add genomics comments

Author: steve-fischer-200

Model/bin/ssLoadBatch

@@ -155,6 +155,7 @@ the corrupted batch."""
                 sys.exit(exit_code)
             except UnboundLocalError:
                 # If exit_code hasn't been set, then Houston, we've had a problem
+                print('Error: exit code has not been set', flush=True)
                 sys.exit(1)
 
 def index(solr_url, batch_dir=None, replace=False, validate_only=False):

Model/lib/wdk/ApiCommon/geneQueries.xml

@@ -89,6 +89,7 @@
           from apidb.TextSearchableComment@COMMENT_DBLINK@ tsc,
                @COMMENT_SCHEMA@MappedComment@COMMENT_DBLINK@ mc
           where mc.comment_id = tsc.comment_id
+            and tsc.comment_target_type = 'gene'
             and mc.review_status_id != 'rejected'
             and mc.is_visible = 1
         ]]>
@@ -104,6 +105,7 @@
           from apidb.textsearchablecomment@COMMENT_DBLINK@ tsc,
                @COMMENT_SCHEMA@mappedComment@COMMENT_DBLINK@ mc
           where mc.comment_id = tsc.comment_id
+            and tsc.comment_target_type = 'gene'
             and mc.review_status_id != 'rejected'
             and mc.is_visible = 1
         ]]>

Model/lib/wdk/ApiCommon/sequenceQueries.xml

@@ -103,6 +103,39 @@
       </sql>
     </sqlQuery>
 
+    <!-- needed for commentupdater -->
+    <sqlQuery name="UserCommentIDs">
+      <column name="source_id"/>
+      <column name="comment_id"/>
+      <sql>
+        <![CDATA[
+          select tsc.source_id, tsc.comment_id
+          from apidb.TextSearchableComment@COMMENT_DBLINK@ tsc,
+               @COMMENT_SCHEMA@MappedComment@COMMENT_DBLINK@ mc
+          where mc.comment_id = tsc.comment_id
+            and tsc.comment_target_type = 'genome'
+            and mc.review_status_id != 'rejected'
+            and mc.is_visible = 1
+        ]]>
+      </sql>
+    </sqlQuery>
+
+    <sqlQuery name="UserCommentContent">
+      <column name="source_id"/>
+      <column name="comment_content"/>
+      <sql>
+        <![CDATA[
+          select tsc.source_id, tsc.content
+          from apidb.TextSearchableComment@COMMENT_DBLINK@ tsc,
+               @COMMENT_SCHEMA@MappedComment@COMMENT_DBLINK@ mc
+          where mc.comment_id = tsc.comment_id
+            and tsc.comment_target_type = 'genome'
+            and mc.review_status_id != 'rejected'
+            and mc.is_visible = 1
+        ]]>
+      </sql>
+    </sqlQuery>
+
   </querySet>
 
 </wdkModel>

Model/lib/wdk/ApiCommon/siteSearchRecords.xml

@@ -151,6 +151,19 @@
 	<columnAttribute name="organism"/>  
       </table>
 
+      <!-- needed for the user comment updater. -->
+      <table name="userCommentIds"
+             internal="true"
+             queryRef="SequenceTables.UserCommentIDs">
+        <columnAttribute name="comment_id"/>
+      </table>
+
+      <table name="userCommentContent"
+             displayName="User Comments"
+             queryRef="SequenceTables.UserCommentContent">
+        <columnAttribute name="content"/>
+      </table>
+
       <table name="Aliases"
              displayName="Previous IDs and aliases"
              queryRef="SequenceTables.Aliases">