Fixed bug with conflicting views handler filter name. Experimenting with Entity Query API... added form to content list page

tripal/includes/TripalEntityUIController.inc

@@ -162,18 +162,80 @@ function tripal_view_entity($entity, $view_mode = 'full') {
   *   A form array describing this listing to the Form API.
   */
  function tripal_content_overview_form($form, &$form_state) {
-
+   $filter_status = '';
+   $filter_type = '';
+   if (array_key_exists('values', $form_state)) {
+     if ($form_state['values']['status'] != '[any]') {
+       $filter_status = preg_replace('/status-(\d+)/', '\1', $form_state['values']['status']);
+     }
+     if ($form_state['values']['type'] != '[any]') {
+       $filter_type = $form_state['values']['type'];
+     }
+   }
    // Set the title to be informative (defaults to content for some reason).
    drupal_set_title('Tripal Content');
 
+   $form['filter'] = array(
+     '#type' => 'fieldset',
+     '#title' => 'Filter',
+     '#collapsible' => TRUE,
+     '#collapsed' => TRUE,
+   );
+   $etypes = db_select('tripal_bundle', 'tb')
+     ->fields('tb', array('id', 'label'))
+     ->execute()
+     ->fetchAllKeyed();
+   $etypes = array('[any]' => 'any') +  $etypes;
+   $form['filter']['type'] = array(
+     '#type' => 'select',
+     '#title' => 'Content Type',
+     '#options' => $etypes,
+   );
+   $form['filter']['status'] = array(
+     '#type' => 'select',
+     '#title' => 'Status',
+     '#options' => array(
+       '[any]' => 'any',
+       'status-1' => 'published',
+       'status-0' => 'not published'
+     ),
+   );
+   $form['filter']['filterbtn'] = array(
+     '#type' => 'submit',
+     '#value' => 'Filter',
+   );
+
    // Retrieve a pages list of all tripal entitles (ie: biological data).
    // This will return the 25 most recently created entities.
-   $entities = db_select('tripal_entity', 'td')
-     ->fields('td')
-     ->orderBy('created', 'DESC')
+   $query = db_select('tripal_entity', 'td')
+     ->fields('td');
+   if ($filter_type) {
+     $query = $query->condition('term_id', $filter_type);
+   }
+   if (is_numeric($filter_status)) {
+     $query = $query->condition('status', $filter_status);
+   }
+   $entities = $query->orderBy('created', 'DESC')
      ->range(0,25)
      ->execute();
 
+   global $user;
+   $query = new EntityFieldQuery();
+   $query->entityCondition('entity_type', 'TripalEntity');
+   if ($filter_type) {
+     $query = $query->propertyCondition('term_id', $filter_type);
+   }
+   if (is_numeric($filter_status)) {
+     $query = $query->propertyCondition('status', $filter_status);
+   }
+//   $query = $query->fieldCondition('feature__name', 'value', 'orange1.1g022797m');
+//   $query = $query->fieldCondition('feature__uniquename', 'value', 'PAC:18136225');
+
+   $result = $query->range(0, 25)
+     ->addMetaData('account', $user)
+     ->execute();
+   dpm($result);
+
    $headers = array('Title', 'Vocabulary', 'Term', 'Author', 'Status', 'Updated', 'Operations');
    $rows = array();
 
@@ -214,7 +276,7 @@ function tripal_view_entity($entity, $view_mode = 'full') {
    if (empty($rows)) {
      $rows[] = array(
        array(
-         'data' => t('No Tripal content available.'),
+         'data' => t('No content can be found.'),
          'colspan' => 7
        )
      );
@@ -238,6 +300,21 @@ function tripal_view_entity($entity, $view_mode = 'full') {
    return $form;
  }
 
+ /**
+  *
+  */
+ function tripal_content_overview_form_validate($form, &$form_state) {
+ }
+
+ /**
+  *
+  */
+ function tripal_content_overview_form_submit($form, &$form_state) {
+   // Always just rebuild the form on submit.  that will update the
+   // result table using the filters provided.
+   $form_state['rebuild'] = TRUE;
+ }
+
  /**
   *
   */

tripal/includes/TripalTermViewsController.inc

@@ -17,7 +17,7 @@ class TripalTermViewsController extends EntityDefaultViewsController {
 
     $data['tripal_term']['name']['title'] = 'Content Type';
     $data['tripal_term']['name']['help'] = t('The name of a Tripal content type.');
-    $data['tripal_term']['name']['filter']['handler'] = 'tripal_views_handler_filter_select_string';
+    $data['tripal_term']['name']['filter']['handler'] = 'tripal_views_handler_filter_string_selectbox';
 
