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

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cdm-dataportal/modules/cdm_dataportal/cdm_api/cdm_api.module @ c0223d83

-            6657531f
+<?php
-cfa718
+  /**
    * @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)
    */
-            6657531f
+            Andreas Kohlbecker
-cfa718
+  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');
-            6657531f
+            Andreas Kohlbecker
-cfa718
+  /**
    * 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);
-dbc0
+            Andreas Kohlbecker
-ca5ef1e
+            Andreas Kohlbecker
 /**
  * orderBy webservice query parameter value
  */
-            f8234b76
+define('CDM_ORDER_BY_ID_ASC', 'BY_ID_ASC');
-ca5ef1e
+            Andreas Kohlbecker
 /**
  * orderBy webservice query parameter value
  */
-            f8234b76
+define('CDM_ORDER_BY_ID_DESC', 'BY_ID_DESC');
-ca5ef1e
+/**
  * orderBy webservice query parameter value
  */
-            f8234b76
+define('CDM_ORDER_BY_TITLE_CACHE_ASC', 'BY_TITLE_CACHE_ASC');
-ca5ef1e
+/**
  * orderBy webservice query parameter value
  */
-            f8234b76
+define('CDM_ORDER_BY_TITLE_CACHE_DESC', 'BY_TITLE_CACHE_DESC');
-ca5ef1e
+/**
  * orderBy webservice query parameter value
  */
-            a33be830
+define('CDM_ORDER_BY_NOMENCLATURAL_ORDER_ASC', 'BY_NOMENCLATURAL_ORDER_ASC');
-ca5ef1e
+/**
  * orderBy webservice query parameter value
  */
-            a33be830
+define('CDM_ORDER_BY_NOMENCLATURAL_ORDER_DESC', 'BY_NOMENCLATURAL_ORDER_DESC');
-ca5ef1e
+/**
  * 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');
-            fa782b11
+            Andreas Kohlbecker
-            6657531f
+/**
  * 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(
-            c6fe437b
+      'access cdm content',
-            6657531f
+    ),
     'type' => MENU_CALLBACK,
   );
   $items['cdm_api/setvalue/session'] = array(
     'page callback' => 'setvalue_session',
     'access arguments' => array(
-            c6fe437b
+      'access cdm content',
-            6657531f
+    ),
     'type' => MENU_CALLBACK,
   );
   return $items;
+}
-            e2464cf8
+/**
  * 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':
-b5815cd
+    $cdm_ws_url = variable_get('cdm_webservice_url', '');
-            e2464cf8
+    $field_map = array(
-b5815cd
+        'ws_uri' => t('URI') . ' <code>(' . $cdm_ws_url .'...)</code>',
-            e2464cf8
+        'time' => t('Time'),
         'fetch_seconds' => t('Fetching [s]'),
         'parse_seconds' => t('Parsing [s]'),
         'size_kb' => t('Size [kb]'),
         'status' => t('Status'),
         'data_links' =>  t('Links'),
     );
     if (!isset($_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){
-b5815cd
+            Andreas Kohlbecker
-            e2464cf8
+      $data = unserialize($data);
-b5815cd
+            Andreas Kohlbecker
       // stip of webservice base url
       $data['ws_uri'] = str_replace($cdm_ws_url, '', $data['ws_uri']);
-ebf0428
+      if($data['method'] == 'POST'){
         $data['ws_uri'] = 'POST: ' . $data['ws_uri'] . '?' . $data['post_data'];
+      }
-b5815cd
+            Andreas Kohlbecker
       $cells = array();
-            e2464cf8
+      foreach ($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();
-b65fa0
+    $block['subject'] = ''; // no subject, title in content for having a defined element id
     // otherwise it would depend on the theme
-f6d312
+    $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
-b65fa0
+        . '<div id="cdm-ws-debug-table-container"><table id="cdm-ws-debug-table">'
-            e2464cf8
+        . $header
         . '<tbody>' . join('', $rows) . '</tbody>'
         . $footer
-f6d312
+        . '</table></div>',
       '#attached' => array(
         'css' => array(
           drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_ws_debug.css'
+        )
+      )
     );
-            e2464cf8
+    return $block;
+  }
+}
-            6657531f
+/**
  * Implements hook_cron().
+ *
  * Expire outdated cache entries.
  */
 function cdm_api_cron() {
   cache_clear_all(NULL, 'cache_cdm_ws');
+}
-            e90899ac
+// ===================== Tagged Text functions ================== //
-            6657531f
+/**
  * 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.
  */
-            e90899ac
+function cdm_tagged_text_to_markup(array $taggedtxt, $tag = 'span', $glue = ' ', $skiptags = array()) {
-            6657531f
+  $out = '';
   $i = 0;
   foreach ($taggedtxt as $tt) {
     if (!in_array($tt->type, $skiptags) && strlen($tt->text) > 0) {
-            55083981
+      $class_attr = $tt->type;
       if(isset($tt->entityReference)){
         $class_attr .= " " . html_class_attribute_ref($tt->entityReference);
+      }
-cc085da
+      $out .= (strlen($out) > 0 && ++$i < count($taggedtxt) ? $glue : '')
-            55083981
+        . '<' . $tag . ' class="' . $class_attr . '">'
-cc085da
+        . t('@text', array('@text' => $tt->text))
         . '</' . $tag . '>';
-            6657531f
+            Andreas Kohlbecker
+  }
   return $out;
+}
-aad9da8
+            Andreas Kohlbecker
-            6657531f
+/**
  * Finds the text tagged with $tag_type in an array of taggedText instances.
+ *
-            e90899ac
+ * Note: This function is currently unused.
-            6657531f
+            Andreas Kohlbecker
  * @param array $taggedtxt
  *   Array with text items.
  * @param string $tag_type
-aad9da8
+ *   The type of tag for which to find text items in the $taggedtxt array, or NULL
  *   to return all texts.
-            6657531f
+            Andreas Kohlbecker
  * @return array
  *   An array with the texts mapped by $tag_type.
  */
-aad9da8
+function cdm_tagged_text_values(array $taggedtxt, $tag_type = NULL) {
-            6657531f
+  $tokens = array();
   if (!empty($taggedtxt)) {
     foreach ($taggedtxt as $tagtxt) {
-aad9da8
+      if ($tag_type === NULL || $tagtxt->type == $tag_type) {
-            6657531f
+        $tokens[] = $tagtxt->text;
+      }
+    }
+  }
   return $tokens;
+}
-            e90899ac
+/**
  * Preprocess the taggedTitle arrays.
+ *
  * Step 1: Turns 'newly' introduces tag types ("hybridSign")
  * into tag type "name"
+ *
  * Step 2: Two taggedTexts which have the same type and which have
  * a separator between them are merged together.
+ *
  * @param array $taggedTextList
  *    An array of TaggedText objects
  */
 function normalize_tagged_text(&$taggedTextList) {
   if (is_array($taggedTextList)) {
     // First pass: rename.
     for ($i = 0; $i < count($taggedTextList); $i++) {
       if ($taggedTextList[$i]->type == "hybridSign") {
         $taggedTextList[$i]->type = "name";
+      }
+    }
     // Second pass: resolve separators.
