diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
index e3614d5bb4eda32a71b24d0b6229cdde783a253e..3840b12cdd855ca3d7ed1a3a200387e9e36c3f8b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java
+++ b/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;
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index 8f1cc44b8194b62c33423b5ec454f01dc07e24e1..6904550a3b34d016817ade64be5903d96949fef7 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/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"));
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java
index f54fa31e7325844e2cb19c60ea7ee28d5b41604c..a5a64fa45128ca6f169bc1256ee616a0a94a2017 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParserTest.java
+++ b/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"));
diff --git a/converter-sbml/testFiles/small/reaction/heterodimer_association_with_single_reactant.xml b/converter-sbml/testFiles/small/reaction/heterodimer_association_with_single_reactant.xml
new file mode 100644
index 0000000000000000000000000000000000000000..de28ae0c8cd360aab3c5a5f5db276c0c4b17777f
--- /dev/null
+++ b/converter-sbml/testFiles/small/reaction/heterodimer_association_with_single_reactant.xml
@@ -0,0 +1,39 @@
+<?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
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/InvalidReactionParticipantNumberException.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/InvalidReactionParticipantNumberException.java
new file mode 100644
index 0000000000000000000000000000000000000000..95c6c52c4d90e86baecb46aa8be832aded5107ee
--- /dev/null
+++ b/model/src/main/java/lcsb/mapviewer/model/map/reaction/InvalidReactionParticipantNumberException.java
@@ -0,0 +1,59 @@
+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);
+ }
+
+}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java b/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
index afa12884c7f1c6e288744fdf1e3e4077ef2d7b0d..bcabc050f42a742757c05d55251d5b93a4a4ea52 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/reaction/Reaction.java
+++ b/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);
}
}