/7.x/modules/cdm_dataportal/cdm_api/cdm_api.module - Annotate - EDIT - EDIT Project Management

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cdm-dataportal/7.x/modules/cdm_dataportal/cdm_api/cdm_api.module @ 4c5c3be4

-            6657531f
+<?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', 'webservice_uris');
 module_load_include('php', 'cdm_api', 'cdm_node');
 /**
  * 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 content',
     ),
     'type' => MENU_CALLBACK,
   );
   $items['cdm_api/setvalue/session'] = array(
     'page callback' => 'setvalue_session',
     'access arguments' => array(
       'access content',
     ),
     'type' => MENU_CALLBACK,
   );
   return $items;
+}
 /**
  * Implements hook_cron().
+ *
  * Expire outdated cache entries.
  */
 function cdm_api_cron() {
   cache_clear_all(NULL, 'cache_cdm_ws');
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_api_permission() {
   return array(
     'administer cdm_api' => array(
       'title' => t('administer cdm_api'),
       'description' => t("TODO Add a description for 'administer cdm_api'"),
     ),
   );
+}
 /**
  * Converts an array of TaggedText items into corresponding html tags.
+ *
  * Each item is provided with a class attribute which is set to the key of the
  * TaggedText item.
+ *
  * @param array $taggedtxt
  *   Array with text items to convert.
  * @param string $tag
  *   Html tag name to convert the items into, default is 'span'.
  * @param string $glue
  *   The string by which the chained text tokens are concatenated together.
  *   Default is a blank character.
+ *
  * @return string
  *   A string with HTML.
  */
 function cdm_taggedtext2html(array $taggedtxt, $tag = 'span', $glue = ' ', $skiptags = array()) {
   $out = '';
   $i = 0;
   foreach ($taggedtxt as $tt) {
     if (!in_array($tt->type, $skiptags) && strlen($tt->text) > 0) {
       $out .= (strlen($out) > 0 && ++$i < count($taggedtxt) ? $glue : '') . '<' . $tag . ' class="' . $tt->type . '">' . t($tt->text) . '</' . $tag . '>';
+    }
+  }
   return $out;
+}
 /**
  * Finds the text tagged with $tag_type in an array of taggedText instances.
+ *
  * Comment @WA: this function seems unused.
+ *
  * @param array $taggedtxt
  *   Array with text items.
  * @param string $tag_type
  *   The type of tag for which to find text items in the $taggedtxt array.
+ *
  * @return array
  *   An array with the texts mapped by $tag_type.
  */
 function cdm_taggedtext_values(array $taggedtxt, $tag_type) {
   $tokens = array();
   if (!empty($taggedtxt)) {
     foreach ($taggedtxt as $tagtxt) {
       if ($tagtxt->type == $tag_type) {
         $tokens[] = $tagtxt->text;
+      }
+    }
+  }
   return $tokens;
+}
 /**
  * Returns the currently classification tree in use.
  */
 function get_taxonomictree_uuid_selected() {
   if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
     return $_SESSION['cdm']['taxonomictree_uuid'];
+  }
   else {
     return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
+  }
+}
 /**
  * Returns the FeatureTree profile as selected.
+ *
  * The FeatureTree profile 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 feature profile tree object.
  */
 function get_profile_featureTree() {
   $profile_featureTree = cdm_ws_get(
     CDM_WS_FEATURETREE,
     variable_get(CDM_PROFILE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
   );
   if (!$profile_featureTree) {
     $profile_featureTree = cdm_ws_get(
       CDM_WS_FEATURETREE,
       UUID_DEFAULT_FEATURETREE
     );
+  }
   return $profile_featureTree;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function switch_to_taxonomictree_uuid($taxonomictree_uuid) {
   $_SESSION['cdm']['taxonomictree_uuid'] = $taxonomictree_uuid;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function reset_taxonomictree_uuid($taxonomictree_uuid) {
   unset($_SESSION['cdm']['taxonomictree_uuid']);
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function set_last_taxon_page_tab($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;
+  }
+}
 /**
  * @todo Improve the documentation of this function.
+ *
  * media Array [4]
  * representations Array [3]
  * mimeType image/jpeg
  * representationParts Array [1]
  * duration 0
  * heigth 0
  * size 0
  * uri
  * http://wp5.e-taxonomy.eu/dataportal/cichorieae/media/protolog/jpeg/Acanthocephalus_p1.jpg
  * uuid 15c687f1-f79d-4b79-992f-7ba0f55e610b
  * width 0
  * suffix jpg
  * uuid 930b7d51-e7b6-4350-b21e-8124b14fe29b
  * title
  * uuid 17e514f1-7a8e-4daa-87ea-8f13f8742cf9
+ *
  * @param object $media
  * @param array $mimeTypes
  * @param int $width
  * @param int $height
+ *
  * @return array
  *   An array with preferred media representations or else an empty array.
