Merge branch 'devel_12.2.x'

.gitlab-ci.yml

@@ -392,3 +392,36 @@ test_deploy_with_db_without_superadmin_rights:
     - test 200 = $(curl --write-out %{http_code} --silent --output /dev/null -c cookie.txt http://localhost:8080/minerva/api/doLogin)
     - test 200 = $(curl --write-out %{http_code} --silent --output /dev/null --cookie cookie.txt http://localhost:8080/minerva/api/projects/)
 
+test_postgres_9_3_compatibility:
+  image: maven:3.6.0-jdk-8
+  services:
+    - postgres:9.3
+  stage: test
+  script:
+    - mkdir /etc/minerva/
+    - cp test-db-ci.properties /etc/minerva/db.properties
+    - mvn -DskipTests=true clean install -pl persist -am
+    - mvn test -pl persist
+
+test_postgres_10_compatibility:
+  image: maven:3.6.0-jdk-8
+  services:
+    - postgres:10
+  stage: test
+  script:
+    - mkdir /etc/minerva/
+    - cp test-db-ci.properties /etc/minerva/db.properties
+    - mvn -DskipTests=true clean install -pl persist -am
+    - mvn test -pl persist
+
+test_postgres_11_compatibility:
+  image: maven:3.6.0-jdk-8
+  services:
+    - postgres:11
+  stage: test
+  script:
+    - mkdir /etc/minerva/
+    - cp test-db-ci.properties /etc/minerva/db.properties
+    - mvn -DskipTests=true clean install -pl persist -am
+    - mvn test -pl persist
+

CHANGELOG

 minerva (12.3.0~alpha.0) unstable; urgency=low
-  * Feature: annotators are more flexible - you can define set of input and 
+  * Feature: annotators are more flexible - you can define set of input and
     outputs used by annotator (#617)
   * Small improvement: validation of the organism and disease id on map upload
     added (#618)
-  * Small improvement: added current username next to logout button in admin 
+  * Small improvement: added current username next to logout button in admin
     panel (#660)
-  * Small improvement: New comment dialog does not contain content of previous 
+  * Small improvement: New comment dialog does not contain content of previous
     comment dialog (#680)
   * Small improvement: Left logo is configurable (#731)
   * Small improvement: Plugin API provides list of overview images (#702)
   * Small improvement: Plugin API allows to show/hide overview images (#702)
   * Small improvement: Plugin API allows to trigger search on the map (#702)
   * Small improvement: Plugin API allows to clear search results on map (#702)
-  * Small improvement: edit/remove project button is disabled until project is 
+  * Small improvement: edit/remove project button is disabled until project is
     uploaded (#683)
-  * Small improvement: warning about capslock is visible on login page when 
+  * Small improvement: warning about capslock is visible on login page when
     necessary (#658)
-  * Small improvement: names of columns in data overlay are unified: no 
+  * Small improvement: names of columns in data overlay are unified: no
     whitespace, "_" used as separator (#596)
   * Small improvement: list of references in drug panel contains PUBMED prefix
     (#666)
-  * Small improvement: passwords to email account and ldap are not sent over 
+  * Small improvement: passwords to email account and ldap are not sent over
     API (#732)
-  * Small improvement: reactant/product/modifier specific colors are parsed 
+  * Small improvement: reactant/product/modifier specific colors are parsed
     properly from CellDesigner file (#597)
   * Small improvement: Info tab contains information about disease and
     organism when info is provided
   * Small improvement: Info tab provides information about model annotations
     and submap tabs provide information about submaps annotations if applicable
     (#591)
-  * Bug fix: progress bar of gene genome mapping upload is refreshing properly 
+  * Bug fix: progress bar of gene genome mapping upload is refreshing properly
     (#728)
-  * Bug fix: when editing project Disease and Organism could not be removed 
+  * Bug fix: when editing project Disease and Organism could not be removed
     (#616)
-  * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and 
-    "Unknown Inhibition" reactions (#664) 
-  * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is 
+  * Bug fix: dashed line partially wasn't dashed in "Unknown Catalysis" and
+    "Unknown Inhibition" reactions (#664)
+  * Bug fix: "Unknown Catalysis" and "Unknown Inhibition" reaction end is
     slightly separated from target phenotype (#664)
 
