Merge branch '1316-dapi-over-ssl' into 'devel_15.0.x'

Resolve "when dapi is down minerva crash"

See merge request !1198

CHANGELOG

+minerva (15.0.1) stable; urgency=medium
+  * Bug fix: when there was problem with DAPI minerva threw unexpected error
+    (#1316) 
+  * Bug fix: DAPI connection must go over HTTPS (#1316)
+
+ -- Piotr Gawron <piotr.gawron@uni.lu>  Fri, 26 Jun 2020 11:00:00 +0200
+
 minerva (15.0.0) stable; urgency=medium
   * Backward incompatible: old connection to CTD is removed and replaced with
     new Data-API interface that closely check license compliance

annotation/src/main/java/lcsb/mapviewer/annotation/services/dapi/DapiConnectorImpl.java

@@ -26,7 +26,7 @@ public class DapiConnectorImpl extends CachableInterface implements DapiConnecto
   private static Logger logger = LogManager.getLogger();
 
   private static final String DAPI_DOMAIN = "dapi.lcsb.uni.lu";
-  private static final String DAPI_BASE_URL = "http://" + DAPI_DOMAIN + "/api/";
+  private static final String DAPI_BASE_URL = "https://" + DAPI_DOMAIN + "/api/";
 
   private ConfigurationDao configurationDao;
 
@@ -220,6 +220,7 @@ public class DapiConnectorImpl extends CachableInterface implements DapiConnecto
       List<String> result = new ArrayList<>();
       String url = DAPI_BASE_URL + "database/";
       String content = getWebPageDownloader().getFromNetwork(url);
+      logger.debug(content);
       JsonArray array = new JsonParser()
           .parse(content)
           .getAsJsonObject()
@@ -230,7 +231,7 @@ public class DapiConnectorImpl extends CachableInterface implements DapiConnecto
         result.add(array.get(i).getAsJsonObject().get("name").getAsString());
       }
       return result;
-    } catch (IOException e) {
+    } catch (Exception e) {
       throw new DapiConnectionException("Problem with accessing dapi", e);
     }
   }

annotation/src/test/java/lcsb/mapviewer/annotation/services/MiriamConnectorTest.java

@@ -91,7 +91,6 @@ public class MiriamConnectorTest extends AnnotationTestFunctions {
       }
 
       if (!deprecated) {
-
         assertTrue("Invalid MiriamType (" + mt + ") for MiriamType: " + mt, miriamConnector.isValidMiriamType(mt));
       }
     }

annotation/src/test/java/lcsb/mapviewer/annotation/services/dapi/CtdDapiConfiguration.java

@@ -26,7 +26,7 @@ public class CtdDapiConfiguration {
   public DapiConnector dapiConnector() throws DapiConnectionException {
     DapiConnectorImpl mock = (DapiConnectorImpl) Mockito.spy(dapiConnector);
 
-    Mockito.doReturn("http://dapi.lcsb.uni.lu/api/database/CTD/releases/2019.02/").when(mock)
+    Mockito.doReturn("https://dapi.lcsb.uni.lu/api/database/CTD/releases/2019.02/").when(mock)
     .getLatestReleaseUrl("CTD");
 
     Mockito.doReturn(true).when(mock).isValidConnection();

annotation/src/test/java/lcsb/mapviewer/annotation/services/dapi/DrugBankDapiConfiguration.java

@@ -26,7 +26,7 @@ public class DrugBankDapiConfiguration {
   public DapiConnector dapiConnector() throws DapiConnectionException {
     DapiConnectorImpl mock = (DapiConnectorImpl) Mockito.spy(dapiConnector);
 
-    Mockito.doReturn("http://dapi.lcsb.uni.lu/api/database/DrugBank/releases/5.1/").when(mock)
+    Mockito.doReturn("https://dapi.lcsb.uni.lu/api/database/DrugBank/releases/5.1/").when(mock)
     .getLatestReleaseUrl("DrugBank");
 
     Mockito.doReturn(true).when(mock).isValidConnection();

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

@@ -266,17 +266,18 @@ final public class XmlParser {
       t.setOutputProperty(OutputKeys.INDENT, "yes");
       t.setOutputProperty(OutputKeys.METHOD, "xml");
 
