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

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cdm-dataportal/modules/cdm_dataportal/cdm_taxontree/cdm_taxontree.module @ 7ac8c744

       <?php
       /**
        * @file
        * Displays a taxon tree in a CDM Dataportal.
+       *
        * @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)
        */
       /**
        * Implements hook_menu()
        */
       function cdm_taxontree_menu() {
         $items = array();
         $items['cdm_taxontree/set'] = array(
           'page callback' => 'cdm_taxontree_set',
           'access arguments' => array('access cdm content'),
           'type' => MENU_CALLBACK,
         );
         $items['cdm_taxontree/filter'] = array(
           'page callback' => 'cdm_taxontree_view_filter',
           'access arguments' => array('access cdm content'),
           'type' => MENU_CALLBACK,
         );
         $items['cdm_taxontree/taxonomy/children'] = array(
           'page callback' => 'cdm_taxontree_taxonomy_children',
           'access arguments' => array('access cdm content'),
           'type' => MENU_CALLBACK,
         );
         return $items;
+      }
       /**
        * Implements hook_block_info().
        */
       function cdm_taxontree_block_info() {
         $block['cdm_tree'] = array(
               "info" => t('CDM taxon tree'),
               "cache" => DRUPAL_NO_CACHE
             );
         $block['cdm_tree_filters']['info'] = t('Active filters');
         $block['cdm_tree_drupal_taxonomy']['info'] = t('Drupal taxonomy tree');
         return $block;
+      }
       /**
        * Implements hook_block_view().
        */
       function cdm_taxontree_block_view($delta) {
         switch ($delta) {
           case 'cdm_tree':
             $block['subject'] = t('Classification');
             $taxonUuid_inFocus = _cdm_get_taxonuuid();
             $tree = cdm_taxontree_build_tree($taxonUuid_inFocus);
             // cdm_taxontree_magicbox_enable is not yet made available via the settings, so $magicbox_enable is always 0
             $magicbox_enable = variable_get('cdm_taxontree_magicbox_enable', 0);
             $block['content'] = '';
             $taxonomictree_selector_form = cdm_taxonomictree_selector();
             if (count($taxonomictree_selector_form['val']['#options']) > 1) {
               $block['content'] = drupal_render($taxonomictree_selector_form);
+            }
             $block['content'] .= theme('cdm_taxontree_block', array(
               'tree' => $tree,
               'delta' => $delta,
               'magicbox' => $magicbox_enable == 1,
               'show_filter_switch' => FALSE,
               // 'cdm_taxontree_node_concept_switch'
              ));
             cdm_taxontree_add_js('#block-cdm-taxontree-cdm-tree', $magicbox_enable);
             return $block;
           case 'cdm_tree_filters':
             $block['subject'] = t('Active filters');
             $block['content'] = cdm_taxontree_view_filter('list');
             return $block;
           case 'cdm_tree_drupal_taxonomy':
             // cdm tree for a drupal taxonomy
             $block['subject'] = t('Taxonomy tree');
             $term_inFocus = arg(0) == 'taxonomy' && arg(1) == 'term' ? arg(2) : 0;
             $tree = cdm_taxontree_build_tree($term_inFocus, TRUE, variable_get('cdm_taxontree_block_1_vid', 0));
             $block['content'] = theme('cdm_taxontree_block', array(
               'tree' => $tree,
               'delta' => $delta,
               'magicbox' => FALSE,
             ));
             cdm_taxontree_add_js('#block-cdm-taxontree-cdm-tree-drupal-taxonomy');
             return $block;
+        }
+      }
       /**
        * Implements hook_block_configure().
        */
       function cdm_taxontree_block_configure($delta) {
         $form = array();
           switch ($delta) {
             case 'cdm_tree':
               /* TODO The option to use the cdm_taxontree for drupal vocabulaties also has been removed, the below code should be
                  removed, see #7565
               $vocs = taxonomy_get_vocabularies();
               $options = array();
               foreach ($vocs as $voc) {
                 $options[$voc->vid] = $voc->name;
+              }
               $form['vid'] = array(
                 '#type' => 'select',
                 '#title' => t('Category'),
                 '#default_value' => variable_get('cdm_taxontree_block_1_vid', 0),
                 '#options' => $options,
               );
               */
+          }
         return $form;
+      }
       /**
        * Implements hook_block_save().
        */
       function cdm_taxontree_block_save($delta, $edit) {
         // TODO Rename block deltas (e.g. '1') to readable strings.
         if (TRUE) {
           switch ($delta) {
             case '1':
               variable_set('cdm_taxontree_block_1_vid', $edit['vid']);
               return;
+          }
+        }
+      }
       /**
        * Implements hook_help().
        */
       function cdm_taxontree_help($path, $arg) {
         switch ($path) {
           case 'admin/modules#description':
             return t('Defines a selection widget for massive taxonomy structures.');
+        }
+      }
       /**
        * Implements hook_field_info().
        */
       function cdm_taxontree_field_info() {
         return array(
           'cdm_taxontree' => array('label' => 'CDM Taxontree'),
         );
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_taxontree_field_formatter_info() {
         return array(
           'default' => array(
             'label' => t('Default'),
             'field types' => array('cdm_taxontree'),
           ),
           'link' => array(
             'label' => t('With link'),
             'field types' => array('cdm_taxontree'),
           ),
         );
+      }
       /**
        * Formatters to prepare the correct links for taxa.
