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@@ -1,110 +1,20 @@
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<?php
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-// http://www.bluespark.com/blog/drupal-entities-part-3-programming-hello-drupal-entity
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-// http://dikini.net/31.08.2010/entities_bundles_fields_and_field_instances
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-/**
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- * Implement hook_entity_info().
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- */
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-function tripal_entities_entity_info() {
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- $entities = array();
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-
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- $entities['chado_data'] = array(
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- // A human readable label to identify our entity.
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- 'label' => t('Chado Data'),
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- 'plural label' => t('Vocabulary Terms'),
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-
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- // The controller for our Entity, extending the Drupal core controller.
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- 'controller class' => 'ChadoDataController',
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-
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- // The table for this entity defined in hook_schema()
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- 'base table' => 'chado_data',
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-
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- // Returns the uri elements of an entity.
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- 'uri callback' => 'tripal_entities_vocbulary_term_uri',
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-
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- // IF fieldable == FALSE, we can't attach fields.
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- 'fieldable' => TRUE,
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-
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- // entity_keys tells the controller what database fields are used for key
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- // functions. It is not required if we don't have bundles or revisions.
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- // Here we do not support a revision, so that entity key is omitted.
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- 'entity keys' => array(
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- 'id' => 'entity_id',
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- 'bundle' => 'type',
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- ),
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- 'bundle keys' => array(
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- 'bundle' => 'type',
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- ),
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-
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- // FALSE disables caching. Caching functionality is handled by Drupal core.
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- 'static cache' => FALSE,
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-
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- // Bundles are defined by the model types below
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- 'bundles' => array(),
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- );
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-
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- // Bundles are alternative groups of fields or configuration
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- // associated with a base entity type.
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- // We want to dynamically add the bundles (or term types) to the entity.
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- $values = array(
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- 'cv_id' => array(
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- 'name' => 'sequence'
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- ),
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- 'name' => 'gene',
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- );
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- $cvterm = chado_generate_var('cvterm', $values);
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- $label = preg_replace('/_/', ' ', ucwords($cvterm->name));
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- $bundle_id = $cvterm->dbxref_id->db_id->name . '_' . $cvterm->dbxref_id->accession;
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- $entities['trp_vocabulary_term']['bundles'][$bundle_id] = array(
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- 'label' => $label,
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- 'admin' => array(
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- 'path' => 'admin/structure/chado_data/manage',
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- 'access arguments' => array('administer chado_data entities'),
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- ),
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- 'entity keys' => array(
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- 'id' => 'entity_id',
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- 'bundle' => 'bundle',
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- ),
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- );
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- return $entities;
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-}
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-/**
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- * Fetch a basic object.
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- *
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- * This function ends up being a shim between the menu system and
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- * chado_data_load_multiple().
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- *
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- * @param int $entity_id
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- * Integer specifying the basic entity id.
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- * @param bool $reset
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- * A boolean indicating that the internal cache should be reset.
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- *
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- * @return object
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- * A fully-loaded $chado_data object or FALSE if it cannot be loaded.
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- *
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- */
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-function chado_data_load($entity_id = NULL, $reset = FALSE) {
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- $entity_ids = (isset($entity_id) ? array($entity_id) : array());
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- $basic = chado_data_load_multiple($entity_ids, array(), $reset);
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- return $basic ? reset($basic) : FALSE;
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-}
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-
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-/**
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- * Loads multiple basic entities.
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- *
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- * We only need to pass this request along to entity_load(), which
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- * will in turn call the load() method of our entity controller class.
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- */
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-function chado_data_load_multiple($entity_ids = array(), $conditions = array(), $reset = FALSE){
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- return entity_load('chado_data', $entity_ids, $conditions, $reset);
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-}
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+require_once "includes/tripal_entities.field_storage.inc";
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+require_once "includes/tripal_entities.fields.inc";
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+require_once "includes/ChadoData.inc";
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+require_once "includes/ChadoDataController.inc";
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+require_once "includes/ChadoDataUIController.inc";
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+require_once "includes/ChadoDataType.inc";
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+require_once "includes/ChadoDataTypeController.inc";
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+require_once "includes/ChadoDataTypeUIController.inc";
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/**
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* Implements hook_menu().
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*/
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function tripal_entities_menu() {
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- // This provides a place for Field API to hang its own
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+/* // This provides a place for Field API to hang its own
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// interface and has to be the same as what was defined
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// in basic_entity_info() above.
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$items['admin/structure/chado_data/manage'] = array(
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@@ -125,768 +35,86 @@ function tripal_entities_menu() {
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$items['admin/structure/chado_data/manage/list'] = array(
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'title' => 'List',
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'type' => MENU_DEFAULT_LOCAL_TASK,
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- );
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+ ); */
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// The page to view our entities - needs to follow what
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// is defined in basic_uri and will use load_basic to retrieve
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// the necessary entity info.
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- $items['chado_data/%chado_data'] = array(
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- 'title callback' => 'chado_data_title',
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- 'title arguments' => array(1),
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- 'page callback' => 'chado_data_view',
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- 'page arguments' => array(1),
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- 'access arguments' => array('view chado_data'),
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- 'type' => MENU_CALLBACK,
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- );
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- // 'View' tab for an individual entity page.
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- $items['chado_data/%chado_data/view'] = array(
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- 'title' => 'View',
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- 'type' => MENU_DEFAULT_LOCAL_TASK,
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- 'weight' => -10,
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- );
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+// $items['chado_data/%chado_data'] = array(
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+// 'title callback' => 'chado_data_title',
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+// 'title arguments' => array(1),
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+// 'page callback' => 'chado_data_view',
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+// 'page arguments' => array(1),
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+// 'access arguments' => array('view chado_data'),
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+// 'type' => MENU_CALLBACK,
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+// );
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- // 'Edit' tab for an individual entity page.
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- $items['chado_data/%chado_data/edit'] = array(
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- 'title' => 'Edit',
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('chado_data_form', 1),
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- 'access arguments' => array('edit any chado_data entity'),
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- 'type' => MENU_LOCAL_TASK,
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- );
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+// // 'View' tab for an individual entity page.
