Bugfix to mGAP ETL

bbimber · bbimber · commit 0fe26b1bea28 · 2025-05-02T09:20:52.000-07:00
diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java
@@ -266,7 +266,7 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip
                     throw new PipelineJobException("File should have been deleted: " + localCopy.getPath());
                 }
 
-                Files.createSymbolicLink(f.toPath(), localCopy.toPath());
+                Files.createSymbolicLink(localCopy.toPath(), f.toPath());
             }
             catch (IOException e)
             {
@@ -289,7 +289,7 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip
                 getStatusLogger().info("Creating symlink copy of VCF index: " + index.getPath() + " / " + indexLocal.getPath());
                 try
                 {
-                    Files.createSymbolicLink(index.toPath(), indexLocal.toPath());
+                    Files.createSymbolicLink(indexLocal.toPath(), index.toPath());
                 }
                 catch (IOException e)
                 {

Original file line number	Diff line number	Diff line change
`@@ -266,7 +266,7 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip`
`266`	`266`	`throw new PipelineJobException("File should have been deleted: " + localCopy.getPath());`
`267`	`267`	`}`
`268`	`268`
`269`		`- Files.createSymbolicLink(f.toPath(), localCopy.toPath());`
	`269`	`+ Files.createSymbolicLink(localCopy.toPath(), f.toPath());`
`270`	`270`	`}`
`271`	`271`	`catch (IOException e)`
`272`	`272`	`{`
`@@ -289,7 +289,7 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip`
`289`	`289`	`getStatusLogger().info("Creating symlink copy of VCF index: " + index.getPath() + " / " + indexLocal.getPath());`
`290`	`290`	`try`
`291`	`291`	`{`
`292`		`- Files.createSymbolicLink(index.toPath(), indexLocal.toPath());`
	`292`	`+ Files.createSymbolicLink(indexLocal.toPath(), index.toPath());`
`293`	`293`	`}`
`294`	`294`	`catch (IOException e)`
`295`	`295`	`{`