Merge remote-tracking branch 'origin/master' into...

Merge remote-tracking branch 'origin/master' into 1471-arrows-without-a-process-box-have-an-irregular-empty-space-in-their-lines

CHANGELOG

 minerva (16.0.0~alpha.2) stable; urgency=medium
   * Backward incompatibility: debian package cannot be upgraded from version
     prior to 12.1.0 (#1464)
+  * Small improvement: artifitial source and sink is created separately for
+    each uncomplete reaction (#1475)
   * Small improvement: homomultimer information is provided in API (#1468)
+  * Small improvement: missing info about species for SBML parsing warning
+    (#1472)
+  * Small improvement: glyph quality is improved (#1458)
   * Bug fix: arrows without a "process" box had an irregular empty space in
     their lines (#1471)
 

CellDesigner-plugin/src/main/java/lcsb/mapviewer/cdplugin/copypaste/CopyPasteAbstractAction.java

@@ -88,7 +88,7 @@ public class CopyPasteAbstractAction {
    */
   protected String getCopyString(String annotationString, String notesString) throws InvalidXmlSchemaException {
     XmlAnnotationParser xap = new XmlAnnotationParser();
-    Set<MiriamData> set = xap.parse(annotationString);
+    Set<MiriamData> set = xap.parse(annotationString, null);
     StringBuilder result = new StringBuilder();
     for (MiriamData md : set) {
       result.append(serialize(md) + "\n");

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

@@ -395,7 +395,7 @@ public class CellDesignerXmlParser extends Converter {
   private void processModelRdfNode(Model model, Node node) throws InvalidXmlSchemaException {
     XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
         CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
-    model.addMiriamData(xmlAnnotationParser.parseRdfNode(node));
+    model.addMiriamData(xmlAnnotationParser.parseRdfNode(node, null));
     model.addAuthors(xmlAnnotationParser.getAuthorsFromRdf(node));
     model.setCreationDate(xmlAnnotationParser.getCreateDateFromRdf(node));
     model.addModificationDates(xmlAnnotationParser.getModificationDatesFromRdf(node));

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

@@ -885,7 +885,8 @@ public class RestAnnotationParser {
     Matcher nodeMatcher = rdfNodePattern.matcher(notes);
     if (nodeMatcher.find()) {
       String rdfString = "<rdf:RDF" + nodeMatcher.group(1) + "</rdf:RDF>";
-      element.addMiriamData(xmlAnnotationParser.parse(rdfString));
+      element.addMiriamData(
+          xmlAnnotationParser.parse(rdfString, new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element)));
 
       notes = notes.substring(0, nodeMatcher.start() - "<rdf:RDF".length())
           + notes.substring(nodeMatcher.end() + "</rdf:RDF>".length());

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

@@ -15,6 +15,8 @@ import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationPars
 import lcsb.mapviewer.converter.model.celldesigner.species.AbstractElementXmlParser;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerCompartment;
 import lcsb.mapviewer.converter.model.celldesigner.structure.CellDesignerElement;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
 
@@ -144,7 +146,9 @@ public class CompartmentXmlParser extends AbstractElementXmlParser<CellDesignerC
       Node node = annotationNodes.item(y);
       if (node.getNodeType() == Node.ELEMENT_NODE) {
         if (node.getNodeName().equalsIgnoreCase("rdf:RDF")) {
-          compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(node));
+          compartment.addMiriamData(xmlAnnotationParser.parseRdfNode(node, 
+              new LogMarker(ProjectLogEntryType.PARSING_ISSUE, compartment.getClass().getSimpleName(), 
+                  compartment.getElementId(), "")));
         } else if (node.getNodeName().equalsIgnoreCase("celldesigner:extension")) {
           parseExtensionNode(compartment, node);
         } else if (node.getNodeName().equalsIgnoreCase("celldesigner:name")) {

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

@@ -19,6 +19,8 @@ import lcsb.mapviewer.converter.model.celldesigner.geometry.ReactionCellDesigner
 import lcsb.mapviewer.converter.model.celldesigner.geometry.helper.*;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.*;
 import lcsb.mapviewer.converter.model.celldesigner.types.*;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.graphics.*;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.model.Model;
@@ -313,7 +315,8 @@ public class ReactionFromXml {
           try {
             XmlAnnotationParser xmlParser = new XmlAnnotationParser(
                 CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
-            result.addMiriamData(xmlParser.parseRdfNode(node));
+            result.addMiriamData(xmlParser.parseRdfNode(node, new LogMarker(ProjectLogEntryType.PARSING_ISSUE,
+                result.getClass().getSimpleName(), result.getElementId(), model.getName())));
           } catch (InvalidXmlSchemaException e) {
             throw new ReactionParserException("Problem with parsing RDF", result, e);
           }

