parsing of CellDesigner 2.5 should work

CHANGELOG

@@ -10,6 +10,7 @@ minerva (15.0.0~alpha.1) stable; urgency=medium
   * Small improvement: list of genomes is automatically refreshed during genome
     upload (#820)
   * Small improvement: items in context menu are reorganized (#787)
+  * Small improvement: CellDesigner files from version 2.5 should be parseable
   * Bug fix: compartments limited by corner (left-top corner compartment, etc)
     are parsed properly from CellDesigner files
   * Bug fix: structural states of proteins are imported properly from SBGNML PD

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

@@ -62,7 +62,7 @@ public class CellDesignerXmlParser extends Converter {
   /**
    * Default class logger.
    */
-  private static Logger logger = LogManager.getLogger(CellDesignerXmlParser.class.getName());
+  private static Logger logger = LogManager.getLogger();
 
   /**
    * CellDesigner parser for layers.
@@ -89,8 +89,11 @@ public class CellDesignerXmlParser extends Converter {
    */
   private RestAnnotationParser rap = new RestAnnotationParser();
 
+  private boolean oldCellDesignerVersion;
+
   @Override
   public Model createModel(ConverterParams params) throws InvalidInputDataExecption {
+    oldCellDesignerVersion = false;
     CellDesignerElementCollection elements = new CellDesignerElementCollection();
     FunctionCollectionXmlParser functionParser = new FunctionCollectionXmlParser();
     UnitCollectionXmlParser unitParser = new UnitCollectionXmlParser();
@@ -213,7 +216,7 @@ public class CellDesignerXmlParser extends Converter {
 
       if (reactionsNode != null) {
         ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements,
-            params.isSbgnFormat());
+            params.isSbgnFormat(), oldCellDesignerVersion);
         List<Reaction> reactions = reactionCollectionXmlParser.parseXmlReactionCollection(reactionsNode);
         model.addReactions(reactions);
       }
@@ -376,7 +379,11 @@ public class CellDesignerXmlParser extends Converter {
           model.addAuthors(xmlAnnotationParser.getAuthorsFromRdf(node));
           model.setCreationDate(xmlAnnotationParser.getCreateDateFromRdf(node));
           model.addModificationDates(xmlAnnotationParser.getModificationDatesFromRdf(node));
-        } else {
+        } else if (node.getNodeName().equalsIgnoreCase("celldesigner:modelVersion")) {
+          logger.warn("Old version of cell designer found: " + XmlParser.getNodeValue(node));
+          oldCellDesignerVersion = true;
+          extensionNode = annotationNode;
+        } else if (!oldCellDesignerVersion) {
           throw new InvalidXmlSchemaException("Unknown element of annotation: " + node.getNodeName());
         }
       }
@@ -601,8 +608,9 @@ public class CellDesignerXmlParser extends Converter {
     try {
       CellDesignerElementCollection elements = new CellDesignerElementCollection();
 
-      SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements, model.getUnits());
-      ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, false);
+      SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements,
+          model.getUnits());
+      ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, false, oldCellDesignerVersion);
       UnitCollectionXmlParser unitCollectionXmlParser = new UnitCollectionXmlParser();
       FunctionCollectionXmlParser functionCollectionXmlParser = new FunctionCollectionXmlParser();
       ParameterCollectionXmlParser parameterCollectionXmlParser = new ParameterCollectionXmlParser(model);

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java

@@ -53,9 +53,10 @@ public class ReactionCollectionXmlParser {
    * @param model
    *          model that is parsed/transformed into xml
    */
-  public ReactionCollectionXmlParser(Model model, CellDesignerElementCollection elements, boolean sbgn) {
+  public ReactionCollectionXmlParser(Model model, CellDesignerElementCollection elements, boolean sbgn,
+      boolean oldCellDesignerVersion) {
     this.model = model;
-    xmlStructureFactory = new ReactionXmlParser(elements, sbgn);
+    xmlStructureFactory = new ReactionXmlParser(elements, sbgn, oldCellDesignerVersion);
   }
 
   /**

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXml.java

@@ -96,15 +96,18 @@ public class ReactionFromXml {
    */
   private boolean sbgn;
 
+  private boolean oldCellDesignerVersion;
+
   /**
    * Default constructor.
    * 
    * @param sbgn
    *          Should the converter use SBGN standard
    */
-  public ReactionFromXml(CellDesignerElementCollection elements, boolean sbgn) {
+  public ReactionFromXml(CellDesignerElementCollection elements, boolean sbgn, boolean oldCellDesignerVersion) {
     this.elements = elements;
     this.sbgn = sbgn;
+    this.oldCellDesignerVersion = oldCellDesignerVersion;
   }
 
