Bugfix to UpdateReadsetFilesHandler

BimberLab · Aug 20, 2024 · 0b52dce · 0b52dce
1 parent 075a2ee
commit 0b52dce
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Showing 2 changed files with 27 additions and 0 deletions.
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/UpdateReadsetFilesHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/UpdateReadsetFilesHandler.java
@@ -1,5 +1,6 @@
 package org.labkey.sequenceanalysis.analysis;
 
+import com.google.common.io.Files;
 import htsjdk.samtools.SAMFileHeader;
 import htsjdk.samtools.SAMFileWriter;
 import htsjdk.samtools.SAMFileWriterFactory;
@@ -111,6 +112,10 @@ else if (SequenceUtil.FILETYPE.gvcf.getFileType().isType(so.getFile()) | Sequenc
             {
                 getAndValidateHeaderForVcf(so, newRsName);
             }
+            else
+            {
+                throw new PipelineJobException("Unexpected file type: " + so.getFile().getPath());
+            }
 
             ctx.getSequenceSupport().cacheObject("readsetId", newRsName);
         }
@@ -207,6 +212,18 @@ private void reheaderVcf(SequenceOutputFile so, JobContext ctx, String newRsName
             String existingSample = header.getGenotypeSamples().get(0);
 
             File sampleNamesFile =  new File(ctx.getWorkingDirectory(), "sampleNames.txt");
+            if (!sampleNamesFile.exists())
+            {
+                try
+                {
+                    Files.touch(sampleNamesFile);
+                }
+                catch (IOException e)
+                {
+                    throw new PipelineJobException(e);
+                }
+            }
+
             try (PrintWriter writer = PrintWriters.getPrintWriter(sampleNamesFile, StandardOpenOption.APPEND))
             {
                 writer.println(newRsName);
@@ -243,6 +260,11 @@ private void addTracker(SequenceOutputFile so, String existingSample, String new
         {
             File tracker = new File(so.getFile().getParentFile(), "reheaderHistory.txt");
             boolean preExisting = tracker.exists();
+            if (!preExisting)
+            {
+                Files.touch(tracker);
+            }
+
             try (PrintWriter writer = PrintWriters.getPrintWriter(tracker, StandardOpenOption.APPEND))
             {
                 if (!preExisting)

diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendSaturation.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendSaturation.java
@@ -65,6 +65,11 @@ public void init(SequenceOutputHandler.JobContext ctx, List<SequenceOutputFile>
             {
                 if (!LOUPE_TYPE.isType(so.getFile()))
                 {
+                    if (!so.getFile().getName().endsWith("seurat.rds"))
+                    {
+                        throw new PipelineJobException("Unexpected file type: " + so.getFile().getPath());
+                    }
+
                     File meta = new File(so.getFile().getPath().replaceAll(".seurat.rds", ".cellBarcodes.csv"));
                     if (!meta.exists())
                     {