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<?php
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/**
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* @file
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* Page functions.
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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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* Composes a render array representing the ocurrences associetad with the $taxon.
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*
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* The resulting render array contains two elements:
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* - 'map': A map showing all point locations of the occurences is availabale
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* - 'specimen_list': the list of occurences prepated as table for theme_table()
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*
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* @param object $taxon
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* A cdm Taxon object
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* @return
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* A render array suitable for drupal_render()
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*
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* @ingroup Compose
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*
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*/
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function compose_cdm_taxon_page_specimens($taxon) {
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$render_array = array();
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RenderHints::pushToRenderStack('taxon_page_specimens');
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$fieldUnitDTOs = null;
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$specimensOrObservations = null;
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if (variable_get('cdm_dataportal_specimen_derivate_tree')){
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// get fieldUnitDTOs
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$fieldUnitDTOs = cdm_ws_get(CDM_WS_TAXON_FIELDUNIT_DTOS, array( $taxon->uuid));
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$fieldUnitDTOs = order_fieldUnitDtos_by_date_and_type($fieldUnitDTOs);
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} else {
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// $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservations'));
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// extend by associated taxas occurrences
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$relationship_filter_query_parameters = relationship_filter_query_parameters();
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if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
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$relationship_filter_query_parameters = array_merge($relationship_filter_query_parameters, $_REQUEST['pager']);
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}
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$by_associatedtaxon_query = http_build_query($relationship_filter_query_parameters);
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$pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
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null,
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$by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
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);
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$specimensOrObservations = array();
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if (isset($pager->records[0])) {
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$specimensOrObservations = $pager->records;
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}
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// cdm_ws_get(CDM_WS_OCCURRENCE_FIELDUNIT_DTO_BY_ASSOCIATEDTAXON,
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// null,
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// $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
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// );
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// $specimensOrObservations = array();
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// if(isset($pager->records[0])){
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// $specimensOrObservations = $pager->records;
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// }
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// Collect media (fieldObjectMedia, derivedUnitMedia) and add as a custom field
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foreach ($specimensOrObservations as &$occurrence) {
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$occurrence->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
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$occurrence->uuid,
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'fieldObjectMediaDTO',
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));
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$occurrence->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
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$occurrence->uuid,
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'derivedUnitMedia',
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));
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}
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$specimensOrObservations = order_specimens_or_observations_by_date_and_type($specimensOrObservations);
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}
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// --- get map service HTTP query parameters
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if (count($specimensOrObservations) > 0 || $fieldUnitDTOs > 0) {
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$render_array['map'] = occurrence_map_query_parameters($taxon);
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}
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// -------------------------------------------------------
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if(variable_get('cdm_dataportal_compressed_specimen_derivate_table')){
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//COMPRESSED SPECIMEN DERIVATE TABLE
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$associatedFieldUnitsQuery_parameters = array();
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if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
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$associatedFieldUnitsQuery_parameters = array_merge($associatedFieldUnitsQuery_parameters, $_REQUEST['pager']);
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}
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$by_associatedtaxon_query = http_build_query($associatedFieldUnitsQuery_parameters);
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$pager_field_units = cdm_ws_get(CDM_WS_PORTAL_TAXON,
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array($taxon->uuid, 'associatedFieldUnits'),
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$by_associatedtaxon_query . '&pageSize=' . variable_get('cdm_dataportal_compressed_specimen_derivate_table_page_size')
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);
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if (isset($pager_field_units->records[0])) {
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$field_unit_uuids = array();
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foreach ($pager_field_units->records as $field_unit) {
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$field_unit_uuids[] = $field_unit->uuid;
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}
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$render_array['derivate_hierarchy_table'] = compose_compressed_specimen_derivate_table($field_unit_uuids);
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}
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$render_array['pager'] = markup_to_render_array(
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theme('cdm_pager', array(
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'pager' => $pager_field_units,
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'path' => $_REQUEST['q'],
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'parameters' => $_REQUEST
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)),
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10 // weight
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);
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}
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else if(variable_get('cdm_dataportal_specimen_derivate_tree')){
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$render_array['specimen_list'] = compose_specimen_table_top_down($fieldUnitDTOs);
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$render_array['specimen_list']['#weight'] = 2;
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} else {
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$specimen_table = compose_specimens_table_bottom_up($specimensOrObservations);
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$render_array['specimen_list'] = $specimen_table;
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$render_array['pager'] = markup_to_render_array(
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theme('cdm_pager', array(
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'pager' => $pager,
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'path' => $_REQUEST['q'],
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'parameters' => $_REQUEST,
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)),
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10 // weight
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);
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}
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RenderHints::popFromRenderStack();
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return $render_array;
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}
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/**
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* @return array
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*
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* TODO move to cdm_dataportal.module or api.module?
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*/
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function relationship_filter_query_parameters()
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{
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$relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
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$relationship_choice['direct'] = get_selection($relationship_choice['direct']);
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$relationship_choice['invers'] = get_selection($relationship_choice['invers']);
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$by_associatedtaxon_query_parameters = array(
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'relationshipsInvers' => implode(',', $relationship_choice['invers']),
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'relationships' => implode(',', $relationship_choice['direct']),
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);
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return $by_associatedtaxon_query_parameters;
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}
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function create_html_link($link, $openInExternalWindow=false){
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$html = "";
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if($link->uri && $link->uri!=""){
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$html .= '<a href="' . $link->uri . '"';
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if($openInExternalWindow){
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$html .= ' target="_blank"';
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}
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$html .= '>' . $link->linkText . '</a>';
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}
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else{
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$html .= $link->linkText;
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}
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return $html;
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}
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/**
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* Creates HTML links from the given link list concatenated by default by a comma.
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* @param $linkList the list with Link objects having "uri" and "linkText" as members
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* @return string the assembled HTML string containing the links
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*/
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function create_html_links($linkList, $openInExternalWindow=false, $separator=", ")
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{
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$html = "";
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if ($linkList) {
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foreach ($linkList as $link) {
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$html .= create_html_link($link, $openInExternalWindow).$separator;
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}
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$html = rtrim($html, $separator);
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}
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return $html;
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}
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/**
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* Composes a taxon page which can consist of multiple parts like
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* 'General', 'Synonymy', 'Images', 'Keys'. These parts can be displayed
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* as tabs or as sections of a single page.
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*
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* It is headed by the name of the accepted taxon without author and reference.
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*
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* @param $taxon
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* The CDM Taxon Instance to compose the page for.
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* @param $page_part
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* Name of the part to display, valid values are:
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* - 'description' - for the general part
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* - 'images'
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* - 'synonymy'
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* - 'keys'
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* - 'all'
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*
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* @return array
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* A drupal render array
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*
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* @ingroup compose
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*/
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function compose_cdm_taxon_page($taxon, $page_part = 'description') {
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// we better cache here since drupal_get_query_parameters has no internal static cache variable
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$http_request_params = drupal_get_query_parameters();
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// add all mandatory js sources
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_add_js_footnotes();
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$render_array = array();
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$weight = 0; // the weight for the render array elements
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$tabsToDisplay = variable_get('cdm_taxonpage_tabs_visibility', unserialize(TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT));
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$page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';
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$synonymy_as_tab = variable_get(CDM_SYNONYMY_AS_TAB, CDM_SYNONYMY_AS_TAB_DEFAULT) === 1;
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if(!$synonymy_as_tab){
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unset($tabsToDisplay["Synonymy"]);
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// the synonymy is located in the general part in this case
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if($page_part == 'synonymy'){
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$page_part = 'description';
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}
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}
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$media = _load_media_for_taxon($taxon);
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if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {
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taxon_page_tabs_hidden_add('images');
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}
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// --- GET specimensOrObservations --- //
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$specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservationsCount'));
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$specimensOrObservationsCount = $specimensOrObservations != null ? $specimensOrObservations->result : 0;
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if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {
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taxon_page_tabs_hidden_add('specimens');
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}
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// --- GET polytomousKeys --- //
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$polytomousKeysPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, NULL, "findByTaxonomicScope=$taxon->uuid");
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$identificationKeyCount = 0;
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if ($polytomousKeysPager) {
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$identificationKeyCount += $polytomousKeysPager->count;
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}
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if ($identificationKeyCount == 0 || ($tabsToDisplay["Keys"] == '0')) {
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taxon_page_tabs_hidden_add('keys');
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}
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// --- GET TaxonNodeAgentRelations --- //
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$current_classification_uuid = get_current_classification_uuid();
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$taxon_node_agent_relations_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
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array(
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$taxon->uuid,
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$current_classification_uuid,
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),
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"pageSize=1&pageIndex=0"// we are only interested into the count so we are fetching only one item, o is not possible!
