Merge branch 'v12.2-release' into 'devel_12.2.x'

V12.2 release

See merge request !714

CHANGELOG

-minerva (12.2.0~beta.3) unstable; urgency=medium
-  * Bug fix: Icons are still not properly loaded on Safari (#661)
-  * Bug fix: fetching information about publication with invalid (non numeric)
-    pubmed id triggered exception (#737)
-  * Bug fix: proper id is used in list of publications when publication id is
-    invalid (#735)
-  * Bug fix: closing Add Project window was taking infinity (#734)
-  * Bug fix: align of checkboxes in top right corner fixed (#733)
-  * Bug fix: uploading SBML file without layout resulted in overlapping 
-    compartments (#736)
-  * Bug fix: migration scripts are compatibile with postgres 9.3 version that 
-    is default on Ubuntu 14 (#762)
-  * Bug fix: after project was modified it could happen that user was unable to
-    upload data overlay (#752)
-  * 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)
-
- -- Piotr Gawron <piotr.gawron@uni.lu>  Wed, 25 Mar 2019 10:00:00 +0200
-
-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
@@ -125,6 +11,15 @@ 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
@@ -158,7 +53,48 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium
     has proper access level
   * 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
+  * 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
@@ -174,9 +110,9 @@ 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)

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

@@ -138,7 +138,7 @@ 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());
       assertEquals((Integer) 48895, res.getSpecies().getDbId());
-      assertEquals((Integer) 11373937, res.getReferenceGenes().get(0).getDbId());
+      assertEquals((Integer) 10586616, res.getReferenceGenes().get(0).getDbId());
 
     } catch (Exception e) {
       e.printStackTrace();

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

@@ -39,7 +39,7 @@ public class ReactomeReferenceIsoformParserTest extends ReactomeTestFunctions {
 			assertEquals((Integer) 2, res.getReferenceDatabase().getDbId());
 			assertEquals("false", res.getIsSequenceChanged());
 			assertEquals((Integer) 48887, res.getSpecies().getDbId());
-			assertEquals((Integer) 11373937, res.getReferenceGenes().get(0).getDbId());
+			assertEquals((Integer) 10586616, res.getReferenceGenes().get(0).getDbId());
 			assertEquals((Integer) 192971, res.getReferenceTranscripts().get(0).getDbId());
 			assertEquals((Integer) 402286, res.getIsoformParents().get(0).getDbId());
 			assertEquals("UniProt:P02545-1 LMNA", res.getDisplayName());

reactome/testFiles/reactome/referenceGeneProduct.xml

@@ -20,7 +20,7 @@
 		<schemaClass>Species</schemaClass>
 	</species>
 	<referenceGene>
-		<dbId>11373937</dbId>
+		<dbId>10586616</dbId>
 		<displayName>BioGPS Gene:1 A1BG</displayName>
 		<schemaClass>ReferenceDNASequence</schemaClass>
 	</referenceGene>

reactome/testFiles/reactome/referenceIsoform.xml

@@ -382,7 +382,7 @@
 		<schemaClass>Species</schemaClass>
 	</species>
 	<referenceGene>
-		<dbId>11373937</dbId>
+		<dbId>10586616</dbId>
 		<displayName>BioGPS Gene:1 A1BG</displayName>
 		<schemaClass>ReferenceDNASequence</schemaClass>
 	</referenceGene>