From 9cbe83f7fb07d06de4002501f16f9c8d446108a4 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 21 Nov 2017 16:53:06 +0100
Subject: [PATCH] every map has optional default center coordinates where map
should be focused after first open during session
---
frontend-js/src/main/js/ServerConnector.js | 25 +
.../main/js/gui/admin/EditProjectDialog.js | 1508 ++++++------
.../src/main/js/map/AbstractCustomMap.js | 2121 +++++++++--------
frontend-js/src/main/js/map/CustomMap.js | 18 +-
frontend-js/src/main/js/map/data/MapModel.js | 1626 ++++++-------
.../js/gui/admin/EditProjectDialog-test.js | 246 +-
.../PATCH_model.id=15781&token=MOCK_TOKEN_ID& | 1 +
.../lcsb/mapviewer/model/map/model/Model.java | 1100 ++++-----
.../mapviewer/model/map/model/ModelData.java | 1428 +++++------
.../model/map/model/ModelFullIndexed.java | 1207 +++++-----
persist/src/db/12.0.0/fix_db_20171121.sql | 5 +
.../api/projects/models/ModelController.java | 108 +-
.../api/projects/models/ModelMetaData.java | 33 +
.../api/projects/models/ModelRestImpl.java | 88 +
.../mapviewer/services/impl/ModelService.java | 1132 ++++-----
.../services/interfaces/IModelService.java | 258 +-
16 files changed, 5688 insertions(+), 5216 deletions(-)
create mode 100644 frontend-js/testFiles/apiCalls/projects/sample/models/15781/PATCH_model.id=15781&token=MOCK_TOKEN_ID&
diff --git a/frontend-js/src/main/js/ServerConnector.js b/frontend-js/src/main/js/ServerConnector.js
index da7011f327..470e139378 100644
--- a/frontend-js/src/main/js/ServerConnector.js
+++ b/frontend-js/src/main/js/ServerConnector.js
@@ -408,6 +408,12 @@ ServerConnector.updateOverlayUrl = function (queryParams) {
});
};
+ServerConnector.updateModelUrl = function (queryParams) {
+ return this.getApiUrl({
+ url: this.getModelsUrl(queryParams)
+ });
+};
+
ServerConnector.deleteOverlayUrl = function (queryParams) {
return this.getApiUrl({
url: this.getOverlayByIdUrl(queryParams)
@@ -1638,6 +1644,25 @@ ServerConnector.updateOverlay = function (overlay) {
return self.sendPatchRequest(self.updateOverlayUrl(queryParams), filterParams);
};
+ServerConnector.updateModel = function (params) {
+ var self = this;
+ var model = params.model;
+ var queryParams = {
+ projectId: params.projectId,
+ modelId: model.getId()
+ };
+ var filterParams = {
+ model: {
+ id: model.getId(),
+ defaultCenterX: model.getDefaultCenterX(),
+ defaultCenterY: model.getDefaultCenterY(),
+ defaultZoomLevel: model.getDefaultZoomLevel()
+ }
+ };
+ return self.sendPatchRequest(self.updateModelUrl(queryParams), filterParams);
+};
+
+
ServerConnector.removeOverlay = function (params) {
var self = this;
var queryParams = {
diff --git a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
index e2787d5492..9101aa7659 100644
--- a/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
+++ b/frontend-js/src/main/js/gui/admin/EditProjectDialog.js
@@ -1,687 +1,821 @@
-"use strict";
-
-/* exported logger */
-var Promise = require("bluebird");
-
-var AbstractGuiElement = require('../AbstractGuiElement');
-var AddOverlayDialog = require('../AddOverlayDialog');
-var Annotation = require('../../map/data/Annotation');
-var GuiConnector = require('../../GuiConnector');
-
-var Functions = require('../../Functions');
-var logger = require('../../logger');
-
-var guiUtils = new (require('../leftPanel/GuiUtils'))();
-
-function EditProjectDialog(params) {
- AbstractGuiElement.call(this, params);
- var self = this;
- $(self.getElement()).addClass("minerva-edit-project-dialog");
-
- self.createGui();
-}
-
-EditProjectDialog.prototype = Object.create(AbstractGuiElement.prototype);
-EditProjectDialog.prototype.constructor = EditProjectDialog;
-
-EditProjectDialog.prototype.createGui = function () {
- var self = this;
- var element = self.getElement();
-
- var tabDiv = Functions.createElement({
- type: "div",
- name: "tabView",
- className: "tabbable boxed parentTabs"
- });
- 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"
- });
- tabDiv.appendChild(tabContentDiv);
-
- self.createGeneralTab(tabMenuDiv, tabContentDiv);
- self.createOverlaysTab(tabMenuDiv, tabContentDiv);
- self.createUsersTab(tabMenuDiv, tabContentDiv);
-};
-
-EditProjectDialog.prototype.createGeneralTab = function (tabMenuDiv, tabContentDiv) {
- var self = this;
- self.addTab({
- tabMenuDiv: tabMenuDiv,
- tabContentDiv: tabContentDiv,
- name: "GENERAL",
- id: self.getProject().getProjectId() + "_general_tab",
- content: self.createGeneralTabContent()
- });
-
-};
-
-EditProjectDialog.prototype.addTab = function (params) {
- var navLi = guiUtils.createTabMenuObject({
- id: params.id,
- name: params.name,
- navigationBar: params.tabMenuDiv
- });
- params.tabMenuDiv.appendChild(navLi);
-
- var contentDiv = guiUtils.createTabContentObject({
- id: params.id,
- navigationObject: navLi,
- navigationBar: params.tabMenuDiv
- });
-
- if (params.content !== undefined) {
- contentDiv.appendChild(params.content);
- }
-
- params.tabContentDiv.appendChild(contentDiv);
-};
-
-EditProjectDialog.prototype.createGeneralTabContent = function () {
- var self = this;
- var project = self.getProject();
-
- var result = new Functions.createElement({
- type: "div"
- });
-
- var table = new Functions.createElement({
- type: "div",
- style: "display:table"
- });
- result.appendChild(table);
-
- var projectIdRow = new Functions.createElement({
- type: "div",
- style: "display:table-row"
- });
- table.appendChild(projectIdRow);
- projectIdRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "ProjectId"
- }));
- projectIdRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: project.getProjectId()
- }));
-
- var nameRow = new Functions.createElement({
- type: "div",
- style: "display:table-row"
- });
- table.appendChild(nameRow);
- nameRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "Name"
- }));
- nameRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "<input name='projectName' value='" + project.getName() + "'/>"
- }));
-
- var versionRow = new Functions.createElement({
- type: "div",
- style: "display:table-row"
- });
- table.appendChild(versionRow);
- versionRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "Version"
- }));
- versionRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "<input name='projectVersion' value='" + project.getVersion() + "'/>"
- }));
-
- var diseaseRow = new Functions.createElement({
- type: "div",
- style: "display:table-row"
- });
- table.appendChild(diseaseRow);
- diseaseRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "Disease"
- }));
- var disease = "";
- if (project.getDisease() !== undefined) {
- disease = project.getDisease().getResource();
- }
- diseaseRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "<input name='projectDisease' value='" + disease + "'/>"
- }));
-
- var organismRow = new Functions.createElement({
- type: "div",
- style: "display:table-row"
- });
- table.appendChild(organismRow);
- organismRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "Organism"
- }));
- var organism = "";
- if (project.getOrganism() !== undefined) {
- organism = project.getOrganism().getResource();
- }
- organismRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "<input name='projectOrganism' value='" + organism + "'/>"
- }));
-
- var emailRow = new Functions.createElement({
- type: "div",
- style: "display:table-row"
- });
- table.appendChild(emailRow);
- emailRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "Notify email"
- }));
- var email = "";
- if (project.getNotifyEmail() !== undefined) {
- email = project.getNotifyEmail();
- }
- emailRow.appendChild(new Functions.createElement({
- type: "div",
- style: "display:table-cell",
- content: "<input name='projectNotifyEmail' value='" + email + "'/>"
- }));
-
- var menuRow = Functions.createElement({
- type: "div",
- className: "minerva-menu-row",
- style: "display:table-row; margin:10px"
- });
- result.appendChild(menuRow);
-
- var saveProjectButton = Functions.createElement({
- type: "button",
- name: "saveProject",
- content: '<span class="ui-icon ui-icon-disk"></span> SAVE',
- onclick: function () {
- return self.onSaveClicked().then(function () {
- return self.close();
- }, GuiConnector.alert);
- }
- });
- var cancelButton = Functions.createElement({
- type: "button",
- name: "cancelProject",
- content: '<span class="ui-icon ui-icon-cancel"></span> CANCEL',
- onclick: function () {
- return self.close();
- }
- });
- menuRow.appendChild(saveProjectButton);
- menuRow.appendChild(cancelButton);
-
- return result;
-
-};
-
-EditProjectDialog.prototype.createOverlaysTab = function (tabMenuDiv, tabContentDiv) {
- var self = this;
- self.addTab({
- tabMenuDiv: tabMenuDiv,
- tabContentDiv: tabContentDiv,
- name: "OVERLAYS",
- id: self.getProject().getProjectId() + "_overlays_tab",
- content: self.createOverlaysTabContent()
- });
-};
-
-EditProjectDialog.prototype.createOverlaysTabContent = function () {
- var self = this;
- var result = Functions.createElement({
- type: "div"
- });
- result.appendChild(self._createOverlayTable());
- return result;
-};
-
-EditProjectDialog.prototype._createOverlayTable = function () {
- var self = this;
-
- var result = Functions.createElement({
- type: "div",
- style: "margin-top:10px;"
- });
-
- var overlaysTable = Functions.createElement({
- type: "table",
- name: "overlaysTable",
- className: "display",
- style: "width:100%"
- });
- result.appendChild(overlaysTable);
-
- $(overlaysTable).DataTable({
- fnRowCallback: function (nRow, aData) {
- nRow.setAttribute('id', "overlay-" + aData[0]);
- },
- columns: [{
- title: 'Id'
- }, {
- title: 'Name'
- }, {
- title: 'Description'
- }, {
- title: 'Public'
- }, {
- title: 'Default'
- }, {
- title: 'Owner'
- }, {
- title: 'Data'
- }, {
- title: 'Update'
- }, {
- title: 'Remove'
- }],
- dom: '<"minerva-datatable-toolbar">frtip',
- initComplete: function () {
- $("div.minerva-datatable-toolbar", $(result)).html('<button name="addOverlay">Add overlay</button>');
- }
-
- });
-
- $(overlaysTable).on("click", "[name='removeOverlay']", function () {
- var button = this;
- return self.removeOverlay($(button).attr("data")).then(null, GuiConnector.alert);
- });
-
- $(overlaysTable).on("click", "[name='saveOverlay']", function () {
- var button = this;
- GuiConnector.showProcessing("Updating");
- return self.saveOverlay($(button).attr("data")).then(function () {
- GuiConnector.hideProcessing();
- GuiConnector.info("Overlay updated successfully");
- }, function (error) {
- GuiConnector.hideProcessing();
- GuiConnector.alert(error);
- });
- });
-
- $(overlaysTable).on("click", "[name='downloadSource']", function () {
- var button = this;
- return ServerConnector.getOverlaySourceDownloadUrl({
- overlayId: $(button).attr("data")
- }).then(function (url) {
- return self.downloadFile(url);
- }).then(null, GuiConnector.alert);
- });
-
- $(result).on("click", "[name='addOverlay']", function () {
- return self.openAddOverlayDialog();
- });
-
- return result;
-};
-
-EditProjectDialog.prototype.createUsersTab = function (tabMenuDiv, tabContentDiv) {
- var self = this;
- self.addTab({
- tabMenuDiv: tabMenuDiv,
- tabContentDiv: tabContentDiv,
- name: "USERS",
- id: self.getProject().getProjectId() + "_users_tab",
- content: self.createUsersTabContent()
- });
-};
-
-EditProjectDialog.prototype.createUsersTabContent = function () {
- var self = this;
-
- var result = Functions.createElement({
- type: "div",
- style: "margin-top:10px;"
- });
-
- var usersTable = Functions.createElement({
- type: "table",
- name: "usersTable",
- className: "display",
- style: "width:100%"
- });
- result.appendChild(usersTable);
-
- $(usersTable).on("click", "[name='saveUser']", function () {
- var button = this;
- GuiConnector.showProcessing("Updating");
- return self.saveUser($(button).attr("data")).then(function () {
- GuiConnector.hideProcessing();
- GuiConnector.info("User updated successfully");
- }, function (error) {
- GuiConnector.hideProcessing();
- GuiConnector.alert(error);
- });
- });
-
- return result;
-};
-
-EditProjectDialog.prototype.createUserPrivilegeColumns = function () {
- var self = this;
-
- if (self._userPrivilegeColumns !== undefined) {
- return Promise.resolve(self._userPrivilegeColumns);
- }
-
- return ServerConnector.getConfiguration().then(function (configuration) {
- self._userPrivilegeColumns = [{
- title: "Name"
- }];
- 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
- });
- }
- }
- self._userPrivilegeColumns.push({
- "title": "Update"
- });
- return self._userPrivilegeColumns;
- });
-
-};
-
-EditProjectDialog.prototype.init = function () {
- var self = this;
- return self.initUsersTab().then(function () {
- return self.refreshUsers();
- }).then(function () {
- return self.refreshOverlays();
- }).then(function () {
- $(window).trigger('resize');
- });
-};
-
-EditProjectDialog.prototype.initUsersTab = function () {
- var self = this;
-
- var usersTable = $("[name=usersTable]", self.getElement())[0];
-
- return self.createUserPrivilegeColumns().then(function (columns) {
- $(usersTable).DataTable({
- columns: columns
- });
- });
-};
-
-EditProjectDialog.prototype.refreshOverlays = function () {
- var self = this;
- return ServerConnector.getOverlays({
- projectId: self.getProject().getProjectId()
- }).then(function (overlays) {
- return self.setOverlays(overlays);
- });
-};
-
-EditProjectDialog.prototype.refreshUsers = function () {
- var self = this;
- return ServerConnector.getUsers().then(function (users) {
- return self.setUsers(users);
- });
-};
-
-EditProjectDialog.prototype.setOverlays = function (overlays) {
- var self = this;
- self._overlayById = [];
- return ServerConnector.getUsers().then(function (users) {
- var dataTable = $($("[name='overlaysTable']", self.getElement())[0]).DataTable();
- var data = [];
- for (var i = 0; i < overlays.length; i++) {
- var overlay = overlays[i];
- self._overlayById[overlay.getId()] = overlay;
- var rowData = self.overlayToTableRow(overlay, users);
- data.push(rowData);
- }
- dataTable.clear().rows.add(data).draw();
- });
-};
-
-EditProjectDialog.prototype.setUsers = function (users) {
- var self = this;
- self._userByLogin = [];
- return self.createUserPrivilegeColumns().then(function (columns) {
- var dataTable = $($("[name='usersTable']", self.getElement())[0]).DataTable();
- var data = [];
- for (var i = 0; i < users.length; i++) {
- var user = users[i];
- self._userByLogin[user.getLogin()] = user;
- var rowData = self.userToTableRow(user, columns);
- data.push(rowData);
- }
- dataTable.clear().rows.add(data).draw();
- });
-};
-
-EditProjectDialog.prototype.userToTableRow = function (user, columns) {
- var self = this;
- var row = [];
- var login = user.getLogin();
-
- row[0] = user.getName() + " " + user.getSurname() + " (" + login + ")";
- for (var i = 1; i < columns.length; i++) {
- var column = columns[i];
- if (column.privilegeType !== undefined) {
- if (column.privilegeType.getValueType() === "boolean") {
- var checked = '';
- if (user.hasPrivilege(column.privilegeType, self.getProject().getId())) {
- checked = 'checked';
- }
- row[i] = "<input type='checkbox' name='privilege-" + login + "' data='" + column.privilegeType.getName() + "' "
- + checked + "/>";
- } else {
- throw new Error("Unsupported type: " + column.privilegeType.getValueType());
- }
- }
- }
-
- row.push("<button name='saveUser' data='" + login + "'>SAVE</button>");
-
- return row;
-};
-
-EditProjectDialog.prototype.overlayToTableRow = function (overlay, users) {
- var row = [];
- var id = overlay.getId();
- var creatorSelect;
- if (overlay.getCreator() === "") {
- creatorSelect = "<select name='creator-" + id + "' value=''>";
- } else {
- creatorSelect = "<select name='creator-" + id + "'>";
- }
-
- creatorSelect += "<option value='' >---</option>";
- for (var i = 0; i < users.length; i++) {
- var selected = "";
- var user = users[i];
- if (overlay.getCreator() === user.getLogin()) {
- selected = "selected";
- } else {
- selected = "";
- }
-
- creatorSelect += "<option value='" + user.getLogin() + "' " + selected + ">" + user.getLogin() + "("
- + user.getName() + " " + user.getSurname() + ")</option>";
- }
- creatorSelect += "</select>";
-
- var checked = '';
- if (overlay.getPublicOverlay()) {
- checked = "checked";
- }
- var publicOverlayCheckbox = "<input type='checkbox' name='publicOverlay-" + id + "' " + checked + "/>";
-
- checked = '';
- if (overlay.isDefaultOverlay()) {
- checked = "checked";
- }
- var defaultOverlayCheckbox = "<input type='checkbox' name='defaultOverlay-" + id + "' " + checked + "/>";
-
- var downloadSourceButton;
- if (overlay.getInputDataAvailable()) {
- downloadSourceButton = "<button name='downloadSource' data='" + id + "'>"
- + "<span class='ui-icon ui-icon-arrowthickstop-1-s'></span>" + "</button>";
- } else {
- downloadSourceButton = "N/A";
- }
-
- row[0] = id;
- row[1] = "<input name='name-" + id + "' value='" + overlay.getName() + "'/>";
- row[2] = "<input name='description-" + id + "' value='" + overlay.getDescription() + "'/>";
- row[3] = publicOverlayCheckbox;
- row[4] = defaultOverlayCheckbox;
- row[5] = creatorSelect;
- row[6] = downloadSourceButton;
- row[7] = "<button name='saveOverlay' data='" + id + "'>SAVE</button>";
- row[8] = "<button name='removeOverlay' data='" + id + "'>REMOVE</button>";
-
- return row;
-};
-
-EditProjectDialog.prototype.destroy = function () {
- var self = this;
- var div = self.getElement();
- var usersTable = $("[name=usersTable]", self.getElement())[0];
- var overlaysTable = $("[name=overlaysTable]", self.getElement())[0];
- if ($.fn.DataTable.isDataTable(usersTable)) {
- $(usersTable).DataTable().destroy();
- }
- if ($.fn.DataTable.isDataTable(overlaysTable)) {
- $(overlaysTable).DataTable().destroy();
- }
-
- if ($(div).hasClass("ui-dialog-content")) {
- $(div).dialog("destroy");
- }
- if (self._addOverlayDialog !== undefined) {
- self._addOverlayDialog.destroy();
- delete self._addOverlayDialog;
- }
-};
-
-EditProjectDialog.prototype.open = function () {
- var self = this;
- var div = self.getElement();
- if (!$(div).hasClass("ui-dialog-content")) {
- $(div).dialog({
- title: self.getProject().getProjectId(),
- width: window.innerWidth / 2,
- height: window.innerHeight / 2
- });
- }
- $(div).dialog("open");
-};
-
-var prepareMiriamData = function (type, resource) {
- if (resource === "" || resource === undefined || resource === null) {
- return null;
- } else {
- return new Annotation({
- type: type,
- resource: resource
- });
- }
-};
-
-EditProjectDialog.prototype.onSaveClicked = function () {
- var self = this;
- var project = self.getProject();
- var element = self.getElement();
- project.setName($("[name='projectName']", element)[0].value);
- project.setVersion($("[name='projectVersion']", element)[0].value);
- project.setNotifyEmail($("[name='projectNotifyEmail']", element)[0].value);
- var organism = prepareMiriamData("TAXONOMY", $("[name='projectOrganism']", element)[0].value);
- project.setOrganism(organism);
- var disease = prepareMiriamData("MESH_2012", $("[name='projectDisease']", element)[0].value);
- project.setDisease(disease);
- return ServerConnector.updateProject(project);
-};
-EditProjectDialog.prototype.close = function () {
- var self = this;
- $(self.getElement()).dialog("close");
-};
-
-EditProjectDialog.prototype.saveOverlay = function (overlayId) {
- var self = this;
- var overlay = self._overlayById[overlayId];
- overlay.setName($("[name='name-" + overlayId + "']", self.getElement())[0].value);
- overlay.setDescription($("[name='description-" + overlayId + "']", self.getElement())[0].value);
- overlay.setPublicOverlay($("[name='publicOverlay-" + overlayId + "']", self.getElement())[0].checked);
- overlay.setDefaultOverlay($("[name='defaultOverlay-" + overlayId + "']", self.getElement())[0].checked);
- overlay.setCreator($("[name='creator-" + overlayId + "']", self.getElement())[0].value);
-
- return ServerConnector.updateOverlay(overlay);
-};
-
-EditProjectDialog.prototype.saveUser = function (login) {
- var self = this;
- var checkboxes = $("[name='privilege-" + login + "']", self.getElement());
- var privileges = {};
- for (var i = 0; i < checkboxes.length; i++) {
- var checkbox = checkboxes[i];
- var privilege = {};
- privilege[self.getProject().getId()] = checkbox.checked;
- privileges[$(checkbox).attr("data")] = privilege;
- }
-
- return ServerConnector.updateUserPrivileges({
- user: self._userByLogin[login],
- privileges: privileges
- });
-};
-
-EditProjectDialog.prototype.removeOverlay = function (overlayId) {
- var self = this;
- return ServerConnector.removeOverlay({
- overlayId: overlayId
- }).then(function () {
- return self.refreshOverlays();
- });
-};
-
-EditProjectDialog.prototype.openAddOverlayDialog = function () {
- var self = this;
- if (self._addOverlayDialog !== undefined) {
- self._addOverlayDialog.destroy();
- }
- self._addOverlayDialog = new AddOverlayDialog({
- project: self.getProject(),
- customMap: null,
- element: document.createElement("div")
- });
- self._addOverlayDialog.addListener("onAddOverlay", function () {
- return self.refreshOverlays();
- });
- return self._addOverlayDialog.init().then(function () {
- return self._addOverlayDialog.open();
- });
-};
-
-module.exports = EditProjectDialog;
+"use strict";
+
+/* exported logger */
+var Promise = require("bluebird");
+
+var AbstractGuiElement = require('../AbstractGuiElement');
+var AddOverlayDialog = require('../AddOverlayDialog');
+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'))();
+
+function EditProjectDialog(params) {
+ AbstractGuiElement.call(this, params);
+ var self = this;
+ $(self.getElement()).addClass("minerva-edit-project-dialog");
+
+ self.createGui();
+}
+
+EditProjectDialog.prototype = Object.create(AbstractGuiElement.prototype);
+EditProjectDialog.prototype.constructor = EditProjectDialog;
+
+EditProjectDialog.prototype.createGui = function () {
+ var self = this;
+ var element = self.getElement();
+
+ var tabDiv = Functions.createElement({
+ type: "div",
+ name: "tabView",
+ className: "tabbable boxed parentTabs"
+ });
+ 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"
+ });
+ tabDiv.appendChild(tabContentDiv);
+
+ self.createGeneralTab(tabMenuDiv, tabContentDiv);
+ self.createOverlaysTab(tabMenuDiv, tabContentDiv);
+ self.createMapsTab(tabMenuDiv, tabContentDiv);
+ self.createUsersTab(tabMenuDiv, tabContentDiv);
+};
+
+EditProjectDialog.prototype.createGeneralTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "GENERAL",
+ id: self.getProject().getProjectId() + "_general_tab",
+ content: self.createGeneralTabContent()
+ });
+
+};
+
+EditProjectDialog.prototype.addTab = function (params) {
+ var navLi = guiUtils.createTabMenuObject({
+ id: params.id,
+ name: params.name,
+ navigationBar: params.tabMenuDiv
+ });
+ params.tabMenuDiv.appendChild(navLi);
+
+ var contentDiv = guiUtils.createTabContentObject({
+ id: params.id,
+ navigationObject: navLi,
+ navigationBar: params.tabMenuDiv
+ });
+
+ if (params.content !== undefined) {
+ contentDiv.appendChild(params.content);
+ }
+
+ params.tabContentDiv.appendChild(contentDiv);
+};
+
+EditProjectDialog.prototype.createGeneralTabContent = function () {
+ var self = this;
+ var project = self.getProject();
+
+ var result = new Functions.createElement({
+ type: "div"
+ });
+
+ var table = new Functions.createElement({
+ type: "div",
+ style: "display:table"
+ });
+ result.appendChild(table);
+
+ var projectIdRow = new Functions.createElement({
+ type: "div",
+ style: "display:table-row"
+ });
+ table.appendChild(projectIdRow);
+ projectIdRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "ProjectId"
+ }));
+ projectIdRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: project.getProjectId()
+ }));
+
+ var nameRow = new Functions.createElement({
+ type: "div",
+ style: "display:table-row"
+ });
+ table.appendChild(nameRow);
+ nameRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "Name"
+ }));
+ nameRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "<input name='projectName' value='" + project.getName() + "'/>"
+ }));
+
+ var versionRow = new Functions.createElement({
+ type: "div",
+ style: "display:table-row"
+ });
+ table.appendChild(versionRow);
+ versionRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "Version"
+ }));
+ versionRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "<input name='projectVersion' value='" + project.getVersion() + "'/>"
+ }));
+
+ var diseaseRow = new Functions.createElement({
+ type: "div",
+ style: "display:table-row"
+ });
+ table.appendChild(diseaseRow);
+ diseaseRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "Disease"
+ }));
+ var disease = "";
+ if (project.getDisease() !== undefined) {
+ disease = project.getDisease().getResource();
+ }
+ diseaseRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "<input name='projectDisease' value='" + disease + "'/>"
+ }));
+
+ var organismRow = new Functions.createElement({
+ type: "div",
+ style: "display:table-row"
+ });
+ table.appendChild(organismRow);
+ organismRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "Organism"
+ }));
+ var organism = "";
+ if (project.getOrganism() !== undefined) {
+ organism = project.getOrganism().getResource();
+ }
+ organismRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "<input name='projectOrganism' value='" + organism + "'/>"
+ }));
+
+ var emailRow = new Functions.createElement({
+ type: "div",
+ style: "display:table-row"
+ });
+ table.appendChild(emailRow);
+ emailRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "Notify email"
+ }));
+ var email = "";
+ if (project.getNotifyEmail() !== undefined) {
+ email = project.getNotifyEmail();
+ }
+ emailRow.appendChild(new Functions.createElement({
+ type: "div",
+ style: "display:table-cell",
+ content: "<input name='projectNotifyEmail' value='" + email + "'/>"
+ }));
+
+ var menuRow = Functions.createElement({
+ type: "div",
+ className: "minerva-menu-row",
+ style: "display:table-row; margin:10px"
+ });
+ result.appendChild(menuRow);
+
+ var saveProjectButton = Functions.createElement({
+ type: "button",
+ name: "saveProject",
+ content: '<span class="ui-icon ui-icon-disk"></span> SAVE',
+ onclick: function () {
+ return self.onSaveClicked().then(function () {
+ return self.close();
+ }, GuiConnector.alert);
+ }
+ });
+ var cancelButton = Functions.createElement({
+ type: "button",
+ name: "cancelProject",
+ content: '<span class="ui-icon ui-icon-cancel"></span> CANCEL',
+ onclick: function () {
+ return self.close();
+ }
+ });
+ menuRow.appendChild(saveProjectButton);
+ menuRow.appendChild(cancelButton);
+
+ return result;
+
+};
+
+EditProjectDialog.prototype.createMapsTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "MAPS",
+ id: self.getProject().getProjectId() + "_maps_tab",
+ content: self.createMapsTabContent()
+ });
+};
+
+EditProjectDialog.prototype.createMapsTabContent = function () {
+ var self = this;
+ var result = Functions.createElement({
+ type: "div"
+ });
+ result.appendChild(self._createMapsTable());
+ return result;
+};
+
+EditProjectDialog.prototype._createMapsTable = function () {
+ var self = this;
+
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var mapsTable = Functions.createElement({
+ type: "table",
+ name: "mapsTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(mapsTable);
+
+ $(mapsTable).DataTable({
+ fnRowCallback: function (nRow, aData) {
+ nRow.setAttribute('id', "map-" + aData[0]);
+ },
+ columns: [{
+ title: 'Id'
+ }, {
+ title: 'Name'
+ }, {
+ title: 'Default center x'
+ }, {
+ title: 'Default center y'
+ }, {
+ title: 'Default zoom level'
+ }, {
+ title: 'Update'
+ }]
+ });
+
+ $(mapsTable).on("click", "[name='saveMap']", function () {
+ var button = this;
+ GuiConnector.showProcessing("Updating");
+ return self.saveMap($(button).attr("data")).then(function () {
+ GuiConnector.hideProcessing();
+ GuiConnector.info("Map updated successfully");
+ }, function (error) {
+ GuiConnector.hideProcessing();
+ GuiConnector.alert(error);
+ });
+ });
+
+ return result;
+};
+
+
+EditProjectDialog.prototype.createOverlaysTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "OVERLAYS",
+ id: self.getProject().getProjectId() + "_overlays_tab",
+ content: self.createOverlaysTabContent()
+ });
+};
+
+EditProjectDialog.prototype.createOverlaysTabContent = function () {
+ var self = this;
+ var result = Functions.createElement({
+ type: "div"
+ });
+ result.appendChild(self._createOverlayTable());
+ return result;
+};
+
+EditProjectDialog.prototype._createOverlayTable = function () {
+ var self = this;
+
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var overlaysTable = Functions.createElement({
+ type: "table",
+ name: "overlaysTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(overlaysTable);
+
+ $(overlaysTable).DataTable({
+ fnRowCallback: function (nRow, aData) {
+ nRow.setAttribute('id', "overlay-" + aData[0]);
+ },
+ columns: [{
+ title: 'Id'
+ }, {
+ title: 'Name'
+ }, {
+ title: 'Description'
+ }, {
+ title: 'Public'
+ }, {
+ title: 'Default'
+ }, {
+ title: 'Owner'
+ }, {
+ title: 'Data'
+ }, {
+ title: 'Update'
+ }, {
+ title: 'Remove'
+ }],
+ dom: '<"minerva-datatable-toolbar">frtip',
+ initComplete: function () {
+ $("div.minerva-datatable-toolbar", $(result)).html('<button name="addOverlay">Add overlay</button>');
+ }
+
+ });
+
+ $(overlaysTable).on("click", "[name='removeOverlay']", function () {
+ var button = this;
+ return self.removeOverlay($(button).attr("data")).then(null, GuiConnector.alert);
+ });
+
+ $(overlaysTable).on("click", "[name='saveOverlay']", function () {
+ var button = this;
+ GuiConnector.showProcessing("Updating");
+ return self.saveOverlay($(button).attr("data")).then(function () {
+ GuiConnector.hideProcessing();
+ GuiConnector.info("Overlay updated successfully");
+ }, function (error) {
+ GuiConnector.hideProcessing();
+ GuiConnector.alert(error);
+ });
+ });
+
+ $(overlaysTable).on("click", "[name='downloadSource']", function () {
+ var button = this;
+ return ServerConnector.getOverlaySourceDownloadUrl({
+ overlayId: $(button).attr("data")
+ }).then(function (url) {
+ return self.downloadFile(url);
+ }).then(null, GuiConnector.alert);
+ });
+
+ $(result).on("click", "[name='addOverlay']", function () {
+ return self.openAddOverlayDialog();
+ });
+
+ return result;
+};
+
+EditProjectDialog.prototype.createUsersTab = function (tabMenuDiv, tabContentDiv) {
+ var self = this;
+ self.addTab({
+ tabMenuDiv: tabMenuDiv,
+ tabContentDiv: tabContentDiv,
+ name: "USERS",
+ id: self.getProject().getProjectId() + "_users_tab",
+ content: self.createUsersTabContent()
+ });
+};
+
+EditProjectDialog.prototype.createUsersTabContent = function () {
+ var self = this;
+
+ var result = Functions.createElement({
+ type: "div",
+ style: "margin-top:10px;"
+ });
+
+ var usersTable = Functions.createElement({
+ type: "table",
+ name: "usersTable",
+ className: "display",
+ style: "width:100%"
+ });
+ result.appendChild(usersTable);
+
+ $(usersTable).on("click", "[name='saveUser']", function () {
+ var button = this;
+ GuiConnector.showProcessing("Updating");
+ return self.saveUser($(button).attr("data")).then(function () {
+ GuiConnector.hideProcessing();
+ GuiConnector.info("User updated successfully");
+ }, function (error) {
+ GuiConnector.hideProcessing();
+ GuiConnector.alert(error);
+ });
+ });
+
+ return result;
+};
+
+EditProjectDialog.prototype.createUserPrivilegeColumns = function () {
+ var self = this;
+
+ if (self._userPrivilegeColumns !== undefined) {
+ return Promise.resolve(self._userPrivilegeColumns);
+ }
+
+ return ServerConnector.getConfiguration().then(function (configuration) {
+ self._userPrivilegeColumns = [{
+ title: "Name"
+ }];
+ 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
+ });
+ }
+ }
+ self._userPrivilegeColumns.push({
+ "title": "Update"
+ });
+ return self._userPrivilegeColumns;
+ });
+
+};
+
+EditProjectDialog.prototype.init = function () {
+ var self = this;
+ return self.initUsersTab().then(function () {
+ return self.refreshUsers();
+ }).then(function () {
+ return self.refreshMaps();
+ }).then(function () {
+ return self.refreshOverlays();
+ }).then(function () {
+ $(window).trigger('resize');
+ });
+};
+
+EditProjectDialog.prototype.initUsersTab = function () {
+ var self = this;
+
+ var usersTable = $("[name=usersTable]", self.getElement())[0];
+
+ return self.createUserPrivilegeColumns().then(function (columns) {
+ $(usersTable).DataTable({
+ columns: columns
+ });
+ });
+};
+
+EditProjectDialog.prototype.refreshOverlays = function () {
+ var self = this;
+ return ServerConnector.getOverlays({
+ projectId: self.getProject().getProjectId()
+ }).then(function (overlays) {
+ return self.setOverlays(overlays);
+ });
+};
+
+EditProjectDialog.prototype.refreshMaps = function () {
+ var self = this;
+ return ServerConnector.getModels(self.getProject().getProjectId()).then(function (maps) {
+ return self.setMaps(maps);
+ });
+};
+
+EditProjectDialog.prototype.refreshUsers = function () {
+ var self = this;
+ return ServerConnector.getUsers().then(function (users) {
+ return self.setUsers(users);
+ });
+};
+
+EditProjectDialog.prototype.setOverlays = function (overlays) {
+ var self = this;
+ self._overlayById = [];
+ return ServerConnector.getUsers().then(function (users) {
+ var dataTable = $($("[name='overlaysTable']", self.getElement())[0]).DataTable();
+ var data = [];
+ for (var i = 0; i < overlays.length; i++) {
+ var overlay = overlays[i];
+ self._overlayById[overlay.getId()] = overlay;
+ var rowData = self.overlayToTableRow(overlay, users);
+ data.push(rowData);
+ }
+ dataTable.clear().rows.add(data).draw();
+ });
+};
+
+EditProjectDialog.prototype.setMaps = function (maps) {
+ var self = this;
+ self._mapsById = [];
+ var dataTable = $($("[name='mapsTable']", self.getElement())[0]).DataTable();
+ var data = [];
+ for (var i = 0; i < maps.length; i++) {
+ var map = maps[i];
+ self._mapsById[map.getId()] = map;
+ var rowData = self.mapToTableRow(map);
+ data.push(rowData);
+ }
+ dataTable.clear().rows.add(data).draw();
+};
+
+EditProjectDialog.prototype.setUsers = function (users) {
+ var self = this;
+ self._userByLogin = [];
+ return self.createUserPrivilegeColumns().then(function (columns) {
+ var dataTable = $($("[name='usersTable']", self.getElement())[0]).DataTable();
+ var data = [];
+ for (var i = 0; i < users.length; i++) {
+ var user = users[i];
+ self._userByLogin[user.getLogin()] = user;
+ var rowData = self.userToTableRow(user, columns);
+ data.push(rowData);
+ }
+ dataTable.clear().rows.add(data).draw();
+ });
+};
+
+EditProjectDialog.prototype.userToTableRow = function (user, columns) {
+ var self = this;
+ var row = [];
+ var login = user.getLogin();
+
+ row[0] = user.getName() + " " + user.getSurname() + " (" + login + ")";
+ for (var i = 1; i < columns.length; i++) {
+ var column = columns[i];
+ if (column.privilegeType !== undefined) {
+ if (column.privilegeType.getValueType() === "boolean") {
+ var checked = '';
+ if (user.hasPrivilege(column.privilegeType, self.getProject().getId())) {
+ checked = 'checked';
+ }
+ row[i] = "<input type='checkbox' name='privilege-" + login + "' data='" + column.privilegeType.getName() + "' "
+ + checked + "/>";
+ } else {
+ throw new Error("Unsupported type: " + column.privilegeType.getValueType());
+ }
+ }
+ }
+
+ row.push("<button name='saveUser' data='" + login + "'>SAVE</button>");
+
+ return row;
+};
+
+EditProjectDialog.prototype.overlayToTableRow = function (overlay, users) {
+ var row = [];
+ var id = overlay.getId();
+ var creatorSelect;
+ if (overlay.getCreator() === "") {
+ creatorSelect = "<select name='creator-" + id + "' value=''>";
+ } else {
+ creatorSelect = "<select name='creator-" + id + "'>";
+ }
+
+ creatorSelect += "<option value='' >---</option>";
+ for (var i = 0; i < users.length; i++) {
+ var selected = "";
+ var user = users[i];
+ if (overlay.getCreator() === user.getLogin()) {
+ selected = "selected";
+ } else {
+ selected = "";
+ }
+
+ creatorSelect += "<option value='" + user.getLogin() + "' " + selected + ">" + user.getLogin() + "("
+ + user.getName() + " " + user.getSurname() + ")</option>";
+ }
+ creatorSelect += "</select>";
+
+ var checked = '';
+ if (overlay.getPublicOverlay()) {
+ checked = "checked";
+ }
+ var publicOverlayCheckbox = "<input type='checkbox' name='publicOverlay-" + id + "' " + checked + "/>";
+
+ checked = '';
+ if (overlay.isDefaultOverlay()) {
+ checked = "checked";
+ }
+ var defaultOverlayCheckbox = "<input type='checkbox' name='defaultOverlay-" + id + "' " + checked + "/>";
+
+ var downloadSourceButton;
+ if (overlay.getInputDataAvailable()) {
+ downloadSourceButton = "<button name='downloadSource' data='" + id + "'>"
+ + "<span class='ui-icon ui-icon-arrowthickstop-1-s'></span>" + "</button>";
+ } else {
+ downloadSourceButton = "N/A";
+ }
+
+ row[0] = id;
+ row[1] = "<input name='name-" + id + "' value='" + overlay.getName() + "'/>";
+ row[2] = "<input name='description-" + id + "' value='" + overlay.getDescription() + "'/>";
+ row[3] = publicOverlayCheckbox;
+ row[4] = defaultOverlayCheckbox;
+ row[5] = creatorSelect;
+ row[6] = downloadSourceButton;
+ row[7] = "<button name='saveOverlay' data='" + id + "'>SAVE</button>";
+ row[8] = "<button name='removeOverlay' data='" + id + "'>REMOVE</button>";
+
+ return row;
+};
+
+function getValueOrEmpty(value) {
+ if (value !== undefined && value !== null) {
+ return value;
+ } else {
+ return "";
+ }
+}
+
+EditProjectDialog.prototype.mapToTableRow = function (map, users) {
+ var row = [];
+ var id = map.getId();
+ var centerX = getValueOrEmpty(map.getDefaultCenterX());
+ var centerY = getValueOrEmpty(map.getDefaultCenterY());
+ var zoomLevel = getValueOrEmpty(map.getDefaultZoomLevel());
+ row[0] = id;
+ row[1] = map.getName();
+ row[2] = "<input name='defaultCenterX-" + id + "' value='" + centerX + "'/>";
+ row[3] = "<input name='defaultCenterY-" + id + "' value='" + centerY + "'/>";
+ row[4] = "<input name='defaultZoomLevel-" + id + "' value='" + zoomLevel + "'/>";
+ row[5] = "<button name='saveMap' data='" + id + "'>SAVE</button>";
+
+ return row;
+};
+
+EditProjectDialog.prototype.destroy = function () {
+ var self = this;
+ var div = self.getElement();
+ var usersTable = $("[name=usersTable]", self.getElement())[0];
+ var overlaysTable = $("[name=overlaysTable]", self.getElement())[0];
+ var mapsTable = $("[name=mapsTable]", self.getElement())[0];
+ if ($.fn.DataTable.isDataTable(usersTable)) {
+ $(usersTable).DataTable().destroy();
+ }
+ if ($.fn.DataTable.isDataTable(overlaysTable)) {
+ $(overlaysTable).DataTable().destroy();
+ }
+ if ($.fn.DataTable.isDataTable(mapsTable)) {
+ $(mapsTable).DataTable().destroy();
+ }
+
+ if ($(div).hasClass("ui-dialog-content")) {
+ $(div).dialog("destroy");
+ }
+ if (self._addOverlayDialog !== undefined) {
+ self._addOverlayDialog.destroy();
+ delete self._addOverlayDialog;
+ }
+};
+
+EditProjectDialog.prototype.open = function () {
+ var self = this;
+ var div = self.getElement();
+ if (!$(div).hasClass("ui-dialog-content")) {
+ $(div).dialog({
+ title: self.getProject().getProjectId(),
+ width: window.innerWidth / 2,
+ height: window.innerHeight / 2
+ });
+ }
+ $(div).dialog("open");
+};
+
+var prepareMiriamData = function (type, resource) {
+ if (resource === "" || resource === undefined || resource === null) {
+ return null;
+ } else {
+ return new Annotation({
+ type: type,
+ resource: resource
+ });
+ }
+};
+
+EditProjectDialog.prototype.onSaveClicked = function () {
+ var self = this;
+ var project = self.getProject();
+ var element = self.getElement();
+ project.setName($("[name='projectName']", element)[0].value);
+ project.setVersion($("[name='projectVersion']", element)[0].value);
+ project.setNotifyEmail($("[name='projectNotifyEmail']", element)[0].value);
+ var organism = prepareMiriamData("TAXONOMY", $("[name='projectOrganism']", element)[0].value);
+ project.setOrganism(organism);
+ var disease = prepareMiriamData("MESH_2012", $("[name='projectDisease']", element)[0].value);
+ project.setDisease(disease);
+ return ServerConnector.updateProject(project);
+};
+EditProjectDialog.prototype.close = function () {
+ var self = this;
+ $(self.getElement()).dialog("close");
+};
+
+EditProjectDialog.prototype.saveOverlay = function (overlayId) {
+ var self = this;
+ var overlay = self._overlayById[overlayId];
+ overlay.setName($("[name='name-" + overlayId + "']", self.getElement())[0].value);
+ overlay.setDescription($("[name='description-" + overlayId + "']", self.getElement())[0].value);
+ overlay.setPublicOverlay($("[name='publicOverlay-" + overlayId + "']", self.getElement())[0].checked);
+ overlay.setDefaultOverlay($("[name='defaultOverlay-" + overlayId + "']", self.getElement())[0].checked);
+ overlay.setCreator($("[name='creator-" + overlayId + "']", self.getElement())[0].value);
+
+ return ServerConnector.updateOverlay(overlay);
+};
+
+EditProjectDialog.prototype.saveMap = function (mapId) {
+ var self = this;
+ var map = self._mapsById[mapId];
+ map.setDefaultCenterX($("[name='defaultCenterX-" + mapId + "']", self.getElement())[0].value);
+ map.setDefaultCenterY($("[name='defaultCenterY-" + mapId + "']", self.getElement())[0].value);
+ map.setDefaultZoomLevel($("[name='defaultZoomLevel-" + mapId + "']", self.getElement())[0].value);
+
+ return ServerConnector.updateModel({projectId: self.getProject().getProjectId(), model: map});
+};
+
+EditProjectDialog.prototype.saveUser = function (login) {
+ var self = this;
+ var checkboxes = $("[name='privilege-" + login + "']", self.getElement());
+ var privileges = {};
+ for (var i = 0; i < checkboxes.length; i++) {
+ var checkbox = checkboxes[i];
+ var privilege = {};
+ privilege[self.getProject().getId()] = checkbox.checked;
+ privileges[$(checkbox).attr("data")] = privilege;
+ }
+
+ return ServerConnector.updateUserPrivileges({
+ user: self._userByLogin[login],
+ privileges: privileges
+ });
+};
+
+EditProjectDialog.prototype.removeOverlay = function (overlayId) {
+ var self = this;
+ return ServerConnector.removeOverlay({
+ overlayId: overlayId
+ }).then(function () {
+ return self.refreshOverlays();
+ });
+};
+
+EditProjectDialog.prototype.openAddOverlayDialog = function () {
+ var self = this;
+ if (self._addOverlayDialog !== undefined) {
+ self._addOverlayDialog.destroy();
+ }
+ self._addOverlayDialog = new AddOverlayDialog({
+ project: self.getProject(),
+ customMap: null,
+ element: document.createElement("div")
+ });
+ self._addOverlayDialog.addListener("onAddOverlay", function () {
+ return self.refreshOverlays();
+ });
+ return self._addOverlayDialog.init().then(function () {
+ return self._addOverlayDialog.open();
+ });
+};
+
+module.exports = EditProjectDialog;
diff --git a/frontend-js/src/main/js/map/AbstractCustomMap.js b/frontend-js/src/main/js/map/AbstractCustomMap.js
index d67620f0bd..78f7c7216d 100644
--- a/frontend-js/src/main/js/map/AbstractCustomMap.js
+++ b/frontend-js/src/main/js/map/AbstractCustomMap.js
@@ -1,1053 +1,1068 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var logger = require('../logger');
-var functions = require('../Functions');
-
-var AliasInfoWindow = require('./window/AliasInfoWindow');
-var AliasSurface = require('./surface/AliasSurface');
-var GuiConnector = require('../GuiConnector');
-var IdentifiedElement = require('./data/IdentifiedElement');
-var ObjectWithListeners = require('../ObjectWithListeners');
-var PointInfoWindow = require('./window/PointInfoWindow');
-var ReactionInfoWindow = require('./window/ReactionInfoWindow');
-var ReactionSurface = require('./surface/ReactionSurface');
-
-var MarkerSurfaceCollection = require('./marker/MarkerSurfaceCollection');
-
-/**
- * Default constructor.
