Edit

<?php

/**

 * @file

 * Module to provide 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)

 */

  module_load_include('php', 'cdm_dataportal', 'node_types');

  module_load_include('php', 'cdm_dataportal', 'settings');

  module_load_include('php', 'cdm_dataportal', 'help');

  module_load_include('php', 'cdm_dataportal', 'cdm_dataportal.search');

  module_load_include('inc', 'cdm_dataportal', 'includes/common');

  module_load_include('inc', 'cdm_dataportal', 'includes/name');

  module_load_include('inc', 'cdm_dataportal', 'includes/taxon');

  module_load_include('inc', 'cdm_dataportal', 'includes/references');

  module_load_include('inc', 'cdm_dataportal', 'includes/pages');

  module_load_include('inc', 'cdm_dataportal', 'includes/media');

  module_load_include('inc', 'cdm_dataportal', 'includes/maps');

  module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');

  module_load_include('inc', 'cdm_dataportal', 'includes/descriptions');

  module_load_include('inc', 'cdm_dataportal', 'includes/pre-drupal8');

  module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');

  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');

  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');

  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');

  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');

  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');

  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');

  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');

  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');

  module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');

  module_load_include('php', 'cdm_dataportal', 'classes/footnote');

  module_load_include('php', 'cdm_dataportal', 'classes/footnotekey');

  module_load_include('php', 'cdm_dataportal', 'classes/renderhints');

  /* ============================ java script functions ============================= */

  /**

  * loads external java script files asynchronously.

  *

  * @param unknown_type $script_url

  */

  function drupal_add_js_async($script_url, $callback){

    drupal_add_js("

          jQuery(document).ready(function() {

            jQuery.ajax({

              url: '" . $script_url . "',

              dataType: 'script',

              cache: true, // otherwise will get fresh copy every page load

              success: function() {

                    " . $callback . "

              }

            });

          });"

    , 'inline');

  }

  /**

   */

  function drupal_add_js_rowToggle($tableId){

      drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/table_modification.js');

      drupal_add_js('jQuery(document).ready(function(){

          addRowToggle("' . $tableId . '");

      });

      ', array('type' => 'inline'));

  }

  /**

   * @param unknown_type $link_element_selector

   * @param unknown_type $progress_element_selector

   */

  function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){

    $callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";

    drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);

    //   drupal_add_js("

    //   	  if (Drupal.jsEnabled) {

    //         $(document).ready(function() {

    //       		$('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');

    //         });

    //       }", 'inline');

    }

  /**

   * @todo Please document this function.

   * @see http://drupal.org/node/1354

   */

  function _add_js_treeselector() {

    // drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');

    drupal_add_js("

        jQuery(document).ready(function() {

           jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {

                jQuery('#cdm-taxonomictree-selector-form').submit();

            });

        });

      ",

      array(

        'type' => 'inline',

        'scope' => 'footer'

      )

    );

  }

  function _add_js_resizable_element($selector, $y_axis_only) {

    _add_jquery_ui();

    $options = "";

    if($y_axis_only) {

      $options = "resize: function(event, ui) {

        ui.size.width = ui.originalSize.width;

        },

        handles: \"s\"";

    }

    drupal_add_js("

          jQuery(document).ready(function() {

             jQuery('" . $selector . "').resizable({". $options ."});

          });

        ",

      array(

        'type' => 'inline',

        'scope' => 'footer'

      )

    );

  }

  function _add_js_openlayers() {

    $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';

    $proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';

    if(variable_get('cdm_js_devel_mode', FALSE)){

      // develooper mode libs

  //     $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';

      $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';

      $proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';

    }

    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,

      array(

        'type' => 'file',

        'group' => JS_LIBRARY,

        'weight' => 0,

        'cache' => TRUE,

        'preprocess' => FALSE

      )

    );

    // see https://github.com/proj4js/proj4js

    // http://openlayers.org/dev/examples/using-proj4js.html

    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $proj4js,

      array(

        'type' => 'file',

        'group' => JS_LIBRARY,

        'weight' => -1, // before open layers

        'cache' => TRUE,

      )

    );

    // configure the theme

    $openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';

    $openlayers_imp_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/img/dark/';

    drupal_add_js('OpenLayers.ImgPath="' . base_path() . $openlayers_imp_path . '";', array(

        'type' => 'inline',

        'group' => JS_LIBRARY,

        'weight' => 1, // after openlayers

        'cache' => TRUE,

        'preprocess' => FALSE

      ));

    drupal_add_css($openlayers_theme_path . 'style.tidy.css',

      array(

        'type' => 'file',

        'cache' => TRUE,

        'preprocess' => FALSE

      )

    );

  }

  /**

   * @todo Please document this function.

   * @see http://drupal.org/node/1354

   */

  function _add_js_thickbox() {

    // ---- jQuery thickbox:

    /*

    * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is

    * not triggered because of problems with compat-1.0.js' see INSTALL.txt

    */

    // drupal_add_js(drupal_get_path('module',

    // 'cdm_dataportal').'/js/jquery.imagetool.min.js');

    //

    // Add a setting for the path to cdm_dataportal module, used to find the path

    // for the loading animation image in thickbox.

    drupal_add_js(array(

    'cdm_dataportal' => array(

    'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),

    )

    ),

    'setting'

        );

        drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');

        drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');

  }

  /**

   * @todo Please document this function.

