Commit a28d3a6b authored by Piotr Gawron's avatar Piotr Gawron
Browse files

Merge branch '1573-export-issue' into 'devel_16.0.x'

Resolve "cannot export submap as image/map"

See merge request !1370
parents a5130eb1 e3524287
Pipeline #48964 passed with stage
in 28 minutes
minerva (16.0.0~beta.3) stable; urgency=medium
* Bug fix: show genetic data overlays in InfoWindow even when no data is
available (#1562)
* Bug fix: speed of opening map is improved (#1558)
* Bug fix: typo (#1555)
* Bug fix: gene mapping with empty url caused issues when opening info window
(#1557)
* Bug fix: issues with exporting map to file or image fixed (#1561, #1560,
#1559)
* Bug fix: sometimes wrong icn numbers were attached to search results
(#1556)
-- Piotr Gawron <piotr.gawron@uni.lu> Mon, 27 Sep 2021 14:00:00 +0200
minerva (16.0.0~beta.2) stable; urgency=medium
* Small improvement: backgrounds are separated from general overlays (#1532)
* Small improvement: layout of pin popup window is slitghly improved (#1493)
* Small improvement: search results are grouped by submap with hits (#1505)
* Bug fix: correct background order for old projects restored (#1533)
* Bug fix: search chemicals by target returned chemicals not bounded by
disease (#1535)
* Bug fix: problem with export map with submaps fixed (#1540)
* Bug fix: clear does not show warning about missing disease ID (#1541)
* Bug fix: removing user removed backgrounds in projects created by user
(#1527)
* Bug fix: removing background did not remove images from server (#1526)
* Bug fix: two genomic data overlay with two different reference genomes
caused issue (#1546)
* Bug fix: search results were limited to 10 elements
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 9 Sep 2021 11:00:00 +0200
minerva (16.0.0~beta.1) stable; urgency=medium
* Backward incompatibility: layout parameter in minerva url is not supported
anymore
* Small improvement: info about background and data overlays is separated in
edit project panel (#1515)
* Bug fix: there was issue with updating data overlay in admin panel "Unknown
parameter: defaultOverlay" (#1489)
* Bug fix: data overlays uploaded in complex map were not processed properly
(#1485)
* Bug fix: sort of the overlays in General Overlays in the left panel was
wrong (#1486)
* Bug fix: overlay owner must be defined (#1488)
* Bug fix: there was issue when upgrading backgrounds in admin panel (#1514)
* Bug fix: there was issue when editing and saving data overlay (#1494)
* Bug fix: problem with adding comments (#1495)
* Bug fix: project with invalid data might cause problem on
create/update/delete (#1509)
* Bug fix: exporting part of map as image caused removing not drawn species
from the database (#1508)
* Bug fix: adding user with already existing login and changing his
privileges occured with error (#1507)
* Bug fix: export model as model could cause an issue (#1500, #1502)
* Bug fix: problem with export as image with data overlays (#1503, #1498,
#1496)
* Bug fix: chrome autofill is disabled for "Search: " in admin panel tables
* Bug fix: top map was not selected properly sometimes (#1487)
* Bug fix: data overlays in comlex upload prevented error to be propagated
to user (#1499)
* Bug fix: searching for all chemicals by target did not work (#1490)
* Bug fix: searching by chemical/drug/mirna in left panel focus the proper
tab in the InfoWindow (#1492)
* Bug fix: search tab becomes active when drug/chemical/mirna result are
available (#1491)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 25 Jun 2021 08:00:00 +0200
minerva (16.0.0~beta.0) stable; urgency=medium
minerva (16.0.0) stable; urgency=medium
* Backward incompatibility: debian package cannot be upgraded from version
prior to 12.1.0 (#1464)
* Small improvement: artifitial source and sink is created separately for
each uncomplete reaction (#1475)
* Small improvement: homomultimer information is provided in API (#1468)
* Small improvement: missing info about species for SBML parsing warning
(#1472)
* Small improvement: information about dimer in sbgn is provided only once
if the information is duplicated in sbgn data (#1358)
* Small improvement: glyph quality is improved (#1458)
* Small improvement: search results are group by diagram (#1451)
* Small improvement: "Failed to fetch" errors are reported in a way that
suggest retrying before submitting error report (#738)
* Small improvement: reverse search pop-up reorganized (#1366)
* Bug fix: arrows without a "process" box had an irregular empty space in
their lines (#1471)
* Bug fix: when selecting drug in the alias window the input text is updated
(#1365)
* Bug fix: zoom slider was not updated when clicking on +/- in genome browser
(#1064)
* Bug fix: there was no possibility to see gene variants
(regression 16.0.0~alpha.1)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 30 Apr 2021 16:30:00 +0200
