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Commit 14cea5ea authored by Piotr Gawron's avatar Piotr Gawron
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simple export of species implemeted

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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/SbmlCompartmentExporter.java
+ 11
− 51
View file @ 14cea5ea
package lcsb.mapviewer.converter.model.sbml;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.xml.stream.XMLStreamException;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.BoundingBox;
import org.sbml.jsbml.ext.layout.CompartmentGlyph;
import org.sbml.jsbml.ext.layout.Dimensions;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.Point;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.compartment.Compartment;
public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment> {
public class SbmlCompartmentExporter extends SbmlElementExporter<Compartment, org.sbml.jsbml.Compartment> {
Logger logger = Logger.getLogger(SbmlCompartmentExporter.class);
Map<String, org.sbml.jsbml.Compartment> sbmlCompartmentByElementId = new HashMap<>();
Map<String, org.sbml.jsbml.Compartment> sbmlCompartmentByName = new HashMap<>();
Map<String, CompartmentGlyph> sbmlCompartmentGlyphByElementId = new HashMap<>();
public SbmlCompartmentExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel) {
super(layout, minervaModel);
}
@Override
public void exportElements(Model model) throws InconsistentModelException {
List<Compartment> compartments = minervaModel.getCompartments();
for (Compartment compartment : compartments) {
if (sbmlCompartmentByName.get(compartment.getName()) == null) {
org.sbml.jsbml.Compartment sbmlCompartment = model.createCompartment("comp_" + compartment.getName());
try {
sbmlCompartment.setNotes(compartment.getNotes());
} catch (XMLStreamException e) {
throw new InvalidStateException(e);
}
sbmlCompartmentByName.put(compartment.getName(), sbmlCompartment);
}
org.sbml.jsbml.Compartment sbmlCompartment = sbmlCompartmentByName.get(compartment.getName());
if (sbmlCompartmentByElementId.get(compartment.getElementId()) != null) {
throw new InconsistentModelException("More than one compartment with id: " + compartment.getElementId());
}
sbmlCompartmentByElementId.put(compartment.getElementId(), sbmlCompartment);
}
for (Compartment compartment : compartments) {
CompartmentGlyph compartmentGlyph = createCompartmentGlyph(compartment);
sbmlCompartmentGlyphByElementId.put(compartment.getElementId(), compartmentGlyph);
}
public org.sbml.jsbml.Compartment createSbmlElement(Compartment element) throws InconsistentModelException {
return sbmlModel.createCompartment("comp_" + element.getName());
}
private CompartmentGlyph createCompartmentGlyph(Compartment compartment) {
String sbmlCompartmentId = sbmlCompartmentByElementId.get(compartment.getElementId()).getId();
String glyphId = compartment.getElementId();
CompartmentGlyph compartmentGlyph = layout.createCompartmentGlyph(glyphId, sbmlCompartmentId);
BoundingBox boundingBox = new BoundingBox();
@Override
protected List<Compartment> getElementList() {
return minervaModel.getCompartments();
}
boundingBox.setPosition(new Point(compartment.getX(), compartment.getY()));
Dimensions dimensions = new Dimensions();
dimensions.setWidth(compartment.getWidth());
dimensions.setHeight(compartment.getHeight());
boundingBox.setDimensions(dimensions);
compartmentGlyph.setBoundingBox(boundingBox);
return compartmentGlyph;
@Override
protected AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId) {
return layout.createCompartmentGlyph(glyphId, sbmlCompartmentId);
}
}
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
+ 76
− 3
View file @ 14cea5ea
package lcsb.mapviewer.converter.model.sbml;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.xml.stream.XMLStreamException;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.BoundingBox;
import org.sbml.jsbml.ext.layout.Dimensions;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.Point;
import lcsb.mapviewer.common.exception.InvalidStateException;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Element;
public abstract class SbmlElementExporter<T extends Element> {
public abstract class SbmlElementExporter<T extends Element, S extends org.sbml.jsbml.Symbol> {
Logger logger = Logger.getLogger(SbmlElementExporter.class);
Layout layout;
lcsb.mapviewer.model.map.model.Model minervaModel;
Model sbmlModel;
