Fixed chado_linker_cvterm_adder and chado_linker_cvterm

tripal_chado/includes/TripalFields/chado_base__dbxref_id.inc

@@ -68,11 +68,11 @@ class chado_base__dbxref_id extends TripalField {
 
     // Check $form_state['values'] to see if an AJAX call set the values.
     if (array_key_exists('values', $form_state)) {
-      $fk_val = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $field_column];
-      $db_id = $form_state['values'][$field_name]['und'][$delta]['db_id'];
-      $accession = $form_state['values'][$field_name]['und'][$delta]['accession'];
-      $version = $form_state['values'][$field_name]['und'][$delta]['version'];
-      $description = $form_state['values'][$field_name]['und'][$delta]['description'];
+      $fk_val = isset($form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $field_column]) ? $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $field_column] : '';
+      $db_id = isset($form_state['values'][$field_name]['und'][$delta]['db_id']) ? $form_state['values'][$field_name]['und'][$delta]['db_id'] : '';
+      $accession = isset($form_state['values'][$field_name]['und'][$delta]['accession']) ? $form_state['values'][$field_name]['und'][$delta]['accession'] : '';
+      $version = isset($form_state['values'][$field_name]['und'][$delta]['version']) ? $form_state['values'][$field_name]['und'][$delta]['version'] : '';
+      $description = isset($form_state['values'][$field_name]['und'][$delta]['description']) ? $form_state['values'][$field_name]['und'][$delta]['description'] : '';
     }
 
     $schema = chado_get_schema('dbxref');
@@ -213,10 +213,10 @@ class chado_base__dbxref_id extends TripalField {
     $field_table = $this->field['settings']['chado_table'];
     $field_column = $this->field['settings']['chado_column'];
 
-    $fk_val = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__' . $field_column];
-    $db_id = $form_state['values'][$field_name][$langcode][$delta]['db_id'];
-    $accession = $form_state['values'][$field_name][$langcode][$delta]['accession'];
-    $version = $form_state['values'][$field_name][$langcode][$delta]['version'];
+    $fk_val = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__' . $field_column]) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__' . $field_column] : '';
+    $db_id = isset($form_state['values'][$field_name][$langcode][$delta]['db_id']) ? $form_state['values'][$field_name][$langcode][$delta]['db_id'] : '';
+    $accession = isset($form_state['values'][$field_name][$langcode][$delta]['accession']) ? $form_state['values'][$field_name][$langcode][$delta]['accession'] : '';
+    $version = isset($form_state['values'][$field_name][$langcode][$delta]['version']) ? $form_state['values'][$field_name][$langcode][$delta]['version'] : '';
 
     // If user did not select a database, we want to remove dbxref_id from the
     // field.

tripal_chado/includes/TripalFields/chado_feature__md5checksum.inc

@@ -77,7 +77,7 @@ class chado_feature__md5checksum  extends TripalField {
     $field_column = $field['settings']['chado_column'];
 
     // Get the residues so we can calculate teh length.
-    $residues = $form_state['values']['feature__residues'][$langcode][0]['chado-feature__residues'];
+    $residues = isset($form_state['values']['feature__residues'][$langcode][0]['chado-feature__residues']) ? $form_state['values']['feature__residues'][$langcode][0]['chado-feature__residues'] : '';
 
     if ($residues) {
       // Remove spaces and new lines from the residues string.

tripal_chado/includes/TripalFields/chado_feature__residues.inc

@@ -106,7 +106,7 @@ class chado_feature__residues extends TripalField {
     $field_name = $this->field['field_name'];
 
     // Remove any white spaces.
-    $residues = $form_state['values'][$field_name][$langcode][$delta]['chado-feature__residues'];
+    $residues = isset($form_state['values'][$field_name][$langcode][$delta]['chado-feature__residues']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-feature__residues'] : '';
     if ($residues) {
       $residues = preg_replace('/\s/', '', $residues);
       $form_state['values'][$field_name][$langcode][$delta]['chado-feature__residues'] = $residues;

tripal_chado/includes/TripalFields/chado_linker__contact.inc

@@ -164,9 +164,9 @@ class chado_linker__contact extends TripalField {
     $field_name = $this->field['field_name'];
 
