| 1 |
6657531f
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Andreas Kohlbecker
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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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| 7 |
e2617c7e
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Andreas Kohlbecker
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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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| 10 |
a6ae799b
|
Andreas Kohlbecker
|
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| 11 |
6657531f
|
Andreas Kohlbecker
|
/**
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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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| 29 |
dc435632
|
Andreas Kohlbecker
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CDM_WS_PORTAL_TAXON_SEARCH => "cdm_dataportal/search",
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| 30 |
6657531f
|
Andreas Kohlbecker
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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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| 39 |
103a1463
|
Andreas Kohlbecker
|
* dataportal. The form returned is populated with all necessary fields
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| 40 |
6657531f
|
Andreas Kohlbecker
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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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| 50 |
632a697a
|
Andreas Kohlbecker
|
* A default text for the query field
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| 51 |
6657531f
|
Andreas Kohlbecker
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* @param string $query_field_description
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| 52 |
632a697a
|
Andreas Kohlbecker
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* The description text for the query field
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| 53 |
6657531f
|
Andreas Kohlbecker
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*
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* @return array
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* The prepared form array.
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*/
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24797d7f
|
Andreas Kohlbecker
|
function cdm_dataportal_search_form_prepare($action_path, $search_webservice, $query_field_default_value, $query_field_description) {
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| 58 |
2d0d855a
|
Andreas Kohlbecker
|
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6657531f
|
Andreas Kohlbecker
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$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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632a697a
|
Andreas Kohlbecker
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// This causes the description to display also when hovering over
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2d0d855a
|
Andreas Kohlbecker
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// the textfield.
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// This is wanted behaviour for the simple seach but could
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| 78 |
632a697a
|
Andreas Kohlbecker
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// be disabled for the advances search.
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6657531f
|
Andreas Kohlbecker
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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' => $query_field_description,
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);
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| 86 |
023c4a03
|
Patrick Plitzner
|
if(variable_get(SIMPLE_SEARCH_AUTO_SUGGEST)){
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| 87 |
24f57e45
|
Patrick Plitzner
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$form['query']['#autocomplete_path'] = 'cdm_dataportal/taxon/autosuggest////';
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| 88 |
35bea66c
|
Patrick Plitzner
|
}
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6657531f
|
Andreas Kohlbecker
|
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| 90 |
93ae67cc
|
Patrick Plitzner
|
$form['search'] = array(
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6657531f
|
Andreas Kohlbecker
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'#weight' => 3,
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'#tree' => TRUE,
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7b4c053d
|
Andreas Kohlbecker
|
// '#type' => $advanced_form ? 'fieldset': 'hidden',
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6657531f
|
Andreas Kohlbecker
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'#title' => t('Options'),
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);
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// Clean URL get forms breaks if we don't give it a 'q'.
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if (!(bool) variable_get('clean_url', '0')) {
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$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 $form;
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}
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| 116 |
24f57e45
|
Patrick Plitzner
|
function cdm_dataportal_taxon_autosuggest($classificationUuid = NULL, $areaUuid = NULL, $status = NULL, $string) {
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| 117 |
93ae67cc
|
Patrick Plitzner
|
$matches = array();
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$queryParams = array();
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| 120 |
04a1d647
|
Patrick Plitzner
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$queryParams['query'] = $string.'*';
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| 121 |
24f57e45
|
Patrick Plitzner
|
if((is_null($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'] = $classificationUuid;
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| 126 |
04a1d647
|
Patrick Plitzner
|
}
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if($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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| 133 |
93ae67cc
|
Patrick Plitzner
|
$queryParams['pageNumber'] = '0';
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| 134 |
04a1d647
|
Patrick Plitzner
|
$queryParams['pageSize'] = '10';
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| 135 |
93ae67cc
|
Patrick Plitzner
|
$queryParams['doTaxa'] = true;
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$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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| 143 |
01fff74a
|
Andreas Kohlbecker
|
preg_match('/(.*) sec.*/', $titleCache, $trimmedTitle); //remove sec reference
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| 144 |
93ae67cc
|
Patrick Plitzner
|
$trimmedTitle = trim($trimmedTitle[1]);
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| 145 |
f35d3f4a
|
Patrick Plitzner
|
$matches[$trimmedTitle] = check_plain($trimmedTitle);
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| 146 |
93ae67cc
|
Patrick Plitzner
|
}
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drupal_json_output($matches);
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}
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| 151 |
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/**
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| 152 |
dbf4b8a8
|
Andreas Kohlbecker
|
* Creates a search form for searching on taxa.
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| 153 |
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*
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| 154 |
7b4c053d
|
Andreas Kohlbecker
|
* If advanced $advanced_form id TRUE the form will offer additional choices
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| 155 |
dbf4b8a8
|
Andreas Kohlbecker
|
*
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| 156 |
73874c48
|
Andreas Kohlbecker
|
* @param array $form
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| 157 |
7b4c053d
|
Andreas Kohlbecker
|
* A drupal form array
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| 158 |
73874c48
|
Andreas Kohlbecker
|
* @param array $form_state
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| 159 |
7b4c053d
|
Andreas Kohlbecker
|
* The drupal form state passed as reference
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| 160 |
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* @param bool $advanced_form
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| 161 |
73874c48
|
Andreas Kohlbecker
|
* default is FALSE
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| 162 |
7b4c053d
|
Andreas Kohlbecker
|
* @param bool $classification_select
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| 163 |
01fff74a
|
Andreas Kohlbecker
|
* set TRUE to offer a classification selector in the form - default is FALSE
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| 164 |
73874c48
|
Andreas Kohlbecker
|
* if only available in the advanced mode
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| 165 |
dbf4b8a8
|
Andreas Kohlbecker
|
*
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| 166 |
7b4c053d
|
Andreas Kohlbecker
|
* @return array
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| 167 |
dbf4b8a8
|
Andreas Kohlbecker
|
* the form array
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| 168 |
6657531f
|
Andreas Kohlbecker
|
*/
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| 169 |
6eaec849
|
Katja Luther
|
function cdm_dataportal_search_taxon_form($form, &$form_state, $advanced_form = FALSE, $classification_select = TRUE)
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| 170 |
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{
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| 171 |
6657531f
|
Andreas Kohlbecker
|
|
| 172 |
6eaec849
|
Katja Luther
|
if ($form_state['build_info']['form_id'] == 'cdm_dataportal_search_blast_form') {
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| 173 |
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$form = cdm_dataportal_search_blast_form($form, $form_state);
|
| 174 |
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} else {
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| 175 |
6657531f
|
Andreas Kohlbecker
|
|
| 176 |
2d0d855a
|
Andreas Kohlbecker
|
|
| 177 |
6eaec849
|
Katja Luther
|
$query_field_default_value = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');
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| 178 |
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| 179 |
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if ($advanced_form || variable_get(SIMPLE_SEARCH_USE_LUCENE_BACKEND, FALSE)) {
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| 180 |
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$search_service_endpoint = CDM_WS_PORTAL_TAXON_SEARCH;
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| 181 |
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} else {
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| 182 |
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$search_service_endpoint = CDM_WS_PORTAL_TAXON_FIND;
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| 183 |
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}
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| 184 |
cd64df61
|
Andreas Kohlbecker
|
|
| 185 |
6eaec849
|
Katja Luther
|
$form = cdm_dataportal_search_form_prepare(
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| 186 |
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'cdm_dataportal/search/results/taxon',
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| 187 |
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$search_service_endpoint,
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| 188 |
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$query_field_default_value,
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| 189 |
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t('Enter the name or part of a name you wish to search for.