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

@@ -17,6 +17,8 @@ import lcsb.mapviewer.converter.model.celldesigner.annotation.RestAnnotationPars
 import lcsb.mapviewer.converter.model.celldesigner.structure.*;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.CellDesignerModificationResidue;
 import lcsb.mapviewer.converter.model.celldesigner.structure.fields.SpeciesState;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.compartment.Compartment;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
 import lcsb.mapviewer.model.map.kinetics.SbmlUnit;
@@ -198,7 +200,8 @@ public class SpeciesSbmlParser extends AbstractElementXmlParser<CellDesignerSpec
     if (rdfNode != null) {
       XmlAnnotationParser xmlAnnotationParser = new XmlAnnotationParser(
           CommonXmlParser.RELATION_TYPES_SUPPORTED_BY_CELL_DESIGNER);
-      species.addMiriamData(xmlAnnotationParser.parseRdfNode(rdfNode));
+      species.addMiriamData(xmlAnnotationParser.parseRdfNode(rdfNode, new LogMarker(ProjectLogEntryType.PARSING_ISSUE,
+          species.getClass().getSimpleName(), species.getElementId(), "")));
     }
 
     return result;

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

@@ -984,7 +984,8 @@ public class SbgnmlXmlParser {
           "No rdf node provided in annotation extension");
     } else {
       try {
-        element.addMiriamData(new XmlAnnotationParser().parseRdfNode(rdf));
+        element.addMiriamData(
+            new XmlAnnotationParser().parseRdfNode(rdf, new LogMarker(ProjectLogEntryType.PARSING_ISSUE, element)));
       } catch (InvalidXmlSchemaException e) {
         logger.error(e, e);
       }
@@ -1677,7 +1678,7 @@ public class SbgnmlXmlParser {
         List<Line2D> lines = new ArrayList<>(product.getLine().getLines());
         product.getLine().removeLines();
         Collections.reverse(lines);
-        for (Line2D l: lines) {
+        for (Line2D l : lines) {
           product.getLine().addLine(l.getP2(), l.getP1());
         }
       }

converter-graphics/src/main/java/lcsb/mapviewer/converter/graphics/bioEntity/element/ElementConverter.java

@@ -99,10 +99,11 @@ public abstract class ElementConverter<T extends Element> extends BioEntityConve
   protected void drawGlyph(T bioEntity, Graphics2D graphics) throws DrawingException {
     try {
       Image img = ImageIO.read(new ByteArrayInputStream(bioEntity.getGlyph().getFile().getFileContent()));
-      graphics.drawImage(img,
+      
+      Image scaledImage = img.getScaledInstance(bioEntity.getWidth().intValue(), bioEntity.getHeight().intValue(), Image.SCALE_SMOOTH);
+
+      graphics.drawImage(scaledImage,
           bioEntity.getX().intValue(), bioEntity.getY().intValue(),
-          (int) (bioEntity.getX() + bioEntity.getWidth()), (int) (bioEntity.getY() + bioEntity.getHeight()),
-          0, 0, img.getWidth(null), img.getHeight(null),
           null);
     } catch (IOException e) {
       throw new DrawingException(

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/GraphicsTestFunctions.java

@@ -16,6 +16,7 @@ import lcsb.mapviewer.common.UnitTestFailedWatcher;
 import lcsb.mapviewer.model.graphics.*;
 import lcsb.mapviewer.model.map.compartment.PathwayCompartment;
 import lcsb.mapviewer.model.map.compartment.SquareCompartment;
+import lcsb.mapviewer.model.map.layout.graphics.LayerText;
 import lcsb.mapviewer.model.map.modifier.Catalysis;
 import lcsb.mapviewer.model.map.reaction.*;
 import lcsb.mapviewer.model.map.species.*;
@@ -93,6 +94,19 @@ public abstract class GraphicsTestFunctions {
     return complex;
   }
 
+  protected LayerText createText() {
+    LayerText layerText = new LayerText();
+    layerText.setX(256.0);
+    layerText.setY(79.0);
+    layerText.setWidth(233.0);
+    layerText.setHeight(188.0);
+    layerText.setZ(0);
+    layerText.setNotes("asd as");
+    layerText.setColor(Color.BLACK);
+    return layerText;
+  }
+
+
   protected List<Color> removeAlpha(List<Color> allValues) {
     List<Color> result = new ArrayList<>();
     for (Color color : allValues) {

