import of sbml kinetics

converter-sbml/.settings/org.eclipse.wst.common.component

+<?xml version="1.0" encoding="UTF-8"?><project-modules id="moduleCoreId" project-version="1.5.0">
+    <wb-module deploy-name="converter-sbml">
+        <wb-resource deploy-path="/" source-path="/src/main/java"/>
+        <wb-resource deploy-path="/" source-path="/src/main/resources"/>
+    </wb-module>
+</project-modules>

converter-sbml/.settings/org.eclipse.wst.common.project.facet.core.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<faceted-project>
+  <installed facet="java" version="1.8"/>
+  <installed facet="jst.utility" version="1.0"/>
+</faceted-project>

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

@@ -16,7 +16,7 @@ import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 
-public class SbmlBioEntityParser extends XmlParser{
+public class SbmlBioEntityParser extends XmlParser {
   Logger logger = Logger.getLogger(SbmlBioEntityParser.class);
 
   protected Layout layout;

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

@@ -65,11 +65,15 @@ public class SbmlParser implements IConverter {
       SbmlCompartmentParser compartmentParser = new SbmlCompartmentParser(layout, model);
       SbmlSpeciesParser speciesParser = new SbmlSpeciesParser(layout, model);
       SbmlReactionParser reactionParser = new SbmlReactionParser(layout, model, speciesParser);
+      SbmlUnitsParser unitParser = new SbmlUnitsParser(model);
 
       Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
       if (annotations.size() > 0) {
         throw new NotImplementedException("Annotations not implemented for model");
       }
+
+      model.addUnits(unitParser.parseList(sbmlModel));
+
       model.addElements(compartmentParser.parseList(sbmlModel));
       model.addElements(speciesParser.parseList(sbmlModel));
       model.addReactions(reactionParser.parseList(sbmlModel));
@@ -112,9 +116,6 @@ public class SbmlParser implements IConverter {
       if (sbmlModel.getRuleCount() > 0) {
         throw new NotImplementedException("Rule not implemented for model");
       }
-      if (sbmlModel.getUnitDefinitionCount() > 0) {
-        logger.warn("Units are not supported");
-      }
 
       createLayout(model, layout);
       return model;

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

+package lcsb.mapviewer.converter.model.sbml;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.Model;
+
+import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+
+public class SbmlUnitsParser extends SbmlBioEntityParser {
+  Logger logger = Logger.getLogger(SbmlUnitsParser.class);
+
+  public SbmlUnitsParser(lcsb.mapviewer.model.map.model.Model minervaModel) {
+    this.minervaModel = minervaModel;
+  }
+
+  protected SbmlUnit parse(org.sbml.jsbml.UnitDefinition unitDefinition, Model sbmlModel) {
+    SbmlUnit result = new SbmlUnit(unitDefinition.getId());
+    result.setName(unitDefinition.getName());
+    return result;
+  }
+
+  protected ListOf<org.sbml.jsbml.UnitDefinition> getSbmlElementList(Model sbmlModel) {
+    return sbmlModel.getListOfUnitDefinitions();
+  }
+
+  public Collection<SbmlUnit> parseList(Model sbmlModel) {
+    List<SbmlUnit> result = new ArrayList<>();
+    for (org.sbml.jsbml.UnitDefinition unitDefinition : getSbmlElementList(sbmlModel)) {
+      result.add(parse(unitDefinition, sbmlModel));
+    }
+    return result;
+  }
+}