Fixed saving to Chado for new field classes. Also fixed bugs in relationship field

tripal/includes/TripalEntityUIController.inc

@@ -435,13 +435,11 @@ function tripal_entity_form_ajax_callback($form, $form_state) {
          if (!preg_match('/^\d+$/', $delta)) {
            continue;
          }
-         if (array_key_exists('#field', $field_form)) {
+         $widget_type = $instance['widget']['type'];
+         if (tripal_load_include_field_class($widget_type)) {
            $field = $field_form['#field'];
-           $field_type = $field['type'];
-           if (class_exists($field_type)) {
-             $tfield = new $field_type($field, $instance);
-             $tfield->widgetFormSubmit($form, $form_state, $entity_type, $entity, $langcode, $delta);
-           }
+           $widget = new $widget_type($field, $instance);
+           $widget->submit($form, $form_state, $entity_type, $entity, $langcode, $delta);
          }
        }
      }

tripal_chado/includes/TripalFields/chado_linker__contact_widget.inc

@@ -13,9 +13,10 @@ class chado_linker__contact_widget extends TripalFieldWidget {
    */
   public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
     parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+
     $entity = $form['#entity'];
     $field_name = $this->field['field_name'];
-    
+
     // Get the FK column that links to the base table.
     $table_name = $this->field['settings']['chado_table'];
     $base_table = $this->field['settings']['base_table'];
@@ -23,13 +24,13 @@ class chado_linker__contact_widget extends TripalFieldWidget {
     $pkey = $schema['primary key'][0];
     $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
     $fkey = $fkeys[0];
-    
+
     // Get the field defaults.
     $record_id = '';
     $fkey_value = $element['#entity']->chado_record_id;
     $contact_id = '';
     $name = '';
-    
+
     // 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)) {
@@ -40,20 +41,20 @@ class chado_linker__contact_widget extends TripalFieldWidget {
         $name = $contact->name;
       }
     }
-    
+
     $schema = chado_get_schema('contact');
-    
+
     $widget['#table_name'] = $table_name;
     $widget['#fkey_field'] = $fkey;
     $widget['#theme'] = 'chado_linker__contact_widget';
     $widget['#prefix'] =  "<span id='$table_name-$delta'>";
     $widget['#suffix'] =  "</span>";
-    
+
     $widget['value'] = array(
       '#type' => 'value',
       '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
     );
-    
+
     $widget['chado-' . $table_name . '__' . $pkey] = array(
       '#type' => 'value',
       '#default_value' => $record_id,
@@ -66,7 +67,7 @@ class chado_linker__contact_widget extends TripalFieldWidget {
       '#type' => 'value',
       '#default_value' => $contact_id,
     );
-    
+
     $widget['name'] = array(
       '#type' => 'textfield',
       '#title' => t('Contact'),
@@ -110,19 +111,19 @@ class chado_linker__contact_widget extends TripalFieldWidget {
     $fkeys = array_values($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'] : '';
     $contact_id = isset($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
     if ($name and !$contact_id) {
       $contact = chado_generate_var('contact', array('name' => $name));
       $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__contact_id'] = $contact->contact_id;
     }
-    
+
     // In the widgetForm function we automatically add the foreign key
     // record.  But if the user did not provide a contact we want to take
     // it out so that the Chado field_storage infrastructure won't try to
@@ -130,7 +131,7 @@ class chado_linker__contact_widget extends TripalFieldWidget {
     if (!$name and !$contact_id) {
       $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $fkey] = '';
     }
-    
+
     // If the user removed the contact from the contact_name field
     // then we want to clear out the rest of the hidden values.
     // Leave the primary key so the record can be deleted.

tripal_chado/includes/TripalFields/chado_linker__dbxref_widget.inc

@@ -17,7 +17,7 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
     $field_type = $this->field['type'];
     $field_table = $this->field['settings']['chado_table'];
     $field_column = $this->field['settings']['chado_column'];
-    
+
     // Get the FK column that links to the base table.
     $chado_table = $this->field['settings']['chado_table'];
     $base_table = $this->field['settings']['base_table'];
@@ -25,16 +25,16 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
     $pkey = $schema['primary key'][0];
     $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
     $fkey = $fkeys[0];
-    
+
     // Get the field defaults.
     $record_id = '';
-    $fkey_value = $element['#entity']->chado_record_id;
+    $fkey_value = $element['#entity'] ? $element['#entity']->chado_record_id : '';
     $dbxref_id = '';
     $db_id = '';
     $accession = '';
     $version = '';
     $description = '';
-    
+
     // 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)) {
@@ -46,7 +46,7 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
       $version = tripal_get_field_item_keyval($items, $delta, 'version', $version);
       $description = tripal_get_field_item_keyval($items, $delta, 'description', $description);
     }
-    
+
     // Check $form_state['values'] to see if an AJAX call set the values.
     if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
       $record_id = $form_state['values'][$field_name]['und'][$delta][$field_table . '__' . $pkey];
@@ -57,23 +57,23 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
       $version = $form_state['values'][$field_name]['und'][$delta]['version'];
       $description = $form_state['values'][$field_name]['und'][$delta]['description'];
     }
-    
+
     $schema = chado_get_schema('dbxref');
     $options = tripal_get_db_select_options();
-    
+
     $widget['#table_name'] = $chado_table;
     $widget['#fkey_field'] = $fkey;
     //$widget['#element_validate'] = array('chado_linker__dbxref_widget_validate');
     $widget['#theme'] = 'chado_linker__dbxref_widget';
     $widget['#prefix'] =  "<span id='$field_name-dbxref--db-id-$delta'>";
     $widget['#suffix'] =  "</span>";
-    
-    
+
+
     $widget['value'] = array(
       '#type' => 'value',
       '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
     );
-    
+
     $widget['chado-' . $field_table . '__' . $pkey] = array(
       '#type' => 'value',
       '#default_value' => $record_id,
@@ -163,18 +163,18 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
     $pkey = $schema['primary key'][0];
     $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
     $fkey = $fkeys[0];
-    
-    
+
+
     // Get the field values.
     foreach ($items as $delta => $values) {
-    
+
       // Get the field values.
       $dbxref_id = $values['chado-' . $field_table . '__dbxref_id'];
       $db_id = $values['db_id'];
       $accession = $values['accession'];
       $version = $values['version'];
       $description = $values['description'];
-    
+
       // Make sure that if a database ID is provided that an accession is also
       // provided.  Here we use the form_set_error function rather than the
       // form_error function because the form_error will add a red_highlight
@@ -219,14 +219,14 @@ class chado_linker__dbxref_widget extends TripalFieldWidget {
     $pkey = $schema['primary key'][0];
     $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
     $fkey = $fkeys[0];
-    
+
     // Get the field values.
     $dbxref_id = isset($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
     // value accordingly.

