Merge pull request #913 from tripal/892_SOFP_issue

resolve SOFP vocabulary warning on T2 migrated sites

tripal_chado/tripal_chado.install

@@ -29,6 +29,10 @@ function tripal_chado_install() {
       )
     ";
     chado_query($sql);
+
+    // Fix the SOFP feature_property issue from the legacy feature_property.
+    tripal_chado_fix_legacy_SOFP_7338();
+
   }
 
   tripal_insert_variable('bundle_category', 'Bundles can be categorized to allow for grouping');
@@ -683,6 +687,63 @@ function tripal_chado_chado_cvterm_mapping_schema() {
   return $schema;
 }
 
+
+
+/**
+ * Fixes a problem with the legacy feature_property/SOFP
+ * ontology loaded with previous verions of Chado and all terms are
+ * relationships.
+ *
+ * This function is called by the tripal_chado_install() for a
+ * new Tripal setup, and the tripal_chado_update_7338 for an existing
+ * site.
+ */
+
+function tripal_chado_fix_legacy_SOFP_7338() {
+
+  $sofp =  chado_get_db(['name' => 'SOFP']);
+  $fp = chado_get_cv(['name' => 'feature_property']);
+
+  // No need to update unless the SOFP db exists
+  if (!$sofp || !$fp) {
+    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.
+  $mview_id = chado_get_mview_id('db2cv_mview');
+  global $user;
+  tripal_add_job(
+    'Repopulating db2cv to fix legacy SOFP',
+    'tripal_chado',
+    'chado_populate_mview',
+    [$mview_id],
+    $user->uid
+  );
+}
+
 /**
  * Fixes the phase on the tripal_gffcds_temp table used for importing GFF files, and fixes the db.name term mapping.
  *
@@ -1859,7 +1920,7 @@ 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 +1929,21 @@ 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
+
+    tripal_chado_fix_legacy_SOFP_7338();
+
+  } catch (\PDOException $e) {
+    $error = $e->getMessage();
+    throw new DrupalUpdateException('Could not perform update: ' . $error);
+  }
+
+}