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<?php
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/**
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* @file
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* Functions for dealing with CDM entities from the package model.common
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*
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* @copyright
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* (C) 2007-2012 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this module are subject to the Mozilla
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* Public License Version 1.1.
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* @see http://www.mozilla.org/MPL/MPL-1.1.html
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*
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* @author
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* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
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*/
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/**
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* @defgroup compose Compose functions
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* @{
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* Functions which are composing Drupal render arays
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*
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* The cdm_dataportal module needs to compose rather complex render arrays from
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* the data returned by the CDM REST service. The compose functions are
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* responsible for creating the render arrays.
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*
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* All these functions are also implementations of the compose_hook()
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* which is used in the proxy_content() function.
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* @}
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*/
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/**
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* Composes an HTML element class attribute value composed of
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* the short-name of the cdm class and the uuid of the entity.
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* This class attribute should be used wherever an cdm-entity is rendered.
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*
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* In case of Taxon entities or TaxonNodeDTOs the secReference is also added
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* to the class attributes as 'sec_uuid:<uuid>'. In case of TaxonNodeDTOs the
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* Taxon uuid is added also as taxon_uuid:<uuid>
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*
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* These according class selectors in css must be escaped, eg:
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* .cdm\:TextData
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*
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* @param $cdm_entity
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* A CDM entity, TaxonNodeDTO or TypedEntityReference
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*/
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function html_class_attribute_ref($cdm_entity) {
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$attributes = '';
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if (is_cdm_entity($cdm_entity)) {
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// Entities
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$attributes = "cdm:" . $cdm_entity->class . " uuid:" . $cdm_entity->uuid;
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switch ($cdm_entity->class){
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case 'Taxon':
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if(isset($cdm_entity->sec->uuid)){
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$attributes .= " sec_uuid:" . $cdm_entity->sec->uuid;
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}
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break;
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}
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} elseif (isset($cdm_entity->class)) {
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// DTOs
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if(isset_not_empty($cdm_entity->type) && isset_not_empty($cdm_entity->uuid)){
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$attributes = "cdm:" . $cdm_entity->type . " uuid:" . $cdm_entity->uuid;
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}
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// additional data of specific DTOs
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switch ($cdm_entity->class){
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case 'TaxonNodeDto':
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$attributes .= "taxon_uuid:" . $cdm_entity->taxonUuid . " sec_uuid:" . $cdm_entity->secUuid;;
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break;
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}
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}
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return $attributes;
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}
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/**
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* Compose an render array from a CDM Marker object.
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*
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* compose_hook() implementation
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*
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* @param object $marker
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* CDM instance of type Marker
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* @return array
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* A drupal render array
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*
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* @ingroup compose
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*/
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function compose_cdm_marker($marker) {
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$label = $marker->markerType->representation_L10n . ': ' . (($marker->flag !== TRUE ? t('yes') : t('no')));
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return markup_to_render_array('<span class="' . html_class_attribute_ref($marker) . '">' . $label . '</span>');
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}
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/**
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* Checks if the given $cdm_entitiy has a marker the type references by the
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* $marker_type_uuid and returns TRUE if a matching marker has been found.
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*
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* @param object $cdm_entitiy A CDM Entity
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* @param string $marker_type_uuid
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*/
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function cdm_entity_has_marker($cdm_entitiy, $marker_type_uuid) {
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if(isset($cdm_entitiy->markers[0]) && !is_uuid($marker_type_uuid)){
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foreach ($cdm_entitiy->markers as $marker) {
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if(isset($marker->markerType) && $marker->markerType->uuid == $marker_type_uuid){
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return TRUE;
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}
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}
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}
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return FALSE;
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}
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/**
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* Sorts an array of CDM IdentifiableSource instances by 1. by the
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* author teams family names and 2. by the publication date.
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*
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* @param array $sources
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* The array of CDM IdentifiableSource instances
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* @return array
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* An array of drupal render arrays
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*/
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function oder_and_render_original_sources($sources){
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$sort_array = array();
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foreach ($sources as $source) {
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$order_key = '';
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// find the familynames
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if(isset($source->citation->uuid) && !isset($source->citation->authorship)){
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$authorteam = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $source->citation->uuid);
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$persons = array();
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if($authorteam->class == 'Team'){
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if(isset($authorteam->teamMembers)){
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$persons = $authorteam->teamMembers;
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}
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} else {
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$persons[] = $authorteam;
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}
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foreach($persons as $person){
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if(!empty($person->lastname)){
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$order_key .= $person->lastname;
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} else {
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$order_key .= $person->titleCache;
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}
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}
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if(empty($order_key)){
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$order_key = $authorteam->titleCache;
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}
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}
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$order_key = str_pad($order_key, 50);
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// add publication date to the key
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if(isset($source->citation->datePublished)){
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$order_key .= '_' . timePeriodAsOrderKey($source->citation->datePublished);
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} else {
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$order_key .= '_' . "0000";
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}
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// padd key until unique
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while(array_key_exists($order_key, $sort_array)){
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$order_key .= "_";
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}
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$sort_array[$order_key] = render_original_source($source);
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}
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ksort($sort_array);
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return array_values ($sort_array);
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}
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/**
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* Compare callback to be used in usort to sort image sources of CDM OriginalSource instances.