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);
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if (!$taxon_node_agent_relations_pager || $taxon_node_agent_relations_pager->count == 0){
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taxon_page_tabs_hidden_add('experts');
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}
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if (!isset($tabsToDisplay["Synonymy"]) || $tabsToDisplay["Synonymy"] == '0') {
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taxon_page_tabs_hidden_add('synonymy');
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}
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// -------------------------------------------- //
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if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {
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$render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);
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}
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// --- PAGE PART: DESCRIPTION --- //
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if (!taxon_page_tabs_hidden_check('description') && ($page_part == 'description' || $page_part == 'all')) {
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$merged_tree = merged_taxon_feature_tree($taxon);
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$render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, !$synonymy_as_tab);
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$render_array['general']['#weight'] = $weight++;
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$render_array['general']['#prefix'] = '<div id="general" class="page-part">';
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$render_array['general']['#suffix'] = '</div>';
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}
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// --- PAGE PART: IMAGES --- //
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if (!taxon_page_tabs_hidden_check('images') && ($page_part == 'images' || $page_part == 'all')) {
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$images_html = '<div id="images" class="page-part">';
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if ($page_part == 'all') {
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$images_html .= '<h2>' . t(cdm_taxonpage_tab_label('Images')) . '</h2>';
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}
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// Get the image gallery as configured by the admin.
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$configured_image_gallery_viewer = variable_get(CDM_MEDIA_GALLERY_VIEWER, CDM_MEDIA_GALLERY_VIEWER_DEFAULT);
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if($configured_image_gallery_viewer != 'fsi'){
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$images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);
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} else {
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// the fsi_gallery requires a flash plugin, in case the client browser is not supporting
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// flash we also need to provide an the default gallery as alternative
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$images_html .= render_taxon_media_gallery($taxon, CDM_MEDIA_GALLERY_VIEWER_DEFAULT, $media);
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$images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);
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}
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$images_html .= '</div>'; // END of <div id="images">
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$render_array['images'] = markup_to_render_array($images_html, $weight++);
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}
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// --- PAGE PART: SYNONYMY --- //
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if (!taxon_page_tabs_hidden_check('synonymy') && (($page_part == 'synonymy' || $page_part == 'all') && $synonymy_as_tab)) {
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$synonymy_html = '<div id="synonymy" class="page-part">';
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if ($page_part == 'all') {
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$synonymy_html .= '<h2>' . t(cdm_taxonpage_tab_label('Synonymy')) . '</h2>';
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}
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$addAcceptedTaxon = variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE);
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$synonym_a = compose_cdm_taxon_page_synonymy($taxon, $addAcceptedTaxon);
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333
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$synonymy_html .= drupal_render($synonym_a);
|
|
334
|
|
|
335
|
$synonymy_html .= '</div>';
|
|
336
|
$render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
|
|
337
|
|
|
338
|
}
|
|
339
|
|
|
340
|
// --- PAGE PART: SPECIMENS --- //
|
|
341
|
if (!taxon_page_tabs_hidden_check('specimens') && ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all'))) {
|
|
342
|
$render_array['specimens'] = array(
|
|
343
|
'#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Specimens')) . '</h2>' : ''),
|
|
344
|
'content' => compose_cdm_taxon_page_specimens($taxon), // returns render array
|
|
345
|
'#suffix' => '</div>',
|
|
346
|
);
|
|
347
|
}
|
|
348
|
|
|
349
|
// --- PAGE PART: KEYS --- //
|
|
350
|
if(!taxon_page_tabs_hidden_check('keys')){
|
|
351
|
if ($identificationKeyCount == 1 && $page_part == 'keys'){
|
|
352
|
drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));
|
|
353
|
}
|
|
354
|
else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {
|
|
355
|
$keys_html = '<div id="keys" class="page-part">';
|
|
356
|
if ($page_part == 'all') {
|
|
357
|
$keys_html .= '<h2>' . t(cdm_taxonpage_tab_label('Keys')) . '</h2>';
|
|
358
|
}
|
|
359
|
$keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
|
|
360
|
$keys_html .= '</div>';
|
|
361
|
$render_array['keys'] = markup_to_render_array($keys_html, $weight++);
|
|
362
|
}
|
|
363
|
}
|
|
364
|
|
|
365
|
// --- PAGE PART: EXPERTS --- //
|
|
366
|
|
|
367
|
if (!taxon_page_tabs_hidden_check('experts') && ($page_part == 'experts' || $page_part == 'all')) {
|
|
368
|
$render_array['experts'] = array(
|
|
369
|
'#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Experts')) . '</h2>' : ''),
|
|
370
|
'content' => compose_cdm_taxon_page_experts($taxon), // returns render array
|
|
371
|
'#suffix' => '</div>',
|
|
372
|
);
|
|
373
|
}
|
|
374
|
|
|
375
|
// ------------------ END OF PARTS -------------- //
|
|
376
|
|
|
377
|
// adjust weights of page and toc elements according to the settings
|
|
378
|
$taxontabs_weights = get_array_variable_merged(CDM_TAXONPAGE_TAB_WEIGHT, CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
|
|
379
|
foreach($taxontabs_weights as $tab_key => $weight){
|
|
380
|
if(isset($render_array[$tab_key])){
|
|
381
|
$render_array[$tab_key]['#weight'] = $weight;
|
|
382
|
}
|
|
383
|
}
|
|
384
|
|
|
385
|
|
|
386
|
// set up the TOC for the pages which contain all pageparts
|
|
387
|
if($page_part == 'all') {
|
|
388
|
|
|
389
|
asort($taxontabs_weights);
|
|
390
|
foreach(array_keys($taxontabs_weights) as $tab_key){
|
|
391
|
if(isset($render_array[$tab_key])){
|
|
392
|
if($tab_key != 'general'){
|
|
393
|
// add entry for page part
|
|
394
|
$toc_elements[] = array(
|
|
395
|
'data' => l(t(cdm_taxonpage_tab_label(ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),
|
|
396
|
'class' => array('page-part-toc-item-' . $tab_key)
|
|
397
|
);
|
|
398
|
} else {
|
|
399
|
// add content of profile part instead
|
|
400
|
if(isset($render_array['general'])) {
|
|
401
|
// in case all tabs are shown at once the feature tocs
|
|
402
|
// should be integrated into the tabs toc as sub list
|
|
403
|
// and the profile image should be on top of the page
|
|
404
|
if(isset($render_array['general']['taxon_description_feature_toc'])){;
|
|
405
|
foreach ($render_array['general']['taxon_description_feature_toc']['#items'] as $profile_toc_item){
|
|
406
|
$toc_elements[] = $profile_toc_item;
|
|
407
|
}
|
|
408
|
unset($render_array['general']['taxon_description_feature_toc']);
|
|
409
|
}
|
|
410
|
}
|
|
411
|
}
|
|
412
|
}
|
|
413
|
}
|
|
414
|
|
|
415
|
// move profile image in page structure
|
|
416
|
if(isset($render_array['general']['taxon_profile_image'])){
|
|
417
|
$render_array['profile_image'] = $render_array['general']['taxon_profile_image'];
|
|
418
|
$render_array['profile_image']['#weight'] = -100;
|
|
419
|
unset($render_array['general']['taxon_profile_image']);
|
|
420
|
}
|
|
421
|
|
|
422
|
// finally add the table of contents to the render array
|
|
423
|
$render_array['toc'] = array(
|
|
424
|
'#theme' => 'item_list',
|
|
425
|
'#items' => $toc_elements,
|
|
426
|
'#title' => t('Content'),
|
|
427
|
'#weight' => -101,
|
|
428
|
'#suffix' => '</div>',
|
|
429
|
'#prefix'=> '<div id="page-toc">'
|
|
430
|
);
|
|
431
|
}
|
|
432
|
|
|
433
|
|
|
434
|
return $render_array;
|
|
435
|
}
|
|
436
|
|
|
437
|
/**
|
|
438
|
* TODO should this function really be a compose function?