     $taggedNameListNew = array();
     for ($i = 0; $i < count($taggedTextList); $i++) {
       // elements of the same type concatenated by a separator should be merged together
       if (isset($taggedTextList[$i + 2]) && $taggedTextList[$i + 1]->type == "separator" && $taggedTextList[$i]->type == $taggedTextList[$i + 2]->type) {
         $taggedName = clone $taggedTextList[$i];
         $taggedName->text = $taggedName->text . $taggedTextList[$i + 1]->text . $taggedTextList[$i + 2]->text;
         $taggedNameListNew[] = $taggedName;
         ++$i;
         ++$i;
         continue;
+      }
       // no special handling
       $taggedNameListNew[] = $taggedTextList[$i];
+    }
     $taggedTextList = $taggedNameListNew;
+  }
+}
-d0407b7
+function split_secref_from_tagged_text(&$tagged_text) {
   $extracted_tt = array();
   if (is_array($tagged_text)) {
     for ($i = 0; $i < count($tagged_text) - 1; $i++) {
       if ($tagged_text[$i + 1]->type == "secReference" && $tagged_text[$i]->type == "separator"){
         $extracted_tt[0] = $tagged_text[$i];
         $extracted_tt[1] = $tagged_text[$i + 1];
         unset($tagged_text[$i]);
         unset($tagged_text[$i + 1]);
-b8afcd8
+        // also get the microfererence which could be in $tagged_text[$i + 3]
         if(isset($tagged_text[$i + 3])  && $tagged_text[$i + 2]->type == "separator" && $tagged_text[$i + 3]->type == "secReference"){
           $extracted_tt[2] = $tagged_text[$i + 2];
           $extracted_tt[3] = $tagged_text[$i + 3];
+        }
-d0407b7
+        break;
-            e90899ac
+            Andreas Kohlbecker
+    }
+  }
-d0407b7
+  return $extracted_tt;
-            e90899ac
+            Andreas Kohlbecker
-d0407b7
+function split_nomstatus_from_tagged_text(&$tagged_text) {
-            e90899ac
+            Andreas Kohlbecker
-d0407b7
+  $extracted_tt = array();
   if (is_array($tagged_text)) {
     for ($i = 0; $i < count($tagged_text) - 1; $i++) {
       if ($tagged_text[$i]->type == "nomStatus"){
         $extracted_tt[] = $tagged_text[$i];
         if(isset($tagged_text[$i + 1]) && $tagged_text[$i + 1]->type == "postSeparator"){
           $extracted_tt[] = $tagged_text[$i + 1];
           unset($tagged_text[$i + 1]);
+        }
         if ($tagged_text[$i - 1]->type == "separator"){
           array_unshift($extracted_tt, $tagged_text[$i - 1]);
           unset($tagged_text[$i - 1]);
-            e90899ac
+            Andreas Kohlbecker
-d0407b7
+        unset($tagged_text[$i]);
         break;
-            e90899ac
+            Andreas Kohlbecker
+    }
+  }
-d0407b7
+  return $extracted_tt;
-            e90899ac
+            Andreas Kohlbecker
 function find_tagged_text_elements($taggedTextList, $type){
   $matching_elements = array();
   if (is_array($taggedTextList)) {
     for ($i = 0; $i < count($taggedTextList) - 1; $i++) {
       if($taggedTextList[$i]->type == $type){
         $matching_elements[] = $taggedTextList[$i];
+      }
+    }
+  }
   return $matching_elements;
+}
 // ===================== END of Tagged Text functions ================== //
-b6ee11
+/**
  * 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);;
+}
-            6657531f
+/**
-            bfb2b81a
+ * Returns the chosen FeatureTree for the taxon profile.
-            6657531f
+            Andreas Kohlbecker
  * 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
-            bfb2b81a
+ *   A cdm FeatureTree object.
-            6657531f
+ */
-b323b
+function get_profile_feature_tree() {
-            bfb2b81a
+  static $profile_featureTree;
   if($profile_featureTree == NULL) {
-            6657531f
+    $profile_featureTree = cdm_ws_get(
       CDM_WS_FEATURETREE,
-            bfb2b81a
+      variable_get(CDM_PROFILE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
-            6657531f
+    );
-            bfb2b81a
+    if (!$profile_featureTree) {
       $profile_featureTree = cdm_ws_get(CDM_WS_FEATURETREE, UUID_DEFAULT_FEATURETREE);
+    }
-            6657531f
+            Andreas Kohlbecker
-e1
+            Andreas Kohlbecker
-            6657531f
+  return $profile_featureTree;
+}
-            f19f47fa
+/**
  * Returns the chosen FeatureTree for SpecimenDescriptions.
+ *
  * The FeatureTree returned is the one that has been set in the
  * dataportal settings (layout->taxon:specimen).
  * 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.
-            bfb2b81a
+ */
-            f19f47fa
+function cdm_get_occurrence_featureTree() {
-            bfb2b81a
+  static $occurrence_featureTree;
   if($occurrence_featureTree == NULL) {
     $occurrence_featureTree = cdm_ws_get(
       CDM_WS_FEATURETREE,
       variable_get(CDM_OCCURRENCE_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
     );
     if (!$occurrence_featureTree) {
       $occurrence_featureTree = cdm_ws_get(CDM_WS_FEATURETREE, UUID_DEFAULT_FEATURETREE);
+    }
+  }
-            f19f47fa
+  return $occurrence_featureTree;
-            bfb2b81a
+            Andreas Kohlbecker
-            f19f47fa
+/**
  * 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 $structured_description_featureTree;
-            bfb2b81a
+  if($structured_description_featureTree == NULL) {
-            f19f47fa
+    $structured_description_featureTree = cdm_ws_get(
         CDM_WS_FEATURETREE,
         variable_get(CDM_DATAPORTAL_STRUCTURED_DESCRIPTION_FEATURETREE_UUID, UUID_DEFAULT_FEATURETREE)
     );
     if (!$structured_description_featureTree) {
       $structured_description_featureTree = cdm_ws_get(
           CDM_WS_FEATURETREE,
           UUID_DEFAULT_FEATURETREE
       );
-            bfb2b81a
+            Andreas Kohlbecker
-            f19f47fa
+            Andreas Kohlbecker
   return $structured_description_featureTree;
-            bfb2b81a
+            Andreas Kohlbecker
-            6657531f
+            Andreas Kohlbecker
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function set_last_taxon_page_tab($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;
+  }
+}
 /**
+ *
  * @param object $media
  * @param array $mimeTypes
-fa6f9ba
+ *    an array of mimetypes in their order of preference. e.g:
  *    array('application/pdf', 'image/png', 'image/jpeg', 'image/gif', 'text/html')
-            6657531f
+ * @param int $width
-dd
+ *    The width of the optimal image. If null, the method will return the representation with the biggest expansion
-            6657531f
+ * @param int $height
-dd
+ *    The height of the optimal image. If null, the method will return the representation with the biggest expansion
-            6657531f
+            Andreas Kohlbecker
  * @return array
  *   An array with preferred media representations or else an empty array.
  */
-dc25a7d
+function cdm_preferred_media_representations($media, array $mimeTypes, $width = NULL, $height = NULL) {
-            6657531f
+  $prefRepr = array();
   if (!isset($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();
-dd
+        $expansionDeltaSum = 0;
-b2642
+        $valid_parts_cnt = 0;
-            6657531f
+        // Look for part with the best matching size.
         foreach ($representation->parts as $part) {
-fa6f9ba
+          if (empty($part->uri)) {
-b2642
+            // skip part if URI is missing
             continue;
+          }
           $valid_parts_cnt++;
-            f6408572
+          $expansionDelta = PHP_INT_MAX; // biggest delta for unknown sizes
-fa6f9ba
+            Andreas Kohlbecker
           // determine the optimal size
-            6657531f
+          if (isset($part->width) && isset($part->height)) {
-dd
+            $expansion = $part->width * $part->height;
-fa6f9ba
+            if ($width != null && $height != null) {
-dd
+              $optimalExpansion = $height * $width;
-fa6f9ba
+            } else {
-dd
+              $optimalExpansion = PHP_INT_MAX;
-fa6f9ba
+            Andreas Kohlbecker
             // determine the difference
-dd
+            $expansionDelta = $expansion > $optimalExpansion ? $expansion - $optimalExpansion : $optimalExpansion - $expansion;
-            6657531f
+            Andreas Kohlbecker
-dd
+          // sum up the expansionDeltas of all parts contained in the representation
           $expansionDeltaSum += $expansionDelta;
-            6657531f
+            Andreas Kohlbecker
-b2642
+        if($valid_parts_cnt > 0){
-dd
+          $expansionDeltaSum = $expansionDeltaSum / $valid_parts_cnt;
           $prefRepr[$expansionDeltaSum] = $representation;
-b2642
+            Andreas Kohlbecker
-            6657531f
+            Andreas Kohlbecker
+    }
+  }
-fa6f9ba
+  // Sort the array so that the smallest key value is the first in the array
   ksort($prefRepr);
-            6657531f
+  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;
+    }
+  }
-            c7f92453
+  return '';
-            6657531f
+            Andreas Kohlbecker
 /**
  * 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;
+    }
+  }
-            c7f92453
+  return '';
-            6657531f
+            Andreas Kohlbecker
 /**
  * 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)) {
-a93702a
+    $day = substr($partial, 8, 2);
-            6657531f
+    if (preg_match("/[0-9][0-9]/", $day)) {
       return $day;
+    }
+  }
-            c7f92453
+  return '';
-            6657531f
+            Andreas Kohlbecker
 /**
  * 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 $stripZeros
  *   If set to TRUE the zero (00) month and days will be hidden:
  *   eg 1956-00-00 becomes 1956. The default is TRUE.