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/NormalImageGeneratorTest.java

 package lcsb.mapviewer.converter.graphics;
 
-import java.awt.*;
+import java.awt.Color;
+import java.awt.Desktop;
 import java.awt.geom.Point2D;
 import java.awt.geom.Rectangle2D;
+import java.io.File;
+import java.nio.file.Files;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
@@ -10,12 +13,12 @@ import org.junit.*;
 
 import lcsb.mapviewer.commands.CreateHierarchyCommand;
 import lcsb.mapviewer.converter.graphics.AbstractImageGenerator.Params;
+import lcsb.mapviewer.model.cache.UploadedFileEntry;
 import lcsb.mapviewer.model.graphics.PolylineData;
-import lcsb.mapviewer.model.map.layout.graphics.Layer;
-import lcsb.mapviewer.model.map.layout.graphics.LayerText;
+import lcsb.mapviewer.model.map.layout.graphics.*;
 import lcsb.mapviewer.model.map.model.Model;
 import lcsb.mapviewer.model.map.model.ModelFullIndexed;
-import lcsb.mapviewer.model.map.species.Complex;
+import lcsb.mapviewer.model.map.species.*;
 
 public class NormalImageGeneratorTest extends GraphicsTestFunctions {
   static Logger logger = LogManager.getLogger();
@@ -33,27 +36,15 @@ public class NormalImageGeneratorTest extends GraphicsTestFunctions {
     model.setWidth(526);
     model.setHeight(346);
 
-    LayerText compAlias = new LayerText();
-    compAlias.setX(256.0);
-    compAlias.setY(79.0);
-    compAlias.setWidth(233.0);
-    compAlias.setHeight(188.0);
-    compAlias.setNotes("asd as");
-    compAlias.setColor(Color.BLACK);
+    LayerText layerText = createText();
     Layer layer = new Layer();
-    layer.addLayerText(compAlias);
+    layer.addLayerText(layerText);
     layer.setVisible(true);
     model.addLayer(layer);
 
     layer.addLayerLine(new PolylineData(new Point2D.Double(0, 0), new Point2D.Double(100, 100)));
 
-    Complex alias = new Complex("1");
-    alias.setName("a");
-    alias.setX(300);
-    alias.setY(90);
-    alias.setWidth(100);
-    alias.setHeight(50);
-    model.addElement(alias);
+    model.addElement(createComplex());
 
     return model;
   }

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/BioEntityConverterImplTest.java

@@ -83,8 +83,7 @@ public class BioEntityConverterImplTest extends GraphicsTestFunctions {
     BioEntityConverterImpl converter = new BioEntityConverterImpl(alias, false, colorExtractor);
     converter.draw(alias, graphics, new ConverterParams());
 
-    verify(graphics, times(1)).drawImage(any(Image.class), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(),
-        anyInt(), anyInt(), nullable(ImageObserver.class));
+    verify(graphics, times(1)).drawImage(any(Image.class), anyInt(), anyInt(), nullable(ImageObserver.class));
   }
 
   private Reaction createReaction(double lineWidth) {

converter-graphics/src/test/java/lcsb/mapviewer/converter/graphics/bioEntity/element/species/SpeciesConverterTest.java

@@ -367,8 +367,7 @@ public class SpeciesConverterTest extends GraphicsTestFunctions {
     alias.setGlyph(glyph);
     rc.draw(alias, graphics, new ConverterParams());
 
-    verify(graphics, times(1)).drawImage(any(Image.class), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(), anyInt(),
-        anyInt(), anyInt(), nullable(ImageObserver.class));
+    verify(graphics, times(1)).drawImage(any(Image.class), anyInt(), anyInt(), nullable(ImageObserver.class));
   }
 
   protected GenericProtein createProtein() {

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

@@ -18,6 +18,8 @@ import lcsb.mapviewer.common.exception.InvalidXmlSchemaException;
 import lcsb.mapviewer.converter.InvalidInputDataExecption;
 import lcsb.mapviewer.converter.annotation.XmlAnnotationParser;
 import lcsb.mapviewer.converter.model.sbml.species.ElementColorEnum;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.BioEntity;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -68,13 +70,13 @@ public class SbmlBioEntityParser {
     this.layout = getSbmlLayout(sbmlModel);
   }
 
