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<?php
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/**
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* @file
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* Search related functions.
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*/
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const SESSION_KEY_SEARCH_REGISTRATION_FILTER = "SESSION_KEY_SEARCH_REGISTRATION_FILTER";
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const SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER = 'SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER';
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const SESSION_KEY_SEARCH_AGENT_FILTER = 'SEARCH_AGENT_FILTER';
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/**
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* Returns a Drupal path to a search form for a CDM webservice.
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*
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* For a given CDM webservice end-point, the drupal page path to the
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* according search form is returned.
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* cdm webservice end points are defined in constant variables like:
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* <code>CDM_WS_PORTAL_TAXON_FIND</code> and
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* <code>CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT</code>
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*
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* @param string $ws_endpoint
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* The cdm webservice endpoint for which to find the search form path.
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*
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* @return string
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* The Drupal path found.
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*/
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function cdm_dataportal_search_form_path_for_ws($ws_endpoint) {
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static $form_ws_map = array(
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CDM_WS_PORTAL_TAXON_FIND => "cdm_dataportal/search",
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CDM_WS_PORTAL_TAXON_SEARCH => "cdm_dataportal/search",
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CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT => "cdm_dataportal/search/taxon_by_description",
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);
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return $form_ws_map[$ws_endpoint];
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}
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/**
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* Prepares a form array for a general purpose search form.
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*
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* The form is used for general purpose search functionality in the
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* dataportal. The form returned is populated with all necessary fields
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* for internal processing and has the textfield element $form['query']
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* which holds the query term.
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*
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* @param string $action_path
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* The Drupal path to be put into the action url to which the form will
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* be submitted.
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* @param string $search_webservice
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* The cdm-remote webservice to be used, valid values are defined by
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* the constants: FIXME.
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* @param string $query_field_default_value
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* A default text for the query field
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* @param string $query_field_description
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* The description text for the query field
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*
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* @return array
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* The prepared form array.
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*/
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function cdm_dataportal_search_form_prepare($action_path, $search_webservice, $query_field_default_value, $query_field_description) {
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$form['#method'] = 'get';
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$form['#action'] = url($action_path, array(
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'absolute' => TRUE,
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));
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$form['ws'] = array(
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'#type' => 'hidden',
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'#value' => $search_webservice,
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'#name' => 'ws',
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);
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$form['query'] = array(
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'#weight' => 0,
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'#type' => 'textfield',
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'#size' => 68,
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// This causes the description to display also when hovering over
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// the textfield.
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// This is wanted behaviour for the simple seach but could
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// be disabled for the advances search.
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'#attributes' => array(
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'title' => $query_field_description,
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),
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'#description' => $query_field_description,
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'#value' => $query_field_default_value,
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// '#description' => $query_field_description,
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);
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if(variable_get(SIMPLE_SEARCH_AUTO_SUGGEST)){
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$form['query']['#autocomplete_path'] = 'cdm_dataportal/taxon/autosuggest////';
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}
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$form['search'] = array(
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'#weight' => 3,
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'#tree' => TRUE,
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// '#type' => $advanced_form ? 'fieldset': 'hidden',
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'#title' => t('Options'),
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);
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// Clean URL get forms breaks if we don't give it a 'q'.
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if (!(bool) variable_get('clean_url', '0')) {
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$form['search']['q'] = array(
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'#type' => 'hidden',
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'#value' => $action_path,
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'#name' => 'q',
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);
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}
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$form['submit'] = array(
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'#weight' => 5,
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'#type' => 'submit',
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'#name' => '',
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'#value' => t('Search'),
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);
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return $form;
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}
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function cdm_dataportal_taxon_autosuggest($classificationUuid = NULL, $areaUuid = NULL, $status = NULL, $string) {
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$matches = array();
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$queryParams = array();
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$queryParams['query'] = $string.'*';
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if((is_null($classificationUuid) || $classificationUuid=='') && isset($_SESSION['cdm']['taxonomictree_uuid'])){
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$classificationUuid = $_SESSION['cdm']['taxonomictree_uuid'];// if no classification uuid is set use the current one
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}
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if($classificationUuid){
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$queryParams['classificationUuid'] = $classificationUuid;
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}
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if($areaUuid){
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$queryParams['area'] = $areaUuid;
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}
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if($status){
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$queryParams['status'] = $status ;
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}
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$queryParams['pageNumber'] = '0';
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$queryParams['pageSize'] = '10';
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$queryParams['doTaxa'] = true;
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$queryParams['doSynonyms'] = true;
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$queryParams['doMisappliedNames'] = true;
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$queryParams['doTaxaByCommonNames'] = true;
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$search_results = cdm_ws_get(CDM_WS_TAXON_SEARCH, NULL, queryString($queryParams));
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foreach($search_results->records as $record){
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$titleCache = $record->entity->titleCache;
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preg_match('/(.*) sec.*/', $titleCache, $trimmedTitle); //remove sec reference
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$trimmedTitle = trim($trimmedTitle[1]);
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$matches[$trimmedTitle] = check_plain($trimmedTitle);
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}
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drupal_json_output($matches);
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}
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/**
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* Creates a search form for searching on taxa.
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*
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* If advanced $advanced_form id TRUE the form will offer additional choices
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*
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* @param array $form
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* A drupal form array
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* @param array $form_state
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* The drupal form state passed as reference
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* @param bool $advanced_form
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* default is FALSE
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* @param bool $classification_select
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* set TRUE to offer a classification selector in the form - default is FALSE
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* if only available in the advanced mode
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*
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* @return array
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* the form array
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*/
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function cdm_dataportal_search_taxon_form($form, &$form_state, $advanced_form = FALSE, $classification_select = TRUE)
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{
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if ($form_state['build_info']['form_id'] == 'cdm_dataportal_search_blast_form') {
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$form = cdm_dataportal_search_blast_form($form, $form_state);
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} else {
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$query_field_default_value = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');
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if ($advanced_form || variable_get(SIMPLE_SEARCH_USE_LUCENE_BACKEND, FALSE)) {
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$search_service_endpoint = CDM_WS_PORTAL_TAXON_SEARCH;
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} else {
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$search_service_endpoint = CDM_WS_PORTAL_TAXON_FIND;
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}
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$form = cdm_dataportal_search_form_prepare(
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'cdm_dataportal/search/results/taxon',
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$search_service_endpoint,
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$query_field_default_value,
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t('Enter the name or part of a name you wish to search for.
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The asterisk character * can be used as wildcard, but must not be used as first character.')
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);
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}
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if (!$advanced_form) {
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$form['query']['#size'] = 20;
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}
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$form['search']['pageSize'] = array(
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'#weight' => -1,
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'#type' => 'hidden',
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'#value' => variable_get(CDM_SEARCH_RESULT_PAGE_SIZE, CDM_SEARCH_RESULT_PAGE_SIZE_DEFAULT),
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);
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$form['search']['pageNumber'] = array(
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'#weight' => -1,
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'#type' => 'hidden',
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'#value' => 0,
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);
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$search_taxa_mode_settings = get_array_variable_merged(
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CDM_SEARCH_TAXA_MODE,
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CDM_SEARCH_TAXA_MODE_DEFAULT
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);
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$preset_do_taxa = $search_taxa_mode_settings['doTaxa'] !== 0;
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$preset_do_synonyms = $search_taxa_mode_settings['doSynonyms'] !== 0;
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$preset_do_taxa_by_common_names = $search_taxa_mode_settings['doTaxaByCommonNames'] !== 0;
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$preset_do_misapplied_names = $search_taxa_mode_settings['doMisappliedNames'] !== 0;
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if ($advanced_form) {
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// --- ADVANCED SEARCH FORM ---
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//
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// Get presets from settings.
