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

 *   A default text for the query field

 * @param string $query_field_description

 *   The description text for the query field

 * @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,

  );

  if(variable_get('cdm_dataportal_taxon_auto_suggest')){

      $form['query']['#autocomplete_path'] = 'cdm_dataportal/taxonSearch/autocomplete';

  }

    $form['search'] = array(

    '#weight' => 3,

    '#tree' => TRUE,

    // '#type' => $advanced_form ? '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;

}

function cdm_dataportal_taxon_search_autocomplete($string) {

  $matches = array();

  $queryParams = array();

  $queryParams['query'] = $string."*";

  $queryParams['pageNumber'] = '0';

  $queryParams['pageSize'] = '100';

  $queryParams['doTaxa'] = true;

  $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;

      preg_match('/(.*) sec.*/', $titleCache, $trimmedTitle); //remove sec reference

      $trimmedTitle = trim($trimmedTitle[1]);

      $matches[$trimmedTitle] = $trimmedTitle;

  }

  drupal_json_output($matches);

}

  /**

 * Creates a search form for searching on taxa.

 *

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

 *

 * @param array $form

 *   A drupal form array

 * @param array $form_state

 *   The drupal form state passed as reference

 * @param bool $advanced_form

 *   default is FALSE

 * @param bool $classification_select

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

 *   if only available in the advanced mode

 *

 * @return array

 *   the form array

 */

function cdm_dataportal_search_taxon_form($form, &$form_state, $advanced_form = FALSE, $classification_select = TRUE) {

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

  if ($advanced_form || 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 be used as wildcard, but must not be used as first character.'),

      NULL

  );

  if (!$advanced_form) {

    $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_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;

  if ($advanced_form) {

    // --- ADVANCED SEARCH FORM ---

    //

    // Get presets from settings.

    $preset_classification_uuid = get_current_classification_uuid();

    // Overwrite presets by user choice stored in session.

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

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

      $preset_do_synonyms = (isset($_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);

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

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

      }

    }

    if ($classification_select === TRUE) {

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

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

        '#weight' => 1,

        '#type' => 'select',

        '#default_value' => get_current_classification_uuid(),

        '#options' => cdm_get_taxontrees_as_options(TRUE),

        '#description' => t('A filter to limit the search to a specific classification. Choosing <em>--- ALL ---</em> will disable this filter.'),

      );

    }

    // General search parameters.

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

      '#weight' => 2,

      '#type' => 'checkbox',

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

      '#value' => $preset_do_taxa,

    );

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

      '#weight' => 3,

      '#type' => 'checkbox',

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

      '#value' => $preset_do_synonyms,

    );

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

      '#weight' => 4,

      '#type' => 'checkbox',

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

      '#value' => $preset_do_misapplied_names,

    );

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

      '#weight' => 5,

      '#type' => 'checkbox',

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

      '#value' => $preset_do_taxa_by_common_names,

    );

    $area_term_dtos = cdm_ws_fetch_all(

      CDM_WS_DESCRIPTION_NAMEDAREAS_IN_USE,

      array('includeAllParents' => 'true')

    );

    // create map: term_uuid => term

    $term_map = array();

    foreach ($area_term_dtos as $term_dto) {

      $term_map[$term_dto->uuid] = $term_dto;

    }

    $term_tree = array();

    // mixed_vocabularies will contain the uuid vocabularies which

    // also contain terms of foreign vocabularies due to the term

    // hierarchy

    $mixed_vocabularies = array();

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

    foreach ($term_map as $term_dto) {

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

        // Children.

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

        if ($parent) {

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

            $parent->children = array();

          }

          $parent->children[$term_dto->uuid] = $term_dto;

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

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

          }

        }

      }

      else {

        // 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;

      }

    }

    $show_area_filter = ! variable_get(CDM_SEARCH_AREA_FILTER_PRESET, '');

    if($show_area_filter){

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

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

        jQuery(\'#edit-search-areas\').search_area_filter(\'#edit-search-areas-areas-filter\');

      });

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

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

        '#type' => 'fieldset',

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

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

        information for at least one of the selected areas.') . ' '