-            fe2edf33
+ * @param string @format
  * 	 Can ve used to specify the format of the date string, currently the following format strings are supported
  *    - "YYYY": Year only
  *    - "YYYY-MM-DD": this is the default
-            6657531f
+            Andreas Kohlbecker
  * @return string
  *   YYYY-MM-DD formatted year, month, day.
  */
-            fe2edf33
+function partialToDate($partial, $stripZeros = TRUE, $format= "YYYY-MM-DD") {
   $y = NULL; $m = NULL; $d = NULL;
-dfe695c
+  if(strpos($format, 'YY') !== FALSE){
-            fe2edf33
+    $y = partialToYear($partial);
+  }
-dfe695c
+  if(strpos($format, 'MM') !== FALSE){
-            fe2edf33
+    $m = partialToMonth($partial);
+  }
-dfe695c
+  if(strpos($format, 'DD') !== FALSE){
-            fe2edf33
+    $d = partialToDay($partial);
+  }
-            6657531f
+            Andreas Kohlbecker
   $y = $y ? $y : '00';
   $m = $m ? $m : '00';
   $d = $d ? $d : '00';
   $date = '';
   if ($y == '00' && $stripZeros) {
-            c7f92453
+    return '';
-            6657531f
+            Andreas Kohlbecker
   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 $stripZeros
  *   If set to True, the zero (00) month and days will be hidden:
  *   eg 1956-00-00 becomes 1956. The default is TRUE.
-            fe2edf33
+ * @param string @format
  * 	 Can ve used to specify the format of the date string, currently the following format strings are supported
  *    - "YYYY": Year only
  *    - "YYYY-MM-DD": this is the default
-            6657531f
+            Andreas Kohlbecker
  * @return string
  *   Returns a date in the form of a string.
  */
-            fe2edf33
+function timePeriodToString($period, $stripZeros = TRUE, $format = "YYYY-MM-DD") {
-            6657531f
+  $dateString = '';
-a288588
+  if($period->freeText){
     $dateString = $period->freeText;
   } else {
     if ($period->start) {
       $dateString = partialToDate($period->start, $stripZeros, $format);
+    }
     if ($period->end) {
-            c0223d83
+      $end_str = partialToDate($period->end, $stripZeros, $format);
       $dateString .= ($dateString && $end_str > 0 ? ' ' . t('to') . ' ' : '') . $end_str;
-a288588
+            Andreas Kohlbecker
-            6657531f
+            Andreas Kohlbecker
   return $dateString;
+}
-            fe2edf33
+            Andreas Kohlbecker
-            c2486c6b
+/**
  * 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;
+}
-            6657531f
+            Andreas Kohlbecker
 /**
-f2e1e0
+ * Composes a absolute CDM web service URI with parameters and querystring.
-            6657531f
+            Andreas Kohlbecker
  * @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();
+  }
   // (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) {
-cc085da
+        drupal_set_message(
           t('cdm_compose_url(): missing pathParameter @index for !uri_pattern',
             array('@index' => $i, '!uri-pattern' => $uri_pattern )),
           'error');
-            6657531f
+      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;
+  }
   $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) {
-ebf0428
+            Andreas Kohlbecker
-            6657531f
+  $args = func_get_args();
-dde69
+  $do_gzip = function_exists('gzencode');
-            6657531f
+  $uriEncoded = array_shift($args);
   $uri = urldecode($uriEncoded);
-            f1f05758
+  $hook = array_shift($args);
-ebf0428
+  $request_method = strtoupper($_SERVER["REQUEST_METHOD"]);
-ab2885
+  $post_data = null;
-ebf0428
+  if ($request_method == "POST" || $request_method == "PUT") {
     // read response body via inputstream module
     $post_data = file_get_contents("php://input");
+  }
-            6657531f
+            Andreas Kohlbecker
   // Find and deserialize arrays.
   foreach ($args as &$arg) {
     // FIXME use regex to find serialized arrays.
-ebf0428
+    //       or should we accept json instead of php serializations?
-            6657531f
+    if (strpos($arg, "a:") === 0) {
       $arg = unserialize($arg);
+    }
+  }
-ebf0428
+  // In all these cases perform a simple get request.
   // TODO reconsider caching logic in this function.
-            6657531f
+            Andreas Kohlbecker
-ebf0428
+  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, $hvalue);
-e1
+            Andreas Kohlbecker
-ebf0428
+            Andreas Kohlbecker
     if (isset($http_response->data)) {
       print $http_response->data;
       flush();
+    }
     exit(); // leave drupal here
   } else {
     // $hook has been supplied
     // handle $hook either as compose ot theme hook
     // pass through theme or comose hook
-af3ce28
+    // compose hooks can be called without data, therefore
     // passing the $uri in this case is not always a requirement
-ebf0428
+            Andreas Kohlbecker
-af3ce28
+    if($uri && $uri != 'NULL') {
-ebf0428
+    // do a security check since the $uri will be passed
     // as absolute URI to cdm_ws_get()
-af3ce28
+      if (!_is_cdm_ws_uri($uri)) {
         drupal_set_message(
           'Invalid call of proxy_content() with callback parameter \'' . $hook . '\' and URI:' . $uri,
           'error'
         );
         return '';
+      }
-e1
+            Andreas Kohlbecker
-af3ce28
+      $obj = cdm_ws_get($uri, NULL, $post_data, $request_method, TRUE);
     } else {
       $obj = NULL;
+    }
-fe78f3c
+            Andreas Kohlbecker
-ebf0428
+    $reponse_data = NULL;
-b3d713e
+            Andreas Kohlbecker
-ebf0428
+    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(
-c9d11f7
+            '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,
             );
-ebf0428
+          $reponse_data = theme($hook, $variables);
           break;
-c9d11f7
+        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;
-ebf0428
+        case 'cdm_media_caption':
           $variables = array(
-            f79d32d6
+            'media' => $obj,
             // $args[0] is set in taxon_image_gallery_default in
             // cdm_dataportal.page.theme.
             'elements' => isset($args[0]) ? $args[0] : array(
             'title',
             'description',
             'artist',
             'location',
             'rights',
-ebf0428
+          ),
-            f79d32d6
+            'sources_as_content' =>  isset($args[1]) ? $args[1] : FALSE
-ebf0428
+          );
           $reponse_data = theme($hook, $variables);
           break;
         default:
           drupal_set_message(t(
-c9d11f7
+          'Theme !theme is not yet supported by the function !function.', array(
-ebf0428
+          '!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 $hook either as compose ot theme hook
-b3d713e
+            Andreas Kohlbecker
-            6657531f
+            Andreas Kohlbecker
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function setvalue_session() {
   if ($_REQUEST['var'] && strlen($_REQUEST['var']) > 4) {
-af3ce28
+    $var_keys = substr($_REQUEST['var'], 1, strlen($_REQUEST['var']) - 2);
     $var_keys = explode('][', $var_keys);
-            6657531f
+            Andreas Kohlbecker
   else {
     return;
+  }
-d69a96c
+  $val = isset($_REQUEST['val']) ? $_REQUEST['val'] : NULL;
-            6657531f
+            Andreas Kohlbecker
   // Prevent from malicous tags.