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$preset_classification_uuid = get_current_classification_uuid();
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// Overwrite presets by user choice stored in session.
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if (isset($_SESSION['cdm']['search'])) {
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$preset_do_taxa = (isset($_SESSION['cdm']['search']['doTaxa']) ? 1 : 0);
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$preset_do_synonyms = (isset($_SESSION['cdm']['search']['doSynonyms']) ? 1 : 0);
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$preset_do_misapplied_names = (isset($_SESSION['cdm']['search']['doMisappliedNames']) ? 1 : 0);
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$preset_do_taxa_by_common_names = (isset($_SESSION['cdm']['search']['doTaxaByCommonNames']) ? 1 : 0);
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if (isset($_SESSION['cdm']['search']['tree'])) {
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$preset_classification_uuid = $_SESSION['cdm']['search']['tree'];
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}
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}
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if ($classification_select === TRUE) {
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$form['search']['tree'] = array(
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'#title' => t('Classification'),
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'#weight' => 1,
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'#type' => 'select',
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'#default_value' => $preset_classification_uuid,
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'#options' => cdm_get_taxontrees_as_options(TRUE),
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'#description' => t('A filter to limit the search to a specific classification. Choosing <em>--- ALL ---</em> will disable this filter.'),
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);
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}
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// General search parameters.
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$form['search']['doTaxa'] = array(
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'#weight' => 2,
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'#type' => 'checkbox',
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'#title' => t('Include') . ' ' . t('accepted taxa'),
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'#value' => $preset_do_taxa,
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);
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$form['search']['doSynonyms'] = array(
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'#weight' => 3,
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'#type' => 'checkbox',
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'#title' => t('Include') . ' ' . t('synonyms'),
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'#value' => $preset_do_synonyms,
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);
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$form['search']['doMisappliedNames'] = array(
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'#weight' => 4,
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'#type' => 'checkbox',
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'#title' => t('Include') . ' ' . t('misapplied names'),
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'#value' => $preset_do_misapplied_names,
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);
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$form['search']['doTaxaByCommonNames'] = array(
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'#weight' => 5,
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'#type' => 'checkbox',
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'#title' => t('Include') . ' ' . t('common names'),
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'#value' => $preset_do_taxa_by_common_names,
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);
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$area_term_dtos = cdm_ws_fetch_all(
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CDM_WS_DESCRIPTION_NAMEDAREAS_IN_USE,
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array('includeAllParents' => 'true')
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);
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// create map: term_uuid => term
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$term_map = array();
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foreach ($area_term_dtos as $term_dto) {
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$term_map[$term_dto->uuid] = $term_dto;
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}
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$term_tree = array();
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// mixed_vocabularies will contain the uuid vocabularies which
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// also contain terms of foreign vocabularies due to the term
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// hierarchy
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$mixed_vocabularies = array();
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// Build hierarchy of the terms regardless of the vocabulary.
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foreach ($term_map as $term_dto) {
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if (!empty($term_dto->partOfUuid)) {
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// Children.
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$parent =& $term_map[$term_dto->partOfUuid];
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if ($parent) {
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if (!isset($parent->children)) {
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$parent->children = array();
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}
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$parent->children[$term_dto->uuid] = $term_dto;
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if ($parent->vocabularyUuid != $term_dto->vocabularyUuid) {
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$mixed_vocabularies[$parent->vocabularyUuid] = $parent->vocabularyUuid;
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}
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}
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}
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else {
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// group root nodes by vocabulary
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if (!isset($term_tree[$term_dto->vocabularyUuid])) {
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$term_tree[$term_dto->vocabularyUuid] = array();
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}
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$term_tree[$term_dto->vocabularyUuid][$term_dto->uuid] = $term_dto;
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}
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}
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$show_area_filter = ! variable_get(CDM_SEARCH_AREA_FILTER_PRESET, '');
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if($show_area_filter){
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drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/search_area_filter.js');
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drupal_add_js('jQuery(document).ready(function() {
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jQuery(\'#edit-search-areas\').search_area_filter(\'#edit-search-areas-areas-filter\');
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});
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', array('type' => 'inline'));
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$form['search']['areas'] = array(
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'#type' => 'fieldset',
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'#title' => t('Filter by distribution areas'),
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'#description' => t('The search will return taxa having distribution
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information for at least one of the selected areas.') . ' '
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.(count($term_tree) > 1 ? t('The areas are grouped
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by the vocabularies to which the highest level areas belong.') : ''),
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);
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$form['search']['areas']['areas_filter'] = array(
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'#type' => 'textfield',
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'#description' => t('Type to filter the areas listed below.'),
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);
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$vocab_cnt = 0;
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$areas_defaults = array();
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if (isset($_SESSION['cdm']['search']['area'])) {
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$areas_defaults = explode(',', $_SESSION['cdm']['search']['area']);
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}
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_add_js_resizable_element('.resizable-box', true);
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foreach ($term_tree as $vocab_uuid => $term_dto_tree) {
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344
|
$vocabulary = cdm_ws_get(CDM_WS_TERMVOCABULARY, array($vocab_uuid));
|
|
345
|
$areas_options = term_tree_as_options($term_dto_tree);
|
|
346
|
$form['search']['areas']['area'][$vocab_cnt++] = array(
|
|
347
|
'#prefix' => '<strong>' . $vocabulary->representation_L10n
|
|
348
|
. (isset($mixed_vocabularies[$vocab_uuid]) ? ' <span title="Contains terms of at least one other area vocabulary.">(' . t('mixed') . ')</span>': '')
|
|
349
|
. '</strong><div class="resizable-container"><div class="resizable-box">',
|
|
350
|
'#type' => 'checkboxes',
|
|
351
|
'#default_value' => $areas_defaults,
|
|
352
|
'#options' => $areas_options,
|
|
353
|
'#suffix' => '</div></div>'
|
|
354
|
);
|
|
355
|
}
|
|
356
|
}
|
|
357
|
|
|
358
|
}
|
|
359
|
else {
|
|
360
|
// --- SIMPLE SEARCH FORM ---
|
|
361
|
//
|
|
362
|
|
|
363
|
// Overwrite presets by user choice stored in session.
|
|
364
|
if (isset($_SESSION['cdm']['search'])) {
|
|
365
|
$preset_do_misapplied_names = (isset($_SESSION['cdm']['search']['doMisappliedNames']) ? 1 : 0);
|
|
366
|
}
|
|
367
|
|
|
368
|
$form['search']['doTaxa'] = array(
|
|
369
|
'#weight' => -2,
|
|
370
|
'#type' => 'hidden',
|
|
371
|
'#value' => $preset_do_taxa,
|
|
372
|
);
|
|
373
|
$form['search']['doSynonyms'] = array(
|
|
374
|
'#weight' => -3,
|
|
375
|
'#type' => 'hidden',
|
|
376
|
'#value' => $preset_do_synonyms,
|
|
377
|
);
|
|
378
|
$form['search']['doMisappliedNames'] = array(
|
|
379
|
'#weight' => -4,
|
|
380
|
'#type' => 'checkbox',
|
|
381
|
'#title' => t('Misapplied names'),
|
|
382
|
'#value' => $preset_do_misapplied_names,
|
|
383
|
);
|
|
384
|
$form['search']['doTaxaByCommonNames'] = array(
|
|
385
|
'#weight' => -5,
|
|
386
|
'#type' => 'hidden',
|
|
387
|
'#value' => $preset_do_taxa_by_common_names,
|
|
388
|
);
|
|
389
|
}
|
|
390
|
|
|
391
|
return $form;
|
|
392
|
}
|
|
393
|
|
|
394
|
/**
|
|
395
|
* Creates a search form for searching on taxa.
