import from sbml could be problematic when provided layout placed two elements...

import from sbml could be problematic when provided layout placed two elements in exactly the same position

CHANGELOG

 minerva (12.2.0~beta.2) unstable; urgency=medium
+  * Bug fix: import from sbml with layout could crash when two elements 
+    occupied the exact same position (#717) 
   * Bug fix: overlays added via API couldn't be visualized after refresh (#718) 
   * Bug fix: Safari sometimes cached server responses and used wrong data, for 
     example in admin panel configuration tab (#719)

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

@@ -19,7 +19,6 @@ import org.sbml.jsbml.ext.SBasePlugin;
 import org.sbml.jsbml.ext.layout.Layout;
 import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
 import org.sbml.jsbml.ext.multi.MultiModelPlugin;
-import org.sbml.jsbml.ext.render.LocalStyle;
 
 import lcsb.mapviewer.commands.CommandExecutionException;
 import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
@@ -157,7 +156,7 @@ public class SbmlParser implements IConverter {
       if (element instanceof Complex && element != species) {
         Complex complex = (Complex) element;
         if (complex.getWidth() != 0 || complex.getHeight() != 0) {
-          if (complex.contains(species)) {
+          if (complex.contains(species) && complex.getSize() > species.getSize()) {
             if (result == null) {
               result = complex;
             } else if (result.getSize() > complex.getSize()) {

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

@@ -5,9 +5,10 @@ import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertNotNull;
 import static org.junit.Assert.assertTrue;
 
-import java.awt.Color;
 import java.io.FileNotFoundException;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Set;
 
 import org.apache.log4j.Logger;
 import org.apache.log4j.spi.LoggingEvent;
@@ -15,7 +16,7 @@ import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 
-import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.commands.CreateHierarchyCommand;
 import lcsb.mapviewer.common.EventStorageLoggerAppender;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
@@ -23,6 +24,7 @@ import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Gene;
 import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
@@ -199,9 +201,32 @@ public class SbmlParserTest {
 
   @Test
   public void testParseConflictingTypesFromMulti() throws Exception {
-    Model model = parser.createModel(new ConverterParams().filename("testFiles/multi_features/conflicting_species_type.xml"));
+    Model model = parser
+        .createModel(new ConverterParams().filename("testFiles/multi_features/conflicting_species_type.xml"));
     assertTrue(model.getElementByElementId("species_0") instanceof GenericProtein);
     assertEquals(1, getWarnings().size());
   }
 
+  @Test
+  public void testCyclicComplexes() throws Exception {
+    try {
+      Model model = parser.createModel(new ConverterParams().filename("testFiles/cyclic_complex.xml"));
+
+      new CreateHierarchyCommand(model, 8, 80).execute();
+
+      for (Species species : model.getSpeciesList()) {
+        Set<Element> parents = new HashSet<Element>();
+        while (species.getComplex() != null) {
+          assertFalse("Cyclic nesting", parents.contains(species.getComplex()));
+          species= species.getComplex();
+          parents.add(species);
+        }
+
+      }
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
 }