tripal_chado/includes/TripalFields/chado_linker__relationship.inc

@@ -76,19 +76,19 @@ class chado_linker__relationship extends TripalField {
    */
   public function load($entity, $details = array()) {
     $settings = $this->field['settings'];
-    
+
     $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'];
-    
+
     // Get the PKey for this table
     $schema = chado_get_schema($field_table);
     $pkey = $schema['primary key'][0];
-    
+
     // Get the Pkeys for the subject and object tables
     $subject_fkey_table = '';
     $object_fkey_table = '';
@@ -107,19 +107,19 @@ class chado_linker__relationship extends TripalField {
     $object_schema = chado_get_schema($object_fkey_table);
     $subject_pkey = $subject_schema['primary key'][0];
     $object_pkey = $object_schema['primary key'][0];
-    
+
     // Get the FK that links to the base record.
     $schema = chado_get_schema($field_table);
     $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
     $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
-    
+
     // Set some defaults for the empty record.
     $entity->{$field_name}['und'][0] = array(
       'value' => array(),
-      $field_table . '__' . $pkey => '',
-      $field_table . '__subject_id' => '',
-      $field_table . '__object_id' => '',
-      $field_table . '__type_id' => '',
+      'chado-' . $field_table . '__' . $pkey => '',
+      'chado-' . $field_table . '__subject_id' => '',
+      'chado-' . $field_table . '__object_id' => '',
+      'chado-' . $field_table . '__type_id' => '',
       // These elements don't need to follow the naming scheme above
       // becasue we don't need the chado_field_storage to try and
       // save these values.
@@ -127,21 +127,21 @@ class chado_linker__relationship extends TripalField {
       'subject_name' => '',
       'type_name' => '',
     );
-    
+
     // If the table has rank and value fields then add those to the default
     // value array.
     if (array_key_exists('value', $schema['fields'])) {
-      $entity->{$field_name}['und'][0][$field_table . '__value'] = '';
+      $entity->{$field_name}['und'][0]['chado-' . $field_table . '__value'] = '';
     }
     if (array_key_exists('rank', $schema['fields'])) {
-      $entity->{$field_name}['und'][0][$field_table . '__rank'] = '';
+      $entity->{$field_name}['und'][0]['chado-' . $field_table . '__rank'] = '';
     }
-    
+
     // If we have no record then just return.
     if (!$record) {
       return;
     }
-    
+
     // Expand the object to include the relationships.
     $options = array(
       'return_array' => 1,
@@ -168,11 +168,7 @@ class chado_linker__relationship extends TripalField {
     }
     $srelationships = null;
     $orelationships = null;
-    if ($rel_table == 'organism_relationship') {
-      $srelationships = $record->$rel_table->subject_organism_id;
-      $orelationships = $record->$rel_table->object_organism_id;
-    }
-    else if ($rel_table == 'nd_reagent_relationship') {
+    if ($rel_table == 'nd_reagent_relationship') {
       $srelationships = $record->$rel_table->subject_reagent_id;
       $orelationships = $record->$rel_table->object_reagent_id;
     }
@@ -184,7 +180,7 @@ class chado_linker__relationship extends TripalField {
       $srelationships = $record->$rel_table->subject_id;
       $orelationships = $record->$rel_table->object_id;
     }
-    
+
     $i = 0;
     if ($orelationships) {
       foreach ($orelationships as $relationship) {
@@ -222,31 +218,31 @@ class chado_linker__relationship extends TripalField {
         $entity->{$field_name}['und'][$i]['value']['phrase'] = 'The ' . $subject_type . ', ' .
             $subject_name . ', ' . $verb . ' '  . $rel_type_clean . ' this '  .
             $object_type . '.';
-    
+
             $entity->{$field_name}['und'][$i]['semantic_web'] = array(
               'type' => $rel_acc,
               'subject' => $relationship->subject_id->type_id->dbxref_id->db_id->name . ':' . $relationship->subject_id->type_id->dbxref_id->accession,
               'object' => $relationship->object_id->type_id->dbxref_id->db_id->name . ':' . $relationship->object_id->type_id->dbxref_id->accession,
             );
-    
-            $entity->{$field_name}['und'][$i][$field_table . '__' . $pkey] = $relationship->$pkey;
-            $entity->{$field_name}['und'][$i][$field_table . '__subject_id'] = $relationship->subject_id->$subject_pkey;
-            $entity->{$field_name}['und'][$i][$field_table . '__type_id'] = $relationship->type_id->cvterm_id;
-            $entity->{$field_name}['und'][$i][$field_table . '__object_id'] = $relationship->object_id->$object_pkey;
-    
+
+            $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . $pkey] = $relationship->$pkey;
+            $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__subject_id'] = $relationship->subject_id->$subject_pkey;
+            $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__type_id'] = $relationship->type_id->cvterm_id;
+            $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__object_id'] = $relationship->object_id->$object_pkey;
+
             $entity->{$field_name}['und'][$i]['type_name'] = $relationship->type_id->name;
             $entity->{$field_name}['und'][$i]['subject_name'] = $relationship->subject_id->name . ' [id: ' . $relationship->subject_id->$fkey_rcolumn . ']';
             $entity->{$field_name}['und'][$i]['object_name'] = $relationship->object_id->name  . ' [id: ' . $relationship->object_id->$fkey_rcolumn . ']';
             if (array_key_exists('value', $schema['fields'])) {
-              $entity->{$field_name}['und'][$i][$field_table . '__value'] = $relationship->value;
+              $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__value'] = $relationship->value;
             }
             if (array_key_exists('rank', $schema['fields'])) {
-              $entity->{$field_name}['und'][$i][$field_table . '__rank'] = $relationship->rank;
+              $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__rank'] = $relationship->rank;
             }
             $i++;
       }
     }
-    
+
     if ($srelationships) {
       foreach ($srelationships as $relationship) {
         $rel_acc = $relationship->type_id->dbxref_id->db_id->name . ':' . $relationship->type_id->dbxref_id->accession;
@@ -283,29 +279,29 @@ class chado_linker__relationship extends TripalField {
         $entity->{$field_name}['und'][$i]['value']['phrase'] = 'This  ' .
             $subject_type . ' ' . $verb . ' '  . $rel_type_clean . ' the '  .
             $object_type . ', ' . $object_name . '.';
-    
-    
+
+
             $entity->{$field_name}['und'][$i]['semantic_web'] = array(
               'type' => $rel_acc,
               'subject' => $relationship->subject_id->type_id->dbxref_id->db_id->name . ':' . $relationship->subject_id->type_id->dbxref_id->accession,
               'object' => $relationship->object_id->type_id->dbxref_id->db_id->name . ':' . $relationship->object_id->type_id->dbxref_id->accession,
             );
-    
-    
-            $entity->{$field_name}['und'][$i][$field_table . '__' . $pkey] = $relationship->$pkey;
-            $entity->{$field_name}['und'][$i][$field_table . '__subject_id'] = $relationship->subject_id->$subject_pkey;
-            $entity->{$field_name}['und'][$i][$field_table . '__type_id'] = $relationship->type_id->cvterm_id;
-            $entity->{$field_name}['und'][$i][$field_table . '__object_id'] = $relationship->object_id->$object_pkey;
-    
+
+
+            $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . $pkey] = $relationship->$pkey;
+            $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__subject_id'] = $relationship->subject_id->$subject_pkey;
+            $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__type_id'] = $relationship->type_id->cvterm_id;
+            $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__object_id'] = $relationship->object_id->$object_pkey;
+
             $entity->{$field_name}['und'][$i]['type_name'] = $relationship->type_id->name;
             $entity->{$field_name}['und'][$i]['subject_name'] = $relationship->subject_id->name  . ' [id: ' . $relationship->subject_id->$fkey_rcolumn . ']';
             $entity->{$field_name}['und'][$i]['object_name'] = $relationship->object_id->name  . ' [id: ' . $relationship->object_id->$fkey_rcolumn . ']';
-    
+
             if (array_key_exists('value', $schema['fields'])) {
-              $entity->{$field_name}['und'][$i][$field_table . '__value'] = $relationship->value;
+              $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__value'] = $relationship->value;
             }
             if (array_key_exists('rank', $schema['fields'])) {
-              $entity->{$field_name}['und'][$i][$field_table . '__rank'] = $relationship->rank;
+              $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__rank'] = $relationship->rank;
             }
             $i++;
       }
@@ -355,17 +351,17 @@ class chado_linker__relationship extends TripalField {
       default:
         $verb = 'is';
     }
-  
+
     return $verb;
   }
-  
+
   /**
    *
    * @see TripalField::settingsForm()
    */
   public function settingsForm($has_data) {
     $element = parent::instanceSettingsForm();
-    
+
     //$element = parent::instanceSettingsForm();
     $element['relationships'] = array(
       '#type' => 'fieldset',
@@ -393,7 +389,7 @@ class chado_linker__relationship extends TripalField {
         could use to specify relationship types. With this option any term in .
         the vocabulary can be used for the relationship type. You may select
         more than one vocabulary.'),
-    
+
     );
     $element['relationships']['option1_vocabs'] = array(
       '#type' => 'select',
@@ -403,7 +399,7 @@ class chado_linker__relationship extends TripalField {
       '#default_value' => $this->instance['settings']['relationships']['option1_vocabs'],
       // TODO add ajax here so that the relationship autocomplete below works
     );
-    
+
     $element['relationships']['option2'] = array(
       '#type' => 'item',
       '#title' => '<b>Option #2</b>',
@@ -445,7 +441,7 @@ class chado_linker__relationship extends TripalField {
       '#type' => 'textarea',
       '#default_value' => $this->instance['settings']['relationships']['relationship_types'],
     );
-    
+
     return $element;
   }
   /**
@@ -457,7 +453,7 @@ class chado_linker__relationship extends TripalField {
     // Get relationships settings
     $settings = $form_state['values']['instance']['settings']['relationships'];
     $form_state['values']['instance']['settings']['relationships']['relationship_types']= trim($settings['relationship_types']);
-    
+
     // Make sure only one option is selected
     $option1test = $settings['option1_vocabs'];
     $option1 = isset($settings['option1_vocabs']) && array_pop($option1test);
@@ -473,7 +469,7 @@ class chado_linker__relationship extends TripalField {
               );
           return;
         }
-    
+
         // For option3, make sure the supplied types are valid cvterms
         if ($option3) {
           $rel_types = explode(PHP_EOL, $settings['relationship_types']);
@@ -546,7 +542,7 @@ class chado_linker__relationship extends TripalField {
             }
           }
         }
-    
+
         // For option2: Make sure the parent term is a valid cvterm
         if ($option2) {
           $cv_id = $settings['option2_vocab'];

