Merge pull request #1396 from tripal/1266-tv3-part2_use-pull-1328

Use new api function chado_get_organism_id_from_scientific_name
tripal · Feb 14, 2023 · 4fbc231 · 4fbc231
2 parents 8fd59e9 + 72c70a0
commit 4fbc231
Showing 1 changed file with 19 additions and 5 deletions.
diff --git a/tripal_chado/includes/TripalFields/sbo__relationship/sbo__relationship_widget.inc b/tripal_chado/includes/TripalFields/sbo__relationship/sbo__relationship_widget.inc
@@ -421,14 +421,21 @@ class sbo__relationship_widget extends ChadoFieldWidget {
         }
         // Otherwise we need to look it up using the name field determined in the
         // constructor for the current field. There may be more than one name field
-        // (e.g. organism: genus + species) so we want to check both.
+        // so we want to check all. Special case for organism where lookup is complicated.
         else {
           $sql = 'SELECT ' . $fkey_rcolumn . ' FROM {' . $base_table . '} WHERE ' . implode("||' '||", $this->base_name_columns) . '=:keyword';
           $subject = chado_query($sql, [':keyword' => $subject_name])->fetchAll();
           if (count($subject) == 1) {
             $subject_id = $subject[0]->$fkey_rcolumn;
           }
-          else {
+          // Handle special case of looking up organism by its scientific name.
+          if ((!$subject_id) and ($base_table == 'organism')) {
+            $organism_id = chado_get_organism_id_from_scientific_name($subject_name, []);
+            if (count($organism_id) == 1) {
+              $subject_id = $organism_id[0];
+            }
+          }
+          if (!$subject_id) {
             form_set_error('sbo__relationship][' . $langcode . '][' . $delta . '][subject_name', 'The subject does not exist');
           }
         }
@@ -449,14 +456,21 @@ class sbo__relationship_widget extends ChadoFieldWidget {
         }
         // Otherwise we need to look it up using the name field determined in the
         // constructor for the current field. There may be more than one name field
-        // (e.g. organism: genus + species) so we want to check both.
-        elseif ($object_name) {
+        // so we want to check all. Special case for organism where lookup is complicated.
+        else {
           $sql = 'SELECT ' . $fkey_rcolumn . ' FROM {' . $base_table . '} WHERE ' . implode("||' '||", $this->base_name_columns) . '=:keyword';
           $object = chado_query($sql, [':keyword' => $object_name])->fetchAll();
           if (count($object) == 1) {
             $object_id = $object[0]->$fkey_rcolumn;
           }
-          else {
+          // Handle special case of looking up organism by its scientific name.
+          if ((!$object_id) and ($base_table == 'organism')) {
+            $organism_id = chado_get_organism_id_from_scientific_name($object_name, []);
+            if (count($organism_id) == 1) {
+              $object_id = $organism_id[0];
+            }
+          }
+          if (!$object_id) {
             form_set_error('sbo__relationship][' . $langcode . '][' . $delta . '][object_name', 'The object does not exist');
           }
         }