Issue #2567053: Moved hard-coding of public schema into a single spot in chado query as well as added todo comments to highlight points where external chado support is broken.

tripal_analysis/api/tripal_analysis.api.inc

@@ -172,9 +172,10 @@ function tripal_get_analysis_select_options($syncd_only = TRUE) {
   $analysis_list[] = 'Select an analysis';
 
   if ($syncd_only) {
+    // @todo: Re-write to support external chado databases.
     $sql = "
       SELECT *
-      FROM public.chado_analysis CA
+      FROM [chado_analysis] CA
         INNER JOIN {analysis} A ON A.analysis_id = CO.analysis_id
       ORDER BY A.name
     ";
@@ -196,4 +197,4 @@ function tripal_get_analysis_select_options($syncd_only = TRUE) {
     }
   }
   return $analysis_list;
-}
+}

tripal_core/api/tripal_core.chado_nodes.api.inc

@@ -550,9 +550,10 @@ function chado_node_sync_form($form, &$form_state) {
       // Build Query, we do a left join on the chado_xxxx table in the Drupal schema
       // so that if no criteria are specified we only get those items that have not
       // yet been synced.
+      // @todo: re-write the query to support external chado databases.
       $query = "SELECT " . implode(', ', $select) . ' ' .
                'FROM {' . $base_table . '} ' . $base_table . ' ' . implode(' ', $joins) . ' '.
-               "  LEFT JOIN public.$linking_table CT ON CT.$base_table_id = $base_table.$base_table_id " .
+               "  LEFT JOIN [$linking_table] CT ON CT.$base_table_id = $base_table.$base_table_id " .
                "WHERE CT.$base_table_id IS NULL";
 
       // extend the where clause if needed
@@ -859,10 +860,11 @@ function chado_node_sync_records($base_table, $max_sync = FALSE,
   // Build Query, we do a left join on the chado_xxxx table in the Drupal schema
   // so that if no criteria are specified we only get those items that have not
   // yet been synced.
+  // @todo: re-write to support external chado databases.
   $query = "
     SELECT " . implode(', ', $select) . ' ' .
     'FROM {' . $base_table . '} ' . $base_table . ' ' . implode(' ', $joins) . ' '.
-    "  LEFT JOIN public.$linking_table CT ON CT.$base_table_id = $base_table.$base_table_id " .
+    "  LEFT JOIN [$linking_table] CT ON CT.$base_table_id = $base_table.$base_table_id " .
     "WHERE CT.$base_table_id IS NULL ";
 
   // extend the where clause if needed

tripal_feature/tripal_feature.module

@@ -481,6 +481,7 @@ function tripal_feature_match_features_page($id) {
     drupal_goto($match->source);
     return;
   }
+  // @todo: re-write to support external chado databases.
   $sql = "
     SELECT
       F.name, F.uniquename, F.feature_id,
@@ -493,7 +494,7 @@ function tripal_feature_match_features_page($id) {
       INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id
       LEFT JOIN {feature_synonym} FS on FS.feature_id = F.feature_id
       LEFT JOIN {synonym} S on S.synonym_id = FS.synonym_id
-      INNER JOIN public.chado_feature CF on CF.feature_id = F.feature_id
+      INNER JOIN [chado_feature] CF on CF.feature_id = F.feature_id
     WHERE
       F.uniquename = :uname or
       F.name = :fname or
@@ -592,4 +593,4 @@ function tripal_feature_form_alter(&$form, &$form_state, $form_id) {
  */
 function tripal_feature_exclude_field_from_feature_by_default() {
   return array('residues' => 'TRUE');
-}
+}

tripal_organism/api/tripal_organism.api.inc

@@ -143,9 +143,10 @@ function tripal_get_organism_select_options($syncd_only = TRUE) {
   $org_list[] = 'Select an organism';
 
   if ($syncd_only) {
+    // @todo: Re-write to support external chado databases.
     $sql = "
       SELECT *
-      FROM public.chado_organism CO
+      FROM [chado_organism] CO
         INNER JOIN {organism} O ON O.organism_id = CO.organism_id
       ORDER BY O.genus, O.species
     ";
@@ -265,4 +266,4 @@ function tripal_autocomplete_organism($text) {
     $items[$name] = $name;
   }
   drupal_json_output($items);
-}
+}

tripal_pub/includes/tripal_pub.pub_search.inc

@@ -573,9 +573,10 @@ function theme_tripal_pub_search_setup_form_elements($variables) {
 function tripal_search_publications($search_array, $offset, $limit, &$total_records) {
 
   // build the SQL based on the criteria provided by the user
+  // @todo: re-write to support external chado databases.
   $select = "SELECT DISTINCT P.*, CP.nid ";
   $from   = "FROM {pub} P
-               LEFT JOIN public.chado_pub CP on P.pub_id = CP.pub_id
+               LEFT JOIN [chado_pub] CP on P.pub_id = CP.pub_id
                INNER JOIN {cvterm} CVT on CVT.cvterm_id = P.type_id
             ";
   $where  = "WHERE (NOT P.title = 'null') "; // always exclude the dummy pub

tripal_stock/tripal_stock.module

@@ -374,6 +374,7 @@ function tripal_stock_match_stocks_page($id) {
     drupal_goto($id);
   }
 
+  // @todo: re-write to support external chado databases.
   $sql = "
     SELECT
       S.name, S.uniquename, S.stock_id,
@@ -383,7 +384,7 @@ function tripal_stock_match_stocks_page($id) {
     FROM {stock} S
       INNER JOIN {organism} O on S.organism_id = O.organism_id
       INNER JOIN {cvterm} CVT on CVT.cvterm_id = S.type_id
-      INNER JOIN public.chado_stock CS on CS.stock_id = S.stock_id
+      INNER JOIN [chado_stock] CS on CS.stock_id = S.stock_id
     WHERE
       S.uniquename = :uname or S.name = :name
   ";