- */
-function AbstractCustomMap(model, options) {
- // call super constructor
- ObjectWithListeners.call(this);
-
- if (model === undefined) {
- throw Error("Model must be defined");
- }
-
- this.setElement(options.getElement());
- this.setConfiguration(options.getConfiguration());
-
- this.setModel(model);
-
- // this array contains elements that are presented on a specific layout (set
- // of google map object representing lines/areas that are associated with
- // layout)
- this.selectedLayoutOverlays = [];
-
- // following fields are used in conversion between x,y coordinates and lat,lng
- // coordinates
- this.pixelOrigin_ = new google.maps.Point(this.getTileSize() / 2, this.getTileSize() / 2);
- this.pixelsPerLonDegree_ = this.getTileSize() / 360;
- this.pixelsPerLonRadian_ = this.getTileSize() / (2 * Math.PI);
-
- /* jshint bitwise: false */
- this.zoomFactor = this.getPictureSize() / (this.getTileSize() / (1 << this.getMinZoom()));
-
- // array with info windows for Marker pointing to aliases
- this._aliasInfoWindow = [];
-
- // array with info windows for Marker pointing to points
- this._pointInfoWindow = [];
-
- // array with info windows for reactions
- this._reactionInfoWindow = [];
-
- this._markerSurfaceCollection = new MarkerSurfaceCollection({map: this});
-
- // this is google.maps.drawing.DrawingManager that will allow user to draw
- // elements in the client
- this._drawingManager = null;
-
- // this is the polygon that was selected (clicked) last time on the map
- this._selectedArea = null;
-
- // markers should be optimized by default,
- // however, for testing purpose this function could be turned of by javascript
- // the other possibility is that it should be off in the touch mode
- // (bigButtons=true)
- this._markerOptimization = options.isMarkerOptimization();
-
- this._bigLogo = options.isBigLogo();
- this._customTouchInterface = options.isCustomTouchInterface();
-
- this.setDebug(options.isDebug());
-}
-
-// define super constructor
-AbstractCustomMap.prototype = Object.create(ObjectWithListeners.prototype);
-AbstractCustomMap.prototype.constructor = AbstractCustomMap;
-
-
-AbstractCustomMap.prototype.getMarkerSurfaceCollection = function () {
- return this._markerSurfaceCollection;
-};
-/**
- * Assigns layouts with images to the google map (which set of images should be
- * used by google maps api for which layout).
- *
- */
-AbstractCustomMap.prototype.setupLayouts = function () {
- for (var i = 0; i < this.getLayouts().length; i++) {
- var layout = this.getLayouts()[i];
- var typeOptions = this.createTypeOptions(layout);
- var mapType = new google.maps.ImageMapType(typeOptions);
- this.getGoogleMap().mapTypes.set(layout.getId().toString(), mapType);
- }
- this.getGoogleMap().setMapTypeId(this.getLayouts()[0].getId().toString());
-};
-
-/**
- * Creates general google maps options used in this map.
- *
- */
-AbstractCustomMap.prototype.createMapOptions = function () {
- var self = this;
-
- var centerPoint = this.getModel().getCenterLatLng();
-
- // if we have coordinate data stored in session then restore it
- var point = ServerConnector.getSessionData(self.getProject()).getCenter(self.getModel());
- if (point !== undefined) {
- centerPoint = self.fromPointToLatLng(point);
- }
-
- var result = {
- center: centerPoint,
- rotateControl: true,
- panControl: true,
- mapTypeControl: false,
- zoom: this.getMinZoom(),
- streetViewControl: false,
-
- panControlOptions: {
- position: google.maps.ControlPosition.LEFT_TOP
- },
- zoomControlOptions: {
- style: google.maps.ZoomControlStyle.LARGE,
- position: google.maps.ControlPosition.LEFT_TOP
- }
-
- };
- return result;
-};
-
-/**
- * Create google maps configuration options object for a specific layout.
- *
- * @param param
- * object with information about layout
- */
-AbstractCustomMap.prototype.createTypeOptions = function (param) {
- var self = this;
- var result = {
- // this is a function that will retrieve valid url to png images for
- // tiles on different zoom levels
- getTileUrl: function (coord, zoom) {
- // we have 1 tile on self.getConfiguration().MIN_ZOOM and
- // therefore must limit tails according to this
- /* jshint bitwise: false */
- var tileRange = 1 << (zoom - self.getMinZoom());
- if (coord.y < 0 || coord.y >= tileRange || coord.x < 0 || coord.x >= tileRange) {
- return null;
- }
- var addr = "../map_images/" + param.getDirectory() + "/" + zoom + "/" + coord.x + "/" + coord.y + ".PNG";
- return addr;
- },
- tileSize: new google.maps.Size(this.getTileSize(), this.getTileSize()),
- maxZoom: this.getMaxZoom(),
- minZoom: this.getMinZoom(),
- radius: 360,
- name: param.name
- };
- return result;
-};
-
-/**
- * Sets maximum zoom level on google map.
- *
- */
-AbstractCustomMap.prototype.setMaxZoomLevel = function () {
- this.getGoogleMap().setZoom(this.getMaxZoom());
-};
-
-/**
- * Returns mouse coordinate on the map in lat,lng system.
- *
- */
-AbstractCustomMap.prototype.getMouseLatLng = function () {
- // this method is tricky, the main problem is how to map mouse coordinate to
- // google map
- // to do that we need a point of reference in both systems (x,y and lat,lng)
- // this will be center of the map that is currently visible
- // next, we will have to find distance from this point in x,y coordinates and
- // transform it to lat,lng
-
- var self = this;
- // center point visible on the map
- var latLngCoordinates = self.getGoogleMap().getCenter();
- var point = self.fromLatLngToPoint(latLngCoordinates);
-
- // this is magic :)
- // find offset of the div where google map is located related to top left
- // corner of the browser
- var el = self.getGoogleMap().getDiv();
- for (var lx = 0, ly = 0; el !== null && el !== undefined; lx += el.offsetLeft, ly += el.offsetTop, el = el.offsetParent) {
- }
-
- var offset = {
- x: lx,
- y: ly
- };
-
- var center = {
- x: self.getGoogleMap().getDiv().offsetWidth / 2,
- y: self.getGoogleMap().getDiv().offsetHeight / 2
- };
-
- // and now find how far from center point we are (in pixels)
- var relativeDist = {
- x: (GuiConnector.xPos - offset.x - center.x),
- y: (GuiConnector.yPos - offset.y - center.y)
- };
-
- // transform pixels into x,y distance
- var pointDist = self.fromPixelsToPoint(relativeDist, self.getGoogleMap().getZoom());
-
- // now we have offset in x,y and center point on the map in x,y, so we have
- // final position in x,y
- var newCoordinates = new google.maps.Point(point.x + pointDist.x, point.y + pointDist.y);
-
- // change it to lat,lng
- var latLngResult = self.fromPointToLatLng(newCoordinates);
-
- return latLngResult;
-};
-
-/**
- * Transform distance (coordinates) in pixels into x,y distance on the map.
- *
- * @param pixels
- * x,y distance in pixels
- * @param zoomLevel
- * at which zoom level this pixels where measured
- *
- */
-AbstractCustomMap.prototype.fromPixelsToPoint = function (pixels, zoomLevel) {
- var zoomScale = this.getPictureSize() / (Math.pow(2, zoomLevel - this.getMinZoom()) * this.getTileSize());
- var pointX = pixels.x * zoomScale;
- var pointY = pixels.y * zoomScale;
- return new google.maps.Point(pointX, pointY);
-};
-
-/**
- * Transforms coordinates on the map from google.maps.LatLng to
- * google.maps.Point
- *
- * @param latLng
- * in lat,lng format
- * @param coordinates in x,y format
- *
- */
-AbstractCustomMap.prototype.fromLatLngToPoint = function (latLng) {
- var me = this;
- var point = new google.maps.Point(0, 0);
- var origin = me.pixelOrigin_;
-
- point.x = origin.x + latLng.lng() * me.pixelsPerLonDegree_;
-
- // Truncating to 0.9999 effectively limits latitude to 89.189. This is
- // about a third of a tile past the edge of the world tile.
- var siny = functions.bound(Math.sin(functions.degreesToRadians(latLng.lat())), -0.9999, 0.9999);
- point.y = origin.y + 0.5 * Math.log((1 + siny) / (1 - siny)) * -me.pixelsPerLonRadian_;
-
- // rescale the point (all computations are done assuming that we work on
- // TILE_SIZE square)
- point.x *= me.zoomFactor;
- point.y *= me.zoomFactor;
- return point;
-};
-
-/**
- * Transforms coordinates on the map from google.maps.Point to
- * google.maps.LatLng
- *
- * @param point
- * coordinates in standard x,y format
- * @return coordinates in lat,lng format
- */
-AbstractCustomMap.prototype.fromPointToLatLng = function (point) {
- var me = this;
-
- // rescale the point (all computations are done assuming that we work on
- // TILE_SIZE square)
- var p = new google.maps.Point(point.x / me.zoomFactor, point.y / me.zoomFactor);
- var origin = me.pixelOrigin_;
- var lng = (p.x - origin.x) / me.pixelsPerLonDegree_;
- var latRadians = (p.y - origin.y) / -me.pixelsPerLonRadian_;
- var lat = functions.radiansToDegrees(2 * Math.atan(Math.exp(latRadians)) - Math.PI / 2);
- return new google.maps.LatLng(lat, lng);
-};
-
-/**
- * Transforms google.maps.LatLng to tile coordinate (for instance on which tile
- * mouse clicked).
- *
- *
- * @param latLng
- * coordinates in latlng format
- * @param z
- * zoom level at which we want to find coordinates of tile
- * @return coordinates of a tile
- */
-AbstractCustomMap.prototype.latLngToTile = function (latLng, z) {
- var worldCoordinate = this.fromLatLngToPoint(latLng);
- var pixelCoordinate = new google.maps.Point(worldCoordinate.x * Math.pow(2, z), worldCoordinate.y * Math.pow(2, z));
- var tileCoordinate = new google.maps.Point(Math.floor(pixelCoordinate.x / this.getTileSize()), Math
- .floor(pixelCoordinate.y / this.getTileSize()));
- return tileCoordinate;
-};
-
-/**
- * Register events responsible for click events
- */
-AbstractCustomMap.prototype.registerMapClickEvents = function () {
-
- // find top map (CustomMap)
- //
- var customMap = this.getTopMap();
-
- var self = this;
-
- // search event
- google.maps.event.addListener(this.getGoogleMap(), 'click', function (mouseEvent) {
- var point = self.fromLatLngToPoint(mouseEvent.latLng);
- var searchDb = customMap.getOverlayByName('search');
- if (searchDb !== undefined) {
- return searchDb.searchByCoordinates({
- modelId: self.getModel().getId(),
- coordinates: point,
- zoom: self.getGoogleMap().getZoom()
- }).then(null, GuiConnector.alert);
- } else {
- logger.warn("Search is impossible because search db is not present");
- }
- });
-
- // select last clicked map
- google.maps.event.addListener(this.getGoogleMap(), 'click', function (mouseEvent) {
- customMap.setActiveSubmapId(self.getId());
- customMap.setActiveSubmapClickCoordinates(self.fromLatLngToPoint(mouseEvent.latLng));
- });
-
- // select last clicked map
- google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function (mouseEvent) {
- customMap.setActiveSubmapId(self.getId());
- customMap.setActiveSubmapClickCoordinates(self.fromLatLngToPoint(mouseEvent.latLng));
- });
-
- // prepare for image export
- google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function () {
- var bounds = self.getGoogleMap().getBounds();
- var polygon = "";
-
- var ne = bounds.getNorthEast();
- var sw = bounds.getSouthWest();
-
- var westLng = sw.lng();
- var eastLng = ne.lng();
-
- if (westLng > 0) {
- westLng = -180;
- }
- if (eastLng - westLng > 90) {
- eastLng = -90;
- } else if (eastLng > -90) {
- eastLng = -90;
- }
-
- polygon += ne.lat() + "," + westLng + ";";
- polygon += ne.lat() + "," + eastLng + ";";
- polygon += sw.lat() + "," + eastLng + ";";
- polygon += sw.lat() + "," + westLng + ";";
- self.getTopMap().setSelectedPolygon(polygon);
- });
-
- // context menu event
- google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function () {
- self.getTopMap().getContextMenu().open(GuiConnector.xPos, GuiConnector.yPos, new Date().getTime());
- });
-};
-
-/**
- * It toggle drawing manager used on the map: if it's on then it will turn it
- * off, if it's off it will turn it on
- *
- */
-AbstractCustomMap.prototype._turnOnOffDrawing = function () {
- if (this.isDrawingOn()) {
- this.turnOffDrawing();
- } else {
- this.turnOnDrawing();
- }
-};
-
-/**
- * Checks if the drawing manager for the map is on.
- *
- */
-AbstractCustomMap.prototype.isDrawingOn = function () {
- return this._drawingManager !== null;
-};
-
-/**
- * Turns on drawing manager on the map.
- */
-AbstractCustomMap.prototype.turnOnDrawing = function () {
- if (this.isDrawingOn()) {
- logger.warn("Trying to turn on drawing manager, but it is already available.");
- return;
- }
- var customMap = this.getTopMap();
- var self = this;
- this._drawingManager = new google.maps.drawing.DrawingManager({
- drawingMode: google.maps.drawing.OverlayType.MARKER,
- drawingControl: true,
- drawingControlOptions: {
- position: google.maps.ControlPosition.TOP_CENTER,
- drawingModes: [google.maps.drawing.OverlayType.POLYGON]
- },
- markerOptions: {
- icon: 'images/beachflag.png'
- },
- circleOptions: {
- fillColor: '#ffff00',
- fillOpacity: 1,
- strokeWeight: 5,
- clickable: false,
- editable: true,
- zIndex: 1
- }
- });
- this._drawingManager.setMap(this.getGoogleMap());
- this._drawingManager.setDrawingMode(google.maps.drawing.OverlayType.POLYGON);
-
- google.maps.event.addListener(this._drawingManager, 'overlaycomplete', function (e) {
- if (e.type !== google.maps.drawing.OverlayType.MARKER) {
- // Switch back to non-drawing mode after drawing a shape.
- self._drawingManager.setDrawingMode(null);
-
- // Add an event listener that selects the newly-drawn shape when the
- // user mouses down on it.
- var newShape = e.overlay;
- newShape.type = e.type;
- google.maps.event.addListener(newShape, 'rightclick', function (e) {
- // select map that was clicked
- customMap.setActiveSubmapId(self.getId());
-
- self.setSelectedArea(newShape);
- newShape.position = e.latLng;
-
- self.getTopMap().setSelectedPolygon(self.areaToString(newShape));
-
- self.getTopMap().getSelectionContextMenu().open(GuiConnector.xPos, GuiConnector.yPos, new Date().getTime());
- });
- }
- });
-
-};
-
-/**
- * Sets selectedArea on this map.
- *
- */
-AbstractCustomMap.prototype.setSelectedArea = function (area) {
- this._selectedArea = area;
-};
-
-/**
- * Returns selectedArea on this map.
- *
- */
-AbstractCustomMap.prototype.getSelectedArea = function () {
- return this._selectedArea;
-};
-
-/**
- * Transforms google.maps.Polygon into string with coordinates.
- *
- */
-AbstractCustomMap.prototype.areaToString = function (area) {
- var len = area.getPath().length;
- var path = area.getPath();
- var res = "";
- for (var i = 0; i < len; i++) {
- var latLng = path.getAt(i);
- res += latLng.lat() + "," + latLng.lng() + ";";
- }
- return res;
-};
-
-/**
- * Removes selected area (polygon) from the map.
- */
-AbstractCustomMap.prototype._removeSelection = function () {
- if (this._selectedArea) {
- this._selectedArea.setMap(null);
- this._selectedArea = null;
- } else {
- logger.warn("Cannot remove selected area. No area was selected");
- }
-};
-
-/**
- * Turns off drawing manager on the map.
- */
-AbstractCustomMap.prototype.turnOffDrawing = function () {
- if (this.isDrawingOn()) {
- this._drawingManager.setMap(null);
- this._drawingManager = null;
- } else {
- logger.warn("Trying to turn off drawing manager, but it is not available.");
- }
-};
-
-/**
- * Returns top map. TODO implementation of this function should be probably
- * moved to Submap and CustomMap classes and here only abstract function
- * definition
- *
- * @returns {CustomMap}
- */
-AbstractCustomMap.prototype.getTopMap = function () {
- logger.fatal("Not implemented");
-};
-
-/**
- * Method that should be called when number of layouts to visualize changed to
- * modify boundaries of the elements to visualize. When few layouts are
- * visualized at the same time then index contains information where this new
- * layout is placed in the list (starting from 0) and length contains
- * information how many layouts we visualize in total.
- *
- * @param layoutId
- * identifier of a layout
- * @param index
- * when visualizing more than one layout at the same time index
- * contains information at which position in the list this layout is
- * placed
- * @param length
- * number of layouts that are currently visualized
- */
-AbstractCustomMap.prototype._resizeSelectedLayout = function (layoutId, index, length) {
- var self = this;
- return new Promise(function (resolve) {
- // if map is not initialized then don't perform this operation
- if (!self.initialized) {
- logger.debug("Model " + self.getId() + " not initialized");
- resolve();
- }
- logger.debug("Resize layout: " + layoutId);
- // start ratio
- var startX = index * (1.0 / length);
- // end ratio
- var endX = (index + 1) * (1.0 / length);
-
- for (var i = 0; i < self.selectedLayoutOverlays[layoutId].length; i++) {
- self.selectedLayoutOverlays[layoutId][i].setBoundsForAlias(startX, endX);
- }
- resolve();
- });
-};
-
-/**
- * Shows all elements from a given layout. When few layouts are visualized at
- * the same time then index contains information where this new layout is placed
- * in the list (starting from 0) and length contains information how many
- * layouts we visualize in total.
- *
- * @param layoutId
- * identifier of a layout
- * @param index
- * when visualizing more than one layout at the same time index
- * contains information at which position in the list this layout is
- * placed
- * @param length
- * number of layouts that are currently visualized
- */
-AbstractCustomMap.prototype._showSelectedLayout = function (layoutId, index, length) {
- var self = this;
- // if map is not initialized then don't perform this operation
- return new Promise(function (resolve, reject) {
- if (!self.initialized) {
- logger.debug("Model " + self.getId() + " not initialized");
- resolve();
- return;
- } else {
- logger.debug("Showing model " + self.getId());
- }
-
- self.selectedLayoutOverlays[layoutId] = [];
-
- // start ratio
- var startX = index * (1.0 / length);
- // end ratio
- var endX = (index + 1) * (1.0 / length);
-
- var layoutAliases;
- var layoutReactions;
-
- return self.getTopMap().getModel().getLayoutDataById(layoutId).then(function (layout) {
- layoutAliases = layout.getAliases();
- layoutReactions = layout.getReactions();
-
- var identifiedElements = [];
- var i;
- for (i = 0; i < layoutAliases.length; i++) {
- if (layoutAliases[i].getModelId() === self.getId()) {
- identifiedElements.push(new IdentifiedElement(layoutAliases[i]));
- }
- }
- var reactionIds = [];
- for (i = 0; i < layoutReactions.length; i++) {
- if (layoutReactions[i].getModelId() === self.getId()) {
- identifiedElements.push(new IdentifiedElement(layoutReactions[i]));
- }
- }
- return self.getModel().getByIdentifiedElements(identifiedElements, false);
- }).then(function () {
- return Promise.each(layoutAliases, function (layoutAlias) {
- if (layoutAlias.getModelId() === self.getId()) {
- var surface;
- var element;
- return self.getModel().getAliasById(layoutAlias.getId()).then(function (aliasData) {
- element = new IdentifiedElement(aliasData);
- return AliasSurface.create({
- overlayAlias: layoutAlias,
- alias: aliasData,
- map: self,
- startX: startX,
- endX: endX,
- onClick: [function () {
- return self._openInfoWindowForAlias(aliasData, surface.getGoogleMarker());
- }, function () {
- return self.getTopMap().callListeners("onBioEntityClick", element);
- }]
- });
- }).then(function (result) {
- surface = result;
- self.selectedLayoutOverlays[layoutId].push(surface);
- });
- }
- });
- }).then(function () {
- return Promise.each(layoutReactions, function (layoutReaction) {
- if (layoutReaction.getModelId() === self.getId()) {
- return self.getModel().getReactionById(layoutReaction.getId()).then(function (reactionData) {
- var surface;
- var element = new IdentifiedElement(reactionData);
- return ReactionSurface.create({
- layoutReaction: layoutReaction,
- reaction: reactionData,
- map: self,
- onClick: [function () {
- return self._openInfoWindowForReaction(reactionData, surface.getGoogleMarker());
- }, function () {
- return self.getTopMap().callListeners("onBioEntityClick", element);
- }],
- customized: (length === 1)
- }).then(function (result) {
- surface = result;
- self.selectedLayoutOverlays[layoutId].push(surface);
- surface.show();
- });
- });
- }
- });
- }).then(function () {
- resolve();
- }).then(null, reject);
- });
-};
-
-/**
- * Hides all elements from layout.
- *
- * @param layoutId
- * identifier of a layout
- */
-AbstractCustomMap.prototype._hideSelectedLayout = function (layoutId) {
- // if map is not initialized then don't perform this operation
- if (!this.initialized) {
- logger.debug("Model " + this.getId() + " not initialized");
- return;
- }
- for (var i = 0; i < this.selectedLayoutOverlays[layoutId].length; i++) {
- this.selectedLayoutOverlays[layoutId][i].setMap(null);
- }
- this.selectedLayoutOverlays[layoutId] = [];
-};
-
-/**
- * Opens {@link AliasInfoWindow} for given alias.
- *
- * @param aliasId
- * identifier of the alias
- */
-AbstractCustomMap.prototype._openInfoWindowForAlias = function (alias, googleMarker) {
- var self = this;
-
- var infoWindow = this.getAliasInfoWindowById(alias.getId());
- if (infoWindow !== null && infoWindow !== undefined) {
- if (!infoWindow.isOpened()) {
- infoWindow.open(googleMarker);
- } else {
- logger.warn("Info window for alias: " + alias.getId() + " is already opened");
- }
- return Promise.resolve(infoWindow);
- } else {
- self._aliasInfoWindow[alias.getId()] = new AliasInfoWindow({
- alias: alias,
- map: self,
- marker: googleMarker,
- });
- return self._aliasInfoWindow[alias.getId()].init();
- }
-};
-
-/**
- * Returns promise of a list of {@link LayoutAlias} information for a given
- * {@link Alias} in all currently visualized layouts.
- *
- * @param aliasId
- * identifier of the {@link Alias}
- * @returns promise of an {Array} with list of {@link LayoutAlias} information
- * for a given {@link Alias} in all currently visualized layouts
- */
-AbstractCustomMap.prototype.getAliasVisibleLayoutsData = function (aliasId) {
- var self = this;
- return self.getTopMap().getVisibleDataOverlays().then(function (visibleDataOverlays) {
- var result = [];
- for (var i = 0; i < visibleDataOverlays.length; i++) {
- var layout = visibleDataOverlays[i];
- result.push(layout.getFullAliasById(aliasId));
- }
- return Promise.all(result);
- });
-};
-
-/**
- * Refresh content of all {@link AliasInfoWindow} in this map.
- */
-AbstractCustomMap.prototype._refreshInfoWindows = function () {
- var promises = [];
- for (var key in this._pointInfoWindow) {
- if (this._pointInfoWindow.hasOwnProperty(key)) {
- if (this._pointInfoWindow[key].isOpened()) {
- promises.push(this._pointInfoWindow[key].update());
- }
- }
- }
- for (var aliasKey in this._aliasInfoWindow) {
- if (this._aliasInfoWindow.hasOwnProperty(aliasKey)) {
- if (this._aliasInfoWindow[aliasKey].isOpened()) {
- promises.push(this._aliasInfoWindow[aliasKey].update());
- }
- }
- }
- return Promise.all(promises);
-};
-
-
-/**
- * Opens {@link ReactionInfoWindow} for given reaction identifier.
- *
- * @param reactionId
- * reaction identifier
- */
-AbstractCustomMap.prototype._openInfoWindowForReaction = function (reaction, googleMarker) {
- var infoWindow = this.getReactionInfoWindowById(reaction.getId());
- var self = this;
- if (infoWindow !== null && infoWindow !== undefined) {
- if (!infoWindow.isOpened()) {
- infoWindow.open(googleMarker);
- } else {
- logger.warn("Info window for reaction: " + reaction.getId() + " is already opened");
- }
- return Promise.resolve(infoWindow);
- } else {
- return self.getModel().getReactionById(reaction.getId()).then(function (reaction) {
- infoWindow = new ReactionInfoWindow({
- reaction: reaction,
- map: self,
- marker: googleMarker,
- });
- self._reactionInfoWindow[reaction.getId()] = infoWindow;
- return infoWindow.init();
- }).then(function () {
- return infoWindow;
- });
- }
-};
-
-AbstractCustomMap.prototype._openInfoWindowForPoint = function (pointData, googleMarker) {
- var self = this;
-
- var infoWindow = this.getPointInfoWindowById(pointData.getId());
- if (infoWindow !== null && infoWindow !== undefined) {
- if (!infoWindow.isOpened()) {
- infoWindow.open(googleMarker);
- } else {
- logger.warn("Info window for point: " + pointData.getId() + " is already opened");
- }
- } else {
- infoWindow = new PointInfoWindow({
- point: pointData,
- map: self,
- marker: googleMarker,
- });
- this._pointInfoWindow[pointData.getId()] = infoWindow;
- }
- return Promise.resolve(infoWindow);
-};
-
-/**
- * Opens {@link AbstractInfoWindow} for a marker.
- *
- * @param marker
- * marker for which we are opening window
- */
-AbstractCustomMap.prototype.returnInfoWindowForIdentifiedElement = function (element) {
- var markerId = element.getId();
- if (element.getType() === "ALIAS") {
- return this.getAliasInfoWindowById(markerId);
- } else if (element.getType() === "POINT") {
- return this.getPointInfoWindowById(markerId);
- } else if (element.getType() === "REACTION") {
- return this.getReactionInfoWindowById(markerId);
- } else {
- throw new Error("Unknown marker type: ", element);
- }
-};
-
-/**
- * Returns identifier.
- *
- * @returns identifier
- */
-AbstractCustomMap.prototype.getId = function () {
- return this.getModel().getId();
-};
-
-AbstractCustomMap.prototype.getConfiguration = function () {
- return this._configuration;
-};
-
-AbstractCustomMap.prototype.setConfiguration = function (configuration) {
- this._configuration = configuration;
-};
-
-AbstractCustomMap.prototype._createMapChangedCallbacks = function () {
- var self = this;
- var sessionData = ServerConnector.getSessionData(self.getTopMap().getProject());
- // listener for changing zoom level
- google.maps.event.addListener(this.getGoogleMap(), 'zoom_changed', function () {
- sessionData.setZoomLevel(self.getModel(), self.getGoogleMap().getZoom());
- });
- // listener for changing location of the map (moving left/right/top/bottom
- google.maps.event.addListener(this.getGoogleMap(), 'center_changed', function () {
- var coord = self.getGoogleMap().getCenter();
- var point = self.fromLatLngToPoint(coord);
- sessionData.setCenter(self.getModel(), point);
- });
-};
-
-/**
- * Returns {@link ReactionInfoWindow} for given reaction identifier
- *
- * @param reactionId
- * reaction identifier
- * @returns {@link ReactionInfoWindow} for given reaction identifier
- */
-AbstractCustomMap.prototype.getReactionInfoWindowById = function (reactionId) {
- return this._reactionInfoWindow[reactionId];
-};
-
-/**
- * Returns {@link AliasInfoWindow} for given alias identifier
- *
- * @param aliasId
- * alias identifier
- * @returns {@link AliasInfoWindow} for given alias identifier
- */
-AbstractCustomMap.prototype.getAliasInfoWindowById = function (aliasId) {
- return this._aliasInfoWindow[aliasId];
-};
-
-/**
- * Returns {@link PointInfoWindow} for given point identifier
- *
- * @param pointId
- * point identifier
- * @returns {@link PointInfoWindow} for given point identifier
- */
-AbstractCustomMap.prototype.getPointInfoWindowById = function (pointId) {
- return this._pointInfoWindow[pointId];
-};
-
-AbstractCustomMap.prototype.getModel = function () {
- return this._model;
-};
-
-AbstractCustomMap.prototype.setModel = function (model) {
- this._model = model;
-};
-
-AbstractCustomMap.prototype.getTileSize = function () {
- return this.getModel().getTileSize();
-};
-
-AbstractCustomMap.prototype.getMinZoom = function () {
- return this.getModel().getMinZoom();
-};
-
-AbstractCustomMap.prototype.getMaxZoom = function () {
- return this.getModel().getMaxZoom();
-};
-
-AbstractCustomMap.prototype.getLayouts = function () {
- return this.getModel().getLayouts();
-};
-
-AbstractCustomMap.prototype.getPictureSize = function () {
- return this.getModel().getPictureSize();
-};
-
-/**
- * Returns array containing elements that are presented on a specific layout
- * (set of google map objects representing lines/areas that are associated with
- * layout).
- *
- * @returns {Array} containing elements that are presented on a specific
- * layout (set of google map objects representing lines/areas that are
- * associated with layout).
