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Commit e819e032 authored by Piotr Gawron's avatar Piotr Gawron
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species types and species feature are created when necessary

parent 293aa8d1
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2 merge requests!630WIP: Resolve "The privileges of a new user are not saved in some cases",!560Resolve "add support for modifications and states in sbml export/import"
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converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+ 1
− 95
View file @ e819e032
......@@ -20,8 +20,6 @@ import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
import org.sbml.jsbml.ext.render.GlobalRenderInformation;
import org.sbml.jsbml.ext.render.RenderLayoutPlugin;
......@@ -29,23 +27,16 @@ import lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
import lcsb.mapviewer.converter.model.sbml.reaction.SbmlReactionExporter;
import lcsb.mapviewer.converter.model.sbml.species.SBOTermSpeciesType;
import lcsb.mapviewer.converter.model.sbml.species.SbmlSpeciesExporter;
import lcsb.mapviewer.converter.model.sbml.units.SbmlUnitExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlExporter {
@SuppressWarnings("unused")
private static Logger logger = Logger.getLogger(SbmlExporter.class);
private int idCounter = 0;
/**
* Set of SBML extensions that should be used during export.
*/
......@@ -94,10 +85,8 @@ public class SbmlExporter {
createSbmlLayout(model, result);
}
MultiModelPlugin multiPlugin = null;
if (usedExtensions.contains(SbmlExtension.MULTI)) {
multiPlugin = createSbmlMultiPlugin(result);
assignModelDataToTypes(multiPlugin, model);
createSbmlMultiPlugin(result);
}
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(result, model, usedExtensions);
......@@ -119,40 +108,6 @@ public class SbmlExporter {
return doc;
}
private void assignModelDataToTypes(MultiModelPlugin multiPlugin, lcsb.mapviewer.model.map.model.Model model) {
for (Species species : model.getSpeciesList()) {
MultiSpeciesType speciesType = speciesTypeByClass.get(species.getClass());
addStructuralStateToPossibleValues(speciesType, species);
if (species instanceof Species) {
addPositionToCompartmentToPossibleValues(speciesType, ((Species) species));
}
}
}
private void addStructuralStateToPossibleValues(MultiSpeciesType speciesType, Species species) {
String structuralState = null;
if (species instanceof Protein) {
structuralState = ((Protein) species).getStructuralState();
} else if (species instanceof Complex) {
structuralState = ((Complex) species).getStructuralState();
}
if (structuralState != null) {
SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
.get(MultiPackageNamingUtils.getStructuralStateFeatureId(species));
addPosibleValueToFeature(feature, structuralState);
}
}
private void addPositionToCompartmentToPossibleValues(MultiSpeciesType speciesType, Species species) {
if (species.getPositionToCompartment() != null) {
SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
.get(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(species));
addPosibleValueToFeature(feature, species.getPositionToCompartment().name());
}
}
/**
* Create SBML layout for the given model.
