diff --git a/CHANGELOG b/CHANGELOG
index 27846d35f885565812fe10b3aaa33fdf41a86b97..6cc7604fddcab7277a2b77bf0a25b625282b1d74 100644
--- a/CHANGELOG
+++ b/CHANGELOG
@@ -1,3 +1,9 @@
+minerva (18.1.1) stable; urgency=medium
+ * Bug fix: SBGN-ML import/export should not use compartmentOrder for
+ non-compartment entities (#2193)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu> Tue, 04 Feb 2025 16:00:00 +0200
+
minerva (18.1.0) stable; urgency=medium
* Small improvement: SBGN-ML import/export is processing notes (#2192)
* Small improvement: SBGN-ML import/export is processing compartmentOrder
diff --git a/CellDesigner-plugin/pom.xml b/CellDesigner-plugin/pom.xml
index f196ae52a36c970a3631fb0002fc2b31edfdb5ed..8b4f056695b8fd90cce5ae6825286ee6de0f66b5 100644
--- a/CellDesigner-plugin/pom.xml
+++ b/CellDesigner-plugin/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>CellDesigner-plugin</artifactId>
<!-- dependency from the MapViewer model -->
@@ -50,19 +50,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
diff --git a/annotation/pom.xml b/annotation/pom.xml
index 4f120e85c46f44f56dacae1e61f22a2a7d040615..638da580c3ee78b2caa19bc82d88efe16357c410 100644
--- a/annotation/pom.xml
+++ b/annotation/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>annotation</artifactId>
<name>Annotation module</name>
@@ -19,7 +19,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -27,7 +27,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser (we need access
@@ -35,13 +35,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- Log4J2 -->
diff --git a/commons/pom.xml b/commons/pom.xml
index 4fc21cf7cf6d475e8356d5f772c698eb8827f86b..2f6112442c1769a4b93bdd2e74730de78c06f8b3 100644
--- a/commons/pom.xml
+++ b/commons/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>commons</artifactId>
<name>Mapviewer commons</name>
diff --git a/converter-CellDesigner/pom.xml b/converter-CellDesigner/pom.xml
index 7d84518701bdae3e7a0dcde533b7cc70bfe100a2..38b05a88d2995936f20557e785dde0f507844033 100644
--- a/converter-CellDesigner/pom.xml
+++ b/converter-CellDesigner/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>converter-CellDesigner</artifactId>
<name>CellDesigner converter</name>
@@ -17,13 +17,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- Log4J2 -->
diff --git a/converter-SBGNML/pom.xml b/converter-SBGNML/pom.xml
index 1d56b0ac8303c7f32a48e0b3689fdc27434c65dc..78cf9295a016e5140fb766c994f2873fb4d7cfea 100644
--- a/converter-SBGNML/pom.xml
+++ b/converter-SBGNML/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>converter-SBGNML</artifactId>
@@ -20,26 +20,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
<scope>test</scope>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
diff --git a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
index cc94a4a40b40b103077dbb88e81537b87987dedd..62c8aadb932f260acf9db8c0c97e42e31856968f 100644
--- a/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
+++ b/converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java
@@ -274,9 +274,6 @@ public class SbgnmlXmlExporter {
newGlyph.setClazz(getGlyphClazzFromElement(element).getClazz());
newGlyph.setLabel(getGlyphLabelFromAlias(element));
newGlyph.setNotes(notesConverter.createNotesNode(element.getNotes()));
- if (element.getZ() != null) {
- newGlyph.setCompartmentOrder(element.getZ().floatValue());
- }
final Bbox bbox = new Bbox();
bbox.setX(element.getX().floatValue());
@@ -285,7 +282,11 @@ public class SbgnmlXmlExporter {
bbox.setH(element.getHeight().floatValue());
newGlyph.setBbox(bbox);
- if (element instanceof Species) {
+ if (element instanceof Compartment) {
+ if (element.getZ() != null) {
+ newGlyph.setCompartmentOrder(element.getZ().floatValue());
+ }
+ } else if (element instanceof Species) {
final Species species = (Species) element;
if (element instanceof Protein) {
final Protein protein = (Protein) element;
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
index 4f90c7ec36fa85c0a802e3dfd803d7f6b74e114a..a834093676e7c6a36902ee96489cda16f7cefd28 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java
@@ -141,12 +141,12 @@ public class SbgnmlTestFunctions extends TestUtils {
model2.setIdModel(model.getIdModel());
model2.setName(model.getName());
for (final Drawable d : model.getDrawables()) {
- if (!(d instanceof Element)) {
+ if (!(d instanceof Compartment)) {
d.setZ(null);
}
}
for (final Drawable d : model2.getDrawables()) {
- if (!(d instanceof Element)) {
+ if (!(d instanceof Compartment)) {
d.setZ(null);
}
}
diff --git a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
index 2f1143c6a905602ad53f1d11d94b48339b0fab1b..34655cfe5df8cc06dfee66b6c0759707eb78eb81 100644
--- a/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
+++ b/converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java
@@ -175,17 +175,12 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
@Test
public void importExportZ() throws Exception {
- GenericProtein protein = createProtein();
- protein.setZ(3);
-
Compartment compartment = createCompartment();
compartment.setZ(4);
- compartment.addElement(protein);
Model model = new ModelFullIndexed(null);
model.setWidth(2000);
model.setHeight(2000);
- model.addElement(protein);
model.addElement(compartment);
Model model2 = serializeAndCleanOverSbgn(model);
diff --git a/converter-graphics/pom.xml b/converter-graphics/pom.xml
index b930fb55b0996679a65c882e6ff86bc040073fdf..e39210329eb33e7aa21b3655ca773b526f9d0ddd 100644
--- a/converter-graphics/pom.xml
+++ b/converter-graphics/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>converter-graphics</artifactId>
<name>MapViewer graphics converter</name>