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| 190 |
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The asterisk character * can be used as wildcard, but must not be used as first character.')
|
| 191 |
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);
|
| 192 |
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}
|
| 193 |
7b4c053d
|
Andreas Kohlbecker
|
if (!$advanced_form) {
|
| 194 |
6657531f
|
Andreas Kohlbecker
|
$form['query']['#size'] = 20;
|
| 195 |
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}
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| 196 |
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| 197 |
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$form['search']['pageSize'] = array(
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| 198 |
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'#weight' => -1,
|
| 199 |
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'#type' => 'hidden',
|
| 200 |
44458b04
|
Andreas Kohlbecker
|
'#value' => variable_get(CDM_SEARCH_RESULT_PAGE_SIZE, CDM_SEARCH_RESULT_PAGE_SIZE_DEFAULT),
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| 201 |
6657531f
|
Andreas Kohlbecker
|
);
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| 202 |
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| 203 |
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$form['search']['pageNumber'] = array(
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| 204 |
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'#weight' => -1,
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| 205 |
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'#type' => 'hidden',
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| 206 |
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'#value' => 0,
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| 207 |
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);
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| 208 |
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| 209 |
7b4c053d
|
Andreas Kohlbecker
|
$search_taxa_mode_settings = get_array_variable_merged(
|
| 210 |
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CDM_SEARCH_TAXA_MODE,
|
| 211 |
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CDM_SEARCH_TAXA_MODE_DEFAULT
|
| 212 |
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);
|
| 213 |
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$preset_do_taxa = $search_taxa_mode_settings['doTaxa'] !== 0;
|
| 214 |
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$preset_do_synonyms = $search_taxa_mode_settings['doSynonyms'] !== 0;
|
| 215 |
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$preset_do_taxa_by_common_names = $search_taxa_mode_settings['doTaxaByCommonNames'] !== 0;
|
| 216 |
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$preset_do_misapplied_names = $search_taxa_mode_settings['doMisappliedNames'] !== 0;
|
| 217 |
6657531f
|
Andreas Kohlbecker
|
|
| 218 |
7b4c053d
|
Andreas Kohlbecker
|
if ($advanced_form) {
|
| 219 |
642b323b
|
Andreas Kohlbecker
|
|
| 220 |
6280e639
|
Andreas Kohlbecker
|
// --- ADVANCED SEARCH FORM ---
|
| 221 |
61b6ee11
|
Andreas Kohlbecker
|
//
|
| 222 |
dbf4b8a8
|
Andreas Kohlbecker
|
|
| 223 |
6657531f
|
Andreas Kohlbecker
|
// Get presets from settings.
|
| 224 |
7663cd0b
|
Andreas Kohlbecker
|
$preset_classification_uuid = get_current_classification_uuid();
|
| 225 |
6657531f
|
Andreas Kohlbecker
|
|
| 226 |
|
|
// Overwrite presets by user choice stored in session.
|
| 227 |
6280e639
|
Andreas Kohlbecker
|
if (isset($_SESSION['cdm']['search'])) {
|
| 228 |
7b4c053d
|
Andreas Kohlbecker
|
$preset_do_taxa = (isset($_SESSION['cdm']['search']['doTaxa']) ? 1 : 0);
|
| 229 |
|
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$preset_do_synonyms = (isset($_SESSION['cdm']['search']['doSynonyms']) ? 1 : 0);
|
| 230 |
|
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$preset_do_misapplied_names = (isset($_SESSION['cdm']['search']['doMisappliedNames']) ? 1 : 0);
|
| 231 |
|
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$preset_do_taxa_by_common_names = (isset($_SESSION['cdm']['search']['doTaxaByCommonNames']) ? 1 : 0);
|
| 232 |
61b6ee11
|
Andreas Kohlbecker
|
if (isset($_SESSION['cdm']['search']['tree'])) {
|
| 233 |
|
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$preset_classification_uuid = $_SESSION['cdm']['search']['tree'];
|
| 234 |
|
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}
|
| 235 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 236 |
dbf4b8a8
|
Andreas Kohlbecker
|
|
| 237 |
7b4c053d
|
Andreas Kohlbecker
|
if ($classification_select === TRUE) {
|
| 238 |
f56b1626
|
Andreas Kohlbecker
|
$form['search']['tree'] = array(
|
| 239 |
642b323b
|
Andreas Kohlbecker
|
'#title' => t('Classification'),
|
| 240 |
|
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'#weight' => 1,
|
| 241 |
|
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'#type' => 'select',
|
| 242 |
7d42c393
|
Andreas Kohlbecker
|
'#default_value' => $preset_classification_uuid,
|
| 243 |
f56b1626
|
Andreas Kohlbecker
|
'#options' => cdm_get_taxontrees_as_options(TRUE),
|
| 244 |
8ae3cfe3
|
Andreas Kohlbecker
|
'#description' => t('A filter to limit the search to a specific classification. Choosing <em>--- ALL ---</em> will disable this filter.'),
|
| 245 |
dbf4b8a8
|
Andreas Kohlbecker
|
);
|
| 246 |
632a697a
|
Andreas Kohlbecker
|
}
|
| 247 |
dbf4b8a8
|
Andreas Kohlbecker
|
|
| 248 |
6657531f
|
Andreas Kohlbecker
|
// General search parameters.
