Merge branch '6.x-1.x' of git.drupal.org:sandbox/spficklin/1337878 into 6.x-1.x

tripal_bulk_loader/tripal_bulk_loader.constants.inc

@@ -274,12 +274,14 @@ function tripal_bulk_loader_set_constants_form_validate($form, $form_state) {
       foreach ($indexes as $record_id => $array) {
         foreach ($array as $field_id) {
           if ($template[$record_id]['fields'][$field_id]['exposed_validate']) {
+            $previous_db = tripal_db_set_active('chado');
             $result = db_fetch_object(db_query(
               "SELECT 1 as valid FROM %s WHERE %s='%s'",
               $template[$record_id]['table'],
               $template[$record_id]['fields'][$field_id]['field'],
               $form_state['values'][$record_id . '-' . $field_id]
             ));
+            tripal_db_set_active($previous_db);
 
             if (!$result->valid) {
               $msg = 'A ' . $form['exposed_fields']['new'][$record_id . '-' . $field_id]['#title'] . ' of "' . $form['exposed_fields']['new'][$record_id . '-' . $field_id]['#value'] . '" must already exist!';

tripal_core/api/tripal_core.api.inc

@@ -336,7 +336,7 @@ function tripal_core_chado_insert($table, $values, $options = array()) {
       watchdog('tripal_core', "tripal_core_chado_insert: %table not defined in tripal schema api", array('%table' => $table), 'WATCHDOG WARNING');
     }
     foreach ($table_desc['primary key'] as $field) {
-      $value = db_last_insert_id($table, $field);
+      $value =  db_result(chado_query("SELECT CURRVAL('" . $table . "_" . $field . "_seq')"));
       $values[$field] = $value;
     }
     return $values;
@@ -2362,7 +2362,7 @@ function tripal_db_set_active($dbname) {
 
     // if this is the default database then set the search path and return
     if (strcmp($dbname, 'default')==0) {
-//      tripal_db_set_default_search_path();
+      tripal_db_set_default_search_path();
       return db_set_active($dbname);
     }
     // if the user requests a database other than the default
@@ -2371,12 +2371,12 @@ function tripal_db_set_active($dbname) {
     // fails then we assume the database is not local and we'll
     // set it as normal.
     else {
-//      if (tripal_db_set_chado_search_path($dbname)) {
+      if (tripal_db_set_chado_search_path($dbname)) {
          return $dbname;
-//      }
-//      else {
-//        return db_set_active($dbname);
-//      }
+      }
+      else {
+        return db_set_active($dbname);
+      }
     }
   }
   else {
@@ -2618,7 +2618,7 @@ function tripal_db_persistent_chado() {
       $connection = db_connect($db_url['chado']);
       if (!$connection) {
         watchdog('tripal_core', "Could not create persistant connection", array(), WATCHDOG_ERROR);
-        return FALSE;       
+        return FALSE;
       }
       variable_set('tripal_persistent_chado', serialize($connection));
     }
@@ -2626,7 +2626,7 @@ function tripal_db_persistent_chado() {
       $connection = db_connect($db_url);
       if (!$connection) {
         watchdog('tripal_core', "Could not create persistant connection", array(), WATCHDOG_ERROR);
-        return FALSE;      	
+        return FALSE;
       }
       variable_set('tripal_persistent_chado', serialize($connection));
     }

tripal_organism/tripal_organism.module

@@ -964,6 +964,7 @@ function chado_organism_load($node) {
   // find the organism and add in the details
   $organism_id = chado_get_id_for_node('organism', $node);
   $values = array('organism_id' => $organism_id);
+
   $organism = tripal_core_generate_chado_var('organism', $values);
 
   // add in the description field