diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
index 18190f46ee7396e650e572f980f405d8d913667a..917ca54b971a73596161c3d9ccde1298dd572528 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/function/FunctionXmlParser.java
@@ -22,7 +22,7 @@ public class FunctionXmlParser extends XmlParser {
if (mathDefinition == null) {
throw new InvalidXmlSchemaException("Function " + functionId + " doesn't contain MathML definition (math node)");
}
- result.setDefinition(nodeToString(mathDefinition));
+ result.setDefinition(nodeToString(mathDefinition).replace(" xmlns=\"http://www.w3.org/1998/Math/MathML\"", ""));
result.setArguments(parseArgumentsFromMath(mathDefinition, functionId));
return result;
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 2124b0065ba3b252e690dde923141ebfdc56537a..d05941bef41cf587f4e9ac39e7a0952dda198a7a 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
@@ -25,16 +25,18 @@ public class SbmlExporter {
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
compartmentExporter);
- SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter, compartmentExporter);
+ SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter,
+ compartmentExporter);
SbmlUnitExporter unitExporter = new SbmlUnitExporter(model);
SbmlParameterExporter parameterExporter = new SbmlParameterExporter(model);
-
+ SbmlFunctionExporter functionExporter = new SbmlFunctionExporter(model);
+
compartmentExporter.exportElements(result);
speciesExporter.exportElements(result);
reactionExporter.exportElements(result);
unitExporter.exportUnits(result);
parameterExporter.exportParameter(result);
-
+ functionExporter.exportFunction(result);
ByteArrayOutputStream stream = new ByteArrayOutputStream();
SBMLWriter.write(doc, stream, "minerva", "1.0");
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java
new file mode 100644
index 0000000000000000000000000000000000000000..1ef4edfa9b7d1806171388d4aa2b8d662582610d
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionExporter.java
@@ -0,0 +1,35 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.ASTNode;
+import org.sbml.jsbml.FunctionDefinition;
+
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class SbmlFunctionExporter {
+ Logger logger = Logger.getLogger(SbmlFunctionExporter.class);
+ private Model minervaModel;
+
+ public SbmlFunctionExporter(lcsb.mapviewer.model.map.model.Model minervaModel) {
+ this.minervaModel = minervaModel;
+ }
+
+ public void exportFunction(org.sbml.jsbml.Model result) {
+ for (SbmlFunction unit : minervaModel.getFunctions()) {
+ result.addFunctionDefinition(createFunction(unit));
+ }
+ }
+
+ private FunctionDefinition createFunction(SbmlFunction unit) {
+ FunctionDefinition result = new FunctionDefinition();
+ result.setName(unit.getName());
+ String definition = unit.getDefinition();
+ definition = definition.replace(" xmlns=\"http://www.sbml.org/sbml/level2/version4\"", "");
+ definition = "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">" + definition + "</math>";
+ result.setMath(ASTNode.parseMathML(definition));
+ result.setId(unit.getFunctionId());
+ return result;
+ }
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..c2facb4d7c10f6cf97fd17ddbddcacd3f546b88c
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlFunctionParser.java
@@ -0,0 +1,62 @@
+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 org.w3c.dom.Node;
+
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
+
+public class SbmlFunctionParser extends SbmlBioEntityParser {
+ Logger logger = Logger.getLogger(SbmlFunctionParser.class);
+
+ public SbmlFunctionParser(lcsb.mapviewer.model.map.model.Model minervaModel) {
+ this.minervaModel = minervaModel;
+ }
+
+ protected SbmlFunction parse(org.sbml.jsbml.FunctionDefinition unitDefinition, Model sbmlModel) throws InvalidInputDataExecption {
+ try {
+ SbmlFunction result = new SbmlFunction(unitDefinition.getId());
+ result.setName(unitDefinition.getName());
+ Node node = super.getXmlDocumentFromString(unitDefinition.getMath().toMathML());
+ Node mathDefinition = getNode("math", node);
+ result.setDefinition(super.nodeToString(mathDefinition));
+ result.setArguments(parseArgumentsFromMath(mathDefinition, result.getFunctionId()));