  */
 function cdm_preferred_media_representations($media, array $mimeTypes, $width = 400, $height = 300) {
   $prefRepr = array();
   if (!isset($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();
         $dwa = 0;
         $dw = 0;
         // Look for part with the best matching size.
         foreach ($representation->parts as $part) {
           if (isset($part->width) && isset($part->height)) {
             $dw = $part->width * $part->height - $height * $width;
+          }
           if ($dw < 0) {
             $dw *= -1;
+          }
           $dwa += $dw;
+        }
         $dwa = (count($representation->parts) > 0) ? $dwa / count($representation->parts) : 0;
         // @WA: $mimeTypeKey is not defined.
         // $prefRepr[$dwa.'_'.$mimeTypeKey] = $representation;
         $prefRepr[$dwa . '_'] = $representation;
+      }
+    }
+  }
   // Sort the array.
   krsort($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';
+  }
+}
 /**
  * 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)) {
     $year = substr($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)) {
     $month = substr($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)) {
     $day = substr($partial, 7, 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 $stripZeros
  *   If set to TRUE the zero (00) month and days will be hidden:
  *   eg 1956-00-00 becomes 1956. The default is TRUE.
+ *
  * @return string
  *   YYYY-MM-DD formatted year, month, day.
  */
 function partialToDate($partial, $stripZeros = TRUE) {
   $y = partialToYear($partial);
   $m = partialToMonth($partial);
   $d = partialToDay($partial);
   $y = $y ? $y : '00';
   $m = $m ? $m : '00';
   $d = $d ? $d : '00';
   $date = '';
   if ($y == '00' && $stripZeros) {
     return;
+  }
   else {
     $date = $y;
+  }
   if ($m == '00' && $stripZeros) {
     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 $stripZeros
  *   If set to True, the zero (00) month and days will be hidden:
  *   eg 1956-00-00 becomes 1956. The default is TRUE.
+ *
  * @return string
  *   Returns a date in the form of a string.
  */
 function timePeriodToString($period, $stripZeros = TRUE) {
   $dateString = '';
   if ($period->start) {
     $dateString = partialToDate($period->start, $stripZeros);
+  }
   if ($period->end) {
     $dateString .= (strlen($dateString) > 0 ? ' ' . t('to') . ' ' : '') . partialToDate($period->end, $stripZeros);
+  }
   return $dateString;
+}
 /**
  * Composes a CDM webservice 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 $query
  *   A query string to append to the URL.
+ *
  * @return string
  *   A complete URL with parameters to a CDM webservice.
  */
 function cdm_compose_url($uri_pattern, $pathParameters = array(), $query = NULL) {
   if (empty($pathParameters)) {
     $pathParameters = array();
+  }
   $request_params = '';
   $path_params = '';
   // (1)
   // Substitute all place holders ($0, $1, ..) in the $uri_pattern by the
   // according element of the $pathParameters array.
   static $helperArray = array();
   if (isset($pathParameters) && !is_array($pathParameters)) {
     $helperArray[0] = $pathParameters;
     $pathParameters = $helperArray;
+  }
   $i = 0;
   while (strpos($uri_pattern, "$" . $i) !== FALSE) {
     if (count($pathParameters) <= $i) {
       if (module_exists("user") && user_access('administer')) {
         drupal_set_message(t('cdm_compose_url(): missing pathParameters'), 'debug');
+      }
       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 $query.
   if (isset($query)) {
     $uri_pattern .= (strpos($uri_pattern, '?') !== FALSE ? '&' : '?') . $query;
+  }
   // @WA: $ws_name seems unused
   // $path = $ws_name.$uri_pattern;
   $path = $uri_pattern;
   $uri = variable_get('cdm_webservice_url', '') . $path;
   return $uri;
+}
 /**
-ba85170
+ * @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?
-e1
+            Andreas Kohlbecker
  * @param string $uri
  *     A URI to a CDM Rest service from which to retrieve an object
-            f1f05758
+ * @param string|null $hook
  *     (optional) The hook name to which the retrieved object should be passed.
  *     Hooks can either be a theme_hook() or compose_hook() implementation
  *     'theme' hook functions return a string whereas 'compose' hooks are returning render arrays
-e1
+ *     suitable for drupal_render()
+ *
-            6657531f
+ * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
-            f1f05758
+function proxy_content($uri, $hook = NULL) {
-            6657531f
+  $args = func_get_args();
   $uriEncoded = array_shift($args);
   $uri = urldecode($uriEncoded);
-            f1f05758
+  $hook = array_shift($args);
-            6657531f
+            Andreas Kohlbecker
   // Find and deserialize arrays.
   foreach ($args as &$arg) {
     // FIXME use regex to find serialized arrays.
-            f1f05758
+    //       or should we accept json instead pf php serializations?
-            6657531f
+    if (strpos($arg, "a:") === 0) {
       $arg = unserialize($arg);
+    }
+  }
   $request_method = strtoupper($_SERVER["REQUEST_METHOD"]);
   if ($request_method == "POST") {
-            f1f05758
+    // this is an experimental feature which will allow to
     // write data inot the cdm via the RESTfull web service
-            6657531f
+    $parameters = $_POST;
     $post_data = array();
     foreach ($parameters as $k => $v) {
       $post_data[] = "$k=" . utf8_encode($v);
+    }
     $post_data = implode(',', $post_data);
     // For testing.
