diff --git a/frontend-js/src/main/js/ConfigurationOption.js b/frontend-js/src/main/js/ConfigurationOption.js
index 53841aa0dc6b8dd5d4963324477207ef48648bd6..d7ce2f8fd3c94d4c958dd1e01144e45a79551f3d 100644
--- a/frontend-js/src/main/js/ConfigurationOption.js
+++ b/frontend-js/src/main/js/ConfigurationOption.js
@@ -1,71 +1,71 @@
-"use strict";
-
-var ObjectWithListeners = require('./ObjectWithListeners');
-
-var logger = require('./logger');
-
-function ConfigurationOption(data) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- var self = this;
- if (data instanceof ConfigurationOption) {
- self.setType(data.getType());
- self.setCommonName(data.getCommonName());
- self.setValue(data.getValue());
- self.setGroup(data.getGroup());
- self.setValueType(data.getValueType());
- } else {
- self.setType(data.type);
- self.setCommonName(data.commonName);
- self.setGroup(data.group);
- self.setValue(data.value);
- self.setValueType(data.valueType);
- }
-}
-
-ConfigurationOption.prototype = Object.create(ObjectWithListeners.prototype);
-ConfigurationOption.prototype.constructor = ConfigurationOption;
-
-ConfigurationOption.prototype.setType = function (type) {
- this._type = type;
-};
-
-ConfigurationOption.prototype.getType = function () {
- return this._type;
-};
-
-ConfigurationOption.prototype.setValue = function (value) {
- this._value = value;
-};
-
-ConfigurationOption.prototype.getValue = function () {
- return this._value;
-};
-
-ConfigurationOption.prototype.setValueType = function (valueType) {
- this._valueType = valueType;
-};
-
-ConfigurationOption.prototype.getValueType = function () {
- return this._valueType;
-};
-
-ConfigurationOption.prototype.setCommonName = function (commonName) {
- this._commonName = commonName;
-};
-
-ConfigurationOption.prototype.getCommonName = function () {
- return this._commonName;
-};
-
-ConfigurationOption.prototype.setGroup = function (group) {
- this._group = group;
-};
-
-ConfigurationOption.prototype.getGroup = function () {
- return this._group;
-};
-
-
-module.exports = ConfigurationOption;
+"use strict";
+
+var ObjectWithListeners = require('./ObjectWithListeners');
+
+var logger = require('./logger');
+
+function ConfigurationOption(data) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ var self = this;
+ if (data instanceof ConfigurationOption) {
+ self.setType(data.getType());
+ self.setCommonName(data.getCommonName());
+ self.setValue(data.getValue());
+ self.setGroup(data.getGroup());
+ self.setValueType(data.getValueType());
+ } else {
+ self.setType(data.type);
+ self.setCommonName(data.commonName);
+ self.setGroup(data.group);
+ self.setValue(data.value);
+ self.setValueType(data.valueType);
+ }
+}
+
+ConfigurationOption.prototype = Object.create(ObjectWithListeners.prototype);
+ConfigurationOption.prototype.constructor = ConfigurationOption;
+
+ConfigurationOption.prototype.setType = function (type) {
+ this._type = type;
+};
+
+ConfigurationOption.prototype.getType = function () {
+ return this._type;
+};
+
+ConfigurationOption.prototype.setValue = function (value) {
+ this._value = value;
+};
+
+ConfigurationOption.prototype.getValue = function () {
+ return this._value;
+};
+
+ConfigurationOption.prototype.setValueType = function (valueType) {
+ this._valueType = valueType;
+};
+
+ConfigurationOption.prototype.getValueType = function () {
+ return this._valueType;
+};
+
+ConfigurationOption.prototype.setCommonName = function (commonName) {
+ this._commonName = commonName;
+};
+
+ConfigurationOption.prototype.getCommonName = function () {
+ return this._commonName;
+};
+
+ConfigurationOption.prototype.setGroup = function (group) {
+ this._group = group;
+};
+
+ConfigurationOption.prototype.getGroup = function () {
+ return this._group;
+};
+
+
+module.exports = ConfigurationOption;
diff --git a/frontend-js/src/main/js/ConfigurationType.js b/frontend-js/src/main/js/ConfigurationType.js
index 5ebf5f1e7d5148b7b7a0fd321f1a4ff3032fe41b..33e11d3ba6e4080eb7d18869a9c466ad7bc6030e 100644
--- a/frontend-js/src/main/js/ConfigurationType.js
+++ b/frontend-js/src/main/js/ConfigurationType.js
@@ -1,25 +1,25 @@
-"use strict";
-
-var ConfigurationType = {
- DEFAULT_MAP: "DEFAULT_MAP",
- GOOGLE_ANALYTICS_IDENTIFIER: "GOOGLE_ANALYTICS_IDENTIFIER",
- GOOGLE_MAPS_API_KEY: "GOOGLE_MAPS_API_KEY",
- LOGO_IMG: "LOGO_IMG",
- LOGO_LINK: "LOGO_LINK",
- LOGO_TEXT: "LOGO_TEXT",
- LEGEND_FILES: "LEGEND_FILES",
- MIN_COLOR_VAL: "MIN_COLOR_VAL",
- MAX_COLOR_VAL: "MAX_COLOR_VAL",
- NEUTRAL_COLOR_VAL: "NEUTRAL_COLOR_VAL",
- OVERLAY_OPACITY: "OVERLAY_OPACITY",
- REQUEST_ACCOUNT_EMAIL: "REQUEST_ACCOUNT_EMAIL",
- REQUEST_ACCOUNT_DEFAULT_CONTENT: "REQUEST_ACCOUNT_DEFAULT_CONTENT",
- SIMPLE_COLOR_VAL: "SIMPLE_COLOR_VAL",
- SHOW_REACTION_TYPE: "SHOW_REACTION_TYPE",
- SEARCH_DISTANCE: "SEARCH_DISTANCE",
- SEARCH_RESULT_NUMBER: "SEARCH_RESULT_NUMBER",
- TERMS_OF_USE: "TERMS_OF_USE",
- USER_MANUAL_FILE: "USER_MANUAL_FILE"
-};
-
-module.exports = ConfigurationType;
+"use strict";
+
+var ConfigurationType = {
+ DEFAULT_MAP: "DEFAULT_MAP",
+ GOOGLE_ANALYTICS_IDENTIFIER: "GOOGLE_ANALYTICS_IDENTIFIER",
+ GOOGLE_MAPS_API_KEY: "GOOGLE_MAPS_API_KEY",
+ LOGO_IMG: "LOGO_IMG",
+ LOGO_LINK: "LOGO_LINK",
+ LOGO_TEXT: "LOGO_TEXT",
+ LEGEND_FILES: "LEGEND_FILES",
+ MIN_COLOR_VAL: "MIN_COLOR_VAL",
+ MAX_COLOR_VAL: "MAX_COLOR_VAL",
+ NEUTRAL_COLOR_VAL: "NEUTRAL_COLOR_VAL",
+ OVERLAY_OPACITY: "OVERLAY_OPACITY",
+ REQUEST_ACCOUNT_EMAIL: "REQUEST_ACCOUNT_EMAIL",
+ REQUEST_ACCOUNT_DEFAULT_CONTENT: "REQUEST_ACCOUNT_DEFAULT_CONTENT",
+ SIMPLE_COLOR_VAL: "SIMPLE_COLOR_VAL",
+ SHOW_REACTION_TYPE: "SHOW_REACTION_TYPE",
+ SEARCH_DISTANCE: "SEARCH_DISTANCE",
+ SEARCH_RESULT_NUMBER: "SEARCH_RESULT_NUMBER",
+ TERMS_OF_USE: "TERMS_OF_USE",
+ USER_MANUAL_FILE: "USER_MANUAL_FILE"
+};
+
+module.exports = ConfigurationType;
diff --git a/frontend-js/src/main/js/Export.js b/frontend-js/src/main/js/Export.js
index ee603b203e1665952909c620dd890a61ed4d6bd4..1c15300edfe892e8aa5db2ea2a45a822aecc45a9 100644
--- a/frontend-js/src/main/js/Export.js
+++ b/frontend-js/src/main/js/Export.js
@@ -1,168 +1,168 @@
-"use strict";
-
-/* exported logger */
-
-var Promise = require("bluebird");
-
-var CustomMapOptions = require('./map/CustomMapOptions');
-var ElementExportPanel = require('./gui/export/ElementExportPanel');
-var GraphicsExportPanel = require('./gui/export/GraphicsExportPanel');
-var NetworkExportPanel = require('./gui/export/NetworkExportPanel');
-var Header = require('./gui/Header');
-var ObjectWithListeners = require('./ObjectWithListeners');
-
-var logger = require('./logger');
-var Functions = require('./Functions');
-
-/**
- * Default constructor.
- *
- * @param options
- * CustomMapOptions object representing all parameters needed for map
- * creation
- */
-function Export(options) {
- var self = this;
- self._panels = [];
- self._tabIdCount = 0;
- if (!(options instanceof CustomMapOptions)) {
- options = new CustomMapOptions(options);
- }
- self.setProject(options.getProject());
- self.setElement(options.getElement());
-
- self.setConfiguration(options.getConfiguration());
- self._createGui();
-}
-
-Export.prototype = Object.create(ObjectWithListeners.prototype);
-Export.prototype.constructor = ObjectWithListeners;
-
-Export.prototype._createGui = function() {
- var self = this;
- self.getElement().innerHTML = "";
- var headerDiv = Functions.createElement({
- type : "div"
- });
- new Header({
- element : headerDiv,
- customMap : null,
- project : self.getProject()
- });
- self.getElement().appendChild(headerDiv);
-
- var panels = [ {
- name : "ELEMENTS",
- panelClass : ElementExportPanel
- }, {
- name : "NETWORK",
- panelClass : NetworkExportPanel
- }, {
- name : "GRAPHICS",
- panelClass : GraphicsExportPanel
- } ];
-
- var tabDiv = Functions.createElement({
- type : "div",
- name : "tabView",
- className : "tabbable boxed parentTabs"
- });
- self.getElement().appendChild(tabDiv);
-
- var tabMenuDiv = Functions.createElement({
- type : "ul",
- className : "nav nav-tabs"
- });
- tabDiv.appendChild(tabMenuDiv);
-
- var tabContentDiv = Functions.createElement({
- type : "div",
- className : "tab-content"
- });
- tabDiv.appendChild(tabContentDiv);
-
- for (var i = 0; i < panels.length; i++) {
- self.addTab(panels[i], tabMenuDiv, tabContentDiv);
- }
-};
-
-Export.prototype.addTab = function(params, navElement, contentElement) {
- var self = this;
-
- var name = params.name;
-
- var tabId = "export_panel_tab_" + this._tabIdCount;
- self._tabIdCount++;
-
- var navClass = '';
- var contentClass = 'tab-pane';
- if (navElement.children.length === 0) {
- navClass = "active";
- contentClass = "tab-pane active";
- }
-
- var navLi = document.createElement("li");
- navLi.className = navClass;
-
- var navLink = document.createElement("a");
- navLink.href = "#" + tabId;
- if (name !== undefined) {
- if (name.length > 12) {
- name = name.substring(0, 10) + "...";
- }
- navLink.innerHTML = name;
- }
- navLink.onclick = function() {
- $(this).tab('show');
- };
- navLi.appendChild(navLink);
- if (name !== undefined) {
- navLink.innerHTML = name;
- }
- navElement.appendChild(navLi);
-
- var contentDiv = document.createElement("div");
- contentDiv.style.height = "100%";
- contentDiv.className = contentClass;
- contentDiv.id = tabId;
-
- contentElement.appendChild(contentDiv);
-
- this._panels.push(new params.panelClass({
- element : contentDiv,
- project : self.getProject(),
- configuration : self.getConfiguration()
- }));
-};
-
-Export.prototype.setProject = function(project) {
- this._project = project;
-};
-Export.prototype.getProject = function() {
- return this._project;
-};
-
-Export.prototype.setElement = function(element) {
- this._element = element;
-};
-Export.prototype.getElement = function() {
- return this._element;
-};
-
-Export.prototype.init = function() {
- var promises = [];
- for (var i = 0; i < this._panels.length; i++) {
- promises.push(this._panels[i].init());
- }
- return Promise.all(promises);
-};
-
-Export.prototype.setConfiguration = function(configuration) {
- this._configuration = configuration;
-};
-
-Export.prototype.getConfiguration = function() {
- return this._configuration;
-};
-
-module.exports = Export;
+"use strict";
+
+/* exported logger */
+
+var Promise = require("bluebird");
+
+var CustomMapOptions = require('./map/CustomMapOptions');
+var ElementExportPanel = require('./gui/export/ElementExportPanel');
+var GraphicsExportPanel = require('./gui/export/GraphicsExportPanel');
+var NetworkExportPanel = require('./gui/export/NetworkExportPanel');
+var Header = require('./gui/Header');
+var ObjectWithListeners = require('./ObjectWithListeners');
+
+var logger = require('./logger');
+var Functions = require('./Functions');
+
+/**
+ * Default constructor.
+ *
+ * @param options
+ * CustomMapOptions object representing all parameters needed for map
+ * creation
+ */
+function Export(options) {
+ var self = this;
+ self._panels = [];
+ self._tabIdCount = 0;
+ if (!(options instanceof CustomMapOptions)) {
+ options = new CustomMapOptions(options);
+ }
+ self.setProject(options.getProject());
+ self.setElement(options.getElement());
+
+ self.setConfiguration(options.getConfiguration());
+ self._createGui();
+}
+
+Export.prototype = Object.create(ObjectWithListeners.prototype);
+Export.prototype.constructor = ObjectWithListeners;
+
+Export.prototype._createGui = function() {
+ var self = this;
+ self.getElement().innerHTML = "";
+ var headerDiv = Functions.createElement({
+ type : "div"
+ });
+ new Header({
+ element : headerDiv,
+ customMap : null,
+ project : self.getProject()
+ });
+ self.getElement().appendChild(headerDiv);
+
+ var panels = [ {
+ name : "ELEMENTS",
+ panelClass : ElementExportPanel
+ }, {
+ name : "NETWORK",
+ panelClass : NetworkExportPanel
+ }, {
+ name : "GRAPHICS",
+ panelClass : GraphicsExportPanel
+ } ];
+
+ var tabDiv = Functions.createElement({
+ type : "div",
+ name : "tabView",
+ className : "tabbable boxed parentTabs"
+ });
+ self.getElement().appendChild(tabDiv);
+
+ var tabMenuDiv = Functions.createElement({
+ type : "ul",
+ className : "nav nav-tabs"
+ });
+ tabDiv.appendChild(tabMenuDiv);
+
+ var tabContentDiv = Functions.createElement({
+ type : "div",
+ className : "tab-content"
+ });
+ tabDiv.appendChild(tabContentDiv);
+
+ for (var i = 0; i < panels.length; i++) {
+ self.addTab(panels[i], tabMenuDiv, tabContentDiv);
+ }
+};
+
+Export.prototype.addTab = function(params, navElement, contentElement) {
+ var self = this;
+
+ var name = params.name;
+
+ var tabId = "export_panel_tab_" + this._tabIdCount;
+ self._tabIdCount++;
+
+ var navClass = '';
+ var contentClass = 'tab-pane';
+ if (navElement.children.length === 0) {
+ navClass = "active";
+ contentClass = "tab-pane active";
+ }
+
+ var navLi = document.createElement("li");
+ navLi.className = navClass;
+
+ var navLink = document.createElement("a");
+ navLink.href = "#" + tabId;
+ if (name !== undefined) {
+ if (name.length > 12) {
+ name = name.substring(0, 10) + "...";
+ }
+ navLink.innerHTML = name;
+ }
+ navLink.onclick = function() {
+ $(this).tab('show');
+ };
+ navLi.appendChild(navLink);
+ if (name !== undefined) {
+ navLink.innerHTML = name;
+ }
+ navElement.appendChild(navLi);
+
+ var contentDiv = document.createElement("div");
+ contentDiv.style.height = "100%";
+ contentDiv.className = contentClass;
+ contentDiv.id = tabId;
+
+ contentElement.appendChild(contentDiv);
+
+ this._panels.push(new params.panelClass({
+ element : contentDiv,
+ project : self.getProject(),
+ configuration : self.getConfiguration()
+ }));
+};
+
+Export.prototype.setProject = function(project) {
+ this._project = project;
+};
+Export.prototype.getProject = function() {
+ return this._project;
+};
+
+Export.prototype.setElement = function(element) {
+ this._element = element;
+};
+Export.prototype.getElement = function() {
+ return this._element;
+};
+
+Export.prototype.init = function() {
+ var promises = [];
+ for (var i = 0; i < this._panels.length; i++) {
+ promises.push(this._panels[i].init());
+ }
+ return Promise.all(promises);
+};
+
+Export.prototype.setConfiguration = function(configuration) {
+ this._configuration = configuration;
+};
+
+Export.prototype.getConfiguration = function() {
+ return this._configuration;
+};
+
+module.exports = Export;
diff --git a/frontend-js/src/main/js/GuiConnector.js b/frontend-js/src/main/js/GuiConnector.js
index c5e6d90f515b9e5d14bd9b0fce0f2772c4deefd6..137259eee36ccedff2b6025f7d0de55877a02873 100644
--- a/frontend-js/src/main/js/GuiConnector.js
+++ b/frontend-js/src/main/js/GuiConnector.js
@@ -1,340 +1,340 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var logger = require('./logger');
-
-var Functions = require('./Functions');
-var SecurityError = require('./SecurityError');
-var ValidationError = require('./ValidationError');
-var GuiMessageError = require('./gui/GuiMessageError');
-var NetworkError = require('./NetworkError');
-
-/**
- * This static global object contains set of functions that returns/set data in
- * the Gui (html).
- */
-function GuiConnector() {
- // X coordinate of the mouse in a browser.
- //@type {number}
- this.xPos = 0;
- // coordinate of the mouse in a browser.
- //@type {number}
- this.yPos = 0;
-
- this.getParams = [];
-}
-
-function returnThisOrSingleton(object) {
- if (object === undefined || object === null) {
- return GuiConnector.singleton;
- } else {
- return object;
- }
-}
-
-/**
- * List of GET params passed via url.
- */
-
-GuiConnector.prototype.init = function () {
- var self = returnThisOrSingleton(this);
-
- if (!String.prototype.endsWith) {
- String.prototype.endsWith = function (pattern) {
- var d = this.length - pattern.length;
- return d >= 0 && this.lastIndexOf(pattern) === d;
- };
- }
- var isIE = /* @cc_on!@ */false || !!document.documentMode;
-
- if (isIE) {
- alert("This web page works well with Chrome, Firefox and Safari.");
- }
- // bootstrap tab initialization
- $("ul.nav-tabs a").click(function (e) {
- e.preventDefault();
- $(this).tab('show');
- });
-
- self.getParams = [];
-
- // find GuiConnector.getParams
- window.location.search.replace(/\??(?:([^=]+)=([^&]*)&?)/g, function () {
- function decode(s) {
- return decodeURIComponent(s.split("+").join(" "));
- }
-
- self.getParams[decode(arguments[1])] = decode(arguments[2]);
- });
-
- self._touchStartEvent = function (e) {
- if (e.originalEvent !== undefined) {
- self.updateMouseCoordinates(e.originalEvent.touches[0].pageX, e.originalEvent.touches[0].pageY);
- }
- };
- self._touchMoveEvent = function (e) {
- if (e.originalEvent !== undefined) {
- self.updateMouseCoordinates(e.originalEvent.touches[0].pageX, e.originalEvent.touches[0].pageY);
- }
- };
-
- // force browser to update mouse coordinates whenever mouse move
- jQuery(document).ready(function () {
- $(document).mousemove(function (e) {
- self.updateMouseCoordinates(e.pageX, e.pageY);
- });
- $(document).on('touchstart', self._touchStartEvent);
- $(document).on('touchmove', self._touchMoveEvent);
- });
-
- if (self._windowResizeEvents === undefined) {
- self._windowResizeEvents = [];
-
- if (window.onresize !== null && window.onresize !== undefined) {
- self.addWindowResizeEvent(window.onresize);
- }
-
- window.onresize = function () {
- for (var i = 0; i < self._windowResizeEvents.length; i++) {
- self._windowResizeEvents[i]();
- }
- };
- }
-};
-
-GuiConnector.prototype.addWindowResizeEvent = function (handler) {
- this._windowResizeEvents.push(handler);
-};
-
-GuiConnector.prototype.removeWindowResizeEvent = function (handler) {
- var events = this._windowResizeEvents;
- var index = events.indexOf(handler);
- if (index > -1) {
- events.splice(index, 1);
- } else {
- logger.warn("Cannot find listener", handler);
- }
-};
-
-/**
- * Returns name of the file with LCSB logo.
- *
- * @param bigLogo
- * {@link Boolean} value determining if we want to have big logo or
- * small one
- */
-GuiConnector.prototype.getLcsbLogoImg = function (bigLogo) {
- if (bigLogo) {
- return 'lcsb_logo_mid.png';
- } else {
- return 'lcsb_logo.png';
- }
-};
-
-/**
- * Returns name of the file with image that should be presented when we are
- * waiting for data to be loaded.
- */
-GuiConnector.prototype.getLoadingImg = function () {
- return "icons/ajax-loader.gif";
-};
-
-
-GuiConnector.prototype.getEmptyTileUrl = function () {
- return "resources/images/empty_tile.png";
-};
-
-/**
- * Returns home directory for images in the application.
- */
-GuiConnector.prototype.getImgPrefix = function () {
- return "resources/images/";
-};
-
-/**
- * Updates coordinates of the mouse in the browser.
- */
-GuiConnector.prototype.updateMouseCoordinates = function (x, y) {
- var self = returnThisOrSingleton(this);
- self.xPos = x;
- self.yPos = y;
-};
-
-GuiConnector.prototype.showProcessing = function (messageText) {
- var self = returnThisOrSingleton(this);
- if (self._processingDialog === undefined) {
- self._processingDialog = document.createElement("div");
- self._processingDialogContent = document.createElement("div");
- self._processingDialog.appendChild(self._processingDialogContent);
- document.body.appendChild(self._processingDialog);
- $(self._processingDialog).dialog({
- modal: true,
- title: "PROCESSING",
- width: "150px",
- closeOnEscape: false,
- dialogClass: 'minerva-no-close'
- });
- }
- if (messageText === undefined) {
- messageText = "PROCESSING";
- }
- var messageImg = Functions.createElement({
- type: "img",
- src: 'resources/images/icons/ajax-loader.gif'
- });
- self._processingDialogContent.innerHTML = "";
- self._processingDialogContent.style.textAlign = "center";
- self._processingDialogContent.appendChild(messageImg);
-
- $(self._processingDialog).dialog("option", "title", messageText);
-
- $(self._processingDialog).dialog("open");
-};
-
-GuiConnector.prototype.hideProcessing = function () {
- var self = returnThisOrSingleton(this);
- $(self._processingDialog).dialog("close");
-};
-
-GuiConnector.prototype.alert = function (error, redirectIfSecurityError) {
- if (redirectIfSecurityError === undefined) {
- redirectIfSecurityError = false;
- }
- if (redirectIfSecurityError && error instanceof SecurityError && ServerConnector.getSessionData().getLogin() === "anonymous") {
- window.location.href = ServerConnector.getServerBaseUrl() + "login.xhtml?from=" + encodeURI(window.location.href);
- } else {
- var self = returnThisOrSingleton(this);
- logger.error(error);
- if (self._errorDialog === undefined) {
- self._errorDialog = document.createElement("div");
- self._errorDialogContent = document.createElement("div");
- self._errorDialog.appendChild(self._errorDialogContent);
- document.body.appendChild(self._errorDialog);
- $(self._errorDialog).dialog({
- classes: {
- "ui-dialog": "ui-state-error"
- },
- modal: true,
- title: "ERROR"
- }).siblings('.ui-dialog-titlebar').css("background", "red");
- }
- self._errorDialogContent.innerHTML = self.getErrorMessageForError(error);
- $(self._errorDialog).dialog("open");
- }
-};
-
-GuiConnector.prototype.getErrorMessageForError = function (error) {
- var message = error;
- if (message instanceof SecurityError) {
- if (ServerConnector.getSessionData().getLogin() === "anonymous") {
- message = error.message + "<p>Please <a href=\"login.xhtml?from=" + encodeURI(window.location.href) + "\">login</a> to access this resource</p>";
- } else {
- message = error.message + "<p>Please <a href=\"login.xhtml?from=" + encodeURI(window.location.href) + "\">login</a> " +
- "as a different user or ask your administrator to change the permissions to access this resource.</p>";
- }
- } else if (message instanceof ValidationError) {
- message = error.message;
- } else if (message instanceof GuiMessageError) {
- message = error.message;
- } else if (message instanceof Error) {
- message = "Unexpected error occurred:<p>" + error.message + "</p>";
- }
- return message;
-};
-
-GuiConnector.prototype.info = function (message) {
- var self = returnThisOrSingleton(this);
- if (self._infoDialog === undefined) {
- self._infoDialog = document.createElement("div");
- self._infoDialogContent = document.createElement("div");
- self._infoDialog.appendChild(self._infoDialogContent);
- document.body.appendChild(self._infoDialog);
- $(self._infoDialog).dialog({
- classes: {
- "ui-dialog": "ui-state-info"
- },
- modal: true,
- title: "INFO"
- });
- }
- self._infoDialogContent.innerHTML = message;
- $(self._infoDialog).dialog("open");
-
-};
-
-GuiConnector.prototype.showConfirmationDialog = function (params) {
- var message = params.message;
- var title = params.title;
- if (title === undefined) {
- title = "Confirm";
- }
- return new Promise(function (resolve) {
- $('<div></div>').appendTo('body')
- .html('<div><h6>' + message + '</h6></div>')
- .dialog({
- modal: true, title: title, zIndex: 10000, autoOpen: true,
- width: 'auto', resizable: false,
- buttons: {
- Yes: function () {
- $(this).dialog("close");
- resolve(true);
- },
- No: function () {
- $(this).dialog("close");
- resolve(false);
- }
- },
- close: function (event, ui) {
- $(this).remove();
- }
- });
- });
-};
-
-GuiConnector.prototype.destroy = function () {
- var self = returnThisOrSingleton(this);
-
- if (self._infoDialog !== undefined) {
- $(self._infoDialog).dialog("destroy").remove();
- }
- if (self._warnDialog !== undefined) {
- $(self._warnDialog).dialog("destroy").remove();
- }
- if (self._processingDialog !== undefined) {
- $(self._processingDialog).dialog("destroy").remove();
- }
-
- if (self._errorDialog !== undefined) {
- $(self._errorDialog).dialog("destroy").remove();
- }
-
- self._windowResizeEvents = undefined;
- $(document).off('touchstart', self._touchStartEvent);
- $(document).off('touchmove', self._touchMoveEvent);
-
-};
-
-GuiConnector.prototype.warn = function (message) {
- var self = GuiConnector;
- logger.warn(message);
- if (self._warnDialog === undefined) {
- self._warnDialog = document.createElement("div");
- self._warnDialogContent = document.createElement("div");
- self._warnDialog.appendChild(self._warnDialogContent);
- document.body.appendChild(self._warnDialog);
- $(self._warnDialog).dialog({
- classes: {
- "ui-dialog": "ui-state-highlight"
- },
- modal: true,
- title: "WARNING"
- });
- }
- self._warnDialogContent.innerHTML = message;
- $(self._warnDialog).dialog("open");
-};
-
-GuiConnector.singleton = new GuiConnector();
-
-module.exports = GuiConnector.singleton;
+"use strict";
+
+var Promise = require("bluebird");
+
+var logger = require('./logger');
+
+var Functions = require('./Functions');
+var SecurityError = require('./SecurityError');
+var ValidationError = require('./ValidationError');
+var GuiMessageError = require('./gui/GuiMessageError');
+var NetworkError = require('./NetworkError');
+
+/**
+ * This static global object contains set of functions that returns/set data in
+ * the Gui (html).
+ */
+function GuiConnector() {
+ // X coordinate of the mouse in a browser.
+ //@type {number}
+ this.xPos = 0;
+ // coordinate of the mouse in a browser.
+ //@type {number}
+ this.yPos = 0;
+
+ this.getParams = [];
+}
+
+function returnThisOrSingleton(object) {
+ if (object === undefined || object === null) {
+ return GuiConnector.singleton;
+ } else {
+ return object;
+ }
+}
+
+/**
+ * List of GET params passed via url.
+ */
+
+GuiConnector.prototype.init = function () {
+ var self = returnThisOrSingleton(this);
+
+ if (!String.prototype.endsWith) {
+ String.prototype.endsWith = function (pattern) {
+ var d = this.length - pattern.length;
+ return d >= 0 && this.lastIndexOf(pattern) === d;
+ };
+ }
+ var isIE = /* @cc_on!@ */false || !!document.documentMode;
+
+ if (isIE) {
+ alert("This web page works well with Chrome, Firefox and Safari.");
+ }
+ // bootstrap tab initialization
+ $("ul.nav-tabs a").click(function (e) {
+ e.preventDefault();
+ $(this).tab('show');
+ });
+
+ self.getParams = [];
+
+ // find GuiConnector.getParams
+ window.location.search.replace(/\??(?:([^=]+)=([^&]*)&?)/g, function () {
+ function decode(s) {
+ return decodeURIComponent(s.split("+").join(" "));
+ }
+
+ self.getParams[decode(arguments[1])] = decode(arguments[2]);
+ });
+
+ self._touchStartEvent = function (e) {
+ if (e.originalEvent !== undefined) {
+ self.updateMouseCoordinates(e.originalEvent.touches[0].pageX, e.originalEvent.touches[0].pageY);
+ }
+ };
+ self._touchMoveEvent = function (e) {
+ if (e.originalEvent !== undefined) {
+ self.updateMouseCoordinates(e.originalEvent.touches[0].pageX, e.originalEvent.touches[0].pageY);
+ }
+ };
+
+ // force browser to update mouse coordinates whenever mouse move
+ jQuery(document).ready(function () {
+ $(document).mousemove(function (e) {
+ self.updateMouseCoordinates(e.pageX, e.pageY);
+ });
+ $(document).on('touchstart', self._touchStartEvent);
+ $(document).on('touchmove', self._touchMoveEvent);
+ });
+
+ if (self._windowResizeEvents === undefined) {
+ self._windowResizeEvents = [];
+
+ if (window.onresize !== null && window.onresize !== undefined) {
+ self.addWindowResizeEvent(window.onresize);
+ }
+
+ window.onresize = function () {
+ for (var i = 0; i < self._windowResizeEvents.length; i++) {
+ self._windowResizeEvents[i]();
+ }
+ };
+ }
+};
+
+GuiConnector.prototype.addWindowResizeEvent = function (handler) {
+ this._windowResizeEvents.push(handler);
+};
+
+GuiConnector.prototype.removeWindowResizeEvent = function (handler) {
+ var events = this._windowResizeEvents;
+ var index = events.indexOf(handler);
+ if (index > -1) {
+ events.splice(index, 1);
+ } else {
+ logger.warn("Cannot find listener", handler);
+ }
+};
+
+/**
+ * Returns name of the file with LCSB logo.
+ *
+ * @param bigLogo
+ * {@link Boolean} value determining if we want to have big logo or
+ * small one
+ */
+GuiConnector.prototype.getLcsbLogoImg = function (bigLogo) {
+ if (bigLogo) {
+ return 'lcsb_logo_mid.png';
+ } else {
+ return 'lcsb_logo.png';
+ }
+};
+
+/**
+ * Returns name of the file with image that should be presented when we are
+ * waiting for data to be loaded.
+ */
+GuiConnector.prototype.getLoadingImg = function () {
+ return "icons/ajax-loader.gif";
+};
+
+
+GuiConnector.prototype.getEmptyTileUrl = function () {
+ return "resources/images/empty_tile.png";
+};
+
+/**
+ * Returns home directory for images in the application.
+ */
+GuiConnector.prototype.getImgPrefix = function () {
+ return "resources/images/";
+};
+
+/**
+ * Updates coordinates of the mouse in the browser.
+ */
+GuiConnector.prototype.updateMouseCoordinates = function (x, y) {
+ var self = returnThisOrSingleton(this);
+ self.xPos = x;
+ self.yPos = y;
+};
+
+GuiConnector.prototype.showProcessing = function (messageText) {
+ var self = returnThisOrSingleton(this);
+ if (self._processingDialog === undefined) {
+ self._processingDialog = document.createElement("div");
+ self._processingDialogContent = document.createElement("div");
+ self._processingDialog.appendChild(self._processingDialogContent);
+ document.body.appendChild(self._processingDialog);
+ $(self._processingDialog).dialog({
+ modal: true,
+ title: "PROCESSING",
+ width: "150px",
+ closeOnEscape: false,
+ dialogClass: 'minerva-no-close'
+ });
+ }
+ if (messageText === undefined) {
+ messageText = "PROCESSING";
+ }
+ var messageImg = Functions.createElement({
+ type: "img",
+ src: 'resources/images/icons/ajax-loader.gif'
+ });
+ self._processingDialogContent.innerHTML = "";
+ self._processingDialogContent.style.textAlign = "center";
+ self._processingDialogContent.appendChild(messageImg);
+
+ $(self._processingDialog).dialog("option", "title", messageText);
+
+ $(self._processingDialog).dialog("open");
+};
+
+GuiConnector.prototype.hideProcessing = function () {
+ var self = returnThisOrSingleton(this);
+ $(self._processingDialog).dialog("close");
+};
+
+GuiConnector.prototype.alert = function (error, redirectIfSecurityError) {
+ if (redirectIfSecurityError === undefined) {
+ redirectIfSecurityError = false;
+ }
+ if (redirectIfSecurityError && error instanceof SecurityError && ServerConnector.getSessionData().getLogin() === "anonymous") {
+ window.location.href = ServerConnector.getServerBaseUrl() + "login.xhtml?from=" + encodeURI(window.location.href);
+ } else {
+ var self = returnThisOrSingleton(this);
+ logger.error(error);
+ if (self._errorDialog === undefined) {
+ self._errorDialog = document.createElement("div");
+ self._errorDialogContent = document.createElement("div");
+ self._errorDialog.appendChild(self._errorDialogContent);
+ document.body.appendChild(self._errorDialog);
+ $(self._errorDialog).dialog({
+ classes: {
+ "ui-dialog": "ui-state-error"
+ },
+ modal: true,
+ title: "ERROR"
+ }).siblings('.ui-dialog-titlebar').css("background", "red");
+ }
+ self._errorDialogContent.innerHTML = self.getErrorMessageForError(error);
+ $(self._errorDialog).dialog("open");
+ }
+};
+
+GuiConnector.prototype.getErrorMessageForError = function (error) {
+ var message = error;
+ if (message instanceof SecurityError) {
+ if (ServerConnector.getSessionData().getLogin() === "anonymous") {
+ message = error.message + "<p>Please <a href=\"login.xhtml?from=" + encodeURI(window.location.href) + "\">login</a> to access this resource</p>";
+ } else {
+ message = error.message + "<p>Please <a href=\"login.xhtml?from=" + encodeURI(window.location.href) + "\">login</a> " +
+ "as a different user or ask your administrator to change the permissions to access this resource.</p>";
+ }
+ } else if (message instanceof ValidationError) {
+ message = error.message;
+ } else if (message instanceof GuiMessageError) {
+ message = error.message;
+ } else if (message instanceof Error) {
+ message = "Unexpected error occurred:<p>" + error.message + "</p>";
+ }
+ return message;
+};
+
+GuiConnector.prototype.info = function (message) {
+ var self = returnThisOrSingleton(this);
+ if (self._infoDialog === undefined) {
+ self._infoDialog = document.createElement("div");
+ self._infoDialogContent = document.createElement("div");
+ self._infoDialog.appendChild(self._infoDialogContent);
+ document.body.appendChild(self._infoDialog);
+ $(self._infoDialog).dialog({
+ classes: {
+ "ui-dialog": "ui-state-info"
+ },
+ modal: true,
+ title: "INFO"
+ });
+ }
+ self._infoDialogContent.innerHTML = message;
+ $(self._infoDialog).dialog("open");
+
+};
+
+GuiConnector.prototype.showConfirmationDialog = function (params) {
+ var message = params.message;
+ var title = params.title;
+ if (title === undefined) {
+ title = "Confirm";
+ }
+ return new Promise(function (resolve) {
+ $('<div></div>').appendTo('body')
+ .html('<div><h6>' + message + '</h6></div>')
+ .dialog({
+ modal: true, title: title, zIndex: 10000, autoOpen: true,
+ width: 'auto', resizable: false,
+ buttons: {
+ Yes: function () {
+ $(this).dialog("close");
+ resolve(true);
+ },
+ No: function () {
+ $(this).dialog("close");
+ resolve(false);
+ }
+ },
+ close: function (event, ui) {
+ $(this).remove();
+ }
+ });
+ });
+};
+
+GuiConnector.prototype.destroy = function () {
+ var self = returnThisOrSingleton(this);
+
+ if (self._infoDialog !== undefined) {
+ $(self._infoDialog).dialog("destroy").remove();
+ }
+ if (self._warnDialog !== undefined) {
+ $(self._warnDialog).dialog("destroy").remove();
+ }
+ if (self._processingDialog !== undefined) {
+ $(self._processingDialog).dialog("destroy").remove();
+ }
+
+ if (self._errorDialog !== undefined) {
+ $(self._errorDialog).dialog("destroy").remove();
+ }
+
+ self._windowResizeEvents = undefined;
+ $(document).off('touchstart', self._touchStartEvent);
+ $(document).off('touchmove', self._touchMoveEvent);
+
+};
+
+GuiConnector.prototype.warn = function (message) {
+ var self = GuiConnector;
+ logger.warn(message);
+ if (self._warnDialog === undefined) {
+ self._warnDialog = document.createElement("div");
+ self._warnDialogContent = document.createElement("div");
+ self._warnDialog.appendChild(self._warnDialogContent);
+ document.body.appendChild(self._warnDialog);
+ $(self._warnDialog).dialog({
+ classes: {
+ "ui-dialog": "ui-state-highlight"
+ },
+ modal: true,
+ title: "WARNING"
+ });
+ }
+ self._warnDialogContent.innerHTML = message;
+ $(self._warnDialog).dialog("open");
+};
+
+GuiConnector.singleton = new GuiConnector();
+
+module.exports = GuiConnector.singleton;
diff --git a/frontend-js/src/main/js/InvalidArgumentError.js b/frontend-js/src/main/js/InvalidArgumentError.js
index 2e8fb4c330b614e4710c8022dd2c5867d8be7281..b0166479773294956cd6f3db57b3c202029f4a12 100644
--- a/frontend-js/src/main/js/InvalidArgumentError.js
+++ b/frontend-js/src/main/js/InvalidArgumentError.js
@@ -1,15 +1,15 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('./logger');
-
-function InvalidArgumentError(message) {
- this.message = message;
- this.stack = (new Error()).stack;
-}
-
-InvalidArgumentError.prototype = Object.create(Error.prototype);
-InvalidArgumentError.prototype.constructor = InvalidArgumentError;
-
-module.exports = InvalidArgumentError;
+"use strict";
+
+/* exported logger */
+
+var logger = require('./logger');
+
+function InvalidArgumentError(message) {
+ this.message = message;
+ this.stack = (new Error()).stack;
+}
+
+InvalidArgumentError.prototype = Object.create(Error.prototype);
+InvalidArgumentError.prototype.constructor = InvalidArgumentError;
+
+module.exports = InvalidArgumentError;
diff --git a/frontend-js/src/main/js/InvalidCredentialsError.js b/frontend-js/src/main/js/InvalidCredentialsError.js
index 1cd1e91ec86db950b28e09de87606d397bfe62f5..7e5f85ce4ff2dfb4e206e6b1fe2e41dd2e543620 100644
--- a/frontend-js/src/main/js/InvalidCredentialsError.js
+++ b/frontend-js/src/main/js/InvalidCredentialsError.js
@@ -1,17 +1,17 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('./logger');
-
-var SecurityError = require("./SecurityError");
-
-function InvalidCredentialsError(message) {
- this.message = message;
- this.stack = (new Error()).stack;
-}
-
-InvalidCredentialsError.prototype = Object.create(SecurityError.prototype);
-InvalidCredentialsError.prototype.constructor = InvalidCredentialsError;
-
-module.exports = InvalidCredentialsError;
+"use strict";
+
+/* exported logger */
+
+var logger = require('./logger');
+
+var SecurityError = require("./SecurityError");
+
+function InvalidCredentialsError(message) {
+ this.message = message;
+ this.stack = (new Error()).stack;
+}
+
+InvalidCredentialsError.prototype = Object.create(SecurityError.prototype);
+InvalidCredentialsError.prototype.constructor = InvalidCredentialsError;
+
+module.exports = InvalidCredentialsError;
diff --git a/frontend-js/src/main/js/NetworkError.js b/frontend-js/src/main/js/NetworkError.js
index 109b0ff5e62cf286e464960b45957e0240b41032..0b693ae0ba40dd17cfbf9e223c329caaa93cc907 100644
--- a/frontend-js/src/main/js/NetworkError.js
+++ b/frontend-js/src/main/js/NetworkError.js
@@ -1,25 +1,25 @@
-"use strict";
-
-/* exported logger */
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('./logger');
-
-function NetworkError(message, connectionParams) {
- this.message = message;
- this.stack = (new Error()).stack;
- if (connectionParams === undefined || connectionParams === null) {
- connectionParams = {};
- }
- this.statusCode = connectionParams.statusCode;
- this.url = connectionParams.url;
- this.content = connectionParams.content;
- if (this.content === undefined) {
- this.content = "";
- }
-}
-
-NetworkError.prototype = Object.create(Error.prototype);
-NetworkError.prototype.constructor = NetworkError;
-
-module.exports = NetworkError;
+"use strict";
+
+/* exported logger */
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('./logger');
+
+function NetworkError(message, connectionParams) {
+ this.message = message;
+ this.stack = (new Error()).stack;
+ if (connectionParams === undefined || connectionParams === null) {
+ connectionParams = {};
+ }
+ this.statusCode = connectionParams.statusCode;
+ this.url = connectionParams.url;
+ this.content = connectionParams.content;
+ if (this.content === undefined) {
+ this.content = "";
+ }
+}
+
+NetworkError.prototype = Object.create(Error.prototype);
+NetworkError.prototype.constructor = NetworkError;
+
+module.exports = NetworkError;
diff --git a/frontend-js/src/main/js/ObjectWithListeners.js b/frontend-js/src/main/js/ObjectWithListeners.js
index 633390bd4eff7dae5921512606b660f10e4d9083..c930048dd6690ce6f9741d1e1c6eb50f5ea029ba 100644
--- a/frontend-js/src/main/js/ObjectWithListeners.js
+++ b/frontend-js/src/main/js/ObjectWithListeners.js
@@ -1,211 +1,211 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var logger = require('./logger');
-
-/**
- * An abstract class that allows to register listeners and call them in case of
- * events.
- * @constructor
- */
-function ObjectWithListeners() {
- this._validListeners = [];
- this._validPropertyListeners = [];
-}
-
-/**
- * @callback ListenerCallback
- * @param event
- */
-/**
- * Adds a listener function to the object.
- *
- * @param {string} type
- * string defining type of the listener
- * @param {ListenerCallback} fun
- * function that should be thrown when type event occurs
- */
-ObjectWithListeners.prototype.addListener = function (type, fun) {
- if (this._validListeners[type] === undefined) {
- throw new Error("Unknown listener type: " + type);
- }
-
- if (typeof fun !== "function") {
- throw new Error("Second parameter must be a function but \"" + typeof (fun) + "\" found.");
- }
-
- this._validListeners[type].push(fun);
-};
-
-/**
- * Adds a property change listener function to the object.
- *
- * @param {string} name
- * string defining property name
- * @param {function} fun
- * function that should be thrown when firePropertyChangeListener is
- * called
- */
-ObjectWithListeners.prototype.addPropertyChangeListener = function (name, fun) {
- if (this._validPropertyListeners[name] === undefined) {
- throw new Error("Unknown property type: " + name);
- }
-
- if (typeof fun !== "function") {
- throw new Error("Second parameter must be a function but \"" + typeof (fun) + "\" found.");
- }
-
- this._validPropertyListeners[name].push(fun);
-};
-
-/**
- * Register new type of listener.
- *
- * @param type
- * string identifying new type of listener
- */
-ObjectWithListeners.prototype.registerListenerType = function (type) {
- if (this._validListeners[type] !== undefined) {
- throw new Error("Listener type already registered: " + type);
- }
- this._validListeners[type] = [];
-};
-
-/**
- * Register new property for listening.
- *
- * @param name
- * string identifying property
- */
-ObjectWithListeners.prototype.registerPropertyType = function (name) {
- if (this._validPropertyListeners[name] !== undefined) {
- throw new Error("Property already registered: " + name);
- }
- this._validPropertyListeners[name] = [];
-};
-
-/**
- * Removes listener from the object.
- *
- * @param type
- * type of the listener
- * @param fun
- * function that was call when event occurred that should be removed
- */
-ObjectWithListeners.prototype.removeListener = function (type, fun) {
- if (this._validListeners[type] === undefined) {
- throw new Error("Unknown listener type: " + type);
- }
-
- if (typeof (fun) !== "function") {
- throw new Error("Second parameter must be a function but \"" + typeof (fun) + "\" found.");
- }
-
- var listenerList = this._validListeners[type];
-
- var index = listenerList.indexOf(fun);
- if (index > -1) {
- listenerList.splice(index, 1);
- } else {
- logger.warn("Cannot remove listener. It doesn't exist", type, fun);
- }
-};
-
-/**
- * Removes property listener from the object.
- *
- * @param name
- * name of the property
- * @param fun
- * function that was call when event occurred that should be removed
- */
-ObjectWithListeners.prototype.removePropertyListener = function (name, fun) {
- if (this._validPropertyListeners[name] === undefined) {
- throw new Error("Unknown property: " + name);
- }
-
- if (typeof (fun) !== "function") {
- throw new Error("Second parameter must be a function but \"" + typeof (fun) + "\" found.");
- }
-
- var listenerList = this._validPropertyListeners[name];
-
- var index = listenerList.indexOf(fun);
- if (index > -1) {
- listenerList.splice(index, 1);
- } else {
- logger.warn("Cannot remove listener. It doesn't exist", name, fun);
- }
-};
-
-/**
- * Fires listeners of a given type.
- *
- * @param {string} type
- * type of the listener (string)
- * @param arg
- * argument data passed to the handler
- *
- * @returns {PromiseLike}
- */
-ObjectWithListeners.prototype.callListeners = function (type, arg) {
- if (this._validListeners[type] === undefined) {
- throw new Error("Unknown listener type: " + type);
- }
- var listenerList = this._validListeners[type];
- var promises = [];
- if (listenerList.length > 0) {
- for (var i in listenerList) {
- if (listenerList.hasOwnProperty(i)) {
- var e = {
- type: type,
- object: this,
- arg: arg
- };
- promises.push(listenerList[i](e));
- }
- }
- }
- return Promise.all(promises);
-};
-
-ObjectWithListeners.prototype.getListeners = function (type) {
- if (this._validListeners[type] === undefined) {
- throw new Error("Unknown listener type: " + type);
- }
- return this._validListeners[type];
-};
-
-/**
- * Fires property change listeners for a given property name.
- *
- * @param propertyName
- * name of the property
- * @param oldValue
- * old value of the property
- * @param newValue
- * new value of the property
- */
-ObjectWithListeners.prototype.firePropertyChangeListener = function (propertyName, oldValue, newValue) {
- var self = this;
- if (this._validPropertyListeners[propertyName] === undefined) {
- throw new Error("Unknown property type: " + propertyName);
- }
- var listenerList = this._validPropertyListeners[propertyName];
- var promises = [];
- if (listenerList.length > 0) {
- for (var i in listenerList) {
- var e = {
- propertyName: propertyName,
- object: self,
- oldVal: oldValue,
- newVal: newValue
- };
- promises.push(listenerList[i](e));
- }
- }
- return Promise.all(promises);
-};
-
-module.exports = ObjectWithListeners;
+"use strict";
+
+var Promise = require("bluebird");
+
+var logger = require('./logger');
+
+/**
+ * An abstract class that allows to register listeners and call them in case of
+ * events.
+ * @constructor
+ */
+function ObjectWithListeners() {
+ this._validListeners = [];
+ this._validPropertyListeners = [];
+}
+
+/**
+ * @callback ListenerCallback
+ * @param event
+ */
+/**
+ * Adds a listener function to the object.
+ *
+ * @param {string} type
+ * string defining type of the listener
+ * @param {ListenerCallback} fun
+ * function that should be thrown when type event occurs
+ */
+ObjectWithListeners.prototype.addListener = function (type, fun) {
+ if (this._validListeners[type] === undefined) {
+ throw new Error("Unknown listener type: " + type);
+ }
+
+ if (typeof fun !== "function") {
+ throw new Error("Second parameter must be a function but \"" + typeof (fun) + "\" found.");
+ }
+
+ this._validListeners[type].push(fun);
+};
+
+/**
+ * Adds a property change listener function to the object.
+ *
+ * @param {string} name
+ * string defining property name
+ * @param {function} fun
+ * function that should be thrown when firePropertyChangeListener is
+ * called
+ */
+ObjectWithListeners.prototype.addPropertyChangeListener = function (name, fun) {
+ if (this._validPropertyListeners[name] === undefined) {
+ throw new Error("Unknown property type: " + name);
+ }
+
+ if (typeof fun !== "function") {
+ throw new Error("Second parameter must be a function but \"" + typeof (fun) + "\" found.");
+ }
+
+ this._validPropertyListeners[name].push(fun);
+};
+
+/**
+ * Register new type of listener.
+ *
+ * @param type
+ * string identifying new type of listener
+ */
+ObjectWithListeners.prototype.registerListenerType = function (type) {
+ if (this._validListeners[type] !== undefined) {
+ throw new Error("Listener type already registered: " + type);
+ }
+ this._validListeners[type] = [];
+};
+
+/**
+ * Register new property for listening.
+ *
+ * @param name
+ * string identifying property
+ */
+ObjectWithListeners.prototype.registerPropertyType = function (name) {
+ if (this._validPropertyListeners[name] !== undefined) {
+ throw new Error("Property already registered: " + name);
+ }
+ this._validPropertyListeners[name] = [];
+};
+
+/**
+ * Removes listener from the object.
+ *
+ * @param type
+ * type of the listener
+ * @param fun
+ * function that was call when event occurred that should be removed
+ */
+ObjectWithListeners.prototype.removeListener = function (type, fun) {
+ if (this._validListeners[type] === undefined) {
+ throw new Error("Unknown listener type: " + type);
+ }
+
+ if (typeof (fun) !== "function") {
+ throw new Error("Second parameter must be a function but \"" + typeof (fun) + "\" found.");
+ }
+
+ var listenerList = this._validListeners[type];
+
+ var index = listenerList.indexOf(fun);
+ if (index > -1) {
+ listenerList.splice(index, 1);
+ } else {
+ logger.warn("Cannot remove listener. It doesn't exist", type, fun);
+ }
+};
+
+/**
+ * Removes property listener from the object.
+ *
+ * @param name
+ * name of the property
+ * @param fun
+ * function that was call when event occurred that should be removed
+ */
+ObjectWithListeners.prototype.removePropertyListener = function (name, fun) {
+ if (this._validPropertyListeners[name] === undefined) {
+ throw new Error("Unknown property: " + name);
+ }
+
+ if (typeof (fun) !== "function") {
+ throw new Error("Second parameter must be a function but \"" + typeof (fun) + "\" found.");
+ }
+
+ var listenerList = this._validPropertyListeners[name];
+
+ var index = listenerList.indexOf(fun);
+ if (index > -1) {
+ listenerList.splice(index, 1);
+ } else {
+ logger.warn("Cannot remove listener. It doesn't exist", name, fun);
+ }
+};
+
+/**
+ * Fires listeners of a given type.
+ *
+ * @param {string} type
+ * type of the listener (string)
+ * @param arg
+ * argument data passed to the handler
+ *
+ * @returns {PromiseLike}
+ */
+ObjectWithListeners.prototype.callListeners = function (type, arg) {
+ if (this._validListeners[type] === undefined) {
+ throw new Error("Unknown listener type: " + type);
+ }
+ var listenerList = this._validListeners[type];
+ var promises = [];
+ if (listenerList.length > 0) {
+ for (var i in listenerList) {
+ if (listenerList.hasOwnProperty(i)) {
+ var e = {
+ type: type,
+ object: this,
+ arg: arg
+ };
+ promises.push(listenerList[i](e));
+ }
+ }
+ }
+ return Promise.all(promises);
+};
+
+ObjectWithListeners.prototype.getListeners = function (type) {
+ if (this._validListeners[type] === undefined) {
+ throw new Error("Unknown listener type: " + type);
+ }
+ return this._validListeners[type];
+};
+
+/**
+ * Fires property change listeners for a given property name.
+ *
+ * @param propertyName
+ * name of the property
+ * @param oldValue
+ * old value of the property
+ * @param newValue
+ * new value of the property
+ */
+ObjectWithListeners.prototype.firePropertyChangeListener = function (propertyName, oldValue, newValue) {
+ var self = this;
+ if (this._validPropertyListeners[propertyName] === undefined) {
+ throw new Error("Unknown property type: " + propertyName);
+ }
+ var listenerList = this._validPropertyListeners[propertyName];
+ var promises = [];
+ if (listenerList.length > 0) {
+ for (var i in listenerList) {
+ var e = {
+ propertyName: propertyName,
+ object: self,
+ oldVal: oldValue,
+ newVal: newValue
+ };
+ promises.push(listenerList[i](e));
+ }
+ }
+ return Promise.all(promises);
+};
+
+module.exports = ObjectWithListeners;
diff --git a/frontend-js/src/main/js/SecurityError.js b/frontend-js/src/main/js/SecurityError.js
index 7d180d91f4e4b54855719e6d8f610f9f4a1a4682..c5755cafbf7c01cf49adac587591c5641cd1b456 100644
--- a/frontend-js/src/main/js/SecurityError.js
+++ b/frontend-js/src/main/js/SecurityError.js
@@ -1,15 +1,15 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('./logger');
-
-function SecurityError(message) {
- this.message = message;
- this.stack = (new Error()).stack;
-}
-
-SecurityError.prototype = Object.create(Error.prototype);
-SecurityError.prototype.constructor = SecurityError;
-
-module.exports = SecurityError;
+"use strict";
+
+/* exported logger */
+
+var logger = require('./logger');
+
+function SecurityError(message) {
+ this.message = message;
+ this.stack = (new Error()).stack;
+}
+
+SecurityError.prototype = Object.create(Error.prototype);
+SecurityError.prototype.constructor = SecurityError;
+
+module.exports = SecurityError;
diff --git a/frontend-js/src/main/js/SessionData.js b/frontend-js/src/main/js/SessionData.js
index 3d3776a211ce0151e1beae29383c1daf55ff4f34..30b8d32347b85aba7f3ae332b534edc97f9e808b 100644
--- a/frontend-js/src/main/js/SessionData.js
+++ b/frontend-js/src/main/js/SessionData.js
@@ -1,225 +1,225 @@
-"use strict";
-
-/* exported logger */
-
-var Point = require('./map/canvas/Point');
-var SessionObjectType = require('./SessionObjectType');
-
-var Cookies = require('js-cookie');
-
-var logger = require('./logger');
-
-function SessionData(project) {
- if (project === undefined) {
- throw new Error("Project must be passed as an argument");
- }
- this.setProject(project);
-}
-
-SessionData.prototype.setProject = function(project) {
- this._project = project;
-};
-
-SessionData.prototype.getProject = function() {
- return this._project;
-};
-
-SessionData.prototype.getProjectId = function() {
- return this._project.getProjectId();
-};
-
-SessionData.prototype.getShowComments = function() {
- var key = this.getKey(SessionObjectType.SHOW_COMMENT);
- return Cookies.get(key) === "true";
-};
-
-SessionData.prototype.setSearchQuery = function(value) {
- var key = this.getKey(SessionObjectType.SEARCH_QUERY);
- Cookies.set(key, JSON.stringify(value));
-};
-
-SessionData.prototype.setQuery = function(param) {
- if (param.type === "drug") {
- this.setDrugQuery(param.query);
- } else if (param.type === "search") {
- this.setSearchQuery(param.query);
- } else if (param.type === "chemical") {
- this.setChemicalQuery(param.query);
- } else if (param.type === "mirna") {
- this.setMiRnaQuery(param.query);
- } else {
- throw new Error("Invalid query type: " + param.type);
- }
-};
-
-SessionData.prototype.getSearchQuery = function() {
- var key = this.getKey(SessionObjectType.SEARCH_QUERY);
- var result = Cookies.get(key);
- if (result !== undefined) {
- result = JSON.parse(result);
- }
- return result;
-};
-
-SessionData.prototype.setDrugQuery = function(value) {
- var key = this.getKey(SessionObjectType.DRUG_QUERY);
- Cookies.set(key, JSON.stringify(value));
-};
-
-SessionData.prototype.getDrugQuery = function() {
- var key = this.getKey(SessionObjectType.DRUG_QUERY);
- var result = Cookies.get(key);
- if (result !== undefined) {
- result = JSON.parse(result);
- }
- return result;
-};
-
-SessionData.prototype.setMiRnaQuery = function(value) {
- var key = this.getKey(SessionObjectType.MI_RNA_QUERY);
- Cookies.set(key, JSON.stringify(value));
-};
-
-SessionData.prototype.getMiRnaQuery = function() {
- var key = this.getKey(SessionObjectType.MI_RNA_QUERY);
- var result = Cookies.get(key);
- if (result !== undefined) {
- result = JSON.parse(result);
- }
- return result;
-};
-
-SessionData.prototype.setChemicalQuery = function(value) {
- var key = this.getKey(SessionObjectType.CHEMICAL_QUERY);
- Cookies.set(key, JSON.stringify(value));
-};
-
-SessionData.prototype.getChemicalQuery = function() {
- var key = this.getKey(SessionObjectType.CHEMICAL_QUERY);
- var result = Cookies.get(key);
- if (result !== undefined) {
- result = JSON.parse(result);
- }
- return result;
-};
-
-SessionData.prototype.setShowComments = function(value) {
- var key = this.getKey(SessionObjectType.SHOW_COMMENT);
- Cookies.set(key, value + "");
-};
-
-SessionData.prototype.getSelectedBackgroundOverlay = function() {
- var key = this.getKey(SessionObjectType.SELECTED_BACKGROUND_OVERLAY);
- return Cookies.get(key);
-};
-
-SessionData.prototype.setSelectedBackgroundOverlay = function(value) {
- var key = this.getKey(SessionObjectType.SELECTED_BACKGROUND_OVERLAY);
- Cookies.set(key, value + "");
-};
-
-SessionData.prototype.getVisibleOverlays = function() {
- var key = this.getKey(SessionObjectType.VISIBLE_OVERLAYS);
- var value = Cookies.get(key);
- if (value === undefined || value === "") {
- value = [];
- } else {
- value = value.split(",");
- }
- return value;
-};
-
-SessionData.prototype.setVisibleOverlays = function(value) {
- var key = this.getKey(SessionObjectType.VISIBLE_OVERLAYS);
- Cookies.set(key, value + "");
-};
-
-/**
- *
- * @param {MapModel} model
- * @param {number} value
- */
-SessionData.prototype.setZoomLevel = function(model, value) {
- var key = this.getKey(SessionObjectType.ZOOM_LEVEL, [ model.getId() ]);
- Cookies.set(key, value + "");
-};
-
-/**
- *
- * @param {MapModel} model
- * @returns {number}
- */
-SessionData.prototype.getZoomLevel = function(model) {
- var key = this.getKey(SessionObjectType.ZOOM_LEVEL, [ model.getId() ]);
- var value = Cookies.get(key);
- if (value !== undefined) {
- value = parseInt(value);
- }
- return value;
-};
-
-SessionData.prototype.setToken = function(token) {
- var key = SessionObjectType.TOKEN;
- if (token === undefined) {
- Cookies.remove(key);
- } else {
- Cookies.set(key, token);
- }
-};
-
-SessionData.prototype.getToken = function() {
- var key = SessionObjectType.TOKEN;
- return Cookies.get(key);
-};
-
-SessionData.prototype.setLogin = function(login) {
- var key = SessionObjectType.LOGIN;
- if (login === undefined) {
- Cookies.remove(key);
- } else {
- Cookies.set(key, login);
- }
-};
-
-SessionData.prototype.getLogin = function() {
- var key = SessionObjectType.LOGIN;
- return Cookies.get(key);
-};
-
-SessionData.prototype.setCenter = function(model, value) {
- var key = this.getKey(SessionObjectType.CENTER, [ model.getId() ]);
- Cookies.set(key, value.x + "," + value.y);
-};
-
-/**
- *
- * @param {MapModel} model
- * @returns {Point}
- */
-SessionData.prototype.getCenter = function(model) {
- var key = this.getKey(SessionObjectType.CENTER, [ model.getId() ]);
- var value = Cookies.get(key);
- if (value !== undefined) {
- var tmp = value.split(",");
- value = new Point(tmp[0], tmp[1]);
- }
- return value;
-};
-
-/**
- *
- * @param {string} type
- * @param {Array} [args]
- * @returns {string}
- */
-SessionData.prototype.getKey = function(type, args) {
- if (type === undefined) {
- throw new Error("Undefined type");
- }
- if (args === undefined) {
- args = [];
- }
- return type + "_" + this.getProjectId() + "_" + args.join("_");
-};
-
-module.exports = SessionData;
+"use strict";
+
+/* exported logger */
+
+var Point = require('./map/canvas/Point');
+var SessionObjectType = require('./SessionObjectType');
+
+var Cookies = require('js-cookie');
+
+var logger = require('./logger');
+
+function SessionData(project) {
+ if (project === undefined) {
+ throw new Error("Project must be passed as an argument");
+ }
+ this.setProject(project);
+}
+
+SessionData.prototype.setProject = function(project) {
+ this._project = project;
+};
+
+SessionData.prototype.getProject = function() {
+ return this._project;
+};
+
+SessionData.prototype.getProjectId = function() {
+ return this._project.getProjectId();
+};
+
+SessionData.prototype.getShowComments = function() {
+ var key = this.getKey(SessionObjectType.SHOW_COMMENT);
+ return Cookies.get(key) === "true";
+};
+
+SessionData.prototype.setSearchQuery = function(value) {
+ var key = this.getKey(SessionObjectType.SEARCH_QUERY);
+ Cookies.set(key, JSON.stringify(value));
+};
+
+SessionData.prototype.setQuery = function(param) {
+ if (param.type === "drug") {
+ this.setDrugQuery(param.query);
+ } else if (param.type === "search") {
+ this.setSearchQuery(param.query);
+ } else if (param.type === "chemical") {
+ this.setChemicalQuery(param.query);
+ } else if (param.type === "mirna") {
+ this.setMiRnaQuery(param.query);
+ } else {
+ throw new Error("Invalid query type: " + param.type);
+ }
+};
+
+SessionData.prototype.getSearchQuery = function() {
+ var key = this.getKey(SessionObjectType.SEARCH_QUERY);
+ var result = Cookies.get(key);
+ if (result !== undefined) {
+ result = JSON.parse(result);
+ }
+ return result;
+};
+
+SessionData.prototype.setDrugQuery = function(value) {
+ var key = this.getKey(SessionObjectType.DRUG_QUERY);
+ Cookies.set(key, JSON.stringify(value));
+};
+
+SessionData.prototype.getDrugQuery = function() {
+ var key = this.getKey(SessionObjectType.DRUG_QUERY);
+ var result = Cookies.get(key);
+ if (result !== undefined) {
+ result = JSON.parse(result);
+ }
+ return result;
+};
+
+SessionData.prototype.setMiRnaQuery = function(value) {
+ var key = this.getKey(SessionObjectType.MI_RNA_QUERY);
+ Cookies.set(key, JSON.stringify(value));
+};
+
+SessionData.prototype.getMiRnaQuery = function() {
+ var key = this.getKey(SessionObjectType.MI_RNA_QUERY);
+ var result = Cookies.get(key);
+ if (result !== undefined) {
+ result = JSON.parse(result);
+ }
+ return result;
+};
+
+SessionData.prototype.setChemicalQuery = function(value) {
+ var key = this.getKey(SessionObjectType.CHEMICAL_QUERY);
+ Cookies.set(key, JSON.stringify(value));
+};
+
+SessionData.prototype.getChemicalQuery = function() {
+ var key = this.getKey(SessionObjectType.CHEMICAL_QUERY);
+ var result = Cookies.get(key);
+ if (result !== undefined) {
+ result = JSON.parse(result);
+ }
+ return result;
+};
+
+SessionData.prototype.setShowComments = function(value) {
+ var key = this.getKey(SessionObjectType.SHOW_COMMENT);
+ Cookies.set(key, value + "");
+};
+
+SessionData.prototype.getSelectedBackgroundOverlay = function() {
+ var key = this.getKey(SessionObjectType.SELECTED_BACKGROUND_OVERLAY);
+ return Cookies.get(key);
+};
+
+SessionData.prototype.setSelectedBackgroundOverlay = function(value) {
+ var key = this.getKey(SessionObjectType.SELECTED_BACKGROUND_OVERLAY);
+ Cookies.set(key, value + "");
+};
+
+SessionData.prototype.getVisibleOverlays = function() {
+ var key = this.getKey(SessionObjectType.VISIBLE_OVERLAYS);
+ var value = Cookies.get(key);
+ if (value === undefined || value === "") {
+ value = [];
+ } else {
+ value = value.split(",");
+ }
+ return value;
+};
+
+SessionData.prototype.setVisibleOverlays = function(value) {
+ var key = this.getKey(SessionObjectType.VISIBLE_OVERLAYS);
+ Cookies.set(key, value + "");
+};
+
+/**
+ *
+ * @param {MapModel} model
+ * @param {number} value
+ */
+SessionData.prototype.setZoomLevel = function(model, value) {
+ var key = this.getKey(SessionObjectType.ZOOM_LEVEL, [ model.getId() ]);
+ Cookies.set(key, value + "");
+};
+
+/**
+ *
+ * @param {MapModel} model
+ * @returns {number}
+ */
+SessionData.prototype.getZoomLevel = function(model) {
+ var key = this.getKey(SessionObjectType.ZOOM_LEVEL, [ model.getId() ]);
+ var value = Cookies.get(key);
+ if (value !== undefined) {
+ value = parseInt(value);
+ }
+ return value;
+};
+
+SessionData.prototype.setToken = function(token) {
+ var key = SessionObjectType.TOKEN;
+ if (token === undefined) {
+ Cookies.remove(key);
+ } else {
+ Cookies.set(key, token);
+ }
+};
+
+SessionData.prototype.getToken = function() {
+ var key = SessionObjectType.TOKEN;
+ return Cookies.get(key);
+};
+
+SessionData.prototype.setLogin = function(login) {
+ var key = SessionObjectType.LOGIN;
+ if (login === undefined) {
+ Cookies.remove(key);
+ } else {
+ Cookies.set(key, login);
+ }
+};
+
+SessionData.prototype.getLogin = function() {
+ var key = SessionObjectType.LOGIN;
+ return Cookies.get(key);
+};
+
+SessionData.prototype.setCenter = function(model, value) {
+ var key = this.getKey(SessionObjectType.CENTER, [ model.getId() ]);
+ Cookies.set(key, value.x + "," + value.y);
+};
+
+/**
+ *
+ * @param {MapModel} model
+ * @returns {Point}
+ */
+SessionData.prototype.getCenter = function(model) {
+ var key = this.getKey(SessionObjectType.CENTER, [ model.getId() ]);
+ var value = Cookies.get(key);
+ if (value !== undefined) {
+ var tmp = value.split(",");
+ value = new Point(tmp[0], tmp[1]);
+ }
+ return value;
+};
+
+/**
+ *
+ * @param {string} type
+ * @param {Array} [args]
+ * @returns {string}
+ */
+SessionData.prototype.getKey = function(type, args) {
+ if (type === undefined) {
+ throw new Error("Undefined type");
+ }
+ if (args === undefined) {
+ args = [];
+ }
+ return type + "_" + this.getProjectId() + "_" + args.join("_");
+};
+
+module.exports = SessionData;
diff --git a/frontend-js/src/main/js/SessionObjectType.js b/frontend-js/src/main/js/SessionObjectType.js
index 6240a50fff5210bfaf92ec6b7466e4f9aa2fc9d6..f2c0caa4c7336ff0496ed33589a7eeaca68c3b3a 100644
--- a/frontend-js/src/main/js/SessionObjectType.js
+++ b/frontend-js/src/main/js/SessionObjectType.js
@@ -1,19 +1,19 @@
-"use strict";
-
-var SessionObjectType = {
- CHEMICAL_QUERY : "CHEMICAL_QUERY",
- DRUG_QUERY : "DRUG_QUERY",
- MI_RNA_QUERY : "MI_RNA_QUERY",
- SHOW_COMMENT : "SHOW_COMMENT",
- SELECTED_BACKGROUND_OVERLAY : "SELECTED_BACKGROUND_OVERLAY",
- SEARCH_QUERY : "SEARCH_QUERY",
- VISIBLE_OVERLAYS : "VISIBLE_OVERLAYS",
-
- CENTER : "CENTER",
- ZOOM_LEVEL : "ZOOM_LEVEL",
-
- TOKEN: "MINERVA_AUTH_TOKEN",
- LOGIN: "LOGIN"
-};
-
-module.exports = SessionObjectType;
+"use strict";
+
+var SessionObjectType = {
+ CHEMICAL_QUERY : "CHEMICAL_QUERY",
+ DRUG_QUERY : "DRUG_QUERY",
+ MI_RNA_QUERY : "MI_RNA_QUERY",
+ SHOW_COMMENT : "SHOW_COMMENT",
+ SELECTED_BACKGROUND_OVERLAY : "SELECTED_BACKGROUND_OVERLAY",
+ SEARCH_QUERY : "SEARCH_QUERY",
+ VISIBLE_OVERLAYS : "VISIBLE_OVERLAYS",
+
+ CENTER : "CENTER",
+ ZOOM_LEVEL : "ZOOM_LEVEL",
+
+ TOKEN: "MINERVA_AUTH_TOKEN",
+ LOGIN: "LOGIN"
+};
+
+module.exports = SessionObjectType;
diff --git a/frontend-js/src/main/js/ValidationError.js b/frontend-js/src/main/js/ValidationError.js
index e23e2abe0257e48d6f75528bbc63074c921e1819..aaa83e2edfdeed9654d988ad15ec67ac4b6e77a1 100644
--- a/frontend-js/src/main/js/ValidationError.js
+++ b/frontend-js/src/main/js/ValidationError.js
@@ -1,15 +1,15 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('./logger');
-
-function ValidationError(message) {
- this.message = message;
- this.stack = (new Error()).stack;
-}
-
-ValidationError.prototype = Object.create(Error.prototype);
-ValidationError.prototype.constructor = ValidationError;
-
-module.exports = ValidationError;
+"use strict";
+
+/* exported logger */
+
+var logger = require('./logger');
+
+function ValidationError(message) {
+ this.message = message;
+ this.stack = (new Error()).stack;
+}
+
+ValidationError.prototype = Object.create(Error.prototype);
+ValidationError.prototype.constructor = ValidationError;
+
+module.exports = ValidationError;
diff --git a/frontend-js/src/main/js/gui/AbstractGuiElement.js b/frontend-js/src/main/js/gui/AbstractGuiElement.js
index 739abfa07a8a4c91685a8480f0fd49310d8a205c..d5be62beb61320ee976f5a500c173896b9d61b9b 100644
--- a/frontend-js/src/main/js/gui/AbstractGuiElement.js
+++ b/frontend-js/src/main/js/gui/AbstractGuiElement.js
@@ -1,229 +1,229 @@
-"use strict";
-
-/* exported logger */
-
-var ObjectWithListeners = require('../ObjectWithListeners');
-var PanelControlElementType = require('./PanelControlElementType');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../logger');
-var Functions = require('../Functions');
-
-/**
- *
- * @param {Object} params
- * @param {HTMLElement} params.element
- * @param {CustomMap} [params.customMap]
- * @param {Configuration} params.configuration
- * @param {Project} [params.project]
- * @param {ServerConnector} [params.serverConnector]
- *
- * @constructor
- *
- * @extends ObjectWithListeners
- */
-function AbstractGuiElement(params) {
- ObjectWithListeners.call(this, params);
-
- var self = this;
-
- self.setElement(params.element);
- self.setConfiguration(params.configuration);
- self.setProject(params.project);
- self.setMap(params.customMap);
- self.setServerConnector(params.serverConnector);
-
- self._controlElements = [];
-
-}
-
-AbstractGuiElement.prototype = Object.create(ObjectWithListeners.prototype);
-AbstractGuiElement.prototype.constructor = AbstractGuiElement;
-
-/**
- *
- * @param {CustomMap} map
- */
-AbstractGuiElement.prototype.setMap = function (map) {
- this._map = map;
-};
-
-/**
- *
- * @returns {CustomMap}
- */
-AbstractGuiElement.prototype.getMap = function () {
- return this._map;
-};
-
-/**
- *
- * @param {HTMLElement} element
- */
-AbstractGuiElement.prototype.setElement = function (element) {
- if (element === undefined || element === null) {
- throw new Error("DOM Element must be defined");
- }
- this._element = element;
-};
-
-/**
- *
- * @returns {HTMLElement}
- */
-AbstractGuiElement.prototype.getElement = function () {
- return this._element;
-};
-
-/**
- *
- * @param {Project} project
- */
-AbstractGuiElement.prototype.setProject = function (project) {
- this._project = project;
-};
-
-/**
- *
- * @returns {Project}
- */
-AbstractGuiElement.prototype.getProject = function () {
- if (this._project === undefined || this._project === null) {
- if (this.getMap()) {
- return this.getMap().getProject();
- } else {
- return null;
- }
- } else {
- return this._project;
- }
-};
-
-
-/**
- *
- * @param {string} type
- * @param {HTMLElement} element
- */
-AbstractGuiElement.prototype.setControlElement = function (type, element) {
- if (type === null || type === undefined) {
- throw new Error("Unknown control element type");
- }
- if (PanelControlElementType[type] === undefined) {
- throw new Error("Unknown control element type: " + type);
- }
-
- this._controlElements[type] = element;
-};
-
-/**
- *
- * @param {string} type
- * @returns {HTMLElement}
- */
-AbstractGuiElement.prototype.getControlElement = function (type) {
- if (type === null || type === undefined) {
- throw new Error("Unknown control element type");
- }
- if (PanelControlElementType[type] === undefined) {
- throw new Error("Unknown control element type: " + type);
- }
-
- return this._controlElements[type];
-};
-
-/**
- *
- * @param {string} url
- */
-AbstractGuiElement.prototype.downloadFile = function (url) {
- this._downloadFile = url;
- window.open(url, '_blank');
-};
-
-/**
- *
- * @returns {string}
- */
-AbstractGuiElement.prototype.getLastDownloadUrl = function () {
- return this._downloadFile;
-};
-
-/**
- *
- * @param {Configuration} configuration
- */
-AbstractGuiElement.prototype.setConfiguration = function (configuration) {
- this._configuration = configuration;
-};
-
-/**
- *
- * @returns {Configuration}
- */
-AbstractGuiElement.prototype.getConfiguration = function () {
- return this._configuration;
-};
-
-/**
- *
- * @param {ServerConnector} serverConnector
- */
-AbstractGuiElement.prototype.setServerConnector = function (serverConnector) {
- this._serverConnector = serverConnector;
-};
-
-/**
- *
- * @returns {ServerConnector}
- */
-AbstractGuiElement.prototype.getServerConnector = function () {
- if (this._serverConnector !== undefined) {
- return this._serverConnector;
- } else {
- return this.getMap().getServerConnector();
- }
-};
-
-/**
- *
- * @param {string} [params.content]
- * @param {string} params.title
- * @param {boolean} [params.input]
- * @returns {Promise}
- */
-AbstractGuiElement.prototype.askConfirmRemoval = function (params) {
- return new Promise(function (resolve) {
- var html;
- var content = '';
- if (params.content) {
- content = params.content;
- }
- if (params.input) {
- html = '<form><input type="text" style="z-index:10000" name="reason-value"><br></form>';
- } else {
- html = '<form><span>' + content + '</span><input type="text" style="z-index:10000;visibility: hidden" name="reason-value"><br></form>';
- }
- $(html).dialog({
- modal: true,
- title: params.title,
- close: function () {
- $(this).dialog('destroy').remove();
- resolve({status: false});
- },
- buttons: {
- 'OK': function () {
- var reason = $('input[name="reason-value"]').val();
- $(this).dialog('destroy').remove();
- resolve({reason: reason, status: true});
- },
- 'Cancel': function () {
- $(this).dialog('destroy').remove();
- resolve({status: false});
- }
- }
- });
- })
-};
-
-module.exports = AbstractGuiElement;
+"use strict";
+
+/* exported logger */
+
+var ObjectWithListeners = require('../ObjectWithListeners');
+var PanelControlElementType = require('./PanelControlElementType');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../logger');
+var Functions = require('../Functions');
+
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} [params.customMap]
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends ObjectWithListeners
+ */
+function AbstractGuiElement(params) {
+ ObjectWithListeners.call(this, params);
+
+ var self = this;
+
+ self.setElement(params.element);
+ self.setConfiguration(params.configuration);
+ self.setProject(params.project);
+ self.setMap(params.customMap);
+ self.setServerConnector(params.serverConnector);
+
+ self._controlElements = [];
+
+}
+
+AbstractGuiElement.prototype = Object.create(ObjectWithListeners.prototype);
+AbstractGuiElement.prototype.constructor = AbstractGuiElement;
+
+/**
+ *
+ * @param {CustomMap} map
+ */
+AbstractGuiElement.prototype.setMap = function (map) {
+ this._map = map;
+};
+
+/**
+ *
+ * @returns {CustomMap}
+ */
+AbstractGuiElement.prototype.getMap = function () {
+ return this._map;
+};
+
+/**
+ *
+ * @param {HTMLElement} element
+ */
+AbstractGuiElement.prototype.setElement = function (element) {
+ if (element === undefined || element === null) {
+ throw new Error("DOM Element must be defined");
+ }
+ this._element = element;
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
+AbstractGuiElement.prototype.getElement = function () {
+ return this._element;
+};
+
+/**
+ *
+ * @param {Project} project
+ */
+AbstractGuiElement.prototype.setProject = function (project) {
+ this._project = project;
+};
+
+/**
+ *
+ * @returns {Project}
+ */
+AbstractGuiElement.prototype.getProject = function () {
+ if (this._project === undefined || this._project === null) {
+ if (this.getMap()) {
+ return this.getMap().getProject();
+ } else {
+ return null;
+ }
+ } else {
+ return this._project;
+ }
+};
+
+
+/**
+ *
+ * @param {string} type
+ * @param {HTMLElement} element
+ */
+AbstractGuiElement.prototype.setControlElement = function (type, element) {
+ if (type === null || type === undefined) {
+ throw new Error("Unknown control element type");
+ }
+ if (PanelControlElementType[type] === undefined) {
+ throw new Error("Unknown control element type: " + type);
+ }
+
+ this._controlElements[type] = element;
+};
+
+/**
+ *
+ * @param {string} type
+ * @returns {HTMLElement}
+ */
+AbstractGuiElement.prototype.getControlElement = function (type) {
+ if (type === null || type === undefined) {
+ throw new Error("Unknown control element type");
+ }
+ if (PanelControlElementType[type] === undefined) {
+ throw new Error("Unknown control element type: " + type);
+ }
+
+ return this._controlElements[type];
+};
+
+/**
+ *
+ * @param {string} url
+ */
+AbstractGuiElement.prototype.downloadFile = function (url) {
+ this._downloadFile = url;
+ window.open(url, '_blank');
+};
+
+/**
+ *
+ * @returns {string}
+ */
+AbstractGuiElement.prototype.getLastDownloadUrl = function () {
+ return this._downloadFile;
+};
+
+/**
+ *
+ * @param {Configuration} configuration
+ */
+AbstractGuiElement.prototype.setConfiguration = function (configuration) {
+ this._configuration = configuration;
+};
+
+/**
+ *
+ * @returns {Configuration}
+ */
+AbstractGuiElement.prototype.getConfiguration = function () {
+ return this._configuration;
+};
+
+/**
+ *
+ * @param {ServerConnector} serverConnector
+ */
+AbstractGuiElement.prototype.setServerConnector = function (serverConnector) {
+ this._serverConnector = serverConnector;
+};
+
+/**
+ *
+ * @returns {ServerConnector}
+ */
+AbstractGuiElement.prototype.getServerConnector = function () {
+ if (this._serverConnector !== undefined) {
+ return this._serverConnector;
+ } else {
+ return this.getMap().getServerConnector();
+ }
+};
+
+/**
+ *
+ * @param {string} [params.content]
+ * @param {string} params.title
+ * @param {boolean} [params.input]
+ * @returns {Promise}
+ */
+AbstractGuiElement.prototype.askConfirmRemoval = function (params) {
+ return new Promise(function (resolve) {
+ var html;
+ var content = '';
+ if (params.content) {
+ content = params.content;
+ }
+ if (params.input) {
+ html = '<form><input type="text" style="z-index:10000" name="reason-value"><br></form>';
+ } else {
+ html = '<form><span>' + content + '</span><input type="text" style="z-index:10000;visibility: hidden" name="reason-value"><br></form>';
+ }
+ $(html).dialog({
+ modal: true,
+ title: params.title,
+ close: function () {
+ $(this).dialog('destroy').remove();
+ resolve({status: false});
+ },
+ buttons: {
+ 'OK': function () {
+ var reason = $('input[name="reason-value"]').val();
+ $(this).dialog('destroy').remove();
+ resolve({reason: reason, status: true});
+ },
+ 'Cancel': function () {
+ $(this).dialog('destroy').remove();
+ resolve({status: false});
+ }
+ }
+ });
+ })
+};
+
+module.exports = AbstractGuiElement;
diff --git a/frontend-js/src/main/js/gui/AddOverlayDialog.js b/frontend-js/src/main/js/gui/AddOverlayDialog.js
index c1ebf8a420f517009c356d065a73b9d95f8ae0fa..d4d8871d96742d872e950466be9e4f898f38200c 100644
--- a/frontend-js/src/main/js/gui/AddOverlayDialog.js
+++ b/frontend-js/src/main/js/gui/AddOverlayDialog.js
@@ -1,296 +1,296 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractGuiElement = require('./AbstractGuiElement');
-var GuiConnector = require('../GuiConnector');
-var GuiUtils = require('./leftPanel/GuiUtils');
-var DataOverlay = require('../map/data/DataOverlay');
-var NetworkError = require('../NetworkError');
-
-var OverlayParser = require('../map/OverlayParser');
-
-var Functions = require('../Functions');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../logger');
-var HttpStatus = require('http-status-codes');
-
-var Promise = require("bluebird");
-var TextEncoder = require('text-encoding').TextEncoder;
-
-/**
- *
- * @param {Object} params
- * @param {HTMLElement} params.element
- * @param {CustomMap} params.customMap
- * @param {Configuration} params.configuration
- * @param {Project} params.project
- * @param {ServerConnector} [params.serverConnector]
- *
- * @constructor
- *
- * @extends AbstractGuiElement
- */
-function AddOverlayDialog(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
- self.registerListenerType("onAddOverlay");
- self.createGui();
-}
-
-AddOverlayDialog.prototype = Object.create(AbstractGuiElement.prototype);
-AddOverlayDialog.prototype.constructor = AddOverlayDialog;
-
-/**
- *
- */
-AddOverlayDialog.prototype.createGui = function () {
- var self = this;
- var guiUtils = new GuiUtils(self.getConfiguration());
- var content = document.createElement("div");
- content.style.width = "100%";
- content.style.height = "100%";
- content.appendChild(guiUtils.createLabel("Name: "));
- var nameInput = Functions.createElement({
- type: "input",
- inputType: "text",
- name: "overlay-name"
- });
- content.appendChild(nameInput);
- content.appendChild(guiUtils.createNewLine());
-
- content.appendChild(guiUtils.createLabel("Description: "));
- content.appendChild(guiUtils.createNewLine());
- var descriptionInput = Functions.createElement({
- type: "textarea",
- name: "overlay-description"
- });
- content.appendChild(descriptionInput);
- content.appendChild(guiUtils.createNewLine());
-
- content.appendChild(guiUtils.createLabel("Type: "));
- content.appendChild(guiUtils.createNewLine());
- var types = self.getConfiguration().getOverlayTypes();
- var typeSelect = Functions.createElement({
- type: "select",
- name: "overlay-type",
- value: types[0]
- });
- for (var i = 0; i < types.length; i++) {
- $(typeSelect).append($('<option>', {
- value: types[i],
- text: types[i]
- }));
- }
-
- content.appendChild(typeSelect);
- content.appendChild(guiUtils.createNewLine());
-
- content.appendChild(guiUtils.createLabel("Upload file: "));
- var fileInput = Functions.createElement({
- type: "input",
- inputType: "file",
- name: "overlay-file"
- });
- fileInput.addEventListener("change", function () {
- return self.processFile(fileInput.files[0]).then(null, GuiConnector.alert);
- }, false);
- content.appendChild(fileInput);
- content.appendChild(guiUtils.createNewLine());
-
- content.appendChild(guiUtils.createLabel("Or provide list of elements here (one per line): "));
- content.appendChild(guiUtils.createNewLine());
- var contentInput = Functions.createElement({
- type: "textarea",
- name: "overlay-content"
- });
- content.appendChild(contentInput);
- content.appendChild(guiUtils.createNewLine());
-
- var consentCheckbox = Functions.createElement({type: "input", name: "overlay-google-consent"});
- consentCheckbox.type = "checkbox";
- content.appendChild(consentCheckbox);
- content.appendChild(guiUtils.createLabel("I am aware that if this map is displayed using Google Maps API, " +
- "it falls under their license <a href='https://cloud.google.com/maps-platform/terms/' target='_blank'>" +
- "https://cloud.google.com/maps-platform/terms/</a>, to which I agree. I warrant that this dataset contains no " +
- "Protected Health Information (as defined in and subject to HIPAA)."));
-
- content.appendChild(guiUtils.createNewLine());
-
- self.getElement().appendChild(content);
-};
-
-AddOverlayDialog.prototype.processFile = function (file) {
- var self = this;
- self.setFileContent(null);
- if (file) {
- return new Promise(function (resolve, reject) {
- var reader = new FileReader();
- reader.readAsArrayBuffer(file);
- reader.onload = function (evt) {
- try {
- var overlayParser = new OverlayParser();
- self.setFileContent(evt.target.result);
- var overlay = overlayParser.parse(evt.target.result);
- var nameInput = $("[name='overlay-name']", self.getElement())[0];
- var descriptionInput = $("[name='overlay-description']", self.getElement())[0];
- var typeSelect = $("[name='overlay-type']", self.getElement());
- if (overlay.getName() !== undefined) {
- nameInput.value = overlay.getName();
- } else {
- var filename = $("[name='overlay-file']", self.getElement())[0].value;
- if (filename.indexOf(".") > 0) {
- filename = filename.substr(0, filename.indexOf("."));
- }
- if (filename.lastIndexOf("\\") >= 0) {
- filename = filename.substr(filename.lastIndexOf("\\") + 1);
- }
- nameInput.value = filename;
-
- }
- if (overlay.getDescription() !== undefined) {
- descriptionInput.value = overlay.getDescription();
- }
- if (overlay.getType() !== undefined) {
- typeSelect.val(overlay.getType());
- }
- if (overlayParser.containsMixedNewLineCharacters(evt.target.result)) {
- GuiConnector.warn("Selected file contains new line characters from different operating systems " +
- "(MAC/Windows/Linux). This might cause confusion when reading the file in the editor later on.")
- }
- resolve(self.getFileContent());
- } catch (error) {
- reject(error);
- }
- };
- reader.onerror = function () {
- reject(new Error("Problem reading file"));
- };
- });
- } else {
- return Promise.resolve(null);
- }
-};
-
-AddOverlayDialog.prototype.setFileContent = function (fileContent) {
- if (typeof fileContent === 'string' || fileContent instanceof String) {
- fileContent = new TextEncoder("UTF8").encode(fileContent);
- }
-
- this._fileContent = fileContent;
-};
-
-AddOverlayDialog.prototype.getFileContent = function () {
- var self = this;
- var contentInput = $("[name='overlay-content']", self.getElement())[0];
-
- if (contentInput.value !== undefined && contentInput.value !== null) {
- contentInput.value = contentInput.value.trim();
- if (contentInput.value !== "") {
- self.setFileContent(contentInput.value);
- }
- }
- if (self._fileContent === undefined) {
- return null;
- } else {
- return self._fileContent;
- }
-};
-
-/**
- *
- * @returns {Promise}
- */
-AddOverlayDialog.prototype.init = function () {
- return Promise.resolve();
-};
-
-
-AddOverlayDialog.prototype.addOverlay = function () {
- var self = this;
- var nameInput = $("[name='overlay-name']", self.getElement())[0];
- var descriptionInput = $("[name='overlay-description']", self.getElement())[0];
- var filename = $("[name='overlay-file']", self.getElement())[0].value;
- var type = $("[name='overlay-type']", self.getElement()).val();
- var consent = $("[name='overlay-google-consent']", self.getElement()).is(":checked");
- var overlay = new DataOverlay({
- name: nameInput.value,
- description: descriptionInput.value,
- filename: filename,
- googleLicenseConsent: consent,
- type: type
- });
-
- if (filename === undefined || filename === "") {
- filename = "unknown.txt";
- }
- GuiConnector.showProcessing();
- return self.getServerConnector().uploadFile({
- filename: filename,
- content: self.getFileContent()
- }).then(function (file) {
- return self.getServerConnector().addOverlay({
- fileId: file.id,
- overlay: overlay,
- projectId: self.getProject().getProjectId()
- });
- }).then(function (result) {
- overlay = result;
- GuiConnector.hideProcessing();
- return self.callListeners("onAddOverlay", overlay);
- });
-};
-
-/**
- *
- * @returns {PromiseLike}
- */
-AddOverlayDialog.prototype.destroy = function () {
- $(this.getElement()).dialog("destroy");
- return Promise.resolve();
-};
-
-AddOverlayDialog.prototype.open = function () {
- var self = this;
- var div = self.getElement();
- if (!$(div).hasClass("ui-dialog-content")) {
- var buttons = [{
- text: "UPLOAD",
- click: function () {
- var dialog = this;
- var fileContent = self.getFileContent();
- if (fileContent === null) {
- GuiConnector.alert("Neither file was selected nor data was entered");
- } else {
- return self.addOverlay().then(function (result) {
- $(dialog).dialog("close");
- return result;
- }, function (error) {
- GuiConnector.hideProcessing();
- if (error instanceof NetworkError && error.statusCode === HttpStatus.BAD_REQUEST) {
- var errorMessage = JSON.parse(error.content);
- GuiConnector.alert("Problematic input: <br/>" + errorMessage.reason);
- } else {
- GuiConnector.alert(error);
- }
- });
- }
- }
- }, {
- text: "CANCEL",
- click: function () {
- $(this).dialog("close");
- }
- }];
-
- $(div).dialog({
- title: "Add overlay",
- buttons: buttons,
- modal: true
- });
- }
-
- $(div).dialog("open");
-};
-
-module.exports = AddOverlayDialog;
+"use strict";
+
+/* exported logger */
+
+var AbstractGuiElement = require('./AbstractGuiElement');
+var GuiConnector = require('../GuiConnector');
+var GuiUtils = require('./leftPanel/GuiUtils');
+var DataOverlay = require('../map/data/DataOverlay');
+var NetworkError = require('../NetworkError');
+
+var OverlayParser = require('../map/OverlayParser');
+
+var Functions = require('../Functions');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../logger');
+var HttpStatus = require('http-status-codes');
+
+var Promise = require("bluebird");
+var TextEncoder = require('text-encoding').TextEncoder;
+
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} params.project
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
+function AddOverlayDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ self.registerListenerType("onAddOverlay");
+ self.createGui();
+}
+
+AddOverlayDialog.prototype = Object.create(AbstractGuiElement.prototype);
+AddOverlayDialog.prototype.constructor = AddOverlayDialog;
+
+/**
+ *
+ */
+AddOverlayDialog.prototype.createGui = function () {
+ var self = this;
+ var guiUtils = new GuiUtils(self.getConfiguration());
+ var content = document.createElement("div");
+ content.style.width = "100%";
+ content.style.height = "100%";
+ content.appendChild(guiUtils.createLabel("Name: "));
+ var nameInput = Functions.createElement({
+ type: "input",
+ inputType: "text",
+ name: "overlay-name"
+ });
+ content.appendChild(nameInput);
+ content.appendChild(guiUtils.createNewLine());
+
+ content.appendChild(guiUtils.createLabel("Description: "));
+ content.appendChild(guiUtils.createNewLine());
+ var descriptionInput = Functions.createElement({
+ type: "textarea",
+ name: "overlay-description"
+ });
+ content.appendChild(descriptionInput);
+ content.appendChild(guiUtils.createNewLine());
+
+ content.appendChild(guiUtils.createLabel("Type: "));
+ content.appendChild(guiUtils.createNewLine());
+ var types = self.getConfiguration().getOverlayTypes();
+ var typeSelect = Functions.createElement({
+ type: "select",
+ name: "overlay-type",
+ value: types[0]
+ });
+ for (var i = 0; i < types.length; i++) {
+ $(typeSelect).append($('<option>', {
+ value: types[i],
+ text: types[i]
+ }));
+ }
+
+ content.appendChild(typeSelect);
+ content.appendChild(guiUtils.createNewLine());
+
+ content.appendChild(guiUtils.createLabel("Upload file: "));
+ var fileInput = Functions.createElement({
+ type: "input",
+ inputType: "file",
+ name: "overlay-file"
+ });
+ fileInput.addEventListener("change", function () {
+ return self.processFile(fileInput.files[0]).then(null, GuiConnector.alert);
+ }, false);
+ content.appendChild(fileInput);
+ content.appendChild(guiUtils.createNewLine());
+
+ content.appendChild(guiUtils.createLabel("Or provide list of elements here (one per line): "));
+ content.appendChild(guiUtils.createNewLine());
+ var contentInput = Functions.createElement({
+ type: "textarea",
+ name: "overlay-content"
+ });
+ content.appendChild(contentInput);
+ content.appendChild(guiUtils.createNewLine());
+
+ var consentCheckbox = Functions.createElement({type: "input", name: "overlay-google-consent"});
+ consentCheckbox.type = "checkbox";
+ content.appendChild(consentCheckbox);
+ content.appendChild(guiUtils.createLabel("I am aware that if this map is displayed using Google Maps API, " +
+ "it falls under their license <a href='https://cloud.google.com/maps-platform/terms/' target='_blank'>" +
+ "https://cloud.google.com/maps-platform/terms/</a>, to which I agree. I warrant that this dataset contains no " +
+ "Protected Health Information (as defined in and subject to HIPAA)."));
+
+ content.appendChild(guiUtils.createNewLine());
+
+ self.getElement().appendChild(content);
+};
+
+AddOverlayDialog.prototype.processFile = function (file) {
+ var self = this;
+ self.setFileContent(null);
+ if (file) {
+ return new Promise(function (resolve, reject) {
+ var reader = new FileReader();
+ reader.readAsArrayBuffer(file);
+ reader.onload = function (evt) {
+ try {
+ var overlayParser = new OverlayParser();
+ self.setFileContent(evt.target.result);
+ var overlay = overlayParser.parse(evt.target.result);
+ var nameInput = $("[name='overlay-name']", self.getElement())[0];
+ var descriptionInput = $("[name='overlay-description']", self.getElement())[0];
+ var typeSelect = $("[name='overlay-type']", self.getElement());
+ if (overlay.getName() !== undefined) {
+ nameInput.value = overlay.getName();
+ } else {
+ var filename = $("[name='overlay-file']", self.getElement())[0].value;
+ if (filename.indexOf(".") > 0) {
+ filename = filename.substr(0, filename.indexOf("."));
+ }
+ if (filename.lastIndexOf("\\") >= 0) {
+ filename = filename.substr(filename.lastIndexOf("\\") + 1);
+ }
+ nameInput.value = filename;
+
+ }
+ if (overlay.getDescription() !== undefined) {
+ descriptionInput.value = overlay.getDescription();
+ }
+ if (overlay.getType() !== undefined) {
+ typeSelect.val(overlay.getType());
+ }
+ if (overlayParser.containsMixedNewLineCharacters(evt.target.result)) {
+ GuiConnector.warn("Selected file contains new line characters from different operating systems " +
+ "(MAC/Windows/Linux). This might cause confusion when reading the file in the editor later on.")
+ }
+ resolve(self.getFileContent());
+ } catch (error) {
+ reject(error);
+ }
+ };
+ reader.onerror = function () {
+ reject(new Error("Problem reading file"));
+ };
+ });
+ } else {
+ return Promise.resolve(null);
+ }
+};
+
+AddOverlayDialog.prototype.setFileContent = function (fileContent) {
+ if (typeof fileContent === 'string' || fileContent instanceof String) {
+ fileContent = new TextEncoder("UTF8").encode(fileContent);
+ }
+
+ this._fileContent = fileContent;
+};
+
+AddOverlayDialog.prototype.getFileContent = function () {
+ var self = this;
+ var contentInput = $("[name='overlay-content']", self.getElement())[0];
+
+ if (contentInput.value !== undefined && contentInput.value !== null) {
+ contentInput.value = contentInput.value.trim();
+ if (contentInput.value !== "") {
+ self.setFileContent(contentInput.value);
+ }
+ }
+ if (self._fileContent === undefined) {
+ return null;
+ } else {
+ return self._fileContent;
+ }
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+AddOverlayDialog.prototype.init = function () {
+ return Promise.resolve();
+};
+
+
+AddOverlayDialog.prototype.addOverlay = function () {
+ var self = this;
+ var nameInput = $("[name='overlay-name']", self.getElement())[0];
+ var descriptionInput = $("[name='overlay-description']", self.getElement())[0];
+ var filename = $("[name='overlay-file']", self.getElement())[0].value;
+ var type = $("[name='overlay-type']", self.getElement()).val();
+ var consent = $("[name='overlay-google-consent']", self.getElement()).is(":checked");
+ var overlay = new DataOverlay({
+ name: nameInput.value,
+ description: descriptionInput.value,
+ filename: filename,
+ googleLicenseConsent: consent,
+ type: type
+ });
+
+ if (filename === undefined || filename === "") {
+ filename = "unknown.txt";
+ }
+ GuiConnector.showProcessing();
+ return self.getServerConnector().uploadFile({
+ filename: filename,
+ content: self.getFileContent()
+ }).then(function (file) {
+ return self.getServerConnector().addOverlay({
+ fileId: file.id,
+ overlay: overlay,
+ projectId: self.getProject().getProjectId()
+ });
+ }).then(function (result) {
+ overlay = result;
+ GuiConnector.hideProcessing();
+ return self.callListeners("onAddOverlay", overlay);
+ });
+};
+
+/**
+ *
+ * @returns {PromiseLike}
+ */
+AddOverlayDialog.prototype.destroy = function () {
+ $(this.getElement()).dialog("destroy");
+ return Promise.resolve();
+};
+
+AddOverlayDialog.prototype.open = function () {
+ var self = this;
+ var div = self.getElement();
+ if (!$(div).hasClass("ui-dialog-content")) {
+ var buttons = [{
+ text: "UPLOAD",
+ click: function () {
+ var dialog = this;
+ var fileContent = self.getFileContent();
+ if (fileContent === null) {
+ GuiConnector.alert("Neither file was selected nor data was entered");
+ } else {
+ return self.addOverlay().then(function (result) {
+ $(dialog).dialog("close");
+ return result;
+ }, function (error) {
+ GuiConnector.hideProcessing();
+ if (error instanceof NetworkError && error.statusCode === HttpStatus.BAD_REQUEST) {
+ var errorMessage = JSON.parse(error.content);
+ GuiConnector.alert("Problematic input: <br/>" + errorMessage.reason);
+ } else {
+ GuiConnector.alert(error);
+ }
+ });
+ }
+ }
+ }, {
+ text: "CANCEL",
+ click: function () {
+ $(this).dialog("close");
+ }
+ }];
+
+ $(div).dialog({
+ title: "Add overlay",
+ buttons: buttons,
+ modal: true
+ });
+ }
+
+ $(div).dialog("open");
+};
+
+module.exports = AddOverlayDialog;
diff --git a/frontend-js/src/main/js/gui/CommentDialog.js b/frontend-js/src/main/js/gui/CommentDialog.js
index 0ca87663084dad9a3f1217e80ac3c515b973a3dc..4a9dea6082de56d5d990a1032815e4514f7412a4 100644
--- a/frontend-js/src/main/js/gui/CommentDialog.js
+++ b/frontend-js/src/main/js/gui/CommentDialog.js
@@ -1,317 +1,317 @@
-"use strict";
-
-/* exported logger */
-
-var Promise = require("bluebird");
-
-var AbstractGuiElement = require('./AbstractGuiElement');
-var Alias = require('../map/data/Alias');
-var Reaction = require('../map/data/Reaction');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../logger');
-var Functions = require('../Functions');
-
-function CommentDialog(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
- self._createGui();
- $(self.getElement()).dialog({
- autoOpen: false,
- resizable: false,
- width: window.innerWidth / 2,
- height: window.innerHeight / 2
- });
-}
-
-CommentDialog.prototype = Object.create(AbstractGuiElement.prototype);
-CommentDialog.prototype.constructor = CommentDialog;
-
-CommentDialog.GENERAL = "<General>";
-
-function createRow(elements) {
- var row = document.createElement('tr');
- for (var i = 0; i < elements.length; i++) {
- var container = document.createElement('td');
- container.appendChild(elements[i]);
- row.appendChild(container);
- }
- return row;
-}
-
-CommentDialog.prototype.open = function (identifiedElements) {
- var self = this;
- self.setTypes([CommentDialog.GENERAL]);
-
- var promises = [CommentDialog.GENERAL];
- for (var i = 0; i < identifiedElements.length; i++) {
- var ie = identifiedElements[i];
- if (ie.getType() === "ALIAS") {
- promises.push(self.getMap().getSubmapById(ie.getModelId()).getModel().getAliasById(ie.getId(), true));
- } else if (ie.getType() === "REACTION") {
- promises.push(self.getMap().getSubmapById(ie.getModelId()).getModel().getReactionById(ie.getId(), true));
- } else {
- throw new Error("Unknown element type: " + ie.getType());
- }
- }
- return Promise.all(promises).then(function (elements) {
- self.setTypes(elements);
- return self.getMap().getServerConnector().getLoggedUser();
- }).then(function (user) {
- if (user.getLogin() !== "anonymous") {
- self.setEmail(user.getEmail());
- self.setName(user.getName() + " " + user.getSurname());
- }
-
- $(self.getElement()).dialog("open");
- });
-};
-
-CommentDialog.prototype._createGui = function () {
- var self = this;
-
- var table = document.createElement('table');
-
- var typeLabel = document.createElement('label');
- typeLabel.innerHTML = "Type";
- var typeOptions = document.createElement("select");
- this.setTypeOptions(typeOptions);
-
- table.appendChild(createRow([typeLabel, typeOptions]));
-
- var detailDiv = document.createElement('div');
-
- table.appendChild(createRow([document.createElement('div'), detailDiv]));
-
- var pinnedLabel = document.createElement('label');
- pinnedLabel.innerHTML = "Pinned";
- var pinnedCheckbox = document.createElement('input');
- pinnedCheckbox.type = "checkbox";
- $(pinnedCheckbox).prop("checked", true);
-
-
- table.appendChild(createRow([pinnedLabel, pinnedCheckbox]));
- this.setPinnedCheckbox(pinnedCheckbox);
-
- var nameLabel = document.createElement('label');
- nameLabel.innerHTML = "Name:<br/>(Visible to moderators only)";
- var nameInput = document.createElement('input');
- nameInput.type = "text";
-
- table.appendChild(createRow([nameLabel, nameInput]));
- this.setNameInput(nameInput);
-
- var emailLabel = document.createElement('label');
- emailLabel.innerHTML = "Email:<br/>(Visible to moderators only)";
- var emailInput = document.createElement('input');
- emailInput.type = "text";
-
- table.appendChild(createRow([emailLabel, emailInput]));
- this.setEmailInput(emailInput);
-
- var contentLabel = document.createElement('label');
- contentLabel.innerHTML = "Content:";
- var contentInput = document.createElement('textarea');
- contentInput.cols = 80;
- contentInput.rows = 3;
-
- table.appendChild(createRow([contentLabel, contentInput]));
- this.setContentInput(contentInput);
-
- var sendButton = document.createElement('button');
- sendButton.innerHTML = "Send";
- sendButton.onclick = function () {
- return self.addComment().then(function () {
- $(self.getElement()).dialog("close");
- });
- };
-
- table.appendChild(createRow([sendButton]));
-
- self.getElement().appendChild(table);
-
- typeOptions.onchange = function () {
- var option = self.getSelectedType();
- var text = "";
- if (option instanceof Alias) {
- if (option.getFullName() !== undefined) {
- text = option.getFullName();
- }
- } else if (option instanceof Reaction) {
- text = "Reactants: ";
- var reactants = option.getReactants();
- var i;
- for (i = 0; i < reactants.length; i++) {
- text += reactants[i].getAlias().getName() + ",";
- }
- text += "<br/>";
- text += "Modifiers: ";
- var modifiers = option.getModifiers();
- for (i = 0; i < modifiers.length; i++) {
- text += modifiers[i].getAlias().getName() + ",";
- }
- text += "<br/>";
- text += "Products: ";
- var products = option.getProducts();
- for (i = 0; i < products.length; i++) {
- text += products[i].getAlias().getName() + ",";
- }
- text += "<br/>";
- }
- detailDiv.innerHTML = text;
- };
-};
-CommentDialog.prototype.setTypes = function (types) {
- var typeOptions = this.getTypeOptions();
- while (typeOptions.firstChild) {
- typeOptions.removeChild(typeOptions.firstChild);
- }
-
- for (var i = 0; i < types.length; i++) {
- var option = document.createElement("option");
- option.value = i.toString();
- var element = types[i];
- var text = element;
- if (element instanceof Alias) {
- text = element.getType() + ": " + element.getName();
- } else if (element instanceof Reaction) {
- text = "Reaction: " + element.getReactionId();
- }
- option.text = text;
- typeOptions.appendChild(option);
- }
- typeOptions.value = 0;
-
- this._types = types;
- typeOptions.onchange();
-};
-
-CommentDialog.prototype.getTypes = function () {
- return this._types;
-};
-
-CommentDialog.prototype.getSelectedType = function () {
- return this._types[this.getTypeOptions().value];
-};
-
-CommentDialog.prototype.setSelectedType = function (value) {
- if (Functions.isInt(value)) {
- this.getTypeOptions().value = value;
- this.getTypeOptions().onchange();
- } else {
- throw new Error("Unknown value type: " + value);
- }
-};
-
-CommentDialog.prototype.getTypeOptions = function () {
- return this._typeOptions;
-};
-CommentDialog.prototype.setTypeOptions = function (typeOptions) {
- this._typeOptions = typeOptions;
-};
-CommentDialog.prototype.setContentInput = function (contentInput) {
- this._contentInput = contentInput;
-};
-CommentDialog.prototype.getContentInput = function () {
- return this._contentInput;
-};
-CommentDialog.prototype.setNameInput = function (nameInput) {
- this._nameInput = nameInput;
-};
-CommentDialog.prototype.getNameInput = function () {
- return this._nameInput;
-};
-CommentDialog.prototype.setEmailInput = function (emailInput) {
- this._emailInput = emailInput;
-};
-CommentDialog.prototype.getEmailInput = function () {
- return this._emailInput;
-};
-CommentDialog.prototype.setPinnedCheckbox = function (pinnedCheckbox) {
- this._pinnedCheckbox = pinnedCheckbox;
-};
-
-CommentDialog.prototype.getPinnedCheckbox = function () {
- return this._pinnedCheckbox;
-};
-
-CommentDialog.prototype.getTypes = function () {
- return this._types;
-};
-
-CommentDialog.prototype.setName = function (name) {
- this.getNameInput().value = name;
-};
-
-CommentDialog.prototype.getName = function () {
- return this.getNameInput().value;
-};
-
-CommentDialog.prototype.getEmail = function () {
- return this.getEmailInput().value;
-};
-
-CommentDialog.prototype.setEmail = function (email) {
- this.getEmailInput().value = email;
-};
-
-CommentDialog.prototype.getContent = function () {
- return this.getContentInput().value;
-};
-
-CommentDialog.prototype.isPinned = function () {
- return this.getPinnedCheckbox().checked;
-};
-CommentDialog.prototype.getSelectedTypeId = function () {
- var selected = this.getSelectedType();
- if (selected instanceof Alias) {
- return selected.getId();
- } else if (selected instanceof Reaction) {
- return selected.getId();
- } else {
- return "";
- }
-};
-
-CommentDialog.prototype.getSelectedTypeClass = function () {
- var selected = this.getSelectedType();
- if (selected instanceof Alias) {
- return "ALIAS";
- } else if (selected instanceof Reaction) {
- return "REACTION";
- } else {
- return "POINT";
- }
-};
-
-/**
- *
- * @returns {Promise}
- */
-CommentDialog.prototype.addComment = function () {
- var self = this;
- var name = self.getName();
- return self.getMap().getServerConnector().addComment({
- modelId: self.getMap().getActiveSubmapId(),
- coordinates: self.getMap().getActiveSubmapClickCoordinates(),
- name: name,
- email: self.getEmail(),
- content: self.getContent(),
- pinned: self.isPinned(),
- elementId: self.getSelectedTypeId(),
- elementType: self.getSelectedTypeClass()
-
- }).then(function (comment) {
- //if we visualize comments add it to data set
- if (self.getMap().getServerConnector().getSessionData(self.getProject()).getShowComments() && comment.isPinned()) {
- return self.getMap().getOverlayByName("comment").addComment(comment);
- } else {
- return [];
- }
- });
-};
-
-CommentDialog.prototype.destroy = function () {
- $(this.getElement()).dialog("destroy");
-};
-
-module.exports = CommentDialog;
+"use strict";
+
+/* exported logger */
+
+var Promise = require("bluebird");
+
+var AbstractGuiElement = require('./AbstractGuiElement');
+var Alias = require('../map/data/Alias');
+var Reaction = require('../map/data/Reaction');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../logger');
+var Functions = require('../Functions');
+
+function CommentDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ self._createGui();
+ $(self.getElement()).dialog({
+ autoOpen: false,
+ resizable: false,
+ width: window.innerWidth / 2,
+ height: window.innerHeight / 2
+ });
+}
+
+CommentDialog.prototype = Object.create(AbstractGuiElement.prototype);
+CommentDialog.prototype.constructor = CommentDialog;
+
+CommentDialog.GENERAL = "<General>";
+
+function createRow(elements) {
+ var row = document.createElement('tr');
+ for (var i = 0; i < elements.length; i++) {
+ var container = document.createElement('td');
+ container.appendChild(elements[i]);
+ row.appendChild(container);
+ }
+ return row;
+}
+
+CommentDialog.prototype.open = function (identifiedElements) {
+ var self = this;
+ self.setTypes([CommentDialog.GENERAL]);
+
+ var promises = [CommentDialog.GENERAL];
+ for (var i = 0; i < identifiedElements.length; i++) {
+ var ie = identifiedElements[i];
+ if (ie.getType() === "ALIAS") {
+ promises.push(self.getMap().getSubmapById(ie.getModelId()).getModel().getAliasById(ie.getId(), true));
+ } else if (ie.getType() === "REACTION") {
+ promises.push(self.getMap().getSubmapById(ie.getModelId()).getModel().getReactionById(ie.getId(), true));
+ } else {
+ throw new Error("Unknown element type: " + ie.getType());
+ }
+ }
+ return Promise.all(promises).then(function (elements) {
+ self.setTypes(elements);
+ return self.getMap().getServerConnector().getLoggedUser();
+ }).then(function (user) {
+ if (user.getLogin() !== "anonymous") {
+ self.setEmail(user.getEmail());
+ self.setName(user.getName() + " " + user.getSurname());
+ }
+
+ $(self.getElement()).dialog("open");
+ });
+};
+
+CommentDialog.prototype._createGui = function () {
+ var self = this;
+
+ var table = document.createElement('table');
+
+ var typeLabel = document.createElement('label');
+ typeLabel.innerHTML = "Type";
+ var typeOptions = document.createElement("select");
+ this.setTypeOptions(typeOptions);
+
+ table.appendChild(createRow([typeLabel, typeOptions]));
+
+ var detailDiv = document.createElement('div');
+
+ table.appendChild(createRow([document.createElement('div'), detailDiv]));
+
+ var pinnedLabel = document.createElement('label');
+ pinnedLabel.innerHTML = "Pinned";
+ var pinnedCheckbox = document.createElement('input');
+ pinnedCheckbox.type = "checkbox";
+ $(pinnedCheckbox).prop("checked", true);
+
+
+ table.appendChild(createRow([pinnedLabel, pinnedCheckbox]));
+ this.setPinnedCheckbox(pinnedCheckbox);
+
+ var nameLabel = document.createElement('label');
+ nameLabel.innerHTML = "Name:<br/>(Visible to moderators only)";
+ var nameInput = document.createElement('input');
+ nameInput.type = "text";
+
+ table.appendChild(createRow([nameLabel, nameInput]));
+ this.setNameInput(nameInput);
+
+ var emailLabel = document.createElement('label');
+ emailLabel.innerHTML = "Email:<br/>(Visible to moderators only)";
+ var emailInput = document.createElement('input');
+ emailInput.type = "text";
+
+ table.appendChild(createRow([emailLabel, emailInput]));
+ this.setEmailInput(emailInput);
+
+ var contentLabel = document.createElement('label');
+ contentLabel.innerHTML = "Content:";
+ var contentInput = document.createElement('textarea');
+ contentInput.cols = 80;
+ contentInput.rows = 3;
+
+ table.appendChild(createRow([contentLabel, contentInput]));
+ this.setContentInput(contentInput);
+
+ var sendButton = document.createElement('button');
+ sendButton.innerHTML = "Send";
+ sendButton.onclick = function () {
+ return self.addComment().then(function () {
+ $(self.getElement()).dialog("close");
+ });
+ };
+
+ table.appendChild(createRow([sendButton]));
+
+ self.getElement().appendChild(table);
+
+ typeOptions.onchange = function () {
+ var option = self.getSelectedType();
+ var text = "";
+ if (option instanceof Alias) {
+ if (option.getFullName() !== undefined) {
+ text = option.getFullName();
+ }
+ } else if (option instanceof Reaction) {
+ text = "Reactants: ";
+ var reactants = option.getReactants();
+ var i;
+ for (i = 0; i < reactants.length; i++) {
+ text += reactants[i].getAlias().getName() + ",";
+ }
+ text += "<br/>";
+ text += "Modifiers: ";
+ var modifiers = option.getModifiers();
+ for (i = 0; i < modifiers.length; i++) {
+ text += modifiers[i].getAlias().getName() + ",";
+ }
+ text += "<br/>";
+ text += "Products: ";
+ var products = option.getProducts();
+ for (i = 0; i < products.length; i++) {
+ text += products[i].getAlias().getName() + ",";
+ }
+ text += "<br/>";
+ }
+ detailDiv.innerHTML = text;
+ };
+};
+CommentDialog.prototype.setTypes = function (types) {
+ var typeOptions = this.getTypeOptions();
+ while (typeOptions.firstChild) {
+ typeOptions.removeChild(typeOptions.firstChild);
+ }
+
+ for (var i = 0; i < types.length; i++) {
+ var option = document.createElement("option");
+ option.value = i.toString();
+ var element = types[i];
+ var text = element;
+ if (element instanceof Alias) {
+ text = element.getType() + ": " + element.getName();
+ } else if (element instanceof Reaction) {
+ text = "Reaction: " + element.getReactionId();
+ }
+ option.text = text;
+ typeOptions.appendChild(option);
+ }
+ typeOptions.value = 0;
+
+ this._types = types;
+ typeOptions.onchange();
+};
+
+CommentDialog.prototype.getTypes = function () {
+ return this._types;
+};
+
+CommentDialog.prototype.getSelectedType = function () {
+ return this._types[this.getTypeOptions().value];
+};
+
+CommentDialog.prototype.setSelectedType = function (value) {
+ if (Functions.isInt(value)) {
+ this.getTypeOptions().value = value;
+ this.getTypeOptions().onchange();
+ } else {
+ throw new Error("Unknown value type: " + value);
+ }
+};
+
+CommentDialog.prototype.getTypeOptions = function () {
+ return this._typeOptions;
+};
+CommentDialog.prototype.setTypeOptions = function (typeOptions) {
+ this._typeOptions = typeOptions;
+};
+CommentDialog.prototype.setContentInput = function (contentInput) {
+ this._contentInput = contentInput;
+};
+CommentDialog.prototype.getContentInput = function () {
+ return this._contentInput;
+};
+CommentDialog.prototype.setNameInput = function (nameInput) {
+ this._nameInput = nameInput;
+};
+CommentDialog.prototype.getNameInput = function () {
+ return this._nameInput;
+};
+CommentDialog.prototype.setEmailInput = function (emailInput) {
+ this._emailInput = emailInput;
+};
+CommentDialog.prototype.getEmailInput = function () {
+ return this._emailInput;
+};
+CommentDialog.prototype.setPinnedCheckbox = function (pinnedCheckbox) {
+ this._pinnedCheckbox = pinnedCheckbox;
+};
+
+CommentDialog.prototype.getPinnedCheckbox = function () {
+ return this._pinnedCheckbox;
+};
+
+CommentDialog.prototype.getTypes = function () {
+ return this._types;
+};
+
+CommentDialog.prototype.setName = function (name) {
+ this.getNameInput().value = name;
+};
+
+CommentDialog.prototype.getName = function () {
+ return this.getNameInput().value;
+};
+
+CommentDialog.prototype.getEmail = function () {
+ return this.getEmailInput().value;
+};
+
+CommentDialog.prototype.setEmail = function (email) {
+ this.getEmailInput().value = email;
+};
+
+CommentDialog.prototype.getContent = function () {
+ return this.getContentInput().value;
+};
+
+CommentDialog.prototype.isPinned = function () {
+ return this.getPinnedCheckbox().checked;
+};
+CommentDialog.prototype.getSelectedTypeId = function () {
+ var selected = this.getSelectedType();
+ if (selected instanceof Alias) {
+ return selected.getId();
+ } else if (selected instanceof Reaction) {
+ return selected.getId();
+ } else {
+ return "";
+ }
+};
+
+CommentDialog.prototype.getSelectedTypeClass = function () {
+ var selected = this.getSelectedType();
+ if (selected instanceof Alias) {
+ return "ALIAS";
+ } else if (selected instanceof Reaction) {
+ return "REACTION";
+ } else {
+ return "POINT";
+ }
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+CommentDialog.prototype.addComment = function () {
+ var self = this;
+ var name = self.getName();
+ return self.getMap().getServerConnector().addComment({
+ modelId: self.getMap().getActiveSubmapId(),
+ coordinates: self.getMap().getActiveSubmapClickCoordinates(),
+ name: name,
+ email: self.getEmail(),
+ content: self.getContent(),
+ pinned: self.isPinned(),
+ elementId: self.getSelectedTypeId(),
+ elementType: self.getSelectedTypeClass()
+
+ }).then(function (comment) {
+ //if we visualize comments add it to data set
+ if (self.getMap().getServerConnector().getSessionData(self.getProject()).getShowComments() && comment.isPinned()) {
+ return self.getMap().getOverlayByName("comment").addComment(comment);
+ } else {
+ return [];
+ }
+ });
+};
+
+CommentDialog.prototype.destroy = function () {
+ $(this.getElement()).dialog("destroy");
+};
+
+module.exports = CommentDialog;
diff --git a/frontend-js/src/main/js/gui/ContextMenu.js b/frontend-js/src/main/js/gui/ContextMenu.js
index 4425389f9262e500fa09bfd28be684a93915eaeb..f8fdbc8c05402036cebddda660905089440a7cb2 100644
--- a/frontend-js/src/main/js/gui/ContextMenu.js
+++ b/frontend-js/src/main/js/gui/ContextMenu.js
@@ -1,196 +1,196 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractGuiElement = require('./AbstractGuiElement');
-var GuiConnector = require('../GuiConnector');
-var SubMenu = require('./SubMenu');
-
-var Functions = require('../Functions');
-
-var logger = require('../logger');
-
-var MARGIN = 5;
-
-function ContextMenu(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
-
- var element = self.getElement();
- element.className = "dropdown-menu";
- element.setAttribute("role", "menu");
- $(element).hide();
-
- self._handledTimeStamp = undefined;
-
- self.MIN_SHOW_TIME = 250;
-
- self._documentClickListener = function (e) {
- var className = e.target.className;
- if (typeof className === 'string' || className instanceof String) {
- if (className.indexOf("dropdown-link") === -1) {
- self.hide(new Date().getTime() - self.MIN_SHOW_TIME);
- }
- } else {
- self.hide(new Date().getTime() - self.MIN_SHOW_TIME);
- }
- };
- $(document).on('click', self._documentClickListener);
- $(document).on('touchstart', self._documentClickListener);
-}
-
-ContextMenu.prototype = Object.create(AbstractGuiElement.prototype);
-ContextMenu.prototype.constructor = ContextMenu;
-
-ContextMenu.prototype.destroy = function () {
- var self = this;
- $(document).off('click', self._documentClickListener);
- $(document).off('touchstart', self._documentClickListener);
-};
-
-ContextMenu.prototype.addOption = function (name, handler, disabled) {
- if (!disabled) disabled = false;
- var self = this;
- if (name instanceof SubMenu) {
- self.getElement().appendChild(name.getElement());
- } else {
- var option = Functions.createElement({
- type: "li"
- });
- var link = Functions.createElement({
- type: "a",
- className: "dropdown-link",
- content: name
- });
- if (!disabled) {
- link.href = "#";
- } else {
- link.className = 'disabled-link';
- }
- $(link).data("handler", handler);
- option.appendChild(link);
- self.getElement().appendChild(option);
- }
-};
-
-/**
- *
- * @param {number} x
- * @param {number} y
- * @param {number} timestamp
- */
-ContextMenu.prototype.open = function (x, y, timestamp) {
- var self = this;
- self._handledTimeStamp = timestamp;
-
- var left = x;
- var right = "";
-
- if ($(self.getElement()).width() + x + MARGIN > $(document).width()) {
- left = Math.max(0, $(document).width() - $(self.getElement()).width() - MARGIN);
- right = 0;
- }
-
- $(self.getElement()).show().css({
- position: "absolute",
- left: left,
- right: right,
- top: y
- }).off('click').on('click', 'a', function (e) {
- //close if this is not a submenu
- if (this.parentNode === undefined || this.parentNode.className.indexOf("dropdown-submenu") === -1) {
- self.hide(new Date().getTime());
- if ($(this).data("handler") !== undefined) {
- return $(this).data("handler")();
- } else {
- logger.debug("Nothing to do");
- }
- }
- });
-};
-
-ContextMenu.prototype.hide = function (timestamp) {
- var self = this;
- if (self._handledTimeStamp < timestamp) {
- self._handledTimeStamp = timestamp;
- $(this.getElement()).hide();
- }
-};
-
-function extractDataOverlayIds(dataOverlays) {
- var ids = [];
- for (var i = 0; i < dataOverlays.length; i++) {
- ids.push(dataOverlays[i].getId());
- }
- return ids;
-}
-
-ContextMenu.prototype.createExportAsImageSubmenu = function () {
- var self = this;
- return self.getMap().getServerConnector().getImageConverters().then(function (converters) {
- var li = Functions.createElement({
- type: "li"
- });
- var submenu = new SubMenu({
- element: li,
- name: "Export as image",
- customMap: self.getMap()
- });
-
- var map = self.getMap();
- converters.forEach(function (converter) {
- submenu.addOption(converter.name, function () {
- return map.getVisibleDataOverlays().then(function (visibleDataOverlays) {
- var submapId = map.getActiveSubmapId();
-
- return map.getServerConnector().getImageDownloadUrl({
- polygonString: map.getSelectedPolygon(),
- modelId: submapId,
- handlerClass: converter.handler,
- backgroundOverlayId: map.getBackgroundDataOverlay().getId(),
- zoomLevel: map.getSubmapById(submapId).getZoom(),
- overlayIds: extractDataOverlayIds(visibleDataOverlays)
- });
- }).then(function (url) {
- return self.downloadFile(url);
- }).catch(GuiConnector.alert);
- });
- });
- return submenu;
- });
-};
-
-ContextMenu.prototype.createExportAsModelSubmenu = function () {
- var self = this;
- return self.getMap().getServerConnector().getModelConverters().then(function (converters) {
- var li = Functions.createElement({
- type: "li"
- });
- var submenu = new SubMenu({
- element: li,
- name: "Export as map",
- customMap: self.getMap()
- });
-
- var map = self.getMap();
- converters.forEach(function (converter) {
- submenu.addOption(converter.name, function () {
- return map.getVisibleDataOverlays().then(function (visibleDataOverlays) {
- return map.getServerConnector().getModelDownloadUrl({
- polygonString: map.getSelectedPolygon(),
- modelId: map.getActiveSubmapId(),
- handlerClass: converter.handler,
- backgroundOverlayId: map.getBackgroundDataOverlay().getId(),
- zoomLevel: map.getZoom(),
- overlayIds: extractDataOverlayIds(visibleDataOverlays)
- });
- }).then(function (url) {
- return self.downloadFile(url);
- }).catch(GuiConnector.alert);
- });
- });
- return submenu;
- });
-};
-
-module.exports = ContextMenu;
+"use strict";
+
+/* exported logger */
+
+var AbstractGuiElement = require('./AbstractGuiElement');
+var GuiConnector = require('../GuiConnector');
+var SubMenu = require('./SubMenu');
+
+var Functions = require('../Functions');
+
+var logger = require('../logger');
+
+var MARGIN = 5;
+
+function ContextMenu(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+
+ var element = self.getElement();
+ element.className = "dropdown-menu";
+ element.setAttribute("role", "menu");
+ $(element).hide();
+
+ self._handledTimeStamp = undefined;
+
+ self.MIN_SHOW_TIME = 250;
+
+ self._documentClickListener = function (e) {
+ var className = e.target.className;
+ if (typeof className === 'string' || className instanceof String) {
+ if (className.indexOf("dropdown-link") === -1) {
+ self.hide(new Date().getTime() - self.MIN_SHOW_TIME);
+ }
+ } else {
+ self.hide(new Date().getTime() - self.MIN_SHOW_TIME);
+ }
+ };
+ $(document).on('click', self._documentClickListener);
+ $(document).on('touchstart', self._documentClickListener);
+}
+
+ContextMenu.prototype = Object.create(AbstractGuiElement.prototype);
+ContextMenu.prototype.constructor = ContextMenu;
+
+ContextMenu.prototype.destroy = function () {
+ var self = this;
+ $(document).off('click', self._documentClickListener);
+ $(document).off('touchstart', self._documentClickListener);
+};
+
+ContextMenu.prototype.addOption = function (name, handler, disabled) {
+ if (!disabled) disabled = false;
+ var self = this;
+ if (name instanceof SubMenu) {
+ self.getElement().appendChild(name.getElement());
+ } else {
+ var option = Functions.createElement({
+ type: "li"
+ });
+ var link = Functions.createElement({
+ type: "a",
+ className: "dropdown-link",
+ content: name
+ });
+ if (!disabled) {
+ link.href = "#";
+ } else {
+ link.className = 'disabled-link';
+ }
+ $(link).data("handler", handler);
+ option.appendChild(link);
+ self.getElement().appendChild(option);
+ }
+};
+
+/**
+ *
+ * @param {number} x
+ * @param {number} y
+ * @param {number} timestamp
+ */
+ContextMenu.prototype.open = function (x, y, timestamp) {
+ var self = this;
+ self._handledTimeStamp = timestamp;
+
+ var left = x;
+ var right = "";
+
+ if ($(self.getElement()).width() + x + MARGIN > $(document).width()) {
+ left = Math.max(0, $(document).width() - $(self.getElement()).width() - MARGIN);
+ right = 0;
+ }
+
+ $(self.getElement()).show().css({
+ position: "absolute",
+ left: left,
+ right: right,
+ top: y
+ }).off('click').on('click', 'a', function (e) {
+ //close if this is not a submenu
+ if (this.parentNode === undefined || this.parentNode.className.indexOf("dropdown-submenu") === -1) {
+ self.hide(new Date().getTime());
+ if ($(this).data("handler") !== undefined) {
+ return $(this).data("handler")();
+ } else {
+ logger.debug("Nothing to do");
+ }
+ }
+ });
+};
+
+ContextMenu.prototype.hide = function (timestamp) {
+ var self = this;
+ if (self._handledTimeStamp < timestamp) {
+ self._handledTimeStamp = timestamp;
+ $(this.getElement()).hide();
+ }
+};
+
+function extractDataOverlayIds(dataOverlays) {
+ var ids = [];
+ for (var i = 0; i < dataOverlays.length; i++) {
+ ids.push(dataOverlays[i].getId());
+ }
+ return ids;
+}
+
+ContextMenu.prototype.createExportAsImageSubmenu = function () {
+ var self = this;
+ return self.getMap().getServerConnector().getImageConverters().then(function (converters) {
+ var li = Functions.createElement({
+ type: "li"
+ });
+ var submenu = new SubMenu({
+ element: li,
+ name: "Export as image",
+ customMap: self.getMap()
+ });
+
+ var map = self.getMap();
+ converters.forEach(function (converter) {
+ submenu.addOption(converter.name, function () {
+ return map.getVisibleDataOverlays().then(function (visibleDataOverlays) {
+ var submapId = map.getActiveSubmapId();
+
+ return map.getServerConnector().getImageDownloadUrl({
+ polygonString: map.getSelectedPolygon(),
+ modelId: submapId,
+ handlerClass: converter.handler,
+ backgroundOverlayId: map.getBackgroundDataOverlay().getId(),
+ zoomLevel: map.getSubmapById(submapId).getZoom(),
+ overlayIds: extractDataOverlayIds(visibleDataOverlays)
+ });
+ }).then(function (url) {
+ return self.downloadFile(url);
+ }).catch(GuiConnector.alert);
+ });
+ });
+ return submenu;
+ });
+};
+
+ContextMenu.prototype.createExportAsModelSubmenu = function () {
+ var self = this;
+ return self.getMap().getServerConnector().getModelConverters().then(function (converters) {
+ var li = Functions.createElement({
+ type: "li"
+ });
+ var submenu = new SubMenu({
+ element: li,
+ name: "Export as map",
+ customMap: self.getMap()
+ });
+
+ var map = self.getMap();
+ converters.forEach(function (converter) {
+ submenu.addOption(converter.name, function () {
+ return map.getVisibleDataOverlays().then(function (visibleDataOverlays) {
+ return map.getServerConnector().getModelDownloadUrl({
+ polygonString: map.getSelectedPolygon(),
+ modelId: map.getActiveSubmapId(),
+ handlerClass: converter.handler,
+ backgroundOverlayId: map.getBackgroundDataOverlay().getId(),
+ zoomLevel: map.getZoom(),
+ overlayIds: extractDataOverlayIds(visibleDataOverlays)
+ });
+ }).then(function (url) {
+ return self.downloadFile(url);
+ }).catch(GuiConnector.alert);
+ });
+ });
+ return submenu;
+ });
+};
+
+module.exports = ContextMenu;
diff --git a/frontend-js/src/main/js/gui/GuiMessageError.js b/frontend-js/src/main/js/gui/GuiMessageError.js
index 52ccf03be23abafbcad02be87411e6aeea94734d..9cb6b8367a053c84f8e685288bb47fb4b845b033 100644
--- a/frontend-js/src/main/js/gui/GuiMessageError.js
+++ b/frontend-js/src/main/js/gui/GuiMessageError.js
@@ -1,15 +1,15 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('../logger');
-
-function GuiMessageError(message) {
- this.message = message;
- this.stack = (new Error()).stack;
-}
-
-GuiMessageError.prototype = Object.create(Error.prototype);
-GuiMessageError.prototype.constructor = GuiMessageError;
-
-module.exports = GuiMessageError;
+"use strict";
+
+/* exported logger */
+
+var logger = require('../logger');
+
+function GuiMessageError(message) {
+ this.message = message;
+ this.stack = (new Error()).stack;
+}
+
+GuiMessageError.prototype = Object.create(Error.prototype);
+GuiMessageError.prototype.constructor = GuiMessageError;
+
+module.exports = GuiMessageError;
diff --git a/frontend-js/src/main/js/gui/Header.js b/frontend-js/src/main/js/gui/Header.js
index 384ac53da084fc69117b7de30dde46a54037a272..2e2eeab613db1a7d42d0b1175a644ae73bc05a99 100644
--- a/frontend-js/src/main/js/gui/Header.js
+++ b/frontend-js/src/main/js/gui/Header.js
@@ -1,169 +1,169 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractGuiElement = require('./AbstractGuiElement');
-var GuiConnector = require('../GuiConnector');
-var PanelControlElementType = require('./PanelControlElementType');
-var Functions = require('../Functions');
-var OptionsMenu = require('./OptionsMenu');
-
-var Promise = require("bluebird");
-
-var logger = require('../logger');
-var xss = require('xss');
-
-function Header(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
-
- var guiParams = {
- adminLink: true,
- optionsMenu: params.optionsMenu
- };
- if (params.adminLink !== undefined) {
- guiParams.adminLink = params.adminLink;
- }
-
- self._createHeaderGui(guiParams);
-}
-
-Header.prototype = Object.create(AbstractGuiElement.prototype);
-Header.prototype.constructor = Header;
-
-Header.prototype._createHeaderGui = function (guiParams) {
- var self = this;
- self.getElement().className = "minerva-header";
-
- var projectId = self.getProject().getProjectId();
- var projectName = xss(self.getProject().getName());
-
- var loadingDiv = Functions.createElement({
- type: "div",
- style: "display:none; "
- });
- loadingDiv.style.float = "right";
-
- var loadingImg = Functions.createElement({
- type: "img",
- src: 'resources/images/icons/ajax-loader.gif'
- });
- loadingImg.style.height = "35px";
- loadingDiv.appendChild(loadingImg);
- this.setControlElement(PanelControlElementType.FOOTER_LOADING_DIV, loadingDiv);
-
- if (guiParams.adminLink) {
- var link = Functions.createElement({
- type: "a",
- style: "padding-right:15px; float:right",
- content: '<i class="fa fa-lock" style="font-size:17px"></i> ',
- xss: false
- });
- link.href = ServerConnector.getServerBaseUrl() + "admin.xhtml?id=" + projectId;
- self.getElement().appendChild(link);
- }
-
- if (guiParams.optionsMenu) {
- var optionsElement = Functions.createElement({type: "ul"});
- document.body.appendChild(optionsElement);
- self._optionsMenu = new OptionsMenu({
- customMap: self.getMap(),
- element: optionsElement
- });
-
- var menuLink = Functions.createElement({
- type: "a",
- style: "padding-right:5px; float:right",
- content: '<i class="fa fa-bars" style="font-size:17px"></i> ',
- href: "#",
- onclick: function (e) {
- var link = $(menuLink);
- var offset = link.offset();
-
- var top = offset.top;
- var left = offset.left;
-
- var bottom = top + link.outerHeight();
-
- return self._optionsMenu.open(left, bottom, new Date().getTime());
- },
- xss: false
- });
- self.getElement().appendChild(menuLink);
- }
-
- self.getElement().appendChild(loadingDiv);
-
- var homeLink = Functions.createElement({
- type: "a",
- content: '<i class="fa fa-home" style="font-size:17px"></i> ' + projectName,
- xss: false
- });
- homeLink.href = ServerConnector.getServerBaseUrl() + "?id=" + projectId;
- self.getElement().appendChild(homeLink);
-};
-
-Header.prototype.addLoadMessage = function (message) {
- var self = this;
- self._loadMessages.push(message);
-};
-Header.prototype.removeLoadMessage = function (message) {
- var self = this;
- var index = self._loadMessages.indexOf(message);
- if (index > -1) {
- self._loadMessages.splice(index, 1);
- } else {
- logger.debug("Removing message that is not there: " + message);
- }
-};
-
-Header.prototype.init = function () {
- var self = this;
- return new Promise(function (resolve) {
- var div = self.getControlElement(PanelControlElementType.FOOTER_LOADING_DIV);
-
- self._loadMessages = [];
- self._onDataLoadStart = function (e) {
- self.addLoadMessage(e.arg);
- div.style.display = "block";
- div.title = e.arg;
- };
-
- self._onDataLoadStop = function (e) {
- self.removeLoadMessage(e.arg);
- if (self._loadMessages.length > 0) {
- div.title = self._loadMessages[0];
- } else {
- div.style.display = "none";
- }
- };
- ServerConnector.addListener("onDataLoadStart", self._onDataLoadStart);
- ServerConnector.addListener("onDataLoadStop", self._onDataLoadStop);
- resolve();
- });
-};
-
-Header.prototype.destroy = function () {
- var self = this;
- if (self._onDataLoadStart) {
- ServerConnector.removeListener("onDataLoadStart", self._onDataLoadStart);
- ServerConnector.removeListener("onDataLoadStop", self._onDataLoadStop);
- }
- if (self._optionsMenu !== undefined) {
- document.body.removeChild(self._optionsMenu.getElement());
- }
-};
-
-Header.prototype.setPluginManager = function (pluginManager) {
- var self = this;
- self._pluginManager = pluginManager;
- if (self._optionsMenu !== undefined) {
- self._optionsMenu.setPluginManager(pluginManager);
- }
-};
-
-Header.prototype.getPluginManager = function () {
- return this._pluginManager;
-};
-
-module.exports = Header;
+"use strict";
+
+/* exported logger */
+
+var AbstractGuiElement = require('./AbstractGuiElement');
+var GuiConnector = require('../GuiConnector');
+var PanelControlElementType = require('./PanelControlElementType');
+var Functions = require('../Functions');
+var OptionsMenu = require('./OptionsMenu');
+
+var Promise = require("bluebird");
+
+var logger = require('../logger');
+var xss = require('xss');
+
+function Header(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+
+ var guiParams = {
+ adminLink: true,
+ optionsMenu: params.optionsMenu
+ };
+ if (params.adminLink !== undefined) {
+ guiParams.adminLink = params.adminLink;
+ }
+
+ self._createHeaderGui(guiParams);
+}
+
+Header.prototype = Object.create(AbstractGuiElement.prototype);
+Header.prototype.constructor = Header;
+
+Header.prototype._createHeaderGui = function (guiParams) {
+ var self = this;
+ self.getElement().className = "minerva-header";
+
+ var projectId = self.getProject().getProjectId();
+ var projectName = xss(self.getProject().getName());
+
+ var loadingDiv = Functions.createElement({
+ type: "div",
+ style: "display:none; "
+ });
+ loadingDiv.style.float = "right";
+
+ var loadingImg = Functions.createElement({
+ type: "img",
+ src: 'resources/images/icons/ajax-loader.gif'
+ });
+ loadingImg.style.height = "35px";
+ loadingDiv.appendChild(loadingImg);
+ this.setControlElement(PanelControlElementType.FOOTER_LOADING_DIV, loadingDiv);
+
+ if (guiParams.adminLink) {
+ var link = Functions.createElement({
+ type: "a",
+ style: "padding-right:15px; float:right",
+ content: '<i class="fa fa-lock" style="font-size:17px"></i> ',
+ xss: false
+ });
+ link.href = ServerConnector.getServerBaseUrl() + "admin.xhtml?id=" + projectId;
+ self.getElement().appendChild(link);
+ }
+
+ if (guiParams.optionsMenu) {
+ var optionsElement = Functions.createElement({type: "ul"});
+ document.body.appendChild(optionsElement);
+ self._optionsMenu = new OptionsMenu({
+ customMap: self.getMap(),
+ element: optionsElement
+ });
+
+ var menuLink = Functions.createElement({
+ type: "a",
+ style: "padding-right:5px; float:right",
+ content: '<i class="fa fa-bars" style="font-size:17px"></i> ',
+ href: "#",
+ onclick: function (e) {
+ var link = $(menuLink);
+ var offset = link.offset();
+
+ var top = offset.top;
+ var left = offset.left;
+
+ var bottom = top + link.outerHeight();
+
+ return self._optionsMenu.open(left, bottom, new Date().getTime());
+ },
+ xss: false
+ });
+ self.getElement().appendChild(menuLink);
+ }
+
+ self.getElement().appendChild(loadingDiv);
+
+ var homeLink = Functions.createElement({
+ type: "a",
+ content: '<i class="fa fa-home" style="font-size:17px"></i> ' + projectName,
+ xss: false
+ });
+ homeLink.href = ServerConnector.getServerBaseUrl() + "?id=" + projectId;
+ self.getElement().appendChild(homeLink);
+};
+
+Header.prototype.addLoadMessage = function (message) {
+ var self = this;
+ self._loadMessages.push(message);
+};
+Header.prototype.removeLoadMessage = function (message) {
+ var self = this;
+ var index = self._loadMessages.indexOf(message);
+ if (index > -1) {
+ self._loadMessages.splice(index, 1);
+ } else {
+ logger.debug("Removing message that is not there: " + message);
+ }
+};
+
+Header.prototype.init = function () {
+ var self = this;
+ return new Promise(function (resolve) {
+ var div = self.getControlElement(PanelControlElementType.FOOTER_LOADING_DIV);
+
+ self._loadMessages = [];
+ self._onDataLoadStart = function (e) {
+ self.addLoadMessage(e.arg);
+ div.style.display = "block";
+ div.title = e.arg;
+ };
+
+ self._onDataLoadStop = function (e) {
+ self.removeLoadMessage(e.arg);
+ if (self._loadMessages.length > 0) {
+ div.title = self._loadMessages[0];
+ } else {
+ div.style.display = "none";
+ }
+ };
+ ServerConnector.addListener("onDataLoadStart", self._onDataLoadStart);
+ ServerConnector.addListener("onDataLoadStop", self._onDataLoadStop);
+ resolve();
+ });
+};
+
+Header.prototype.destroy = function () {
+ var self = this;
+ if (self._onDataLoadStart) {
+ ServerConnector.removeListener("onDataLoadStart", self._onDataLoadStart);
+ ServerConnector.removeListener("onDataLoadStop", self._onDataLoadStop);
+ }
+ if (self._optionsMenu !== undefined) {
+ document.body.removeChild(self._optionsMenu.getElement());
+ }
+};
+
+Header.prototype.setPluginManager = function (pluginManager) {
+ var self = this;
+ self._pluginManager = pluginManager;
+ if (self._optionsMenu !== undefined) {
+ self._optionsMenu.setPluginManager(pluginManager);
+ }
+};
+
+Header.prototype.getPluginManager = function () {
+ return this._pluginManager;
+};
+
+module.exports = Header;
diff --git a/frontend-js/src/main/js/gui/Legend.js b/frontend-js/src/main/js/gui/Legend.js
index 1dad46e65334a2e339966306c741dcb0feb3d55a..be280e82258b54357bdafd661e31af2a5d982a27 100644
--- a/frontend-js/src/main/js/gui/Legend.js
+++ b/frontend-js/src/main/js/gui/Legend.js
@@ -1,151 +1,151 @@
-"use strict";
-
-var AbstractGuiElement = require('./AbstractGuiElement');
-var ConfigurationType = require('../ConfigurationType');
-var Functions = require('../Functions');
-var PanelControlElementType = require('./PanelControlElementType');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../logger');
-
-function Legend(params) {
- AbstractGuiElement.call(this, params);
-
- this._initializeGui();
-}
-
-Legend.prototype = Object.create(AbstractGuiElement.prototype);
-Legend.prototype.constructor = Legend;
-
-Legend.prototype._initializeGui = function () {
- var self = this;
-
- var legendDiv = Functions.createElement({
- type: "div",
- id: "legend-div",
- className: "carousel slide"
- });
- self.getElement().appendChild(legendDiv);
-
- var indicators = Functions.createElement({
- type: "ol",
- name: "indicators",
- className: "carousel-indicators"
- });
- legendDiv.appendChild(indicators);
- self.setControlElement(PanelControlElementType.LEGEND_INDICATORS_OL, indicators);
-
- var slidesDiv = Functions.createElement({
- type: "div",
- name: "slides",
- className: "carousel-inner",
- role: "listbox"
- });
- legendDiv.appendChild(slidesDiv);
- self.setControlElement(PanelControlElementType.LEGEND_SLIDES_DIV, slidesDiv);
-
- var leftButton = Functions
- .createElement({
- type: "a",
- className: "left carousel-control",
- role: "button",
- href: "#legend-div",
- content: '<span class="glyphicon glyphicon-chevron-left" aria-hidden="true"></span><span class="sr-only">Previous</span>',
- xss: false
- });
- leftButton.setAttribute("data-slide", "prev");
- legendDiv.appendChild(leftButton);
-
- var rightButton = Functions
- .createElement({
- type: "a",
- className: "right carousel-control",
- role: "button",
- href: "#legend-div",
- content: '<span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span><span class="sr-only">Next</span>',
- xss: false
- });
- rightButton.setAttribute("data-slide", "next");
- legendDiv.appendChild(rightButton);
-};
-
-Legend.prototype.hide = function () {
- this.getElement().style.display = "none";
-};
-Legend.prototype.show = function () {
- var maxZIndex = Math.max.apply(null,
- $.map($('body *'), function (e) {
- if ($(e).css('position') !== 'static') {
- return parseInt($(e).css('z-index')) || 1;
- }
- }));
-
- this.getElement().style.display = "block";
- $(this.getElement()).css('z-index', maxZIndex + 1);
-};
-
-function createLegendIndicator(file, index) {
- var result = document.createElement("li");
- result.setAttribute("data-target", "legend");
- result.setAttribute("data-slide-to", "" + index);
- if (index === 0) {
- result.className = "active";
- }
- return result;
-}
-
-function createLegendSlide(file, index) {
- var result = document.createElement("div");
- if (index === 0) {
- result.className = "item active";
- } else {
- result.className = "item";
- }
- var img = document.createElement("img");
- img.src = file.getValue();
- result.appendChild(img);
- return result;
-}
-
-function getValidLegendFiles(legendFiles) {
- var result = [];
-
- var promises = [];
- legendFiles.forEach(function (file) {
- result.push(file);
- var url = file.getValue();
- if (url.indexOf("http") !== 0 && "" !== url) {
- url = ServerConnector.getServerBaseUrl() + url;
- }
- promises.push(ServerConnector.sendGetRequest(url).catch(function (error) {
- var index = result.indexOf(file);
- if (index > -1) {
- result.splice(index, 1);
- }
- }));
- });
-
- return Promise.all(promises).then(function () {
- return result;
- });
-}
-
-Legend.prototype.init = function () {
- var self = this;
- var element = self.getElement();
- var menu = self.getControlElement(PanelControlElementType.LEGEND_INDICATORS_OL);
- var slides = self.getControlElement(PanelControlElementType.LEGEND_SLIDES_DIV);
- return ServerConnector.getConfigurationParam(ConfigurationType.LEGEND_FILES).then(function (legendFiles) {
- return getValidLegendFiles(legendFiles);
- }).then(function (legendFiles) {
- for (var i = 0; i < legendFiles.length; i++) {
- var legendFile = legendFiles[i];
- menu.appendChild(createLegendIndicator(legendFile, i));
- slides.appendChild(createLegendSlide(legendFile, i));
- }
- $(element).carousel();
- });
-
-};
-
-module.exports = Legend;
+"use strict";
+
+var AbstractGuiElement = require('./AbstractGuiElement');
+var ConfigurationType = require('../ConfigurationType');
+var Functions = require('../Functions');
+var PanelControlElementType = require('./PanelControlElementType');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../logger');
+
+function Legend(params) {
+ AbstractGuiElement.call(this, params);
+
+ this._initializeGui();
+}
+
+Legend.prototype = Object.create(AbstractGuiElement.prototype);
+Legend.prototype.constructor = Legend;
+
+Legend.prototype._initializeGui = function () {
+ var self = this;
+
+ var legendDiv = Functions.createElement({
+ type: "div",
+ id: "legend-div",
+ className: "carousel slide"
+ });
+ self.getElement().appendChild(legendDiv);
+
+ var indicators = Functions.createElement({
+ type: "ol",
+ name: "indicators",
+ className: "carousel-indicators"
+ });
+ legendDiv.appendChild(indicators);
+ self.setControlElement(PanelControlElementType.LEGEND_INDICATORS_OL, indicators);
+
+ var slidesDiv = Functions.createElement({
+ type: "div",
+ name: "slides",
+ className: "carousel-inner",
+ role: "listbox"
+ });
+ legendDiv.appendChild(slidesDiv);
+ self.setControlElement(PanelControlElementType.LEGEND_SLIDES_DIV, slidesDiv);
+
+ var leftButton = Functions
+ .createElement({
+ type: "a",
+ className: "left carousel-control",
+ role: "button",
+ href: "#legend-div",
+ content: '<span class="glyphicon glyphicon-chevron-left" aria-hidden="true"></span><span class="sr-only">Previous</span>',
+ xss: false
+ });
+ leftButton.setAttribute("data-slide", "prev");
+ legendDiv.appendChild(leftButton);
+
+ var rightButton = Functions
+ .createElement({
+ type: "a",
+ className: "right carousel-control",
+ role: "button",
+ href: "#legend-div",
+ content: '<span class="glyphicon glyphicon-chevron-right" aria-hidden="true"></span><span class="sr-only">Next</span>',
+ xss: false
+ });
+ rightButton.setAttribute("data-slide", "next");
+ legendDiv.appendChild(rightButton);
+};
+
+Legend.prototype.hide = function () {
+ this.getElement().style.display = "none";
+};
+Legend.prototype.show = function () {
+ var maxZIndex = Math.max.apply(null,
+ $.map($('body *'), function (e) {
+ if ($(e).css('position') !== 'static') {
+ return parseInt($(e).css('z-index')) || 1;
+ }
+ }));
+
+ this.getElement().style.display = "block";
+ $(this.getElement()).css('z-index', maxZIndex + 1);
+};
+
+function createLegendIndicator(file, index) {
+ var result = document.createElement("li");
+ result.setAttribute("data-target", "legend");
+ result.setAttribute("data-slide-to", "" + index);
+ if (index === 0) {
+ result.className = "active";
+ }
+ return result;
+}
+
+function createLegendSlide(file, index) {
+ var result = document.createElement("div");
+ if (index === 0) {
+ result.className = "item active";
+ } else {
+ result.className = "item";
+ }
+ var img = document.createElement("img");
+ img.src = file.getValue();
+ result.appendChild(img);
+ return result;
+}
+
+function getValidLegendFiles(legendFiles) {
+ var result = [];
+
+ var promises = [];
+ legendFiles.forEach(function (file) {
+ result.push(file);
+ var url = file.getValue();
+ if (url.indexOf("http") !== 0 && "" !== url) {
+ url = ServerConnector.getServerBaseUrl() + url;
+ }
+ promises.push(ServerConnector.sendGetRequest(url).catch(function (error) {
+ var index = result.indexOf(file);
+ if (index > -1) {
+ result.splice(index, 1);
+ }
+ }));
+ });
+
+ return Promise.all(promises).then(function () {
+ return result;
+ });
+}
+
+Legend.prototype.init = function () {
+ var self = this;
+ var element = self.getElement();
+ var menu = self.getControlElement(PanelControlElementType.LEGEND_INDICATORS_OL);
+ var slides = self.getControlElement(PanelControlElementType.LEGEND_SLIDES_DIV);
+ return ServerConnector.getConfigurationParam(ConfigurationType.LEGEND_FILES).then(function (legendFiles) {
+ return getValidLegendFiles(legendFiles);
+ }).then(function (legendFiles) {
+ for (var i = 0; i < legendFiles.length; i++) {
+ var legendFile = legendFiles[i];
+ menu.appendChild(createLegendIndicator(legendFile, i));
+ slides.appendChild(createLegendSlide(legendFile, i));
+ }
+ $(element).carousel();
+ });
+
+};
+
+module.exports = Legend;
diff --git a/frontend-js/src/main/js/gui/LoginDialog.js b/frontend-js/src/main/js/gui/LoginDialog.js
index 7a652643d9157fc10d709381730bf9c0c7989d75..a32a49e44fc012a54414433380dca59124efa06e 100644
--- a/frontend-js/src/main/js/gui/LoginDialog.js
+++ b/frontend-js/src/main/js/gui/LoginDialog.js
@@ -1,146 +1,146 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractGuiElement = require('./AbstractGuiElement');
-var GuiConnector = require('../GuiConnector');
-var InvalidCredentialsError = require('../InvalidCredentialsError');
-var PanelControlElementType = require('./PanelControlElementType');
-var ConfigurationType = require("../ConfigurationType");
-
-var Functions = require('../Functions');
-var logger = require('../logger');
-
-function LoginDialog(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
- self._createLoginTab();
-
- var loginButton = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_BUTTON);
- loginButton.onclick = function() {
- var login = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_INPUT_TEXT).value;
- var password = self.getControlElement(PanelControlElementType.USER_TAB_PASSWORD_INPUT_TEXT).value;
-
- return ServerConnector.login(login, password).then(function() {
- window.location.reload(false);
- }).then(null, function(error) {
- if (error instanceof InvalidCredentialsError) {
- GuiConnector.alert("invalid credentials");
- } else {
- GuiConnector.alert(error);
- }
- });
- };
-
-}
-
-LoginDialog.prototype = Object.create(AbstractGuiElement.prototype);
-LoginDialog.prototype.constructor = LoginDialog;
-
-LoginDialog.prototype.createTableRow = function (elements) {
- var row = Functions.createElement({
- type: "div",
- style: "display: table-row;"
- });
-
- for (var i = 0; i < elements.length; i++) {
- var cell = Functions.createElement({
- type : "div",
- style : "display: table-cell;"
- });
- cell.appendChild(elements[i]);
- row.appendChild(cell);
- }
- return row;
-};
-
-LoginDialog.prototype._createLoginTab = function () {
- var self = this;
-
- var authorizationFormTab = Functions.createElement({
- type: "div",
- style: "width:100%;display: table;border-spacing: 10px;"
- });
- this.getElement().appendChild(authorizationFormTab);
-
- var loginLabel = Functions.createElement({
- type: "div",
- content: "LOGIN:"
- });
- var loginInput = Functions.createElement({
- type: "input",
- inputType: "text",
- style: "width:100%",
- name: "loginText"
- });
- this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_INPUT_TEXT, loginInput);
-
- authorizationFormTab.appendChild(self.createTableRow([loginLabel, loginInput]));
-
- var passwordLabel = Functions.createElement({
- type: "div",
- content: "PASSWORD:"
- });
- var passwordInput = Functions.createElement({
- type: "input",
- inputType: "password",
- style: "width:100%",
- name: "passwordText"
- });
- this.setControlElement(PanelControlElementType.USER_TAB_PASSWORD_INPUT_TEXT, passwordInput);
-
- authorizationFormTab.appendChild(self.createTableRow([passwordLabel, passwordInput]));
-
- var centerTag = Functions.createElement({
- type: "center"
- });
- this.getElement().appendChild(centerTag);
-
- var loginButton = Functions.createElement({
- type: "button",
- name: "loginButton",
- content: "LOGIN"
- });
- centerTag.appendChild(loginButton);
- this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_BUTTON, loginButton);
- this.getElement().appendChild(Functions.createElement({type: "br"}));
-
- this.getElement().appendChild(Functions.createElement({
- type: "a",
- name: "requestAccount",
- content: "Request an account",
- href: "#"
- }));
-
-};
-
-LoginDialog.prototype.init = function () {
- var self = this;
- return ServerConnector.getConfigurationParam(ConfigurationType.REQUEST_ACCOUNT_EMAIL).then(function (value) {
- var link = $("[name=requestAccount]", self.getElement());
- link.attr("href", "mailto:" + value + "?subject=MINERVA account request");
- });
-};
-
-LoginDialog.prototype.open = function () {
- var self = this;
- var div = self.getElement();
- if (!$(div).hasClass("ui-dialog-content")) {
- $(div).dialog({
- autoOpen: false,
- resizable: false
- });
- }
-
- $(div).dialog('option', 'title', 'AUTHORIZATION FORM');
- $(div).dialog("open");
-};
-
-LoginDialog.prototype.destroy = function () {
- var self = this;
- if ($(self.getElement()).hasClass("ui-dialog-content")) {
- $(self.getElement()).dialog("destroy");
- }
-};
-
-module.exports = LoginDialog;
+"use strict";
+
+/* exported logger */
+
+var AbstractGuiElement = require('./AbstractGuiElement');
+var GuiConnector = require('../GuiConnector');
+var InvalidCredentialsError = require('../InvalidCredentialsError');
+var PanelControlElementType = require('./PanelControlElementType');
+var ConfigurationType = require("../ConfigurationType");
+
+var Functions = require('../Functions');
+var logger = require('../logger');
+
+function LoginDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ self._createLoginTab();
+
+ var loginButton = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_BUTTON);
+ loginButton.onclick = function() {
+ var login = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_INPUT_TEXT).value;
+ var password = self.getControlElement(PanelControlElementType.USER_TAB_PASSWORD_INPUT_TEXT).value;
+
+ return ServerConnector.login(login, password).then(function() {
+ window.location.reload(false);
+ }).then(null, function(error) {
+ if (error instanceof InvalidCredentialsError) {
+ GuiConnector.alert("invalid credentials");
+ } else {
+ GuiConnector.alert(error);
+ }
+ });
+ };
+
+}
+
+LoginDialog.prototype = Object.create(AbstractGuiElement.prototype);
+LoginDialog.prototype.constructor = LoginDialog;
+
+LoginDialog.prototype.createTableRow = function (elements) {
+ var row = Functions.createElement({
+ type: "div",
+ style: "display: table-row;"
+ });
+
+ for (var i = 0; i < elements.length; i++) {
+ var cell = Functions.createElement({
+ type : "div",
+ style : "display: table-cell;"
+ });
+ cell.appendChild(elements[i]);
+ row.appendChild(cell);
+ }
+ return row;
+};
+
+LoginDialog.prototype._createLoginTab = function () {
+ var self = this;
+
+ var authorizationFormTab = Functions.createElement({
+ type: "div",
+ style: "width:100%;display: table;border-spacing: 10px;"
+ });
+ this.getElement().appendChild(authorizationFormTab);
+
+ var loginLabel = Functions.createElement({
+ type: "div",
+ content: "LOGIN:"
+ });
+ var loginInput = Functions.createElement({
+ type: "input",
+ inputType: "text",
+ style: "width:100%",
+ name: "loginText"
+ });
+ this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_INPUT_TEXT, loginInput);
+
+ authorizationFormTab.appendChild(self.createTableRow([loginLabel, loginInput]));
+
+ var passwordLabel = Functions.createElement({
+ type: "div",
+ content: "PASSWORD:"
+ });
+ var passwordInput = Functions.createElement({
+ type: "input",
+ inputType: "password",
+ style: "width:100%",
+ name: "passwordText"
+ });
+ this.setControlElement(PanelControlElementType.USER_TAB_PASSWORD_INPUT_TEXT, passwordInput);
+
+ authorizationFormTab.appendChild(self.createTableRow([passwordLabel, passwordInput]));
+
+ var centerTag = Functions.createElement({
+ type: "center"
+ });
+ this.getElement().appendChild(centerTag);
+
+ var loginButton = Functions.createElement({
+ type: "button",
+ name: "loginButton",
+ content: "LOGIN"
+ });
+ centerTag.appendChild(loginButton);
+ this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_BUTTON, loginButton);
+ this.getElement().appendChild(Functions.createElement({type: "br"}));
+
+ this.getElement().appendChild(Functions.createElement({
+ type: "a",
+ name: "requestAccount",
+ content: "Request an account",
+ href: "#"
+ }));
+
+};
+
+LoginDialog.prototype.init = function () {
+ var self = this;
+ return ServerConnector.getConfigurationParam(ConfigurationType.REQUEST_ACCOUNT_EMAIL).then(function (value) {
+ var link = $("[name=requestAccount]", self.getElement());
+ link.attr("href", "mailto:" + value + "?subject=MINERVA account request");
+ });
+};
+
+LoginDialog.prototype.open = function () {
+ var self = this;
+ var div = self.getElement();
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ autoOpen: false,
+ resizable: false
+ });
+ }
+
+ $(div).dialog('option', 'title', 'AUTHORIZATION FORM');
+ $(div).dialog("open");
+};
+
+LoginDialog.prototype.destroy = function () {
+ var self = this;
+ if ($(self.getElement()).hasClass("ui-dialog-content")) {
+ $(self.getElement()).dialog("destroy");
+ }
+};
+
+module.exports = LoginDialog;
diff --git a/frontend-js/src/main/js/gui/MapContextMenu.js b/frontend-js/src/main/js/gui/MapContextMenu.js
index c66c5f077c6c852f9b27d31b1233cae6f2e12846..048e16d10b15aa8221e6978002ca7373464f99d9 100644
--- a/frontend-js/src/main/js/gui/MapContextMenu.js
+++ b/frontend-js/src/main/js/gui/MapContextMenu.js
@@ -1,49 +1,49 @@
-"use strict";
-
-/* exported logger */
-
-var ContextMenu = require('./ContextMenu');
-
-var logger = require('../logger');
-
-function MapContextMenu(params) {
- ContextMenu.call(this, params);
- var self = this;
-
- self._createMapContextMenuGui();
- self.setMolArt(params.molArt);
-}
-
-MapContextMenu.prototype = Object.create(ContextMenu.prototype);
-MapContextMenu.prototype.constructor = MapContextMenu;
-
-
-MapContextMenu.prototype._createMapContextMenuGui = function() {
- var self = this;
- self.addOption("Add comment", function() {
- return self.getMap().openCommentDialog();
- });
- self.addOption("Select mode", function() {
- return self.getMap().toggleDrawing();
- });
-};
-
-MapContextMenu.prototype.init = function() {
- var self = this;
- return self.createExportAsImageSubmenu().then(function(submenu){
- self.addOption(submenu);
- return self.createExportAsModelSubmenu();
- }).then(function(submenu){
- self.addOption(submenu);
- });
-};
-
-MapContextMenu.prototype.setMolArt = function(molArt){
- this._molArt = molArt;
-};
-
-MapContextMenu.prototype.getMolArt = function(){
- return this._molArt;
-};
-
-module.exports = MapContextMenu;
+"use strict";
+
+/* exported logger */
+
+var ContextMenu = require('./ContextMenu');
+
+var logger = require('../logger');
+
+function MapContextMenu(params) {
+ ContextMenu.call(this, params);
+ var self = this;
+
+ self._createMapContextMenuGui();
+ self.setMolArt(params.molArt);
+}
+
+MapContextMenu.prototype = Object.create(ContextMenu.prototype);
+MapContextMenu.prototype.constructor = MapContextMenu;
+
+
+MapContextMenu.prototype._createMapContextMenuGui = function() {
+ var self = this;
+ self.addOption("Add comment", function() {
+ return self.getMap().openCommentDialog();
+ });
+ self.addOption("Select mode", function() {
+ return self.getMap().toggleDrawing();
+ });
+};
+
+MapContextMenu.prototype.init = function() {
+ var self = this;
+ return self.createExportAsImageSubmenu().then(function(submenu){
+ self.addOption(submenu);
+ return self.createExportAsModelSubmenu();
+ }).then(function(submenu){
+ self.addOption(submenu);
+ });
+};
+
+MapContextMenu.prototype.setMolArt = function(molArt){
+ this._molArt = molArt;
+};
+
+MapContextMenu.prototype.getMolArt = function(){
+ return this._molArt;
+};
+
+module.exports = MapContextMenu;
diff --git a/frontend-js/src/main/js/gui/OptionsMenu.js b/frontend-js/src/main/js/gui/OptionsMenu.js
index 9ef28aaeb490653ccbb1d3e7b6d13edef02f740b..178fa188aea9f3d883f450f2ed8e722e5cd1ba91 100644
--- a/frontend-js/src/main/js/gui/OptionsMenu.js
+++ b/frontend-js/src/main/js/gui/OptionsMenu.js
@@ -1,56 +1,56 @@
-"use strict";
-
-var ContextMenu = require('./ContextMenu');
-var PluginDialog = require('./PluginDialog');
-var Promise = require('bluebird');
-
-function OptionsMenu(params) {
- ContextMenu.call(this, params);
- var self = this;
-
- self._createMenuGui();
-}
-
-OptionsMenu.prototype = Object.create(ContextMenu.prototype);
-OptionsMenu.prototype.constructor = OptionsMenu;
-
-
-OptionsMenu.prototype._createMenuGui = function () {
- var self = this;
- self.addOption("Plugins", function () {
- var initPromise = Promise.resolve();
- if (self._pluginDialog === undefined) {
- self._pluginDialog = new PluginDialog({
- element: document.createElement("div"),
- customMap: self.getMap(),
- pluginManager: self.getPluginManager()
- });
- initPromise = self._pluginDialog.init();
- }
- return initPromise.then(function () {
- return self._pluginDialog.open();
- })
- });
-};
-
-OptionsMenu.prototype.init = function () {
- return Promise.resolve();
-};
-OptionsMenu.prototype.destroy = function () {
- var self = this;
- var promises = [];
- if (self._pluginDialog !== undefined) {
- promises.push(self._pluginDialog.destroy());
- }
- return Promise.all(promises);
-};
-
-OptionsMenu.prototype.setPluginManager = function (pluginManager) {
- this._pluginManager = pluginManager;
-};
-
-OptionsMenu.prototype.getPluginManager = function () {
- return this._pluginManager;
-};
-
-module.exports = OptionsMenu;
+"use strict";
+
+var ContextMenu = require('./ContextMenu');
+var PluginDialog = require('./PluginDialog');
+var Promise = require('bluebird');
+
+function OptionsMenu(params) {
+ ContextMenu.call(this, params);
+ var self = this;
+
+ self._createMenuGui();
+}
+
+OptionsMenu.prototype = Object.create(ContextMenu.prototype);
+OptionsMenu.prototype.constructor = OptionsMenu;
+
+
+OptionsMenu.prototype._createMenuGui = function () {
+ var self = this;
+ self.addOption("Plugins", function () {
+ var initPromise = Promise.resolve();
+ if (self._pluginDialog === undefined) {
+ self._pluginDialog = new PluginDialog({
+ element: document.createElement("div"),
+ customMap: self.getMap(),
+ pluginManager: self.getPluginManager()
+ });
+ initPromise = self._pluginDialog.init();
+ }
+ return initPromise.then(function () {
+ return self._pluginDialog.open();
+ })
+ });
+};
+
+OptionsMenu.prototype.init = function () {
+ return Promise.resolve();
+};
+OptionsMenu.prototype.destroy = function () {
+ var self = this;
+ var promises = [];
+ if (self._pluginDialog !== undefined) {
+ promises.push(self._pluginDialog.destroy());
+ }
+ return Promise.all(promises);
+};
+
+OptionsMenu.prototype.setPluginManager = function (pluginManager) {
+ this._pluginManager = pluginManager;
+};
+
+OptionsMenu.prototype.getPluginManager = function () {
+ return this._pluginManager;
+};
+
+module.exports = OptionsMenu;
diff --git a/frontend-js/src/main/js/gui/OverviewDialog.js b/frontend-js/src/main/js/gui/OverviewDialog.js
index ae3a5c4023cab0f5cca9978a6c536001c853fb5f..864743375a6f03efd4037d0f905894bf137f1235 100644
--- a/frontend-js/src/main/js/gui/OverviewDialog.js
+++ b/frontend-js/src/main/js/gui/OverviewDialog.js
@@ -1,227 +1,227 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractGuiElement = require('./AbstractGuiElement');
-var GuiConnector = require('../GuiConnector');
-var Point = require('../map/canvas/Point');
-
-var functions = require('../Functions');
-var logger = require('../logger');
-
-function OverviewDialog(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
- $(self.getElement()).dialog({
- autoOpen: false,
- resizable: false
- });
-}
-
-OverviewDialog.prototype = Object.create(AbstractGuiElement.prototype);
-OverviewDialog.prototype.constructor = OverviewDialog;
-
-OverviewDialog.prototype.showOverview = function (overviewImageId) {
- var self = this;
- var map = self.getMap();
-
- var project = map.getProject();
-
- // resize dialog
- var htmlTag = self.getElement();
-
- var width = Math.floor(window.innerWidth * 2 / 3);
- var height = Math.floor(window.innerHeight * 2 / 3);
-
- $(self.getElement()).dialog("option", "width", width + 60);
- $(self.getElement()).dialog("option", "height", height + 60);
-
- // remove all child nodes from overview div
- while (htmlTag.hasChildNodes()) {
- htmlTag.removeChild(htmlTag.lastChild);
- }
-
- var content = document.createElement("div");
- htmlTag.appendChild(content);
-
- var canvasDebug = document.createElement("canvas");
- canvasDebug.className = "canvasDebugClass";
- canvasDebug.style.display = "none";
- htmlTag.appendChild(canvasDebug);
-
- if (overviewImageId === undefined) {
- this.overviewImage = project.getTopOverviewImage();
- } else {
- this.overviewImage = null;
- var images = project.getOverviewImages();
- for (var i = 0; i < images.length; i++) {
- if (images[i].idObject === overviewImageId) {
- this.overviewImage = images[i];
- }
- }
-
- if (this.overviewImage === null) {
- logger.warn("Unknown overview image with id = " + overviewImageId);
- this.overviewImage = project.getTopOverviewImage();
- }
- }
-
- // add image to overview div
- this.overviewImageTag = document.createElement("IMG");
- this.overviewImageTag.src = "../map_images/" + this.overviewImage.filename;
- content.appendChild(this.overviewImageTag);
-
- var ratio = 1.0;
-
- // check how image should be re-sized to fit dialog and resize it manually!!!
