EDIT

<?php

/**

 * @file

 * Search related functions.

 */

 * Returns a Drupal path to a search form for a CDM webservice.

 *

 * For a given CDM webservice end-point, the drupal page path to the

 * according search form is returned.

 * cdm webservice end points are defined in constant variables like:

 * <code>CDM_WS_PORTAL_TAXON_FIND</code> and

 * <code>CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT</code>

 *

 * @param string $ws_endpoint

 *   The cdm webservice endpoint for which to find the search form path.

 *

 * @return string

 *   The Drupal path found.

 */

function cdm_dataportal_search_form_path_for_ws($ws_endpoint) {

  static $form_ws_map = array(

    CDM_WS_PORTAL_TAXON_FIND => "cdm_dataportal/search",

  );

  return $form_ws_map[$ws_endpoint];

}

/**

 * Prepares a form array for a general purpose search form.

 *

 * The form is used for general purpose search functionality in the

 * which holds the query term.

 *

 * @param string $action_path

 *   The Drupal path to be put into the action url to which the form will

 *   be submitted.

 * @param string $search_webservice

 *   The cdm-remote webservice to be used, valid values are defined by

 *   the constants: FIXME.

 * @param string $query_field_default_value

 * @return array

 *   The prepared form array.

 */

  $form['#action'] = url($action_path, array(

    'absolute' => TRUE,

  ));

  $form['ws'] = array(

    '#type' => 'hidden',

    '#value' => $search_webservice,

    '#name' => 'ws',

  );

  $form['query'] = array(

    '#weight' => 0,

    '#type' => 'textfield',

    '#size' => 68,

    // This is wanted behaviour for the simple seach but could

      'title' => $query_field_description,

    ),

    '#description' => $query_field_description,

    '#value' => $query_field_default_value,

    // '#description' => $query_field_description,

  );

    '#tree' => TRUE,

  );

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

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

    $form['search']['q'] = array(

      '#type' => 'hidden',

      '#value' => $action_path,

      '#name' => 'q',

    );

  }

  $form['submit'] = array(

    '#weight' => 5,

    '#type' => 'submit',

    '#name' => '',

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

  );

  return $form;

}

  $queryParams = array();

    $classificationUuid = $_SESSION['cdm']['taxonomictree_uuid'];// if no classification uuid is set use the current one

  }

  if($classificationUuid){

    $queryParams['classificationUuid'] = $classificationUuid;

  if($areaUuid){

    $queryParams['area'] = $areaUuid;

  }

  if($status){

    $queryParams['status'] = $status ;

  }

  $queryParams['doSynonyms'] = true;

  $queryParams['doMisappliedNames'] = true;

  $queryParams['doTaxaByCommonNames'] = true;

  $search_results = cdm_ws_get(CDM_WS_TAXON_SEARCH, NULL, queryString($queryParams));

  foreach($search_results->records as $record){

      $titleCache = $record->entity->titleCache;

  drupal_json_output($matches);

}

  /**

 *

 * @param bool $advanced_form

  $query_field_default_value = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');

  else {

  }

  $form = cdm_dataportal_search_form_prepare(

    'cdm_dataportal/search/results/taxon',

    $search_service_endpoint,

    $query_field_default_value,

    t('Enter the name or part of a name you wish to search for.

  }

  $form['search']['pageSize'] = array(

    '#weight' => -1,

    '#type' => 'hidden',

    '#value' => variable_get('cdm_dataportal_search_items_on_page', 25),

  );

  $form['search']['pageNumber'] = array(

    '#weight' => -1,

    '#type' => 'hidden',

    '#value' => 0,

  );

    CDM_SEARCH_TAXA_MODE,

    CDM_SEARCH_TAXA_MODE_DEFAULT

  );

  $preset_do_taxa = $search_taxa_mode_settings['doTaxa'] !== 0;

  $preset_do_synonyms = $search_taxa_mode_settings['doSynonyms'] !== 0;

  $preset_do_taxa_by_common_names = $search_taxa_mode_settings['doTaxaByCommonNames'] !== 0;

  $preset_do_misapplied_names = $search_taxa_mode_settings['doMisappliedNames'] !== 0;

    // Overwrite presets by user choice stored in session.

