Additional error handling for picard and testing

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/run/PicardWrapper.java

@@ -30,6 +30,11 @@ public PicardWrapper(@Nullable Logger logger)
 
     public String getVersion() throws PipelineJobException
     {
+        if (!jarExists())
+        {
+            throw new PipelineJobException("Unable to find picard.jar");
+        }
+
         List<String> params = new LinkedList<>();
         params.add(SequencePipelineService.get().getJava8FilePath());
         params.add("-jar");
@@ -77,13 +82,18 @@ public void setStringency(ValidationStringency stringency)
 
     abstract protected String getToolName();
 
-    protected List<String> getBaseArgs()
+    protected List<String> getBaseArgs() throws PipelineJobException
     {
         return getBaseArgs(false);
     }
 
-    protected List<String> getBaseArgs(boolean basicArgsOnly)
+    protected List<String> getBaseArgs(boolean basicArgsOnly) throws PipelineJobException
     {
+        if (!jarExists())
+        {
+            throw new PipelineJobException("Unable to find picard.jar");
+        }
+
         List<String> params = new LinkedList<>();
         params.add(SequencePipelineService.get().getJava8FilePath());
         params.addAll(SequencePipelineService.get().getJavaOpts());

SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java

@@ -353,7 +353,7 @@ public RecordedActionSet run() throws PipelineJobException
                 CreateSequenceDictionaryWrapper wrapper = new CreateSequenceDictionaryWrapper(getJob().getLogger());
                 wrapper.execute(fasta, true);
             }
-            catch (PipelineJobException e)
+            catch (PipelineJobException | IllegalArgumentException e)
             {
                 getJob().getLogger().warn("Unable to create sequence dictionary");
             }