|
|
396
|
*
|
|
397
|
* If advanced $advanced_form id TRUE the form will offer additional choices
|
|
398
|
*
|
|
399
|
* @param array $form
|
|
400
|
* A drupal form array
|
|
401
|
* @param array $form_state
|
|
402
|
* The drupal form state passed as reference
|
|
403
|
* @param bool $advanced_form
|
|
404
|
* default is FALSE
|
|
405
|
* @param bool $classification_select
|
|
406
|
* set TRUE to offer a classification selector in the form - default is FALSE
|
|
407
|
* if only available in the advanced mode
|
|
408
|
*
|
|
409
|
* @return array
|
|
410
|
* the form array
|
|
411
|
*/
|
|
412
|
function cdm_dataportal_search_blast_form($form, &$form_state) {
|
|
413
|
|
|
414
|
$query_field_default_value = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');
|
|
415
|
|
|
416
|
$search_service_endpoint = CDM_SEARCH_BLAST_SERVICE_URI;
|
|
417
|
|
|
418
|
|
|
419
|
$form = cdm_dataportal_search_blast_form_prepare(
|
|
420
|
'cdm_dataportal/search/results/specimen',
|
|
421
|
$search_service_endpoint,
|
|
422
|
$query_field_default_value,
|
|
423
|
t('Enter the sequence or part of a sequence you wish to search for.')
|
|
424
|
);
|
|
425
|
|
|
426
|
|
|
427
|
|
|
428
|
$form['search']['pageSize'] = array(
|
|
429
|
'#weight' => -1,
|
|
430
|
'#type' => 'hidden',
|
|
431
|
'#value' => variable_get(CDM_SEARCH_RESULT_PAGE_SIZE, CDM_SEARCH_RESULT_PAGE_SIZE_DEFAULT),
|
|
432
|
);
|
|
433
|
|
|
434
|
$form['search']['pageNumber'] = array(
|
|
435
|
'#weight' => -1,
|
|
436
|
'#type' => 'hidden',
|
|
437
|
'#value' => 0,
|
|
438
|
);
|
|
439
|
|
|
440
|
|
|
441
|
|
|
442
|
|
|
443
|
|
|
444
|
return $form;
|
|
445
|
}
|
|
446
|
|
|
447
|
/**
|
|
448
|
* Prepares a form array for a general purpose search form.
|
|
449
|
*
|
|
450
|
* The form is used for general purpose search functionality in the
|
|
451
|
* dataportal. The form returned is populated with all necessary fields
|
|
452
|
* for internal processing and has the textfield element $form['query']
|
|
453
|
* which holds the query term.
|
|
454
|
*
|
|
455
|
* @param string $action_path
|
|
456
|
* The Drupal path to be put into the action url to which the form will
|
|
457
|
* be submitted.
|
|
458
|
* @param string $search_webservice
|
|
459
|
* The cdm-remote webservice to be used, valid values are defined by
|
|
460
|
* the constants: FIXME.
|
|
461
|
* @param string $query_field_default_value
|
|
462
|
* A default text for the query field
|
|
463
|
* @param string $query_field_description
|
|
464
|
* The description text for the query field
|
|
465
|
* @param string $process
|
|
466
|
* The value for #process, if NULL (default), 'cdm_dataportal_search_process'
|
|
467
|
* is used.
|
|
468
|
*
|
|
469
|
* @return array
|
|
470
|
* The prepared form array.
|
|
471
|
*/
|
|
472
|
function cdm_dataportal_search_blast_form_prepare($action_path, $search_webservice, $query_field_default_value, $query_field_description, $process = NULL) {
|
|
473
|
|
|
474
|
if ($process == NULL) {
|
|
475
|
$process = 'cdm_dataportal_search_process';
|
|
476
|
}
|
|
477
|
|
|
478
|
$form['#method'] = 'get';
|
|
479
|
//
|
|
480
|
// $form['#process'] = array(
|
|
481
|
// $process => array(),
|
|
482
|
// );
|
|
483
|
//
|
|
484
|
$form['#action'] = url($action_path, array(
|
|
485
|
'absolute' => TRUE,
|
|
486
|
));
|
|
487
|
|
|
488
|
$form['ws'] = array(
|
|
489
|
'#type' => 'hidden',
|
|
490
|
'#value' => $search_webservice,
|
|
491
|
'#name' => 'ws',
|
|
492
|
);
|
|
493
|
|
|
494
|
$form['query'] = array(
|
|
495
|
'#weight' => 0,
|
|
496
|
'#type' => 'textarea',
|
|
497
|
'#size' => 68,
|
|
498
|
// This causes the description to display also when hovering over
|
|
499
|
// the textfield.
|
|
500
|
// This is wanted behaviour for the simple seach but could
|
|
501
|
// be disabled for the advances search.
|
|
502
|
'#attributes' => array(
|
|
503
|
'title' => $query_field_description,
|
|
504
|
),
|
|
505
|
'#description' => $query_field_description,
|
|
506
|
// '#value' => $query_field_default_value,
|
|
507
|
// '#description' => $query_field_description,
|
|
508
|
);
|
|
509
|
|
|
510
|
|
|
511
|
$form['search'] = array(
|
|
512
|
'#weight' => 3,
|
|
513
|
'#tree' => TRUE,
|
|
514
|
// '#type' => $advanced_form ? 'fieldset': 'hidden',
|
|
515
|
'#title' => t('Options'),
|
|
516
|
);
|
|
517
|
|
|
518
|
// Clean URL get forms breaks if we don't give it a 'q'.
|
|
519
|
if (!(bool) variable_get('clean_url', '0')) {
|
|
520
|
$form['search']['q'] = array(
|
|
521
|
'#type' => 'hidden',
|
|
522
|
'#value' => $action_path,
|
|
523
|
'#name' => 'q',
|
|
524
|
);
|
|
525
|
}
|
|
526
|
|
|
527
|
$form['search']['word_size'] = array(
|
|
528
|
'#weight' => 1,
|
|
529
|
'#type' => 'textfield',
|
|
530
|
'#title' => t('Word size'),
|
|
531
|
'#default_value' => 7,
|
|
532
|
'#description' => t('Length of initial exact match'),
|
|
533
|
);
|
|
534
|
|
|
535
|
$form['search']['reward'] = array(
|
|
536
|
'#weight' => 2,
|
|
537
|
'#type' => 'textfield',
|
|
538
|
'#title' => t('Reward'),
|
|
539
|
'#default_value' => 1,
|
|
540
|
'#description' => t('Reward for Matching'),
|
|
541
|
);
|
|
542
|
|
|
543
|
$form['search']['penalty'] = array(
|
|
544
|
'#weight' => 3,
|
|
545
|
'#type' => 'textfield',
|
|
546
|
'#title' => t('Penalty'),
|
|
547
|
'#default_value' => -2,
|
|
548
|
'#description' => t('Penalty for mismatching'),
|
|
549
|
);
|
|
550
|
|
|
551
|
$form['search']['gap_open'] = array(
|
|
552
|
'#weight' => 4,
|
|
553
|
'#type' => 'textfield',
|
|
554
|
'#title' => t('Gap open'),
|
|
555
|
'#default_value' => 5,
|
|
556
|
'#description' => t('Cost to open a gap'),
|
|
557
|
);
|
|
558
|
|
|
559
|
$form['search']['gap_extend'] = array(
|
|
560
|
'#weight' => 5,
|
|
561
|
'#type' => 'textfield',
|
|
562
|
'#title' => t('Gap extend'),
|
|
563
|
'#default_value' => -2,
|
|
564
|
'#description' => t('Cost for extend a gap'),
|
|
565
|
);
|
|
566
|
|
|
567
|
$form['submit'] = array(
|
|
568
|
'#weight' => 5,
|
|
569
|
'#type' => 'submit',
|
|
570
|
'#name' => '',
|
|
571
|
'#value' => t('Search'),
|
|
572
|
);
|
|
573
|
|
|
574
|
return $form;
|
|
575
|
}
|
|
576
|
/**
|
|
577
|
* Wrapper function for cdm_dataportal_search_taxon_form().
