/modules/cdm_dataportal/cdm_api/cdm_api.module - EDIT - EDIT Project Management

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cdm-dataportal/modules/cdm_dataportal/cdm_api/cdm_api.module @ d8001ede

       <?php
         /**
          * @file
          * Required or useful functions for using CDM Data Store Webservices.
+         *
          * Naming conventions:
          * ----------------------
          * - All webservice access methods are prefixed with cdm_ws.
+         *
          * @copyright
          *   (C) 2007-2012 EDIT
          *   European Distributed Institute of Taxonomy
          *   http://www.e-taxonomy.eu
+         *
          *   The contents of this module are subject to the Mozilla
          *   Public License Version 1.1.
          * @see http://www.mozilla.org/MPL/MPL-1.1.html
+         *
          * @author
          *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
          *   - Wouter Addink <w.addink@eti.uva.nl> (migration from Drupal 5 to Drupal7)
          */
         module_load_include('php', 'cdm_api', 'xml2json');
         module_load_include('php', 'cdm_api', 'commons');
         module_load_include('php', 'cdm_api', 'uuids');
         module_load_include('php', 'cdm_api', 'enums');
         module_load_include('php', 'cdm_api', 'webservice_uris');
         module_load_include('php', 'cdm_api', 'cdm_node');
         module_load_include('inc', 'cdm_api', 'tagged_text');
         /**
          * Timeout used to override the default of 30 seconds
          * in @see drupal_http_request()
+         *
          * @var CDM_HTTP_REQUEST_TIMEOUT: A float representing the maximum number of seconds the function
          *     call may take
          */
         define('CDM_HTTP_REQUEST_TIMEOUT', 90.0);
       /**
        * orderBy webservice query parameter value
        */
       define('CDM_ORDER_BY_ID_ASC', 'BY_ID_ASC');
       /**
        * orderBy webservice query parameter value
        */
       define('CDM_ORDER_BY_ID_DESC', 'BY_ID_DESC');
       /**
        * orderBy webservice query parameter value
        */
       define('CDM_ORDER_BY_TITLE_CACHE_ASC', 'BY_TITLE_CACHE_ASC');
       /**
        * orderBy webservice query parameter value
        */
       define('CDM_ORDER_BY_TITLE_CACHE_DESC', 'BY_TITLE_CACHE_DESC');
       /**
        * orderBy webservice query parameter value
        */
       define('CDM_ORDER_BY_NOMENCLATURAL_ORDER_ASC', 'BY_NOMENCLATURAL_ORDER_ASC');
       /**
        * orderBy webservice query parameter value
        */
       define('CDM_ORDER_BY_NOMENCLATURAL_ORDER_DESC', 'BY_NOMENCLATURAL_ORDER_DESC');
       /**
        * orderBy webservice query parameter value
        */
       define('CDM_ORDER_BY_ORDER_INDEX_ASC', 'BY_ORDER_INDEX_ASC');
       /**
        * orderBy webservice query parameter value
        */
       define('CDM_ORDER_BY_ORDER_INDEX_DESC', 'BY_ORDER_INDEX_DESC');
       /**
        * Implements hook_menu().
        */
       function cdm_api_menu() {
         $items = array();
         // usage: url('cdm_api/proxy/'.urlencode($content_url)."/$theme");
         $items['cdm_api/proxy'] = array(
           'page callback' => 'proxy_content',
           'access arguments' => array(
             'access cdm content',
           ),
           'type' => MENU_CALLBACK,
         );
         $items['cdm_api/setvalue/session'] = array(
           'page callback' => 'setvalue_session',
           'access arguments' => array(
             'access cdm content',
           ),
           'type' => MENU_CALLBACK,
         );
         return $items;
+      }
       /**
        * Implements hook_block_info().
        */
       function cdm_api_block_info() {
         $block['cdm_ws_debug'] = array(
             "info" => t("CDM web service debug"),
             "cache" => DRUPAL_NO_CACHE
         );
         return $block;
+      }
       /**
        * Implements hook_block_view().
        */
       function cdm_api_block_view($delta) {
         switch ($delta) {
           case 'cdm_ws_debug':
           $cdm_ws_url = variable_get('cdm_webservice_url', '');
           $field_map = array(
               'ws_uri' => t('URI') . ' <code>(' . $cdm_ws_url .'...)</code>',
               'time' => t('Time'),
               'fetch_seconds' => t('Fetching [s]'),
               'parse_seconds' => t('Parsing [s]'),
               'size_kb' => t('Size [kb]'),
               'status' => t('Status'),
               'data_links' =>  t('Links'),
           );
           if (!isset($_SESSION['cdm']['ws_debug'])) {
             $_SESSION['cdm']['ws_debug'] = array();
+          }
           $header = '<thead><tr><th>' . join('</th><th>' , array_values($field_map)) . '</th></thead>';
           $footer = '<tfoot><tr><th>' . join('</th><th>' , array_values($field_map)) . '</th></tfoot>';
           $rows = array();
           foreach ($_SESSION['cdm']['ws_debug'] as $data){
             $data = unserialize($data);
             // stip of webservice base url
             $data['ws_uri'] = str_replace($cdm_ws_url, '', $data['ws_uri']);
             if($data['method'] == 'POST'){
               $data['ws_uri'] = 'POST: ' . $data['ws_uri'] . '?' . $data['post_data'];
+            }
             $cells = array();
             foreach ($field_map as $field => $label){
               $cells[] = '<td class="' . $field . '">' .  $data[$field] . '</td>';
+            }
             $rows[] = '<tr class="' . $data['status']  . '">' . join('' , $cells). '</tr>';
+          }
           // clear session again
           $_SESSION['cdm']['ws_debug'] = array();
           _add_js_ws_debug();
           $block['subject'] = ''; // no subject, title in content for having a defined element id
           // otherwise it would depend on the theme
           $block['content'] = array(
             '#markup' => '<h4 id="cdm-ws-debug-button">' . t('CDM Debug') . '</h4>'
               // cannot use theme_table() since table footer is not jet supported in D7
               . '<div id="cdm-ws-debug-table-container"><table id="cdm-ws-debug-table">'
               . $header
               . '<tbody>' . join('', $rows) . '</tbody>'
               . $footer
               . '</table></div>',
             '#attached' => array(
               'css' => array(
                 drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_ws_debug.css'
+              )
+            )
           );
           return $block;
+        }
+      }
       /**
        * Implements hook_cron().
+       *
        * Expire outdated cache entries.
        */
       function cdm_api_cron() {
         cache_clear_all(NULL, 'cache_cdm_ws');
+      }
       /**
        * Lists the classifications a taxon belongs to
+       *
        * @param CDM type Taxon $taxon
        *   the taxon
+       *
        * @return array
        *   aray of CDM instances of Type Classification
        */
       function get_classifications_for_taxon($taxon) {
         return cdm_ws_get(CDM_WS_TAXON_CLASSIFICATIONS, $taxon->uuid);
+      }
       /**
        * Returns the chosen FeatureTree to be used as FeatureTree for the taxon profile.
+       *
        * The FeatureTree returned is the term tree one that has been set in the
        * dataportal settings (layout->taxon:profile).
        * When the chosen FeatureTree is not found in the database,
        * the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.
+       *
        * @return object
        *   A cdm TermTree object.
        */
       function get_profile_feature_tree() {
         static $profile_featureTree;
         if($profile_featureTree == NULL) {
           $profile_featureTree = cdm_ws_get(
             CDM_WS_TERMTREE,
             variable_get(CDM_PROFILE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
           );
           if (!$profile_featureTree) {
             $profile_featureTree = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
+          }
+        }
         return $profile_featureTree;
+      }
       /**
        * Returns the chosen TermTree to be used as FeatureTree for SpecimenDescriptions.
+       *
        * The TermTree returned is the one that has been set in the
        * dataportal settings (layout->taxon:specimen).
        * When the chosen TermTree is not found in the database,
        * the standard term tree (UUID_DEFAULT_TERMTREE) will be returned.
+       *
        * @return object
        *   A cdm TermTree object.
        */
       function cdm_get_occurrence_featureTree() {
         static $occurrence_featureTree;
         if($occurrence_featureTree == NULL) {
           $occurrence_featureTree = cdm_ws_get(
             CDM_WS_TERMTREE,
             variable_get(CDM_OCCURRENCE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
           );
           if (!$occurrence_featureTree) {
             $occurrence_featureTree = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
+          }
+        }
         return $occurrence_featureTree;
+      }
       /**
        * Returns the FeatureTree for structured descriptions
+       *
        * The FeatureTree returned is the one that has been set in the
        * dataportal settings (layout->taxon:profile).
        * When the chosen FeatureTree is not found in the database,
        * the standard feature tree (UUID_DEFAULT_FEATURETREE) will be returned.
+       *
        * @return mixed
        *   A cdm FeatureTree object.
        */
       function get_structured_description_featureTree() {
         static $structured_description_featureTree;
         if($structured_description_featureTree == NULL) {
           $structured_description_featureTree = cdm_ws_get(
               CDM_WS_TERMTREE,
               variable_get(CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
           );
           if (!$structured_description_featureTree) {
             $structured_description_featureTree = cdm_ws_get(
                 CDM_WS_TERMTREE,
                 UUID_DEFAULT_FEATURETREE
             );
+          }
+        }
         return $structured_description_featureTree;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function set_last_taxon_page_tab($taxonPageTab) {
         $_SESSION['cdm']['taxon_page_tab'] = $taxonPageTab;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function get_last_taxon_page_tab() {
         if (isset($_SESSION['cdm']['taxon_page_tab'])) {
           return $_SESSION['cdm']['taxon_page_tab'];
+        }
         else {
           return FALSE;
+        }
+      }
       /**
        * NOTE: The cdm-library provides a very similar server side function. See
        * eu.etaxonomy.cdm.model.media.MediaUtils.filterAndOrderMediaRepresentations()
+       *
        * @param object $media
        * @param array $mimeTypes
        *    an array of mimetypes in their order of preference. e.g:
        *    array('application/pdf', 'image/png', 'image/jpeg', 'image/gif', 'text/html')
        * @param int $width
        *    The width of the optimal image. If null, the method will return the representation with the biggest expansion
        * @param int $height
        *    The height of the optimal image. If null, the method will return the representation with the biggest expansion
+       *
        * @return array
        *   An array with preferred media representations or else an empty array.
        */
       function cdm_preferred_media_representations($media, array $mimeTypes, $width = NULL, $height = NULL) {
         $prefRepr = array();
         if (!isset($media->representations[0])) {
           return $prefRepr;
+        }
         while (count($mimeTypes) > 0) {
           // getRepresentationByMimeType
           $mimeType = array_shift($mimeTypes);
           foreach ($media->representations as &$representation) {
             // If the mimetype is not known, try inferring it.
             if (!$representation->mimeType) {
               if (isset($representation->parts[0])) {
                 $representation->mimeType = infer_mime_type($representation->parts[0]->uri);
+              }
+            }
             if ($representation->mimeType == $mimeType) {
               // Preferred mimetype found -> erase all remaining mimetypes
               // to end loop.
               $mimeTypes = array();
               $expansionDeltaSum = 0;
               $valid_parts_cnt = 0;
               // Look for part with the best matching size.
               foreach ($representation->parts as $part) {
                 if (empty($part->uri)) {
                   // skip part if URI is missing
                   continue;
+                }
                 $valid_parts_cnt++;
                 $expansionDelta = PHP_INT_MAX; // biggest delta for unknown sizes
                 // determine the optimal size
                 if (isset($part->width) && isset($part->height)) {
                   $expansion = $part->width * $part->height;
                   if ($width != null && $height != null) {
                     $optimalExpansion = $height * $width;
                   } else {
                     $optimalExpansion = PHP_INT_MAX;
+                  }
                   // determine the difference
                   $expansionDelta = $expansion > $optimalExpansion ? $expansion - $optimalExpansion : $optimalExpansion - $expansion;
+                }
                 // sum up the expansionDeltas of all parts contained in the representation
                 $expansionDeltaSum += $expansionDelta;
+              }
               if($valid_parts_cnt > 0){
                 $expansionDeltaSum = $expansionDeltaSum / $valid_parts_cnt;
                 $prefRepr[$expansionDeltaSum] = $representation;
+              }
+            }
+          }
+        }
         // Sort the array so that the smallest key value is the first in the array
         ksort($prefRepr);
         return $prefRepr;
+      }
       /**
        * Infers the mime type of a file using the filename extension.