|
|
439
|
* For a compose function must there always be a theme function with the same name? (ak 8.8.2013)
|
|
440
|
*
|
|
441
|
* composes and returns an render array containing the components of the taxon profile tab:
|
|
442
|
* - 'taxon_profile_image'
|
|
443
|
* - 'taxon_description_feature_toc'
|
|
444
|
* - 'taxon_description_features'
|
|
445
|
*
|
|
446
|
*
|
|
447
|
* @param object taxon
|
|
448
|
* @param object $merged_tree
|
|
449
|
* @param object media
|
|
450
|
* @param bool $add_synonymy
|
|
451
|
*
|
|
452
|
* @return array
|
|
453
|
* A Drupal render array with the following elements:
|
|
454
|
* - 'taxon_profile_image'
|
|
455
|
* - 'taxon_description_feature_toc'
|
|
456
|
* - 'taxon_description_features'
|
|
457
|
*
|
|
458
|
* @throws Exception
|
|
459
|
*
|
|
460
|
* @ingroup compose
|
|
461
|
*/
|
|
462
|
function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, $add_synonymy) {
|
|
463
|
|
|
464
|
$render_array = array();
|
|
465
|
|
|
466
|
$taxon_profile_image_settings = variable_get(CDM_TAXON_PROFILE_IMAGE, unserialize(CDM_TAXON_PROFILE_IMAGE_DEFAULT));
|
|
467
|
|
|
468
|
$hide_taxon_profile_image = FALSE;
|
|
469
|
if (variable_get('image_hide_rank', '0') != '0' && isset($taxon->name->rank->uuid)) {
|
|
470
|
$rankCompare = rank_compare($taxon->name->rank->uuid, variable_get('image_hide_rank', '-99'));
|
|
471
|
$hide_taxon_profile_image = ($rankCompare > -1);
|
|
472
|
}
|
|
473
|
|
|
474
|
if ($taxon_profile_image_settings['show'] && !$hide_taxon_profile_image) {
|
|
475
|
|
|
476
|
$representationPart = new stdClass();
|
|
477
|
$attributes = array();
|
|
478
|
if (isset($media[0])) {
|
|
479
|
// due to a bug the portal/taxon/{uuid}/media service only delivers a filtered media object
|
|
480
|
// which only contains the thumbnail representation even if the height and width filters are not set.
|
|
481
|
// -->
|
|
482
|
$preferred_media = cdm_ws_get(CDM_WS_MEDIA, $media[0]->uuid);
|
|
483
|
$preferred_representations = cdm_preferred_media_representations($preferred_media, array(
|
|
484
|
'image/jpg',
|
|
485
|
'image/jpeg',
|
|
486
|
'image/png',
|
|
487
|
'image/gif',
|
|
488
|
),
|
|
489
|
$taxon_profile_image_settings['maxextend'],
|
|
490
|
$taxon_profile_image_settings['maxextend']
|
|
491
|
);
|
|
492
|
if(count($preferred_representations) > 0){
|
|
493
|
|
|
494
|
$representation = array_shift($preferred_representations);
|
|
495
|
$representationPart = $representation->parts[0];
|
|
496
|
$attributes['alt'] = $representationPart->uri;
|
|
497
|
|
|
498
|
if (!empty($taxon_profile_image_settings['media_uri_query'])) {
|
|
499
|
$representationPart->uri = $representationPart->uri
|
|
500
|
. (strpos($representationPart->uri, '?') !== FALSE ? '&' : '?')
|
|
501
|
. $taxon_profile_image_settings['media_uri_query'];
|
|
502
|
}
|
|
503
|
}
|
|
504
|
}
|
|
505
|
else {
|
|
506
|
if ($taxon_profile_image_settings['custom_placeholder_enabled']) {
|
|
507
|
// show placeholder image instead
|
|
508
|
if (!empty($taxon_profile_image_settings['custom_placeholder_image_on']) && !empty($taxon_profile_image_settings['custom_placeholder_image_fid'])) {
|
|
509
|
// use the user provided image
|
|
510
|
$profile_image_file = file_load($taxon_profile_image_settings['custom_placeholder_image_fid']);
|
|
511
|
$url = file_create_url($profile_image_file->uri);
|
|
512
|
$image_info = image_get_info($profile_image_file->uri);
|
|
513
|
$representationPart->width = $image_info['width'];
|
|
514
|
$representationPart->height = $image_info['height'];
|
|
515
|
$representationPart->uri = $url;
|
|
516
|
}
|
|
517
|
else {
|
|
518
|
// use the hard coded default
|
|
519
|
$representationPart->width = 184;
|
|
520
|
$representationPart->height = 144;
|
|
521
|
$representationPart->uri = base_path() . drupal_get_path('module',
|
|
522
|
'cdm_dataportal') . '/images/no_picture.png';
|
|
523
|
}
|
|
524
|
$attributes['alt'] = "no image available";
|
|
525
|
}
|
|
526
|
}
|
|
527
|
|
|
528
|
if (isset($representationPart->uri)) {
|
|
529
|
$profile_image = cdm_media_gallerie_image($representationPart, $taxon_profile_image_settings['maxextend'], FALSE, $attributes);
|
|
530
|
// NOTE: style="width:${maxextend}px' is needed for IE8 !!!
