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Commit eaea8d6f authored by Piotr Gawron's avatar Piotr Gawron
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parsing of global parameters supported

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1 merge request!186Resolve "upload of sbml"
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converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+ 3
− 0
View file @ eaea8d6f
......@@ -27,10 +27,13 @@ public class SbmlExporter {
compartmentExporter);
SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter, compartmentExporter);
SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
SbmlParameterExporter parameterExporter = new SbmlParameterExporter(model);
compartmentExporter.exportElements(result);
speciesExporter.exportElements(result);
reactionExporter.exportElements(result);
unitExporter.exportUnits(result);
parameterExporter.exportParameter(result);
ByteArrayOutputStream stream = new ByteArrayOutputStream();
......
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterExporter.java 0 → 100644
+ 32
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View file @ eaea8d6f
package lcsb.mapviewer.converter.model.sbml;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Parameter;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.model.Model;
public class SbmlParameterExporter {
Logger logger = Logger.getLogger(SbmlParameterExporter.class);
private Model minervaModel;
public SbmlParameterExporter(lcsb.mapviewer.model.map.model.Model minervaModel) {
this.minervaModel = minervaModel;
}
public void exportParameter(org.sbml.jsbml.Model result) {
for (SbmlParameter unit : minervaModel.getParameters()) {
result.addParameter(createParameter(unit));
}
}
private Parameter createParameter(SbmlParameter unit) {
Parameter result = new Parameter();
result.setName(unit.getName());
result.setValue(unit.getValue());
result.setId(unit.getParameterId());
result.setUnits(unit.getUnits().getUnitId());
return result;
}
}
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterParser.java 0 → 100644
+ 39
− 0
View file @ eaea8d6f
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.SbmlParameter;
public class SbmlParameterParser extends SbmlBioEntityParser {
Logger logger = Logger.getLogger(SbmlParameterParser.class);
public SbmlParameterParser(lcsb.mapviewer.model.map.model.Model minervaModel) {
this.minervaModel = minervaModel;
}
protected SbmlParameter parse(org.sbml.jsbml.Parameter unitDefinition, Model sbmlModel) {
SbmlParameter result = new SbmlParameter(unitDefinition.getId());
result.setName(unitDefinition.getName());
result.setValue(unitDefinition.getValue());
result.setUnits(minervaModel.getUnitsByUnitId(unitDefinition.getUnits()));
return result;
}
protected ListOf<org.sbml.jsbml.Parameter> getSbmlElementList(Model sbmlModel) {
return sbmlModel.getListOfParameters();
}
public Collection<SbmlParameter> parseList(Model sbmlModel) {
List<SbmlParameter> result = new ArrayList<>();
for (org.sbml.jsbml.Parameter unitDefinition : getSbmlElementList(sbmlModel)) {
result.add(parse(unitDefinition, sbmlModel));
}
return result;
}
}
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+ 4
− 5
View file @ eaea8d6f
......@@ -66,6 +66,7 @@ public class SbmlParser implements IConverter {
SbmlSpeciesParser speciesParser = new SbmlSpeciesParser(layout, model);
SbmlReactionParser reactionParser = new SbmlReactionParser(layout, model, speciesParser, compartmentParser);
SbmlUnitsParser unitParser = new SbmlUnitsParser(model);
SbmlParameterParser parameterParser = new SbmlParameterParser(model);
Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
if (annotations.size() > 0) {
......@@ -73,6 +74,7 @@ public class SbmlParser implements IConverter {
}
model.addUnits(unitParser.parseList(sbmlModel));
model.addParameters(parameterParser.parseList(sbmlModel));
model.addElements(compartmentParser.parseList(sbmlModel));
