From c0857fb0c25288fb79d54e768104f12b5fe514b2 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Tue, 4 Feb 2025 15:28:59 +0100
Subject: [PATCH] don't export z-index as compartmentOrder for not compartments
---
CHANGELOG | 6 ++++++
.../converter/model/sbgnml/SbgnmlXmlExporter.java | 9 +++++----
.../converter/model/sbgnml/SbgnmlTestFunctions.java | 4 ++--
.../converter/model/sbgnml/SbgnmlXmlExporterTest.java | 5 -----
4 files changed, 13 insertions(+), 11 deletions(-)
diff --git a/CHANGELOG b/CHANGELOG
index 27846d35f8..6cc7604fdd 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/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 cc94a4a40b..62c8aadb93 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 4f90c7ec36..a834093676 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 2f1143c6a9..34655cfe5d 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);
--
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