   $val = strip_tags($val);
-af3ce28
+  $session_var = &$_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();
-            6657531f
+            Andreas Kohlbecker
-af3ce28
+    $session_var = &$session_var[$key];
-            6657531f
+            Andreas Kohlbecker
-af3ce28
+  $session_var = $val;
-            6657531f
+  if (isset($_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" : ''));
+}
 /**
-f2e1e0
+ * 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 $cdmBase
  *   The CDM entity to construct the annotations pager uri for
-            6657531f
+ */
-f2e1e0
+function cdm_compose_annotations_uri($cdmBase) {
-            6657531f
+  if (!$cdmBase->uuid) {
     return;
+  }
   $ws_base_uri = NULL;
   switch ($cdmBase->class) {
     case 'TaxonBase':
     case 'Taxon':
     case 'Synonym':
       $ws_base_uri = CDM_WS_TAXON;
       break;
-            b20f6a5f
+    case 'TaxonName':
-            6657531f
+      $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
-            b5dca1e2
+ * @param int $pageSize
  *   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
-            6657531f
+ *   to return all entities in a single page).
  * @param int $pageNumber
  *   The number of the page to be returned, the first page has the
-            b5dca1e2
+ *   pageNumber = 0
-ebf0428
+ * @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"
-f2e1e0
+ * @param bool $absoluteURI
  *   TRUE when the URL should be treated as absolute URL.
-ebf0428
+            Andreas Kohlbecker
-            b5dca1e2
+ * @return the a CDM Pager object
-            6657531f
+            Andreas Kohlbecker
  */
-ebf0428
+function cdm_ws_page($resourceURI, $pageSize, $pageNumber, array $query = array(), $method = 'GET', $absoluteURI = FALSE) {
   $query['pageNumber'] = $pageNumber;
   $query['pageSize'] = $pageSize;
   return cdm_ws_get($resourceURI, NULL, queryString($query), $method, $absoluteURI);
-            6657531f
+            Andreas Kohlbecker
-            b5dca1e2
+/**
  * Fetches all entities from the given REST endpoint using the pager mechanism.
+ *
  * @param string $resourceURI
-ebf0428
+ * @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";
-f2e1e0
+ * @param bool $absoluteURI
  *   TRUE when the URL should be treated as absolute URL.
-            b5dca1e2
+            Andreas Kohlbecker
  * @return array
  *     A list of CDM entitites
+ *
  */
-ebf0428
+function cdm_ws_fetch_all($resourceURI, array $query = array(), $method = 'GET', $absoluteURI = FALSE) {
-            b5dca1e2
+  $page_index = 0;
   // using a bigger page size to avoid to many multiple requests
-            f9da0eb9
+  $page_size = 500;
-            b5dca1e2
+  $entities = array();
   while ($page_index !== FALSE){
-ebf0428
+    $pager =  cdm_ws_page($resourceURI, $page_size, $page_index, $query,  $method, $absoluteURI);
-            b5dca1e2
+    if(isset($pager->records) && is_array($pager->records)) {
-            dc66315d
+      $entities = array_merge($entities, $pager->records);
-            b5dca1e2
+      if(!empty($pager->nextIndex)){
         $page_index = $pager->nextIndex;
       } else {
         $page_index = FALSE;
+      }
     } else {
       $page_index = FALSE;
+    }
+  }
   return $entities;
+}
-            6657531f
+/*
 function cdm_ws_taxonomy_compose_resourcePath($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 $ignore_rank_limit
  *   Whether to ignore the variable 'taxontree_ranklimit' set by admin in the settings
-            6657531f
+            Andreas Kohlbecker
-            aaa81689
+ * @return string
  *   A cdm REST service URL path to a Classification
-            6657531f
+ */
-c55
+function cdm_compose_taxonomy_root_level_path($taxon_uuid = FALSE, $ignore_rank_limit = FALSE) {
-cd0b
+  $view_uuid = get_current_classification_uuid();
-c55
+  $rank_uuid = NULL;
   if (!$ignore_rank_limit) {
-            aaa81689
+    $rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
-c55
+            Andreas Kohlbecker
-            6657531f
+            Andreas Kohlbecker
-c55
+  if (!empty($taxon_uuid)) {
-            6657531f
+    return cdm_compose_url(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
-c55
+      $view_uuid,
       $taxon_uuid,
-            6657531f
+    ));
+  }
   else {
-            aaa81689
+    if (is_uuid($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
-ebf0428
+    $response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid), NULL, NULL, 'GET', TRUE);
-c55
+            Andreas Kohlbecker
     if ($response == NULL) {
       // 2dn try by ignoring the rank limit
-ebf0428
+      $response = cdm_ws_get(cdm_compose_taxonomy_root_level_path($taxon_uuid, TRUE), NULL, NULL, 'GET', 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']);
-fcdb3
+        drupal_set_message("Could not find a valid classification, falling back to the default classification.", 'warning');
-c55
+        return cdm_ws_taxonomy_root_level($taxon_uuid);
+      }
       else {
         // Check if taxonomictree_uuid is valid.
-            a50c8468
+        // expecting an array of taxonNodes,
         // empty classifications are ok so no warning in this case!
-ebf0428
+        $test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
-            a50c8468
+        if (!is_array($test)) {
-c55
+          // The default set by the admin seems to be invalid or is not even set.
           drupal_set_message(_no_classfication_uuid_message(), 'warning');
+        }
-            a50c8468
+        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');
+        }
-            6657531f
+            Andreas Kohlbecker
+    }
   return $response;
+}
 /**
-            aaa81689
+ * 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.
-            6657531f
+            Andreas Kohlbecker
-c55
+ * @param string $taxon_uuid
-            6657531f
+            Andreas Kohlbecker
-            eb9fdcf7
+ * @return array
-            aaa81689
+ *   An array of CDM TaxonNodeDTO objects
-            6657531f
+ */
-c55
+function cdm_ws_taxonomy_pathFromRoot($taxon_uuid) {
-cd0b
+  $view_uuid = get_current_classification_uuid();
-            aaa81689
+  $rank_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
-            6657531f
+            Andreas Kohlbecker
   $response = NULL;
-            aaa81689
+  if (is_uuid($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.
-af3ce28
+//    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 {
-            6657531f
+      // Check if taxonomictree_uuid is valid.
-ebf0428
+      $test = cdm_ws_get(cdm_compose_taxonomy_root_level_path(), NULL, NULL, 'GET', TRUE);
-            6657531f
+      if ($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');
+      }
-af3ce28
+//    }
-            6657531f
+            Andreas Kohlbecker
   return $response;
+}
-            d8e85b2d
+            Andreas Kohlbecker
 // =============================Terms and Vocabularies ========================================= //
-            6657531f
+            Andreas Kohlbecker
 /**
-f307
+ * Returns the localized representation for the given term.
-            6657531f
+            Andreas Kohlbecker
  * @param Object $definedTermBase
  * 	  of cdm type DefinedTermBase
  * @return string
  * 	  the localized representation_L10n of the term,
  *    otherwise the titleCache as fall back,
-c5c87a
+ *    otherwise the default_representation which defaults to an empty string
-            6657531f
+ */
-c5c87a
+function cdm_term_representation($definedTermBase, $default_representation = '') {
-            6657531f
+  if ( isset($definedTermBase->representation_L10n) ) {
     return $definedTermBase->representation_L10n;
   } elseif ( isset($definedTermBase->titleCache)) {
     return $definedTermBase->titleCache;
+  }
-c5c87a
+  return $default_representation;
-            6657531f
+            Andreas Kohlbecker
-f307
+/**
  * 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);
+  }
+}
-            d8e85b2d
+/**
  * 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
+ *
-            a6ae799b
+ * @param bool $empty_option
  *   An additional element do be placed at the beginning og the list. This element will be the default option.
+ *
-            d8e85b2d
+ * @return array
  *   the terms in an array as options for a form element that allows multiple choices.