     $data = drupal_http_request($uri, array('headers' => "POST", 'method' => $post_data));
     print $data;
-            f1f05758
+  } else {
     // Not a "POST" request
     // In all these cases perform a simple get request.
-            6657531f
+    // TODO reconsider caching logic in this function.
-            f1f05758
+            Andreas Kohlbecker
     if (empty($hook)) {
       // simply return the webservice response
-            6657531f
+      // Print out JSON, the cache cannot be used since it contains objects.
       $http_response = drupal_http_request($uri);
       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;
+      }
       exit();
-            f1f05758
+    } else {
       // $hook has been supplied
       // handle $hook either as compose ot theme hook
       // pass through theme or comose hook
       // do a security check since the $uri will be passed
       // as absolute URI to cdm_ws_get()
-e1
+      if( !_is_cdm_ws_uri($uri)) {
         drupal_set_message(
-            f1f05758
+            'Invalid call of proxy_content() with callback parameter \'' . $hook . '\' and URI:' . $uri,
-e1
+            'error'
         );
         return '';
+      }
-            6657531f
+      $obj = cdm_ws_get($uri, NULL, NULL, NULL, TRUE);
-            f1f05758
+      $theme_result = NULL;
-b3d713e
+            Andreas Kohlbecker
-            f1f05758
+      if (function_exists('compose_' . $hook)){
         // call compose hook
-b3d713e
+            Andreas Kohlbecker
-            f1f05758
+        $elements =  call_user_func('compose_' . $hook, $obj);
         // pass the render array to drupal_render()
         $theme_result = drupal_render($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,
             );
             $theme_result = theme($hook, $variables);
             break;
           case 'cdm_media_caption':
             $variables = array(
               'media' => $obj,
               // $args[0] is set in taxon_image_gallery_default in
               // cdm_dataportal.page.theme.
               'elements' => isset($args[0]) ? $args[0] : array(
                 'title',
                 'description',
                 'artist',
                 'location',
                 'rights',
               ),
               'fileUri' => isset($args[1]) ? $args[1] : NULL,
             );
             $theme_result = theme($hook, $variables);
             break;
           default:
             drupal_set_message(t(
             'Theme !theme is not supported yet by function !function.', array(
             '!theme' => $hook,
             '!function' => __FUNCTION__,
             )), 'error');
             break;
         } // END of theme hook switch
       } // END of tread as theme hook
       print $theme_result;
     } // END of handle $hook either as compose ot theme hook
-            6657531f
+            Andreas Kohlbecker
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function setvalue_session() {
   if ($_REQUEST['var'] && strlen($_REQUEST['var']) > 4) {
     $keys = substr($_REQUEST['var'], 1, strlen($_REQUEST['var']) - 2);
     $keys = explode('][', $keys);
+  }
   else {
     return;
+  }
   $val = $_REQUEST['val'] ? $_REQUEST['val'] : NULL;
   // Prevent from malicous tags.
   $val = strip_tags($val);
   $var = &$_SESSION;
   $i = 0;
   foreach ($keys as $key) {
     $hasMoreKeys = ++$i < count($var);
     if ($hasMoreKeys && (!isset($var[$key]) || !is_array($var[$key]))) {
       $var[$key] = array();
+    }
     $var = &$var[$key];
+  }
   $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" : ''));
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_compose_annotations_url($cdmBase) {
   if (!$cdmBase->uuid) {
     return;
+  }
   $ws_base_uri = NULL;
   switch ($cdmBase->class) {
     case 'TaxonBase':
     case 'Taxon':
     case 'Synonym':
       $ws_base_uri = CDM_WS_TAXON;
       break;
     case 'TaxonNameBase':
     case 'NonViralName':
     case 'BacterialName':
     case 'BotanicalName':
     case 'CultivarPlantName':
     case 'ZoologicalName':
     case 'ViralName':
       $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 'Distribution':
     case 'TextData':
     case 'TaxonInteraction':
     case 'QuantitativeData':
     case 'IndividualsAssociation':
     case 'Distribution':
     case 'CommonTaxonName':
     case 'CategoricalData':
       $ws_base_uri = CDM_WS_DESCRIPTIONELEMENT;
       break;
     case 'PolytomousKey':
     case 'MediaKey':
     case 'MultiAccessKey':
       $ws_base_uri = $cdmBase->class;
       $ws_base_uri{0} = strtolower($ws_base_uri{0});
       break;
     default:
       trigger_error(check_plain('Unsupported CDM Class - no annotations available for ' . $cdmBase->class), E_USER_ERROR);
       return;
+  }
   return cdm_compose_url($ws_base_uri, array(
     $cdmBase->uuid,
     'annotations',
   ));
+}
 /**
  * Enter description here...
+ *
  * @param string $resourceURI
  * @param mixed $pageSize
  *   The maximum number of entities returned per page (can be NULL
  *   to return all entities in a single page).
  * @param int $pageNumber
  *   The number of the page to be returned, the first page has the
  *   pageNumber = 1.