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+// $items['chado_data/%chado_data/view'] = array(
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+// 'title' => 'View',
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+// 'type' => MENU_DEFAULT_LOCAL_TASK,
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+// 'weight' => -10,
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+// );
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+
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+// // 'Edit' tab for an individual entity page.
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+// $items['chado_data/%chado_data/edit'] = array(
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+// 'title' => 'Edit',
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+// 'page callback' => 'drupal_get_form',
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+// 'page arguments' => array('chado_data_form', 1),
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+// 'access arguments' => array('edit any chado_data entity'),
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+// 'type' => MENU_LOCAL_TASK,
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+// );
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- // Add example entities.
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- $items['examples/entity_example/basic/add'] = array(
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- 'title' => 'Add Chado Data',
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- 'page callback' => 'drupal_get_form',
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- 'page arguments' => array('chado_data_form'),
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- 'access arguments' => array('create chado_data entities'),
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- );
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return $items;
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}
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-/**
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- * We save the entity by calling the controller.
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- */
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-function chado_data_save(&$entity) {
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- return entity_get_controller('chado_data')->save($entity);
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-}
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-/**
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- * Use the controller to delete the entity.
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- */
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-function chado_data_delete($entity) {
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- entity_get_controller('chado_data')->delete($entity);
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-}
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/**
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* Implements hook_permission().
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*/
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function tripal_entities_permission() {
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+ // We set up permisssions to manage entity types, manage all entities and the
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+ // permissions for each individual entity
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$permissions = array(
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- 'administer chado_data entities' => array(
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- 'title' => t('Administer Chado data entity'),
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- ),
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- 'view any chado_data entity' => array(
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- 'title' => t('View any Chado data entity'),
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- ),
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- 'edit any chado_data entity' => array(
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- 'title' => t('Edit any Chado data entity'),
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+ 'administer chado data types' => array(
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+ 'title' => t('Administer Chado data types'),
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+ 'description' => t('Create and delete fields for Chado data types, and set their permissions.'),
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),
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- 'create chado_data entities' => array(
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- 'title' => t('Create Chado data entities'),
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+ 'administer chado data' => array(
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+ 'title' => t('Administer Chado data'),
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+ 'description' => t('Edit and delete all chado data'),
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),
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);
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- return $permissions;
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-}
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-/**
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- * Returns a render array with all chado_data entities.
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- *
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- * @see pager_example.module
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- */
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-function tripal_entities_list_entities() {
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- $content = array();
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- // Load all of our entities.
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- $entities = chado_data_load_multiple();
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- if (!empty($entities)) {
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- foreach ($entities as $entity) {
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- // Create tabular rows for our entities.
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- $rows[] = array(
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- 'data' => array(
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- 'id' => $entity->entity_id,
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- 'title' => l($entity->title, 'chado_data/' . $entity->entity_id),
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- 'type' => $entity->type,
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- ),
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- );
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- }
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- // Put our entities into a themed table. See theme_table() for details.
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- $content['entity_table'] = array(
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- '#theme' => 'table',
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- '#rows' => $rows,
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- '#header' => array(t('ID'), t('Item Description'), t('Bundle')),
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- );
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- }
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- else {
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- // There were no entities. Tell the user.
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- $content[] = array(
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- '#type' => 'item',
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- '#markup' => t('No chado data entities currently exist.'),
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- );
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- }
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- return $content;
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-}
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-
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-/**
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- *
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- */
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-function chado_data_title($entity){
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- return $entity->title;
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-}
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-
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-/**
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- * Implements the uri callback.
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- */
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-function chado_data_uri($entity) {
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- return array(
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- 'path' => 'chado_data/' . $entity->entity_id,
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- );
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-}
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-
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-/**
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- * Menu callback to display an entity.
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- *
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- * As we load the entity for display, we're responsible for invoking a number
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- * of hooks in their proper order.
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- *
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- * @see hook_entity_prepare_view()
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- * @see hook_entity_view()
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- * @see hook_entity_view_alter()
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- */
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-function chado_data_view($entity, $view_mode = 'full') {
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-
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- // Our entity type, for convenience.
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- $entity_type = 'chado_data';
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-
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- // Start setting up the content.
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- $entity->content = array(
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- '#view_mode' => $view_mode,
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- );
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-
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- // Build fields content - this is where the Field API really comes in to play.
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- // The task has very little code here because it all gets taken care of by
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- // field module. field_attach_prepare_view() lets the fields load any
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- // data they need before viewing.
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- field_attach_prepare_view($entity_type, array($entity->entity_id => $entity),
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- $view_mode);
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-
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- // We call entity_prepare_view() so it can invoke hook_entity_prepare_view()
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- // for us.
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- entity_prepare_view($entity_type, array($entity->entity_id => $entity));
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-
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- // Now field_attach_view() generates the content for the fields.
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- $entity->content += field_attach_view($entity_type, $entity, $view_mode);
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-
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- // OK, Field API done, now we can set up some of our own data.
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-// $entity->content['created'] = array(
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-// '#type' => 'item',
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-// '#title' => t('Created date'),
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-// '#markup' => format_date($entity->created),
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-// );
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-
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- // Now to invoke some hooks. We need the language code for
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- // hook_entity_view(), so let's get that.
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- global $language;
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- $langcode = $language->language;
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-
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- // And now invoke hook_entity_view().
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- module_invoke_all('entity_view', $entity, $entity_type, $view_mode, $langcode);
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-
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- // Now invoke hook_entity_view_alter().
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- drupal_alter(array('chado_data', 'entity_view'), $entity->content, $entity_type);
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-
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-
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- // And finally return the content.
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- return $entity->content;
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-}
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-
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-/**
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- *
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- */
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-function chado_data_page_view($entity, $view_mode = 'full'){
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- $entity->content = array();
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-
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- // Build fields content.
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- field_attach_prepare_view('chado_data', array($entity->entity_id => $entity), $view_mode);
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- entity_prepare_view('chado_data', array($entity->entity_id => $entity));
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- $entity->content += field_attach_view('chado_data', $entity, $view_mode);
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-
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- return $entity->content;
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-}
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-
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-/**
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- *
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- */
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-function tripal_entities_vocbulary_term_uri($entity) {
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- return array(
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- 'path' => 'chado_data/' . $entity->entity_id,
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- );
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-}
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-
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-/**
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- *
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- */
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-function chado_data_form($form, &$form_state, $entity = NULL) {
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-
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- // Set the defaults.