- */
-AbstractCustomMap.prototype.getSelectedLayoutOverlays = function () {
- return this.selectedLayoutOverlays;
-};
-
-/**
- * Returns google.maps.map object used to representing data.
- *
- * @returns google.maps.map object used to representing data
- */
-AbstractCustomMap.prototype.getGoogleMap = function () {
- return this._map;
-};
-
-/**
- * Sets google.maps.map object used to representing data.
- *
- */
-AbstractCustomMap.prototype.setGoogleMap = function (googleMap) {
- this._map = googleMap;
-};
-
-AbstractCustomMap.prototype.isMarkerOptimization = function () {
- return this._markerOptimization;
-};
-
-AbstractCustomMap.prototype.isBigLogo = function () {
- return this._bigLogo;
-};
-
-AbstractCustomMap.prototype.isCustomTouchInterface = function () {
- return this._customTouchInterface;
-};
-
-AbstractCustomMap.prototype.setDebug = function (debug) {
- if (debug !== undefined) {
- if (typeof debug !== "boolean") {
- logger.warn("param must be boolean");
- }
- this._debug = debug;
- }
-};
-
-AbstractCustomMap.prototype.isDebug = function () {
- return this._debug === true;
-};
-
-AbstractCustomMap.prototype.getTopLeftLatLng = function () {
- return this.getModel().getTopLeftLatLng();
-};
-
-AbstractCustomMap.prototype.getBottomRightLatLng = function () {
- return this.getModel().getBottomRightLatLng();
-};
-
-AbstractCustomMap.prototype.getElement = function () {
- return this._element;
-};
-AbstractCustomMap.prototype.setElement = function (element) {
- this._element = element;
-};
-
-/**
- * Sets center point for google maps.
- *
- * @param coordinates
- * new center point on map
- */
-AbstractCustomMap.prototype.setCenter = function (coordinates) {
- if (coordinates instanceof google.maps.Point) {
- coordinates = this.fromPointToLatLng(coordinates);
- }
- if (this.initialized) {
- return Promise.resolve(this.getGoogleMap().setCenter(coordinates));
- } else {
- logger.warn("cannot center map that is not opened yet");
- return Promise.resolve();
- }
-};
-
-/**
- * Sets zoom level for google maps.
- *
- * @param mapIdentifier
- * id of the model for which we change zoom level
- * @param zoom
- * new zoom level on map
- */
-AbstractCustomMap.prototype.setZoom = function (zoom) {
- if (this.initialized) {
- return Promise.resolve(this.getGoogleMap().setZoom(zoom));
- } else {
- logger.warn("cannot center map that is not opened yet");
- return Promise.resolve();
- }
-};
-
-AbstractCustomMap.prototype.fitBounds = function (markers) {
- var self = this;
- var map = self.getGoogleMap();
- if (map !== undefined) {
- var bounds = new google.maps.LatLngBounds();
-
- for (var i = 0; i < markers.length; i++) {
- var marker = markers[i];
- if (marker.getModelId() === self.getId()) {
- var markerBounds = marker.getBounds();
- bounds.extend(markerBounds.getNorthEast());
- bounds.extend(markerBounds.getSouthWest());
- }
- }
- if (!bounds.isEmpty()) {
- map.fitBounds(bounds);
- }
- }
-};
-
-module.exports = AbstractCustomMap;
+"use strict";
+
+var Promise = require("bluebird");
+
+var logger = require('../logger');
+var functions = require('../Functions');
+
+var AliasInfoWindow = require('./window/AliasInfoWindow');
+var AliasSurface = require('./surface/AliasSurface');
+var GuiConnector = require('../GuiConnector');
+var IdentifiedElement = require('./data/IdentifiedElement');
+var ObjectWithListeners = require('../ObjectWithListeners');
+var PointInfoWindow = require('./window/PointInfoWindow');
+var ReactionInfoWindow = require('./window/ReactionInfoWindow');
+var ReactionSurface = require('./surface/ReactionSurface');
+
+var MarkerSurfaceCollection = require('./marker/MarkerSurfaceCollection');
+
+/**
+ * Default constructor.
+ */
+function AbstractCustomMap(model, options) {
+ // call super constructor
+ ObjectWithListeners.call(this);
+
+ if (model === undefined) {
+ throw Error("Model must be defined");
+ }
+
+ this.setElement(options.getElement());
+ this.setConfiguration(options.getConfiguration());
+
+ this.setModel(model);
+
+ // this array contains elements that are presented on a specific layout (set
+ // of google map object representing lines/areas that are associated with
+ // layout)
+ this.selectedLayoutOverlays = [];
+
+ // following fields are used in conversion between x,y coordinates and lat,lng
+ // coordinates
+ this.pixelOrigin_ = new google.maps.Point(this.getTileSize() / 2, this.getTileSize() / 2);
+ this.pixelsPerLonDegree_ = this.getTileSize() / 360;
+ this.pixelsPerLonRadian_ = this.getTileSize() / (2 * Math.PI);
+
+ /* jshint bitwise: false */
+ this.zoomFactor = this.getPictureSize() / (this.getTileSize() / (1 << this.getMinZoom()));
+
+ // array with info windows for Marker pointing to aliases
+ this._aliasInfoWindow = [];
+
+ // array with info windows for Marker pointing to points
+ this._pointInfoWindow = [];
+
+ // array with info windows for reactions
+ this._reactionInfoWindow = [];
+
+ this._markerSurfaceCollection = new MarkerSurfaceCollection({map: this});
+
+ // this is google.maps.drawing.DrawingManager that will allow user to draw
+ // elements in the client
+ this._drawingManager = null;
+
+ // this is the polygon that was selected (clicked) last time on the map
+ this._selectedArea = null;
+
+ // markers should be optimized by default,
+ // however, for testing purpose this function could be turned of by javascript
+ // the other possibility is that it should be off in the touch mode
+ // (bigButtons=true)
+ this._markerOptimization = options.isMarkerOptimization();
+
+ this._bigLogo = options.isBigLogo();
+ this._customTouchInterface = options.isCustomTouchInterface();
+
+ this.setDebug(options.isDebug());
+}
+
+// define super constructor
+AbstractCustomMap.prototype = Object.create(ObjectWithListeners.prototype);
+AbstractCustomMap.prototype.constructor = AbstractCustomMap;
+
+
+AbstractCustomMap.prototype.getMarkerSurfaceCollection = function () {
+ return this._markerSurfaceCollection;
+};
+/**
+ * Assigns layouts with images to the google map (which set of images should be
+ * used by google maps api for which layout).
+ *
+ */
+AbstractCustomMap.prototype.setupLayouts = function () {
+ for (var i = 0; i < this.getLayouts().length; i++) {
+ var layout = this.getLayouts()[i];
+ var typeOptions = this.createTypeOptions(layout);
+ var mapType = new google.maps.ImageMapType(typeOptions);
+ this.getGoogleMap().mapTypes.set(layout.getId().toString(), mapType);
+ }
+ this.getGoogleMap().setMapTypeId(this.getLayouts()[0].getId().toString());
+};
+
+/**
+ * Creates general google maps options used in this map.
+ *
+ */
+AbstractCustomMap.prototype.createMapOptions = function () {
+ var self = this;
+ var model = self.getModel();
+
+ var centerPoint = this.getModel().getCenterLatLng();
+
+ var zoom = ServerConnector.getSessionData(self.getProject()).getZoomLevel(model);
+ if (zoom === undefined) {
+ zoom = this.getMinZoom();
+ }
+
+ // if we have coordinate data stored in session then restore it
+ var point = ServerConnector.getSessionData(self.getProject()).getCenter(model);
+ if (point !== undefined) {
+ centerPoint = self.fromPointToLatLng(point);
+ // if we have default coordinates defined for model
+ } else if (model.getDefaultCenterX() !== undefined &&
+ model.getDefaultCenterY() !== undefined &&
+ model.getDefaultZoomLevel() !== undefined &&
+ model.getDefaultCenterX() !== null &&
+ model.getDefaultCenterY() !== null &&
+ model.getDefaultZoomLevel() !== null) {
+
+ centerPoint = self.fromPointToLatLng(new google.maps.Point(model.getDefaultCenterX(), model.getDefaultCenterY()));
+ zoom = model.getDefaultZoomLevel();
+ }
+
+ return {
+ center: centerPoint,
+ rotateControl: true,
+ panControl: true,
+ mapTypeControl: false,
+ zoom: zoom,
+ streetViewControl: false,
+
+ panControlOptions: {
+ position: google.maps.ControlPosition.LEFT_TOP
+ },
+ zoomControlOptions: {
+ style: google.maps.ZoomControlStyle.LARGE,
+ position: google.maps.ControlPosition.LEFT_TOP
+ }
+
+ };
+};
+
+/**
+ * Create google maps configuration options object for a specific layout.
+ *
+ * @param param
+ * object with information about layout
+ */
+AbstractCustomMap.prototype.createTypeOptions = function (param) {
+ var self = this;
+ var result = {
+ // this is a function that will retrieve valid url to png images for
+ // tiles on different zoom levels
+ getTileUrl: function (coord, zoom) {
+ // we have 1 tile on self.getConfiguration().MIN_ZOOM and
+ // therefore must limit tails according to this
+ /* jshint bitwise: false */
+ var tileRange = 1 << (zoom - self.getMinZoom());
+ if (coord.y < 0 || coord.y >= tileRange || coord.x < 0 || coord.x >= tileRange) {
+ return null;
+ }
+ var addr = "../map_images/" + param.getDirectory() + "/" + zoom + "/" + coord.x + "/" + coord.y + ".PNG";
+ return addr;
+ },
+ tileSize: new google.maps.Size(this.getTileSize(), this.getTileSize()),
+ maxZoom: this.getMaxZoom(),
+ minZoom: this.getMinZoom(),
+ radius: 360,
+ name: param.name
+ };
+ return result;
+};
+
+/**
+ * Sets maximum zoom level on google map.
+ *
+ */
+AbstractCustomMap.prototype.setMaxZoomLevel = function () {
+ this.getGoogleMap().setZoom(this.getMaxZoom());
+};
+
+/**
+ * Returns mouse coordinate on the map in lat,lng system.
+ *
+ */
+AbstractCustomMap.prototype.getMouseLatLng = function () {
+ // this method is tricky, the main problem is how to map mouse coordinate to
+ // google map
+ // to do that we need a point of reference in both systems (x,y and lat,lng)
+ // this will be center of the map that is currently visible
+ // next, we will have to find distance from this point in x,y coordinates and
+ // transform it to lat,lng
+
+ var self = this;
+ // center point visible on the map
+ var latLngCoordinates = self.getGoogleMap().getCenter();
+ var point = self.fromLatLngToPoint(latLngCoordinates);
+
+ // this is magic :)
+ // find offset of the div where google map is located related to top left
+ // corner of the browser
+ var el = self.getGoogleMap().getDiv();
+ for (var lx = 0, ly = 0; el !== null && el !== undefined; lx += el.offsetLeft, ly += el.offsetTop, el = el.offsetParent) {
+ }
+
+ var offset = {
+ x: lx,
+ y: ly
+ };
+
+ var center = {
+ x: self.getGoogleMap().getDiv().offsetWidth / 2,
+ y: self.getGoogleMap().getDiv().offsetHeight / 2
+ };
+
+ // and now find how far from center point we are (in pixels)
+ var relativeDist = {
+ x: (GuiConnector.xPos - offset.x - center.x),
+ y: (GuiConnector.yPos - offset.y - center.y)
+ };
+
+ // transform pixels into x,y distance
+ var pointDist = self.fromPixelsToPoint(relativeDist, self.getGoogleMap().getZoom());
+
+ // now we have offset in x,y and center point on the map in x,y, so we have
+ // final position in x,y
+ var newCoordinates = new google.maps.Point(point.x + pointDist.x, point.y + pointDist.y);
+
+ // change it to lat,lng
+ var latLngResult = self.fromPointToLatLng(newCoordinates);
+
+ return latLngResult;
+};
+
+/**
+ * Transform distance (coordinates) in pixels into x,y distance on the map.
+ *
+ * @param pixels
+ * x,y distance in pixels
+ * @param zoomLevel
+ * at which zoom level this pixels where measured
+ *
+ */
+AbstractCustomMap.prototype.fromPixelsToPoint = function (pixels, zoomLevel) {
+ var zoomScale = this.getPictureSize() / (Math.pow(2, zoomLevel - this.getMinZoom()) * this.getTileSize());
+ var pointX = pixels.x * zoomScale;
+ var pointY = pixels.y * zoomScale;
+ return new google.maps.Point(pointX, pointY);
+};
+
+/**
+ * Transforms coordinates on the map from google.maps.LatLng to
+ * google.maps.Point
+ *
+ * @param latLng
+ * in lat,lng format
+ * @param coordinates in x,y format
+ *
+ */
+AbstractCustomMap.prototype.fromLatLngToPoint = function (latLng) {
+ var me = this;
+ var point = new google.maps.Point(0, 0);
+ var origin = me.pixelOrigin_;
+
+ point.x = origin.x + latLng.lng() * me.pixelsPerLonDegree_;
+
+ // Truncating to 0.9999 effectively limits latitude to 89.189. This is
+ // about a third of a tile past the edge of the world tile.
+ var siny = functions.bound(Math.sin(functions.degreesToRadians(latLng.lat())), -0.9999, 0.9999);
+ point.y = origin.y + 0.5 * Math.log((1 + siny) / (1 - siny)) * -me.pixelsPerLonRadian_;
+
+ // rescale the point (all computations are done assuming that we work on
+ // TILE_SIZE square)
+ point.x *= me.zoomFactor;
+ point.y *= me.zoomFactor;
+ return point;
+};
+
+/**
+ * Transforms coordinates on the map from google.maps.Point to
+ * google.maps.LatLng
+ *
+ * @param point
+ * coordinates in standard x,y format
+ * @return coordinates in lat,lng format
+ */
+AbstractCustomMap.prototype.fromPointToLatLng = function (point) {
+ var me = this;
+
+ // rescale the point (all computations are done assuming that we work on
+ // TILE_SIZE square)
+ var p = new google.maps.Point(point.x / me.zoomFactor, point.y / me.zoomFactor);
+ var origin = me.pixelOrigin_;
+ var lng = (p.x - origin.x) / me.pixelsPerLonDegree_;
+ var latRadians = (p.y - origin.y) / -me.pixelsPerLonRadian_;
+ var lat = functions.radiansToDegrees(2 * Math.atan(Math.exp(latRadians)) - Math.PI / 2);
+ return new google.maps.LatLng(lat, lng);
+};
+
+/**
+ * Transforms google.maps.LatLng to tile coordinate (for instance on which tile
+ * mouse clicked).
+ *
+ *
+ * @param latLng
+ * coordinates in latlng format
+ * @param z
+ * zoom level at which we want to find coordinates of tile
+ * @return coordinates of a tile
+ */
+AbstractCustomMap.prototype.latLngToTile = function (latLng, z) {
+ var worldCoordinate = this.fromLatLngToPoint(latLng);
+ var pixelCoordinate = new google.maps.Point(worldCoordinate.x * Math.pow(2, z), worldCoordinate.y * Math.pow(2, z));
+ var tileCoordinate = new google.maps.Point(Math.floor(pixelCoordinate.x / this.getTileSize()), Math
+ .floor(pixelCoordinate.y / this.getTileSize()));
+ return tileCoordinate;
+};
+
+/**
+ * Register events responsible for click events
+ */
+AbstractCustomMap.prototype.registerMapClickEvents = function () {
+
+ // find top map (CustomMap)
+ //
+ var customMap = this.getTopMap();
+
+ var self = this;
+
+ // search event
+ google.maps.event.addListener(this.getGoogleMap(), 'click', function (mouseEvent) {
+ var point = self.fromLatLngToPoint(mouseEvent.latLng);
+ var searchDb = customMap.getOverlayByName('search');
+ if (searchDb !== undefined) {
+ return searchDb.searchByCoordinates({
+ modelId: self.getModel().getId(),
+ coordinates: point,
+ zoom: self.getGoogleMap().getZoom()
+ }).then(null, GuiConnector.alert);
+ } else {
+ logger.warn("Search is impossible because search db is not present");
+ }
+ });
+
+ // select last clicked map
+ google.maps.event.addListener(this.getGoogleMap(), 'click', function (mouseEvent) {
+ customMap.setActiveSubmapId(self.getId());
+ customMap.setActiveSubmapClickCoordinates(self.fromLatLngToPoint(mouseEvent.latLng));
+ });
+
+ // select last clicked map
+ google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function (mouseEvent) {
+ customMap.setActiveSubmapId(self.getId());
+ customMap.setActiveSubmapClickCoordinates(self.fromLatLngToPoint(mouseEvent.latLng));
+ });
+
+ // prepare for image export
+ google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function () {
+ var bounds = self.getGoogleMap().getBounds();
+ var polygon = "";
+
+ var ne = bounds.getNorthEast();
+ var sw = bounds.getSouthWest();
+
+ var westLng = sw.lng();
+ var eastLng = ne.lng();
+
+ if (westLng > 0) {
+ westLng = -180;
+ }
+ if (eastLng - westLng > 90) {
+ eastLng = -90;
+ } else if (eastLng > -90) {
+ eastLng = -90;
+ }
+
+ polygon += ne.lat() + "," + westLng + ";";
+ polygon += ne.lat() + "," + eastLng + ";";
+ polygon += sw.lat() + "," + eastLng + ";";
+ polygon += sw.lat() + "," + westLng + ";";
+ self.getTopMap().setSelectedPolygon(polygon);
+ });
+
+ // context menu event
+ google.maps.event.addListener(this.getGoogleMap(), 'rightclick', function () {
+ self.getTopMap().getContextMenu().open(GuiConnector.xPos, GuiConnector.yPos, new Date().getTime());
+ });
+};
+
+/**
+ * It toggle drawing manager used on the map: if it's on then it will turn it
+ * off, if it's off it will turn it on
+ *
+ */
+AbstractCustomMap.prototype._turnOnOffDrawing = function () {
+ if (this.isDrawingOn()) {
+ this.turnOffDrawing();
+ } else {
+ this.turnOnDrawing();
+ }
+};
+
+/**
+ * Checks if the drawing manager for the map is on.
+ *
+ */
+AbstractCustomMap.prototype.isDrawingOn = function () {
+ return this._drawingManager !== null;
+};
+
+/**
+ * Turns on drawing manager on the map.
+ */
+AbstractCustomMap.prototype.turnOnDrawing = function () {
+ if (this.isDrawingOn()) {
+ logger.warn("Trying to turn on drawing manager, but it is already available.");
+ return;
+ }
+ var customMap = this.getTopMap();
+ var self = this;
+ this._drawingManager = new google.maps.drawing.DrawingManager({
+ drawingMode: google.maps.drawing.OverlayType.MARKER,
+ drawingControl: true,
+ drawingControlOptions: {
+ position: google.maps.ControlPosition.TOP_CENTER,
+ drawingModes: [google.maps.drawing.OverlayType.POLYGON]
+ },
+ markerOptions: {
+ icon: 'images/beachflag.png'
+ },
+ circleOptions: {
+ fillColor: '#ffff00',
+ fillOpacity: 1,
+ strokeWeight: 5,
+ clickable: false,
+ editable: true,
+ zIndex: 1
+ }
+ });
+ this._drawingManager.setMap(this.getGoogleMap());
+ this._drawingManager.setDrawingMode(google.maps.drawing.OverlayType.POLYGON);
+
+ google.maps.event.addListener(this._drawingManager, 'overlaycomplete', function (e) {
+ if (e.type !== google.maps.drawing.OverlayType.MARKER) {
+ // Switch back to non-drawing mode after drawing a shape.
+ self._drawingManager.setDrawingMode(null);
+
+ // Add an event listener that selects the newly-drawn shape when the
+ // user mouses down on it.
+ var newShape = e.overlay;
+ newShape.type = e.type;
+ google.maps.event.addListener(newShape, 'rightclick', function (e) {
+ // select map that was clicked
+ customMap.setActiveSubmapId(self.getId());
+
+ self.setSelectedArea(newShape);
+ newShape.position = e.latLng;
+
+ self.getTopMap().setSelectedPolygon(self.areaToString(newShape));
+
+ self.getTopMap().getSelectionContextMenu().open(GuiConnector.xPos, GuiConnector.yPos, new Date().getTime());
+ });
+ }
+ });
+
+};
+
+/**
+ * Sets selectedArea on this map.
+ *
+ */
+AbstractCustomMap.prototype.setSelectedArea = function (area) {
+ this._selectedArea = area;
+};
+
+/**
+ * Returns selectedArea on this map.
+ *
+ */
+AbstractCustomMap.prototype.getSelectedArea = function () {
+ return this._selectedArea;
+};
+
+/**
+ * Transforms google.maps.Polygon into string with coordinates.
+ *
+ */
+AbstractCustomMap.prototype.areaToString = function (area) {
+ var len = area.getPath().length;
+ var path = area.getPath();
+ var res = "";
+ for (var i = 0; i < len; i++) {
+ var latLng = path.getAt(i);
+ res += latLng.lat() + "," + latLng.lng() + ";";
+ }
+ return res;
+};
+
+/**
+ * Removes selected area (polygon) from the map.
+ */
+AbstractCustomMap.prototype._removeSelection = function () {
+ if (this._selectedArea) {
+ this._selectedArea.setMap(null);
+ this._selectedArea = null;
+ } else {
+ logger.warn("Cannot remove selected area. No area was selected");
+ }
+};
+
+/**
+ * Turns off drawing manager on the map.
+ */
+AbstractCustomMap.prototype.turnOffDrawing = function () {
+ if (this.isDrawingOn()) {
+ this._drawingManager.setMap(null);
+ this._drawingManager = null;
+ } else {
+ logger.warn("Trying to turn off drawing manager, but it is not available.");
+ }
+};
+
+/**
+ * Returns top map. TODO implementation of this function should be probably
+ * moved to Submap and CustomMap classes and here only abstract function
+ * definition
+ *
+ * @returns {CustomMap}
+ */
+AbstractCustomMap.prototype.getTopMap = function () {
+ logger.fatal("Not implemented");
+};
+
+/**
+ * Method that should be called when number of layouts to visualize changed to
+ * modify boundaries of the elements to visualize. When few layouts are
+ * visualized at the same time then index contains information where this new
+ * layout is placed in the list (starting from 0) and length contains
+ * information how many layouts we visualize in total.
+ *
+ * @param layoutId
+ * identifier of a layout
+ * @param index
+ * when visualizing more than one layout at the same time index
+ * contains information at which position in the list this layout is
+ * placed
+ * @param length
+ * number of layouts that are currently visualized
+ */
+AbstractCustomMap.prototype._resizeSelectedLayout = function (layoutId, index, length) {
+ var self = this;
+ return new Promise(function (resolve) {
+ // if map is not initialized then don't perform this operation
+ if (!self.initialized) {
+ logger.debug("Model " + self.getId() + " not initialized");
+ resolve();
+ }
+ logger.debug("Resize layout: " + layoutId);
+ // start ratio
+ var startX = index * (1.0 / length);
+ // end ratio
+ var endX = (index + 1) * (1.0 / length);
+
+ for (var i = 0; i < self.selectedLayoutOverlays[layoutId].length; i++) {
+ self.selectedLayoutOverlays[layoutId][i].setBoundsForAlias(startX, endX);
+ }
+ resolve();
+ });
+};
+
+/**
+ * Shows all elements from a given layout. When few layouts are visualized at
+ * the same time then index contains information where this new layout is placed
+ * in the list (starting from 0) and length contains information how many
+ * layouts we visualize in total.
+ *
+ * @param layoutId
+ * identifier of a layout
+ * @param index
+ * when visualizing more than one layout at the same time index
+ * contains information at which position in the list this layout is
+ * placed
+ * @param length
+ * number of layouts that are currently visualized
+ */
+AbstractCustomMap.prototype._showSelectedLayout = function (layoutId, index, length) {
+ var self = this;
+ // if map is not initialized then don't perform this operation
+ return new Promise(function (resolve, reject) {
+ if (!self.initialized) {
+ logger.debug("Model " + self.getId() + " not initialized");
+ resolve();
+ return;
+ } else {
+ logger.debug("Showing model " + self.getId());
+ }
+
+ self.selectedLayoutOverlays[layoutId] = [];
+
+ // start ratio
+ var startX = index * (1.0 / length);
+ // end ratio
+ var endX = (index + 1) * (1.0 / length);
+
+ var layoutAliases;
+ var layoutReactions;
+
+ return self.getTopMap().getModel().getLayoutDataById(layoutId).then(function (layout) {
+ layoutAliases = layout.getAliases();
+ layoutReactions = layout.getReactions();
+
+ var identifiedElements = [];
+ var i;
+ for (i = 0; i < layoutAliases.length; i++) {
+ if (layoutAliases[i].getModelId() === self.getId()) {
+ identifiedElements.push(new IdentifiedElement(layoutAliases[i]));
+ }
+ }
+ var reactionIds = [];
+ for (i = 0; i < layoutReactions.length; i++) {
+ if (layoutReactions[i].getModelId() === self.getId()) {
+ identifiedElements.push(new IdentifiedElement(layoutReactions[i]));
+ }
+ }
+ return self.getModel().getByIdentifiedElements(identifiedElements, false);
+ }).then(function () {
+ return Promise.each(layoutAliases, function (layoutAlias) {
+ if (layoutAlias.getModelId() === self.getId()) {
+ var surface;
+ var element;
+ return self.getModel().getAliasById(layoutAlias.getId()).then(function (aliasData) {
+ element = new IdentifiedElement(aliasData);
+ return AliasSurface.create({
+ overlayAlias: layoutAlias,
+ alias: aliasData,
+ map: self,
+ startX: startX,
+ endX: endX,
+ onClick: [function () {
+ return self._openInfoWindowForAlias(aliasData, surface.getGoogleMarker());
+ }, function () {
+ return self.getTopMap().callListeners("onBioEntityClick", element);
+ }]
+ });
+ }).then(function (result) {
+ surface = result;
+ self.selectedLayoutOverlays[layoutId].push(surface);
+ });
+ }
+ });
+ }).then(function () {
+ return Promise.each(layoutReactions, function (layoutReaction) {
+ if (layoutReaction.getModelId() === self.getId()) {
+ return self.getModel().getReactionById(layoutReaction.getId()).then(function (reactionData) {
+ var surface;
+ var element = new IdentifiedElement(reactionData);
+ return ReactionSurface.create({
+ layoutReaction: layoutReaction,
+ reaction: reactionData,
+ map: self,
+ onClick: [function () {
+ return self._openInfoWindowForReaction(reactionData, surface.getGoogleMarker());
+ }, function () {
+ return self.getTopMap().callListeners("onBioEntityClick", element);
+ }],
+ customized: (length === 1)
+ }).then(function (result) {
+ surface = result;
+ self.selectedLayoutOverlays[layoutId].push(surface);
+ surface.show();
+ });
+ });
+ }
+ });
+ }).then(function () {
+ resolve();
+ }).then(null, reject);
+ });
+};
+
+/**
+ * Hides all elements from layout.
+ *
+ * @param layoutId
+ * identifier of a layout
+ */
+AbstractCustomMap.prototype._hideSelectedLayout = function (layoutId) {
+ // if map is not initialized then don't perform this operation
+ if (!this.initialized) {
+ logger.debug("Model " + this.getId() + " not initialized");
+ return;
+ }
+ for (var i = 0; i < this.selectedLayoutOverlays[layoutId].length; i++) {
+ this.selectedLayoutOverlays[layoutId][i].setMap(null);
+ }
+ this.selectedLayoutOverlays[layoutId] = [];
+};
+
+/**
+ * Opens {@link AliasInfoWindow} for given alias.
+ *
+ * @param aliasId
+ * identifier of the alias
+ */
+AbstractCustomMap.prototype._openInfoWindowForAlias = function (alias, googleMarker) {
+ var self = this;
+
+ var infoWindow = this.getAliasInfoWindowById(alias.getId());
+ if (infoWindow !== null && infoWindow !== undefined) {
+ if (!infoWindow.isOpened()) {
+ infoWindow.open(googleMarker);
+ } else {
+ logger.warn("Info window for alias: " + alias.getId() + " is already opened");
+ }
+ return Promise.resolve(infoWindow);
+ } else {
+ self._aliasInfoWindow[alias.getId()] = new AliasInfoWindow({
+ alias: alias,
+ map: self,
+ marker: googleMarker,
+ });
+ return self._aliasInfoWindow[alias.getId()].init();
+ }
+};
+
+/**
+ * Returns promise of a list of {@link LayoutAlias} information for a given
+ * {@link Alias} in all currently visualized layouts.
+ *
+ * @param aliasId
+ * identifier of the {@link Alias}
+ * @returns promise of an {Array} with list of {@link LayoutAlias} information
+ * for a given {@link Alias} in all currently visualized layouts
+ */
+AbstractCustomMap.prototype.getAliasVisibleLayoutsData = function (aliasId) {
+ var self = this;
+ return self.getTopMap().getVisibleDataOverlays().then(function (visibleDataOverlays) {
+ var result = [];
+ for (var i = 0; i < visibleDataOverlays.length; i++) {
+ var layout = visibleDataOverlays[i];
+ result.push(layout.getFullAliasById(aliasId));
+ }
+ return Promise.all(result);
+ });
+};
+
+/**
+ * Refresh content of all {@link AliasInfoWindow} in this map.
+ */
+AbstractCustomMap.prototype._refreshInfoWindows = function () {
+ var promises = [];
+ for (var key in this._pointInfoWindow) {
+ if (this._pointInfoWindow.hasOwnProperty(key)) {
+ if (this._pointInfoWindow[key].isOpened()) {
+ promises.push(this._pointInfoWindow[key].update());
+ }
+ }
+ }
+ for (var aliasKey in this._aliasInfoWindow) {
+ if (this._aliasInfoWindow.hasOwnProperty(aliasKey)) {
+ if (this._aliasInfoWindow[aliasKey].isOpened()) {
+ promises.push(this._aliasInfoWindow[aliasKey].update());
+ }
+ }
+ }
+ return Promise.all(promises);
+};
+
+
+/**
+ * Opens {@link ReactionInfoWindow} for given reaction identifier.
+ *
+ * @param reactionId
+ * reaction identifier
+ */
+AbstractCustomMap.prototype._openInfoWindowForReaction = function (reaction, googleMarker) {
+ var infoWindow = this.getReactionInfoWindowById(reaction.getId());
+ var self = this;
+ if (infoWindow !== null && infoWindow !== undefined) {
+ if (!infoWindow.isOpened()) {
+ infoWindow.open(googleMarker);
+ } else {
+ logger.warn("Info window for reaction: " + reaction.getId() + " is already opened");
+ }
+ return Promise.resolve(infoWindow);
+ } else {
+ return self.getModel().getReactionById(reaction.getId()).then(function (reaction) {
+ infoWindow = new ReactionInfoWindow({
+ reaction: reaction,
+ map: self,
+ marker: googleMarker,
+ });
+ self._reactionInfoWindow[reaction.getId()] = infoWindow;
+ return infoWindow.init();
+ }).then(function () {
+ return infoWindow;
+ });
+ }
+};
+
+AbstractCustomMap.prototype._openInfoWindowForPoint = function (pointData, googleMarker) {
+ var self = this;
+
+ var infoWindow = this.getPointInfoWindowById(pointData.getId());
+ if (infoWindow !== null && infoWindow !== undefined) {
+ if (!infoWindow.isOpened()) {
+ infoWindow.open(googleMarker);
+ } else {
+ logger.warn("Info window for point: " + pointData.getId() + " is already opened");
+ }
+ } else {
+ infoWindow = new PointInfoWindow({
+ point: pointData,
+ map: self,
+ marker: googleMarker,
+ });
+ this._pointInfoWindow[pointData.getId()] = infoWindow;
+ }
+ return Promise.resolve(infoWindow);
+};
+
+/**
+ * Opens {@link AbstractInfoWindow} for a marker.
+ *
+ * @param marker
+ * marker for which we are opening window
+ */
+AbstractCustomMap.prototype.returnInfoWindowForIdentifiedElement = function (element) {
+ var markerId = element.getId();
+ if (element.getType() === "ALIAS") {
+ return this.getAliasInfoWindowById(markerId);
+ } else if (element.getType() === "POINT") {
+ return this.getPointInfoWindowById(markerId);
+ } else if (element.getType() === "REACTION") {
+ return this.getReactionInfoWindowById(markerId);
+ } else {
+ throw new Error("Unknown marker type: ", element);
+ }
+};
+
+/**
+ * Returns identifier.
+ *
+ * @returns identifier
+ */
+AbstractCustomMap.prototype.getId = function () {
+ return this.getModel().getId();
+};
+
+AbstractCustomMap.prototype.getConfiguration = function () {
+ return this._configuration;
+};
+
+AbstractCustomMap.prototype.setConfiguration = function (configuration) {
+ this._configuration = configuration;
+};
+
+AbstractCustomMap.prototype._createMapChangedCallbacks = function () {
+ var self = this;
+ var sessionData = ServerConnector.getSessionData(self.getTopMap().getProject());
+ // listener for changing zoom level
+ google.maps.event.addListener(this.getGoogleMap(), 'zoom_changed', function () {
+ sessionData.setZoomLevel(self.getModel(), self.getGoogleMap().getZoom());
+ });
+ // listener for changing location of the map (moving left/right/top/bottom
+ google.maps.event.addListener(this.getGoogleMap(), 'center_changed', function () {
+ var coord = self.getGoogleMap().getCenter();
+ var point = self.fromLatLngToPoint(coord);
+ sessionData.setCenter(self.getModel(), point);
+ });
+};
+
+/**
+ * Returns {@link ReactionInfoWindow} for given reaction identifier
+ *
+ * @param reactionId
+ * reaction identifier
+ * @returns {@link ReactionInfoWindow} for given reaction identifier
+ */
+AbstractCustomMap.prototype.getReactionInfoWindowById = function (reactionId) {
+ return this._reactionInfoWindow[reactionId];
+};
+
+/**
+ * Returns {@link AliasInfoWindow} for given alias identifier
+ *
+ * @param aliasId
+ * alias identifier
+ * @returns {@link AliasInfoWindow} for given alias identifier
+ */
+AbstractCustomMap.prototype.getAliasInfoWindowById = function (aliasId) {
+ return this._aliasInfoWindow[aliasId];
+};
+
+/**
+ * Returns {@link PointInfoWindow} for given point identifier
+ *
+ * @param pointId
+ * point identifier
+ * @returns {@link PointInfoWindow} for given point identifier
+ */
+AbstractCustomMap.prototype.getPointInfoWindowById = function (pointId) {
+ return this._pointInfoWindow[pointId];
+};
+
+AbstractCustomMap.prototype.getModel = function () {
+ return this._model;
+};
+
+AbstractCustomMap.prototype.setModel = function (model) {
+ this._model = model;
+};
+
+AbstractCustomMap.prototype.getTileSize = function () {
+ return this.getModel().getTileSize();
+};
+
+AbstractCustomMap.prototype.getMinZoom = function () {
+ return this.getModel().getMinZoom();
+};
+
+AbstractCustomMap.prototype.getMaxZoom = function () {
+ return this.getModel().getMaxZoom();
+};
+
+AbstractCustomMap.prototype.getLayouts = function () {
+ return this.getModel().getLayouts();
+};
+
+AbstractCustomMap.prototype.getPictureSize = function () {
+ return this.getModel().getPictureSize();
+};
+
+/**
+ * Returns array containing elements that are presented on a specific layout
+ * (set of google map objects representing lines/areas that are associated with
+ * layout).
+ *
+ * @returns {Array} containing elements that are presented on a specific
+ * layout (set of google map objects representing lines/areas that are
+ * associated with layout).
+ */
+AbstractCustomMap.prototype.getSelectedLayoutOverlays = function () {
+ return this.selectedLayoutOverlays;
+};
+
+/**
+ * Returns google.maps.map object used to representing data.
+ *
+ * @returns google.maps.map object used to representing data
+ */
+AbstractCustomMap.prototype.getGoogleMap = function () {
+ return this._map;
+};
+
+/**
+ * Sets google.maps.map object used to representing data.
+ *
+ */
+AbstractCustomMap.prototype.setGoogleMap = function (googleMap) {
+ this._map = googleMap;
+};
+
+AbstractCustomMap.prototype.isMarkerOptimization = function () {
+ return this._markerOptimization;
+};
+
+AbstractCustomMap.prototype.isBigLogo = function () {
+ return this._bigLogo;
+};
+
+AbstractCustomMap.prototype.isCustomTouchInterface = function () {
+ return this._customTouchInterface;
+};
+
+AbstractCustomMap.prototype.setDebug = function (debug) {
+ if (debug !== undefined) {
+ if (typeof debug !== "boolean") {
+ logger.warn("param must be boolean");
+ }
+ this._debug = debug;
+ }
+};
+
+AbstractCustomMap.prototype.isDebug = function () {
+ return this._debug === true;
+};
+
+AbstractCustomMap.prototype.getTopLeftLatLng = function () {
+ return this.getModel().getTopLeftLatLng();
+};
+
+AbstractCustomMap.prototype.getBottomRightLatLng = function () {
+ return this.getModel().getBottomRightLatLng();
+};
+
+AbstractCustomMap.prototype.getElement = function () {
+ return this._element;
+};
+AbstractCustomMap.prototype.setElement = function (element) {
+ this._element = element;
+};
+
+/**
+ * Sets center point for google maps.
+ *
+ * @param coordinates
+ * new center point on map
+ */
+AbstractCustomMap.prototype.setCenter = function (coordinates) {
+ if (coordinates instanceof google.maps.Point) {
+ coordinates = this.fromPointToLatLng(coordinates);
+ }
+ if (this.initialized) {
+ return Promise.resolve(this.getGoogleMap().setCenter(coordinates));
+ } else {
+ logger.warn("cannot center map that is not opened yet");
+ return Promise.resolve();
+ }
+};
+
+/**
+ * Sets zoom level for google maps.