+ *
  * @return unknown
  */
 function cdm_ws_page($resourceURI, $pageSize, $pageNumber) {
   return cdm_ws_get($resourceURI, NULL, queryString(array(
     "page" => $pageNumber,
     'pageSize' => $pageSize,
   )));
+}
 /*
 function cdm_ws_taxonomy_compose_resourcePath($path = NULL){
   $viewrank = _cdm_taxonomy_compose_viewrank();
   return CDM_WS_PORTAL_TAXONOMY . '/' . ($viewrank ? $viewrank : '' ) . ($path
   ? '/' . $path : '') ;
+}
 */
 /**
  * @todo Enter description here...
+ *
-c55
+ * @param string $taxon_uuid
  *  The UUID of a cdm taxon instance
  * @param string $ignore_rank_limit
  *   Whether to ignore the variable 'taxontree_ranklimit' set by admin in the settings
-            6657531f
+            Andreas Kohlbecker
-c55
+ * @return A cdm REST service URL path to a Classification
-            6657531f
+ */
-c55
+function cdm_compose_taxonomy_root_level_path($taxon_uuid = FALSE, $ignore_rank_limit = FALSE) {
   $view_uuid = get_taxonomictree_uuid_selected();
   $rank_uuid = NULL;
   if (!$ignore_rank_limit) {
     $rank_uuid = variable_get('taxontree_ranklimit', DEFAULT_TAXONTREE_RANKLIMIT);
+  }
-            6657531f
+            Andreas Kohlbecker
-c55
+  if (!empty($taxon_uuid)) {
-            6657531f
+    return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
-c55
+      $view_uuid,
       $taxon_uuid,
-            6657531f
+    ));
+  }
   else {
-c55
+    if (!empty($rank_uuid)) {
-            6657531f
+      return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_AT_RANK, array(
-c55
+        $view_uuid,
         $rank_uuid,
-            6657531f
+      ));
+    }
     else {
-c55
+      return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES, array(
         $view_uuid,
-            6657531f
+      ));
+    }
+  }
+}
 /**
-c55
+ * 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 $taxon_uuid
  *   The UUID of a cdm taxon instance
-            6657531f
+ */
-c55
+function cdm_ws_taxonomy_root_level($taxon_uuid = NULL) {
-            6657531f
+            Andreas Kohlbecker
-c55
+    $response = NULL;
-            6657531f
+            Andreas Kohlbecker
-c55
+    // 1st try
     $response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid), NULL, NULL, NULL, 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, NULL, TRUE);
-            6657531f
+            Andreas Kohlbecker
-c55
+            Andreas Kohlbecker
     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']);
         return cdm_ws_taxonomy_root_level($taxon_uuid);
+      }
       else {
         // Check if taxonomictree_uuid is valid.
         $test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, NULL, TRUE);
         if ($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');
+        }
-            6657531f
+            Andreas Kohlbecker
+    }
   return $response;
+}
 /**
  * @todo Enter description here...
+ *
-c55
+ * @param string $taxon_uuid
-            6657531f
+            Andreas Kohlbecker
  * @return unknown
  */
-c55
+function cdm_ws_taxonomy_pathFromRoot($taxon_uuid) {
   $view_uuid = get_taxonomictree_uuid_selected();
   $rank_uuid = variable_get('taxontree_ranklimit', DEFAULT_TAXONTREE_RANKLIMIT);
-            6657531f
+            Andreas Kohlbecker
   $response = NULL;
-c55
+  if ($rank_uuid) {
-            6657531f
+    $response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM_TO_RANK, array(
-c55
+      $view_uuid,
       $taxon_uuid,
       $rank_uuid,
-            6657531f
+    ));
+  }
   else {
     $response = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_PATH_FROM, array(
-c55
+      $view_uuid,
       $taxon_uuid,
-            6657531f
+    ));
+  }
   if ($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']);
-c55
+      return cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
-            6657531f
+            Andreas Kohlbecker
     else {
       // Check if taxonomictree_uuid is valid.
-c55
+      $test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, NULL, TRUE);
-            6657531f
+      if ($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;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_rankVocabulary_as_option() {
-c55
+  $options = cdm_Vocabulary_as_option(UUID_RANK);
   array_unshift ($options, "");
   return $options;
-            6657531f
+            Andreas Kohlbecker
 /**
+ *
  * @param Object $definedTermBase
  * 	  of cdm type DefinedTermBase
  * @return string
  * 	  the localized representation_L10n of the term,
  *    otherwise the titleCache as fall back,
  *    otherwise an empty string
  */
 function cdm_term_representation($definedTermBase) {
   if ( isset($definedTermBase->representation_L10n) ) {
     return $definedTermBase->representation_L10n;
   } elseif ( isset($definedTermBase->titleCache)) {
     return $definedTermBase->titleCache;
+  }
   return '';
+}
 /**
  * @todo Improve documentation of this function.
+ *
  * eu.etaxonomy.cdm.model.description.