        */
       function cdm_taxontree_field_formatter($field, $item, $formatter, $node) {
         switch ($formatter) {
           // TODO remove case, see #7565
           case 'link':
             $term = taxonomy_term_load($item['tid']);
             $taxa = db_query('SELECT name FROM {taxonomy_vocabulary} WHERE vid = :vid', array(':vid' => $term->vid))->fetchField();
             switch ($taxa) {
               case 'Taxonomy':
                 $link = 'interest_by_taxonomy/';
                 break;
               case 'Georegion':
                 $link = 'interest_by_georegion/';
                 break;
               default:
                 $link = 'taxonomy/term/';
+            }
             return l($term->name, $link . $term->tid);
           default:
             $name = db_query('SELECT name FROM {taxonomy_term_data} WHERE tid = :tid', array(':tid' => $item['tid']))->fetchField();
             return $name;
+        }
+      }
       /**
        * Transforms an unpredictably and irregularly nested set of tids (as returned
        * from a taxonomy form) into a linear array of tids.
        * borrow from taxonomy_browser.module
        */
       function _cdm_taxontree_get_all_children($tids = NULL, $include_children = FALSE) {
         static $tid_list = array();
         if (isset($tids) && is_array($tids)) {
           foreach ($tids as $key => $tid) {
             if (!empty($tid)) {
               if (is_array($tid)) {
                 foreach ($tid as $key2 => $tid2) {
                   if (!empty($tid2)) {
                     $tid_list[$tid2] = $tid2;
+                  }
+                }
+              }
               else {
                 $tid_list[$tid] = $tid;
+              }
             } /* end !empty */
           } /* end foreach */
+        }
         if ($include_children) {
           foreach ($tid_list as $tid) {
             _cdm_taxontree_get_children($tid_list, $tid);
+          }
+        }
         return $tid_list;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function _cdm_taxontree_get_children(&$tid_list, $tid) {
         $child_nodes = taxonomy_get_children($tid);
         if (!empty($child_nodes)) {
           foreach ($child_nodes as $child_tid => $child_term) {
             $tid_list[$tid] = $tid;
             _cdm_taxontree_get_children($tid_list, $child_tid);
+          }
+        }
         else {
           $tid_list[$tid] = $tid;
+        }
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_taxontree_set($key, $value) {
         if (is_string($key)) {
           $_SESSION['cdm']['taxontree'][$key] = $value;
+        }
         if ($_GET['destination']) {
           $destination = $_GET['destination'];
           unset($_GET['destination']);
           drupal_goto($destination);
+        }
+      }
       /**
        * Enter description here...
+       *
        * @param string $secUuid
+       *
        * @return unknown
        */
       function cdm_taxontree_secRefTitle_for($secUuid) {
         $reference = cdm_api_secref_cache_get($secUuid);
         if ($reference) {
           $cit = $reference->titleCache;
+        }
         else {
           $cit = '[no title for:' . $secUuid . ']';
+        }
         return $cit;
+      }
       /**
        * Queries the Drupal db for location of a certain block with the given $delta.
+       *
        * @param mixed $delta
        *   String or number identifying the block.
+       *
        * @return string
        *   The location: left, right or <empty>.
        */
       function _get_block_region($delta) {
         global $user, $theme_key;
         // Comment @WA you need to repace this with db_select if other modules
         // should be able to overrride this.
         $result = db_query("
           SELECT DISTINCT b.region
           FROM {block} b
           LEFT JOIN {block_role} r
           ON b.module = r.module
           AND b.delta = r.delta
           WHERE b.theme = :b.theme
           AND b.status = :b.status
           AND (r.rid IN (:r.rid) OR r.rid IS NULL)
           AND b.module = :b.module
           AND b.delta = :b.delta
         ", array(
           ':b.theme' => $theme_key,
           ':b.status' => 1,
           ':r.rid' => implode(',', array_keys($user->roles)),
           ':b.module' => 'cdm_taxontree',
           ':b.delta' => $delta,
         ))->fetch();
         return $result['region'];
+      }
       /**
        * Enter description here...
+       *
        * @return unknown
        */
       function _get_compact_mode() {
         if (!isset($_SESSION['cdm']['taxontree']['compact_mode'])) {
           $_SESSION['cdm']['taxontree']['compact_mode'] = 'expanded';
+        }
         return $_SESSION['cdm']['taxontree']['compact_mode'];
+      }
       /**
        * Converts Drupal taxonomy terms into preliminary cdm tree nodes.
+       *
        * An array of drupal taxonomy terms are converted into an
        * array of partially instantiated cdm tree nodes by adding the fields
        * relevant for tree node processing in cdm_taxontree.
+       *
        * term => cdm tree node
        * ------------------------------------
        * tid -> uuid
        * name -> titleCache
        * taggedName
        * secUuid
        * isAccepted
        * taxonomicChildrenCount
        * alternativeConceptRefs
+       *
        * @param array $terms
+       *
        * TODO remove method, see #7565
        */
       function cdm_taxontree_terms2treenodes(&$terms) {
         foreach ($terms as &$term) {
           $term->uuid = $term->tid;
           $term->titleCache = $term->name;
           $term->taxonomicChildrenCount = count(taxonomy_get_children($term->tid, $term->vid));
+        }
         return $terms;
+      }
       /**
        * Enter description here...