|
|
531
|
$max_extend_with = $taxon_profile_image_settings['maxextend'] . 'px';
|
|
532
|
$render_array['taxon_profile_image'] = markup_to_render_array('<div id="taxonProfileImage" style="width:' . $max_extend_with . '">' . $profile_image . '</div>',
|
|
533
|
-101);
|
|
534
|
}
|
|
535
|
}
|
|
536
|
|
|
537
|
if($add_synonymy){
|
|
538
|
$synonymy_a = compose_cdm_taxon_page_synonymy($taxon, true);
|
|
539
|
$synonymy_a['#weight'] = -102;
|
|
540
|
$render_array['synonymy'] = $synonymy_a;
|
|
541
|
}
|
|
542
|
|
|
543
|
// $pseudo_feature_block_toc_items = array();
|
|
544
|
|
|
545
|
|
|
546
|
// Render the sections for each real feature
|
|
547
|
$feature_block_list = make_feature_block_list($merged_tree->root->childNodes, $taxon);
|
|
548
|
|
|
549
|
// >>>>>>>>>>>>>>>>>>> PSEUDO FEATURES >>>>>>>>>>>>>>>>>>>
|
|
550
|
$pseudo_feature_weights = get_array_variable_merged(CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS, CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS_DEFAULT);
|
|
551
|
// Bibliography
|
|
552
|
$bibliography_settings = get_bibliography_settings();
|
|
553
|
if($bibliography_settings['enabled'] == 1){
|
|
554
|
$bibliography_markup = FootnoteManager::renderFootnoteList(PSEUDO_FEATURE_BIBLIOGRAPHY, '');
|
|
555
|
if($bibliography_markup) {
|
|
556
|
$feature_bibliography = make_pseudo_feature('Bibliography', PSEUDO_FEATURE_BIBLIOGRAPHY);
|
|
557
|
$bibliography_item = markup_to_render_array($bibliography_markup);
|
|
558
|
$bibliography_block = feature_block(t('Bibliography'), $feature_bibliography);
|
|
559
|
$bibliography_block->content = array();
|
|
560
|
$bibliography_block->content[] = compose_feature_block_wrap_elements(array($bibliography_item), $feature_bibliography);
|
|
561
|
|
|
562
|
$feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]] = $bibliography_block;
|
|
563
|
cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]);
|
|
564
|
}
|
|
565
|
}
|
|
566
|
|
|
567
|
// Descriptions (aggregated)
|
|
568
|
$descriptionTypes = array();
|
|
569
|
$descriptionTypes['descriptionTypes'] = ("AGGREGATED_STRUC_DESC");
|
|
570
|
$aggregatedDescriptions = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXON . '/' . $taxon->uuid . '/descriptions', $descriptionTypes);
|
|
571
|
if (isset($aggregatedDescriptions) and !empty($aggregatedDescriptions)) {
|
|
572
|
// if($feature_block_list) ....TODO
|
|
573
|
$feature_description = make_pseudo_feature('Descriptions (aggregated)', PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS);
|
|
574
|
$description_item = '';
|
|
575
|
foreach ($aggregatedDescriptions as $description) {
|
|
576
|
$description_item = '<div class="' . html_class_attribute_ref($description) . '">';
|
|
577
|
$description_item .= render_description_string(get_root_nodes_for_dataset($description));
|
|
578
|
$description_item .= ' ' . icon_link(path_to_description($description->uuid));
|
|
579
|
$description_item .= '<div class="content-caption">'. statistical_values_explanation() . '</div>';
|
|
580
|
$description_item .= '</div>';
|
|
581
|
}
|
|
582
|
$description_block = feature_block(t('Descriptions (aggregated)'), $feature_description);
|
|
583
|
$description_block->content = [];
|
|
584
|
$description_block->content[] = compose_feature_block_wrap_elements([$description_item], $feature_description);
|
|
585
|
|
|
586
|
$feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]] = $description_block;
|
|
587
|
cdm_toc_list_add_item('Descriptions (aggregated)', 'aggregation_descriptions', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]);
|
|
588
|
|
|
589
|
|
|
590
|
}
|
|
591
|
|
|
592
|
// sort by weight
|
|
593
|
ksort($feature_block_list);
|
|
594
|
$render_array['taxon_description_features'] = _block_get_renderable_array($feature_block_list);
|
|
595
|
|
|
596
|
/* // update TOC
|
|
597
|
if ($pseudo_feature_block_toc_items){
|
|
598
|
foreach ($pseudo_feature_block_toc_items as $label=>$fragment){
|
|
599
|
cdm_toc_list_add_item($label, $fragment);
|
|
600
|
}
|
|
601
|
}
|
|
602
|
*/
|
|
603
|
// <<<<<<<<<<<<<<<<<<< PSEUDO FEATURES <<<<<<<<<<<<<<<<<<<
|
|
604
|
|
|
605
|
// create the table of content
|
|
606
|
$toc = array(
|
|
607
|
'#theme' => 'item_list',
|
|
608
|
'#items' => cdm_toc_list(),
|
|
609
|
'#title' => t('Content'),
|
|
610
|
'#weight' => -100, // move to the top
|
|
611
|
'#suffix' => '</div>',
|
|
612
|
'#prefix'=> '<div id="page-toc">'
|
|
613
|
);
|
|
614
|
$render_array['taxon_description_feature_toc'] = $toc;
|
|
615
|
|
|
616
|
return $render_array;
|
|
617
|
}
|
|
618
|
|
|
619
|
|
|
620
|
/**
|
|
621
|
* Renders the link which will lead to the specimen detail page
|
|
622
|
* @param object $specimen
|
|
623
|
* the cdm specimen entity which will be linked to
|
|
624
|
*
|
|
625
|
* @return string
|
|
626
|
* the markup for the link
|
|
627
|
*/
|
|
628
|
function render_cdm_specimen_link($specimen) {
|
|
629
|
$path = path_to_specimen($specimen->uuid);
|
|
630
|
$attributes['class'][] = html_class_attribute_ref($specimen);
|
|
631
|
return $specimen->titleCache.icon_link($path);
|
|
632
|
}
|
|
633
|
|
|
634
|
/**
|
|
635
|
* Returns HTML containing the synonymy for the accepted taxon.
|
|
636
|
*
|
|
637
|
* Shows the whole synonymy for the accepted taxon.
|
|
638
|
* The synonymy list is headed by the complete scientific name
|
|
639
|
* of the accepted taxon with nomenclatural reference.
|
|
640
|
*
|
|
641
|
* @param object $taxon
|
|
642
|
* @param boolean $add_accepted_taxon
|
|
643
|
*
|
|
644
|
* @return array
|
|
645
|
* Drupal render array for the synonymy
|
|
646
|
*
|
|
647
|
* @throws Exception
|
|
648
|
*
|
|
649
|
* @ingroup compose
|
|
650
|
*/
|
|
651
|
function compose_cdm_taxon_page_synonymy($taxon, $add_accepted_taxon) {
|
|
652
|
|
|
653
|
RenderHints::pushToRenderStack('taxon_page_synonymy');
|
|
654
|
|
|
655
|
// footnote key for the homotypic group and accepted taxon,
|
|
656
|
// both should have the same footnote key
|
|
657
|
RenderHints::setFootnoteListKey(RenderHints::getRenderPath());
|
|
658
|
|
|
659
|
$synomymie = cdm_ws_get(CDM_WS_PORTAL_TAXON_SYNONYMY, array($taxon->uuid));
|
|
660
|
|
|
661
|
$out = '';
|
|
662
|
|
|
663
|
// Render accepted taxon.
|
|
664
|
//
|
|
665
|
// foonotes of the accepted taxon will be rendered in the homotypic group section
|
|
666
|
// even if there are not synonyms in the homotypic group
|
|
667
|
// homotypic group and accepted taxon should have the same footnote key
|
|
668
|
$referenceUri = '';
|
|
669
|
if ($add_accepted_taxon) {
|
|
670
|
// remember the last part of the render path
|
|
671
|
$synonymy_render_path = RenderHints::getRenderPath();
|
|
672
|
// set new render path for the accepted taxon so
|
|
673
|
// it can be styled differently via the name render part definitions
|
|
674
|
RenderHints::pushToRenderStack('accepted_taxon');
|
|
675
|
$accepted_name = '';
|
|
676
|
if (variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE, 0)) {
|
|
677
|
$label = variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL, CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL_DEFAULT);
|
|
678
|
$accepted_name .= '<div class="secReference"><span class="label">' . t($label) . ':</span> ' . $taxon->sec->titleCache . '</div>';
|
|
679
|
}
|
|
680
|
if (isset($taxon->name->nomenclaturalReference)) {
|
|
681
|
$referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
|
|
682
|
}
|
|
683
|
|
|
684
|
$accepted_name .= '<div class="accepted-name">';
|
|
685
|
$accepted_name .= render_taxon_or_name($taxon, NULL, $referenceUri);
|
|
686
|
|
|
687
|
$name_relations = cdm_name_relationships_for_taxon($taxon);
|
|
688
|
$name_relationships = compose_name_relationships_inline($name_relations, $taxon->name->uuid, $taxon->uuid);
|
|
689
|
// Render relationships of accepted name.
|
|
690
|
if(isset($name_relationships['list']['items'][0])){
|
|
691
|
$accepted_name .= ' ' . drupal_render($name_relationships);
|
|
692
|
}
|
|
693
|
|
|
694
|
// handle annotations of the name and taxon
|
|
695
|
$special_annotations_array = array();
|
|
696
|
$special_annotations_array[] = $taxon->name;
|
|
697
|
$special_annotations_array[] = $taxon;
|
|
698
|
$accepted_name .= theme('cdm_annotations_as_footnotekeys', array(
|
|
699
|
'cdmBase_list' => $special_annotations_array,
|
|
700
|
'footnote_list_key' => $synonymy_render_path . '-annotations')
|
|
701
|
);
|
|
702
|
$accepted_name .= '</div>';
|
|
703
|
RenderHints::popFromRenderStack();
|
|
704
|
}
|
|
705
|
|
|
706
|
// --- Render homotypic synonymy group
|
|
707
|
if (!empty($accepted_name)) {
|
|
708
|
$out .= $accepted_name;
|
|
709
|
}
|
|
710
|
|
|
711
|
// Render the homotypicSynonymyGroup including the type information.
