Additional support for VCF indexing

Author: bbimber

jbrowse/src/org/labkey/jbrowse/model/JBrowseSession.java

@@ -406,7 +406,7 @@ public static JBrowseSession getGenericGenomeSession(int genomeId)
 
     public JsonFile getTrack(User u, String trackGUID)
     {
-        for (JsonFile jf : getGenomeTracks(u, false))
+        for (JsonFile jf : getJsonFiles(u, false))
         {
             if (trackGUID.equalsIgnoreCase(jf.getObjectId()))
             {

jbrowse/src/org/labkey/jbrowse/model/JsonFile.java

@@ -929,12 +929,32 @@ public File prepareResource(Logger log, boolean throwIfNotPrepared, boolean forc
                 }
             }
 
-            prepareLuceneIndex(log);
+            if (forceReprocess || !doesLuceneIndexExist())
+            {
+                prepareLuceneIndex(log);
+            }
+            else
+            {
+                log.debug("Existing lucene index found, will not re-create: " + luceneDir.getPath());
+            }
         }
 
         return targetFile;
     }
 
+    private boolean doesLuceneIndexExist()
+    {
+        File luceneDir = getExpectedLocationOfLuceneIndex(false);
+        if (luceneDir == null)
+        {
+            return false;
+        }
+
+        // NOTE: is this the best file to test?
+        luceneDir = new File(luceneDir, "write.lock");
+        return luceneDir.exists();
+    }
+
     private void prepareLuceneIndex(Logger log) throws PipelineJobException
     {
         log.debug("Generating VCF full text index for file: " + getExpData().getFile().getName());