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- $cv_id = NULL;
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- $term_name = NULL;
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- $entity_id = NULL;
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- $cvterm = NULL;
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-
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- // Set defaults if an entity was provided.
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- if ($entity) {
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- $entity_id = $entity->entity_id;
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- $values = array('cvterm_id' => $entity->cvterm_id);
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- $cvterm = chado_generate_var('cvterm', $values);
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- $cv_id = $cvterm->cv_id->cv_id;
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- $term_name = $cvterm->name;
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- }
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-
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- // Set defaults using the form state.
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- if (array_key_exists('values', $form_state)) {
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- $cv_id = array_key_exists('cv_id', $form_state['values']) ? $form_state['values']['cv_id'] : NULL;
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- $term_name = array_key_exists('term_name', $form_state['values']) ? $form_state['values']['term_name'] : NULL;
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- // Get the cvterm that matches
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- $values = array(
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- 'cv_id' => $cv_id,
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- 'name' => $term_name
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- );
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- $cvterm = chado_generate_var('cvterm', $values);
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- }
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-
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- // Add in the IDs for the entity.
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- if ($entity) {
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- $form['entity_id'] = array(
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- '#type' => 'hidden',
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- '#value' => $entity_id,
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- );
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- $form['entity'] = array(
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- '#type' => 'value',
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|
- '#value' => $entity,
|
|
|
- );
|
|
|
- $form['record_id'] = array(
|
|
|
- '#type' => 'hidden',
|
|
|
- '#value' => $entity->record_id,
|
|
|
- );
|
|
|
- }
|
|
|
-
|
|
|
- // Let the user select the vocabulary and chado_data but only if they haven't
|
|
|
- // already selected a chado_data.
|
|
|
- $cvs = tripal_get_cv_select_options();
|
|
|
- if (!$term_name) {
|
|
|
- $form['cv_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Vocabulary'),
|
|
|
- '#options' => $cvs,
|
|
|
- '#required' => TRUE,
|
|
|
- '#description' => t('Select a vocabulary that contains the term for the type of data you want to add.'),
|
|
|
- '#default_value' => $cv_id,
|
|
|
- '#ajax' => array(
|
|
|
- 'callback' => "chado_data_form_ajax_callback",
|
|
|
- 'wrapper' => 'chado_data_form',
|
|
|
- 'effect' => 'fade',
|
|
|
- 'method' => 'replace'
|
|
|
- )
|
|
|
- );
|
|
|
- }
|
|
|
-
|
|
|
- // If we have a CV ID then we want to provide an autocomplete field
|
|
|
- if ($cv_id and !$term_name) {
|
|
|
- $form['cvterm_select']['term_name'] = array(
|
|
|
- '#title' => t('Record Type'),
|
|
|
- '#type' => 'textfield',
|
|
|
- '#description' => t("Enter the name of a term within the selected vocabulary for the record type you want to enter."),
|
|
|
- '#required' => TRUE,
|
|
|
- '#default_value' => $term_name,
|
|
|
- '#autocomplete_path' => "admin/tripal/chado/tripal_cv/cvterm/auto_name/$cv_id",
|
|
|
- );
|
|
|
-
|
|
|
- $form['cvterm_select']['select_button'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => t('Use this term'),
|
|
|
- '#name' => 'select_cvterm',
|
|
|
- );
|
|
|
- }
|
|
|
-
|
|
|
- // Once the CV term is selected then provide the other fields.
|
|
|
- if ($cvterm) {
|
|
|
- $bundle_id = $cvterm->dbxref_id->db_id->name . '_' . $cvterm->dbxref_id->accession;
|
|
|
-
|
|
|
- $form['cv_id'] = array(
|
|
|
- '#type' => 'hidden',
|
|
|
- '#value' => $cv_id,
|
|
|
- );
|
|
|
- $form['term_name'] = array(
|
|
|
- '#type' => 'hidden',
|
|
|
- '#value' => $term_name,
|
|
|
- );
|
|
|
- $form['cvterm_id'] = array(
|
|
|
- '#type' => 'hidden',
|
|
|
- '#value' => $cvterm->cvterm_id,
|
|
|
- );
|
|
|
- $form['type'] = array(
|
|
|
- '#type' => 'hidden',
|
|
|
- '#value' => $bundle_id,
|
|
|
- );
|
|
|
- $form['details'] = array(
|
|
|
- '#type' => 'fieldset',
|
|
|
- '#title' => 'Record Type',
|
|
|
- '#collapsable' => FALSE,
|
|
|
- '#weight' => -100,
|
|
|
- );
|
|
|
- $form['details']['cv_name_shown'] = array(
|
|
|
- '#type' => 'item',
|
|
|
- '#title' => 'Vocabulary',
|
|
|
- '#markup' => $cvterm->cv_id->name,
|
|
|
- );
|
|
|
- $form['details']['term_name_shown'] = array(
|
|
|
- '#type' => 'item',
|
|
|
- '#title' => 'Term',
|
|
|
- '#markup' => $cvterm->name,
|
|
|
- );
|
|
|
-/*
|
|
|
-
|
|
|
- // Drupal field types and settings:
|
|
|
- // https://www.drupal.org/node/1879542
|
|
|
- $field = array(
|
|
|
- 'field_name' => 'feature__name',
|
|
|
- 'type' => 'text',
|
|
|
- 'cardinality' => 1,
|
|
|
- 'storage' => array(
|
|
|
- 'type' => 'tripal_entities_storage'
|
|
|
- ),
|
|
|
- );
|
|
|
- field_create_field($field);
|
|
|
- $field_instance = array(
|
|
|
- 'field_name' => 'feature__name',
|
|
|
- 'label' => 'Name',
|
|
|
- 'widget' => array(
|
|
|
- 'type' => 'text_textfield'
|
|
|
- ),
|
|
|
- 'entity_type' => 'chado_data',
|
|
|
- 'required' => 'true',
|
|
|
- 'settings' => array(
|
|
|
- 'max_length' => 255
|
|
|
- ),
|
|
|
- 'bundle' => $bundle_id,
|
|
|
- );
|
|
|
- field_create_instance($field_instance);
|
|
|
- $field = array(
|
|
|
- 'field_name' => 'feature__uniquename',
|
|
|
- 'type' => 'text',
|
|
|
- 'cardinality' => 1,
|
|
|
- 'storage' => array(
|
|
|
- 'type' => 'tripal_entities_storage'
|
|
|
- ),
|
|
|
- );
|
|
|
- field_create_field($field);
|
|
|
- $field_instance = array(
|
|
|
- 'field_name' => 'feature__uniquename',
|
|
|
- 'label' => 'Unique Name',
|
|
|
- 'widget' => array(
|
|
|
- 'type' => 'text_textfield'
|
|
|
+ // Generate permissions per each data type.