-      NodeList list = node.getChildNodes();
-      for (int i = 0; i < list.getLength(); i++) {
-        Node element = list.item(i);
-        t.transform(new DOMSource(element), new StreamResult(sw));
+      if (includeHeadNode) {
+        t.transform(new DOMSource(node), new StreamResult(sw));
+      } else {
+        NodeList list = node.getChildNodes();
+        for (int i = 0; i < list.getLength(); i++) {
+          Node element = list.item(i);
+          t.transform(new DOMSource(element), new StreamResult(sw));
+        }
       }
     } catch (TransformerException te) {
       logger.debug("nodeToString Transformer Exception");
     }
-    if (includeHeadNode) {
-      return "<" + node.getNodeName() + ">" + sw.toString() + "</" + node.getNodeName() + ">";
-    }
     return sw.toString();
   }
 

commons/src/test/java/lcsb/mapviewer/common/XmlParserTest.java

@@ -99,6 +99,14 @@ public class XmlParserTest extends CommonTestFunctions {
     assertTrue(str.contains(xml));
   }
 
+  @Test
+  public void testNodeToStringWithHeaderAndAttrib() throws Exception {
+    String xml = "<test_node x=\"y\">test_x</test_node>";
+    Node validDoc = XmlParser.getXmlDocumentFromString(xml).getDocumentElement();
+    String str = XmlParser.nodeToString(validDoc, true);
+    assertTrue(str.contains(xml));
+  }
+
   @Test
   public void testConcurrencyParse() throws Exception {
     StringBuilder builder = new StringBuilder("<doc>");

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

@@ -393,7 +393,7 @@ public class CellDesignerXmlParser extends Converter {
   }
 
   private void processModelRdfNode(Model model, Node node) throws InvalidXmlSchemaException {
-    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
     model.addMiriamData(xmlAnnotationParser.parseRdfNode(node));
     model.addAuthors(xmlAnnotationParser.getAuthorsFromRdf(node));
     model.setCreationDate(xmlAnnotationParser.getCreateDateFromRdf(node));
@@ -728,7 +728,8 @@ public class CellDesignerXmlParser extends Converter {
     result.append(layerParser.layerCollectionToXml(model.getLayers()));
 
     result.append("</celldesigner:extension>\n");
-    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+
+    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
     result.append(xmlAnnotationParser.dataSetToXmlString(model.getMiriamData(), model.getAuthors(),
         model.getCreationDate(), model.getModificationDates(), model.getIdModel()));
     result.append("</annotation>\n");

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

@@ -4,6 +4,7 @@ import java.awt.Color;
 import java.awt.geom.Dimension2D;
 import java.awt.geom.Point2D;
 import java.io.ByteArrayInputStream;
+import java.util.*;
 
 import javax.xml.parsers.*;
 
@@ -15,6 +16,7 @@ import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidStateException;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SingleLine;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.View;
+import lcsb.mapviewer.model.map.MiriamRelationType;
 
 /**
  * Class with parsers for common CellDesigner objects.
@@ -47,6 +49,13 @@ public class CommonXmlParser {
 
   }
 
+  public static Set<MiriamRelationType> RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER;
+  {
+    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER = new HashSet<>();
+    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.addAll(Arrays.asList(MiriamRelationType.values()));
+    RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER.remove(MiriamRelationType.BQ_MODEL_IS_DERIVED_FROM);
+  }
+
   private DocumentBuilderFactory dbFactory;
   private DocumentBuilder dBuilder;
 

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

@@ -496,16 +496,6 @@ public class LayerXmlParser {
       if (node.getNodeType() == Node.ELEMENT_NODE) {
         if (node.getNodeName().equalsIgnoreCase("celldesigner:layerNotes")) {
           String notes = XmlParser.getNodeValue(node).trim();
-          Color backgroundColor = extractBackgroundColor(notes);
-          if (backgroundColor != null) {
-            result.setBackgroundColor(backgroundColor);
-            notes = removeBackgroundColor(notes);
-          }
-          Color borderColor = extractBorderColor(notes);
-          if (borderColor != null) {
-            result.setBorderColor(borderColor);
-            notes = removeBorderColor(notes);
-          }
           result.setNotes(notes);
         } else if (node.getNodeName().equalsIgnoreCase("celldesigner:paint")) {
           result.setColor(commonParser.getColor(node));
@@ -545,25 +535,6 @@ public class LayerXmlParser {
     return result.toString();
   }
 
