EDIT

<?php

// $Id$

/*

 * @file

 * cdm_dataportal

 *

 * Copyright (C) 2007 EDIT

 * European Distributed Institute of Taxonomy

 * http://www.e-taxonomy.eu

 *

 */

require_once('cdm_dataportal.theme.php');

define(CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE, 25);

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

/**

 * Implementation of hook_help()

 *

 * Display help and module information

 * @param section which section of the site we're displaying help

 * @return help text for section

 */

function cdm_dataportal_help($section='') {

  $out = '';

  switch ($section) {

    case "admin/modules#description":

      $out = t("The dataportal publishes CDM data hosted in a CommunityStore on the web.");

      break;

  }

  return $out;

}

/**

 * Implementation of hook_perm()

 *

 * Valid permissions for this module

 * @return array An array of valid permissions for the portfolio module

 */

function cdm_dataportal_perm() {

  return array(

    	'administer cdm_dataportal',

        'cdm_dataportal view notes',

  //TODO which else permission are required? -> check the WP6 requirements document

  );

}

/**

 * Implementation of hook_menu()

 */

function cdm_dataportal_menu($may_cache) {

  $items = array();

  if ($may_cache) {

    $items[] = array(

      'path' => 'admin/settings/cdm_dataportal',

      'title' => t('CDM Dataportal'),

      'description' => t('Setting for the CDM Dataportal'),

      'access' => user_access('administer cdm_dataportal'),

      'callback' => 'drupal_get_form',

      'callback arguments' => 'cdm_dataportal_settings',

    );

    /*$items[] = array(

      'path' => 'admin/settings/cdm_dataportal/ws',

      'title' => t('Web Service'),

      'description' => t('Setting for the CDM Dataportal'),

      'access' => user_access('administer cdm_dataportal'),

      'callback' => 'drupal_get_form',

      'callback arguments' => 'cdm_dataportal_settings',

      'weight' => 1,

      'type' => MENU_DEFAULT_LOCAL_TASK,

    );*/

    $items[] = array(

	    'path' => 'cdm_dataportal/names',

	    'callback' => 'cdm_dataportal_view_names',

	    'access' => true,

	    'type' => MENU_CALLBACK,

    );

    // optional callback arguments: page

    $items[] = array(

      'path' => 'cdm_dataportal/taxon',

      'callback' => 'cdm_dataportal_view_taxon',

      'access' => true,

      'type' => MENU_CALLBACK,

    // expected callback arguments: name_uuid

    );

    $items[] = array(

      'path' => 'cdm_dataportal/reference',

      'callback' => 'cdm_dataportal_view_reference',

      'access' => true,

      'type' => MENU_CALLBACK,

    // expected callback arguments: name_uuid

    );

    $items[] = array(

      'path' => 'cdm_dataportal/reference/list',

      'callback' => 'cdm_dataportal_view_reference_list',

      'access' => true,

      'type' => MENU_CALLBACK,

    // expected callback arguments: name_uuid

    );

    $items[] = array(

      'path' => 'cdm_dataportal/search/taxon',

      'callback' => 'cdm_dataportal_view_search_taxon',

      'access' => true,

      'type' => MENU_CALLBACK,

    );

    $items[] = array(

      'path' => 'cdm/xml2json',

      'callback' => 'cdm_view_xml2json',

      'access' => true,

      'type' => MENU_CALLBACK,

    );

  } else {

    // may not cache

        // --- local tasks for Taxon

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

       $items[] = array(

      'path' => 'cdm_dataportal/taxon/'.arg(2),

      'title' => t('General'),

      'callback' => 'cdm_dataportal_view_taxon',

      'access' => true,

      'type' => MENU_CALLBACK,

      'weight' => 1,

      'callback arguments' => array(arg(2))

      // expected callback arguments: name_uuid

      );

      $items[] = array(

      'path' => 'cdm_dataportal/taxon/'.arg(2).'/description',

      'title' => t('General'),

      'callback' => 'cdm_dataportal_view_taxon',

      'access' => true,

      'type' => MENU_DEFAULT_LOCAL_TASK,

      'weight' => 2,

      'callback arguments' => array(arg(2), "description")

      // expected callback arguments: name_uuid

      );

      $items[] = array(

      'path' => 'cdm_dataportal/taxon/'.arg(2).'/synonymy',

      'title' => t('Synonymy'),

      'callback' => 'cdm_dataportal_view_taxon',

      'access' => true,

      'type' => MENU_LOCAL_TASK,

      'weight' => 3,

      'callback arguments' => array(arg(2), "synonymy")

