Migrating theming to modules

tripal_contact/includes/tripal_contact.admin.inc

@@ -77,7 +77,7 @@ function get_tripal_contact_admin_form_reindex_set(&$form) {
 
   // iterate through all of the maps
   $lib_boxes = array();
-  while ($contact = db_fetch_object($lib_rset)) {
+  while ($contact = $lib_rset->fetchObject()) {
     $lib_boxes[$contact->contact_id] = "$contact->name";
   }
   $form['reindex']['description'] = array(
@@ -118,7 +118,7 @@ function tripal_contact_admin_validate($form, &$form_state) {
       if ($contact_id and preg_match("/^\d+$/i", $contact_id)) {
         // get the map info
         $sql = "SELECT * FROM {contact} WHERE contact_id = :contact_id";
-        $contact = db_fetch_object(chado_query($sql, array(':contact_id' => $contact_id)));
+        $contact = chado_query($sql, array(':contact_id' => $contact_id))->fetchObject();
         $job_args[0] = $contact_id;
         tripal_add_job("Reindex features for map: $contact->name", 'tripal_contact',
          'tripal_contact_reindex_features', $job_args, $user->uid);

tripal_contact/includes/tripal_contact.form.inc

@@ -79,7 +79,7 @@ function chado_contact_form(&$node, $form_state) {
   ";
   $results = chado_query($sql);
   $contact_types = array();
-  while ($contact_type = db_fetch_object($results)) {
+  while ($contact_type = $results->fetchObject()) {
     $contact_types[$contact_type->cvterm_id] = $contact_type->name;
     if (strcmp($contact_type->name,"Person") == 0 and !$d_type_id) {
       $d_type_id = $contact_type->cvterm_id;
@@ -102,7 +102,7 @@ function chado_contact_form(&$node, $form_state) {
     ORDER BY CVTS.name ASC 
   ";
   $prop_types = chado_query($sql);
-  while ($prop = db_fetch_object($prop_types)) {
+  while ($prop = $prop_types->fetchObject()) {
     $properties_select[$prop->cvterm_id] = $prop->name;
     $properties_list[$prop->cvterm_id] = $prop;
   }
@@ -172,11 +172,11 @@ function chado_contact_validate($node, &$form) {
       SELECT * FROM {contact} 
       WHERE name = :name AND NOT contact_id = :contact_id
     ";
-    $contact = db_fetch_object(chado_query($sql, array(':name' => $title, ':contact_id' => $contact_id)));
+    $contact = chado_query($sql, array(':name' => $title, ':contact_id' => $contact_id))->fetchObject();
   }
   else {
     $sql = "SELECT * FROM {contact} WHERE name = :name";
-    $contact = db_fetch_object(chado_query($sql, array(':name' => $title)));
+    $contact = chado_query($sql, array(':name' => $title))->fetchObject();
   }
   if ($contact) {
     form_set_error('title', t('The contact name already exists. Please choose another'));
@@ -366,7 +366,7 @@ function chado_contact_node_form_add_contactprop_table_props(&$form, $form_state
     ORDER BY CVT.name, PP.rank
   ";
   $contact_props = chado_query($sql, array(':contact_id' => $contact_id));
-  while ($prop = db_fetch_object($contact_props)) {
+  while ($prop = $contact_props->fetchObject()) {
 
     $type_id = $prop->cvterm_id;
     $rank = count($d_properties[$type_id]);