     $data['tripal_term']['vocab_id']['title'] = t('Vocabulary ID');
     $data['tripal_term']['vocab_id']['help'] = t('The internal numeric ID for the vocabulary to which the content type term belongs.');

tripal/tripal.info

@@ -9,7 +9,7 @@ configure = admin/tripal
 stylesheets[all][] = theme/css/tripal.css
 scripts[]          = theme/js/tripal.js
 
-files[] = views_handlers/tripal_views_handler_filter_select_string.inc
+files[] = views_handlers/tripal_views_handler_filter_string_selectbox.inc
 files[] = views_handlers/tripal_views_handler_field_entity.inc
 files[] = views_handlers/tripal_views_handler_field_entity_status.inc
 

tripal/tripal.views.inc

@@ -279,59 +279,4 @@ function tripal_views_data_jobs($data) {
   );
 
   return $data;
-}
-
-
-/**
- * Implements hook_views_handlers().
- *
- * Purpose: Register all custom handlers with views
- *   where a handler describes either "the type of field",
- *   "how a field should be filtered", "how a field should be sorted"
- *
- * @return
- *   An array of handler definitions
- *
- * @ingroup tripal_views
- */
-function tripal_views_views_handlers() {
-
-  return array(
-    'info' => array(
-      'path' => drupal_get_path('module', 'tripal') . '/views_handlers',
-    ),
-    'handlers' => array(
-//       // Custom area handler
-//       'tripal_views_handler_area_action_links' => array(
-//         'parent' => 'views_handler_area',
-//       ),
-
-      // Custom Tripal Filter Handlers
-//       'tripal_views_handler_filter_no_results' => array(
-//         'parent' => 'views_handler_filter'
-//       ),
-//       'tripal_views_handler_filter_select_cvterm' => array(
-//         'parent' => 'tripal_views_handler_filter_select_string',
-//       ),
-//       'tripal_views_handler_filter_select_id' => array(
-//         'parent' => 'tripal_views_handler_filter_select_string',
-//       ),
-      'tripal_views_handler_filter_select_string' => array(
-        'parent' => 'views_handler_filter_string',
-      ),
-      'tripal_views_handler_field_entity' => array(
-        'parent' => 'tripal_views_handler_field_entity',
-      ),
-      'tripal_views_handler_field_entity_status' => array(
-        'parent' => 'tripal_views_handler_field_entity_status',
-      ),
-//       'tripal_views_handler_filter_textarea' => array(
-//         'parent' => 'views_handler_filter',
-//       ),
-//       'tripal_views_handler_filter_file_upload' => array(
-//         'parent' => 'views_handler_filter',
-//       ),
-
-    ),
-  );
 }

tripal/views_handlers/tripal_views_handler_filter_select_string.inc

@@ -1,7 +1,7 @@
 <?php
 /**
  * @file
-* Contains tripal_views_handler_filter_select_string Filter Handler
+* Contains tripal_views_handler_filter_string_selectbox Filter Handler
 */
 
 /**
@@ -10,7 +10,7 @@
 *
 * @ingroup tripal_views
 */
-class tripal_views_handler_filter_select_string extends views_handler_filter_string {
+class tripal_views_handler_filter_string_selectbox extends views_handler_filter_string {
 
   /**
    * {@inheritdoc}

tripal_chado/includes/fields/chado_feature__md5checksum.inc

@@ -127,7 +127,7 @@ class chado_feature__md5checksum  extends TripalField {
 
     $field_name = $field['field_name'];
     if ($record and property_exists($record, 'md5checksum')) {
-      $entity->{$field_name}['und'][] = array('value' => $record->md5checksum);
+      $entity->{$field_name}['und'][0]['value'] = $record->md5checksum;
     }
   }
 }

tripal_chado/includes/fields/chado_linker__featureloc.inc

@@ -56,10 +56,10 @@ class chado_linker__featureloc extends TripalField {
         'chado_column' => $pkey,
         'base_table' => 'feature',
         'semantic_web' => array(
-          'name' => '',
-          'accession' => '',
-          'ns' => '',
-          'nsurl' => '',
+          'name' => 'position_of',
+          'accession' => 'position_of',
+          'ns' => 'SO',
+          'nsurl' => 'http://www.sequenceontology.org/',
         ),
       ),
     );

tripal_chado/includes/tripal_chado.field_storage.inc

@@ -406,4 +406,12 @@ function tripal_chado_field_storage_unnest_fields($fields, $entity_type, $entity
  * NOTE: This function needs to exist or errors are triggered but so far it doesn't
  * appear to actually need to do anything...
  */
-function tripal_chado_field_storage_query($query) { }
+function tripal_chado_field_storage_query($query) {
+  dpm($query);
+  $fieldConditions = $query->fieldConditions;
+  foreach ($fieldConditions as $condition) {
+    $field = $condition['field'];
+    $field_name = $field['field_name'];
+    $column = $condition['column'];
+  }
+}