+ return result;
+ } catch (InvalidXmlSchemaException e) {
+ throw new InvalidInputDataExecption(e);
+ }
+
+ }
+
+ private List<String> parseArgumentsFromMath(Node mathDefinition, String functionId) throws InvalidXmlSchemaException {
+ List<String> result = new ArrayList<>();
+ Node lambdaDefinition = getNode("lambda", mathDefinition);
+ if (lambdaDefinition == null) {
+ throw new InvalidXmlSchemaException("Function " + functionId + " doesn't contain valid MathML lambda node");
+ }
+ List<Node> variables = super.getNodes("bvar", lambdaDefinition.getChildNodes());
+ for (Node node : variables) {
+ result.add(getNodeValue(getNode("ci", node)).trim());
+ }
+ return result;
+ }
+
+ protected ListOf<org.sbml.jsbml.FunctionDefinition> getSbmlElementList(Model sbmlModel) {
+ return sbmlModel.getListOfFunctionDefinitions();
+ }
+
+ public Collection<SbmlFunction> parseList(Model sbmlModel) throws InvalidInputDataExecption {
+ List<SbmlFunction> result = new ArrayList<>();
+ for (org.sbml.jsbml.FunctionDefinition unitDefinition : getSbmlElementList(sbmlModel)) {
+ result.add(parse(unitDefinition, sbmlModel));
+ }
+ return result;
+ }
+}
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
index a89e7aebdf0d14bef465ff4bc73d3cb0bc1bcee8..ab52589200989af11b4c3865caad90415f14aa4f 100644
--- 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
@@ -25,7 +25,9 @@ public class SbmlParameterExporter {
result.setName(unit.getName());
result.setValue(unit.getValue());
result.setId(unit.getParameterId());
- result.setUnits(unit.getUnits().getUnitId());
+ if (unit.getUnits() != null) {
+ 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
index 111f6fe8b874cac340256fb29ff8b79a4baac21c..f2a9f645e0ee9050a393d8a870be3726523c5ffe 100644
--- 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
@@ -7,6 +7,7 @@ import java.util.List;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
+import org.sbml.jsbml.QuantityWithUnit;
import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
@@ -17,7 +18,7 @@ public class SbmlParameterParser extends SbmlBioEntityParser {
this.minervaModel = minervaModel;
}
- protected SbmlParameter parse(org.sbml.jsbml.Parameter unitDefinition, Model sbmlModel) {
+ protected SbmlParameter parse(org.sbml.jsbml.QuantityWithUnit unitDefinition) {
SbmlParameter result = new SbmlParameter(unitDefinition.getId());
result.setName(unitDefinition.getName());
result.setValue(unitDefinition.getValue());
@@ -30,10 +31,16 @@ public class SbmlParameterParser extends SbmlBioEntityParser {
}
public Collection<SbmlParameter> parseList(Model sbmlModel) {
+ Collection<SbmlParameter> result = parseList(getSbmlElementList(sbmlModel));
+ return result;
+ }
+
+ public Collection<SbmlParameter> parseList(Collection<? extends QuantityWithUnit> parameters) {
List<SbmlParameter> result = new ArrayList<>();
- for (org.sbml.jsbml.Parameter unitDefinition : getSbmlElementList(sbmlModel)) {
- result.add(parse(unitDefinition, sbmlModel));
+ for (org.sbml.jsbml.QuantityWithUnit unitDefinition : parameters) {
+ result.add(parse(unitDefinition));
}
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 b7eb54f4ac0eee14c0cecfa754ee269ada365d6c..ee244ef5616df3ff148e939cb7fad5e871bc549c 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
@@ -31,6 +31,7 @@ import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.MiriamData;
+import lcsb.mapviewer.model.map.kinetics.SbmlFunction;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
import lcsb.mapviewer.model.map.modifier.Modulation;
@@ -67,6 +68,7 @@ public class SbmlParser implements IConverter {
SbmlReactionParser reactionParser = new SbmlReactionParser(layout, model, speciesParser, compartmentParser);
SbmlUnitsParser unitParser = new SbmlUnitsParser(model);
SbmlParameterParser parameterParser = new SbmlParameterParser(model);
+ SbmlFunctionParser functionParser = new SbmlFunctionParser(model);
Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
if (annotations.size() > 0) {
@@ -75,6 +77,7 @@ public class SbmlParser implements IConverter {
model.addUnits(unitParser.parseList(sbmlModel));
model.addParameters(parameterParser.parseList(sbmlModel));