   * @see http://drupal.org/node/1354

   */

  function _add_js_lightbox($galleryID) {

    /*

     * Important Notice: The jquery.lightbox-0.5.js has been modified in order to

     * allow using the "alt" attribute for captions instead of the "title"

     * attribute

     */

    $lightbox_base_path =  drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';

    $lightbox_image_path = base_path() . $lightbox_base_path . '/images/';

    drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');

    drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');

    drupal_add_js('jQuery(document).ready(function() {

        jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({

          fixedNavigation:  true,

          imageLoading:     \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',

          imageBtnPrev:     \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',

          imageBtnNext:     \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',

          imageBtnClose:    \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',

          imageBlank:       \'' . $lightbox_image_path . 'lightbox-blank.gif\',

          adjustToWindow: true

        });

      });

      ', array('type' => 'inline'));

  }

  /**

   * @todo Please document this function.

   * @see http://drupal.org/node/1354

   */

  function _add_js_footnotes() {

    _add_js_domEvent();

    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');

  }

  /**

   * @todo Please document this function.

   * @see http://drupal.org/node/1354

   */

  function _add_js_ahah() {

    _add_js_domEvent(); // requires domEvent.js

    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');

  }

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

function _add_js_taxonomic_children($jquery_selector) {

  global $base_url;

  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');

  drupal_add_js('jQuery(document).ready(function() {

        jQuery(\'' . $jquery_selector . '\').taxonomic_children({

          // hoverClass: "fa-rotate-90",

          // activeClass: "fa-rotate-90",

          classificationUuid: "' . get_current_classification_uuid() . '",

          taxonUuid: "' . get_current_taxon_uuid() . '",

          cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",

          proxyBaseUri: "' . $base_url . '",

        });

      });

      ', array('type' => 'inline'));

}

  /**

   * Adds the external javascript file for domEvent.js.

   *

   * @see drupal_add_js()

   */

  function _add_js_domEvent() {

    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');

  }

  function _add_jquery_ui()

  {

    drupal_add_css(drupal_get_path('module',

        'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');

    drupal_add_js(drupal_get_path('module',

        'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',

      array(

        'type' => 'file',

        'weight' => JS_LIBRARY,

        'cache' => TRUE,

        'preprocess' => FALSE

      )

    );

  }

  function _add_js_ui_accordion(){

    _add_jquery_ui();

    drupal_add_js('jQuery(document).ready(function() {

        jQuery( "#accordion" ).accordion();

      });',

      array('type' => 'inline')

    );

  }

  /**

   * Provides the markup for an font awesome icon.

   *

   * The icons is created in default size without any extra features.

   *

   * The available icons are listed here http://fontawesome.io/cheatsheet/

   * fontawesome icons have much more features than implemented here in this function,

   * for spinning icons, fixed width icons, rotation, etc please checkout the

   * examples at http://fontawesome.io/examples/

   *

   * @parameter $icon_name

   *  The name of the icon which starts with 'fa-'

   *

   * @return String

   *    the markup for the icon in an <i> tag

   *

   */

  function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){

    _add_font_awesome_font();

    if($icon_name){

      if(!isset($attributes['class'])){

        $attributes['class'] = array();

      }

      $attributes['class'][] = 'fa';

      $attributes['class'][] = $icon_name;

      return '<i ' . drupal_attributes($attributes) . '></i>';

    }

    return '';

  }

/**

 * Adds the css  containing the font awesome icons to the html header.

 */

function _add_font_awesome_font()

{

//<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">

  $font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/font-awesome-4.6.3/css/font-awesome.min.css';

  //$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";

  drupal_add_html_head_link(

    array(

      'href' => $font_awesome_css_uri,

      'rel' => 'stylesheet'

    )

  );

}

/* ====================== hook implementations ====================== */

  /**

   * Implements hook_permission().

   *

   * Valid permissions for this module.

   *

   * @return array

   *   An array of valid permissions for the cdm_dataportal module.

   */

  function cdm_dataportal_permission() {

    return array(

      'administer cdm_dataportal' => array(

        'title' => t('Administer CDM DataPortal settings'),

        'description' => t("Access the settings pages specific for the cdm_dataportal module"),

      ),

      'access cdm content' => array(

        'title' => t('Access CDM content'),

        'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),

      ),

    );

  }

/**

 * Implements hook_menu().

 */

function cdm_dataportal_menu() {

  $items = array();

  // @see settings.php.

  cdm_dataportal_menu_admin($items);

  cdm_dataportal_menu_help($items);

  $items['cdm_dataportal/names'] = array(

    'page callback' => 'cdm_dataportal_view_names',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

  );

  // Optional callback arguments: page.

  $items['cdm_dataportal/taxon'] = array(

    'page callback' => 'cdm_dataportal_taxon_page_view',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

    // Expected callback arguments: uuid.