  */
-            a6ae799b
+function cdm_terms_as_options($terms, $term_label_callback = NULL, $empty_option = FALSE){
-            d8e85b2d
+  $options = array();
-ca5ef1e
+  if(isset($terms) && is_array($terms)) {
     foreach ($terms as $term) {
-            d8e85b2d
+      if ($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?
-cc085da
+        $options[$term->uuid] = t('@term', array('@term' => $term->representation_L10n));
-            d8e85b2d
+            Andreas Kohlbecker
+    }
+  }
-            a6ae799b
+  if($empty_option !== FALSE){
     array_unshift ($options, "");
+  }
-            d8e85b2d
+  return $options;
+}
 /**
-ca5ef1e
+ * 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
-            a6ae799b
+ * @param bool $empty_option
-ca5ef1e
+ *   An additional element do be placed at the beginning og the list. This element will be the default option.
-            efa372e9
+ * @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 $order_by
-ca5ef1e
+ *   One of the order by constants defined in this file
-            efa372e9
+ * @return mixed
-            d8e85b2d
+ */
-            a6ae799b
+function cdm_vocabulary_as_option($vocabulary_uuid, $term_label_callback = NULL, $empty_option = FALSE,
-            efa372e9
+                                  array $include_filter = null, $order_by = CDM_ORDER_BY_ORDER_INDEX_ASC) {
-            d8e85b2d
+  static $vocabularyOptions = array();
-ca5ef1e
+  if (!isset($vocabularyOptions[$vocabulary_uuid])) {
     $terms = cdm_ws_fetch_all('termVocabulary/' . $vocabulary_uuid . '/terms',
       array(
         'orderBy' => $order_by
+      )
     );
-            efa372e9
+            Andreas Kohlbecker
     // apply the include filter
     if($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
-            a6ae799b
+    $vocabularyOptions[$vocabulary_uuid] = cdm_terms_as_options($terms, $term_label_callback, $empty_option);
-            d8e85b2d
+            Andreas Kohlbecker
-            f5bc56a0
+            Andreas Kohlbecker
-ca5ef1e
+  $options = $vocabularyOptions[$vocabulary_uuid];
-            a6ae799b
+            Andreas Kohlbecker
-            f5bc56a0
+  return $options;
-            d8e85b2d
+            Andreas Kohlbecker
 /**
-            a6ae799b
+ * @param $term_type string one of
-            d8e85b2d
+ *  - 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
-ca5ef1e
+            Andreas Kohlbecker
  * @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!!)
-            a6ae799b
+ * @param bool $empty_option
  *   An additional element do be placed at the beginning og the list. This element will be the default option.
-d3d6556
+ * @return array
  *    the terms in an array as options for a form element that allows multiple choices.
-            d8e85b2d
+ */
-            a6ae799b
+function cdm_terms_by_type_as_option($term_type, $order_by = CDM_ORDER_BY_TITLE_CACHE_ASC, $term_label_callback = NULL, $empty_option = FALSE){
-ca5ef1e
+  $terms = cdm_ws_fetch_all(
     CDM_WS_TERM,
     array(
       'class' => $term_type,
       'orderBy' => $order_by
+    )
   );
-            a6ae799b
+  return cdm_terms_as_options($terms, $term_label_callback, $empty_option);
-            d8e85b2d
+            Andreas Kohlbecker
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _cdm_relationship_type_term_label_callback($term) {
   if (isset($term->representation_L10n_abbreviatedLabel)) {
-cc085da
+    return $term->representation_L10n_abbreviatedLabel . ' : '
     . t('@term', array('@term' => $term->representation_L10n));
-            d8e85b2d
+            Andreas Kohlbecker
 else {
-cc085da
+    return t('@term', array('@term' => $term->representation_L10n));
-            d8e85b2d
+            Andreas Kohlbecker
+}
 // ========================================================================================== //
-            6657531f
+/**
  * @todo Improve documentation of this function.
+ *
  * eu.etaxonomy.cdm.model.description.
  * CategoricalData
  * CommonTaxonName
  * Distribution
  * IndividualsAssociation
  * QuantitativeData
  * TaxonInteraction
  * TextData
  */
 function cdm_descriptionElementTypes_as_option($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;
+}
 /**
-cbbc22a
+ * Fetches all TaxonDescription descriptions elements which are associated to the
  * Taxon specified by the $taxon_uuid and merges the elements into the given
-            37252893
+ * feature tree.
  * @param $feature_tree
  *     The CDM FeatureTree to be used as template
  * @param $taxon_uuid
  *     The UUID of the taxon
-e1
+ * @param $excludes
  *     UUIDs of features to be excluded
-            37252893
+ * @return$feature_tree
-cbbc22a
+ *     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 $descriptionElements.
-            6657531f
+ */
-e1
+function cdm_ws_descriptions_by_featuretree($feature_tree, $taxon_uuid, $exclude_uuids = array()) {
-            37252893
+            Andreas Kohlbecker
   if (!$feature_tree) {
-            6657531f
+    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;
+  }
-e1
+  $description_elements = cdm_ws_fetch_all(CDM_WS_DESCRIPTIONELEMENT_BY_TAXON,
-            37252893
+      array(
       'taxon' => $taxon_uuid,
-e1
+      'features' => cdm_featureTree_elements_toString($feature_tree->root, ',', 'uuid', $exclude_uuids)
-ebf0428
+      ),
       'POST'
-            37252893
+  );
-            6657531f
+            Andreas Kohlbecker
-            7508605c
+  // Combine all descriptions into one feature tree.
-e1
+  $merged_nodes = _mergeFeatureTreeDescriptions($feature_tree->root->childNodes, $description_elements);
-            fae36a2a
+  $feature_tree->root->childNodes = $merged_nodes;
-            6657531f
+            Andreas Kohlbecker
-            37252893
+  return $feature_tree;
-            6657531f
+            Andreas Kohlbecker
 /**
-a15731a
+ * Returns a filtered a list of annotations for the cdm entity given as parameter $cdmBase.
  * If the annotations are not yet already loded with the cdm entity the cdm REST service will
  * be requested for the annotations.
-            6657531f
+            Andreas Kohlbecker
  * @param string $cdmBase
  *   An annotatable cdm entity.
  * @param array $includeTypes
  *   If an array of annotation type uuids is supplied by this parameter the
  *   list of annotations is resticted to those which belong to this type.
+ *
  * @return array
  *   An array of Annotation objects or an empty array.
  */
-a15731a
+function cdm_ws_getAnnotationsFor(&$cdmBase, $includeTypes = FALSE) {
   if(!isset($cdmBase->annotations)){
-f2e1e0
+    $annotationUrl = cdm_compose_annotations_uri($cdmBase);
-f01b13
+    $cdmBase->annotations = cdm_ws_fetch_all($annotationUrl, array(), 'GET', TRUE);
-            6657531f
+            Andreas Kohlbecker
-a15731a
+            Andreas Kohlbecker
-            b5dca1e2
+  $annotations = array();
-a15731a
+  foreach ($cdmBase->annotations as $annotation) {
     if ($includeTypes) {
-            d8e85b2d
+      if (
         ( isset($annotation->annotationType->uuid) && in_array($annotation->annotationType->uuid, $includeTypes, TRUE) )
         || ($annotation->annotationType === NULL && in_array('NULL_VALUE', $includeTypes, TRUE))
       ) {
-a15731a
+        $annotations[] = $annotation;
+      }
+    }
     else {
       $annotations[] = $annotation;
+    }
+  }
   return $annotations;
-            6657531f
+            Andreas Kohlbecker
-            eeb98da8
+/**
  * Loads the annotations from the REST service an adds them as field to the given $annotatable_entity.