+       *
        * The filename extension is used to infer the mime type.
+       *
        * @param string $filepath
        *   The path to the respective file.
+       *
        * @return string
        *   The mimetype for the file or FALSE if the according mime type could
        *   not be found.
        */
       function infer_mime_type($filepath) {
         static $mimemap = NULL;
         if (!$mimemap) {
           $mimemap = array(
             'jpg' => 'image/jpeg',
             'jpeg' => 'image/jpeg',
             'png' => 'image/png',
             'gif' => 'image/gif',
             'giff' => 'image/gif',
             'tif' => 'image/tif',
             'tiff' => 'image/tif',
             'pdf' => 'application/pdf',
             'html' => 'text/html',
             'htm' => 'text/html',
           );
+        }
         $extension = substr($filepath, strrpos($filepath, '.') + 1);
         if (isset($mimemap[$extension])) {
           return $mimemap[$extension];
+        }
         else {
           // FIXME remove this hack just return FALSE;
           return 'text/html';
+        }
+      }
       /**
        * Formats a mysql datatime as string
+       *
        * @param $datetime
        * @param string $format
+       *
        * @return
        *  the formatted string representation of the $datetime
        */
       function format_datetime($datetime, $format = 'Y-m-d H:i:s', $strip_zeros = true){
         return date($format, strtotime($datetime));
+      }
       /**
        * Converts an ISO 8601 org.joda.time.Partial to a year.
+       *
        * The function expects an ISO 8601 time representation of a
        * org.joda.time.Partial of the form yyyy-MM-dd.
+       *
        * @param string $partial
        *   ISO 8601 time representation of a org.joda.time.Partial.
+       *
        * @return string
        *   Returns the year. In case the year is unknown (= ????), it returns NULL.
        */
       function partialToYear($partial) {
         if (is_string($partial)) {
           $year = drupal_substr($partial, 0, 4);
           if (preg_match("/[0-9][0-9][0-9][0-9]/", $year)) {
             return $year;
+          }
+        }
         return '';
+      }
       /**
        * Converts an ISO 8601 org.joda.time.Partial to a month.
+       *
        * This function expects an ISO 8601 time representation of a
        * org.joda.time.Partial of the form yyyy-MM-dd.
        * In case the month is unknown (= ???) NULL is returned.
+       *
        * @param string $partial
        *   ISO 8601 time representation of a org.joda.time.Partial.
+       *
        * @return string
        *   A month.
        */
       function partialToMonth($partial) {
         if (is_string($partial)) {
           $month = drupal_substr($partial, 5, 2);
           if (preg_match("/[0-9][0-9]/", $month)) {
             return $month;
+          }
+        }
         return '';
+      }
       /**
        * Converts an ISO 8601 org.joda.time.Partial to a day.
+       *
        * This function expects an ISO 8601 time representation of a
        * org.joda.time.Partial of the form yyyy-MM-dd and returns the day as string.
        * In case the day is unknown (= ???) NULL is returned.
+       *
        * @param string $partial
        *   ISO 8601 time representation of a org.joda.time.Partial.
+       *
        * @return string
        *   A day.
        */
       function partialToDay($partial) {
         if (is_string($partial)) {
           $day = drupal_substr($partial, 8, 2);
           if (preg_match("/[0-9][0-9]/", $day)) {
             return $day;
+          }
+        }
         return '';
+      }
       /**
        * Converts an ISO 8601 org.joda.time.Partial to YYYY-MM-DD.
+       *
        * This function expects an ISO 8601 time representations of a
        * org.joda.time.Partial of the form yyyy-MM-dd and returns
        * four digit year, month and day with dashes:
        * YYYY-MM-DD eg: "2012-06-30", "1956-00-00"
+       *
        * The partial may contain question marks eg: "1973-??-??",
        * these are turned in to '00' or are stripped depending of the $stripZeros
        * parameter.
+       *
        * @param string $partial
        *   org.joda.time.Partial.
        * @param bool $stripZeros
        *   If set to TRUE the zero (00) month and days will be hidden:
        *   eg 1956-00-00 becomes 1956. The default is TRUE.
        * @param string @format
        * 	 Can ve used to specify the format of the date string, currently the following format strings are supported
        *    - "YYYY": Year only
        *    - "YYYY-MM-DD": this is the default
+       *
        * @return string
        *   YYYY-MM-DD formatted year, month, day.
        */
       function partialToDate($partial, $stripZeros = TRUE, $format= "YYYY-MM-DD") {
         $y = NULL; $m = NULL; $d = NULL;
         if(strpos($format, 'YY') !== FALSE){
           $y = partialToYear($partial);
+        }
         if(strpos($format, 'MM') !== FALSE){
           $m = partialToMonth($partial);
+        }
         if(strpos($format, 'DD') !== FALSE){
           $d = partialToDay($partial);
+        }
         $y = $y ? $y : '0000';
         $m = $m ? $m : '00';
         $d = $d ? $d : '00';
         $date = '';
         if ($y == '0000' && $stripZeros && $m == '00' && $d == '00') {
           return '';
+        }
         else {
           $date = $y;
+        }
         if ($m == '00' && $stripZeros && $d == '00') {
           return $date;
+        }
         else {
           $date .= "-" . $m;
+        }
         if ($d == '00' && $stripZeros) {
           return $date;
+        }
         else {
           $date .= "-" . $d;
+        }
         return $date;
+      }
       /**
        * Converts a time period to a string.
+       *
        * See also partialToDate($partial, $stripZeros).
+       *
        * @param object $period
        *   An JodaTime org.joda.time.Period object.
        * @param bool $stripZeros
        *   If set to True, the zero (00) month and days will be hidden:
        *   eg 1956-00-00 becomes 1956. The default is TRUE.
        * @param string @format
        * 	 Can ve used to specify the format of the date string, currently the following format strings are supported
        *    - "YYYY": Year only
        *    - "YYYY-MM-DD": this is the default
+       *
        * @return string
        *   Returns a date in the form of a string.
        */
       function timePeriodToString($period, $stripZeros = TRUE, $format = "YYYY-MM-DD") {
         $dateString = '';
         if($period->freeText){
           $dateString = $period->freeText;
         } else {
           if ($period->start) {
             $dateString = partialToDate($period->start, $stripZeros, $format);
+          }
           if ($period->end) {
             $end_str = partialToDate($period->end, $stripZeros, $format);
             $dateString .= ($dateString && $end_str ? ' ' . t('to') . ' ' : '') . $end_str;
+          }
+        }
         return $dateString;
+      }
       /**
        * returns the earliest date available in the $period in a normalized
        * form suitable for sorting, e.g.:
+       *
        *  - 1956-00-00
        *  - 0000-00-00
        *  - 1957-03-00
+       *
        * that is either the start date is returned if set otherwise the
        * end date
+       *
        * @param  $period
        *    An JodaTime org.joda.time.Period object.
        * @return string normalized form of the date
        *   suitable for sorting
        */
       function timePeriodAsOrderKey($period) {
         $dateString = '';
         if ($period->start) {
           $dateString = partialToDate($period->start, false);
+        }
         if ($period->end) {
           $dateString .= partialToDate($period->end, false);
+        }
         return $dateString;
+      }
       /**
        * Composes a absolute CDM web service URI with parameters and querystring.
+       *
        * @param string $uri_pattern
        *   String with place holders ($0, $1, ..) that should be replaced by the
        *   according element of the $pathParameters array.
        * @param array $pathParameters
        *   An array of path elements, or a single element.
        * @param string $query
        *   A query string to append to the URL.
+       *
        * @return string
        *   A complete URL with parameters to a CDM webservice.
        */
       function cdm_compose_ws_url($uri_pattern, $pathParameters = array(), $query = NULL) {
         if (empty($pathParameters)) {
           $pathParameters = array();
+        }
         $path = cdm_compose_url($uri_pattern, $pathParameters, $query);
         $uri = variable_get('cdm_webservice_url', '') . $path;
         return $uri;
+      }
       /**
        * Composes a relative Url with parameters and querystring.
+       *
        * @param string $uri_pattern
        *   String with place holders ($0, $1, ..) that should be replaced by the
        *   according element of the $pathParameters array.
        * @param array $pathParameters
        *   An array of path elements, or a single element.
        * @param string $query
        *   A query string to append to the URL.
+       *
        * @return string
        *   A relative URL with query parameters.
        */
       function cdm_compose_url($uri_pattern, $pathParameters, $query = NULL) {
         // (1)
         // Substitute all place holders ($0, $1, ..) in the $uri_pattern by the
         // according element of the $pathParameters array.
         static $helperArray = [];
         if (isset($pathParameters) && !is_array($pathParameters)) {
           $helperArray[0] = $pathParameters;
           $pathParameters = $helperArray;
+        }
         $i = 0;
         while (strpos($uri_pattern, "$" . $i) !== FALSE) {
           if (count($pathParameters) <= $i) {
             drupal_set_message('cdm_compose_url(): missing pathParameter ' . $i .' for ' . $uri_pattern, 'error');
             break;
+          }
           $uri_pattern = str_replace("$" . $i, rawurlencode($pathParameters[$i]), $uri_pattern);
           ++$i;
+        }
         // (2)
         // Append all remaining element of the $pathParameters array as path
         // elements.
         if (count($pathParameters) > $i) {
           // Strip trailing slashes.
           if (strrchr($uri_pattern, '/') == strlen($uri_pattern)) {
             $uri_pattern = substr($uri_pattern, 0, strlen($uri_pattern) - 1);
+          }
           while (count($pathParameters) > $i) {
             $uri_pattern .= '/' . rawurlencode($pathParameters[$i]);
             ++$i;
+          }
+        }
         // (3)
         // Append the query string supplied by $query.
         $uri_pattern = append_query_parameters($uri_pattern, $query);
         $path = $uri_pattern;
         return $path;
+      }
       /**
        * @param string $uri
+       *
        * @param $query_string
+       *
        * @return string
        */
       function append_query_parameters($uri, $query_string) {
         if (isset($query_string)) {
           $uri .= (strpos($uri, '?') !== FALSE ? '&' : '?') . $query_string;
+        }
         return $uri;
+      }
       /**
        * @todo wouldn't it more elegant and secure to only pass a uuid and additional function parameters
        *     together with a theme name to such a proxy function?
        *     Well this would not be covering all use cases but maybe all which involve AHAH.
        *     Maybe we want to have two different proxy functions, one with theming and one without?
+       *
        * @param string $uri
        *     A URI to a CDM Rest service from which to retrieve an object
        * @param string|null $hook
        *     (optional) The hook name to which the retrieved object should be passed.
        *     Hooks can either be a theme_hook() or compose_hook() implementation
        *     'theme' hook functions return a string whereas 'compose' hooks are returning render arrays
        *     suitable for drupal_render()
+       *
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function proxy_content($uri, $hook = NULL) {
         $args = func_get_args();
         $do_gzip = function_exists('gzencode');
         $uriEncoded = array_shift($args);
         $uri = urldecode($uriEncoded);
         $hook = array_shift($args);
         $request_method = strtoupper($_SERVER["REQUEST_METHOD"]);
         $post_data = null;
         if ($request_method == "POST" || $request_method == "PUT") {
           // read response body via inputstream module
           $post_data = file_get_contents("php://input");
+        }
         // Find and deserialize arrays.
         foreach ($args as &$arg) {
           // FIXME use regex to find serialized arrays.
