Fixed issue saving properties. Moved field admin form alter to the Chado module. Fixed labels and descriptions on property widgets

tripal/includes/tripal.fields.inc

@@ -128,32 +128,6 @@ function tripal_field_no_delete() {
   return '';
 }
 
-/**
- *
- * Implements hook_form_FORM_ID_alter().
- *
- * The field_ui_field_edit_form is used for customizing the settings of
- * a field attached to an entity.
- *
- * This alter function disables some of the form widgets when the storage
- * backend indicates they are not appropriate.
- */
-function tripal_form_field_ui_field_edit_form_alter(&$form, &$form_state, $form_id) {
-
-  // For entity fields added by Tripal Entities we don't want the
-  // the end-user to change the cardinality and the required fields
-  // such that record can't be saved in Chado.
-
-  // TODO: this shouldn't be hardcoded here.  These settings
-  // should be part of the field and handled by the tripal_entity module.
-  if ($form['#instance']['entity_type'] == 'TripalEntity') {
-    $form['field']['cardinality']['#access'] = FALSE;
-    $form['instance']['required']['#access'] = FALSE;
-  }
-
-  // TODO: don't the the maximum length be larger than the field size.
-}
-
 /**
  *
  * Implements hook_form_FORM_ID_alter().

tripal_chado/includes/TripalFields/chado_linker__prop.inc

@@ -53,7 +53,7 @@ class chado_linker__prop extends TripalField {
     $field_type = $this->field['type'];
     $field_table = $this->field['settings']['chado_table'];
     $field_column = $this->field['settings']['chado_column'];
-
+    $instance = $this->instance;
 
     // Get the table name and cvterm that this field maps to.
     $matches = array();
@@ -81,17 +81,6 @@ class chado_linker__prop extends TripalField {
       $propval = tripal_get_field_item_keyval($items, $delta, 'chado-' . $table_name . '__value', $propval);
     }
 
-    // The group of elements all-together need some extra functionality
-    // after building up the full list (like draggable table rows).
-    $widget['#theme'] = 'field_multiple_value_form';
-    $widget['#title'] = $element['#title'];
-    $widget['#description'] = $element['#description'];
-    $widget['#field_name'] = $element['#field_name'];
-    $widget['#language'] = $element['#language'];
-    $widget['#weight'] = isset($element['#weight']) ? $element['#weight'] : 0;
-    //$widget['#element_validate'] = array('chado_linker__prop_widget_validate');
-    $widget['#cardinality'] = 1;
-
     $widget['value'] = array(
       '#type' => 'value',
       '#value' => key_exists($delta, $items) ? $items[$delta]['value'] : '',
@@ -108,6 +97,8 @@ class chado_linker__prop extends TripalField {
     $widget['chado-' . $table_name . '__value'] = array(
       '#type' => 'textfield',
       '#default_value' => $propval,
+      '#title' => $instance['label'] . ' value',
+      '#description' => $instance['description'],
     );
     $widget['chado-' . $table_name . '__type_id'] = array(
       '#type' => 'hidden',
@@ -124,68 +115,32 @@ class chado_linker__prop extends TripalField {
    * @see TripalField::validate()
    */
   public function validate($entity_type, $entity, $field, $items, &$errors) {
-/*     $field_name = $this->field['field_name'];
-
-    $matches = array();
-
-    // Get the record and table mapping info.
-    $chado_table = $entity->chado_table;
-    $chado_column = $entity->chado_column;
-
-    // Get the table name and cvterm_id for this field.
-    preg_match('/(.*?)__(\d+)/', $field_name, $matches);
-    $table_name = $matches[1];
-    $cvterm_id = $matches[2];
-
-    // Get the name of the pkey field for this property table and the name
-    // of the FK field that links to the base table.
-    $schema = chado_get_schema($table_name);
-    $pkey = $schema['primary key'][0];
-    $lfkey_field = key($schema['foreign keys'][$chado_table]['columns']);
-
-    // If we don't have a property value then we need to set all other fields
-    // to be empty so that when the module tries to save the field on the
-    // entity it won't try to save a partial record.
-//     $pkey_val = tripal_chado_get_field_form_values($field_name, $form_state, $delta);
-//     $prop_value = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $table_name . "__value");
-//     $fk_val = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $table_name . '__' . $lfkey_field);
-//     $type_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $table_name . '__type_id');
 
