tripal/tripal_entities/tripal_entities.module

<?php

require_once "api/tripal_entities.api.inc";
require_once "includes/tripal_entities.field_storage.inc";
require_once "includes/tripal_entities.fields.inc";
require_once "includes/ChadoData.inc";
require_once "includes/ChadoDataController.inc";
require_once "includes/ChadoDataUIController.inc";
require_once "includes/ChadoDataType.inc";
require_once "includes/ChadoDataTypeController.inc";
require_once "includes/ChadoDataTypeUIController.inc";

/**
 * Implements hook_menu().
 */
function tripal_entities_menu() {

/*   // This provides a place for Field API to hang its own
  // interface and has to be the same as what was defined
  // in basic_entity_info() above.
  $items['admin/structure/chado_data/manage'] = array(
    'title' => 'Chado Data',
    'description' => t('Manage chado records, including default status, fields, settings, etc.'),
    'page callback' => 'tripal_entities_list_entities',
    'access arguments' => array('administer chado_data'),
  );
  // Add entities.
  $items['admin/structure/chado_data/manage/add'] = array(
    'title' => 'Add Chado Data',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('chado_data_form'),
    'access arguments' => array('create chado_data entities'),
    'type' => MENU_LOCAL_ACTION,
  );
  // List of all chado_data entities.
  $items['admin/structure/chado_data/manage/list'] = array(
    'title' => 'List',
    'type' => MENU_DEFAULT_LOCAL_TASK,
  ); */
  // The page to view our entities - needs to follow what
  // is defined in basic_uri and will use load_basic to retrieve
  // the necessary entity info.

//   $items['chado_data/%chado_data'] = array(
//     'title callback' => 'chado_data_title',
//     'title arguments' => array(1),
//     'page callback' => 'chado_data_view',
//     'page arguments' => array(1),
//     'access arguments' => array('view chado_data'),
//     'type' => MENU_CALLBACK,
//   );

//   // 'View' tab for an individual entity page.
//   $items['chado_data/%chado_data/view'] = array(
//     'title' => 'View',
//     'type' => MENU_DEFAULT_LOCAL_TASK,
//     'weight' => -10,
//   );

//   // 'Edit' tab for an individual entity page.
//   $items['chado_data/%chado_data/edit'] = array(
//     'title' => 'Edit',
//     'page callback' => 'drupal_get_form',
//     'page arguments' => array('chado_data_form', 1),
//     'access arguments' => array('edit any chado_data entity'),
//     'type' => MENU_LOCAL_TASK,
//   );


  return $items;
}



/**
 * Implements hook_permission().
 */
function tripal_entities_permission() {
  // We set up permisssions to manage entity types, manage all entities and the
  // permissions for each individual entity
  $permissions = array(
    'administer chado data types' => array(
      'title' => t('Administer Chado data types'),
      'description' => t('Create and delete fields for Chado data types, and set their permissions.'),
    ),
    'administer chado data' => array(
      'title' => t('Administer Chado data'),
      'description' => t('Edit and delete all chado data'),
    ),
  );

  // 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)),
      ),
      "view any $type_name data" => array(
        'title' => t('%type_name: View any', array('%type_name' => $type->label)),
      ),
    );
  }
  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',
    ),
  );
}

/**
 * https://api.drupal.org/api/drupal/modules!rdf!rdf.module/group/rdf/7
 */
function tripal_entities_rdf_mapping() {
  return array();
/*   return array(
    'type' => 'chado_data',
    'bundle' => 'gene',
    'mapping' => array(
      'rdftype' => array('sioc:Item', 'foaf:Document'),
      'title' => array(
        'predicates' => array('dc:title'),
      ),
      'uid' => array(
        'predicates' => array('sioc:has_creator'),
        'type' => 'rel',
      ),
      'name' => array(
        'predicates' => array('foaf:name'),
      ),
      'uniquename' => array(
        'predicates' => array('foaf:name'),
      ),
      'organism_id' => array(
        'predicates' => array('sioc:has_parent'),
        'type' => 'rel'
      )
    ),
  ); */
}

// 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
/**
 * Implement hook_entity_info().
 */
function tripal_entities_entity_info() {
  $entities = array();

  $entities['chado_data'] = array(
    // A human readable label to identify our entity.
    'label' => t('Chado Data'),
    'plural label' => t('Vocabulary Terms'),

    // The entity class and controller class extend the classes provided by the
    // Entity API.
    'entity class' => 'ChadoData',
    'controller class' => 'ChadoDataController',

    // 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',

    // IF fieldable == FALSE, we can't attach fields.
    'fieldable' => TRUE,

    // 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',
    ),

    // Callback function for access to this entity.
    'access callback' => 'chado_data_access',

    // FALSE disables caching. Caching functionality is handled by Drupal core.
    'static cache' => FALSE,

    // Bundles are defined below.
    'bundles' => array(),

    'label callback' => 'entity_class_label',
    'creation callback' => 'chado_data_create',

    // 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',
    ),
  );

  // 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',
    ),
  );

  // 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',
      'controller class' => 'ChadoDataTypeUIController',
    ),
  );
  return $entities;
}

/**
 * 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,
        ),
      );
    }
    // 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;
}