+ *
+ * @param mapIdentifier
+ * id of the model for which we change zoom level
+ * @param zoom
+ * new zoom level on map
+ */
+AbstractCustomMap.prototype.setZoom = function (zoom) {
+ if (this.initialized) {
+ return Promise.resolve(this.getGoogleMap().setZoom(zoom));
+ } else {
+ logger.warn("cannot center map that is not opened yet");
+ return Promise.resolve();
+ }
+};
+
+AbstractCustomMap.prototype.fitBounds = function (markers) {
+ var self = this;
+ var map = self.getGoogleMap();
+ if (map !== undefined) {
+ var bounds = new google.maps.LatLngBounds();
+
+ for (var i = 0; i < markers.length; i++) {
+ var marker = markers[i];
+ if (marker.getModelId() === self.getId()) {
+ var markerBounds = marker.getBounds();
+ bounds.extend(markerBounds.getNorthEast());
+ bounds.extend(markerBounds.getSouthWest());
+ }
+ }
+ if (!bounds.isEmpty()) {
+ map.fitBounds(bounds);
+ }
+ }
+};
+
+module.exports = AbstractCustomMap;
diff --git a/frontend-js/src/main/js/map/CustomMap.js b/frontend-js/src/main/js/map/CustomMap.js
index 931fb1673a..82e5f7fef8 100644
--- a/frontend-js/src/main/js/map/CustomMap.js
+++ b/frontend-js/src/main/js/map/CustomMap.js
@@ -441,7 +441,14 @@ CustomMap.prototype.customizeGoogleMapView = function (div) {
// center map and zoom in to fit into browser window if there is no
// information about coordinates in the session
- if (ServerConnector.getSessionData(this.getProject()).getCenter(this.getModel()) === undefined) {
+ if (ServerConnector.getSessionData(this.getProject()).getCenter(this.getModel()) === undefined &&
+ (this.getModel().getDefaultCenterX() === undefined ||
+ this.getModel().getDefaultCenterY() === undefined ||
+ this.getModel().getDefaultZoomLevel() === undefined ||
+ this.getModel().getDefaultCenterX() === null ||
+ this.getModel().getDefaultCenterY() === null ||
+ this.getModel().getDefaultZoomLevel() === null
+ )) {
var bounds = new google.maps.LatLngBounds();
bounds.extend(this.getTopLeftLatLng());
bounds.extend(this.getBottomRightLatLng());
@@ -459,15 +466,6 @@ CustomMap.prototype.createMapChangedCallbacks = function () {
var self = this;
var sessionData = ServerConnector.getSessionData(self.getProject());
- // if we have zoom level data stored in session then restore it
- var level = sessionData.getZoomLevel(self.getModel());
- if (parseInt(level) > 0) {
- level = parseInt(level);
- this.getGoogleMap().setZoom(level);
- } else {
- sessionData.setZoomLevel(self.getModel(), self.getGoogleMap().getZoom());
- }
-
// listener for changing type of layout
google.maps.event.addListener(self.getGoogleMap(), 'maptypeid_changed', function () {
sessionData.setSelectedBackgroundOverlay(self.getGoogleMap().getMapTypeId());
diff --git a/frontend-js/src/main/js/map/data/MapModel.js b/frontend-js/src/main/js/map/data/MapModel.js
index 000602857d..7bbd84fc8d 100644
--- a/frontend-js/src/main/js/map/data/MapModel.js
+++ b/frontend-js/src/main/js/map/data/MapModel.js
@@ -1,798 +1,828 @@
-"use strict";
-
-var Promise = require("bluebird");
-
-var logger = require('../../logger');
-
-var Alias = require('./Alias');
-var IdentifiedElement = require('./IdentifiedElement');
-var LayoutData = require('./LayoutData');
-var PointData = require('./PointData');
-var Reaction = require('./Reaction');
-
-// This file describes javascript representation of Java Model class that
-// represents content of the map.
-
-/**
- * Default constructor.
- *
- */
-
-function MapModel(configuration) {
-
- // list of aliases is empty (it will be filled dynamically - when necessary)
- this._aliases = [];
-
- // list of reactions is empty (it will be filled dynamically - when necessary)
- this._reactions = [];
- this._reactionsByParticipantElementId = [];
-
- // list of aliases that should be updated from server side during the next
- // connection
- this._missingAliases = [];
-
- // list of reactions that should be updated from server side during the next
- // connection
- this._missingReactions = [];
-
- // list of layouts is empty (it will be filled when necessary)
- this._layoutsData = [];
-
- // information about points and associated data (for now we have only comments
- // associated to the point,
- // but it can be extended)
- this._pointsData = [];
-
- this._submodels = [];
-
- if (configuration !== undefined) {
- if (configuration instanceof MapModel) {
- this.setId(configuration.getId());
- this.setName(configuration.getName());
- this.setTileSize(configuration.getTileSize());
- this.setWidth(configuration.getWidth());
- this.setHeight(configuration.getHeight());
- this.setMinZoom(configuration.getMinZoom());
- this.setMaxZoom(configuration.getMaxZoom());
- this.addLayouts(configuration.getLayouts());
- this.addSubmodels(configuration.getSubmodels());
- this.setCenterLatLng(configuration.getCenterLatLng());
- this.setTopLeftLatLng(configuration.getTopLeftLatLng());
- this.setBottomRightLatLng(configuration.getBottomRightLatLng());
- this.setSubmodelType(configuration.getSubmodelType());
- } else {
- this.setId(configuration.idObject);
- this.setName(configuration.name);
- this.setTileSize(configuration.tileSize);
- this.setWidth(configuration.width);
- this.setHeight(configuration.height);
- this.setMinZoom(configuration.minZoom);
- this.setMaxZoom(configuration.maxZoom);
- this.addLayouts(configuration.layouts);
- this.addSubmodels(configuration.submodels);
- this.setCenterLatLng(configuration.centerLatLng);
- this.setTopLeftLatLng(configuration.topLeftLatLng);
- this.setBottomRightLatLng(configuration.bottomRightLatLng);
- this.setSubmodelType(configuration.submodelType);
- }
- }
-}
-
-/**
- * Returns list of {@link LayoutData} on this model.
- *
- * @returns {Array} with list of {@link LayoutData} on this model
- */
-MapModel.prototype.getLayoutsData = function() {
- var result = [];
- for ( var id in this._layoutsData) {
- if (this._layoutsData.hasOwnProperty(id)) {
- result.push(this._layoutsData[id]);
- }
- }
- return result;
-};
-
-MapModel.prototype.getLayouts = function() {
- return this.getLayoutsData();
-};
-
-/**
- * Return list of all aliases that were added to the model.
- */
-MapModel.prototype.getAliases = function(params) {
- var self = this;
- return ServerConnector.getAliases({
- columns : "id,modelId",
- type : params.type,
- modelId : self.getId(),
- includedCompartmentIds : params.includedCompartmentIds,
- excludedCompartmentIds : params.excludedCompartmentIds,
-
- }).then(function(lightAliases) {
- var identifiedElements = [];
- for (var i = 0; i < lightAliases.length; i++) {
- self.addAlias(lightAliases[i]);
- identifiedElements.push(new IdentifiedElement(lightAliases[i]));
- }
- return self.getByIdentifiedElements(identifiedElements, params.complete);
- });
-};
-
-/**
- * Returns {@link Alias} by identifier.
- *
- * @param id
- * identifier of the {@link Alias}
- * @returns {@link Alias} by identifier
- */
-MapModel.prototype.getAliasById = function(id, complete) {
- var self = this;
- if (complete) {
- return this.getCompleteAliasById(id);
- }
- if (self._aliases[id] !== undefined) {
- return Promise.resolve(self._aliases[id]);
- } else {
- return self.getMissingElements({
- aliasIds : [ id ]
- }).then(function() {
- return self._aliases[id];
- });
- }
-};
-
-MapModel.prototype.getCompleteAliasById = function(id) {
- var self = this;
- if (self._aliases[id] !== undefined && self._aliases[id].isComplete()) {
- return Promise.resolve(self._aliases[id]);
- } else {
- return ServerConnector.getAliases({
- ids : id
- }).then(function(aliases) {
- if (self._aliases[id] === undefined) {
- self._aliases[id] = aliases[0];
- } else {
- self._aliases[id].update(aliases[0]);
- }
- return self._aliases[id];
- });
- }
-};
-
-/**
- * Returns {@link Reaction} by identifier.
- *
- * @param id
- * identifier of the {@link Reaction}
- * @returns {@link Reaction} by identifier
- */
-MapModel.prototype.getReactionById = function(id, complete) {
- var self = this;
- if (complete) {
- return this.getCompleteReactionById(id);
- }
- if (self._reactions[id] !== undefined) {
- return Promise.resolve(self._reactions[id]);
- } else {
- return self.getMissingElements({
- reactionIds : [ id ]
- }).then(function() {
- return self._reactions[id];
- });
- }
-};
-
-MapModel.prototype._getMissingReactionsElementIds = function(reactions) {
- var self = this;
- var result = [];
- var ids = [];
- for (var i = 0; i < reactions.length; i++) {
- var reaction = reactions[i];
- var elements = reaction.getElements();
- for (var j = 0; j < elements.length; j++) {
- var element = elements[j];
- if (!(element instanceof Alias)) {
- if (self._aliases[element] === undefined || !self._aliases[element].isComplete()) {
- if (!ids[element]) {
- ids[element] = true;
- result.push(element);
- }
- }
- }
- }
- }
- return result;
-};
-
-MapModel.prototype.getCompleteReactionById = function(id) {
- var self = this;
- if (self._reactions[id] instanceof Reaction && self._reactions[id].isComplete()) {
- return Promise.resolve(self._reactions[id]);
- } else {
- var result;
- return self.getReactionById(id).then(function(result) {
- var ids = self._getMissingReactionsElementIds([ result ]);
- return self.getMissingElements({
- aliasIds : ids,
- complete : true
- });
- }).then(function() {
- var i;
- result = self._reactions[id];
- for (i = 0; i < result.getReactants().length; i++) {
- if (!(result.getReactants()[i] instanceof Alias)) {
- result.getReactants()[i] = self._aliases[result.getReactants()[i]];
- }
- }
- for (i = 0; i < result.getProducts().length; i++) {
- if (!(result.getProducts()[i] instanceof Alias)) {
- result.getProducts()[i] = self._aliases[result.getProducts()[i]];
- }
- }
- for (i = 0; i < result.getModifiers().length; i++) {
- if (!(result.getModifiers()[i] instanceof Alias)) {
- result.getModifiers()[i] = self._aliases[result.getModifiers()[i]];
- }
- }
- return result;
- });
- }
-};
-
-MapModel.prototype.getMissingElements = function(elements) {
- var self = this;
-
- var layouts = this._getLayouts();
- var aliasIds = [];
- var reactionIds = [];
-
- var i = 0;
- if (elements.reactionIds !== undefined) {
- reactionIds.push.apply(reactionIds, elements.reactionIds);
- for (i = 0; i < reactionIds.length; i++) {
- this._missingReactions[reactionIds[i]] = reactionIds[i];
- }
-
- }
- if (elements.aliasIds !== undefined) {
- aliasIds.push.apply(aliasIds, elements.aliasIds);
- for (i = 0; i < aliasIds.length; i++) {
- this._missingAliases[aliasIds[i]] = aliasIds[i];
- }
- }
-
- for (i = 0; i < layouts.length; i++) {
- var layout = layouts[i];
- if (layout.isInitialized()) {
- var aliases = layout.getAliases();
- for (var j = 0; j < aliases.length; j++) {
- var alias = aliases[j];
- if (this._aliases[alias.getId()] === undefined && this._missingAliases[alias.getId()] === undefined) {
- this._missingAliases[alias.getId()] = alias.getId();
- aliasIds.push(alias.getId());
- }
- }
-
- var reactions = layout.getReactions();
- for (var k = 0; k < reactions.length; k++) {
- var reaction = reactions[k];
- if (this._reactions[reaction.getId()] === undefined && this._missingReactions[reaction.getId()] === undefined) {
- this._missingReactions[reaction.getId()] = reaction.getId();
- reactionIds.push(reaction.getId());
- }
- }
- }
- }
- var reactionPromise = null;
- if (reactionIds.length > 0) {
- reactionPromise = ServerConnector.getReactions({
- ids : reactionIds,
- complete : elements.complete
- });
- }
-
- var aliasPromise = null;
- if (aliasIds.length > 0) {
- if (elements.complete) {
- aliasPromise = ServerConnector.getAliases({
- ids : aliasIds
- });
- } else {
- aliasPromise = ServerConnector.getAliases({
- ids : aliasIds,
- columns : "id,bounds,modelId"
- });
-
- }
- }
-
- var result = [];
- return Promise.all([ reactionPromise, aliasPromise ]).then(function(values) {
- var i;
- var reactions = values[0];
- var aliases = values[1];
- var ids = [];
-
- if (reactions !== null) {
- for (i = 0; i < reactions.length; i++) {
- var reaction = reactions[i];
- self.addReaction(reaction);
- result.push(reaction);
- }
- ids = self._getMissingReactionsElementIds(reactions);
- }
- if (aliases !== null) {
- for (i = 0; i < aliases.length; i++) {
- var alias = aliases[i];
- self.addAlias(alias);
- result.push(alias);
- }
- }
- if (ids.length > 0) {
- return self.getMissingElements({
- aliasIds : ids,
- complete : true
- });
- } else {
- return Promise.resolve([]);
- }
- }).then(function() {
- return result;
- });
-};
-
-/**
- * Returns layout data for a given layout identifier.
- *
- * @param layoutId
- * layout identifier
- * @returns {LayoutData} for a given layout identifier
- */
-MapModel.prototype.getLayoutDataById = function(layoutId) {
- var self = this;
- if (self._layoutsData[layoutId] !== undefined) {
- return Promise.resolve(self._layoutsData[layoutId]);
- } else {
- return ServerConnector.getOverlayById(layoutId).then(function(layout) {
- self.addLayout(layout);
- return self._layoutsData[layoutId];
- });
- }
-};
-
-/**
- * Adds information about alias.
- *
- * @param aliasData
- * raw data about alias
- */
-MapModel.prototype.addAlias = function(aliasData) {
- var alias = aliasData;
- if (!(aliasData instanceof Alias)) {
- alias = new Alias(aliasData);
- }
- if (this._aliases[alias.getId()] !== undefined) {
- this._aliases[alias.getId()].update(alias);
- } else {
- this._aliases[alias.getId()] = alias;
- if (this._missingAliases[alias.getId()] !== undefined) {
- this._missingAliases[alias.getId()] = null;
- delete this._missingAliases[alias.getId()];
- }
- }
-};
-
-/**
- * Adds information about reaction.
- *
- * @param reactionData
- * raw data about reaction
- */
-MapModel.prototype.addReaction = function(reactionData) {
- var reaction = null;
- if (reactionData instanceof Reaction) {
- reaction = reactionData;
- } else {
- reaction = new Reaction(reactionData);
- }
- if (this._reactions[reaction.getId()] !== undefined) {
- logger.warn("Reaction with id: " + reaction.getId() + " already exists");
- } else {
- this._reactions[reaction.getId()] = reaction;
- if (this._missingReactions[reaction.getId()] !== undefined) {
- this._missingReactions[reaction.getId()] = null;
- delete this._missingReactions[reaction.getId()];
- }
- }
-};
-
-/**
- * Returns {@link PointData} for a given point on the map.
- *
- * @param point
- * {@link google.maps.Point} where we are requesting data
- * @returns {@link PointData} for a given point on the map
- */
-MapModel.prototype.getPointDataByPoint = function(inputPoint) {
- if (inputPoint instanceof google.maps.Point) {
- var point = this._roundPoint(inputPoint);
- var id = this._pointToId(point);
- var result = this._pointsData[id];
- if (result === undefined) {
- result = new PointData(point, this.getId());
- this._pointsData[id] = result;
- }
- return result;
- } else {
- logger.warn("point must be of class: google.maps.Point");
- return null;
- }
-};
-
-/**
- * Returns point where x and y coordinate are rounded to 2 decimal places.
- *
- * @param point
- * input point
- * @returns {google.maps.Point} point where x and y coordinate are rounded to 2
- * decimal places
- */
-MapModel.prototype._roundPoint = function(point) {
- var x = parseFloat(point.x).toFixed(2);
- var y = parseFloat(point.y).toFixed(2);
- return new google.maps.Point(x, y);
-};
-
-/**
- * Transform point into string identifier.
- *
- * @param point
- * {google.maps.Point} to transform
- * @returns {String} string identifier for a given point
- */
-MapModel.prototype._pointToId = function(point) {
- if (point instanceof google.maps.Point) {
- return "(" + point.x + ", " + point.y + ")";
- } else {
- return point.replace(/ /g, '');
- }
-};
-
-MapModel.prototype.getId = function() {
- return this.id;
-};
-
-MapModel.prototype.setId = function(id) {
- this.id = parseInt(id);
-};
-
-MapModel.prototype.getWidth = function() {
- return this._width;
-};
-
-MapModel.prototype.setWidth = function(width) {
- this._width = width;
-};
-
-MapModel.prototype.getHeight = function() {
- return this._height;
-};
-
-MapModel.prototype.setHeight = function(height) {
- this._height = height;
-};
-
-MapModel.prototype.getName = function() {
- return this._name;
-};
-
-MapModel.prototype.setName = function(name) {
- this._name = name;
-};
-
-MapModel.prototype.getMinZoom = function() {
- return this._minZoom;
-};
-
-MapModel.prototype.setMinZoom = function(minZoom) {
- this._minZoom = minZoom;
-};
-
-MapModel.prototype.getSubmodelType = function() {
- return this._submodelType;
-};
-
-MapModel.prototype.setSubmodelType = function(submodelType) {
- this._submodelType = submodelType;
-};
-
-function createLatLng(param) {
- if (param === undefined) {
- return null;
- }
- if (param instanceof google.maps.LatLng) {
- return new google.maps.LatLng(param.lat(), param.lng());
- } else {
- return new google.maps.LatLng(param.lat, param.lng);
- }
-}
-
-MapModel.prototype.setCenterLatLng = function(centerLatLng) {
- var newVal = createLatLng(centerLatLng);
- if (newVal === null) {
- logger.warn("centerLatLng is invalid");
- } else {
- this._centerLatLng = newVal;
- }
-};
-
-MapModel.prototype.getCenterLatLng = function() {
- return this._centerLatLng;
-};
-
-MapModel.prototype.setTopLeftLatLng = function(topLeftLatLng) {
- var newVal = createLatLng(topLeftLatLng);
- if (newVal === null) {
- logger.warn("topLeftLatLng is invalid");
- } else {
- this._topLeftLatLng = newVal;
- }
-};
-
-MapModel.prototype.getTopLeftLatLng = function() {
- return this._topLeftLatLng;
-};
-
-MapModel.prototype.setBottomRightLatLng = function(bottomRightLatLng) {
- var newVal = createLatLng(bottomRightLatLng);
- if (newVal === null) {
- logger.warn("bottomRightLatLng is invalid");
- } else {
- this._bottomRightLatLng = newVal;
- }
-};
-
-MapModel.prototype.getBottomRightLatLng = function() {
- return this._bottomRightLatLng;
-};
-
-MapModel.prototype.getMaxZoom = function() {
- return this._maxZoom;
-};
-
-MapModel.prototype.setMaxZoom = function(maxZoom) {
- this._maxZoom = maxZoom;
-};
-
-MapModel.prototype.getTileSize = function() {
- return this._tileSize;
-};
-
-MapModel.prototype.getPictureSize = function() {
- return Math.max(this.getWidth(), this.getHeight());
-};
-
-MapModel.prototype.setTileSize = function(tileSize) {
- this._tileSize = tileSize;
-};
-
-MapModel.prototype.addLayouts = function(layouts) {
- if (layouts === undefined) {
- logger.warn("Layouts are undefined...");
- } else {
- for (var i = 0; i < layouts.length; i++) {
- this.addLayout(layouts[i]);
- }
- }
-};
-MapModel.prototype.addLayout = function(layout) {
- var layoutData = null;
- if (layout instanceof LayoutData) {
- layoutData = layout;
- } else {
- layoutData = new LayoutData(layout);
- }
- var object = this._layoutsData[layoutData.getId()];
- if (object === undefined) {
- this._layoutsData[layoutData.getId()] = layoutData;
- } else {
- logger.warn("Layout " + layoutData.getId() + " already exists in a model: " + this.getId());
- }
-};
-
-MapModel.prototype.addSubmodels = function(submodels) {
- if (submodels !== undefined) {
- for (var i = 0; i < submodels.length; i++) {
- this.addSubmodel(submodels[i]);
- }
- }
-};
-
-MapModel.prototype.addSubmodel = function(submodel) {
- if (!(submodel instanceof MapModel)) {
- submodel = new MapModel(submodel);
- }
- this._submodels.push(submodel);
-};
-
-MapModel.prototype.getSubmodels = function() {
- return this._submodels;
-};
-
-MapModel.prototype.getSubmodelById = function(id) {
- if (this.getId() === id) {
- return this;
- }
- for (var i = 0; i < this._submodels.length; i++) {
- if (this._submodels[i].getId() === id) {
- return this._submodels[i];
- }
- }
- return null;
-};
-
-MapModel.prototype._getLayouts = function() {
- var result = [];
- for ( var id in this._layoutsData) {
- if (this._layoutsData.hasOwnProperty(id)) {
- result.push(this._layoutsData[id]);
- }
- }
- return result;
-};
-
-MapModel.prototype.getByIdentifiedElement = function(ie, complete) {
- var self = this;
- if (ie.getType() === "ALIAS") {
- return self.getAliasById(ie.getId(), complete);
- } else if (ie.getType() === "REACTION") {
- return self.getReactionById(ie.getId(), complete);
- } else if (ie.getType() === "POINT") {
- var id = self._pointToId(ie.getId());
- var result = this._pointsData[id];
- if (result === undefined) {
- result = new PointData(ie);
- this._pointsData[id] = result;
- }
- return Promise.resolve(result);
- } else {
- throw new Error("Unknown type: " + ie.getType());
- }
-};
-
-MapModel.prototype.getByIdentifiedElements = function(identifiedElements, complete) {
- var self = this;
- var missingAliases = [];
- var missingReactions = [];
-
- for (var i = 0; i < identifiedElements.length; i++) {
- var ie = identifiedElements[i];
- if (!this.isAvailable(ie, complete)) {
- if (ie.getType() === "ALIAS") {
- missingAliases.push(ie.getId());
- } else if (ie.getType() === "REACTION") {
- missingReactions.push(ie.getId());
- } else {
- throw new Error("Unknown type " + ie);
- }
- }
- }
-
- return self.getMissingElements({
- aliasIds : missingAliases,
- reactionIds : missingReactions,
- complete : complete
- }).then(function() {
- var promises = [];
- for (var i = 0; i < identifiedElements.length; i++) {
- promises.push(self.getByIdentifiedElement(identifiedElements[i], complete));
- }
- return Promise.all(promises);
- });
-
-};
-
-MapModel.prototype.isAvailable = function(ie, complete) {
- var element;
- if (ie.getType() === "ALIAS") {
- element = this._aliases[ie.getId()];
- } else if (ie.getType() === "REACTION") {
- element = this._reactions[ie.getId()];
- } else if (ie.getType() === "POINT") {
- var id = this._pointToId(ie.getId());
- var result = this._pointsData[id];
- if (result === undefined) {
- result = new PointData(ie);
- this._pointsData[id] = result;
- }
- element = this._pointsData[id];
- } else {
- throw new Error("Unknown type: " + ie.getType(), complete);
- }
- if (element === undefined) {
- return false;
- } else if (complete) {
- return element.isComplete();
- } else {
- return true;
- }
-};
-
-MapModel.prototype.getReactionsForElement = function(element, complete) {
- return this.getReactionsForElements([ element ], complete);
-};
-
-MapModel.prototype.getReactionsForElements = function(elements, complete) {
- var self = this;
- var ids = [];
- var i;
- for (i = 0; i < elements.length; i++) {
- ids.push(elements[i].getId());
- }
- var idString = ids.join();
- if (this._reactionsByParticipantElementId[idString]) {
- var reactions = self._reactionsByParticipantElementId[idString];
- if (!complete) {
- return Promise.resolve(reactions);
- } else {
- var promises = [];
- for (i = 0; i < reactions.length; i++) {
- promises.push(self.getCompleteReactionById(reactions[i].getId()));
- }
- return Promise.all(promises);
- }
- }
-
- var result = [];
- return ServerConnector.getReactions({
- modelId: self.getId(),
- participantId : ids
- }).then(function(reactions) {
- result = reactions;
-
- for (var i = 0; i < reactions.length; i++) {
- var reaction = reactions[i];
- var id = reaction.getId();
- if (self._reactions[id] === undefined) {
- self._reactions[id] = reaction;
- } else {
- self._reactions[id].update(reaction);
- }
- }
- var ids = self._getMissingReactionsElementIds(reactions);
- return self.getMissingElements({
- aliasIds : ids,
- complete : true
- });
- }).then(function() {
- var promises = [];
- for (var i = 0; i < result.length; i++) {
- promises.push(self.getCompleteReactionById(result[i].getId()));
- }
- return Promise.all(promises);
- });
-};
-
-MapModel.prototype.getCompartments = function() {
- var self = this;
-
- var promise = Promise.resolve();
- if (self._compartments === undefined) {
- promise = ServerConnector.getAliases({
- columns : "id,bounds,modelId",
- type : "Compartment",
- modelId : self.getId()
- }).then(function(compartments) {
- self._compartments = [];
- for (var i = 0; i < compartments.length; i++) {
- self._compartments.push(new IdentifiedElement(compartments[i]));
- }
- });
- }
- return promise.then(function() {
- return self.getByIdentifiedElements(self._compartments, true);
- });
-};
-
-module.exports = MapModel;
+"use strict";
+
+var Promise = require("bluebird");
+
+var logger = require('../../logger');
+
+var Alias = require('./Alias');
+var IdentifiedElement = require('./IdentifiedElement');
+var LayoutData = require('./LayoutData');
+var PointData = require('./PointData');
+var Reaction = require('./Reaction');
+
+// This file describes javascript representation of Java Model class that
+// represents content of the map.
+
+/**
+ * Default constructor.
+ *
+ */
+
+function MapModel(configuration) {
+
+ // list of aliases is empty (it will be filled dynamically - when necessary)
+ this._aliases = [];
+
+ // list of reactions is empty (it will be filled dynamically - when necessary)
+ this._reactions = [];
+ this._reactionsByParticipantElementId = [];
+
+ // list of aliases that should be updated from server side during the next
+ // connection
+ this._missingAliases = [];
+
+ // list of reactions that should be updated from server side during the next
+ // connection
+ this._missingReactions = [];
+
+ // list of layouts is empty (it will be filled when necessary)
+ this._layoutsData = [];
+
+ // information about points and associated data (for now we have only comments
+ // associated to the point,
+ // but it can be extended)
+ this._pointsData = [];
+
+ this._submodels = [];
+
+ if (configuration !== undefined) {
+ if (configuration instanceof MapModel) {
+ this.setId(configuration.getId());
+ this.setName(configuration.getName());
+ this.setTileSize(configuration.getTileSize());
+ this.setWidth(configuration.getWidth());
+ this.setHeight(configuration.getHeight());
+ this.setMinZoom(configuration.getMinZoom());
+ this.setMaxZoom(configuration.getMaxZoom());
+ this.addLayouts(configuration.getLayouts());
+ this.addSubmodels(configuration.getSubmodels());
+ this.setCenterLatLng(configuration.getCenterLatLng());
+ this.setTopLeftLatLng(configuration.getTopLeftLatLng());
+ this.setBottomRightLatLng(configuration.getBottomRightLatLng());
+ this.setSubmodelType(configuration.getSubmodelType());
+ this.setDefaultCenterX(configuration.getDefaultCenterX());
+ this.setDefaultCenterY(configuration.getDefaultCenterY());
+ this.setDefaultZoomLevel(configuration.getDefaultZoomLevel());
+ } else {
+ this.setId(configuration.idObject);
+ this.setName(configuration.name);
+ this.setTileSize(configuration.tileSize);
+ this.setWidth(configuration.width);
+ this.setHeight(configuration.height);
+ this.setMinZoom(configuration.minZoom);
+ this.setMaxZoom(configuration.maxZoom);
+ this.addLayouts(configuration.layouts);
+ this.addSubmodels(configuration.submodels);
+ this.setCenterLatLng(configuration.centerLatLng);
+ this.setTopLeftLatLng(configuration.topLeftLatLng);
+ this.setBottomRightLatLng(configuration.bottomRightLatLng);
+ this.setSubmodelType(configuration.submodelType);
+ this.setDefaultCenterX(configuration.defaultCenterX);
+ this.setDefaultCenterY(configuration.defaultCenterY);
+ this.setDefaultZoomLevel(configuration.defaultZoomLevel);
+ }
+ }
+}
+
+/**
+ * Returns list of {@link LayoutData} on this model.
+ *
+ * @returns {Array} with list of {@link LayoutData} on this model
+ */
+MapModel.prototype.getLayoutsData = function() {
+ var result = [];
+ for ( var id in this._layoutsData) {
+ if (this._layoutsData.hasOwnProperty(id)) {
+ result.push(this._layoutsData[id]);
+ }
+ }
+ return result;
+};
+
+MapModel.prototype.getLayouts = function() {
+ return this.getLayoutsData();
+};
+
+/**
+ * Return list of all aliases that were added to the model.
+ */
+MapModel.prototype.getAliases = function(params) {
+ var self = this;
+ return ServerConnector.getAliases({
+ columns : "id,modelId",
+ type : params.type,
+ modelId : self.getId(),
+ includedCompartmentIds : params.includedCompartmentIds,
+ excludedCompartmentIds : params.excludedCompartmentIds,
+
+ }).then(function(lightAliases) {
+ var identifiedElements = [];
+ for (var i = 0; i < lightAliases.length; i++) {
+ self.addAlias(lightAliases[i]);
+ identifiedElements.push(new IdentifiedElement(lightAliases[i]));
+ }
+ return self.getByIdentifiedElements(identifiedElements, params.complete);
+ });
+};
+
+/**
+ * Returns {@link Alias} by identifier.
+ *
+ * @param id
+ * identifier of the {@link Alias}
+ * @returns {@link Alias} by identifier
+ */
+MapModel.prototype.getAliasById = function(id, complete) {
+ var self = this;
+ if (complete) {
+ return this.getCompleteAliasById(id);
+ }
+ if (self._aliases[id] !== undefined) {
+ return Promise.resolve(self._aliases[id]);
+ } else {
+ return self.getMissingElements({
+ aliasIds : [ id ]
+ }).then(function() {
+ return self._aliases[id];
+ });
+ }
+};
+
+MapModel.prototype.getCompleteAliasById = function(id) {
+ var self = this;
+ if (self._aliases[id] !== undefined && self._aliases[id].isComplete()) {
+ return Promise.resolve(self._aliases[id]);
+ } else {
+ return ServerConnector.getAliases({
+ ids : id
+ }).then(function(aliases) {
+ if (self._aliases[id] === undefined) {
+ self._aliases[id] = aliases[0];
+ } else {
+ self._aliases[id].update(aliases[0]);
+ }
+ return self._aliases[id];
+ });
+ }
+};
+
+/**
+ * Returns {@link Reaction} by identifier.
+ *
+ * @param id
+ * identifier of the {@link Reaction}
+ * @returns {@link Reaction} by identifier
+ */
+MapModel.prototype.getReactionById = function(id, complete) {
+ var self = this;
+ if (complete) {
+ return this.getCompleteReactionById(id);
+ }
+ if (self._reactions[id] !== undefined) {
+ return Promise.resolve(self._reactions[id]);
+ } else {
+ return self.getMissingElements({
+ reactionIds : [ id ]
+ }).then(function() {
+ return self._reactions[id];
+ });
+ }
+};
+
+MapModel.prototype._getMissingReactionsElementIds = function(reactions) {
+ var self = this;
+ var result = [];
+ var ids = [];
+ for (var i = 0; i < reactions.length; i++) {
+ var reaction = reactions[i];
+ var elements = reaction.getElements();
+ for (var j = 0; j < elements.length; j++) {
+ var element = elements[j];
+ if (!(element instanceof Alias)) {
+ if (self._aliases[element] === undefined || !self._aliases[element].isComplete()) {
+ if (!ids[element]) {
+ ids[element] = true;
+ result.push(element);
+ }
+ }
+ }
+ }
+ }
+ return result;
+};
+
+MapModel.prototype.getCompleteReactionById = function(id) {
+ var self = this;
+ if (self._reactions[id] instanceof Reaction && self._reactions[id].isComplete()) {
+ return Promise.resolve(self._reactions[id]);
+ } else {
+ var result;
+ return self.getReactionById(id).then(function(result) {
+ var ids = self._getMissingReactionsElementIds([ result ]);
+ return self.getMissingElements({
+ aliasIds : ids,
+ complete : true
+ });
+ }).then(function() {
+ var i;
+ result = self._reactions[id];
+ for (i = 0; i < result.getReactants().length; i++) {
+ if (!(result.getReactants()[i] instanceof Alias)) {
+ result.getReactants()[i] = self._aliases[result.getReactants()[i]];
+ }
+ }
+ for (i = 0; i < result.getProducts().length; i++) {
+ if (!(result.getProducts()[i] instanceof Alias)) {
+ result.getProducts()[i] = self._aliases[result.getProducts()[i]];
+ }
+ }
+ for (i = 0; i < result.getModifiers().length; i++) {
+ if (!(result.getModifiers()[i] instanceof Alias)) {
+ result.getModifiers()[i] = self._aliases[result.getModifiers()[i]];
+ }
+ }
+ return result;
+ });
+ }
+};
+
+MapModel.prototype.getMissingElements = function(elements) {
+ var self = this;
+
+ var layouts = this._getLayouts();
+ var aliasIds = [];
+ var reactionIds = [];
+
+ var i = 0;
+ if (elements.reactionIds !== undefined) {
+ reactionIds.push.apply(reactionIds, elements.reactionIds);
+ for (i = 0; i < reactionIds.length; i++) {
+ this._missingReactions[reactionIds[i]] = reactionIds[i];
+ }
+
+ }
+ if (elements.aliasIds !== undefined) {
+ aliasIds.push.apply(aliasIds, elements.aliasIds);
+ for (i = 0; i < aliasIds.length; i++) {
+ this._missingAliases[aliasIds[i]] = aliasIds[i];
+ }
+ }
+
+ for (i = 0; i < layouts.length; i++) {
+ var layout = layouts[i];
+ if (layout.isInitialized()) {
+ var aliases = layout.getAliases();
+ for (var j = 0; j < aliases.length; j++) {
+ var alias = aliases[j];
+ if (this._aliases[alias.getId()] === undefined && this._missingAliases[alias.getId()] === undefined) {
+ this._missingAliases[alias.getId()] = alias.getId();
+ aliasIds.push(alias.getId());
+ }
+ }
+
+ var reactions = layout.getReactions();
+ for (var k = 0; k < reactions.length; k++) {
+ var reaction = reactions[k];
+ if (this._reactions[reaction.getId()] === undefined && this._missingReactions[reaction.getId()] === undefined) {
+ this._missingReactions[reaction.getId()] = reaction.getId();
+ reactionIds.push(reaction.getId());
+ }
+ }
+ }
+ }
+ var reactionPromise = null;
+ if (reactionIds.length > 0) {
+ reactionPromise = ServerConnector.getReactions({
+ ids : reactionIds,
+ complete : elements.complete
+ });
+ }
+
+ var aliasPromise = null;
+ if (aliasIds.length > 0) {
+ if (elements.complete) {
+ aliasPromise = ServerConnector.getAliases({
+ ids : aliasIds
+ });
+ } else {
+ aliasPromise = ServerConnector.getAliases({
+ ids : aliasIds,
+ columns : "id,bounds,modelId"
+ });
+
+ }
+ }
+
+ var result = [];
+ return Promise.all([ reactionPromise, aliasPromise ]).then(function(values) {
+ var i;
+ var reactions = values[0];
+ var aliases = values[1];
+ var ids = [];
+
+ if (reactions !== null) {
+ for (i = 0; i < reactions.length; i++) {
+ var reaction = reactions[i];
+ self.addReaction(reaction);
+ result.push(reaction);
+ }
+ ids = self._getMissingReactionsElementIds(reactions);
+ }
+ if (aliases !== null) {
+ for (i = 0; i < aliases.length; i++) {
+ var alias = aliases[i];
+ self.addAlias(alias);
+ result.push(alias);
+ }
+ }
+ if (ids.length > 0) {
+ return self.getMissingElements({
+ aliasIds : ids,
+ complete : true
+ });
+ } else {
+ return Promise.resolve([]);
+ }
+ }).then(function() {
+ return result;
+ });
+};
+
+/**
+ * Returns layout data for a given layout identifier.
+ *
+ * @param layoutId
+ * layout identifier
+ * @returns {LayoutData} for a given layout identifier
+ */
+MapModel.prototype.getLayoutDataById = function(layoutId) {
+ var self = this;
+ if (self._layoutsData[layoutId] !== undefined) {
+ return Promise.resolve(self._layoutsData[layoutId]);
+ } else {
+ return ServerConnector.getOverlayById(layoutId).then(function(layout) {
+ self.addLayout(layout);
+ return self._layoutsData[layoutId];
+ });
+ }
+};
+
+/**
+ * Adds information about alias.
+ *
+ * @param aliasData
+ * raw data about alias
+ */
+MapModel.prototype.addAlias = function(aliasData) {
+ var alias = aliasData;
+ if (!(aliasData instanceof Alias)) {
+ alias = new Alias(aliasData);
+ }
+ if (this._aliases[alias.getId()] !== undefined) {
+ this._aliases[alias.getId()].update(alias);
+ } else {
+ this._aliases[alias.getId()] = alias;
+ if (this._missingAliases[alias.getId()] !== undefined) {
+ this._missingAliases[alias.getId()] = null;
+ delete this._missingAliases[alias.getId()];
+ }
+ }
+};
+
+/**
+ * Adds information about reaction.