|
|
578
|
*
|
|
579
|
* This function makes ot possible possible to just pass the
|
|
580
|
* correct $form_id 'cdm_dataportal_search_taxon_form_advanced' to
|
|
581
|
* drupal_get_form like:
|
|
582
|
* drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
|
|
583
|
*
|
|
584
|
* @param array $form
|
|
585
|
* A drupal form array
|
|
586
|
* @param array $form_state
|
|
587
|
* The drupal form state passed as reference
|
|
588
|
*
|
|
589
|
* @return array
|
|
590
|
* The form array
|
|
591
|
*/
|
|
592
|
function cdm_dataportal_search_taxon_form_advanced($form, &$form_state) {
|
|
593
|
return cdm_dataportal_search_taxon_form($form, $form_state, TRUE);
|
|
594
|
}
|
|
595
|
|
|
596
|
/**
|
|
597
|
* Form for searching taxa by the findByDescriptionElementFullText rest service.
|
|
598
|
*/
|
|
599
|
function cdm_dataportal_search_taxon_by_description_form() {
|
|
600
|
$query_field_default_value = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');
|
|
601
|
|
|
602
|
$form = cdm_dataportal_search_form_prepare(
|
|
603
|
'cdm_dataportal/search/results/taxon',
|
|
604
|
CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT,
|
|
605
|
$query_field_default_value,
|
|
606
|
t("Enter the text you wish to search for. The asterisk character * can be
|
|
607
|
used as wildcard, but must not be used as first character. Terms can be combined with 'AND'. To search for a
|
|
608
|
full phrase enclose the terms in parentheses. For more syntactical
|
|
609
|
options please refer to the !link.",
|
|
610
|
array(
|
|
611
|
'!link' => l(
|
|
612
|
t('Apache Lucene - Query Parser Syntax'),
|
|
613
|
'http://lucene.apache.org/core/old_versioned_docs/versions/2_9_1/queryparsersyntax.html', array(
|
|
614
|
'attributes' => array(
|
|
615
|
'absolute' => TRUE,
|
|
616
|
'html' => TRUE),
|
|
617
|
)
|
|
618
|
),
|
|
619
|
)
|
|
620
|
)
|
|
621
|
);
|
|
622
|
|
|
623
|
$form['search']['tree'] = array(
|
|
624
|
'#weight' => -1,
|
|
625
|
'#type' => 'hidden',
|
|
626
|
'#value' => get_current_classification_uuid(),
|
|
627
|
);
|
|
628
|
|
|
629
|
$form['search']['hl'] = array(
|
|
630
|
'#weight' => -1,
|
|
631
|
'#type' => 'hidden',
|
|
632
|
'#value' => 1,
|
|
633
|
);
|
|
634
|
|
|
635
|
// Only available to admins:
|
|
636
|
if (!isset($_SESSION['cdm']['search']['clazz'])) {
|
|
637
|
$_SESSION['cdm']['search']['clazz'] = '';
|
|
638
|
}
|
|
639
|
if (module_exists("user") && user_access('administer')) {
|
|
640
|
$form['search']['clazz'] = array(
|
|
641
|
'#type' => 'select',
|
|
642
|
'#title' => t('Limit to description item type'),
|
|
643
|
'#default_value' => $_SESSION['cdm']['search']['clazz'],
|
|
644
|
'#options' => cdm_descriptionElementTypes_as_option(TRUE),
|
|
645
|
);
|
|
646
|
}
|
|
647
|
|
|
648
|
$profile_feature_tree = get_profile_feature_tree();
|
|
649
|
$feature_options = _featureTree_nodes_as_feature_options($profile_feature_tree->root);
|
|
650
|
if (isset($_SESSION['cdm']['search']['features'])) {
|
|
651
|
$form['search']['features'] = array(
|
|
652
|
'#type' => 'checkboxes',
|
|
653
|
'#title' => t('Limit to selected features'),
|
|
654
|
'#default_value' => $_SESSION['cdm']['search']['features'],
|
|
655
|
'#options' => $feature_options,
|
|
656
|
);
|
|
657
|
}
|
|
658
|
else {
|
|
659
|
$form['search']['features'] = array(
|
|
660
|
'#type' => 'checkboxes',
|
|
661
|
'#title' => t('Limit to selected features'),
|
|
662
|
'#options' => $feature_options,
|
|
663
|
);
|
|
664
|
}
|
|
665
|
return $form;
|
|
666
|
}
|
|
667
|
|
|
668
|
/**
|
|
669
|
* Processes the query parameters of the search form.
|
|
670
|
*
|
|
671
|
* Reads the query parameters from $_REQUEST and modifies and adds additional
|
|
672
|
* query parameters if necessary.
|
|
673
|
*
|
|
674
|
* - Filters $_REQUEST by a list of valid request parameters
|
|
675
|
* - modifies geographic_range parameters
|
|
676
|
* - adds taxon tree uuid if it is missing and if it should not be
|
|
677
|
* ignored (parameter value = 'IGNORE')
|
|
678
|
* - and more
|
|
679
|
*
|
|
680
|
* @param $search_endpoint string
|
|
681
|
* The web service endpoint which will be used for executing the search.
|
|
682
|
* Usually one of CDM_WS_PORTAL_TAXON_SEARCH, CDM_WS_PORTAL_TAXON_FIND,
|
|
683
|
* CDM_WS_PORTAL_TAXON_FINDBY_DESCRIPTIONELEMENT_FULLTEXT.
|
|
684
|
* @return array
|
|
685
|
* the processed request parameters submitted by the search form and
|
|
686
|
* also stores them in $_SESSION['cdm']['search']
|
|
687
|
*/
|
|
688
|
function cdm_dataportal_search_request($search_endpoint)
|
|
689
|
{
|
|
690
|
|
|
691
|
$form_params = array();
|
|
692
|
|
|
693
|
if (isset($_REQUEST['search']) && is_array($_REQUEST['search'])) {
|
|
694
|
array_deep_copy($_REQUEST['search'], $form_params);
|
|
695
|
}
|
|
696
|
|
|
697
|
if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
|
|
698
|
$form_params = array_merge($form_params, $_REQUEST['pager']);
|
|
699
|
}
|
|
700
|
|
|
701
|
$form_params['query'] = trim($_REQUEST['query']);
|
|
702
|
|
|
703
|
|
|
704
|
// --- handle geographic range
|
|
705
|
// Split of geographic range.
|
|
706
|
unset($form_params['areas']);
|
|
707
|
|
|
708
|
$area_filter_preset = null;
|
|
709
|
if (variable_get(CDM_SEARCH_AREA_FILTER_PRESET, '')) {
|
|
710
|
$area_filter_preset = explode(',', variable_get(CDM_SEARCH_AREA_FILTER_PRESET, ''));
|
|
711
|
}
|
|
712
|
|
|
713
|
$area_uuids = array();
|
|
714
|
if($area_filter_preset){
|
|
715
|
$area_uuids = $area_filter_preset;
|
|
716
|
}
|
|
717
|
elseif (isset($_REQUEST['search']['areas']['area']) && is_array($_REQUEST['search']['areas']['area'])) {
|
|
718
|
foreach ($_REQUEST['search']['areas']['area'] as $areas) {
|
|
719
|
$area_uuids = array_merge($area_uuids, $areas);
|
|
720
|
}
|
|
721
|
// The area filter is limited to areas with non absent distribution status
|
|
722
|
$presence_terms_options = cdm_vocabulary_as_option(UUID_PRESENCE_ABSENCE_TERM, null, FALSE, array('absenceTerm' => '/false/'));
|
|
723
|
$presence_term_uuids = array_keys($presence_terms_options);
|
|
724
|
$form_params['status'] = $presence_term_uuids;
|
|
725
|
}
|
|
726
|
if(count($area_uuids) > 0){
|
|
727
|
$form_params['area'] = implode(',', $area_uuids);
|
|
728
|
}
|
|
729
|
|
|
730
|
// Simple search will not submit a 'tree' query parameter,
|
|
731
|
// so we add it here from what is stored in the session unless
|
|
732
|
// SIMPLE_SEARCH_IGNORE_CLASSIFICATION is checked in the settings.
