From 82eee8811eb3d0b6ae137d0d7c7846bbb3eda669 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Wed, 23 May 2018 11:42:54 +0200
Subject: [PATCH] when exporting reaction that has the same product and
reactant system doesn't crash
Instead of crashing reaction is omitted and proper info is added to the model notes.
---
.../celldesigner/CellDesignerXmlParser.java | 78 +++++++++++--------
.../reaction/ReactionCollectionXmlParser.java | 4 +
.../celldesigner/reaction/ReactionToXml.java | 4 +
.../reaction/SelfReactionException.java | 31 ++++++++
.../CellDesignerXmlParserTest.java | 37 +++++++++
.../reaction/ReactionToXmlTest.java | 47 ++++++-----
6 files changed, 151 insertions(+), 50 deletions(-)
create mode 100644 converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/SelfReactionException.java
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
index 6a7e6d10c7..8ab5a64b64 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
@@ -13,11 +13,13 @@ import java.util.List;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.lang3.StringEscapeUtils;
import org.apache.log4j.Logger;
+import org.apache.log4j.spi.LoggingEvent;
import org.apache.xerces.parsers.DOMParser;
import org.w3c.dom.Document;
import org.w3c.dom.Node;
import org.w3c.dom.NodeList;
+import lcsb.mapviewer.common.EventStorageLoggerAppender;
import lcsb.mapviewer.common.MimeType;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.common.XmlParser;
@@ -563,47 +565,59 @@ public class CellDesignerXmlParser extends XmlParser implements IConverter {
* thrown when then model is invalid
* @throws InconsistentModelException
*/
- public String toXml(Model model) throws InconsistentModelException, InconsistentModelException {
- CellDesignerElementCollection elements = new CellDesignerElementCollection();
+ public String toXml(Model model) throws InconsistentModelException {
+ EventStorageLoggerAppender appender = new EventStorageLoggerAppender();
+ try {
+ Logger.getRootLogger().addAppender(appender);
+ CellDesignerElementCollection elements = new CellDesignerElementCollection();
- SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
- ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, false);
- UnitCollectionXmlParser unitCollectionXmlParser = new UnitCollectionXmlParser();
- FunctionCollectionXmlParser functionCollectionXmlParser = new FunctionCollectionXmlParser();
- ParameterCollectionXmlParser parameterCollectionXmlParser = new ParameterCollectionXmlParser(model);
+ SpeciesCollectionXmlParser speciesCollectionXmlParser = new SpeciesCollectionXmlParser(elements);
+ ReactionCollectionXmlParser reactionCollectionXmlParser = new ReactionCollectionXmlParser(model, elements, false);
+ UnitCollectionXmlParser unitCollectionXmlParser = new UnitCollectionXmlParser();
+ FunctionCollectionXmlParser functionCollectionXmlParser = new FunctionCollectionXmlParser();
+ ParameterCollectionXmlParser parameterCollectionXmlParser = new ParameterCollectionXmlParser(model);
- aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
+ aliasCollectionParser = new AliasCollectionXmlParser(elements, model);
- StringBuilder result = new StringBuilder();
- result.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
- result.append("<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" "
- + "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
- // metaid is a string cell designer id, usually it's model id and as far as
- // we can tell it's not used at all
- result.append("<model metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\">\n");
-
- if (model.getNotes() != null) {
- result.append("<notes>");
- result.append(escapeXml(model.getNotes()));
- result.append("</notes>");
- }
+ StringBuilder result = new StringBuilder();
+ result.append("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n");
+ result.append("<sbml xmlns=\"http://www.sbml.org/sbml/level2/version4\" "
+ + "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
+ // metaid is a string cell designer id, usually it's model id and as far as
+ // we can tell it's not used at all