- if (width / this.overviewImage.width > height / this.overviewImage.height) {
- this.overviewImageTag.style.height = height + "px";
- ratio = height / this.overviewImage.height;
- width = this.overviewImage.width * ratio;
- $(self.getElement()).dialog("option", "width", width + 60);
- } else {
- this.overviewImageTag.style.width = width + "px";
- ratio = width / this.overviewImage.width;
- height = this.overviewImage.height * ratio;
- $(self.getElement()).dialog("option", "height", height + 60);
- }
-
- // on click event (what should happen when we click on the image)
- var onClickEvent = function getClickPosition(e) {
- var parentPosition = functions.getPosition(e.currentTarget);
- var xPosition = e.clientX - parentPosition.x;
- var yPosition = e.clientY - parentPosition.y;
-
- var imgWidth = self.overviewImageTag.offsetWidth;
-
- var currentRatio = imgWidth / self.overviewImage.width;
-
- var xNormal = xPosition / currentRatio;
- var yNormal = yPosition / currentRatio;
- var point = new Point(xNormal, yNormal);
-
- var link = null;
- for (var i = 0; i < self.overviewImage.links.length; i++) {
- if (functions.pointInsidePolygon(point, self.overviewImage.links[i].polygon)) {
- if (link === null) {
- link = self.overviewImage.links[i];
- } else {
- logger.warn("More than one link found. Skipping");
- }
- }
- }
- if (link !== null) {
- self.openLink(link);
- }
- };
-
- this.overviewImageTag.onclick = onClickEvent;
-
- // resize canvas where on mouse over highlight will appear
-
- // in debug mode draw clickable shapes
- if (map.isDebug()) {
- canvasDebug.style.display = "";
- canvasDebug.width = width;
- canvasDebug.height = height;
- canvasDebug.onclick = onClickEvent;
- this.drawClickableShapes(canvasDebug, ratio);
- }
-
- this.overviewImage.mousePos = {
- x: 0,
- y: 0
- };
-
- // this listener should be called when mouse moves over image, it purpose is
- // to change cursor to pointer when mouse enters clickable polygon and back
- // to normal when mouse leaves such region
- var onMouseMove = function getMouseOverPosition(e) {
- var position = functions.getPosition(e.currentTarget);
- position.x = e.clientX - position.x;
- position.y = e.clientY - position.y;
-
- var imgWidth = self.overviewImageTag.offsetWidth;
-
- var currentRatio = imgWidth / self.overviewImage.width;
-
- var xNormal = position.x / currentRatio;
- var yNormal = position.y / currentRatio;
- var point = new Point(xNormal, yNormal);
-
- if (self.overviewImage.mousePos.x !== position.x || self.overviewImage.mousePos.y !== position.y) {
- self.overviewImage.mousePos = position;
- var link = null;
- for (var i = 0; i < self.overviewImage.links.length; i++) {
- if (functions.pointInsidePolygon(point, self.overviewImage.links[i].polygon)) {
- link = self.overviewImage.links[i];
- }
- }
- if (link === null) {
- e.currentTarget.style.cursor = "auto";
- } else {
- e.currentTarget.style.cursor = "pointer";
- }
- }
- };
-
- // onMouseMove listener should be assigned to canvas (which is on top of the
- // image) and overviewImage (just in case something went wrong with resizing
- // canvas)
- canvasDebug.onmousemove = onMouseMove;
- this.overviewImageTag.onmousemove = onMouseMove;
-
- $(self.getElement()).dialog("open");
-};
-
-OverviewDialog.prototype.openLink = function (link) {
- var self = this;
- var map = self.getMap();
- if (link.type === "OverviewModelLink") {
- logger.debug("Opening model from overview. ModelId: " + link.modelLinkId);
- logger.debug("link coordinates [" + link.idObject + "]: " + link.modelPoint);
-
- map.openSubmap(link.modelLinkId);
- var submap = map.getSubmapById(link.modelLinkId);
- logger.debug("zoom [" + link.idObject + "]: " + link.zoomLevel + submap.getMinZoom());
- submap.setCenter(new Point(link.modelPoint));
- submap.setZoom(link.zoomLevel + submap.getMinZoom());
-
- $(self.getElement()).dialog("close");
- } else if (link.type === "OverviewImageLink") {
- logger.debug("Opening image from overview. ImageId: " + link.imageLinkId);
- self.showOverview(link.imageLinkId);
- } else if (link.type === "OverviewSearchLink") {
- logger.debug("Sending search query. Query: " + link.query);
- return map.getOverlayByName("search").searchByQuery(link.query).then(function () {
- $(self.getElement()).dialog("close");
- }, GuiConnector.alert);
- } else {
- logger.warn("Unknown type of link: " + link.type + ". Don't know what to do... LinkId: " + link.idObject);
- }
-};
-
-OverviewDialog.prototype.drawClickableShapes = function (canvas, ratio) {
- var ctx = canvas.getContext("2d");
- // clear canvas
- ctx.clearRect(0, 0, canvas.width, canvas.height);
- for (var i = 0; i < this.overviewImage.links.length; i++) {
- ctx.beginPath();
- var polygon = this.overviewImage.links[i].polygon;
- for (var j = 0; j < polygon.length; j++) {
- var x = polygon[j].x * ratio;
- var y = polygon[j].y * ratio;
- ctx.moveTo(x, y);
- x = polygon[(j + 1) % polygon.length].x * ratio;
- y = polygon[(j + 1) % polygon.length].y * ratio;
- ctx.lineTo(x, y);
- }
- ctx.stroke();
- }
-};
-
-OverviewDialog.prototype.destroy = function () {
- $(this.getElement()).dialog("destroy");
-};
-
-module.exports = OverviewDialog;
+"use strict";
+
+/* exported logger */
+
+var AbstractGuiElement = require('./AbstractGuiElement');
+var GuiConnector = require('../GuiConnector');
+var Point = require('../map/canvas/Point');
+
+var functions = require('../Functions');
+var logger = require('../logger');
+
+function OverviewDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ $(self.getElement()).dialog({
+ autoOpen: false,
+ resizable: false
+ });
+}
+
+OverviewDialog.prototype = Object.create(AbstractGuiElement.prototype);
+OverviewDialog.prototype.constructor = OverviewDialog;
+
+OverviewDialog.prototype.showOverview = function (overviewImageId) {
+ var self = this;
+ var map = self.getMap();
+
+ var project = map.getProject();
+
+ // resize dialog
+ var htmlTag = self.getElement();
+
+ var width = Math.floor(window.innerWidth * 2 / 3);
+ var height = Math.floor(window.innerHeight * 2 / 3);
+
+ $(self.getElement()).dialog("option", "width", width + 60);
+ $(self.getElement()).dialog("option", "height", height + 60);
+
+ // remove all child nodes from overview div
+ while (htmlTag.hasChildNodes()) {
+ htmlTag.removeChild(htmlTag.lastChild);
+ }
+
+ var content = document.createElement("div");
+ htmlTag.appendChild(content);
+
+ var canvasDebug = document.createElement("canvas");
+ canvasDebug.className = "canvasDebugClass";
+ canvasDebug.style.display = "none";
+ htmlTag.appendChild(canvasDebug);
+
+ if (overviewImageId === undefined) {
+ this.overviewImage = project.getTopOverviewImage();
+ } else {
+ this.overviewImage = null;
+ var images = project.getOverviewImages();
+ for (var i = 0; i < images.length; i++) {
+ if (images[i].idObject === overviewImageId) {
+ this.overviewImage = images[i];
+ }
+ }
+
+ if (this.overviewImage === null) {
+ logger.warn("Unknown overview image with id = " + overviewImageId);
+ this.overviewImage = project.getTopOverviewImage();
+ }
+ }
+
+ // add image to overview div
+ this.overviewImageTag = document.createElement("IMG");
+ this.overviewImageTag.src = "../map_images/" + this.overviewImage.filename;
+ content.appendChild(this.overviewImageTag);
+
+ var ratio = 1.0;
+
+ // check how image should be re-sized to fit dialog and resize it manually!!!
+ if (width / this.overviewImage.width > height / this.overviewImage.height) {
+ this.overviewImageTag.style.height = height + "px";
+ ratio = height / this.overviewImage.height;
+ width = this.overviewImage.width * ratio;
+ $(self.getElement()).dialog("option", "width", width + 60);
+ } else {
+ this.overviewImageTag.style.width = width + "px";
+ ratio = width / this.overviewImage.width;
+ height = this.overviewImage.height * ratio;
+ $(self.getElement()).dialog("option", "height", height + 60);
+ }
+
+ // on click event (what should happen when we click on the image)
+ var onClickEvent = function getClickPosition(e) {
+ var parentPosition = functions.getPosition(e.currentTarget);
+ var xPosition = e.clientX - parentPosition.x;
+ var yPosition = e.clientY - parentPosition.y;
+
+ var imgWidth = self.overviewImageTag.offsetWidth;
+
+ var currentRatio = imgWidth / self.overviewImage.width;
+
+ var xNormal = xPosition / currentRatio;
+ var yNormal = yPosition / currentRatio;
+ var point = new Point(xNormal, yNormal);
+
+ var link = null;
+ for (var i = 0; i < self.overviewImage.links.length; i++) {
+ if (functions.pointInsidePolygon(point, self.overviewImage.links[i].polygon)) {
+ if (link === null) {
+ link = self.overviewImage.links[i];
+ } else {
+ logger.warn("More than one link found. Skipping");
+ }
+ }
+ }
+ if (link !== null) {
+ self.openLink(link);
+ }
+ };
+
+ this.overviewImageTag.onclick = onClickEvent;
+
+ // resize canvas where on mouse over highlight will appear
+
+ // in debug mode draw clickable shapes
+ if (map.isDebug()) {
+ canvasDebug.style.display = "";
+ canvasDebug.width = width;
+ canvasDebug.height = height;
+ canvasDebug.onclick = onClickEvent;
+ this.drawClickableShapes(canvasDebug, ratio);
+ }
+
+ this.overviewImage.mousePos = {
+ x: 0,
+ y: 0
+ };
+
+ // this listener should be called when mouse moves over image, it purpose is
+ // to change cursor to pointer when mouse enters clickable polygon and back
+ // to normal when mouse leaves such region
+ var onMouseMove = function getMouseOverPosition(e) {
+ var position = functions.getPosition(e.currentTarget);
+ position.x = e.clientX - position.x;
+ position.y = e.clientY - position.y;
+
+ var imgWidth = self.overviewImageTag.offsetWidth;
+
+ var currentRatio = imgWidth / self.overviewImage.width;
+
+ var xNormal = position.x / currentRatio;
+ var yNormal = position.y / currentRatio;
+ var point = new Point(xNormal, yNormal);
+
+ if (self.overviewImage.mousePos.x !== position.x || self.overviewImage.mousePos.y !== position.y) {
+ self.overviewImage.mousePos = position;
+ var link = null;
+ for (var i = 0; i < self.overviewImage.links.length; i++) {
+ if (functions.pointInsidePolygon(point, self.overviewImage.links[i].polygon)) {
+ link = self.overviewImage.links[i];
+ }
+ }
+ if (link === null) {
+ e.currentTarget.style.cursor = "auto";
+ } else {
+ e.currentTarget.style.cursor = "pointer";
+ }
+ }
+ };
+
+ // onMouseMove listener should be assigned to canvas (which is on top of the
+ // image) and overviewImage (just in case something went wrong with resizing
+ // canvas)
+ canvasDebug.onmousemove = onMouseMove;
+ this.overviewImageTag.onmousemove = onMouseMove;
+
+ $(self.getElement()).dialog("open");
+};
+
+OverviewDialog.prototype.openLink = function (link) {
+ var self = this;
+ var map = self.getMap();
+ if (link.type === "OverviewModelLink") {
+ logger.debug("Opening model from overview. ModelId: " + link.modelLinkId);
+ logger.debug("link coordinates [" + link.idObject + "]: " + link.modelPoint);
+
+ map.openSubmap(link.modelLinkId);
+ var submap = map.getSubmapById(link.modelLinkId);
+ logger.debug("zoom [" + link.idObject + "]: " + link.zoomLevel + submap.getMinZoom());
+ submap.setCenter(new Point(link.modelPoint));
+ submap.setZoom(link.zoomLevel + submap.getMinZoom());
+
+ $(self.getElement()).dialog("close");
+ } else if (link.type === "OverviewImageLink") {
+ logger.debug("Opening image from overview. ImageId: " + link.imageLinkId);
+ self.showOverview(link.imageLinkId);
+ } else if (link.type === "OverviewSearchLink") {
+ logger.debug("Sending search query. Query: " + link.query);
+ return map.getOverlayByName("search").searchByQuery(link.query).then(function () {
+ $(self.getElement()).dialog("close");
+ }, GuiConnector.alert);
+ } else {
+ logger.warn("Unknown type of link: " + link.type + ". Don't know what to do... LinkId: " + link.idObject);
+ }
+};
+
+OverviewDialog.prototype.drawClickableShapes = function (canvas, ratio) {
+ var ctx = canvas.getContext("2d");
+ // clear canvas
+ ctx.clearRect(0, 0, canvas.width, canvas.height);
+ for (var i = 0; i < this.overviewImage.links.length; i++) {
+ ctx.beginPath();
+ var polygon = this.overviewImage.links[i].polygon;
+ for (var j = 0; j < polygon.length; j++) {
+ var x = polygon[j].x * ratio;
+ var y = polygon[j].y * ratio;
+ ctx.moveTo(x, y);
+ x = polygon[(j + 1) % polygon.length].x * ratio;
+ y = polygon[(j + 1) % polygon.length].y * ratio;
+ ctx.lineTo(x, y);
+ }
+ ctx.stroke();
+ }
+};
+
+OverviewDialog.prototype.destroy = function () {
+ $(this.getElement()).dialog("destroy");
+};
+
+module.exports = OverviewDialog;
diff --git a/frontend-js/src/main/js/gui/Panel.js b/frontend-js/src/main/js/gui/Panel.js
index ae0f4900331f9769f5c8d93ec74ac02b5512d7af..309fc1c6740d2e25c9c5512183782e1d296c55d7 100644
--- a/frontend-js/src/main/js/gui/Panel.js
+++ b/frontend-js/src/main/js/gui/Panel.js
@@ -1,309 +1,309 @@
-"use strict";
-
-/* exported logger */
-
-var GuiConnector = require('../GuiConnector');
-var AbstractGuiElement = require('./AbstractGuiElement');
-var GuiUtils = require('./leftPanel/GuiUtils');
-var PanelControlElementType = require('./PanelControlElementType');
-var Functions = require('../Functions');
-
-var logger = require('../logger');
-var xss = require('xss');
-
-/**
- *
- * @param {Configuration} [params.configuration]
- * @param {HTMLElement} params.element
- * @param {Project} params.project
- * @param {CustomMap} [params.customMap]
- * @param {string} params.panelName
- * @param {boolean} params.scrollable
- * @param {string} [params.helpTip]
- * @param params.parent
- *
- * @constructor
- * @extends AbstractGuiElement
- */
-
-function Panel(params) {
- AbstractGuiElement.call(this, params);
-
- var self = this;
-
- self.setParent(params.parent);
- var configuration = params.configuration;
- if (params.configuration === undefined) {
- configuration = self.getMap().getConfiguration();
- }
- var guiUtils = new GuiUtils(configuration);
- self.setGuiUtils(guiUtils);
- if (self.getMap() !== undefined) {
- this.getGuiUtils().setMap(self.getMap());
- }
- self.setPanelName(params.panelName);
-
- if (params.scrollable) {
- $(self.getElement()).addClass("pre-scrollable");
- } else {
- $(self.getElement()).css("overflow-y", "auto");
- }
-
- $(self.getElement()).css("position", "relative");
- if (params.helpTip !== undefined) {
- self.setHelpTip(params.helpTip);
- }
-
- GuiConnector.addWindowResizeEvent(function () {
- self.onresize();
- });
-
- $("a[href='#" + self.getElement().id + "']").on('shown.bs.tab', function () {
- self.onresize();
- });
-
-}
-
-Panel.prototype = Object.create(AbstractGuiElement.prototype);
-Panel.prototype.constructor = Panel;
-
-Panel.prototype.createHelpButton = function () {
- var self = this;
- var helpTipButton = self.getGuiUtils().createHelpButton(self.getHelpTip());
- self.getElement().appendChild(helpTipButton);
-};
-
-Panel.prototype.disablePanel = function (message) {
- var self = this;
-
- $(self.getElement()).children().css("visibility", "hidden");
- $("[class='minerva-help-button']", self.getElement()).children().css("visibility", "visible");
- var hideReasonDiv = document.createElement("div");
- hideReasonDiv.className = "searchPanel";
-
- var center = document.createElement("center");
- var messageDiv = document.createElement("h4");
- messageDiv.innerHTML = message;
- center.appendChild(messageDiv);
- hideReasonDiv.appendChild(center);
-
- $(self.getElement()).prepend(hideReasonDiv);
-};
-
-Panel.prototype.isDisabled = function () {
- var self = this;
- var searchQueryElement = self.getControlElement(PanelControlElementType.SEARCH_DIV);
- return searchQueryElement.style.visibility === "hidden";
-};
-Panel.prototype.setMap = function (map) {
- this._map = map;
-};
-
-Panel.prototype.setPanelName = function (panelName) {
- this._panelName = panelName;
-};
-
-Panel.prototype.getPanelName = function () {
- return this._panelName;
-};
-
-/**
- *
- * @param {HTMLElement} element
- */
-Panel.prototype.setElement = function (element) {
- if (element === undefined || element === null) {
- throw new Error("DOM Element must be defined");
- }
- this._element = element;
-};
-
-/**
- *
- * @returns {HTMLElement}
- */
-Panel.prototype.getElement = function () {
- return this._element;
-};
-
-Panel.prototype.getElementByName = function (element, name) {
- if (element !== undefined) {
- if (element.getAttribute("name") === name) {
- return element;
- }
- var children = element.children;
- for (var i = 0; i < children.length; i++) {
- var child = children[i];
- var res = this.getElementByName(child, name);
- if (res !== undefined) {
- return res;
- }
- }
- }
- return undefined;
-};
-
-Panel.prototype.getDialogDiv = function (id) {
- var dialogs = this.getElementByName(this.getElement(), "dialogs");
- if (dialogs === undefined) {
- dialogs = document.createElement("div");
- dialogs.setAttribute("name", "dialogs");
- this.getElement().appendChild(dialogs);
-
- this._dialogs = [];
- }
-
- var dialogDiv = this._dialogs[id];
-
- if (dialogDiv === undefined) {
- dialogDiv = document.createElement("div");
- dialogDiv.className = "ui-widget";
- dialogDiv.setAttribute("name", "dialog-" + id);
-
- var contentDiv = document.createElement("div");
- contentDiv.setAttribute("name", "content");
- dialogDiv.appendChild(contentDiv);
-
- dialogs.appendChild(dialogDiv);
-
- this._dialogs[id] = dialogDiv;
- }
- return dialogDiv;
-};
-
-Panel.prototype.assignDialogOptions = function (div, params) {
- var dialog = $(div);
- for (var key in params) {
- if (params.hasOwnProperty(key)) {
- if (key === "id") {
- div.setAttribute("name", "dialog-" + params[key]);
- } else if (key === "modal") {
- dialog.dialog('option', 'modal', params[key]);
- } else if (key === "buttons") {
- dialog.dialog('option', 'buttons', params[key]);
- } else if (key === "className") {
- dialog.dialog('option', 'dialogClass', params[key]);
- } else if (key === "title") {
- dialog.dialog('option', 'title', params[key]);
- } else if (key === "width") {
- dialog.dialog('option', 'width', params[key]);
- } else {
- throw new Error("Unknown dialog param: " + key + " - " + params[key]);
- }
- }
- }
-};
-
-Panel.prototype.openDialog = function (content, options) {
- if (options === undefined) {
- options = {};
- }
-
- if (options.id === undefined) {
- logger.warn("Id of dialog is not defined");
- }
-
- var div = this.getDialogDiv(options.id);
-
- var contentDiv = this.getElementByName(div, "content");
- while (contentDiv.hasChildNodes()) {
- contentDiv.removeChild(contentDiv.lastChild);
- }
- contentDiv.appendChild(content);
- contentDiv.style.display = "block";
-
- $(div).dialog({
- close: function () {
- contentDiv.style.display = "none";
- $(this).dialog('destroy');
- },
- dialogClass: options.className
- });
-
- this.assignDialogOptions(div, options);
-
- $(div).dialog("open");
-};
-
-Panel.prototype.init = function () {
- throw new Error(this.getPanelName() + " Not implemented");
-};
-
-Panel.prototype.setParent = function (parent) {
- this._parent = parent;
-};
-
-Panel.prototype.getParent = function () {
- return this._parent;
-};
-
-/**
- *
- * @param {GuiUtils} guiUtils
- */
-Panel.prototype.setGuiUtils = function (guiUtils) {
- this._guiUtils = guiUtils;
-};
-
-/**
- *
- * @returns {GuiUtils}
- */
-Panel.prototype.getGuiUtils = function () {
- return this._guiUtils;
-};
-
-Panel.prototype.setHelpTip = function (helpTip) {
- if (this._helpTip === undefined && helpTip !== undefined) {
- this._helpTip = helpTip;
- this.createHelpButton();
- }
-};
-
-Panel.prototype.getHelpTip = function () {
- return this._helpTip;
-};
-
-Panel.prototype.onresize = function () {
- var self = this;
- var footerPosition = window.innerHeight;
-
- // compute the width (we can only compute it for visible elements)
- var size = 100000;
-
- if ($(self.getElement()).is(":visible")) {
-
- $(".pre-scrollable", self.getElement()).each(function (index, element) {
- if ($(element).is(":visible")) {
- size = Math.min(size, footerPosition - $(element).offset().top);
- }
- });
- if ($(self.getElement()).hasClass("pre-scrollable") && $(self.getElement()).is(":visible")) {
- size = Math.min(size, footerPosition - $(self.getElement()).offset().top);
- }
- if (size !== 100000) {
- $(".pre-scrollable", self.getElement()).each(function (index, element) {
- $(element).css('max-height', size);
- $(element).css('height', size);
- });
- }
- if ($(self.getElement()).hasClass("pre-scrollable") && $(self.getElement()).is(":visible")) {
- $(self.getElement()).css('max-height', size);
- $(self.getElement()).css('height', size);
- }
- }
-
-};
-
-Panel.prototype.destroy = function () {
- for (var id in this._dialogs) {
- if (this._dialogs.hasOwnProperty(id)) {
- var div = this._dialogs[id];
- if ($(div).hasClass("ui-dialog-content")) {
- $(div).dialog("destroy");
- }
- }
- }
-};
-
-module.exports = Panel;
+"use strict";
+
+/* exported logger */
+
+var GuiConnector = require('../GuiConnector');
+var AbstractGuiElement = require('./AbstractGuiElement');
+var GuiUtils = require('./leftPanel/GuiUtils');
+var PanelControlElementType = require('./PanelControlElementType');
+var Functions = require('../Functions');
+
+var logger = require('../logger');
+var xss = require('xss');
+
+/**
+ *
+ * @param {Configuration} [params.configuration]
+ * @param {HTMLElement} params.element
+ * @param {Project} params.project
+ * @param {CustomMap} [params.customMap]
+ * @param {string} params.panelName
+ * @param {boolean} params.scrollable
+ * @param {string} [params.helpTip]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
+
+function Panel(params) {
+ AbstractGuiElement.call(this, params);
+
+ var self = this;
+
+ self.setParent(params.parent);
+ var configuration = params.configuration;
+ if (params.configuration === undefined) {
+ configuration = self.getMap().getConfiguration();
+ }
+ var guiUtils = new GuiUtils(configuration);
+ self.setGuiUtils(guiUtils);
+ if (self.getMap() !== undefined) {
+ this.getGuiUtils().setMap(self.getMap());
+ }
+ self.setPanelName(params.panelName);
+
+ if (params.scrollable) {
+ $(self.getElement()).addClass("pre-scrollable");
+ } else {
+ $(self.getElement()).css("overflow-y", "auto");
+ }
+
+ $(self.getElement()).css("position", "relative");
+ if (params.helpTip !== undefined) {
+ self.setHelpTip(params.helpTip);
+ }
+
+ GuiConnector.addWindowResizeEvent(function () {
+ self.onresize();
+ });
+
+ $("a[href='#" + self.getElement().id + "']").on('shown.bs.tab', function () {
+ self.onresize();
+ });
+
+}
+
+Panel.prototype = Object.create(AbstractGuiElement.prototype);
+Panel.prototype.constructor = Panel;
+
+Panel.prototype.createHelpButton = function () {
+ var self = this;
+ var helpTipButton = self.getGuiUtils().createHelpButton(self.getHelpTip());
+ self.getElement().appendChild(helpTipButton);
+};
+
+Panel.prototype.disablePanel = function (message) {
+ var self = this;
+
+ $(self.getElement()).children().css("visibility", "hidden");
+ $("[class='minerva-help-button']", self.getElement()).children().css("visibility", "visible");
+ var hideReasonDiv = document.createElement("div");
+ hideReasonDiv.className = "searchPanel";
+
+ var center = document.createElement("center");
+ var messageDiv = document.createElement("h4");
+ messageDiv.innerHTML = message;
+ center.appendChild(messageDiv);
+ hideReasonDiv.appendChild(center);
+
+ $(self.getElement()).prepend(hideReasonDiv);
+};
+
+Panel.prototype.isDisabled = function () {
+ var self = this;
+ var searchQueryElement = self.getControlElement(PanelControlElementType.SEARCH_DIV);
+ return searchQueryElement.style.visibility === "hidden";
+};
+Panel.prototype.setMap = function (map) {
+ this._map = map;
+};
+
+Panel.prototype.setPanelName = function (panelName) {
+ this._panelName = panelName;
+};
+
+Panel.prototype.getPanelName = function () {
+ return this._panelName;
+};
+
+/**
+ *
+ * @param {HTMLElement} element
+ */
+Panel.prototype.setElement = function (element) {
+ if (element === undefined || element === null) {
+ throw new Error("DOM Element must be defined");
+ }
+ this._element = element;
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
+Panel.prototype.getElement = function () {
+ return this._element;
+};
+
+Panel.prototype.getElementByName = function (element, name) {
+ if (element !== undefined) {
+ if (element.getAttribute("name") === name) {
+ return element;
+ }
+ var children = element.children;
+ for (var i = 0; i < children.length; i++) {
+ var child = children[i];
+ var res = this.getElementByName(child, name);
+ if (res !== undefined) {
+ return res;
+ }
+ }
+ }
+ return undefined;
+};
+
+Panel.prototype.getDialogDiv = function (id) {
+ var dialogs = this.getElementByName(this.getElement(), "dialogs");
+ if (dialogs === undefined) {
+ dialogs = document.createElement("div");
+ dialogs.setAttribute("name", "dialogs");
+ this.getElement().appendChild(dialogs);
+
+ this._dialogs = [];
+ }
+
+ var dialogDiv = this._dialogs[id];
+
+ if (dialogDiv === undefined) {
+ dialogDiv = document.createElement("div");
+ dialogDiv.className = "ui-widget";
+ dialogDiv.setAttribute("name", "dialog-" + id);
+
+ var contentDiv = document.createElement("div");
+ contentDiv.setAttribute("name", "content");
+ dialogDiv.appendChild(contentDiv);
+
+ dialogs.appendChild(dialogDiv);
+
+ this._dialogs[id] = dialogDiv;
+ }
+ return dialogDiv;
+};
+
+Panel.prototype.assignDialogOptions = function (div, params) {
+ var dialog = $(div);
+ for (var key in params) {
+ if (params.hasOwnProperty(key)) {
+ if (key === "id") {
+ div.setAttribute("name", "dialog-" + params[key]);
+ } else if (key === "modal") {
+ dialog.dialog('option', 'modal', params[key]);
+ } else if (key === "buttons") {
+ dialog.dialog('option', 'buttons', params[key]);
+ } else if (key === "className") {
+ dialog.dialog('option', 'dialogClass', params[key]);
+ } else if (key === "title") {
+ dialog.dialog('option', 'title', params[key]);
+ } else if (key === "width") {
+ dialog.dialog('option', 'width', params[key]);
+ } else {
+ throw new Error("Unknown dialog param: " + key + " - " + params[key]);
+ }
+ }
+ }
+};
+
+Panel.prototype.openDialog = function (content, options) {
+ if (options === undefined) {
+ options = {};
+ }
+
+ if (options.id === undefined) {
+ logger.warn("Id of dialog is not defined");
+ }
+
+ var div = this.getDialogDiv(options.id);
+
+ var contentDiv = this.getElementByName(div, "content");
+ while (contentDiv.hasChildNodes()) {
+ contentDiv.removeChild(contentDiv.lastChild);
+ }
+ contentDiv.appendChild(content);
+ contentDiv.style.display = "block";
+
+ $(div).dialog({
+ close: function () {
+ contentDiv.style.display = "none";
+ $(this).dialog('destroy');
+ },
+ dialogClass: options.className
+ });
+
+ this.assignDialogOptions(div, options);
+
+ $(div).dialog("open");
+};
+
+Panel.prototype.init = function () {
+ throw new Error(this.getPanelName() + " Not implemented");
+};
+
+Panel.prototype.setParent = function (parent) {
+ this._parent = parent;
+};
+
+Panel.prototype.getParent = function () {
+ return this._parent;
+};
+
+/**
+ *
+ * @param {GuiUtils} guiUtils
+ */
+Panel.prototype.setGuiUtils = function (guiUtils) {
+ this._guiUtils = guiUtils;
+};
+
+/**
+ *
+ * @returns {GuiUtils}
+ */
+Panel.prototype.getGuiUtils = function () {
+ return this._guiUtils;
+};
+
+Panel.prototype.setHelpTip = function (helpTip) {
+ if (this._helpTip === undefined && helpTip !== undefined) {
+ this._helpTip = helpTip;
+ this.createHelpButton();
+ }
+};
+
+Panel.prototype.getHelpTip = function () {
+ return this._helpTip;
+};
+
+Panel.prototype.onresize = function () {
+ var self = this;
+ var footerPosition = window.innerHeight;
+
+ // compute the width (we can only compute it for visible elements)
+ var size = 100000;
+
+ if ($(self.getElement()).is(":visible")) {
+
+ $(".pre-scrollable", self.getElement()).each(function (index, element) {
+ if ($(element).is(":visible")) {
+ size = Math.min(size, footerPosition - $(element).offset().top);
+ }
+ });
+ if ($(self.getElement()).hasClass("pre-scrollable") && $(self.getElement()).is(":visible")) {
+ size = Math.min(size, footerPosition - $(self.getElement()).offset().top);
+ }
+ if (size !== 100000) {
+ $(".pre-scrollable", self.getElement()).each(function (index, element) {
+ $(element).css('max-height', size);
+ $(element).css('height', size);
+ });
+ }
+ if ($(self.getElement()).hasClass("pre-scrollable") && $(self.getElement()).is(":visible")) {
+ $(self.getElement()).css('max-height', size);
+ $(self.getElement()).css('height', size);
+ }
+ }
+
+};
+
+Panel.prototype.destroy = function () {
+ for (var id in this._dialogs) {
+ if (this._dialogs.hasOwnProperty(id)) {
+ var div = this._dialogs[id];
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
+ }
+ }
+ }
+};
+
+module.exports = Panel;
diff --git a/frontend-js/src/main/js/gui/PanelControlElementType.js b/frontend-js/src/main/js/gui/PanelControlElementType.js
index dd7610f6830145ebee9d41cc7f9e0c973af60bcd..9f66700a416c7eb8fa883313c4365f3aa80dffed 100644
--- a/frontend-js/src/main/js/gui/PanelControlElementType.js
+++ b/frontend-js/src/main/js/gui/PanelControlElementType.js
@@ -1,60 +1,60 @@
-"use strict";
-
-var PanelControlElementType = {
- SEARCH_DIV : "SEARCH_DIV",
- SEARCH_LABEL : "SEARCH_LABEL",
- SEARCH_INPUT : "SEARCH_INPUT",
- SEARCH_BUTTON : "SEARCH_BUTTON",
- SEARCH_RESULTS_DIV : "SEARCH_RESULTS_DIV",
- SEARCH_RESULTS_NAV_TAB : "SEARCH_RESULTS_NAV_TAB",
- SEARCH_RESULTS_CONTENT_TAB : "SEARCH_RESULTS_CONTENT_TAB",
-
- SEARCH_PERFECT_MATCH_CHECKBOX : "SEARCH_PERFECT_MATCH_CHECKBOX",
-
- OVERLAY_GENERAL_OVERLAY_DIV : "OVERLAY_GENERAL_OVERLAY_DIV",
- OVERLAY_GENERAL_OVERLAY_TABLE : "OVERLAY_GENERAL_OVERLAY_TABLE",
- OVERLAY_CUSTOM_OVERLAY_DIV : "OVERLAY_CUSTOM_OVERLAY_DIV",
- OVERLAY_CUSTOM_OVERLAY_TABLE : "OVERLAY_CUSTOM_OVERLAY_TABLE",
- OVERLAY_CUSTOM_OVERLAY_TITLE : "OVERLAY_CUSTOM_OVERLAY_TITLE",
- OVERLAY_ADD_OVERLAY_BUTTON : "OVERLAY_ADD_OVERLAY_BUTTON",
-
- USER_TAB_LOGIN_DIV : "USER_TAB_LOGIN_DIV",
- USER_TAB_LOGIN_INPUT_TEXT : "USER_TAB_LOGIN_INPUT_TEXT",
- USER_TAB_PASSWORD_INPUT_TEXT : "USER_TAB_PASSWORD_INPUT_TEXT",
- USER_TAB_LOGIN_BUTTON : "USER_TAB_LOGIN_BUTTON",
-
- USER_TAB_USER_DIV : "USER_TAB_USER_DIV",
- USER_TAB_LOGIN_TEXT : "USER_TAB_LOGIN_TEXT",
- USER_TAB_NAME_TEXT : "USER_TAB_NAME_TEXT",
- USER_TAB_SURNAME_TEXT : "USER_TAB_SURNAME_TEXT",
- USER_TAB_EMAIL_TEXT : "USER_TAB_EMAIL_TEXT",
- USER_TAB_LOGOUT_BUTTON : "USER_TAB_LOGOUT_BUTTON",
-
- SUBMAP_TABLE : "SUBMAP_TABLE",
- SUBMAP_DIV : "SUBMAP_DIV",
-
- INFO_DIV : "INFO_DIV",
- INFO_PROJECT_NAME_TEXT : "INFO_PROJECT_NAME_TEXT",
- INFO_PROJECT_VERSION_TEXT : "INFO_PROJECT_VERSION_TEXT",
- INFO_PROJECT_DESCRIPTION_TEXT : "INFO_PROJECT_DESCRIPTION_TEXT",
- INFO_PROJECT_PUBLICATIONS_TEXT : "INFO_PROJECT_PUBLICATIONS_TEXT",
- INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON : "INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON",
- INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON : "INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON",
-
- LEGEND_INDICATORS_OL : "LEGEND_INDICATORS_OL",
- LEGEND_SLIDES_DIV : "LEGEND_SLIDES_DIV",
-
- MENU_LEGEND_CHECKBOX : "MENU_LEGEND_CHECKBOX",
- MENU_HIDE_LEFT_PANEL_BUTTON : "MENU_HIDE_LEFT_PANEL_BUTTON",
- MENU_HIDE_LEFT_PANEL_BUTTON_ICON : "MENU_HIDE_LEFT_PANEL_BUTTON_ICON",
- MENU_COMMENTS_CHECKBOX : "MENU_COMMENTS_CHECKBOX",
- MENU_REFRESH_COMMENTS_BUTTON : "MENU_REFRESH_COMMENTS_BUTTON",
- MENU_CLEAR_BUTTON : "MENU_CLEAR_BUTTON",
- OVERVIEW_DIALOG_DIV : "OVERVIEW_DIALOG_DIV",
- MENU_SHOW_OVERVIEW_BUTTON : "MENU_SHOW_OVERVIEW_BUTTON",
- MENU_VERSION_DIV : "MENU_VERSION_DIV",
-
- FOOTER_LOADING_DIV : "FOOTER_LOADING_DIV"
-};
-
-module.exports = PanelControlElementType;
+"use strict";
+
+var PanelControlElementType = {
+ SEARCH_DIV : "SEARCH_DIV",
+ SEARCH_LABEL : "SEARCH_LABEL",
+ SEARCH_INPUT : "SEARCH_INPUT",
+ SEARCH_BUTTON : "SEARCH_BUTTON",
+ SEARCH_RESULTS_DIV : "SEARCH_RESULTS_DIV",
+ SEARCH_RESULTS_NAV_TAB : "SEARCH_RESULTS_NAV_TAB",
+ SEARCH_RESULTS_CONTENT_TAB : "SEARCH_RESULTS_CONTENT_TAB",
+
+ SEARCH_PERFECT_MATCH_CHECKBOX : "SEARCH_PERFECT_MATCH_CHECKBOX",
+
+ OVERLAY_GENERAL_OVERLAY_DIV : "OVERLAY_GENERAL_OVERLAY_DIV",
+ OVERLAY_GENERAL_OVERLAY_TABLE : "OVERLAY_GENERAL_OVERLAY_TABLE",
+ OVERLAY_CUSTOM_OVERLAY_DIV : "OVERLAY_CUSTOM_OVERLAY_DIV",
+ OVERLAY_CUSTOM_OVERLAY_TABLE : "OVERLAY_CUSTOM_OVERLAY_TABLE",
+ OVERLAY_CUSTOM_OVERLAY_TITLE : "OVERLAY_CUSTOM_OVERLAY_TITLE",
+ OVERLAY_ADD_OVERLAY_BUTTON : "OVERLAY_ADD_OVERLAY_BUTTON",
+
+ USER_TAB_LOGIN_DIV : "USER_TAB_LOGIN_DIV",
+ USER_TAB_LOGIN_INPUT_TEXT : "USER_TAB_LOGIN_INPUT_TEXT",
+ USER_TAB_PASSWORD_INPUT_TEXT : "USER_TAB_PASSWORD_INPUT_TEXT",
+ USER_TAB_LOGIN_BUTTON : "USER_TAB_LOGIN_BUTTON",
+
+ USER_TAB_USER_DIV : "USER_TAB_USER_DIV",
+ USER_TAB_LOGIN_TEXT : "USER_TAB_LOGIN_TEXT",
+ USER_TAB_NAME_TEXT : "USER_TAB_NAME_TEXT",
+ USER_TAB_SURNAME_TEXT : "USER_TAB_SURNAME_TEXT",
+ USER_TAB_EMAIL_TEXT : "USER_TAB_EMAIL_TEXT",
+ USER_TAB_LOGOUT_BUTTON : "USER_TAB_LOGOUT_BUTTON",
+
+ SUBMAP_TABLE : "SUBMAP_TABLE",
+ SUBMAP_DIV : "SUBMAP_DIV",
+
+ INFO_DIV : "INFO_DIV",
+ INFO_PROJECT_NAME_TEXT : "INFO_PROJECT_NAME_TEXT",
+ INFO_PROJECT_VERSION_TEXT : "INFO_PROJECT_VERSION_TEXT",
+ INFO_PROJECT_DESCRIPTION_TEXT : "INFO_PROJECT_DESCRIPTION_TEXT",
+ INFO_PROJECT_PUBLICATIONS_TEXT : "INFO_PROJECT_PUBLICATIONS_TEXT",
+ INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON : "INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON",
+ INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON : "INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON",
+
+ LEGEND_INDICATORS_OL : "LEGEND_INDICATORS_OL",
+ LEGEND_SLIDES_DIV : "LEGEND_SLIDES_DIV",
+
+ MENU_LEGEND_CHECKBOX : "MENU_LEGEND_CHECKBOX",
+ MENU_HIDE_LEFT_PANEL_BUTTON : "MENU_HIDE_LEFT_PANEL_BUTTON",
+ MENU_HIDE_LEFT_PANEL_BUTTON_ICON : "MENU_HIDE_LEFT_PANEL_BUTTON_ICON",
+ MENU_COMMENTS_CHECKBOX : "MENU_COMMENTS_CHECKBOX",
+ MENU_REFRESH_COMMENTS_BUTTON : "MENU_REFRESH_COMMENTS_BUTTON",
+ MENU_CLEAR_BUTTON : "MENU_CLEAR_BUTTON",
+ OVERVIEW_DIALOG_DIV : "OVERVIEW_DIALOG_DIV",
+ MENU_SHOW_OVERVIEW_BUTTON : "MENU_SHOW_OVERVIEW_BUTTON",
+ MENU_VERSION_DIV : "MENU_VERSION_DIV",
+
+ FOOTER_LOADING_DIV : "FOOTER_LOADING_DIV"
+};
+
+module.exports = PanelControlElementType;
diff --git a/frontend-js/src/main/js/gui/PluginDialog.js b/frontend-js/src/main/js/gui/PluginDialog.js
index fd351bac1583f542de07b0ec827cf139b45bf52f..0837775528057939b0911029563120c6567e86b6 100644
--- a/frontend-js/src/main/js/gui/PluginDialog.js
+++ b/frontend-js/src/main/js/gui/PluginDialog.js
@@ -1,162 +1,162 @@
-"use strict";
-var AbstractGuiElement = require('./AbstractGuiElement');
-var GuiConnector = require('../GuiConnector');
-var GuiUtils = require('./leftPanel/GuiUtils');
-
-var Functions = require('../Functions');
-
-function PluginDialog(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
- self.setPluginManager(params.pluginManager);
- self._knownPlugins = [];
-}
-
-PluginDialog.prototype = Object.create(AbstractGuiElement.prototype);
-PluginDialog.prototype.constructor = PluginDialog;
-
-PluginDialog.prototype._createPluginGui = function () {
- var self = this;
- var guiUtils = new GuiUtils();
-
- self.getElement().innerHTML = "";
-
- var pluginFormTab = Functions.createElement({
- type: "div",
- name: "minerva-plugin-list-tab",
- style: "width:100%;display: table;border-spacing: 10px;"
- });
- self.getElement().appendChild(pluginFormTab);
-
- var pluginUrlLabel = Functions.createElement({
- type: "span",
- content: "URL:",
- style: "color:#999999"
- });
- var pluginUrlInput = Functions.createElement({
- type: "input",
- name: "pluginUrlValue"
- });
-
- var loadPluginButton = Functions.createElement({
- type: "button",
- name: "loadPluginButton",
- content: "LOAD",
- onclick: function () {
- return self.getPluginManager().addPlugin({url: pluginUrlInput.value}).then(function () {
- self.close();
- }).then(null, GuiConnector.alert);
- }
- });
- pluginFormTab.appendChild(guiUtils.createTableRow([pluginUrlLabel, pluginUrlInput, loadPluginButton]));
-
- var pluginManager = self.getPluginManager();
-
- var loadedPlugins = [];
- var plugins = pluginManager.getPlugins();
- var i;
- for (i = 0; i < plugins.length; i++) {
- loadedPlugins[plugins[i].getOptions().url] = true;
- }
-
- for (i = 0; i < self._knownPlugins.length; i++) {
- var pluginData = self._knownPlugins[i];
- var url = pluginData.url;
-
- var pluginUrl = Functions.createElement({
- type: "input",
- value: url,
- style: "color:#999999"
- });
- pluginUrl.readOnly = true;
- var button;
- if (!loadedPlugins[url]) {
- button = Functions.createElement({
- type: "button",
- content: "LOAD",
- onclick: function () {
- return pluginManager.addPlugin({url: $(this).data("url")}).then(function () {
- self.close();
- }).then(null, GuiConnector.alert);
- }
- });
- }
- $(button).data("url", url);
-
- pluginFormTab.appendChild(guiUtils.createTableRow([Functions.createElement({type: "span"}), pluginUrl, button]));
- }
- for (i = 0; i < plugins.length; i++) {
- var plugin = plugins[i];
- var removePlugin = (function () {
- var pluginToRemove = plugin;
- return function () {
- return pluginManager.removePlugin(pluginToRemove).then(function () {
- self.close();
- }).then(null, GuiConnector.alert);
- }
- })();
- pluginUrl = Functions.createElement({
- type: "input",
- value: plugins[i].getOptions().url,
- style: "color:#999999"
- });
- pluginUrl.readOnly = true;
- button = Functions.createElement({
- type: "button",
- content: "UNLOAD",
- onclick: removePlugin
- });
-
- pluginFormTab.appendChild(guiUtils.createTableRow([Functions.createElement({type: "span"}), pluginUrl, button]));
-
- }
-};
-
-PluginDialog.prototype.init = function () {
- var self = this;
- return ServerConnector.getConfiguration().then(function (configuration) {
- var pluginsData = configuration.getPluginsData();
- for (var i = 0; i < pluginsData.length; i++) {
- var pluginData = pluginsData[i];
- self._knownPlugins.push({url: ServerConnector.getServerBaseUrl() + pluginData.url});
- }
- });
-};
-
-PluginDialog.prototype.open = function () {
- var self = this;
- self._createPluginGui();
- var div = self.getElement();
- if (!$(div).hasClass("ui-dialog-content")) {
- $(div).dialog({
- autoOpen: false,
- resizable: false,
- width: 400
- });
- }
-
- $(div).dialog('option', 'title', 'PLUGINS');
- $(div).dialog("open");
-};
-PluginDialog.prototype.close = function () {
- var self = this;
- $(self.getElement()).dialog("close");
-};
-
-PluginDialog.prototype.destroy = function () {
- var self = this;
- var div = self.getElement();
- if ($(div).hasClass("ui-dialog-content")) {
- $(div).dialog("destroy");
- }
-};
-
-PluginDialog.prototype.setPluginManager = function (pluginManager) {
- this._pluginManager = pluginManager;
-};
-
-PluginDialog.prototype.getPluginManager = function () {
- return this._pluginManager;
-};
-
-module.exports = PluginDialog;
+"use strict";
+var AbstractGuiElement = require('./AbstractGuiElement');
+var GuiConnector = require('../GuiConnector');
+var GuiUtils = require('./leftPanel/GuiUtils');
+
+var Functions = require('../Functions');
+
+function PluginDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ self.setPluginManager(params.pluginManager);
+ self._knownPlugins = [];
+}
+
+PluginDialog.prototype = Object.create(AbstractGuiElement.prototype);
+PluginDialog.prototype.constructor = PluginDialog;
+
+PluginDialog.prototype._createPluginGui = function () {
+ var self = this;
+ var guiUtils = new GuiUtils();
+
+ self.getElement().innerHTML = "";
+
+ var pluginFormTab = Functions.createElement({
+ type: "div",
+ name: "minerva-plugin-list-tab",
+ style: "width:100%;display: table;border-spacing: 10px;"
+ });
+ self.getElement().appendChild(pluginFormTab);
+
+ var pluginUrlLabel = Functions.createElement({
+ type: "span",
+ content: "URL:",
+ style: "color:#999999"
+ });
+ var pluginUrlInput = Functions.createElement({
+ type: "input",
+ name: "pluginUrlValue"
+ });
+
+ var loadPluginButton = Functions.createElement({
+ type: "button",
+ name: "loadPluginButton",
+ content: "LOAD",
+ onclick: function () {
+ return self.getPluginManager().addPlugin({url: pluginUrlInput.value}).then(function () {
+ self.close();
+ }).then(null, GuiConnector.alert);
+ }
+ });
+ pluginFormTab.appendChild(guiUtils.createTableRow([pluginUrlLabel, pluginUrlInput, loadPluginButton]));
+
+ var pluginManager = self.getPluginManager();
+
+ var loadedPlugins = [];
+ var plugins = pluginManager.getPlugins();
+ var i;
+ for (i = 0; i < plugins.length; i++) {
+ loadedPlugins[plugins[i].getOptions().url] = true;
+ }
+
+ for (i = 0; i < self._knownPlugins.length; i++) {
+ var pluginData = self._knownPlugins[i];
+ var url = pluginData.url;
+
+ var pluginUrl = Functions.createElement({
+ type: "input",
+ value: url,
+ style: "color:#999999"
+ });
+ pluginUrl.readOnly = true;
+ var button;
+ if (!loadedPlugins[url]) {
+ button = Functions.createElement({
+ type: "button",
+ content: "LOAD",
+ onclick: function () {
+ return pluginManager.addPlugin({url: $(this).data("url")}).then(function () {
+ self.close();
+ }).then(null, GuiConnector.alert);
+ }
+ });
+ }
+ $(button).data("url", url);
+
+ pluginFormTab.appendChild(guiUtils.createTableRow([Functions.createElement({type: "span"}), pluginUrl, button]));
+ }
+ for (i = 0; i < plugins.length; i++) {
+ var plugin = plugins[i];
+ var removePlugin = (function () {
+ var pluginToRemove = plugin;
+ return function () {
+ return pluginManager.removePlugin(pluginToRemove).then(function () {
+ self.close();
+ }).then(null, GuiConnector.alert);
+ }
+ })();
+ pluginUrl = Functions.createElement({
+ type: "input",
+ value: plugins[i].getOptions().url,
+ style: "color:#999999"
+ });
+ pluginUrl.readOnly = true;
+ button = Functions.createElement({
+ type: "button",
+ content: "UNLOAD",
+ onclick: removePlugin
+ });
+
+ pluginFormTab.appendChild(guiUtils.createTableRow([Functions.createElement({type: "span"}), pluginUrl, button]));
+
+ }
+};
+
+PluginDialog.prototype.init = function () {
+ var self = this;
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ var pluginsData = configuration.getPluginsData();
+ for (var i = 0; i < pluginsData.length; i++) {
+ var pluginData = pluginsData[i];
+ self._knownPlugins.push({url: ServerConnector.getServerBaseUrl() + pluginData.url});
+ }
+ });
+};
+
+PluginDialog.prototype.open = function () {
+ var self = this;
+ self._createPluginGui();
+ var div = self.getElement();
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ autoOpen: false,
+ resizable: false,
+ width: 400
+ });
+ }
+
+ $(div).dialog('option', 'title', 'PLUGINS');
+ $(div).dialog("open");
+};
+PluginDialog.prototype.close = function () {
+ var self = this;
+ $(self.getElement()).dialog("close");
+};
+
+PluginDialog.prototype.destroy = function () {
+ var self = this;
+ var div = self.getElement();
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
+ }
+};
+
+PluginDialog.prototype.setPluginManager = function (pluginManager) {
+ this._pluginManager = pluginManager;
+};
+
+PluginDialog.prototype.getPluginManager = function () {
+ return this._pluginManager;
+};
+
+module.exports = PluginDialog;
diff --git a/frontend-js/src/main/js/gui/SelectionContextMenu.js b/frontend-js/src/main/js/gui/SelectionContextMenu.js
index 16a7629ebbdc3a33f2660bb6c45291d8383fde83..1c22528851fdb0f3f0209a8b306fab2dcdad48d1 100644
--- a/frontend-js/src/main/js/gui/SelectionContextMenu.js
+++ b/frontend-js/src/main/js/gui/SelectionContextMenu.js
@@ -1,39 +1,39 @@
-"use strict";
-
-/* exported logger */
-
-var ContextMenu = require('./ContextMenu');
-
-var logger = require('../logger');
-
-function SelectionContextMenu(params) {
- ContextMenu.call(this, params);
- var self = this;
-
- self._createSelectionContextMenuGui();
-}
-
-SelectionContextMenu.prototype = Object.create(ContextMenu.prototype);
-SelectionContextMenu.prototype.constructor = SelectionContextMenu;
-
-SelectionContextMenu.prototype.init = function () {
- var self = this;
- return self.createExportAsImageSubmenu().then(function (submenu) {
- self.addOption(submenu);
- return self.createExportAsModelSubmenu();
- }).then(function (submenu) {
- self.addOption(submenu);
- });
-};
-
-SelectionContextMenu.prototype._createSelectionContextMenuGui = function () {
- var self = this;
- self.addOption("Remove Selection", function () {
- self.getMap().removeSelection();
- if (self.getMap().isDrawingOn()) {
- self.getMap().toggleDrawing();
- }
- });
-};
-
-module.exports = SelectionContextMenu;
+"use strict";
+
+/* exported logger */
+
+var ContextMenu = require('./ContextMenu');
+
+var logger = require('../logger');
+
+function SelectionContextMenu(params) {
+ ContextMenu.call(this, params);
+ var self = this;
+
+ self._createSelectionContextMenuGui();
+}
+
+SelectionContextMenu.prototype = Object.create(ContextMenu.prototype);
+SelectionContextMenu.prototype.constructor = SelectionContextMenu;
+
+SelectionContextMenu.prototype.init = function () {
+ var self = this;
+ return self.createExportAsImageSubmenu().then(function (submenu) {
+ self.addOption(submenu);
+ return self.createExportAsModelSubmenu();
+ }).then(function (submenu) {
+ self.addOption(submenu);
+ });
+};
+
+SelectionContextMenu.prototype._createSelectionContextMenuGui = function () {
+ var self = this;
+ self.addOption("Remove Selection", function () {
+ self.getMap().removeSelection();
+ if (self.getMap().isDrawingOn()) {
+ self.getMap().toggleDrawing();
+ }
+ });
+};
+
+module.exports = SelectionContextMenu;
diff --git a/frontend-js/src/main/js/gui/SubMenu.js b/frontend-js/src/main/js/gui/SubMenu.js
index 5fe63088015b1a82538be890e6cd428231f1d699..88924fb023f5f5f9af3a1a5d0bee00af62045aea 100644
--- a/frontend-js/src/main/js/gui/SubMenu.js
+++ b/frontend-js/src/main/js/gui/SubMenu.js
@@ -1,73 +1,73 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractGuiElement = require('./AbstractGuiElement');
-var Functions = require('../Functions');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../logger');
-
-function SubMenu(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
-
- self._createGui(params);
-
-}
-
-SubMenu.prototype = Object.create(AbstractGuiElement.prototype);
-SubMenu.prototype.constructor = SubMenu;
-
-SubMenu.prototype._createGui = function (params) {
- var self = this;
-
- var element = self.getElement();
- element.className = "dropdown-submenu";
-
- var link = Functions.createElement({
- type: "a",
- href: "#",
- className: "dropdown-link",
- content: params.name
- });
- link.tabIndex = -1;
- self.getElement().appendChild(link);
-
- var ul = Functions.createElement({
- type: "ul",
- className: "dropdown-menu"
- });
- self.getElement().appendChild(ul);
- self.setUl(ul);
-
-};
-SubMenu.prototype.addOption = function (name, handler) {
- var self = this;
- if (name instanceof SubMenu) {
- self.getElement().appendChild(name.getElement());
- } else {
- var option = Functions.createElement({
- type: "li"
- });
- var link = Functions.createElement({
- type: "a",
- href: "#",
- className: "dropdown-link",
- content: name
- });
- $(link).data("handler", handler);
- option.appendChild(link);
- self.getUl().appendChild(option);
- }
-};
-
-SubMenu.prototype.setUl = function (ul) {
- this._ul = ul;
-};
-
-SubMenu.prototype.getUl = function () {
- return this._ul;
-};
-
-module.exports = SubMenu;
+"use strict";
+
+/* exported logger */
+
+var AbstractGuiElement = require('./AbstractGuiElement');
+var Functions = require('../Functions');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../logger');
+
+function SubMenu(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+
+ self._createGui(params);
+
+}
+
+SubMenu.prototype = Object.create(AbstractGuiElement.prototype);
+SubMenu.prototype.constructor = SubMenu;
+
+SubMenu.prototype._createGui = function (params) {
+ var self = this;
+
+ var element = self.getElement();
+ element.className = "dropdown-submenu";
+
+ var link = Functions.createElement({
+ type: "a",
+ href: "#",
+ className: "dropdown-link",
+ content: params.name
+ });
+ link.tabIndex = -1;
+ self.getElement().appendChild(link);
+
+ var ul = Functions.createElement({
+ type: "ul",
+ className: "dropdown-menu"
+ });
+ self.getElement().appendChild(ul);
+ self.setUl(ul);
+
+};
+SubMenu.prototype.addOption = function (name, handler) {
+ var self = this;
+ if (name instanceof SubMenu) {
+ self.getElement().appendChild(name.getElement());
+ } else {
+ var option = Functions.createElement({
+ type: "li"
+ });
+ var link = Functions.createElement({
+ type: "a",
+ href: "#",
+ className: "dropdown-link",
+ content: name
+ });
+ $(link).data("handler", handler);
+ option.appendChild(link);
+ self.getUl().appendChild(option);
+ }
+};
+
+SubMenu.prototype.setUl = function (ul) {
+ this._ul = ul;
+};
+
+SubMenu.prototype.getUl = function () {
+ return this._ul;
+};
+
+module.exports = SubMenu;
diff --git a/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js b/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js
index 3780b8749497a11a6018655e42f606d4e09443ab..6d0c3434a8d7e1c635ab9f5a3db8b5d3b42f1a76 100644
--- a/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/AbstractAdminPanel.js
@@ -1,99 +1,99 @@
-"use strict";
-
-/* exported logger */
-/* exported Promise*/
-
-var Panel = require('../Panel');
-var UserPreferences = require('../../map/data/UserPreferences');
-var GuiConnector = require('../../GuiConnector');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-// noinspection JSUnusedLocalSymbols
-var Functions = require('../../Functions');
-var Promise = require("bluebird");
-
-/**
- *
- * @param {Configuration} [params.configuration]
- * @param {HTMLElement} params.element
- * @param {Project} params.project
- * @param {CustomMap} params.customMap
- * @param {string} params.panelName
- * @param {string} [params.helpTip]
- * @param params.parent
- *
- * @constructor
- * @extends Panel
- */
-function AbstractAdminPanel(params) {
- params["scrollable"] = true;
- Panel.call(this, params);
- this._createHeader(params.name);
-
- this._initPromises = [];
- this._eventBinds = [];
-}
-
-AbstractAdminPanel.prototype = Object.create(Panel.prototype);
-AbstractAdminPanel.prototype.constructor = AbstractAdminPanel;
-
-AbstractAdminPanel.prototype._createHeader = function (name) {
- // this.getElement().appendChild(Functions.createElement({
- // type: "h1",
- // content: name
- // }));
-};
-
-/**
- *
- * @returns {Promise}
- */
-AbstractAdminPanel.prototype.init = function () {
- return Promise.all(this._initPromises);
-};
-
-/**
- *
- * @param {Object} params
- * @param {string} params.event
- * @param {jQuery} params.jQueryObject
- * @param {string} params.preferenceName
- * @param {Object} params.defaultValue
- * @param {function} params.getter
- * @param {function} params.setter
- */
-AbstractAdminPanel.prototype.bindUserGuiPreference = function (params) {
- params.jQueryObject.on(params.event, function () {
- return ServerConnector.getLoggedUser().then(function (user) {
- var oldValue = user.getPreferences().getGuiPreference(params.preferenceName, params.defaultValue);
- var newValue = params.getter();
- if (oldValue !== newValue) {
- user.getPreferences().setGuiPreference(params.preferenceName, newValue);
-
- var data = new UserPreferences();
- data.setGuiPreference(params.preferenceName, newValue);
- return ServerConnector.updateUserPreferences({user: user, preferences: data});
- }
- }).catch(GuiConnector.alert);
- });
- this._initPromises.push(ServerConnector.getLoggedUser().then(function (user) {
- var value = user.getPreferences().getGuiPreference(params.preferenceName, params.defaultValue);
- return params.setter(value);
- }));
-
- this._eventBinds.push(params);
-};
-
-/**
- *
- * @returns {Promise}
- */
-AbstractAdminPanel.prototype.destroy = function () {
- return Promise.each(this._eventBinds, function (params) {
- params.jQueryObject.off(params.event);
- });
-};
-
-
-module.exports = AbstractAdminPanel;
+"use strict";
+
+/* exported logger */
+/* exported Promise*/
+
+var Panel = require('../Panel');
+var UserPreferences = require('../../map/data/UserPreferences');
+var GuiConnector = require('../../GuiConnector');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+// noinspection JSUnusedLocalSymbols
+var Functions = require('../../Functions');
+var Promise = require("bluebird");
+
+/**
+ *
+ * @param {Configuration} [params.configuration]
+ * @param {HTMLElement} params.element
+ * @param {Project} params.project
+ * @param {CustomMap} params.customMap
+ * @param {string} params.panelName
+ * @param {string} [params.helpTip]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends Panel
+ */
+function AbstractAdminPanel(params) {
+ params["scrollable"] = true;
+ Panel.call(this, params);
+ this._createHeader(params.name);
+
+ this._initPromises = [];
+ this._eventBinds = [];
+}
+
+AbstractAdminPanel.prototype = Object.create(Panel.prototype);
+AbstractAdminPanel.prototype.constructor = AbstractAdminPanel;
+
+AbstractAdminPanel.prototype._createHeader = function (name) {
+ // this.getElement().appendChild(Functions.createElement({
+ // type: "h1",
+ // content: name
+ // }));
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+AbstractAdminPanel.prototype.init = function () {
+ return Promise.all(this._initPromises);
+};
+
+/**
+ *
+ * @param {Object} params
+ * @param {string} params.event
+ * @param {jQuery} params.jQueryObject
+ * @param {string} params.preferenceName
+ * @param {Object} params.defaultValue
+ * @param {function} params.getter
+ * @param {function} params.setter
+ */
+AbstractAdminPanel.prototype.bindUserGuiPreference = function (params) {
+ params.jQueryObject.on(params.event, function () {
+ return ServerConnector.getLoggedUser().then(function (user) {
+ var oldValue = user.getPreferences().getGuiPreference(params.preferenceName, params.defaultValue);
+ var newValue = params.getter();
+ if (oldValue !== newValue) {
+ user.getPreferences().setGuiPreference(params.preferenceName, newValue);
+
+ var data = new UserPreferences();
+ data.setGuiPreference(params.preferenceName, newValue);
+ return ServerConnector.updateUserPreferences({user: user, preferences: data});
+ }
+ }).catch(GuiConnector.alert);
+ });
+ this._initPromises.push(ServerConnector.getLoggedUser().then(function (user) {
+ var value = user.getPreferences().getGuiPreference(params.preferenceName, params.defaultValue);
+ return params.setter(value);
+ }));
+
+ this._eventBinds.push(params);
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+AbstractAdminPanel.prototype.destroy = function () {
+ return Promise.each(this._eventBinds, function (params) {
+ params.jQueryObject.off(params.event);
+ });
+};
+
+
+module.exports = AbstractAdminPanel;
diff --git a/frontend-js/src/main/js/gui/admin/AbstractAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/AbstractAnnotatorsDialog.js
index bd6441728532085b3ce19efdb1a72656562a4dbc..275de12a40094856c98f056dfee4910da14695ac 100644
--- a/frontend-js/src/main/js/gui/admin/AbstractAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/AbstractAnnotatorsDialog.js
@@ -1,42 +1,42 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractGuiElement = require('../AbstractGuiElement');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-function AbstractAnnotatorsDialog(params) {
- AbstractGuiElement.call(this, params);
-}
-
-AbstractAnnotatorsDialog.prototype = Object.create(AbstractGuiElement.prototype);
-AbstractAnnotatorsDialog.prototype.constructor = AbstractAnnotatorsDialog;
-
-/**
- *
- * @param {BioEntityType} elementType
- * @param {boolean} [includeChildren=false]
- *
- * @returns {BioEntityType[]}
- */
-AbstractAnnotatorsDialog.prototype.getAllChildrenTypesIfNeeded = function (elementType, includeChildren) {
- var result = [elementType];
- if (includeChildren) {
- var queue = [elementType];
- var elementTypes = this.getConfiguration().getElementTypes();
- while (queue.length > 0) {
- var type = queue.shift();
- for (var i = 0; i < elementTypes.length; i++) {
- if (type.className === elementTypes[i].parentClass) {
- queue.push(elementTypes[i]);
- result.push(elementTypes[i]);
- }
- }
- }
- }
- return result;
-};
-
-module.exports = AbstractAnnotatorsDialog;
+"use strict";
+
+/* exported logger */
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+function AbstractAnnotatorsDialog(params) {
+ AbstractGuiElement.call(this, params);
+}
+
+AbstractAnnotatorsDialog.prototype = Object.create(AbstractGuiElement.prototype);
+AbstractAnnotatorsDialog.prototype.constructor = AbstractAnnotatorsDialog;
+
+/**
+ *
+ * @param {BioEntityType} elementType
+ * @param {boolean} [includeChildren=false]
+ *
+ * @returns {BioEntityType[]}
+ */
+AbstractAnnotatorsDialog.prototype.getAllChildrenTypesIfNeeded = function (elementType, includeChildren) {
+ var result = [elementType];
+ if (includeChildren) {
+ var queue = [elementType];
+ var elementTypes = this.getConfiguration().getElementTypes();
+ while (queue.length > 0) {
+ var type = queue.shift();
+ for (var i = 0; i < elementTypes.length; i++) {
+ if (type.className === elementTypes[i].parentClass) {
+ queue.push(elementTypes[i]);
+ result.push(elementTypes[i]);
+ }
+ }
+ }
+ }
+ return result;
+};
+
+module.exports = AbstractAnnotatorsDialog;
diff --git a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
index f7969805f7927a073312f7882d0af621483d2c09..63bc240de4603d9ab8ed3f11ae1c4252e776bd51 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseAnnotatorsDialog.js
@@ -1,357 +1,357 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractAnnotatorsDialog = require('./AbstractAnnotatorsDialog');
-var GuiConnector = require("../../GuiConnector");
-var MultiCheckboxList = require("multi-checkbox-list");
-var UserPreferences = require("../../map/data/UserPreferences");
-
-var Functions = require('../../Functions');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-function ChooseAnnotatorsDialog(params) {
- AbstractAnnotatorsDialog.call(this, params);
- var self = this;
- self.createGui();
-}
-
-ChooseAnnotatorsDialog.prototype = Object.create(AbstractAnnotatorsDialog.prototype);
-ChooseAnnotatorsDialog.prototype.constructor = ChooseAnnotatorsDialog;
-
-ChooseAnnotatorsDialog.prototype.createGui = function () {
- var self = this;
- var content = Functions.createElement({
- type: "div",
- style: "display:table;height:100%;width:100%"
- });
- content.appendChild(Functions.createElement({
- type: "div",
- style: "display:table-cell;height:100%;",
- content: "<div name='elementTree' style='height:100%;overflow-y:scroll;'/>",
- xss: false
- }));
-
- var annotatorsDiv = Functions.createElement({
- type: "div",
- style: "display:table-cell;width:100%",
- content: "<div style='height:100%;width:100%;overflow-y:auto;'><div name='annotatorListBox'></div><div class='minerva-annotators-params'></div></div>",
- xss: false
- });
- content.appendChild(annotatorsDiv);
-
- self.getElement().appendChild(content);
-};
-
-function onChangeParameterValue(element, user) {
- var name = $(element).siblings(".minerva-annotator-param-name")[0].childNodes[0].nodeValue;
- var annotatorClassName = $(element).parent().parent().attr('name');
-
- var data = new UserPreferences();
-
- var annotatorsParams = {};
- annotatorsParams[annotatorClassName] = {};
- if (element.type == 'checkbox') annotatorsParams[annotatorClassName][name] = element.checked.toString();
- else annotatorsParams[annotatorClassName][name] = element.value;
- data.setAnnotatorsParameters(annotatorsParams);
-
- return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
-}
-
-ChooseAnnotatorsDialog.prototype.saveAnnotatorsInfo = function (elementTypes, selectedAnnotators) {
- selectedAnnotators = selectedAnnotators.slice();
- return ServerConnector.getLoggedUser().then(function (user) {
-
- var data = new UserPreferences();
-
- var elementAnnotators = {};
- for (var i = 0; i < elementTypes.length; i++) {
- elementAnnotators[elementTypes[i].className] = selectedAnnotators;
-
- var userAnnotators = user.getPreferences().getElementAnnotators(elementTypes[i].className);
- userAnnotators.length = 0;
- userAnnotators.push.apply(userAnnotators, selectedAnnotators);
- }
- data.setElementAnnotators(elementAnnotators);
- return ServerConnector.updateUserPreferences({
- user: user,
- preferences: data
- });
- }).catch(GuiConnector.alert);
-};
-
-ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
- var self = this;
-
- var configuration = self.getConfiguration();
-
- return ServerConnector.getLoggedUser().then(function (user) {
- var element = $("[name='annotatorListBox']", self.getElement())[0];
- var annotatorsParams = $(".minerva-annotators-params", self.getElement())[0];
- Functions.removeChildren(element);
-
- var selectElement = Functions.createElement({
- type: "div",
- style: "width:50%; height:200px;float:left; OVERFLOW-Y:scroll"
- });
-
- element.appendChild(selectElement);
- var includeChildrenCheckbox = Functions.createElement({type: "input", inputType: "checkbox"});
- element.appendChild(includeChildrenCheckbox);
- element.appendChild(Functions.createElement({type: "span", content: "Apply to all in subtree"}));
- element.appendChild(Functions.createElement({type: "br"}));
- var copyFromButton = Functions.createElement({
- type: "button", content: "Copy from", onclick: function () {
- var typeClassName = copyFromSelect.value;
- var annotators;
- for (var i = 0; i < configuration.getElementTypes().length; i++) {
- var type = configuration.getElementTypes()[i];
- if (typeClassName === type.className) {
- annotators = user.getPreferences().getElementAnnotators(typeClassName);
- }
- }
- if (annotators === undefined) {
- return GuiConnector.alert("Invalid element type: " + copyFromSelect.value);
- } else {
- var includeChildren = includeChildrenCheckbox.checked;
- return self.saveAnnotatorsInfo(self.getAllChildrenTypesIfNeeded(elementType, includeChildren), annotators).then(function () {
- return self.setElementType(elementType);
- });
- }
- }
- });
- element.appendChild(copyFromButton);
- var copyFromSelect = Functions.createElement({type: "select", style: "margin:5px"});
- element.appendChild(copyFromSelect);
- var options = [], i;
- for (i = 0; i < configuration.getElementTypes().length; i++) {
- var type = configuration.getElementTypes()[i];
- var name = type.className;
- if (name.indexOf(".") > 0) {
- name = name.substr(name.lastIndexOf(".") + 1);
- }
- options.push(Functions.createElement({
- type: "option",
- value: type.className,
- content: name
- }));
- }
- options.sort(function (a, b) {
- return a.text === b.text ? 0 : a.text < b.text ? -1 : 1
- });
- for (i = 0; i < options.length; i++) {
- copyFromSelect.appendChild(options[i]);
- }
-
- var annotators = configuration.getElementAnnotators(elementType);
-
- var selectedAnnotators = user.getPreferences().getElementAnnotators(elementType.className);
-
- var entries = [];
-
- for (i = 0; i < annotators.length; i++) {
- var annotator = annotators[i];
- var entry = {name: annotator.getName(), value: annotator.getClassName(), selected: false};
- for (var j = 0; j < selectedAnnotators.length; j++) {
- if (annotator.getName() === selectedAnnotators[j]) {
- entry.selected = true;
- }
- }
- entries.push(entry);
- }
- var checkboxList = new MultiCheckboxList(selectElement, {
- entries: entries,
- listTitle: "Available annotators",
- selectedTitle: "Selected annotators",
- selectedList: true
- });
- var changeSelection = function (elementId, selected) {
-
- var annotators = configuration.getElementAnnotators();
- var annotator;
- for (var i = 0; i < annotators.length; i++) {
- if (elementId === annotators[i].getClassName()) {
- annotator = annotators[i];
- }
- }
- if (selected) {
- selectedAnnotators.push(annotator.getName());
- } else {
- var index = selectedAnnotators.indexOf(annotator.getName());
- if (index > -1) {
- selectedAnnotators.splice(index, 1);
- }
- }
- createAnnotatorsParams();
- var includeChildren = includeChildrenCheckbox.checked;
- return self.saveAnnotatorsInfo(self.getAllChildrenTypesIfNeeded(elementType, includeChildren), selectedAnnotators);
- };
- includeChildrenCheckbox.onchange = function () {
- var includeChildren = includeChildrenCheckbox.checked;
- return self.saveAnnotatorsInfo(self.getAllChildrenTypesIfNeeded(elementType, includeChildren), selectedAnnotators);
- };
-
- checkboxList.addListener("select", function (element) {
- return changeSelection(element.value, true);
- });
- checkboxList.addListener("deselect", function (element) {
- return changeSelection(element.value, false);
- });
-
-
- function createAnnotatorsParams() {
-
- var existingAnnotatorsParameters = user.getPreferences().getAnnotatorsParameters();
-
- Functions.removeChildren(annotatorsParams);
- for (var i = 0; i < annotators.length; i++) {
- var annotator = annotators[i];
- for (var j = 0; j < selectedAnnotators.length; j++) {
- if (annotator.getName() === selectedAnnotators[j]) {
- var paramsDefs = annotator.getParametersDefinitions();
- if (paramsDefs.length > 0) {
-
- annotatorsParams.appendChild(Functions.createElement({
- type: "div",
- className: "minerva-annotators-params-header",
- content: '<div>Available parameters</div>'
- }));
-
- var annotatorParams = Functions.createElement({
- type: "div",
- className: "minerva-annotator-params",
- name: annotator.getClassName()
- });
-
- annotatorParams.appendChild(Functions.createElement({
- type: "div",
- className: "minerva-annotator-params-header",
- content: annotator.getName()
- }));
-
- for (var k = 0; k < paramsDefs.length; k++) {
- var param = paramsDefs[k];
- var paramElement = Functions.createElement({
- type: "div",
- className: "minerva-annotator-param"
- });
-
- var paramName = Functions.createElement({
- type: "div",
- className: "minerva-annotator-param-name",
- content: param.name
- });
-
- var tooltipContainer = Functions.createElement({
- type: "span"
- });
- tooltipContainer.appendChild(Functions.createElement({
- type: "span",
- className: "glyphicon glyphicon-question-sign tooltip-icon"
- }));
- tooltipContainer.appendChild(Functions.createElement({
- type: "span",
- className: "annotator-tooltip",
- content: param.description
- }));
-
- paramName.appendChild(tooltipContainer);
- paramElement.appendChild(paramName);
-
- var paramValue;
-
- var existingParamValue;
- if (existingAnnotatorsParameters[annotator.getClassName()]) {
- existingParamValue = existingAnnotatorsParameters[annotator.getClassName()][param.name]
- }
-
- if (param.type.indexOf("String") >= 0) {
- paramValue = Functions.createElement({
- type: "textarea",
- onchange: function () {
- return onChangeParameterValue(this, user);
- }
- });
- if (existingParamValue) paramValue.value = existingParamValue;
- } else if (param.type.indexOf("Integer") >= 0) {
- paramValue = Functions.createElement({
- type: "input",
- inputType: "number",
- onchange: function () {
- return onChangeParameterValue(this, user);
- }
- });
- if (existingParamValue) paramValue.value = existingParamValue;
- } else if (param.type.indexOf("Boolean") >= 0) {
- paramValue = Functions.createElement({
- type: "input",
- inputType: "checkbox",
- onchange: function () {
- return onChangeParameterValue(this, user);
- }
- });
- paramValue.checked = (existingParamValue && existingParamValue === 'true');
- } else {
- throw new Error("Unknown annotator parameter type");
- }
-
- paramElement.appendChild(paramValue);
- annotatorParams.appendChild(paramElement);
- }
-
- annotatorsParams.appendChild(annotatorParams);
- }
- }
- }
- }
- }
-
- createAnnotatorsParams();
-
- });
-
-};
-
-ChooseAnnotatorsDialog.prototype.init = function () {
- var self = this;
- return ServerConnector.getConfiguration().then(function (configuration) {
-
- var treeData = configuration.getElementTypeTree();
-
- var element = $('[name="elementTree"]', self.getElement());
- element.jstree({
- core: {
- data: treeData
- }
- }).on('ready.jstree', function () {
- element.jstree("open_all");
- }).on("select_node.jstree",
- function (evt, data) {
- return self.setElementType(data.node.data);
- }
- );
- });
-};
-
-ChooseAnnotatorsDialog.prototype.destroy = function () {
- $(this.getElement()).dialog("destroy");
-};
-
-ChooseAnnotatorsDialog.prototype.open = function () {
- var self = this;
- var div = self.getElement();
- if (!$(div).hasClass("ui-dialog-content")) {
- $(div).dialog({
- title: "Select annotators",
- modal: true,
- width: window.innerWidth / 2,
- height: window.innerHeight / 2
-
- });
- }
- $(div).dialog("open");
- $(div).css("overflow", "hidden");
-};
-
-module.exports = ChooseAnnotatorsDialog;
+"use strict";
+
+/* exported logger */
+
+var AbstractAnnotatorsDialog = require('./AbstractAnnotatorsDialog');
+var GuiConnector = require("../../GuiConnector");
+var MultiCheckboxList = require("multi-checkbox-list");
+var UserPreferences = require("../../map/data/UserPreferences");
+
+var Functions = require('../../Functions');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+function ChooseAnnotatorsDialog(params) {
+ AbstractAnnotatorsDialog.call(this, params);
+ var self = this;
+ self.createGui();
+}
+
+ChooseAnnotatorsDialog.prototype = Object.create(AbstractAnnotatorsDialog.prototype);
+ChooseAnnotatorsDialog.prototype.constructor = ChooseAnnotatorsDialog;
+
+ChooseAnnotatorsDialog.prototype.createGui = function () {
+ var self = this;
+ var content = Functions.createElement({
+ type: "div",
+ style: "display:table;height:100%;width:100%"
+ });
+ content.appendChild(Functions.createElement({
+ type: "div",
+ style: "display:table-cell;height:100%;",
+ content: "<div name='elementTree' style='height:100%;overflow-y:scroll;'/>",
+ xss: false
+ }));
+
+ var annotatorsDiv = Functions.createElement({
+ type: "div",
+ style: "display:table-cell;width:100%",
+ content: "<div style='height:100%;width:100%;overflow-y:auto;'><div name='annotatorListBox'></div><div class='minerva-annotators-params'></div></div>",
+ xss: false
+ });
+ content.appendChild(annotatorsDiv);
+
+ self.getElement().appendChild(content);
+};
+
+function onChangeParameterValue(element, user) {
+ var name = $(element).siblings(".minerva-annotator-param-name")[0].childNodes[0].nodeValue;
+ var annotatorClassName = $(element).parent().parent().attr('name');
+
+ var data = new UserPreferences();
+
+ var annotatorsParams = {};
+ annotatorsParams[annotatorClassName] = {};
+ if (element.type == 'checkbox') annotatorsParams[annotatorClassName][name] = element.checked.toString();
+ else annotatorsParams[annotatorClassName][name] = element.value;
+ data.setAnnotatorsParameters(annotatorsParams);
+
+ return ServerConnector.updateUserPreferences({user: user, preferences: data}).then(null, GuiConnector.alert);
+}
+
+ChooseAnnotatorsDialog.prototype.saveAnnotatorsInfo = function (elementTypes, selectedAnnotators) {
+ selectedAnnotators = selectedAnnotators.slice();
+ return ServerConnector.getLoggedUser().then(function (user) {
+
+ var data = new UserPreferences();
+
+ var elementAnnotators = {};
+ for (var i = 0; i < elementTypes.length; i++) {
+ elementAnnotators[elementTypes[i].className] = selectedAnnotators;
+
+ var userAnnotators = user.getPreferences().getElementAnnotators(elementTypes[i].className);
+ userAnnotators.length = 0;
+ userAnnotators.push.apply(userAnnotators, selectedAnnotators);
+ }
+ data.setElementAnnotators(elementAnnotators);
+ return ServerConnector.updateUserPreferences({
+ user: user,
+ preferences: data
+ });
+ }).catch(GuiConnector.alert);
+};
+
+ChooseAnnotatorsDialog.prototype.setElementType = function (elementType) {
+ var self = this;
+
+ var configuration = self.getConfiguration();
+
+ return ServerConnector.getLoggedUser().then(function (user) {
+ var element = $("[name='annotatorListBox']", self.getElement())[0];
+ var annotatorsParams = $(".minerva-annotators-params", self.getElement())[0];
+ Functions.removeChildren(element);
+
+ var selectElement = Functions.createElement({
+ type: "div",
+ style: "width:50%; height:200px;float:left; OVERFLOW-Y:scroll"
+ });
+
+ element.appendChild(selectElement);
+ var includeChildrenCheckbox = Functions.createElement({type: "input", inputType: "checkbox"});
+ element.appendChild(includeChildrenCheckbox);
+ element.appendChild(Functions.createElement({type: "span", content: "Apply to all in subtree"}));
+ element.appendChild(Functions.createElement({type: "br"}));
+ var copyFromButton = Functions.createElement({
+ type: "button", content: "Copy from", onclick: function () {
+ var typeClassName = copyFromSelect.value;
+ var annotators;
+ for (var i = 0; i < configuration.getElementTypes().length; i++) {
+ var type = configuration.getElementTypes()[i];
+ if (typeClassName === type.className) {
+ annotators = user.getPreferences().getElementAnnotators(typeClassName);
+ }
+ }
+ if (annotators === undefined) {
+ return GuiConnector.alert("Invalid element type: " + copyFromSelect.value);
+ } else {
+ var includeChildren = includeChildrenCheckbox.checked;
+ return self.saveAnnotatorsInfo(self.getAllChildrenTypesIfNeeded(elementType, includeChildren), annotators).then(function () {
+ return self.setElementType(elementType);
+ });
+ }
+ }
+ });
+ element.appendChild(copyFromButton);
+ var copyFromSelect = Functions.createElement({type: "select", style: "margin:5px"});
+ element.appendChild(copyFromSelect);
+ var options = [], i;
+ for (i = 0; i < configuration.getElementTypes().length; i++) {
+ var type = configuration.getElementTypes()[i];
+ var name = type.className;
+ if (name.indexOf(".") > 0) {
+ name = name.substr(name.lastIndexOf(".") + 1);
+ }
+ options.push(Functions.createElement({
+ type: "option",
+ value: type.className,
+ content: name
+ }));
+ }
+ options.sort(function (a, b) {
+ return a.text === b.text ? 0 : a.text < b.text ? -1 : 1
+ });
+ for (i = 0; i < options.length; i++) {
+ copyFromSelect.appendChild(options[i]);
+ }
+
+ var annotators = configuration.getElementAnnotators(elementType);
+
+ var selectedAnnotators = user.getPreferences().getElementAnnotators(elementType.className);
+
+ var entries = [];
+
+ for (i = 0; i < annotators.length; i++) {
+ var annotator = annotators[i];
+ var entry = {name: annotator.getName(), value: annotator.getClassName(), selected: false};
+ for (var j = 0; j < selectedAnnotators.length; j++) {
+ if (annotator.getName() === selectedAnnotators[j]) {
+ entry.selected = true;
+ }
+ }
+ entries.push(entry);
+ }
+ var checkboxList = new MultiCheckboxList(selectElement, {
+ entries: entries,
+ listTitle: "Available annotators",
+ selectedTitle: "Selected annotators",
+ selectedList: true
+ });
+ var changeSelection = function (elementId, selected) {
+
+ var annotators = configuration.getElementAnnotators();
+ var annotator;
+ for (var i = 0; i < annotators.length; i++) {
+ if (elementId === annotators[i].getClassName()) {
+ annotator = annotators[i];
+ }
+ }
+ if (selected) {
+ selectedAnnotators.push(annotator.getName());
+ } else {
+ var index = selectedAnnotators.indexOf(annotator.getName());
+ if (index > -1) {
+ selectedAnnotators.splice(index, 1);
+ }
+ }
+ createAnnotatorsParams();
+ var includeChildren = includeChildrenCheckbox.checked;
+ return self.saveAnnotatorsInfo(self.getAllChildrenTypesIfNeeded(elementType, includeChildren), selectedAnnotators);
+ };
+ includeChildrenCheckbox.onchange = function () {
+ var includeChildren = includeChildrenCheckbox.checked;
+ return self.saveAnnotatorsInfo(self.getAllChildrenTypesIfNeeded(elementType, includeChildren), selectedAnnotators);
+ };
+
+ checkboxList.addListener("select", function (element) {
+ return changeSelection(element.value, true);
+ });
+ checkboxList.addListener("deselect", function (element) {
+ return changeSelection(element.value, false);
+ });
+
+
+ function createAnnotatorsParams() {
+
+ var existingAnnotatorsParameters = user.getPreferences().getAnnotatorsParameters();
+
+ Functions.removeChildren(annotatorsParams);
+ for (var i = 0; i < annotators.length; i++) {
+ var annotator = annotators[i];
+ for (var j = 0; j < selectedAnnotators.length; j++) {
+ if (annotator.getName() === selectedAnnotators[j]) {
+ var paramsDefs = annotator.getParametersDefinitions();
+ if (paramsDefs.length > 0) {
+
+ annotatorsParams.appendChild(Functions.createElement({
+ type: "div",
+ className: "minerva-annotators-params-header",
+ content: '<div>Available parameters</div>'
+ }));
+
+ var annotatorParams = Functions.createElement({
+ type: "div",
+ className: "minerva-annotator-params",
+ name: annotator.getClassName()
+ });
+
+ annotatorParams.appendChild(Functions.createElement({
+ type: "div",
+ className: "minerva-annotator-params-header",
+ content: annotator.getName()
+ }));
+
+ for (var k = 0; k < paramsDefs.length; k++) {
+ var param = paramsDefs[k];
+ var paramElement = Functions.createElement({
+ type: "div",
+ className: "minerva-annotator-param"
+ });
+
+ var paramName = Functions.createElement({
+ type: "div",
+ className: "minerva-annotator-param-name",
+ content: param.name
+ });
+
+ var tooltipContainer = Functions.createElement({
+ type: "span"
+ });
+ tooltipContainer.appendChild(Functions.createElement({
+ type: "span",
+ className: "glyphicon glyphicon-question-sign tooltip-icon"
+ }));
+ tooltipContainer.appendChild(Functions.createElement({
+ type: "span",
+ className: "annotator-tooltip",
+ content: param.description
+ }));
+
+ paramName.appendChild(tooltipContainer);
+ paramElement.appendChild(paramName);
+
+ var paramValue;
+
+ var existingParamValue;
+ if (existingAnnotatorsParameters[annotator.getClassName()]) {
+ existingParamValue = existingAnnotatorsParameters[annotator.getClassName()][param.name]
+ }
+
+ if (param.type.indexOf("String") >= 0) {
+ paramValue = Functions.createElement({
+ type: "textarea",
+ onchange: function () {
+ return onChangeParameterValue(this, user);
+ }
+ });
+ if (existingParamValue) paramValue.value = existingParamValue;
+ } else if (param.type.indexOf("Integer") >= 0) {
+ paramValue = Functions.createElement({
+ type: "input",
+ inputType: "number",
+ onchange: function () {
+ return onChangeParameterValue(this, user);
+ }
+ });
+ if (existingParamValue) paramValue.value = existingParamValue;
+ } else if (param.type.indexOf("Boolean") >= 0) {
+ paramValue = Functions.createElement({
+ type: "input",
+ inputType: "checkbox",
+ onchange: function () {
+ return onChangeParameterValue(this, user);
+ }
+ });
+ paramValue.checked = (existingParamValue && existingParamValue === 'true');
+ } else {
+ throw new Error("Unknown annotator parameter type");
+ }
+
+ paramElement.appendChild(paramValue);
+ annotatorParams.appendChild(paramElement);
+ }
+
+ annotatorsParams.appendChild(annotatorParams);
+ }
+ }
+ }
+ }
+ }
+
+ createAnnotatorsParams();
+
+ });
+
+};
+
+ChooseAnnotatorsDialog.prototype.init = function () {
+ var self = this;
+ return ServerConnector.getConfiguration().then(function (configuration) {
+
+ var treeData = configuration.getElementTypeTree();
+
+ var element = $('[name="elementTree"]', self.getElement());
+ element.jstree({
+ core: {
+ data: treeData
+ }
+ }).on('ready.jstree', function () {
+ element.jstree("open_all");
+ }).on("select_node.jstree",
+ function (evt, data) {
+ return self.setElementType(data.node.data);
+ }
+ );
+ });
+};
+
+ChooseAnnotatorsDialog.prototype.destroy = function () {
+ $(this.getElement()).dialog("destroy");
+};
+
+ChooseAnnotatorsDialog.prototype.open = function () {
+ var self = this;
+ var div = self.getElement();
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ title: "Select annotators",
+ modal: true,
+ width: window.innerWidth / 2,
+ height: window.innerHeight / 2
+
+ });
+ }
+ $(div).dialog("open");
+ $(div).css("overflow", "hidden");
+};
+
+module.exports = ChooseAnnotatorsDialog;
diff --git a/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js b/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
index 2e5e45c36fff45804aa80ec812d79223817e0455..10f77ba75aa204312d8f2b37d2e0d721a209f778 100644
--- a/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
+++ b/frontend-js/src/main/js/gui/admin/ChooseValidatorsDialog.js
@@ -1,409 +1,409 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractAnnotatorsDialog = require('./AbstractAnnotatorsDialog');
-var GuiConnector = require("../../GuiConnector");
-var UserPreferences = require("../../map/data/UserPreferences");
-var MultiCheckboxList = require("multi-checkbox-list");
-
-var Functions = require('../../Functions');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-/**
- *
- /**
- *
- * @param {Object} params
- * @param {HTMLElement} params.element
- * @param {CustomMap} params.customMap
- * @param {Configuration} [params.configuration]
- * @param {ServerConnector} [params.serverConnector]
- *
- * @constructor
- *
- * @extends AbstractGuiElement
- */
-function ChooseValidatorsDialog(params) {
- AbstractAnnotatorsDialog.call(this, params);
- var self = this;
- self.createGui();
-}
-
-ChooseValidatorsDialog.prototype = Object.create(AbstractAnnotatorsDialog.prototype);
-ChooseValidatorsDialog.prototype.constructor = ChooseValidatorsDialog;
-
-/**
- *
- */
-ChooseValidatorsDialog.prototype.createGui = function () {
- var self = this;
- var content = Functions.createElement({
- type: "div",
- style: "display:table;height:100%;width:100%"
- });
- content.appendChild(Functions.createElement({
- type: "div",
- style: "display:table-cell;height:100%;",
- content: "<div name='elementTree' style='height:100%;overflow-y:scroll;'/>",
- xss: false
- }));
-
- content.appendChild(Functions.createElement({
- type: "div",
- style: "display:table-cell;height:100%;width:100%;",
- content: "<div name='annotatorListBox' style='height:100%;width:100%;overflow-y:auto;'><span> </span></div>",
- xss: false
- }));
-
- self.getElement().appendChild(content);
-};
-
-/**
- *
- * @param {BioEntityType} elementType
- * @returns {Promise}
- */
-ChooseValidatorsDialog.prototype.setElementType = function (elementType) {
- var self = this;
-
- var configuration;
-
- return self.getServerConnector().getConfiguration().then(function (result) {
- configuration = result;
- return self.getServerConnector().getLoggedUser();
- }).then(function (user) {
- var element = $("[name='annotatorListBox']", self.getElement())[0];
- Functions.removeChildren(element);
-
- var validAnnotationSelect = Functions.createElement({
- type: "select",
- className: "minerva-multi-select"
- });
- element.appendChild(validAnnotationSelect);
- self.createValidAnnotationsDualListBox(user, configuration, elementType, validAnnotationSelect);
-
- var verifyAnnotationSelect = Functions.createElement({
- type: "select",
- className: "minerva-multi-select"
- });
- element.appendChild(verifyAnnotationSelect);
- self.createVerifyAnnotationsDualListBox(user, configuration, elementType, verifyAnnotationSelect);
-
- element.appendChild(Functions.createElement({type: "br"}));
- var includeChildrenCheckbox = Functions.createElement({type: "input", inputType: "checkbox"});
- var copyFromButton = Functions.createElement({
- type: "button", content: "Copy from", name: "copy-from-validator", onclick: function () {
- var typeClassName = copyFromSelect.value;
- var requiredAnnotations, validAnnotators;
- for (var i = 0; i < configuration.getElementTypes().length; i++) {
- var type = configuration.getElementTypes()[i];
- if (typeClassName === type.className) {
- requiredAnnotations = user.getPreferences().getElementRequiredAnnotations(typeClassName);
- validAnnotators = user.getPreferences().getElementValidAnnotations(typeClassName);
- }
- }
- if (requiredAnnotations === undefined) {
- return GuiConnector.alert("Invalid element type: " + copyFromSelect.value);
- } else {
- var includeChildren = includeChildrenCheckbox.checked;
- return self.saveAnnotationsInfo({
- elementTypes: self.getAllChildrenTypesIfNeeded(elementType, includeChildren),
- requiredAnnotators: requiredAnnotations,
- validAnnotators: validAnnotators
- }).then(function () {
- return self.setElementType(elementType);
- });
- }
- }
- });
- element.appendChild(copyFromButton);
- var copyFromSelect = Functions.createElement({type: "select", style: "margin:5px"});
- element.appendChild(copyFromSelect);
- var options = [], i;
- for (i = 0; i < configuration.getElementTypes().length; i++) {
- var type = configuration.getElementTypes()[i];
- var name = type.className;
- if (name.indexOf(".") > 0) {
- name = name.substr(name.lastIndexOf(".") + 1);
- }
- options.push(Functions.createElement({
- type: "option",
- value: type.className,
- content: name
- }));
- }
- options.sort(function (a, b) {
- return a.text === b.text ? 0 : a.text < b.text ? -1 : 1
- });
- for (i = 0; i < options.length; i++) {
- copyFromSelect.appendChild(options[i]);
- }
- element.appendChild(includeChildrenCheckbox);
- element.appendChild(Functions.createElement({type: "span", content: "Apply to all in subtree"}));
-
- });
-
-};
-
-/**
- *
- * @param {BioEntityType[]} params.elementTypes
- * @param {{list:string[], requiredAtLeastOnce:boolean}} params.requiredAnnotators
- * @param {string[]} params.validAnnotators
- *
- * @returns {Promise}
- */
-ChooseValidatorsDialog.prototype.saveAnnotationsInfo = function (params) {
- var elementTypes = params.elementTypes;
- var requiredAnnotators = params.requiredAnnotators;
- var validAnnotators = params.validAnnotators;
- var self = this;
- return self.getServerConnector().getLoggedUser().then(function (user) {
-
- var data = new UserPreferences();
-
- var elementRequiredAnnotators = {};
- var elementValidAnnotators = {};
- for (var i = 0; i < elementTypes.length; i++) {
- elementRequiredAnnotators[elementTypes[i].className] = {
- "require-at-least-one": requiredAnnotators.requiredAtLeastOnce,
- "annotation-list": requiredAnnotators.list.slice()
- };
- elementValidAnnotators[elementTypes[i].className] = validAnnotators.slice();
- }
- data.setElementRequiredAnnotations(elementRequiredAnnotators);
- data.setElementValidAnnotations(elementValidAnnotators);
- return self.getServerConnector().updateUserPreferences({
- user: user,
- preferences: data
- });
- }).catch(GuiConnector.alert);
-};
-
-
-/**
- *
- * @param {User} user
- * @param {Configuration} configuration
- * @param {BioEntityType} elementType
- * @param {HTMLElement} validAnnotationSelect
- */
-ChooseValidatorsDialog.prototype.createValidAnnotationsDualListBox = function (user, configuration, elementType, validAnnotationSelect) {
- var self = this;
-
- var miriamTypes = configuration.getMiriamTypes();
-
- var validAnnotations = user.getPreferences().getElementValidAnnotations(elementType.className);
-
- var entries = [];
-
-
- for (var i = 0; i < miriamTypes.length; i++) {
- var miriamType = miriamTypes[i];
- var entry = {name: miriamType.getCommonName(), value: miriamType.getName(), selected: false};
-
- for (var j = 0; j < validAnnotations.length; j++) {
- if (miriamType.getName() === validAnnotations[j]) {
- entry.selected = true;
- }
- }
- entries.push(entry);
- }
-
- var checkboxList = new MultiCheckboxList(validAnnotationSelect, {
- entries: entries,
- listTitle: "Available",
- selectedTitle: "Selected",
- selectedList: true
- });
-
- var changeSelection = function (elementId, selected) {
- var miriamTypes = configuration.getMiriamTypes();
- var miriamType;
- for (var i = 0; i < miriamTypes.length; i++) {
- if (elementId === miriamTypes[i].getName()) {
- miriamType = miriamTypes[i];
- }
- }
- if (selected) {
- validAnnotations.push(miriamType.getName());
- } else {
- var index = validAnnotations.indexOf(miriamType.getName());
- if (index > -1) {
- validAnnotations.splice(index, 1);
- }
- }
-
- var data = new UserPreferences();
-
- var elementAnnotators = {};
- elementAnnotators[elementType.className] = validAnnotations;
- data.setElementValidAnnotations(elementAnnotators);
- return self.getServerConnector().updateUserPreferences({
- user: user,
- preferences: data
- }).catch(GuiConnector.alert);
- };
-
- checkboxList.addListener("select", function (element) {
- return changeSelection(element.value, true);
- });
- checkboxList.addListener("deselect", function (element) {
- return changeSelection(element.value, false);
- });
-
-};
-
-/**
- *
- * @param {User} user
- * @param {Configuration} configuration
- * @param {BioEntityType} elementType
- * @param {HTMLElement} verifyAnnotationSelect
- */
-
-ChooseValidatorsDialog.prototype.createVerifyAnnotationsDualListBox = function (user, configuration, elementType, verifyAnnotationSelect) {
- var self = this;
- var requiredAnnotationsData = user.getPreferences().getElementRequiredAnnotations(elementType.className);
-
- var verifyCheckboxDiv = Functions.createElement({type: "div"});
- var checkbox = Functions.createElement({
- type: "input",
- inputType: "checkbox",
- name: "require-at-least-one-checkbox",
- onclick: function () {
- var data = new UserPreferences();
-
- var elementRequiredAnnotations = {};
- elementRequiredAnnotations[elementType.className] = {
- "require-at-least-one": checkbox.checked,
- "annotation-list": requiredAnnotationsData.list
- };
- data.setElementRequiredAnnotations(elementRequiredAnnotations);
- return self.getServerConnector().updateUserPreferences({user: user, preferences: data}).catch(GuiConnector.alert);
- }
- });
- checkbox.checked = requiredAnnotationsData.requiredAtLeastOnce;
- verifyCheckboxDiv.appendChild(Functions.createElement({type: "br"}));
- verifyCheckboxDiv.appendChild(Functions.createElement({type: "br"}));
- verifyCheckboxDiv.appendChild(checkbox);
- verifyCheckboxDiv.appendChild(Functions.createElement({
- type: "span",
- content: "One of these miriam should be required"
- }));
- verifyAnnotationSelect.parentNode.insertBefore(verifyCheckboxDiv, verifyAnnotationSelect);
-
- var miriamTypes = configuration.getMiriamTypes();
-
- var entries = [];
-
- for (var i = 0; i < miriamTypes.length; i++) {
- var miriamType = miriamTypes[i];
- var entry = {name: miriamType.getCommonName(), value: miriamType.getName(), selected: false};
- for (var j = 0; j < requiredAnnotationsData.list.length; j++) {
- if (miriamType.getName() === requiredAnnotationsData.list[j]) {
- entry.selected = true;
- }
- }
- entries.push(entry);
- }
-
- var checkboxList = new MultiCheckboxList(verifyAnnotationSelect, {
- entries: entries,
- listTitle: "Available",
- selectedTitle: "Selected",
- selectedList: true
- });
-
- var changeSelection = function (elementId, selected) {
-
- var miriamTypes = configuration.getMiriamTypes();
- var miriamType;
- for (var i = 0; i < miriamTypes.length; i++) {
- if (elementId === miriamTypes[i].getName()) {
- miriamType = miriamTypes[i];
- }
- }
- if (selected) {
- requiredAnnotationsData.list.push(miriamType.getName());
- } else {
- var index = requiredAnnotationsData.list.indexOf(miriamType.getName());
- if (index > -1) {
- requiredAnnotationsData.list.splice(index, 1);
- }
- }
-
- var data = new UserPreferences();
-
- var elementRequiredAnnotations = {};
- elementRequiredAnnotations[elementType.className] = {
- "require-at-least-one": requiredAnnotationsData.requiredAtLeastOnce,
- "annotation-list": requiredAnnotationsData.list
- };
- data.setElementRequiredAnnotations(elementRequiredAnnotations);
- return self.getServerConnector().updateUserPreferences({user: user, preferences: data}).catch(GuiConnector.alert);
- };
-
- checkboxList.addListener("select", function (element) {
- return changeSelection(element.value, true);
- });
- checkboxList.addListener("deselect", function (element) {
- return changeSelection(element.value, false);
- });
-
-};
-
-/**
- *
- * @returns {Promise}
- */
-ChooseValidatorsDialog.prototype.init = function () {
- var self = this;
- return self.getServerConnector().getConfiguration().then(function (configuration) {
-
- var treeData = configuration.getElementTypeTree();
-
- var element = $('[name="elementTree"]', self.getElement());
- element.jstree({
- core: {
- data: treeData
- }
- }).on('ready.jstree', function () {
- element.jstree("open_all");
- }).on("select_node.jstree",
- function (evt, data) {
- return self.setElementType(data.node.data);
- }
- );
- });
-};
-
-/**
- *
- */
-ChooseValidatorsDialog.prototype.destroy = function () {
- $(this.getElement()).dialog("destroy");
-};
-
-/**
- *
- */
-ChooseValidatorsDialog.prototype.open = function () {
- var self = this;
- var div = self.getElement();
- if (!$(div).hasClass("ui-dialog-content")) {
- $(div).dialog({
- title: "Select valid annotations",
- modal: true,
- width: window.innerWidth / 2,
- height: window.innerHeight / 2
-
- });
- }
-
- $(div).dialog("open");
-};
-
-module.exports = ChooseValidatorsDialog;
+"use strict";
+
+/* exported logger */
+
+var AbstractAnnotatorsDialog = require('./AbstractAnnotatorsDialog');
+var GuiConnector = require("../../GuiConnector");
+var UserPreferences = require("../../map/data/UserPreferences");
+var MultiCheckboxList = require("multi-checkbox-list");
+
+var Functions = require('../../Functions');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+/**
+ *
+ /**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} [params.configuration]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
+function ChooseValidatorsDialog(params) {
+ AbstractAnnotatorsDialog.call(this, params);
+ var self = this;
+ self.createGui();
+}
+
+ChooseValidatorsDialog.prototype = Object.create(AbstractAnnotatorsDialog.prototype);
+ChooseValidatorsDialog.prototype.constructor = ChooseValidatorsDialog;
+
+/**
+ *
+ */
+ChooseValidatorsDialog.prototype.createGui = function () {
+ var self = this;
+ var content = Functions.createElement({
+ type: "div",
+ style: "display:table;height:100%;width:100%"
+ });
+ content.appendChild(Functions.createElement({
+ type: "div",
+ style: "display:table-cell;height:100%;",
+ content: "<div name='elementTree' style='height:100%;overflow-y:scroll;'/>",
+ xss: false
+ }));
+
+ content.appendChild(Functions.createElement({
+ type: "div",
+ style: "display:table-cell;height:100%;width:100%;",
+ content: "<div name='annotatorListBox' style='height:100%;width:100%;overflow-y:auto;'><span> </span></div>",
+ xss: false
+ }));
+
+ self.getElement().appendChild(content);
+};
+
+/**
+ *
+ * @param {BioEntityType} elementType
+ * @returns {Promise}
+ */
+ChooseValidatorsDialog.prototype.setElementType = function (elementType) {
+ var self = this;
+
+ var configuration;
+
+ return self.getServerConnector().getConfiguration().then(function (result) {
+ configuration = result;
+ return self.getServerConnector().getLoggedUser();
+ }).then(function (user) {
+ var element = $("[name='annotatorListBox']", self.getElement())[0];
+ Functions.removeChildren(element);
+
+ var validAnnotationSelect = Functions.createElement({
+ type: "select",
+ className: "minerva-multi-select"
+ });
+ element.appendChild(validAnnotationSelect);
+ self.createValidAnnotationsDualListBox(user, configuration, elementType, validAnnotationSelect);
+
+ var verifyAnnotationSelect = Functions.createElement({
+ type: "select",
+ className: "minerva-multi-select"
+ });
+ element.appendChild(verifyAnnotationSelect);
+ self.createVerifyAnnotationsDualListBox(user, configuration, elementType, verifyAnnotationSelect);
+
+ element.appendChild(Functions.createElement({type: "br"}));
+ var includeChildrenCheckbox = Functions.createElement({type: "input", inputType: "checkbox"});
+ var copyFromButton = Functions.createElement({
+ type: "button", content: "Copy from", name: "copy-from-validator", onclick: function () {
+ var typeClassName = copyFromSelect.value;
+ var requiredAnnotations, validAnnotators;
+ for (var i = 0; i < configuration.getElementTypes().length; i++) {
+ var type = configuration.getElementTypes()[i];
+ if (typeClassName === type.className) {
+ requiredAnnotations = user.getPreferences().getElementRequiredAnnotations(typeClassName);
+ validAnnotators = user.getPreferences().getElementValidAnnotations(typeClassName);
+ }
+ }
+ if (requiredAnnotations === undefined) {
+ return GuiConnector.alert("Invalid element type: " + copyFromSelect.value);
+ } else {
+ var includeChildren = includeChildrenCheckbox.checked;
+ return self.saveAnnotationsInfo({
+ elementTypes: self.getAllChildrenTypesIfNeeded(elementType, includeChildren),
+ requiredAnnotators: requiredAnnotations,
+ validAnnotators: validAnnotators
+ }).then(function () {
+ return self.setElementType(elementType);
+ });
+ }
+ }
+ });
+ element.appendChild(copyFromButton);
+ var copyFromSelect = Functions.createElement({type: "select", style: "margin:5px"});
+ element.appendChild(copyFromSelect);
+ var options = [], i;
+ for (i = 0; i < configuration.getElementTypes().length; i++) {
+ var type = configuration.getElementTypes()[i];
+ var name = type.className;
+ if (name.indexOf(".") > 0) {
+ name = name.substr(name.lastIndexOf(".") + 1);
+ }
+ options.push(Functions.createElement({
+ type: "option",
+ value: type.className,
+ content: name
+ }));
+ }
+ options.sort(function (a, b) {
+ return a.text === b.text ? 0 : a.text < b.text ? -1 : 1
+ });
+ for (i = 0; i < options.length; i++) {
+ copyFromSelect.appendChild(options[i]);
+ }
+ element.appendChild(includeChildrenCheckbox);
+ element.appendChild(Functions.createElement({type: "span", content: "Apply to all in subtree"}));
+
+ });
+
+};
+
+/**
+ *
+ * @param {BioEntityType[]} params.elementTypes
+ * @param {{list:string[], requiredAtLeastOnce:boolean}} params.requiredAnnotators
+ * @param {string[]} params.validAnnotators
+ *
+ * @returns {Promise}
+ */
+ChooseValidatorsDialog.prototype.saveAnnotationsInfo = function (params) {
+ var elementTypes = params.elementTypes;
+ var requiredAnnotators = params.requiredAnnotators;
+ var validAnnotators = params.validAnnotators;
+ var self = this;
+ return self.getServerConnector().getLoggedUser().then(function (user) {
+
+ var data = new UserPreferences();
+
+ var elementRequiredAnnotators = {};
+ var elementValidAnnotators = {};
+ for (var i = 0; i < elementTypes.length; i++) {
+ elementRequiredAnnotators[elementTypes[i].className] = {
+ "require-at-least-one": requiredAnnotators.requiredAtLeastOnce,
+ "annotation-list": requiredAnnotators.list.slice()
+ };
+ elementValidAnnotators[elementTypes[i].className] = validAnnotators.slice();
+ }
+ data.setElementRequiredAnnotations(elementRequiredAnnotators);
+ data.setElementValidAnnotations(elementValidAnnotators);
+ return self.getServerConnector().updateUserPreferences({
+ user: user,
+ preferences: data
+ });
+ }).catch(GuiConnector.alert);
+};
+
+
+/**
+ *
+ * @param {User} user
+ * @param {Configuration} configuration
+ * @param {BioEntityType} elementType
+ * @param {HTMLElement} validAnnotationSelect
+ */
+ChooseValidatorsDialog.prototype.createValidAnnotationsDualListBox = function (user, configuration, elementType, validAnnotationSelect) {
+ var self = this;
+
+ var miriamTypes = configuration.getMiriamTypes();
+
+ var validAnnotations = user.getPreferences().getElementValidAnnotations(elementType.className);
+
+ var entries = [];
+
+
+ for (var i = 0; i < miriamTypes.length; i++) {
+ var miriamType = miriamTypes[i];
+ var entry = {name: miriamType.getCommonName(), value: miriamType.getName(), selected: false};
+
+ for (var j = 0; j < validAnnotations.length; j++) {
+ if (miriamType.getName() === validAnnotations[j]) {
+ entry.selected = true;
+ }
+ }
+ entries.push(entry);
+ }
+
+ var checkboxList = new MultiCheckboxList(validAnnotationSelect, {
+ entries: entries,
+ listTitle: "Available",
+ selectedTitle: "Selected",
+ selectedList: true
+ });
+
+ var changeSelection = function (elementId, selected) {
+ var miriamTypes = configuration.getMiriamTypes();
+ var miriamType;
+ for (var i = 0; i < miriamTypes.length; i++) {
+ if (elementId === miriamTypes[i].getName()) {
+ miriamType = miriamTypes[i];
+ }
+ }
+ if (selected) {
+ validAnnotations.push(miriamType.getName());
+ } else {
+ var index = validAnnotations.indexOf(miriamType.getName());
+ if (index > -1) {
+ validAnnotations.splice(index, 1);
+ }
+ }
+
+ var data = new UserPreferences();
+
+ var elementAnnotators = {};
+ elementAnnotators[elementType.className] = validAnnotations;
+ data.setElementValidAnnotations(elementAnnotators);
+ return self.getServerConnector().updateUserPreferences({
+ user: user,
+ preferences: data
+ }).catch(GuiConnector.alert);
+ };
+
+ checkboxList.addListener("select", function (element) {
+ return changeSelection(element.value, true);
+ });
+ checkboxList.addListener("deselect", function (element) {
+ return changeSelection(element.value, false);
+ });
+
+};
+
+/**
+ *
+ * @param {User} user
+ * @param {Configuration} configuration
+ * @param {BioEntityType} elementType
+ * @param {HTMLElement} verifyAnnotationSelect
+ */
+
+ChooseValidatorsDialog.prototype.createVerifyAnnotationsDualListBox = function (user, configuration, elementType, verifyAnnotationSelect) {
+ var self = this;
+ var requiredAnnotationsData = user.getPreferences().getElementRequiredAnnotations(elementType.className);
+
+ var verifyCheckboxDiv = Functions.createElement({type: "div"});
+ var checkbox = Functions.createElement({
+ type: "input",
+ inputType: "checkbox",
+ name: "require-at-least-one-checkbox",
+ onclick: function () {
+ var data = new UserPreferences();
+
+ var elementRequiredAnnotations = {};
+ elementRequiredAnnotations[elementType.className] = {
+ "require-at-least-one": checkbox.checked,
+ "annotation-list": requiredAnnotationsData.list
+ };
+ data.setElementRequiredAnnotations(elementRequiredAnnotations);
+ return self.getServerConnector().updateUserPreferences({user: user, preferences: data}).catch(GuiConnector.alert);
+ }
+ });
+ checkbox.checked = requiredAnnotationsData.requiredAtLeastOnce;
+ verifyCheckboxDiv.appendChild(Functions.createElement({type: "br"}));
+ verifyCheckboxDiv.appendChild(Functions.createElement({type: "br"}));
+ verifyCheckboxDiv.appendChild(checkbox);
+ verifyCheckboxDiv.appendChild(Functions.createElement({
+ type: "span",
+ content: "One of these miriam should be required"
+ }));
+ verifyAnnotationSelect.parentNode.insertBefore(verifyCheckboxDiv, verifyAnnotationSelect);
+
+ var miriamTypes = configuration.getMiriamTypes();
+
+ var entries = [];
+
+ for (var i = 0; i < miriamTypes.length; i++) {
+ var miriamType = miriamTypes[i];
+ var entry = {name: miriamType.getCommonName(), value: miriamType.getName(), selected: false};
+ for (var j = 0; j < requiredAnnotationsData.list.length; j++) {
+ if (miriamType.getName() === requiredAnnotationsData.list[j]) {
+ entry.selected = true;
+ }
+ }
+ entries.push(entry);
+ }
+
+ var checkboxList = new MultiCheckboxList(verifyAnnotationSelect, {
+ entries: entries,
+ listTitle: "Available",
+ selectedTitle: "Selected",
+ selectedList: true
+ });
+
+ var changeSelection = function (elementId, selected) {
+
+ var miriamTypes = configuration.getMiriamTypes();
+ var miriamType;
+ for (var i = 0; i < miriamTypes.length; i++) {
+ if (elementId === miriamTypes[i].getName()) {
+ miriamType = miriamTypes[i];
+ }
+ }
+ if (selected) {
+ requiredAnnotationsData.list.push(miriamType.getName());
+ } else {
+ var index = requiredAnnotationsData.list.indexOf(miriamType.getName());
+ if (index > -1) {
+ requiredAnnotationsData.list.splice(index, 1);
+ }
+ }
+
+ var data = new UserPreferences();
+
+ var elementRequiredAnnotations = {};
+ elementRequiredAnnotations[elementType.className] = {
+ "require-at-least-one": requiredAnnotationsData.requiredAtLeastOnce,
+ "annotation-list": requiredAnnotationsData.list
+ };
+ data.setElementRequiredAnnotations(elementRequiredAnnotations);
+ return self.getServerConnector().updateUserPreferences({user: user, preferences: data}).catch(GuiConnector.alert);
+ };
+
+ checkboxList.addListener("select", function (element) {
+ return changeSelection(element.value, true);
+ });
+ checkboxList.addListener("deselect", function (element) {
+ return changeSelection(element.value, false);
+ });
+
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+ChooseValidatorsDialog.prototype.init = function () {
+ var self = this;
+ return self.getServerConnector().getConfiguration().then(function (configuration) {
+
+ var treeData = configuration.getElementTypeTree();
+
+ var element = $('[name="elementTree"]', self.getElement());
+ element.jstree({
+ core: {
+ data: treeData
+ }
+ }).on('ready.jstree', function () {
+ element.jstree("open_all");
+ }).on("select_node.jstree",
+ function (evt, data) {
+ return self.setElementType(data.node.data);
+ }
+ );
+ });
+};
+
+/**
+ *
+ */
+ChooseValidatorsDialog.prototype.destroy = function () {
+ $(this.getElement()).dialog("destroy");
+};
+
+/**
+ *
+ */
+ChooseValidatorsDialog.prototype.open = function () {
+ var self = this;
+ var div = self.getElement();
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ title: "Select valid annotations",
+ modal: true,
+ width: window.innerWidth / 2,
+ height: window.innerHeight / 2
+
+ });
+ }
+
+ $(div).dialog("open");
+};
+
+module.exports = ChooseValidatorsDialog;
diff --git a/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js b/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
index bfaf2efb6d1c77efb49be4211659e0acb8afbf5a..5c9f1c7791fab00acf1dc27fc94665f6da6c8e88 100644
--- a/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/CommentsAdminPanel.js
@@ -1,151 +1,151 @@
-"use strict";
-
-var AbstractGuiElement = require('../AbstractGuiElement');
-
-var Functions = require('../../Functions');
-var GuiConnector = require('../../GuiConnector');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-// noinspection JSUnusedLocalSymbols
-var Promise = require("bluebird");
-var xss = require('xss');
-
-function CommentsAdminPanel(params) {
- params.customMap = null;
- AbstractGuiElement.call(this, params);
-
- this._createGui();
-}
-
-CommentsAdminPanel.prototype = Object.create(AbstractGuiElement.prototype);
-CommentsAdminPanel.prototype.constructor = CommentsAdminPanel;
-
-CommentsAdminPanel.prototype._createGui = function () {
- var self = this;
-
- var commentsTable = Functions.createElement({
- type: "table",
- name: "commentsTable",
- className: "display",
- style: "width:100%"
- });
-
- self.getElement().appendChild(commentsTable);
-
- $(commentsTable).DataTable({
- columns: [{
- title: 'Id'
- }, {
- title: 'Title'
- }, {
- title: 'Author'
- }, {
- title: 'Email'
- }, {
- title: 'Content'
- }, {
- title: 'Removed'
- }, {
- title: 'Pinned'
- }]
- });
-
-};
-
-CommentsAdminPanel.prototype.init = function () {
- var self = this;
- return self.refreshProjects();
-};
-
-CommentsAdminPanel.prototype.refreshComments = function () {
- var self = this;
-
- return ServerConnector.getComments({
- projectId: self.getProject().getProjectId()
- }).then(function (comments) {
- var dataTable = $($("[name='commentsTable']", self.getElement())[0]).DataTable();
- var data = [];
- for (var i = 0; i < comments.length; i++) {
- data.push(self.commentToTableRow(comments[i]));
- }
- dataTable.clear().rows.add(data).draw();
- $("[name='commentsTable']", self.getElement()).on("click", "[name='removeComment']", function () {
- var button = this;
- return self.askConfirmRemoval({
- title: "Why do you want to remove this comment?",
- input: true
- }).then(function (param) {
- if (param.status) {
- return ServerConnector.removeComment({
- commentId: $(button).attr("data"),
- reason: param.reason,
- projectId: self.getProject().getProjectId()
- }).then(function () {
- $(button).after("<span>YES (" + param.reason + ")</span>");
- button.style.display = "none";
- });
- }
- }).catch(GuiConnector.alert)
- });
- });
-};
-
-CommentsAdminPanel.prototype.commentToTableRow = function (comment) {
- var self = this;
- var projectId = self.getProject().getProjectId();
- var toYesNo = function (val) {
- if (val) {
- return "YES";
- } else {
- return "NO";
- }
- };
- var title = null;
- if (!comment.isRemoved()) {
- var commentLink = "index.xhtml?id=" + projectId + //
- "&x=" + comment.getCoordinates().x + //
- "&y=" + comment.getCoordinates().y + //
- "&zoom=12" + //
- "&comments=on";
- title = "<a href='" + commentLink + "' target='" + projectId + "'>" + comment.getTitle() + "</a>";
- } else {
- title = comment.getTitle();
- }
-
- var remove = null;
- if (comment.isRemoved()) {
- remove = "YES (" + comment.getRemoveReason() + ")";
- } else {
- remove = "<button name='removeComment' data='" + comment.getId() + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
- }
-
- var author = comment.getAuthor();
- if (author === undefined) {
- author = "N/A";
- }
-
- var email = comment.getEmail();
- if (email === undefined) {
- email = "N/A";
- }
-
- return [comment.getId(), //
- xss(title), //
- xss(author), //
- xss(email), //
- xss(comment.getContent()), //
- remove, //
- toYesNo(comment.isPinned())];
-};
-
-CommentsAdminPanel.prototype.destroy = function () {
- var self = this;
- var table = $("[name='commentsTable']", self.getElement())[0];
- if ($.fn.DataTable.isDataTable(table)) {
- $(table).DataTable().destroy();
- }
-};
-
-
-module.exports = CommentsAdminPanel;
+"use strict";
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+
+var Functions = require('../../Functions');
+var GuiConnector = require('../../GuiConnector');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+// noinspection JSUnusedLocalSymbols
+var Promise = require("bluebird");
+var xss = require('xss');
+
+function CommentsAdminPanel(params) {
+ params.customMap = null;
+ AbstractGuiElement.call(this, params);
+
+ this._createGui();
+}
+
+CommentsAdminPanel.prototype = Object.create(AbstractGuiElement.prototype);
+CommentsAdminPanel.prototype.constructor = CommentsAdminPanel;
+
+CommentsAdminPanel.prototype._createGui = function () {
+ var self = this;
+
+ var commentsTable = Functions.createElement({
+ type: "table",
+ name: "commentsTable",
+ className: "display",
+ style: "width:100%"
+ });
+
+ self.getElement().appendChild(commentsTable);
+
+ $(commentsTable).DataTable({
+ columns: [{
+ title: 'Id'
+ }, {
+ title: 'Title'
+ }, {
+ title: 'Author'
+ }, {
+ title: 'Email'
+ }, {
+ title: 'Content'
+ }, {
+ title: 'Removed'
+ }, {
+ title: 'Pinned'
+ }]
+ });
+
+};
+
+CommentsAdminPanel.prototype.init = function () {
+ var self = this;
+ return self.refreshProjects();
+};
+
+CommentsAdminPanel.prototype.refreshComments = function () {
+ var self = this;
+
+ return ServerConnector.getComments({
+ projectId: self.getProject().getProjectId()
+ }).then(function (comments) {
+ var dataTable = $($("[name='commentsTable']", self.getElement())[0]).DataTable();
+ var data = [];
+ for (var i = 0; i < comments.length; i++) {
+ data.push(self.commentToTableRow(comments[i]));
+ }
+ dataTable.clear().rows.add(data).draw();
+ $("[name='commentsTable']", self.getElement()).on("click", "[name='removeComment']", function () {
+ var button = this;
+ return self.askConfirmRemoval({
+ title: "Why do you want to remove this comment?",
+ input: true
+ }).then(function (param) {
+ if (param.status) {
+ return ServerConnector.removeComment({
+ commentId: $(button).attr("data"),
+ reason: param.reason,
+ projectId: self.getProject().getProjectId()
+ }).then(function () {
+ $(button).after("<span>YES (" + param.reason + ")</span>");
+ button.style.display = "none";
+ });
+ }
+ }).catch(GuiConnector.alert)
+ });
+ });
+};
+
+CommentsAdminPanel.prototype.commentToTableRow = function (comment) {
+ var self = this;
+ var projectId = self.getProject().getProjectId();
+ var toYesNo = function (val) {
+ if (val) {
+ return "YES";
+ } else {
+ return "NO";
+ }
+ };
+ var title = null;
+ if (!comment.isRemoved()) {
+ var commentLink = "index.xhtml?id=" + projectId + //
+ "&x=" + comment.getCoordinates().x + //
+ "&y=" + comment.getCoordinates().y + //
+ "&zoom=12" + //
+ "&comments=on";
+ title = "<a href='" + commentLink + "' target='" + projectId + "'>" + comment.getTitle() + "</a>";
+ } else {
+ title = comment.getTitle();
+ }
+
+ var remove = null;
+ if (comment.isRemoved()) {
+ remove = "YES (" + comment.getRemoveReason() + ")";
+ } else {
+ remove = "<button name='removeComment' data='" + comment.getId() + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
+ }
+
+ var author = comment.getAuthor();
+ if (author === undefined) {
+ author = "N/A";
+ }
+
+ var email = comment.getEmail();
+ if (email === undefined) {
+ email = "N/A";
+ }
+
+ return [comment.getId(), //
+ xss(title), //
+ xss(author), //
+ xss(email), //
+ xss(comment.getContent()), //
+ remove, //
+ toYesNo(comment.isPinned())];
+};
+
+CommentsAdminPanel.prototype.destroy = function () {
+ var self = this;
+ var table = $("[name='commentsTable']", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(table)) {
+ $(table).DataTable().destroy();
+ }
+};
+
+
+module.exports = CommentsAdminPanel;
diff --git a/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
index db63e854dc8534215b76cd1b12bf8fada93cf2ce..ff90758262320a867554675444ff8f73eeba6d23 100644
--- a/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditGenomeDialog.js
@@ -1,703 +1,703 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var AbstractGuiElement = require('../AbstractGuiElement');
-var Annotation = require('../../map/data/Annotation');
-var GuiConnector = require('../../GuiConnector');
-
-var Functions = require('../../Functions');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-var guiUtils = new (require('../leftPanel/GuiUtils'))();
-
-/**
- *
- * @param {Object} params
- * @param {HTMLElement} params.element
- * @param {CustomMap} params.customMap
- * @param {Configuration} params.configuration
- * @param {ReferenceGenome} params.referenceGenome
- * @param {ServerConnector} [params.serverConnector]
-
- * @constructor
- *
- * @extends AbstractGuiElement
- */
-function EditGenomeDialog(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
- self.setReferenceGenome(params.referenceGenome);
-
- $(self.getElement()).css({overflow: "hidden"});
-
- self.createGui();
- self.registerListenerType("onSave");
-}
-
-EditGenomeDialog.prototype = Object.create(AbstractGuiElement.prototype);
-EditGenomeDialog.prototype.constructor = EditGenomeDialog;
-
-/**
- *
- * @param {ReferenceGenome} referenceGenome
- */
-EditGenomeDialog.prototype.setReferenceGenome = function (referenceGenome) {
- this._referenceGenome = referenceGenome;
-};
-
-/**
- *
- * @returns {ReferenceGenome}
- */
-EditGenomeDialog.prototype.getReferenceGenome = function () {
- return this._referenceGenome;
-};
-
-/**
- *
- * @returns {boolean}
- */
-EditGenomeDialog.prototype.isNew = function () {
- return this.getReferenceGenome().getId() === undefined;
-};
-
-/**
- *
- */
-EditGenomeDialog.prototype.createGui = function () {
- var self = this;
- var element = self.getElement();
-
- var tabDiv = Functions.createElement({
- type: "div",
- name: "tabView",
- className: "tabbable boxed parentTabs",
- style: "position:absolute;top:10px;bottom:40px;left:10px;right:10px"
- });
- element.appendChild(tabDiv);
-
- var tabMenuDiv = Functions.createElement({
- type: "ul",
- className: "nav nav-tabs"
- });
- tabDiv.appendChild(tabMenuDiv);
-
- var tabContentDiv = Functions.createElement({
- type: "div",
- className: "tab-content",
- style: "height:100%"
- });
- tabDiv.appendChild(tabContentDiv);
-
- self.createGeneralTab(tabMenuDiv, tabContentDiv);
- self.createGeneMappingTab(tabMenuDiv, tabContentDiv);
- $("a", tabMenuDiv).bind("click", function () {
- //workaround for some css issues...
- tabDiv.style.top = "40px";
- tabDiv.style.bottom = "10px";
- });
-
-};
-
-/**
- *
- * @param {HTMLElement} tabMenuDiv
- * @param {HTMLElement} tabContentDiv
- */
-EditGenomeDialog.prototype.createGeneralTab = function (tabMenuDiv, tabContentDiv) {
- var self = this;
- self.addTab({
- tabMenuDiv: tabMenuDiv,
- tabContentDiv: tabContentDiv,
- name: "DETAILS",
- content: self.createGeneralTabContent()
- });
-
-};
-
-/**
- *
- * @param {HTMLElement} tabMenuDiv
- * @param {HTMLElement} tabContentDiv
- */
-EditGenomeDialog.prototype.createGeneMappingTab = function (tabMenuDiv, tabContentDiv) {
- var self = this;
- self.addTab({
- tabMenuDiv: tabMenuDiv,
- tabContentDiv: tabContentDiv,
- name: "GENE MAPPING",
- content: self.createGeneMappingTabContent()
- });
-
-};
-
-var id_counter = 0;
-
-/**
- *
- * @param {string} tab_name
- * @returns {string}
- */
-EditGenomeDialog.prototype.generateTabId = function (tab_name) {
- var self = this;
- var id = self.getReferenceGenome().getId();
- if (id === undefined) {
- id = "new_genome_" + (id_counter++);
- }
- return id + tab_name.replace(" ", "_") + "_TAB";
-};
-
-EditGenomeDialog.prototype.addTab = function (params) {
- var id = this.generateTabId(params.name);
-
- var navLi = guiUtils.createTabMenuObject({
- id: id,
- name: params.name,
- navigationBar: params.tabMenuDiv
- });
- params.tabMenuDiv.appendChild(navLi);
-
- var contentDiv = guiUtils.createTabContentObject({
- id: id,
- navigationObject: navLi,
- navigationBar: params.tabMenuDiv
- });
-
- $(contentDiv).css("overflow", "auto");
- if (params.content !== undefined) {
- contentDiv.appendChild(params.content);
- }
-
- params.tabContentDiv.appendChild(contentDiv);
-};
-
-/**
- *
- * @returns {HTMLElement}
- */
-EditGenomeDialog.prototype.createGeneralTabContent = function () {
-
- var self = this;
-
- var result = Functions.createElement({
- type: "div",
- style: "margin-top:10px;"
- });
-
- var table = Functions.createElement({
- type: "table",
- name: "detailsTable",
- className: "display",
- style: "width:100%"
- });
- result.appendChild(table);
-
- $(table).on("change", "[name='genomeOrganismSelect']", function () {
- return self._fillTypeSelect(self.getReferenceGenome(), self.getSelectedOrganism());
- });
-
- $(table).on("change", "[name='genomeTypeSelect']", function () {
- return self._fillVersionSelect(self.getReferenceGenome(), self.getSelectedOrganism(), self.getSelectedType());
- });
-
- $(table).on("change", "[name='genomeVersionSelect']", function () {
- return self._fillUrl(self.getReferenceGenome(), self.getSelectedOrganism(), self.getSelectedType(), self.getSelectedVersion());
- });
-
-
- var menuRow = Functions.createElement({
- type: "div",
- className: "minerva-menu-row",
- style: "display:table-row; margin:10px"
- });
- result.appendChild(menuRow);
-
- var saveUserButton = Functions.createElement({
- type: "button",
- name: "saveGenome",
- content: '<span class="ui-icon ui-icon-disk"></span> SAVE',
- onclick: function () {
- return self.onSaveClicked().then(function () {
- return self.close();
- }).catch(GuiConnector.alert);
- },
- xss: false
- });
- var cancelButton = Functions.createElement({
- type: "button",
- name: "cancelGenome",
- content: '<span class="ui-icon ui-icon-cancel"></span> CANCEL',
- onclick: function () {
- return self.close();
- },
- xss: false
- });
- menuRow.appendChild(saveUserButton);
- menuRow.appendChild(cancelButton);
-
- return result;
-};
-
-/**
- *
- * @returns {HTMLElement}
- */
-EditGenomeDialog.prototype.createGeneMappingTabContent = function () {
-
- var self = this;
-
- var result = Functions.createElement({
- type: "div",
- style: "margin-top:10px;"
- });
-
- var geneMappingTable = Functions.createElement({
- type: "table",
- name: "geneMappingTable",
- className: "display",
- style: "width:100%"
- });
- result.appendChild(geneMappingTable);
-
- // noinspection JSUnusedGlobalSymbols
- $(geneMappingTable).DataTable({
- columns: [{
- title: 'Name'
- }, {
- title: 'Source'
- }, {
- title: 'Progress'
- }, {
- title: 'Remove',
- orderable: false
- }],
- order: [[1, "asc"]]
- });
-
- $(geneMappingTable).on("click", "[name='removeMapping']", function () {
- var button = this;
- return self.askConfirmRemoval({
- title: "INFO",
- content: "Do you really want to remove this gene mapping?",
- input: false
- }).then(function (param) {
- if (param.status) {
- return self.getServerConnector().removeReferenceGenomeGeneMapping({
- mappingId: $(button).attr("data").toString(),
- genomeId: self.getReferenceGenome().getId().toString()
- }).then(function () {
- return self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()});
- }).then(function (referenceGenome) {
- self.setReferenceGenome(referenceGenome);
- return self.refresh();
- });
- }
- }).catch(GuiConnector.alert);
- });
-
- var menuRow = Functions.createElement({
- type: "div",
- className: "minerva-menu-row",
- style: "display:table-row; margin:10px"
- });
- result.appendChild(menuRow);
-
- var addGeneMappingButton = Functions.createElement({
- type: "button",
- name: "saveGenome",
- content: '<span class="ui-icon ui-icon-disk"></span> ADD GENE MAPPING',
- onclick: function () {
- return self.openAddGeneMapping();
- },
- xss: false
- });
-
- menuRow.appendChild(addGeneMappingButton);
-
- return result;
-};
-
-/**
- *
- * @returns {Promise|PromiseLike}
- */
-EditGenomeDialog.prototype.onSaveClicked = function () {
- var self = this;
- if (!self.isNew()) {
- return self.callListeners("onSave");
- } else {
- var genome = self.getReferenceGenome();
- genome.setSourceUrl(self.getSourceUrl());
- genome.setOrganism(self.getSelectedOrganism());
- genome.setType(self.getSelectedType());
- genome.setVersion(self.getSelectedVersion());
- return self.getServerConnector().addReferenceGenome(genome).then(function () {
- return self.callListeners("onSave");
- });
- }
-};
-/**
- *
- * @param {ReferenceGenome} genome
- * @returns {Promise}
- * @private
- */
-EditGenomeDialog.prototype._fillOrganismSelect = function (genome) {
- var self = this;
- return self.getServerConnector().getReferenceGenomeOrganisms().then(function (organisms) {
- var genomeOrganismSelect = $("[name=genomeOrganismSelect]", self.getElement());
- genomeOrganismSelect.empty();
- var selectedOrganism;
- if (self.isNew()) {
- selectedOrganism = organisms[0];
- for (var i = 0; i < organisms.length; i++) {
- if (organisms[i].getResource() === "9606") {
- selectedOrganism = organisms[i];
- }
- }
- } else {
- selectedOrganism = genome.getOrganism();
- }
- $.each(organisms, function (i, organism) {
- var disable = false;
- if (organism.getResource() !== selectedOrganism.getResource() && !self.isNew()) {
- disable = true;
- }
- genomeOrganismSelect.append($('<option>', {
- value: organism.getResource(),
- text: organism.getResource(),
- disabled: disable
- }));
- });
- genomeOrganismSelect.val(selectedOrganism.getResource());
- return self._fillTypeSelect(genome, selectedOrganism);
- });
-};
-
-/**
- *
- * @param {ReferenceGenome} genome
- * @param {Annotation} selectedOrganism
- * @returns {Promise}
- * @private
- */
-EditGenomeDialog.prototype._fillTypeSelect = function (genome, selectedOrganism) {
- var self = this;
- return self.getServerConnector().getReferenceGenomeTypes({organism: selectedOrganism}).then(function (types) {
-
- var genomeTypeSelect = $("[name=genomeTypeSelect]", self.getElement());
- genomeTypeSelect.empty();
-
- var selectedType;
- if (self.isNew()) {
- selectedType = types[0].type;
- } else {
- selectedType = genome.getType();
- }
- $.each(types, function (i, type) {
- var disable = false;
- if (type.type !== selectedType && !self.isNew()) {
- disable = true;
- }
- genomeTypeSelect.append($('<option>', {
- value: type.type,
- text: type.type,
- disabled: disable
- }));
- });
- genomeTypeSelect.val(selectedType);
- return self._fillVersionSelect(genome, selectedOrganism, selectedType);
- })
-};
-
-/**
- *
- * @param {ReferenceGenome} genome
- * @param {Annotation} selectedOrganism
- * @param {string} selectedType
- * @returns {Promise}
- * @private
- */
-EditGenomeDialog.prototype._fillVersionSelect = function (genome, selectedOrganism, selectedType) {
- var self = this;
- return self.getServerConnector().getReferenceGenomeVersions({
- organism: selectedOrganism,
- type: selectedType
- }).then(function (versions) {
- var genomeVersionSelect = $("[name=genomeVersionSelect]", self.getElement());
- genomeVersionSelect.empty();
-
- var selectedVersion;
- if (self.isNew()) {
- selectedVersion = versions[0].version;
- } else {
- selectedVersion = genome.getVersion();
- }
- $.each(versions, function (i, version) {
- var disable = false;
- if (version.version !== selectedVersion && !self.isNew()) {
- disable = true;
- }
- genomeVersionSelect.append($('<option>', {
- value: version.version,
- text: version.version,
- disabled: disable
- }));
- });
- genomeVersionSelect.val(selectedVersion);
- return self._fillUrl(genome, selectedOrganism, selectedType, selectedVersion);
- })
-};
-
-/**
- *
- * @param {ReferenceGenome} genome
- * @param {Annotation} organism
- * @param {string} type
- * @param {string} version
- * @returns {Promise}
- * @private
- */
-EditGenomeDialog.prototype._fillUrl = function (genome, organism, type, version) {
- var self = this;
- var genomeSourceUrlInput = $("[name=genomeSourceUrl]", self.getElement());
- var genomeLocalUrlInput = $("[name=genomeLocalUrl]", self.getElement());
- var genomeProgressInput = $("[name=genomeProgress]", self.getElement());
- genomeLocalUrlInput.prop("disabled", true);
- genomeProgressInput.val(genome.getDownloadProgressStatus());
- genomeProgressInput.prop("disabled", true);
- if (!self.isNew()) {
- genomeSourceUrlInput.val(genome.getSourceUrl());
- genomeSourceUrlInput.prop("disabled", true);
-
- genomeLocalUrlInput.val(genome.getLocalUrl());
- } else {
- genomeSourceUrlInput.prop("disabled", false);
-
- genomeLocalUrlInput.val("");
- return self.getServerConnector().getAvailableGenomeUrls({
- organism: organism,
- type: type,
- version: version
- }).then(function (urls) {
- if (urls.length > 0) {
- genomeSourceUrlInput.val(urls[0]);
- } else {
- genomeSourceUrlInput.val("");
- }
- })
- }
- return Promise.resolve();
-}
-;
-
-
-/**
- *
- * @param {ReferenceGenomeGeneMapping} geneMapping
- * @returns {Array}
- */
-EditGenomeDialog.prototype.geneMappingToTableRow = function (geneMapping) {
- var row = [];
- row[0] = geneMapping.getName();
- row[1] = geneMapping.getSourceUrl();
- row[2] = geneMapping.getProgress();
- row[3] = "<button name='removeMapping' data='" + geneMapping.getId() + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
- return row;
-};
-/**
- *
- * @returns {Promise}
- */
-EditGenomeDialog.prototype.init = function () {
- var self = this;
-
- var detailsTable = $("[name=detailsTable]", self.getElement())[0];
-
- // noinspection JSCheckFunctionSignatures
- $(detailsTable).DataTable({
- columns: [{
- title: "Name"
- }, {
- title: "Value"
- }],
- paging: false,
- ordering: false,
- searching: false,
- bInfo: false
- });
-
- return self.refresh();
-};
-
-/**
- *
- * @returns {Promise}
- */
-EditGenomeDialog.prototype.refresh = function () {
- var self = this;
-
- var genome = self.getReferenceGenome();
-
- var dataTable = $("[name=detailsTable]", self.getElement()).DataTable();
- var data = [];
-
- data.push(['Organism', Functions.createElement({type: "select", name: "genomeOrganismSelect"}).outerHTML]);
- data.push(['Type', Functions.createElement({type: "select", name: "genomeTypeSelect"}).outerHTML]);
- data.push(['Version', Functions.createElement({type: "select", name: "genomeVersionSelect"}).outerHTML]);
- data.push(['Source url', Functions.createElement({type: "input", name: "genomeSourceUrl"}).outerHTML]);
- data.push(['Local url', Functions.createElement({type: "input", name: "genomeLocalUrl"}).outerHTML]);
- data.push(['Progress', Functions.createElement({type: "input", name: "genomeProgress"}).outerHTML]);
-
- dataTable.clear().rows.add(data).draw();
-
- dataTable = $("[name=geneMappingTable]", self.getElement()).DataTable();
- data = [];
- var page = dataTable.page();
-
- for (var i = 0; i < genome.getGeneMappings().length; i++) {
- var geneMapping = genome.getGeneMappings()[i];
- var rowData = self.geneMappingToTableRow(geneMapping);
- data.push(rowData);
- }
- //it should be simplified, but I couldn't make it work
- dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
-
- return self._fillOrganismSelect(genome);
-};
-
-/**
- *
- */
-EditGenomeDialog.prototype.destroy = function () {
- var self = this;
- var div = self.getElement();
-
- var detailsTable = $("[name=detailsTable]", div)[0];
- if ($.fn.DataTable.isDataTable(detailsTable)) {
- $(detailsTable).DataTable().destroy();
- }
-
- var geneMappingTable = $("[name=geneMappingTable]", div)[0];
- if ($.fn.DataTable.isDataTable(geneMappingTable)) {
- $(geneMappingTable).DataTable().destroy();
- }
-
- if ($(div).hasClass("ui-dialog-content")) {
- $(div).dialog("destroy");
- }
-};
-
-/**
- *
- */
-EditGenomeDialog.prototype.open = function () {
- var self = this;
- var div = self.getElement();
- var title;
- if (self.isNew()) {
- title = "Download genome";
- } else {
- var genome = self.getReferenceGenome();
- title = genome.getType() + " " + genome.getOrganism().getResource() + " " + genome.getVersion();
- }
- if (!$(div).hasClass("ui-dialog-content")) {
- $(div).dialog({
- title: title,
- width: window.innerWidth / 2,
- height: window.innerHeight / 2
- });
- }
- $(div).dialog("open");
-};
-
-/**
- *
- */
-EditGenomeDialog.prototype.close = function () {
- var self = this;
- $(self.getElement()).dialog("close");
-};
-
-/**
- *
- * @returns {Annotation}
- */
-EditGenomeDialog.prototype.getSelectedOrganism = function () {
- var self = this;
- return new Annotation({
- resource: ($("[name='genomeOrganismSelect']", self.getElement()).val()).toString(),
- link: '',
- id: 0,
- type: ''
- })
-};
-
-/**
- *
- * @returns {string}
- */
-EditGenomeDialog.prototype.getSelectedType = function () {
- var self = this;
- return ($("[name='genomeTypeSelect']", self.getElement()).val()).toString();
-};
-
-/**
- *
- * @returns {string}
- */
-EditGenomeDialog.prototype.getSelectedVersion = function () {
- var self = this;
- return ($("[name='genomeVersionSelect']", self.getElement()).val()).toString();
-};
-
-/**
- *
- * @returns {string}
- */
-EditGenomeDialog.prototype.getSourceUrl = function () {
- var self = this;
- return ($("[name='genomeSourceUrl']", self.getElement()).val()).toString();
-};
-
-/**
- *
- */
-EditGenomeDialog.prototype.openAddGeneMapping = function () {
- var self = this;
- var html = '<form style="z-index:10000"><span>Name: </span><input type="text" name="gene-mapping-name"><br>' +
- '<span>Url: </span><input type="text" name="gene-mapping-url"><br></form>';
- $(html).dialog({
- modal: true,
- title: "Add gene mapping",
- close: function () {
- $(this).dialog('destroy').remove();
- },
- buttons: {
- 'ADD': function () {
- var dialog = this;
- var name = $('input[name="gene-mapping-name"]').val().toString();
- var url = $('input[name="gene-mapping-url"]').val().toString();
- return self.getServerConnector().addGeneMapping({
- genomeId: self.getReferenceGenome().getId(),
- mappingName: name,
- mappingUrl: url
- }).then(function () {
- return self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()});
- }).then(function (referenceGenome) {
- self.setReferenceGenome(referenceGenome);
- return self.refresh();
- }).then(function () {
- $(dialog).dialog('destroy').remove();
- });
- },
- 'Cancel': function () {
- $(this).dialog('destroy').remove();
- }
- }
- });
-};
-
-module.exports = EditGenomeDialog;
+"use strict";
+
+var Promise = require("bluebird");
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+var Annotation = require('../../map/data/Annotation');
+var GuiConnector = require('../../GuiConnector');
+
+var Functions = require('../../Functions');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var guiUtils = new (require('../leftPanel/GuiUtils'))();
+
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {ReferenceGenome} params.referenceGenome
+ * @param {ServerConnector} [params.serverConnector]
+
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
+function EditGenomeDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ self.setReferenceGenome(params.referenceGenome);
+
+ $(self.getElement()).css({overflow: "hidden"});
+
+ self.createGui();
+ self.registerListenerType("onSave");
+}
+
+EditGenomeDialog.prototype = Object.create(AbstractGuiElement.prototype);
+EditGenomeDialog.prototype.constructor = EditGenomeDialog;
+
+/**
+ *
+ * @param {ReferenceGenome} referenceGenome
+ */
+EditGenomeDialog.prototype.setReferenceGenome = function (referenceGenome) {
+ this._referenceGenome = referenceGenome;
+};
+
+/**
+ *
+ * @returns {ReferenceGenome}
+ */
+EditGenomeDialog.prototype.getReferenceGenome = function () {
+ return this._referenceGenome;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+EditGenomeDialog.prototype.isNew = function () {
+ return this.getReferenceGenome().getId() === undefined;
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.createGui = function () {
+ var self = this;
+ var element = self.getElement();
+
+ var tabDiv = Functions.createElement({
+ type: "div",
+ name: "tabView",
+ className: "tabbable boxed parentTabs",
+ style: "position:absolute;top:10px;bottom:40px;left:10px;right:10px"
+ });
+ element.appendChild(tabDiv);
+
+ var tabMenuDiv = Functions.createElement({
+ type: "ul",
+ className: "nav nav-tabs"
+ });
+ tabDiv.appendChild(tabMenuDiv);
+
+ var tabContentDiv = Functions.createElement({
+ type: "div",
+ className: "tab-content",
+ style: "height:100%"
+ });
+ tabDiv.appendChild(tabContentDiv);
+
+ self.createGeneralTab(tabMenuDiv, tabContentDiv);
+ self.createGeneMappingTab(tabMenuDiv, tabContentDiv);
+ $("a", tabMenuDiv).bind("click", function () {
+ //workaround for some css issues...
