Bugfix to RestoreSraDataHandler for new SRA datasets

Author: bbimber

SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceTriggerHelper.java

@@ -36,6 +36,7 @@
 import org.labkey.sequenceanalysis.SequenceAnalysisSchema;
 import org.labkey.sequenceanalysis.SequenceAnalysisServiceImpl;
 import org.labkey.sequenceanalysis.SequenceReadsetImpl;
+import org.labkey.sequenceanalysis.pipeline.ReadsetImportJob;
 import org.labkey.vfs.FileLike;
 
 import java.io.File;
@@ -302,7 +303,8 @@ public void createReaddataForSra(int readsetId, String sraAccessions)
             }
 
             String folderName = "SequenceImport_RS" + rs.getRowId() + "_" + FileUtil.getTimestamp();
-            FileLike outDir = AssayFileWriter.findUniqueFileName(folderName, pr.getRootFileLike());
+            FileLike sequenceImport = FileUtil.appendPath(pr.getRootFileLike(), Path.parse(ReadsetImportJob.NAME));
+            FileLike outDir = AssayFileWriter.findUniqueFileName(folderName, sequenceImport);
 
             FileLike expectedFile1 = FileUtil.appendPath(outDir, Path.parse(token + "_1.fastq.gz"));
             ExpData exp1 = ExperimentService.get().createData(c, new DataType("Data"));

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

@@ -158,8 +158,13 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Reads
                             throw new PipelineJobException("Missing Expdata: " + rd.getFileId1());
                         }
 
-                        if (!f1.getFile().exists() && !f1.getFile().getParentFile().exists())
+                        if (!f1.getFile().exists())
                         {
+                            if (f1.getFile().getParentFile().exists())
+                            {
+                                job.getLogger().warn("Parent file unexpectedly exists: " + f1.getFile().getParentFile().getPath());
+                            }
+
                             f1.setDataFileURI(new File(outputDir, accession + "_1.fastq.gz").toURI());
                             f1.save(job.getUser());
                             job.getLogger().debug("Updating filepath: " + f1.getFile().getPath());