|  | @@ -60,7 +60,7 @@ function hook_tripal_ws_value(&$items, $field, $instance) {
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				|  |  |   *
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				|  |  |   * @return
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				|  |  |   *   A list of TripalWebService names.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_get_web_services() {
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				|  | @@ -91,19 +91,15 @@ function tripal_get_web_services() {
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				|  |  |   *
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				|  |  |   * @return
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				|  |  |   *   TRUE if the field type class file was found, FALSE otherwise.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_load_include_web_service_class($class) {
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				|  |  | -
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				|  |  |    $modules = module_list(TRUE);
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				|  |  |    foreach ($modules as $module) {
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				|  |  | -    $file_path = realpath(".") . '/' . drupal_get_path('module', $module) . '/includes/TripalWebService/' . $class . '.inc';
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				|  |  | -    if (file_exists($file_path)) {
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				|  |  | -      module_load_include('inc', $module, 'includes/TripalWebService/' . $class);
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				|  |  | -      if (class_exists($class)) {
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				|  |  | -        return TRUE;
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				|  |  | -      }
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				|  |  | +    module_load_include('inc', $module, 'includes/TripalWebService/' . $class);
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				|  |  | +    if (class_exists($class)) {
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				|  |  | +      return TRUE;
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				|  |  |      }
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				|  |  |    }
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				|  |  |    return FALSE;
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				|  | @@ -124,7 +120,7 @@ function tripal_load_include_web_service_class($class) {
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				|  |  |   *
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				|  |  |   * @return
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				|  |  |   *   TRUE if the site is successfully added, FALSE otherwise.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_add_site($name, $url, $version, $description) {
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				|  | @@ -180,7 +176,7 @@ function tripal_add_site($name, $url, $version, $description) {
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				|  |  |   *
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				|  |  |   * @return
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				|  |  |   *   TRUE if the record was successfully deleted, FALSE otherwise.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_remove_site($record_id) {
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				|  | @@ -196,7 +192,7 @@ function tripal_remove_site($record_id) {
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				|  |  |  
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				|  |  |  /**
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				|  |  |   * Constructs a URL for a remote Tripal web service.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @param $remote_site
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				|  |  |   *   A remote Tripal site object.
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				|  |  |   * @param $path
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				|  | @@ -205,8 +201,8 @@ function tripal_remove_site($record_id) {
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				|  |  |   *   leave this paramter empty.
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				|  |  |   * @param $query
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				|  |  |   *   An query string to appear after the ? in a URL.
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				|  |  | - *   
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				|  |  | - * @return  
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				|  |  | + *
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				|  |  | + * @return
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				|  |  |   *   The full URL within the content service.
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				|  |  |   */
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				|  |  |  function tripal_build_remote_content_url($remote_site, $path = '', $query = '') {
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				|  | @@ -215,12 +211,12 @@ function tripal_build_remote_content_url($remote_site, $path = '', $query = '')
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				|  |  |    $ws_url = $remote_site->url;
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				|  |  |    $ws_url = trim($ws_url, '/');
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				|  |  |    $ws_url .= '/web-services/content/' . $ws_version . '/' . $path;
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				|  |  | -  
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				|  |  | +
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				|  |  |    // Build the Query and make and substitions needed.
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				|  |  |    if ($query) {
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				|  |  |      $ws_url = $ws_url . '?' . $query;
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				|  |  |    }
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				|  |  | -  
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				|  |  | +
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				|  |  |    return $ws_url;
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				|  |  |  }
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				|  |  |  
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				|  | @@ -238,7 +234,7 @@ function tripal_build_remote_content_url($remote_site, $path = '', $query = '')
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				|  |  |   *
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				|  |  |   * @return
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				|  |  |   *   The JSON response formatted in a PHP array or FALSE if a problem occured.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_get_remote_content($site_id, $path = '', $query = '') {
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				|  | @@ -262,7 +258,7 @@ function tripal_get_remote_content($site_id, $path = '', $query = '') {
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				|  |  |      _tripal_report_ws_error($data);
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				|  |  |      return $data;
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				|  |  |    }
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				|  |  | -  
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				|  |  | +
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				|  |  |    // Make the remote query.
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				|  |  |    $ws_url = tripal_build_remote_content_url($remote_site, $path, $query);
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				|  |  |    $data = drupal_http_request($ws_url);
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				|  | @@ -287,7 +283,7 @@ function tripal_get_remote_content($site_id, $path = '', $query = '') {
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				|  |  |  
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				|  |  |    // We got a response, so convert it to a PHP array.
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				|  |  |    $data = drupal_json_decode($data->data);
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				|  |  | -  
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				|  |  | +