+ model.addFunctions(functionParser.parseList(sbmlModel));
model.addElements(compartmentParser.parseList(sbmlModel));
model.addElements(speciesParser.parseList(sbmlModel));
@@ -109,9 +112,6 @@ public class SbmlParser implements IConverter {
if (sbmlModel.getInitialAssignmentCount() > 0) {
throw new NotImplementedException("InitialAssignment 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/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
index acb2305454f134420d39435fbe2a023b14383f89..a623cd369572180ca7b2618e67f2c92976e96596 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
@@ -34,7 +34,6 @@ import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.PolylineData;
import lcsb.mapviewer.model.map.kinetics.SbmlArgument;
import lcsb.mapviewer.model.map.kinetics.SbmlKinetics;
-import lcsb.mapviewer.model.map.kinetics.SbmlParameter;
import lcsb.mapviewer.model.map.modifier.Inhibition;
import lcsb.mapviewer.model.map.modifier.Modulation;
import lcsb.mapviewer.model.map.modifier.Trigger;
@@ -301,13 +300,9 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
private SbmlKinetics createMinervaKinetics(KineticLaw kineticLaw) throws InvalidInputDataExecption {
SbmlKinetics result = new SbmlKinetics();
result.setDefinition(kineticLaw.getMath().toMathML());
- for (LocalParameter parameter : kineticLaw.getListOfLocalParameters()) {
- SbmlParameter minervaParameter = new SbmlParameter(parameter.getId());
- minervaParameter.setName(parameter.getName());
- minervaParameter.setValue(parameter.getValue());
- minervaParameter.setUnits(minervaModel.getUnitsByUnitId(parameter.getUnits()));
- result.addParameter(minervaParameter);
- }
+
+ SbmlParameterParser parameterParser = new SbmlParameterParser(minervaModel);
+ result.addParameters(parameterParser.parseList((Collection<LocalParameter>)kineticLaw.getListOfLocalParameters()));
try {
Node node = super.getXmlDocumentFromString(result.getDefinition());
diff --git a/converter-sbml/testFiles/layoutExample/kinetic_function.xml b/converter-sbml/testFiles/layoutExample/kinetic_function.xml
new file mode 100644
index 0000000000000000000000000000000000000000..5285496d41d09a3646c5f904c846291e561c2175
--- /dev/null
+++ b/converter-sbml/testFiles/layoutExample/kinetic_function.xml
@@ -0,0 +1,106 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<sbml level="2" version="3" xmlns="http://www.sbml.org/sbml/level2/version3">
+ <model name="EnzymaticReaction">
+<listOfFunctionDefinitions>
+<functionDefinition metaid="function_id" id="function_id" name="Function name">
+<math xmlns="http://www.w3.org/1998/Math/MathML">
+<lambda>
+<bvar>
+<ci> x </ci>
+</bvar>
+<bvar>
+<ci> y </ci>
+</bvar>
+<apply>
+<plus/>
+<ci> x </ci>
+<ci> y </ci>
+</apply>
+</lambda>
+</math>
+</functionDefinition>
+</listOfFunctionDefinitions>
+ <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>
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
index 74d4ea82313ecaebd2695e1cc27ab37bfa96f53a..15f90d66f8b719dc2e4931e7b7ede0c43c830254 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlFunctionComparator.java
@@ -28,6 +28,8 @@ public class SbmlFunctionComparator extends Comparator<SbmlFunction> {
if (stringComparator.compare(arg0.getDefinition(), arg1.getDefinition()) != 0) {
logger.debug("definition different");
+ logger.debug(arg0.getDefinition());
+ logger.debug(arg1.getDefinition());
return stringComparator.compare(arg0.getDefinition(), arg1.getDefinition());
}
diff --git a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
index 9420e5e4d53debfdb48837b241003f2e92df0459..a4f1ec484c05dfbc35162710d95d8fd1c7a9de2b 100644
--- a/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
+++ b/model/src/main/java/lcsb/mapviewer/model/map/kinetics/SbmlKinetics.java
@@ -2,6 +2,7 @@ package lcsb.mapviewer.model.map.kinetics;
import java.io.Serializable;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
@@ -109,7 +110,7 @@ public class SbmlKinetics implements Serializable {
}
}
- public void addParameters(Set<SbmlParameter> parameters) {
+ public void addParameters(Collection<SbmlParameter> parameters) {
for (SbmlParameter parameter : parameters) {
addParameter(parameter);
}