+ *
+ * @param reactionData
+ * raw data about reaction
+ */
+MapModel.prototype.addReaction = function(reactionData) {
+ var reaction = null;
+ if (reactionData instanceof Reaction) {
+ reaction = reactionData;
+ } else {
+ reaction = new Reaction(reactionData);
+ }
+ if (this._reactions[reaction.getId()] !== undefined) {
+ logger.warn("Reaction with id: " + reaction.getId() + " already exists");
+ } else {
+ this._reactions[reaction.getId()] = reaction;
+ if (this._missingReactions[reaction.getId()] !== undefined) {
+ this._missingReactions[reaction.getId()] = null;
+ delete this._missingReactions[reaction.getId()];
+ }
+ }
+};
+
+/**
+ * Returns {@link PointData} for a given point on the map.
+ *
+ * @param point
+ * {@link google.maps.Point} where we are requesting data
+ * @returns {@link PointData} for a given point on the map
+ */
+MapModel.prototype.getPointDataByPoint = function(inputPoint) {
+ if (inputPoint instanceof google.maps.Point) {
+ var point = this._roundPoint(inputPoint);
+ var id = this._pointToId(point);
+ var result = this._pointsData[id];
+ if (result === undefined) {
+ result = new PointData(point, this.getId());
+ this._pointsData[id] = result;
+ }
+ return result;
+ } else {
+ logger.warn("point must be of class: google.maps.Point");
+ return null;
+ }
+};
+
+/**
+ * Returns point where x and y coordinate are rounded to 2 decimal places.
+ *
+ * @param point
+ * input point
+ * @returns {google.maps.Point} point where x and y coordinate are rounded to 2
+ * decimal places
+ */
+MapModel.prototype._roundPoint = function(point) {
+ var x = parseFloat(point.x).toFixed(2);
+ var y = parseFloat(point.y).toFixed(2);
+ return new google.maps.Point(x, y);
+};
+
+/**
+ * Transform point into string identifier.
+ *
+ * @param point
+ * {google.maps.Point} to transform
+ * @returns {String} string identifier for a given point
+ */
+MapModel.prototype._pointToId = function(point) {
+ if (point instanceof google.maps.Point) {
+ return "(" + point.x + ", " + point.y + ")";
+ } else {
+ return point.replace(/ /g, '');
+ }
+};
+
+MapModel.prototype.getId = function() {
+ return this.id;
+};
+
+MapModel.prototype.setId = function(id) {
+ this.id = parseInt(id);
+};
+
+MapModel.prototype.getWidth = function() {
+ return this._width;
+};
+
+MapModel.prototype.setWidth = function(width) {
+ this._width = width;
+};
+
+MapModel.prototype.getHeight = function() {
+ return this._height;
+};
+
+MapModel.prototype.setHeight = function(height) {
+ this._height = height;
+};
+
+MapModel.prototype.getName = function() {
+ return this._name;
+};
+
+MapModel.prototype.setName = function(name) {
+ this._name = name;
+};
+
+MapModel.prototype.getMinZoom = function() {
+ return this._minZoom;
+};
+
+MapModel.prototype.setMinZoom = function(minZoom) {
+ this._minZoom = minZoom;
+};
+
+MapModel.prototype.getDefaultZoomLevel = function() {
+ return this._defaultZoomLevel;
+};
+
+MapModel.prototype.setDefaultZoomLevel = function(defaultZoomLevel) {
+ this._defaultZoomLevel = defaultZoomLevel;
+};
+
+MapModel.prototype.getDefaultCenterX = function() {
+ return this._defaultCenterX;
+};
+
+MapModel.prototype.setDefaultCenterX = function(defaultCenterX) {
+ this._defaultCenterX = defaultCenterX;
+};
+
+MapModel.prototype.getDefaultCenterY = function() {
+ return this._defaultCenterY;
+};
+
+MapModel.prototype.setDefaultCenterY = function(defaultCenterY) {
+ this._defaultCenterY = defaultCenterY;
+};
+
+MapModel.prototype.getSubmodelType = function() {
+ return this._submodelType;
+};
+
+MapModel.prototype.setSubmodelType = function(submodelType) {
+ this._submodelType = submodelType;
+};
+
+function createLatLng(param) {
+ if (param === undefined) {
+ return null;
+ }
+ if (param instanceof google.maps.LatLng) {
+ return new google.maps.LatLng(param.lat(), param.lng());
+ } else {
+ return new google.maps.LatLng(param.lat, param.lng);
+ }
+}
+
+MapModel.prototype.setCenterLatLng = function(centerLatLng) {
+ var newVal = createLatLng(centerLatLng);
+ if (newVal === null) {
+ logger.warn("centerLatLng is invalid");
+ } else {
+ this._centerLatLng = newVal;
+ }
+};
+
+MapModel.prototype.getCenterLatLng = function() {
+ return this._centerLatLng;
+};
+
+MapModel.prototype.setTopLeftLatLng = function(topLeftLatLng) {
+ var newVal = createLatLng(topLeftLatLng);
+ if (newVal === null) {
+ logger.warn("topLeftLatLng is invalid");
+ } else {
+ this._topLeftLatLng = newVal;
+ }
+};
+
+MapModel.prototype.getTopLeftLatLng = function() {
+ return this._topLeftLatLng;
+};
+
+MapModel.prototype.setBottomRightLatLng = function(bottomRightLatLng) {
+ var newVal = createLatLng(bottomRightLatLng);
+ if (newVal === null) {
+ logger.warn("bottomRightLatLng is invalid");
+ } else {
+ this._bottomRightLatLng = newVal;
+ }
+};
+
+MapModel.prototype.getBottomRightLatLng = function() {
+ return this._bottomRightLatLng;
+};
+
+MapModel.prototype.getMaxZoom = function() {
+ return this._maxZoom;
+};
+
+MapModel.prototype.setMaxZoom = function(maxZoom) {
+ this._maxZoom = maxZoom;
+};
+
+MapModel.prototype.getTileSize = function() {
+ return this._tileSize;
+};
+
+MapModel.prototype.getPictureSize = function() {
+ return Math.max(this.getWidth(), this.getHeight());
+};
+
+MapModel.prototype.setTileSize = function(tileSize) {
+ this._tileSize = tileSize;
+};
+
+MapModel.prototype.addLayouts = function(layouts) {
+ if (layouts === undefined) {
+ logger.warn("Layouts are undefined...");
+ } else {
+ for (var i = 0; i < layouts.length; i++) {
+ this.addLayout(layouts[i]);
+ }
+ }
+};
+MapModel.prototype.addLayout = function(layout) {
+ var layoutData = null;
+ if (layout instanceof LayoutData) {
+ layoutData = layout;
+ } else {
+ layoutData = new LayoutData(layout);
+ }
+ var object = this._layoutsData[layoutData.getId()];
+ if (object === undefined) {
+ this._layoutsData[layoutData.getId()] = layoutData;
+ } else {
+ logger.warn("Layout " + layoutData.getId() + " already exists in a model: " + this.getId());
+ }
+};
+
+MapModel.prototype.addSubmodels = function(submodels) {
+ if (submodels !== undefined) {
+ for (var i = 0; i < submodels.length; i++) {
+ this.addSubmodel(submodels[i]);
+ }
+ }
+};
+
+MapModel.prototype.addSubmodel = function(submodel) {
+ if (!(submodel instanceof MapModel)) {
+ submodel = new MapModel(submodel);
+ }
+ this._submodels.push(submodel);
+};
+
+MapModel.prototype.getSubmodels = function() {
+ return this._submodels;
+};
+
+MapModel.prototype.getSubmodelById = function(id) {
+ if (this.getId() === id) {
+ return this;
+ }
+ for (var i = 0; i < this._submodels.length; i++) {
+ if (this._submodels[i].getId() === id) {
+ return this._submodels[i];
+ }
+ }
+ return null;
+};
+
+MapModel.prototype._getLayouts = function() {
+ var result = [];
+ for ( var id in this._layoutsData) {
+ if (this._layoutsData.hasOwnProperty(id)) {
+ result.push(this._layoutsData[id]);
+ }
+ }
+ return result;
+};
+
+MapModel.prototype.getByIdentifiedElement = function(ie, complete) {
+ var self = this;
+ if (ie.getType() === "ALIAS") {
+ return self.getAliasById(ie.getId(), complete);
+ } else if (ie.getType() === "REACTION") {
+ return self.getReactionById(ie.getId(), complete);
+ } else if (ie.getType() === "POINT") {
+ var id = self._pointToId(ie.getId());
+ var result = this._pointsData[id];
+ if (result === undefined) {
+ result = new PointData(ie);
+ this._pointsData[id] = result;
+ }
+ return Promise.resolve(result);
+ } else {
+ throw new Error("Unknown type: " + ie.getType());
+ }
+};
+
+MapModel.prototype.getByIdentifiedElements = function(identifiedElements, complete) {
+ var self = this;
+ var missingAliases = [];
+ var missingReactions = [];
+
+ for (var i = 0; i < identifiedElements.length; i++) {
+ var ie = identifiedElements[i];
+ if (!this.isAvailable(ie, complete)) {
+ if (ie.getType() === "ALIAS") {
+ missingAliases.push(ie.getId());
+ } else if (ie.getType() === "REACTION") {
+ missingReactions.push(ie.getId());
+ } else {
+ throw new Error("Unknown type " + ie);
+ }
+ }
+ }
+
+ return self.getMissingElements({
+ aliasIds : missingAliases,
+ reactionIds : missingReactions,
+ complete : complete
+ }).then(function() {
+ var promises = [];
+ for (var i = 0; i < identifiedElements.length; i++) {
+ promises.push(self.getByIdentifiedElement(identifiedElements[i], complete));
+ }
+ return Promise.all(promises);
+ });
+
+};
+
+MapModel.prototype.isAvailable = function(ie, complete) {
+ var element;
+ if (ie.getType() === "ALIAS") {
+ element = this._aliases[ie.getId()];
+ } else if (ie.getType() === "REACTION") {
+ element = this._reactions[ie.getId()];
+ } else if (ie.getType() === "POINT") {
+ var id = this._pointToId(ie.getId());
+ var result = this._pointsData[id];
+ if (result === undefined) {
+ result = new PointData(ie);
+ this._pointsData[id] = result;
+ }
+ element = this._pointsData[id];
+ } else {
+ throw new Error("Unknown type: " + ie.getType(), complete);
+ }
+ if (element === undefined) {
+ return false;
+ } else if (complete) {
+ return element.isComplete();
+ } else {
+ return true;
+ }
+};
+
+MapModel.prototype.getReactionsForElement = function(element, complete) {
+ return this.getReactionsForElements([ element ], complete);
+};
+
+MapModel.prototype.getReactionsForElements = function(elements, complete) {
+ var self = this;
+ var ids = [];
+ var i;
+ for (i = 0; i < elements.length; i++) {
+ ids.push(elements[i].getId());
+ }
+ var idString = ids.join();
+ if (this._reactionsByParticipantElementId[idString]) {
+ var reactions = self._reactionsByParticipantElementId[idString];
+ if (!complete) {
+ return Promise.resolve(reactions);
+ } else {
+ var promises = [];
+ for (i = 0; i < reactions.length; i++) {
+ promises.push(self.getCompleteReactionById(reactions[i].getId()));
+ }
+ return Promise.all(promises);
+ }
+ }
+
+ var result = [];
+ return ServerConnector.getReactions({
+ modelId: self.getId(),
+ participantId : ids
+ }).then(function(reactions) {
+ result = reactions;
+
+ for (var i = 0; i < reactions.length; i++) {
+ var reaction = reactions[i];
+ var id = reaction.getId();
+ if (self._reactions[id] === undefined) {
+ self._reactions[id] = reaction;
+ } else {
+ self._reactions[id].update(reaction);
+ }
+ }
+ var ids = self._getMissingReactionsElementIds(reactions);
+ return self.getMissingElements({
+ aliasIds : ids,
+ complete : true
+ });
+ }).then(function() {
+ var promises = [];
+ for (var i = 0; i < result.length; i++) {
+ promises.push(self.getCompleteReactionById(result[i].getId()));
+ }
+ return Promise.all(promises);
+ });
+};
+
+MapModel.prototype.getCompartments = function() {
+ var self = this;
+
+ var promise = Promise.resolve();
+ if (self._compartments === undefined) {
+ promise = ServerConnector.getAliases({
+ columns : "id,bounds,modelId",
+ type : "Compartment",
+ modelId : self.getId()
+ }).then(function(compartments) {
+ self._compartments = [];
+ for (var i = 0; i < compartments.length; i++) {
+ self._compartments.push(new IdentifiedElement(compartments[i]));
+ }
+ });
+ }
+ return promise.then(function() {
+ return self.getByIdentifiedElements(self._compartments, true);
+ });
+};
+
+module.exports = MapModel;
diff --git a/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js b/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js
index 886be16557..d5d1638bba 100644
--- a/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js
+++ b/frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js
@@ -1,114 +1,132 @@
-"use strict";
-
-require("../../mocha-config");
-
-var EditProjectDialog = require('../../../../main/js/gui/admin/EditProjectDialog');
-var ServerConnector = require('../../ServerConnector-mock');
-var logger = require('../../logger');
-
-var assert = require('assert');
-
-describe('EditProjectDialog', function () {
-
- it('open', function () {
- var dialog;
- var project;
- return ServerConnector.getProject().then(function (result) {
- project = result;
- dialog = new EditProjectDialog({
- element: testDiv,
- project: project,
- customMap: null
- });
- return dialog.open();
- }).then(function () {
- assert.equal(0, logger.getWarnings().length);
- dialog.destroy();
- });
- });
-
- it('init', function () {
- var dialog;
- var project;
- return ServerConnector.getProject().then(function (result) {
- project = result;
- dialog = new EditProjectDialog({
- element: testDiv,
- project: project,
- customMap: null
- });
- return dialog.init();
- }).then(function () {
- dialog.destroy();
- });
- });
- it('saveOverlay', function () {
- var dialog;
- var project;
- return ServerConnector.getProject().then(function (result) {
- project = result;
- dialog = new EditProjectDialog({
- element: testDiv,
- project: project,
- customMap: null
- });
- return dialog.init();
- }).then(function () {
- return dialog.saveOverlay(14081);
- }).then(function () {
- dialog.destroy();
- });
- });
-
- it('saveUser', function () {
- var dialog;
- var project;
- return ServerConnector.getProject().then(function (result) {
- project = result;
- dialog = new EditProjectDialog({
- element: testDiv,
- project: project,
- customMap: null
- });
- return dialog.init();
- }).then(function () {
- return dialog.saveUser("anonymous");
- }).then(function () {
- dialog.destroy();
- });
- });
-
-
- it('onSaveClicked', function () {
- var dialog;
- var project;
- return ServerConnector.getProject().then(function (result) {
- project = result;
- project.setVersion("2.01");
- dialog = new EditProjectDialog({
- element: testDiv,
- project: project,
- customMap: null
- });
- return dialog.onSaveClicked();
- }).then(function (result) {
- assert.ok(project === result);
- dialog.destroy();
- });
- });
-
- it('openAddOverlayDialog', function () {
- var dialog;
- return ServerConnector.getProject().then(function (project) {
- dialog = new EditProjectDialog({
- element: testDiv,
- project: project,
- customMap: null
- });
- return dialog.openAddOverlayDialog();
- }).then(function () {
- dialog.destroy();
- });
- });
-
-});
+"use strict";
+
+require("../../mocha-config");
+
+var EditProjectDialog = require('../../../../main/js/gui/admin/EditProjectDialog');
+var ServerConnector = require('../../ServerConnector-mock');
+var logger = require('../../logger');
+
+var assert = require('assert');
+
+describe('EditProjectDialog', function () {
+
+ it('open', function () {
+ var dialog;
+ var project;
+ return ServerConnector.getProject().then(function (result) {
+ project = result;
+ dialog = new EditProjectDialog({
+ element: testDiv,
+ project: project,
+ customMap: null
+ });
+ return dialog.open();
+ }).then(function () {
+ assert.equal(0, logger.getWarnings().length);
+ dialog.destroy();
+ });
+ });
+
+ it('init', function () {
+ var dialog;
+ var project;
+ return ServerConnector.getProject().then(function (result) {
+ project = result;
+ dialog = new EditProjectDialog({
+ element: testDiv,
+ project: project,
+ customMap: null
+ });
+ return dialog.init();
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
+ it('saveOverlay', function () {
+ var dialog;
+ var project;
+ return ServerConnector.getProject().then(function (result) {
+ project = result;
+ dialog = new EditProjectDialog({
+ element: testDiv,
+ project: project,
+ customMap: null
+ });
+ return dialog.init();
+ }).then(function () {
+ return dialog.saveOverlay(14081);
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
+
+ it('saveMap', function () {
+ var dialog;
+ var project;
+ return ServerConnector.getProject().then(function (result) {
+ project = result;
+ dialog = new EditProjectDialog({
+ element: testDiv,
+ project: project,
+ customMap: null
+ });
+ return dialog.init();
+ }).then(function () {
+ return dialog.saveMap(15781);
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
+
+ it('saveUser', function () {
+ var dialog;
+ var project;
+ return ServerConnector.getProject().then(function (result) {
+ project = result;
+ dialog = new EditProjectDialog({
+ element: testDiv,
+ project: project,
+ customMap: null
+ });
+ return dialog.init();
+ }).then(function () {
+ return dialog.saveUser("anonymous");
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
+
+
+ it('onSaveClicked', function () {
+ var dialog;
+ var project;
+ return ServerConnector.getProject().then(function (result) {
+ project = result;
+ project.setVersion("2.01");
+ dialog = new EditProjectDialog({
+ element: testDiv,
+ project: project,
+ customMap: null
+ });
+ return dialog.onSaveClicked();
+ }).then(function (result) {
+ assert.ok(project === result);
+ dialog.destroy();
+ });
+ });
+
+ it('openAddOverlayDialog', function () {
+ var dialog;
+ return ServerConnector.getProject().then(function (project) {
+ dialog = new EditProjectDialog({
+ element: testDiv,
+ project: project,
+ customMap: null
+ });
+ return dialog.openAddOverlayDialog();
+ }).then(function () {
+ dialog.destroy();
+ });
+ });
+
+});
diff --git a/frontend-js/testFiles/apiCalls/projects/sample/models/15781/PATCH_model.id=15781&token=MOCK_TOKEN_ID& b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/PATCH_model.id=15781&token=MOCK_TOKEN_ID&
new file mode 100644
index 0000000000..689b1eb3d8
--- /dev/null
+++ b/frontend-js/testFiles/apiCalls/projects/sample/models/15781/PATCH_model.id=15781&token=MOCK_TOKEN_ID&
@@ -0,0 +1 @@
+{"version":null,"name":"UNKNOWN DISEASE MAP","idObject":15781,"tileSize":256,"width":1305,"height":473,"defaultCenterX":3.0,"defaultCenterY":4.0,"defaultZoomLevel":null,"minZoom":2,"maxZoom":5,"layouts":[{"idObject":14081,"modelId":15781,"name":"Pathways and compartments","description":"","status":"Not available","publicOverlay":true,"defaultOverlay":false,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_nested0","creator":"","inputDataAvailable":"false"},{"idObject":14082,"modelId":15781,"name":"Network","description":"","status":"Not available","publicOverlay":true,"defaultOverlay":false,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_normal0","creator":"","inputDataAvailable":"false"},{"idObject":14083,"modelId":15781,"name":"Empty","description":"","status":"Not available","publicOverlay":true,"defaultOverlay":true,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/_empty0","creator":"","inputDataAvailable":"false"},{"idObject":18076,"modelId":15781,"name":"C:\\fakepath\\test.txt","description":"xxx","status":"OK","publicOverlay":true,"defaultOverlay":false,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18076","creator":"","inputDataAvailable":"true"},{"idObject":18077,"modelId":15781,"name":"xxx","description":"yyy","status":"OK","publicOverlay":true,"defaultOverlay":false,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.18077","creator":"","inputDataAvailable":"true"},{"idObject":22750,"modelId":15781,"name":"new-global","description":"","status":"OK","publicOverlay":true,"defaultOverlay":false,"progress":"0.00","directory":"5e8ff9bf55ba3508199d22e984129be6/.22750","creator":"","inputDataAvailable":"true"}],"submodels":[],"centerLatLng":{"lat":79.18277721779353,"lng":-135.06093781915757},"topLeftLatLng":{"lat":85.05112877980659,"lng":-180.0},"bottomRightLatLng":{"lat":81.26928406550978,"lng":-90.0},"submodelType":"UNKNOWN"}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
index f5d4a32637..f20bbd35a4 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/Model.java
@@ -21,7 +21,7 @@ import lcsb.mapviewer.model.map.species.Species;
/**
* This interface defines functionality that the model container class should
- * implement to access data effitiently. It shouldn't be implemented by data
+ * implement to access data efficiently. It shouldn't be implemented by data
* model.
*
* @author Piotr Gawron
@@ -29,543 +29,563 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public interface Model {
- /**
- * Adds element to the model.
- *
- * @param element
- * element to add
- */
- void addElement(Element element);
-
- /**
- *
- * @return model width
- */
- Double getWidth();
-
- /**
- * Sets model width.
- *
- * @param width
- * new model width
- */
- void setWidth(Double width);
-
- /**
- *
- * @return model hieght
- */
- Double getHeight();
-
- /**
- * Sets model height.
- *
- * @param height
- * new model height
- */
- void setHeight(Double height);
-
- /**
- * Sets model width.
- *
- * @param text
- * new model width
- */
- void setWidth(String text);
-
- /**
- * Sets model height.
- *
- * @param text
- * new model height
- */
- void setHeight(String text);
-
- /**
- * Returns set of all alisaes.
- *
- * @return set of all alisaes
- */
- Set<Element> getElements();
-
- /**
- * Returns element with the given element identfier ({@link Element#elementId}
- * ).
- *
- * @param idElement
- * element identifier
- * @param <T>
- * type of the object to be returned
- * @return {@link Element} with the given id
- */
- <T extends Element> T getElementByElementId(String idElement);
-
- /**
- * Adds reaction to the model.
- *
- * @param reaction
- * reaction to add
- */
- void addReaction(Reaction reaction);
-
- /**
- * Returns set of reactions.
- *
- * @return set of reaction in the model
- */
- Set<Reaction> getReactions();
-
- /**
- * @return list of compartments
- */
- List<Compartment> getCompartments();
-
- /**
- * Adds layer to the model.
- *
- * @param layer
- * object to add
- */
- void addLayer(Layer layer);
-
- /**
- *
- * @return set of layers
- */
- Set<Layer> getLayers();
-
- /**
- * Adds list of elements into model.
- *
- * @param elements
- * list of elements
- */
- void addElements(List<? extends Element> elements);
-
- /**
- * Sets new short description of the model.
- *
- * @param notes
- * new short description
- */
- void setNotes(String notes);
-
- /**
- *
- * @return short description of the model
- */
- String getNotes();
-
- /**
- * Returns reaction with the id given in the parameter.
- *
- * @param idReaction
- * reaction identifier ({@link Reaction#idReaction})
- * @return reaction with the id given in the parameter
- */
- Reaction getReactionByReactionId(String idReaction);
-
- /**
- * Adds set of layers to the model.
- *
- * @param layers
- * object to add
- */
- void addLayers(Collection<Layer> layers);
-
- /**
- * Adds {@link ElementGroup} to the model.
- *
- * @param elementGroup
- * object to add
- */
- void addElementGroup(ElementGroup elementGroup);
-
- /**
- * Adds {@link BlockDiagram} to the model.
- *
- * @param blockDiagram
- * object to add
- */
- void addBlockDiagream(BlockDiagram blockDiagram);
-
- /**
- * @param idModel
- * the idModel to set
- * @see Model#idModel
- */
- void setIdModel(String idModel);
-
- /**
- * @return the idModel
- * @see Model#idModel
- */
- String getIdModel();
-
- /**
- * @param tileSize
- * the tileSize to set
- * @see ModelData#tileSize
- */
- void setTileSize(int tileSize);
-
- /**
- * @return the tileSize
- * @see ModelData#tileSize
- */
- int getTileSize();
-
- /**
- * @param zoomLevels
- * the zoomLevels to set
- * @see ModelData#zoomLevels
- */
- void setZoomLevels(int zoomLevels);
-
- /**
- * @return the zoomLevels
- * @see ModelData#zoomLevels
- */
- int getZoomLevels();
-
- /**
- * Removes reaction from model.
- *
- * @param reaction
- * reaction to remove
- */
- void removeReaction(Reaction reaction);
-
- /**
- * Removes {@link Element} from the model.
- *
- * @param element
- * element to remove
- */
- void removeElement(Element element);
-
- /**
- * Returns list of reactions sorted by reaction id.
- *
- * @return list of reactions sorted by reaction id
- */
- List<Reaction> getSortedReactions();
-
- /**
- * Return list of elements sorted by the size.
- *
- * @return list of elements sorted by the size
- */
- List<Element> getSortedSpeciesList();
-
- /**
- * Returns collection of all {@link Species} excluding {@link Complex}.
- *
- * @return collection of all {@link Species} excluding {@link Complex}.
- */
- Collection<Species> getNotComplexSpeciesList();
-
- /**
- * Returns list of all {@link Species} in the model.
- *
- * @return list of all {@link Species} in the model
- */
- List<Species> getSpeciesList();
-
- /**
- * Returns collection of {@link Complex}.
- *
- * @return collection of {@link Complex}
- */
- Collection<Complex> getComplexList();
-
- /**
- * Adds reactions to model.
- *
- * @param reactions2
- * list of reaction to add
- */
- void addReactions(List<Reaction> reactions2);
-
- /**
- * Returns list of elements annotated by the {@link MiriamData}.
- *
- * @param miriamData
- * {@link MiriamData}
- * @return list of elements
- */
- Set<BioEntity> getElementsByAnnotation(MiriamData miriamData);
-
- /**
- * Returns list of elements with given name.
- *
- * @param name
- * name of the element
- * @return list of elements with given name
- */
- List<Element> getElementsByName(String name);
-
- /**
- *
- * @param height
- * new {@link ModelData#height}
- */
- void setHeight(int height);
-
- /**
- *
- * @param width
- * new {@link ModelData#width}
- */
- void setWidth(int width);
-
- /**
- * Adds layout to model.
- *
- * @param layout
- * layout to add
- */
- void addLayout(Layout layout);
-
- /**
- *
- * @param layouts
- * new {@link ModelData#layouts}
- */
- void setLayouts(List<Layout> layouts);
-
- /**
- *
- * @return {@link ModelData#layouts}
- */
- List<Layout> getLayouts();
-
- /**
- *
- * @param creationDate
- * new {@link ModelData#creationDate}
- */
- void setCreationDate(Calendar creationDate);
-
- /**
- *
- * @return {@link ModelData#creationDate}
- */
- Calendar getCreationDate();
-
- /**
- * Returns {@link Element} for given database identifier.
- *
- * @param dbId
- * element database identifier ({@link Element#id})
- * @return {@link Element} for a given id
- */
- <T extends Element> T getElementByDbId(Integer dbId);
-
- /**
- * Returns {@link Reaction} for given database identifier.
- *
- * @param dbId
- * reaction database identifier ({@link Reaction#id})
- * @return {@link Reaction} for a given id
- */
- Reaction getReactionByDbId(Integer dbId);
-
- /**
- * Returns sorted by size list of compartments.
- *
- * @return list of compartment sorted by size
- */
- List<Compartment> getSortedCompartments();
-
- /**
- * Returns list of elements sorted by the size.
- *
- * @return list of elements sorted by the size
- */
- List<Element> getElementsSortedBySize();
-
- /**
- *
- * @param project
- * new {@link ModelData#project}
- */
- void setProject(Project project);
-
- /**
- *
- * @return {@link ModelData#project}
- */
- Project getProject();
-
- /**
- *
- * @param elements
- * new {@link ModelData#elements} collection
- */
- void setElements(Set<Element> elements);
-
- /**
- * @return the modelData
- */
- ModelData getModelData();
-
- /**
- *
- * @return {@link ModelData#id}
- */
- Integer getId();
-
- /**
- * Adds submodel connection.
- *
- * @param submodel
- * submodel to add
- */
- void addSubmodelConnection(ModelSubmodelConnection submodel);
-
- /**
- * Returns set of submodel connections.
- *
- * @return collection of submodels
- */
- Collection<ModelSubmodelConnection> getSubmodelConnections();
-
- /**
- * Returns name of the model.
- *
- * @return name of the model
- */
- String getName();
-
- /**
- * Sets name of the model.
- *
- * @param name
- * name of the model
- */
- void setName(String name);
-
- /**
- * Returns {@link Model submodel} by the {@link ModelData#id database
- * identifier} given in the parameter.
- *
- * @param idObject
- * the {@link ModelData#id database identifier} that identifies
- * submodel
- * @return {@link Model submodel} by the {@link ModelData#id database
- * identifier} given in the parameter
- */
- Model getSubmodelById(Integer idObject);
-
- /**
- * Returns set of connections that point to this model. Be very carefoul with
- * using this function as the implementation forces lazy loading of the maps.
- *
- * @return set of connections that point to this model
- */
- Collection<SubmodelConnection> getParentModels();
-
- /**
- * Returns connection to a submodel identified by connection name.
- *
- * @param name
- * name of the connection
- * @return connection to a submodel identified by connection name
- */
- Model getSubmodelByConnectionName(String name);
-
- /**
- * Returns connection to a submodel identified by connection identifier.
- *
- * @param id
- * id of the connection
- * @return connection to a submodel identified by connection identifier
- */
- SubmodelConnection getSubmodelConnectionById(Integer id);
-
- /**
- * Returns submodel identified by submodel identifier.
- *
- * @param identifier
- * identifier of the model
- * @return submodel identified by identifiere
- */
- Model getSubmodelById(String identifier);
-
- /**
- * Returns collection of {@link Model submodels}.
- *
- * @return collection of {@link Model submodels}
- */
- Collection<Model> getSubmodels();
-
- /**
- * Returns {@link Model submodel} identified by the {@link ModelData#name
- * model name}. It returns this 'parent' object when the names matches.
- *
- * @param name
- * name of the submodel that should be returned
- * @return {@link Model submodel} identified by the {@link ModelData#name
- * model name}
- */
- Model getSubmodelByName(String name);
-
- /**
- * Adds layout to list of layouts on a given position.
- *
- * @param index
- * where the new layout should be added
- * @param layout
- * object to add
- */
- void addLayout(int index, Layout layout);
-
- /**
- * Adds new {@link DataMiningSet} to the model.
- *
- * @param dataMiningSet
- * object to add
- */
- void addDataMiningSet(DataMiningSet dataMiningSet);
-
- /**
- * Returns list of {@link DataMiningSet} associated with the model.
- *
- * @return list of {@link DataMiningSet} associated with the model
- */
- List<DataMiningSet> getDataMiningSets();
-
- /**
- * Adds set of {@link DataMiningSet} to the model.
- *
- * @param dataMiningSets
- * objects to add
- */
- void addDataMiningSets(Collection<DataMiningSet> dataMiningSets);
-
- /**
- * Returns layout identified by {@link Layout#id database identifier}.
- *
- * @param layoutIdentfier
- * layout {@link Layout#id database identifier}
- * @return layout identified by {@link Layout#id database identifier}
- */
- Layout getLayoutByIdentifier(Integer layoutIdentfier);
-
- /**
- * Sets database identifier of the model.
- *
- * @param id
- * database identifier
- */
- void setId(int id);
-
- /**
- * Return list od all {@link BioEntity} in the map. This includes all
- * {@link Reaction reactions} and {@link Element elements}.
- *
- * @return list od all {@link BioEntity} in the map
- */
- List<BioEntity> getBioEntities();
+ /**
+ * Adds element to the model.
+ *
+ * @param element
+ * element to add
+ */
+ void addElement(Element element);
+
+ /**
+ *
+ * @return model width
+ */
+ Double getWidth();
+
+ /**
+ * Sets model width.
+ *
+ * @param width
+ * new model width
+ */
+ void setWidth(Double width);
+
+ /**
+ *
+ * @return model height
+ */
+ Double getHeight();
+
+ /**
+ * Sets model height.
+ *
+ * @param height
+ * new model height
+ */
+ void setHeight(Double height);
+
+ /**
+ * Sets model width.
+ *
+ * @param text
+ * new model width
+ */
+ void setWidth(String text);
+
+ /**
+ * Sets model height.
+ *
+ * @param text
+ * new model height
+ */
+ void setHeight(String text);
+
+ /**
+ * Returns set of all elements.
+ *
+ * @return set of all elements
+ */
+ Set<Element> getElements();
+
+ /**
+ * Returns element with the given element identifier ({@link Element#elementId}
+ * ).
+ *
+ * @param idElement
+ * element identifier
+ * @param <T>
+ * type of the object to be returned
+ * @return {@link Element} with the given id
+ */
+ <T extends Element> T getElementByElementId(String idElement);
+
+ /**
+ * Adds reaction to the model.
+ *
+ * @param reaction
+ * reaction to add
+ */
+ void addReaction(Reaction reaction);
+
+ /**
+ * Returns set of reactions.
+ *
+ * @return set of reaction in the model
+ */
+ Set<Reaction> getReactions();
+
+ /**
+ * @return list of compartments
+ */
+ List<Compartment> getCompartments();
+
+ /**
+ * Adds layer to the model.
+ *
+ * @param layer
+ * object to add
+ */
+ void addLayer(Layer layer);
+
+ /**
+ *
+ * @return set of layers
+ */
+ Set<Layer> getLayers();
+
+ /**
+ * Adds list of elements into model.
+ *
+ * @param elements
+ * list of elements
+ */
+ void addElements(List<? extends Element> elements);
+
+ /**
+ * Sets new short description of the model.
+ *
+ * @param notes
+ * new short description
+ */
+ void setNotes(String notes);
+
+ /**
+ *
+ * @return short description of the model
+ */
+ String getNotes();
+
+ /**
+ * Returns reaction with the id given in the parameter.
+ *
+ * @param idReaction
+ * reaction identifier ({@link Reaction#idReaction})
+ * @return reaction with the id given in the parameter
+ */
+ Reaction getReactionByReactionId(String idReaction);
+
+ /**
+ * Adds set of layers to the model.
+ *
+ * @param layers
+ * object to add
+ */
+ void addLayers(Collection<Layer> layers);
+
+ /**
+ * Adds {@link ElementGroup} to the model.
+ *
+ * @param elementGroup
+ * object to add
+ */
+ void addElementGroup(ElementGroup elementGroup);
+
+ /**
+ * Adds {@link BlockDiagram} to the model.
+ *
+ * @param blockDiagram
+ * object to add
+ */
+ void addBlockDiagream(BlockDiagram blockDiagram);
+
+ /**
+ * @param idModel
+ * the idModel to set
+ * @see Model#idModel
+ */
+ void setIdModel(String idModel);
+
+ /**
+ * @return the idModel
+ * @see Model#idModel
+ */
+ String getIdModel();
+
+ /**
+ * @param tileSize
+ * the tileSize to set
+ * @see ModelData#tileSize
+ */
+ void setTileSize(int tileSize);
+
+ /**
+ * @return the tileSize
+ * @see ModelData#tileSize
+ */
+ int getTileSize();
+
+ /**
+ * @param zoomLevels
+ * the zoomLevels to set
+ * @see ModelData#zoomLevels
+ */
+ void setZoomLevels(int zoomLevels);
+
+ /**
+ * @return the zoomLevels
+ * @see ModelData#zoomLevels
+ */
+ int getZoomLevels();
+
+ /**
+ * Removes reaction from model.
+ *
+ * @param reaction
+ * reaction to remove
+ */
+ void removeReaction(Reaction reaction);
+
+ /**
+ * Removes {@link Element} from the model.
+ *
+ * @param element
+ * element to remove
+ */
+ void removeElement(Element element);
+
+ /**
+ * Returns list of reactions sorted by reaction id.
+ *
+ * @return list of reactions sorted by reaction id
+ */
+ List<Reaction> getSortedReactions();
+
+ /**
+ * Return list of elements sorted by the size.
+ *
+ * @return list of elements sorted by the size
+ */
+ List<Element> getSortedSpeciesList();
+
+ /**
+ * Returns collection of all {@link Species} excluding {@link Complex}.
+ *
+ * @return collection of all {@link Species} excluding {@link Complex}.
+ */
+ Collection<Species> getNotComplexSpeciesList();
+
+ /**
+ * Returns list of all {@link Species} in the model.
+ *
+ * @return list of all {@link Species} in the model
+ */
+ List<Species> getSpeciesList();
+
+ /**
+ * Returns collection of {@link Complex}.
+ *
+ * @return collection of {@link Complex}
+ */
+ Collection<Complex> getComplexList();
+
+ /**
+ * Adds reactions to model.
+ *
+ * @param reactions2
+ * list of reaction to add
+ */
+ void addReactions(List<Reaction> reactions2);
+
+ /**
+ * Returns list of elements annotated by the {@link MiriamData}.
+ *
+ * @param miriamData
+ * {@link MiriamData}
+ * @return list of elements
+ */
+ Set<BioEntity> getElementsByAnnotation(MiriamData miriamData);
+
+ /**
+ * Returns list of elements with given name.
+ *
+ * @param name
+ * name of the element
+ * @return list of elements with given name
+ */
+ List<Element> getElementsByName(String name);
+
+ /**
+ *
+ * @param height
+ * new {@link ModelData#height}
+ */
+ void setHeight(int height);
+
+ /**
+ *
+ * @param width
+ * new {@link ModelData#width}
+ */
+ void setWidth(int width);
+
+ /**
+ * Adds layout to model.
+ *
+ * @param layout
+ * layout to add
+ */
+ void addLayout(Layout layout);
+
+ /**
+ *
+ * @param layouts
+ * new {@link ModelData#layouts}
+ */
+ void setLayouts(List<Layout> layouts);
+
+ /**
+ *
+ * @return {@link ModelData#layouts}
+ */
+ List<Layout> getLayouts();
+
+ /**
+ *
+ * @param creationDate
+ * new {@link ModelData#creationDate}
+ */
+ void setCreationDate(Calendar creationDate);
+
+ /**
+ *
+ * @return {@link ModelData#creationDate}
+ */
+ Calendar getCreationDate();
+
+ /**
+ * Returns {@link Element} for given database identifier.