|
|
|
+ foreach (chado_data_get_types() as $type) {
|
|
|
+ $type_name = check_plain($type->type);
|
|
|
+ $permissions += array(
|
|
|
+ "edit any $type_name data" => array(
|
|
|
+ 'title' => t('%type_name: Edit any', array('%type_name' => $type->label)),
|
|
|
),
|
|
|
- 'entity_type' => 'chado_data',
|
|
|
- 'required' => 'true',
|
|
|
- 'settings' => array(
|
|
|
- 'max_length' => 255
|
|
|
+ "view any $type_name data" => array(
|
|
|
+ 'title' => t('%type_name: View any', array('%type_name' => $type->label)),
|
|
|
),
|
|
|
- 'bundle' => $bundle_id,
|
|
|
);
|
|
|
- field_create_instance($field_instance);
|
|
|
- $field = array(
|
|
|
- 'field_name' => 'feature__organism_id',
|
|
|
- 'type' => 'organism_id',
|
|
|
- 'cardinality' => 1,
|
|
|
- 'storage' => array(
|
|
|
- 'type' => 'tripal_entities_storage'
|
|
|
- ),
|
|
|
- );
|
|
|
- field_create_field($field);
|
|
|
- $field_instance = array(
|
|
|
- 'field_name' => 'feature__organism_id',
|
|
|
- 'label' => 'Organism',
|
|
|
- 'entity_type' => 'chado_data',
|
|
|
- 'required' => 'true',
|
|
|
- 'settings' => array(),
|
|
|
- 'bundle' => $bundle_id,
|
|
|
- );
|
|
|
- field_create_instance($field_instance);
|
|
|
- */
|
|
|
-
|
|
|
-
|
|
|
- // Create the object for this entity instance. The entity instance type
|
|
|
- // is always the name of the term.
|
|
|
- if (!$entity) {
|
|
|
- $entity = new stdClass();
|
|
|
- $entity->entity_id = NULL;
|
|
|
- $entity->type = $bundle_id;
|
|
|
- }
|
|
|
- $form['#parents'] = array('attached');
|
|
|
- field_attach_form('chado_data', $entity, $form, $form_state);
|
|
|
-
|
|
|
- if (!$entity_id) {
|
|
|
- $form['submit'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => t('Add a new ' . $cvterm->name),
|
|
|
- '#name' => 'add_data',
|
|
|
- '#weight' => 1000
|
|
|
- );
|
|
|
- }
|
|
|
- else {
|
|
|
- $form['submit'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => t('Update'),
|
|
|
- '#name' => 'update_data',
|
|
|
- '#weight' => 1000
|
|
|
- );
|
|
|
- }
|
|
|
- }
|
|
|
- $form['cancel'] = array(
|
|
|
- '#type' => 'submit',
|
|
|
- '#value' => t('Cancel'),
|
|
|
- '#name' => 'cancel',
|
|
|
- '#weight' => 1000
|
|
|
- );
|
|
|
- $form['#prefix'] = '<div id="chado_data_form">';
|
|
|
- $form['#suffix'] = '</div>';
|
|
|
- return $form;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_field_info().
|
|
|
- */
|
|
|
-function tripal_entities_field_info() {
|
|
|
- $fields = array(
|
|
|
- 'organism_id' => array(
|
|
|
- 'label' => t('Organism'),
|
|
|
- 'description' => t('A field for specifying an organism.'),
|
|
|
- 'default_widget' => 'tripal_entities_organism_select_widget',
|
|
|
- 'default_formatter' => 'tripal_entities_organism_formatter',
|
|
|
- 'settings' => array(),
|
|
|
- 'storage' => array(
|
|
|
- 'type' => 'tripal_entities_storage',
|
|
|
- 'module' => 'tripal_entities',
|
|
|
- 'active' => TRUE
|
|
|
- ),
|
|
|
- ),
|
|
|
- );
|
|
|
- return $fields;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_field_widget_info().
|
|
|
- */
|
|
|
-function tripal_entities_field_widget_info() {
|
|
|
- return array(
|
|
|
- 'tripal_entities_organism_select_widget' => array(
|
|
|
- 'label' => t('Organism Select'),
|
|
|
- 'field types' => array('organism_id')
|
|
|
- ),
|
|
|
- );
|
|
|
-}
|
|
|
-/**
|
|
|
- * Implements hook_field_formatter_info().
|
|
|
- */
|
|
|
-function tripal_entities_field_formatter_info() {
|
|
|
- return array(
|
|
|
- 'tripal_entities_organism_formatter' => array(
|
|
|
- 'label' => t('Organism'),
|
|
|
- 'field types' => array('organism_id')
|
|
|
- ),
|
|
|
- );
|
|
|
-}
|
|
|
-/**
|
|
|
- * Implements hook_field_formatter_view().
|
|
|
- *
|
|
|
- * Two formatters are implemented.
|
|
|
- * - field_example_simple_text just outputs markup indicating the color that
|
|
|
- * was entered and uses an inline style to set the text color to that value.
|
|
|
- * - field_example_color_background does the same but also changes the
|
|
|
- * background color of div.region-content.
|
|
|
- *
|
|
|
- * @see field_example_field_formatter_info()
|
|
|
- */
|
|
|
-function tripal_entities_field_formatter_view($entity_type, $entity, $field, $instance, $langcode, $items, $display) {
|
|
|
- $element = array();
|
|
|
-
|
|
|
- switch ($display['type']) {
|
|
|
- // This formatter simply outputs the field as text and with a color.
