Improve error handling

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/util/SequenceUtil.java

@@ -162,7 +162,7 @@ public static boolean hasMinLineCount(File f, long minLines) throws PipelineJobE
         }
         catch (IOException e)
         {
-            throw new PipelineJobException(e);
+            throw new PipelineJobException("Error processing file: " + f.getPath(), e);
         }
     }
 

jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java

@@ -217,7 +217,14 @@ public void ensureJsonFilesPrepared(User u, Logger log) throws PipelineJobExcept
     {
         for (JsonFile x : getJsonFiles(u, true))
         {
-            x.prepareResource(log, false, false);
+            try
+            {
+                x.prepareResource(log, false, false);
+            }
+            catch (Exception e)
+            {
+                log.error("Unable to process JsonFile: " + getObjectId(), e);
+            }
         }
     }