parsing type from species type SBO term added

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

@@ -14,6 +14,7 @@ import org.sbml.jsbml.Annotation;
 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.LocalRenderInformation;
 import org.sbml.jsbml.ext.render.LocalStyle;
 import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
@@ -52,15 +53,17 @@ public class SbmlBioEntityParser extends XmlParser {
   private lcsb.mapviewer.model.map.model.Model minervaModel;
 
   /**
-   * Counter for identifiers that cannot be inferred from SBML. 
+   * Counter for identifiers that cannot be inferred from SBML.
    */
   private int idCounter = 0;
 
   /**
    * Default constructor.
    * 
-   * @param sbmlModel SBML model that we are parsing
-   * @param minervaModel Minerva model to which we are extracting data
+   * @param sbmlModel
+   *          SBML model that we are parsing
+   * @param minervaModel
+   *          Minerva model to which we are extracting data
    */
   public SbmlBioEntityParser(org.sbml.jsbml.Model sbmlModel, Model minervaModel) {
     super();
@@ -222,4 +225,8 @@ public class SbmlBioEntityParser extends XmlParser {
     return layout;
   }
 
+  protected MultiModelPlugin getMultiPlugin() {
+    return (MultiModelPlugin) sbmlModel.getExtension("multi");
+  }
+
 }
\ No newline at end of file

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesParser.java

@@ -10,6 +10,8 @@ import org.sbml.jsbml.Model;
 import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
 import org.sbml.jsbml.ext.layout.CompartmentGlyph;
 import org.sbml.jsbml.ext.layout.SpeciesGlyph;
+import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
+import org.sbml.jsbml.ext.multi.MultiSpeciesType;
 import org.sbml.jsbml.ext.render.LocalStyle;
 
 import lcsb.mapviewer.common.Pair;
@@ -35,6 +37,19 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
   @Override
   protected Species parse(org.sbml.jsbml.Species species) throws InvalidInputDataExecption {
     String sboTerm = species.getSBOTermID();
+    MultiSpeciesPlugin multiExtension = (MultiSpeciesPlugin) species.getExtension("multi");
+    if (multiExtension != null) {
+      MultiSpeciesType speciesType = getMultiPlugin().getListOfSpeciesTypes().get(multiExtension.getSpeciesType());
+      if (speciesType != null) {
+        String sboTerm2 = speciesType.getSBOTermID();
+        if (sboTerm != null && !sboTerm.isEmpty() && !sboTerm2.equals(sboTerm)) {
+          logger.warn("Different SBO terms defining species and speciesType: " + species.getId() + ". " + sboTerm + ";"
+              + sboTerm2);
+        } else {
+          sboTerm = sboTerm2;
+        }
+      }
+    }
     Class<? extends Species> clazz = SBOTermSpeciesType.getTypeSBOTerm(sboTerm);
     try {
       Species result = clazz.getConstructor(String.class).newInstance(species.getId());

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

@@ -7,23 +7,48 @@ import static org.junit.Assert.assertTrue;
 
 import java.awt.Color;
 import java.io.FileNotFoundException;
+import java.util.List;
 
 import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
+import org.junit.After;
+import org.junit.Before;
 import org.junit.Test;
 
 import lcsb.mapviewer.common.Configuration;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 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.Gene;
+import lcsb.mapviewer.model.map.species.GenericProtein;
 import lcsb.mapviewer.model.map.species.Species;
 
 public class SbmlParserTest {
   Logger logger = Logger.getLogger(SbmlParserTest.class);
   SbmlParser parser = new SbmlParser();
 
+  private EventStorageLoggerAppender appender;
+
+  @Before
+  public final void _setUp() throws Exception {
+    Logger.getRootLogger().removeAppender(appender);
+    appender = new EventStorageLoggerAppender();
+    Logger.getRootLogger().addAppender(appender);
+  }
+
+  @After
+  public final void _tearDown() throws Exception {
+    Logger.getRootLogger().removeAppender(appender);
+  }
+
+  protected List<LoggingEvent> getWarnings() {
+    return appender.getWarnings();
+  }
+
   @Test
   public void testParseCompartment() throws FileNotFoundException, InvalidInputDataExecption {
     Model model = parser.createModel(
@@ -191,4 +216,17 @@ public class SbmlParserTest {
     assertTrue(model.getHeight() > 0);
   }
 
+  @Test
+  public void testParseTypeFromMulti() throws Exception {
+    Model model = parser.createModel(new ConverterParams().filename("testFiles/multi_features/species_type.xml"));
+    assertTrue(model.getElementByElementId("species_0") instanceof Gene);
+  }
+
+  @Test
+  public void testParseConflictingTypesFromMulti() throws Exception {
+    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());
+  }
+
 }

converter-sbml/testFiles/multi_features/conflicting_species_type.xml

+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<!-- Created by minerva version Unknown on 2018-12-31 at 12:23:42 CET with 
+	JSBML version 1.4. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"
+	layout:required="false" level="3" multi:required="true"
+	render:required="false" version="2"
+	xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+	xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
+	xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
+	<model id="id1" name="UNKNOWN DISEASE MAP">
+		<multi:listOfSpeciesTypes
+			xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1">
+			<multi:speciesType
+				multi:id="minerva_species_type_Gene" multi:name="Gene"
+				sboTerm="SBO:0000243" />
+		</multi:listOfSpeciesTypes>
+		<listOfSpecies>
+			<species id="species_0"
+				multi:speciesType="minerva_species_type_Gene" name="test name"
+				sboTerm="SBO:0000252">
+			</species>
+		</listOfSpecies>
+	</model>
+</sbml>
\ No newline at end of file

converter-sbml/testFiles/multi_features/species_type.xml

+<?xml version='1.0' encoding='UTF-8' standalone='no'?>
+<!-- Created by minerva version Unknown on 2018-12-31 at 12:23:42 CET with 
+	JSBML version 1.4. -->
+<sbml xmlns="http://www.sbml.org/sbml/level3/version2/core"
+	layout:required="false" level="3" multi:required="true"
+	render:required="false" version="2"
+	xmlns:layout="http://www.sbml.org/sbml/level3/version1/layout/version1"
+	xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
+	xmlns:render="http://www.sbml.org/sbml/level3/version1/render/version1">
+	<model id="id1" name="UNKNOWN DISEASE MAP">
+		<multi:listOfSpeciesTypes
+			xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1">
+			<multi:speciesType
+				multi:id="minerva_species_type_Gene" multi:name="Gene"
+				sboTerm="SBO:0000243" />
+		</multi:listOfSpeciesTypes>
+		<listOfSpecies>
+			<species id="species_0"
+				multi:speciesType="minerva_species_type_Gene" name="test name">
+			</species>
+		</listOfSpecies>
+	</model>
+</sbml>
\ No newline at end of file