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Commit 660e66bd authored by Piotr Gawron's avatar Piotr Gawron
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common parsing interface for bioentities exracted

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1 merge request!186Resolve "upload of sbml"
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converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlBioEntityParser.java 0 → 100644
+ 47
− 0
View file @ 660e66bd
package lcsb.mapviewer.converter.model.sbml;
import java.util.HashSet;
import java.util.Set;
import javax.xml.stream.XMLStreamException;
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.util.NotImplementedException;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.BioEntity;
import lcsb.mapviewer.model.map.MiriamData;
public class SbmlBioEntityParser {
protected Layout layout;
protected lcsb.mapviewer.model.map.model.Model minervaModel;
public SbmlBioEntityParser() {
super();
}
protected Set<MiriamData> parseAnnotation(Annotation annotation) {
if (annotation.getCVTermCount() > 0) {
throw new NotImplementedException();
}
Set<MiriamData> result = new HashSet<>();
return result;
}
protected void assignBioEntityData(AbstractNamedSBase sbmlElement, BioEntity result) throws InvalidInputDataExecption {
result.addMiriamData(parseAnnotation(sbmlElement.getAnnotation()));
result.setName(sbmlElement.getName());
if (result.getName() == null || result.getName().isEmpty()) {
result.setName(result.getElementId());
}
try {
result.setNotes(sbmlElement.getNotesString());
} catch (XMLStreamException e) {
throw new InvalidInputDataExecption(sbmlElement.getId() + " Invalid notes", e);
}
}
}
\ No newline at end of file
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
+ 1
− 12
View file @ 660e66bd
......@@ -3,8 +3,6 @@ package lcsb.mapviewer.converter.model.sbml;
import java.util.ArrayList;
import java.util.List;
import javax.xml.stream.XMLStreamException;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
......@@ -29,16 +27,7 @@ public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Comp
protected Compartment parse(org.sbml.jsbml.Compartment compartment, Model sbmlModel)
throws InvalidInputDataExecption {
Compartment result = new SquareCompartment(compartment.getId());
result.setMiriamData(parseAnnotation(compartment.getAnnotation()));
result.setName(compartment.getName());
if (result.getName() == null || result.getName().isEmpty()) {
result.setName(result.getElementId());
}
try {
result.setNotes(compartment.getNotesString());
} catch (XMLStreamException e) {
throw new InvalidInputDataExecption(compartment.getId() + " Invalid compartment notes", e);
}
assignBioEntityData(compartment, result);
return result;
}
......
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
+ 1
− 16
View file @ 660e66bd
......@@ -8,25 +8,18 @@ import java.util.Map;
import java.util.Set;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.util.NotImplementedException;
import lcsb.mapviewer.common.Pair;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.MiriamData;
import lcsb.mapviewer.model.map.species.Element;
public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> {
public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> extends SbmlBioEntityParser {
Logger logger = Logger.getLogger(SbmlElementParser.class);
Layout layout;
lcsb.mapviewer.model.map.model.Model minervaModel;
public SbmlElementParser(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel) {
this.layout = sbmlLayout;
this.minervaModel = minervaModel;
......@@ -92,12 +85,4 @@ public abstract class SbmlElementParser<T extends org.sbml.jsbml.Symbol> {
protected abstract Element parse(T species, Model sbmlModel) throws InvalidInputDataExecption;
protected Set<MiriamData> parseAnnotation(Annotation annotation) {
if (annotation.getCVTermCount() > 0) {
throw new NotImplementedException();
}
Set<MiriamData> result = new HashSet<>();
return result;
}
}
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionExporter.java
+ 24
− 20
View file @ 660e66bd
......@@ -5,6 +5,8 @@ import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
import javax.xml.stream.XMLStreamException;
import org.apache.log4j.Logger;
import org.sbml.jsbml.SimpleSpeciesReference;
import org.sbml.jsbml.Species;
......@@ -18,6 +20,7 @@ import org.sbml.jsbml.ext.layout.ReactionGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceGlyph;
import org.sbml.jsbml.ext.layout.SpeciesReferenceRole;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.modifier.Inhibition;
import lcsb.mapviewer.model.map.reaction.Modifier;
......@@ -40,25 +43,28 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
@Override
public org.sbml.jsbml.Reaction createSbmlElement(Reaction reaction) throws InconsistentModelException {
logger.debug(reaction);
org.sbml.jsbml.Reaction result = sbmlModel.createReaction("reaction_" + (getNextId()));
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
speciesReferenceByReactionNode.put(product, speciesReference);
}
for (Reactant reactant : reaction.getReactants()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(reactant.getElement().getElementId());
SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
logger.debug(reactant);
speciesReferenceByReactionNode.put(reactant, speciesReference);
}
for (Modifier modifier : reaction.getModifiers()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(modifier.getElement().getElementId());
SimpleSpeciesReference speciesReference = result.createModifier(sbmlSymbol);
speciesReferenceByReactionNode.put(modifier, speciesReference);
try {
org.sbml.jsbml.Reaction result = sbmlModel.createReaction("reaction_" + (getNextId()));
result.setNotes(reaction.getNotes());
for (Product product : reaction.getProducts()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(product.getElement().getElementId());
SpeciesReference speciesReference = result.createProduct(sbmlSymbol);
speciesReferenceByReactionNode.put(product, speciesReference);
}
for (Reactant reactant : reaction.getReactants()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(reactant.getElement().getElementId());
SpeciesReference speciesReference = result.createReactant(sbmlSymbol);
speciesReferenceByReactionNode.put(reactant, speciesReference);
}
for (Modifier modifier : reaction.getModifiers()) {
Species sbmlSymbol = speciesExporter.sbmlElementByElementId.get(modifier.getElement().getElementId());
SimpleSpeciesReference speciesReference = result.createModifier(sbmlSymbol);
speciesReferenceByReactionNode.put(modifier, speciesReference);
}
return result;
} catch (XMLStreamException e) {
throw new InvalidStateException(e);
}
return result;
}
@Override
......@@ -75,7 +81,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
@Override
protected void assignLayoutToGlyph(Reaction reaction, AbstractReferenceGlyph compartmentGlyph) {
logger.debug(reaction);
ReactionGlyph reactionGlyph = (ReactionGlyph) compartmentGlyph;
boolean firstReactant = true;
for (Reactant reactant : reaction.getReactants()) {
......@@ -112,7 +117,6 @@ public class SbmlReactionExporter extends SbmlBioEntityExporter<Reaction, org.sb
SpeciesReferenceGlyph reactantGlyph = reactionGlyph.createSpeciesReferenceGlyph("node_" + getNextId());
reactantGlyph.setSpeciesGlyph(speciesExporter.sbmlGlyphByElementId.get(node.getElement().getElementId()).getId());
reactantGlyph.setCurve(createCurve(node));
logger.debug(node);
reactantGlyph.setSpeciesReference(speciesReferenceByReactionNode.get(node));
return reactantGlyph;
}
......
