Merge branch '204-uploading-of-data-overlay-fails' into 'master'

uploading of big data overlay gives proper error message

See merge request !110

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/ConverterTest.java

 package lcsb.mapviewer.converter.graphics;
 
 import java.awt.Color;
+import java.awt.Desktop;
+import java.awt.Graphics2D;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.IOException;
+
+import javax.imageio.ImageIO;
 
 import org.junit.After;
 import org.junit.Before;
+import org.junit.Ignore;
 import org.junit.Test;
 
 import lcsb.mapviewer.commands.ColorExtractor;
@@ -37,4 +45,42 @@ public class ConverterTest {
 		}
 	}
 
+	@Test
+	@Ignore("it's just code for generating scale")
+	public void testX() throws IOException {
+		BufferedImage tmpBI = new BufferedImage(900, 100, BufferedImage.TYPE_INT_ARGB);
+		Graphics2D tmpGraphics = tmpBI.createGraphics();
+		int startX = 10;
+		int startY = 15;
+		int stepSize = 40;
+		int height = 25;
+		tmpGraphics.setColor(Color.BLACK);
+		for (int i = 0; i < 21; i++) {
+			tmpGraphics.drawLine(startX + i * stepSize, height+startY, startX + i * stepSize, height*2);
+			String str = ""+((double)(i-10))/((double)(10));
+			tmpGraphics.drawString(str, startX + i * stepSize, height*2+startY);
+		}
+		for (int i = 0; i < 10 * stepSize; i++) {
+			double ratio = ((double) i) / ((double) (10 * stepSize));
+			tmpGraphics.setBackground(getColor(ratio, Color.BLUE, Color.WHITE));
+			tmpGraphics.setColor(getColor(ratio, Color.BLUE, Color.WHITE));
+			tmpGraphics.drawRect(startX + i, startY , 1, height);
+		}
+		for (int i = 0; i < 10 * stepSize; i++) {
+			double ratio = ((double) i) / ((double) (10 * stepSize));
+			tmpGraphics.setBackground(getColor(ratio, Color.WHITE, Color.RED));
+			tmpGraphics.setColor(getColor(ratio, Color.WHITE, Color.RED));
+			tmpGraphics.drawRect(10 * stepSize + startX + i, startY , 1, height);
+		}
+		ImageIO.write(tmpBI, "PNG", new File("tmp.png"));
+		Desktop.getDesktop().open(new File("tmp.png"));
+	}
+
+	private Color getColor(double d, Color startColor, Color endColor) {
+
+		return new Color((int) (startColor.getRed() + d * (endColor.getRed() - startColor.getRed())), //
+				(int) (startColor.getGreen() + d * (endColor.getGreen() - startColor.getGreen())), //
+				(int) (startColor.getBlue() + d * (endColor.getBlue() - startColor.getBlue())));
+	}
+
 }

frontend-js/.gitignore

+.idea/workspace.xml
 /dist/
 /coverage/
 /node_modules/

frontend-js/.idea/dictionaries/piotr_gawron.xml

+<component name="ProjectDictionaryState">
+  <dictionary name="piotr.gawron">
+    <words>
+      <w>mailto</w>
+    </words>
+  </dictionary>
+</component>
\ No newline at end of file

frontend-js/.idea/frontend-js.iml

+<?xml version="1.0" encoding="UTF-8"?>
+<module type="WEB_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$">
+      <excludeFolder url="file://$MODULE_DIR$/.tmp" />
+      <excludeFolder url="file://$MODULE_DIR$/temp" />
+      <excludeFolder url="file://$MODULE_DIR$/tmp" />
+    </content>
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+</module>
\ No newline at end of file

frontend-js/.idea/modules.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/frontend-js.iml" filepath="$PROJECT_DIR$/.idea/frontend-js.iml" />
+    </modules>
+  </component>
+</project>
\ No newline at end of file

frontend-js/.idea/vcs.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$/.." vcs="Git" />
+  </component>
+</project>
\ No newline at end of file

frontend-js/src/main/js/GuiConnector.js

@@ -4,6 +4,7 @@ var logger = require('./logger');
 
 var Functions = require('./Functions');
 var SecurityError = require('./SecurityError');
+var NetworkError = require('./NetworkError');
 