   /**
@@ -276,6 +279,9 @@ public class ReactionFromXml {
   private Reaction parseReactionAnnotation(Node annotationNode, Reaction result, Model model)
       throws ReactionParserException {
     NodeList nodes = annotationNode.getChildNodes();
+    if (oldCellDesignerVersion) {
+      result = parseReactionExtension(result, annotationNode, model);
+    }
     for (int x = 0; x < nodes.getLength(); x++) {
       Node node = nodes.item(x);
       if (node.getNodeType() == Node.ELEMENT_NODE) {
@@ -288,11 +294,12 @@ public class ReactionFromXml {
           } catch (InvalidXmlSchemaException e) {
             throw new ReactionParserException("Problem with parsing RDF", result, e);
           }
-        } else {
+        } else if (!oldCellDesignerVersion) {
           throw new ReactionParserException("Unknown element of reaction/annotation: " + node.getNodeName(), result);
         }
       }
     }
+
     return result;
   }
 
@@ -409,7 +416,7 @@ public class ReactionFromXml {
       }
       applyStylingToLine(line, result.getLine());
 
-      if (booleanLogicGateType!=null) {
+      if (booleanLogicGateType != null) {
         assignColorFromGateMembers(result, gateMembers);
       }
       if (reactantsLinkNode != null) {
@@ -954,7 +961,7 @@ public class ReactionFromXml {
                 polylines.add(result.getReactants().get(elementIndex - 1).getLine());
               }
             }
-            for (PolylineData polyline: polylines) {
+            for (PolylineData polyline : polylines) {
               polyline.setColor(line.getColor());
               polyline.setWidth(line.getWidth());
             }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionXmlParser.java

@@ -39,9 +39,9 @@ public class ReactionXmlParser {
    *          collection of {@link CellDesignerElement cell designer elements}
    *          parsed from xml
    */
-  public ReactionXmlParser(CellDesignerElementCollection elements, boolean sbgn) {
+  public ReactionXmlParser(CellDesignerElementCollection elements, boolean sbgn, boolean oldCellDesignerVersion) {
     reactionToXml = new ReactionToXml(elements, sbgn);
-    reactionFromXml = new ReactionFromXml(elements, sbgn);
+    reactionFromXml = new ReactionFromXml(elements, sbgn, oldCellDesignerVersion);
   }
 
   /**

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/species/SpeciesSbmlParser.java

@@ -88,6 +88,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
     list = annotationNode.getChildNodes();
     Node extensionNode = null;
     Node rdfNode = null;
+    Node speciesIdentity = null;
+    Node positionToCompartment = null;
 
     for (int i = 0; i < list.getLength(); i++) {
       Node node = list.item(i);
@@ -96,36 +98,45 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
           extensionNode = node;
         } else if (node.getNodeName().equals("rdf:RDF")) {
           rdfNode = node;
-        } else {
-          throw new InvalidXmlSchemaException("Unknown element of annotation " + node.getNodeName());
-        }
-      }
-    }
-
-    if (extensionNode == null) {
-      throw new InvalidXmlSchemaException(
-          "No celldesigner:extension node in SBML/model/listOfSpecies/species/annotation");
-    }
-
-    list = extensionNode.getChildNodes();
-    Node speciesIdentity = null;
-    Node positionToCompartment = null;
-    for (int i = 0; i < list.getLength(); i++) {
-      Node node = list.item(i);
-      if (node.getNodeType() == Node.ELEMENT_NODE) {
-        if (node.getNodeName().equals("celldesigner:speciesIdentity")) {
-          speciesIdentity = node;
         } else if (node.getNodeName().equals("celldesigner:positionToCompartment")) {
           positionToCompartment = node;
+        } else if (node.getNodeName().equals("celldesigner:speciesIdentity")) {
+          speciesIdentity = node;
         } else if (node.getNodeName().equals("celldesigner:listOfCatalyzedReactions")) {
           // we can ignore it - every node on the map contains information about
           // itself
           continue;
         } else {
-          throw new InvalidXmlSchemaException("[" + XmlParser.getNodeAttr("id", spieciesNode)
-              + "]\tUnknown element of celldesigner:extension " + node.getNodeName());
+          logger.debug(XmlParser.nodeToString(spieciesNode, true));
+          throw new InvalidXmlSchemaException("Unknown element of annotation " + node.getNodeName());
+        }
+      }
+    }
+
+    if (extensionNode != null) {
+      list = extensionNode.getChildNodes();
+      for (int i = 0; i < list.getLength(); i++) {
+        Node node = list.item(i);
+        if (node.getNodeType() == Node.ELEMENT_NODE) {
+          if (node.getNodeName().equals("celldesigner:speciesIdentity")) {
+            speciesIdentity = node;
+          } else if (node.getNodeName().equals("celldesigner:positionToCompartment")) {
+            positionToCompartment = node;
+          } else if (node.getNodeName().equals("celldesigner:listOfCatalyzedReactions")) {
+            // we can ignore it - every node on the map contains information about
+            // itself
+            continue;
+          } else {
+            throw new InvalidXmlSchemaException("[" + XmlParser.getNodeAttr("id", spieciesNode)
+                + "]\tUnknown element of celldesigner:extension " + node.getNodeName());
+          }
         }
       }
+    } else {
+      if (speciesIdentity == null) { // speciesIdentity was placed in the parent node in CD 2.5
+        throw new InvalidXmlSchemaException(
+            "No celldesigner:extension node in SBML/model/listOfSpecies/species/annotation");
+      }
     }
 