      // expected callback arguments: name_uuid

      );

      $items[] = array(

      'path' => 'cdm_dataportal/taxon/'.arg(2).'/images',

      'title' => t('Images'),

      'callback' => 'cdm_dataportal_view_taxon',

      'access' => true,

      'type' => MENU_LOCAL_TASK,

      'weight' => 4,

      'callback arguments' => array(arg(2), "images")

      // expected callback arguments: name_uuid

      );

    } 

  }

  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', 'screen');

  return $items;

}

/**

 * Implementation of hook_block()

 *

 * Provides the following blocks:

 *  0: list of links useful during development

 *

 * @param String $op

 * @param int $delta

 */

function cdm_dataportal_block($op='list', $delta=0) {

  // listing of blocks, such as on the admin/block page

  if ($op == "list") {

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

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

    $block[2]["info"] = t("CDM Search Taxa");

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

    return $block;

  }

  else if ($op == 'view') {

    switch($delta){

      case 0:

        $block['subject'] = t('CDM DataPortal DevLinks');

        $block['content'] = '<ul>

        <li>'.l('A Taxon Page', cdm_dataportal_taxon_path('5000001-stub')).'</li>

        <li>'.l('Name List - page1 of A', 'cdm_dataportal/names/A/1')

        //.'</li><li>'.l('xml2json', 'cdm/xml2json/namelist;startwith=A.xml')

        .'</li>

        </ul>';

        return $block;

      case 1:

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

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

        return $block;

      case 2:

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

        $block['content'] = drupal_get_form('cdm_dataportal_search_taxon_form');

        return $block;

    }

  }

}

/**

 * Implementation of hook_validate()

 *

 * @param $element

 */

function cdm_dataportal_settings_validate($form_id, $form_values){

  if (!str_endsWith($form_values['cdm_webservice_url'], '/')) {

    form_set_error('cdm_webservice_url', t("The URL to the CDM Web Service must end with a slash: '/'."));

  }

  $cdm_webservice_url_changed = variable_get('cdm_webservice_url', '') != $form_values['cdm_webservice_url'];

  if ($cdm_webservice_url_changed) {

    $form_values['cdm_secUuid_default'] = '';

    //TODO does the currentSecUuid need to be stored?

    //   Yes - if switching to another concept is permanent until an other concept switch is used.

    //   NO  - if a user only 'visits' other concepts until this context is left by visiting a non taxon page

    //         , or explicitly when a concept switch is used.

    //         other concept could be activated permanently by personal preference settings

    //

    //  >> NO seems to be the desired solution <<

    //

    _cdm_dataportal_set_currentSecUuid(false);

    // reset all cdm related data stored in the session

    // cdm_dataportal_session_clear($form_values['cdm_webservice_url']); // cdm_webservice_url is not further stored here

    // clear the cdm webservice cache

    cache_clear_all(NULL, 'cache_cdm_ws');

    // better clear secref_cache since i can not be sure if the cache has not be used during this response

    cdm_api_secref_cache_clear();

  }

  if($form_values['cdm_webservice_cache'] != variable_get('cdm_webservice_cache', 1)){

    cache_clear_all(NULL, 'cache_cdm_ws');

    // better clear secref_cache since i can not be sure if the cache has not be used during this response

    cdm_api_secref_cache_clear();

  }

}

/*

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));

  }

}

*/

function cdm_dataportal_search_taxon_form(){

  $url = 'cdm_dataportal/search/taxon';

  $form['#method'] = 'get';

  $form['#process'] = array('cdm_dataportal_search_process' => array());

  $form['#action'] = url($url, NULL, NULL, true);

  $form['queryString'] = array(

    '#type' => 'textfield',

    '#size' => 20,

    '#attributes' => array('title' => t('Enter the name or part of a name you wish to search for. The asterisk  character * can always be used as wildcard')),

    '#default_value' => (isset($_SESSION['cdm']['search']['queryString']) ? $_SESSION['cdm']['search']['queryString'] : ''),

  );

  $form['mode'] =  array(

    '#type' => 'hidden',

    '#value' => 'BEGINNING'

    );

  $form['onlyAccepted'] =  array(

    '#type' => 'hidden',

    '#value' => '0',

    );

 /* $form['onlyAccepted'] = array(

    '#type' => 'checkbox',

    '#title' => t('Only Accepted'),

    '#attributes' => array('title' => t('Search only for accepted taxa.')),

    '#default_value' => isset($_SESSION['cdm']['search']['onlyAccepted']) && $_SESSION['cdm']['search']['onlyAccepted'],