 /**
  * This static global object contains set of functions that returns/set data in
@@ -25,11 +26,11 @@ GuiConnector.yPos = 0;
  * List of GET params passed via url.
  */
 
-GuiConnector.init = function() {
+GuiConnector.init = function () {
   var self = this;
 
   if (!String.prototype.endsWith) {
-    String.prototype.endsWith = function(pattern) {
+    String.prototype.endsWith = function (pattern) {
       var d = this.length - pattern.length;
       return d >= 0 && this.lastIndexOf(pattern) === d;
     };
@@ -40,7 +41,7 @@ GuiConnector.init = function() {
     alert("This webpage works well with Chrome, Firefox and Safari.");
   }
   // bootstrap tab initialization
-  $("ul.nav-tabs a").click(function(e) {
+  $("ul.nav-tabs a").click(function (e) {
     e.preventDefault();
     $(this).tab('show');
   });
@@ -48,16 +49,17 @@ GuiConnector.init = function() {
   self.getParams = [];
 
   // find GuiConnector.getParams
-  window.location.search.replace(/\??(?:([^=]+)=([^&]*)&?)/g, function() {
+  window.location.search.replace(/\??(?:([^=]+)=([^&]*)&?)/g, function () {
     function decode(s) {
       return decodeURIComponent(s.split("+").join(" "));
     }
+
     GuiConnector.getParams[decode(arguments[1])] = decode(arguments[2]);
   });
 
   // forser browser to update mouse coordinates whenever mouse move
-  jQuery(document).ready(function() {
-    $(document).mousemove(function(e) {
+  jQuery(document).ready(function () {
+    $(document).mousemove(function (e) {
       GuiConnector.updateMouseCoordinates(e.pageX, e.pageY);
     });
   });
@@ -69,7 +71,7 @@ GuiConnector.init = function() {
       self.addWindowResizeEvent(window.onresize);
     }
 
-    window.onresize = function() {
+    window.onresize = function () {
       for (var i = 0; i < self._windowResizeEvents.length; i++) {
         self._windowResizeEvents[i]();
       }
@@ -77,18 +79,18 @@ GuiConnector.init = function() {
   }
 };
 
-GuiConnector.addWindowResizeEvent = function(handler) {
+GuiConnector.addWindowResizeEvent = function (handler) {
   this._windowResizeEvents.push(handler);
 };
 
 /**
  * Returns name of the file with LCSB logo.
- * 
+ *
  * @param bigLogo
  *          {@link Boolean} value determining if we want to have big logo or
  *          small one
  */
-GuiConnector.getLcsbLogoImg = function(bigLogo) {
+GuiConnector.getLcsbLogoImg = function (bigLogo) {
   if (bigLogo) {
     return 'lcsb_logo_mid.png';
   } else {
@@ -100,26 +102,26 @@ GuiConnector.getLcsbLogoImg = function(bigLogo) {
  * Returns name of the file with image that should be presented when we are
  * wainting for data to be loaded.
  */
-GuiConnector.getLoadingImg = function() {
+GuiConnector.getLoadingImg = function () {
   return "icons/ajax-loader.gif";
 };
 
 /**
  * Returns home directory for images in the application.
  */
-GuiConnector.getImgPrefix = function() {
+GuiConnector.getImgPrefix = function () {
   return "resources/images/";
 };
 
 /**
  * Updates coordinates of the mouse in the browser.
  */
-GuiConnector.updateMouseCoordinates = function(x, y) {
+GuiConnector.updateMouseCoordinates = function (x, y) {
   this.xPos = x;
   this.yPos = y;
 };
 
