Merge remote-tracking branch 'origin/develop' into fb_bound_containerfilter

Author: labkey-matthewb

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceAnalysisService.java

@@ -89,10 +89,10 @@ static public void setInstance(SequenceAnalysisService instance)
 
     abstract public String getVCFLineCount(File vcf, Logger log, boolean passOnly) throws PipelineJobException;
 
-    abstract public File getPicardJar();
-
     abstract public File writeAllCellHashingBarcodes(File webserverDir, User u, Container c) throws PipelineJobException;
 
+    abstract public File writeAllCiteSeqBarcodes(File webserverDir, User u, Container c) throws PipelineJobException;
+
     abstract public String createReferenceLibrary(List<Integer> sequenceIds, Container c, User u, String name, String assemblyId, String description, boolean skipCacheIndexes, boolean skipTriggers) throws IOException;
 
     abstract public String createReferenceLibrary(List<Integer> sequenceIds, Container c, User u, String name, String assemblyId, String description, boolean skipCacheIndexes, boolean skipTriggers, Set<GenomeTrigger> extraTriggers) throws IOException;

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/SequenceOutputFile.java

@@ -222,7 +222,7 @@ public ExpData getExpData()
             throw new IllegalAccessError("This method should only be called from the webserver");
         }
 
-        return _dataId > 0 ? ExperimentService.get().getExpData(_dataId) : null;
+        return _dataId != null && _dataId > 0 ? ExperimentService.get().getExpData(_dataId) : null;
     }
 
     public File getFile()

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

@@ -25,21 +25,23 @@
 abstract public class AbstractPipelineStep implements PipelineStep
 {
     private PipelineContext _ctx;
-    private PipelineStepProvider _provider;
+    private PipelineStepProvider<?> _provider;
     private int _stepIdx = 0;
 
-    public AbstractPipelineStep(PipelineStepProvider provider, PipelineContext ctx)
+    public AbstractPipelineStep(PipelineStepProvider<?> provider, PipelineContext ctx)
     {
         _ctx = ctx;
         _provider = provider;
     }
 
+    @Override
     public PipelineContext getPipelineCtx()
     {
         return _ctx;
     }
 
-    public PipelineStepProvider getProvider()
+    @Override
+    public PipelineStepProvider<?> getProvider()
     {
         return _provider;
     }

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

@@ -29,6 +29,16 @@ public interface BamProcessingStep extends PipelineStep
 {
     public BamProcessingStep.Output processBam(Readset rs, File inputBam, ReferenceGenome referenceGenome, File outputDirectory) throws PipelineJobException;
 
+    /**
+     * The BamProcessingStep must call Output.setBam() to explicitly specify the modified file.  This method exists as a check
+     * to prevent the developer from forgetting this.  Unless this is overridden, the pipeline will error if the original BAM is returned
+     * instead.
+     */
+    default boolean expectToCreateNewBam()
+    {
+        return true;
+    }
+
     public static interface Output extends PipelineStepOutput
     {
         /**

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

@@ -77,6 +77,12 @@ public List<File> getIntermediateFiles()
         return Collections.unmodifiableList(_intermediateFiles);
     }
 
+    @Override
+    public void removeIntermediateFiles(File toRemove)
+    {
+        _intermediateFiles.remove(toRemove);
+    }
+
     @Override
     public List<PicardMetricsOutput> getPicardMetricsFiles()
     {

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

@@ -28,7 +28,7 @@ public interface PipelineStep
 {
     public PipelineContext getPipelineCtx();
 
-    public PipelineStepProvider getProvider();
+    public PipelineStepProvider<?> getProvider();
 
     public int getStepIdx();
 

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

@@ -55,6 +55,12 @@ public interface PipelineStepOutput
      */
     public List<File> getIntermediateFiles();
 
+    /**
+     * Remove a previously added intermediate file
+     * @param toRemove The file to remove
+     */
+    public void removeIntermediateFiles(File toRemove);
+
     public List<PicardMetricsOutput> getPicardMetricsFiles();
 
     /**

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

@@ -83,7 +83,7 @@ public void run()
                     try (BufferedReader procReader = new BufferedReader(new InputStreamReader(_readStdErr ? tmpProcess.getErrorStream() : tmpProcess.getInputStream(), StringUtilsLabKey.DEFAULT_CHARSET)))
                     {
                         String line;
-                        while (tmpProcess.isAlive() && (line = procReader.readLine()) != null)
+                        while ((line = procReader.readLine()) != null)
                         {
                             if (_writeOutputToLog)
                                 _log.log(Level.DEBUG, "\t" + line);

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

@@ -124,5 +124,5 @@ static public void setInstance(SequencePipelineService instance)
 
     abstract public PreprocessingStep.Output simpleTrimFastqPair(File fq1, File fq2, List<String> params, File outDir, Logger log) throws PipelineJobException;
 
-    abstract public File runCiteSeqCount(PipelineStepOutput output, @Nullable String outputCategory, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId) throws PipelineJobException;
+    abstract public File runCiteSeqCount(PipelineStepOutput output, @Nullable String outputCategory, Readset htoReadset, File htoList, File cellBarcodeList, File outputDir, String basename, Logger log, List<String> extraArgs, boolean doHtoFiltering, @Nullable Integer minCountPerCell, File localPipelineDir, @Nullable Integer editDistance, boolean scanEditDistances, Readset parentReadset, @Nullable Integer genomeId, boolean generateHtoCalls) throws PipelineJobException;
 }

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

@@ -263,6 +263,11 @@ protected void setLogLevel(Level logLevel)
         _logLevel = logLevel;
     }
 
+    public Level getLogLevel()
+    {
+        return _logLevel;
+    }
+
     public void setWarnNonZeroExits(boolean warnNonZeroExits)
     {
         _warnNonZeroExits = warnNonZeroExits;