tripal/tripal_chado/includes/tripal_chado.entity.inc

<?php

/**
 * Implements hook_entity_presave().
 */
function tripal_chado_entity_presave($entity, $type) { }

/**
 * Implements hook_entity_postsave().
 */
function tripal_chado_entity_postsave($entity, $type) { }

/**
 *
 * Implements hook_entity_load().
 */
function tripal_chado_entity_load($entities, $type) {
 // TODO: we should add the cvterm record and the Chado record to the
 // entity.  This way the kvproperty field (or any other's we add in the
 // future do not need to load all of that information.  This can create
 // multiple loading of the same records all over the place.
}

/**
 *
 * Implements hook_entity_insert().
 */
function tripal_chado_entity_insert($entity, $type) { }

/**
 *
 * Implements hook_entity_update().
 */
function tripal_chado_entity_update($entity, $type) { }

/**
 *
 * Implements hook_entity_delete().
 */
function tripal_chaddo_entity_delete($entity, $type) {
  $record = db_select('chado_entity', 'ce')
   ->fields('ce', array('chado_entity_id', 'data_table', 'record_id'))
   ->condition('entity_id', $entity->id)
   ->execute()
   ->fetchObject();

  if ($record && property_exists($record, 'chado_entity_id')) {
    // Delete the corresponding record in Chado
    $table = $record->data_table;
    $record_id = $record->record_id;
    chado_delete_record($table, array($table . '_id' => $record_id));

    //Delete the record in the public.chado_entity table
    $sql = "DELETE FROM {chado_entity} WHERE chado_entity_id = :id";
    db_query($sql, array(':id' => $record->chado_entity_id));
  }
}

/**
 * This theme function is meant to override the data_combo theme.
 *
 * @param $variables
 */
function theme_tripal_chado_date_combo($variables) {
  $element = $variables['element'];
  $field = field_info_field($element['#field_name']);
  $instance = field_info_instance($element['#entity_type'], $element['#field_name'], $element['#bundle']);

  // Group start/end items together in fieldset.
  $fieldset = array(
    '#title' => t($element['#title']) . ' ' . ($element['#delta'] > 0 ? intval($element['#delta'] + 1) : ''),
    '#value' => '',
    '#description' => !empty($element['#fieldset_description']) ? $element['#fieldset_description'] : '',
    '#attributes' => array(),
    '#children' => $element['#children'],
    '#attributes' => array('class' => array('collapsible', 'collapsed')),
  );
  return theme('fieldset', array('element' => $fieldset));
}


/**
 * Determines whether the given user has access to a tripal data entity.
 *
 * TODO: I'm not sure this function should be at this level. I think all
 * access controls should be handled by the tripal_entity module and that
 * storage backends should just attach data as requested.
 *
 * @param $op
 *   The operation being performed. One of 'view', 'update', 'create', 'delete'
 *   or just 'edit' (being the same as 'create' or 'update').
 * @param $entity
 *   Optionally a tripal data entity or a tripal data type to check access for.
 *   If nothing is given, access for all types is determined.
 * @param $account
 *   The user to check for. Leave it to NULL to check for the global user.
 * @return boolean
 *   Whether access is allowed or not.
 */
function tripal_chado_entity_access($op, $entity = NULL, $account = NULL) {
  if (user_access('administer tripal data', $account)) {
    return TRUE;
  }
  if (isset($entity) && $type_name = $entity->type) {
    $op = ($op == 'view') ? 'view' : 'edit';
    if (user_access("$op any $type_name data", $account)) {
      return TRUE;
    }
  }
  return FALSE;
}

/**
 * Menu callback to display an entity.
 *
 * As we load the entity for display, we're responsible for invoking a number
 * of hooks in their proper order.
 *
 * @see hook_entity_prepare_view()
 * @see hook_entity_view()
 * @see hook_entity_view_alter()
 */
function tripal_chado_view_entity($entity, $view_mode = 'full') {
  $content = '';
  $controller = entity_get_controller($entity->type);
  $content = $controller->view(array($entity->id => $entity));
  drupal_set_title($entity->title);
  return $content;
}

/**
 * Menu title callback for showing individual entities
 */
function tripal_chado_entity_title($entity){
  if ($entity) {
    return $entity->title;
  }
}