-GuiConnector.showProcessing = function(messageText) {
+GuiConnector.showProcessing = function (messageText) {
   var self = GuiConnector;
   if (self._processingDialog === undefined) {
     self._processingDialog = document.createElement("div");
@@ -127,11 +129,11 @@ GuiConnector.showProcessing = function(messageText) {
     self._processingDialog.appendChild(self._errorDialogContent);
     document.body.appendChild(self._processingDialog);
     $(self._processingDialog).dialog({
-      modal : true,
-      title : "PROCESSING",
-      width : "150px",
-      closeOnEscape : false,
-      open : function(event, ui) {
+      modal: true,
+      title: "PROCESSING",
+      width: "150px",
+      closeOnEscape: false,
+      open: function (event, ui) {
         $(".ui-dialog-titlebar-close", ui).hide();
       },
     });
@@ -140,8 +142,8 @@ GuiConnector.showProcessing = function(messageText) {
     messageText = "PROCESSING";
   }
   var messageImg = Functions.createElement({
-    type : "img",
-    src : 'resources/images/icons/ajax-loader.gif',
+    type: "img",
+    src: 'resources/images/icons/ajax-loader.gif',
   });
   self._errorDialogContent.innerHTML = "";
   self._errorDialogContent.style.textAlign = "center";
@@ -152,12 +154,12 @@ GuiConnector.showProcessing = function(messageText) {
   $(self._processingDialog).dialog("open");
 };
 
-GuiConnector.hideProcessing = function() {
+GuiConnector.hideProcessing = function () {
   var self = GuiConnector;
   $(self._processingDialog).dialog("close");
 };
 
-GuiConnector.alert = function(error) {
+GuiConnector.alert = function (error) {
   var self = GuiConnector;
   logger.error(error);
   if (self._errorDialog === undefined) {
@@ -166,18 +168,20 @@ GuiConnector.alert = function(error) {
     self._errorDialog.appendChild(self._errorDialogContent);
     document.body.appendChild(self._errorDialog);
     $(self._errorDialog).dialog({
-      classes : {
-        "ui-dialog" : "ui-state-error"
+      classes: {
+        "ui-dialog": "ui-state-error"
       },
-      modal : true,
-      title : "ERROR"
+      modal: true,
+      title: "ERROR"
     }).siblings('.ui-dialog-titlebar').css("background", "red");
   }
   var message = error;
   if (message instanceof SecurityError) {
-    message = error.message + "<p>Please <a href=\"login.xhtml\">login</a> to access this resuorce</p>";
+    message = error.message + "<p>Please <a href=\"login.xhtml\">login</a> to access this resource</p>";
+  } else if (message instanceof NetworkError && (error.message === "XHR error" || error.message === "Failed to fetch")) {
+    message = "File to big.<br>Please reduce file size or contact administrators.";
   } else if (message instanceof Error) {
-    message = "Unexpected error occured:<p>" + error.message + "</p>";
+    message = "Unexpected error occurred:<p>" + error.message + "</p>";
   }
   self._errorDialogContent.innerHTML = message;
   $(self._errorDialog).dialog("open");

frontend-js/src/main/js/ServerConnector.js

@@ -155,7 +155,7 @@ ServerConnector.sendPostRequest = function (url, params) {
       form: params
     }, function (error, response, body) {
       if (error) {
-        reject(new NetworkError(error, {
+        reject(new NetworkError(error.message, {
           content: body,
           url: url
         }));