+ tabDiv.style.top = "40px";
+ tabDiv.style.bottom = "10px";
+ });
+
+};
+
+/**
+ *
+ * @param {HTMLElement} tabMenuDiv
+ * @param {HTMLElement} tabContentDiv
+ */
+EditGenomeDialog.prototype.createGeneralTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "DETAILS",
+ content: self.createGeneralTabContent()
+ });
+
+};
+
+/**
+ *
+ * @param {HTMLElement} tabMenuDiv
+ * @param {HTMLElement} tabContentDiv
+ */
+EditGenomeDialog.prototype.createGeneMappingTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "GENE MAPPING",
+ content: self.createGeneMappingTabContent()
+ });
+
+};
+
+var id_counter = 0;
+
+/**
+ *
+ * @param {string} tab_name
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.generateTabId = function (tab_name) {
+ var self = this;
+ var id = self.getReferenceGenome().getId();
+ if (id === undefined) {
+ id = "new_genome_" + (id_counter++);
+ }
+ return id + tab_name.replace(" ", "_") + "_TAB";
+};
+
+EditGenomeDialog.prototype.addTab = function (params) {
+ var id = this.generateTabId(params.name);
+
+ var navLi = guiUtils.createTabMenuObject({
+ id: id,
+ name: params.name,
+ navigationBar: params.tabMenuDiv
+ });
+ params.tabMenuDiv.appendChild(navLi);
+
+ var contentDiv = guiUtils.createTabContentObject({
+ id: id,
+ navigationObject: navLi,
+ navigationBar: params.tabMenuDiv
+ });
+
+ $(contentDiv).css("overflow", "auto");
+ if (params.content !== undefined) {
+ contentDiv.appendChild(params.content);
+ }
+
+ params.tabContentDiv.appendChild(contentDiv);
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
+EditGenomeDialog.prototype.createGeneralTabContent = function () {
+
+ var self = this;
+
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var table = Functions.createElement({
+ type: "table",
+ name: "detailsTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(table);
+
+ $(table).on("change", "[name='genomeOrganismSelect']", function () {
+ return self._fillTypeSelect(self.getReferenceGenome(), self.getSelectedOrganism());
+ });
+
+ $(table).on("change", "[name='genomeTypeSelect']", function () {
+ return self._fillVersionSelect(self.getReferenceGenome(), self.getSelectedOrganism(), self.getSelectedType());
+ });
+
+ $(table).on("change", "[name='genomeVersionSelect']", function () {
+ return self._fillUrl(self.getReferenceGenome(), self.getSelectedOrganism(), self.getSelectedType(), self.getSelectedVersion());
+ });
+
+
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+ result.appendChild(menuRow);
+
+ var saveUserButton = Functions.createElement({
+ type: "button",
+ name: "saveGenome",
+ content: '<span class="ui-icon ui-icon-disk"></span> SAVE',
+ onclick: function () {
+ return self.onSaveClicked().then(function () {
+ return self.close();
+ }).catch(GuiConnector.alert);
+ },
+ xss: false
+ });
+ var cancelButton = Functions.createElement({
+ type: "button",
+ name: "cancelGenome",
+ content: '<span class="ui-icon ui-icon-cancel"></span> CANCEL',
+ onclick: function () {
+ return self.close();
+ },
+ xss: false
+ });
+ menuRow.appendChild(saveUserButton);
+ menuRow.appendChild(cancelButton);
+
+ return result;
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
+EditGenomeDialog.prototype.createGeneMappingTabContent = function () {
+
+ var self = this;
+
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var geneMappingTable = Functions.createElement({
+ type: "table",
+ name: "geneMappingTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(geneMappingTable);
+
+ // noinspection JSUnusedGlobalSymbols
+ $(geneMappingTable).DataTable({
+ columns: [{
+ title: 'Name'
+ }, {
+ title: 'Source'
+ }, {
+ title: 'Progress'
+ }, {
+ title: 'Remove',
+ orderable: false
+ }],
+ order: [[1, "asc"]]
+ });
+
+ $(geneMappingTable).on("click", "[name='removeMapping']", function () {
+ var button = this;
+ return self.askConfirmRemoval({
+ title: "INFO",
+ content: "Do you really want to remove this gene mapping?",
+ input: false
+ }).then(function (param) {
+ if (param.status) {
+ return self.getServerConnector().removeReferenceGenomeGeneMapping({
+ mappingId: $(button).attr("data").toString(),
+ genomeId: self.getReferenceGenome().getId().toString()
+ }).then(function () {
+ return self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()});
+ }).then(function (referenceGenome) {
+ self.setReferenceGenome(referenceGenome);
+ return self.refresh();
+ });
+ }
+ }).catch(GuiConnector.alert);
+ });
+
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+ result.appendChild(menuRow);
+
+ var addGeneMappingButton = Functions.createElement({
+ type: "button",
+ name: "saveGenome",
+ content: '<span class="ui-icon ui-icon-disk"></span> ADD GENE MAPPING',
+ onclick: function () {
+ return self.openAddGeneMapping();
+ },
+ xss: false
+ });
+
+ menuRow.appendChild(addGeneMappingButton);
+
+ return result;
+};
+
+/**
+ *
+ * @returns {Promise|PromiseLike}
+ */
+EditGenomeDialog.prototype.onSaveClicked = function () {
+ var self = this;
+ if (!self.isNew()) {
+ return self.callListeners("onSave");
+ } else {
+ var genome = self.getReferenceGenome();
+ genome.setSourceUrl(self.getSourceUrl());
+ genome.setOrganism(self.getSelectedOrganism());
+ genome.setType(self.getSelectedType());
+ genome.setVersion(self.getSelectedVersion());
+ return self.getServerConnector().addReferenceGenome(genome).then(function () {
+ return self.callListeners("onSave");
+ });
+ }
+};
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @returns {Promise}
+ * @private
+ */
+EditGenomeDialog.prototype._fillOrganismSelect = function (genome) {
+ var self = this;
+ return self.getServerConnector().getReferenceGenomeOrganisms().then(function (organisms) {
+ var genomeOrganismSelect = $("[name=genomeOrganismSelect]", self.getElement());
+ genomeOrganismSelect.empty();
+ var selectedOrganism;
+ if (self.isNew()) {
+ selectedOrganism = organisms[0];
+ for (var i = 0; i < organisms.length; i++) {
+ if (organisms[i].getResource() === "9606") {
+ selectedOrganism = organisms[i];
+ }
+ }
+ } else {
+ selectedOrganism = genome.getOrganism();
+ }
+ $.each(organisms, function (i, organism) {
+ var disable = false;
+ if (organism.getResource() !== selectedOrganism.getResource() && !self.isNew()) {
+ disable = true;
+ }
+ genomeOrganismSelect.append($('<option>', {
+ value: organism.getResource(),
+ text: organism.getResource(),
+ disabled: disable
+ }));
+ });
+ genomeOrganismSelect.val(selectedOrganism.getResource());
+ return self._fillTypeSelect(genome, selectedOrganism);
+ });
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {Annotation} selectedOrganism
+ * @returns {Promise}
+ * @private
+ */
+EditGenomeDialog.prototype._fillTypeSelect = function (genome, selectedOrganism) {
+ var self = this;
+ return self.getServerConnector().getReferenceGenomeTypes({organism: selectedOrganism}).then(function (types) {
+
+ var genomeTypeSelect = $("[name=genomeTypeSelect]", self.getElement());
+ genomeTypeSelect.empty();
+
+ var selectedType;
+ if (self.isNew()) {
+ selectedType = types[0].type;
+ } else {
+ selectedType = genome.getType();
+ }
+ $.each(types, function (i, type) {
+ var disable = false;
+ if (type.type !== selectedType && !self.isNew()) {
+ disable = true;
+ }
+ genomeTypeSelect.append($('<option>', {
+ value: type.type,
+ text: type.type,
+ disabled: disable
+ }));
+ });
+ genomeTypeSelect.val(selectedType);
+ return self._fillVersionSelect(genome, selectedOrganism, selectedType);
+ })
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {Annotation} selectedOrganism
+ * @param {string} selectedType
+ * @returns {Promise}
+ * @private
+ */
+EditGenomeDialog.prototype._fillVersionSelect = function (genome, selectedOrganism, selectedType) {
+ var self = this;
+ return self.getServerConnector().getReferenceGenomeVersions({
+ organism: selectedOrganism,
+ type: selectedType
+ }).then(function (versions) {
+ var genomeVersionSelect = $("[name=genomeVersionSelect]", self.getElement());
+ genomeVersionSelect.empty();
+
+ var selectedVersion;
+ if (self.isNew()) {
+ selectedVersion = versions[0].version;
+ } else {
+ selectedVersion = genome.getVersion();
+ }
+ $.each(versions, function (i, version) {
+ var disable = false;
+ if (version.version !== selectedVersion && !self.isNew()) {
+ disable = true;
+ }
+ genomeVersionSelect.append($('<option>', {
+ value: version.version,
+ text: version.version,
+ disabled: disable
+ }));
+ });
+ genomeVersionSelect.val(selectedVersion);
+ return self._fillUrl(genome, selectedOrganism, selectedType, selectedVersion);
+ })
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {Annotation} organism
+ * @param {string} type
+ * @param {string} version
+ * @returns {Promise}
+ * @private
+ */
+EditGenomeDialog.prototype._fillUrl = function (genome, organism, type, version) {
+ var self = this;
+ var genomeSourceUrlInput = $("[name=genomeSourceUrl]", self.getElement());
+ var genomeLocalUrlInput = $("[name=genomeLocalUrl]", self.getElement());
+ var genomeProgressInput = $("[name=genomeProgress]", self.getElement());
+ genomeLocalUrlInput.prop("disabled", true);
+ genomeProgressInput.val(genome.getDownloadProgressStatus());
+ genomeProgressInput.prop("disabled", true);
+ if (!self.isNew()) {
+ genomeSourceUrlInput.val(genome.getSourceUrl());
+ genomeSourceUrlInput.prop("disabled", true);
+
+ genomeLocalUrlInput.val(genome.getLocalUrl());
+ } else {
+ genomeSourceUrlInput.prop("disabled", false);
+
+ genomeLocalUrlInput.val("");
+ return self.getServerConnector().getAvailableGenomeUrls({
+ organism: organism,
+ type: type,
+ version: version
+ }).then(function (urls) {
+ if (urls.length > 0) {
+ genomeSourceUrlInput.val(urls[0]);
+ } else {
+ genomeSourceUrlInput.val("");
+ }
+ })
+ }
+ return Promise.resolve();
+}
+;
+
+
+/**
+ *
+ * @param {ReferenceGenomeGeneMapping} geneMapping
+ * @returns {Array}
+ */
+EditGenomeDialog.prototype.geneMappingToTableRow = function (geneMapping) {
+ var row = [];
+ row[0] = geneMapping.getName();
+ row[1] = geneMapping.getSourceUrl();
+ row[2] = geneMapping.getProgress();
+ row[3] = "<button name='removeMapping' data='" + geneMapping.getId() + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
+ return row;
+};
+/**
+ *
+ * @returns {Promise}
+ */
+EditGenomeDialog.prototype.init = function () {
+ var self = this;
+
+ var detailsTable = $("[name=detailsTable]", self.getElement())[0];
+
+ // noinspection JSCheckFunctionSignatures
+ $(detailsTable).DataTable({
+ columns: [{
+ title: "Name"
+ }, {
+ title: "Value"
+ }],
+ paging: false,
+ ordering: false,
+ searching: false,
+ bInfo: false
+ });
+
+ return self.refresh();
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+EditGenomeDialog.prototype.refresh = function () {
+ var self = this;
+
+ var genome = self.getReferenceGenome();
+
+ var dataTable = $("[name=detailsTable]", self.getElement()).DataTable();
+ var data = [];
+
+ data.push(['Organism', Functions.createElement({type: "select", name: "genomeOrganismSelect"}).outerHTML]);
+ data.push(['Type', Functions.createElement({type: "select", name: "genomeTypeSelect"}).outerHTML]);
+ data.push(['Version', Functions.createElement({type: "select", name: "genomeVersionSelect"}).outerHTML]);
+ data.push(['Source url', Functions.createElement({type: "input", name: "genomeSourceUrl"}).outerHTML]);
+ data.push(['Local url', Functions.createElement({type: "input", name: "genomeLocalUrl"}).outerHTML]);
+ data.push(['Progress', Functions.createElement({type: "input", name: "genomeProgress"}).outerHTML]);
+
+ dataTable.clear().rows.add(data).draw();
+
+ dataTable = $("[name=geneMappingTable]", self.getElement()).DataTable();
+ data = [];
+ var page = dataTable.page();
+
+ for (var i = 0; i < genome.getGeneMappings().length; i++) {
+ var geneMapping = genome.getGeneMappings()[i];
+ var rowData = self.geneMappingToTableRow(geneMapping);
+ data.push(rowData);
+ }
+ //it should be simplified, but I couldn't make it work
+ dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
+
+ return self._fillOrganismSelect(genome);
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.destroy = function () {
+ var self = this;
+ var div = self.getElement();
+
+ var detailsTable = $("[name=detailsTable]", div)[0];
+ if ($.fn.DataTable.isDataTable(detailsTable)) {
+ $(detailsTable).DataTable().destroy();
+ }
+
+ var geneMappingTable = $("[name=geneMappingTable]", div)[0];
+ if ($.fn.DataTable.isDataTable(geneMappingTable)) {
+ $(geneMappingTable).DataTable().destroy();
+ }
+
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
+ }
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.open = function () {
+ var self = this;
+ var div = self.getElement();
+ var title;
+ if (self.isNew()) {
+ title = "Download genome";
+ } else {
+ var genome = self.getReferenceGenome();
+ title = genome.getType() + " " + genome.getOrganism().getResource() + " " + genome.getVersion();
+ }
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ title: title,
+ width: window.innerWidth / 2,
+ height: window.innerHeight / 2
+ });
+ }
+ $(div).dialog("open");
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.close = function () {
+ var self = this;
+ $(self.getElement()).dialog("close");
+};
+
+/**
+ *
+ * @returns {Annotation}
+ */
+EditGenomeDialog.prototype.getSelectedOrganism = function () {
+ var self = this;
+ return new Annotation({
+ resource: ($("[name='genomeOrganismSelect']", self.getElement()).val()).toString(),
+ link: '',
+ id: 0,
+ type: ''
+ })
+};
+
+/**
+ *
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.getSelectedType = function () {
+ var self = this;
+ return ($("[name='genomeTypeSelect']", self.getElement()).val()).toString();
+};
+
+/**
+ *
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.getSelectedVersion = function () {
+ var self = this;
+ return ($("[name='genomeVersionSelect']", self.getElement()).val()).toString();
+};
+
+/**
+ *
+ * @returns {string}
+ */
+EditGenomeDialog.prototype.getSourceUrl = function () {
+ var self = this;
+ return ($("[name='genomeSourceUrl']", self.getElement()).val()).toString();
+};
+
+/**
+ *
+ */
+EditGenomeDialog.prototype.openAddGeneMapping = function () {
+ var self = this;
+ var html = '<form style="z-index:10000"><span>Name: </span><input type="text" name="gene-mapping-name"><br>' +
+ '<span>Url: </span><input type="text" name="gene-mapping-url"><br></form>';
+ $(html).dialog({
+ modal: true,
+ title: "Add gene mapping",
+ close: function () {
+ $(this).dialog('destroy').remove();
+ },
+ buttons: {
+ 'ADD': function () {
+ var dialog = this;
+ var name = $('input[name="gene-mapping-name"]').val().toString();
+ var url = $('input[name="gene-mapping-url"]').val().toString();
+ return self.getServerConnector().addGeneMapping({
+ genomeId: self.getReferenceGenome().getId(),
+ mappingName: name,
+ mappingUrl: url
+ }).then(function () {
+ return self.getServerConnector().getReferenceGenome({genomeId: self.getReferenceGenome().getId()});
+ }).then(function (referenceGenome) {
+ self.setReferenceGenome(referenceGenome);
+ return self.refresh();
+ }).then(function () {
+ $(dialog).dialog('destroy').remove();
+ });
+ },
+ 'Cancel': function () {
+ $(this).dialog('destroy').remove();
+ }
+ }
+ });
+};
+
+module.exports = EditGenomeDialog;
diff --git a/frontend-js/src/main/js/gui/admin/EditUserDialog.js b/frontend-js/src/main/js/gui/admin/EditUserDialog.js
index 3030c8cab407a8ce2f5c38275cba2f4acd858435..7cf9719e85ae2c81b8da50ba758bb3f4b86dd64e 100644
--- a/frontend-js/src/main/js/gui/admin/EditUserDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditUserDialog.js
@@ -1,630 +1,630 @@
-"use strict";
-
-var Promise = require("bluebird");
-var xss = require('xss');
-
-var AbstractGuiElement = require('../AbstractGuiElement');
-var GuiConnector = require('../../GuiConnector');
-var ValidationError = require('../../ValidationError');
-
-var Functions = require('../../Functions');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-var guiUtils = new (require('../leftPanel/GuiUtils'))();
-
-function EditUserDialog(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
- self.setUser(params.user);
-
- $(self.getElement()).css({overflow: "hidden"});
-
- self.createGui();
- self.registerListenerType("onSave");
-}
-
-EditUserDialog.prototype = Object.create(AbstractGuiElement.prototype);
-EditUserDialog.prototype.constructor = EditUserDialog;
-
-EditUserDialog.prototype.setUser = function (user) {
- this._user = user;
- this.setIsNewUser(user.getLogin() === undefined);
-};
-EditUserDialog.prototype.getUser = function () {
- return this._user;
-};
-
-EditUserDialog.prototype.setIsNewUser = function (isNewUser) {
- this._isNewUser = isNewUser;
-};
-EditUserDialog.prototype.getIsNewUser = function () {
- return this._isNewUser;
-};
-
-EditUserDialog.prototype.createGui = function () {
- var self = this;
- var element = self.getElement();
-
- var tabDiv = Functions.createElement({
- type: "div",
- name: "tabView",
- className: "tabbable boxed parentTabs",
- style: "position:absolute;top:10px;bottom:40px;left:10px;right:10px"
- });
- element.appendChild(tabDiv);
-
- var tabMenuDiv = Functions.createElement({
- type: "ul",
- className: "nav nav-tabs"
- });
- tabDiv.appendChild(tabMenuDiv);
-
- var tabContentDiv = Functions.createElement({
- type: "div",
- className: "tab-content",
- style: "height:100%"
- });
- tabDiv.appendChild(tabContentDiv);
-
- self.createGeneralTab(tabMenuDiv, tabContentDiv);
- self.createPrivilegesTab(tabMenuDiv, tabContentDiv);
- self.createProjectsTab(tabMenuDiv, tabContentDiv);
- $("a", tabMenuDiv).bind("click", function () {
- //workaround for some css issues...
- tabDiv.style.top = "40px";
- tabDiv.style.bottom = "10px";
- });
-};
-
-EditUserDialog.prototype.createGeneralTab = function (tabMenuDiv, tabContentDiv) {
- var self = this;
- self.addTab({
- tabMenuDiv: tabMenuDiv,
- tabContentDiv: tabContentDiv,
- name: "DETAILS",
- content: self.createGeneralTabContent()
- });
-
-};
-
-var login_counter = 0;
-
-EditUserDialog.prototype.generateTabId = function (tab_name) {
- var self = this;
- var login = self.getUser().getLogin();
- if (login === undefined) {
- login = "new_user_" + (login_counter++);
- }
- return login.replace(".", "_") + tab_name.replace(" ", "_") + "_TAB";
-};
-
-EditUserDialog.prototype.createPrivilegesTab = function (tabMenuDiv, tabContentDiv) {
- var self = this;
- self.addTab({
- tabMenuDiv: tabMenuDiv,
- tabContentDiv: tabContentDiv,
- name: "GLOBAL PRIVILEGES",
- content: self.createPrivilegesTabContent()
- });
-
-};
-
-EditUserDialog.prototype.addTab = function (params) {
- var id = this.generateTabId(params.name);
-
- var navLi = guiUtils.createTabMenuObject({
- id: id,
- name: params.name,
- navigationBar: params.tabMenuDiv
- });
- params.tabMenuDiv.appendChild(navLi);
-
- var contentDiv = guiUtils.createTabContentObject({
- id: id,
- navigationObject: navLi,
- navigationBar: params.tabMenuDiv
- });
-
- $(contentDiv).css("overflow","auto");
- if (params.content !== undefined) {
- contentDiv.appendChild(params.content);
- }
-
- params.tabContentDiv.appendChild(contentDiv);
-};
-
-function getStringIfDefined(value) {
- if (value === undefined) {
- return "";
- }
- return xss(value);
-}
-
-EditUserDialog.prototype.createGeneralTabContent = function () {
-
- var self = this;
-
- var result = Functions.createElement({
- type: "div",
- style: "margin-top:10px;"
- });
-
- var table = Functions.createElement({
- type: "table",
- name: "detailsTable",
- className: "display",
- style: "width:100%"
- });
- result.appendChild(table);
-
- var menuRow = Functions.createElement({
- type: "div",
- className: "minerva-menu-row",
- style: "display:table-row; margin:10px"
- });
- result.appendChild(menuRow);
-
- var saveUserButton = Functions.createElement({
- type: "button",
- name: "saveUser",
- content: '<span class="ui-icon ui-icon-disk"></span> SAVE',
- onclick: function () {
- return self.onSaveClicked().then(function () {
- return self.close();
- }, GuiConnector.alert);
- },
- xss: false
- });
- var cancelButton = Functions.createElement({
- type: "button",
- name: "cancelProject",
- content: '<span class="ui-icon ui-icon-cancel"></span> CANCEL',
- onclick: function () {
- return self.close();
- },
- xss: false
- });
- menuRow.appendChild(saveUserButton);
- menuRow.appendChild(cancelButton);
-
- return result;
-
-};
-
-EditUserDialog.prototype.createPrivilegesTabContent = function () {
- var self = this;
- var result = Functions.createElement({
- type: "div",
- style: "margin-top:10px;"
- });
- result.appendChild(self._createPrivilegesTable());
- return result;
-};
-
-EditUserDialog.prototype._createPrivilegesTable = function () {
- var result = Functions.createElement({
- type: "div",
- style: "margin-top:10px;"
- });
-
- var privilegesTable = Functions.createElement({
- type: "table",
- name: "privilegesTable",
- className: "display",
- style: "width:100%"
- });
- result.appendChild(privilegesTable);
-
- return result;
-};
-
-
-EditUserDialog.prototype.createProjectsTab = function (tabMenuDiv, tabContentDiv) {
- var self = this;
- self.addTab({
- tabMenuDiv: tabMenuDiv,
- tabContentDiv: tabContentDiv,
- name: "PROJECT PRIVILEGES",
- content: self.createProjectsTabContent()
- });
-};
-
-EditUserDialog.prototype.createProjectsTabContent = function () {
- var self = this;
- var result = Functions.createElement({
- type: "div",
- style: "margin-top:10px;"
- });
- result.appendChild(self._createProjectsTable());
- return result;
-};
-
-EditUserDialog.prototype._createProjectsTable = function () {
- var result = Functions.createElement({
- type: "div",
- style: "margin-top:10px;"
- });
-
- result.appendChild(Functions.createElement({
- type: "div",
- name: "defaultProjectsRow",
- style: "width:100%"
- }));
-
- result.appendChild(Functions.createElement({
- type: "table",
- name: "projectsTable",
- className: "display",
- style: "width:100%"
- }));
-
- return result;
-};
-
-EditUserDialog.prototype.init = function () {
- var self = this;
-
- var detailsTable = $("[name=detailsTable]", self.getElement())[0];
-
- var dataTable = $(detailsTable).DataTable({
- columns: [{
- title: "Name"
- }, {
- title: "Value"
- }],
- paging: false,
- ordering: false,
- searching: false,
- bInfo: false
- });
- var data = [];
-
- var user = self.getUser();
-
- var readonly = '';
- if (user.getLogin() !== undefined) {
- readonly = ' readonly ';
- }
- data.push(['Login', '<input name="userLogin" value="' + getStringIfDefined(user.getLogin()) + '" ' + readonly + '/>']);
- data.push(['Password', '<input type="password" name="userPassword" value=""/>']);
- data.push(['Confirm password', '<input type="password" name="userPassword2" value=""/>']);
- data.push(['Name', '<input name="userName" value="' + getStringIfDefined(user.getName()) + '"/>']);
- data.push(['Surname', '<input name="userSurname" value="' + getStringIfDefined(user.getSurname()) + '"/>']);
- data.push(['Email', '<input name="userEmail" value="' + getStringIfDefined(user.getEmail()) + '"/>']);
-
- dataTable.clear().rows.add(data).draw();
-
- return self.initProjectsTab().then(function () {
- return self.refreshProjects();
- }).then(function () {
- return self.initPrivilegesTab();
- }).then(function () {
- $(window).trigger('resize');
- });
-};
-
-EditUserDialog.prototype.initProjectsTab = function () {
- var self = this;
-
- var usersTable = $("[name=projectsTable]", self.getElement())[0];
-
- var configuration;
- return ServerConnector.getConfiguration().then(function (result) {
- configuration = result;
- return self.createUserPrivilegeColumns()
- }).then(function (columns) {
- $(usersTable).DataTable({
- columns: columns
- });
- $(usersTable).on("click", "[name='project-privilege-checkbox']", function () {
- var data = $(this).attr("data").split("-");
- var privilegeType = data[0];
- var objectId = data[1];
- var value = $(this).is(":checked");
- for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
- var privilege = configuration.getPrivilegeTypes()[i];
- if (privilege.getName() === privilegeType) {
- self.getUser().setPrivilege({type: privilege, value: value, objectId: objectId});
- }
- }
- });
-
- $("[name='defaultProjectsRow']", self.getElement()).on("click", "[name='project-privilege-checkbox']", function () {
- var data = $(this).attr("data").split("-");
- var privilegeType = data[0];
- var objectId = data[1];
- var value = $(this).is(":checked");
- for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
- var privilege = configuration.getPrivilegeTypes()[i];
- if (privilege.getName() === privilegeType) {
- self.getUser().setPrivilege({type: privilege, value: value, objectId: objectId});
- }
- }
- });
-
- });
-};
-
-EditUserDialog.prototype.initPrivilegesTab = function () {
- var self = this;
-
- var usersTable = $("[name=privilegesTable]", self.getElement())[0];
-
- return ServerConnector.getConfiguration().then(function (configuration) {
- var columns = [{
- title: "Name"
- }, {
- title: "Value"
- }];
- var dataTable = $(usersTable).DataTable({
- columns: columns
- });
- var data = [];
-
- for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
- var privilege = configuration.getPrivilegeTypes()[i];
- if (privilege.getObjectType() === null) {
- if (privilege.getValueType() === "boolean") {
- var checked = "";
- if (self.getUser().hasPrivilege(privilege)) {
- checked = "checked"
- }
- data.push([
- "<span>" + privilege.getCommonName() + "</span>",
- "<input type='checkbox' name='privilege-checkbox' data='" + privilege.getName() + "' " + checked + " />"
- ]);
- } else if (privilege.getValueType() === "int") {
- data.push([
- "<span>" + privilege.getCommonName() + "</span>",
- "<input name='privilege-int' data='" + privilege.getName() + "' value='" + self.getUser().getPrivilegeValue(privilege) + "' />"
- ]);
-
- }
- }
- }
- dataTable.clear().rows.add(data).draw();
- $(usersTable).on("click", "[name='privilege-checkbox']", function () {
- var privilegeType = $(this).attr("data");
- for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
- var privilege = configuration.getPrivilegeTypes()[i];
- if (privilege.getName() === privilegeType) {
- self.getUser().setPrivilege({type: privilege, value: $(this).is(":checked")});
- }
- }
- });
- $(usersTable).on("change", "[name='privilege-int']", function () {
- var privilegeType = $(this).attr("data");
- var value = $(this).val();
- value = parseInt(value);
- if (Functions.isInt(value)) {
- for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
- var privilege = configuration.getPrivilegeTypes()[i];
- if (privilege.getName() === privilegeType) {
- self.getUser().setPrivilege({type: privilege, value: value});
- }
- }
- }
- });
- });
-};
-
-EditUserDialog.prototype.refreshProjects = function () {
- var self = this;
- return ServerConnector.getProjects().then(function (projects) {
- return self.setProjects(projects);
- });
-};
-
-EditUserDialog.prototype.setProjects = function (projects) {
- var self = this;
- self._userByLogin = [];
- return self.createUserPrivilegeColumns().then(function (columns) {
- var dataTable = $("[name='projectsTable']", self.getElement()).DataTable();
- var data = [], i;
-
- var rowData = self.projectToTableRow(null, columns);
- var defaultRow = $("[name='defaultProjectsRow']", self.getElement())[0];
- defaultRow.innerHTML = "";
- defaultRow.appendChild(Functions.createElement({
- type: "span",
- content: rowData[0],
- xss: false
- }));
- defaultRow.appendChild(Functions.createElement({type: "br"}));
- for (i = 1; i < columns.length; i++) {
- defaultRow.appendChild(Functions.createElement({
- type: "div",
- content: rowData[i] + columns[i].title,
- style: "float:left;padding:5px;",
- xss: false
- }));
- }
- defaultRow.appendChild(Functions.createElement({type: "br"}));
- defaultRow.appendChild(Functions.createElement({type: "hr"}));
- // data.push(rowData);
- for (i = 0; i < projects.length; i++) {
- var project = projects[i];
- rowData = self.projectToTableRow(project, columns);
- data.push(rowData);
- }
- dataTable.clear().rows.add(data).draw();
- });
-};
-
-EditUserDialog.prototype.projectToTableRow = function (project, columns) {
- var user = this.getUser();
- var row = [];
- var id = null;
- var projectId = "<b>DEFAULT PRIVILEGE FOR NEW PROJECT</b>";
- if (project !== null) {
- id = project.getId();
- projectId = project.getProjectId();
- }
-
- row[0] = "<span data='" + id + "'>" + projectId + "</span>";
-
- for (var i = 1; i < columns.length; i++) {
- var privilege = columns[i].privilegeType;
- var checked = "";
- if (user.hasPrivilege(privilege, id)) {
- checked = "checked";
- }
- row.push("<input type='checkbox' name='project-privilege-checkbox' data='" + privilege.getName() + "-" + id + "' " + checked + " />");
- }
-
- return row;
-};
-
-
-EditUserDialog.prototype.destroy = function () {
- var self = this;
- var div = self.getElement();
- var usersTable = $("[name=projectsTable]", div)[0];
- if ($.fn.DataTable.isDataTable(usersTable)) {
- $(usersTable).DataTable().destroy();
- }
-
- var privilegesTable = $("[name=privilegesTable]", div)[0];
- if ($.fn.DataTable.isDataTable(privilegesTable)) {
- $(privilegesTable).DataTable().destroy();
- }
-
- var detailsTable = $("[name=detailsTable]", div)[0];
- if ($.fn.DataTable.isDataTable(detailsTable)) {
- $(detailsTable).DataTable().destroy();
- }
-
-
- if ($(div).hasClass("ui-dialog-content")) {
- $(div).dialog("destroy");
- }
-};
-
-EditUserDialog.prototype.open = function () {
- var self = this;
- var div = self.getElement();
- var title = self.getUser().getLogin();
- if (title === undefined) {
- title = "NEW USER";
- }
- if (!$(div).hasClass("ui-dialog-content")) {
- $(div).dialog({
- title: title,
- width: window.innerWidth / 2,
- height: window.innerHeight / 2
- });
- }
- $(div).dialog("open");
-};
-
-EditUserDialog.prototype.onSaveClicked = function () {
- var self = this;
- var user = self.getUser();
- return self.checkValidity().then(function () {
- user.setLogin(self.getLogin());
- user.setPassword(self.getPassword());
- user.setEmail(self.getEmail());
- user.setName(self.getName());
- user.setSurname(self.getSurname());
- if (self.getIsNewUser()) {
- return ServerConnector.addUser(user);
- } else {
- return ServerConnector.updateUser(user);
- }
- }).then(function () {
- return self.callListeners("onSave", user);
- });
-};
-
-EditUserDialog.prototype.checkValidity = function () {
- var self = this;
- var isValid = true;
- var error = "<b>Some data is missing.</b><ul>";
- if (self.getPassword() !== self.getPassword2()) {
- error += "<li>Password doesn't match</li>";
- isValid = false;
- }
- if (self.getLogin() === "" || self.getLogin() === undefined || self.getLogin() === null) {
- error += "<li>Login must not be empty</li>";
- isValid = false;
- }
- var promise = Promise.resolve();
- if (self.getUser().getLogin() !== self.getLogin()) {
- promise = ServerConnector.getUser(self.getLogin()).then(function (remoteUser) {
- if (remoteUser !== null) {
- error += "<li>Login already used</li>";
- isValid = false;
- }
- });
- }
- return promise.then(function () {
- if (isValid) {
- return Promise.resolve(true);
- } else {
- return Promise.reject(new ValidationError(error));
- }
- });
-};
-
-EditUserDialog.prototype.getPassword = function () {
- var self = this;
- return $("[name='userPassword']", self.getElement()).val();
-};
-EditUserDialog.prototype.getPassword2 = function () {
- var self = this;
- return $("[name='userPassword2']", self.getElement()).val();
-};
-
-EditUserDialog.prototype.getLogin = function () {
- var self = this;
- return $("[name='userLogin']", self.getElement()).val();
-};
-
-EditUserDialog.prototype.getEmail = function () {
- var self = this;
- return $("[name='userEmail']", self.getElement()).val();
-};
-EditUserDialog.prototype.getName = function () {
- var self = this;
- return $("[name='userName']", self.getElement()).val();
-};
-EditUserDialog.prototype.getSurname = function () {
- var self = this;
- return $("[name='userSurname']", self.getElement()).val();
-};
-
-
-EditUserDialog.prototype.close = function () {
- var self = this;
- $(self.getElement()).dialog("close");
-};
-
-EditUserDialog.prototype.createUserPrivilegeColumns = function () {
- var self = this;
-
- if (self._userPrivilegeColumns !== undefined) {
- return Promise.resolve(self._userPrivilegeColumns);
- }
-
- return ServerConnector.getConfiguration().then(function (configuration) {
- self._userPrivilegeColumns = [{
- title: "ProjectId"
- }];
- var privilegeTypes = configuration.getPrivilegeTypes();
- for (var i = 0; i < privilegeTypes.length; i++) {
- var type = privilegeTypes[i];
- if (type.getObjectType() === "Project") {
- self._userPrivilegeColumns.push({
- "title": type.getCommonName(),
- privilegeType: type
- });
- }
- }
- return self._userPrivilegeColumns;
- });
-
-};
-
-
-module.exports = EditUserDialog;
+"use strict";
+
+var Promise = require("bluebird");
+var xss = require('xss');
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+var GuiConnector = require('../../GuiConnector');
+var ValidationError = require('../../ValidationError');
+
+var Functions = require('../../Functions');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var guiUtils = new (require('../leftPanel/GuiUtils'))();
+
+function EditUserDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ self.setUser(params.user);
+
+ $(self.getElement()).css({overflow: "hidden"});
+
+ self.createGui();
+ self.registerListenerType("onSave");
+}
+
+EditUserDialog.prototype = Object.create(AbstractGuiElement.prototype);
+EditUserDialog.prototype.constructor = EditUserDialog;
+
+EditUserDialog.prototype.setUser = function (user) {
+ this._user = user;
+ this.setIsNewUser(user.getLogin() === undefined);
+};
+EditUserDialog.prototype.getUser = function () {
+ return this._user;
+};
+
+EditUserDialog.prototype.setIsNewUser = function (isNewUser) {
+ this._isNewUser = isNewUser;
+};
+EditUserDialog.prototype.getIsNewUser = function () {
+ return this._isNewUser;
+};
+
+EditUserDialog.prototype.createGui = function () {
+ var self = this;
+ var element = self.getElement();
+
+ var tabDiv = Functions.createElement({
+ type: "div",
+ name: "tabView",
+ className: "tabbable boxed parentTabs",
+ style: "position:absolute;top:10px;bottom:40px;left:10px;right:10px"
+ });
+ element.appendChild(tabDiv);
+
+ var tabMenuDiv = Functions.createElement({
+ type: "ul",
+ className: "nav nav-tabs"
+ });
+ tabDiv.appendChild(tabMenuDiv);
+
+ var tabContentDiv = Functions.createElement({
+ type: "div",
+ className: "tab-content",
+ style: "height:100%"
+ });
+ tabDiv.appendChild(tabContentDiv);
+
+ self.createGeneralTab(tabMenuDiv, tabContentDiv);
+ self.createPrivilegesTab(tabMenuDiv, tabContentDiv);
+ self.createProjectsTab(tabMenuDiv, tabContentDiv);
+ $("a", tabMenuDiv).bind("click", function () {
+ //workaround for some css issues...
+ tabDiv.style.top = "40px";
+ tabDiv.style.bottom = "10px";
+ });
+};
+
+EditUserDialog.prototype.createGeneralTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "DETAILS",
+ content: self.createGeneralTabContent()
+ });
+
+};
+
+var login_counter = 0;
+
+EditUserDialog.prototype.generateTabId = function (tab_name) {
+ var self = this;
+ var login = self.getUser().getLogin();
+ if (login === undefined) {
+ login = "new_user_" + (login_counter++);
+ }
+ return login.replace(".", "_") + tab_name.replace(" ", "_") + "_TAB";
+};
+
+EditUserDialog.prototype.createPrivilegesTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "GLOBAL PRIVILEGES",
+ content: self.createPrivilegesTabContent()
+ });
+
+};
+
+EditUserDialog.prototype.addTab = function (params) {
+ var id = this.generateTabId(params.name);
+
+ var navLi = guiUtils.createTabMenuObject({
+ id: id,
+ name: params.name,
+ navigationBar: params.tabMenuDiv
+ });
+ params.tabMenuDiv.appendChild(navLi);
+
+ var contentDiv = guiUtils.createTabContentObject({
+ id: id,
+ navigationObject: navLi,
+ navigationBar: params.tabMenuDiv
+ });
+
+ $(contentDiv).css("overflow","auto");
+ if (params.content !== undefined) {
+ contentDiv.appendChild(params.content);
+ }
+
+ params.tabContentDiv.appendChild(contentDiv);
+};
+
+function getStringIfDefined(value) {
+ if (value === undefined) {
+ return "";
+ }
+ return xss(value);
+}
+
+EditUserDialog.prototype.createGeneralTabContent = function () {
+
+ var self = this;
+
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var table = Functions.createElement({
+ type: "table",
+ name: "detailsTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(table);
+
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+ result.appendChild(menuRow);
+
+ var saveUserButton = Functions.createElement({
+ type: "button",
+ name: "saveUser",
+ content: '<span class="ui-icon ui-icon-disk"></span> SAVE',
+ onclick: function () {
+ return self.onSaveClicked().then(function () {
+ return self.close();
+ }, GuiConnector.alert);
+ },
+ xss: false
+ });
+ var cancelButton = Functions.createElement({
+ type: "button",
+ name: "cancelProject",
+ content: '<span class="ui-icon ui-icon-cancel"></span> CANCEL',
+ onclick: function () {
+ return self.close();
+ },
+ xss: false
+ });
+ menuRow.appendChild(saveUserButton);
+ menuRow.appendChild(cancelButton);
+
+ return result;
+
+};
+
+EditUserDialog.prototype.createPrivilegesTabContent = function () {
+ var self = this;
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+ result.appendChild(self._createPrivilegesTable());
+ return result;
+};
+
+EditUserDialog.prototype._createPrivilegesTable = function () {
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var privilegesTable = Functions.createElement({
+ type: "table",
+ name: "privilegesTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(privilegesTable);
+
+ return result;
+};
+
+
+EditUserDialog.prototype.createProjectsTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "PROJECT PRIVILEGES",
+ content: self.createProjectsTabContent()
+ });
+};
+
+EditUserDialog.prototype.createProjectsTabContent = function () {
+ var self = this;
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+ result.appendChild(self._createProjectsTable());
+ return result;
+};
+
+EditUserDialog.prototype._createProjectsTable = function () {
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ result.appendChild(Functions.createElement({
+ type: "div",
+ name: "defaultProjectsRow",
+ style: "width:100%"
+ }));
+
+ result.appendChild(Functions.createElement({
+ type: "table",
+ name: "projectsTable",
+ className: "display",
+ style: "width:100%"
+ }));
+
+ return result;
+};
+
+EditUserDialog.prototype.init = function () {
+ var self = this;
+
+ var detailsTable = $("[name=detailsTable]", self.getElement())[0];
+
+ var dataTable = $(detailsTable).DataTable({
+ columns: [{
+ title: "Name"
+ }, {
+ title: "Value"
+ }],
+ paging: false,
+ ordering: false,
+ searching: false,
+ bInfo: false
+ });
+ var data = [];
+
+ var user = self.getUser();
+
+ var readonly = '';
+ if (user.getLogin() !== undefined) {
+ readonly = ' readonly ';
+ }
+ data.push(['Login', '<input name="userLogin" value="' + getStringIfDefined(user.getLogin()) + '" ' + readonly + '/>']);
+ data.push(['Password', '<input type="password" name="userPassword" value=""/>']);
+ data.push(['Confirm password', '<input type="password" name="userPassword2" value=""/>']);
+ data.push(['Name', '<input name="userName" value="' + getStringIfDefined(user.getName()) + '"/>']);
+ data.push(['Surname', '<input name="userSurname" value="' + getStringIfDefined(user.getSurname()) + '"/>']);
+ data.push(['Email', '<input name="userEmail" value="' + getStringIfDefined(user.getEmail()) + '"/>']);
+
+ dataTable.clear().rows.add(data).draw();
+
+ return self.initProjectsTab().then(function () {
+ return self.refreshProjects();
+ }).then(function () {
+ return self.initPrivilegesTab();
+ }).then(function () {
+ $(window).trigger('resize');
+ });
+};
+
+EditUserDialog.prototype.initProjectsTab = function () {
+ var self = this;
+
+ var usersTable = $("[name=projectsTable]", self.getElement())[0];
+
+ var configuration;
+ return ServerConnector.getConfiguration().then(function (result) {
+ configuration = result;
+ return self.createUserPrivilegeColumns()
+ }).then(function (columns) {
+ $(usersTable).DataTable({
+ columns: columns
+ });
+ $(usersTable).on("click", "[name='project-privilege-checkbox']", function () {
+ var data = $(this).attr("data").split("-");
+ var privilegeType = data[0];
+ var objectId = data[1];
+ var value = $(this).is(":checked");
+ for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
+ var privilege = configuration.getPrivilegeTypes()[i];
+ if (privilege.getName() === privilegeType) {
+ self.getUser().setPrivilege({type: privilege, value: value, objectId: objectId});
+ }
+ }
+ });
+
+ $("[name='defaultProjectsRow']", self.getElement()).on("click", "[name='project-privilege-checkbox']", function () {
+ var data = $(this).attr("data").split("-");
+ var privilegeType = data[0];
+ var objectId = data[1];
+ var value = $(this).is(":checked");
+ for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
+ var privilege = configuration.getPrivilegeTypes()[i];
+ if (privilege.getName() === privilegeType) {
+ self.getUser().setPrivilege({type: privilege, value: value, objectId: objectId});
+ }
+ }
+ });
+
+ });
+};
+
+EditUserDialog.prototype.initPrivilegesTab = function () {
+ var self = this;
+
+ var usersTable = $("[name=privilegesTable]", self.getElement())[0];
+
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ var columns = [{
+ title: "Name"
+ }, {
+ title: "Value"
+ }];
+ var dataTable = $(usersTable).DataTable({
+ columns: columns
+ });
+ var data = [];
+
+ for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
+ var privilege = configuration.getPrivilegeTypes()[i];
+ if (privilege.getObjectType() === null) {
+ if (privilege.getValueType() === "boolean") {
+ var checked = "";
+ if (self.getUser().hasPrivilege(privilege)) {
+ checked = "checked"
+ }
+ data.push([
+ "<span>" + privilege.getCommonName() + "</span>",
+ "<input type='checkbox' name='privilege-checkbox' data='" + privilege.getName() + "' " + checked + " />"
+ ]);
+ } else if (privilege.getValueType() === "int") {
+ data.push([
+ "<span>" + privilege.getCommonName() + "</span>",
+ "<input name='privilege-int' data='" + privilege.getName() + "' value='" + self.getUser().getPrivilegeValue(privilege) + "' />"
+ ]);
+
+ }
+ }
+ }
+ dataTable.clear().rows.add(data).draw();
+ $(usersTable).on("click", "[name='privilege-checkbox']", function () {
+ var privilegeType = $(this).attr("data");
+ for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
+ var privilege = configuration.getPrivilegeTypes()[i];
+ if (privilege.getName() === privilegeType) {
+ self.getUser().setPrivilege({type: privilege, value: $(this).is(":checked")});
+ }
+ }
+ });
+ $(usersTable).on("change", "[name='privilege-int']", function () {
+ var privilegeType = $(this).attr("data");
+ var value = $(this).val();
+ value = parseInt(value);
+ if (Functions.isInt(value)) {
+ for (var i = 0; i < configuration.getPrivilegeTypes().length; i++) {
+ var privilege = configuration.getPrivilegeTypes()[i];
+ if (privilege.getName() === privilegeType) {
+ self.getUser().setPrivilege({type: privilege, value: value});
+ }
+ }
+ }
+ });
+ });
+};
+
+EditUserDialog.prototype.refreshProjects = function () {
+ var self = this;
+ return ServerConnector.getProjects().then(function (projects) {
+ return self.setProjects(projects);
+ });
+};
+
+EditUserDialog.prototype.setProjects = function (projects) {
+ var self = this;
+ self._userByLogin = [];
+ return self.createUserPrivilegeColumns().then(function (columns) {
+ var dataTable = $("[name='projectsTable']", self.getElement()).DataTable();
+ var data = [], i;
+
+ var rowData = self.projectToTableRow(null, columns);
+ var defaultRow = $("[name='defaultProjectsRow']", self.getElement())[0];
+ defaultRow.innerHTML = "";
+ defaultRow.appendChild(Functions.createElement({
+ type: "span",
+ content: rowData[0],
+ xss: false
+ }));
+ defaultRow.appendChild(Functions.createElement({type: "br"}));
+ for (i = 1; i < columns.length; i++) {
+ defaultRow.appendChild(Functions.createElement({
+ type: "div",
+ content: rowData[i] + columns[i].title,
+ style: "float:left;padding:5px;",
+ xss: false
+ }));
+ }
+ defaultRow.appendChild(Functions.createElement({type: "br"}));
+ defaultRow.appendChild(Functions.createElement({type: "hr"}));
+ // data.push(rowData);
+ for (i = 0; i < projects.length; i++) {
+ var project = projects[i];
+ rowData = self.projectToTableRow(project, columns);
+ data.push(rowData);
+ }
+ dataTable.clear().rows.add(data).draw();
+ });
+};
+
+EditUserDialog.prototype.projectToTableRow = function (project, columns) {
+ var user = this.getUser();
+ var row = [];
+ var id = null;
+ var projectId = "<b>DEFAULT PRIVILEGE FOR NEW PROJECT</b>";
+ if (project !== null) {
+ id = project.getId();
+ projectId = project.getProjectId();
+ }
+
+ row[0] = "<span data='" + id + "'>" + projectId + "</span>";
+
+ for (var i = 1; i < columns.length; i++) {
+ var privilege = columns[i].privilegeType;
+ var checked = "";
+ if (user.hasPrivilege(privilege, id)) {
+ checked = "checked";
+ }
+ row.push("<input type='checkbox' name='project-privilege-checkbox' data='" + privilege.getName() + "-" + id + "' " + checked + " />");
+ }
+
+ return row;
+};
+
+
+EditUserDialog.prototype.destroy = function () {
+ var self = this;
+ var div = self.getElement();
+ var usersTable = $("[name=projectsTable]", div)[0];
+ if ($.fn.DataTable.isDataTable(usersTable)) {
+ $(usersTable).DataTable().destroy();
+ }
+
+ var privilegesTable = $("[name=privilegesTable]", div)[0];
+ if ($.fn.DataTable.isDataTable(privilegesTable)) {
+ $(privilegesTable).DataTable().destroy();
+ }
+
+ var detailsTable = $("[name=detailsTable]", div)[0];
+ if ($.fn.DataTable.isDataTable(detailsTable)) {
+ $(detailsTable).DataTable().destroy();
+ }
+
+
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
+ }
+};
+
+EditUserDialog.prototype.open = function () {
+ var self = this;
+ var div = self.getElement();
+ var title = self.getUser().getLogin();
+ if (title === undefined) {
+ title = "NEW USER";
+ }
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ title: title,
+ width: window.innerWidth / 2,
+ height: window.innerHeight / 2
+ });
+ }
+ $(div).dialog("open");
+};
+
+EditUserDialog.prototype.onSaveClicked = function () {
+ var self = this;
+ var user = self.getUser();
+ return self.checkValidity().then(function () {
+ user.setLogin(self.getLogin());
+ user.setPassword(self.getPassword());
+ user.setEmail(self.getEmail());
+ user.setName(self.getName());
+ user.setSurname(self.getSurname());
+ if (self.getIsNewUser()) {
+ return ServerConnector.addUser(user);
+ } else {
+ return ServerConnector.updateUser(user);
+ }
+ }).then(function () {
+ return self.callListeners("onSave", user);
+ });
+};
+
+EditUserDialog.prototype.checkValidity = function () {
+ var self = this;
+ var isValid = true;
+ var error = "<b>Some data is missing.</b><ul>";
+ if (self.getPassword() !== self.getPassword2()) {
+ error += "<li>Password doesn't match</li>";
+ isValid = false;
+ }
+ if (self.getLogin() === "" || self.getLogin() === undefined || self.getLogin() === null) {
+ error += "<li>Login must not be empty</li>";
+ isValid = false;
+ }
+ var promise = Promise.resolve();
+ if (self.getUser().getLogin() !== self.getLogin()) {
+ promise = ServerConnector.getUser(self.getLogin()).then(function (remoteUser) {
+ if (remoteUser !== null) {
+ error += "<li>Login already used</li>";
+ isValid = false;
+ }
+ });
+ }
+ return promise.then(function () {
+ if (isValid) {
+ return Promise.resolve(true);
+ } else {
+ return Promise.reject(new ValidationError(error));
+ }
+ });
+};
+
+EditUserDialog.prototype.getPassword = function () {
+ var self = this;
+ return $("[name='userPassword']", self.getElement()).val();
+};
+EditUserDialog.prototype.getPassword2 = function () {
+ var self = this;
+ return $("[name='userPassword2']", self.getElement()).val();
+};
+
+EditUserDialog.prototype.getLogin = function () {
+ var self = this;
+ return $("[name='userLogin']", self.getElement()).val();
+};
+
+EditUserDialog.prototype.getEmail = function () {
+ var self = this;
+ return $("[name='userEmail']", self.getElement()).val();
+};
+EditUserDialog.prototype.getName = function () {
+ var self = this;
+ return $("[name='userName']", self.getElement()).val();
+};
+EditUserDialog.prototype.getSurname = function () {
+ var self = this;
+ return $("[name='userSurname']", self.getElement()).val();
+};
+
+
+EditUserDialog.prototype.close = function () {
+ var self = this;
+ $(self.getElement()).dialog("close");
+};
+
+EditUserDialog.prototype.createUserPrivilegeColumns = function () {
+ var self = this;
+
+ if (self._userPrivilegeColumns !== undefined) {
+ return Promise.resolve(self._userPrivilegeColumns);
+ }
+
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ self._userPrivilegeColumns = [{
+ title: "ProjectId"
+ }];
+ var privilegeTypes = configuration.getPrivilegeTypes();
+ for (var i = 0; i < privilegeTypes.length; i++) {
+ var type = privilegeTypes[i];
+ if (type.getObjectType() === "Project") {
+ self._userPrivilegeColumns.push({
+ "title": type.getCommonName(),
+ privilegeType: type
+ });
+ }
+ }
+ return self._userPrivilegeColumns;
+ });
+
+};
+
+
+module.exports = EditUserDialog;
diff --git a/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
index 7abf854ec353de6035bb7ca3caf24739982c2efd..afece10d70d1c7d0ee1dcb3574f75b270ccf6c8b 100644
--- a/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/GenomeAdminPanel.js
@@ -1,326 +1,326 @@
-"use strict";
-
-var AbstractAdminPanel = require('./AbstractAdminPanel');
-var EditGenomeDialog = require('./EditGenomeDialog');
-
-var Functions = require('../../Functions');
-var GuiConnector = require('../../GuiConnector');
-var PrivilegeType = require('../../map/data/PrivilegeType');
-var ReferenceGenome = require('../../map/data/ReferenceGenome');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-var Promise = require('bluebird');
-
-/**
- *
- * @param {Configuration} params.configuration
- * @param {HTMLElement} params.element
- *
- * @constructor
- */
-function GenomeAdminPanel(params) {
- params["panelName"] = "genomes";
- AbstractAdminPanel.call(this, params);
-
- var self = this;
- $(self.getElement()).addClass("minerva-genome-tab");
-
- self._createGui();
-}
-
-GenomeAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
-GenomeAdminPanel.prototype.constructor = GenomeAdminPanel;
-
-/**
- *
- * @private
- */
-GenomeAdminPanel.prototype._createGui = function () {
- var self = this;
- var genomeDiv = Functions.createElement({
- type: "div"
- });
- self.getElement().appendChild(genomeDiv);
-
- genomeDiv.appendChild(self._createMenuRow());
-
- var genomesTable = Functions.createElement({
- type: "table",
- name: "genomeTable",
- className: "display",
- style: "width:100%"
- });
- genomeDiv.appendChild(genomesTable);
-
- // noinspection JSUnusedGlobalSymbols
- $(genomesTable).DataTable({
- columns: [{
- title: 'Type'
- }, {
- title: 'Organism'
- }, {
- title: 'Version'
- }, {
- title: 'Progress'
- }, {
- title: 'Source'
- }, {
- title: 'Edit',
- orderable: false
- }, {
- title: 'Remove',
- orderable: false
- }],
- order: [[1, "asc"]]
- });
- self.bindUserGuiPreference({
- jQueryObject: $(genomesTable),
- event: 'length.dt',
- preferenceName: 'admin-genome-datatable-length',
- defaultValue: '10',
- getter: function () {
- return $(genomesTable).DataTable().page.len() + '';
- },
- setter: function (value) {
- return $(genomesTable).DataTable().page.len(value).draw();
- }
- });
-
- $(genomesTable).on("click", "[name='removeGenome']", function () {
- var button = this;
- return self.askConfirmRemoval({
- title: "INFO",
- content: "Do you really want to remove this genome?",
- input: false
- }).then(function (param) {
- if (param.status) {
- return self.getServerConnector().removeReferenceGenome({genomeId: $(button).attr("data")});
- }
- }).catch(GuiConnector.alert);
- });
-
- $(genomesTable).on("click", "[name='editGenome']", function () {
- var button = this;
- return self.showEditDialog(parseInt($(button).attr("data"))).catch(GuiConnector.alert);
- });
-
- genomeDiv.appendChild(self._createMenuRow());
-
-};
-
-/**
- *
- * @returns {HTMLElement}
- * @private
- */
-GenomeAdminPanel.prototype._createMenuRow = function () {
- var self = this;
- var menuRow = Functions.createElement({
- type: "div",
- className: "minerva-menu-row",
- style: "display:table-row; margin:10px"
- });
-
- var addProjectButton = Functions.createElement({
- type: "button",
- name: "addGenome",
- content: '<span class="ui-icon ui-icon-circle-plus"></span> ADD GENOME',
- onclick: function () {
- return self.onAddClicked().catch(GuiConnector.alert);
- },
- xss: false
- });
- var refreshButton = Functions.createElement({
- type: "button",
- name: "refreshGenomes",
- content: '<span class="ui-icon ui-icon-refresh"></span> REFRESH',
- onclick: function () {
- return self.onRefreshClicked().catch(GuiConnector.alert);
- },
- xss: false
- });
- menuRow.appendChild(addProjectButton);
- menuRow.appendChild(refreshButton);
- return menuRow;
-};
-
-/**
- *
- * @returns {Promise}
- */
-GenomeAdminPanel.prototype.init = function () {
- var self = this;
- return AbstractAdminPanel.prototype.init.call(this).then(function () {
- return self.getServerConnector().getLoggedUser();
- }).then(function (user) {
- if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.MANAGE_GENOMES))) {
- return self.onRefreshClicked();
- } else {
- self.disablePanel("You have no privilege to manage genomes");
- }
- });
-};
-
-/**
- *
- * @returns {Promise}
- */
-GenomeAdminPanel.prototype.onRefreshClicked = function () {
- var self = this;
- return self.getServerConnector().getReferenceGenomes().then(function (referenceGenomes) {
- return self.setReferenceGenomes(referenceGenomes);
- });
-};
-
-/**
- *
- * @param {ReferenceGenome[]} referenceGenomes
- *
- * @returns {Promise}
- *
- */
-GenomeAdminPanel.prototype.setReferenceGenomes = function (referenceGenomes) {
- var self = this;
-
- return self.getServerConnector().getLoggedUser().then(function (user) {
-
- var dataTable = $("[name='genomeTable']", self.getElement()).DataTable();
- var data = [];
- var page = dataTable.page();
-
- for (var i = 0; i < referenceGenomes.length; i++) {
- var genome = referenceGenomes[i];
- var rowData = self.genomeToTableRow(genome, user);
- data.push(rowData);
- }
- //it should be simplified, but I couldn't make it work
- dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
- })
-};
-
-/**
- *
- * @param {ReferenceGenome} genome
- * @param {User} user
- * @returns {Array}
- */
-GenomeAdminPanel.prototype.genomeToTableRow = function (genome, user) {
- var self = this;
- var row = [];
-
- row[0] = genome.getType();
- row[1] = self.getGuiUtils().createAnnotationLink(genome.getOrganism()).outerHTML;
- row[2] = genome.getVersion();
- row[3] = genome.getDownloadProgressStatus();
- row[4] = genome.getSourceUrl();
-
- var disabled = " disabled ";
- if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.MANAGE_GENOMES))) {
- disabled = "";
- }
- row[5] = "<button name='editGenome' data='" + genome.getId() + "'" + disabled + "><i class='fa fa-edit' style='font-size:17px'></i></button>";
- row[6] = "<button name='removeGenome' data='" + genome.getId() + "'" + disabled + "><i class='fa fa-trash-o' style='font-size:17px'></button>";
- return row;
-};
-
-
-/**
- *
- * @returns {Promise}
- */
-GenomeAdminPanel.prototype.destroy = function () {
- var self = this;
- var table = $("[name='genomeTable']", self.getElement())[0];
- if ($.fn.DataTable.isDataTable(table)) {
- $(table).DataTable().destroy();
- }
- var promises = [];
- for (var key in self._dialogs) {
- if (self._dialogs.hasOwnProperty(key)) {
- promises.push(self._dialogs[key].destroy());
- }
- }
- promises.push(AbstractAdminPanel.prototype.destroy.call(self));
-
- return Promise.all(promises);
-};
-
-/**
- *
- * @param {ReferenceGenome} [genome]
- * @returns {Promise}
- */
-GenomeAdminPanel.prototype.getDialog = function (genome) {
- var self = this;
- if (self._dialogs === undefined) {
- self._dialogs = [];
- }
- var id = genome.getId();
- var dialog = self._dialogs[id];
- if (dialog === undefined) {
- dialog = new EditGenomeDialog({
- element: Functions.createElement({
- type: "div"
- }),
- configuration: self.getConfiguration(),
- referenceGenome: genome,
- customMap: null,
- serverConnector: self.getServerConnector()
- });
- self._dialogs[id] = dialog;
- if (id === undefined) {
- dialog.addListener("onSave", function () {
- return self.onRefreshClicked();
- });
- }
- return dialog.init().then(function () {
- return dialog;
- });
- } else {
- return Promise.resolve(dialog);
- }
-};
-
-/**
- *
- * @param {number} id
- * @returns {Promise}
- */
-GenomeAdminPanel.prototype.showEditDialog = function (id) {
- var self = this;
- GuiConnector.showProcessing();
- return self.getServerConnector().getReferenceGenome({genomeId: id}).then(function (referenceGenome) {
- if (referenceGenome === null) {
- referenceGenome = new ReferenceGenome();
- }
- return self.getDialog(referenceGenome);
- }).then(function (dialog) {
- dialog.open();
- GuiConnector.hideProcessing();
- }).catch(function (error) {
- GuiConnector.hideProcessing();
- return Promise.reject(error);
- });
-};
-
-/**
- *
- * @returns {Promise}
- */
-GenomeAdminPanel.prototype.onAddClicked = function () {
- var self = this;
- GuiConnector.showProcessing();
- var referenceGenome = new ReferenceGenome();
- return self.getDialog(referenceGenome).then(function (dialog) {
- dialog.open();
- GuiConnector.hideProcessing();
- }).catch(function (error) {
- GuiConnector.hideProcessing();
- return Promise.reject(error);
- });
-};
-
-
-module.exports = GenomeAdminPanel;
+"use strict";
+
+var AbstractAdminPanel = require('./AbstractAdminPanel');
+var EditGenomeDialog = require('./EditGenomeDialog');
+
+var Functions = require('../../Functions');
+var GuiConnector = require('../../GuiConnector');
+var PrivilegeType = require('../../map/data/PrivilegeType');
+var ReferenceGenome = require('../../map/data/ReferenceGenome');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var Promise = require('bluebird');
+
+/**
+ *
+ * @param {Configuration} params.configuration
+ * @param {HTMLElement} params.element
+ *
+ * @constructor
+ */
+function GenomeAdminPanel(params) {
+ params["panelName"] = "genomes";
+ AbstractAdminPanel.call(this, params);
+
+ var self = this;
+ $(self.getElement()).addClass("minerva-genome-tab");
+
+ self._createGui();
+}
+
+GenomeAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
+GenomeAdminPanel.prototype.constructor = GenomeAdminPanel;
+
+/**
+ *
+ * @private
+ */
+GenomeAdminPanel.prototype._createGui = function () {
+ var self = this;
+ var genomeDiv = Functions.createElement({
+ type: "div"
+ });
+ self.getElement().appendChild(genomeDiv);
+
+ genomeDiv.appendChild(self._createMenuRow());
+
+ var genomesTable = Functions.createElement({
+ type: "table",
+ name: "genomeTable",
+ className: "display",
+ style: "width:100%"
+ });
+ genomeDiv.appendChild(genomesTable);
+
+ // noinspection JSUnusedGlobalSymbols
+ $(genomesTable).DataTable({
+ columns: [{
+ title: 'Type'
+ }, {
+ title: 'Organism'
+ }, {
+ title: 'Version'
+ }, {
+ title: 'Progress'
+ }, {
+ title: 'Source'
+ }, {
+ title: 'Edit',
+ orderable: false
+ }, {
+ title: 'Remove',
+ orderable: false
+ }],
+ order: [[1, "asc"]]
+ });
+ self.bindUserGuiPreference({
+ jQueryObject: $(genomesTable),
+ event: 'length.dt',
+ preferenceName: 'admin-genome-datatable-length',
+ defaultValue: '10',
+ getter: function () {
+ return $(genomesTable).DataTable().page.len() + '';
+ },
+ setter: function (value) {
+ return $(genomesTable).DataTable().page.len(value).draw();
+ }
+ });
+
+ $(genomesTable).on("click", "[name='removeGenome']", function () {
+ var button = this;
+ return self.askConfirmRemoval({
+ title: "INFO",
+ content: "Do you really want to remove this genome?",
+ input: false
+ }).then(function (param) {
+ if (param.status) {
+ return self.getServerConnector().removeReferenceGenome({genomeId: $(button).attr("data")});
+ }
+ }).catch(GuiConnector.alert);
+ });
+
+ $(genomesTable).on("click", "[name='editGenome']", function () {
+ var button = this;
+ return self.showEditDialog(parseInt($(button).attr("data"))).catch(GuiConnector.alert);
+ });
+
+ genomeDiv.appendChild(self._createMenuRow());
+
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
+GenomeAdminPanel.prototype._createMenuRow = function () {
+ var self = this;
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+
+ var addProjectButton = Functions.createElement({
+ type: "button",
+ name: "addGenome",
+ content: '<span class="ui-icon ui-icon-circle-plus"></span> ADD GENOME',
+ onclick: function () {
+ return self.onAddClicked().catch(GuiConnector.alert);
+ },
+ xss: false
+ });
+ var refreshButton = Functions.createElement({
+ type: "button",
+ name: "refreshGenomes",
+ content: '<span class="ui-icon ui-icon-refresh"></span> REFRESH',
+ onclick: function () {
+ return self.onRefreshClicked().catch(GuiConnector.alert);
+ },
+ xss: false
+ });
+ menuRow.appendChild(addProjectButton);
+ menuRow.appendChild(refreshButton);
+ return menuRow;
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.init = function () {
+ var self = this;
+ return AbstractAdminPanel.prototype.init.call(this).then(function () {
+ return self.getServerConnector().getLoggedUser();
+ }).then(function (user) {
+ if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.MANAGE_GENOMES))) {
+ return self.onRefreshClicked();
+ } else {
+ self.disablePanel("You have no privilege to manage genomes");
+ }
+ });
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.onRefreshClicked = function () {
+ var self = this;
+ return self.getServerConnector().getReferenceGenomes().then(function (referenceGenomes) {
+ return self.setReferenceGenomes(referenceGenomes);
+ });
+};
+
+/**
+ *
+ * @param {ReferenceGenome[]} referenceGenomes
+ *
+ * @returns {Promise}
+ *
+ */
+GenomeAdminPanel.prototype.setReferenceGenomes = function (referenceGenomes) {
+ var self = this;
+
+ return self.getServerConnector().getLoggedUser().then(function (user) {
+
+ var dataTable = $("[name='genomeTable']", self.getElement()).DataTable();
+ var data = [];
+ var page = dataTable.page();
+
+ for (var i = 0; i < referenceGenomes.length; i++) {
+ var genome = referenceGenomes[i];
+ var rowData = self.genomeToTableRow(genome, user);
+ data.push(rowData);
+ }
+ //it should be simplified, but I couldn't make it work
+ dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
+ })
+};
+
+/**
+ *
+ * @param {ReferenceGenome} genome
+ * @param {User} user
+ * @returns {Array}
+ */
+GenomeAdminPanel.prototype.genomeToTableRow = function (genome, user) {
+ var self = this;
+ var row = [];
+
+ row[0] = genome.getType();
+ row[1] = self.getGuiUtils().createAnnotationLink(genome.getOrganism()).outerHTML;
+ row[2] = genome.getVersion();
+ row[3] = genome.getDownloadProgressStatus();
+ row[4] = genome.getSourceUrl();
+
+ var disabled = " disabled ";
+ if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.MANAGE_GENOMES))) {
+ disabled = "";
+ }
+ row[5] = "<button name='editGenome' data='" + genome.getId() + "'" + disabled + "><i class='fa fa-edit' style='font-size:17px'></i></button>";
+ row[6] = "<button name='removeGenome' data='" + genome.getId() + "'" + disabled + "><i class='fa fa-trash-o' style='font-size:17px'></button>";
+ return row;
+};
+
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.destroy = function () {
+ var self = this;
+ var table = $("[name='genomeTable']", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(table)) {
+ $(table).DataTable().destroy();
+ }
+ var promises = [];
+ for (var key in self._dialogs) {
+ if (self._dialogs.hasOwnProperty(key)) {
+ promises.push(self._dialogs[key].destroy());
+ }
+ }
+ promises.push(AbstractAdminPanel.prototype.destroy.call(self));
+
+ return Promise.all(promises);
+};
+
+/**
+ *
+ * @param {ReferenceGenome} [genome]
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.getDialog = function (genome) {
+ var self = this;
+ if (self._dialogs === undefined) {
+ self._dialogs = [];
+ }
+ var id = genome.getId();
+ var dialog = self._dialogs[id];
+ if (dialog === undefined) {
+ dialog = new EditGenomeDialog({
+ element: Functions.createElement({
+ type: "div"
+ }),
+ configuration: self.getConfiguration(),
+ referenceGenome: genome,
+ customMap: null,
+ serverConnector: self.getServerConnector()
+ });
+ self._dialogs[id] = dialog;
+ if (id === undefined) {
+ dialog.addListener("onSave", function () {
+ return self.onRefreshClicked();
+ });
+ }
+ return dialog.init().then(function () {
+ return dialog;
+ });
+ } else {
+ return Promise.resolve(dialog);
+ }
+};
+
+/**
+ *
+ * @param {number} id
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.showEditDialog = function (id) {
+ var self = this;
+ GuiConnector.showProcessing();
+ return self.getServerConnector().getReferenceGenome({genomeId: id}).then(function (referenceGenome) {
+ if (referenceGenome === null) {
+ referenceGenome = new ReferenceGenome();
+ }
+ return self.getDialog(referenceGenome);
+ }).then(function (dialog) {
+ dialog.open();
+ GuiConnector.hideProcessing();
+ }).catch(function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+GenomeAdminPanel.prototype.onAddClicked = function () {
+ var self = this;
+ GuiConnector.showProcessing();
+ var referenceGenome = new ReferenceGenome();
+ return self.getDialog(referenceGenome).then(function (dialog) {
+ dialog.open();
+ GuiConnector.hideProcessing();
+ }).catch(function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+
+module.exports = GenomeAdminPanel;
diff --git a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
index f09ccc985410b0478df811e8365d18119e36d6d6..e99f74c9480b6ddd4042797ff7550fbf2d400d5c 100644
--- a/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/MapsAdminPanel.js
@@ -1,433 +1,433 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractAdminPanel = require('./AbstractAdminPanel');
-var AddProjectDialog = require('./AddProjectDialog');
-var EditProjectDialog = require('./EditProjectDialog');
-var LogListDialog = require('./LogListDialog');
-var PrivilegeType = require('../../map/data/PrivilegeType');
-var UserPreferences = require('../../map/data/UserPreferences');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-var Functions = require('../../Functions');
-var GuiConnector = require('../../GuiConnector');
-var Promise = require("bluebird");
-
-function MapsAdminPanel(params) {
- var self = this;
- AbstractAdminPanel.call(self, params);
- self._createGui();
-
- $(self.getElement()).addClass("minerva-projects-tab");
-
-}
-
-MapsAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
-MapsAdminPanel.prototype.constructor = MapsAdminPanel;
-
-MapsAdminPanel.prototype._createGui = function () {
- var self = this;
- var projectsDiv = Functions.createElement({
- type: "div"
- });
- self.getElement().appendChild(projectsDiv);
-
- var dataDiv = Functions.createElement({
- type: "div",
- style: "display:table; width:100%"
- });
- projectsDiv.appendChild(dataDiv);
-
- dataDiv.appendChild(self._createMenuRow());
- dataDiv.appendChild(self._createProjectTableRow());
- dataDiv.appendChild(self._createMenuRow());
-
-};
-
-MapsAdminPanel.prototype._createMenuRow = function () {
- var self = this;
- var menuRow = Functions.createElement({
- type: "div",
- className: "minerva-menu-row",
- style: "display:table-row; margin:10px"
- });
-
- var addProjectButton = Functions.createElement({
- type: "button",
- name: "addProject",
- content: '<span class="ui-icon ui-icon-circle-plus"></span> ADD PROJECT',
- onclick: function () {
- return self.onAddClicked().then(null, GuiConnector.alert);
- },
- xss: false
- });
- var refreshButton = Functions.createElement({
- type: "button",
- name: "refreshProject",
- content: '<span class="ui-icon ui-icon-refresh"></span> REFRESH',
- onclick: function () {
- return self.onRefreshClicked().then(null, GuiConnector.alert);
- },
- xss: false
- });
- menuRow.appendChild(addProjectButton);
- menuRow.appendChild(refreshButton);
- return menuRow;
-};
-
-MapsAdminPanel.prototype._createProjectTableRow = function () {
- var self = this;
- var projectsRow = Functions.createElement({
- type: "div",
- style: "display:table-row; width:100%"
- });
-
- var projectsTable = Functions.createElement({
- type: "table",
- name: "projectsTable",
- className: "display",
- style: "width:100%"
- });
- projectsRow.appendChild(projectsTable);
-
- $(projectsTable).DataTable({
- columns: [{
- title: 'ProjectId'
- }, {
- title: 'Name'
- }, {
- title: 'Disease'
- }, {
- title: 'Organism'
- }, {
- title: 'Status'
- }, {
- title: 'Edit'
- }, {
- title: 'Remove'
- }]
- });
- self.bindUserGuiPreference({
- jQueryObject: $(projectsTable),
- event: 'length.dt',
- preferenceName: 'admin-projects-datatable-length',
- defaultValue: '10',
- getter: function () {
- return $(projectsTable).DataTable().page.len() + '';
- },
- setter: function (value) {
- return $(projectsTable).DataTable().page.len(value).draw();
- }
- });
-
- $(projectsTable).on("click", "[name='removeProject']", function () {
- var button = this;
- return self.askConfirmRemoval({
- title: "INFO",
- content: "Do you really want to remove '" + $(button).attr("data") + "' map?",
- input: false
- }).then(function (param) {
- if (param.status) {
- return self.removeProject($(button).attr("data"))
- }
- }).catch(GuiConnector.alert);
- });
-
- $(projectsTable).on("click", "[name='showEditDialog']", function () {
- var button = this;
- return self.showEditDialog($(button).attr("data")).then(null, GuiConnector.alert);
- });
- $(projectsTable).on("click", "[name='showErrors']", function () {
- var button = this;
- return self.showLogs($(button).attr("data"), 'error').then(null, GuiConnector.alert);
- });
- $(projectsTable).on("click", "[name='showWarnings']", function () {
- var button = this;
- return self.showLogs($(button).attr("data"), 'warning').then(null, GuiConnector.alert);
- });
-
- return projectsRow;
-};
-
-/**
- *
- * @returns {Promise}
- */
-MapsAdminPanel.prototype.init = function () {
- var self = this;
- return self.getServerConnector().getProjects().then(function (projects) {
- return self.setProjects(projects);
- });
-};
-
-/**
- *
- * @param {Project} project
- * @param {Array} [row]
- * @param {User} user
- * @returns {Array}
- */
-MapsAdminPanel.prototype.projectToTableRow = function (project, row, user) {
- var self = this;
- var disease = self.getHtmlStringLink(project.getDisease());
- var organism = self.getHtmlStringLink(project.getOrganism());
-
- if (row === undefined) {
- row = [];
- }
- var projectId = project.getProjectId();
- var formattedProjectId;
- if (project.getStatus().toLowerCase() === "ok") {
- formattedProjectId = "<a href='" + "index.xhtml?id=" + projectId + "' target='" + projectId + "'>" + projectId + "</a>";
- } else {
- formattedProjectId = projectId;
- }
- var status = project.getStatus();
- if (project.hasErrors()) {
- status += "<a name='showErrors' href='#' data='" + project.getProjectId() + "'>" +
- "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:red'></i>" +
- "</a>";
- }
- if (project.hasWarnings()) {
- status += "<a name='showWarnings' href='#' data='" + project.getProjectId() + "'>" +
- "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:black'></i>" +
- "</a>";
- }
-
- row[0] = formattedProjectId;
- row[1] = project.getName();
- row[2] = disease;
- row[3] = organism;
- row[4] = status;
-
- var disabled = " disabled ";
- if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.CONFIGURATION_MANAGE))) {
- disabled = "";
- }
- row[5] = "<button name='showEditDialog' data='" + project.getProjectId() + "'" + disabled + "><i class='fa fa-edit' style='font-size:17px'></i></button>";
- row[6] = "<button name='removeProject' data='" + project.getProjectId() + "'" + disabled + "><i class='fa fa-trash-o' style='font-size:17px'></button>";
-
- return row;
-};
-
-MapsAdminPanel.prototype.getHtmlStringLink = function (annotation) {
- var self = this;
- if (annotation !== undefined && annotation !== null) {
- var link = self.getGuiUtils().createAnnotationLink(annotation, true);
- var tmp = document.createElement("div");
- tmp.appendChild(link);
- return tmp.innerHTML;
- } else {
- return "N/A";
- }
-
-};
-
-/**
- *
- * @param {Project[]} projects
- * @returns {Promise}
- */
-MapsAdminPanel.prototype.setProjects = function (projects) {
- var self = this;
-
- return self.getServerConnector().getLoggedUser().then(function (user) {
- var dataTable = $("[name='projectsTable']", self.getElement()).DataTable();
- var data = [];
- var page = dataTable.page();
-
- for (var i = 0; i < projects.length; i++) {
- var project = projects[i];
- var rowData = self.projectToTableRow(project, undefined, user);
- self.addUpdateListener(project, rowData);
- data.push(rowData);
- }
- //it should be simplified, but I couldn't make it work
- dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
- });
-};
-
-MapsAdminPanel.prototype.addUpdateListener = function (project, dataTableRow) {
- var self = this;
-
- var listenerName = "PROJECT_LIST_LISTENER";
- var listeners = project.getListeners("onreload");
- for (var i = 0; i < listeners.length; i++) {
- if (listeners[i].listenerName === listenerName) {
- project.removeListener("onreload", listeners[i]);
- }
- }
- var listener = function () {
- return self.getServerConnector().getLoggedUser().then(function (user) {
- self.projectToTableRow(project, dataTableRow, user);
- var row = $($("[name='projectsTable']", self.getElement())[0]).DataTable().row("#" + project.getProjectId());
- if (row.length > 0) {
- row.data(dataTableRow).draw();
- }
- });
- };
- listener.listenerName = listenerName;
- project.addListener("onreload", listener);
-};
-
-MapsAdminPanel.prototype.onAddClicked = function () {
- var self = this;
- var dialog = self._addDialog;
- if (dialog === undefined) {
- dialog = new AddProjectDialog({
- element: Functions.createElement({
- type: "div"
- }),
- customMap: null,
- configuration: self.getConfiguration(),
- serverConnector: self.getServerConnector()
- });
- self._addDialog = dialog;
- dialog.addListener("onProjectAdd", function () {
- return self.onRefreshClicked()
- });
- return dialog.init().then(function () {
- return dialog.open();
- });
- } else {
- dialog.clear();
- dialog.open();
- return Promise.resolve();
- }
-};
-
-MapsAdminPanel.prototype.destroy = function () {
- var promises = [];
- var self = this;
- var dialog = self._addDialog;
- if (dialog !== undefined) {
- promises.push(dialog.destroy());
- }
- var table = $("[name='projectsTable']", self.getElement())[0];
- if ($.fn.DataTable.isDataTable(table)) {
- promises.push($(table).DataTable().destroy());
- }
-
- var key;
- for (key in self._logDialogs) {
- if (self._logDialogs.hasOwnProperty(key)) {
- promises.push(self._logDialogs[key].destroy());
- }
- }
- for (key in self._dialogs) {
- if (self._dialogs.hasOwnProperty(key)) {
- promises.push(self._dialogs[key].destroy());
- }
- }
- return Promise.all(promises);
-};
-
-MapsAdminPanel.prototype.onRefreshClicked = function () {
- var self = this;
- return ServerConnector.getProjects(true).then(function (projects) {
- return self.setProjects(projects);
- }).then(function () {
- return ServerConnector.getLoggedUser();
- }).then(function (user) {
- var privilege = self.getConfiguration().getPrivilegeType(PrivilegeType.USER_MANAGEMENT);
- //we need to refresh users as well because of privileges
- if (user.hasPrivilege(privilege)) {
- return ServerConnector.getUsers(true);
- } else {
- return Promise.resolve();
- }
- });
-};
-
-MapsAdminPanel.prototype.getDialog = function (project) {
- var self = this;
- if (self._dialogs === undefined) {
- self._dialogs = [];
- }
- var dialog = self._dialogs[project.getProjectId()];
- if (dialog === undefined) {
- dialog = new EditProjectDialog({
- element: Functions.createElement({
- type: "div"
- }),
- project: project,
- configuration: self.getConfiguration(),
- customMap: null
- });
- self._dialogs[project.getProjectId()] = dialog;
- return dialog.init().then(function () {
- return dialog.addListener("onSave", function () {
- return self.onRefreshClicked()
- });
- }).then(function () {
- return dialog;
- });
- } else {
- return Promise.resolve(dialog);
- }
-};
-
-MapsAdminPanel.prototype.getLogDialog = function (projectId, level) {
- var self = this;
- if (self._logDialogs === undefined) {
- self._logDialogs = [];
- }
- var dialog = self._logDialogs[projectId + "-" + level];
- if (dialog === undefined) {
- dialog = new LogListDialog({
- element: Functions.createElement({
- type: "div"
- }),
- projectId: projectId,
- customMap: null,
- level: level
- });
- self._logDialogs[projectId + "-" + level] = dialog;
- return dialog.init().then(function () {
- return dialog;
- });
- } else {
- return Promise.resolve(dialog);
- }
-};
-
-MapsAdminPanel.prototype.showEditDialog = function (id) {
- var self = this;
- GuiConnector.showProcessing();
- return ServerConnector.getProject(id).then(function (project) {
- return self.getDialog(project);
- }).then(function (dialog) {
-
- dialog.open();
- GuiConnector.hideProcessing();
- }).then(null, function (error) {
- GuiConnector.hideProcessing();
- return Promise.reject(error);
- });
-};
-
-MapsAdminPanel.prototype.showLogs = function (id, level) {
- var self = this;
- GuiConnector.showProcessing();
- return self.getLogDialog(id, level).then(function (dialog) {
- return dialog.open();
- }).then(function () {
- GuiConnector.hideProcessing();
- }, function (error) {
- GuiConnector.hideProcessing();
- return Promise.reject(error);
- });
-};
-
-
-MapsAdminPanel.prototype.removeProject = function (id) {
- var self = this;
- return ServerConnector.removeProject(id).then(function () {
- return self.onRefreshClicked();
- });
-};
-
-module.exports = MapsAdminPanel;
+"use strict";
+
+/* exported logger */
+
+var AbstractAdminPanel = require('./AbstractAdminPanel');
+var AddProjectDialog = require('./AddProjectDialog');
+var EditProjectDialog = require('./EditProjectDialog');
+var LogListDialog = require('./LogListDialog');
+var PrivilegeType = require('../../map/data/PrivilegeType');
+var UserPreferences = require('../../map/data/UserPreferences');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var Functions = require('../../Functions');
+var GuiConnector = require('../../GuiConnector');
+var Promise = require("bluebird");
+
+function MapsAdminPanel(params) {
+ var self = this;
+ AbstractAdminPanel.call(self, params);
+ self._createGui();
+
+ $(self.getElement()).addClass("minerva-projects-tab");
+
+}
+
+MapsAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
+MapsAdminPanel.prototype.constructor = MapsAdminPanel;
+
+MapsAdminPanel.prototype._createGui = function () {
+ var self = this;
+ var projectsDiv = Functions.createElement({
+ type: "div"
+ });
+ self.getElement().appendChild(projectsDiv);
+
+ var dataDiv = Functions.createElement({
+ type: "div",
+ style: "display:table; width:100%"
+ });
+ projectsDiv.appendChild(dataDiv);
+
+ dataDiv.appendChild(self._createMenuRow());
+ dataDiv.appendChild(self._createProjectTableRow());
+ dataDiv.appendChild(self._createMenuRow());
+
+};
+
+MapsAdminPanel.prototype._createMenuRow = function () {
+ var self = this;
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+
+ var addProjectButton = Functions.createElement({
+ type: "button",
+ name: "addProject",
+ content: '<span class="ui-icon ui-icon-circle-plus"></span> ADD PROJECT',
+ onclick: function () {
+ return self.onAddClicked().then(null, GuiConnector.alert);
+ },
+ xss: false
+ });
+ var refreshButton = Functions.createElement({
+ type: "button",
+ name: "refreshProject",
+ content: '<span class="ui-icon ui-icon-refresh"></span> REFRESH',
+ onclick: function () {
+ return self.onRefreshClicked().then(null, GuiConnector.alert);
+ },
+ xss: false
+ });
+ menuRow.appendChild(addProjectButton);
+ menuRow.appendChild(refreshButton);
+ return menuRow;
+};
+
+MapsAdminPanel.prototype._createProjectTableRow = function () {
+ var self = this;
+ var projectsRow = Functions.createElement({
+ type: "div",
+ style: "display:table-row; width:100%"
+ });
+
+ var projectsTable = Functions.createElement({
+ type: "table",
+ name: "projectsTable",
+ className: "display",
+ style: "width:100%"
+ });
+ projectsRow.appendChild(projectsTable);
+
+ $(projectsTable).DataTable({
+ columns: [{
+ title: 'ProjectId'
+ }, {
+ title: 'Name'
+ }, {
+ title: 'Disease'
+ }, {
+ title: 'Organism'
+ }, {
+ title: 'Status'
+ }, {
+ title: 'Edit'
+ }, {
+ title: 'Remove'
+ }]
+ });
+ self.bindUserGuiPreference({
+ jQueryObject: $(projectsTable),
+ event: 'length.dt',
+ preferenceName: 'admin-projects-datatable-length',
+ defaultValue: '10',
+ getter: function () {
+ return $(projectsTable).DataTable().page.len() + '';
+ },
+ setter: function (value) {
+ return $(projectsTable).DataTable().page.len(value).draw();
+ }
+ });
+
+ $(projectsTable).on("click", "[name='removeProject']", function () {
+ var button = this;
+ return self.askConfirmRemoval({
+ title: "INFO",
+ content: "Do you really want to remove '" + $(button).attr("data") + "' map?",
+ input: false
+ }).then(function (param) {
+ if (param.status) {
+ return self.removeProject($(button).attr("data"))
+ }
+ }).catch(GuiConnector.alert);
+ });
+
+ $(projectsTable).on("click", "[name='showEditDialog']", function () {
+ var button = this;
+ return self.showEditDialog($(button).attr("data")).then(null, GuiConnector.alert);
+ });
+ $(projectsTable).on("click", "[name='showErrors']", function () {
+ var button = this;
+ return self.showLogs($(button).attr("data"), 'error').then(null, GuiConnector.alert);
+ });
+ $(projectsTable).on("click", "[name='showWarnings']", function () {
+ var button = this;
+ return self.showLogs($(button).attr("data"), 'warning').then(null, GuiConnector.alert);
+ });
+
+ return projectsRow;
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+MapsAdminPanel.prototype.init = function () {
+ var self = this;
+ return self.getServerConnector().getProjects().then(function (projects) {
+ return self.setProjects(projects);
+ });
+};
+
+/**
+ *
+ * @param {Project} project
+ * @param {Array} [row]
+ * @param {User} user
+ * @returns {Array}
+ */
+MapsAdminPanel.prototype.projectToTableRow = function (project, row, user) {
+ var self = this;
+ var disease = self.getHtmlStringLink(project.getDisease());
+ var organism = self.getHtmlStringLink(project.getOrganism());
+
+ if (row === undefined) {
+ row = [];
+ }
+ var projectId = project.getProjectId();
+ var formattedProjectId;
+ if (project.getStatus().toLowerCase() === "ok") {
+ formattedProjectId = "<a href='" + "index.xhtml?id=" + projectId + "' target='" + projectId + "'>" + projectId + "</a>";
+ } else {
+ formattedProjectId = projectId;
+ }
+ var status = project.getStatus();
+ if (project.hasErrors()) {
+ status += "<a name='showErrors' href='#' data='" + project.getProjectId() + "'>" +
+ "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:red'></i>" +
+ "</a>";
+ }
+ if (project.hasWarnings()) {
+ status += "<a name='showWarnings' href='#' data='" + project.getProjectId() + "'>" +
+ "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:black'></i>" +
+ "</a>";
+ }
+
+ row[0] = formattedProjectId;
+ row[1] = project.getName();
+ row[2] = disease;
+ row[3] = organism;
+ row[4] = status;
+
+ var disabled = " disabled ";
+ if (user.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.CONFIGURATION_MANAGE))) {
+ disabled = "";
+ }
+ row[5] = "<button name='showEditDialog' data='" + project.getProjectId() + "'" + disabled + "><i class='fa fa-edit' style='font-size:17px'></i></button>";
+ row[6] = "<button name='removeProject' data='" + project.getProjectId() + "'" + disabled + "><i class='fa fa-trash-o' style='font-size:17px'></button>";
+
+ return row;
+};
+
+MapsAdminPanel.prototype.getHtmlStringLink = function (annotation) {
+ var self = this;
+ if (annotation !== undefined && annotation !== null) {
+ var link = self.getGuiUtils().createAnnotationLink(annotation, true);
+ var tmp = document.createElement("div");
+ tmp.appendChild(link);
+ return tmp.innerHTML;
+ } else {
+ return "N/A";
+ }
+
+};
+
+/**
+ *
+ * @param {Project[]} projects
+ * @returns {Promise}
+ */
+MapsAdminPanel.prototype.setProjects = function (projects) {
+ var self = this;
+
+ return self.getServerConnector().getLoggedUser().then(function (user) {
+ var dataTable = $("[name='projectsTable']", self.getElement()).DataTable();
+ var data = [];
+ var page = dataTable.page();
+
+ for (var i = 0; i < projects.length; i++) {
+ var project = projects[i];
+ var rowData = self.projectToTableRow(project, undefined, user);
+ self.addUpdateListener(project, rowData);
+ data.push(rowData);
+ }
+ //it should be simplified, but I couldn't make it work
+ dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
+ });
+};
+
+MapsAdminPanel.prototype.addUpdateListener = function (project, dataTableRow) {
+ var self = this;
+
+ var listenerName = "PROJECT_LIST_LISTENER";
+ var listeners = project.getListeners("onreload");
+ for (var i = 0; i < listeners.length; i++) {
+ if (listeners[i].listenerName === listenerName) {
+ project.removeListener("onreload", listeners[i]);
+ }
+ }
+ var listener = function () {
+ return self.getServerConnector().getLoggedUser().then(function (user) {
+ self.projectToTableRow(project, dataTableRow, user);
+ var row = $($("[name='projectsTable']", self.getElement())[0]).DataTable().row("#" + project.getProjectId());
+ if (row.length > 0) {
+ row.data(dataTableRow).draw();
+ }
+ });
+ };
+ listener.listenerName = listenerName;
+ project.addListener("onreload", listener);
+};
+
+MapsAdminPanel.prototype.onAddClicked = function () {
+ var self = this;
+ var dialog = self._addDialog;
+ if (dialog === undefined) {
+ dialog = new AddProjectDialog({
+ element: Functions.createElement({
+ type: "div"
+ }),
+ customMap: null,
+ configuration: self.getConfiguration(),
+ serverConnector: self.getServerConnector()
+ });
+ self._addDialog = dialog;
+ dialog.addListener("onProjectAdd", function () {
+ return self.onRefreshClicked()
+ });
+ return dialog.init().then(function () {
+ return dialog.open();
+ });
+ } else {
+ dialog.clear();
+ dialog.open();
+ return Promise.resolve();
+ }
+};
+
+MapsAdminPanel.prototype.destroy = function () {
+ var promises = [];
+ var self = this;
+ var dialog = self._addDialog;
+ if (dialog !== undefined) {
+ promises.push(dialog.destroy());
+ }
+ var table = $("[name='projectsTable']", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(table)) {
+ promises.push($(table).DataTable().destroy());
+ }
+
+ var key;
+ for (key in self._logDialogs) {
+ if (self._logDialogs.hasOwnProperty(key)) {
+ promises.push(self._logDialogs[key].destroy());
+ }
+ }
+ for (key in self._dialogs) {
+ if (self._dialogs.hasOwnProperty(key)) {
+ promises.push(self._dialogs[key].destroy());
+ }
+ }
+ return Promise.all(promises);
+};
+
+MapsAdminPanel.prototype.onRefreshClicked = function () {
+ var self = this;
+ return ServerConnector.getProjects(true).then(function (projects) {
+ return self.setProjects(projects);
+ }).then(function () {
+ return ServerConnector.getLoggedUser();
+ }).then(function (user) {
+ var privilege = self.getConfiguration().getPrivilegeType(PrivilegeType.USER_MANAGEMENT);
+ //we need to refresh users as well because of privileges
+ if (user.hasPrivilege(privilege)) {
+ return ServerConnector.getUsers(true);
+ } else {
+ return Promise.resolve();
+ }
+ });
+};
+
+MapsAdminPanel.prototype.getDialog = function (project) {
+ var self = this;
+ if (self._dialogs === undefined) {
+ self._dialogs = [];
+ }
+ var dialog = self._dialogs[project.getProjectId()];
+ if (dialog === undefined) {
+ dialog = new EditProjectDialog({
+ element: Functions.createElement({
+ type: "div"
+ }),
+ project: project,
+ configuration: self.getConfiguration(),
+ customMap: null
+ });
+ self._dialogs[project.getProjectId()] = dialog;
+ return dialog.init().then(function () {
+ return dialog.addListener("onSave", function () {
+ return self.onRefreshClicked()
+ });
+ }).then(function () {
+ return dialog;
+ });
+ } else {
+ return Promise.resolve(dialog);
+ }
+};
+
+MapsAdminPanel.prototype.getLogDialog = function (projectId, level) {
+ var self = this;
+ if (self._logDialogs === undefined) {
+ self._logDialogs = [];
+ }
+ var dialog = self._logDialogs[projectId + "-" + level];
+ if (dialog === undefined) {
+ dialog = new LogListDialog({
+ element: Functions.createElement({
+ type: "div"
+ }),
+ projectId: projectId,
+ customMap: null,
+ level: level
+ });
+ self._logDialogs[projectId + "-" + level] = dialog;
+ return dialog.init().then(function () {
+ return dialog;
+ });
+ } else {
+ return Promise.resolve(dialog);
+ }
+};
+
+MapsAdminPanel.prototype.showEditDialog = function (id) {
+ var self = this;
+ GuiConnector.showProcessing();
+ return ServerConnector.getProject(id).then(function (project) {
+ return self.getDialog(project);
+ }).then(function (dialog) {
+
+ dialog.open();
+ GuiConnector.hideProcessing();
+ }).then(null, function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+MapsAdminPanel.prototype.showLogs = function (id, level) {
+ var self = this;
+ GuiConnector.showProcessing();
+ return self.getLogDialog(id, level).then(function (dialog) {
+ return dialog.open();
+ }).then(function () {
+ GuiConnector.hideProcessing();
+ }, function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+
+MapsAdminPanel.prototype.removeProject = function (id) {
+ var self = this;
+ return ServerConnector.removeProject(id).then(function () {
+ return self.onRefreshClicked();
+ });
+};
+
+module.exports = MapsAdminPanel;
diff --git a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js b/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
index 1bbc720da8c241f3792adc69edae5d5705e3f409..2eb25ce86ccf98dcca46ae0316b02f832fd6855b 100644
--- a/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
+++ b/frontend-js/src/main/js/gui/admin/UsersAdminPanel.js
@@ -1,404 +1,404 @@
-"use strict";
-
-var Promise = require('bluebird');
-
-var PrivilegeType = require('../../map/data/PrivilegeType');
-
-var AbstractAdminPanel = require('./AbstractAdminPanel');
-var EditUserDialog = require('./EditUserDialog');
-
-var User = require("../../map/data/User");
-
-var Functions = require('../../Functions');
-var GuiConnector = require('../../GuiConnector');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-/**
- *
- * @param {Object} params
- *
- * @constructor
- * @extends AbstractAdminPanel
- */
-function UsersAdminPanel(params) {
- var self = this;
- AbstractAdminPanel.call(self, params);
- self._createGui();
- $(self.getElement()).addClass("minerva-users-tab");
-}
-
-UsersAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
-UsersAdminPanel.prototype.constructor = UsersAdminPanel;
-
-/**
- *
- * @private
- */
-UsersAdminPanel.prototype._createGui = function () {
- var self = this;
- var usersDiv = Functions.createElement({
- type: "div"
- });
- self.getElement().appendChild(usersDiv);
-
- var dataDiv = Functions.createElement({
- type: "div",
- style: "display:table; width:100%"
- });
- usersDiv.appendChild(dataDiv);
-
- dataDiv.appendChild(self._createMenuRow());
- dataDiv.appendChild(self._createUsersTableRow());
- dataDiv.appendChild(self._createMenuRow());
-
-};
-
-/**
- *
- * @returns {HTMLElement}
- * @private
- */
-UsersAdminPanel.prototype._createMenuRow = function () {
- var self = this;
- var menuRow = Functions.createElement({
- type: "div",
- className: "minerva-menu-row",
- style: "display:table-row; margin:10px"
- });
-
- var addUserButton = Functions.createElement({
- type: "button",
- name: "addProject",
- content: '<span class="ui-icon ui-icon-circle-plus"></span> ADD USER',
- onclick: function () {
- return self.onAddClicked().then(null, GuiConnector.alert);
- },
- xss: false
- });
- var refreshButton = Functions.createElement({
- type: "button",
- name: "refreshProject",
- content: '<span class="ui-icon ui-icon-refresh"></span> REFRESH',
- onclick: function () {
- return self.onRefreshClicked().then(null, GuiConnector.alert);
- },
- xss: false
- });
- menuRow.appendChild(addUserButton);
- menuRow.appendChild(refreshButton);
- return menuRow;
-};
-
-/**
- *
- * @returns {HTMLElement}
- * @private
- */
-UsersAdminPanel.prototype._createUsersTableRow = function () {
- var self = this;
- var projectsRow = Functions.createElement({
- type: "div",
- style: "display:table-row; width:100%"
- });
-
- var usersTable = Functions.createElement({
- type: "table",
- name: "usersTable",
- className: "display",
- style: "width:100%"
- });
- projectsRow.appendChild(usersTable);
-
- // noinspection JSCheckFunctionSignatures
- $(usersTable).DataTable({
- fnRowCallback: function (nRow, aData) {
- nRow.setAttribute('id', aData[0]);
- },
- columns: [{
- title: 'Login'
- }, {
- title: 'Name'
- }, {
- title: 'Surname'
- }, {
- title: 'Email'
- }, {
- title: 'Authentication'
- }, {
- title: 'Edit'
- }, {
- title: 'Remove'
- }]
- });
-
- self.bindUserGuiPreference({
- jQueryObject: $(usersTable),
- event: 'length.dt',
- preferenceName: 'admin-users-datatable-length',
- defaultValue: '10',
- getter: function () {
- return $(usersTable).DataTable().page.len() + '';
- },
- setter: function (value) {
- return $(usersTable).DataTable().page.len(value).draw();
- }
- });
-
- $(usersTable).on("click", "[name='removeUser']", function () {
- var button = this;
- return self.askConfirmRemoval({
- title: "INFO",
- content: "Do you really want to remove '" + $(button).attr("data") + "'user?",
- input: false
- }).then(function (param) {
- if (param.status) {
- return self.removeUser($(button).attr("data"))
- }
- }).catch(GuiConnector.alert);
- });
-
- $(usersTable).on("click", "[name='ldap-auth']", function () {
- var field = this;
- var login = $(this).attr('data');
- GuiConnector.showProcessing();
- return self.getServerConnector().getUser(login).then(function (user) {
- var newIsConnected = $('input:checked', field).val() === "LDAP";
- var isConnected = user.isConnectedToLdap();
- if (isConnected !== newIsConnected) {
- user.setConnectedToLdap(newIsConnected);
- return self.getServerConnector().updateUser(user);
- }
- }).catch(function (error) {
- GuiConnector.alert(error);
- }).finally(function(){
- GuiConnector.hideProcessing();
- });
- });
-
- $(usersTable).on("click", "[name='showEditDialog']", function () {
- var button = this;
- return self.showEditDialog($(button).attr("data")).then(null, GuiConnector.alert);
- });
-
- return projectsRow;
-};
-
-/**
- *
- * @param {String} login
- * @returns {Promise}
- */
-UsersAdminPanel.prototype.showEditDialog = function (login) {
- var self = this;
- GuiConnector.showProcessing();
- return self.getServerConnector().getUser(login).then(function (user) {
- return self.getDialog(user);
- }).then(function (dialog) {
- dialog.open();
- GuiConnector.hideProcessing();
- }).then(null, function (error) {
- GuiConnector.hideProcessing();
- return Promise.reject(error);
- });
-};
-
-/**
- *
- * @param {User} user
- * @returns {Promise}
- */
-UsersAdminPanel.prototype.getDialog = function (user) {
- var self = this;
- if (self._dialogs === undefined) {
- self._dialogs = [];
- }
- var dialog = self._dialogs[user.getLogin()];
- if (dialog === undefined) {
- dialog = new EditUserDialog({
- element: Functions.createElement({
- type: "div"
- }),
- user: user,
- customMap: null
- });
- self._dialogs[user.getLogin()] = dialog;
- if (user.getLogin() === undefined) {
- dialog.addListener("onSave", function () {
- return self.onRefreshClicked();
- });
- }
- return dialog.init().then(function () {
- return dialog;
- });
- } else {
- return Promise.resolve(dialog);
- }
-};
-
-/**
- *
- * @returns {Promise}
- */
-UsersAdminPanel.prototype.init = function () {
- var self = this;
- return AbstractAdminPanel.prototype.init.call(this).then(function () {
- return self.getServerConnector().getLoggedUser();
- }).then(function (user) {
- var privilege = self.getConfiguration().getPrivilegeType(PrivilegeType.USER_MANAGEMENT);
- if (user.hasPrivilege(privilege)) {
- return self.getServerConnector().getUsers().then(function (users) {
- return self.setUsers(users);
- });
- } else {
- self.disablePanel("You have no privilege to manage users");
- }
- });
-};
-
-/**
- *
- * @param {User[]} users
- */
-UsersAdminPanel.prototype.setUsers = function (users) {
- var self = this;
- var dataTable = $($("[name='usersTable']", self.getElement())[0]).DataTable();
- var page = dataTable.page();
- var data = [];
- for (var i = 0; i < users.length; i++) {
- var user = users[i];
- var rowData = self.userToTableRow(user);
- self.addUpdateListener(user, rowData);
- data.push(rowData);
- }
- //it should be simplified, but I couldn't make it work
- dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
-};
-
-
-/**
- *
- * @param {User} user
- * @param {Array} dataTableRow
- */
-UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
- var self = this;
-
- var listenerName = "USER_LIST_LISTENER";
- var listeners = user.getListeners("onreload");
- for (var i = 0; i < listeners.length; i++) {
- if (listeners[i].listenerName === listenerName) {
- user.removeListener("onreload", listeners[i]);
- }
- }
- var listener = function () {
- var login = user.getLogin().replace(".", "\\.");
- self.userToTableRow(user, dataTableRow);
- var row = $($("[name='usersTable']", self.getElement())[0]).DataTable().row("#" + login);
- if (row.length > 0) {
- row.data(dataTableRow).draw();
- }
-
- };
- listener.listenerName = listenerName;
- user.addListener("onreload", listener);
-};
-
-/**
- *
- * @param {User} user
- * @param {Array} [row]
- * @returns {Array}
- */
-UsersAdminPanel.prototype.userToTableRow = function (user, row) {
- if (row === undefined) {
- row = [];
- }
-
- row[0] = user.getLogin();
- row[1] = user.getName();
- row[2] = user.getSurname();
- row[3] = user.getEmail();
- var ldapFieldId = 'ldap-auth-' + user.getLogin();
- if (user.isConnectedToLdap()) {
- row[4] = "<fieldset name='ldap-auth' id='" + ldapFieldId + "' data='" + user.getLogin() + "'> <input type='radio' name='" + ldapFieldId + "' value='LOCAL'> LOCAL <input type='radio' name='" + ldapFieldId + "' checked value='LDAP'> LDAP </fieldset>";
- } else {
- if (user.isLdapAccountAvailable()) {
- row[4] = "<fieldset name='ldap-auth' id='" + ldapFieldId + "' data='" + user.getLogin() + "'> <input type='radio' name='" + ldapFieldId + "' value='LOCAL' checked> LOCAL <input type='radio' name='" + ldapFieldId + "' value='LDAP'> LDAP </fieldset>";
- // row[4] = "LOCAL <button name='connectLdap' data='" + user.getLogin() + "'>CONNECT LDAP</button>"
- } else {
- row[4] = "<fieldset name='ldap-auth' id='" + ldapFieldId + "' data='" + user.getLogin() + "'> <input type='radio' name='" + ldapFieldId + "' value='LOCAL' checked> LOCAL</fieldset>";
- }
- }
-
- row[5] = "<button name='showEditDialog' data='" + user.getLogin() + "'><i class='fa fa-edit' style='font-size:17px'></i></button>";
- row[6] = "<button name='removeUser' data='" + user.getLogin() + "'><i class='fa fa-trash-o' style='font-size:17px'></i></button>";
-
- return row;
-};
-
-/**
- *
- * @returns {Promise}
- */
-UsersAdminPanel.prototype.onRefreshClicked = function () {
- var self = this;
- return self.getServerConnector().getUsers(true).then(function (users) {
- return self.setUsers(users);
- });
-};
-
-
-/**
- *
- */
-UsersAdminPanel.prototype.destroy = function () {
- var self = this;
- var table = $("[name='usersTable']", self.getElement())[0];
- if ($.fn.DataTable.isDataTable(table)) {
- $(table).DataTable().destroy();
- }
-
- for (var key in self._dialogs) {
- if (self._dialogs.hasOwnProperty(key)) {
- self._dialogs[key].destroy();
- }
- }
-};
-
-/**
- *
- * @returns {Promise}
- */
-UsersAdminPanel.prototype.onAddClicked = function () {
- var self = this;
- var user = new User({});
- GuiConnector.showProcessing();
- return self.getDialog(user).then(function (dialog) {
- dialog.open();
- GuiConnector.hideProcessing();
- }).then(null, function (error) {
- GuiConnector.hideProcessing();
- return Promise.reject(error);
- });
-};
-
-/**
- *
- * @param {string} login
- * @returns {Promise}
- */
-UsersAdminPanel.prototype.removeUser = function (login) {
- var self = this;
- GuiConnector.showProcessing();
- return self.getServerConnector().removeUser(login).then(function () {
- return self.onRefreshClicked();
- }).then(function () {
- GuiConnector.hideProcessing();
- }).then(null, function (error) {
- GuiConnector.hideProcessing();
- return Promise.reject(error);
- });
-};
-
-module.exports = UsersAdminPanel;
+"use strict";
+
+var Promise = require('bluebird');
+
+var PrivilegeType = require('../../map/data/PrivilegeType');
+
+var AbstractAdminPanel = require('./AbstractAdminPanel');
+var EditUserDialog = require('./EditUserDialog');
+
+var User = require("../../map/data/User");
+
+var Functions = require('../../Functions');
+var GuiConnector = require('../../GuiConnector');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+/**
+ *
+ * @param {Object} params
+ *
+ * @constructor
+ * @extends AbstractAdminPanel
+ */
+function UsersAdminPanel(params) {
+ var self = this;
+ AbstractAdminPanel.call(self, params);
+ self._createGui();
+ $(self.getElement()).addClass("minerva-users-tab");
+}
+
+UsersAdminPanel.prototype = Object.create(AbstractAdminPanel.prototype);
+UsersAdminPanel.prototype.constructor = UsersAdminPanel;
+
+/**
+ *
+ * @private
+ */
+UsersAdminPanel.prototype._createGui = function () {
+ var self = this;
+ var usersDiv = Functions.createElement({
+ type: "div"
+ });
+ self.getElement().appendChild(usersDiv);
+
+ var dataDiv = Functions.createElement({
+ type: "div",
+ style: "display:table; width:100%"
+ });
+ usersDiv.appendChild(dataDiv);
+
+ dataDiv.appendChild(self._createMenuRow());
+ dataDiv.appendChild(self._createUsersTableRow());
+ dataDiv.appendChild(self._createMenuRow());
+
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
+UsersAdminPanel.prototype._createMenuRow = function () {
+ var self = this;
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+
+ var addUserButton = Functions.createElement({
+ type: "button",
+ name: "addProject",
+ content: '<span class="ui-icon ui-icon-circle-plus"></span> ADD USER',
+ onclick: function () {
+ return self.onAddClicked().then(null, GuiConnector.alert);
+ },
+ xss: false
+ });
+ var refreshButton = Functions.createElement({
+ type: "button",
+ name: "refreshProject",
+ content: '<span class="ui-icon ui-icon-refresh"></span> REFRESH',
+ onclick: function () {
+ return self.onRefreshClicked().then(null, GuiConnector.alert);
+ },
+ xss: false
+ });
+ menuRow.appendChild(addUserButton);
+ menuRow.appendChild(refreshButton);
+ return menuRow;
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ * @private
+ */
+UsersAdminPanel.prototype._createUsersTableRow = function () {
+ var self = this;
+ var projectsRow = Functions.createElement({
+ type: "div",
+ style: "display:table-row; width:100%"
+ });
+
+ var usersTable = Functions.createElement({
+ type: "table",
+ name: "usersTable",
+ className: "display",
+ style: "width:100%"
+ });
+ projectsRow.appendChild(usersTable);
+
+ // noinspection JSCheckFunctionSignatures
+ $(usersTable).DataTable({
+ fnRowCallback: function (nRow, aData) {
+ nRow.setAttribute('id', aData[0]);
+ },
+ columns: [{
+ title: 'Login'
+ }, {
+ title: 'Name'
+ }, {
+ title: 'Surname'
+ }, {
+ title: 'Email'
+ }, {
+ title: 'Authentication'
+ }, {
+ title: 'Edit'
+ }, {
+ title: 'Remove'
+ }]
+ });
+
+ self.bindUserGuiPreference({
+ jQueryObject: $(usersTable),
+ event: 'length.dt',
+ preferenceName: 'admin-users-datatable-length',
+ defaultValue: '10',
+ getter: function () {
+ return $(usersTable).DataTable().page.len() + '';
+ },
+ setter: function (value) {
+ return $(usersTable).DataTable().page.len(value).draw();
+ }
+ });
+
+ $(usersTable).on("click", "[name='removeUser']", function () {
+ var button = this;
+ return self.askConfirmRemoval({
+ title: "INFO",
+ content: "Do you really want to remove '" + $(button).attr("data") + "'user?",
+ input: false
+ }).then(function (param) {
+ if (param.status) {
+ return self.removeUser($(button).attr("data"))
+ }
+ }).catch(GuiConnector.alert);
+ });
+
+ $(usersTable).on("click", "[name='ldap-auth']", function () {
+ var field = this;
+ var login = $(this).attr('data');
+ GuiConnector.showProcessing();
+ return self.getServerConnector().getUser(login).then(function (user) {
+ var newIsConnected = $('input:checked', field).val() === "LDAP";
+ var isConnected = user.isConnectedToLdap();
+ if (isConnected !== newIsConnected) {
+ user.setConnectedToLdap(newIsConnected);
+ return self.getServerConnector().updateUser(user);
+ }
+ }).catch(function (error) {
+ GuiConnector.alert(error);
+ }).finally(function(){
+ GuiConnector.hideProcessing();
+ });
+ });
+
+ $(usersTable).on("click", "[name='showEditDialog']", function () {
+ var button = this;
+ return self.showEditDialog($(button).attr("data")).then(null, GuiConnector.alert);
+ });
+
+ return projectsRow;
+};
+
+/**
+ *
+ * @param {String} login
+ * @returns {Promise}
+ */
+UsersAdminPanel.prototype.showEditDialog = function (login) {
+ var self = this;
+ GuiConnector.showProcessing();
+ return self.getServerConnector().getUser(login).then(function (user) {
+ return self.getDialog(user);
+ }).then(function (dialog) {
+ dialog.open();
+ GuiConnector.hideProcessing();
+ }).then(null, function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+/**
+ *
+ * @param {User} user
+ * @returns {Promise}
+ */
+UsersAdminPanel.prototype.getDialog = function (user) {
+ var self = this;
+ if (self._dialogs === undefined) {
+ self._dialogs = [];
+ }
+ var dialog = self._dialogs[user.getLogin()];
+ if (dialog === undefined) {
+ dialog = new EditUserDialog({
+ element: Functions.createElement({
+ type: "div"
+ }),
+ user: user,
+ customMap: null
+ });
+ self._dialogs[user.getLogin()] = dialog;
+ if (user.getLogin() === undefined) {
+ dialog.addListener("onSave", function () {
+ return self.onRefreshClicked();
+ });
+ }
+ return dialog.init().then(function () {
+ return dialog;
+ });
+ } else {
+ return Promise.resolve(dialog);
+ }
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+UsersAdminPanel.prototype.init = function () {
+ var self = this;
+ return AbstractAdminPanel.prototype.init.call(this).then(function () {
+ return self.getServerConnector().getLoggedUser();
+ }).then(function (user) {
+ var privilege = self.getConfiguration().getPrivilegeType(PrivilegeType.USER_MANAGEMENT);
+ if (user.hasPrivilege(privilege)) {
+ return self.getServerConnector().getUsers().then(function (users) {
+ return self.setUsers(users);
+ });
+ } else {
+ self.disablePanel("You have no privilege to manage users");
+ }
+ });
+};
+
+/**
+ *
+ * @param {User[]} users
+ */
+UsersAdminPanel.prototype.setUsers = function (users) {
+ var self = this;
+ var dataTable = $($("[name='usersTable']", self.getElement())[0]).DataTable();
+ var page = dataTable.page();
+ var data = [];
+ for (var i = 0; i < users.length; i++) {
+ var user = users[i];
+ var rowData = self.userToTableRow(user);
+ self.addUpdateListener(user, rowData);
+ data.push(rowData);
+ }
+ //it should be simplified, but I couldn't make it work
+ dataTable.clear().rows.add(data).page(page).draw(false).page(page).draw(false);
+};
+
+
+/**
+ *
+ * @param {User} user
+ * @param {Array} dataTableRow
+ */
+UsersAdminPanel.prototype.addUpdateListener = function (user, dataTableRow) {
+ var self = this;
+
+ var listenerName = "USER_LIST_LISTENER";
+ var listeners = user.getListeners("onreload");
+ for (var i = 0; i < listeners.length; i++) {
+ if (listeners[i].listenerName === listenerName) {
+ user.removeListener("onreload", listeners[i]);
+ }
+ }
+ var listener = function () {
+ var login = user.getLogin().replace(".", "\\.");
+ self.userToTableRow(user, dataTableRow);
+ var row = $($("[name='usersTable']", self.getElement())[0]).DataTable().row("#" + login);
+ if (row.length > 0) {
+ row.data(dataTableRow).draw();
+ }
+
+ };
+ listener.listenerName = listenerName;
+ user.addListener("onreload", listener);
+};
+
+/**
+ *
+ * @param {User} user
+ * @param {Array} [row]
+ * @returns {Array}
+ */
+UsersAdminPanel.prototype.userToTableRow = function (user, row) {
+ if (row === undefined) {
+ row = [];
+ }
+
+ row[0] = user.getLogin();
+ row[1] = user.getName();
+ row[2] = user.getSurname();
+ row[3] = user.getEmail();
+ var ldapFieldId = 'ldap-auth-' + user.getLogin();
+ if (user.isConnectedToLdap()) {
+ row[4] = "<fieldset name='ldap-auth' id='" + ldapFieldId + "' data='" + user.getLogin() + "'> <input type='radio' name='" + ldapFieldId + "' value='LOCAL'> LOCAL <input type='radio' name='" + ldapFieldId + "' checked value='LDAP'> LDAP </fieldset>";
+ } else {
+ if (user.isLdapAccountAvailable()) {
+ row[4] = "<fieldset name='ldap-auth' id='" + ldapFieldId + "' data='" + user.getLogin() + "'> <input type='radio' name='" + ldapFieldId + "' value='LOCAL' checked> LOCAL <input type='radio' name='" + ldapFieldId + "' value='LDAP'> LDAP </fieldset>";
+ // row[4] = "LOCAL <button name='connectLdap' data='" + user.getLogin() + "'>CONNECT LDAP</button>"
+ } else {
+ row[4] = "<fieldset name='ldap-auth' id='" + ldapFieldId + "' data='" + user.getLogin() + "'> <input type='radio' name='" + ldapFieldId + "' value='LOCAL' checked> LOCAL</fieldset>";
+ }
+ }
+
+ row[5] = "<button name='showEditDialog' data='" + user.getLogin() + "'><i class='fa fa-edit' style='font-size:17px'></i></button>";
+ row[6] = "<button name='removeUser' data='" + user.getLogin() + "'><i class='fa fa-trash-o' style='font-size:17px'></i></button>";
+
+ return row;
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+UsersAdminPanel.prototype.onRefreshClicked = function () {
+ var self = this;
+ return self.getServerConnector().getUsers(true).then(function (users) {
+ return self.setUsers(users);
+ });
+};
+
+
+/**
+ *
+ */
+UsersAdminPanel.prototype.destroy = function () {
+ var self = this;
+ var table = $("[name='usersTable']", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(table)) {
+ $(table).DataTable().destroy();
+ }
+
+ for (var key in self._dialogs) {
+ if (self._dialogs.hasOwnProperty(key)) {
+ self._dialogs[key].destroy();
+ }
+ }
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+UsersAdminPanel.prototype.onAddClicked = function () {
+ var self = this;
+ var user = new User({});
+ GuiConnector.showProcessing();
+ return self.getDialog(user).then(function (dialog) {
+ dialog.open();
+ GuiConnector.hideProcessing();
+ }).then(null, function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+/**
+ *
+ * @param {string} login
+ * @returns {Promise}
+ */
+UsersAdminPanel.prototype.removeUser = function (login) {
+ var self = this;
+ GuiConnector.showProcessing();
+ return self.getServerConnector().removeUser(login).then(function () {
+ return self.onRefreshClicked();
+ }).then(function () {
+ GuiConnector.hideProcessing();
+ }).then(null, function (error) {
+ GuiConnector.hideProcessing();
+ return Promise.reject(error);
+ });
+};
+
+module.exports = UsersAdminPanel;
diff --git a/frontend-js/src/main/js/gui/admin/ZipEntry.js b/frontend-js/src/main/js/gui/admin/ZipEntry.js
index c3891a3a013e1b131353649c320471edd8671b7c..d774a223327fec74db0eb7ebedf9b6b8b7183cc5 100644
--- a/frontend-js/src/main/js/gui/admin/ZipEntry.js
+++ b/frontend-js/src/main/js/gui/admin/ZipEntry.js
@@ -1,37 +1,37 @@
-"use strict";
-
-var types = ["IMAGE", "OVERLAY", "MAP"];
-
-function ZipEntry(params) {
- var self = this;
- self.setType(params.type);
- self.setFilename(params.filename);
- self.setData(params.data);
-}
-
-ZipEntry.prototype.setType = function (type) {
- if (types.indexOf(type) === -1) {
- throw new Error("Unknown ZipEntryType: " + type + ".")
- }
- this._type = type;
-};
-ZipEntry.prototype.getType = function () {
- return this._type;
-};
-
-ZipEntry.prototype.setFilename = function (filename) {
- this._filename = filename;
-};
-
-ZipEntry.prototype.getFilename = function () {
- return this._filename;
-};
-
-ZipEntry.prototype.setData = function (data) {
- this._data = data;
-};
-ZipEntry.prototype.getData = function () {
- return this._data;
-};
-
-module.exports = ZipEntry;
+"use strict";
+
+var types = ["IMAGE", "OVERLAY", "MAP"];
+
+function ZipEntry(params) {
+ var self = this;
+ self.setType(params.type);
+ self.setFilename(params.filename);
+ self.setData(params.data);
+}
+
+ZipEntry.prototype.setType = function (type) {
+ if (types.indexOf(type) === -1) {
+ throw new Error("Unknown ZipEntryType: " + type + ".")
+ }
+ this._type = type;
+};
+ZipEntry.prototype.getType = function () {
+ return this._type;
+};
+
+ZipEntry.prototype.setFilename = function (filename) {
+ this._filename = filename;
+};
+
+ZipEntry.prototype.getFilename = function () {
+ return this._filename;
+};
+
+ZipEntry.prototype.setData = function (data) {
+ this._data = data;
+};
+ZipEntry.prototype.getData = function () {
+ return this._data;
+};
+
+module.exports = ZipEntry;
diff --git a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
index d18f91310c421d3350a7b9e44e19123f6639fe51..b38d50a2c1329bda595a51ee73c1b9ac68f410f6 100644
--- a/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/AbstractExportPanel.js
@@ -1,453 +1,453 @@
-"use strict";
-
-/* exported logger */
-
-var Panel = require('../Panel');
-
-var GuiConnector = require('../../GuiConnector');
-var logger = require('../../logger');
-var Functions = require('../../Functions');
-var DualListbox = require('dual-listbox').DualListbox;
-var Promise = require("bluebird");
-
-function AbstractExportPanel(params) {
- params.scrollable = true;
- Panel.call(this, params);
-
-}
-
-AbstractExportPanel.prototype = Object.create(Panel.prototype);
-AbstractExportPanel.prototype.constructor = AbstractExportPanel;
-
-AbstractExportPanel.prototype.init = function () {
-
-};
-
-function compareSimple(val1, val2) {
- if (val1 < val2) {
- return -1;
- } else if (val1 > val2) {
- return 1;
- } else {
- return 0;
- }
-}
-
-AbstractExportPanel.prototype._createMiriamTypeDiv = function (annotations) {
- var self = this;
- var typeDiv = Functions.createElement({
- type: "div",
- name: "miriamSelectDiv",
- className: "minerva-export-dual-listbox-container"
- });
- typeDiv.appendChild(Functions.createElement({
- type: "h4",
- content: " Annotations:"
- }));
-
- var selectElement = Functions.createElement({
- type: "select",
- className: "minerva-multi-select"
- });
- typeDiv.appendChild(selectElement);
-
- function compare(entry1, entry2) {
- if ((entry1.count === 0 && entry2.count === 0) || (entry1.count !== 0 && entry2.count !== 0)) {
- return compareSimple(entry1.miriamType.getCommonName(), entry2.miriamType.getCommonName());
- } else {
- return compareSimple(-entry1.count, -entry2.count);
- }
- }
-
- annotations.sort(compare);
-
- for (var i = 0; i < annotations.length; i++) {
- var miriamType = annotations[i].miriamType;
- var count = annotations[i].count;
-
- var option = new Option();
- option.value = miriamType.getName();
- if (count > 0) {
- option.innerHTML = "<div class='minerva-multi-select-special'>" + miriamType.getCommonName() + " (" + count
- + ")</div>";
- } else {
- option.innerHTML = "<div >" + miriamType.getCommonName() + "</div>";
- }
- selectElement.appendChild(option);
- }
-
- self.setMiriamTypesDualListbox(self.createDualListbox(selectElement));
- return typeDiv;
-};
-
-AbstractExportPanel.prototype.createDualListbox = function (selectElement) {
- return new DualListbox(selectElement, {
- availableTitle: 'Available',
- selectedTitle: 'Used',
- addButtonText: '>',
- removeButtonText: '<',
- addAllButtonText: '>>',
- removeAllButtonText: '<<'
- });
-};
-
-AbstractExportPanel.prototype._createSelectTypeDiv = function (elementTypes) {
- var typeDiv = Functions.createElement({
- type: "div",
- name: "typeSelectDiv"
- });
- typeDiv.appendChild(Functions.createElement({
- type: "h4",
- content: " TYPE:"
- }));
- var choicesContainer = Functions.createElement({
- type: "ul",
- className: "minerva-checkbox-grid"
- });
- typeDiv.appendChild(choicesContainer);
- var i;
- var toBeExcluded = [];
- for (i = 0; i < elementTypes.length; i++) {
- toBeExcluded[elementTypes[i].parentClass] = true;
- }
- var processedNames = [];
- for (i = 0; i < elementTypes.length; i++) {
- var elementType = elementTypes[i];
- var name = elementType.name;
- if (processedNames[name] === undefined && toBeExcluded[elementType.className] === undefined) {
- processedNames[name] = true;
- var row = Functions.createElement({
- type: "li",
- content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + name + "\" value=\"" + name + "\" />" + name + "</label></div>",
- xss: false
- });
- choicesContainer.appendChild(row);
- }
- }
- choicesContainer.appendChild(Functions.createElement({
- type: "li",
- content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>",
- xss: false
- }));
- return typeDiv;
-};
-
-AbstractExportPanel.prototype.getSelectedTypes = function () {
- var self = this;
-
- var div = $("div[name='typeSelectDiv']", $(self.getElement()))[0];
- var result = [];
- var selectedAll = false;
- $(":checked", $(div)).each(function (index, element) {
- if (element.value === "ALL") {
- selectedAll = true;
- }
- result.push(element.value);
- });
- if (selectedAll) {
- return ServerConnector.getConfiguration().then(function (configuration) {
- return configuration.getSimpleElementTypeNames();
- });
- }
-
- return Promise.resolve(result);
-};
-
-AbstractExportPanel.prototype.setMiriamTypesDualListbox = function (dualListbox) {
- this._miriamTypesDualListbox = dualListbox;
-};
-AbstractExportPanel.prototype.getMiriamTypesDualListbox = function () {
- return this._miriamTypesDualListbox;
-};
-
-AbstractExportPanel.prototype._createSelectColumnDiv = function (columnTypes) {
- var columnDiv = Functions.createElement({
- type: "div",
- name: "columnSelectDiv"
- });
- columnDiv.appendChild(Functions.createElement({
- type: "h4",
- content: " COLUMN:"
- }));
- var choicesContainer = Functions.createElement({
- type: "ul",
- className: "minerva-checkbox-grid"
- });
-
- columnDiv.appendChild(choicesContainer);
- for (var i = 0; i < columnTypes.length; i++) {
- var columnType = columnTypes[i];
- var row = Functions.createElement({
- type: "li",
- content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"column_" + columnType.columnName
- + "\" value=\"" + columnType.columnName + "\" />" + columnType.name + "</label></div>",
- xss: false
- });
- choicesContainer.appendChild(row);
- }
- choicesContainer.appendChild(Functions.createElement({
- type: "li",
- content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>",
- xss: false
- }));
- return columnDiv;
-};
-
-AbstractExportPanel.prototype.getSelectedMiriamTypes = function () {
- var self = this;
- return ServerConnector.getConfiguration().then(function (configuration) {
- var selected = self.getMiriamTypesDualListbox().selected;
- var result = [];
- for (var i = 0; i < selected.length; i++) {
- var miriamType = configuration.getMiriamTypeByName(selected[i].dataset.id);
- result.push(miriamType);
- }
- return result;
- });
-};
-
-AbstractExportPanel.prototype.getSelectedColumns = function () {
- var self = this;
-
- var div = $("div[name='columnSelectDiv']", $(self.getElement()))[0];
- var selectedColumnMap = [];
- var selectedAll = false;
- $(":checked", $(div)).each(function (index, element) {
- if (element.value === "ALL") {
- selectedAll = true;
- }
- selectedColumnMap[element.value] = true;
- });
- var columnTypes = self.getAllColumns();
-
- if (selectedAll) {
- return Promise.resolve(columnTypes);
- }
-
- var result = [];
-
- for (var i = 0; i < columnTypes.length; i++) {
- var columnType = columnTypes[i];
- if (selectedColumnMap[columnType.columnName] === true) {
- result.push(columnType);
- }
- }
- return Promise.resolve(result);
-};
-
-AbstractExportPanel.prototype._getCompartmentNames = function () {
- var self = this;
- var compartments = [];
- return self._getAllCompartments().then(function (result) {
-
- var addedNames = [];
- for (var i = 0; i < result.length; i++) {
- if (addedNames[result[i].getName()] === undefined) {
- compartments.push(result[i].getName());
- addedNames[result[i].getName()] = true;
- }
- }
- compartments.sort(compareSimple);
- return compartments;
- });
-};
-
-AbstractExportPanel.prototype.getModels = function () {
- return this.getProject().getModels();
-};
-
-AbstractExportPanel.prototype._getAllCompartments = function () {
- var self = this;
- var compartments = [];
-
- var models = self.getModels();
-
- var promises = [];
- for (var i = 0; i < models.length; i++) {
- promises.push(models[i].getCompartments());
- }
-
- return Promise.all(promises).then(function (result) {
- for (var i = 0; i < result.length; i++) {
- var modelCompartments = result[i];
- for (var j = 0; j < modelCompartments.length; j++) {
- compartments.push(modelCompartments[j]);
- }
- }
- return compartments;
- });
-};
-
-AbstractExportPanel.prototype._createDownloadButton = function () {
- var self = this;
- var downloadDiv = Functions.createElement({
- type: "div",
- name: "downloadDiv",
- style: "clear:both; padding: 10px;"
- });
- var button = Functions.createElement({
- type: "button",
- name: "downloadButton",
- content: " Download",
- onclick: function () {
- GuiConnector.showProcessing();
- return self.createResponseString().then(function (result) {
- var blob = new Blob([result], {
- type: "text/plain;charset=utf-8"
- });
- var FileSaver = require("file-saver");
- return FileSaver.saveAs(blob, self.getSaveFilename());
- }).then(function () {
- GuiConnector.hideProcessing();
- }, function (error) {
- GuiConnector.hideProcessing();
- GuiConnector.alert(error);
- });
- }
- });
- downloadDiv.appendChild(button);
-
- return downloadDiv;
-};
-
-AbstractExportPanel.prototype.getSaveFilename = function () {
- var self = this;
- return self.getProject().getProjectId() + "-" + self.getPanelName() + ".txt";
-};
-
-AbstractExportPanel.prototype._createSelectIncludedCompartmentDiv = function () {
- var self = this;
- var typeDiv = Functions.createElement({
- type: "div",
- name: "includedCompartmentSelectDiv",
- className: "minerva-export-dual-listbox-container"
- });
- typeDiv.appendChild(Functions.createElement({
- type: "h4",
- content: " Included compartment/pathways:"
- }));
-
- return self._getCompartmentNames().then(function (compartmentNames) {
-
- var selectElement = Functions.createElement({
- type: "select",
- className: "minerva-multi-select"
- });
- typeDiv.appendChild(selectElement);
-
- for (var i = 0; i < compartmentNames.length; i++) {
- var name = compartmentNames[i];
-
- var option = new Option();
- option.value = name;
- option.innerHTML = "<div >" + name + "</div>";
- selectElement.appendChild(option);
- }
- self.setIncludedCompartmentsDualListbox(self.createDualListbox(selectElement));
- return typeDiv;
- });
-};
-
-AbstractExportPanel.prototype._createSelectExcludedCompartmentDiv = function () {
- var self = this;
- var typeDiv = Functions.createElement({
- type: "div",
- name: "excludedCompartmentSelectDiv",
- className: "minerva-export-dual-listbox-container"
- });
- typeDiv.appendChild(Functions.createElement({
- type: "h4",
- content: " Excluded compartment/pathways:"
- }));
-
- return self._getCompartmentNames().then(function (compartmentNames) {
-
- var selectElement = Functions.createElement({
- type: "select",
- className: "minerva-multi-select"
- });
- typeDiv.appendChild(selectElement);
-
- for (var i = 0; i < compartmentNames.length; i++) {
- var name = compartmentNames[i];
-
- var option = new Option();
- option.value = name;
- option.innerHTML = "<div >" + name + "</div>";
- selectElement.appendChild(option);
- }
- self.setExcludedCompartmentsDualListbox(self.createDualListbox(selectElement));
- return typeDiv;
- });
-};
-
-AbstractExportPanel.prototype.setIncludedCompartmentsDualListbox = function (dualListbox) {
- this._includedCompartmentsDualListbox = dualListbox;
-};
-AbstractExportPanel.prototype.getIncludedCompartmentsDualListbox = function () {
- return this._includedCompartmentsDualListbox;
-};
-
-AbstractExportPanel.prototype.getSelectedIncludedCompartments = function () {
- var self = this;
- var list = self.getIncludedCompartmentsDualListbox().selected;
- var names = [];
- var result = [];
- for (var i = 0; i < list.length; i++) {
- var element = list[i];
- names[element.dataset.id] = true;
- }
- return self._getAllCompartments().then(function (compartments) {
- for (var i = 0; i < compartments.length; i++) {
- var compartment = compartments[i];
- if (names[compartment.getName()]) {
- result.push(compartment);
- }
- }
- return result;
- });
-};
-
-AbstractExportPanel.prototype.setExcludedCompartmentsDualListbox = function (dualListbox) {
- this._excludedCompartmentsDualListbox = dualListbox;
-};
-AbstractExportPanel.prototype.getExcludedCompartmentsDualListbox = function () {
- return this._excludedCompartmentsDualListbox;
-};
-
-AbstractExportPanel.prototype.getSelectedExcludedCompartments = function () {
- var self = this;
- var list = self.getExcludedCompartmentsDualListbox().selected;
- var names = [];
- var result = [];
- for (var i = 0; i < list.length; i++) {
- var element = list[i];
- names[element.dataset.id] = true;
- }
- return self._getAllCompartments().then(function (compartments) {
- for (var i = 0; i < compartments.length; i++) {
- var compartment = compartments[i];
- if (names[compartment.getName()]) {
- result.push(compartment);
- }
- }
- return result;
- });
-};
-
-AbstractExportPanel.prototype.createResponseHeader = function (columns, miriamTypes) {
- var stringBuilder = [];
- var i;
- for (i = 0; i < columns.length; i++) {
- var column = columns[i];
- stringBuilder.push(column.name);
- }
- for (i = 0; i < miriamTypes.length; i++) {
- var miriamType = miriamTypes[i];
- stringBuilder.push(miriamType.getCommonName());
- }
- return stringBuilder.join("\t");
-
-};
-
-module.exports = AbstractExportPanel;
+"use strict";
+
+/* exported logger */
+
+var Panel = require('../Panel');
+
+var GuiConnector = require('../../GuiConnector');
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+var DualListbox = require('dual-listbox').DualListbox;
+var Promise = require("bluebird");
+
+function AbstractExportPanel(params) {
+ params.scrollable = true;
+ Panel.call(this, params);
+
+}
+
+AbstractExportPanel.prototype = Object.create(Panel.prototype);
+AbstractExportPanel.prototype.constructor = AbstractExportPanel;
+
+AbstractExportPanel.prototype.init = function () {
+
+};
+
+function compareSimple(val1, val2) {
+ if (val1 < val2) {
+ return -1;
+ } else if (val1 > val2) {
+ return 1;
+ } else {
+ return 0;
+ }
+}
+
+AbstractExportPanel.prototype._createMiriamTypeDiv = function (annotations) {
+ var self = this;
+ var typeDiv = Functions.createElement({
+ type: "div",
+ name: "miriamSelectDiv",
+ className: "minerva-export-dual-listbox-container"
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type: "h4",
+ content: " Annotations:"
+ }));
+
+ var selectElement = Functions.createElement({
+ type: "select",
+ className: "minerva-multi-select"
+ });
+ typeDiv.appendChild(selectElement);
+
+ function compare(entry1, entry2) {
+ if ((entry1.count === 0 && entry2.count === 0) || (entry1.count !== 0 && entry2.count !== 0)) {
+ return compareSimple(entry1.miriamType.getCommonName(), entry2.miriamType.getCommonName());
+ } else {
+ return compareSimple(-entry1.count, -entry2.count);
+ }
+ }
+
+ annotations.sort(compare);
+
+ for (var i = 0; i < annotations.length; i++) {
+ var miriamType = annotations[i].miriamType;
+ var count = annotations[i].count;
+
+ var option = new Option();
+ option.value = miriamType.getName();
+ if (count > 0) {
+ option.innerHTML = "<div class='minerva-multi-select-special'>" + miriamType.getCommonName() + " (" + count
+ + ")</div>";
+ } else {
+ option.innerHTML = "<div >" + miriamType.getCommonName() + "</div>";
+ }
+ selectElement.appendChild(option);
+ }
+
+ self.setMiriamTypesDualListbox(self.createDualListbox(selectElement));
+ return typeDiv;
+};
+
+AbstractExportPanel.prototype.createDualListbox = function (selectElement) {
+ return new DualListbox(selectElement, {
+ availableTitle: 'Available',
+ selectedTitle: 'Used',
+ addButtonText: '>',
+ removeButtonText: '<',
+ addAllButtonText: '>>',
+ removeAllButtonText: '<<'
+ });
+};
+
+AbstractExportPanel.prototype._createSelectTypeDiv = function (elementTypes) {
+ var typeDiv = Functions.createElement({
+ type: "div",
+ name: "typeSelectDiv"
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type: "h4",
+ content: " TYPE:"
+ }));
+ var choicesContainer = Functions.createElement({
+ type: "ul",
+ className: "minerva-checkbox-grid"
+ });
+ typeDiv.appendChild(choicesContainer);
+ var i;
+ var toBeExcluded = [];
+ for (i = 0; i < elementTypes.length; i++) {
+ toBeExcluded[elementTypes[i].parentClass] = true;
+ }
+ var processedNames = [];
+ for (i = 0; i < elementTypes.length; i++) {
+ var elementType = elementTypes[i];
+ var name = elementType.name;
+ if (processedNames[name] === undefined && toBeExcluded[elementType.className] === undefined) {
+ processedNames[name] = true;
+ var row = Functions.createElement({
+ type: "li",
+ content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"" + name + "\" value=\"" + name + "\" />" + name + "</label></div>",
+ xss: false
+ });
+ choicesContainer.appendChild(row);
+ }
+ }
+ choicesContainer.appendChild(Functions.createElement({
+ type: "li",
+ content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>",
+ xss: false
+ }));
+ return typeDiv;
+};
+
+AbstractExportPanel.prototype.getSelectedTypes = function () {
+ var self = this;
+
+ var div = $("div[name='typeSelectDiv']", $(self.getElement()))[0];
+ var result = [];
+ var selectedAll = false;
+ $(":checked", $(div)).each(function (index, element) {
+ if (element.value === "ALL") {
+ selectedAll = true;
+ }
+ result.push(element.value);
+ });
+ if (selectedAll) {
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ return configuration.getSimpleElementTypeNames();
+ });
+ }
+
+ return Promise.resolve(result);
+};
+
+AbstractExportPanel.prototype.setMiriamTypesDualListbox = function (dualListbox) {
+ this._miriamTypesDualListbox = dualListbox;
+};
+AbstractExportPanel.prototype.getMiriamTypesDualListbox = function () {
+ return this._miriamTypesDualListbox;
+};
+
+AbstractExportPanel.prototype._createSelectColumnDiv = function (columnTypes) {
+ var columnDiv = Functions.createElement({
+ type: "div",
+ name: "columnSelectDiv"
+ });
+ columnDiv.appendChild(Functions.createElement({
+ type: "h4",
+ content: " COLUMN:"
+ }));
+ var choicesContainer = Functions.createElement({
+ type: "ul",
+ className: "minerva-checkbox-grid"
+ });
+
+ columnDiv.appendChild(choicesContainer);
+ for (var i = 0; i < columnTypes.length; i++) {
+ var columnType = columnTypes[i];
+ var row = Functions.createElement({
+ type: "li",
+ content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"column_" + columnType.columnName
+ + "\" value=\"" + columnType.columnName + "\" />" + columnType.name + "</label></div>",
+ xss: false
+ });
+ choicesContainer.appendChild(row);
+ }
+ choicesContainer.appendChild(Functions.createElement({
+ type: "li",
+ content: "<div class=\"checkbox\"><label> <input type=\"checkbox\" name=\"ALL\" value=\"ALL\" />ALL</label></div>",
+ xss: false
+ }));
+ return columnDiv;
+};
+
+AbstractExportPanel.prototype.getSelectedMiriamTypes = function () {
+ var self = this;
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ var selected = self.getMiriamTypesDualListbox().selected;
+ var result = [];
+ for (var i = 0; i < selected.length; i++) {
+ var miriamType = configuration.getMiriamTypeByName(selected[i].dataset.id);
+ result.push(miriamType);
+ }
+ return result;
+ });
+};
+
+AbstractExportPanel.prototype.getSelectedColumns = function () {
+ var self = this;
+
+ var div = $("div[name='columnSelectDiv']", $(self.getElement()))[0];
+ var selectedColumnMap = [];
+ var selectedAll = false;
+ $(":checked", $(div)).each(function (index, element) {
+ if (element.value === "ALL") {
+ selectedAll = true;
+ }
+ selectedColumnMap[element.value] = true;
+ });
+ var columnTypes = self.getAllColumns();
+
+ if (selectedAll) {
+ return Promise.resolve(columnTypes);
+ }
+
+ var result = [];
+
+ for (var i = 0; i < columnTypes.length; i++) {
+ var columnType = columnTypes[i];
+ if (selectedColumnMap[columnType.columnName] === true) {
+ result.push(columnType);
+ }
+ }
+ return Promise.resolve(result);
+};
+
+AbstractExportPanel.prototype._getCompartmentNames = function () {
+ var self = this;
+ var compartments = [];
+ return self._getAllCompartments().then(function (result) {
+
+ var addedNames = [];
+ for (var i = 0; i < result.length; i++) {
+ if (addedNames[result[i].getName()] === undefined) {
+ compartments.push(result[i].getName());
+ addedNames[result[i].getName()] = true;
+ }
+ }
+ compartments.sort(compareSimple);
+ return compartments;
+ });
+};
+
+AbstractExportPanel.prototype.getModels = function () {
+ return this.getProject().getModels();
+};
+
+AbstractExportPanel.prototype._getAllCompartments = function () {
+ var self = this;
+ var compartments = [];
+
+ var models = self.getModels();
+
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getCompartments());
+ }
+
+ return Promise.all(promises).then(function (result) {
+ for (var i = 0; i < result.length; i++) {
+ var modelCompartments = result[i];
+ for (var j = 0; j < modelCompartments.length; j++) {
+ compartments.push(modelCompartments[j]);
+ }
+ }
+ return compartments;
+ });
+};
+
+AbstractExportPanel.prototype._createDownloadButton = function () {
+ var self = this;
+ var downloadDiv = Functions.createElement({
+ type: "div",
+ name: "downloadDiv",
+ style: "clear:both; padding: 10px;"
+ });
+ var button = Functions.createElement({
+ type: "button",
+ name: "downloadButton",
+ content: " Download",
+ onclick: function () {
+ GuiConnector.showProcessing();
+ return self.createResponseString().then(function (result) {
+ var blob = new Blob([result], {
+ type: "text/plain;charset=utf-8"
+ });
+ var FileSaver = require("file-saver");
+ return FileSaver.saveAs(blob, self.getSaveFilename());
+ }).then(function () {
+ GuiConnector.hideProcessing();
+ }, function (error) {
+ GuiConnector.hideProcessing();
+ GuiConnector.alert(error);
+ });
+ }
+ });
+ downloadDiv.appendChild(button);
+
+ return downloadDiv;
+};
+
+AbstractExportPanel.prototype.getSaveFilename = function () {
+ var self = this;
+ return self.getProject().getProjectId() + "-" + self.getPanelName() + ".txt";
+};
+
+AbstractExportPanel.prototype._createSelectIncludedCompartmentDiv = function () {
+ var self = this;
+ var typeDiv = Functions.createElement({
+ type: "div",
+ name: "includedCompartmentSelectDiv",
+ className: "minerva-export-dual-listbox-container"
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type: "h4",
+ content: " Included compartment/pathways:"
+ }));
+
+ return self._getCompartmentNames().then(function (compartmentNames) {
+
+ var selectElement = Functions.createElement({
+ type: "select",
+ className: "minerva-multi-select"
+ });
+ typeDiv.appendChild(selectElement);
+
+ for (var i = 0; i < compartmentNames.length; i++) {
+ var name = compartmentNames[i];
+
+ var option = new Option();
+ option.value = name;
+ option.innerHTML = "<div >" + name + "</div>";
+ selectElement.appendChild(option);
+ }
+ self.setIncludedCompartmentsDualListbox(self.createDualListbox(selectElement));
+ return typeDiv;
+ });
+};
+
+AbstractExportPanel.prototype._createSelectExcludedCompartmentDiv = function () {
+ var self = this;
+ var typeDiv = Functions.createElement({
+ type: "div",
+ name: "excludedCompartmentSelectDiv",
+ className: "minerva-export-dual-listbox-container"
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type: "h4",
+ content: " Excluded compartment/pathways:"
+ }));
+
+ return self._getCompartmentNames().then(function (compartmentNames) {
+
+ var selectElement = Functions.createElement({
+ type: "select",
+ className: "minerva-multi-select"
+ });
+ typeDiv.appendChild(selectElement);
+
+ for (var i = 0; i < compartmentNames.length; i++) {
+ var name = compartmentNames[i];
+
+ var option = new Option();
+ option.value = name;
+ option.innerHTML = "<div >" + name + "</div>";
+ selectElement.appendChild(option);
+ }
+ self.setExcludedCompartmentsDualListbox(self.createDualListbox(selectElement));
+ return typeDiv;
+ });
+};
+
+AbstractExportPanel.prototype.setIncludedCompartmentsDualListbox = function (dualListbox) {
+ this._includedCompartmentsDualListbox = dualListbox;
+};
+AbstractExportPanel.prototype.getIncludedCompartmentsDualListbox = function () {
+ return this._includedCompartmentsDualListbox;
+};
+
+AbstractExportPanel.prototype.getSelectedIncludedCompartments = function () {
+ var self = this;
+ var list = self.getIncludedCompartmentsDualListbox().selected;
+ var names = [];
+ var result = [];
+ for (var i = 0; i < list.length; i++) {
+ var element = list[i];
+ names[element.dataset.id] = true;
+ }
+ return self._getAllCompartments().then(function (compartments) {
+ for (var i = 0; i < compartments.length; i++) {
+ var compartment = compartments[i];
+ if (names[compartment.getName()]) {
+ result.push(compartment);
+ }
+ }
+ return result;
+ });
+};
+
+AbstractExportPanel.prototype.setExcludedCompartmentsDualListbox = function (dualListbox) {
+ this._excludedCompartmentsDualListbox = dualListbox;
+};
+AbstractExportPanel.prototype.getExcludedCompartmentsDualListbox = function () {
+ return this._excludedCompartmentsDualListbox;
+};
+
+AbstractExportPanel.prototype.getSelectedExcludedCompartments = function () {
+ var self = this;
+ var list = self.getExcludedCompartmentsDualListbox().selected;
+ var names = [];
+ var result = [];
+ for (var i = 0; i < list.length; i++) {
+ var element = list[i];
+ names[element.dataset.id] = true;
+ }
+ return self._getAllCompartments().then(function (compartments) {
+ for (var i = 0; i < compartments.length; i++) {
+ var compartment = compartments[i];
+ if (names[compartment.getName()]) {
+ result.push(compartment);
+ }
+ }
+ return result;
+ });
+};
+
+AbstractExportPanel.prototype.createResponseHeader = function (columns, miriamTypes) {
+ var stringBuilder = [];
+ var i;
+ for (i = 0; i < columns.length; i++) {
+ var column = columns[i];
+ stringBuilder.push(column.name);
+ }
+ for (i = 0; i < miriamTypes.length; i++) {
+ var miriamType = miriamTypes[i];
+ stringBuilder.push(miriamType.getCommonName());
+ }
+ return stringBuilder.join("\t");
+
+};
+
+module.exports = AbstractExportPanel;
diff --git a/frontend-js/src/main/js/gui/export/ElementExportPanel.js b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
index 2d0c3028e9ba97c227f248d7ab5ee0ee3f58d0b6..5b1b0ae483623095bea32f795bee918fc822d26c 100644
--- a/frontend-js/src/main/js/gui/export/ElementExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/ElementExportPanel.js
@@ -1,215 +1,215 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractExportPanel = require('./AbstractExportPanel');
-var GuiMessageError = require('../GuiMessageError');
-
-var logger = require('../../logger');
-
-var Promise = require("bluebird");
-
-function ElementExportPanel(params) {
- params.panelName = "elementExport";
- AbstractExportPanel.call(this, params);
-}
-
-ElementExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
-ElementExportPanel.prototype.constructor = ElementExportPanel;
-
-ElementExportPanel.prototype.init = function () {
- var self = this;
- var element = self.getElement();
- var configuration;
- return ServerConnector.getConfiguration().then(function (result) {
- configuration = result;
- var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
- element.appendChild(typeDiv);
- element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
- return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
- }).then(function (statistics) {
- return self._createMiriamTypeDiv(statistics.getElementAnnotations());
- }).then(function (div) {
- element.appendChild(div);
- return self._createSelectIncludedCompartmentDiv();
- }).then(function (div) {
- element.appendChild(div);
- return self._createSelectExcludedCompartmentDiv();
- }).then(function (div) {
- element.appendChild(div);
- element.appendChild(self._createDownloadButton());
- }).then(function () {
- $(window).trigger('resize');
- });
-};
-
-ElementExportPanel.prototype.createResponseString = function () {
- var self = this;
- var types, miriamTypes;
- var includedCompartmentIds = [];
- var excludedCompartmentIds = [];
- var models = self.getProject().getModels();
-
- var elements = [];
- return self.getSelectedTypes().then(function (result) {
- if (result.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one type"));
- }
- types = result;
- return self.getSelectedIncludedCompartments();
- }).then(function (result) {
- result.forEach(function (compartment) {
- includedCompartmentIds.push(compartment.getId());
- });
- return self.getSelectedExcludedCompartments();
- }).then(function (result) {
- result.forEach(function (compartment) {
- excludedCompartmentIds.push(compartment.getId());
- });
-
- var promises = [];
- for (var i = 0; i < models.length; i++) {
- promises.push(models[i].getAliases({
- type: types,
- complete: true,
- includedCompartmentIds: includedCompartmentIds,
- excludedCompartmentIds: excludedCompartmentIds
- }));
- }
