Bugfix to UpdateSeuratPrototype

bbimber · bbimber · commit af0c4ba16568 · 2025-03-04T16:49:23.000-08:00
diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java
@@ -140,7 +140,8 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
                 toReplace.delete();
             }
 
-            FileUtils.moveFile(wrapper.getFile(), toReplace);
+            FileUtils.copyFile(wrapper.getFile(), toReplace);
+            ctx.getFileManager().addIntermediateFile(wrapper.getFile());
 
             // Also metadata:
             File meta = CellHashingServiceImpl.get().getMetaTableFromSeurat(wrapper.getFile());
@@ -149,7 +150,8 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
             {
                 metaOrig.delete();
             }
-            FileUtils.moveFile(meta, metaOrig);
+            FileUtils.copyFile(meta, metaOrig);
+            ctx.getFileManager().addIntermediateFile(meta);
 
             // Also cellbarcodes:
             File cellbarcodes = CellHashingServiceImpl.get().getCellBarcodesFromSeurat(wrapper.getFile());
@@ -158,7 +160,8 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra
             {
                 cellbarcodesOrig.delete();
             }
-            FileUtils.moveFile(cellbarcodes, cellbarcodesOrig);
+            FileUtils.copyFile(cellbarcodes, cellbarcodesOrig);
+            ctx.getFileManager().addIntermediateFile(cellbarcodes);
         }
         catch (IOException e)
         {

Original file line number	Diff line number	Diff line change
`@@ -140,7 +140,8 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra`
`140`	`140`	`toReplace.delete();`
`141`	`141`	`}`
`142`	`142`
`143`		`- FileUtils.moveFile(wrapper.getFile(), toReplace);`
	`143`	`+ FileUtils.copyFile(wrapper.getFile(), toReplace);`
	`144`	`+ ctx.getFileManager().addIntermediateFile(wrapper.getFile());`
`144`	`145`
`145`	`146`	`// Also metadata:`
`146`	`147`	`File meta = CellHashingServiceImpl.get().getMetaTableFromSeurat(wrapper.getFile());`
`@@ -149,7 +150,8 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra`
`149`	`150`	`{`
`150`	`151`	`metaOrig.delete();`
`151`	`152`	`}`
`152`		`- FileUtils.moveFile(meta, metaOrig);`
	`153`	`+ FileUtils.copyFile(meta, metaOrig);`
	`154`	`+ ctx.getFileManager().addIntermediateFile(meta);`
`153`	`155`
`154`	`156`	`// Also cellbarcodes:`
`155`	`157`	`File cellbarcodes = CellHashingServiceImpl.get().getCellBarcodesFromSeurat(wrapper.getFile());`
`@@ -158,7 +160,8 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List<SeuratObjectWra`
`158`	`160`	`{`
`159`	`161`	`cellbarcodesOrig.delete();`
`160`	`162`	`}`
`161`		`- FileUtils.moveFile(cellbarcodes, cellbarcodesOrig);`
	`163`	`+ FileUtils.copyFile(cellbarcodes, cellbarcodesOrig);`
	`164`	`+ ctx.getFileManager().addIntermediateFile(cellbarcodes);`
`162`	`165`	`}`
`163`	`166`	`catch (IOException e)`
`164`	`167`	`{`