-    if (!$prop_value) {
-      tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__' . $lfkey_field);
-      tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__value');
-      tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__type_id');
-      tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__rank');
-    }
-    else {
-      $rank = tripal_chado_get_field_form_values($field_name, $form_state, $delta, '_weight');
-      tripal_chado_set_field_form_values($field_name, $form_state, $rank, $delta, $table_name . '__rank');
-    }
-    // Remove the properties for this record. We will re-add it. Otherwise,
-    // if we change ranks, we wind up with multiple records in the property table.
-    if ($pkey_val) {
-      $match = array(
-        $pkey => $pkey_val
-      );
-      chado_delete_record($table_name, $match);
-    } */
   }
 
   /**
    * @see TripalField::widgetFormSubmit()
    */
   public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
-    
+
     $field_name = $this->field['field_name'];
-    $field_table = $this->field['settings']['chado_table'];
+    $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];
 
-    // Don't save if there is no value for the property
-    if (!trim($form_state['values'][$field_name][$langcode][$delta]['chado-' . $field_table . '__' . 'value'])) {
-      foreach($form_state['values'][$field_name][$langcode][$delta] AS $key => $value) {
-        if (preg_match('/^chado-/', $key)) {
-          $form_state['values'][$field_name][$langcode][$delta][$key] = '__NULL__';
-        }
-      }
+    $prop_value = $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__value'];
+
+    // If the user removed the contact from the contact_name field
+    // then we want to clear out the rest of the hidden values.
+    // Leave the primary key so the record can be deleted.
+    if (!$prop_value) {
+      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $pkey] = '';
+      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__rank'] = '';
+      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__type_id'] = '';
+      $form_state['values'][$field_name][$langcode][$delta]['chado-' . $table_name . '__' . $lfkey_field] = '';
     }
   }
 
@@ -248,12 +203,3 @@ class chado_linker__prop extends TripalField {
     }
   }
 }
-/**
- *
- * @param unknown $form
- * @param unknown $form_state
- */
-function chado_linker__prop_widget_form_ajax_callback($form, $form_state) {
-  $field_name = $form_state['triggering_element']['#parents'][0];
-  return $form[$field_name];
-}

tripal_chado/includes/TripalFields/chado_linker__prop_adder.inc

@@ -137,7 +137,7 @@ class chado_linker__prop_adder extends TripalField {
         $widget['wrapper']['cardinality'] = array(
           '#title'       => t('Number of Values'),
           '#type'        => 'textfield',
-          '#description' => t("The number of values allowed for this property. 0 for unlimited values"),
+          '#description' => t("A number of 1 or more indicating the number of values allowed for this property. Enter -1 for unlimited values"),
           '#size' => 10,
           '#default_value' => 1,
         );
@@ -162,10 +162,10 @@ class chado_linker__prop_adder extends TripalField {
       // If the user has clicked the 'user_term_button' then we need to makes
       // sure that the cardinality textbox contains a positive integer.
       $cardinality = $form_state['values'][$field_name][$langcode][$delta]['wrapper']['cardinality'];
-      if (!preg_match('/^\d+$/', $cardinality) or $cardinality < 0) {
-        form_set_error("$field_name][$langcode][$delta][wrapper][cardinality", "Please provide positive number for the number of values.");
+      if (!preg_match('/^-*\d+$/', $cardinality) or $cardinality < -2 or $cardinality == 0) {
+        form_set_error("$field_name][$langcode][$delta][wrapper][cardinality", "Please provide positive number for the number of values, or -1 for unlimited.");
       }
-      
+
       // Get selected terms
       $terms_list = $form_state['values'][$field_name][$langcode][$delta]['wrapper']['terms_list'];
       $counter = 0;
@@ -204,7 +204,6 @@ class chado_linker__prop_adder extends TripalField {
    */
   public function widgetFormSubmit($form, &$form_state, $entity_type, $entity, $langcode, $delta) {
 