*
......@@ -192,58 +147,9 @@ public class SbmlExporter {
protected MultiModelPlugin createSbmlMultiPlugin(Model result) {
MultiModelPlugin multiPlugin = new MultiModelPlugin(result);
result.addExtension("multi", multiPlugin);
for (Class<? extends Element> clazz : new ElementUtils().getAvailableElementSubclasses()) {
if (Species.class.isAssignableFrom(clazz)) {
createSpeciesTypeForClass(multiPlugin, clazz);
}
}
return multiPlugin;
}
@SuppressWarnings("unchecked")
private void createSpeciesTypeForClass(MultiModelPlugin multiPlugin, Class<? extends Element> clazz) {
MultiSpeciesType speciesType = new MultiSpeciesType();
speciesType.setName(clazz.getSimpleName());
speciesType.setId(MultiPackageNamingUtils.getSpeciesTypeId(clazz));
if (Protein.class.isAssignableFrom(clazz) || Complex.class.isAssignableFrom(clazz)) {
createStructuralStateFeature(clazz, speciesType);
}
createPositionToCompartmentFeature(clazz, speciesType);
multiPlugin.getListOfSpeciesTypes().add(speciesType);
speciesTypeByClass.put(clazz, speciesType);
speciesType.setSBOTerm(SBOTermSpeciesType.getTermByType((Class<? extends Species>) clazz));
}
private void createStructuralStateFeature(Class<? extends Element> clazz, MultiSpeciesType speciesType) {
SpeciesFeatureType feature = new SpeciesFeatureType();
feature.setName("Structural state");
feature.setId(MultiPackageNamingUtils.getStructuralStateFeatureId(clazz));
addPosibleValueToFeature(feature, "");
speciesType.getListOfSpeciesFeatureTypes().add(feature);
}
private void createPositionToCompartmentFeature(Class<? extends Element> clazz, MultiSpeciesType speciesType) {
SpeciesFeatureType feature = new SpeciesFeatureType();
feature.setName("Position to compartment");
feature.setId(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(clazz));
addPosibleValueToFeature(feature, "undefined");
speciesType.getListOfSpeciesFeatureTypes().add(feature);
}
private void addPosibleValueToFeature(SpeciesFeatureType feature, String value) {
boolean alreadyExists = false;
for (PossibleSpeciesFeatureValue existingValue : feature.getListOfPossibleSpeciesFeatureValues()) {
if (existingValue.getName().equals(value)) {
alreadyExists = true;
}
}
if (!alreadyExists) {
PossibleSpeciesFeatureValue featureEmptyValue = new PossibleSpeciesFeatureValue();
featureEmptyValue.setId(feature.getId() + "_" + (idCounter++));
featureEmptyValue.setName(value);
feature.getListOfPossibleSpeciesFeatureValues().add(featureEmptyValue);
}
}
/**
* Creates SBML render plugin for SBML model.
......
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporter.java
+ 91
− 30
View file @ e819e032
......@@ -6,6 +6,7 @@ import java.util.List;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.multi.MultiModelPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesPlugin;
import org.sbml.jsbml.ext.multi.MultiSpeciesType;
import org.sbml.jsbml.ext.multi.PossibleSpeciesFeatureValue;
......@@ -14,19 +15,20 @@ import org.sbml.jsbml.ext.multi.SpeciesFeatureType;
import org.sbml.jsbml.ext.multi.SpeciesFeatureValue;
import org.sbml.jsbml.ext.render.LocalStyle;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.converter.model.sbml.MultiPackageNamingUtils;
import lcsb.mapviewer.converter.model.sbml.SbmlElementExporter;
import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.Protein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.modelutils.map.ElementUtils;
public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.jsbml.Species> {
private static int idCounter = 0;
/**
* Default class logger.
*/
......@@ -84,18 +86,9 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
structuralState = ((Complex) element).getStructuralState();
}
if (structuralState != null) {
SpeciesFeatureType structuralStateFeature = speciesType
.getSpeciesFeatureType(MultiPackageNamingUtils.getStructuralStateFeatureId(element));
PossibleSpeciesFeatureValue structuralStateFeatureValue = null;
for (PossibleSpeciesFeatureValue value : structuralStateFeature.getListOfPossibleSpeciesFeatureValues()) {
if (value.getName().equals(structuralState)) {
structuralStateFeatureValue = value;
}
}
if (structuralStateFeatureValue == null) {