tripal_chado/includes/TripalFields/chado_linker__relationship_widget.inc

@@ -13,131 +13,141 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
    */
   public function form(&$widget, &$form, &$form_state, $langcode, $items, $delta, $element) {
     parent::form($widget, $form, $form_state, $langcode, $items, $delta, $element);
+
+    // Get the field settings.
+    $entity = $form['#entity'];
     $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'];
-    
-    // Get the instance settings
-    $instance = $this->instance;
-    $settings = $instance['settings']['relationships'];
-    
-    $option1_vocabs = $settings['option1_vocabs'];
-    $option2_vocab  = $settings['option2_vocab'];
-    $option2_parent = $settings['option2_parent'];
-    $option3_rtypes = $settings['relationship_types'];
-    
-    // For testing if there are selected vocabs for option1 we'll copy the
-    // contents in a special variable for later.
-    $option1_test   = $option1_vocabs;
-    
+    $base_table = $this->field['settings']['base_table'];
+
     // Get the FK column that links to the base table.
-    $chado_table = $this->field['settings']['chado_table'];
     $base_table = $this->field['settings']['base_table'];
-    $schema = chado_get_schema($chado_table);
+    $schema = chado_get_schema($field_table);
     $pkey = $schema['primary key'][0];
     $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
     $fkey = $fkeys[0];
-    
+
+    // Get the instance settings. There are three options for how this widget
+    // will be displayed. Those are controlled in the instance settings
+    // of the field.
+    // Option 1:  relationship types are limited to a specific vocabulary.
+    // Option 2:  relationship types are limited to a subset of one vocabulary.
+    // Option 3:  relationship types are limited to a predefined set.
+    $instance = $this->instance;
+    $settings = '';
+    $option1_vocabs = '';
+    $option2_parent = '';
+    $option2_vocab = '';
+    $option3_rtypes  = '';
+    if (array_key_exists('relationships', $instance)) {
+      $settings = $instance['settings']['relationships'];
+      $option1_vocabs = $settings['option1_vocabs'];
+      $option2_vocab  = $settings['option2_vocab'];
+      $option2_parent = $settings['option2_parent'];
+      $option3_rtypes = $settings['relationship_types'];
+    }
+
+    // For testing if there are selected vocabs for option1 we'll copy the
+    // contents in a special variable for later.
+    $option1_test = $option1_vocabs;
+
     // Get the field defaults.
     $record_id = '';
-    $fkey_value = $element['#entity'] ? $element['#entity']->chado_record_id : '';
     $subject_id = '';
-    $subject_uniquename = '';
-    $type_id = '';
-    $type = '';
     $object_id = '';
-    $object_uniquename = '';
+    $type_id = '';
     $value = '';
     $rank = '';
-    
+    $subject_uniquename = '';
+    $object_uniquename = '';
+    $type = '';
+
     // Handle special cases
     $subject_id_key = 'subject_id';
     $object_id_key = 'object_id';
-    if ($chado_table == 'organism_relationship') {
-      $subject_id_key = 'subject_organism_id';
-      $object_id_key = 'object_organism_id';
-    }
-    else if ($chado_table == 'nd_reagent_relationship') {
+    if ($field_table == 'nd_reagent_relationship') {
       $subject_id_key = 'subject_reagent_id';
       $object_id_key = 'object_reagent_id';
     }
-    else if ($chado_table == 'project_relationship') {
+    else if ($field_table == 'project_relationship') {
       $subject_id_key = 'subject_project_id';
       $object_id_key = 'object_project_id';
     }
-    
+
     // If the field already has a value then it will come through the $items
     // array.  This happens when editing an existing record.
-    if (array_key_exists($delta, $items)) {
-      $record_id = isset($items[$delta][$field_table . '__' . $pkey]) ? $items[$delta][$field_table . '__' . $pkey] : '';
-      $subject_id = isset($items[$delta][$field_table . '__' . $subject_id_key]) ? $items[$delta][$field_table . '__' . $subject_id_key] : '';
-      $type_id = isset($items[$delta][$field_table . '__type_id']) ? $items[$delta][$field_table . '__type_id'] : '';
-      $object_id = isset($items[$delta][$field_table . '__' . $object_id_key]) ? $items[$delta][$field_table . '__' . $object_id_key] : '';
-    
-      if (isset($items[$delta][$field_table . '__value'])) {
-        $value = $items[$delta][$field_table . '__value'];
+    if (count($items) > 0 and array_key_exists($delta, $items)) {
+      // Check for element values that correspond to fields in the Chado table.
+      $record_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__' . $pkey, $record_id);
+      $subject_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__' . $subject_id_key, $subject_id);
+      $object_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__' . $object_id_key, $object_id);
+      $type_id = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__type_id', $type_id);
+      // Not all Chado tables have a value and rank.  So we'll only get
+      // those if applicable.
+      if (array_key_exists('value', $schema['fields'])) {
+        $value = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__value', $value);
       }
-      if (isset($items[$delta][$field_table . '__rank'])) {
-        $rank = $items[$delta][$field_table . '__rank'];
+      if (array_key_exists('rank', $schema['fields'])) {
+        $rank = tripal_get_field_item_keyval($items, $delta, 'chado-' . $field_table . '__rank', $rank);
       }
-    
-      $object_uniquename = isset($items[$delta]['object_name']) ? $items[$delta]['object_name'] : '';
-      $subject_uniquename = isset($items[$delta]['subject_name']) ? $items[$delta]['subject_name'] : '';
-      $type = isset($items[$delta]['type_name']) ? $items[$delta]['type_name'] : '';
+      // Get element values added to help support insert/updates.
+      $object_uniquename = tripal_get_field_item_keyval($items, $delta, 'object_name', $object_uniquename);
+      $subject_uniquename = tripal_get_field_item_keyval($items, $delta, 'subject_name', $subject_uniquename);
+      $type = tripal_get_field_item_keyval($items, $delta, 'type_name', $type);
     }
-    
+
     // Check $form_state['values'] to see if an AJAX call set the values.
     if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
-      //       $record_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__' . $pkey);
-      //       $subject_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__subject_id');
