Commit b2d45f06 authored by Piotr Gawron's avatar Piotr Gawron
Browse files

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

parents ea956483 b2b9808d
Pipeline #11171 passed with stage
in 9 minutes and 34 seconds
......@@ -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
......
......@@ -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 {
......
......@@ -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
......
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