+       *
        * @param unknown_type $tid
        * @param unknown_type $vid
        * @param unknown_type $theme
        */
       function cdm_taxontree_taxonomy_children($tid, $vid, $theme) {
         $args = func_get_args();
         $tid = array_shift($args);
         $vid = array_shift($args);
         $theme = array_shift($args);
         $children = cdm_taxontree_get_children($tid, $vid);
         $children = cdm_taxontree_terms2treenodes($children);
         array_unshift($args, $theme, $children);
         print call_user_func_array('theme', $args);
+      }
       /**
        * Get the root level of the tree
        */
       function cdm_taxontree_get_root($vid = NULL) {
         if (is_numeric($vid)) {
           // vid, $parent = 0, $depth = -1, $max_depth = NULL) {
           $terms = taxonomy_get_tree($vid, 0, 1);
           return cdm_taxontree_terms2treenodes($terms);
+        }
         else {
           return cdm_ws_taxonomy_root_level();
+        }
+      }
       /**
        * @todo Enter description here...
+       *
        * @param unknown_type $uuid
        * @param unknown_type $vid
+       *
        * @return unknown
        */
       function cdm_taxontree_get_children($uuid, $vid = NULL) {
         if (is_numeric($vid)) {
           $terms = taxonomy_get_children($uuid, $vid);
           return cdm_taxontree_terms2treenodes($terms);
+        }
         else {
           // FIXME Replace $uuid by path of parent $uuids.
           return cdm_ws_taxonomy_root_level($uuid);
+        }
+      }
       /**
        * @todo Enter description here...
+       *
        * @param unknown_type $uuid
+       *
        * @return unknown
        */
       function cdm_taxontree_get_parents($uuid) {
         if (!is_uuid($uuid)) {
           // Using Drupal taxonomy.
           $terms = taxonomy_get_parents($uuid);
           array_push($terms, taxonomy_term_load($uuid));
           $terms = array_reverse($terms);
           return cdm_taxontree_terms2treenodes($terms);
+        }
         else {
           // Using cdm.
           $terms = cdm_ws_taxonomy_pathFromRoot($uuid);
           if (!$terms) {
             return;
+          }
           $terms = array_reverse($terms);
           return $terms;
+        }
+      }
       /**
        * Builds a tree of TaxonNode instances
+       *
        * When building the tree, the instances are extended by some fields:
        *  - $node->filter: values ( 'on', 'excluded', 'included' )
        *  - $node->expanded: values ( 'expanded', 'collapsed' )
+       *
        * @param string $taxonUuid
+       *
        * @return unknown
        */
       function cdm_taxontree_build_tree($taxonUuid = NULL, $hideOtherConcepts = TRUE, $vid = NULL) {
         // TODO Remove $hideOtherConcepts from method signature.
         if (is_null($vid)) {
           if ($taxonUuid) {
             $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $taxonUuid);
+          }
           $compact_tree = cdm_taxontree_filters_active() && _get_compact_mode() != 'expanded';
+        }
         // Valid compact_modes: 'expanded', 'compact', 'flattened'.
         // Get the root level.
         $root_tree = cdm_taxontree_get_root($vid);
         /*
         if(!$root_tree || !is_array($root_tree)){
           return array();
+        }
         */
         $root_tree = _cdm_resultset2nodelist($root_tree, cdm_taxontree_filters_active());
         if (cdm_taxontree_filters_active()) {
           // The paths up to active filters are inactive in the user interface and
           // thus cannot be browsed by expanding nodes.
           // Therefore we need to build up the branches for all nodes which are set
           // as filters. The branches are merged with the root.
           foreach (cdm_taxontree_filters_get() as $uuid => $filter) {
             $branch = cdm_taxontree_build_path($uuid, TRUE, ($compact_tree === FALSE ? TRUE : NULL));
             $root_tree = _cdm_taxontree_merge($root_tree, $branch);
+          }
+        }
         // Build the the branch for the focused node and merge it with the root.
         if ($taxonUuid) {
           $taxon_in_current_tree = taxon_in_current_classification($taxonUuid);
           if ($taxon_in_current_tree) {
             $branch = cdm_taxontree_build_path($taxonUuid, NULL, (cdm_taxontree_filters_active() ? NULL : TRUE));
             $root_tree = _cdm_taxontree_merge($root_tree, $branch);
+          }
+        }
          // Reorder siblings & populate expanded nodes with children and propagate
          // the filter attribute.
          $root_tree = cdm_taxontree_populate($root_tree, $compact_tree === FALSE);
         // Flatten tree.
         if ($compact_tree) {
           if (_get_compact_mode() == 'flattened') {
             $root_tree = cdm_taxontree_flatten($root_tree);
+          }
           elseif (_get_compact_mode() == 'compact') {
             foreach ($root_tree as $uuid => $node) {
               if ($node->filter == 'excluded' && !$node->children) {
                 unset($root_tree[$uuid]);
+              }
+            }
+          }
+        }
         return $root_tree;
+      }
       /**
        * Builds the specific branch path for $taxonUuid.
+       *
        * The branch path reaches from the parent root node of
        * $taxonUuid up to $taxonUuid.