|
|
733
|
if (!isset($form_params['tree']) && !variable_get(SIMPLE_SEARCH_IGNORE_CLASSIFICATION, 0)) {
|
|
734
|
$form_params['tree'] = get_current_classification_uuid();
|
|
735
|
}
|
|
736
|
// Store in session.
|
|
737
|
$_SESSION['cdm']['search'] = $form_params;
|
|
738
|
|
|
739
|
// ----------- further processing that must not be store in the session --------- //
|
|
740
|
|
|
741
|
if($search_endpoint == CDM_WS_PORTAL_TAXON_SEARCH){
|
|
742
|
// HACK to allow using dot characters
|
|
743
|
$form_params['query'] = str_replace('.', '*', $form_params['query']);
|
|
744
|
// lucene based taxon search always as phrase search if the query string contains a whitespace --> enclose it in "
|
|
745
|
if(preg_match("/\s+/", $form_params['query'])){
|
|
746
|
if(!str_beginsWith($form_params['query'], '"')){
|
|
747
|
$form_params['query'] = '"' . $form_params['query'];
|
|
748
|
}
|
|
749
|
if(!str_endsWith($form_params['query'], '"')){
|
|
750
|
$form_params['query'] = $form_params['query'] . '"' ;
|
|
751
|
}
|
|
752
|
}
|
|
753
|
}
|
|
754
|
|
|
755
|
// If the 'NONE' classification has been chosen (advanced search)
|
|
756
|
// delete the tree information to avoid unknown uuid exceptions in the
|
|
757
|
// cdm service.
|
|
758
|
if (isset($form_params['tree'])
|
|
759
|
&& ($form_params['tree'] == 'NONE' || !is_uuid($form_params['tree']))
|
|
760
|
) {
|
|
761
|
// $form_params['ignore_classification'] = TRUE;
|
|
762
|
unset($form_params['tree']);
|
|
763
|
}
|
|
764
|
// else {
|
|
765
|
// $form_params['ignore_classification'] = NULL;
|
|
766
|
// }
|
|
767
|
|
|
768
|
|
|
769
|
return $form_params;
|
|
770
|
}
|
|
771
|
|
|
772
|
/**
|
|
773
|
* Processes the query parameters of the blast search form.
|
|
774
|
*
|
|
775
|
* Reads the query parameters from $_REQUEST and modifies and adds additional
|
|
776
|
* query parameters if necessary.
|
|
777
|
*
|
|
778
|
* - Filters $_REQUEST by a list of valid request parameters
|
|
779
|
*
|
|
780
|
*
|
|
781
|
* @param $search_endpoint string
|
|
782
|
* The web service endpoint which will be used for executing the search.
|
|
783
|
*
|
|
784
|
* @return array
|
|
785
|
* the processed request parameters submitted by the search form and
|
|
786
|
* also stores them in $_SESSION['cdm']['search']
|
|
787
|
*/
|
|
788
|
function cdm_dataportal_blast_search_request($search_endpoint)
|
|
789
|
{
|
|
790
|
$form_params = array();
|
|
791
|
|
|
792
|
if (isset($_REQUEST['search']) && is_array($_REQUEST['search'])) {
|
|
793
|
array_deep_copy($_REQUEST['search'], $form_params['data']);
|
|
794
|
}
|
|
795
|
$form_params['data'] = formatWSParams($_REQUEST['search']);
|
|
796
|
$form_params['query']= trim($_REQUEST['query']).$form_params['data'];
|
|
797
|
// Store in session.
|
|
798
|
$_SESSION['cdm']['search'] = $form_params;
|
|
799
|
return $form_params;
|
|
800
|
}
|
|
801
|
|
|
802
|
/**
|
|
803
|
* Provides the classification to which the last search has been limited to..
|
|
804
|
*
|
|
805
|
* This function should only be used after the cdm_dataportal_search_taxon_execute()
|
|
806
|
* handler has been run, otherwise it will return the information from the last
|
|
807
|
* search executed. The information is retrieved from
|
|
808
|
* the $_SESSION variable: $_SESSION['cdm']['search']['tree']
|
|
809
|
*
|
|
810
|
* @return object
|
|
811
|
* the CDM classification instance which has been used a filter for the
|
|
812
|
* last processed search
|
|
813
|
* or NULL, it it was on all classifications
|
|
814
|
*/
|
|
815
|
function cdm_dataportal_searched_in_classification() {
|
|
816
|
|
|
817
|
$classification = &drupal_static(__FUNCTION__);
|
|
818
|
|
|
819
|
if (!isset($classification)) {
|
|
820
|
if (isset($_SESSION['cdm']['search']['tree'])) {
|
|
821
|
$classification = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY, ($_SESSION['cdm']['search']['tree']));
|
|
822
|
}
|
|
823
|
else {
|
|
824
|
$classification = FALSE;
|
|
825
|
}
|
|
826
|
}
|
|
827
|
|
|
828
|
return $classification !== FALSE ? $classification : NULL;
|
|
829
|
}
|
|
830
|
|
|
831
|
/**
|
|
832
|
* Removed the drupal internal form parameters 'form_id', 'form_token', 'form_build_id' from the request array.
|
|
833
|
*
|
|
834
|
* @param $request array
|
|
835
|
* Pass $_REQUEST as paramter
|
|
836
|
* @return array
|
|
837
|
* The $request array without drupal internal form parameters
|
|
838
|
*/
|
|
839
|
function remove_drupal_form_params($request) {
|
|
840
|
|
|
841
|
static $exclude_keys = array('form_id', 'form_token', 'form_build_id');
|
|
842
|
$request_sanitized = array();
|
|
843
|
foreach ($request as $key => $value) {
|
|
844
|
if(!array_search($key, $exclude_keys)){
|
|
845
|
$request_sanitized[$key] = $value;
|
|
846
|
}
|
|
847
|
}
|
|
848
|
|
|
849
|
return $request_sanitized;
|
|
850
|
}
|
|
851
|
|
|
852
|
/**
|
|
853
|
* Sends a search request to the cdm server.
|
|
854
|
*
|
|
855
|
* The parameters to build the query are taken obtained by calling
|
|
856
|
* cdm_dataportal_search_request() which reads the query parameters
|
|
857
|
* from $_REQUEST and add additional query parameters if nessecary.
|
|
858
|
*
|
|
859
|
* @see cdm_dataportal_search_request()
|
|
860
|
*/
|
|
861
|
function cdm_dataportal_search_taxon_execute() {
|
|
862
|
|
|
863
|
// Store as last search in session.