|
| 249 |
|
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$form['search']['doTaxa'] = array(
|
| 250 |
|
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'#weight' => 2,
|
| 251 |
|
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'#type' => 'checkbox',
|
| 252 |
51384c70
|
Andreas Kohlbecker
|
'#title' => t('Include') . ' ' . t('accepted taxa'),
|
| 253 |
7b4c053d
|
Andreas Kohlbecker
|
'#value' => $preset_do_taxa,
|
| 254 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 255 |
|
|
$form['search']['doSynonyms'] = array(
|
| 256 |
|
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'#weight' => 3,
|
| 257 |
|
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'#type' => 'checkbox',
|
| 258 |
51384c70
|
Andreas Kohlbecker
|
'#title' => t('Include') . ' ' . t('synonyms'),
|
| 259 |
7b4c053d
|
Andreas Kohlbecker
|
'#value' => $preset_do_synonyms,
|
| 260 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 261 |
|
|
$form['search']['doMisappliedNames'] = array(
|
| 262 |
|
|
'#weight' => 4,
|
| 263 |
|
|
'#type' => 'checkbox',
|
| 264 |
51384c70
|
Andreas Kohlbecker
|
'#title' => t('Include') . ' ' . t('misapplied names'),
|
| 265 |
7b4c053d
|
Andreas Kohlbecker
|
'#value' => $preset_do_misapplied_names,
|
| 266 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 267 |
|
|
$form['search']['doTaxaByCommonNames'] = array(
|
| 268 |
|
|
'#weight' => 5,
|
| 269 |
|
|
'#type' => 'checkbox',
|
| 270 |
51384c70
|
Andreas Kohlbecker
|
'#title' => t('Include') . ' ' . t('common names'),
|
| 271 |
7b4c053d
|
Andreas Kohlbecker
|
'#value' => $preset_do_taxa_by_common_names,
|
| 272 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 273 |
|
|
|
| 274 |
7b4c053d
|
Andreas Kohlbecker
|
$area_term_dtos = cdm_ws_fetch_all(
|
| 275 |
|
|
CDM_WS_DESCRIPTION_NAMEDAREAS_IN_USE,
|
| 276 |
|
|
array('includeAllParents' => 'true')
|
| 277 |
|
|
);
|
| 278 |
446cffc5
|
Andreas Kohlbecker
|
|
| 279 |
86424a78
|
Andreas Kohlbecker
|
// create map: term_uuid => term
|
| 280 |
41c6dd13
|
Andreas Kohlbecker
|
$term_map = array();
|
| 281 |
7b4c053d
|
Andreas Kohlbecker
|
foreach ($area_term_dtos as $term_dto) {
|
| 282 |
41c6dd13
|
Andreas Kohlbecker
|
$term_map[$term_dto->uuid] = $term_dto;
|
| 283 |
632a697a
|
Andreas Kohlbecker
|
}
|
| 284 |
41c6dd13
|
Andreas Kohlbecker
|
|
| 285 |
632a697a
|
Andreas Kohlbecker
|
$term_tree = array();
|
| 286 |
41c6dd13
|
Andreas Kohlbecker
|
// mixed_vocabularies will contain the uuid vocabularies which
|
| 287 |
86424a78
|
Andreas Kohlbecker
|
// also contain terms of foreign vocabularies due to the term
|
| 288 |
41c6dd13
|
Andreas Kohlbecker
|
// hierarchy
|
| 289 |
|
|
$mixed_vocabularies = array();
|
| 290 |
|
|
|
| 291 |
|
|
// Build hierarchy of the terms regardless of the vocabulary.
|
| 292 |
a783afbc
|
Andreas Kohlbecker
|
foreach ($term_map as $term_dto) {
|
| 293 |
|
|
if (!empty($term_dto->partOfUuid)) {
|
| 294 |
|
|
// Children.
|
| 295 |
|
|
$parent =& $term_map[$term_dto->partOfUuid];
|
| 296 |
|
|
if ($parent) {
|
| 297 |
|
|
if (!isset($parent->children)) {
|
| 298 |
|
|
$parent->children = array();
|
| 299 |
446cffc5
|
Andreas Kohlbecker
|
}
|
| 300 |
a783afbc
|
Andreas Kohlbecker
|
$parent->children[$term_dto->uuid] = $term_dto;
|
| 301 |
|
|
if ($parent->vocabularyUuid != $term_dto->vocabularyUuid) {
|
| 302 |
|
|
$mixed_vocabularies[$parent->vocabularyUuid] = $parent->vocabularyUuid;
|
| 303 |
41c6dd13
|
Andreas Kohlbecker
|
}
|
| 304 |
632a697a
|
Andreas Kohlbecker
|
}
|
| 305 |
446cffc5
|
Andreas Kohlbecker
|
}
|
| 306 |
a783afbc
|
Andreas Kohlbecker
|
else {
|
| 307 |
|
|
// group root nodes by vocabulary
|
| 308 |
|
|
if (!isset($term_tree[$term_dto->vocabularyUuid])) {
|
| 309 |
|
|
$term_tree[$term_dto->vocabularyUuid] = array();
|
| 310 |
|
|
}
|
| 311 |
|
|
$term_tree[$term_dto->vocabularyUuid][$term_dto->uuid] = $term_dto;
|
| 312 |
|
|
}
|
| 313 |
|
|
}
|
| 314 |
|
|
|
| 315 |
072122ee
|
Andreas Kohlbecker
|
$show_area_filter = ! variable_get(CDM_SEARCH_AREA_FILTER_PRESET, '');
|
| 316 |
446cffc5
|
Andreas Kohlbecker
|
|
| 317 |
072122ee
|
Andreas Kohlbecker
|
if($show_area_filter){
|
| 318 |
|
|
drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/search_area_filter.js');
|
| 319 |
|
|
|
| 320 |
|
|
drupal_add_js('jQuery(document).ready(function() {
|
| 321 |
446cffc5
|
Andreas Kohlbecker
|
jQuery(\'#edit-search-areas\').search_area_filter(\'#edit-search-areas-areas-filter\');
|
| 322 |
|
|
});
|
| 323 |
|
|
', array('type' => 'inline'));
|
| 324 |
|
|
|
| 325 |
072122ee
|
Andreas Kohlbecker
|
$form['search']['areas'] = array(
|
| 326 |
|
|
'#type' => 'fieldset',
|
| 327 |
|
|
'#title' => t('Filter by distribution areas'),
|
| 328 |
|
|
'#description' => t('The search will return taxa having distribution
|
| 329 |
722b1688
|
Andreas Kohlbecker
|
information for at least one of the selected areas.') . ' '
|
| 330 |
072122ee
|
Andreas Kohlbecker
|
.(count($term_tree) > 1 ? t('The areas are grouped
|
| 331 |
722b1688
|
Andreas Kohlbecker
|
by the vocabularies to which the highest level areas belong.') : ''),
|
| 332 |
632a697a
|
Andreas Kohlbecker
|
);
|
| 333 |
072122ee
|
Andreas Kohlbecker
|
$form['search']['areas']['areas_filter'] = array(
|
| 334 |
|
|
'#type' => 'textfield',
|
| 335 |
|
|
'#description' => t('Type to filter the areas listed below.'),
|
| 336 |
|
|
);
|
| 337 |
|
|
$vocab_cnt = 0;
|
| 338 |
|
|
$areas_defaults = array();
|
| 339 |
|
|
if (isset($_SESSION['cdm']['search']['area'])) {
|
| 340 |
|
|
$areas_defaults = explode(',', $_SESSION['cdm']['search']['area']);
|
| 341 |
|
|
}
|
| 342 |
6b605d3b
|
Andreas Kohlbecker
|
_add_js_resizable_element('.resizable-box', true);
|
| 343 |
072122ee
|
Andreas Kohlbecker
|
foreach ($term_tree as $vocab_uuid => $term_dto_tree) {
|
| 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 |
6b605d3b
|
Andreas Kohlbecker
|
. '</strong><div class="resizable-container"><div class="resizable-box">',
|
| 350 |
072122ee
|
Andreas Kohlbecker
|
'#type' => 'checkboxes',
|
| 351 |
|
|
'#default_value' => $areas_defaults,
|
| 352 |
|
|
'#options' => $areas_options,
|
| 353 |
6b605d3b
|
Andreas Kohlbecker
|
'#suffix' => '</div></div>'
|
| 354 |
072122ee
|
Andreas Kohlbecker
|
);
|
| 355 |
|
|
}
|
| 356 |
632a697a
|
Andreas Kohlbecker
|
}
|
| 357 |
446cffc5
|
Andreas Kohlbecker
|
|
| 358 |
7b4c053d
|
Andreas Kohlbecker
|
}
|
| 359 |
|
|
else {
|
| 360 |
61b6ee11
|
Andreas Kohlbecker
|
// --- SIMPLE SEARCH FORM ---
|
| 361 |
|
|
//
|
| 362 |
|
|
|
| 363 |
6657531f
|
Andreas Kohlbecker
|
// Overwrite presets by user choice stored in session.
