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",

    CDM_WS_PORTAL_TAXON_SEARCH => "cdm_dataportal/search",

    CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT => "cdm_dataportal/search/taxon_by_description",

  );

  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

 * dataportal. The form returned is populated with all nessecary fields

 * for internal processing and has the textfield element $form['query']

 * which holds the query term.

 * he sub tree array can be extended to contain additional search parameters.

 *

 * @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

 * @param string $query_field_description

 * @param string $process

 *   The value for #process, if NULL (default), 'cdm_dataportal_search_process'

 *   is used.

 *

 * @return array

 *   The prepared form array.

 */

function cdm_dataportal_search_form_prepare($action_path, $search_webservice, $query_field_default_value, $query_field_description, $process = NULL) {

  if ($process == NULL) {

    $process = 'cdm_dataportal_search_process';

  }

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

  /*

  $form['#process'] = array(

    $process => 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 causes the description to display also when hovering over

    // the textfield.

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

    // be disabled for the advances search

    '#attributes' => array(

      'title' => $query_field_description,

    ),

    '#description' => $query_field_description,

    '#value' => $query_field_default_value,

    // '#description' => $query_field_description,

  );

  $form['search'] = array(

    '#weight' => 3,

    '#tree' => TRUE,

    // '#type' => $advancedForm ? 'fieldset': 'hidden',

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

  );

  // 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;

}

/**

 * Creates a search form for searching on taxa.

 *

 * If advanced $advancedForm id TRUE the form will offer additional choices

 *

 * @param array $form

 * @param array $form_state

 * @param bool $advancedForm

 *   default is FALSE

 * @param bool $classificationSelect

 *   set TRUE to offer a classifiaction selector in the form - default is FALSE

 *   if only available in the advanced mode

 *

 * @return

 *   the form array

 *

 */

function cdm_dataportal_search_taxon_form($form, &$form_state, $advancedForm = FALSE, $classificationSelect = TRUE) {

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

  if ($advancedForm || variable_get(SIMPLE_SEARCH_USE_LUCENE_BACKEND, FALSE)) {

    $search_service_endpoint = CDM_WS_PORTAL_TAXON_SEARCH;

  } else {

    $search_service_endpoint = CDM_WS_PORTAL_TAXON_FIND;

  }

  $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.

      The asterisk  character * can always be used as wildcard.'),

      NULL

  );

  if (!$advancedForm){

    $form['query']['#size'] = 20;

  }

  $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,

  );

  $search_taxa_mode_settings = get_array_variable_merged(CDM_SEARCH_TAXA_MODE, CDM_SEARCH_TAXA_MODE_DEFAULT);

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

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

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

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

  if ($advancedForm) {

    // --- ADVANCED SEARCH FORM ---

    //

    // Get presets from settings.

    $preset_classification_uuid = get_taxonomictree_uuid_selected();

    // Overwrite presets by user choice stored in session.

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

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

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

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

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

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

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

      }

    }

   if ($classificationSelect === TRUE) {

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

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

        '#weight' => 1,

        '#type' => 'select',

        '#default_value' => get_taxonomictree_uuid_selected(),

        '#options' => cdm_get_taxontrees_as_options(TRUE),

        '#description' => t('A filter to limit the search to a specific classification. Choosing <em>-- None --</em> will disable this filter.'),

      );

   }

    // General search parameters.

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

      '#weight' => 2,

      '#type' => 'checkbox',

      '#title' => t('Search for accepted taxa'),

      '#value' => $preset_doTaxa,

    );

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

      '#weight' => 3,

      '#type' => 'checkbox',

      '#title' => t('Search for synonyms'),

      '#value' => $preset_doSynonyms,

    );

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

      '#weight' => 4,

      '#type' => 'checkbox',

      '#title' => t('Search for misapplied names'),

      '#value' => $preset_doMisappliedNames,

    );

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

      '#weight' => 5,

      '#type' => 'checkbox',

      '#title' => t('Search for common names'),

      '#value' => $preset_doTaxaByCommonNames,

    );

    $areas_options = cdm_terms_as_options(cdm_ws_fetch_all(CDM_WS_DESCRIPTION_NAMEDAREAS_IN_USE));

    $areas_defaults = array();

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

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

    }

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

      '#type' => 'checkboxes',

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

      '#default_value' =>  $areas_defaults,

      '#options' => $areas_options,

      '#description' => t('Check one or multiple areas to filter by distribution.'),

    );

  } else {

    // --- SIMPLE SEARCH FORM ---

    //

    // Overwrite presets by user choice stored in session.

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

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

    }

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

      '#weight' => -2,

      '#type' => 'hidden',

      '#value' => $preset_doTaxa,

    );

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

      '#weight' => -3,

      '#type' => 'hidden',

      '#value' => $preset_doSynonyms,

    );

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

      '#weight' => -4,

      '#type' => 'checkbox',

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

      '#value' => $preset_doMisappliedNames,

    );

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

      '#weight' => -5,

      '#type' => 'hidden',

      '#value' => $preset_doTaxaByCommonNames,

    );

  }

  return $form;

}

/**

 * @todo Please document this function.