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlReactionParser.java
+ 2
− 9
View file @ 660e66bd
......@@ -47,7 +47,7 @@ import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlReactionParser {
public class SbmlReactionParser extends SbmlBioEntityParser {
Logger logger = Logger.getLogger(SbmlReactionParser.class);
Layout layout;
......@@ -244,6 +244,7 @@ public class SbmlReactionParser {
protected Reaction parse(org.sbml.jsbml.Reaction sbmlReaction, Model sbmlModel) throws InvalidInputDataExecption {
Reaction reaction = new StateTransitionReaction();
assignBioEntityData(sbmlReaction, reaction);
reaction.setIdReaction(sbmlReaction.getId());
reaction.setReversible(sbmlReaction.isReversible());
if (sbmlReaction.getKineticLaw() != null) {
......@@ -266,14 +267,6 @@ public class SbmlReactionParser {
return reaction;
}
protected Set<MiriamData> parseAnnotation(Annotation annotation) {
if (annotation.getCVTermCount() > 0) {
throw new NotImplementedException();
}
Set<MiriamData> result = new HashSet<>();
return result;
}
public void validateReactions(Set<Reaction> reactions) throws InvalidInputDataExecption {
for (Reaction reaction : reactions) {
if (reaction.getReactants().size() == 0) {
......
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
+ 3
− 15
View file @ 660e66bd
......@@ -4,8 +4,6 @@ import java.lang.reflect.InvocationTargetException;
import java.util.ArrayList;
import java.util.List;
import javax.xml.stream.XMLStreamException;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
......@@ -39,19 +37,9 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
if (clazz == null) {
throw new InvalidInputDataExecption("Unknown species type: " + type);
}
Species result;
try {
result = clazz.getConstructor(String.class).newInstance(species.getId());
result.setMiriamData(parseAnnotation(species.getAnnotation()));
result.setName(species.getName());
if (result.getName() == null || result.getName().isEmpty()) {
result.setName(result.getElementId());
}
try {
result.setNotes(species.getNotesString());
} catch (XMLStreamException e) {
throw new InvalidInputDataExecption(species.getId() + " Invalid Species notes", e);
}
Species result = clazz.getConstructor(String.class).newInstance(species.getId());
assignBioEntityData(species, result);
return result;
} catch (SecurityException | NoSuchMethodException | InstantiationException | IllegalAccessException
| IllegalArgumentException | InvocationTargetException e) {
......@@ -91,7 +79,7 @@ public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species>
compartment = compartment2;
}
}
}
if (compartment != null) {
compartment.addElement(element);
......
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+ 25
− 2
View file @ 660e66bd
......@@ -161,6 +161,20 @@ public class SbmlExporterTest {
@Test
public void testExportReactionWithLayout() throws Exception {
Model model = createModelWithReaction();
Reaction reaction = model.getReactions().iterator().next();
Model deserializedModel = getModelAfterSerializing(model);
Reaction deserializedReaction = deserializedModel.getReactions().iterator().next();
assertEquals(reaction.getReactants().get(0).getLine().length(),
deserializedReaction.getReactants().get(0).getLine().length(), Configuration.EPSILON);
assertEquals(reaction.getProducts().get(0).getLine().length(),
deserializedReaction.getProducts().get(0).getLine().length(), Configuration.EPSILON);
}
private Model createModelWithReaction() {
Model model = new ModelFullIndexed(null);
GenericProtein p1 = new GenericProtein("s1");
p1.setWidth(100);
......@@ -188,10 +202,19 @@ public class SbmlExporterTest {
reaction.addReactant(reactant);
reaction.addProduct(product);
model.addReaction(reaction);
return model;
}
@Test
public void testExportReactionWithNotes() throws Exception {
Model model = createModelWithReaction();
Reaction reaction = model.getReactions().iterator().next();
reaction.setNotes("XYZ");
Model deserializedModel = getModelAfterSerializing(model);
Reaction deserializedReaction = deserializedModel.getReactions().iterator().next();
assertEquals(reactantLine.length(), deserializedReaction.getReactants().get(0).getLine().length(), Configuration.EPSILON);
assertEquals(productLine.length(), deserializedReaction.getProducts().get(0).getLine().length(), Configuration.EPSILON);
assertEquals(reaction.getNotes(), deserializedReaction.getNotes());
}
......
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