           //       or should we accept json instead of php serializations?
           if (strpos($arg, "a:") === 0) {
             $arg = unserialize($arg);
+          }
+        }
         // In all these cases perform a simple get request.
         // TODO reconsider caching logic in this function.
         if (empty($hook)) {
           // simply return the webservice response
           // Print out JSON, the cache cannot be used since it contains objects.
           $http_response = cdm_http_request($uri, $request_method, $post_data);
           if (isset($http_response->headers)) {
             foreach ($http_response->headers as $hname => $hvalue) {
               drupal_add_http_header($hname, $hvalue);
+            }
+          }
           if (isset($http_response->data)) {
             print $http_response->data;
             flush();
+          }
           exit(); // leave drupal here
         } else {
           // $hook has been supplied
           // handle $hook either as compose or theme hook
           // pass through theme or compose hook
           // compose hooks can be called without data, therefore
           // passing the $uri in this case is not always a requirement
           if($uri && $uri != 'NULL') {
           // do a security check since the $uri will be passed
           // as absolute URI to cdm_ws_get()
             if (!_is_cdm_ws_uri($uri)) {
               drupal_set_message(
                 'Invalid call of proxy_content() with callback parameter \'' . $hook . '\' and URI:' . $uri,
                 'error'
               );
               return '';
+            }
             $obj = cdm_ws_get($uri, NULL, $post_data, $request_method, TRUE);
           } else {
             $obj = NULL;
+          }
           $reponse_data = NULL;
           if (function_exists('compose_' . $hook)){
             // call compose hook
             $elements =  call_user_func('compose_' . $hook, $obj);
             // pass the render array to drupal_render()
             $reponse_data = drupal_render($elements);
           } else {
             // call theme hook
             // TODO use theme registry to get the registered hook info and
             //    use these defaults
             switch($hook) {
               case 'cdm_taxontree':
                 $variables = array(
                   'tree' => $obj,
                   'filterIncludes' => isset($args[0]) ? $args[0] : NULL,
                   'show_filter_switch' => isset($args[1]) ? $args[1] : FALSE,
                   'tree_node_callback' => isset($args[2]) ? $args[2] : FALSE,
                   'element_name'=> isset($args[3]) ? $args[3] : FALSE,
                   );
                 $reponse_data = theme($hook, $variables);
                 break;
               case 'cdm_list_of_taxa':
                   $variables = array(
                     'records' => $obj,
                     'freetextSearchResults' => isset($args[0]) ? $args[0] : array(),
                     'show_classification' => isset($args[1]) ? $args[1] : FALSE);
                   $reponse_data = theme($hook, $variables);
                   break;
               case 'cdm_media_caption':
                 $variables = $arg;
                 $variables['media'] = $obj;
                 $reponse_data = theme($hook, $variables);
                 break;
               default:
                 drupal_set_message(t(
                 'Theme !theme is not yet supported by the function !function.', array(
                 '!theme' => $hook,
                 '!function' => __FUNCTION__,
                 )), 'error');
                 break;
             } // END of theme hook switch
           } // END of tread as theme hook
           if($do_gzip){
             $reponse_data = gzencode($reponse_data, 2, FORCE_GZIP);
             drupal_add_http_header('Content-Encoding', 'gzip');
+          }
           drupal_add_http_header('Content-Type', 'text/html; charset=utf-8');
           drupal_add_http_header('Content-Length', strlen($reponse_data));
           print $reponse_data;
         } // END of handle $hook either as compose ot theme hook
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function setvalue_session() {
         if ($_REQUEST['var'] && strlen($_REQUEST['var']) > 4) {
           $var_keys = substr($_REQUEST['var'], 1, strlen($_REQUEST['var']) - 2);
           $var_keys = explode('][', $var_keys);
+        }
         else {
           return;
+        }
         $val = isset($_REQUEST['val']) ? $_REQUEST['val'] : NULL;
         // Prevent from malicous tags.
         $val = strip_tags($val);
         $session_var = &$_SESSION;
         //$i = 0;
         foreach ($var_keys as $key) {
           // $hasMoreKeys = ++$i < count($session);
           if (!isset($session_var[$key]) || !is_array($session_var[$key])) {
             $session_var[$key] = array();
+          }
           $session_var = &$session_var[$key];
+        }
         $session_var = $val;
         if (isset($_REQUEST['destination'])) {
           drupal_goto($_REQUEST['destination']);
+        }
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function uri_uriByProxy($uri, $theme = FALSE) {
         // usage: url('cdm_api/proxy/'.urlencode($content_url)."/$theme");)
         return url('cdm_api/proxy/' . urlencode($uri) . (isset($theme) ? "/$theme" : ''));
+      }
       /**
        * Composes the the absolute REST service URI to the annotations pager
        * for the given CDM entity.
+       *
        * NOTE: Not all CDM Base types are yet supported.
+       *
        * @param $cdm_entity
        *   The CDM entity to construct the annotations pager uri for
        */
       function cdm_compose_annotations_uri($cdm_entity) {
         $cdm_entity_type = $cdm_entity->class;
         if($cdm_entity_type == 'DerivedUnitFacade'){
           // TODO with the below code we may miss annotations.
           //  Better implement a derivedUnitFacade/{uuid}/annotations service and use that instead
           if(isset($cdm_entity->fieldUnitEntityReference)){
             $cdm_entity_type = $cdm_entity->fieldUnitEntityReference->type;
             $cdm_entity_uuid = $cdm_entity->fieldUnitEntityReference->uuid;
           } elseif(isset($cdm_entity->baseUnitEntityReference)){
             $cdm_entity_type = $cdm_entity->baseUnitEntityReference->type;
             $cdm_entity_uuid = $cdm_entity->baseUnitEntityReference->uuid;
+          }
         } elseif ($cdm_entity_type == 'TypedEntityReference'){
           $cdm_entity_type = $cdm_entity->type;
           $cdm_entity_uuid = $cdm_entity->uuid;
         } else {
           if (isset($cdm_entity->uuid)) {
             $cdm_entity_uuid = $cdm_entity->uuid;
+          }
+        }
         if(!isset($cdm_entity_uuid) || !isset($cdm_entity_type) || !$cdm_entity_type ){
           // silently give up
           return;
+        }
         $ws_base_uri = cdm_ws_base_uri($cdm_entity_type);
         if($ws_base_uri === null){
             trigger_error(check_plain('Unsupported CDM Class - no annotations available for ' . $cdm_entity_type), E_USER_ERROR);
+        }
         return cdm_compose_ws_url($ws_base_uri, array(
           $cdm_entity_uuid,
           'annotations',
         ));
+      }
       /**
        * Provides the base URI of the cdm REST service responsible for the passed simple name
        * of a CDM java class. For example 'TaxonName' is the simple name of 'eu.etaxonomy.cdm.model.name.TaxonName'
+       *
        * @param $cdm_type_simple
        *    simple name of a CDM java class
        * @return null|string
        */
       function cdm_ws_base_uri($cdm_type_simple)
+      {
         $ws_base_uri = NULL;
         switch ($cdm_type_simple) {
           case 'TaxonNode':
           case 'TaxonNodeDto':
             $ws_base_uri = CDM_WS_TAXONNODE;
           case 'TaxonBase':
           case 'Taxon':
           case 'Synonym':
             $ws_base_uri = CDM_WS_TAXON;
             break;
           case 'TaxonName':
             $ws_base_uri = CDM_WS_NAME;
             break;
           case 'Media':
             $ws_base_uri = CDM_WS_MEDIA;
             break;
           case 'Reference':
             $ws_base_uri = CDM_WS_REFERENCE;
             break;
           case 'Registration':
             $ws_base_uri = CDM_WS_REFERENCE;
             break;
           case 'FieldUnit':
           case 'DerivedUnit':
           case 'DnaSample':
           case 'MediaSpecimen':
             $ws_base_uri = CDM_WS_OCCURRENCE;
             break;
           case 'Amplification':
           case 'DerivationEvent':
           case 'DeterminationEvent':
           case 'GatheringEvent':
           case 'MaterialOrMethodEvent':
           case 'SingleRead':
             $ws_base_uri = CDM_WS_EVENTBASE;
             break;
           case 'Distribution':
           case 'TextData':
           case 'TaxonInteraction':
           case 'QuantitativeData':
           case 'IndividualsAssociation':
           case 'CommonTaxonName':
           case 'CategoricalData':
             $ws_base_uri = CDM_WS_DESCRIPTIONELEMENT;
             break;
           case 'Person':
           case 'Team':
           case 'AgentBase':
             $ws_base_uri = CDM_WS_AGENT;
             break;
           case 'PolytomousKey':
           case 'MediaKey':
           case 'MultiAccessKey':
             $ws_base_uri = $cdm_type_simple;
             $ws_base_uri[0] = strtolower($ws_base_uri[0]);
             break;
           case 'TextualTypeDesignation':
           case 'SpecimenTypeDesignation':
           case 'NameTypeDesignation':
           case 'TypeDesignationDTO':
             $ws_base_uri = CDM_WS_TYPEDESIGNATION;
             break;
           default:
             $ws_base_uri = null;
             drupal_set_message(
               t('cdm_ws_base_uri()  - cdm type name "@cdm_type_simple" unsupported',
                 array('@cdm_type_simple' => $cdm_type_simple )),
               'error');
+        }
         return $ws_base_uri;
+      }
       /**
        * Enter description here...
+       *
        * @param string $resource_uri
        * @param int $page_size
        *   The maximum number of entities returned per page.
        *   The default page size as configured in the cdm server
        *   will be used if set to NULL
        *   to return all entities in a single page).
        * @param int $page_index
        *   The number of the page to be returned, the first page has the
        *   page_index = 0
        * @param array $query
        *   A array holding the HTTP request query parameters for the request
        * @param string $method
        *   The HTTP method to use, valid values are "GET" or "POST"
        * @param bool $absolute_uri
        *   TRUE when the URL should be treated as absolute URL.
+       *
        * @return object
        *   A CDM Pager object
+       *
        */
       function cdm_ws_page($resource_uri, $page_size, $page_index, array $query = array(), $method = 'GET', $absolute_uri = FALSE) {
         $query['pageNumber'] = $page_index;
         $query['pageSize'] = $page_size;
         $pager = cdm_ws_get($resource_uri, NULL, queryString($query), $method, $absolute_uri);
         if(is_array($pager)){
           trigger_error("Expecting web service to return pager objects but received an array:<br/>" . $resource_uri . '?' . queryString($query) . '<br/>Wrapping response in pager to recover from error.', E_USER_WARNING);
           $records = $pager;
           $pager = new stdClass();
           $pager->records = $records;
           $pager->count = count($records);
           $pager->pageSize = $pager->count;
           $pager->nextIndex = null;
+        }
         return $pager;
+      }
       /**
        * Sends a http GET request to the generic page method which allows for filtering entities by Restrictions.
+       *
        * @param $cdm_entity_type
        * @param $class_restriction
        *   Optional param to narrow down polymorph types to a specific type.
        * @param array $restrictions
        *   An array of Restriction objects
        * @param array $init_strategy
        *   The init strategy to initialize the entity beans while being loaded from the
        *   persistent storage by the cdm
        * @param int $page_size
        *   The maximum number of entities returned per page.
        *   The default page size as configured in the cdm server
        *   will be used if set to NULL
        *   to return all entities in a single page).
        * @param int $page_index
        *   The number of the page to be returned, the first page has the
        *   pageNumber = 0
+       *
        * @return object
        *   A CDM Pager object
        */
       function cdm_ws_page_by_restriction($cdm_entity_type, $class_restriction, array $restrictions, array $init_strategy, $page_size, $page_index) {
         $restrictions_json = array(); // json_encode($restrictions);
         foreach ($restrictions as $restr){
           $restrictions_json[] = json_encode($restr);
+        }
         $filter_parameters = [
           'restriction' => $restrictions_json,
           'initStrategy' => $init_strategy
         ];
         if($class_restriction){
           $filter_parameters['class'] = $class_restriction;
+        }
         return cdm_ws_page(
             'portal/' . cdm_ws_base_uri($cdm_entity_type),
             $page_size,
             $page_index,
           $filter_parameters,
           "GET"
           );
+      }
       /**
        * Fetches all entities returned by the the generic page method for the Restrictions applied as filter.