  );

  $items['cdm_dataportal/specimen'] = array(

      'page callback' => 'cdm_dataportal_specimen_page_view',

      'access arguments' => array('access cdm content'),

      'type' => MENU_CALLBACK,

      // Expected callback arguments: uuid.

  );

  $items['cdm_dataportal/named_area'] = array(

    'page callback' => 'cdm_dataportal_named_area_page_view',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

    // Expected callback arguments: uuid.

  );

  $items['cdm_dataportal/name'] = array(

    'page callback' => 'cdm_dataportal_name_page_view',

      /*

    'page arguments' => array(

       'taxon_name_uuid',

       'taxon_to_hide_uuid',

       'synonym_uuid' => NULL

      ),

      */

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

    // Expected callback arguments: uuid.

  );

  $items['cdm_dataportal/reference'] = array(

    'page callback' => 'cdm_dataportal_view_reference',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

    // Expected callback arguments: uuid.

  );

  $items['cdm_dataportal/reference/list'] = array(

    'page callback' => 'cdm_dataportal_view_reference_list',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

    // Expected callback arguments: uuid.

  );

  $items['cdm_dataportal/media'] = array(

    'page callback' => 'cdm_dataportal_view_media',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

    // Expected callback arguments:

    // uuid, mediarepresentation_uuid, part_uuid or part#.

  );

  $items['cdm_dataportal/polytomousKey'] = array(

    'page callback' => 'cdm_dataportal_view_polytomousKey',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

    // Expected callback arguments: polytomousKey->uuid.

  );

  $items['cdm_dataportal/search'] = array(

    'page callback' => 'cdm_dataportal_view_search_advanced',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

  );

  $items['cdm_dataportal/search/advanced'] = array(

    'title' => 'Advanced', // will be passed through t()

    'page callback' => 'cdm_dataportal_view_search_advanced',

    'access arguments' => array('access cdm content'),

    'type' => MENU_DEFAULT_LOCAL_TASK,

  );

  $items['cdm_dataportal/search/taxon_by_description'] = array(

    'title' => 'By content category', // will be passed through t()

    'page callback' => 'cdm_dataportal_view_search_taxon_by_description',

    'access arguments' => array('access cdm content'),

    'type' => MENU_LOCAL_TASK,

  );

  $items['cdm_dataportal/search/results/taxon'] = array(

    'page callback' => 'cdm_dataportal_view_search_results_taxon',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

  );

  /*

   * MENU_CALLBACK at cdm_dataportal/registration-search is needed to make the

   * tabs in the subordinate paths work, accessing this 'page' will cause the

   * MENU_DEFAULT_LOCAL_TASK being displayed

   */

  $items['cdm_dataportal/registration-search'] = array(

    'title' => 'Search', // will be passed through t()

    'page callback' => 'cdm_dataportal_view_search_registrations_results',

    'page arguments' => array("filter"),

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

  );

  /*

   * the MENU_DEFAULT_LOCAL_TASK creates a tab for the MENU_CALLBACK

   * defined at a higher level of the path (cdm_dataportal/registration-search)

   */

  $items['cdm_dataportal/registration-search/filter'] = array(

    'title' => 'Search', // will be passed through t()

    'page callback' => 'cdm_dataportal_view_search_registrations_results',

    'page arguments' => array("filter"),

    'access arguments' => array('access cdm content'),

    'type' => MENU_DEFAULT_LOCAL_TASK,

  );

  /*

   * the MENU_LOCAL_TASK creates another tab

   */

  $items['cdm_dataportal/registration-search/taxongraph'] = array(

    'title' => 'Taxonomic search', // will be passed through t()

    'page callback' => 'cdm_dataportal_view_search_registrations_results',

    'page arguments' => array("taxongraph"),

    'access arguments' => array('access cdm content'),

    'type' => MENU_LOCAL_TASK,

  );

  // Optional callback arguments: page.

  $items['cdm_dataportal/registration'] = array(

    'page callback' => 'cdm_dataportal_registration_page_view',

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

    // Expected callback arguments: uuid.

  );

  /*

   $items['cdm/xml2json'] = array(

   'page callback' => 'cdm_view_xml2json',

   'access arguments' => array('access cdm content'),

   'type' => MENU_CALLBACK,

   );

   */

  // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {

  // User configuration of cdm_dataportal.

  $items['user/%/cdm_dataportal'] = array(

    'title' => 'cdm_dataportal',

    'access arguments' => array('access cdm content'),

    'page callback' => 'drupal_get_form',

    'page arguments' => array('cdm_dataportal_user_form'),

    'type' => MENU_LOCAL_TASK,

    'weight' => 10,

  );

  // }

  // 'May not cache' in D5.

  $items['cdm_dataportal/name/%'] = array(

    // 'page callback' => 'cdm_dataportal_view_name',

    'page callback' => 'cdm_dataportal_name_page_view',

    'page arguments' => array(2, 3, 4),

    'access arguments' => array('access cdm content'),

    'type' => MENU_CALLBACK,

  );

  // --- Local tasks for Taxon.