-minerva (12.2.0~beta.2) unstable; urgency=medium
-  * Bug fix: order of the overlays is defined explicitly also for general
-    overlays (#684)
-  * Bug fix: files are saved in proper folder (#694, #670)
-  * Bug fix: removing comments in a project asked for confirmation twice after
-    edit project dialog for specific project was opened; closed and opened
-    again (#697)
-  * Bug fix: clicking on compartment border inside pathway should return
-    compartment, not a pathway (#324)
-  * Bug fix: clicking outside of the element sometimes resulted with the
-    invalid element highlighted  (#324)
-  * Bug fix: parent compartment/pathway use proper type name in left panel
-    (#324)
-  * Bug fix: editing/removing project requires Map Management privilege (#681)
-  * Bug fix: when removeAllListeners is called list of registered listeners is
-    cleaned (#687)
-  * Bug fix: when plugin is removed the html elements associated with it are
-    removed as well (#686)
-  * Bug fix: when creating new user default privileges are set properly (#692)
-  * Bug fix: import from SBML issue - reaction with product and modifier being
-    the same element caused exception (#703)
-  * Bug fix: plugin can be added after plugin has been removed in admin plugin
-    panel (#686)
-  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
-    (#708)
-  * Bug fix: text was outside the popup window (#711)
-  * Bug fix: custom semantic zooming contains multiple overlays checkbox was
-    disabled (#715)
-  * Bug fix: export to svg contains viewBox info (#716)
-  * Bug fix: import from sbml with layout could crash when two elements
-    occupied the exact same position (#717)
-  * Bug fix: overlays added via API couldn't be visualized after refresh (#718)
-  * Bug fix: Safari sometimes cached server responses and used wrong data, for
-    example in admin panel configuration tab (#719)
-  * Bug fix: description of transcription site is centered (#720)
-  * Bug fix: selecting too few parameters in export doesn't throw reportable
-    error (#721)
-  * Bug fix: changes in selected checkbox in add project dialog block UI (#722)
-  * Bug fix: providing invalid overlay id in url could break minerva (#726)
-  * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
-  * Bug fix: Editing project with images and submaps could cause a problem
-    (#725)
-  * Bug fix: opening map with invalid id shows proper error message (#724)
-  * Bug fix: Fixing an issue where search panel was not properly resized on
-    expansion (#682)
-  * Small improvement: highlighting table rows in admin panel uses better
-    contrast color (#706)
-
- -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 20 Feb 2019 14:00:00 +0200
-
-minerva (12.2.0~beta.1) unstable; urgency=medium
-  * Small improvement: list of publication can be filtered by submap (#614)
-  * Small improvement: report bug utility shows confirmation dialog on success
-    (#648)
-  * Small improvement: size of add overlay window adjusted to show more data
-    without scrollbars (#657)
-  * Small improvement: all popup dialogs in the app have dialog specific css
-    class names (#665)
-  * Bug fix: loading icon is not overlapping input in the search panel (#404)
-  * Bug fix: position of transcription sites in genes are computed properly
-    (#553)
-  * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
-    (#626)
-  * Bug fix: layout exported to SBML can be properly visualized by COPASI
-    (#654)
-  * Bug fix: working with too many maps within the single session could crash
-    connection to server (#651)
-  * Bug fix: invalid pubmed id could crash listing/downloading publications
-    (#656)
-  * Bug fix: icons in safari sometimes disappear (#661)
-  * Bug fix: downloading reference genome for the second time resulted in an
-    error (#670)
-  * Bug fix: plugin validation in admin panel improved to catch more problems
-    (#672)
-  * Bug fix: drawing corrupted heterodimer association in CellDesigner could
-    crash map upload (#673)
-  * Bug fix: custom semantic zooming didn't work with pathways imported from
-    CellDesigner layers (#678)
-
- -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 7 Feb 2019 14:00:00 +0200
-
-minerva (12.2.0~beta.0) unstable; urgency=medium
+minerva (12.2.0) stable; urgency=medium
   * Feature: bug report utility
-  * Small improvement: JS plugin can create listener that is triggered on
-    search results focus change
-
- -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 23 Jan 2019 15:00:00 +0200
-
-minerva (12.2.0~alpha.1) unstable; urgency=medium
-  * Bug fix: problems with SBML-CellDesigner translation fixed