-  protected Set<MiriamData> extractMiriamDataFromAnnotation(Annotation annotation) throws InvalidInputDataExecption {
+  protected Set<MiriamData> extractMiriamDataFromAnnotation(Annotation annotation, LogMarker marker) throws InvalidInputDataExecption {
     XmlAnnotationParser parser = new XmlAnnotationParser();
     Set<MiriamData> result = new HashSet<>();
     try {
       Node rdfNode = getRdfNodeFromAnnotation(annotation);
       if (rdfNode != null) {
-        result.addAll(parser.parseRdfNode(rdfNode));
+        result.addAll(parser.parseRdfNode(rdfNode, marker));
       }
     } catch (InvalidXmlSchemaException e) {
       throw new InvalidInputDataExecption(e);
@@ -136,7 +138,7 @@ public class SbmlBioEntityParser {
 
   protected void assignBioEntityData(AbstractNamedSBase sbmlElement, BioEntity result)
       throws InvalidInputDataExecption {
-    result.addMiriamData(extractMiriamDataFromAnnotation(sbmlElement.getAnnotation()));
+    result.addMiriamData(extractMiriamDataFromAnnotation(sbmlElement.getAnnotation(), new LogMarker(ProjectLogEntryType.PARSING_ISSUE, result)));
     result.setName(sbmlElement.getName());
     String notes = NotesUtility.extractNotes(sbmlElement);
     result.setNotes(notes);

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

@@ -4,12 +4,15 @@ import java.awt.Color;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.sbml.jsbml.AbstractNamedSBase;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.ext.SBasePlugin;
 import org.sbml.jsbml.ext.layout.*;
 import org.sbml.jsbml.ext.render.*;
 
 import lcsb.mapviewer.common.XmlParser;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.graphics.ArrowType;
 
 public class SbmlModelUtils {
@@ -247,4 +250,14 @@ public class SbmlModelUtils {
     return result;
   }
 
+  public static LogMarker createMarker(ProjectLogEntryType type, AbstractNamedSBase element) {
+    if (element == null) {
+      return new LogMarker(type, "", "N/A", "N/A");
+    } else if (element.getModel() == null) {
+      return new LogMarker(type, element.getClass().getSimpleName(), element.getId(), "");
+    } else {
+      return new LogMarker(type, element.getClass().getSimpleName(), element.getId(), element.getModel().getName());
+    }
+  }
+
 }

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

@@ -72,7 +72,7 @@ public class SbmlParser extends Converter {
       SbmlParameterParser parameterParser = new SbmlParameterParser(sbmlModel, model);
       SbmlFunctionParser functionParser = new SbmlFunctionParser(sbmlModel, model);
 
-      model.addMiriamData(compartmentParser.extractMiriamDataFromAnnotation(sbmlModel.getAnnotation()));
+      model.addMiriamData(compartmentParser.extractMiriamDataFromAnnotation(sbmlModel.getAnnotation(), null));
       model.addAuthors(compartmentParser.extractAuthorsFromAnnotation(sbmlModel.getAnnotation()));
       model.addModificationDates(compartmentParser.extractModificationDatesFromAnnotation(sbmlModel.getAnnotation()));
       model.setCreationDate(compartmentParser.extractCreationDateFromAnnotation(sbmlModel.getAnnotation()));

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierType.java

@@ -5,7 +5,10 @@ import java.util.List;
 
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
+import org.sbml.jsbml.ModifierSpeciesReference;
 
+import lcsb.mapviewer.converter.model.sbml.SbmlModelUtils;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.modifier.*;
 import lcsb.mapviewer.model.map.reaction.Modifier;
 
@@ -31,7 +34,8 @@ public enum SBOTermModifierType {
     }
   }
 
-  public static Class<? extends Modifier> getTypeSBOTerm(String sboTerm) {
+  public static Class<? extends Modifier> getTypeSBOTerm(ModifierSpeciesReference modifier) {
+    String sboTerm = modifier.getSBOTermID();
     if (sboTerm == null || sboTerm.isEmpty()) {
       return Modifier.class;
     }
@@ -43,8 +47,10 @@ public enum SBOTermModifierType {
         }
       }
     }
+
     if (result == null) {
-      logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for modifier");
+      logger.warn(SbmlModelUtils.createMarker(ProjectLogEntryType.PARSING_ISSUE, modifier),
+          "Don't know how to handle SBOTerm " + sboTerm + " for modifier");
       result = Modifier.class;
     }
     return result;

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermReactionType.java

@@ -6,6 +6,8 @@ import java.util.List;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
+import lcsb.mapviewer.converter.model.sbml.SbmlModelUtils;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.reaction.Reaction;
 import lcsb.mapviewer.model.map.reaction.type.*;
 