minerva (16.0.0~alpha.1) stable; urgency=medium
* Backward incompatibility: layout parameter in minerva url is not supported
anymore
* Backward incompatibility: deprecated columns in data overlays are no longer
supported (#958)
* Backward incompatibility: comment does not contain name anymore (#1070)
......@@ -100,11 +10,35 @@ minerva (16.0.0~alpha.1) stable; urgency=medium
(#1007)
* Backward incompatibility: elements in data overlay are returned differently
when using data overlay API (#1007)
* Improvement: performance improved - map is available immediatelly after
* Backward incompatibility: deprecated columns in data overlay table are no
longer supported: reverseReaction, reaction_identifier, reactionIdentifier,
reference_genome_type, reference_genome_version, allel_frequency, lineWidth,
elementIdentifier, references, model_name (#958)
* Backward incompatibility: information about old search queries removed from
database (it can be still accessed using proper log managing)
* Improvement: automatically generated API documentation available in the
package (#1016)
* Improvement: performance improved - map is available immediately after
tomcat starts (#1007)
* Improvement: minerva does not require huge amounts of memory anymore
(#1007)
* Improvement: data overlay allows for multiple hits per element (#1007)
* Small improvement: backgrounds are separated from general overlays (#1532,
#1515)
* Small improvement: layout of pin popup window is slightly improved (#1493)
* Small improvement: search results are grouped by submap with hits (#1505)
* Small improvement: artificial source and sink is created separately for
each incomplete reaction (#1475)
* Small improvement: homomultimer information is provided in API (#1468)
* Small improvement: missing info about species for SBML parsing warning
(#1472)
* Small improvement: information about dimer in sbgn is provided only once
if the information is duplicated in sbgn data (#1358)
* Small improvement: glyph quality is improved (#1458)
* Small improvement: search results are group by diagram (#1451)
* Small improvement: "Failed to fetch" errors are reported in a way that
suggest retrying before submitting error report (#738)
* Small improvement: reverse search pop-up reorganized (#1366)
* Small improvement: "dbSNP", "IMGT HLA", "PMC", "Complex Portal" identifiers
are supported (#1452, #1450, #1420)
* Small improvement: information about perfect search are stored in the url
......@@ -120,28 +54,32 @@ minerva (16.0.0~alpha.1) stable; urgency=medium
(#1456)
* Small improvement: SBML render contains process rectangle for reactions
(#1457)
* Bug fix: show genetic data overlays in InfoWindow even when no data is
available (#1562)
* Bug fix: gene mapping with empty url caused issues when opening info window
(#1557)
* Bug fix: clear does not show warning about missing disease ID (#1541)
* Bug fix: two genomic data overlay with two different reference genomes
caused issue (#1546)
* Bug fix: search results were limited to 10 elements
* Bug fix: Chrome autofill is disabled for "Search: " in admin panel tables
* Bug fix: search tab becomes active when drug/chemical/mirna result are
available (#1491)
* Bug fix: arrows without a "process" box had an irregular empty space in
their lines (#1471)
* Bug fix: when selecting drug in the alias window the input text is updated
(#1365)
* Bug fix: zoom slider was not updated when clicking on +/- in genome browser
(#1064)
* Bug fix: refreshing page after removing last project on the page redirect to
proper page (#1051)
* Bug fix: removing plugin that does not exist anymore does not raise an error
(#1289)
* Bug fix: broken overlays crashed minerva upgrade (#1453)
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 19 Mar 2021 10:00:00 +0200
minerva (16.0.0~alpha.0) stable; urgency=medium
* Backward incompatibility: deprecated columns in data overlay table are no
longer supported: reverseReaction, reaction_identifier, reactionIdentifier,
reference_genome_type, reference_genome_version, allel_frequency, lineWidth,
elementIdentifier, references, model_name (#958)
* Backward incompatibility: information about old search queries removed from
database (it can be still accessed using proper log managing)
* Improvement: automatically generated API documentation available in the
package (#1016)
* Bug fix: md5 hash function of plugin was not computed properly
* Bug fix: exported gpml for every compartment contained list of species name
in the comment section
-- Piotr Gawron <piotr.gawron@uni.lu> Thu, 27 Aug 2020 13:00:00 +0200
-- Piotr Gawron <piotr.gawron@uni.lu> Fri, 29 Oct 2021 13:00:00 +0200
minerva (15.1.4) stable; urgency=medium
* Bug fix: structural state information data was not available for complexes
......