|
|
712
|
$out .= theme(
|
|
713
|
'cdm_homotypicSynonymyGroup',
|
|
714
|
array(
|
|
715
|
'synonymList' => $synomymie->homotypicSynonymsByHomotypicGroup,
|
|
716
|
'accepted_taxon_name_uuid' => $taxon->name->uuid
|
|
717
|
)
|
|
718
|
);
|
|
719
|
|
|
720
|
|
|
721
|
// Render accepted taxon heterotypic synonymy groups.
|
|
722
|
if ($synomymie->heterotypicSynonymyGroups) {
|
|
723
|
foreach ($synomymie->heterotypicSynonymyGroups as $homotypicalGroup) {
|
|
724
|
$out .= theme('cdm_heterotypicSynonymyGroup', array('homotypicalGroup' => $homotypicalGroup));
|
|
725
|
}
|
|
726
|
}
|
|
727
|
// Render taxon relationships.
|
|
728
|
if (variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT)) {
|
|
729
|
$taxonRelationshipsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, $taxon->uuid);
|
|
730
|
$out .= cdm_taxonRelationships($taxonRelationshipsDTO, $taxon);
|
|
731
|
}
|
|
732
|
|
|
733
|
RenderHints::popFromRenderStack();
|
|
734
|
|
|
735
|
return markup_to_render_array($out);
|
|
736
|
}
|
|
737
|
|
|
738
|
|
|
739
|
/**
|
|
740
|
* composes and returns an render array for the experts associated with the given taxon
|
|
741
|
*
|
|
742
|
* @param object taxon
|
|
743
|
*
|
|
744
|
* @return array
|
|
745
|
* A Drupal render array for a table with the experts
|
|
746
|
*
|
|
747
|
* @ingroup compose
|
|
748
|
*/
|
|
749
|
function compose_cdm_taxon_page_experts($taxon){
|
|
750
|
|
|
751
|
$render_array = array();
|
|
752
|
if(!isset($taxon->uuid)){
|
|
753
|
return $render_array;
|
|
754
|
}
|
|
755
|
|
|
756
|
$current_classification_uuid = get_current_classification_uuid();
|
|
757
|
// TODO use cdm_ws_fetchall below but this failes! needs fix!
|
|
758
|
$taxon_node_agent_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
|
|
759
|
array(
|
|
760
|
$taxon->uuid,
|
|
761
|
$current_classification_uuid
|
|
762
|
)
|
|
763
|
);
|
|
764
|
|
|
765
|
$header = array(
|
|
766
|
array('data' => t('Expert')),
|
|
767
|
array('data' => t('Role'))
|
|
768
|
);
|
|
769
|
$rows = array();
|
|
770
|
|
|
771
|
|
|
772
|
foreach($taxon_node_agent_relations->records as $taxon_node_agent_relation){
|
|
773
|
|
|
774
|
|
|
775
|
$expert_role_id = $taxon_node_agent_relation->agent->uuid . '-' . $taxon_node_agent_relation->type->uuid;
|
|
776
|
$expert_details_container_id = 'expert_details_' . $expert_role_id;
|
|
777
|
|
|
778
|
$agent_label_markup = cdm_dynabox(
|
|
779
|
'expert_' . $expert_role_id,
|
|
780
|
$taxon_node_agent_relation->agent->titleCache,
|
|
781
|
// specifying both ends of the relationship will return only one record in the pager
|
|
782
|
cdm_compose_url(CDM_WS_PORTAL_AGENT,
|
|
783
|
array($taxon_node_agent_relation->agent->uuid, 'taxonNodeAgentRelations'),
|
|
784
|
'taxon_uuid=' . $taxon->uuid . '&relType_uuid=' . $taxon_node_agent_relation->type->uuid),
|
|
785
|
'cdm_taxon_expert',
|
|
786
|
'Click for details',
|
|
787
|
array('div', 'div'),
|
|
788
|
array(), // attributes
|
|
789
|
'#' . $expert_details_container_id // $content_element_selector
|
|
790
|
);
|
|
791
|
|
|
792
|
// Expert and Role
|
|
793
|
$rows[] = array(
|
|
794
|
'data' => array(
|
|
795
|
array(
|
|
796
|
'data' => $agent_label_markup,
|
|
797
|
'class' => array(html_class_attribute_ref($taxon_node_agent_relation->agent))
|
|
798
|
),
|
|
799
|
array(
|
|
800
|
'data' => $taxon_node_agent_relation->type->representation_L10n,
|
|
801
|
'class' => array(html_class_attribute_ref($taxon_node_agent_relation->type))
|
|
802
|
)
|
|
803
|
)
|
|
804
|
);
|
|
805
|
// Agent details
|
|
806
|
$rows[] = array(
|
|
807
|
'data' => array(
|
|
808
|
array(
|
|
809
|
'data' => '<!-- expert_details_container -->',
|
|
810
|
'id' => $expert_details_container_id,
|
|
811
|
'colspan' => 2
|
|
812
|
)
|
|
813
|
)
|
|
814
|
);
|
|
815
|
|
|
816
|
}
|
|
817
|
|
|
818
|
|
|
819
|
$render_array['experts_table'] = array(
|
|
820
|
'#theme' => 'table',
|
|
821
|
'#header' => $header,
|
|
822
|
'#rows' => $rows,
|
|
823
|
);
|
|
824
|
|
|
825
|
|
|
826
|
return $render_array;
|
|
827
|
}
|
|
828
|
|
|
829
|
|
|
830
|
/**
|
|
831
|
* Manages the tabs to be hidden in the taxon page.
|
|
832
|
*
|
|
833
|
* The tabs are identified by their last menu link path element:
|
|
834
|
* - description
|
|
835
|
* - synonymy
|
|
836
|
* - images
|
|
837
|
* - specimens
|
|
838
|
* - key
|
|
839
|
*
|
|
840
|
* Internally the tabs are stored in a static variable which is
|
|
841
|
* managed by drupal_static().
|
|
842
|
*
|
|
843
|
* @param string $add_tab
|
|
844
|
* Optional parameter. The given string will be added to the array of tabs
|
|
845
|
*
|
|
846
|
* @return
|
|
847
|
* The array of tabs
|
|
848
|
*/
|
|
849
|
function taxon_page_tabs_hidden_add($add_tab = NULL) {
|
|
850
|
$tabs = &drupal_static('taxon_page_tabs_hidden');
|
|
851
|
|
|
852
|
if(!isset($tabs)){
|
|
853
|
$tabs = array();
|
|
854
|
}
|
|
855
|
|
|
856
|
if (isset($add_tab) && !array_key_exists($add_tab, $tabs)) {
|
|
857
|
$tabs[] = $add_tab;
|
|
858
|
}
|
|
859
|
|
|
860
|
return $tabs;
|
|
861
|
}
|
|
862
|
|
|
863
|
/**
|
|
864
|
* Manages the tabs to be hidden in the taxon page.
|
|
865
|
*
|
|
866
|
* The tabs names are identified by their last menu link path element:
|
|
867
|
* - description
|
|
868
|
* - synonymy
|
|
869
|
* - images
|
|
870
|
* - specimens
|
|
871
|
* - key
|
|
872
|
*
|
|
873
|
* Internally the tabs are stored in a static variable which is
|
|
874
|
* managed by drupal_static().
