Issue #2624452: tripal_insert_cvterm(), ensure the accession can be updated correctly in the rare case that it needs to be.

tripal_cv/api/tripal_cv.api.inc

@@ -524,9 +524,9 @@ function tripal_insert_cvterm($term, $options = array()) {
   }
 
   // This SQL statement will be used a lot to find a cvterm so just set it
-  // here for easy reference below.  Because CV terms can change their names
-  // but accessions don't change, the following SQL finds cvterms based on
-  // their accession rather than the name.
+  // here for easy reference below.  The following SQL tries to cover both the following:
+  // 1) The cvterm name may have changed but the accession remains constant
+  // 2) The cvterm name remains constant but the daccession/db may have changed (rare).
   $cvtermsql = "
     SELECT CVT.name, CVT.cvterm_id, CV.cv_id, CV.name as cvname,
       DB.name as dbname, DB.db_id, DBX.accession
@@ -534,7 +534,7 @@ function tripal_insert_cvterm($term, $options = array()) {
       INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
       INNER JOIN {db} DB on DBX.db_id = DB.db_id
       INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
-    WHERE DBX.accession = :accession and DB.name = :name
+    WHERE (DBX.accession = :accession and DB.name = :dbname) OR (CVT.name = :term and CV.name = :cvname)
   ";
 
   // Add the database. The function will just return the DB object if the
@@ -648,7 +648,7 @@ function tripal_insert_cvterm($term, $options = array()) {
         }
       }
       // get the original cvterm with the same name and return that.
-      $result = chado_query($cvtermsql, array(':accession' => $dbxref->accession, ':name' => $dbname));
+      $result = chado_query($cvtermsql, array(':accession' => $dbxref->accession, ':dbname' => $dbname, ':term' => $name, ':cvname' => $cvname));
       $cvterm = $result->fetchObject();
       return $cvterm;
     }
@@ -658,7 +658,7 @@ function tripal_insert_cvterm($term, $options = array()) {
   }
 
   // Get the CVterm record.  If it doesn't exist then create it.
-  $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
+  $result = chado_query($cvtermsql, array(':accession' => $dbxref->accession, ':dbname' => $dbname, ':term' => $name, ':cvname' => $cvname));
   $cvterm = $result->fetchObject();
   if (!$cvterm) {
 
@@ -705,11 +705,13 @@ function tripal_insert_cvterm($term, $options = array()) {
       tripal_report_error('tripal_cv', TRIPAL_WARNING, "The dbxref already exists for another cvterm record: $name (cv: " . $cvname . " db: $dbname)", NULL);
       return 0;
     }
-    $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
+    $result = chado_query($cvtermsql, array(':accession' => $dbxref->accession, ':dbname' => $dbname, ':term' => $name, ':cvname' => $cvname));
     $cvterm = $result->fetchObject();
   }
   // Update the cvterm.
   elseif ($update) {
+
+    // First, basic update of the term.
     $match = array('cvterm_id' => $cvterm->cvterm_id);
     $upd_values = array(
       'name'                => $name,
@@ -723,7 +725,43 @@ function tripal_insert_cvterm($term, $options = array()) {
       tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to update the term: $name", NULL);
       return 0;
     }
-    $result = chado_query($cvtermsql, array(':accession' => $accession, ':name' => $dbname));
+
+    // Second, check that the dbxref has not changed and if it has then update it.
+    $checksql = "
+      SELECT cvterm_id
+      FROM {cvterm} CVT
+        INNER JOIN {dbxref} DBX on CVT.dbxref_id = DBX.dbxref_id
+        INNER JOIN {db} DB on DBX.db_id = DB.db_id
+        INNER JOIN {cv} CV on CV.cv_id = CVT.cv_id
+      WHERE DBX.accession = :accession and DB.name = :dbname and CVT.name = :term and CV.name = :cvname
+    ";
+    $check = chado_query($checksql, array(':accession' => $dbxref->accession, ':dbname' => $dbname, ':term' => $name, ':cvname' => $cvname))->fetchObject();
+    if (!$check) {
+
+      // check to see if the dbxref exists if not, add it.
+      $dbxref =  tripal_insert_dbxref(array(
+        'db_id' => $db->db_id,
+        'accession' => $accession
+      ));
+      if (!$dbxref) {
+        tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to find or insert the dbxref record for cvterm, " .
+          "$name (id: $accession), for database $dbname", NULL);
+        return 0;
+      }
+
+      $match = array('cvterm_id' => $cvterm->cvterm_id);
+      $upd_values = array(
+        'dbxref_id' => $dbxref->dbxref_id,
+      );
+      $success = chado_update_record('cvterm', $match, $upd_values);
+      if (!$success) {
+        tripal_report_error('tripal_cv', TRIPAL_WARNING, "Failed to update the term $name with new accession $db:$accession", NULL);
+        return 0;
+      }
+    }
+
+    // Finally grab the updated details.
+    $result = chado_query($cvtermsql, array(':accession' => $dbxref->accession, ':dbname' => $dbname, ':term' => $name, ':cvname' => $cvname));
     $cvterm = $result->fetchObject();
   }
   else {
@@ -1111,4 +1149,4 @@ function tripal_get_cvterm_default_select_options($table, $field, $field_desc) {
   }
 
   return $options;
-}
+}