Merge branch '7.x-2.x' of github.com:tripal/tripal into 7.x-2.x

tripal_core/api/tripal_core.chado_query.api.inc

@@ -829,8 +829,8 @@ function chado_delete_record($table, $match, $options = NULL) {
   $table_desc = chado_get_schema($table);
   $fields = $table_desc['fields'];
   if (empty($table_desc)) {
-    chado_delete_record('tripal_core', TRIPAL_WARNING,
-      'chado_insert_record; There is no table description for !table_name',
+    tripal_report_error('tripal_core', TRIPAL_WARNING,
+      'chado_delete_record; There is no table description for !table_name',
       array('!table_name' => $table), array('print' => $print_errors)
     );
   }
@@ -1091,8 +1091,6 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
     return FALSE;
   }
 
-  $select = '';
-  $from = '';
   $where = array();
   $args = array();
 
@@ -1197,8 +1195,6 @@ function chado_select_record($table, $columns, $values, $options = NULL) {
       return array();
     }
 
-    $select[] = $field;
-
     // CASE 1: We have an array for a value.
     if (is_array($value)) {
 

tripal_feature/includes/tripal_feature.gff_loader.inc

@@ -676,7 +676,7 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
       $attr_fmax_partial = 'f';
       $attr_is_obsolete = 'f';
       $attr_is_analysis = 'f';
-      $attr_others = '';
+      $attr_others = [];
       $residues = '';
 
       // the organism to which a feature belongs can be set in the GFF
@@ -982,13 +982,15 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
             CVT.cvterm_id, CVT.name as feature_type,
             min(TGCT.fmin) as fmin, max(TGCT.fmax) as fmax,
             TGPT.feature_id as protein_id, TGPT.fmin as protein_fmin,
-            TGPT.fmax as protein_fmax
+            TGPT.fmax as protein_fmax, FLM.uniquename as landmark
           FROM {tripal_gffcds_temp} TGCT
             INNER JOIN {feature} F on F.feature_id = TGCT.parent_id
             INNER JOIN {cvterm} CVT on CVT.cvterm_id = F.type_id
+            INNER JOIN {featureloc} L on F.feature_id = L.feature_id
+            INNER JOIN {feature} FLM on L.srcfeature_id = FLM.feature_id
             LEFT JOIN {tripal_gffprotein_temp} TGPT on TGPT.parent_id = F.feature_id
           GROUP BY F.feature_id, F.name, F.uniquename, CVT.cvterm_id, CVT.name,
-            TGPT.feature_id, TGPT.fmin, TGPT.fmax, TGCT.strand
+            TGPT.feature_id, TGPT.fmin, TGPT.fmax, TGCT.strand, FLM.uniquename
         ";
         $results = chado_query($sql);
         $protein_cvterm = tripal_get_cvterm(array(
@@ -1041,8 +1043,8 @@ function tripal_feature_load_gff3($gff_file, $organism_id, $analysis_id,
               $result->uniquename, $organism, $pfmin, $pfmax);
             // Add the featureloc record. Set the start of the protein to
             // be the start of the coding sequence minus the phase.
-            tripal_feature_load_gff3_featureloc($feature, $organism, $landmark,
-              $pfmin, $pfmax, $strand, '', 'f', 'f', '', 0);
+            tripal_feature_load_gff3_featureloc($feature, $organism, $result->landmark,
+              $pfmin, $pfmax, $result->strand, '', 'f', 'f', '', 0);
           }
         }
       }