From abd318d18c02ff9da2efb24080d945d69813fe99 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Fri, 2 Feb 2018 11:16:53 +0100
Subject: [PATCH] import of sbml reaction kinetics added
---
converter-sbml/.gitignore | 1 +
.../model/sbml/SbmlBioEntityParser.java | 3 +-
.../converter/model/sbml/SbmlParser.java | 3 --
.../model/sbml/SbmlReactionParser.java | 53 +++++++++++++++++--
.../converter/model/sbml/SbmlParserTest.java | 19 +++++++
5 files changed, 71 insertions(+), 8 deletions(-)
diff --git a/converter-sbml/.gitignore b/converter-sbml/.gitignore
index 7bca1630c9..3ef28bc255 100644
--- a/converter-sbml/.gitignore
+++ b/converter-sbml/.gitignore
@@ -1,2 +1,3 @@
/bin/
tmp.png
+tmp.xml
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
index 2a03a7bd52..fc53759d70 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java
@@ -11,11 +11,12 @@ import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.util.NotImplementedException;
+import lcsb.mapviewer.common.XmlParser;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
-public class SbmlBioEntityParser {
+public class SbmlBioEntityParser extends XmlParser{
Logger logger = Logger.getLogger(SbmlBioEntityParser.class);
protected Layout layout;
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 32a2964d99..7cbaa961dc 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
@@ -106,9 +106,6 @@ public class SbmlParser implements IConverter {
if (sbmlModel.getInitialAssignmentCount() > 0) {
throw new NotImplementedException("InitialAssignment not implemented for model");
}
- if (sbmlModel.getKineticLawCount() > 0) {
- throw new NotImplementedException("KineticLaw not implemented for model");
- }
if (sbmlModel.getParameterCount() > 0) {
throw new NotImplementedException("Parameter 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 fc91aa0314..0f91b7a80c 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
@@ -11,8 +11,9 @@ import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
-import org.sbml.jsbml.Annotation;
+import org.sbml.jsbml.KineticLaw;
import org.sbml.jsbml.ListOf;
+import org.sbml.jsbml.LocalParameter;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ModifierSpeciesReference;
import org.sbml.jsbml.SpeciesReference;
@@ -21,16 +22,19 @@ import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
-import org.sbml.jsbml.util.NotImplementedException;
+import org.w3c.dom.Node;
import lcsb.mapviewer.common.exception.InvalidArgumentException;
import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
import lcsb.mapviewer.model.graphics.ArrowType;
import lcsb.mapviewer.model.graphics.ArrowTypeData;
import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.MiriamData;
+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;
@@ -248,7 +252,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
reaction.setIdReaction(sbmlReaction.getId());
reaction.setReversible(sbmlReaction.isReversible());
if (sbmlReaction.getKineticLaw() != null) {
- throw new NotImplementedException("KineticLaw not implemented");
+ reaction.setKinetics(createMinervaKinetics(sbmlReaction.getKineticLaw()));
}
for (SpeciesReference reactant : sbmlReaction.getListOfReactants()) {
Species element = minervaModel.getElementByElementId(reactant.getSpecies());
@@ -267,6 +271,47 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
return reaction;
}
+ 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);
+ }
+
+ try {
+ Node node = super.getXmlDocumentFromString(result.getDefinition());
+ Set<SbmlArgument> elementsUsedInKinetics = new HashSet<>();
+ for (Node ciNode : super.getAllNotNecessirellyDirectChild("ci", node)) {
+ String id = super.getNodeValue(ciNode).trim();
+ SbmlArgument element = minervaModel.getElementByElementId(id);
+ if (element == null) {
+ element = result.getParameterById(id);
+ }
+ if (element == null) {
+ element = minervaModel.getParameterById(id);
+ }
+ if (element == null) {
+ element = minervaModel.getFunctionById(id);
+ }
+ if (element != null) {
+ ciNode.setTextContent(element.getElementId());
+ } else {
+ throw new InvalidXmlSchemaException("Unknown symbol in kinetics: " + id);
+ }
+ elementsUsedInKinetics.add(element);
+ }
+ result.addArguments(elementsUsedInKinetics);
+ } catch (InvalidXmlSchemaException e) {
+ throw new InvalidInputDataExecption(e);
+ }
+
+ return result;
+ }
+
public void validateReactions(Set<Reaction> reactions) throws InvalidInputDataExecption {
for (Reaction reaction : reactions) {
if (reaction.getReactants().size() == 0) {
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 aa8225c4f0..91893ec7d4 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
@@ -40,6 +40,25 @@ public class SbmlParserTest {
assertFalse(compartment.getClass().equals(Compartment.class));
}
+ @Test
+ public void testParseUnits() throws FileNotFoundException, InvalidInputDataExecption {
+ Model model = parser.createModel(
+ new ConverterParams().filename("testFiles/layoutExample/CompartmentGlyph_Example_level2_level3.xml"));
+ assertNotNull(model);
+ assertTrue("Units weren't parsed", model.getUnits().size() > 0);
+ }
+
+ @Test
+ public void testParseKinetics() throws FileNotFoundException, InvalidInputDataExecption {
+ Model model = parser.createModel(new ConverterParams().filename("testFiles/layoutExample/SBML.xml"));
+ for (Reaction reaction : model.getReactions()) {
+ assertNotNull("Kinetics is not parsed", reaction.getKinetics());
+ assertNotNull("No math definition for kinetic law", reaction.getKinetics().getDefinition());
+ assertTrue("There should be a kinetic parameter defined", reaction.getKinetics().getParameters().size() > 0);
+ assertTrue("Elements used by kinetics are not available", reaction.getKinetics().getElements().size() > 0);
+ }
+ }
+
@Test
public void testParseSpecies() throws FileNotFoundException, InvalidInputDataExecption {
Model model = parser
--
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