|
| 364 |
6280e639
|
Andreas Kohlbecker
|
if (isset($_SESSION['cdm']['search'])) {
|
| 365 |
7b4c053d
|
Andreas Kohlbecker
|
$preset_do_misapplied_names = (isset($_SESSION['cdm']['search']['doMisappliedNames']) ? 1 : 0);
|
| 366 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 367 |
|
|
|
| 368 |
|
|
$form['search']['doTaxa'] = array(
|
| 369 |
|
|
'#weight' => -2,
|
| 370 |
|
|
'#type' => 'hidden',
|
| 371 |
7b4c053d
|
Andreas Kohlbecker
|
'#value' => $preset_do_taxa,
|
| 372 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 373 |
|
|
$form['search']['doSynonyms'] = array(
|
| 374 |
|
|
'#weight' => -3,
|
| 375 |
|
|
'#type' => 'hidden',
|
| 376 |
7b4c053d
|
Andreas Kohlbecker
|
'#value' => $preset_do_synonyms,
|
| 377 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 378 |
|
|
$form['search']['doMisappliedNames'] = array(
|
| 379 |
|
|
'#weight' => -4,
|
| 380 |
|
|
'#type' => 'checkbox',
|
| 381 |
|
|
'#title' => t('Misapplied names'),
|
| 382 |
7b4c053d
|
Andreas Kohlbecker
|
'#value' => $preset_do_misapplied_names,
|
| 383 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 384 |
|
|
$form['search']['doTaxaByCommonNames'] = array(
|
| 385 |
|
|
'#weight' => -5,
|
| 386 |
|
|
'#type' => 'hidden',
|
| 387 |
7b4c053d
|
Andreas Kohlbecker
|
'#value' => $preset_do_taxa_by_common_names,
|
| 388 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 389 |
|
|
}
|
| 390 |
|
|
|
| 391 |
|
|
return $form;
|
| 392 |
|
|
}
|
| 393 |
632a697a
|
Andreas Kohlbecker
|
|
| 394 |
6eaec849
|
Katja Luther
|
/**
|
| 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 |
2f30124c
|
Andreas Kohlbecker
|
$search_service_endpoint = CDM_SEARCH_BLAST_SERVICE_URI;
|
| 417 |
6eaec849
|
Katja Luther
|
|
| 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 |
44458b04
|
Andreas Kohlbecker
|
'#value' => variable_get(CDM_SEARCH_RESULT_PAGE_SIZE, CDM_SEARCH_RESULT_PAGE_SIZE_DEFAULT),
|
| 432 |
6eaec849
|
Katja Luther
|
);
|
| 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 |
6657531f
|
Andreas Kohlbecker
|
/**
|
| 577 |
7b4c053d
|
Andreas Kohlbecker
|
* 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 $form_state
|
| 587 |
|
|
* The drupal form state passed as reference
|
| 588 |
|
|
*
|
| 589 |
|
|
* @return array
|
| 590 |
|
|
* The form array
|
| 591 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 592 |
|
|
function cdm_dataportal_search_taxon_form_advanced($form, &$form_state) {
|
| 593 |
|
|
return cdm_dataportal_search_taxon_form($form, $form_state, TRUE);
|
| 594 |
|
|
}
|
| 595 |
|
|
|
| 596 |
|
|
/**
|
| 597 |
7b4c053d
|
Andreas Kohlbecker
|
* Form for searching taxa by the findByDescriptionElementFullText rest service.
|
| 598 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 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 |
632a697a
|
Andreas Kohlbecker
|
'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 |
20624f5a
|
Andreas Kohlbecker
|
used as wildcard, but must not be used as first character. Terms can be combined with 'AND'. To search for a
|
| 608 |
36af8b60
|
Andreas Kohlbecker
|
full phrase enclose the terms in parentheses. For more syntactical
|
| 609 |
7b4c053d
|
Andreas Kohlbecker
|
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 |
a6ae799b
|
Andreas Kohlbecker
|
)
|
| 621 |
632a697a
|
Andreas Kohlbecker
|
);
|
| 622 |
6657531f
|
Andreas Kohlbecker
|
|
| 623 |
|
|
$form['search']['tree'] = array(
|
| 624 |
|
|
'#weight' => -1,
|
| 625 |
|
|
'#type' => 'hidden',
|
| 626 |
7663cd0b
|
Andreas Kohlbecker
|
'#value' => get_current_classification_uuid(),
|
| 627 |
6657531f
|
Andreas Kohlbecker
|
);
|
| 628 |
|
|
|
| 629 |
|
|
$form['search']['hl'] = array(
|
| 630 |
|
|
'#weight' => -1,
|
| 631 |
|
|
'#type' => 'hidden',
|
| 632 |
|
|
'#value' => 1,
|
| 633 |
|
|
);
|
| 634 |
|
|
|
| 635 |
b58fcc1f
|
Andreas Kohlbecker
|
// Only available to admins:
|
| 636 |
6657531f
|
Andreas Kohlbecker
|
if (!isset($_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 |
b58fcc1f
|
Andreas Kohlbecker
|
'#title' => t('Limit to description item type'),
|
| 643 |
6657531f
|
Andreas Kohlbecker
|
'#default_value' => $_SESSION['cdm']['search']['clazz'],
|
| 644 |
|
|
'#options' => cdm_descriptionElementTypes_as_option(TRUE),
|
| 645 |
|
|
);
|
| 646 |
|
|
}
|
| 647 |
|
|
|
| 648 |
7b4c053d
|
Andreas Kohlbecker
|
$profile_feature_tree = get_profile_feature_tree();
|
| 649 |
|
|
$feature_options = _featureTree_nodes_as_feature_options($profile_feature_tree->root);
|
| 650 |
6657531f
|
Andreas Kohlbecker
|
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 |
7b4c053d
|
Andreas Kohlbecker
|
* Processes the query parameters of the search form.