-  Color extractBackgroundColor(String notes) {
-    return extractColor(notes, "BackgroundColor");
-  }
-
-  Color extractBorderColor(String notes) {
-    return extractColor(notes, "BorderColor");
-  }
-
-  private Color extractColor(String notes, String string) {
-    String lines[] = notes.split("[\n\r]+");
-    for (String line : lines) {
-      if (line.startsWith(string + "=") || line.startsWith(string + ":")) {
-        String colorString = line.replace(string + "=", "").replace(string + ":", "");
-        return new ColorParser().parse(colorString);
-      }
-    }
-    return null;
-  }
-
   /**
    * Transforms LayerText object into CellDesigner xml node.
    * 

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

 package lcsb.mapviewer.converter.model.celldesigner.annotation;
 
 import lcsb.mapviewer.model.map.*;
+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;
@@ -134,6 +135,12 @@ public enum NoteField {
   @ImportOnly
   TRANSPARENCY_ZOOM_LEVEL_VISIBILITY("SemanticZoomLevelTransparency", Element.class, null),
 
+  @ImportOnly
+  BACKGROUND_COLOR("BackgroundColor", LayerText.class, null),
+
+  @ImportOnly
+  BORDER_COLOR("BorderColor", LayerText.class, null),
+
   /**
    * {@link Element#getSemanticZoomLevelVisibility()}.
    */

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

 package lcsb.mapviewer.converter.model.celldesigner.annotation;
 
+import java.awt.Color;
 import java.lang.annotation.Annotation;
 import java.lang.reflect.Field;
 import java.util.*;
@@ -14,7 +15,11 @@ import org.w3c.dom.Node;
 import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.comparator.*;
 import lcsb.mapviewer.common.exception.*;
+import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
+import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.*;
 import lcsb.mapviewer.model.map.layout.graphics.LayerText;
 import lcsb.mapviewer.model.map.reaction.Reaction;
@@ -44,13 +49,17 @@ public class RestAnnotationParser {
   /**
    * Parser used for parsing annotations in rdf format.
    */
-  private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+  private XmlAnnotationParser xmlAnnotationParser;
 
   /**
    * Class used for some simple operations on {@link BioEntity} elements.
    */
   private ElementUtils elementUtils = new ElementUtils();
 
+  public RestAnnotationParser() {
+    xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
+  }
+
   /**
    * This method parse the string with annotations provided by the lcsb team.
    * Parsing has been prepared based on the information provided by Kazuhiro
@@ -761,10 +770,13 @@ public class RestAnnotationParser {
     for (String string2 : string) {
       boolean remove = false;
       for (NoteField field : NoteField.values()) {
-
         if (string2.startsWith(field.getCommonName() + ":") && field.getClazz().isAssignableFrom(object.getClass())) {
           remove = true;
+        } else if (string2.startsWith(field.getCommonName() + "=")
+            && field.getClazz().isAssignableFrom(object.getClass())) {
+          remove = true;
         }
+
       }
       if (remove) {
         annotations.append(string2 + "\n");
@@ -775,7 +787,10 @@ public class RestAnnotationParser {
     String ann = annotations.toString();
     setZIndex(object, ann);
     if (object instanceof LayerText) {
-      ((LayerText) object).setNotes(newNotes.toString().trim());
+      LayerText layerText = (LayerText) object;
+      setBackgroundColor(layerText, ann);
+      setBorderColor(layerText, ann);
+      layerText.setNotes(newNotes.toString().trim());
     }
     if (object instanceof BioEntity) {
       BioEntity bioEntity = (BioEntity) object;
@@ -814,6 +829,47 @@ public class RestAnnotationParser {
     }
   }
 