+       *
        * @param string $taxonUuid
        *   The UUID of the taxon.
        * @param bool $is_filter_path
        *   Whether the upmost node of this path is mapped by an active filter.
        * @param bool $is_expanded
        *   Whether all nodes along the tree are expanded.
+       *
        * @return mixed
        *   A subtree.
        */
       function cdm_taxontree_build_path($taxonUuid, $is_filter_path = NULL, $is_expanded = NULL) {
         $branch_path = array();
         $parents = cdm_taxontree_get_parents($taxonUuid);
         if (!$parents) {
           if ($is_filter_path) {
             // \remove invalid filter.
             cdm_taxontree_filters_remove($taxonUuid);
+          }
           return FALSE;
+        }
         $parents = _cdm_resultset2nodelist($parents, NULL);
         $lastParent = NULL;
         foreach ($parents as $pnode) {
           if ($lastParent) {
             $pnode->children = array($lastParent->taxonUuid => $lastParent);
             if (!is_null($is_filter_path)) {
               $pnode->filter = ($is_filter_path ? 'excludes' : 'included');
+            }
             if (!is_null($is_expanded)) {
               $pnode->expanded = ($is_expanded ? 'expanded' : 'collapsed');
+            }
+          }
           else {
             // The uppermost node of branch.
             if (!is_null($is_filter_path)) {
               $pnode->filter = ($is_filter_path ? 'on' : 'includes');
+            }
             $pnode->expanded = ($pnode->taxonomicChildrenCount ? 'expanded' : 'collapsed');
+          }
           $lastParent = $pnode;
+        }
         $branch_path[$pnode->taxonUuid] = $pnode;
         return $branch_path;
+      }
       /**
        * Order a tree and populate expanded nodes.
+       *
        * Performs two steps on each level of the tree:
        *  1. Reorder siblings except root (which is expected to be ordered already)
        *     alphabetically.
        *  2. Populate children of expanded nodes  & propagate the filter attribute
+       *
        * @param array $tree
        * @param unknown $expand_excluded
        * @param unknown $filter_default
+       *
        * @return unknown
        */
       function cdm_taxontree_populate($tree, $expand_excluded, $filter_default = NULL) {
         if (!is_array($tree)) {
           return FALSE;
+        }
         foreach (array_keys($tree) as $uuid) {
           if (!isset($tree[$uuid]->filter)) {
             $tree[$uuid]->filter = $filter_default;
+          }
           if (isset($tree[$uuid]->expanded) && $tree[$uuid]->expanded == 'expanded' && ($expand_excluded || $tree[$uuid]->filter != 'excluded')) {
             if (isset($tree[$uuid]->vid)) {
               //  TODO remove case, see #7565
               $children = cdm_taxontree_get_children($uuid, $tree[$uuid]->vid);
+            }
             else {
               $children = cdm_taxontree_get_children($uuid);
+            }
             $children = _cdm_resultset2nodelist($children, ($tree[$uuid]->filter == 'excludes'));
             // Store the children of the node for later processing.
             if (isset($tree[$uuid]->children) && is_array($tree[$uuid]->children)) {
               $pnode_children = $tree[$uuid]->children;
+            }
             else {
               $pnode_children = FALSE;
+            }
             // Replace the children by the newly retrieved child nodes.
             $tree[$uuid]->children = $children;
             if ($pnode_children) {
               // Recurse into the childtree which was stored before.
               $pnode_children = cdm_taxontree_populate($pnode_children, $expand_excluded, $tree[$uuid]->filter);
               // Recombine.
               foreach ($pnode_children as $childUuid => $cnode) {
                 $tree[$uuid]->children[$childUuid] = $cnode;
+              }
+            }
+          }
           else {
             // Reorder nodes which are not expanded, expanded nodes are reordered
             // implicitly above.
             if (isset($tree[$uuid]->children) && count($tree[$uuid]->children) > 1) {
               // Copy the children into an array which can be sorted by its keys.
               $ordered = array();
               foreach ($tree[$uuid]->children as $cnode) {
                 // Concatenate full name and uid.
                 $reordered[str_pad($cnode->titleCache, 255, '-') . $cnode->taxonUuid] = $cnode;
+              }
               // Sort.
               ksort($reordered);
               // Move the children back into the parent node.
               $tree[$uuid]->children = array();
               foreach ($reordered as $cnode) {
                 $tree[$uuid]->children[$cnode->taxonUuid] = $cnode;
+              }
+            }
             if (!isset($tree[$uuid]->children)) {
               $tree[$uuid]->children = FALSE;
+            }
             $tree[$uuid]->children = cdm_taxontree_populate($tree[$uuid]->children, $expand_excluded, $tree[$uuid]->filter);
+          }
+        }
         return $tree;
+      }
       /**
        * Enter description here...
+       *
        * @param array $tree
        *   Tree to flatten.
        * @param array $new_root
+       *
        * @return unknown
        */
       function cdm_taxontree_flatten($tree, &$new_root = NULL) {
         if (empty($new_root)) {
           $new_root = array();
+        }
         foreach ($tree as $node) {
           if ($node->filter == 'on') {
             $new_root[$node->taxonUuid] = $node;
+          }
           elseif (is_array($node->children)) {
             cdm_taxontree_flatten($node->children, $new_root);
+          }
+        }
         return $new_root;
+      }
       /**
        * Merge a branch into a tree.