|
|
|
- case 'tripal_entities_organism_formatter':
|
|
|
- foreach ($items as $delta => $item) {
|
|
|
- $organism = chado_select_record('organism', array('genus', 'species'), array('organism_id' => $item['value']));
|
|
|
- $element[$delta] = array(
|
|
|
- // We create a render array to produce the desired markup,
|
|
|
- // "<p>Genus Species</p>".
|
|
|
- // See theme_html_tag().
|
|
|
- '#type' => 'html_tag',
|
|
|
- '#tag' => 'p',
|
|
|
- '#value' => '<i>' . $organism[0]->genus .' ' . $organism[0]->species . '</i>',
|
|
|
- );
|
|
|
- }
|
|
|
- break;
|
|
|
-
|
|
|
- }
|
|
|
-
|
|
|
- return $element;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_field_widget_form().
|
|
|
- */
|
|
|
-function tripal_entities_field_widget_form(&$form, &$form_state, $field,
|
|
|
- $instance, $langcode, $items, $delta, $element) {
|
|
|
-
|
|
|
- $widget = $element;
|
|
|
- $widget['#delta'] = $delta;
|
|
|
-
|
|
|
- switch ($instance['widget']['type']) {
|
|
|
- case 'tripal_entities_organism_select_widget':
|
|
|
- $options = tripal_get_organism_select_options();
|
|
|
- $widget += array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => $element['#title'],
|
|
|
- '#description' => $element['#description'],
|
|
|
- '#options' => $options,
|
|
|
- '#default_value' => $items[0]['value'],
|
|
|
- '#required' => $element['#required'],
|
|
|
- '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
|
|
|
- '#delta' => $delta,
|
|
|
- '#element_validate' => array('tripal_entities_organism_select_widget_validate'),
|
|
|
- );
|
|
|
- $element['value'] = $widget;
|
|
|
- break;
|
|
|
- }
|
|
|
- return $element;
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Callback function for validating the tripal_entities_organism_select_widget.
|
|
|
- */
|
|
|
-function tripal_entities_organism_select_widget_validate($element, &$form_state) {
|
|
|
-
|
|
|
- $field_name = $element['#field_name'];
|
|
|
- // Make sure we have a valid organism
|
|
|
- foreach ($form_state['values'][$field_name] as $langcode => $items) {
|
|
|
- foreach ($items as $delta => $value) {
|
|
|
- $organism_id = chado_select_record('organism', array('organism_id'),
|
|
|
- array('organism_id' => $value['value']), array('has_record' => TRUE));
|
|
|
- if (!$organism_id) {
|
|
|
- form_error($element, t("Please specify an organism that already exists in the database."));
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_field_is_empty().
|
|
|
- */
|
|
|
-function tripal_entities_field_is_empty($item, $field) {
|
|
|
- if (empty($item['tripal_entities_organism_select_widget'])) {
|
|
|
- return TRUE;
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_field_storage_info().
|
|
|
- */
|
|
|
-function tripal_entities_field_storage_info() {
|
|
|
- return array(
|
|
|
- 'tripal_entities_storage' => array(
|
|
|
- 'label' => t('Chado storage'),
|
|
|
- 'description' => t('Stores fields in the local Chado database.'),
|
|
|
- 'settings' => array(),
|
|
|
- ),
|
|
|
- );
|
|
|
-}
|
|
|
-
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_field_storage_write().
|
|
|
- */
|
|
|
-function tripal_entities_field_storage_write($entity_type, $entity, $op, $fields) {
|
|
|
-
|
|
|
- // Get the IDs for this entity.
|
|
|
- list($id, $vid, $bundle) = entity_extract_ids($entity_type, $entity);
|
|
|
-
|
|
|
- // Find out which table should receive the insert.
|
|
|
- $tablename = 'feature';
|
|
|
- $type_field = 'type_id';
|
|
|
- $schema = chado_get_schema($tablename);
|
|
|
- $pkey_field = $schema['primary key'][0];
|
|
|
-
|
|
|
- // Construct the values array that will be used to insert into the table.
|
|
|
- $values = array();
|
|
|
- foreach ($fields as $field_id) {
|
|
|
- $field = field_info_field_by_id($field_id);
|
|
|
- $field_name = $field['field_name'];
|
|
|
-
|
|
|
- $matches = array();
|
|
|
- if (preg_match('/^' . $tablename . '__(.*)/', $field_name, $matches)) {
|
|
|
- $chado_field = $matches[1];
|
|
|
- // Currently, we only support one language, but for for the sake of
|
|
|
- // thoroughness we'll iterate through all possible languages.
|
|
|
- $all_languages = field_available_languages($entity_type, $field);
|
|
|
- $field_languages = array_intersect($all_languages, array_keys((array) $entity->$field_name));
|
|
|
- foreach ($field_languages as $langcode) {
|
|
|
- $items = (array) $entity->{$field_name}[$langcode];
|
|
|
- // The number of items is related to the cardinatily of the field.
|
|
|
- foreach ($items as $delta => $item) {
|
|
|
- $values[$chado_field] = $item['value'];
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
- // Add in the type_id field.
|
|
|
- $values[$type_field] = $entity->cvterm_id;
|
|
|
-
|
|
|
- switch ($op) {
|
|
|
- case FIELD_STORAGE_INSERT:
|
|
|
- $record = chado_insert_record($tablename, $values);
|
|
|
- if ($record === FALSE) {
|
|
|
- drupal_set_message('Could not insert Chado record.', 'error');
|
|
|
- }
|
|
|
- $entity->record_id = $record[$pkey_field];
|
|
|
- break;
|
|
|
- case FIELD_STORAGE_UPDATE:
|
|
|
- $match[$pkey_field] = $entity->record_id;
|
|
|
- chado_update_record($tablename, $match, $values);
|
|
|
- break;
|
|
|
- }
|
|
|
-}
|
|
|
-/**
|
|
|
- * Implements hook_field_storage_load().
|
|
|
- *
|
|
|
- * Responsible for loading the fields from the Chado database and adding
|
|
|
- * their values to the entity.
