Fixes to schema__publication field.

tripal_chado/includes/TripalFields/schema__publication/schema__publication_formatter.inc

@@ -20,16 +20,23 @@ class schema__publication_formatter extends ChadoFieldFormatter {
       if (empty($item['value'])) {
         continue;
       }
+      // Ignore the null publication.
+      if ($item['uniquename'] == 'null') {
+        continue;
+      }
+
       $title = isset($item['value']['TPUB:0000039']) ? $item['value']['TPUB:0000039'] : '';
       $citation = isset($item['value']['TPUB:0000003']) ? $item['value']['TPUB:0000003'] : '';
       $entity = array_key_exists('entity', $item['value']) ? $item['value']['entity'] : '';
       if ($entity) {
         list($entity_type, $entity_id) = explode(':', $entity);
         $new_title = l($title, 'bio_data/' . $entity_id);
-        // If a title has parens we need to escape them for the
+        // If a title has parenthesis we need to escape them for the
         // regular expression to work.
         $title = preg_replace('/\(/', '\(', $title);
         $title = preg_replace('/\)/', '\)', $title);
+        // We also need to escape any forward slashes.
+        $title = preg_replace('/\//', '\/', $title);
         $citation = preg_replace("/$title/", $new_title, $citation);
       }
       $list_items[] = $citation;

tripal_chado/includes/TripalFields/schema__publication/schema__publication_widget.inc

@@ -26,15 +26,38 @@ class schema__publication_widget extends ChadoFieldWidget {
 
     // Get the field defaults.
     $fkey_value = (array_key_exists('#entity', $element) and is_object($element['#entity'])) ? $element['#entity']->chado_record_id : NULL;
+    $pkey_value = '';
     $pub_id = '';
     $uname = '';
 
     // If the field already has a value then it will come through the $items
     // array.  This happens when editing an existing record.
     if (count($items) > 0 and array_key_exists($delta, $items)) {
+      $pkey_value = tripal_get_field_item_keyval($items, $delta, 'chado-' . $table_name . '__' . $pkey, $pkey_value);
       $pub_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $table_name . '__pub_id', $pub_id);
       $uname = tripal_get_field_item_keyval($items, $delta, 'uniquename', $uname);
     }
+    // We also need to take into account the case where a field is changed by a user.
+    // In this case the info is in the form state.
+    if (isset($form_state['values']) AND !empty($form_state['values'])) {
+      // If the user entered a new publication then we only have the uniquename...
+      // so we need to query the db for the rest of the information.
+      if (empty($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'])) {
+        $uname = $form_state['values'][$field_name][$langcode][$delta]['uniquename'];
+        $pub_id = chado_query('SELECT pub_id FROM {pub} WHERE uniquename=:uniquename',
+          array(':uniquename' => $uname))->fetchField();
+      }
+      // If the user changed an existing publication...
+      // then we have to update the pub_id and reset the pkey.
+      // We can tell if this element was changed by comparing it to the triggering element.
+      $current_value = $form_state['values'][$field_name][$langcode][$delta]['value'];
+      $triggering_value = $form_state['triggering_element']['#value'];
+      if ($triggering_value == $current_value) {
+        $uname = $form_state['values'][$field_name][$langcode][$delta]['uniquename'];
+        $pub_id = chado_query('SELECT pub_id FROM {pub} WHERE uniquename=:uniquename',
+          array(':uniquename' => $uname))->fetchField();
+      }
+    }
 
     $schema = chado_get_schema('pub');
 
@@ -49,16 +72,16 @@ class schema__publication_widget extends ChadoFieldWidget {
     );
 
     $widget['chado-' . $table_name . '__' . $pkey] = array(
-      '#type' => 'value',
-      '#default_value' => '',
+      '#type' => 'hidden',
+      '#value' => $pkey_value,
     );
     $widget['chado-' . $table_name . '__' . $fkey] = array(
-      '#type' => 'value',
-      '#default_value' => $fkey_value,
+      '#type' => 'hidden',
+      '#value' => $fkey_value,
     );
     $widget['chado-' . $table_name . '__pub_id'] = array(
-      '#type' => 'value',
-      '#default_value' => $pub_id,
+      '#type' => 'hidden',
+      '#value' => $pub_id,
     );
 
     $widget['uniquename'] = array(
@@ -76,47 +99,33 @@ class schema__publication_widget extends ChadoFieldWidget {
     );
   }
 
-
   /**
    *
-   * @see TripalFieldWidget::submit()
+   * @see TripalFieldWidget::validate()
    */
-  public function submit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-    // Get the FK column that links to the base table.
-    $table_name = $this->instance['settings']['chado_table'];
+  public function validate($element, $form, &$form_state, $langcode, $delta) {
+    $field_name = $this->field['field_name'];
+    $field_type = $this->field['type'];
     $base_table = $this->instance['settings']['base_table'];
-    $schema = chado_get_schema($table_name);
+    $field_table = $this->instance['settings']['chado_table'];
+    $chado_column = $this->instance['settings']['chado_column'];
+    $instance = $this->instance;
+
+    $schema = chado_get_schema($field_table);
     $pkey = $schema['primary key'][0];
     $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
     $fkey = $fkeys[0];
-    $field_name = $this->field['field_name'];
-
-    // Get the field values.
-    $fkey_value = isset($form_state['values'][$field_name][$langcode][$delta]['value']) ? $form_state['values'][$field_name][$langcode][$delta]['value'] : '';
-    $pub_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] : '';
-    $uname = isset($form_state['values'][$field_name][$langcode][$delta]['uniquename']) ? $form_state['values'][$field_name][$langcode][$delta]['uniquename'] : '';
 
-    // If the user provided a uniquename then we want to set the foreign key
-    // value to be the chado_record_id
-    if ($uname and !$pub_id) {
-      $pub = chado_generate_var('pub', array('uniquename' => $uname));
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] = $pub->pub_id;
-    }
-
-    // In the widgetFrom function we automatically add the foreign key
-    // record.  But if the user did not provide a publication we want to take
-    // it out so that the Chado field_storage infrastructure won't try to
-    // write a record.
-    if (!$uname and !$pub_id) {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] = '';
-    }
+    $value = $form_state['values'][$field_name]['und'][$delta]['uniquename'];
+    $form_state['values'][$field_name]['und'][$delta]['value'] = $value;
 
-    // If the user removed the publication from the pub_uniquename field
-    // then we want to clear out the rest of the hidden values.
-    // Leave the primary key so the record can be deleted.
-    if (!$uname and $pub_id) {
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] = '';
-      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] = '';
+    // If the user removed the publication then we want to clear out the other
+    // fields except the pkey value. If the pkey field is present and the value
+    // is present then the chado storage backend will delete the record.
+    if (!$value) {
+      $form_state['values'][$field_name]['und'][$delta]['value'] = 'delete_me';
+      $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $fkey] = '';
+      $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__pub_id'] = '';
     }
   }