+       *
        * @param $cdm_entity_type
        * @param $class_restriction
        *   Optional param to narrow down polymorph types to a specific type.
        * @param array $restrictions
        *   An array of Restriction objects
        * @param array $init_strategy
        *   The init strategy to initialize the entity beans while being loaded from the
        *   persistent storage by the cdm
+       *
        * @return array
        *   A array of CDM entities
        */
       function cdm_ws_fetch_all_by_restriction($cdm_entity_type, $class_restriction, array $restrictions, array $init_strategy){
         $page_index = 0;
         // using a bigger page size to avoid to many multiple requests
         $page_size = 500;
         $entities = array();
         while ($page_index !== FALSE && $page_index < 1){
           $pager =  cdm_ws_page_by_restriction($cdm_entity_type, $class_restriction, $restrictions, $init_strategy, $page_size, $page_index);
           if(isset($pager->records) && is_array($pager->records)) {
             $entities = array_merge($entities, $pager->records);
             if(!empty($pager->nextIndex)){
               $page_index = $pager->nextIndex;
             } else {
               $page_index = FALSE;
+            }
           } else {
             $page_index = FALSE;
+          }
+        }
         return $entities;
+      }
         /**
        * Fetches all entities from the given REST endpoint using the pager mechanism.
+       *
        * @param string $resourceURI
        * @param array $query
        *   A array holding the HTTP request query parameters for the request
        * @param string $method
        *   The HTTP method to use, valid values are "GET" or "POST";
        * @param bool $absoluteURI
        *   TRUE when the URL should be treated as absolute URL.
+       *
        * @return array
        *     A list of CDM entitites
+       *
        */
       function cdm_ws_fetch_all($resourceURI, array $query = array(), $method = 'GET', $absoluteURI = FALSE) {
         $page_index = 0;
         // using a bigger page size to avoid too many multiple requests
         $page_size = 500;
         $entities = [];
         while ($page_index !== FALSE){
           $pager =  cdm_ws_page($resourceURI, $page_size, $page_index, $query,  $method, $absoluteURI);
           if(isset($pager->records) && is_array($pager->records)) {
             $entities = array_merge($entities, $pager->records);
             if(!empty($pager->nextIndex)){
               $page_index = $pager->nextIndex;
             } else {
               $page_index = FALSE;
+            }
           } else {
             $page_index = FALSE;
+          }
+        }
         return $entities;
+      }
       /*
       function cdm_ws_taxonomy_compose_resourcePath($path = NULL){
         $viewrank = _cdm_taxonomy_compose_viewrank();
         return CDM_WS_PORTAL_TAXONOMY . '/' . ($viewrank ? $viewrank : '' ) . ($path
         ? '/' . $path : '') ;
+      }
       */
       /**
        * @todo Enter description here...
+       *
        * @param string $taxon_uuid
        *  The UUID of a cdm taxon instance
        * @param string $ignore_rank_limit
        *   Whether to ignore the variable 'taxontree_ranklimit' set by admin in the settings
+       *
        * @return string
        *   A cdm REST service URL path to a Classification
        */
       function cdm_compose_taxonomy_root_level_path($taxon_uuid = FALSE, $ignore_rank_limit = FALSE) {
         $view_uuid = get_current_classification_uuid();
         $rank_uuid = NULL;
         if (!$ignore_rank_limit) {
           $rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
+        }
         if (!empty($taxon_uuid)) {
           return cdm_compose_ws_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
             $view_uuid,
             $taxon_uuid,
           ));
+        }
         else {
           if (is_uuid($rank_uuid)) {
             return cdm_compose_ws_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_AT_RANK, array(
               $view_uuid,
               $rank_uuid,
             ));
+          }
           else {
             return cdm_compose_ws_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES, array(
               $view_uuid,
             ));
+          }
+        }
+      }
       /**
        * Retrieves from the cdm web service with the first level of childnodes of a classification.
+       *
        * The level is either the real root level ot it is a lover level if a rank limit has been set.
        * (@see  cdm_compose_taxonomy_root_level_path() for more on the rank limit).
+       *
        * Operates in two modes depending on whether the parameter
        * $taxon_uuid is set or NULL.
+       *
        * A) $taxon_uuid = NULL:
        *  1. retrieve the Classification for the uuid set in the $_SESSION['cdm']['taxonomictree_uuid']
        *  2. otherwise return the default classification as defined by the admin via the settings
+       *
        * b) $taxon_uuid is set:
        *   return the classification to whcih the taxon belongs to.
+       *
        * @param UUID $taxon_uuid
        *   The UUID of a cdm taxon instance
        */
       function cdm_ws_taxonomy_root_level($taxon_uuid = NULL) {
           $response = NULL;
           // 1st try
           $response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid), NULL, NULL, 'GET', TRUE);
           if ($response == NULL) {
             // 2dn try by ignoring the rank limit
             $response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid, TRUE), NULL, NULL, 'GET', TRUE);
+          }
           if ($response == NULL) {
             // 3rd try, last fallback:
             //    return the default classification
             if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
               // Delete the session value and try again with the default.
               unset($_SESSION['cdm']['taxonomictree_uuid']);
               drupal_set_message("Could not find a valid classification, falling back to the default classification.", 'warning');
               return cdm_ws_taxonomy_root_level($taxon_uuid);
+            }
             else {
               // Check if taxonomictree_uuid is valid.
               // expecting an array of taxonNodes,
               // empty classifications are ok so no warning in this case!
               $test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
               if (!is_array($test)) {
                 // The default set by the admin seems to be invalid or is not even set.
                 drupal_set_message(_no_classfication_uuid_message(), 'warning');
+              }
               if (count($test) == 0) {
                 // The default set by the admin seems to be invalid or is not even set.
                 drupal_set_message("The chosen classification is empty.", 'status');
+              }
+            }
+          }
         return $response;
+      }
       /**
        * Determines the tree path of the taxon given as uuid to the root of the classification tree.
+       *
        * The root either is the absolute root of the tree or a rank specific root if the TAXONTREE_RANKLIMIT
        * variable is set.
+       *
        * @param string $taxon_uuid
+       *
        * @return array
        *   An array of CDM TaxonNodeDTO objects
        */
       function cdm_ws_taxonomy_pathFromRoot($taxon_uuid) {
         $view_uuid = get_current_classification_uuid();
         $rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
         $response = NULL;
         if (is_uuid($rank_uuid)) {
           $response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM_TO_RANK, array(
             $view_uuid,
             $taxon_uuid,
             $rank_uuid,
           ));
+        }
         else {
           $response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM, array(
             $view_uuid,
             $taxon_uuid,
           ));
+        }
         if ($response == NULL) {
           // Error handing.
       //    if (is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
       //      // Delete the session value and try again with the default.
       //      unset($_SESSION['cdm']['taxonomictree_uuid']);
       //      return cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
       //    }
       //    else {
             // Check if taxonomictree_uuid is valid.
             $test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
             if ($test == NULL) {
               // The default set by the admin seems to be invalid or is not even set.
               drupal_set_message(_no_classfication_uuid_message(), 'warning');
+            }
       //    }
+        }
         return $response;
+      }
       // =============================Terms and Vocabularies ========================================= //
       /**
        * Returns the localized representation for the given term.
+       *
        * @param Object $definedTermBase
        * 	  of cdm type DefinedTermBase
        * @return string
        * 	  the localized representation_L10n of the term,
        *    otherwise the titleCache as fall back,
        *    otherwise the default_representation which defaults to an empty string
        */
       function cdm_term_representation($definedTermBase, $default_representation = '') {
         if ( isset($definedTermBase->representation_L10n) ) {
           return $definedTermBase->representation_L10n;
         } elseif ( isset($definedTermBase->titleCache)) {
           return $definedTermBase->titleCache;
+        }
         return $default_representation;
+      }
       /**
        * Returns the abbreviated localized representation for the given term.
+       *
        * @param Object $definedTermBase
        * 	  of cdm type DefinedTermBase
        * @return string
        * 	  the localized representation_L10n_abbreviatedLabel of the term,
        *    if this representation is not available the function delegates the
        *    call to cdm_term_representation()
        */
       function cdm_term_representation_abbreviated($definedTermBase, $default_representation = '') {
         if ( isset($definedTermBase->representation_L10n_abbreviatedLabel) ) {
           return $definedTermBase->representation_L10n_abbreviatedLabel;
         } else {
           cdm_term_representation($definedTermBase, $default_representation);
+        }
+      }
       /**
        * Transforms the list of the given term base instances to a alphabetical ordered options array.
+       *
        * The options array is suitable for drupal form API elements that allow multiple choices.
        * @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
+       *
        * @param array $terms
        *   a list of CDM DefinedTermBase instances
+       *
        * @param $term_label_callback
        *   A callback function to override the term representations
+       *
        * @param bool $empty_option
        *   An additional element do be placed at the beginning og the list. This element will be the default option.
+       *
        * @return array
        *   the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
        */
       function cdm_terms_as_options($terms, $term_label_callback = NULL, $empty_option = FALSE){
         $options = array();
         if(isset($terms) && is_array($terms)) {
           foreach ($terms as $term) {
             if ($term_label_callback && function_exists($term_label_callback)) {
               $options[$term->uuid] = call_user_func($term_label_callback, $term);
             } else {
               //TODO use cdm_term_representation() here?
               $options[$term->uuid] = t('@term', array('@term' => $term->representation_L10n));
+            }
+          }
+        }
         if($empty_option !== FALSE){
           array_unshift ($options, "");
+        }
         return $options;
+      }
       /**
        * Creates and array of options for drupal select form elements.
+       *
        * @param $vocabulary_uuid
        *   The UUID of the CDM Term Vocabulary
        * @param $term_label_callback
        *   An optional call back function which can be used to modify the term label
        * @param bool $empty_option
        *   An additional element do be placed at the beginning og the list. This element will be the default option.
        * @param array $include_filter
        *   An associative array consisting of a field name an regular expression. All term matching
        *   these filter are included. The value of the field is converted to a String by var_export()
        *   so a boolean 'true' can be matched by '/true/'
        * @param string $order_by
        *   One of the order by constants defined in this file
        * @return array
        *   the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
        */
       function cdm_vocabulary_as_option($vocabulary_uuid, $term_label_callback = NULL, $empty_option = FALSE,
                                         array $include_filter = null, $order_by = CDM_ORDER_BY_ORDER_INDEX_ASC) {
         static $vocabularyOptions = array();
         if (!isset($vocabularyOptions[$vocabulary_uuid])) {
           $terms = cdm_ws_fetch_all('termVocabulary/' . $vocabulary_uuid . '/terms',
             array(
               'orderBy' => $order_by
+            )
           );
           // apply the include filter
           if($include_filter != null){
             $included_terms = array();
             foreach ($terms as $term){
               $include = true;
               foreach ($include_filter as $field=>$regex){
                 $include =  preg_match($regex, var_export($term->$field, true)) === 1;
                 if(!$include){
                   break;
+                }
+              }
               if($include){
                 $included_terms[] = $term;
+              }
+            }
             $terms = $included_terms;
+          }
           // make options list
           $vocabularyOptions[$vocabulary_uuid] = cdm_terms_as_options($terms, $term_label_callback, $empty_option);
+        }
         $options = $vocabularyOptions[$vocabulary_uuid];
         return $options;
+      }
       /**
        * Creates and array of defaults for drupal select form elements.
