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

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cdm-dataportal/modules/cdm_dataportal/cdm_taxontree/cdm_taxontree.module @ 8a4d078d

-            6657531f
+<?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)
  */
-a4d078d
+const CDM_TAXONTREE_LINK_TYPE = 'cdm_taxontree_link_type';
-            6657531f
+/**
-            f555e0ec
+ * Implements hook_menu()
  */
-            6657531f
+function cdm_taxontree_menu() {
   $items = array();
   $items['cdm_taxontree/set'] = array(
     'page callback' => 'cdm_taxontree_set',
-            c6fe437b
+    'access arguments' => array('access cdm content'),
-            6657531f
+    'type' => MENU_CALLBACK,
   );
   $items['cdm_taxontree/filter'] = array(
     'page callback' => 'cdm_taxontree_view_filter',
-            c6fe437b
+    'access arguments' => array('access cdm content'),
-            6657531f
+    'type' => MENU_CALLBACK,
   );
   $items['cdm_taxontree/taxonomy/children'] = array(
     'page callback' => 'cdm_taxontree_taxonomy_children',
-            c6fe437b
+    'access arguments' => array('access cdm content'),
-            6657531f
+    'type' => MENU_CALLBACK,
   );
   return $items;
+}
 /**
  * Implements hook_block_info().
  */
 function cdm_taxontree_block_info() {
-            fc13aa30
+  $block['cdm_tree'] = array(
         "info" => t('CDM taxon tree'),
         "cache" => DRUPAL_NO_CACHE
       );
-            6657531f
+            Andreas Kohlbecker
-            0375638f
+  $block['cdm_tree_filters']['info'] = t('Active filters');
   $block['cdm_tree_drupal_taxonomy']['info'] = t('Drupal taxonomy tree');
-            6657531f
+  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);
-            0375638f
+            Andreas Kohlbecker
       // cdm_taxontree_magicbox_enable is not yet made available via the settings, so $magicbox_enable is always 0
-            6657531f
+      $magicbox_enable = variable_get('cdm_taxontree_magicbox_enable', 0);
       $block['content'] = '';
-            d7588d36
+      $taxonomictree_selector_form = cdm_taxonomictree_selector();
       if (count($taxonomictree_selector_form['val']['#options']) > 1) {
         $block['content'] = drupal_render($taxonomictree_selector_form);
-            6657531f
+            Andreas Kohlbecker
       $block['content'] .= theme('cdm_taxontree_block', array(
         'tree' => $tree,
         'delta' => $delta,
-            0375638f
+        'magicbox' => $magicbox_enable == 1,
-            6657531f
+        'show_filter_switch' => FALSE,
         // 'cdm_taxontree_node_concept_switch'
        ));
-            0375638f
+      cdm_taxontree_add_js('#block-cdm-taxontree-cdm-tree', $magicbox_enable);
-            6657531f
+      return $block;
-            0375638f
+    case 'cdm_tree_filters':
-            6657531f
+      $block['subject'] = t('Active filters');
       $block['content'] = cdm_taxontree_view_filter('list');
       return $block;
-            0375638f
+    case 'cdm_tree_drupal_taxonomy':
       // cdm tree for a drupal taxonomy
-            6657531f
+      $block['subject'] = t('Taxonomy tree');
       $term_inFocus = arg(0) == 'taxonomy' && arg(1) == 'term' ? arg(2) : 0;
-a4d078d
+      $tree = cdm_taxontree_build_tree($term_inFocus, TRUE);
-            6657531f
+      $block['content'] = theme('cdm_taxontree_block', array(
         'tree' => $tree,
         'delta' => $delta,
         'magicbox' => FALSE,
       ));
-            0375638f
+      cdm_taxontree_add_js('#block-cdm-taxontree-cdm-tree-drupal-taxonomy');
-            6657531f
+      return $block;
+  }
+}
 /**
  * Implements hook_block_configure().
