Merge branch '1055-copasi-does-not-preserve-elements-shape' into 'master'

Resolve "COPASI does not preserve elements shape"

Closes #1055

See merge request !1282

CHANGELOG

@@ -15,6 +15,9 @@ minerva (16.0.0~alpha.1) stable; urgency=medium
     (#1376)
   * Small improvement: context menu exporting map is more precise about scope
     (#1447)
+  * Small improvement: styling of GENERIC search tab title improved (#1364)
+  * Small improvement: SBML render contains information about species shapes
+    (#1055)
   * Bug fix: refreshing page after removing last project on the page redirect to
     proper page (#1051)
   * Bug fix: removing plugin that does not exist anymore does not raise an error

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

@@ -54,7 +54,9 @@ public class SbmlExporter {
       return stream.toString("UTF-8")
           // TODO bug: https://github.com/sbmlteam/jsbml/issues/158
           .replace("<listOfSpeciesFeatures>", "<multi:listOfSpeciesFeatures>")
-          .replace("</listOfSpeciesFeatures>", "</multi:listOfSpeciesFeatures>");
+          .replace("</listOfSpeciesFeatures>", "</multi:listOfSpeciesFeatures>")
+          //TODO bug: https://github.com/sbmlteam/jsbml/pull/222
+          .replace("render:basepoint", "render:basePoint");
     } catch (UnsupportedEncodingException | XMLStreamException e) {
       throw new InvalidStateException(e);
     }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/AllSbmlSpeciesTests.java

@@ -5,7 +5,11 @@ import org.junit.runners.Suite;
 import org.junit.runners.Suite.SuiteClasses;
 
 @RunWith(Suite.class)
-@SuiteClasses({ SbmlSpeciesExporterTest.class, SbmlSpeciesParserTest.class })
+@SuiteClasses({
+  SbmlSpeciesExporterRenderShapeTest.class,
+  SbmlSpeciesExporterTest.class,
+  
+  SbmlSpeciesParserTest.class })
 public class AllSbmlSpeciesTests {
 
 }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterRenderShapeTest.java

+package lcsb.mapviewer.converter.model.sbml.species;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import java.util.ArrayList;
+import java.util.Collection;
+
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
+import org.junit.Before;
+import org.junit.Test;
+import org.junit.runner.RunWith;
+import org.junit.runners.Parameterized;
+import org.junit.runners.Parameterized.Parameters;
+import org.sbml.jsbml.ext.render.LocalStyle;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlTestFunctions;
+import lcsb.mapviewer.model.map.model.Model;
+import lcsb.mapviewer.model.map.model.ModelFullIndexed;
+import lcsb.mapviewer.model.map.species.Species;
+import lcsb.mapviewer.modelutils.map.ElementUtils;
+
+@RunWith(Parameterized.class)
+public class SbmlSpeciesExporterRenderShapeTest extends SbmlTestFunctions {
+
+  static Logger logger = LogManager.getLogger();
+
+  private Species species;
+
+  public SbmlSpeciesExporterRenderShapeTest(String name, Species species) {
+    this.species = species;
+  }
+
+  SbmlSpeciesExporterTestHelper helper;
+
+  @Before
+  public void setUp()  {
+    helper = new SbmlSpeciesExporterTestHelper();
+  }
+
+  @Parameters(name = "{index} : {0}")
+  public static Collection<Object[]> data() throws Exception {
+    Collection<Object[]> data = new ArrayList<Object[]>();
+    for (Class<?> clazz : new ElementUtils().getAvailableElementSubclasses()) {
+      if (Species.class.isAssignableFrom(clazz)) {
+        Species species = (Species) (clazz.getConstructor(String.class).newInstance("s1"));
+        species.setX(10);
+        species.setY(20);
+        species.setWidth(50);
+        species.setHeight(50);
+        data.add(new Object[] { species.getClass().getName(), species });
+      }
+    }
+    return data;
+  }
+
+  @Test
+  public void createModelTest() throws Exception {
+    Model model = new ModelFullIndexed(null);
+    model.addElement(species);
+    
+    SbmlSpeciesExporter exporter = helper.createExporter(model);
+    
+    LocalStyle style = exporter.createStyle(species);
+    assertNotNull(style);
+    assertEquals("Style was not generated without issues", 0, super.getWarnings().size());
+  }
+
+  
+}

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTest.java

@@ -4,15 +4,14 @@ import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
 
 import java.util.Arrays;
-import java.util.Collection;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.junit.Before;
 import org.junit.Test;
-import org.sbml.jsbml.SBMLDocument;
 
-import lcsb.mapviewer.converter.model.sbml.*;
-import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
+import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
+import lcsb.mapviewer.converter.model.sbml.SbmlTestFunctions;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
@@ -24,7 +23,12 @@ public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
 
   Logger logger = LogManager.getLogger();
 
-  org.sbml.jsbml.Model sbmlModel;
+  SbmlSpeciesExporterTestHelper helper;
+
+  @Before
+  public void setUp()  {
+    helper = new SbmlSpeciesExporterTestHelper();
+  }
 
   @Test
   public void testOneElementWithTwoAliases() throws InconsistentModelException {
@@ -34,11 +38,11 @@ public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
     model.addElement(protein1);
     model.addElement(protein2);
 
-    SbmlSpeciesExporter exporter = createExporter(model);
+    SbmlSpeciesExporter exporter = helper.createExporter(model);
 
     exporter.exportElements();
 
-    assertEquals(1, sbmlModel.getSpeciesCount());
+    assertEquals(1, helper.sbmlModel.getSpeciesCount());
   }
 
   @Test
@@ -54,31 +58,11 @@ public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
     model.addElement(protein2);
     model.addElement(compartment);
 
-    SbmlSpeciesExporter exporter = createExporter(model);
+    SbmlSpeciesExporter exporter = helper.createExporter(model);
 
     exporter.exportElements();
 
-    assertEquals(2, sbmlModel.getSpeciesCount());
-  }
-
-  private SbmlSpeciesExporter createExporter(Model model) throws InconsistentModelException {
-    return createExporter(model, Arrays.asList(new SbmlExtension[] { SbmlExtension.RENDER, SbmlExtension.LAYOUT }));
-  }
-
-  private SbmlSpeciesExporter createExporter(Model model, Collection<SbmlExtension> sbmlExtensions)
-      throws InconsistentModelException {
-    SBMLDocument doc = new SBMLDocument(3, 1);
-    sbmlModel = doc.createModel(model.getIdModel());
-
-    SbmlExporter sbmlExporter = new SbmlExporter();
-    sbmlExporter.createSbmlLayout(model, sbmlModel);
-
-    SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(sbmlModel, model,
-        Arrays.asList(SbmlExtension.values()));
-    compartmentExporter.exportElements();
-
-    SbmlSpeciesExporter result = new SbmlSpeciesExporter(sbmlModel, model, sbmlExtensions, compartmentExporter);
-    return result;
+    assertEquals(2, helper.sbmlModel.getSpeciesCount());
   }
 
   @Test
@@ -92,7 +76,7 @@ public class SbmlSpeciesExporterTest extends SbmlTestFunctions {
     model.addElement(protein1);
     model.addElement(protein2);
 
-    SbmlSpeciesExporter exporter = createExporter(model, Arrays.asList(SbmlExtension.values()));
+    SbmlSpeciesExporter exporter = helper.createExporter(model, Arrays.asList(SbmlExtension.values()));
 
     assertFalse(exporter.getSbmlIdKey(protein1).equals(exporter.getSbmlIdKey(protein2)));
   }

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/species/SbmlSpeciesExporterTestHelper.java

+package lcsb.mapviewer.converter.model.sbml.species;
+
+import java.util.Arrays;
+import java.util.Collection;
+
+import org.sbml.jsbml.SBMLDocument;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlExporter;
+import lcsb.mapviewer.converter.model.sbml.SbmlExtension;
+import lcsb.mapviewer.converter.model.sbml.compartment.SbmlCompartmentExporter;
+import lcsb.mapviewer.model.map.InconsistentModelException;
+import lcsb.mapviewer.model.map.model.Model;
+
+public class SbmlSpeciesExporterTestHelper {
+  org.sbml.jsbml.Model sbmlModel;
+  
+  public SbmlSpeciesExporter createExporter(Model model, Collection<SbmlExtension> sbmlExtensions)
+      throws InconsistentModelException {
+    SBMLDocument doc = new SBMLDocument(3, 1);
+    sbmlModel = doc.createModel(model.getIdModel());
+
+    SbmlExporter sbmlExporter = new SbmlExporter();
+    sbmlExporter.createSbmlLayout(model, sbmlModel);
+
+    SbmlCompartmentExporter compartmentExporter = new SbmlCompartmentExporter(sbmlModel, model,
+        Arrays.asList(SbmlExtension.values()));
+    compartmentExporter.exportElements();
+
+    SbmlSpeciesExporter result = new SbmlSpeciesExporter(sbmlModel, model, sbmlExtensions, compartmentExporter);
+    return result;
+  }
+
+  public SbmlSpeciesExporter createExporter(Model model) throws InconsistentModelException {
+    return createExporter(model, Arrays.asList(new SbmlExtension[] { SbmlExtension.RENDER, SbmlExtension.LAYOUT }));
+  }
+
+
+}

frontend-js/src/main/js/gui/leftPanel/GenericSearchPanel.js

@@ -35,9 +35,10 @@ function GenericSearchPanel(params) {
   params["placeholder"] = "keyword";
 
   AbstractDbPanel.call(self, params);
+  self.getControlElement(PanelControlElementType.SEARCH_LABEL).innerHTML = "SEARCH IN CONTENT:";
 
   $(params.element).addClass("minerva-generic-search-panel");
-
+  $(".minerva-generic-search-tab-link").css("border-top-color", "white");
   self.createSearchGui();
 
   self.getMap().addListener("onBioEntityClick", function (e) {

frontend-js/src/main/js/gui/leftPanel/LeftPanel.js

@@ -192,7 +192,7 @@ LeftPanel.prototype.showElementDetails = function (element) {
     openTabName = undefined;
   }
 
-  if (element !== undefined && openTabName !== undefined && (openTabName.indexOf("SEARCH") === -1 || searchTabName !== "GENERIC")) {
+  if (element !== undefined && openTabName !== undefined && (openTabName.indexOf("SEARCH") === -1 || searchTabName !== "CONTENT")) {
     var model = self.getMap().getSubmapById(element.getModelId()).getModel();
     var bioEntity;
     return model.getByIdentifiedElement(element, true).then(function (result) {

frontend-js/src/main/js/gui/leftPanel/SearchPanel.js

@@ -57,7 +57,7 @@ SearchPanel.prototype._createPanelGui = function () {
  */
 SearchPanel.prototype.getPanelsDefinition = function () {
   return [{
-    name: "GENERIC",
+    name: "CONTENT",
     panelClass: GenericSearchPanel,
     linkClassName: "minerva-generic-search-tab-link",
     options: {parent: this}