+       *
        * Merge a branch into a tree whereas the tree dominated the branch except
        * nodes having property filter set to "on". These always dominate
        * nevertheless if they are in tree or branch.
+       *
        * @param array $tree
        *   The dominant tree.
        * @param array $branch
        *   The tree to be merged in.
+       *
        * @return array
        *   The merged $tree.
        */
       function _cdm_taxontree_merge($tree, $branch) {
         if (!$branch || !is_array($branch)) {
           return $tree;
+        }
         if (!is_array($tree)) {
           return;
+        }
         foreach (array_keys($tree) as $uuid) {
           // Check if node exists in $branch.
           if (!empty($branch[$uuid])) {
             // Preserve filter property.
             if (isset($tree[$uuid]->filter) && !(isset($branch[$uuid]->filter) && $branch[$uuid]->filter == 'on')) {
               $branch[$uuid]->filter = $tree[$uuid]->filter;
+            }
             elseif (isset($branch[$uuid]->filter)) {
               $tree[$uuid]->filter = $branch[$uuid]->filter;
+            }
             // Preserve expanded property.
             if (isset($tree[$uuid]->expanded)) {
               $branch[$uuid]->expanded = $tree[$uuid]->expanded;
+            }
             elseif (isset($branch[$uuid]->expanded)) {
               $tree[$uuid]->expanded = $branch[$uuid]->expanded;
+            }
             // $Uuid exists check if the node in tree1 or tree2 contains children.
             if (isset($branch[$uuid]->children) && is_array($branch[$uuid]->children) && isset($tree[$uuid]->children) && is_array($tree[$uuid]->children)) {
               // Merge recursive.
               $tree[$uuid]->children = _cdm_taxontree_merge($tree[$uuid]->children, $branch[$uuid]->children);
+            }
             elseif (isset($branch[$uuid]->children) && is_array($branch[$uuid]->children)) {
               $tree[$uuid] = $branch[$uuid];
+            }
             unset($branch[$uuid]);
+          }
+        }
         // Append remaining items from branch to tree.
         foreach (array_keys($branch) as $uuid) {
           $tree[$uuid] = $branch[$uuid];
+        }
         return $tree;
+      }
       /**
        * Alter a resultset into an array of TreeNode instances with taxonUuid as keys.
+       *
        * Replaces the keys of an array of TreeNode instances
        * by the $treenode->taxonUuid of the single array elements and sets
        * additional fields.
+       *
        * @param array $resultset
        *   Array of TreeNode instances as +returned by the cdm web service.
        * @param mixed $excluded
        *   Whether the $resultset is included by a active filter. Is ignored if NULL.
        * @param mixed $expanded
        *   Whether the children of the nodes in the $resultset are expanded or not.
        *   Is ignored if NULL.
+       *
        * @return array
        *   A tree of TreeNode instances with altered keys.
        */
       function _cdm_resultset2nodelist($resultset, $excluded = NULL, $expanded = NULL) {
         if (!is_array($resultset)) {
           return FALSE;
+        }
         $tree = array();
         foreach ($resultset as $treeNode) {
           if (!is_null($excluded)) {
             $treeNode->filter = ($excluded ? 'excluded' : 'included');
+          }
           if (!is_null($expanded)) {
             $treeNode->expanded = ($expanded ? 'expanded' : 'collapsed');
+          }
           $tree[$treeNode->taxonUuid] = $treeNode;
+        }
         return $tree;
+      }
       /**
        * Adds all java script files and also initializes the cdm_taxontree java script behaviours
+       *
        * @param string $parent_element_selector
        *    jQuery selector of a parent element of the cdm_taxontree, This is usually a drupal block id
        *    selector: #block-cdm-taxontree-cdm-tree or #block-cdm-taxontree-cdm-tree-drupal-taxonomy
+       *
        * @param bool $magicbox_enable
        *    If set to TRUE the cdm_taxontree will get the magic box behavoir, which means that it
        *    will extend on mouse over events in order to
        *    show the entrys without truncation through cropping
        */
       function cdm_taxontree_add_js($parent_element_selector, $magicbox_enable = FALSE) {
         $path_cdm_taxontree = drupal_get_path('module', 'cdm_taxontree');
         $path_preferred_module = drupal_get_path('module', 'cdm_dataportal') ? drupal_get_path('module', 'cdm_dataportal') : $path_cdm_taxontree;
         drupal_add_css($path_cdm_taxontree . '/cdm_taxontree.css');
         drupal_add_js($path_cdm_taxontree . '/js/cdm_taxontree.js');
         drupal_add_js('
             jQuery(document).ready(function()
+            {
               jQuery(\'' . $parent_element_selector . '\').cdm_taxontree();
             });
             ', array('type' => 'inline'));
+      }
       // ------------------------ THEME --------------------------- //
       /**
        *  Returns HTML for a Taxontree block.
+       *
        * @param array $variables
        *   An associative array containing:
        *   - tree: The tree of TreeNode to be displayed.
        *   - magicbox: Boolean. If TRUE, the tree will be embedded into a set of
        *       div tags which allow the tree to expand and overlap other content.
        *       This is useful if the node titles are quite long or if the tree is
        *       nested deeply. If $magicbox ist set to the delta of the containing
        *       block the direction into which the box expands is dependent on the
        *       region in which the block is located. See also $left_expand_region
        *       in this function!