  );*/

  /*

  $form['vernacular'] = array(

    '#type' => 'checkbox',

    '#title' => t('Vernacular Names'),

    '#attributes' => array('title' => t('Search for vernacular names.')),

    '#default_value' => isset($_SESSION['cdm']['search']['vernacular']) && $_SESSION['cdm']['search']['vernacular'],

  );

  $form['language'] =  array(

    '#type' => 'select',

    '#title' => t('Language'),

    '#options' => array(

        '*' => t('ALL')

        ),

    '#description'   => t('The language of the vernacular name'),

    '#default_value' => (isset($_SESSION['cdm']['search']['language']) ? $_SESSION['cdm']['search']['language'] : ''),

  );

  */

  $form['page'] = array(

  '#type' => 'hidden',

  '#value' => '1',

  );

  $form['submit'] = array(

  '#type' => 'submit',

  '#name' => '',

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

  );

  // clean URL get forms breaks if we don't give it a 'q'.

  if (!(bool)variable_get('clean_url', '0')) {

    $form['q'] = array(

      '#type' => 'hidden',

      '#value' => $url,

      '#name' => 'q',

    );

  }

  return $form;

}

//TODO is this function REACHABLE and thus in use??

function cdm_dataportal_search_process($form) {

  unset($form['form_id']);

  unset($form['form_token']);

  return $form;

}

/**

 * Filters $_REQUEST by a list of valid request  parameters and also sets defaults if required.

 * returns the processed request parameters submitted by the search form.

 */

function cdm_dataportal_search_form_request(){

  $currentSecRefArray = _cdm_dataportal_currentSecRef_array();

  // keys map $REQUEST Keys values are optional default parameters if not null

  $search_form_params = array( 	'queryString' => null,

  										'onlyAccepted' => '0',

  										'page' => null,

  										'pagesize' => variable_get('cdm_dataportal_search_items_on_page', 25),

  										'mode' => null,

                      'sec' => $currentSecRefArray['uuid']);

  $form_params = array();

  foreach($search_form_params as $key=>$default ){

    $form_params[$key] = ( isset($_REQUEST[$key]) && $_REQUEST[$key] != '' ? $_REQUEST[$key] : $default);

  }

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

  return $form_params;

}

/* 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/', $paramstr);

}

*/

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

/**

 * Generate main administration form.

 *

 * @return

 *   An array containing form items to place on the module settings page.

 */

function cdm_dataportal_settings(){

  $form = cdm_api_settings_form();

  //TODO: settings are still incomplete, compare with trunk/dataportal/inc/config_default.php.inc

  $form['cdm_dataportal'] = array(

      '#type' => 'fieldset',

      '#title' => t('CDM DataPortal'),

      '#collapsible' => FALSE,

      '#collapsed' => TRUE,

  );

  $form['cdm_dataportal']['secuuid_widget'] = array(

    '#type' => 'select_secuuid', // => will be themed by theme_select_secuuid(...)

    '#title' => t('Default Concept References'),

    '#description'   => t('The default \'sensu\' reference to start the CDM DataPortal with. Per user choices are possible and may override this value.'),

    '#varname' => 'cdm_secUuid_default',

    '#multiple' => false

  );

  //------------------ FEATURE TREE --------------------//

  $form['cdm_dataportal']['feature_tree'] = array(

    '#type' => 'fieldset',

    '#title' => t('Feature Tree'),

    '#collapsible' => TRUE,

    '#collapsed' => TRUE,

  );

    $form['cdm_dataportal']['feature_tree']['cdm_dataportal_feature_tree_active'] = array(

    '#type' => 'select',

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

    '#default_value' => variable_get('cdm_dataportal_feature_tree_active', 'ae9615b8-bc60-4ed0-ad96-897f9226d568'),

	'#options' => _get_feature_trees(),

    '#description'   => t('Select a FeatureTree for this webservice. If there is no applicable FeatureTree you can create a new one using the <a href="">FeatureTreeManager</a>')

  );

  //------------------ LAYOUT --------------------//

  $form['cdm_dataportal']['layout'] = array(

    '#type' => 'fieldset',

    '#title' => t('Layout'),

    '#collapsible' => TRUE,

    '#collapsed' => TRUE,

  );

   $form['cdm_dataportal']['layout']['cdm_taxonname_type'] = array(

    '#type' => 'select',

    '#title'         => t('Taxon name type'),

    '#default_value' => variable_get('cdm_taxonname_type', 'BotanicalName'),

    '#options' => array( 'BotanicalName'=>t('BotanicalName'), 'ZoologicalName'=>t('ZoologicalName')),

    '#description'   => t('')

  );

  $form['cdm_dataportal']['layout']['cdm_dataportal_nomref_in_title'] = array(

    '#type' => 'checkbox',

    '#title' => t('Hide full nomenclatural reference in title'),

    '#default_value' => variable_get('cdm_dataportal_nomref_in_title', 1),

    '#description' => t('Uncheck this, if you want the title of a taxon page consisting of name and author plus publication year only.