  */
 function cdm_taxontree_block_configure($delta) {
-ac8c744
+            Andreas Kohlbecker
   $form = array();
-            6657531f
+    switch ($delta) {
-ac8c744
+      case 'cdm_tree':
-a4d078d
+            Andreas Kohlbecker
         $form[CDM_TAXONTREE_LINK_TYPE] = array(
           '#type' => 'radios',
           '#title' => t('Link to '),
           '#default_value' => variable_get(CDM_TAXONTREE_LINK_TYPE,  'taxon_page'),
           '#options' => array('taxon_page' => 'Taxon pages', 'search_registrations' =>'Registration search page' ),
         );
-ac8c744
+        /* TODO The option to use the cdm_taxontree for drupal vocabulaties also has been removed, the below code should be
            removed, see #7565
-            6657531f
+        $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,
         );
-ac8c744
+        */
-            6657531f
+            Andreas Kohlbecker
-ac8c744
+  return $form;
-            6657531f
+            Andreas Kohlbecker
 /**
  * Implements hook_block_save().
  */
 function cdm_taxontree_block_save($delta, $edit) {
-a4d078d
+            Andreas Kohlbecker
-            6657531f
+    switch ($delta) {
-a4d078d
+      case 'cdm_tree':
         variable_set(CDM_TAXONTREE_LINK_TYPE,  $edit[CDM_TAXONTREE_LINK_TYPE]);
         /* TODO The option to use the cdm_taxontree for drupal vocabulaties also has been removed, the below code should be
            removed, see #7565
-            6657531f
+        variable_set('cdm_taxontree_block_1_vid', $edit['vid']);
         return;
-a4d078d
+        */
-            6657531f
+            Andreas Kohlbecker
-a4d078d
+            Andreas Kohlbecker
-            6657531f
+            Andreas Kohlbecker
 /**
  * Implements hook_help().
  */
 function cdm_taxontree_help($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) {
-ac8c744
+    // TODO remove case, see #7565
-            6657531f
+    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)
-c55
+    AND b.module = :b.module
-            6657531f
+    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 $terms
-ac8c744
+            Andreas Kohlbecker
  * TODO remove method, see #7565
-            6657531f
+ */
 function cdm_taxontree_terms2treenodes(&$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 $theme
-            a3228c59
+            Andreas Kohlbecker
  * * TODO remove method, see #7565
-            6657531f
+ */
 function cdm_taxontree_taxonomy_children($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', $args);
+}
 /**
-c55
+ * Get the root level of the tree
-            6657531f
+ */
 function cdm_taxontree_get_root($vid = NULL) {
   if (is_numeric($vid)) {
-            a3228c59
+    //  TODO remove case, see #7565
-            6657531f
+    // vid, $parent = 0, $depth = -1, $max_depth = NULL) {
     $terms = taxonomy_get_tree($vid, 0, 1);
     return cdm_taxontree_terms2treenodes($terms);
+  }
   else {
-c55
+    return cdm_ws_taxonomy_root_level();
-            6657531f
+            Andreas Kohlbecker
+}
 /**
  * @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)) {
-            a3228c59
+    //  TODO remove case, see #7565
-            6657531f
+    $terms = taxonomy_get_children($uuid, $vid);
     return cdm_taxontree_terms2treenodes($terms);
+  }
   else {
     // FIXME Replace $uuid by path of parent $uuids.
-c55
+    return cdm_ws_taxonomy_root_level($uuid);
-            6657531f
+            Andreas Kohlbecker
+}
 /**
  * @todo Enter description here...
+ *
  * @param unknown_type $uuid
+ *
  * @return unknown
  */
 function cdm_taxontree_get_parents($uuid) {
   if (!is_uuid($uuid)) {
     // Using Drupal taxonomy.
-            a3228c59
+    //  TODO remove case, see #7565
-            6657531f
+    $terms = taxonomy_get_parents($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)) {
-            a3228c59
+    //  TODO remove case, see #7565
-            6657531f
+    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.
-            a3228c59
+            Andreas Kohlbecker
   $root_tree = cdm_taxontree_get_root($vid); //  TODO remove $vid, see #7565 ?
-            6657531f
+  /*
   if(!$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) {
-cd0b
+    $taxon_in_current_tree = taxon_in_current_classification($taxonUuid);
-            6657531f
+    if ($taxon_in_current_tree) {
-af3ce28
+      $branch = cdm_taxontree_build_path($taxonUuid, NULL, (cdm_taxontree_filters_active() ? NULL : TRUE));
-            6657531f
+      $root_tree = _cdm_taxontree_merge($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 $is_expanded
  *   Whether all nodes along the tree are expanded.