        *   - show_filter_switch: The tree can offer buttons to add a node to a set of
        *       filters which can then be applied to the tree to limit the visible
        *       subtrees and thus to compact the tree. Three different compact modes
        *       are available.
        *   - tree_node_callback: Name of a callback method which will be called
        *       for each node in theme_cdm_taxontree_node(). The output of this
        *       callback, which takes the $node object as single arument, is appended
        *       to the end of the rendered node.
+       *
        * @ingroup themeable
        */
       function theme_cdm_taxontree_block($variables) {
         $tree = $variables['tree'];
         $delta = $variables['delta'];
         $magicbox = $variables['magicbox'];
         $show_filter_switch = $variables['show_filter_switch'];
         $tree_node_callback = $variables['tree_node_callback'];
         // THEMERS: change the line below according to the
         // specific regions of your theme.
         $left_expand_region = 'right';
         $out = '';
         if (cdm_taxontree_filters_active()) {
           $out .= theme('cdm_taxontree_controller', array('compact_mode' => _get_compact_mode()));
+        }
         $region = null;
         if (!empty($magicbox)) {
           if (is_numeric($magicbox) || is_string($magicbox)) {
             $region = _get_block_region($magicbox);
+          }
           // The magicbox expands to the right by default,
           // if the class 'expand-left' to  the cdm_taxontree_scroller_x the box will
           // expand to the left.
           $expand_direction = ($region == 'right' ? 'expand-left' : '');
           $out .= '<div class="cdm_taxontree_scroller_x ' . $expand_direction . '"><div class="cdm_taxontree_container"><div class="cdm_taxontree_scroller_y">';
+        }
         else {
           $out .= '<div class="cdm_taxontree_scroller_xy">';
+        }
         $out .= theme('cdm_taxontree', array(
           'tree' => $tree,
           'filterIncludes' => !cdm_taxontree_filters_active(),
           'show_filter_switch' => $show_filter_switch,
           'tree_node_callback' => $tree_node_callback,
           ));
         if ($magicbox) {
           $out .= '</div></div></div>';
+        }
         else {
           $out .= '</div>';
+        }
         return $out;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function theme_cdm_taxontree_controller($variables) {
         $compact_mode = $variables['compact_mode'];
         static $modes = array('expanded', 'compact', 'flattened');
         $out = '<div class="settings">';
         foreach ($modes as $mode) {
           if ($compact_mode == $mode) {
             $out .= t('@mode', array('@mode' => $mode));
+          }
           else {
             $out .= l(t('@mode', array('@mode' => $mode)), 'cdm_taxontree/set/compact_mode/' . $mode, array('query' => drupal_get_destination()));
+          }
           $out .= ' ';
+        }
         return $out . '</div>';
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function theme_cdm_taxontree($variables) {
         $tree = $variables['tree'];
         $filterIncludes = $variables['filterIncludes'];
         $show_filter_switch = $variables['show_filter_switch'];
         $tree_node_callback = $variables['tree_node_callback'];
         $element_name = $variables['element_name'];
         if(isset($tree->records)){
           // unwrap from pager object
           $tree = $tree->records;
+        }
         if (!is_array($tree)) {
           return FALSE;
+        }
         if (is_null($filterIncludes)) {
           // Set $filterIncludes TRUE if no filters are set.
           $filterIncludes = !cdm_taxontree_filters_active();
+        }
         // Append element name to get multiple taxontrees on one page working.
         $out = '<ul class="taxon-nodes ' . (($element_name) ? ' ' . $element_name : '') . '">';
         foreach ($tree as $node) {
           if($node == null){
             continue;
+          }
           $out .= theme('cdm_taxontree_node', array(
             'node' => $node,
             'filterIncludes' => $filterIncludes,
             'show_filter_switch' => $show_filter_switch,
             'tree_node_callback' => $tree_node_callback
             ));
+        }
         $out .= '</ul>';
         return $out;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function theme_cdm_taxontree_node($variables) {
         $node = $variables['node'];
         $filterIncludes = $variables['filterIncludes'];
         $show_filter_switch = $variables['show_filter_switch'];
         $tree_node_callback = $variables['tree_node_callback'];
         $is_leaf = !$node->taxonomicChildrenCount || $node->taxonomicChildrenCount == 0;
         $is_expanded = isset($node->expanded) && $node->expanded = 'expanded';
         $focused_taxon_uuid = get_current_taxon_uuid();
         if (isset($node->tid)) {
           $node_name = $node->name;
           $path = "taxonomy/term/" . $node->tid;
           // disable filterswitch
           $show_filter_switch = FALSE;
+        }
         elseif (module_exists('cdm_dataportal')) {
           $node_name = cdm_dataportal_shortname_of($node);
           $path = path_to_taxon($node->taxonUuid);
+        }
         else {
           $node_name = "module cdm_dataportal missing";
           $path = "";
+        }
         if ($filterIncludes) {
           $name = l($node_name, $path);
           // No names for terms in filter widget; as discussed with A. Müller.