  // --- tabbed taxon page

  if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {

    $items['cdm_dataportal/taxon/%'] = array(

      'title' => cdm_taxonpage_tab_label('General'),

      'page callback' => 'cdm_dataportal_taxon_page_view',

      'access arguments' => array('access cdm content'),

      'type' => MENU_CALLBACK,

      'weight' => 1,

      'page arguments' => array(2, "description")

      , // Expected callback arguments: taxon_uuid.

    );

    $items['cdm_dataportal/taxon/%/all'] = array(

      'title' => cdm_taxonpage_tab_label('General'),

      'page callback' => 'cdm_dataportal_taxon_page_view',

      'access arguments' => array('access cdm content'),

      'type' => MENU_CALLBACK,

      'weight' => 2,

      'page arguments' => array(2, "all")

      , // Expected callback arguments: taxon_uuid.

    );

    $items['cdm_dataportal/taxon/%/description'] = array(

      'title' => cdm_taxonpage_tab_label('General'),

      'page callback' => 'cdm_dataportal_taxon_page_view',

      'access arguments' => array('access cdm content'),

      'type' => MENU_DEFAULT_LOCAL_TASK,

      'weight' => 2,

      'page arguments' => array(2, "description")

      , // Expected callback arguments: taxon_uuid.

    );

    $items['cdm_dataportal/taxon/%/synonymy'] = array(

      'title' => cdm_taxonpage_tab_label('Synonymy'),

      'page callback' => 'cdm_dataportal_taxon_page_view',

      'access arguments' => array('access cdm content'),

      'type' => MENU_LOCAL_TASK,

      'weight' => 4,

      'page arguments' => array(2, "synonymy", 4)

      , // Expected callback arguments: taxon_uuid and ...

    );

    $items['cdm_dataportal/taxon/%/images'] = array( // Images

      'title' => cdm_taxonpage_tab_label('Images'),

      'page callback' => 'cdm_dataportal_taxon_page_view',

      'access arguments' => array('access cdm content'),

      'type' => MENU_LOCAL_TASK,

      'weight' => 5,

      'page arguments' => array(2, "images")

      , // Expected callback arguments: taxon_uuid.

    );

    $items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens

      'title' => cdm_taxonpage_tab_label('Specimens'),

      'page callback' => 'cdm_dataportal_taxon_page_view',

      'access arguments' => array('access cdm content'),

      'type' => MENU_LOCAL_TASK,

      'weight' => 6,

      'page arguments' => array(2, "specimens")

      , // Expected callback arguments: taxon_uuid.

    );

    $items['cdm_dataportal/taxon/%/keys'] = array( // Keys

      'title' => cdm_taxonpage_tab_label('Keys'),

      'page callback' => 'cdm_dataportal_taxon_page_view',

      'access arguments' => array('access cdm content'),

      'type' => MENU_LOCAL_TASK,

      'weight' => 6,

      'page arguments' => array(2, "keys")

      , // Expected callback arguments: taxon_uuid.

    );

    $items['cdm_dataportal/taxon/%/experts'] = array( // Experts

      'title' => cdm_taxonpage_tab_label('Experts'),

        'page callback' => 'cdm_dataportal_taxon_page_view',

        'access arguments' => array('access cdm content'),

        'type' => MENU_LOCAL_TASK,

        'weight' => 6,

        'page arguments' => array(2, "experts")

    , // Expected callback arguments: taxon_uuid.

    );

    $items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(

        'page callback' => 'cdm_dataportal_taxon_autosuggest',

        'access arguments' => array('access cdm content'),

        'page arguments' => array(3,4,5),

        'type' => MENU_CALLBACK

    );

  }

  // --- refresh link for all cdmnode types

  foreach (cdm_get_nodetypes() as $type=>$name) {

    $items['cdm_dataportal/' . $name . '/%/refresh'] = array(

        'title' => 'Refresh',

        'page callback' => 'cdm_dataportal_refresh_node',

        'access arguments' => array('administer cdm_dataportal'),

        'type' => MENU_LOCAL_TASK,

        'weight' => 100,

        'page arguments' => array($name, 2)

    );

  }

  return $items;

}

/**

 * Implements hook_init().

 *

 */

function cdm_dataportal_init() {

  if (!path_is_admin(current_path())) {

    //FIXME To add CSS or JS that should be present on all pages, modules

    //      should not implement this hook, but declare these files in their .info file.

    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');

    // drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');

    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));

  } else {

    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');

  }

  if(variable_get('cdm_debug_mode', FALSE)){

    $file = 'temporary://drupal_debug.txt';

    file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file

  }

  $bibliography_settings = get_bibliography_settings();

  $enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';

  FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);

}

function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){

  $base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;

  if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){

    // force reloading of all and notify user about this special loading

    drupal_set_message(t('The level 2 cache has been cleared for all tabs of this taxon page at once, please click here to return to the tabbed page: ')

        . l('Back to tabbed taxon page', $base_path));

    $base_path .= '/all';

  } else {

    drupal_set_message(t('The level 2 cache has been cleared for this page'));

  }

  $parameters['cacheL2_refresh'] ='1';

  drupal_goto($base_path, array('query' => $parameters));

}

/**

 * Implements hook_requirements($phase)

 */

function cdm_dataportal_requirements($phase) {

    $requirements = array();

    if($phase == 'runtime'){

    }

    return $requirements;

}

/**

 * The function generate form for own user cdm dataportal configurations.