- return Promise.all(promises);
- }).then(function (aliasesByModel) {
- for (var i = 0; i < aliasesByModel.length; i++) {
- for (var j = 0; j < aliasesByModel[i].length; j++) {
- elements.push(aliasesByModel[i][j]);
- }
- }
-
- return self.getSelectedMiriamTypes();
- }).then(function (result) {
- miriamTypes = result;
- return self.getSelectedColumns();
- }).then(function (selectedColumns) {
- if (selectedColumns.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one column"));
- }
-
- var rows = [];
- rows.push(self.createResponseHeader(selectedColumns, miriamTypes));
- for (var i = 0; i < elements.length; i++) {
- rows.push(self.createResponseRow(elements[i], selectedColumns, miriamTypes));
- }
- return rows.join("\n");
- });
-};
-
-ElementExportPanel.prototype.createResponseRow = function (alias, columns, miriamTypes) {
- var stringBuilder = [];
- var i, value;
- for (i = 0; i < columns.length; i++) {
- var column = columns[i];
- value = alias[column.method]();
- if (column.formatFunction !== undefined) {
- value = column.formatFunction(value);
- }
- if (value instanceof String || typeof value === "string") {
- value = value.replace(/[\n\r]/g, ' ');
- }
- stringBuilder.push(value);
- }
- for (i = 0; i < miriamTypes.length; i++) {
- value = "";
- var miriamType = miriamTypes[i];
- var references = alias.getReferences();
- for (var j = 0; j < references.length; j++) {
- var reference = references[j];
- if (reference.getType() === miriamType.getName()) {
- value += reference.getResource() + ",";
- }
- }
- stringBuilder.push(value);
- }
- return stringBuilder.join("\t");
-};
-
-ElementExportPanel.prototype.getAllColumns = function () {
- return [{
- "columnName": "id",
- "method": "getId",
- "name": "Id"
- }, {
- "columnName": "name",
- "method": "getName",
- "name": "Name"
- }, {
- "columnName": "description",
- "method": "getDescription",
- "name": "Description"
- }, {
- "columnName": "modelId",
- "method": "getModelId",
- "name": "Model"
- }, {
- "columnName": "type",
- "method": "getType",
- "name": "Type"
- }, {
- "columnName": "complexId",
- "method": "getComplexId",
- "name": "Complex"
- }, {
- "columnName": "compartmentId",
- "method": "getCompartmentId",
- "name": "Compartment"
- }, {
- "columnName": "charge",
- "method": "getCharge",
- "name": "Charge"
- }, {
- "columnName": "symbol",
- "method": "getSymbol",
- "name": "Symbol"
- }, {
- "columnName": "fullName",
- "method": "getFullName",
- "name": "Full name"
- }, {
- "columnName": "abbreviation",
- "method": "getAbbreviation",
- "name": "Abbreviation"
- }, {
- "columnName": "formula",
- "method": "getFormula",
- "name": "Formula"
- }, {
- "columnName": "synonyms",
- "method": "getSynonyms",
- "name": "Synonyms"
- }, {
- "columnName": "formerSymbols",
- "method": "getFormerSymbols",
- "name": "Former symbols"
- }, {
- "columnName": "references",
- "method": "getReferences",
- "name": "References",
- "formatFunction": function (references) {
- var stringBuilder = [];
- for (var i = 0; i < references.length; i++) {
- var reference = references[i];
- stringBuilder.push(reference.getType() + ":" + reference.getResource());
- }
- return stringBuilder.join(",");
- }
- }, {
- "columnName": "linkedSubmodelId",
- "method": "getLinkedSubmodelId",
- "name": "Linked submodel"
- }, {
- "columnName": "elementId",
- "method": "getElementId",
- "name": "Element external id"
- }];
-};
-
-
-module.exports = ElementExportPanel;
+"use strict";
+
+/* exported logger */
+
+var AbstractExportPanel = require('./AbstractExportPanel');
+var GuiMessageError = require('../GuiMessageError');
+
+var logger = require('../../logger');
+
+var Promise = require("bluebird");
+
+function ElementExportPanel(params) {
+ params.panelName = "elementExport";
+ AbstractExportPanel.call(this, params);
+}
+
+ElementExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
+ElementExportPanel.prototype.constructor = ElementExportPanel;
+
+ElementExportPanel.prototype.init = function () {
+ var self = this;
+ var element = self.getElement();
+ var configuration;
+ return ServerConnector.getConfiguration().then(function (result) {
+ configuration = result;
+ var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
+ element.appendChild(typeDiv);
+ element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
+ return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
+ }).then(function (statistics) {
+ return self._createMiriamTypeDiv(statistics.getElementAnnotations());
+ }).then(function (div) {
+ element.appendChild(div);
+ return self._createSelectIncludedCompartmentDiv();
+ }).then(function (div) {
+ element.appendChild(div);
+ return self._createSelectExcludedCompartmentDiv();
+ }).then(function (div) {
+ element.appendChild(div);
+ element.appendChild(self._createDownloadButton());
+ }).then(function () {
+ $(window).trigger('resize');
+ });
+};
+
+ElementExportPanel.prototype.createResponseString = function () {
+ var self = this;
+ var types, miriamTypes;
+ var includedCompartmentIds = [];
+ var excludedCompartmentIds = [];
+ var models = self.getProject().getModels();
+
+ var elements = [];
+ return self.getSelectedTypes().then(function (result) {
+ if (result.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one type"));
+ }
+ types = result;
+ return self.getSelectedIncludedCompartments();
+ }).then(function (result) {
+ result.forEach(function (compartment) {
+ includedCompartmentIds.push(compartment.getId());
+ });
+ return self.getSelectedExcludedCompartments();
+ }).then(function (result) {
+ result.forEach(function (compartment) {
+ excludedCompartmentIds.push(compartment.getId());
+ });
+
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getAliases({
+ type: types,
+ complete: true,
+ includedCompartmentIds: includedCompartmentIds,
+ excludedCompartmentIds: excludedCompartmentIds
+ }));
+ }
+ return Promise.all(promises);
+ }).then(function (aliasesByModel) {
+ for (var i = 0; i < aliasesByModel.length; i++) {
+ for (var j = 0; j < aliasesByModel[i].length; j++) {
+ elements.push(aliasesByModel[i][j]);
+ }
+ }
+
+ return self.getSelectedMiriamTypes();
+ }).then(function (result) {
+ miriamTypes = result;
+ return self.getSelectedColumns();
+ }).then(function (selectedColumns) {
+ if (selectedColumns.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one column"));
+ }
+
+ var rows = [];
+ rows.push(self.createResponseHeader(selectedColumns, miriamTypes));
+ for (var i = 0; i < elements.length; i++) {
+ rows.push(self.createResponseRow(elements[i], selectedColumns, miriamTypes));
+ }
+ return rows.join("\n");
+ });
+};
+
+ElementExportPanel.prototype.createResponseRow = function (alias, columns, miriamTypes) {
+ var stringBuilder = [];
+ var i, value;
+ for (i = 0; i < columns.length; i++) {
+ var column = columns[i];
+ value = alias[column.method]();
+ if (column.formatFunction !== undefined) {
+ value = column.formatFunction(value);
+ }
+ if (value instanceof String || typeof value === "string") {
+ value = value.replace(/[\n\r]/g, ' ');
+ }
+ stringBuilder.push(value);
+ }
+ for (i = 0; i < miriamTypes.length; i++) {
+ value = "";
+ var miriamType = miriamTypes[i];
+ var references = alias.getReferences();
+ for (var j = 0; j < references.length; j++) {
+ var reference = references[j];
+ if (reference.getType() === miriamType.getName()) {
+ value += reference.getResource() + ",";
+ }
+ }
+ stringBuilder.push(value);
+ }
+ return stringBuilder.join("\t");
+};
+
+ElementExportPanel.prototype.getAllColumns = function () {
+ return [{
+ "columnName": "id",
+ "method": "getId",
+ "name": "Id"
+ }, {
+ "columnName": "name",
+ "method": "getName",
+ "name": "Name"
+ }, {
+ "columnName": "description",
+ "method": "getDescription",
+ "name": "Description"
+ }, {
+ "columnName": "modelId",
+ "method": "getModelId",
+ "name": "Model"
+ }, {
+ "columnName": "type",
+ "method": "getType",
+ "name": "Type"
+ }, {
+ "columnName": "complexId",
+ "method": "getComplexId",
+ "name": "Complex"
+ }, {
+ "columnName": "compartmentId",
+ "method": "getCompartmentId",
+ "name": "Compartment"
+ }, {
+ "columnName": "charge",
+ "method": "getCharge",
+ "name": "Charge"
+ }, {
+ "columnName": "symbol",
+ "method": "getSymbol",
+ "name": "Symbol"
+ }, {
+ "columnName": "fullName",
+ "method": "getFullName",
+ "name": "Full name"
+ }, {
+ "columnName": "abbreviation",
+ "method": "getAbbreviation",
+ "name": "Abbreviation"
+ }, {
+ "columnName": "formula",
+ "method": "getFormula",
+ "name": "Formula"
+ }, {
+ "columnName": "synonyms",
+ "method": "getSynonyms",
+ "name": "Synonyms"
+ }, {
+ "columnName": "formerSymbols",
+ "method": "getFormerSymbols",
+ "name": "Former symbols"
+ }, {
+ "columnName": "references",
+ "method": "getReferences",
+ "name": "References",
+ "formatFunction": function (references) {
+ var stringBuilder = [];
+ for (var i = 0; i < references.length; i++) {
+ var reference = references[i];
+ stringBuilder.push(reference.getType() + ":" + reference.getResource());
+ }
+ return stringBuilder.join(",");
+ }
+ }, {
+ "columnName": "linkedSubmodelId",
+ "method": "getLinkedSubmodelId",
+ "name": "Linked submodel"
+ }, {
+ "columnName": "elementId",
+ "method": "getElementId",
+ "name": "Element external id"
+ }];
+};
+
+
+module.exports = ElementExportPanel;
diff --git a/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
index 4b3c3d2a124e6b5914054439155c7d1d54084b6b..9976880791a52ebec5572738f01d8372ac865f19 100644
--- a/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/GraphicsExportPanel.js
@@ -1,159 +1,159 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractExportPanel = require('./AbstractExportPanel');
-var Functions = require('../../Functions');
-var GuiConnector = require('../../GuiConnector');
-
-var logger = require('../../logger');
-var xss = require('xss');
-
-function GraphicsExportPanel(params) {
- params.panelName = "graphicsExport";
- AbstractExportPanel.call(this, params);
-}
-
-GraphicsExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
-GraphicsExportPanel.prototype.constructor = GraphicsExportPanel;
-
-GraphicsExportPanel.prototype.init = function () {
- var self = this;
- var element = self.getElement();
- var configuration;
- element.appendChild(self._createSelectProjectDiv());
- return ServerConnector.getConfiguration().then(function (result) {
- configuration = result;
- element.appendChild(self._createSelectGraphicsFormatDiv(configuration.getImageConverters()));
- element.appendChild(self._createDownloadButton());
- }).then(function () {
- $(window).trigger('resize');
- });
-};
-
-GraphicsExportPanel.prototype._createSelectProjectDiv = function () {
- var self = this;
- var typeDiv = Functions.createElement({
- type: "div",
- name: "modelSelectDiv"
- });
- typeDiv.appendChild(Functions.createElement({
- type: "h4",
- content: "(Sub)map:"
- }));
-
- var choicesContainer = Functions.createElement({
- type: "ul"
- });
- typeDiv.appendChild(choicesContainer);
-
- var models = self.getModels();
-
- for (var i = 0; i < models.length; i++) {
- var model = models[i];
- var checkedString = "";
- if (i === 0) {
- checkedString = ' checked="checked" ';
- }
- var modelName = xss(model.getName());
- var row = Functions.createElement({
- type: "li",
- content: '<div><label> <input type="radio" name="model" value="' + model.getId() + '"' + checkedString + '/>'
- + modelName + '</label></div>',
- xss: false
- });
- choicesContainer.appendChild(row);
- }
-
- return typeDiv;
-};
-
-GraphicsExportPanel.prototype._createSelectGraphicsFormatDiv = function (formats) {
- var typeDiv = Functions.createElement({
- type: "div",
- name: "formatSelectDiv"
- });
- typeDiv.appendChild(Functions.createElement({
- type: "h4",
- content: "Format:"
- }));
-
- var choicesContainer = Functions.createElement({
- type: "ul"
- });
- typeDiv.appendChild(choicesContainer);
-
- for (var i = 0; i < formats.length; i++) {
- var format = formats[i];
- var checkedString = "";
- if (i === 0) {
- checkedString = ' checked="checked" ';
- }
- var row = Functions.createElement({
- type: "li",
- content: '<div><label> <input type="radio" name="format" value="' + format.handler + '"' + checkedString + '/>'
- + format.name + '</label></div>',
- xss: false
-
- });
- choicesContainer.appendChild(row);
- }
-
- return typeDiv;
-};
-
-GraphicsExportPanel.prototype.getSubmapId = function () {
- var self = this;
- var div = $("div[name='modelSelectDiv']", $(self.getElement()))[0];
- var id = null;
- $(":checked", $(div)).each(function (index, element) {
- id = element.value;
- });
- return id;
-};
-GraphicsExportPanel.prototype.getFormatHandler = function () {
- var self = this;
- var div = $("div[name='formatSelectDiv']", $(self.getElement()))[0];
- var format = null;
- $(":checked", $(div)).each(function (index, element) {
- format = element.value;
- });
- return format;
-};
-
-GraphicsExportPanel.prototype._createDownloadButton = function () {
- var self = this;
- var downloadDiv = Functions.createElement({
- type: "div",
- name: "downloadDiv",
- style: "clear:both; padding: 10px;"
- });
- var button = Functions.createElement({
- type: "button",
- name: "downloadButton",
- content: " Download",
- onclick: function () {
- var identifier = null;
- var defaultOverlayName = "Network";
- for (var i = 0; i < self.getProject().getDataOverlays().length; i++) {
- var overlay = self.getProject().getDataOverlays()[i];
- if (identifier === null || overlay.getName() === defaultOverlayName) {
- identifier = overlay.getId();
- }
- }
-
- return ServerConnector.getImageDownloadUrl({
- modelId: self.getSubmapId(),
- backgroundOverlayId: identifier,
- handlerClass: self.getFormatHandler()
- }).then(function (url) {
- return self.downloadFile(url);
- }).then(null, GuiConnector.alert);
- }
- });
- downloadDiv.appendChild(button);
-
- return downloadDiv;
-};
-
-module.exports = GraphicsExportPanel;
+"use strict";
+
+/* exported logger */
+
+var AbstractExportPanel = require('./AbstractExportPanel');
+var Functions = require('../../Functions');
+var GuiConnector = require('../../GuiConnector');
+
+var logger = require('../../logger');
+var xss = require('xss');
+
+function GraphicsExportPanel(params) {
+ params.panelName = "graphicsExport";
+ AbstractExportPanel.call(this, params);
+}
+
+GraphicsExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
+GraphicsExportPanel.prototype.constructor = GraphicsExportPanel;
+
+GraphicsExportPanel.prototype.init = function () {
+ var self = this;
+ var element = self.getElement();
+ var configuration;
+ element.appendChild(self._createSelectProjectDiv());
+ return ServerConnector.getConfiguration().then(function (result) {
+ configuration = result;
+ element.appendChild(self._createSelectGraphicsFormatDiv(configuration.getImageConverters()));
+ element.appendChild(self._createDownloadButton());
+ }).then(function () {
+ $(window).trigger('resize');
+ });
+};
+
+GraphicsExportPanel.prototype._createSelectProjectDiv = function () {
+ var self = this;
+ var typeDiv = Functions.createElement({
+ type: "div",
+ name: "modelSelectDiv"
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type: "h4",
+ content: "(Sub)map:"
+ }));
+
+ var choicesContainer = Functions.createElement({
+ type: "ul"
+ });
+ typeDiv.appendChild(choicesContainer);
+
+ var models = self.getModels();
+
+ for (var i = 0; i < models.length; i++) {
+ var model = models[i];
+ var checkedString = "";
+ if (i === 0) {
+ checkedString = ' checked="checked" ';
+ }
+ var modelName = xss(model.getName());
+ var row = Functions.createElement({
+ type: "li",
+ content: '<div><label> <input type="radio" name="model" value="' + model.getId() + '"' + checkedString + '/>'
+ + modelName + '</label></div>',
+ xss: false
+ });
+ choicesContainer.appendChild(row);
+ }
+
+ return typeDiv;
+};
+
+GraphicsExportPanel.prototype._createSelectGraphicsFormatDiv = function (formats) {
+ var typeDiv = Functions.createElement({
+ type: "div",
+ name: "formatSelectDiv"
+ });
+ typeDiv.appendChild(Functions.createElement({
+ type: "h4",
+ content: "Format:"
+ }));
+
+ var choicesContainer = Functions.createElement({
+ type: "ul"
+ });
+ typeDiv.appendChild(choicesContainer);
+
+ for (var i = 0; i < formats.length; i++) {
+ var format = formats[i];
+ var checkedString = "";
+ if (i === 0) {
+ checkedString = ' checked="checked" ';
+ }
+ var row = Functions.createElement({
+ type: "li",
+ content: '<div><label> <input type="radio" name="format" value="' + format.handler + '"' + checkedString + '/>'
+ + format.name + '</label></div>',
+ xss: false
+
+ });
+ choicesContainer.appendChild(row);
+ }
+
+ return typeDiv;
+};
+
+GraphicsExportPanel.prototype.getSubmapId = function () {
+ var self = this;
+ var div = $("div[name='modelSelectDiv']", $(self.getElement()))[0];
+ var id = null;
+ $(":checked", $(div)).each(function (index, element) {
+ id = element.value;
+ });
+ return id;
+};
+GraphicsExportPanel.prototype.getFormatHandler = function () {
+ var self = this;
+ var div = $("div[name='formatSelectDiv']", $(self.getElement()))[0];
+ var format = null;
+ $(":checked", $(div)).each(function (index, element) {
+ format = element.value;
+ });
+ return format;
+};
+
+GraphicsExportPanel.prototype._createDownloadButton = function () {
+ var self = this;
+ var downloadDiv = Functions.createElement({
+ type: "div",
+ name: "downloadDiv",
+ style: "clear:both; padding: 10px;"
+ });
+ var button = Functions.createElement({
+ type: "button",
+ name: "downloadButton",
+ content: " Download",
+ onclick: function () {
+ var identifier = null;
+ var defaultOverlayName = "Network";
+ for (var i = 0; i < self.getProject().getDataOverlays().length; i++) {
+ var overlay = self.getProject().getDataOverlays()[i];
+ if (identifier === null || overlay.getName() === defaultOverlayName) {
+ identifier = overlay.getId();
+ }
+ }
+
+ return ServerConnector.getImageDownloadUrl({
+ modelId: self.getSubmapId(),
+ backgroundOverlayId: identifier,
+ handlerClass: self.getFormatHandler()
+ }).then(function (url) {
+ return self.downloadFile(url);
+ }).then(null, GuiConnector.alert);
+ }
+ });
+ downloadDiv.appendChild(button);
+
+ return downloadDiv;
+};
+
+module.exports = GraphicsExportPanel;
diff --git a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
index d34f0b40a9b60d9e9e6368ae5e63b0cd9bcb718e..1543fafae775f649c2e207e4251c34681a63ce7f 100644
--- a/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
+++ b/frontend-js/src/main/js/gui/export/NetworkExportPanel.js
@@ -1,251 +1,251 @@
-"use strict";
-
-/* exported logger */
-
-var AbstractExportPanel = require('./AbstractExportPanel');
-
-var Promise = require("bluebird");
-var logger = require('../../logger');
-var GuiMessageError = require('../GuiMessageError');
-
-
-function NetworkExportPanel(params) {
- params.panelName = "networkExport";
- AbstractExportPanel.call(this, params);
-}
-
-NetworkExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
-NetworkExportPanel.prototype.constructor = NetworkExportPanel;
-
-NetworkExportPanel.prototype.init = function () {
-
- var self = this;
- var element = self.getElement();
- var configuration;
- return ServerConnector.getConfiguration().then(function (result) {
- configuration = result;
- var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
- element.appendChild(typeDiv);
- element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
- return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
- }).then(function (statistics) {
- return self._createMiriamTypeDiv(statistics.getReactionAnnotations());
- }).then(function (div) {
- element.appendChild(div);
- return self._createSelectIncludedCompartmentDiv();
- }).then(function (div) {
- element.appendChild(div);
- return self._createSelectExcludedCompartmentDiv();
- }).then(function (div) {
- element.appendChild(div);
- element.appendChild(self._createDownloadButton());
- }).then(function () {
- $(window).trigger('resize');
- });
-
-};
-
-NetworkExportPanel.prototype.getAllColumns = function () {
- return [{
- "columnName": "elements",
- "method": "getElements",
- "name": "Elements",
- "formatFunction": function (elements, reaction, elementIds) {
- var stringBuilder = [];
- var type;
- var elementFormat = function (element) {
- if (elementIds[element.getAlias().getId()]) {
- stringBuilder.push(type + ":" + element.getAlias().getId());
- }
- };
- type = "REACTANT";
- reaction.getReactants().forEach(elementFormat);
- type = "PRODUCT";
- reaction.getProducts().forEach(elementFormat);
- type = "MODIFIER";
- reaction.getModifiers().forEach(elementFormat);
-
- return stringBuilder.join(",");
- }
- }, {
- "columnName": "id",
- "method": "getId",
- "name": "Id"
- }, {
- "columnName": "description",
- "method": "getDescription",
- "name": "Description"
- }, {
- "columnName": "modelId",
- "method": "getModelId",
- "name": "Model"
- }, {
- "columnName": "type",
- "method": "getType",
- "name": "Type"
- }, {
- "columnName": "symbol",
- "method": "getSymbol",
- "name": "Symbol"
- }, {
- "columnName": "abbreviation",
- "method": "getAbbreviation",
- "name": "Abbreviation"
- }, {
- "columnName": "formula",
- "method": "getFormula",
- "name": "Formula"
- }, {
- "columnName": "synonyms",
- "method": "getSynonyms",
- "name": "Synonyms"
- }, {
- "columnName": "references",
- "method": "getReferences",
- "name": "References",
- "formatFunction": function (references) {
- var stringBuilder = [];
- for (var i = 0; i < references.length; i++) {
- var reference = references[i];
- stringBuilder.push(reference.getType() + ":" + reference.getResource());
- }
- return stringBuilder.join(",");
- }
- }, {
- "columnName": "reactionId",
- "method": "getReactionId",
- "name": "Element external id"
- }, {
- "columnName": "mechanicalConfidenceScore",
- "method": "getMechanicalConfidenceScore",
- "name": "Mechanical Confidence Score"
- }, {
- "columnName": "lowerBound",
- "method": "getLowerBound",
- "name": "Lower Bound"
- }, {
- "columnName": "upperBound",
- "method": "getUpperBound",
- "name": "Upper Bound"
- }, {
- "columnName": "geneProteinReaction",
- "method": "getGeneProteinReaction",
- "name": "Gene Protein Reaction"
- }, {
- "columnName": "subsystem",
- "method": "getSubsystem",
- "name": "Subsystem"
- }];
-};
-
-function matchReaction(reaction, elementIds) {
- var count = 0;
- reaction.getElements().forEach(function (element) {
- if (elementIds[element.getId()]) {
- count++;
- }
- });
- return count > 1;
-}
-
-NetworkExportPanel.prototype.createResponseString = function () {
- var self = this;
- var types, miriamTypes;
- var includedCompartmentIds = [];
- var excludedCompartmentIds = [];
- var models = self.getProject().getModels();
-
- var elementIds = [];
- var reactions = [];
- return self.getSelectedTypes().then(function (result) {
- if (result.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one type"));
- }
- types = result;
- return self.getSelectedIncludedCompartments();
- }).then(function (result) {
- result.forEach(function (compartment) {
- includedCompartmentIds.push(compartment.getId());
- });
- return self.getSelectedExcludedCompartments();
- }).then(function (result) {
- result.forEach(function (compartment) {
- excludedCompartmentIds.push(compartment.getId());
- });
-
- var promises = [];
- for (var i = 0; i < models.length; i++) {
- promises.push(models[i].getAliases({
- type: types,
- complete: true,
- includedCompartmentIds: includedCompartmentIds,
- excludedCompartmentIds: excludedCompartmentIds
- }));
- }
- return Promise.all(promises);
- }).then(function (aliasesByModel) {
- var promises = [];
- for (var i = 0; i < models.length; i++) {
- promises.push(models[i].getReactionsForElements(aliasesByModel[i], true));
- for (var j = 0; j < aliasesByModel[i].length; j++) {
- elementIds[aliasesByModel[i][j].getId()] = true;
- }
- }
- return Promise.all(promises);
- }).then(function (reactionsByModel) {
- for (var i = 0; i < models.length; i++) {
- for (var j = 0; j < reactionsByModel[i].length; j++) {
- var reaction = reactionsByModel[i][j];
- if (matchReaction(reaction, elementIds)) {
- reactions.push(reaction);
- }
- }
- }
- return self.getSelectedMiriamTypes();
- }).then(function (result) {
- miriamTypes = result;
- return self.getSelectedColumns();
- }).then(function (selectedColumns) {
- if (selectedColumns.length === 0) {
- return Promise.reject(new GuiMessageError("You must select at least one column"));
- }
-
- var rows = [];
- rows.push(self.createResponseHeader(selectedColumns, miriamTypes));
- for (var i = 0; i < reactions.length; i++) {
- rows.push(self.createResponseRow(reactions[i], selectedColumns, miriamTypes, elementIds));
- }
- return rows.join("\n");
- });
-};
-
-NetworkExportPanel.prototype.createResponseRow = function (reaction, columns, miriamTypes, elementIds) {
- var stringBuilder = [];
- var i, value;
- for (i = 0; i < columns.length; i++) {
- var column = columns[i];
- value = reaction[column.method]();
- if (column.formatFunction !== undefined) {
- value = column.formatFunction(value, reaction, elementIds);
- }
- if (value instanceof String || typeof value === "string") {
- value = value.replace(/[\n\r]/g, ' ');
- }
- stringBuilder.push(value);
- }
- for (i = 0; i < miriamTypes.length; i++) {
- value = "";
- var miriamType = miriamTypes[i];
- var references = reaction.getReferences();
- for (var j = 0; j < references.length; j++) {
- var reference = references[j];
- if (reference.getType() === miriamType.getName()) {
- value += reference.getResource() + ",";
- }
- }
- stringBuilder.push(value);
- }
- return stringBuilder.join("\t");
-};
-
-module.exports = NetworkExportPanel;
+"use strict";
+
+/* exported logger */
+
+var AbstractExportPanel = require('./AbstractExportPanel');
+
+var Promise = require("bluebird");
+var logger = require('../../logger');
+var GuiMessageError = require('../GuiMessageError');
+
+
+function NetworkExportPanel(params) {
+ params.panelName = "networkExport";
+ AbstractExportPanel.call(this, params);
+}
+
+NetworkExportPanel.prototype = Object.create(AbstractExportPanel.prototype);
+NetworkExportPanel.prototype.constructor = NetworkExportPanel;
+
+NetworkExportPanel.prototype.init = function () {
+
+ var self = this;
+ var element = self.getElement();
+ var configuration;
+ return ServerConnector.getConfiguration().then(function (result) {
+ configuration = result;
+ var typeDiv = self._createSelectTypeDiv(configuration.getElementTypes());
+ element.appendChild(typeDiv);
+ element.appendChild(self._createSelectColumnDiv(self.getAllColumns()));
+ return ServerConnector.getProjectStatistics(self.getProject().getProjectId());
+ }).then(function (statistics) {
+ return self._createMiriamTypeDiv(statistics.getReactionAnnotations());
+ }).then(function (div) {
+ element.appendChild(div);
+ return self._createSelectIncludedCompartmentDiv();
+ }).then(function (div) {
+ element.appendChild(div);
+ return self._createSelectExcludedCompartmentDiv();
+ }).then(function (div) {
+ element.appendChild(div);
+ element.appendChild(self._createDownloadButton());
+ }).then(function () {
+ $(window).trigger('resize');
+ });
+
+};
+
+NetworkExportPanel.prototype.getAllColumns = function () {
+ return [{
+ "columnName": "elements",
+ "method": "getElements",
+ "name": "Elements",
+ "formatFunction": function (elements, reaction, elementIds) {
+ var stringBuilder = [];
+ var type;
+ var elementFormat = function (element) {
+ if (elementIds[element.getAlias().getId()]) {
+ stringBuilder.push(type + ":" + element.getAlias().getId());
+ }
+ };
+ type = "REACTANT";
+ reaction.getReactants().forEach(elementFormat);
+ type = "PRODUCT";
+ reaction.getProducts().forEach(elementFormat);
+ type = "MODIFIER";
+ reaction.getModifiers().forEach(elementFormat);
+
+ return stringBuilder.join(",");
+ }
+ }, {
+ "columnName": "id",
+ "method": "getId",
+ "name": "Id"
+ }, {
+ "columnName": "description",
+ "method": "getDescription",
+ "name": "Description"
+ }, {
+ "columnName": "modelId",
+ "method": "getModelId",
+ "name": "Model"
+ }, {
+ "columnName": "type",
+ "method": "getType",
+ "name": "Type"
+ }, {
+ "columnName": "symbol",
+ "method": "getSymbol",
+ "name": "Symbol"
+ }, {
+ "columnName": "abbreviation",
+ "method": "getAbbreviation",
+ "name": "Abbreviation"
+ }, {
+ "columnName": "formula",
+ "method": "getFormula",
+ "name": "Formula"
+ }, {
+ "columnName": "synonyms",
+ "method": "getSynonyms",
+ "name": "Synonyms"
+ }, {
+ "columnName": "references",
+ "method": "getReferences",
+ "name": "References",
+ "formatFunction": function (references) {
+ var stringBuilder = [];
+ for (var i = 0; i < references.length; i++) {
+ var reference = references[i];
+ stringBuilder.push(reference.getType() + ":" + reference.getResource());
+ }
+ return stringBuilder.join(",");
+ }
+ }, {
+ "columnName": "reactionId",
+ "method": "getReactionId",
+ "name": "Element external id"
+ }, {
+ "columnName": "mechanicalConfidenceScore",
+ "method": "getMechanicalConfidenceScore",
+ "name": "Mechanical Confidence Score"
+ }, {
+ "columnName": "lowerBound",
+ "method": "getLowerBound",
+ "name": "Lower Bound"
+ }, {
+ "columnName": "upperBound",
+ "method": "getUpperBound",
+ "name": "Upper Bound"
+ }, {
+ "columnName": "geneProteinReaction",
+ "method": "getGeneProteinReaction",
+ "name": "Gene Protein Reaction"
+ }, {
+ "columnName": "subsystem",
+ "method": "getSubsystem",
+ "name": "Subsystem"
+ }];
+};
+
+function matchReaction(reaction, elementIds) {
+ var count = 0;
+ reaction.getElements().forEach(function (element) {
+ if (elementIds[element.getId()]) {
+ count++;
+ }
+ });
+ return count > 1;
+}
+
+NetworkExportPanel.prototype.createResponseString = function () {
+ var self = this;
+ var types, miriamTypes;
+ var includedCompartmentIds = [];
+ var excludedCompartmentIds = [];
+ var models = self.getProject().getModels();
+
+ var elementIds = [];
+ var reactions = [];
+ return self.getSelectedTypes().then(function (result) {
+ if (result.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one type"));
+ }
+ types = result;
+ return self.getSelectedIncludedCompartments();
+ }).then(function (result) {
+ result.forEach(function (compartment) {
+ includedCompartmentIds.push(compartment.getId());
+ });
+ return self.getSelectedExcludedCompartments();
+ }).then(function (result) {
+ result.forEach(function (compartment) {
+ excludedCompartmentIds.push(compartment.getId());
+ });
+
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getAliases({
+ type: types,
+ complete: true,
+ includedCompartmentIds: includedCompartmentIds,
+ excludedCompartmentIds: excludedCompartmentIds
+ }));
+ }
+ return Promise.all(promises);
+ }).then(function (aliasesByModel) {
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getReactionsForElements(aliasesByModel[i], true));
+ for (var j = 0; j < aliasesByModel[i].length; j++) {
+ elementIds[aliasesByModel[i][j].getId()] = true;
+ }
+ }
+ return Promise.all(promises);
+ }).then(function (reactionsByModel) {
+ for (var i = 0; i < models.length; i++) {
+ for (var j = 0; j < reactionsByModel[i].length; j++) {
+ var reaction = reactionsByModel[i][j];
+ if (matchReaction(reaction, elementIds)) {
+ reactions.push(reaction);
+ }
+ }
+ }
+ return self.getSelectedMiriamTypes();
+ }).then(function (result) {
+ miriamTypes = result;
+ return self.getSelectedColumns();
+ }).then(function (selectedColumns) {
+ if (selectedColumns.length === 0) {
+ return Promise.reject(new GuiMessageError("You must select at least one column"));
+ }
+
+ var rows = [];
+ rows.push(self.createResponseHeader(selectedColumns, miriamTypes));
+ for (var i = 0; i < reactions.length; i++) {
+ rows.push(self.createResponseRow(reactions[i], selectedColumns, miriamTypes, elementIds));
+ }
+ return rows.join("\n");
+ });
+};
+
+NetworkExportPanel.prototype.createResponseRow = function (reaction, columns, miriamTypes, elementIds) {
+ var stringBuilder = [];
+ var i, value;
+ for (i = 0; i < columns.length; i++) {
+ var column = columns[i];
+ value = reaction[column.method]();
+ if (column.formatFunction !== undefined) {
+ value = column.formatFunction(value, reaction, elementIds);
+ }
+ if (value instanceof String || typeof value === "string") {
+ value = value.replace(/[\n\r]/g, ' ');
+ }
+ stringBuilder.push(value);
+ }
+ for (i = 0; i < miriamTypes.length; i++) {
+ value = "";
+ var miriamType = miriamTypes[i];
+ var references = reaction.getReferences();
+ for (var j = 0; j < references.length; j++) {
+ var reference = references[j];
+ if (reference.getType() === miriamType.getName()) {
+ value += reference.getResource() + ",";
+ }
+ }
+ stringBuilder.push(value);
+ }
+ return stringBuilder.join("\t");
+};
+
+module.exports = NetworkExportPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
index 53abb947aab7dd1e45d4decba0233d025d9b5e3d..b6ead02a0d361ed46a2d7ee86733b8deb993d8e1 100644
--- a/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/AbstractDbPanel.js
@@ -1,426 +1,426 @@
-"use strict";
-
-/* exported logger */
-
-var Promise = require("bluebird");
-
-var GuiConnector = require('../../GuiConnector');
-var Panel = require('../Panel');
-var PanelControlElementType = require('../PanelControlElementType');
-
-var logger = require('../../logger');
-var Functions = require('../../Functions');
-
-/**
- *
- * @param {string} params.placeholder
- * @param {string} params.panelName
- * @constructor
- * @extends Panel
- */
-function AbstractDbPanel(params) {
- Panel.call(this, params);
- var self = this;
-
- this._initializeGui(params.placeholder);
- this.setOverlayDb(self.getMap().getOverlayByName(params.panelName));
- this._createEventHandlers();
-
- this._tabIdCount = 0;
-
-}
-
-AbstractDbPanel.prototype = Object.create(Panel.prototype);
-AbstractDbPanel.prototype.constructor = AbstractDbPanel;
-
-AbstractDbPanel.prototype._createEventHandlers = function () {
- var self = this;
- var searchButton = self.getControlElement(PanelControlElementType.SEARCH_BUTTON);
- var searchInput = self.getControlElement(PanelControlElementType.SEARCH_INPUT);
-
- var searchByQuery = function () {
- var busyImage = $("[name=busyImage]", self.getElement());
- busyImage.show();
- return self.searchByQuery().finally(function () {
- busyImage.hide();
- });
- };
-
- searchButton.onclick = searchByQuery;
- searchInput.onkeypress = function (event) {
- if (event.keyCode === 13) {
- return searchByQuery().then(null, GuiConnector.alert);
- }
- };
-
- $(searchInput).typeahead({
- minLength: 1,
- hint: true,
- highlight: true
- }, {
- source: function (query, callback) {
- callback(self.getAutocomplete(query.toLowerCase()));
- }
- });
-
- $(searchInput).on('typeahead:select', function () {
- searchByQuery();
- });
-
- self.getOverlayDb().addListener("onSearch", function () {
- return self.refreshSearchResults();
- });
-
- self.getOverlayDb().addListener("onClear", function () {
- searchInput.value = "";
- });
-
-};
-
-AbstractDbPanel.prototype._initializeGui = function (placeholder) {
- var searchQueryDiv = Functions.createElement({
- type: "div",
- name: "searchQuery",
- className: "searchPanel"
- });
- this.getElement().appendChild(searchQueryDiv);
- this.setControlElement(PanelControlElementType.SEARCH_DIV, searchQueryDiv);
-
- var busyImage = Functions.createElement({
- type: "img",
- name: "busyImage",
- style: "display:block;position: absolute;margin-left: 80px;z-index: 10;display:none",
- src: "resources/images/icons/ajax-loader.gif"
- });
- searchQueryDiv.appendChild(busyImage);
-
- var searchLabel = Functions.createElement({
- type: "div",
- name: "searchLabel",
- content: "SEARCH:"
- });
- searchQueryDiv.appendChild(searchLabel);
- this.setControlElement(PanelControlElementType.SEARCH_LABEL, searchLabel);
-
- var searchInputDiv = Functions.createElement({
- type: "table"
- });
- searchQueryDiv.appendChild(searchInputDiv);
-
- var searchInputRow = Functions.createElement({
- type: "tr"
- });
- searchInputDiv.appendChild(searchInputRow);
-
- var searchInputCell = Functions.createElement({
- type: "td"
- });
- searchInputRow.appendChild(searchInputCell);
-
- var searchInput = Functions.createElement({
- type: "input",
- name: "searchInput",
- className: "input-field typeahead"
- });
- if (placeholder !== undefined) {
- searchInput.placeholder = placeholder;
- }
- searchInputCell.appendChild(searchInput);
- this.setControlElement(PanelControlElementType.SEARCH_INPUT, searchInput);
-
- var searchButtonCell = Functions.createElement({
- type: "td"
- });
- searchInputRow.appendChild(searchButtonCell);
-
- var searchButton = Functions.createElement({
- type: "a",
- content: '<img src="resources/images/icons/search.png"/>',
- xss: false
- });
- searchButton.href = "#";
- searchButtonCell.appendChild(searchButton);
- this.setControlElement(PanelControlElementType.SEARCH_BUTTON, searchButton);
-
- var searchResultsDiv = Functions.createElement({
- type: "div",
- name: "searchResults",
- className: "tabbable boxed parentTabs"
- });
- this.getElement().appendChild(searchResultsDiv);
- this.setControlElement(PanelControlElementType.SEARCH_RESULTS_DIV, searchResultsDiv);
-
- var searchResultsNavTabDiv = Functions.createElement({
- type: "ul",
- className: "nav nav-tabs",
- content: '<li class="active"><a href="#set1"/></li>',
- xss: false
- });
- searchResultsDiv.appendChild(searchResultsNavTabDiv);
- this.setControlElement(PanelControlElementType.SEARCH_RESULTS_NAV_TAB, searchResultsNavTabDiv);
-
- var searchResultsContentTabDiv = Functions.createElement({
- type: "div",
- className: "tab-content",
- content: '<div class="tab-pane fade active in" name="set1" id="set1"/>',
- xss: false
- });
- searchResultsDiv.appendChild(searchResultsContentTabDiv);
- this.setControlElement(PanelControlElementType.SEARCH_RESULTS_CONTENT_TAB, searchResultsContentTabDiv);
-
-};
-
-AbstractDbPanel.prototype.setOverlayDb = function (overlayDb) {
- if (overlayDb === undefined) {
- throw new Error("Undefined overlayDb for panel: " + this.getPanelName());
- }
- this._overlayDb = overlayDb;
-};
-
-/**
- *
- * @returns {AbstractDbOverlay}
- */
-AbstractDbPanel.prototype.getOverlayDb = function () {
- return this._overlayDb;
-};
-
-AbstractDbPanel.prototype.clearResults = function () {
- var navElement = this.getControlElement(PanelControlElementType.SEARCH_RESULTS_NAV_TAB);
- while (navElement.firstChild) {
- navElement.removeChild(navElement.firstChild);
- }
-
- var contentElement = this.getControlElement(PanelControlElementType.SEARCH_RESULTS_CONTENT_TAB);
- while (contentElement.firstChild) {
- contentElement.removeChild(contentElement.firstChild);
- }
-};
-
-AbstractDbPanel.prototype.refreshSearchResults = function () {
- var self = this;
- self.clearResults();
- var searchDb = self.getOverlayDb();
- var queries = searchDb.getQueries();
-
- var promises = [];
- for (var i = 0; i < queries.length; i++) {
- promises.push(searchDb.getElementsByQuery(queries[i]));
- }
- return Promise.all(promises).then(function (results) {
- return Promise.each(queries, function(query, index){
- return self.addResultTab(query, results[index]);
- });
- }).then(function(){
- self.onresize();
- });
-};
-
-AbstractDbPanel.prototype.getAutocomplete = function () {
- logger.warn("Get autocomplete not implemented");
-};
-
-AbstractDbPanel.prototype.searchByQuery = function () {
- throw new Error("searchByQuery is not implemented");
-};
-
-AbstractDbPanel.prototype.addResultTab = function (query, elements) {
- var self = this;
- var name = JSON.parse(query).query;
-
- var tabId = this.getPanelName() + "Tab_" + this._tabIdCount;
- this._tabIdCount++;
-
- var navElement = this.getControlElement(PanelControlElementType.SEARCH_RESULTS_NAV_TAB);
- var contentElement = this.getControlElement(PanelControlElementType.SEARCH_RESULTS_CONTENT_TAB);
- var navClass = '';
- var contentClass = 'tab-pane';
- if (navElement.children.length === 0) {
- navClass = "active";
- contentClass = "tab-pane active";
- }
-
- var navLi = document.createElement("li");
- navLi.className = navClass;
-
- var navLink = Functions.createElement({
- type: "a",
- href: "#" + tabId,
- onclick: function () {
- $(this).tab('show');
- }
- });
- if (name !== undefined) {
- if (name.length > 12) {
- name = name.substring(0, 10) + "...";
- }
- navLink.innerHTML = name;
- }
- navLi.appendChild(navLink);
- if (query.name !== undefined) {
- navLink.innerHTML = query.name;
- }
- navElement.appendChild(navLi);
-
- var contentDiv = document.createElement("div");
- contentDiv.className = "pre-scrollable " + contentClass;
- contentDiv.style.maxHeight = "10px";
-
- contentDiv.id = tabId;
-
- contentElement.appendChild(contentDiv);
-
- contentDiv.appendChild(this.createPreamble(elements.element));
-
- var tableDiv = document.createElement("table");
- tableDiv.className = "table table-bordered";
- contentDiv.appendChild(tableDiv);
- var tableBody = document.createElement("tbody");
- tableDiv.appendChild(tableBody);
-
- return Promise.each(elements, function (entry) {
- var element = entry.element;
- var icon = entry.icon;
- return self.createTableElement(element, icon).then(function (div) {
- return tableBody.appendChild(div);
- });
- });
-};
-
-/**
- *
- * @returns {Promise<HTMLTableRowElement>}
- */
-AbstractDbPanel.prototype.createTableElement = function () {
- throw new Error("Not implemented");
-};
-
-/**
- *
- * @param {Target} target
- * @param {string} icon
- * @returns {Promise<HTMLTableRowElement>}
- */
-AbstractDbPanel.prototype.createTargetRow = function (target, icon) {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var result = document.createElement("tr");
- var iconColumn = document.createElement("td");
- iconColumn.style.width = "20px";
- iconColumn.style.verticalAlign = "middle";
- iconColumn.style.textAlign = "center";
- result.appendChild(iconColumn);
- var submaps = [];
- var i;
- if (target.getTargetElements().length > 0) {
- var submapAddedIds = [];
- iconColumn.appendChild(guiUtils.createIcon(icon));
- var checkbox = document.createElement('input');
- checkbox.type = "checkbox";
- checkbox.checked = target.isVisible();
- checkbox.onclick = function () {
- target.setIsVisible(!target.isVisible());
- self.getOverlayDb().callListeners("onTargetVisibilityChange");
- };
-
- iconColumn.appendChild(checkbox);
- var elements = target.getTargetElements();
- for (i = 0; i < elements.length; i++) {
- var elementId = elements[i].getModelId();
- if (elementId !== self.getMap().getId() && !submapAddedIds[elementId]) {
- submaps.push(elementId);
- submapAddedIds[elementId] = true;
- }
- }
- }
-
- var descColumn = document.createElement("td");
- result.appendChild(descColumn);
-
- descColumn.appendChild(guiUtils.createParamLine("Name: ", target.getName()));
- descColumn.appendChild(guiUtils.createAnnotations("Elements: ", target.getTargetParticipants(), {
- showType: false,
- inline: true,
- groupAnnotations: false
- }));
- descColumn.appendChild(guiUtils.createAnnotations("References: ", target.getReferences(), {
- showType: false,
- groupAnnotations: false
- }));
- if (submaps.length > 0) {
- descColumn.appendChild(guiUtils.createLabel("Available in submaps: "));
- for (i = 0; i < submaps.length; i++) {
- var model = self.getMap().getSubmapById(submaps[i]).getModel();
- var onclick = (function () {
- var id = model.getId();
- return function () {
- self.getMap().openSubmap(id);
- };
- }());
- var button = Functions.createElement({
- type: "button",
- className: "minerva-open-submap-button",
- content: model.getName(),
- onclick: onclick
- });
- descColumn.appendChild(button);
- }
- }
- return Promise.resolve(result);
-};
-
-AbstractDbPanel.prototype.computeAutocompleteDictionary = function (queries) {
- var result = {};
-
- var i, j, k, mainString, substring, list;
- //compute dict for prefixes
- for (i = 0; i < queries.length; i++) {
- mainString = queries[i].toLowerCase();
- for (j = 0; j < mainString.length; j++) {
- substring = mainString.substring(0, j + 1);
- if (result[substring] !== undefined) {
- continue;
- }
-
- list = [];
- for (k = 0; k < 5; k++) {
- if (k + i >= queries.length) {
- break;
- } else if (queries[k + i].toLowerCase().indexOf(substring.toLowerCase()) === 0) {
- list.push(queries[k + i]);
- }
- }
-
- result[substring] = list;
- }
- }
-
- //and now we add substring from inside
- for (i = 0; i < queries.length; i++) {
- mainString = queries[i].toLowerCase();
- for (var startSubstring = 1; startSubstring < mainString.length; startSubstring++) {
- for (var endSubstring = startSubstring + 1; endSubstring <= mainString.length; endSubstring++) {
- substring = mainString.substring(startSubstring, endSubstring);
- if (mainString.indexOf(substring) !== 0) {
- if (result[substring] === undefined) {
- result[substring] = [];
- }
- if (result[substring].length < 5) {
- var found = false;
- for (k = 0; k < result[substring].length; k++) {
- found |= result[substring][k] === mainString;
- }
- if (!found) {
- result[substring].push(mainString);
- }
- }
- }
- }
- }
- }
-
- return result;
-};
-
-
-module.exports = AbstractDbPanel;
+"use strict";
+
+/* exported logger */
+
+var Promise = require("bluebird");
+
+var GuiConnector = require('../../GuiConnector');
+var Panel = require('../Panel');
+var PanelControlElementType = require('../PanelControlElementType');
+
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+
+/**
+ *
+ * @param {string} params.placeholder
+ * @param {string} params.panelName
+ * @constructor
+ * @extends Panel
+ */
+function AbstractDbPanel(params) {
+ Panel.call(this, params);
+ var self = this;
+
+ this._initializeGui(params.placeholder);
+ this.setOverlayDb(self.getMap().getOverlayByName(params.panelName));
+ this._createEventHandlers();
+
+ this._tabIdCount = 0;
+
+}
+
+AbstractDbPanel.prototype = Object.create(Panel.prototype);
+AbstractDbPanel.prototype.constructor = AbstractDbPanel;
+
+AbstractDbPanel.prototype._createEventHandlers = function () {
+ var self = this;
+ var searchButton = self.getControlElement(PanelControlElementType.SEARCH_BUTTON);
+ var searchInput = self.getControlElement(PanelControlElementType.SEARCH_INPUT);
+
+ var searchByQuery = function () {
+ var busyImage = $("[name=busyImage]", self.getElement());
+ busyImage.show();
+ return self.searchByQuery().finally(function () {
+ busyImage.hide();
+ });
+ };
+
+ searchButton.onclick = searchByQuery;
+ searchInput.onkeypress = function (event) {
+ if (event.keyCode === 13) {
+ return searchByQuery().then(null, GuiConnector.alert);
+ }
+ };
+
+ $(searchInput).typeahead({
+ minLength: 1,
+ hint: true,
+ highlight: true
+ }, {
+ source: function (query, callback) {
+ callback(self.getAutocomplete(query.toLowerCase()));
+ }
+ });
+
+ $(searchInput).on('typeahead:select', function () {
+ searchByQuery();
+ });
+
+ self.getOverlayDb().addListener("onSearch", function () {
+ return self.refreshSearchResults();
+ });
+
+ self.getOverlayDb().addListener("onClear", function () {
+ searchInput.value = "";
+ });
+
+};
+
+AbstractDbPanel.prototype._initializeGui = function (placeholder) {
+ var searchQueryDiv = Functions.createElement({
+ type: "div",
+ name: "searchQuery",
+ className: "searchPanel"
+ });
+ this.getElement().appendChild(searchQueryDiv);
+ this.setControlElement(PanelControlElementType.SEARCH_DIV, searchQueryDiv);
+
+ var busyImage = Functions.createElement({
+ type: "img",
+ name: "busyImage",
+ style: "display:block;position: absolute;margin-left: 80px;z-index: 10;display:none",
+ src: "resources/images/icons/ajax-loader.gif"
+ });
+ searchQueryDiv.appendChild(busyImage);
+
+ var searchLabel = Functions.createElement({
+ type: "div",
+ name: "searchLabel",
+ content: "SEARCH:"
+ });
+ searchQueryDiv.appendChild(searchLabel);
+ this.setControlElement(PanelControlElementType.SEARCH_LABEL, searchLabel);
+
+ var searchInputDiv = Functions.createElement({
+ type: "table"
+ });
+ searchQueryDiv.appendChild(searchInputDiv);
+
+ var searchInputRow = Functions.createElement({
+ type: "tr"
+ });
+ searchInputDiv.appendChild(searchInputRow);
+
+ var searchInputCell = Functions.createElement({
+ type: "td"
+ });
+ searchInputRow.appendChild(searchInputCell);
+
+ var searchInput = Functions.createElement({
+ type: "input",
+ name: "searchInput",
+ className: "input-field typeahead"
+ });
+ if (placeholder !== undefined) {
+ searchInput.placeholder = placeholder;
+ }
+ searchInputCell.appendChild(searchInput);
+ this.setControlElement(PanelControlElementType.SEARCH_INPUT, searchInput);
+
+ var searchButtonCell = Functions.createElement({
+ type: "td"
+ });
+ searchInputRow.appendChild(searchButtonCell);
+
+ var searchButton = Functions.createElement({
+ type: "a",
+ content: '<img src="resources/images/icons/search.png"/>',
+ xss: false
+ });
+ searchButton.href = "#";
+ searchButtonCell.appendChild(searchButton);
+ this.setControlElement(PanelControlElementType.SEARCH_BUTTON, searchButton);
+
+ var searchResultsDiv = Functions.createElement({
+ type: "div",
+ name: "searchResults",
+ className: "tabbable boxed parentTabs"
+ });
+ this.getElement().appendChild(searchResultsDiv);
+ this.setControlElement(PanelControlElementType.SEARCH_RESULTS_DIV, searchResultsDiv);
+
+ var searchResultsNavTabDiv = Functions.createElement({
+ type: "ul",
+ className: "nav nav-tabs",
+ content: '<li class="active"><a href="#set1"/></li>',
+ xss: false
+ });
+ searchResultsDiv.appendChild(searchResultsNavTabDiv);
+ this.setControlElement(PanelControlElementType.SEARCH_RESULTS_NAV_TAB, searchResultsNavTabDiv);
+
+ var searchResultsContentTabDiv = Functions.createElement({
+ type: "div",
+ className: "tab-content",
+ content: '<div class="tab-pane fade active in" name="set1" id="set1"/>',
+ xss: false
+ });
+ searchResultsDiv.appendChild(searchResultsContentTabDiv);
+ this.setControlElement(PanelControlElementType.SEARCH_RESULTS_CONTENT_TAB, searchResultsContentTabDiv);
+
+};
+
+AbstractDbPanel.prototype.setOverlayDb = function (overlayDb) {
+ if (overlayDb === undefined) {
+ throw new Error("Undefined overlayDb for panel: " + this.getPanelName());
+ }
+ this._overlayDb = overlayDb;
+};
+
+/**
+ *
+ * @returns {AbstractDbOverlay}
+ */
+AbstractDbPanel.prototype.getOverlayDb = function () {
+ return this._overlayDb;
+};
+
+AbstractDbPanel.prototype.clearResults = function () {
+ var navElement = this.getControlElement(PanelControlElementType.SEARCH_RESULTS_NAV_TAB);
+ while (navElement.firstChild) {
+ navElement.removeChild(navElement.firstChild);
+ }
+
+ var contentElement = this.getControlElement(PanelControlElementType.SEARCH_RESULTS_CONTENT_TAB);
+ while (contentElement.firstChild) {
+ contentElement.removeChild(contentElement.firstChild);
+ }
+};
+
+AbstractDbPanel.prototype.refreshSearchResults = function () {
+ var self = this;
+ self.clearResults();
+ var searchDb = self.getOverlayDb();
+ var queries = searchDb.getQueries();
+
+ var promises = [];
+ for (var i = 0; i < queries.length; i++) {
+ promises.push(searchDb.getElementsByQuery(queries[i]));
+ }
+ return Promise.all(promises).then(function (results) {
+ return Promise.each(queries, function(query, index){
+ return self.addResultTab(query, results[index]);
+ });
+ }).then(function(){
+ self.onresize();
+ });
+};
+
+AbstractDbPanel.prototype.getAutocomplete = function () {
+ logger.warn("Get autocomplete not implemented");
+};
+
+AbstractDbPanel.prototype.searchByQuery = function () {
+ throw new Error("searchByQuery is not implemented");
+};
+
+AbstractDbPanel.prototype.addResultTab = function (query, elements) {
+ var self = this;
+ var name = JSON.parse(query).query;
+
+ var tabId = this.getPanelName() + "Tab_" + this._tabIdCount;
+ this._tabIdCount++;
+
+ var navElement = this.getControlElement(PanelControlElementType.SEARCH_RESULTS_NAV_TAB);
+ var contentElement = this.getControlElement(PanelControlElementType.SEARCH_RESULTS_CONTENT_TAB);
+ var navClass = '';
+ var contentClass = 'tab-pane';
+ if (navElement.children.length === 0) {
+ navClass = "active";
+ contentClass = "tab-pane active";
+ }
+
+ var navLi = document.createElement("li");
+ navLi.className = navClass;
+
+ var navLink = Functions.createElement({
+ type: "a",
+ href: "#" + tabId,
+ onclick: function () {
+ $(this).tab('show');
+ }
+ });
+ if (name !== undefined) {
+ if (name.length > 12) {
+ name = name.substring(0, 10) + "...";
+ }
+ navLink.innerHTML = name;
+ }
+ navLi.appendChild(navLink);
+ if (query.name !== undefined) {
+ navLink.innerHTML = query.name;
+ }
+ navElement.appendChild(navLi);
+
+ var contentDiv = document.createElement("div");
+ contentDiv.className = "pre-scrollable " + contentClass;
+ contentDiv.style.maxHeight = "10px";
+
+ contentDiv.id = tabId;
+
+ contentElement.appendChild(contentDiv);
+
+ contentDiv.appendChild(this.createPreamble(elements.element));
+
+ var tableDiv = document.createElement("table");
+ tableDiv.className = "table table-bordered";
+ contentDiv.appendChild(tableDiv);
+ var tableBody = document.createElement("tbody");
+ tableDiv.appendChild(tableBody);
+
+ return Promise.each(elements, function (entry) {
+ var element = entry.element;
+ var icon = entry.icon;
+ return self.createTableElement(element, icon).then(function (div) {
+ return tableBody.appendChild(div);
+ });
+ });
+};
+
+/**
+ *
+ * @returns {Promise<HTMLTableRowElement>}
+ */
+AbstractDbPanel.prototype.createTableElement = function () {
+ throw new Error("Not implemented");
+};
+
+/**
+ *
+ * @param {Target} target
+ * @param {string} icon
+ * @returns {Promise<HTMLTableRowElement>}
+ */
+AbstractDbPanel.prototype.createTargetRow = function (target, icon) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var result = document.createElement("tr");
+ var iconColumn = document.createElement("td");
+ iconColumn.style.width = "20px";
+ iconColumn.style.verticalAlign = "middle";
+ iconColumn.style.textAlign = "center";
+ result.appendChild(iconColumn);
+ var submaps = [];
+ var i;
+ if (target.getTargetElements().length > 0) {
+ var submapAddedIds = [];
+ iconColumn.appendChild(guiUtils.createIcon(icon));
+ var checkbox = document.createElement('input');
+ checkbox.type = "checkbox";
+ checkbox.checked = target.isVisible();
+ checkbox.onclick = function () {
+ target.setIsVisible(!target.isVisible());
+ self.getOverlayDb().callListeners("onTargetVisibilityChange");
+ };
+
+ iconColumn.appendChild(checkbox);
+ var elements = target.getTargetElements();
+ for (i = 0; i < elements.length; i++) {
+ var elementId = elements[i].getModelId();
+ if (elementId !== self.getMap().getId() && !submapAddedIds[elementId]) {
+ submaps.push(elementId);
+ submapAddedIds[elementId] = true;
+ }
+ }
+ }
+
+ var descColumn = document.createElement("td");
+ result.appendChild(descColumn);
+
+ descColumn.appendChild(guiUtils.createParamLine("Name: ", target.getName()));
+ descColumn.appendChild(guiUtils.createAnnotations("Elements: ", target.getTargetParticipants(), {
+ showType: false,
+ inline: true,
+ groupAnnotations: false
+ }));
+ descColumn.appendChild(guiUtils.createAnnotations("References: ", target.getReferences(), {
+ showType: false,
+ groupAnnotations: false
+ }));
+ if (submaps.length > 0) {
+ descColumn.appendChild(guiUtils.createLabel("Available in submaps: "));
+ for (i = 0; i < submaps.length; i++) {
+ var model = self.getMap().getSubmapById(submaps[i]).getModel();
+ var onclick = (function () {
+ var id = model.getId();
+ return function () {
+ self.getMap().openSubmap(id);
+ };
+ }());
+ var button = Functions.createElement({
+ type: "button",
+ className: "minerva-open-submap-button",
+ content: model.getName(),
+ onclick: onclick
+ });
+ descColumn.appendChild(button);
+ }
+ }
+ return Promise.resolve(result);
+};
+
+AbstractDbPanel.prototype.computeAutocompleteDictionary = function (queries) {
+ var result = {};
+
+ var i, j, k, mainString, substring, list;
+ //compute dict for prefixes
+ for (i = 0; i < queries.length; i++) {
+ mainString = queries[i].toLowerCase();
+ for (j = 0; j < mainString.length; j++) {
+ substring = mainString.substring(0, j + 1);
+ if (result[substring] !== undefined) {
+ continue;
+ }
+
+ list = [];
+ for (k = 0; k < 5; k++) {
+ if (k + i >= queries.length) {
+ break;
+ } else if (queries[k + i].toLowerCase().indexOf(substring.toLowerCase()) === 0) {
+ list.push(queries[k + i]);
+ }
+ }
+
+ result[substring] = list;
+ }
+ }
+
+ //and now we add substring from inside
+ for (i = 0; i < queries.length; i++) {
+ mainString = queries[i].toLowerCase();
+ for (var startSubstring = 1; startSubstring < mainString.length; startSubstring++) {
+ for (var endSubstring = startSubstring + 1; endSubstring <= mainString.length; endSubstring++) {
+ substring = mainString.substring(startSubstring, endSubstring);
+ if (mainString.indexOf(substring) !== 0) {
+ if (result[substring] === undefined) {
+ result[substring] = [];
+ }
+ if (result[substring].length < 5) {
+ var found = false;
+ for (k = 0; k < result[substring].length; k++) {
+ found |= result[substring][k] === mainString;
+ }
+ if (!found) {
+ result[substring].push(mainString);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return result;
+};
+
+
+module.exports = AbstractDbPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js b/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
index 579599f37bf08ff04d7f457a460cc08dd3077123..3a72aec79e68944c957934608a452687ff4752a3 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js
@@ -1,121 +1,121 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-/* exported logger */
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-var AbstractDbPanel = require('./AbstractDbPanel');
-var PanelControlElementType = require('../PanelControlElementType');
-
-/**
- *
- * @param params
- * @constructor
- * @extends AbstractDbPanel
- */
-function ChemicalPanel(params) {
- var self = this;
- params.panelName = "chemical";
- params.placeholder = "full chemical name (CTD)";
-
-
- AbstractDbPanel.call(self, params);
-
- if (self.getMap().getProject().getDisease() === undefined) {
- self.disablePanel("The Comparative Toxicogenomics Database (CTD) requires a disease context. " +
- "Choose an appropriate MeSH code and provide it in the via the Admin section of this MINERVA platform. " +
- "See User Manual for more details ");
- } else {
- self.getControlElement(PanelControlElementType.SEARCH_LABEL).innerHTML = "SEARCH FOR TARGETS OF:";
- }
-}
-
-ChemicalPanel.prototype = Object.create(AbstractDbPanel.prototype);
-ChemicalPanel.prototype.constructor = ChemicalPanel;
-
-ChemicalPanel.prototype.createPreamble = function (chemical) {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var result = document.createElement("div");
- if (chemical === undefined || chemical.getName() === undefined) {
- result.appendChild(guiUtils.createLabel("NOT FOUND"));
- } else {
- result.appendChild(guiUtils.createParamLine("Chemical: ", chemical.getName()));
- result.appendChild(guiUtils.createParamLine("Description: ", chemical.getDescription()));
- result.appendChild(guiUtils.createArrayParamLine("Synonyms: ", chemical.getSynonyms()));
- result.appendChild(guiUtils.createParamLine("Direct Evidence: ", chemical.getDirectEvidence()));
- result.appendChild(guiUtils
- .createAnnotations("Direct Evidence Publications: ", chemical.getDirectEvidenceReferences(), {groupAnnotations: false}));
- result.appendChild(guiUtils.createAnnotations("Sources: ", chemical.getReferences()));
- result.appendChild(guiUtils.createNewLine());
- }
-
- return result;
-};
-
-ChemicalPanel.prototype.createTableElement = function (target, icon) {
- return this.createTargetRow(target, icon);
-};
-
-ChemicalPanel.prototype.searchByQuery = function () {
- var self = this;
- var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
-
- return self.getOverlayDb().searchByQuery(query);
-};
-
-ChemicalPanel.prototype.init = function () {
- var self = this;
- return self.getToolTipForAnnotation(self.getProject().getDisease()).then(function (toolTip) {
- self.setHelpTip(toolTip);
- var query = ServerConnector.getSessionData().getChemicalQuery();
- if (query !== undefined) {
- return self.getOverlayDb().searchByEncodedQuery(query);
- }
- });
-};
-
-ChemicalPanel.prototype.destroy = function () {
- return Promise.resolve();
-};
-
-ChemicalPanel.prototype.getAutocomplete = function (query) {
- if (this._searchAutocomplete === undefined) {
- this.refreshSearchAutocomplete();
- return [];
- }
-
- return this._searchAutocomplete[query];
-};
-
-ChemicalPanel.prototype.refreshSearchAutocomplete = function () {
- var self = this;
- self._searchAutocomplete = [];
- return ServerConnector.getChemicalSuggestedQueryList().then(function (queries) {
- self._searchAutocomplete = self.computeAutocompleteDictionary(queries);
- return self._searchAutocomplete;
- });
-};
-
-ChemicalPanel.prototype.getToolTipForAnnotation = function (annotation) {
- var self = this;
- var promise = Promise.resolve('disease');
- if (annotation !== null && annotation !== undefined) {
- promise = ServerConnector.getMesh({id: annotation.getResource()}).then(function (mesh) {
- return mesh.getName() + " (" + self.getGuiUtils().createAnnotationLink(annotation).outerHTML + ")";
- });
- }
- return promise.then(function (diseaseString) {
- var result = '<p>source: Comparative Toxicogenomics Database <a target="_ctd" href="http://ctdbase.org/">ctdbase.org</a></p>'
- + '<p>only associations between genes and chemicals with direct evidence to '
- + diseaseString + ' are displayed</p>'
- + '<p>use only the full name of chemicals according to <a target="_ctd_chemicals" href="http://ctdbase.org/voc.go?type=chem"> ctdbase/chem</a> for search</p>'
- + 'if the chemical name includes comma(s), place a semicolon behind the name to avoid a segmentation of the name</p>'
- + '<p>separate multiple search by semicolon';
- return Promise.resolve(result);
- });
-};
-
-module.exports = ChemicalPanel;
+"use strict";
+
+var Promise = require("bluebird");
+
+/* exported logger */
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var AbstractDbPanel = require('./AbstractDbPanel');
+var PanelControlElementType = require('../PanelControlElementType');
+
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractDbPanel
+ */
+function ChemicalPanel(params) {
+ var self = this;
+ params.panelName = "chemical";
+ params.placeholder = "full chemical name (CTD)";
+
+
+ AbstractDbPanel.call(self, params);
+
+ if (self.getMap().getProject().getDisease() === undefined) {
+ self.disablePanel("The Comparative Toxicogenomics Database (CTD) requires a disease context. " +
+ "Choose an appropriate MeSH code and provide it in the via the Admin section of this MINERVA platform. " +
+ "See User Manual for more details ");
+ } else {
+ self.getControlElement(PanelControlElementType.SEARCH_LABEL).innerHTML = "SEARCH FOR TARGETS OF:";
+ }
+}
+
+ChemicalPanel.prototype = Object.create(AbstractDbPanel.prototype);
+ChemicalPanel.prototype.constructor = ChemicalPanel;
+
+ChemicalPanel.prototype.createPreamble = function (chemical) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var result = document.createElement("div");
+ if (chemical === undefined || chemical.getName() === undefined) {
+ result.appendChild(guiUtils.createLabel("NOT FOUND"));
+ } else {
+ result.appendChild(guiUtils.createParamLine("Chemical: ", chemical.getName()));
+ result.appendChild(guiUtils.createParamLine("Description: ", chemical.getDescription()));
+ result.appendChild(guiUtils.createArrayParamLine("Synonyms: ", chemical.getSynonyms()));
+ result.appendChild(guiUtils.createParamLine("Direct Evidence: ", chemical.getDirectEvidence()));
+ result.appendChild(guiUtils
+ .createAnnotations("Direct Evidence Publications: ", chemical.getDirectEvidenceReferences(), {groupAnnotations: false}));
+ result.appendChild(guiUtils.createAnnotations("Sources: ", chemical.getReferences()));
+ result.appendChild(guiUtils.createNewLine());
+ }
+
+ return result;
+};
+
+ChemicalPanel.prototype.createTableElement = function (target, icon) {
+ return this.createTargetRow(target, icon);
+};
+
+ChemicalPanel.prototype.searchByQuery = function () {
+ var self = this;
+ var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
+
+ return self.getOverlayDb().searchByQuery(query);
+};
+
+ChemicalPanel.prototype.init = function () {
+ var self = this;
+ return self.getToolTipForAnnotation(self.getProject().getDisease()).then(function (toolTip) {
+ self.setHelpTip(toolTip);
+ var query = ServerConnector.getSessionData().getChemicalQuery();
+ if (query !== undefined) {
+ return self.getOverlayDb().searchByEncodedQuery(query);
+ }
+ });
+};
+
+ChemicalPanel.prototype.destroy = function () {
+ return Promise.resolve();
+};
+
+ChemicalPanel.prototype.getAutocomplete = function (query) {
+ if (this._searchAutocomplete === undefined) {
+ this.refreshSearchAutocomplete();
+ return [];
+ }
+
+ return this._searchAutocomplete[query];
+};
+
+ChemicalPanel.prototype.refreshSearchAutocomplete = function () {
+ var self = this;
+ self._searchAutocomplete = [];
+ return ServerConnector.getChemicalSuggestedQueryList().then(function (queries) {
+ self._searchAutocomplete = self.computeAutocompleteDictionary(queries);
+ return self._searchAutocomplete;
+ });
+};
+
+ChemicalPanel.prototype.getToolTipForAnnotation = function (annotation) {
+ var self = this;
+ var promise = Promise.resolve('disease');
+ if (annotation !== null && annotation !== undefined) {
+ promise = ServerConnector.getMesh({id: annotation.getResource()}).then(function (mesh) {
+ return mesh.getName() + " (" + self.getGuiUtils().createAnnotationLink(annotation).outerHTML + ")";
+ });
+ }
+ return promise.then(function (diseaseString) {
+ var result = '<p>source: Comparative Toxicogenomics Database <a target="_ctd" href="http://ctdbase.org/">ctdbase.org</a></p>'
+ + '<p>only associations between genes and chemicals with direct evidence to '
+ + diseaseString + ' are displayed</p>'
+ + '<p>use only the full name of chemicals according to <a target="_ctd_chemicals" href="http://ctdbase.org/voc.go?type=chem"> ctdbase/chem</a> for search</p>'
+ + 'if the chemical name includes comma(s), place a semicolon behind the name to avoid a segmentation of the name</p>'
+ + '<p>separate multiple search by semicolon';
+ return Promise.resolve(result);
+ });
+};
+
+module.exports = ChemicalPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js b/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
index ee96cfe765e6810c7b0c462c661f0e075dcdabf3..d2b5c8447d7b1131e23521adfdf5487530816edc 100644
--- a/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/DrugPanel.js
@@ -1,97 +1,97 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-/* exported logger */
-var logger = require('../../logger');
-
-var AbstractDbPanel = require('./AbstractDbPanel');
-var PanelControlElementType = require('../PanelControlElementType');
-
-/**
- *
- * @param params
- * @constructor
- * @extends AbstractDbPanel
- */
-function DrugPanel(params) {
- params.panelName = "drug";
- params.helpTip = '<p>source: <a target="_drugbank" href="http://www.drugbank.ca/">DrugBank</a> and '
- + '<a target="_drugbank" href="https://www.ebi.ac.uk/chembl/">ChEMBL</a></p>'
- + "<p>use of drug names, synonyms and brand names is supported<p>separate multiple search by semicolon</p>";
- params.placeholder = "drug, synonym, brand name";
-
- AbstractDbPanel.call(this, params);
- var self = this;
- self.getControlElement(PanelControlElementType.SEARCH_LABEL).innerHTML = "SEARCH FOR TARGETS OF:";
-}
-
-DrugPanel.prototype = Object.create(AbstractDbPanel.prototype);
-DrugPanel.prototype.constructor = DrugPanel;
-
-/**
- *
- * @param {Drug} drug
- * @returns {HTMLDivElement}
- */
-DrugPanel.prototype.createPreamble = function (drug) {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var result = document.createElement("div");
- if (drug === undefined || drug.getName() === undefined) {
- result.appendChild(guiUtils.createLabel("NOT FOUND"));
- } else {
- result.appendChild(guiUtils.createParamLine("Drug: ", drug.getName()));
- result.appendChild(guiUtils.createParamLine("Description: ", drug.getDescription()));
- result.appendChild(guiUtils.createArrayParamLine("Synonyms: ", drug.getSynonyms()));
- result.appendChild(guiUtils.createArrayParamLine("Brand names: ", drug.getBrandNames()));
- result.appendChild(guiUtils.createParamLine("Blood brain barrier: ", drug.getBloodBrainBarrier()));
- result.appendChild(guiUtils.createAnnotations("Sources: ", drug.getReferences(), {groupAnnotations: false}));
- result.appendChild(guiUtils.createNewLine());
- }
-
- return result;
-};
-
-DrugPanel.prototype.createTableElement = function (target, icon) {
- return this.createTargetRow(target, icon);
-};
-
-DrugPanel.prototype.searchByQuery = function () {
- var self = this;
- var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
- return self.getOverlayDb().searchByQuery(query);
-};
-
-DrugPanel.prototype.init = function () {
- var query = ServerConnector.getSessionData().getDrugQuery();
- if (query !== undefined) {
- return this.getOverlayDb().searchByEncodedQuery(query);
- } else {
- return Promise.resolve();
- }
-};
-
-DrugPanel.prototype.destroy = function () {
- return Promise.resolve();
-};
-
-DrugPanel.prototype.getAutocomplete = function (query) {
- if (this._searchAutocomplete === undefined) {
- this.refreshSearchAutocomplete();
- return [];
- }
-
- return this._searchAutocomplete[query];
-};
-
-DrugPanel.prototype.refreshSearchAutocomplete = function () {
- var self = this;
- self._searchAutocomplete = [];
- return ServerConnector.getDrugSuggestedQueryList().then(function (queries) {
- self._searchAutocomplete = self.computeAutocompleteDictionary(queries);
- return self._searchAutocomplete;
- });
-};
-
-module.exports = DrugPanel;
+"use strict";
+
+var Promise = require("bluebird");
+
+/* exported logger */
+var logger = require('../../logger');
+
+var AbstractDbPanel = require('./AbstractDbPanel');
+var PanelControlElementType = require('../PanelControlElementType');
+
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractDbPanel
+ */
+function DrugPanel(params) {
+ params.panelName = "drug";
+ params.helpTip = '<p>source: <a target="_drugbank" href="http://www.drugbank.ca/">DrugBank</a> and '
+ + '<a target="_drugbank" href="https://www.ebi.ac.uk/chembl/">ChEMBL</a></p>'
+ + "<p>use of drug names, synonyms and brand names is supported<p>separate multiple search by semicolon</p>";
+ params.placeholder = "drug, synonym, brand name";
+
+ AbstractDbPanel.call(this, params);
+ var self = this;
+ self.getControlElement(PanelControlElementType.SEARCH_LABEL).innerHTML = "SEARCH FOR TARGETS OF:";
+}
+
+DrugPanel.prototype = Object.create(AbstractDbPanel.prototype);
+DrugPanel.prototype.constructor = DrugPanel;
+
+/**
+ *
+ * @param {Drug} drug
+ * @returns {HTMLDivElement}
+ */
+DrugPanel.prototype.createPreamble = function (drug) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var result = document.createElement("div");
+ if (drug === undefined || drug.getName() === undefined) {
+ result.appendChild(guiUtils.createLabel("NOT FOUND"));
+ } else {
+ result.appendChild(guiUtils.createParamLine("Drug: ", drug.getName()));
+ result.appendChild(guiUtils.createParamLine("Description: ", drug.getDescription()));
+ result.appendChild(guiUtils.createArrayParamLine("Synonyms: ", drug.getSynonyms()));
+ result.appendChild(guiUtils.createArrayParamLine("Brand names: ", drug.getBrandNames()));
+ result.appendChild(guiUtils.createParamLine("Blood brain barrier: ", drug.getBloodBrainBarrier()));
+ result.appendChild(guiUtils.createAnnotations("Sources: ", drug.getReferences(), {groupAnnotations: false}));
+ result.appendChild(guiUtils.createNewLine());
+ }
+
+ return result;
+};
+
+DrugPanel.prototype.createTableElement = function (target, icon) {
+ return this.createTargetRow(target, icon);
+};
+
+DrugPanel.prototype.searchByQuery = function () {
+ var self = this;
+ var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
+ return self.getOverlayDb().searchByQuery(query);
+};
+
+DrugPanel.prototype.init = function () {
+ var query = ServerConnector.getSessionData().getDrugQuery();
+ if (query !== undefined) {
+ return this.getOverlayDb().searchByEncodedQuery(query);
+ } else {
+ return Promise.resolve();
+ }
+};
+
+DrugPanel.prototype.destroy = function () {
+ return Promise.resolve();
+};
+
+DrugPanel.prototype.getAutocomplete = function (query) {
+ if (this._searchAutocomplete === undefined) {
+ this.refreshSearchAutocomplete();
+ return [];
+ }
+
+ return this._searchAutocomplete[query];
+};
+
+DrugPanel.prototype.refreshSearchAutocomplete = function () {
+ var self = this;
+ self._searchAutocomplete = [];
+ return ServerConnector.getDrugSuggestedQueryList().then(function (queries) {
+ self._searchAutocomplete = self.computeAutocompleteDictionary(queries);
+ return self._searchAutocomplete;
+ });
+};
+
+module.exports = DrugPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
index e1b3d6fa419a879bf18c388d3bebeafea431b6ae..cb400d39b6b2e80471713333a89a548c0afb8280 100644
--- a/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js
@@ -1,179 +1,179 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-/* exported logger */
-
-var AbstractDbPanel = require('./AbstractDbPanel');
-var Alias = require('../../map/data/Alias');
-var InvalidArgumentError = require('../../InvalidArgumentError');
-var PanelControlElementType = require('../PanelControlElementType');
-var Reaction = require('../../map/data/Reaction');
-var SearchBioEntityGroup = require('../../map/data/SearchBioEntityGroup');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-var Functions = require('../../Functions');
-
-function GenericSearchPanel(params) {
- params.panelName = "search";
- params.helpTip = "<p>search tab allows to search for particular elements or interactions in the map</p>"
- + "<p>perfect match tick box active: only terms with an exact match to the query will be returned</p>"
- + "<p>separate multiple search by semicolon</p>";
- params.placeholder = "keyword";
-
- AbstractDbPanel.call(this, params);
-
- this.createSearchGui();
-}
-
-GenericSearchPanel.prototype = Object.create(AbstractDbPanel.prototype);
-GenericSearchPanel.prototype.constructor = GenericSearchPanel;
-
-GenericSearchPanel.prototype.createSearchGui = function () {
- var searchDiv = this.getControlElement(PanelControlElementType.SEARCH_DIV);
-
- var perfectMatchCheckbox = Functions.createElement({
- type: "input",
- name: "searchPerfectMatch",
- inputType: "checkbox"
- });
- searchDiv.appendChild(perfectMatchCheckbox);
- this.setControlElement(PanelControlElementType.SEARCH_PERFECT_MATCH_CHECKBOX, perfectMatchCheckbox);
-
- var perfectMatchLabel = Functions.createElement({
- type: "span",
- content: "PERFECT MATCH"
- });
- searchDiv.appendChild(perfectMatchLabel);
-};
-
-/**
- *
- * @param {SearchBioEntityGroup|BioEntity} element
- * @param {string} icon
- * @returns {Promise<HTMLTableRowElement>}
- */
-GenericSearchPanel.prototype.createTableElement = function (element, icon) {
- if (element instanceof Alias) {
- return this.createAliasElement(element, icon);
- } else if (element instanceof Reaction) {
- return this.createReactionElement(element);
- } else if (element instanceof SearchBioEntityGroup) {
- return this.createSearchBioEntityGroupElement(element);
- } else {
- throw new Error("Unknown element type: " + element.constructor.name);
- }
-};
-
-GenericSearchPanel.prototype.createPreamble = function () {
- return document.createElement("div");
-};
-
-/**
- *
- * @param {Reaction} reaction
- * @returns {Promise<HTMLTableRowElement>}
- */
-GenericSearchPanel.prototype.createReactionElement = function (reaction) {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var result = document.createElement("tr");
- var td = document.createElement("td");
- result.appendChild(td);
-
- return guiUtils.createReactionElement({reaction: reaction}).then((function (div) {
- div.appendChild(guiUtils.createSeparator());
- td.appendChild(div);
- return result;
- }));
-};
-
-/**
- *
- * @param {Alias} alias
- * @param {string} icon
- * @returns {Promise<HTMLTableRowElement>}
- */
-GenericSearchPanel.prototype.createAliasElement = function (alias, icon) {
- var self = this;
- var guiUtils = self.getGuiUtils();
-
- var result = document.createElement("tr");
- var td = document.createElement("td");
- result.appendChild(td);
- return guiUtils.createAliasElement({
- alias: alias,
- icon: icon
- }).then(function (div) {
- div.appendChild(guiUtils.createSeparator());
- td.appendChild(div);
-
- return result;
- });
-
-};
-
-/**
- *
- * @param {SearchBioEntityGroup} group
- * @returns {Promise<HTMLTableRowElement>}
- */
-GenericSearchPanel.prototype.createSearchBioEntityGroupElement = function (group) {
- var self = this;
- var guiUtils = self.getGuiUtils();
-
- var result = document.createElement("tr");
- var td = document.createElement("td");
- result.appendChild(td);
- return guiUtils.createSearchBioEntityGroupElement(group).then(function (div) {
- div.appendChild(guiUtils.createSeparator());
- td.appendChild(div);
-
- return result;
- });
-
-};
-
-GenericSearchPanel.prototype.searchByQuery = function () {
- var self = this;
- var query = this.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
- var perfect = this.getControlElement(PanelControlElementType.SEARCH_PERFECT_MATCH_CHECKBOX).checked;
- return self.getOverlayDb().searchByQuery(query, perfect, true);
-};
-
-GenericSearchPanel.prototype.getAutocomplete = function (query) {
- if (this._searchAutocomplete === undefined) {
- this.refreshSearchAutocomplete();
- return [];
- }
-
- return this._searchAutocomplete[query];
-};
-
-GenericSearchPanel.prototype.refreshSearchAutocomplete = function () {
- var self = this;
- self._searchAutocomplete = [];
- return ServerConnector.getSuggestedQueryList().then(function (queries) {
- self._searchAutocomplete = self.computeAutocompleteDictionary(queries);
- return self._searchAutocomplete;
- });
-};
-
-GenericSearchPanel.prototype.init = function () {
- var query = ServerConnector.getSessionData().getSearchQuery();
- if (query !== undefined) {
- return this.getOverlayDb().searchByEncodedQuery(query, false).catch(function (error) {
- if (error instanceof InvalidArgumentError) {
- logger.warn(error.message);
- } else {
- throw error;
- }
- });
- } else {
- return Promise.resolve();
- }
-};
-
-
-module.exports = GenericSearchPanel;
+"use strict";
+
+var Promise = require("bluebird");
+
+/* exported logger */
+
+var AbstractDbPanel = require('./AbstractDbPanel');
+var Alias = require('../../map/data/Alias');
+var InvalidArgumentError = require('../../InvalidArgumentError');
+var PanelControlElementType = require('../PanelControlElementType');
+var Reaction = require('../../map/data/Reaction');
+var SearchBioEntityGroup = require('../../map/data/SearchBioEntityGroup');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+
+function GenericSearchPanel(params) {
+ params.panelName = "search";
+ params.helpTip = "<p>search tab allows to search for particular elements or interactions in the map</p>"
+ + "<p>perfect match tick box active: only terms with an exact match to the query will be returned</p>"
+ + "<p>separate multiple search by semicolon</p>";
+ params.placeholder = "keyword";
+
+ AbstractDbPanel.call(this, params);
+
+ this.createSearchGui();
+}
+
+GenericSearchPanel.prototype = Object.create(AbstractDbPanel.prototype);
+GenericSearchPanel.prototype.constructor = GenericSearchPanel;
+
+GenericSearchPanel.prototype.createSearchGui = function () {
+ var searchDiv = this.getControlElement(PanelControlElementType.SEARCH_DIV);
+
+ var perfectMatchCheckbox = Functions.createElement({
+ type: "input",
+ name: "searchPerfectMatch",
+ inputType: "checkbox"
+ });
+ searchDiv.appendChild(perfectMatchCheckbox);
+ this.setControlElement(PanelControlElementType.SEARCH_PERFECT_MATCH_CHECKBOX, perfectMatchCheckbox);
+
+ var perfectMatchLabel = Functions.createElement({
+ type: "span",
+ content: "PERFECT MATCH"
+ });
+ searchDiv.appendChild(perfectMatchLabel);
+};
+
+/**
+ *
+ * @param {SearchBioEntityGroup|BioEntity} element
+ * @param {string} icon
+ * @returns {Promise<HTMLTableRowElement>}
+ */
+GenericSearchPanel.prototype.createTableElement = function (element, icon) {
+ if (element instanceof Alias) {
+ return this.createAliasElement(element, icon);
+ } else if (element instanceof Reaction) {
+ return this.createReactionElement(element);
+ } else if (element instanceof SearchBioEntityGroup) {
+ return this.createSearchBioEntityGroupElement(element);
+ } else {
+ throw new Error("Unknown element type: " + element.constructor.name);
+ }
+};
+
+GenericSearchPanel.prototype.createPreamble = function () {
+ return document.createElement("div");
+};
+
+/**
+ *
+ * @param {Reaction} reaction
+ * @returns {Promise<HTMLTableRowElement>}
+ */
+GenericSearchPanel.prototype.createReactionElement = function (reaction) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var result = document.createElement("tr");
+ var td = document.createElement("td");
+ result.appendChild(td);
+
+ return guiUtils.createReactionElement({reaction: reaction}).then((function (div) {
+ div.appendChild(guiUtils.createSeparator());
+ td.appendChild(div);
+ return result;
+ }));
+};
+
+/**
+ *
+ * @param {Alias} alias
+ * @param {string} icon
+ * @returns {Promise<HTMLTableRowElement>}
+ */
+GenericSearchPanel.prototype.createAliasElement = function (alias, icon) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+
+ var result = document.createElement("tr");
+ var td = document.createElement("td");
+ result.appendChild(td);
+ return guiUtils.createAliasElement({
+ alias: alias,
+ icon: icon
+ }).then(function (div) {
+ div.appendChild(guiUtils.createSeparator());
+ td.appendChild(div);
+
+ return result;
+ });
+
+};
+
+/**
+ *
+ * @param {SearchBioEntityGroup} group
+ * @returns {Promise<HTMLTableRowElement>}
+ */
+GenericSearchPanel.prototype.createSearchBioEntityGroupElement = function (group) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+
+ var result = document.createElement("tr");
+ var td = document.createElement("td");
+ result.appendChild(td);
+ return guiUtils.createSearchBioEntityGroupElement(group).then(function (div) {
+ div.appendChild(guiUtils.createSeparator());
+ td.appendChild(div);
+
+ return result;
+ });
+
+};
+
+GenericSearchPanel.prototype.searchByQuery = function () {
+ var self = this;
+ var query = this.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
+ var perfect = this.getControlElement(PanelControlElementType.SEARCH_PERFECT_MATCH_CHECKBOX).checked;
+ return self.getOverlayDb().searchByQuery(query, perfect, true);
+};
+
+GenericSearchPanel.prototype.getAutocomplete = function (query) {
+ if (this._searchAutocomplete === undefined) {
+ this.refreshSearchAutocomplete();
+ return [];
+ }
+
+ return this._searchAutocomplete[query];
+};
+
+GenericSearchPanel.prototype.refreshSearchAutocomplete = function () {
+ var self = this;
+ self._searchAutocomplete = [];
+ return ServerConnector.getSuggestedQueryList().then(function (queries) {
+ self._searchAutocomplete = self.computeAutocompleteDictionary(queries);
+ return self._searchAutocomplete;
+ });
+};
+
+GenericSearchPanel.prototype.init = function () {
+ var query = ServerConnector.getSessionData().getSearchQuery();
+ if (query !== undefined) {
+ return this.getOverlayDb().searchByEncodedQuery(query, false).catch(function (error) {
+ if (error instanceof InvalidArgumentError) {
+ logger.warn(error.message);
+ } else {
+ throw error;
+ }
+ });
+ } else {
+ return Promise.resolve();
+ }
+};
+
+
+module.exports = GenericSearchPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
index 646c317f8edc13bfb5ec7d0355fa6354ca7a92ef..c9777db198c6ddee2f101290246de87fc4beb139 100644
--- a/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/LeftPanel.js
@@ -1,361 +1,361 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-/* exported logger */
-
-var AbstractGuiElement = require('../AbstractGuiElement');
-var AbstractDbOverlay = require('../../map/overlay/AbstractDbOverlay');
-var Alias = require('../../map/data/Alias');
-var GuiUtils = require('./GuiUtils');
-var Header = require('../Header');
-var LoginDialog = require('../LoginDialog');
-var OverlayPanel = require('./OverlayPanel');
-var PointData = require('../../map/data/PointData');
-var ProjectInfoPanel = require('./ProjectInfoPanel');
-var Reaction = require('../../map/data/Reaction');
-var SearchPanel = require('./SearchPanel');
-var SubmapPanel = require('./SubmapPanel');
-
-var Functions = require('../../Functions');
-var logger = require('../../logger');
-
-/**
- *
- * @param {Object} params
- * @param {HTMLElement} params.element
- * @param {CustomMap} params.customMap
- * @param {Configuration} params.configuration
- * @param {Project} [params.project]
- * @param {ServerConnector} [params.serverConnector]
- *
- * @constructor
- *
- * @extends AbstractGuiElement
- */
-function LeftPanel(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
-
- this._tabIdCount = 0;
- this._panels = [];
-
- self._createPanelGui();
-
-}
-
-LeftPanel.prototype = Object.create(AbstractGuiElement.prototype);
-LeftPanel.prototype.constructor = LeftPanel;
-
-LeftPanel.prototype._createPanelGui = function () {
- var self = this;
- var panels = self.getPanelsDefinition();
-
- var headerDiv = Functions.createElement({
- type: "div",
- id: "headerPanel"
- });
- var header = new Header({
- element: headerDiv,
- customMap: self.getMap(),
- optionsMenu: true
- });
- self.getElement().appendChild(headerDiv);
-
- var loginDialogDiv = Functions.createElement({
- type: "div",
- name: "loginDialog",
- style: "display:none"
- });
- self.getElement().appendChild(loginDialogDiv);
- this.setLoginDialog(new LoginDialog({
- element: loginDialogDiv,
- customMap: self.getMap()
- }));
-
- var guiUtils = self.getGuiUtils();
- var tabData = guiUtils.createTabDiv({
- element: self.getElement(),
- id: "left_panel"
- });
-
- self.setHeader(header);
-
- self.elementInfoDiv = Functions.createElement({
- name: "elementInfoDiv",
- type: "div",
- style: "background-color:#f3f3f3",
- className: "minerva-element-info-div"
- });
-
- for (var i = 0; i < panels.length; i++) {
- self.addTab(panels[i], tabData);
- }
-};
-
-LeftPanel.prototype.getPanelsDefinition = function () {
- return [{
- name: "SEARCH",
- className: "fa-search",
- panelClass: SearchPanel
- }, {
- name: "OVERLAYS",
- className: "fa-th-list",
- panelClass: OverlayPanel
- }, {
- name: "SUBMAPS",
- className: "fa-sitemap",
- panelClass: SubmapPanel
- }, {
- name: "INFO",
- className: "fa-info",
- panelClass: ProjectInfoPanel
- }];
-};
-
-LeftPanel.prototype.hideTab = function (panel) {
- var self = this;
- var panelDefinitions = self.getPanelsDefinition();
- for (var i = 0; i < panelDefinitions.length; i++) {
- if (panel instanceof panelDefinitions[i].panelClass) {
- var liElement = $("li:has(a[data='left_tab_" + i + "'])", $(self.getElement()))[0];
- if (liElement !== undefined) {
- liElement.style.display = "none";
- } else {
- logger.warn("Cannot find tab link for panel: " + panel.getPanelName());
- }
- }
- }
-};
-
-LeftPanel.prototype.init = function () {
- var self = this;
-
- var promises = [];
- for (var i = 0; i < self._panels.length; i++) {
- promises.push(self._panels[i].init());
- }
- promises.push(self.getHeader().init());
-
- var initEvents = new Promise(function (resolve) {
- self.getMap().addListener("onBioEntityClick", function (e) {
- return self.showElementDetails(e.arg);
- });
- self.getMap().getOverlayByName("search").addListener("onSearch", function (e) {
- if (e.arg.type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES ||
- e.arg.type === AbstractDbOverlay.QueryType.SEARCH_BY_TARGET) {
- return self.showElementDetails(e.arg.identifiedElements[0][0]);
- } else {
- return self.showElementDetails(undefined);
- }
- });
- resolve();
- });
- promises.push(initEvents);
- promises.push(self.getLoginDialog().init());
- return Promise.all(promises);
-};
-
-LeftPanel.prototype.showElementDetails = function (element) {
- var self = this;
- var div = self.elementInfoDiv;
- if (!$(div).hasClass("ui-dialog-content")) {
- $(div).dialog({
- resizable: false,
- width: $(self.getElement()).width(),
- height: 200,
- beforeclose: function () {
- $(this).dialog('option', 'position', [$(this).offset().left, $(this).offset().top]);
- $(this).dialog('option', 'width', $(this).width());
- $(this).dialog('option', 'height', $(this).height());
- },
- position: {
- my: "left bottom",
- at: "left bottom",
- of: $(self.getElement())
- }
- }).siblings('.ui-dialog-titlebar').css("background", "gray");
- }
-
- var openedTabs = $("[name='tabView'] > ul > li.active > a");
- var openTabName = openedTabs[0].innerHTML;
- var searchTabName = openedTabs[1].innerHTML;
- var isPanelHidden = (self.getElement().style.display === "none");
- if (isPanelHidden) {
- openTabName = undefined;
- }
-
- if (element !== undefined && openTabName !== undefined && (openTabName.indexOf("SEARCH") === -1 || searchTabName !== "GENERIC")) {
- var model = self.getMap().getSubmapById(element.getModelId()).getModel();
- var bioEntity;
- return model.getByIdentifiedElement(element, true).then(function (result) {
- bioEntity=result;
- return self.prepareElementDetailsContent(bioEntity);
- }).then(function(elementDetailsDiv){
- div.innerHTML = "";
- div.appendChild(elementDetailsDiv);
- $(div).dialog("open");
- $(div).dialog("option", "title", self.getElementTitle(bioEntity));
- $(div).scrollTop(0);
- });
- } else {
- $(div).dialog("close");
- return Promise.resolve();
- }
-};
-
-/**
- *
- * @param {BioEntity} bioEntity
- *
- * @returns {Promise<HTMLDivElement>}
- */
-LeftPanel.prototype.prepareElementDetailsContent = function (bioEntity) {
- var guiUtils = this.getGuiUtils();
- if (bioEntity instanceof Reaction) {
- return guiUtils.createReactionElement({
- reaction: bioEntity,
- showTitle: false
- });
- } else if (bioEntity instanceof Alias) {
- return guiUtils.createAliasElement({
- alias: bioEntity,
- showTitle: false
- });
- } else if (bioEntity instanceof PointData) {
- return Promise.resolve(Functions.createElement({
- type: "div"
- }));
- } else {
- throw new Error("Unknown element type:" + bioEntity);
- }
-};
-
-/**
- *
- * @returns {GuiUtils}
- */
-LeftPanel.prototype.getGuiUtils = function () {
- var self = this;
- if (self._guiUtils === undefined) {
- self._guiUtils = new GuiUtils(self.getMap().getConfiguration());
- self._guiUtils.setMap(self.getMap());
- }
- return self._guiUtils;
-};
-
-/**
- *
- * @param {BioEntity} bioEntity
- * @returns {string}
- */
-LeftPanel.prototype.getElementTitle = function (bioEntity) {
- if (bioEntity instanceof Reaction) {
- return bioEntity.getType() + ": " + bioEntity.getReactionId();
- } else if (bioEntity instanceof Alias) {
- return bioEntity.getType() + ": " + bioEntity.getName();
- } else if (bioEntity instanceof PointData) {
- return "POINT: " + bioEntity.getId();
- } else {
- throw new Error("Unknown element type:" + bioEntity);
- }
-};
-
-LeftPanel.prototype.addTab = function (params, tabData) {
- var self = this;
-
- var name = params.name;
- if (name !== undefined) {
- if (name.length > 12) {
- name = name.substring(0, 10) + "...";
- }
- } else {
- name = "";
- }
-
-
- var guiUtils = self.getGuiUtils();
- var data = guiUtils.createTab({
- tabData: tabData,
- title: '<div class="maintabdiv"><i class="fa ' + params.className + ' maintab"></i><br>' + name
- + '</div>',
- content: ""
- });
-
- $(data.title).attr("data", "left_tab_" + this._panels.length);
-
- this._panels.push(new params.panelClass({
- element: data.content,
- customMap: self.getMap(),
- configuration: self.getConfiguration(),
- parent: self
- }));
-
-};
-
-LeftPanel.prototype.hide = function () {
- this.getElement().style.display = "none";
-};
-LeftPanel.prototype.show = function () {
- this.getElement().style.display = "block";
-};
-
-LeftPanel.prototype.setHeader = function (header) {
- this._header = header;
-};
-
-LeftPanel.prototype.getHeader = function () {
- return this._header;
-};
-
-LeftPanel.prototype.setLoginDialog = function (loginDialog) {
- this._loginDialog = loginDialog;
-};
-
-LeftPanel.prototype.getLoginDialog = function () {
- return this._loginDialog;
-};
-
-LeftPanel.prototype.setPluginManager = function (pluginManager) {
- this._pluginManager = pluginManager;
- this.getHeader().setPluginManager(pluginManager);
-};
-
-LeftPanel.prototype.getPluginManager = function () {
- return this._pluginManager;
-};
-
-LeftPanel.prototype.destroy = function () {
- var self = this;
- var promises = [];
- promises.push(self.getHeader().destroy());
- var div = self.elementInfoDiv;
-
- var destroyPanel = new Promise(function (resolve) {
- if ($(div).hasClass("ui-dialog-content")) {
- $(div).dialog("destroy");
- }
- resolve();
- });
- promises.push(destroyPanel);
- promises.push(self.getLoginDialog().destroy());
- for (var i = 0; i < self._panels.length; i++) {
- promises.push(self._panels[i].destroy());
- }
-
- if (self._pluginManager !== undefined) {
- promises.push(self._pluginManager.destroy());
- }
-
- return Promise.all(promises);
-};
-
-LeftPanel.prototype.setGoogleLicenseConsentRequired = function (value) {
- this._googleLicenseConsentRequired = value;
-};
-
-LeftPanel.prototype.isGoogleLicenseConsentRequired = function () {
- return this._googleLicenseConsentRequired;
-};
-
-module.exports = LeftPanel;
+"use strict";
+
+var Promise = require("bluebird");
+
+/* exported logger */
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+var AbstractDbOverlay = require('../../map/overlay/AbstractDbOverlay');
+var Alias = require('../../map/data/Alias');
+var GuiUtils = require('./GuiUtils');
+var Header = require('../Header');
+var LoginDialog = require('../LoginDialog');
+var OverlayPanel = require('./OverlayPanel');
+var PointData = require('../../map/data/PointData');
+var ProjectInfoPanel = require('./ProjectInfoPanel');
+var Reaction = require('../../map/data/Reaction');
+var SearchPanel = require('./SearchPanel');
+var SubmapPanel = require('./SubmapPanel');
+
+var Functions = require('../../Functions');
+var logger = require('../../logger');
+
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {ServerConnector} [params.serverConnector]
+ *
+ * @constructor
+ *
+ * @extends AbstractGuiElement
+ */
+function LeftPanel(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+
+ this._tabIdCount = 0;
+ this._panels = [];
+
+ self._createPanelGui();
+
+}
+
+LeftPanel.prototype = Object.create(AbstractGuiElement.prototype);
+LeftPanel.prototype.constructor = LeftPanel;
+
+LeftPanel.prototype._createPanelGui = function () {
+ var self = this;
+ var panels = self.getPanelsDefinition();
+
+ var headerDiv = Functions.createElement({
+ type: "div",
+ id: "headerPanel"
+ });
+ var header = new Header({
+ element: headerDiv,
+ customMap: self.getMap(),
+ optionsMenu: true
+ });
+ self.getElement().appendChild(headerDiv);
+
+ var loginDialogDiv = Functions.createElement({
+ type: "div",
+ name: "loginDialog",
+ style: "display:none"
+ });
+ self.getElement().appendChild(loginDialogDiv);
+ this.setLoginDialog(new LoginDialog({
+ element: loginDialogDiv,
+ customMap: self.getMap()
+ }));
+
+ var guiUtils = self.getGuiUtils();
+ var tabData = guiUtils.createTabDiv({
+ element: self.getElement(),
+ id: "left_panel"
+ });
+
+ self.setHeader(header);
+
+ self.elementInfoDiv = Functions.createElement({
+ name: "elementInfoDiv",
+ type: "div",
+ style: "background-color:#f3f3f3",
+ className: "minerva-element-info-div"
+ });
+
+ for (var i = 0; i < panels.length; i++) {
+ self.addTab(panels[i], tabData);
+ }
+};
+
+LeftPanel.prototype.getPanelsDefinition = function () {
+ return [{
+ name: "SEARCH",
+ className: "fa-search",
+ panelClass: SearchPanel
+ }, {
+ name: "OVERLAYS",
+ className: "fa-th-list",
+ panelClass: OverlayPanel
+ }, {
+ name: "SUBMAPS",
+ className: "fa-sitemap",
+ panelClass: SubmapPanel
+ }, {
+ name: "INFO",
+ className: "fa-info",
+ panelClass: ProjectInfoPanel
+ }];
+};
+
+LeftPanel.prototype.hideTab = function (panel) {
+ var self = this;
+ var panelDefinitions = self.getPanelsDefinition();
+ for (var i = 0; i < panelDefinitions.length; i++) {
+ if (panel instanceof panelDefinitions[i].panelClass) {
+ var liElement = $("li:has(a[data='left_tab_" + i + "'])", $(self.getElement()))[0];
+ if (liElement !== undefined) {
+ liElement.style.display = "none";
+ } else {
+ logger.warn("Cannot find tab link for panel: " + panel.getPanelName());
+ }
+ }
+ }
+};
+
+LeftPanel.prototype.init = function () {
+ var self = this;
+
+ var promises = [];
+ for (var i = 0; i < self._panels.length; i++) {
+ promises.push(self._panels[i].init());
+ }
+ promises.push(self.getHeader().init());
+
+ var initEvents = new Promise(function (resolve) {
+ self.getMap().addListener("onBioEntityClick", function (e) {
+ return self.showElementDetails(e.arg);
+ });
+ self.getMap().getOverlayByName("search").addListener("onSearch", function (e) {
+ if (e.arg.type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES ||
+ e.arg.type === AbstractDbOverlay.QueryType.SEARCH_BY_TARGET) {
+ return self.showElementDetails(e.arg.identifiedElements[0][0]);
+ } else {
+ return self.showElementDetails(undefined);
+ }
+ });
+ resolve();
+ });
+ promises.push(initEvents);
+ promises.push(self.getLoginDialog().init());
+ return Promise.all(promises);
+};
+
+LeftPanel.prototype.showElementDetails = function (element) {
+ var self = this;
+ var div = self.elementInfoDiv;
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ resizable: false,
+ width: $(self.getElement()).width(),
+ height: 200,
+ beforeclose: function () {
+ $(this).dialog('option', 'position', [$(this).offset().left, $(this).offset().top]);
+ $(this).dialog('option', 'width', $(this).width());
+ $(this).dialog('option', 'height', $(this).height());
+ },
+ position: {
+ my: "left bottom",
+ at: "left bottom",
+ of: $(self.getElement())
+ }
+ }).siblings('.ui-dialog-titlebar').css("background", "gray");
+ }
+
+ var openedTabs = $("[name='tabView'] > ul > li.active > a");
+ var openTabName = openedTabs[0].innerHTML;
+ var searchTabName = openedTabs[1].innerHTML;
+ var isPanelHidden = (self.getElement().style.display === "none");
+ if (isPanelHidden) {
+ openTabName = undefined;
+ }
+
+ if (element !== undefined && openTabName !== undefined && (openTabName.indexOf("SEARCH") === -1 || searchTabName !== "GENERIC")) {
+ var model = self.getMap().getSubmapById(element.getModelId()).getModel();
+ var bioEntity;
+ return model.getByIdentifiedElement(element, true).then(function (result) {
+ bioEntity=result;
+ return self.prepareElementDetailsContent(bioEntity);
+ }).then(function(elementDetailsDiv){
+ div.innerHTML = "";
+ div.appendChild(elementDetailsDiv);
+ $(div).dialog("open");
+ $(div).dialog("option", "title", self.getElementTitle(bioEntity));
+ $(div).scrollTop(0);
+ });
+ } else {
+ $(div).dialog("close");
+ return Promise.resolve();
+ }
+};
+
+/**
+ *
+ * @param {BioEntity} bioEntity
+ *
+ * @returns {Promise<HTMLDivElement>}
+ */
+LeftPanel.prototype.prepareElementDetailsContent = function (bioEntity) {
+ var guiUtils = this.getGuiUtils();
+ if (bioEntity instanceof Reaction) {
+ return guiUtils.createReactionElement({
+ reaction: bioEntity,
+ showTitle: false
+ });
+ } else if (bioEntity instanceof Alias) {
+ return guiUtils.createAliasElement({
+ alias: bioEntity,
+ showTitle: false
+ });
+ } else if (bioEntity instanceof PointData) {
+ return Promise.resolve(Functions.createElement({
+ type: "div"
+ }));
+ } else {
+ throw new Error("Unknown element type:" + bioEntity);
+ }
+};
+
+/**
+ *
+ * @returns {GuiUtils}
+ */
+LeftPanel.prototype.getGuiUtils = function () {
+ var self = this;
+ if (self._guiUtils === undefined) {
+ self._guiUtils = new GuiUtils(self.getMap().getConfiguration());
+ self._guiUtils.setMap(self.getMap());
+ }
+ return self._guiUtils;
+};
+
+/**
+ *
+ * @param {BioEntity} bioEntity
+ * @returns {string}
+ */
+LeftPanel.prototype.getElementTitle = function (bioEntity) {
+ if (bioEntity instanceof Reaction) {
+ return bioEntity.getType() + ": " + bioEntity.getReactionId();
+ } else if (bioEntity instanceof Alias) {
+ return bioEntity.getType() + ": " + bioEntity.getName();
+ } else if (bioEntity instanceof PointData) {
+ return "POINT: " + bioEntity.getId();
+ } else {
+ throw new Error("Unknown element type:" + bioEntity);
+ }
+};
+
+LeftPanel.prototype.addTab = function (params, tabData) {
+ var self = this;
+
+ var name = params.name;
+ if (name !== undefined) {
+ if (name.length > 12) {
+ name = name.substring(0, 10) + "...";
+ }
+ } else {
+ name = "";
+ }
+
+
+ var guiUtils = self.getGuiUtils();
+ var data = guiUtils.createTab({
+ tabData: tabData,
+ title: '<div class="maintabdiv"><i class="fa ' + params.className + ' maintab"></i><br>' + name
+ + '</div>',
+ content: ""
+ });
+
+ $(data.title).attr("data", "left_tab_" + this._panels.length);
+
+ this._panels.push(new params.panelClass({
+ element: data.content,
+ customMap: self.getMap(),
+ configuration: self.getConfiguration(),
+ parent: self
+ }));
+
+};
+
+LeftPanel.prototype.hide = function () {
+ this.getElement().style.display = "none";
+};
+LeftPanel.prototype.show = function () {
+ this.getElement().style.display = "block";
+};
+
+LeftPanel.prototype.setHeader = function (header) {
+ this._header = header;
+};
+
+LeftPanel.prototype.getHeader = function () {
+ return this._header;
+};
+
+LeftPanel.prototype.setLoginDialog = function (loginDialog) {
+ this._loginDialog = loginDialog;
+};
+
+LeftPanel.prototype.getLoginDialog = function () {
+ return this._loginDialog;
+};
+
+LeftPanel.prototype.setPluginManager = function (pluginManager) {
+ this._pluginManager = pluginManager;
+ this.getHeader().setPluginManager(pluginManager);
+};
+
+LeftPanel.prototype.getPluginManager = function () {
+ return this._pluginManager;
+};
+
+LeftPanel.prototype.destroy = function () {
+ var self = this;
+ var promises = [];
+ promises.push(self.getHeader().destroy());
+ var div = self.elementInfoDiv;
+
+ var destroyPanel = new Promise(function (resolve) {
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
+ }
+ resolve();
+ });
+ promises.push(destroyPanel);
+ promises.push(self.getLoginDialog().destroy());
+ for (var i = 0; i < self._panels.length; i++) {
+ promises.push(self._panels[i].destroy());
+ }
+
+ if (self._pluginManager !== undefined) {
+ promises.push(self._pluginManager.destroy());
+ }
+
+ return Promise.all(promises);
+};
+
+LeftPanel.prototype.setGoogleLicenseConsentRequired = function (value) {
+ this._googleLicenseConsentRequired = value;
+};
+
+LeftPanel.prototype.isGoogleLicenseConsentRequired = function () {
+ return this._googleLicenseConsentRequired;
+};
+
+module.exports = LeftPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js b/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
index db300dedd1e78d52a89be252499282ae54cc8351..eb678ae5a4daa80374ae7b8e8cbd1d04cc5f5e86 100644
--- a/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/MiRnaPanel.js
@@ -1,84 +1,84 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-/* exported logger */
-var logger = require('../../logger');
-
-var AbstractDbPanel = require('./AbstractDbPanel');
-var PanelControlElementType = require('../PanelControlElementType');
-
-function MiRnaPanel(params) {
- params.panelName = "mirna";
- params.helpTip = '<p>source: <a target="_mirtarbase" href="http://mirtarbase.mbc.nctu.edu.tw/">miRTarBase</a></p>'
- + '<p>use only mature sequence IDs according to <a target="_mirbase" href="http://www.mirbase.org">www.mirbase.org</a> (e.g., hsa-miR-125a-3p)</p>'
- + '<p>only targets with strong evidence as defined by miRTarBase are displayed<p>separate multiple search by semicolon</p>';
- params.placeholder = "mature seq. ID (miRTarBase)";
- AbstractDbPanel.call(this, params);
- this.getControlElement(PanelControlElementType.SEARCH_LABEL).innerHTML = "SEARCH FOR TARGETS OF:";
-}
-MiRnaPanel.prototype = Object.create(AbstractDbPanel.prototype);
-MiRnaPanel.prototype.constructor = MiRnaPanel;
-
-MiRnaPanel.prototype.createPreamble = function(miRna) {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var result = document.createElement("div");
- if (miRna === undefined || miRna.getName() === undefined) {
- result.appendChild(guiUtils.createLabel("NOT FOUND"));
- } else {
- var line = document.createElement("div");
- line.appendChild(guiUtils.createLabel("MiRNA: "));
- line.appendChild(guiUtils.createLink("http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" + miRna.getName(), miRna
- .getName()));
- line.appendChild(guiUtils.createNewLine());
-
- result.appendChild(line);
- result.appendChild(guiUtils.createNewLine());
- }
-
- return result;
-};
-
-MiRnaPanel.prototype.createTableElement = function(target, icon) {
- return this.createTargetRow(target, icon);
-};
-
-MiRnaPanel.prototype.searchByQuery = function() {
- var self = this;
- var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
- return self.getOverlayDb().searchByQuery(query);
-};
-
-MiRnaPanel.prototype.init = function() {
- var query = ServerConnector.getSessionData().getMiRnaQuery();
- if (query !== undefined) {
- return this.getOverlayDb().searchByEncodedQuery(query);
- } else {
- return Promise.resolve();
- }
-};
-
-MiRnaPanel.prototype.destroy = function () {
- return Promise.resolve();
-};
-
-MiRnaPanel.prototype.getAutocomplete = function (query) {
- if (this._searchAutocomplete === undefined) {
- this.refreshSearchAutocomplete();
- return [];
- }
-
- return this._searchAutocomplete[query];
-};
-
-MiRnaPanel.prototype.refreshSearchAutocomplete = function () {
- var self = this;
- self._searchAutocomplete = [];
- return ServerConnector.getMiRnaSuggestedQueryList().then(function (queries) {
- self._searchAutocomplete = self.computeAutocompleteDictionary(queries);
- return self._searchAutocomplete;
- });
-};
-
-module.exports = MiRnaPanel;
+"use strict";
+
+var Promise = require("bluebird");
+
+/* exported logger */
+var logger = require('../../logger');
+
+var AbstractDbPanel = require('./AbstractDbPanel');
+var PanelControlElementType = require('../PanelControlElementType');
+
+function MiRnaPanel(params) {
+ params.panelName = "mirna";
+ params.helpTip = '<p>source: <a target="_mirtarbase" href="http://mirtarbase.mbc.nctu.edu.tw/">miRTarBase</a></p>'
+ + '<p>use only mature sequence IDs according to <a target="_mirbase" href="http://www.mirbase.org">www.mirbase.org</a> (e.g., hsa-miR-125a-3p)</p>'
+ + '<p>only targets with strong evidence as defined by miRTarBase are displayed<p>separate multiple search by semicolon</p>';
+ params.placeholder = "mature seq. ID (miRTarBase)";
+ AbstractDbPanel.call(this, params);
+ this.getControlElement(PanelControlElementType.SEARCH_LABEL).innerHTML = "SEARCH FOR TARGETS OF:";
+}
+MiRnaPanel.prototype = Object.create(AbstractDbPanel.prototype);
+MiRnaPanel.prototype.constructor = MiRnaPanel;
+
+MiRnaPanel.prototype.createPreamble = function(miRna) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var result = document.createElement("div");
+ if (miRna === undefined || miRna.getName() === undefined) {
+ result.appendChild(guiUtils.createLabel("NOT FOUND"));
+ } else {
+ var line = document.createElement("div");
+ line.appendChild(guiUtils.createLabel("MiRNA: "));
+ line.appendChild(guiUtils.createLink("http://www.mirbase.org/cgi-bin/mirna_entry.pl?acc=" + miRna.getName(), miRna
+ .getName()));
+ line.appendChild(guiUtils.createNewLine());
+
+ result.appendChild(line);
+ result.appendChild(guiUtils.createNewLine());
+ }
+
+ return result;
+};
+
+MiRnaPanel.prototype.createTableElement = function(target, icon) {
+ return this.createTargetRow(target, icon);
+};
+
+MiRnaPanel.prototype.searchByQuery = function() {
+ var self = this;
+ var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
+ return self.getOverlayDb().searchByQuery(query);
+};
+
+MiRnaPanel.prototype.init = function() {
+ var query = ServerConnector.getSessionData().getMiRnaQuery();
+ if (query !== undefined) {
+ return this.getOverlayDb().searchByEncodedQuery(query);
+ } else {
+ return Promise.resolve();
+ }
+};
+
+MiRnaPanel.prototype.destroy = function () {
+ return Promise.resolve();
+};
+
+MiRnaPanel.prototype.getAutocomplete = function (query) {
+ if (this._searchAutocomplete === undefined) {
+ this.refreshSearchAutocomplete();
+ return [];
+ }
+
+ return this._searchAutocomplete[query];
+};
+
+MiRnaPanel.prototype.refreshSearchAutocomplete = function () {
+ var self = this;
+ self._searchAutocomplete = [];
+ return ServerConnector.getMiRnaSuggestedQueryList().then(function (queries) {
+ self._searchAutocomplete = self.computeAutocompleteDictionary(queries);
+ return self._searchAutocomplete;
+ });
+};
+
+module.exports = MiRnaPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
index 862b8f9f46349a84796d866ffea8f3016e8cca71..0a178c5e3008042600a77549ff2ab443b0a34706 100644
--- a/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js
@@ -1,668 +1,668 @@
-"use strict";
-
-/* exported logger */
-
-var AddOverlayDialog = require('../AddOverlayDialog');
-var Panel = require('../Panel');
-var PanelControlElementType = require('../PanelControlElementType');
-
-var GuiConnector = require('../../GuiConnector');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-var Functions = require('../../Functions');
-
-var Promise = require('bluebird');
-
-/**
- *
- * @param {Object} params
- * @param {HTMLElement} params.element
- * @param {CustomMap} params.customMap
- * @param {Configuration} [params.configuration]
- * @param {Project} [params.project]
- * @param params.parent
- *
- * @constructor
- * @extends Panel
- */
-function OverlayPanel(params) {
- params["panelName"] = "overlays";
- params["scrollable"] = true;
- params["helpTip"] = "<p>Overlays tab allows to display or generate custom coloring of elements and interactions in the map.</p>"
- + "<p>General overlays are overlays accessible for every user viewing the content.</p>"
- + "<p>Custom overlays are user-provided overlays, this menu becomes available upon login (see below).</p>";
- if (params.project === undefined) {
- params.project = params.customMap.getProject();
- }
- Panel.call(this, params);
-
- //overflow is defined in minerva-overlay-panel, so remove the one that is already there
- $(params.element).css("overflow", "");
- $(params.element).addClass("minerva-overlay-panel");
-
- var self = this;
-
- self._createOverlayPanelGui();
-
- var addButton = this.getControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON);
-
- addButton.onclick = function () {
- return self.openAddOverlayDialog();
- };
-
- var titleElement = this.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE);
- self.setCustomOverlaysMessage(titleElement.innerHTML);
-
- $(self.getElement()).on("click", "[name='overlayToggle']", function () {
- var thisCheckbox = this;
- var overlayId = $(thisCheckbox).attr("data");
- var toggleOverlayPromise;
- if (thisCheckbox.checked) {
- toggleOverlayPromise = self.getMap().openDataOverlay(overlayId);
- } else {
- toggleOverlayPromise = self.getMap().hideDataOverlay(overlayId);
- }
- $(thisCheckbox).prop("disabled", true);
- return toggleOverlayPromise.catch(GuiConnector.alert).finally(function () {
- $(thisCheckbox).prop("disabled", false);
- });
- });
- $(self.getElement()).on("click", "[name='overlayLink']", function () {
- var overlayId = $(this).attr("data");
- return self.getMap().openDataOverlay(overlayId);
- });
- self.getMap().addListener("onBackgroundOverlayChange", function (e) {
- var overlayId = e.arg.toString();
- var buttons = $("[name='overlayLink']", self.getElement());
- for (var i = 0; i < buttons.length; i++) {
- var button = buttons[i];
- if ($(button).attr("data").toString() === overlayId) {
- $(button.parentNode.parentNode).addClass('active').siblings().removeClass('active');
- }
- }
- });
- $(self.getElement()).on("click", "[name='download-overlay']", function () {
- var overlayId = $(this).attr("data");
- return self.getServerConnector().getOverlaySourceDownloadUrl({
- overlayId: overlayId
- }).then(function (url) {
- return self.downloadFile(url);
- }).then(null, GuiConnector.alert);
- });
- $(self.getElement()).on("click", "[name='editButton']", function () {
- var overlayId = $(this).attr("data");
- return self.getProject().getDataOverlayById(overlayId).then(function (overlay) {
- return self.openEditOverlayDialog(overlay);
- });
- });
-}
-
-OverlayPanel.prototype = Object.create(Panel.prototype);
-OverlayPanel.prototype.constructor = OverlayPanel;
-
-/**
- *
- * @private
- */
-OverlayPanel.prototype._createOverlayPanelGui = function () {
- var generalOverlaysDiv = Functions.createElement({
- type: "div",
- name: "generalOverlays",
- className: "searchPanel"
- });
- this.getElement().appendChild(generalOverlaysDiv);
- this.setControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_DIV, generalOverlaysDiv);
-
- var generalOverlaysTitle = Functions.createElement({
- type: "h5",
- content: "GENERAL OVERLAYS:"
- });
- generalOverlaysDiv.appendChild(generalOverlaysTitle);
-
- var generalOverlaysTableDiv = Functions.createElement({
- type: "table",
- name: "generalOverlaysTab",
- className: "table table-bordered",
- style: "width:100%"
- });
- generalOverlaysDiv.appendChild(generalOverlaysTableDiv);
- this.setControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE, generalOverlaysTableDiv);
-
- var customOverlaysDiv = Functions.createElement({
- type: "div",
- name: "customOverlays",
- className: "searchPanel"
- });
- this.getElement().appendChild(customOverlaysDiv);
- this.setControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_DIV, customOverlaysDiv);
-
- var customOverlaysTitle = Functions.createElement({
- type: "h5",
- name: "customOverlaysTitle",
- content: "USER-PROVIDED OVERLAYS:"
- });
- customOverlaysDiv.appendChild(customOverlaysTitle);
- this.setControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE, customOverlaysTitle);
-
- var customOverlaysTableDiv = Functions.createElement({
- type: "table",
- name: "customOverlaysTab",
- className: "table table-bordered",
- style: "width:100%"
- });
- customOverlaysDiv.appendChild(customOverlaysTableDiv);
- this.setControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE, customOverlaysTableDiv);
-
- var centerTag = Functions.createElement({
- type: "center"
- });
- customOverlaysDiv.appendChild(centerTag);
-
- var addOverlayButton = Functions.createElement({
- type: "button",
- name: "addOverlay",
- content: "Add overlay"
- });
- centerTag.appendChild(addOverlayButton);
- this.setControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON, addOverlayButton);
-};
-
-OverlayPanel.prototype.clear = function () {
- var table = this.getControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE);
- while (table.firstChild) {
- table.removeChild(table.firstChild);
- }
-
- table = $(this.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE)).DataTable();
- table.clear().draw();
-};
-
-/**
- *
- * @param {boolean} [edit=false]
- * @returns {HTMLElement}
- */
-OverlayPanel.prototype.createTableHeader = function (edit) {
- if (edit === undefined) {
- edit = false;
- }
- var result = document.createElement("thead");
-
- var row = document.createElement("tr");
-
- var nameTd = document.createElement("th");
- nameTd.innerHTML = "Name";
- row.appendChild(nameTd);
-
- var viewTd = document.createElement("th");
- viewTd.innerHTML = "View";
- row.appendChild(viewTd);
-
- var dataTd = document.createElement("th");
- dataTd.innerHTML = "Data";
- row.appendChild(dataTd);
-
- if (edit) {
- var editTd = document.createElement("th");
- editTd.innerHTML = "Edit";
- row.appendChild(editTd);
- }
-
- result.appendChild(row);
- return result;
-};
-
-/**
- *
- * @param {DataOverlay} overlay
- * @param {boolean} [checked=false]
- * @param {boolean} [disabled=false]
- * @returns {HTMLElement}
- */
-OverlayPanel.prototype.createOverlayRow = function (overlay, checked, disabled) {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var result = document.createElement("tr");
-
- if (checked && !overlay.getInputDataAvailable()) {
- result.className = "active";
- }
-
- var nameTd = Functions.createElement({type: "td", content: overlay.getName(), xss: true});
- result.appendChild(nameTd);
-
- var viewTd = document.createElement("td");
- if (overlay.getInputDataAvailable()) {
- var checkbox = Functions.createElement({
- type: "input",
- inputType: "checkbox",
- name: "overlayToggle",
- data: overlay.getId()
- });
- checkbox.checked = checked;
- $(checkbox).prop("disabled", disabled);
- if (disabled) {
- var warningDiv = Functions.createElement({
- type: "div",
- content: "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:orange'></i>",
- xss: false
- });
- warningDiv.title = "You did not consent to terms of the license of Google Maps Platform. Click the \"Edit\" button to do so.";
- viewTd.appendChild(warningDiv)
- } else {
- viewTd.appendChild(checkbox);
- }
- } else {
- var img = guiUtils.createIcon("icons/search.png");
- var link = Functions.createElement({type: "a", href: "#", name: "overlayLink", data: overlay.getId()});
- link.appendChild(img);
- viewTd.appendChild(link);
- }
- result.appendChild(viewTd);
-
- var dataTd = document.createElement("td");
- if (overlay.getInputDataAvailable()) {
- var button = Functions.createElement({
- type: "button",
- name: "download-overlay",
- data: overlay.getId(),
- content: "<span class='ui-icon ui-icon-arrowthickstop-1-s'></span>",
- xss: false
- });
- dataTd.appendChild(button);
- }
-
- result.appendChild(dataTd);
-
- if (overlay.getCreator() !== "" && overlay.getCreator() !== undefined) {
- var editTd = document.createElement("td");
- button = Functions.createElement({
- type: "button",
- name: "editButton",
- data: overlay.getId(),
- content: "<span class='ui-icon ui-icon-document'></span>",
- xss: false
- });
- editTd.appendChild(button);
- result.appendChild(editTd);
- }
- result.title = overlay.getDescription();
- return result;
-};
-
-/**
- *
- * @param {DataOverlay} overlay
- * @param {boolean} checked
- * @param {boolean} disabled
- * @returns {Array}
- */
-OverlayPanel.prototype.overlayToDataRow = function (overlay, checked, disabled) {
- var result = [];
- result[0] = overlay.getOrder();
- result[1] = overlay.getName();
-
- if (overlay.getInputDataAvailable()) {
- if (disabled) {
- result[2] = "<div title='You did not consent to terms of the license of Google Maps Platform. Click the \"Edit\" button to do so.'>" +
- "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:orange'></i></div>";
- } else {
- var checkedString = "";
- if (checked) {
- checkedString = " checked ";
- }
- result[2] = "<input type='checkbox' " + checkedString + " data='" + overlay.getId() + "' name='overlayToggle'/>";
- }
-
- result[3] = "<button data='" + overlay.getId() + "' name='download-overlay'><span class='ui-icon ui-icon-arrowthickstop-1-s'></span></button>";
- } else {
- result[2] = "<a href='#' data='" + overlay.getId() + "' name='overlayLink'><img src='" + GuiConnector.getImgPrefix() + "icons/search.png' style='float: left' hspace='5'/></a>";
- result[3] = "";
- }
-
- if (overlay.getCreator() !== "" && overlay.getCreator() !== undefined) {
- result[4] = "<button data='" + overlay.getId() + "' name='editButton'><span class='ui-icon ui-icon-document'></span></button>";
- } else {
- result[4] = "";
- }
- if (overlay.getDescription() !== "") {
- for (var i = 0; i < result.length; i++) {
-
- result[i] = "<div class=\"minerva-tooltip\">" + result[i] +
- "<span class=\"minerva-tooltip-text\">" + overlay.getDescription() + "</span>" +
- "</div>";
- }
- }
- return result;
-};
-
-/**
- *
- * @param {DataOverlay} overlay
- */
-OverlayPanel.prototype.openEditOverlayDialog = function (overlay) {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var content = document.createElement("fieldset");
- var nameInput = guiUtils.createInputText(overlay.getName());
- var row = guiUtils.createTableRow([guiUtils.createLabel("Name: "), nameInput]);
- content.appendChild(row);
-
- var descriptionInput = guiUtils.createTextArea(overlay.getDescription());
- row = guiUtils.createTableRow([guiUtils.createLabel("Description: "), descriptionInput]);
- content.appendChild(row);
-
- var consentCheckbox = document.createElement("input");
- consentCheckbox.type = "checkbox";
- consentCheckbox.checked = overlay.isGoogleLicenseConsent();
-
- row = guiUtils.createTableRow([guiUtils.createLabel("I am aware that if this map is displayed using Google Maps API, " +
- "it falls under their license <a href='https://cloud.google.com/maps-platform/terms/' target='_blank'>" +
- "https://cloud.google.com/maps-platform/terms/</a>, to which I agree. I warrant that this dataset contains no " +
- "Protected Health Information (as defined in and subject to HIPAA)."), consentCheckbox]);
- content.appendChild(row);
-
- var buttons = [{
- text: "SAVE",
- click: function () {
- var windowSelf = this;
- overlay.setName(nameInput.value);
- overlay.setDescription(descriptionInput.value);
- overlay.setGoogleLicenseConsent(consentCheckbox.checked);
-
- return self.getServerConnector().updateOverlay(overlay).then(function () {
- return self.refresh();
- }).then(function () {
- $(windowSelf).dialog("close");
- }).then(null, GuiConnector.alert);
- }
- }, {
- text: "REMOVE",
- click: function () {
- var windowSelf = this;
- return GuiConnector.showConfirmationDialog({
- message: "Do you want to delete overlay: " + overlay.getName() + "?"
- }).then(function (confirmation) {
- if (confirmation) {
- return self.removeOverlay(overlay).then(function () {
- $(windowSelf).dialog("close");
- }).then(null, GuiConnector.alert);
- }
- });
- }
- }, {
- text: "CANCEL",
- click: function () {
- $(this).dialog("close");
- }
- }];
- self.openDialog(content, {
- width: "600px",
- id: overlay.getId(),
- buttons: buttons,
- title: "Data overlay: " + overlay.getName(),
- className: "minerva-overlay-dialog"
- });
-};
-
-/**
- *
- * @param {boolean} [showDefault=false]
- * @returns {PromiseLike}
- */
-OverlayPanel.prototype.refresh = function (showDefault) {
- if (showDefault === undefined) {
- showDefault = false;
- }
- var self = this;
- var user = null;
-
- var overlayTypes = [];
- var selectedOverlay = [];
-
- return self.getServerConnector().getOverlayTypes().then(function (types) {
- overlayTypes = types;
- return self.getServerConnector().getLoggedUser();
- }).then(function (loggedUser) {
- user = loggedUser;
- return self.getMap().getVisibleDataOverlays();
- }).then(function (visibleDataOverlays) {
- for (var j = 0; j < visibleDataOverlays.length; j++) {
- selectedOverlay[visibleDataOverlays[j].getId()] = true;
- }
-
- return self.getServerConnector().getOverlays({
- publicOverlay: false,
- creator: user.getLogin()
- });
- }).then(function (customOverlays) {
-
- if (!showDefault) {
- var id = self.getMap().getBackgroundDataOverlay().getId();
- selectedOverlay[id] = true;
- }
-
- self.clear();
-
- var generalOverlays = [];
- var overlay;
-
- var overlays = self.getProject().getDataOverlays();
- for (var i = 0; i < overlays.length; i++) {
- overlay = overlays[i];
- if (overlay.getCreator() === undefined || overlay.getCreator() === "") {
- generalOverlays.push(overlay);
- if (showDefault && overlay.isDefaultOverlay()) {
- selectedOverlay[overlay.getId()] = true;
- }
- }
- }
-
- var table = self.getControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE);
- table.appendChild(self.createTableHeader());
-
- var body = document.createElement("tbody");
- table.appendChild(body);
- for (i = 0; i < generalOverlays.length; i++) {
- overlay = generalOverlays[i];
- body.appendChild(self.createOverlayRow(overlay, selectedOverlay[overlay.getId()], false));
- }
-
- var title = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE);
- var addButton = self.getControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON);
- var tableElement = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE);
- if (user.getLogin() === "anonymous") {
- title.innerHTML = 'YOU ARE NOT LOGGED IN. PLEASE, <a href="#">LOG IN</a> '
- + 'TO UPLOAD AND VIEW CUSTOM OVERLAYS<br/><center><button>LOGIN</button></center>';
- var openLoginDialog = function () {
- return self.getParent().getLoginDialog().open();
- };
- $(title).find("a")[0].onclick = openLoginDialog;
- $(title).find("button")[0].onclick = openLoginDialog;
- addButton.style.display = "none";
- $(tableElement).hide();
- } else {
- $(tableElement).show();
- title.innerHTML = self.getCustomOverlaysMessage();
- addButton.style.display = "block";
-
- table = $(tableElement).on('order.dt', function () {
- if ($(tableElement).dataTable().fnSettings().aaSorting[0][0] === 0) {
- table.rowReorder.enable();
- } else {
- table.rowReorder.disable();
- }
- }).DataTable();
- var data = [];
- self.setGoogleLicenseConsentRequired(false);
- for (i = 0; i < customOverlays.length; i++) {
- overlay = customOverlays[i];
- if (showDefault && overlay.isDefaultOverlay()) {
- selectedOverlay[overlay.getId()] = true;
- }
- var disabled = !overlay.isGoogleLicenseConsent() && self.getMap().getProject().getMapCanvasType() === "GOOGLE_MAPS_API";
- data.push(self.overlayToDataRow(overlay, selectedOverlay[overlay.getId()], disabled));
- if (disabled) {
- self.setGoogleLicenseConsentRequired(true);
- }
- }
- table.clear().rows.add(data).draw();
-
- }
-
- self.onresize();
-
- var promises = [];
- if (showDefault) {
- for (var key in selectedOverlay) {
- if (selectedOverlay.hasOwnProperty(key) && selectedOverlay[key]) {
- promises.push(self.getMap().openDataOverlay(key));
- }
- }
- }
- return Promise.all(promises);
- });
-};
-
-/**
- *
- * @param {string} customOverlaysMessage
- */
-OverlayPanel.prototype.setCustomOverlaysMessage = function (customOverlaysMessage) {
- this._customOverlaysMessage = customOverlaysMessage;
-};
-
-/**
- *
- * @returns {string}
- */
-OverlayPanel.prototype.getCustomOverlaysMessage = function () {
- return this._customOverlaysMessage;
-};
-
-
-/**
- *
- * @returns {PromiseLike}
- */
-OverlayPanel.prototype.openAddOverlayDialog = function () {
- var self = this;
- if (self._addOverlayDialog !== undefined) {
- self._addOverlayDialog.destroy();
- }
- self._addOverlayDialog = new AddOverlayDialog({
- project: self.getProject(),
- customMap: self.getMap(),
- element: document.createElement("div"),
- configuration: self.getConfiguration()
- });
- self._addOverlayDialog.addListener("onAddOverlay", function (e) {
- self.getProject().addDataOverlay(e.arg);
- return self.refresh();
- });
- return self._addOverlayDialog.init().then(function () {
- return self._addOverlayDialog.open();
- });
-};
-
-/**
- *
- * @returns {PromiseLike}
- */
-OverlayPanel.prototype.init = function () {
- var self = this;
- var backgroundOverlay = self.getServerConnector().getSessionData().getSelectedBackgroundOverlay();
- var showDefault = (backgroundOverlay === undefined || backgroundOverlay === "undefined");
- var table = $(this.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE)).DataTable({
- columns: [{
- title: 'No',
- className: "no_padding"
- }, {
- title: 'Name'
- }, {
- title: 'View',
- orderable: false,
- className: "no_padding"
- }, {
- title: 'Data',
- orderable: false,
- className: "no_padding"
- }, {
- title: 'Edit',
- orderable: false,
- className: "no_padding"
- }],
- paging: false,
- searching: false,
- info: false,
- rowReorder: true
- });
- table.on('row-reorder', function (e, diff) {
- var promises = [];
-
- for (var i = 0, ien = diff.length; i < ien; i++) {
- var rowData = table.row(diff[i].node).data();
- var overlayId = $(rowData[2]).attr("data");
- promises.push(self.updateOverlayOrder(overlayId, diff[i].newData));
- }
- promises.push(self.getMap().redrawSelectedDataOverlays());
- return Promise.all(promises);
- });
-
- return this.refresh(showDefault);
-};
-
-/**
- *
- * @param {number} overlayId
- * @param {number} order
- * @returns {PromiseLike}
- */
-OverlayPanel.prototype.updateOverlayOrder = function (overlayId, order) {
- var self = this;
- return self.getProject().getDataOverlayById(overlayId).then(function (overlay) {
- overlay.setOrder(order);
- return self.getServerConnector().updateOverlay(overlay);
- });
-};
-
-/**
- *
- * @param {DataOverlay} overlay
- * @returns {PromiseLike<any>}
- */
-OverlayPanel.prototype.removeOverlay = function (overlay) {
- var self = this;
- return self.getMap().hideDataOverlay(overlay.getId()).then(function () {
- return self.getServerConnector().removeOverlay({overlayId: overlay.getId()});
- }).then(function () {
- return self.refresh();
- })
-};
-
-/**
- *
- * @returns {PromiseLike}
- */
-OverlayPanel.prototype.destroy = function () {
- var self = this;
- Panel.prototype.destroy.call(this);
- var customOverlayDataTable = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE);
- if ($.fn.DataTable.isDataTable(customOverlayDataTable)) {
- $(customOverlayDataTable).DataTable().destroy();
- }
-
- if (self._addOverlayDialog !== undefined) {
- return self._addOverlayDialog.destroy();
- } else {
- return Promise.resolve();
- }
-};
-
-OverlayPanel.prototype.setGoogleLicenseConsentRequired = function (value) {
- var leftPanel = this.getParent();
- if (leftPanel !== undefined) {
- leftPanel.setGoogleLicenseConsentRequired(value);
- }
-};
-module.exports = OverlayPanel;
+"use strict";
+
+/* exported logger */
+
+var AddOverlayDialog = require('../AddOverlayDialog');
+var Panel = require('../Panel');
+var PanelControlElementType = require('../PanelControlElementType');
+
+var GuiConnector = require('../../GuiConnector');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+
+var Promise = require('bluebird');
+
+/**
+ *
+ * @param {Object} params
+ * @param {HTMLElement} params.element
+ * @param {CustomMap} params.customMap
+ * @param {Configuration} [params.configuration]
+ * @param {Project} [params.project]
+ * @param params.parent
+ *
+ * @constructor
+ * @extends Panel
+ */
+function OverlayPanel(params) {
+ params["panelName"] = "overlays";
+ params["scrollable"] = true;
+ params["helpTip"] = "<p>Overlays tab allows to display or generate custom coloring of elements and interactions in the map.</p>"
+ + "<p>General overlays are overlays accessible for every user viewing the content.</p>"
+ + "<p>Custom overlays are user-provided overlays, this menu becomes available upon login (see below).</p>";
+ if (params.project === undefined) {
+ params.project = params.customMap.getProject();
+ }
+ Panel.call(this, params);
+
+ //overflow is defined in minerva-overlay-panel, so remove the one that is already there
+ $(params.element).css("overflow", "");
+ $(params.element).addClass("minerva-overlay-panel");
+
+ var self = this;
+
+ self._createOverlayPanelGui();
+
+ var addButton = this.getControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON);
+
+ addButton.onclick = function () {
+ return self.openAddOverlayDialog();
+ };
+
+ var titleElement = this.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE);
+ self.setCustomOverlaysMessage(titleElement.innerHTML);
+
+ $(self.getElement()).on("click", "[name='overlayToggle']", function () {
+ var thisCheckbox = this;
+ var overlayId = $(thisCheckbox).attr("data");
+ var toggleOverlayPromise;
+ if (thisCheckbox.checked) {
+ toggleOverlayPromise = self.getMap().openDataOverlay(overlayId);
+ } else {
+ toggleOverlayPromise = self.getMap().hideDataOverlay(overlayId);
+ }
+ $(thisCheckbox).prop("disabled", true);
+ return toggleOverlayPromise.catch(GuiConnector.alert).finally(function () {
+ $(thisCheckbox).prop("disabled", false);
+ });
+ });
+ $(self.getElement()).on("click", "[name='overlayLink']", function () {
+ var overlayId = $(this).attr("data");
+ return self.getMap().openDataOverlay(overlayId);
+ });
+ self.getMap().addListener("onBackgroundOverlayChange", function (e) {
+ var overlayId = e.arg.toString();
+ var buttons = $("[name='overlayLink']", self.getElement());
+ for (var i = 0; i < buttons.length; i++) {
+ var button = buttons[i];
+ if ($(button).attr("data").toString() === overlayId) {
+ $(button.parentNode.parentNode).addClass('active').siblings().removeClass('active');
+ }
+ }
+ });
+ $(self.getElement()).on("click", "[name='download-overlay']", function () {
+ var overlayId = $(this).attr("data");
+ return self.getServerConnector().getOverlaySourceDownloadUrl({
+ overlayId: overlayId
+ }).then(function (url) {
+ return self.downloadFile(url);
+ }).then(null, GuiConnector.alert);
+ });
+ $(self.getElement()).on("click", "[name='editButton']", function () {
+ var overlayId = $(this).attr("data");
+ return self.getProject().getDataOverlayById(overlayId).then(function (overlay) {
+ return self.openEditOverlayDialog(overlay);
+ });
+ });
+}
+
+OverlayPanel.prototype = Object.create(Panel.prototype);
+OverlayPanel.prototype.constructor = OverlayPanel;
+
+/**
+ *
+ * @private
+ */
+OverlayPanel.prototype._createOverlayPanelGui = function () {
+ var generalOverlaysDiv = Functions.createElement({
+ type: "div",
+ name: "generalOverlays",
+ className: "searchPanel"
+ });
+ this.getElement().appendChild(generalOverlaysDiv);
+ this.setControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_DIV, generalOverlaysDiv);
+
+ var generalOverlaysTitle = Functions.createElement({
+ type: "h5",
+ content: "GENERAL OVERLAYS:"
+ });
+ generalOverlaysDiv.appendChild(generalOverlaysTitle);
+
+ var generalOverlaysTableDiv = Functions.createElement({
+ type: "table",
+ name: "generalOverlaysTab",
+ className: "table table-bordered",
+ style: "width:100%"
+ });
+ generalOverlaysDiv.appendChild(generalOverlaysTableDiv);
+ this.setControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE, generalOverlaysTableDiv);
+
+ var customOverlaysDiv = Functions.createElement({
+ type: "div",
+ name: "customOverlays",
+ className: "searchPanel"
+ });
+ this.getElement().appendChild(customOverlaysDiv);
+ this.setControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_DIV, customOverlaysDiv);
+
+ var customOverlaysTitle = Functions.createElement({
+ type: "h5",
+ name: "customOverlaysTitle",
+ content: "USER-PROVIDED OVERLAYS:"
+ });
+ customOverlaysDiv.appendChild(customOverlaysTitle);
+ this.setControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE, customOverlaysTitle);
+
+ var customOverlaysTableDiv = Functions.createElement({
+ type: "table",
+ name: "customOverlaysTab",
+ className: "table table-bordered",
+ style: "width:100%"
+ });
+ customOverlaysDiv.appendChild(customOverlaysTableDiv);
+ this.setControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE, customOverlaysTableDiv);
+
+ var centerTag = Functions.createElement({
+ type: "center"
+ });
+ customOverlaysDiv.appendChild(centerTag);
+
+ var addOverlayButton = Functions.createElement({
+ type: "button",
+ name: "addOverlay",
+ content: "Add overlay"
+ });
+ centerTag.appendChild(addOverlayButton);
+ this.setControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON, addOverlayButton);
+};
+
+OverlayPanel.prototype.clear = function () {
+ var table = this.getControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE);
+ while (table.firstChild) {
+ table.removeChild(table.firstChild);
+ }
+
+ table = $(this.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE)).DataTable();
+ table.clear().draw();
+};
+
+/**
+ *
+ * @param {boolean} [edit=false]
+ * @returns {HTMLElement}
+ */
+OverlayPanel.prototype.createTableHeader = function (edit) {
+ if (edit === undefined) {
+ edit = false;
+ }
+ var result = document.createElement("thead");
+
+ var row = document.createElement("tr");
+
+ var nameTd = document.createElement("th");
+ nameTd.innerHTML = "Name";
+ row.appendChild(nameTd);
+
+ var viewTd = document.createElement("th");
+ viewTd.innerHTML = "View";
+ row.appendChild(viewTd);
+
+ var dataTd = document.createElement("th");
+ dataTd.innerHTML = "Data";
+ row.appendChild(dataTd);
+
+ if (edit) {
+ var editTd = document.createElement("th");
+ editTd.innerHTML = "Edit";
+ row.appendChild(editTd);
+ }
+
+ result.appendChild(row);
+ return result;
+};
+
+/**
+ *
+ * @param {DataOverlay} overlay
+ * @param {boolean} [checked=false]
+ * @param {boolean} [disabled=false]
+ * @returns {HTMLElement}
+ */
+OverlayPanel.prototype.createOverlayRow = function (overlay, checked, disabled) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var result = document.createElement("tr");
+
+ if (checked && !overlay.getInputDataAvailable()) {
+ result.className = "active";
+ }
+
+ var nameTd = Functions.createElement({type: "td", content: overlay.getName(), xss: true});
+ result.appendChild(nameTd);
+
+ var viewTd = document.createElement("td");
+ if (overlay.getInputDataAvailable()) {
+ var checkbox = Functions.createElement({
+ type: "input",
+ inputType: "checkbox",
+ name: "overlayToggle",
+ data: overlay.getId()
+ });
+ checkbox.checked = checked;
+ $(checkbox).prop("disabled", disabled);
+ if (disabled) {
+ var warningDiv = Functions.createElement({
+ type: "div",
+ content: "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:orange'></i>",
+ xss: false
+ });
+ warningDiv.title = "You did not consent to terms of the license of Google Maps Platform. Click the \"Edit\" button to do so.";
+ viewTd.appendChild(warningDiv)
+ } else {
+ viewTd.appendChild(checkbox);
+ }
+ } else {
+ var img = guiUtils.createIcon("icons/search.png");
+ var link = Functions.createElement({type: "a", href: "#", name: "overlayLink", data: overlay.getId()});
+ link.appendChild(img);
+ viewTd.appendChild(link);
+ }
+ result.appendChild(viewTd);
+
+ var dataTd = document.createElement("td");
+ if (overlay.getInputDataAvailable()) {
+ var button = Functions.createElement({
+ type: "button",
+ name: "download-overlay",
+ data: overlay.getId(),
+ content: "<span class='ui-icon ui-icon-arrowthickstop-1-s'></span>",
+ xss: false
+ });
+ dataTd.appendChild(button);
+ }
+
+ result.appendChild(dataTd);
+
+ if (overlay.getCreator() !== "" && overlay.getCreator() !== undefined) {
+ var editTd = document.createElement("td");
+ button = Functions.createElement({
+ type: "button",
+ name: "editButton",
+ data: overlay.getId(),
+ content: "<span class='ui-icon ui-icon-document'></span>",
+ xss: false
+ });
+ editTd.appendChild(button);
+ result.appendChild(editTd);
+ }
+ result.title = overlay.getDescription();
+ return result;
+};
+
+/**
+ *
+ * @param {DataOverlay} overlay
+ * @param {boolean} checked
+ * @param {boolean} disabled
+ * @returns {Array}
+ */
+OverlayPanel.prototype.overlayToDataRow = function (overlay, checked, disabled) {
+ var result = [];
+ result[0] = overlay.getOrder();
+ result[1] = overlay.getName();
+
+ if (overlay.getInputDataAvailable()) {
+ if (disabled) {
+ result[2] = "<div title='You did not consent to terms of the license of Google Maps Platform. Click the \"Edit\" button to do so.'>" +
+ "<i class='fa fa-exclamation-triangle' style='font-size:18px; font-weight:400; padding-right:10px;color:orange'></i></div>";
+ } else {
+ var checkedString = "";
+ if (checked) {
+ checkedString = " checked ";
+ }
+ result[2] = "<input type='checkbox' " + checkedString + " data='" + overlay.getId() + "' name='overlayToggle'/>";
+ }
+
+ result[3] = "<button data='" + overlay.getId() + "' name='download-overlay'><span class='ui-icon ui-icon-arrowthickstop-1-s'></span></button>";
+ } else {
+ result[2] = "<a href='#' data='" + overlay.getId() + "' name='overlayLink'><img src='" + GuiConnector.getImgPrefix() + "icons/search.png' style='float: left' hspace='5'/></a>";
+ result[3] = "";
+ }
+
+ if (overlay.getCreator() !== "" && overlay.getCreator() !== undefined) {
+ result[4] = "<button data='" + overlay.getId() + "' name='editButton'><span class='ui-icon ui-icon-document'></span></button>";
+ } else {
+ result[4] = "";
+ }
+ if (overlay.getDescription() !== "") {
+ for (var i = 0; i < result.length; i++) {
+
+ result[i] = "<div class=\"minerva-tooltip\">" + result[i] +
+ "<span class=\"minerva-tooltip-text\">" + overlay.getDescription() + "</span>" +
+ "</div>";
+ }
+ }
+ return result;
+};
+
+/**
+ *
+ * @param {DataOverlay} overlay
+ */
+OverlayPanel.prototype.openEditOverlayDialog = function (overlay) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var content = document.createElement("fieldset");
+ var nameInput = guiUtils.createInputText(overlay.getName());
+ var row = guiUtils.createTableRow([guiUtils.createLabel("Name: "), nameInput]);
+ content.appendChild(row);
+
+ var descriptionInput = guiUtils.createTextArea(overlay.getDescription());
+ row = guiUtils.createTableRow([guiUtils.createLabel("Description: "), descriptionInput]);
+ content.appendChild(row);
+
+ var consentCheckbox = document.createElement("input");
+ consentCheckbox.type = "checkbox";
+ consentCheckbox.checked = overlay.isGoogleLicenseConsent();
+
+ row = guiUtils.createTableRow([guiUtils.createLabel("I am aware that if this map is displayed using Google Maps API, " +
+ "it falls under their license <a href='https://cloud.google.com/maps-platform/terms/' target='_blank'>" +
+ "https://cloud.google.com/maps-platform/terms/</a>, to which I agree. I warrant that this dataset contains no " +
+ "Protected Health Information (as defined in and subject to HIPAA)."), consentCheckbox]);
+ content.appendChild(row);
+
+ var buttons = [{
+ text: "SAVE",
+ click: function () {
+ var windowSelf = this;
+ overlay.setName(nameInput.value);
+ overlay.setDescription(descriptionInput.value);
+ overlay.setGoogleLicenseConsent(consentCheckbox.checked);
+
+ return self.getServerConnector().updateOverlay(overlay).then(function () {
+ return self.refresh();
+ }).then(function () {
+ $(windowSelf).dialog("close");
+ }).then(null, GuiConnector.alert);
+ }
+ }, {
+ text: "REMOVE",
+ click: function () {
+ var windowSelf = this;
+ return GuiConnector.showConfirmationDialog({
+ message: "Do you want to delete overlay: " + overlay.getName() + "?"