-  * Bug fix: gitlab CI tests fixed
-
- -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 17 Jan 2019 15:00:00 +0200
-
-minerva (12.2.0~alpha.0) unstable; urgency=medium
   * Feature: url GET parameters support all kind of search and selected overlays
     highlight
   * Feature: user can create custom logging configuration in file
@@ -144,6 +51,15 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium
     file formats
   * Feature: current state of the browsed map is reflected in the url (position,
     zoom, overlays, search queries, etc.)
+  * Small improvement: highlighting table rows in admin panel uses better
+    contrast color (#706)
+  * Small improvement: list of publication can be filtered by submap (#614)
+  * Small improvement: size of add overlay window adjusted to show more data
+    without scrollbars (#657)
+  * Small improvement: all popup dialogs in the application have dialog
+    specific css class names (#665)
+  * Small improvement: JS plugin can create listener that is triggered on
+    search results focus change
   * Small improvement: export to SBML includes unit factors
   * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
   * Small improvement: genetics information allows to provide information about
@@ -178,6 +94,47 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium
   * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
     email account is provided
   * Small improvement: Plugin API allows to show/hide data overlays
+  * Bug fix: Icons were sometimes not properly loaded on Safari (#661)
+  * Bug fix: migration scripts are compatibile with postgres 9.3 version that
+    is default on Ubuntu 14 (#762)
+  * Bug fix: update/remove button is disabled when user has no privileges for
+    managing overlays (#742)
+  * Bug fix: when user cannot manage users information in overlays and users
+    tab in edit project dialog is provided instead of hiding tabs (#756)
+  * Bug fix: removing comments in a project asked for confirmation twice after
+    edit project dialog for specific project was opened; closed and opened
+    again (#697)
+  * Bug fix: editing/removing project requires Map Management privilege (#681)
+  * Bug fix: when removeAllListeners is called list of registered listeners is
+    cleaned (#687)
+  * Bug fix: when plugin is removed the html elements associated with it are
+    removed as well (#686)
+  * Bug fix: when creating new user default privileges are set properly (#692)
+  * Bug fix: plugin can be added after plugin has been removed in admin plugin
+    panel (#686)
+  * Bug fix: too many annotations (>=100) caused misaligning in the left panel
+    (#708)
+  * Bug fix: export to svg contains viewBox info (#716)
+  * Bug fix: overlays added via API couldn't be visualized after refresh (#718)
+  * Bug fix: Safari sometimes cached server responses and used wrong data, for
+    example in admin panel configuration tab (#719)
+  * Bug fix: description of transcription site is centered (#720)
+  * Bug fix: selecting too few parameters in export doesn't throw reportable
+    error (#721)
+  * Bug fix: providing invalid overlay id in url could break minerva (#726)
+  * Bug fix: removing project that doesn't exist doesn't cause 500 error (#723)
+  * Bug fix: opening map with invalid id shows proper error message (#724)
+  * Bug fix: Fixing an issue where search panel was not properly resized on
+    expansion (#682)
+  * Bug fix: loading icon is not overlapping input in the search panel (#404)
+  * Bug fix: position of transcription sites in genes are computed properly
+    (#553)
+  * Bug fix: REQUEST AN ACCOUNT was enabled when associated email was invalid
+    (#626)
+  * Bug fix: working with too many maps within the single session could crash
+    connection to server (#651)
+  * Bug fix: drawing corrupted heterodimer association in CellDesigner could
+    crash map upload (#673)
   * Bug fix: export to CellDesigner align inhibition reaction properly
   * Bug fix: export/import to/from SBML handles Heterodimer Association
     reaction properly
@@ -193,9 +150,9 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium
   * Bug fix: type of the data overlay can be defined in the file content
     (useful when uploading genetic variants)
   * Bug fix: CLEAR button clears comment checkbox if necessary
-  * Bug fix: minerva install problem on ubuntu 16 fixed
+  * Bug fix: minerva install problem on ubuntu 18 fixed
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 11 Jan 2019 12:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 25 Mar 2019 17:00:00 +0200
 