 */

function cdm_dataportal_user_form($form, &$form_state) {

  global $user;

  $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';

  $form['taxon_page_tabs'] = array(

      '#type' => 'fieldset',

      '#tree' => true,

      '#title' => t('Taxon page tabs'),

  );

  $form['taxon_page_tabs']['user_defined'] = array(

    '#type' => 'checkbox',

    '#title' => t('Activate user default configuration'),

    '#default_value' => variable_get($checkbox_value, 0),

    '#description' => t('Check this if you want configure your own default tab from the below menu.'),

  );

  $form['taxon_page_tabs']['default_tab'] = array(

    '#type' => 'select',

    '#title' => t('Default tab to display'),

    '#default_value' => get_default_taxon_tab(TRUE),

    '#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),

    '#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>

              <strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab

              to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),

  );

  if(false){

    $form['developer_options'] = array(

        '#type' => 'fieldset',

        '#tree' => true,

        '#title' => t('Developer options'),

    );

    $form['developer_options']['show_render_path'] = array(

      '#type' => 'checkbox',

      '#title' => t('Display the render path for each taxon name.'),

      '#default_value' => variable_get($checkbox_value, 0),

      '#description' => t('This option is very helpful if you are editing the !link for taxon names.',

        array(

            '!link' => l(

              'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))

            )

        ),

    );

  }

  $form['submit'] = array(

    '#type' => 'submit',

    '#value' => t('Submit'),

  );

  return $form;

}

/**

 * Form submission handler for user_form().

 *

 * Submits the user cdm dataportal configurations.

 */

function cdm_dataportal_user_form_submit($form, &$form_state) {

  global $user;

  $msg_type = 'status';

  $username = $user->name;

  $variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';

  // FIXME: this is completely wrong, see user_profile_form_submit()

  // it is only possible to change own user settings

  if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {

    // DEFAULT_TAXON_TAB

    $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);

    variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);

    variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);

    if ($form_state['values']['taxon_page_tabs']['user_defined']) {

      drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));

      drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(

        '!tab' => $variable[variable_get($variable_to_use, 0)],

        '!user' => $username,

      ))), $msg_type);

    }

    else {

      drupal_set_message(check_plain(t('The user default tab wont be used for

        the next taxon site, check the box if you want to use the user default configuration.')));

    }

  }

  else {

    // Problem with the user id => variables wont be saved.

    $msg_type = 'warning';

    drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);

  }

}

/**

 * Implements hook_block_info().

 */

function cdm_dataportal_block_info() {

    // $block[0]["info"] = t("CDM DataPortal DevLinks");

    // $block[1]["info"] = t("CDM DataPortal Credits");

    $block["2"] = array(

        "info" => t("CDM - Search Taxa"),

        "cache" => DRUPAL_NO_CACHE

      );

    // $block[3]["info"] = t("CDM Filters");

    $block["4"]["info"] = t("CDM  - Dataportal Print");

    $block["keys"]["info"] = t("CDM - Identification keys");

    $block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');

    $block["classification_breadcrumbs"] =  array(

        'info' => t('CDM - Classification breadcrumbs'),

        'cache' => DRUPAL_CACHE_PER_PAGE

      );

    $block["taxonomic_children"] =  array(

      'info' => t('CDM - Taxonomic children'),

      'cache' => DRUPAL_CACHE_PER_PAGE

    );

    $block["back_to_search_results"] =  array(

      'title' => '<none>',

      'info' => t('CDM - Back to search Results'),

      'cache' => DRUPAL_CACHE_PER_PAGE,

      'visibility' => BLOCK_VISIBILITY_LISTED,

      'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!!

    );

  $block['registrations_search_filter'] =  array(

    'title' => 'Filter registrations',

    'info' => t('CDM - Registrations search filter'),

    'cache' => DRUPAL_CACHE_PER_PAGE,

    'visibility' => BLOCK_VISIBILITY_NOTLISTED,

    'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!

  );

  $block['registrations_search_taxongraph'] =  array(

    'title' => 'Taxonomic registration search',

    'info' => t('CDM - Registrations search by taxon graph'),

    'cache' => DRUPAL_CACHE_PER_PAGE,

    'visibility' => BLOCK_VISIBILITY_NOTLISTED,

    'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!

  );

  $block['registrations_search'] =  array(

    'title' => 'Search',

    'info' => t('CDM - Registrations search combining filter and taxon graph search' ),

    'cache' => DRUPAL_CACHE_PER_PAGE,

    'visibility' => BLOCK_VISIBILITY_NOTLISTED,

    'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!

  );

  return $block;

}

/**

 * Implements hook_block_view().