@@ -18,13 +18,13 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- Log4J2 -->
diff --git a/converter-sbml/pom.xml b/converter-sbml/pom.xml
index dc07a47f36ff66bd91c50cef13f3e4191038ebf7..d0c6e4105a9e9d6d03f91dbbbcbfe789a3d25e8a 100644
--- a/converter-sbml/pom.xml
+++ b/converter-sbml/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>converter-sbml</artifactId>
<name>converter-sbml</name>
@@ -40,22 +40,22 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- Log4J2 -->
@@ -167,7 +167,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
<scope>test</scope>
</dependency>
diff --git a/converter/pom.xml b/converter/pom.xml
index 2b7328f0f48cea06e1493e7147f0d86443bd4102..f6e53dd58ab98742e450874329f9372773c17266 100644
--- a/converter/pom.xml
+++ b/converter/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>converter</artifactId>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>xerces</groupId>
diff --git a/frontend-js/pom.xml b/frontend-js/pom.xml
index 682044db84ea0b1c7939cd3ca7490f533a363a2e..daec87d496ea05af35838ed4180cec4270145617 100644
--- a/frontend-js/pom.xml
+++ b/frontend-js/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>frontend-js</artifactId>
<name>frontend-js</name>
diff --git a/model-command/pom.xml b/model-command/pom.xml
index 023c9c1f0a0d1b51026c6daaf60d9aa29cd7cf6b..0ea553bece32b80c7ba215b0b907fd3ebf21acd4 100644
--- a/model-command/pom.xml
+++ b/model-command/pom.xml
@@ -3,7 +3,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>model-command</artifactId>
<name>Model commands</name>
@@ -16,7 +16,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
@@ -24,7 +24,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- Log4J2-->
diff --git a/model/pom.xml b/model/pom.xml
index 5172f0a04eb9f7c0337ddd6b6b26c9f65647a683..5cbdcfe395d865a17f0faf0a8739ae9778f6255b 100644
--- a/model/pom.xml
+++ b/model/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>model</artifactId>
<name>model MapViewer</name>
@@ -15,7 +15,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>commons</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- Java xml serialization -->
diff --git a/pathvisio/pom.xml b/pathvisio/pom.xml
index 3549eb953bf6b638aed3aa88b8549427296c7468..db2cc0845e8c7fb53eae2b60d550c018b9fbfdf6 100644
--- a/pathvisio/pom.xml
+++ b/pathvisio/pom.xml
@@ -5,7 +5,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>pathvisio</artifactId>
<name>Pathvisio plugin</name>
@@ -77,26 +77,26 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
<scope>test</scope>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- Log4J2 -->
diff --git a/persist/pom.xml b/persist/pom.xml
index 24678fa8391ffd3ab67ce57fb40b26d08961d182..9d4f4f2f6ed517234f83f1691d1968490e307b6e 100644
--- a/persist/pom.xml
+++ b/persist/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>persist</artifactId>
@@ -26,7 +26,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- Hibernate -->
diff --git a/pom.xml b/pom.xml
index 60799bd1b535b763eb2c753bb0f8d60de59a4afc..918085bc04c4b33d27c5d506e7d95139bf0dc57a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,7 +6,7 @@
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
<packaging>pom</packaging>
<name>parent MapViewer</name>
diff --git a/rest-api/pom.xml b/rest-api/pom.xml
index 35dfb9cb44e0d0fb73e264514a0054c9f097d2b4..f92e224b3f69c46cc3add662e599ff4eb2b1811a 100644
--- a/rest-api/pom.xml
+++ b/rest-api/pom.xml
@@ -7,7 +7,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>rest-api</artifactId>
<name>rest-api</name>
@@ -19,19 +19,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>pathvisio</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
diff --git a/service/pom.xml b/service/pom.xml
index 624ca59f523a1215cadee2828f0694ed40ef3423..b1131cba882e95d958b840e48b6484ee1c9aa6cd 100644
--- a/service/pom.xml
+++ b/service/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>service</artifactId>
@@ -19,7 +19,7 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- dependency from the MapViewer dao -->
@@ -27,47 +27,47 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>persist</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>model-command</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>annotation</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- dependency from the MapViewer cell designer parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-CellDesigner</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- dependency from the MapViewer SBGN-ML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-SBGNML</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- dependency from the MapViewer graphics converter -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-graphics</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- dependency from the SBML parser -->
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>converter-sbml</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<!-- Log4J2 -->
diff --git a/web/pom.xml b/web/pom.xml
index 503ad0060d576cf033c06312e0b8072bbf92179c..a7feec46e84d6994eefafd9bd66e7f97b7d29c98 100644
--- a/web/pom.xml
+++ b/web/pom.xml
@@ -6,7 +6,7 @@
<parent>
<groupId>lcsb.mapviewer</groupId>
<artifactId>parent</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</parent>
<artifactId>web</artifactId>
<packaging>jar</packaging>
@@ -36,19 +36,19 @@
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>service</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>rest-api</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>
<groupId>lcsb.mapviewer</groupId>
<artifactId>frontend-js</artifactId>
- <version>18.1.0</version>
+ <version>18.1.1</version>
</dependency>
<dependency>