|
| 670 |
|
|
*
|
| 671 |
|
|
* Reads the query parameters from $_REQUEST and modifies and adds additional
|
| 672 |
103a1463
|
Andreas Kohlbecker
|
* query parameters if necessary.
|
| 673 |
dbf4b8a8
|
Andreas Kohlbecker
|
*
|
| 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 |
b3d49e6e
|
Andreas Kohlbecker
|
* @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 |
7b4c053d
|
Andreas Kohlbecker
|
* @return array
|
| 685 |
dbf4b8a8
|
Andreas Kohlbecker
|
* the processed request parameters submitted by the search form and
|
| 686 |
|
|
* also stores them in $_SESSION['cdm']['search']
|
| 687 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 688 |
b3d49e6e
|
Andreas Kohlbecker
|
function cdm_dataportal_search_request($search_endpoint)
|
| 689 |
f48cede0
|
Andreas Kohlbecker
|
{
|
| 690 |
61b6ee11
|
Andreas Kohlbecker
|
|
| 691 |
6657531f
|
Andreas Kohlbecker
|
$form_params = array();
|
| 692 |
61b6ee11
|
Andreas Kohlbecker
|
|
| 693 |
34dd7be9
|
Andreas Kohlbecker
|
if (isset($_REQUEST['search']) && is_array($_REQUEST['search'])) {
|
| 694 |
6657531f
|
Andreas Kohlbecker
|
array_deep_copy($_REQUEST['search'], $form_params);
|
| 695 |
|
|
}
|
| 696 |
34dd7be9
|
Andreas Kohlbecker
|
|
| 697 |
|
|
if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
|
| 698 |
|
|
$form_params = array_merge($form_params, $_REQUEST['pager']);
|
| 699 |
|
|
}
|
| 700 |
|
|
|
| 701 |
6657531f
|
Andreas Kohlbecker
|
$form_params['query'] = trim($_REQUEST['query']);
|
| 702 |
|
|
|
| 703 |
b3d49e6e
|
Andreas Kohlbecker
|
|
| 704 |
6657531f
|
Andreas Kohlbecker
|
// --- handle geographic range
|
| 705 |
|
|
// Split of geographic range.
|
| 706 |
44756fcd
|
Andreas Kohlbecker
|
unset($form_params['areas']);
|
| 707 |
072122ee
|
Andreas Kohlbecker
|
|
| 708 |
9bbe3bcd
|
Andreas Kohlbecker
|
$area_filter_preset = null;
|
| 709 |
f48cede0
|
Andreas Kohlbecker
|
if (variable_get(CDM_SEARCH_AREA_FILTER_PRESET, '')) {
|
| 710 |
|
|
$area_filter_preset = explode(',', variable_get(CDM_SEARCH_AREA_FILTER_PRESET, ''));
|
| 711 |
|
|
}
|
| 712 |
072122ee
|
Andreas Kohlbecker
|
|
| 713 |
30399ffa
|
Andreas Kohlbecker
|
$area_uuids = array();
|
| 714 |
072122ee
|
Andreas Kohlbecker
|
if($area_filter_preset){
|
| 715 |
|
|
$area_uuids = $area_filter_preset;
|
| 716 |
|
|
}
|
| 717 |
|
|
elseif (isset($_REQUEST['search']['areas']['area']) && is_array($_REQUEST['search']['areas']['area'])) {
|
| 718 |
7b4c053d
|
Andreas Kohlbecker
|
foreach ($_REQUEST['search']['areas']['area'] as $areas) {
|
| 719 |
|
|
$area_uuids = array_merge($area_uuids, $areas);
|
| 720 |
|
|
}
|
| 721 |
efa372e9
|
Andreas Kohlbecker
|
// 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'] = $presence_term_uuids;
|
| 725 |
072122ee
|
Andreas Kohlbecker
|
}
|
| 726 |
30399ffa
|
Andreas Kohlbecker
|
if(count($area_uuids) > 0){
|
| 727 |
7b4c053d
|
Andreas Kohlbecker
|
$form_params['area'] = implode(',', $area_uuids);
|
| 728 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 729 |
|
|
|
| 730 |
7b4c053d
|
Andreas Kohlbecker
|
// Simple search will not submit a 'tree' query parameter,
|
| 731 |
|
|
// so we add it here from what is stored in the session unless
|
| 732 |
90a6166e
|
Andreas Kohlbecker
|
// SIMPLE_SEARCH_IGNORE_CLASSIFICATION is checked in the settings.
|
| 733 |
|
|
if (!isset($form_params['tree']) && !variable_get(SIMPLE_SEARCH_IGNORE_CLASSIFICATION, 0)) {
|
| 734 |
7663cd0b
|
Andreas Kohlbecker
|
$form_params['tree'] = get_current_classification_uuid();
|
| 735 |
61b6ee11
|
Andreas Kohlbecker
|
}
|
| 736 |
38753115
|
Andreas Kohlbecker
|
// Store in session.
|
| 737 |
|
|
$_SESSION['cdm']['search'] = $form_params;
|
| 738 |
|
|
|
| 739 |
|
|
// ----------- further processing that must not be store in the session --------- //
|
| 740 |
|
|
|
| 741 |
67a5cafa
|
Andreas Kohlbecker
|
if($search_endpoint == CDM_WS_PORTAL_TAXON_SEARCH){
|
| 742 |
a15edbb0
|
Andreas Kohlbecker
|
// HACK to allow using dot characters
|
| 743 |
|
|
$form_params['query'] = str_replace('.', '*', $form_params['query']);
|
| 744 |
a0557101
|
Andreas Kohlbecker
|
// 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'] = $form_params['query'] . '"' ;
|
| 751 |
|
|
}
|
| 752 |
67a5cafa
|
Andreas Kohlbecker
|
}
|
| 753 |
|
|
}
|
| 754 |
|
|
|
| 755 |
efa372e9
|
Andreas Kohlbecker
|
// If the 'NONE' classification has been chosen (advanced search)
|
| 756 |
7b4c053d
|
Andreas Kohlbecker
|
// delete the tree information to avoid unknown uuid exceptions in the
|
| 757 |
|
|
// cdm service.