 */

function cdm_dataportal_block_view($delta) {

  // TODO Rename block deltas (e.g. '2') to readable strings.

  switch ($delta) {

    // case 'delta-1':

    // $block['subject'] = t('Credits');

    // $block['content'] = theme('cdm_credits');

    // return $block;

    case '2':

      $block['subject'] = t('Search taxa');

      $form = drupal_get_form('cdm_dataportal_search_taxon_form');

      $block['content'] = drupal_render($form);

      if (variable_get('cdm_dataportal_show_advanced_search', 1)) {

        $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';

      }

      return $block;

    case '4':

      $block['subject'] = '';

      $block['content'] = theme('cdm_print_button');

      return $block;

    case "keys":

      $block['subject'] = t('Identification Keys');

      $block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));

      return $block;

    case "fundedByEDIT":

      // t('Funded by EDIT');

      $text = '<none>';

      $block['subject'] = $text;

      $img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';

      $block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(

        'attributes' => array("target" => "EDIT"),

        'absolute' => TRUE,

        'html' => TRUE,

      ));

      return $block;

    case 'classification_breadcrumbs':

      $taxon_uuid = get_current_taxon_uuid();

      $block['subject'] = '<none>';

      $block['content'] = compose_classification_breadcrumbs($taxon_uuid);

      return $block;

    case 'taxonomic_children':

      $taxon_uuid = get_current_taxon_uuid();

      $block['subject'] = '<none>';

      $block['content'] = compose_taxonomic_children($taxon_uuid);

      return $block;

    case 'back_to_search_results':

      $block['subject'] = '<none>';

      if (isset($_SESSION['cdm']['search'])) {

        $block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);

      }

      return $block;

    case 'registrations_search_filter':

      $block['subject'] = '<none>';

      $block['content'] = drupal_get_form('cdm_dataportal_search_registration_filter_form'); // see cdm_dataportal_search_registration_filter_form($form, &$form_state)

      return $block;

    case 'registrations_search_taxongraph':

      $block['subject'] = '<none>';

      $block['content'] = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form'); // see cdm_dataportal_search_registration_taxongraph_form($form, &$form_state)

      return $block;

    case 'registrations_search':

      _add_js_ui_accordion();

      _add_font_awesome_font();

      $block['subject'] = '<none>';

      $filter_form = drupal_get_form('cdm_dataportal_search_registration_filter_form');

      $filter_form['#prefix'] = '<div>';

      $filter_form['#suffix'] = '</div>';

      $taxongraph_form = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form');

      $taxongraph_form['#prefix'] = '<div>';

      $taxongraph_form['#suffix'] = '</div>';

      $block['content'] = array(

        'accordion' => array(

          '#markup' => '',

          '#prefix' => '<div id="accordion">',

          '#suffix' => '</div>',

          'content' => array(

            array('#markup' => '<h3>Filter</h3>'),

            $filter_form,

            array('#markup' => '<h3>Taxon graph</h3>'),

            $taxongraph_form,

          )

        )

    );

       return $block;

    default:

      return null;

  }

}

/**

 * Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}

 *

 * @return string

 *   the taxon uuid or NULL

 */

function get_current_taxon_uuid()

{

  static $taxon_uuid;

  if(!isset($taxon_uuid)){

    if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {

      $taxon_uuid = $_REQUEST['currentTaxon'];

    } else if (arg(1) == 'taxon' && is_uuid(arg(2))) {

      $taxon_uuid = arg(2);

    } else {

      $taxon_uuid = null;

    }

  }

  return $taxon_uuid;

}

/**

 * Returns the currently classification tree in use.

 *

 * @return string

 *   The uuid of the currently focused classification

 */

function get_current_classification_uuid() {

  if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {

    return $_SESSION['cdm']['taxonomictree_uuid'];

  }

  else {

    return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);

  }

}

/*

 function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){

 $_SESSION['cdm'] = NULL;

 if(is_string($cdm_ws_uri_update)){

 $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);

 }

 }

 function cdm_dataportal_session_validate(){

 if(!isset($_SESSION['cdm']['ws_uri'])){

 $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));

 } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){

 cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));

 }

 }

 */

/**

 * creates a  selector form for taxonomic trees.

 *

 * @return array

 *  a drupal form array

 */

function cdm_taxonomictree_selector() {

  _add_js_treeselector();

  $form = drupal_get_form('cdm_taxonomictree_selector_form');

  return $form;

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 *

 * @deprecated use compose_classification_selector instead

 */

function cdm_taxonomictree_selector_form($form, &$form_state) {

  $url = url('cdm_api/setvalue/session', array('query' => NULL));

  $form['#action'] = $url;

  $form['var'] = array(

    '#weight' => -3,

    '#type' => 'hidden',

    '#value' => '[cdm][taxonomictree_uuid]',

  );

  $destination_array = drupal_get_destination();

  $destination = $destination_array['destination'];

  $form['destination'] = array(

    '#weight' => -3,

    '#type' => 'hidden',

    '#value' =>  $destination,

  );

  $options = cdm_get_taxontrees_as_options();

