issues that were discovered during biohackathon 2019 in Paris

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/XML/DataNodeParser.java

@@ -11,6 +11,8 @@ import lcsb.mapviewer.common.Pair;
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
 import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.converter.ConverterException;
+import lcsb.mapviewer.model.LogMarker;
+import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.MiriamData;
 import lcsb.mapviewer.wikipathway.model.*;
 
@@ -33,6 +35,8 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
    */
   private final ReferenceParser referenceParser;
 
+  private int counter = 0;
+
   public DataNodeParser(String mapName) {
     super(mapName);
     referenceParser = new ReferenceParser(mapName);
@@ -43,7 +47,14 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
     if (!eElement.getNodeName().equals("DataNode")) {
       throw new InvalidArgumentException(ShapeParser.class.getSimpleName() + " can parse only DataNode xml nodes");
     }
-    DataNode node = new DataNode(eElement.getAttribute("GraphId"), getMapName());
+
+    String id = eElement.getAttribute("GraphId");
+    if (id == null || id.isEmpty()) {
+      id = "gen_dn_" + counter++;
+      logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, "DataNode", null, getMapName()),
+          "Empty GraphId found. Replacing with: " + id);
+    }
+    DataNode node = new DataNode(id, getMapName());
 
     for (Pair<String, String> entry : getAttributes(eElement)) {
       switch (entry.getLeft()) {
@@ -59,7 +70,7 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
         node.setType(entry.getRight());
         break;
       default:
-        logger.warn("Unknown attribute of " + eElement.getNodeName() + " node: " + entry.getLeft());
+        logger.warn(node.getLogMarker(), "Unknown attribute: " + entry.getLeft());
         break;
       }
     }
@@ -77,7 +88,7 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
           node.addBiopaxReference(eTmp.getTextContent());
           break;
         case ("Xref"):
-          MiriamData data = referenceParser.parse(eTmp);
+          MiriamData data = referenceParser.parse(eTmp, node.getLogMarker());
           if (data != null) {
             node.addReference(data);
           }
@@ -89,7 +100,8 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
           parseAttribute(eTmp, node);
           break;
         default:
-          logger.warn("Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
+          logger.warn(node.getLogMarker(),
+              "Unknown sub-node of " + eElement.getNodeName() + " node: " + eTmp.getNodeName());
           break;
         }
       }
@@ -189,12 +201,12 @@ public class DataNodeParser extends GraphicalPathwayElementParser<DataNode> {
     case ("org.pathvisio.model.GenMAPP-Xref"):
       // skip it when it's empty
       if (!value.isEmpty()) {
-        logger.warn(shape.getLogMarker() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+        logger.warn(shape.getLogMarker(), "Unknown attribute of node. Key: " + key + "; value: " + value);
         break;
       }
       break;
     default:
-      logger.warn(shape.getLogMarker() + "Unknown attribute of node. Key: " + key + "; value: " + value);
+      logger.warn(shape.getLogMarker(), "Unknown attribute of node. Key: " + key + "; value: " + value);
       break;
     }
   }