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Commit e9ffb42c authored by Piotr Gawron's avatar Piotr Gawron
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species type contains list of all structural state values in the proper feature

parent f9e55b64
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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
+ 48
− 5
View file @ e9ffb42c
......@@ -3,7 +3,9 @@ package lcsb.mapviewer.converter.model.sbml;
import java.io.UnsupportedEncodingException;
import java.util.Arrays;
import java.util.Collection;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Map;
import java.util.Set;
import javax.xml.stream.XMLStreamException;
......@@ -42,6 +44,8 @@ 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.
*/
......@@ -88,8 +92,10 @@ public class SbmlExporter {
layout = createSbmlLayout(model, result);
}
MultiModelPlugin multiPlugin = null;
if (usedExtensions.contains(SbmlExtension.MULTI)) {
createSbmlMultiPlugin(result);
multiPlugin = createSbmlMultiPlugin(result);
assignStructuralStatesToTypes(multiPlugin, model);
}
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model, usedExtensions);
......@@ -111,6 +117,28 @@ public class SbmlExporter {
return doc;
}
private void assignStructuralStatesToTypes(MultiModelPlugin multiPlugin, lcsb.mapviewer.model.map.model.Model model) {
for (Element element : model.getElements()) {
String structuralState = null;
if (element instanceof Protein) {
structuralState = ((Protein) element).getStructuralState();
} else if (element instanceof Complex) {
structuralState = ((Complex) element).getStructuralState();
}
if (structuralState != null) {
MultiSpeciesType speciesType = speciesTypeByClass.get(element.getClass());
addStructuralStateToPossibleValues(speciesType, structuralState);
}
}
}
private void addStructuralStateToPossibleValues(MultiSpeciesType speciesType, String structuralState) {
SpeciesFeatureType feature = speciesType.getListOfSpeciesFeatureTypes()
.get("minerva_structural_state_" + speciesType.getName());
addPosibleValueToFeature(feature, structuralState);
}
/**
* Create SBML layout for the given model.
*
......@@ -145,6 +173,8 @@ public class SbmlExporter {
return layout;
}
private Map<Class<?>, MultiSpeciesType> speciesTypeByClass = new HashMap<>();
@SuppressWarnings("unchecked")
protected MultiModelPlugin createSbmlMultiPlugin(Model result) {
MultiModelPlugin multiPlugin = new MultiModelPlugin(result);
......@@ -158,19 +188,32 @@ public class SbmlExporter {
SpeciesFeatureType feature = new SpeciesFeatureType();
feature.setName("Structural state");
feature.setId("minerva_structural_state_" + clazz.getSimpleName());
PossibleSpeciesFeatureValue featureEmptyValue = new PossibleSpeciesFeatureValue();
featureEmptyValue.setId("minerva_structural_state_" + clazz.getSimpleName() + "_empty");
featureEmptyValue.setName("");
feature.getListOfPossibleSpeciesFeatureValues().add(featureEmptyValue);
addPosibleValueToFeature(feature, "");
speciesType.getListOfSpeciesFeatureTypes().add(feature);
}
multiPlugin.getListOfSpeciesTypes().add(speciesType);
speciesTypeByClass.put(clazz, speciesType);
speciesType.setSBOTerm(SBOTermSpeciesType.getTermByType((Class<? extends Species>) clazz));
}
}
return multiPlugin;
}
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/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+ 74
− 18
View file @ e9ffb42c
......@@ -22,6 +22,8 @@ import org.reflections.Reflections;
import org.sbml.jsbml.SBMLDocument;
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 lcsb.mapviewer.common.Configuration;
import lcsb.mapviewer.converter.ConverterParams;
......@@ -194,9 +196,7 @@ public class SbmlExporterTest {
}
private Model createModelWithReaction() {
Model model = new ModelFullIndexed(null);
model.setWidth(1000);
model.setHeight(1000);
Model model = createEmptyModel();
GenericProtein p1 = new GenericProtein("s1");
p1.setWidth(100);
p1.setHeight(20);