|
| 758 |
|
|
if (isset($form_params['tree'])
|
| 759 |
|
|
&& ($form_params['tree'] == 'NONE' || !is_uuid($form_params['tree']))
|
| 760 |
|
|
) {
|
| 761 |
|
|
// $form_params['ignore_classification'] = TRUE;
|
| 762 |
dbf4b8a8
|
Andreas Kohlbecker
|
unset($form_params['tree']);
|
| 763 |
|
|
}
|
| 764 |
7b4c053d
|
Andreas Kohlbecker
|
// else {
|
| 765 |
|
|
// $form_params['ignore_classification'] = NULL;
|
| 766 |
|
|
// }
|
| 767 |
dbf4b8a8
|
Andreas Kohlbecker
|
|
| 768 |
6657531f
|
Andreas Kohlbecker
|
|
| 769 |
|
|
return $form_params;
|
| 770 |
|
|
}
|
| 771 |
|
|
|
| 772 |
6eaec849
|
Katja Luther
|
/**
|
| 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 |
72d57201
|
Katja Luther
|
$form_params['data'] = formatWSParams($_REQUEST['search']);
|
| 796 |
|
|
$form_params['query']= trim($_REQUEST['query']).$form_params['data'];
|
| 797 |
6eaec849
|
Katja Luther
|
// Store in session.
|
| 798 |
|
|
$_SESSION['cdm']['search'] = $form_params;
|
| 799 |
|
|
return $form_params;
|
| 800 |
|
|
}
|
| 801 |
|
|
|
| 802 |
61b6ee11
|
Andreas Kohlbecker
|
/**
|
| 803 |
44756fcd
|
Andreas Kohlbecker
|
* Provides the classification to which the last search has been limited to..
|
| 804 |
61b6ee11
|
Andreas Kohlbecker
|
*
|
| 805 |
24797d7f
|
Andreas Kohlbecker
|
* This function should only be used after the cdm_dataportal_search_taxon_execute()
|
| 806 |
efa372e9
|
Andreas Kohlbecker
|
* handler has been run, otherwise it will return the information from the last
|
| 807 |
7b4c053d
|
Andreas Kohlbecker
|
* search executed. The information is retrieved from
|
| 808 |
61b6ee11
|
Andreas Kohlbecker
|
* the $_SESSION variable: $_SESSION['cdm']['search']['tree']
|
| 809 |
|
|
*
|
| 810 |
7b4c053d
|
Andreas Kohlbecker
|
* @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 |
61b6ee11
|
Andreas Kohlbecker
|
*/
|
| 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 |
7b4c053d
|
Andreas Kohlbecker
|
}
|
| 823 |
|
|
else {
|
| 824 |
61b6ee11
|
Andreas Kohlbecker
|
$classification = FALSE;
|
| 825 |
|
|
}
|
| 826 |
|
|
}
|
| 827 |
|
|
|
| 828 |
7b4c053d
|
Andreas Kohlbecker
|
return $classification !== FALSE ? $classification : NULL;
|
| 829 |
61b6ee11
|
Andreas Kohlbecker
|
}
|
| 830 |
|
|
|
| 831 |
a6ae799b
|
Andreas Kohlbecker
|
/**
|
| 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 |
6657531f
|
Andreas Kohlbecker
|
/**
|
| 853 |
103a1463
|
Andreas Kohlbecker
|
* Sends a search request to the cdm server.
|
| 854 |
dbf4b8a8
|
Andreas Kohlbecker
|
*
|
| 855 |
|
|
* The parameters to build the query are taken obtained by calling
|
| 856 |
efa372e9
|
Andreas Kohlbecker
|
* cdm_dataportal_search_request() which reads the query parameters
|
| 857 |
dbf4b8a8
|
Andreas Kohlbecker
|
* from $_REQUEST and add additional query parameters if nessecary.
|
| 858 |
|
|
*
|
| 859 |
efa372e9
|
Andreas Kohlbecker
|
* @see cdm_dataportal_search_request()
|
| 860 |
6657531f
|
Andreas Kohlbecker
|
*/
|
| 861 |
24797d7f
|
Andreas Kohlbecker
|
function cdm_dataportal_search_taxon_execute() {
|
| 862 |
6657531f
|
Andreas Kohlbecker
|
|
| 863 |
|
|
// Store as last search in session.
|
| 864 |
|
|
$_SESSION['cdm']['last_search'] = $_SERVER['REQUEST_URI'];
|
| 865 |
|
|
|
| 866 |
|
|
// Validate the search webservice parameter:
|
| 867 |
7b4c053d
|
Andreas Kohlbecker
|
if (!isset($_REQUEST['ws'])) {
|
| 868 |
|
|
drupal_set_message(
|
| 869 |
103a1463
|
Andreas Kohlbecker
|
t("Invalid search, webservice parameter 'ws' is missing"), 'warning'
|
| 870 |
7b4c053d
|
Andreas Kohlbecker
|
);
|
| 871 |
61b6ee11
|
Andreas Kohlbecker
|
return NULL;
|
| 872 |
|
|
}
|
| 873 |
7b4c053d
|
Andreas Kohlbecker
|
if (!cdm_dataportal_search_form_path_for_ws($_REQUEST['ws'])) {
|
| 874 |
6657531f
|
Andreas Kohlbecker
|
// Endpoint is unknown.
|
| 875 |
7b4c053d
|
Andreas Kohlbecker
|
drupal_set_message(
|
| 876 |
78ec4159
|
Andreas Kohlbecker
|
t("Invalid search webservice parameter 'ws' given"), 'warning'
|
| 877 |
7b4c053d
|
Andreas Kohlbecker
|
);
|
| 878 |
6657531f
|
Andreas Kohlbecker
|
return NULL;
|
| 879 |
|
|
}
|
| 880 |
|
|
|
| 881 |
7b4c053d
|
Andreas Kohlbecker
|
// Read the query parameters from $_REQUEST and add additional query
|
| 882 |
|
|
// parameters if necessary.
|
| 883 |
b3d49e6e
|
Andreas Kohlbecker
|
$request_params = cdm_dataportal_search_request($_REQUEST['ws']);
|
| 884 |
dbf4b8a8
|
Andreas Kohlbecker
|
|
| 885 |
446cffc5
|
Andreas Kohlbecker
|
$taxon_pager = cdm_ws_get($_REQUEST['ws'], NULL, queryString($request_params));
|
| 886 |
|
|
|
| 887 |
|
|
return $taxon_pager;
|
| 888 |
|
|
}
|
| 889 |
|
|
|
| 890 |
6eaec849
|
Katja Luther
|
/**
|
| 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 |
72d57201
|
Katja Luther
|
$request_params['timeout'] = 200;
|
| 924 |
6eaec849
|
Katja Luther
|
$taxon_pager = drupal_http_request($_REQUEST['ws'].'?sequence='.$request_params['query'], $request_params);
|
| 925 |
|
|
|
| 926 |
|
|
return $taxon_pager;
|
| 927 |
|
|
}
|
| 928 |
|
|
|
| 929 |
|
|
|
| 930 |
a6ae799b
|
Andreas Kohlbecker
|
|
| 931 |
|
|
/**
|
| 932 |
efbff4b3
|
Andreas Kohlbecker
|
* Sends a request for a registrations filter search to the cdm server.
