commit tripal_chado_update_7338 which fixes a legacy t2 vocab warning

tripal_chado/tripal_chado.install

@@ -1859,7 +1859,7 @@ function tripal_chado_update_7336() {
 /**
  * Update the NCBITaxon DB entry.
  */
-function tripal_chado_update_7337(){
+function tripal_chado_update_7337() {
 
   chado_insert_db(array(
     'name' => 'NCBITaxon',
@@ -1868,3 +1868,54 @@ function tripal_chado_update_7337(){
     'urlprefix' => 'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id={accession}',
   ));
 }
+/**
+ * Correctly flag SOFP terms as "not" relationships, allowing the mview to
+ * populate them.
+ */
+function tripal_chado_update_7338() {
+
+  try {
+    // Get all SOFP terms and set their is_relationshiptype to 0
+
+    $sofp =  chado_get_db(['name' => 'SOFP']);
+    $fp = chado_get_cv(['name' => 'feature_property']);
+
+    if (!$sofp || !$fp) {
+      // No need to update unless the SOFP db exists
+      return;
+    }
+    $terms = chado_select_record('cvterm', ['cvterm_id', 'name'], [
+      'dbxref_id' => [
+        'db_id' => [
+          'name' => 'SOFP',
+        ],
+      ],
+      'cv_id' => ['name' => 'feature_property'],
+    ]);
+
+    if (empty($terms)) {
+      return;
+    }
+
+    foreach ($terms as $term) {
+
+      $id = $term->cvterm_id;
+      $name = $term->name;
+
+      if ($name == 'linked_to') {
+        continue;
+      }
+      chado_update_record('cvterm', ['cvterm_id' => $id], ['is_relationshiptype' => 0]);
+    }
+
+    //repopulate the mview.
+    print("repopulating the db2cv mview...");
+    $mview_id = chado_get_mview_id('db2cv_mview');
+    chado_populate_mview($mview_id);
+
+  } catch (\PDOException $e) {
+    $error = $e->getMessage();
+    throw new DrupalUpdateException('Could not perform update: ' . $error);
+  }
+
+}