tripal/tripal_entities/tripal_entities.module

<?php

require_once "api/tripal_entities.api.inc";
require_once "includes/tripal_entities.chado_entity.inc";
require_once "includes/tripal_entities.entity_form.inc";
require_once "includes/tripal_entities.tables.inc";
require_once "includes/TripalEntity.inc";
require_once "includes/TripalEntityController.inc";
require_once "includes/TripalEntityUIController.inc";
require_once "includes/TripalBundle.inc";
require_once "includes/TripalBundleController.inc";
require_once "includes/TripalBundleUIController.inc";

/**
 * Implements hook_views_api().
 */
function tripal_entities_views_api() {
  return array(
    'api' => 3,
  );
}

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

  $items = array();

  // The administative settings menu.
  $items['admin/tripal/BioData'] = array(
    'title' => 'Biological Data',
    'description' => 'Tools for publishing, configurating and managing biological data.',
    'page callback' => 'tripal_entities_admin_view',
    'access arguments' => array('administer tripal data types'),
    'file' =>  'includes/tripal_entities.admin.inc',
    'type' => MENU_NORMAL_ITEM,
  );

  // The default tab.
  $items['admin/tripal/BioData/default'] = array(
    'title' => 'Biological Data',
    'type' => MENU_DEFAULT_LOCAL_TASK,
    'weight' =>  1,
  );

  $items['admin/tripal/BioData/access'] = array(
    'title' => 'Access',
    'description' => 'Set default access permissions for collections of data.',
    'page callback' => 'drupal_get_form',
    'page arguments' => array('tripal_entities_admin_access_form'),
    'access arguments' => array('administer tripal data types'),
    'file' =>  'includes/tripal_entities.admin.inc',
    'type' => MENU_LOCAL_TASK,
    'weight' => 3
  );

  return $items;
}

/**
 * Implements hook_admin_paths().
 * Define administrative paths.
 */
function tripal_entities_admin_paths() {
  if (variable_get('node_admin_theme')) {
    $paths = array(
      'BioData/*/edit' => TRUE,
      'BioData/*/delete' => TRUE,
      'BioData/add' => TRUE,
      'BioData/add/*' => TRUE,
    );
    return $paths;
  }
}

/**
 * Implements hook_menu_local_tasks_alter().
 * Used to add action links to pages.
 */
function tripal_entities_menu_local_tasks_alter(&$data, $router_item, $root_path) {

  // Add an "Add Biological Data" action link to the Admin > Content > Biological Data page.
  if ($root_path == 'admin/content/BioData') {
    $item = menu_get_item('BioData/add');
    if ($item['access']) {
      $data['actions']['output'][] = array(
        '#theme' => 'menu_local_action',
        '#link' => $item,
      );
    }
  }
}

/**
 * Implements hook_shortcut_default_set().
 * Modify the shortcut menu to include Biological data links.
 *
 * @param object $account
 *   The user account whose default shortcut set will be returned. If not provided, the 
 *   function will return the currently logged-in user's default shortcut set.
 *
 * @return
 *   An object representing the default shortcut set.
 */
function tripal_entities_shortcut_default_set($account) {
  $sets = shortcut_sets();
  $found = FALSE;
  foreach ($sets as $set) {
    if ($set->title == 'TripalDefault') {
      $found = TRUE;
    }
  }
  if (!$found) {
    $t = get_t();
    // Create an initial default shortcut set.
    $shortcut_set = new stdClass();
    $shortcut_set->title = $t('TripalDefault');
    $shortcut_set->links = array(
      array(
        'link_path' => 'BioData/add',
        'link_title' => 'Add Biological Data',
        'weight' => -23,
      ),
      array(
        'link_path' => 'admin/content/BioData',
        'link_title' => 'Find Biological Data',
        'weight' => -22,
      ),
      array(
        'link_path' => 'node/add',
        'link_title' => $t('Add content'),
        'weight' => -21,
      ),
      array(
        'link_path' => 'admin/content',
        'link_title' => $t('Find content'),
        'weight' => -20,
      ),
    );
    shortcut_set_save($shortcut_set);
  }

  $sets = shortcut_sets();
  foreach ($sets as $set) {
   if ($set->title == 'TripalDefault') {
     return $set->set_name;
   }
  }
}

/**
 * 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 tripal data types' => array(
      'title' => t('Administer Tripal data types'),
      'description' => t('Create and delete fields for Tripal data types, and set their permissions.'),
    ),
    'administer tripal data' => array(
      'title' => t('Administer Tripal data'),
      'description' => t('Edit and delete all tripal data'),
    ),
  );
  
  return $permissions;
}

/**
 * Implements hook_theme().
 */
function tripal_entities_theme($existing, $type, $theme, $path) {
  return array(
    'tripal_entity' => array(
      'render element' => 'elements',
      'template' => 'tripal_entity',
      'path' => "$path/theme/templates"
    ),
    'tripal_entities_date_combo' => array(
      'render element' => 'element',
      'file' => 'includes/tripal_entities.chado_entity.inc',
    ),
    'tripal_entities_add_list' => array(
      'variables' => array('content' => NULL),
      'file' => 'includes/tripal_entities.entity_form.inc',
    ),

  );
}

/**
 * https://api.drupal.org/api/drupal/modules!rdf!rdf.module/group/rdf/7
 */
function tripal_entities_rdf_mapping() {
  return array();
/*   return array(
    'type' => 'tripal_entity',
    '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['BioData'] = array (
    // A human readable label to identify our entity.
    'label' => 'Biological Data',
    'plural label' => 'Biological Data',

