Improve handling of mGAP releases with or without lucene indexes

bbimber · bbimber · commit ef0d1cb6cd93 · 2023-12-06T11:07:55.000-08:00
diff --git a/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java b/jbrowse/src/org/labkey/jbrowse/model/JsonFile.java
@@ -964,10 +964,23 @@ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, bool
             }
             else if (existingLuceneDir != null && existingLuceneDir.exists())
             {
+                if (doesLuceneIndexExist())
+                {
+                    log.info("Deleting existing lucene index dir: " + luceneDir.getPath());
+                    try
+                    {
+                        FileUtils.deleteDirectory(luceneDir);
+                    }
+                    catch (IOException e)
+                    {
+                        throw new PipelineJobException(e);
+                    }
+                }
+
                 log.debug("Creating symlink to existing index: " + existingLuceneDir.getPath());
                 try
                 {
-                    Files.createSymbolicLink(existingLuceneDir.toPath(), existingLuceneDir.toPath());
+                    Files.createSymbolicLink(existingLuceneDir.toPath(), luceneDir.toPath());
                 }
                 catch (IOException e)
                 {

Original file line number	Diff line number	Diff line change
`@@ -964,10 +964,23 @@ public File prepareResource(User u, Logger log, boolean throwIfNotPrepared, bool`
`964`	`964`	`}`
`965`	`965`	`else if (existingLuceneDir != null && existingLuceneDir.exists())`
`966`	`966`	`{`
	`967`	`+ if (doesLuceneIndexExist())`
	`968`	`+ {`
	`969`	`+ log.info("Deleting existing lucene index dir: " + luceneDir.getPath());`
	`970`	`+ try`
	`971`	`+ {`
	`972`	`+ FileUtils.deleteDirectory(luceneDir);`
	`973`	`+ }`
	`974`	`+ catch (IOException e)`
	`975`	`+ {`
	`976`	`+ throw new PipelineJobException(e);`
	`977`	`+ }`
	`978`	`+ }`
	`979`	`+`
`967`	`980`	`log.debug("Creating symlink to existing index: " + existingLuceneDir.getPath());`
`968`	`981`	`try`
`969`	`982`	`{`
`970`		`- Files.createSymbolicLink(existingLuceneDir.toPath(), existingLuceneDir.toPath());`
	`983`	`+ Files.createSymbolicLink(existingLuceneDir.toPath(), luceneDir.toPath());`
`971`	`984`	`}`
`972`	`985`	`catch (IOException e)`
`973`	`986`	`{`