|
| 933 |
a6ae799b
|
Andreas Kohlbecker
|
*/
|
| 934 |
efbff4b3
|
Andreas Kohlbecker
|
function cdm_dataportal_search_registrations_filter_execute()
|
| 935 |
a6ae799b
|
Andreas Kohlbecker
|
{
|
| 936 |
|
|
|
| 937 |
|
|
static $query_param_map = array(
|
| 938 |
|
|
'identifier' => 'identifierFilterPattern',
|
| 939 |
|
|
'taxon_name'=> 'taxonNameFilterPattern',
|
| 940 |
c5089cec
|
Andreas Kohlbecker
|
'reference_citation' => 'referenceFilterPattern',
|
| 941 |
dc58a71b
|
Andreas Kohlbecker
|
'type_designation_status_uuids' => 'typeDesignationStatusUuids',
|
| 942 |
a6ae799b
|
Andreas Kohlbecker
|
);
|
| 943 |
|
|
|
| 944 |
efbff4b3
|
Andreas Kohlbecker
|
$session_key = SESSION_KEY_SEARCH_REGISTRATION_FILTER;
|
| 945 |
|
|
$request_params = cdm_dataportal_search_request_params($session_key, $query_param_map);
|
| 946 |
a6ae799b
|
Andreas Kohlbecker
|
|
| 947 |
|
|
// cleanup
|
| 948 |
|
|
if(isset($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 |
bb177c82
|
Andreas Kohlbecker
|
}
|
| 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 |
a6ae799b
|
Andreas Kohlbecker
|
}
|
| 962 |
c5089cec
|
Andreas Kohlbecker
|
// 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 |
a6ae799b
|
Andreas Kohlbecker
|
|
| 971 |
|
|
$registration_pager = cdm_ws_get('registrationDTO/find', NULL, queryString($request_params));
|
| 972 |
|
|
|
| 973 |
|
|
return $registration_pager;
|
| 974 |
|
|
}
|
| 975 |
|
|
|
| 976 |
efbff4b3
|
Andreas Kohlbecker
|
/**
|
| 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 |
e2617c7e
|
Andreas Kohlbecker
|
* The key to be used for storing the search params in $_SESSION['cdm'][]
|
| 1006 |
efbff4b3
|
Andreas Kohlbecker
|
* @param $query_param_map
|
| 1007 |
e2617c7e
|
Andreas Kohlbecker
|
* An array which maps the filter_key to the web service query parameter.
|
| 1008 |
|
|
* The filter key may be used as form element name or as drupal url
|
| 1009 |
|
|
* query parameter.
|
| 1010 |
efbff4b3
|
Andreas Kohlbecker
|
* @return array
|
| 1011 |
|
|
*/
|
| 1012 |
|
|
function cdm_dataportal_search_request_params($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 |
7b4c053d
|
Andreas Kohlbecker
|
/**
|
| 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(), $prefix = '') {
|
| 1073 |
|
|
|
| 1074 |
c079337e
|
Andreas Kohlbecker
|
uasort($term_dto_tree, 'compare_terms_by_order_index');
|
| 1075 |
7b4c053d
|
Andreas Kohlbecker
|
foreach ($term_dto_tree as $uuid => $dto) {
|
| 1076 |
|
|
$label = $prefix . '<span class="child-label">'
|
| 1077 |
|
|
. $dto->representation_L10n
|
| 1078 |
35619936
|
Andreas Kohlbecker
|
. '</span><span class="child-label-abbreviated"> (' . $dto->representation_L10n_abbreviatedLabel . ')</span>';
|
| 1079 |
7b4c053d
|
Andreas Kohlbecker
|
$options[$uuid] = $label;
|
| 1080 |
|
|
if (isset($dto->children) && is_array($dto->children)) {
|
| 1081 |
|
|
term_tree_as_options(
|
| 1082 |
|
|
$dto->children,
|
| 1083 |
|
|
$options, $prefix
|
| 1084 |
fdf52d6a
|
Andreas Kohlbecker
|
. '<span data-cdm-parent="' . $uuid . '" class="parent"></span>'
|
| 1085 |
|
|
);
|
| 1086 |
446cffc5
|
Andreas Kohlbecker
|
}
|
| 1087 |
7b4c053d
|
Andreas Kohlbecker
|
}
|
| 1088 |
6657531f
|
Andreas Kohlbecker
|
|
| 1089 |
7b4c053d
|
Andreas Kohlbecker
|
return $options;
|
| 1090 |
6657531f
|
Andreas Kohlbecker
|
}
|
| 1091 |
a6ae799b
|
Andreas Kohlbecker
|
|
| 1092 |
|
|
|
| 1093 |
efbff4b3
|
Andreas Kohlbecker
|
function cdm_dataportal_search_registration_filter_form($form, &$form_state) {
|
| 1094 |
a6ae799b
|
Andreas Kohlbecker
|
|
| 1095 |
d68a30b0
|
Andreas Kohlbecker
|
static $filter_presets_empty = array(
|
| 1096 |
|
|
'identifier'=> null,
|
| 1097 |
|
|
'taxon_name'=> null,
|
| 1098 |
c5089cec
|
Andreas Kohlbecker
|
'reference_citation'=> null,
|
| 1099 |
dc58a71b
|
Andreas Kohlbecker
|
'type_designation_status_uuids' => null
|
| 1100 |
d68a30b0
|
Andreas Kohlbecker
|
);
|
| 1101 |
|
|
|
| 1102 |
6d9071b7
|
Andreas Kohlbecker
|
_add_font_awesome_font();
|
| 1103 |
bb177c82
|
Andreas Kohlbecker
|
|
| 1104 |
5195ddf2
|
Andreas Kohlbecker
|
if(isset($_REQUEST['q']) && ($_REQUEST['q'] == 'cdm_dataportal/registration-search/filter' || $_REQUEST['q'] == 'cdm_dataportal/registration-search')){
|
| 1105 |
efbff4b3
|
Andreas Kohlbecker
|
// 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 |
a6ae799b
|
Andreas Kohlbecker
|
$filter_presets = (isset($_SESSION['cdm'][SESSION_KEY_SEARCH_REGISTRATION_FILTER]) ? $_SESSION['cdm'][SESSION_KEY_SEARCH_REGISTRATION_FILTER] : array());
|
| 1111 |
efbff4b3
|
Andreas Kohlbecker
|
$filter_presets = array_merge($filter_presets_empty, $filter_presets, $request_params);
|
| 1112 |
|
|
$form['#action'] = url('/cdm_dataportal/registration-search/filter');
|
| 1113 |
a6ae799b
|
Andreas Kohlbecker
|
$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 |
c5089cec
|
Andreas Kohlbecker
|