+ *
+ * @param dbId
+ * element database identifier ({@link Element#id})
+ * @return {@link Element} for a given id
+ */
+ <T extends Element> T getElementByDbId(Integer dbId);
+
+ /**
+ * Returns {@link Reaction} for given database identifier.
+ *
+ * @param dbId
+ * reaction database identifier ({@link Reaction#id})
+ * @return {@link Reaction} for a given id
+ */
+ Reaction getReactionByDbId(Integer dbId);
+
+ /**
+ * Returns sorted by size list of compartments.
+ *
+ * @return list of compartment sorted by size
+ */
+ List<Compartment> getSortedCompartments();
+
+ /**
+ * Returns list of elements sorted by the size.
+ *
+ * @return list of elements sorted by the size
+ */
+ List<Element> getElementsSortedBySize();
+
+ /**
+ *
+ * @param project
+ * new {@link ModelData#project}
+ */
+ void setProject(Project project);
+
+ /**
+ *
+ * @return {@link ModelData#project}
+ */
+ Project getProject();
+
+ /**
+ *
+ * @param elements
+ * new {@link ModelData#elements} collection
+ */
+ void setElements(Set<Element> elements);
+
+ /**
+ * @return the modelData
+ */
+ ModelData getModelData();
+
+ /**
+ *
+ * @return {@link ModelData#id}
+ */
+ Integer getId();
+
+ /**
+ * Adds submodel connection.
+ *
+ * @param submodel
+ * submodel to add
+ */
+ void addSubmodelConnection(ModelSubmodelConnection submodel);
+
+ /**
+ * Returns set of submodel connections.
+ *
+ * @return collection of submodels
+ */
+ Collection<ModelSubmodelConnection> getSubmodelConnections();
+
+ /**
+ * Returns name of the model.
+ *
+ * @return name of the model
+ */
+ String getName();
+
+ /**
+ * Sets name of the model.
+ *
+ * @param name
+ * name of the model
+ */
+ void setName(String name);
+
+ /**
+ * Returns {@link Model submodel} by the {@link ModelData#id database
+ * identifier} given in the parameter.
+ *
+ * @param idObject
+ * the {@link ModelData#id database identifier} that identifies
+ * submodel
+ * @return {@link Model submodel} by the {@link ModelData#id database
+ * identifier} given in the parameter
+ */
+ Model getSubmodelById(Integer idObject);
+
+ /**
+ * Returns set of connections that point to this model. Be very carefoul with
+ * using this function as the implementation forces lazy loading of the maps.
+ *
+ * @return set of connections that point to this model
+ */
+ Collection<SubmodelConnection> getParentModels();
+
+ /**
+ * Returns connection to a submodel identified by connection name.
+ *
+ * @param name
+ * name of the connection
+ * @return connection to a submodel identified by connection name
+ */
+ Model getSubmodelByConnectionName(String name);
+
+ /**
+ * Returns connection to a submodel identified by connection identifier.
+ *
+ * @param id
+ * id of the connection
+ * @return connection to a submodel identified by connection identifier
+ */
+ SubmodelConnection getSubmodelConnectionById(Integer id);
+
+ /**
+ * Returns submodel identified by submodel identifier.
+ *
+ * @param identifier
+ * identifier of the model
+ * @return submodel identified by identifiere
+ */
+ Model getSubmodelById(String identifier);
+
+ /**
+ * Returns collection of {@link Model submodels}.
+ *
+ * @return collection of {@link Model submodels}
+ */
+ Collection<Model> getSubmodels();
+
+ /**
+ * Returns {@link Model submodel} identified by the {@link ModelData#name model
+ * name}. It returns this 'parent' object when the names matches.
+ *
+ * @param name
+ * name of the submodel that should be returned
+ * @return {@link Model submodel} identified by the {@link ModelData#name model
+ * name}
+ */
+ Model getSubmodelByName(String name);
+
+ /**
+ * Adds layout to list of layouts on a given position.
+ *
+ * @param index
+ * where the new layout should be added
+ * @param layout
+ * object to add
+ */
+ void addLayout(int index, Layout layout);
+
+ /**
+ * Adds new {@link DataMiningSet} to the model.
+ *
+ * @param dataMiningSet
+ * object to add
+ */
+ void addDataMiningSet(DataMiningSet dataMiningSet);
+
+ /**
+ * Returns list of {@link DataMiningSet} associated with the model.
+ *
+ * @return list of {@link DataMiningSet} associated with the model
+ */
+ List<DataMiningSet> getDataMiningSets();
+
+ /**
+ * Adds set of {@link DataMiningSet} to the model.
+ *
+ * @param dataMiningSets
+ * objects to add
+ */
+ void addDataMiningSets(Collection<DataMiningSet> dataMiningSets);
+
+ /**
+ * Returns layout identified by {@link Layout#id database identifier}.
+ *
+ * @param layoutIdentfier
+ * layout {@link Layout#id database identifier}
+ * @return layout identified by {@link Layout#id database identifier}
+ */
+ Layout getLayoutByIdentifier(Integer layoutIdentfier);
+
+ /**
+ * Sets database identifier of the model.
+ *
+ * @param id
+ * database identifier
+ */
+ void setId(int id);
+
+ /**
+ * Return list of all {@link BioEntity} in the map. This includes all
+ * {@link Reaction reactions} and {@link Element elements}.
+ *
+ * @return list of all {@link BioEntity} in the map
+ */
+ List<BioEntity> getBioEntities();
+
+ Double getDefaultCenterX();
+
+ void setDefaultCenterX(Double defaultCenterX);
+
+ Double getDefaultCenterY();
+
+ void setDefaultCenterY(Double defaultCenterY);
+
+ Integer getDefaultZoomLevel();
+
+ void setDefaultZoomLevel(Integer defaultZoomLevel);
+
+ /**
+ * Remove layout from model.
+ *
+ * @param dbLayout
+ * layout to remove
+ */
+ void removeLayout(Layout dbLayout);
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
index 448470f1d8..e5c17ee798 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelData.java
@@ -1,695 +1,735 @@
-package lcsb.mapviewer.model.map.model;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OrderBy;
-import javax.persistence.Table;
-import javax.persistence.Transient;
-import javax.xml.bind.annotation.XmlTransient;
-
-import org.apache.log4j.Logger;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.Project;
-import lcsb.mapviewer.model.map.graph.DataMiningSet;
-import lcsb.mapviewer.model.map.layout.BlockDiagram;
-import lcsb.mapviewer.model.map.layout.ElementGroup;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-
-/**
- * Representation of the model data. It contains all information about single
- * map:
- * <ul>
- * <li>species and compartments ({@link #elements} field)</li>
- * <li>list of reactions ({@link #reactions})</li>
- * <li>layers with additional graphical objects ({@link #layers})</li>
- * <li>different graphical visualizations of the whole map ({@link #layouts})
- * </li>
- * <li>some other meta data (like: creation date, version, etc)</li>
- * </ul>
- *
- * @author Piotr Gawron
- *
- */
-@Entity
-@Table(name = "model_table")
-public class ModelData implements Serializable {
-
- /**
- *
- */
- private static final long serialVersionUID = 1L;
-
- /**
- * Default class logger.
- */
- private static Logger logger = Logger.getLogger(ModelData.class);
-
- /**
- * Set of all elements in the map.
- *
- * @see Element
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "model", orphanRemoval = true)
- private Set<Element> elements = new HashSet<>();
-
- /**
- * Set of all layers in the map.
- *
- * @see Layer
- *
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "model", orphanRemoval = true)
- private Set<Layer> layers = new HashSet<>();
-
- /**
- * Unique database identifier.
- */
- @Id
- @GeneratedValue(strategy = GenerationType.IDENTITY)
- @Column(name = "idDb", unique = true, nullable = false)
- private int id;
-
- /**
- * Collection of all reactions in the map.
- *
- * @see Reaction
- *
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "model", orphanRemoval = true)
- private Set<Reaction> reactions = new HashSet<>();
-
- /**
- * When the map was created.
- */
- private Calendar creationDate = Calendar.getInstance();
-
- /**
- * Width of the map.
- */
- private Double width;
- /**
- * Height of the map.
- */
- private Double height;
-
- /**
- * Description of the map.
- */
- @Column(name = "notes", columnDefinition = "TEXT")
- private String notes;
-
- /**
- * Name of the map.
- */
- private String name;
-
- /**
- * Another CellDesigner identifier.
- */
- private String idModel;
-
- /**
- * How many hierarchical levels are in this map.
- */
- private int zoomLevels;
-
- /**
- * Size of the image tile that are used in this model.
- */
- private int tileSize;
-
- /**
- * List of layouts.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "model", orphanRemoval = true)
- @OrderBy("id")
- private List<Layout> layouts = new ArrayList<>();
-
- /**
- * Project to which this model belong to.
- */
- @ManyToOne(fetch = FetchType.LAZY, optional = false)
- private Project project;
-
- // This field should be transient in hibernate and during the transformation
- // to xml
- /**
- * {@link Model} object that is a container where data is being placed.
- */
- @Transient
- @XmlTransient
- private Model model;
-
- /**
- * List of submodels.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.EAGER, mappedBy = "parentModel", orphanRemoval = true)
- private Set<ModelSubmodelConnection> submodels = new HashSet<>();
-
- /**
- * List of connections with parent model (by definition one map can be a
- * submodel of few maps).
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(fetch = FetchType.LAZY, mappedBy = "submodel")
- private Set<SubmodelConnection> parentModels = new HashSet<>();
-
- /**
- * List of {@link DataMiningSet} in the model. These data mining sets are used
- * to create suggested (but missing) connections in the model.
- */
- @Cascade({ CascadeType.ALL })
- @OneToMany(mappedBy = "model", orphanRemoval = true)
- @OrderBy("id")
- private List<DataMiningSet> dataMiningSets = new ArrayList<>();
-
- /**
- * Default constructor.
- */
- public ModelData() {
- }
-
- /**
- * Adds {@link Element} to model data.
- *
- * @param element
- * element to add
- */
- public void addElement(Element element) {
- element.setModelData(this);
- elements.add(element);
- }
-
- /**
- * Adds {@link Reaction} to model data.
- *
- * @param reaction
- * reaction to add
- */
- public void addReaction(Reaction reaction) {
- reaction.setModelData(this);
- reactions.add(reaction);
- }
-
- /**
- * Adds {@link Layer} to model data.
- *
- * @param layer
- * layer to add
- */
- public void addLayer(Layer layer) {
- layer.setModel(this);
- layers.add(layer);
- }
-
- /**
- * Adds collection of {@link Element elements} to model data.
- *
- * @param elements
- * elements to add
- */
- public void addElements(List<? extends Element> elements) {
- for (Element element : elements) {
- addElement(element);
- }
- }
-
- /**
- *
- * @return {@link #id}
- */
- public Integer getId() {
- return id;
- }
-
- /**
- *
- * @param id
- * new {@link #id}
- */
- public void setId(int id) {
- this.id = id;
- }
-
- /**
- *
- * @param elements
- * new {@link #elements} collection
- */
- public void setElements(Set<Element> elements) {
- this.elements = elements;
- }
-
- /**
- *
- * @return {@link #project}
- */
- public Project getProject() {
- return project;
- }
-
- /**
- *
- * @param project
- * new {@link #project}
- */
- public void setProject(Project project) {
- this.project = project;
- }
-
- /**
- *
- * @return {@link #creationDate}
- */
- public Calendar getCreationDate() {
- return creationDate;
- }
-
- /**
- *
- * @param creationDate
- * new {@link #creationDate}
- */
- public void setCreationDate(Calendar creationDate) {
- this.creationDate = creationDate;
- }
-
- /**
- *
- * @return {@link #layouts}
- */
- public List<Layout> getLayouts() {
- return layouts;
- }
-
- /**
- *
- * @param layouts
- * new {@link #layouts}
- */
- public void setLayouts(List<Layout> layouts) {
- this.layouts = layouts;
- }
-
- /**
- * Adds layout to model.
- *
- * @param layout
- * layout to add
- */
- public void addLayout(Layout layout) {
- layouts.add(layout);
- layout.setModel(this);
- }
-
- /**
- *
- * @param width
- * new {@link #width}
- */
- public void setWidth(int width) {
- setWidth(Double.valueOf(width));
- }
-
- /**
- *
- * @param height
- * new {@link #height}
- */
- public void setHeight(int height) {
- setHeight(Double.valueOf(height));
- }
-
- /**
- * Adds reactions to model.
- *
- * @param reactions2
- * list of reaction to add
- */
- public void addReactions(List<Reaction> reactions2) {
- for (Reaction reaction : reactions2) {
- addReaction(reaction);
- }
- }
-
- /**
- * Adds collection of {@link Layer layers} to the model data.
- *
- * @param layers
- * objets to add
- */
- public void addLayers(Collection<Layer> layers) {
- for (Layer layer : layers) {
- addLayer(layer);
- }
- }
-
- /**
- * Remove layout from model.
- *
- * @param dbLayout
- * layout to remove
- */
- public void removeLayout(Layout dbLayout) {
- List<Layout> toRemove = new ArrayList<Layout>();
- for (Layout layout : layouts) {
- if (layout.getId() == dbLayout.getId()) {
- toRemove.add(layout);
- }
- }
-
- if (toRemove.size() == 0) {
- logger.warn("Cannot remove layout: " + dbLayout.getId());
- } else {
- layouts.removeAll(toRemove);
- }
- }
-
- /**
- * Adds {@link ElementGroup} to the model data.
- *
- * @param elementGroup
- * object to add
- */
- public void addElementGroup(ElementGroup elementGroup) {
- // for now we ignore this information
- }
-
- /**
- * Adds {@link BlockDiagram} to the model data.
- *
- * @param blockDiagram
- * object to add
- */
- public void addBlockDiagream(BlockDiagram blockDiagram) {
- // for now we ignore this information
- }
-
- /**
- * Removes {@link Element} from the model.
- *
- * @param element
- * element to remove
- */
- public void removeElement(Element element) {
- if (element == null) {
- throw new InvalidArgumentException("Cannot remove null");
- }
- if (!elements.contains(element)) {
- logger.warn("Element doesn't exist in the map: " + element.getElementId());
- return;
- }
-
- element.setModelData(null);
- elements.remove(element);
- }
-
- /**
- * Removes reaction from model.
- *
- * @param reaction
- * reaction to remove
- */
- public void removeReaction(Reaction reaction) {
- if (!reactions.contains(reaction)) {
- logger.warn("Reaction doesn't exist in the model: " + reaction.getIdReaction());
- return;
- }
- reaction.setModelData(null);
- reactions.remove(reaction);
- }
-
- /**
- * @return the zoomLevels
- * @see #zoomLevels
- */
- public int getZoomLevels() {
- return zoomLevels;
- }
-
- /**
- * @param zoomLevels
- * the zoomLevels to set
- * @see #zoomLevels
- */
- public void setZoomLevels(int zoomLevels) {
- this.zoomLevels = zoomLevels;
- }
-
- /**
- * @return the tileSize
- * @see #tileSize
- */
- public int getTileSize() {
- return tileSize;
- }
-
- /**
- * @param tileSize
- * the tileSize to set
- * @see #tileSize
- */
- public void setTileSize(int tileSize) {
- this.tileSize = tileSize;
- }
-
- /**
- * @return the idModel
- * @see #idModel
- */
- public String getIdModel() {
- return idModel;
- }
-
- /**
- * @param idModel
- * the idModel to set
- * @see #idModel
- */
- public void setIdModel(String idModel) {
- this.idModel = idModel;
- }
-
- /**
- * @return the model
- * @see #model
- */
- @XmlTransient
- public Model getModel() {
- if (model == null) {
- logger.warn("Model not set in model data.");
- }
- return model;
- }
-
- /**
- * @param model
- * the model to set
- * @see #model
- */
- public void setModel(Model model) {
- this.model = model;
- }
-
- /**
- * @return the elements
- * @see #elements
- */
- public Set<Element> getElements() {
- return elements;
- }
-
- /**
- * @return the layers
- * @see #layers
- */
- public Set<Layer> getLayers() {
- return layers;
- }
-
- /**
- * @param layers
- * the layers to set
- * @see #layers
- */
- public void setLayers(Set<Layer> layers) {
- this.layers = layers;
- }
-
- /**
- * @return the reactions
- * @see #reactions
- */
- public Set<Reaction> getReactions() {
- return reactions;
- }
-
- /**
- * @param reactions
- * the reactions to set
- * @see #reactions
- */
- public void setReactions(Set<Reaction> reactions) {
- this.reactions = reactions;
- }
-
- /**
- * @return the width
- * @see #width
- */
- public Double getWidth() {
- return width;
- }
-
- /**
- * @param width
- * the width to set
- * @see #width
- */
- public void setWidth(Double width) {
- this.width = width;
- }
-
- /**
- * @return the height
- * @see #height
- */
- public Double getHeight() {
- return height;
- }
-
- /**
- * @param height
- * the height to set
- * @see #height
- */
- public void setHeight(Double height) {
- this.height = height;
- }
-
- /**
- * @return the notes
- * @see #notes
- */
- public String getNotes() {
- return notes;
- }
-
- /**
- * @param notes
- * the notes to set
- * @see #notes
- */
- public void setNotes(String notes) {
- this.notes = notes;
- }
-
- /**
- * Adds submodel.
- *
- * @param submodel
- * object to add
- */
- public void addSubmodel(ModelSubmodelConnection submodel) {
- this.submodels.add(submodel);
- submodel.setParentModel(this);
- }
-
- /**
- * Returns collection of submodels.
- *
- * @return collection of submodels.
- */
- public Collection<ModelSubmodelConnection> getSubmodels() {
- return this.submodels;
- }
-
- /**
- * @return the name
- * @see #name
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set
- * @see #name
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * @return the parentModels
- * @see #parentModels
- */
- public Set<SubmodelConnection> getParentModels() {
- return parentModels;
- }
-
- /**
- * @param parentModels
- * the parentModels to set
- * @see #parentModels
- */
- public void setParentModels(Set<SubmodelConnection> parentModels) {
- this.parentModels = parentModels;
- }
-
- /**
- * @return the dataMining
- * @see #dataMiningSets
- */
- public List<DataMiningSet> getDataMiningSets() {
- return dataMiningSets;
- }
-
- /**
- * @param dataMining
- * the dataMining to set
- * @see #dataMiningSets
- */
- public void setDataMiningSets(List<DataMiningSet> dataMining) {
- this.dataMiningSets = dataMining;
- }
-
- /**
- * Adds layout to the list of layouts at a given position.
- *
- * @param index
- * position at which new object will be inserted
- * @param layout
- * object to add
- */
- public void addLayout(int index, Layout layout) {
- layouts.add(index, layout);
- layout.setModel(this);
- }
+package lcsb.mapviewer.model.map.model;
+
+import java.io.Serializable;
+import java.util.ArrayList;
+import java.util.Calendar;
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import javax.persistence.Column;
+import javax.persistence.Entity;
+import javax.persistence.FetchType;
+import javax.persistence.GeneratedValue;
+import javax.persistence.GenerationType;
+import javax.persistence.Id;
+import javax.persistence.ManyToOne;
+import javax.persistence.OneToMany;
+import javax.persistence.OrderBy;
+import javax.persistence.Table;
+import javax.persistence.Transient;
+import javax.xml.bind.annotation.XmlTransient;
+
+import org.apache.log4j.Logger;
+import org.hibernate.annotations.Cascade;
+import org.hibernate.annotations.CascadeType;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.Project;
+import lcsb.mapviewer.model.map.graph.DataMiningSet;
+import lcsb.mapviewer.model.map.layout.BlockDiagram;
+import lcsb.mapviewer.model.map.layout.ElementGroup;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.layout.graphics.Layer;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+
+/**
+ * Representation of the model data. It contains all information about single
+ * map:
+ * <ul>
+ * <li>species and compartments ({@link #elements} field)</li>
+ * <li>list of reactions ({@link #reactions})</li>
+ * <li>layers with additional graphical objects ({@link #layers})</li>
+ * <li>different graphical visualizations of the whole map ({@link #layouts})
+ * </li>
+ * <li>some other meta data (like: creation date, version, etc)</li>
+ * </ul>
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Entity
+@Table(name = "model_table")
+public class ModelData implements Serializable {
+
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default class logger.
+ */
+ private static Logger logger = Logger.getLogger(ModelData.class);
+
+ /**
+ * Set of all elements in the map.
+ *
+ * @see Element
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "model", orphanRemoval = true)
+ private Set<Element> elements = new HashSet<>();
+
+ /**
+ * Set of all layers in the map.
+ *
+ * @see Layer
+ *
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "model", orphanRemoval = true)
+ private Set<Layer> layers = new HashSet<>();
+
+ /**
+ * Unique database identifier.
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Column(name = "idDb", unique = true, nullable = false)
+ private int id;
+
+ /**
+ * Collection of all reactions in the map.
+ *
+ * @see Reaction
+ *
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "model", orphanRemoval = true)
+ private Set<Reaction> reactions = new HashSet<>();
+
+ /**
+ * When the map was created.
+ */
+ private Calendar creationDate = Calendar.getInstance();
+
+ /**
+ * Width of the map.
+ */
+ private Double width;
+
+ /**
+ * Height of the map.
+ */
+ private Double height;
+
+ /**
+ * X coordinate that should be used when initially showing map.
+ */
+ private Double defaultCenterX;
+
+ /**
+ * Y coordinate that should be used when initially showing map.
+ */
+ private Double defaultCenterY;
+
+ /**
+ * Description of the map.
+ */
+ @Column(name = "notes", columnDefinition = "TEXT")
+ private String notes;
+
+ /**
+ * Name of the map.
+ */
+ private String name;
+
+ /**
+ * Another CellDesigner identifier.
+ */
+ private String idModel;
+
+ /**
+ * How many hierarchical levels are in this map.
+ */
+ private int zoomLevels;
+
+ /**
+ * Zoom level that should be used when initially showing map.
+ */
+ private Integer defaultZoomLevel;
+
+ /**
+ * Size of the image tile that are used in this model.
+ */
+ private int tileSize;
+
+ /**
+ * List of layouts.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "model", orphanRemoval = true)
+ @OrderBy("id")
+ private List<Layout> layouts = new ArrayList<>();
+
+ /**
+ * Project to which this model belong to.
+ */
+ @ManyToOne(fetch = FetchType.LAZY, optional = false)
+ private Project project;
+
+ // This field should be transient in hibernate and during the transformation
+ // to xml
+ /**
+ * {@link Model} object that is a container where data is being placed.
+ */
+ @Transient
+ @XmlTransient
+ private Model model;
+
+ /**
+ * List of submodels.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.EAGER, mappedBy = "parentModel", orphanRemoval = true)
+ private Set<ModelSubmodelConnection> submodels = new HashSet<>();
+
+ /**
+ * List of connections with parent model (by definition one map can be a
+ * submodel of few maps).
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(fetch = FetchType.LAZY, mappedBy = "submodel")
+ private Set<SubmodelConnection> parentModels = new HashSet<>();
+
+ /**
+ * List of {@link DataMiningSet} in the model. These data mining sets are used
+ * to create suggested (but missing) connections in the model.
+ */
+ @Cascade({ CascadeType.ALL })
+ @OneToMany(mappedBy = "model", orphanRemoval = true)
+ @OrderBy("id")
+ private List<DataMiningSet> dataMiningSets = new ArrayList<>();
+
+ /**
+ * Default constructor.
+ */
+ public ModelData() {
+ }
+
+ /**
+ * Adds {@link Element} to model data.
+ *
+ * @param element
+ * element to add
+ */
+ public void addElement(Element element) {
+ element.setModelData(this);
+ elements.add(element);
+ }
+
+ /**
+ * Adds {@link Reaction} to model data.
+ *
+ * @param reaction
+ * reaction to add
+ */
+ public void addReaction(Reaction reaction) {
+ reaction.setModelData(this);
+ reactions.add(reaction);
+ }
+
+ /**
+ * Adds {@link Layer} to model data.
+ *
+ * @param layer
+ * layer to add
+ */
+ public void addLayer(Layer layer) {
+ layer.setModel(this);
+ layers.add(layer);
+ }
+
+ /**
+ * Adds collection of {@link Element elements} to model data.
+ *
+ * @param elements
+ * elements to add
+ */
+ public void addElements(List<? extends Element> elements) {
+ for (Element element : elements) {
+ addElement(element);
+ }
+ }
+
+ /**
+ *
+ * @return {@link #id}
+ */
+ public Integer getId() {
+ return id;
+ }
+
+ /**
+ *
+ * @param id
+ * new {@link #id}
+ */
+ public void setId(int id) {
+ this.id = id;
+ }
+
+ /**
+ *
+ * @param elements
+ * new {@link #elements} collection
+ */
+ public void setElements(Set<Element> elements) {
+ this.elements = elements;
+ }
+
+ /**
+ *
+ * @return {@link #project}
+ */
+ public Project getProject() {
+ return project;
+ }
+
+ /**
+ *
+ * @param project
+ * new {@link #project}
+ */
+ public void setProject(Project project) {
+ this.project = project;
+ }
+
+ /**
+ *
+ * @return {@link #creationDate}
+ */
+ public Calendar getCreationDate() {
+ return creationDate;
+ }
+
+ /**
+ *
+ * @param creationDate
+ * new {@link #creationDate}
+ */
+ public void setCreationDate(Calendar creationDate) {
+ this.creationDate = creationDate;
+ }
+
+ /**
+ *
+ * @return {@link #layouts}
+ */
+ public List<Layout> getLayouts() {
+ return layouts;
+ }
+
+ /**
+ *
+ * @param layouts
+ * new {@link #layouts}
+ */
+ public void setLayouts(List<Layout> layouts) {
+ this.layouts = layouts;
+ }
+
+ /**
+ * Adds layout to model.
+ *
+ * @param layout
+ * layout to add
+ */
+ public void addLayout(Layout layout) {
+ layouts.add(layout);
+ layout.setModel(this);
+ }
+
+ /**
+ *
+ * @param width
+ * new {@link #width}
+ */
+ public void setWidth(int width) {
+ setWidth(Double.valueOf(width));
+ }
+
+ /**
+ *
+ * @param height
+ * new {@link #height}
+ */
+ public void setHeight(int height) {
+ setHeight(Double.valueOf(height));
+ }
+
+ /**
+ * Adds reactions to model.
+ *
+ * @param reactions2
+ * list of reaction to add
+ */
+ public void addReactions(List<Reaction> reactions2) {
+ for (Reaction reaction : reactions2) {
+ addReaction(reaction);
+ }
+ }
+
+ /**
+ * Adds collection of {@link Layer layers} to the model data.
+ *
+ * @param layers
+ * objets to add
+ */
+ public void addLayers(Collection<Layer> layers) {
+ for (Layer layer : layers) {
+ addLayer(layer);
+ }
+ }
+
+ /**
+ * Remove layout from model.
+ *
+ * @param dbLayout
+ * layout to remove
+ */
+ public void removeLayout(Layout dbLayout) {
+ List<Layout> toRemove = new ArrayList<Layout>();
+ for (Layout layout : layouts) {
+ if (layout.getId() == dbLayout.getId()) {
+ toRemove.add(layout);
+ }
+ }
+
+ if (toRemove.size() == 0) {
+ logger.warn("Cannot remove layout: " + dbLayout.getId());
+ } else {
+ layouts.removeAll(toRemove);
+ }
+ }
+
+ /**
+ * Adds {@link ElementGroup} to the model data.
+ *
+ * @param elementGroup
+ * object to add
+ */
+ public void addElementGroup(ElementGroup elementGroup) {
+ // for now we ignore this information
+ }
+
+ /**
+ * Adds {@link BlockDiagram} to the model data.
+ *
+ * @param blockDiagram
+ * object to add
+ */
+ public void addBlockDiagream(BlockDiagram blockDiagram) {
+ // for now we ignore this information
+ }
+
+ /**
+ * Removes {@link Element} from the model.
+ *
+ * @param element
+ * element to remove
+ */
+ public void removeElement(Element element) {
+ if (element == null) {
+ throw new InvalidArgumentException("Cannot remove null");
+ }
+ if (!elements.contains(element)) {
+ logger.warn("Element doesn't exist in the map: " + element.getElementId());
+ return;
+ }
+
+ element.setModelData(null);
+ elements.remove(element);
+ }
+
+ /**
+ * Removes reaction from model.
+ *
+ * @param reaction
+ * reaction to remove
+ */
+ public void removeReaction(Reaction reaction) {
+ if (!reactions.contains(reaction)) {
+ logger.warn("Reaction doesn't exist in the model: " + reaction.getIdReaction());
+ return;
+ }
+ reaction.setModelData(null);
+ reactions.remove(reaction);
+ }
+
+ /**
+ * @return the zoomLevels
+ * @see #zoomLevels
+ */
+ public int getZoomLevels() {
+ return zoomLevels;
+ }
+
+ /**
+ * @param zoomLevels
+ * the zoomLevels to set
+ * @see #zoomLevels
+ */
+ public void setZoomLevels(int zoomLevels) {
+ this.zoomLevels = zoomLevels;
+ }
+
+ /**
+ * @return the tileSize
+ * @see #tileSize
+ */
+ public int getTileSize() {
+ return tileSize;
+ }
+
+ /**
+ * @param tileSize
+ * the tileSize to set
+ * @see #tileSize
+ */
+ public void setTileSize(int tileSize) {
+ this.tileSize = tileSize;
+ }
+
+ /**
+ * @return the idModel
+ * @see #idModel
+ */
+ public String getIdModel() {
+ return idModel;
+ }
+
+ /**
+ * @param idModel
+ * the idModel to set
+ * @see #idModel
+ */
+ public void setIdModel(String idModel) {
+ this.idModel = idModel;
+ }
+
+ /**
+ * @return the model
+ * @see #model
+ */
+ @XmlTransient
+ public Model getModel() {
+ if (model == null) {
+ logger.warn("Model not set in model data.");
+ }
+ return model;
+ }
+
+ /**
+ * @param model
+ * the model to set
+ * @see #model
+ */
+ public void setModel(Model model) {
+ this.model = model;
+ }
+
+ /**
+ * @return the elements
+ * @see #elements
+ */
+ public Set<Element> getElements() {
+ return elements;
+ }
+
+ /**
+ * @return the layers
+ * @see #layers
+ */
+ public Set<Layer> getLayers() {
+ return layers;
+ }
+
+ /**
+ * @param layers
+ * the layers to set
+ * @see #layers
+ */
+ public void setLayers(Set<Layer> layers) {
+ this.layers = layers;
+ }
+
+ /**
+ * @return the reactions
+ * @see #reactions
+ */
+ public Set<Reaction> getReactions() {
+ return reactions;
+ }
+
+ /**
+ * @param reactions
+ * the reactions to set
+ * @see #reactions
+ */
+ public void setReactions(Set<Reaction> reactions) {
+ this.reactions = reactions;
+ }
+
+ /**
+ * @return the width
+ * @see #width
+ */
+ public Double getWidth() {
+ return width;
+ }
+
+ /**
+ * @param width
+ * the width to set
+ * @see #width
+ */
+ public void setWidth(Double width) {
+ this.width = width;
+ }
+
+ /**
+ * @return the height
+ * @see #height
+ */
+ public Double getHeight() {
+ return height;
+ }
+
+ /**
+ * @param height
+ * the height to set
+ * @see #height
+ */
+ public void setHeight(Double height) {
+ this.height = height;
+ }
+
+ /**
+ * @return the notes
+ * @see #notes
+ */
+ public String getNotes() {
+ return notes;
+ }
+
+ /**
+ * @param notes
+ * the notes to set
+ * @see #notes
+ */
+ public void setNotes(String notes) {
+ this.notes = notes;
+ }
+
+ /**
+ * Adds submodel.
+ *
+ * @param submodel
+ * object to add
+ */
+ public void addSubmodel(ModelSubmodelConnection submodel) {
+ this.submodels.add(submodel);
+ submodel.setParentModel(this);
+ }
+
+ /**
+ * Returns collection of submodels.
+ *
+ * @return collection of submodels.
+ */
+ public Collection<ModelSubmodelConnection> getSubmodels() {
+ return this.submodels;
+ }
+
+ /**
+ * @return the name
+ * @see #name
+ */
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name
+ * the name to set
+ * @see #name
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the parentModels
+ * @see #parentModels
+ */
+ public Set<SubmodelConnection> getParentModels() {
+ return parentModels;
+ }
+
+ /**
+ * @param parentModels
+ * the parentModels to set
+ * @see #parentModels
+ */
+ public void setParentModels(Set<SubmodelConnection> parentModels) {
+ this.parentModels = parentModels;
+ }
+
+ /**
+ * @return the dataMining
+ * @see #dataMiningSets
+ */
+ public List<DataMiningSet> getDataMiningSets() {
+ return dataMiningSets;
+ }
+
+ /**
+ * @param dataMining
+ * the dataMining to set
+ * @see #dataMiningSets
+ */
+ public void setDataMiningSets(List<DataMiningSet> dataMining) {
+ this.dataMiningSets = dataMining;
+ }
+
+ /**
+ * Adds layout to the list of layouts at a given position.
+ *
+ * @param index
+ * position at which new object will be inserted
+ * @param layout
+ * object to add
+ */
+ public void addLayout(int index, Layout layout) {
+ layouts.add(index, layout);
+ layout.setModel(this);
+ }
+
+ public Double getDefaultCenterX() {
+ return defaultCenterX;
+ }
+
+ public void setDefaultCenterX(Double defaultCenterX) {
+ this.defaultCenterX = defaultCenterX;
+ }
+
+ public Double getDefaultCenterY() {
+ return defaultCenterY;
+ }
+
+ public void setDefaultCenterY(Double defaultCenterY) {
+ this.defaultCenterY = defaultCenterY;
+ }
+
+ public Integer getDefaultZoomLevel() {
+ return defaultZoomLevel;
+ }
+
+ public void setDefaultZoomLevel(Integer defaultZoomLevel) {
+ this.defaultZoomLevel = defaultZoomLevel;
+ }
}
\ No newline at end of file
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
index cef95d6fd2..9a5c504bc3 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java
@@ -28,7 +28,7 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
/**
- * This class implemets {@link Model} interface. It's is very simple
+ * This class implements {@link Model} interface. It's is very simple
* implementation containing structures that index the data from
* {@link ModelData} structure and provide access method to this indexed data.
*
@@ -37,594 +37,619 @@ import lcsb.mapviewer.model.map.species.Species;
*/
public class ModelFullIndexed implements Model {
- /**
- * Default class logger.
- */
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(ModelFullIndexed.class);
-
- /**
- * Object that map {@link Element#elementId element identifier} into
- * {@link Element}.
- */
- private Map<String, Element> elementByElementId = new HashMap<>();
-
- /**
- * Object that map {@link Element#id element database identifier} into
- * {@link Element}.
- */
- private Map<Integer, Element> elementByDbId = new HashMap<>();
-
- /**
- * Object that map {@link Reaction#idReaction reaction identifier} into
- * {@link Reaction}.
- */
- private Map<String, Reaction> reactionByReactionId = new HashMap<>();
-
- /**
- * Object that map {@link Reaction#id reaction database identifier} into
- * {@link Reaction}.
- */
- private Map<Integer, Reaction> reactionByDbId = new HashMap<>();
-
- /**
- * {@link ModelData} object containing "raw" data about the model.
- */
- private ModelData modelData = null;
-
- /**
- * Default constructor.