|
|
|
- */
|
|
|
-function tripal_entities_field_storage_load($entity_type, $entities, $age, $fields, $options) {
|
|
|
- $load_current = $age == FIELD_LOAD_CURRENT;
|
|
|
-
|
|
|
- global $language;
|
|
|
- $langcode = $language->language;
|
|
|
-
|
|
|
- foreach ($entities as $entity_id => $entity) {
|
|
|
- // Find out which table should receive the insert.
|
|
|
- $tablename = 'feature';
|
|
|
- $type_field = 'type_id';
|
|
|
- $schema = chado_get_schema($tablename);
|
|
|
- $pkey_field = $schema['primary key'][0];
|
|
|
- $record_id = $entity->record_id;
|
|
|
-
|
|
|
- // Iterate through the field names to get the list of tables and fields
|
|
|
- // that should be queried.
|
|
|
- $columns = array();
|
|
|
- foreach ($fields as $field_id => $ids) {
|
|
|
- // By the time this hook runs, the relevant field definitions have been
|
|
|
- // populated and cached in FieldInfo, so calling field_info_field_by_id()
|
|
|
- // on each field individually is more efficient than loading all fields in
|
|
|
- // memory upfront with field_info_field_by_ids().
|
|
|
- $field = field_info_field_by_id($field_id);
|
|
|
- $field_name = $field['field_name'];
|
|
|
-
|
|
|
- $matches = array();
|
|
|
- if (preg_match('/^(.*?)__(.*?)$/', $field_name, $matches)) {
|
|
|
- $table = $matches[1];
|
|
|
- $field = $matches[2];
|
|
|
- $columns[$table][] = $field;
|
|
|
- }
|
|
|
- }
|
|
|
-
|
|
|
- // Get the record
|
|
|
- $record = chado_select_record($tablename, $columns[$tablename], array($pkey_field => $entity->record_id));
|
|
|
-
|
|
|
- // Now set the field values
|
|
|
- foreach ($fields as $field_id => $ids) {
|
|
|
- $field = field_info_field_by_id($field_id);
|
|
|
- $field_name = $field['field_name'];
|
|
|
- $matches = array();
|
|
|
- if (preg_match('/^(.*?)__(.*?)$/', $field_name, $matches)) {
|
|
|
- $table = $matches[1];
|
|
|
- $field = $matches[2];
|
|
|
- $entity->{$field_name}['und'][] = array('value' => $record[0]->$field);
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * An Ajax callback for the chado_data_form.
|
|
|
- */
|
|
|
-function chado_data_form_ajax_callback($form, $form_state) {
|
|
|
- // return the form so Drupal can update the content on the page
|
|
|
- return $form;
|
|
|
-
|
|
|
-}
|
|
|
-/**
|
|
|
- * Implements hook_validate() for the chado_data_form.
|
|
|
- */
|
|
|
-function chado_data_form_validate($form, &$form_state) {
|
|
|
-
|
|
|
- if ($form_state['clicked_button']['#name'] == 'add_data') {
|
|
|
- $chado_data = (object) $form_state['values'];
|
|
|
- field_attach_form_validate('chado_data', $chado_data, $form, $form_state);
|
|
|
- }
|
|
|
-}
|
|
|
-
|
|
|
-/**
|
|
|
- * Implements hook_submit() for the chado_data_form.
|
|
|
- *
|
|
|
- */
|
|
|
-function chado_data_form_submit($form, &$form_state) {
|
|
|
- if ($form_state['clicked_button']['#name'] == 'cancel') {
|
|
|
- if (array_key_exists('entity_id', $form_state['values'])){
|
|
|
- $entity = $form_state['values']['entity'];
|
|
|
- $form_state['redirect'] = "chado_data/$entity->entity_id";
|
|
|
- }
|
|
|
- else {
|
|
|
- $form_state['redirect'] = "admin/structure/chado_data/manage";
|
|
|
- }
|
|
|
- return;
|
|
|
- }
|
|
|
- if ($form_state['clicked_button']['#name'] == 'select_cvterm') {
|
|
|
- // don't do anything, we just need to know what the term name is.
|
|
|
- $form_state['rebuild'] = TRUE;
|
|
|
- }
|
|
|
- else {
|
|
|
- // Build and entity instance object.
|
|
|
- $entity = (object) $form_state['values'];
|
|
|
-
|
|
|
- // This is an update if the entity_id is in the form_state.
|
|
|
- if (array_key_exists('entity_id', $form_state['values'])) {
|
|
|
- $entity->entity_id = $form_state['values']['entity_id'];
|
|
|
- field_attach_update('chado_data', $entity);
|
|
|
- }
|
|
|
- else {
|
|
|
- field_attach_insert('chado_data', $entity);
|
|
|
- }
|
|
|
-
|
|
|
- // Now save the entity
|
|
|
- $entity = chado_data_save($entity);
|
|
|
-
|
|
|
- $form_state['redirect'] = "chado_data/$entity->entity_id";
|
|
|
}
|
|
|
+ return $permissions;
|
|
|
}
|
|
|
|
|
|
-
|
|
|
/**
|
|
|
* Implements hook_theme().
|
|
|
*/
|
|
|
function tripal_entities_theme($existing, $type, $theme, $path) {
|
|
|
return array(
|
|
|
-
|
|
|
+ 'chado_data_add_list' => array(
|
|
|
+ 'variables' => array('content' => array()),
|
|
|
+ ),
|
|
|
+ 'chado_data' => array(
|
|
|
+ 'render element' => 'elements',
|
|
|
+ 'template' => 'chado_data',
|
|
|
+ ),
|
|
|
);
|
|
|
}
|
|
|
|
|
|
@@ -921,157 +149,149 @@ function tripal_entities_rdf_mapping() {
|
|
|
); */
|
|
|
}
|
|
|
|
|
|
+// http://www.bluespark.com/blog/drupal-entities-part-3-programming-hello-drupal-entity
|
|
|
+// http://dikini.net/31.08.2010/entities_bundles_fields_and_field_instances
|
|
|
/**
|
|
|
- * ChadoDataControllerInterface definition.
|
|
|
- *
|
|
|
- * We create an interface here because anyone could come along and
|
|
|
- * use hook_entity_info_alter() to change our controller class.
|
|
|
- * We want to let them know what methods our class needs in order
|
|
|
- * to function with the rest of the module, so here's a handy list.