     // Get the field values.
-    $fkey_value = $form_state['values'][$field_name][$langcode][$delta]['value'];
-    $contact_id = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__contact_id'];
-    $name = $form_state['values'][$field_name][$langcode][$delta]['name'];
+    $fkey_value = isset($form_state['values'][$field_name][$langcode][$delta]['value']) ? $form_state['values'][$field_name][$langcode][$delta]['value'] : '';
+    $contact_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__contact_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__contact_id'] : '';
+    $name = isset($form_state['values'][$field_name][$langcode][$delta]['name']) ? $form_state['values'][$field_name][$langcode][$delta]['name'] : '';
 
     // If the user provided a name then we want to set the foreign key
     // value to be the chado_record_id

tripal_chado/includes/TripalFields/chado_linker__cvterm.inc

@@ -89,8 +89,6 @@ class chado_linker__cvterm extends TripalField {
   public function widgetForm(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
     parent::widgetForm($widget, $form, $form_state, $langcode, $items, $delta, $element);
 
-
-    $entity = $form['#entity'];
     $field_name = $this->field['field_name'];
 
     $matches = array();
@@ -123,7 +121,6 @@ class chado_linker__cvterm extends TripalField {
     // array.  This happens when editing an existing record.
     if (array_key_exists($delta, $items)) {
       $record_id = $items[$delta]['value'];
-      $fkey_value = $items[$delta]['chado-' . $table_name . '__' . $fkey];
       $cvterm_name = $items[$delta]['cvterm__name'];
       $is_not = $items[$delta]['chado-' . $table_name . '__is_not'];
       $cvterm_id = $items[$delta]['chado-' . $table_name . '__cvterm_id'];
@@ -147,14 +144,13 @@ class chado_linker__cvterm extends TripalField {
 
     $widget['#table_name'] = $chado_table;
     $widget['#fkey_field'] = $fkey;
-    $widget['#element_validate'] = array('chado_linker__cvterm_widget_validate');
     $widget['#theme'] = 'chado_linker__cvterm_widget';
     $widget['#prefix'] =  "<span id='$table_name-$delta'>";
     $widget['#suffix'] =  "</span>";
 
     $widget['value'] = array(
       '#type' => 'value',
-      '#value' => $items[$delta]['value'],
+      '#value' => key_exists($delta, $items) ? $items[$delta]['value'] : '',
     );
 
     $widget['chado-' . $table_name . '__' . $pkey] = array(
@@ -206,7 +202,13 @@ class chado_linker__cvterm extends TripalField {
   public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
 
     $field_name = $this->field['field_name'];
-    $field_type = $this->field['type'];
+    $table_name = $this->field['settings']['chado_table'];
+    $schema = chado_get_schema($table_name);
+    $pkey = $schema['primary key'][0];
+    $base_table = $this->field['settings']['base_table'];
+    $lfkey_field = key($schema['foreign keys'][$base_table]['columns']);
+    $rfkey_field = $schema['foreign keys'][$base_table]['columns'][$lfkey_field];
+
 
     // If the form ID is field_ui_field_edit_form, then the user is editing the
     // field's values in the manage fields form of Drupal.  We don't want
@@ -215,35 +217,16 @@ class chado_linker__cvterm extends TripalField {
       return;
     }
 
-    // Get the field values.
-    //   $cvterm_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $table_name . '__cvterm_id');
-    //   $cv_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $table_name . '--cvterm__cv_id--cv__cv_id');
-    //   $cvterm_name = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $table_name . '--cvterm__name');
-    //   $cvterm_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $table_name . '__cvterm_id');
-    //   $pub_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $table_name . '__pub_id');
-
     // If the user provided a cv_id and a name then we want to set the
     // foreign key value to be the chado_record_idd
-    if ($cvterm_name) {
+    $cvterm_name = isset($form_state['values'][$field_name][$langcode][$delta]['cvterm__name']) ? $form_state['values'][$field_name][$langcode][$delta]['cvterm__name'] : '';
 
