Allow certain jobs to run when the readset has archived reads

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceAnalysisJobSupport.java

@@ -47,6 +47,8 @@ public interface SequenceAnalysisJobSupport extends Serializable
 
     public void cacheReadset(int readsetId, User u);
 
+    public void cacheReadset(int readsetId, User u, boolean allowReadsetsWithArchivedData);
+
     public List<AnalysisModel> getCachedAnalyses();
 
     public void cacheGenome(ReferenceGenome m);

SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java

@@ -236,8 +236,11 @@ private File getFile(int fileIdx, Integer fileId)
 
     public void cacheForRemoteServer()
     {
-        getFile1();
-        getFile2();
+        if (!isArchived())
+        {
+            getFile1();
+            getFile2();
+        }
     }
 
     @Transient

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

@@ -73,12 +73,19 @@ public AnalysisModel getCachedAnalysis(int rowId)
         return _cachedAnalyses.get(rowId);
     }
 
+    @Override
     public void cacheReadset(int readsetId, User u)
+    {
+        cacheReadset(readsetId,u, false);
+    }
+
+    @Override
+    public void cacheReadset(int readsetId, User u, boolean allowReadsetsWithArchivedData)
     {
         SequenceReadsetImpl rs = SequenceAnalysisServiceImpl.get().getReadset(readsetId, u);
         if (rs != null)
         {
-            cacheReadset(rs);
+            cacheReadset(rs, allowReadsetsWithArchivedData);
         }
         else
         {
@@ -88,9 +95,14 @@ public void cacheReadset(int readsetId, User u)
 
     public void cacheReadset(SequenceReadsetImpl m)
     {
-        if (m.hasArchivedData())
+        cacheReadset(m, false);
+    }
+
+    public void cacheReadset(SequenceReadsetImpl m, boolean allowReadsetsWithArchivedData)
+    {
+        if (!allowReadsetsWithArchivedData && m.hasArchivedData())
         {
-            throw new IllegalArgumentException("Readset has archived data, cannot be used for pipeline jobs");
+            throw new IllegalArgumentException("Readset has archived data, cannot be used for pipeline jobs", new Exception());
         }
 
         m.cacheForRemoteServer();
@@ -113,6 +125,11 @@ public void cacheReadset(SequenceReadsetImpl m)
     }
 
     public void cacheAnalysis(AnalysisModelImpl m, PipelineJob job)
+    {
+        cacheAnalysis(m, job, false);
+    }
+
+    public void cacheAnalysis(AnalysisModelImpl m, PipelineJob job, boolean allowReadsetsWithArchivedData)
     {
         if (m.getAlignmentFile() != null)
         {
@@ -122,7 +139,7 @@ public void cacheAnalysis(AnalysisModelImpl m, PipelineJob job)
         if (m.getReadset() != null)
         {
             SequenceReadsetImpl rs = SequenceAnalysisServiceImpl.get().getReadset(m.getReadset(), job.getUser());
-            cacheReadset(rs);
+            cacheReadset(rs, allowReadsetsWithArchivedData);
         }
 
         if (m.getLibraryId() != null)

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

@@ -96,12 +96,12 @@ public RecordedActionSet run() throws PipelineJobException
 
             if (f.getReadset() != null)
             {
-                getPipelineJob().getSequenceSupport().cacheReadset(f.getReadset(), getJob().getUser());
+                getPipelineJob().getSequenceSupport().cacheReadset(f.getReadset(), getJob().getUser(), true);
             }
 
             if (f.getAnalysis_id() != null)
             {
-                getPipelineJob().getSequenceSupport().cacheAnalysis(AnalysisModelImpl.getFromDb(f.getAnalysis_id(), getJob().getUser()), getJob());
+                getPipelineJob().getSequenceSupport().cacheAnalysis(AnalysisModelImpl.getFromDb(f.getAnalysis_id(), getJob().getUser()), getJob(), true);
             }
         }
 

cluster/src/org/labkey/cluster/ClusterController.java

@@ -201,7 +201,7 @@ public boolean handlePost(JobIdsForm form, BindException errors) throws Exceptio
                     return false;
                 }
 
-                if (!PipelineJob.TaskStatus.running.name().equalsIgnoreCase(sf.getStatus()))
+                if (PipelineJob.TaskStatus.running.name().equalsIgnoreCase(sf.getStatus()))
                 {
                     errors.reject(ERROR_MSG, "This cannot be used on actively running jobs.  Status was: " + sf.getStatus());
                     return false;