Merge remote-tracking branch 'origin/devel_13.1.x' into merge-13.1.0

CHANGELOG

@@ -5,12 +5,12 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
   * Feature: Replaced connection pool manager C3P0 with better maintained
     Hikari (#564)
   * Feature removal: BioCompendium annotator removed (#32)
-  * Small improvement: caching is active by default for new users when 
+  * Small improvement: caching is active by default for new users when
     uploading project (#202)
-  * Small improvement: when removing overlay in admin panel there is a 
+  * Small improvement: when removing overlay in admin panel there is a
     confirmation dialog (#696)
   * Small improvement: overlay name is obligatory (#698)
-  * Small improvement: target gene in search panel contains also information 
+  * Small improvement: target gene in search panel contains also information
     about type of database that identifies the target (#66)
   * Bug fix: export to CellDesigner of reaction with two modifiers connected
     with boolean operator resulted was skipping some layout information
@@ -20,57 +20,24 @@ minerva (14.0.0~alpha.0) unstable; urgency=low
     inside boolean gateway
   * Bug fix: CellDesigner file exported from minerva was not fully compliant
     with SBML standard (#831)
-  * Bug fix: MiRNA targets are limited only to the organism associated with the 
+  * Bug fix: MiRNA targets are limited only to the organism associated with the
     map (#66)
-  * Bug fix: Search drug by target element did not return values when this 
+  * Bug fix: Search drug by target element did not return values when this
     element was annotated automatically (#216)
 
  -- Sascha Herzinger <sascha.herzinger@uni.lu>  Wed, 22 May 2019 10:30:00 +0200
 
-minerva (13.1.0~beta.1) unstable; urgency=low
-  * Small improvement: model_name renamed to map_name in data overlay columns
-    (#827)
-  * Small improvement: name, type, reference_genome_type and
-    reference_genome_version column in genetic variant data overlay are
-    deprecated (#827)
-  * Bug fix: deprecated columns in data overlay are not visible to the end user
-    (#827)
-  * Bug fix: invalid color in data overlay provides proper feedback to the user
-    (#822)
-  * Bug fix: genetic variant overlay without name caused problems (#832)
-  * Bug fix: tair locus identifiers were used improperly - instead of id the
-    name was used
-  * Bug fix: plugin tab header wasn't properly resized after adding plugins
-    that introduced second line for tab selection (#758)
-  * Bug fix: invisible layer shouldn't be shown in the on th map (#813)
-  * Bug fix: list of availbale annotators is sorted alphabetically (#815)
-  * Bug fix: redirect url from export panel is fixed (#819)
-  * Bug fix: allow to reupload the same file without closing add overlay dialog
-    (#833)
-  * Bug fix: gene_name column is allowed only in the genetic variant data
-    overlay
-  * Bug fix: protein types are sorted properly in "Select valid annotations"
-    dialog (#815)
-  * Bug fix: if there is a description of (sub)map then it is available in
-    info/submap panel (#824)
-  * Bug fix: when changing data in edit user dialog there was a need to click
-    close button twice (#818)
-  * Bug fix: empty type for data overlay is allowed (#827)
-  * Bug fix: genetic variants data overlay was ignoring color parameter (#827)
-  * Bug fix: pathways can be drawn using glyphs (#825)
-  * Bug fix: empty background overlay doesn't show glyphs, instead standard
-    visualization is used (#826)
-  * Bug fix: asynchronous cals on showing/hiding data overlays might cause
-    problems due to network latency (#830)
-
- -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 7 Jun 2019 17:00:00 +0200
-
-minerva (13.1.0~beta.0) unstable; urgency=low
+minerva (13.1.0) stable; urgency=medium
   * Feature: annotators are more flexible - you can define set of input and
     outputs used by annotator (#617)
   * Feature: changes in admin panel doesn't require saving - they are saved
     automatically (#676)
   * Feature: elements can have custom glyphs used for visualization (#487)
+  * Small improvement: model_name renamed to map_name in data overlay columns
+    (#827)
+  * Small improvement: name, type, reference_genome_type and
+    reference_genome_version column in genetic variant data overlay are
+    deprecated (#827)
   * Small improvement: all bio entities have z-index associated with them
     (#487)
   * Small improvement: validation of the organism and disease id on map upload
@@ -120,6 +87,32 @@ minerva (13.1.0~beta.0) unstable; urgency=low
     SemanticZoomLevelTransparency (#801)
   * Small improvement: export/import from SBML support z-index in LAYOUT
     extension
+  * Bug fix: due to blocking of our requests from ctdbase the autocomplete for
+    this database is disabled
+  * Bug fix: deprecated columns in data overlay are not visible to the end user
+    (#827)
+  * Bug fix: invalid color in data overlay provides proper feedback to the user
+    (#822)
+  * Bug fix: genetic variant overlay without name caused problems (#832)
+  * Bug fix: tair locus identifiers were used improperly - instead of id the
+    name was used
+  * Bug fix: plugin tab header wasn't properly resized after adding plugins
+    that introduced second line for tab selection (#758)
+  * Bug fix: invisible layer shouldn't be shown on the map (#813)
+  * Bug fix: list of availbale annotators is sorted alphabetically (#815)
+  * Bug fix: redirect url from export panel is fixed (#819)
+  * Bug fix: allow to reupload the same file without closing add overlay dialog
+    (#833)
+  * Bug fix: gene_name column is allowed only in the genetic variant data
+    overlay
+  * Bug fix: protein types are sorted properly in "Select valid annotations"
+    dialog (#815)
+  * Bug fix: if there is a description of (sub)map then it is available in
+    info/submap panel (#824)
+  * Bug fix: empty type for data overlay is allowed (#827)
+  * Bug fix: genetic variants data overlay was ignoring color parameter (#827)
+  * Bug fix: asynchronous calls on showing/hiding data overlays might cause
+    problems due to network latency (#830)
   * 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
@@ -138,7 +131,7 @@ minerva (13.1.0~beta.0) unstable; urgency=low
   * Bug fix: layout data was ignored for some reactions when importing from
     SBML (#812)
 