|
|
864
|
$_SESSION['cdm']['last_search'] = $_SERVER['REQUEST_URI'];
|
|
865
|
|
|
866
|
// Validate the search webservice parameter:
|
|
867
|
if (!isset($_REQUEST['ws'])) {
|
|
868
|
drupal_set_message(
|
|
869
|
t("Invalid search, webservice parameter 'ws' is missing"), 'warning'
|
|
870
|
);
|
|
871
|
return NULL;
|
|
872
|
}
|
|
873
|
if (!cdm_dataportal_search_form_path_for_ws($_REQUEST['ws'])) {
|
|
874
|
// Endpoint is unknown.
|
|
875
|
drupal_set_message(
|
|
876
|
t("Invalid search webservice parameter 'ws' given"), 'warning'
|
|
877
|
);
|
|
878
|
return NULL;
|
|
879
|
}
|
|
880
|
|
|
881
|
// Read the query parameters from $_REQUEST and add additional query
|
|
882
|
// parameters if necessary.
|
|
883
|
$request_params = cdm_dataportal_search_request($_REQUEST['ws']);
|
|
884
|
|
|
885
|
$taxon_pager = cdm_ws_get($_REQUEST['ws'], NULL, queryString($request_params));
|
|
886
|
|
|
887
|
return $taxon_pager;
|
|
888
|
}
|
|
889
|
|
|
890
|
/**
|
|
891
|
* Sends a search request to the cdm server.
|
|
892
|
*
|
|
893
|
* The parameters to build the query are taken obtained by calling
|
|
894
|
* cdm_dataportal_search_request() which reads the query parameters
|
|
895
|
* from $_REQUEST and add additional query parameters if nessecary.
|
|
896
|
*
|
|
897
|
* @see cdm_dataportal_search_request()
|
|
898
|
*/
|
|
899
|
function cdm_dataportal_search_blast_execute() {
|
|
900
|
|
|
901
|
// Store as last search in session.
|
|
902
|
$_SESSION['cdm']['last_blast_search'] = $_SERVER['REQUEST_URI'];
|
|
903
|
|
|
904
|
// Validate the search webservice parameter:
|
|
905
|
if (!isset($_REQUEST['ws'])) {
|
|
906
|
drupal_set_message(
|
|
907
|
t("Invalid search, webservice parameter 'ws' is missing"), 'warning'
|
|
908
|
);
|
|
909
|
return NULL;
|
|
910
|
}
|
|
911
|
// if (!cdm_dataportal_search_form_path_for_ws($_REQUEST['ws'])) {
|
|
912
|
// // Endpoint is unknown.
|
|
913
|
// drupal_set_message(
|
|
914
|
// t("Invalid search webservice parameter 'ws' given"), 'warning'
|
|
915
|
// );
|
|
916
|
// return NULL;
|
|
917
|
// }
|
|
918
|
|
|
919
|
// Read the query parameters from $_REQUEST and add additional query
|
|
920
|
// parameters if necessary.
|
|
921
|
$request_params = cdm_dataportal_blast_search_request($_REQUEST['ws']);
|
|
922
|
// $url = drupal_http_build_query($_REQUEST['ws'], $request_params);
|
|
923
|
$request_params['timeout'] = 200;
|
|
924
|
$taxon_pager = drupal_http_request($_REQUEST['ws'].'?sequence='.$request_params['query'], $request_params);
|
|
925
|
|
|
926
|
return $taxon_pager;
|
|
927
|
}
|
|
928
|
|
|
929
|
|
|
930
|
|
|
931
|
/**
|
|
932
|
* Sends a request for a registrations filter search to the cdm server.
|
|
933
|
*/
|
|
934
|
function cdm_dataportal_search_registrations_filter_execute()
|
|
935
|
{
|
|
936
|
|
|
937
|
static $query_param_map = array(
|
|
938
|
'identifier' => 'identifierFilterPattern',
|
|
939
|
'taxon_name'=> 'taxonNameFilterPattern',
|
|
940
|
'reference_citation' => 'referenceFilterPattern',
|
|
941
|
'type_designation_status_uuids' => 'typeDesignationStatusUuids',
|
|
942
|
);
|
|
943
|
|
|
944
|
$session_key = SESSION_KEY_SEARCH_REGISTRATION_FILTER;
|
|
945
|
$request_params = cdm_dataportal_search_request_params($session_key, $query_param_map);
|
|
946
|
|
|
947
|
// cleanup
|
|
948
|
if(isset($request_params['typeDesignationStatusUuids'])){
|
|
949
|
if(!$request_params['typeDesignationStatusUuids']
|
|
950
|
|| $request_params['typeDesignationStatusUuids'] == "0"
|
|
951
|
|| (isset($request_params['typeDesignationStatusUuids'][0]) && !$request_params['typeDesignationStatusUuids'][0])){
|
|
952
|
unset($request_params['typeDesignationStatusUuids']);
|
|
953
|
}
|
|
954
|
}
|
|
955
|
if(isset($request_params['taxonNameFilterPattern'])){
|
|
956
|
// trim and remove empty taxon name query strings
|
|
957
|
$request_params['taxonNameFilterPattern'] = trim($request_params['taxonNameFilterPattern']);
|
|
958
|
if(!$request_params['taxonNameFilterPattern']){
|
|
959
|
unset($request_params['taxonNameFilterPattern']);
|
|
960
|
}
|
|
961
|
}
|
|
962
|
// reference_citation
|
|
963
|
if(isset($request_params['referenceFilterPattern'])){
|
|
964
|
// trim and remove empty taxon name query strings
|
|
965
|
$request_params['referenceFilterPattern'] = trim($request_params['referenceFilterPattern']);
|
|
966
|
if(!$request_params['referenceFilterPattern']){
|
|
967
|
unset($request_params['referenceFilterPattern']);
|
|
968
|
}
|
|
969
|
}
|
|
970
|
|
|
971
|
$registration_pager = cdm_ws_get('registrationDTO/find', NULL, queryString($request_params));
|
|
972
|
|
|
973
|
return $registration_pager;
|
|
974
|
}
|
|
975
|
|
|
976
|
/**
|
|
977
|
* Sends a request for a registrations taxongraph search to the cdm server.
|
|
978
|
*/
|
|
979
|
function cdm_dataportal_search_registrations_taxongraph_execute()
|
|
980
|
{
|
|
981
|
|
|
982
|
static $query_param_map = array(
|
|
983
|
'taxon_name'=> 'taxonNameFilter'
|
|
984
|
);
|
|
985
|
|
|
986
|
$session_key = SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER;
|
|
987
|
$request_params = cdm_dataportal_search_request_params($session_key, $query_param_map);
|
|
988
|
|
|
989
|
// cleanup
|
|
990
|
if(isset($request_params['taxonNameFilter'])){
|
|
991
|
// trim and remove empty taxon name query strings
|
|
992
|
$request_params['taxonNameFilter'] = trim($request_params['taxonNameFilter']);
|
|
993
|
if(!$request_params['taxonNameFilter']){
|
|
994
|
unset($request_params['taxonNameFilter']);
|
|
995
|
}
|
|
996
|
}
|
|
997
|
|
|
998
|
$registration_pager = cdm_ws_get('registrationDTO/findInTaxonGraph', NULL, queryString($request_params));
|
|
999
|
|
|
1000
|
return $registration_pager;
|
|
1001
|
}
|
|
1002
|
|
|
1003
|
/**
|
|
1004
|
* @param $session_key
|
|
1005
|
* The key to be used for storing the search params in $_SESSION['cdm'][]
|
|
1006
|
* @param $query_param_map
|
|
1007
|
* An array which maps the filter_key to the web service query parameter.
|
|
1008
|
* The filter key may be used as form element name or as drupal url
|
|
1009
|
* query parameter.
|
|
1010
|
* @return array
|
|
1011
|
*/
|
|
1012
|
function cdm_dataportal_search_request_params($session_key, $query_param_map)
|
|
1013
|
{
|
|
1014
|
// Read the query parameters from $_REQUEST and add additional query
|
|
1015
|
// parameters if necessary.