-      //       $subject_uniquename = tripal_chado_get_field_form_values($field_name, $form_state, $delta, 'subject_name');
-      //       $type_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__type_id');
-      //       $type = tripal_chado_get_field_form_values($field_name, $form_state, $delta, 'type_name');
-      //       $object_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__object_id');
-      //       $object_uniquename = tripal_chado_get_field_form_values($field_name, $form_state, $delta, 'object_name');
-      //       $value = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__value');
-      //       $rank = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_table . '__rank');
+      $record_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $pkey];
+      $subject_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $subject_id_key];
+      $object_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__' . $object_id_key];
+      $type_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__type_id'];
+      if (array_key_exists('value', $schema['fields'])) {
+        $value = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__value'];
+      }
+      if (array_key_exists('rank', $schema['fields'])) {
+        $rank = $form_state['values'][$field_name]['und'][$delta]['chado-' . $field_table . '__rank'];
+      }
+      $object_uniquename = $form_state['values'][$field_name]['und'][$delta]['object_name'];
+      $subject_uniquename = $form_state['values'][$field_name]['und'][$delta]['subject_name'];
+      $type = $form_state['values'][$field_name]['und'][$delta]['type_name'];
     }
-    
-    $widget['#table_name'] = $chado_table;
-    
-    $widget['#fkeys'] = $schema['foreign keys'];
-    $widget['#base_table'] = $base_table;
-    $widget['#chado_record_id'] = isset($form['#entity']) ? $form['#entity']->chado_record_id : '';
+
     //$widget['#element_validate'] = array('chado_linker__relationship_validate');
     $widget['#theme'] = 'chado_linker__relationship_widget';
-    $widget['#prefix'] =  "<span id='$chado_table-$delta'>";
+    $widget['#prefix'] =  "<span id='$field_table-$delta'>";
     $widget['#suffix'] =  "</span>";
-    
+
     $widget['value'] = array(
       '#type' => 'value',
       '#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
     );
-    $widget[$field_table . '__' . $pkey] = array(
+    $widget['chado-' . $field_table . '__' . $pkey] = array(
       '#type' => 'value',
       '#default_value' => $record_id,
     );
-    $widget[$field_table . '__' . $subject_id_key] = array(
+    $widget['chado-' . $field_table . '__' . $subject_id_key] = array(
       '#type' => 'value',
       '#default_value' => $subject_id,
     );
-    $widget[$field_table . '__type_id'] = array(
+    $widget['chado-' . $field_table . '__type_id'] = array(
       '#type' => 'value',
       '#default_value' => $type_id,
     );
-    $widget[$field_table . '__' . $object_id_key] = array(
+    $widget['chado-' . $field_table . '__' . $object_id_key] = array(
       '#type' => 'value',
       '#default_value' => $object_id,
     );
     if (array_key_exists('value', $schema['fields'])) {
-      $widget[$field_table . '__value'] = array(
+      $widget['chado-' . $field_table . '__value'] = array(
         '#type' => 'value',
         '#default_value' => $value,
       );
     }
     if (array_key_exists('rank', $schema['fields'])) {
-      $widget[$field_table . '__rank'] = array(
+      $widget['chado-' . $field_table . '__rank'] = array(
         '#type' => 'value',
         '#default_value' => $rank,
       );
@@ -151,8 +161,8 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
       '#size' => 35,
       '#autocomplete_path' => "admin/tripal/storage/chado/auto_name/$base_table",
     );
-    
-    // Getting default values
+
+    // Getting default values for the relationship type element.
     $default_voc = '';
     if (isset($form_state['field'][$field_name]['und']['instance']['default_value'][0]['vocabulary'])) {
       $default_voc = $form_state['field'][$field_name]['und']['instance']['default_value'][0]['vocabulary'];
@@ -161,7 +171,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
     if (isset($form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_name'])) {
       $default_term = $form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_name'];
     }
-    
+
     $default_type_id = $type_id;
     if (!$type_id && isset($form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_id'])) {
       $default_type_id = $form_state['field'][$field_name]['und']['instance']['default_value'][0]['type_id'];
@@ -203,7 +213,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
         'name' => $option2_parent
       );
       $parent_term = tripal_get_cvterm($values);
-    
+
       // If the term wasn't found then see if it's a synonym.
       if(!$parent_term) {
         $values = array(
@@ -217,16 +227,14 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
         }
       }
       // Get the child terms of the parent term found above.
-      $sql =
-      "SELECT
-           subject_id,
-           (SELECT name from {cvterm} where cvterm_id = subject_id) AS name
-         FROM {cvtermpath}
-         WHERE
-           object_id = :parent_cvterm_id
-         AND
-           cv_id = :parent_cv_id
-         ORDER BY name
+      $sql = "
+        SELECT subject_id,
+          (SELECT name from {cvterm} where cvterm_id = subject_id) AS name
+        FROM {cvtermpath}
+        WHERE
+          object_id = :parent_cvterm_id AND
+          cv_id = :parent_cv_id
+        ORDER BY name
        ";
       $args = array(
         ':parent_cvterm_id' => $parent_term->cvterm_id,
@@ -288,7 +296,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
         '#default_value' => $cv_id,
         '#ajax' => array(
           'callback' => "chado_linker__relationship_widget_form_ajax_callback",
-          'wrapper' => "$chado_table-$delta",
+          'wrapper' => "$field_table-$delta",
           'effect' => 'fade',
           'method' => 'replace'
         ),
@@ -304,7 +312,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
         );
       }
     }
-    
+
     $widget['object_name'] = array(
       '#type' => 'textfield',
       '#title' => t('Object'),
@@ -332,18 +340,14 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
     $field_table = $this->field['settings']['chado_table'];
     $field_column = $this->field['settings']['chado_column'];
     $base_table = $this->field['settings']['base_table'];
-    
+
     $schema = chado_get_schema($field_table);
     $fkeys = $schema['foreign keys'];