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

    // The table for this entity defined in hook_schema()
    'base table' => 'tripal_entity',

    // 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' => 'id',
      'bundle' => 'bundle'
    ),
    'bundle keys' => array (
      'bundle' => 'bundle'
    ),

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

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

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

    'label callback' => 'tripal_entity_label',

    // The information below is used by the TripalEntityUIController
    // (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/BioData',
      'controller class' => 'TripalEntityUIController',
      'menu wildcard' => '%tripal_entity',
      'file' => 'includes/TripalEntityUIController.inc'
    ),
    'view modes' => array (
      'full' => array (
        'label' => t ('Full content'),
        'custom settings' => FALSE
      ),
      'teaser' => array (
        'label' => t ('Teaser'),
        'custom settings' => TRUE
      )
    )
  );

  // The entity that holds information about the entity types.
  $entities['BioData_bundles'] = array (
    'label' => 'Biological Data Type', //$voc->db_id->name . ' (' . $voc->cv_id->name . ') Data Type',
    'entity class' => 'TripalBundle',
    'controller class' => 'TripalBundleController',
    'base table' => 'tripal_bundle',
    'fieldable' => FALSE,
    'bundle of' => 'BioData',
    'exportable' => FALSE,
    'entity keys' => array (
      'id' => 'id',
      'name' => 'bundle',
      'label' => 'label'
    ),
    'access callback' => 'tripal_bundle_access',
    'module' => 'tripal_entities',
    // Enable the entity API's admin UI.
    'admin ui' => array (
      'path' => 'admin/structure/BioData',
      'controller class' => 'TripalBundleUIController',
      'file' => 'includes/TripalBundleUIController.inc',
      'menu wildcard' => '%tripal_bundle',
    )
  );

  // Dynamically add in the bundles. Bundles are alternative groups of fields
  // or configuration associated with an entity type .We want to dynamically
  // add the bundles to the entity.
  $published_terms = chado_generate_var('tripal_term', array('publish' => 1), array('return_array' => 1));
  foreach ($published_terms as $term) {

    $cvterm = $term->cvterm_id;
    $bundle_id = 'dbxref_' . $cvterm->dbxref_id->dbxref_id;
    $label = preg_replace('/_/', ' ', ucwords($cvterm->name));

    $entities['BioData']['bundles'][$bundle_id] = array (
      'label' => $label,
      'admin' => array (
        'path' => 'admin/structure/BioData/manage/%tripal_bundle',
        'real path' => 'admin/structure/BioData/manage/' . $bundle_id,
        'bundle argument' => 4,
        'access arguments' => array (
          'administer tripal data types'
        )
      )
    );
  }
  return $entities;
}

/**
 * Get published vocabularies as select options
 * @return multitype:NULL
 */
function tripal_entities_get_published_vocabularies_as_select_options() {
  $published_vocs = chado_generate_var('tripal_vocabulary', array('publish' => 1), array('return_array' => 1));
  $options = array();
  foreach ($published_vocs as $voc) {
    $options [$voc->cv_id->cv_id] = $voc->cv_id->name;
  }
  return $options;
}

/**
 * Get published vocabularies as select options
 * @return multitype:NULL
 */
function tripal_entities_get_db_names_for_published_vocabularies() {
  $published_vocs = chado_generate_var('tripal_vocabulary', array('publish' => 1), array('return_array' => 1));
  $db = array();
  foreach ($published_vocs as $voc) {
    $db [$voc->db_id->db_id] = $voc->db_id->name;
  }
  return $db;
}

/**
 * Get published terms as select options
 * @return multitype:NULL
 */
function tripal_entities_get_published_terms_as_select_options($cv_id = NULL) {
  $where = array('publish' => 1);
  $published_terms = chado_generate_var('tripal_term', $where, array('return_array' => 1));
  $options = array();
  foreach ($published_terms as $term) {
    if (!$cv_id) {
      $options [$term->cvterm_id->name] = $term->cvterm_id->name;
    }
    else {
      if ($term->cvterm_id->cv_id->cv_id == $cv_id) {
        $options [$term->cvterm_id->name] = $term->cvterm_id->name;
      }
    }
  }
  return $options;
}

/**
 * Menu argument loader; Load a tripal data type by string.
 *
 * @param $type
 *   The machine-readable name of a tripal data type to load.
 * @return
 *   A tripal data type array or FALSE if $type does not exist.
 */

function tripal_bundle_load($bundle_type, $reset = FALSE) {
  // Get the type of entity by the ID.
  $bundle_types = db_select('tripal_bundle', 'tdt')
    ->fields('tdt', array('id', 'type'))
    ->condition('bundle', $bundle_type)
    ->execute()
    ->fetchObject();

  if ($bundle_types) {
    $entity = entity_load('BioData_bundles', array($bundle_types->id), array(), $reset);
    return reset($entity);
  }
  return FALSE;
}

/**
 * Allows the menu system to use a wildcard to fetch the entity.
 *
 * Make sure that the wildcard you choose in the tripal_entity entity
 * definition fits the function name here.
 *
 * @param $id
 *   Integer specifying the tripal_entity id.
 * @param $reset
 *   A boolean indicating that the internal cache should be reset.
 * @return
 *   A fully-loaded $tripal_entity object or FALSE if it cannot be loaded.
 *
 * @see tripal_entity_load_multiple()
 */
function tripal_entity_load($id, $reset = FALSE) {
    $entity = entity_load('BioData', array($id), array(), $reset);
    return reset($entity);
}