Bugfixes around mGAP lucene indexes

Author: bbimber

mGAP/src/org/labkey/mgap/columnTransforms/LuceneIndexTransform.java

@@ -33,7 +33,7 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip
                 "rsync", "-r", "-a", "--delete", "--no-owner", "--no-group", "--chmod=D2770,F660", sourceDir.getPath(), targetDir.getPath()
         ));
 
-        return new File(targetDir, f.getName());
+        return new File(targetDir, sourceDir.getName() + "/" + f.getName());
     }
 
     @Override

mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java

@@ -181,7 +181,7 @@ private void inspectReleaseFolder(String releaseId, File baseDir, Container c, U
             checkSymlink(log, new File(f.getPath() + ".tbi"), releaseId, commandsToRun);
         });
 
-        final Set<String> fields = PageFlowUtil.set("vcfId", "variantTable", "liftedVcfId", "sitesOnlyVcfId", "novelSitesVcfId");
+        final Set<String> fields = PageFlowUtil.set("vcfId", "variantTable", "liftedVcfId", "sitesOnlyVcfId", "novelSitesVcfId", "luceneIndex");
         new TableSelector(QueryService.get().getUserSchema(u, c, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_CATALOG_RELEASES), fields, new SimpleFilter(FieldKey.fromString("objectid"), releaseId), null).forEachResults(rs -> {
             for (String field : fields)
             {
@@ -205,6 +205,12 @@ private void inspectReleaseFolder(String releaseId, File baseDir, Container c, U
                     continue;
                 }
 
+                // NOTE: lucene points to a file, but the parent dir is what we need to manage:
+                if ("write.lock".equals(f.getName()))
+                {
+                    expectedFiles.add(f.getParentFile().getParentFile());
+                }
+
                 expectedFiles.add(f);
                 if (f.getPath().toLowerCase().endsWith("vcf.gz"))
                 {