issues that were discovered during biohackathon 2019 in Paris

pathvisio/src/main/java/lcsb/mapviewer/wikipathway/model/biopax/BiopaxFactory.java

@@ -2,10 +2,12 @@ package lcsb.mapviewer.wikipathway.model.biopax;
 
 import java.util.*;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 
 import lcsb.mapviewer.common.exception.InvalidArgumentException;
+import lcsb.mapviewer.common.exception.NotImplementedException;
 import lcsb.mapviewer.model.LogMarker;
 import lcsb.mapviewer.model.ProjectLogEntryType;
 import lcsb.mapviewer.model.map.*;
@@ -30,10 +32,14 @@ public class BiopaxFactory {
       if (publication.getId() == null || publication.getId().equals("")) {
         return null;
       } else {
-        return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, publication.getId());
+        if (StringUtils.isNumeric(publication.getId().trim())) {
+          return new MiriamData(MiriamRelationType.BQ_BIOL_IS_DESCRIBED_BY, MiriamType.PUBMED, publication.getId());
+        } else {
+          return null;
+        }
       }
     } else {
-      throw new InvalidArgumentException("Unknown biopax database: " + publication.getDb());
+      throw new NotImplementedException("Unknown biopax database: " + publication.getDb());
     }
   }
 
@@ -55,10 +61,15 @@ public class BiopaxFactory {
       if (biopaxData != null) {
         BiopaxPublication bp = biopaxData.getPublicationByReference(string);
         if (bp != null) {
-          MiriamData md = createMiriamData(bp);
-          if (md != null) {
-            result.add(md);
-          } else {
+          try {
+            MiriamData md = createMiriamData(bp);
+            if (md != null) {
+              result.add(md);
+            } else {
+              logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, "BiopaxReference", string, getMapName()),
+                  "Publication is invalid.");
+            }
+          } catch (NotImplementedException e) {
             logger.warn(new LogMarker(ProjectLogEntryType.PARSING_ISSUE, "BiopaxReference", string, getMapName()),
                 "Publication is invalid.");
           }