Issue #72: Updating API to include 2.1 improvements: 9a05f03

legacy/tripal_core/api/tripal_core.chado_nodes.api.inc

@@ -552,7 +552,7 @@ function chado_node_sync_form($form, &$form_state) {
       // yet been synced.
       $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
@@ -862,7 +862,7 @@ function chado_node_sync_records($base_table, $max_sync = FALSE,
   $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

legacy/tripal_feature/tripal_feature.module

@@ -472,7 +472,7 @@ 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

legacy/tripal_pub/includes/tripal_pub.pub_search.inc

@@ -575,7 +575,7 @@ function tripal_search_publications($search_array, $offset, $limit, &$total_reco
   // build the SQL based on the criteria provided by the user
   $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

legacy/tripal_stock/tripal_stock.module

@@ -392,7 +392,7 @@ 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
   ";

tripal_chado/api/modules/tripal_chado.organism.api.inc

@@ -145,7 +145,7 @@ function tripal_get_organism_select_options($syncd_only = TRUE) {
   if ($syncd_only) {
     $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
     ";

tripal_chado/api/tripal_chado.api.inc

@@ -70,14 +70,14 @@ function tripal_chado_publish_records($values, $job_id = NULL) {
   $select = "SELECT T.$pkey_field as record_id ";
   $from = "
     FROM {" . $table . "} T
-      LEFT JOIN public.$chado_entity_table CE on CE.record_id = T.$pkey_field
+      LEFT JOIN {" . $chado_entity_table . "} CE on CE.record_id = T.$pkey_field
   ";
 
   // For migration of Tripal v2 nodes to entities we want to include the
   // coresponding chado linker table.
   if ($sync_node && db_table_exists('chado_' . $table)) {
     $select = "SELECT T.$pkey_field as record_id, CT.nid ";
-    $from .= " INNER JOIN public.chado_$table CT ON CT.$pkey_field = T.$pkey_field";
+    $from .= " INNER JOIN {chado_" . $table . "} CT ON CT.$pkey_field = T.$pkey_field";
   }
   $where = " WHERE CE.record_id IS NULL ";
 

tripal_chado/includes/tripal_chado.migrate.inc

@@ -131,7 +131,7 @@ function tripal_chado_migrate_form($form, &$form_state) {
         $sql =
            "SELECT count(*)
             FROM {organism} O
-            INNER JOIN public.chado_organism CO ON O.organism_id = CO.organism_id
+            INNER JOIN {chado_organism} CO ON O.organism_id = CO.organism_id
           ";
         $org_count = chado_query($sql)->fetchField();
         if ($org_count > 0) {
@@ -147,7 +147,7 @@ function tripal_chado_migrate_form($form, &$form_state) {
         $sql =
         "SELECT count(*)
           FROM {analysis} A
-          INNER JOIN public.chado_analysis CA ON A.analysis_id = CA.analysis_id
+          INNER JOIN {chado_analysis} CA ON A.analysis_id = CA.analysis_id
          ";
         $ana_count = chado_query($sql)->fetchField();
         if ($ana_count > 0) {
@@ -163,7 +163,7 @@ function tripal_chado_migrate_form($form, &$form_state) {
         $sql =
           "SELECT count(*)
            FROM {project} P
-           INNER JOIN public.chado_project CP ON P.project_id = CP.project_id
+           INNER JOIN {chado_project} CP ON P.project_id = CP.project_id
           ";
         $proj_count = chado_query($sql)->fetchField();
         if ($proj_count > 0) {
@@ -179,7 +179,7 @@ function tripal_chado_migrate_form($form, &$form_state) {
         $sql =
           "SELECT count(*)
             FROM {featuremap} M
-            INNER JOIN public.chado_featuremap CM ON M.featuremap_id = CM.featuremap_id
+            INNER JOIN {chado_featuremap} CM ON M.featuremap_id = CM.featuremap_id
           ";
         $map_count = chado_query($sql)->fetchField();
         if ($map_count > 0) {
@@ -195,7 +195,7 @@ function tripal_chado_migrate_form($form, &$form_state) {
         $sql =
           "SELECT count(*)
            FROM {pub} P
-           INNER JOIN public.chado_pub CP ON P.pub_id = CP.pub_id
+           INNER JOIN {chado_pub} CP ON P.pub_id = CP.pub_id
          ";
         $proj_count = chado_query($sql)->fetchField();
         if ($proj_count > 0) {
@@ -212,7 +212,7 @@ function tripal_chado_migrate_form($form, &$form_state) {
         $sql =
             "SELECT V.name AS type, X.accession, db.name AS vocabulary , count(*) AS num
               FROM {" . $table . "} T
-              INNER JOIN public.$tv2_content_type CT ON T.$pkey = CT.$pkey
+              INNER JOIN {" . $tv2_content_type CT . "} ON T.$pkey = CT.$pkey
               INNER JOIN {cvterm} V ON V.cvterm_id = T.type_id
               INNER JOIN {dbxref} X ON X.dbxref_id = V.dbxref_id
               INNER JOIN {db} ON db.db_id = X.db_id
@@ -671,7 +671,7 @@ function tripal_chado_migrate_map_types($tv2_content_types) {
       $sql = "
         SELECT V.name AS type, X.accession, db.name AS vocabulary
         FROM {" . $table . "} T
-          INNER JOIN public.$tv2_content_type CT ON T.$pkey = CT.$pkey
+          INNER JOIN {" . $tv2_content_type . "} CT ON T.$pkey = CT.$pkey
           INNER JOIN {cvterm} V ON V.cvterm_id = T.type_id
           INNER JOIN {dbxref} X ON X.dbxref_id = V.dbxref_id
           INNER JOIN {db} ON db.db_id = X.db_id