Add parseGenes option to FBCparser

The parsing of the gene association is often the most time consuming step of the sbml reading.
Setting the parseGenes option to false allows not to parse genes when it's not useful

met4j-io/src/main/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/plugin/FBCParser.java

@@ -91,6 +91,11 @@ public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Comp
 	 */
 	public FBCModelPlugin fbcModel;
 
+	/**
+	 * Indicates if the genes are parsed or not
+	 */
+	public Boolean parseGenes = true;
+
 	/** {@inheritDoc} */
 	@Override
 	public String getAssociatedPackageName() {
@@ -103,6 +108,17 @@ public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Comp
 		return model.isPackageURIEnabled(PackageNamespace);
 	}
 
+
+	public FBCParser(Boolean parseGenes) {
+
+        this.parseGenes = parseGenes;
+    }
+
+	public FBCParser() {
+
+		this.parseGenes = true;
+	}
+
 	/**
 	 * {@inheritDoc}
 	 *
@@ -129,7 +145,10 @@ public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Comp
 		this.setStrictFromFbcModel();
 
 		this.parseParameters();
-		this.parseListOfGeneProducts();
+
+		if(parseGenes) {
+			this.parseListOfGeneProducts();
+		}
 		try {
 			this.parseFluxReactions();
 		} catch (GeneSetException | Met4jSbmlReaderException e) {
@@ -239,7 +258,7 @@ public class FBCParser implements PackageParser, PrimaryDataTag, ReaderSBML3Comp
 			GeneAssociation geneAssociation = new GeneAssociation();
 
 			// System.err.println(rxn.getId());
-			if (rxnPlugin.isSetGeneProductAssociation()) {
+			if (parseGenes && rxnPlugin.isSetGeneProductAssociation()) {
 				geneAssociation = this.computeGeneAssocations(rxnPlugin.getGeneProductAssociation().getAssociation());
 			}
 			// System.err.println("out of recursion");

met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/JsbmlReaderTest.java

@@ -37,11 +37,15 @@
 package fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader;
 
 import fr.inrae.toulouse.metexplore.met4j_core.biodata.BioNetwork;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.FBCParser;
+import fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader.plugin.PackageParser;
 import org.junit.Test;
 import org.sbml.jsbml.SBMLDocument;
 
 import javax.xml.stream.XMLStreamException;
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
 
 import static org.junit.Assert.*;
 import static org.mockito.Mockito.doReturn;
@@ -65,10 +69,33 @@ public class JsbmlReaderTest {
 
         assertEquals(3, network.getReactionsView().size());
 
+        assertEquals(2, network.getGenesView().size());
+
         // Other tests are done on JsbmlToBioNetwork
 
     }
 
+    @Test
+    public void readWithoutGenes() throws IOException, XMLStreamException, Met4jSbmlReaderException {
+
+        JsbmlReader reader = spy(new JsbmlReader("test"));
+
+        SbmlDocMock docMockGenerator  = new SbmlDocMock();
+        SBMLDocument doc = docMockGenerator.doc;
+
+        doReturn(doc).when(reader).sbmlRead();
+
+        BioNetwork network = reader.read(new ArrayList<PackageParser>(Arrays.asList(new FBCParser(false))));
+
+        assertNotNull(network);
+
+        assertEquals(3, network.getReactionsView().size());
+
+        assertEquals(0, network.getGenesView().size());
+
+
+    }
+
     @Test
     public void readWithoutNotes() throws IOException, XMLStreamException, Met4jSbmlReaderException {
         JsbmlReader reader = spy(new JsbmlReader("test"));

met4j-io/src/test/java/fr/inrae/toulouse/metexplore/met4j_io/jsbml/reader/SbmlDocMock.java

@@ -35,9 +35,13 @@
  */
 package fr.inrae.toulouse.metexplore.met4j_io.jsbml.reader;
 
+import fr.inrae.toulouse.metexplore.met4j_io.utils.StringUtils;
 import org.sbml.jsbml.*;
+import org.sbml.jsbml.ext.fbc.*;
 
 import javax.xml.stream.XMLStreamException;
+import java.util.ArrayList;
+import java.util.List;
 
 public class SbmlDocMock {
 
@@ -51,7 +55,7 @@ public class SbmlDocMock {
 
     public SbmlDocMock() {
 
-        doc = new SBMLDocument(3, 1);
+        doc = new SBMLDocument(3, 2);
 
         model = doc.createModel();
 
@@ -83,6 +87,21 @@ public class SbmlDocMock {
         m1.setInitialAmount(2.0);
         m2.setInitialAmount(3.0);
 
+        // Create genes
+        FBCModelPlugin fbcModel = (FBCModelPlugin)  model.getPlugin("http://www.sbml.org/sbml/level3/version1/fbc/version2");
+        GeneProduct gene1 = fbcModel.createGeneProduct();
+        gene1.setId("g1");
+        gene1.setName("g1");
+        gene1.setLabel("g1");
+
+        fbcModel.addGeneProduct(gene1);
+
+        GeneProduct gene2 = fbcModel.createGeneProduct();
+        gene2.setId("g2");
+        gene2.setName("g2");
+        gene2.setLabel("g2");
+
+        fbcModel.addGeneProduct(gene2);
 
         r1 = model.createReaction("r1");
         r1.setName("name1");
@@ -90,8 +109,22 @@ public class SbmlDocMock {
 
         r1.setSBOTerm("SBO:0000167");
 
+        GeneProductRef geneRef1 = new GeneProductRef();
+        geneRef1.setGeneProduct(StringUtils.convertToSID("g1"));
+
+        FBCReactionPlugin rxnPlugin = (FBCReactionPlugin) r1.getPlugin("fbc");
+        GeneProductAssociation GPA = rxnPlugin.createGeneProductAssociation();
+        GPA.setAssociation(geneRef1);
+
         r2 = model.createReaction("r2");
 
+        GeneProductRef geneRef2 = new GeneProductRef();
+        geneRef2.setGeneProduct(StringUtils.convertToSID("g2"));
+
+        FBCReactionPlugin rxn2Plugin = (FBCReactionPlugin) r2.getPlugin("fbc");
+        GeneProductAssociation GPA2 = rxnPlugin.createGeneProductAssociation();
+        GPA.setAssociation(geneRef2);
+
         SpeciesReference m1Ref = new SpeciesReference(m1);
         m1Ref.setStoichiometry(2.0);