diff --git a/.gitignore b/.gitignore
index bbcea90463b8d87b5fec80ccacfd75fdaa3587b7..5f2ce9bf39d3f4369734360f98a8e770780ca767 100644
--- a/.gitignore
+++ b/.gitignore
@@ -10,6 +10,7 @@ web/src/main/webapp/svnversion.txt
/target/
service/minerva-big/
npm-debug.log
+converter-sbml/jsbml.log
.idea/workspace.xml
.idea/libraries/
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
index 27cc67f3126ab3b670d497aeb02af8bcc2f2a573..9e119bfbaffaa72f7ad2b08d3636aa66e7ae074a 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentParser.java
@@ -1,84 +1,32 @@
package lcsb.mapviewer.converter.model.sbml;
import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
import java.util.List;
-import java.util.Map;
-import java.util.Set;
import javax.xml.stream.XMLStreamException;
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.CompartmentGlyph;
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.compartment.Compartment;
import lcsb.mapviewer.model.map.compartment.SquareCompartment;
-public class SbmlCompartmentParser {
+public class SbmlCompartmentParser extends SbmlElementParser<org.sbml.jsbml.Compartment> {
Logger logger = Logger.getLogger(SbmlCompartmentParser.class);
- Layout layout;
-
public SbmlCompartmentParser(Layout layout) {
- this.layout = layout;
- }
-
- public List<Compartment> parseList(Model sbmlModel) throws InvalidInputDataExecption {
- List<Compartment> result = new ArrayList<>();
- for (org.sbml.jsbml.Compartment compartment : sbmlModel.getListOfCompartments()) {
- result.add(parse(compartment));
- }
- if (layout != null) {
- return mergeLayout(result, layout);
- } else {
- return result;
- }
- }
-
- private List<Compartment> mergeLayout(List<Compartment> compartments, Layout sbmlLayout)
- throws InvalidInputDataExecption {
- Set<Compartment> used = new HashSet<>();
- Map<String, Compartment> compartmentById = new HashMap<>();
- for (Compartment compartment : compartments) {
- if (compartmentById.get(compartment.getElementId()) != null) {
- throw new InvalidInputDataExecption("Duplicated element id: " + compartment.getElementId());
- }
- compartmentById.put(compartment.getElementId(), compartment);
- }
- List<Compartment> result = new ArrayList<>();
-
- for (CompartmentGlyph glyph : sbmlLayout.getListOfCompartmentGlyphs()) {
- Compartment source = compartmentById.get(glyph.getCompartment());
- if (source==null) {
- throw new InvalidInputDataExecption("Layout contains invalid compartment id: "+glyph.getCompartment());
- }
- used.add(source);
- Compartment compartmentWithLayout = new SquareCompartment(source);
- compartmentWithLayout.setElementId(glyph.getId());
- compartmentWithLayout.setX(glyph.getBoundingBox().getPosition().getX());
- compartmentWithLayout.setY(glyph.getBoundingBox().getPosition().getY());
- compartmentWithLayout.setWidth(glyph.getBoundingBox().getDimensions().getWidth());
- compartmentWithLayout.setHeight(glyph.getBoundingBox().getDimensions().getHeight());
- result.add(compartmentWithLayout);
- }
- for (Compartment compartment : compartments) {
- if (!used.contains(compartment)) {
- logger.warn("Layout doesn't contain information about compartment: "+compartment.getElementId());
- result.add(compartment);
- }
- }
- return result;
+ super(layout);
}
- private Compartment parse(org.sbml.jsbml.Compartment compartment) throws InvalidInputDataExecption {
- Compartment result = new Compartment(compartment.getId());
+ @Override
+ protected Compartment parse(org.sbml.jsbml.Compartment compartment) throws InvalidInputDataExecption {
+ Compartment result = new SquareCompartment(compartment.getId());
result.setMiriamData(parseAnnotation(compartment.getAnnotation()));
result.setName(compartment.getName());
try {
@@ -89,11 +37,17 @@ public class SbmlCompartmentParser {
return result;
}
- protected Set<MiriamData> parseAnnotation(Annotation annotation) {
- if (annotation.getCVTermCount() > 0) {
- throw new NotImplementedException();
+ @Override
+ protected ListOf<org.sbml.jsbml.Compartment> getSbmlElementList(Model sbmlModel) {
+ return sbmlModel.getListOfCompartments();
+ }
+
+ @Override
+ protected List<Pair<String, AbstractReferenceGlyph>> getGlyphs(Layout sbmlLayout) {
+ List<Pair<String, AbstractReferenceGlyph>> result = new ArrayList<>();
+ for (CompartmentGlyph glyph : sbmlLayout.getListOfCompartmentGlyphs()) {
+ result.add(new Pair<String, AbstractReferenceGlyph>(glyph.getCompartment(), glyph));
}
- Set<MiriamData> result = new HashSet<>();
return result;
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..5b7c7edcb98e8b050fb3f0aca830347bd81dd201