+ *
  * @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)) {
     $annotations = cdm_ws_getAnnotationsFor($annotatable_entity);
     if (is_array($annotations)) {
       $annotatable_entity->annotations = $annotations;
+    }
+  }
+}
-c2b9b9d
+/**
  * 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;
+  }
+}
-            6657531f
+/**
  * 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, $microreference) {
-            ecb8526d
+            Andreas Kohlbecker
   // TODO the below statement avoids error boxes due to #4644 remove it once this ticket is solved
   if(is_array($microreference) || is_object($microreference)) {
     return '';
+  }
-            6657531f
+  $obj = cdm_ws_get(CDM_WS_NOMENCLATURAL_REFERENCE_CITATION, array(
     $referenceUuid,
   ), "microReference=" . urlencode($microreference));
   if ($obj) {
     return $obj->String;
+  }
   else {
     return NULL;
+  }
+}
-e1
+/**
  * 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 $feature_uuid
  *    The UUID of the Feature
  * @return returns the FeatureNode or null
  */
 function &cdm_feature_tree_find_node($feature_tree_nodes, $feature_uuid){
   // 1. scan this level
   foreach ($feature_tree_nodes as $node){
     if($node->feature->uuid == $feature_uuid){
       return $node;
+    }
+  }
   // 2. descend into childen
   foreach ($feature_tree_nodes as $node){
     if(is_array($node->childNodes)){
-b4ae204
+      $node = cdm_feature_tree_find_node($node->childNodes, $feature_uuid);
-e1
+      if($node) {
         return $node;
+      }
+    }
+  }
-b4ae204
+  $null_var = null; // kludgy workaround to avoid "PHP Notice: Only variable references should be returned by reference"
   return $null_var;
-e1
+            Andreas Kohlbecker
-            6657531f
+/**
-            bfb2b81a
+ * Merges the given featureNodes structure with the descriptionElements.
+ *
  * This method is used in preparation for rendering the descriptionElements.
-c5c87a
+ * The descriptionElements which belong to a specific feature node are appended
-            fae36a2a
+ * to a the feature node by creating a new field:
-fd
+ *  - descriptionElements: the CDM DescriptionElements which belong to this feature
  * The descriptionElements will be cleared in advance in order to allow reusing the
-c5c87a
+ * same feature tree without the risk of mixing sets of description elements.
-fd
+            Andreas Kohlbecker
-            bfb2b81a
+ * which originally is not existing in the cdm.
+ *
-fd
+            Andreas Kohlbecker
+ *
-            bfb2b81a
+ * @param array $featureNodes
-c5c87a
+ *    An array of cdm FeatureNodes which may be hierarchical since feature nodes
-            bfb2b81a
+ *    may have children.
  * @param array $descriptionElements
  *    An flat array of cdm DescriptionElements
  * @return array
-c5c87a
+ *    The $featureNodes structure enriched with the according $descriptionElements
-            6657531f
+ */
 function _mergeFeatureTreeDescriptions($featureNodes, $descriptionElements) {
-            a67e7364
+            Andreas Kohlbecker
-            6657531f
+  foreach ($featureNodes as &$node) {
-            a67e7364
+    // since the $featureNodes array is reused for each description
-c5c87a
+    // it is necessary to clear the custom node fields in advance
-            a67e7364
+    if(isset($node->descriptionElements)){
       unset($node->descriptionElements);
+    }
-            6657531f
+    // 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[] = $element;
+      }
+    }
     // Recurse into node children.
-            fae36a2a
+    if (isset($node->childNodes[0])) {
       $mergedChildNodes = _mergeFeatureTreeDescriptions($node->childNodes, $descriptionElements);
       $node->childNodes = $mergedChildNodes;
-            6657531f
+            Andreas Kohlbecker
-            a67e7364
+            Andreas Kohlbecker
-            fae36a2a
+    if(!isset($node->descriptionElements) && !isset($node->childNodes[0])){
-fd
+      unset($node);
+    }
-            6657531f
+            Andreas Kohlbecker
-            a67e7364
+            Andreas Kohlbecker
-            6657531f
+  return $featureNodes;
+}
 /**
-fdac2a
+ * Sends a GET or POST request to a CDM RESTService and returns a de-serialized object.
-            6657531f
+            Andreas Kohlbecker
  * The response from the HTTP GET request is returned as object.
  * The response objects coming from the webservice configured in the
-fdac2a
+ * 'cdm_webservice_url' variable are being cached in a level 1 (L1) and / or
-            6657531f
+ *  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
-fdac2a
+ * long as the drupal cache is not being cleared and are available across
-            6657531f
+ * 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 $absoluteURI
  *   TRUE when the URL should be treated as absolute URL.
+ *
-d3c2389
+ * @return object| array
-fdac2a
+ *   The de-serialized webservice response object.
-            6657531f
+ */
 function cdm_ws_get($uri, $pathParameters = array(), $query = NULL, $method = "GET", $absoluteURI = FALSE) {
-            d071bed7
+            Andreas Kohlbecker
-            6657531f
+  static $cacheL1 = array();
-ebf0428
+  $data = NULL;
   // store query string in $data and clear the query, $data will be set as HTTP request body
   if($method == 'POST'){
     $data = $query;
     $query = NULL;
+  }
-e1
+  // Transform the given uri path or pattern into a proper webservice uri.
-            6657531f
+  if (!$absoluteURI) {
     $uri = cdm_compose_url($uri, $pathParameters, $query);
+  }
-ea6
+  // read request parameter 'cacheL2_refresh'
-fdac2a
+  // which allows refreshing the level 2 cache
-ea6
+  $do_cacheL2_refresh = isset($_REQUEST['cacheL2_refresh']) && $_REQUEST['cacheL2_refresh'] == 1;
-            6657531f
+  $is_cdm_ws_uri = _is_cdm_ws_uri($uri);
   $use_cacheL2 = variable_get('cdm_webservice_cache', 1);
-ebf0428
+  if($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)) {
-            6657531f
+    $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;
   $cacheL2_entry = FALSE;
-ea6
+  if ($use_cacheL2 && !$do_cacheL2_refresh) {
-            6657531f
+    // Try to get object from cacheL2.
-ebf0428
+    $cacheL2_entry = cache_get($cache_key, 'cache_cdm_ws');
-            6657531f
+            Andreas Kohlbecker
   if (isset($cacheL1_obj)) {
     //
     // The object has been found in the L1 cache.
     //
     $obj = $cacheL1_obj;
-            a4f964ee
+    if (cdm_debug_block_visible()) {
-ebf0428
+      cdm_ws_debug_add($uri, $method, $data, 0, 0, NULL, 'cacheL1');
-            6657531f
+            Andreas Kohlbecker
+  }
   elseif ($cacheL2_entry) {
     //
     // The object has been found in the L2 cache.
     //
-            e2464cf8
+    $duration_parse_start = microtime(TRUE);
-            6657531f
+    $obj = unserialize($cacheL2_entry->data);
-            e2464cf8
+    $duration_parse = microtime(TRUE) - $duration_parse_start;
-            6657531f
+            Andreas Kohlbecker
-            a4f964ee
+    if (cdm_debug_block_visible()) {
-ebf0428
+      cdm_ws_debug_add($uri, $method, $data, 0, $duration_parse, NULL, 'cacheL2');
-            6657531f
+            Andreas Kohlbecker
+  }
   else {
     //
     // Get the object from the webservice and cache it.
     //
-            e2464cf8
+    $duration_fetch_start = microtime(TRUE);
-            6657531f
+    // Request data from webservice JSON or XML.
-ebf0428
+    $response = cdm_http_request($uri, $method, $data);
     $response_body = NULL;
-fe78f3c
+    if (isset($response->data)) {
-ebf0428
+      $response_body = $response->data;
-fe78f3c
+            Andreas Kohlbecker
-            e2464cf8
+    $duration_fetch = microtime(TRUE) - $duration_fetch_start;
     $duration_parse_start = microtime(TRUE);
-            6657531f
+            Andreas Kohlbecker
     // Parse data and create object.