model.addElements(speciesParser.parseList(sbmlModel));
......@@ -104,14 +106,11 @@ public class SbmlParser implements IConverter {
if (sbmlModel.getEventAssignmentCount() > 0) {
throw new NotImplementedException("EventAssignemnts not implemented for model");
}
if (sbmlModel.getFunctionDefinitionCount() > 0) {
throw new NotImplementedException("FunctionDefinition not implemented for model");
}
if (sbmlModel.getInitialAssignmentCount() > 0) {
throw new NotImplementedException("InitialAssignment not implemented for model");
}
if (sbmlModel.getParameterCount() > 0) {
throw new NotImplementedException("Parameter not implemented for model");
if (sbmlModel.getFunctionDefinitionCount() > 0) {
throw new NotImplementedException("Function not implemented for model");
}
if (sbmlModel.getRuleCount() > 0) {
throw new NotImplementedException("Rule not implemented for model");
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+ 13
− 0
View file @ eaea8d6f
......@@ -59,6 +59,19 @@ public class SbmlParserTest {
}
}
@Test
public void testParseGlobalParameters() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser
.createModel(new ConverterParams().filename("testFiles/layoutExample/kinetic_global_paramter.xml"));
assertTrue("There should be a kinetic parameter defined", model.getParameters().size() > 0);
}
@Test
public void testParseFunctions() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/kinetic_function.xml"));
assertTrue("There should be a kinetic function defined", model.getFunctions().size() > 0);
}
@Test
public void testParseSpecies() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser
......
converter-sbml/testFiles/layoutExample/kinetic_global_paramter.xml 0 → 100644
+ 90
− 0
View file @ eaea8d6f
<?xml version="1.0" encoding="UTF-8"?>
<sbml level="2" version="3" xmlns="http://www.sbml.org/sbml/level2/version3">
<model name="EnzymaticReaction">
<listOfParameters>
<parameter metaid="param_id" id="param_id" name="Parameter name" value="12" units="volume"/>
</listOfParameters>
<listOfUnitDefinitions>
<unitDefinition id="per_second">
<listOfUnits>
<unit kind="second" exponent="-1"/>
</listOfUnits>
</unitDefinition>
<unitDefinition id="litre_per_mole_per_second">
<listOfUnits>
<unit kind="mole" exponent="-1"/>
<unit kind="litre" exponent="1"/>
<unit kind="second" exponent="-1"/>
</listOfUnits>
</unitDefinition>
</listOfUnitDefinitions>
<listOfCompartments>
<compartment id="cytosol" size="1e-14"/>
</listOfCompartments>
<listOfSpecies>
<species compartment="cytosol" id="ES" initialAmount="0" name="ES"/>
<species compartment="cytosol" id="P" initialAmount="0" name="P"/>
<species compartment="cytosol" id="S" initialAmount="1e-20" name="S"/>
<species compartment="cytosol" id="E" initialAmount="5e-21" name="E"/>
</listOfSpecies>
<listOfReactions>
<reaction id="veq">
<listOfReactants>
<speciesReference species="E"/>
<speciesReference species="S"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="ES"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci>cytosol</ci>
<apply>
<minus/>
<apply>
<times/>
<ci>kon</ci>
<ci>E</ci>
<ci>S</ci>
</apply>
<apply>
<times/>
<ci>koff</ci>
<ci>ES</ci>
</apply>
</apply>
</apply>
</math>
<listOfParameters>
<parameter id="kon" value="1000000" units="litre_per_mole_per_second"/>
<parameter id="koff" value="0.2" units="per_second"/>
</listOfParameters>
</kineticLaw>
</reaction>
<reaction id="vcat" reversible="false">
<listOfReactants>
<speciesReference species="ES"/>
</listOfReactants>
<listOfProducts>
<speciesReference species="E"/>
<speciesReference species="P"/>
</listOfProducts>
<kineticLaw>
<math xmlns="http://www.w3.org/1998/Math/MathML">
<apply>
<times/>
<ci>cytosol</ci>
<ci>kcat</ci>
<ci>ES</ci>
</apply>
</math>
<listOfParameters>
<parameter id="kcat" value="0.1" units="per_second"/>
</listOfParameters>
</kineticLaw>
</reaction>
</listOfReactions>
</model>
</sbml>
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