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
......@@ -50,19 +50,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
......
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
......@@ -18,7 +18,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- dependency from the MapViewer dao -->
......@@ -26,7 +26,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
......@@ -34,13 +34,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- Log4J2 -->
......
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
......
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>converter-CellDesigner</artifactId>
<name>CellDesigner converter</name>
......@@ -17,13 +17,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- Log4J2 -->
......
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>converter-SBGNML</artifactId>
......@@ -20,26 +20,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
......
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>converter-graphics</artifactId>
<name>MapViewer graphics converter</name>
......@@ -18,13 +18,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- Log4J2-->
......
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>converter-sbml</artifactId>
<name>converter-sbml</name>
......@@ -40,22 +40,22 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- Log4J2 -->
......@@ -154,7 +154,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
<scope>test</scope>
</dependency>
......
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>converter</artifactId>
......@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
......
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>frontend-js</artifactId>
<name>frontend-js</name>
......
......@@ -3,7 +3,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>model-command</artifactId>
<name>Model commands</name>
......@@ -16,7 +16,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
......@@ -24,7 +24,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- Log4J2-->
......
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>model</artifactId>
<name>model MapViewer</name>
......@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- Java xml serialization -->
......
......@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>pathvisio</artifactId>
<name>Pathvisio plugin</name>
......@@ -77,20 +77,20 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<scope>test</scope>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- Log4J2 -->
......
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>persist</artifactId>
......@@ -27,7 +27,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- apache ftp -->
......
......@@ -6,7 +6,7 @@
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
<packaging>pom</packaging>
<name>parent MapViewer</name>
......
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>rest-api</artifactId>
<name>rest-api</name>
......@@ -19,19 +19,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>pathvisio</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<dependency>
......
......@@ -185,7 +185,7 @@ public class ModelRestImpl extends BaseRestImpl {
ConverterException, InconsistentModelException {
Model originalModel = getModelService().getAndFetchModelByMapId(projectId, parseInteger(modelId, "modelId"));
originalModel.setProject(null);
Path2D polygon = stringToPolygon(polygonString, originalModel);
Set<Integer> elementIdsList = stringListToIntegerSet(elementIds);
......@@ -283,6 +283,8 @@ public class ModelRestImpl extends BaseRestImpl {
}
Model originalModel = getModelService().getAndFetchModelByMapId(projectId, mapId);
boolean sbgn = originalModel.getProject().isSbgnFormat();
originalModel.setProject(null);
Model colorModel = new CopyCommand(originalModel).execute();
......@@ -344,7 +346,7 @@ public class ModelRestImpl extends BaseRestImpl {
Params params = new Params().x(minX).y(minY).height((maxY - minY) /
scale).width((maxX - minX) / scale)
.level(level - Configuration.MIN_ZOOM_LEVEL).nested(false). // automatically set nested view as invalid
scale(scale).colorExtractor(colorExtractor).sbgn(originalModel.getProject().isSbgnFormat()).model(part);
scale(scale).colorExtractor(colorExtractor).sbgn(sbgn).model(part);
if (background != null) {
params.nested(background.isHierarchicalView());
}
......
......@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</parent>
<artifactId>service</artifactId>
......@@ -20,7 +20,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
<version>16.0.0~beta.3</version>
<version>16.0.0</version>
</dependency>
<!-- dependency from the MapViewer dao -->
......@@ -28,47 +28,47 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>