          .(count($term_tree) > 1 ? t('The areas are grouped

        by the vocabularies to which the highest level areas belong.') : ''),

      );

      $form['search']['areas']['areas_filter'] = array(

        '#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']);

      }

      foreach ($term_tree as $vocab_uuid => $term_dto_tree) {

        $vocabulary = cdm_ws_get(CDM_WS_TERMVOCABULARY, array($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>': '')

            . '</strong>',

          '#type' => 'checkboxes',

          '#default_value' => $areas_defaults,

          '#options' => $areas_options,

        );

      }

    }

  }

  else {

    // --- SIMPLE SEARCH FORM ---

    //

    // Overwrite presets by user choice stored in session.

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

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

    }

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

      '#weight' => -2,

      '#type' => 'hidden',

      '#value' => $preset_do_taxa,

    );

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

      '#weight' => -3,

      '#type' => 'hidden',

      '#value' => $preset_do_synonyms,

    );

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

      '#weight' => -4,

      '#type' => 'checkbox',

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

      '#value' => $preset_do_misapplied_names,

    );

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

      '#weight' => -5,

      '#type' => 'hidden',

      '#value' => $preset_do_taxa_by_common_names,

    );

  }

  return $form;

}

/**

 * Wrapper function for cdm_dataportal_search_taxon_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);

}

/**

 * Form for 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, but must not be used as first character. Terms can be combined with 'AND'. To search for a

        full phrase enclose the terms in parentheses. For more syntactical

        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_current_classification_uuid(),

  );

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

    '#weight' => -1,

    '#type' => 'hidden',

    '#value' => 1,

  );

  // Only available 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 description item type'),

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

      '#options' => cdm_descriptionElementTypes_as_option(TRUE),

    );

  }

  $profile_feature_tree = get_profile_feature_tree();

  $feature_options = _featureTree_nodes_as_feature_options($profile_feature_tree->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;

}

/**

 * Processes the query parameters of the search 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 array

 *   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['areas']);

  $area_filter_preset = null;

  if (variable_get(CDM_SEARCH_AREA_FILTER_PRESET, '')) {

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

  }

  $area_uuids = array();

  if($area_filter_preset){

    $area_uuids = $area_filter_preset;

  }

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

    foreach ($_REQUEST['search']['areas']['area'] as $areas) {

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

    }

  }

  if(count($area_uuids) > 0){

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

  }

  // 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, 0)) {

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

  }

  // 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 to 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 object

 *   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'])) {

    drupal_set_message(

      t("Invalid search webservice parameter 'ws' given"), 'warning'

    );

    return NULL;

  }

  if (!cdm_dataportal_search_form_path_for_ws($_REQUEST['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 necessary.

  $request_params = cdm_dataportal_search_form_request();

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

  return $taxon_pager;

}

/**

 * Transforms the termDTO tree into options array.

 *

 *   TermDto:

 *      - partOfUuid:

 *      - representation_L10n:

 *      - representation_L10n_abbreviatedLabel:

 *      - uuid:

 *      - vocabularyUuid:

 *      - children: array of TermDto

 *

 * The options array is suitable for drupal form API elements that

 * allow multiple choices.

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

 *

 * @param array $term_dto_tree

 *   a hierarchic array of CDM TermDto instances, with additional

 * 'children' field:

 * @param array $options

 *   Internally used for recursive calls

 * @param string $prefix

 *   Internally used for recursive calls

 *

 * @return array

 *   the terms in an array as options for a form element that allows

 *   multiple choices.

 */

function term_tree_as_options($term_dto_tree, &$options = array(), $prefix = '') {

  foreach ($term_dto_tree as $uuid => $dto) {

    $label = $prefix . '<span class="child-label">'

      .  $dto->representation_L10n

      . '</span><span class="child-label-abbreviated"> (' . $dto->representation_L10n_abbreviatedLabel . ')</span>';

    $options[$uuid] = $label;

    if (isset($dto->children) && is_array($dto->children)) {

      uasort($dto->children, 'compare_terms_by_representationL10n');

      term_tree_as_options(

        $dto->children,

        $options, $prefix

          . '<span data-cdm-parent="' . $uuid . '" class="parent"></span>');

    }

  }

  return $options;

}