Catch errors and throw exceptions earlier

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/CellHashingHandler.java

@@ -805,7 +805,11 @@ private HtoMergeResult possiblyMergeHtoFastqs(Readset htoReadset, File outdir, L
         File file1;
         File file2;
 
-        if (htoReadset.getReadData().size() != 1)
+        if (htoReadset.getReadData().isEmpty())
+        {
+            throw new PipelineJobException("No HTO fastqs exist for readset: " + htoReadset.getName());
+        }
+        else if (htoReadset.getReadData().size() != 1)
         {
             log.info("Merging HTO data");
             file1 = new File(outdir, FileUtil.makeLegalName(htoReadset.getName() + "hto.R1.fastq.gz"));

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

@@ -88,6 +88,11 @@ public void cacheReadset(int readsetId, User u)
 
     public void cacheReadset(SequenceReadsetImpl m)
     {
+        if (m.hasArchivedData())
+        {
+            throw new IllegalArgumentException("Readset has archived data, cannot be used for pipeline jobs");
+        }
+
         m.cacheForRemoteServer();
         if (m.existsInDatabase())
         {

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

@@ -84,7 +84,7 @@ private void mergeUsingCat(File output, List<File> inputs) throws PipelineJobExc
                 writer.write("{\n");
                 bashCommands.forEach(x -> writer.write(x + '\n'));
 
-                writer.write("} | gzip -c > " + output + "\n");
+                writer.write("} | gzip -c > " + output.getPath() + "\n");
             }
 
             SimpleScriptWrapper wrapper = new SimpleScriptWrapper(_logger);

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

@@ -508,7 +508,7 @@ else if (!samples.equals(header.getGenotypeSamples()))
                     threads = Math.max(1, threads - 1);
                 }
 
-                writer.write("} | bgzip -f" + (compressionLevel == null ? "" : " --compress-level 9") + (threads == null ? "" : " --threads " + threads) + " > " + outputGzip + "\n");
+                writer.write("} | bgzip -f" + (compressionLevel == null ? "" : " --compress-level 9") + (threads == null ? "" : " --threads " + threads) + " > " + outputGzip.getPath() + "\n");
             }
 
             SimpleScriptWrapper wrapper = new SimpleScriptWrapper(log);