  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);

  if($taxontree_includes){

    $filtered_options = array();

    foreach($options as $uuid=>$label){

      if(!empty($taxontree_includes[$uuid])){

        $filtered_options[$uuid] = $label;

      }

    }

    $options = $filtered_options;

  }

  $form['val'] = array(

    '#type' => 'select',

    '#title' => t('Available classifications'),

    '#default_value' => get_current_classification_uuid(),

    '#options' => $options,

    '#attributes' => array('class' => array('highlite-first-child')),

  );

  return $form;

}

/**

 *

 * @ingroup compose

 */

function compose_classification_selector() {

  $destination_array = drupal_get_destination();

  $destination = $destination_array['destination'];

  $options = cdm_get_taxontrees_as_options();

  $items = array();

  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);

  $current_classification_uuid = get_current_classification_uuid();

  foreach($options as $uuid=>$label){

    if(!$taxontree_includes || !empty($taxontree_includes[$uuid])){

      $class_attributes = '';

      if($current_classification_uuid == $uuid){

        $class_attributes  = array('focused');

      }

      $items[] = array(

        'data' => l($label,

          'cdm_api/setvalue/session',

          array(

            'query' => array(

              'destination' => $destination,

              'val' => $uuid,

              'var' => '[cdm][taxonomictree_uuid]'

            ),

          )

        ),

        'class' => $class_attributes

      );

    }

  }

  $render_array = array(

    '#theme' => 'item_list',

    '#type' => 'ul',

    '#items' => $items

  );

  return $render_array;

}

/* UNREACHABLE since action of form directly links to view.

 function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {

 $_SESSION['cdm']['search'] = $form_values;

 //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];

 return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');

 //$paramstr = compose_url_prameterstr($form_values);

 //return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));

 }

 */

/* ====================== menu callback functions ====================== */

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

/*

function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {

  static $comment_node_disabled =  0;

  static $comment_node_read_only =  1;

  static $comment_node_read_write =  2;

  if ($form_id == 'node_type_form'

   && isset($form['identity']['type'])

   && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())

  ) {

    $form['workflow']['comment'] = array(

      '#type' => 'radios',

      '#title' => t('Default comment setting'),

      '#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),

      '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),

      '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),

    );

  }

}

*/

/**

 * Displays a list of the known taxonomic names.

 *

 * When the list of taxonomic names is displayed, long lists are split up into

 * multiple pages.

 *

 * TODO: Parameters are still preliminary.

 *

 * @param string $beginsWith

 * @param string $page

 *   Page number to diplay defaults to page 1.

 * @param bool $onlyAccepted

 */

function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {

  $out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');

  /*

  // FIXME the filter for accepted names will be a form element, thus this

  // widget should be generated via form api preferably as block.

  $out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);

  $out .= theme('cdm_dataportal_widget_names_list', $names, $page);

  $out .= theme('cdm_listof_taxa', $taxonPager);

  return $out;

  */

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 * @throws Exception

 */

function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {

  cdm_check_valid_portal_page();

  return compose_cdm_reference_page($uuid);

}

/**

 * Creates a view on a all references contained in the portal.

 *

 * This function is used at the path cdm_dataportal/reference/list

 */

function cdm_dataportal_view_reference_list($pageNumber) {

  $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);

  cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {

  cdm_check_valid_portal_page();

  $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);

  return theme('cdm_media_page', array(

    'media' => $media,

    'mediarepresentation_uuid' => $mediarepresentation_uuid,

    'partId' => $part,

    ));

}

/**

 * @todo Please document this function.

 * @see http://drupal.org/node/1354

 */

function _load_taxonBase(&$taxonBase) {

  if (isset($taxonBase->uuid)) {

    $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));

    $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));

    $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));

  }

}

/**

 * Loads the media associated to the given taxon from the cdm server.

 * The aggregation settings regarding taxon relathionships and

 * taxonnomic childen are taken into account.

 *

 * The media lists are cached in a static variable.

 *

 * @param Taxon $taxon

 *   A CDM Taxon entitiy

 *

 * @return array

 *   An array of CDM Media entities

 *

 */

function _load_media_for_taxon($taxon) {

  static $media = NULL;

  if(!isset($media)) {

    $media = array();

  }

  if (!isset($media[$taxon->uuid])) {

    // --- GET Images --- //

    $mediaQueryParameters = array(

        "type" => "ImageFile",

    );

    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));

    $mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));

    $mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));

    $taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));

    $mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;

    $mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;

    $mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;

    $ws_endpoint = NULL;

    if ( variable_get('cdm_images_include_children', 0) == 0) {

      $ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;

    } else {

      $ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;

    }

    $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,

        array(

            $taxon->uuid,

        ),

        queryString($mediaQueryParameters)

       );

  }

  return $media[$taxon->uuid];

}

/**

 *

 * @param Taxon $taxon

 *   A CDM Taxon entitiy

 *

 * @return array

 *   An array of CDM SpecimenOrObservation entities

 *

function _load_occurences_for_taxon($taxon){

  static $occurences = NULL;

  if(!isset($occurences)) {

    $occurences = array();

  }

  if (!isset($occurences[$taxon->uuid])){

    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));

    $relationship_choice['direct'] = get_selection($relationship_choice['direct']);

    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);

    $by_associatedtaxon_query = http_build_query(array(

        'relationshipsInvers' => implode(',', $relationship_choice['invers']),

        'relationships' => implode(',', $relationship_choice['direct']),

        'pageSize' => null // all hits in one page

    )

    );

    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,

        null,

        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid

    );

    if(isset($pager->records[0])){

      $occurences[$taxon->uuid] =  $pager->records;

    }

  }

  return $occurences[$taxon->uuid];

}

 */

/**

 * Gets a Drupal variable, string or array and returns it.

