Fix bug in the order of gzip and deletion for SRA download

bbimber · bbimber · commit 04882ed4f663 · 2022-03-30T05:42:09.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java
@@ -279,8 +279,8 @@ public Pair<File, File> downloadSra(String dataset, File outDir) throws Pipeline
             {
                 throw new PipelineJobException("Missing file: " + file1.getPath());
             }
-            files.remove(file1);
             file1 = doGzip(file1);
+            files.remove(file1);
 
             File file2 = new File(outDir, dataset + "_2.fastq");
             if (!file2.exists())
@@ -289,8 +289,8 @@ public Pair<File, File> downloadSra(String dataset, File outDir) throws Pipeline
             }
             else
             {
-                files.remove(file2);
                 file2 = doGzip(file2);
+                files.remove(file2);
             }
 
             if (!files.isEmpty())

Original file line number	Diff line number	Diff line change
`@@ -279,8 +279,8 @@ public Pair<File, File> downloadSra(String dataset, File outDir) throws Pipeline`
`279`	`279`	`{`
`280`	`280`	`throw new PipelineJobException("Missing file: " + file1.getPath());`
`281`	`281`	`}`
`282`		`- files.remove(file1);`
`283`	`282`	`file1 = doGzip(file1);`
	`283`	`+ files.remove(file1);`
`284`	`284`
`285`	`285`	`File file2 = new File(outDir, dataset + "_2.fastq");`
`286`	`286`	`if (!file2.exists())`
`@@ -289,8 +289,8 @@ public Pair<File, File> downloadSra(String dataset, File outDir) throws Pipeline`
`289`	`289`	`}`
`290`	`290`	`else`
`291`	`291`	`{`
`292`		`- files.remove(file2);`
`293`	`292`	`file2 = doGzip(file2);`
	`293`	`+ files.remove(file2);`
`294`	`294`	`}`
`295`	`295`
`296`	`296`	`if (!files.isEmpty())`