properly handle compartments defined by CellDesigner 2.5

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentXmlParser.java

@@ -137,15 +137,17 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
   private void parseAnnotationNode(CellDesignerCompartment compartment, Node xmlNode) throws InvalidXmlSchemaException {
     NodeList annotationNodes = xmlNode.getChildNodes();
     for (int y = 0; y < annotationNodes.getLength(); y++) {
-      Node annotationNode = annotationNodes.item(y);
-      if (annotationNode.getNodeType() == Node.ELEMENT_NODE) {
-        if (annotationNode.getNodeName().equalsIgnoreCase("rdf:RDF")) {
-          compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(annotationNode));
-        } else if (annotationNode.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
-          parseExtensionNode(compartment, annotationNode);
+      Node node = annotationNodes.item(y);
+      if (node.getNodeType() == Node.ELEMENT_NODE) {
+        if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
+          compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(node));
+        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
+          parseExtensionNode(compartment, node);
+        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:name")) {
+          compartment.setName(decodeName(XmlParser.getNodeValue(node)));
         } else {
           throw new InvalidXmlSchemaException(
-              "Unknown xml tag of compartment->annotation: " + annotationNode.getNodeName());
+              "Unknown xml tag of compartment->annotation: " + node.getNodeName());
         }
       }
     }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/compartment/CompartmentParserTests.java

@@ -118,4 +118,12 @@ public class CompartmentParserTests extends CellDesignerTestFunctions {
     assertEquals(1, model.getElements().size());
   }
 
+  @Test
+  public void testOldCellDesignerCompartment() throws Exception {
+    Model model = getModelForFile("testFiles/compartment/old_compartment.xml");
+    Compartment c = model.getElementByElementId("ca1");
+
+    assertEquals(1, model.getElements().size());
+  }
+
 }

converter-CellDesigner/testFiles/compartment/old_compartment.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" xmlns:celldesigner="http://www.sbml.org/2001/ns/celldesigner" level="2" version="1">
+<model id="Activin_beta_signaling_pathway">
+<annotation>
+<celldesigner:extension>
+<celldesigner:modelVersion>2.5</celldesigner:modelVersion>
+<celldesigner:modelDisplay sizeX="2262" sizeY="2010"/>
+<celldesigner:listOfCompartmentAliases>
+<celldesigner:compartmentAlias id="ca1" compartment="c1">
+<celldesigner:class>SQUARE_CLOSEUP_NORTH</celldesigner:class>
+<celldesigner:point x="85.0" y="648.0"/>
+<celldesigner:namePoint x="802.0" y="1973.5"/>
+<celldesigner:doubleLine thickness="12.0" outerWidth="2.0" innerWidth="1.0"/>
+<celldesigner:paint color="ffcccc00" scheme="Color"/>
+<celldesigner:info state="empty" angle="-1.5707963267948966"/>
+</celldesigner:compartmentAlias>
+</celldesigner:listOfCompartmentAliases>
+<celldesigner:listOfComplexSpeciesAliases/>
+<celldesigner:listOfSpeciesAliases/>
+<celldesigner:listOfGroups/>
+<celldesigner:listOfProteins/>
+<celldesigner:listOfGenes/>
+<celldesigner:listOfRNAs/>
+<celldesigner:listOfAntisenseRNAs/>
+<celldesigner:listOfLayers/>
+<celldesigner:listOfBlockDiagrams/>
+</celldesigner:extension>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+<compartment id="c1" name="cytosol" outside="default">
+<annotation>
+<celldesigner:name>cytosol</celldesigner:name>
+</annotation>
+</compartment>
+</listOfCompartments>
+</model>
+</sbml>