-      $fkey_value = $element['#entity']->chado_record_id;
-      tripal_chado_set_field_form_values($field_name, $form_state, $fkey_value, $delta, $table_name . '__' . $fkey);
-
-      // Get the cvterm ID. If one is not available because it's a newly added
-      // record, then we need to retrieve it and set the form element.
-      if (!$cvterm_id) {
-        $cvterm = tripal_get_cvterm(array('cv_id' => $cv_id, 'name' => $cvterm_name));
-        tripal_chado_set_field_form_values($field_name, $form_state, $cvterm->cvterm_id, $delta, $table_name . '__cvterm_id');
-      }
-
-      if (!$pub_id) {
-        $pub = chado_generate_var('pub', array('uniquename' => 'null'));
-        tripal_chado_set_field_form_values($field_name, $form_state, $pub->pub_id, $delta, $table_name . '__pub_id');
-      }
+    if (!$cvterm_name) {
+      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__cvterm_id'] = '';
+      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $lfkey_field] = '';
     }
     else {
-      // If the $cv_id and name are not set, then remove the linker FK value to the base table.
-      tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__' . $fkey);
+      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] = 1;
     }
   }
 
@@ -252,12 +235,11 @@ class chado_linker__cvterm extends TripalField {
    */
   public function load($entity, $details = array()) {
 
-    $record = $details['record'];
-
     $field_name = $this->field['field_name'];
     $field_type = $this->field['type'];
     $field_table = $this->field['settings']['chado_table'];
     $field_column = $this->field['settings']['chado_column'];
+    $base_table = $this->field['settings']['base_table'];
 
     $matches = array();
     preg_match('/(.*?)__(\d+)/', $field_name, $matches);
@@ -271,6 +253,7 @@ class chado_linker__cvterm extends TripalField {
     $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
 
     // Set some defaults for the empty record.
+    $chado_record = $entity->chado_record;
     $entity->{$field_name}['und'][0] = array(
       'value' => '',
       'chado-' . $field_table . '__' . $fkey_lcolumn => '',
@@ -295,7 +278,7 @@ class chado_linker__cvterm extends TripalField {
     // Get the annotations associated with this base record for this fields type.
     $columns = array('*');
     $match = array(
-      $fkey_lcolumn => $record->$fkey_rcolumn,
+      $fkey_lcolumn => $chado_record->$fkey_rcolumn,
       'cvterm_id' => array(
         'cv_id' => $cv_id,
       ),

tripal_chado/includes/TripalFields/chado_linker__cvterm_adder.inc

@@ -48,7 +48,7 @@ class chado_linker__cvterm_adder extends TripalField {
     $widget['cvterm_class_adder_instructions'] = array(
       '#type' => 'item',
       '#markup' => t('You may add annotation types to this form by
-          providing a vocabulary name in the field below
+          providing a vocabulary name in the field above
           and clicking the "Add Annotation Type" button.  This will add a
           new field to the form above for the vocabulary you entered which
           will allow users to associate terms from that vocabulary to
@@ -82,6 +82,35 @@ class chado_linker__cvterm_adder extends TripalField {
     );
   }
 
+  /**
+   * @see TripalField::widgetFormValidate()
+   */
+  public function widgetFormValidate($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
+  
+    if (array_key_exists('triggering_element', $form_state) and
+        $form_state['triggering_element']['#name'] == 'cvterm_class_adder_button') {
+          $this_field = $this->field;
+          $field_name = $this_field['field_name'];
+          $bundle = $entity->bundle;
+          
+          // Get the base table name from the field annotations.
+          $base_table = $entity->chado_table;
+          $cvterm_class_adder = $form_state['values'][$base_table . '_cvterm'][$langcode][$delta]['value'];
+          $cv = chado_generate_var('cv', array('cv_id' => $cvterm_class_adder));
+          
+          // Make sure a valid vocabulary is selected
+          if (!$cv) {
+            form_set_error("$field_name][$langcode][$delta][value", "Please select a vocabulary.");
+          }
+          else {
+            // Make sure this vocabulary doesn't already have a field
+            if (key_exists($field_name . '__' . $cv->cv_id, $form_state['values'])) {
+              form_set_error("$field_name][$langcode][$delta][wrapper][terms_name", "Field for this vocabulary already exists. Please select another vocabulary.");
+            }
+          }
+        }
+  }
+  
   /**
    * @see TripalField::widgetFormSubmit()
    */
@@ -92,20 +121,19 @@ class chado_linker__cvterm_adder extends TripalField {
         $form_state['triggering_element']['#name'] == 'cvterm_class_adder_button') {
 
