From 154f1e686a6114ab89fc4dcf5abff717c3a9a699 Mon Sep 17 00:00:00 2001
From: Piotr Gawron <piotr.gawron@uni.lu>
Date: Tue, 19 Dec 2017 17:01:50 +0100
Subject: [PATCH] export of compartments implemented
---
.../java/lcsb/mapviewer/common/MimeType.java | 130 +++++++++---------
.../model/sbml/SbmlCompartmentExporter.java | 74 ++++++++++
.../model/sbml/SbmlElementExporter.java | 24 ++++
.../converter/model/sbml/SbmlExporter.java | 62 +++++++++
.../converter/model/sbml/SbmlParser.java | 32 +++--
.../model/sbml/AllSbmlConverterTests.java | 7 +-
.../sbml/GenericSbmlToXmlParserTest.java | 88 ++++++++++++
.../model/sbml/SbmlExporterTest.java | 111 +++++++++++++++
8 files changed, 453 insertions(+), 75 deletions(-)
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
create mode 100644 converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
create mode 100644 converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
create mode 100644 converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
diff --git a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
index 54c7c29e1b..ca6960532a 100644
--- a/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
+++ b/commons/src/main/java/lcsb/mapviewer/common/MimeType.java
@@ -1,86 +1,86 @@
package lcsb.mapviewer.common;
/**
- * Mime content types of data used in the system. If there is publically
- * available class with all posible types then we should use it, but I couldn't
- * quickly find it. For the full list see <a
- * href="http://www.iana.org/assignments/media-types/media-types.xhtml">IANA
+ * Mime content types of data used in the system. If there is publicly available
+ * class with all possible types then we should use it, but I couldn't quickly
+ * find it. For the full list see
+ * <a href="http://www.iana.org/assignments/media-types/media-types.xhtml">IANA
* MIME media types list</a>
*
* @author Piotr Gawron
*
*/
public enum MimeType {
- /**
- * SBML type of file.
- */
- SBML("application/sbml+xml"), //
+ /**
+ * SBML type of file.
+ */
+ SBML("application/sbml+xml"), //
- /**
- * Standard text file.
- */
- TEXT("text/plain"), //
+ /**
+ * Standard text file.
+ */
+ TEXT("text/plain"), //
- /**
- * Standard XML file.
- */
- XML("application/xml"),
+ /**
+ * Standard XML file.
+ */
+ XML("application/xml"),
- /**
- * <a href="http://www.w3.org/TR/SVG11/mimereg.html">SVG</a> file type.
- */
- SVG("image/svg+xml"),
+ /**
+ * <a href="http://www.w3.org/TR/SVG11/mimereg.html">SVG</a> file type.
+ */
+ SVG("image/svg+xml"),
- /**
- * JPG image file type.
- */
- JPG("image/jpeg"),
+ /**
+ * JPG image file type.
+ */
+ JPG("image/jpeg"),
- /**
- * PNG image file type.
- */
- PNG("image/png"),
+ /**
+ * PNG image file type.
+ */
+ PNG("image/png"),
- /**
- * PDF files (see <a href="http://www.rfc-editor.org/rfc/rfc3778.txt"> RFC
- * 3778, The application/pdf Media Type</a>).
- */
- PDF("application/pdf"), //
+ /**
+ * PDF files (see <a href="http://www.rfc-editor.org/rfc/rfc3778.txt"> RFC 3778,
+ * The application/pdf Media Type</a>).
+ */
+ PDF("application/pdf"), //
- /**
- * CSS files.
- */
- CSS("text/css"), //
+ /**
+ * CSS files.
+ */
+ CSS("text/css"), //
- /**
- * Javascript files.
- */
- JS("text/javascript"),
-
- /**
- * Zip files.
- */
- ZIP("application/zip"); //
+ /**
+ * JavaScript files.
+ */
+ JS("text/javascript"),
- /**
- * String representation of the MIME content.
- */
- private String textRepresentation;
+ /**
+ * Zip files.
