when parsing sbml reaction with invalid number of reactant/products is...

when parsing sbml reaction with invalid number of reactant/products is encountered the default reaction type is used

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java

@@ -51,6 +51,7 @@ import lcsb.mapviewer.model.map.reaction.AbstractNode;
 import lcsb.mapviewer.model.map.reaction.AndOperator;
 import lcsb.mapviewer.model.map.reaction.AssociationOperator;
 import lcsb.mapviewer.model.map.reaction.DissociationOperator;
+import lcsb.mapviewer.model.map.reaction.InvalidReactionParticipantNumberException;
 import lcsb.mapviewer.model.map.reaction.Modifier;
 import lcsb.mapviewer.model.map.reaction.NodeOperator;
 import lcsb.mapviewer.model.map.reaction.Product;
@@ -453,14 +454,34 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
       }
     }
 
+    String sboTerm = sbmlReaction.getSBOTermID();
+
+    reaction = createProperReactionClassForSboTerm(reaction, sboTerm);
+
+    return reaction;
+  }
+
+  private Reaction createProperReactionClassForSboTerm(Reaction reaction, String sboTerm)
+      throws InvalidInputDataExecption {
+    Class<? extends Reaction> reactionClass = SBOTermReactionType.getTypeSBOTerm(sboTerm);
     try {
-      Class<? extends Reaction> reactionClass = SBOTermReactionType.getTypeSBOTerm(sbmlReaction.getSBOTermID());
       reaction = reactionClass.getConstructor(Reaction.class).newInstance(reaction);
     } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException
         | NoSuchMethodException | SecurityException e) {
-      throw new InvalidInputDataExecption("Problem with creating reaction", e);
+      if (e.getCause() instanceof InvalidReactionParticipantNumberException) {
+        try {
+          logger.warn(eu.getElementTag(reaction) + "SBO term indicated " + reactionClass.getSimpleName()
+              + " class. However number of reactants/products is insufficient for such class type. Using default.");
+          reactionClass = SBOTermReactionType.getTypeSBOTerm(null);
+          reaction = reactionClass.getConstructor(Reaction.class).newInstance(reaction);
+        } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException
+            | NoSuchMethodException | SecurityException e1) {
+          throw new InvalidInputDataExecption(eu.getElementTag(reaction) + "Problem with creating reaction", e);
+        }
+      } else {
+        throw new InvalidInputDataExecption(eu.getElementTag(reaction) + "Problem with creating reaction", e);
+      }
     }
-
     return reaction;
   }
 

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

@@ -159,6 +159,17 @@ public class SbmlParserTest {
         new ConverterParams().filename("testFiles/invalidReaction/reaction_with_missing_part_of_layout.xml"));
   }
 
+  @Test
+  public void test() throws Exception {
+    try {
+    parser.createModel(
+        new ConverterParams().filename("/home/gawi/Desktop/biomodels/BIOMD0000000001_url.xml"));
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testDefaultColors() throws Exception {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/default_colors.xml"));

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java

@@ -125,6 +125,21 @@ public class SbmlReactionParserTest {
     assertTrue(reaction instanceof HeterodimerAssociationReaction);
   }
 
+  @Test
+  public void testParseHeterodimerAssociationWithSingleReactant() throws Exception {
+    try {
+      Model model = parser
+          .createModel(new ConverterParams()
+              .filename("testFiles/small/reaction/heterodimer_association_with_single_reactant.xml"));
+      Reaction reaction = model.getReactions().iterator().next();
+      assertNotNull(reaction);
+      assertTrue(reaction instanceof Reaction);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testParseDissociation() throws FileNotFoundException, InvalidInputDataExecption {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/small/reaction/dissociation.xml"));

converter-sbml/testFiles/small/reaction/heterodimer_association_with_single_reactant.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+  <model id="TestGEN">
+    <annotation/>
+    <listOfCompartments>
+      <compartment constant="true" id="cell" name="cell" sboTerm="SBO:0000290" size="1">
+        <annotation>
+          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
+            <rdf:Description rdf:about="#">
+              <bqbiol:isVersionOf>
+                <rdf:Bag>
+                  <rdf:li rdf:resource="urn:miriam:obo.go:GO:0005623"/>
+                </rdf:Bag>
+              </bqbiol:isVersionOf>
+            </rdf:Description>
+          </rdf:RDF>
+        </annotation>
+      </compartment>
+    </listOfCompartments>
+    <listOfSpecies>
+      <species compartment="cell" initialConcentration="1" id="s1" name="nm1">
+        <annotation/>
+      </species>
+      <species compartment="cell" initialConcentration="1" id="s2" name="nm2">
+        <annotation/>
+      </species>
+    </listOfSpecies>
+    <listOfReactions>
+      <reaction id="re1" sboTerm="SBO:0000177">
+        <listOfReactants>
+          <speciesReference species="s1" stoichiometry="1"/>
+        </listOfReactants>
+        <listOfProducts>
+          <speciesReference species="s2" stoichiometry="1"/>
+        </listOfProducts>
+      </reaction>
+    </listOfReactions>
+  </model>
+</sbml>
\ No newline at end of file

model/src/main/java/lcsb/mapviewer/model/map/reaction/InvalidReactionParticipantNumberException.java

+package lcsb.mapviewer.model.map.reaction;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+
+/**
+ * Exception to be thrown when number of reactants or products is invalid when
+ * creating reaction.
+ * 
+ * @author Piotr Gawron
+ * 
+ */
+public class InvalidReactionParticipantNumberException extends InvalidArgumentException {
+  /**
+   * 
+   */
+  private static final long serialVersionUID = 1L;
+
+  /**
+   * Default constructor - initializes instance variable to unknown.
+   */
+
+  public InvalidReactionParticipantNumberException() {
+    super(); // call superclass constructor
+  }
+
+  /**
+   * Public constructor with parent exception that was caught.
+   * 
+   * @param e
+   *          parent exception
+   */
+
+  public InvalidReactionParticipantNumberException(final String e) {
+    super(e);
+  }
+
+  /**
+   * Public constructor with parent exception that was caught.
+   * 
+   * @param e
+   *          parent exception
+   */
+  public InvalidReactionParticipantNumberException(final Exception e) {
+    super(e);
+  }
+
+  /**
+   * Public constructor with parent exception that was caught.
+   * 
+   * @param message
+   *          exception message
+   * @param e
+   *          parent exception
+   */
+  public InvalidReactionParticipantNumberException(final String message, final Exception e) {
+    super(message, e);
+  }
+
+}

model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java

@@ -268,12 +268,12 @@ public class Reaction implements BioEntity {
       minProducts = 2;
     }
     if (original.getProducts().size() < minProducts) {
-      throw new InvalidArgumentException(new ElementUtils().getElementTag(original)
+      throw new InvalidReactionParticipantNumberException(new ElementUtils().getElementTag(original)
           + "Invalid source reaction: number of products must be at least " + minProducts);
     }
 
     if (original.getReactants().size() < minReactants) {
-      throw new InvalidArgumentException(new ElementUtils().getElementTag(original)
+      throw new InvalidReactionParticipantNumberException(new ElementUtils().getElementTag(original)
           + "Invalid source reaction: number of reactants must be at least " + minReactants);
     }
   }