-    
+
     // Handle special cases
     $subject_id_key = 'subject_id';
     $object_id_key = 'object_id';
-    if ($field_table == 'organism_relationship') {
-      $subject_id_key = 'subject_organism_id';
-      $object_id_key = 'object_organism_id';
-    }
-    else if ($field_table == 'nd_reagent_relationship') {
+    if ($field_table == 'nd_reagent_relationship') {
       $subject_id_key = 'subject_reagent_id';
       $object_id_key = 'object_reagent_id';
     }
@@ -351,22 +355,22 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
       $subject_id_key = 'subject_project_id';
       $object_id_key = 'object_project_id';
     }
-    
+
     foreach ($items as $delta => $item) {
-      $subject_id = $item[$field_table . '__' . $subject_id_key];
-      $object_id = $item[ $field_table . '__' . $object_id_key];
-      $type_id = $item[$field_table . '__type_id'];
-      $type_id = isset($item['type_id']) ? $item['type_id'] : $type_id;
+      $subject_id = $item['chado' . $field_table . '__' . $subject_id_key];
+      $object_id = $item['chado' . $field_table . '__' . $object_id_key];
+      $type_id = $item['chado' . $field_table . '__type_id'];
+      $type_id = isset($item['type_id']) ? $item['chado' . $field_table . '__type_id'] : $type_id;
       $type_name = isset($item['type_name']) ? $item['type_name'] : '';
       $subject_name = $item['subject_name'];
       $object_name = $item['object_name'];
-    
-    
+
+
       // If the row is empty then just continue, there's nothing to validate.
       if (!$type_id and !$type_name and !$subject_name and !$object_name) {
         continue;
       }
-    
+
       // Make sure we have values for all of the fields.
       $form_error = FALSE;
       if (!$type_name && !$type_id) {
@@ -390,9 +394,9 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
       if ($form_error) {
         continue;
       }
-    
+
       // Before submitting this form we need to make sure that our subject_id and
-      // object_ids are real values.  There are two ways to get the value, either
+      // object_ids are real records.  There are two ways to get the record, either
       // just with the text value or with an [id: \d+] string embedded.  If the
       // later we will pull it out.
       $subject_id = '';
@@ -427,7 +431,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
           }
         }
       }
-    
+
       // Now check for a matching object.
       $object_id = '';
       $fkey_rcolumn = $fkeys[$base_table]['columns'][$object_id_key];
@@ -461,7 +465,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
           }
         }
       }
-    
+
       // Make sure that either our object or our subject refers to the base record.
       if ($entity) {
         $chado_record_id = $entity->chado_record_id;
@@ -471,7 +475,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
             'message' =>  t("Either the subject or the object in the relationship must refer to this record."),
           );
         }
-    
+
         // Make sure that the object and subject are not both the same thing.
         if ($object_id == $subject_id) {
           $errors[$this->field['field_name']][$langcode][$delta][] = array(
@@ -495,23 +499,35 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
     $field_column = $this->field['settings']['chado_column'];
     $base_table = $this->field['settings']['base_table'];
     $chado_record_id = $entity->chado_record_id;
-    
+
     $schema = chado_get_schema($field_table);
     $fkeys = $schema['foreign keys'];
-    
+
+    // Handle special cases
+    $subject_id_key = 'subject_id';
+    $object_id_key = 'object_id';
+    if ($field_table == 'nd_reagent_relationship') {
+      $subject_id_key = 'subject_reagent_id';
+      $object_id_key = 'object_reagent_id';
+    }
+    else if ($field_table == 'project_relationship') {
+      $subject_id_key = 'subject_project_id';
+      $object_id_key = 'object_project_id';
+    }
+
     $type_name = array_key_exists('type_name', $item) ? $item['type_name'] : '';
-    $subject_id = $form_state['values'][$field_name][$langcode][$delta][$field_table . '__subject_id'];
-    $object_id = $form_state['values'][$field_name][$langcode][$delta][ $field_table . '__object_id'];
-    $type_id = $form_state['values'][$field_name][$langcode][$delta][$field_table . '__type_id'];
-    
+    $subject_id = $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__' . $subject_id_key];
+    $object_id = $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__' . $object_id_key];
+    $type_id = $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__type_id'];
+
     $subject_name = $form_state['values'][$field_name][$langcode][$delta]['subject_name'];
     $object_name = $form_state['values'][$field_name][$langcode][$delta]['object_name'];
-    
+
     // If the row is empty then skip this one, there's nothing to validate.
     if (!($type_id or !$type_name) and !$subject_name and !$object_name) {
       return;
     }
-    
+
     // Get the subject ID.
     $subject_id = '';
     $fkey_rcolumn = $fkeys[$base_table]['columns']['subject_id'];
@@ -524,7 +540,7 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
       $subject = chado_select_record($base_table, array($fkey_rcolumn), $values);
       $subject_id = $subject[0]->$fkey_rcolumn;
     }
-    
+
     // Get the object ID.
     $object_id = '';
     $fkey_rcolumn = $fkeys[$base_table]['columns']['object_id'];
@@ -537,12 +553,12 @@ class chado_linker__relationship_widget extends TripalFieldWidget {
       $object = chado_select_record($base_table, array($fkey_rcolumn), $values);
       $object_id = $object[0]->$fkey_rcolumn;
     }
-    
+
     // Set the IDs according to the values that were determined above.
-    $form_state['values'][$field_name][$langcode][$delta][$field_table . '__subject_id'] = $subject_id;
-    $form_state['values'][$field_name][$langcode][$delta][$field_table . '__object_id'] = $object_id;
-    $form_state['values'][$field_name][$langcode][$delta][$field_table . '__type_id'] = $type_name;
-    $form_state['values'][$field_name][$langcode][$delta][$field_table . '__rank'] = $item['_weight'];
+    $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__' . $subject_id_key] = $subject_id;
+    $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__' . $object_id_key] = $object_id;
+    $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__type_id'] = $type_name;
+    $form_state['values'][$field_name][$langcode][$delta]['chado' . $field_table . '__rank'] = $item['_weight'];
   }
 }
 

