element info added to modifier warnings: Don't know how to handle SBOTerm

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/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/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);

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/AllSbmlReactionParserTests.java

@@ -8,7 +8,8 @@ import org.junit.runners.Suite.SuiteClasses;
 @SuiteClasses({ SbmlReactionExportArrowType.class,
     SbmlReactionExporterTest.class,
     SbmlReactionParserTest.class,
-    SbmlReactionParserExtractCurveTest.class
+    SbmlReactionParserExtractCurveTest.class,
+    SBOTermModifierTypeTest.class
 })
 public class AllSbmlReactionParserTests {
 

converter-sbml/src/test/java/lcsb/mapviewer/converter/model/sbml/reaction/SBOTermModifierTypeTest.java

+package lcsb.mapviewer.converter.model.sbml.reaction;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertNotNull;
+
+import org.junit.Test;
+import org.sbml.jsbml.ModifierSpeciesReference;
+
+import lcsb.mapviewer.converter.model.sbml.SbmlTestFunctions;
+import lcsb.mapviewer.model.map.reaction.Modifier;
+
+public class SBOTermModifierTypeTest extends SbmlTestFunctions {
+
+  @Test
+  public void testUnknownId() {
+    ModifierSpeciesReference reference = new ModifierSpeciesReference(3, 2);
+    reference.setSBOTerm("SBO:0000000");
+    Class<? extends Modifier> clazz = SBOTermModifierType.getTypeSBOTerm(reference);
+    assertNotNull(clazz);
+    assertEquals(1, super.getWarnings().size());
+    assertNotNull(super.getWarnings().get(0).getMarker());
+  }
+
+}