- *
- * @param model
- * {@link ModelData} object containing "raw" data about the model
- */
- public ModelFullIndexed(ModelData model) {
- if (model == null) {
- this.modelData = new ModelData();
- } else {
- this.modelData = model;
- for (Element element : model.getElements()) {
- elementByElementId.put(element.getElementId(), element);
- elementByDbId.put(element.getId(), element);
- }
- for (Reaction reaction : model.getReactions()) {
- reactionByReactionId.put(reaction.getIdReaction(), reaction);
- reactionByDbId.put(reaction.getId(), reaction);
- }
- if (getProject() != null) {
- getProject().getProjectId();
- }
-
- for (ModelSubmodelConnection connection : model.getSubmodels()) {
- if (connection.getSubmodel().getModel() == null) {
- connection.getSubmodel().setModel(new ModelFullIndexed(connection.getSubmodel()));
- }
- }
- // fetch creators of layouts
- for (Layout layout : modelData.getLayouts()) {
- if (layout.getCreator() != null) {
- layout.getCreator().getId();
- }
- }
- }
- modelData.setModel(this);
- }
-
- @Override
- public void addElement(Element element) {
- if (element.getElementId() == null || element.getElementId().isEmpty()) {
- throw new InvalidArgumentException("Element identifier cannot be empty");
- }
- Element element2 = elementByElementId.get(element.getElementId());
- if (element2 == null) {
- modelData.addElement(element);
- elementByElementId.put(element.getElementId(), element);
- elementByDbId.put(element.getId(), element);
- } else {
- throw new InvalidArgumentException("Element with duplicated id: " + element.getElementId());
- }
- }
-
- @Override
- public Double getWidth() {
- return modelData.getWidth();
- }
-
- @Override
- public void setWidth(Double width) {
- modelData.setWidth(width);
- }
-
- @Override
- public Double getHeight() {
- return modelData.getHeight();
- }
-
- @Override
- public void setHeight(Double height) {
- modelData.setHeight(height);
- }
-
- @Override
- public void setWidth(String text) {
- modelData.setWidth(Double.parseDouble(text));
- }
-
- @Override
- public void setHeight(String text) {
- modelData.setHeight(Double.parseDouble(text));
- }
-
- @Override
- public Set<Element> getElements() {
- return modelData.getElements();
- }
-
- @SuppressWarnings("unchecked")
- @Override
- public <T extends Element> T getElementByElementId(String elementId) {
- return (T) elementByElementId.get(elementId);
- }
-
- @Override
- public void addReaction(Reaction reaction) {
- modelData.addReaction(reaction);
- reactionByReactionId.put(reaction.getIdReaction(), reaction);
- reactionByDbId.put(reaction.getId(), reaction);
- }
-
- @Override
- public Set<Reaction> getReactions() {
- return modelData.getReactions();
- }
-
- @Override
- public List<Compartment> getCompartments() {
- List<Compartment> result = new ArrayList<Compartment>();
- for (Element element : modelData.getElements()) {
- if (element instanceof Compartment) {
- result.add((Compartment) element);
- }
- }
- return result;
- }
-
- @Override
- public void addLayer(Layer layer) {
- modelData.addLayer(layer);
- }
-
- @Override
- public Set<Layer> getLayers() {
- return modelData.getLayers();
- }
-
- @Override
- public void addElements(List<? extends Element> elements) {
- for (Element element : elements) {
- addElement(element);
- }
- }
-
- @Override
- public void setNotes(String notes) {
- if (notes != null && notes.contains("<html")) {
- throw new InvalidArgumentException("notes cannot contain <html> tag");
- }
- modelData.setNotes(notes);
- }
-
- @Override
- public String getNotes() {
- return modelData.getNotes();
- }
-
- @Override
- public void setElements(Set<Element> elements) {
- this.modelData.setElements(elements);
- }
-
- @Override
- public Reaction getReactionByReactionId(String idReaction) {
- return reactionByReactionId.get(idReaction);
- }
-
- @Override
- public Project getProject() {
- return modelData.getProject();
- }
-
- @Override
- public void setProject(Project project) {
- modelData.setProject(project);
- }
-
- @Override
- public List<Element> getElementsSortedBySize() {
- List<Element> sortedElements = new ArrayList<>();
- sortedElements.addAll(getElements());
- Collections.sort(sortedElements, Element.SIZE_COMPARATOR);
- return sortedElements;
- }
-
- @Override
- public List<Compartment> getSortedCompartments() {
- List<Compartment> result = getCompartments();
- Collections.sort(result, Element.SIZE_COMPARATOR);
- return result;
- }
-
- @Override
- public Reaction getReactionByDbId(Integer dbId) {
- return reactionByDbId.get(dbId);
- }
-
- @Override
- public Element getElementByDbId(Integer dbId) {
- return elementByDbId.get(dbId);
- }
-
- @Override
- public Calendar getCreationDate() {
- return modelData.getCreationDate();
- }
-
- @Override
- public void setCreationDate(Calendar creationDate) {
- this.modelData.setCreationDate(creationDate);
- }
-
- @Override
- public List<Layout> getLayouts() {
- return modelData.getLayouts();
- }
-
- @Override
- public void setLayouts(List<Layout> layouts) {
- this.modelData.setLayouts(layouts);
- }
-
- @Override
- public void addLayout(Layout layout) {
- modelData.addLayout(layout);
- }
-
- @Override
- public void setWidth(int width) {
- setWidth(Double.valueOf(width));
- }
-
- @Override
- public void setHeight(int height) {
- setHeight(Double.valueOf(height));
- }
-
- @Override
- public Set<BioEntity> getElementsByAnnotation(MiriamData miriamData) {
- Set<BioEntity> result = new HashSet<>();
- for (Element element : getElements()) {
- for (MiriamData md : element.getMiriamData()) {
- if (md.equals(miriamData)) {
- result.add(element);
- }
- }
- }
-
- for (Reaction element : getReactions()) {
- for (MiriamData md : element.getMiriamData()) {
- if (md.equals(miriamData)) {
- result.add(element);
- }
- }
- }
-
- return result;
- }
-
- @Override
- public void addReactions(List<Reaction> reactions2) {
- for (Reaction reaction : reactions2) {
- addReaction(reaction);
- }
- }
-
- @Override
- public Collection<Complex> getComplexList() {
- List<Complex> result = new ArrayList<>();
- for (Element element : modelData.getElements()) {
- if (element instanceof Complex) {
- result.add((Complex) element);
- }
- }
- return result;
- }
-
- @Override
- public Collection<Species> getNotComplexSpeciesList() {
- List<Species> result = new ArrayList<>();
- for (Element element : modelData.getElements()) {
- if (element instanceof Species && !(element instanceof Complex)) {
- result.add((Species) element);
- }
- }
- return result;
- }
-
- @Override
- public void addLayers(Collection<Layer> layers) {
- for (Layer layer : layers) {
- addLayer(layer);
- }
- }
-
- @Override
- public List<Element> getSortedSpeciesList() {
- List<Element> result = new ArrayList<>();
- result.addAll(getElements());
- Collections.sort(result, Element.SIZE_COMPARATOR);
- return result;
- }
-
- @Override
- public List<Reaction> getSortedReactions() {
- List<Reaction> result = new ArrayList<Reaction>();
- result.addAll(getReactions());
- Collections.sort(result, Reaction.ID_COMPARATOR);
- return result;
- }
-
- /**
- * Remove layout from model.
- *
- * @param dbLayout
- * layout to remove
- */
- public void removeLayout(Layout dbLayout) {
- modelData.removeLayout(dbLayout);
- }
-
- @Override
- public void addElementGroup(ElementGroup elementGroup) {
- modelData.addElementGroup(elementGroup);
- }
-
- @Override
- public void addBlockDiagream(BlockDiagram blockDiagram) {
- modelData.addBlockDiagream(blockDiagram);
- }
-
- @Override
- public void removeElement(Element element) {
- modelData.removeElement(element);
- elementByElementId.remove(element.getElementId());
- elementByDbId.remove(element.getId());
-
- if (element.getCompartment() != null) {
- Compartment ca = element.getCompartment();
- ca.removeElement(element);
- }
-
- if (element instanceof Species) {
- Species al = (Species) element;
- if (al.getComplex() != null) {
- Complex ca = ((Species) element).getComplex();
- ca.removeElement(al);
- }
- }
- }
-
- @Override
- public void removeReaction(Reaction reaction) {
- modelData.removeReaction(reaction);
- reactionByReactionId.remove(reaction.getIdReaction());
- reactionByDbId.remove(reaction.getId());
- }
-
- @Override
- public int getZoomLevels() {
- return modelData.getZoomLevels();
- }
-
- @Override
- public void setZoomLevels(int zoomLevels) {
- this.modelData.setZoomLevels(zoomLevels);
- }
-
- @Override
- public int getTileSize() {
- return modelData.getTileSize();
- }
-
- @Override
- public void setTileSize(int tileSize) {
- this.modelData.setTileSize(tileSize);
- }
-
- @Override
- public String getIdModel() {
- return modelData.getIdModel();
- }
-
- @Override
- public void setIdModel(String idModel) {
- this.modelData.setIdModel(idModel);
- }
-
- @Override
- public ModelData getModelData() {
- return modelData;
- }
-
- @Override
- public Integer getId() {
- return modelData.getId();
- }
-
- @Override
- public void addSubmodelConnection(ModelSubmodelConnection submodel) {
- modelData.addSubmodel(submodel);
- submodel.setParentModel(this);
- }
-
- @Override
- public Collection<ModelSubmodelConnection> getSubmodelConnections() {
- return modelData.getSubmodels();
- }
-
- @Override
- public String getName() {
- return modelData.getName();
- }
-
- @Override
- public void setName(String name) {
- modelData.setName(name);
- }
-
- @Override
- public Model getSubmodelById(Integer id) {
- if (id == null) {
- return null;
- }
- if (id.equals(getId())) {
- return this;
- }
- SubmodelConnection connection = getSubmodelConnectionById(id);
- if (connection != null) {
- return connection.getSubmodel().getModel();
- } else {
- return null;
- }
- }
-
- @Override
- public Collection<SubmodelConnection> getParentModels() {
- return modelData.getParentModels();
- }
-
- @Override
- public Model getSubmodelByConnectionName(String name) {
- if (name == null) {
- return null;
- }
- for (ModelSubmodelConnection connection : getSubmodelConnections()) {
- if (name.equals(connection.getName())) {
- return connection.getSubmodel().getModel();
- }
- }
- return null;
- }
-
- @Override
- public SubmodelConnection getSubmodelConnectionById(Integer id) {
- for (ModelSubmodelConnection connection : getSubmodelConnections()) {
- if (id.equals(connection.getSubmodel().getId())) {
- return connection;
- }
- }
- return null;
- }
-
- @Override
- public Model getSubmodelById(String identifier) {
- if (identifier == null) {
- return null;
- }
- Integer id = Integer.parseInt(identifier);
- return getSubmodelById(id);
- }
-
- @Override
- public Collection<Model> getSubmodels() {
- List<Model> models = new ArrayList<Model>();
- for (ModelSubmodelConnection connection : getSubmodelConnections()) {
- models.add(connection.getSubmodel().getModel());
- }
- return models;
- }
-
- @Override
- public Model getSubmodelByName(String name) {
- if (name == null) {
- return null;
- }
- for (ModelSubmodelConnection connection : getSubmodelConnections()) {
- if (name.equals(connection.getSubmodel().getName())) {
- return connection.getSubmodel().getModel();
- }
- }
- if (name.equals(getName())) {
- return this;
- }
- return null;
- }
-
- @Override
- public void addLayout(int index, Layout layout) {
- this.modelData.getLayouts().add(index, layout);
- layout.setModel(this);
- }
-
- @Override
- public void addDataMiningSet(DataMiningSet dataMiningSet) {
- this.modelData.getDataMiningSets().add(dataMiningSet);
- dataMiningSet.setModel(this);
- }
-
- @Override
- public List<DataMiningSet> getDataMiningSets() {
- return modelData.getDataMiningSets();
- }
-
- @Override
- public void addDataMiningSets(Collection<DataMiningSet> dataMiningSets) {
- for (DataMiningSet dataMiningSet : dataMiningSets) {
- addDataMiningSet(dataMiningSet);
- }
- }
-
- @Override
- public Layout getLayoutByIdentifier(Integer layoutDbIdentfier) {
- for (Layout layout : getLayouts()) {
- if (layout.getId() == layoutDbIdentfier) {
- return layout;
- }
- }
- return null;
- }
-
- @Override
- public void setId(int id) {
- modelData.setId(id);
- }
-
- @Override
- public List<BioEntity> getBioEntities() {
- List<BioEntity> result = new ArrayList<>();
- result.addAll(getElements());
- result.addAll(getReactions());
- return result;
- }
-
- @Override
- public List<Element> getElementsByName(String name) {
- List<Element> result = new ArrayList<>();
- for (Element element : getElements()) {
- if (element.getName().equalsIgnoreCase(name)) {
- result.add(element);
- }
- }
- return result;
- }
-
- @Override
- public List<Species> getSpeciesList() {
- List<Species> result = new ArrayList<>();
- for (Element element : modelData.getElements()) {
- if (element instanceof Species) {
- result.add((Species) element);
- }
- }
- return result;
- }
+ /**
+ * Default class logger.
+ */
+ @SuppressWarnings("unused")
+ private static Logger logger = Logger.getLogger(ModelFullIndexed.class);
+
+ /**
+ * Object that map {@link Element#elementId element identifier} into
+ * {@link Element}.
+ */
+ private Map<String, Element> elementByElementId = new HashMap<>();
+
+ /**
+ * Object that map {@link Element#id element database identifier} into
+ * {@link Element}.
+ */
+ private Map<Integer, Element> elementByDbId = new HashMap<>();
+
+ /**
+ * Object that map {@link Reaction#idReaction reaction identifier} into
+ * {@link Reaction}.
+ */
+ private Map<String, Reaction> reactionByReactionId = new HashMap<>();
+
+ /**
+ * Object that map {@link Reaction#id reaction database identifier} into
+ * {@link Reaction}.
+ */
+ private Map<Integer, Reaction> reactionByDbId = new HashMap<>();
+
+ /**
+ * {@link ModelData} object containing "raw" data about the model.
+ */
+ private ModelData modelData = null;
+
+ /**
+ * Default constructor.
+ *
+ * @param model
+ * {@link ModelData} object containing "raw" data about the model
+ */
+ public ModelFullIndexed(ModelData model) {
+ if (model == null) {
+ this.modelData = new ModelData();
+ } else {
+ this.modelData = model;
+ for (Element element : model.getElements()) {
+ elementByElementId.put(element.getElementId(), element);
+ elementByDbId.put(element.getId(), element);
+ }
+ for (Reaction reaction : model.getReactions()) {
+ reactionByReactionId.put(reaction.getIdReaction(), reaction);
+ reactionByDbId.put(reaction.getId(), reaction);
+ }
+ if (getProject() != null) {
+ getProject().getProjectId();
+ }
+
+ for (ModelSubmodelConnection connection : model.getSubmodels()) {
+ if (connection.getSubmodel().getModel() == null) {
+ connection.getSubmodel().setModel(new ModelFullIndexed(connection.getSubmodel()));
+ }
+ }
+ // fetch creators of layouts
+ for (Layout layout : modelData.getLayouts()) {
+ if (layout.getCreator() != null) {
+ layout.getCreator().getId();
+ }
+ }
+ }
+ modelData.setModel(this);
+ }
+
+ @Override
+ public void addElement(Element element) {
+ if (element.getElementId() == null || element.getElementId().isEmpty()) {
+ throw new InvalidArgumentException("Element identifier cannot be empty");
+ }
+ Element element2 = elementByElementId.get(element.getElementId());
+ if (element2 == null) {
+ modelData.addElement(element);
+ elementByElementId.put(element.getElementId(), element);
+ elementByDbId.put(element.getId(), element);
+ } else {
+ throw new InvalidArgumentException("Element with duplicated id: " + element.getElementId());
+ }
+ }
+
+ @Override
+ public Double getWidth() {
+ return modelData.getWidth();
+ }
+
+ @Override
+ public void setWidth(Double width) {
+ modelData.setWidth(width);
+ }
+
+ @Override
+ public Double getHeight() {
+ return modelData.getHeight();
+ }
+
+ @Override
+ public void setHeight(Double height) {
+ modelData.setHeight(height);
+ }
+
+ @Override
+ public void setWidth(String text) {
+ modelData.setWidth(Double.parseDouble(text));
+ }
+
+ @Override
+ public void setHeight(String text) {
+ modelData.setHeight(Double.parseDouble(text));
+ }
+
+ @Override
+ public Set<Element> getElements() {
+ return modelData.getElements();
+ }
+
+ @SuppressWarnings("unchecked")
+ @Override
+ public <T extends Element> T getElementByElementId(String elementId) {
+ return (T) elementByElementId.get(elementId);
+ }
+
+ @Override
+ public void addReaction(Reaction reaction) {
+ modelData.addReaction(reaction);
+ reactionByReactionId.put(reaction.getIdReaction(), reaction);
+ reactionByDbId.put(reaction.getId(), reaction);
+ }
+
+ @Override
+ public Set<Reaction> getReactions() {
+ return modelData.getReactions();
+ }
+
+ @Override
+ public List<Compartment> getCompartments() {
+ List<Compartment> result = new ArrayList<Compartment>();
+ for (Element element : modelData.getElements()) {
+ if (element instanceof Compartment) {
+ result.add((Compartment) element);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public void addLayer(Layer layer) {
+ modelData.addLayer(layer);
+ }
+
+ @Override
+ public Set<Layer> getLayers() {
+ return modelData.getLayers();
+ }
+
+ @Override
+ public void addElements(List<? extends Element> elements) {
+ for (Element element : elements) {
+ addElement(element);
+ }
+ }
+
+ @Override
+ public void setNotes(String notes) {
+ if (notes != null && notes.contains("<html")) {
+ throw new InvalidArgumentException("notes cannot contain <html> tag");
+ }
+ modelData.setNotes(notes);
+ }
+
+ @Override
+ public String getNotes() {
+ return modelData.getNotes();
+ }
+
+ @Override
+ public void setElements(Set<Element> elements) {
+ this.modelData.setElements(elements);
+ }
+
+ @Override
+ public Reaction getReactionByReactionId(String idReaction) {
+ return reactionByReactionId.get(idReaction);
+ }
+
+ @Override
+ public Project getProject() {
+ return modelData.getProject();
+ }
+
+ @Override
+ public void setProject(Project project) {
+ modelData.setProject(project);
+ }
+
+ @Override
+ public List<Element> getElementsSortedBySize() {
+ List<Element> sortedElements = new ArrayList<>();
+ sortedElements.addAll(getElements());
+ Collections.sort(sortedElements, Element.SIZE_COMPARATOR);
+ return sortedElements;
+ }
+
+ @Override
+ public List<Compartment> getSortedCompartments() {
+ List<Compartment> result = getCompartments();
+ Collections.sort(result, Element.SIZE_COMPARATOR);
+ return result;
+ }
+
+ @Override
+ public Reaction getReactionByDbId(Integer dbId) {
+ return reactionByDbId.get(dbId);
+ }
+
+ @Override
+ public Element getElementByDbId(Integer dbId) {
+ return elementByDbId.get(dbId);
+ }
+
+ @Override
+ public Calendar getCreationDate() {
+ return modelData.getCreationDate();
+ }
+
+ @Override
+ public void setCreationDate(Calendar creationDate) {
+ this.modelData.setCreationDate(creationDate);
+ }
+
+ @Override
+ public List<Layout> getLayouts() {
+ return modelData.getLayouts();
+ }
+
+ @Override
+ public void setLayouts(List<Layout> layouts) {
+ this.modelData.setLayouts(layouts);
+ }
+
+ @Override
+ public void addLayout(Layout layout) {
+ modelData.addLayout(layout);
+ }
+
+ @Override
+ public void setWidth(int width) {
+ setWidth(Double.valueOf(width));
+ }
+
+ @Override
+ public void setHeight(int height) {
+ setHeight(Double.valueOf(height));
+ }
+
+ @Override
+ public Set<BioEntity> getElementsByAnnotation(MiriamData miriamData) {
+ Set<BioEntity> result = new HashSet<>();
+ for (Element element : getElements()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (md.equals(miriamData)) {
+ result.add(element);
+ }
+ }
+ }
+
+ for (Reaction element : getReactions()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (md.equals(miriamData)) {
+ result.add(element);
+ }
+ }
+ }
+
+ return result;
+ }
+
+ @Override
+ public void addReactions(List<Reaction> reactions2) {
+ for (Reaction reaction : reactions2) {
+ addReaction(reaction);
+ }
+ }
+
+ @Override
+ public Collection<Complex> getComplexList() {
+ List<Complex> result = new ArrayList<>();
+ for (Element element : modelData.getElements()) {
+ if (element instanceof Complex) {
+ result.add((Complex) element);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public Collection<Species> getNotComplexSpeciesList() {
+ List<Species> result = new ArrayList<>();
+ for (Element element : modelData.getElements()) {
+ if (element instanceof Species && !(element instanceof Complex)) {
+ result.add((Species) element);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public void addLayers(Collection<Layer> layers) {
+ for (Layer layer : layers) {
+ addLayer(layer);
+ }
+ }
+
+ @Override
+ public List<Element> getSortedSpeciesList() {
+ List<Element> result = new ArrayList<>();
+ result.addAll(getElements());
+ Collections.sort(result, Element.SIZE_COMPARATOR);
+ return result;
+ }
+
+ @Override
+ public List<Reaction> getSortedReactions() {
+ List<Reaction> result = new ArrayList<Reaction>();
+ result.addAll(getReactions());
+ Collections.sort(result, Reaction.ID_COMPARATOR);
+ return result;
+ }
+
+ @Override
+ public void removeLayout(Layout dbLayout) {
+ modelData.removeLayout(dbLayout);
+ }
+
+ @Override
+ public void addElementGroup(ElementGroup elementGroup) {
+ modelData.addElementGroup(elementGroup);
+ }
+
+ @Override
+ public void addBlockDiagream(BlockDiagram blockDiagram) {
+ modelData.addBlockDiagream(blockDiagram);
+ }
+
+ @Override
+ public void removeElement(Element element) {
+ modelData.removeElement(element);
+ elementByElementId.remove(element.getElementId());
+ elementByDbId.remove(element.getId());
+
+ if (element.getCompartment() != null) {
+ Compartment ca = element.getCompartment();
+ ca.removeElement(element);
+ }
+
+ if (element instanceof Species) {
+ Species al = (Species) element;
+ if (al.getComplex() != null) {
+ Complex ca = ((Species) element).getComplex();
+ ca.removeElement(al);
+ }
+ }
+ }
+
+ @Override
+ public void removeReaction(Reaction reaction) {
+ modelData.removeReaction(reaction);
+ reactionByReactionId.remove(reaction.getIdReaction());
+ reactionByDbId.remove(reaction.getId());
+ }
+
+ @Override
+ public int getZoomLevels() {
+ return modelData.getZoomLevels();
+ }
+
+ @Override
+ public void setZoomLevels(int zoomLevels) {
+ this.modelData.setZoomLevels(zoomLevels);
+ }
+
+ @Override
+ public int getTileSize() {
+ return modelData.getTileSize();
+ }
+
+ @Override
+ public void setTileSize(int tileSize) {
+ this.modelData.setTileSize(tileSize);
+ }
+
+ @Override
+ public String getIdModel() {
+ return modelData.getIdModel();
+ }
+
+ @Override
+ public void setIdModel(String idModel) {
+ this.modelData.setIdModel(idModel);
+ }
+
+ @Override
+ public ModelData getModelData() {
+ return modelData;
+ }
+
+ @Override
+ public Integer getId() {
+ return modelData.getId();
+ }
+
+ @Override
+ public void addSubmodelConnection(ModelSubmodelConnection submodel) {
+ modelData.addSubmodel(submodel);
+ submodel.setParentModel(this);
+ }
+
+ @Override
+ public Collection<ModelSubmodelConnection> getSubmodelConnections() {
+ return modelData.getSubmodels();
+ }
+
+ @Override
+ public String getName() {
+ return modelData.getName();
+ }
+
+ @Override
+ public void setName(String name) {
+ modelData.setName(name);
+ }
+
+ @Override
+ public Model getSubmodelById(Integer id) {
+ if (id == null) {
+ return null;
+ }
+ if (id.equals(getId())) {
+ return this;
+ }
+ SubmodelConnection connection = getSubmodelConnectionById(id);
+ if (connection != null) {
+ return connection.getSubmodel().getModel();
+ } else {
+ return null;
+ }
+ }
+
+ @Override
+ public Collection<SubmodelConnection> getParentModels() {
+ return modelData.getParentModels();
+ }
+
+ @Override
+ public Model getSubmodelByConnectionName(String name) {
+ if (name == null) {
+ return null;
+ }
+ for (ModelSubmodelConnection connection : getSubmodelConnections()) {
+ if (name.equals(connection.getName())) {
+ return connection.getSubmodel().getModel();
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public SubmodelConnection getSubmodelConnectionById(Integer id) {
+ for (ModelSubmodelConnection connection : getSubmodelConnections()) {
+ if (id.equals(connection.getSubmodel().getId())) {
+ return connection;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public Model getSubmodelById(String identifier) {
+ if (identifier == null) {
+ return null;
+ }
+ Integer id = Integer.parseInt(identifier);
+ return getSubmodelById(id);
+ }
+
+ @Override
+ public Collection<Model> getSubmodels() {
+ List<Model> models = new ArrayList<Model>();
+ for (ModelSubmodelConnection connection : getSubmodelConnections()) {
+ models.add(connection.getSubmodel().getModel());
+ }
+ return models;
+ }
+
+ @Override
+ public Model getSubmodelByName(String name) {
+ if (name == null) {
+ return null;
+ }
+ for (ModelSubmodelConnection connection : getSubmodelConnections()) {
+ if (name.equals(connection.getSubmodel().getName())) {
+ return connection.getSubmodel().getModel();
+ }
+ }
+ if (name.equals(getName())) {
+ return this;
+ }
+ return null;
+ }
+
+ @Override
+ public void addLayout(int index, Layout layout) {
+ this.modelData.getLayouts().add(index, layout);
+ layout.setModel(this);
+ }
+
+ @Override
+ public void addDataMiningSet(DataMiningSet dataMiningSet) {
+ this.modelData.getDataMiningSets().add(dataMiningSet);
+ dataMiningSet.setModel(this);
+ }
+
+ @Override
+ public List<DataMiningSet> getDataMiningSets() {
+ return modelData.getDataMiningSets();
+ }
+
+ @Override
+ public void addDataMiningSets(Collection<DataMiningSet> dataMiningSets) {
+ for (DataMiningSet dataMiningSet : dataMiningSets) {
+ addDataMiningSet(dataMiningSet);
+ }
+ }
+
+ @Override
+ public Layout getLayoutByIdentifier(Integer layoutDbIdentfier) {
+ for (Layout layout : getLayouts()) {
+ if (layout.getId() == layoutDbIdentfier) {
+ return layout;
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public void setId(int id) {
+ modelData.setId(id);
+ }
+
+ @Override
+ public List<BioEntity> getBioEntities() {
+ List<BioEntity> result = new ArrayList<>();
+ result.addAll(getElements());
+ result.addAll(getReactions());
+ return result;
+ }
+
+ @Override
+ public List<Element> getElementsByName(String name) {
+ List<Element> result = new ArrayList<>();
+ for (Element element : getElements()) {
+ if (element.getName().equalsIgnoreCase(name)) {
+ result.add(element);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public List<Species> getSpeciesList() {
+ List<Species> result = new ArrayList<>();
+ for (Element element : modelData.getElements()) {
+ if (element instanceof Species) {
+ result.add((Species) element);
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public Double getDefaultCenterX() {
+ return modelData.getDefaultCenterX();
+ }
+
+ @Override
+ public void setDefaultCenterX(Double defaultCenterX) {
+ modelData.setDefaultCenterX(defaultCenterX);
+ }
+
+ @Override
+ public Double getDefaultCenterY() {
+ return modelData.getDefaultCenterY();
+ }
+
+ @Override
+ public void setDefaultCenterY(Double defaultCenterY) {
+ modelData.setDefaultCenterY(defaultCenterY);
+ }
+
+ @Override
+ public Integer getDefaultZoomLevel() {
+ return modelData.getDefaultZoomLevel();
+ }
+
+ @Override
+ public void setDefaultZoomLevel(Integer defaultZoomLevel) {
+ modelData.setDefaultZoomLevel(defaultZoomLevel);
+ }
}
diff --git a/persist/src/db/12.0.0/fix_db_20171121.sql b/persist/src/db/12.0.0/fix_db_20171121.sql
index 98a7685a7e..3769716cac 100644
--- a/persist/src/db/12.0.0/fix_db_20171121.sql
+++ b/persist/src/db/12.0.0/fix_db_20171121.sql
@@ -1,2 +1,7 @@
-- column which indicates that this overlay should be shown on startup
alter table layout add column defaultoverlay boolean default false;
+
+-- default positioning of map when session data is not available
+alter table model_table add column defaultzoomlevel integer default null;
+alter table model_table add column defaultcenterx double precision default null;
+alter table model_table add column defaultcentery double precision default null;
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
index 1cecb23458..93beeb54c1 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelController.java
@@ -1,44 +1,66 @@
-package lcsb.mapviewer.api.projects.models;
-
-import java.util.List;
-
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.MediaType;
-import org.springframework.web.bind.annotation.CookieValue;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-
-import lcsb.mapviewer.api.BaseController;
-import lcsb.mapviewer.api.ObjectNotFoundException;
-import lcsb.mapviewer.common.Configuration;
-import lcsb.mapviewer.services.SecurityException;
-
-@RestController
-public class ModelController extends BaseController {
- @Autowired
- private ModelRestImpl modelController;
-
- @RequestMapping(value = "/projects/{projectId:.+}/models/", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public List<ModelMetaData> getModels(//
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, ObjectNotFoundException {
- return modelController.getModels(projectId, token);
- }
-
- @RequestMapping(value = "/projects/{projectId:.+}/models/{modelId:.+}", method = { RequestMethod.GET }, produces = { MediaType.APPLICATION_JSON_VALUE })
- public Object getModel(//
- @PathVariable(value = "modelId") String modelId, //
- @PathVariable(value = "projectId") String projectId, //
- @CookieValue(value = Configuration.AUTH_TOKEN) String token //
- ) throws SecurityException, ObjectNotFoundException {
- if (modelId.equals("*")) {
- return modelController.getModels(projectId, token);
- } else {
- return modelController.getModel(projectId, modelId, token);
- }
- }
-
+package lcsb.mapviewer.api.projects.models;
+
+import java.io.IOException;
+import java.util.List;
+import java.util.Map;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
+import org.springframework.web.bind.annotation.CookieValue;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.RestController;
+
+import com.fasterxml.jackson.core.JsonParseException;
+import com.fasterxml.jackson.databind.JsonMappingException;
+
+import lcsb.mapviewer.api.BaseController;
+import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.services.SecurityException;
+
+@RestController
+public class ModelController extends BaseController {
+ @Autowired
+ private ModelRestImpl modelController;
+
+ @RequestMapping(value = "/projects/{projectId:.+}/models/", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public List<ModelMetaData> getModels(//
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ return modelController.getModels(projectId, token);
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}/models/{modelId:.+}", method = { RequestMethod.GET }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Object getModel(//
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "projectId") String projectId, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, ObjectNotFoundException {
+ if (modelId.equals("*")) {
+ return modelController.getModels(projectId, token);
+ } else {
+ return modelController.getModel(projectId, modelId, token);
+ }
+ }
+
+ @RequestMapping(value = "/projects/{projectId:.+}/models/{modelId:.+}", method = { RequestMethod.PATCH }, produces = {
+ MediaType.APPLICATION_JSON_VALUE })
+ public Object updateModel(//
+ @PathVariable(value = "modelId") String modelId, //
+ @PathVariable(value = "projectId") String projectId, //
+ @RequestBody String body, //
+ @CookieValue(value = Configuration.AUTH_TOKEN) String token //
+ ) throws SecurityException, JsonParseException, JsonMappingException, IOException, QueryException {
+ Map<String, Object> node = parseBody(body);
+ Map<String, Object> data = getData(node, "model");
+ return modelController.updateModel(projectId, modelId, data, token);
+ }
+
}
\ No newline at end of file
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
index 2ff2bc4932..e7effa77c3 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelMetaData.java
@@ -46,6 +46,12 @@ public class ModelMetaData implements Serializable {
private Integer height;
+ private Double defaultCenterX;
+
+ private Double defaultCenterY;
+
+ private Integer defaultZoomLevel;
+
/**
* Minimum zoom level that should be allowed by the Google Maps API.
*/
@@ -104,6 +110,9 @@ public class ModelMetaData implements Serializable {
this.setCenterLatLng(cConverter.toLatLng(new Point2D.Double(size / 2, size / 2)));
this.setBottomRightLatLng(cConverter.toLatLng(new Point2D.Double(model.getWidth(), model.getHeight())));
this.setTopLeftLatLng(cConverter.toLatLng(new Point2D.Double(0, 0)));
+ this.setDefaultCenterX(model.getDefaultCenterX());
+ this.setDefaultCenterY(model.getDefaultCenterY());
+ this.setDefaultZoomLevel(model.getDefaultZoomLevel());
List<ModelMetaData> submodels = new ArrayList<>();
for (ModelSubmodelConnection connection : model.getSubmodels()) {
@@ -362,4 +371,28 @@ public class ModelMetaData implements Serializable {
this.submodelType = submodelType;
}
+ public Integer getDefaultZoomLevel() {
+ return defaultZoomLevel;
+ }
+
+ public void setDefaultZoomLevel(Integer defaultZoomLevel) {
+ this.defaultZoomLevel = defaultZoomLevel;
+ }
+
+ public Double getDefaultCenterX() {
+ return defaultCenterX;
+ }
+
+ public void setDefaultCenterX(Double defaultCenterX) {
+ this.defaultCenterX = defaultCenterX;
+ }
+
+ public Double getDefaultCenterY() {
+ return defaultCenterY;
+ }
+
+ public void setDefaultCenterY(Double defaultCenterY) {
+ this.defaultCenterY = defaultCenterY;
+ }
+
}
diff --git a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
index 7e26e7430e..2fd1d56ad5 100644
--- a/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
+++ b/rest-api/src/main/java/lcsb/mapviewer/api/projects/models/ModelRestImpl.java
@@ -2,6 +2,8 @@ package lcsb.mapviewer.api.projects.models;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
+import java.util.Set;
import org.apache.log4j.Logger;
import org.springframework.beans.factory.annotation.Autowired;
@@ -9,8 +11,12 @@ import org.springframework.transaction.annotation.Transactional;
import lcsb.mapviewer.api.BaseRestImpl;
import lcsb.mapviewer.api.ObjectNotFoundException;
+import lcsb.mapviewer.api.QueryException;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.model.Project;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.user.PrivilegeType;
import lcsb.mapviewer.services.SecurityException;
import lcsb.mapviewer.services.interfaces.ILayoutService;
import lcsb.mapviewer.services.view.AuthenticationToken;
@@ -72,4 +78,86 @@ public class ModelRestImpl extends BaseRestImpl {
}
return result;
}
+
+ public ModelMetaData updateModel(String projectId, String modelId, Map<String, Object> data, String token)
+ throws SecurityException, QueryException {
+ AuthenticationToken authenticationToken = getUserService().getToken(token);
+ Project project = getProjectService().getProjectByProjectId(projectId, authenticationToken);
+ if (project == null) {
+ throw new ObjectNotFoundException("Project with given id doesn't exist");
+ }
+ boolean canModify = getUserService().userHasPrivilege(authenticationToken, PrivilegeType.ADD_MAP);
+ if (!canModify) {
+ throw new SecurityException("You cannot update projects");
+ }
+ ModelData model = null;
+ Integer id = Integer.valueOf(modelId);
+ for (ModelData m : project.getModels()) {
+ if (m.getId().equals(id)) {
+ model = m;
+ }
+ }
+ if (model == null) {
+ throw new ObjectNotFoundException("Model with given id doesn't exist");
+ }
+
+ Set<String> fields = data.keySet();
+ for (String fieldName : fields) {
+ Object value = data.get(fieldName);
+ if (fieldName.equalsIgnoreCase("defaultCenterX")) {
+ model.setDefaultCenterX(parseDouble(value));
+ } else if (fieldName.equalsIgnoreCase("defaultCenterY")) {
+ model.setDefaultCenterY(parseDouble(value));
+ } else if (fieldName.equalsIgnoreCase("defaultZoomLevel")) {
+ model.setDefaultZoomLevel(parseInteger(value));
+ } else if (fieldName.equalsIgnoreCase("id")) {
+ if (!model.getId().equals(parseInteger(value))) {
+ throw new QueryException("Id doesn't match: " + value + ", " + model.getId());
+ }
+ } else {
+ throw new QueryException("Unknown field: " + fieldName);
+ }
+ }
+ getModelService().updateModel(model, authenticationToken);
+ return getModel(projectId, modelId, token);
+ }
+
+ private Integer parseInteger(Object value) throws QueryException {
+ if (value instanceof Integer) {
+ return (Integer) value;
+ } else if (value instanceof String) {
+ if (((String) value).equalsIgnoreCase("")) {
+ return null;
+ } else {
+ try {
+ return Integer.parseInt((String) value);
+ } catch (NumberFormatException e) {
+ throw new QueryException("Invalid double value: " + value);
+ }
+ }
+ } else {
+ throw new InvalidArgumentException();
+ }
+
+ }
+
+ private Double parseDouble(Object value) throws QueryException {
+ if (value instanceof Double) {
+ return (Double) value;
+ } else if (value instanceof String) {
+ if (((String) value).equalsIgnoreCase("")) {
+ return null;
+ } else {
+ try {
+ return Double.parseDouble((String) value);
+ } catch (NumberFormatException e) {
+ throw new QueryException("Invalid double value: " + value);
+ }
+ }
+ } else if (value == null) {
+ return null;
+ } else {
+ throw new InvalidArgumentException();
+ }
+ }
}
diff --git a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
index 4d7a63ac46..d3634f6b8d 100644
--- a/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/impl/ModelService.java
@@ -1,558 +1,574 @@
-package lcsb.mapviewer.services.impl;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.apache.log4j.Logger;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.transaction.annotation.Transactional;
-
-import lcsb.mapviewer.annotation.data.Article;
-import lcsb.mapviewer.annotation.services.MeSHParser;
-import lcsb.mapviewer.annotation.services.MiriamConnector;
-import lcsb.mapviewer.annotation.services.PubmedParser;
-import lcsb.mapviewer.annotation.services.PubmedSearchException;
-import lcsb.mapviewer.annotation.services.TaxonomyBackend;
-import lcsb.mapviewer.annotation.services.TaxonomySearchException;
-import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
-import lcsb.mapviewer.commands.CopyCommand;
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.common.exception.InvalidArgumentException;
-import lcsb.mapviewer.model.map.MiriamData;
-import lcsb.mapviewer.model.map.MiriamType;
-import lcsb.mapviewer.model.map.layout.Layout;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.reaction.Reaction;
-import lcsb.mapviewer.model.map.species.Element;
-import lcsb.mapviewer.model.user.PrivilegeType;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.persist.dao.ProjectDao;
-import lcsb.mapviewer.persist.dao.map.ModelDao;
-import lcsb.mapviewer.services.interfaces.ILayoutService;
-import lcsb.mapviewer.services.interfaces.IModelService;
-import lcsb.mapviewer.services.interfaces.IUserService;
-import lcsb.mapviewer.services.search.data.LightAliasView;
-import lcsb.mapviewer.services.search.data.LightAliasViewFactory;
-import lcsb.mapviewer.services.search.data.LightReactionView;
-import lcsb.mapviewer.services.view.AuthenticationToken;
-import lcsb.mapviewer.services.view.LayoutView;
-import lcsb.mapviewer.services.view.ModelView;
-import lcsb.mapviewer.services.view.ModelViewFactory;
-import lcsb.mapviewer.services.view.ProjectView;
-
-/**
- * Implementation of the service that manages models.
- *
- * @author Piotr Gawron
- *
- */
-@Transactional(value = "txManager")
-public class ModelService implements IModelService {
-
- /**
- * Default class logger.
- */
- private Logger logger = Logger.getLogger(ModelService.class);
-
- /**
- * List of cached models.
- */
- private static Map<String, Model> models = new HashMap<String, Model>();
-
- /**
- * List of models that are currently being loaded from databsae.
