Commit 31199bb0 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

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

V12.2 release

See merge request minerva/core!714
parents ad58b81d a29e4489
Pipeline #9475 passed with stages
in 22 minutes and 34 seconds
minerva (12.2.0~beta.3) unstable; urgency=medium minerva (12.2.0) stable; 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
* Feature: bug report utility * 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 * Feature: url GET parameters support all kind of search and selected overlays
highlight highlight
* Feature: user can create custom logging configuration in file * Feature: user can create custom logging configuration in file
...@@ -125,6 +11,15 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium ...@@ -125,6 +11,15 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium
file formats file formats
* Feature: current state of the browsed map is reflected in the url (position, * Feature: current state of the browsed map is reflected in the url (position,
zoom, overlays, search queries, etc.) 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: export to SBML includes unit factors
* Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls * Small improvement: mesh identifiers are resolved to meshb.nlm.nih.gov urls
* Small improvement: genetics information allows to provide information about * Small improvement: genetics information allows to provide information about
...@@ -158,7 +53,48 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium ...@@ -158,7 +53,48 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium
has proper access level has proper access level
* Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact * Small improvement: 'REQUEST AN ACCOUNT' link is available only the contact
email account is provided 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 to CellDesigner align inhibition reaction properly
* Bug fix: export/import to/from SBML handles Heterodimer Association * Bug fix: export/import to/from SBML handles Heterodimer Association
reaction properly reaction properly
...@@ -174,9 +110,9 @@ minerva (12.2.0~alpha.0) unstable; urgency=medium ...@@ -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 * Bug fix: type of the data overlay can be defined in the file content
(useful when uploading genetic variants) (useful when uploading genetic variants)
* Bug fix: CLEAR button clears comment checkbox if necessary * 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 minerva (12.1.8) stable; urgency=medium
* Bug fix: add a project reset users custom overlays limit to default (#679) * Bug fix: add a project reset users custom overlays limit to default (#679)
......
...@@ -138,7 +138,7 @@ public class ReactomeConnector extends CachableInterface implements DataSourceUp ...@@ -138,7 +138,7 @@ public class ReactomeConnector extends CachableInterface implements DataSourceUp
/** /**
* Url used for accessing Reactome RestFULL API. * 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 @Override
public List<ReactomePhysicalEntity> getEntitiesForName(String name) throws IOException { public List<ReactomePhysicalEntity> getEntitiesForName(String name) throws IOException {
......
...@@ -173,7 +173,7 @@ public class ReactomeConnectorTest extends ReactomeTestFunctions { ...@@ -173,7 +173,7 @@ public class ReactomeConnectorTest extends ReactomeTestFunctions {
@Test(timeout = 15000) @Test(timeout = 15000)
public void testCachableInterfaceByParams() throws Exception { 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 query = "identifier=2562550\n" + url;
String newRes = "hello"; String newRes = "hello";
try { try {
......
...@@ -53,7 +53,7 @@ public class ReactomeReferenceGeneProductParserTest extends ReactomeTestFunction ...@@ -53,7 +53,7 @@ public class ReactomeReferenceGeneProductParserTest extends ReactomeTestFunction
assertEquals((Integer) 2, res.getReferenceDatabase().getDbId()); assertEquals((Integer) 2, res.getReferenceDatabase().getDbId());
assertEquals((Integer) 48895, res.getSpecies().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) { } catch (Exception e) {
e.printStackTrace(); e.printStackTrace();
......
...@@ -39,7 +39,7 @@ public class ReactomeReferenceIsoformParserTest extends ReactomeTestFunctions { ...@@ -39,7 +39,7 @@ public class ReactomeReferenceIsoformParserTest extends ReactomeTestFunctions {
assertEquals((Integer) 2, res.getReferenceDatabase().getDbId()); assertEquals((Integer) 2, res.getReferenceDatabase().getDbId());
assertEquals("false", res.getIsSequenceChanged()); assertEquals("false", res.getIsSequenceChanged());
assertEquals((Integer) 48887, res.getSpecies().getDbId()); 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) 192971, res.getReferenceTranscripts().get(0).getDbId());
assertEquals((Integer) 402286, res.getIsoformParents().get(0).getDbId()); assertEquals((Integer) 402286, res.getIsoformParents().get(0).getDbId());
assertEquals("UniProt:P02545-1 LMNA", res.getDisplayName()); assertEquals("UniProt:P02545-1 LMNA", res.getDisplayName());
......
...@@ -20,7 +20,7 @@ ...@@ -20,7 +20,7 @@
<schemaClass>Species</schemaClass> <schemaClass>Species</schemaClass>
</species> </species>
<referenceGene> <referenceGene>
<dbId>11373937</dbId> <dbId>10586616</dbId>
<displayName>BioGPS Gene:1 A1BG</displayName> <displayName>BioGPS Gene:1 A1BG</displayName>
<schemaClass>ReferenceDNASequence</schemaClass> <schemaClass>ReferenceDNASequence</schemaClass>
</referenceGene> </referenceGene>
......
...@@ -382,7 +382,7 @@ ...@@ -382,7 +382,7 @@
<schemaClass>Species</schemaClass> <schemaClass>Species</schemaClass>
</species> </species>
<referenceGene> <referenceGene>
<dbId>11373937</dbId> <dbId>10586616</dbId>
<displayName>BioGPS Gene:1 A1BG</displayName> <displayName>BioGPS Gene:1 A1BG</displayName>
<schemaClass>ReferenceDNASequence</schemaClass> <schemaClass>ReferenceDNASequence</schemaClass>
</referenceGene> </referenceGene>
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment