Merge branch '487-custom-images-as-overlay-levels-or-background' into 'master'

Resolve "Custom images as overlay levels  or background"

Closes #487

See merge request !768

CHANGELOG

@@ -3,6 +3,9 @@ minerva (13.1.0~alpha.0) unstable; urgency=low
     outputs used by annotator (#617)
   * Feature: changes in admin panel doesn't require saving - they are saved
     automatically (#676)
+  * Feature: elements can have custom glyphs used for visualization (#487)
+  * Small improvement: all bio entities have z-index associated with them 
+    (#487)
   * Small improvement: validation of the organism and disease id on map upload
     added (#618)
   * Small improvement: added current username next to logout button in admin
@@ -48,6 +51,8 @@ minerva (13.1.0~alpha.0) unstable; urgency=low
   * Small improvement: allow admin to disable CORS check (#802)
   * Small improvement: TransparencyZoomLevelVisibility parameter renamed to
     SemanticZoomLevelTransparency (#801)
+  * Small improvement: export/import from SBML support z-index in LAYOUT 
+    extension
   * Bug fix: progress bar of gene genome mapping upload is refreshing properly
     (#728)
   * Bug fix: when editing project Disease and Organism could not be removed

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

@@ -8,7 +8,10 @@ import org.apache.log4j.Logger;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 
 public abstract class Comparator<T extends Object> implements java.util.Comparator<T> {
-  Logger logger = Logger.getLogger(Comparator.class);
+  /**
+   * Default class logger.
+   */
+  private static Logger logger = Logger.getLogger(Comparator.class);
   private Class<T> comparatorClazz;
   private boolean exactClassMatch;
   private List<Comparator<? extends T>> subClassComparatorList = new ArrayList<>();

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParser.java

@@ -22,6 +22,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.Converter;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ZIndexPopulator;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.alias.AliasCollectionXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
@@ -144,7 +145,10 @@ public class CellDesignerXmlParser extends Converter {
       }
       // we ignore metaid - it's useless and obstruct data model
       // model.setMetaId(XmlParser.getNodeAttr("metaId", modelNode));
-      model.setIdModel(XmlParser.getNodeAttr("id", modelNode));
+      String modelId = XmlParser.getNodeAttr("id", modelNode);
+      if (modelId != null && !modelId.isEmpty()) {
+        model.setIdModel(modelId);
+      }
 
       Node compartmentNode = XmlParser.getNode("listOfCompartments", modelNode.getChildNodes());
       if (compartmentNode != null) {
@@ -236,6 +240,7 @@ public class CellDesignerXmlParser extends Converter {
         model.setWidth(width);
         model.setHeight(height);
       }
+      new ZIndexPopulator().populateZIndex(model);
     } catch (InvalidXmlSchemaException e) {
       throw new InvalidInputDataExecption(e);
     } catch (CellDesignerParserException e) {
@@ -610,7 +615,11 @@ public class CellDesignerXmlParser extends Converter {
           + "xmlns:celldesigner=\"http://www.sbml.org/2001/ns/celldesigner\" level=\"2\" version=\"4\">\n");
       // metaid is a string cell designer id, usually it's model id and as far as
       // we can tell it's not used at all
-      result.append("<model metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\">\n");
+      result.append("<model ");
+      if (model.getIdModel() != null) {
+        result.append("metaid=\"" + model.getIdModel() + "\" id=\"" + model.getIdModel() + "\"");
+      }
+      result.append(">\n");
 
       result.append(unitCollectionXmlParser.toXml(model.getUnits()));
       result.append(functionCollectionXmlParser.toXml(model.getFunctions()));
@@ -697,7 +706,8 @@ public class CellDesignerXmlParser extends Converter {
 
     result.append("</celldesigner:extension>\n");
     XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
-    result.append(xmlAnnotationParser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(), model.getCreationDate(), model.getModificationDates()));
+    result.append(xmlAnnotationParser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(),
+        model.getCreationDate(), model.getModificationDates()));
     result.append("</annotation>\n");
     return result.toString();
   }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/InvalidGroupException.java

@@ -3,7 +3,7 @@ package lcsb.mapviewer.converter.model.celldesigner;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 
 /**
- * Exception that shold be thrown when the group in xml schema is invalid.
+ * Exception that should be thrown when the group in xml schema is invalid.
  * 
  * @author Piotr Gawron
  * 
@@ -20,7 +20,7 @@ public class InvalidGroupException extends InvalidXmlSchemaException {
 	 */
 
 	public InvalidGroupException() {
-		super(); // call superclass constructor
+		super();
 	}
 
 	/**

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParser.java

@@ -13,6 +13,7 @@ import org.w3c.dom.NodeList;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.common.geometry.ColorParser;
+import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.graphics.LineType;
 import lcsb.mapviewer.model.graphics.PolylineData;
@@ -522,6 +523,7 @@ public class LayerXmlParser {
         }
       }
     }
+    new RestAnnotationParser().processNotes(result.getNotes(), result);
     return result;
   }
 

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/ImportOnly.java

+package lcsb.mapviewer.converter.model.celldesigner.annotation;
+
+import static java.lang.annotation.ElementType.FIELD;
+import static java.lang.annotation.RetentionPolicy.RUNTIME;
+
+import java.lang.annotation.Retention;
+import java.lang.annotation.Target;
+
+@Retention(RUNTIME)
+@Target(FIELD)
+public @interface ImportOnly {
+
+}

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/NoteField.java

 package lcsb.mapviewer.converter.model.celldesigner.annotation;
 
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
-import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerSpecies;
 import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
 import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
@@ -53,12 +52,12 @@ public enum NoteField {
   /**
    * {@link Element#symbol}.
    */
-	SYMBOL("Symbol", CellDesignerElement.class, null),
+  SYMBOL("Symbol", BioEntity.class, null),
 
   /**
    * {@link Element#fullName}.
    */
-	NAME("Name", CellDesignerElement.class, null),
+  NAME("Name", BioEntity.class, null),
 
   /**
    * {@link Element#notes} or {@link Reaction#notes} .
@@ -68,7 +67,7 @@ public enum NoteField {
   /**
    * {@link Element#formerSymbols}.
    */
-	PREVIOUS_SYMBOLS("Previous Symbols", CellDesignerElement.class, null),
+  PREVIOUS_SYMBOLS("Previous Symbols", Element.class, null),
 
   /**
    * {@link Element#synonyms} or {@link Reaction#synonyms}.
@@ -113,12 +112,12 @@ public enum NoteField {
   /**
    * {@link Element#formula}.
    */
-	CHARGED_FORMULA("ChargedFormula", CellDesignerElement.class, null),
+  CHARGED_FORMULA("ChargedFormula", Element.class, null),
 
   /**
    * {@link Species#charge}.
    */
-	CHARGE("Charge", CellDesignerSpecies.class, null),
+  CHARGE("Charge", Species.class, null),
 
   /**
    * {@link Element#getSemanticZoomLevelVisibility()}.
@@ -135,6 +134,10 @@ public enum NoteField {
    */
   @Deprecated
   TRANSPARENCY_ZOOM_LEVEL_VISIBILITY_OLD("TransparencyZoomLevelVisibility", Element.class, null),
+
+  @ImportOnly
+  Z_INDEX("Z-Index", Drawable.class, null),
+
   ;
 
   /**
@@ -145,7 +148,7 @@ public enum NoteField {
   /**
    * What object class can have this field.
    */
-	private Class<?>	 clazz;
+  private Class<? extends Drawable> clazz;
 
   /**
    * What {@link MiriamType} is associated with the field.
@@ -160,7 +163,7 @@ public enum NoteField {
    * @param clazz
    *          {@link #clazz}
    */
-	NoteField(String name, Class<?> clazz) {
+  NoteField(String name, Class<? extends Drawable> clazz) {
     this.commonName = name;
     this.clazz = clazz;
   }
@@ -175,7 +178,7 @@ public enum NoteField {
    * @param type
    *          {@link #miriamType}
    */
-	NoteField(String name, Class<?> clazz, MiriamType type) {
+  NoteField(String name, Class<? extends Drawable> clazz, MiriamType type) {
     this(name, clazz);
     this.miriamType = type;
   }

converter-CellDesigner/src/main/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParser.java

@@ -23,9 +23,11 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.model.map.BioEntity;
+import lcsb.mapviewer.model.map.Drawable;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.MiriamRelationType;
 import lcsb.mapviewer.model.map.MiriamType;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.Element;
 import lcsb.mapviewer.model.map.species.Species;
@@ -702,6 +704,24 @@ public class RestAnnotationParser {
     }
   }
 
+  private void setZIndex(Drawable element, String annotationString) {
+    String zIndex = getParamByPrefix(annotationString,
+        NoteField.Z_INDEX.getCommonName() + ":");
+    if (zIndex != null) {
+      try {
+        Integer z = Integer.valueOf(zIndex);
+        if (element.getZ() == null) {
+          element.setZ(z);
+        } else if (!element.getZ().equals(z)) {
+          logger.warn(elementUtils.getElementTag(element) + " New " + NoteField.Z_INDEX.getCommonName()
+              + " different than default [" + zIndex + "][" + element.getZ() + "]. Ignoring.");
+        }
+      } catch (NumberFormatException e) {
+        logger.warn("Invalid e index", e);
+      }
+    }
+  }
+
   /**
    * Assigns notes to the element from notes string. This might look strange. The
    * idea is that sometimes we have notes from more then one source. And the data
@@ -739,7 +759,7 @@ public class RestAnnotationParser {
    * @param object
    *          where the structural data should be put
    */
-  public void processNotes(String notes, BioEntity object) {
+  public void processNotes(String notes, Drawable object) {
     StringBuilder annotations = new StringBuilder();
 
     String[] string = notes.split("\n");
@@ -748,7 +768,7 @@ public class RestAnnotationParser {
       boolean remove = false;
       for (NoteField field : NoteField.values()) {
 
-        if (string2.startsWith(field.getCommonName() + ":")) {
+        if (string2.startsWith(field.getCommonName() + ":")&& field.getClazz().isAssignableFrom(object.getClass())) {
           remove = true;
         }
       }
@@ -758,15 +778,21 @@ public class RestAnnotationParser {
         newNotes.append(string2 + "\n");
       }
     }
-    object.setNotes(newNotes.toString().trim());
-
     String ann = annotations.toString();
-    setNotes(object, ann);
-    setSymbol(object, ann);
-    setSynonyms(object, ann);
-    setSemanticZoomLevelVisibility(object, ann);
-    setAbbreviation(object, ann);
-    setFormula(object, ann);
+    setZIndex(object, ann);
+    if (object instanceof LayerText) {
+      ((LayerText) object).setNotes(newNotes.toString().trim());
+    }
+    if (object instanceof BioEntity) {
+      BioEntity bioEntity = (BioEntity) object;
+      bioEntity.setNotes(newNotes.toString().trim());
+
+      setNotes(bioEntity, ann);
+      setSymbol(bioEntity, ann);
+      setSynonyms(bioEntity, ann);
+      setSemanticZoomLevelVisibility(bioEntity, ann);
+      setAbbreviation(bioEntity, ann);
+      setFormula(bioEntity, ann);
       if (object instanceof Reaction) {
         Reaction reaction = (Reaction) object;
         setMechanicalConfidenceScoreToReaction(reaction, ann);
@@ -786,12 +812,13 @@ public class RestAnnotationParser {
       }
 
       try {
-      processRdfDescription(object);
+        processRdfDescription(bioEntity);
       } catch (InvalidXmlSchemaException e) {
         String warning = elementUtils.getElementTag(object) + " Problem with processing notes. Invalid RDF node.";
         logger.warn(warning);
       }
     }
+  }
 
   /**
    * Process rdf description from notes, removes it from the description and adds

