diff --git a/CHANGELOG b/CHANGELOG
index 815f1be6299476b0d92eb14e41707bb66e67917b..6f8d5521f29db56d315411cee5c119ba47217d85 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,119 +1,5 @@
-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)
diff --git a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java b/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
index dcc5cdb14ec81803fbffab2d59318a2717d3aae1..c793c508178fd795557b2e2e809dc2df40d8be44 100644
--- a/reactome/src/main/java/lcsb/mapviewer/reactome/utils/ReactomeConnector.java
+++ b/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 {
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java
index cfc792e5f612d0caad2fad0009e871be3fb2ccb6..6dc740d05a21fc8e810c6670e6b9c47bfa2f98ad 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/utils/ReactomeConnectorTest.java
+++ b/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 {
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
index 5412d92cafa5ca788bd8e42436993a411517d073..2c51193790a348d9229da562ba4b1413212b49dc 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceGeneProductParserTest.java
+++ b/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();
diff --git a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java b/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java
index 1cfb460fdd0e475b183fc36a0f44ef9cf4880bc6..fc18b30ee840e7c8a35747f728832f10c14a76e2 100644
--- a/reactome/src/test/java/lcsb/mapviewer/reactome/xml/ReactomeReferenceIsoformParserTest.java
+++ b/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());
diff --git a/reactome/testFiles/reactome/referenceGeneProduct.xml b/reactome/testFiles/reactome/referenceGeneProduct.xml
index 502894eef6af22255c140af50ca417422668445a..a3458d75e34352146a9dd6b4d329e5c4dae5bddc 100644
--- a/reactome/testFiles/reactome/referenceGeneProduct.xml
+++ b/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>
diff --git a/reactome/testFiles/reactome/referenceIsoform.xml b/reactome/testFiles/reactome/referenceIsoform.xml
index 8d08e978b194355ce6d27192a52b759c8a67989c..415b1bba7b619d406c2a81d0a8f83a290cf441d1 100644
--- a/reactome/testFiles/reactome/referenceIsoform.xml
+++ b/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>