 minerva (12.1.8) stable; urgency=medium
   * Bug fix: add a project reset users custom overlays limit to default (#679)

frontend-js/src/main/css/global.css

@@ -616,7 +616,7 @@ Plugin tabs
     float: left;
 }
 
-.minerva-top-checkbox-div input {
+.minerva-top-checkbox-div input[type=checkbox] {
     margin-top: 12px;
     display: inline;
     float: left;

frontend-js/src/main/js/gui/admin/AddProjectDialog.js

@@ -788,10 +788,10 @@ AddProjectDialog.prototype.bindProjectUploadPreferences = function (user, type,
   var value = user.getPreferences().getProjectUpload()[type];
   element.prop('checked', value);
 
-  GuiConnector.showProcessing();
   element.change(function () {
     var data = new UserPreferences();
     data.getProjectUpload()[type] = element.is(":checked");
+    GuiConnector.showProcessing();
     return ServerConnector.updateUserPreferences({
       user: user,
       preferences: data

frontend-js/src/main/js/gui/admin/EditProjectDialog.js

@@ -641,7 +641,7 @@ EditProjectDialog.prototype.refreshOverlays = function () {
         return self.setOverlays(overlays);
       });
     } else {
-      guiUtils.hideTab(self, $(".minerva-project-overlays-tab", self.getElement())[0]);
+      guiUtils.disableTab($(".minerva-project-overlays-tab", self.getElement())[0], "You have no privileges to manage users data");
     }
   });
 };
@@ -671,7 +671,7 @@ EditProjectDialog.prototype.refreshUsers = function () {
         return self.setUsers(users);
       });
     } else {
-      guiUtils.hideTab(self, $(".minerva-project-users-tab", self.getElement())[0]);
+      guiUtils.disableTab($(".minerva-project-users-tab", self.getElement())[0], "You have no privileges to manage users data");
     }
   });
 };
@@ -774,9 +774,13 @@ EditProjectDialog.prototype.userToTableRow = function (user, columns) {
  * @returns {Array}
  */
 EditProjectDialog.prototype.overlayToTableRow = function (overlay, users) {
+  var self = this;
   var row = [];
   var id = overlay.getId();
   var creatorSelect;
+
+  var loggedUser = null;
+
   if (overlay.getCreator() === "") {
     creatorSelect = "<select name='creator-" + id + "' value=''>";
   } else {
@@ -795,6 +799,10 @@ EditProjectDialog.prototype.overlayToTableRow = function (overlay, users) {
 
     creatorSelect += "<option value='" + user.getLogin() + "' " + selected + ">" + user.getLogin() + "("
       + user.getName() + " " + user.getSurname() + ")</option>";
+
+    if (user.getLogin() === self.getServerConnector().getSessionData().getLogin()) {
+      loggedUser = user;
+    }
   }
   creatorSelect += "</select>";
 
@@ -825,8 +833,15 @@ EditProjectDialog.prototype.overlayToTableRow = function (overlay, users) {
   row[4] = defaultOverlayCheckbox;
   row[5] = creatorSelect;
   row[6] = downloadSourceButton;
-  row[7] = "<button name='saveOverlay' data='" + id + "'><i class=\"fa fa-save\" style=\"font-size:17px\"></i></button>";
-  row[8] = "<button name='removeOverlay' data='" + id + "'><i class='fa fa-trash-o' style='font-size:17px'></button>";
+
+  var disabled = " disabled ";
+  if (loggedUser.hasPrivilege(self.getConfiguration().getPrivilegeType(PrivilegeType.LAYOUT_MANAGEMENT), self.getProject().getId())) {
+    disabled = "";
+  }
+
+
+  row[7] = "<button name='saveOverlay' data='" + id + "'" + disabled + "><i class=\"fa fa-save\" style=\"font-size:17px\"></i></button>";
+  row[8] = "<button name='removeOverlay' data='" + id + "'" + disabled + "><i class='fa fa-trash-o' style='font-size:17px'></button>";
 
   return row;
 };
@@ -1053,7 +1068,7 @@ EditProjectDialog.prototype.openAddOverlayDialog = function () {
   });
   return self._addOverlayDialog.init().then(function () {
     return self._addOverlayDialog.open();
-  }).then(function(){
+  }).then(function () {
     return self._addOverlayDialog;
   });
 };

frontend-js/src/main/js/gui/admin/MapsAdminPanel.js

@@ -346,9 +346,9 @@ MapsAdminPanel.prototype.onAddClicked = function () {
       return dialog.open();
     });
   } else {
-    dialog.clear();
-    dialog.open();
-    return Promise.resolve();
+    return dialog.clear().then(function () {
+      return dialog.open();
+    })
   }
 };
 