 *

 * Similar to the variable_get() function of Drupal, except that this function

 * is able to handle arrays correctly. This function is especially useful

 * when dealing with collections of settings form elements (#tree = TRUE).

 *

 * @param string $variableKey

 *   The Unique key of the Drupal variable in the Drupal variables table.

 * @param string $defaultValueString

 *   A string as for example derived from a CONSTANT.

 *

 * @return mixed

 *   usually an array, depending on the nature of the variable.

 *

 * TODO compare with get_array_variable_merged() duplicate functions?

 * @deprecated rather use get_array_variable_merged() since this function

 * used an array as second parameter

 */

function mixed_variable_get($variableKey, $defaultValueString) {

  $systemDefaults = unserialize($defaultValueString);

  $storedSettings = variable_get($variableKey, array());

  if (is_array($storedSettings)) {

    // TODO better use drupal_array_merge_deep() ?

    $settings = array_merge($systemDefaults, $storedSettings);

  }

  else {

    $settings = $systemDefaults;

  }

  return $settings;

}

/**

 * Recursive function to convert an object into an array.

 * also subordinate objects will be converted.

 *

 * @param object $object

 *  the object to be converted

 * @return array

 *  The array

 */

function object_to_array($object) {

  if(is_object($object) || is_array($object)) {

    $array = (array)$object;

    foreach ($array as $key=>$value){

      $array[$key] = object_to_array($value);

    }

    return $array;

  } else {

    return $object;

  }

}

/**

 * Searches the $collection for the cdm entitiy given as $element.

 *

 * The elements are compared by their UUID.

 *

 * @param $element

 *  the CDM entitiy to search for

 * @param $collection

 *  the list of CDM entities to search in

 *

 * @return boolean TRUE if the $collection contains the $element, otheriwse FALSE

 *

 */

function contains_cdm_entitiy($element, $collection) {

  $result = FALSE;

  foreach ($collection as $a) {

    if ($a->uuid == $element->uuid) {

      $result = TRUE;

    }

  }

  return $result;

}

/**

 * Fiters the array $entity_list of CDM entities by the list

 * of $excludes. Any element contained in the $excludes will be removed

 * from included int the retuned list.

 *

 * If the $entity_list is not an array the $excludes will be returned.

 */

function filter_cdm_entity_list($entity_list, $excludes) {

  if (is_array($entity_list)) {

    $result = $entity_list;

    if ($excludes) {

      foreach ($excludes as $exclude) {

        if (!contains_cdm_entitiy($exclude, $entity_list)) {

          $result[] = $exclude;

        }

      }

    }

  }

  else {

    $result = $excludes;

  }

  return $result;

}

/**

 * Wraps the given $html string into a render array suitable for drupal_render()

 *

 * @param $html

 *   the html string, see

 *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup

 * @param $weight

 *   A positive or negative number (integer or decimal).

 *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval

 * @param $prefix

 *   Optional markup for the '#prefix' element of the render array

 * @param $suffix

 *   Optional markup for the '#suffix' element of the render array

 *

 * @return array

 *   A render array

 *

 */

function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {

  $render_array = array(

    '#markup' => $html

      );

  if (is_numeric($weight)) {

    $render_array['#weight'] = $weight;

  }

  if($prefix){

    $render_array['#prefix'] = $prefix;

  }

  if($suffix) {

    $render_array['#suffix'] = $suffix;

  }

  return $render_array;

}

/**

 * Loads the subgraph of a given PolytomousKeyNode.

 *

 * Loads the subgraph of the given PolytomousKeyNode recursively from

 * the CDM REST service.

 *

 * @param mixed $polytomousKeyNode

 *   PolytomousKeyNode passed by reference.

 *

 * @return void

 */

function _load_polytomousKeySubGraph(&$polytomousKeyNode) {

  if (!$polytomousKeyNode) {

    return;

  }

  if ($polytomousKeyNode->class != "PolytomousKeyNode") {

    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');

    return;

  }

  if (!is_uuid($polytomousKeyNode->uuid)) {

    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');

    return;

  }

  $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);

  if (!$polytomousKeyNode) {

    // drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");

    return;

  }

  // Load children.

  foreach ($polytomousKeyNode->children as &$childNode) {

    _load_polytomousKeySubGraph($childNode);

  }

  // Load subkey.

  $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));

  // Load taxon.

  $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));

  _load_taxonBase($polytomousKeyNode->taxon);

  return;

}

/**