+  private void setBackgroundColor(LayerText layerText, String ann) {
+    Color color = getColor(ann, NoteField.BACKGROUND_COLOR.getCommonName());
+    if (color == null) {
+      return;
+    }
+    if (layerText.getBackgroundColor() == null || layerText.getBackgroundColor().equals(Color.LIGHT_GRAY)) {
+      layerText.setBackgroundColor(color);
+    } else if (!layerText.getBackgroundColor().equals(color)) {
+      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, layerText),
+          " New background color different than default [" + color + "]["
+              + layerText.getBackgroundColor() + "]. Ignoring.");
+    }
+
+  }
+
+  private void setBorderColor(LayerText layerText, String ann) {
+    Color color = getColor(ann, NoteField.BORDER_COLOR.getCommonName());
+    if (color == null) {
+      return;
+    }
+    if (layerText.getBorderColor() == null || layerText.getBorderColor().equals(Color.LIGHT_GRAY)) {
+      layerText.setBorderColor(color);
+    } else if (!layerText.getBorderColor().equals(color)) {
+      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, layerText),
+          " New border color different than default [" + color + "]["
+              + layerText.getBorderColor() + "]. Ignoring.");
+    }
+
+  }
+
+  Color getColor(String notes, String string) {
+    String lines[] = notes.split("[\n\r]+");
+    for (String line : lines) {
+      if (line.startsWith(string + "=") || line.startsWith(string + ":")) {
+        String colorString = line.replace(string + "=", "").replace(string + ":", "");
+        return new ColorParser().parse(colorString);
+      }
+    }
+    return null;
+  }
+
   /**
    * Process RDF description from notes, removes it from the description and adds
    * appropriate information to miriam data set.

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

@@ -10,6 +10,7 @@ import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.species.AbstractElementXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
@@ -34,7 +35,7 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
   /**
    * Parser used to retrieve Miriam data for the element.
    */
-  private XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+  private XmlAnnotationParser xmlAnnotationParser;
 
   /**
    * Collection of {@link CellDesignerElement cell designer elements} parsed from
@@ -56,6 +57,7 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
    */
   public CompartmentXmlParser(CellDesignerElementCollection elements) {
     this.elements = elements;
+    xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
   }
 
   @Override

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

@@ -80,7 +80,7 @@ public class KineticsXmlParser {
     try {
       StringBuilder result = new StringBuilder();
       result.append("<kineticLaw>");
-      Node mathNode = XmlParser.getXmlDocumentFromString(kinetics.getDefinition()).getFirstChild();
+      Node mathNode = XmlParser.getXmlDocumentFromString(kinetics.getDefinition()).getDocumentElement();
       for (Node ciNode : XmlParser.getAllNotNecessirellyDirectChild("ci", mathNode)) {
         String id = XmlParser.getNodeValue(ciNode).trim();
         Element element = model.getElementByElementId(id);

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

@@ -12,6 +12,7 @@ import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.*;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesignerConverter;
@@ -311,7 +312,7 @@ public class ReactionFromXml {
           result = parseReactionExtension(result, node, model);
         } else if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
           try {
-            XmlAnnotationParser xmlParser = new XmlAnnotationParser();
+            XmlAnnotationParser xmlParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
             result.addMiriamData(xmlParser.parseRdfNode(node));
           } catch (InvalidXmlSchemaException e) {
             throw new ReactionParserException("Problem with parsing RDF", result, e);

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

@@ -14,6 +14,7 @@ import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.CellDesignerAliasConverter;
 import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.*;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
@@ -494,7 +495,7 @@ public class ReactionToXml {
 
     sb.append(getLineXmlStringForLines(reaction.getLine()));
 
-    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
     sb.append("</celldesigner:extension>\n");
     sb.append(xmlAnnotationParser.dataSetToXmlString(reaction.getMiriamData(), reaction.getIdReaction()));
     sb.append("</annotation>\n");

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

@@ -13,6 +13,7 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.structure.*;
 import lcsb.mapviewer.model.map.InconsistentModelException;
@@ -67,7 +68,7 @@ public class SpeciesCollectionXmlParser {
   /**
    * Parser used for parsing annotation.
    */
-  private XmlAnnotationParser xap = new XmlAnnotationParser();
+  private XmlAnnotationParser xap;
 
   /**
    * Helper class used to decode/encode CellDesigner strings.
@@ -114,6 +115,7 @@ public class SpeciesCollectionXmlParser {
     geneParser = new GeneXmlParser(elements);
     proteinParser = new ProteinXmlParser(elements);
     antisenseRnaParser = new AntisenseRnaXmlParser(elements);
+    xap = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
   }
 