+       *
        * @param $vocabulary_uuid
        *   The UUID of the CDM Term Vocabulary
        * @param $term_label_callback
        *   An optional call back function which can be used to modify the term label
        * @param bool $empty_option
        *   An additional element do be placed at the beginning og the list. This element will be the default option.
        * @param array $include_filter
        *   An associative array consisting of a field name an regular expression. All term matching
        *   these filter are included. The value of the field is converted to a String by var_export()
        *   so a boolean 'true' can be matched by '/true/'
        * @param string $order_by
        *   One of the order by constants defined in this file
        * @return array
        *   the terms in an array (key: uuid => value: uuid) as defaults for a form element that allows multiple choices.
        */
       function cdm_vocabulary_as_defaults($vocabulary_uuid, array $include_filter = null) {
         $options = cdm_vocabulary_as_option($vocabulary_uuid, null, null, $include_filter);
         $defaults = array();
         foreach ($options as $uuid => $value){
           $defaults[$uuid] = $uuid;
+        }
         return $defaults;
+      }
       /**
        * @param $term_type string one of
        *  - Unknown
        *  - Language
        *  - NamedArea
        *  - Rank
        *  - Feature
        *  - AnnotationType
        *  - MarkerType
        *  - ExtensionType
        *  - DerivationEventType
        *  - PresenceAbsenceTerm
        *  - NomenclaturalStatusType
        *  - NameRelationshipType
        *  - HybridRelationshipType
        *  - SynonymRelationshipType
        *  - TaxonRelationshipType
        *  - NameTypeDesignationStatus
        *  - SpecimenTypeDesignationStatus
        *  - InstitutionType
        *  - NamedAreaType
        *  - NamedAreaLevel
        *  - RightsType
        *  - MeasurementUnit
        *  - StatisticalMeasure
        *  - MaterialOrMethod
        *  - Material
        *  - Method
        *  - Modifier
        *  - Scope
        *  - Stage
        *  - KindOfUnit
        *  - Sex
        *  - ReferenceSystem
        *  - State
        *  - NaturalLanguageTerm
        *  - TextFormat
        *  - DeterminationModifier
        *  - DnaMarker
+       *
        * @param  $order_by
        *  Optionally sort option (default: CDM_ORDER_BY_TITLE_CACHE_ASC)
        *  possible values:
        *    - CDM_ORDER_BY_ID_ASC
        *    - CDM_ORDER_BY_ID_DESC
        *    - CDM_ORDER_BY_TITLE_CACHE_ASC
        *    - CDM_ORDER_BY_TITLE_CACHE_DESC
        *    - CDM_ORDER_BY_ORDER_INDEX_ASC (can only be used with OrderedTerms!!)
        *    - CDM_ORDER_BY_ORDER_INDEX_DESC (can only be used with OrderedTerms!!)
        * @param bool $empty_option
        *   An additional element do be placed at the beginning og the list. This element will be the default option.
        * @return array
        *    the terms in an array (key: uuid => value: label) as options for a form element that allows multiple choices.
        */
       function cdm_terms_by_type_as_option($term_type, $order_by = CDM_ORDER_BY_TITLE_CACHE_ASC, $term_label_callback = NULL, $empty_option = FALSE){
         $terms = cdm_ws_fetch_all(
           CDM_WS_TERM,
           array(
             'class' => $term_type,
             'orderBy' => $order_by
+          )
         );
         return cdm_terms_as_options($terms, $term_label_callback, $empty_option);
+      }
       /**
        * @param array $none_option
        *    Will add a filter option to search for NULL values
        * @param $with_empty_option
        *    Will add an empty option to the beginning. Choosing this option will disable the filtering.
        * @return array
        *   An array of options with uuids as key and the localized term representation as value
        */
       function cdm_type_designation_status_filter_terms_as_options($none_option_label, $with_empty_option = false){
         $filter_terms = cdm_ws_get(CDM_WS_TYPE_DESIGNATION_STATUS_FILTER_TERMS);
         if(isset($filter_terms) && is_array($filter_terms)) {
           foreach ($filter_terms as $filter_term) {
             $options[join(',', $filter_term->uuids)] = $filter_term->label;
+          }
+        }
         if(is_string($none_option_label)){
           $options = array_merge(array('NULL' => $none_option_label), $options);
+        }
         if($with_empty_option !== FALSE){
           array_unshift ($options, "");
+        }
         return $options;
+      }
       /**
        * Callback function which provides the localized representation of a cdm term.
+       *
        * The representation is build by concatenating the abbreviated label with the label
        * and thus is especially useful for relationship terms
        * The localized representation provided by the cdm can be overwritten by
        * providing a drupal translation.
+       *
        */
       function _cdm_relationship_type_term_label_callback($term) {
         if (isset($term->representation_L10n_abbreviatedLabel)) {
           return $term->representation_L10n_abbreviatedLabel . ' : '
           . t('@term', array('@term' => $term->representation_L10n));
+        }
       else {
           return t('@term', array('@term' => $term->representation_L10n));
+        }
+      }
       /**
        * Callback function which provides the localized inverse representation of a cdm term.
+       *
        * The representation is build by concatenating the abbreviated label with the label
        * and thus is especially useful for relationship terms
        * The localized representation provided by the cdm can be overwritten by
        * providing a drupal translation.
+       *
        */
       function _cdm_relationship_type_term_inverse_label_callback($term) {
         if (isset($term->inverseRepresentation_L10n_abbreviatedLabel)) {
           return $term->inverseRepresentation_L10n_abbreviatedLabel . ' : '
             . t('@term', array('@term' => $term->inverseRepresentation_L10n));
+        }
         else {
           return t('@term', array('@term' => $term->inverseRepresentation_L10n));
+        }
+      }
       /**
        * Returns the localized abbreviated label of the relationship term.
+       *
        * In case the abbreviated label is not set the normal representation is returned.
+       *
        * @param $term
        * @param bool $is_inverse_relation
        * @return string
        *   The abbreviated label
        */
       function cdm_relationship_type_term_abbreviated_label($term, $is_inverse_relation = false){
         if($is_inverse_relation) {
           if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {
             $abbr_label = $term->inverseResentation_L10n_abbreviatedLabel;
           } else {
             $abbr_label = $term->inverseRepresentation_L10n;
+          }
         } else {
           if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {
             $abbr_label = $term->representation_L10n_abbreviatedLabel;
           } else {
             $abbr_label = $term->representation_L10n;
+          }
+        }
         return $abbr_label;
+      }
       /**
        * Returns the symbol of the relationship term.
+       *
        * In case the symbol is not set the function falls back to use the abbreviated label or
        * the normal representation..
+       *
        * @param $term
        * @param bool $is_inverse_relation
        * @return string
        *   The abbreviated label
        */
       function cdm_relationship_type_term_symbol($term, $is_inverse_relation = false){
         if($is_inverse_relation) {
           if (isset($term->inverseSymbol) && $term->inverseSymbol) {
             $symbol = $term->inverseSymbol;
           } else if (isset($term->inverseRepresentation_L10n_abbreviatedLabel) && $term->inverseRepresentation_L10n_abbreviatedLabel) {
             $symbol = $term->inverseResentation_L10n_abbreviatedLabel;
           } else {
             $symbol = $term->inverseRepresentation_L10n;
+          }
         } else {
           if (isset($term->symbol) && $term->symbol) {
             $symbol = $term->symbol;
           } else if (isset($term->representation_L10n_abbreviatedLabel) && $term->representation_L10n_abbreviatedLabel) {
             $symbol = $term->representation_L10n_abbreviatedLabel;
           } else {
             $symbol = $term->representation_L10n;
+          }
+        }
         return $symbol;
+      }
       // ========================================================================================== //
       /**
        * @todo Improve documentation of this function.
+       *
        * eu.etaxonomy.cdm.model.description.
        * CategoricalData
        * CommonTaxonName
        * Distribution
        * IndividualsAssociation
        * QuantitativeData
        * TaxonInteraction
        * TextData
        */
       function cdm_descriptionElementTypes_as_option($prependEmptyElement = FALSE) {
         static $types = array(
           "CategoricalData",
           "CommonTaxonName",
           "Distribution",
           "IndividualsAssociation",
           "QuantitativeData",
           "TaxonInteraction",
           "TextData",
         );
         static $options = NULL;
         if ($options == NULL) {
           $options = array();
           if ($prependEmptyElement) {
             $options[' '] = '';
+          }
           foreach ($types as $type) {
             // No internatianalization here since these are purely technical terms.
             $options["eu.etaxonomy.cdm.model.description." . $type] = $type;
+          }
+        }
         return $options;
+      }
       /**
        * Fetches all TaxonDescription descriptions elements which are associated to the
        * Taxon specified by the $taxon_uuid and merges the elements into the given
        * feature tree.
        * @param $feature_tree
        *     The CDM FeatureTree to be used as template
        * @param $taxon_uuid
        *     The UUID of the taxon
        * @param $excludes
        *     UUIDs of features to be excluded
        * @return object
        *     The CDM FeatureTree which was given as parameter merged tree whereas the
        *     CDM FeatureNodes are extended by an additional field 'descriptionElements'
        *     witch will hold the according $descriptionElements.
        */
       function cdm_ws_descriptions_by_featuretree($feature_tree, $taxon_uuid, $exclude_uuids = array()) {
         if (!$feature_tree) {
           drupal_set_message(check_plain(t("No 'FeatureTree' has been set so far.
             In order to see the species profiles of your taxa, please select a
             'FeatureTree' in the !settings"), array('!settings' => l(t('CDM Dataportal Settings'), 'admin/config/cdm_dataportal/layout'))), 'warning');
           return FALSE;
+        }
         $description_elements = cdm_ws_fetch_all(CDM_WS_DESCRIPTIONELEMENT_BY_TAXON,
             array(
             'taxon' => $taxon_uuid,
             'features' => cdm_featureTree_elements_toString($feature_tree->root, ',', 'uuid', $exclude_uuids)
             ),
             'POST'
         );
         // Combine all descriptions into one feature tree.
         $merged_nodes = _mergeFeatureTreeDescriptions($feature_tree->root->childNodes, $description_elements);
         $feature_tree->root->childNodes = $merged_nodes;
         return $feature_tree;
+      }
       /**
        * Returns a filtered a list of annotations for the cdm entity given as parameter $cdm_entity.
        * If the annotations are not yet already loded with the cdm entity the cdm REST service will
        * be requested for the annotations.
+       *
        * @param string $cdm_entity
        *   An annotatable cdm entity.
        * @param array $include_types
        *   If an array of annotation type uuids is supplied by this parameter the
        *   list of annotations is resticted to those which belong to this type.
+       *
        * @return array
        *   An array of Annotation objects or an empty array.
        */
       function cdm_ws_fetch_annotations(&$cdm_entity, $include_types = FALSE) {
         if(!isset($cdm_entity->annotations)){
           $annotation_url = cdm_compose_annotations_uri($cdm_entity);
           $cdm_entity->annotations = cdm_ws_fetch_all($annotation_url, array(), 'GET', TRUE);
+        }
         $annotations = array();
         foreach ($cdm_entity->annotations as $annotation) {
           if ($include_types) {
             if (
               ( isset($annotation->annotationType->uuid) && in_array($annotation->annotationType->uuid, $include_types, TRUE) )
               || ($annotation->annotationType === NULL && in_array('NULL_VALUE', $include_types, TRUE))
             ) {
               $annotations[] = $annotation;
+            }
+          }
           else {
             $annotations[] = $annotation;
+          }
+        }
         return $annotations;
+      }
       /**
        * Provides the list of visible annotations for the $cdm_entity.
+       *
        * @param $cdm_entity
        *     The annotatable CDM entity
+       *
        * @return array of the annotations which are visible according to the settings as stored in ANNOTATION_TYPES_VISIBLE
        */
       function cdm_fetch_visible_annotations($cdm_entity){
         static $annotations_types_filter = null;
         if(!$annotations_types_filter) {
           $annotations_types_filter = unserialize(EXTENSION_TYPES_VISIBLE_DEFAULT);
+        }
         return cdm_ws_fetch_annotations($cdm_entity, variable_get(ANNOTATION_TYPES_VISIBLE, $annotations_types_filter));
+      }
       /**
        * Loads the annotations from the REST service an adds them as field to the given $annotatable_entity.
