Merge branch '2194-bug-in-sbgn-ml-export-empty-sets-are-exported-with-a-label' into 'master'

Resolve "bug in SBGN-ML export: empty sets are exported with a label"

See merge request !1859

CHANGELOG

@@ -12,6 +12,8 @@ minerva (18.1.0) stable; urgency=medium
     separated using compartment (#2169)
   * Bug fix: exporting model should provide deterministic output for species and
     compartments (#2187)
+  * Bug fix: exporting degraded to SBGN-ML should not produce a label for it
+    (#2194)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 19 Dec 2024 13:00:00 +0200
 

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporter.java

@@ -615,6 +615,9 @@ public class SbgnmlXmlExporter {
    * @return label for a glyph
    */
   private Label getGlyphLabelFromAlias(final Element element) {
+    if (element instanceof Degraded) {
+      return null;
+    }
     final Label label = new Label();
     label.setText(element.getName());
     final Bbox box = new Bbox();

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlTestFunctions.java

@@ -17,6 +17,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.SquareCompartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.Degraded;
 import lcsb.mapviewer.model.map.species.Drug;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.GenericProtein;
@@ -74,6 +75,14 @@ public class SbgnmlTestFunctions extends TestUtils {
     return protein;
   }
 
+  protected Degraded createDegraded() {
+    Degraded degraded = new Degraded("id" + (counter++));
+    assignLayout(degraded);
+    degraded.setWidth(degraded.getHeight());
+    degraded.setNameWidth(degraded.getHeight());
+    return degraded;
+  }
+
   protected Compartment createCompartment() {
     SquareCompartment compartment = new SquareCompartment("id" + (counter++));
     assignLayout(compartment);

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlExporterTest.java

@@ -12,6 +12,7 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.type.ModifierReactionNotation;
 import lcsb.mapviewer.model.map.reaction.type.ReducedNotation;
+import lcsb.mapviewer.model.map.species.Degraded;
 import lcsb.mapviewer.model.map.species.Drug;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Ion;
@@ -191,4 +192,16 @@ public class SbgnmlXmlExporterTest extends SbgnmlTestFunctions {
     assertEquals(0, new ModelComparator().compare(model, model2));
   }
 
+  @Test
+  public void importExportDegraded() throws Exception {
+    Degraded degraded = createDegraded();
+
+    Model model = new ModelFullIndexed(null);
+    model.setWidth(2000);
+    model.setHeight(2000);
+    model.addElement(degraded);
+
+    serializeAndCleanOverSbgn(model);
+  }
+
 }