Bugfix to track import

bbimber · bbimber · commit 31608d6abe1a · 2023-04-16T06:37:33.000-07:00
diff --git a/mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java b/mGAP/src/org/labkey/mgap/pipeline/GenerateMgapTracksStep.java
@@ -250,13 +250,15 @@ private void createOrUpdateTrack(SequenceOutputFile so, PipelineJob job, String
             }
             else
             {
-                job.getLogger().debug("Updating existing track: " + so.getName());
+                int rowId = ts.getObject(Integer.class)
+                job.getLogger().debug("Updating existing track: " + so.getName() + " / " + rowId);
+
                 Map<String, Object> toUpdate = new CaseInsensitiveHashMap<>();
-                toUpdate.put("rowId", ts.getObject(Integer.class));
+                toUpdate.put("rowId", rowId);
                 toUpdate.put("vcfId", so.getRowid());
 
                 Map<String, Object> oldKeys = new CaseInsensitiveHashMap<>();
-                toUpdate.put("rowId", ts.getObject(Integer.class));
+                oldKeys.put("rowId", rowId);
 
                 releaseTracks.getUpdateService().updateRows(job.getUser(), targetContainer, Arrays.asList(toUpdate), Arrays.asList(oldKeys), null, null);
             }

Original file line number	Diff line number	Diff line change
`@@ -250,13 +250,15 @@ private void createOrUpdateTrack(SequenceOutputFile so, PipelineJob job, String`
`250`	`250`	`}`
`251`	`251`	`else`
`252`	`252`	`{`
`253`		`- job.getLogger().debug("Updating existing track: " + so.getName());`
	`253`	`+ int rowId = ts.getObject(Integer.class)`
	`254`	`+ job.getLogger().debug("Updating existing track: " + so.getName() + " / " + rowId);`
	`255`	`+`
`254`	`256`	`Map<String, Object> toUpdate = new CaseInsensitiveHashMap<>();`
`255`		`- toUpdate.put("rowId", ts.getObject(Integer.class));`
	`257`	`+ toUpdate.put("rowId", rowId);`
`256`	`258`	`toUpdate.put("vcfId", so.getRowid());`
`257`	`259`
`258`	`260`	`Map<String, Object> oldKeys = new CaseInsensitiveHashMap<>();`
`259`		`- toUpdate.put("rowId", ts.getObject(Integer.class));`
	`261`	`+ oldKeys.put("rowId", rowId);`
`260`	`262`
`261`	`263`	`releaseTracks.getUpdateService().updateRows(job.getUser(), targetContainer, Arrays.asList(toUpdate), Arrays.asList(oldKeys), null, null);`
`262`	`264`	`}`