Bugfix to RestoreSraDataHandler for new SRA datasets

Author: bbimber

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

@@ -149,6 +149,36 @@ public void init(PipelineJob job, SequenceAnalysisJobSupport support, List<Reads
                         throw new PipelineJobException("Missing accession for archived readdata: " + rd.getRowid());
                     }
 
+                    // This indicates there is no pipeline job and no file, meaning it was imported as a TSV with SRA info. Therefore use this job's folder as the output location:
+                    if (rd.getRunId() == null)
+                    {
+                        ExpData f1 = ExperimentService.get().getExpData(rd.getFileId1());
+                        if (f1 == null)
+                        {
+                            throw new PipelineJobException("Missing Expdata: " + rd.getFileId1());
+                        }
+
+                        if (!f1.getFile().exists() && !f1.getFile().getParentFile().exists())
+                        {
+                            f1.setDataFileURI(new File(outputDir, accession + "_1.fastq.gz").toURI());
+                            f1.save(job.getUser());
+                            job.getLogger().debug("Updating filepath: " + f1.getFile().getPath());
+
+                            if (rd.getFileId2() != null)
+                            {
+                                ExpData f2 = ExperimentService.get().getExpData(rd.getFileId2());
+                                if (f2 == null)
+                                {
+                                    throw new PipelineJobException("Missing Expdata: " + rd.getFileId2());
+                                }
+
+                                f2.setDataFileURI(new File(outputDir, accession + "_2.fastq.gz").toURI());
+                                f2.save(job.getUser());
+                                job.getLogger().debug("Updating filepath: " + f2.getFile().getPath());
+                            }
+                        }
+                    }
+
                     totalArchivedPairs++;
                     support.cacheExpData(ExperimentService.get().getExpData(rd.getFileId1()));
                     if (rd.getFileId2() != null)