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*
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* TODO the compare strategy implemented in oder_and_render_original_sources() is probably better but is not taking the
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* originalName into account.
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*
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* @param $a
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* @param $b
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*/
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function compare_original_sources($a, $b){
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$a_string = '';
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if(isset($a->citation->titleCache)) {
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$a_string = $a->citation->titleCache;
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}
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if((isset($a->nameUsedInSource))){
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$a_string .= $a->nameUsedInSource->titleCache;
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} elseif (isset($a->originalNameString)){
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$a_string .= $a->originalNameString;
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}
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$b_string = '';
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if(isset($b->citation->titleCache)) {
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$b_string = $b->citation->titleCache;
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};
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if((isset($b->nameUsedInSource))){
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$b_string .= $b->nameUsedInSource->titleCache;
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} elseif (isset($b->originalNameString)){
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$b_string .= $b->originalNameString;
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}
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if ($a_string == $b_string) {
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return 0;
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}
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return ($a_string < $b_string) ? -1 : 1;
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}
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/**
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* Compare callback to be used in usort to sort image sources of CDM Media instances.
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*
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* @param $a
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* @param $b
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*/
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function compare_text_data($a, $b) {
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if ($a->multilanguageText_L10n->text == $b->multilanguageText_L10n->text) {
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return 0;
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}
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return ($a->multilanguageText_L10n->text < $b->multilanguageText_L10n->text) ? -1 : 1;
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}
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/**
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* Provides an explanatory text on the statistical values representation as generated by statistical_values()
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*
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* @return string
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* the text
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*/
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function statistical_values_explanation(){
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return t("A single or the first number in square brackets denotes sample size");
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}
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/**
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* Creates an array suitable to be used in statistical_values()
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* The min max structure is suitable for being used in the context
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* of GatheringEvents and StatisticalMeasures (see render_quantitative_statistics()).
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*
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* The order of the items is important for the display and must not be changed.
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*
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* @return array
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*/
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function statistical_values_array() {
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$min_max = [
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'ExactValue' => NULL,
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'Min' => NULL,
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'TypicalLowerBoundary' => NULL,
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'TypicalUpperBoundary' => NULL,
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'Max' => NULL,
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'SampleSize' => NULL,
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'Average' => NULL,
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'Variance' => NULL,
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'StandardDeviation' => NULL
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];
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return $min_max;
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}
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/**
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* Creates markup from a min max array.
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*
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263
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* NOTE: use statistical_values_array() to create an appropriate array
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*
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265
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* Internally Min will be translated to TypicalLowerBoundary if no such value is present.
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* The same also accounts for Max and TypicalUpperBoundary.
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*
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268
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* For further details see #3742, #8766
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269
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*
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270
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* @param $stat_vals_arr
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271
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* the statistical values array as produced by statistical_values_array()
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* @param $unit
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273
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* Defaults to no unit
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274
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* @return string
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275
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*/
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276
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function statistical_values($stat_vals_arr, $unit = '') {
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277
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278
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static $xbar_equals = 'x̄='; // x̄ is x-bar (http://www.personal.psu.edu/ejp10/blogs/gotunicode/2010/03/dealing-with-x-bar-x-and-p-hat.html)
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279
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280
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$exact_markup = '';
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281
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$min_max_markup = '';
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282
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$other_vals_array = [];
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283
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284
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// --- sanitize values
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285
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if(statistical_values_num_equals($stat_vals_arr, 'Min', 'TypicalLowerBoundary')){
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286
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$stat_vals_arr['Min'] = NULL;
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287
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}
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288
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289
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if(statistical_values_num_equals($stat_vals_arr, 'Max', 'TypicalUpperBoundary')){
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290
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$stat_vals_arr['Max'] = NULL;
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291
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}
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292
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293
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if($stat_vals_arr['TypicalLowerBoundary'] === null && $stat_vals_arr['Min'] !== null){
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294
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$stat_vals_arr['TypicalLowerBoundary'] = $stat_vals_arr['Min'];
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295
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$stat_vals_arr['Min'] = NULL;
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296
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}
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297
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298
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if($stat_vals_arr['TypicalUpperBoundary'] === null && $stat_vals_arr['Max'] !== null){
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299
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$stat_vals_arr['TypicalUpperBoundary'] = $stat_vals_arr['Max'];
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300
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$stat_vals_arr['Max'] = NULL;
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301
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}
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302
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303
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if (statistical_values_num_equals($stat_vals_arr, 'TypicalUpperBoundary', 'TypicalLowerBoundary')) {
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304
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$stat_vals_arr['Average'] = $stat_vals_arr['TypicalUpperBoundary'];
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305