           $form_state['rebuild'] = TRUE;
-          $field_name = $element['#field_name'];
-          $entity_type = $element['#entity']->type;
-          $bundle = $element['#entity']->bundle;
-
+          $this_field = $this->field;
+          $field_name = $this_field['field_name'];
+          $bundle = $entity->bundle;
+          
           // Get the base table name from the field annotations.
-          $field = field_info_field($field_name);
-          $base_table = $field['settings']['base_table'];
+          $base_table = $entity->chado_table;
+          $cvterm_class_adder = $form_state['values'][$base_table . '_cvterm'][$langcode][$delta]['value'];
 
           // Get the vocabulary.
           //$cvterm_class_adder = tripal_chado_get_field_form_values($field_name, $form_state);
           $cv = chado_generate_var('cv', array('cv_id' => $cvterm_class_adder));
 
           if (!$cv) {
-            form_set_error(implode('][', $element ['#parents']) . '][value', t("Please select a vocabulary."));
             return;
           }
 
@@ -120,8 +148,8 @@ class chado_linker__cvterm_adder extends TripalField {
           $field = field_info_field('cvterm');
           if (!$field) {
             $create_info = array(
-              'field_name' => 'cvterm',
-              'type' => 'tripal_chado_cvterm_widget',
+              'field_name' => $type_field_name,
+              'type' => 'chado_linker__cvterm',
               'cardinality' => FIELD_CARDINALITY_UNLIMITED,
               'locked' => FALSE,
               'storage' => array(
@@ -141,15 +169,15 @@ class chado_linker__cvterm_adder extends TripalField {
               !array_key_exists('TripalEntity', $field['bundles']) or
               !in_array($bundle_name, $field['bundles']['TripalEntity'])) {
                 $createInstanceInfo = array(
-                  'field_name' => 'cvtmerm',
+                  'field_name' => $type_field_name,
                   'entity_type' => 'TripalEntity',
-                  'bundle' => $this->bundle->name,
+                  'bundle' => $bundle,
                   'label' => ucfirst(preg_replace('/_/', ' ', $cv->name)),
                   'description' => "Annotations from the $cv->name vocabulary",
                   'required' => FALSE,
                   'settings' => array(),
                   'widget' => array(
-                    'type' => 'tripal_chado_cvterm_widget',
+                    'type' => 'chado_linker__cvterm_widget',
                     'settings' => array(
                       'display_label' => 1,
                     ),
@@ -157,7 +185,7 @@ class chado_linker__cvterm_adder extends TripalField {
                   'display' => array(
                     'default' => array(
                       'label' => 'above',
-                      'type' => 'tripal_chado_cvterm_formatter',
+                      'type' => 'chado_linker__cvterm_formatter',
                       'settings' => array(),
                     ),
                   ),

tripal_chado/includes/TripalFields/chado_linker__dbxref.inc

@@ -268,11 +268,11 @@ class chado_linker__dbxref extends TripalField {
     $fkey = $fkeys[0];
 