    					If not checked, the first homotypic taxon is a repetition of the accepted taxon with

    					the full nomenclatural reference.')

  );

  $form['cdm_dataportal']['layout']['cdm_dataportal_display_name_relations'] = array(

    '#type' => 'checkbox',

    '#title' => t('Show name relations of accepted taxa on taxon page'),

    '#default_value' => variable_get('cdm_dataportal_display_name_relations', 1),

    '#description' => t('')

  );

  $form['cdm_dataportal']['layout']['cdm_dataportal_taxonpage_tabs'] = array(

    '#type' => 'checkbox',

    '#title' => t('Tabbed taxon page'),

    '#default_value' => variable_get('cdm_dataportal_taxonpage_tabs', 1),

    '#description' => t('Split the taxon page into individual tabs for description, images, synonymy')

  );

  $form['cdm_dataportal']['layout']['cdm_dataportal_search_items_on_page'] = array(

    '#type' => 'textfield',

    '#title' => t('Search Page Size'),

    '#default_value' => variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE),

    '#description' => t('Number of Names to display per page in search results.')

  );

  //---------------- GEOSERVICE ----------------//

  $form['cdm_dataportal']['geoservice'] = array(

    '#type' => 'fieldset',

    '#title' => t('Geoservice'),

    '#collapsible' => TRUE,

    '#collapsed' => TRUE,

  );

  $form['cdm_dataportal']['geoservice']['cdm_dataportal_geoservice_access_point'] = array(

    '#type' => 'textfield',

    '#title' => t('Geoservice Access Point'),

    '#default_value' => variable_get('cdm_dataportal_geoservice_access_point', ''),

    '#description' => t('Base URL of the geoservice to be used by this portal')

  );

  $form['cdm_dataportal']['geoservice']['cdm_dataportal_geoservice_display_width'] = array(

    '#type' => 'textfield',

    '#title' => t('Geoservice Display Width'),

    '#default_value' => variable_get('cdm_dataportal_geoservice_display_width', 390),

    '#description' => t('Width of the image generated by geoservice')

  );

  $form['cdm_dataportal']['geoservice']['cdm_dataportal_geoservice_bounding_box'] = array(

    '#type' => 'textfield',

    '#title' => t('Geoservice Bounding Box'),

    '#default_value' => variable_get('cdm_dataportal_geoservice_bounding_box', '-180,-90,180,90'),

    '#description' => t('Define the surrounding area using latitude and longitude. Leave as is for the whole world.')

  );

   //cdm_dataportal_geoservice_labels_on

  $form['cdm_dataportal']['geoservice']['cdm_dataportal_geoservice_labels_on'] = array(

    '#type' => 'checkbox',

    '#title' => t('Display Country Labels'),

    '#default_value' => variable_get('cdm_dataportal_geoservice_labels_on', FALSE),

    '#description' => t('Check this if you like country names to be displayed in the maps. ')

  );

  return system_settings_form($form);

}

/**

 * Implementation of hook_elements().

 */

function cdm_dataportal_elements() {

  $type['select_secuuid'] = array(

    '#input' => TRUE,

    '#process' => array('cdm_dataportal_select_secuuid_expand' => array()),

    //'#validate' => array('cdm_dataportal_select_secuuid_validate' => array()),

    //'#default_value' => array(),

  );

  return $type;

}

/*

 *

 */

function cdm_dataportal_select_secuuid_expand($element){

  $element['#tree'] = FALSE;

  // any value submitted?

  if(isset($element['#post'][$element['#varname']])){

    $selected_values = $element['#post'][$element['#varname']];

  } else {

    // use those store in drupal

    $selected_values = variable_get( $element['#varname'], array());

  }

  if(!is_array($selected_values)){

    $selected_values = array($selected_values);

  }

  $options = array();

  foreach($selected_values as $secUuid){

    $options[$secUuid] = cdm_taxontree_secRefTitle_for($secUuid);