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -44,9 +44,9 @@ function tripal_chado_field_storage_write($entity_type, $entity, $op, $fields) {
   $field_vals = tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $entity);
 
   // First, write the record for the base table.  If we have a record id then
-  // this is an upate and we need to set the primary key.  If not, then this
+  // this is an update and we need to set the primary key.  If not, then this
   // is an insert and we need to set the type_id if the table supports it.
-  $values = $field_vals[$base_table][0];
+  $values = $field_vals[$base_table];
   if ($record_id) {
     $values[$base_pkey] = $record_id;
   }
@@ -109,93 +109,72 @@ function tripal_chado_field_storage_write($entity_type, $entity, $op, $fields) {
  *   The unique record ID.
  */
 function tripal_chado_field_storage_write_table($table_name, $values) {
-   $schema = chado_get_schema($table_name);
-   $fkeys = $schema['foreign keys'];
-   $pkey = $schema['primary key'][0];
-
-
-//    // Before inserting or updating this table, recurse if there are any
-//    // nested FK array values.
-//    foreach ($values as $column => $value) {
-//      // If this value is an array then it must be a FK... let's recurse.
-//      if (is_array($value)) {
-
-//        // Find the name of the FK table for this column.
-//        $fktable_name = '';
-//        foreach ($fkeys as $fktable => $details) {
-//          foreach ($details['columns'] as $fkey_lcolumn => $fkey_rcolumn) {
-//            if ($fkey_lcolumn == $column) {
-//              $fktable_name = $fktable;
-//            }
-//          }
-//        }
-
-//        // Recurse on this recod.
-//        $record_id = tripal_chado_field_storage_write_table($fktable_name, $values[$column]);
-//        $values[$column] = $record_id;
-//      }
-//    }
-
-   // Fields with a cardinality greater than 1 will often submit an
-   // empty form.  We want to remove these empty submissions.  We can detect
-   // them if all of the fields are empty.
-   $num_empty = 0;
-   foreach ($values as $column => $value) {
-     if (!$value) {
-       $num_empty++;
-     }
-   }
-   if ($num_empty == count(array_keys($values))) {
-     return '';
-   }
-   // If the primary key column has a value but all other values are empty then
-   // this is a delete.
-   if (array_key_exists($pkey, $values) and $values[$pkey]) {
-     $num_vals = 0;
-     foreach ($values as $value) {
-       if ($value) {
-         $num_vals++;
-       }
-     }
-     if ($num_vals == 1) {
-       $new_vals[$pkey] = $values[$pkey];
-       if (!chado_delete_record($table_name, $new_vals)) {
-         throw new Exception('Could not delete record from table: "' . $table_name . '".');
-       }
-       return '';
-     }
-   }
+  $schema = chado_get_schema($table_name);
+  $fkeys = $schema['foreign keys'];
+  $pkey = $schema['primary key'][0];
+
+
+  // Fields with a cardinality greater than 1 will often submit an
+  // empty form.  We want to remove these empty submissions.  We can detect
+  // them if all of the fields are empty.
+  $num_empty = 0;
+  foreach ($values as $column => $value) {
+    if (!$value) {
+      $num_empty++;
+    }
+  }
+  if ($num_empty == count(array_keys($values))) {
+    return '';
+  }
 