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

 */

function cdm_dataportal_search_taxon_form_advanced($form, &$form_state) {

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

}

/**

 * Search form for the searching taxa by the findByDescriptionElementFullText

 * rest service.

 */

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_dataportal/search/results/taxon',

      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

        used as wildcard. Terms can be combined with 'AND'. To search for a

        full phrase enclose the terms in parentheses. For more syntactial

        options please refer to the !link.", 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))),

        )),

      NULL

      );

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

    '#weight' => -1,

    '#type' => 'hidden',

    '#value' => get_taxonomictree_uuid_selected(),

  );

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

    '#weight' => -1,

    '#type' => 'hidden',

    '#value' => 1,

  );

  // Only avaiable to admins:

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

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

  }

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

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

      '#type' => 'select',

      '#title' => t('Limit to DescriptionElement type'),

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

      '#options' => cdm_descriptionElementTypes_as_option(TRUE),

    );

  }

  /*

  see cdm_get_featureTrees_as_options() ... $treeRepresentation =

  $featureTree->titleCache; if(is_array($featureTree->root->childNodes) &&

  count($featureTree->root->childNodes) > 0){ // render the hierarchic tree

  structure $treeDetails = '<div class="featuretree_structure">'

  //.cdm_featureTree_elements_toString($featureTree->root)

  .theme('featureTree_hierarchy', $featureTree->uuid) .'</div>'; $form =

  array(); $form['featureTree-'.$featureTree->uuid] = array( '#type' =>

  'fieldset', '#title' => t('Show details'), '#collapsible' => TRUE,

  '#collapsed' => TRUE, );

  $form['featureTree-'.$featureTree->uuid]['details'] =

  array('#value'=>$treeDetails); $treeRepresentation .= drupal_render($form);

  */

  $profile_featureTree = get_profile_feature_tree();

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

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

    $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 query parameters if nessecary.

 *

 *  - 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

 *

 *

 * @return

 *   the processed request parameters submitted by the search form and

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

 */

function cdm_dataportal_search_form_request() {

  $form_params = array();

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

    array_deep_copy($_REQUEST['search'], $form_params);

  }

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

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

  }

  $form_params['query'] = trim($_REQUEST['query']);

  // --- handle geographic range

  // Split of geographic range.

  unset($form_params['area']);

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

    $form_params['area'] = implode(',', $_REQUEST['search']['area']);

  }

  // simple search will not submit a 'tree' query parameter, so we add it here from

  // what is stored in the session unless 'simple_search_ignore_classification'

  // is checked in the settings

  if (!isset($form_params['tree']) && !variable_get('simple_search_ignore_classification', 1)) {

    $form_params['tree'] = get_taxonomictree_uuid_selected();

  }

  // if the 'NONE' classification has been chosen (adanced search) delete the tree information

  // to avoid unknown uuid exceptions in the cdm service

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

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

    unset($form_params['tree']);

  }

//   else {

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

//   }

  // Store in session.

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

  return $form_params;

}

/**

 * Provides the classification ti which the last search has been limited to..

 *

 * This function should only be used after the cdm_dataportal_search_execute() handler has been run,

 * otherwise it will return the infomation from the last search executed. The information is retrieved from

 * the $_SESSION variable:  $_SESSION['cdm']['search']['tree']

 *

 * @return

 *    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 {

      $classification = FALSE;

    }

  }

  return $classification !== FALSE ?  $classification : NULL;

}

/**

 * Removes Drupal internal form elements from query.

 */

function cdm_dataportal_search_process($form, &$form_state) {

  unset($form['form_id']);

  unset($form['form_token']);

  return $form;

}

/**

 * Sends a search request at the cdm web server.

 *

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

 * cdm_dataportal_search_form_request() which reads the query parameters

 * from $_REQUEST and add additional query parameters if nessecary.

 *

 * @see cdm_dataportal_search_form_request()

 *

 */

function cdm_dataportal_search_execute() {

  // Store as last search in session.

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

  // Validate the search webservice parameter:

  if (!isset($_REQUEST['ws'])) {// Check is ws.

    // Endpoint is unknown.

    drupal_set_message(t('webservice parameter \'ws\' missing'), 'warning');

    return NULL;

  }

  if (!cdm_dataportal_search_form_path_for_ws($_REQUEST['ws'])) {// Check is ws.

    // Endpoint is unknown.

    drupal_set_message(t('Invalid search webservice parameter  \'ws\' given'), 'warning');

    return NULL;

  }

  // read the query parameters from $_REQUEST and add additional query parameters if nessecary.

  $request_params = cdm_dataportal_search_form_request();

  $taxonPager = cdm_ws_get($_REQUEST['ws'], NULL, queryString($request_params));

  return $taxonPager;

}