|
|
|
- *
|
|
|
- * @see hook_entity_info_alter()
|
|
|
+ * Implement hook_entity_info().
|
|
|
*/
|
|
|
-interface ChadoDataControllerInterface
|
|
|
-extends DrupalEntityControllerInterface {
|
|
|
+function tripal_entities_entity_info() {
|
|
|
+ $entities = array();
|
|
|
|
|
|
- /**
|
|
|
- * Create an entity.
|
|
|
- */
|
|
|
- public function create();
|
|
|
+ $entities['chado_data'] = array(
|
|
|
+ // A human readable label to identify our entity.
|
|
|
+ 'label' => t('Chado Data'),
|
|
|
+ 'plural label' => t('Vocabulary Terms'),
|
|
|
|
|
|
- /**
|
|
|
- * Save an entity.
|
|
|
- *
|
|
|
- * @param object $entity
|
|
|
- * The entity to save.
|
|
|
- */
|
|
|
- public function save($entity);
|
|
|
+ // The entity class and controller class extend the classes provided by the
|
|
|
+ // Entity API.
|
|
|
+ 'entity class' => 'ChadoData',
|
|
|
+ 'controller class' => 'ChadoDataController',
|
|
|
|
|
|
- /**
|
|
|
- * Delete an entity.
|
|
|
- *
|
|
|
- * @param object $entity
|
|
|
- * The entity to delete.
|
|
|
- */
|
|
|
- public function delete($entity);
|
|
|
+ // The table for this entity defined in hook_schema()
|
|
|
+ 'base table' => 'chado_data',
|
|
|
|
|
|
-}
|
|
|
+ // Returns the uri elements of an entity.
|
|
|
+ 'uri callback' => 'tripal_entities_vocbulary_term_uri',
|
|
|
|
|
|
-/**
|
|
|
- * ChadoDataController extends DrupalDefaultEntityController.
|
|
|
- *
|
|
|
- * Our subclass of DrupalDefaultEntityController lets us add a few
|
|
|
- * important create, update, and delete methods.
|
|
|
- */
|
|
|
-class ChadoDataController
|
|
|
- extends DrupalDefaultEntityController
|
|
|
- implements ChadoDataControllerInterface {
|
|
|
+ // IF fieldable == FALSE, we can't attach fields.
|
|
|
+ 'fieldable' => TRUE,
|
|
|
|
|
|
- /**
|
|
|
- * Create and return a new tripal_entities entity.
|
|
|
- */
|
|
|
- public function create() {
|
|
|
- $entity = new stdClass();
|
|
|
- $entity->type = 'chado_data';
|
|
|
- $entity->entity_id = 0;
|
|
|
- return $entity;
|
|
|
- }
|
|
|
+ // entity_keys tells the controller what database fields are used for key
|
|
|
+ // functions. It is not required if we don't have bundles or revisions.
|
|
|
+ // Here we do not support a revision, so that entity key is omitted.
|
|
|
+ 'entity keys' => array(
|
|
|
+ 'id' => 'entity_id',
|
|
|
+ 'bundle' => 'type',
|
|
|
+ ),
|
|
|
+ 'bundle keys' => array(
|
|
|
+ 'bundle' => 'type',
|
|
|
+ ),
|
|
|
|
|
|
- /**
|
|
|
- * Delete a single entity.
|
|
|
- *
|
|
|
- * Really a convenience function for deleteMultiple().
|
|
|
- */
|
|
|
- public function delete($entity) {
|
|
|
- $this->deleteMultiple(array($entity));
|
|
|
- }
|
|
|
+ // Callback function for access to this entity.
|
|
|
+ 'access callback' => 'chado_data_access',
|
|
|
|
|
|
- /**
|
|
|
- * Delete one or more tripal_entities entities.
|
|
|
- *
|
|
|
- * Deletion is unfortunately not supported in the base
|
|
|
- * DrupalDefaultEntityController class.
|
|
|
- *
|
|
|
- * @param array $entities
|
|
|
- * An array of entity IDs or a single numeric ID.
|
|
|
- */
|
|
|
- public function deleteMultiple($entities) {
|
|
|
- $entity_ids = array();
|
|
|
- if (!empty($entities)) {
|
|
|
- $transaction = db_transaction();
|
|
|
- try {
|
|
|
- foreach ($entities as $entity) {
|
|
|
- // Invoke hook_entity_delete().
|
|
|
- module_invoke_all('entity_delete', $entity, 'chado_data');
|
|
|
- field_attach_delete('chado_data', $entity);
|
|
|
- $entity_ids[] = $entity->entity_id;
|
|
|
- }
|
|
|
- db_delete('chado_data')
|
|
|
- ->condition('entity_id', $entity_ids, 'IN')
|
|
|
- ->execute();
|
|
|
- }
|
|
|
- catch (Exception $e) {
|
|
|
- $transaction->rollback();
|
|
|
- watchdog_exception('entity_example', $e);
|
|
|
- throw $e;
|
|
|
- }
|
|
|
- }
|
|
|
- }
|
|
|
+ // FALSE disables caching. Caching functionality is handled by Drupal core.
|
|
|
+ 'static cache' => FALSE,
|
|
|
|
|
|
- /**
|
|
|
- * Saves the custom fields using drupal_write_record().
|
|
|
- */
|
|
|
- public function save($entity) {
|
|
|
- global $user;
|
|
|
+ // Bundles are defined below.
|
|
|
+ 'bundles' => array(),
|
|
|
|
|
|
- // If our entity has no entity_id, then we need to give it a
|
|
|
- // time of creation.
|
|
|
- if (empty($entity->entity_id)) {
|
|
|
- $entity->created = time();
|
|
|
- $invocation = 'entity_insert';
|
|
|
- }
|
|
|
- else {
|
|
|
- $invocation = 'entity_update';
|
|
|
- }
|
|
|
+ // The information below is used by the ChadoDataUIController
|
|
|
+ // (which extends the EntityDefaultUIController). The admin_ui
|
|
|
+ // key here is mean to appear on the 'Find Content' page of the
|
|
|
+ // administrative menu.