+ */
+ ZIP("application/zip"); //
- /**
- * Default constructor with string definition.
- *
- * @param textRepresentation
- * text representation for MIME type
- */
- MimeType(String textRepresentation) {
- this.textRepresentation = textRepresentation;
- }
+ /**
+ * String representation of the MIME content.
+ */
+ private String textRepresentation;
- /**
- * @return the textRepresentation
- */
- public String getTextRepresentation() {
- return textRepresentation;
- }
+ /**
+ * Default constructor with string definition.
+ *
+ * @param textRepresentation
+ * text representation for MIME type
+ */
+ MimeType(String textRepresentation) {
+ this.textRepresentation = textRepresentation;
+ }
+
+ /**
+ * @return the textRepresentation
+ */
+ public String getTextRepresentation() {
+ return textRepresentation;
+ }
}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java
new file mode 100644
index 0000000000..07844dd698
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java
@@ -0,0 +1,74 @@
+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.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> {
+ 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);
+ }
+
+ }
+
+ 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();
+
+ 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;
+ }
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
new file mode 100644
index 0000000000..bac1ac7b6f
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java
@@ -0,0 +1,24 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import org.apache.log4j.Logger;
+import org.sbml.jsbml.Model;
+import org.sbml.jsbml.ext.layout.Layout;
+
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.species.Element;
+
+public abstract class SbmlElementExporter<T extends Element> {
+ Logger logger = Logger.getLogger(SbmlElementExporter.class);
+
+ Layout layout;
+
+ lcsb.mapviewer.model.map.model.Model minervaModel;
+
+ 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;
+
+}
diff --git a/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
new file mode 100644
index 0000000000..f92b8f5278
--- /dev/null
+++ b/converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java
@@ -0,0 +1,62 @@
+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;
+
+import lcsb.mapviewer.model.map.InconsistentModelException;
+
+public class SbmlExporter {
+ 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);
+ 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);
+
+ // For brevity, we omit error checking, BUT YOU SHOULD CALL
+ // doc.checkConsistency() and check the error log.
+
+ // Write the SBML document to a file.
+ ByteArrayOutputStream stream = new ByteArrayOutputStream();
+ SBMLWriter.write(doc, stream, "minerva", "1.0");
+ return stream.toString();
+ }
+
+ private Layout createSbmlLayout(lcsb.mapviewer.model.map.model.Model model, Model result) {
+ LayoutModelPlugin layoutPlugin = new LayoutModelPlugin(result);
+ Layout layout = new Layout();
+ Dimensions dimensions = new Dimensions();
+ dimensions.setHeight(model.getHeight());
+ dimensions.setWidth(model.getWidth());
+ layout.setDimensions(dimensions);
+ layoutPlugin.add(layout);
+ result.addExtension("layout", layoutPlugin);
+ return layout;
+ }
+}
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 c139cb3546..df96d4d304 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
@@ -2,7 +2,9 @@ package lcsb.mapviewer.converter.model.sbml;
import java.awt.Point;
import java.awt.geom.Point2D;
+import java.io.ByteArrayInputStream;
import java.io.File;
+import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.util.HashSet;
@@ -13,6 +15,7 @@ import javax.xml.stream.XMLStreamException;
import org.apache.commons.io.FilenameUtils;
import org.apache.log4j.Logger;
import org.sbml.jsbml.SBMLDocument;
+import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBMLReader;
import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.ext.layout.Layout;
@@ -326,33 +329,44 @@ public class SbmlParser implements IConverter {
@Override
public InputStream exportModelToInputStream(Model model) throws ConverterException, InconsistentModelException {