-ebf0428
+    $obj = cdm_load_obj($response_body);
-            6657531f
+            Andreas Kohlbecker
-            e2464cf8
+    $duration_parse = microtime(TRUE) - $duration_parse_start;
-            a4f964ee
+            Andreas Kohlbecker
     if (cdm_debug_block_visible()) {
-ebf0428
+      if ($obj || $response_body == "[]") {
-            e2464cf8
+        $status = 'valid';
-            6657531f
+            Andreas Kohlbecker
       else {
-            e2464cf8
+        $status = 'invalid';
-            6657531f
+            Andreas Kohlbecker
-ebf0428
+      cdm_ws_debug_add($uri, $method, $data, $duration_fetch, $duration_parse, strlen($response_body), $status);
-            6657531f
+            Andreas Kohlbecker
     if ($set_cacheL2) {
       // Store the object in cache L2.
-ebf0428
+      // Comment @WA perhaps better if Drupal serializedatas here? Then the
-            6657531f
+      // flag serialized is set properly in the cache table.
-ebf0428
+      cache_set($cache_key, serialize($obj), 'cache_cdm_ws', CACHE_TEMPORARY);
-            6657531f
+            Andreas Kohlbecker
+  }
   if ($obj) {
     // Store the object in cache L1.
     if ($set_cacheL1) {
-ebf0428
+      $cacheL1[$cache_key] = $obj;
-            6657531f
+            Andreas Kohlbecker
+  }
   return $obj;
+}
 /**
-            e2464cf8
+ * 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
-ebf0428
+ * @param string $method
  *    The HTTP request method, either 'GET' or 'POST'
  * @param string $post_data
  *    The datastring send with a post request
-            e2464cf8
+ * @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 $status
  *    A status string, possible values are: 'valid', 'invalid', 'cacheL1', 'cacheL2'
  * @return bool
  *    TRUE if adding the debug information was successful
-            6657531f
+ */
-ebf0428
+function cdm_ws_debug_add($uri, $method, $post_data, $duration_fetch, $duration_parse, $datasize, $status) {
-            6657531f
+            Andreas Kohlbecker
-            e2464cf8
+  static $initial_time = NULL;
   if(!$initial_time) {
     $initial_time = microtime(TRUE);
+  }
   $time = microtime(TRUE) - $initial_time;
-            6657531f
+            Andreas Kohlbecker
   // Decompose uri into path and query element.
   $uri_parts = explode("?", $uri);
-f4c
+  $query = array();
-            6657531f
+  if (count($uri_parts) == 2) {
     $path = $uri_parts[0];
+  }
   else {
     $path = $uri;
+  }
-            c1bcfc1b
+  if(strpos($uri, '?') > 0){
     $json_uri = str_replace('?', '.json?', $uri);
     $xml_uri = str_replace('?', '.xml?', $uri);
   } else {
     $json_uri = $uri . '.json';
     $xml_uri = $json_uri . '.xml';
+  }
-            e2464cf8
+  // data links to make data accecsible as json and xml
   $data_links = '';
-            6657531f
+  if (_is_cdm_ws_uri($path)) {
-ebf0428
+            Andreas Kohlbecker
     // 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>';
+    }
-            6657531f
+            Andreas Kohlbecker
   else {
-            c1bcfc1b
+    $data_links .= '<a href="' . $uri . '" target="data">open</a>';
-            e2464cf8
+            Andreas Kohlbecker
   //
   $data = array(
       'ws_uri' => $uri,
-ebf0428
+      'method' => $method,
       'post_data' => $post_data,
-            e2464cf8
+      '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();
-            6657531f
+            Andreas Kohlbecker
-            e2464cf8
+  $_SESSION['cdm']['ws_debug'][] = serialize($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;
-            6657531f
+            Andreas Kohlbecker
-            a4f964ee
+/**
  * 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');
-            af932304
+      $is_visible = isset($block->status) && $block->status == 1;
-            a4f964ee
+      if($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 $is_visible;
+}
-            6657531f
+/**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
-ebf0428
+function cdm_load_obj($response_body) {
   $obj = json_decode($response_body);
-            6657531f
+            Andreas Kohlbecker
   if (!(is_object($obj) || is_array($obj))) {
     ob_start();
     $obj_dump = ob_get_contents();
     ob_clean();
     return FALSE;
+  }
   return $obj;
+}
 /**
-fe78f3c
+ * Do a http request to a CDM RESTful web service.
-            6657531f
+            Andreas Kohlbecker
  * @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.
-ebf0428
+ * @param $data: A string containing the request body, formatted as
  *     'param=value&param=value&...'. Defaults to NULL.
-            6657531f
+            Andreas Kohlbecker
-fe78f3c
+ * @return object
  *   The object as returned by drupal_http_request():
  *   An object that can have one or more of the following components:
  *   - request: A string containing the request body that was sent.
  *   - code: An integer containing the response status code, or the error code
  *     if an error occurred.
  *   - protocol: The response protocol (e.g. HTTP/1.1 or HTTP/1.0).
  *   - status_message: The status message from the response, if a response was
  *     received.
  *   - redirect_code: If redirected, an integer containing the initial response
  *     status code.
  *   - redirect_url: If redirected, a string containing the URL of the redirect
  *     target.
  *   - error: If an error occurred, the error message. Otherwise not set.
  *   - headers: An array containing the response headers as name/value pairs.
  *     HTTP header names are case-insensitive (RFC 2616, section 4.2), so for
  *     easy access the array keys are returned in lower case.
  *   - data: A string containing the response body that was received.
-            6657531f
+ */
-ebf0428
+function cdm_http_request($uri, $method = "GET", $data = NULL) {
-            6657531f
+  static $acceptLanguage = NULL;
-b606c0d
+  $header = array();
-            af0cde1a
+            Andreas Kohlbecker
   if(!$acceptLanguage && module_exists('i18n')){
     $acceptLanguage = i18n_language_content()->language;
+  }
-            6657531f
+            Andreas Kohlbecker
   if (!$acceptLanguage) {
     if (function_exists('apache_request_headers')) {
       $headers = apache_request_headers();
       if (isset($headers['Accept-Language'])) {
         $acceptLanguage = $headers['Accept-Language'];
+      }
+    }
+  }
   if ($method != "GET" && $method != "POST") {
-ebf0428
+    drupal_set_message('cdm_api.module#cdm_http_request() : unsupported HTTP request method ', 'error');
-            6657531f
+            Andreas Kohlbecker
-b606c0d
+  if (_is_cdm_ws_uri($uri)) {
-db2866c
+    $header['Accept'] = 'application/json';
-            6657531f
+    $header['Accept-Language'] = $acceptLanguage;
     $header['Accept-Charset'] = 'UTF-8';
+  }
-ebf0428
+  if($method == "POST") {
     // content type is application/x-www-form-urlencoded, so the request body uses the same format as the query string
     $header['Content-Type'] = 'application/x-www-form-urlencoded';
+  }
-dd59bb5
+            Andreas Kohlbecker
   cdm_dd($uri);
-fe78f3c
+  return drupal_http_request($uri, array(
       'headers' => $header,
       'method' => $method,
-ebf0428
+      'data' => $data,
-fe78f3c
+      'timeout' => CDM_HTTP_REQUEST_TIMEOUT
+      )
    );
-            6657531f
+            Andreas Kohlbecker
 /**
-            37252893
+ * 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
-e1
+ * @param $excludes
  *     Allows defining a set of values to be excluded. This refers to the values
  *     in the field denoted by the $field_name parameter
+ *
-            6657531f
+ */
-e1
+function cdm_featureTree_elements_toString($root_node, $separator = ', ', $field_name = 'representation_L10n', $excludes = array()) {
-            6657531f
+  $out = '';
-            37252893
+  $pre_child_separator = $separator;
   $post_child_separator = '';
-            fae36a2a
+  foreach ($root_node->childNodes as $feature_node) {
-            6657531f
+    $out .= ($out ? $separator : '');
-e1
+    if(!in_array($feature_node->feature->$field_name, $excludes)) {
       $out .= $feature_node->feature->$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;
+        }
-            6657531f
+            Andreas Kohlbecker
+    }
+  }
   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 = '') {
   $options = array();
-            fae36a2a
+  foreach ($rootNode->childNodes as $featureNode) {
-            6657531f
+    $indent_prefix = '';
     if ($childIndent) {
       $indent_prefix = $childIndent . $node_char . " ";
+    }
     $options[$featureNode->feature->uuid] = $indent_prefix . $featureNode->feature->representation_L10n;
-            fae36a2a
+    if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
       // Foreach ($featureNode->childNodes as $childNode){
-            6657531f
+      $childList = _featureTree_nodes_as_feature_options($featureNode, $node_char, $childIndentStr, $childIndent . $childIndentStr);
       $options = array_merge_recursive($options, $childList);
       // }
+    }
+  }
   return $options;
+}
 /**
-            72294996
+ * Returns an array with all available FeatureTrees and the representations of the selected
  * FeatureTree as a detail view.