- -- Piotr Gawron <piotr.gawron@uni.lu>  Mon, 13 May 2019 19:00:00 +0200
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 27 Jun 2019 14:00:00 +0200
 
 minerva (13.0.0) stable; urgency=medium
   * Bug fix: Since Oracle Java cannot be installed as debian dependency we use

annotation/src/main/java/lcsb/mapviewer/annotation/services/ChemicalParser.java

@@ -687,7 +687,8 @@ public class ChemicalParser extends CachableInterface implements IExternalServic
     String cachedData = getCacheValue(cacheQuery);
     List<String> result;
     if (cachedData == null) {
-      result = getSuggestedQueryListWithoutCache(project, diseaseMiriam);
+//      result = getSuggestedQueryListWithoutCache(project, diseaseMiriam);
+      result = new ArrayList<>();
       cachedData = StringUtils.join(result, "\n");
       setCacheValue(cacheQuery, cachedData);
     } else {

service/src/main/java/lcsb/mapviewer/services/impl/ProjectService.java

@@ -863,13 +863,15 @@ public class ProjectService implements IProjectService {
         updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_MIRIAM, progress, params);
       }
     });
-
-    chemicalService.cacheDataForModel(originalModel, new IProgressUpdater() {
-      @Override
-      public void setProgress(double progress) {
-        updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_CHEMICAL, progress, params);
-      }
-    });
+    
+    logger.warn("Cache of chemicals data is disabled");
+
+//    chemicalService.cacheDataForModel(originalModel, new IProgressUpdater() {
+//      @Override
+//      public void setProgress(double progress) {
+//        updateProjectStatus(originalModel.getProject(), ProjectStatus.CACHING_CHEMICAL, progress, params);
+//      }
+//    });
 
     drugService.cacheDataForModel(originalModel, new IProgressUpdater() {
       @Override