+ }).then(function (confirmation) {
+ if (confirmation) {
+ return self.removeOverlay(overlay).then(function () {
+ $(windowSelf).dialog("close");
+ }).then(null, GuiConnector.alert);
+ }
+ });
+ }
+ }, {
+ text: "CANCEL",
+ click: function () {
+ $(this).dialog("close");
+ }
+ }];
+ self.openDialog(content, {
+ width: "600px",
+ id: overlay.getId(),
+ buttons: buttons,
+ title: "Data overlay: " + overlay.getName(),
+ className: "minerva-overlay-dialog"
+ });
+};
+
+/**
+ *
+ * @param {boolean} [showDefault=false]
+ * @returns {PromiseLike}
+ */
+OverlayPanel.prototype.refresh = function (showDefault) {
+ if (showDefault === undefined) {
+ showDefault = false;
+ }
+ var self = this;
+ var user = null;
+
+ var overlayTypes = [];
+ var selectedOverlay = [];
+
+ return self.getServerConnector().getOverlayTypes().then(function (types) {
+ overlayTypes = types;
+ return self.getServerConnector().getLoggedUser();
+ }).then(function (loggedUser) {
+ user = loggedUser;
+ return self.getMap().getVisibleDataOverlays();
+ }).then(function (visibleDataOverlays) {
+ for (var j = 0; j < visibleDataOverlays.length; j++) {
+ selectedOverlay[visibleDataOverlays[j].getId()] = true;
+ }
+
+ return self.getServerConnector().getOverlays({
+ publicOverlay: false,
+ creator: user.getLogin()
+ });
+ }).then(function (customOverlays) {
+
+ if (!showDefault) {
+ var id = self.getMap().getBackgroundDataOverlay().getId();
+ selectedOverlay[id] = true;
+ }
+
+ self.clear();
+
+ var generalOverlays = [];
+ var overlay;
+
+ var overlays = self.getProject().getDataOverlays();
+ for (var i = 0; i < overlays.length; i++) {
+ overlay = overlays[i];
+ if (overlay.getCreator() === undefined || overlay.getCreator() === "") {
+ generalOverlays.push(overlay);
+ if (showDefault && overlay.isDefaultOverlay()) {
+ selectedOverlay[overlay.getId()] = true;
+ }
+ }
+ }
+
+ var table = self.getControlElement(PanelControlElementType.OVERLAY_GENERAL_OVERLAY_TABLE);
+ table.appendChild(self.createTableHeader());
+
+ var body = document.createElement("tbody");
+ table.appendChild(body);
+ for (i = 0; i < generalOverlays.length; i++) {
+ overlay = generalOverlays[i];
+ body.appendChild(self.createOverlayRow(overlay, selectedOverlay[overlay.getId()], false));
+ }
+
+ var title = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TITLE);
+ var addButton = self.getControlElement(PanelControlElementType.OVERLAY_ADD_OVERLAY_BUTTON);
+ var tableElement = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE);
+ if (user.getLogin() === "anonymous") {
+ title.innerHTML = 'YOU ARE NOT LOGGED IN. PLEASE, <a href="#">LOG IN</a> '
+ + 'TO UPLOAD AND VIEW CUSTOM OVERLAYS<br/><center><button>LOGIN</button></center>';
+ var openLoginDialog = function () {
+ return self.getParent().getLoginDialog().open();
+ };
+ $(title).find("a")[0].onclick = openLoginDialog;
+ $(title).find("button")[0].onclick = openLoginDialog;
+ addButton.style.display = "none";
+ $(tableElement).hide();
+ } else {
+ $(tableElement).show();
+ title.innerHTML = self.getCustomOverlaysMessage();
+ addButton.style.display = "block";
+
+ table = $(tableElement).on('order.dt', function () {
+ if ($(tableElement).dataTable().fnSettings().aaSorting[0][0] === 0) {
+ table.rowReorder.enable();
+ } else {
+ table.rowReorder.disable();
+ }
+ }).DataTable();
+ var data = [];
+ self.setGoogleLicenseConsentRequired(false);
+ for (i = 0; i < customOverlays.length; i++) {
+ overlay = customOverlays[i];
+ if (showDefault && overlay.isDefaultOverlay()) {
+ selectedOverlay[overlay.getId()] = true;
+ }
+ var disabled = !overlay.isGoogleLicenseConsent() && self.getMap().getProject().getMapCanvasType() === "GOOGLE_MAPS_API";
+ data.push(self.overlayToDataRow(overlay, selectedOverlay[overlay.getId()], disabled));
+ if (disabled) {
+ self.setGoogleLicenseConsentRequired(true);
+ }
+ }
+ table.clear().rows.add(data).draw();
+
+ }
+
+ self.onresize();
+
+ var promises = [];
+ if (showDefault) {
+ for (var key in selectedOverlay) {
+ if (selectedOverlay.hasOwnProperty(key) && selectedOverlay[key]) {
+ promises.push(self.getMap().openDataOverlay(key));
+ }
+ }
+ }
+ return Promise.all(promises);
+ });
+};
+
+/**
+ *
+ * @param {string} customOverlaysMessage
+ */
+OverlayPanel.prototype.setCustomOverlaysMessage = function (customOverlaysMessage) {
+ this._customOverlaysMessage = customOverlaysMessage;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+OverlayPanel.prototype.getCustomOverlaysMessage = function () {
+ return this._customOverlaysMessage;
+};
+
+
+/**
+ *
+ * @returns {PromiseLike}
+ */
+OverlayPanel.prototype.openAddOverlayDialog = function () {
+ var self = this;
+ if (self._addOverlayDialog !== undefined) {
+ self._addOverlayDialog.destroy();
+ }
+ self._addOverlayDialog = new AddOverlayDialog({
+ project: self.getProject(),
+ customMap: self.getMap(),
+ element: document.createElement("div"),
+ configuration: self.getConfiguration()
+ });
+ self._addOverlayDialog.addListener("onAddOverlay", function (e) {
+ self.getProject().addDataOverlay(e.arg);
+ return self.refresh();
+ });
+ return self._addOverlayDialog.init().then(function () {
+ return self._addOverlayDialog.open();
+ });
+};
+
+/**
+ *
+ * @returns {PromiseLike}
+ */
+OverlayPanel.prototype.init = function () {
+ var self = this;
+ var backgroundOverlay = self.getServerConnector().getSessionData().getSelectedBackgroundOverlay();
+ var showDefault = (backgroundOverlay === undefined || backgroundOverlay === "undefined");
+ var table = $(this.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE)).DataTable({
+ columns: [{
+ title: 'No',
+ className: "no_padding"
+ }, {
+ title: 'Name'
+ }, {
+ title: 'View',
+ orderable: false,
+ className: "no_padding"
+ }, {
+ title: 'Data',
+ orderable: false,
+ className: "no_padding"
+ }, {
+ title: 'Edit',
+ orderable: false,
+ className: "no_padding"
+ }],
+ paging: false,
+ searching: false,
+ info: false,
+ rowReorder: true
+ });
+ table.on('row-reorder', function (e, diff) {
+ var promises = [];
+
+ for (var i = 0, ien = diff.length; i < ien; i++) {
+ var rowData = table.row(diff[i].node).data();
+ var overlayId = $(rowData[2]).attr("data");
+ promises.push(self.updateOverlayOrder(overlayId, diff[i].newData));
+ }
+ promises.push(self.getMap().redrawSelectedDataOverlays());
+ return Promise.all(promises);
+ });
+
+ return this.refresh(showDefault);
+};
+
+/**
+ *
+ * @param {number} overlayId
+ * @param {number} order
+ * @returns {PromiseLike}
+ */
+OverlayPanel.prototype.updateOverlayOrder = function (overlayId, order) {
+ var self = this;
+ return self.getProject().getDataOverlayById(overlayId).then(function (overlay) {
+ overlay.setOrder(order);
+ return self.getServerConnector().updateOverlay(overlay);
+ });
+};
+
+/**
+ *
+ * @param {DataOverlay} overlay
+ * @returns {PromiseLike<any>}
+ */
+OverlayPanel.prototype.removeOverlay = function (overlay) {
+ var self = this;
+ return self.getMap().hideDataOverlay(overlay.getId()).then(function () {
+ return self.getServerConnector().removeOverlay({overlayId: overlay.getId()});
+ }).then(function () {
+ return self.refresh();
+ })
+};
+
+/**
+ *
+ * @returns {PromiseLike}
+ */
+OverlayPanel.prototype.destroy = function () {
+ var self = this;
+ Panel.prototype.destroy.call(this);
+ var customOverlayDataTable = self.getControlElement(PanelControlElementType.OVERLAY_CUSTOM_OVERLAY_TABLE);
+ if ($.fn.DataTable.isDataTable(customOverlayDataTable)) {
+ $(customOverlayDataTable).DataTable().destroy();
+ }
+
+ if (self._addOverlayDialog !== undefined) {
+ return self._addOverlayDialog.destroy();
+ } else {
+ return Promise.resolve();
+ }
+};
+
+OverlayPanel.prototype.setGoogleLicenseConsentRequired = function (value) {
+ var leftPanel = this.getParent();
+ if (leftPanel !== undefined) {
+ leftPanel.setGoogleLicenseConsentRequired(value);
+ }
+};
+module.exports = OverlayPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
index c981bc420c36799ea77e938bce6b771e01d811ee..004f351df91b8e5d6027366eeff0c325b25bd428 100644
--- a/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js
@@ -1,382 +1,382 @@
-"use strict";
-
-/* exported logger */
-
-var ConfigurationType = require('../../ConfigurationType');
-var GuiConnector = require('../../GuiConnector');
-var Panel = require('../Panel');
-var PanelControlElementType = require('../PanelControlElementType');
-var PublicationListDialog = require('./PublicationListDialog');
-
-var logger = require('../../logger');
-var Functions = require('../../Functions');
-
-function ProjectInfoPanel(params) {
- params.panelName = "info";
- params.scrollable = true;
- Panel.call(this, params);
- var self = this;
- self._createInfoPanelGui();
- self._createInfoPanelLogic();
-
- self._createUserDataTab();
- var logoutButton = self.getControlElement(PanelControlElementType.USER_TAB_LOGOUT_BUTTON);
-
- logoutButton.onclick = function () {
- return ServerConnector.logout().then(function () {
- window.location.reload(false);
- }).then(null, GuiConnector.alert);
- };
-
-}
-
-ProjectInfoPanel.prototype = Object.create(Panel.prototype);
-ProjectInfoPanel.prototype.constructor = ProjectInfoPanel;
-
-ProjectInfoPanel.prototype._createInfoPanelGui = function () {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var projectId = self.getMap().getProject().getProjectId();
-
- var infoDiv = Functions.createElement({
- type: "div",
- name: "infoDiv",
- className: "searchPanel"
- });
- this.getElement().appendChild(infoDiv);
- this.setControlElement(PanelControlElementType.INFO_DIV, infoDiv);
-
- var infoTitle = Functions.createElement({
- type: "h4",
- content: "PROJECT INFO:"
- });
- infoDiv.appendChild(infoTitle);
-
- var dataTab = Functions.createElement({
- type: "div",
- style: "width:100%;display: table;border-spacing: 10px;"
- });
- infoDiv.appendChild(dataTab);
-
- var projectNameLabel = Functions.createElement({
- type: "div",
- content: "Name:"
- });
- var projectNameText = Functions.createElement({
- type: "div",
- style: "width:100%",
- name: "projectNameText"
- });
- this.setControlElement(PanelControlElementType.INFO_PROJECT_NAME_TEXT, projectNameText);
- dataTab.appendChild(guiUtils.createTableRow([projectNameLabel, projectNameText]));
-
- var projectVersionLabel = Functions.createElement({
- type: "div",
- content: "Version:"
- });
- var projectVersionText = Functions.createElement({
- type: "div",
- style: "width:100%",
- name: "projectVersionText"
- });
- this.setControlElement(PanelControlElementType.INFO_PROJECT_VERSION_TEXT, projectVersionText);
- dataTab.appendChild(guiUtils.createTableRow([projectVersionLabel, projectVersionText]));
-
- infoTitle = Functions.createElement({
- type: "h4",
- content: "Data:"
- });
- infoDiv.appendChild(infoTitle);
-
- var dialogDiv = Functions.createElement({
- type: "div"
- });
-
- this.publicationListDialog = new PublicationListDialog({
- customMap: self.getMap(),
- element: dialogDiv
- });
-
- dataTab = Functions.createElement({
- type: "ul"
- });
- infoDiv.appendChild(dataTab);
-
- var projectPublicationsText = Functions.createElement({
- type: "span",
- name: "projectPublicationsText",
- style: "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer"
- });
- this.setControlElement(PanelControlElementType.INFO_PROJECT_PUBLICATIONS_TEXT, projectPublicationsText);
-
- var projectPublicationsButton = Functions.createElement({
- type: "a",
- name: "projectPublicationsButton"
- });
- projectPublicationsButton.appendChild(Functions.createElement({
- type: "span",
- content: "<i class='fa fa-list'> ",
- xss: false
- }));
-
- projectPublicationsButton.appendChild(projectPublicationsText);
- projectPublicationsButton.appendChild(Functions.createElement({
- type: "span",
- style: "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
- content: " publication(s)"
- }));
- this.setControlElement(PanelControlElementType.INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON, projectPublicationsButton);
-
- var liElement = Functions.createElement({
- type: "li",
- style: "line-height: 30px;"
- });
- liElement.appendChild(projectPublicationsButton);
- dataTab.appendChild(liElement);
-
- var projectOriginalFileButton = Functions.createElement({
- type: "a",
- name: "projectOriginalFileButton",
- href: "#",
- content: "<i class='fa fa-files-o'> source file",
- xss: false
- });
- this.setControlElement(PanelControlElementType.INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON, projectOriginalFileButton);
- liElement = Functions.createElement({
- type: "li",
- style: "line-height: 30px"
- });
- liElement.appendChild(projectOriginalFileButton);
- dataTab.appendChild(liElement);
-
- var exportButton = Functions.createElement({
- type: "a",
- href: ServerConnector.getServerBaseUrl() + "/export.xhtml?id=" + projectId,
- content: '<i class="fa fa-mail-forward"> EXPORT',
- xss: false
- });
- liElement = Functions.createElement({
- type: "li",
- style: "line-height: 30px"
- });
- liElement.appendChild(exportButton);
- dataTab.appendChild(liElement);
-
- var manualButton = Functions.createElement({
- type: "a",
- name: "manualLink",
- content: '<i class="fa fa-file"> MANUAL',
- xss: false
- });
- manualButton.href = "#";
- manualButton.onclick = function () {
- return ServerConnector.getConfigurationParam(ConfigurationType.USER_MANUAL_FILE).then(function (manualFileUrl) {
- var win = window.open(manualFileUrl, '_user_manual_');
- win.focus();
- });
- };
- liElement = Functions.createElement({
- type: "li",
- style: "line-height: 30px"
- });
- liElement.appendChild(manualButton);
- dataTab.appendChild(liElement);
-
-};
-
-ProjectInfoPanel.prototype._createInfoPanelLogic = function () {
- var self = this;
-
- var downloadSourceButton = self.getControlElement(PanelControlElementType.INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON);
- var showPublicationsButton = self.getControlElement(PanelControlElementType.INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON);
-
- downloadSourceButton.onclick = function () {
- return self.downloadSourceFile();
- };
- showPublicationsButton.onclick = function () {
- return self.showPublicationListDialog();
- };
-};
-
-ProjectInfoPanel.prototype.downloadSourceFile = function () {
- var self = this;
- return ServerConnector.getProjectSourceDownloadUrl().then(function (url) {
- return self.downloadFile(url);
- }).then(null, GuiConnector.alert);
-};
-
-ProjectInfoPanel.prototype.showPublicationListDialog = function () {
- return this.publicationListDialog.show();
-};
-
-ProjectInfoPanel.prototype.refresh = function () {
- var self = this;
-
- var projectNameText = self.getControlElement(PanelControlElementType.INFO_PROJECT_NAME_TEXT);
- var projectVersionText = self.getControlElement(PanelControlElementType.INFO_PROJECT_VERSION_TEXT);
- var projectPublicationsText = self.getControlElement(PanelControlElementType.INFO_PROJECT_PUBLICATIONS_TEXT);
-
- var project = self.getProject();
- projectNameText.innerHTML = project.getName();
- projectVersionText.innerHTML = project.getVersion();
-
- return ServerConnector.getProjectStatistics().then(function (statistics) {
- projectPublicationsText.innerHTML = statistics.getPublicationCount();
- return ServerConnector.getLoggedUser();
- }).then(function (user) {
- self.showUserProfilePage(user);
- });
-};
-
-ProjectInfoPanel.prototype._createUserDataTab = function () {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var userDataDiv = Functions.createElement({
- type: "div",
- name: "userDataTab",
- className: "searchPanel",
- style: "display:none"
- });
- this.getElement().appendChild(userDataDiv);
- this.setControlElement(PanelControlElementType.USER_TAB_USER_DIV, userDataDiv);
-
- var userDataTitle = Functions.createElement({
- type: "h3",
- content: '<img src="./resources/images/profile.png" border="0" align="left"/><br/>User data<br/>',
- xss: false
- });
- userDataDiv.appendChild(userDataTitle);
-
- var userDataFormTab = Functions.createElement({
- type: "div",
- style: "width:100%;display: table;border-spacing: 10px;"
- });
- userDataDiv.appendChild(userDataFormTab);
-
- var loginLabel = Functions.createElement({
- type: "span",
- content: "LOGIN:",
- style: "color:#999999"
- });
- var loginText = Functions.createElement({
- type: "span",
- name: "loginValue"
- });
- this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_TEXT, loginText);
- userDataDiv.appendChild(guiUtils.createTableRow([loginLabel, loginText]));
-
- var nameLabel = Functions.createElement({
- type: "span",
- content: "NAME:",
- style: "color:#999999"
- });
- var nameText = Functions.createElement({
- type: "span",
- name: "nameValue"
- });
- this.setControlElement(PanelControlElementType.USER_TAB_NAME_TEXT, nameText);
- userDataDiv.appendChild(guiUtils.createTableRow([nameLabel, nameText]));
-
- var surnameLabel = Functions.createElement({
- type: "span",
- content: "SURNAME:",
- style: "color:#999999"
- });
- var surnameText = Functions.createElement({
- type: "span",
- name: "surnameValue"
- });
- this.setControlElement(PanelControlElementType.USER_TAB_SURNAME_TEXT, surnameText);
- userDataDiv.appendChild(guiUtils.createTableRow([surnameLabel, surnameText]));
-
- var emailLabel = Functions.createElement({
- type: "span",
- content: "EMAIL:",
- style: "color:#999999"
- });
- var emailText = Functions.createElement({
- type: "span",
- name: "emailValue"
- });
- self.setControlElement(PanelControlElementType.USER_TAB_EMAIL_TEXT, emailText);
- userDataDiv.appendChild(guiUtils.createTableRow([emailLabel, emailText]));
-
- var centerTag = Functions.createElement({
- type: "center"
- });
- userDataDiv.appendChild(centerTag);
-
- var logoutButton = Functions.createElement({
- type: "button",
- name: "logoutButton",
- content: "LOGOUT"
- });
- centerTag.appendChild(logoutButton);
- self.setControlElement(PanelControlElementType.USER_TAB_LOGOUT_BUTTON, logoutButton);
- self.setControlElement(PanelControlElementType.USER_TAB_USER_DIV, userDataDiv);
-
- var loginTabDiv = Functions.createElement({
- type: "div",
- name: "userLoginTab",
- className: "searchPanel",
- style: "display:none",
- content: '<h3><img src="./resources/images/profile.png" border="0" align="left"/>'
- + '<br/>User data</h3><br/>YOU ARE NOT LOGGED IN.<br/>' + '<center><button>LOGIN</button></center>' +
- '<br/><a href="#" name="requestAccount">Request an account</a>',
- xss: false
-
- });
- $(loginTabDiv).find("button")[0].onclick = function () {
- return self.getParent().getLoginDialog().open();
- };
-
- self.getElement().appendChild(loginTabDiv);
- self.setControlElement(PanelControlElementType.USER_TAB_LOGIN_DIV, loginTabDiv);
-
-};
-
-
-ProjectInfoPanel.prototype.showUserProfilePage = function (user) {
-
- var self = this;
- var userDataTabDiv = self.getControlElement(PanelControlElementType.USER_TAB_USER_DIV);
- var userLoginTabDiv = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_DIV);
- if (user.getLogin() !== "anonymous") {
- var loginText = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_TEXT);
- var nameText = self.getControlElement(PanelControlElementType.USER_TAB_NAME_TEXT);
- var surnameText = self.getControlElement(PanelControlElementType.USER_TAB_SURNAME_TEXT);
- var emailText = self.getControlElement(PanelControlElementType.USER_TAB_EMAIL_TEXT);
-
- userLoginTabDiv.style.display = "none";
- userDataTabDiv.style.display = "block";
-
- loginText.innerHTML = user.getLogin();
- nameText.innerHTML = user.getName();
- surnameText.innerHTML = user.getSurname();
- emailText.innerHTML = user.getEmail();
- } else {
-
- userLoginTabDiv.style.display = "block";
- userDataTabDiv.style.display = "none";
- }
-};
-
-ProjectInfoPanel.prototype.init = function () {
- var self = this;
- var email, content;
- return ServerConnector.getConfigurationParam(ConfigurationType.REQUEST_ACCOUNT_EMAIL).then(function (result) {
- email = result;
- return ServerConnector.getConfigurationParam(ConfigurationType.REQUEST_ACCOUNT_DEFAULT_CONTENT);
- }).then(function (result) {
- content = encodeURIComponent(result);
- var url = 'mailto:' + email + '?subject=MINERVA account request&body=' + content;
- var link = $("[name=requestAccount]", self.getElement());
- link.attr("href", url);
- return self.refresh();
- });
-};
-
-ProjectInfoPanel.prototype.destroy = function () {
- return this.publicationListDialog.destroy();
-};
-module.exports = ProjectInfoPanel;
+"use strict";
+
+/* exported logger */
+
+var ConfigurationType = require('../../ConfigurationType');
+var GuiConnector = require('../../GuiConnector');
+var Panel = require('../Panel');
+var PanelControlElementType = require('../PanelControlElementType');
+var PublicationListDialog = require('./PublicationListDialog');
+
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+
+function ProjectInfoPanel(params) {
+ params.panelName = "info";
+ params.scrollable = true;
+ Panel.call(this, params);
+ var self = this;
+ self._createInfoPanelGui();
+ self._createInfoPanelLogic();
+
+ self._createUserDataTab();
+ var logoutButton = self.getControlElement(PanelControlElementType.USER_TAB_LOGOUT_BUTTON);
+
+ logoutButton.onclick = function () {
+ return ServerConnector.logout().then(function () {
+ window.location.reload(false);
+ }).then(null, GuiConnector.alert);
+ };
+
+}
+
+ProjectInfoPanel.prototype = Object.create(Panel.prototype);
+ProjectInfoPanel.prototype.constructor = ProjectInfoPanel;
+
+ProjectInfoPanel.prototype._createInfoPanelGui = function () {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var projectId = self.getMap().getProject().getProjectId();
+
+ var infoDiv = Functions.createElement({
+ type: "div",
+ name: "infoDiv",
+ className: "searchPanel"
+ });
+ this.getElement().appendChild(infoDiv);
+ this.setControlElement(PanelControlElementType.INFO_DIV, infoDiv);
+
+ var infoTitle = Functions.createElement({
+ type: "h4",
+ content: "PROJECT INFO:"
+ });
+ infoDiv.appendChild(infoTitle);
+
+ var dataTab = Functions.createElement({
+ type: "div",
+ style: "width:100%;display: table;border-spacing: 10px;"
+ });
+ infoDiv.appendChild(dataTab);
+
+ var projectNameLabel = Functions.createElement({
+ type: "div",
+ content: "Name:"
+ });
+ var projectNameText = Functions.createElement({
+ type: "div",
+ style: "width:100%",
+ name: "projectNameText"
+ });
+ this.setControlElement(PanelControlElementType.INFO_PROJECT_NAME_TEXT, projectNameText);
+ dataTab.appendChild(guiUtils.createTableRow([projectNameLabel, projectNameText]));
+
+ var projectVersionLabel = Functions.createElement({
+ type: "div",
+ content: "Version:"
+ });
+ var projectVersionText = Functions.createElement({
+ type: "div",
+ style: "width:100%",
+ name: "projectVersionText"
+ });
+ this.setControlElement(PanelControlElementType.INFO_PROJECT_VERSION_TEXT, projectVersionText);
+ dataTab.appendChild(guiUtils.createTableRow([projectVersionLabel, projectVersionText]));
+
+ infoTitle = Functions.createElement({
+ type: "h4",
+ content: "Data:"
+ });
+ infoDiv.appendChild(infoTitle);
+
+ var dialogDiv = Functions.createElement({
+ type: "div"
+ });
+
+ this.publicationListDialog = new PublicationListDialog({
+ customMap: self.getMap(),
+ element: dialogDiv
+ });
+
+ dataTab = Functions.createElement({
+ type: "ul"
+ });
+ infoDiv.appendChild(dataTab);
+
+ var projectPublicationsText = Functions.createElement({
+ type: "span",
+ name: "projectPublicationsText",
+ style: "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer"
+ });
+ this.setControlElement(PanelControlElementType.INFO_PROJECT_PUBLICATIONS_TEXT, projectPublicationsText);
+
+ var projectPublicationsButton = Functions.createElement({
+ type: "a",
+ name: "projectPublicationsButton"
+ });
+ projectPublicationsButton.appendChild(Functions.createElement({
+ type: "span",
+ content: "<i class='fa fa-list'> ",
+ xss: false
+ }));
+
+ projectPublicationsButton.appendChild(projectPublicationsText);
+ projectPublicationsButton.appendChild(Functions.createElement({
+ type: "span",
+ style: "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
+ content: " publication(s)"
+ }));
+ this.setControlElement(PanelControlElementType.INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON, projectPublicationsButton);
+
+ var liElement = Functions.createElement({
+ type: "li",
+ style: "line-height: 30px;"
+ });
+ liElement.appendChild(projectPublicationsButton);
+ dataTab.appendChild(liElement);
+
+ var projectOriginalFileButton = Functions.createElement({
+ type: "a",
+ name: "projectOriginalFileButton",
+ href: "#",
+ content: "<i class='fa fa-files-o'> source file",
+ xss: false
+ });
+ this.setControlElement(PanelControlElementType.INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON, projectOriginalFileButton);
+ liElement = Functions.createElement({
+ type: "li",
+ style: "line-height: 30px"
+ });
+ liElement.appendChild(projectOriginalFileButton);
+ dataTab.appendChild(liElement);
+
+ var exportButton = Functions.createElement({
+ type: "a",
+ href: ServerConnector.getServerBaseUrl() + "/export.xhtml?id=" + projectId,
+ content: '<i class="fa fa-mail-forward"> EXPORT',
+ xss: false
+ });
+ liElement = Functions.createElement({
+ type: "li",
+ style: "line-height: 30px"
+ });
+ liElement.appendChild(exportButton);
+ dataTab.appendChild(liElement);
+
+ var manualButton = Functions.createElement({
+ type: "a",
+ name: "manualLink",
+ content: '<i class="fa fa-file"> MANUAL',
+ xss: false
+ });
+ manualButton.href = "#";
+ manualButton.onclick = function () {
+ return ServerConnector.getConfigurationParam(ConfigurationType.USER_MANUAL_FILE).then(function (manualFileUrl) {
+ var win = window.open(manualFileUrl, '_user_manual_');
+ win.focus();
+ });
+ };
+ liElement = Functions.createElement({
+ type: "li",
+ style: "line-height: 30px"
+ });
+ liElement.appendChild(manualButton);
+ dataTab.appendChild(liElement);
+
+};
+
+ProjectInfoPanel.prototype._createInfoPanelLogic = function () {
+ var self = this;
+
+ var downloadSourceButton = self.getControlElement(PanelControlElementType.INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON);
+ var showPublicationsButton = self.getControlElement(PanelControlElementType.INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON);
+
+ downloadSourceButton.onclick = function () {
+ return self.downloadSourceFile();
+ };
+ showPublicationsButton.onclick = function () {
+ return self.showPublicationListDialog();
+ };
+};
+
+ProjectInfoPanel.prototype.downloadSourceFile = function () {
+ var self = this;
+ return ServerConnector.getProjectSourceDownloadUrl().then(function (url) {
+ return self.downloadFile(url);
+ }).then(null, GuiConnector.alert);
+};
+
+ProjectInfoPanel.prototype.showPublicationListDialog = function () {
+ return this.publicationListDialog.show();
+};
+
+ProjectInfoPanel.prototype.refresh = function () {
+ var self = this;
+
+ var projectNameText = self.getControlElement(PanelControlElementType.INFO_PROJECT_NAME_TEXT);
+ var projectVersionText = self.getControlElement(PanelControlElementType.INFO_PROJECT_VERSION_TEXT);
+ var projectPublicationsText = self.getControlElement(PanelControlElementType.INFO_PROJECT_PUBLICATIONS_TEXT);
+
+ var project = self.getProject();
+ projectNameText.innerHTML = project.getName();
+ projectVersionText.innerHTML = project.getVersion();
+
+ return ServerConnector.getProjectStatistics().then(function (statistics) {
+ projectPublicationsText.innerHTML = statistics.getPublicationCount();
+ return ServerConnector.getLoggedUser();
+ }).then(function (user) {
+ self.showUserProfilePage(user);
+ });
+};
+
+ProjectInfoPanel.prototype._createUserDataTab = function () {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var userDataDiv = Functions.createElement({
+ type: "div",
+ name: "userDataTab",
+ className: "searchPanel",
+ style: "display:none"
+ });
+ this.getElement().appendChild(userDataDiv);
+ this.setControlElement(PanelControlElementType.USER_TAB_USER_DIV, userDataDiv);
+
+ var userDataTitle = Functions.createElement({
+ type: "h3",
+ content: '<img src="./resources/images/profile.png" border="0" align="left"/><br/>User data<br/>',
+ xss: false
+ });
+ userDataDiv.appendChild(userDataTitle);
+
+ var userDataFormTab = Functions.createElement({
+ type: "div",
+ style: "width:100%;display: table;border-spacing: 10px;"
+ });
+ userDataDiv.appendChild(userDataFormTab);
+
+ var loginLabel = Functions.createElement({
+ type: "span",
+ content: "LOGIN:",
+ style: "color:#999999"
+ });
+ var loginText = Functions.createElement({
+ type: "span",
+ name: "loginValue"
+ });
+ this.setControlElement(PanelControlElementType.USER_TAB_LOGIN_TEXT, loginText);
+ userDataDiv.appendChild(guiUtils.createTableRow([loginLabel, loginText]));
+
+ var nameLabel = Functions.createElement({
+ type: "span",
+ content: "NAME:",
+ style: "color:#999999"
+ });
+ var nameText = Functions.createElement({
+ type: "span",
+ name: "nameValue"
+ });
+ this.setControlElement(PanelControlElementType.USER_TAB_NAME_TEXT, nameText);
+ userDataDiv.appendChild(guiUtils.createTableRow([nameLabel, nameText]));
+
+ var surnameLabel = Functions.createElement({
+ type: "span",
+ content: "SURNAME:",
+ style: "color:#999999"
+ });
+ var surnameText = Functions.createElement({
+ type: "span",
+ name: "surnameValue"
+ });
+ this.setControlElement(PanelControlElementType.USER_TAB_SURNAME_TEXT, surnameText);
+ userDataDiv.appendChild(guiUtils.createTableRow([surnameLabel, surnameText]));
+
+ var emailLabel = Functions.createElement({
+ type: "span",
+ content: "EMAIL:",
+ style: "color:#999999"
+ });
+ var emailText = Functions.createElement({
+ type: "span",
+ name: "emailValue"
+ });
+ self.setControlElement(PanelControlElementType.USER_TAB_EMAIL_TEXT, emailText);
+ userDataDiv.appendChild(guiUtils.createTableRow([emailLabel, emailText]));
+
+ var centerTag = Functions.createElement({
+ type: "center"
+ });
+ userDataDiv.appendChild(centerTag);
+
+ var logoutButton = Functions.createElement({
+ type: "button",
+ name: "logoutButton",
+ content: "LOGOUT"
+ });
+ centerTag.appendChild(logoutButton);
+ self.setControlElement(PanelControlElementType.USER_TAB_LOGOUT_BUTTON, logoutButton);
+ self.setControlElement(PanelControlElementType.USER_TAB_USER_DIV, userDataDiv);
+
+ var loginTabDiv = Functions.createElement({
+ type: "div",
+ name: "userLoginTab",
+ className: "searchPanel",
+ style: "display:none",
+ content: '<h3><img src="./resources/images/profile.png" border="0" align="left"/>'
+ + '<br/>User data</h3><br/>YOU ARE NOT LOGGED IN.<br/>' + '<center><button>LOGIN</button></center>' +
+ '<br/><a href="#" name="requestAccount">Request an account</a>',
+ xss: false
+
+ });
+ $(loginTabDiv).find("button")[0].onclick = function () {
+ return self.getParent().getLoginDialog().open();
+ };
+
+ self.getElement().appendChild(loginTabDiv);
+ self.setControlElement(PanelControlElementType.USER_TAB_LOGIN_DIV, loginTabDiv);
+
+};
+
+
+ProjectInfoPanel.prototype.showUserProfilePage = function (user) {
+
+ var self = this;
+ var userDataTabDiv = self.getControlElement(PanelControlElementType.USER_TAB_USER_DIV);
+ var userLoginTabDiv = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_DIV);
+ if (user.getLogin() !== "anonymous") {
+ var loginText = self.getControlElement(PanelControlElementType.USER_TAB_LOGIN_TEXT);
+ var nameText = self.getControlElement(PanelControlElementType.USER_TAB_NAME_TEXT);
+ var surnameText = self.getControlElement(PanelControlElementType.USER_TAB_SURNAME_TEXT);
+ var emailText = self.getControlElement(PanelControlElementType.USER_TAB_EMAIL_TEXT);
+
+ userLoginTabDiv.style.display = "none";
+ userDataTabDiv.style.display = "block";
+
+ loginText.innerHTML = user.getLogin();
+ nameText.innerHTML = user.getName();
+ surnameText.innerHTML = user.getSurname();
+ emailText.innerHTML = user.getEmail();
+ } else {
+
+ userLoginTabDiv.style.display = "block";
+ userDataTabDiv.style.display = "none";
+ }
+};
+
+ProjectInfoPanel.prototype.init = function () {
+ var self = this;
+ var email, content;
+ return ServerConnector.getConfigurationParam(ConfigurationType.REQUEST_ACCOUNT_EMAIL).then(function (result) {
+ email = result;
+ return ServerConnector.getConfigurationParam(ConfigurationType.REQUEST_ACCOUNT_DEFAULT_CONTENT);
+ }).then(function (result) {
+ content = encodeURIComponent(result);
+ var url = 'mailto:' + email + '?subject=MINERVA account request&body=' + content;
+ var link = $("[name=requestAccount]", self.getElement());
+ link.attr("href", url);
+ return self.refresh();
+ });
+};
+
+ProjectInfoPanel.prototype.destroy = function () {
+ return this.publicationListDialog.destroy();
+};
+module.exports = ProjectInfoPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/SearchPanel.js b/frontend-js/src/main/js/gui/leftPanel/SearchPanel.js
index 22a3c038d76cc1f72e85f01abded2e059b04be99..17b93ec24a5c7b8cb40fb307c2843f41a3324ad5 100644
--- a/frontend-js/src/main/js/gui/leftPanel/SearchPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/SearchPanel.js
@@ -1,118 +1,118 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-/* exported logger */
-
-var Panel = require('../Panel');
-var ChemicalPanel = require('./ChemicalPanel');
-var DrugPanel = require('./DrugPanel');
-var MiRnaPanel = require('./MiRnaPanel');
-var GenericSearchPanel = require('./GenericSearchPanel');
-
-var logger = require('../../logger');
-
-/**
- *
- * @param {Configuration} params.configuration
- * @param {HTMLElement} params.element
- * @param {Project} params.project
- * @param {CustomMap} params.customMap
- * @param params.parent
- *
- * @constructor
- * @extends AbstractGuiElement
- */
-function SearchPanel(params) {
- params["panelName"] = "global-search";
- Panel.call(this, params);
- var self = this;
-
- self._createPanelGui();
-}
-
-SearchPanel.prototype = Object.create(Panel.prototype);
-SearchPanel.prototype.constructor = SearchPanel;
-
-/**
- *
- * @private
- */
-SearchPanel.prototype._createPanelGui = function () {
- var self = this;
-
- self.getGuiUtils().initTabContent(self);
-
- var panels = self.getPanelsDefinition();
- for (var i = 0; i < panels.length; i++) {
- self.getGuiUtils().addTab(self, panels[i]);
- }
-};
-
-/**
- *
- * @returns {*[]}
- */
-SearchPanel.prototype.getPanelsDefinition = function () {
- return [{
- name: "GENERIC",
- panelClass: GenericSearchPanel,
- options: {parent: this}
- }, {
- name: "DRUG",
- panelClass: DrugPanel,
- options: {parent: this}
- }, {
- name: "CHEMICAL",
- panelClass: ChemicalPanel,
- options: {parent: this}
- }, {
- name: "MiRNA",
- panelClass: MiRnaPanel,
- options: {parent: this}
- }];
-};
-
-/**
- *
- * @param {AbstractDbPanel} panel
- */
-SearchPanel.prototype.hideTab = function (panel) {
- var self = this;
- var panelDefinitions = self.getPanelsDefinition();
- for (var i = 0; i < panelDefinitions.length; i++) {
- if (panel instanceof panelDefinitions[i].panelClass) {
- var liElement = $("li:has(a[href='#search_panel_tab_" + i + "'])", $(self.getElement()))[0];
- if (liElement !== undefined) {
- liElement.style.display = "none";
- } else {
- logger.warn("Cannot find tab link for panel: " + panel.getPanelName());
- }
- }
- }
-};
-
-/**
- *
- * @returns {Promise}
- */
-SearchPanel.prototype.init = function () {
- var self = this;
-
- var promises = [];
- for (var i = 0; i < self._panels.length; i++) {
- promises.push(self._panels[i].init());
- }
- return Promise.all(promises);
-};
-
-/**
- *
- * @returns {Promise}
- */
-SearchPanel.prototype.destroy = function () {
- return Promise.resolve();
-};
-
-
-module.exports = SearchPanel;
+"use strict";
+
+var Promise = require("bluebird");
+
+/* exported logger */
+
+var Panel = require('../Panel');
+var ChemicalPanel = require('./ChemicalPanel');
+var DrugPanel = require('./DrugPanel');
+var MiRnaPanel = require('./MiRnaPanel');
+var GenericSearchPanel = require('./GenericSearchPanel');
+
+var logger = require('../../logger');
+
+/**
+ *
+ * @param {Configuration} params.configuration
+ * @param {HTMLElement} params.element
+ * @param {Project} params.project
+ * @param {CustomMap} params.customMap
+ * @param params.parent
+ *
+ * @constructor
+ * @extends AbstractGuiElement
+ */
+function SearchPanel(params) {
+ params["panelName"] = "global-search";
+ Panel.call(this, params);
+ var self = this;
+
+ self._createPanelGui();
+}
+
+SearchPanel.prototype = Object.create(Panel.prototype);
+SearchPanel.prototype.constructor = SearchPanel;
+
+/**
+ *
+ * @private
+ */
+SearchPanel.prototype._createPanelGui = function () {
+ var self = this;
+
+ self.getGuiUtils().initTabContent(self);
+
+ var panels = self.getPanelsDefinition();
+ for (var i = 0; i < panels.length; i++) {
+ self.getGuiUtils().addTab(self, panels[i]);
+ }
+};
+
+/**
+ *
+ * @returns {*[]}
+ */
+SearchPanel.prototype.getPanelsDefinition = function () {
+ return [{
+ name: "GENERIC",
+ panelClass: GenericSearchPanel,
+ options: {parent: this}
+ }, {
+ name: "DRUG",
+ panelClass: DrugPanel,
+ options: {parent: this}
+ }, {
+ name: "CHEMICAL",
+ panelClass: ChemicalPanel,
+ options: {parent: this}
+ }, {
+ name: "MiRNA",
+ panelClass: MiRnaPanel,
+ options: {parent: this}
+ }];
+};
+
+/**
+ *
+ * @param {AbstractDbPanel} panel
+ */
+SearchPanel.prototype.hideTab = function (panel) {
+ var self = this;
+ var panelDefinitions = self.getPanelsDefinition();
+ for (var i = 0; i < panelDefinitions.length; i++) {
+ if (panel instanceof panelDefinitions[i].panelClass) {
+ var liElement = $("li:has(a[href='#search_panel_tab_" + i + "'])", $(self.getElement()))[0];
+ if (liElement !== undefined) {
+ liElement.style.display = "none";
+ } else {
+ logger.warn("Cannot find tab link for panel: " + panel.getPanelName());
+ }
+ }
+ }
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+SearchPanel.prototype.init = function () {
+ var self = this;
+
+ var promises = [];
+ for (var i = 0; i < self._panels.length; i++) {
+ promises.push(self._panels[i].init());
+ }
+ return Promise.all(promises);
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+SearchPanel.prototype.destroy = function () {
+ return Promise.resolve();
+};
+
+
+module.exports = SearchPanel;
diff --git a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
index a2ac63594384c18c00f103efda155667740b21e8..908a50916ea52da4c562df1cc322772ba1162acc 100644
--- a/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
+++ b/frontend-js/src/main/js/gui/leftPanel/SubmapPanel.js
@@ -1,151 +1,151 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var GuiConnector= require('../../GuiConnector');
-var Panel = require('../Panel');
-var PanelControlElementType = require('../PanelControlElementType');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-var Functions = require('../../Functions');
-
-function SubmapPanel(params) {
- params.panelName = "submap";
- params.scrollable = true;
- params.helpTip = "The Submaps tab summarizes all the submap networks uploaded together and linked to the main network of <b>'"
- + params.parent.getMap().getProject().getName() + "'</b> project.";
- Panel.call(this, params);
-
- var self = this;
- self._createSubmapGui();
-}
-
-SubmapPanel.prototype = Object.create(Panel.prototype);
-SubmapPanel.prototype.constructor = SubmapPanel;
-
-SubmapPanel.prototype._createSubmapGui = function () {
- var submapDiv = Functions.createElement({
- type: "div",
- name: "submapDiv",
- className: "searchPanel"
- });
- this.getElement().appendChild(submapDiv);
- this.setControlElement(PanelControlElementType.SUBMAP_DIV, submapDiv);
-
-};
-
-SubmapPanel.prototype.createRow = function (model) {
- var self = this;
- var guiUtils = self.getGuiUtils();
- var result = document.createElement("tr");
-
- var nameTd = document.createElement("td");
- nameTd.innerHTML = model.getName();
- result.appendChild(nameTd);
-
- var openTd = document.createElement("td");
-
- if (model.getId() !== self.getMap().getId()) {
- var img = guiUtils.createIcon("icons/search.png");
- var link = document.createElement("a");
- link.href = "#";
- link.onclick = function () {
- return self.getMap().openSubmap(model.getId()).catch(GuiConnector.alert);
- };
- link.appendChild(img);
- openTd.appendChild(link);
- }
-
- result.appendChild(openTd);
-
- return result;
-};
-
-SubmapPanel.prototype.createTableHeader = function () {
- var result = document.createElement("thead");
-
- var row = document.createElement("tr");
-
- var nameTd = document.createElement("th");
- nameTd.innerHTML = "Name";
- row.appendChild(nameTd);
-
- row.appendChild(Functions.createElement({
- type: "th",
- style: "width: 60px;",
- content: "View"
- }));
-
- result.appendChild(row);
- return result;
-};
-
-SubmapPanel.prototype.init = function () {
- var self = this;
- return new Promise(function (resolve) {
- var div = self.getControlElement(PanelControlElementType.SUBMAP_DIV);
- div.innerHTML = "";
- var models = self.getMap().getProject().getModels();
- var modelsByType = [];
- var types = [];
- var i;
- for (i = 1; i < models.length; i++) {
- var model = models[i];
- if (modelsByType[model.getSubmodelType()] === undefined) {
- modelsByType[model.getSubmodelType()] = [];
- types.push(model.getSubmodelType());
- }
- modelsByType[model.getSubmodelType()].push(model);
- }
- for (i = 0; i < types.length; i++) {
- var type = types[i];
- var tableName = type + " submaps";
- if (type === "UNKNOWN") {
- tableName = ""
- }
- div.appendChild(self.createTable(modelsByType[type], tableName));
- }
- if (models.length <= 1) {
- self.getParent().hideTab(self);
- }
- return resolve();
- });
-};
-
-SubmapPanel.prototype.createTable = function (models, type) {
- var self = this;
- var result = Functions.createElement({
- type: "div"
- });
-
- var title = Functions.createElement({
- type: "h5",
- content: type
- });
- result.appendChild(title);
-
- var table = Functions.createElement({
- type: "table",
- className: "table table-bordered",
- style: "width:100%"
- });
- result.appendChild(table);
-
- table.appendChild(self.createTableHeader());
- var tableBody = Functions.createElement({
- type: "tbody"
- });
- table.appendChild(tableBody);
-
- for (var i = 0; i < models.length; i++) {
- tableBody.appendChild(self.createRow(models[i]));
- }
- return result;
-};
-
-SubmapPanel.prototype.destroy = function () {
- return Promise.resolve();
-};
-
-module.exports = SubmapPanel;
+"use strict";
+
+var Promise = require("bluebird");
+
+var GuiConnector= require('../../GuiConnector');
+var Panel = require('../Panel');
+var PanelControlElementType = require('../PanelControlElementType');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+var Functions = require('../../Functions');
+
+function SubmapPanel(params) {
+ params.panelName = "submap";
+ params.scrollable = true;
+ params.helpTip = "The Submaps tab summarizes all the submap networks uploaded together and linked to the main network of <b>'"
+ + params.parent.getMap().getProject().getName() + "'</b> project.";
+ Panel.call(this, params);
+
+ var self = this;
+ self._createSubmapGui();
+}
+
+SubmapPanel.prototype = Object.create(Panel.prototype);
+SubmapPanel.prototype.constructor = SubmapPanel;
+
+SubmapPanel.prototype._createSubmapGui = function () {
+ var submapDiv = Functions.createElement({
+ type: "div",
+ name: "submapDiv",
+ className: "searchPanel"
+ });
+ this.getElement().appendChild(submapDiv);
+ this.setControlElement(PanelControlElementType.SUBMAP_DIV, submapDiv);
+
+};
+
+SubmapPanel.prototype.createRow = function (model) {
+ var self = this;
+ var guiUtils = self.getGuiUtils();
+ var result = document.createElement("tr");
+
+ var nameTd = document.createElement("td");
+ nameTd.innerHTML = model.getName();
+ result.appendChild(nameTd);
+
+ var openTd = document.createElement("td");
+
+ if (model.getId() !== self.getMap().getId()) {
+ var img = guiUtils.createIcon("icons/search.png");
+ var link = document.createElement("a");
+ link.href = "#";
+ link.onclick = function () {
+ return self.getMap().openSubmap(model.getId()).catch(GuiConnector.alert);
+ };
+ link.appendChild(img);
+ openTd.appendChild(link);
+ }
+
+ result.appendChild(openTd);
+
+ return result;
+};
+
+SubmapPanel.prototype.createTableHeader = function () {
+ var result = document.createElement("thead");
+
+ var row = document.createElement("tr");
+
+ var nameTd = document.createElement("th");
+ nameTd.innerHTML = "Name";
+ row.appendChild(nameTd);
+
+ row.appendChild(Functions.createElement({
+ type: "th",
+ style: "width: 60px;",
+ content: "View"
+ }));
+
+ result.appendChild(row);
+ return result;
+};
+
+SubmapPanel.prototype.init = function () {
+ var self = this;
+ return new Promise(function (resolve) {
+ var div = self.getControlElement(PanelControlElementType.SUBMAP_DIV);
+ div.innerHTML = "";
+ var models = self.getMap().getProject().getModels();
+ var modelsByType = [];
+ var types = [];
+ var i;
+ for (i = 1; i < models.length; i++) {
+ var model = models[i];
+ if (modelsByType[model.getSubmodelType()] === undefined) {
+ modelsByType[model.getSubmodelType()] = [];
+ types.push(model.getSubmodelType());
+ }
+ modelsByType[model.getSubmodelType()].push(model);
+ }
+ for (i = 0; i < types.length; i++) {
+ var type = types[i];
+ var tableName = type + " submaps";
+ if (type === "UNKNOWN") {
+ tableName = ""
+ }
+ div.appendChild(self.createTable(modelsByType[type], tableName));
+ }
+ if (models.length <= 1) {
+ self.getParent().hideTab(self);
+ }
+ return resolve();
+ });
+};
+
+SubmapPanel.prototype.createTable = function (models, type) {
+ var self = this;
+ var result = Functions.createElement({
+ type: "div"
+ });
+
+ var title = Functions.createElement({
+ type: "h5",
+ content: type
+ });
+ result.appendChild(title);
+
+ var table = Functions.createElement({
+ type: "table",
+ className: "table table-bordered",
+ style: "width:100%"
+ });
+ result.appendChild(table);
+
+ table.appendChild(self.createTableHeader());
+ var tableBody = Functions.createElement({
+ type: "tbody"
+ });
+ table.appendChild(tableBody);
+
+ for (var i = 0; i < models.length; i++) {
+ tableBody.appendChild(self.createRow(models[i]));
+ }
+ return result;
+};
+
+SubmapPanel.prototype.destroy = function () {
+ return Promise.resolve();
+};
+
+module.exports = SubmapPanel;
diff --git a/frontend-js/src/main/js/gui/topMenu/TopMenu.js b/frontend-js/src/main/js/gui/topMenu/TopMenu.js
index a38f9a6abf86b758a1f81c8581839dc2c677310c..44016f2259496c840427ef62e1edf8e05e9a575d 100644
--- a/frontend-js/src/main/js/gui/topMenu/TopMenu.js
+++ b/frontend-js/src/main/js/gui/topMenu/TopMenu.js
@@ -1,243 +1,243 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-/* exported logger */
-
-var AbstractGuiElement = require('../AbstractGuiElement');
-var GuiConnector = require('../../GuiConnector');
-var OverviewDialog = require('../OverviewDialog');
-var PanelControlElementType = require('../PanelControlElementType');
-
-var Functions = require('../../Functions');
-var logger = require('../../logger');
-
-function TopMenu(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
-
- self._createGui();
-}
-
-TopMenu.prototype = Object.create(AbstractGuiElement.prototype);
-TopMenu.prototype.constructor = TopMenu;
-
-TopMenu.prototype._createGui = function () {
- var self = this;
-
- var overviewDialogDiv = Functions.createElement({
- type: "div",
- name: "overviewDialog"
- });
- self.getElement().appendChild(overviewDialogDiv);
- self.setControlElement(PanelControlElementType.OVERVIEW_DIALOG_DIV, overviewDialogDiv);
-
- var hideButtonDiv = Functions.createElement({
- type: "div",
- className: "headerHideDivButton"
- });
- self.getElement().appendChild(hideButtonDiv);
-
- var hideButton = Functions.createElement({
- type: "button",
- className: "headerHideButton",
- name: "hideButton"
- });
- hideButtonDiv.appendChild(hideButton);
- self.setControlElement(PanelControlElementType.MENU_HIDE_LEFT_PANEL_BUTTON, hideButton);
-
- var hideButtonIcon = Functions.createElement({
- type: "i",
- className: "fa fa-chevron-left",
- name: "hideButtonIcon"
- });
- hideButton.appendChild(hideButtonIcon);
- self.setControlElement(PanelControlElementType.MENU_HIDE_LEFT_PANEL_BUTTON_ICON, hideButtonIcon);
-
- var versionDiv = Functions.createElement({
- type: "div",
- className: "headerTextBold",
- name: "versionDiv"
- });
- self.getElement().appendChild(versionDiv);
- self.setControlElement(PanelControlElementType.MENU_VERSION_DIV, versionDiv);
-
- var showOverviewDiv = Functions.createElement({
- type: "div",
- style: "float: left;"
- });
- self.getElement().appendChild(showOverviewDiv);
-
- var showOverviewButton = Functions.createElement({
- type: "button",
- className: "minerva-overview-button",
- name: "showOverviewButton",
- content: "<i class='fa fa-sitemap' style='font-size:18px; font-weight:400; padding-right:10px;'></i><span >SHOW OVERVIEW</span>",
- style: "display:none",
- xss: false
- });
- showOverviewDiv.appendChild(showOverviewButton);
- self.setControlElement(PanelControlElementType.MENU_SHOW_OVERVIEW_BUTTON, showOverviewButton);
-
- var rightHeaderMenuDiv = Functions.createElement({
- type: "div",
- className: "rightHeaderMenu"
- });
- self.getElement().appendChild(rightHeaderMenuDiv);
-
- var div4checkboxes = Functions.createElement({
- type: "div",
- className: "minerva-top-checkbox-div"
- });
- rightHeaderMenuDiv.appendChild(div4checkboxes);
-
- var legendCheckbox = Functions.createElement({
- type: "input",
- inputType: "checkbox",
- name: "legendCheckbox"
- });
- div4checkboxes.appendChild(legendCheckbox);
- self.setControlElement(PanelControlElementType.MENU_LEGEND_CHECKBOX, legendCheckbox);
-
- div4checkboxes.appendChild(Functions.createElement({
- type: "label",
- content: "LEGEND"
- }));
-
- var commentCheckbox = Functions.createElement({
- type: "input",
- inputType: "checkbox",
- name: "commentCheckbox"
- });
- div4checkboxes.appendChild(commentCheckbox);
- self.setControlElement(PanelControlElementType.MENU_COMMENTS_CHECKBOX, commentCheckbox);
-
- div4checkboxes.appendChild(Functions.createElement({
- type: "label",
- content: "COMMENTS"
- }));
-
- var refreshCommentButton = Functions.createElement({
- type: "button",
- className: "minerva-overview-button",
- name: "refreshCommentButton",
- content: "<i class='fa fa-refresh' style='font-size:21px; font-weight:400;'></i>",
- style: "display:none",
- xss: false
- });
- div4checkboxes.appendChild(refreshCommentButton);
- self.setControlElement(PanelControlElementType.MENU_REFRESH_COMMENTS_BUTTON, refreshCommentButton);
-
- var clearButton = Functions.createElement({
- type: "button",
- className: "minerva-overview-button",
- name: "clearButton",
- content: "<i class='fa fa-times' style='font-size:18px; font-weight:300; padding-right:10px;'></i>CLEAR",
- xss: false
- });
- rightHeaderMenuDiv.appendChild(clearButton);
- self.setControlElement(PanelControlElementType.MENU_CLEAR_BUTTON, clearButton);
-
-};
-
-TopMenu.prototype.init = function () {
- var self = this;
- self.getControlElement(PanelControlElementType.MENU_LEGEND_CHECKBOX).onclick = function () {
- return self.toggleLegend();
- };
- var hideButton = self.getControlElement(PanelControlElementType.MENU_HIDE_LEFT_PANEL_BUTTON);
- var icon = self.getControlElement(PanelControlElementType.MENU_HIDE_LEFT_PANEL_BUTTON_ICON);
- hideButton.onclick = function () {
- if (icon.className.indexOf("fa-chevron-left") >= 0) {
- icon.className = "fa fa-chevron-right";
- self.getLeftPanel().hide();
- } else {
- icon.className = "fa fa-chevron-left";
- self.getLeftPanel().show();
- }
- self.getMap().getMapCanvas().triggerListeners('resize');
- };
-
- var project = self.getMap().getProject();
- self.getControlElement(PanelControlElementType.MENU_VERSION_DIV).innerHTML = project.getVersion();
-
- var commentCheckbox = self.getControlElement(PanelControlElementType.MENU_COMMENTS_CHECKBOX);
- var refreshCommentButton = self.getControlElement(PanelControlElementType.MENU_REFRESH_COMMENTS_BUTTON);
- commentCheckbox.onclick = function () {
- ServerConnector.getSessionData(project).setShowComments(commentCheckbox.checked);
- if (commentCheckbox.checked) {
- $(refreshCommentButton).css("display","inline");
- } else {
- $(refreshCommentButton).css("display","none");
- }
- return self.getMap().refreshComments().then(null, GuiConnector.alert);
- };
- refreshCommentButton.onclick = (function () {
- return function () {
- self.getMap().refreshComments();
- return false;
- };
- })();
-
- var clearButton = self.getControlElement(PanelControlElementType.MENU_CLEAR_BUTTON);
- clearButton.onclick = (function () {
- return function () {
- return self.getMap().clearDbOverlays();
- };
- })();
-
- if (project.getTopOverviewImage() !== undefined && project.getTopOverviewImage() !== null) {
- self._overviewDialog = new OverviewDialog({
- customMap: self.getMap(),
- element: self.getControlElement(PanelControlElementType.OVERVIEW_DIALOG_DIV)
- });
- var showOverviewButton = self.getControlElement(PanelControlElementType.MENU_SHOW_OVERVIEW_BUTTON);
- showOverviewButton.onclick = function () {
- return self._overviewDialog.showOverview();
- };
- $(showOverviewButton).css("display","inline-block");
- }
-
- if (ServerConnector.getSessionData().getShowComments()) {
- self.getControlElement(PanelControlElementType.MENU_COMMENTS_CHECKBOX).checked = true;
- return self.getMap().refreshComments();
- } else {
- return Promise.resolve();
- }
-};
-
-TopMenu.prototype.setLegend = function (legend) {
- this._legend = legend;
-};
-
-TopMenu.prototype.getLegend = function () {
- return this._legend;
-};
-
-TopMenu.prototype.setLeftPanel = function (leftPanel) {
- this._leftPanel = leftPanel;
-};
-
-TopMenu.prototype.getLeftPanel = function () {
- return this._leftPanel;
-};
-
-TopMenu.prototype.destroy = function () {
- var self = this;
- if (self._overviewDialog !== undefined) {
- self._overviewDialog.destroy();
- }
- return Promise.resolve();
-};
-
-TopMenu.prototype.toggleLegend = function () {
- var self = this;
- var legend = self.getLegend();
- if (self.getControlElement(PanelControlElementType.MENU_LEGEND_CHECKBOX).checked) {
- legend.show();
- } else {
- legend.hide();
- }
-};
-
+"use strict";
+
+var Promise = require("bluebird");
+
+/* exported logger */
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+var GuiConnector = require('../../GuiConnector');
+var OverviewDialog = require('../OverviewDialog');
+var PanelControlElementType = require('../PanelControlElementType');
+
+var Functions = require('../../Functions');
+var logger = require('../../logger');
+
+function TopMenu(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+
+ self._createGui();
+}
+
+TopMenu.prototype = Object.create(AbstractGuiElement.prototype);
+TopMenu.prototype.constructor = TopMenu;
+
+TopMenu.prototype._createGui = function () {
+ var self = this;
+
+ var overviewDialogDiv = Functions.createElement({
+ type: "div",
+ name: "overviewDialog"
+ });
+ self.getElement().appendChild(overviewDialogDiv);
+ self.setControlElement(PanelControlElementType.OVERVIEW_DIALOG_DIV, overviewDialogDiv);
+
+ var hideButtonDiv = Functions.createElement({
+ type: "div",
+ className: "headerHideDivButton"
+ });
+ self.getElement().appendChild(hideButtonDiv);
+
+ var hideButton = Functions.createElement({
+ type: "button",
+ className: "headerHideButton",
+ name: "hideButton"
+ });
+ hideButtonDiv.appendChild(hideButton);
+ self.setControlElement(PanelControlElementType.MENU_HIDE_LEFT_PANEL_BUTTON, hideButton);
+
+ var hideButtonIcon = Functions.createElement({
+ type: "i",
+ className: "fa fa-chevron-left",
+ name: "hideButtonIcon"
+ });
+ hideButton.appendChild(hideButtonIcon);
+ self.setControlElement(PanelControlElementType.MENU_HIDE_LEFT_PANEL_BUTTON_ICON, hideButtonIcon);
+
+ var versionDiv = Functions.createElement({
+ type: "div",
+ className: "headerTextBold",
+ name: "versionDiv"
+ });
+ self.getElement().appendChild(versionDiv);
+ self.setControlElement(PanelControlElementType.MENU_VERSION_DIV, versionDiv);
+
+ var showOverviewDiv = Functions.createElement({
+ type: "div",
+ style: "float: left;"
+ });
+ self.getElement().appendChild(showOverviewDiv);
+
+ var showOverviewButton = Functions.createElement({
+ type: "button",
+ className: "minerva-overview-button",
+ name: "showOverviewButton",
+ content: "<i class='fa fa-sitemap' style='font-size:18px; font-weight:400; padding-right:10px;'></i><span >SHOW OVERVIEW</span>",
+ style: "display:none",
+ xss: false
+ });
+ showOverviewDiv.appendChild(showOverviewButton);
+ self.setControlElement(PanelControlElementType.MENU_SHOW_OVERVIEW_BUTTON, showOverviewButton);
+
+ var rightHeaderMenuDiv = Functions.createElement({
+ type: "div",
+ className: "rightHeaderMenu"
+ });
+ self.getElement().appendChild(rightHeaderMenuDiv);
+
+ var div4checkboxes = Functions.createElement({
+ type: "div",
+ className: "minerva-top-checkbox-div"
+ });
+ rightHeaderMenuDiv.appendChild(div4checkboxes);
+
+ var legendCheckbox = Functions.createElement({
+ type: "input",
+ inputType: "checkbox",
+ name: "legendCheckbox"
+ });
+ div4checkboxes.appendChild(legendCheckbox);
+ self.setControlElement(PanelControlElementType.MENU_LEGEND_CHECKBOX, legendCheckbox);
+
+ div4checkboxes.appendChild(Functions.createElement({
+ type: "label",
+ content: "LEGEND"
+ }));
+
+ var commentCheckbox = Functions.createElement({
+ type: "input",
+ inputType: "checkbox",
+ name: "commentCheckbox"
+ });
+ div4checkboxes.appendChild(commentCheckbox);
+ self.setControlElement(PanelControlElementType.MENU_COMMENTS_CHECKBOX, commentCheckbox);
+
+ div4checkboxes.appendChild(Functions.createElement({
+ type: "label",
+ content: "COMMENTS"
+ }));
+
+ var refreshCommentButton = Functions.createElement({
+ type: "button",
+ className: "minerva-overview-button",
+ name: "refreshCommentButton",
+ content: "<i class='fa fa-refresh' style='font-size:21px; font-weight:400;'></i>",
+ style: "display:none",
+ xss: false
+ });
+ div4checkboxes.appendChild(refreshCommentButton);
+ self.setControlElement(PanelControlElementType.MENU_REFRESH_COMMENTS_BUTTON, refreshCommentButton);
+
+ var clearButton = Functions.createElement({
+ type: "button",
+ className: "minerva-overview-button",
+ name: "clearButton",
+ content: "<i class='fa fa-times' style='font-size:18px; font-weight:300; padding-right:10px;'></i>CLEAR",
+ xss: false
+ });
+ rightHeaderMenuDiv.appendChild(clearButton);
+ self.setControlElement(PanelControlElementType.MENU_CLEAR_BUTTON, clearButton);
+
+};
+
+TopMenu.prototype.init = function () {
+ var self = this;
+ self.getControlElement(PanelControlElementType.MENU_LEGEND_CHECKBOX).onclick = function () {
+ return self.toggleLegend();
+ };
+ var hideButton = self.getControlElement(PanelControlElementType.MENU_HIDE_LEFT_PANEL_BUTTON);
+ var icon = self.getControlElement(PanelControlElementType.MENU_HIDE_LEFT_PANEL_BUTTON_ICON);
+ hideButton.onclick = function () {
+ if (icon.className.indexOf("fa-chevron-left") >= 0) {
+ icon.className = "fa fa-chevron-right";
+ self.getLeftPanel().hide();
+ } else {
+ icon.className = "fa fa-chevron-left";
+ self.getLeftPanel().show();
+ }
+ self.getMap().getMapCanvas().triggerListeners('resize');
+ };
+
+ var project = self.getMap().getProject();
+ self.getControlElement(PanelControlElementType.MENU_VERSION_DIV).innerHTML = project.getVersion();
+
+ var commentCheckbox = self.getControlElement(PanelControlElementType.MENU_COMMENTS_CHECKBOX);
+ var refreshCommentButton = self.getControlElement(PanelControlElementType.MENU_REFRESH_COMMENTS_BUTTON);
+ commentCheckbox.onclick = function () {
+ ServerConnector.getSessionData(project).setShowComments(commentCheckbox.checked);
+ if (commentCheckbox.checked) {
+ $(refreshCommentButton).css("display","inline");
+ } else {
+ $(refreshCommentButton).css("display","none");
+ }
+ return self.getMap().refreshComments().then(null, GuiConnector.alert);
+ };
+ refreshCommentButton.onclick = (function () {
+ return function () {
+ self.getMap().refreshComments();
+ return false;
+ };
+ })();
+
+ var clearButton = self.getControlElement(PanelControlElementType.MENU_CLEAR_BUTTON);
+ clearButton.onclick = (function () {
+ return function () {
+ return self.getMap().clearDbOverlays();
+ };
+ })();
+
+ if (project.getTopOverviewImage() !== undefined && project.getTopOverviewImage() !== null) {
+ self._overviewDialog = new OverviewDialog({
+ customMap: self.getMap(),
+ element: self.getControlElement(PanelControlElementType.OVERVIEW_DIALOG_DIV)
+ });
+ var showOverviewButton = self.getControlElement(PanelControlElementType.MENU_SHOW_OVERVIEW_BUTTON);
+ showOverviewButton.onclick = function () {
+ return self._overviewDialog.showOverview();
+ };
+ $(showOverviewButton).css("display","inline-block");
+ }
+
+ if (ServerConnector.getSessionData().getShowComments()) {
+ self.getControlElement(PanelControlElementType.MENU_COMMENTS_CHECKBOX).checked = true;
+ return self.getMap().refreshComments();
+ } else {
+ return Promise.resolve();
+ }
+};
+
+TopMenu.prototype.setLegend = function (legend) {
+ this._legend = legend;
+};
+
+TopMenu.prototype.getLegend = function () {
+ return this._legend;
+};
+
+TopMenu.prototype.setLeftPanel = function (leftPanel) {
+ this._leftPanel = leftPanel;
+};
+
+TopMenu.prototype.getLeftPanel = function () {
+ return this._leftPanel;
+};
+
+TopMenu.prototype.destroy = function () {
+ var self = this;
+ if (self._overviewDialog !== undefined) {
+ self._overviewDialog.destroy();
+ }
+ return Promise.resolve();
+};
+
+TopMenu.prototype.toggleLegend = function () {
+ var self = this;
+ var legend = self.getLegend();
+ if (self.getControlElement(PanelControlElementType.MENU_LEGEND_CHECKBOX).checked) {
+ legend.show();
+ } else {
+ legend.hide();
+ }
+};
+
module.exports = TopMenu;
\ No newline at end of file
diff --git a/frontend-js/src/main/js/logger.js b/frontend-js/src/main/js/logger.js
index f60d8a4c25c3355a468a715ea767ab7827f45adb..f6cd2db0f6f6a30af3f69278b41e67b3522844db 100644
--- a/frontend-js/src/main/js/logger.js
+++ b/frontend-js/src/main/js/logger.js
@@ -1,20 +1,20 @@
-"use strict";
-
-var log4js = require('log4js');
-
-/**
- * @typedef {Object} Logger
- * @property {function(string):void} setLevel
- * @property {function(Object):void} warn
- * @property {function(Object):void} info
- * @property {function(Object):void} debug
- * @property {function(Object):void} error
- * @property {function(Object):void} fatal
- */
-
-/**
- * @type Logger
- */
-var logger = log4js.getLogger();
-
-module.exports = logger;
+"use strict";
+
+var log4js = require('log4js');
+
+/**
+ * @typedef {Object} Logger
+ * @property {function(string):void} setLevel
+ * @property {function(Object):void} warn
+ * @property {function(Object):void} info
+ * @property {function(Object):void} debug
+ * @property {function(Object):void} error
+ * @property {function(Object):void} fatal
+ */
+
+/**
+ * @type Logger
+ */
+var logger = log4js.getLogger();
+
+module.exports = logger;
diff --git a/frontend-js/src/main/js/map/ControlType.js b/frontend-js/src/main/js/map/ControlType.js
index 9aba0868fe933641990fb124933d97722c444e36..09d41558c3b7c99219f50dd0d899e1998c7364b9 100644
--- a/frontend-js/src/main/js/map/ControlType.js
+++ b/frontend-js/src/main/js/map/ControlType.js
@@ -1,9 +1,9 @@
-"use strict";
-
-var ControlType = {
- SUBMAP_DIALOGS : "SUBMAP_DIALOGS",
- LOGO_IMG : "LOGO_IMG",
- LOGO_2_IMG : "LOGO_2_IMG"
-};
-
-module.exports = ControlType;
+"use strict";
+
+var ControlType = {
+ SUBMAP_DIALOGS : "SUBMAP_DIALOGS",
+ LOGO_IMG : "LOGO_IMG",
+ LOGO_2_IMG : "LOGO_2_IMG"
+};
+
+module.exports = ControlType;
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 949488ace5075ce9bf517502ee6214bda41a3629..e68a051ec5687ef7982a540db7d4d524c7357c3d 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -1,1319 +1,1319 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var logger = require('../logger');
-var Functions = require('../Functions');
-
-var AbstractCustomMap = require('./AbstractCustomMap');
-var Alias = require('./data/Alias');
-var CommentDialog = require('../gui/CommentDialog');
-var ConfigurationType = require('../ConfigurationType');
-var ControlType = require('./ControlType');
-var CustomMapOptions = require('./CustomMapOptions');
-var GuiConnector = require('../GuiConnector');
-var IdentifiedElement = require('./data/IdentifiedElement');
-var DataOverlay = require('./data/DataOverlay');
-var Reaction = require('./data/Reaction');
-var ReferenceGenome = require('./data/ReferenceGenome');
-var SecurityError = require('../SecurityError');
-var Submap = require('./Submap');
-
-var Bounds = require('./canvas/Bounds');
-var Point = require('./canvas/Point');
-
-/**
- * Default constructor.
- *
- * @param {CustomMapOptions} options
- * CustomMapOptions object representing all parameters needed for map
- * creation
- *
- * @constructor
- * @extends AbstractCustomMap
- */
-function CustomMap(options) {
- //@type {HTMLElement[]}
- this._controls = [];
-
- if (!(options instanceof CustomMapOptions)) {
- options = new CustomMapOptions(options);
- }
- AbstractCustomMap.call(this, options.getProject().getModels()[0], options);
-
- this.registerListenerType("onBioEntityClick");
- this.registerListenerType("onShowOverlay");
- this.registerListenerType("onHideOverlay");
- this.registerListenerType("onBackgroundOverlayChange");
-
- // @type {boolean[]}
- this._selectedOverlays = [];
-
- this.customizeGoogleMapView(options.getElement());
-
- this.createMapChangedCallbacks();
-
- /**
- *
- * @type {Object.<string, AbstractDbOverlay>}
- */
- this.overlayCollections = {};
-
- // which submap is active (where user made interaction for the last time)
- // @type {number}
- this._activeSubmapId = null;
-
- // @type {boolean}
- this.initialized = true;
-
- // list of reference genomes
- this._referenceGenome = [];
-
- this.createSubmaps();
-
- //@type {HTMLElement[]}
- this._dialogs = [];
-}
-
-CustomMap.prototype = Object.create(AbstractCustomMap.prototype);
-CustomMap.prototype.constructor = CustomMap;
-
-/**
- * This code must be run after the object is created. It requires to download
- * some data via promises.
- *
- * @return {PromiseLike} with empty result
- */
-CustomMap.prototype.init = function () {
- var self = this;
- var sessionData = self.getServerConnector().getSessionData(self.getProject());
-
- // if we have background overlay stored in the session then restore it
- var mapType = sessionData.getSelectedBackgroundOverlay();
- // if we have user data overlays stored in the session then restore it
- var ids = sessionData.getVisibleOverlays();
- if (mapType !== undefined) {
- ids.push(mapType);
- }
-
- return Promise.all([self.getMapCanvas().triggerListeners('resize'),
- // noinspection SpellCheckingInspection
- self.getMapCanvas().triggerListeners('maptypeid_changed'),
- self.getMapCanvas().triggerListeners('projection_changed')
- ]).then(function () {
-
- // center map and zoom in to fit into browser window if there is no
- // information about coordinates in the session
-
- var x = self.getModel().getDefaultCenterX();
- var y = self.getModel().getDefaultCenterY();
- var zoom = self.getModel().getDefaultZoomLevel();
- if (self.getServerConnector().getSessionData(self.getProject()).getCenter(self.getModel()) === undefined &&
- (x === undefined || y === undefined || zoom === undefined ||
- x === null || y === null || zoom === null
- )) {
- var bounds = new Bounds();
- bounds.extend(self.getTopLeft());
- bounds.extend(self.getBottomRight());
-
- self.getMapCanvas().fitBounds(bounds);
- }
-
-
- return Promise.each(ids, function (overlayId) {
- try {
- return self.openDataOverlay(overlayId);
- } catch (e) {
- if (e instanceof SecurityError) {
- logger.debug(e.message);
- sessionData.setSelectedBackgroundOverlay(self.getProject().getDataOverlays()[0].getId());
- } else {
- return Promise.reject(e);
- }
- }
- });
- }).then(function () {
- return self.getServerConnector().getLogoImg();
- }).then(function (url) {
- var logo2 = self.getControl(ControlType.LOGO_2_IMG);
- if (!/^(f|ht)tps?:\/\//i.test(url)) {
- url = GuiConnector.getImgPrefix() + url;
- }
- logo2.src = url;
- logo2.setAttribute('title', self.getConfiguration().getOption(ConfigurationType.LOGO_TEXT).getValue());
- logo2.setAttribute('alt', self.getConfiguration().getOption(ConfigurationType.LOGO_TEXT).getValue());
- });
-};
-
-/**
- * Create submaps.
- */
-CustomMap.prototype.createSubmaps = function () {
- this.submaps = [];
- for (var i = 1; i < this.getProject().getModels().length; i++) {
- this.submaps.push(new Submap(this, this.getProject().getModels()[i]));
- }
-};
-
-/**
- * Creates logo and put it on the google map.
- */
-CustomMap.prototype.createLogo = function () {
- var self = this;
- var logoControlDiv2 = Functions.createElement({type: "div", index: 0});
- var logo2 = Functions.createElement({
- type: 'IMG',
- style: "cursor: pointer; width: 80px",
- id: ControlType.LOGO_2_IMG,
- onclick: function () {
- return self.getServerConnector().getLogoLink().then(function (url) {
- var win = window.open(url, '_blank');
- win.focus();
- }).catch(GuiConnector.alert);
- }
- });
- this.addControl(logo2);
-
- logoControlDiv2.appendChild(logo2);
-
- this.getMapCanvas().addLeftBottomControl(logoControlDiv2);
-
- var logoControlDiv = Functions.createElement({type: "div", style: "padding: 5px", index: 1});
- var logo = Functions.createElement({
- type: "IMG",
- src: GuiConnector.getImgPrefix() + GuiConnector.getLcsbLogoImg(this.bigButtons),
- style: "cursor: pointer",
- id: ControlType.LOGO_IMG,
- onclick: function () {
- var win = window.open('http://wwwen.uni.lu/lcsb/', '_blank');
- win.focus();
- }
- });
- this.addControl(logo);
- logoControlDiv.appendChild(logo);
-
- this.getMapCanvas().addRightBottomControl(logoControlDiv);
-};
-
-/**
- * Clear all AbstractDbOverlay.
- *
- * @returns {PromiseLike}
- */
-CustomMap.prototype.clearDbOverlays = function () {
- var promises = [];
- var overlays = this.getDbOverlays();
- for (var i = 0; i < overlays.length; i++) {
- promises.push(overlays[i].clear());
- }
- return Promise.all(promises);
-};
-
-/**
- * Open data overlay given in the parameter.
- *
- * @param {DataOverlay|number|string} param
- * identifier or DataOverlay identifying data overlay to open
- *
- * @returns {PromiseLike|Promise}
- */
-CustomMap.prototype.openDataOverlay = function (param) {
- logger.debug("Opening data overlay: " + param);
-
- var self = this;
- var identifier = param;
- if (param instanceof DataOverlay) {
- identifier = param.getId();
- }
- identifier = parseInt(identifier);
-
- if (isNaN(identifier)) {
- throw new Error("invalid id: " + param);
- }
-
- var overlayToOpen = null;
- var overlays = self.getProject().getDataOverlays();
- for (var j = 0; j < overlays.length; j++) {
- var overlay = overlays[j];
- if (overlay.getId() === identifier) {
- overlayToOpen = overlay;
- }
- }
-
- if (overlayToOpen === null) {
- throw new SecurityError("You have no privileges for selected overlay");
- } else {
- return overlayToOpen.init().then(function () {
- if (overlayToOpen.getInputDataAvailable()) {
- if (self._selectedOverlays[identifier] === true) {
- logger.warn("Overlay " + identifier + " already selected");
- return Promise.resolve();
- } else {
- self._selectedOverlays[identifier] = true;
- return self.getVisibleDataOverlays().then(function (visibleDataOverlays) {
- var ids = [];
- for (var i = 0; i < visibleDataOverlays.length; i++) {
- ids.push(visibleDataOverlays[i].getId());
- }
- self.getServerConnector().getSessionData(self.getProject()).setVisibleOverlays(ids);
- return self.redrawSelectedDataOverlays();
- }).then(function () {
- var backgroundToOpen;
- var overlays = self.getProject().getDataOverlays();
- for (var i = 0; i < overlays.length; i++) {
- var overlay = overlays[i];
- if (overlay.getName().toLowerCase() === "empty") {
- backgroundToOpen = overlay;
- }
- }
- if (backgroundToOpen === undefined) {
- logger.warn("Cannot find empty background overlay");
- } else {
- return self.openDataOverlay(backgroundToOpen.getId());
- }
- });
- }
- } else {
- if (identifier.toString() === self.getMapCanvas().getBackgroundId()) {
- return Promise.resolve();
- } else {
- self.getMapCanvas().setBackgroundId(identifier.toString());
-
- var submaps = self.getSubmaps();
- for (var i = 0; i < submaps.length; i++) {
- var submap = submaps[i];
- submap.openDataOverlay(identifier);
- }
- return self.callListeners("onBackgroundOverlayChange", identifier);
- }
- }
- }).then(function () {
- return self.callListeners("onShowOverlay", overlayToOpen);
- });
- }
-};
-
-/**
- * Returns {DataOverlay} that is used as a background.
- *
- * @returns {DataOverlay}
- */
-CustomMap.prototype.getBackgroundDataOverlay = function () {
- var identifier = parseInt(this.getMapCanvas().getBackgroundId());
- var overlays = this.getProject().getDataOverlays();
- for (var i = 0; i < overlays.length; i++) {
- var overlay = overlays[i];
- if (overlay.getId() === identifier) {
- return overlay;
- }
- }
- return null;
-};
-
-/**
- * Register AbstractDbOverlay in the map.
- *
- * @param {AbstractDbOverlay} dbOverlay
- * database overlay to be connected to the map
- */
-CustomMap.prototype.registerDbOverlay = function (dbOverlay) {
- var self = this;
-
- this.overlayCollections[dbOverlay.getName()] = dbOverlay;
-
-
- if (dbOverlay.getName() !== undefined) {
- if (dbOverlay.getName() === "search" || dbOverlay.getName().indexOf("plugin") === 0) {
- dbOverlay.addListener("onSearch", function (e) {
- return self.renderOverlayCollection({
- overlayCollection: dbOverlay,
- fitBounds: e.arg.fitBounds
- });
- });
- }
- if (dbOverlay.getName() === "drug" || dbOverlay.getName() === "chemical" || dbOverlay.getName() === "mirna") {
- dbOverlay.addListener("onSearch", function (e) {
- return self.renderOverlayCollection({
- overlayCollection: dbOverlay,
- fitBounds: e.arg.fitBounds
- });
- });
-
- dbOverlay.addListener("onTargetVisibilityChange", function () {
- return self.renderOverlayCollection({
- overlayCollection: dbOverlay,
- fitBounds: false
- });
- });
- }
- if (dbOverlay.getName() === "comment") {
- var listener = function () {
- return self.renderOverlayCollection({
- overlayCollection: dbOverlay,
- fitBounds: false
- });
- };
- dbOverlay.addListener("onRefresh", listener);
- dbOverlay.addListener("onClear", listener);
- }
- }
-
-};
-
-/**
- * Refresh comment list.
- *
- * @return {PromiseLike} promise that is resolved when comment list is refreshed
- */
-CustomMap.prototype.refreshComments = function () {
- var self = this;
-
- var commentDbOverlay = self.getOverlayByName("comment");
- if (commentDbOverlay !== undefined) {
- if (self.getServerConnector().getSessionData(self.getProject()).getShowComments()) {
- return commentDbOverlay.refresh();
- } else {
- return commentDbOverlay.clear();
- }
- }
- throw new Error("comment DbOverlay not found");
-};
-
-/**
- * Turns on/off drawing module on google maps.
- */
-CustomMap.prototype.toggleDrawing = function () {
- var submap = this.getSubmapById(this.getActiveSubmapId());
- if (submap !== undefined) {
- submap.getMapCanvas().toggleDrawing();
- } else {
- throw new Error("Cannot find submodel with id: " + this.getActiveSubmapId());
- }
-};
-
-/**
- *
- * @returns {PromiseLike}
- */
-CustomMap.prototype.refreshMarkers = function () {
- var promises = [];
- logger.debug("Refresh Markers: ");
-
- var overlays = this.getDbOverlays();
- for (var i = 0; i < overlays.length; i++) {
- promises.push(this.refreshOverlayMarkers(overlays[i]));
- }
-
- return Promise.all(promises);
-};
-
-/**
- *
- * @param {AbstractDbOverlay} overlay
- * @returns {PromiseLike}
- */
-CustomMap.prototype.refreshOverlayMarkers = function (overlay) {
- var promises = [];
- var self = this;
- logger.debug("Refresh overlay: " + overlay.getName());
-
- promises.push(self.getMarkerSurfaceCollection().refreshOverlayMarkers(overlay));
- var submaps = self.getSubmaps();
- for (var i = 0; i < submaps.length; i++) {
- if (submaps[i].isInitialized()) {
- promises.push(submaps[i].getMarkerSurfaceCollection().refreshOverlayMarkers(overlay));
- }
- }
- return Promise.all(promises);
-};
-
-/**
- * Returns HTML div that is attached to jQuery dialog that should be used for
- * opening submap.
- *
- * @param {number} id
- * identifier of the submap
- *
- * @returns {HTMLElement}
- */
-CustomMap.prototype.getSubmapDialogDiv = function (id) {
- var dialogDiv = this._dialogs[id];
-
- if (dialogDiv === undefined) {
- dialogDiv = document.createElement("div");
- dialogDiv.setAttribute("name", "dialog-" + id);
-
- this._dialogs[id] = dialogDiv;
-
- $(dialogDiv).dialog({
- autoOpen: false
- });
- }
- return dialogDiv;
-};
-
-/**
- * Opens a dialog with a submodel.
- *
- * @param {number} id
- * @returns {PromiseLike}
- */
-CustomMap.prototype.openSubmap = function (id) {
- var self = this;
- var submap = self.getSubmapById(id);
- if (submap === null) {
- throw new Error("Unknown submap for id: " + id);
- } else if (submap !== this) {
- var wasInitialized = submap.isInitialized();
-
- var dialogDiv = self.getSubmapDialogDiv(id);
-
- submap.open(dialogDiv);
-
- return this.openDataOverlay(self.getMapCanvas().getBackgroundId()).then(function () {
- if (!wasInitialized) {
- // now we have to visualize overlays
- return self.getVisibleDataOverlays().then(function (overlays) {
- var promises = [];
- // show overlays that should be visualized (resize or show them)
- for (var i = 0; i < overlays.length; i++) {
- promises.push(submap._showSelectedDataOverlay(overlays[i].getId(), i, overlays.length));
- }
- return Promise.all(promises);
- }).then(function () {
- return self.refreshMarkers();
- });
- }
- });
- } else {
- return Promise.resolve();
- }
-
-};
-
-/**
- *
- * @param {HTMLElement} div
- */
-CustomMap.prototype.customizeGoogleMapView = function (div) {
- var self = this;
-
- self.createMapCanvas(div);
-
- self.createLogo();
-};
-
-/**
- * Creates listeners for google.maps.Map object that will actualize the data in
- * user session.
- */
-CustomMap.prototype.createMapChangedCallbacks = function () {
- this._createMapChangedCallbacks();
- var self = this;
- var sessionData = self.getServerConnector().getSessionData(self.getProject());
-
- // listener for changing type of background overlay
- // noinspection SpellCheckingInspection
- this.getMapCanvas().addListener('maptypeid_changed', function () {
- sessionData.setSelectedBackgroundOverlay(self.getMapCanvas().getBackgroundId());
- });
-
-};
-
-/**
- * Returns submap (or this map) by id.
- *
- * @param {number|string} identifier
- * identifier of the submap
- * @returns {AbstractCustomMap} (submap or this map) with given identifier of the model
- */
-CustomMap.prototype.getSubmapById = function (identifier) {
- identifier = parseInt(identifier);
- if (this.getId() === identifier) {
- return this;
- }
- for (var i = 0; i < this.submaps.length; i++) {
- if (this.submaps[i].getId() === identifier) {
- return this.submaps[i];
- }
- }
- logger.warn("Cannot find submodel with id: " + identifier);
- return null;
-};
-
-/**
- *
- */
-CustomMap.prototype.removeSelection = function () {
- var model = this.getSubmapById(this.getActiveSubmapId());
- if (model !== null) {
- model.getMapCanvas().removeSelection();
- } else {
- throw new Error("Cannot find submap with id: " + this.getActiveSubmapId());
- }
-};
-
-/**
- * Removes overlay from visualization.
- *
- * @param {number} identifier
- * identifier of overlay to remove
- *
- * @returns {PromiseLike}
- */
-CustomMap.prototype.hideDataOverlay = function (identifier) {
- var self = this;
- logger.debug("Hiding overlay: " + identifier);
-
- if (this._selectedOverlays[identifier] !== true) {
- logger.warn("Overlay " + identifier + " is not selected");
- return Promise.resolve();
- } else {
- self._selectedOverlays[identifier] = false;
- return self.redrawSelectedDataOverlays().then(function () {
- return self.getVisibleDataOverlays();
- }).then(function (visibleDataOverlays) {
- var ids = [];
- for (var i = 0; i < visibleDataOverlays.length; i++) {
- ids.push(visibleDataOverlays[i].getId());
- }
- self.getServerConnector().getSessionData(self.getProject()).setVisibleOverlays(ids);
- return self.redrawSelectedDataOverlays();
- }).then(function () {
- return self.getProject().getDataOverlayById(identifier);
- }).then(function (overlay) {
- return self.callListeners("onHideOverlay", overlay);
- });
- }
-};
-
-/**
- * Redrawing selected overlays.
- *
- * @returns {PromiseLike|Promise}
- */
-CustomMap.prototype.redrawSelectedDataOverlays = function () {
- logger.debug("Redrawing overlays");
- var self = this;
- return self.getVisibleDataOverlays().then(function (visibleDataOverlays) {
- // show overlays that should be visualized (resize or show them)
- var promises = [];
- for (var i = 0; i < visibleDataOverlays.length; i++) {
- var overlayId = visibleDataOverlays[i].getId();
- if (self.layoutContainsOverlays(overlayId)) {
- // resize element on the map
- promises.push(self.resizeSelectedDataOverlay(overlayId, i, visibleDataOverlays.length));
- } else {
- promises.push(self.showSelectedDataOverlay(overlayId, i, visibleDataOverlays.length));
- }
- }
- return Promise.all(promises);
- }).then(function () {
- var promises = [];
- // hide overlays that were visible
- var overlays = self.getProject().getDataOverlays();
- for (var i = 0; i < overlays.length; i++) {
- var id = overlays[i].getId();
- if (!self._selectedOverlays[id] && self.layoutContainsOverlays(id)) {
- promises.push(self.hideSelectedLayout(id));
- }
- }
- return Promise.all(promises);
- });
-};
-
-/**
- * Hides overlay on the map and all submaps
- *
- * @param {number} overlayId
- * identifier of a overlay to hide
- *
- * @returns {Promise}
- */
-CustomMap.prototype.hideSelectedLayout = function (overlayId) {
- var promises = [];
- promises.push(this._hideSelectedLayout(overlayId));
- for (var i = 0; i < this.submaps.length; i++) {
- promises.push(this.submaps[i]._hideSelectedLayout(overlayId));
- }
- return Promise.all(promises);
-};
-
-/**
- * Resize(refresh) overlay on the map and all submaps. Resizing should be called
- * when number of overlays to visualize change.
- *
- * @param {number} overlayId
- * identifier of overlay to refresh
- * @param {number} index
- * position of the overlay in list of overlays that we visualize
- * @param {number} length
- * number of overlays that we currently visualize
- *
- * @returns {PromiseLike}
- */
-CustomMap.prototype.resizeSelectedDataOverlay = function (overlayId, index, length) {
- logger.debug("Resize overlay: " + overlayId);
- var promises = [];
- promises.push(this._resizeSelectedDataOverlay(overlayId, index, length));
- for (var i = 0; i < this.submaps.length; i++) {
- promises.push(this.submaps[i]._resizeSelectedDataOverlay(overlayId, index, length));
- }
- return Promise.all(promises);
-};
-
-/**
- * Show overlay on the map and all submaps.
- *
- * @param {number} overlayId
- * identifier of overlay to show
- * @param {number} index
- * position of the overlay in list of overlays that we visualize
- * @param {number} length
- * number of overlays that we currently visualize
- *
- * @returns {PromiseLike}
- */
-CustomMap.prototype.showSelectedDataOverlay = function (overlayId, index, length) {
- logger.debug("Show overlay: " + overlayId);
- var promises = [];
- promises.push(this._showSelectedDataOverlay(overlayId, index, length));
-
- for (var i = 0; i < this.submaps.length; i++) {
- promises.push(this.submaps[i]._showSelectedDataOverlay(overlayId, index, length));
- }
- return Promise.all(promises);
-};
-
-/**
- * This method checks if the overlay contains any overlays (like AliasSurface or
- * ReactionSurface) that is currently visible on the map.
- *
- * @param {number} overlayId
- * identifier of the overlay
- * @returns {boolean} <code>true</code> if the overlay contains overlays to
- * visualize, <code>false</code> otherwise
- */
-CustomMap.prototype.layoutContainsOverlays = function (overlayId) {
-
- // first, check top map
- if (this.selectedLayoutOverlays[overlayId] !== undefined && this.selectedLayoutOverlays[overlayId].length > 0) {
- return true;
- }
-
- // now check all submaps
- for (var i = 0; i < this.submaps.length; i++) {
- if (this.submaps[i].isInitialized()) {
- if (this.submaps[i].selectedLayoutOverlays[overlayId] !== undefined
- && this.submaps[i].selectedLayoutOverlays[overlayId].length > 0) {
- return true;
- }
- }
- }
- return false;
-};
-
-/**
- * Renders markers, lines, etc. for elements highlighted in OverlayCollection.
- *
- * @param {boolean} params.fitBounds <code>true</code> if the borders should fit bounds after creating
- * all elements
- * @param {AbstractDbOverlay} params.overlayCollection to be processed
- *
- * @param params
- * @returns {PromiseLike}
- */
-CustomMap.prototype.renderOverlayCollection = function (params) {
- var self = this;
- var fitBounds = params.fitBounds;
- var overlayCollection = params.overlayCollection;
-
- var elements;
- var submaps = self.getSubmaps().concat([self]);
-
- return overlayCollection.getIdentifiedElements().then(function (identifiedElements) {
- return self.appendElementsPointingToSubmap(identifiedElements, overlayCollection);
- }).then(function (identifiedElements) {
- elements = identifiedElements;
- var promises = [];
- for (var i = 0; i < submaps.length; i++) {
- promises.push(submaps[i].getMarkerSurfaceCollection().renderOverlay(identifiedElements, overlayCollection));
- }
- return Promise.all(promises);
- }).then(function () {
- return self.fetchIdentifiedElements(elements, true);
- }).then(function (fullElements) {
- var promises = [];
- if (elements.length > 0 && fitBounds) {
- for (var j = 0; j < submaps.length; j++) {
- promises.push(submaps[j].fitBounds(fullElements));
- }
- }
- return Promise.all(promises);
- });
-};
-
-/**
- *
- * @param {IdentifiedElement[]} identifiedElements
- * @param {AbstractDbOverlay} overlayDb
- * @returns {PromiseLike}
- */
-CustomMap.prototype.appendElementsPointingToSubmap = function (identifiedElements, overlayDb) {
- var self = this;
- var existingElements = {};
- var i;
- for (i = 0; i < identifiedElements.length; i++) {
- var element = identifiedElements[i];
- existingElements[element.getId() + "_" + element.getIcon() + "_" + element.getType()] = true;
- }
- return Promise.each(identifiedElements, function (ie) {
- return self.getProject().getElementsPointingToSubmap(ie.getModelId()).then(function (elementsPointingToSubmap) {
- for (var j = 0; j < elementsPointingToSubmap.length; j++) {
- var element = elementsPointingToSubmap[j];
- if (!existingElements[element.getId() + "_" + ie.getIcon() + "_" + element.getType()]) {
- existingElements[element.getId() + "_" + ie.getIcon() + "_" + element.getType()] = true;
- var newElement = new IdentifiedElement(elementsPointingToSubmap[j]);
- if (ie.getIcon() === undefined) {
- newElement.setIcon(overlayDb.getIcon(0));
- } else {
- newElement.setIcon(ie.getIcon());
- }
-
- identifiedElements.push(newElement);
- }
- }
- })
- });
-};
-
-
-/**
- * Opens {@link AbstractInfoWindow} for a marker.
- *
- * @param {Marker} [marker]
- * for which info window should be opened
- * @param {IdentifiedElement} element
- * for which info window should be opened
- *
- * @returns {PromiseLike<AbstractInfoWindow>|Promise<AbstractInfoWindow>}
- */
-CustomMap.prototype.openInfoWindowForIdentifiedElement = function (element, marker) {
- var self = this;
- var submap = self.getSubmapById(element.getModelId());
- logger.debug(element + ": Opening info window");
-
- var infoWindow;
- return submap._openInfoWindowForIdentifiedElement(element, marker).then(function () {
- infoWindow = submap.returnInfoWindowForIdentifiedElement(element);
- return self.retrieveOverlayDetailDataForElement(element, infoWindow.getOverlayFullViewArray());
- }).then(function () {
- return infoWindow;
- });
-};
-
-/**
- * Sends requests to download detailed data about element in all
- * {OverlayCollection}.
- *
- * @param {IdentifiedElement} element
- * element for which we want to have detailed information
- * @param {Object.<string,boolean>} general
- */
-CustomMap.prototype.retrieveOverlayDetailDataForElement = function (element, general) {
- var promises = [];
- if (general === undefined) {
- logger.warn("general param is undefined!");
- general = {};
- }
- var overlays = this.getDbOverlays();
- for (var i = 0; i < overlays.length; i++) {
- var overlay = overlays[i];
-
- var generalRequest = general[overlay.getName()];
- if (generalRequest === undefined) {
- logger.warn("No information about general overlay request for overlay: " + overlay.getName());
- generalRequest = false;
- }
- generalRequest = generalRequest || (!overlay.allowSearchById() && overlay.allowGeneralSearch());
-
- promises.push(overlay.getDetailDataByIdentifiedElement(element, generalRequest));
- }
- return Promise.all(promises);
-};
-
-/**
- * Returns data from all {OverlayCollection} for a given alias.
- *
- * @param {Alias} alias
- * for which overlay data will be returned
- * @param {Object.<string,boolean>} general
- * if true then all elements will be returned, if false then only ones
- * available right now in the overlay
- * @returns {Promise} of the data from all {OverlayCollection} for a given alias
- */
-CustomMap.prototype.getOverlayDataForAlias = function (alias, general) {
- var identifiedElement = new IdentifiedElement(alias);
- return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
-};
-
-/**
- * Returns data from all {OverlayCollection} for a given reaction.
- *
- * @param {Reaction} reaction
- * for which overlay data will be returned
- * @param {Object.<string,boolean>} general
- * @returns {Promise} of data from all {OverlayCollection} for a given alias
- */
-CustomMap.prototype.getOverlayDataForReaction = function (reaction, general) {
- var identifiedElement = new IdentifiedElement(reaction);
- return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
-};
-
-/**
- * Returns data from all {OverlayCollection} for a given {PointData}
- *
- * @param {Object.<string,boolean>} general
- * @param {PointData} point
- * for which overlay data will be returned
- * @returns {Promise} of data from all {OverlayCollection} for a given
- * {PointData}
- */
-CustomMap.prototype.getOverlayDataForPoint = function (point, general) {
- var identifiedElement = new IdentifiedElement(point);
- return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
-};
-
-/**
- * Returns data from all {OverlayCollection} for element identified by the
- * parameter
- *
- * @param {Object.<string,boolean>} general
- * @param {IdentifiedElement} identifiedElement
- * for which overlay data will be returned
- * @returns {Promise} of data from all {OverlayCollection} for a given
- * {IdentifiedElement}
- */
-CustomMap.prototype.getOverlayDataForIdentifiedElement = function (identifiedElement, general) {
- if (general === undefined) {
- logger.warn("general parameter must be defined");
- general = [];
- }
- var promises = [];
- var overlays = [];
- var allOverlays = this.getDbOverlays();
- for (var i = 0; i < allOverlays.length; i++) {
- var overlay = allOverlays[i];
- if (overlay.allowGeneralSearch() || overlay.allowSearchById()) {
- var generalFlag = general[overlay.getName()];
- if (generalFlag === undefined) {
- logger.warn("General flag for overlay: " + overlay.getName() + " is not defined, assuming false");
- generalFlag = false;
- }
- overlays.push(overlay);
- promises.push(overlay.getDetailDataByIdentifiedElement(identifiedElement, !overlay.allowSearchById()
- || generalFlag));
-
- }
- }
- return Promise.all(promises).then(function (values) {
- var result = [];
- for (var i = 0; i < values.length; i++) {
- result.push({
- overlay: overlays[i],
- data: values[i]
- });
- }
- return result;
- });
-};
-
-/**
- *
- * @param {string} name
- * @returns {AbstractDbOverlay}
- */
-CustomMap.prototype.getOverlayByName = function (name) {
- return this.overlayCollections[name];
-};
-
-/**
- *
- * @returns {AbstractDbOverlay[]}
- */
-CustomMap.prototype.getDbOverlays = function () {
- var result = [];
- for (var overlayName in this.overlayCollections) {
- if (this.overlayCollections.hasOwnProperty(overlayName)) {
- result.push(this.overlayCollections[overlayName]);
- }
- }
- return result;
-};
-
-/**
- * Returns {@link AbstractInfoWindow} for element identified by the parameter.
- *
- * @param {IdentifiedElement} identifiedElement
- * that determines for which element we want
- * {AbstractInfoWindow}
- * @returns {AbstractInfoWindow} for element identified by the parameter
- */
-CustomMap.prototype.getInfoWindowForIdentifiedElement = function (identifiedElement) {
- var model = this.getSubmapById(identifiedElement.modelId);
- var infoWindow = null;
- if (identifiedElement.type === "ALIAS") {
- infoWindow = model.getAliasInfoWindowById(identifiedElement.getId());
- } else if (identifiedElement.type === "POINT") {
- infoWindow = model.getPointInfoWindowById(identifiedElement.getId());
- } else if (identifiedElement.type === "REACTION") {
- infoWindow = model.getReactionInfoWindowById(identifiedElement.getId());
- } else {
- throw new Error("Unknown type of IdentifiedElement: " + identifiedElement.type);
- }
- return infoWindow;
-};
-
-/**
- *
- * @returns {number}
- */
-CustomMap.prototype.getActiveSubmapId = function () {
- return this._activeSubmapId;
-};
-
-/**
- *
- * @param {number} submapId
- */
-CustomMap.prototype.setActiveSubmapId = function (submapId) {
- this._activeSubmapId = submapId;
-};
-
-/**
- *
- * @param {Point} coordinates
- */
-CustomMap.prototype.setActiveSubmapClickCoordinates = function (coordinates) {
- if (!(coordinates instanceof Point)) {
- throw new Error("Coordinates must be provided as Point object, but found: " + coordinates);
- }
- this._activeSubmapCoordinates = coordinates;
-};
-
-/**
- *
- * @returns {Point}
- */
-CustomMap.prototype.getActiveSubmapClickCoordinates = function () {
- return this._activeSubmapCoordinates;
-};
-
-/**
- *
- * @param {string} type
- * @param {string} version
- * @returns {PromiseLike}
- */
-CustomMap.prototype.getReferenceGenome = function (type, version) {
- var self = this;
- if (self.getProject().getOrganism() === undefined) {
- return Promise.resolve(new ReferenceGenome(null));
- }
-
- if (self._referenceGenome[type] === undefined) {
- self._referenceGenome[type] = [];
- }
- if (self._referenceGenome[type][version] === undefined) {
- return self.getServerConnector().getReferenceGenome({
- type: type,
- version: version,
- organism: self.getProject().getOrganism().getResource()
- }).then(function (genome) {
- self._referenceGenome[type][version] = genome;
- return genome;
- });
- } else {
- return Promise.resolve(self._referenceGenome[type][version]);
- }
-};
-
-/**
- *
- * @returns {CustomMap}
- */
-CustomMap.prototype.getTopMap = function () {
- return this;
-};
-
-/**
- *
- * @param {HTMLElement} element
- */
-CustomMap.prototype.addControl = function (element) {
- if (this._controls[element.id] !== undefined) {
- throw new Error("Element with id " + element.id + " already added to controls");
- }
- if (ControlType[element.id] === undefined) {
- throw new Error("Unknown control type: " + element.id);
- }
- this._controls[element.id] = element;
-};
-
-/**
- *
- * @param {string} type
- * @returns {HTMLElement}
- */
-CustomMap.prototype.getControl = function (type) {
- if (ControlType[type] === undefined) {
- throw new Error("Unknown control type: " + type);
- }
- return this._controls[type];
-};
-
-/**
- *
- * @param {CommentDialog} commentDialog
- */
-CustomMap.prototype.setCommentDialog = function (commentDialog) {
- this._commentDialog = commentDialog;
-};
-
-/**
- *
- * @returns {CommentDialog}
- */
-CustomMap.prototype.getCommentDialog = function () {
- return this._commentDialog;
-};
-
-/**
- *
- * @param {ContextMenu} contextMenu
- */
-CustomMap.prototype.setContextMenu = function (contextMenu) {
- this._contextMenu = contextMenu;
-};
-
-/**
- *
- * @returns {ContextMenu}
- */
-CustomMap.prototype.getContextMenu = function () {
- return this._contextMenu;
-};
-
-/**
- *
- * @param {SelectionContextMenu} selectionContextMenu
- */
-CustomMap.prototype.setSelectionContextMenu = function (selectionContextMenu) {
- this._selectionContextMenu = selectionContextMenu;
-};
-
-/**
- *
- * @returns {SelectionContextMenu}
- */
-CustomMap.prototype.getSelectionContextMenu = function () {
- return this._selectionContextMenu;
-};
-
-/**
- *
- * @returns {PromiseLike|Promise}
- */
-CustomMap.prototype.openCommentDialog = function () {
- var self = this;
- return self.getServerConnector().getClosestElementsByCoordinates({
- modelId: this.getActiveSubmapId(),
- coordinates: this.getActiveSubmapClickCoordinates()
- }).then(function (elements) {
- var commentDialog = self.getCommentDialog();
- if (commentDialog === undefined) {
- var div = Functions.createElement({
- type: "div"
- });
- self.getElement().appendChild(div);
- commentDialog = new CommentDialog({
- element: div,
- customMap: self
- });
- self.setCommentDialog(commentDialog);
- }
- self.setCommentDialog(commentDialog);
-
- return commentDialog.open(elements);
- });
-};
-
-/**
- *
- * @param {IdentifiedElement[]} elements
- * @param {boolean} complete
- * @returns {PromiseLike<BioEntity[]> | Promise<BioEntity[]>}
- */
-CustomMap.prototype.fetchIdentifiedElements = function (elements, complete) {
- var modelIds = [];
- var modelElements = [];
- var i;
- for (i = 0; i < elements.length; i++) {
- var element = elements[i];
- if (modelElements[element.getModelId()] === undefined) {
- modelIds.push(element.getModelId());
- modelElements[element.getModelId()] = [];
- }
- modelElements[element.getModelId()].push(element);
- }
-
- var promises = [];
- for (i = 0; i < modelIds.length; i++) {
- var modelId = modelIds[i];
- promises.push(this.getSubmapById(modelId).getModel().getByIdentifiedElements(modelElements[modelId], complete));
- }
- var result = [];
- return Promise.all(promises).then(function (data) {
- for (var i = 0; i < data.length; i++) {
- result.push.apply(result, data[i]);
- }
- return result;
- });
-
-};
-
-
-/**
- *
- * @param {string} polygonData
- */
-CustomMap.prototype.setSelectedPolygon = function (polygonData) {
- this._selectedPolygon = polygonData;
-};
-
-/**
- *
- * @returns {string}
- */
-CustomMap.prototype.getSelectedPolygon = function () {
- return this._selectedPolygon;
-};
-
-/**
- *
- * @param {number} params.modelId
- * @param {IdentifiedElement} params.element
- * @param {Point} params.coordinates
- *
- * @returns {PromiseLike|Promise}
- */
-CustomMap.prototype.getDistance = function (params) {
- var self = this;
- var ie = params.element;
- var model = self.getSubmapById(ie.getModelId()).getModel();
- if (ie.getModelId() !== params.modelId) {
- throw new Error("Element and coordinates are on different maps: " + ie.getModelId() + ", " + params.modelId);
- }
- var x = params.coordinates.x;
- var y = params.coordinates.y;
- var p1 = new Point(x, y);
- return model.getByIdentifiedElement(ie).then(function (element) {
- if (element instanceof Alias) {
- if (element.getX() <= x && element.getX() + element.getWidth() >= x) {
- if (element.getY() <= y && element.getY() + element.getHeight() >= y) {
- return 0;
- } else {
- return Math.min( //
- Math.abs(element.getY() - y), //
- Math.abs(element.getY() + element.getHeight() - y) //
- );
- }
- } else if (element.getY() <= y && element.getY() + element.getHeight() >= y) {
- return Math.min( //
- Math.abs(element.getX() - x), //
- Math.abs(element.getX() + element.getWidth() - x) //
- );
- } else {
- var elementX = element.getX();
- var elementY = element.getY();
- var elementWidth = element.getWidth();
- var elementHeight = element.getHeight();
- return Math.min( //
- Functions.distance(p1, new Point(elementX, y)), //
- Functions.distance(p1, new Point(elementX + elementWidth, elementY)), //
- Functions.distance(p1, new Point(elementX, elementY + elementHeight)), //
- Functions.distance(p1, new Point(elementX + elementWidth, elementY + elementHeight)) //
- );
- }
- } else if (element instanceof Reaction) {
- var distance = Number.POSITIVE_INFINITY;
- var lines = element.getLines();
- for (var i = 0; i < lines.length; i++) {
- distance = Math.min(distance, Functions.distance(p1, lines[i]));
- }
- return distance;
- } else {
- throw new Error("Unknown element type: " + (typeof element));
- }
- });
-};
-
-/**
- *
- * @returns {Submap[]}
- */
-CustomMap.prototype.getSubmaps = function () {
- var submaps = this.submaps;
- if (submaps === undefined) {
- submaps = [];
- }
- return submaps;
-};
-
-CustomMap.prototype.destroy = function () {
- var self = this;
- AbstractCustomMap.prototype.destroy.call(self);
- var commentDialog = self.getCommentDialog();
- if (commentDialog !== undefined) {
- commentDialog.destroy();
- }
- var submaps = self.getSubmaps();
- for (var i = 0; i < submaps.length; i++) {
- submaps[i].destroy();
- }
- if (self.getContextMenu() !== undefined) {
- self.getContextMenu().destroy();
- }
- if (self.getSelectionContextMenu() !== undefined) {
- self.getSelectionContextMenu().destroy();
- }
-};
-
-/**
- *
- * @returns {Promise<DataOverlay[]>}
- */
-CustomMap.prototype.getVisibleDataOverlays = function () {
- var dataOverlayPromises = [];
-
- for (var key in this._selectedOverlays) {
- if (this._selectedOverlays.hasOwnProperty(key) && this._selectedOverlays[key] === true) {
- dataOverlayPromises.push(this.getProject().getDataOverlayById(parseInt(key)));
- }
- }
-
- return Promise.all(dataOverlayPromises).then(function (overlays) {
- overlays.sort(function (dataOverlay1, dataOverlay2) {
- if (dataOverlay1.getOrder() < dataOverlay2.getOrder())
- return -1;
- if (dataOverlay1.getOrder() > dataOverlay2.getOrder())
- return 1;
- return 0;
- });
-
- return overlays;
- });
-};
-
-
-module.exports = CustomMap;
+"use strict";
+
+var Promise = require("bluebird");
+
+var logger = require('../logger');
+var Functions = require('../Functions');
+
+var AbstractCustomMap = require('./AbstractCustomMap');
+var Alias = require('./data/Alias');
+var CommentDialog = require('../gui/CommentDialog');
+var ConfigurationType = require('../ConfigurationType');
+var ControlType = require('./ControlType');
+var CustomMapOptions = require('./CustomMapOptions');
+var GuiConnector = require('../GuiConnector');
+var IdentifiedElement = require('./data/IdentifiedElement');
+var DataOverlay = require('./data/DataOverlay');
+var Reaction = require('./data/Reaction');
+var ReferenceGenome = require('./data/ReferenceGenome');
+var SecurityError = require('../SecurityError');
+var Submap = require('./Submap');
+
+var Bounds = require('./canvas/Bounds');
+var Point = require('./canvas/Point');
+
+/**
+ * Default constructor.
+ *
+ * @param {CustomMapOptions} options
+ * CustomMapOptions object representing all parameters needed for map
+ * creation
+ *
+ * @constructor
+ * @extends AbstractCustomMap
+ */
+function CustomMap(options) {
+ //@type {HTMLElement[]}
+ this._controls = [];
+
+ if (!(options instanceof CustomMapOptions)) {
+ options = new CustomMapOptions(options);
+ }
+ AbstractCustomMap.call(this, options.getProject().getModels()[0], options);
+
+ this.registerListenerType("onBioEntityClick");
+ this.registerListenerType("onShowOverlay");
+ this.registerListenerType("onHideOverlay");
+ this.registerListenerType("onBackgroundOverlayChange");
+
+ // @type {boolean[]}
+ this._selectedOverlays = [];
+
+ this.customizeGoogleMapView(options.getElement());
+
+ this.createMapChangedCallbacks();
+
+ /**
+ *
+ * @type {Object.<string, AbstractDbOverlay>}
+ */
+ this.overlayCollections = {};
+
+ // which submap is active (where user made interaction for the last time)
+ // @type {number}
+ this._activeSubmapId = null;
+
+ // @type {boolean}
+ this.initialized = true;
+
+ // list of reference genomes
+ this._referenceGenome = [];
+
+ this.createSubmaps();
+
+ //@type {HTMLElement[]}
+ this._dialogs = [];
+}
+
+CustomMap.prototype = Object.create(AbstractCustomMap.prototype);
+CustomMap.prototype.constructor = CustomMap;
+
+/**
+ * This code must be run after the object is created. It requires to download
+ * some data via promises.
+ *
+ * @return {PromiseLike} with empty result
+ */
+CustomMap.prototype.init = function () {
+ var self = this;
+ var sessionData = self.getServerConnector().getSessionData(self.getProject());
+
+ // if we have background overlay stored in the session then restore it
+ var mapType = sessionData.getSelectedBackgroundOverlay();
+ // if we have user data overlays stored in the session then restore it
+ var ids = sessionData.getVisibleOverlays();
+ if (mapType !== undefined) {
+ ids.push(mapType);
+ }
+
+ return Promise.all([self.getMapCanvas().triggerListeners('resize'),
+ // noinspection SpellCheckingInspection
+ self.getMapCanvas().triggerListeners('maptypeid_changed'),
+ self.getMapCanvas().triggerListeners('projection_changed')
+ ]).then(function () {
+
+ // center map and zoom in to fit into browser window if there is no
+ // information about coordinates in the session
+
+ var x = self.getModel().getDefaultCenterX();
+ var y = self.getModel().getDefaultCenterY();
+ var zoom = self.getModel().getDefaultZoomLevel();
+ if (self.getServerConnector().getSessionData(self.getProject()).getCenter(self.getModel()) === undefined &&
+ (x === undefined || y === undefined || zoom === undefined ||
+ x === null || y === null || zoom === null
+ )) {
+ var bounds = new Bounds();
+ bounds.extend(self.getTopLeft());
+ bounds.extend(self.getBottomRight());
+
+ self.getMapCanvas().fitBounds(bounds);
+ }
+
+
+ return Promise.each(ids, function (overlayId) {
+ try {
+ return self.openDataOverlay(overlayId);
+ } catch (e) {
+ if (e instanceof SecurityError) {
+ logger.debug(e.message);
+ sessionData.setSelectedBackgroundOverlay(self.getProject().getDataOverlays()[0].getId());
+ } else {
+ return Promise.reject(e);
+ }
+ }
+ });
+ }).then(function () {
+ return self.getServerConnector().getLogoImg();
+ }).then(function (url) {
+ var logo2 = self.getControl(ControlType.LOGO_2_IMG);
+ if (!/^(f|ht)tps?:\/\//i.test(url)) {
+ url = GuiConnector.getImgPrefix() + url;
+ }
+ logo2.src = url;
+ logo2.setAttribute('title', self.getConfiguration().getOption(ConfigurationType.LOGO_TEXT).getValue());
+ logo2.setAttribute('alt', self.getConfiguration().getOption(ConfigurationType.LOGO_TEXT).getValue());
+ });
+};
+
+/**
+ * Create submaps.
+ */
+CustomMap.prototype.createSubmaps = function () {
+ this.submaps = [];
+ for (var i = 1; i < this.getProject().getModels().length; i++) {
+ this.submaps.push(new Submap(this, this.getProject().getModels()[i]));
+ }
+};
+
+/**
+ * Creates logo and put it on the google map.
+ */
+CustomMap.prototype.createLogo = function () {
+ var self = this;
+ var logoControlDiv2 = Functions.createElement({type: "div", index: 0});
+ var logo2 = Functions.createElement({
+ type: 'IMG',
+ style: "cursor: pointer; width: 80px",
+ id: ControlType.LOGO_2_IMG,
+ onclick: function () {
+ return self.getServerConnector().getLogoLink().then(function (url) {
+ var win = window.open(url, '_blank');
+ win.focus();
+ }).catch(GuiConnector.alert);
+ }
+ });
+ this.addControl(logo2);
+
+ logoControlDiv2.appendChild(logo2);
+
+ this.getMapCanvas().addLeftBottomControl(logoControlDiv2);
+
+ var logoControlDiv = Functions.createElement({type: "div", style: "padding: 5px", index: 1});
+ var logo = Functions.createElement({
+ type: "IMG",
+ src: GuiConnector.getImgPrefix() + GuiConnector.getLcsbLogoImg(this.bigButtons),
+ style: "cursor: pointer",
+ id: ControlType.LOGO_IMG,
+ onclick: function () {
+ var win = window.open('http://wwwen.uni.lu/lcsb/', '_blank');
+ win.focus();
+ }
+ });
+ this.addControl(logo);
+ logoControlDiv.appendChild(logo);
+
+ this.getMapCanvas().addRightBottomControl(logoControlDiv);
+};
+
+/**
+ * Clear all AbstractDbOverlay.
+ *
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.clearDbOverlays = function () {
+ var promises = [];
+ var overlays = this.getDbOverlays();
+ for (var i = 0; i < overlays.length; i++) {
+ promises.push(overlays[i].clear());
+ }
+ return Promise.all(promises);
+};
+
+/**
+ * Open data overlay given in the parameter.
+ *
+ * @param {DataOverlay|number|string} param
+ * identifier or DataOverlay identifying data overlay to open
+ *
+ * @returns {PromiseLike|Promise}
+ */
+CustomMap.prototype.openDataOverlay = function (param) {
+ logger.debug("Opening data overlay: " + param);
+
+ var self = this;
+ var identifier = param;
+ if (param instanceof DataOverlay) {
+ identifier = param.getId();
+ }
+ identifier = parseInt(identifier);
+
+ if (isNaN(identifier)) {
+ throw new Error("invalid id: " + param);
+ }
+
+ var overlayToOpen = null;
+ var overlays = self.getProject().getDataOverlays();
+ for (var j = 0; j < overlays.length; j++) {
+ var overlay = overlays[j];
+ if (overlay.getId() === identifier) {
+ overlayToOpen = overlay;
+ }
+ }
+
+ if (overlayToOpen === null) {
+ throw new SecurityError("You have no privileges for selected overlay");
+ } else {
+ return overlayToOpen.init().then(function () {
+ if (overlayToOpen.getInputDataAvailable()) {
+ if (self._selectedOverlays[identifier] === true) {
+ logger.warn("Overlay " + identifier + " already selected");
+ return Promise.resolve();
+ } else {
+ self._selectedOverlays[identifier] = true;
+ return self.getVisibleDataOverlays().then(function (visibleDataOverlays) {
+ var ids = [];
+ for (var i = 0; i < visibleDataOverlays.length; i++) {
+ ids.push(visibleDataOverlays[i].getId());
+ }
+ self.getServerConnector().getSessionData(self.getProject()).setVisibleOverlays(ids);
+ return self.redrawSelectedDataOverlays();
+ }).then(function () {
+ var backgroundToOpen;
+ var overlays = self.getProject().getDataOverlays();
+ for (var i = 0; i < overlays.length; i++) {
+ var overlay = overlays[i];
+ if (overlay.getName().toLowerCase() === "empty") {
+ backgroundToOpen = overlay;
+ }
+ }
+ if (backgroundToOpen === undefined) {
+ logger.warn("Cannot find empty background overlay");
+ } else {
+ return self.openDataOverlay(backgroundToOpen.getId());
+ }
+ });
+ }
+ } else {
+ if (identifier.toString() === self.getMapCanvas().getBackgroundId()) {
+ return Promise.resolve();
+ } else {
+ self.getMapCanvas().setBackgroundId(identifier.toString());
+
+ var submaps = self.getSubmaps();
+ for (var i = 0; i < submaps.length; i++) {
+ var submap = submaps[i];
+ submap.openDataOverlay(identifier);
+ }
+ return self.callListeners("onBackgroundOverlayChange", identifier);
+ }
+ }
+ }).then(function () {
+ return self.callListeners("onShowOverlay", overlayToOpen);
+ });
+ }
+};
+
+/**
+ * Returns {DataOverlay} that is used as a background.
+ *
+ * @returns {DataOverlay}
+ */
+CustomMap.prototype.getBackgroundDataOverlay = function () {
+ var identifier = parseInt(this.getMapCanvas().getBackgroundId());
+ var overlays = this.getProject().getDataOverlays();
+ for (var i = 0; i < overlays.length; i++) {
+ var overlay = overlays[i];
+ if (overlay.getId() === identifier) {
+ return overlay;
+ }
+ }
+ return null;
+};
+
+/**
+ * Register AbstractDbOverlay in the map.
+ *
+ * @param {AbstractDbOverlay} dbOverlay
+ * database overlay to be connected to the map
+ */
+CustomMap.prototype.registerDbOverlay = function (dbOverlay) {
+ var self = this;
+
+ this.overlayCollections[dbOverlay.getName()] = dbOverlay;
+
+
+ if (dbOverlay.getName() !== undefined) {
+ if (dbOverlay.getName() === "search" || dbOverlay.getName().indexOf("plugin") === 0) {
+ dbOverlay.addListener("onSearch", function (e) {
+ return self.renderOverlayCollection({
+ overlayCollection: dbOverlay,
+ fitBounds: e.arg.fitBounds
+ });
+ });
+ }
+ if (dbOverlay.getName() === "drug" || dbOverlay.getName() === "chemical" || dbOverlay.getName() === "mirna") {
+ dbOverlay.addListener("onSearch", function (e) {
+ return self.renderOverlayCollection({
+ overlayCollection: dbOverlay,
+ fitBounds: e.arg.fitBounds
+ });
+ });
+
+ dbOverlay.addListener("onTargetVisibilityChange", function () {
+ return self.renderOverlayCollection({
+ overlayCollection: dbOverlay,
+ fitBounds: false
+ });
+ });
+ }
+ if (dbOverlay.getName() === "comment") {
+ var listener = function () {
+ return self.renderOverlayCollection({
+ overlayCollection: dbOverlay,
+ fitBounds: false
+ });
+ };
+ dbOverlay.addListener("onRefresh", listener);
+ dbOverlay.addListener("onClear", listener);
+ }
+ }
+
+};
+
+/**
+ * Refresh comment list.
+ *
+ * @return {PromiseLike} promise that is resolved when comment list is refreshed
+ */
+CustomMap.prototype.refreshComments = function () {
+ var self = this;
+
+ var commentDbOverlay = self.getOverlayByName("comment");
+ if (commentDbOverlay !== undefined) {
+ if (self.getServerConnector().getSessionData(self.getProject()).getShowComments()) {
+ return commentDbOverlay.refresh();
+ } else {
+ return commentDbOverlay.clear();
+ }
+ }
+ throw new Error("comment DbOverlay not found");
+};
+
+/**
+ * Turns on/off drawing module on google maps.
+ */
+CustomMap.prototype.toggleDrawing = function () {
+ var submap = this.getSubmapById(this.getActiveSubmapId());
+ if (submap !== undefined) {
+ submap.getMapCanvas().toggleDrawing();
+ } else {
+ throw new Error("Cannot find submodel with id: " + this.getActiveSubmapId());
+ }
+};
+
+/**
+ *
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.refreshMarkers = function () {
+ var promises = [];
+ logger.debug("Refresh Markers: ");
+
+ var overlays = this.getDbOverlays();
+ for (var i = 0; i < overlays.length; i++) {
+ promises.push(this.refreshOverlayMarkers(overlays[i]));
+ }
+
+ return Promise.all(promises);
+};
+
+/**
+ *
+ * @param {AbstractDbOverlay} overlay
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.refreshOverlayMarkers = function (overlay) {
+ var promises = [];
+ var self = this;
+ logger.debug("Refresh overlay: " + overlay.getName());
+
+ promises.push(self.getMarkerSurfaceCollection().refreshOverlayMarkers(overlay));
+ var submaps = self.getSubmaps();
+ for (var i = 0; i < submaps.length; i++) {
+ if (submaps[i].isInitialized()) {
+ promises.push(submaps[i].getMarkerSurfaceCollection().refreshOverlayMarkers(overlay));
+ }
+ }
+ return Promise.all(promises);
+};
+
+/**
+ * Returns HTML div that is attached to jQuery dialog that should be used for
+ * opening submap.
+ *
+ * @param {number} id
+ * identifier of the submap
+ *
+ * @returns {HTMLElement}
+ */
+CustomMap.prototype.getSubmapDialogDiv = function (id) {
+ var dialogDiv = this._dialogs[id];
+
+ if (dialogDiv === undefined) {
+ dialogDiv = document.createElement("div");
+ dialogDiv.setAttribute("name", "dialog-" + id);
+
+ this._dialogs[id] = dialogDiv;
+
+ $(dialogDiv).dialog({
+ autoOpen: false
+ });
+ }
+ return dialogDiv;
+};
+
+/**
+ * Opens a dialog with a submodel.
+ *
+ * @param {number} id
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.openSubmap = function (id) {
+ var self = this;
+ var submap = self.getSubmapById(id);
+ if (submap === null) {
+ throw new Error("Unknown submap for id: " + id);
+ } else if (submap !== this) {
+ var wasInitialized = submap.isInitialized();
+
+ var dialogDiv = self.getSubmapDialogDiv(id);
+
+ submap.open(dialogDiv);
+
+ return this.openDataOverlay(self.getMapCanvas().getBackgroundId()).then(function () {
+ if (!wasInitialized) {
+ // now we have to visualize overlays
+ return self.getVisibleDataOverlays().then(function (overlays) {
+ var promises = [];
+ // show overlays that should be visualized (resize or show them)
+ for (var i = 0; i < overlays.length; i++) {
+ promises.push(submap._showSelectedDataOverlay(overlays[i].getId(), i, overlays.length));
+ }
+ return Promise.all(promises);
+ }).then(function () {
+ return self.refreshMarkers();
+ });
+ }
+ });
+ } else {
+ return Promise.resolve();
+ }
+
+};
+
+/**
+ *
+ * @param {HTMLElement} div
+ */
+CustomMap.prototype.customizeGoogleMapView = function (div) {
+ var self = this;
+
+ self.createMapCanvas(div);
+
+ self.createLogo();
+};
+
+/**
+ * Creates listeners for google.maps.Map object that will actualize the data in
+ * user session.
+ */
+CustomMap.prototype.createMapChangedCallbacks = function () {
+ this._createMapChangedCallbacks();
+ var self = this;
+ var sessionData = self.getServerConnector().getSessionData(self.getProject());
+
+ // listener for changing type of background overlay
+ // noinspection SpellCheckingInspection
+ this.getMapCanvas().addListener('maptypeid_changed', function () {
+ sessionData.setSelectedBackgroundOverlay(self.getMapCanvas().getBackgroundId());
+ });
+
+};
+
+/**
+ * Returns submap (or this map) by id.
+ *
+ * @param {number|string} identifier
+ * identifier of the submap
+ * @returns {AbstractCustomMap} (submap or this map) with given identifier of the model
+ */
+CustomMap.prototype.getSubmapById = function (identifier) {
+ identifier = parseInt(identifier);
+ if (this.getId() === identifier) {
+ return this;
+ }
+ for (var i = 0; i < this.submaps.length; i++) {
+ if (this.submaps[i].getId() === identifier) {
+ return this.submaps[i];
+ }
+ }
+ logger.warn("Cannot find submodel with id: " + identifier);
+ return null;
+};
+
+/**
+ *
+ */
+CustomMap.prototype.removeSelection = function () {
+ var model = this.getSubmapById(this.getActiveSubmapId());
+ if (model !== null) {
+ model.getMapCanvas().removeSelection();
+ } else {
+ throw new Error("Cannot find submap with id: " + this.getActiveSubmapId());
+ }
+};
+
+/**
+ * Removes overlay from visualization.
+ *
+ * @param {number} identifier
+ * identifier of overlay to remove
+ *
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.hideDataOverlay = function (identifier) {
+ var self = this;
+ logger.debug("Hiding overlay: " + identifier);
+
+ if (this._selectedOverlays[identifier] !== true) {
+ logger.warn("Overlay " + identifier + " is not selected");
+ return Promise.resolve();
+ } else {
+ self._selectedOverlays[identifier] = false;
+ return self.redrawSelectedDataOverlays().then(function () {
+ return self.getVisibleDataOverlays();
+ }).then(function (visibleDataOverlays) {
+ var ids = [];
+ for (var i = 0; i < visibleDataOverlays.length; i++) {
+ ids.push(visibleDataOverlays[i].getId());
+ }
+ self.getServerConnector().getSessionData(self.getProject()).setVisibleOverlays(ids);
+ return self.redrawSelectedDataOverlays();
+ }).then(function () {
+ return self.getProject().getDataOverlayById(identifier);
+ }).then(function (overlay) {
+ return self.callListeners("onHideOverlay", overlay);
+ });
+ }
+};
+
+/**
+ * Redrawing selected overlays.
+ *
+ * @returns {PromiseLike|Promise}
+ */
+CustomMap.prototype.redrawSelectedDataOverlays = function () {
+ logger.debug("Redrawing overlays");
+ var self = this;
+ return self.getVisibleDataOverlays().then(function (visibleDataOverlays) {
+ // show overlays that should be visualized (resize or show them)
+ var promises = [];
+ for (var i = 0; i < visibleDataOverlays.length; i++) {
+ var overlayId = visibleDataOverlays[i].getId();
+ if (self.layoutContainsOverlays(overlayId)) {
+ // resize element on the map
+ promises.push(self.resizeSelectedDataOverlay(overlayId, i, visibleDataOverlays.length));
+ } else {
+ promises.push(self.showSelectedDataOverlay(overlayId, i, visibleDataOverlays.length));
+ }
+ }
+ return Promise.all(promises);
+ }).then(function () {
+ var promises = [];
+ // hide overlays that were visible
+ var overlays = self.getProject().getDataOverlays();
+ for (var i = 0; i < overlays.length; i++) {
+ var id = overlays[i].getId();
+ if (!self._selectedOverlays[id] && self.layoutContainsOverlays(id)) {
+ promises.push(self.hideSelectedLayout(id));
+ }
+ }
+ return Promise.all(promises);
+ });
+};
+
+/**
+ * Hides overlay on the map and all submaps
+ *
+ * @param {number} overlayId
+ * identifier of a overlay to hide
+ *
+ * @returns {Promise}
+ */
+CustomMap.prototype.hideSelectedLayout = function (overlayId) {
+ var promises = [];
+ promises.push(this._hideSelectedLayout(overlayId));
+ for (var i = 0; i < this.submaps.length; i++) {
+ promises.push(this.submaps[i]._hideSelectedLayout(overlayId));
+ }
+ return Promise.all(promises);
+};
+
+/**
+ * Resize(refresh) overlay on the map and all submaps. Resizing should be called
+ * when number of overlays to visualize change.
+ *
+ * @param {number} overlayId
+ * identifier of overlay to refresh
+ * @param {number} index
+ * position of the overlay in list of overlays that we visualize
+ * @param {number} length
+ * number of overlays that we currently visualize
+ *
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.resizeSelectedDataOverlay = function (overlayId, index, length) {
+ logger.debug("Resize overlay: " + overlayId);
+ var promises = [];
+ promises.push(this._resizeSelectedDataOverlay(overlayId, index, length));
+ for (var i = 0; i < this.submaps.length; i++) {
+ promises.push(this.submaps[i]._resizeSelectedDataOverlay(overlayId, index, length));
+ }
+ return Promise.all(promises);
+};
+
+/**
+ * Show overlay on the map and all submaps.
+ *
+ * @param {number} overlayId
+ * identifier of overlay to show
+ * @param {number} index
+ * position of the overlay in list of overlays that we visualize
+ * @param {number} length
+ * number of overlays that we currently visualize
+ *
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.showSelectedDataOverlay = function (overlayId, index, length) {
+ logger.debug("Show overlay: " + overlayId);
+ var promises = [];
+ promises.push(this._showSelectedDataOverlay(overlayId, index, length));
+
+ for (var i = 0; i < this.submaps.length; i++) {
+ promises.push(this.submaps[i]._showSelectedDataOverlay(overlayId, index, length));
+ }
+ return Promise.all(promises);
+};
+
+/**
+ * This method checks if the overlay contains any overlays (like AliasSurface or
+ * ReactionSurface) that is currently visible on the map.
+ *
+ * @param {number} overlayId
+ * identifier of the overlay
+ * @returns {boolean} <code>true</code> if the overlay contains overlays to
+ * visualize, <code>false</code> otherwise
+ */
+CustomMap.prototype.layoutContainsOverlays = function (overlayId) {
+
+ // first, check top map
+ if (this.selectedLayoutOverlays[overlayId] !== undefined && this.selectedLayoutOverlays[overlayId].length > 0) {
+ return true;
+ }
+
+ // now check all submaps
+ for (var i = 0; i < this.submaps.length; i++) {
+ if (this.submaps[i].isInitialized()) {
+ if (this.submaps[i].selectedLayoutOverlays[overlayId] !== undefined
+ && this.submaps[i].selectedLayoutOverlays[overlayId].length > 0) {
+ return true;
+ }
+ }
+ }
+ return false;
+};
+
+/**
+ * Renders markers, lines, etc. for elements highlighted in OverlayCollection.
+ *
+ * @param {boolean} params.fitBounds <code>true</code> if the borders should fit bounds after creating
+ * all elements
+ * @param {AbstractDbOverlay} params.overlayCollection to be processed
+ *
+ * @param params
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.renderOverlayCollection = function (params) {
+ var self = this;
+ var fitBounds = params.fitBounds;
+ var overlayCollection = params.overlayCollection;
+
+ var elements;
+ var submaps = self.getSubmaps().concat([self]);
+
+ return overlayCollection.getIdentifiedElements().then(function (identifiedElements) {
+ return self.appendElementsPointingToSubmap(identifiedElements, overlayCollection);
+ }).then(function (identifiedElements) {
+ elements = identifiedElements;
+ var promises = [];
+ for (var i = 0; i < submaps.length; i++) {
+ promises.push(submaps[i].getMarkerSurfaceCollection().renderOverlay(identifiedElements, overlayCollection));
+ }
+ return Promise.all(promises);
+ }).then(function () {
+ return self.fetchIdentifiedElements(elements, true);
+ }).then(function (fullElements) {
+ var promises = [];
+ if (elements.length > 0 && fitBounds) {
+ for (var j = 0; j < submaps.length; j++) {
+ promises.push(submaps[j].fitBounds(fullElements));
+ }
+ }
+ return Promise.all(promises);
+ });
+};
+
+/**
+ *
+ * @param {IdentifiedElement[]} identifiedElements
+ * @param {AbstractDbOverlay} overlayDb
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.appendElementsPointingToSubmap = function (identifiedElements, overlayDb) {
+ var self = this;
+ var existingElements = {};
+ var i;
+ for (i = 0; i < identifiedElements.length; i++) {
+ var element = identifiedElements[i];
+ existingElements[element.getId() + "_" + element.getIcon() + "_" + element.getType()] = true;
+ }
+ return Promise.each(identifiedElements, function (ie) {
+ return self.getProject().getElementsPointingToSubmap(ie.getModelId()).then(function (elementsPointingToSubmap) {
+ for (var j = 0; j < elementsPointingToSubmap.length; j++) {
+ var element = elementsPointingToSubmap[j];
+ if (!existingElements[element.getId() + "_" + ie.getIcon() + "_" + element.getType()]) {
+ existingElements[element.getId() + "_" + ie.getIcon() + "_" + element.getType()] = true;
+ var newElement = new IdentifiedElement(elementsPointingToSubmap[j]);
+ if (ie.getIcon() === undefined) {
+ newElement.setIcon(overlayDb.getIcon(0));
+ } else {
+ newElement.setIcon(ie.getIcon());
+ }
+
+ identifiedElements.push(newElement);
+ }
+ }
+ })
+ });
+};
+
+
+/**
+ * Opens {@link AbstractInfoWindow} for a marker.
+ *
+ * @param {Marker} [marker]
+ * for which info window should be opened
+ * @param {IdentifiedElement} element
+ * for which info window should be opened
+ *
+ * @returns {PromiseLike<AbstractInfoWindow>|Promise<AbstractInfoWindow>}
+ */
+CustomMap.prototype.openInfoWindowForIdentifiedElement = function (element, marker) {
+ var self = this;
+ var submap = self.getSubmapById(element.getModelId());
+ logger.debug(element + ": Opening info window");
+
+ var infoWindow;
+ return submap._openInfoWindowForIdentifiedElement(element, marker).then(function () {
+ infoWindow = submap.returnInfoWindowForIdentifiedElement(element);
+ return self.retrieveOverlayDetailDataForElement(element, infoWindow.getOverlayFullViewArray());
+ }).then(function () {
+ return infoWindow;
+ });
+};
+
+/**
+ * Sends requests to download detailed data about element in all
+ * {OverlayCollection}.
+ *
+ * @param {IdentifiedElement} element
+ * element for which we want to have detailed information
+ * @param {Object.<string,boolean>} general
+ */
+CustomMap.prototype.retrieveOverlayDetailDataForElement = function (element, general) {
+ var promises = [];
+ if (general === undefined) {
+ logger.warn("general param is undefined!");
+ general = {};
+ }
+ var overlays = this.getDbOverlays();
+ for (var i = 0; i < overlays.length; i++) {
+ var overlay = overlays[i];
+
+ var generalRequest = general[overlay.getName()];
+ if (generalRequest === undefined) {
+ logger.warn("No information about general overlay request for overlay: " + overlay.getName());
+ generalRequest = false;
+ }
+ generalRequest = generalRequest || (!overlay.allowSearchById() && overlay.allowGeneralSearch());
+
+ promises.push(overlay.getDetailDataByIdentifiedElement(element, generalRequest));
+ }
+ return Promise.all(promises);
+};
+
+/**
+ * Returns data from all {OverlayCollection} for a given alias.
+ *
+ * @param {Alias} alias
+ * for which overlay data will be returned
+ * @param {Object.<string,boolean>} general
+ * if true then all elements will be returned, if false then only ones
+ * available right now in the overlay
+ * @returns {Promise} of the data from all {OverlayCollection} for a given alias
+ */
+CustomMap.prototype.getOverlayDataForAlias = function (alias, general) {
+ var identifiedElement = new IdentifiedElement(alias);
+ return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
+};
+
+/**
+ * Returns data from all {OverlayCollection} for a given reaction.
+ *
+ * @param {Reaction} reaction
+ * for which overlay data will be returned
+ * @param {Object.<string,boolean>} general
+ * @returns {Promise} of data from all {OverlayCollection} for a given alias
+ */
+CustomMap.prototype.getOverlayDataForReaction = function (reaction, general) {
+ var identifiedElement = new IdentifiedElement(reaction);
+ return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
+};
+
+/**
+ * Returns data from all {OverlayCollection} for a given {PointData}
+ *
+ * @param {Object.<string,boolean>} general
+ * @param {PointData} point
+ * for which overlay data will be returned
+ * @returns {Promise} of data from all {OverlayCollection} for a given
+ * {PointData}
+ */
+CustomMap.prototype.getOverlayDataForPoint = function (point, general) {
+ var identifiedElement = new IdentifiedElement(point);
+ return this.getOverlayDataForIdentifiedElement(identifiedElement, general);
+};
+
+/**
+ * Returns data from all {OverlayCollection} for element identified by the
+ * parameter
+ *
+ * @param {Object.<string,boolean>} general
+ * @param {IdentifiedElement} identifiedElement
+ * for which overlay data will be returned
+ * @returns {Promise} of data from all {OverlayCollection} for a given
+ * {IdentifiedElement}
+ */
+CustomMap.prototype.getOverlayDataForIdentifiedElement = function (identifiedElement, general) {
+ if (general === undefined) {
+ logger.warn("general parameter must be defined");
+ general = [];
+ }
+ var promises = [];
+ var overlays = [];
+ var allOverlays = this.getDbOverlays();
+ for (var i = 0; i < allOverlays.length; i++) {
+ var overlay = allOverlays[i];
+ if (overlay.allowGeneralSearch() || overlay.allowSearchById()) {
+ var generalFlag = general[overlay.getName()];
+ if (generalFlag === undefined) {
+ logger.warn("General flag for overlay: " + overlay.getName() + " is not defined, assuming false");
+ generalFlag = false;
+ }
+ overlays.push(overlay);
+ promises.push(overlay.getDetailDataByIdentifiedElement(identifiedElement, !overlay.allowSearchById()
+ || generalFlag));
+
+ }
+ }
+ return Promise.all(promises).then(function (values) {
+ var result = [];
+ for (var i = 0; i < values.length; i++) {
+ result.push({
+ overlay: overlays[i],
+ data: values[i]
+ });
+ }
+ return result;
+ });
+};
+
+/**
+ *
+ * @param {string} name
+ * @returns {AbstractDbOverlay}
+ */
+CustomMap.prototype.getOverlayByName = function (name) {
+ return this.overlayCollections[name];
+};
+
+/**
+ *
+ * @returns {AbstractDbOverlay[]}
+ */
+CustomMap.prototype.getDbOverlays = function () {
+ var result = [];
+ for (var overlayName in this.overlayCollections) {
+ if (this.overlayCollections.hasOwnProperty(overlayName)) {
+ result.push(this.overlayCollections[overlayName]);
+ }
+ }
+ return result;
+};
+
+/**
+ * Returns {@link AbstractInfoWindow} for element identified by the parameter.
+ *
+ * @param {IdentifiedElement} identifiedElement
+ * that determines for which element we want
+ * {AbstractInfoWindow}
+ * @returns {AbstractInfoWindow} for element identified by the parameter
+ */
+CustomMap.prototype.getInfoWindowForIdentifiedElement = function (identifiedElement) {
+ var model = this.getSubmapById(identifiedElement.modelId);
+ var infoWindow = null;
+ if (identifiedElement.type === "ALIAS") {
+ infoWindow = model.getAliasInfoWindowById(identifiedElement.getId());
+ } else if (identifiedElement.type === "POINT") {
+ infoWindow = model.getPointInfoWindowById(identifiedElement.getId());
+ } else if (identifiedElement.type === "REACTION") {
+ infoWindow = model.getReactionInfoWindowById(identifiedElement.getId());
+ } else {
+ throw new Error("Unknown type of IdentifiedElement: " + identifiedElement.type);
+ }
+ return infoWindow;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+CustomMap.prototype.getActiveSubmapId = function () {
+ return this._activeSubmapId;
+};
+
+/**
+ *
+ * @param {number} submapId
+ */
+CustomMap.prototype.setActiveSubmapId = function (submapId) {
+ this._activeSubmapId = submapId;
+};
+
+/**
+ *
+ * @param {Point} coordinates
+ */
+CustomMap.prototype.setActiveSubmapClickCoordinates = function (coordinates) {
+ if (!(coordinates instanceof Point)) {
+ throw new Error("Coordinates must be provided as Point object, but found: " + coordinates);
+ }
+ this._activeSubmapCoordinates = coordinates;
+};
+
+/**
+ *
+ * @returns {Point}
+ */
+CustomMap.prototype.getActiveSubmapClickCoordinates = function () {
+ return this._activeSubmapCoordinates;
+};
+
+/**
+ *
+ * @param {string} type
+ * @param {string} version
+ * @returns {PromiseLike}
+ */
+CustomMap.prototype.getReferenceGenome = function (type, version) {
+ var self = this;
+ if (self.getProject().getOrganism() === undefined) {
+ return Promise.resolve(new ReferenceGenome(null));
+ }
+
+ if (self._referenceGenome[type] === undefined) {
+ self._referenceGenome[type] = [];
+ }
+ if (self._referenceGenome[type][version] === undefined) {
+ return self.getServerConnector().getReferenceGenome({
+ type: type,
+ version: version,
+ organism: self.getProject().getOrganism().getResource()
+ }).then(function (genome) {
+ self._referenceGenome[type][version] = genome;
+ return genome;
+ });
+ } else {
+ return Promise.resolve(self._referenceGenome[type][version]);
+ }
+};
+
+/**
+ *
+ * @returns {CustomMap}
+ */
+CustomMap.prototype.getTopMap = function () {
+ return this;
+};
+
+/**
+ *
+ * @param {HTMLElement} element
+ */
+CustomMap.prototype.addControl = function (element) {
+ if (this._controls[element.id] !== undefined) {
+ throw new Error("Element with id " + element.id + " already added to controls");
+ }
+ if (ControlType[element.id] === undefined) {
+ throw new Error("Unknown control type: " + element.id);
+ }
+ this._controls[element.id] = element;
+};
+
+/**
+ *
+ * @param {string} type
+ * @returns {HTMLElement}
+ */
+CustomMap.prototype.getControl = function (type) {
+ if (ControlType[type] === undefined) {
+ throw new Error("Unknown control type: " + type);
+ }
+ return this._controls[type];
+};
+
+/**
+ *
+ * @param {CommentDialog} commentDialog
+ */
+CustomMap.prototype.setCommentDialog = function (commentDialog) {
+ this._commentDialog = commentDialog;
+};
+
+/**
+ *
+ * @returns {CommentDialog}
+ */
+CustomMap.prototype.getCommentDialog = function () {
+ return this._commentDialog;
+};
+
+/**
+ *
+ * @param {ContextMenu} contextMenu
+ */
+CustomMap.prototype.setContextMenu = function (contextMenu) {
+ this._contextMenu = contextMenu;
+};
+
+/**
+ *
+ * @returns {ContextMenu}
+ */
+CustomMap.prototype.getContextMenu = function () {
+ return this._contextMenu;
+};
+
+/**
+ *
+ * @param {SelectionContextMenu} selectionContextMenu
+ */
+CustomMap.prototype.setSelectionContextMenu = function (selectionContextMenu) {
+ this._selectionContextMenu = selectionContextMenu;
+};
+
+/**
+ *
+ * @returns {SelectionContextMenu}
+ */
+CustomMap.prototype.getSelectionContextMenu = function () {
+ return this._selectionContextMenu;
+};
+
+/**
+ *
+ * @returns {PromiseLike|Promise}
+ */
+CustomMap.prototype.openCommentDialog = function () {
+ var self = this;
+ return self.getServerConnector().getClosestElementsByCoordinates({
+ modelId: this.getActiveSubmapId(),
+ coordinates: this.getActiveSubmapClickCoordinates()
+ }).then(function (elements) {
+ var commentDialog = self.getCommentDialog();
+ if (commentDialog === undefined) {
+ var div = Functions.createElement({
+ type: "div"
+ });
+ self.getElement().appendChild(div);
+ commentDialog = new CommentDialog({
+ element: div,
+ customMap: self
+ });
+ self.setCommentDialog(commentDialog);
+ }
+ self.setCommentDialog(commentDialog);
+
+ return commentDialog.open(elements);
+ });
+};
+
+/**
+ *
+ * @param {IdentifiedElement[]} elements
+ * @param {boolean} complete
+ * @returns {PromiseLike<BioEntity[]> | Promise<BioEntity[]>}
+ */
+CustomMap.prototype.fetchIdentifiedElements = function (elements, complete) {
+ var modelIds = [];
+ var modelElements = [];
+ var i;
+ for (i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ if (modelElements[element.getModelId()] === undefined) {
+ modelIds.push(element.getModelId());
+ modelElements[element.getModelId()] = [];
+ }
+ modelElements[element.getModelId()].push(element);
+ }
+
+ var promises = [];
+ for (i = 0; i < modelIds.length; i++) {
+ var modelId = modelIds[i];
+ promises.push(this.getSubmapById(modelId).getModel().getByIdentifiedElements(modelElements[modelId], complete));
+ }
+ var result = [];
+ return Promise.all(promises).then(function (data) {
+ for (var i = 0; i < data.length; i++) {
+ result.push.apply(result, data[i]);
+ }
+ return result;
+ });
+
+};
+
+
+/**
+ *
+ * @param {string} polygonData
+ */
+CustomMap.prototype.setSelectedPolygon = function (polygonData) {
+ this._selectedPolygon = polygonData;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+CustomMap.prototype.getSelectedPolygon = function () {
+ return this._selectedPolygon;
+};
+
+/**
+ *
+ * @param {number} params.modelId
+ * @param {IdentifiedElement} params.element
+ * @param {Point} params.coordinates
+ *
+ * @returns {PromiseLike|Promise}
+ */
+CustomMap.prototype.getDistance = function (params) {
+ var self = this;
+ var ie = params.element;
+ var model = self.getSubmapById(ie.getModelId()).getModel();
+ if (ie.getModelId() !== params.modelId) {
+ throw new Error("Element and coordinates are on different maps: " + ie.getModelId() + ", " + params.modelId);
+ }
+ var x = params.coordinates.x;
+ var y = params.coordinates.y;
+ var p1 = new Point(x, y);
+ return model.getByIdentifiedElement(ie).then(function (element) {
+ if (element instanceof Alias) {
+ if (element.getX() <= x && element.getX() + element.getWidth() >= x) {
+ if (element.getY() <= y && element.getY() + element.getHeight() >= y) {
+ return 0;
+ } else {
+ return Math.min( //
+ Math.abs(element.getY() - y), //
+ Math.abs(element.getY() + element.getHeight() - y) //
+ );
+ }
+ } else if (element.getY() <= y && element.getY() + element.getHeight() >= y) {
+ return Math.min( //
+ Math.abs(element.getX() - x), //
+ Math.abs(element.getX() + element.getWidth() - x) //
+ );
+ } else {
+ var elementX = element.getX();
+ var elementY = element.getY();
+ var elementWidth = element.getWidth();
+ var elementHeight = element.getHeight();
+ return Math.min( //
+ Functions.distance(p1, new Point(elementX, y)), //
+ Functions.distance(p1, new Point(elementX + elementWidth, elementY)), //
+ Functions.distance(p1, new Point(elementX, elementY + elementHeight)), //
+ Functions.distance(p1, new Point(elementX + elementWidth, elementY + elementHeight)) //
+ );
+ }
+ } else if (element instanceof Reaction) {
+ var distance = Number.POSITIVE_INFINITY;
+ var lines = element.getLines();
+ for (var i = 0; i < lines.length; i++) {
+ distance = Math.min(distance, Functions.distance(p1, lines[i]));
+ }
+ return distance;
+ } else {
+ throw new Error("Unknown element type: " + (typeof element));
+ }
+ });
+};
+
+/**
+ *
+ * @returns {Submap[]}
+ */
+CustomMap.prototype.getSubmaps = function () {
+ var submaps = this.submaps;
+ if (submaps === undefined) {
+ submaps = [];
+ }
+ return submaps;
+};
+
+CustomMap.prototype.destroy = function () {
+ var self = this;
+ AbstractCustomMap.prototype.destroy.call(self);
+ var commentDialog = self.getCommentDialog();
+ if (commentDialog !== undefined) {
+ commentDialog.destroy();
+ }
+ var submaps = self.getSubmaps();
+ for (var i = 0; i < submaps.length; i++) {
+ submaps[i].destroy();
+ }
+ if (self.getContextMenu() !== undefined) {
+ self.getContextMenu().destroy();
+ }
+ if (self.getSelectionContextMenu() !== undefined) {
+ self.getSelectionContextMenu().destroy();
+ }
+};
+
+/**
+ *
+ * @returns {Promise<DataOverlay[]>}
+ */
+CustomMap.prototype.getVisibleDataOverlays = function () {
+ var dataOverlayPromises = [];
+
+ for (var key in this._selectedOverlays) {
+ if (this._selectedOverlays.hasOwnProperty(key) && this._selectedOverlays[key] === true) {
+ dataOverlayPromises.push(this.getProject().getDataOverlayById(parseInt(key)));
+ }
+ }
+
+ return Promise.all(dataOverlayPromises).then(function (overlays) {
+ overlays.sort(function (dataOverlay1, dataOverlay2) {
+ if (dataOverlay1.getOrder() < dataOverlay2.getOrder())
+ return -1;
+ if (dataOverlay1.getOrder() > dataOverlay2.getOrder())
+ return 1;
+ return 0;
+ });
+
+ return overlays;
+ });
+};
+
+
+module.exports = CustomMap;
diff --git a/frontend-js/src/main/js/map/CustomMapOptions.js b/frontend-js/src/main/js/map/CustomMapOptions.js
index e992f2a2e7237dce44b26653de114abe9e2ce35f..900823b53a48303f61ae66ea47b9d544e89aed58 100644
--- a/frontend-js/src/main/js/map/CustomMapOptions.js
+++ b/frontend-js/src/main/js/map/CustomMapOptions.js
@@ -1,170 +1,170 @@
-"use strict";
-
-var logger = require('./../logger');
-
-/**
- * Object representing information needed for constructing {@link CustomMap}
- * objects.
- *
- * @param {Object|CustomMapOptions} params
- * @param {HTMLElement} params.element
- * @param {Configuration} params.configuration
- * @param {Project} [params.project]
- * @param {string} params.projectId
- * @param {ServerConnector} params.serverConnector
- * @param {boolean} [params.bigLogo]
- * @param {boolean} [params.debug]
- * @param {Object} [params.plugins]
- *
- * @constructor
- */
-function CustomMapOptions(params) {
- if (params.element === undefined) {
- throw new Error("element must be defined");
- }
- this.setElement(params.element);
- this.setConfiguration(params.configuration);
- this.setProject(params.project);
- this.setProjectId(params.projectId);
- this.setServerConnector(params.serverConnector);
-
- if (params.bigLogo !== undefined) {
- if (typeof params.bigLogo === "boolean") {
- this._bigLogo = params.bigLogo;
- } else {
- logger.warn("bigLogo must be of type boolean");
- this._bigLogo = false;
- }
- } else {
- this._bigLogo = false;
- }
-
- this.setDebug(params.debug);
- this.setPlugins(params.plugins);
-
-}
-
-/**
- *
- * @returns {boolean}
- */
-CustomMapOptions.prototype.isBigLogo = function () {
- return this._bigLogo;
-};
-
-/**
- *
- * @returns {Project}
- */
-CustomMapOptions.prototype.getProject = function () {
- return this._project;
-};
-
-/**
- *
- * @param {Project} project
- */
-CustomMapOptions.prototype.setProject = function (project) {
- this._project = project;
-};
-
-/**
- *
- * @returns {ServerConnector}
- */
-CustomMapOptions.prototype.getServerConnector = function () {
- return this._serverConnector;
-};
-
-/**
- *
- * @param {ServerConnector} serverConnector
- */
-CustomMapOptions.prototype.setServerConnector = function (serverConnector) {
- this._serverConnector = serverConnector;
-};
-
-CustomMapOptions.prototype.getPlugins = function () {
- return this._plugins;
-};
-CustomMapOptions.prototype.setPlugins = function (plugins) {
- if (plugins === undefined) {
- plugins = [];
- }
- this._plugins = plugins;
-};
-
-/**
- *
- * @returns {Configuration}
- */
-CustomMapOptions.prototype.getConfiguration = function () {
- return this._configuration;
-};
-
-/**
- *
- * @param {Configuration} configuration
- */
-CustomMapOptions.prototype.setConfiguration = function (configuration) {
- this._configuration = configuration;
-};
-
-/**
- *
- * @returns {string}
- */
-CustomMapOptions.prototype.getProjectId = function () {
- if (this.getProject() !== undefined) {
- return this.getProject().getProjectId();
- } else {
- return this._projectId;
- }
-};
-
-/**
- *
- * @param {string} projectId
- */
-CustomMapOptions.prototype.setProjectId = function (projectId) {
- this._projectId = projectId;
-};
-
-/**
- *
- * @param {boolean} debug
- */
-CustomMapOptions.prototype.setDebug = function (debug) {
- if (debug !== undefined) {
- if (typeof debug !== "boolean") {
- logger.warn("Params must be boolean");
- }
- this._debug = debug;
- }
-};
-
-/**
- *
- * @returns {boolean}
- */
-CustomMapOptions.prototype.isDebug = function () {
- return this._debug === true;
-};
-
-/**
- *
- * @param {HTMLElement} element
- */
-CustomMapOptions.prototype.setElement = function (element) {
- this._element = element;
-};
-
-/**
- *
- * @returns {HTMLElement}
- */
-CustomMapOptions.prototype.getElement = function () {
- return this._element;
-};
-
-module.exports = CustomMapOptions;
+"use strict";
+
+var logger = require('./../logger');
+
+/**
+ * Object representing information needed for constructing {@link CustomMap}
+ * objects.
+ *
+ * @param {Object|CustomMapOptions} params
+ * @param {HTMLElement} params.element
+ * @param {Configuration} params.configuration
+ * @param {Project} [params.project]
+ * @param {string} params.projectId
+ * @param {ServerConnector} params.serverConnector
+ * @param {boolean} [params.bigLogo]
+ * @param {boolean} [params.debug]
+ * @param {Object} [params.plugins]
+ *
+ * @constructor
+ */
+function CustomMapOptions(params) {
+ if (params.element === undefined) {
+ throw new Error("element must be defined");
+ }
+ this.setElement(params.element);
+ this.setConfiguration(params.configuration);
+ this.setProject(params.project);
+ this.setProjectId(params.projectId);
+ this.setServerConnector(params.serverConnector);
+
+ if (params.bigLogo !== undefined) {
+ if (typeof params.bigLogo === "boolean") {
+ this._bigLogo = params.bigLogo;
+ } else {
+ logger.warn("bigLogo must be of type boolean");
+ this._bigLogo = false;
+ }
+ } else {
+ this._bigLogo = false;
+ }
+
+ this.setDebug(params.debug);
+ this.setPlugins(params.plugins);
+
+}
+
+/**
+ *
+ * @returns {boolean}
+ */
+CustomMapOptions.prototype.isBigLogo = function () {
+ return this._bigLogo;
+};
+
+/**
+ *
+ * @returns {Project}
+ */
+CustomMapOptions.prototype.getProject = function () {
+ return this._project;
+};
+
+/**
+ *
+ * @param {Project} project
+ */
+CustomMapOptions.prototype.setProject = function (project) {
+ this._project = project;
+};
+
+/**
+ *
+ * @returns {ServerConnector}
+ */
+CustomMapOptions.prototype.getServerConnector = function () {
+ return this._serverConnector;
+};
+
+/**
+ *
+ * @param {ServerConnector} serverConnector
+ */
+CustomMapOptions.prototype.setServerConnector = function (serverConnector) {
+ this._serverConnector = serverConnector;
+};
+
+CustomMapOptions.prototype.getPlugins = function () {
+ return this._plugins;
+};
+CustomMapOptions.prototype.setPlugins = function (plugins) {
+ if (plugins === undefined) {
+ plugins = [];
+ }
+ this._plugins = plugins;
+};
+
+/**
+ *
+ * @returns {Configuration}
+ */
+CustomMapOptions.prototype.getConfiguration = function () {
+ return this._configuration;
+};
+
+/**
+ *
+ * @param {Configuration} configuration
+ */
+CustomMapOptions.prototype.setConfiguration = function (configuration) {
+ this._configuration = configuration;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+CustomMapOptions.prototype.getProjectId = function () {
+ if (this.getProject() !== undefined) {
+ return this.getProject().getProjectId();
+ } else {
+ return this._projectId;
+ }
+};
+
+/**
+ *
+ * @param {string} projectId
+ */
+CustomMapOptions.prototype.setProjectId = function (projectId) {
+ this._projectId = projectId;
+};
+
+/**
+ *
+ * @param {boolean} debug
+ */
+CustomMapOptions.prototype.setDebug = function (debug) {
+ if (debug !== undefined) {
+ if (typeof debug !== "boolean") {
+ logger.warn("Params must be boolean");
+ }
+ this._debug = debug;
+ }
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+CustomMapOptions.prototype.isDebug = function () {
+ return this._debug === true;
+};
+
+/**
+ *
+ * @param {HTMLElement} element
+ */
+CustomMapOptions.prototype.setElement = function (element) {
+ this._element = element;
+};
+
+/**
+ *
+ * @returns {HTMLElement}
+ */
+CustomMapOptions.prototype.getElement = function () {
+ return this._element;
+};
+
+module.exports = CustomMapOptions;
diff --git a/frontend-js/src/main/js/map/OverlayParser.js b/frontend-js/src/main/js/map/OverlayParser.js
index 239de8d595203d790a3d6ec10662ce9c0c8c1dfe..b785ca26b205f407e0c8c9254f1272fa34ee23a0 100644
--- a/frontend-js/src/main/js/map/OverlayParser.js
+++ b/frontend-js/src/main/js/map/OverlayParser.js
@@ -1,88 +1,88 @@
-"use strict";
-
-var logger = require('./../logger');
-var DataOverlay = require('./data/DataOverlay');
-var TextDecoder = require('text-encoding').TextDecoder;
-
-function OverlayParser() {
-}
-
-/**
- *
- * @param {string| Uint8Array | ArrayBuffer} content
- * @returns {string}
- * @private
- */
-OverlayParser.prototype._extractContent = function (content) {
- if (content instanceof Uint8Array || content instanceof ArrayBuffer) {
- content = new TextDecoder("UTF8").decode(content);
- }
- return content;
-};
-
-/**
- *
- * @param {string| Uint8Array|ArrayBuffer} content
- * @returns {DataOverlay}
- */
-OverlayParser.prototype.parse = function (content) {
- content = this._extractContent(content);
- var data = {content: content};
- var lines = content.split("\n");
- for (var i = 0; i < lines.length; i++) {
- var line = lines[i];
- if (line.indexOf("#") === 0) {
- if (line.indexOf("=") > 0) {
- var name = line.substring(1, line.indexOf("=")).trim();
- var value = line.substring(line.indexOf("=") + 1).trim();
- if (name === "NAME") {
- data.name = value;
- } else if (name === "DESCRIPTION") {
- data.description = value;
- } else if (name === "TYPE") {
- data.type = value;
- }
- } else {
- logger.warn("Invalid overlay header line: " + line);
- }
- } else {
- break;
- }
- }
-
- return new DataOverlay(data);
-};
-
-/**
- *
- * @param {string| Uint8Array | ArrayBuffer} content
- * @returns {boolean}
- */
-OverlayParser.prototype.containsMixedNewLineCharacters = function (content) {
- content = this._extractContent(content);
- var newLineRegEx = /[\r\n]+/g;
- var match = newLineRegEx.exec(content);
- var newLineFormats = {};
- var counter = 0;
- while (match !== null && match !== undefined) {
- var foundMultiplication = false;
- var key = '';
- //this is just a heuristic - let's assume there are at most 10 empty lines in a file
- for (var i = 0; i < 10; i++) {
- key += match[0];
- if (newLineFormats[key]) {
- foundMultiplication = true;
- } else {
- newLineFormats[key] = true;
- }
- }
- if (!foundMultiplication) {
- counter++;
- }
- match = newLineRegEx.exec(content);
- }
- return counter > 1;
-};
-
-
-module.exports = OverlayParser;
+"use strict";
+
+var logger = require('./../logger');
+var DataOverlay = require('./data/DataOverlay');
+var TextDecoder = require('text-encoding').TextDecoder;
+
+function OverlayParser() {
+}
+
+/**
+ *
+ * @param {string| Uint8Array | ArrayBuffer} content
+ * @returns {string}
+ * @private
+ */
+OverlayParser.prototype._extractContent = function (content) {
+ if (content instanceof Uint8Array || content instanceof ArrayBuffer) {
+ content = new TextDecoder("UTF8").decode(content);
+ }
+ return content;
+};
+
+/**
+ *
+ * @param {string| Uint8Array|ArrayBuffer} content
+ * @returns {DataOverlay}
+ */
+OverlayParser.prototype.parse = function (content) {
+ content = this._extractContent(content);
+ var data = {content: content};
+ var lines = content.split("\n");
+ for (var i = 0; i < lines.length; i++) {
+ var line = lines[i];
+ if (line.indexOf("#") === 0) {
+ if (line.indexOf("=") > 0) {
+ var name = line.substring(1, line.indexOf("=")).trim();
+ var value = line.substring(line.indexOf("=") + 1).trim();
+ if (name === "NAME") {
+ data.name = value;
+ } else if (name === "DESCRIPTION") {
+ data.description = value;
+ } else if (name === "TYPE") {
+ data.type = value;
+ }
+ } else {
+ logger.warn("Invalid overlay header line: " + line);
+ }
+ } else {
+ break;
+ }
+ }
+
+ return new DataOverlay(data);
+};
+
+/**
+ *
+ * @param {string| Uint8Array | ArrayBuffer} content
+ * @returns {boolean}
+ */
+OverlayParser.prototype.containsMixedNewLineCharacters = function (content) {
+ content = this._extractContent(content);
+ var newLineRegEx = /[\r\n]+/g;
+ var match = newLineRegEx.exec(content);
+ var newLineFormats = {};
+ var counter = 0;
+ while (match !== null && match !== undefined) {
+ var foundMultiplication = false;
+ var key = '';
+ //this is just a heuristic - let's assume there are at most 10 empty lines in a file
+ for (var i = 0; i < 10; i++) {
+ key += match[0];
+ if (newLineFormats[key]) {
+ foundMultiplication = true;
+ } else {
+ newLineFormats[key] = true;
+ }
+ }
+ if (!foundMultiplication) {
+ counter++;
+ }
+ match = newLineRegEx.exec(content);
+ }
+ return counter > 1;
+};
+
+
+module.exports = OverlayParser;
diff --git a/frontend-js/src/main/js/map/Submap.js b/frontend-js/src/main/js/map/Submap.js
index 4811edf5c65d21de79eaa296ef65a820bfb5c222..59ebc5073017f87586196b571f0eece06c90de12 100644
--- a/frontend-js/src/main/js/map/Submap.js
+++ b/frontend-js/src/main/js/map/Submap.js
@@ -1,145 +1,145 @@
-"use strict";
-
-/* exported logger */
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../logger');
-var AbstractCustomMap = require('./AbstractCustomMap');
-var CustomMapOptions = require('./CustomMapOptions');
-
-/**
- * Constructor of a submap. Submaps are created on application start. But dialog
- * (popup window) is initialized on demand using init function.
- *
- * @param {CustomMap} customMap
- * parent CustomMap
- * @param {MapModel} model
- *
- * @constructor
- * @extends AbstractCustomMap
- */
-function Submap(customMap, model) {
- this.setCustomMap(customMap);
-
- AbstractCustomMap.call(this, model, new CustomMapOptions({
- element: customMap.getElement(),
- bigLogo: customMap.isBigLogo(),
- project: customMap.getProject(),
- configuration: customMap.getConfiguration(),
- projectId: customMap.getProject().getProjectId(),
- debug: customMap.isDebug(),
- serverConnector: customMap.getServerConnector()
- }));
-
- this.initialized = false;
-}
-
-// implementation of object inheritance
-Submap.prototype = Object.create(AbstractCustomMap.prototype);
-Submap.prototype.constructor = Submap;
-
-/**
- * This method initializes submap with gui component. Before this point submap
- * is created and contains data, but cannot be visualized in the browser.
- *
- * @param {HTMLElement} htmlTag
- * html div tag where google map should be placed
- */
-Submap.prototype.open = function (htmlTag) {
- var self = this;
-
- if (!this.isInitialized()) {
- self.setElement(htmlTag);
-
- var contentDiv = document.createElement("div");
- contentDiv.setAttribute("name", "submap-div-" + self.getId());
- contentDiv.style.width = "100%";
- contentDiv.style.height = "100%";
- htmlTag.appendChild(contentDiv);
-
- var mapDiv = document.createElement("div");
- mapDiv.style.width = "100%";
- mapDiv.style.height = "100%";
- contentDiv.appendChild(mapDiv);
-
- $(self.getElement()).dialog({
- title: self.getModel().getName(),
- width: Math.floor(window.innerWidth * 2 / 3),
- height: Math.floor(window.innerHeight * 2 / 3),
- position: {
- my: "center",
- at: "center",
- of: $(self.getTopMap().getElement())
- },
- resize: function () {
- self.getMapCanvas().triggerListeners('resize');
- }
- });
-
- $(self.getElement()).dialog("open");
-
- self.createMapCanvas(mapDiv);
-
- self._createMapChangedCallbacks();
-
- self.getMapCanvas().triggerListeners('resize');
- self.getMapCanvas().setBackgroundId(self.getTopMap().getBackgroundDataOverlay().getId());
-
- self.initialized = true;
- } else {
- $(self.getElement()).dialog("open");
- }
-
-};
-
-/**
- *
- * @param {number} identifier
- */
-Submap.prototype.openDataOverlay = function (identifier) {
- if (this.isInitialized()) {
- this.getMapCanvas().setBackgroundId(identifier.toString());
- }
-};
-
-/**
- *
- * @returns {CustomMap}
- */
-Submap.prototype.getTopMap = function () {
- return this.getCustomMap();
-};
-
-/**
- *
- * @returns {CustomMap}
- */
-Submap.prototype.getCustomMap = function () {
- return this._customMap;
-};
-
-/**
- *
- * @param {CustomMap} customMap
- */
-Submap.prototype.setCustomMap = function (customMap) {
- this._customMap = customMap;
-};
-
-/**
- *
- * @returns {Project}
- */
-Submap.prototype.getProject = function () {
- return this.getCustomMap().getProject();
-};
-
-Submap.prototype.destroy = function () {
- var self = this;
- AbstractCustomMap.prototype.destroy.call(self);
- if (self.isInitialized()) {
- $(self.getElement()).dialog("destroy");
- }
-};
-
-module.exports = Submap;
+"use strict";
+
+/* exported logger */
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../logger');
+var AbstractCustomMap = require('./AbstractCustomMap');
+var CustomMapOptions = require('./CustomMapOptions');
+
+/**
+ * Constructor of a submap. Submaps are created on application start. But dialog
+ * (popup window) is initialized on demand using init function.
+ *
+ * @param {CustomMap} customMap
+ * parent CustomMap
+ * @param {MapModel} model
+ *
+ * @constructor
+ * @extends AbstractCustomMap
+ */
+function Submap(customMap, model) {
+ this.setCustomMap(customMap);
+
+ AbstractCustomMap.call(this, model, new CustomMapOptions({
+ element: customMap.getElement(),
+ bigLogo: customMap.isBigLogo(),
+ project: customMap.getProject(),
+ configuration: customMap.getConfiguration(),
+ projectId: customMap.getProject().getProjectId(),
+ debug: customMap.isDebug(),
+ serverConnector: customMap.getServerConnector()
+ }));
+
+ this.initialized = false;
+}
+
+// implementation of object inheritance
+Submap.prototype = Object.create(AbstractCustomMap.prototype);
+Submap.prototype.constructor = Submap;
+
+/**
+ * This method initializes submap with gui component. Before this point submap
+ * is created and contains data, but cannot be visualized in the browser.
+ *
+ * @param {HTMLElement} htmlTag
+ * html div tag where google map should be placed
+ */
+Submap.prototype.open = function (htmlTag) {
+ var self = this;
+
+ if (!this.isInitialized()) {
+ self.setElement(htmlTag);
+
+ var contentDiv = document.createElement("div");
+ contentDiv.setAttribute("name", "submap-div-" + self.getId());
+ contentDiv.style.width = "100%";
+ contentDiv.style.height = "100%";
+ htmlTag.appendChild(contentDiv);
+
+ var mapDiv = document.createElement("div");
+ mapDiv.style.width = "100%";
+ mapDiv.style.height = "100%";
+ contentDiv.appendChild(mapDiv);
+
+ $(self.getElement()).dialog({
+ title: self.getModel().getName(),
+ width: Math.floor(window.innerWidth * 2 / 3),
+ height: Math.floor(window.innerHeight * 2 / 3),
+ position: {
+ my: "center",
+ at: "center",
+ of: $(self.getTopMap().getElement())
+ },
+ resize: function () {
+ self.getMapCanvas().triggerListeners('resize');
+ }
+ });
+
+ $(self.getElement()).dialog("open");
+
+ self.createMapCanvas(mapDiv);
+
+ self._createMapChangedCallbacks();
+
+ self.getMapCanvas().triggerListeners('resize');
+ self.getMapCanvas().setBackgroundId(self.getTopMap().getBackgroundDataOverlay().getId());
+
+ self.initialized = true;
+ } else {
+ $(self.getElement()).dialog("open");
+ }
+
+};
+
+/**
+ *
+ * @param {number} identifier
+ */
+Submap.prototype.openDataOverlay = function (identifier) {
+ if (this.isInitialized()) {
+ this.getMapCanvas().setBackgroundId(identifier.toString());
+ }
+};
+
+/**
+ *
+ * @returns {CustomMap}
+ */
+Submap.prototype.getTopMap = function () {
+ return this.getCustomMap();
+};
+
+/**
+ *
+ * @returns {CustomMap}
+ */
+Submap.prototype.getCustomMap = function () {
+ return this._customMap;
+};
+
+/**
+ *
+ * @param {CustomMap} customMap
+ */
+Submap.prototype.setCustomMap = function (customMap) {
+ this._customMap = customMap;
+};
+
+/**
+ *
+ * @returns {Project}
+ */
+Submap.prototype.getProject = function () {
+ return this.getCustomMap().getProject();
+};
+
+Submap.prototype.destroy = function () {
+ var self = this;
+ AbstractCustomMap.prototype.destroy.call(self);
+ if (self.isInitialized()) {
+ $(self.getElement()).dialog("destroy");
+ }
+};
+
+module.exports = Submap;
diff --git a/frontend-js/src/main/js/map/data/Alias.js b/frontend-js/src/main/js/map/data/Alias.js
index 1bfd76989315b1d645d6a6438a4fad8556fbe213..2dbe094b08b8b8da240ce033edf43fe526a99a06 100644
--- a/frontend-js/src/main/js/map/data/Alias.js
+++ b/frontend-js/src/main/js/map/data/Alias.js
@@ -1,403 +1,403 @@
-"use strict";
-
-var BioEntity = require("./BioEntity");
-var Point = require("../canvas/Point");
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-/**
- * Class representing alias data.
- *
- * @param {Alias|Object} javaObject
- * object de-serialized ajax query to the server side
- */
-function Alias(javaObject) {
- BioEntity.call(this, javaObject);
- if (javaObject.idObject !== undefined) {
- this.setId(javaObject.idObject);
- } else {
- this.setId(javaObject.id);
- }
- this.setModelId(javaObject.modelId);
- if (javaObject.bounds !== undefined) {
- this.setX(javaObject.bounds.x);
- this.setY(javaObject.bounds.y);
- this.setWidth(javaObject.bounds.width);
- this.setHeight(javaObject.bounds.height);
- }
- this.setLinkedSubmodelId(javaObject.linkedSubmodel);
-
- if (this._modelId === undefined) {
- throw new Error("ModelId is not defined for alias" + javaObject);
- }
-
- if (javaObject.name === undefined) {
- this.setIsComplete(false);
- } else {
- this.update(javaObject);
- }
-}
-
-Alias.prototype = Object.create(BioEntity.prototype);
-Alias.prototype.constructor = Alias;
-
-/**
- * Updates alias with full data information. This function should be called when
- * full information about alias is retrieved from server.
- *
- * @param {Alias|Object} javaObject
- * object representing data from server side
- */
-Alias.prototype.update = function (javaObject) {
- if (javaObject instanceof Alias) {
- if (javaObject.getName() === undefined) {
- return;
- }
- this.setDescription(javaObject.getDescription());
- this.setElementId(javaObject.getElementId());
- this.setType(javaObject.getType());
- this.setCharge(javaObject.getCharge());
- this.setSymbol(javaObject.getSymbol());
- this.setFullName(javaObject.getFullName());
- this.setAbbreviation(javaObject.getAbbreviation());
- this.setFormula(javaObject.getFormula());
- this.setName(javaObject.getName());
- this.setSynonyms(javaObject.getSynonyms());
- this.setFormerSymbols(javaObject.getFormerSymbols());
- this.setReferences(javaObject.getReferences());
- this.setOther(javaObject.getOther());
- this.setHierarchyVisibilityLevel(javaObject.getHierarchyVisibilityLevel());
- this.setComplexId(javaObject.getComplexId());
- this.setTransparencyLevel(javaObject.getTransparencyLevel());
- this.setLinkedSubmodelId(javaObject.getLinkedSubmodelId());
- this.setCompartmentId(javaObject.getCompartmentId());
- this.setDescription(javaObject.getDescription());
-
- this.setConstant(javaObject.getConstant());
- this.setBoundaryCondition(javaObject.getBoundaryCondition());
- this.setInitialAmount(javaObject.getInitialAmount());
- this.setInitialConcentration(javaObject.getInitialConcentration());
-
- this.setX(javaObject.getX());
- this.setY(javaObject.getY());
- this.setWidth(javaObject.getWidth());
- this.setHeight(javaObject.getHeight());
-
- this.setIsComplete(true);
- } else {
- if (javaObject.name === undefined) {
- return;
- }
- this.setDescription(javaObject.notes);
- this.setElementId(javaObject.elementId);
- this.setType(javaObject.type);
- this.setCharge(javaObject.charge);
- this.setSymbol(javaObject.symbol);
- this.setFullName(javaObject.fullName);
- this.setAbbreviation(javaObject.abbreviation);
- this.setFormula(javaObject.formula);
- this.setName(javaObject.name);
- this.setSynonyms(javaObject.synonyms);
- this.setFormerSymbols(javaObject.formerSymbols);
- this.setReferences(javaObject.references);
- this.setOther(javaObject.other);
- this.setHierarchyVisibilityLevel(javaObject.hierarchyVisibilityLevel);
- this.setComplexId(javaObject.complexId);
- this.setTransparencyLevel(javaObject.transparencyLevel);
- this.setLinkedSubmodelId(javaObject.linkedSubmodel);
- this.setCompartmentId(javaObject.compartmentId);
-
- this.setConstant(javaObject.constant);
- this.setBoundaryCondition(javaObject.boundaryCondition);
- this.setInitialAmount(javaObject.initialAmount);
- this.setInitialConcentration(javaObject.initialConcentration);
-
-
- if (javaObject.bounds !== undefined) {
- this.setX(javaObject.bounds.x);
- this.setY(javaObject.bounds.y);
- this.setWidth(javaObject.bounds.width);
- this.setHeight(javaObject.bounds.height);
- }
- this.setIsComplete(true);
- }
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getCharge = function () {
- return this.charge;
-};
-
-/**
- *
- * @param {number} charge
- */
-Alias.prototype.setCharge = function (charge) {
- this.charge = charge;
-};
-
-/**
- *
- * @returns {boolean}
- */
-Alias.prototype.getConstant = function () {
- return this._constant;
-};
-
-/**
- *
- * @param {boolean} constant
- */
-Alias.prototype.setConstant = function (constant) {
- this._constant = constant;
-};
-
-/**
- *
- * @returns {boolean}
- */
-Alias.prototype.getBoundaryCondition = function () {
- return this._boundaryCondition;
-};
-
-/**
- *
- * @param {boolean} boundaryCondition
- */
-Alias.prototype.setBoundaryCondition = function (boundaryCondition) {
- this._boundaryCondition = boundaryCondition;
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getInitialAmount = function () {
- return this._initialAmount;
-};
-
-/**
- *
- * @param {number} initialAmount
- */
-Alias.prototype.setInitialAmount = function (initialAmount) {
- this._initialAmount = initialAmount;
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getInitialConcentration = function () {
- return this._initialConcentration;
-};
-
-/**
- *
- * @param {number} initialConcentration
- */
-Alias.prototype.setInitialConcentration = function (initialConcentration) {
- this._initialConcentration = initialConcentration;
-};
-
-/**
- *
- * @returns {string[]}
- */
-Alias.prototype.getFormerSymbols = function () {
- return this.formerSymbols;
-};
-
-/**
- *
- * @param {string[]} formerSymbols
- */
-Alias.prototype.setFormerSymbols = function (formerSymbols) {
- this.formerSymbols = formerSymbols;
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getX = function () {
- return this.x;
-};
-
-/**
- *
- * @param {number} x
- */
-Alias.prototype.setX = function (x) {
- if (x !== undefined) {
- this.x = x;
- }
-};
-
-/**
- *
- * @param {number} y
- */
-Alias.prototype.setY = function (y) {
- if (y !== undefined) {
- this.y = y;
- }
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getY = function () {
- return this.y;
-};
-
-/**
- *
- * @param {number} elementId
- */
-Alias.prototype.setElementId = function (elementId) {
- this._elementId = elementId;
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getElementId = function () {
- return this._elementId;
-};
-
-/**
- *
- * @param {number} width
- */
-Alias.prototype.setWidth = function (width) {
- if (width !== undefined) {
- this.width = width;
- }
-};
-
-/**
- *
- * @param {number} height
- */
-Alias.prototype.setHeight = function (height) {
- if (height !== undefined) {
- this.height = height;
- }
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getWidth = function () {
- return this.width;
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getHeight = function () {
- return this.height;
-};
-
-/**
- *
- * @returns {string}
- */
-Alias.prototype.getName = function () {
- return this.name;
-};
-
-/**
- *
- * @param {string} name
- */
-Alias.prototype.setName = function (name) {
- this.name = name;
-};
-
-/**
- *
- * @returns {string}
- */
-Alias.prototype.getFullName = function () {
- return this.fullName;
-};
-
-/**
- *
- * @param {string} fullName
- */
-Alias.prototype.setFullName = function (fullName) {
- this.fullName = fullName;
-};
-
-/**
- *
- * @returns {number|undefined}
- */
-Alias.prototype.getCompartmentId = function () {
- return this._compartmentId;
-};
-
-/**
- *
- * @param {number} compartmentId
- */
-Alias.prototype.setCompartmentId = function (compartmentId) {
- if (compartmentId !== null) {
- this._compartmentId = compartmentId;
- }
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getComplexId = function () {
- return this._complexId;
-};
-
-/**
- *
- * @param {number} complexId
- */
-Alias.prototype.setComplexId = function (complexId) {
- if (complexId !== null) {
- this._complexId = complexId;
- }
-};
-
-/**
- *
- * @returns {number}
- */
-Alias.prototype.getTransparencyLevel = function () {
- return this._transparencyLevel;
-};
-
-/**
- *
- * @param {number} transparencyLevel
- */
-Alias.prototype.setTransparencyLevel = function (transparencyLevel) {
- this._transparencyLevel = transparencyLevel;
-};
-
-/**
- *
- * @returns {Point}
- */
-Alias.prototype.getCenter = function () {
- return new Point(this.getX() + this.getWidth() / 2, this.getY() + this.getHeight() / 2);
-};
-
-module.exports = Alias;
+"use strict";
+
+var BioEntity = require("./BioEntity");
+var Point = require("../canvas/Point");
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+/**
+ * Class representing alias data.
+ *
+ * @param {Alias|Object} javaObject
+ * object de-serialized ajax query to the server side
+ */
+function Alias(javaObject) {
+ BioEntity.call(this, javaObject);
+ if (javaObject.idObject !== undefined) {
+ this.setId(javaObject.idObject);
+ } else {
+ this.setId(javaObject.id);
+ }
+ this.setModelId(javaObject.modelId);
+ if (javaObject.bounds !== undefined) {
+ this.setX(javaObject.bounds.x);
+ this.setY(javaObject.bounds.y);
+ this.setWidth(javaObject.bounds.width);
+ this.setHeight(javaObject.bounds.height);
+ }
+ this.setLinkedSubmodelId(javaObject.linkedSubmodel);
+
+ if (this._modelId === undefined) {
+ throw new Error("ModelId is not defined for alias" + javaObject);
+ }
+
+ if (javaObject.name === undefined) {
+ this.setIsComplete(false);
+ } else {
+ this.update(javaObject);
+ }
+}
+
+Alias.prototype = Object.create(BioEntity.prototype);
+Alias.prototype.constructor = Alias;
+
+/**
+ * Updates alias with full data information. This function should be called when
+ * full information about alias is retrieved from server.
