Handle nulls

labkey-jeckels · labkey-jeckels · commit 66325249aa4d · 2025-12-03T09:22:27.000-08:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java
@@ -335,7 +335,8 @@ public RecordedActionSet run() throws PipelineJobException
                 {
                     for (FileGroup.FilePair fp : lane)
                     {
-                        File localCopy = _wd.getWorkingCopyForInput(FileSystemLike.wrapFile(fp.file1)).toNioPathForRead().toFile();
+                        FileLike localCopyFileLike = _wd.getWorkingCopyForInput(FileSystemLike.wrapFile(fp.file1));
+                        File localCopy = localCopyFileLike == null ? null : localCopyFileLike.toNioPathForRead().toFile();
                         if (localCopy != null)
                         {
                             getJob().getLogger().debug("using local working copy for file: " + fp.file1.getPath());

Original file line number	Diff line number	Diff line change
`@@ -335,7 +335,8 @@ public RecordedActionSet run() throws PipelineJobException`
`335`	`335`	`{`
`336`	`336`	`for (FileGroup.FilePair fp : lane)`
`337`	`337`	`{`
`338`		`- File localCopy = _wd.getWorkingCopyForInput(FileSystemLike.wrapFile(fp.file1)).toNioPathForRead().toFile();`
	`338`	`+ FileLike localCopyFileLike = _wd.getWorkingCopyForInput(FileSystemLike.wrapFile(fp.file1));`
	`339`	`+ File localCopy = localCopyFileLike == null ? null : localCopyFileLike.toNioPathForRead().toFile();`
`339`	`340`	`if (localCopy != null)`
`340`	`341`	`{`
`341`	`342`	`getJob().getLogger().debug("using local working copy for file: " + fp.file1.getPath());`