      $preset_do_synonyms = (isset($_SESSION['cdm']['search']['doSynonyms']) ? 1 : 0);

      $preset_do_misapplied_names = (isset($_SESSION['cdm']['search']['doMisappliedNames']) ? 1 : 0);

      $preset_do_taxa_by_common_names = (isset($_SESSION['cdm']['search']['doTaxaByCommonNames']) ? 1 : 0);

        $preset_classification_uuid = $_SESSION['cdm']['search']['tree'];

      }

        '#weight' => 1,

        '#type' => 'select',

    $form['search']['doTaxa'] = array(

      '#weight' => 2,

      '#type' => 'checkbox',

    $form['search']['doSynonyms'] = array(

      '#weight' => 3,

      '#type' => 'checkbox',

    $form['search']['doMisappliedNames'] = array(

      '#weight' => 4,

      '#type' => 'checkbox',

    $form['search']['doTaxaByCommonNames'] = array(

      '#weight' => 5,

      '#type' => 'checkbox',

      CDM_WS_DESCRIPTION_NAMEDAREAS_IN_USE,

      array('includeAllParents' => 'true')

    );

    $mixed_vocabularies = array();

    // Build hierarchy of the terms regardless of the vocabulary.

      if (!empty($term_dto->partOfUuid)) {

        // Children.

        $parent =& $term_map[$term_dto->partOfUuid];

        if ($parent) {

          if (!isset($parent->children)) {

            $parent->children = array();

          if ($parent->vocabularyUuid != $term_dto->vocabularyUuid) {

            $mixed_vocabularies[$parent->vocabularyUuid] = $parent->vocabularyUuid;

        // group root nodes by vocabulary

        if (!isset($term_tree[$term_dto->vocabularyUuid])) {

          $term_tree[$term_dto->vocabularyUuid] = array();

        }

        $term_tree[$term_dto->vocabularyUuid][$term_dto->uuid] = $term_dto;

      }

    }

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

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

      });

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

        '#type' => 'fieldset',

        '#title' => t('Filter by distribution areas'),

        '#description' => t('The search will return taxa having distribution

        '#type' => 'textfield',

        '#description' => t('Type to filter the areas listed below.'),

      );

      $vocab_cnt = 0;

      $areas_defaults = array();

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

        $areas_defaults = explode(',', $_SESSION['cdm']['search']['area']);

      }

        $vocabulary = cdm_ws_get(CDM_WS_TERMVOCABULARY, array($vocab_uuid));

        $areas_options = term_tree_as_options($term_dto_tree);

        $form['search']['areas']['area'][$vocab_cnt++] = array(

          '#prefix' => '<strong>' . $vocabulary->representation_L10n

            . (isset($mixed_vocabularies[$vocab_uuid]) ? ' <span title="Contains terms of at least one other area vocabulary.">(' . t('mixed') . ')</span>': '')

          '#default_value' => $areas_defaults,

          '#options' => $areas_options,

      }

  else {

    //

    $form['search']['doTaxa'] = array(

      '#weight' => -2,

      '#type' => 'hidden',

    $form['search']['doSynonyms'] = array(

      '#weight' => -3,

      '#type' => 'hidden',

    $form['search']['doMisappliedNames'] = array(

      '#weight' => -4,

      '#type' => 'checkbox',

      '#title' => t('Misapplied names'),

    $form['search']['doTaxaByCommonNames'] = array(

      '#weight' => -5,

      '#type' => 'hidden',

  }

  return $form;

}

 *

 * This function makes ot possible possible to just pass the

 * correct $form_id 'cdm_dataportal_search_taxon_form_advanced' to

 * drupal_get_form like:

 * drupal_get_form('cdm_dataportal_search_taxon_form_advanced');

 *

 * @param array $form

 *   A drupal form array

 * @param array $form_state

 *   The drupal form state passed as reference

 *

 * @return array

 *   The form array

function cdm_dataportal_search_taxon_form_advanced($form, &$form_state) {

  return cdm_dataportal_search_taxon_form($form, $form_state, TRUE);

}

/**

function cdm_dataportal_search_taxon_by_description_form() {

  $query_field_default_value = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');

  $form = cdm_dataportal_search_form_prepare(

    CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT,

    $query_field_default_value,

    t("Enter the text you wish to search for. The asterisk character * can be

      array(

        '!link' => l(

          t('Apache Lucene - Query Parser Syntax'),

          'http://lucene.apache.org/core/old_versioned_docs/versions/2_9_1/queryparsersyntax.html', array(

            'attributes' => array(

              'absolute' => TRUE,

              'html' => TRUE),

          )

        ),

      )

  $form['search']['tree'] = array(

    '#weight' => -1,

    '#type' => 'hidden',

  $form['search']['hl'] = array(

    '#weight' => -1,

    '#type' => 'hidden',

    '#value' => 1,

  );

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

  }

  if (module_exists("user") && user_access('administer')) {

    $form['search']['clazz'] = array(

      '#type' => 'select',

      '#options' => cdm_descriptionElementTypes_as_option(TRUE),

    );

  }

  $feature_options = _featureTree_nodes_as_feature_options($profile_feature_tree->root);

