sbml unit factors are exported and imported proeprly

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

@@ -16,6 +16,7 @@ import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
 
 import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
 import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
+import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.species.Species;
 

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

@@ -32,6 +32,7 @@ import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.model.celldesigner.structure.ComplexSpeciesTest;
 import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionParser;
 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;

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlUnitExporter.java → converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/SbmlUnitExporter.java

-package lcsb.mapviewer.converter.model.sbml;
+package lcsb.mapviewer.converter.model.sbml.units;
 
 import org.apache.log4j.Logger;
+import org.sbml.jsbml.Unit;
 import org.sbml.jsbml.UnitDefinition;
 
 import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
 import lcsb.mapviewer.model.map.model.Model;
 
 public class SbmlUnitExporter {
-  Logger logger = Logger.getLogger(SbmlUnitExporter.class);
+  @SuppressWarnings("unused")
+  private static Logger logger = Logger.getLogger(SbmlUnitExporter.class);
   private Model minervaModel;
 
   public SbmlUnitExporter(lcsb.mapviewer.model.map.model.Model minervaModel) {
@@ -24,6 +27,14 @@ public class SbmlUnitExporter {
     UnitDefinition result = new UnitDefinition();
     result.setId(unit.getUnitId());
     result.setName(unit.getName());
+    for (SbmlUnitTypeFactor factor : unit.getUnitTypeFactors()) {
+      Unit sbmlUnit = new Unit();
+      sbmlUnit.setKind(UnitMapping.unitTypeToKind(factor.getUnitType()));
+      sbmlUnit.setExponent((double) factor.getExponent());
+      sbmlUnit.setMultiplier(factor.getMultiplier());
+      sbmlUnit.setScale(factor.getScale());
+      result.addUnit(sbmlUnit);
+    }
     return result;
   }
 

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

-package lcsb.mapviewer.converter.model.sbml;
+package lcsb.mapviewer.converter.model.sbml.units;
 
 import java.util.ArrayList;
 import java.util.Collection;
@@ -7,8 +7,11 @@ import java.util.List;
 import org.apache.log4j.Logger;
 import org.sbml.jsbml.ListOf;
 import org.sbml.jsbml.Model;
+import org.sbml.jsbml.Unit;
 
+import lcsb.mapviewer.converter.model.sbml.SbmlBioEntityParser;
 import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitTypeFactor;
 
 public class SbmlUnitsParser extends SbmlBioEntityParser {
   Logger logger = Logger.getLogger(SbmlUnitsParser.class);
@@ -20,6 +23,12 @@ public class SbmlUnitsParser extends SbmlBioEntityParser {
   protected SbmlUnit parse(org.sbml.jsbml.UnitDefinition unitDefinition, Model sbmlModel) {
     SbmlUnit result = new SbmlUnit(unitDefinition.getId());
     result.setName(unitDefinition.getName());
+    for (int i = 0; i < unitDefinition.getUnitCount(); i++) {
+      Unit sbmlUnit = unitDefinition.getUnit(i);
+      SbmlUnitTypeFactor factor = new SbmlUnitTypeFactor(UnitMapping.kindToUnitType(sbmlUnit.getKind()),
+          (int) sbmlUnit.getExponent(), sbmlUnit.getScale(), sbmlUnit.getMultiplier());
+      result.addUnitTypeFactor(factor);
+    }
     return result;
   }
 

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/units/UnitMapping.java

+package lcsb.mapviewer.converter.model.sbml.units;
+
+import org.sbml.jsbml.Unit.Kind;
+
+import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.model.map.kinetics.SbmlUnitType;
+
+public enum UnitMapping {
+  AMPERE(SbmlUnitType.AMPERE, Kind.AMPERE),
+
+  BECQUEREL(SbmlUnitType.BECQUEREL, Kind.BECQUEREL),
+
+  CANDELA(SbmlUnitType.CANDELA, Kind.CANDELA),
+
+  COULUMB(SbmlUnitType.COULUMB, Kind.COULOMB),
+
+  DIMENSIONLESS(SbmlUnitType.DIMENSIONLESS, Kind.DIMENSIONLESS),
+
+  FARAD(SbmlUnitType.FARAD, Kind.FARAD),
+
+  GRAM(SbmlUnitType.GRAM, Kind.GRAM),
+
+  GRAY(SbmlUnitType.GRAY, Kind.GRAY),
+
+  HENRY(SbmlUnitType.HENRY, Kind.HENRY),
+
+  HERTZ(SbmlUnitType.HERTZ, Kind.HERTZ),
+
+  ITEM(SbmlUnitType.ITEM, Kind.ITEM),
+
+  JOULE(SbmlUnitType.JOULE, Kind.JOULE),
+
+  KATAL(SbmlUnitType.KATAL, Kind.KATAL),
+
+  KELVIN(SbmlUnitType.KELVIN, Kind.KELVIN),
+
+  KILOGRAM(SbmlUnitType.KILOGRAM, Kind.KILOGRAM),
+
+  LITRE(SbmlUnitType.LITRE, Kind.LITRE),
+
+  LUMEN(SbmlUnitType.LUMEN, Kind.LUMEN),
+
+  LUX(SbmlUnitType.LUX, Kind.LUX),
+
+  METRE(SbmlUnitType.METRE, Kind.METRE),
+
+  MOLE(SbmlUnitType.MOLE, Kind.MOLE),
+
+  NEWTON(SbmlUnitType.NEWTON, Kind.NEWTON),
+
+  OHM(SbmlUnitType.OHM, Kind.OHM),
+
+  PASCAL(SbmlUnitType.PASCAL, Kind.PASCAL),
+
+  RADIAN(SbmlUnitType.RADIAN, Kind.RADIAN),
+
+  SECOND(SbmlUnitType.SECOND, Kind.SECOND),
+
+  SIEMENS(SbmlUnitType.SIEMENS, Kind.SIEMENS),
+
+  SIEVERT(SbmlUnitType.SIEVERT, Kind.SIEVERT),
+
+  STERADIAN(SbmlUnitType.STERADIAN, Kind.STERADIAN),
+
+  TESLA(SbmlUnitType.TESLA, Kind.TESLA),
+
+  VOLT(SbmlUnitType.VOLT, Kind.VOLT),
+
+  WATT(SbmlUnitType.WATT, Kind.WATT),
+
+  WEBER(SbmlUnitType.WEBER, Kind.WEBER);
+
+  private SbmlUnitType unitType;
+  private Kind sbmlUnitType;
+
+  UnitMapping(SbmlUnitType unitType, Kind sbmlUnitType) {
+    this.unitType = unitType;
+    this.sbmlUnitType = sbmlUnitType;
+  }
+
+  public static Kind unitTypeToKind(SbmlUnitType unitType) {
+    for (UnitMapping mapping : UnitMapping.values()) {
+      if (mapping.unitType == unitType) {
+        return mapping.sbmlUnitType;
+      }
+    }
+    throw new InvalidArgumentException("Unknown sbml unit type: " + unitType);
+  }
+  public static SbmlUnitType kindToUnitType(Kind kind) {
+    for (UnitMapping mapping : UnitMapping.values()) {
+      if (mapping.sbmlUnitType == kind) {
+        return mapping.unitType;
+      }
+    }
+    throw new InvalidArgumentException("Unknown sbml unit type: " + kind);
+  }
+}