           // $name = '';
           $filter_class = 'filter_included';
+        }
         else {
           if ($node->filter == 'on') {
             $name = l($node_name, $path);
             $filter_class = 'filter_on';
+          }
           else {
             $name = $node_name;
             $filter_class = 'filter_excluded';
+          }
+        }
         $nextLevelIncluded = isset($node->filter) && $node->filter == 'on' || $filterIncludes;
         $ahah_url = FALSE;
         if (!$is_leaf && !$is_expanded && $filter_class != 'filter_excluded') {
           if (isset($node->tid)) {
             //  TODO remove case, see #7565
             $ahah_url = url('cdm_taxontree/taxonomy/children/' . $node->tid . '/' . $node->vid . '/cdm_taxontree/' . ($nextLevelIncluded ? 1 : 0) . '/' . ($show_filter_switch ? 1 : 0) . '/' . $tree_node_callback);
+          }
           elseif (module_exists('cdm_dataportal')) {
             $ws_url = cdm_compose_taxonomy_root_level_path($node->taxonUuid);
             $ahah_url = url('cdm_api/proxy/' . urlencode($ws_url) . '/cdm_taxontree/' . ($nextLevelIncluded ? 1 : 0) . '/' . ($show_filter_switch ? 1 : 0) . '/' . $tree_node_callback);
+          }
+        }
         // List item.
         $out = '<li class="'
           . ($node->taxonUuid == $focused_taxon_uuid ? 'focused ' : '')
           . ($is_leaf ? 'leaf ' : ($is_expanded ? 'expanded ' : 'collapsed '))
           . $filter_class . '"'
           . ($ahah_url ? ' data-cdm-ahah-url="' . $ahah_url . '"' : '')
           . '>';
         if ($show_filter_switch) {
           // Filter icon.
           $out .= theme('cdm_taxontree_node_filter_switch', array('node' => $node, 'filter_class' => $filter_class));
+        }
         // Taxon name.
         $out .= '<span class="' . html_class_attribute_ref($node) . '">' . $name . '</span>';
         // Concept_switch or other theme callbacks.
         if ($tree_node_callback) {
            $out .= theme($tree_node_callback, array('node' => $node));
+        }
         if (isset($node->children) && is_array($node->children)) {
           $out .= theme('cdm_taxontree', array(
             'tree' => $node->children,
             'filterIncludes' => $nextLevelIncluded,
             'show_filter_switch' => $show_filter_switch,
             'tree_node_callback' => $tree_node_callback,
           ));
+        }
         $out .= '</li>';
         return $out;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function theme_cdm_taxontree_node_filter_switch($variables) {
         $node = $variables['node'];
         $filter_class = $variables['filter_class'];
         if (!module_exists('cdm_dataportal')) {
           return '';
+        }
         $out = '';
         switch ($filter_class) {
           case 'filter_included':
             $filter_icon = 'visible_implicit_small.gif';
             break;
           case 'filter_excluded':
             $filter_icon = 'invisible_small.gif';
             break;
           case 'filter_on':
             $filter_icon = 'visible_small.gif';
             break;
+        }
         $filter_op = $node->filter == 'on' ? 'remove' : 'add';
         $out .= '&nbsp;'
           . l('<img src="' . base_path() . drupal_get_path('module', 'cdm_taxontree') . '/' . $filter_icon . '" alt="[f]" />',
               'cdm_taxontree/filter/' . $filter_op . '/' . $node->taxonUuid, array(
                 'attributes' => array('class' => 'filter_' . $filter_op),
                 'query' => 'destination=' . path_to_taxon($node->taxonUuid),
                 'fragment' => NULL,
                 'absolute' => TRUE,
                 'html' => TRUE,
               ));
         return $out;
+      }
       /**
        * Returns HTML for a Taxontree-node concept switch.
+       *
        * @param array $variables
        *   An associative array containing:
        *   - node: The node object.
+       *
        * @ingroup themeable
        */
       function theme_cdm_taxontree_node_concept_switch($variables) {
         $node = $variables['node'];
         $out = '';
         if (isset($node->alternativeConceptRefs[0])) {
           $out = l(
             '<img src="' . base_path() . drupal_get_path('module', 'cdm_taxontree') . '/concept_switch.gif" alt="[-&gt;]" />',
             'cdm_dataportal/taxon/alternative/' . $node->taxonUuid, array(
               'attributes' => array('rel' => 'cdm_dataportal/taxon/alternative/' . $node->taxonUuid, 'class' => 'concept_switch'),
               'query' => NULL,
               'fragment' => NULL,
               'absolute' => TRUE,
               'html' => TRUE,
             ));
+        }
         return $out;
+      }
       /**
        * @todo Please document this function.
        * @see http://drupal.org/node/1354
        */
       function cdm_taxontree_theme() {
         return array(
           'cdm_taxontree' => array('variables' => array(
             'tree' => NULL,
             'filterIncludes' => NULL,
             'show_filter_switch' => FALSE,
             'tree_node_callback' => FALSE,
             'element_name' => FALSE
             )),
           'cdm_taxontree_block' => array('variables' => array(
             'tree' => NULL,
             'delta' => NULL,
             'magicbox' => FALSE,
             'show_filter_switch' => FALSE,
             'tree_node_callback' => FALSE,
             )),
           'cdm_taxontree_controller' => array('variables' => array('compact_mode' => NULL)),
           'cdm_taxontree_node' => array('variables' => array(
             'node' => NULL,
             'filterIncludes' => NULL,
             'show_filter_switch' => FALSE,
             'tree_node_callback' => FALSE
             )),
           'cdm_taxontree_node_concept_switch' => array('variables' => array('node' => NULL)),
           'cdm_taxontree_node_filter_switch' => array('variables' => array('node' => NULL, 'filter_class' => NULL)),
         );
+      }
       // ----------------- FILTERS -------------------------- //
       /**
        * Filters on children, overrides already set parent filters and vice versa.