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$stat_vals_arr['TypicalLowerBoundary'] = NULL;
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306
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$stat_vals_arr['TypicalUpperBoundary'] = NULL;
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307
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}
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308
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309
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// --- check for inconsistent cases, eg. only Max and average given
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310
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if ($stat_vals_arr['TypicalLowerBoundary'] === NULL && $stat_vals_arr['TypicalUpperBoundary'] !== null) {
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311
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// min missing
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312
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$stat_vals_arr['TypicalLowerBoundary'] = '?';
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313
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}
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314
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if ($stat_vals_arr['TypicalLowerBoundary'] !== null && $stat_vals_arr['TypicalUpperBoundary'] === NULL) {
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315
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// max missing
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316
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$stat_vals_arr['TypicalUpperBoundary'] = '?';
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317
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}
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318
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319
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if(statistical_values_is_numeric($stat_vals_arr['Average']) && statistical_values_is_numeric($stat_vals_arr['TypicalUpperBoundary']) && statistical_values_is_numeric($stat_vals_arr['TypicalLowerBoundary'])) {
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320
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statistical_values_adjust_significant_figures($stat_vals_arr['Average'], $stat_vals_arr['TypicalLowerBoundary'], $stat_vals_arr['TypicalUpperBoundary']);
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321
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}
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322
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323
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foreach ($stat_vals_arr as $key => $statistical_val) {
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324
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325
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if ($statistical_val !== NULL) {
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326
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if ($statistical_val == '?') {
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327
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$val_markup = $statistical_val;
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328
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}
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329
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else {
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330
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if (is_numeric($statistical_val->_value)) {
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331
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$val_markup = '<span class="'
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332
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. html_class_attribute_ref($statistical_val) . ' '
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333
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. (isset($statistical_val->type) ? $statistical_val->type->termType : '') . ' ' . $key . '" title="' . $key . '">'
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334
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. $statistical_val->_value . '</span>';
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335
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336
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}
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337
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else {
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338
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$val_markup = NULL;
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339
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}
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340
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}
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341
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342
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if ($val_markup) {
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343
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switch ($key) {
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344
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case 'ExactValue':
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345
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$exact_markup = $val_markup;
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346
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break;
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347
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// ---- min_max_element
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348
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case 'Min':
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349
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$min_max_markup .= "($val_markup–)";
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350
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break;
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351
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case 'Max':
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352
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$min_max_markup .= "(–$val_markup)";
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353
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break;
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354
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case 'TypicalLowerBoundary':
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355
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$min_max_markup .= "$val_markup";
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356
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break;
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357
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case 'TypicalUpperBoundary':
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358
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$min_max_markup .= "–$val_markup";
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359
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break;
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360
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// ---- other values
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361
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case 'SampleSize':
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362
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$other_vals_array[$key] = $val_markup;
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363
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break;
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364
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case 'Average':
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365
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$other_vals_array[$key] = $xbar_equals . $val_markup;
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366
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break;
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367
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case 'Variance':
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368
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$other_vals_array[$key] = 'σ²=' . $val_markup;
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369
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break;
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370
|
case 'StandardDeviation':
|
|
371
|
$other_vals_array[$key] = 'σ=' . $val_markup;
|
|
372
|
break;
|
|
373
|
}
|
|
374
|
}
|
|
375
|
}
|
|
376
|
}
|
|
377
|
|
|
378
|
$full_markup = $exact_markup . ($exact_markup ? ' ' : '') . $min_max_markup;
|
|
379
|
|
|
380
|
if(!$full_markup && !empty($other_vals_array['Average'])){
|
|
381
|
// this could be the case in which we only have one value for Average
|
|
382
|
// this trivial case needs to be displayed a simpler way
|
|
383
|
$full_markup = str_replace($xbar_equals, '' , $other_vals_array['Average']);
|
|
384
|
unset($other_vals_array['Average']);
|
|
385
|
}
|
|
386
|
if($unit){
|
|
387
|
$full_markup .= ' ' . $unit;
|
|
388
|
}
|
|
389
|
if(count($other_vals_array)){
|
|
390
|
$full_markup .= ' [' . join(';', $other_vals_array) . ']';
|
|
391
|
}
|
|
392
|
|
|
393
|
return $full_markup;
|
|
394
|
}
|
|
395
|
|
|
396
|
/**
|
|
397
|
* Calculates the required precision for the target value to be significantly different from min and may and rounds it.
|
|
398
|
*
|
|
399
|
* @param $target
|
|
400
|
* The statistical value to be rounded to the least significant precision
|
|
401
|
* @param $min
|
|
402
|
* The lower bound to calculate the least significant precision
|
|
403
|
* @param $max
|
|
404
|
* The upper bound to calculate the least significant precision
|
|
405
|
* @param int $threshold
|
|
406
|
* Per default 1, but can be set to any other value > 0 and < 1 to define
|
|
407
|
* another threshold for the transition to the next precision level.
|
|
408
|
* E.g. A value of 0.5 will cause values > 50 and <= 500 to be shown with
|
|
409
|
* a precision of 2, whereas with a threshold of 1 the values > 10 and <= 100
|
|
410
|
* will be shown with a precision of 2 figures
|
|
411
|
*/
|
|
412
|
function statistical_values_adjust_significant_figures(&$target, $min, $max, $threshold = 1){
|
|
413
|
|
|
414
|
$precision = 1;
|
|
415
|
if($min->_value !== $max->_value){
|
|
416
|
$precision = floor(log10(abs($max->_value - $min->_value) * (1 / $threshold)));
|
|
417
|
// increase precision by one
|
|
418
|
$precision += $precision < 0 ? - 1 : 1;
|
|
419
|
}
|
|
420
|
|
|
421
|
$target->_value = sigFig($target->_value, $precision);
|
|
422
|
}
|
|
423
|
|
|
424
|
/**
|
|
425
|
* based on an idea taken from https://stackoverflow.com/questions/37618679/format-number-to-n-significant-digits-in-php#answer-48283297
|
|
426
|
*
|
|
427
|
* @param $value
|
|
428
|
* @param $digits
|
|
429
|
*
|
|
430
|
* @return float|string
|
|
431
|
*/
|
|
432
|
function sigFig($value, $digits, $round_only = true)
|
|
433
|
{
|
|
434
|
if ($value == 0) {
|
|
435
|
$decimalPlaces = $digits - 1;
|
|
436
|
} elseif ($value < 0) {
|
|
437
|
$decimalPlaces = $digits - floor(log10($value * -1)) - 1;
|
|
438
|
} else {
|
|
439
|
$decimalPlaces = $digits - floor(log10($value)) - 1;
|
|
440
|
}
|
|
441
|
|
|
442
|
$answer = ($decimalPlaces > 0) && !$round_only ?