+ result.append("<model metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\">\n");
- result.append(unitCollectionXmlParser.toXml(model.getUnits()));
- result.append(functionCollectionXmlParser.toXml(model.getFunctions()));
- result.append(parameterCollectionXmlParser.toXml(model.getParameters()));
- result.append(annotationToXml(model, elements));
+ result.append(unitCollectionXmlParser.toXml(model.getUnits()));
+ result.append(functionCollectionXmlParser.toXml(model.getFunctions()));
+ result.append(parameterCollectionXmlParser.toXml(model.getParameters()));
+ result.append(annotationToXml(model, elements));
- compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
+ compartmentCollectionXmlParser = new CompartmentCollectionXmlParser(elements);
- result.append(compartmentCollectionXmlParser.toXml(model.getCompartments()));
+ result.append(compartmentCollectionXmlParser.toXml(model.getCompartments()));
- result.append(speciesCollectionXmlParser.speciesCollectionToSbmlString(model.getSpeciesList()));
+ result.append(speciesCollectionXmlParser.speciesCollectionToSbmlString(model.getSpeciesList()));
- result.append(reactionCollectionXmlParser.reactionCollectionToXmlString(model.getReactions()));
+ result.append(reactionCollectionXmlParser.reactionCollectionToXmlString(model.getReactions()));
+ if (model.getNotes() != null || !appender.getWarnings().isEmpty()) {
+ result.append("<notes>");
+ if (model.getNotes() != null) {
+ result.append(escapeXml(model.getNotes()));
+ }
+ for (LoggingEvent event : appender.getWarnings()) {
+ if (event.getMessage() instanceof String) {
+ result.append("\n" + ((String) event.getMessage()));
+ }
+ }
+ result.append("</notes>");
+ }
- result.append("</model>");
- result.append("</sbml>");
- return result.toString();
+ result.append("</model>");
+ result.append("</sbml>");
+ return result.toString();
+ } finally {
+ Logger.getRootLogger().removeAppender(appender);
+ }
}
/**
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
index e42618f464..cb8166ffe7 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
@@ -101,7 +101,11 @@ public class ReactionCollectionXmlParser extends XmlParser {
String result = "";
result += "<listOfReactions>\n";
for (Reaction reaction : collection) {
+ try {
result += xmlStructureFactory.toXml(reaction);
+ } catch (SelfReactionException e) {
+ logger.warn("Reaction omitted: " + e.getMessage());
+ }
}
result += "</listOfReactions>\n";
return result;
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
index e1656a8ce4..7058ed10ec 100644
--- a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
@@ -108,6 +108,10 @@ public class ReactionToXml extends XmlParser {
* @throws ConverterException
*/
public String toXml(Reaction reaction) throws InconsistentModelException {
+ if (reaction.getReactants().get(0).getElement().equals(reaction.getProducts().get(0).getElement())) {
+ throw new SelfReactionException("Reaction " + reaction.getElementId() + " is a self reference for element "
+ + reaction.getProducts().get(0).getElement().getElementId());
+ }
StringBuilder sb = new StringBuilder();
sb.append("<reaction ");
sb.append("metaid=\"" + reaction.getIdReaction() + "\" ");
diff --git a/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/SelfReactionException.java b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/SelfReactionException.java
new file mode 100644
index 0000000000..b85d6f5537
--- /dev/null
+++ b/converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/SelfReactionException.java
@@ -0,0 +1,31 @@
+package lcsb.mapviewer.converter.model.celldesigner.reaction;
+
+import lcsb.mapviewer.model.map.InconsistentModelException;
+
+/**
+ * Exception thrown when CellDesigner exporter tries to export reaction that
+ * uses the same element as product and reactant.
+ *
+ * @author Piotr Gawron
+ *
+ */
+public class SelfReactionException extends InconsistentModelException {
+ /**
+ *
+ */
+ private static final long serialVersionUID = 1L;
+
+ /**
+ * Default constructor with a message passed in the argument.