  * CategoricalData
  * CommonTaxonName
  * Distribution
  * IndividualsAssociation
  * QuantitativeData
  * TaxonInteraction
  * TextData
  */
 function cdm_descriptionElementTypes_as_option($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 $options;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_Vocabulary_as_option($vocabularyUuid, $term_label_callback = NULL) {
   static $vocabularyOptions = array();
   if (!isset($vocabularyOptions[$vocabularyUuid])) {
     $vocab = cdm_ws_get(CDM_WS_TERMVOCABULARY, $vocabularyUuid);
     $vocabularyOptions[$vocabularyUuid] = array();
     if ($vocab) {
       foreach ($vocab->terms as $term) {
         if ($term_label_callback && function_exists($term_label_callback)) {
           $vocabularyOptions[$vocabularyUuid][$term->uuid] = call_user_func($term_label_callback, $term);
+        }
         else {
           $vocabularyOptions[$vocabularyUuid][$term->uuid] = t($term->representation_L10n);
+        }
+      }
       array_reverse($vocabularyOptions[$vocabularyUuid]);
+    }
+  }
   return $vocabularyOptions[$vocabularyUuid];
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _cdm_relationship_type_term_label_callback($term) {
   if (isset($term->representation_L10n_abbreviatedLabel)) {
     return $term->representation_L10n_abbreviatedLabel . ' : ' . t($term->representation_L10n);
+  }
   else {
     return t($term->representation_L10n);
+  }
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_ws_descriptions_by_featuretree($featureTree, $descriptions, $isDescriptionsSeparated = FALSE) {
   if (!$featureTree) {
     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;
+  }
   $mergedTrees = array();
   if ($isDescriptionsSeparated) {
     // Merge any description into a separate feature tree.
     foreach ($descriptions as $desc) {
       $mergedNodes = _mergeFeatureTreeDescriptions($featureTree->root->children, $desc->elements);
       $mergedTree = clone $featureTree;
       $mergedTree->root->children = $mergedNodes;
       $mergedTrees[] = $mergedTree;
+    }
+  }
   else {
     // Combine all descripions into one feature tree.
     foreach ($descriptions as $desc) {
       $mergedNodes = _mergeFeatureTreeDescriptions($featureTree->root->children, $desc->elements);
       $featureTree->root->children = $mergedNodes;
+    }
     $mergedTrees[] = $featureTree;
+  }
   return $mergedTrees;
+}
 /**
  * Get a list of annotations for a cdm entity.
+ *
  * @param string $cdmBase
  *   An annotatable cdm entity.
  * @param array $includeTypes
  *   If an array of annotation type uuids is supplied by this parameter the
  *   list of annotations is resticted to those which belong to this type.
+ *
  * @return array
  *   An array of Annotation objects or an empty array.
  */
 function cdm_ws_getAnnotationsFor($cdmBase, $includeTypes = FALSE) {
   $annotationUrl = cdm_compose_annotations_url($cdmBase);
   if ($annotationUrl) {
     $annotationPager = cdm_ws_get($annotationUrl, NULL, NULL, NULL, TRUE);
     if (isset($annotationPager->records) && is_array($annotationPager->records)) {
       $annotations = array();
       foreach ($annotationPager->records as $annotation) {
         if ($includeTypes) {
           if ((isset($annotation->annotationType->uuid) && in_array($annotation->annotationType->uuid, $includeTypes, TRUE)) || ($annotation->annotationType === NULL && in_array('NULL_VALUE', $includeTypes, TRUE))) {
             $annotations[] = $annotation;
+          }
+        }
         else {
           $annotations[] = $annotation;
+        }
+      }
       return $annotations;
+    }
+  }
+}
 /**
  * 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) {
   $obj = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array(
     $referenceUuid,
   ), "microReference=" . urlencode($microreference));
   if ($obj) {
     return $obj->String;
+  }
   else {
     return NULL;
+  }
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _mergeFeatureTreeDescriptions($featureNodes, $descriptionElements) {
   foreach ($featureNodes as &$node) {
     // Append corresponding elements to an additional node field:
     // $node->descriptionElements.
     foreach ($descriptionElements as $element) {
       if ($element->feature->uuid == $node->feature->uuid) {
         if (!isset($node->descriptionElements)) {
           $node->descriptionElements = array();
+        }
         $node->descriptionElements[] = $element;
+      }
+    }
     // Recurse into node children.
     if (isset($node->children) && is_array($node->children)) {
       $mergedChildNodes = _mergeFeatureTreeDescriptions($node->children, $descriptionElements);
       $node->children = $mergedChildNodes;
+    }
+  }
   return $featureNodes;
+}
 /**
  * Sends a GET request to a CDM RESTService and returns a deserialized 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 beeing 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 beeing 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
  *   A query string to be appended to the URL.
  * @param string $method
  *   The HTTP method to use, valid values are "GET" or "POST";
  * @param bool $absoluteURI
  *   TRUE when the URL should be treated as absolute URL.
+ *
  * @return object
  *   The deserialized webservice response object.
  */
 function cdm_ws_get($uri, $pathParameters = array(), $query = NULL, $method = "GET", $absoluteURI = FALSE) {
   // static $cacheL1; if(!isset($cacheL1)){ $cacheL1 = array(); }
   static $cacheL1 = array();
-e1
+  // Transform the given uri path or pattern into a proper webservice uri.
-            6657531f
+  if (!$absoluteURI) {
     $uri = cdm_compose_url($uri, $pathParameters, $query);
+  }
   $is_cdm_ws_uri = _is_cdm_ws_uri($uri);
   $use_cacheL2 = variable_get('cdm_webservice_cache', 1);
   if (array_key_exists($uri, $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) {
     // Try to get object from cacheL2.