-
     // Add the new field to the entity but only if the property adder button
     // was clicked
     if (!array_key_exists('triggering_element', $form_state) or
@@ -274,9 +273,11 @@ class chado_linker__prop_adder extends TripalField {
         'label' => ucfirst(preg_replace('/_/', ' ', $cvterm->name)),
         'description' => $cvterm->definition ? $cvterm->definition : '',
         'required' => FALSE,
-        'settings' => array(),
+        'settings' => array(
+          'auto_attach' => FALSE,
+        ),
         'widget' => array(
-          'type' => $field_name . '_widget',
+          'type' => 'chado_linker__prop_widget',
           'settings' => array(
             'display_label' => 1,
           ),
@@ -284,7 +285,7 @@ class chado_linker__prop_adder extends TripalField {
         'display' => array(
           'default' => array(
             'label' => 'inline',
-            'type' => $field_name . '_formatter',
+            'type' => 'chado_linker__prop_formatter',
             'settings' => array(),
           ),
         ),

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -352,7 +352,10 @@ function tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $e
     // Iterate through the field's items. Fields with cardinality ($delta) > 1
     // are multi-valued.
     $items = field_get_items($entity_type, $entity, $field_name);
+    $temp = array();
+
     foreach ($items as $delta => $item) {
+
       // A field may have multiple items. The field can use items
       // indexed with "chado-" to represent values that should map directly
       // to chado tables and fields.
@@ -361,25 +364,25 @@ function tripal_chado_field_storage_write_merge_fields($fields, $entity_type, $e
         if (preg_match('/^chado-(.*?)__(.*?)$/', $item_name, $matches)) {
           $table_name = $matches[1];
           $column_name = $matches[2];
-          // If not seen this table and column then just add it. If we've
-          // already seen it then it means it's a FK field and we've already
-          // added subfields so do nothing.
-          if (!array_key_exists($table_name, $new_fields) or
-              !array_key_exists($delta, $new_fields[$table_name]) or
-              !array_key_exists($column_name, $new_fields[$table_name][$delta])) {
-            $new_fields[$table_name][$delta][$column_name] = $value;
-          }
+          $temp[$table_name][$delta][$column_name] = $value;
         }
       }
       // If there is no value set for the field using the
       // chado-[table_name]__[field name] naming schema then check if a 'value' item
       // is present and if so use that.
-      if ((!array_key_exists($chado_table, $new_fields) or
-           !array_key_exists($delta, $new_fields[$chado_table]) or
-           !array_key_exists($chado_column, $new_fields[$chado_table][$delta])) and
+      if ((!array_key_exists($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'])) {
-        $new_fields[$chado_table][$delta][$chado_column] = $items[$delta]['value'];
+        $temp[$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;
       }
     }
   }

tripal_chado/includes/tripal_chado.fields.inc

@@ -1403,4 +1403,5 @@ function tripal_chado_form_field_ui_field_overview_form_alter(&$form, &$form_sta
       unset($form['fields'][$field_name]);
     }
   }
-}
+}
+

tripal_chado/tripal_chado.module

@@ -768,3 +768,32 @@ function tripal_chado_node_delete($node) {
   db_query($sql, array('nid' => $nid));
 }
 
+
+/**
+ *
+ * Implements hook_form_FORM_ID_alter().
+ *
+ * The field_ui_field_edit_form is used for customizing the settings of
+ * a field attached to an entity.
+ *
+ * This alter function disables some of the form widgets when the storage
+ * backend indicates they are not appropriate.
+ */
+function tripal_chado_form_field_ui_field_edit_form_alter(&$form, &$form_state, $form_id) {
+  // For entity fields added by Tripal Entities we don't want the
+  // the end-user to change the cardinality and the required fields
+  // such that record can't be saved in Chado.
+
+  // TODO: we shouldn't check for specific field types here
+  // (e.g. chaod_linker_prop). That should be done via the TripalField
+  // functions.
+  if ($form['#instance']['entity_type'] == 'TripalEntity') {
+    if ($form['#field']['storage']['type'] == 'field_chado_storage' and
+        $form['#field']['type'] != 'chado_linker__prop') {
+      $form['field']['cardinality']['#access'] = FALSE;
+      $form['instance']['required']['#access'] = FALSE;
+    }
+  }
+
+  // TODO: don't the the maximum length be larger than the field size.
+}