|
|
443
|
number_format($value, $decimalPlaces) : round($value, abs($decimalPlaces));
|
|
444
|
return $answer;
|
|
445
|
}
|
|
446
|
|
|
447
|
|
|
448
|
|
|
449
|
/**
|
|
450
|
* Used internally in statistical_values() do determine numerically equality of stat_vals_arr values
|
|
451
|
*
|
|
452
|
* @param $stat_vals_arr
|
|
453
|
* @param $key1
|
|
454
|
* @param $key2
|
|
455
|
*
|
|
456
|
* @return bool
|
|
457
|
*/
|
|
458
|
function statistical_values_num_equals($stat_vals_arr, $key1, $key2){
|
|
459
|
|
|
460
|
return $stat_vals_arr[$key1] !== NULL && $stat_vals_arr[$key2] !== NULL && $stat_vals_arr[$key1]->_value == $stat_vals_arr[$key2]->_value && is_numeric($stat_vals_arr[$key1]->_value);
|
|
461
|
}
|
|
462
|
|
|
463
|
function statistical_values_is_numeric($stat_val){
|
|
464
|
return $stat_val !== null && is_numeric($stat_val->_value);
|
|
465
|
}
|
|
466
|
|
|
467
|
/**
|
|
468
|
* Creates min max markup to represent a min-average-max measure optionally with an error value.
|
|
469
|
*
|
|
470
|
* The fields that are taken into account are:
|
|
471
|
* - field_base_name = min
|
|
472
|
* - field_base_nameMax = max
|
|
473
|
* - field_base_nameText = free text
|
|
474
|
* - field_base_nameError = error value
|
|
475
|
*
|
|
476
|
* @param $object
|
|
477
|
* The object having min max measurement fields e.g.: GatheringEvent
|
|
478
|
* @param string $field_base_name
|
|
479
|
* The base name for all measurement fields. This name is at the same time the full name of the
|
|
480
|
* min value.
|
|
481
|
* @return string
|
|
482
|
* The markup for the min max
|
|
483
|
*
|
|
484
|
* @see statistical_values()
|
|
485
|
*/
|
|
486
|
function statistical_values_from_gathering_event($object, $field_base_name)
|
|
487
|
{
|
|
488
|
static $default_unit = 'm';
|
|
489
|
|
|
490
|
$field_name = $field_base_name . 'Text';
|
|
491
|
if (isset_not_empty($object->$field_name)) {
|
|
492
|
// Freetext overrides all other data
|
|
493
|
$min_max_markup = ' ' . $object->$field_name;
|
|
494
|
} else {
|
|
495
|
// create markup for the atomized min max data
|
|
496
|
$min_max_array = statistical_values_array();
|
|
497
|
if (isset_numerical($object->$field_base_name)) {
|
|
498
|
$min_max_array['TypicalLowerBoundary'] = new stdClass();
|
|
499
|
$min_max_array['TypicalLowerBoundary']->_value = $object->$field_base_name;
|
|
500
|
}
|
|
501
|
$field_name = $field_base_name . 'Max';
|
|
502
|
if (isset_numerical($object->$field_name)) {
|
|
503
|
$min_max_array['TypicalUpperBoundary'] = new stdClass();
|
|
504
|
$min_max_array['TypicalUpperBoundary']->_value = $object->$field_name;
|
|
505
|
} else {
|
|
506
|
$min_max_array['Average'] = $min_max_array['TypicalLowerBoundary'];
|
|
507
|
$min_max_array['TypicalLowerBoundary'] = null;
|
|
508
|
}
|
|
509
|
$min_max_markup = statistical_values($min_max_array, $default_unit);
|
|
510
|
}
|
|
511
|
|
|
512
|
return $min_max_markup;
|
|
513
|
}
|
|
514
|
|
|
515
|
// TODO move below code into new file: agent.inc
|
|
516
|
|
|
517
|
/*
|
|
518
|
* Compose an render array from a CDM TaxonNodeAgentRelation object as Taxon Expert.