     $cacheL2_entry = cache_get($uri, 'cache_cdm_ws');
+  }
   if (isset($cacheL1_obj)) {
     //
     // The object has been found in the L1 cache.
     //
     $obj = $cacheL1_obj;
     if (variable_get('cdm_webservice_debug', 1) && user_access('administer')) {
       _add_status_message_toggler();
       _add_debugMessageStr('Using cacheL1 for: ' . $uri);
+    }
+  }
   elseif ($cacheL2_entry) {
     //
     // The object has been found in the L2 cache.
     //
     $obj = unserialize($cacheL2_entry->data);
     if (variable_get('cdm_webservice_debug', 1) && user_access('administer')) {
       _add_status_message_toggler();
       _add_debugMessageStr('Using cacheL2 for: ' . $uri);
+    }
+  }
   else {
     //
     // Get the object from the webservice and cache it.
     //
     $time_get_start = microtime(TRUE);
     // Request data from webservice JSON or XML.
     $datastr = cdm_http_request($uri, $method);
     $time_get = microtime(TRUE) - $time_get_start;
     $time_parse_start = microtime(TRUE);
     // Parse data and create object.
     $obj = cdm_load_obj($datastr);
     $time_parse = microtime(TRUE) - $time_parse_start;
     if (variable_get('cdm_webservice_debug', 1) && user_access('administer')) {
       if ($obj || $datastr == "[]") {
         $success_msg = 'valid';
+      }
       else {
         $success_msg = 'invalid';
+      }
       _add_debugMessage($uri, $time_get, $time_parse, strlen($datastr), $success_msg);
+    }
     if ($set_cacheL2) {
       // Store the object in cache L2.
       // Comment @WA perhaps better if Drupal serializes here? Then the
       // flag serialized is set properly in the cache table.
       cache_set($uri, serialize($obj), 'cache_cdm_ws', CACHE_TEMPORARY);
+    }
+  }
   if ($obj) {
     // Store the object in cache L1.
     if ($set_cacheL1) {
       $cacheL1[$uri] = $obj;
+    }
+  }
   return $obj;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_debugMessageStr($message) {
   _add_status_message_toggler();
   drupal_set_message(check_plain($message), 'debug');
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _add_debugMessage($uri, $time_get, $time_parse, $datasize, $success_msg) {
   static $cumulated_time_parse = 0;
   static $cumulated_time_get = 0;
   _add_status_message_toggler();
   $cumulated_time_get += $time_get;
   $cumulated_time_parse += $time_parse;
   // Decompose uri into path and query element.
-c5c3be4
+  // URI query elements are stored in an array
   // suitable for drupal_http_build_query()
-            6657531f
+  $uri_parts = explode("?", $uri);
-f4c
+  $query = array();
-            6657531f
+  if (count($uri_parts) == 2) {
     $path = $uri_parts[0];
-f4c
+    $queryparts = explode("&", $uri_parts[1]);
     foreach ($queryparts as $querypart) {
       $querypart = explode("=", $querypart);
-c5c3be4
+      if(count($querypart) == 2){
         $query[$querypart[0]] = $querypart[1];
       } else {
         $query[$querypart[0]] = null;
+      }
-f4c
+            w.addink
-            6657531f
+            Andreas Kohlbecker
   else {
     $path = $uri;
+  }
   $message = '<span class="uri">' . $uri . '</span><br />';
   $message .= '[fetched in: ' . sprintf('%3.3f', $time_get) . 's(' . sprintf('%3.3f', $cumulated_time_get) . 's); ';
   $message .= 'parsed in ' . sprintf('%3.3f', $time_parse) . ' s(' . sprintf('%3.3f', $cumulated_time_parse) . 's); ';
   $message .= 'size:' . sprintf('%3.1f', ($datasize / 1024)) . ' kb of ' . $success_msg . ' data: ';
   if (_is_cdm_ws_uri($path)) {
     $message .= '<a href="' . url($path . '.xml', array(
       'query' => $query,
     )) . '" target="data" class="' . $success_msg . '">xml</a>-';
     $message .= '<a href="' . url('cdm_api/proxy/' . urlencode(url($path . '.xml', array(
       'query' => $query,
     )))) . '" target="data" class="' . $success_msg . '">proxied</a>,';
     $message .= '<a href="' . url($path . '.json', array(
       'query' => $query,
     )) . '" target="data" class="' . $success_msg . '">json</a>-';
-            e56d4915
+    $message .= '<a href="' . url('cdm_api/proxy/' . urlencode(url($path . '.json', array(
-            6657531f
+      'query' => $query,
-            e56d4915
+    )))) . '" target="data" class="' . $success_msg . '">proxied</a>';
-            6657531f
+            Andreas Kohlbecker
   else {
     $message .= '<a href="' . url($path, array(
       'query' => $query,
     )) . '" target="data" class="' . $success_msg . '">open</a>';
+  }
   $message .= '] ';
   drupal_set_message(($message), 'debug');
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_load_obj($datastr) {
   $obj = json_decode($datastr);
   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 webservice.
