Bugfix to RestoreSraDataHandler

bbimber · bbimber · commit 2ef4efb16085 · 2025-10-17T07:22:40.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java
@@ -401,7 +401,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
 
                     long lines1 = SequenceUtil.getLineCount(files.first) / 4;
                     ctx.getJob().getLogger().debug("Reads in " + files.first.getName() + ": " + lines1);
-                    if (accessionToReads.containsKey(accession) && lines1 != accessionToReads.get(accession))
+                    if (accessionToReads.containsKey(accession) && accessionToReads.get(accession) > 0 && lines1 != accessionToReads.get(accession))
                     {
                         throw new PipelineJobException("Reads found in file, " + lines1 + ", does not match expected: " + accessionToReads.get(accession) + " for file: " + files.first.getPath());
                     }
@@ -410,7 +410,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un
                     {
                         long lines2 = SequenceUtil.getLineCount(files.second) / 4;
                         ctx.getJob().getLogger().debug("Reads in " + files.second.getName() + ": " + lines2);
-                        if (accessionToReads.containsKey(accession) && lines2 != accessionToReads.get(accession))
+                        if (accessionToReads.containsKey(accession) && accessionToReads.get(accession) > 0 && lines2 != accessionToReads.get(accession))
                         {
                             throw new PipelineJobException("Reads found in file, " + lines2 + ", does not match expected: " + accessionToReads.get(accession) + " for file: " + files.second.getPath());
                         }

Original file line number	Diff line number	Diff line change
`@@ -401,7 +401,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un`
`401`	`401`
`402`	`402`	`long lines1 = SequenceUtil.getLineCount(files.first) / 4;`
`403`	`403`	`ctx.getJob().getLogger().debug("Reads in " + files.first.getName() + ": " + lines1);`
`404`		`- if (accessionToReads.containsKey(accession) && lines1 != accessionToReads.get(accession))`
	`404`	`+ if (accessionToReads.containsKey(accession) && accessionToReads.get(accession) > 0 && lines1 != accessionToReads.get(accession))`
`405`	`405`	`{`
`406`	`406`	`throw new PipelineJobException("Reads found in file, " + lines1 + ", does not match expected: " + accessionToReads.get(accession) + " for file: " + files.first.getPath());`
`407`	`407`	`}`
`@@ -410,7 +410,7 @@ public void processFilesRemote(List<Readset> readsets, JobContext ctx) throws Un`
`410`	`410`	`{`
`411`	`411`	`long lines2 = SequenceUtil.getLineCount(files.second) / 4;`
`412`	`412`	`ctx.getJob().getLogger().debug("Reads in " + files.second.getName() + ": " + lines2);`
`413`		`- if (accessionToReads.containsKey(accession) && lines2 != accessionToReads.get(accession))`
	`413`	`+ if (accessionToReads.containsKey(accession) && accessionToReads.get(accession) > 0 && lines2 != accessionToReads.get(accession))`
`414`	`414`	`{`
`415`	`415`	`throw new PipelineJobException("Reads found in file, " + lines2 + ", does not match expected: " + accessionToReads.get(accession) + " for file: " + files.second.getPath());`
`416`	`416`	`}`