|
|
|
+ 'admin ui' => array(
|
|
|
+ 'path' => 'admin/content/chado_data',
|
|
|
+ 'file' => 'includes/tripal_entities.admin.inc',
|
|
|
+ 'controller class' => 'ChadoDataUIController',
|
|
|
+ 'menu wildcard' => '%chado_data',
|
|
|
+ ),
|
|
|
+ );
|
|
|
|
|
|
- // Invoke hook_entity_presave().
|
|
|
- module_invoke_all('entity_presave', $entity, 'chado_data');
|
|
|
+ // Bundles are alternative groups of fields or configuration
|
|
|
+ // associated with a base entity type.
|
|
|
+ // We want to dynamically add the bundles (or term types) to the entity.
|
|
|
+ $values = array(
|
|
|
+ 'cv_id' => array(
|
|
|
+ 'name' => 'sequence'
|
|
|
+ ),
|
|
|
+ 'name' => 'gene',
|
|
|
+ );
|
|
|
+ $cvterm = chado_generate_var('cvterm', $values);
|
|
|
+ $label = preg_replace('/_/', ' ', ucwords($cvterm->name));
|
|
|
+ $bundle_id = $cvterm->dbxref_id->db_id->name . '_' . $cvterm->dbxref_id->accession;
|
|
|
+ $entities['trp_vocabulary_term']['bundles'][$bundle_id] = array(
|
|
|
+ 'label' => $label,
|
|
|
+ 'admin' => array(
|
|
|
+ 'path' => 'admin/structure/chado_data/manage',
|
|
|
+ 'access arguments' => array('administer chado_data entities'),
|
|
|
+ ),
|
|
|
+ 'entity keys' => array(
|
|
|
+ 'id' => 'entity_id',
|
|
|
+ 'bundle' => 'bundle',
|
|
|
+ ),
|
|
|
+ );
|
|
|
|
|
|
- // Write out the entity record.
|
|
|
- $tablename = 'feature';
|
|
|
- $type_field = 'type_id';
|
|
|
- $schema = chado_get_schema($tablename);
|
|
|
- $pkey_field = $schema['primary key'][0];
|
|
|
- $record = array(
|
|
|
- 'cvterm_id' => $entity->cvterm_id,
|
|
|
- 'type' => $entity->type,
|
|
|
- 'tablename' => $tablename,
|
|
|
- 'record_id' => $entity->record_id,
|
|
|
- 'title' => 'title',
|
|
|
- 'uid' => $user->uid,
|
|
|
- 'created' => $entity->created,
|
|
|
- 'changed' => time(),
|
|
|
- );
|
|
|
- $success = drupal_write_record('chado_data', $record);
|
|
|
- if ($success == SAVED_NEW) {
|
|
|
- $entity->entity_id = $record['entity_id'];
|
|
|
- }
|
|
|
+ // The entity that holds information about the entity types
|
|
|
+ $entities['chado_data_type'] = array(
|
|
|
+ 'label' => t('Chado Data Type'),
|
|
|
+ 'entity class' => 'ChadoDataType',
|
|
|
+ 'controller class' => 'ChadoDataTypeController',
|
|
|
+ 'base table' => 'chado_data_type',
|
|
|
+ 'fieldable' => FALSE,
|
|
|
+ 'bundle of' => 'chado_data',
|
|
|
+ 'exportable' => TRUE,
|
|
|
+ 'entity keys' => array(
|
|
|
+ 'id' => 'id',
|
|
|
+ 'name' => 'type',
|
|
|
+ 'label' => 'label',
|
|
|
+ ),
|
|
|
+ 'access callback' => 'chado_data_type_access',
|
|
|
+ 'module' => 'tripal_entities',
|
|
|
+ // Enable the entity API's admin UI.
|
|
|
+ 'admin ui' => array(
|
|
|
+ 'path' => 'admin/structure/chado_data_types',
|
|
|
+ 'file' => 'includes/tripal_entities.admin.inc',
|
|
|
+ 'controller class' => 'ChadoDataTypeUIController',
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ return $entities;
|
|
|
+}
|
|
|
|
|
|
- // Now we need to either insert or update the fields which are
|
|
|
- // attached to this entity. We use the same primary_keys logic
|
|
|
- // to determine whether to update or insert, and which hook we
|
|
|
- // need to invoke.
|
|
|
- if ($invocation == 'entity_insert') {
|
|
|
- field_attach_insert('chado_data', $entity);
|
|
|
- }
|
|
|
- else {
|
|
|
- field_attach_update('chado_data', $entity);
|
|
|
+/**
|
|
|
+ * Returns a render array with all chado_data entities.
|
|
|
+ *
|
|
|
+ * @see pager_example.module
|
|
|
+ */
|
|
|
+function tripal_entities_list_entities() {
|
|
|
+ $content = array();
|
|
|
+ // Load all of our entities.
|
|
|
+ $entities = chado_data_load_multiple();
|
|
|
+ if (!empty($entities)) {
|
|
|
+ foreach ($entities as $entity) {
|
|
|
+ // Create tabular rows for our entities.
|
|
|
+ $rows[] = array(
|
|
|
+ 'data' => array(
|
|
|
+ 'id' => $entity->entity_id,
|
|
|
+ 'title' => l($entity->title, 'chado_data/' . $entity->entity_id),
|
|
|
+ 'type' => $entity->type,
|
|
|
+ ),
|
|
|
+ );
|
|
|
}
|
|
|
- // Invoke either hook_entity_update() or hook_entity_insert().
|
|
|
- module_invoke_all($invocation, $entity, 'chado_data');
|
|
|
-
|
|
|
- return $entity;
|
|
|
+ // Put our entities into a themed table. See theme_table() for details.
|
|
|
+ $content['entity_table'] = array(
|
|
|
+ '#theme' => 'table',
|
|
|
+ '#rows' => $rows,
|
|
|
+ '#header' => array(t('ID'), t('Item Description'), t('Bundle')),
|
|
|
+ );
|
|
|
}
|
|
|
-
|
|
|
+ else {
|
|
|
+ // There were no entities. Tell the user.
|
|
|
+ $content[] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#markup' => t('No chado data entities currently exist.'),
|
|
|
+ );
|
|
|
+ }
|
|
|
+ return $content;
|
|
|
}
|
|
|
|
Stephen Ficklin