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementParser.java
@@ -0,0 +1,94 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+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> {
+ Logger logger = Logger.getLogger(SbmlElementParser.class);
+
+ Layout layout;
+
+ public SbmlElementParser(Layout layout) {
+ this.layout = layout;
+ }
+
+ public List<Element> parseList(Model sbmlModel) throws InvalidInputDataExecption {
+ List<Element> result = new ArrayList<>();
+ for (T sbmlElement : getSbmlElementList(sbmlModel)) {
+ result.add(parse(sbmlElement));
+ }
+ if (layout != null) {
+ return mergeLayout(result, layout);
+ } else {
+ return result;
+ }
+ }
+
+ protected abstract ListOf<T> getSbmlElementList(Model sbmlModel);
+
+ private List<Element> mergeLayout(List<Element> elements, Layout sbmlLayout) throws InvalidInputDataExecption {
+ Set<Element> used = new HashSet<>();
+ Map<String, Element> elementById = new HashMap<>();
+ for (Element species : elements) {
+ if (elementById.get(species.getElementId()) != null) {
+ throw new InvalidInputDataExecption("Duplicated element id: " + species.getElementId());
+ }
+ elementById.put(species.getElementId(), species);
+ }
+ List<Element> result = new ArrayList<>();
+
+ for (Pair<String, AbstractReferenceGlyph> idGlyphPair : getGlyphs(sbmlLayout)) {
+ String id = idGlyphPair.getLeft();
+ Element source = elementById.get(id);
+ if (source == null) {
+ throw new InvalidInputDataExecption("Layout contains invalid Species id: " + idGlyphPair.getLeft());
+ }
+ used.add(source);
+ AbstractReferenceGlyph glyph = idGlyphPair.getRight();
+ Element SpeciesWithLayout = source.copy();
+ SpeciesWithLayout.setElementId(glyph.getId());
+ SpeciesWithLayout.setX(glyph.getBoundingBox().getPosition().getX());
+ SpeciesWithLayout.setY(glyph.getBoundingBox().getPosition().getY());
+ SpeciesWithLayout.setWidth(glyph.getBoundingBox().getDimensions().getWidth());
+ SpeciesWithLayout.setHeight(glyph.getBoundingBox().getDimensions().getHeight());
+ result.add(SpeciesWithLayout);
+ }
+ for (Element Species : elements) {
+ if (!used.contains(Species)) {
+ logger.warn("Layout doesn't contain information about Element: " + Species.getElementId());
+ result.add(Species);
+ }
+ }
+ return result;
+ }
+
+ protected abstract List<Pair<String, AbstractReferenceGlyph>> getGlyphs(Layout sbmlLayout);
+
+ protected abstract Element parse(T species) throws InvalidInputDataExecption;
+
+ protected Set<MiriamData> parseAnnotation(Annotation annotation) {
+ if (annotation.getCVTermCount() > 0) {
+ throw new NotImplementedException();
+ }
+ Set<MiriamData> result = new HashSet<>();
+ return result;
+ }
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
index 357fcfefaf317e53937a7705f6139107c46efda0..7e32722234fe9ed7aaf6598e407dfac2d71d72fa 100644
--- a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlParser.java
@@ -49,12 +49,14 @@ public class SbmlParser implements IConverter {
Layout layout = getSbmlLayout(sbmlModel);
SbmlCompartmentParser compartmentParser = new SbmlCompartmentParser(layout);
+ SbmlSpeciesParser speciesParser = new SbmlSpeciesParser(layout);
Set<MiriamData> annotations = compartmentParser.parseAnnotation(sbmlModel.getAnnotation());
if (annotations.size() > 0) {
throw new NotImplementedException("Annotations not implemented for model");
}
model.addElements(compartmentParser.parseList(sbmlModel));
+ model.addElements(speciesParser.parseList(sbmlModel));
if (sbmlModel.getConstraintCount() > 0) {
throw new NotImplementedException("Constraints not implemented for model");
}
@@ -91,9 +93,6 @@ public class SbmlParser implements IConverter {
if (sbmlModel.getRuleCount() > 0) {
throw new NotImplementedException("Rule not implemented for model");
}
- if (sbmlModel.getSpeciesCount() > 0) {
- throw new NotImplementedException("Species not implemented for model");
- }
if (sbmlModel.getSpeciesReferenceCount() > 0) {
throw new NotImplementedException("SpeciesReference not implemented for model");
}
@@ -120,7 +119,7 @@ public class SbmlParser implements IConverter {
double minX = Double.MAX_VALUE;
double minY = Double.MAX_VALUE;
for (Element element : model.getElements()) {
- if (element.getX() == null) {
+ if (element.getWidth() == 0.0) {
throw new NotImplementedException("Element without layout not implemented");
}
width = Math.max(width, element.getX() + element.getWidth());
@@ -147,7 +146,7 @@ public class SbmlParser implements IConverter {
if (plugin.getClass().equals(org.sbml.jsbml.ext.layout.LayoutModelPlugin.class)) {
LayoutModelPlugin layoutPlugin = (LayoutModelPlugin) plugin;