@@ -480,12 +480,9 @@ MapsAdminPanel.prototype.showEditDialog = function (id) {
   return ServerConnector.getProject(id).then(function (project) {
     return self.getDialog(project);
   }).then(function (dialog) {
-
     dialog.open();
+  }).finally(function () {
     GuiConnector.hideProcessing();
-  }).then(null, function (error) {
-    GuiConnector.hideProcessing();
-    return Promise.reject(error);
   });
 };
 
@@ -500,11 +497,8 @@ MapsAdminPanel.prototype.showLogs = function (id, level) {
   GuiConnector.showProcessing();
   return self.getLogDialog(id, level).then(function (dialog) {
     return dialog.open();
-  }).then(function () {
-    GuiConnector.hideProcessing();
-  }, function (error) {
+  }).finally(function () {
     GuiConnector.hideProcessing();
-    return Promise.reject(error);
   });
 };
 

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

@@ -1142,6 +1142,26 @@ GuiUtils.prototype.hideTab = function (abstractGuiElement, panel) {
   }
 };
 
+/**
+ *
+ * @param {HTMLElement} element
+ * @param {string} message
+ */
+GuiUtils.prototype.disableTab = function (element, message) {
+  $(element).children().css("visibility", "hidden");
+  $("[class='minerva-help-button']", element).children().css("visibility", "visible");
+  var hideReasonDiv = document.createElement("div");
+  hideReasonDiv.className = "searchPanel";
+
+  var center = document.createElement("center");
+  var messageDiv = document.createElement("h4");
+  messageDiv.innerHTML = message;
+  center.appendChild(messageDiv);
+  hideReasonDiv.appendChild(center);
+
+  $(element).prepend(hideReasonDiv);
+};
+
 /**
  *
  * @param {AbstractGuiElement} abstractGuiElement

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

@@ -108,7 +108,7 @@ PublicationListDialog.prototype._dataTableAjaxCall = function (data, callback) {
           row[3] = article.journal;
           row[4] = article.year;
         } else {
-          row[0] = publicationList.data[i].publication.id;
+          row[0] = publicationList.data[i].publication.resource;
           row[1] = "N/A";
           row[2] = "N/A";
           row[3] = "N/A";
@@ -304,7 +304,7 @@ PublicationListDialog.prototype.publicationListToArray = function (publicationLi
         row[3] = article.journal;
         row[4] = article.year;
       } else {
-        row[0] = entry.publication.id;
+        row[0] = entry.publication.resource;
         row[1] = "N/A";
         row[2] = "N/A";
         row[3] = "N/A";

frontend-js/src/main/js/map/data/PrivilegeType.js

@@ -36,6 +36,7 @@ PrivilegeType.MANAGE_PLUGINS = 'MANAGE_PLUGINS';
 PrivilegeType.PROJECT_MANAGEMENT = 'PROJECT_MANAGEMENT';
 PrivilegeType.ADD_MAP = 'ADD_MAP';
 PrivilegeType.USER_MANAGEMENT = 'USER_MANAGEMENT';
+PrivilegeType.LAYOUT_MANAGEMENT = 'LAYOUT_MANAGEMENT';
 
 /**
  *

frontend-js/src/test/js/gui/admin/EditProjectDialog-test.js

@@ -6,7 +6,8 @@ var EditProjectDialog = require('../../../../main/js/gui/admin/EditProjectDialog
 var ServerConnector = require('../../ServerConnector-mock');
 var logger = require('../../logger');
 
-var assert = require('assert');
+var chai = require('chai');
+var assert = chai.assert;
 var Promise = require('bluebird');
 
 describe('EditProjectDialog', function () {
@@ -130,4 +131,37 @@ describe('EditProjectDialog', function () {
     });
   });
 
+  describe('overlayToTableRow', function () {
+    it('as not admin', function () {
+      var dialog;
+      helper.loginAsAdmin();
+      return createDialog().then(function (result) {
+        dialog = result;
+        return ServerConnector.getUsers();
+      }).then(function (users) {
+        helper.loginWithoutAccess();
+        var overlay = helper.createOverlay();
+        var data = dialog.overlayToTableRow(overlay, users);
+        assert.ok(data[7].indexOf("disabled") >= 0)
+      }).then(function () {
+        return dialog.destroy();
+      });
+    });
+    it('as admin', function () {
+      var dialog;
+      helper.loginAsAdmin();
+      return createDialog().then(function (result) {
+        dialog = result;
+        return ServerConnector.getUsers();
+      }).then(function (users) {
+        var overlay = helper.createOverlay();
+        var data = dialog.overlayToTableRow(overlay, users);
+        assert.equal(data[7].indexOf("disabled"), -1)
+      }).then(function () {
+        return dialog.destroy();
+      });
+    });
+  });
+
+
 });

