Merge branch '1622-export-to-sbml' into 'devel_16.0.x'

Resolve "problem with jsbml"

See merge request !1409

CHANGELOG

@@ -13,6 +13,8 @@ minerva (16.0.6) stable; urgency=medium
   * Bug fix: when there is problem with loading data from minerva
     ("Load failed") suggestion about retrying before submitting error report is
     provided (#1623)
+  * Bug fix: export to SBML of model that contained compartment with
+    "default_compartment" id was crashing (#1622)
 
  -- Piotr Gawron <piotr.gawron@uni.lu>  Thu, 16 Dec 2021 11:00:00 +0200
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/compartment/SbmlCompartmentExporter.java

 package lcsb.mapviewer.converter.model.sbml.compartment;
 
-import java.util.*;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.sbml.jsbml.Model;
-import org.sbml.jsbml.ext.layout.*;
+import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.BoundingBox;
+import org.sbml.jsbml.ext.layout.CompartmentGlyph;
+import org.sbml.jsbml.ext.layout.Dimensions;
+import org.sbml.jsbml.ext.layout.Point;
 import org.sbml.jsbml.ext.multi.MultiCompartmentPlugin;
-import org.sbml.jsbml.ext.render.*;
+import org.sbml.jsbml.ext.render.Ellipse;
+import org.sbml.jsbml.ext.render.LocalStyle;
+import org.sbml.jsbml.ext.render.Rectangle;
+import org.sbml.jsbml.ext.render.RelAbsVector;
 
 import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
 import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
@@ -22,8 +31,8 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
   @SuppressWarnings("unused")
   private static Logger logger = LogManager.getLogger();
 
-  public SbmlCompartmentExporter(Model sbmlModel, lcsb.mapviewer.model.map.model.Model minervaModel,
-      Collection<SbmlExtension> sbmlExtensions) {
+  public SbmlCompartmentExporter(final Model sbmlModel, final lcsb.mapviewer.model.map.model.Model minervaModel,
+      final Collection<SbmlExtension> sbmlExtensions) {
     super(sbmlModel, minervaModel, sbmlExtensions);
   }
 
@@ -45,7 +54,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
   }
 
   @Override
-  public org.sbml.jsbml.Compartment createSbmlElement(Compartment element) throws InconsistentModelException {
+  public org.sbml.jsbml.Compartment createSbmlElement(final Compartment element) throws InconsistentModelException {
     org.sbml.jsbml.Compartment result;
     if (element == null || getElementId(element).equals("default")) {
       result = getSbmlModel().createCompartment("default");
@@ -65,7 +74,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
   }
 
   @Override
-  public org.sbml.jsbml.Compartment getSbmlElement(Compartment element) throws InconsistentModelException {
+  public org.sbml.jsbml.Compartment getSbmlElement(final Compartment element) throws InconsistentModelException {
     String mapKey = getSbmlIdKey(element);
     if (element == null && sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
       org.sbml.jsbml.Compartment sbmlElement = createSbmlElement(element);
@@ -75,7 +84,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
   }
 
   @Override
-  protected String getSbmlIdKey(Compartment compartment) {
+  protected String getSbmlIdKey(final Compartment compartment) {
     if (compartment == null || getElementId(compartment).equals("default")) {
       return "default";
     }
@@ -83,16 +92,20 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
   }
 
   @Override
-  protected AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId) {
+  protected AbstractReferenceGlyph createElementGlyph(final String sbmlCompartmentId, String glyphId) {
     if (sbmlCompartmentId.equals("default")) {
       glyphId = "default_compartment";
+      while (getMinervaModel().getElementByElementId(glyphId) != null ||
+          getMinervaModel().getReactionByReactionId(glyphId) != null) {
+        glyphId = "default_compartment_" + getNextId();
+      }
     }
     CompartmentGlyph result = getLayout().createCompartmentGlyph(glyphId, sbmlCompartmentId);
     return result;
   }
 
   @Override
-  protected LocalStyle createStyle(Compartment element) {
+  protected LocalStyle createStyle(final Compartment element) {
     LocalStyle style = super.createStyle(element);
     style.getGroup().setStrokeWidth(element.getThickness());
     style.getGroup().setFill(getColorDefinition(element.getFillColor()).getId());
@@ -119,7 +132,7 @@ public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, or
   }
 
   @Override
-  protected void assignLayoutToGlyph(Compartment element, AbstractReferenceGlyph speciesGlyph) {
+  protected void assignLayoutToGlyph(final Compartment element, final AbstractReferenceGlyph speciesGlyph) {
     if (getElementId(element).equals("default")) {
       BoundingBox boundingBox = new BoundingBox();
 

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java

@@ -770,4 +770,16 @@ public class SbmlExporterTest extends SbmlTestFunctions {
 
   }
 
+  @Test
+  public void testExportWithCompartmentWithProblematicId() throws Exception {
+    Model model = createEmptyModel();
+
+    Compartment defaultCompartment = createCompartment();
+    defaultCompartment.setElementId("default_compartment");
+    model.addElement(defaultCompartment);
+
+    exporter.toXml(model);
+
+  }
+
 }