|
|
519
|
*
|
|
520
|
* compose_hook() implementation
|
|
521
|
*
|
|
522
|
* @param object $taxon_node_agent_relation
|
|
523
|
* CDM instance of type TaxonNodeAgentRelation
|
|
524
|
* @return array
|
|
525
|
* A drupal render array
|
|
526
|
*
|
|
527
|
* @ingroup compose
|
|
528
|
*/
|
|
529
|
function compose_cdm_taxon_expert($taxon_node_agent_relation) {
|
|
530
|
|
|
531
|
$agent_details = null;
|
|
532
|
|
|
533
|
$label_suffix = ':';
|
|
534
|
|
|
535
|
if($taxon_node_agent_relation->class == 'DefaultPagerImpl'){
|
|
536
|
// oops this is a pager
|
|
537
|
// this situation will occur when this compose is executed
|
|
538
|
// through the proxy_content() method
|
|
539
|
$taxon_node_agent_relation = $taxon_node_agent_relation->records[0];
|
|
540
|
|
|
541
|
}
|
|
542
|
|
|
543
|
if(is_object($taxon_node_agent_relation->agent)) {
|
|
544
|
$agent_details = compose_cdm_team_or_person_base($taxon_node_agent_relation->agent);
|
|
545
|
// all data will be added to the groups of the agent_details render array
|
|
546
|
$groups = &$agent_details[0]['#groups'];
|
|
547
|
|
|
548
|
@_description_list_group_add($groups, t('Role'). $label_suffix, $taxon_node_agent_relation->type->representation_L10n);
|
|
549
|
|
|
550
|
$family_tnars = cdm_ws_fetch_all(CDM_WS_PORTAL_AGENT . '/' . $taxon_node_agent_relation->agent->uuid . '/taxonNodeAgentRelations', array("rank"=>"Familia"));
|
|
551
|
|
|
552
|
$taxa_markup = array(
|
|
553
|
'#theme_wrappers' => array('container'),
|
|
554
|
'#attributes' => array('class' => array('managed_taxa')),
|
|
555
|
'#wrapper_attributes' => array('class' => 'sublist-container')
|
|
556
|
);
|
|
557
|
foreach($family_tnars as $tnar){
|
|
558
|
if(is_object($tnar->taxonNode->taxon)){
|
|
559
|
$taxa_markup[$tnar->taxonNode->taxon->titleCache] = markup_to_render_array(render_taxon_or_name($tnar->taxonNode->taxon, url(path_to_taxon($tnar->taxonNode->taxon->uuid))));
|
|
560
|
}
|
|
561
|
}
|
|
562
|
ksort($taxa_markup);
|
|
563
|
|
|
564
|
@_description_list_group_add($groups, t('Families'). $label_suffix, array($taxa_markup));
|
|
565
|
|
|
566
|
}
|
|
567
|
|
|
568
|
return $agent_details;
|
|
569
|
}
|
|
570
|
|
|
571
|
|
|
572
|
/*
|
|
573
|
* Compose an render array from a CDM TeamOrPersonBase object.
|
|
574
|
*
|
|
575
|
* compose_hook() implementation
|
|
576
|
*
|
|
577
|
* TODO: currently mainly implemented for Agent, add Team details
|
|
578
|
*
|
|
579
|
* @param object $team_or_person
|
|
580
|
* CDM instance of type TeamOrPersonBase
|
|
581
|
* @return array
|
|
582
|
* A drupal render array
|
|
583
|
*
|
|
584
|
* @ingroup compose
|
|
585
|
*/
|
|
586
|
function compose_cdm_team_or_person_base($team_or_person, $data = array()) {
|
|
587
|
|
|
588
|
$groups = array();
|
|
589
|
|
|
590
|
$label_suffix = ':';
|
|
591
|
|
|
592
|
// $weight = 0;
|
|
593
|
if($team_or_person){
|
|
594
|
|
|
595
|
if(is_object($team_or_person->lifespan)){
|
|
596
|
// ToDo render as date* - date† ?
|
|
597
|
@_description_list_group_add($groups, t('Lifespan'). $label_suffix, timePeriodToString($team_or_person->lifespan) /*, '' , $weight++ */);
|
|
598
|
}
|
|
599
|
|
|
600
|
// nomenclaturalTitle
|
|
601
|
@_description_list_group_add($groups, "Nomenclatural Title". $label_suffix, $team_or_person->nomenclaturalTitle);
|
|
602
|
// collectorTitle
|
|
603
|
@_description_list_group_add($groups, "Collector Title". $label_suffix, $team_or_person->collectorTitle);
|
|
604
|
|
|
605
|
// institutionalMemberships
|
|
606
|
if(is_array($team_or_person->institutionalMemberships)){
|
|
607
|
|
|
608
|
$institutes_ra = array();
|
|
609
|
foreach($team_or_person->institutionalMemberships as $membership) {
|
|
610
|
$membership_groups = array();
|
|
611
|
@_description_list_group_add($membership_groups, t('Department'). $label_suffix, $membership->department);
|
|
612
|
@_description_list_group_add($membership_groups, t('Role'). $label_suffix, $membership->role);
|
|
613
|
if(is_object($membership->period)){
|
|
614
|
@_description_list_group_add($membership_groups, t('Period'). $label_suffix, timePeriodToString($membership->period));
|
|
615
|
}
|
|
616
|
if(is_object($membership->institute->contact)){
|
|
617
|
$institute_contact_details = compose_cdm_contact($membership->institute->contact, $membership->institute->titleCache);
|
|
618
|
if(is_array($institute_contact_details[0]['#groups'])){
|
|
619
|
$membership_groups = array_merge($membership_groups, $institute_contact_details[0]['#groups']);
|
|
620
|
}
|
|
621
|
}
|
|
622
|
if(count($membership_groups) > 0){
|
|
623
|
$institutes_ra[] = array(
|
|
624
|
'#title' => $membership->institute->titleCache,
|