  }

  $element[$element['#varname']] =  array(

    '#type' => 'select',

    '#options' => $options,

    '#default_value' => array_values($options),

    '#size' => $element['#multiple'] ? 12 : 2,

    '#multiple' => $element['#multiple'],

  );

  return $element;

}

/**

 * Displays a list of the known taxonomic names. Long lists are split up into multiple pages

 *

 * TODO: parameters are still preliminar

 * @param String $page page number to diplay defaults to page 1

 * @param boolean $hide_unaccepted whether to hide nams which are not accepted by the current view

 */

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

  $request_params  = array(

    'q' => $beginsWith,

         //'sec' = '',

         //'higherTaxa' => getFiters(),

          // 'matchAnywhere' => false, // default is false

    'page' => $page,

    'onlyAccepted' => $onlyAccepted,

    'pagesize' => 20  /*$_SESSION['cdm']['namelist_pagesize'] */);

  $taxonPager = cdm_ws_find(CDM_WS_FIND_TAXA, $request_params);

  /*

   * 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;

}

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

    $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);

    return theme('cdm_reference_page', $reference);

}

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);

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

}

/**

 * The taxon page gives detailed information on a taxon, it shows:

 *  - Taxon name

 *  - Full list of synonyms homotypic synonyms on top, followed by the

 *    heterotypic and finally followed by misapplied names.

 *    The list is ordered historically.

 *  - All facts associated with the very taxon concept and taxon name.

 *

 * @param String $uuid the UUID of the taxon

 */

function cdm_dataportal_view_taxon($uuid, $chapter){

    // display the page for the taxon defined by $uuid

    $taxon = cdm_ws_get(CDM_WS_TAXON, $uuid);

    if(!$taxon){

      drupal_set_title(t('Taxon does not exist'));

      return false;

    }

    _cdm_dataportal_set_currentSecUuid($taxon->sec->uuid);

    drupal_set_title(theme('cdm_taxon_page_title', $taxon->name));

    $out = theme('cdm_taxon_page_general', $taxon, $chapter);

    return $out;

  /*}*/

}

/**

 * Expected URL request parameters:

 *  - text

 *  - language

 *  - vernacular

 *

 * future extensions to meet palmweb mockup requirements:

 *  - habitat

 *  - uses

 *  - conservation status

 *  - locality / tdwg region

 */

function cdm_dataportal_view_search_taxon(){

  $_SESSION['cdm']['last_search'] = $_SERVER['REQUEST_URI'];

  $request_params = cdm_dataportal_search_form_request();

  $sw_params = array_replace_key($request_params, array('queryString'=> 10 ));

  $taxonPager = cdm_ws_find(CDM_WS_TAXON, $sw_params);

  //$taxonPager->pageNumber = $request_params['page'];

  return theme('cdm_search_results', $taxonPager, 'cdm_dataportal/search/taxon', $request_params);

}

function cdm_view_xml2json(){

  $file = arg(2);

  $datastr = get_content(variable_get('cdm_webservice_url', '').$file);

  return  xml2json::transformXmlStringToJson($datastr);

}

/* ====================== other functions ====================== */

/**

 * Enter description here...

 *

 * @param String $uuid the UUID of the taxon

 * @return the URL

 */

function cdm_dataportal_taxon_path($uuid){

  return 'cdm_dataportal/taxon/'.$uuid;

}

/**

 * Creates a short taxonname by using the taggename field of NameSTO or NameTO instances.

 * If the taggename if empty the fullname will be returned.

 *

 * @param unknown_type $Name or TreeNode

 * @return string

 */

function cdm_dataportal_shortname_of($name){

  $nameStr = '';

  // get all tagged text tokens of the scientific name

  foreach($name->taggedTitle as $tagtxt){

      if($tagtxt->type == 'name' || $tagtxt->type == 'rank'){

        $nameStr .= ($nameStr ? ' ' : '').$tagtxt->text;

      }

  }

  $nameStr = trim($nameStr);

  if($nameStr){

    // do not return short names for these

    if($nameStr == 'Incertae sedis' || $nameStr ==  'Nomina excludenda'){

      return $nameStr;

    }

    if($pos = stripos($nameStr, ' ')){

      return substr($nameStr, 0, 1).'. '.substr($nameStr, $pos);

    } else {

      return $nameStr;

    }

  } else {

    return $name->titleCache;