+ *
  * @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 array $parameters
  *   Parameters to use in the request.
  * @param array $header
  *   The header to include in the request.
+ *
  * @return
  *   The response data from the request.
  */
 function cdm_http_request($uri, $method = "GET", $parameters = array(), $header = array()) {
   static $acceptLanguage = NULL;
   if (!$acceptLanguage) {
     if (function_exists('apache_request_headers')) {
       $headers = apache_request_headers();
       if (isset($headers['Accept-Language'])) {
         $acceptLanguage = $headers['Accept-Language'];
+      }
+    }
     if (!$acceptLanguage) {
       // DEFAULT TODO make configurable.
       $acceptLanguage = "en";
+    }
+  }
   if ($method != "GET" && $method != "POST") {
     $method = "GET";
+  }
   if (empty($header) && _is_cdm_ws_uri($uri)) {
     $header['Accept'] = (variable_get('cdm_webservice_type', 'json') == 'json' ? 'application/json' : 'text/xml');
     $header['Accept-Language'] = $acceptLanguage;
     $header['Accept-Charset'] = 'UTF-8';
+  }
   if (FALSE && function_exists('curl_init')) {
     // !!!!! CURL Disabled due to problems with following redirects
     // (CURLOPT_FOLLOWLOCATION=1) and safe_mode = on
     // Use the CURL lib if installed, it is supposed to be 20x faster.
     return _http_request_using_curl($uri, $header, $method, $parameters);
+  }
   else {
     return _http_request_using_fsockopen($uri, $header, $method, $parameters);
+  }
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _http_request_using_fsockopen($uri, $header = array(), $method = 'GET') {
   $response = drupal_http_request($uri, array('headers' => $header, 'method' => $method));
   if (isset($response->data)) {
       return $response->data;
+  }
+}
 /**
  * Return string content from a remote file.
+ *
  * @author Luiz Miguel Axcar <lmaxcar@yahoo.com.br>
+ *
  * @param string $uri
  *   The url for which to return content.
+ *
  * @return string
  *   The returned content.
  */
 function _http_request_using_curl($uri, $headers = array(), $method = "GET", $parameters = array()) {
   $ch = curl_init();
   curl_setopt($ch, CURLOPT_URL, $uri);
   curl_setopt($ch, CURLOPT_FOLLOWLOCATION, 1);
   curl_setopt($ch, CURLOPT_MAXREDIRS, 5);
   // Set proxy settings.
   if (variable_get('cdm_webservice_proxy_url', FALSE)) {
     curl_setopt($ch, CURLOPT_PROXY, variable_get('cdm_webservice_proxy_url', ''));
     curl_setopt($ch, CURLOPT_PROXYPORT, variable_get('cdm_webservice_proxy_port', '80'));
     if (variable_get('cdm_webservice_proxy_usr', FALSE)) {
       curl_setopt($ch, CURLOPT_PROXYUSERPWD, variable_get('cdm_webservice_proxy_usr', '') . ':' . variable_get('cdm_webservice_proxy_pwd', ''));
+    }
+  }
   // Modify headers array to be used by curl.
   foreach ($headers as $header_key => $header_val) {
     $curl_headers[] = $header_key . ': ' . $header_val;
+  }
   if (isset($curl_headers)) {
     curl_setopt($ch, CURLOPT_HTTPHEADER, $curl_headers);
+  }
   // Set method if not default.
   if ($method != "GET") {
     if ($method == "POST") {
       curl_setopt($ch, CURLOPT_POST, 1);
       curl_setopt($ch, CURLOPT_POSTFIELDS, $parameters);
+    }
     else {
       // Other obscure http methods get passed to curl directly.
       // TODO generic parameter/body handling
       curl_setopt($ch, CURLOPT_CUSTOMREQUEST, $method);
+    }
+  }
   ob_start();
   curl_exec($ch);
   $info = curl_getinfo($ch);
   if (curl_errno($ch)) {
     watchdog('CDM_API', '_http_request_curl() - ' . curl_error($ch) . '; REQUEST-METHOD:' . $method . ' URL: ' . substr($uri . ' ', 0, 150), WATCHDOG_ERROR);
     if (variable_get('cdm_webservice_debug', 1) && user_access('administer')) {
       drupal_set_message(check_plain(t('_http_request_curl() - !curl_error; REQUEST-METHOD:!method URL: !url', array(
       '!curl_error' => curl_error($ch),
       '!method' => $method,
       '!url' => substr($uri . ' ', 0, 150),
        ))), 'error');
+    }
+  }
   curl_close($ch);
   $string = ob_get_contents();
   ob_end_clean();
   return $string;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _featureTree_elements_toString($rootNode, $separator = ', ') {
   $out = '';
   foreach ($rootNode->children as $featureNode) {
     $out .= ($out ? $separator : '');
     $out .= $featureNode->feature->representation_L10n;
     if (is_array($featureNode->children)) {
       $childlabels = '';
       foreach ($featureNode->children as $childNode) {
         $childlabels .= ($childlabels ? $separator : '');
+      }
       $childlabels .= _featureTree_elements_toString($childNode);
+    }
     if ($childlabels) {
       $out .= '[' . $childlabels . ' ]';
+    }
+  }
   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->children as $featureNode) {
     $indent_prefix = '';
     if ($childIndent) {
       $indent_prefix = $childIndent . $node_char . " ";
+    }
     $options[$featureNode->feature->uuid] = $indent_prefix . $featureNode->feature->representation_L10n;
     if (isset($featureNode->children) && is_array($featureNode->children)) {
       // Foreach ($featureNode->children as $childNode){
       $childList = _featureTree_nodes_as_feature_options($featureNode, $node_char, $childIndentStr, $childIndent . $childIndentStr);
       $options = array_merge_recursive($options, $childList);
       // }
+    }
+  }
   return $options;
+}
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
-d24e
+function cdm_get_featureTrees_as_options($add_default_feature_free = FALSE) {
-            6657531f
+  $feature_trees = array();
   // Set tree that contains all features.