frontend-js/src/test/js/gui/admin/MapsAdminPanel-test.js

@@ -7,6 +7,7 @@ var ServerConnector = require('../../ServerConnector-mock');
 var logger = require('../../logger');
 
 var assert = require('assert');
+var Promise = require('bluebird');
 
 function createMapsAdminPanel() {
   return new MapsAdminPanel({

model-command/src/main/java/lcsb/mapviewer/commands/layout/ApplySimpleLayoutModelCommand.java

@@ -219,7 +219,7 @@ public class ApplySimpleLayoutModelCommand extends ApplyLayoutModelCommand {
         minPoint.getY() + COMPARTMENT_BORDER, dimension.getWidth() - COMPARTMENT_BORDER * 2,
         dimension.getHeight() - COMPARTMENT_BORDER * 2);
     for (Element element : compartment.getElements()) {
-      if (!elements.contains(element) && element.getBorder()!=null) {
+      if (!elements.contains(element) && element.getBorder() != null && element.getX() != 0 && element.getY() != 0) {
         border.add(element.getBorder());
       }
     }

model/src/main/java/lcsb/mapviewer/model/map/model/Model.java

@@ -151,7 +151,7 @@ public interface Model {
    * @param elements
    *          list of elements
    */
-  void addElements(List<? extends Element> elements);
+  void addElements(Collection<? extends Element> elements);
 
   /**
    * Sets new short description of the model.

model/src/main/java/lcsb/mapviewer/model/map/model/ModelFullIndexed.java

@@ -198,7 +198,7 @@ public class ModelFullIndexed implements Model {
   }
 
   @Override
-  public void addElements(List<? extends Element> elements) {
+  public void addElements(Collection<? extends Element> elements) {
     for (Element element : elements) {
       addElement(element);
     }

model/src/main/java/lcsb/mapviewer/model/map/species/Element.java

@@ -322,7 +322,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
    * @see x
    */
   public void setX(String string) {
-    this.x = Double.parseDouble(string);
+    setX(Double.parseDouble(string));
   }
 
   /**
@@ -483,7 +483,7 @@ public abstract class Element implements BioEntity, Serializable, SbmlArgument {
    * @return rectangle border
    */
   public Rectangle2D getBorder() {
-    if (x == null || y == null || width == null || height == null) {
+    if (x == null || y == null || width == null || height == null || width == 0.0 || height == 0.0) {
       return null;
     }
     return new Rectangle2D.Double(x, y, width, height);

persist/src/main/resources/db/migration/V1__base.sql

@@ -13,7 +13,6 @@ SET client_encoding = 'UTF8';
 SET standard_conforming_strings = on;
 SET check_function_bodies = false;
 SET client_min_messages = warning;
-SET row_security = off;
 
 --
 -- TOC entry 1 (class 3079 OID 12355)

reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java

@@ -139,7 +139,7 @@ public class ReactomeConnector extends CachableInterface implements DataSourceUp
 	/**
 	 * Url used for accessing Reactome RestFULL API.
 	 */
-	private static final String									 REACTOME_URL			= "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/";
+	public static final String									 REACTOME_URL			= "http://reactomews.oicr.on.ca:8080/ReactomeRESTfulAPI/RESTfulWS/";
 
 	@Override
 	public List<ReactomePhysicalEntity> getEntitiesForName(String name) throws IOException {

reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java

@@ -173,7 +173,7 @@ public class ReactomeConnectorTest extends ReactomeTestFunctions {
 
   @Test(timeout = 15000)
   public void testCachableInterfaceByParams() throws Exception {
-    String url = "http://reactome.org/ReactomeRESTfulAPI/RESTfulWS/listByQuery/DatabaseObjects";
+    String url = ReactomeConnector.REACTOME_URL + "listByQuery/DatabaseObjects";
     String query = "identifier=2562550\n" + url;
     String newRes = "hello";
     try {

reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java

@@ -53,7 +53,7 @@ public class ReactomeReferenceGeneProductParserTest extends ReactomeTestFunction
 
       assertEquals((Integer) 2, res.getReferenceDatabase().getDbId());