export of compartments implemented

commons/src/main/java/lcsb/mapviewer/common/MimeType.java

 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;
+  }
 }

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlCompartmentExporter.java

+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;
+  }
+
+}

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlElementExporter.java

+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;  
+
+}

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/SbmlExporter.java

+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;
+  }
+}

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";
   }
 
 }

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 {
 
 }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/GenericSbmlToXmlParserTest.java

+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;
+    }
+  }
+
+}

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/SbmlExporterTest.java

+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());
+  }
+
+}