+ *
-            cdafd99f
+ * @param boolean $add_default_feature_free
-            72294996
+ * @return array
-            cdafd99f
+ *  associative array with following keys:
  *  -options: Returns an array with all available Feature Trees
  *  -treeRepresentations: Returns representations of the selected Feature Tree as a detail view
-            72294996
+            Andreas Kohlbecker
-            6657531f
+ */
-d24e
+function cdm_get_featureTrees_as_options($add_default_feature_free = FALSE) {
-f485c6d
+            Andreas Kohlbecker
   $options = array();
   $tree_representations = array();
-            6657531f
+  $feature_trees = array();
   // Set tree that contains all features.
-d24e
+  if ($add_default_feature_free) {
-f485c6d
+    $options[UUID_DEFAULT_FEATURETREE] = t('Default Featuretree (contains all features)');
     $feature_trees[] = cdm_ws_get(CDM_WS_FEATURETREE, UUID_DEFAULT_FEATURETREE);
+  }
   // Get feature trees from database.
-f2e1e0
+  $persited_trees = cdm_ws_fetch_all(CDM_WS_FEATURETREES);
-f485c6d
+  if (is_array($persited_trees)) {
     $feature_trees = array_merge($feature_trees, $persited_trees);
-            6657531f
+            Andreas Kohlbecker
-f485c6d
+  foreach ($feature_trees as $featureTree) {
-            6657531f
+            Andreas Kohlbecker
-c962983
+    if(!is_object($featureTree)){
       continue;
+    }
-f485c6d
+    // Do not add the DEFAULT_FEATURETREE again,
     if ($featureTree->uuid != UUID_DEFAULT_FEATURETREE) {
-            1717116c
+      $options[$featureTree->uuid] = $featureTree->titleCache;
-f485c6d
+            Andreas Kohlbecker
     // Render the hierarchic tree structure
-            fae36a2a
+    if (is_array( $featureTree->root->childNodes) && count( $featureTree->root->childNodes) > 0) {
-f485c6d
+            Andreas Kohlbecker
       // Render the hierarchic tree structure.
       $treeDetails = '<div class="featuretree_structure">'
         . 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,
       );
       $tree_representations[$featureTree->uuid] = drupal_render($form);
-            6657531f
+            Andreas Kohlbecker
-e506
+            Alexander Oppermann
-f485c6d
+  } // END loop over feature trees
-            6657531f
+            Andreas Kohlbecker
-f485c6d
+  // return $options;
   return array('options' => $options, 'treeRepresentations' => $tree_representations);
-            6657531f
+            Andreas Kohlbecker
 /**
-af3ce28
+ * Provides the list of available classifications in form of an options array.
-            de8b5b32
+            Andreas Kohlbecker
  * 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.
+ *
-b6ee11
+ * @param bool $add_none_option
-            1717116c
+ *   is true an addtional 'none' option will be added, optional parameter, defaults to FALSE
-b6ee11
+            Andreas Kohlbecker
-            de8b5b32
+ * @return array
  *   classifications in an array as options for a form element that allows multiple choices.
-            6657531f
+ */
-b6ee11
+function cdm_get_taxontrees_as_options($add_none_option = FALSE) {
-            a488aeb6
+  $taxonTrees = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
-            de8b5b32
+            Andreas Kohlbecker
   $default_classification_uuid = variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
   $default_classification_label = '';
   // add all classifications
-d24e
+  $taxonomic_tree_options = array();
-b6ee11
+  if ($add_none_option) {
     $taxonomic_tree_options['NONE'] = ' '; // one Space character at beginning to force on top;
+  }
-            6657531f
+  if ($taxonTrees) {
     foreach ($taxonTrees as $tree) {
-            de8b5b32
+      if (!$default_classification_uuid || $default_classification_uuid != $tree->uuid) {
         $taxonomic_tree_options[$tree->uuid] = $tree->titleCache;
       } else {
-b6ee11
+        $taxonomic_tree_options[$tree->uuid] = '  '; // two Space characters to force on top but below 'none' option , will be replaced below by titleCache
-            de8b5b32
+        $default_classification_label = $tree->titleCache;
+      }
-            6657531f
+            Andreas Kohlbecker
+  }
-b6ee11
+  // oder alphabetically the space
-            de8b5b32
+  asort($taxonomic_tree_options);
-b6ee11
+  // now set the labels
   //   for none
-            f19f47fa
+  if ($add_none_option) {
-ae3cfe3
+    $taxonomic_tree_options['NONE'] =t('--- ALL ---');
-b6ee11
+            Andreas Kohlbecker
   //   for default_classification
-b6
+  if (is_uuid($default_classification_uuid)) {
-            d88a1df7
+    $taxonomic_tree_options[$default_classification_uuid] =
       $default_classification_label ? $default_classification_label : '--- INVALID CHOICE ---'
-b1e5ae3
+      . (count($taxonTrees) > 1 ? ' [' . t('DEFAULT CLASSIFICATION') . ']': '');
-            de8b5b32
+            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();
+}
-            f26245c8
+            Andreas Kohlbecker
-            6657531f
+/**
  * 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.
-            f19f47fa
+ * The function is null save.
-            6657531f
+            Andreas Kohlbecker
  * @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) {
-            a6ae799b
+  return
     isset($object->class) && is_string($object->class) && strlen($object->class) > 2 && $object->class != 'TypedEntityReference'
     && is_string($object->uuid) && is_uuid($object->uuid);
-            6657531f
+            Andreas Kohlbecker
 /**
  * @todo Please document this function.
  * @see http://drupal.org/node/1354
  */
 function _cdm_api_secref_cache_add($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);
+    }
+  }
+}
-            a783afbc
+/**
  * 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, $term2->representation_L10n);
+}
-            c079337e
+function compare_terms_by_order_index($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 < $b) ? -1 : 1;
+}
-            a783afbc
+            Andreas Kohlbecker
-            6657531f
+/**
  * Make a 'deep copy' of an array.
+ *
  * Make a complete deep copy of an array replacing
  * references with deep copies until a certain depth is reached
  * ($maxdepth) whereupon references are copied as-is...
+ *
  * @see http://us3.php.net/manual/en/ref.array.php
+ *
  * @param array $array
-            cc3c9807
+ * @param array $copy passed by reference
-            6657531f
+ * @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;
+    }
+  }
+}
 /**
-            e2464cf8
+ * Adds java script to create and enable a toggler for the cdm webservice debug block content.
-            6657531f
+            Andreas Kohlbecker
  */
-            e2464cf8
+function _add_js_ws_debug() {
-ea8b301
+  $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,
-            e2464cf8
+    array(
       'type' => 'file',
       'weight' => JS_LIBRARY,
       'cache' => TRUE)
     );
-ea8b301
+  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $colorbox_js,
-            e2464cf8
+    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)
     );
-ebf0428
+  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/http-method-link.js',
     array(
     'type' => 'file',
     'weight' => JS_LIBRARY,
     'cache' => TRUE)
     );
-            6657531f
+            Andreas Kohlbecker
+}
 /**
  * @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');
+}
-            f26245c8
+            Andreas Kohlbecker
-dd59bb5
+/**
  * 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, $label = NULL) {
-            43251923
+  if(module_exists('devel') && variable_get('cdm_debug_mode', FALSE) && file_stream_wrapper_get_class('temporary') ){
-dd59bb5
+    return dd($data, $label);
+  }
+}

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