frontend-js/src/main/js/gui/leftPanel/ChemicalPanel.js

@@ -11,22 +11,25 @@ var PanelControlElementType = require('../PanelControlElementType');
 function ChemicalPanel(params) {
   params.panelName = "chemical";
   params.helpTip = '<p>source: Comparative Toxicogenomics Database <a target="_ctd" href="http://ctdbase.org/">ctdbase.org</a></p>'
-      + '<p>use only the full name of chemicals according to <a target="_ctd_chemicals" href="http://ctdbase.org/voc.go?type=chem"> ctdbase/chem</a> for search</p>'
-      + '<p>only curated associations between genes and chemicals with direct evidence to '
-      + 'Parkinson Disease (<a href="http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300" target="_blank">D010300</a>) are displayed</p>'
-      + '<p>separate multiple search by semicolon';
+    + '<p>only associations between genes and chemicals with direct evidence to '
+    + 'Parkinson Disease (<a href="http://bioportal.bioontology.org/ontologies/1351?p=terms&conceptid=D010300" target="_blank">D010300</a>) are displayed</p>'
+    + '<p>use only the full name of chemicals according to <a target="_ctd_chemicals" href="http://ctdbase.org/voc.go?type=chem"> ctdbase/chem</a> for search</p>'
+    + 'if the chemical name includes comma(s), place a semicolon behind the name to avoid a segmentation of the name</p>'
+    + '<p>separate multiple search by semicolon';
   params.placeholder = "full chemical name (CTD)";
 
+
   AbstractDbPanel.call(this, params);
 
   if (this.getMap().getProject().getDisease() === undefined) {
     this.disablePanel("DISEASE NOT DEFINED FOR PROJECT. PLEASE, DEFINE IT IN THE ADMIN SECTION.");
   }
 }
+
 ChemicalPanel.prototype = Object.create(AbstractDbPanel.prototype);
 ChemicalPanel.prototype.constructor = ChemicalPanel;
 
-ChemicalPanel.prototype.createPreamble = function(chemical) {
+ChemicalPanel.prototype.createPreamble = function (chemical) {
   var self = this;
   var guiUtils = self.getGuiUtils();
   var result = document.createElement("div");
@@ -37,8 +40,7 @@ ChemicalPanel.prototype.createPreamble = function(chemical) {
     result.appendChild(guiUtils.createParamLine("Description: ", chemical.getDescription()));
     result.appendChild(guiUtils.createArrayParamLine("Synonyms: ", chemical.getSynonyms()));
     result.appendChild(guiUtils.createParamLine("Direct Evidence: ", chemical.getDirectEvidence()));
-    result.appendChild(guiUtils
-        .createAnnotations("Directe Evidence Publications: ", chemical.getDirectEvidenceReferences()));
+    result.appendChild(guiUtils.createAnnotations("Direct Evidence Publications: ", chemical.getDirectEvidenceReferences()));
     result.appendChild(guiUtils.createAnnotations("Sources: ", chemical.getReferences()));
     result.appendChild(guiUtils.createNewLine());
   }
@@ -46,18 +48,18 @@ ChemicalPanel.prototype.createPreamble = function(chemical) {
   return result;
 };
 
-ChemicalPanel.prototype.createTableElement = function(target, icon) {
+ChemicalPanel.prototype.createTableElement = function (target, icon) {
   return this.createTargetRow(target, icon);
 };
 
-ChemicalPanel.prototype.searchByQuery = function() {
+ChemicalPanel.prototype.searchByQuery = function () {
   var self = this;
   var query = self.getControlElement(PanelControlElementType.SEARCH_INPUT).value;
 
   return self.getOverlayDb().searchByQuery(query);
 };
 
-ChemicalPanel.prototype.init = function() {
+ChemicalPanel.prototype.init = function () {
   var query = ServerConnector.getSessionData().getChemicalQuery();
   if (query !== undefined) {
     return this.getOverlayDb().searchByEncodedQuery(query);

