Bugfixes around mGAP lucene indexes

Author: bbimber

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

@@ -9,7 +9,6 @@
 import org.labkey.api.util.GUID;
 import org.labkey.api.util.PageFlowUtil;
 
-import java.util.Arrays;
 import java.util.Date;
 import java.util.HashMap;
 import java.util.List;
@@ -30,7 +29,7 @@ protected String getDatabaseName()
     }
 
     @Override
-    protected String getTrackJson(Results rs)
+    protected String getTrackJson(boolean hasLuceneIndex)
     {
         return "{\"category\":\"mGAP Variant Catalog\",\"visibleByDefault\": true,\"additionalFeatureMsg\":\"<h2>**These annotations are created by lifting the macaque variants to human coordinates, and must be viewed in that context.</h2>\"}";
     }
@@ -93,7 +92,7 @@ private String getOrCreateJsonFile()
             row.put("createdby", getContainerUser().getUser().getUserId());
             row.put("modified", new Date());
             row.put("modifiedby", getContainerUser().getUser().getUserId());
-            row.put("trackJson", getTrackJson());
+            row.put("trackJson", getTrackJson(false));
 
             getStatusLogger().info("creating jsonfile for output: " + outputFileId);
             List<Map<String, Object>> rows = jsonFiles.getUpdateService().insertRows(getContainerUser().getUser(), getContainerUser().getContainer(), List.of(row), new BatchValidationException(), null, new HashMap<>());

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

@@ -270,7 +270,8 @@ private String getOrCreateJsonFile(Results rs, String fieldKey) throws SQLExcept
 
             if (isDefaultTrack)
             {
-                row.put("trackJson", getTrackJson(rs));
+                boolean hasLuceneIndex = StringUtils.trimToNull(rs.getString(FieldKey.fromString("luceneIndex/dataid/DataFileUrl"))) != null;
+                row.put("trackJson", getTrackJson(hasLuceneIndex));
             }
             else
             {
@@ -307,22 +308,14 @@ protected String getDatabaseName()
         return "mGAP Release: " + getInputValue("version");
     }
 
-    protected String getTrackJson(Results rs)
+    protected String getTrackJson(boolean hasLuceneIndex)
     {
         String indexString = "";
 
-        try
-        {
-            String luceneIndex = StringUtils.trimToNull(rs.getString(FieldKey.fromString("luceneIndex/dataid/DataFileUrl")));
-            if (luceneIndex != null)
-            {
-                ArrayList<String> infoFields = new TableSelector(QueryService.get().getUserSchema(getContainerUser().getUser(), getContainerUser().getContainer(), mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_ANNOTATIONS), PageFlowUtil.set("infoKey"), new SimpleFilter(FieldKey.fromString("isIndexed"), true), null).getArrayList(String.class);
-                indexString = ", \"createFullTextIndex\": true,\"infoFieldsForFullTextSearch\":\"" + (infoFields.isEmpty() ? "null" : StringUtils.join(infoFields, ",")) + "\"";
-            }
-        }
-        catch (SQLException e)
+        if (hasLuceneIndex)
         {
-            getStatusLogger().error("Error extracting luceneIndex", e);
+            ArrayList<String> infoFields = new TableSelector(QueryService.get().getUserSchema(getContainerUser().getUser(), getContainerUser().getContainer(), mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_ANNOTATIONS), PageFlowUtil.set("infoKey"), new SimpleFilter(FieldKey.fromString("isIndexed"), true), null).getArrayList(String.class);
+            indexString = ", \"createFullTextIndex\": true,\"infoFieldsForFullTextSearch\":\"" + (infoFields.isEmpty() ? "null" : StringUtils.join(infoFields, ",")) + "\"";
         }
 
         return "{\"category\":\"mGAP Variant Catalog\",\"visibleByDefault\": true,\"ensemblId\":\"Macaca_mulatta\",\"additionalFeatureMsg\":\"<h2>**The annotations below are primarily derived from human data sources (not macaque), and must be viewed in that context.</h2>\"" + indexString + "}";