|
|
875
|
*
|
|
876
|
* @param string $tabname
|
|
877
|
* The name of the tab to check
|
|
878
|
*
|
|
879
|
* @return boolean
|
|
880
|
* True if the tab or section is to be hidden
|
|
881
|
*/
|
|
882
|
function taxon_page_tabs_hidden_check($tabname) {
|
|
883
|
|
|
884
|
$tabs = &drupal_static('taxon_page_tabs_hidden');
|
|
885
|
|
|
886
|
if(!isset($tabs)){
|
|
887
|
$tabs = array();
|
|
888
|
}
|
|
889
|
|
|
890
|
return array_search($tabname, $tabs) !== FALSE;
|
|
891
|
}
|
|
892
|
|
|
893
|
/**
|
|
894
|
* Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
|
|
895
|
*
|
|
896
|
* - Removes the tabs to be hidden, @see taxon_page_tabs_hidden_add()
|
|
897
|
* - Renames tabs according to the settings // TODO (this will replace the theme_cdm_taxonpage_tab() function !!!)
|
|
898
|
*
|
|
899
|
* @param array $variables
|
|
900
|
* The variables array
|
|
901
|
*/
|
|
902
|
function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {
|
|
903
|
|
|
904
|
$hidden_tabs = taxon_page_tabs_hidden_add();
|
|
905
|
|
|
906
|
if (!variable_get(CDM_SEARCH_BLAST_ENABLED)) {
|
|
907
|
if (is_array($variables['primary'])) {
|
|
908
|
foreach ($variables['primary'] as $key => &$element) {
|
|
909
|
if ($element['#link']['path'] == 'cdm_dataportal/search/blast') {
|
|
910
|
// remove the tab
|
|
911
|
unset($variables['primary'][$key]);
|
|
912
|
}
|
|
913
|
|
|
914
|
}
|
|
915
|
}
|
|
916
|
}
|
|
917
|
if (is_array($variables['primary'])) {
|
|
918
|
foreach ($variables['primary'] as $key => &$element) {
|
|
919
|
|
|
920
|
// 1. Remove the tabs to be hidden
|
|
921
|
foreach ($hidden_tabs as $tab) {
|
|
922
|
if ($element['#link']['path'] == 'cdm_dataportal/taxon/%/' . $tab) {
|
|
923
|
// remove the tab
|
|
924
|
unset($variables['primary'][$key]);
|
|
925
|
}
|
|
926
|
}
|
|
927
|
}
|
|
928
|
}
|
|
929
|
}
|
|
930
|
|
|
931
|
|
|
932
|
|
|
933
|
/**
|
|
934
|
* Implements the hook_preprocess_HOOK() for theme_menu_local_task()
|
|
935
|
*
|
|
936
|
*
|
|
937
|
* @param array $variables
|
|
938
|
* An associative array containing:
|
|
939
|
* - element: A render element containing:
|
|
940
|
* #link: A menu link array with 'title', 'href', and 'localized_options' keys.
|
|
941
|
* #active: A boolean indicating whether the local task is active.
|
|
942
|
*
|
|
943
|
*/
|
|
944
|
function cdm_dataportal_preprocess_menu_local_task(&$variables) {
|
|
945
|
|
|
946
|
$link = $variables['element']['#link'];
|
|
947
|
if (preg_match('/cdm_dataportal\/.*\/refresh$/', $link['href'])) {
|
|
948
|
$link['title'] = '<img class="refresh" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/view-refresh.png' . '" alt="' . check_plain($link['title']) . '" title="' . check_plain($link['title']) . '"/>';
|
|
949
|
$link['localized_options']['html'] = TRUE;
|
|
950
|
|
|
951
|
$variables['element']['#link'] = $link;
|
|
952
|
}
|
|
953
|
}
|
|
954
|
|
|
955
|
/* =================== block composition ===================== */
|
|
956
|
|
|
957
|
/**
|
|
958
|
* Composes and returns an render array for the classification breadcrumbs of the given taxon.
|
|
959
|
*
|
|
960
|
* @param taxon
|
|
961
|
*
|
|
962
|
* @return array
|
|
963
|
* A Drupal render array for a table with the experts
|
|
964
|
*
|
|
965
|
* @ingroup compose
|
|
966
|
*/
|
|
967
|
function compose_classification_breadcrumbs($taxon_uuid) {
|
|
968
|
|
|
969
|
_add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');
|
|
970
|
|
|
971
|
$render_array = array();
|
|
972
|
|
|
973
|
$render_array['#theme'] = 'item_list';
|
|
974
|
$render_array['#type'] = 'ul';
|
|
975
|
$render_array['#attributes'] = array(
|
|
976
|
'id' => 'classification-breadcrumbs',
|
|
977
|
'class' => 'breadcrumbs inline',
|
|
978
|
);
|
|
979
|
|
|
980
|
$items = array();
|
|
981
|
|
|
982
|
$parent_taxon_nodes = null;
|
|
983
|
if($taxon_uuid){
|
|
984
|
$parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
|
|
985
|
}
|
|
986
|
|
|
987
|
$classifications = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
|
|
988
|
// find current classification in list
|
|
989
|
$classification = null;
|
|
990
|
$current_classification_uuid = get_current_classification_uuid();
|
|
991
|
foreach ($classifications as $classification){
|
|
992
|
if($classification->uuid == $current_classification_uuid){
|
|
993
|
break;
|
|
994
|
}
|
|
995
|
}
|
|
996
|
|
|
997
|
$node_name = '';
|
|
998
|
if(count($classifications) > 1 ){
|
|
999
|
// need to add the current classification as first label
|
|
1000
|
|
|
1001
|
$label = $classification->titleCache;
|
|
1002
|
if(strlen($label) > 20){
|
|
1003
|
$label = substr($label, 0, strpos($label, ' ', 15)) . '...';
|
|
1004
|
}
|
|
1005
|
$node_name = font_awesome_icon_markup('fa-th-list') . ' ' . l($label, '#', array(
|
|
1006
|
'attributes' => array(
|
|
1007
|
'class' => 'taxonomic-children-button classification-chooser',
|
|
1008
|
'data-destination-uri' => drupal_get_destination(),
|
|
1009
|
'data-cdm-align-with' => array('prev')
|
|
1010
|
),
|
|
1011
|
'html' => true
|
|
1012
|
));
|
|
1013
|
}
|
|
1014
|
|
|
1015
|
$rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
|
|
1016
|
|
|
1017
|
$rank_separator = '<span> '
|
|
1018
|
. font_awesome_icon_markup('fa-chevron-right')
|
|
1019
|
. ' </span>';
|
|
1020
|
$more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');
|
|
1021
|
$more_children_label = '...';
|
|
1022
|
|
|
1023
|
$items[] = $node_name;
|
|
1024
|
|
|
1025
|
$more_children_for = null;
|
|
1026
|
if($parent_taxon_nodes){
|
|
1027
|
foreach ($parent_taxon_nodes as $node) {
|
|
1028
|
|
|
1029
|
$is_first_item = count($items) == 0;
|
|
1030
|
$is_last_item = count($items) == count($parent_taxon_nodes);
|
|
1031
|
$node_name = cdm_dataportal_shortname_of($node);
|
|
1032
|
$path = path_to_taxon($node->taxonUuid);
|
|
1033
|
|
|
1034
|
if($node->taxonomicChildrenCount > 0) {
|
|
1035
|
$more_children_for = $node->taxonUuid;
|
|
1036
|
} else {
|
|
1037
|
$more_children_for = null;
|
|
1038
|
}
|
|
1039
|
|
|
1040
|
// 'fa-sitemap'
|
|
1041
|
|
|
1042
|
$items[] =
|
|
1043
|
($is_first_item ? '' : ' ')
|
|
1044
|
. $rank_separator
|
|
1045
|
. l(
|
|
1046
|
'<span class="' . html_class_attribute_ref($node) . '">' . $node_name . '</span>',
|
|
1047
|
$path,
|
|
1048
|
array(
|
|
1049
|
'attributes' => array(
|
|
1050
|
'class' => array('taxonomic-children-button'),
|
|
1051
|
'data-cdm-taxon-uuid' => array($node->taxonUuid),
|
|
1052
|
'data-cdm-classification-mode' => array('siblings'),
|
|
1053
|
'data-cdm-align-with' => array('prev')
|
|
1054
|
),
|
|
1055
|
'html' => true
|
|
1056
|
)
|
|
1057
|
);
|
|
1058
|
}
|
|
1059
|
}
|
|
1060
|
|
|
1061
|
// add more button to the end
|
|
1062
|
if(!$parent_taxon_nodes) {
|
|
1063
|
// not taxon focused yet, adding button to make the root nodes available
|
|
1064
|
$items[] = '<span>'
|
|
1065
|
. $more_children_icon . ' ' .
