export of modelId added

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

@@ -19,30 +19,17 @@ public class SbmlExporter {
       throws SBMLException, XMLStreamException, InconsistentModelException {
     SBMLDocument doc = new SBMLDocument(3, 1);
     Model result = doc.createModel(model.getName());
+    result.setId(model.getIdModel());
     Layout layout = createSbmlLayout(model, result);
 
     SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(layout, model);
-    SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model, compartmentExporter);
+    SbmlBioEntityExporter<Species, org.sbml.jsbml.Species> speciesExporter = new SbmlSpeciesExporter(layout, model,
+        compartmentExporter);
     SbmlReactionExporter reactionExporter = new SbmlReactionExporter(layout, model, speciesExporter);
     compartmentExporter.exportElements(result);
     speciesExporter.exportElements(result);
     reactionExporter.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();
@@ -52,8 +39,16 @@ public class SbmlExporter {
     LayoutModelPlugin layoutPlugin = new LayoutModelPlugin(result);
     Layout layout = new Layout();
     Dimensions dimensions = new Dimensions();
-    dimensions.setHeight(model.getHeight());
-    dimensions.setWidth(model.getWidth());
+    if (model.getHeight() != null) {
+      dimensions.setHeight(model.getHeight());
+    } else {
+      dimensions.setHeight(640);
+    }
+    if (model.getWidth() != null) {
+      dimensions.setWidth(model.getWidth());
+    } else {
+      dimensions.setWidth(480);
+    }
     layout.setDimensions(dimensions);
     layoutPlugin.add(layout);
     result.addExtension("layout", layoutPlugin);

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

@@ -19,9 +19,9 @@ import lcsb.mapviewer.converter.graphics.NormalImageGenerator;
 import lcsb.mapviewer.converter.graphics.PngImageGenerator;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.ReactionNode;
-import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
 
 public class SbmlExporterTest {
@@ -49,11 +49,15 @@ public class SbmlExporterTest {
 
   private Model getModelAfterSerializing(String filename) throws Exception {
     Model originalModel = parser.createModel(new ConverterParams().filename(filename));
+    return getModelAfterSerializing(originalModel);
+  }
+
+  private Model getModelAfterSerializing(Model originalModel) throws Exception {
     String xml = exporter.toXml(originalModel);
     ByteArrayInputStream stream = new ByteArrayInputStream(xml.getBytes("UTF-8"));
     Model result = parser.createModel(new ConverterParams().inputStream(stream));
-//    showImage(originalModel);
-//    showImage(result);
+    // showImage(originalModel);
+    // showImage(result);
     return result;
   }
 
@@ -120,4 +124,13 @@ public class SbmlExporterTest {
     assertEquals(2, reaction.getOperators().size());
   }
 
+  @Test
+  public void testExportModelId() throws Exception {
+    Model model = new ModelFullIndexed(null);
+    model.setIdModel("Test123");
+    Model deserializedModel = getModelAfterSerializing(model);
+
+    assertEquals(model.getIdModel(), deserializedModel.getIdModel());
+  }
+
 }