Chado Node API: updated dbxref/relationship api to handle pre-retrieved records in the update functions and changed the update function params to match the details arry form used elsewhere

tripal_core/api/tripal_core.chado_nodes.dbxrefs.api.inc

@@ -581,23 +581,33 @@ function chado_node_additional_dbxrefs_form_retreive($node) {
  *
  * @param $node
  *    The node passed into hook_insert & hook_update
- * @param $linking_table
- *    The name of the _dbxref linking table (ie: feature_dbxref)
- * @param $foreignkey_name
- *    The name of the foreign key used to link to the node content (ie: feature_id)
- * @param $foreignkey_value
- *    The value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
+ * @param $details
+ *   - linking_table: the name of the _dbxref linking table (ie: feature_dbxref)
+ *   - foreignkey_name: the name of the foreign key used to link to the node content (ie: feature_id)
+ *   - foreignkey_value: the value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
+ * @param $retrieved_dbxrefs
+ *   An array of databa references from chado_node_additional_dbxrefs_form_retreive($node).
+ *   This can be used if you need special handling for some of the database references
  *
  * @ingroup tripal_chado_node_api
  */
-function chado_node_additional_dbxrefs_form_update_dbxrefs($node, $linking_table, $foreignkey_name, $foreignkey_value) {
+function chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details, $retrieved_dbxrefs = FALSE) {
+
+  $linking_table = $details['linking_table'];
+  $foreignkey_name = $details['foreignkey_name'];
+  $foreignkey_value = $details['foreignkey_value'];
 
   if (isset($node->dbxref_table) AND ($foreignkey_value > 0)) {
     // First remove existing dbxref links
     tripal_core_chado_delete($linking_table, array($foreignkey_name => $foreignkey_value));
 
     // Add back in dbxref links and insert dbxrefs as needed
-    $dbxrefs = chado_node_additional_dbxrefs_form_retreive($node);
+    if ($retrieved_dbxrefs) {
+      $dbxrefs = $retrieved_dbxrefs;
+    }
+    else {
+      $dbxrefs = chado_node_additional_dbxrefs_form_retreive($node);
+    }
     foreach ($dbxrefs as $db_id => $versions) {
       foreach ($versions as $version => $elements) {
         foreach ($elements as $dbxref_id => $accession) {

tripal_core/api/tripal_core.chado_nodes.relationships.api.inc

@@ -726,14 +726,19 @@ function chado_node_relationships_form_retreive($node) {
  *
  * @param $node
  *    The node passed into hook_insert & hook_update
- * @param $relationship_table
- *    The name of the _relationship linking table (ie: feature_relationship)
- * @param $current_id
- *    The value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
+ * @param $details
+ *  - relationship_table: the name of the _relationship linking table (ie: feature_relationship)
+ *  - foreignkey_value: the value of the foreign key (ie: 445, if there exists a feature where feature_id=445)
+ * @param $retrieved_relationships
+ *   An array of relationships from chado_node_relationships_form_retreive($node). This
+ *   can be used if you need special handling for some of the relationships.
  *
  * @ingroup tripal_chado_node_api
  */
-function chado_node_relationships_form_update_relationships($node, $relationship_table, $current_id) {
+function chado_node_relationships_form_update_relationships($node, $details, $retrieved_relationships = FALSE) {
+
+  $relationship_table = $details['relationship_table'];
+  $current_id = $details['foreignkey_value'];
 
   if (isset($node->relationship_table) AND ($current_id > 0)) {
     // First remove existing relationships links
@@ -741,7 +746,12 @@ function chado_node_relationships_form_update_relationships($node, $relationship
     tripal_core_chado_delete($relationship_table, array('object_id' => $current_id));
 
     // Add back in relationships as needed
-    $relationships = chado_node_relationships_form_retreive($node);
+    if ($retrieved_relationships) {
+      $relationships = $retrieved_relationships;
+    }
+    else {
+      $relationships = chado_node_relationships_form_retreive($node);
+    }
     foreach ($relationships as $type_id => $ranks) {
       foreach ($ranks as $rank => $element) {
 

tripal_stock/includes/tripal_stock.chado_node.inc

@@ -545,18 +545,19 @@ function chado_stock_insert($node) {
       chado_node_properties_form_update_properties($node, $details);
 
       // Now add the additional references
-      chado_node_additional_dbxrefs_form_update_dbxrefs(
-        $node,
-        'stock_dbxref',
-        'stock_id',
-        $stock_id
+      $details = array(
+        'linking_table' => 'stock_dbxref',
+        'foreignkey_name' => 'stock_id',
+        'foreignkey_value' => $stock_id
       );
+      chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
+
       // Now add in relationships
-      chado_node_relationships_form_update_relationships(
-        $node,
-        'stock_relationship',
-        $stock_id
+      $details = array(
+        'relationship_table' => 'stock_relationship',
+        'foreignkey_value' => $node->stock_id
       );
+      chado_node_relationships_form_update_relationships($node, $details);
     }
   } //end of adding stock to chado
   else {
@@ -722,21 +723,21 @@ function chado_stock_update($node) {
 
   // now update the additional dbxrefs
   if ($node->stock_id > 0) {
-    chado_node_additional_dbxrefs_form_update_dbxrefs(
-      $node,
-      'stock_dbxref',
-      'stock_id',
-      $node->stock_id
+    $details = array(
+      'linking_table' => 'stock_dbxref',
+      'foreignkey_name' => 'stock_id',
+      'foreignkey_value' => $node->stock_id
     );
+    chado_node_additional_dbxrefs_form_update_dbxrefs($node, $details);
   }
 
   // now update relationships
   if ($node->stock_id > 0) {
-    chado_node_relationships_form_update_relationships(
-      $node,
-      'stock_relationship',
-      $node->stock_id
+    $details = array(
+      'relationship_table' => 'stock_relationship',
+      'foreignkey_value' => $node->stock_id
     );
+    chado_node_relationships_form_update_relationships($node, $details);
   }
 }