From eaea8d6f363f781a337d052919d4b24b73092d14 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 6 Feb 2018 14:27:20 +0100
Subject: [PATCH] parsing of global parameters supported
---
.../converter/model/sbml/SbmlExporter.java | 3 +
.../model/sbml/SbmlParameterExporter.java | 32 +++++++
.../model/sbml/SbmlParameterParser.java | 39 ++++++++
.../converter/model/sbml/SbmlParser.java | 9 +-
.../converter/model/sbml/SbmlParserTest.java | 13 +++
.../layoutExample/kinetic_global_paramter.xml | 90 +++++++++++++++++++
6 files changed, 181 insertions(+), 5 deletions(-)
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterExporter.java
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterParser.java
create mode 100644 converter-sbml/testFiles/layoutExample/kinetic_global_paramter.xml
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
index 1b159bd344..2124b0065b 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -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();
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterExporter.java
new file mode 100644
index 0000000000..a89e7aebdf
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterExporter.java
@@ -0,0 +1,32 @@
+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;
+ }
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterParser.java
new file mode 100644
index 0000000000..111f6fe8b8
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParameterParser.java
@@ -0,0 +1,39 @@
+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;
+ }
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 38045d6103..b7eb54f4ac 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -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");
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index 91893ec7d4..19a431f9f7 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -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
diff --git a/converter-sbml/testFiles/layoutExample/kinetic_global_paramter.xml b/converter-sbml/testFiles/layoutExample/kinetic_global_paramter.xml
new file mode 100644
index 0000000000..350fb62672
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/kinetic_global_paramter.xml
@@ -0,0 +1,90 @@
+<?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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