Map<String, S> sbmlElementByElementId = new HashMap<>();
Map<String, AbstractReferenceGlyph> sbmlGlyphByElementId = new HashMap<>();
private Map<String, S> sbmlElementByElementNameAndCompartmentName = new HashMap<>();
public SbmlElementExporter(Layout sbmlLayout, lcsb.mapviewer.model.map.model.Model minervaModel) {
this.layout = sbmlLayout;
this.minervaModel = minervaModel;
}
public abstract void exportElements(Model model) throws InconsistentModelException;
public void exportElements(Model model) throws InconsistentModelException {
sbmlModel = model;
List<T> speciesList = getElementList();
for (T species : speciesList) {
S sbmlCompartment = getSbmlElement(species, null);
if (sbmlElementByElementId.get(species.getElementId()) != null) {
throw new InconsistentModelException("More than one species with id: " + species.getElementId());
}
sbmlElementByElementId.put(species.getElementId(), sbmlCompartment);
}
for (T species : speciesList) {
AbstractReferenceGlyph compartmentGlyph = createCompartmentGlyph(species);
sbmlGlyphByElementId.put(species.getElementId(), compartmentGlyph);
}
}
protected abstract List<T> getElementList();
public abstract S createSbmlElement(T element) throws InconsistentModelException;
protected S getSbmlElement(T element, String compartmentName) throws InconsistentModelException {
String mapKey = element.getName() + "\n" + compartmentName;
if (sbmlElementByElementNameAndCompartmentName.get(mapKey) == null) {
S sbmlElement = createSbmlElement(element);
sbmlElement.setName(element.getName());
try {
sbmlElement.setNotes(element.getNotes());
} catch (XMLStreamException e) {
throw new InvalidStateException(e);
}
sbmlElementByElementNameAndCompartmentName.put(mapKey, sbmlElement);
}
return sbmlElementByElementNameAndCompartmentName.get(mapKey);
}
protected void assignLayoutToGlyph(T element, AbstractReferenceGlyph compartmentGlyph) {
BoundingBox boundingBox = new BoundingBox();
boundingBox.setPosition(new Point(element.getX(), element.getY()));
Dimensions dimensions = new Dimensions();
dimensions.setWidth(element.getWidth());
dimensions.setHeight(element.getHeight());
boundingBox.setDimensions(dimensions);
compartmentGlyph.setBoundingBox(boundingBox);
}
protected AbstractReferenceGlyph createCompartmentGlyph(T compartment) {
String sbmlCompartmentId = sbmlElementByElementId.get(compartment.getElementId()).getId();
String glyphId = compartment.getElementId();
AbstractReferenceGlyph compartmentGlyph = createElementGlyph(sbmlCompartmentId, glyphId);
assignLayoutToGlyph(compartment, compartmentGlyph);
return compartmentGlyph;
}
protected abstract AbstractReferenceGlyph createElementGlyph(String sbmlCompartmentId, String glyphId);
}
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
+ 16
− 19
View file @ 14cea5ea
......@@ -3,16 +3,10 @@ package lcsb.mapviewer.converter.model.sbml;
import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.output.ByteArrayOutputStream;
import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.Creator;
import org.sbml.jsbml.History;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBMLWriter;
import org.sbml.jsbml.Species;
import org.sbml.jsbml.SpeciesReference;
import org.sbml.jsbml.ext.layout.Dimensions;
import org.sbml.jsbml.ext.layout.Layout;
import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
......@@ -20,24 +14,27 @@ import org.sbml.jsbml.ext.layout.LayoutModelPlugin;
import lcsb.mapviewer.model.map.InconsistentModelException;
public class SbmlExporter {
public String toXml(lcsb.mapviewer.model.map.model.Model model) throws SBMLException, XMLStreamException, InconsistentModelException {
public String toXml(lcsb.mapviewer.model.map.model.Model model)
throws SBMLException, XMLStreamException, InconsistentModelException {
SBMLDocument doc = new SBMLDocument(3, 1);
Model result = doc.createModel(model.getName());
Layout layout = createSbmlLayout(model, result);
SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
SbmlSpeciesExporter speciesExporter = new SbmlSpeciesExporter(layout, model, compartmentExporter);
compartmentExporter.exportElements(result);
// // Create some sample content in the SBML model.
// Species specOne = result.createSpecies("test_spec1", compartment);
// Species specTwo = result.createSpecies("test_spec2", compartment);
// Reaction sbReaction = result.createReaction("reaction_id");
//
// // Add a substrate (SBO:0000015) and product (SBO:0000011) to the reaction.