+ *
  * @return mixed
  *   A subtree.
  */
-af3ce28
+function cdm_taxontree_build_path($taxonUuid, $is_filter_path = NULL, $is_expanded = NULL) {
-            6657531f
+            Andreas Kohlbecker
   $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 $uuid) {
-            b5519d3a
+    if (!isset($tree[$uuid]->filter)) {
-            6657531f
+      $tree[$uuid]->filter = $filter_default;
+    }
     if (isset($tree[$uuid]->expanded) && $tree[$uuid]->expanded == 'expanded' && ($expand_excluded || $tree[$uuid]->filter != 'excluded')) {
       if (isset($tree[$uuid]->vid)) {
-ac8c744
+        //  TODO remove case, see #7565
-            6657531f
+        $children = cdm_taxontree_get_children($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;
+}
 /**
-            43251923
+ * Alter a resultset into an array of TreeNode instances with taxonUuid as keys.
-            6657531f
+            Andreas Kohlbecker
  * 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;
+}
 /**
-            0375638f
+ * 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 $magicbox_enable
  *    If set to TRUE the cdm_taxontree will get the magic box behavoir, which means that it
  *    will extend on mouse over events in order to
  *    show the entrys without truncation through cropping
-            6657531f
+ */
-            0375638f
+function cdm_taxontree_add_js($parent_element_selector, $magicbox_enable = FALSE) {
-            6657531f
+  $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');
-            b0adfd32
+            Andreas Kohlbecker
-            0375638f
+  drupal_add_js('
       jQuery(document).ready(function()
+      {
-            b7b43dc2
+        jQuery(\'' . $parent_element_selector . '\').cdm_taxontree();
-            0375638f
+      });
       ', array('type' => 'inline'));
-            6657531f
+            Andreas Kohlbecker
-            0375638f
+// ------------------------ THEME --------------------------- //
-            6657531f
+            Andreas Kohlbecker
 /**
  *  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()));
+  }
-            0375638f
+  $region = null;
-            6657531f
+  if (!empty($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.
-            0375638f
+    $expand_direction = ($region == 'right' ? 'expand-left' : '');
-            6657531f
+    $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) {
-cc085da
+      $out .= t('@mode', array('@mode' => $mode));
-            6657531f
+            Andreas Kohlbecker
     else {
-cc085da
+      $out .= l(t('@mode', array('@mode' => $mode)), 'cdm_taxontree/set/compact_mode/' . $mode, array('query' => drupal_get_destination()));
-            6657531f
+            Andreas Kohlbecker
     $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 = $variables['element_name'];
-da4e54
+  if(isset($tree->records)){
     // unwrap from pager object
     $tree = $tree->records;
+  }
-            6657531f
+  if (!is_array($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.
-            b0adfd32
+  $out = '<ul class="taxon-nodes ' . (($element_name) ? ' ' . $element_name : '') . '">';
-            6657531f
+  foreach ($tree as $node) {
-da4e54
+    if($node == null){
       continue;
+    }
-            6657531f
+    $out .= theme('cdm_taxontree_node', array(
       'node' => $node,
       'filterIncludes' => $filterIncludes,
       'show_filter_switch' => $show_filter_switch,
-af3ce28
+      'tree_node_callback' => $tree_node_callback
-            6657531f
+      ));
+  }
   $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'];
-af3ce28
+            Andreas Kohlbecker
-            6657531f
+  $is_leaf = !$node->taxonomicChildrenCount || $node->taxonomicChildrenCount == 0;
   $is_expanded = isset($node->expanded) && $node->expanded = 'expanded';
-af3ce28
+  $focused_taxon_uuid = get_current_taxon_uuid();
-a4d078d
+  $path = '';
   $query = array();
-            6657531f
+  if (isset($node->tid)) {
-a4d078d
+    //  TODO remove case, see #7565
-            6657531f
+    $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);
-a4d078d
+    $link_type = variable_get(CDM_TAXONTREE_LINK_TYPE,  'taxon_page');
     switch($link_type){
       case 'taxon_page':
         $path = path_to_taxon($node->taxonUuid);
         break;
       case 'search_registrations':
         $path = "cdm_dataportal/search/registration";
         $query['taxon_name'] = $node->titleCache;
         break;
       default:
         $path = "invalid_cdm_taxontree_linktype";
+    }
-            6657531f
+            Andreas Kohlbecker
   else {
     $node_name = "module cdm_dataportal missing";
     $path = "";
+  }
   if ($filterIncludes) {
-a4d078d
+    $name = l($node_name, $path, array('query' => $query));
-            6657531f
+    // No names for terms in filter widget; as discussed with A. Müller.