  }

}

/**

 * TODO Add Comments. I don't get what

 *

 * @param UUID $secUuid

 */

function _cdm_dataportal_set_currentSecUuid($secUuid){

// do not save in session but in database

  //TODO setting the currentSecUuid causes problems in cichorieae in taraxacum, 

  //     thus it is temporary disabled

  return;

  if(is_array($secUuid)){

    $secUuid = $secUuid[0];

  }

  if(!$secUuid){

    variable_set('cdm_currentSecRef', null);

  } else {

    $secRef = cdm_ws_get(CDM_WS_REFERENCE, $secUuid);

    if(isset($secRef[0])){

      variable_set('cdm_currentSecRef', (array)($secRef[0]));

    }

  }

}

/**

 * TODO

 * This will not work with multiple instances of the dataportal running

 * under the same host as there is only one session for all instances.

 * In case you switch instances with the same client, you will definitely

 * run into trouble.

 * Also this is not handling multiple secs.

 *

 *

 * returns the current secRef array from the users session.

 * If the according session variable is not jet set the default

 * as configured in the setting is used otherwise null.

 *

 * currentSecRef['uuid']

 * currentSecRef[....

 *

 * @return array

 */

function _cdm_dataportal_currentSecRef_array(){

    /*

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

     $secUuid = variable_get('cdm_secUuid_default', null);

     _cdm_dataportal_set_currentSecUuid($secUuid);

  }

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

  */

  //TODO setting the currentSecUuid causes problems in cichorieae in taraxacum, 

  //     thus it is temporary DISABLED

  // do not look in session but in database

  if( "DISABLED" != false || variable_get('cdm_currentSecRef', null) == null){

     $secUuid = variable_get('cdm_secUuid_default', null);

     _cdm_dataportal_set_currentSecUuid($secUuid);

  }

  return variable_get('cdm_currentSecRef', null);

}

/**

 * Check if a taxon is accepted by the current secundum

 *

 * @param TaxonTO $taxonTO

 * @return true if $taxonTo is accepted, false otherwise

 */

function _cdm_dataportal_acceptedByCurrentView($taxon){

  $current_secref = _cdm_dataportal_currentSecRef_array();

  return $taxon->class == "Taxon" && $current_secref->uuid == $taxon->sec->uuid;

}

/**

 * Truncates a $string to the specified $length. 

 * If the supplied string is equal to or shorter than the $legth the original is returend.

 * if an $appendix is defined the resulting string will have the specified $length including the $appendix.

 *

 * @param String $string	the string to truncate

 * @param Number $length	the maximun length

 * @param String $appendix	an optional appendix.

 *

 * @return the string

 */

function str_trunk(&$string, $length, $appendix=''){

  if(strlen($string) >= $length ){

    return  substr($string, 0, $length - strlen($appendix)).$appendix;

  } else {

    return $string;

  }

}

/**

 * @param string $str

 * @param string $sub

 * @return boolean

 */

function str_beginsWith( $str, $sub ) {

  return ( substr( $str, 0, strlen( $sub ) ) === $sub );

}

/**

 *

 * @param string $str

 * @param string $sub

 * @return boolean

 */

function str_endsWith( $str, $sub ) {

  return ( substr( $str, strlen( $str ) - strlen( $sub ) ) === $sub );

}

function array_replace_key($array, $replace_map){

  foreach($replace_map as $key=>$newkey){

    if(isset($array[$key])){

      $array[$newkey] = $array[$key];

      unset($array[$key]);

    }

  }

  return $array;

}

/**

 * Replaces all occurrences of space characters with 

 * an underscore and transforms the given

 * string to lowercase.

 *

 * @param String $string

 * @return the transformed string

 */

function generalizeString($string){

  return str_replace(' ', '_', strtolower($string));

}

function compose_url_prameterstr($parameters = array()){

  $pstr = '';

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

     $pstr .= ($pstr ? '&' :'').$key.'='.urlencode($value);

  }

  return $pstr;

}

function _get_feature_trees(){

   $feature_trees = array();

   // set tree that contains all features

   $feature_trees['0'] = 'No FeatureTree';

   // get features from database

   $pager = cdm_ws_page(CDM_WS_FEATURETREE, null, null);

   $persisted_trees = $pager->records;

   if(is_array($persisted_trees)){

     foreach($persisted_trees as $featureTree){

       $featureLabels = array();

       foreach ($featureTree->children as $featureNode){

         $featureLabels[] = $featureNode->feature->representation_L10n;

       }

       $feature_trees[$featureTree->uuid] = implode(", ", $featureLabels);

     }

   }

   return $feature_trees;

}