|
|
1016
|
$request_params = array();
|
|
1017
|
|
|
1018
|
$request = remove_drupal_form_params($_REQUEST);
|
|
1019
|
|
|
1020
|
if (count($request) > 0) {
|
|
1021
|
$_SESSION['cdm'][$session_key] = $request;
|
|
1022
|
foreach ($query_param_map as $filter_key => $query_param) {
|
|
1023
|
if (isset($request[$filter_key])) {
|
|
1024
|
$request_params[$query_param] = $request[$filter_key];
|
|
1025
|
}
|
|
1026
|
}
|
|
1027
|
if (isset($request['pager']['pageNumber'])) {
|
|
1028
|
$request_params['pageNumber'] = $request['pager']['pageNumber'];
|
|
1029
|
}
|
|
1030
|
}
|
|
1031
|
|
|
1032
|
if (count($request_params) == 0 && isset($_SESSION['cdm'][$session_key])) {
|
|
1033
|
foreach ($query_param_map as $filter_key => $query_param) {
|
|
1034
|
if (isset($_SESSION['cdm'][$session_key][$filter_key])) {
|
|
1035
|
$request_params[$query_param] = $_SESSION['cdm'][$session_key][$filter_key];
|
|
1036
|
}
|
|
1037
|
}
|
|
1038
|
if (isset($_SESSION['cdm'][$session_key]['pager']['pageNumber'])) {
|
|
1039
|
$request_params['pageNumber'] = $_SESSION['cdm'][$session_key]['pager']['pageNumber'];
|
|
1040
|
}
|
|
1041
|
}
|
|
1042
|
return $request_params;
|
|
1043
|
}
|
|
1044
|
|
|
1045
|
/**
|
|
1046
|
* Transforms the termDTO tree into options array.
|
|
1047
|
*
|
|
1048
|
* TermDto:
|
|
1049
|
* - partOfUuid:
|
|
1050
|
* - representation_L10n:
|
|
1051
|
* - representation_L10n_abbreviatedLabel:
|
|
1052
|
* - uuid:
|
|
1053
|
* - vocabularyUuid:
|
|
1054
|
* - children: array of TermDto
|
|
1055
|
*
|
|
1056
|
* The options array is suitable for drupal form API elements that
|
|
1057
|
* allow multiple choices.
|
|
1058
|
* @see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#options
|
|
1059
|
*
|
|
1060
|
* @param array $term_dto_tree
|
|
1061
|
* a hierarchic array of CDM TermDto instances, with additional
|
|
1062
|
* 'children' field:
|
|
1063
|
* @param array $options
|
|
1064
|
* Internally used for recursive calls
|
|
1065
|
* @param string $prefix
|
|
1066
|
* Internally used for recursive calls
|
|
1067
|
*
|
|
1068
|
* @return array
|
|
1069
|
* the terms in an array as options for a form element that allows
|
|
1070
|
* multiple choices.
|
|
1071
|
*/
|
|
1072
|
function term_tree_as_options($term_dto_tree, &$options = array(), $prefix = '') {
|
|
1073
|
|
|
1074
|
uasort($term_dto_tree, 'compare_terms_by_order_index');
|
|
1075
|
foreach ($term_dto_tree as $uuid => $dto) {
|
|
1076
|
$label = $prefix . '<span class="child-label">'
|
|
1077
|
. $dto->representation_L10n
|
|
1078
|
. '</span><span class="child-label-abbreviated"> (' . $dto->representation_L10n_abbreviatedLabel . ')</span>';
|
|
1079
|
$options[$uuid] = $label;
|
|
1080
|
if (isset($dto->children) && is_array($dto->children)) {
|
|
1081
|
term_tree_as_options(
|
|
1082
|
$dto->children,
|
|
1083
|
$options, $prefix
|
|
1084
|
. '<span data-cdm-parent="' . $uuid . '" class="parent"></span>'
|
|
1085
|
);
|
|
1086
|
}
|
|
1087
|
}
|
|
1088
|
|
|
1089
|
return $options;
|
|
1090
|
}
|
|
1091
|
|
|
1092
|
|
|
1093
|
function cdm_dataportal_search_registration_filter_form($form, &$form_state) {
|
|
1094
|
|
|
1095
|
static $filter_presets_empty = array(
|
|
1096
|
'identifier'=> null,
|
|
1097
|
'taxon_name'=> null,
|
|
1098
|
'reference_citation'=> null,
|
|
1099
|
'type_designation_status_uuids' => null
|
|
1100
|
);
|
|
1101
|
|
|
1102
|
_add_font_awesome_font();
|
|
1103
|
|
|
1104
|
if(isset($_REQUEST['q']) && ($_REQUEST['q'] == 'cdm_dataportal/registration-search/filter' || $_REQUEST['q'] == 'cdm_dataportal/registration-search')){
|
|
1105
|
// read the $request_params only if it was send from this form
|
|
1106
|
$request_params = remove_drupal_form_params($_REQUEST);
|
|
1107
|
} else {
|
|
1108
|
$request_params = array();
|
|
1109
|
}
|
|
1110
|
$filter_presets = (isset($_SESSION['cdm'][SESSION_KEY_SEARCH_REGISTRATION_FILTER]) ? $_SESSION['cdm'][SESSION_KEY_SEARCH_REGISTRATION_FILTER] : array());
|
|
1111
|
$filter_presets = array_merge($filter_presets_empty, $filter_presets, $request_params);
|
|
1112
|
$form['#action'] = url('/cdm_dataportal/registration-search/filter');
|
|
1113
|
$form['#method'] = 'get';
|
|
1114
|
$form['#attributes'] = array('class' => array('search-filter'));
|
|
1115
|
$form['identifier'] = array(
|
|
1116
|
'#type' => 'textfield',
|
|
1117
|
'#title' => t('Identifier'),
|
|
1118
|
'#default_value' => $filter_presets['identifier'],
|
|
1119
|
'#size' => 20,
|
|
1120
|
'#maxlength' => 128
|
|
1121
|
);
|
|
1122
|
$form['taxon_name'] = array(
|
|
1123
|
'#type' => 'textfield',
|
|
1124
|
'#title' => t('Scientific name'),
|
|
1125
|
'#default_value' => $filter_presets['taxon_name'],
|
|
1126
|
'#size' => 20,
|
|
1127
|
'#maxlength' => 128
|
|
1128
|
);
|
|
1129
|
$form['reference_citation'] = array(
|
|
1130
|
'#type' => 'textfield',
|
|
1131
|
'#title' => t('Publication'),
|
|
1132
|
'#default_value' => $filter_presets['reference_citation'],
|
|
1133
|
'#size' => 20,
|
|
1134
|
'#maxlength' => 128
|
|
1135
|
);
|
|
1136
|
$form['type_designation_status_uuids'] = array(
|
|
1137
|
'#type' => 'select',
|
|
1138
|
'#title' => t('Type designation status'),
|
|
1139
|
'#multiple' => true,
|
|
1140
|
'#options' => cdm_type_designation_status_filter_terms_as_options('- none -'),
|
|
1141
|
'#default_value' => $filter_presets['type_designation_status_uuids'],
|
|
1142
|
"#description" => '<i>' . t('Ctrl + Click to unselect') . '</i>'
|
|
1143
|
);
|
|
1144
|
|
|
1145
|
$form['submit'] = array(
|
|
1146
|
'#markup' => '<button type="submit" title="Search" class="form-submit">' . font_awesome_icon_markup('fa-search') . '</button>'
|
|
1147
|
// '#prefix' => "<div class=\"form-item\"><label> </label>",
|
|
1148
|