+ *
+ * @param {Alias|Object} javaObject
+ * object representing data from server side
+ */
+Alias.prototype.update = function (javaObject) {
+ if (javaObject instanceof Alias) {
+ if (javaObject.getName() === undefined) {
+ return;
+ }
+ this.setDescription(javaObject.getDescription());
+ this.setElementId(javaObject.getElementId());
+ this.setType(javaObject.getType());
+ this.setCharge(javaObject.getCharge());
+ this.setSymbol(javaObject.getSymbol());
+ this.setFullName(javaObject.getFullName());
+ this.setAbbreviation(javaObject.getAbbreviation());
+ this.setFormula(javaObject.getFormula());
+ this.setName(javaObject.getName());
+ this.setSynonyms(javaObject.getSynonyms());
+ this.setFormerSymbols(javaObject.getFormerSymbols());
+ this.setReferences(javaObject.getReferences());
+ this.setOther(javaObject.getOther());
+ this.setHierarchyVisibilityLevel(javaObject.getHierarchyVisibilityLevel());
+ this.setComplexId(javaObject.getComplexId());
+ this.setTransparencyLevel(javaObject.getTransparencyLevel());
+ this.setLinkedSubmodelId(javaObject.getLinkedSubmodelId());
+ this.setCompartmentId(javaObject.getCompartmentId());
+ this.setDescription(javaObject.getDescription());
+
+ this.setConstant(javaObject.getConstant());
+ this.setBoundaryCondition(javaObject.getBoundaryCondition());
+ this.setInitialAmount(javaObject.getInitialAmount());
+ this.setInitialConcentration(javaObject.getInitialConcentration());
+
+ this.setX(javaObject.getX());
+ this.setY(javaObject.getY());
+ this.setWidth(javaObject.getWidth());
+ this.setHeight(javaObject.getHeight());
+
+ this.setIsComplete(true);
+ } else {
+ if (javaObject.name === undefined) {
+ return;
+ }
+ this.setDescription(javaObject.notes);
+ this.setElementId(javaObject.elementId);
+ this.setType(javaObject.type);
+ this.setCharge(javaObject.charge);
+ this.setSymbol(javaObject.symbol);
+ this.setFullName(javaObject.fullName);
+ this.setAbbreviation(javaObject.abbreviation);
+ this.setFormula(javaObject.formula);
+ this.setName(javaObject.name);
+ this.setSynonyms(javaObject.synonyms);
+ this.setFormerSymbols(javaObject.formerSymbols);
+ this.setReferences(javaObject.references);
+ this.setOther(javaObject.other);
+ this.setHierarchyVisibilityLevel(javaObject.hierarchyVisibilityLevel);
+ this.setComplexId(javaObject.complexId);
+ this.setTransparencyLevel(javaObject.transparencyLevel);
+ this.setLinkedSubmodelId(javaObject.linkedSubmodel);
+ this.setCompartmentId(javaObject.compartmentId);
+
+ this.setConstant(javaObject.constant);
+ this.setBoundaryCondition(javaObject.boundaryCondition);
+ this.setInitialAmount(javaObject.initialAmount);
+ this.setInitialConcentration(javaObject.initialConcentration);
+
+
+ if (javaObject.bounds !== undefined) {
+ this.setX(javaObject.bounds.x);
+ this.setY(javaObject.bounds.y);
+ this.setWidth(javaObject.bounds.width);
+ this.setHeight(javaObject.bounds.height);
+ }
+ this.setIsComplete(true);
+ }
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getCharge = function () {
+ return this.charge;
+};
+
+/**
+ *
+ * @param {number} charge
+ */
+Alias.prototype.setCharge = function (charge) {
+ this.charge = charge;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+Alias.prototype.getConstant = function () {
+ return this._constant;
+};
+
+/**
+ *
+ * @param {boolean} constant
+ */
+Alias.prototype.setConstant = function (constant) {
+ this._constant = constant;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+Alias.prototype.getBoundaryCondition = function () {
+ return this._boundaryCondition;
+};
+
+/**
+ *
+ * @param {boolean} boundaryCondition
+ */
+Alias.prototype.setBoundaryCondition = function (boundaryCondition) {
+ this._boundaryCondition = boundaryCondition;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getInitialAmount = function () {
+ return this._initialAmount;
+};
+
+/**
+ *
+ * @param {number} initialAmount
+ */
+Alias.prototype.setInitialAmount = function (initialAmount) {
+ this._initialAmount = initialAmount;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getInitialConcentration = function () {
+ return this._initialConcentration;
+};
+
+/**
+ *
+ * @param {number} initialConcentration
+ */
+Alias.prototype.setInitialConcentration = function (initialConcentration) {
+ this._initialConcentration = initialConcentration;
+};
+
+/**
+ *
+ * @returns {string[]}
+ */
+Alias.prototype.getFormerSymbols = function () {
+ return this.formerSymbols;
+};
+
+/**
+ *
+ * @param {string[]} formerSymbols
+ */
+Alias.prototype.setFormerSymbols = function (formerSymbols) {
+ this.formerSymbols = formerSymbols;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getX = function () {
+ return this.x;
+};
+
+/**
+ *
+ * @param {number} x
+ */
+Alias.prototype.setX = function (x) {
+ if (x !== undefined) {
+ this.x = x;
+ }
+};
+
+/**
+ *
+ * @param {number} y
+ */
+Alias.prototype.setY = function (y) {
+ if (y !== undefined) {
+ this.y = y;
+ }
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getY = function () {
+ return this.y;
+};
+
+/**
+ *
+ * @param {number} elementId
+ */
+Alias.prototype.setElementId = function (elementId) {
+ this._elementId = elementId;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getElementId = function () {
+ return this._elementId;
+};
+
+/**
+ *
+ * @param {number} width
+ */
+Alias.prototype.setWidth = function (width) {
+ if (width !== undefined) {
+ this.width = width;
+ }
+};
+
+/**
+ *
+ * @param {number} height
+ */
+Alias.prototype.setHeight = function (height) {
+ if (height !== undefined) {
+ this.height = height;
+ }
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getWidth = function () {
+ return this.width;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getHeight = function () {
+ return this.height;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Alias.prototype.getName = function () {
+ return this.name;
+};
+
+/**
+ *
+ * @param {string} name
+ */
+Alias.prototype.setName = function (name) {
+ this.name = name;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Alias.prototype.getFullName = function () {
+ return this.fullName;
+};
+
+/**
+ *
+ * @param {string} fullName
+ */
+Alias.prototype.setFullName = function (fullName) {
+ this.fullName = fullName;
+};
+
+/**
+ *
+ * @returns {number|undefined}
+ */
+Alias.prototype.getCompartmentId = function () {
+ return this._compartmentId;
+};
+
+/**
+ *
+ * @param {number} compartmentId
+ */
+Alias.prototype.setCompartmentId = function (compartmentId) {
+ if (compartmentId !== null) {
+ this._compartmentId = compartmentId;
+ }
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getComplexId = function () {
+ return this._complexId;
+};
+
+/**
+ *
+ * @param {number} complexId
+ */
+Alias.prototype.setComplexId = function (complexId) {
+ if (complexId !== null) {
+ this._complexId = complexId;
+ }
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Alias.prototype.getTransparencyLevel = function () {
+ return this._transparencyLevel;
+};
+
+/**
+ *
+ * @param {number} transparencyLevel
+ */
+Alias.prototype.setTransparencyLevel = function (transparencyLevel) {
+ this._transparencyLevel = transparencyLevel;
+};
+
+/**
+ *
+ * @returns {Point}
+ */
+Alias.prototype.getCenter = function () {
+ return new Point(this.getX() + this.getWidth() / 2, this.getY() + this.getHeight() / 2);
+};
+
+module.exports = Alias;
diff --git a/frontend-js/src/main/js/map/data/Annotation.js b/frontend-js/src/main/js/map/data/Annotation.js
index 7b6f82bef9bf4a6518da736cb18df40c06c23303..ea2c3d71f43e792a40ea8f7dc63a58a8e080d17b 100644
--- a/frontend-js/src/main/js/map/data/Annotation.js
+++ b/frontend-js/src/main/js/map/data/Annotation.js
@@ -1,149 +1,149 @@
-"use strict";
-
-/* exported logger */
-
-var Article = require("./Article");
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-/**
- * @typedef {Object} AnnotationOptions
- * @property {string} link
- * @property {number} id
- * @property {Article|ArticleOptions} [article]
- * @property {string} type
- * @property {string} resource
- * @property {string} [annotatorClassName]
- */
-
-/**
- *
- * @param {AnnotationOptions|Annotation} javaObject
- * @constructor
- */
-function Annotation(javaObject) {
- if (javaObject instanceof Annotation) {
- this.setLink(javaObject.getLink());
- this.setId(javaObject.getId());
- if (javaObject.getArticle() !== undefined) {
- this.setArticle(new Article(javaObject.getArticle()));
- }
- this.setType(javaObject.getType());
- this.setResource(javaObject.getResource());
- this.setAnnotatorClassName(javaObject.getAnnotatorClassName());
- } else {
- this.setLink(javaObject.link);
- this.setId(javaObject.id);
- if (javaObject.article !== undefined && javaObject.article !== null) {
- this.setArticle(new Article(javaObject.article));
- }
- this.setType(javaObject.type);
- this.setResource(javaObject.resource);
- this.setAnnotatorClassName(javaObject.annotatorClassName);
- }
-}
-
-/**
- *
- * @param {string} link
- */
-Annotation.prototype.setLink = function (link) {
- this._link = link;
-};
-
-/**
- *
- * @returns {string}
- */
-Annotation.prototype.getLink = function () {
- return this._link;
-};
-
-/**
- *
- * @param {number} id
- */
-Annotation.prototype.setId = function (id) {
- this._id = id;
-};
-
-/**
- *
- * @returns {number}
- */
-Annotation.prototype.getId = function () {
- return this._id;
-};
-
-/**
- *
- * @param {string} resource
- */
-Annotation.prototype.setResource = function (resource) {
- if (resource === undefined) {
- throw new Error("resource cannot be undefined");
- }
- this._resource = resource;
-};
-
-/**
- *
- * @returns {string}
- */
-Annotation.prototype.getResource = function () {
- return this._resource;
-};
-
-/**
- *
- * @param {string} type
- */
-Annotation.prototype.setType = function (type) {
- if (type === undefined) {
- throw new Error("type cannot be undefined");
- }
- this._type = type;
-};
-
-/**
- *
- * @returns {string}
- */
-Annotation.prototype.getType = function () {
- return this._type;
-};
-
-/**
- *
- * @param {Article} article
- */
-Annotation.prototype.setArticle = function (article) {
- this._article = article;
-};
-
-/**
- *
- * @returns {Article}
- */
-Annotation.prototype.getArticle = function () {
- return this._article;
-};
-
-/**
- *
- * @param {string} annotatorClassName
- */
-Annotation.prototype.setAnnotatorClassName = function (annotatorClassName) {
- this._annotatorClassName = annotatorClassName;
-};
-
-/**
- *
- * @returns {string|undefined}
- */
-Annotation.prototype.getAnnotatorClassName = function () {
- return this._annotatorClassName;
-};
-
-module.exports = Annotation;
+"use strict";
+
+/* exported logger */
+
+var Article = require("./Article");
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+/**
+ * @typedef {Object} AnnotationOptions
+ * @property {string} link
+ * @property {number} id
+ * @property {Article|ArticleOptions} [article]
+ * @property {string} type
+ * @property {string} resource
+ * @property {string} [annotatorClassName]
+ */
+
+/**
+ *
+ * @param {AnnotationOptions|Annotation} javaObject
+ * @constructor
+ */
+function Annotation(javaObject) {
+ if (javaObject instanceof Annotation) {
+ this.setLink(javaObject.getLink());
+ this.setId(javaObject.getId());
+ if (javaObject.getArticle() !== undefined) {
+ this.setArticle(new Article(javaObject.getArticle()));
+ }
+ this.setType(javaObject.getType());
+ this.setResource(javaObject.getResource());
+ this.setAnnotatorClassName(javaObject.getAnnotatorClassName());
+ } else {
+ this.setLink(javaObject.link);
+ this.setId(javaObject.id);
+ if (javaObject.article !== undefined && javaObject.article !== null) {
+ this.setArticle(new Article(javaObject.article));
+ }
+ this.setType(javaObject.type);
+ this.setResource(javaObject.resource);
+ this.setAnnotatorClassName(javaObject.annotatorClassName);
+ }
+}
+
+/**
+ *
+ * @param {string} link
+ */
+Annotation.prototype.setLink = function (link) {
+ this._link = link;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Annotation.prototype.getLink = function () {
+ return this._link;
+};
+
+/**
+ *
+ * @param {number} id
+ */
+Annotation.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Annotation.prototype.getId = function () {
+ return this._id;
+};
+
+/**
+ *
+ * @param {string} resource
+ */
+Annotation.prototype.setResource = function (resource) {
+ if (resource === undefined) {
+ throw new Error("resource cannot be undefined");
+ }
+ this._resource = resource;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Annotation.prototype.getResource = function () {
+ return this._resource;
+};
+
+/**
+ *
+ * @param {string} type
+ */
+Annotation.prototype.setType = function (type) {
+ if (type === undefined) {
+ throw new Error("type cannot be undefined");
+ }
+ this._type = type;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Annotation.prototype.getType = function () {
+ return this._type;
+};
+
+/**
+ *
+ * @param {Article} article
+ */
+Annotation.prototype.setArticle = function (article) {
+ this._article = article;
+};
+
+/**
+ *
+ * @returns {Article}
+ */
+Annotation.prototype.getArticle = function () {
+ return this._article;
+};
+
+/**
+ *
+ * @param {string} annotatorClassName
+ */
+Annotation.prototype.setAnnotatorClassName = function (annotatorClassName) {
+ this._annotatorClassName = annotatorClassName;
+};
+
+/**
+ *
+ * @returns {string|undefined}
+ */
+Annotation.prototype.getAnnotatorClassName = function () {
+ return this._annotatorClassName;
+};
+
+module.exports = Annotation;
diff --git a/frontend-js/src/main/js/map/data/Annotator.js b/frontend-js/src/main/js/map/data/Annotator.js
index 0905f0f7b4e5960b348a2496080dcb03ab732994..e5653d2b4105f70e9eed69f4803ac17a4e056576 100644
--- a/frontend-js/src/main/js/map/data/Annotator.js
+++ b/frontend-js/src/main/js/map/data/Annotator.js
@@ -1,98 +1,98 @@
-"use strict";
-
-/* exported logger */
-
-var Article = require("./Article");
-
-var logger = require('../../logger');
-
-function Annotator(javaObject, configuration) {
- var self = this;
- if (javaObject instanceof Annotator) {
- self.setClassName(javaObject.getClassName());
- this._elementTypes = javaObject.getElementTypes();
- self.setName(javaObject.getName());
- self.setDescription(javaObject.getDescription());
- self.setParametersDefinitions(javaObject.getParametersDefinitions());
- self.setUrl(javaObject.getUrl());
- } else {
- self.setClassName(javaObject.className);
- self.setElementTypes(javaObject.elementClassNames, configuration);
- self.setName(javaObject.name);
- self.setDescription(javaObject.description);
- self.setParametersDefinitions(javaObject.parametersDefinitions);
- self.setUrl(javaObject.url);
- }
-}
-
-Annotator.prototype.setClassName = function (className) {
- this._className = className;
-};
-
-Annotator.prototype.getClassName = function () {
- return this._className;
-};
-
-Annotator.prototype.setName = function (name) {
- this._name = name;
-};
-
-Annotator.prototype.getName = function () {
- return this._name;
-};
-
-Annotator.prototype.setDescription = function (description) {
- this._description = description;
-};
-
-Annotator.prototype.getDescription = function () {
- return this._description;
-};
-
-Annotator.prototype.setUrl = function (url) {
- this._url = url;
-};
-
-Annotator.prototype.getUrl = function () {
- return this._url;
-};
-
-Annotator.prototype.getParametersDefinitions = function () {
- return this._parametersDefinitions;
-};
-
-Annotator.prototype.setParametersDefinitions = function (parametersDefinitions) {
- this._parametersDefinitions = parametersDefinitions;
-};
-
-Annotator.prototype.setElementTypes = function (elementTypesClassNames, configuration) {
- this._elementTypes = [];
- var typeByClassName = {};
- var types = configuration.getElementTypes();
- var i, type;
- for (i = 0; i < types.length; i++) {
- type = types[i];
- typeByClassName[type.className] = type;
- }
- types = configuration.getReactionTypes();
- for (i = 0; i < types.length; i++) {
- type = types[i];
- typeByClassName[type.className] = type;
- }
-
- for (i = 0; i < elementTypesClassNames.length; i++) {
- type = typeByClassName[elementTypesClassNames[i]];
- if (type !== undefined) {
- this._elementTypes.push(type)
- } else {
- throw new Error("Unknown elementType: " + elementTypesClassNames[i]);
- }
- }
-};
-
-Annotator.prototype.getElementTypes = function () {
- return this._elementTypes;
-};
-
-
-module.exports = Annotator;
+"use strict";
+
+/* exported logger */
+
+var Article = require("./Article");
+
+var logger = require('../../logger');
+
+function Annotator(javaObject, configuration) {
+ var self = this;
+ if (javaObject instanceof Annotator) {
+ self.setClassName(javaObject.getClassName());
+ this._elementTypes = javaObject.getElementTypes();
+ self.setName(javaObject.getName());
+ self.setDescription(javaObject.getDescription());
+ self.setParametersDefinitions(javaObject.getParametersDefinitions());
+ self.setUrl(javaObject.getUrl());
+ } else {
+ self.setClassName(javaObject.className);
+ self.setElementTypes(javaObject.elementClassNames, configuration);
+ self.setName(javaObject.name);
+ self.setDescription(javaObject.description);
+ self.setParametersDefinitions(javaObject.parametersDefinitions);
+ self.setUrl(javaObject.url);
+ }
+}
+
+Annotator.prototype.setClassName = function (className) {
+ this._className = className;
+};
+
+Annotator.prototype.getClassName = function () {
+ return this._className;
+};
+
+Annotator.prototype.setName = function (name) {
+ this._name = name;
+};
+
+Annotator.prototype.getName = function () {
+ return this._name;
+};
+
+Annotator.prototype.setDescription = function (description) {
+ this._description = description;
+};
+
+Annotator.prototype.getDescription = function () {
+ return this._description;
+};
+
+Annotator.prototype.setUrl = function (url) {
+ this._url = url;
+};
+
+Annotator.prototype.getUrl = function () {
+ return this._url;
+};
+
+Annotator.prototype.getParametersDefinitions = function () {
+ return this._parametersDefinitions;
+};
+
+Annotator.prototype.setParametersDefinitions = function (parametersDefinitions) {
+ this._parametersDefinitions = parametersDefinitions;
+};
+
+Annotator.prototype.setElementTypes = function (elementTypesClassNames, configuration) {
+ this._elementTypes = [];
+ var typeByClassName = {};
+ var types = configuration.getElementTypes();
+ var i, type;
+ for (i = 0; i < types.length; i++) {
+ type = types[i];
+ typeByClassName[type.className] = type;
+ }
+ types = configuration.getReactionTypes();
+ for (i = 0; i < types.length; i++) {
+ type = types[i];
+ typeByClassName[type.className] = type;
+ }
+
+ for (i = 0; i < elementTypesClassNames.length; i++) {
+ type = typeByClassName[elementTypesClassNames[i]];
+ if (type !== undefined) {
+ this._elementTypes.push(type)
+ } else {
+ throw new Error("Unknown elementType: " + elementTypesClassNames[i]);
+ }
+ }
+};
+
+Annotator.prototype.getElementTypes = function () {
+ return this._elementTypes;
+};
+
+
+module.exports = Annotator;
diff --git a/frontend-js/src/main/js/map/data/Article.js b/frontend-js/src/main/js/map/data/Article.js
index 584cd35a1eff35bd56791234b8cb3decd78c4336..92f4beb6b50fea6a2f671358dcfee3cc5e68447b 100644
--- a/frontend-js/src/main/js/map/data/Article.js
+++ b/frontend-js/src/main/js/map/data/Article.js
@@ -1,159 +1,159 @@
-"use strict";
-
-/**
- * @typedef {Object} ArticleOptions
- * @property {string} title
- * @property {string[]} authors
- * @property {string} journal
- * @property {number} year
- * @property {string} link
- * @property {number} citationCount
- * @property {string} id
- */
-
-/**
- *
- * @param {Article|ArticleOptions} javaObject
- * @constructor
- */
-function Article(javaObject) {
- if (javaObject instanceof Article) {
- this.setTitle(javaObject.getTitle());
- this.setAuthors(javaObject.getAuthors());
- this.setJournal(javaObject.getJournal());
- this.setYear(javaObject.getYear());
- this.setLink(javaObject.getLink());
- this.setCitationCount(javaObject.getCitationCount());
- this.setId(javaObject.getId());
- } else {
- this.setTitle(javaObject.title);
- this.setAuthors(javaObject.authors);
- this.setJournal(javaObject.journal);
- this.setYear(javaObject.year);
- this.setLink(javaObject.link);
- this.setCitationCount(javaObject.citationCount);
- this.setId(javaObject.id);
- }
-}
-
-/**
- *
- * @param {string} title
- */
-Article.prototype.setTitle = function (title) {
- this._title = title;
-};
-
-/**
- *
- * @returns {string}
- */
-Article.prototype.getTitle = function () {
- return this._title;
-};
-
-/**
- *
- * @param {string} id
- */
-Article.prototype.setId = function (id) {
- this._id = id;
-};
-
-/**
- *
- * @returns {string[]}
- */
-Article.prototype.getAuthors = function () {
- return this._authors;
-};
-
-/**
- *
- * @param {string[]} authors
- */
-Article.prototype.setAuthors = function (authors) {
- this._authors = authors;
-};
-
-/**
- *
- * @param {string} id
- */
-Article.prototype.setId = function (id) {
- this._id = id;
-};
-
-/**
- *
- * @returns {string}
- */
-Article.prototype.getId = function () {
- return this._id;
-};
-
-/**
- *
- * @param {string} journal
- */
-Article.prototype.setJournal = function (journal) {
- this._journal = journal;
-};
-
-/**
- *
- * @returns {string}
- */
-Article.prototype.getJournal = function () {
- return this._journal;
-};
-
-/**
- *
- * @param {number} year
- */
-Article.prototype.setYear = function (year) {
- this._year = year;
-};
-
-/**
- *
- * @returns {number}
- */
-Article.prototype.getYear = function () {
- return this._year;
-};
-
-/**
- *
- * @param {string} link
- */
-Article.prototype.setLink = function (link) {
- this._link = link;
-};
-
-/**
- *
- * @returns {string}
- */
-Article.prototype.getLink = function () {
- return this._link;
-};
-
-/**
- *
- * @param {number} citationCount
- */
-Article.prototype.setCitationCount = function (citationCount) {
- this._citationCount = citationCount;
-};
-
-/**
- *
- * @returns {number}
- */
-Article.prototype.getCitationCount = function () {
- return this._citationCount;
-};
-
-module.exports = Article;
+"use strict";
+
+/**
+ * @typedef {Object} ArticleOptions
+ * @property {string} title
+ * @property {string[]} authors
+ * @property {string} journal
+ * @property {number} year
+ * @property {string} link
+ * @property {number} citationCount
+ * @property {string} id
+ */
+
+/**
+ *
+ * @param {Article|ArticleOptions} javaObject
+ * @constructor
+ */
+function Article(javaObject) {
+ if (javaObject instanceof Article) {
+ this.setTitle(javaObject.getTitle());
+ this.setAuthors(javaObject.getAuthors());
+ this.setJournal(javaObject.getJournal());
+ this.setYear(javaObject.getYear());
+ this.setLink(javaObject.getLink());
+ this.setCitationCount(javaObject.getCitationCount());
+ this.setId(javaObject.getId());
+ } else {
+ this.setTitle(javaObject.title);
+ this.setAuthors(javaObject.authors);
+ this.setJournal(javaObject.journal);
+ this.setYear(javaObject.year);
+ this.setLink(javaObject.link);
+ this.setCitationCount(javaObject.citationCount);
+ this.setId(javaObject.id);
+ }
+}
+
+/**
+ *
+ * @param {string} title
+ */
+Article.prototype.setTitle = function (title) {
+ this._title = title;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Article.prototype.getTitle = function () {
+ return this._title;
+};
+
+/**
+ *
+ * @param {string} id
+ */
+Article.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @returns {string[]}
+ */
+Article.prototype.getAuthors = function () {
+ return this._authors;
+};
+
+/**
+ *
+ * @param {string[]} authors
+ */
+Article.prototype.setAuthors = function (authors) {
+ this._authors = authors;
+};
+
+/**
+ *
+ * @param {string} id
+ */
+Article.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Article.prototype.getId = function () {
+ return this._id;
+};
+
+/**
+ *
+ * @param {string} journal
+ */
+Article.prototype.setJournal = function (journal) {
+ this._journal = journal;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Article.prototype.getJournal = function () {
+ return this._journal;
+};
+
+/**
+ *
+ * @param {number} year
+ */
+Article.prototype.setYear = function (year) {
+ this._year = year;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Article.prototype.getYear = function () {
+ return this._year;
+};
+
+/**
+ *
+ * @param {string} link
+ */
+Article.prototype.setLink = function (link) {
+ this._link = link;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Article.prototype.getLink = function () {
+ return this._link;
+};
+
+/**
+ *
+ * @param {number} citationCount
+ */
+Article.prototype.setCitationCount = function (citationCount) {
+ this._citationCount = citationCount;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Article.prototype.getCitationCount = function () {
+ return this._citationCount;
+};
+
+module.exports = Article;
diff --git a/frontend-js/src/main/js/map/data/BioEntity.js b/frontend-js/src/main/js/map/data/BioEntity.js
index f2deb9b7686a2f9fc60e57f141c172d0b665ebba..bacd7e36e82ca036f8bdf9da282890b45f9bf77f 100644
--- a/frontend-js/src/main/js/map/data/BioEntity.js
+++ b/frontend-js/src/main/js/map/data/BioEntity.js
@@ -1,243 +1,243 @@
-"use strict";
-
-var Annotation = require("./Annotation");
-var Functions = require("../../Functions");
-
-/**
- * Class representing BioEntity.
- *
- * @constructor
- */
-function BioEntity() {
-}
-
-/**
- *
- * @returns {number|undefined}
- */
-BioEntity.prototype.getLinkedSubmodelId = function () {
- return this._linkedSubmodelId;
-};
-
-/**
- *
- * @param {number} linkedSubmodelId
- */
-BioEntity.prototype.setLinkedSubmodelId = function (linkedSubmodelId) {
- this._linkedSubmodelId = Functions.getIntOrUndefined(linkedSubmodelId);
-};
-
-/**
- * Returns identifier of the BioEntity.
- *
- * @returns {number} identifier of the BioEntity
- */
-BioEntity.prototype.getId = function () {
- return this.id;
-};
-
-/**
- *
- * @param {number} id
- */
-BioEntity.prototype.setId = function (id) {
- this.id = id;
-};
-
-/**
- * Returns model identifier where {@link BioEntity} is located.
- *
- * @returns {number} model identifier where {@link BioEntity} is located
- */
-BioEntity.prototype.getModelId = function () {
- return this._modelId;
-};
-
-/**
- *
- * @param {number} modelId
- */
-BioEntity.prototype.setModelId = function (modelId) {
- this._modelId = modelId;
-};
-
-/**
- *
- * @returns {boolean}
- */
-BioEntity.prototype.isComplete = function () {
- return this._complete;
-};
-
-/**
- *
- * @param {boolean} complete
- */
-BioEntity.prototype.setIsComplete = function (complete) {
- this._complete = complete;
-};
-
-/**
- *
- * @returns {string}
- */
-BioEntity.prototype.getSymbol = function () {
- return this.symbol;
-};
-
-/**
- *
- * @param {string} symbol
- */
-BioEntity.prototype.setSymbol = function (symbol) {
- this.symbol = symbol;
-};
-
-/**
- *
- * @returns {string}
- */
-BioEntity.prototype.getAbbreviation = function () {
- return this._abbreviation;
-};
-
-/**
- *
- * @param {string} abbreviation
- */
-BioEntity.prototype.setAbbreviation = function (abbreviation) {
- this._abbreviation = abbreviation;
-};
-
-/**
- *
- * @returns {string}
- */
-BioEntity.prototype.getFormula = function () {
- return this._formula;
-};
-
-/**
- *
- * @param {string} formula
- */
-BioEntity.prototype.setFormula = function (formula) {
- this._formula = formula;
-};
-
-/**
- *
- * @param {string[]} synonyms
- */
-BioEntity.prototype.setSynonyms = function (synonyms) {
- this._synonyms = synonyms;
-};
-
-/**
- *
- * @returns {string[]}
- */
-BioEntity.prototype.getSynonyms = function () {
- return this._synonyms;
-};
-
-/**
- *
- * @param {string} description
- */
-BioEntity.prototype.setDescription = function (description) {
- this._description = description;
-};
-
-/**
- *
- * @returns {string}
- */
-BioEntity.prototype.getDescription = function () {
- return this._description;
-};
-
-/**
- *
- * @param {string} type
- */
-BioEntity.prototype.setType = function (type) {
- if (type === undefined) {
- throw new Error("type cannot be undefined");
- }
- this._type = type;
-};
-
-/**
- *
- * @returns {string}
- */
-BioEntity.prototype.getType = function () {
- return this._type;
-};
-
-/**
- *
- * @param {string} type
- * @returns {Object}
- */
-BioEntity.prototype.getOther = function (type) {
- if (this._other !== undefined) {
- return (type === undefined) ? this._other : this._other[type];
- }
-};
-
-/**
- *
- * @param {Object} other
- */
-BioEntity.prototype.setOther = function (other) {
- this._other = other;
-};
-
-/**
- *
- * @returns {number}
- */
-BioEntity.prototype.getHierarchyVisibilityLevel = function () {
- return this._hierarchyVisibilityLevel;
-};
-
-/**
- *
- * @param {number} hierarchyVisibilityLevel
- */
-BioEntity.prototype.setHierarchyVisibilityLevel = function (hierarchyVisibilityLevel) {
- this._hierarchyVisibilityLevel = hierarchyVisibilityLevel;
-};
-
-/**
- *
- * @returns {Annotation[]}
- */
-BioEntity.prototype.getReferences = function () {
- return this.references;
-};
-
-/**
- *
- * @param {Annotation[]} references
- */
-BioEntity.prototype.setReferences = function (references) {
- if (references === undefined) {
- throw new Error("references must be defined");
- }
- this.references = [];
- for (var i = 0; i < references.length; i++) {
- this.references.push(new Annotation(references[i]));
- }
-};
-
-/**
- * @returns {Point}
- */
-BioEntity.prototype.getCenter = function () {
- throw new Error("Not implemented");
-};
-
-module.exports = BioEntity;
+"use strict";
+
+var Annotation = require("./Annotation");
+var Functions = require("../../Functions");
+
+/**
+ * Class representing BioEntity.
+ *
+ * @constructor
+ */
+function BioEntity() {
+}
+
+/**
+ *
+ * @returns {number|undefined}
+ */
+BioEntity.prototype.getLinkedSubmodelId = function () {
+ return this._linkedSubmodelId;
+};
+
+/**
+ *
+ * @param {number} linkedSubmodelId
+ */
+BioEntity.prototype.setLinkedSubmodelId = function (linkedSubmodelId) {
+ this._linkedSubmodelId = Functions.getIntOrUndefined(linkedSubmodelId);
+};
+
+/**
+ * Returns identifier of the BioEntity.
+ *
+ * @returns {number} identifier of the BioEntity
+ */
+BioEntity.prototype.getId = function () {
+ return this.id;
+};
+
+/**
+ *
+ * @param {number} id
+ */
+BioEntity.prototype.setId = function (id) {
+ this.id = id;
+};
+
+/**
+ * Returns model identifier where {@link BioEntity} is located.
+ *
+ * @returns {number} model identifier where {@link BioEntity} is located
+ */
+BioEntity.prototype.getModelId = function () {
+ return this._modelId;
+};
+
+/**
+ *
+ * @param {number} modelId
+ */
+BioEntity.prototype.setModelId = function (modelId) {
+ this._modelId = modelId;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+BioEntity.prototype.isComplete = function () {
+ return this._complete;
+};
+
+/**
+ *
+ * @param {boolean} complete
+ */
+BioEntity.prototype.setIsComplete = function (complete) {
+ this._complete = complete;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+BioEntity.prototype.getSymbol = function () {
+ return this.symbol;
+};
+
+/**
+ *
+ * @param {string} symbol
+ */
+BioEntity.prototype.setSymbol = function (symbol) {
+ this.symbol = symbol;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+BioEntity.prototype.getAbbreviation = function () {
+ return this._abbreviation;
+};
+
+/**
+ *
+ * @param {string} abbreviation
+ */
+BioEntity.prototype.setAbbreviation = function (abbreviation) {
+ this._abbreviation = abbreviation;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+BioEntity.prototype.getFormula = function () {
+ return this._formula;
+};
+
+/**
+ *
+ * @param {string} formula
+ */
+BioEntity.prototype.setFormula = function (formula) {
+ this._formula = formula;
+};
+
+/**
+ *
+ * @param {string[]} synonyms
+ */
+BioEntity.prototype.setSynonyms = function (synonyms) {
+ this._synonyms = synonyms;
+};
+
+/**
+ *
+ * @returns {string[]}
+ */
+BioEntity.prototype.getSynonyms = function () {
+ return this._synonyms;
+};
+
+/**
+ *
+ * @param {string} description
+ */
+BioEntity.prototype.setDescription = function (description) {
+ this._description = description;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+BioEntity.prototype.getDescription = function () {
+ return this._description;
+};
+
+/**
+ *
+ * @param {string} type
+ */
+BioEntity.prototype.setType = function (type) {
+ if (type === undefined) {
+ throw new Error("type cannot be undefined");
+ }
+ this._type = type;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+BioEntity.prototype.getType = function () {
+ return this._type;
+};
+
+/**
+ *
+ * @param {string} type
+ * @returns {Object}
+ */
+BioEntity.prototype.getOther = function (type) {
+ if (this._other !== undefined) {
+ return (type === undefined) ? this._other : this._other[type];
+ }
+};
+
+/**
+ *
+ * @param {Object} other
+ */
+BioEntity.prototype.setOther = function (other) {
+ this._other = other;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+BioEntity.prototype.getHierarchyVisibilityLevel = function () {
+ return this._hierarchyVisibilityLevel;
+};
+
+/**
+ *
+ * @param {number} hierarchyVisibilityLevel
+ */
+BioEntity.prototype.setHierarchyVisibilityLevel = function (hierarchyVisibilityLevel) {
+ this._hierarchyVisibilityLevel = hierarchyVisibilityLevel;
+};
+
+/**
+ *
+ * @returns {Annotation[]}
+ */
+BioEntity.prototype.getReferences = function () {
+ return this.references;
+};
+
+/**
+ *
+ * @param {Annotation[]} references
+ */
+BioEntity.prototype.setReferences = function (references) {
+ if (references === undefined) {
+ throw new Error("references must be defined");
+ }
+ this.references = [];
+ for (var i = 0; i < references.length; i++) {
+ this.references.push(new Annotation(references[i]));
+ }
+};
+
+/**
+ * @returns {Point}
+ */
+BioEntity.prototype.getCenter = function () {
+ throw new Error("Not implemented");
+};
+
+module.exports = BioEntity;
diff --git a/frontend-js/src/main/js/map/data/Chemical.js b/frontend-js/src/main/js/map/data/Chemical.js
index b81080341613ea28776fca293cfeea911c381cc5..1bb0049a9631c423eb8c5469f929ae4bedb212a4 100644
--- a/frontend-js/src/main/js/map/data/Chemical.js
+++ b/frontend-js/src/main/js/map/data/Chemical.js
@@ -1,113 +1,113 @@
-"use strict";
-
-var Annotation = require("./Annotation");
-var TargettingStructure = require("./TargettingStructure");
-
-/**
- *
- * @param javaObject
- * @constructor
- */
-function Chemical(javaObject) {
- TargettingStructure.call(this, javaObject);
- if (javaObject !== undefined) {
- this.setReferences(javaObject.references);
- this.setDescription(javaObject.description);
- this.setSynonyms(javaObject.synonyms);
-
- this.setDirectEvidence(javaObject.directEvidence);
- this.setDirectEvidenceReferences(javaObject.directEvidenceReferences);
- }
-}
-
-Chemical.prototype = Object.create(TargettingStructure.prototype);
-Chemical.prototype.constructor = Chemical;
-
-/**
- *
- * @param {string} directEvidence
- */
-Chemical.prototype.setDirectEvidence = function (directEvidence) {
- this._directEvidence = directEvidence;
-};
-
-/**
- *
- * @returns {string}
- */
-Chemical.prototype.getDirectEvidence = function () {
- return this._directEvidence;
-};
-
-/**
- *
- * @param {Annotation[]} directEvidenceReferences
- */
-Chemical.prototype.setDirectEvidenceReferences = function (directEvidenceReferences) {
- this._directEvidenceReferences = [];
- for (var i = 0; i < directEvidenceReferences.length; i++) {
- this._directEvidenceReferences.push(new Annotation(directEvidenceReferences[i]));
- }
-};
-
-
-/**
- *
- * @returns {Annotation[]}
- */
-Chemical.prototype.getDirectEvidenceReferences = function () {
- return this._directEvidenceReferences;
-};
-
-/**
- *
- * @param {Annotation[]} references
- */
-Chemical.prototype.setReferences = function (references) {
- this._references = [];
- for (var i = 0; i < references.length; i++) {
- this._references.push(new Annotation(references[i]));
- }
-};
-
-/**
- *
- * @returns {Annotation[]}
- */
-Chemical.prototype.getReferences = function () {
- return this._references;
-};
-
-/**
- *
- * @param {string[]} synonyms
- */
-Chemical.prototype.setSynonyms = function (synonyms) {
- this._synonyms = synonyms;
-};
-
-/**
- *
- * @returns {string[]}
- */
-Chemical.prototype.getSynonyms = function () {
- return this._synonyms;
-};
-
-/**
- *
- * @param {string} description
- */
-Chemical.prototype.setDescription = function (description) {
- this._description = description;
-};
-
-/**
- *
- * @returns {string}
- */
-Chemical.prototype.getDescription = function () {
- return this._description;
-};
-
-module.exports = Chemical;
+"use strict";
+
+var Annotation = require("./Annotation");
+var TargettingStructure = require("./TargettingStructure");
+
+/**
+ *
+ * @param javaObject
+ * @constructor
+ */
+function Chemical(javaObject) {
+ TargettingStructure.call(this, javaObject);
+ if (javaObject !== undefined) {
+ this.setReferences(javaObject.references);
+ this.setDescription(javaObject.description);
+ this.setSynonyms(javaObject.synonyms);
+
+ this.setDirectEvidence(javaObject.directEvidence);
+ this.setDirectEvidenceReferences(javaObject.directEvidenceReferences);
+ }
+}
+
+Chemical.prototype = Object.create(TargettingStructure.prototype);
+Chemical.prototype.constructor = Chemical;
+
+/**
+ *
+ * @param {string} directEvidence
+ */
+Chemical.prototype.setDirectEvidence = function (directEvidence) {
+ this._directEvidence = directEvidence;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Chemical.prototype.getDirectEvidence = function () {
+ return this._directEvidence;
+};
+
+/**
+ *
+ * @param {Annotation[]} directEvidenceReferences
+ */
+Chemical.prototype.setDirectEvidenceReferences = function (directEvidenceReferences) {
+ this._directEvidenceReferences = [];
+ for (var i = 0; i < directEvidenceReferences.length; i++) {
+ this._directEvidenceReferences.push(new Annotation(directEvidenceReferences[i]));
+ }
+};
+
+
+/**
+ *
+ * @returns {Annotation[]}
+ */
+Chemical.prototype.getDirectEvidenceReferences = function () {
+ return this._directEvidenceReferences;
+};
+
+/**
+ *
+ * @param {Annotation[]} references
+ */
+Chemical.prototype.setReferences = function (references) {
+ this._references = [];
+ for (var i = 0; i < references.length; i++) {
+ this._references.push(new Annotation(references[i]));
+ }
+};
+
+/**
+ *
+ * @returns {Annotation[]}
+ */
+Chemical.prototype.getReferences = function () {
+ return this._references;
+};
+
+/**
+ *
+ * @param {string[]} synonyms
+ */
+Chemical.prototype.setSynonyms = function (synonyms) {
+ this._synonyms = synonyms;
+};
+
+/**
+ *
+ * @returns {string[]}
+ */
+Chemical.prototype.getSynonyms = function () {
+ return this._synonyms;
+};
+
+/**
+ *
+ * @param {string} description
+ */
+Chemical.prototype.setDescription = function (description) {
+ this._description = description;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Chemical.prototype.getDescription = function () {
+ return this._description;
+};
+
+module.exports = Chemical;
diff --git a/frontend-js/src/main/js/map/data/Comment.js b/frontend-js/src/main/js/map/data/Comment.js
index 526ef4294432e5f00a22d020e1e47397c4d7bafd..78c6e950a557af1fc83406cef79d623b7ecc2abd 100644
--- a/frontend-js/src/main/js/map/data/Comment.js
+++ b/frontend-js/src/main/js/map/data/Comment.js
@@ -1,192 +1,192 @@
-"use strict";
-
-var IdentifiedElement = require('./IdentifiedElement');
-var Point = require('../canvas/Point');
-
-/**
- *
- * @param javaObject
- * @constructor
- */
-function Comment(javaObject) {
- this.setIdentifiedElement(new IdentifiedElement({
- id: javaObject.elementId,
- type: javaObject.type,
- modelId: javaObject.modelId,
- icon: javaObject.icon
- }));
- this.setId(javaObject.id);
- this.setRemoved(javaObject.removed);
- this.setRemoveReason(javaObject.removeReason);
- this.setPinned(javaObject.pinned);
-
- if (javaObject.title !== undefined) {
- this.setCoordinates(javaObject.coord);
- this.setTitle(javaObject.title);
- this.setContent(javaObject.content);
- }
- this.setAuthor(javaObject.author);
- this.setEmail(javaObject.email);
-}
-
-/**
- *
- * @param {IdentifiedElement} ie
- */
-Comment.prototype.setIdentifiedElement = function (ie) {
- this._ie = ie;
-};
-
-/**
- *
- * @returns {IdentifiedElement}
- */
-Comment.prototype.getIdentifiedElement = function () {
- return this._ie;
-};
-
-/**
- *
- * @param {boolean} pinned
- */
-Comment.prototype.setPinned = function (pinned) {
- this._pinned = (pinned === true);
-};
-
-/**
- *
- * @param {{x:number, y:number}} coordinates
- */
-Comment.prototype.setCoordinates = function (coordinates) {
- this._coordinates = new Point(coordinates.x, coordinates.y);
-};
-
-/**
- *
- * @param {boolean} removed
- */
-Comment.prototype.setRemoved = function (removed) {
- this._removed = (removed === true);
-};
-
-/**
- *
- * @param {number} id
- */
-Comment.prototype.setId = function (id) {
- this._id = id;
-};
-
-/**
- *
- * @param {string} content
- */
-Comment.prototype.setContent = function (content) {
- this._content = content;
-};
-
-/**
- *
- * @returns {boolean}
- */
-Comment.prototype.isPinned = function () {
- return this._pinned;
-};
-
-/**
- *
- * @returns {Point}
- */
-Comment.prototype.getCoordinates = function () {
- return this._coordinates;
-};
-
-/**
- *
- * @returns {boolean}
- */
-Comment.prototype.isRemoved = function () {
- return this._removed;
-};
-
-/**
- *
- * @returns {number}
- */
-Comment.prototype.getId = function () {
- return this._id;
-};
-
-/**
- *
- * @param {string} title
- */
-Comment.prototype.setTitle = function (title) {
- this._title = title;
-};
-
-/**
- *
- * @returns {string}
- */
-Comment.prototype.getTitle = function () {
- return this._title;
-};
-
-/**
- *
- * @returns {string}
- */
-Comment.prototype.getContent = function () {
- return this._content;
-};
-
-/**
- *
- * @param {string} author
- */
-Comment.prototype.setAuthor = function (author) {
- this._author = author;
-};
-
-/**
- *
- * @returns {string}
- */
-Comment.prototype.getAuthor = function () {
- return this._author;
-};
-
-/**
- *
- * @param {string} email
- */
-Comment.prototype.setEmail = function (email) {
- this._email = email;
-};
-
-/**
- *
- * @returns {string}
- */
-Comment.prototype.getEmail = function () {
- return this._email;
-};
-
-/**
- *
- * @param {string} removeReason
- */
-Comment.prototype.setRemoveReason = function (removeReason) {
- this._removeReason = removeReason;
-};
-
-/**
- *
- * @returns {string}
- */
-Comment.prototype.getRemoveReason = function () {
- return this._removeReason;
-};
-
-module.exports = Comment;
+"use strict";
+
+var IdentifiedElement = require('./IdentifiedElement');
+var Point = require('../canvas/Point');
+
+/**
+ *
+ * @param javaObject
+ * @constructor
+ */
+function Comment(javaObject) {
+ this.setIdentifiedElement(new IdentifiedElement({
+ id: javaObject.elementId,
+ type: javaObject.type,
+ modelId: javaObject.modelId,
+ icon: javaObject.icon
+ }));
+ this.setId(javaObject.id);
+ this.setRemoved(javaObject.removed);
+ this.setRemoveReason(javaObject.removeReason);
+ this.setPinned(javaObject.pinned);
+
+ if (javaObject.title !== undefined) {
+ this.setCoordinates(javaObject.coord);
+ this.setTitle(javaObject.title);
+ this.setContent(javaObject.content);
+ }
+ this.setAuthor(javaObject.author);
+ this.setEmail(javaObject.email);
+}
+
+/**
+ *
+ * @param {IdentifiedElement} ie
+ */
+Comment.prototype.setIdentifiedElement = function (ie) {
+ this._ie = ie;
+};
+
+/**
+ *
+ * @returns {IdentifiedElement}
+ */
+Comment.prototype.getIdentifiedElement = function () {
+ return this._ie;
+};
+
+/**
+ *
+ * @param {boolean} pinned
+ */
+Comment.prototype.setPinned = function (pinned) {
+ this._pinned = (pinned === true);
+};
+
+/**
+ *
+ * @param {{x:number, y:number}} coordinates
+ */
+Comment.prototype.setCoordinates = function (coordinates) {
+ this._coordinates = new Point(coordinates.x, coordinates.y);
+};
+
+/**
+ *
+ * @param {boolean} removed
+ */
+Comment.prototype.setRemoved = function (removed) {
+ this._removed = (removed === true);
+};
+
+/**
+ *
+ * @param {number} id
+ */
+Comment.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @param {string} content
+ */
+Comment.prototype.setContent = function (content) {
+ this._content = content;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+Comment.prototype.isPinned = function () {
+ return this._pinned;
+};
+
+/**
+ *
+ * @returns {Point}
+ */
+Comment.prototype.getCoordinates = function () {
+ return this._coordinates;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+Comment.prototype.isRemoved = function () {
+ return this._removed;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Comment.prototype.getId = function () {
+ return this._id;
+};
+
+/**
+ *
+ * @param {string} title
+ */
+Comment.prototype.setTitle = function (title) {
+ this._title = title;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Comment.prototype.getTitle = function () {
+ return this._title;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Comment.prototype.getContent = function () {
+ return this._content;
+};
+
+/**
+ *
+ * @param {string} author
+ */
+Comment.prototype.setAuthor = function (author) {
+ this._author = author;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Comment.prototype.getAuthor = function () {
+ return this._author;
+};
+
+/**
+ *
+ * @param {string} email
+ */
+Comment.prototype.setEmail = function (email) {
+ this._email = email;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Comment.prototype.getEmail = function () {
+ return this._email;
+};
+
+/**
+ *
+ * @param {string} removeReason
+ */
+Comment.prototype.setRemoveReason = function (removeReason) {
+ this._removeReason = removeReason;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Comment.prototype.getRemoveReason = function () {
+ return this._removeReason;
+};
+
+module.exports = Comment;
diff --git a/frontend-js/src/main/js/map/data/DataOverlay.js b/frontend-js/src/main/js/map/data/DataOverlay.js
index c957147c37c78b05fc84220366908b2f2aa5ab7f..2e8b47eacd0cc9f65b75fba0c38b0517337dc621 100644
--- a/frontend-js/src/main/js/map/data/DataOverlay.js
+++ b/frontend-js/src/main/js/map/data/DataOverlay.js
@@ -1,397 +1,397 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var IdentifiedElement = require('./IdentifiedElement');
-var LayoutAlias = require('./LayoutAlias');
-var LayoutReaction = require('./LayoutReaction');
-var logger = require('../../logger');
-
-/**
- * Class representing data in a specific overlay.
- *
- * @param {number|Object} overlayId
- * @param {string} [name]
- * @constructor
- */
-function DataOverlay(overlayId, name) {
- this.setInitialized(false);
-
- if (name === undefined) {
- // from json structure
- var object = overlayId;
- this.setId(object.idObject);
- this.setOrder(object.order);
- this.setName(object.name);
- this.setImagesDirectory(object.images);
- this.setDescription(object.description);
- this.setCreator(object.creator);
- this.setContent(object.content);
- this.setFilename(object.filename);
- this.setPublicOverlay(object.publicOverlay);
- this.setDefaultOverlay(object.defaultOverlay);
- this.setGoogleLicenseConsent(object.googleLicenseConsent);
- this.setInputDataAvailable(object.inputDataAvailable);
- this.setType(object.type);
- if (!this.getInputDataAvailable()) {
- this.setInitialized(true);
- }
- } else {
- // default two param call
- this.setId(overlayId);
- this.setName(name);
- }
- this.aliases = [];
- this.aliasById = [];
- this.reactions = [];
-}
-
-/**
- * Adds alias to the {@link DataOverlay}
- *
- * @param {LayoutAlias} overlayAlias
- * information about alias in the overlay
- */
-DataOverlay.prototype.addAlias = function (overlayAlias) {
- this.aliases.push(overlayAlias);
- this.aliasById[overlayAlias.getId()] = overlayAlias;
-};
-
-/**
- * Adds reaction to the {@link DataOverlay}
- *
- * @param {LayoutReaction} overlayReaction
- * information about reaction in the overlay
- */
-DataOverlay.prototype.addReaction = function (overlayReaction) {
- this.reactions.push(overlayReaction);
-};
-
-/**
- *
- * @returns {number}
- */
-DataOverlay.prototype.getId = function () {
- return this.id;
-};
-
-/**
- *
- * @param {number|string} id
- */
-DataOverlay.prototype.setId = function (id) {
- this.id = parseInt(id);
-};
-
-/**
- *
- * @returns {string}
- */
-DataOverlay.prototype.getDescription = function () {
- return this._description;
-};
-
-/**
- *
- * @param {string} description
- */
-DataOverlay.prototype.setDescription = function (description) {
- this._description = description;
-};
-
-/**
- *
- * @returns {string}
- */
-DataOverlay.prototype.getCreator = function () {
- return this._creator;
-};
-
-/**
- *
- * @param {string} creator
- */
-DataOverlay.prototype.setCreator = function (creator) {
- this._creator = creator;
-};
-
-/**
- *
- * @returns {boolean}
- */
-DataOverlay.prototype.getInputDataAvailable = function () {
- return this._inputDataAvailable;
-};
-
-/**
- *
- * @param {string|boolean} inputDataAvailable
- */
-DataOverlay.prototype.setInputDataAvailable = function (inputDataAvailable) {
- var value = inputDataAvailable;
- if (inputDataAvailable === undefined) {
- value = false;
- } else if (inputDataAvailable === "true") {
- value = true;
- } else if (inputDataAvailable === "false") {
- value = false;
- } else if (typeof (inputDataAvailable) !== "boolean") {
- logger.warn("inputDataAvailable should be boolean");
- value = false;
- }
- this._inputDataAvailable = value;
-};
-
-/**
- *
- * @returns {string}
- */
-DataOverlay.prototype.getName = function () {
- return this.name;
-};
-
-/**
- *
- * @param {string} name
- */
-DataOverlay.prototype.setName = function (name) {
- this.name = name;
-};
-
-/**
- *
- * @param {number} modelId
- * @returns {string|null}
- */
-DataOverlay.prototype.getImagesDirectory = function (modelId) {
- for (var i = 0; i < this._imagesDirectory.length; i++) {
- if (parseInt(this._imagesDirectory[i].modelId) === modelId) {
- return this._imagesDirectory[i].path;
- }
- }
- return null;
-};
-
-/**
- *
- * @param {Object.<number,string>} imagesDirectory
- */
-DataOverlay.prototype.setImagesDirectory = function (imagesDirectory) {
- this._imagesDirectory = imagesDirectory;
-};
-
-/**
- *
- * @param {LayoutAlias} overlayAlias
- */
-DataOverlay.prototype.updateAlias = function (overlayAlias) {
- if (this.aliasById[overlayAlias.getId()] === undefined) {
- logger.warn("Cannot update alias, it doesn't exist. Alias: " + overlayAlias.getId());
- } else {
- this.aliasById[overlayAlias.getId()].update(overlayAlias);
- }
-};
-
-/**
- *
- * @param {number} id
- * @returns {LayoutAlias}
- */
-DataOverlay.prototype.getAliasById = function (id) {
- return this.aliasById[id];
-};
-
-/**
- *
- * @param {number} id
- * @returns {Promise<LayoutAlias>}
- */
-DataOverlay.prototype.getFullAliasById = function (id) {
- var self = this;
- var alias = self.getAliasById(id);
- if (alias !== undefined) {
- if (alias.getType() === LayoutAlias.LIGHT) {
- return ServerConnector.getFullOverlayElement({
- element: new IdentifiedElement(alias),
- overlay: self
- }).then(function (data) {
- self.updateAlias(data);
- return alias;
- });
- }
- }
- return Promise.resolve(alias);
-};
-
-/**
- *
- * @param {boolean} value
- */
-DataOverlay.prototype.setInitialized = function (value) {
- this._initialized = value;
-};
-
-/**
- *
- * @returns {boolean}
- */
-DataOverlay.prototype.isInitialized = function () {
- return this._initialized;
-};
-
-/**
- *
- * @returns {LayoutAlias[]}
- */
-DataOverlay.prototype.getAliases = function () {
- return this.aliases;
-};
-
-/**
- *
- * @returns {LayoutReaction[]}
- */
-DataOverlay.prototype.getReactions = function () {
- return this.reactions;
-};
-
-/**
- *
- * @returns {Promise}
- */
-DataOverlay.prototype.init = function () {
- var self = this;
- if (this.isInitialized()) {
- return Promise.resolve();
- }
- return ServerConnector.getOverlayElements(self.getId()).then(function (data) {
- for (var i = 0; i < data.length; i++) {
- if (data[i] instanceof LayoutAlias) {
- self.addAlias(data[i]);
- } else if (data[i] instanceof LayoutReaction) {
- self.addReaction(data[i]);
- } else {
- return Promise.reject("Unknown element type: " + typeof (data[i]));
- }
-
- }
- self.setInitialized(true);
- });
-
-};
-
-/**
- *
- * @returns {boolean}
- */
-DataOverlay.prototype.getPublicOverlay = function () {
- return this._publicOverlay;
-};
-
-/**
- *
- * @param {boolean} publicOverlay
- */
-DataOverlay.prototype.setPublicOverlay = function (publicOverlay) {
- this._publicOverlay = publicOverlay;
-};
-
-/**
- *
- * @returns {boolean}
- */
-DataOverlay.prototype.isDefaultOverlay = function () {
- return this._defaultOverlay;
-};
-
-/**
- *
- * @param {boolean} defaultOverlay
- */
-DataOverlay.prototype.setDefaultOverlay = function (defaultOverlay) {
- this._defaultOverlay = defaultOverlay;
-};
-
-/**
- *
- * @returns {string}
- */
-DataOverlay.prototype.getContent = function () {
- return this._content;
-};
-
-/**
- *
- * @param {string} content
- */
-DataOverlay.prototype.setContent = function (content) {
- this._content = content;
-};
-
-/**
- *
- * @returns {number}
- */
-DataOverlay.prototype.getOrder = function () {
- return this._order;
-};
-
-/**
- *
- * @param {number} order
- */
-DataOverlay.prototype.setOrder = function (order) {
- this._order = order;
-};
-
-/**
- *
- * @returns {string}
- */
-DataOverlay.prototype.getFilename = function () {
- return this._filename;
-};
-
-/**
- *
- * @param {string} filename
- */
-DataOverlay.prototype.setFilename = function (filename) {
- this._filename = filename;
-};
-
-/**
- *
- * @returns {string}
- */
-DataOverlay.prototype.getType = function () {
- return this._type;
-};
-
-/**
- *
- * @param {string} type
- */
-DataOverlay.prototype.setType = function (type) {
- this._type = type;
-};
-
-DataOverlay.prototype.setGoogleLicenseConsent = function(value) {
- this._googleLicenseConsent = value;
-};
-
-DataOverlay.prototype.isGoogleLicenseConsent = function() {
- return this._googleLicenseConsent;
-};
-
-/**
- *
- * @param {DataOverlay} overlay
- */
-DataOverlay.prototype.update = function (overlay) {
- this.setName(overlay.getName());
- this.setDescription(overlay.getDescription());
-};
-
-
-module.exports = DataOverlay;
+"use strict";
+
+var Promise = require("bluebird");
+
+var IdentifiedElement = require('./IdentifiedElement');
+var LayoutAlias = require('./LayoutAlias');
+var LayoutReaction = require('./LayoutReaction');
+var logger = require('../../logger');
+
+/**
+ * Class representing data in a specific overlay.
+ *
+ * @param {number|Object} overlayId
+ * @param {string} [name]
+ * @constructor
+ */
+function DataOverlay(overlayId, name) {
+ this.setInitialized(false);
+
+ if (name === undefined) {
+ // from json structure
+ var object = overlayId;
+ this.setId(object.idObject);
+ this.setOrder(object.order);
+ this.setName(object.name);
+ this.setImagesDirectory(object.images);
+ this.setDescription(object.description);
+ this.setCreator(object.creator);
+ this.setContent(object.content);
+ this.setFilename(object.filename);
+ this.setPublicOverlay(object.publicOverlay);
+ this.setDefaultOverlay(object.defaultOverlay);
+ this.setGoogleLicenseConsent(object.googleLicenseConsent);
+ this.setInputDataAvailable(object.inputDataAvailable);
+ this.setType(object.type);
+ if (!this.getInputDataAvailable()) {
+ this.setInitialized(true);
+ }
+ } else {
+ // default two param call
+ this.setId(overlayId);
+ this.setName(name);
+ }
+ this.aliases = [];
+ this.aliasById = [];
+ this.reactions = [];
+}
+
+/**
+ * Adds alias to the {@link DataOverlay}
+ *
+ * @param {LayoutAlias} overlayAlias
+ * information about alias in the overlay
+ */
+DataOverlay.prototype.addAlias = function (overlayAlias) {
+ this.aliases.push(overlayAlias);
+ this.aliasById[overlayAlias.getId()] = overlayAlias;
+};
+
+/**
+ * Adds reaction to the {@link DataOverlay}
+ *
+ * @param {LayoutReaction} overlayReaction
+ * information about reaction in the overlay
+ */
+DataOverlay.prototype.addReaction = function (overlayReaction) {
+ this.reactions.push(overlayReaction);
+};
+
+/**
+ *
+ * @returns {number}
+ */
+DataOverlay.prototype.getId = function () {
+ return this.id;
+};
+
+/**
+ *
+ * @param {number|string} id
+ */
+DataOverlay.prototype.setId = function (id) {
+ this.id = parseInt(id);
+};
+
+/**
+ *
+ * @returns {string}
+ */
+DataOverlay.prototype.getDescription = function () {
+ return this._description;
+};
+
+/**
+ *
+ * @param {string} description
+ */
+DataOverlay.prototype.setDescription = function (description) {
+ this._description = description;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+DataOverlay.prototype.getCreator = function () {
+ return this._creator;
+};
+
+/**
+ *
+ * @param {string} creator
+ */
+DataOverlay.prototype.setCreator = function (creator) {
+ this._creator = creator;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+DataOverlay.prototype.getInputDataAvailable = function () {
+ return this._inputDataAvailable;
+};
+
+/**
+ *
+ * @param {string|boolean} inputDataAvailable
+ */
+DataOverlay.prototype.setInputDataAvailable = function (inputDataAvailable) {
+ var value = inputDataAvailable;
+ if (inputDataAvailable === undefined) {
+ value = false;
+ } else if (inputDataAvailable === "true") {
+ value = true;
+ } else if (inputDataAvailable === "false") {
+ value = false;
+ } else if (typeof (inputDataAvailable) !== "boolean") {
+ logger.warn("inputDataAvailable should be boolean");
+ value = false;
+ }
+ this._inputDataAvailable = value;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+DataOverlay.prototype.getName = function () {
+ return this.name;
+};
+
+/**
+ *
+ * @param {string} name
+ */
+DataOverlay.prototype.setName = function (name) {
+ this.name = name;
+};
+
+/**
+ *
+ * @param {number} modelId
+ * @returns {string|null}
+ */
+DataOverlay.prototype.getImagesDirectory = function (modelId) {
+ for (var i = 0; i < this._imagesDirectory.length; i++) {
+ if (parseInt(this._imagesDirectory[i].modelId) === modelId) {
+ return this._imagesDirectory[i].path;
+ }
+ }
+ return null;
+};
+
+/**
+ *
+ * @param {Object.<number,string>} imagesDirectory
+ */
+DataOverlay.prototype.setImagesDirectory = function (imagesDirectory) {
+ this._imagesDirectory = imagesDirectory;
+};
+
+/**
+ *
+ * @param {LayoutAlias} overlayAlias
+ */
+DataOverlay.prototype.updateAlias = function (overlayAlias) {
+ if (this.aliasById[overlayAlias.getId()] === undefined) {
+ logger.warn("Cannot update alias, it doesn't exist. Alias: " + overlayAlias.getId());
+ } else {
+ this.aliasById[overlayAlias.getId()].update(overlayAlias);
+ }
+};
+
+/**
+ *
+ * @param {number} id
+ * @returns {LayoutAlias}
+ */
+DataOverlay.prototype.getAliasById = function (id) {
+ return this.aliasById[id];
+};
+
+/**
+ *
+ * @param {number} id
+ * @returns {Promise<LayoutAlias>}
+ */
+DataOverlay.prototype.getFullAliasById = function (id) {
+ var self = this;
+ var alias = self.getAliasById(id);
+ if (alias !== undefined) {
+ if (alias.getType() === LayoutAlias.LIGHT) {
+ return ServerConnector.getFullOverlayElement({
+ element: new IdentifiedElement(alias),
+ overlay: self
+ }).then(function (data) {
+ self.updateAlias(data);
+ return alias;
+ });
+ }
+ }
+ return Promise.resolve(alias);
+};
+
+/**
+ *
+ * @param {boolean} value
+ */
+DataOverlay.prototype.setInitialized = function (value) {
+ this._initialized = value;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+DataOverlay.prototype.isInitialized = function () {
+ return this._initialized;
+};
+
+/**
+ *
+ * @returns {LayoutAlias[]}
+ */
+DataOverlay.prototype.getAliases = function () {
+ return this.aliases;
+};
+
+/**
+ *
+ * @returns {LayoutReaction[]}
+ */
+DataOverlay.prototype.getReactions = function () {
+ return this.reactions;
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+DataOverlay.prototype.init = function () {
+ var self = this;
+ if (this.isInitialized()) {
+ return Promise.resolve();
+ }
+ return ServerConnector.getOverlayElements(self.getId()).then(function (data) {
+ for (var i = 0; i < data.length; i++) {
+ if (data[i] instanceof LayoutAlias) {
+ self.addAlias(data[i]);
+ } else if (data[i] instanceof LayoutReaction) {
+ self.addReaction(data[i]);
+ } else {
+ return Promise.reject("Unknown element type: " + typeof (data[i]));
+ }
+
+ }
+ self.setInitialized(true);
+ });
+
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+DataOverlay.prototype.getPublicOverlay = function () {
+ return this._publicOverlay;
+};
+
+/**
+ *
+ * @param {boolean} publicOverlay
+ */
+DataOverlay.prototype.setPublicOverlay = function (publicOverlay) {
+ this._publicOverlay = publicOverlay;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+DataOverlay.prototype.isDefaultOverlay = function () {
+ return this._defaultOverlay;
+};
+
+/**
+ *
+ * @param {boolean} defaultOverlay
+ */
+DataOverlay.prototype.setDefaultOverlay = function (defaultOverlay) {
+ this._defaultOverlay = defaultOverlay;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+DataOverlay.prototype.getContent = function () {
+ return this._content;
+};
+
+/**
+ *
+ * @param {string} content
+ */
+DataOverlay.prototype.setContent = function (content) {
+ this._content = content;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+DataOverlay.prototype.getOrder = function () {
+ return this._order;
+};
+
+/**
+ *
+ * @param {number} order
+ */
+DataOverlay.prototype.setOrder = function (order) {
+ this._order = order;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+DataOverlay.prototype.getFilename = function () {
+ return this._filename;
+};
+
+/**
+ *
+ * @param {string} filename
+ */
+DataOverlay.prototype.setFilename = function (filename) {
+ this._filename = filename;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+DataOverlay.prototype.getType = function () {
+ return this._type;
+};
+
+/**
+ *
+ * @param {string} type
+ */
+DataOverlay.prototype.setType = function (type) {
+ this._type = type;
+};
+
+DataOverlay.prototype.setGoogleLicenseConsent = function(value) {
+ this._googleLicenseConsent = value;
+};
+
+DataOverlay.prototype.isGoogleLicenseConsent = function() {
+ return this._googleLicenseConsent;
+};
+
+/**
+ *
+ * @param {DataOverlay} overlay
+ */
+DataOverlay.prototype.update = function (overlay) {
+ this.setName(overlay.getName());
+ this.setDescription(overlay.getDescription());
+};
+
+
+module.exports = DataOverlay;
diff --git a/frontend-js/src/main/js/map/data/Drug.js b/frontend-js/src/main/js/map/data/Drug.js
index cebafe5a1cac2227db9a1e0f8496d22fa35b751d..3addb61d5c5ae5ac878e3a8be9683ebf277d776a 100644
--- a/frontend-js/src/main/js/map/data/Drug.js
+++ b/frontend-js/src/main/js/map/data/Drug.js
@@ -1,108 +1,108 @@
-"use strict";
-
-var Annotation = require("./Annotation");
-var TargettingStructure = require("./TargettingStructure");
-
-/**
- *
- * @param javaObject
- * @constructor
- */
-function Drug(javaObject) {
- TargettingStructure.call(this, javaObject);
- if (javaObject !== undefined) {
- this.setBrandNames(javaObject.brandNames);
- this.setReferences(javaObject.references);
- this.setSynonyms(javaObject.synonyms);
- this.setDescription(javaObject.description);
- this.setBloodBrainBarrier(javaObject.bloodBrainBarrier);
- }
-}
-
-Drug.prototype = Object.create(TargettingStructure.prototype);
-Drug.prototype.constructor = Drug;
-
-/**
- *
- * @param {string[]} brandNames
- */
-Drug.prototype.setBrandNames = function (brandNames) {
- this._brandNames = brandNames;
-};
-
-/**
- *
- * @returns {string[]}
- */
-Drug.prototype.getBrandNames = function () {
- return this._brandNames;
-};
-
-/**
- *
- * @param {Annotation[]}references
- */
-Drug.prototype.setReferences = function (references) {
- this._references = [];
- for (var i = 0; i < references.length; i++) {
- this._references.push(new Annotation(references[i]));
- }
-};
-
-/**
- *
- * @returns {Annotation[]}
- */
-Drug.prototype.getReferences = function () {
- return this._references;
-};
-
-/**
- *
- * @param {string[]} synonyms
- */
-Drug.prototype.setSynonyms = function (synonyms) {
- this._synonyms = synonyms;
-};
-
-/**
- *
- * @returns {string[]}
- */
-Drug.prototype.getSynonyms = function () {
- return this._synonyms;
-};
-
-/**
- *
- * @param {string} description
- */
-Drug.prototype.setDescription = function (description) {
- this._description = description;
-};
-
-/**
- *
- * @returns {string}
- */
-Drug.prototype.getDescription = function () {
- return this._description;
-};
-
-/**
- *
- * @param {boolean} bloodBrainBarrier
- */
-Drug.prototype.setBloodBrainBarrier = function (bloodBrainBarrier) {
- this._bloodBrainBarrier = bloodBrainBarrier;
-};
-
-/**
- *
- * @returns {boolean}
- */
-Drug.prototype.getBloodBrainBarrier = function () {
- return this._bloodBrainBarrier;
-};
-
-module.exports = Drug;
+"use strict";
+
+var Annotation = require("./Annotation");
+var TargettingStructure = require("./TargettingStructure");
+
+/**
+ *
+ * @param javaObject
+ * @constructor
+ */
+function Drug(javaObject) {
+ TargettingStructure.call(this, javaObject);
+ if (javaObject !== undefined) {
+ this.setBrandNames(javaObject.brandNames);
+ this.setReferences(javaObject.references);
+ this.setSynonyms(javaObject.synonyms);
+ this.setDescription(javaObject.description);
+ this.setBloodBrainBarrier(javaObject.bloodBrainBarrier);
+ }
+}
+
+Drug.prototype = Object.create(TargettingStructure.prototype);
+Drug.prototype.constructor = Drug;
+
+/**
+ *
+ * @param {string[]} brandNames
+ */
+Drug.prototype.setBrandNames = function (brandNames) {
+ this._brandNames = brandNames;
+};
+
+/**
+ *
+ * @returns {string[]}
+ */
+Drug.prototype.getBrandNames = function () {
+ return this._brandNames;
+};
+
+/**
+ *
+ * @param {Annotation[]}references
+ */
+Drug.prototype.setReferences = function (references) {
+ this._references = [];
+ for (var i = 0; i < references.length; i++) {
+ this._references.push(new Annotation(references[i]));
+ }
+};
+
+/**
+ *
+ * @returns {Annotation[]}
+ */
+Drug.prototype.getReferences = function () {
+ return this._references;
+};
+
+/**
+ *
+ * @param {string[]} synonyms
+ */
+Drug.prototype.setSynonyms = function (synonyms) {
+ this._synonyms = synonyms;
+};
+
+/**
+ *
+ * @returns {string[]}
+ */
+Drug.prototype.getSynonyms = function () {
+ return this._synonyms;
+};
+
+/**
+ *
+ * @param {string} description
+ */
+Drug.prototype.setDescription = function (description) {
+ this._description = description;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Drug.prototype.getDescription = function () {
+ return this._description;
+};
+
+/**
+ *
+ * @param {boolean} bloodBrainBarrier
+ */
+Drug.prototype.setBloodBrainBarrier = function (bloodBrainBarrier) {
+ this._bloodBrainBarrier = bloodBrainBarrier;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+Drug.prototype.getBloodBrainBarrier = function () {
+ return this._bloodBrainBarrier;
+};
+
+module.exports = Drug;
diff --git a/frontend-js/src/main/js/map/data/GeneVariant.js b/frontend-js/src/main/js/map/data/GeneVariant.js
index 50fa4462f2eecc232ad702e927cdd6dfbed6928b..166b1edb754f5c2b62cd0d5abc43f18ceb15de00 100644
--- a/frontend-js/src/main/js/map/data/GeneVariant.js
+++ b/frontend-js/src/main/js/map/data/GeneVariant.js
@@ -1,164 +1,164 @@
-"use strict";
-
-/**
- *
- * @param {Object} javaObject
- * @param {number} javaObject.position
- * @param {string} javaObject.originalDna
- * @param {string} javaObject.modifiedDna
- * @param {string} javaObject.referenceGenomeType
- * @param {string} javaObject.referenceGenomeVersion
- * @param {string} javaObject.contig
- * @param {null|number} [javaObject.allelFrequency]
- * @param {null|string} [javaObject.variantIdentifier]
- *
- * @constructor
- */
-function GeneVariant(javaObject) {
- this.setPosition(javaObject.position);
- this.setOriginalDna(javaObject.originalDna);
- this.setModifiedDna(javaObject.modifiedDna);
- this.setReferenceGenomeType(javaObject.referenceGenomeType);
- this.setReferenceGenomeVersion(javaObject.referenceGenomeVersion);
- this.setContig(javaObject.contig);
- this.setAllelFrequency(javaObject.allelFrequency);
- this.setVariantIdentifier(javaObject.variantIdentifier);
-}
-
-/**
- *
- * @param {number} position
- */
-GeneVariant.prototype.setPosition = function (position) {
- this._position = position;
-};
-
-/**
- *
- * @returns {number}
- */
-GeneVariant.prototype.getPosition = function () {
- return this._position;
-};
-
-/**
- *
- * @param {string} originalDna
- */
-GeneVariant.prototype.setOriginalDna = function (originalDna) {
- this._original = originalDna;
-};
-
-/**
- *
- * @returns {string}
- */
-GeneVariant.prototype.getOriginalDna = function () {
- return this._original;
-};
-
-/**
- *
- * @param {string} modifiedDna
- */
-GeneVariant.prototype.setModifiedDna = function (modifiedDna) {
- this._modifiedDna = modifiedDna;
-};
-
-/**
- *
- * @returns {string}
- */
-GeneVariant.prototype.getModifiedDna = function () {
- return this._modifiedDna;
-};
-
-/**
- *
- * @param {string} contig
- */
-GeneVariant.prototype.setContig = function (contig) {
- this._contig = contig;
-};
-
-/**
- *
- * @returns {string}
- */
-GeneVariant.prototype.getContig = function () {
- return this._contig;
-};
-
-/**
- *
- * @param {number} allelFrequency
- */
-GeneVariant.prototype.setAllelFrequency = function (allelFrequency) {
- if (allelFrequency === null) {
- this._allelFrequency = undefined;
- } else {
- this._allelFrequency = allelFrequency;
- }
-};
-
-/**
- *
- * @returns {number}
- */
-GeneVariant.prototype.getAllelFrequency = function () {
- return this._allelFrequency;
-};
-
-/**
- *
- * @param {string} variantIdentifier
- */
-GeneVariant.prototype.setVariantIdentifier = function (variantIdentifier) {
- if (variantIdentifier === null) {
- this._variantIdentifier = undefined;
- } else {
- this._variantIdentifier = variantIdentifier;
- }
-};
-
-/**
- *
- * @returns {string}
- */
-GeneVariant.prototype.getVariantIdentifier = function () {
- return this._variantIdentifier;
-};
-
-/**
- *
- * @param {string} referenceGenomeType
- */
-GeneVariant.prototype.setReferenceGenomeType = function (referenceGenomeType) {
- this._referenceGenomeType = referenceGenomeType;
-};
-
-/**
- *
- * @returns {string}
- */
-GeneVariant.prototype.getReferenceGenomeType = function () {
- return this._referenceGenomeType;
-};
-
-/**
- *
- * @param {string} referenceGenomeVersion
- */
-GeneVariant.prototype.setReferenceGenomeVersion = function (referenceGenomeVersion) {
- this._referenceGenomeVersion = referenceGenomeVersion;
-};
-
-/**
- *
- * @returns {string}
- */
-GeneVariant.prototype.getReferenceGenomeVersion = function () {
- return this._referenceGenomeVersion;
-};
-
-module.exports = GeneVariant;
+"use strict";
+
+/**
+ *
+ * @param {Object} javaObject
+ * @param {number} javaObject.position
+ * @param {string} javaObject.originalDna
+ * @param {string} javaObject.modifiedDna
+ * @param {string} javaObject.referenceGenomeType
+ * @param {string} javaObject.referenceGenomeVersion
+ * @param {string} javaObject.contig
+ * @param {null|number} [javaObject.allelFrequency]
+ * @param {null|string} [javaObject.variantIdentifier]
+ *
+ * @constructor
+ */
+function GeneVariant(javaObject) {
+ this.setPosition(javaObject.position);
+ this.setOriginalDna(javaObject.originalDna);
+ this.setModifiedDna(javaObject.modifiedDna);
+ this.setReferenceGenomeType(javaObject.referenceGenomeType);
+ this.setReferenceGenomeVersion(javaObject.referenceGenomeVersion);
+ this.setContig(javaObject.contig);
+ this.setAllelFrequency(javaObject.allelFrequency);
+ this.setVariantIdentifier(javaObject.variantIdentifier);
+}
+
+/**
+ *
+ * @param {number} position
+ */
+GeneVariant.prototype.setPosition = function (position) {
+ this._position = position;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+GeneVariant.prototype.getPosition = function () {
+ return this._position;
+};
+
+/**
+ *
+ * @param {string} originalDna
+ */
+GeneVariant.prototype.setOriginalDna = function (originalDna) {
+ this._original = originalDna;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getOriginalDna = function () {
+ return this._original;
+};
+
+/**
+ *
+ * @param {string} modifiedDna
+ */
+GeneVariant.prototype.setModifiedDna = function (modifiedDna) {
+ this._modifiedDna = modifiedDna;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getModifiedDna = function () {
+ return this._modifiedDna;
+};
+
+/**
+ *
+ * @param {string} contig
+ */
+GeneVariant.prototype.setContig = function (contig) {
+ this._contig = contig;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getContig = function () {
+ return this._contig;
+};
+
+/**
+ *
+ * @param {number} allelFrequency
+ */
+GeneVariant.prototype.setAllelFrequency = function (allelFrequency) {
+ if (allelFrequency === null) {
+ this._allelFrequency = undefined;
+ } else {
+ this._allelFrequency = allelFrequency;
+ }
+};
+
+/**
+ *
+ * @returns {number}
+ */
+GeneVariant.prototype.getAllelFrequency = function () {
+ return this._allelFrequency;
+};
+
+/**
+ *
+ * @param {string} variantIdentifier
+ */
+GeneVariant.prototype.setVariantIdentifier = function (variantIdentifier) {
+ if (variantIdentifier === null) {
+ this._variantIdentifier = undefined;
+ } else {
+ this._variantIdentifier = variantIdentifier;
+ }
+};
+
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getVariantIdentifier = function () {
+ return this._variantIdentifier;
+};
+
+/**
+ *
+ * @param {string} referenceGenomeType
+ */
+GeneVariant.prototype.setReferenceGenomeType = function (referenceGenomeType) {
+ this._referenceGenomeType = referenceGenomeType;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getReferenceGenomeType = function () {
+ return this._referenceGenomeType;
+};
+
+/**
+ *
+ * @param {string} referenceGenomeVersion
+ */
+GeneVariant.prototype.setReferenceGenomeVersion = function (referenceGenomeVersion) {
+ this._referenceGenomeVersion = referenceGenomeVersion;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+GeneVariant.prototype.getReferenceGenomeVersion = function () {
+ return this._referenceGenomeVersion;
+};
+
+module.exports = GeneVariant;
diff --git a/frontend-js/src/main/js/map/data/IdentifiedElement.js b/frontend-js/src/main/js/map/data/IdentifiedElement.js
index 59d26d826ed8f1c0d22ef80dbd2dba4459cdf471..855cdf88c3bf000faa5a37f4c6747939e682691a 100644
--- a/frontend-js/src/main/js/map/data/IdentifiedElement.js
+++ b/frontend-js/src/main/js/map/data/IdentifiedElement.js
@@ -1,250 +1,250 @@
-"use strict";
-
-var Alias = require('./Alias');
-var LayoutAlias = require('./LayoutAlias');
-var Reaction = require('./Reaction');
-var LayoutReaction = require('./LayoutReaction');
-var PointData = require('./PointData');
-var Point = require('../canvas/Point');
-
-var logger = require('../../logger');
-
-/**
- * @typedef {Object} IdentifiedElementInput
- * @property {string|number} [id]
- * @property {string|number} [objectId]
- * @property {number} modelId
- * @property {string} type
- * @property {string} [icon]
- */
-
-/**
- * This is object representing element tha should be visualized on the map. It's
- * very light and contains only the most important data. There are three types
- * of objects to visualize:
- * <ul>
- * <li>"ALIAS" - for {@link Alias} objects</li>
- * <li>"REACTION" - for {@link Reaction} objects</li>
- * <li>"POINT" - for any point on the map, the data connected to this kind of
- * objects are stored in {@link PointData}</li>
- * </ul>
- *
- * @param {BioEntity|LayoutAlias|LayoutReaction|PointData|IdentifiedElementInput} object
- * @constructor
- */
-function IdentifiedElement(object) {
- this._visualizationdata = {};
- if (object instanceof Alias) {
- this.setId(object.getId());
- this.setModelId(object.getModelId());
- this.setType("ALIAS");
- } else if (object instanceof LayoutAlias) {
- this.setId(object.getId());
- this.setModelId(object.getModelId());
- this.setType("ALIAS");
- } else if (object instanceof Reaction) {
- this.setId(object.getId());
- this.setModelId(object.getModelId());
- this.setType("REACTION");
- } else if (object instanceof LayoutReaction) {
- this.setId(object.getId());
- this.setModelId(object.getModelId());
- this.setType("REACTION");
- } else if (object instanceof PointData) {
- this.setId(object.getId());
- this.setModelId(object.getModelId());
- this.setType("POINT");
- } else {
- // identifier of the object to visualize
- if (object.objectId === undefined) {
- this.setId(object.id);
- } else {
- this.setId(object.objectId);
- }
- // which marker should be used to show this object
- this.setIcon(object.icon);
- // on which model the element is located
- this.setModelId(object.modelId);
- // what kind of object we are talking about
- this.setType(object.type);
- }
-
- if (this.getType() === "POINT") {
- var tmp = this.getId();
- if (tmp.indexOf("Point2D.Double") >= 0) {
- tmp = tmp.replace("Point2D.Double", "");
- tmp = JSON.parse(tmp);
- } else {
- tmp = tmp.replace("(", "");
- tmp = tmp.replace(")", "");
- tmp = tmp.split(",");
- }
- var x = parseFloat(tmp[0]).toFixed(2);
- var y = parseFloat(tmp[1]).toFixed(2);
- this._point = new Point(x, y);
- this.setId("(" + x + "," + y + ")");
- } else if (this.getType() !== "ALIAS" && this.getType() !== "REACTION") {
- throw new Error("Unknown type of identified element: " + this.getType());
- }
-
- if (this.getId() === undefined) {
- throw new Error("Id not defined for element: " + object);
- }
-}
-
-/**
- * Returns point where it should be visualized when the type of object is
- * "POINT".
- *
- * @returns {Point|null} where it should be visualized when the
- * type of object is "POINT".
- */
-IdentifiedElement.prototype.getPoint = function () {
- if (this._point === undefined || this._point === null) {
- logger.warn("No point associated with IdentifiedElement");
- return null;
- } else {
- return this._point;
- }
-};
-
-/**
- * Returns element identifier.
- *
- * @returns {string|number} element identifier
- */
-IdentifiedElement.prototype.getId = function () {
- return this.id;
-};
-
-IdentifiedElement.prototype.setId = function (id) {
- // some elements are identified by id that is not a number (like point on the
- // map)
- if (!isNaN(id)) {
- id = parseInt(id);
- }
- this.id = id;
-};
-
-/**
- *
- * @param {number|string} modelId
- */
-IdentifiedElement.prototype.setModelId = function (modelId) {
- if (modelId === undefined || modelId === null) {
- throw new Error("ModelId is invalid");
- }
- this.modelId = parseInt(modelId);
-};
-
-/**
- * Returns model identifier where element is placed.
- *
- * @returns {number} model identifier
- */
-IdentifiedElement.prototype.getModelId = function () {
- return this.modelId;
-};
-
-/**
- * Returns type of the element. For now only three types are allowed:
- * <ul>
- * <li>"ALIAS" - for {@link Alias} objects</li>
- * <li>"REACTION" - for {@link Reaction} objects</li>
- * <li>"POINT" - for any point on the map, the data connected to this kind of
- * objects are stored in {@link PointData}</li>
- * </ul>
- *
- * @returns {string} type of the element
- */
-IdentifiedElement.prototype.getType = function () {
- return this.type;
-};
-
-IdentifiedElement.prototype.setType = function (type) {
- if (type === undefined || type === null) {
- throw new Error("Type not defined");
- }
-
- this.type = type.toUpperCase();
-};
-
-/**
- * Returns icon that should be used for visualization.
- *
- * @returns {string|undefined} icon that should be used for visualization
- */
-IdentifiedElement.prototype.getIcon = function () {
- return this._visualizationdata._icon;
-};
-
-/**
- *
- * @param {string} icon
- */
-IdentifiedElement.prototype.setIcon = function (icon) {
- this._visualizationdata._icon = icon;
-};
-
-/**
- * @returns {string|undefined}
- */
-IdentifiedElement.prototype.getColor = function () {
- return this._visualizationdata._color;
-};
-
-IdentifiedElement.prototype.setColor = function (color) {
- this._visualizationdata._color = color;
-};
-
-IdentifiedElement.prototype.getOpacity = function () {
- return this._visualizationdata._opacity;
-};
-
-IdentifiedElement.prototype.setOpacity = function (opacity) {
- this._visualizationdata._opacity = opacity;
-};
-
-IdentifiedElement.prototype.getLineWeight = function () {
- return this._visualizationdata._lineWeight;
-};
-
-IdentifiedElement.prototype.setLineWeight = function (lineWeight) {
- this._visualizationdata._lineWeight = lineWeight;
-};
-IdentifiedElement.prototype.getLineOpacity = function () {
- return this._visualizationdata._lineOpacity;
-};
-
-IdentifiedElement.prototype.setLineOpacity = function (lineOpacity) {
- this._visualizationdata._lineOpacity = lineOpacity;
-};
-IdentifiedElement.prototype.getLineColor = function () {
- return this._visualizationdata._lineColor;
-};
-
-IdentifiedElement.prototype.setLineColor = function (lineColor) {
- this._visualizationdata._lineColor = lineColor;
-};
-
-IdentifiedElement.prototype.equals = function (argument) {
- if (argument instanceof IdentifiedElement) {
- return (this.getType() === argument.getType() && //
- this.getId() === argument.getId() && //
- this.getModelId() === argument.getModelId());
- } else {
- return false;
- }
-};
-
-/**
- *
- * @returns {string}
- */
-IdentifiedElement.prototype.toString = function () {
- var self = this;
- return "[" + IdentifiedElement.prototype.constructor.name + "] " + self.getType() + " " + self.getId() + " (model: "
- + self.getModelId() + ")";
-};
-
-module.exports = IdentifiedElement;
+"use strict";
+
+var Alias = require('./Alias');
+var LayoutAlias = require('./LayoutAlias');
+var Reaction = require('./Reaction');
+var LayoutReaction = require('./LayoutReaction');
+var PointData = require('./PointData');
+var Point = require('../canvas/Point');
+
+var logger = require('../../logger');
+
+/**
+ * @typedef {Object} IdentifiedElementInput
+ * @property {string|number} [id]
+ * @property {string|number} [objectId]
+ * @property {number} modelId
+ * @property {string} type
+ * @property {string} [icon]
+ */
+
+/**
+ * This is object representing element tha should be visualized on the map. It's
+ * very light and contains only the most important data. There are three types
+ * of objects to visualize:
+ * <ul>
+ * <li>"ALIAS" - for {@link Alias} objects</li>
+ * <li>"REACTION" - for {@link Reaction} objects</li>
+ * <li>"POINT" - for any point on the map, the data connected to this kind of
+ * objects are stored in {@link PointData}</li>
+ * </ul>
+ *
+ * @param {BioEntity|LayoutAlias|LayoutReaction|PointData|IdentifiedElementInput} object
+ * @constructor
+ */
+function IdentifiedElement(object) {
+ this._visualizationdata = {};
+ if (object instanceof Alias) {
+ this.setId(object.getId());
+ this.setModelId(object.getModelId());
+ this.setType("ALIAS");
+ } else if (object instanceof LayoutAlias) {
+ this.setId(object.getId());
+ this.setModelId(object.getModelId());
+ this.setType("ALIAS");
+ } else if (object instanceof Reaction) {
+ this.setId(object.getId());
+ this.setModelId(object.getModelId());
+ this.setType("REACTION");
+ } else if (object instanceof LayoutReaction) {
+ this.setId(object.getId());
+ this.setModelId(object.getModelId());
+ this.setType("REACTION");
+ } else if (object instanceof PointData) {
+ this.setId(object.getId());
+ this.setModelId(object.getModelId());
+ this.setType("POINT");
+ } else {
+ // identifier of the object to visualize
+ if (object.objectId === undefined) {
+ this.setId(object.id);
+ } else {
+ this.setId(object.objectId);
+ }
+ // which marker should be used to show this object
+ this.setIcon(object.icon);
+ // on which model the element is located
+ this.setModelId(object.modelId);
+ // what kind of object we are talking about
+ this.setType(object.type);
+ }
+
+ if (this.getType() === "POINT") {
+ var tmp = this.getId();
+ if (tmp.indexOf("Point2D.Double") >= 0) {
+ tmp = tmp.replace("Point2D.Double", "");
+ tmp = JSON.parse(tmp);
+ } else {
+ tmp = tmp.replace("(", "");
+ tmp = tmp.replace(")", "");
+ tmp = tmp.split(",");
+ }
+ var x = parseFloat(tmp[0]).toFixed(2);
+ var y = parseFloat(tmp[1]).toFixed(2);
+ this._point = new Point(x, y);
+ this.setId("(" + x + "," + y + ")");
+ } else if (this.getType() !== "ALIAS" && this.getType() !== "REACTION") {
+ throw new Error("Unknown type of identified element: " + this.getType());
+ }
+
+ if (this.getId() === undefined) {
+ throw new Error("Id not defined for element: " + object);
+ }
+}
+
+/**
+ * Returns point where it should be visualized when the type of object is
+ * "POINT".
+ *
+ * @returns {Point|null} where it should be visualized when the
+ * type of object is "POINT".
+ */
+IdentifiedElement.prototype.getPoint = function () {
+ if (this._point === undefined || this._point === null) {
+ logger.warn("No point associated with IdentifiedElement");
+ return null;
+ } else {
+ return this._point;
+ }
+};
+
+/**
+ * Returns element identifier.
+ *
+ * @returns {string|number} element identifier
+ */
+IdentifiedElement.prototype.getId = function () {
+ return this.id;
+};
+
+IdentifiedElement.prototype.setId = function (id) {
+ // some elements are identified by id that is not a number (like point on the
+ // map)
+ if (!isNaN(id)) {
+ id = parseInt(id);
+ }
+ this.id = id;
+};
+
+/**
+ *
+ * @param {number|string} modelId
+ */
+IdentifiedElement.prototype.setModelId = function (modelId) {
+ if (modelId === undefined || modelId === null) {
+ throw new Error("ModelId is invalid");
+ }
+ this.modelId = parseInt(modelId);
+};
+
+/**
+ * Returns model identifier where element is placed.
+ *
+ * @returns {number} model identifier
+ */
+IdentifiedElement.prototype.getModelId = function () {
+ return this.modelId;
+};
+
+/**
+ * Returns type of the element. For now only three types are allowed:
+ * <ul>
+ * <li>"ALIAS" - for {@link Alias} objects</li>
+ * <li>"REACTION" - for {@link Reaction} objects</li>
+ * <li>"POINT" - for any point on the map, the data connected to this kind of
+ * objects are stored in {@link PointData}</li>
+ * </ul>
+ *
+ * @returns {string} type of the element
+ */
+IdentifiedElement.prototype.getType = function () {
+ return this.type;
+};
+
+IdentifiedElement.prototype.setType = function (type) {
+ if (type === undefined || type === null) {
+ throw new Error("Type not defined");
+ }
+
+ this.type = type.toUpperCase();
+};
+
+/**
+ * Returns icon that should be used for visualization.
+ *
+ * @returns {string|undefined} icon that should be used for visualization
+ */
+IdentifiedElement.prototype.getIcon = function () {
+ return this._visualizationdata._icon;
+};
+
+/**
+ *
+ * @param {string} icon
+ */
+IdentifiedElement.prototype.setIcon = function (icon) {
+ this._visualizationdata._icon = icon;
+};
+
+/**
+ * @returns {string|undefined}
+ */
+IdentifiedElement.prototype.getColor = function () {
+ return this._visualizationdata._color;
+};
+
+IdentifiedElement.prototype.setColor = function (color) {
+ this._visualizationdata._color = color;
+};
+
+IdentifiedElement.prototype.getOpacity = function () {
+ return this._visualizationdata._opacity;
+};
+
+IdentifiedElement.prototype.setOpacity = function (opacity) {
+ this._visualizationdata._opacity = opacity;
+};
+
+IdentifiedElement.prototype.getLineWeight = function () {
+ return this._visualizationdata._lineWeight;
+};
+
+IdentifiedElement.prototype.setLineWeight = function (lineWeight) {
+ this._visualizationdata._lineWeight = lineWeight;
+};
+IdentifiedElement.prototype.getLineOpacity = function () {
+ return this._visualizationdata._lineOpacity;
+};
+
+IdentifiedElement.prototype.setLineOpacity = function (lineOpacity) {
+ this._visualizationdata._lineOpacity = lineOpacity;
+};
+IdentifiedElement.prototype.getLineColor = function () {
+ return this._visualizationdata._lineColor;
+};
+
+IdentifiedElement.prototype.setLineColor = function (lineColor) {
+ this._visualizationdata._lineColor = lineColor;
+};
+
+IdentifiedElement.prototype.equals = function (argument) {
+ if (argument instanceof IdentifiedElement) {
+ return (this.getType() === argument.getType() && //
+ this.getId() === argument.getId() && //
+ this.getModelId() === argument.getModelId());
+ } else {
+ return false;
+ }
+};
+
+/**
+ *
+ * @returns {string}
+ */
+IdentifiedElement.prototype.toString = function () {
+ var self = this;
+ return "[" + IdentifiedElement.prototype.constructor.name + "] " + self.getType() + " " + self.getId() + " (model: "
+ + self.getModelId() + ")";
+};
+
+module.exports = IdentifiedElement;
diff --git a/frontend-js/src/main/js/map/data/KineticLaw.js b/frontend-js/src/main/js/map/data/KineticLaw.js
index fb4ecc6deb8ed953caa823fada83fb9864b18e73..0fd2129d88a49b3ad49e28b4152573663580ec46 100644
--- a/frontend-js/src/main/js/map/data/KineticLaw.js
+++ b/frontend-js/src/main/js/map/data/KineticLaw.js
@@ -1,39 +1,39 @@
-"use strict";
-
-function KineticLaw(jsonObject) {
- var self = this;
- self.setParameterIds(jsonObject.parameterIds);
- self.setFunctionIds(jsonObject.functionIds);
- self.setDefinition(jsonObject.definition);
- self.setMathMlPresentation(jsonObject.mathMlPresentation);
-}
-
-KineticLaw.prototype.setParameterIds = function (parameterIds) {
- this._parameterIds = parameterIds;
-};
-KineticLaw.prototype.getParameterIds = function () {
- return this._parameterIds;
-};
-
-KineticLaw.prototype.setFunctionIds = function (functionIds) {
- this._functionIds = functionIds;
-};
-KineticLaw.prototype.getFunctionIds = function () {
- return this._functionIds;
-};
-
-KineticLaw.prototype.setDefinition = function (definition) {
- this._definition = definition;
-};
-KineticLaw.prototype.getDefinition = function () {
- return this._definition;
-};
-
-KineticLaw.prototype.setMathMlPresentation = function (mathMlPresentation) {
- this._mathMlPresentation = mathMlPresentation;
-};
-KineticLaw.prototype.getMathMlPresentation = function () {
- return this._mathMlPresentation;
-};
-
-module.exports = KineticLaw;
+"use strict";
+
+function KineticLaw(jsonObject) {
+ var self = this;
+ self.setParameterIds(jsonObject.parameterIds);
+ self.setFunctionIds(jsonObject.functionIds);
+ self.setDefinition(jsonObject.definition);
+ self.setMathMlPresentation(jsonObject.mathMlPresentation);
+}
+
+KineticLaw.prototype.setParameterIds = function (parameterIds) {
+ this._parameterIds = parameterIds;
+};
+KineticLaw.prototype.getParameterIds = function () {
+ return this._parameterIds;
+};
+
+KineticLaw.prototype.setFunctionIds = function (functionIds) {
+ this._functionIds = functionIds;
+};
+KineticLaw.prototype.getFunctionIds = function () {
+ return this._functionIds;
+};
+
+KineticLaw.prototype.setDefinition = function (definition) {
+ this._definition = definition;
+};
+KineticLaw.prototype.getDefinition = function () {
+ return this._definition;
+};
+
+KineticLaw.prototype.setMathMlPresentation = function (mathMlPresentation) {
+ this._mathMlPresentation = mathMlPresentation;
+};
+KineticLaw.prototype.getMathMlPresentation = function () {
+ return this._mathMlPresentation;
+};
+
+module.exports = KineticLaw;
diff --git a/frontend-js/src/main/js/map/data/LayoutReaction.js b/frontend-js/src/main/js/map/data/LayoutReaction.js
index 4026262f1371b037036a02890a46d9f2e4d55802..4c880969b5597d31acbc5b8093ecc1aae54e3989 100644
--- a/frontend-js/src/main/js/map/data/LayoutReaction.js
+++ b/frontend-js/src/main/js/map/data/LayoutReaction.js
@@ -1,55 +1,55 @@
-"use strict";
-
-/**
- * Class representing reaction visualized in a overlay.
- *
- * @param javaObject
- * object de-serialized from ajax query to the server side
- */
-function LayoutReaction(javaObject) {
- this.setId(javaObject.idObject);
- this.setModelId(javaObject.modelId);
- this.setWidth(javaObject.width);
- this.setColor(javaObject.color);
- this.setReverse(javaObject.reverse);
-}
-
-LayoutReaction.prototype.getId = function() {
- return this.id;
-};
-
-LayoutReaction.prototype.setId = function(id) {
- this.id = parseInt(id);
-};
-
-LayoutReaction.prototype.getModelId = function() {
- return this._modelId;
-};
-
-LayoutReaction.prototype.setModelId = function(modelId) {
- this._modelId = parseInt(modelId);
-};
-
-LayoutReaction.prototype.setWidth = function(width) {
- this.width = width;
-};
-
-LayoutReaction.prototype.setColor = function(color) {
- this.color = color;
-};
-
-LayoutReaction.prototype.setReverse= function(reverse) {
- this.reverse = reverse;
-};
-
-LayoutReaction.prototype.getWidth = function() {
- return this.width;
-};
-LayoutReaction.prototype.getColor = function() {
- return this.color;
-};
-LayoutReaction.prototype.getReverse = function() {
- return this.reverse;
-};
-
-module.exports = LayoutReaction;
+"use strict";
+
+/**
+ * Class representing reaction visualized in a overlay.
+ *
+ * @param javaObject
+ * object de-serialized from ajax query to the server side
+ */
+function LayoutReaction(javaObject) {
+ this.setId(javaObject.idObject);
+ this.setModelId(javaObject.modelId);
+ this.setWidth(javaObject.width);
+ this.setColor(javaObject.color);
+ this.setReverse(javaObject.reverse);
+}
+
+LayoutReaction.prototype.getId = function() {
+ return this.id;
+};
+
+LayoutReaction.prototype.setId = function(id) {
+ this.id = parseInt(id);
+};
+
+LayoutReaction.prototype.getModelId = function() {
+ return this._modelId;
+};
+
+LayoutReaction.prototype.setModelId = function(modelId) {
+ this._modelId = parseInt(modelId);
+};
+
+LayoutReaction.prototype.setWidth = function(width) {
+ this.width = width;
+};
+
+LayoutReaction.prototype.setColor = function(color) {
+ this.color = color;
+};
+
+LayoutReaction.prototype.setReverse= function(reverse) {
+ this.reverse = reverse;
+};
+
+LayoutReaction.prototype.getWidth = function() {
+ return this.width;
+};
+LayoutReaction.prototype.getColor = function() {
+ return this.color;
+};
+LayoutReaction.prototype.getReverse = function() {
+ return this.reverse;
+};
+
+module.exports = LayoutReaction;
diff --git a/frontend-js/src/main/js/map/data/Mesh.js b/frontend-js/src/main/js/map/data/Mesh.js
index 500ef3a9a107101e11642b1478ca03731a5652a7..433f5ca9924e89bd38fd7ac5486e332a8b5e4bac 100644
--- a/frontend-js/src/main/js/map/data/Mesh.js
+++ b/frontend-js/src/main/js/map/data/Mesh.js
@@ -1,36 +1,36 @@
-"use strict";
-
-function Mesh(jsonObject) {
- var self = this;
- self.setSynonyms(jsonObject.synonyms);
- self.setName(jsonObject.name);
- self.setId(jsonObject.id);
- self.setDescription(jsonObject.description);
-}
-
-Mesh.prototype.setSynonyms = function (synonyms) {
- this._synonyms = synonyms;
-};
-Mesh.prototype.getSynonyms = function () {
- return this._synonyms;
-};
-Mesh.prototype.setName = function (name) {
- this._name = name;
-};
-Mesh.prototype.getName = function () {
- return this._name;
-};
-Mesh.prototype.setId = function (id) {
- this._id = id;
-};
-Mesh.prototype.getId = function () {
- return this._id;
-};
-Mesh.prototype.setDescription = function (description) {
- this._description = description;
-};
-Mesh.prototype.getDescription = function () {
- return this._description;
-};
-
-module.exports = Mesh;
+"use strict";
+
+function Mesh(jsonObject) {
+ var self = this;
+ self.setSynonyms(jsonObject.synonyms);
+ self.setName(jsonObject.name);
+ self.setId(jsonObject.id);
+ self.setDescription(jsonObject.description);
+}
+
+Mesh.prototype.setSynonyms = function (synonyms) {
+ this._synonyms = synonyms;
+};
+Mesh.prototype.getSynonyms = function () {
+ return this._synonyms;
+};
+Mesh.prototype.setName = function (name) {
+ this._name = name;
+};
+Mesh.prototype.getName = function () {
+ return this._name;
+};
+Mesh.prototype.setId = function (id) {
+ this._id = id;
+};
+Mesh.prototype.getId = function () {
+ return this._id;
+};
+Mesh.prototype.setDescription = function (description) {
+ this._description = description;
+};
+Mesh.prototype.getDescription = function () {
+ return this._description;
+};
+
+module.exports = Mesh;
diff --git a/frontend-js/src/main/js/map/data/MiRna.js b/frontend-js/src/main/js/map/data/MiRna.js
index ddc024e2d8bedef67c13a02a9f9f2ac3be488985..a5b79965334b131f4d55b41a2a6fe2757fb7a835 100644
--- a/frontend-js/src/main/js/map/data/MiRna.js
+++ b/frontend-js/src/main/js/map/data/MiRna.js
@@ -1,12 +1,12 @@
-"use strict";
-
-var TargettingStructure = require("./TargettingStructure");
-
-function MiRna(javaObject) {
- TargettingStructure.call(this, javaObject);
-}
-
-MiRna.prototype = Object.create(TargettingStructure.prototype);
-MiRna.prototype.constructor = MiRna;
-
-module.exports = MiRna;
+"use strict";
+
+var TargettingStructure = require("./TargettingStructure");
+
+function MiRna(javaObject) {
+ TargettingStructure.call(this, javaObject);
+}
+
+MiRna.prototype = Object.create(TargettingStructure.prototype);
+MiRna.prototype.constructor = MiRna;
+
+module.exports = MiRna;
diff --git a/frontend-js/src/main/js/map/data/MiriamType.js b/frontend-js/src/main/js/map/data/MiriamType.js
index 57b7387244aaadd90aeef121fad18de1f763dd96..80772a63e06c33e7501686360b99ace8785d5cd5 100644
--- a/frontend-js/src/main/js/map/data/MiriamType.js
+++ b/frontend-js/src/main/js/map/data/MiriamType.js
@@ -1,60 +1,60 @@
-"use strict";
-
-var ObjectWithListeners = require('../../ObjectWithListeners');
-
-function MiriamType(data, name) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- var self = this;
- self.setUris(data.uris);
- self.setHomepage(data.homepage);
- self.setName(name);
- self.setCommonName(data.commonName);
- self.setRegistryIdentifier(data.registryIdentifier);
-}
-
-MiriamType.prototype = Object.create(ObjectWithListeners.prototype);
-MiriamType.prototype.constructor = MiriamType;
-
-MiriamType.prototype.setUris = function(uris) {
- this._uris = uris;
-};
-
-MiriamType.prototype.getUris = function() {
- return this._uris;
-};
-
-MiriamType.prototype.setHomepage = function(homepage) {
- this._homepage = homepage;
-};
-
-MiriamType.prototype.getHomepage = function() {
- return this._homepage;
-};
-
-MiriamType.prototype.setName = function(name) {
- this._name = name;
-};
-
-MiriamType.prototype.getName = function() {
- return this._name;
-};
-
-MiriamType.prototype.setCommonName = function(commonName) {
- this._commonName = commonName;
-};
-
-MiriamType.prototype.getCommonName = function() {
- return this._commonName;
-};
-
-MiriamType.prototype.setRegistryIdentifier = function(registryIdentifier) {
- this._registryIdentifier = registryIdentifier;
-};
-
-MiriamType.prototype.getRegistryIdentifier = function() {
- return this._registryIdentifier;
-};
-
-module.exports = MiriamType;
+"use strict";
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+function MiriamType(data, name) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ var self = this;
+ self.setUris(data.uris);
+ self.setHomepage(data.homepage);
+ self.setName(name);
+ self.setCommonName(data.commonName);
+ self.setRegistryIdentifier(data.registryIdentifier);
+}
+
+MiriamType.prototype = Object.create(ObjectWithListeners.prototype);
+MiriamType.prototype.constructor = MiriamType;
+
+MiriamType.prototype.setUris = function(uris) {
+ this._uris = uris;
+};
+
+MiriamType.prototype.getUris = function() {
+ return this._uris;
+};
+
+MiriamType.prototype.setHomepage = function(homepage) {
+ this._homepage = homepage;
+};
+
+MiriamType.prototype.getHomepage = function() {
+ return this._homepage;
+};
+
+MiriamType.prototype.setName = function(name) {
+ this._name = name;
+};
+
+MiriamType.prototype.getName = function() {
+ return this._name;
+};
+
+MiriamType.prototype.setCommonName = function(commonName) {
+ this._commonName = commonName;
+};
+
+MiriamType.prototype.getCommonName = function() {
+ return this._commonName;
+};
+
+MiriamType.prototype.setRegistryIdentifier = function(registryIdentifier) {
+ this._registryIdentifier = registryIdentifier;
+};
+
+MiriamType.prototype.getRegistryIdentifier = function() {
+ return this._registryIdentifier;
+};
+
+module.exports = MiriamType;
diff --git a/frontend-js/src/main/js/map/data/ModificationStateType.js b/frontend-js/src/main/js/map/data/ModificationStateType.js
index 7f5612b996c30cd90adb6b1b5faed6a7f47631cc..3343d4de4264502072158c61ccda92fb6d2d293a 100644
--- a/frontend-js/src/main/js/map/data/ModificationStateType.js
+++ b/frontend-js/src/main/js/map/data/ModificationStateType.js
@@ -1,42 +1,42 @@
-"use strict";
-
-var ObjectWithListeners = require('../../ObjectWithListeners');
-
-function ModificationStateType(data, name) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- var self = this;
- self.setAbbreviation(data.abbreviation);
- self.setName(name);
- self.setCommonName(data.commonName);
-}
-
-ModificationStateType.prototype = Object.create(ObjectWithListeners.prototype);
-ModificationStateType.prototype.constructor = ModificationStateType;
-
-ModificationStateType.prototype.setName = function(name) {
- this._name = name;
-};
-
-ModificationStateType.prototype.getName = function() {
- return this._name;
-};
-
-ModificationStateType.prototype.setAbbreviation= function(abbreviation) {
- this._abbreviation = abbreviation;
-};
-
-ModificationStateType.prototype.getAbbreviation = function() {
- return this._abbreviation;
-};
-
-ModificationStateType.prototype.setCommonName = function(commonName) {
- this._commonName = commonName;
-};
-
-ModificationStateType.prototype.getCommonName = function() {
- return this._commonName;
-};
-
-module.exports = ModificationStateType;
+"use strict";
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+function ModificationStateType(data, name) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ var self = this;
+ self.setAbbreviation(data.abbreviation);
+ self.setName(name);
+ self.setCommonName(data.commonName);
+}
+
+ModificationStateType.prototype = Object.create(ObjectWithListeners.prototype);
+ModificationStateType.prototype.constructor = ModificationStateType;
+
+ModificationStateType.prototype.setName = function(name) {
+ this._name = name;
+};
+
+ModificationStateType.prototype.getName = function() {
+ return this._name;
+};
+
+ModificationStateType.prototype.setAbbreviation= function(abbreviation) {
+ this._abbreviation = abbreviation;
+};
+
+ModificationStateType.prototype.getAbbreviation = function() {
+ return this._abbreviation;
+};
+
+ModificationStateType.prototype.setCommonName = function(commonName) {
+ this._commonName = commonName;
+};
+
+ModificationStateType.prototype.getCommonName = function() {
+ return this._commonName;
+};
+
+module.exports = ModificationStateType;
diff --git a/frontend-js/src/main/js/map/data/Modifier.js b/frontend-js/src/main/js/map/data/Modifier.js
index 9d488e0ee94e30955d8b4ba947f4bfa5800518b6..ea94bdd8b443c683131f82b324c250be34392cf0 100644
--- a/frontend-js/src/main/js/map/data/Modifier.js
+++ b/frontend-js/src/main/js/map/data/Modifier.js
@@ -1,22 +1,22 @@
-"use strict";
-
-
-function Modifier(javaObject) {
- this.setAlias(javaObject.aliasId);
- this.setStoichiometry(javaObject.stoichiometry);
-}
-
-Modifier.prototype.getAlias = function () {
- return this._alias;
-};
-Modifier.prototype.setAlias = function (alias) {
- this._alias = alias;
-};
-Modifier.prototype.getStoichiometry = function () {
- return this._stoichiometry;
-};
-Modifier.prototype.setStoichiometry = function (stoichiometry) {
- this._stoichiometry = stoichiometry;
-};
-
-module.exports = Modifier;
+"use strict";
+
+
+function Modifier(javaObject) {
+ this.setAlias(javaObject.aliasId);
+ this.setStoichiometry(javaObject.stoichiometry);
+}
+
+Modifier.prototype.getAlias = function () {
+ return this._alias;
+};
+Modifier.prototype.setAlias = function (alias) {
+ this._alias = alias;
+};
+Modifier.prototype.getStoichiometry = function () {
+ return this._stoichiometry;
+};
+Modifier.prototype.setStoichiometry = function (stoichiometry) {
+ this._stoichiometry = stoichiometry;
+};
+
+module.exports = Modifier;
diff --git a/frontend-js/src/main/js/map/data/PointData.js b/frontend-js/src/main/js/map/data/PointData.js
index c97186d002ff55a144528fc60bd471d11ded4e96..0d23a5dd3ca2493d15e120ca7691d9515a6ae6f3 100644
--- a/frontend-js/src/main/js/map/data/PointData.js
+++ b/frontend-js/src/main/js/map/data/PointData.js
@@ -1,56 +1,56 @@
-"use strict";
-
-var Point = require('../canvas/Point');
-
-/**
- * Object representing information for specific point on the map.
- */
-function PointData(javaObject, modelId) {
- if (javaObject instanceof Point) {
- this._point = javaObject;
- this._modelId = modelId;
- } else if (javaObject.constructor.name === "IdentifiedElement") {
- this._point = javaObject.getPoint();
- this._modelId = javaObject.getModelId();
- } else {
- var tmp = javaObject.idObject.replace("Point2D.Double", "");
- tmp = JSON.parse(tmp);
- var x = parseFloat(tmp[0]).toFixed(2);
- var y = parseFloat(tmp[1]).toFixed(2);
- this._point = new Point(x, y);
- this._modelId = modelId;
- }
- this._id = "(" + parseFloat(this._point.x).toFixed(2) + "," + parseFloat(this._point.y).toFixed(2) + ")";
-}
-
-/**
- * Returns identifier of the object.
- *
- * @returns {string} that is identifier of the object
- */
-PointData.prototype.getId = function() {
- return this._id;
-};
-
-/**
- * Returns point to which this object corresponds.
- *
- * @returns {Point} to which this object corresponds
- */
-PointData.prototype.getPoint = function() {
- return this._point;
-};
-
-/**
- *
- * @returns {number}
- */
-PointData.prototype.getModelId = function() {
- return this._modelId;
-};
-
-PointData.prototype.isComplete = function() {
- return true;
-};
-
-module.exports = PointData;
+"use strict";
+
+var Point = require('../canvas/Point');
+
+/**
+ * Object representing information for specific point on the map.
+ */
+function PointData(javaObject, modelId) {
+ if (javaObject instanceof Point) {
+ this._point = javaObject;
+ this._modelId = modelId;
+ } else if (javaObject.constructor.name === "IdentifiedElement") {
+ this._point = javaObject.getPoint();
+ this._modelId = javaObject.getModelId();
+ } else {
+ var tmp = javaObject.idObject.replace("Point2D.Double", "");
+ tmp = JSON.parse(tmp);
+ var x = parseFloat(tmp[0]).toFixed(2);
+ var y = parseFloat(tmp[1]).toFixed(2);
+ this._point = new Point(x, y);
+ this._modelId = modelId;
+ }
+ this._id = "(" + parseFloat(this._point.x).toFixed(2) + "," + parseFloat(this._point.y).toFixed(2) + ")";
+}
+
+/**
+ * Returns identifier of the object.
+ *
+ * @returns {string} that is identifier of the object
+ */
+PointData.prototype.getId = function() {
+ return this._id;
+};
+
+/**
+ * Returns point to which this object corresponds.
+ *
+ * @returns {Point} to which this object corresponds
+ */
+PointData.prototype.getPoint = function() {
+ return this._point;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+PointData.prototype.getModelId = function() {
+ return this._modelId;
+};
+
+PointData.prototype.isComplete = function() {
+ return true;
+};
+
+module.exports = PointData;
diff --git a/frontend-js/src/main/js/map/data/PrivilegeType.js b/frontend-js/src/main/js/map/data/PrivilegeType.js
index 45af426283985ab02e2165bc19cd799600a71254..be25207f9d7654aea14014486271468d3736bce7 100644
--- a/frontend-js/src/main/js/map/data/PrivilegeType.js
+++ b/frontend-js/src/main/js/map/data/PrivilegeType.js
@@ -1,54 +1,54 @@
-"use strict";
-
-var ObjectWithListeners = require('../../ObjectWithListeners');
-
-function PrivilegeType(data, name) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- var self = this;
- self.setName(name);
- self.setCommonName(data.commonName);
- self.setObjectType(data.objectType);
- self.setValueType(data.valueType);
-}
-
-PrivilegeType.prototype = Object.create(ObjectWithListeners.prototype);
-PrivilegeType.prototype.constructor = PrivilegeType;
-
-PrivilegeType.CONFIGURATION_MANAGE = 'CONFIGURATION_MANAGE';
-PrivilegeType.MANAGE_GENOMES = 'MANAGE_GENOMES';
-PrivilegeType.PROJECT_MANAGEMENT = 'PROJECT_MANAGEMENT';
-PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
-
-PrivilegeType.prototype.setObjectType = function (objectType) {
- this._objectType = objectType;
-};
-
-PrivilegeType.prototype.getObjectType = function () {
- return this._objectType;
-};
-PrivilegeType.prototype.setValueType = function (valueType) {
- this._valueType = valueType;
-};
-
-PrivilegeType.prototype.getValueType = function () {
- return this._valueType;
-};
-PrivilegeType.prototype.setCommonName = function (commonName) {
- this._commonName = commonName;
-};
-
-PrivilegeType.prototype.getCommonName = function () {
- return this._commonName;
-};
-
-PrivilegeType.prototype.setName = function (name) {
- this._name = name;
-};
-
-PrivilegeType.prototype.getName = function () {
- return this._name;
-};
-
-module.exports = PrivilegeType;
+"use strict";
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+function PrivilegeType(data, name) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ var self = this;
+ self.setName(name);
+ self.setCommonName(data.commonName);
+ self.setObjectType(data.objectType);
+ self.setValueType(data.valueType);
+}
+
+PrivilegeType.prototype = Object.create(ObjectWithListeners.prototype);
+PrivilegeType.prototype.constructor = PrivilegeType;
+
+PrivilegeType.CONFIGURATION_MANAGE = 'CONFIGURATION_MANAGE';
+PrivilegeType.MANAGE_GENOMES = 'MANAGE_GENOMES';
+PrivilegeType.PROJECT_MANAGEMENT = 'PROJECT_MANAGEMENT';
+PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
+
+PrivilegeType.prototype.setObjectType = function (objectType) {
+ this._objectType = objectType;
+};
+
+PrivilegeType.prototype.getObjectType = function () {
+ return this._objectType;
+};
+PrivilegeType.prototype.setValueType = function (valueType) {
+ this._valueType = valueType;
+};
+
+PrivilegeType.prototype.getValueType = function () {
+ return this._valueType;
+};
+PrivilegeType.prototype.setCommonName = function (commonName) {
+ this._commonName = commonName;
+};
+
+PrivilegeType.prototype.getCommonName = function () {
+ return this._commonName;
+};
+
+PrivilegeType.prototype.setName = function (name) {
+ this._name = name;
+};
+
+PrivilegeType.prototype.getName = function () {
+ return this._name;
+};
+
+module.exports = PrivilegeType;
diff --git a/frontend-js/src/main/js/map/data/Product.js b/frontend-js/src/main/js/map/data/Product.js
index ba1f61311296f2db7a700911d8c0cc8e247fbff2..d14459e57650a493485678fbc7efc59af204769d 100644
--- a/frontend-js/src/main/js/map/data/Product.js
+++ b/frontend-js/src/main/js/map/data/Product.js
@@ -1,23 +1,23 @@
-"use strict";
-
-
-function Product(javaObject) {
- this.setAlias(javaObject.aliasId);
- this.setStoichiometry(javaObject.stoichiometry);
-}
-
-Product.prototype.getAlias = function () {
- return this._alias;
-};
-Product.prototype.setAlias = function (alias) {
- this._alias = alias;
-};
-Product.prototype.getStoichiometry = function () {
- return this._stoichiometry;
-};
-Product.prototype.setStoichiometry = function (stoichiometry) {
- this._stoichiometry = stoichiometry;
-};
-
-
-module.exports = Product;
+"use strict";
+
+
+function Product(javaObject) {
+ this.setAlias(javaObject.aliasId);
+ this.setStoichiometry(javaObject.stoichiometry);
+}
+
+Product.prototype.getAlias = function () {
+ return this._alias;
+};
+Product.prototype.setAlias = function (alias) {
+ this._alias = alias;
+};
+Product.prototype.getStoichiometry = function () {
+ return this._stoichiometry;
+};
+Product.prototype.setStoichiometry = function (stoichiometry) {
+ this._stoichiometry = stoichiometry;
+};
+
+
+module.exports = Product;
diff --git a/frontend-js/src/main/js/map/data/Project.js b/frontend-js/src/main/js/map/data/Project.js
index e5053fbc932bb3d7674196add1a69008caece753..0f9114d09d04f2e00b528e66fea312b03ea25473 100644
--- a/frontend-js/src/main/js/map/data/Project.js
+++ b/frontend-js/src/main/js/map/data/Project.js
@@ -1,526 +1,526 @@
-"use strict";
-
-/* exported logger */
-
-var ObjectWithListeners = require('../../ObjectWithListeners');
-
-var Annotation = require("./Annotation");
-var DataOverlay = require("./DataOverlay");
-var Model = require('./MapModel');
-
-var Promise = require('bluebird');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-/**
- *
- * @param {Project|string|Object} [data]
- * @constructor
- */
-function Project(data) {
- // call super constructor
- ObjectWithListeners.call(this);
- this.registerListenerType("onreload");
-
- this._dataOverlays = [];
- this._models = [];
- this._elementsPointingToSubmap = [];
-
- if (data !== undefined) {
- this.loadFromData(data);
- }
-}
-
-// this class inherits from ObjectWithListeners class where generic methods for
-// listeners are set
-Project.prototype = Object.create(ObjectWithListeners.prototype);
-Project.prototype.constructor = Project;
-
-/**
- *
- * @param {Project|string} data
- * @private
- */
-Project.prototype.loadFromData = function (data) {
- var self = this;
- if (typeof data === "string") {
- // replace is due to some strange problem with serialization
- data = JSON.parse(data.replace(/\n/g, " "));
- }
- if (data instanceof Project) {
- self._update(data);
- } else {
- self.setId(parseInt(data.idObject));
- self.setProjectId(data.projectId);
- self.setDirectory(data.directory);
- self.setVersion(data.version);
- self.setName(data.name);
- self.setOverviewImages(data.overviewImageViews);
- self.setTopOverviewImage(data.topOverviewImage);
- self.setDisease(data.disease);
- self.setOrganism(data.organism);
- self.setStatus(data.status);
- self.setNotifyEmail(data.notifyEmail);
- self.setProgress(data.progress);
- self.setHasWarnings(data.warnings);
- self.setHasErrors(data.errors);
- self.setMapCanvasType(data.mapCanvasType);
- }
-};
-
-/**
- *
- * @param {Project} data
- * @returns {PromiseLike}
- */
-Project.prototype.update = function (data) {
- this._update(data);
- return this.callListeners("onreload");
-};
-
-/**
- *
- * @param {Project} data
- * @private
- */
-Project.prototype._update = function (data) {
- var self = this;
- self.setId(data.getId());
- self.setProjectId(data.getProjectId());
- self.setDirectory(data.getDirectory());
- self.setVersion(data.getVersion());
- self.setName(data.getName());
- self.setOverviewImages(data.getOverviewImages());
- self.setTopOverviewImage(data.getTopOverviewImage());
- self.setDisease(data.getDisease());
- self.setOrganism(data.getOrganism());
- self.setStatus(data.getStatus());
- self.setProgress(data.getProgress());
- self.setNotifyEmail(data.getNotifyEmail());
- self.setHasWarnings(data.hasWarnings());
- self.setHasErrors(data.hasErrors());
- self.setMapCanvasType(data.getMapCanvasType());
-
- if (data.getModels() !== undefined) {
- var models = data.getModels();
- for (var i = 0; i < models.length; i++) {
- self.addModel(new Model(models[i]));
- }
- }
-};
-
-/**
- *
- * @returns {number}
- */
-Project.prototype.getId = function () {
- return this._id;
-};
-
-/**
- *
- * @param {number|string} id
- */
-Project.prototype.setId = function (id) {
- this._id = parseInt(id);
-};
-
-/**
- *
- * @returns {boolean}
- */
-Project.prototype.hasErrors = function () {
- return this._hasErrors === true;
-};
-
-/**
- *
- * @param {boolean} hasErrors
- */
-Project.prototype.setHasErrors = function (hasErrors) {
- this._hasErrors = hasErrors;
-};
-
-/**
- *
- * @returns {boolean}
- */
-Project.prototype.hasWarnings = function () {
- return this._hasWarnings === true;
-};
-
-/**
- *
- * @param {boolean} hasWarnings
- */
-Project.prototype.setHasWarnings = function (hasWarnings) {
- this._hasWarnings = hasWarnings;
-};
-
-/**
- *
- * @returns {string}
- */
-Project.prototype.getProjectId = function () {
- return this._projectId;
-};
-
-/**
- *
- * @param {string} projectId
- */
-Project.prototype.setProjectId = function (projectId) {
- this._projectId = projectId;
-};
-
-/**
- *
- * @returns {string}
- */
-Project.prototype.getDirectory = function () {
- return this._directory;
-};
-
-/**
- *
- * @param {string} directory
- */
-Project.prototype.setDirectory = function (directory) {
- this._directory = directory;
-};
-
-/**
- *
- * @returns {string}
- */
-Project.prototype.getVersion = function () {
- return this._version;
-};
-
-/**
- *
- * @param {string} version
- */
-Project.prototype.setVersion = function (version) {
- this._version = version;
-};
-
-/**
- *
- * @returns {string}
- */
-Project.prototype.getName = function () {
- return this._name;
-};
-
-/**
- *
- * @param {string} name
- */
-Project.prototype.setName = function (name) {
- this._name = name;
-};
-
-/**
- *
- * @returns {MapModel[]}
- */
-Project.prototype.getModels = function () {
- return this._models;
-};
-
-/**
- *
- * @param modelId
- * @returns {MapModel|null}
- */
-Project.prototype.getModelById = function (modelId) {
- for (var i = 0; i < this._models.length; i++) {
- if (this._models[i].getId() === modelId) {
- return this._models[i];
- }
- }
- return null;
-};
-
-/**
- *
- * @param {MapModel[]} models
- */
-Project.prototype.setModels = function (models) {
- this._models = models;
-};
-
-/**
- *
- * @param {MapModel} model
- */
-Project.prototype.addModel = function (model) {
- this._models.push(model);
-};
-
-Project.prototype.getOverviewImages = function () {
- return this._overviewImages;
-};
-Project.prototype.setOverviewImages = function (overviewImages) {
- this._overviewImages = overviewImages;
-};
-
-Project.prototype.getTopOverviewImage = function () {
- return this._topOverviewImage;
-};
-Project.prototype.setTopOverviewImage = function (topOverviewImage) {
- this._topOverviewImage = topOverviewImage;
-};
-
-/**
- *
- * @returns {Annotation}
- */
-Project.prototype.getDisease = function () {
- return this._disease;
-};
-
-/**
- *
- * @param {Object} disease
- */
-Project.prototype.setDisease = function (disease) {
- if (disease !== undefined && disease !== null) {
- this._disease = new Annotation(disease);
- } else {
- this._disease = undefined;
- }
-};
-
-/**
- *
- * @returns {Annotation}
- */
-Project.prototype.getOrganism = function () {
- return this._organism;
-};
-
-/**
- *
- * @param {Object} organism
- */
-Project.prototype.setOrganism = function (organism) {
- if (organism !== undefined && organism !== null) {
- this._organism = new Annotation(organism);
- } else {
- this._organism = undefined;
- }
-};
-
-/**
- *
- * @returns {string}
- */
-Project.prototype.getMapCanvasType = function () {
- return this._mapCanvasType;
-};
-
-/**
- *
- * @param {string} mapCanvasType
- */
-Project.prototype.setMapCanvasType = function (mapCanvasType) {
- this._mapCanvasType = mapCanvasType;
-};
-
-/**
- *
- * @returns {string}
- */
-Project.prototype.getStatus = function () {
- return this._status;
-};
-
-/**
- *
- * @param {string} status
- */
-Project.prototype.setStatus = function (status) {
- this._status = status;
-};
-
-/**
- *
- * @returns {number}
- */
-Project.prototype.getProgress = function () {
- return this._progress;
-};
-
-/**
- *
- * @param {number} progress
- */
-Project.prototype.setProgress = function (progress) {
- this._progress = progress;
-};
-
-/**
- *
- * @returns {string}
- */
-Project.prototype.getNotifyEmail = function () {
- return this._notifyEmail;
-};
-
-/**
- *
- * @param {string} notifyEmail
- */
-Project.prototype.setNotifyEmail = function (notifyEmail) {
- this._notifyEmail = notifyEmail;
-};
-
-/**
- *
- * @param {DataOverlay} overlay
- * @param {boolean} [updateWhenExists=false]
- */
-Project.prototype.addDataOverlay = function (overlay, updateWhenExists) {
- var overlayToAdd = null;
- if (overlay instanceof DataOverlay) {
- overlayToAdd = overlay;
- } else {
- overlayToAdd = new DataOverlay(overlay);
- }
- var object = this._dataOverlays[overlayToAdd.getId()];
- if (object === undefined) {
- this._dataOverlays[overlayToAdd.getId()] = overlayToAdd;
- } else {
- if (updateWhenExists) {
- object.update(overlay);
- } else {
- throw new Error("Overlay " + overlayToAdd.getId() + " already exists in a project " + this.getProjectId());
- }
- }
-};
-
-/**
- *
- * @param {DataOverlay} overlay
- */
-Project.prototype.addOrUpdateDataOverlay = function (overlay) {
- this.addDataOverlay(overlay, true);
-};
-
-
-/**
- *
- * @param {DataOverlay[]} overlay
- */
-Project.prototype.addOrUpdateDataOverlays = function (overlay) {
- this.addDataOverlays(overlay, true);
-};
-
-/**
- *
- * @param {DataOverlay[]} overlays
- * @param {boolean} updateWhenExists
- */
-Project.prototype.addDataOverlays = function (overlays, updateWhenExists) {
- if (overlays === undefined) {
- logger.warn("Overlays are undefined...");
- } else {
- for (var i = 0; i < overlays.length; i++) {
- this.addDataOverlay(overlays[i], updateWhenExists);
- }
- }
-};
-
-/**
- *
- * @returns {DataOverlay[]}
- */
-Project.prototype.getDataOverlays = function () {
- var result = [];
- for (var id in this._dataOverlays) {
- if (this._dataOverlays.hasOwnProperty(id)) {
- result.push(this._dataOverlays[id]);
- }
- }
- result.sort(function (dataOverlay1, dataOverlay2) {
- if (dataOverlay1.getOrder() < dataOverlay2.getOrder())
- return -1;
- if (dataOverlay1.getOrder() > dataOverlay2.getOrder())
- return 1;
- return 0;
- });
- return result;
-};
-
-
-/**
- * Returns data overlay for a given overlay identifier.
- *
- * @param {number} overlayId
- * overlay identifier
- * @returns {PromiseLike<DataOverlay>} for a given overlay identifier
- */
-Project.prototype.getDataOverlayById = function (overlayId) {
- var self = this;
- if (self._dataOverlays[overlayId] !== undefined) {
- return Promise.resolve(self._dataOverlays[overlayId]);
- } else {
- return ServerConnector.getOverlayById(overlayId).then(function (overlay) {
- self.addDataOverlay(overlay, false);
- return self._dataOverlays[overlayId];
- });
- }
-};
-
-/**
- * Returns promise with list of elements pointing to the submap.
- *
- * @param {number} modelId id of the submap
- * @returns {Promise} for a given overlay identifier
- */
-Project.prototype.getElementsPointingToSubmap = function (modelId) {
- var self = this;
- if (self._elementsPointingToSubmap[modelId] !== undefined) {
- return Promise.resolve(self._elementsPointingToSubmap[modelId]);
- }
- var promise = Promise.resolve();
- if (self._submapConnections === undefined) {
- promise = ServerConnector.getSubmapConnections().then(function (data) {
- self._submapConnections = data;
- });
- }
- return promise.then(function () {
- self._elementsPointingToSubmap[modelId] = [];
-
- var queue = [modelId];
-
- while (queue.length > 0) {
- var id = queue.shift();
- for (var i = 0; i < self._submapConnections.length; i++) {
- var connection = self._submapConnections[i];
- if (connection.to === id) {
- var elementToAdd = connection.from;
- var alreadyAdded = false;
- for (var j = 0; j < self._elementsPointingToSubmap[modelId].length; j++) {
- var elementAlreadyAdded = self._elementsPointingToSubmap[modelId][j];
- if (elementToAdd.getId() === elementAlreadyAdded.getId()) {
- alreadyAdded = true;
- }
- }
- if (!alreadyAdded) {
- self._elementsPointingToSubmap[modelId].push(elementToAdd);
- queue.push(elementToAdd.getModelId());
- }
- }
- }
- }
-
- return self._elementsPointingToSubmap[modelId];
- });
-};
-
-
-module.exports = Project;
+"use strict";
+
+/* exported logger */
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+var Annotation = require("./Annotation");
+var DataOverlay = require("./DataOverlay");
+var Model = require('./MapModel');
+
+var Promise = require('bluebird');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+/**
+ *
+ * @param {Project|string|Object} [data]
+ * @constructor
+ */
+function Project(data) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+ this.registerListenerType("onreload");
+
+ this._dataOverlays = [];
+ this._models = [];
+ this._elementsPointingToSubmap = [];
+
+ if (data !== undefined) {
+ this.loadFromData(data);
+ }
+}
+
+// this class inherits from ObjectWithListeners class where generic methods for
+// listeners are set
+Project.prototype = Object.create(ObjectWithListeners.prototype);
+Project.prototype.constructor = Project;
+
+/**
+ *
+ * @param {Project|string} data
+ * @private
+ */
+Project.prototype.loadFromData = function (data) {
+ var self = this;
+ if (typeof data === "string") {
+ // replace is due to some strange problem with serialization
+ data = JSON.parse(data.replace(/\n/g, " "));
+ }
+ if (data instanceof Project) {
+ self._update(data);
+ } else {
+ self.setId(parseInt(data.idObject));
+ self.setProjectId(data.projectId);
+ self.setDirectory(data.directory);
+ self.setVersion(data.version);
+ self.setName(data.name);
+ self.setOverviewImages(data.overviewImageViews);
+ self.setTopOverviewImage(data.topOverviewImage);
+ self.setDisease(data.disease);
+ self.setOrganism(data.organism);
+ self.setStatus(data.status);
+ self.setNotifyEmail(data.notifyEmail);
+ self.setProgress(data.progress);
+ self.setHasWarnings(data.warnings);
+ self.setHasErrors(data.errors);
+ self.setMapCanvasType(data.mapCanvasType);
+ }
+};
+
+/**
+ *
+ * @param {Project} data
+ * @returns {PromiseLike}
+ */
+Project.prototype.update = function (data) {
+ this._update(data);
+ return this.callListeners("onreload");
+};
+
+/**
+ *
+ * @param {Project} data
+ * @private
+ */
+Project.prototype._update = function (data) {
+ var self = this;
+ self.setId(data.getId());
+ self.setProjectId(data.getProjectId());
+ self.setDirectory(data.getDirectory());
+ self.setVersion(data.getVersion());
+ self.setName(data.getName());
+ self.setOverviewImages(data.getOverviewImages());
+ self.setTopOverviewImage(data.getTopOverviewImage());
+ self.setDisease(data.getDisease());
+ self.setOrganism(data.getOrganism());
+ self.setStatus(data.getStatus());
+ self.setProgress(data.getProgress());
+ self.setNotifyEmail(data.getNotifyEmail());
+ self.setHasWarnings(data.hasWarnings());
+ self.setHasErrors(data.hasErrors());
+ self.setMapCanvasType(data.getMapCanvasType());
+
+ if (data.getModels() !== undefined) {
+ var models = data.getModels();
+ for (var i = 0; i < models.length; i++) {
+ self.addModel(new Model(models[i]));
+ }
+ }
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Project.prototype.getId = function () {
+ return this._id;
+};
+
+/**
+ *
+ * @param {number|string} id
+ */
+Project.prototype.setId = function (id) {
+ this._id = parseInt(id);
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+Project.prototype.hasErrors = function () {
+ return this._hasErrors === true;
+};
+
+/**
+ *
+ * @param {boolean} hasErrors
+ */
+Project.prototype.setHasErrors = function (hasErrors) {
+ this._hasErrors = hasErrors;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+Project.prototype.hasWarnings = function () {
+ return this._hasWarnings === true;
+};
+
+/**
+ *
+ * @param {boolean} hasWarnings
+ */
+Project.prototype.setHasWarnings = function (hasWarnings) {
+ this._hasWarnings = hasWarnings;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Project.prototype.getProjectId = function () {
+ return this._projectId;
+};
+
+/**
+ *
+ * @param {string} projectId
+ */
+Project.prototype.setProjectId = function (projectId) {
+ this._projectId = projectId;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Project.prototype.getDirectory = function () {
+ return this._directory;
+};
+
+/**
+ *
+ * @param {string} directory
+ */
+Project.prototype.setDirectory = function (directory) {
+ this._directory = directory;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Project.prototype.getVersion = function () {
+ return this._version;
+};
+
+/**
+ *
+ * @param {string} version
+ */
+Project.prototype.setVersion = function (version) {
+ this._version = version;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Project.prototype.getName = function () {
+ return this._name;
+};
+
+/**
+ *
+ * @param {string} name
+ */
+Project.prototype.setName = function (name) {
+ this._name = name;
+};
+
+/**
+ *
+ * @returns {MapModel[]}
+ */
+Project.prototype.getModels = function () {
+ return this._models;
+};
+
+/**
+ *
+ * @param modelId
+ * @returns {MapModel|null}
+ */
+Project.prototype.getModelById = function (modelId) {
+ for (var i = 0; i < this._models.length; i++) {
+ if (this._models[i].getId() === modelId) {
+ return this._models[i];
+ }
+ }
+ return null;
+};
+
+/**
+ *
+ * @param {MapModel[]} models
+ */
+Project.prototype.setModels = function (models) {
+ this._models = models;
+};
+
+/**
+ *
+ * @param {MapModel} model
+ */
+Project.prototype.addModel = function (model) {
+ this._models.push(model);
+};
+
+Project.prototype.getOverviewImages = function () {
+ return this._overviewImages;
+};
+Project.prototype.setOverviewImages = function (overviewImages) {
+ this._overviewImages = overviewImages;
+};
+
+Project.prototype.getTopOverviewImage = function () {
+ return this._topOverviewImage;
+};
+Project.prototype.setTopOverviewImage = function (topOverviewImage) {
+ this._topOverviewImage = topOverviewImage;
+};
+
+/**
+ *
+ * @returns {Annotation}
+ */
+Project.prototype.getDisease = function () {
+ return this._disease;
+};
+
+/**
+ *
+ * @param {Object} disease
+ */
+Project.prototype.setDisease = function (disease) {
+ if (disease !== undefined && disease !== null) {
+ this._disease = new Annotation(disease);
+ } else {
+ this._disease = undefined;
+ }
+};
+
+/**
+ *
+ * @returns {Annotation}
+ */
+Project.prototype.getOrganism = function () {
+ return this._organism;
+};
+
+/**
+ *
+ * @param {Object} organism
+ */
+Project.prototype.setOrganism = function (organism) {
+ if (organism !== undefined && organism !== null) {
+ this._organism = new Annotation(organism);
+ } else {
+ this._organism = undefined;
+ }
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Project.prototype.getMapCanvasType = function () {
+ return this._mapCanvasType;
+};
+
+/**
+ *
+ * @param {string} mapCanvasType
+ */
+Project.prototype.setMapCanvasType = function (mapCanvasType) {
+ this._mapCanvasType = mapCanvasType;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Project.prototype.getStatus = function () {
+ return this._status;
+};
+
+/**
+ *
+ * @param {string} status
+ */
+Project.prototype.setStatus = function (status) {
+ this._status = status;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+Project.prototype.getProgress = function () {
+ return this._progress;
+};
+
+/**
+ *
+ * @param {number} progress
+ */
+Project.prototype.setProgress = function (progress) {
+ this._progress = progress;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+Project.prototype.getNotifyEmail = function () {
+ return this._notifyEmail;
+};
+
+/**
+ *
+ * @param {string} notifyEmail
+ */
+Project.prototype.setNotifyEmail = function (notifyEmail) {
+ this._notifyEmail = notifyEmail;
+};
+
+/**
+ *
+ * @param {DataOverlay} overlay
+ * @param {boolean} [updateWhenExists=false]
+ */
+Project.prototype.addDataOverlay = function (overlay, updateWhenExists) {
+ var overlayToAdd = null;
+ if (overlay instanceof DataOverlay) {
+ overlayToAdd = overlay;
+ } else {
+ overlayToAdd = new DataOverlay(overlay);
+ }
+ var object = this._dataOverlays[overlayToAdd.getId()];
+ if (object === undefined) {
+ this._dataOverlays[overlayToAdd.getId()] = overlayToAdd;
+ } else {
+ if (updateWhenExists) {
+ object.update(overlay);
+ } else {
+ throw new Error("Overlay " + overlayToAdd.getId() + " already exists in a project " + this.getProjectId());
+ }
+ }
+};
+
+/**
+ *
+ * @param {DataOverlay} overlay
+ */
+Project.prototype.addOrUpdateDataOverlay = function (overlay) {
+ this.addDataOverlay(overlay, true);
+};
+
+
+/**
+ *
+ * @param {DataOverlay[]} overlay
+ */
+Project.prototype.addOrUpdateDataOverlays = function (overlay) {
+ this.addDataOverlays(overlay, true);
+};
+
+/**
+ *
+ * @param {DataOverlay[]} overlays
+ * @param {boolean} updateWhenExists
+ */
+Project.prototype.addDataOverlays = function (overlays, updateWhenExists) {
+ if (overlays === undefined) {
+ logger.warn("Overlays are undefined...");
+ } else {
+ for (var i = 0; i < overlays.length; i++) {
+ this.addDataOverlay(overlays[i], updateWhenExists);
+ }
+ }
+};
+
+/**
+ *
+ * @returns {DataOverlay[]}
+ */
+Project.prototype.getDataOverlays = function () {
+ var result = [];
+ for (var id in this._dataOverlays) {
+ if (this._dataOverlays.hasOwnProperty(id)) {
+ result.push(this._dataOverlays[id]);
+ }
+ }
+ result.sort(function (dataOverlay1, dataOverlay2) {
+ if (dataOverlay1.getOrder() < dataOverlay2.getOrder())
+ return -1;
+ if (dataOverlay1.getOrder() > dataOverlay2.getOrder())
+ return 1;
+ return 0;
+ });
+ return result;
+};
+
+
+/**
+ * Returns data overlay for a given overlay identifier.
+ *
+ * @param {number} overlayId
+ * overlay identifier
+ * @returns {PromiseLike<DataOverlay>} for a given overlay identifier
+ */
+Project.prototype.getDataOverlayById = function (overlayId) {
+ var self = this;
+ if (self._dataOverlays[overlayId] !== undefined) {
+ return Promise.resolve(self._dataOverlays[overlayId]);
+ } else {
+ return ServerConnector.getOverlayById(overlayId).then(function (overlay) {
+ self.addDataOverlay(overlay, false);
+ return self._dataOverlays[overlayId];
+ });
+ }
+};
+
+/**
+ * Returns promise with list of elements pointing to the submap.
+ *
+ * @param {number} modelId id of the submap
+ * @returns {Promise} for a given overlay identifier
+ */
+Project.prototype.getElementsPointingToSubmap = function (modelId) {
+ var self = this;
+ if (self._elementsPointingToSubmap[modelId] !== undefined) {
+ return Promise.resolve(self._elementsPointingToSubmap[modelId]);
+ }
+ var promise = Promise.resolve();
+ if (self._submapConnections === undefined) {
+ promise = ServerConnector.getSubmapConnections().then(function (data) {
+ self._submapConnections = data;
+ });
+ }
+ return promise.then(function () {
+ self._elementsPointingToSubmap[modelId] = [];
+
+ var queue = [modelId];
+
+ while (queue.length > 0) {
+ var id = queue.shift();
+ for (var i = 0; i < self._submapConnections.length; i++) {
+ var connection = self._submapConnections[i];
+ if (connection.to === id) {
+ var elementToAdd = connection.from;
+ var alreadyAdded = false;
+ for (var j = 0; j < self._elementsPointingToSubmap[modelId].length; j++) {
+ var elementAlreadyAdded = self._elementsPointingToSubmap[modelId][j];
+ if (elementToAdd.getId() === elementAlreadyAdded.getId()) {
+ alreadyAdded = true;
+ }
+ }
+ if (!alreadyAdded) {
+ self._elementsPointingToSubmap[modelId].push(elementToAdd);
+ queue.push(elementToAdd.getModelId());
+ }
+ }
+ }
+ }
+
+ return self._elementsPointingToSubmap[modelId];
+ });
+};
+
+
+module.exports = Project;
diff --git a/frontend-js/src/main/js/map/data/ProjectStatistics.js b/frontend-js/src/main/js/map/data/ProjectStatistics.js
index 0e5cd484641a1a04e88b51e38391628854617a04..5230dbdad6e498ecec6d2b459e7777d169bdf255 100644
--- a/frontend-js/src/main/js/map/data/ProjectStatistics.js
+++ b/frontend-js/src/main/js/map/data/ProjectStatistics.js
@@ -1,63 +1,63 @@
-"use strict";
-
-/* exported logger */
-
-var ObjectWithListeners = require('../../ObjectWithListeners');
-
-var logger = require('../../logger');
-
-function ProjectStatistics(data, configuration) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- this.setReactionAnnotations(data.reactionAnnotations, configuration);
- this.setElementAnnotations(data.elementAnnotations, configuration);
- this.setPublicationCount(data.publications, configuration);
-}
-
-ProjectStatistics.prototype = Object.create(ObjectWithListeners.prototype);
-ProjectStatistics.prototype.constructor = ProjectStatistics;
-
-ProjectStatistics.prototype.setReactionAnnotations = function(reactionAnnotations, configuration) {
- var self = this;
- self._reactionAnnotations = [];
- for ( var key in reactionAnnotations) {
- if (reactionAnnotations.hasOwnProperty(key)) {
- var miriamType = configuration.getMiriamTypeByName(key);
- self._reactionAnnotations.push({
- miriamType : miriamType,
- count : reactionAnnotations[key]
- });
- }
- }
-};
-
-ProjectStatistics.prototype.setElementAnnotations = function(elementAnnotations, configuration) {
- var self = this;
- self._elementAnnotations = [];
- for ( var key in elementAnnotations) {
- if (elementAnnotations.hasOwnProperty(key)) {
- var miriamType = configuration.getMiriamTypeByName(key);
- self._elementAnnotations.push({
- miriamType : miriamType,
- count : elementAnnotations[key]
- });
- }
- }
-};
-
-ProjectStatistics.prototype.getElementAnnotations = function() {
- return this._elementAnnotations;
-};
-ProjectStatistics.prototype.getReactionAnnotations = function() {
- return this._reactionAnnotations;
-};
-
-ProjectStatistics.prototype.setPublicationCount = function(count) {
- this._publicationsCount = count;
-};
-ProjectStatistics.prototype.getPublicationCount = function() {
- return this._publicationsCount;
-};
-
-module.exports = ProjectStatistics;
+"use strict";
+
+/* exported logger */
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+var logger = require('../../logger');
+
+function ProjectStatistics(data, configuration) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ this.setReactionAnnotations(data.reactionAnnotations, configuration);
+ this.setElementAnnotations(data.elementAnnotations, configuration);
+ this.setPublicationCount(data.publications, configuration);
+}
+
+ProjectStatistics.prototype = Object.create(ObjectWithListeners.prototype);
+ProjectStatistics.prototype.constructor = ProjectStatistics;
+
+ProjectStatistics.prototype.setReactionAnnotations = function(reactionAnnotations, configuration) {
+ var self = this;
+ self._reactionAnnotations = [];
+ for ( var key in reactionAnnotations) {
+ if (reactionAnnotations.hasOwnProperty(key)) {
+ var miriamType = configuration.getMiriamTypeByName(key);
+ self._reactionAnnotations.push({
+ miriamType : miriamType,
+ count : reactionAnnotations[key]
+ });
+ }
+ }
+};
+
+ProjectStatistics.prototype.setElementAnnotations = function(elementAnnotations, configuration) {
+ var self = this;
+ self._elementAnnotations = [];
+ for ( var key in elementAnnotations) {
+ if (elementAnnotations.hasOwnProperty(key)) {
+ var miriamType = configuration.getMiriamTypeByName(key);
+ self._elementAnnotations.push({
+ miriamType : miriamType,
+ count : elementAnnotations[key]
+ });
+ }
+ }
+};
+
+ProjectStatistics.prototype.getElementAnnotations = function() {
+ return this._elementAnnotations;
+};
+ProjectStatistics.prototype.getReactionAnnotations = function() {
+ return this._reactionAnnotations;
+};
+
+ProjectStatistics.prototype.setPublicationCount = function(count) {
+ this._publicationsCount = count;
+};
+ProjectStatistics.prototype.getPublicationCount = function() {
+ return this._publicationsCount;
+};
+
+module.exports = ProjectStatistics;
diff --git a/frontend-js/src/main/js/map/data/Reactant.js b/frontend-js/src/main/js/map/data/Reactant.js
index 8643fc280213b264e5d6342d6999c468cde02a7f..d6f65d317556d6534e84f9740efb3b25041aa762 100644
--- a/frontend-js/src/main/js/map/data/Reactant.js
+++ b/frontend-js/src/main/js/map/data/Reactant.js
@@ -1,30 +1,30 @@
-"use strict";
-
-var Alias = require("./Alias");
-
-
-function Reactant(javaObject) {
- this.setAlias(javaObject.aliasId);
- this.setStoichiometry(javaObject.stoichiometry);
-}
-
-Reactant.prototype.getAlias = function () {
- return this._alias;
-};
-
-Reactant.prototype.setAlias = function (alias) {
- this._alias = alias;
-};
-
-Reactant.prototype.isComplete = function (alias) {
- return this.getAlias() instanceof Alias;
-};
-Reactant.prototype.getStoichiometry = function () {
- return this._stoichiometry;
-};
-Reactant.prototype.setStoichiometry = function (stoichiometry) {
- this._stoichiometry = stoichiometry;
-};
-
-
-module.exports = Reactant;
+"use strict";
+
+var Alias = require("./Alias");
+
+
+function Reactant(javaObject) {
+ this.setAlias(javaObject.aliasId);
+ this.setStoichiometry(javaObject.stoichiometry);
+}
+
+Reactant.prototype.getAlias = function () {
+ return this._alias;
+};
+
+Reactant.prototype.setAlias = function (alias) {
+ this._alias = alias;
+};
+
+Reactant.prototype.isComplete = function (alias) {
+ return this.getAlias() instanceof Alias;
+};
+Reactant.prototype.getStoichiometry = function () {
+ return this._stoichiometry;
+};
+Reactant.prototype.setStoichiometry = function (stoichiometry) {
+ this._stoichiometry = stoichiometry;
+};
+
+
+module.exports = Reactant;
diff --git a/frontend-js/src/main/js/map/data/Reaction.js b/frontend-js/src/main/js/map/data/Reaction.js
index 8a0499c487eda93207e340385d29b1367444edb3..9e9efffa7dc1f8163e6d9c27f6298c1d2a16fe62 100644
--- a/frontend-js/src/main/js/map/data/Reaction.js
+++ b/frontend-js/src/main/js/map/data/Reaction.js
@@ -1,257 +1,257 @@
-"use strict";
-
-/* exported logger */
-
-var BioEntity = require("./BioEntity");
-var KineticLaw = require("./KineticLaw");
-var Point = require("../canvas/Point");
-
-var Modifier = require('./Modifier');
-var Product = require('./Product');
-var Reactant = require('./Reactant');
-
-var logger = require('../../logger');
-
-/**
- * Class representing reaction data.
- *
- * @param javaObject
- * object de-serialized from ajax query to the server side
- */
-function Reaction(javaObject) {
- BioEntity.call(this, javaObject);
- this.startLines = [];
- this.endLines = [];
- this.midLines = [];
- if (javaObject instanceof Reaction) {
- this.setId(javaObject.getId());
- this.setCenter(javaObject.getCenter());
- this.setModelId(javaObject.getModelId());
-
- this.startLines.push.apply(this.startLines, javaObject.getStartLines());
- this.endLines.push.apply(this.endLines, javaObject.getEndLines());
- this.midLines.push.apply(this.midLines, javaObject.getMidLines());
-
- } else {
- if (javaObject.idObject !== undefined) {
- this.setId(javaObject.idObject);
- } else {
- this.setId(javaObject.id);
- }
- for (var i = 0; i < javaObject.lines.length; i++) {
- var line = javaObject.lines[i];
- if (line.type === "START") {
- this.startLines.push(line);
- } else if (line.type === "END") {
- this.endLines.push(line);
- } else if (line.type === "MIDDLE") {
- this.midLines.push(line);
- } else {
- throw new Error("Unknown line type: " + line.type);
- }
- }
- this.setCenter(javaObject.centerPoint);
- this.setModelId(javaObject.modelId);
- this.setIsComplete(false);
- this.update(javaObject);
- }
-}
-
-Reaction.prototype = Object.create(BioEntity.prototype);
-Reaction.prototype.constructor = Reaction;
-
-/**
- *
- * @returns {Point}
- */
-Reaction.prototype.getCenter = function () {
- return this._center;
-};
-
-/**
- *
- * @returns {Object[]}
- */
-Reaction.prototype.getLines = function () {
- var result = [];
- result = result.concat(this.startLines);
- result = result.concat(this.endLines);
- result = result.concat(this.midLines);
- return result;
-};
-
-Reaction.prototype.getMidLines = function () {
- return this.midLines;
-};
-Reaction.prototype.getStartLines = function () {
- return this.startLines;
-};
-Reaction.prototype.getEndLines = function () {
- return this.endLines;
-};
-
-Reaction.prototype.setCenter = function (center) {
- if (center === null || center === undefined) {
- throw new Error("Setting undefined center: " + center);
- }
- this._center = new Point(center);
-};
-
-Reaction.prototype.update = function (javaObject) {
- if (javaObject.reactionId === undefined) {
- return;
- }
- this.setReactionId(javaObject.reactionId);
- this.setSymbol(javaObject.symbol);
- this.setAbbreviation(javaObject.abbreviation);
- this.setFormula(javaObject.formula);
- this.setMechanicalConfidenceScore(javaObject.mechanicalConfidenceScore);
- this.setLowerBound(javaObject.lowerBound);
- this.setUpperBound(javaObject.upperBound);
- this.setGeneProteinReaction(javaObject.geneProteinReaction);
- this.setSubsystem(javaObject.subsystem);
- this.setSynonyms(javaObject.synonyms);
- this.setDescription(javaObject.notes);
- this.setOther(javaObject.other);
- this.setReferences(javaObject.references);
- this.setType(javaObject.type);
-
- var reactants = [];
- var products = [];
- var modifiers = [];
- var i;
- if (javaObject.reactants !== undefined) {
- for (i = 0; i < javaObject.reactants.length; i++) {
- reactants.push(new Reactant(javaObject.reactants[i]));
- }
- }
- if (javaObject.products !== undefined) {
- for (i = 0; i < javaObject.products.length; i++) {
- products.push(new Product(javaObject.products[i]));
- }
- }
- if (javaObject.modifiers !== "" && javaObject.modifiers !== undefined) {
- for (i = 0; i < javaObject.modifiers.length; i++) {
- modifiers.push(new Modifier(javaObject.modifiers[i]));
- }
- }
- this.setReactants(reactants);
- this.setProducts(products);
- this.setModifiers(modifiers);
-
- if (javaObject.kineticLaw !== undefined && javaObject.kineticLaw !== null) {
- this.setKineticLaw(new KineticLaw(javaObject.kineticLaw));
- }
-
- this.setHierarchyVisibilityLevel(javaObject.hierarchyVisibilityLevel);
- this.setIsComplete(true);
-};
-
-Reaction.prototype.isComplete = function () {
- var self = this;
- var result = self._complete;
- if (result) {
- var reactants = self.getReactants();
- if (reactants.length === 0) {
- result = false;
- } else {
- result = reactants[0].isComplete();
- }
- }
- return result;
-};
-
-Reaction.prototype.getReactionId = function () {
- return this._reactionId;
-};
-
-Reaction.prototype.setReactionId = function (reactionId) {
- this._reactionId = reactionId;
-};
-
-Reaction.prototype.getMechanicalConfidenceScore = function () {
- return this._mechanicalConfidenceScore;
-};
-
-Reaction.prototype.setMechanicalConfidenceScore = function (mechanicalConfidenceScore) {
- this._mechanicalConfidenceScore = mechanicalConfidenceScore;
-};
-
-Reaction.prototype.getLowerBound = function () {
- return this._lowerBound;
-};
-
-Reaction.prototype.setLowerBound = function (lowerBound) {
- this._lowerBound = lowerBound;
-};
-
-Reaction.prototype.getUpperBound = function () {
- return this._upperBound;
-};
-
-Reaction.prototype.setUpperBound = function (upperBound) {
- this._upperBound = upperBound;
-};
-
-Reaction.prototype.setGeneProteinReaction = function (geneProteinReaction) {
- this._geneProteinReaction = geneProteinReaction;
-};
-
-Reaction.prototype.getGeneProteinReaction = function () {
- return this._geneProteinReaction;
-};
-
-Reaction.prototype.setSubsystem = function (subsystem) {
- this._subsystem = subsystem;
-};
-
-Reaction.prototype.getSubsystem = function () {
- return this._subsystem;
-};
-
-Reaction.prototype.getReactants = function () {
- return this._reactants;
-};
-
-Reaction.prototype.setReactants = function (reactants) {
- this._reactants = reactants;
-};
-
-Reaction.prototype.setProducts = function (products) {
- this._products = products;
-};
-
-Reaction.prototype.getProducts = function () {
- return this._products;
-};
-
-Reaction.prototype.getElements = function () {
- var result = [], i;
- for (i = 0; i < this.getReactants().length; i++) {
- result.push(this.getReactants()[i].getAlias());
- }
- for (i = 0; i < this.getProducts().length; i++) {
- result.push(this.getProducts()[i].getAlias());
- }
- for (i = 0; i < this.getModifiers().length; i++) {
- result.push(this.getModifiers()[i].getAlias());
- }
- return result;
-};
-
-Reaction.prototype.setModifiers = function (modifiers) {
- this._modifiers = modifiers;
-};
-
-Reaction.prototype.getModifiers = function () {
- return this._modifiers;
-};
-
-Reaction.prototype.setKineticLaw = function (kineticLaw) {
- this._kineticLaw = kineticLaw;
-};
-Reaction.prototype.getKineticLaw = function () {
- return this._kineticLaw;
-};
-
-module.exports = Reaction;
+"use strict";
+
+/* exported logger */
+
+var BioEntity = require("./BioEntity");
+var KineticLaw = require("./KineticLaw");
+var Point = require("../canvas/Point");
+
+var Modifier = require('./Modifier');
+var Product = require('./Product');
+var Reactant = require('./Reactant');
+
+var logger = require('../../logger');
+
+/**
+ * Class representing reaction data.
+ *
+ * @param javaObject
+ * object de-serialized from ajax query to the server side
+ */
+function Reaction(javaObject) {
+ BioEntity.call(this, javaObject);
+ this.startLines = [];
+ this.endLines = [];
+ this.midLines = [];
+ if (javaObject instanceof Reaction) {
+ this.setId(javaObject.getId());
+ this.setCenter(javaObject.getCenter());
+ this.setModelId(javaObject.getModelId());
+
+ this.startLines.push.apply(this.startLines, javaObject.getStartLines());
+ this.endLines.push.apply(this.endLines, javaObject.getEndLines());
+ this.midLines.push.apply(this.midLines, javaObject.getMidLines());
+
+ } else {
+ if (javaObject.idObject !== undefined) {
+ this.setId(javaObject.idObject);
+ } else {
+ this.setId(javaObject.id);
+ }
+ for (var i = 0; i < javaObject.lines.length; i++) {
+ var line = javaObject.lines[i];
+ if (line.type === "START") {
+ this.startLines.push(line);
+ } else if (line.type === "END") {
+ this.endLines.push(line);
+ } else if (line.type === "MIDDLE") {
+ this.midLines.push(line);
+ } else {
+ throw new Error("Unknown line type: " + line.type);
+ }
+ }
+ this.setCenter(javaObject.centerPoint);
+ this.setModelId(javaObject.modelId);
+ this.setIsComplete(false);
+ this.update(javaObject);
+ }
+}
+
+Reaction.prototype = Object.create(BioEntity.prototype);
+Reaction.prototype.constructor = Reaction;
+
+/**
+ *
+ * @returns {Point}
+ */
+Reaction.prototype.getCenter = function () {
+ return this._center;
+};
+
+/**
+ *
+ * @returns {Object[]}
+ */
+Reaction.prototype.getLines = function () {
+ var result = [];
+ result = result.concat(this.startLines);
+ result = result.concat(this.endLines);
+ result = result.concat(this.midLines);
+ return result;
+};
+
+Reaction.prototype.getMidLines = function () {
+ return this.midLines;
+};
+Reaction.prototype.getStartLines = function () {
+ return this.startLines;
+};
+Reaction.prototype.getEndLines = function () {
+ return this.endLines;
+};
+
+Reaction.prototype.setCenter = function (center) {
+ if (center === null || center === undefined) {
+ throw new Error("Setting undefined center: " + center);
+ }
+ this._center = new Point(center);
+};
+
+Reaction.prototype.update = function (javaObject) {
+ if (javaObject.reactionId === undefined) {
+ return;
+ }
+ this.setReactionId(javaObject.reactionId);
+ this.setSymbol(javaObject.symbol);
+ this.setAbbreviation(javaObject.abbreviation);
+ this.setFormula(javaObject.formula);
+ this.setMechanicalConfidenceScore(javaObject.mechanicalConfidenceScore);
+ this.setLowerBound(javaObject.lowerBound);
+ this.setUpperBound(javaObject.upperBound);
+ this.setGeneProteinReaction(javaObject.geneProteinReaction);
+ this.setSubsystem(javaObject.subsystem);
+ this.setSynonyms(javaObject.synonyms);
+ this.setDescription(javaObject.notes);
+ this.setOther(javaObject.other);
+ this.setReferences(javaObject.references);
+ this.setType(javaObject.type);
+
+ var reactants = [];
+ var products = [];
+ var modifiers = [];
+ var i;
+ if (javaObject.reactants !== undefined) {
+ for (i = 0; i < javaObject.reactants.length; i++) {
+ reactants.push(new Reactant(javaObject.reactants[i]));
+ }
+ }
+ if (javaObject.products !== undefined) {
+ for (i = 0; i < javaObject.products.length; i++) {
+ products.push(new Product(javaObject.products[i]));
+ }
+ }
+ if (javaObject.modifiers !== "" && javaObject.modifiers !== undefined) {
+ for (i = 0; i < javaObject.modifiers.length; i++) {
+ modifiers.push(new Modifier(javaObject.modifiers[i]));
+ }
+ }
+ this.setReactants(reactants);
+ this.setProducts(products);
+ this.setModifiers(modifiers);
+
+ if (javaObject.kineticLaw !== undefined && javaObject.kineticLaw !== null) {
+ this.setKineticLaw(new KineticLaw(javaObject.kineticLaw));
+ }
+
+ this.setHierarchyVisibilityLevel(javaObject.hierarchyVisibilityLevel);
+ this.setIsComplete(true);
+};
+
+Reaction.prototype.isComplete = function () {
+ var self = this;
+ var result = self._complete;
+ if (result) {
+ var reactants = self.getReactants();
+ if (reactants.length === 0) {
+ result = false;
+ } else {
+ result = reactants[0].isComplete();
+ }
+ }
+ return result;
+};
+
+Reaction.prototype.getReactionId = function () {
+ return this._reactionId;
+};
+
+Reaction.prototype.setReactionId = function (reactionId) {
+ this._reactionId = reactionId;
+};
+
+Reaction.prototype.getMechanicalConfidenceScore = function () {
+ return this._mechanicalConfidenceScore;
+};
+
+Reaction.prototype.setMechanicalConfidenceScore = function (mechanicalConfidenceScore) {
+ this._mechanicalConfidenceScore = mechanicalConfidenceScore;
+};
+
+Reaction.prototype.getLowerBound = function () {
+ return this._lowerBound;
+};
+
+Reaction.prototype.setLowerBound = function (lowerBound) {
+ this._lowerBound = lowerBound;
+};
+
+Reaction.prototype.getUpperBound = function () {
+ return this._upperBound;
+};
+
+Reaction.prototype.setUpperBound = function (upperBound) {
+ this._upperBound = upperBound;
+};
+
+Reaction.prototype.setGeneProteinReaction = function (geneProteinReaction) {
+ this._geneProteinReaction = geneProteinReaction;
+};
+
+Reaction.prototype.getGeneProteinReaction = function () {
+ return this._geneProteinReaction;
+};
+
+Reaction.prototype.setSubsystem = function (subsystem) {
+ this._subsystem = subsystem;
+};
+
+Reaction.prototype.getSubsystem = function () {
+ return this._subsystem;
+};
+
+Reaction.prototype.getReactants = function () {
+ return this._reactants;
+};
+
+Reaction.prototype.setReactants = function (reactants) {
+ this._reactants = reactants;
+};
+
+Reaction.prototype.setProducts = function (products) {
+ this._products = products;
+};
+
+Reaction.prototype.getProducts = function () {
+ return this._products;
+};
+
+Reaction.prototype.getElements = function () {
+ var result = [], i;
+ for (i = 0; i < this.getReactants().length; i++) {
+ result.push(this.getReactants()[i].getAlias());
+ }
+ for (i = 0; i < this.getProducts().length; i++) {
+ result.push(this.getProducts()[i].getAlias());
+ }
+ for (i = 0; i < this.getModifiers().length; i++) {
+ result.push(this.getModifiers()[i].getAlias());
+ }
+ return result;
+};
+
+Reaction.prototype.setModifiers = function (modifiers) {
+ this._modifiers = modifiers;
+};
+
+Reaction.prototype.getModifiers = function () {
+ return this._modifiers;
+};
+
+Reaction.prototype.setKineticLaw = function (kineticLaw) {
+ this._kineticLaw = kineticLaw;
+};
+Reaction.prototype.getKineticLaw = function () {
+ return this._kineticLaw;
+};
+
+module.exports = Reaction;
diff --git a/frontend-js/src/main/js/map/data/ReferenceGenome.js b/frontend-js/src/main/js/map/data/ReferenceGenome.js
index 8ed9b5445016bb0b1a922580129e125079e4c7be..cc90df69f73c79e6cc97d1c31d5a0b7ef91ea6a9 100644
--- a/frontend-js/src/main/js/map/data/ReferenceGenome.js
+++ b/frontend-js/src/main/js/map/data/ReferenceGenome.js
@@ -1,193 +1,193 @@
-"use strict";
-
-var Annotation = require('./Annotation');
-var ReferenceGenomeGeneMapping = require('./ReferenceGenomeGeneMapping');
-
-function ReferenceGenome(javaObject) {
- if (javaObject !== undefined && javaObject !== null) {
- this.setId(javaObject.idObject);
- this.setType(javaObject.type);
- this.setVersion(javaObject.version);
- this.setLocalUrl(javaObject.localUrl);
- this.setSourceUrl(javaObject.sourceUrl);
- if (javaObject.localUrl !== undefined) {
- this.setUrl(javaObject.localUrl);
- } else {
- this.setUrl(javaObject.sourceUrl);
- }
- this.setOrganism(new Annotation(javaObject.organism));
- this.setDownloadProgress(javaObject.downloadProgress);
- this._geneMapping = [];
- if (javaObject.geneMapping !== undefined) {
- for (var i = 0; i < javaObject.geneMapping.length; i++) {
- this._geneMapping.push(new ReferenceGenomeGeneMapping(javaObject.geneMapping[i]));
- }
- }
- } else {
- this._geneMapping = [];
- }
-}
-
-/**
- *
- * @param {string} type
- */
-ReferenceGenome.prototype.setType = function (type) {
- this._type = type;
-};
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenome.prototype.getType = function () {
- return this._type;
-};
-
-/**
- *
- * @param {number} id
- */
-ReferenceGenome.prototype.setId = function (id) {
- this._id = id;
-};
-
-/**
- *
- * @returns {number}
- */
-ReferenceGenome.prototype.getId = function () {
- return this._id;
-};
-
-/**
- *
- * @returns {number}
- */
-ReferenceGenome.prototype.getDownloadProgress = function () {
- return this._downloadProgress;
-};
-
-/**
- *
- * @param {number} downloadProgress
- */
-ReferenceGenome.prototype.setDownloadProgress = function (downloadProgress) {
- this._downloadProgress = downloadProgress;
-};
-
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenome.prototype.getDownloadProgressStatus = function () {
- if (this.getDownloadProgress() === 100) {
- if (this.getLocalUrl() !== undefined) {
- return "READY";
- } else {
- return "ERROR";
- }
- } else {
- if (this.getDownloadProgress() === undefined) {
- return "N/A";
- } else {
- return this.getDownloadProgress().toString();
- }
- }
-};
-
-
-/**
- *
- * @param {Annotation} organism
- */
-ReferenceGenome.prototype.setOrganism = function (organism) {
- this._organism = organism;
-};
-
-/**
- *
- * @returns {Annotation}
- */
-ReferenceGenome.prototype.getOrganism = function () {
- return this._organism;
-};
-
-/**
- *
- * @param {string} url
- */
-ReferenceGenome.prototype.setUrl = function (url) {
- this._url = url;
-};
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenome.prototype.getUrl = function () {
- return this._url;
-};
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenome.prototype.getSourceUrl = function () {
- return this._sourceUrl;
-};
-
-/**
- *
- * @param {string} sourceUrl
- */
-ReferenceGenome.prototype.setSourceUrl = function (sourceUrl) {
- this._sourceUrl = sourceUrl;
-};
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenome.prototype.getLocalUrl = function () {
- return this._localUrl;
-};
-
-/**
- *
- * @param {string} localUrl
- */
-ReferenceGenome.prototype.setLocalUrl = function (localUrl) {
- if (localUrl === null) {
- this._localUrl = undefined;
- } else {
- this._localUrl = localUrl;
- }
-};
-
-/**
- *
- * @param {string} version
- */
-ReferenceGenome.prototype.setVersion = function (version) {
- this._version = version;
-};
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenome.prototype.getVersion = function () {
- return this._version;
-};
-
-/**
- *
- * @returns {ReferenceGenomeGeneMapping[]}
- */
-ReferenceGenome.prototype.getGeneMappings = function () {
- return this._geneMapping;
-};
-
-module.exports = ReferenceGenome;
+"use strict";
+
+var Annotation = require('./Annotation');
+var ReferenceGenomeGeneMapping = require('./ReferenceGenomeGeneMapping');
+
+function ReferenceGenome(javaObject) {
+ if (javaObject !== undefined && javaObject !== null) {
+ this.setId(javaObject.idObject);
+ this.setType(javaObject.type);
+ this.setVersion(javaObject.version);
+ this.setLocalUrl(javaObject.localUrl);
+ this.setSourceUrl(javaObject.sourceUrl);
+ if (javaObject.localUrl !== undefined) {
+ this.setUrl(javaObject.localUrl);
+ } else {
+ this.setUrl(javaObject.sourceUrl);
+ }
+ this.setOrganism(new Annotation(javaObject.organism));
+ this.setDownloadProgress(javaObject.downloadProgress);
+ this._geneMapping = [];
+ if (javaObject.geneMapping !== undefined) {
+ for (var i = 0; i < javaObject.geneMapping.length; i++) {
+ this._geneMapping.push(new ReferenceGenomeGeneMapping(javaObject.geneMapping[i]));
+ }
+ }
+ } else {
+ this._geneMapping = [];
+ }
+}
+
+/**
+ *
+ * @param {string} type
+ */
+ReferenceGenome.prototype.setType = function (type) {
+ this._type = type;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getType = function () {
+ return this._type;
+};
+
+/**
+ *
+ * @param {number} id
+ */
+ReferenceGenome.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenome.prototype.getId = function () {
+ return this._id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenome.prototype.getDownloadProgress = function () {
+ return this._downloadProgress;
+};
+
+/**
+ *
+ * @param {number} downloadProgress
+ */
+ReferenceGenome.prototype.setDownloadProgress = function (downloadProgress) {
+ this._downloadProgress = downloadProgress;
+};
+
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getDownloadProgressStatus = function () {
+ if (this.getDownloadProgress() === 100) {
+ if (this.getLocalUrl() !== undefined) {
+ return "READY";
+ } else {
+ return "ERROR";
+ }
+ } else {
+ if (this.getDownloadProgress() === undefined) {
+ return "N/A";
+ } else {
+ return this.getDownloadProgress().toString();
+ }
+ }
+};
+
+
+/**
+ *
+ * @param {Annotation} organism
+ */
+ReferenceGenome.prototype.setOrganism = function (organism) {
+ this._organism = organism;
+};
+
+/**
+ *
+ * @returns {Annotation}
+ */
+ReferenceGenome.prototype.getOrganism = function () {
+ return this._organism;
+};
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenome.prototype.setUrl = function (url) {
+ this._url = url;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getUrl = function () {
+ return this._url;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getSourceUrl = function () {
+ return this._sourceUrl;
+};
+
+/**
+ *
+ * @param {string} sourceUrl
+ */
+ReferenceGenome.prototype.setSourceUrl = function (sourceUrl) {
+ this._sourceUrl = sourceUrl;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getLocalUrl = function () {
+ return this._localUrl;
+};
+
+/**
+ *
+ * @param {string} localUrl
+ */
+ReferenceGenome.prototype.setLocalUrl = function (localUrl) {
+ if (localUrl === null) {
+ this._localUrl = undefined;
+ } else {
+ this._localUrl = localUrl;
+ }
+};
+
+/**
+ *
+ * @param {string} version
+ */
+ReferenceGenome.prototype.setVersion = function (version) {
+ this._version = version;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenome.prototype.getVersion = function () {
+ return this._version;
+};
+
+/**
+ *
+ * @returns {ReferenceGenomeGeneMapping[]}
+ */
+ReferenceGenome.prototype.getGeneMappings = function () {
+ return this._geneMapping;
+};
+
+module.exports = ReferenceGenome;
diff --git a/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js b/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
index b28f702bb5667b2d93d8672502bb26faa1b602a8..d8e955bf20522b4192b69389e800bc9a697e9025 100644
--- a/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
+++ b/frontend-js/src/main/js/map/data/ReferenceGenomeGeneMapping.js
@@ -1,112 +1,112 @@
-"use strict";
-
-function ReferenceGenomeGeneMapping(javaObject) {
- this.setName(javaObject.name);
- if (javaObject.localUrl !== undefined) {
- this.setUrl(javaObject.localUrl);
- } else {
- this.setUrl(javaObject.sourceUrl);
- }
- this.setLocalUrl(javaObject.localUrl);
- this.setSourceUrl(javaObject.sourceUrl);
- this.setProgress(javaObject.downloadProgress);
- this.setId(javaObject.idObject);
-}
-
-/**
- *
- * @param {string} name
- */
-ReferenceGenomeGeneMapping.prototype.setName = function (name) {
- this._name = name;
-};
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenomeGeneMapping.prototype.getName = function () {
- return this._name;
-};
-
-/**
- *
- * @param {string} url
- */
-ReferenceGenomeGeneMapping.prototype.setUrl = function (url) {
- this._url = url;
-};
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenomeGeneMapping.prototype.getUrl = function () {
- return this._url;
-};
-
-/**
- *
- * @param {string} url
- */
-ReferenceGenomeGeneMapping.prototype.setLocalUrl = function (url) {
- this._localUrl = url;
-};
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenomeGeneMapping.prototype.getLocalUrl = function () {
- return this._localUrl;
-};
-
-/**
- *
- * @returns {string}
- */
-ReferenceGenomeGeneMapping.prototype.getSourceUrl = function () {
- return this._sourceUrl;
-};
-
-/**
- *
- * @param {string} url
- */
-ReferenceGenomeGeneMapping.prototype.setSourceUrl = function (url) {
- this._sourceUrl = url;
-};
-
-/**
- *
- * @param {number} progress
- */
-ReferenceGenomeGeneMapping.prototype.setProgress = function (progress) {
- this._progress = progress;
-};
-
-/**
- *
- * @returns {number}
- */
-ReferenceGenomeGeneMapping.prototype.getProgress = function () {
- return this._progress;
-};
-
-/**
- *
- * @param {number} id
- */
-ReferenceGenomeGeneMapping.prototype.setId = function (id) {
- this._id = id;
-};
-
-/**
- *
- * @returns {number}
- */
-ReferenceGenomeGeneMapping.prototype.getId = function () {
- return this._id;
-};
-
-module.exports = ReferenceGenomeGeneMapping;
+"use strict";
+
+function ReferenceGenomeGeneMapping(javaObject) {
+ this.setName(javaObject.name);
+ if (javaObject.localUrl !== undefined) {
+ this.setUrl(javaObject.localUrl);
+ } else {
+ this.setUrl(javaObject.sourceUrl);
+ }
+ this.setLocalUrl(javaObject.localUrl);
+ this.setSourceUrl(javaObject.sourceUrl);
+ this.setProgress(javaObject.downloadProgress);
+ this.setId(javaObject.idObject);
+}
+
+/**
+ *
+ * @param {string} name
+ */
+ReferenceGenomeGeneMapping.prototype.setName = function (name) {
+ this._name = name;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getName = function () {
+ return this._name;
+};
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenomeGeneMapping.prototype.setUrl = function (url) {
+ this._url = url;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getUrl = function () {
+ return this._url;
+};
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenomeGeneMapping.prototype.setLocalUrl = function (url) {
+ this._localUrl = url;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getLocalUrl = function () {
+ return this._localUrl;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+ReferenceGenomeGeneMapping.prototype.getSourceUrl = function () {
+ return this._sourceUrl;
+};
+
+/**
+ *
+ * @param {string} url
+ */
+ReferenceGenomeGeneMapping.prototype.setSourceUrl = function (url) {
+ this._sourceUrl = url;
+};
+
+/**
+ *
+ * @param {number} progress
+ */
+ReferenceGenomeGeneMapping.prototype.setProgress = function (progress) {
+ this._progress = progress;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenomeGeneMapping.prototype.getProgress = function () {
+ return this._progress;
+};
+
+/**
+ *
+ * @param {number} id
+ */
+ReferenceGenomeGeneMapping.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReferenceGenomeGeneMapping.prototype.getId = function () {
+ return this._id;
+};
+
+module.exports = ReferenceGenomeGeneMapping;
diff --git a/frontend-js/src/main/js/map/data/SbmlFunction.js b/frontend-js/src/main/js/map/data/SbmlFunction.js
index c6d52947cda17dce905e60047e9779c0a7a4f2d1..077b8a23770a11f9db4374fa9bd13c3fc227b40a 100644
--- a/frontend-js/src/main/js/map/data/SbmlFunction.js
+++ b/frontend-js/src/main/js/map/data/SbmlFunction.js
@@ -1,55 +1,55 @@
-"use strict";
-
-function SbmlFunction(jsonObject) {
- var self = this;
- self.setFunctionId(jsonObject.functionId);
- self.setName(jsonObject.name);
- self.setId(jsonObject.id);
- self.setArguments(jsonObject["arguments"]);
- self.setDefinition(jsonObject.definition);
- self.setMathMlPresentation(jsonObject.mathMlPresentation);
-}
-
-SbmlFunction.prototype.setFunctionId = function (functionId) {
- this._functionId = functionId;
-};
-SbmlFunction.prototype.getFunctionId = function () {
- return this._functionId;
-};
-
-SbmlFunction.prototype.setDefinition = function (definition) {
- this._definition = definition;
-};
-SbmlFunction.prototype.getDefinition = function () {
- return this._definition;
-};
-
-SbmlFunction.prototype.setMathMlPresentation = function (mathMlPresentation) {
- this._mathMlPresentation = mathMlPresentation;
-};
-SbmlFunction.prototype.getMathMlPresentation = function () {
- return this._mathMlPresentation;
-};
-
-SbmlFunction.prototype.setName = function (name) {
- this._name = name;
-};
-SbmlFunction.prototype.getName = function () {
- return this._name;
-};
-SbmlFunction.prototype.setArguments = function (args) {
- this._arguments = args;
-};
-SbmlFunction.prototype.getArguments = function () {
- return this._arguments;
-};
-
-SbmlFunction.prototype.setId = function (id) {
- this._id = id;
-};
-SbmlFunction.prototype.getId = function () {
- return this._id;
-};
-
-
-module.exports = SbmlFunction;
+"use strict";
+
+function SbmlFunction(jsonObject) {
+ var self = this;
+ self.setFunctionId(jsonObject.functionId);
+ self.setName(jsonObject.name);
+ self.setId(jsonObject.id);
+ self.setArguments(jsonObject["arguments"]);
+ self.setDefinition(jsonObject.definition);
+ self.setMathMlPresentation(jsonObject.mathMlPresentation);
+}
+
+SbmlFunction.prototype.setFunctionId = function (functionId) {
+ this._functionId = functionId;
+};
+SbmlFunction.prototype.getFunctionId = function () {
+ return this._functionId;
+};
+
+SbmlFunction.prototype.setDefinition = function (definition) {
+ this._definition = definition;
+};
+SbmlFunction.prototype.getDefinition = function () {
+ return this._definition;
+};
+
+SbmlFunction.prototype.setMathMlPresentation = function (mathMlPresentation) {
+ this._mathMlPresentation = mathMlPresentation;
+};
+SbmlFunction.prototype.getMathMlPresentation = function () {
+ return this._mathMlPresentation;
+};
+
+SbmlFunction.prototype.setName = function (name) {
+ this._name = name;
+};
+SbmlFunction.prototype.getName = function () {
+ return this._name;
+};
+SbmlFunction.prototype.setArguments = function (args) {
+ this._arguments = args;
+};
+SbmlFunction.prototype.getArguments = function () {
+ return this._arguments;
+};
+
+SbmlFunction.prototype.setId = function (id) {
+ this._id = id;
+};
+SbmlFunction.prototype.getId = function () {
+ return this._id;
+};
+
+
+module.exports = SbmlFunction;
diff --git a/frontend-js/src/main/js/map/data/SbmlParameter.js b/frontend-js/src/main/js/map/data/SbmlParameter.js
index 86c52d8b1b00e328939a4410c0c9898015c4fe6e..3bf2430104b657afefc8ced3696407e48ff97884 100644
--- a/frontend-js/src/main/js/map/data/SbmlParameter.js
+++ b/frontend-js/src/main/js/map/data/SbmlParameter.js
@@ -1,56 +1,56 @@
-"use strict";
-
-function SbmlParameter(jsonObject) {
- var self = this;
- self.setParameterId(jsonObject.parameterId);
- self.setValue(jsonObject.value);
- self.setGlobal(jsonObject.global);
- self.setName(jsonObject.name);
- self.setId(jsonObject.id);
- self.setUnitsId(jsonObject.unitsId);
-}
-
-SbmlParameter.prototype.setParameterId = function (parameterId) {
- this._parameterId = parameterId;
-};
-SbmlParameter.prototype.getParameterId = function () {
- return this._parameterId;
-};
-
-SbmlParameter.prototype.setUnitsId = function (unitsId) {
- this._unitsId = unitsId;
-};
-SbmlParameter.prototype.getUnitsId = function () {
- return this._unitsId;
-};
-
-SbmlParameter.prototype.setValue = function (value) {
- this._value = value;
-};
-SbmlParameter.prototype.getValue = function () {
- return this._value;
-};
-
-SbmlParameter.prototype.setGlobal = function (global) {
- this._global = global;
-};
-SbmlParameter.prototype.getGlobal = function () {
- return this._global;
-};
-
-SbmlParameter.prototype.setName = function (name) {
- this._name = name;
-};
-SbmlParameter.prototype.getName = function () {
- return this._name;
-};
-
-SbmlParameter.prototype.setId = function (id) {
- this._id = id;
-};
-SbmlParameter.prototype.getId = function () {
- return this._id;
-};
-
-
-module.exports = SbmlParameter;
+"use strict";
+
+function SbmlParameter(jsonObject) {
+ var self = this;
+ self.setParameterId(jsonObject.parameterId);
+ self.setValue(jsonObject.value);
+ self.setGlobal(jsonObject.global);
+ self.setName(jsonObject.name);
+ self.setId(jsonObject.id);
+ self.setUnitsId(jsonObject.unitsId);
+}
+
+SbmlParameter.prototype.setParameterId = function (parameterId) {
+ this._parameterId = parameterId;
+};
+SbmlParameter.prototype.getParameterId = function () {
+ return this._parameterId;
+};
+
+SbmlParameter.prototype.setUnitsId = function (unitsId) {
+ this._unitsId = unitsId;
+};
+SbmlParameter.prototype.getUnitsId = function () {
+ return this._unitsId;
+};
+
+SbmlParameter.prototype.setValue = function (value) {
+ this._value = value;
+};
+SbmlParameter.prototype.getValue = function () {
+ return this._value;
+};
+
+SbmlParameter.prototype.setGlobal = function (global) {
+ this._global = global;
+};
+SbmlParameter.prototype.getGlobal = function () {
+ return this._global;
+};
+
+SbmlParameter.prototype.setName = function (name) {
+ this._name = name;
+};
+SbmlParameter.prototype.getName = function () {
+ return this._name;
+};
+
+SbmlParameter.prototype.setId = function (id) {
+ this._id = id;
+};
+SbmlParameter.prototype.getId = function () {
+ return this._id;
+};
+
+
+module.exports = SbmlParameter;
diff --git a/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js b/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
index 16e07a3fe3d759e763ed2b449944a8e7fd57e0ac..a7ce5c1c9c20fc33853d414bcc19a0a77f1ee6c1 100644
--- a/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
+++ b/frontend-js/src/main/js/map/data/SearchBioEntityGroup.js
@@ -1,227 +1,227 @@
-"use strict";
-
-var Alias = require("./Alias");
-var BioEntity = require("./BioEntity");
-var Reaction = require("./Reaction");
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-/**
- * Class representing merged search bioEntities.