+       *
        * NOTE: The annotations are not filtered by the ANNOTATION_TYPES_VISIBLE settings since this method is meant to act
        * like the annotations have been fetched in the ORM-framework in the service.
+       *
        * @param object $annotatable_entity
        *   The CDM AnnotatableEntity to load annotations for
        */
       function cdm_load_annotations(&$annotatable_entity) {
         if (isset($annotatable_entity) && !isset($annotatable_entity->annotations)) {
           $annotations = cdm_ws_fetch_annotations($annotatable_entity);
           if (is_array($annotations)) {
             $annotatable_entity->annotations = $annotations;
+          }
+        }
+      }
       function cdm_load_tagged_full_title($taxon_name){
         if(isset($taxon_name) && !isset($taxon_name->taggedFullTitle)){
           $tagged_full_title = cdm_ws_get(CDM_WS_NAME, array($taxon_name->uuid, 'taggedFullTitle'));
           if(is_array($tagged_full_title)){
             $taxon_name->taggedFullTitle = $tagged_full_title;
+          }
+        }
+      }
       /**
        * Extends the $cdm_entity object by the field if it is not already existing.
+       *
        * This function can only be used for fields with 1 to many relations.
+        *
        * @param $cdm_base_type
        * @param $field_name
        * @param $cdm_entity
        */
       function cdm_lazyload_array_field($cdm_base_type, $field_name, &$cdm_entity)
+      {
         if (!isset($cdm_entity->$field_name)) {
           $items = cdm_ws_fetch_all('portal/' . $cdm_base_type . '/' . $cdm_entity->uuid . '/' . $field_name);
           $cdm_entity->$field_name = $items;
+        }
+      }
       /**
        * Get a NomenclaturalReference string.
+       *
        * Returns the NomenclaturalReference string with correctly placed
        * microreference (= reference detail) e.g.
        * in Phytotaxa 43: 1-48. 2012.
+       *
        * @param string $referenceUuid
        *   UUID of the reference.
        * @param string $microreference
        *   Reference detail.
+       *
        * @return string
        *   a NomenclaturalReference.
        */
       function cdm_ws_getNomenclaturalReference($referenceUuid, $microreference) {
         // TODO the below statement avoids error boxes due to #4644 remove it once this ticket is solved
         if(is_array($microreference) || is_object($microreference)) {
           return '';
+        }
         $obj = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array(
           $referenceUuid,
         ), "microReference=" . urlencode($microreference));
         if ($obj) {
           return $obj->String;
+        }
         else {
           return NULL;
+        }
+      }
       /**
        * finds and returns the FeatureNode denoted by the given $feature_uuid
+       *
        * @param $feature_tree_nodes
        *    The nodes contained in CDM FeatureTree entitiy: $feature->root->childNodes
        * @param $feature_uuid
        *    The UUID of the Feature
        * @return object
        *    the FeatureNode or null
        */
       function &cdm_feature_tree_find_node($feature_tree_nodes, $feature_uuid){
         // 1. scan this level
         foreach ($feature_tree_nodes as $node){
           if($node->term->uuid == $feature_uuid){
             return $node;
+          }
+        }
         // 2. descend into childen
         foreach ($feature_tree_nodes as $node){
           if(is_array($node->childNodes)){
             $node = cdm_feature_tree_find_node($node->childNodes, $feature_uuid);
             if($node) {
               return $node;
+            }
+          }
+        }
         $null_var = null; // kludgy workaround to avoid "PHP Notice: Only variable references should be returned by reference"
         return $null_var;
+      }
       /**
        * Merges the given featureNodes structure with the descriptionElements.
+       *
        * This method is used in preparation for rendering the descriptionElements.
        * The descriptionElements which belong to a specific feature node are appended
        * to a the feature node by creating a new field:
        *  - descriptionElements: the CDM DescriptionElements which belong to this feature
        * The descriptionElements will be cleared in advance in order to allow reusing the
        * same feature tree without the risk of mixing sets of description elements.
+       *
        * which originally is not existing in the cdm.
+       *
+       *
+       *
        * @param array $featureNodes
        *    An array of cdm FeatureNodes which may be hierarchical since feature nodes
        *    may have children.
        * @param array $descriptionElements
        *    An flat array of cdm DescriptionElements
        * @return array
        *    The $featureNodes structure enriched with the according $descriptionElements
        */
       function _mergeFeatureTreeDescriptions($featureNodes, $descriptionElements) {
         foreach ($featureNodes as &$feature_node) {
           // since the $featureNodes array is reused for each description
           // it is necessary to clear the custom node fields in advance
           if(isset($feature_node->descriptionElements)){
             unset($feature_node->descriptionElements);
+          }
           // Append corresponding elements to an additional node field:
           // $node->descriptionElements.
           foreach ($descriptionElements as $element) {
             if ($element->feature->uuid == $feature_node->term->uuid) {
               if (!isset($feature_node->descriptionElements)) {
                 $feature_node->descriptionElements = array();
+              }
               $feature_node->descriptionElements[] = $element;
+            }
+          }
           // Recurse into node children.
           if (isset($feature_node->childNodes[0])) {
             $mergedChildNodes = _mergeFeatureTreeDescriptions($feature_node->childNodes, $descriptionElements);
             $feature_node->childNodes = $mergedChildNodes;
+          }
           if(!isset($feature_node->descriptionElements) && !isset($feature_node->childNodes[0])){
             unset($feature_node);
+          }
+        }
         return $featureNodes;
+      }
       /**
        * Sends a GET or POST request to a CDM RESTService and returns a de-serialized object.
+       *
        * The response from the HTTP GET request is returned as object.
        * The response objects coming from the webservice configured in the
        * 'cdm_webservice_url' variable are being cached in a level 1 (L1) and / or
        *  in a level 2 (L2) cache.
+       *
        * Since the L1 cache is implemented as static variable of the cdm_ws_get()
        * function, this cache persists only per each single page execution.
        * Any object coming from the webservice is stored into it by default.
        * In contrast to this default caching mechanism the L2 cache only is used if
        * the 'cdm_webservice_cache' variable is set to TRUE,
        * which can be set using the modules administrative settings section.
        * Objects stored in this L2 cache are serialized and stored
        * using the drupal cache in the '{prefix}cache_cdm_ws' cache table. So the
        * objects that are stored in the database will persist as
        * long as the drupal cache is not being cleared and are available across
        * multiple script executions.
+       *
        * @param string $uri
        *   URL to the webservice.
        * @param array $pathParameters
        *   An array of path parameters.
        * @param string $query_string
        *   A query_string string to be appended to the URL.
        * @param string $method
        *   The HTTP method to use, valid values are "GET" or "POST";
        * @param bool $absoluteURI
        *   TRUE when the URL should be treated as absolute URL.
+       *
        * @return object| array
        *   The de-serialized webservice response object.
        */
       function cdm_ws_get($uri, $pathParameters = array(), $query_string = NULL, $method = "GET", $absoluteURI = FALSE) {
         static $cacheL1 = array();
         $data = NULL;
         // store query_string string in $data and clear the query_string, $data will be set as HTTP request body
         if($method == 'POST'){
           $data = $query_string;
           $query_string = NULL;
+        }
         // Transform the given uri path or pattern into a proper webservice uri.
         if (!$absoluteURI) {
           $uri = cdm_compose_ws_url($uri, $pathParameters, $query_string);
         } else {
           if($query_string){
             $uri = append_query_parameters($uri, $query_string);
+          }
+        }
         cdm_ws_apply_classification_subtree_filter($uri);
         // read request parameter 'cacheL2_refresh'
         // which allows refreshing the level 2 cache
         $do_cacheL2_refresh = isset($_REQUEST['cacheL2_refresh']) && $_REQUEST['cacheL2_refresh'] == 1;
         $is_cdm_ws_uri = _is_cdm_ws_uri($uri);
         $use_cacheL2 = variable_get('cdm_webservice_cache', 1);
         if($method == 'GET'){
           $cache_key = $uri;
         } else {
           // sha1 creates longer hashes and thus will cause fewer collisions than md5.
           // crc32 is faster but creates much shorter hashes
           $cache_key = $uri . '[' . $method . ':' . sha1($data) .']';
+        }
         if (array_key_exists($cache_key, $cacheL1)) {
           $cacheL1_obj = $cacheL1[$uri];
+        }
         $set_cacheL1 = FALSE;
         if ($is_cdm_ws_uri && !isset($cacheL1_obj)) {
           $set_cacheL1 = TRUE;
+        }
         // Only cache cdm webservice URIs.
         $set_cacheL2 = $use_cacheL2 && $is_cdm_ws_uri && $set_cacheL1;
         $cacheL2_entry = FALSE;
         if ($use_cacheL2 && !$do_cacheL2_refresh) {
           // Try to get object from cacheL2.
           $cacheL2_entry = cache_get($cache_key, 'cache_cdm_ws');
+        }
         if (isset($cacheL1_obj)) {
           //
           // The object has been found in the L1 cache.
           //
           $obj = $cacheL1_obj;
           if (cdm_debug_block_visible()) {
             cdm_ws_debug_add($uri, $method, $data, 0, 0, NULL, 'cacheL1');
+          }
+        }
         elseif ($cacheL2_entry) {
           //
           // The object has been found in the L2 cache.
           //
           $duration_parse_start = microtime(TRUE);
           $obj = unserialize($cacheL2_entry->data);
           $duration_parse = microtime(TRUE) - $duration_parse_start;
           if (cdm_debug_block_visible()) {
             cdm_ws_debug_add($uri, $method, $data, 0, $duration_parse, NULL, 'cacheL2');
+          }
+        }
         else {
           //
           // Get the object from the webservice and cache it.
           //
           $duration_fetch_start = microtime(TRUE);
           // Request data from webservice JSON or XML.
           $response = cdm_http_request($uri, $method, $data);
           $response_body = NULL;
           if (isset($response->data)) {
             $response_body = $response->data;
+          }
           $duration_fetch = microtime(TRUE) - $duration_fetch_start;
           $duration_parse_start = microtime(TRUE);
           // Parse data and create object.
           $obj = cdm_load_obj($response_body);
           if(isset($obj->servlet) && isset($obj->status) && is_numeric($obj->status)){
             // this is json error message returned by jetty #8914
             // wee need to replace it by null to avoid breaking existing assumptions in the code here
             // this is also related to #2711
             $obj = null;
+          }
           $duration_parse = microtime(TRUE) - $duration_parse_start;
           if (cdm_debug_block_visible()) {
             if ($obj || $response_body == "[]") {
               $status = 'valid';
+            }
             else {
               $status = 'invalid';
+            }
             cdm_ws_debug_add($uri, $method, $data, $duration_fetch, $duration_parse, strlen($response_body), $status);
+          }
           if ($set_cacheL2) {
             // Store the object in cache L2.
