Edit

<?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)

 */

const CDM_TAXONTREE_LINK_TYPE = 'cdm_taxontree_link_type';

/**

 * 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);

      $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':

        $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' ),

        );

        /* 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) {

    switch ($delta) {

      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

        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

 *

 * * TODO remove method, see #7565

 */

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)) {

    //  TODO remove case, see #7565

    // 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)) {

    //  TODO remove case, see #7565

    $terms = taxonomy_get_children($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.

    //  TODO remove case, see #7565

    $terms = taxonomy_get_parents($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)) {

    //  TODO remove case, see #7565

    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); //  TODO remove $vid, see #7565 ?

  /*

  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();

  $path = '';

  $query = array();

  if (isset($node->tid)) {

    //  TODO remove case, see #7565

    $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);

    $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";

    }

  }

  else {

    $node_name = "module cdm_dataportal missing";

    $path = "";

  }

  if ($filterIncludes) {

    $name = l($node_name, $path, array('query' => $query));

    // 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, array('query' => $query));

      $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 .= ' '

    . 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;

}