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				|  |  |    // Check if there was a Tripal Web Services error.
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				|  |  |    if (array_key_exists('error', $data)) {
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				|  |  |      _tripal_report_ws_error($data);
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				|  | @@ -298,12 +294,12 @@ function tripal_get_remote_content($site_id, $path = '', $query = '') {
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				|  |  |  
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				|  |  |  /**
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				|  |  |   * A helper function for reporting an error when retrieving remote content.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @param $data
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				|  |  |   *   A data array containing at a minimum the 'error' key containing the
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				|  |  |   *   error message.
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				|  |  |   */
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				|  |  | -function _tripal_report_ws_error($data) {  
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				|  |  | +function _tripal_report_ws_error($data) {
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				|  |  |    $error = '</pre>' . print_r($data['error'], TRUE) . '</pre>';
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				|  |  |    tripal_report_error('tripal_ws', TRIPAL_ERROR,
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				|  |  |      'Tripal remote web services reports the following error: !error.',
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				|  | @@ -323,7 +319,7 @@ function _tripal_report_ws_error($data) {
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				|  |  |   * @return
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				|  |  |   *   The JSON-LD context mapping array, or FALSE if the context could not
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				|  |  |   *   be retrieved.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_get_remote_context($context_url, $cache_id) {
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				|  | @@ -374,7 +370,7 @@ function tripal_get_remote_context($context_url, $cache_id) {
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				|  |  |   *   the Class (i.e. content type).
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				|  |  |   * @return
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				|  |  |   *   The JSON-LD context mapping array.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_get_remote_content_context($site_id, $context_url, $bundle_accession, $field_accession = '') {
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				|  | @@ -392,7 +388,7 @@ function tripal_get_remote_content_context($site_id, $context_url, $bundle_acces
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				|  |  |   *
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				|  |  |   * @param $site_id
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				|  |  |   *   The numeric site ID for the remote Tripal site.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_clear_remote_cache($site_id) {
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				|  | @@ -410,7 +406,7 @@ function tripal_clear_remote_cache($site_id) {
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				|  |  |   * @return
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				|  |  |   *   The vocabulary of a remote Tripal web service, or FALSE if an error
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				|  |  |   *   occured.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_get_remote_API_doc($site_id) {
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				|  | @@ -498,7 +494,7 @@ function tripal_get_remote_API_doc($site_id) {
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				|  |  |   * @return
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				|  |  |   *    An array of fake entity objects where the key is the entity_id and
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				|  |  |   *    the value is the object.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_load_remote_entities($remote_entity_ids, $site_id, $bundle_accession, $field_ids) {
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				|  | @@ -531,7 +527,7 @@ function tripal_load_remote_entities($remote_entity_ids, $site_id, $bundle_acces
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				|  |  |      '&fields=' . urlencode(implode(",", $field_ids));
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				|  |  |  
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				|  |  |    $results = tripal_get_remote_content($site_id, $bundle_accession, $query);
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				|  |  | -  
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				|  |  | +
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				|  |  |    // If we encountered an error just return;
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				|  |  |    if (array_key_exists('error', $results)) {
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				|  |  |      return FALSE;
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				|  | @@ -591,7 +587,7 @@ function tripal_load_remote_entities($remote_entity_ids, $site_id, $bundle_acces
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				|  |  |   *   be added to the entity returned.
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				|  |  |   * @return
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				|  |  |   *    A fake entity object.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_load_remote_entity($remote_entity_id, $site_id, $bundle_accession, $field_ids) {
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				|  | @@ -601,7 +597,7 @@ function tripal_load_remote_entity($remote_entity_id, $site_id, $bundle_accessio
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				|  |  |  
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				|  |  |    // Get the remote entity and create the fake entity.
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				|  |  |    $remote_entity = tripal_get_remote_content($site_id, $bundle_accession . '/' . $remote_entity_id);
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				|  |  | -  
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				|  |  | +
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				|  |  |    // If we encountered an error just return;
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				|  |  |    if (array_key_exists('error', $results)) {
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				|  |  |      return FALSE;
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				|  | @@ -700,7 +696,7 @@ function tripal_load_remote_entity($remote_entity_id, $site_id, $bundle_accessio
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				|  |  |   *   The field array as returned by web services.
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				|  |  |   * @param $context
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				|  |  |   *   The web service JSON-LD context for the bundle to which the field belongs.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function _tripal_update_remote_entity_field($field_data, $context, $depth = 0) {
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				|  | @@ -764,7 +760,7 @@ function _tripal_update_remote_entity_field($field_data, $context, $depth = 0) {
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				|  |  |   * @return
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				|  |  |   *   An array similar to that returned by the field_info_field function
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				|  |  |   *   of Drupal for local fields.
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				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_get_remote_field_info($site_id, $bundle_accession, $field_accession){
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				|  | @@ -806,7 +802,7 @@ function tripal_get_remote_field_info($site_id, $bundle_accession, $field_access
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				|  |  |   * @return
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				|  |  |   *   An array similar to that returned by the field_info_instance function
 | 
	