frontend-js/src/main/js/gui/leftPanel/OverlayPanel.js

@@ -449,7 +449,9 @@ OverlayPanel.prototype.openAddOverlayDialog = function () {
         }
       }
       if (fileContent === null) {
-        GuiConnector.alert("Neither file was selected nor data was enterd");
+        GuiConnector.alert("Neither file was selected nor data was entered");
+      } else if (fileContent.length > 1024 * 256) {
+        GuiConnector.alert("File to big.<br>Please reduce file size or contact administrators.");
       } else {
         var data = {
           name: nameInput.value,
@@ -466,15 +468,11 @@ OverlayPanel.prototype.openAddOverlayDialog = function () {
           $(dialog).dialog("close");
         }, function (error) {
           GuiConnector.hideProcessing();
-          if (error instanceof NetworkError) {
-            if (error.statusCode === HttpStatus.BAD_REQUEST) {
-              var errorMessage = JSON.parse(error.content);
-              GuiConnector.alert("Problematic input: <br/>" + errorMessage.reason);
-            } else {
-              throw error;
-            }
+          if (error instanceof NetworkError && error.statusCode === HttpStatus.BAD_REQUEST) {
+            var errorMessage = JSON.parse(error.content);
+            GuiConnector.alert("Problematic input: <br/>" + errorMessage.reason);
           } else {
-            throw error;
+            GuiConnector.alert(error);
           }
         });
       }

frontend-js/src/main/js/gui/leftPanel/ProjectInfoPanel.js

@@ -21,8 +21,8 @@ function ProjectInfoPanel(params) {
   self._createUserDataTab();
   var logoutButton = self.getControlElement(PanelControlElementType.USER_TAB_LOGOUT_BUTTON);
 
-  logoutButton.onclick = function() {
-    return ServerConnector.logout().then(function() {
+  logoutButton.onclick = function () {
+    return ServerConnector.logout().then(function () {
       window.location.reload(false);
     }).then(null, GuiConnector.alert);
   };
@@ -32,191 +32,191 @@ function ProjectInfoPanel(params) {
 ProjectInfoPanel.prototype = Object.create(Panel.prototype);
 ProjectInfoPanel.prototype.constructor = ProjectInfoPanel;
 
-ProjectInfoPanel.prototype._createInfoPanelGui = function() {
+ProjectInfoPanel.prototype._createInfoPanelGui = function () {
   var self = this;
   var guiUtils = self.getGuiUtils();
   var projectId = self.getMap().getProject().getProjectId();
 
   var infoDiv = Functions.createElement({
-    type : "div",
-    name : "infoDiv",
-    className : "searchPanel"
+    type: "div",
+    name: "infoDiv",
+    className: "searchPanel"
   });
   this.getElement().appendChild(infoDiv);
   this.setControlElement(PanelControlElementType.INFO_DIV, infoDiv);
 
   var infoTitle = Functions.createElement({
-    type : "h4",
-    content : "PROJECT INFO:"
+    type: "h4",
+    content: "PROJECT INFO:"
   });
   infoDiv.appendChild(infoTitle);
 
   var dataTab = Functions.createElement({
-    type : "div",
-    style : "width:100%;display: table;border-spacing: 10px;"
+    type: "div",
+    style: "width:100%;display: table;border-spacing: 10px;"
   });
   infoDiv.appendChild(dataTab);
 
   var projectNameLabel = Functions.createElement({
-    type : "div",
-    content : "Name:"
+    type: "div",
+    content: "Name:"
   });
   var projectNameText = Functions.createElement({
-    type : "div",
-    style : "width:100%",
-    name : "projectNameText"
+    type: "div",
+    style: "width:100%",
+    name: "projectNameText"
   });
   this.setControlElement(PanelControlElementType.INFO_PROJECT_NAME_TEXT, projectNameText);
-  dataTab.appendChild(guiUtils.createTableRow([ projectNameLabel, projectNameText ]));
+  dataTab.appendChild(guiUtils.createTableRow([projectNameLabel, projectNameText]));
 
   var projectVersionLabel = Functions.createElement({
-    type : "div",
-    content : "Version:"
+    type: "div",
+    content: "Version:"
   });
   var projectVersionText = Functions.createElement({
-    type : "div",
-    style : "width:100%",
-    name : "projectVersionText"
+    type: "div",
+    style: "width:100%",
+    name: "projectVersionText"
   });
   this.setControlElement(PanelControlElementType.INFO_PROJECT_VERSION_TEXT, projectVersionText);
-  dataTab.appendChild(guiUtils.createTableRow([ projectVersionLabel, projectVersionText ]));
+  dataTab.appendChild(guiUtils.createTableRow([projectVersionLabel, projectVersionText]));
 