     if (speciesIdentity == null) {
@@ -213,7 +224,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
     }
     if (species.getSubstanceUnits() != null) {
       if (species.getSubstanceUnits() instanceof SbmlUnit) {
-        attributesBuilder.append(" substanceUnits=\"" + ((SbmlUnit)species.getSubstanceUnits()).getUnitId().toLowerCase() + "\"");
+        attributesBuilder
+            .append(" substanceUnits=\"" + ((SbmlUnit) species.getSubstanceUnits()).getUnitId().toLowerCase() + "\"");
       } else {
         attributesBuilder.append(" substanceUnits=\"" + species.getSubstanceUnits().toString().toLowerCase() + "\"");
       }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/types/ModifierType.java

@@ -48,7 +48,20 @@ public enum ModifierType {
   /**
    * Trigger.
    */
-  TRIGGER_STRING("TRIGGER", Trigger.class, ArrowType.BLANK_CROSSBAR);
+  TRIGGER_STRING("TRIGGER", Trigger.class, ArrowType.BLANK_CROSSBAR),
+  
+  /**
+   * CellDesigner 2.5 modification type.
+   */
+  TRANSCRIPTIONAL_ACTIVATION("TRANSCRIPTIONAL_ACTIVATION", Trigger.class, ArrowType.BLANK_CROSSBAR),
+  
+  /**
+   * CellDesigner 2.5 modification type.
+   */
+  TRANSCRIPTIONAL_INHIBITION("TRANSCRIPTIONAL_INHIBITION", Inhibition.class, ArrowType.CROSSBAR, 8.0, ReactionCellDesignerConverter.RECT_SIZE / 2 - 1),
+
+  
+  ;
 
   /**
    * CellDesigner string describing this type.

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

@@ -78,6 +78,16 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
     super.testXmlSerialization(model);
   }
 
+  @Test
+  public void testCellDesigner2_5() throws Exception {
+    CellDesignerXmlParser parser = new CellDesignerXmlParser();
+    Model model = parser
+        .createModel(new ConverterParams().filename("testFiles/problematic/MYO_signaling_pathway.xml")
+            .sizeAutoAdjust(false));
+    assertNotNull(model);
+    super.testXmlSerialization(model);
+  }
+
   @Test
   public void testUnknownCatalysisWithGate() throws Exception {
     CellDesignerXmlParser parser = new CellDesignerXmlParser();

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParserTest.java

@@ -36,7 +36,7 @@ public class ReactionCollectionXmlParserTest extends CellDesignerTestFunctions {
       Model model = getModelFilledWithSpecies();
 
       CellDesignerElementCollection elements = new CellDesignerElementCollection();
-      ReactionCollectionXmlParser parser = new ReactionCollectionXmlParser(model, elements, false);
+      ReactionCollectionXmlParser parser = new ReactionCollectionXmlParser(model, elements, false, false);
 
       String xmlString = readFile("testFiles/reactions/listOfReactions.xml");
       Node node = getNodeFromXmlString(xmlString);
@@ -56,19 +56,19 @@ public class ReactionCollectionXmlParserTest extends CellDesignerTestFunctions {
       Model model = getModelFilledWithSpecies();
 