     // $name = '';
     $filter_class = 'filter_included';
+  }
   else {
     if ($node->filter == 'on') {
-a4d078d
+      $name = l($node_name, $path, array('query' => $query));
-            6657531f
+      $filter_class = 'filter_on';
+    }
     else {
-af3ce28
+      $name = $node_name;
-            6657531f
+      $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)) {
-ac8c744
+      //  TODO remove case, see #7565
-            6657531f
+      $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')) {
-c55
+      $ws_url = cdm_compose_taxonomy_root_level_path($node->taxonUuid);
-            6657531f
+      $ahah_url = url('cdm_api/proxy/' . urlencode($ws_url) . '/cdm_taxontree/' . ($nextLevelIncluded ? 1 : 0) . '/' . ($show_filter_switch ? 1 : 0) . '/' . $tree_node_callback);
+    }
+  }
   // List item.
   $out = '<li class="'
-af3ce28
+    . ($node->taxonUuid == $focused_taxon_uuid ? 'focused ' : '')
-            6657531f
+    . ($is_leaf ? 'leaf ' : ($is_expanded ? 'expanded ' : 'collapsed '))
     . $filter_class . '"'
-            cbc77aa9
+    . ($ahah_url ? ' data-cdm-ahah-url="' . $ahah_url . '"' : '')
-            6657531f
+    . '>';
   if ($show_filter_switch) {
     // Filter icon.
     $out .= theme('cdm_taxontree_node_filter_switch', array('node' => $node, 'filter_class' => $filter_class));
+  }
   // Taxon name.
-b3be949
+  $out .= '<span class="' . html_class_attribute_ref($node) . '">' . $name . '</span>';
-            6657531f
+            Andreas Kohlbecker
   // Concept_switch or other theme callbacks.
   if ($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;'
-            d5f0e39e
+    . l('<img src="' . base_path() . drupal_get_path('module', 'cdm_taxontree') . '/' . $filter_icon . '" alt="[f]" />',
-            6657531f
+        '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(
-            d5f0e39e
+      '<img src="' . base_path() . drupal_get_path('module', 'cdm_taxontree') . '/concept_switch.gif" alt="[-&gt;]" />',
-            6657531f
+      '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,
-af3ce28
+      'element_name' => FALSE
-            6657531f
+      )),
     '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,
-af3ce28
+      'tree_node_callback' => FALSE
-            6657531f
+      )),
     '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 $taxonUuid
+ *
-            a0e3ae5c
+ * @return string
-            6657531f
+ */
 function cdm_taxontree_view_filter($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.
-af3ce28
+            Andreas Kohlbecker
  * @deprecated use get_current_taxon_uuid() instead
-            6657531f
+ */
 function _cdm_get_taxonuuid() {
-af3ce28
+            Andreas Kohlbecker
-            6657531f
+  if (arg(0) == "cdm_dataportal" && arg(1) == "taxon" && arg(2) !== 0) {
     $taxon_uuid = arg(2);
+  }
   else {
     $taxon_uuid = FALSE;
-af3ce28
+    // TODO is this SESSION variable ['cdm_dataportal']['tree']['taxon_uuid'] use at all?
-            6657531f
+    if (isset($_SESSION['cdm_dataportal']['tree']['taxon_uuid'])) {
       $taxon_uuid = $_SESSION['cdm_dataportal']['tree']['taxon_uuid'];
+    }
+  }
   return $taxon_uuid;
+}

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