             // Comment @WA perhaps better if Drupal serializedatas here? Then the
             // flag serialized is set properly in the cache table.
             cache_set($cache_key, serialize($obj), 'cache_cdm_ws', CACHE_TEMPORARY);
+          }
+        }
         if ($obj) {
           // Store the object in cache L1.
           if ($set_cacheL1) {
             $cacheL1[$cache_key] = $obj;
+          }
+        }
         return $obj;
+      }
       function cdm_ws_apply_classification_subtree_filter(&$uri){
         $classification_subtree_filter_patterns = &drupal_static('classification_subtree_filter_patterns', array(
           "#/classification/[0-9a-f\-]{36}/childNodes#",
           /* covered by above pattern:
           "#/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
           '#/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
           */
           "#/portal/classification/[0-9a-f\-]{36}/childNodes#",
           /* covered by above pattern:
           "#/portal/classification/[0-9a-f\-]{36}/childNodesAt/[0-9a-f\-]{36}#",
           '#/portal/classification/[0-9a-f\-]{36}/childNodesOf/[0-9a-f\-]{36}#',
           */
           '#/portal/classification/[0-9a-f\-]{36}/pathFrom/[0-9a-f\-]{36}#',
           "#/portal/taxon/search#",
           "#/portal/taxon/find#",
           /* covered by above pattern:
           "#/portal/taxon/findByDescriptionElementFullText#",
           "#/portal/taxon/findByFullText#",
           "#/portal/taxon/findByEverythingFullText#",
           "#/portal/taxon/findByIdentifier#",
           "#/portal/taxon/findByMarker#",
           "#/portal/taxon/findByMarker#",
           "#/portal/taxon/findByMarker#",
           */
           "#/portal/taxon/[0-9a-f\-]{36}#"
           /* covered by above pattern:
           "#/portal/taxon/[0-9a-f\-]{36}/taxonNodes#",
           */
         ));
         $sub_tree_filter_uuid_value = variable_get(CDM_SUB_TREE_FILTER_UUID, FALSE);
         if(is_uuid($sub_tree_filter_uuid_value)){
           foreach($classification_subtree_filter_patterns as $preg_pattern){
             if(preg_match($preg_pattern, $uri)){
               // no need to take care for uri fragments with ws uris!
               if(strpos( $uri, '?')){
                 $uri .= '&subtree=' . $sub_tree_filter_uuid_value;
               } else {
                 $uri .= '?subtree='. $sub_tree_filter_uuid_value;
+              }
               break;
+            }
+          }
+        }
+      }
       /**
        * Processes and stores the given information in $_SESSION['cdm']['ws_debug'] as table row.
+       *
        * The cdm_ws_debug block will display the debug information.
+       *
        * @param $uri
        *    The CDM REST URI to which the request has been send
        * @param string $method
        *    The HTTP request method, either 'GET' or 'POST'
        * @param string $post_data
        *    The datastring send with a post request
        * @param $duration_fetch
        *    The time in seconds it took to fetch the data from the web service
        * @param $duration_parse
        *    Time in seconds which was needed to parse the json response
        * @param $datasize
        *    Size of the data received from the server
        * @param $status
        *    A status string, possible values are: 'valid', 'invalid', 'cacheL1', 'cacheL2'
        * @return bool
        *    TRUE if adding the debug information was successful
        */
       function cdm_ws_debug_add($uri, $method, $post_data, $duration_fetch, $duration_parse, $datasize, $status) {
         static $initial_time = NULL;
         if(!$initial_time) {
           $initial_time = microtime(TRUE);
+        }
         $time = microtime(TRUE) - $initial_time;
         // Decompose uri into path and query element.
         $uri_parts = explode("?", $uri);
         $query = array();
         if (count($uri_parts) == 2) {
           $path = $uri_parts[0];
+        }
         else {
           $path = $uri;
+        }
         if(strpos($uri, '?') > 0){
           $json_uri = str_replace('?', '.json?', $uri);
           $xml_uri = str_replace('?', '.xml?', $uri);
         } else {
           $json_uri = $uri . '.json';
           $xml_uri = $json_uri . '.xml';
+        }
         // data links to make data accecsible as json and xml
         $data_links = '';
         if (_is_cdm_ws_uri($path)) {
           // see ./js/http-method-link.js
           if($method == 'GET'){
             $data_links .= '<a href="' . $xml_uri . '" target="data">xml</a>-';
             $data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">proxied</a>';
             $data_links .= '<br/>';
             $data_links .= '<a href="' . $json_uri . '" target="data">json</a>-';
             $data_links .= '<a href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">proxied</a>';
           } else {
             $js_link_activation = 'class="http-' . $method . '-link" data-cdm-http-post="' . $post_data . '" type="application/x-www-form-urlencoded"';
             $data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($xml_uri)) . '" target="data">xml-proxied</a>';
             $data_links .= '<br/>';
             $data_links .= '<a ' . $js_link_activation . ' href="' . url('cdm_api/proxy/' . urlencode($json_uri)) . '" target="data">json-proxied</a>';
+          }
+        }
         else {
           $data_links .= '<a href="' . $uri . '" target="data">open</a>';
+        }
         //
         $data = array(
             'ws_uri' => $uri,
             'method' => $method,
             'post_data' => $post_data,
             'time' => sprintf('%3.3f', $time),
             'fetch_seconds' => sprintf('%3.3f', $duration_fetch),
             'parse_seconds' => sprintf('%3.3f', $duration_parse),
             'size_kb' => sprintf('%3.1f', ($datasize / 1024)) ,
             'status' => $status,
             'data_links' => $data_links
         );
         if (!isset($_SESSION['cdm']['ws_debug'])) {
           $_SESSION['cdm']['ws_debug'] = array();
+        }
         $_SESSION['cdm']['ws_debug'][] = serialize($data);
         // Mark this page as being uncacheable.
         // taken over from drupal_get_messages() but it is unsure if we really need this here
         drupal_page_is_cacheable(FALSE);
         // Messages not set when DB connection fails.
         return isset($_SESSION['cdm']['ws_debug']) ? $_SESSION['cdm']['ws_debug'] : NULL;
+      }
       /**
        * helper function to dtermine if the cdm_debug_block should be displayed or not
        * the visibility depends on whether
        *  - the block is enabled
        *  - the visibility restrictions in the block settings are satisfied
        */
       function cdm_debug_block_visible() {
         static $is_visible = null;
         if($is_visible === null){
             $block = block_load('cdm_api', 'cdm_ws_debug');
             $is_visible = isset($block->status) && $block->status == 1;
             if($is_visible){
               $blocks = array($block);
               // Checks the page, user role, and user-specific visibilty settings.
               block_block_list_alter($blocks);
               $is_visible = count($blocks) > 0;
+            }
+        }
         return $is_visible;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_load_obj($response_body) {
         $obj = json_decode($response_body);
         if (!(is_object($obj) || is_array($obj))) {
           ob_start();
           $obj_dump = ob_get_contents();
           ob_clean();
           return FALSE;
+        }
         return $obj;
+      }
       /**
        * Do a http request to a CDM RESTful web service.
+       *
        * @param string $uri
        *   The webservice url.
        * @param string $method
        *   The HTTP method to use, valid values are "GET" or "POST"; defaults to
        *   "GET" even if NULL, FALSE or any invalid value is supplied.
        * @param $data: A string containing the request body, formatted as
        *     'param=value&param=value&...'. Defaults to NULL.
+       *
        * @return object
        *   The object as returned by drupal_http_request():
        *   An object that can have one or more of the following components:
        *   - request: A string containing the request body that was sent.
        *   - code: An integer containing the response status code, or the error code
        *     if an error occurred.
        *   - protocol: The response protocol (e.g. HTTP/1.1 or HTTP/1.0).
        *   - status_message: The status message from the response, if a response was
        *     received.
        *   - redirect_code: If redirected, an integer containing the initial response
        *     status code.
        *   - redirect_url: If redirected, a string containing the URL of the redirect
        *     target.
        *   - error: If an error occurred, the error message. Otherwise not set.
        *   - headers: An array containing the response headers as name/value pairs.
        *     HTTP header names are case-insensitive (RFC 2616, section 4.2), so for
        *     easy access the array keys are returned in lower case.
        *   - data: A string containing the response body that was received.
        */
       function cdm_http_request($uri, $method = "GET", $data = NULL) {
         static $acceptLanguage = NULL;
         $header = array();
         if(!$acceptLanguage && module_exists('i18n')){
           $acceptLanguage = i18n_language_content()->language;
+        }
         if (!$acceptLanguage) {
           if (function_exists('apache_request_headers')) {
             $headers = apache_request_headers();
             if (isset($headers['Accept-Language'])) {
               $acceptLanguage = $headers['Accept-Language'];
+            }
+          }
+        }
         if ($method != "GET" && $method != "POST") {
           drupal_set_message('cdm_api.module#cdm_http_request() : unsupported HTTP request method ', 'error');
+        }
         if (_is_cdm_ws_uri($uri)) {
           $header['Accept'] = 'application/json';
           $header['Accept-Language'] = $acceptLanguage;
           $header['Accept-Charset'] = 'UTF-8';
+        }
         if($method == "POST") {
           // content type is application/x-www-form-urlencoded, so the request body uses the same format as the query string
           $header['Content-Type'] = 'application/x-www-form-urlencoded';
+        }
         cdm_dd($uri);
         return drupal_http_request($uri, array(
             'headers' => $header,
             'method' => $method,
             'data' => $data,
             'timeout' => CDM_HTTP_REQUEST_TIMEOUT
+            )
          );
+      }
       /**
        * Concatenates recursively the fields of all features contained in the given
        * CDM FeatureTree root node.
+       *
        * @param $rootNode
        *     A CDM FeatureTree node
        * @param
        *     The character to be used as glue for concatenation, default is ', '
        * @param $field_name
        *     The field name of the CDM Features
        * @param $excludes
        *     Allows defining a set of values to be excluded. This refers to the values
        *     in the field denoted by the $field_name parameter
+       *
        */
       function cdm_featureTree_elements_toString($root_node, $separator = ', ', $field_name = 'representation_L10n', $excludes = array()) {
         $out = '';
         $pre_child_separator = $separator;
         $post_child_separator = '';
         foreach ($root_node->childNodes as $feature_node) {
           $out .= ($out ? $separator : '');
           if(!in_array($feature_node->term->$field_name, $excludes)) {
             $out .= $feature_node->term->$field_name;
             if (is_array($feature_node->childNodes) && count($feature_node->childNodes) > 0) {
               $childlabels = cdm_featureTree_elements_toString($feature_node, $separator, $field_name);
               if (strlen($childlabels)) {
                   $out .=  $pre_child_separator . $childlabels . $post_child_separator;
+              }
+            }
+          }
+        }
         return $out;
+      }
       /**
        * Create a one-dimensional form options array.
+       *
        * Creates an array of all features in the feature tree of feature nodes,
        * the node labels are indented by $node_char and $childIndent depending on the
        * hierachy level.
+       *
        * @param - $rootNode
        * @param - $node_char
        * @param - $childIndentStr
        * @param - $childIndent
        *   ONLY USED INTERNALLY!
+       *
        * @return array
        *   A one dimensional Drupal form options array.
        */
       function _featureTree_nodes_as_feature_options($rootNode, $node_char = "&#9500;&#9472; ", $childIndentStr = '&nbsp;', $childIndent = '') {
         $options = array();
         foreach ($rootNode->childNodes as $featureNode) {
           $indent_prefix = '';
           if ($childIndent) {
             $indent_prefix = $childIndent . $node_char . " ";
+          }
           $options[$featureNode->term->uuid] = $indent_prefix . $featureNode->term->representation_L10n;
           if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
             // Foreach ($featureNode->childNodes as $childNode){
             $childList = _featureTree_nodes_as_feature_options($featureNode, $node_char, $childIndentStr, $childIndent . $childIndentStr);
             $options = array_merge_recursive($options, $childList);
             // }
+          }
+        }
         return $options;
+      }
       /**
        * Returns an array with all available FeatureTrees and the representations of the selected
        * FeatureTree as a detail view.
+       *
        * @param boolean $add_default_feature_free
        * @param boolean $show_weight
        *     Show the weight which will be applied to the according feature block
        * @return array
        *  associative array with following keys:
        *  -options: Returns an array with all available Feature Trees
        *  -treeRepresentations: Returns representations of the selected Feature Tree as a detail view
+       *
        */
       function cdm_get_featureTrees_as_options($add_default_feature_free = FALSE, $show_weight = FALSE) {
         $options = array();
         $tree_representations = array();
         $feature_trees = array();
         // Set tree that contains all features.
         if ($add_default_feature_free) {
           $options[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
           $feature_trees[] = cdm_ws_get(CDM_WS_TERMTREE, UUID_DEFAULT_FEATURETREE);
+        }
         // Get feature trees from database.