       CellDesignerElementCollection elements = new CellDesignerElementCollection();
-      ReactionCollectionXmlParser parser = new ReactionCollectionXmlParser(model, elements, false);
+      ReactionCollectionXmlParser parser = new ReactionCollectionXmlParser(model, elements, false, false);
 
       String xmlString = readFile("testFiles/reactions/listOfReactions.xml");
       Node node = getNodeFromXmlString(xmlString);
       List<Reaction> reactions = parser.parseXmlReactionCollection(node);
 
       elements = new CellDesignerElementCollection();
-      parser = new ReactionCollectionXmlParser(model, elements, false);
+      parser = new ReactionCollectionXmlParser(model, elements, false, false);
       String xmlString2 = parser.reactionCollectionToXmlString(reactions);
       assertNotNull(xmlString2);
 
       elements = new CellDesignerElementCollection();
-      parser = new ReactionCollectionXmlParser(model, elements, false);
+      parser = new ReactionCollectionXmlParser(model, elements, false, false);
       node = getNodeFromXmlString(xmlString2);
       List<Reaction> reactions2 = parser.parseXmlReactionCollection(node);
 

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionFromXmlTest.java

@@ -27,7 +27,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
   @Before
   public void setUp() throws Exception {
     elements = new CellDesignerElementCollection();
-    parser = new ReactionXmlParser(elements, false);
+    parser = new ReactionXmlParser(elements, false, false);
 
     Species alias = new GenericProtein("sa1");
     model.addElement(alias);
@@ -195,7 +195,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
   public void testInvalidReaction() throws Exception {
     // test situation when createProperTypeReaction returns reaction of
     // unknown type
-    ReactionFromXml parser = new ReactionFromXml(null, false) {
+    ReactionFromXml parser = new ReactionFromXml(null, false, false) {
       Reaction createProperTypeReaction(String type, Reaction result) {
         return result;
       }
@@ -209,7 +209,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
     // test situation when createProperTypeReaction returns reaction of
     // unknown type that implements TwoProductReactionInterface
 
-    ReactionFromXml parser = new ReactionFromXml(null, false) {
+    ReactionFromXml parser = new ReactionFromXml(null, false, false) {
       Reaction createProperTypeReaction(String type, Reaction reaction) {
         Reaction result = Mockito.mock(Reaction.class,
             Mockito.withSettings().extraInterfaces(TwoProductReactionInterface.class));
@@ -229,7 +229,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
     // test situation when createOperatorsForTwoProductReaction encounter
     // reaction with two many base reactants
 
-    ReactionFromXml parser = new ReactionFromXml(null, false) {
+    ReactionFromXml parser = new ReactionFromXml(null, false, false) {
       Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
         Reaction r = super.createProperTypeReaction(type, result);
         r.addReactant(new Reactant());
@@ -246,7 +246,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
     // test situation when createOperatorsForTwoProductReaction encounter
     // reaction with two many base products
 
-    ReactionFromXml parser = new ReactionFromXml(null, false) {
+    ReactionFromXml parser = new ReactionFromXml(null, false, false) {
       Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
         Reaction r = super.createProperTypeReaction(type, result);
         r.addProduct(new Product());
@@ -263,7 +263,7 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
     // test situation when createOperatorsForTwoReactantReaction encounter
     // reaction with two many base products
 
-    ReactionFromXml parser = new ReactionFromXml(null, false) {
+    ReactionFromXml parser = new ReactionFromXml(null, false, false) {
       Reaction createProperTypeReaction(String type, Reaction result) throws ReactionParserException {
         Reaction r = super.createProperTypeReaction(type, result);
         r.addProduct(new Product());
@@ -276,14 +276,14 @@ public class ReactionFromXmlTest extends CellDesignerTestFunctions {
 
   @Test(expected = InvalidArgumentException.class)
   public void testParseInvalidEditPointsString() throws Exception {
-    ReactionFromXml parser = new ReactionFromXml(null, false);
+    ReactionFromXml parser = new ReactionFromXml(null, false, false);
 
     parser.parseEditPointsString("1");
   }
 
   @Test(expected = InvalidArgumentException.class)
   public void testParseInvalidEditPointsString2() throws Exception {
-    ReactionFromXml parser = new ReactionFromXml(null, false);
+    ReactionFromXml parser = new ReactionFromXml(null, false, false);
 
     parser.parseEditPointsString("1,Infinity");
   }