|
625
|
'#theme' => 'description_list',
|
|
626
|
'#groups' => $membership_groups,
|
|
627
|
'#attributes' => array('class' => html_class_attribute_ref($membership)),
|
|
628
|
'#wrapper_attributes' => array('class' => 'sublist-container')
|
|
629
|
);
|
|
630
|
} else {
|
|
631
|
// no further details for the membership, display the title
|
|
632
|
$institutes_ra[] = markup_to_render_array('<h3>' . $membership->institute->titleCache . '</h3>');
|
|
633
|
}
|
|
634
|
|
|
635
|
}
|
|
636
|
|
|
637
|
$label = count($institutes_ra) > 1 ? t('Institutes'): t('Institute');
|
|
638
|
@_description_list_group_add($groups, $label. $label_suffix, $institutes_ra /*, '' , $weight++ */);
|
|
639
|
}
|
|
640
|
|
|
641
|
|
|
642
|
// Contact
|
|
643
|
$agent_contact_details = compose_cdm_contact($team_or_person->contact, $team_or_person->titleCache);
|
|
644
|
if(is_array($agent_contact_details[0]['#groups'])){
|
|
645
|
$groups = array_merge($groups, $agent_contact_details[0]['#groups']);
|
|
646
|
}
|
|
647
|
|
|
648
|
// additional data
|
|
649
|
foreach($data as $key=>$value){
|
|
650
|
@_description_list_group_add($sub_dl_groups, t('@key', array('@key' => $key)), $value /*, '' , $weight++ */);
|
|
651
|
}
|
|
652
|
|
|
653
|
}
|
|
654
|
|
|
655
|
$team_or_person_details = array(
|
|
656
|
'#title' => $team_or_person->titleCache,
|
|
657
|
'#theme' => 'description_list',
|
|
658
|
'#groups' => $groups,
|
|
659
|
'#attributes' => array('class' => html_class_attribute_ref($team_or_person)),
|
|
660
|
);
|
|
661
|
return array($team_or_person_details);
|
|
662
|
}
|
|
663
|
|
|
664
|
|
|
665
|
/*
|
|
666
|
* Compose an render array from a CDM Contact object.
|
|
667
|
*
|
|
668
|
* compose_hook() implementation
|
|
669
|
*
|
|
670
|
* TODO: currently mainly implemented for Agent, add Team details
|
|
671
|
*
|
|
672
|
* @param object $contact
|
|
673
|
* CDM instance of type Contact
|
|
674
|
* @param $title
|
|
675
|
* The title for the description list header
|
|
676
|
* @param $weight
|
|
677
|
* Optional weight for the description list entries
|
|
678
|
* @return array
|
|
679
|
* A drupal render array
|
|
680
|
*
|
|
681
|
* @ingroup compose
|
|
682
|
*/
|
|
683
|
function compose_cdm_contact($contact, $title, $weight = 0)
|
|
684
|
{
|
|
685
|
|
|
686
|
$groups = array();
|
|
687
|
|
|
688
|
$contact_details = null;
|
|
689
|
|
|
690
|
$label_suffix = ':';
|
|
691
|
|
|
692
|
$contact_field_names_map = array(
|
|
693
|
'emailAddresses' => t('Email'),
|
|
694
|
'urls' => t('Urls'),
|
|
695
|
'phoneNumbers' => t('Phone'),
|
|
696
|
'faxNumbers' => t('Fax'),
|
|
697
|
);
|
|
698
|
|
|
699
|
// Contact
|
|
700
|
if(is_object($contact)){
|
|
701
|
if(isset($contact->addresses)){
|
|
702
|
// TODO ....
|
|
703
|
// $sub_groups = array();
|
|
704
|
// foreach($contact->addresses as $address){
|
|
705
|
// @_description_list_group_add($sub_groups, $label, $contact->$fieldName, '', $weight++);
|
|
706
|
// }
|
|
707
|
}
|
|
708
|
foreach($contact_field_names_map as $fieldName => $label){
|
|
709
|
if(is_array($contact->$fieldName)){
|
|
710
|
@_description_list_group_add($groups, $label . $label_suffix, $contact->$fieldName, '', $weight++);
|
|
711
|
}
|
|
712
|
}
|
|
713
|
$contact_details = array(
|
|
714
|
'#title' => $title,
|
|
715
|
'#theme' => 'description_list',
|
|
716
|
'#groups' => $groups
|
|
717
|
);
|
|
718
|
|
|
719
|
|
|
720
|
} else if(is_string($title)) {
|
|
721
|
// if the contact entity is empty but the title is given anyway
|
|
722
|
// we are only adding the title, using the description_list
|
|
723
|
// structure is not possible since it would be empty due to
|
|
724
|
// missing group data
|
|
725
|
$contact_details = array('#markup' => '<h3>' . $title . '</h3>');
|
|
726
|
}
|
|
727
|
|
|
728
|
return array($contact_details);
|
|
729
|
|
|
730
|
}
|
|
731
|
|
|
732
|
function visible_extensions_sorted($cdm_entity) {
|
|
733
|
|
|
734
|
$visible_extensions_sorted = [];
|
|
735
|
$extension_types_visible = variable_get(EXTENSION_TYPES_VISIBLE, unserialize(EXTENSION_TYPES_VISIBLE_DEFAULT));
|
|
736
|
if (isset($cdm_entity->extensions)) {
|
|
737
|
foreach ($cdm_entity->extensions as $ext) {
|
|
738
|
if (array_search($ext->type->uuid, $extension_types_visible)) {
|
|
739
|
if (!array_key_exists($ext->type->uuid, $visible_extensions_sorted)) {
|
|
740
|
$visible_extensions_sorted[$ext->type->uuid] = [];
|
|
741
|
}
|
|
742
|
$visible_extensions_sorted[$ext->type->uuid][] = $ext;
|
|
743
|
}
|
|
744
|
}
|
|
745
|
}
|
|
746
|
return $visible_extensions_sorted;
|
|
747
|
}
|
|
748
|
|
|
749
|
/**
|
|
750
|
* Compose an render array from a CDM Extension objects.