- *
- * @param bioEntity
- * initial bioEntity from which group is created
- */
-function SearchBioEntityGroup(bioEntity) {
- if (!(bioEntity instanceof BioEntity)) {
- throw new Error("Invalid argument");
- }
- this._bioEntites = [bioEntity];
-}
-
-SearchBioEntityGroup.prototype.bioEntityMatch = function (newBioEntity) {
- var result = true;
- var self = this;
-
- for (var i = 0; i < self._bioEntites.length; i++) {
- var bioEntity = self._bioEntites[i];
- if (self.bioEntityComparator(bioEntity, newBioEntity) !== 0) {
- result = false;
- }
- }
- return result;
-};
-
-SearchBioEntityGroup.prototype.addBioEntity = function (newBioEntity) {
- this._bioEntites.push(newBioEntity);
-};
-
-SearchBioEntityGroup.prototype.getBioEntities = function () {
- return this._bioEntites;
-};
-
-SearchBioEntityGroup.prototype.bioEntityComparator = function (bioEntity1, bioEntity2) {
- if (bioEntity1 instanceof Alias && bioEntity2 instanceof Alias) {
- if (bioEntity1.getName() !== bioEntity2.getName()) {
- return -1;
- }
- if (bioEntity1.getModelId() !== bioEntity2.getModelId()) {
- return -2;
- }
- if (bioEntity1.getCompartmentId() !== bioEntity2.getCompartmentId()) {
- return -3;
- }
- if (bioEntity1.getType() !== bioEntity2.getType()) {
- return -4;
- }
- if (bioEntity1.getOther("structuralState") !== bioEntity2.getOther("structuralState")) {
- return -5;
- }
-
- var computeSerializedModifications = function (modifications) {
- if (modifications === undefined) {
- return [];
- }
- var result = [];
- for (var i = 0; i < modifications.length; i++) {
- var modification = modifications[i];
- result.push(modification.name + "_" + modification.state);
- }
- result.sort();
- return result;
- };
- var serializedModifications1 = computeSerializedModifications(bioEntity1.getOther("modifications"));
- var serializedModifications2 = computeSerializedModifications(bioEntity2.getOther("modifications"));
- if (serializedModifications1.length !== serializedModifications2.length) {
- return -6;
- }
- for (var i = 0; i < serializedModifications1.length; i++) {
- if (serializedModifications1[i] !== serializedModifications2[i]) {
- return -7;
- }
- }
- return 0;
- }
- if (bioEntity1 instanceof Reaction && bioEntity2 instanceof Reaction) {
- if (bioEntity1.getId() !== bioEntity2.getId()) {
- return -8;
- }
- return 0;
- }
- return -9;
-};
-
-SearchBioEntityGroup.prototype.setIcon = function (icon) {
- this._icon = icon;
-};
-
-SearchBioEntityGroup.prototype.getIcon = function () {
- return this._icon;
-};
-
-//aggregated data
-SearchBioEntityGroup.prototype.getType = function () {
- return this._bioEntites[0].getType();
-};
-
-SearchBioEntityGroup.prototype.getName = function () {
- return this._bioEntites[0].getName();
-};
-
-SearchBioEntityGroup.prototype.getModelId = function () {
- return this._bioEntites[0].getModelId();
-};
-
-SearchBioEntityGroup.prototype.getCompartmentId = function () {
- return this._bioEntites[0].getCompartmentId();
-};
-
-SearchBioEntityGroup.prototype.getReactants = function () {
- return this._bioEntites[0].getReactants();
-};
-SearchBioEntityGroup.prototype.getProducts = function () {
- return this._bioEntites[0].getProducts();
-};
-SearchBioEntityGroup.prototype.getModifiers = function () {
- return this._bioEntites[0].getModifiers();
-};
-
-SearchBioEntityGroup.prototype.getFullName = function () {
- return this.getMergedParameterByFunction("getFullName");
-};
-
-SearchBioEntityGroup.prototype.getReactionId = function () {
- return this.getMergedParameterByFunction("getReactionId");
-};
-SearchBioEntityGroup.prototype.getLinkedSubmodelId = function () {
- return this.getMergedParameterByFunction("getLinkedSubmodelId");
-};
-SearchBioEntityGroup.prototype.getSymbol = function () {
- return this.getMergedParameterByFunction("getSymbol");
-};
-SearchBioEntityGroup.prototype.getAbbreviation = function () {
- return this.getMergedParameterByFunction("getAbbreviation");
-};
-SearchBioEntityGroup.prototype.getFormula = function () {
- return this.getMergedParameterByFunction("getFormula");
-};
-SearchBioEntityGroup.prototype.getMechanicalConfidenceScore = function () {
- return this.getMergedParameterByFunction("getMechanicalConfidenceScore");
-};
-SearchBioEntityGroup.prototype.getLowerBound = function () {
- return this.getMergedParameterByFunction("getLowerBound");
-};
-SearchBioEntityGroup.prototype.getUpperBound = function () {
- return this.getMergedParameterByFunction("getUpperBound");
-};
-SearchBioEntityGroup.prototype.getGeneProteinReaction = function () {
- return this.getMergedParameterByFunction("getGeneProteinReaction");
-};
-SearchBioEntityGroup.prototype.getSubsystem = function () {
- return this.getMergedParameterByFunction("getSubsystem");
-};
-SearchBioEntityGroup.prototype.getDescription = function () {
- return this.getMergedParameterByFunction("getDescription");
-};
-SearchBioEntityGroup.prototype.getCharge = function () {
- return this.getMergedParameterByFunction("getCharge");
-};
-SearchBioEntityGroup.prototype.getSynonyms = function () {
- return this.getIntersectionListByFunction("getSynonyms");
-};
-SearchBioEntityGroup.prototype.getFormerSymbols = function () {
- return this.getIntersectionListByFunction("getFormerSymbols");
-};
-
-SearchBioEntityGroup.prototype.getReferences = function () {
- return this.getIntersectionListByFunction("getReferences");
-};
-
-SearchBioEntityGroup.prototype.getOther = function (param) {
- if (param === "modifications") {
- return this.getIntersectionListByFunction(function (alias) {
- return alias.getOther(param)
- });
- } else {
- throw new Error("Don't now how to handle: " + param);
- }
-};
-
-SearchBioEntityGroup.prototype.getMergedParameterByFunction = function (functionName) {
- var bioEntities = this.getBioEntities();
- var result = bioEntities[0][functionName]();
- for (var i = 1; i < bioEntities.length; i++) {
- var newEntry = bioEntities[i][functionName]();
- if (newEntry !== result) {
- result = "Value different among merged elements";
- }
- }
- return result;
-};
-
-SearchBioEntityGroup.prototype.getIntersectionListByFunction = function (functionName) {
- var bioEntities = this.getBioEntities();
- var result;
- if (typeof functionName === "function") {
- result = functionName(bioEntities[0]);
- } else {
- result = bioEntities[0][functionName]();
- }
- for (var i = 1; i < bioEntities.length; i++) {
- var newList;
- if (typeof functionName === "function") {
- newList = functionName(bioEntities[i]);
- } else {
- newList = bioEntities[0][functionName]();
- }
- //intersection of two arrays
- result = result.filter(function (n) {
- return newList.indexOf(n) !== -1;
- });
- }
- return result;
-};
-
-
-module.exports = SearchBioEntityGroup;
+"use strict";
+
+var Alias = require("./Alias");
+var BioEntity = require("./BioEntity");
+var Reaction = require("./Reaction");
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+/**
+ * Class representing merged search bioEntities.
+ *
+ * @param bioEntity
+ * initial bioEntity from which group is created
+ */
+function SearchBioEntityGroup(bioEntity) {
+ if (!(bioEntity instanceof BioEntity)) {
+ throw new Error("Invalid argument");
+ }
+ this._bioEntites = [bioEntity];
+}
+
+SearchBioEntityGroup.prototype.bioEntityMatch = function (newBioEntity) {
+ var result = true;
+ var self = this;
+
+ for (var i = 0; i < self._bioEntites.length; i++) {
+ var bioEntity = self._bioEntites[i];
+ if (self.bioEntityComparator(bioEntity, newBioEntity) !== 0) {
+ result = false;
+ }
+ }
+ return result;
+};
+
+SearchBioEntityGroup.prototype.addBioEntity = function (newBioEntity) {
+ this._bioEntites.push(newBioEntity);
+};
+
+SearchBioEntityGroup.prototype.getBioEntities = function () {
+ return this._bioEntites;
+};
+
+SearchBioEntityGroup.prototype.bioEntityComparator = function (bioEntity1, bioEntity2) {
+ if (bioEntity1 instanceof Alias && bioEntity2 instanceof Alias) {
+ if (bioEntity1.getName() !== bioEntity2.getName()) {
+ return -1;
+ }
+ if (bioEntity1.getModelId() !== bioEntity2.getModelId()) {
+ return -2;
+ }
+ if (bioEntity1.getCompartmentId() !== bioEntity2.getCompartmentId()) {
+ return -3;
+ }
+ if (bioEntity1.getType() !== bioEntity2.getType()) {
+ return -4;
+ }
+ if (bioEntity1.getOther("structuralState") !== bioEntity2.getOther("structuralState")) {
+ return -5;
+ }
+
+ var computeSerializedModifications = function (modifications) {
+ if (modifications === undefined) {
+ return [];
+ }
+ var result = [];
+ for (var i = 0; i < modifications.length; i++) {
+ var modification = modifications[i];
+ result.push(modification.name + "_" + modification.state);
+ }
+ result.sort();
+ return result;
+ };
+ var serializedModifications1 = computeSerializedModifications(bioEntity1.getOther("modifications"));
+ var serializedModifications2 = computeSerializedModifications(bioEntity2.getOther("modifications"));
+ if (serializedModifications1.length !== serializedModifications2.length) {
+ return -6;
+ }
+ for (var i = 0; i < serializedModifications1.length; i++) {
+ if (serializedModifications1[i] !== serializedModifications2[i]) {
+ return -7;
+ }
+ }
+ return 0;
+ }
+ if (bioEntity1 instanceof Reaction && bioEntity2 instanceof Reaction) {
+ if (bioEntity1.getId() !== bioEntity2.getId()) {
+ return -8;
+ }
+ return 0;
+ }
+ return -9;
+};
+
+SearchBioEntityGroup.prototype.setIcon = function (icon) {
+ this._icon = icon;
+};
+
+SearchBioEntityGroup.prototype.getIcon = function () {
+ return this._icon;
+};
+
+//aggregated data
+SearchBioEntityGroup.prototype.getType = function () {
+ return this._bioEntites[0].getType();
+};
+
+SearchBioEntityGroup.prototype.getName = function () {
+ return this._bioEntites[0].getName();
+};
+
+SearchBioEntityGroup.prototype.getModelId = function () {
+ return this._bioEntites[0].getModelId();
+};
+
+SearchBioEntityGroup.prototype.getCompartmentId = function () {
+ return this._bioEntites[0].getCompartmentId();
+};
+
+SearchBioEntityGroup.prototype.getReactants = function () {
+ return this._bioEntites[0].getReactants();
+};
+SearchBioEntityGroup.prototype.getProducts = function () {
+ return this._bioEntites[0].getProducts();
+};
+SearchBioEntityGroup.prototype.getModifiers = function () {
+ return this._bioEntites[0].getModifiers();
+};
+
+SearchBioEntityGroup.prototype.getFullName = function () {
+ return this.getMergedParameterByFunction("getFullName");
+};
+
+SearchBioEntityGroup.prototype.getReactionId = function () {
+ return this.getMergedParameterByFunction("getReactionId");
+};
+SearchBioEntityGroup.prototype.getLinkedSubmodelId = function () {
+ return this.getMergedParameterByFunction("getLinkedSubmodelId");
+};
+SearchBioEntityGroup.prototype.getSymbol = function () {
+ return this.getMergedParameterByFunction("getSymbol");
+};
+SearchBioEntityGroup.prototype.getAbbreviation = function () {
+ return this.getMergedParameterByFunction("getAbbreviation");
+};
+SearchBioEntityGroup.prototype.getFormula = function () {
+ return this.getMergedParameterByFunction("getFormula");
+};
+SearchBioEntityGroup.prototype.getMechanicalConfidenceScore = function () {
+ return this.getMergedParameterByFunction("getMechanicalConfidenceScore");
+};
+SearchBioEntityGroup.prototype.getLowerBound = function () {
+ return this.getMergedParameterByFunction("getLowerBound");
+};
+SearchBioEntityGroup.prototype.getUpperBound = function () {
+ return this.getMergedParameterByFunction("getUpperBound");
+};
+SearchBioEntityGroup.prototype.getGeneProteinReaction = function () {
+ return this.getMergedParameterByFunction("getGeneProteinReaction");
+};
+SearchBioEntityGroup.prototype.getSubsystem = function () {
+ return this.getMergedParameterByFunction("getSubsystem");
+};
+SearchBioEntityGroup.prototype.getDescription = function () {
+ return this.getMergedParameterByFunction("getDescription");
+};
+SearchBioEntityGroup.prototype.getCharge = function () {
+ return this.getMergedParameterByFunction("getCharge");
+};
+SearchBioEntityGroup.prototype.getSynonyms = function () {
+ return this.getIntersectionListByFunction("getSynonyms");
+};
+SearchBioEntityGroup.prototype.getFormerSymbols = function () {
+ return this.getIntersectionListByFunction("getFormerSymbols");
+};
+
+SearchBioEntityGroup.prototype.getReferences = function () {
+ return this.getIntersectionListByFunction("getReferences");
+};
+
+SearchBioEntityGroup.prototype.getOther = function (param) {
+ if (param === "modifications") {
+ return this.getIntersectionListByFunction(function (alias) {
+ return alias.getOther(param)
+ });
+ } else {
+ throw new Error("Don't now how to handle: " + param);
+ }
+};
+
+SearchBioEntityGroup.prototype.getMergedParameterByFunction = function (functionName) {
+ var bioEntities = this.getBioEntities();
+ var result = bioEntities[0][functionName]();
+ for (var i = 1; i < bioEntities.length; i++) {
+ var newEntry = bioEntities[i][functionName]();
+ if (newEntry !== result) {
+ result = "Value different among merged elements";
+ }
+ }
+ return result;
+};
+
+SearchBioEntityGroup.prototype.getIntersectionListByFunction = function (functionName) {
+ var bioEntities = this.getBioEntities();
+ var result;
+ if (typeof functionName === "function") {
+ result = functionName(bioEntities[0]);
+ } else {
+ result = bioEntities[0][functionName]();
+ }
+ for (var i = 1; i < bioEntities.length; i++) {
+ var newList;
+ if (typeof functionName === "function") {
+ newList = functionName(bioEntities[i]);
+ } else {
+ newList = bioEntities[0][functionName]();
+ }
+ //intersection of two arrays
+ result = result.filter(function (n) {
+ return newList.indexOf(n) !== -1;
+ });
+ }
+ return result;
+};
+
+
+module.exports = SearchBioEntityGroup;
diff --git a/frontend-js/src/main/js/map/data/Target.js b/frontend-js/src/main/js/map/data/Target.js
index d35c1731eb30095f3743171b7732f7e2a15c0cd0..08e5f713038ef7d5ae87b38b6a6a60db770a830b 100644
--- a/frontend-js/src/main/js/map/data/Target.js
+++ b/frontend-js/src/main/js/map/data/Target.js
@@ -1,67 +1,67 @@
-"use strict";
-
-/* exported logger */
-
-var Annotation = require("./Annotation");
-var IdentifiedElement = require('./IdentifiedElement');
-
-var logger = require('../../logger');
-
-function Target(javaObject) {
- this.setName(javaObject.name);
- this.setTargetElements(javaObject.targetElements);
- this.setTargetParticipants(javaObject.targetParticipants);
- this.setReferences(javaObject.references);
-}
-
-Target.prototype.setTargetElements = function(targetElements) {
- this._targetElements = [];
- for (var i = 0; i < targetElements.length; i++) {
- this._targetElements.push(new IdentifiedElement(targetElements[i]));
- }
- this.setIsVisible(this._targetElements.length > 0);
-};
-
-Target.prototype.getTargetElements = function() {
- return this._targetElements;
-};
-
-Target.prototype.setTargetParticipants = function(targetParticipants) {
- this._targetParticipants = [];
- for (var i = 0; i < targetParticipants.length; i++) {
- this._targetParticipants.push(new Annotation(targetParticipants[i]));
- }
-};
-
-Target.prototype.getTargetParticipants = function() {
- return this._targetParticipants;
-};
-
-Target.prototype.setName = function(name) {
- this._name = name;
-};
-
-Target.prototype.getName = function() {
- return this._name;
-};
-
-Target.prototype.setIsVisible = function(visible) {
- this._isVisible = visible;
-};
-
-Target.prototype.isVisible = function() {
- return this._isVisible;
-};
-
-Target.prototype.setReferences = function(references) {
- this._references = [];
- for (var i = 0; i < references.length; i++) {
- this._references.push(new Annotation(references[i]));
- }
-};
-
-Target.prototype.getReferences = function() {
- return this._references;
-};
-
-module.exports = Target;
+"use strict";
+
+/* exported logger */
+
+var Annotation = require("./Annotation");
+var IdentifiedElement = require('./IdentifiedElement');
+
+var logger = require('../../logger');
+
+function Target(javaObject) {
+ this.setName(javaObject.name);
+ this.setTargetElements(javaObject.targetElements);
+ this.setTargetParticipants(javaObject.targetParticipants);
+ this.setReferences(javaObject.references);
+}
+
+Target.prototype.setTargetElements = function(targetElements) {
+ this._targetElements = [];
+ for (var i = 0; i < targetElements.length; i++) {
+ this._targetElements.push(new IdentifiedElement(targetElements[i]));
+ }
+ this.setIsVisible(this._targetElements.length > 0);
+};
+
+Target.prototype.getTargetElements = function() {
+ return this._targetElements;
+};
+
+Target.prototype.setTargetParticipants = function(targetParticipants) {
+ this._targetParticipants = [];
+ for (var i = 0; i < targetParticipants.length; i++) {
+ this._targetParticipants.push(new Annotation(targetParticipants[i]));
+ }
+};
+
+Target.prototype.getTargetParticipants = function() {
+ return this._targetParticipants;
+};
+
+Target.prototype.setName = function(name) {
+ this._name = name;
+};
+
+Target.prototype.getName = function() {
+ return this._name;
+};
+
+Target.prototype.setIsVisible = function(visible) {
+ this._isVisible = visible;
+};
+
+Target.prototype.isVisible = function() {
+ return this._isVisible;
+};
+
+Target.prototype.setReferences = function(references) {
+ this._references = [];
+ for (var i = 0; i < references.length; i++) {
+ this._references.push(new Annotation(references[i]));
+ }
+};
+
+Target.prototype.getReferences = function() {
+ return this._references;
+};
+
+module.exports = Target;
diff --git a/frontend-js/src/main/js/map/data/TargettingStructure.js b/frontend-js/src/main/js/map/data/TargettingStructure.js
index d36d2288d4c41380c3655c36b395bd252b356434..b35a23713cf33b03fc45246791a2184710ecbeaa 100644
--- a/frontend-js/src/main/js/map/data/TargettingStructure.js
+++ b/frontend-js/src/main/js/map/data/TargettingStructure.js
@@ -1,60 +1,60 @@
-"use strict";
-
-/* exported logger */
-
-var Target = require("./Target");
-
-var logger = require('../../logger');
-
-function TargettingStructure(javaObject) {
- if (javaObject !== undefined) {
- this.setName(javaObject.name);
- this.setId(javaObject.id);
- this.setTargets(javaObject.targets);
- }
-}
-
-TargettingStructure.prototype.setName = function(name) {
- this._name = name;
-};
-
-TargettingStructure.prototype.getName = function() {
- return this._name;
-};
-
-TargettingStructure.prototype.setId = function(id) {
- this._id = id;
-};
-
-TargettingStructure.prototype.getId = function() {
- return this._id;
-};
-
-TargettingStructure.prototype.setTargets = function(targets) {
- this._targets = [];
- for (var i = 0; i < targets.length; i++) {
- this._targets.push(new Target(targets[i]));
- }
-};
-
-TargettingStructure.prototype.getTargets = function() {
- return this._targets;
-};
-
-TargettingStructure.prototype.getTargetsForIdentifiedElement = function(targetIdentifiedElement) {
- var result = [];
- this.getTargets().forEach(function(target) {
- var targetOk = false;
- target.getTargetElements().forEach(function(identifiedElement){
- if (targetIdentifiedElement.equals(identifiedElement)) {
- targetOk = true;
- }
- });
- if (targetOk) {
- result.push(target);
- }
- });
- return result;
-};
-
-module.exports = TargettingStructure;
+"use strict";
+
+/* exported logger */
+
+var Target = require("./Target");
+
+var logger = require('../../logger');
+
+function TargettingStructure(javaObject) {
+ if (javaObject !== undefined) {
+ this.setName(javaObject.name);
+ this.setId(javaObject.id);
+ this.setTargets(javaObject.targets);
+ }
+}
+
+TargettingStructure.prototype.setName = function(name) {
+ this._name = name;
+};
+
+TargettingStructure.prototype.getName = function() {
+ return this._name;
+};
+
+TargettingStructure.prototype.setId = function(id) {
+ this._id = id;
+};
+
+TargettingStructure.prototype.getId = function() {
+ return this._id;
+};
+
+TargettingStructure.prototype.setTargets = function(targets) {
+ this._targets = [];
+ for (var i = 0; i < targets.length; i++) {
+ this._targets.push(new Target(targets[i]));
+ }
+};
+
+TargettingStructure.prototype.getTargets = function() {
+ return this._targets;
+};
+
+TargettingStructure.prototype.getTargetsForIdentifiedElement = function(targetIdentifiedElement) {
+ var result = [];
+ this.getTargets().forEach(function(target) {
+ var targetOk = false;
+ target.getTargetElements().forEach(function(identifiedElement){
+ if (targetIdentifiedElement.equals(identifiedElement)) {
+ targetOk = true;
+ }
+ });
+ if (targetOk) {
+ result.push(target);
+ }
+ });
+ return result;
+};
+
+module.exports = TargettingStructure;
diff --git a/frontend-js/src/main/js/map/data/User.js b/frontend-js/src/main/js/map/data/User.js
index 8c129f086c3f34238fc1b46169f8458b21b4398d..d0befc57c8f7cb0305724f860df026726b8d9d68 100644
--- a/frontend-js/src/main/js/map/data/User.js
+++ b/frontend-js/src/main/js/map/data/User.js
@@ -1,403 +1,403 @@
-"use strict";
-
-/* exported logger */
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-var UserPreferences = require('./UserPreferences');
-var ObjectWithListeners = require('../../ObjectWithListeners');
-
-/**
- *
- * @param javaObject
- * @constructor
- */
-function User(javaObject) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- this.registerListenerType("onreload");
-
- this.setLogin(javaObject.login);
- this.setName(javaObject.name);
- this.setSurname(javaObject.surname);
- this.setEmail(javaObject.email);
- this.setRemoved(javaObject.removed);
- this.setPrivileges(javaObject.privileges);
- this.setPreferences(javaObject.preferences);
- this.setMinColor(javaObject.minColor);
- this.setMaxColor(javaObject.maxColor);
- this.setNeutralColor(javaObject.neutralColor);
- this.setSimpleColor(javaObject.simpleColor);
- this.setTermsOfUseConsent(javaObject.termsOfUseConsent);
- this.setLdapAccountAvailable(javaObject.ldapAccountAvailable);
- this.setConnectedToLdap(javaObject.connectedToLdap);
-}
-
-// this class inherits from ObjectWithListeners class where generic methods for
-// listeners are set
-User.prototype = Object.create(ObjectWithListeners.prototype);
-User.prototype.constructor = User;
-
-/**
- *
- * @param {string} login
- */
-User.prototype.setLogin = function (login) {
- this._login = login;
-};
-
-/**
- *
- * @returns {string}
- */
-User.prototype.getLogin = function () {
- return this._login;
-};
-
-/**
- *
- * @param {string} name
- */
-User.prototype.setName = function (name) {
- this._name = name;
-};
-
-/**
- *
- * @returns {string}
- */
-User.prototype.getName = function () {
- return this._name;
-};
-
-/**
- *
- * @param {string} surname
- */
-User.prototype.setSurname = function (surname) {
- this._surname = surname;
-};
-
-/**
- *
- * @returns {string}
- */
-User.prototype.getSurname = function () {
- return this._surname;
-};
-
-/**
- *
- * @param {string} email
- */
-User.prototype.setEmail = function (email) {
- this._email = email;
-};
-
-/**
- *
- * @returns {string}
- */
-User.prototype.getEmail = function () {
- return this._email;
-};
-
-/**
- *
- * @param {boolean} removed
- */
-User.prototype.setRemoved = function (removed) {
- this._removed = removed;
-};
-
-/**
- *
- * @returns {boolean}
- */
-User.prototype.getRemoved = function () {
- return this._removed;
-};
-
-/**
- *
- * @param {string} minColor
- */
-User.prototype.setMinColor = function (minColor) {
- this._minColor = minColor;
-};
-
-/**
- *
- * @returns {string}
- */
-User.prototype.getMinColor = function () {
- return this._minColor;
-};
-
-/**
- *
- * @param {string} simpleColor
- */
-User.prototype.setSimpleColor = function (simpleColor) {
- this._simpleColor = simpleColor;
-};
-
-/**
- *
- * @returns {string}
- */
-User.prototype.getSimpleColor = function () {
- return this._simpleColor;
-};
-
-/**
- *
- * @param {string} neutralColor
- */
-User.prototype.setNeutralColor = function (neutralColor) {
- this._neutralColor = neutralColor;
-};
-
-/**
- *
- * @returns {string}
- */
-User.prototype.getNeutralColor = function () {
- return this._neutralColor;
-};
-
-/**
- *
- * @param {string} maxColor
- */
-User.prototype.setMaxColor = function (maxColor) {
- this._maxColor = maxColor;
-};
-
-/**
- *
- * @returns {string}
- */
-User.prototype.getMaxColor = function () {
- return this._maxColor;
-};
-
-/**
- *
- * @param {string} password
- */
-User.prototype.setPassword = function (password) {
- this._password = password;
-};
-
-/**
- *
- * @returns {string}
- */
-User.prototype.getPassword = function () {
- return this._password;
-};
-
-/**
- *
- * @param {Object[]} privileges
- */
-User.prototype.setPrivileges = function (privileges) {
- this._privileges = privileges;
- if (this._privileges === undefined) {
- this._privileges = [];
- }
-};
-
-/**
- *
- * @returns {Array}
- */
-User.prototype.getPrivileges = function () {
- return this._privileges;
-};
-
-/**
- *
- * @param {UserPreferences|Object} preferences
- */
-User.prototype.setPreferences = function (preferences) {
- if (!(preferences instanceof UserPreferences)) {
- preferences = new UserPreferences(preferences);
- }
- this._preferences = preferences;
-};
-
-/**
- *
- * @returns {UserPreferences}
- */
-User.prototype.getPreferences = function () {
- return this._preferences;
-};
-
-/**
- *
- * @param {PrivilegeType} type
- * @param {number} [objectId]
- * @returns {boolean}
- */
-User.prototype.hasPrivilege = function (type, objectId) {
- return this.getPrivilegeValue(type, objectId) > 0;
-};
-
-/**
- *
- * @param {Object} params
- * @param {number} params.objectId
- * @param {PrivilegeType} params.type
- * @param {number} [params.value=1]
- */
-User.prototype.setPrivilege = function (params) {
- var objectId = params.objectId;
- var type = params.type;
- var value = params.value;
- if (value === undefined) {
- value = 1;
- } else if (value === true) {
- value = 1;
- } else if (value === false) {
- value = 0;
- }
- for (var i = 0; i < this._privileges.length; i++) {
- var privilege = this._privileges[i];
- if (privilege.type === type.getName()) {
- if (objectId === privilege.objectId) {
- privilege.value = value;
- return;
- }
- }
- }
- this._privileges.push({
- type: type.getName(),
- value: value,
- objectId: objectId
- });
-};
-
-/**
- *
- * @param {PrivilegeType} type
- * @param {number} [objectId]
- *
- * @returns {number}
- */
-User.prototype.getPrivilegeValue = function (type, objectId) {
- for (var i = 0; i < this._privileges.length; i++) {
- var privilege = this._privileges[i];
- if (privilege.type === type.getName()) {
- if (objectId === privilege.objectId) {
- return privilege.value;
- }
- }
- }
- return 0;
-};
-
-/**
- *
- * @param {Configuration} configuration
- *
- * @returns {Object}
- */
-User.prototype.privilegesToExport = function (configuration) {
- var self = this;
- var result = {};
- var validTypes = {};
- var i;
- for (i = 0; i < configuration.getPrivilegeTypes().length; i++) {
- validTypes[configuration.getPrivilegeTypes()[i].getName()] = true;
- }
- for (i = 0; i < self.getPrivileges().length; i++) {
- var privilege = self.getPrivileges()[i];
- if (validTypes[privilege.type]) {
- if (result[privilege.type] === undefined) {
- result[privilege.type] = {};
- }
- if (privilege.objectId !== undefined) {
- result[privilege.type][privilege.objectId] = privilege.value;
- } else {
- result[privilege.type] = privilege.value;
- }
- }
- }
- return result;
-};
-
-/**
- *
- * @param {User} user
- * @returns {PromiseLike}
- */
-User.prototype.update = function (user) {
- var self = this;
- self.setLogin(user.getLogin());
- self.setName(user.getName());
- self.setSurname(user.getSurname());
- self.setEmail(user.getEmail());
- self.setRemoved(user.getRemoved());
- self.setPrivileges(user.getPrivileges());
- self.getPreferences().update(user.getPreferences());
- self.setMinColor(user.getMinColor());
- self.setMaxColor(user.getMaxColor());
- self.setSimpleColor(user.getSimpleColor());
-
- return self.callListeners("onreload");
-};
-
-/**
- *
- * @param {boolean} termsOfUseConsent
- */
-User.prototype.setTermsOfUseConsent = function (termsOfUseConsent) {
- this._termsOfUseConsent = termsOfUseConsent;
-};
-
-/**
- *
- * @returns {boolean}
- */
-User.prototype.isTermsOfUseConsent = function () {
- return this._termsOfUseConsent;
-};
-
-/**
- *
- * @param {boolean} ldapAccountAvailable
- */
-User.prototype.setLdapAccountAvailable = function (ldapAccountAvailable) {
- this._ldapAccountAvailable = ldapAccountAvailable;
-};
-
-/**
- *
- * @returns {boolean}
- */
-User.prototype.isLdapAccountAvailable = function () {
- return this._ldapAccountAvailable;
-};
-
-/**
- *
- * @param {boolean} connectedToLdap
- */
-User.prototype.setConnectedToLdap = function (connectedToLdap) {
- this._connectedToLdap = connectedToLdap;
-};
-
-/**
- *
- * @returns {boolean}
- */
-User.prototype.isConnectedToLdap = function () {
- return this._connectedToLdap;
-};
-
-module.exports = User;
+"use strict";
+
+/* exported logger */
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var UserPreferences = require('./UserPreferences');
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+/**
+ *
+ * @param javaObject
+ * @constructor
+ */
+function User(javaObject) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ this.registerListenerType("onreload");
+
+ this.setLogin(javaObject.login);
+ this.setName(javaObject.name);
+ this.setSurname(javaObject.surname);
+ this.setEmail(javaObject.email);
+ this.setRemoved(javaObject.removed);
+ this.setPrivileges(javaObject.privileges);
+ this.setPreferences(javaObject.preferences);
+ this.setMinColor(javaObject.minColor);
+ this.setMaxColor(javaObject.maxColor);
+ this.setNeutralColor(javaObject.neutralColor);
+ this.setSimpleColor(javaObject.simpleColor);
+ this.setTermsOfUseConsent(javaObject.termsOfUseConsent);
+ this.setLdapAccountAvailable(javaObject.ldapAccountAvailable);
+ this.setConnectedToLdap(javaObject.connectedToLdap);
+}
+
+// this class inherits from ObjectWithListeners class where generic methods for
+// listeners are set
+User.prototype = Object.create(ObjectWithListeners.prototype);
+User.prototype.constructor = User;
+
+/**
+ *
+ * @param {string} login
+ */
+User.prototype.setLogin = function (login) {
+ this._login = login;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+User.prototype.getLogin = function () {
+ return this._login;
+};
+
+/**
+ *
+ * @param {string} name
+ */
+User.prototype.setName = function (name) {
+ this._name = name;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+User.prototype.getName = function () {
+ return this._name;
+};
+
+/**
+ *
+ * @param {string} surname
+ */
+User.prototype.setSurname = function (surname) {
+ this._surname = surname;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+User.prototype.getSurname = function () {
+ return this._surname;
+};
+
+/**
+ *
+ * @param {string} email
+ */
+User.prototype.setEmail = function (email) {
+ this._email = email;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+User.prototype.getEmail = function () {
+ return this._email;
+};
+
+/**
+ *
+ * @param {boolean} removed
+ */
+User.prototype.setRemoved = function (removed) {
+ this._removed = removed;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+User.prototype.getRemoved = function () {
+ return this._removed;
+};
+
+/**
+ *
+ * @param {string} minColor
+ */
+User.prototype.setMinColor = function (minColor) {
+ this._minColor = minColor;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+User.prototype.getMinColor = function () {
+ return this._minColor;
+};
+
+/**
+ *
+ * @param {string} simpleColor
+ */
+User.prototype.setSimpleColor = function (simpleColor) {
+ this._simpleColor = simpleColor;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+User.prototype.getSimpleColor = function () {
+ return this._simpleColor;
+};
+
+/**
+ *
+ * @param {string} neutralColor
+ */
+User.prototype.setNeutralColor = function (neutralColor) {
+ this._neutralColor = neutralColor;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+User.prototype.getNeutralColor = function () {
+ return this._neutralColor;
+};
+
+/**
+ *
+ * @param {string} maxColor
+ */
+User.prototype.setMaxColor = function (maxColor) {
+ this._maxColor = maxColor;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+User.prototype.getMaxColor = function () {
+ return this._maxColor;
+};
+
+/**
+ *
+ * @param {string} password
+ */
+User.prototype.setPassword = function (password) {
+ this._password = password;
+};
+
+/**
+ *
+ * @returns {string}
+ */
+User.prototype.getPassword = function () {
+ return this._password;
+};
+
+/**
+ *
+ * @param {Object[]} privileges
+ */
+User.prototype.setPrivileges = function (privileges) {
+ this._privileges = privileges;
+ if (this._privileges === undefined) {
+ this._privileges = [];
+ }
+};
+
+/**
+ *
+ * @returns {Array}
+ */
+User.prototype.getPrivileges = function () {
+ return this._privileges;
+};
+
+/**
+ *
+ * @param {UserPreferences|Object} preferences
+ */
+User.prototype.setPreferences = function (preferences) {
+ if (!(preferences instanceof UserPreferences)) {
+ preferences = new UserPreferences(preferences);
+ }
+ this._preferences = preferences;
+};
+
+/**
+ *
+ * @returns {UserPreferences}
+ */
+User.prototype.getPreferences = function () {
+ return this._preferences;
+};
+
+/**
+ *
+ * @param {PrivilegeType} type
+ * @param {number} [objectId]
+ * @returns {boolean}
+ */
+User.prototype.hasPrivilege = function (type, objectId) {
+ return this.getPrivilegeValue(type, objectId) > 0;
+};
+
+/**
+ *
+ * @param {Object} params
+ * @param {number} params.objectId
+ * @param {PrivilegeType} params.type
+ * @param {number} [params.value=1]
+ */
+User.prototype.setPrivilege = function (params) {
+ var objectId = params.objectId;
+ var type = params.type;
+ var value = params.value;
+ if (value === undefined) {
+ value = 1;
+ } else if (value === true) {
+ value = 1;
+ } else if (value === false) {
+ value = 0;
+ }
+ for (var i = 0; i < this._privileges.length; i++) {
+ var privilege = this._privileges[i];
+ if (privilege.type === type.getName()) {
+ if (objectId === privilege.objectId) {
+ privilege.value = value;
+ return;
+ }
+ }
+ }
+ this._privileges.push({
+ type: type.getName(),
+ value: value,
+ objectId: objectId
+ });
+};
+
+/**
+ *
+ * @param {PrivilegeType} type
+ * @param {number} [objectId]
+ *
+ * @returns {number}
+ */
+User.prototype.getPrivilegeValue = function (type, objectId) {
+ for (var i = 0; i < this._privileges.length; i++) {
+ var privilege = this._privileges[i];
+ if (privilege.type === type.getName()) {
+ if (objectId === privilege.objectId) {
+ return privilege.value;
+ }
+ }
+ }
+ return 0;
+};
+
+/**
+ *
+ * @param {Configuration} configuration
+ *
+ * @returns {Object}
+ */
+User.prototype.privilegesToExport = function (configuration) {
+ var self = this;
+ var result = {};
+ var validTypes = {};
+ var i;
+ for (i = 0; i < configuration.getPrivilegeTypes().length; i++) {
+ validTypes[configuration.getPrivilegeTypes()[i].getName()] = true;
+ }
+ for (i = 0; i < self.getPrivileges().length; i++) {
+ var privilege = self.getPrivileges()[i];
+ if (validTypes[privilege.type]) {
+ if (result[privilege.type] === undefined) {
+ result[privilege.type] = {};
+ }
+ if (privilege.objectId !== undefined) {
+ result[privilege.type][privilege.objectId] = privilege.value;
+ } else {
+ result[privilege.type] = privilege.value;
+ }
+ }
+ }
+ return result;
+};
+
+/**
+ *
+ * @param {User} user
+ * @returns {PromiseLike}
+ */
+User.prototype.update = function (user) {
+ var self = this;
+ self.setLogin(user.getLogin());
+ self.setName(user.getName());
+ self.setSurname(user.getSurname());
+ self.setEmail(user.getEmail());
+ self.setRemoved(user.getRemoved());
+ self.setPrivileges(user.getPrivileges());
+ self.getPreferences().update(user.getPreferences());
+ self.setMinColor(user.getMinColor());
+ self.setMaxColor(user.getMaxColor());
+ self.setSimpleColor(user.getSimpleColor());
+
+ return self.callListeners("onreload");
+};
+
+/**
+ *
+ * @param {boolean} termsOfUseConsent
+ */
+User.prototype.setTermsOfUseConsent = function (termsOfUseConsent) {
+ this._termsOfUseConsent = termsOfUseConsent;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+User.prototype.isTermsOfUseConsent = function () {
+ return this._termsOfUseConsent;
+};
+
+/**
+ *
+ * @param {boolean} ldapAccountAvailable
+ */
+User.prototype.setLdapAccountAvailable = function (ldapAccountAvailable) {
+ this._ldapAccountAvailable = ldapAccountAvailable;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+User.prototype.isLdapAccountAvailable = function () {
+ return this._ldapAccountAvailable;
+};
+
+/**
+ *
+ * @param {boolean} connectedToLdap
+ */
+User.prototype.setConnectedToLdap = function (connectedToLdap) {
+ this._connectedToLdap = connectedToLdap;
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+User.prototype.isConnectedToLdap = function () {
+ return this._connectedToLdap;
+};
+
+module.exports = User;
diff --git a/frontend-js/src/main/js/map/data/UserPreferences.js b/frontend-js/src/main/js/map/data/UserPreferences.js
index a42b804aad16f17f893c01fd6412c0018018d192..6d2fa23a5c1f19fe09420238018e00dd625a14b9 100644
--- a/frontend-js/src/main/js/map/data/UserPreferences.js
+++ b/frontend-js/src/main/js/map/data/UserPreferences.js
@@ -1,176 +1,176 @@
-"use strict";
-
-/* exported logger */
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-function UserPreferences(javaObject) {
- if (javaObject !== undefined) {
- this.setProjectUpload(javaObject["project-upload"]);
- this.setElementAnnotators(javaObject["element-annotators"]);
- this.setElementRequiredAnnotations(javaObject["element-required-annotations"]);
- this.setElementValidAnnotations(javaObject["element-valid-annotations"]);
- this.setAnnotatorsParameters(javaObject["annotators-parameters"]);
- this.setGuiPreferences(javaObject["gui-preferences"]);
- } else {
- this._projectUpload = {};
- this._elementAnnotators = {};
- this._elementRequiredAnnotations = {};
- this._elementValidAnnotations = {};
- this._annotatorsParameters = {};
- this._guiPreferences = {};
- }
-}
-
-UserPreferences.prototype.update = function (userPreferences) {
- var updateDict = function (originalDict, newDict) {
- for (var key in newDict) {
- if (newDict.hasOwnProperty(key)) {
- originalDict[key] = newDict[key];
- }
- }
- };
-
- updateDict(this._projectUpload, userPreferences.getProjectUpload());
- updateDict(this._elementAnnotators, userPreferences.getElementAnnotators);
- updateDict(this._elementValidAnnotations, userPreferences._elementValidAnnotations);
- updateDict(this._elementRequiredAnnotations, userPreferences._elementRequiredAnnotations);
- updateDict(this._annotatorsParameters, userPreferences.getAnnotatorsParameters());
- updateDict(this._guiPreferences, userPreferences.getGuiPreferences());
-};
-
-UserPreferences.prototype.setProjectUpload = function (projectUpload) {
- this._projectUpload = {
- autoResize: projectUpload["auto-resize"],
- validateMiriam: projectUpload["validate-miriam"],
- annotateModel: projectUpload["annotate-model"],
- cacheData: projectUpload["cache-data"],
- semanticZooming: projectUpload["semantic-zooming"],
- sbgn: projectUpload["sbgn"]
- };
-};
-UserPreferences.prototype.getAnnotatorsParameters = function () {
- return this._annotatorsParameters;
-};
-UserPreferences.prototype.setAnnotatorsParameters = function (annotatorsParameters) {
- this._annotatorsParameters = annotatorsParameters;
-};
-UserPreferences.prototype.getGuiPreferences = function () {
- return this._guiPreferences;
-};
-UserPreferences.prototype.setGuiPreference = function (key, value) {
- this._guiPreferences[key] = value;
-};
-UserPreferences.prototype.getGuiPreference = function (key, defaultValue) {
- var result = this._guiPreferences[key];
- if (result === undefined) {
- result = defaultValue;
- }
- return result;
-};
-UserPreferences.prototype.setGuiPreferences = function (guiPreferences) {
- this._guiPreferences = guiPreferences;
-};
-UserPreferences.prototype.getProjectUpload = function () {
- return this._projectUpload;
-};
-UserPreferences.prototype.setElementAnnotators = function (elementAnnotators) {
- this._elementAnnotators = elementAnnotators;
-};
-
-/**
- *
- * @param {string} className
- * @returns {string[]}
- */
-UserPreferences.prototype.getElementAnnotators = function (className) {
- var result = this._elementAnnotators[className];
- if (result === undefined) {
- this._elementAnnotators[className] = [];
- result = this._elementAnnotators[className];
- }
- return result;
-};
-
-/**
- *
- * @param {Object<string, Object>} elementRequiredAnnotations
- */
-UserPreferences.prototype.setElementRequiredAnnotations = function (elementRequiredAnnotations) {
- this._elementRequiredAnnotations = {};
- for (var key in elementRequiredAnnotations) {
- if (elementRequiredAnnotations.hasOwnProperty(key)) {
- var data = elementRequiredAnnotations[key];
- this._elementRequiredAnnotations[key] = {
- requiredAtLeastOnce: data["require-at-least-one"],
- list: data["annotation-list"]
- };
- }
- }
-};
-
-/**
- *
- * @param {string} className
- * @returns {{list:string[], requiredAtLeastOnce:boolean}}
- */
-UserPreferences.prototype.getElementRequiredAnnotations = function (className) {
- var result = this._elementRequiredAnnotations[className];
- if (result === undefined) {
- result = {list: [], requiredAtLeastOnce: false};
- }
- return result;
-};
-
-/**
- *
- * @param {Object<string,string[]>}elementValidAnnotations
- */
-UserPreferences.prototype.setElementValidAnnotations = function (elementValidAnnotations) {
- this._elementValidAnnotations = elementValidAnnotations;
-};
-
-/**
- *
- * @param {string} className
- * @returns {string[]}
- */
-UserPreferences.prototype.getElementValidAnnotations = function (className) {
- var result = this._elementValidAnnotations[className];
- if (result === undefined) {
- result = [];
- }
- return result;
-};
-
-UserPreferences.prototype.toExport = function () {
- var requiredAnnotations = {};
- for (var key in this._elementRequiredAnnotations) {
- if (this._elementRequiredAnnotations.hasOwnProperty(key)) {
- var data = this._elementRequiredAnnotations[key];
- requiredAnnotations[key] = {
- "require-at-least-one": data.requiredAtLeastOnce,
- "annotation-list": data.list
- };
- }
- }
-
- return {
- "project-upload": {
- "auto-resize": this._projectUpload.autoResize,
- "validate-miriam": this._projectUpload.validateMiriam,
- "annotate-model": this._projectUpload.annotateModel,
- "cache-data": this._projectUpload.cacheData,
- "sbgn": this._projectUpload.sbgn,
- "semantic-zooming": this._projectUpload.semanticZooming
- },
- "element-annotators": this._elementAnnotators,
- "element-valid-annotations": this._elementValidAnnotations,
- "element-required-annotations": requiredAnnotations,
- "annotators-parameters": this.getAnnotatorsParameters(),
- "gui-preferences": this.getGuiPreferences()
- };
-};
-
-module.exports = UserPreferences;
+"use strict";
+
+/* exported logger */
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+function UserPreferences(javaObject) {
+ if (javaObject !== undefined) {
+ this.setProjectUpload(javaObject["project-upload"]);
+ this.setElementAnnotators(javaObject["element-annotators"]);
+ this.setElementRequiredAnnotations(javaObject["element-required-annotations"]);
+ this.setElementValidAnnotations(javaObject["element-valid-annotations"]);
+ this.setAnnotatorsParameters(javaObject["annotators-parameters"]);
+ this.setGuiPreferences(javaObject["gui-preferences"]);
+ } else {
+ this._projectUpload = {};
+ this._elementAnnotators = {};
+ this._elementRequiredAnnotations = {};
+ this._elementValidAnnotations = {};
+ this._annotatorsParameters = {};
+ this._guiPreferences = {};
+ }
+}
+
+UserPreferences.prototype.update = function (userPreferences) {
+ var updateDict = function (originalDict, newDict) {
+ for (var key in newDict) {
+ if (newDict.hasOwnProperty(key)) {
+ originalDict[key] = newDict[key];
+ }
+ }
+ };
+
+ updateDict(this._projectUpload, userPreferences.getProjectUpload());
+ updateDict(this._elementAnnotators, userPreferences.getElementAnnotators);
+ updateDict(this._elementValidAnnotations, userPreferences._elementValidAnnotations);
+ updateDict(this._elementRequiredAnnotations, userPreferences._elementRequiredAnnotations);
+ updateDict(this._annotatorsParameters, userPreferences.getAnnotatorsParameters());
+ updateDict(this._guiPreferences, userPreferences.getGuiPreferences());
+};
+
+UserPreferences.prototype.setProjectUpload = function (projectUpload) {
+ this._projectUpload = {
+ autoResize: projectUpload["auto-resize"],
+ validateMiriam: projectUpload["validate-miriam"],
+ annotateModel: projectUpload["annotate-model"],
+ cacheData: projectUpload["cache-data"],
+ semanticZooming: projectUpload["semantic-zooming"],
+ sbgn: projectUpload["sbgn"]
+ };
+};
+UserPreferences.prototype.getAnnotatorsParameters = function () {
+ return this._annotatorsParameters;
+};
+UserPreferences.prototype.setAnnotatorsParameters = function (annotatorsParameters) {
+ this._annotatorsParameters = annotatorsParameters;
+};
+UserPreferences.prototype.getGuiPreferences = function () {
+ return this._guiPreferences;
+};
+UserPreferences.prototype.setGuiPreference = function (key, value) {
+ this._guiPreferences[key] = value;
+};
+UserPreferences.prototype.getGuiPreference = function (key, defaultValue) {
+ var result = this._guiPreferences[key];
+ if (result === undefined) {
+ result = defaultValue;
+ }
+ return result;
+};
+UserPreferences.prototype.setGuiPreferences = function (guiPreferences) {
+ this._guiPreferences = guiPreferences;
+};
+UserPreferences.prototype.getProjectUpload = function () {
+ return this._projectUpload;
+};
+UserPreferences.prototype.setElementAnnotators = function (elementAnnotators) {
+ this._elementAnnotators = elementAnnotators;
+};
+
+/**
+ *
+ * @param {string} className
+ * @returns {string[]}
+ */
+UserPreferences.prototype.getElementAnnotators = function (className) {
+ var result = this._elementAnnotators[className];
+ if (result === undefined) {
+ this._elementAnnotators[className] = [];
+ result = this._elementAnnotators[className];
+ }
+ return result;
+};
+
+/**
+ *
+ * @param {Object<string, Object>} elementRequiredAnnotations
+ */
+UserPreferences.prototype.setElementRequiredAnnotations = function (elementRequiredAnnotations) {
+ this._elementRequiredAnnotations = {};
+ for (var key in elementRequiredAnnotations) {
+ if (elementRequiredAnnotations.hasOwnProperty(key)) {
+ var data = elementRequiredAnnotations[key];
+ this._elementRequiredAnnotations[key] = {
+ requiredAtLeastOnce: data["require-at-least-one"],
+ list: data["annotation-list"]
+ };
+ }
+ }
+};
+
+/**
+ *
+ * @param {string} className
+ * @returns {{list:string[], requiredAtLeastOnce:boolean}}
+ */
+UserPreferences.prototype.getElementRequiredAnnotations = function (className) {
+ var result = this._elementRequiredAnnotations[className];
+ if (result === undefined) {
+ result = {list: [], requiredAtLeastOnce: false};
+ }
+ return result;
+};
+
+/**
+ *
+ * @param {Object<string,string[]>}elementValidAnnotations
+ */
+UserPreferences.prototype.setElementValidAnnotations = function (elementValidAnnotations) {
+ this._elementValidAnnotations = elementValidAnnotations;
+};
+
+/**
+ *
+ * @param {string} className
+ * @returns {string[]}
+ */
+UserPreferences.prototype.getElementValidAnnotations = function (className) {
+ var result = this._elementValidAnnotations[className];
+ if (result === undefined) {
+ result = [];
+ }
+ return result;
+};
+
+UserPreferences.prototype.toExport = function () {
+ var requiredAnnotations = {};
+ for (var key in this._elementRequiredAnnotations) {
+ if (this._elementRequiredAnnotations.hasOwnProperty(key)) {
+ var data = this._elementRequiredAnnotations[key];
+ requiredAnnotations[key] = {
+ "require-at-least-one": data.requiredAtLeastOnce,
+ "annotation-list": data.list
+ };
+ }
+ }
+
+ return {
+ "project-upload": {
+ "auto-resize": this._projectUpload.autoResize,
+ "validate-miriam": this._projectUpload.validateMiriam,
+ "annotate-model": this._projectUpload.annotateModel,
+ "cache-data": this._projectUpload.cacheData,
+ "sbgn": this._projectUpload.sbgn,
+ "semantic-zooming": this._projectUpload.semanticZooming
+ },
+ "element-annotators": this._elementAnnotators,
+ "element-valid-annotations": this._elementValidAnnotations,
+ "element-required-annotations": requiredAnnotations,
+ "annotators-parameters": this.getAnnotatorsParameters(),
+ "gui-preferences": this.getGuiPreferences()
+ };
+};
+
+module.exports = UserPreferences;
diff --git a/frontend-js/src/main/js/map/marker/AbstractMarker.js b/frontend-js/src/main/js/map/marker/AbstractMarker.js
index 2ea04f698cdc2578d292e6f48f78675a42c2e2f1..5fa0da4a9e490f1844ca2d0537ac8b92fd237219 100644
--- a/frontend-js/src/main/js/map/marker/AbstractMarker.js
+++ b/frontend-js/src/main/js/map/marker/AbstractMarker.js
@@ -1,334 +1,334 @@
-"use strict";
-
-var GuiConnector = require('../../GuiConnector');
-
-var logger = require('../../logger');
-var Promise = require("bluebird");
-
-var ObjectWithListeners = require('../../ObjectWithListeners');
-
-/**
- * Class representing Marker (called sometimes bubble) that we visualize on the
- * map.
- *
- * @param {IdentifiedElement} params.element
- * @param {AbstractCustomMap} params.map
- * @param {function|function[]} [params.onClick]
- * @constructor
- */
-function AbstractMarker(params) {
- var self = this;
- // call super constructor
- ObjectWithListeners.call(this);
-
- self._icons = [];
- if (params.element.getIcon()) {
- self._icons.push(params.element.getIcon());
- }
- self.setIdentifiedElement(params.element);
- self.setCustomMap(params.map);
-
- self.registerListenerType("onClick");
- if (params.onClick !== undefined) {
- if (typeof params.onClick !== "function") {
- for (var i = 0; i < params.onClick.length; i++) {
- self.addListener("onClick", params.onClick[i]);
- }
- } else {
- self.addListener("onClick", params.onClick);
- }
- }
-
-}
-
-AbstractMarker.prototype = Object.create(ObjectWithListeners.prototype);
-AbstractMarker.prototype.constructor = AbstractMarker;
-
-/**
- * Returns identifier of this object.
- *
- * @returns {number|string} identifier of this object
- */
-AbstractMarker.prototype.getId = function () {
- return this.getIdentifiedElement().getId();
-};
-
-/**
- * Returns icon of the marker.
- *
- * @returns {string|undefined} identifying icon of the marker
- */
-AbstractMarker.prototype.getIcon = function () {
- var icons = this._icons;
- if (icons.length === 0) {
- return undefined;
- } else if (icons.length === 1) {
- return icons[0];
- } else {
- var result = icons[0];
- //if we have many identical icons then return this specific icon
- for (var i = 1; i < icons.length; i++) {
- if (icons[i] !== result) {
- return "marker/multi.png";
-
- }
- }
- return result;
- }
-};
-
-/**
- *
- * @returns {Promise}
- * @private
- */
-AbstractMarker.prototype._updateIcon = function () {
- var self = this;
- var marker = self.getMarker();
- if (marker !== undefined) {
- if (self.getIcon() === undefined) {
- return self.hide();
- } else {
- marker.setIcon(GuiConnector.getImgPrefix() + self.getIcon());
- if (!marker.isShown()) {
- return self.show();
- }
- }
- }
- return Promise.resolve();
-};
-
-/**
- *
- * @param {string|null|undefined} icon
- * @returns {Promise}
- */
-AbstractMarker.prototype.setIcon = function (icon) {
- var self = this;
- if (icon === null || icon === undefined) {
- self._icons = [];
- } else {
- self._icons = [icon];
- }
- return self._updateIcon();
-};
-
-/**
- *
- * @param {string[]} icons
- * @returns {Promise}
- */
-AbstractMarker.prototype.setIcons = function (icons) {
- var self = this;
- self._icons = icons;
- return self._updateIcon();
-};
-
-/**
- *
- * @param {string} icon
- * @returns {Promise}
- */
-AbstractMarker.prototype.addIcon = function (icon) {
- var self = this;
- self._icons.push(icon);
- return self._updateIcon();
-};
-
-/**
- *
- * @param {string[]} icons
- * @returns {Promise}
- */
-AbstractMarker.prototype.addIcons = function (icons) {
- var self = this;
- for (var i = 0; i < icons.length; i++) {
- self._icons.push(icons[i]);
- }
- return self._updateIcon();
-};
-
-/**
- *
- * @param {string[]} icons
- * @returns {Promise}
- */
-AbstractMarker.prototype.removeIcons = function (icons) {
- var self = this;
- var promises = [];
- for (var i = 0; i < icons.length; i++) {
- promises.push(self.removeIcon(icons[i], true));
- }
- return Promise.all(promises).then(function () {
- return self._updateIcon();
- });
-};
-
-/**
- *
- * @param {string} icon
- * @param {boolean} [preventMarkerUpdate]
- * @returns {Promise}
- */
-AbstractMarker.prototype.removeIcon = function (icon, preventMarkerUpdate) {
- var self = this;
- var index = self._icons.indexOf(icon);
-
- if (index > -1) {
- self._icons.splice(index, 1);
- if (!preventMarkerUpdate) {
- return self._updateIcon();
- }
- } else {
- logger.warn("Unknown icon for marker: " + icon);
- }
- return Promise.resolve();
-};
-
-/**
- * Shows marker on the map.
- *
- * @returns {Promise}
- */
-AbstractMarker.prototype.show = function () {
- var self = this;
- if (this.getMarker() === undefined) {
- return this.init().then(function () {
- return self.getMarker().show();
- });
- } else {
- return this.getMarker().show();
- }
-};
-
-/**
- *
- * @returns {Promise}
- */
-AbstractMarker.prototype.hide = function () {
- var self = this;
- if (this.getMarker() === undefined) {
- return this.init().then(function () {
- return self.getMarker().hide();
- });
- } else {
- return Promise.resolve(this.getMarker().hide());
- }
-};
-
-/**
- *
- * @returns {boolean}
- */
-AbstractMarker.prototype.isShown = function () {
- if (this.getMarker() === undefined) {
- return false;
- }
- return this.getMarker().isShown();
-};
-
-/**
- * Returns {@link AbstractCustomMap} where marker is located.
- *
- * @returns {AbstractCustomMap} where marker is located
- */
-AbstractMarker.prototype.getCustomMap = function () {
- return this._map;
-};
-
-/**
- *
- * @param {AbstractCustomMap} map
- */
-AbstractMarker.prototype.setCustomMap = function (map) {
- this._map = map;
-};
-
-/**
- * Returns {Bounds} of the marker (it's a single point).
- *
- * @returns {Bounds|null} bounds of the marker (it's a single point)
- */
-AbstractMarker.prototype.getBounds = function () {
- var marker = this.getMarker();
- if (marker === undefined || marker === null) {
- logger.warn("Marker not initialized");
- return null;
- }
-
- return marker.getBounds();
-};
-
-/**
- * Initializes {@link Marker} object connected to this object.
- *
- * @returns {Promise}
- * @protected
- */
-AbstractMarker.prototype._init = function () {
- var self = this;
- var point = this.getCoordinates();
-
- this._marker = this.getCustomMap().getMapCanvas().createMarker({
- position: point,
- icon: GuiConnector.getImgPrefix() + self.getIcon(),
- id: self.getId()
- });
-
- this._marker.addListener('click', function () {
- return self.onClickHandler().then(null, GuiConnector.alert);
- });
- return Promise.resolve();
-};
-
-/**
- *
- * @returns {Promise|PromiseLike}
- */
-AbstractMarker.prototype.onClickHandler = function () {
- return this.callListeners("onClick");
-};
-
-/**
- * Returns {google.maps.Marker} connected to this object.
- *
- * @returns {Marker} connected to this object
- */
-AbstractMarker.prototype.getMarker = function () {
- return this._marker;
-};
-
-/**
- * Abstract function returning string marker type.
- *
- * @returns {string} marker type
- */
-AbstractMarker.prototype.getType = function () {
- return this.getIdentifiedElement().getType();
-};
-
-/**
- *
- * @returns {number}
- */
-AbstractMarker.prototype.getModelId = function () {
- return this.getIdentifiedElement().getModelId();
-};
-
-/**
- *
- * @returns {IdentifiedElement}
- */
-AbstractMarker.prototype.getIdentifiedElement = function () {
- return this._identifiedElement;
-};
-
-/**
- *
- * @param {IdentifiedElement} identifiedElement
- */
-AbstractMarker.prototype.setIdentifiedElement = function (identifiedElement) {
- this._identifiedElement = identifiedElement;
-};
-
-module.exports = AbstractMarker;
+"use strict";
+
+var GuiConnector = require('../../GuiConnector');
+
+var logger = require('../../logger');
+var Promise = require("bluebird");
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+/**
+ * Class representing Marker (called sometimes bubble) that we visualize on the
+ * map.
+ *
+ * @param {IdentifiedElement} params.element
+ * @param {AbstractCustomMap} params.map
+ * @param {function|function[]} [params.onClick]
+ * @constructor
+ */
+function AbstractMarker(params) {
+ var self = this;
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ self._icons = [];
+ if (params.element.getIcon()) {
+ self._icons.push(params.element.getIcon());
+ }
+ self.setIdentifiedElement(params.element);
+ self.setCustomMap(params.map);
+
+ self.registerListenerType("onClick");
+ if (params.onClick !== undefined) {
+ if (typeof params.onClick !== "function") {
+ for (var i = 0; i < params.onClick.length; i++) {
+ self.addListener("onClick", params.onClick[i]);
+ }
+ } else {
+ self.addListener("onClick", params.onClick);
+ }
+ }
+
+}
+
+AbstractMarker.prototype = Object.create(ObjectWithListeners.prototype);
+AbstractMarker.prototype.constructor = AbstractMarker;
+
+/**
+ * Returns identifier of this object.
+ *
+ * @returns {number|string} identifier of this object
+ */
+AbstractMarker.prototype.getId = function () {
+ return this.getIdentifiedElement().getId();
+};
+
+/**
+ * Returns icon of the marker.
+ *
+ * @returns {string|undefined} identifying icon of the marker
+ */
+AbstractMarker.prototype.getIcon = function () {
+ var icons = this._icons;
+ if (icons.length === 0) {
+ return undefined;
+ } else if (icons.length === 1) {
+ return icons[0];
+ } else {
+ var result = icons[0];
+ //if we have many identical icons then return this specific icon
+ for (var i = 1; i < icons.length; i++) {
+ if (icons[i] !== result) {
+ return "marker/multi.png";
+
+ }
+ }
+ return result;
+ }
+};
+
+/**
+ *
+ * @returns {Promise}
+ * @private
+ */
+AbstractMarker.prototype._updateIcon = function () {
+ var self = this;
+ var marker = self.getMarker();
+ if (marker !== undefined) {
+ if (self.getIcon() === undefined) {
+ return self.hide();
+ } else {
+ marker.setIcon(GuiConnector.getImgPrefix() + self.getIcon());
+ if (!marker.isShown()) {
+ return self.show();
+ }
+ }
+ }
+ return Promise.resolve();
+};
+
+/**
+ *
+ * @param {string|null|undefined} icon
+ * @returns {Promise}
+ */
+AbstractMarker.prototype.setIcon = function (icon) {
+ var self = this;
+ if (icon === null || icon === undefined) {
+ self._icons = [];
+ } else {
+ self._icons = [icon];
+ }
+ return self._updateIcon();
+};
+
+/**
+ *
+ * @param {string[]} icons
+ * @returns {Promise}
+ */
+AbstractMarker.prototype.setIcons = function (icons) {
+ var self = this;
+ self._icons = icons;
+ return self._updateIcon();
+};
+
+/**
+ *
+ * @param {string} icon
+ * @returns {Promise}
+ */
+AbstractMarker.prototype.addIcon = function (icon) {
+ var self = this;
+ self._icons.push(icon);
+ return self._updateIcon();
+};
+
+/**
+ *
+ * @param {string[]} icons
+ * @returns {Promise}
+ */
+AbstractMarker.prototype.addIcons = function (icons) {
+ var self = this;
+ for (var i = 0; i < icons.length; i++) {
+ self._icons.push(icons[i]);
+ }
+ return self._updateIcon();
+};
+
+/**
+ *
+ * @param {string[]} icons
+ * @returns {Promise}
+ */
+AbstractMarker.prototype.removeIcons = function (icons) {
+ var self = this;
+ var promises = [];
+ for (var i = 0; i < icons.length; i++) {
+ promises.push(self.removeIcon(icons[i], true));
+ }
+ return Promise.all(promises).then(function () {
+ return self._updateIcon();
+ });
+};
+
+/**
+ *
+ * @param {string} icon
+ * @param {boolean} [preventMarkerUpdate]
+ * @returns {Promise}
+ */
+AbstractMarker.prototype.removeIcon = function (icon, preventMarkerUpdate) {
+ var self = this;
+ var index = self._icons.indexOf(icon);
+
+ if (index > -1) {
+ self._icons.splice(index, 1);
+ if (!preventMarkerUpdate) {
+ return self._updateIcon();
+ }
+ } else {
+ logger.warn("Unknown icon for marker: " + icon);
+ }
+ return Promise.resolve();
+};
+
+/**
+ * Shows marker on the map.
+ *
+ * @returns {Promise}
+ */
+AbstractMarker.prototype.show = function () {
+ var self = this;
+ if (this.getMarker() === undefined) {
+ return this.init().then(function () {
+ return self.getMarker().show();
+ });
+ } else {
+ return this.getMarker().show();
+ }
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+AbstractMarker.prototype.hide = function () {
+ var self = this;
+ if (this.getMarker() === undefined) {
+ return this.init().then(function () {
+ return self.getMarker().hide();
+ });
+ } else {
+ return Promise.resolve(this.getMarker().hide());
+ }
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+AbstractMarker.prototype.isShown = function () {
+ if (this.getMarker() === undefined) {
+ return false;
+ }
+ return this.getMarker().isShown();
+};
+
+/**
+ * Returns {@link AbstractCustomMap} where marker is located.
+ *
+ * @returns {AbstractCustomMap} where marker is located
+ */
+AbstractMarker.prototype.getCustomMap = function () {
+ return this._map;
+};
+
+/**
+ *
+ * @param {AbstractCustomMap} map
+ */
+AbstractMarker.prototype.setCustomMap = function (map) {
+ this._map = map;
+};
+
+/**
+ * Returns {Bounds} of the marker (it's a single point).
+ *
+ * @returns {Bounds|null} bounds of the marker (it's a single point)
+ */
+AbstractMarker.prototype.getBounds = function () {
+ var marker = this.getMarker();
+ if (marker === undefined || marker === null) {
+ logger.warn("Marker not initialized");
+ return null;
+ }
+
+ return marker.getBounds();
+};
+
+/**
+ * Initializes {@link Marker} object connected to this object.
+ *
+ * @returns {Promise}
+ * @protected
+ */
+AbstractMarker.prototype._init = function () {
+ var self = this;
+ var point = this.getCoordinates();
+
+ this._marker = this.getCustomMap().getMapCanvas().createMarker({
+ position: point,
+ icon: GuiConnector.getImgPrefix() + self.getIcon(),
+ id: self.getId()
+ });
+
+ this._marker.addListener('click', function () {
+ return self.onClickHandler().then(null, GuiConnector.alert);
+ });
+ return Promise.resolve();
+};
+
+/**
+ *
+ * @returns {Promise|PromiseLike}
+ */
+AbstractMarker.prototype.onClickHandler = function () {
+ return this.callListeners("onClick");
+};
+
+/**
+ * Returns {google.maps.Marker} connected to this object.
+ *
+ * @returns {Marker} connected to this object
+ */
+AbstractMarker.prototype.getMarker = function () {
+ return this._marker;
+};
+
+/**
+ * Abstract function returning string marker type.
+ *
+ * @returns {string} marker type
+ */
+AbstractMarker.prototype.getType = function () {
+ return this.getIdentifiedElement().getType();
+};
+
+/**
+ *
+ * @returns {number}
+ */
+AbstractMarker.prototype.getModelId = function () {
+ return this.getIdentifiedElement().getModelId();
+};
+
+/**
+ *
+ * @returns {IdentifiedElement}
+ */
+AbstractMarker.prototype.getIdentifiedElement = function () {
+ return this._identifiedElement;
+};
+
+/**
+ *
+ * @param {IdentifiedElement} identifiedElement
+ */
+AbstractMarker.prototype.setIdentifiedElement = function (identifiedElement) {
+ this._identifiedElement = identifiedElement;
+};
+
+module.exports = AbstractMarker;
diff --git a/frontend-js/src/main/js/map/marker/AliasMarker.js b/frontend-js/src/main/js/map/marker/AliasMarker.js
index 7186290000c78c821ad50fef9ae0d7634033505e..9418c84a7840a0d02d6767257726660b08f12336 100644
--- a/frontend-js/src/main/js/map/marker/AliasMarker.js
+++ b/frontend-js/src/main/js/map/marker/AliasMarker.js
@@ -1,66 +1,66 @@
-"use strict";
-
-var AbstractMarker = require('./AbstractMarker');
-var Point = require('../canvas/Point');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-/**
- * This class describes Google maps marker (connected to {@link Alias}) that is
- * visualized on the map.
- *
- * @param {IdentifiedElement} params.element
- * @param {AbstractCustomMap} params.map
- * @param {function|function[]} [params.onClick]
- * @constructor
- * @extends AbstractMarker
- */
-function AliasMarker(params) {
- AbstractMarker.call(this, params);
-}
-
-AliasMarker.prototype = Object.create(AbstractMarker.prototype);
-AliasMarker.prototype.constructor = AliasMarker;
-
-/**
- * Returns {@link Alias} data for this marker.
- *
- * @returns {Alias} data for this marker
- */
-AliasMarker.prototype.getAliasData = function () {
- return this._aliasData;
-};
-
-/**
- * Sets {@link Alias} data for this marker.
- *
- * @param {Alias} data
- * data for this marker
- */
-AliasMarker.prototype.setAliasData = function (data) {
- this._aliasData = data;
-};
-
-/**
- * Returns coordinates where marker is pointing.
- *
- * @returns {Point} - coordinates where marker is pointing
- */
-AliasMarker.prototype.getCoordinates = function () {
- var alias = this.getAliasData();
- return new Point(alias.getX() + alias.getWidth() / 2, alias.getY() + alias.getHeight() / 2);
-};
-
-AliasMarker.prototype.init = function () {
- var self = this;
- var model = self.getCustomMap().getModel();
- return model.getByIdentifiedElement(self.getIdentifiedElement()).then(function (aliasData) {
- self.setAliasData(aliasData);
- return self._init();
- }).then(function () {
- return self.show();
- });
-};
-
-module.exports = AliasMarker;
+"use strict";
+
+var AbstractMarker = require('./AbstractMarker');
+var Point = require('../canvas/Point');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+/**
+ * This class describes Google maps marker (connected to {@link Alias}) that is
+ * visualized on the map.
+ *
+ * @param {IdentifiedElement} params.element
+ * @param {AbstractCustomMap} params.map
+ * @param {function|function[]} [params.onClick]
+ * @constructor
+ * @extends AbstractMarker
+ */
+function AliasMarker(params) {
+ AbstractMarker.call(this, params);
+}
+
+AliasMarker.prototype = Object.create(AbstractMarker.prototype);
+AliasMarker.prototype.constructor = AliasMarker;
+
+/**
+ * Returns {@link Alias} data for this marker.
+ *
+ * @returns {Alias} data for this marker
+ */
+AliasMarker.prototype.getAliasData = function () {
+ return this._aliasData;
+};
+
+/**
+ * Sets {@link Alias} data for this marker.
+ *
+ * @param {Alias} data
+ * data for this marker
+ */
+AliasMarker.prototype.setAliasData = function (data) {
+ this._aliasData = data;
+};
+
+/**
+ * Returns coordinates where marker is pointing.
+ *
+ * @returns {Point} - coordinates where marker is pointing
+ */
+AliasMarker.prototype.getCoordinates = function () {
+ var alias = this.getAliasData();
+ return new Point(alias.getX() + alias.getWidth() / 2, alias.getY() + alias.getHeight() / 2);
+};
+
+AliasMarker.prototype.init = function () {
+ var self = this;
+ var model = self.getCustomMap().getModel();
+ return model.getByIdentifiedElement(self.getIdentifiedElement()).then(function (aliasData) {
+ self.setAliasData(aliasData);
+ return self._init();
+ }).then(function () {
+ return self.show();
+ });
+};
+
+module.exports = AliasMarker;
diff --git a/frontend-js/src/main/js/map/marker/MarkerSurfaceCollection.js b/frontend-js/src/main/js/map/marker/MarkerSurfaceCollection.js
index 5ecac222035e50ca0a651b3284e545ba702535c1..7189f9a8c4da11ea3054d5df2b7f855a314df489 100644
--- a/frontend-js/src/main/js/map/marker/MarkerSurfaceCollection.js
+++ b/frontend-js/src/main/js/map/marker/MarkerSurfaceCollection.js
@@ -1,562 +1,562 @@
-"use strict";
-
-var AliasMarker = require('./AliasMarker');
-var IdentifiedElement = require('../data/IdentifiedElement');
-var PointMarker = require('./PointMarker');
-var ReactionMarker = require('./ReactionMarker');
-
-var AbstractSurfaceElement = require('../surface/AbstractSurfaceElement');
-var AliasSurface = require('../surface/AliasSurface');
-var ReactionSurface = require('../surface/ReactionSurface');
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-var Promise = require("bluebird");
-
-var ObjectWithListeners = require('../../ObjectWithListeners');
-
-/**
- * @typedef {Object} IconData
- * @property {IdentifiedElement} element
- * @property {string[]} icons
- */
-
-/**
- *
- * @param {AbstractCustomMap} params.map
- * @constructor
- */
-function MarkerSurfaceCollection(params) {
- var self = this;
- ObjectWithListeners.call(this);
-
- /**
- * @type {Object.<string, IconData>}
- */
- self._overlayIcons = {};
- // @type {Object.<string, AbstractMarker>}
- self._markers = {};
- // @type {Object.<string, Object.<string,AbstractMarker>>}
- self._overlaySurfaces = {
- ALIAS: [],
- REACTION: [],
- POINT: []
- };
-
- self.setMap(params.map);
-}
-
-MarkerSurfaceCollection.prototype = Object.create(ObjectWithListeners.prototype);
-MarkerSurfaceCollection.prototype.constructor = MarkerSurfaceCollection;
-
-/**
- *
- * @param {AbstractCustomMap} map
- */
-MarkerSurfaceCollection.prototype.setMap = function (map) {
- if (map === undefined) {
- throw new Error("Map must be defined");
- }
- this._map = map;
-};
-
-/**
- *
- * @returns {AbstractCustomMap}
- */
-MarkerSurfaceCollection.prototype.getMap = function () {
- return this._map;
-};
-
-/**
- *
- * @param {AbstractDbOverlay} overlay
- * @returns {Promise}
- */
-MarkerSurfaceCollection.prototype.refreshOverlayMarkers = function (overlay) {
- var promises = [];
- var self = this;
- var overlayData = self._overlayIcons[overlay.getName()];
- for (var elementId in overlayData) {
- if (overlayData.hasOwnProperty(elementId)) {
- var x = function () {
- var marker = self._markers[elementId];
- promises.push(marker.hide().then(function () {
- return marker.show();
- }));
- }();
- }
- }
- overlayData = self._overlaySurfaces[overlay.getName()];
- for (elementId in overlayData) {
- if (overlayData.hasOwnProperty(elementId)) {
- x = function () {
- var surface = overlayData[elementId];
- promises.push(surface.hide().then(function () {
- return surface.show();
- }));
- }();
- }
- }
- return Promise.all(promises);
-};
-
-/**
- *
- * @param {string[]} params.icons
- * @param {IdentifiedElement} params.element
- * @returns {Promise}
- */
-MarkerSurfaceCollection.prototype.addMarker = function (params) {
- var element = params.element;
- var icons = params.icons;
-
- var self = this;
-
- var result = self.getMarker(element);
- if (result !== undefined) {
- return result.addIcons(icons).then(function () {
- return Promise.resolve(result);
- });
- }
-
- var MarkerConstructor = null;
- if (element.getType() === "ALIAS") {
- MarkerConstructor = AliasMarker;
- } else if (element.getType() === "REACTION") {
- MarkerConstructor = ReactionMarker;
- } else if (element.getType() === "POINT") {
- MarkerConstructor = PointMarker;
- } else {
- throw new Error("Unknown type of the element in overlay: " + element.type);
- }
- result = new MarkerConstructor({
- element: element,
- map: self.getMap(),
- onClick: [function () {
- return self.getMap()._openInfoWindowForIdentifiedElement(element, result.getMarker());
- }, function () {
- return self.getMap().getTopMap().callListeners("onBioEntityClick", element);
- }]
- });
- self.putMarker(element, result);
- return result.setIcons(icons).then(function () {
- if (self.getMap().isInitialized()) {
- return result.init().then(function () {
- return result;
- });
- } else {
- return Promise.resolve(result);
- }
- });
-};
-
-/**
- *
- * @param {string[]} params.icons
- * @param {IdentifiedElement} params.element
- * @returns {Promise}
- */
-MarkerSurfaceCollection.prototype.removeMarker = function (params) {
- var element = params.element;
- var icons = params.icons;
-
- var self = this;
-
- var result = self.getMarker(element);
- return result.removeIcons(icons);
-};
-
-/**
- *
- * @param {IdentifiedElement} element
- * @param {AbstractDbOverlay} dbOverlay
- * @returns {PromiseLike<any>}
- */
-MarkerSurfaceCollection.prototype.createSurfaceForDbOverlay = function (element, dbOverlay) {
- var self = this;
-
- var result = self.getSurface({element: element, overlay: dbOverlay});
- if (result !== undefined) {
- result.updateIdentifiedElement(element);
- return Promise.resolve(result);
- }
-
- var map = self.getMap();
- /**
- * @type {function[]}
- */
- var onclickFunctions = [function () {
- return self.getMap().getTopMap().callListeners("onBioEntityClick", element);
- }];
- if (element.getType() === "ALIAS") {
- return map.getModel().getAliasById(element.getId()).then(function (alias) {
- result = new AliasSurface({
- alias: alias,
- map: map,
- onClick: onclickFunctions,
- color: element.getColor(),
- fillOpacity: element.getOpacity(),
- strokeWeight: element.getLineWeight(),
- strokeColor: element.getLineColor(),
- strokeOpacity: element.getLineOpacity()
- });
- self.putSurface({element: element, overlay: dbOverlay}, result);
- if (self.getMap().isInitialized()) {
- return result.init().then(function () {
- return result.show();
- }).then(function () {
- return result;
- });
- } else {
- return result;
- }
- });
- } else if (element.getType() === "REACTION") {
- return map.getModel().getReactionById(element.getId()).then(function (reactionData) {
- result = new ReactionSurface({
- reaction: reactionData,
- map: map,
- customized: true,
- color: element.getColor(),
- onClick: onclickFunctions
- });
- result.addListener("onClick", function(){
- return map.getTopMap().openInfoWindowForIdentifiedElement(element);
- });
- self.putSurface({element: element, overlay: dbOverlay}, result);
- if (self.getMap().isInitialized()) {
- return result.init().then(function () {
- return result.show();
- }).then(function () {
- return result;
- });
- } else {
- return result;
- }
- });
- } else if (element.getType() === "POINT") {
- throw new Error("Not implemented");
- } else {
- throw new Error("Unknown type of the element in overlay: " + element.getType());
- }
-};
-
-/**
- *
- * @returns {AbstractMarker[]}
- */
-MarkerSurfaceCollection.prototype.getMarkers = function () {
- var result = [];
- var markers = this._markers;
- for (var key in markers) {
- if (markers.hasOwnProperty(key)) {
- var marker = markers[key];
- if (marker.isShown()) {
- result.push(marker);
- }
- }
- }
-
- return result;
-};
-
-/**
- *
- * @returns {AbstractSurfaceElement[]}
- */
-MarkerSurfaceCollection.prototype.getSurfaces = function () {
- var result = [];
-
- var overlaySurfaces = this._overlaySurfaces;
- for (var overlayName in overlaySurfaces) {
- if (overlaySurfaces.hasOwnProperty(overlayName)) {
- var surfaces = overlaySurfaces[overlayName];
- for (var key in surfaces) {
- if (surfaces.hasOwnProperty(key)) {
- result.push(surfaces[key]);
- }
- }
- }
- }
-
- return result;
-};
-
-/**
- *
- * @param {IdentifiedElement} element
- * @returns {AbstractMarker|undefined}
- */
-MarkerSurfaceCollection.prototype.getMarker = function (element) {
- return this._markers[element.toString()];
-};
-
-/**
- *
- * @param {IdentifiedElement} element
- * @param {AbstractMarker} marker
- */
-MarkerSurfaceCollection.prototype.putMarker = function (element, marker) {
- this._markers[element.toString()] = marker;
-};
-
-/**
- *
- * @param params
- * @returns {AbstractSurfaceElement|undefined}
- */
-MarkerSurfaceCollection.prototype.getSurface = function (params) {
- var element = new IdentifiedElement(params.element);
- var overlay = params.overlay;
-
- var overlaySurfaces = this._overlaySurfaces[overlay.getName()];
- if (overlaySurfaces === undefined) {
- this._overlaySurfaces[overlay.getName()] = [];
- overlaySurfaces = this._overlaySurfaces[overlay.getName()];
- }
- return overlaySurfaces[element.toString()];
-};
-
-/**
- *
- * @param {Object} params
- * @param {IdentifiedElement} params.element
- * @param {AbstractDbOverlay} params.overlay
- * @param {AbstractSurfaceElement} surface
- */
-MarkerSurfaceCollection.prototype.putSurface = function (params, surface) {
- var element = params.element;
- var overlay = params.overlay;
-
- var overlaySurfaces = this._overlaySurfaces[overlay.getName()];
- if (overlaySurfaces === undefined) {
- this._overlaySurfaces[overlay.getName()] = [];
- overlaySurfaces = this._overlaySurfaces[overlay.getName()];
- }
- overlaySurfaces[element.toString()] = surface;
-};
-
-/**
- *
- * @param {AbstractSurfaceElement[]} modifiedMarkersAndSurfaces
- * @param {AbstractDbOverlay} dbOverlay
- */
-MarkerSurfaceCollection.prototype.removeUnmodifiedSurfaces = function (modifiedMarkersAndSurfaces, dbOverlay) {
- var modifiedSurfaces = {
- "ALIAS": [],
- "REACTION": [],
- "POINT": []
- };
-
- for (var i = 0; i < modifiedMarkersAndSurfaces.length; i++) {
- var object = modifiedMarkersAndSurfaces[i];
- var identifiedElement = object.getIdentifiedElement();
- if (object instanceof AbstractSurfaceElement) {
- modifiedSurfaces[identifiedElement.toString()] = true;
- } else {
- throw new Error("Unknown class type: " + object.prototype.name);
- }
- }
-
- var surfaceOverlaysPerType = this._overlaySurfaces[dbOverlay.getName()];
- for (var key in surfaceOverlaysPerType) {
- if (surfaceOverlaysPerType.hasOwnProperty(key)) {
- if (!modifiedSurfaces[key]) {
- surfaceOverlaysPerType[key].hide();
- delete surfaceOverlaysPerType[key];
- }
- }
- }
-};
-
-/**
- *
- * @param {IdentifiedElement[]} allElements
- * @param {AbstractDbOverlay} overlay
- * @returns {PromiseLike<any>}
- */
-MarkerSurfaceCollection.prototype.renderOverlay = function (allElements, overlay) {
- var self = this;
- var markerElements = [];
- var surfaceElements = [];
- for (var i = 0; i < allElements.length; i++) {
- var element = allElements[i];
- if (element.getModelId() === self.getMap().getId()) {
- if (element.getIcon() !== null && element.getIcon() !== undefined) {
- markerElements.push(element);
- } else {
- surfaceElements.push(element);
- }
- }
- }
-
- var markers;
- return self.renderOverlayMarkers(markerElements, overlay).then(function (result) {
- markers = result;
- return self.renderOverlaySurfaces(surfaceElements, overlay);
- }).then(function (surfaces) {
- return markers.concat(surfaces);
- });
-};
-
-/**
- *
- * @param {IdentifiedElement} element
- * @constructor
- */
-function IconDifference(element) {
- this.element = element;
- this.iconsToAdd = [];
- this.iconsToRemove = [];
-}
-
-/**
- *
- * @param {string} icon
- */
-IconDifference.prototype.addIcon = function (icon) {
- var index = this.iconsToRemove.indexOf(icon);
- if (index > -1) {
- this.iconsToRemove.splice(index, 1);
- } else {
- this.iconsToAdd.push(icon);
- }
-};
-
-/**
- *
- * @param {string} icon
- */
-IconDifference.prototype.removeIcon = function (icon) {
- var index = this.iconsToAdd.indexOf(icon);
- if (index > -1) {
- this.iconsToAdd.splice(index, 1);
- } else {
- this.iconsToRemove.push(icon);
- }
-};
-
-/**
- *
- * @param {string[]} icons
- */
-IconDifference.prototype.removeIcons = function (icons) {
- for (var i = 0; i < icons.length; i++) {
- this.removeIcon(icons[i]);
- }
-};
-
-/**
- *
- * @param {IdentifiedElement[]} elements
- * @param {AbstractDbOverlay} overlay
- * @returns {PromiseLike<any>}
- */
-MarkerSurfaceCollection.prototype.renderOverlayMarkers = function (elements, overlay) {
- var self = this;
-
- var markers = [];
- return self.getMap().getModel().getByIdentifiedElements(elements).then(function () {
- var elementsToProcess = [];
- var i, element, icon, data, entry, key;
- for (i = 0; i < elements.length; i++) {
- element = elements[i];
- icon = element.getIcon();
- data = elementsToProcess[element.toString()];
- if (data === undefined) {
- elementsToProcess[element.toString()] = new IconDifference(element);
- data = elementsToProcess[element.toString()]
- }
- data.addIcon(icon);
- }
- var iconData = self.getOverlayIconData(overlay);
- for (key in iconData) {
- if (iconData.hasOwnProperty(key)) {
- entry = iconData[key];
- element = entry.element;
- data = elementsToProcess[element.toString()];
- if (data === undefined) {
- elementsToProcess[element.toString()] = new IconDifference(element);
- data = elementsToProcess[element.toString()]
- }
- data.removeIcons(entry.icons);
- }
- }
-
- var promises = [];
-
- for (key in elementsToProcess) {
- if (elementsToProcess.hasOwnProperty(key)) {
- data = elementsToProcess[key];
- if (data.iconsToAdd.length > 0) {
- promises.push(self.addMarker({element: data.element, icons: data.iconsToAdd}).then(function (marker) {
- markers.push(marker);
- }));
- }
- if (data.iconsToRemove.length > 0) {
- promises.push(self.removeMarker({element: data.element, icons: data.iconsToRemove}));
- }
- }
- }
- return Promise.all(promises);
- }).then(function () {
- self.createOverlayIconData(elements, overlay);
- return markers;
- });
-};
-
-/**
- *
- * @param {AbstractDbOverlay} overlay
- * @returns {IconData}
- */
-MarkerSurfaceCollection.prototype.getOverlayIconData = function (overlay) {
- var iconData = this._overlayIcons[overlay.getName()];
- if (iconData === undefined) {
- this._overlayIcons[overlay.getName()] = {};
- iconData = this._overlayIcons[overlay.getName()]
- }
- return iconData;
-};
-
-/**
- *
- * @param {IdentifiedElement[]} elements
- * @param {AbstractDbOverlay} overlay
- */
-MarkerSurfaceCollection.prototype.createOverlayIconData = function (elements, overlay) {
- var iconData = {};
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i];
- if (iconData[element.toString()] === undefined) {
- iconData[element.toString()] = {icons: [], element: element};
- }
- iconData[element.toString()].icons.push(element.getIcon());
- }
- this._overlayIcons[overlay.getName()] = iconData;
-};
-
-/**
- *
- * @param {IdentifiedElement[]} elements
- * @param {AbstractDbOverlay} overlay
- * @returns {PromiseLike<AbstractSurfaceElement>}
- */
-MarkerSurfaceCollection.prototype.renderOverlaySurfaces = function (elements, overlay) {
- var self = this;
- var surfaces = [];
- return self.getMap().getModel().getByIdentifiedElements(elements).then(function () {
- return Promise.each(elements, function (element) {
- return self.createSurfaceForDbOverlay(element, overlay).then(function (mapOverlay) {
- surfaces.push(mapOverlay);
- });
- });
- }).then(function () {
- self.removeUnmodifiedSurfaces(surfaces, overlay);
- return surfaces;
- });
-
-};
-
-module.exports = MarkerSurfaceCollection;
+"use strict";
+
+var AliasMarker = require('./AliasMarker');
+var IdentifiedElement = require('../data/IdentifiedElement');
+var PointMarker = require('./PointMarker');
+var ReactionMarker = require('./ReactionMarker');
+
+var AbstractSurfaceElement = require('../surface/AbstractSurfaceElement');
+var AliasSurface = require('../surface/AliasSurface');
+var ReactionSurface = require('../surface/ReactionSurface');
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+var Promise = require("bluebird");
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+
+/**
+ * @typedef {Object} IconData
+ * @property {IdentifiedElement} element
+ * @property {string[]} icons
+ */
+
+/**
+ *
+ * @param {AbstractCustomMap} params.map
+ * @constructor
+ */
+function MarkerSurfaceCollection(params) {
+ var self = this;
+ ObjectWithListeners.call(this);
+
+ /**
+ * @type {Object.<string, IconData>}
+ */
+ self._overlayIcons = {};
+ // @type {Object.<string, AbstractMarker>}
+ self._markers = {};
+ // @type {Object.<string, Object.<string,AbstractMarker>>}
+ self._overlaySurfaces = {
+ ALIAS: [],
+ REACTION: [],
+ POINT: []
+ };
+
+ self.setMap(params.map);
+}
+
+MarkerSurfaceCollection.prototype = Object.create(ObjectWithListeners.prototype);
+MarkerSurfaceCollection.prototype.constructor = MarkerSurfaceCollection;
+
+/**
+ *
+ * @param {AbstractCustomMap} map
+ */
+MarkerSurfaceCollection.prototype.setMap = function (map) {
+ if (map === undefined) {
+ throw new Error("Map must be defined");
+ }
+ this._map = map;
+};
+
+/**
+ *
+ * @returns {AbstractCustomMap}
+ */
+MarkerSurfaceCollection.prototype.getMap = function () {
+ return this._map;
+};
+
+/**
+ *
+ * @param {AbstractDbOverlay} overlay
+ * @returns {Promise}
+ */
+MarkerSurfaceCollection.prototype.refreshOverlayMarkers = function (overlay) {
+ var promises = [];
+ var self = this;
+ var overlayData = self._overlayIcons[overlay.getName()];
+ for (var elementId in overlayData) {
+ if (overlayData.hasOwnProperty(elementId)) {
+ var x = function () {
+ var marker = self._markers[elementId];
+ promises.push(marker.hide().then(function () {
+ return marker.show();
+ }));
+ }();
+ }
+ }
+ overlayData = self._overlaySurfaces[overlay.getName()];
+ for (elementId in overlayData) {
+ if (overlayData.hasOwnProperty(elementId)) {
+ x = function () {
+ var surface = overlayData[elementId];
+ promises.push(surface.hide().then(function () {
+ return surface.show();
+ }));
+ }();
+ }
+ }
+ return Promise.all(promises);
+};
+
+/**
+ *
+ * @param {string[]} params.icons
+ * @param {IdentifiedElement} params.element
+ * @returns {Promise}
+ */
+MarkerSurfaceCollection.prototype.addMarker = function (params) {
+ var element = params.element;
+ var icons = params.icons;
+
+ var self = this;
+
+ var result = self.getMarker(element);
+ if (result !== undefined) {
+ return result.addIcons(icons).then(function () {
+ return Promise.resolve(result);
+ });
+ }
+
+ var MarkerConstructor = null;
+ if (element.getType() === "ALIAS") {
+ MarkerConstructor = AliasMarker;
+ } else if (element.getType() === "REACTION") {
+ MarkerConstructor = ReactionMarker;
+ } else if (element.getType() === "POINT") {
+ MarkerConstructor = PointMarker;
+ } else {
+ throw new Error("Unknown type of the element in overlay: " + element.type);
+ }
+ result = new MarkerConstructor({
+ element: element,
+ map: self.getMap(),
+ onClick: [function () {
+ return self.getMap()._openInfoWindowForIdentifiedElement(element, result.getMarker());
+ }, function () {
+ return self.getMap().getTopMap().callListeners("onBioEntityClick", element);
+ }]
+ });
+ self.putMarker(element, result);
+ return result.setIcons(icons).then(function () {
+ if (self.getMap().isInitialized()) {
+ return result.init().then(function () {
+ return result;
+ });
+ } else {
+ return Promise.resolve(result);
+ }
+ });
+};
+
+/**
+ *
+ * @param {string[]} params.icons
+ * @param {IdentifiedElement} params.element
+ * @returns {Promise}
+ */
+MarkerSurfaceCollection.prototype.removeMarker = function (params) {
+ var element = params.element;
+ var icons = params.icons;
+
+ var self = this;
+
+ var result = self.getMarker(element);
+ return result.removeIcons(icons);
+};
+
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @param {AbstractDbOverlay} dbOverlay
+ * @returns {PromiseLike<any>}
+ */
+MarkerSurfaceCollection.prototype.createSurfaceForDbOverlay = function (element, dbOverlay) {
+ var self = this;
+
+ var result = self.getSurface({element: element, overlay: dbOverlay});
+ if (result !== undefined) {
+ result.updateIdentifiedElement(element);
+ return Promise.resolve(result);
+ }
+
+ var map = self.getMap();
+ /**
+ * @type {function[]}
+ */
+ var onclickFunctions = [function () {
+ return self.getMap().getTopMap().callListeners("onBioEntityClick", element);
+ }];
+ if (element.getType() === "ALIAS") {
+ return map.getModel().getAliasById(element.getId()).then(function (alias) {
+ result = new AliasSurface({
+ alias: alias,
+ map: map,
+ onClick: onclickFunctions,
+ color: element.getColor(),
+ fillOpacity: element.getOpacity(),
+ strokeWeight: element.getLineWeight(),
+ strokeColor: element.getLineColor(),
+ strokeOpacity: element.getLineOpacity()
+ });
+ self.putSurface({element: element, overlay: dbOverlay}, result);
+ if (self.getMap().isInitialized()) {
+ return result.init().then(function () {
+ return result.show();
+ }).then(function () {
+ return result;
+ });
+ } else {
+ return result;
+ }
+ });
+ } else if (element.getType() === "REACTION") {
+ return map.getModel().getReactionById(element.getId()).then(function (reactionData) {
+ result = new ReactionSurface({
+ reaction: reactionData,
+ map: map,
+ customized: true,
+ color: element.getColor(),
+ onClick: onclickFunctions
+ });
+ result.addListener("onClick", function(){
+ return map.getTopMap().openInfoWindowForIdentifiedElement(element);
+ });
+ self.putSurface({element: element, overlay: dbOverlay}, result);
+ if (self.getMap().isInitialized()) {
+ return result.init().then(function () {
+ return result.show();
+ }).then(function () {
+ return result;
+ });
+ } else {
+ return result;
+ }
+ });
+ } else if (element.getType() === "POINT") {
+ throw new Error("Not implemented");
+ } else {
+ throw new Error("Unknown type of the element in overlay: " + element.getType());
+ }
+};
+
+/**
+ *
+ * @returns {AbstractMarker[]}
+ */
+MarkerSurfaceCollection.prototype.getMarkers = function () {
+ var result = [];
+ var markers = this._markers;
+ for (var key in markers) {
+ if (markers.hasOwnProperty(key)) {
+ var marker = markers[key];
+ if (marker.isShown()) {
+ result.push(marker);
+ }
+ }
+ }
+
+ return result;
+};
+
+/**
+ *
+ * @returns {AbstractSurfaceElement[]}
+ */
+MarkerSurfaceCollection.prototype.getSurfaces = function () {
+ var result = [];
+
+ var overlaySurfaces = this._overlaySurfaces;
+ for (var overlayName in overlaySurfaces) {
+ if (overlaySurfaces.hasOwnProperty(overlayName)) {
+ var surfaces = overlaySurfaces[overlayName];
+ for (var key in surfaces) {
+ if (surfaces.hasOwnProperty(key)) {
+ result.push(surfaces[key]);
+ }
+ }
+ }
+ }
+
+ return result;
+};
+
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @returns {AbstractMarker|undefined}
+ */
+MarkerSurfaceCollection.prototype.getMarker = function (element) {
+ return this._markers[element.toString()];
+};
+
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @param {AbstractMarker} marker
+ */
+MarkerSurfaceCollection.prototype.putMarker = function (element, marker) {
+ this._markers[element.toString()] = marker;
+};
+
+/**
+ *
+ * @param params
+ * @returns {AbstractSurfaceElement|undefined}
+ */
+MarkerSurfaceCollection.prototype.getSurface = function (params) {
+ var element = new IdentifiedElement(params.element);
+ var overlay = params.overlay;
+
+ var overlaySurfaces = this._overlaySurfaces[overlay.getName()];
+ if (overlaySurfaces === undefined) {
+ this._overlaySurfaces[overlay.getName()] = [];
+ overlaySurfaces = this._overlaySurfaces[overlay.getName()];
+ }
+ return overlaySurfaces[element.toString()];
+};
+
+/**
+ *
+ * @param {Object} params
+ * @param {IdentifiedElement} params.element
+ * @param {AbstractDbOverlay} params.overlay
+ * @param {AbstractSurfaceElement} surface
+ */
+MarkerSurfaceCollection.prototype.putSurface = function (params, surface) {
+ var element = params.element;
+ var overlay = params.overlay;
+
+ var overlaySurfaces = this._overlaySurfaces[overlay.getName()];
+ if (overlaySurfaces === undefined) {
+ this._overlaySurfaces[overlay.getName()] = [];
+ overlaySurfaces = this._overlaySurfaces[overlay.getName()];
+ }
+ overlaySurfaces[element.toString()] = surface;
+};
+
+/**
+ *
+ * @param {AbstractSurfaceElement[]} modifiedMarkersAndSurfaces
+ * @param {AbstractDbOverlay} dbOverlay
+ */
+MarkerSurfaceCollection.prototype.removeUnmodifiedSurfaces = function (modifiedMarkersAndSurfaces, dbOverlay) {
+ var modifiedSurfaces = {
+ "ALIAS": [],
+ "REACTION": [],
+ "POINT": []
+ };
+
+ for (var i = 0; i < modifiedMarkersAndSurfaces.length; i++) {
+ var object = modifiedMarkersAndSurfaces[i];
+ var identifiedElement = object.getIdentifiedElement();
+ if (object instanceof AbstractSurfaceElement) {
+ modifiedSurfaces[identifiedElement.toString()] = true;
+ } else {
+ throw new Error("Unknown class type: " + object.prototype.name);
+ }
+ }
+
+ var surfaceOverlaysPerType = this._overlaySurfaces[dbOverlay.getName()];
+ for (var key in surfaceOverlaysPerType) {
+ if (surfaceOverlaysPerType.hasOwnProperty(key)) {
+ if (!modifiedSurfaces[key]) {
+ surfaceOverlaysPerType[key].hide();
+ delete surfaceOverlaysPerType[key];
+ }
+ }
+ }
+};
+
+/**
+ *
+ * @param {IdentifiedElement[]} allElements
+ * @param {AbstractDbOverlay} overlay
+ * @returns {PromiseLike<any>}
+ */
+MarkerSurfaceCollection.prototype.renderOverlay = function (allElements, overlay) {
+ var self = this;
+ var markerElements = [];
+ var surfaceElements = [];
+ for (var i = 0; i < allElements.length; i++) {
+ var element = allElements[i];
+ if (element.getModelId() === self.getMap().getId()) {
+ if (element.getIcon() !== null && element.getIcon() !== undefined) {
+ markerElements.push(element);
+ } else {
+ surfaceElements.push(element);
+ }
+ }
+ }
+
+ var markers;
+ return self.renderOverlayMarkers(markerElements, overlay).then(function (result) {
+ markers = result;
+ return self.renderOverlaySurfaces(surfaceElements, overlay);
+ }).then(function (surfaces) {
+ return markers.concat(surfaces);
+ });
+};
+
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @constructor
+ */
+function IconDifference(element) {
+ this.element = element;
+ this.iconsToAdd = [];
+ this.iconsToRemove = [];
+}
+
+/**
+ *
+ * @param {string} icon
+ */
+IconDifference.prototype.addIcon = function (icon) {
+ var index = this.iconsToRemove.indexOf(icon);
+ if (index > -1) {
+ this.iconsToRemove.splice(index, 1);
+ } else {
+ this.iconsToAdd.push(icon);
+ }
+};
+
+/**
+ *
+ * @param {string} icon
+ */
+IconDifference.prototype.removeIcon = function (icon) {
+ var index = this.iconsToAdd.indexOf(icon);
+ if (index > -1) {
+ this.iconsToAdd.splice(index, 1);
+ } else {
+ this.iconsToRemove.push(icon);
+ }
+};
+
+/**
+ *
+ * @param {string[]} icons
+ */
+IconDifference.prototype.removeIcons = function (icons) {
+ for (var i = 0; i < icons.length; i++) {
+ this.removeIcon(icons[i]);
+ }
+};
+
+/**
+ *
+ * @param {IdentifiedElement[]} elements
+ * @param {AbstractDbOverlay} overlay
+ * @returns {PromiseLike<any>}
+ */
+MarkerSurfaceCollection.prototype.renderOverlayMarkers = function (elements, overlay) {
+ var self = this;
+
+ var markers = [];
+ return self.getMap().getModel().getByIdentifiedElements(elements).then(function () {
+ var elementsToProcess = [];
+ var i, element, icon, data, entry, key;
+ for (i = 0; i < elements.length; i++) {
+ element = elements[i];
+ icon = element.getIcon();
+ data = elementsToProcess[element.toString()];
+ if (data === undefined) {
+ elementsToProcess[element.toString()] = new IconDifference(element);
+ data = elementsToProcess[element.toString()]
+ }
+ data.addIcon(icon);
+ }
+ var iconData = self.getOverlayIconData(overlay);
+ for (key in iconData) {
+ if (iconData.hasOwnProperty(key)) {
+ entry = iconData[key];
+ element = entry.element;
+ data = elementsToProcess[element.toString()];
+ if (data === undefined) {
+ elementsToProcess[element.toString()] = new IconDifference(element);
+ data = elementsToProcess[element.toString()]
+ }
+ data.removeIcons(entry.icons);
+ }
+ }
+
+ var promises = [];
+
+ for (key in elementsToProcess) {
+ if (elementsToProcess.hasOwnProperty(key)) {
+ data = elementsToProcess[key];
+ if (data.iconsToAdd.length > 0) {
+ promises.push(self.addMarker({element: data.element, icons: data.iconsToAdd}).then(function (marker) {
+ markers.push(marker);
+ }));
+ }
+ if (data.iconsToRemove.length > 0) {
+ promises.push(self.removeMarker({element: data.element, icons: data.iconsToRemove}));
+ }
+ }
+ }
+ return Promise.all(promises);
+ }).then(function () {
+ self.createOverlayIconData(elements, overlay);
+ return markers;
+ });
+};
+
+/**
+ *
+ * @param {AbstractDbOverlay} overlay
+ * @returns {IconData}
+ */
+MarkerSurfaceCollection.prototype.getOverlayIconData = function (overlay) {
+ var iconData = this._overlayIcons[overlay.getName()];
+ if (iconData === undefined) {
+ this._overlayIcons[overlay.getName()] = {};
+ iconData = this._overlayIcons[overlay.getName()]
+ }
+ return iconData;
+};
+
+/**
+ *
+ * @param {IdentifiedElement[]} elements
+ * @param {AbstractDbOverlay} overlay
+ */
+MarkerSurfaceCollection.prototype.createOverlayIconData = function (elements, overlay) {
+ var iconData = {};
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ if (iconData[element.toString()] === undefined) {
+ iconData[element.toString()] = {icons: [], element: element};
+ }
+ iconData[element.toString()].icons.push(element.getIcon());
+ }
+ this._overlayIcons[overlay.getName()] = iconData;
+};
+
+/**
+ *
+ * @param {IdentifiedElement[]} elements
+ * @param {AbstractDbOverlay} overlay
+ * @returns {PromiseLike<AbstractSurfaceElement>}
+ */
+MarkerSurfaceCollection.prototype.renderOverlaySurfaces = function (elements, overlay) {
+ var self = this;
+ var surfaces = [];
+ return self.getMap().getModel().getByIdentifiedElements(elements).then(function () {
+ return Promise.each(elements, function (element) {
+ return self.createSurfaceForDbOverlay(element, overlay).then(function (mapOverlay) {
+ surfaces.push(mapOverlay);
+ });
+ });
+ }).then(function () {
+ self.removeUnmodifiedSurfaces(surfaces, overlay);
+ return surfaces;
+ });
+
+};
+
+module.exports = MarkerSurfaceCollection;
diff --git a/frontend-js/src/main/js/map/marker/PointMarker.js b/frontend-js/src/main/js/map/marker/PointMarker.js
index 63decdbe6674bb7f10a6e20f5a6fbc5e74d87a50..e477cfa41cd6c9cef123cfbcde740874d7b716f3 100644
--- a/frontend-js/src/main/js/map/marker/PointMarker.js
+++ b/frontend-js/src/main/js/map/marker/PointMarker.js
@@ -1,70 +1,70 @@
-"use strict";
-
-var AbstractMarker = require('./AbstractMarker');
-var PointData = require('../data/PointData');
-
-/**
- * This class describes Google maps marker (connected to some specific point,
- * but not to any element) that is visualized on the map.
- *
- * @param {IdentifiedElement} params.element
- * @param {AbstractCustomMap} params.map
- * @param {function|function[]} params.onclick
- * @constructor
- * @extends AbstractMarker
- */
-function PointMarker(params) {
- var self = this;
- AbstractMarker.call(self, params);
- self.setPointData(new PointData(self.getIdentifiedElement()));
-}
-
-PointMarker.prototype = Object.create(AbstractMarker.prototype);
-PointMarker.prototype.constructor = PointMarker;
-
-/**
- *
- * @returns {Promise<any>}
- */
-PointMarker.prototype.init = function () {
- var self = this;
- return self._init().then(function () {
- return self.show();
- });
-};
-
-/**
- * Returns identifier of the object.
- *
- * @returns {string} identifier of the object
- */
-PointMarker.prototype.getId = function () {
- return this.getPointData().getId();
-};
-
-/**
- * Returns a {@link PointData} that is connected to this marker.
- *
- * @returns {PointData} that is connected to this marker
- */
-PointMarker.prototype.getPointData = function () {
- return this._pointData;
-};
-
-/**
- *
- * @param {PointData} pointData
- */
-PointMarker.prototype.setPointData = function (pointData) {
- this._pointData = pointData;
-};
-
-/**
- *
- * @returns {Point}
- */
-PointMarker.prototype.getCoordinates = function () {
- return this._pointData.getPoint();
-};
-
-module.exports = PointMarker;
+"use strict";
+
+var AbstractMarker = require('./AbstractMarker');
+var PointData = require('../data/PointData');
+
+/**
+ * This class describes Google maps marker (connected to some specific point,
+ * but not to any element) that is visualized on the map.
+ *
+ * @param {IdentifiedElement} params.element
+ * @param {AbstractCustomMap} params.map
+ * @param {function|function[]} params.onclick
+ * @constructor
+ * @extends AbstractMarker
+ */
+function PointMarker(params) {
+ var self = this;
+ AbstractMarker.call(self, params);
+ self.setPointData(new PointData(self.getIdentifiedElement()));
+}
+
+PointMarker.prototype = Object.create(AbstractMarker.prototype);
+PointMarker.prototype.constructor = PointMarker;
+
+/**
+ *
+ * @returns {Promise<any>}
+ */
+PointMarker.prototype.init = function () {
+ var self = this;
+ return self._init().then(function () {
+ return self.show();
+ });
+};
+
+/**
+ * Returns identifier of the object.
+ *
+ * @returns {string} identifier of the object
+ */
+PointMarker.prototype.getId = function () {
+ return this.getPointData().getId();
+};
+
+/**
+ * Returns a {@link PointData} that is connected to this marker.
+ *
+ * @returns {PointData} that is connected to this marker
+ */
+PointMarker.prototype.getPointData = function () {
+ return this._pointData;
+};
+
+/**
+ *
+ * @param {PointData} pointData
+ */
+PointMarker.prototype.setPointData = function (pointData) {
+ this._pointData = pointData;
+};
+
+/**
+ *
+ * @returns {Point}
+ */
+PointMarker.prototype.getCoordinates = function () {
+ return this._pointData.getPoint();
+};
+
+module.exports = PointMarker;
diff --git a/frontend-js/src/main/js/map/marker/ReactionMarker.js b/frontend-js/src/main/js/map/marker/ReactionMarker.js
index d7c793a7c81c03d5550202fc0a10a95f05155d38..e062ed356af1e7c93235413e4d1a7df4aa7dfba1 100644
--- a/frontend-js/src/main/js/map/marker/ReactionMarker.js
+++ b/frontend-js/src/main/js/map/marker/ReactionMarker.js
@@ -1,65 +1,65 @@
-"use strict";
-
-var AbstractMarker = require('./AbstractMarker');
-var Point = require('../canvas/Point');
-
-/**
- * This class describes Google maps marker (connected to {@link Reaction}) that
- * is visualized on the map.
- *
- * @param {IdentifiedElement} params.element
- * @param {AbstractCustomMap} params.map
- * @param {function|function[]} params.onclick
- * @constructor
- * @extends AbstractMarker
- */
-function ReactionMarker(params) {
- AbstractMarker.call(this, params);
-}
-
-ReactionMarker.prototype = Object.create(AbstractMarker.prototype);
-ReactionMarker.prototype.constructor = ReactionMarker;
-
-/**
- *
- * @returns {PromiseLike<any>}
- */
-ReactionMarker.prototype.init = function () {
- var self = this;
- return self.getCustomMap().getModel().getReactionById(self.getId()).then(function (reactionData) {
- self.setReactionData(reactionData);
- return self._init();
- }).then(function () {
- return self.show();
- });
-};
-
-/**
- * Returns {@link Reaction} data for this marker.
- *
- * @returns {Reaction} data for this marker
- */
-ReactionMarker.prototype.getReactionData = function () {
- return this._reactionData;
-};
-
-/**
- * Sets {@link Reaction} data for this marker.
- *
- * @param {Reaction} data
- * data for this marker
- */
-ReactionMarker.prototype.setReactionData = function (data) {
- this._reactionData = data;
-};
-
-/**
- * Returns coordinates where marker is pointing.
- *
- * @returns {Point} - coordinates where marker is pointing
- */
-ReactionMarker.prototype.getCoordinates = function () {
- return new Point(this._reactionData.getCenter().x, this._reactionData.getCenter().y);
-};
-
-module.exports = ReactionMarker;
+"use strict";
+
+var AbstractMarker = require('./AbstractMarker');
+var Point = require('../canvas/Point');
+
+/**
+ * This class describes Google maps marker (connected to {@link Reaction}) that
+ * is visualized on the map.
+ *
+ * @param {IdentifiedElement} params.element
+ * @param {AbstractCustomMap} params.map
+ * @param {function|function[]} params.onclick
+ * @constructor
+ * @extends AbstractMarker
+ */
+function ReactionMarker(params) {
+ AbstractMarker.call(this, params);
+}
+
+ReactionMarker.prototype = Object.create(AbstractMarker.prototype);
+ReactionMarker.prototype.constructor = ReactionMarker;
+
+/**
+ *
+ * @returns {PromiseLike<any>}
+ */
+ReactionMarker.prototype.init = function () {
+ var self = this;
+ return self.getCustomMap().getModel().getReactionById(self.getId()).then(function (reactionData) {
+ self.setReactionData(reactionData);
+ return self._init();
+ }).then(function () {
+ return self.show();
+ });
+};
+
+/**
+ * Returns {@link Reaction} data for this marker.
+ *
+ * @returns {Reaction} data for this marker
+ */
+ReactionMarker.prototype.getReactionData = function () {
+ return this._reactionData;
+};
+
+/**
+ * Sets {@link Reaction} data for this marker.
+ *
+ * @param {Reaction} data
+ * data for this marker
+ */
+ReactionMarker.prototype.setReactionData = function (data) {
+ this._reactionData = data;
+};
+
+/**
+ * Returns coordinates where marker is pointing.
+ *
+ * @returns {Point} - coordinates where marker is pointing
+ */
+ReactionMarker.prototype.getCoordinates = function () {
+ return new Point(this._reactionData.getCenter().x, this._reactionData.getCenter().y);
+};
+
+module.exports = ReactionMarker;
diff --git a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js b/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
index 85906d905631f2323f1f1d6e243da80ff87f7c49..aedfaaa67dfbab6ad3ed8636a30b2dc31c471d89 100644
--- a/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/AbstractDbOverlay.js
@@ -1,318 +1,318 @@
-"use strict";
-
-/* exported logger */
-
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-var Promise = require("bluebird");
-
-var IdentifiedElement = require('../data/IdentifiedElement');
-var ObjectWithListeners = require('../../ObjectWithListeners');
-var Point= require('../canvas/Point');
-
-var ServerConnector = require('../../ServerConnector');
-
-function AbstractDbOverlay(params) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- if (params.map === undefined) {
- throw new Error("map param must be defined");
- }
-
- this.setName(params.name);
- this.setMap(params.map);
-
- this.setAllowSearchById(params.allowSearchById);
- this.setAllowGeneralSearch(params.allowGeneralSearch);
-
- this.setIconType(params.iconType);
- this.setIconStart(params.iconColorStart);
-
- this._elementsByQuery = [];
- this._elementsByQuery[""] = [];
- this.registerListenerType('onSearch');
- this.registerListenerType('onClear');
- this.registerListenerType('onTargetVisibilityChange');
-
- this.setQueries([]);
-
- this.mapOverlays = {
- ALIAS: [],
- REACTION: [],
- POINT: []
- };
-
-}
-
-AbstractDbOverlay.prototype = Object.create(ObjectWithListeners.prototype);
-AbstractDbOverlay.prototype.constructor = AbstractDbOverlay;
-
-AbstractDbOverlay.QueryType = {
- SEARCH_BY_COORDINATES: "SEARCH_BY_COORDINATES",
- SEARCH_BY_TARGET: "SEARCH_BY_TARGET",
- SEARCH_BY_QUERY: "SEARCH_BY_QUERY"
-};
-
-AbstractDbOverlay.prototype.encodeQuery = function (type, arg0, arg1, arg2) {
- if (type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
- var modelId = arg0;
- var coordinates = arg1;
- // noinspection UnnecessaryLocalVariableJS
- var zoom = arg2;
- return JSON.stringify({
- type: type,
- modelId: modelId,
- coordinates: coordinates,
- zoom: zoom
- });
- } else if (type === AbstractDbOverlay.QueryType.SEARCH_BY_TARGET) {
- // noinspection UnnecessaryLocalVariableJS
- var target = arg0;
- return JSON.stringify({
- type: type,
- target: target
- });
- } else if (type === AbstractDbOverlay.QueryType.SEARCH_BY_QUERY) {
- var query = arg0;
- // noinspection UnnecessaryLocalVariableJS
- var perfect = arg1;
- return JSON.stringify({
- type: type,
- query: query,
- perfect: perfect
- });
- } else {
- throw new Error("Unknown query type: " + type);
- }
-};
-
-AbstractDbOverlay.prototype.decodeQuery = function (query) {
- return JSON.parse(query);
-};
-
-AbstractDbOverlay.prototype.searchByQuery = function (originalQuery, perfect, fitBounds) {
- var self = this;
- var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery, perfect);
- ServerConnector.getSessionData().setQuery({
- type: self.getName(),
- query: query
- });
-
- var res;
- var encodedQueries = [];
-
- var resultPromise;
- if (originalQuery.indexOf(";") >= 0) {
- var queries = self.splitQuery(originalQuery);
-
- var promises = [];
- for (var i = 0; i < queries.length; i++) {
- encodedQueries.push(self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, queries[i], perfect));
- promises.push(self.searchBySingleQuery(queries[i], perfect));
- }
- resultPromise = Promise.all(promises);
- } else {
- resultPromise = self.searchBySingleQuery(originalQuery, perfect).then(function (results) {
- if (results.length > 0) {
- encodedQueries.push(query);
- return [results];
- } else {
- var queries = self.splitQuery(originalQuery);
-
- var promises = [];
- for (var i = 0; i < queries.length; i++) {
- encodedQueries.push(self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, queries[i], perfect));
- promises.push(self.searchBySingleQuery(queries[i], perfect));
- }
-
- return Promise.all(promises);
- }
- });
- }
- return resultPromise.then(function (results) {
- self.setQueries(encodedQueries);
- res = results;
- return self.callListeners('onSearch', {
- fitBounds: fitBounds,
- identifiedElements: res,
- type: AbstractDbOverlay.QueryType.SEARCH_BY_QUERY
- });
- }).then(function () {
- return res;
- });
-}
-;
-
-AbstractDbOverlay.prototype.setQueries = function (queries) {
- this._queries = queries;
-};
-
-AbstractDbOverlay.prototype.getQueries = function () {
- return this._queries;
-};
-
-AbstractDbOverlay.prototype.createIdentifiedElementsForTargetingClass = function (targetingElement, colourId) {
- var self = this;
- var result = [];
- var iconCounter = 1;
- var targets = targetingElement.getTargets();
- for (var k = 0; k < targets.length; k++) {
- var target = targets[k];
- if (target.isVisible()) {
- var elements = target.getTargetElements();
- for (var l = 0; l < elements.length; l++) {
- var element = elements[l];
- var ie = new IdentifiedElement(element);
- if (element.getType() === "ALIAS") {
- ie.setIcon(self.getIcon(colourId, iconCounter));
- } else if (element.getType() !== "REACTION") {
- throw new Error("Unknown element type: " + element.getType());
- }
- result.push(ie);
- }
- }
- iconCounter++;
- }
- return result;
-};
-
-/**
- * @returns {PromiseLike}
- */
-AbstractDbOverlay.prototype.refresh = function () {
- throw new Error("Refreshing shouldn't be called");
-};
-
-/**
- *
- * @param {IdentifiedElement} element
- * @returns {Promise}
- */
-AbstractDbOverlay.prototype.searchByTarget = function (element) {
- throw new Error("Not implemented");
-};
-
-AbstractDbOverlay.prototype.searchByEncodedQuery = function (originalQuery, fitBounds) {
- var query = this.decodeQuery(originalQuery);
- query.fitBounds = fitBounds;
- if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_QUERY) {
- return this.searchByQuery(query.query, query.perfect);
- } else if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_TARGET) {
- return this.searchByTarget(new IdentifiedElement(query.target));
- } else if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
- query.coordinates = new Point(query.coordinates.x, query.coordinates.y);
- if (this.getMap().getSubmapById(query.modelId) === null) {
- //this can happen when cached data comes from project that was removed and something else
- //was uploaded with the same name
- logger.warn("Invalid search query. Model doesn't exist: " + query.modelId);
- return Promise.resolve();
- }
- return this.searchByCoordinates(query);
- } else {
- throw new Error("Unknown type of query: " + query.type);
- }
-};
-
-AbstractDbOverlay.prototype.clear = function () {
- var self = this;
- return self.searchByQuery("").then(function () {
- return self.callListeners('onClear');
- });
-};
-
-/**
- * Returns true if overlay allows to get general data for element.
- */
-AbstractDbOverlay.prototype.allowGeneralSearch = function () {
- return this._allowGeneralSearch;
-};
-
-/**
- * Returns true if overlay allows to get data for element by search id.
- */
-AbstractDbOverlay.prototype.allowSearchById = function () {
- return this._allowSearchById;
-};
-
-AbstractDbOverlay.prototype.setMap = function (map) {
- this._map = map;
-};
-
-AbstractDbOverlay.prototype.getMap = function () {
- return this._map;
-};
-
-AbstractDbOverlay.prototype.setName = function (name) {
- this.name = name;
-};
-
-AbstractDbOverlay.prototype.getName = function () {
- return this.name;
-};
-
-AbstractDbOverlay.prototype.setAllowSearchById = function (allowSearchById) {
- // configure if the overlay can contain detailed data about elements that
- // should be visualized in detailed mode of the Info Window
- if (typeof allowSearchById === "boolean") {
- this._allowSearchById = allowSearchById;
- } else if (allowSearchById === undefined) {
- this._allowSearchById = false;
- } else {
- throw new Error("Unknown type of allowSearchById: " + allowSearchById);
- }
-};
-
-AbstractDbOverlay.prototype.setAllowGeneralSearch = function (allowGeneralSearch) {
- if (typeof allowGeneralSearch === "boolean") {
- this._allowGeneralSearch = allowGeneralSearch;
- } else if (allowGeneralSearch === undefined) {
- this._allowGeneralSearch = false;
- } else {
- throw new Error("Unknown type of allowSearchById: " + allowGeneralSearch);
- }
-};
-
-AbstractDbOverlay.prototype.setIconType = function (iconType) {
- this._iconType = iconType;
-};
-AbstractDbOverlay.prototype.setIconStart = function (iconStart) {
- this._iconStart = iconStart;
-};
-
-AbstractDbOverlay.IconColors = ["red", "blue", "green", "purple", "yellow", "pink", "paleblue", "brown", "orange"];
-
-AbstractDbOverlay.prototype.getColor = function (colorId) {
- var id = colorId + this._iconStart;
- id %= AbstractDbOverlay.IconColors.length;
- return AbstractDbOverlay.IconColors[id];
-};
-
-AbstractDbOverlay.prototype.getIcon = function (colorId, id) {
- var suffix = "_" + id;
- if (id >= 100 || id === undefined) {
- suffix = "";
- }
- var color = this.getColor(colorId);
- return "marker/" + this._iconType + "/" + this._iconType + "_" + color + suffix + ".png";
-};
-
-AbstractDbOverlay.prototype.splitQuery = function (query, useFullName) {
- var result = [];
- if (query.indexOf(";") >= 0) {
- result = query.split(";");
- } else {
- result = query.split(",");
- }
-
- for (var i = 0; i < result.length; i++) {
- result[i] = result[i].trim();
- }
- if (result.length > 1 && useFullName) {
- result.push(query);
- }
- return result;
-};
-
-module.exports = AbstractDbOverlay;
+"use strict";
+
+/* exported logger */
+
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var Promise = require("bluebird");
+
+var IdentifiedElement = require('../data/IdentifiedElement');
+var ObjectWithListeners = require('../../ObjectWithListeners');
+var Point= require('../canvas/Point');
+
+var ServerConnector = require('../../ServerConnector');
+
+function AbstractDbOverlay(params) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ if (params.map === undefined) {
+ throw new Error("map param must be defined");
+ }
+
+ this.setName(params.name);
+ this.setMap(params.map);
+
+ this.setAllowSearchById(params.allowSearchById);
+ this.setAllowGeneralSearch(params.allowGeneralSearch);
+
+ this.setIconType(params.iconType);
+ this.setIconStart(params.iconColorStart);
+
+ this._elementsByQuery = [];
+ this._elementsByQuery[""] = [];
+ this.registerListenerType('onSearch');
+ this.registerListenerType('onClear');
+ this.registerListenerType('onTargetVisibilityChange');
+
+ this.setQueries([]);
+
+ this.mapOverlays = {
+ ALIAS: [],
+ REACTION: [],
+ POINT: []
+ };
+
+}
+
+AbstractDbOverlay.prototype = Object.create(ObjectWithListeners.prototype);
+AbstractDbOverlay.prototype.constructor = AbstractDbOverlay;
+
+AbstractDbOverlay.QueryType = {
+ SEARCH_BY_COORDINATES: "SEARCH_BY_COORDINATES",
+ SEARCH_BY_TARGET: "SEARCH_BY_TARGET",
+ SEARCH_BY_QUERY: "SEARCH_BY_QUERY"
+};
+
+AbstractDbOverlay.prototype.encodeQuery = function (type, arg0, arg1, arg2) {
+ if (type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
+ var modelId = arg0;
+ var coordinates = arg1;
+ // noinspection UnnecessaryLocalVariableJS
+ var zoom = arg2;
+ return JSON.stringify({
+ type: type,
+ modelId: modelId,
+ coordinates: coordinates,
+ zoom: zoom
+ });
+ } else if (type === AbstractDbOverlay.QueryType.SEARCH_BY_TARGET) {
+ // noinspection UnnecessaryLocalVariableJS
+ var target = arg0;
+ return JSON.stringify({
+ type: type,
+ target: target
+ });
+ } else if (type === AbstractDbOverlay.QueryType.SEARCH_BY_QUERY) {
+ var query = arg0;
+ // noinspection UnnecessaryLocalVariableJS
+ var perfect = arg1;
+ return JSON.stringify({
+ type: type,
+ query: query,
+ perfect: perfect
+ });
+ } else {
+ throw new Error("Unknown query type: " + type);
+ }
+};
+
+AbstractDbOverlay.prototype.decodeQuery = function (query) {
+ return JSON.parse(query);
+};
+
+AbstractDbOverlay.prototype.searchByQuery = function (originalQuery, perfect, fitBounds) {
+ var self = this;
+ var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery, perfect);
+ ServerConnector.getSessionData().setQuery({
+ type: self.getName(),
+ query: query
+ });
+
+ var res;
+ var encodedQueries = [];
+
+ var resultPromise;
+ if (originalQuery.indexOf(";") >= 0) {
+ var queries = self.splitQuery(originalQuery);
+
+ var promises = [];
+ for (var i = 0; i < queries.length; i++) {
+ encodedQueries.push(self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, queries[i], perfect));
+ promises.push(self.searchBySingleQuery(queries[i], perfect));
+ }
+ resultPromise = Promise.all(promises);
+ } else {
+ resultPromise = self.searchBySingleQuery(originalQuery, perfect).then(function (results) {
+ if (results.length > 0) {
+ encodedQueries.push(query);
+ return [results];
+ } else {
+ var queries = self.splitQuery(originalQuery);
+
+ var promises = [];
+ for (var i = 0; i < queries.length; i++) {
+ encodedQueries.push(self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, queries[i], perfect));
+ promises.push(self.searchBySingleQuery(queries[i], perfect));
+ }
+
+ return Promise.all(promises);
+ }
+ });
+ }
+ return resultPromise.then(function (results) {
+ self.setQueries(encodedQueries);
+ res = results;
+ return self.callListeners('onSearch', {
+ fitBounds: fitBounds,
+ identifiedElements: res,
+ type: AbstractDbOverlay.QueryType.SEARCH_BY_QUERY
+ });
+ }).then(function () {
+ return res;
+ });
+}
+;
+
+AbstractDbOverlay.prototype.setQueries = function (queries) {
+ this._queries = queries;
+};
+
+AbstractDbOverlay.prototype.getQueries = function () {
+ return this._queries;
+};
+
+AbstractDbOverlay.prototype.createIdentifiedElementsForTargetingClass = function (targetingElement, colourId) {
+ var self = this;
+ var result = [];
+ var iconCounter = 1;
+ var targets = targetingElement.getTargets();
+ for (var k = 0; k < targets.length; k++) {
+ var target = targets[k];
+ if (target.isVisible()) {
+ var elements = target.getTargetElements();
+ for (var l = 0; l < elements.length; l++) {
+ var element = elements[l];
+ var ie = new IdentifiedElement(element);
+ if (element.getType() === "ALIAS") {
+ ie.setIcon(self.getIcon(colourId, iconCounter));
+ } else if (element.getType() !== "REACTION") {
+ throw new Error("Unknown element type: " + element.getType());
+ }
+ result.push(ie);
+ }
+ }
+ iconCounter++;
+ }
+ return result;
+};
+
+/**
+ * @returns {PromiseLike}
+ */
+AbstractDbOverlay.prototype.refresh = function () {
+ throw new Error("Refreshing shouldn't be called");
+};
+
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @returns {Promise}
+ */
+AbstractDbOverlay.prototype.searchByTarget = function (element) {
+ throw new Error("Not implemented");
+};
+
+AbstractDbOverlay.prototype.searchByEncodedQuery = function (originalQuery, fitBounds) {
+ var query = this.decodeQuery(originalQuery);
+ query.fitBounds = fitBounds;
+ if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_QUERY) {
+ return this.searchByQuery(query.query, query.perfect);
+ } else if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_TARGET) {
+ return this.searchByTarget(new IdentifiedElement(query.target));
+ } else if (query.type === AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES) {
+ query.coordinates = new Point(query.coordinates.x, query.coordinates.y);
+ if (this.getMap().getSubmapById(query.modelId) === null) {
+ //this can happen when cached data comes from project that was removed and something else
+ //was uploaded with the same name
+ logger.warn("Invalid search query. Model doesn't exist: " + query.modelId);
+ return Promise.resolve();
+ }
+ return this.searchByCoordinates(query);
+ } else {
+ throw new Error("Unknown type of query: " + query.type);
+ }
+};
+
+AbstractDbOverlay.prototype.clear = function () {
+ var self = this;
+ return self.searchByQuery("").then(function () {
+ return self.callListeners('onClear');
+ });
+};
+
+/**
+ * Returns true if overlay allows to get general data for element.
+ */
+AbstractDbOverlay.prototype.allowGeneralSearch = function () {
+ return this._allowGeneralSearch;
+};
+
+/**
+ * Returns true if overlay allows to get data for element by search id.