- // TODO Auto-generated method stub
- return null;
+ String exportedString = toXml(model);
+ InputStream inputStream = new ByteArrayInputStream(exportedString.getBytes());
+ return inputStream;
+ }
+
+ private String toXml(Model model) throws ConverterException {
+ try {
+ return new SbmlExporter().toXml(model);
+ } catch (SBMLException | XMLStreamException | InconsistentModelException e) {
+ throw new ConverterException(e);
+ }
}
@Override
public File exportModelToFile(Model model, String filePath)
throws ConverterException, InconsistentModelException, IOException {
- // TODO Auto-generated method stub
+ File file = new File(filePath);
+ String exportedString = toXml(model);
+ FileWriter fileWriter = new FileWriter(file);
+ fileWriter.write(exportedString);
+ fileWriter.flush();
+ fileWriter.close();
return null;
}
@Override
public String getCommonName() {
- // TODO Auto-generated method stub
- return null;
+ return "SBML";
}
@Override
public MimeType getMimeType() {
- // TODO Auto-generated method stub
- return null;
+ return MimeType.SBML;
}
@Override
public String getFileExtension() {
- // TODO Auto-generated method stub
- return null;
+ return "xml";
}
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
index 5841758afb..337bc2c992 100644
--- a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/AllSbmlConverterTests.java
@@ -5,7 +5,12 @@ import org.junit.runners.Suite;
import org.junit.runners.Suite.SuiteClasses;
@RunWith(Suite.class)
-@SuiteClasses({ GenericSbmlParserTest.class, SbmlPareserForInvalidReactionTest.class, SbmlParserTest.class })
+@SuiteClasses({ GenericSbmlParserTest.class, //
+ GenericSbmlToXmlParserTest.class, //
+ SbmlExporterTest.class, //
+ SbmlPareserForInvalidReactionTest.class, //
+ SbmlParserTest.class,//
+})
public class AllSbmlConverterTests {
}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
new file mode 100644
index 0000000000..65e7242d23
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java
@@ -0,0 +1,88 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.awt.Desktop;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.PrintWriter;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.converter.IConverter;
+import lcsb.mapviewer.converter.graphics.AbstractImageGenerator;
+import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
+import lcsb.mapviewer.converter.graphics.PngImageGenerator;
+import lcsb.mapviewer.converter.model.celldesigner.CellDesignerXmlParser;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelComparator;
+import lcsb.mapviewer.model.map.species.Element;
+
+@RunWith(Parameterized.class)
+public class GenericSbmlToXmlParserTest {
+
+ static Logger logger = Logger.getLogger(GenericSbmlToXmlParserTest.class.getName());
+
+ private Path filePath;
+
+ public GenericSbmlToXmlParserTest(Path filePath) {
+ this.filePath = filePath;
+ }
+
+ @Parameters(name = "{index} : {0}")
+ public static Collection<Object[]> data() throws IOException {
+ Collection<Object[]> data = new ArrayList<Object[]>();
+ Files.walk(Paths.get("testFiles/layoutExample")).forEach(fPath -> {
+ if (Files.isRegularFile(fPath) && fPath.toString().endsWith(".xml")) {
+ data.add(new Object[] { fPath });
+ }
+ });
+ return data;
+ }
+
+ @Test
+ public void toXmlModelTest() throws Exception {
+ try {
+ String dir = Files.createTempDirectory("sbgn-temp-images-dir").toFile().getAbsolutePath();
+
+ IConverter converter = new SbmlParser();
+
+ Model model = converter.createModel(new ConverterParams().filename(filePath.toString()));
+ model.setName(null);
+
+ String pathWithouExtension = dir + "/"
+ + filePath.getFileName().toString().substring(0, filePath.getFileName().toString().indexOf(".xml"));
+ String xmlFilePath = pathWithouExtension.concat(".xml");
+ converter.exportModelToFile(model, xmlFilePath);
+
+ Model model2 = converter.createModel(new ConverterParams().filename(xmlFilePath));
+ model.setName(null);
+
+ assertNotNull(model2);
+ ModelComparator comparator = new ModelComparator(1.0);
+ assertEquals(0, comparator.compare(model, model2));
+ FileUtils.deleteDirectory(new File(dir));