......@@ -263,11 +263,7 @@ public class SbmlExporterTest {
String tempFilename = File.createTempFile("tmp", ".xml").getAbsolutePath();
IConverter converter = new SbmlParser();
Model model = new ModelFullIndexed(null);
model.setWidth(100);
model.setHeight(100);
model.setName("UNKNOWN DISEASE MAP");
model.setIdModel("id1");
Model model = createEmptyModel();
converter.exportModelToFile(model, tempFilename);
......@@ -279,6 +275,15 @@ public class SbmlExporterTest {
}
private Model createEmptyModel() {
Model model = new ModelFullIndexed(null);
model.setWidth(1000);
model.setHeight(1000);
model.setName("UNKNOWN DISEASE MAP");
model.setIdModel("id1");
return model;
}
@Test
public void testExportProblematicNotes() throws Exception {
Model model = createModelWithReaction();
......@@ -332,11 +337,7 @@ public class SbmlExporterTest {
Set<Class<? extends Species>> classes = reflections.getSubTypesOf(Species.class);
for (Class<? extends Element> class1 : classes) {
if (!Modifier.isAbstract(class1.getModifiers())) {
Model model = new ModelFullIndexed(null);
model.setIdModel("Test123");
model.setName("x");
model.setWidth("300");
model.setHeight("300");
Model model = createEmptyModel();
Element element = class1.getConstructor(String.class).newInstance("x");
element.setName("test name");
element.setX(10);
......@@ -463,11 +464,7 @@ public class SbmlExporterTest {
@Test
public void testExportProteinState() throws Exception {
Model model = new ModelFullIndexed(null);
model.setIdModel("Test123");
model.setName("x");
model.setWidth("300");
model.setHeight("300");
Model model = createEmptyModel();
GenericProtein element = new GenericProtein("id");
element.setName("test name");
element.setX(10);
......@@ -481,4 +478,63 @@ public class SbmlExporterTest {
assertEquals("Structural state not exported/imported properly", 0, comparator.compare(model, deserializedModel));
}
@Test
public void testMultiExtensionProteinStateInTypes() throws Exception {
String structuralState = "xxx";
Model model = createEmptyModel();
GenericProtein element = new GenericProtein("id");
element.setName("test name");
element.setX(10);
element.setWidth(10);
element.setY(10);
element.setHeight(10);
element.setStructuralState(structuralState);
model.addElement(element);
org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
MultiModelPlugin multiPlugin = (MultiModelPlugin) sbmlModel.getExtension("multi");
boolean structuralStateValueFound = false;
for (MultiSpeciesType speciesType : multiPlugin.getListOfSpeciesTypes()) {
for (SpeciesFeatureType featureType : speciesType.getListOfSpeciesFeatureTypes()) {
for (PossibleSpeciesFeatureValue featureValue : featureType.getListOfPossibleSpeciesFeatureValues()) {
if (featureValue.getName().equals(structuralState)) {
structuralStateValueFound = true;
}
}
}
}
assertTrue("Structural state not defined in the list of possible values", structuralStateValueFound);
}
@Test
public void testMultiExtensionProteinStateSuplicateInTypes() throws Exception {
String structuralState = "xxx";
Model model = createEmptyModel();
GenericProtein element = new GenericProtein("id");
element.setName("test name");
element.setX(10);
element.setWidth(10);
element.setY(10);
element.setHeight(10);
element.setStructuralState(structuralState);
model.addElement(element);
element = new GenericProtein("id2");
element.setName("test name");
element.setX(10);
element.setWidth(10);
element.setY(10);
element.setHeight(10);
element.setStructuralState(structuralState);
model.addElement(element);
org.sbml.jsbml.Model sbmlModel = exporter.toSbmlDocument(model).getModel();
MultiModelPlugin multiPlugin = (MultiModelPlugin) sbmlModel.getExtension("multi");
for (MultiSpeciesType speciesType : multiPlugin.getListOfSpeciesTypes()) {
for (SpeciesFeatureType featureType : speciesType.getListOfSpeciesFeatureTypes()) {
assertTrue(featureType.getListOfPossibleSpeciesFeatureValues().size() <= 2);
}
}
}
}
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