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Commit b06d14fe authored by Piotr Gawron's avatar Piotr Gawron
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Merge branch '416-error-when-exporting-model-generated-from-sbml' into 'master' 

Resolve "error when exporting model generated from SBML"

Closes #416

See merge request piotr.gawron/minerva!300
parents 909c0b91 82eee881
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1 merge request!300Resolve "error when exporting model generated from SBML"
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converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java
+ 46
− 32
View file @ b06d14fe
......@@ -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);
}
}
/**
......
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionCollectionXmlParser.java
+ 4
− 0
View file @ b06d14fe
......@@ -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;
......
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXml.java
+ 4
− 0
View file @ b06d14fe
......@@ -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() + "\" ");
......
converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/reaction/SelfReactionException.java 0 → 100644
+ 31
− 0
View file @ b06d14fe
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);
}
}
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java
+ 37
− 0
View file @ b06d14fe
......@@ -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;
}
}
}
converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/reaction/ReactionToXmlTest.java
+ 29
− 18
View file @ b06d14fe
......@@ -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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