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerTestFunctions.java

@@ -44,6 +44,7 @@ import lcsb.mapviewer.common.EventStorageLoggerAppender;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.InconsistentModelException;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelComparator;
@@ -234,14 +235,30 @@ public abstract class CellDesignerTestFunctions {
 
   protected void testXmlSerialization(Model model)
       throws InconsistentModelException, UnsupportedEncodingException, InvalidInputDataExecption {
-    CellDesignerXmlParser parser = new CellDesignerXmlParser();
-    String xml = parser.model2String(model);
-    InputStream is = new ByteArrayInputStream(xml.getBytes("UTF-8"));
-    Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+    for (BioEntity bioEntity : model.getBioEntities()) {
+      bioEntity.setZ(null);
+    }
+
+    Model model2 = serializeModel(model);
 
     model.setName(null);
     ModelComparator comparator = new ModelComparator();
     assertEquals(0, comparator.compare(model, model2));
   }
 
+
+  protected Model serializeModel(Model model)
+      throws InconsistentModelException, UnsupportedEncodingException, InvalidInputDataExecption {
+    CellDesignerXmlParser parser = new CellDesignerXmlParser();
+    String xmlString = parser.model2String(model);
+    InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
+
+    Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+    for (BioEntity bioEntity : model2.getBioEntities()) {
+      bioEntity.setZ(null);
+    }
+    return model2;
+  }
+
+
 }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/CellDesignerXmlParserTest.java

@@ -36,6 +36,7 @@ import lcsb.mapviewer.converter.ConverterParams;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.model.graphics.PolylineData;
+import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.layout.graphics.Layer;
 import lcsb.mapviewer.model.map.layout.graphics.LayerOval;
@@ -82,6 +83,20 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
     }
   }
 
+  @Test
+  public void testZIndexAvailableForBioEntities() throws Exception {
+    try {
+      CellDesignerXmlParser parser = new CellDesignerXmlParser();
+      Model model = parser.createModel(new ConverterParams().filename("testFiles/sample.xml"));
+      for (BioEntity bioEntity : model.getBioEntities()) {
+        assertNotNull(bioEntity.getZ());
+      }
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testOpenFromFile() throws Exception {
     try {
@@ -455,11 +470,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
       alias2.setName("PDK2");
       model.addElement(alias2);
 
-      CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xmlString = parser.model2String(model);
-
-      InputStream is = new ByteArrayInputStream(xmlString.getBytes());
-      Model model2 = parser.createModel(new ConverterParams().inputStream(is).sizeAutoAdjust(false));
+      Model model2 = serializeModel(model);
 
       assertEquals(0, modelComparator.compare(model, model2));
 
@@ -1063,11 +1074,7 @@ public class CellDesignerXmlParserTest extends CellDesignerTestFunctions {
       protein.addSynonym("&");
       model.addElement(protein);
 
-      CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String xmlString = parser.model2String(model);
-      InputStream is = new ByteArrayInputStream(xmlString.getBytes("UTF-8"));
-
-      Model model2 = parser.createModel(new ConverterParams().inputStream(is));
+      Model model2 = serializeModel(model);
 
       assertEquals(0, modelComparator.compare(model, model2));
 

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/ComplexParserTests.java

@@ -7,8 +7,6 @@ import static org.junit.Assert.assertTrue;
 
 import java.awt.Color;
 import java.io.ByteArrayInputStream;
-import java.io.InputStream;
-import java.nio.charset.StandardCharsets;
 import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
@@ -98,7 +96,6 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
     }
   }
 
-
   @Test
   public void testParseTextWithBackground() throws Exception {
     try {
@@ -413,14 +410,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
       alias.setName("name & no-name");
       model.addElement(alias);
 
-      CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String string = parser.model2String(model);
-
-      InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
-
-      ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
-
-      Model model2 = parser.createModel(params);
+      Model model2 = serializeModel(model);
 
       ModelComparator comparator = new ModelComparator();
 
@@ -443,14 +433,7 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
       alias.setName("name\rno-name");
       model.addElement(alias);
 
-      CellDesignerXmlParser parser = new CellDesignerXmlParser();
-      String string = parser.model2String(model);
-
-      InputStream stream = new ByteArrayInputStream(string.getBytes(StandardCharsets.UTF_8));
-
-      ConverterParams params = new ConverterParams().inputStream(stream).sizeAutoAdjust(false);
-
-      Model model2 = parser.createModel(params);
+      Model model2 = serializeModel(model);
 