   var projectDescriptionLabel = Functions.createElement({
-    type : "div",
-    content : "Description:"
+    type: "div",
+    content: "Description:"
   });
   var projectDescriptionText = Functions.createElement({
-    type : "div",
-    style : "width:100%",
-    name : "projectDescriptionText"
+    type: "div",
+    style: "width:100%",
+    name: "projectDescriptionText"
   });
   this.setControlElement(PanelControlElementType.INFO_PROJECT_DESCRIOPTION_TEXT, projectDescriptionText);
-  dataTab.appendChild(guiUtils.createTableRow([ projectDescriptionLabel, projectDescriptionText ]));
+  dataTab.appendChild(guiUtils.createTableRow([projectDescriptionLabel, projectDescriptionText]));
 
   infoTitle = Functions.createElement({
-    type : "h4",
-    content : "Data:"
+    type: "h4",
+    content: "Data:"
   });
   infoDiv.appendChild(infoTitle);
 
   var dialogDiv = Functions.createElement({
-    type : "div",
+    type: "div",
   });
 
   this.publicationListDialog = new PublicationListDialog({
-    customMap : self.getMap(),
-    element : dialogDiv,
+    customMap: self.getMap(),
+    element: dialogDiv,
   });
 
   dataTab = Functions.createElement({
-    type : "ul",
+    type: "ul",
   });
   infoDiv.appendChild(dataTab);
 
   var projectPublicationsText = Functions.createElement({
-    type : "span",
-    name : "projectPublicationsText",
-    style : "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
+    type: "span",
+    name: "projectPublicationsText",
+    style: "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
   });
   this.setControlElement(PanelControlElementType.INFO_PROJECT_PUBLICATIONS_TEXT, projectPublicationsText);
 
   var projectPublicationsButton = Functions.createElement({
-    type : "a",
-    name : "projectPublicationsButton",
+    type: "a",
+    name: "projectPublicationsButton",
   });
   projectPublicationsButton.appendChild(Functions.createElement({
-    type : "span",
-    content : "<i class='fa fa-list'>&nbsp;",
+    type: "span",
+    content: "<i class='fa fa-list'>&nbsp;",
   }));
 
   projectPublicationsButton.appendChild(projectPublicationsText);
   projectPublicationsButton.appendChild(Functions.createElement({
-    type : "span",
-    style : "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
-    content : "&nbsp;publication(s)",
+    type: "span",
+    style: "font-family:FontAwesome; font-weight: normal;font-style: normal;cursor: pointer",
+    content: "&nbsp;publication(s)",
   }));
   this.setControlElement(PanelControlElementType.INFO_PROJECT_SHOW_PUBLICATIONS_BUTTON, projectPublicationsButton);
 
   var liElement = Functions.createElement({
-    type : "li",
-    style : "line-height: 30px;",
+    type: "li",
+    style: "line-height: 30px;",
   });
   liElement.appendChild(projectPublicationsButton);
   dataTab.appendChild(liElement);
 
   var projectOriginalFileButton = Functions.createElement({
-    type : "a",
-    name : "projectOriginalFileButton",
-    href : "#",
-    content : "<i class='fa fa-files-o'>&nbsp;source file",
+    type: "a",
+    name: "projectOriginalFileButton",
+    href: "#",
+    content: "<i class='fa fa-files-o'>&nbsp;source file",
   });
   this.setControlElement(PanelControlElementType.INFO_PROJECT_GET_ORIGINAL_FILE_BUTTON, projectOriginalFileButton);
   liElement = Functions.createElement({
-    type : "li",
-    style : "line-height: 30px",
+    type: "li",
+    style: "line-height: 30px",
   });
   liElement.appendChild(projectOriginalFileButton);
   dataTab.appendChild(liElement);
 
   var exportButton = Functions.createElement({
-    type : "a",