|
|
1066
|
'<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
|
|
1067
|
. '" data-rank-limit-uuid="' . $rank_limit_uuid . '" data-cdm-align-with="prev"> ' . $more_children_label . '<span>'
|
|
1068
|
. '</span>';
|
|
1069
|
} else if($more_children_for){
|
|
1070
|
// last parent item has child taxon nodes
|
|
1071
|
$items[] = ' <span>'
|
|
1072
|
. $more_children_icon . ' ' .
|
|
1073
|
'<span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
|
|
1074
|
. '" data-cdm-classification-mode="children" data-cdm-align-with="prev"> ' . $more_children_label . '</span>'
|
|
1075
|
. '</span>';
|
|
1076
|
|
|
1077
|
}
|
|
1078
|
|
|
1079
|
$render_array['#items'] = $items;
|
|
1080
|
|
|
1081
|
return $render_array;
|
|
1082
|
}
|
|
1083
|
|
|
1084
|
|
|
1085
|
/**
|
|
1086
|
* @param $specimen_uuid
|
|
1087
|
* @return array
|
|
1088
|
* The drupal render array for the page
|
|
1089
|
*
|
|
1090
|
* @ingroup compose
|
|
1091
|
*/
|
|
1092
|
function compose_cdm_specimen_page($specimen_uuid)
|
|
1093
|
{
|
|
1094
|
drupal_set_title("Specimen Details");
|
|
1095
|
RenderHints::pushToRenderStack('specimen_page');
|
|
1096
|
|
|
1097
|
$specimen_table = array(
|
|
1098
|
'#theme' => 'table',
|
|
1099
|
'#weight' => 2,
|
|
1100
|
// prefix attributes and rows with '#' to let it pass to the theme function,
|
|
1101
|
// otherwise it is handled as child render array
|
|
1102
|
|
|
1103
|
'#attributes' => array('class' => 'specimens'),
|
|
1104
|
'#rows' => array(),
|
|
1105
|
'#prefix' => '<div id="specimens">',
|
|
1106
|
'#suffix' => '</div>',
|
|
1107
|
|
|
1108
|
|
|
1109
|
);
|
|
1110
|
$specimen = compose_cdm_specimen_or_observation($specimen_uuid, true);
|
|
1111
|
$render_array = array(
|
|
1112
|
'#theme' => 'item_list',
|
|
1113
|
'#items' => array($specimen),
|
|
1114
|
'#type' => 'ul');
|
|
1115
|
$output = drupal_render($render_array);
|
|
1116
|
|
|
1117
|
$specimen_table['#rows'][] = array(
|
|
1118
|
// An array of table rows. Every row is an array of cells, or an associative array
|
|
1119
|
'data' => $specimen,
|
|
1120
|
'class' => array(
|
|
1121
|
'descriptionElement',
|
|
1122
|
'descriptionElement_IndividualsAssociation'
|
|
1123
|
),
|
|
1124
|
);
|
|
1125
|
|
|
1126
|
|
|
1127
|
// $detail_html = compose_cdm_specimen_or_observation($specimen_uuid, true);
|
|
1128
|
// $render_array['markup'] = array(
|
|
1129
|
// '#prefix' => '<div id="specimens" class="page">',
|
|
1130
|
// 'content' => $specimen_table,
|
|
1131
|
// '#suffix' => '</div>',
|
|
1132
|
// );
|
|
1133
|
$render_array['specimen_table'] = $specimen_table;
|
|
1134
|
|
|
1135
|
RenderHints::popFromRenderStack();
|
|
1136
|
return $specimen; // $render_array;
|
|
1137
|
}
|
|
1138
|
|
|
1139
|
/**
|
|
1140
|
* @param $named_area_uuid
|
|
1141
|
* @return array
|
|
1142
|
* The drupal render array for the page
|
|
1143
|
*
|
|
1144
|
* @ingroup compose
|
|
1145
|
*/
|
|
1146
|
function compose_cdm_named_area_page($named_area_uuid)
|
|
1147
|
{
|
|
1148
|
|
|
1149
|
$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid));
|
|
1150
|
|
|
1151
|
$render_array = array();
|
|
1152
|
RenderHints::pushToRenderStack('named_area_page');
|
|
1153
|
|
|
1154
|
$groups = array();
|
|
1155
|
@_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);
|
|
1156
|
@_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);
|
|
1157
|
if(isset($named_area->level)) {
|
|
1158
|
@_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);
|
|
1159
|
}
|
|
1160
|
|
|
1161
|
$name_area_details_elements = array(
|
|
1162
|
// '#title' => $title,
|
|
1163
|
'#theme' => 'description_list',
|
|
1164
|
'#groups' => $groups,
|
|
1165
|
'#attributes' => array('class' => html_class_attribute_ref($named_area)),
|
|
1166
|
);
|
|
1167
|
|
|
1168
|
$render_array[] = $name_area_details_elements;
|
|
1169
|
|
|
1170
|
RenderHints::popFromRenderStack();
|
|
1171
|
return $render_array;
|
|
1172
|
}
|
|
1173
|
|
|
1174
|
|
|
1175
|
/**
|
|
1176
|
* Returns a drupal render array for a single reference page.
|
|
1177
|
*
|
|
1178
|
* Composes a page with all data on a single reference.
|
|
1179
|
*
|
|
1180
|
* @param string $uuid
|
|
1181
|
* An uuid for a cdm reference.
|
|
1182
|
*
|
|
1183
|
* @return array
|
|
1184
|
* A drupal render array
|
|
1185
|
*
|
|
1186
|
* @throws Exception
|
|
1187
|
*
|
|
1188
|
* @ingroup compose
|
|
1189
|
*/
|
|
1190
|
function compose_cdm_reference_page($uuid) {
|
|
1191
|
|
|
1192
|
$pathelement = "reference_page";
|
|
1193
|
RenderHints::pushToRenderStack($pathelement);
|
|
1194
|
$reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
|
|
1195
|
if (!$reference) {
|
|
1196
|
drupal_set_title(t('Reference does not exist'), PASS_THROUGH);
|
|
1197
|
return "";
|
|
1198
|
}
|
|
1199
|
if (isset($reference->titleCache)) {
|
|
1200
|
drupal_set_title($reference->titleCache, PASS_THROUGH);
|
|
1201
|
}
|
|
1202
|
|
|
1203
|
$field_order = array(
|
|
1204
|
"title",
|
|
1205
|
"abbrevTitle",
|
|
1206
|
// "titleCache" abbrevTitleCache
|
|
1207
|
// "citation",
|
|
1208
|
"authorship",
|
|
1209
|
"editor",
|
|
1210
|
"publisher",
|
|
1211
|
"placePublished",
|
|
1212
|
"datePublished",
|
|
1213
|
"year",
|
|
1214
|
"edition",// Class Book.
|
|
1215
|
"volume",// Class Article.
|
|
1216
|
"seriesPart",
|
|
1217
|
"inReference",
|
|
1218
|
"nomRefBase", // Class BookSection, Book, Article.
|
|
1219
|
"pages",// Class Article.
|
|
1220
|
"series",// Class Article, PrintSeries.
|
|
1221
|
"school",// Class Thesis.
|
|
1222
|
"institution",// Class Report.
|
|
1223
|
"organization",// Class Proceedings.
|
|
1224
|
"nextVersion",
|
|
1225
|
"previousVersion",
|
|
1226
|
"isbn",// Class Book.
|
|
1227
|
"issn",// Class Journal.