-   // If the primary key column does not have a value then this is an insert.
-   if (!array_key_exists($pkey, $values) or !$values[$pkey] or !isset($values[$pkey])) {
-     // Before inserting, we want to make sure the record does not
-     // already exist.  Using the unique constraint check for a matching record.
-     $options = array('is_duplicate' => TRUE);
-     $is_duplicate = chado_select_record($table_name, array('*'), $values, $options);
-     if($is_duplicate) {
-       $record = chado_select_record($table_name, array('*'), $values);
-       return $record[0]->$pkey;
-     }
+  // If the primary key column has a value but all other values are empty then
+  // this is a delete.
+  if (array_key_exists($pkey, $values) and $values[$pkey]) {
+    $num_vals = 0;
+    foreach ($values as $value) {
+      if ($value) {
+        $num_vals++;
+      }
+    }
+    if ($num_vals == 1) {
+      $new_vals[$pkey] = $values[$pkey];
+      if (!chado_delete_record($table_name, $new_vals)) {
+        throw new Exception('Could not delete record from table: "' . $table_name . '".');
+      }
+      return '';
+    }
+  }
 
-     // Insert the values array as a new record in the table but remove the
-     // pkey as it should be set.
-     $new_vals = $values;
-     unset($new_vals[$pkey]);
-     $record = chado_insert_record($table_name, $new_vals);
-     if ($record === FALSE) {
-       throw new Exception('Could not insert Chado record into table: "' . $table_name . '".');
-     }
-     return $record[$pkey];
-   }
+  // If the primary key column does not have a value then this is an insert.
+  if (!array_key_exists($pkey, $values) or !$values[$pkey] or !isset($values[$pkey])) {
+    // Before inserting, we want to make sure the record does not
+    // already exist.  Using the unique constraint check for a matching record.
+    $options = array('is_duplicate' => TRUE);
+    $is_duplicate = chado_select_record($table_name, array('*'), $values, $options);
+    if($is_duplicate) {
+      $record = chado_select_record($table_name, array('*'), $values);
+      return $record[0]->$pkey;
+    }
 
-   // If we've made it to this point then this is an update.
-   // TODO: what if the unique constraint matches another record?  That is
-   // not being tested for here.
-   $match[$pkey] = $values[$pkey];
-   if (!chado_update_record($table_name, $match, $values)) {
-     drupal_set_message("Could not update Chado record in table: $table_name.", 'error');
-   }
-   return $values[$pkey];
+    // Insert the values array as a new record in the table but remove the
+    // pkey as it should be set.
+    $new_vals = $values;
+    unset($new_vals[$pkey]);
+    $record = chado_insert_record($table_name, $new_vals);
+    if ($record === FALSE) {
+      throw new Exception('Could not insert Chado record into table: "' . $table_name . '".');
+    }
+    return $record[$pkey];
+  }
+
+  // If we've made it to this point then this is an update.
+  // TODO: what if the unique constraint matches another record?  That is
+  // not being tested for here.
+  $match[$pkey] = $values[$pkey];
+  if (!chado_update_record($table_name, $match, $values)) {
+    drupal_set_message("Could not update Chado record in table: $table_name.", 'error');
+  }
+  return $values[$pkey];
 }
 
 /**
@@ -331,7 +310,8 @@ function tripal_chado_field_storage_load($entity_type, $entities, $age,
  * Merges the values of all fields into a single array keyed by table name.
  */
 function tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $entity) {
-  $new_fields = array();
+  $all_fields = array();
+  $base_fields = array();
 
   // Iterate through all of the fields and organize them into a
   // new fields array keyed by the table name
@@ -348,12 +328,12 @@ function tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $e
     }
     $chado_table = $field['settings']['chado_table'];
     $chado_column = $field['settings']['chado_column'];
+    $base_table = $field['settings']['base_table'];
 
     // Iterate through the field's items. Fields with cardinality ($delta) > 1
     // are multi-valued.
     $items = field_get_items($entity_type, $entity, $field_name);
     $temp = array();
-
     foreach ($items as $delta => $item) {
 
       // A field may have multiple items. The field can use items
@@ -364,30 +344,45 @@ function tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $e
         if (preg_match('/^chado-(.*?)__(.*?)$/', $item_name, $matches)) {
           $table_name = $matches[1];
           $column_name = $matches[2];
-          $temp[$table_name][$delta][$column_name] = $value;
+          // If this field belongs to the base table then we just add
+          // those values in... there's no delta.
+          if ($table_name == $base_table) {
+            $base_fields[$table_name][$column_name] = $value;
+          }
+          else {
+            $temp[$table_name][$delta][$column_name] = $value;
+          }
         }
       }
       // If there is no value set for the field using the
-      // chado-[table_name]__[field name] naming schema then check if a 'value' item
-      // is present and if so use that.
+      // chado-[table_name]__[field name] naming schema then check if a 'value'
+      // item is present and if so use that for the table column value.
       if ((!array_key_exists($chado_table, $temp) or
            !array_key_exists($delta, $temp[$chado_table]) or
            !array_key_exists($chado_column, $temp[$chado_table][$delta])) and
           array_key_exists('value', $items[$delta]) and
           !is_array($items[$delta]['value'])) {
-        $temp[$chado_table][$delta][$chado_column] = $items[$delta]['value'];
+        // If this field belongs to the base table then we just add
+        // those values in... there's no delta.
+        if ($base_table == $chado_table) {
+          $base_fields[$chado_table][$chado_column] = $items[$delta]['value'];
+        }
+        else {
+          $temp[$chado_table][$delta][$chado_column] = $items[$delta]['value'];
+        }
       }
     }
 