         $persited_trees = cdm_ws_fetch_all(CDM_WS_TERMTREES, array("termType" => "Feature"));
         if (is_array($persited_trees)) {
           $feature_trees = array_merge($feature_trees, $persited_trees);
+        }
         foreach ($feature_trees as $featureTree) {
           if(!is_object($featureTree)){
             continue;
+          }
           // Do not add the DEFAULT_FEATURETREE again,
           if ($featureTree->uuid != UUID_DEFAULT_FEATURETREE) {
             $options[$featureTree->uuid] = $featureTree->representation_L10n;
+          }
           // Render the hierarchic tree structure
           if (is_array( $featureTree->root->childNodes) && count( $featureTree->root->childNodes) > 0) {
             // Render the hierarchic tree structure.
             $treeDetails = '<div class="featuretree_structure">'
               . render_feature_tree_hierarchy($featureTree->uuid, $show_weight)
               . '</div>';
             $form = array();
             $form['featureTree-' .  $featureTree->uuid] = array(
               '#type' => 'fieldset',
               '#title' => 'Show details',
               '#attributes' => array('class' => array('collapsible collapsed')),
               // '#collapsible' => TRUE,
               // '#collapsed' => TRUE,
             );
             $form['featureTree-' .  $featureTree->uuid]['details'] = array(
               '#markup' => $treeDetails,
             );
             $tree_representations[$featureTree->uuid] = drupal_render($form);
+          }
         } // END loop over feature trees
         // return $options;
         return array('options' => $options, 'treeRepresentations' => $tree_representations);
+      }
       /**
        * Provides the list of available classifications in form of an options array.
+       *
        * The options array is suitable for drupal form API elements that allow multiple choices.
        * @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
+       *
        * The classifications are ordered alphabetically whereas the classification
        * chosen as default will always appear on top of the array, followed by a
        * blank line below.
+       *
        * @param bool $add_none_option
        *   is true an addtional 'none' option will be added, optional parameter, defaults to FALSE
+       *
        * @return array
        *   classifications in an array as options for a form element that allows multiple choices.
        */
       function cdm_get_taxontrees_as_options($add_none_option = FALSE) {
         $taxonTrees = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
         $default_classification_uuid = variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
         $default_classification_label = '';
         // add all classifications
         $taxonomic_tree_options = array();
         if ($add_none_option) {
           $taxonomic_tree_options['NONE'] = ' '; // one Space character at beginning to force on top;
+        }
         if ($taxonTrees) {
           foreach ($taxonTrees as $tree) {
             if (!$default_classification_uuid || $default_classification_uuid != $tree->uuid) {
               $taxonomic_tree_options[$tree->uuid] = $tree->titleCache;
             } else {
               $taxonomic_tree_options[$tree->uuid] = '  '; // two Space characters to force on top but below 'none' option , will be replaced below by titleCache
               $default_classification_label = $tree->titleCache;
+            }
+          }
+        }
         // oder alphabetically the space
         asort($taxonomic_tree_options);
         // now set the labels
         //   for none
         if ($add_none_option) {
           $taxonomic_tree_options['NONE'] =t('--- ALL ---');
+        }
         //   for default_classification
         if (is_uuid($default_classification_uuid)) {
           $taxonomic_tree_options[$default_classification_uuid] =
             $default_classification_label ? $default_classification_label : '--- INVALID CHOICE ---'
             . (count($taxonTrees) > 1 ? ' [' . t('DEFAULT CLASSIFICATION') . ']': '');
+        }
         return $taxonomic_tree_options;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_api_secref_cache_prefetch(&$secUuids) {
         // Comment @WA: global variables should start with a single underscore
         // followed by the module and another underscore.
         global $_cdm_api_secref_cache;
         if (!is_array($_cdm_api_secref_cache)) {
           $_cdm_api_secref_cache = array();
+        }
         $uniqueUuids = array_unique($secUuids);
         $i = 0;
         $param = '';
         while ($i++ < count($uniqueUuids)) {
           $param .= $secUuids[$i] . ',';
           if (strlen($param) + 37 > 2000) {
             _cdm_api_secref_cache_add($param);
             $param = '';
+          }
+        }
         if ($param) {
           _cdm_api_secref_cache_add($param);
+        }
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_api_secref_cache_get($secUuid) {
         global $_cdm_api_secref_cache;
         if (!is_array($_cdm_api_secref_cache)) {
           $_cdm_api_secref_cache = array();
+        }
         if (!array_key_exists($secUuid, $_cdm_api_secref_cache)) {
           _cdm_api_secref_cache_add($secUuid);
+        }
         return $_cdm_api_secref_cache[$secUuid];
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_api_secref_cache_clear() {
         global $_cdm_api_secref_cache;
         $_cdm_api_secref_cache = array();
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function _cdm_api_secref_cache_add($secUuidsStr) {
         global $_cdm_api_secref_cache;
         $ref = cdm_ws_get(CDM_WS_REFERENCE, $secUuidsStr);
         // Batch fetching not jet reimplemented thus:
         /*
         $assocRefSTOs = array(); if($refSTOs) { foreach($refSTOs as $ref){
         $assocRefSTOs[$ref->uuid] = $ref; } $_cdm_api_secref_cache =
         array_merge($_cdm_api_secref_cache, $assocRefSTOs); }
         */
         $_cdm_api_secref_cache[$ref->uuid] = $ref;
+      }
       /**
        * Checks if the given uri starts with a cdm webservice url.
+       *
        * Checks if the uri starts with the cdm webservice url stored in the
        * Drupal variable 'cdm_webservice_url'.
        * The 'cdm_webservice_url' can be set in the admins section of the portal.
+       *
        * @param string $uri
        *   The URI to test.
+       *
        * @return bool
        *   True if the uri starts with a cdm webservice url.
        */
       function _is_cdm_ws_uri($uri) {
         return str_beginsWith($uri, variable_get('cdm_webservice_url', '#EMPTY#'));
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function queryString($elements) {
         $query = '';
         foreach ($elements as $key => $value) {
           if (is_array($value)) {
             foreach ($value as $v) {
               $query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($v);
+            }
+          }
           else {
             $query .= (strlen($query) > 0 ? '&' : '') . $key . '=' . urlencode($value);
+          }
+        }
         return $query;
+      }
       /**
        * Compares the given CDM Term instances by the  representationL10n.
+       *
        * Can also be used with TermDTOs. To be used in usort()
+       *
        * @see http://php.net/manual/en/function.usort.php
+       *
        * @param $term1
        *   The first CDM Term instance
        * @param $term2
        *   The second CDM Term instance
        * @return int
        *   The result of the comparison
        */
       function compare_terms_by_representationL10n($term1, $term2) {
         if (!isset($term1->representation_L10n)) {
           $term1->representationL10n = '';
+        }
         if (!isset($term2->representation_L10n)) {
           $term2->representationL10n = '';
+        }
         return strcmp($term1->representation_L10n, $term2->representation_L10n);
+      }
       function compare_terms_by_order_index($term1, $term2) {
         if (!isset($term1->orderIndex)) {
           $a = 0;
         } else {
           $a = $term1->orderIndex;
+        }
         if (!isset($term2->orderIndex)) {
           $b = 0;
         } else {
           $b = $term2->orderIndex;
+        }
         if ($a == $b) {
           return 0;
+        }
         return ($a < $b) ? -1 : 1;
+      }
       /**
        * Make a 'deep copy' of an array.
+       *
        * Make a complete deep copy of an array replacing
        * references with deep copies until a certain depth is reached
        * ($maxdepth) whereupon references are copied as-is...
+       *
        * @see http://us3.php.net/manual/en/ref.array.php
+       *
        * @param array $array
        * @param array $copy passed by reference
        * @param int $maxdepth
        * @param int $depth
        */
       function array_deep_copy(&$array, &$copy, $maxdepth = 50, $depth = 0) {
         if ($depth > $maxdepth) {
           $copy = $array;
           return;
+        }
         if (!is_array($copy)) {
           $copy = array();
+        }
         foreach ($array as $k => &$v) {
           if (is_array($v)) {
             array_deep_copy($v, $copy[$k], $maxdepth, ++$depth);
+          }
           else {
             $copy[$k] = $v;
+          }
+        }
+      }
       /**
        * Concatenated the uuids of the passed cdm entity with `,` as glue.
        * The returned string is suitable for cdm webservices consuming UUIDList as
        * parameter
+       *
        * @param array $cdm_entities
+       *
        * @return string
        */
       function cdm_uuid_list_parameter_value(array $cdm_entities){
         $uuids = [];
         foreach ($cdm_entities as $entity){
           if(isset($entity) && is_uuid($entity->uuid) ){
             $uuids[] = $entity->uuid;
+          }
+        }
         return  join(',', $uuids);
+      }
       /**
        * Adds java script to create and enable a toggler for the cdm webservice debug block content.
+       *
        */
       function _add_js_ws_debug() {
         $data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.min.js';
         $colorbox_js = '/js/colorbox/jquery.colorbox-min.js';
         if (variable_get('cdm_js_devel_mode', FALSE)) {
           // use the developer versions of js libs
           $data_tables_js = '/js/DataTables-1.9.4/media/js/jquery.dataTables.js';
           $colorbox_js = '/js/colorbox/jquery.colorbox.js';
+        }
         drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $data_tables_js,
           array(
             'type' => 'file',
             'weight' => JS_LIBRARY,
             'cache' => TRUE)
           );
         drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $colorbox_js,
           array(
             'type' => 'file',
             'weight' => JS_LIBRARY,
             'cache' => TRUE)
           );
         drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/colorbox/colorbox.css');
         drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/DataTables-1.9.4/media/css/cdm_debug_table.css');
         drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ws_debug_block.js',
           array(
             'type' => 'file',
             'weight' => JS_LIBRARY,
             'cache' => TRUE)
           );
         drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/http-method-link.js',
           array(
           'type' => 'file',
           'weight' => JS_LIBRARY,
           'cache' => TRUE)
           );
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function _no_classfication_uuid_message() {
         if (!cdm_ws_get(CDM_WS_PORTAL_TAXONOMY)) {
           return t('This DataPortal is not configured properly or the CDM-Server may be absent.') . ' Please check the ' . l(t('CDM web service URL'), 'admin/config/cdm_dataportal/settings/general') . t(', or contact the maintainer of this DataPortal.');
+        }
         return t('This DataPortal is not configured properly.') . l(t('Please choose a valid classification'), 'admin/config/cdm_dataportal/settings/general') . t(', or contact the maintainer of this DataPortal.');
+      }
       /**
        * Implementation of hook flush_caches
+       *
        * Add custom cache tables to the list of cache tables that
        * will be cleared by the Clear button on the Performance page or whenever
        * drupal_flush_all_caches is invoked.
+       *
        * @author W.Addink <waddink@eti.uva.nl>
+       *
        * @return array
        *   An array with custom cache tables to include.
        */
       function cdm_api_flush_caches() {
         return array('cache_cdm_ws');
+      }
       /**
        * Logs if the drupal variable 'cdm_debug_mode' ist set true to drupal_debug.txt in the site's temp directory.
+       *
        * @param $data
        *   The variable to log to the drupal_debug.txt log file.
        * @param $label
        *   (optional) If set, a label to output before $data in the log file.
+       *
        * @return
        *   No return value if successful, FALSE if the log file could not be written
        *   to.
+       *
        * @see cdm_dataportal_init() where the log file is reset on each requests
        * @see dd()
        * @see http://drupal.org/node/314112
+       *
        */
       function cdm_dd($data, $label = NULL) {
         if(module_exists('devel') && variable_get('cdm_debug_mode', FALSE) && file_stream_wrapper_get_class('temporary') ){
           return dd($data, $label);
+        }
+      }

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