From 54134e725afd93491dcc247487431fcc7a551994 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 6 Feb 2018 13:42:56 +0100
Subject: [PATCH] full import/export of reaction kinetics
---
.../model/sbml/SbmlElementParser.java | 7 +++++
.../converter/model/sbml/SbmlParser.java | 3 +-
.../model/sbml/SbmlReactionExporter.java | 8 -----
.../model/sbml/SbmlReactionParser.java | 29 ++++++++++++++++++-
4 files changed, 36 insertions(+), 11 deletions(-)
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
index 7cd9676e7a..c84692525e 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -40,10 +40,16 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
Map<String, Element> elementBySbmlId = new HashMap<>();
+ Map<String, String> sbmlIdByElementId = new HashMap<>();
+
public Element getAnyElementBySbmlElementId(String id) {
return elementBySbmlId.get(id);
}
+ public String getSbmlIdByElementId(String compartmentId) {
+ return sbmlIdByElementId.get(compartmentId);
+ }
+
protected List<Element> mergeLayout(List<? extends Element> elements, Layout sbmlLayout, Model sbmlModel)
throws InvalidInputDataExecption {
Set<String> used = new HashSet<>();
@@ -70,6 +76,7 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends
result.add(elementWithLayout);
elementBySbmlId.put(id, elementWithLayout);
elementBySbmlId.put(elementWithLayout.getElementId(), elementWithLayout);
+ sbmlIdByElementId.put(elementWithLayout.getElementId(), id);
}
for (Element element : elements) {
if (!used.contains(element.getElementId())) {
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 07429d9d30..38045d6103 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
@@ -64,7 +64,7 @@ public class SbmlParser implements IConverter {
SbmlCompartmentParser compartmentParser = new SbmlCompartmentParser(layout, model);
SbmlSpeciesParser speciesParser = new SbmlSpeciesParser(layout, model);
- SbmlReactionParser reactionParser = new SbmlReactionParser(layout, model, speciesParser);
+ SbmlReactionParser reactionParser = new SbmlReactionParser(layout, model, speciesParser, compartmentParser);
SbmlUnitsParser unitParser = new SbmlUnitsParser(model);
Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
@@ -226,7 +226,6 @@ public class SbmlParser implements IConverter {
throws ConverterException, InconsistentModelException, IOException {
File file = new File(filePath);
String exportedString = toXml(model);
- logger.debug(exportedString);
FileWriter fileWriter = new FileWriter(file);
fileWriter.write(exportedString);
fileWriter.flush();
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
index 02ec6cbdf8..7f39759342 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
@@ -111,21 +111,13 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
} else {
sbmlId = compartmentExporter.sbmlElementByElementId.get(id).getId();
}
-
- logger.debug(id);
- logger.debug(element.getElementId());
- logger.debug(speciesExporter);
- logger.debug(speciesExporter.sbmlElementByElementId);
- logger.debug(speciesExporter.sbmlElementByElementId.get(element.getElementId()));
ciNode.setTextContent(sbmlId);
}
}
String definition = super.nodeToString(node);
definition = definition.replace(" xmlns=\"http://www.sbml.org/sbml/level2/version4\"", "");
definition = definition.replace("<math>", "<math xmlns=\"http://www.w3.org/1998/Math/MathML\">");
- logger.debug(definition);
result.setMath(ASTNode.parseMathML(definition));
- logger.debug(result.getMathMLString());
return result;
} catch (InvalidXmlSchemaException e) {
throw new InconsistentModelException(e);
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 cceec32e95..acb2305454 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
@@ -60,12 +60,14 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
ElementUtils eu = new ElementUtils();
SbmlSpeciesParser speciesParser;
+ SbmlCompartmentParser compartmentParser;
public SbmlReactionParser(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel,
- SbmlSpeciesParser speciesParser) {
+ SbmlSpeciesParser speciesParser, SbmlCompartmentParser compartmentParser) {
this.layout = sbmlLayout;
this.minervaModel = minervaModel;
this.speciesParser = speciesParser;
+ this.compartmentParser = compartmentParser;
}
public List<Reaction> parseList(Model sbmlModel) throws InvalidInputDataExecption {
@@ -184,6 +186,12 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
}
}
+ updateKinetics(reactionWithLayout, minervaElement.getElementId(), minervaNode.getElement().getElementId());
+ if (minervaElement.getCompartment() != null) {
+ String newCompartmentId = minervaElement.getCompartment().getElementId();
+ String oldCompartmentId = compartmentParser.getSbmlIdByElementId(newCompartmentId);
+ updateKinetics(reactionWithLayout, newCompartmentId, oldCompartmentId);
+ }
minervaNode.setLine(line);
minervaNode.setElement(minervaElement);
if (nodeClass != minervaNode.getClass()) {
@@ -246,6 +254,25 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
}
}
+ private void updateKinetics(Reaction reactionWithLayout, String newElementId, String oldElementId) {
+ SbmlKinetics kinetics = reactionWithLayout.getKinetics();
+ if (kinetics != null) {
+ String newDefinition = kinetics.getDefinition().replace(">" + oldElementId + "<", ">" + newElementId + "<");
+ kinetics.setDefinition(newDefinition);
+ Element elementToRemove = null;
+ for (Element element : kinetics.getElements()) {
+ if (element.getElementId().equals(oldElementId)) {
+ elementToRemove = element;
+ }
+ }
+ if (elementToRemove != null) {
+ kinetics.removeElement(elementToRemove);
+ kinetics.addElement(minervaModel.getElementByElementId(newElementId));
+ }
+ }
+
+ }
+
protected Reaction parse(org.sbml.jsbml.Reaction sbmlReaction, Model sbmlModel) throws InvalidInputDataExecption {
Reaction reaction = new StateTransitionReaction();
assignBioEntityData(sbmlReaction, reaction);
--
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