       ModelComparator comparator = new ModelComparator();
 
@@ -485,5 +468,4 @@ public class ComplexParserTests extends CellDesignerTestFunctions {
     }
   }
 
-
 }

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/LayerXmlParserTest.java

@@ -391,6 +391,19 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
     }
   }
 
+  @Test
+  public void testGetLayerTextWithZIndex() throws Exception {
+    try {
+      String xmlString = readFile("testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml");
+      Node node = getNodeFromXmlString(xmlString);
+      LayerText layer = parser.getLayerText(node);
+      assertEquals((Integer) 19, layer.getZ());
+    } catch (Exception e) {
+      e.printStackTrace();
+      throw e;
+    }
+  }
+
   @Test
   public void testParseInvalidLayerText() throws Exception {
     try {

converter-CellDesigner/src/test/java/lcsb/mapviewer/converter/model/celldesigner/annotation/RestAnnotationParserTest.java

@@ -295,17 +295,19 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
 
       for (NoteField field : NoteField.values()) {
         boolean deprecated = false;
+        boolean importOnly = false;
         try {
           Field f = NoteField.class.getField(field.name());
           if (f.isAnnotationPresent(Deprecated.class))
             deprecated = true;
+          if (f.isAnnotationPresent(ImportOnly.class))
+            importOnly = true;
 
         } catch (NoSuchFieldException | SecurityException e) {
         }
 
-        if (!deprecated) {
+        if (!deprecated && !importOnly) {
           if (field.getClazz().isAssignableFrom(element.getClass())
-
               || CellDesignerElement.class.isAssignableFrom(field.getClazz())) {
             assertTrue("Export string doesn't contain info about: " + field.getCommonName(),
                 str.indexOf(field.getCommonName()) >= 0);

converter-CellDesigner/testFiles/xmlNodeTestExamples/layer_text_with_z_index.xml

+<celldesigner:layerSpeciesAlias x="0.0" y="0.0">
+<celldesigner:layerNotes>
+text node
+Z-Index: 19
+</celldesigner:layerNotes>
+<celldesigner:bounds x="55.0" y="37.0" w="152.0" h="105.0"/>
+<celldesigner:paint color="ff000000"/>
+<celldesigner:font size="11"/>
+</celldesigner:layerSpeciesAlias>

converter-SBGNML/src/main/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParser.java

@@ -24,6 +24,7 @@ import org.sbgn.bindings.Sbgn;
 import lcsb.mapviewer.common.comparator.DoubleComparator;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
+import lcsb.mapviewer.converter.ZIndexPopulator;
 import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
 import lcsb.mapviewer.converter.model.celldesigner.types.ModifierType;
@@ -186,6 +187,8 @@ public class SbgnmlXmlParser {
       }
     }
     
+    new ZIndexPopulator().populateZIndex(model);
+
     return model;
   }
 

converter-SBGNML/src/test/java/lcsb/mapviewer/converter/model/sbgnml/SbgnmlXmlParserTest2.java

@@ -46,11 +46,12 @@ public class SbgnmlXmlParserTest2 {
       Converter converter = new SbgnmlXmlConverter();
 
       Model model = converter
-            .createModel(new ConverterParams().filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml"));
+          .createModel(new ConverterParams()
+              .filename("testFiles/sbgnmlParserTestFiles/sbgnmlFiles/elements_inside_compartment.xml"));
       Complex complexInsideCompartment = model.getElementByElementId("csa1830");
       assertNotNull("Complex inside compartment has undefined compartment", complexInsideCompartment.getCompartment());
       Complex complexOutsideCompartment = model.getElementByElementId("csa1831");
-        assertNull("Complex outside compartment has not null compartment",complexOutsideCompartment.getCompartment());
+      assertNull("Complex outside compartment has not null compartment", complexOutsideCompartment.getCompartment());
       Compartment compartment = model.getElementByElementId("ca107");
       assertNull("Top compartment has not null compartment", compartment.getCompartment());
     } catch (Exception e) {
@@ -59,4 +60,20 @@ public class SbgnmlXmlParserTest2 {
     }
   }