empty kinetic law was throwing an exception

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

@@ -431,7 +431,11 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
     reaction.setIdReaction(sbmlReaction.getId());
     reaction.setReversible(sbmlReaction.isReversible());
     if (sbmlReaction.getKineticLaw() != null) {
-      reaction.setKinetics(createMinervaKinetics(sbmlReaction.getKineticLaw()));
+      if (sbmlReaction.getKineticLaw().getMath() == null) {
+        logger.warn(eu.getElementTag(reaction) + "Reaction contains empty kinetic law.");
+      } else {
+        reaction.setKinetics(createMinervaKinetics(sbmlReaction.getKineticLaw()));
+      }
     }
     for (SpeciesReference reactant : sbmlReaction.getListOfReactants()) {
       Species element = minervaModel.getElementByElementId(reactant.getSpecies());

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

@@ -233,4 +233,19 @@ public class SbmlReactionParserTest {
     }
   }
 
+  @Test
+  public void testParseReactionWithEmptyKinetics() throws Exception {
+    try {
+      Model model = parser
+          .createModel(new ConverterParams()
+              .filename("testFiles/small/reaction/reaction_with_empty_kinetics.xml"));
+      Reaction reaction = model.getReactions().iterator().next();
+      assertNotNull(reaction);
+      assertTrue(reaction instanceof Reaction);
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
 }

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

+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" version="1">
+	<model>
+		<notes>
+		</notes>
+		<annotation>
+		</annotation>
+		<listOfUnitDefinitions>
+			<unitDefinition id="substance" metaid="metaid_0000023"
+				name="micromole (default)">
+				<notes>
+				</notes>
+				<listOfUnits>
+					<unit kind="mole" metaid="_289328" scale="-6" />
+				</listOfUnits>
+			</unitDefinition>
+			<unitDefinition id="time" metaid="metaid_0000024"
+				name="heure (default)">
+				<notes>
+				</notes>
+				<listOfUnits>
+					<unit kind="second" metaid="_289340" multiplier="3600" />
+				</listOfUnits>
+			</unitDefinition>
+		</listOfUnitDefinitions>
+		<listOfCompartments>
+			<compartment id="default" metaid="_741863" size="1E-15" />
+			<compartment id="CYTOPLASM" metaid="_741901"
+				outside="default" size="1E-15">
+			</compartment>
+			<compartment id="compartment_0000004"
+				metaid="metaid_0000026" name="NUCLEUS" outside="CYTOPLASM"
+				size="1E-15">
+			</compartment>
+		</listOfCompartments>
+		<listOfSpecies>
+			<species boundaryCondition="true" compartment="default"
+				constant="true" id="EmptySet" initialAmount="0" metaid="_741921">
+			</species>
+			<species compartment="CYTOPLASM" id="M"
+				initialConcentration="0.1" metaid="_741942" name="PER mRNA">
+			</species>
+			<species compartment="CYTOPLASM" id="P0"
+				initialConcentration="0.25" metaid="_741962"
+				name="unphosphorylated PER">
+			</species>
+			<species compartment="CYTOPLASM" id="P1"
+				initialConcentration="0.25" metaid="_741981"
+				name="monophosphorylated PER">
+			</species>
+			<species compartment="CYTOPLASM" id="P2"
+				initialConcentration="0.25" metaid="_742001"
+				name="biphosphorylated PER">
+			</species>
+			<species compartment="compartment_0000004" id="Pn"
+				initialConcentration="0.25" metaid="_742021" name="nuclear PER">
+			</species>
+			<species compartment="CYTOPLASM" id="Pt"
+				initialConcentration="1" metaid="_742041" name="total PER">
+			</species>
+		</listOfSpecies>
+		<listOfReactions>
+			<reaction id="rM" metaid="_742062"
+				name="transcription of PER" reversible="false">
+				<listOfReactants>
+					<speciesReference metaid="_289353"
+						species="EmptySet" />
+				</listOfReactants>
+				<listOfProducts>
+					<speciesReference metaid="_289365" species="M" />
+				</listOfProducts>
+				<listOfModifiers>
+					<modifierSpeciesReference metaid="_289377"
+						species="Pn" />
+				</listOfModifiers>
+				<kineticLaw />
+			</reaction>
+		</listOfReactions>
+	</model>
+</sbml>
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