Update logic in JBrowseMaintenanceTask

Author: bbimber

jbrowse/src/org/labkey/jbrowse/JBrowseMaintenanceTask.java

@@ -264,15 +264,21 @@ private void processContainer(Container c, Logger log) throws IOException
             {
                 File expectedFile = j.getLocationOfProcessedTrack(false);
                 boolean error = false;
-                if (expectedFile != null && !expectedFile.exists())
+                if (j.shouldBeCopiedToProcessDir() && expectedFile != null && !expectedFile.exists())
                 {
                     log.error("Missing expected file: " + expectedFile.getPath());
                     error = true;
                 }
 
                 if (!j.doExpectedSearchIndexesExist())
                 {
-                    log.error("Missing search indexes: " + expectedFile.getPath());
+                    log.error("Missing trix search indexes: " + expectedFile.getPath());
+                    error = true;
+                }
+
+                if (j.shouldHaveFreeTextSearch() && !j.getExpectedLocationOfLuceneIndex(false).exists())
+                {
+                    log.error("Missing lucene search indexes: " + expectedFile.getPath());
                     error = true;
                 }
 

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

@@ -774,6 +774,11 @@ public boolean needsProcessing()
         return (needsGzip() && !isGzipped()) || doIndex() || shouldHaveFreeTextSearch();
     }
 
+    public boolean shouldBeCopiedToProcessDir()
+    {
+        return (needsGzip() && !isGzipped());
+    }
+
     public boolean isGzipped()
     {
         String fn = getSourceFileName();