$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 |
dc58a71b
|
Andreas Kohlbecker
|
$form['type_designation_status_uuids'] = array(
|
| 1137 |
a6ae799b
|
Andreas Kohlbecker
|
'#type' => 'select',
|
| 1138 |
|
|
'#title' => t('Type designation status'),
|
| 1139 |
88131480
|
Andreas Kohlbecker
|
'#multiple' => true,
|
| 1140 |
dc58a71b
|
Andreas Kohlbecker
|
'#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 |
a6ae799b
|
Andreas Kohlbecker
|
);
|
| 1144 |
|
|
|
| 1145 |
|
|
$form['submit'] = array(
|
| 1146 |
c8624e9a
|
Andreas Kohlbecker
|
'#markup' => '<button type="submit" title="Search" class="form-submit">' . font_awesome_icon_markup('fa-search') . '</button>'
|
| 1147 |
098b6358
|
Andreas Kohlbecker
|
// '#prefix' => "<div class=\"form-item\"><label> </label>",
|
| 1148 |
|
|
// '#suffix' => "</div>"
|
| 1149 |
a6ae799b
|
Andreas Kohlbecker
|
|
| 1150 |
|
|
);
|
| 1151 |
|
|
return $form;
|
| 1152 |
|
|
}
|
| 1153 |
|
|
|
| 1154 |
|
|
|
| 1155 |
efbff4b3
|
Andreas Kohlbecker
|
function cdm_dataportal_search_registration_taxongraph_form($form, &$form_state) {
|
| 1156 |
|
|
|
| 1157 |
|
|
static $filter_presets_empty = array(
|
| 1158 |
|
|
'taxon_name'=> null
|
| 1159 |
|
|
);
|
| 1160 |
|
|
|
| 1161 |
|
|
_add_font_awesome_font();
|
| 1162 |
|
|
|
| 1163 |
5195ddf2
|
Andreas Kohlbecker
|
if(isset($_REQUEST['q']) && $_REQUEST['q'] == 'cdm_dataportal/registration-search/taxongraph'){
|
| 1164 |
efbff4b3
|
Andreas Kohlbecker
|
// 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 |
a6ae799b
|
Andreas Kohlbecker
|
/**
|
| 1195 |
|
|
* Compose the result set of a registration search from a pager object
|
| 1196 |
|
|
*
|
| 1197 |
e2617c7e
|
Andreas Kohlbecker
|
* @param $cdm_item_pager
|
| 1198 |
a6ae799b
|
Andreas Kohlbecker
|
* The pager containing registration objects
|
| 1199 |
|
|
*
|
| 1200 |
|
|
* @return
|
| 1201 |
|
|
* A drupal render array.
|
| 1202 |
|
|
*
|
| 1203 |
|
|
* @ingroup compose
|
| 1204 |
|
|
*
|
| 1205 |
|
|
* TODO compose function into search.inc ?
|
| 1206 |
|
|
*/
|
| 1207 |
e2617c7e
|
Andreas Kohlbecker
|
function compose_search_results($cdm_item_pager, ItemComposeHandler $item_compose_handler){
|
| 1208 |
a6ae799b
|
Andreas Kohlbecker
|
|
| 1209 |
|
|
$render_array = array();
|
| 1210 |
6789eff8
|
Andreas Kohlbecker
|
$render_array['pre'] = markup_to_render_array("<div class=\"cdm-item-list\">");
|
| 1211 |
0b494565
|
Andreas Kohlbecker
|
|
| 1212 |
e2617c7e
|
Andreas Kohlbecker
|
if($cdm_item_pager != null && count($cdm_item_pager->records) > 0){
|
| 1213 |
a6ae799b
|
Andreas Kohlbecker
|
$items_render_array = array();
|
| 1214 |
e2617c7e
|
Andreas Kohlbecker
|
foreach($cdm_item_pager->records as $registration_dto) {
|
| 1215 |
26b8a1bc
|
Andreas Kohlbecker
|
|
| 1216 |
|
|
$items_render_array[] = array(
|
| 1217 |
e2617c7e
|
Andreas Kohlbecker
|
'#prefix' => "<div class=\"item\"><div class=\"" . $item_compose_handler->getClassAttributes($registration_dto) . "\">",
|
| 1218 |
|
|
'item_data' => $item_compose_handler->composeItem($registration_dto),
|
| 1219 |
26b8a1bc
|
Andreas Kohlbecker
|
'#suffix' => "</div></div>"
|
| 1220 |
a6ae799b
|
Andreas Kohlbecker
|
);
|
| 1221 |
|
|
;
|
| 1222 |
|
|
}
|
| 1223 |
efbff4b3
|
Andreas Kohlbecker
|
|
| 1224 |
a6ae799b
|
Andreas Kohlbecker
|
$render_array['items'] = $items_render_array;
|
| 1225 |
|
|
$render_array['pager'] = markup_to_render_array(theme('cdm_pager', array(
|
| 1226 |
e2617c7e
|
Andreas Kohlbecker
|
'pager' => $cdm_item_pager,
|
| 1227 |
efbff4b3
|
Andreas Kohlbecker
|
'path' => $_REQUEST['q'], // stay on same page
|
| 1228 |
a6ae799b
|
Andreas Kohlbecker
|
'parameters' => $_REQUEST,
|
| 1229 |
|
|
)));
|
| 1230 |
|
|
|
| 1231 |
|
|
} else {
|
| 1232 |
e2617c7e
|
Andreas Kohlbecker
|
if($cdm_item_pager != null && $cdm_item_pager->count > 0 && count($cdm_item_pager->records) == 0){
|
| 1233 |
0b494565
|
Andreas Kohlbecker
|
$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 |
a6ae799b
|
Andreas Kohlbecker
|
}
|
| 1238 |
|
|
$render_array['post'] = markup_to_render_array("</div>");
|
| 1239 |
|
|
|
| 1240 |
|
|
return $render_array;
|
| 1241 |
|
|
|
| 1242 |
e2617c7e
|
Andreas Kohlbecker
|
}
|
| 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 |
77451b2a
|
Andreas Kohlbecker
|
$restrictions = [];
|
| 1268 |
|
|
if( isset($request_params['markerType'])){
|
| 1269 |
|
|
$restrictions = array(new Restriction("markers.markerType.uuid","EXACT", array($request_params['markerType']), 'AND'));
|
| 1270 |
|
|
}
|
| 1271 |
e2617c7e
|
Andreas Kohlbecker
|
$init_strategy = array(
|
| 1272 |
|
|
"$",
|
| 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 |
77451b2a
|
Andreas Kohlbecker
|
$page_index = 0;
|
| 1283 |
|
|
if(isset($_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 |
e2617c7e
|
Andreas Kohlbecker
|
|
| 1288 |
|
|
return $pager;
|
| 1289 |
|
|
}
|