// '#suffix' => "</div>"
|
|
1149
|
|
|
1150
|
);
|
|
1151
|
return $form;
|
|
1152
|
}
|
|
1153
|
|
|
1154
|
|
|
1155
|
function cdm_dataportal_search_registration_taxongraph_form($form, &$form_state) {
|
|
1156
|
|
|
1157
|
static $filter_presets_empty = array(
|
|
1158
|
'taxon_name'=> null
|
|
1159
|
);
|
|
1160
|
|
|
1161
|
_add_font_awesome_font();
|
|
1162
|
|
|
1163
|
if(isset($_REQUEST['q']) && $_REQUEST['q'] == 'cdm_dataportal/registration-search/taxongraph'){
|
|
1164
|
// read the $request_params only if it was send from this form
|
|
1165
|
$request_params = remove_drupal_form_params($_REQUEST);
|
|
1166
|
} else {
|
|
1167
|
$request_params = array();
|
|
1168
|
}
|
|
1169
|
$filter_presets = (isset($_SESSION['cdm'][SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER]) ? $_SESSION['cdm'][SESSION_KEY_SEARCH_TAXONGRAPH_FOR_REGISTRATION_FILTER] : array());
|
|
1170
|
$filter_presets = array_merge($filter_presets_empty, $filter_presets, $request_params);
|
|
1171
|
|
|
1172
|
$form['#action'] = url('/cdm_dataportal/registration-search/taxongraph');
|
|
1173
|
$form['#method'] = 'get';
|
|
1174
|
$form['#attributes'] = array('class' => array('search-filter'));
|
|
1175
|
$form['taxon_name'] = array(
|
|
1176
|
'#type' => 'textfield',
|
|
1177
|
'#title' => t('Scientific name'),
|
|
1178
|
'#default_value' => $filter_presets['taxon_name'],
|
|
1179
|
'#size' => 20,
|
|
1180
|
'#maxlength' => 128
|
|
1181
|
);
|
|
1182
|
|
|
1183
|
$form['submit'] = array(
|
|
1184
|
'#type' => 'submit',
|
|
1185
|
'#attributes' => array('class' => array('fa-icon'), 'title' => t('Search')),
|
|
1186
|
'#value' => decode_entities(''), // fontawesome search icon
|
|
1187
|
// '#prefix' => "<div class=\"form-item\"><label> </label>",
|
|
1188
|
// '#suffix' => "</div>"
|
|
1189
|
|
|
1190
|
);
|
|
1191
|
return $form;
|
|
1192
|
}
|
|
1193
|
|
|
1194
|
/**
|
|
1195
|
* Compose the result set of a registration search from a pager object
|
|
1196
|
*
|
|
1197
|
* @param $cdm_item_pager
|
|
1198
|
* The pager containing registration objects
|
|
1199
|
*
|
|
1200
|
* @return
|
|
1201
|
* A drupal render array.
|
|
1202
|
*
|
|
1203
|
* @ingroup compose
|
|
1204
|
*
|
|
1205
|
* TODO compose function into search.inc ?
|
|
1206
|
*/
|
|
1207
|
function compose_search_results($cdm_item_pager, ItemComposeHandler $item_compose_handler){
|
|
1208
|
|
|
1209
|
$render_array = array();
|
|
1210
|
$render_array['pre'] = markup_to_render_array("<div class=\"cdm-item-list\">");
|
|
1211
|
|
|
1212
|
if($cdm_item_pager != null && count($cdm_item_pager->records) > 0){
|
|
1213
|
$items_render_array = array();
|
|
1214
|
foreach($cdm_item_pager->records as $registration_dto) {
|
|
1215
|
|
|
1216
|
$items_render_array[] = array(
|
|
1217
|
'#prefix' => "<div class=\"item\"><div class=\"" . $item_compose_handler->getClassAttributes($registration_dto) . "\">",
|
|
1218
|
'item_data' => $item_compose_handler->composeItem($registration_dto),
|
|
1219
|
'#suffix' => "</div></div>"
|
|
1220
|
);
|
|
1221
|
;
|
|
1222
|
}
|
|
1223
|
|
|
1224
|
$render_array['items'] = $items_render_array;
|
|
1225
|
$render_array['pager'] = markup_to_render_array(theme('cdm_pager', array(
|
|
1226
|
'pager' => $cdm_item_pager,
|
|
1227
|
'path' => $_REQUEST['q'], // stay on same page
|
|
1228
|
'parameters' => $_REQUEST,
|
|
1229
|
)));
|
|
1230
|
|
|
1231
|
} else {
|
|
1232
|
if($cdm_item_pager != null && $cdm_item_pager->count > 0 && count($cdm_item_pager->records) == 0){
|
|
1233
|
$render_array['items'] = markup_to_render_array("<div id=\"no_results\">Result page out of range.</div>");
|
|
1234
|
} else {
|
|
1235
|
$render_array['items'] = markup_to_render_array("<div id=\"no_results\">No results found.</div>");
|
|
1236
|
}
|
|
1237
|
}
|
|
1238
|
$render_array['post'] = markup_to_render_array("</div>");
|
|
1239
|
|
|
1240
|
return $render_array;
|
|
1241
|
|
|
1242
|
}
|
|
1243
|
|
|
1244
|
|
|
1245
|
/**
|
|
1246
|
* Sends a search request for agents to the cdm server.
|
|
1247
|
*/
|
|
1248
|
function cdm_dataportal_search_agent_execute()
|
|
1249
|
{
|
|
1250
|
|
|
1251
|
static $query_param_map = array(
|
|
1252
|
'markerType' => 'markerType',
|
|
1253
|
'cdmType' => 'class'
|
|
1254
|
);
|
|
1255
|
|
|
1256
|
$session_key = SESSION_KEY_SEARCH_AGENT_FILTER;
|
|
1257
|
$request_params = cdm_dataportal_search_request_params($session_key, $query_param_map);
|
|
1258
|
|
|
1259
|
// cleanup
|
|
1260
|
if(isset($request_params['taxonNameFilter'])){
|
|
1261
|
// trim and remove empty taxon name query strings
|
|
1262
|
$request_params['taxonNameFilter'] = trim($request_params['taxonNameFilter']);
|
|
1263
|
if(!$request_params['taxonNameFilter']){
|
|
1264
|
unset($request_params['taxonNameFilter']);
|
|
1265
|
}
|
|
1266
|
}
|
|
1267
|
$restrictions = [];
|
|
1268
|
if( isset($request_params['markerType'])){
|
|
1269
|
$restrictions = array(new Restriction("markers.markerType.uuid","EXACT", array($request_params['markerType']), 'AND'));
|
|
1270
|
}
|
|
1271
|
$init_strategy = array(
|
|
1272
|
"$",
|
|
1273
|
"titleCache",
|
|
1274
|
"extensions.$",
|
|
1275
|
"identifiers.type"
|
|
1276
|
);
|
|
1277
|
|
|
1278
|
$type_restriction = null;
|
|
1279
|
if(isset($query_param_map['class']) && ($query_param_map['class'] == 'Team' || $query_param_map['class'] == 'Person')){
|
|
1280
|
$type_restriction = $query_param_map['class'];
|
|
1281
|
}
|
|
1282
|
$page_index = 0;
|
|
1283
|
if(isset($_REQUEST['pager']['pageNumber'])){
|
|
1284
|
$page_index = $_REQUEST['pager']['pageNumber'];
|
|
1285
|
}
|
|
1286
|
$pager = cdm_ws_page_by_restriction('AgentBase', $type_restriction, $restrictions, $init_strategy, 50, $page_index);
|
|
1287
|
|
|
1288
|
return $pager;
|
|
1289
|
}
|
|
1290
|
|