recognition of reduced notation is done over proper java interface

CHANGELOG

@@ -25,6 +25,8 @@ minerva (15.1.0) unstable; urgency=medium
     index
   * Small improvement: pathways with glyphs and z index below 0 are not
     clickable (#1314)
+  * Small improvement: Modifier Reaction from CellDesigner are exported properly
+    to SBGN-ML PD (#1320)
   * Bug fix: export to image from selected polygon contained all elements
     inside rectangle bounded by the polygon coordinates (#1096)
   * Bug fix: continuous refreshing list of project when uploading/removing

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

@@ -139,18 +139,21 @@ public class SbgnmlXmlExporter {
 
     for (Reaction reaction : model.getReactions()) {
       try {
-        map.getGlyph().add(getProcessGlyphFromReaction(reaction));
-      } catch (InvalidArgumentException ex) {
-        // Reduced notation
-        try {
-          map.getArc().add(getArcFromReducedReaction(reaction));
-        } catch (InvalidArgumentException e) {
-          logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction), "Invalid arc type."
-              + " Reduced notation reaction found of type that is not compliant with SBGN-ML format.");
+        Glyph glyph = getProcessGlyphFromReaction(reaction);
+        if (glyph != null) {
+          map.getGlyph().add(glyph);
+          map.getArc().addAll(getArcsFromReaction(reaction, map.getGlyph()));
+        } else {
+          Arc arc = getArcFromReducedReaction(reaction);
+          if (arc != null) {
+            map.getArc().add(arc);
+          }
         }
-        continue;
+      } catch (Exception ex) {
+        ex.printStackTrace();
+        logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction),
+            "Unexpected problem with exporting reaction.");
       }
-      map.getArc().addAll(getArcsFromReaction(reaction, map.getGlyph()));
     }
     try {
       RenderUtil.setRenderInformation(map, renderInformation);
@@ -599,7 +602,11 @@ public class SbgnmlXmlExporter {
   private Glyph getProcessGlyphFromReaction(Reaction reaction) {
     Glyph processGlyph = new Glyph();
     processGlyph.setId(reaction.getIdReaction());
-    processGlyph.setClazz(getGlyphClazzFromReaction(reaction).getClazz());
+    GlyphClazz clazz = getGlyphClazzFromReaction(reaction);
+    if (clazz == null) {
+      return null;
+    }
+    processGlyph.setClazz(clazz.getClazz());
     Bbox bbox = new Bbox();
 
     PolylineData line = reaction.getLine();
@@ -708,12 +715,6 @@ public class SbgnmlXmlExporter {
    * @return {@link GlyphClazz} appropriate to given reaction
    */
   private GlyphClazz getGlyphClazzFromReaction(Reaction reaction) {
-    if (reaction instanceof StateTransitionReaction ||
-        reaction instanceof TransportReaction ||
-        reaction instanceof TranslationReaction ||
-        reaction instanceof TranscriptionReaction) {
-      return GlyphClazz.PROCESS;
-    }
     if (reaction instanceof HeterodimerAssociationReaction) {
       return GlyphClazz.ASSOCIATION;
     }
@@ -726,7 +727,10 @@ public class SbgnmlXmlExporter {
     if (reaction instanceof UnknownTransitionReaction) {
       return GlyphClazz.UNCERTAIN_PROCESS;
     }
-    throw new InvalidArgumentException();
+    if (reaction instanceof ReducedNotation) {
+      return null;
+    }
+    return GlyphClazz.PROCESS;
   }
 
   /**
@@ -738,7 +742,9 @@ public class SbgnmlXmlExporter {
    */
   private Arc getArcFromReducedReaction(Reaction reaction) {
     if ((reaction.getReactants().size() != 1) || (reaction.getProducts().size() != 1)) {
-      throw new InvalidArgumentException();
+      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction),
+          "Reduced notation does not allow to have multiple reactants/products. Reaction skipped");
+      return null;
     }
     Arc arc = new Arc();
     arc.setId(reaction.getIdReaction());
@@ -752,7 +758,9 @@ public class SbgnmlXmlExporter {
     } else if (reaction instanceof ReducedPhysicalStimulationReaction) {
       arc.setClazz(ArcClazz.STIMULATION.getClazz());
     } else {
-      throw new InvalidArgumentException();
+      logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction), "Invalid arc type."
+          + " Reduced notation reaction found of type that is not compliant with SBGN-ML format.");
+      return null;
     }
 
     if (reaction.getProducts().get(0).getElement() instanceof Phenotype) {
@@ -941,7 +949,8 @@ public class SbgnmlXmlExporter {
         }
       }
     } else if (node instanceof NodeOperator) {
-      if ((node instanceof DissociationOperator) || (node instanceof AssociationOperator)) {
+      if ((node instanceof DissociationOperator) || (node instanceof AssociationOperator)
+          || (node instanceof TruncationOperator)) {
         throw new InvalidArgumentException();
       }
       arc.setSource(sourceTargetMap.get(operatorIds.get(node).concat(".2")));

model/src/main/java/lcsb/mapviewer/model/map/reaction/type/ReducedNotation.java

@@ -4,7 +4,7 @@ package lcsb.mapviewer.model.map.reaction.type;
  * 
  * Interface used for marking {@link lcsb.mapviewer.model.map.reaction.Reaction
  * Reaction} extensions that implements reduced notation in CellDesigner. These
- * classes should have more than one reactant and product and cannot have any
+ * classes should have no more than one reactant and product and cannot have any
  * modifiers.
  * 
  * @author Piotr Gawron