		
			
				|  |  |   *   of Drupal for local fields.
 | 
	
		
			
				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
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				|  |  |   */
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				|  |  |  function tripal_get_remote_field_instance_info($site_id, $bundle_accession, $field_accession){
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				|  | @@ -851,7 +847,7 @@ function tripal_get_remote_field_instance_info($site_id, $bundle_accession, $fie
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				|  |  |   * @return
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				|  |  |   *   A PHP array corresponding to the Hydra Class stanza (i.e. a content type).
 | 
	
		
			
				|  |  |   *   Returns NULL if the class ID cannot be found.
 | 
	
		
			
				|  |  | - * 
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				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
 | 
	
		
			
				|  |  |   */
 | 
	
		
			
				|  |  |  function tripal_get_remote_content_doc($site_id, $bundle_accession){
 | 
	
	
		
			
				|  | @@ -888,7 +884,7 @@ function tripal_get_remote_content_doc($site_id, $bundle_accession){
 | 
	
		
			
				|  |  |   *   A PHP array corresponding to the Hydra property stanza (field) that
 | 
	
		
			
				|  |  |   *   belongs to the given Class (i.e. a content type).  Retruns NULL if the
 | 
	
		
			
				|  |  |   *   property cannot be found.
 | 
	
		
			
				|  |  | - * 
 | 
	
		
			
				|  |  | + *
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				|  |  |   * @ingroup tripal_ws_api
 | 
	
		
			
				|  |  |   */
 | 
	
		
			
				|  |  |  function tripal_get_remote_field_doc($site_id, $bundle_accession, $field_accession){
 | 
	
	
		
			
				|  | @@ -926,7 +922,7 @@ function tripal_get_remote_field_doc($site_id, $bundle_accession, $field_accessi
 | 
	
		
			
				|  |  |   * @return
 | 
	
		
			
				|  |  |   *   An array of field downloader class names that are compoatible with the
 | 
	
		
			
				|  |  |   *   field and which exist on this site.
 | 
	
		
			
				|  |  | - * 
 | 
	
		
			
				|  |  | + *
 | 
	
		
			
				|  |  |   * @ingroup tripal_ws_api
 | 
	
		
			
				|  |  |   */
 | 
	
		
			
				|  |  |  function tripal_get_remote_field_formatters($site_id, $bundle_accession, $field_accession) {
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				|  | @@ -947,4 +943,4 @@ function tripal_get_remote_field_formatters($site_id, $bundle_accession, $field_
 | 
	
		
			
				|  |  |      }
 | 
	
		
			
				|  |  |    }
 | 
	
		
			
				|  |  |    return $flist;
 | 
	
		
			
				|  |  | -}
 | 
	
		
			
				|  |  | +}
 |