Resolve "Export to SBGN does not export some reactions"

Closes #713 (closed)

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

@@ -26,6 +26,8 @@ import lcsb.mapviewer.common.geometry.ColorParser;
 import lcsb.mapviewer.converter.ConverterException;
 import lcsb.mapviewer.converter.graphics.bioEntity.element.species.SpeciesConverter;
 import lcsb.mapviewer.converter.graphics.bioEntity.reaction.ReactionConverter;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.graphics.ArrowType;
 import lcsb.mapviewer.model.graphics.PolylineData;
 import lcsb.mapviewer.model.map.compartment.Compartment;
@@ -66,18 +68,15 @@ public class SbgnmlXmlExporter {
    */
   private static final double PROCESS_PORT_DISTANCE = 10.0;
   /**
-   * Length of random alphabetic string added in the begining of ID, if it is a
+   * Length of random alphabetic string added in the beginning of ID, if it is a
    * number. SBGN-ML doesn't accept numbers as ID.
    */
   private static final int ID_RANDOM_STRING_LENGTH = 5;
-  /**
-   * Helps in providing human readable identifiers of elements for logging.
-   */
-  private ElementUtils eu = new ElementUtils();
+
   /**
    * Default class logger.
    */
-  private Logger logger = LogManager.getLogger(SbgnmlXmlExporter.class.getName());
+  private Logger logger = LogManager.getLogger();
   /**
    * Counter of the arcs parsed so far, used in generating arc's id.
    */
@@ -141,7 +140,7 @@ public class SbgnmlXmlExporter {
         try {
           map.getArc().add(getArcFromReducedReaction(reaction));
         } catch (InvalidArgumentException e) {
-          logger.warn(eu.getElementTag(reaction) + "Invalid arc type."
+          logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, reaction), "Invalid arc type."
               + " Reduced notation reaction found of type that is not compliant with SBGN-ML format.");
         }
         continue;
@@ -263,7 +262,7 @@ public class SbgnmlXmlExporter {
     float height = structuralState.getHeight().floatValue();
     bbox.setH(height);
     bbox.setW(width);
-    
+
     bbox.setX((float) structuralState.getPosition().getX());
     bbox.setY((float) structuralState.getPosition().getY());
 
@@ -423,8 +422,8 @@ public class SbgnmlXmlExporter {
       return GlyphClazz.UNSPECIFIED_ENTITY;
     }
 
-    logger.warn(eu.getElementTag(element)
-        + "Element type is not supported by SBGN-ML format. Unspecified Entity type assigned.");
+    logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, element),
+        "Element type is not supported by SBGN-ML format. Unspecified Entity type assigned.");
     return GlyphClazz.UNSPECIFIED_ENTITY;
   }
 
@@ -721,8 +720,8 @@ public class SbgnmlXmlExporter {
     }
 
     if (reaction.getProducts().get(0).getElement() instanceof Phenotype) {
-      logger.warn(eu.getElementTag(reaction.getProducts().get(0).getElement())
-          + "Found Phenotype being a reactant in process. That is discouraged");
+      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, reaction.getProducts().get(0).getElement()),
+          "Found Phenotype being a reactant in process. That is discouraged");
     }
 
     arc.setSource(sourceTargetMap.get(reaction.getReactants().get(0).getElement().getElementId()));
@@ -820,8 +819,9 @@ public class SbgnmlXmlExporter {
       try {
         arcList.add(getArcFromNode(node, glyphList));
       } catch (InvalidArgumentException ex) {
-        logger.warn(
-            eu.getElementTag(node) + "Node skipped in export process, since it is not compliant with SBGN-ML format.");
+        logger.warn(new LogMarker(ProjectLogEntryType.EXPORT_ISSUE, node),
+            new ElementUtils().getElementTag(node.getElement()) +
+                "Node skipped in export process, since it is not compliant with SBGN-ML format.");
         continue;
       }
     }
@@ -839,7 +839,7 @@ public class SbgnmlXmlExporter {
       try {
         arcList.add(getArcFromNode(node, glyphList));
       } catch (InvalidArgumentException ex) {
-        logger.warn("Node skipped in export process, since it is not compliant with SBGN-ML format: "
+        logger.warn("Node skipped in export process, since it is not compliant with SBGN-ML format."
             + node.getClass().getName());
         continue;
       }