     // Now merge the records for this field with the $new_fields array
     foreach ($temp as $table_name => $details) {
       foreach ($details as $delta => $list) {
-        $new_fields[$table_name][] = $list;
+        $all_fields[$table_name][] = $list;
       }
     }
   }
 
-  return $new_fields;
+  $all_fields = array_merge($base_fields, $all_fields);
+  return $all_fields;
 }
 
 /**

tripal_chado/includes/tripal_chado.fields.inc

@@ -134,6 +134,7 @@ function tripal_chado_bundle_create_fields_base(&$info, $details, $entity_type,
       'settings' => array(
         'chado_table' => $table_name,
         'chado_column' => $column_name,
+        'base_table' => $table_name,
         'semantic_web' => tripal_get_chado_semweb_term($table_name, $column_name),
       ),
     );
@@ -234,6 +235,7 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
       'settings' => array(
         'chado_table' => $table_name,
         'chado_column' => 'organism_id',
+        'base_table' => $table_name,
       ),
     );
   }
@@ -253,6 +255,7 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
       'settings' => array(
         'chado_table' => $table_name,
         'chado_column' => 'dbxref_id',
+        'base_table' => $table_name,
         'semantic_web' => tripal_get_chado_semweb_term($table_name, 'dbxref_id'),
       ),
     );
@@ -273,6 +276,7 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
       'settings' => array(
         'chado_table' => $table_name,
         'chado_column' => 'md5checksum',
+        'base_table' => $table_name,
         'semantic_web' => tripal_get_chado_semweb_term($table_name, 'md5checksum'),
       ),
     );
@@ -293,11 +297,12 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
       'settings' => array(
         'chado_table' => $table_name,
         'chado_column' => 'residues',
+        'base_table' => $table_name,
         'semantic_web' => tripal_get_chado_semweb_term($table_name, 'residues'),
       ),
     );
   }
-  
+
   // FEATURE SEQLEN
   if ($table_name == 'feature') {
     $field_name = 'data__sequence_length';
@@ -313,6 +318,7 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
       'settings' => array(
         'chado_table' => $table_name,
         'chado_column' => 'seqlen',
+        'base_table' => $table_name,
         'semantic_web' => tripal_get_chado_semweb_term($table_name, 'seqlen'),
       ),
     );
@@ -341,24 +347,24 @@ function tripal_chado_bundle_create_fields_custom(&$info, $details, $entity_type
   }
 
   // ORGANISM TYPE_ID
-  if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
-    $field_name = 'taxarank__infraspecific_taxon';
-    $field_type = 'taxarank__infraspecific_taxon';
-    $info[$field_name] = array(
-      'field_name' => $field_name,
-      'type' => $field_type,
-      'cardinality' => 1,
-      'locked' => FALSE,
-      'storage' => array(
-        'type' => 'field_chado_storage',
-      ),
-      'settings' => array(
-        'chado_table' => 'organism',
-        'chado_column' => 'type_id',
-        'semantic_web' => 'TAXRANK:0000046',
-      ),
-    );
-  }
+//   if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
+//     $field_name = 'taxarank__infraspecific_taxon';
+//     $field_type = 'taxarank__infraspecific_taxon';
+//     $info[$field_name] = array(
+//       'field_name' => $field_name,
+//       'type' => $field_type,
+//       'cardinality' => 1,
+//       'locked' => FALSE,
+//       'storage' => array(
+//         'type' => 'field_chado_storage',
+//       ),
+//       'settings' => array(
+//         'chado_table' => 'organism',
+//         'chado_column' => 'type_id',
+//         'semantic_web' => 'TAXRANK:0000046',
+//       ),
+//     );
+//   }
 }
 
 /**
@@ -1076,33 +1082,33 @@ function tripal_chado_bundle_create_instances_custom(&$info, $entity_type, $bund
   }
 
   // ORGANISM TYPE_ID
-  if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
-    $field_name = 'taxarank__infraspecific_taxon';
-    $info[$field_name] = array(
-      'field_name' => $field_name,
-      'entity_type' => $entity_type,
-      'bundle' => $bundle->name,
-      'label' => 'Infraspecific Taxon',
-      'description' => 'The Infraspecific Taxon.',
-      'required' => FALSE,
-      'settings' => array(
-        'auto_attach' => TRUE,
-      ),
-      'widget' => array(
-        'type' => 'taxarank__infraspecific_taxon_widget',
-        'settings' => array(
-          'display_label' => 1,
-        ),
-      ),
-      'display' => array(
-        'default' => array(
-          'label' => 'inline',
-          'type' => 'taxarank__infraspecific_taxon_formatter',
-          'settings' => array(),
-        ),
-      ),
-    );
-  }
+//   if ($table_name == 'organism' and array_key_exists('type_id', $schema['fields'])) {
+//     $field_name = 'taxarank__infraspecific_taxon';
+//     $info[$field_name] = array(
+//       'field_name' => $field_name,
+//       'entity_type' => $entity_type,
+//       'bundle' => $bundle->name,
+//       'label' => 'Infraspecific Taxon',
+//       'description' => 'The Infraspecific Taxon.',
+//       'required' => FALSE,
+//       'settings' => array(
+//         'auto_attach' => TRUE,
+//       ),
+//       'widget' => array(
+//         'type' => 'taxarank__infraspecific_taxon_widget',
+//         'settings' => array(
+//           'display_label' => 1,
+//         ),
+//       ),
+//       'display' => array(
+//         'default' => array(
+//           'label' => 'inline',
+//           'type' => 'taxarank__infraspecific_taxon_formatter',
+//           'settings' => array(),
+//         ),
+//       ),
+//     );
+//   }
 }
 
 /**
@@ -1148,7 +1154,7 @@ function tripal_chado_bundle_create_instances_linker(&$info, $entity_type, $bund
       ),
     );
   }
-  
+
   // CVTERM
   $cvterm_table = $table_name . '_cvterm';
   if (chado_table_exists($cvterm_table)) {