     // Get the field values.
-    $dbxref_id = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__dbxref_id'];
-    $db_id = $form_state['values'][$field_name][$langcode][$delta]['db_id'];
-    $accession = $form_state['values'][$field_name][$langcode][$delta]['accession'];
-    $version = $form_state['values'][$field_name][$langcode][$delta]['version'];
-    $description = $form_state['values'][$field_name][$langcode][$delta]['description'];
+    $dbxref_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__dbxref_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__dbxref_id'] : '';
+    $db_id = isset($form_state['values'][$field_name][$langcode][$delta]['db_id']) ? $form_state['values'][$field_name][$langcode][$delta]['db_id'] : '';
+    $accession = isset($form_state['values'][$field_name][$langcode][$delta]['accession']) ? $form_state['values'][$field_name][$langcode][$delta]['accession'] : '';
+    $version = isset($form_state['values'][$field_name][$langcode][$delta]['version']) ? $form_state['values'][$field_name][$langcode][$delta]['version'] : '';
+    $description = isset($form_state['values'][$field_name][$langcode][$delta]['description']) ? $form_state['values'][$field_name][$langcode][$delta]['description'] : '';
 
     // If the dbxref_id does not match the db_id + accession then the user
     // has selected a new dbxref record and we need to update the hidden

tripal_chado/includes/TripalFields/chado_linker__prop.inc

@@ -131,7 +131,7 @@ class chado_linker__prop extends TripalField {
     $lfkey_field = key($schema['foreign keys'][$base_table]['columns']);
     $rfkey_field = $schema['foreign keys'][$base_table]['columns'][$lfkey_field];
 
-    $prop_value = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__value'];
+    $prop_value = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__value']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__value'] : '';
 
     // If the user removed the contact from the contact_name field
     // then we want to clear out the rest of the hidden values.

tripal_chado/includes/TripalFields/chado_linker__prop_adder.inc

@@ -58,7 +58,7 @@ class chado_linker__prop_adder extends TripalField {
           of this type.'),
     );
 
-    $term_name = array_key_exists('values', $form_state) ? $form_state['values'][$field_name]['und'][0]['wrapper']['term_name'] : '';
+    $term_name = isset($form_state['values'][$field_name]['und'][0]['wrapper']['term_name']) ? $form_state['values'][$field_name]['und'][0]['wrapper']['term_name'] : '';
 
     // Drupal's vertical feild set is a bit quirky in that we can't just
     // add a prefix and suffix to the weidget.  If we do, then the

tripal_chado/includes/TripalFields/chado_linker__pub.inc

@@ -141,9 +141,9 @@ class chado_linker__pub extends TripalField {
     $field_name = $this->field['field_name'];
 
     // Get the field values.
-    $fkey_value = $form_state['values'][$field_name][$langcode][$delta]['value'];
-    $pub_id = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'];
-    $uname = $form_state['values'][$field_name][$langcode][$delta]['uniquename'];
+    $fkey_value = isset($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

tripal_chado/includes/TripalFields/chado_linker__synonym.inc

@@ -219,14 +219,14 @@ class chado_linker__synonym extends TripalField {
     $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
     $fkey = $fkeys[0];
 
-    $record_id = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $pkey];
-    $fkey_value = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey];
-    $synonym_id = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__synonym_id'];
-    $pub_id = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'];
-    $is_current = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_current'];
-    $is_internal = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_internal'];
-    $syn_name = $form_state['values'][$field_name][$langcode][$delta]['name'];
-    $syn_type = $form_state['values'][$field_name][$langcode][$delta]['type_id'];
+    $record_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $pkey]) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $pkey] : '';
+    $fkey_value = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey]) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] : '';
+    $synonym_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__synonym_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__synonym_id'] : '';
+    $pub_id = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__pub_id'] : '';
+    $is_current = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_current']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_current'] : '';
+    $is_internal = isset($form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_internal']) ? $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__is_internal'] : '';
+    $syn_name = isset($form_state['values'][$field_name][$langcode][$delta]['name']) ? $form_state['values'][$field_name][$langcode][$delta]['name'] : '';
+    $syn_type = isset($form_state['values'][$field_name][$langcode][$delta]['type_id']) ? $form_state['values'][$field_name][$langcode][$delta]['type_id'] : '';
 
     // If the user provided a $syn_name and a $syn_type then we want to set
     // the foreign key value to be the chado_record_id.