+ */
+AbstractDbOverlay.prototype.allowSearchById = function () {
+ return this._allowSearchById;
+};
+
+AbstractDbOverlay.prototype.setMap = function (map) {
+ this._map = map;
+};
+
+AbstractDbOverlay.prototype.getMap = function () {
+ return this._map;
+};
+
+AbstractDbOverlay.prototype.setName = function (name) {
+ this.name = name;
+};
+
+AbstractDbOverlay.prototype.getName = function () {
+ return this.name;
+};
+
+AbstractDbOverlay.prototype.setAllowSearchById = function (allowSearchById) {
+ // configure if the overlay can contain detailed data about elements that
+ // should be visualized in detailed mode of the Info Window
+ if (typeof allowSearchById === "boolean") {
+ this._allowSearchById = allowSearchById;
+ } else if (allowSearchById === undefined) {
+ this._allowSearchById = false;
+ } else {
+ throw new Error("Unknown type of allowSearchById: " + allowSearchById);
+ }
+};
+
+AbstractDbOverlay.prototype.setAllowGeneralSearch = function (allowGeneralSearch) {
+ if (typeof allowGeneralSearch === "boolean") {
+ this._allowGeneralSearch = allowGeneralSearch;
+ } else if (allowGeneralSearch === undefined) {
+ this._allowGeneralSearch = false;
+ } else {
+ throw new Error("Unknown type of allowSearchById: " + allowGeneralSearch);
+ }
+};
+
+AbstractDbOverlay.prototype.setIconType = function (iconType) {
+ this._iconType = iconType;
+};
+AbstractDbOverlay.prototype.setIconStart = function (iconStart) {
+ this._iconStart = iconStart;
+};
+
+AbstractDbOverlay.IconColors = ["red", "blue", "green", "purple", "yellow", "pink", "paleblue", "brown", "orange"];
+
+AbstractDbOverlay.prototype.getColor = function (colorId) {
+ var id = colorId + this._iconStart;
+ id %= AbstractDbOverlay.IconColors.length;
+ return AbstractDbOverlay.IconColors[id];
+};
+
+AbstractDbOverlay.prototype.getIcon = function (colorId, id) {
+ var suffix = "_" + id;
+ if (id >= 100 || id === undefined) {
+ suffix = "";
+ }
+ var color = this.getColor(colorId);
+ return "marker/" + this._iconType + "/" + this._iconType + "_" + color + suffix + ".png";
+};
+
+AbstractDbOverlay.prototype.splitQuery = function (query, useFullName) {
+ var result = [];
+ if (query.indexOf(";") >= 0) {
+ result = query.split(";");
+ } else {
+ result = query.split(",");
+ }
+
+ for (var i = 0; i < result.length; i++) {
+ result[i] = result[i].trim();
+ }
+ if (result.length > 1 && useFullName) {
+ result.push(query);
+ }
+ return result;
+};
+
+module.exports = AbstractDbOverlay;
diff --git a/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js b/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
index 50540c08d777d15b6e3e2075b3e7b1b54e5efd16..c357e9cabd5175f13ef53a07c513843abc97b73d 100644
--- a/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/AbstractTargettingDbOverlay.js
@@ -1,187 +1,187 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('../../logger');
-
-var Promise = require("bluebird");
-
-var IdentifiedElement = require('../data/IdentifiedElement');
-var AbstractDbOverlay = require('./AbstractDbOverlay');
-
-function AbstractTargettingDbOverlay(params) {
- // call super constructor
- AbstractDbOverlay.call(this, params);
-}
-
-AbstractTargettingDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
-AbstractTargettingDbOverlay.prototype.constructor = AbstractTargettingDbOverlay;
-
-AbstractTargettingDbOverlay.prototype.getElementsByQuery = function (query) {
- var self = this;
- return new Promise(function (resolve) {
- var i;
- var queryId = null;
- var queries = self.getQueries();
- for (i = 0; i < queries.length; i++) {
- if (queries[i] === query) {
- queryId = i;
- }
- }
- if (queryId === null) {
- throw new Error("Invalid query: " + query);
- }
- var colourId = queryId;
- var elements = self._elementsByQuery[query];
-
- var result = [];
- if (elements.length > 0) {
- if (elements.length > 1) {
- logger.warn("More than one element per query not implemented");
- }
- var element = elements[0];
- result.element = element;
- var iconCounter = 1;
- for (i = 0; i < element.getTargets().length; i++) {
- var target = element.getTargets()[i];
- var icon = self.getIcon(colourId, iconCounter++);
- if (target.getTargetElements().length === 0) {
- icon = null;
- }
- result.push({
- element: target,
- icon: icon
- });
- }
- }
- resolve(result);
- });
-};
-
-AbstractTargettingDbOverlay.prototype.searchBySingleQuery = function (originalQuery) {
- var self = this;
- var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery);
- if (self._elementsByQuery[query] !== undefined) {
- return Promise.resolve(self._elementsByQuery[query]);
- } else {
- return self.getElementsByQueryFromServer({
- query: originalQuery
- }).then(function (elements) {
- self._elementsByQuery[query] = elements;
-
- var identifiedElements = [];
- for (var i = 0; i < elements.length; i++) {
- var targets = elements[i].getTargets();
- for (var j = 0; j < targets.length; j++) {
- var target = targets[j];
- for (var k = 0; k < target.targetElements; k++) {
- identifiedElements.push(new IdentifiedElement(target.targetElements[i]));
- }
- }
- }
- return self.getMap().fetchIdentifiedElements(identifiedElements, true);
- }).then(function () {
- return self._elementsByQuery[query];
- });
- }
-};
-
-AbstractTargettingDbOverlay.prototype.getIdentifiedElements = function () {
- var self = this;
-
- return new Promise(function (resolve) {
- var queries = self.getQueries();
- var result = [];
- var colourId = 0;
- for (var i = 0; i < queries.length; i++) {
- var query = queries[i];
- var elements = self._elementsByQuery[query];
-
- for (var j = 0; j < elements.length; j++) {
- var element = elements[j];
-
- var targetElements = self.createIdentifiedElementsForTargetingClass(element, colourId);
-
- result.push.apply(result, targetElements);
-
- colourId++;
- }
- }
- resolve(result);
- });
-};
-
-/**
- *
- * @param {IdentifiedElement} element
- * @returns {Promise}
- */
-AbstractTargettingDbOverlay.prototype.searchByTarget = function (element) {
- return this.searchNamesByTarget(element);
-};
-
-AbstractTargettingDbOverlay.prototype.searchNamesByTarget = function (element) {
- var self = this;
- var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_TARGET, element);
-
- if (self._elementsByQuery[query] !== undefined) {
- return Promise.resolve(self._elementsByQuery[query]);
- } else {
- return self.getNamesByTargetFromServer({
- target: element
- }).then(function (drugNames) {
- self._elementsByQuery[query] = drugNames;
- return self._elementsByQuery[query];
- });
- }
-};
-
-
-AbstractTargettingDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element, general) {
- var self = this;
- if (general) {
- return self.searchNamesByTarget(element).then(function (names) {
- var promises = [];
- names.forEach(function (name) {
- promises.push(self.searchBySingleQuery(name));
- });
- return Promise.all(promises);
- }).then(function (drugs) {
- var result = [];
- drugs.forEach(function (drugList) {
- drugList.forEach(function (drug) {
- result.push(drug);
- });
- });
- return result;
- });
- } else {
- return new Promise(function (resolve) {
- var drugNames = [];
- var result = [];
- var queries = self.getQueries();
- for (var i = 0; i < queries.length; i++) {
- var drugs = self._elementsByQuery[queries[i]];
- if (drugs === undefined) {
- drugs = [];
- }
- for (var j = 0; j < drugs.length; j++) {
- var drug = drugs[j];
- var targets = drug.getTargets();
- for (var k = 0; k < targets.length; k++) {
- var elements = targets[k].getTargetElements();
- for (var l = 0; l < elements.length; l++) {
- if (element.equals(elements[l]) && drugNames[drug.getName()] === undefined) {
- result.push(drug);
- drugNames[drug.getName()] = true;
- }
- }
- }
- }
- }
- resolve(result);
- });
- }
-};
-
-module.exports = AbstractTargettingDbOverlay;
+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+var Promise = require("bluebird");
+
+var IdentifiedElement = require('../data/IdentifiedElement');
+var AbstractDbOverlay = require('./AbstractDbOverlay');
+
+function AbstractTargettingDbOverlay(params) {
+ // call super constructor
+ AbstractDbOverlay.call(this, params);
+}
+
+AbstractTargettingDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
+AbstractTargettingDbOverlay.prototype.constructor = AbstractTargettingDbOverlay;
+
+AbstractTargettingDbOverlay.prototype.getElementsByQuery = function (query) {
+ var self = this;
+ return new Promise(function (resolve) {
+ var i;
+ var queryId = null;
+ var queries = self.getQueries();
+ for (i = 0; i < queries.length; i++) {
+ if (queries[i] === query) {
+ queryId = i;
+ }
+ }
+ if (queryId === null) {
+ throw new Error("Invalid query: " + query);
+ }
+ var colourId = queryId;
+ var elements = self._elementsByQuery[query];
+
+ var result = [];
+ if (elements.length > 0) {
+ if (elements.length > 1) {
+ logger.warn("More than one element per query not implemented");
+ }
+ var element = elements[0];
+ result.element = element;
+ var iconCounter = 1;
+ for (i = 0; i < element.getTargets().length; i++) {
+ var target = element.getTargets()[i];
+ var icon = self.getIcon(colourId, iconCounter++);
+ if (target.getTargetElements().length === 0) {
+ icon = null;
+ }
+ result.push({
+ element: target,
+ icon: icon
+ });
+ }
+ }
+ resolve(result);
+ });
+};
+
+AbstractTargettingDbOverlay.prototype.searchBySingleQuery = function (originalQuery) {
+ var self = this;
+ var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery);
+ if (self._elementsByQuery[query] !== undefined) {
+ return Promise.resolve(self._elementsByQuery[query]);
+ } else {
+ return self.getElementsByQueryFromServer({
+ query: originalQuery
+ }).then(function (elements) {
+ self._elementsByQuery[query] = elements;
+
+ var identifiedElements = [];
+ for (var i = 0; i < elements.length; i++) {
+ var targets = elements[i].getTargets();
+ for (var j = 0; j < targets.length; j++) {
+ var target = targets[j];
+ for (var k = 0; k < target.targetElements; k++) {
+ identifiedElements.push(new IdentifiedElement(target.targetElements[i]));
+ }
+ }
+ }
+ return self.getMap().fetchIdentifiedElements(identifiedElements, true);
+ }).then(function () {
+ return self._elementsByQuery[query];
+ });
+ }
+};
+
+AbstractTargettingDbOverlay.prototype.getIdentifiedElements = function () {
+ var self = this;
+
+ return new Promise(function (resolve) {
+ var queries = self.getQueries();
+ var result = [];
+ var colourId = 0;
+ for (var i = 0; i < queries.length; i++) {
+ var query = queries[i];
+ var elements = self._elementsByQuery[query];
+
+ for (var j = 0; j < elements.length; j++) {
+ var element = elements[j];
+
+ var targetElements = self.createIdentifiedElementsForTargetingClass(element, colourId);
+
+ result.push.apply(result, targetElements);
+
+ colourId++;
+ }
+ }
+ resolve(result);
+ });
+};
+
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @returns {Promise}
+ */
+AbstractTargettingDbOverlay.prototype.searchByTarget = function (element) {
+ return this.searchNamesByTarget(element);
+};
+
+AbstractTargettingDbOverlay.prototype.searchNamesByTarget = function (element) {
+ var self = this;
+ var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_TARGET, element);
+
+ if (self._elementsByQuery[query] !== undefined) {
+ return Promise.resolve(self._elementsByQuery[query]);
+ } else {
+ return self.getNamesByTargetFromServer({
+ target: element
+ }).then(function (drugNames) {
+ self._elementsByQuery[query] = drugNames;
+ return self._elementsByQuery[query];
+ });
+ }
+};
+
+
+AbstractTargettingDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element, general) {
+ var self = this;
+ if (general) {
+ return self.searchNamesByTarget(element).then(function (names) {
+ var promises = [];
+ names.forEach(function (name) {
+ promises.push(self.searchBySingleQuery(name));
+ });
+ return Promise.all(promises);
+ }).then(function (drugs) {
+ var result = [];
+ drugs.forEach(function (drugList) {
+ drugList.forEach(function (drug) {
+ result.push(drug);
+ });
+ });
+ return result;
+ });
+ } else {
+ return new Promise(function (resolve) {
+ var drugNames = [];
+ var result = [];
+ var queries = self.getQueries();
+ for (var i = 0; i < queries.length; i++) {
+ var drugs = self._elementsByQuery[queries[i]];
+ if (drugs === undefined) {
+ drugs = [];
+ }
+ for (var j = 0; j < drugs.length; j++) {
+ var drug = drugs[j];
+ var targets = drug.getTargets();
+ for (var k = 0; k < targets.length; k++) {
+ var elements = targets[k].getTargetElements();
+ for (var l = 0; l < elements.length; l++) {
+ if (element.equals(elements[l]) && drugNames[drug.getName()] === undefined) {
+ result.push(drug);
+ drugNames[drug.getName()] = true;
+ }
+ }
+ }
+ }
+ }
+ resolve(result);
+ });
+ }
+};
+
+module.exports = AbstractTargettingDbOverlay;
diff --git a/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js b/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js
index 778f9e8ba5e6af9dbce4ebb2f10911950da63f6d..e77a9894107b3fa667c3d8b4170b1ab4fa7bb3d8 100644
--- a/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/ChemicalDbOverlay.js
@@ -1,30 +1,30 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('../../logger');
-
-var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
-
-var ServerConnector = require('../../ServerConnector');
-
-function ChemicalDbOverlay(params) {
- params.iconType= "ball";
- params.iconColorStart = 1;
- // call super constructor
- AbstractTargettingDbOverlay.call(this, params);
-
-}
-
-ChemicalDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
-ChemicalDbOverlay.prototype.constructor = ChemicalDbOverlay;
-
-ChemicalDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
- return ServerConnector.getChemicalNamesByTarget(param);
-};
-
-ChemicalDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
- return ServerConnector.getChemicalsByQuery(param);
-};
-
-module.exports = ChemicalDbOverlay;
+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
+
+var ServerConnector = require('../../ServerConnector');
+
+function ChemicalDbOverlay(params) {
+ params.iconType= "ball";
+ params.iconColorStart = 1;
+ // call super constructor
+ AbstractTargettingDbOverlay.call(this, params);
+
+}
+
+ChemicalDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
+ChemicalDbOverlay.prototype.constructor = ChemicalDbOverlay;
+
+ChemicalDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
+ return ServerConnector.getChemicalNamesByTarget(param);
+};
+
+ChemicalDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
+ return ServerConnector.getChemicalsByQuery(param);
+};
+
+module.exports = ChemicalDbOverlay;
diff --git a/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js b/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js
index 4c86c71aa82e99c614a9739745550451bbc43f9f..da24726b03fcd373e989671c7e623c7836e9dad8 100644
--- a/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/CommentDbOverlay.js
@@ -1,85 +1,85 @@
-"use strict";
-
-/* exported logger */
-
-var Promise = require("bluebird");
-
-var AbstractDbOverlay = require('./AbstractDbOverlay');
-var ServerConnector = require('../../ServerConnector');
-
-var logger = require('../../logger');
-
-function CommentDbOverlay(params) {
- // call super constructor
- AbstractDbOverlay.call(this, params);
-
- this._elements = [];
- this._detailDataByIdentifiedElement = [];
- this.registerListenerType('onRefresh');
-}
-
-CommentDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
-CommentDbOverlay.prototype.constructor = CommentDbOverlay;
-
-CommentDbOverlay.prototype.refresh = function() {
- var self = this;
- return ServerConnector.getLightComments({}).then(function(comments) {
- self._elements = comments;
- return self.callListeners('onRefresh');
- }).then(function() {
- return self._elements;
- });
-};
-
-CommentDbOverlay.prototype.addComment = function(newComment) {
- var self = this;
- self._elements.push(newComment);
- return self.callListeners('onRefresh').then(function() {
- return self._elements;
- });
-};
-
-CommentDbOverlay.prototype.clear = function() {
- var self = this;
- self._elements = [];
- self._detailDataByIdentifiedElement = [];
- return self.callListeners('onClear');
-};
-
-CommentDbOverlay.prototype.getDetailDataByIdentifiedElement = function(element) {
- var self = this;
- var elementKey = element.getId() + "," + element.getType() + "," + element.getModelId();
- if (this._detailDataByIdentifiedElement[elementKey] !== undefined) {
- return Promise.resolve(this._detailDataByIdentifiedElement[elementKey]);
- } else {
- var coordinates;
- if (element.getType() === "POINT") {
- coordinates = element.getPoint().x.toFixed(2) + "," + element.getPoint().y.toFixed(2);
- }
- return ServerConnector.getComments({
- elementId : element.getId(),
- elementType : element.getType(),
- coordinates : coordinates
- }).then(function(comments) {
- self._detailDataByIdentifiedElement[elementKey] = comments;
- return comments;
- });
- }
-};
-
-CommentDbOverlay.prototype.getIdentifiedElements = function() {
- var self = this;
- return new Promise(function(resolve) {
- var result = [];
- for (var i = 0; i < self._elements.length; i++) {
- // we return only elements that are pinned to the map and weren't removed
- var comment = self._elements[i];
- if (!comment.isRemoved() && comment.isPinned()) {
- result.push(comment.getIdentifiedElement());
- }
- }
- resolve(result);
- });
-};
-
-module.exports = CommentDbOverlay;
+"use strict";
+
+/* exported logger */
+
+var Promise = require("bluebird");
+
+var AbstractDbOverlay = require('./AbstractDbOverlay');
+var ServerConnector = require('../../ServerConnector');
+
+var logger = require('../../logger');
+
+function CommentDbOverlay(params) {
+ // call super constructor
+ AbstractDbOverlay.call(this, params);
+
+ this._elements = [];
+ this._detailDataByIdentifiedElement = [];
+ this.registerListenerType('onRefresh');
+}
+
+CommentDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
+CommentDbOverlay.prototype.constructor = CommentDbOverlay;
+
+CommentDbOverlay.prototype.refresh = function() {
+ var self = this;
+ return ServerConnector.getLightComments({}).then(function(comments) {
+ self._elements = comments;
+ return self.callListeners('onRefresh');
+ }).then(function() {
+ return self._elements;
+ });
+};
+
+CommentDbOverlay.prototype.addComment = function(newComment) {
+ var self = this;
+ self._elements.push(newComment);
+ return self.callListeners('onRefresh').then(function() {
+ return self._elements;
+ });
+};
+
+CommentDbOverlay.prototype.clear = function() {
+ var self = this;
+ self._elements = [];
+ self._detailDataByIdentifiedElement = [];
+ return self.callListeners('onClear');
+};
+
+CommentDbOverlay.prototype.getDetailDataByIdentifiedElement = function(element) {
+ var self = this;
+ var elementKey = element.getId() + "," + element.getType() + "," + element.getModelId();
+ if (this._detailDataByIdentifiedElement[elementKey] !== undefined) {
+ return Promise.resolve(this._detailDataByIdentifiedElement[elementKey]);
+ } else {
+ var coordinates;
+ if (element.getType() === "POINT") {
+ coordinates = element.getPoint().x.toFixed(2) + "," + element.getPoint().y.toFixed(2);
+ }
+ return ServerConnector.getComments({
+ elementId : element.getId(),
+ elementType : element.getType(),
+ coordinates : coordinates
+ }).then(function(comments) {
+ self._detailDataByIdentifiedElement[elementKey] = comments;
+ return comments;
+ });
+ }
+};
+
+CommentDbOverlay.prototype.getIdentifiedElements = function() {
+ var self = this;
+ return new Promise(function(resolve) {
+ var result = [];
+ for (var i = 0; i < self._elements.length; i++) {
+ // we return only elements that are pinned to the map and weren't removed
+ var comment = self._elements[i];
+ if (!comment.isRemoved() && comment.isPinned()) {
+ result.push(comment.getIdentifiedElement());
+ }
+ }
+ resolve(result);
+ });
+};
+
+module.exports = CommentDbOverlay;
diff --git a/frontend-js/src/main/js/map/overlay/DbOverlayCollection.js b/frontend-js/src/main/js/map/overlay/DbOverlayCollection.js
index e98f689b21ec0ff72b5b2eef195b8f8119f93f6c..97eb7f90aaf00ebfd60061b0e94bf5f55b7783a2 100644
--- a/frontend-js/src/main/js/map/overlay/DbOverlayCollection.js
+++ b/frontend-js/src/main/js/map/overlay/DbOverlayCollection.js
@@ -1,67 +1,67 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('../../logger');
-
-var ObjectWithListeners = require('../../ObjectWithListeners');
-var ChemicalDbOverlay = require('./ChemicalDbOverlay');
-var CommentDbOverlay = require('./CommentDbOverlay');
-var DrugDbOverlay = require('./DrugDbOverlay');
-var MiRnaDbOverlay = require('./MiRnaDbOverlay');
-var SearchDbOverlay = require('./SearchDbOverlay');
-
-function DbOverlayCollection(params) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- var hasDisease = params.map.getProject().getDisease() !== undefined;
-
- var dataCollections = [ {
- name : "search"
- }, {
- name : "drug",
- allowSearchById : true,
- allowGeneralSearch : true
- }, {
- name : "chemical",
- allowSearchById : hasDisease,
- allowGeneralSearch : hasDisease
- }, {
- name : "mirna",
- allowSearchById : true,
- allowGeneralSearch : true
- }, {
- name : "comment",
- allowSearchById : false,
- allowGeneralSearch : true
- } ];
-
- var map = params.map;
-
- for (var i = 0; i < dataCollections.length; i++) {
- var collectionParams = dataCollections[i];
- collectionParams.map = map;
- var collection = null;
- if (collectionParams.name === "comment") {
- collection = new CommentDbOverlay(collectionParams);
- } else if (collectionParams.name === "search") {
- collection = new SearchDbOverlay(collectionParams);
- } else if (collectionParams.name === "drug") {
- collection = new DrugDbOverlay(collectionParams);
- } else if (collectionParams.name === "mirna") {
- collection = new MiRnaDbOverlay(collectionParams);
- } else if (collectionParams.name === "chemical") {
- collection = new ChemicalDbOverlay(collectionParams);
- } else {
- throw new Error("Unknown overlay db: " + collectionParams.name);
- }
- map.registerDbOverlay(collection);
- }
-
-}
-
-DbOverlayCollection.prototype = Object.create(ObjectWithListeners.prototype);
-DbOverlayCollection.prototype.constructor = DbOverlayCollection;
-
-module.exports = DbOverlayCollection;
+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+var ObjectWithListeners = require('../../ObjectWithListeners');
+var ChemicalDbOverlay = require('./ChemicalDbOverlay');
+var CommentDbOverlay = require('./CommentDbOverlay');
+var DrugDbOverlay = require('./DrugDbOverlay');
+var MiRnaDbOverlay = require('./MiRnaDbOverlay');
+var SearchDbOverlay = require('./SearchDbOverlay');
+
+function DbOverlayCollection(params) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ var hasDisease = params.map.getProject().getDisease() !== undefined;
+
+ var dataCollections = [ {
+ name : "search"
+ }, {
+ name : "drug",
+ allowSearchById : true,
+ allowGeneralSearch : true
+ }, {
+ name : "chemical",
+ allowSearchById : hasDisease,
+ allowGeneralSearch : hasDisease
+ }, {
+ name : "mirna",
+ allowSearchById : true,
+ allowGeneralSearch : true
+ }, {
+ name : "comment",
+ allowSearchById : false,
+ allowGeneralSearch : true
+ } ];
+
+ var map = params.map;
+
+ for (var i = 0; i < dataCollections.length; i++) {
+ var collectionParams = dataCollections[i];
+ collectionParams.map = map;
+ var collection = null;
+ if (collectionParams.name === "comment") {
+ collection = new CommentDbOverlay(collectionParams);
+ } else if (collectionParams.name === "search") {
+ collection = new SearchDbOverlay(collectionParams);
+ } else if (collectionParams.name === "drug") {
+ collection = new DrugDbOverlay(collectionParams);
+ } else if (collectionParams.name === "mirna") {
+ collection = new MiRnaDbOverlay(collectionParams);
+ } else if (collectionParams.name === "chemical") {
+ collection = new ChemicalDbOverlay(collectionParams);
+ } else {
+ throw new Error("Unknown overlay db: " + collectionParams.name);
+ }
+ map.registerDbOverlay(collection);
+ }
+
+}
+
+DbOverlayCollection.prototype = Object.create(ObjectWithListeners.prototype);
+DbOverlayCollection.prototype.constructor = DbOverlayCollection;
+
+module.exports = DbOverlayCollection;
diff --git a/frontend-js/src/main/js/map/overlay/DrugDbOverlay.js b/frontend-js/src/main/js/map/overlay/DrugDbOverlay.js
index bea3f1141d94da8cc26102deb6b39a014a056d64..23582176ede30f6ccc5aad12301aea9bb6e61048 100644
--- a/frontend-js/src/main/js/map/overlay/DrugDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/DrugDbOverlay.js
@@ -1,29 +1,29 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('../../logger');
-
-var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
-
-var ServerConnector = require('../../ServerConnector');
-
-function DrugDbOverlay(params) {
- params.iconType= "drug";
- params.iconColorStart = 5;
- // call super constructor
- AbstractTargettingDbOverlay.call(this, params);
-}
-
-DrugDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
-DrugDbOverlay.prototype.constructor = DrugDbOverlay;
-
-DrugDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
- return ServerConnector.getDrugNamesByTarget(param);
-};
-
-DrugDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
- return ServerConnector.getDrugsByQuery(param);
-};
-
-module.exports = DrugDbOverlay;
+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
+
+var ServerConnector = require('../../ServerConnector');
+
+function DrugDbOverlay(params) {
+ params.iconType= "drug";
+ params.iconColorStart = 5;
+ // call super constructor
+ AbstractTargettingDbOverlay.call(this, params);
+}
+
+DrugDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
+DrugDbOverlay.prototype.constructor = DrugDbOverlay;
+
+DrugDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
+ return ServerConnector.getDrugNamesByTarget(param);
+};
+
+DrugDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
+ return ServerConnector.getDrugsByQuery(param);
+};
+
+module.exports = DrugDbOverlay;
diff --git a/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js b/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js
index 141c864befe0525ddd21de0fcd8fbc0050febb46..8526cf7c809040eea06a14a3397e2433725b5d21 100644
--- a/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/MiRnaDbOverlay.js
@@ -1,30 +1,30 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('../../logger');
-
-var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
-
-var ServerConnector = require('../../ServerConnector');
-
-function MiRnaDbOverlay(params) {
- params.iconType= "target";
- params.iconColorStart = 2;
- // call super constructor
- AbstractTargettingDbOverlay.call(this, params);
-
-}
-
-MiRnaDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
-MiRnaDbOverlay.prototype.constructor = MiRnaDbOverlay;
-
-MiRnaDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
- return ServerConnector.getMiRnaNamesByTarget(param);
-};
-
-MiRnaDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
- return ServerConnector.getMiRnasByQuery(param);
-};
-
-module.exports = MiRnaDbOverlay;
+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+var AbstractTargettingDbOverlay = require('./AbstractTargettingDbOverlay');
+
+var ServerConnector = require('../../ServerConnector');
+
+function MiRnaDbOverlay(params) {
+ params.iconType= "target";
+ params.iconColorStart = 2;
+ // call super constructor
+ AbstractTargettingDbOverlay.call(this, params);
+
+}
+
+MiRnaDbOverlay.prototype = Object.create(AbstractTargettingDbOverlay.prototype);
+MiRnaDbOverlay.prototype.constructor = MiRnaDbOverlay;
+
+MiRnaDbOverlay.prototype.getNamesByTargetFromServer = function(param) {
+ return ServerConnector.getMiRnaNamesByTarget(param);
+};
+
+MiRnaDbOverlay.prototype.getElementsByQueryFromServer = function(param) {
+ return ServerConnector.getMiRnasByQuery(param);
+};
+
+module.exports = MiRnaDbOverlay;
diff --git a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
index 5f199aad9f22cb3dd89a040d47c0f3b0738a8d38..4720bfcac3877c8872918b68cbc7141f6932ab01 100644
--- a/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/SearchDbOverlay.js
@@ -1,355 +1,355 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('../../logger');
-
-var Promise = require("bluebird");
-
-var AbstractDbOverlay = require('./AbstractDbOverlay');
-var Alias = require('../data/Alias');
-var IdentifiedElement = require('../data/IdentifiedElement');
-var InvalidArgumentException = require('../../InvalidArgumentError');
-var Reaction = require('../data/Reaction');
-var SearchBioEntityGroup = require('../data/SearchBioEntityGroup');
-
-
-var ServerConnector = require('../../ServerConnector');
-
-/**
- *
- * @param params
- * @constructor
- * @extends AbstractDbOverlay
- */
-function SearchDbOverlay(params) {
- params.iconType = "marker";
- params.iconColorStart = 0;
- // call super constructor
- AbstractDbOverlay.call(this, params);
-
-}
-
-SearchDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
-SearchDbOverlay.prototype.constructor = SearchDbOverlay;
-
-SearchDbOverlay.prototype.getElementsByQuery = function (query) {
- var self = this;
- var i;
- var queryId = null;
- var queries = self.getQueries();
- for (i = 0; i < queries.length; i++) {
- if (queries[i] === query) {
- queryId = i;
- }
- }
- if (queryId === null) {
- throw new Error("Invalid query: " + query);
- }
- var elements = self._elementsByQuery[query];
- var promises = [];
- for (i = 0; i < elements.length; i++) {
- var model = self.getMap().getSubmapById(elements[0].getModelId()).getModel();
- promises.push(model.getByIdentifiedElement(elements[i], true));
- }
- return Promise.all(promises).then(function (elements) {
- var result = [];
- var iconCounter = 1;
- var groups = [];
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i];
- var alreadyExists = false;
- var group;
- for (var j = 0; j < groups.length; j++) {
- group = groups[j];
- if (group.bioEntityMatch(element)) {
- alreadyExists = true;
- group.addBioEntity(element);
- }
- }
-
- if (!alreadyExists) {
- var icon;
- if (element instanceof Alias) {
- icon = self.getIcon(queryId, iconCounter++)
- }
- group = new SearchBioEntityGroup(element);
- group.setIcon(icon);
- groups.push(group);
- result.push({
- element: group,
- icon: icon
- });
- }
- }
- return result;
- });
-};
-
-SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedElement, zoomLevel, coordinates) {
- if (identifiedElement === undefined) {
- return Promise.resolve();
- }
- var self = this;
- var model = self.getMap().getSubmapById(identifiedElement.getModelId()).getModel();
- return model.getByIdentifiedElement(identifiedElement, true).then(function (fullElement) {
- if (fullElement.getHierarchyVisibilityLevel() <= zoomLevel) {
- if (fullElement instanceof Alias) {
- //transparent compartments shouldn't be clickable
- if (fullElement.getTransparencyLevel() <= zoomLevel && fullElement.getType() === "Compartment") {
- return undefined;
- }
- }
- return identifiedElement;
- } else {
- var parentId;
- if (fullElement instanceof Alias) {
- if (fullElement.getComplexId() !== undefined) {
- parentId = fullElement.getComplexId();
- } else if (fullElement.getCompartmentId() !== undefined) {
- parentId = fullElement.getCompartmentId();
- }
- }
- if (parentId !== undefined) {
- var parent = new IdentifiedElement({
- id: parentId,
- type: "ALIAS",
- modelId: identifiedElement.getModelId()
- });
- return self._getFirstVisibleParentOrObject(parent, zoomLevel, coordinates);
- } else {
- logger.warn("Cannot find visible parent for object. (zoomLevel=" + zoomLevel + ")");
- logger.warn(fullElement);
- return identifiedElement;
- }
- }
- });
-};
-SearchDbOverlay.prototype.searchByCoordinates = function (params) {
- var modelId = params.modelId;
- var coordinates = params.coordinates;
- var zoom = params.zoom;
-
- var self = this;
- var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES, modelId, coordinates, zoom);
-
- ServerConnector.getSessionData().setSearchQuery(query);
-
- if (self._elementsByQuery[query] !== undefined) {
- self.setQueries([query]);
- return self.callListeners('onSearch', {
- fitBounds: false,
- identifiedElements: [self._elementsByQuery[query]],
- type: AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES
- }).then(function () {
- return Promise.resolve(self._elementsByQuery[query]);
- });
- } else {
- var searchResult = null;
- var maxDistance;
- var map = self.getMap().getSubmapById(modelId);
- if (map === null) {
- return Promise.reject(new InvalidArgumentException("model doesn't exist for modelId: " + modelId));
- }
- var model = map.getModel();
- return ServerConnector.getMaxSearchDistance().then(function (distance) {
- var maxZoom = model.getMaxZoom();
- var zoomDiff = maxZoom - zoom;
- for (var i = 0; i < zoomDiff; i++) {
- distance = distance * 1.5;
- }
- maxDistance = distance;
- return ServerConnector.getClosestElementsByCoordinates({
- modelId: modelId,
- coordinates: coordinates,
- count: 1
- });
- }).then(function (elements) {
- var nestedOverlay = "Pathways and compartments";
- if (elements.length === 0) {
- return undefined;
- } else {
- if (self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
- return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom());
- } else {
- return elements[0];
- }
- }
- }).then(function (visibleObject) {
- if (visibleObject !== undefined) {
- searchResult = [visibleObject];
- if (searchResult[0].getType() === "REACTION") {
- return model.getReactionById(searchResult[0].getId(), true).then(function (reaction) {
- var reactionElements = reaction.getElements();
- for (var i = 0; i < reactionElements.length; i++) {
- searchResult.push(new IdentifiedElement(reactionElements[i]));
- }
- });
- }
- } else {
- searchResult = [];
- }
- }).then(function () {
- if (searchResult.length > 0) {
- return self.getMap().getDistance({
- modelId: modelId,
- coordinates: coordinates,
- element: searchResult[0]
- });
- } else {
- return Number.POSITIVE_INFINITY;
- }
- }).then(function (distance) {
- if (distance <= maxDistance) {
- self._elementsByQuery[query] = searchResult;
- } else {
- return ServerConnector.getClosestElementsByCoordinates({
- modelId: modelId,
- coordinates: coordinates,
- count: 1,
- type: ["Compartment"]
- }).then(function (elements) {
- var nestedOverlay = "Pathways and compartments";
- if (elements.length === 0) {
- return undefined;
- } else {
- if (self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
- return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom());
- } else {
- return undefined;
- }
- }
- }).then(function (visibleObject) {
- if (visibleObject !== undefined) {
- self._elementsByQuery[query] = [visibleObject];
- } else {
- self._elementsByQuery[query] = [];
- }
- });
- }
- }).then(function () {
- self.setQueries([query]);
-
- return self.callListeners('onSearch', {
- fitBounds: params.fitBounds,
- identifiedElements: [self._elementsByQuery[query]],
- type: AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES
- });
- }).then(function () {
- return self._elementsByQuery[query];
- });
- }
-};
-
-SearchDbOverlay.prototype.searchBySingleQuery = function (originalQuery, perfect) {
- var self = this;
- var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery, perfect);
- if (self._elementsByQuery[query] !== undefined) {
- return Promise.resolve(self._elementsByQuery[query]);
- } else {
- return ServerConnector.getElementsByQuery({
- query: originalQuery,
- perfectMatch: perfect
- }).then(function (elements) {
- var result = [];
- for (var i = 0; i < elements.length; i++) {
- result.push(new IdentifiedElement(elements[i]));
- }
- self._elementsByQuery[query] = result;
- return self.getMap().fetchIdentifiedElements(result, true);
- }).then(function () {
- return self._elementsByQuery[query];
- });
- }
-};
-
-/**
- *
- * @param {IdentifiedElement} element
- * @returns {Promise|PromiseLike}
- */
-SearchDbOverlay.prototype.searchByTarget = function (element) {
- var self = this;
- var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_TARGET, element);
-
- ServerConnector.getSessionData().setSearchQuery(query);
-
- if (self._elementsByQuery[query] === undefined) {
- self._elementsByQuery[query] = [element];
- }
- return self.getMap().fetchIdentifiedElements([element], true).then(function () {
- self.setQueries([query]);
- return self.callListeners('onSearch', {
- fitBounds: false,
- identifiedElements: [self._elementsByQuery[query]],
- type: AbstractDbOverlay.QueryType.SEARCH_BY_TARGET
- });
- }).then(function () {
- return Promise.resolve(self._elementsByQuery[query]);
- });
-};
-
-
-SearchDbOverlay.prototype.getIdentifiedElements = function () {
- var self = this;
- var queries = self.getQueries();
- var result = [];
-
- return Promise.each(queries, function (query, index) {
- var identifiedElements = self._elementsByQuery[query];
- return self.getMap().fetchIdentifiedElements(identifiedElements, true).then(function (elements) {
- var iconCounter = 1;
- var groups = [];
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i];
- var alreadyExists = false;
- var icon = null;
- var group;
- for (var j = 0; j < groups.length; j++) {
- group = groups[j];
- if (group.bioEntityMatch(element)) {
- alreadyExists = true;
- group.addBioEntity(element);
- icon = group.getIcon();
- }
- }
-
- if (!alreadyExists) {
- if (element instanceof Alias) {
- icon = self.getIcon(index, iconCounter++)
- }
- group = new SearchBioEntityGroup(element);
- group.setIcon(icon);
- groups.push(group);
-
- }
- var ie = new IdentifiedElement(element);
- if (element instanceof Alias) {
- ie.setIcon(icon);
- } else if (!(element instanceof Reaction)) {
- throw new Error("Unknown element type: " + ie.getType());
- }
- result.push(ie);
-
- }
- });
-
- }).then(function () {
- return result;
- });
-};
-
-/**
- *
- * @param element
- * @returns {Promise<BioEntity[]>}
- */
-SearchDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element) {
- if (element.getType() === "POINT") {
- return Promise.resolve(null);
- }
- var model = this.getMap().getSubmapById(element.getModelId()).getModel();
- return model.getByIdentifiedElement(element, true);
-};
-
-module.exports = SearchDbOverlay;
+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+var Promise = require("bluebird");
+
+var AbstractDbOverlay = require('./AbstractDbOverlay');
+var Alias = require('../data/Alias');
+var IdentifiedElement = require('../data/IdentifiedElement');
+var InvalidArgumentException = require('../../InvalidArgumentError');
+var Reaction = require('../data/Reaction');
+var SearchBioEntityGroup = require('../data/SearchBioEntityGroup');
+
+
+var ServerConnector = require('../../ServerConnector');
+
+/**
+ *
+ * @param params
+ * @constructor
+ * @extends AbstractDbOverlay
+ */
+function SearchDbOverlay(params) {
+ params.iconType = "marker";
+ params.iconColorStart = 0;
+ // call super constructor
+ AbstractDbOverlay.call(this, params);
+
+}
+
+SearchDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
+SearchDbOverlay.prototype.constructor = SearchDbOverlay;
+
+SearchDbOverlay.prototype.getElementsByQuery = function (query) {
+ var self = this;
+ var i;
+ var queryId = null;
+ var queries = self.getQueries();
+ for (i = 0; i < queries.length; i++) {
+ if (queries[i] === query) {
+ queryId = i;
+ }
+ }
+ if (queryId === null) {
+ throw new Error("Invalid query: " + query);
+ }
+ var elements = self._elementsByQuery[query];
+ var promises = [];
+ for (i = 0; i < elements.length; i++) {
+ var model = self.getMap().getSubmapById(elements[0].getModelId()).getModel();
+ promises.push(model.getByIdentifiedElement(elements[i], true));
+ }
+ return Promise.all(promises).then(function (elements) {
+ var result = [];
+ var iconCounter = 1;
+ var groups = [];
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ var alreadyExists = false;
+ var group;
+ for (var j = 0; j < groups.length; j++) {
+ group = groups[j];
+ if (group.bioEntityMatch(element)) {
+ alreadyExists = true;
+ group.addBioEntity(element);
+ }
+ }
+
+ if (!alreadyExists) {
+ var icon;
+ if (element instanceof Alias) {
+ icon = self.getIcon(queryId, iconCounter++)
+ }
+ group = new SearchBioEntityGroup(element);
+ group.setIcon(icon);
+ groups.push(group);
+ result.push({
+ element: group,
+ icon: icon
+ });
+ }
+ }
+ return result;
+ });
+};
+
+SearchDbOverlay.prototype._getFirstVisibleParentOrObject = function (identifiedElement, zoomLevel, coordinates) {
+ if (identifiedElement === undefined) {
+ return Promise.resolve();
+ }
+ var self = this;
+ var model = self.getMap().getSubmapById(identifiedElement.getModelId()).getModel();
+ return model.getByIdentifiedElement(identifiedElement, true).then(function (fullElement) {
+ if (fullElement.getHierarchyVisibilityLevel() <= zoomLevel) {
+ if (fullElement instanceof Alias) {
+ //transparent compartments shouldn't be clickable
+ if (fullElement.getTransparencyLevel() <= zoomLevel && fullElement.getType() === "Compartment") {
+ return undefined;
+ }
+ }
+ return identifiedElement;
+ } else {
+ var parentId;
+ if (fullElement instanceof Alias) {
+ if (fullElement.getComplexId() !== undefined) {
+ parentId = fullElement.getComplexId();
+ } else if (fullElement.getCompartmentId() !== undefined) {
+ parentId = fullElement.getCompartmentId();
+ }
+ }
+ if (parentId !== undefined) {
+ var parent = new IdentifiedElement({
+ id: parentId,
+ type: "ALIAS",
+ modelId: identifiedElement.getModelId()
+ });
+ return self._getFirstVisibleParentOrObject(parent, zoomLevel, coordinates);
+ } else {
+ logger.warn("Cannot find visible parent for object. (zoomLevel=" + zoomLevel + ")");
+ logger.warn(fullElement);
+ return identifiedElement;
+ }
+ }
+ });
+};
+SearchDbOverlay.prototype.searchByCoordinates = function (params) {
+ var modelId = params.modelId;
+ var coordinates = params.coordinates;
+ var zoom = params.zoom;
+
+ var self = this;
+ var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES, modelId, coordinates, zoom);
+
+ ServerConnector.getSessionData().setSearchQuery(query);
+
+ if (self._elementsByQuery[query] !== undefined) {
+ self.setQueries([query]);
+ return self.callListeners('onSearch', {
+ fitBounds: false,
+ identifiedElements: [self._elementsByQuery[query]],
+ type: AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES
+ }).then(function () {
+ return Promise.resolve(self._elementsByQuery[query]);
+ });
+ } else {
+ var searchResult = null;
+ var maxDistance;
+ var map = self.getMap().getSubmapById(modelId);
+ if (map === null) {
+ return Promise.reject(new InvalidArgumentException("model doesn't exist for modelId: " + modelId));
+ }
+ var model = map.getModel();
+ return ServerConnector.getMaxSearchDistance().then(function (distance) {
+ var maxZoom = model.getMaxZoom();
+ var zoomDiff = maxZoom - zoom;
+ for (var i = 0; i < zoomDiff; i++) {
+ distance = distance * 1.5;
+ }
+ maxDistance = distance;
+ return ServerConnector.getClosestElementsByCoordinates({
+ modelId: modelId,
+ coordinates: coordinates,
+ count: 1
+ });
+ }).then(function (elements) {
+ var nestedOverlay = "Pathways and compartments";
+ if (elements.length === 0) {
+ return undefined;
+ } else {
+ if (self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
+ return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom());
+ } else {
+ return elements[0];
+ }
+ }
+ }).then(function (visibleObject) {
+ if (visibleObject !== undefined) {
+ searchResult = [visibleObject];
+ if (searchResult[0].getType() === "REACTION") {
+ return model.getReactionById(searchResult[0].getId(), true).then(function (reaction) {
+ var reactionElements = reaction.getElements();
+ for (var i = 0; i < reactionElements.length; i++) {
+ searchResult.push(new IdentifiedElement(reactionElements[i]));
+ }
+ });
+ }
+ } else {
+ searchResult = [];
+ }
+ }).then(function () {
+ if (searchResult.length > 0) {
+ return self.getMap().getDistance({
+ modelId: modelId,
+ coordinates: coordinates,
+ element: searchResult[0]
+ });
+ } else {
+ return Number.POSITIVE_INFINITY;
+ }
+ }).then(function (distance) {
+ if (distance <= maxDistance) {
+ self._elementsByQuery[query] = searchResult;
+ } else {
+ return ServerConnector.getClosestElementsByCoordinates({
+ modelId: modelId,
+ coordinates: coordinates,
+ count: 1,
+ type: ["Compartment"]
+ }).then(function (elements) {
+ var nestedOverlay = "Pathways and compartments";
+ if (elements.length === 0) {
+ return undefined;
+ } else {
+ if (self.getMap().getBackgroundDataOverlay().getName() === nestedOverlay) {
+ return self._getFirstVisibleParentOrObject(elements[0], zoom - model.getMinZoom());
+ } else {
+ return undefined;
+ }
+ }
+ }).then(function (visibleObject) {
+ if (visibleObject !== undefined) {
+ self._elementsByQuery[query] = [visibleObject];
+ } else {
+ self._elementsByQuery[query] = [];
+ }
+ });
+ }
+ }).then(function () {
+ self.setQueries([query]);
+
+ return self.callListeners('onSearch', {
+ fitBounds: params.fitBounds,
+ identifiedElements: [self._elementsByQuery[query]],
+ type: AbstractDbOverlay.QueryType.SEARCH_BY_COORDINATES
+ });
+ }).then(function () {
+ return self._elementsByQuery[query];
+ });
+ }
+};
+
+SearchDbOverlay.prototype.searchBySingleQuery = function (originalQuery, perfect) {
+ var self = this;
+ var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY, originalQuery, perfect);
+ if (self._elementsByQuery[query] !== undefined) {
+ return Promise.resolve(self._elementsByQuery[query]);
+ } else {
+ return ServerConnector.getElementsByQuery({
+ query: originalQuery,
+ perfectMatch: perfect
+ }).then(function (elements) {
+ var result = [];
+ for (var i = 0; i < elements.length; i++) {
+ result.push(new IdentifiedElement(elements[i]));
+ }
+ self._elementsByQuery[query] = result;
+ return self.getMap().fetchIdentifiedElements(result, true);
+ }).then(function () {
+ return self._elementsByQuery[query];
+ });
+ }
+};
+
+/**
+ *
+ * @param {IdentifiedElement} element
+ * @returns {Promise|PromiseLike}
+ */
+SearchDbOverlay.prototype.searchByTarget = function (element) {
+ var self = this;
+ var query = self.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_TARGET, element);
+
+ ServerConnector.getSessionData().setSearchQuery(query);
+
+ if (self._elementsByQuery[query] === undefined) {
+ self._elementsByQuery[query] = [element];
+ }
+ return self.getMap().fetchIdentifiedElements([element], true).then(function () {
+ self.setQueries([query]);
+ return self.callListeners('onSearch', {
+ fitBounds: false,
+ identifiedElements: [self._elementsByQuery[query]],
+ type: AbstractDbOverlay.QueryType.SEARCH_BY_TARGET
+ });
+ }).then(function () {
+ return Promise.resolve(self._elementsByQuery[query]);
+ });
+};
+
+
+SearchDbOverlay.prototype.getIdentifiedElements = function () {
+ var self = this;
+ var queries = self.getQueries();
+ var result = [];
+
+ return Promise.each(queries, function (query, index) {
+ var identifiedElements = self._elementsByQuery[query];
+ return self.getMap().fetchIdentifiedElements(identifiedElements, true).then(function (elements) {
+ var iconCounter = 1;
+ var groups = [];
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ var alreadyExists = false;
+ var icon = null;
+ var group;
+ for (var j = 0; j < groups.length; j++) {
+ group = groups[j];
+ if (group.bioEntityMatch(element)) {
+ alreadyExists = true;
+ group.addBioEntity(element);
+ icon = group.getIcon();
+ }
+ }
+
+ if (!alreadyExists) {
+ if (element instanceof Alias) {
+ icon = self.getIcon(index, iconCounter++)
+ }
+ group = new SearchBioEntityGroup(element);
+ group.setIcon(icon);
+ groups.push(group);
+
+ }
+ var ie = new IdentifiedElement(element);
+ if (element instanceof Alias) {
+ ie.setIcon(icon);
+ } else if (!(element instanceof Reaction)) {
+ throw new Error("Unknown element type: " + ie.getType());
+ }
+ result.push(ie);
+
+ }
+ });
+
+ }).then(function () {
+ return result;
+ });
+};
+
+/**
+ *
+ * @param element
+ * @returns {Promise<BioEntity[]>}
+ */
+SearchDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element) {
+ if (element.getType() === "POINT") {
+ return Promise.resolve(null);
+ }
+ var model = this.getMap().getSubmapById(element.getModelId()).getModel();
+ return model.getByIdentifiedElement(element, true);
+};
+
+module.exports = SearchDbOverlay;
diff --git a/frontend-js/src/main/js/map/overlay/UserDbOverlay.js b/frontend-js/src/main/js/map/overlay/UserDbOverlay.js
index f8298eab0302c99b85c5add04a166297ad08594f..eac4eea005536b9c957edbfd2bfc12ef98b79470 100644
--- a/frontend-js/src/main/js/map/overlay/UserDbOverlay.js
+++ b/frontend-js/src/main/js/map/overlay/UserDbOverlay.js
@@ -1,248 +1,248 @@
-"use strict";
-
-/* exported logger */
-
-var logger = require('../../logger');
-
-var AbstractDbOverlay = require('./AbstractDbOverlay');
-
-var IdentifiedElement = require('../data/IdentifiedElement');
-var InvalidArgumentError = require('../../InvalidArgumentError');
-
-var Promise = require("bluebird");
-
-function UserDbOverlay(params) {
- params.iconType = "marker";
- params.iconColorStart = 1;
- // call super constructor
- AbstractDbOverlay.call(this, params);
-
- this._markerIdentifiedElements = {
- ALIAS: [],
- REACTION: [],
- POINT: []
- };
- this._surfaceIdentifiedElements = {
- ALIAS: [],
- REACTION: [],
- POINT: []
- };
-}
-
-UserDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
-UserDbOverlay.prototype.constructor = UserDbOverlay;
-
-UserDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element) {
- if (element.getType() === "POINT") {
- return Promise.resolve(null);
- }
- var model = this.getMap().getSubmapById(element.getModelId()).getModel();
- return model.getByIdentifiedElement(element, true);
-};
-
-UserDbOverlay.prototype._createIdentifiedElements = function (params, sourceArray, mustBeUndefined) {
- var self = this;
- var result = [];
- var promises = [];
- var mustBeDefined = !mustBeUndefined;
- for (var i = 0; i < params.length; i++) {
- var singleElementParam = params[i];
- var element = new IdentifiedElement(singleElementParam.element);
- if (singleElementParam.icon !== undefined) {
- element.setIcon(singleElementParam.icon);
- }
- if (singleElementParam.options !== undefined) {
- element.setColor(singleElementParam.options.color);
- element.setOpacity(singleElementParam.options.opacity);
- element.setLineColor(singleElementParam.options.lineColor);
- element.setLineWeight(singleElementParam.options.lineWeight);
- element.setLineOpacity(singleElementParam.options.lineOpacity);
- }
- if (sourceArray[element.getType()][element.getId()] !== undefined && mustBeUndefined) {
- return Promise.reject(new Error("Element already highlighted: " + element.getId()));
- }
- if (sourceArray[element.getType()][element.getId()] === undefined && mustBeDefined) {
- return Promise.reject(new Error("Element is not highlighted: " + element.getId()));
- }
- result.push(element);
- var submap = self.getMap().getSubmapById(element.getModelId());
- if (submap === null) {
- return Promise.reject(new InvalidArgumentError("Submap doesn't exist: " + result[i].getModelId()));
- }
- promises.push(submap.getModel().getByIdentifiedElement(element));
- }
- return Promise.all(promises).then(function (elementsFromModel) {
- for (var i = 0; i < elementsFromModel.length; i++) {
- if (elementsFromModel[i] === undefined || elementsFromModel[i] === null) {
- return Promise.reject(new InvalidArgumentError("Element doesn't exist: " + result[i].getId()));
- }
- }
- return result;
- });
-};
-
-UserDbOverlay.prototype.addMarker = function (params) {
- var self = this;
- self.disableAddRemoveElements();
-
- if (params.length === undefined) {
- params = [params];
- }
- return self._createIdentifiedElements(params, self._markerIdentifiedElements, true).then(function (elements) {
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i];
- self._markerIdentifiedElements[element.getType()][element.getId()] = element;
- }
- return self.getIdentifiedElements();
- }).then(function (elements) {
- self.enableAddRemoveElements();
- return self.callListeners("onSearch", {
- fitBounds: false,
- identifiedElements: elements
- });
- }).then(null, function (error) {
- self.enableAddRemoveElements();
- return Promise.reject(error);
- });
-};
-
-UserDbOverlay.prototype.addSurface = function (params) {
- var self = this;
- self.disableAddRemoveElements();
-
- if (params.length === undefined) {
- params = [params];
- }
-
- return self._createIdentifiedElements(params, self._surfaceIdentifiedElements, true).then(function (elements) {
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i];
- self._surfaceIdentifiedElements[element.getType()][element.getId()] = element;
- }
- return self.getIdentifiedElements();
- }).then(function (elements) {
- self.enableAddRemoveElements();
- return self.callListeners("onSearch", {
- fitBounds: false,
- identifiedElements: elements
- });
- }).then(null, function (error) {
- self.enableAddRemoveElements();
- return Promise.reject(error);
- });
-};
-
-UserDbOverlay.prototype.removeMarker = function (params) {
- var self = this;
- self.disableAddRemoveElements();
-
- if (params.length === undefined) {
- params = [params];
- }
-
- return self._createIdentifiedElements(params, self._markerIdentifiedElements, false).then(function (elements) {
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i];
- self._markerIdentifiedElements[element.getType()][element.getId()] = undefined;
- delete self._markerIdentifiedElements[element.getType()][element.getId()];
- }
- return self.getIdentifiedElements();
- }).then(function (elements) {
- self.enableAddRemoveElements();
- return self.callListeners("onSearch", {
- fitBounds: false,
- identifiedElements: elements
- });
- }).then(null, function (error) {
- self.enableAddRemoveElements();
- return Promise.reject(error);
- });
-};
-
-UserDbOverlay.prototype.removeSurface = function (params) {
- var self = this;
- self.disableAddRemoveElements();
-
- if (params.length === undefined) {
- params = [params];
- }
- return self._createIdentifiedElements(params, self._surfaceIdentifiedElements, false).then(function (elements) {
- for (var i = 0; i < elements.length; i++) {
- var element = elements[i];
- self._surfaceIdentifiedElements[element.getType()][element.getId()] = undefined;
- delete self._surfaceIdentifiedElements[element.getType()][element.getId()];
- }
- return self.getIdentifiedElements();
- }).then(function (elements) {
- self.enableAddRemoveElements();
- return self.callListeners("onSearch", {
- fitBounds: false,
- identifiedElements: elements
- });
- }).then(null, function (error) {
- self.enableAddRemoveElements();
- return Promise.reject(error);
- });
-};
-
-UserDbOverlay.prototype.disableAddRemoveElements = function () {
- if (this._addRemoveElementsDisabled) {
- throw new Error("wait until previous Promise for showBioEntity/hideBioEntity is resolved");
- } else {
- this._addRemoveElementsDisabled = true;
- }
-};
-UserDbOverlay.prototype.enableAddRemoveElements = function () {
- if (this._addRemoveElementsDisabled) {
- this._addRemoveElementsDisabled = false;
- } else {
- logger.warn("showBioEntity/hideBioEntity is not disabled");
- }
-};
-
-UserDbOverlay.prototype.getIdentifiedElements = function () {
- var result = [];
- var markerType, key, markers;
- for (markerType in this._markerIdentifiedElements) {
- if (this._markerIdentifiedElements.hasOwnProperty(markerType)) {
- markers = this._markerIdentifiedElements[markerType];
- for (key in markers) {
- if (markers.hasOwnProperty(key)) {
- var identifiedElement = markers[key];
- if (identifiedElement.getIcon() === undefined) {
- identifiedElement.setIcon("marker/generic/search_red.png");
- }
- result.push(identifiedElement);
- }
- }
- }
- }
-
- for (markerType in this._surfaceIdentifiedElements) {
- if (this._surfaceIdentifiedElements.hasOwnProperty(markerType)) {
- markers = this._surfaceIdentifiedElements[markerType];
- for (key in markers) {
- if (markers.hasOwnProperty(key)) {
- result.push(markers[key]);
- }
- }
- }
- }
-
- return Promise.resolve(result);
-};
-
-UserDbOverlay.prototype.clear = function () {
- var self = this;
- self._markerIdentifiedElements = {
- ALIAS: [],
- REACTION: [],
- POINT: []
- };
- return self.callListeners("onSearch", {
- fitBounds: false,
- identifiedElements: []
- });
-};
-
-module.exports = UserDbOverlay;
+"use strict";
+
+/* exported logger */
+
+var logger = require('../../logger');
+
+var AbstractDbOverlay = require('./AbstractDbOverlay');
+
+var IdentifiedElement = require('../data/IdentifiedElement');
+var InvalidArgumentError = require('../../InvalidArgumentError');
+
+var Promise = require("bluebird");
+
+function UserDbOverlay(params) {
+ params.iconType = "marker";
+ params.iconColorStart = 1;
+ // call super constructor
+ AbstractDbOverlay.call(this, params);
+
+ this._markerIdentifiedElements = {
+ ALIAS: [],
+ REACTION: [],
+ POINT: []
+ };
+ this._surfaceIdentifiedElements = {
+ ALIAS: [],
+ REACTION: [],
+ POINT: []
+ };
+}
+
+UserDbOverlay.prototype = Object.create(AbstractDbOverlay.prototype);
+UserDbOverlay.prototype.constructor = UserDbOverlay;
+
+UserDbOverlay.prototype.getDetailDataByIdentifiedElement = function (element) {
+ if (element.getType() === "POINT") {
+ return Promise.resolve(null);
+ }
+ var model = this.getMap().getSubmapById(element.getModelId()).getModel();
+ return model.getByIdentifiedElement(element, true);
+};
+
+UserDbOverlay.prototype._createIdentifiedElements = function (params, sourceArray, mustBeUndefined) {
+ var self = this;
+ var result = [];
+ var promises = [];
+ var mustBeDefined = !mustBeUndefined;
+ for (var i = 0; i < params.length; i++) {
+ var singleElementParam = params[i];
+ var element = new IdentifiedElement(singleElementParam.element);
+ if (singleElementParam.icon !== undefined) {
+ element.setIcon(singleElementParam.icon);
+ }
+ if (singleElementParam.options !== undefined) {
+ element.setColor(singleElementParam.options.color);
+ element.setOpacity(singleElementParam.options.opacity);
+ element.setLineColor(singleElementParam.options.lineColor);
+ element.setLineWeight(singleElementParam.options.lineWeight);
+ element.setLineOpacity(singleElementParam.options.lineOpacity);
+ }
+ if (sourceArray[element.getType()][element.getId()] !== undefined && mustBeUndefined) {
+ return Promise.reject(new Error("Element already highlighted: " + element.getId()));
+ }
+ if (sourceArray[element.getType()][element.getId()] === undefined && mustBeDefined) {
+ return Promise.reject(new Error("Element is not highlighted: " + element.getId()));
+ }
+ result.push(element);
+ var submap = self.getMap().getSubmapById(element.getModelId());
+ if (submap === null) {
+ return Promise.reject(new InvalidArgumentError("Submap doesn't exist: " + result[i].getModelId()));
+ }
+ promises.push(submap.getModel().getByIdentifiedElement(element));
+ }
+ return Promise.all(promises).then(function (elementsFromModel) {
+ for (var i = 0; i < elementsFromModel.length; i++) {
+ if (elementsFromModel[i] === undefined || elementsFromModel[i] === null) {
+ return Promise.reject(new InvalidArgumentError("Element doesn't exist: " + result[i].getId()));
+ }
+ }
+ return result;
+ });
+};
+
+UserDbOverlay.prototype.addMarker = function (params) {
+ var self = this;
+ self.disableAddRemoveElements();
+
+ if (params.length === undefined) {
+ params = [params];
+ }
+ return self._createIdentifiedElements(params, self._markerIdentifiedElements, true).then(function (elements) {
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ self._markerIdentifiedElements[element.getType()][element.getId()] = element;
+ }
+ return self.getIdentifiedElements();
+ }).then(function (elements) {
+ self.enableAddRemoveElements();
+ return self.callListeners("onSearch", {
+ fitBounds: false,
+ identifiedElements: elements
+ });
+ }).then(null, function (error) {
+ self.enableAddRemoveElements();
+ return Promise.reject(error);
+ });
+};
+
+UserDbOverlay.prototype.addSurface = function (params) {
+ var self = this;
+ self.disableAddRemoveElements();
+
+ if (params.length === undefined) {
+ params = [params];
+ }
+
+ return self._createIdentifiedElements(params, self._surfaceIdentifiedElements, true).then(function (elements) {
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ self._surfaceIdentifiedElements[element.getType()][element.getId()] = element;
+ }
+ return self.getIdentifiedElements();
+ }).then(function (elements) {
+ self.enableAddRemoveElements();
+ return self.callListeners("onSearch", {
+ fitBounds: false,
+ identifiedElements: elements
+ });
+ }).then(null, function (error) {
+ self.enableAddRemoveElements();
+ return Promise.reject(error);
+ });
+};
+
+UserDbOverlay.prototype.removeMarker = function (params) {
+ var self = this;
+ self.disableAddRemoveElements();
+
+ if (params.length === undefined) {
+ params = [params];
+ }
+
+ return self._createIdentifiedElements(params, self._markerIdentifiedElements, false).then(function (elements) {
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ self._markerIdentifiedElements[element.getType()][element.getId()] = undefined;
+ delete self._markerIdentifiedElements[element.getType()][element.getId()];
+ }
+ return self.getIdentifiedElements();
+ }).then(function (elements) {
+ self.enableAddRemoveElements();
+ return self.callListeners("onSearch", {
+ fitBounds: false,
+ identifiedElements: elements
+ });
+ }).then(null, function (error) {
+ self.enableAddRemoveElements();
+ return Promise.reject(error);
+ });
+};
+
+UserDbOverlay.prototype.removeSurface = function (params) {
+ var self = this;
+ self.disableAddRemoveElements();
+
+ if (params.length === undefined) {
+ params = [params];
+ }
+ return self._createIdentifiedElements(params, self._surfaceIdentifiedElements, false).then(function (elements) {
+ for (var i = 0; i < elements.length; i++) {
+ var element = elements[i];
+ self._surfaceIdentifiedElements[element.getType()][element.getId()] = undefined;
+ delete self._surfaceIdentifiedElements[element.getType()][element.getId()];
+ }
+ return self.getIdentifiedElements();
+ }).then(function (elements) {
+ self.enableAddRemoveElements();
+ return self.callListeners("onSearch", {
+ fitBounds: false,
+ identifiedElements: elements
+ });
+ }).then(null, function (error) {
+ self.enableAddRemoveElements();
+ return Promise.reject(error);
+ });
+};
+
+UserDbOverlay.prototype.disableAddRemoveElements = function () {
+ if (this._addRemoveElementsDisabled) {
+ throw new Error("wait until previous Promise for showBioEntity/hideBioEntity is resolved");
+ } else {
+ this._addRemoveElementsDisabled = true;
+ }
+};
+UserDbOverlay.prototype.enableAddRemoveElements = function () {
+ if (this._addRemoveElementsDisabled) {
+ this._addRemoveElementsDisabled = false;
+ } else {
+ logger.warn("showBioEntity/hideBioEntity is not disabled");
+ }
+};
+
+UserDbOverlay.prototype.getIdentifiedElements = function () {
+ var result = [];
+ var markerType, key, markers;
+ for (markerType in this._markerIdentifiedElements) {
+ if (this._markerIdentifiedElements.hasOwnProperty(markerType)) {
+ markers = this._markerIdentifiedElements[markerType];
+ for (key in markers) {
+ if (markers.hasOwnProperty(key)) {
+ var identifiedElement = markers[key];
+ if (identifiedElement.getIcon() === undefined) {
+ identifiedElement.setIcon("marker/generic/search_red.png");
+ }
+ result.push(identifiedElement);
+ }
+ }
+ }
+ }
+
+ for (markerType in this._surfaceIdentifiedElements) {
+ if (this._surfaceIdentifiedElements.hasOwnProperty(markerType)) {
+ markers = this._surfaceIdentifiedElements[markerType];
+ for (key in markers) {
+ if (markers.hasOwnProperty(key)) {
+ result.push(markers[key]);
+ }
+ }
+ }
+ }
+
+ return Promise.resolve(result);
+};
+
+UserDbOverlay.prototype.clear = function () {
+ var self = this;
+ self._markerIdentifiedElements = {
+ ALIAS: [],
+ REACTION: [],
+ POINT: []
+ };
+ return self.callListeners("onSearch", {
+ fitBounds: false,
+ identifiedElements: []
+ });
+};
+
+module.exports = UserDbOverlay;
diff --git a/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js b/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
index 4e058339ecb3da145ffd68e12a64579818dc171d..e3fd29c3ed937a7845360b6c1d1f5cf52728e3cb 100644
--- a/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
+++ b/frontend-js/src/main/js/map/surface/AbstractSurfaceElement.js
@@ -1,221 +1,221 @@
-"use strict";
-
-var logger = require('../../logger');
-
-var Bounds = require('../canvas/Bounds');
-var ObjectWithListeners = require('../../ObjectWithListeners');
-var Promise = require('bluebird');
-
-/**
- * Class representing abstract overlay element on the map relevant for a
- * specific overlay.
- *
- * @param {IdentifiedElement} params.element
- * @param {AbstractCustomMap} params.map
- * @param {function|function[]} params.onClick
- * @constructor
- */
-function AbstractSurfaceElement(params) {
- var self = this;
- // call super constructor
- ObjectWithListeners.call(this);
-
- self.registerListenerType("onClick");
- self.setCustomMap(params.map);
- if (params.element !== undefined && params.element !== null) {
- self.setIdentifiedElement(params.element);
- }
- self._mapCanvasObjects = [];
-
- if (params.onClick !== undefined) {
- if (typeof params.onClick !== "function") {
- for (var i = 0; i < params.onClick.length; i++) {
- self.addListener("onClick", params.onClick[i]);
- }
- } else {
- self.addListener("onClick", params.onClick);
- }
- }
-}
-
-AbstractSurfaceElement.prototype = Object.create(ObjectWithListeners.prototype);
-AbstractSurfaceElement.prototype.constructor = AbstractSurfaceElement;
-
-/**
- *
- * @returns {boolean}
- */
-AbstractSurfaceElement.prototype.isShown = function () {
- var result = false;
- for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
- if (this.getMapCanvasObjects()[i].isShown()) {
- result = true;
- }
- }
- return result;
-};
-
-/**
- *
- * @returns {Promise}
- */
-AbstractSurfaceElement.prototype.show = function () {
- var self = this;
- if (!this.isInitialized()) {
- return this.init().then(function () {
- return self.show();
- });
- }
- if (this.isShown()) {
- logger.warn("Surface already shown");
- return Promise.resolve();
- }
- var promises = [];
- for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
- promises.push(this.getMapCanvasObjects()[i].show());
- }
- return Promise.all(promises);
-};
-
-/**
- *
- * @returns {boolean}
- */
-AbstractSurfaceElement.prototype.isInitialized = function () {
- return this.getMapCanvasObjects().length > 0;
-};
-
-/**
- *
- * @returns {Promise}
- */
-AbstractSurfaceElement.prototype.hide = function () {
- var promises = [];
- for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
- promises.push(this.getMapCanvasObjects()[i].hide());
- }
- return Promise.all(promises);
-};
-
-/**
- *
- * @returns {Promise|PromiseLike}
- */
-AbstractSurfaceElement.prototype.onClickHandler = function () {
- return this.callListeners("onClick");
-};
-
-/**
- *
- * @returns {Array}
- */
-AbstractSurfaceElement.prototype.getMapCanvasObjects = function () {
- return this._mapCanvasObjects;
-};
-
-/**
- *
- * @param {Rectangle|Polyline} object
- */
-AbstractSurfaceElement.prototype.addMapCanvasObject = function (object) {
- this._mapCanvasObjects.push(object);
-
- var self = this;
- var onclick = function () {
- return self.onClickHandler();
- };
- object.addListener('click', onclick);
-};
-
-/**
- *
- * @returns {IdentifiedElement}
- */
-AbstractSurfaceElement.prototype.getIdentifiedElement = function () {
- return this._identifiedElement;
-};
-
-/**
- *
- * @param {IdentifiedElement} identifiedElement
- */
-AbstractSurfaceElement.prototype.setIdentifiedElement = function (identifiedElement) {
- this._identifiedElement = identifiedElement;
-};
-
-/**
- *
- * @returns {BioEntity}
- */
-AbstractSurfaceElement.prototype.getBioEntity = function () {
- return this._bioEntity;
-};
-
-/**
- *
- * @param {BioEntity} bioEntity
- */
-AbstractSurfaceElement.prototype.setBioEntity = function (bioEntity) {
- this._bioEntity = bioEntity;
-};
-
-
-/**
- *
- * @returns {number}
- */
-AbstractSurfaceElement.prototype.getModelId = function () {
- return this.getIdentifiedElement().getModelId();
-};
-
-/**
- *
- * @param {IdentifiedElement} identifiedElement
- */
-AbstractSurfaceElement.prototype.updateIdentifiedElement = function (identifiedElement) {
- if (identifiedElement.getColor() !== undefined) {
- this.setColor(identifiedElement.getColor());
- }
-};
-
-/**
- *
- * @returns {Bounds}
- */
-AbstractSurfaceElement.prototype.getBounds = function () {
- var self = this;
- var bounds = new Bounds();
- for (var i = 0; i < self.getMapCanvasObjects().length; i++) {
- var elementBounds = self.getMapCanvasObjects()[i].getBounds();
- bounds.extend(elementBounds.getTopLeft());
- bounds.extend(elementBounds.getRightBottom());
- }
- return bounds;
-};
-
-/**
- * Returns {@link AbstractCustomMap} where surface is located.
- *
- * @returns {AbstractCustomMap} where surface is located
- */
-AbstractSurfaceElement.prototype.getCustomMap = function () {
- return this._customMap;
-};
-
-/**
- *
- * @param {AbstractCustomMap} customMap
- */
-AbstractSurfaceElement.prototype.setCustomMap = function (customMap) {
- this._customMap = customMap;
-};
-
-/**
- *
- * @returns {Point}
- */
-AbstractSurfaceElement.prototype.getCenter = function () {
- return this.getBioEntity().getCenter();
-};
-
-module.exports = AbstractSurfaceElement;
+"use strict";
+
+var logger = require('../../logger');
+
+var Bounds = require('../canvas/Bounds');
+var ObjectWithListeners = require('../../ObjectWithListeners');
+var Promise = require('bluebird');
+
+/**
+ * Class representing abstract overlay element on the map relevant for a
+ * specific overlay.
+ *
+ * @param {IdentifiedElement} params.element
+ * @param {AbstractCustomMap} params.map
+ * @param {function|function[]} params.onClick
+ * @constructor
+ */
+function AbstractSurfaceElement(params) {
+ var self = this;
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ self.registerListenerType("onClick");
+ self.setCustomMap(params.map);
+ if (params.element !== undefined && params.element !== null) {
+ self.setIdentifiedElement(params.element);
+ }
+ self._mapCanvasObjects = [];
+
+ if (params.onClick !== undefined) {
+ if (typeof params.onClick !== "function") {
+ for (var i = 0; i < params.onClick.length; i++) {
+ self.addListener("onClick", params.onClick[i]);
+ }
+ } else {
+ self.addListener("onClick", params.onClick);
+ }
+ }
+}
+
+AbstractSurfaceElement.prototype = Object.create(ObjectWithListeners.prototype);
+AbstractSurfaceElement.prototype.constructor = AbstractSurfaceElement;
+
+/**
+ *
+ * @returns {boolean}
+ */
+AbstractSurfaceElement.prototype.isShown = function () {
+ var result = false;
+ for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
+ if (this.getMapCanvasObjects()[i].isShown()) {
+ result = true;
+ }
+ }
+ return result;
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+AbstractSurfaceElement.prototype.show = function () {
+ var self = this;
+ if (!this.isInitialized()) {
+ return this.init().then(function () {
+ return self.show();
+ });
+ }
+ if (this.isShown()) {
+ logger.warn("Surface already shown");
+ return Promise.resolve();
+ }
+ var promises = [];
+ for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
+ promises.push(this.getMapCanvasObjects()[i].show());
+ }
+ return Promise.all(promises);
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+AbstractSurfaceElement.prototype.isInitialized = function () {
+ return this.getMapCanvasObjects().length > 0;
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+AbstractSurfaceElement.prototype.hide = function () {
+ var promises = [];
+ for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
+ promises.push(this.getMapCanvasObjects()[i].hide());
+ }
+ return Promise.all(promises);
+};
+
+/**
+ *
+ * @returns {Promise|PromiseLike}
+ */
+AbstractSurfaceElement.prototype.onClickHandler = function () {
+ return this.callListeners("onClick");
+};
+
+/**
+ *
+ * @returns {Array}
+ */
+AbstractSurfaceElement.prototype.getMapCanvasObjects = function () {
+ return this._mapCanvasObjects;
+};
+
+/**
+ *
+ * @param {Rectangle|Polyline} object
+ */
+AbstractSurfaceElement.prototype.addMapCanvasObject = function (object) {
+ this._mapCanvasObjects.push(object);
+
+ var self = this;
+ var onclick = function () {
+ return self.onClickHandler();
+ };
+ object.addListener('click', onclick);
+};
+
+/**
+ *
+ * @returns {IdentifiedElement}
+ */
+AbstractSurfaceElement.prototype.getIdentifiedElement = function () {
+ return this._identifiedElement;
+};
+
+/**
+ *
+ * @param {IdentifiedElement} identifiedElement
+ */
+AbstractSurfaceElement.prototype.setIdentifiedElement = function (identifiedElement) {
+ this._identifiedElement = identifiedElement;
+};
+
+/**
+ *
+ * @returns {BioEntity}
+ */
+AbstractSurfaceElement.prototype.getBioEntity = function () {
+ return this._bioEntity;
+};
+
+/**
+ *
+ * @param {BioEntity} bioEntity
+ */
+AbstractSurfaceElement.prototype.setBioEntity = function (bioEntity) {
+ this._bioEntity = bioEntity;
+};
+
+
+/**
+ *
+ * @returns {number}
+ */
+AbstractSurfaceElement.prototype.getModelId = function () {
+ return this.getIdentifiedElement().getModelId();
+};
+
+/**
+ *
+ * @param {IdentifiedElement} identifiedElement
+ */
+AbstractSurfaceElement.prototype.updateIdentifiedElement = function (identifiedElement) {
+ if (identifiedElement.getColor() !== undefined) {
+ this.setColor(identifiedElement.getColor());
+ }
+};
+
+/**
+ *
+ * @returns {Bounds}
+ */
+AbstractSurfaceElement.prototype.getBounds = function () {
+ var self = this;
+ var bounds = new Bounds();
+ for (var i = 0; i < self.getMapCanvasObjects().length; i++) {
+ var elementBounds = self.getMapCanvasObjects()[i].getBounds();
+ bounds.extend(elementBounds.getTopLeft());
+ bounds.extend(elementBounds.getRightBottom());
+ }
+ return bounds;
+};
+
+/**
+ * Returns {@link AbstractCustomMap} where surface is located.
+ *
+ * @returns {AbstractCustomMap} where surface is located
+ */
+AbstractSurfaceElement.prototype.getCustomMap = function () {
+ return this._customMap;
+};
+
+/**
+ *
+ * @param {AbstractCustomMap} customMap
+ */
+AbstractSurfaceElement.prototype.setCustomMap = function (customMap) {
+ this._customMap = customMap;
+};
+
+/**
+ *
+ * @returns {Point}
+ */
+AbstractSurfaceElement.prototype.getCenter = function () {
+ return this.getBioEntity().getCenter();
+};
+
+module.exports = AbstractSurfaceElement;
diff --git a/frontend-js/src/main/js/map/surface/ReactionSurface.js b/frontend-js/src/main/js/map/surface/ReactionSurface.js
index 8b8a0520a82df550b515ef5d53bd6d8143cae473..b750368fcbf609325c0c9f31d3c5835b3cf59167 100644
--- a/frontend-js/src/main/js/map/surface/ReactionSurface.js
+++ b/frontend-js/src/main/js/map/surface/ReactionSurface.js
@@ -1,313 +1,313 @@
-"use strict";
-
-var Bounds = require('../canvas/Bounds');
-var Point = require('../canvas/Point');
-var Promise = require("bluebird");
-
-/* exported logger */
-
-var functions = require('../../Functions');
-// noinspection JSUnusedLocalSymbols
-var logger = require('../../logger');
-
-var AbstractSurfaceElement = require('./AbstractSurfaceElement');
-var IdentifiedElement = require('../data/IdentifiedElement');
-
-/**
- *
- * @param {IdentifiedElement} [params.element]
- * @param {AbstractCustomMap} params.map
- * @param {function|function[]} [params.onClick]
- * @param {Reaction} params.reaction
- * @param {LayoutReaction} [params.layoutReaction]
- * @param {boolean} params.customized
- * @param {string} [params.color]
- * @constructor
- * @extends AbstractSurfaceElement
- */
-function ReactionSurface(params) {
- // call super constructor
- AbstractSurfaceElement.call(this, params);
-
- this.setWidth(5.0);
- this.setOverlayData(params.layoutReaction);
- this.setBioEntity(params.reaction);
-
- var color = params.color;
-
- if (color === undefined) {
- color = "#0000FF";
- }
-
- this.setColor(color);
- this.setCustomized(params.customized);
- this.setIdentifiedElement(new IdentifiedElement(this.getBioEntity()));
-}
-
-ReactionSurface.prototype = Object.create(AbstractSurfaceElement.prototype);
-ReactionSurface.prototype.constructor = ReactionSurface;
-
-/**
- * Returns {@link Bounds} of all google maps elements
- * included in the object.
- *
- * @returns {Bounds} of all google maps elements
- * included in the object
- */
-ReactionSurface.prototype.getBounds = function () {
- var bounds = new Bounds();
-
- for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
- var line = this.getMapCanvasObjects()[i];
- bounds.extend(line.getBounds());
- }
- return bounds;
-};
-
-/**
- *
- * @param {boolean} customized
- */
-ReactionSurface.prototype.setCustomized = function (customized) {
- this.customized = customized;
-};
-
-/**
- * Sets color to be used by the reaction overlay visualization when visualized
- * in customized mode.
- *
- * @param {string} color
- * new color value
- */
-ReactionSurface.prototype.setColor = function (color) {
- this._color = color;
- var mapCanvasObjects = this.getMapCanvasObjects();
- for (var i = 0; i < mapCanvasObjects.length; i++) {
- mapCanvasObjects[i].setOptions({
- strokeColor: color
- });
- }
- this.customized = true;
-};
-
-/**
- * Sets width of line to be used by the reaction overlay visualization when
- * visualized in customized mode.
- *
- * @param {number} width
- * new width value
- */
-ReactionSurface.prototype.setWidth = function (width) {
- if (width !== undefined && width !== null) {
- this.width = width;
- } else {
- this.width = 1.0;
- }
-
-};
-
-/**
- * Returns color that should be used when visualized in customized mode.
- *
- * @returns {string} color that should be used when visualized in customized mode.
- */
-ReactionSurface.prototype.getColor = function () {
- return this._color;
-};
-
-/**
- * Returns width that should be used when visualized in customized mode.
- *
- * @returns {number} width that should be used when visualized in customized mode.
- */
-ReactionSurface.prototype.getWidth = function () {
- return this.width;
-};
-
-/**
- * This function is used when some overlays are added/removed from visualization.
- * The syntax is compatible with AliasSurface class so they can be handled in
- * the same way. When visualizing more than one overlay startX or endX will be
- * set to a value between 0..1 (not inclusive). In such case the visualization
- * of reaction should turn to some default mode where we know that reaction is
- * highlighted, but we have no more information. In this way user will know that
- * he should investigate the reaction manually.
- *
- * @param {number} startX
- * see {AliasSurface} class for details, in this implementation the
- * only important information is that when there are more than one
- * overlay visualized at least one of the two parameters (startX,endX)
- * will differ from {0.0, 1.0} values
- * @param {number} endX
- * see {AliasSurface} class for details, in this implementation the
- * only important information is that when there are more than one
- * overlay visualized at least one of the two parameters (startX,endX)
- * will differ from {0.0, 1.0} values
- */
-ReactionSurface.prototype.setBoundsForAlias = function (startX, endX) {
- if (this.isCustomized() && (startX > 0 || endX < 1)) {
- this.changedToDefault();
- } else if (!this.isCustomized() && (startX <= 0 && endX >= 1)) {
- this.changedToCustomized();
- }
-};
-
-/**
- * Changes visualization of the ReactionSurface to default mode where we mark
- * reaction as highlighted, but we skip customized reaction overlay data.
- */
-ReactionSurface.prototype.changedToDefault = function () {
- for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
- this.getMapCanvasObjects()[i].setOptions({
- strokeColor: "#0000FF",
- strokeWeight: 5
- });
- }
- this.customized = false;
-};
-
-/**
- * Changes visualization of the ReactionSurface to customized mode where we mark
- * reaction as highlighted with customized reaction overlay data.
- */
-ReactionSurface.prototype.changedToCustomized = function () {
- for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
- this.getMapCanvasObjects()[i].setOptions({
- strokeColor: this.getColor(),
- strokeWeight: this.getWidth()
- });
- }
- this.customized = true;
-};
-
-/**
- * Creates {google.maps.Polyline} from input data.
- *
- * @param {Object} line
- * raw data about line taken from server
- * @param {number} line.start.x
- * @param {number} line.start.y
- * @param {number} line.end.x
- * @param {number} line.end.y
- *
- * @param {string} color
- * color that should be used for visualization of the line
- * @param {number} width
- * width that should be used for visualization of the line
- * @param {AbstractCustomMap} map
- * where line should be visualized
- * @returns {Polyline} from input data
- */
-ReactionSurface.createLine = function (line, color, width, map) {
- var pointA = new Point(line.start.x, line.start.y);
- var pointB = new Point(line.end.x, line.end.y);
- var path = [pointA, pointB];
-
- return map.getMapCanvas().createPolyline({
- strokeColor: color,
- strokeOpacity: 1.0,
- strokeWeight: width,
- path: path
- });
-};
-
-/**
- *
- * @returns {number}
- */
-ReactionSurface.prototype.getId = function () {
- return this._id;
-};
-
-/**
- *
- * @param {number} id
- */
-ReactionSurface.prototype.setId = function (id) {
- this._id = id;
-};
-
-/**
- *
- * @returns {LayoutReaction}
- */
-ReactionSurface.prototype.getOverlayData = function () {
- return this._overlayData;
-};
-
-/**
- *
- * @param {LayoutReaction} overlayData
- */
-ReactionSurface.prototype.setOverlayData = function (overlayData) {
- this._overlayData = overlayData;
- if (overlayData !== undefined) {
- if (overlayData.width) {
- this.setWidth(overlayData.width);
- }
- }
-};
-
-/**
- *
- * @param {BioEntity} bioEntity
- */
-ReactionSurface.prototype.setBioEntity = function (bioEntity) {
- if (bioEntity === undefined || bioEntity === null) {
- throw new Error("Reaction must be defined");
- }
- AbstractSurfaceElement.prototype.setBioEntity.call(this, bioEntity);
- this.setId(bioEntity.getId());
-};
-
-/**
- *
- * @returns {boolean}
- */
-ReactionSurface.prototype.isCustomized = function () {
- return this.customized;
-};
-
-/**
- *
- * @returns {Promise}
- */
-ReactionSurface.prototype.init = function () {
- var self = this;
- var reaction = this.getBioEntity();
- var overlayData = this.getOverlayData();
-
- var promise = Promise.resolve(self.getColor());
- if (overlayData !== undefined && overlayData !== null) {
- promise = functions.overlayToColor(overlayData);
- }
- return promise.then(function (color) {
- if (color === undefined) {
- color = "#0000FF";
- }
- self.setColor(color);
- var i;
- var line;
- var googleLine;
- for (i = 0; i < reaction.startLines.length; i++) {
- line = reaction.startLines[i];
- googleLine = ReactionSurface.createLine(line, self.getColor(), self.getWidth(), self.getCustomMap());
- self.addMapCanvasObject(googleLine);
- }
- for (i = 0; i < reaction.endLines.length; i++) {
- line = reaction.endLines[i];
- googleLine = ReactionSurface.createLine(line, self.getColor(), self.getWidth(), self.getCustomMap());
- self.addMapCanvasObject(googleLine);
- }
- for (i = 0; i < reaction.midLines.length; i++) {
- line = reaction.midLines[i];
- googleLine = ReactionSurface.createLine(line, self.getColor(), self.getWidth(), self.getCustomMap());
- self.addMapCanvasObject(googleLine);
- }
- if (!self.isCustomized()) {
- self.changedToDefault();
- }
- });
-};
-
-module.exports = ReactionSurface;
+"use strict";
+
+var Bounds = require('../canvas/Bounds');
+var Point = require('../canvas/Point');
+var Promise = require("bluebird");
+
+/* exported logger */
+
+var functions = require('../../Functions');
+// noinspection JSUnusedLocalSymbols
+var logger = require('../../logger');
+
+var AbstractSurfaceElement = require('./AbstractSurfaceElement');
+var IdentifiedElement = require('../data/IdentifiedElement');
+
+/**
+ *
+ * @param {IdentifiedElement} [params.element]
+ * @param {AbstractCustomMap} params.map
+ * @param {function|function[]} [params.onClick]
+ * @param {Reaction} params.reaction
+ * @param {LayoutReaction} [params.layoutReaction]
+ * @param {boolean} params.customized
+ * @param {string} [params.color]
+ * @constructor
+ * @extends AbstractSurfaceElement
+ */
+function ReactionSurface(params) {
+ // call super constructor
+ AbstractSurfaceElement.call(this, params);
+
+ this.setWidth(5.0);
+ this.setOverlayData(params.layoutReaction);
+ this.setBioEntity(params.reaction);
+
+ var color = params.color;
+
+ if (color === undefined) {
+ color = "#0000FF";
+ }
+
+ this.setColor(color);
+ this.setCustomized(params.customized);
+ this.setIdentifiedElement(new IdentifiedElement(this.getBioEntity()));
+}
+
+ReactionSurface.prototype = Object.create(AbstractSurfaceElement.prototype);
+ReactionSurface.prototype.constructor = ReactionSurface;
+
+/**
+ * Returns {@link Bounds} of all google maps elements
+ * included in the object.
+ *
+ * @returns {Bounds} of all google maps elements
+ * included in the object
+ */
+ReactionSurface.prototype.getBounds = function () {
+ var bounds = new Bounds();
+
+ for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
+ var line = this.getMapCanvasObjects()[i];
+ bounds.extend(line.getBounds());
+ }
+ return bounds;
+};
+
+/**
+ *
+ * @param {boolean} customized
+ */
+ReactionSurface.prototype.setCustomized = function (customized) {
+ this.customized = customized;
+};
+
+/**
+ * Sets color to be used by the reaction overlay visualization when visualized
+ * in customized mode.
+ *
+ * @param {string} color
+ * new color value
+ */
+ReactionSurface.prototype.setColor = function (color) {
+ this._color = color;
+ var mapCanvasObjects = this.getMapCanvasObjects();
+ for (var i = 0; i < mapCanvasObjects.length; i++) {
+ mapCanvasObjects[i].setOptions({
+ strokeColor: color
+ });
+ }
+ this.customized = true;
+};
+
+/**
+ * Sets width of line to be used by the reaction overlay visualization when
+ * visualized in customized mode.
+ *
+ * @param {number} width
+ * new width value
+ */
+ReactionSurface.prototype.setWidth = function (width) {
+ if (width !== undefined && width !== null) {
+ this.width = width;
+ } else {
+ this.width = 1.0;
+ }
+
+};
+
+/**
+ * Returns color that should be used when visualized in customized mode.
+ *
+ * @returns {string} color that should be used when visualized in customized mode.
+ */
+ReactionSurface.prototype.getColor = function () {
+ return this._color;
+};
+
+/**
+ * Returns width that should be used when visualized in customized mode.
+ *
+ * @returns {number} width that should be used when visualized in customized mode.
+ */
+ReactionSurface.prototype.getWidth = function () {
+ return this.width;
+};
+
+/**
+ * This function is used when some overlays are added/removed from visualization.
+ * The syntax is compatible with AliasSurface class so they can be handled in
+ * the same way. When visualizing more than one overlay startX or endX will be
+ * set to a value between 0..1 (not inclusive). In such case the visualization
+ * of reaction should turn to some default mode where we know that reaction is
+ * highlighted, but we have no more information. In this way user will know that
+ * he should investigate the reaction manually.
+ *
+ * @param {number} startX
+ * see {AliasSurface} class for details, in this implementation the
+ * only important information is that when there are more than one
+ * overlay visualized at least one of the two parameters (startX,endX)
+ * will differ from {0.0, 1.0} values
+ * @param {number} endX
+ * see {AliasSurface} class for details, in this implementation the
+ * only important information is that when there are more than one
+ * overlay visualized at least one of the two parameters (startX,endX)
+ * will differ from {0.0, 1.0} values
+ */
+ReactionSurface.prototype.setBoundsForAlias = function (startX, endX) {
+ if (this.isCustomized() && (startX > 0 || endX < 1)) {
+ this.changedToDefault();
+ } else if (!this.isCustomized() && (startX <= 0 && endX >= 1)) {
+ this.changedToCustomized();
+ }
+};
+
+/**
+ * Changes visualization of the ReactionSurface to default mode where we mark
+ * reaction as highlighted, but we skip customized reaction overlay data.
+ */
+ReactionSurface.prototype.changedToDefault = function () {
+ for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
+ this.getMapCanvasObjects()[i].setOptions({
+ strokeColor: "#0000FF",
+ strokeWeight: 5
+ });
+ }
+ this.customized = false;
+};
+
+/**
+ * Changes visualization of the ReactionSurface to customized mode where we mark
+ * reaction as highlighted with customized reaction overlay data.
+ */
+ReactionSurface.prototype.changedToCustomized = function () {
+ for (var i = 0; i < this.getMapCanvasObjects().length; i++) {
+ this.getMapCanvasObjects()[i].setOptions({
+ strokeColor: this.getColor(),
+ strokeWeight: this.getWidth()
+ });
+ }
+ this.customized = true;
+};
+
+/**
+ * Creates {google.maps.Polyline} from input data.
+ *
+ * @param {Object} line
+ * raw data about line taken from server
+ * @param {number} line.start.x
+ * @param {number} line.start.y
+ * @param {number} line.end.x
+ * @param {number} line.end.y
+ *
+ * @param {string} color
+ * color that should be used for visualization of the line
+ * @param {number} width
+ * width that should be used for visualization of the line
+ * @param {AbstractCustomMap} map
+ * where line should be visualized
+ * @returns {Polyline} from input data
+ */
+ReactionSurface.createLine = function (line, color, width, map) {
+ var pointA = new Point(line.start.x, line.start.y);
+ var pointB = new Point(line.end.x, line.end.y);
+ var path = [pointA, pointB];
+
+ return map.getMapCanvas().createPolyline({
+ strokeColor: color,
+ strokeOpacity: 1.0,
+ strokeWeight: width,
+ path: path
+ });
+};
+
+/**
+ *
+ * @returns {number}
+ */
+ReactionSurface.prototype.getId = function () {
+ return this._id;
+};
+
+/**
+ *
+ * @param {number} id
+ */
+ReactionSurface.prototype.setId = function (id) {
+ this._id = id;
+};
+
+/**
+ *
+ * @returns {LayoutReaction}
+ */
+ReactionSurface.prototype.getOverlayData = function () {
+ return this._overlayData;
+};
+
+/**
+ *
+ * @param {LayoutReaction} overlayData
+ */
+ReactionSurface.prototype.setOverlayData = function (overlayData) {
+ this._overlayData = overlayData;
+ if (overlayData !== undefined) {
+ if (overlayData.width) {
+ this.setWidth(overlayData.width);
+ }
+ }
+};
+
+/**
+ *
+ * @param {BioEntity} bioEntity
+ */
+ReactionSurface.prototype.setBioEntity = function (bioEntity) {
+ if (bioEntity === undefined || bioEntity === null) {
+ throw new Error("Reaction must be defined");
+ }
+ AbstractSurfaceElement.prototype.setBioEntity.call(this, bioEntity);
+ this.setId(bioEntity.getId());
+};
+
+/**
+ *
+ * @returns {boolean}
+ */
+ReactionSurface.prototype.isCustomized = function () {
+ return this.customized;
+};
+
+/**
+ *
+ * @returns {Promise}
+ */
+ReactionSurface.prototype.init = function () {
+ var self = this;
+ var reaction = this.getBioEntity();
+ var overlayData = this.getOverlayData();
+
+ var promise = Promise.resolve(self.getColor());
+ if (overlayData !== undefined && overlayData !== null) {
+ promise = functions.overlayToColor(overlayData);
+ }
+ return promise.then(function (color) {
+ if (color === undefined) {
+ color = "#0000FF";
+ }
+ self.setColor(color);
+ var i;
+ var line;
+ var googleLine;
+ for (i = 0; i < reaction.startLines.length; i++) {
+ line = reaction.startLines[i];
+ googleLine = ReactionSurface.createLine(line, self.getColor(), self.getWidth(), self.getCustomMap());
+ self.addMapCanvasObject(googleLine);
+ }
+ for (i = 0; i < reaction.endLines.length; i++) {
+ line = reaction.endLines[i];
+ googleLine = ReactionSurface.createLine(line, self.getColor(), self.getWidth(), self.getCustomMap());
+ self.addMapCanvasObject(googleLine);
+ }
+ for (i = 0; i < reaction.midLines.length; i++) {
+ line = reaction.midLines[i];
+ googleLine = ReactionSurface.createLine(line, self.getColor(), self.getWidth(), self.getCustomMap());
+ self.addMapCanvasObject(googleLine);
+ }
+ if (!self.isCustomized()) {
+ self.changedToDefault();
+ }
+ });
+};
+
+module.exports = ReactionSurface;
diff --git a/frontend-js/src/main/js/minerva.js b/frontend-js/src/main/js/minerva.js
index 88c4a9baf3c732deb5eaa3f16b0fa6050360b402..3a7e83e4f4c693eae4d6db66666c232a58f0c9b1 100644
--- a/frontend-js/src/main/js/minerva.js
+++ b/frontend-js/src/main/js/minerva.js
@@ -1,654 +1,654 @@
-'use strict';
-
-var functions = require('./Functions');
-
-var AbstractDbOverlay = require('./map/overlay/AbstractDbOverlay');
-var Admin = require('./Admin');
-var DbOverlayCollection = require('./map/overlay/DbOverlayCollection');
-var ConfigurationType = require('./ConfigurationType');
-var CustomMap = require('./map/CustomMap');
-var CustomMapOptions = require('./map/CustomMapOptions');
-var Export = require('./Export');
-var GuiUtils = require('./gui/leftPanel/GuiUtils');
-var PluginManager = require('./plugin/PluginManager');
-var Point = require('./map/canvas/Point');
-var SearchDbOverlay = require('./map/overlay/SearchDbOverlay');
-
-var LeftPanel = require('./gui/leftPanel/LeftPanel');
-var TopMenu = require('./gui/topMenu/TopMenu');
-var Legend = require('./gui/Legend');
-var MapContextMenu = require('./gui/MapContextMenu');
-var SelectionContextMenu = require('./gui/SelectionContextMenu');
-
-var GuiConnector = require('./GuiConnector');
-var ServerConnector = require('./ServerConnector');
-
-var MolArt = require('./map/structure/MolArt');
-
-var Promise = require("bluebird");
-
-var logger = require('./logger');
-
-
-var customMap, leftPanel, topMenu, legend, mapContextMenu, selectionContextMenu;
-
-function processUrlGetParams(params) {
- var project = params.getProject();
- var sessionData = ServerConnector.getSessionData(project);
-
- var modelId;
- if (GuiConnector.getParams["submap"] !== undefined) {
- modelId = parseInt(GuiConnector.getParams["submap"]);
- } else {
- modelId = project.getModels()[0].getId()
- }
-
- var model = project.getModelById(modelId);
-
- if (GuiConnector.getParams["x"] !== undefined && GuiConnector.getParams["y"] !== undefined) {
- var point = new Point(GuiConnector.getParams["x"], GuiConnector.getParams["y"]);
- sessionData.setCenter(model, point);
- }
- if (GuiConnector.getParams["zoom"] !== undefined) {
- sessionData.setZoomLevel(model, GuiConnector.getParams["zoom"]);
- }
-
- if (GuiConnector.getParams["comments"] === "on") {
- sessionData.setShowComments(true);
- }
- if (GuiConnector.getParams["search"] !== undefined) {
- var query = SearchDbOverlay.prototype.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY,
- GuiConnector.getParams["search"]);
- sessionData.setSearchQuery(query);
- }
-
-}
-
-/**
- *
- * @param {User} user
- * @param {string} termsOfUseUrl
- */
-function requestConsent(user, termsOfUseUrl) {
- if (termsOfUseUrl === "") {
- return;
- }
- var dialog = document.createElement("div");
- var dialogContent = document.createElement("div");
- dialogContent.appendChild(functions.createElement({
- type: "span",
- content: "I agree to the minerva <a href='" + termsOfUseUrl + "' target='_blank'>Terms of Use</a>."
- }));
- var checkbox = functions.createElement({type: "input", inputType: "checkbox", style: "float: left"});
- var okButton = functions.createElement({
- type: "button",
- content: "OK",
- className: "ui-button ui-corner-all ui-widget",
- onclick: function () {
- user.setTermsOfUseConsent($(checkbox).is(':checked'));
- return ServerConnector.updateUser(user).then(function () {
- $(dialog).dialog("close");
- }).catch(GuiConnector.alert);
- }
- });
- var cancelButton = functions.createElement({
- type: "button",
- content: "I disagree",
- className: "ui-button ui-corner-all ui-widget",
- onclick: function () {
- return ServerConnector.logout().catch(GuiConnector.alert);
- }
- });
- $(okButton).prop("disabled", true);
- $(checkbox).change(function () {
- $(okButton).prop("disabled", !$(checkbox).is(':checked'));
- });
- dialogContent.appendChild(checkbox);
- dialogContent.appendChild(okButton);
- dialogContent.appendChild(cancelButton);
-
- dialog.appendChild(dialogContent);
- document.body.appendChild(dialog);
- $(dialog).dialog({
- classes: {
- "ui-dialog": "ui-state-error"
- },
- modal: true,
- closeOnEscape: false,
- title: "Terms of Use"
- }).siblings('.ui-dialog-titlebar').css("background", "red");
- $(".ui-dialog-titlebar-close", $(dialog).dialog().siblings('.ui-dialog-titlebar')).hide();
- $(dialog).dialog("open");
-}
-
-function insertGoogleAnalyticsCode() {
- return ServerConnector.getConfigurationParam(ConfigurationType.GOOGLE_ANALYTICS_IDENTIFIER).then(function (identifier) {
- if (identifier === "" || identifier === undefined || identifier === null) {
- return Promise.resolve();
- } else {
- global._gaq = global._gaq || [];
- global._gaq.push(['_setAccount', identifier]);
- global._gaq.push(['_trackPageview']);
-
- (function () {
- var ga = document.createElement('script');
- ga.type = 'text/javascript';
- ga.async = true;
- ga.src = ('https:' === document.location.protocol ? 'https://ssl' : 'http://www')
- + '.google-analytics.com/ga.js';
- var s = document.getElementsByTagName('script')[0];
- s.parentNode.insertBefore(ga, s);
- })();
- return Promise.resolve();
- }
- });
-}
-
-function createDivStructure(element) {
- var tableDiv = functions.createElement({
- type: "div",
- className: "minerva-root"
- });
- element.appendChild(tableDiv);
- var leftPanelDiv = functions.createElement({
- type: "div",
- className: "minerva-left-panel"
- });
- tableDiv.appendChild(leftPanelDiv);
- var middlePanelDiv = functions.createElement({
- type: "div",
- className: "minerva-middle-panel"
- });
- tableDiv.appendChild(middlePanelDiv);
-
- //this container is required because google maps API modifies DOM and it will crash
- var middlePanelContainerDiv = functions.createElement({type: "div"});
- middlePanelDiv.appendChild(middlePanelContainerDiv);
-
- var splitBar = functions.createElement({
- type: "div",
- className: "minerva-plugin-split-bar",
- content: " "
- });
- tableDiv.appendChild(splitBar);
-
- var rightPanelDiv = functions.createElement({
- type: "div",
- className: "minerva-plugin"
- });
- tableDiv.appendChild(rightPanelDiv);
-
- var menuDiv = functions.createElement({
- type: "div",
- className: "minerva-top-menu"
- });
- middlePanelContainerDiv.appendChild(menuDiv);
-
- var mapDiv = functions.createElement({
- type: "div",
- className: "minerva-map"
- });
- middlePanelContainerDiv.appendChild(mapDiv);
-
- var legendDiv = functions.createElement({
- type: "div",
- name: "legendDiv",
- className: "minerva-legend",
- style: "display:none"
- });
- middlePanelContainerDiv.appendChild(legendDiv);
-
- var contextMenu = functions.createElement({
- type: "ul",
- name: "contextMenu"
- });
- element.appendChild(contextMenu);
- var selectionContextMenu = functions.createElement({
- type: "ul",
- name: "selectionContextMenu"
- });
- element.appendChild(selectionContextMenu);
-}
-
-
-function initGlobals(params) {
- if (global.ServerConnector === undefined) {
- global.ServerConnector = ServerConnector;
- if (params.isDebug()) {
- logger.setLevel("debug");
- } else {
- logger.setLevel("info");
- }
- GuiConnector.init();
- if (GuiConnector.getParams['debug'] !== undefined) {
- logger.setLevel("debug");
- }
- } else {
- logger.warn("global ServerConnector found");
- }
-
-}
-
-function verifyBrowser() {
-
- var browser = functions.browser;
- if (browser.name === "IE") {
- if (browser.version <= 8 || browser.compatibilityMode) {
- var message = "This web page works only with Internet Explorer version 9 or greater.\n"
- + "If you have Internet Explorer version 9 or greater and still see this message, please, turn the 'Compatibility mode off:\n"
- + "Open Internet Explorer and press the Alt key on your keyboard.\n"
- + "Select 'Tools' menu item. \n"
- + "Select the 'Compatibility View' settings option. \n"
- + "Make sure the 'Display all websites in Compatibility View' check box is unchecked and that the 'Compatibility View; list of websites is cleared.\n"
- + "\n" + "Alternatively, please, use other browsers: Chrome, Firefox or Safari.";
- GuiConnector.alert(message);
- }
- }
-}
-
-function getProject(params) {
- if (params.getProject() !== undefined) {
- return Promise.resolve(params.getProject());
- } else {
- return ServerConnector.getProject(params.getProjectId());
- }
-}
-
-function modifyParamsForTouchTable(params) {
- if (params.bigLogo === undefined) {
- // noinspection UnnecessaryLocalVariableJS
- var isTouchTable = ((navigator.appVersion.indexOf("Win") > -1) && ('ontouchstart' in document.documentElement));
- params.bigLogo = isTouchTable;
- }
- return params;
-}
-
-function assignSplitBarHandler(customMap, pluginManager) {
- var splitBar = $('.minerva-plugin-split-bar');
- var rightPanelDiv = $('.minerva-plugin');
- var mouseDownHandler = function (e) {
- e.preventDefault();
- //TODO should use global size (but element size)
- var x = $("body").width() - e.pageX;
- $(rightPanelDiv).css("flex", "0 0 " + x + "px");
- customMap.getMapCanvas().triggerListeners('resize');
- return pluginManager.callListeners("onResize");
- };
- $(splitBar).mousedown(function (e) {
- e.preventDefault();
- $(document).mousemove(mouseDownHandler);
- });
- $(document).mouseup(function () {
- $(document).unbind('mousemove', mouseDownHandler);
- });
-}
-
-function create(params) {
- params = modifyParamsForTouchTable(params);
- if (!(params instanceof CustomMapOptions)) {
- params = new CustomMapOptions(params);
- }
- params.setServerConnector(ServerConnector);
- initGlobals(params);
- params.getElement().innerHTML = "<div style='position:relative; width:100%;height:100%'>"
- + "<img src='resources/images/icons/ajax-loader.gif' style='position:absolute;top:0;bottom:0;left:0;right:0;margin:auto;'/>" + "</div>";
-
- // make sure that we are logged in
- return ServerConnector.createSession().then(function () {
- return ServerConnector.getConfiguration();
- }).then(function (configuration) {
- params.setConfiguration(configuration);
- return getProject(params);
- }).then(function (project) {
- if (project === null) {
- var message = "Project with given id doesn't exist.";
- message += "<p>Please go to <a href='" + ServerConnector.getServerBaseUrl() + "'>default map</a>";
- return Promise.reject(new Error(message));
- }
- params.setProject(project);
- var promise = Promise.resolve();
- if (params.getProject().getMapCanvasType() === "GOOGLE_MAPS_API") {
- var apiKeySuffixString = '';
- if (params.getConfiguration().getOption(ConfigurationType.GOOGLE_MAPS_API_KEY).getValue()) {
- apiKeySuffixString = '&key=' + params.getConfiguration().getOption(ConfigurationType.GOOGLE_MAPS_API_KEY).getValue();
- }
- promise = functions.loadScript("https://maps.google.com/maps/api/js?libraries=drawing" + apiKeySuffixString);
- }
- return promise;
- }).then(function () {
- var element = params.getElement();
-
- verifyBrowser();
-
- processUrlGetParams(params);
-
- params.getElement().innerHTML = "";
- createDivStructure(element);
- params.setElement(functions.getElementByClassName(element, "minerva-map"));
-
- customMap = new CustomMap(params);
-
-
- new DbOverlayCollection({
- map: customMap
- });
-
- leftPanel = new LeftPanel({
- element: functions.getElementByClassName(element, "minerva-left-panel"),
- customMap: customMap,
- configuration: params.getConfiguration()
- });
-
- var pluginManager = new PluginManager({
- element: functions.getElementByClassName(element, "minerva-plugin"),
- map: customMap,
- project: params.getProject(),
- configuration: params.getConfiguration()
- });
- leftPanel.setPluginManager(pluginManager);
- assignSplitBarHandler(customMap, pluginManager);
-
- topMenu = new TopMenu({
- element: functions.getElementByClassName(element, "minerva-top-menu"),
- customMap: customMap
- });
-
- legend = new Legend({
- element: functions.getElementByName(element, "legendDiv"),
- customMap: customMap
- });
-
- mapContextMenu = new MapContextMenu({
- element: functions.getElementByName(element, "contextMenu"),
- customMap: customMap,
- molArt: new MolArt(element, customMap)
- });
- customMap.setContextMenu(mapContextMenu);
-
- selectionContextMenu = new SelectionContextMenu({
- element: functions.getElementByName(element, "selectionContextMenu"),
- customMap: customMap
- });
- customMap.setSelectionContextMenu(selectionContextMenu);
-
- topMenu.setLegend(legend);
- topMenu.setLeftPanel(leftPanel);
-
- return customMap.init();
- }).then(function () {
- return insertGoogleAnalyticsCode(customMap);
- }).then(function () {
- return leftPanel.init();
- }).then(function () {
- return legend.init();
- }).then(function () {
- return topMenu.init();
- }).then(function () {
- return selectionContextMenu.init();
- }).then(function () {
- return mapContextMenu.init();
- }).then(function () {
- if (GuiConnector.getParams["layout"] !== undefined) {
- var overlays = params.getProject().getDataOverlays();
- for (var j = 0; j < overlays.length; j++) {
- var overlay = overlays[j];
- if (overlay.getName() === GuiConnector.getParams["layout"]) {
- return customMap.openDataOverlay(overlay);
- }
- }
- }
- }).then(function () {
-
- var submapId = GuiConnector.getParams["submap"];
- if (submapId !== undefined) {
- return customMap.openSubmap(submapId);
- }
- }).then(function () {
- var promises = [];
- for (var i = 0; i < params.getPlugins().length; i++) {
- promises.push(leftPanel.getPluginManager().addPlugin(params.getPlugins()[i]))
- }
- return Promise.all(promises);
- }).then(function () {
- return ServerConnector.getLoggedUser();
- }).then(function (user) {
- if (leftPanel.isGoogleLicenseConsentRequired()) {
- GuiConnector.warn("Visualization of data overlays (Overlays tab) requires consent to terms of the <a href='https://cloud.google.com/maps-platform/terms/' target='_blank'>license of Google Maps Platform</a>. Click the \"Edit\" button for the overlay to do so.");
- }
- if (user.getLogin() !== "anonymous" && !user.isTermsOfUseConsent()) {
- requestConsent(user, params.getConfiguration().getOption(ConfigurationType.TERMS_OF_USE).getValue());
- }
- var result = {
- destroy: function () {
- return leftPanel.destroy().then(function () {
- customMap.destroy();
- return topMenu.destroy();
- });
- },
- getProject: function () {
- return customMap.getProject();
- }
- };
-
- if (params.isDebug()) {
- result.leftPanel = leftPanel;
- result.customMap = customMap;
- }
- return result;
- });
-
-}
-
-function createFooter() {
- var logoLink, logoText, logoImg;
- return ServerConnector.getConfigurationParam(ConfigurationType.LOGO_LINK).then(function (result) {
- logoLink = result;
- return ServerConnector.getConfigurationParam(ConfigurationType.LOGO_TEXT);
- }).then(function (result) {
- logoText = result;
- return ServerConnector.getConfigurationParam(ConfigurationType.LOGO_IMG);
- }).then(function (result) {
- logoImg = result;
- return ServerConnector.getConfiguration();
- }).then(function (configuration) {
- return functions.createElement({
- type: "div",
- className: "minerva-footer-table",
- content: '<table width="100%" border="0" cellspacing="0" cellpadding="0">' +
- '<tr>' +
- '<td align="left"><a href="' + logoLink + '" title="' + logoText + '" target="_blank">' +
- '<img src="' + GuiConnector.getImgPrefix() + logoImg + '" width="80" height="80" border="0" alt="' + logoText + '"/>' +
- '</a></td>' +
- '<td align="center" class="minerva-footer-text">MiNERVA version ' + configuration.getVersion() + ';<br/>' +
- 'build ' + configuration.getBuildDate() + ';<br/>' +
- 'git: ' + configuration.getGitHash() + '</td>' +
- '<td align="right"><a href="http://wwwen.uni.lu/lcsb/" title="LCSB - Luxembourg Centre for Systems Biomedicine" target="_blank">' +
- '<img src="' + GuiConnector.getImgPrefix() + 'lcsb.png" width="80" height="80" border="0" alt="LCSB - Luxembourg Centre for Systems Biomedicine"/>' +
- '</a></td>' +
- '</tr>\n' +
- '</table>', xss: false
- });
- })
-}
-
-function createLoginDiv() {
- var loggedIn = false;
-
- var result = functions.createElement({type: "center"});
- var resultDiv = functions.createElement({type: "div", className: "minerva-login-form", style: "text-align:left"});
- result.appendChild(resultDiv);
- resultDiv.appendChild(functions.createElement({
- type: "div",
- className: "minerva-login-form-title",
- content: "AUTHORIZATION FORM"
- }));
- var guiUtils = new GuiUtils();
- var table = functions.createElement({
- type: "div",
- className: "loginDataPanelGrid",
- style: "display: table;border-spacing:5px"
- });
- table.appendChild(guiUtils.createTableRow([
- functions.createElement({type: "label", className: "labelText", content: "LOGIN:"}),
- functions.createElement({type: "input", className: "minerva-input-text", id: "username"})]
- ));
- table.appendChild(guiUtils.createTableRow([
- functions.createElement({type: "label", className: "labelText", content: "PASSWORD:"}),
- functions.createElement({
- type: "input",
- inputType: "password",
- className: "minerva-input-password",
- id: "password"
- })]
- ));
-
- table.appendChild(guiUtils.createTableRow([
- functions.createElement({type: "label", className: "labelText"}),
- functions.createElement({type: "button", className: "labelText", id: "login", content: "LOGIN"})]
- ));
-
- resultDiv.appendChild(table);
- resultDiv.appendChild(functions.createElement({type: "br"}));
- resultDiv.appendChild(functions.createElement({type: "br"}));
- resultDiv.appendChild(functions.createElement({
- type: "a",
- href: "javascript:;",
- id: "go_to_map_button",
- className: "adminLink",
- content: '<i class="fa fa-chevron-right"></i> BACK TO MAP',
- xss: false
- }));
- resultDiv.appendChild(functions.createElement({type: "br"}));
- resultDiv.appendChild(functions.createElement({
- type: "a",
- href: "javascript:;",
- id: "register_button",
- className: "adminLink",
- content: '<i class="fa fa-chevron-right"></i> REQUEST AN ACCOUNT</a>',
- xss: false
- }));
-
- var fromPage = GuiConnector.getParams["from"];
-
- $("#login", result).on("click", function login() {
- var loginString = document.getElementById('username').value;
- var passwordString = document.getElementById('password').value;
- return ServerConnector.login(loginString, passwordString).then(function () {
- loggedIn = true;
- if (fromPage !== undefined) {
- window.location.href = fromPage;
- } else {
- window.location.href = ServerConnector.getServerBaseUrl();
- }
- }, function (error) {
- if (error.constructor.name === "InvalidCredentialsError") {
- GuiConnector.alert("invalid credentials");
- } else {
- GuiConnector.alert(error);
- }
- });
- });
- $('#go_to_map_button', result).click(function () {
- return ServerConnector.getProjectId().then(function (projectId) {
- window.location.href = ServerConnector.getServerBaseUrl() + '?id=' + projectId;
- });
- });
- $('#register_button', result).click(function () {
- var email, content;
- return ServerConnector.getConfigurationParam("REQUEST_ACCOUNT_EMAIL").then(function (result) {
- email = result;
- return ServerConnector.getConfigurationParam("REQUEST_ACCOUNT_DEFAULT_CONTENT");
- }).then(function (result) {
- content = encodeURIComponent(result);
- document.location.href = 'mailto:' + email + '?subject=MINERVA account request&body=' + content;
- });
- });
-
- return result;
-}
-
-
-function createLogin(params) {
- params = modifyParamsForTouchTable(params);
- if (!(params instanceof CustomMapOptions)) {
- params = new CustomMapOptions(params);
- }
- initGlobals(params);
- // make sure that we are logged in
- return ServerConnector.createSession().then(function () {
- return ServerConnector.getConfiguration();
- }).then(function () {
- var loginDiv = createLoginDiv(params);
- params.getElement().appendChild(loginDiv);
- return createFooter();
- }).then(function (footer) {
- params.getElement().appendChild(footer);
- return insertGoogleAnalyticsCode();
- })
-}
-
-function createExport(params) {
- params = modifyParamsForTouchTable(params);
- if (!(params instanceof CustomMapOptions)) {
- params = new CustomMapOptions(params);
- }
- initGlobals(params);
- params.getElement().style.display = "table";
- params.getElement().innerHTML = "<div style='vertical-align:middle;display:table-cell;text-align: center'>"
- + "<img src='resources/images/icons/ajax-loader.gif'/>" + "</div>";
-
- var result;
- // make sure that we are logged in
- return ServerConnector.getConfiguration().then(function (configuration) {
- params.setConfiguration(configuration);
- return getProject(params);
- }).then(function (project) {
- params.setProject(project);
- result = new Export(params);
- return result.init();
- }).then(function () {
- return result;
- });
-}
-
-function createAdmin(params) {
- params = modifyParamsForTouchTable(params);
- if (!(params instanceof CustomMapOptions)) {
- params = new CustomMapOptions(params);
- }
- params.setServerConnector(ServerConnector);
- initGlobals(params);
- params.getElement().style.display = "table";
- params.getElement().innerHTML = "<div style='vertical-align:middle;display:table-cell;text-align: center'>"
- + "<img src='resources/images/icons/ajax-loader.gif'/>" + "</div>";
- if (ServerConnector.getSessionData(null).getLogin() === "anonymous") {
- window.location.href = ServerConnector.getServerBaseUrl() + "login.xhtml?from=" + encodeURI(window.location.href);
- return Promise.resolve()
- }
-
- var result;
- // make sure that we are logged in
- return ServerConnector.createSession().then(function () {
- return ServerConnector.getConfiguration();
- }).then(function (configuration) {
- params.setConfiguration(configuration);
- result = new Admin(params);
- return createFooter();
- }).then(function (footer) {
- params.getElement().appendChild(footer);
- return result.init();
- }).then(function () {
- return result;
- });
-}
-
-var minerva = {
- create: create,
- createLogin: createLogin,
- createExport: createExport,
- createAdmin: createAdmin,
- ServerConnector: ServerConnector,
- GuiConnector: GuiConnector
-};
-
-module.exports = minerva;
+'use strict';
+
+var functions = require('./Functions');
+
+var AbstractDbOverlay = require('./map/overlay/AbstractDbOverlay');
+var Admin = require('./Admin');
+var DbOverlayCollection = require('./map/overlay/DbOverlayCollection');
+var ConfigurationType = require('./ConfigurationType');
+var CustomMap = require('./map/CustomMap');
+var CustomMapOptions = require('./map/CustomMapOptions');
+var Export = require('./Export');
+var GuiUtils = require('./gui/leftPanel/GuiUtils');
+var PluginManager = require('./plugin/PluginManager');
+var Point = require('./map/canvas/Point');
+var SearchDbOverlay = require('./map/overlay/SearchDbOverlay');
+
+var LeftPanel = require('./gui/leftPanel/LeftPanel');
+var TopMenu = require('./gui/topMenu/TopMenu');
+var Legend = require('./gui/Legend');
+var MapContextMenu = require('./gui/MapContextMenu');
+var SelectionContextMenu = require('./gui/SelectionContextMenu');
+
+var GuiConnector = require('./GuiConnector');
+var ServerConnector = require('./ServerConnector');
+
+var MolArt = require('./map/structure/MolArt');
+
+var Promise = require("bluebird");
+
+var logger = require('./logger');
+
+
+var customMap, leftPanel, topMenu, legend, mapContextMenu, selectionContextMenu;
+
+function processUrlGetParams(params) {
+ var project = params.getProject();
+ var sessionData = ServerConnector.getSessionData(project);
+
+ var modelId;
+ if (GuiConnector.getParams["submap"] !== undefined) {
+ modelId = parseInt(GuiConnector.getParams["submap"]);
+ } else {
+ modelId = project.getModels()[0].getId()
+ }
+
+ var model = project.getModelById(modelId);
+
+ if (GuiConnector.getParams["x"] !== undefined && GuiConnector.getParams["y"] !== undefined) {
+ var point = new Point(GuiConnector.getParams["x"], GuiConnector.getParams["y"]);
+ sessionData.setCenter(model, point);
+ }
+ if (GuiConnector.getParams["zoom"] !== undefined) {
+ sessionData.setZoomLevel(model, GuiConnector.getParams["zoom"]);
+ }
+
+ if (GuiConnector.getParams["comments"] === "on") {
+ sessionData.setShowComments(true);
+ }
+ if (GuiConnector.getParams["search"] !== undefined) {
+ var query = SearchDbOverlay.prototype.encodeQuery(AbstractDbOverlay.QueryType.SEARCH_BY_QUERY,
+ GuiConnector.getParams["search"]);
+ sessionData.setSearchQuery(query);
+ }
+
+}
+
+/**
+ *
+ * @param {User} user
+ * @param {string} termsOfUseUrl
+ */
+function requestConsent(user, termsOfUseUrl) {
+ if (termsOfUseUrl === "") {
+ return;
+ }
+ var dialog = document.createElement("div");
+ var dialogContent = document.createElement("div");
+ dialogContent.appendChild(functions.createElement({
+ type: "span",
+ content: "I agree to the minerva <a href='" + termsOfUseUrl + "' target='_blank'>Terms of Use</a>."
+ }));
+ var checkbox = functions.createElement({type: "input", inputType: "checkbox", style: "float: left"});
+ var okButton = functions.createElement({
+ type: "button",
+ content: "OK",
+ className: "ui-button ui-corner-all ui-widget",
+ onclick: function () {
+ user.setTermsOfUseConsent($(checkbox).is(':checked'));
+ return ServerConnector.updateUser(user).then(function () {
+ $(dialog).dialog("close");
+ }).catch(GuiConnector.alert);
+ }
+ });
+ var cancelButton = functions.createElement({
+ type: "button",
+ content: "I disagree",
+ className: "ui-button ui-corner-all ui-widget",
+ onclick: function () {
+ return ServerConnector.logout().catch(GuiConnector.alert);
+ }
+ });
+ $(okButton).prop("disabled", true);
+ $(checkbox).change(function () {
+ $(okButton).prop("disabled", !$(checkbox).is(':checked'));
+ });
+ dialogContent.appendChild(checkbox);
+ dialogContent.appendChild(okButton);
+ dialogContent.appendChild(cancelButton);
+
+ dialog.appendChild(dialogContent);
+ document.body.appendChild(dialog);
+ $(dialog).dialog({
+ classes: {
+ "ui-dialog": "ui-state-error"
+ },
+ modal: true,
+ closeOnEscape: false,
+ title: "Terms of Use"
+ }).siblings('.ui-dialog-titlebar').css("background", "red");
+ $(".ui-dialog-titlebar-close", $(dialog).dialog().siblings('.ui-dialog-titlebar')).hide();
+ $(dialog).dialog("open");
+}
+
+function insertGoogleAnalyticsCode() {
+ return ServerConnector.getConfigurationParam(ConfigurationType.GOOGLE_ANALYTICS_IDENTIFIER).then(function (identifier) {
+ if (identifier === "" || identifier === undefined || identifier === null) {
+ return Promise.resolve();
+ } else {
+ global._gaq = global._gaq || [];
+ global._gaq.push(['_setAccount', identifier]);
+ global._gaq.push(['_trackPageview']);
+
+ (function () {
+ var ga = document.createElement('script');
+ ga.type = 'text/javascript';
+ ga.async = true;
+ ga.src = ('https:' === document.location.protocol ? 'https://ssl' : 'http://www')
+ + '.google-analytics.com/ga.js';
+ var s = document.getElementsByTagName('script')[0];
+ s.parentNode.insertBefore(ga, s);
+ })();
+ return Promise.resolve();
+ }
+ });
+}
+
+function createDivStructure(element) {
+ var tableDiv = functions.createElement({
+ type: "div",
+ className: "minerva-root"
+ });
+ element.appendChild(tableDiv);
+ var leftPanelDiv = functions.createElement({
+ type: "div",
+ className: "minerva-left-panel"
+ });
+ tableDiv.appendChild(leftPanelDiv);
+ var middlePanelDiv = functions.createElement({
+ type: "div",
+ className: "minerva-middle-panel"
+ });
+ tableDiv.appendChild(middlePanelDiv);
+
+ //this container is required because google maps API modifies DOM and it will crash
+ var middlePanelContainerDiv = functions.createElement({type: "div"});
+ middlePanelDiv.appendChild(middlePanelContainerDiv);
+
+ var splitBar = functions.createElement({
+ type: "div",
+ className: "minerva-plugin-split-bar",
+ content: " "
+ });
+ tableDiv.appendChild(splitBar);
+
+ var rightPanelDiv = functions.createElement({
+ type: "div",
+ className: "minerva-plugin"
+ });
+ tableDiv.appendChild(rightPanelDiv);
+
+ var menuDiv = functions.createElement({
+ type: "div",
+ className: "minerva-top-menu"
+ });
+ middlePanelContainerDiv.appendChild(menuDiv);
+
+ var mapDiv = functions.createElement({
+ type: "div",
+ className: "minerva-map"
+ });
+ middlePanelContainerDiv.appendChild(mapDiv);
+
+ var legendDiv = functions.createElement({
+ type: "div",
+ name: "legendDiv",
+ className: "minerva-legend",
+ style: "display:none"
+ });
+ middlePanelContainerDiv.appendChild(legendDiv);
+
+ var contextMenu = functions.createElement({
+ type: "ul",
+ name: "contextMenu"
+ });
+ element.appendChild(contextMenu);
+ var selectionContextMenu = functions.createElement({
+ type: "ul",
+ name: "selectionContextMenu"
+ });
+ element.appendChild(selectionContextMenu);
+}
+
+
+function initGlobals(params) {
+ if (global.ServerConnector === undefined) {
+ global.ServerConnector = ServerConnector;
+ if (params.isDebug()) {
+ logger.setLevel("debug");
+ } else {
+ logger.setLevel("info");
+ }
+ GuiConnector.init();
+ if (GuiConnector.getParams['debug'] !== undefined) {
+ logger.setLevel("debug");
+ }
+ } else {
+ logger.warn("global ServerConnector found");
+ }
+
+}
+
+function verifyBrowser() {
+
+ var browser = functions.browser;
+ if (browser.name === "IE") {
+ if (browser.version <= 8 || browser.compatibilityMode) {
+ var message = "This web page works only with Internet Explorer version 9 or greater.\n"
+ + "If you have Internet Explorer version 9 or greater and still see this message, please, turn the 'Compatibility mode off:\n"
+ + "Open Internet Explorer and press the Alt key on your keyboard.\n"
+ + "Select 'Tools' menu item. \n"
+ + "Select the 'Compatibility View' settings option. \n"
+ + "Make sure the 'Display all websites in Compatibility View' check box is unchecked and that the 'Compatibility View; list of websites is cleared.\n"
+ + "\n" + "Alternatively, please, use other browsers: Chrome, Firefox or Safari.";
+ GuiConnector.alert(message);
+ }
+ }
+}
+
+function getProject(params) {
+ if (params.getProject() !== undefined) {
+ return Promise.resolve(params.getProject());
+ } else {
+ return ServerConnector.getProject(params.getProjectId());
+ }
+}
+
+function modifyParamsForTouchTable(params) {
+ if (params.bigLogo === undefined) {
+ // noinspection UnnecessaryLocalVariableJS
+ var isTouchTable = ((navigator.appVersion.indexOf("Win") > -1) && ('ontouchstart' in document.documentElement));
+ params.bigLogo = isTouchTable;
+ }
+ return params;
+}
+
+function assignSplitBarHandler(customMap, pluginManager) {
+ var splitBar = $('.minerva-plugin-split-bar');
+ var rightPanelDiv = $('.minerva-plugin');
+ var mouseDownHandler = function (e) {
+ e.preventDefault();
+ //TODO should use global size (but element size)
+ var x = $("body").width() - e.pageX;
+ $(rightPanelDiv).css("flex", "0 0 " + x + "px");
+ customMap.getMapCanvas().triggerListeners('resize');
+ return pluginManager.callListeners("onResize");
+ };
+ $(splitBar).mousedown(function (e) {
+ e.preventDefault();
+ $(document).mousemove(mouseDownHandler);
+ });
+ $(document).mouseup(function () {
+ $(document).unbind('mousemove', mouseDownHandler);
+ });
+}
+
+function create(params) {
+ params = modifyParamsForTouchTable(params);
+ if (!(params instanceof CustomMapOptions)) {
+ params = new CustomMapOptions(params);
+ }
+ params.setServerConnector(ServerConnector);
+ initGlobals(params);
+ params.getElement().innerHTML = "<div style='position:relative; width:100%;height:100%'>"
+ + "<img src='resources/images/icons/ajax-loader.gif' style='position:absolute;top:0;bottom:0;left:0;right:0;margin:auto;'/>" + "</div>";
+
+ // make sure that we are logged in
+ return ServerConnector.createSession().then(function () {
+ return ServerConnector.getConfiguration();
+ }).then(function (configuration) {
+ params.setConfiguration(configuration);
+ return getProject(params);
+ }).then(function (project) {
+ if (project === null) {
+ var message = "Project with given id doesn't exist.";
+ message += "<p>Please go to <a href='" + ServerConnector.getServerBaseUrl() + "'>default map</a>";
+ return Promise.reject(new Error(message));
+ }
+ params.setProject(project);
+ var promise = Promise.resolve();
+ if (params.getProject().getMapCanvasType() === "GOOGLE_MAPS_API") {
+ var apiKeySuffixString = '';
+ if (params.getConfiguration().getOption(ConfigurationType.GOOGLE_MAPS_API_KEY).getValue()) {
+ apiKeySuffixString = '&key=' + params.getConfiguration().getOption(ConfigurationType.GOOGLE_MAPS_API_KEY).getValue();
+ }
+ promise = functions.loadScript("https://maps.google.com/maps/api/js?libraries=drawing" + apiKeySuffixString);
+ }
+ return promise;
+ }).then(function () {
+ var element = params.getElement();
+
+ verifyBrowser();
+
+ processUrlGetParams(params);
+
+ params.getElement().innerHTML = "";
+ createDivStructure(element);
+ params.setElement(functions.getElementByClassName(element, "minerva-map"));
+
+ customMap = new CustomMap(params);
+
+
+ new DbOverlayCollection({
+ map: customMap
+ });
+
+ leftPanel = new LeftPanel({
+ element: functions.getElementByClassName(element, "minerva-left-panel"),
+ customMap: customMap,
+ configuration: params.getConfiguration()
+ });
+
+ var pluginManager = new PluginManager({
+ element: functions.getElementByClassName(element, "minerva-plugin"),
+ map: customMap,
+ project: params.getProject(),
+ configuration: params.getConfiguration()
+ });
+ leftPanel.setPluginManager(pluginManager);
+ assignSplitBarHandler(customMap, pluginManager);
+
+ topMenu = new TopMenu({
+ element: functions.getElementByClassName(element, "minerva-top-menu"),
+ customMap: customMap
+ });
+
+ legend = new Legend({
+ element: functions.getElementByName(element, "legendDiv"),
+ customMap: customMap
+ });
+
+ mapContextMenu = new MapContextMenu({
+ element: functions.getElementByName(element, "contextMenu"),
+ customMap: customMap,
+ molArt: new MolArt(element, customMap)
+ });
+ customMap.setContextMenu(mapContextMenu);
+
+ selectionContextMenu = new SelectionContextMenu({
+ element: functions.getElementByName(element, "selectionContextMenu"),
+ customMap: customMap
+ });
+ customMap.setSelectionContextMenu(selectionContextMenu);
+
+ topMenu.setLegend(legend);
+ topMenu.setLeftPanel(leftPanel);
+
+ return customMap.init();
+ }).then(function () {
+ return insertGoogleAnalyticsCode(customMap);
+ }).then(function () {
+ return leftPanel.init();
+ }).then(function () {
+ return legend.init();
+ }).then(function () {
+ return topMenu.init();
+ }).then(function () {
+ return selectionContextMenu.init();
+ }).then(function () {
+ return mapContextMenu.init();
+ }).then(function () {
+ if (GuiConnector.getParams["layout"] !== undefined) {
+ var overlays = params.getProject().getDataOverlays();
+ for (var j = 0; j < overlays.length; j++) {
+ var overlay = overlays[j];
+ if (overlay.getName() === GuiConnector.getParams["layout"]) {
+ return customMap.openDataOverlay(overlay);
+ }
+ }
+ }
+ }).then(function () {
+
+ var submapId = GuiConnector.getParams["submap"];
+ if (submapId !== undefined) {
+ return customMap.openSubmap(submapId);
+ }
+ }).then(function () {
+ var promises = [];
+ for (var i = 0; i < params.getPlugins().length; i++) {
+ promises.push(leftPanel.getPluginManager().addPlugin(params.getPlugins()[i]))
+ }
+ return Promise.all(promises);
+ }).then(function () {
+ return ServerConnector.getLoggedUser();
+ }).then(function (user) {
+ if (leftPanel.isGoogleLicenseConsentRequired()) {
+ GuiConnector.warn("Visualization of data overlays (Overlays tab) requires consent to terms of the <a href='https://cloud.google.com/maps-platform/terms/' target='_blank'>license of Google Maps Platform</a>. Click the \"Edit\" button for the overlay to do so.");
+ }
+ if (user.getLogin() !== "anonymous" && !user.isTermsOfUseConsent()) {
+ requestConsent(user, params.getConfiguration().getOption(ConfigurationType.TERMS_OF_USE).getValue());
+ }
+ var result = {
+ destroy: function () {
+ return leftPanel.destroy().then(function () {
+ customMap.destroy();
+ return topMenu.destroy();
+ });
+ },
+ getProject: function () {
+ return customMap.getProject();
+ }
+ };
+
+ if (params.isDebug()) {
+ result.leftPanel = leftPanel;
+ result.customMap = customMap;
+ }
+ return result;
+ });
+
+}
+
+function createFooter() {
+ var logoLink, logoText, logoImg;
+ return ServerConnector.getConfigurationParam(ConfigurationType.LOGO_LINK).then(function (result) {
+ logoLink = result;
+ return ServerConnector.getConfigurationParam(ConfigurationType.LOGO_TEXT);
+ }).then(function (result) {
+ logoText = result;
+ return ServerConnector.getConfigurationParam(ConfigurationType.LOGO_IMG);
+ }).then(function (result) {
+ logoImg = result;
+ return ServerConnector.getConfiguration();
+ }).then(function (configuration) {
+ return functions.createElement({
+ type: "div",
+ className: "minerva-footer-table",
+ content: '<table width="100%" border="0" cellspacing="0" cellpadding="0">' +
+ '<tr>' +
+ '<td align="left"><a href="' + logoLink + '" title="' + logoText + '" target="_blank">' +
+ '<img src="' + GuiConnector.getImgPrefix() + logoImg + '" width="80" height="80" border="0" alt="' + logoText + '"/>' +
+ '</a></td>' +
+ '<td align="center" class="minerva-footer-text">MiNERVA version ' + configuration.getVersion() + ';<br/>' +
+ 'build ' + configuration.getBuildDate() + ';<br/>' +
+ 'git: ' + configuration.getGitHash() + '</td>' +
+ '<td align="right"><a href="http://wwwen.uni.lu/lcsb/" title="LCSB - Luxembourg Centre for Systems Biomedicine" target="_blank">' +
+ '<img src="' + GuiConnector.getImgPrefix() + 'lcsb.png" width="80" height="80" border="0" alt="LCSB - Luxembourg Centre for Systems Biomedicine"/>' +
+ '</a></td>' +
+ '</tr>\n' +
+ '</table>', xss: false
+ });
+ })
+}
+
+function createLoginDiv() {
+ var loggedIn = false;
+
+ var result = functions.createElement({type: "center"});
+ var resultDiv = functions.createElement({type: "div", className: "minerva-login-form", style: "text-align:left"});
+ result.appendChild(resultDiv);
+ resultDiv.appendChild(functions.createElement({
+ type: "div",
+ className: "minerva-login-form-title",
+ content: "AUTHORIZATION FORM"
+ }));
+ var guiUtils = new GuiUtils();
+ var table = functions.createElement({
+ type: "div",
+ className: "loginDataPanelGrid",
+ style: "display: table;border-spacing:5px"
+ });
+ table.appendChild(guiUtils.createTableRow([
+ functions.createElement({type: "label", className: "labelText", content: "LOGIN:"}),
+ functions.createElement({type: "input", className: "minerva-input-text", id: "username"})]
+ ));
+ table.appendChild(guiUtils.createTableRow([
+ functions.createElement({type: "label", className: "labelText", content: "PASSWORD:"}),
+ functions.createElement({
+ type: "input",
+ inputType: "password",
+ className: "minerva-input-password",
+ id: "password"
+ })]
+ ));
+
+ table.appendChild(guiUtils.createTableRow([
+ functions.createElement({type: "label", className: "labelText"}),
+ functions.createElement({type: "button", className: "labelText", id: "login", content: "LOGIN"})]
+ ));
+
+ resultDiv.appendChild(table);
+ resultDiv.appendChild(functions.createElement({type: "br"}));
+ resultDiv.appendChild(functions.createElement({type: "br"}));
+ resultDiv.appendChild(functions.createElement({
+ type: "a",
+ href: "javascript:;",
+ id: "go_to_map_button",
+ className: "adminLink",
+ content: '<i class="fa fa-chevron-right"></i> BACK TO MAP',
+ xss: false
+ }));
+ resultDiv.appendChild(functions.createElement({type: "br"}));
+ resultDiv.appendChild(functions.createElement({
+ type: "a",
+ href: "javascript:;",
+ id: "register_button",
+ className: "adminLink",
+ content: '<i class="fa fa-chevron-right"></i> REQUEST AN ACCOUNT</a>',
+ xss: false
+ }));
+
+ var fromPage = GuiConnector.getParams["from"];
+
+ $("#login", result).on("click", function login() {
+ var loginString = document.getElementById('username').value;
+ var passwordString = document.getElementById('password').value;
+ return ServerConnector.login(loginString, passwordString).then(function () {
+ loggedIn = true;
+ if (fromPage !== undefined) {
+ window.location.href = fromPage;
+ } else {
+ window.location.href = ServerConnector.getServerBaseUrl();
+ }
+ }, function (error) {
+ if (error.constructor.name === "InvalidCredentialsError") {
+ GuiConnector.alert("invalid credentials");
+ } else {
+ GuiConnector.alert(error);
+ }
+ });
+ });
+ $('#go_to_map_button', result).click(function () {
+ return ServerConnector.getProjectId().then(function (projectId) {
+ window.location.href = ServerConnector.getServerBaseUrl() + '?id=' + projectId;
+ });
+ });
+ $('#register_button', result).click(function () {
+ var email, content;
+ return ServerConnector.getConfigurationParam("REQUEST_ACCOUNT_EMAIL").then(function (result) {
+ email = result;
+ return ServerConnector.getConfigurationParam("REQUEST_ACCOUNT_DEFAULT_CONTENT");
+ }).then(function (result) {
+ content = encodeURIComponent(result);
+ document.location.href = 'mailto:' + email + '?subject=MINERVA account request&body=' + content;
+ });
+ });
+
+ return result;
+}
+
+
+function createLogin(params) {
+ params = modifyParamsForTouchTable(params);
+ if (!(params instanceof CustomMapOptions)) {
+ params = new CustomMapOptions(params);
+ }
+ initGlobals(params);
+ // make sure that we are logged in
+ return ServerConnector.createSession().then(function () {
+ return ServerConnector.getConfiguration();
+ }).then(function () {
+ var loginDiv = createLoginDiv(params);
+ params.getElement().appendChild(loginDiv);
+ return createFooter();
+ }).then(function (footer) {
+ params.getElement().appendChild(footer);
+ return insertGoogleAnalyticsCode();
+ })
+}
+
+function createExport(params) {
+ params = modifyParamsForTouchTable(params);
+ if (!(params instanceof CustomMapOptions)) {
+ params = new CustomMapOptions(params);
+ }
+ initGlobals(params);
+ params.getElement().style.display = "table";
+ params.getElement().innerHTML = "<div style='vertical-align:middle;display:table-cell;text-align: center'>"
+ + "<img src='resources/images/icons/ajax-loader.gif'/>" + "</div>";
+
+ var result;
+ // make sure that we are logged in
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ params.setConfiguration(configuration);
+ return getProject(params);
+ }).then(function (project) {
+ params.setProject(project);
+ result = new Export(params);
+ return result.init();
+ }).then(function () {
+ return result;
+ });
+}
+
+function createAdmin(params) {
+ params = modifyParamsForTouchTable(params);
+ if (!(params instanceof CustomMapOptions)) {
+ params = new CustomMapOptions(params);
+ }
+ params.setServerConnector(ServerConnector);
+ initGlobals(params);
+ params.getElement().style.display = "table";
+ params.getElement().innerHTML = "<div style='vertical-align:middle;display:table-cell;text-align: center'>"
+ + "<img src='resources/images/icons/ajax-loader.gif'/>" + "</div>";
+ if (ServerConnector.getSessionData(null).getLogin() === "anonymous") {
+ window.location.href = ServerConnector.getServerBaseUrl() + "login.xhtml?from=" + encodeURI(window.location.href);
+ return Promise.resolve()
+ }
+
+ var result;
+ // make sure that we are logged in
+ return ServerConnector.createSession().then(function () {
+ return ServerConnector.getConfiguration();
+ }).then(function (configuration) {
+ params.setConfiguration(configuration);
+ result = new Admin(params);
+ return createFooter();
+ }).then(function (footer) {
+ params.getElement().appendChild(footer);
+ return result.init();
+ }).then(function () {
+ return result;
+ });
+}
+
+var minerva = {
+ create: create,
+ createLogin: createLogin,
+ createExport: createExport,
+ createAdmin: createAdmin,
+ ServerConnector: ServerConnector,
+ GuiConnector: GuiConnector
+};
+
+module.exports = minerva;
diff --git a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
index 3675b654a26f5b9c20f46fed88277bc5de95a6ab..4116d900b1e145cc06b4963a4202a730399c56eb 100644
--- a/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
+++ b/frontend-js/src/main/js/plugin/MinervaPluginProxy.js
@@ -1,500 +1,500 @@
-"use strict";
-
-var Annotation = require('../map/data/Annotation');
-var IdentifiedElement = require('../map/data/IdentifiedElement');
-var UserDbOverlay = require('../map/overlay/UserDbOverlay');
-var Configuration = require('../Configuration');
-
-var Bounds = require('../map/canvas/Bounds');
-var Point = require('../map/canvas/Point');
-
-var logger = require('../logger');
-
-var Promise = require("bluebird");
-
-function getOverlayByName(customMap, dbOverlayName) {
- var dbOverlay = customMap.getOverlayByName(dbOverlayName);
- if (dbOverlay === null) {
- var validOverlays = "";
- var overlays = customMap.getDbOverlays();
- for (var overlay in overlays) {
- if (overlays.hasOwnProperty(overlay)) {
- validOverlays += overlay.getName() + ", ";
- }
- }
- throw new Error("Invalid DbOverlay: " + dbOverlayName + ". Valid DbOverlays: " + validOverlays);
- } else {
- return dbOverlay;
- }
-}
-
-function getFullElements(customMap, identifiedElements) {
- var result = [];
- return Promise.each(
- identifiedElements,
- function (item) {
- if (item.length === undefined) {
- return customMap.getSubmapById(item.getModelId()).getModel().getByIdentifiedElement(item, true).then(
- function (fullElement) {
- result.push(fullElement);
- });
- } else {
- return getFullElements(customMap, item).then(function (resultRow) {
- result.push(resultRow);
- });
- }
- }).then(function () {
- return result;
- });
-}
-
-function getElements(elementIdentifiers, customMap) {
- var identifiedElements = [];
-
- var elementsByModelId = [];
- for (var i = 0; i < elementIdentifiers.length; i++) {
- var identifiedElement = new IdentifiedElement(elementIdentifiers[i]);
- if (elementsByModelId[identifiedElement.getModelId()] === undefined) {
- elementsByModelId[identifiedElement.getModelId()] = [];
- }
- elementsByModelId[identifiedElement.getModelId()].push(identifiedElement);
- identifiedElements.push(identifiedElement);
- }
-
- var modelScopePromises = [];
- for (var key in elementsByModelId) {
- if (elementsByModelId.hasOwnProperty(key)) {
- var model = customMap.getProject().getModelById(parseInt(key));
- modelScopePromises.push(model.getByIdentifiedElements(elementsByModelId[key], true));
- }
- }
- // first promise fetch all data
- return Promise.all(modelScopePromises).then(function () {
- // this promise return result in the right order
- var elementPromises = [];
- for (var i = 0; i < identifiedElements.length; i++) {
- var element = identifiedElements[i];
- var model = customMap.getProject().getModelById(element.getModelId());
- var promise = model.getByIdentifiedElement(element, true);
- elementPromises.push(promise);
- }
- return Promise.all(elementPromises);
- });
-}
-
-
-function createProjectData(options) {
- var map = options.map;
- return {
- getBioEntityById: function (param) {
- var isArray = true;
- if (param.length === undefined) {
- param = [param];
- isArray = false;
- }
- return getElements(param, map).then(function (result) {
- if (!isArray) {
- return result[0];
- } else {
- return result;
- }
- });
- },
- getAllBioEntities: function () {
- var models = map.getProject().getModels();
- var result = [];
- var promises = [];
- for (var i = 0; i < models.length; i++) {
- promises.push(models[i].getAliases({
- type: map.getConfiguration().getSimpleElementTypeNames(),
- complete: true
- }));
- }
- return Promise.all(promises).then(function (aliasesByModel) {
- var promises = [];
- for (var i = 0; i < models.length; i++) {
- promises.push(models[i].getReactionsForElements(aliasesByModel[i], true));
- for (var j = 0; j < aliasesByModel[i].length; j++) {
- result.push(aliasesByModel[i][j]);
- }
- }
- return Promise.all(promises);
- }).then(function (reactionsByModel) {
- for (var i = 0; i < models.length; i++) {
- for (var j = 0; j < reactionsByModel[i].length; j++) {
- result.push(reactionsByModel[i][j]);
- }
- }
- return result;
- });
- },
- getReactionsWithElement: function (param) {
- if (param.length === undefined) {
- param = [param];
- }
- return getReactionsForElements(param, map);
- },
- getProjectId: function () {
- return map.getProject().getProjectId();
- },
- getName: function () {
- return map.getProject().getName();
- },
- getVersion: function () {
- return map.getProject().getVersion();
- },
- getDisease: function () {
- if (map.getProject().getDisease() !== undefined) {
- return new Annotation(map.getProject().getDisease());
- } else {
- return null;
- }
- },
- getOrganism: function () {
- if (map.getProject().getOrganism() !== undefined) {
- return new Annotation(map.getProject().getOrganism());
- } else {
- return null;
- }
- },
- getModels: function () {
- var result = [{modelId: map.getId()}];
- for (var i = 0; i < map.getSubmaps().length; i++) {
- var subModel = map.getSubmaps()[i].getModel();
- result.push({
- modelId: subModel.getId(),
- name: subModel.getName(),
- width: subModel.getWidth(),
- height: subModel.getHeight()
- });
- }
- return result;
- }
- };
-}
-
-function getReactionsForElements(elementIdentifiers, customMap) {
- var elementsByModelId = [];
- for (var i = 0; i < elementIdentifiers.length; i++) {
- var identifiedElement = new IdentifiedElement(elementIdentifiers[i]);
- if (elementsByModelId[identifiedElement.getModelId()] === undefined) {
- elementsByModelId[identifiedElement.getModelId()] = [];
- }
- elementsByModelId[identifiedElement.getModelId()].push(identifiedElement);
- }
-
- var modelScopePromises = [];
- for (var key in elementsByModelId) {
- if (elementsByModelId.hasOwnProperty(key)) {
- var model = customMap.getProject().getModelById(parseInt(key));
- var promise = model.getReactionsForElements(elementsByModelId[key], true);
- modelScopePromises.push(promise);
- }
- }
-
- // first promise fetch all data
- return Promise.all(modelScopePromises).then(function (reactionResult) {
- var result = [];
- for (var i = 0; i < reactionResult.length; i++) {
- result = result.concat(reactionResult[i]);
- }
- return result;
- });
-}
-
-
-function createMarkerElements(options) {
- var params = options.params;
- var filteredType = options.filteredType;
- var isDefault = options.isDefault;
-
- var markerElements = [];
- if (params.length === undefined) {
- params = [params];
- }
- for (var i = 0; i < params.length; i++) {
- var elementParam = params[i];
- if (elementParam.type === undefined && isDefault) {
- markerElements.push({
- element: elementParam.element
- });
- } else if (elementParam.type === filteredType) {
- markerElements.push({
- element: elementParam.element,
- options: elementParam.options
- });
- } else if (elementParam.type !== "ICON" && elementParam.type !== "SURFACE") {
- throw new Error("Unknown type:" + elementParam.type);
- }
- }
- return markerElements;
-}
-
-function createProjectMap(options) {
- var map = options.map;
- var pluginId = options.pluginId;
-
- map.registerDbOverlay(new UserDbOverlay({name: pluginId, map: map}));
-
- var listenersData = [];
-
- return {
- getVisibleDataOverlays: function () {
- return map.getVisibleDataOverlays();
- },
- addListener: function (param) {
- var objects = [];
- var listenerWrapper = null;
- var listenerType = param.type;
- if (param.dbOverlayName !== undefined) {
- objects.push(getOverlayByName(map, param.dbOverlayName));
- listenerWrapper = function (e) {
- return getFullElements(map, e.arg.identifiedElements).then(function (result) {
- return param.callback(result);
- });
- };
- } else if (param.object === "plugin") {
- objects.push(options.plugin);
- listenerWrapper = function () {
- return param.callback();
- };
- } else if (param.object === "overlay") {
- objects.push(map);
- if (param.type === "onShow") {
- listenerType = "onShowOverlay";
- } else if (param.type === "onHide") {
- listenerType = "onHideOverlay";
- } else {
- throw new Error("Unknown listener type: " + param.type);
- }
- listenerWrapper = function (e) {
- return param.callback(e.arg);
- };
- } else if (param.object === "map") {
- objects.push(map);
- if (param.type === "onZoomChanged") {
- listenerWrapper = function (e) {
- return param.callback({modelId: e.object.getId(), zoom: e.arg});
- };
- } else if (param.type === "onCenterChanged") {
- listenerWrapper = function (e) {
- return param.callback({modelId: e.object.getId(), center: e.arg});
- };
- } else {
- throw new Error("Unknown listener type: " + param.type);
- }
- objects = objects.concat(map.getSubmaps());
- } else {
- throw new Error("Invalid argument");
- }
-
- for (var i = 0; i < objects.length; i++) {
- var object = objects[i];
- object.addListener(listenerType, listenerWrapper);
- listenersData.push({listener: param.callback, wrapper: listenerWrapper, object: object, type: listenerType});
- }
- },
- removeListener: function (param) {
- var dbOverlay = getOverlayByName(map, param.dbOverlayName);
- var indexToBeRemoved = -1;
-
- for (var i = 0; i < listenersData.length; i++) {
- var listenerData = listenersData[i];
- if (listenerData.listener === param.callback &&
- listenerData.object === dbOverlay &&
- listenerData.type === param.type) {
- indexToBeRemoved = i;
- }
- }
- if (indexToBeRemoved === -1) {
- throw new Error("Listener doesn't exist");
- }
- var listenerWrapper = listenersData[indexToBeRemoved].wrapper;
-
- dbOverlay.removeListener(param.type, listenerWrapper);
-
- listenersData.splice(indexToBeRemoved, 1);
- },
- removeAllListeners: function () {
- var removedListeners = [];
- for (var i = 0; i < listenersData.length; i++) {
- var listenerData = listenersData[i];
- var listenerWrapper = listenersData[i].wrapper;
- listenerData.object.removeListener(listenerData.type, listenerWrapper);
- removedListeners.push(listenerData.listener);
- }
- return removedListeners;
- },
- getHighlightedBioEntities: function (dbOverlayName) {
- if (dbOverlayName === undefined) {
- dbOverlayName = pluginId;
- }
- var dbOverlay = getOverlayByName(map, dbOverlayName);
- var identifiedElements;
- return dbOverlay.getIdentifiedElements().then(function (result) {
- identifiedElements = result;
- return getFullElements(map, identifiedElements);
- }).then(function (fullElements) {
- var result = [];
- for (var i = 0; i < identifiedElements.length; i++) {
- var type;
- if (identifiedElements[i].getIcon() !== undefined) {
- type = "ICON";
- } else {
- type = "SURFACE";
- }
- var row = {
- element: fullElements[i],
- type: type,
- options: {
- icon: identifiedElements[i].getIcon(),
- color: identifiedElements[i].getColor(),
- opacity: identifiedElements[i].getOpacity()
- }
- };
- result.push(row);
- }
- return result;
- });
- },
- showBioEntity: function (params) {
- var iconElements = createMarkerElements({
- params: params,
- filteredType: "ICON",
- isDefault: true
- });
- var surfaceElements = createMarkerElements({
- params: params,
- filteredType: "SURFACE",
- isDefault: false
- });
- var promise = Promise.resolve();
- if (iconElements.length > 0) {
- promise = map.getOverlayByName(pluginId).addMarker(iconElements);
- }
- return promise.then(function () {
- if (surfaceElements.length > 0) {
- return map.getOverlayByName(pluginId).addSurface(surfaceElements);
- } else {
- return Promise.resolve();
- }
- });
- },
- hideBioEntity: function (params) {
- var iconElements = createMarkerElements({
- params: params,
- filteredType: "ICON",
- isDefault: true
- });
- var surfaceElements = createMarkerElements({
- params: params,
- filteredType: "SURFACE",
- isDefault: false
- });
- return map.getOverlayByName(pluginId).removeMarker(iconElements).then(function () {
- return map.getOverlayByName(pluginId).removeSurface(surfaceElements);
- });
- },
- setCenter: function (params) {
- var submap = map.getSubmapById(params.modelId);
- if (submap === null) {
- throw new Error("Unknown modelId: " + params.modelId);
- }
- return submap.setCenter(new Point(params.x, params.y));
- },
- getCenter: function (params) {
- var submap = map.getSubmapById(params.modelId);
- if (submap === null) {
- throw new Error("Unknown modelId: " + params.modelId);
- }
- return submap.getCenter();
- },
- getBounds: function (params) {
- var submap = map.getSubmapById(params.modelId);
- if (submap === null) {
- throw new Error("Unknown modelId: " + params.modelId);
- }
- return submap.getBounds();
- },
- fitBounds: function (params) {
- var submap = map.getSubmapById(params.modelId);
- if (submap === null) {
- throw new Error("Unknown modelId: " + params.modelId);
- }
- var p1 = new Point(params.x1, params.y1);
- var p2 = new Point(params.x2, params.y2);
- return submap.getMapCanvas().fitBounds(new Bounds(p1, p2));
- },
- setZoom: function (params) {
- var submap = map.getSubmapById(params.modelId);
- if (submap === null) {
- throw new Error("Unknown modelId: " + params.modelId);
- }
- return submap.setZoom(params.zoom);
- },
- getZoom: function (params) {
- var submap = map.getSubmapById(params.modelId);
- if (submap === null) {
- throw new Error("Unknown modelId: " + params.modelId);
- }
- return submap.getZoom();
- },
- openMap: function (params) {
- return map.openSubmap(params.id);
- }
- }
-}
-
-function createProject(options) {
- return {
- data: createProjectData(options),
- map: createProjectMap(options)
- };
-}
-
-function createConfiguration(options) {
- var configuration = new Configuration(options.configuration);
- return {
- options: configuration.getOptions(),
- overlayTypes: configuration.getOverlayTypes(),
- imageConverters: configuration.getImageConverters(),
- modelConverters: configuration.getModelConverters(),
- elementTypes: configuration.getElementTypes(),
- reactionTypes: configuration.getReactionTypes(),
- miriamTypes: configuration.getMiriamTypes(),
- mapTypes: configuration.getMapTypes(),
- modificationStateTypes: configuration.getModificationStateTypes(),
- privilegeTypes: configuration.getPrivilegeTypes(),
- annotators: configuration.getAnnotators()
- };
-}
-
-function createPluginData(options) {
- return {
- setGlobalParam: function (key, value) {
- return ServerConnector.setPluginGlobalParam({hash: options.hash, key: key, value: value});
- },
- getGlobalParam: function (key) {
- return ServerConnector.getPluginGlobalParam({hash: options.hash, key: key});
- },
- setUserParam: function (key, value) {
- return ServerConnector.setPluginUserParam({hash: options.hash, key: key, value: value});
- },
- getUserParam: function (key) {
- return ServerConnector.getPluginUserParam({hash: options.hash, key: key});
- }
- };
-}
-
-
-function MinervaPluginProxy(options) {
- return {
- pluginId: options.pluginId,
- element: options.element,
- project: createProject(options),
- configuration: createConfiguration(options),
- pluginData: createPluginData(options)
- };
-}
-
-module.exports = MinervaPluginProxy;
+"use strict";
+
+var Annotation = require('../map/data/Annotation');
+var IdentifiedElement = require('../map/data/IdentifiedElement');
+var UserDbOverlay = require('../map/overlay/UserDbOverlay');
+var Configuration = require('../Configuration');
+
+var Bounds = require('../map/canvas/Bounds');
+var Point = require('../map/canvas/Point');
+
+var logger = require('../logger');
+
+var Promise = require("bluebird");
+
+function getOverlayByName(customMap, dbOverlayName) {
+ var dbOverlay = customMap.getOverlayByName(dbOverlayName);
+ if (dbOverlay === null) {
+ var validOverlays = "";
+ var overlays = customMap.getDbOverlays();
+ for (var overlay in overlays) {
+ if (overlays.hasOwnProperty(overlay)) {
+ validOverlays += overlay.getName() + ", ";
+ }
+ }
+ throw new Error("Invalid DbOverlay: " + dbOverlayName + ". Valid DbOverlays: " + validOverlays);
+ } else {
+ return dbOverlay;
+ }
+}
+
+function getFullElements(customMap, identifiedElements) {
+ var result = [];
+ return Promise.each(
+ identifiedElements,
+ function (item) {
+ if (item.length === undefined) {
+ return customMap.getSubmapById(item.getModelId()).getModel().getByIdentifiedElement(item, true).then(
+ function (fullElement) {
+ result.push(fullElement);
+ });
+ } else {
+ return getFullElements(customMap, item).then(function (resultRow) {
+ result.push(resultRow);
+ });
+ }
+ }).then(function () {
+ return result;
+ });
+}
+
+function getElements(elementIdentifiers, customMap) {
+ var identifiedElements = [];
+
+ var elementsByModelId = [];
+ for (var i = 0; i < elementIdentifiers.length; i++) {
+ var identifiedElement = new IdentifiedElement(elementIdentifiers[i]);
+ if (elementsByModelId[identifiedElement.getModelId()] === undefined) {
+ elementsByModelId[identifiedElement.getModelId()] = [];
+ }
+ elementsByModelId[identifiedElement.getModelId()].push(identifiedElement);
+ identifiedElements.push(identifiedElement);
+ }
+
+ var modelScopePromises = [];
+ for (var key in elementsByModelId) {
+ if (elementsByModelId.hasOwnProperty(key)) {
+ var model = customMap.getProject().getModelById(parseInt(key));
+ modelScopePromises.push(model.getByIdentifiedElements(elementsByModelId[key], true));
+ }
+ }
+ // first promise fetch all data
+ return Promise.all(modelScopePromises).then(function () {
+ // this promise return result in the right order
+ var elementPromises = [];
+ for (var i = 0; i < identifiedElements.length; i++) {
+ var element = identifiedElements[i];
+ var model = customMap.getProject().getModelById(element.getModelId());
+ var promise = model.getByIdentifiedElement(element, true);
+ elementPromises.push(promise);
+ }
+ return Promise.all(elementPromises);
+ });
+}
+
+
+function createProjectData(options) {
+ var map = options.map;
+ return {
+ getBioEntityById: function (param) {
+ var isArray = true;
+ if (param.length === undefined) {
+ param = [param];
+ isArray = false;
+ }
+ return getElements(param, map).then(function (result) {
+ if (!isArray) {
+ return result[0];
+ } else {
+ return result;
+ }
+ });
+ },
+ getAllBioEntities: function () {
+ var models = map.getProject().getModels();
+ var result = [];
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getAliases({
+ type: map.getConfiguration().getSimpleElementTypeNames(),
+ complete: true
+ }));
+ }
+ return Promise.all(promises).then(function (aliasesByModel) {
+ var promises = [];
+ for (var i = 0; i < models.length; i++) {
+ promises.push(models[i].getReactionsForElements(aliasesByModel[i], true));
+ for (var j = 0; j < aliasesByModel[i].length; j++) {
+ result.push(aliasesByModel[i][j]);
+ }
+ }
+ return Promise.all(promises);
+ }).then(function (reactionsByModel) {
+ for (var i = 0; i < models.length; i++) {
+ for (var j = 0; j < reactionsByModel[i].length; j++) {
+ result.push(reactionsByModel[i][j]);
+ }
+ }
+ return result;
+ });
+ },
+ getReactionsWithElement: function (param) {
+ if (param.length === undefined) {
+ param = [param];
+ }
+ return getReactionsForElements(param, map);
+ },
+ getProjectId: function () {
+ return map.getProject().getProjectId();
+ },
+ getName: function () {
+ return map.getProject().getName();
+ },
+ getVersion: function () {
+ return map.getProject().getVersion();
+ },
+ getDisease: function () {
+ if (map.getProject().getDisease() !== undefined) {
+ return new Annotation(map.getProject().getDisease());
+ } else {
+ return null;
+ }
+ },
+ getOrganism: function () {
+ if (map.getProject().getOrganism() !== undefined) {
+ return new Annotation(map.getProject().getOrganism());
+ } else {
+ return null;
+ }
+ },
+ getModels: function () {
+ var result = [{modelId: map.getId()}];
+ for (var i = 0; i < map.getSubmaps().length; i++) {
+ var subModel = map.getSubmaps()[i].getModel();
+ result.push({
+ modelId: subModel.getId(),
+ name: subModel.getName(),
+ width: subModel.getWidth(),
+ height: subModel.getHeight()
+ });
+ }
+ return result;
+ }
+ };
+}
+
+function getReactionsForElements(elementIdentifiers, customMap) {
+ var elementsByModelId = [];
+ for (var i = 0; i < elementIdentifiers.length; i++) {
+ var identifiedElement = new IdentifiedElement(elementIdentifiers[i]);
+ if (elementsByModelId[identifiedElement.getModelId()] === undefined) {
+ elementsByModelId[identifiedElement.getModelId()] = [];
+ }
+ elementsByModelId[identifiedElement.getModelId()].push(identifiedElement);
+ }
+
+ var modelScopePromises = [];
+ for (var key in elementsByModelId) {
+ if (elementsByModelId.hasOwnProperty(key)) {
+ var model = customMap.getProject().getModelById(parseInt(key));
+ var promise = model.getReactionsForElements(elementsByModelId[key], true);
+ modelScopePromises.push(promise);
+ }
+ }
+
+ // first promise fetch all data
+ return Promise.all(modelScopePromises).then(function (reactionResult) {
+ var result = [];
+ for (var i = 0; i < reactionResult.length; i++) {
+ result = result.concat(reactionResult[i]);
+ }
+ return result;
+ });
+}
+
+
+function createMarkerElements(options) {
+ var params = options.params;
+ var filteredType = options.filteredType;
+ var isDefault = options.isDefault;
+
+ var markerElements = [];
+ if (params.length === undefined) {
+ params = [params];
+ }
+ for (var i = 0; i < params.length; i++) {
+ var elementParam = params[i];
+ if (elementParam.type === undefined && isDefault) {
+ markerElements.push({
+ element: elementParam.element
+ });
+ } else if (elementParam.type === filteredType) {
+ markerElements.push({
+ element: elementParam.element,
+ options: elementParam.options
+ });
+ } else if (elementParam.type !== "ICON" && elementParam.type !== "SURFACE") {
+ throw new Error("Unknown type:" + elementParam.type);
+ }
+ }
+ return markerElements;
+}
+
+function createProjectMap(options) {
+ var map = options.map;
+ var pluginId = options.pluginId;
+
+ map.registerDbOverlay(new UserDbOverlay({name: pluginId, map: map}));
+
+ var listenersData = [];
+
+ return {
+ getVisibleDataOverlays: function () {
+ return map.getVisibleDataOverlays();
+ },
+ addListener: function (param) {
+ var objects = [];
+ var listenerWrapper = null;
+ var listenerType = param.type;
+ if (param.dbOverlayName !== undefined) {
+ objects.push(getOverlayByName(map, param.dbOverlayName));
+ listenerWrapper = function (e) {
+ return getFullElements(map, e.arg.identifiedElements).then(function (result) {
+ return param.callback(result);
+ });
+ };
+ } else if (param.object === "plugin") {
+ objects.push(options.plugin);
+ listenerWrapper = function () {
+ return param.callback();
+ };
+ } else if (param.object === "overlay") {
+ objects.push(map);
+ if (param.type === "onShow") {
+ listenerType = "onShowOverlay";
+ } else if (param.type === "onHide") {
+ listenerType = "onHideOverlay";
+ } else {
+ throw new Error("Unknown listener type: " + param.type);
+ }
+ listenerWrapper = function (e) {
+ return param.callback(e.arg);
+ };
+ } else if (param.object === "map") {
+ objects.push(map);
+ if (param.type === "onZoomChanged") {
+ listenerWrapper = function (e) {
+ return param.callback({modelId: e.object.getId(), zoom: e.arg});
+ };
+ } else if (param.type === "onCenterChanged") {
+ listenerWrapper = function (e) {
+ return param.callback({modelId: e.object.getId(), center: e.arg});
+ };
+ } else {
+ throw new Error("Unknown listener type: " + param.type);
+ }
+ objects = objects.concat(map.getSubmaps());
+ } else {
+ throw new Error("Invalid argument");
+ }
+
+ for (var i = 0; i < objects.length; i++) {
+ var object = objects[i];
+ object.addListener(listenerType, listenerWrapper);
+ listenersData.push({listener: param.callback, wrapper: listenerWrapper, object: object, type: listenerType});
+ }
+ },
+ removeListener: function (param) {
+ var dbOverlay = getOverlayByName(map, param.dbOverlayName);
+ var indexToBeRemoved = -1;
+
+ for (var i = 0; i < listenersData.length; i++) {
+ var listenerData = listenersData[i];
+ if (listenerData.listener === param.callback &&
+ listenerData.object === dbOverlay &&
+ listenerData.type === param.type) {
+ indexToBeRemoved = i;
+ }
+ }
+ if (indexToBeRemoved === -1) {
+ throw new Error("Listener doesn't exist");
+ }
+ var listenerWrapper = listenersData[indexToBeRemoved].wrapper;
+
+ dbOverlay.removeListener(param.type, listenerWrapper);
+
+ listenersData.splice(indexToBeRemoved, 1);
+ },
+ removeAllListeners: function () {
+ var removedListeners = [];
+ for (var i = 0; i < listenersData.length; i++) {
+ var listenerData = listenersData[i];
+ var listenerWrapper = listenersData[i].wrapper;
+ listenerData.object.removeListener(listenerData.type, listenerWrapper);
+ removedListeners.push(listenerData.listener);
+ }
+ return removedListeners;
+ },
+ getHighlightedBioEntities: function (dbOverlayName) {
+ if (dbOverlayName === undefined) {
+ dbOverlayName = pluginId;
+ }
+ var dbOverlay = getOverlayByName(map, dbOverlayName);
+ var identifiedElements;
+ return dbOverlay.getIdentifiedElements().then(function (result) {
+ identifiedElements = result;
+ return getFullElements(map, identifiedElements);
+ }).then(function (fullElements) {
+ var result = [];
+ for (var i = 0; i < identifiedElements.length; i++) {
+ var type;
+ if (identifiedElements[i].getIcon() !== undefined) {
+ type = "ICON";
+ } else {
+ type = "SURFACE";
+ }
+ var row = {
+ element: fullElements[i],
+ type: type,
+ options: {
+ icon: identifiedElements[i].getIcon(),
+ color: identifiedElements[i].getColor(),
+ opacity: identifiedElements[i].getOpacity()
+ }
+ };
+ result.push(row);
+ }
+ return result;
+ });
+ },
+ showBioEntity: function (params) {
+ var iconElements = createMarkerElements({
+ params: params,
+ filteredType: "ICON",
+ isDefault: true
+ });
+ var surfaceElements = createMarkerElements({
+ params: params,
+ filteredType: "SURFACE",
+ isDefault: false
+ });
+ var promise = Promise.resolve();
+ if (iconElements.length > 0) {
+ promise = map.getOverlayByName(pluginId).addMarker(iconElements);
+ }
+ return promise.then(function () {
+ if (surfaceElements.length > 0) {
+ return map.getOverlayByName(pluginId).addSurface(surfaceElements);
+ } else {
+ return Promise.resolve();
+ }
+ });
+ },
+ hideBioEntity: function (params) {
+ var iconElements = createMarkerElements({
+ params: params,
+ filteredType: "ICON",
+ isDefault: true
+ });
+ var surfaceElements = createMarkerElements({
+ params: params,
+ filteredType: "SURFACE",
+ isDefault: false
+ });
+ return map.getOverlayByName(pluginId).removeMarker(iconElements).then(function () {
+ return map.getOverlayByName(pluginId).removeSurface(surfaceElements);
+ });
+ },
+ setCenter: function (params) {
+ var submap = map.getSubmapById(params.modelId);
+ if (submap === null) {
+ throw new Error("Unknown modelId: " + params.modelId);
+ }
+ return submap.setCenter(new Point(params.x, params.y));
+ },
+ getCenter: function (params) {
+ var submap = map.getSubmapById(params.modelId);
+ if (submap === null) {
+ throw new Error("Unknown modelId: " + params.modelId);
+ }
+ return submap.getCenter();
+ },
+ getBounds: function (params) {
+ var submap = map.getSubmapById(params.modelId);
+ if (submap === null) {
+ throw new Error("Unknown modelId: " + params.modelId);
+ }
+ return submap.getBounds();
+ },
+ fitBounds: function (params) {
+ var submap = map.getSubmapById(params.modelId);
+ if (submap === null) {
+ throw new Error("Unknown modelId: " + params.modelId);
+ }
+ var p1 = new Point(params.x1, params.y1);
+ var p2 = new Point(params.x2, params.y2);
+ return submap.getMapCanvas().fitBounds(new Bounds(p1, p2));
+ },
+ setZoom: function (params) {
+ var submap = map.getSubmapById(params.modelId);
+ if (submap === null) {
+ throw new Error("Unknown modelId: " + params.modelId);
+ }
+ return submap.setZoom(params.zoom);
+ },
+ getZoom: function (params) {
+ var submap = map.getSubmapById(params.modelId);
+ if (submap === null) {
+ throw new Error("Unknown modelId: " + params.modelId);
+ }
+ return submap.getZoom();
+ },
+ openMap: function (params) {
+ return map.openSubmap(params.id);
+ }
+ }
+}
+
+function createProject(options) {
+ return {
+ data: createProjectData(options),
+ map: createProjectMap(options)
+ };
+}
+
+function createConfiguration(options) {
+ var configuration = new Configuration(options.configuration);
+ return {
+ options: configuration.getOptions(),
+ overlayTypes: configuration.getOverlayTypes(),
+ imageConverters: configuration.getImageConverters(),
+ modelConverters: configuration.getModelConverters(),
+ elementTypes: configuration.getElementTypes(),
+ reactionTypes: configuration.getReactionTypes(),
+ miriamTypes: configuration.getMiriamTypes(),
+ mapTypes: configuration.getMapTypes(),
+ modificationStateTypes: configuration.getModificationStateTypes(),
+ privilegeTypes: configuration.getPrivilegeTypes(),
+ annotators: configuration.getAnnotators()
+ };
+}
+
+function createPluginData(options) {
+ return {
+ setGlobalParam: function (key, value) {
+ return ServerConnector.setPluginGlobalParam({hash: options.hash, key: key, value: value});
+ },
+ getGlobalParam: function (key) {
+ return ServerConnector.getPluginGlobalParam({hash: options.hash, key: key});
+ },
+ setUserParam: function (key, value) {
+ return ServerConnector.setPluginUserParam({hash: options.hash, key: key, value: value});
+ },
+ getUserParam: function (key) {
+ return ServerConnector.getPluginUserParam({hash: options.hash, key: key});
+ }
+ };
+}
+
+
+function MinervaPluginProxy(options) {
+ return {
+ pluginId: options.pluginId,
+ element: options.element,
+ project: createProject(options),
+ configuration: createConfiguration(options),
+ pluginData: createPluginData(options)
+ };
+}
+
+module.exports = MinervaPluginProxy;
diff --git a/frontend-js/src/main/js/plugin/Plugin.js b/frontend-js/src/main/js/plugin/Plugin.js
index 9ae61f686353d96d29afe0324ba92b0f6b9828a1..60b5df465ec4277cf9a1f439f5d44a7c7217a207 100644
--- a/frontend-js/src/main/js/plugin/Plugin.js
+++ b/frontend-js/src/main/js/plugin/Plugin.js
@@ -1,161 +1,161 @@
-"use strict";
-
-var MinervaPluginProxy = require('./MinervaPluginProxy');
-var ObjectWithListeners = require('../ObjectWithListeners');
-
-var Promise = require("bluebird");
-
-var logger = require('../logger');
-var Functions = require('../Functions');
-
-var pluginId = 0;
-
-function Plugin(options) {
- ObjectWithListeners.call(this);
- var self = this;
- self.setOptions(options);
- self.registerListenerType("onUnload");
- self.registerListenerType("onResize");
-}
-
-Plugin.prototype = Object.create(ObjectWithListeners.prototype);
-Plugin.prototype.constructor = ObjectWithListeners;
-
-Plugin.prototype.setOptions = function (options) {
- this._options = options;
-};
-
-Plugin.prototype.getOptions = function () {
- return this._options;
-};
-
-Plugin.prototype.setLoadedPluginData = function (loadedPluginData) {
- this._loadedPluginData = loadedPluginData;
-};
-Plugin.prototype.getLoadedPluginData = function () {
- return this._loadedPluginData;
-};
-
-Plugin.prototype.setMinervaPluginProxy = function (minervaPluginProxy) {
- this._minervaPluginProxy = minervaPluginProxy;
-};
-Plugin.prototype.getMinervaPluginProxy = function () {
- return this._minervaPluginProxy;
-};
-Plugin.prototype.getPluginId = function () {
- return this.getMinervaPluginProxy().pluginId;
-};
-
-Plugin.prototype.load = function () {
- var self = this;
- var options = self.getOptions();
-
- var hash;
- var error = false;
- var registerPromise = null;
-
- return ServerConnector.sendRequest({
- url: options.url,
- description: "Loading plugin: " + options.url,
- method: "GET"
- }).then(function (content) {
- hash = Functions.computeMD5(content);
- var pluginData = undefined;
- try {
- // noinspection JSUnusedLocalSymbols
- var minervaDefine = function (pluginFunction) {
- try {
- if (typeof pluginFunction === "function") {
- pluginData = pluginFunction();
- } else {
- pluginData = pluginFunction;
- }
-
- var minervaPluginProxy = new MinervaPluginProxy({
- hash: hash,
- map: options.map,
- configuration: options.configuration,
- element: options.element,
- plugin: self,
- pluginId: "plugin" + (pluginId++)
- });
- self.setLoadedPluginData(pluginData);
- self.setMinervaPluginProxy(minervaPluginProxy);
- registerPromise = new Promise(function (resolve) {
- resolve(pluginData.register(minervaPluginProxy));
- });
- } catch (e) {
- error = e;
- }
- };
- content += "//# sourceURL=" + options.url;
- eval(content);
- } catch (e) {
- error = e;
- }
- return ServerConnector.registerPlugin({
- hash: hash,
- url: options.url,
- name: self.getName(),
- version: self.getVersion()
- });
- }).then(function () {
- if (error) {
- return Promise.reject(error);
- }
- return registerPromise;
- });
-
-};
-
-Plugin.prototype.getMinWidth = function () {
- var value;
- var data = this.getLoadedPluginData();
- if (data.minWidth !== undefined) {
- if (typeof data.minWidth === "function") {
- value = parseInt(data.minWidth());
- } else {
- value = parseInt(data.minWidth);
- }
- }
- return value;
-};
-
-Plugin.prototype.unload = function () {
- var self = this;
- return Promise.resolve().then(function () {
- return self.getLoadedPluginData().unregister();
- }).then(function () {
- var removedListeners = self.getMinervaPluginProxy().project.map.removeAllListeners();
- if (removedListeners.length > 0) {
- logger.warn("'" + self.getLoadedPluginData().getName() + "' plugin didn't remove all registered listeners");
- }
- return self.callListeners("onUnload");
- }).then(function () {
- return self.destroy();
- });
-};
-
-Plugin.prototype.getName = function () {
- if (this.getLoadedPluginData() === undefined) {
- return "";
- }
- return this.getLoadedPluginData().getName();
-};
-
-Plugin.prototype.getVersion = function () {
- if (this.getLoadedPluginData() === undefined) {
- return "";
- }
- return this.getLoadedPluginData().getVersion();
-};
-
-Plugin.prototype.destroy = function () {
- return Promise.resolve();
-};
-
-Plugin.prototype.setHash = function (hash) {
- this.getMinervaPluginProxy().hash = hash;
-};
-
-module.exports = Plugin;
+"use strict";
+
+var MinervaPluginProxy = require('./MinervaPluginProxy');
+var ObjectWithListeners = require('../ObjectWithListeners');
+
+var Promise = require("bluebird");
+
+var logger = require('../logger');
+var Functions = require('../Functions');
+
+var pluginId = 0;
+
+function Plugin(options) {
+ ObjectWithListeners.call(this);
+ var self = this;
+ self.setOptions(options);
+ self.registerListenerType("onUnload");
+ self.registerListenerType("onResize");
+}
+
+Plugin.prototype = Object.create(ObjectWithListeners.prototype);
+Plugin.prototype.constructor = ObjectWithListeners;
+
+Plugin.prototype.setOptions = function (options) {
+ this._options = options;
+};
+
+Plugin.prototype.getOptions = function () {
+ return this._options;
+};
+
+Plugin.prototype.setLoadedPluginData = function (loadedPluginData) {
+ this._loadedPluginData = loadedPluginData;
+};
+Plugin.prototype.getLoadedPluginData = function () {
+ return this._loadedPluginData;
+};
+
+Plugin.prototype.setMinervaPluginProxy = function (minervaPluginProxy) {
+ this._minervaPluginProxy = minervaPluginProxy;
+};
+Plugin.prototype.getMinervaPluginProxy = function () {
+ return this._minervaPluginProxy;
+};
+Plugin.prototype.getPluginId = function () {
+ return this.getMinervaPluginProxy().pluginId;
+};
+
+Plugin.prototype.load = function () {
+ var self = this;
+ var options = self.getOptions();
+
+ var hash;
+ var error = false;
+ var registerPromise = null;
+
+ return ServerConnector.sendRequest({
+ url: options.url,
+ description: "Loading plugin: " + options.url,
+ method: "GET"
+ }).then(function (content) {
+ hash = Functions.computeMD5(content);
+ var pluginData = undefined;
+ try {
+ // noinspection JSUnusedLocalSymbols
+ var minervaDefine = function (pluginFunction) {
+ try {
+ if (typeof pluginFunction === "function") {
+ pluginData = pluginFunction();
+ } else {
+ pluginData = pluginFunction;
+ }
+
+ var minervaPluginProxy = new MinervaPluginProxy({
+ hash: hash,
+ map: options.map,
+ configuration: options.configuration,
+ element: options.element,
+ plugin: self,
+ pluginId: "plugin" + (pluginId++)
+ });
+ self.setLoadedPluginData(pluginData);
+ self.setMinervaPluginProxy(minervaPluginProxy);
+ registerPromise = new Promise(function (resolve) {
+ resolve(pluginData.register(minervaPluginProxy));
+ });
+ } catch (e) {
+ error = e;
+ }
+ };
+ content += "//# sourceURL=" + options.url;
+ eval(content);
+ } catch (e) {
+ error = e;
+ }
+ return ServerConnector.registerPlugin({
+ hash: hash,
+ url: options.url,
+ name: self.getName(),
+ version: self.getVersion()
+ });
+ }).then(function () {
+ if (error) {
+ return Promise.reject(error);
+ }
+ return registerPromise;
+ });
+
+};
+
+Plugin.prototype.getMinWidth = function () {
+ var value;
+ var data = this.getLoadedPluginData();
+ if (data.minWidth !== undefined) {
+ if (typeof data.minWidth === "function") {
+ value = parseInt(data.minWidth());
+ } else {
+ value = parseInt(data.minWidth);
+ }
+ }
+ return value;
+};
+
+Plugin.prototype.unload = function () {
+ var self = this;
+ return Promise.resolve().then(function () {
+ return self.getLoadedPluginData().unregister();
+ }).then(function () {
+ var removedListeners = self.getMinervaPluginProxy().project.map.removeAllListeners();
+ if (removedListeners.length > 0) {
+ logger.warn("'" + self.getLoadedPluginData().getName() + "' plugin didn't remove all registered listeners");
+ }
+ return self.callListeners("onUnload");
+ }).then(function () {
+ return self.destroy();
+ });
+};
+
+Plugin.prototype.getName = function () {
+ if (this.getLoadedPluginData() === undefined) {
+ return "";
+ }
+ return this.getLoadedPluginData().getName();
+};
+
+Plugin.prototype.getVersion = function () {
+ if (this.getLoadedPluginData() === undefined) {
+ return "";
+ }
+ return this.getLoadedPluginData().getVersion();
+};
+
+Plugin.prototype.destroy = function () {
+ return Promise.resolve();
+};
+
+Plugin.prototype.setHash = function (hash) {
+ this.getMinervaPluginProxy().hash = hash;
+};
+
+module.exports = Plugin;