+       *
        * @param string $op
        *   [add | remove] a taxon from the filtered taxa.
        *   TODO at the moment there is also a 'list' operation that displays all
        *   set filters and provides the ability to delete them.
        *   This option depends on function is defined in cdm_dataportal.
        *   Problem is, that the dependency is the other way round.
        * @param string $taxonUuid
+       *
        * @return string
        */
       function cdm_taxontree_view_filter($op, $taxonUuid = NULL) {
         if (!isset($_SESSION['cdm']['filters'])) {
           $_SESSION['cdm']['filters'] = array();
+        }
         if ($taxonUuid || $op == 'list') {
           switch ($op) {
             case 'add':
               cdm_taxontree_filters_add($taxonUuid);
               break;
             case 'remove':
               cdm_taxontree_filters_remove($taxonUuid);
               break;
             case 'list':
               // TODO put in cdm_dataportal_theme to decouple both modules by this!!!
               $out = '<ul>';
               foreach ($_SESSION['cdm']['filters'] as $uuid => $node) {
                 $out .= '<li>' . cdm_dataportal_shortname_of($node) . ' ' . l(t('[x]'), 'cdm_dataportal/filter/remove/' . $uuid, array('query' => drupal_get_destination())) . '</li>';
+              }
               $out .= '</ul>';
               return $out;
+          }
+        }
         if ($_GET['destination']) {
           $destination = $_GET['destination'];
           unset($_GET['destination']);
           drupal_goto($destination);
+        }
+      }
       /**
        * Checks if there are active filters.
+       *
        * Filters are set in cdm_dataportal_view_filter().
        * functions using filters should remove invalid filters.
+       *
        * @return bool
        *   TRUE if any filter is active.
        */
       function cdm_taxontree_filters_active() {
         return isset($_SESSION['cdm']['filters']) && count($_SESSION['cdm']['filters']) > 0;
+      }
       /**
        * Filters are set in cdm_dataportal_view_filter().
+       *
        * @return mixed
        *   A reference on the filters array stored in the SESSION.
        */
       function &cdm_taxontree_filters_get() {
         if (!isset($_SESSION['cdm']['filters'])) {
           $_SESSION['cdm']['filters'] = array();
+        }
         return $_SESSION['cdm']['filters'];
+      }
       /**
        * Adds a taxon to the filtered taxa array
+       *
        * @param UUID $taxonUuid
        */
       function cdm_taxontree_filters_add($taxonUuid) {
         $parents = cdm_ws_taxonomy_pathFromRoot($taxonUuid);
         $parents = array_reverse($parents);
         // Pop off last element since this is the TreeNode object for $taxonUuid!
         $this_node = array_pop($parents);
         // Will contain the uuid of the parent nodes excluding the
         // $taxonUuid node itself.
         $parent_uuids = array();
         // Children override parents rule: remove all parent filters.
         foreach ($parents as $pnode) {
           unset($_SESSION['cdm']['filters'][$pnode->taxonUuid]);
           $parent_uuids[] = $pnode->taxonUuid;
+        }
         // Search for potential children of this $taxonUuid.
         foreach ($_SESSION['cdm']['filters'] as $uuid => $node) {
           if (in_array($taxonUuid, $node->parentUuids)) {
             unset($_SESSION['cdm']['filters'][$node->taxonUuid]);
+          }
+        }
         // Finally add this $taxonUuid as new filter.
         $this_node->parentUuids = $parent_uuids;
         $_SESSION['cdm']['filters'][$taxonUuid] = $this_node;
+      }
       /**
        * Unsets a taxon from the filtered taxa array.
+       *
        * @param string $taxonUuid
        */
       function cdm_taxontree_filters_remove($taxonUuid) {
         unset($_SESSION['cdm']['filters'][$taxonUuid]);
+      }
       // ------------------------ PRIVATE --------------------------- //
       /**
        * Analyses the current Drupal path to get the taxon UUID.
+       *
        * If a certain taxon was requested in the request, returns the UUID
        * of that taxon. Returns a stored UUID if no taxon was requested.
        * TODO where does the stored UUID come from?
+       *
        * @return string
        *   The taxon id found, or FALSE.
+       *
        * @deprecated use get_current_taxon_uuid() instead
        */
       function _cdm_get_taxonuuid() {
         if (arg(0) == "cdm_dataportal" && arg(1) == "taxon" && arg(2) !== 0) {
           $taxon_uuid = arg(2);
+        }
         else {
           $taxon_uuid = FALSE;
           // TODO is this SESSION variable ['cdm_dataportal']['tree']['taxon_uuid'] use at all?
           if (isset($_SESSION['cdm_dataportal']['tree']['taxon_uuid'])) {
             $taxon_uuid = $_SESSION['cdm_dataportal']['tree']['taxon_uuid'];
+          }
+        }
         return $taxon_uuid;
+      }

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