Add check for orphan GenomicsDB folders

bbimber · bbimber · commit ff0747c80122 · 2024-10-01T10:56:30.000-07:00
diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/OrphanFilePipelineJob.java
@@ -542,6 +542,14 @@ private void getOrphanFilesForDirectory(Set<Integer> knownExpDatas, Map<URI, Set
 
                 if (f.isDirectory())
                 {
+                    if (f.getName().endsWith(".gdb"))
+                    {
+                        if (!knownExpDatas.contains(new File(f, "__tiledb_workspace.tdb").toURI()))
+                        {
+                            orphanSequenceFiles.add(f);
+                        }
+                    }
+
                     getOrphanFilesForDirectory(knownExpDatas, dataMap, f, orphanSequenceFiles, orphanIndexes);
                 }
                 else

Original file line number	Diff line number	Diff line change
`@@ -542,6 +542,14 @@ private void getOrphanFilesForDirectory(Set<Integer> knownExpDatas, Map<URI, Set`
`542`	`542`
`543`	`543`	`if (f.isDirectory())`
`544`	`544`	`{`
	`545`	`+ if (f.getName().endsWith(".gdb"))`
	`546`	`+ {`
	`547`	`+ if (!knownExpDatas.contains(new File(f, "__tiledb_workspace.tdb").toURI()))`
	`548`	`+ {`
	`549`	`+ orphanSequenceFiles.add(f);`
	`550`	`+ }`
	`551`	`+ }`
	`552`	`+`
`545`	`553`	`getOrphanFilesForDirectory(knownExpDatas, dataMap, f, orphanSequenceFiles, orphanIndexes);`
`546`	`554`	`}`
`547`	`555`	`else`