error reporting includes more info when there is a problem with exporting some elements to sbml

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityExporter.java

@@ -37,6 +37,7 @@ import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.sbml.jsbml.AbstractNamedSBase>
     extends XmlParser {
@@ -81,18 +82,28 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
 
   public void exportElements() throws InconsistentModelException {
     Collection<T> speciesList = getElementList();
-    for (T species : speciesList) {
-      S sbmlElement = getSbmlElement(species);
+    for (T bioEntity : speciesList) {
+      try {
+        S sbmlElement = getSbmlElement(bioEntity);
 
-      if (sbmlElementByElementId.get(species.getElementId()) != null) {
-        throw new InconsistentModelException("More than one species with id: " + species.getElementId());
+        if (sbmlElementByElementId.get(bioEntity.getElementId()) != null) {
+          throw new InconsistentModelException("More than one species with id: " + bioEntity.getElementId());
+        }
+        sbmlElementByElementId.put(bioEntity.getElementId(), sbmlElement);
+      } catch (Exception e) {
+        throw new InconsistentModelException(new ElementUtils().getElementTag(bioEntity) +
+            "Problem with exporting bioEntity", e);
       }
-      sbmlElementByElementId.put(species.getElementId(), sbmlElement);
     }
     if (isExtensionEnabled(SbmlExtension.LAYOUT)) {
-      for (T species : speciesList) {
-        AbstractReferenceGlyph elementGlyph = createGlyph(species);
-        sbmlGlyphByElementId.put(species.getElementId(), elementGlyph);
+      for (T bioEntity : speciesList) {
+        try {
+          AbstractReferenceGlyph elementGlyph = createGlyph(bioEntity);
+          sbmlGlyphByElementId.put(bioEntity.getElementId(), elementGlyph);
+        } catch (Exception e) {
+          throw new InconsistentModelException(new ElementUtils().getElementTag(bioEntity) +
+              "Problem with exporting bioEntity", e);
+        }
       }
     }
   }
@@ -294,7 +305,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     BoundingBox boundingBox = createBoundingBox(-2, 0, 4, 4);
     result.getGroup().setFill(getColorDefinition(Color.WHITE).getId());
     result.setBoundingBox(boundingBox);
-    Ellipse ellipse= new Ellipse();
+    Ellipse ellipse = new Ellipse();
     ellipse.setAbsoluteCx(false);
     ellipse.setAbsoluteCy(false);
     ellipse.setAbsoluteRx(true);
@@ -366,7 +377,7 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
     polygon.addElement(createRenderPoint(33, 100));
     polygon.addElement(createRenderPoint(33, 0));
     result.getGroup().addElement(polygon);
-    
+
     Polygon crossBar = new Polygon();
     crossBar.addElement(createRenderPoint(0, 0));
     crossBar.addElement(createRenderPoint(0, 100));
@@ -408,12 +419,11 @@ public abstract class SbmlBioEntityExporter<T extends BioEntity, S extends org.s
   }
 
   public void setProvideDefaults(boolean provideDefaults) {
-    this.provideDefaults= provideDefaults;
+    this.provideDefaults = provideDefaults;
   }
 
   protected boolean isProvideDefaults() {
     return provideDefaults;
   }
 
-
 }