|
|
1228
|
"doi",
|
|
1229
|
"uri"
|
|
1230
|
);
|
|
1231
|
|
|
1232
|
$table_rows = array();
|
|
1233
|
|
|
1234
|
if (!isset($reference->authorship)) {
|
|
1235
|
$authorship = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid);
|
|
1236
|
$reference->authorship = isset($authorship->titleCache) ? $authorship->titleCache : '';
|
|
1237
|
}
|
|
1238
|
|
|
1239
|
if (!isset($reference->inReference)) {
|
|
1240
|
$reference->inReference = cdm_ws_get(CDM_WS_REFERENCE, array(
|
|
1241
|
$reference->uuid,
|
|
1242
|
"inReference",
|
|
1243
|
));
|
|
1244
|
}
|
|
1245
|
|
|
1246
|
foreach ($field_order as $fieldname) {
|
|
1247
|
|
|
1248
|
if (isset($reference->$fieldname)) {
|
|
1249
|
|
|
1250
|
if ($fieldname == "datePublished") {
|
|
1251
|
$period = $reference->$fieldname;
|
|
1252
|
$datePublished = timePeriodToString($period);
|
|
1253
|
if (isset($datePublished) && $datePublished != '') {
|
|
1254
|
$table_rows[] = array(
|
|
1255
|
t("Date published"),
|
|
1256
|
$datePublished,
|
|
1257
|
);
|
|
1258
|
}
|
|
1259
|
}
|
|
1260
|
elseif ($fieldname == "doi" && is_object($reference->doi)) {
|
|
1261
|
$table_rows[] = array(
|
|
1262
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
|
1263
|
cdm_doi($reference->doi, false)
|
|
1264
|
);
|
|
1265
|
}
|
|
1266
|
elseif ($fieldname == "uri" && isset($reference->uri) && $reference->uri) {
|
|
1267
|
$table_rows[] = array(
|
|
1268
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
|
1269
|
cdm_external_uri($reference->uri, false)
|
|
1270
|
);
|
|
1271
|
}
|
|
1272
|
elseif (is_object($reference->$fieldname)) {
|
|
1273
|
if ($fieldname == "authorship") {
|
|
1274
|
$dump = $reference->$fieldname;
|
|
1275
|
$teammembers = "teamMembers";
|
|
1276
|
$team = $dump->$teammembers;
|
|
1277
|
$nameArray = array();
|
|
1278
|
|
|
1279
|
foreach ($team as $member) {
|
|
1280
|
if (strlen($member->lastname) > 0) {
|
|
1281
|
$nname = $member->lastname;
|
|
1282
|
$name = $nname;
|
|
1283
|
if (strlen($member->firstname) > 0) {
|
|
1284
|
$vname = $member->firstname;
|
|
1285
|
$name = $vname . " " . $nname;
|
|
1286
|
}
|
|
1287
|
$nameArray[] = $name;
|
|
1288
|
}
|
|
1289
|
else {
|
|
1290
|
if (strlen($member->titleCache) > 0) {
|
|
1291
|
$nameArray[] = $member->titleCache;
|
|
1292
|
}
|
|
1293
|
}
|
|
1294
|
}
|
|
1295
|
$value = join($nameArray, ", ");
|
|
1296
|
}
|
|
1297
|
elseif ($fieldname == "inReference") {
|
|
1298
|
$type = $reference->$fieldname->type;
|
|
1299
|
$value = l($reference->$fieldname->titleCache, path_to_reference($reference->$fieldname->uuid));
|
|
1300
|
switch ($type) {
|
|
1301
|
case "Book":
|
|
1302
|
$fieldname = "in book";
|
|
1303
|
break;
|
|
1304
|
case "Journal":
|
|
1305
|
$fieldname = "in journal";
|
|
1306
|
break;
|
|
1307
|
case "Proceedings":
|
|
1308
|
$fieldname = "in proceedings";
|
|
1309
|
break;
|
|
1310
|
}
|
|
1311
|
}
|
|
1312
|
else {
|
|
1313
|
$value = $reference->$fieldname->titleCache;
|
|
1314
|
}
|
|
1315
|
|
|
1316
|
|
|
1317
|
if (isset($value) && $value != '') {
|
|
1318
|
$table_rows[] = array(
|
|
1319
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
|
1320
|
$value,
|
|
1321
|
);
|
|
1322
|
}
|
|
1323
|
|
|
1324
|
}
|
|
1325
|
else {
|
|
1326
|
if (isset($reference->$fieldname) && $reference->$fieldname != '') {
|
|
1327
|
$table_rows[] = array(
|
|
1328
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
|
1329
|
$reference->$fieldname,
|
|
1330
|
);
|
|
1331
|
}
|
|
1332
|
}
|
|
1333
|
}
|
|
1334
|
}
|
|
1335
|
|
|
1336
|
$out = theme_table(array(
|
|
1337
|
'header' => array(),
|
|
1338
|
'rows' => $table_rows,
|
|
1339
|
'attributes' => array(
|
|
1340
|
'class' => html_class_attribute_ref($reference)
|
|
1341
|
),
|
|
1342
|
'caption' => NULL,
|
|
1343
|
'colgroups' => NULL,
|
|
1344
|
'sticky' => NULL,
|
|
1345
|
'empty' => NULL,
|
|
1346
|
));
|
|
1347
|
|
|
1348
|
if(isset($reference->referenceAbstract)){
|
|
1349
|
$out .= '<h2 class="block-title">Abstract</h2><div class="abstract">' . $reference->referenceAbstract . '</div>';
|
|
1350
|
}
|
|
1351
|
|
|
1352
|
|
|
1353
|
// Annotations below the table
|
|
1354
|
$annotations = cdm_fetch_visible_annotations($reference);
|
|
1355
|
$out .= theme("cdm_annotations", array('annotations' => $annotations));
|
|
1356
|
|
|
1357
|
$registration_working_set = cdm_ws_get("registrationWorkingSetDTO", array($uuid));
|
|
1358
|
if($registration_working_set && count($registration_working_set->registrationDTOs) > 0){
|
|
1359
|
$out .= "<h3>Nomenclatural acts:</h3><div class=\"cdm-item-list registration-item-list\">";
|
|
1360
|
foreach($registration_working_set->registrationDTOs as $registration_dto){
|
|
1361
|
if($registration_dto->status == "PUBLISHED"){
|
|
1362
|
$registration_render_a = compose_registration_dto_compact($registration_dto, 'citation');
|
|
1363
|
$registration_render_a["#prefix"] = "<div class=\"item item-registration\">";
|
|
1364
|
$registration_render_a["#suffix"] = "</div>";
|
|
1365
|
$out .= drupal_render($registration_render_a);
|
|
1366
|
}
|
|
1367
|
}
|
|
1368
|
$out .= "</div>";
|
|
1369
|
}
|
|
1370
|
|
|
1371
|
RenderHints::popFromRenderStack();
|
|
1372
|
|
|
1373
|
return markup_to_render_array($out);
|
|
1374
|
}
|
|
1375
|
|
|
1376
|
/**
|
|
1377
|
* Provides the the label string for taxon page tabs.
|
|
1378
|
*
|
|
1379
|
* The $tabname as passed to the method will be returned if no override
|
|
1380
|
* label is configured in the settings.
|
|
1381
|
*/
|
|
1382
|
function cdm_taxonpage_tab_label($tabname) {
|
|
1383
|
static $taxon_tabs_labels = null;
|
|
1384
|
if($taxon_tabs_labels == null){
|
|
1385
|
$taxon_tabs_labels = get_array_variable_merged(CDM_TAXONPAGE_TAB_LABELS, CDM_TAXONPAGE_TAB_LABELS_DEFAULT);
|
|
1386
|
}
|
|
1387
|
$tabname_key = strtolower($tabname);
|
|
1388
|
if(isset($taxon_tabs_labels[$tabname_key]) && $taxon_tabs_labels[$tabname_key]){
|
|
1389
|
return $taxon_tabs_labels[$tabname_key];
|
|
1390
|
}
|
|
1391
|
return $tabname;
|
|
1392
|
}
|