   /**

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

@@ -12,6 +12,7 @@ import lcsb.mapviewer.common.XmlParser;
 import lcsb.mapviewer.common.exception.*;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerElementCollection;
+import lcsb.mapviewer.converter.model.celldesigner.CommonXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationParser;
 import lcsb.mapviewer.converter.model.celldesigner.structure.*;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
@@ -195,7 +196,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
     }
 
     if (rdfNode != null) {
-      XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+      XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
       species.addMiriamData(xmlAnnotationParser.parseRdfNode(rdfNode));
     }
 
@@ -286,7 +287,7 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
 
     builder.append("</celldesigner:extension>\n");
 
-    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser();
+    XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
     builder.append(xmlAnnotationParser.dataSetToXmlString(species.getMiriamData(), elements.getElementId(species)));
 
     builder.append("</annotation>\n");

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

@@ -279,24 +279,6 @@ public class LayerXmlParserTest extends CellDesignerTestFunctions {
     assertNotNull(xml);
   }
 
-  @Test
-  public void testExtractBackgroundColor() throws Exception {
-    Color color = parser.extractBackgroundColor("dcxvxcvxcvx\nBackgroundColor=#ccffcc");
-    assertNotNull(color);
-  }
-
-  @Test
-  public void testExtractBackgroundColorWithColon() throws Exception {
-    Color color = parser.extractBackgroundColor("dcxvxcvxcvx\nBackgroundColor:#ccffcc");
-    assertNotNull(color);
-  }
-
-  @Test
-  public void testExtractNonExistingBackgroundColor() throws Exception {
-    Color color = parser.extractBackgroundColor("dcxvxcvxcvx\nBackgroundCffcc");
-    assertNull(color);
-  }
-
   @Test
   public void testRemoveBackgroundColor() throws Exception {
     String notes = parser.removeBackgroundColor("dcxvxcvxcvx\nBackgroundColor=#ccffcc");

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

@@ -45,7 +45,7 @@ public class SbmlValidationTests extends CellDesignerTestFunctions {
     result.add(new Object[] { "testFiles/model_with_annotations.xml" });
     result.add(new Object[] { "testFiles/reactions/modifier_with_operator.xml" });
     result.add(new Object[] { "testFiles/problematic/problematic_reaction_name.xml" });
-    
+    result.add(new Object[] { "testFiles/reactions/kinetics.xml" });
     return result;
   }
 

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

@@ -2,6 +2,7 @@ package lcsb.mapviewer.converter.model.celldesigner.annotation;
 
 import static org.junit.Assert.*;
 
+import java.awt.Color;
 import java.util.List;
 import java.util.Set;
 
@@ -18,6 +19,7 @@ import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.model.celldesigner.CellDesignerTestFunctions;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
 import lcsb.mapviewer.model.map.*;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.species.*;
@@ -333,4 +335,27 @@ public class RestAnnotationParserTest extends CellDesignerTestFunctions {
     assertFalse(protein.getNotes().contains("Description"));
   }
 
+  @Test
+  public void testExtractBackgroundColor() throws Exception {
+    RestAnnotationParser parser = new RestAnnotationParser();
+
+    Color color = parser.getColor("dcxvxcvxcvx\nBackgroundColor=#ccffcc", NoteField.BACKGROUND_COLOR.getCommonName());
+    assertNotNull(color);
+  }
+
+  @Test
+  public void testExtractBackgroundColorWithColon() throws Exception {
+    RestAnnotationParser parser = new RestAnnotationParser();
+    Color color = parser.getColor("dcxvxcvxcvx\nBackgroundColor:#ccffcc", NoteField.BACKGROUND_COLOR.getCommonName());
+    assertNotNull(color);
+  }
+
+  @Test
+  public void testExtractNonExistingBackgroundColor() throws Exception {
+    RestAnnotationParser parser = new RestAnnotationParser();
+    Color color = parser.getColor("dcxvxcvxcvx\nBackgroundCffcc", NoteField.BACKGROUND_COLOR.getCommonName());
+    assertNull(color);
+  }
+
+
 }