throw new InvalidStateException(
new ElementUtils().getElementTag(element) + "Cannot find structural state value for: " + structuralState);
}
SpeciesFeatureType structuralStateFeature = getStructuralStateFeature(element.getClass(), speciesType);
PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(structuralState,
structuralStateFeature);
SpeciesFeature feature = multiExtension.createSpeciesFeature();
feature.setSpeciesFeatureType(structuralStateFeature.getId());
......@@ -105,25 +98,29 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
}
private void assignPostionToCompartmentToMulti(Species element, MultiSpeciesPlugin multiExtension,
MultiSpeciesType speciesType) {
String positionToCompartmentName = "undefined";
if (element.getPositionToCompartment() != null) {
positionToCompartmentName = element.getPositionToCompartment().name();
}
SpeciesFeatureType structuralStateFeature = speciesType
.getSpeciesFeatureType(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(element));
private PossibleSpeciesFeatureValue getPosibleFeatureIdByName(String featureValueName,
SpeciesFeatureType speciesFeature) {
PossibleSpeciesFeatureValue structuralStateFeatureValue = null;
for (PossibleSpeciesFeatureValue value : structuralStateFeature.getListOfPossibleSpeciesFeatureValues()) {
if (value.getName().equals(positionToCompartmentName)) {
for (PossibleSpeciesFeatureValue value : speciesFeature.getListOfPossibleSpeciesFeatureValues()) {
if (value.getName().equals(featureValueName)) {
structuralStateFeatureValue = value;
}
}
if (structuralStateFeatureValue == null) {
throw new InvalidStateException(
new ElementUtils().getElementTag(element) + "Cannot find position to compartment value for: "
+ positionToCompartmentName);
structuralStateFeatureValue = addPosibleValueToFeature(speciesFeature, featureValueName);
}
return structuralStateFeatureValue;
}
private void assignPostionToCompartmentToMulti(Species element, MultiSpeciesPlugin multiExtension,
MultiSpeciesType speciesType) {
String positionToCompartmentName = "undefined";
if (element.getPositionToCompartment() != null) {
positionToCompartmentName = element.getPositionToCompartment().name();
}
SpeciesFeatureType structuralStateFeature = getPositionToCompartmentFeature(element.getClass(), speciesType);
PossibleSpeciesFeatureValue structuralStateFeatureValue = getPosibleFeatureIdByName(positionToCompartmentName,
structuralStateFeature);
SpeciesFeature feature = multiExtension.createSpeciesFeature();
feature.setSpeciesFeatureType(structuralStateFeature.getId());
......@@ -133,8 +130,10 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
private MultiSpeciesType getMultiSpeciesType(Species element) {
MultiSpeciesType speciesType = getMultiPlugin()
.getSpeciesType(MultiPackageNamingUtils.getSpeciesTypeId(element));
MultiSpeciesType speciesType = getMultiPlugin().getSpeciesType(MultiPackageNamingUtils.getSpeciesTypeId(element));
if (speciesType == null) {
speciesType = createSpeciesTypeForClass(getMultiPlugin(), element.getClass());
}
return speciesType;
}
......@@ -170,7 +169,8 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
}
multiDistinguisher = structuralState;
}
String result =element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n" + complexName
String result = element.getClass().getSimpleName() + "\n" + element.getName() + "\n" + compartmentName + "\n"
+ complexName
+ "\n" + multiDistinguisher;
return result;
}
......@@ -181,4 +181,65 @@ public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.j
return style;
}
@SuppressWarnings("unchecked")
private MultiSpeciesType createSpeciesTypeForClass(MultiModelPlugin multiPlugin, Class<? extends Element> clazz) {
MultiSpeciesType speciesType = new MultiSpeciesType();
speciesType.setName(clazz.getSimpleName());
speciesType.setId(MultiPackageNamingUtils.getSpeciesTypeId(clazz));
multiPlugin.getListOfSpeciesTypes().add(speciesType);
speciesType.setSBOTerm(SBOTermSpeciesType.getTermByType((Class<? extends Species>) clazz));
return speciesType;
}
private SpeciesFeatureType getStructuralStateFeature(Class<? extends Element> clazz, MultiSpeciesType speciesType) {