|
|
751
|
*
|
|
752
|
* @param $extensions
|
|
753
|
* An array of CDM Extension objects
|
|
754
|
* @return array
|
|
755
|
* A render array containing the fields of the supplied $sequence
|
|
756
|
*
|
|
757
|
* @ingroup compose
|
|
758
|
*/
|
|
759
|
function compose_extensions($extensions)
|
|
760
|
{
|
|
761
|
$render_array= null;
|
|
762
|
$extensions_by_type = array();
|
|
763
|
foreach ($extensions as $extension) {
|
|
764
|
if (@is_string($extension->value)) {
|
|
765
|
if (!isset($extensions_by_type[$extension->type->representation_L10n])) {
|
|
766
|
$extensions_by_type[$extension->type->representation_L10n] = array();
|
|
767
|
}
|
|
768
|
$extensions_by_type[$extension->type->representation_L10n][] = markup_to_render_array($extension->value);
|
|
769
|
}
|
|
770
|
}
|
|
771
|
|
|
772
|
if (count($extensions_by_type)) {
|
|
773
|
$sub_dl_groups = array();
|
|
774
|
foreach ($extensions_by_type as $type_label => $text_list) {
|
|
775
|
@_description_list_group_add($sub_dl_groups, $type_label . ':', $text_list);
|
|
776
|
}
|
|
777
|
$render_array = array(
|
|
778
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
779
|
);
|
|
780
|
return $render_array;
|
|
781
|
}
|
|
782
|
return $render_array;
|
|
783
|
}
|
|
784
|
|
|
785
|
/**
|
|
786
|
* Compose an render array from a CDM Identifier objects.
|
|
787
|
*
|
|
788
|
* @param $extensions
|
|
789
|
* An array of CDM Identifier objects
|
|
790
|
* @return array
|
|
791
|
* A render array containing the fields of the supplied $sequence
|
|
792
|
*
|
|
793
|
* @ingroup compose
|
|
794
|
*/
|
|
795
|
function compose_identifiers($identifiers){
|
|
796
|
|
|
797
|
$render_array = [];
|
|
798
|
// // urn:lsid:ipni.org:authors:20009164-1 UUID_IDENTIFIER_TYPE_LSID
|
|
799
|
foreach($identifiers as $identifier){
|
|
800
|
if($identifier->identifier){
|
|
801
|
$render_array[] = markup_to_render_array('<span class="label">' . $identifier->type->representation_L10n . ':</span> ' . $identifier->identifier, null, '<span class="'. html_class_attribute_ref($identifier) . '">', '</span>');
|
|
802
|
}
|
|
803
|
}
|
|
804
|
|
|
805
|
return $render_array;
|
|
806
|
|
|
807
|
}
|
|
808
|
|
|
809
|
function formatParams($params) {
|
|
810
|
$paramString = null;
|
|
811
|
if (is_array($params)){
|
|
812
|
$keys =array_keys($params);
|
|
813
|
$paramString = '';
|
|
814
|
foreach ($keys as $k ){
|
|
815
|
if ($k != 'pageNumber' && $k != 'pageSize'){
|
|
816
|
$paramString .= ' -'.$k.'='.urlencode($params[$k]);
|
|
817
|
}
|
|
818
|
}
|
|
819
|
}
|
|
820
|
return $paramString;
|
|
821
|
}
|
|
822
|
|
|
823
|
function formatWSParams($params) {
|
|
824
|
$paramString = null;
|
|
825
|
if (is_array($params)){
|
|
826
|
$keys =array_keys($params);
|
|
827
|
$paramString = '';
|
|
828
|
foreach ($keys as $k ){
|
|
829
|
if ($k != 'pageNumber' && $k != 'pageSize'){
|
|
830
|
$paramString .= '&'.$k.'='.urlencode($params[$k]);
|
|
831
|
}
|
|
832
|
}
|
|
833
|
}
|
|
834
|
return $paramString;
|
|
835
|
}
|
|
836
|
|
|
837
|
/**
|
|
838
|
*
|
|
839
|
* @param $cdm_entity
|
|
840
|
*
|
|
841
|
* @return string the markup
|
|
842
|
*/
|
|
843
|
function render_cdm_entity_link($cdm_entity) {
|
|
844
|
|
|
845
|
switch ($cdm_entity->class) {
|
|
846
|
case 'TaxonDescription':
|
|
847
|
case 'NameDescription':
|
|
848
|
case 'SpecimenDescription':
|
|
849
|
$link = '<span class="' . html_class_attribute_ref($cdm_entity) . '">' . $cdm_entity->titleCache . '</span> ' . icon_link(path_to_description($cdm_entity->uuid));