@@ -49,7 +51,12 @@ public enum SBOTermReactionType {
     }
   }
 
-  public static Class<? extends Reaction> getTypeSBOTerm(String sboTerm) {
+  public static Class<? extends Reaction> getTypeSBOTerm(org.sbml.jsbml.Reaction reaction) {
+    if (reaction == null) {
+      return StateTransitionReaction.class;
+
+    }
+    String sboTerm = reaction.getSBOTermID();
     if (sboTerm == null || sboTerm.isEmpty()) {
       return StateTransitionReaction.class;
     }
@@ -62,7 +69,8 @@ public enum SBOTermReactionType {
       }
     }
     if (result == null) {
-      logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for reaction");
+      logger.warn(SbmlModelUtils.createMarker(ProjectLogEntryType.PARSING_ISSUE, reaction),
+          "Don't know how to handle SBOTerm " + sboTerm + " for reaction");
       result = StateTransitionReaction.class;
     }
     return result;

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/reaction/SbmlReactionParser.java

@@ -707,7 +707,7 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
 
     for (ModifierSpeciesReference modifier : sbmlReaction.getListOfModifiers()) {
       Species element = getMinervaModel().getElementByElementId(modifier.getSpecies());
-      Class<? extends Modifier> nodeClass = SBOTermModifierType.getTypeSBOTerm(modifier.getSBOTermID());
+      Class<? extends Modifier> nodeClass = SBOTermModifierType.getTypeSBOTerm(modifier);
       try {
         Modifier newNode = nodeClass.getConstructor(Element.class).newInstance(element);
         reaction.addModifier(newNode);
@@ -740,16 +740,14 @@ public class SbmlReactionParser extends SbmlBioEntityParser {
       reaction.addProduct(new Product(element));
     }
 
-    String sboTerm = sbmlReaction.getSBOTermID();
-
-    reaction = createProperReactionClassForSboTerm(reaction, sboTerm);
+    reaction = createProperReactionClassForSboTerm(reaction, sbmlReaction);
 
     return reaction;
   }
 
-  private Reaction createProperReactionClassForSboTerm(Reaction reaction, String sboTerm)
+  private Reaction createProperReactionClassForSboTerm(Reaction reaction, org.sbml.jsbml.Reaction sbmlReaction)
       throws InvalidInputDataExecption {
-    Class<? extends Reaction> reactionClass = SBOTermReactionType.getTypeSBOTerm(sboTerm);
+    Class<? extends Reaction> reactionClass = SBOTermReactionType.getTypeSBOTerm(sbmlReaction);
     try {
       reaction = reactionClass.getConstructor(Reaction.class).newInstance(reaction);
     } catch (InstantiationException | IllegalAccessException | IllegalArgumentException | InvocationTargetException

converter-sbml/src/main/java/lcsb/mapviewer/converter/model/sbml/species/SBOTermSpeciesType.java

@@ -8,6 +8,8 @@ import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.InvalidStateException;
+import lcsb.mapviewer.converter.model.sbml.SbmlModelUtils;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.species.*;
 
 public enum SBOTermSpeciesType {
@@ -50,7 +52,7 @@ public enum SBOTermSpeciesType {
     this.hypothetical = hypothetical;
   }
 
-  private static SBOTermSpeciesType getTypeSBOTerm(String sboTerm) {
+  private static SBOTermSpeciesType getTypeSBOTerm(String sboTerm, org.sbml.jsbml.Species species) {
     if (sboTerm == null || sboTerm.isEmpty()) {
       return SIMPLE_MOLECULE;
     }
@@ -63,17 +65,18 @@ public enum SBOTermSpeciesType {
       }
     }
     if (result == null) {
-      logger.warn("Don't know how to handle SBOTerm " + sboTerm + " for species");
+      logger.warn(SbmlModelUtils.createMarker(ProjectLogEntryType.PARSING_ISSUE, species),
+          "Don't know how to handle SBOTerm " + sboTerm);
       result = SIMPLE_MOLECULE;
     }
     return result;
   }
 
-  public static Species createElementForSBOTerm(String sboTerm, String elementId) {
+  public static Species createElementForSBOTerm(String sboTerm, org.sbml.jsbml.Species species) {
     try {
-      SBOTermSpeciesType type = getTypeSBOTerm(sboTerm);
+      SBOTermSpeciesType type = getTypeSBOTerm(sboTerm, species);
       Class<? extends Species> clazz = type.clazz;
-      Species result = clazz.getConstructor(String.class).newInstance(elementId);
+      Species result = clazz.getConstructor(String.class).newInstance(species.getId());
       if (type.hypothetical) {
         result.setHypothetical(true);
       }