+ *
+ * @param message
+ * text message of this exception
+ */
+ public SelfReactionException(String message) {
+ super(message);
+ }
+
+ public SelfReactionException(Exception e) {
+ super(e);
+ }
+}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
index efa2ee8835..6f97c0fbcd 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
@@ -39,7 +39,10 @@ import lcsb.mapviewer.model.map.layout.graphics.LayerText;
import lcsb.mapviewer.model.map.model.Model;
import lcsb.mapviewer.model.map.model.ModelComparator;
import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.reaction.Product;
+import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Gene;
import lcsb.mapviewer.model.map.species.GenericProtein;
@@ -962,4 +965,38 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
}
}
+ @Test
+ public void testModelWithSelfReactionToXml() throws Exception {
+ try {
+ Model model = new ModelFullIndexed(null);
+ model.setIdModel("as");
+ model.setWidth(10);
+ model.setHeight(10);
+ Species protein = new GenericProtein("id1");
+ protein.setName("ROS");
+ model.addElement(protein);
+
+ Reaction reaction = new StateTransitionReaction();
+ reaction.setIdReaction("re1");
+ Product product = new Product(protein);
+ product.setLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(20, 20)));
+ reaction.addProduct(product);
+ Reactant reactant = new Reactant(protein);
+ reactant.setLine(new PolylineData(new Point2D.Double(20, 20), new Point2D.Double(0, 0)));
+ reaction.addReactant(reactant);
+ model.addReaction(reaction);
+
+ CellDesignerXmlParser parser = new CellDesignerXmlParser();
+ String xmlString = parser.toXml(model);
+
+ assertNotNull(xmlString);
+ assertTrue(xmlString.contains("omitted"));
+ assertTrue(xmlString.contains("re1"));
+
+ } catch (Exception e) {
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
}
diff --git a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
index fdc5a88fc6..892243e5b3 100644
--- a/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
+++ b/converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
@@ -57,24 +57,26 @@ public class ReactionToXmlTest {
@Test
public void testInvalidModification() throws InconsistentModelException {
Model model = new ModelFullIndexed(null);
- Species alias = new GenericProtein("2");
+ Species protein1 = new GenericProtein("2");
+ Species protein2 = new GenericProtein("3");
- model.addElement(alias);
+ model.addElement(protein1);
+ model.addElement(protein2);
Reaction reaction = new TransportReaction();
- Reactant reactant = new Reactant(alias);
+ Reactant reactant = new Reactant(protein1);
reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
- Product product = new Product(alias);
+ Product product = new Product(protein2);
product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
reaction.addReactant(reactant);
reaction.addProduct(product);
- Modifier modifier = new Catalysis(alias);
+ Modifier modifier = new Catalysis(protein1);
modifier.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(30, 0)));
- Modifier modifier2 = new Catalysis(alias);
+ Modifier modifier2 = new Catalysis(protein1);
List<Point2D> points = new ArrayList<>();
points.add(new Point2D.Double(0, 0));
points.add(new Point2D.Double(30, 30));
@@ -114,28 +116,30 @@ public class ReactionToXmlTest {
public void testModificationFromInsideComplex() throws InconsistentModelException {
Model model = new ModelFullIndexed(null);
- Species alias = new GenericProtein("2");
+ Species protein1 = new GenericProtein("2");
+ Species protein2 = new GenericProtein("3");
- model.addElement(alias);
+ model.addElement(protein1);
+ model.addElement(protein2);
Complex complex = new Complex("4");
- complex.addSpecies(alias);
+ complex.addSpecies(protein1);
- alias.setComplex(complex);
+ protein1.setComplex(complex);
model.addElement(complex);
Reaction reaction = new TransportReaction();
- Reactant reactant = new Reactant(alias);
+ Reactant reactant = new Reactant(protein1);
reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
- Product product = new Product(alias);
+ Product product = new Product(protein2);
product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
reaction.addReactant(reactant);
reaction.addProduct(product);
- Modifier modifier = new Catalysis(alias);
+ Modifier modifier = new Catalysis(protein1);
modifier.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(30, 0)));
reaction.addModifier(modifier);
@@ -154,12 +158,17 @@ public class ReactionToXmlTest {
Complex complex = new Complex("4");
complex.setComplex(complex);
model.addElement(complex);
+
+ Species protein1 = new GenericProtein("2");
+
+ model.addElement(protein1);
+
Reaction reaction = new TransportReaction();
Reactant reactant = new Reactant(complex);
reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
- Product product = new Product(complex);
+ Product product = new Product(protein1);
product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
reaction.addReactant(reactant);
@@ -178,15 +187,17 @@ public class ReactionToXmlTest {
public void testInvalidReaction() throws InconsistentModelException {
Model model = new ModelFullIndexed(null);
- Species alias = new GenericProtein("2");
+ Species protein1 = new GenericProtein("2");
+ Species protein2 = new GenericProtein("3");
- model.addElement(alias);
+ model.addElement(protein1);
+ model.addElement(protein2);
Reaction reaction = new Reaction();
- Reactant reactant = new Reactant(alias);
+ Reactant reactant = new Reactant(protein1);
reactant.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(10, 0)));
- Product product = new Product(alias);
+ Product product = new Product(protein2);
product.setLine(new PolylineData(new Point2D.Double(), new Point2D.Double(20, 0)));
reaction.addReactant(reactant);
--
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