Bugfix to SRA restore with single-end data

Author: bbimber

SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/model/ReadData.java

@@ -61,4 +61,6 @@ public interface ReadData extends Serializable
     String getSra_accession();
 
     boolean isArchived();
+
+    boolean isPairedEnd();
 }

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

@@ -307,10 +307,11 @@ public void cacheForRemoteServer()
         }
     }
 
+    @Override
     @Transient
     public boolean isPairedEnd()
     {
-        return getFile2() != null;
+        return getFileId2() != null;
     }
 
     @Override

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

@@ -1941,7 +1941,7 @@ else if (sraIDs.contains(rd.getSra_accession()))
                 RestoreSraDataHandler.FastqDumpWrapper sra = new RestoreSraDataHandler.FastqDumpWrapper(getJob().getLogger());
                 if (doneFile.exists())
                 {
-                    rdi.setFile(new File(outDir, rd.getSra_accession() + "_1.fastq.gz"), 1);
+                    rdi.setFile(new File(outDir, rd.getSra_accession() + (rd.isPairedEnd() ? "_1" : "") + ".fastq.gz"), 1);
                     if (rd.getFileId2() != null)
                     {
                         rdi.setFile(new File(outDir, rd.getSra_accession() + "_2.fastq.gz"), 2);
@@ -1954,7 +1954,7 @@ else if (sraIDs.contains(rd.getSra_accession()))
                         outDir.mkdirs();
                     }
 
-                    Pair<File, File> downloaded = sra.downloadSra(rd.getSra_accession(), outDir);
+                    Pair<File, File> downloaded = sra.downloadSra(rd.getSra_accession(), outDir, rd.isPairedEnd());
                     rdi.setFile(downloaded.first, 1);
                     rdi.setFile(downloaded.second, 2);
 

SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java

@@ -384,7 +384,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
                     File expectedFile2 = rd.getFileId2() == null ? null : ctx.getSequenceSupport().getCachedData(rd.getFileId2());
 
                     FastqDumpWrapper wrapper = new FastqDumpWrapper(ctx.getLogger());
-                    Pair<File, File> files = wrapper.downloadSra(accession, ctx.getOutputDir());
+                    Pair<File, File> files = wrapper.downloadSra(accession, ctx.getOutputDir(), rd.isPairedEnd());
 
                     long lines1 = SequenceUtil.getLineCount(files.first) / 4;
                     ctx.getJob().getLogger().debug("Reads in " + files.first.getName() + ": " + lines1);
@@ -459,7 +459,7 @@ public FastqDumpWrapper(@Nullable Logger logger)
             super(logger);
         }
 
-        public Pair<File, File> downloadSra(String dataset, File outDir) throws PipelineJobException
+        public Pair<File, File> downloadSra(String dataset, File outDir, boolean expectPaired) throws PipelineJobException
         {
             List<String> args = new ArrayList<>();
             args.add(getExe().getPath());
@@ -491,7 +491,7 @@ public Pair<File, File> downloadSra(String dataset, File outDir) throws Pipeline
 
             List<File> files = new ArrayList<>(Arrays.asList(Objects.requireNonNull(outDir.listFiles((dir, name) -> name.startsWith(dataset)))));
 
-            File file1 = new File(outDir, dataset + "_1.fastq");
+            File file1 = new File(outDir, dataset + (expectPaired ? "_1" : "") + ".fastq");
             if (!file1.exists())
             {
                 throw new PipelineJobException("Missing file: " + file1.getPath());
@@ -500,7 +500,12 @@ public Pair<File, File> downloadSra(String dataset, File outDir) throws Pipeline
             files.remove(file1);
 
             File file2 = new File(outDir, dataset + "_2.fastq");
-            if (!file2.exists())
+            if (expectPaired & !file2.exists())
+            {
+                throw new PipelineJobException("Missing file: " + file2.getPath());
+            }
+
+            if (!expectPaired)
             {
                 file2 = null;
             }