- */
- private static Set<String> modelsInLoadStage = new HashSet<>();
-
- /**
- * Service that manages and gives access to user information.
- */
- @Autowired
- private IUserService userService;
-
- /**
- * Data access object for models.
- */
- @Autowired
- private ModelDao modelDao;
-
- @Autowired
- private ProjectDao projectDao;
-
- /**
- * Object allowing access to the mesh database.
- */
- @Autowired
- private MeSHParser meshParser;
-
- /**
- * Local backend to the pubmed data.
- */
- @Autowired
- private PubmedParser backend;
-
- /**
- * Service used for managing layouts.
- */
- @Autowired
- private ILayoutService layoutService;
-
- /**
- * Connector used for accessing data from miriam registry.
- */
- @Autowired
- private MiriamConnector miriamConnector;
-
- /**
- * Factory object used for creation of {@link ModelView} elements.
- */
- @Autowired
- private ModelViewFactory modelViewFactory;
-
- /**
- * Access point and parser for the online ctd database.
- */
- @Autowired
- private TaxonomyBackend taxonomyBackend;
-
- @Override
- public Model getLastModelByProjectId(String projectName, AuthenticationToken token) {
- if (projectName == null) {
- return null;
- }
-
- // check if model is being loaded by another thread
- boolean waitForModel = false;
- do {
- synchronized (modelsInLoadStage) {
- waitForModel = modelsInLoadStage.contains(projectName);
- }
- // if model is being loaded then wait until it's loaded
- if (waitForModel) {
- try {
- Thread.sleep(100);
- } catch (InterruptedException e) {
- logger.fatal(e, e);
- }
- }
- } while (waitForModel);
-
- Model model = models.get(projectName);
- if (model == null) {
- try {
- // mark model as being load stage, so other threads that want to access
- // it will wait
- synchronized (modelsInLoadStage) {
- modelsInLoadStage.add(projectName);
- }
- logger.debug("Unknown model, trying to load the model into memory.");
-
- ModelData modelData = modelDao.getLastModelForProjectIdentifier(projectName, false);
-
- if (modelData == null) {
- logger.debug("Model doesn't exist");
- return null;
- }
- logger.debug("Model loaded from db.");
- model = new ModelFullIndexed(modelData);
-
- // this is a trick to load all required subelements of the model... ;/
- // lets copy model - it will access all elements...
- new CopyCommand(model).execute();
-
- for (ModelData m : model.getProject().getModels()) {
- new CopyCommand(m.getModel()).execute();
- }
-
- logger.debug("Model loaded successfullly");
- models.put(projectName, model);
- } finally {
- // model is not being loaded anymore
- synchronized (modelsInLoadStage) {
- modelsInLoadStage.remove(projectName);
- }
- }
- }
- if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, model.getProject())) {
- return model;
- } else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
- return model;
- } else {
- logger.debug(userService.getUserByToken(token).getLogin());
- throw new SecurityException("User doesn't have access to project");
- }
- }
-
- @Override
- public void cacheAllPubmedIds(Model model, IProgressUpdater updater) {
- logger.debug("Caching pubmed ids...");
- if (model != null) {
- Set<Integer> pubmedIds = new HashSet<>();
-
- for (Element element : model.getElements()) {
- for (MiriamData md : element.getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- try {
- pubmedIds.add(Integer.parseInt(md.getResource()));
- } catch (NumberFormatException e) {
- logger.error("Problem with parsing: " + e.getMessage(), e);
- }
- }
- }
- }
- for (Reaction reaction : model.getReactions()) {
- for (MiriamData md : reaction.getMiriamData()) {
- if (MiriamType.PUBMED.equals(md.getDataType())) {
- try {
- pubmedIds.add(Integer.parseInt(md.getResource()));
- } catch (NumberFormatException e) {
- logger.error("Problem with parsing: " + e.getMessage(), e);
- }
- }
- }
- }
- double amount = pubmedIds.size();
- double counter = 0;
- for (Integer id : pubmedIds) {
- try {
- Article art = backend.getPubmedArticleById(id);
- if (art == null) {
- logger.warn("Cannot find pubmed article. Pubmed_id = " + id);
- }
- } catch (PubmedSearchException e) {
- logger.warn("Problem with accessing info about pubmed: " + id, e);
- }
- counter++;
- updater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
- }
- }
- logger.debug("Caching finished");
- }
-
- @Override
- public void updateModel(ModelData model, ProjectView selectedProject) {
-
- for (Model cachedModel : models.values()) {
- if (cachedModel.getId().equals(selectedProject.getModelId())) {
- setModel(cachedModel.getModelData(), selectedProject);
- }
- }
- setModel(model, selectedProject);
- modelDao.update(model);
- }
-
- /**
- * Sets the data from selectedProject into model.
- *
- * @param model
- * destination of the data
- * @param selectedProject
- * source of the data
- */
- private void setModel(ModelData model, ProjectView selectedProject) {
- model.setNotes(selectedProject.getDescription());
- List<Layout> toRemove = new ArrayList<Layout>();
- for (Layout layout : model.getLayouts()) {
- boolean exists = false;
- for (LayoutView row : selectedProject.getLayouts()) {
- if (layout.getId() == row.getIdObject()) {
- exists = true;
- // don't allow client side to edit layouts
- // layout.setDirectory(row.getDirectory());
- layout.setTitle(row.getName());
- layout.setDescription(row.getDescription());
- }
- }
- if (!exists) {
- toRemove.add(layout);
- }
- }
- model.getLayouts().removeAll(toRemove);
-
- MiriamData disease = null;
- if (selectedProject.getNewDiseaseName() != null) {
- disease = new MiriamData(MiriamType.MESH_2012, selectedProject.getNewDiseaseName());
- }
-
- try {
- if (meshParser.isValidMeshId(disease)) {
- model.getProject().setDisease(disease);
- } else {
- model.getProject().setDisease(null);
- selectedProject.setNewDiseaseName(null);
- }
- } catch (AnnotatorException e) {
- logger.warn("Problem with accessing mesh db");
- }
-
- if (model.getProject() != null) {
- MiriamData organism = null;
- if (selectedProject.getNewOrganismName() != null && !selectedProject.getNewOrganismName().isEmpty()) {
- organism = new MiriamData(MiriamType.TAXONOMY, selectedProject.getNewOrganismName());
- }
-
- try {
- if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
- model.getProject().setOrganism(organism);
- } else {
- model.getProject().setOrganism(null);
- }
- } catch (TaxonomySearchException e) {
- logger.error("Problem with accessing taxonomy db", e);
- model.getProject().setOrganism(null);
- }
- }
-
- }
-
- @Override
- public void removeModelFromCache(Model model) {
- models.remove(model.getProject().getProjectId());
-
- }
-
- /**
- * @return the modelDao
- * @see #modelDao
- */
- public ModelDao getModelDao() {
- return modelDao;
- }
-
- /**
- * @param modelDao
- * the modelDao to set
- * @see #modelDao
- */
- public void setModelDao(ModelDao modelDao) {
- this.modelDao = modelDao;
- }
-
- /**
- * @return the backend
- * @see #backend
- */
- public PubmedParser getBackend() {
- return backend;
- }
-
- /**
- * @param backend
- * the backend to set
- * @see #backend
- */
- public void setBackend(PubmedParser backend) {
- this.backend = backend;
- }
-
- @Override
- public void cacheAllMiriamLinks(Model model, IProgressUpdater updater) {
- logger.debug("Caching miriam ids...");
- if (model != null) {
- Set<MiriamData> pubmedIds = new HashSet<MiriamData>();
-
- for (Element element : model.getElements()) {
- pubmedIds.addAll(element.getMiriamData());
- }
- for (Reaction reaction : model.getReactions()) {
- pubmedIds.addAll(reaction.getMiriamData());
- }
- double amount = pubmedIds.size();
- double counter = 0;
- for (MiriamData md : pubmedIds) {
- miriamConnector.getUrlString(md);
- counter++;
- updater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
- }
- }
- logger.debug("Caching finished");
-
- }
-
- @Override
- public ModelView getModelView(Model model, User user) {
- ModelView result = modelViewFactory.create(model);
- if (user != null) {
- result.setCustomLayouts(layoutService.getCustomLayouts(model, user, true, user));
- for (ModelView view : result.getSubmodels()) {
- view.setCustomLayouts(layoutService.getCustomLayouts(model.getSubmodelById(view.getIdObject()), user, true, user));
- }
- }
- return result;
- }
-
- @Override
- public void removeModelFromCache(ModelData model) {
- models.remove(model.getProject().getProjectId());
- }
-
- /**
- * @return the layoutService
- * @see #layoutService
- */
- public ILayoutService getLayoutService() {
- return layoutService;
- }
-
- /**
- * @param layoutService
- * the layoutService to set
- * @see #layoutService
- */
- public void setLayoutService(ILayoutService layoutService) {
- this.layoutService = layoutService;
- }
-
- @Override
- public void removeModelFromCacheByProjectId(String projectId) {
- models.remove(projectId);
- }
-
- @Override
- public List<LightAliasView> getLightAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
- LightAliasViewFactory lightAliasViewFactory = new LightAliasViewFactory();
- List<LightAliasView> result = lightAliasViewFactory.createList(getAliasesByIds(model, identifiers));
- return result;
- }
-
- /**
- * Returns list of {@link Element aliases} for given identifiers.
- *
- * @param model
- * model where aliases are located
- * @param identifiers
- * list of alias identifiers in a given submodel. Every {@link Pair}
- * contains information about {@link Model#getId() model identifier}
- * (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
- * identifier} (in {@link Pair#right}).
- * @return list of {@link Element aliases} for given identifiers
- */
- private List<Element> getAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
- Map<Integer, Set<Integer>> identifiersForMap = new HashMap<>();
- for (Pair<Integer, Integer> pair : identifiers) {
- Set<Integer> set = identifiersForMap.get(pair.getLeft());
- if (set == null) {
- set = new HashSet<>();
- identifiersForMap.put(pair.getLeft(), set);
- }
- set.add(pair.getRight());
- }
-
- List<Element> result = new ArrayList<>();
- List<Model> models = new ArrayList<>();
- models.add(model);
- models.addAll(model.getSubmodels());
- for (Model model2 : models) {
- Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
- if (set != null) {
- for (Element alias : model2.getElements()) {
- if (set.contains(alias.getId())) {
- result.add(alias);
- set.remove(alias.getId());
- }
- if (set.size() == 0) {
- break;
- }
- }
- if (set.size() > 0) {
- Integer aliasId = set.iterator().next();
- throw new InvalidArgumentException("Cannot find alias (id: " + aliasId + ") in a model (id: " + model2.getModelData().getId() + ")");
- }
- identifiersForMap.remove(model2.getModelData().getId());
- }
- }
- if (identifiersForMap.keySet().size() > 0) {
- Integer modelId = identifiersForMap.keySet().iterator().next();
- Integer aliasId = identifiersForMap.get(modelId).iterator().next();
- throw new InvalidArgumentException("Cannot find alias (id: " + aliasId + ") in a model (id: " + modelId + "). Model doesn't exist.");
- }
- return result;
- }
-
- @Override
- public List<LightReactionView> getLightReactionsByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
-
- Map<Integer, Set<Integer>> identifiersForMap = new HashMap<>();
- for (Pair<Integer, Integer> pair : identifiers) {
- Set<Integer> set = identifiersForMap.get(pair.getLeft());
- if (set == null) {
- set = new HashSet<>();
- identifiersForMap.put(pair.getLeft(), set);
- }
- set.add(pair.getRight());
- }
-
- List<LightReactionView> result = new ArrayList<>();
- List<Model> models = new ArrayList<>();
- models.add(model);
- models.addAll(model.getSubmodels());
- for (Model model2 : models) {
- Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
- if (set != null) {
- for (Reaction reaction : model2.getReactions()) {
- if (set.contains(reaction.getId())) {
- result.add(new LightReactionView(reaction));
- set.remove(reaction.getId());
- }
- if (set.size() == 0) {
- break;
- }
- }
- if (set.size() > 0) {
- Integer aliasId = set.iterator().next();
- throw new InvalidArgumentException("Cannot find reaction (id: " + aliasId + ") in a model (id: " + model2.getModelData().getId() + ")");
- }
- identifiersForMap.remove(model2.getModelData().getId());
- }
- }
- if (identifiersForMap.keySet().size() > 0) {
- Integer modelId = identifiersForMap.keySet().iterator().next();
- Integer aliasId = identifiersForMap.get(modelId).iterator().next();
- throw new InvalidArgumentException("Cannot find reaction (id: " + aliasId + ") in a model (id: " + modelId + "). Model doesn't exist.");
- }
- return result;
- }
-
- /**
- * @return the userService
- * @see #userService
- */
- public IUserService getUserService() {
- return userService;
- }
-
- /**
- * @param userService
- * the userService to set
- * @see #userService
- */
- public void setUserService(IUserService userService) {
- this.userService = userService;
- }
-
- /**
- * @return the projectDao
- * @see #projectDao
- */
- public ProjectDao getProjectDao() {
- return projectDao;
- }
-
- /**
- * @param projectDao
- * the projectDao to set
- * @see #projectDao
- */
- public void setProjectDao(ProjectDao projectDao) {
- this.projectDao = projectDao;
- }
-
-}
+package lcsb.mapviewer.services.impl;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.log4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.transaction.annotation.Transactional;
+
+import lcsb.mapviewer.annotation.data.Article;
+import lcsb.mapviewer.annotation.services.MeSHParser;
+import lcsb.mapviewer.annotation.services.MiriamConnector;
+import lcsb.mapviewer.annotation.services.PubmedParser;
+import lcsb.mapviewer.annotation.services.PubmedSearchException;
+import lcsb.mapviewer.annotation.services.TaxonomyBackend;
+import lcsb.mapviewer.annotation.services.TaxonomySearchException;
+import lcsb.mapviewer.annotation.services.annotators.AnnotatorException;
+import lcsb.mapviewer.commands.CopyCommand;
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.Layout;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.species.Element;
+import lcsb.mapviewer.model.user.PrivilegeType;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.persist.dao.ProjectDao;
+import lcsb.mapviewer.persist.dao.map.ModelDao;
+import lcsb.mapviewer.services.interfaces.ILayoutService;
+import lcsb.mapviewer.services.interfaces.IModelService;
+import lcsb.mapviewer.services.interfaces.IUserService;
+import lcsb.mapviewer.services.search.data.LightAliasView;
+import lcsb.mapviewer.services.search.data.LightAliasViewFactory;
+import lcsb.mapviewer.services.search.data.LightReactionView;
+import lcsb.mapviewer.services.view.AuthenticationToken;
+import lcsb.mapviewer.services.view.LayoutView;
+import lcsb.mapviewer.services.view.ModelView;
+import lcsb.mapviewer.services.view.ModelViewFactory;
+import lcsb.mapviewer.services.view.ProjectView;
+
+/**
+ * Implementation of the service that manages models.
+ *
+ * @author Piotr Gawron
+ *
+ */
+@Transactional(value = "txManager")
+public class ModelService implements IModelService {
+
+ /**
+ * Default class logger.
+ */
+ private Logger logger = Logger.getLogger(ModelService.class);
+
+ /**
+ * List of cached models.
+ */
+ private static Map<String, Model> models = new HashMap<String, Model>();
+
+ /**
+ * List of models that are currently being loaded from database.
+ */
+ private static Set<String> modelsInLoadStage = new HashSet<>();
+
+ /**
+ * Service that manages and gives access to user information.
+ */
+ @Autowired
+ private IUserService userService;
+
+ /**
+ * Data access object for models.
+ */
+ @Autowired
+ private ModelDao modelDao;
+
+ @Autowired
+ private ProjectDao projectDao;
+
+ /**
+ * Object allowing access to the mesh database.
+ */
+ @Autowired
+ private MeSHParser meshParser;
+
+ /**
+ * Local backend to the pubmed data.
+ */
+ @Autowired
+ private PubmedParser backend;
+
+ /**
+ * Service used for managing layouts.
+ */
+ @Autowired
+ private ILayoutService layoutService;
+
+ /**
+ * Connector used for accessing data from miriam registry.
+ */
+ @Autowired
+ private MiriamConnector miriamConnector;
+
+ /**
+ * Factory object used for creation of {@link ModelView} elements.
+ */
+ @Autowired
+ private ModelViewFactory modelViewFactory;
+
+ /**
+ * Access point and parser for the online ctd database.
+ */
+ @Autowired
+ private TaxonomyBackend taxonomyBackend;
+
+ @Override
+ public Model getLastModelByProjectId(String projectName, AuthenticationToken token) {
+ if (projectName == null) {
+ return null;
+ }
+
+ // check if model is being loaded by another thread
+ boolean waitForModel = false;
+ do {
+ synchronized (modelsInLoadStage) {
+ waitForModel = modelsInLoadStage.contains(projectName);
+ }
+ // if model is being loaded then wait until it's loaded
+ if (waitForModel) {
+ try {
+ Thread.sleep(100);
+ } catch (InterruptedException e) {
+ logger.fatal(e, e);
+ }
+ }
+ } while (waitForModel);
+
+ Model model = models.get(projectName);
+ if (model == null) {
+ try {
+ // mark model as being load stage, so other threads that want to access
+ // it will wait
+ synchronized (modelsInLoadStage) {
+ modelsInLoadStage.add(projectName);
+ }
+ logger.debug("Unknown model, trying to load the model into memory.");
+
+ ModelData modelData = modelDao.getLastModelForProjectIdentifier(projectName, false);
+
+ if (modelData == null) {
+ logger.debug("Model doesn't exist");
+ return null;
+ }
+ logger.debug("Model loaded from db.");
+ model = new ModelFullIndexed(modelData);
+
+ // this is a trick to load all required subelements of the model... ;/
+ // lets copy model - it will access all elements...
+ new CopyCommand(model).execute();
+
+ for (ModelData m : model.getProject().getModels()) {
+ new CopyCommand(m.getModel()).execute();
+ }
+
+ logger.debug("Model loaded successfullly");
+ models.put(projectName, model);
+ } finally {
+ // model is not being loaded anymore
+ synchronized (modelsInLoadStage) {
+ modelsInLoadStage.remove(projectName);
+ }
+ }
+ }
+ if (userService.userHasPrivilege(token, PrivilegeType.VIEW_PROJECT, model.getProject())) {
+ return model;
+ } else if (userService.userHasPrivilege(token, PrivilegeType.ADD_MAP)) {
+ return model;
+ } else {
+ logger.debug(userService.getUserByToken(token).getLogin());
+ throw new SecurityException("User doesn't have access to project");
+ }
+ }
+
+ @Override
+ public void cacheAllPubmedIds(Model model, IProgressUpdater updater) {
+ logger.debug("Caching pubmed ids...");
+ if (model != null) {
+ Set<Integer> pubmedIds = new HashSet<>();
+
+ for (Element element : model.getElements()) {
+ for (MiriamData md : element.getMiriamData()) {
+ if (MiriamType.PUBMED.equals(md.getDataType())) {
+ try {
+ pubmedIds.add(Integer.parseInt(md.getResource()));
+ } catch (NumberFormatException e) {
+ logger.error("Problem with parsing: " + e.getMessage(), e);
+ }
+ }
+ }
+ }
+ for (Reaction reaction : model.getReactions()) {
+ for (MiriamData md : reaction.getMiriamData()) {
+ if (MiriamType.PUBMED.equals(md.getDataType())) {
+ try {
+ pubmedIds.add(Integer.parseInt(md.getResource()));
+ } catch (NumberFormatException e) {
+ logger.error("Problem with parsing: " + e.getMessage(), e);
+ }
+ }
+ }
+ }
+ double amount = pubmedIds.size();
+ double counter = 0;
+ for (Integer id : pubmedIds) {
+ try {
+ Article art = backend.getPubmedArticleById(id);
+ if (art == null) {
+ logger.warn("Cannot find pubmed article. Pubmed_id = " + id);
+ }
+ } catch (PubmedSearchException e) {
+ logger.warn("Problem with accessing info about pubmed: " + id, e);
+ }
+ counter++;
+ updater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
+ }
+ }
+ logger.debug("Caching finished");
+ }
+
+ @Override
+ public void updateModel(ModelData model, ProjectView selectedProject) {
+
+ for (Model cachedModel : models.values()) {
+ if (cachedModel.getId().equals(selectedProject.getModelId())) {
+ setModel(cachedModel.getModelData(), selectedProject);
+ }
+ }
+ setModel(model, selectedProject);
+ modelDao.update(model);
+ }
+
+ /**
+ * Sets the data from selectedProject into model.
+ *
+ * @param model
+ * destination of the data
+ * @param selectedProject
+ * source of the data
+ */
+ private void setModel(ModelData model, ProjectView selectedProject) {
+ model.setNotes(selectedProject.getDescription());
+ List<Layout> toRemove = new ArrayList<Layout>();
+ for (Layout layout : model.getLayouts()) {
+ boolean exists = false;
+ for (LayoutView row : selectedProject.getLayouts()) {
+ if (layout.getId() == row.getIdObject()) {
+ exists = true;
+ // don't allow client side to edit layouts
+ // layout.setDirectory(row.getDirectory());
+ layout.setTitle(row.getName());
+ layout.setDescription(row.getDescription());
+ }
+ }
+ if (!exists) {
+ toRemove.add(layout);
+ }
+ }
+ model.getLayouts().removeAll(toRemove);
+
+ MiriamData disease = null;
+ if (selectedProject.getNewDiseaseName() != null) {
+ disease = new MiriamData(MiriamType.MESH_2012, selectedProject.getNewDiseaseName());
+ }
+
+ try {
+ if (meshParser.isValidMeshId(disease)) {
+ model.getProject().setDisease(disease);
+ } else {
+ model.getProject().setDisease(null);
+ selectedProject.setNewDiseaseName(null);
+ }
+ } catch (AnnotatorException e) {
+ logger.warn("Problem with accessing mesh db");
+ }
+
+ if (model.getProject() != null) {
+ MiriamData organism = null;
+ if (selectedProject.getNewOrganismName() != null && !selectedProject.getNewOrganismName().isEmpty()) {
+ organism = new MiriamData(MiriamType.TAXONOMY, selectedProject.getNewOrganismName());
+ }
+
+ try {
+ if (taxonomyBackend.getNameForTaxonomy(organism) != null) {
+ model.getProject().setOrganism(organism);
+ } else {
+ model.getProject().setOrganism(null);
+ }
+ } catch (TaxonomySearchException e) {
+ logger.error("Problem with accessing taxonomy db", e);
+ model.getProject().setOrganism(null);
+ }
+ }
+
+ }
+
+ @Override
+ public void removeModelFromCache(Model model) {
+ models.remove(model.getProject().getProjectId());
+
+ }
+
+ /**
+ * @return the modelDao
+ * @see #modelDao
+ */
+ public ModelDao getModelDao() {
+ return modelDao;
+ }
+
+ /**
+ * @param modelDao
+ * the modelDao to set
+ * @see #modelDao
+ */
+ public void setModelDao(ModelDao modelDao) {
+ this.modelDao = modelDao;
+ }
+
+ /**
+ * @return the backend
+ * @see #backend
+ */
+ public PubmedParser getBackend() {
+ return backend;
+ }
+
+ /**
+ * @param backend
+ * the backend to set
+ * @see #backend
+ */
+ public void setBackend(PubmedParser backend) {
+ this.backend = backend;
+ }
+
+ @Override
+ public void cacheAllMiriamLinks(Model model, IProgressUpdater updater) {
+ logger.debug("Caching miriam ids...");
+ if (model != null) {
+ Set<MiriamData> pubmedIds = new HashSet<MiriamData>();
+
+ for (Element element : model.getElements()) {
+ pubmedIds.addAll(element.getMiriamData());
+ }
+ for (Reaction reaction : model.getReactions()) {
+ pubmedIds.addAll(reaction.getMiriamData());
+ }
+ double amount = pubmedIds.size();
+ double counter = 0;
+ for (MiriamData md : pubmedIds) {
+ miriamConnector.getUrlString(md);
+ counter++;
+ updater.setProgress(IProgressUpdater.MAX_PROGRESS * counter / amount);
+ }
+ }
+ logger.debug("Caching finished");
+
+ }
+
+ @Override
+ public ModelView getModelView(Model model, User user) {
+ ModelView result = modelViewFactory.create(model);
+ if (user != null) {
+ result.setCustomLayouts(layoutService.getCustomLayouts(model, user, true, user));
+ for (ModelView view : result.getSubmodels()) {
+ view.setCustomLayouts(
+ layoutService.getCustomLayouts(model.getSubmodelById(view.getIdObject()), user, true, user));
+ }
+ }
+ return result;
+ }
+
+ @Override
+ public void removeModelFromCache(ModelData model) {
+ models.remove(model.getProject().getProjectId());
+ }
+
+ /**
+ * @return the layoutService
+ * @see #layoutService
+ */
+ public ILayoutService getLayoutService() {
+ return layoutService;
+ }
+
+ /**
+ * @param layoutService
+ * the layoutService to set
+ * @see #layoutService
+ */
+ public void setLayoutService(ILayoutService layoutService) {
+ this.layoutService = layoutService;
+ }
+
+ @Override
+ public void removeModelFromCacheByProjectId(String projectId) {
+ models.remove(projectId);
+ }
+
+ @Override
+ public List<LightAliasView> getLightAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
+ LightAliasViewFactory lightAliasViewFactory = new LightAliasViewFactory();
+ List<LightAliasView> result = lightAliasViewFactory.createList(getAliasesByIds(model, identifiers));
+ return result;
+ }
+
+ /**
+ * Returns list of {@link Element aliases} for given identifiers.
+ *
+ * @param model
+ * model where aliases are located
+ * @param identifiers
+ * list of alias identifiers in a given submodel. Every {@link Pair}
+ * contains information about {@link Model#getId() model identifier}
+ * (in {@link Pair#left}) and
+ * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
+ * identifier} (in {@link Pair#right}).
+ * @return list of {@link Element aliases} for given identifiers
+ */
+ private List<Element> getAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
+ Map<Integer, Set<Integer>> identifiersForMap = new HashMap<>();
+ for (Pair<Integer, Integer> pair : identifiers) {
+ Set<Integer> set = identifiersForMap.get(pair.getLeft());
+ if (set == null) {
+ set = new HashSet<>();
+ identifiersForMap.put(pair.getLeft(), set);
+ }
+ set.add(pair.getRight());
+ }
+
+ List<Element> result = new ArrayList<>();
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+ for (Model model2 : models) {
+ Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
+ if (set != null) {
+ for (Element alias : model2.getElements()) {
+ if (set.contains(alias.getId())) {
+ result.add(alias);
+ set.remove(alias.getId());
+ }
+ if (set.size() == 0) {
+ break;
+ }
+ }
+ if (set.size() > 0) {
+ Integer aliasId = set.iterator().next();
+ throw new InvalidArgumentException(
+ "Cannot find alias (id: " + aliasId + ") in a model (id: " + model2.getModelData().getId() + ")");
+ }
+ identifiersForMap.remove(model2.getModelData().getId());
+ }
+ }
+ if (identifiersForMap.keySet().size() > 0) {
+ Integer modelId = identifiersForMap.keySet().iterator().next();
+ Integer aliasId = identifiersForMap.get(modelId).iterator().next();
+ throw new InvalidArgumentException(
+ "Cannot find alias (id: " + aliasId + ") in a model (id: " + modelId + "). Model doesn't exist.");
+ }
+ return result;
+ }
+
+ @Override
+ public List<LightReactionView> getLightReactionsByIds(Model model, List<Pair<Integer, Integer>> identifiers) {
+
+ Map<Integer, Set<Integer>> identifiersForMap = new HashMap<>();
+ for (Pair<Integer, Integer> pair : identifiers) {
+ Set<Integer> set = identifiersForMap.get(pair.getLeft());
+ if (set == null) {
+ set = new HashSet<>();
+ identifiersForMap.put(pair.getLeft(), set);
+ }
+ set.add(pair.getRight());
+ }
+
+ List<LightReactionView> result = new ArrayList<>();
+ List<Model> models = new ArrayList<>();
+ models.add(model);
+ models.addAll(model.getSubmodels());
+ for (Model model2 : models) {
+ Set<Integer> set = identifiersForMap.get(model2.getModelData().getId());
+ if (set != null) {
+ for (Reaction reaction : model2.getReactions()) {
+ if (set.contains(reaction.getId())) {
+ result.add(new LightReactionView(reaction));
+ set.remove(reaction.getId());
+ }
+ if (set.size() == 0) {
+ break;
+ }
+ }
+ if (set.size() > 0) {
+ Integer aliasId = set.iterator().next();
+ throw new InvalidArgumentException(
+ "Cannot find reaction (id: " + aliasId + ") in a model (id: " + model2.getModelData().getId() + ")");
+ }
+ identifiersForMap.remove(model2.getModelData().getId());
+ }
+ }
+ if (identifiersForMap.keySet().size() > 0) {
+ Integer modelId = identifiersForMap.keySet().iterator().next();
+ Integer aliasId = identifiersForMap.get(modelId).iterator().next();
+ throw new InvalidArgumentException(
+ "Cannot find reaction (id: " + aliasId + ") in a model (id: " + modelId + "). Model doesn't exist.");
+ }
+ return result;
+ }
+
+ /**
+ * @return the userService
+ * @see #userService
+ */
+ public IUserService getUserService() {
+ return userService;
+ }
+
+ /**
+ * @param userService
+ * the userService to set
+ * @see #userService
+ */
+ public void setUserService(IUserService userService) {
+ this.userService = userService;
+ }
+
+ /**
+ * @return the projectDao
+ * @see #projectDao
+ */
+ public ProjectDao getProjectDao() {
+ return projectDao;
+ }
+
+ /**
+ * @param projectDao
+ * the projectDao to set
+ * @see #projectDao
+ */
+ public void setProjectDao(ProjectDao projectDao) {
+ this.projectDao = projectDao;
+ }
+
+ @Override
+ public void updateModel(ModelData model, AuthenticationToken token) {
+ Model topCachedData = getLastModelByProjectId(model.getProject().getProjectId(), token);
+ Model cachedData = topCachedData.getSubmodelById(model.getId());
+ cachedData.setDefaultCenterX(model.getDefaultCenterX());
+ cachedData.setDefaultCenterY(model.getDefaultCenterY());
+ cachedData.setDefaultZoomLevel(model.getDefaultZoomLevel());
+ modelDao.update(model);
+
+ }
+
+}
diff --git a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
index 43cc0ff508..53fda094d0 100644
--- a/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
+++ b/service/src/main/java/lcsb/mapviewer/services/interfaces/IModelService.java
@@ -1,128 +1,130 @@
-package lcsb.mapviewer.services.interfaces;
-
-import java.util.List;
-
-import lcsb.mapviewer.common.IProgressUpdater;
-import lcsb.mapviewer.common.Pair;
-import lcsb.mapviewer.model.map.model.Model;
-import lcsb.mapviewer.model.map.model.ModelData;
-import lcsb.mapviewer.model.user.User;
-import lcsb.mapviewer.services.search.data.LightAliasView;
-import lcsb.mapviewer.services.search.data.LightReactionView;
-import lcsb.mapviewer.services.view.AuthenticationToken;
-import lcsb.mapviewer.services.view.ModelView;
-import lcsb.mapviewer.services.view.ProjectView;
-
-/**
- * Service that manages models (maps).
- *
- * @author Piotr Gawron
- *
- */
-public interface IModelService {
-
- /**
- * Returns the newest model for the project identified by the
- * {@link lcsb.mapviewer.model.Project#projectId project identifier}.
- *
- * @param projectId
- * {@link lcsb.mapviewer.model.Project#projectId project identifier}
- * @return the newest model for the project
- */
- Model getLastModelByProjectId(String projectId, AuthenticationToken token);
-
- /**
- * Caches information about all pubmed articles for the given model.
- *
- * @param model
- * model in which we are caching the data
- * @param updater
- * callback interface that update progress information
- */
- void cacheAllPubmedIds(Model model, IProgressUpdater updater);
-
- /**
- * Updates information in the model with the one taken from selectedProject.
- *
- * @param model
- * model to update
- * @param selectedProject
- * source of data that should be used in the update
- */
- void updateModel(ModelData model, ProjectView selectedProject);
-
- /**
- * Removes model from application cache.
- *
- * @param model
- * model to remove
- */
- void removeModelFromCache(Model model);
-
- /**
- * Caches information about all miriam resources in the model.
- *
- * @param model
- * model in which we are caching the data
- * @param updater
- * callback interface that update progress information
- */
- void cacheAllMiriamLinks(Model model, IProgressUpdater updater);
-
- /**
- * Returns {@link ModelView} for the given model.
- *
- * @param model
- * model fgor which view is returned.
- * @param user
- * user for which custom layouts should be added
- * @return {@link ModelView} for the given {@link Model}
- */
- ModelView getModelView(Model model, User user);
-
- /**
- * Removes model from application cache.
- *
- * @param model
- * model to remove
- */
- void removeModelFromCache(ModelData model);
-
- /**
- * Removes model from application cache.
- *
- * @param projectId
- * identifier of the project
- */
- void removeModelFromCacheByProjectId(String projectId);
-
- /**
- * Returns list of {@link LightAliasView aliases} for given identifiers.
- *
- * @param model
- * model where aliases are located
- * @param identifiers
- * list of alias identifiers in a given submodel. Every {@link Pair}
- * contains information about {@link Model#getId() model identifier}
- * (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
- * identifier} (in {@link Pair#right}).
- * @return list of {@link LightAliasView aliases} for given identifiers
- */
- List<LightAliasView> getLightAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers);
-
- /**
- * Returns list of {@link LightReactionView reactions} for given identifiers.
- *
- * @param model
- * model where aliases are located
- * @param identifiers
- * list of reaction identifiers in a given submodel. Every
- * {@link Pair} contains information about {@link Model#getId() model
- * identifier} (in {@link Pair#left}) and
- * {@link lcsb.mapviewer.model.map.reaction.Reaction#getId() reaction
- * identifier} (in {@link Pair#right}).
- * @return list of {@link LightReactionView reactions} for given identifiers
- */
- List<LightReactionView> getLightReactionsByIds(Model model, List<Pair<Integer, Integer>> identifiers);
-}
+package lcsb.mapviewer.services.interfaces;
+
+import java.util.List;
+
+import lcsb.mapviewer.common.IProgressUpdater;
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelData;
+import lcsb.mapviewer.model.user.User;
+import lcsb.mapviewer.services.search.data.LightAliasView;
+import lcsb.mapviewer.services.search.data.LightReactionView;
+import lcsb.mapviewer.services.view.AuthenticationToken;
+import lcsb.mapviewer.services.view.ModelView;
+import lcsb.mapviewer.services.view.ProjectView;
+
+/**
+ * Service that manages models (maps).
+ *
+ * @author Piotr Gawron
+ *
+ */
+public interface IModelService {
+
+ /**
+ * Returns the newest model for the project identified by the
+ * {@link lcsb.mapviewer.model.Project#projectId project identifier}.
+ *
+ * @param projectId
+ * {@link lcsb.mapviewer.model.Project#projectId project identifier}
+ * @return the newest model for the project
+ */
+ Model getLastModelByProjectId(String projectId, AuthenticationToken token);
+
+ /**
+ * Caches information about all pubmed articles for the given model.
+ *
+ * @param model
+ * model in which we are caching the data
+ * @param updater
+ * callback interface that update progress information
+ */
+ void cacheAllPubmedIds(Model model, IProgressUpdater updater);
+
+ /**
+ * Updates information in the model with the one taken from selectedProject.
+ *
+ * @param model
+ * model to update
+ * @param selectedProject
+ * source of data that should be used in the update
+ */
+ void updateModel(ModelData model, ProjectView selectedProject);
+
+ /**
+ * Removes model from application cache.
+ *
+ * @param model
+ * model to remove
+ */
+ void removeModelFromCache(Model model);
+
+ /**
+ * Caches information about all miriam resources in the model.
+ *
+ * @param model
+ * model in which we are caching the data
+ * @param updater
+ * callback interface that update progress information
+ */
+ void cacheAllMiriamLinks(Model model, IProgressUpdater updater);
+
+ /**
+ * Returns {@link ModelView} for the given model.
+ *
+ * @param model
+ * model for which view is returned.
+ * @param user
+ * user for which custom layouts should be added
+ * @return {@link ModelView} for the given {@link Model}
+ */
+ ModelView getModelView(Model model, User user);
+
+ /**
+ * Removes model from application cache.
+ *
+ * @param model
+ * model to remove
+ */
+ void removeModelFromCache(ModelData model);
+
+ /**
+ * Removes model from application cache.
+ *
+ * @param projectId
+ * identifier of the project
+ */
+ void removeModelFromCacheByProjectId(String projectId);
+
+ /**
+ * Returns list of {@link LightAliasView aliases} for given identifiers.
+ *
+ * @param model
+ * model where aliases are located
+ * @param identifiers
+ * list of alias identifiers in a given submodel. Every {@link Pair}
+ * contains information about {@link Model#getId() model identifier}
+ * (in {@link Pair#left}) and
+ * {@link lcsb.mapviewer.model.map.species.Element#getId() alias
+ * identifier} (in {@link Pair#right}).
+ * @return list of {@link LightAliasView aliases} for given identifiers
+ */
+ List<LightAliasView> getLightAliasesByIds(Model model, List<Pair<Integer, Integer>> identifiers);
+
+ /**
+ * Returns list of {@link LightReactionView reactions} for given identifiers.
+ *
+ * @param model
+ * model where aliases are located
+ * @param identifiers
+ * list of reaction identifiers in a given submodel. Every {@link Pair}
+ * contains information about {@link Model#getId() model identifier}
+ * (in {@link Pair#left}) and
+ * {@link lcsb.mapviewer.model.map.reaction.Reaction#getId() reaction
+ * identifier} (in {@link Pair#right}).
+ * @return list of {@link LightReactionView reactions} for given identifiers
+ */
+ List<LightReactionView> getLightReactionsByIds(Model model, List<Pair<Integer, Integer>> identifiers);
+
+ void updateModel(ModelData model, AuthenticationToken token);
+}
--
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