if (layoutPlugin.getLayoutCount() == 0) {
- logger.warn("Layout plugin available but not layouts defined");
+ logger.warn("Layout plugin available but no layouts defined");
} else if (layoutPlugin.getLayoutCount() > 1) {
logger.warn(layoutPlugin.getLayoutCount() + " layouts defined. Using first one.");
layout = layoutPlugin.getLayout(0);
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
new file mode 100644
index 0000000000000000000000000000000000000000..e5d5547c4de7caab6e0d8323379a5dfd7fb5ecee
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlSpeciesParser.java
@@ -0,0 +1,69 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+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;
+import org.sbml.jsbml.ext.layout.AbstractReferenceGlyph;
+import org.sbml.jsbml.ext.layout.Layout;
+import org.sbml.jsbml.ext.layout.SpeciesGlyph;
+
+import lcsb.mapviewer.common.Pair;
+import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.model.map.species.Unknown;
+
+public class SbmlSpeciesParser extends SbmlElementParser<org.sbml.jsbml.Species> {
+ Logger logger = Logger.getLogger(SbmlSpeciesParser.class);
+
+ public SbmlSpeciesParser(Layout layout) {
+ super(layout);
+ }
+
+ protected Species parse(org.sbml.jsbml.Species species) throws InvalidInputDataExecption {
+ String type = species.getSpeciesType();
+ Class<? extends Species> clazz = null;
+ if (type == null || type.isEmpty()) {
+ clazz = Unknown.class;
+ }
+ 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());
+ try {
+ result.setNotes(species.getNotesString());
+ } catch (XMLStreamException e) {
+ throw new InvalidInputDataExecption(species.getId() + " Invalid Species notes", e);
+ }
+ return result;
+ } catch (SecurityException | NoSuchMethodException | InstantiationException | IllegalAccessException
+ | IllegalArgumentException | InvocationTargetException e) {
+ throw new InvalidStateException(e);
+ }
+ }
+
+ @Override
+ protected ListOf<org.sbml.jsbml.Species> getSbmlElementList(Model sbmlModel) {
+ return sbmlModel.getListOfSpecies();
+ }
+
+ @Override
+ protected List<Pair<String, AbstractReferenceGlyph>> getGlyphs(Layout sbmlLayout) {
+ List<Pair<String, AbstractReferenceGlyph>> result = new ArrayList<>();
+ for (SpeciesGlyph glyph : sbmlLayout.getListOfSpeciesGlyphs()) {
+ result.add(new Pair<String, AbstractReferenceGlyph>(glyph.getSpecies(), glyph));
+ }
+ return result;
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
index 835fe52df8cb3c10948025d3883a51de1c596c3b..d28517873a9e0e59e7528df3e46041049e2161fa 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlParserTest.java
@@ -64,8 +64,6 @@ public class GenericSbmlParserTest {
Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
model.setName(null);
- Compartment c = new SquareCompartment((Compartment) model.getElements().iterator().next());
-
// Create and display image of parsed map
AbstractImageGenerator.Params params = new AbstractImageGenerator.Params().height(model.getHeight())
.width(model.getWidth()).nested(true).scale(1).level(20).x(0).y(0).model(model);
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
index b0da6b65b91d7c8aada9ef31d8342aa868c2bf50..72a079086fa04dceed1ee2d1033a3e1b12aed2ec 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlParserTest.java
@@ -14,6 +14,7 @@ import lcsb.mapviewer.converter.ConverterParams;
import lcsb.mapviewer.converter.InvalidInputDataExecption;
import lcsb.mapviewer.model.map.compartment.Compartment;
import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.species.Species;
public class SbmlParserTest {
Logger logger = Logger.getLogger(SbmlParserTest.class);
@@ -37,4 +38,23 @@ public class SbmlParserTest {
assertFalse(compartment.getClass().equals(Compartment.class));
}
+ @Test
+ public void testParseSpecies() throws FileNotFoundException, InvalidInputDataExecption {
+ Model model = parser.createModel(
+ new ConverterParams().filename("testFiles/layoutExample/SpeciesGlyph_Example_level2_level3.xml"));
+ assertNotNull(model);
+ assertEquals(1, model.getElements().size());
+ Species glucoseSpecies = model.getElementByElementId("SpeciesGlyph_Glucose");
+ assertNotNull(glucoseSpecies.getX());
+ assertNotNull(glucoseSpecies.getY());
+ assertTrue(glucoseSpecies.getWidth()>0);
+ assertTrue(glucoseSpecies.getHeight()>0);
+ assertNotNull(model.getHeight());
+ assertNotNull(model.getWidth());
+ assertTrue(model.getWidth() >= glucoseSpecies.getX() + glucoseSpecies.getWidth());
+ assertTrue(model.getHeight() >= glucoseSpecies.getY() + glucoseSpecies.getHeight());
+ assertFalse(glucoseSpecies.getClass().equals(Species.class));
+ }
+
+
}