Merge pull request #1547 from tripal/tv4g1-issue1544-organism-infrasp…

…ecies-validation Tripal 4 change chado storage handling of empty fields
tripal · Jun 21, 2023 · 4f42251 · 4f42251
2 parents 0e78c14 + 16b7ffa
commit 4f42251
Show file tree

Hide file tree

Showing 2 changed files with 21 additions and 9 deletions.
diff --git a/tripal_chado/config/install/tripal.tripalfield_collection.default_chado.yml b/tripal_chado/config/install/tripal.tripalfield_collection.default_chado.yml
@@ -7,7 +7,7 @@ fields:
         content_type: bio_data_1
         label: Abbreviation
         type: chado_string_type
-        description: A shortened name (or abbreviation) for the organism (e.g. O.sativa).
+        description: A shortened name (or abbreviation) for the organism (e.g. O. sativa).
         cardinality: 1
         required: false
         storage_settings:
@@ -61,7 +61,7 @@ fields:
         content_type: bio_data_1
         label: Species
         type: chado_string_type
-        description: "The species name of the organism"
+        description: "The species name of the organism."
         cardinality: 1
         required: true
         storage_settings:
@@ -88,7 +88,7 @@ fields:
         content_type: bio_data_1
         label: Common Name
         type: chado_string_type
-        description: "The common name for the organism"
+        description: "The common name for the organism."
         cardinality: 1
         required: false
         storage_settings:

diff --git a/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php b/tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php
@@ -1122,14 +1122,26 @@ private function validateUnique($values, $chado_table, $record_id, $record, &$vi
           if (array_key_exists($col, $record['fields'])) {
             $col_val = $record['fields'][$col];
           }
-          // There is an issue with postgreSQL that if the value is allowed
-          // to be null but it is in a unique constraint then it will allow
-          // it to be inserted because a Null != NULL. So, skip checking
-          // these columns in the unique constraint if they are empty.
+          // If there is not a NOT NULL constraint on this column,
+          // and it is of a string type, then we need to handle
+          // empty values specially, since they might be stored
+          // as either NULL or as an empty string in the database
+          // table. Create a condition that checks for both. For
+          // other types, e.g. integer, just check for null.
           if ($table_def['fields'][$col]['not null'] == FALSE and !$col_val) {
-            continue;
+            if (in_array($table_def['fields'][$col]['type'],
+                ['character', 'character varying', 'text'])) {
+              $query->condition($query->orConditionGroup()
+                ->condition($col, '', '=')
+                ->isNull($col));
+            }
+            else {
+              $query->isNull($col);
+            }
+          }
+          else {
+            $query->condition($col, $col_val);
           }
-          $query->condition($col, $col_val);
         }
 
         // If we have matching record, check for a unique constraint