-d24e
+  if ($add_default_feature_free) {
-            6657531f
+    $feature_trees[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
+  }
   // Get features from database.
   $persisted_trees = cdm_ws_get(CDM_WS_FEATURETREES);
-d24e
+  $tree_representation = NULL;
-            6657531f
+  if (is_array($persisted_trees)) {
     foreach ($persisted_trees as $featureTree) {
       // Do not add the DEFAULT_FEATURETREE again,
       if ($featureTree->uuid == UUID_DEFAULT_FEATURETREE) {
         continue;
+      }
-d24e
+      // $tree_representation = $featureTree->titleCache;
       $tree_representation = '';
-            6657531f
+      if (is_array($featureTree->root->children) && count($featureTree->root->children) > 0) {
         // Render the hierarchic tree structure.
         $treeDetails = '<div class="featuretree_structure">'
           // ._featureTree_elements_toString($featureTree->root)
           . theme('FeatureTree_hierarchy', array('FeatureTreeUuid' => $featureTree->uuid))
           . '</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' => $treeDetails,
         );
         // echo drupal_render($form);
-d24e
+        $tree_representation .= drupal_render($form);
-            6657531f
+            Andreas Kohlbecker
       $feature_trees[$featureTree->uuid] = $featureTree->titleCache;
-d24e
+      // $feature_trees[$featureTree->uuid] = $tree_representation;
-            6657531f
+            Andreas Kohlbecker
+  }
   // return $feature_trees;
-d24e
+  return array('options' => $feature_trees, 'treeRepresentations' => $tree_representation);
-            6657531f
+            Andreas Kohlbecker
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_get_taxontrees_as_options() {
   $taxonTrees = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY);
-d24e
+  $taxonomic_tree_options = array();
-            6657531f
+  if ($taxonTrees) {
     foreach ($taxonTrees as $tree) {
-d24e
+      $taxonomic_tree_options[$tree->uuid] = $tree->titleCache;
-            6657531f
+            Andreas Kohlbecker
+  }
-d24e
+  return $taxonomic_tree_options;
-            6657531f
+            Andreas Kohlbecker
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function cdm_api_secref_cache_prefetch(&$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();
+}
 /**
  * Validates if the given string is a uuid.
+ *
  * @param string $str
  *   The string to validate.
+ *
  * return bool
  *   TRUE if the string is a UUID.
  */
 function is_uuid($str) {
   return is_string($str) && strlen($str) == 36 && strpos($str, '-');
+}
 /**
  * Checks if the given $object is a valid cdm entity.
+ *
  * An object is considered a cdm entity if it has a string field $object->class
  * with at least 3 characters and if it has a valid uuid in $object->uuid.
+ *
  * @author a.kohlbecker <a.kohlbecker@bgbm.org>
+ *
  * @param mixed $object
  *   The object to validate
+ *
  * @return bool
  *   True if the object is a cdm entity.
  */
 function is_cdm_entity($object) {
   return is_string($object->class) && strlen($object->class) > 2 && is_string($object->uuid) && is_uuid($object->uuid);
+}
 /**
  * @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 $query;
+}
 /**
  * Implementation of the magic method __clone to allow deep cloning of objects
  * and arrays.
  */
 function __clone() {
   foreach ($this as $name => $value) {
     if (gettype($value) == 'object' || gettype($value) == 'array') {
       $this->$name = clone($this->$name);
+    }
+  }
+}
 /**
  * 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
  * @param int $maxdepth
  * @param int $depth
+ *
  * @return void
  */
 function array_deep_copy(&$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] = $v;
+    }
+  }
+}
 /**
  * Implementation of theme_status_messages($display = NULL).
+ *
  * @see includes/theme.inc
+ *
  * @return void
  */
 function _add_status_message_toggler() {
   static $isAdded = FALSE;
   if (!$isAdded) {
     drupal_add_js(
     'jQuery(document).ready(function($){
        $(\'.messages.debug\').before( \'<h6 class="messages_toggler debug">Debug Messages (click to toggle)</h6>\' );
        $(\'.messages_toggler\').click(function(){
          $(this).next().slideToggle(\'fast\');
-a2a14b3
+         return false;
-            6657531f
+       }).next().hide();
      });', array('type' => 'inline'));
     $isAdded = 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');
+}

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