Improve logging

bbimber · bbimber · commit 7aade9e0a3c6 · 2025-01-02T17:03:54.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java
@@ -1955,6 +1955,7 @@ else if (sraIDs.contains(rd.getSra_accession()))
                 RestoreSraDataHandler.FastqDumpWrapper sra = new RestoreSraDataHandler.FastqDumpWrapper(getJob().getLogger());
                 if (doneFile.exists())
                 {
+                    getPipelineJob().getLogger().debug("Re-using existing SRA download: " + rd.getSra_accession());
                     rdi.setFile(new File(outDir, rd.getSra_accession() + (rd.isPairedEnd() ? "_1" : "") + ".fastq.gz"), 1);
                     if (rd.getFileId2() != null)
                     {

Original file line number	Diff line number	Diff line change
`@@ -1955,6 +1955,7 @@ else if (sraIDs.contains(rd.getSra_accession()))`
`1955`	`1955`	`RestoreSraDataHandler.FastqDumpWrapper sra = new RestoreSraDataHandler.FastqDumpWrapper(getJob().getLogger());`
`1956`	`1956`	`if (doneFile.exists())`
`1957`	`1957`	`{`
	`1958`	`+ getPipelineJob().getLogger().debug("Re-using existing SRA download: " + rd.getSra_accession());`
`1958`	`1959`	`rdi.setFile(new File(outDir, rd.getSra_accession() + (rd.isPairedEnd() ? "_1" : "") + ".fastq.gz"), 1);`
`1959`	`1960`	`if (rd.getFileId2() != null)`
`1960`	`1961`	`{`