parsing of sbml model annotations implemented

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

 package lcsb.mapviewer.converter.model.sbml;
 
-import java.io.ByteArrayInputStream;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.io.InputStream;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.Set;
@@ -23,9 +18,9 @@ import org.sbml.jsbml.ext.multi.MultiModelPlugin;
 import lcsb.mapviewer.commands.CommandExecutionException;
 import lcsb.mapviewer.commands.layout.ApplySimpleLayoutModelCommand;
 import lcsb.mapviewer.common.MimeType;
+import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.ConverterParams;
-import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentParser;
 import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser;
@@ -33,7 +28,6 @@ import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesParser;
 import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitsParser;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.InconsistentModelException;
-import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.modifier.Modulation;
@@ -82,10 +76,7 @@ public class SbmlParser extends Converter {
       SbmlParameterParser parameterParser = new SbmlParameterParser(sbmlModel, model);
       SbmlFunctionParser functionParser = new SbmlFunctionParser(sbmlModel, model);
 
-      Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
-      if (annotations.size() > 0) {
-        logger.warn("Annotations for model not implemented");
-      }
+      model.addMiriamData(compartmentParser.parseAnnotation(sbmlModel.getAnnotation()));
 
       model.addUnits(unitParser.parseList(sbmlModel));
       model.addParameters(parameterParser.parseList(sbmlModel));

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

@@ -82,6 +82,14 @@ public class SbmlParserTest {
     assertTrue("Units weren't parsed", model.getUnits().size() > 0);
   }
 
+  @Test
+  public void testParseModelAnnotations() throws FileNotFoundException, InvalidInputDataExecption {
+    Model model = parser.createModel(
+        new ConverterParams().filename("testFiles/small/model_with_annotations.xml"));
+    assertNotNull(model);
+    assertEquals(2,model.getMiriamData().size());
+  }
+
   @Test
   public void testParseKinetics() throws FileNotFoundException, InvalidInputDataExecption {
     Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/SBML.xml"));

converter-sbml/testFiles/small/model_with_annotations.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" version="4">
+<model metaid="untitled" id="untitled">
+<annotation>
+<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
+<rdf:Description rdf:about="#untitled">
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A12345"/>
+</rdf:Bag>
+</bqmodel:is>
+<bqmodel:is>
+<rdf:Bag>
+<rdf:li rdf:resource="urn:miriam:taxonomy:9606"/>
+</rdf:Bag>
+</bqmodel:is>
+</rdf:Description>
+</rdf:RDF>
+</annotation>
+<listOfUnitDefinitions>
+<unitDefinition metaid="substance" id="substance" name="substance">
+<listOfUnits>
+<unit metaid="CDMT00001" kind="mole"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="volume" id="volume" name="volume">
+<listOfUnits>
+<unit metaid="CDMT00002" kind="litre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="area" id="area" name="area">
+<listOfUnits>
+<unit metaid="CDMT00003" kind="metre" exponent="2"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="length" id="length" name="length">
+<listOfUnits>
+<unit metaid="CDMT00004" kind="metre"/>
+</listOfUnits>
+</unitDefinition>
+<unitDefinition metaid="time" id="time" name="time">
+<listOfUnits>
+<unit metaid="CDMT00005" kind="second"/>
+</listOfUnits>
+</unitDefinition>
+</listOfUnitDefinitions>
+<listOfCompartments>
+<compartment metaid="default" id="default" size="1" units="volume"/>
+</listOfCompartments>
+</model>
+</sbml>