// SpeciesReference subs = sbReaction.createReactant(specOne);
// subs.setSBOTerm(15);
// SpeciesReference prod = sbReaction.createProduct(specTwo);
// prod.setSBOTerm(11);
speciesExporter.exportElements(result);
// // Create some sample content in the SBML model.
// Species specOne = result.createSpecies("test_spec1", compartment);
// Species specTwo = result.createSpecies("test_spec2", compartment);
// Reaction sbReaction = result.createReaction("reaction_id");
//
// // Add a substrate (SBO:0000015) and product (SBO:0000011) to the reaction.
// SpeciesReference subs = sbReaction.createReactant(specOne);
// subs.setSBOTerm(15);
// SpeciesReference prod = sbReaction.createProduct(specTwo);
// prod.setSBOTerm(11);
// For brevity, we omit error checking, BUT YOU SHOULD CALL
// doc.checkConsistency() and check the error log.
......
converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesExporter.java 0 → 100644
+ 44
− 0
View file @ 14cea5ea
package lcsb.mapviewer.converter.model.sbml;
import java.util.List;
import org.apache.log4j.Logger;
import org.sbml.jsbml.Symbol;
import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
import org.sbml.jsbml.ext.layout.Layout;
import lcsb.mapviewer.model.map.InconsistentModelException;
import lcsb.mapviewer.model.map.species.Species;
public class SbmlSpeciesExporter extends SbmlElementExporter<Species, org.sbml.jsbml.Species> {
Logger logger = Logger.getLogger(SbmlSpeciesExporter.class);
private int idCounter = 0;
private SbmlCompartmentExporter compartmentExporter;
public SbmlSpeciesExporter(Layout layout, lcsb.mapviewer.model.map.model.Model minervaModel,
SbmlCompartmentExporter compartmentExporter) {
super(layout, minervaModel);
this.compartmentExporter = compartmentExporter;
}
@Override
public org.sbml.jsbml.Species createSbmlElement(Species element) throws InconsistentModelException {
org.sbml.jsbml.Species result = sbmlModel.createSpecies("species_" + (idCounter++));
if (element.getCompartment() != null) {
result.setCompartment(compartmentExporter.getSbmlElement(element.getCompartment(), null));
}
return result;
}
@Override
protected AbstractReferenceGlyph createElementGlyph(String sbmlElementId, String glyphId) {
AbstractReferenceGlyph speciesGlyph = layout.createSpeciesGlyph(glyphId, sbmlElementId);
return speciesGlyph;
}
@Override
protected List<Species> getElementList() {
return minervaModel.getSpeciesList();
}
}
converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
+ 5
− 4
View file @ 14cea5ea
......@@ -23,7 +23,7 @@ public class SbmlExporterTest {
SbmlExporter exporter = new SbmlExporter();
@Test
public void testParseCompartment() throws Exception {
public void testExportCompartment() throws Exception {
Model model = getModelAfterSerializing("testFiles/layoutExample/CompartmentGlyph_Example_level2_level3.xml");
assertNotNull(model);
assertEquals(1, model.getCompartments().size());
......@@ -43,12 +43,13 @@ public class SbmlExporterTest {
private Model getModelAfterSerializing(String filename) throws Exception {
Model originalModel = parser.createModel(new ConverterParams().filename(filename));
String xml = exporter.toXml(originalModel);
logger.debug(xml);
ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
return parser.createModel(new ConverterParams().inputStream(stream));
}
@Test
public void testParseSpecies() throws Exception {
public void testExportSpecies() throws Exception {
Model model = getModelAfterSerializing("testFiles/layoutExample/SpeciesGlyph_Example_level2_level3.xml");
assertNotNull(model);
assertEquals(1, model.getElements().size());
......@@ -65,7 +66,7 @@ public class SbmlExporterTest {
}
@Test
public void testParseSpeciesInCompartments() throws Exception {
public void testExportSpeciesInCompartments() throws Exception {
Model model = getModelAfterSerializing("testFiles/layoutExample/SpeciesGlyph_Example.xml");
assertNotNull(model);
assertEquals(2, model.getElements().size());
......@@ -83,7 +84,7 @@ public class SbmlExporterTest {
}
@Test
public void testParseReaction() throws Exception {
public void testExportReaction() throws Exception {
Model model = getModelAfterSerializing("testFiles/layoutExample/Complete_Example.xml");
assertNotNull(model);
assertEquals(1, model.getReactions().size());
......
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