+
+ } catch (Exception e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ throw e;
+ }
+ }
+
+}
diff --git a/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
new file mode 100644
index 0000000000..8128f83717
--- /dev/null
+++ b/converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java
@@ -0,0 +1,111 @@
+package lcsb.mapviewer.converter.model.sbml;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
+import static org.junit.Assert.assertTrue;
+
+import java.io.ByteArrayInputStream;
+
+import org.apache.log4j.Logger;
+import org.junit.Test;
+
+import lcsb.mapviewer.converter.ConverterParams;
+import lcsb.mapviewer.model.map.compartment.Compartment;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.reaction.Reaction;
+import lcsb.mapviewer.model.map.reaction.ReactionNode;
+import lcsb.mapviewer.model.map.species.Species;
+
+public class SbmlExporterTest {
+ Logger logger = Logger.getLogger(SbmlExporterTest.class);
+ SbmlParser parser = new SbmlParser();
+ SbmlExporter exporter = new SbmlExporter();
+
+ @Test
+ public void testParseCompartment() throws Exception {
+ Model model = getModelAfterSerializing("testFiles/layoutExample/CompartmentGlyph_Example_level2_level3.xml");
+ assertNotNull(model);
+ assertEquals(1, model.getCompartments().size());
+ Compartment compartment = model.getElementByElementId("CompartmentGlyph_1");
+ assertNotNull(compartment);
+ assertNotNull(compartment.getX());
+ assertNotNull(compartment.getY());
+ assertTrue(compartment.getWidth() > 0);
+ assertTrue(compartment.getHeight() > 0);
+ assertNotNull(model.getHeight());
+ assertNotNull(model.getWidth());
+ assertTrue(model.getWidth() >= compartment.getX() + compartment.getWidth());
+ assertTrue(model.getHeight() >= compartment.getY() + compartment.getHeight());
+ assertFalse(compartment.getClass().equals(Compartment.class));
+ }
+
+ private Model getModelAfterSerializing(String filename) throws Exception {
+ Model originalModel = parser.createModel(new ConverterParams().filename(filename));
+ String xml = exporter.toXml(originalModel);
+ ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
+ return parser.createModel(new ConverterParams().inputStream(stream));
+ }
+
+ @Test
+ public void testParseSpecies() throws Exception {
+ Model model = getModelAfterSerializing("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));
+ }
+
+ @Test
+ public void testParseSpeciesInCompartments() throws Exception {
+ Model model = getModelAfterSerializing("testFiles/layoutExample/SpeciesGlyph_Example.xml");
+ assertNotNull(model);
+ assertEquals(2, model.getElements().size());
+ Compartment compartment = model.getElementByElementId("Yeast");
+ assertNotNull(compartment.getX());
+ assertNotNull(compartment.getY());
+ assertTrue(compartment.getWidth() > 0);
+ assertTrue(compartment.getHeight() > 0);
+ assertNotNull(model.getHeight());
+ assertNotNull(model.getWidth());
+ assertTrue(model.getWidth() >= compartment.getX() + compartment.getWidth());
+ assertTrue(model.getHeight() >= compartment.getY() + compartment.getHeight());
+ assertFalse(compartment.getClass().equals(Compartment.class));
+ assertTrue(compartment.getElements().size() > 0);
+ }
+
+ @Test
+ public void testParseReaction() throws Exception {
+ Model model = getModelAfterSerializing("testFiles/layoutExample/Complete_Example.xml");
+ assertNotNull(model);
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ assertNotNull(node.getLine());
+ assertTrue(node.getLine().length() > 0);
+ }
+ assertEquals(2, reaction.getOperators().size());
+ }
+
+ @Test
+ public void testReactionWithoutLayout() throws Exception {
+ Model model = getModelAfterSerializing("testFiles/layoutExample/Complete_Example_level2.xml");
+ assertNotNull(model);
+ assertEquals(1, model.getReactions().size());
+ Reaction reaction = model.getReactions().iterator().next();
+ for (ReactionNode node : reaction.getReactionNodes()) {
+ assertNotNull(node.getLine());
+ assertTrue(node.getLine().length() > 0);
+ }
+ assertEquals(2, reaction.getOperators().size());
+ }
+
+}
--
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