|
|
850
|
break;
|
|
851
|
default:
|
|
852
|
$link = '<span class="error">UNSUPPORTED CDM ENTITY TYPE</span>';
|
|
853
|
}
|
|
854
|
return $link;
|
|
855
|
}
|
|
856
|
|
|
857
|
/**
|
|
858
|
* @param $point
|
|
859
|
* @param bool $do_link_to_geohack
|
|
860
|
* @param string $geohack_link_pagename
|
|
861
|
*
|
|
862
|
* @return string
|
|
863
|
*/
|
|
864
|
function render_point($point, $do_link_to_geohack = true, $geohack_link_pagename = ''){
|
|
865
|
if(!isset($point->sexagesimalString)){
|
|
866
|
return '';
|
|
867
|
}
|
|
868
|
$markup = $point->sexagesimalString;
|
|
869
|
if($do_link_to_geohack) {
|
|
870
|
// see https://www.mediawiki.org/wiki/GeoHack
|
|
871
|
$geohack_url = sprintf(
|
|
872
|
"https://geohack.toolforge.org/geohack.php?language=en¶ms=%f;%f&pagename=%s",
|
|
873
|
$point->latitude,
|
|
874
|
$point->longitude,
|
|
875
|
$geohack_link_pagename);
|
|
876
|
$markup = l($markup, $geohack_url, ['attributes' => ['target' => 'geohack']]);
|
|
877
|
}
|
|
878
|
if(isset($point->errorRadius) && $point->errorRadius){
|
|
879
|
$markup .= ' +/-' . $point->errorRadius . ' m';
|
|
880
|
}
|
|
881
|
if(isset($point->referenceSystem) && $point->referenceSystem){
|
|
882
|
$refsystem = '(' . $point->referenceSystem->representation_L10n . ')';
|
|
883
|
$markup = str_replace($refsystem, '', $markup);
|
|
884
|
$markup .= ' ' . $refsystem;
|
|
885
|
}
|
|
886
|
return $markup;
|
|
887
|
}
|
|
888
|
|
|
889
|
/**
|
|
890
|
* Creates an icon which links to the given path
|
|
891
|
*
|
|
892
|
* @param $path
|
|
893
|
*
|
|
894
|
* @param string $fragment
|
|
895
|
* The URL fragment to link to
|
|
896
|
* @param bool $superscript
|
|
897
|
* If TRUE, the Icon will be be displayed in superscript position. Default is TRUE.
|
|
898
|
*
|
|
899
|
* @return string
|
|
900
|
*/
|
|
901
|
function icon_link($path, $fragment = '', $superscript = FALSE) {
|
|
902
|
if($superscript){
|
|
903
|
$attributes = ['class' => ['superscript']];
|
|
904
|
} else {
|
|
905
|
$attributes = [];
|
|
906
|
}
|
|
907
|
$icon_link = l(custom_icon_font_markup('icon-interal-link-alt-solid', $attributes), $path, ['html' => TRUE, 'fragment' => $fragment] );
|
|
908
|
return $icon_link;
|
|
909
|
}
|
|
910
|
|
|
911
|
/**
|
|
912
|
* Determine if a variable is set and is not NULL an is not empty.
|
|
913
|
*
|
|
914
|
* @param $var
|
|
915
|
* The variable to test
|
|
916
|
*
|
|
917
|
* @return bool
|
|
918
|
* True if the variable is set and is not NULL an is not empty.
|
|
919
|
*/
|
|
920
|
function isset_not_empty(&$var, $numerical_non_zero = FALSE){
|
|
921
|
if (!isset($var)){
|
|
922
|
return false;
|
|
923
|
}
|
|
924
|
if(is_numeric($var)) {
|
|
925
|
if($numerical_non_zero){
|
|
926
|
return $var;
|
|
927
|
} else {
|
|
928
|
true;
|
|
929
|
};
|
|
930
|
} else if(is_array($var)){
|
|
931
|
return count($var) > 0;
|
|
932
|
}else if(is_string($var)){
|
|
933
|
return !!trim($var);
|
|
934
|
} else {
|
|
935
|
return !!$var;
|
|
936
|
}
|
|
937
|
}
|
|
938
|
|
|
939
|
function isset_numerical(&$var){
|
|
940
|
if (!isset($var)){
|
|
941
|
return false;
|
|
942
|
}
|
|
943
|
return is_numeric($var);
|
|
944
|
}
|
|
945
|
|
|
946
|
function normalize_to_class_attribute($string){
|
|
947
|
$string = strtolower($string);
|
|
948
|
$string = preg_replace('/\s/', '_', $string);
|
|
949
|
$string = preg_replace('/[^a-z0-9\-_]/', '', $string);
|
|
950
|
return $string;
|
|
951
|
}
|