    $form['search']['features'] = array(

      '#type' => 'checkboxes',

      '#title' => t('Limit to selected features'),

      '#default_value' => $_SESSION['cdm']['search']['features'],

      '#options' => $feature_options,

    );

  }

  else {

    $form['search']['features'] = array(

      '#type' => 'checkboxes',

      '#title' => t('Limit to selected features'),

      '#options' => $feature_options,

    );

  }

  return $form;

}

/**

 *

 * Reads the query parameters from $_REQUEST and modifies and adds additional

 *  - Filters $_REQUEST by a list of valid request parameters

 *  - modifies geographic_range parameters

 *  - adds taxon tree uuid if it is missing and if it should not be

 *    ignored (parameter value = 'IGNORE')

 *  - and more

 *

 *    The web service endpoint which will be used for executing the search.

 *    Usually one of CDM_WS_PORTAL_TAXON_SEARCH, CDM_WS_PORTAL_TAXON_FIND,

 *    CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT.

 *   also stores them in $_SESSION['cdm']['search']

  }

  if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {

    $form_params = array_merge($form_params, $_REQUEST['pager']);

  }

  // Split of geographic range.

    $area_filter_preset = explode(',', variable_get(CDM_SEARCH_AREA_FILTER_PRESET, ''));

  }

    $area_uuids = $area_filter_preset;

  }

  elseif (isset($_REQUEST['search']['areas']['area']) && is_array($_REQUEST['search']['areas']['area'])) {

      $area_uuids = array_merge($area_uuids, $areas);

    }

    $presence_terms_options = cdm_vocabulary_as_option(UUID_PRESENCE_ABSENCE_TERM, null, FALSE, array('absenceTerm' => '/false/'));

    $presence_term_uuids = array_keys($presence_terms_options);

    $form_params['status'] = $presence_term_uuids;

  // so we add it here from what is stored in the session unless

  if (!isset($form_params['tree']) && !variable_get(SIMPLE_SEARCH_IGNORE_CLASSIFICATION, 0)) {

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

  // ----------- further processing that must not be store in the session --------- //

    $form_params['query'] = str_replace('.', '*', $form_params['query']);

    if(preg_match("/\s+/", $form_params['query'])){

      if(!str_beginsWith($form_params['query'], '"')){

        $form_params['query'] = '"' . $form_params['query'];

      }

      if(!str_endsWith($form_params['query'], '"')){

        $form_params['query'] = $form_params['query'] . '"' ;

      }

  }

  // cdm service.

  if (isset($form_params['tree'])

    && ($form_params['tree'] == 'NONE' || !is_uuid($form_params['tree']))

  ) {

    // $form_params['ignore_classification'] =  TRUE;

  }

  //   $form_params['ignore_classification'] =  NULL;

  // }

  return $form_params;

}

 *

 *   the CDM classification instance which has been used a filter for the

 *   last processed search

 *   or NULL, it it was on all classifications

function cdm_dataportal_searched_in_classification() {

  $classification = &drupal_static(__FUNCTION__);

  if (!isset($classification)) {

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

      $classification = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY, ($_SESSION['cdm']['search']['tree']));

    else {

    }

  }

 * Removed the drupal internal form parameters 'form_id', 'form_token', 'form_build_id' from the request array.

 *

 * @param $request array

 *   Pass $_REQUEST as paramter

 * @return array

 *  The $request array without drupal internal form parameters

 */

function remove_drupal_form_params($request) {

  static $exclude_keys = array('form_id', 'form_token', 'form_build_id');

  $request_sanitized = array();

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

    if(!array_search($key, $exclude_keys)){

      $request_sanitized[$key] = $value;

    }

  }

  return $request_sanitized;

}

 * The parameters to build the query are taken obtained by calling

 *

  // Store as last search in session.

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

  // Validate the search webservice parameter:

    drupal_set_message(

  }

  }

  // parameters if necessary.

  return $taxon_pager;

}

/**

 * Sends a request to search for registrations to the cdm server.

 */

function cdm_dataportal_search_registrations_execute()

{

  static $query_param_map = array(

    'identifier' => 'identifierFilterPattern',

    'taxon_name'=> 'taxonNameFilterPattern',

    'type_designation_status' => 'typeDesignationStatusUuids',

  );

  // Read the query parameters from $_REQUEST and add additional query

  // parameters if necessary.

  $request_params = array();

  $request = remove_drupal_form_params($_REQUEST);

  if(count($request) > 0){

    $_SESSION['cdm'][SESSION_KEY_SEARCH_REGISTRATION_FILTER] = $request;

    foreach ($query_param_map as $filter_key => $query_param){

      if (isset($request[$filter_key])) {

        $request_params[$query_param] = $request[$filter_key];