SpeciesFeatureType feature = speciesType
.getSpeciesFeatureType(MultiPackageNamingUtils.getStructuralStateFeatureId(clazz));
if (feature == null) {
feature = new SpeciesFeatureType();
feature.setName("Structural state");
feature.setId(MultiPackageNamingUtils.getStructuralStateFeatureId(clazz));
addPosibleValueToFeature(feature, "");
speciesType.getListOfSpeciesFeatureTypes().add(feature);
}
return feature;
}
private SpeciesFeatureType getPositionToCompartmentFeature(Class<? extends Element> clazz,
MultiSpeciesType speciesType) {
SpeciesFeatureType feature = speciesType
.getSpeciesFeatureType(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(clazz));
if (feature == null) {
feature = new SpeciesFeatureType();
feature.setName("Position to compartment");
feature.setId(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(clazz));
addPosibleValueToFeature(feature, "undefined");
speciesType.getListOfSpeciesFeatureTypes().add(feature);
}
return feature;
}
private PossibleSpeciesFeatureValue addPosibleValueToFeature(SpeciesFeatureType feature, String value) {
PossibleSpeciesFeatureValue result = null;
for (PossibleSpeciesFeatureValue existingValue : feature.getListOfPossibleSpeciesFeatureValues()) {
if (existingValue.getName().equals(value)) {
result = existingValue;
}
}
if (result == null) {
result = new PossibleSpeciesFeatureValue();
result.setId(feature.getId() + "_" + (idCounter++));
result.setName(value);
feature.getListOfPossibleSpeciesFeatureValues().add(result);
}
return result;
}
private void addPositionToCompartmentToPossibleValues(MultiSpeciesType speciesType, Species species) {
if (species.getPositionToCompartment() != null) {
SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
.get(MultiPackageNamingUtils.getPositionToCompartmentFeatureId(species));
addPosibleValueToFeature(feature, species.getPositionToCompartment().name());
}
}
}
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+ 0
− 25
View file @ e819e032
......@@ -13,7 +13,6 @@ import java.io.File;
import java.lang.reflect.Modifier;
import java.nio.file.Files;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Set;
import org.apache.log4j.Logger;
......@@ -43,13 +42,9 @@ import lcsb.mapviewer.model.map.reaction.Reactant;
import lcsb.mapviewer.model.map.reaction.Reaction;
import lcsb.mapviewer.model.map.reaction.ReactionNode;
import lcsb.mapviewer.model.map.reaction.type.StateTransitionReaction;
import lcsb.mapviewer.model.map.species.Complex;
import lcsb.mapviewer.model.map.species.Element;
import lcsb.mapviewer.model.map.species.GenericProtein;
import lcsb.mapviewer.model.map.species.IonChannelProtein;
import lcsb.mapviewer.model.map.species.ReceptorProtein;
import lcsb.mapviewer.model.map.species.Species;
import lcsb.mapviewer.model.map.species.TruncatedProtein;
import lcsb.mapviewer.model.map.species.field.ModificationState;
import lcsb.mapviewer.model.map.species.field.PositionToCompartment;
import lcsb.mapviewer.model.map.species.field.Residue;
......@@ -431,26 +426,6 @@ public class SbmlExporterTest {
assertTrue("Species types are not exported", multiPlugin.getListOfSpeciesTypes().size() > 0);
}
@Test
public void testMultiExtensionTypeWithStructuralState() throws Exception {
SbmlExporter exporter = new SbmlExporter();
SBMLDocument doc = new SBMLDocument(3, 2);
org.sbml.jsbml.Model result = doc.createModel("id");
MultiModelPlugin multiPlugin = exporter.createSbmlMultiPlugin(result);
Set<Class<?>> typesWithStructuralStates = new HashSet<>();
typesWithStructuralStates.addAll(Arrays.asList(new Class<?>[] { GenericProtein.class, TruncatedProtein.class,
Complex.class, IonChannelProtein.class, ReceptorProtein.class }));
for (Class<?> clazz : typesWithStructuralStates) {
MultiSpeciesType speciesType = multiPlugin.getSpeciesType(MultiPackageNamingUtils.getSpeciesTypeId(clazz));
assertTrue(clazz.getSimpleName() + " doesn't have any features, but at least structuralState expected",
speciesType.getListOfSpeciesFeatureTypes().size() > 0);
}
}
@Test
public void testMultiExtensionSBOTermsForTypes() throws Exception {
SbmlExporter exporter = new SbmlExporter();
......
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