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c70b93c3
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Andreas Kohlbecker
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<?php
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f19f47fa
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Andreas Kohlbecker
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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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c70b93c3
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Andreas Kohlbecker
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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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f19f47fa
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Andreas Kohlbecker
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* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
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*/
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/**
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02e8615c
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Andreas Kohlbecker
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* Composes a render array representing the ocurrences associetad with the $taxon.
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f19f47fa
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Andreas Kohlbecker
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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 $taxon
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* A cdm Taxon object
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* @return
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* A render array suitable for drupal_render()
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*
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02e8615c
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Andreas Kohlbecker
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* @ingroup Compose
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*
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c70b93c3
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Andreas Kohlbecker
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*/
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35 |
02e8615c
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Andreas Kohlbecker
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function compose_cdm_taxon_page_specimens($taxon) {
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36 |
f19f47fa
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Andreas Kohlbecker
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1ce9afb7
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Patric Plitzner
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$render_array = array();
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RenderHints::pushToRenderStack('taxon_page_specimens');
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39 |
30f78c59
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Andreas Kohlbecker
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961319fe
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Andreas Kohlbecker
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$fieldUnitDTOs = null;
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$specimensOrObservations = null;
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42 |
276f39f6
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Katja Luther
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if (variable_get('cdm_dataportal_specimen_derivate_tree')){
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43 |
961319fe
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Andreas Kohlbecker
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// get fieldUnitDTOs
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a0be8d7e
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Andreas Kohlbecker
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$fieldUnitDTOs = cdm_ws_get(CDM_WS_TAXON_FIELDUNIT_DTOS, array( $taxon->uuid));
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45 |
961319fe
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Andreas Kohlbecker
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$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($specimensOrObservations);
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7965ef92
|
Katja Luther
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}
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85 |
b8afc4bb
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Patric Plitzner
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b5c89485
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Patric Plitzner
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// --- get map service HTTP query parameters
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961319fe
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Andreas Kohlbecker
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if (count($specimensOrObservations) > 0 || $fieldUnitDTOs > 0) {
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$render_array['map'] = occurrence_map_query_parameters($taxon);
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b8afc4bb
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Patric Plitzner
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}
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db725031
|
Andreas Kohlbecker
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// -------------------------------------------------------
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106e1cf9
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Katja Luther
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1ce9afb7
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Patric Plitzner
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if(variable_get('cdm_dataportal_compressed_specimen_derivate_table')){
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//COMPRESSED SPECIMEN DERIVATE TABLE
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4cb163f8
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Patric Plitzner
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$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($associatedFieldUnitsQuery_parameters);
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09f028e2
|
Andreas Kohlbecker
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$pager_field_units = cdm_ws_get(CDM_WS_PORTAL_TAXON,
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2e82a602
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Patrick Plitzner
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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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106 |
1e87f89f
|
Andreas Kohlbecker
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09f028e2
|
Andreas Kohlbecker
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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[] = $field_unit->uuid;
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}
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961319fe
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Andreas Kohlbecker
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$render_array['derivate_hierarchy_table'] = compose_compressed_specimen_derivate_table($field_unit_uuids);
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02f3768c
|
Andreas Kohlbecker
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}
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115 |
f19f47fa
|
Andreas Kohlbecker
|
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1e87f89f
|
Andreas Kohlbecker
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$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' => $_REQUEST
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)),
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10 // weight
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);
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124 |
f19f47fa
|
Andreas Kohlbecker
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}
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125 |
276f39f6
|
Katja Luther
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else if(variable_get('cdm_dataportal_specimen_derivate_tree')){
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126 |
961319fe
|
Andreas Kohlbecker
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$render_array['specimen_list'] = compose_specimen_table_top_down($fieldUnitDTOs);
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127 |
ae177dac
|
Andreas Kohlbecker
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$render_array['specimen_list']['#weight'] = 2;
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128 |
961319fe
|
Andreas Kohlbecker
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} else {
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129 |
84849c31
|
Andreas Kohlbecker
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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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f19f47fa
|
Andreas Kohlbecker
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84849c31
|
Andreas Kohlbecker
|
RenderHints::popFromRenderStack();
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return $render_array;
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}
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146 |
1e87f89f
|
Andreas Kohlbecker
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/**
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* @return array
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*
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149 |
961319fe
|
Andreas Kohlbecker
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* TODO move to cdm_dataportal.module or api.module?
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150 |
1e87f89f
|
Andreas Kohlbecker
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*/
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151 |
961319fe
|
Andreas Kohlbecker
|
function relationship_filter_query_parameters()
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152 |
1e87f89f
|
Andreas Kohlbecker
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{
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153 |
961319fe
|
Andreas Kohlbecker
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$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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156 |
1e87f89f
|
Andreas Kohlbecker
|
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157 |
961319fe
|
Andreas Kohlbecker
|
$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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160 |
1e87f89f
|
Andreas Kohlbecker
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);
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161 |
961319fe
|
Andreas Kohlbecker
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return $by_associatedtaxon_query_parameters;
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162 |
1e87f89f
|
Andreas Kohlbecker
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}
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164 |
961319fe
|
Andreas Kohlbecker
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165 |
65a4de51
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Patrick Plitzner
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function create_html_link($link, $openInExternalWindow=false){
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166 |
7d8ef9fa
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Patric Plitzner
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$html = "";
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167 |
65a4de51
|
Patrick Plitzner
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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 .= '>' . $link->linkText . '</a>';
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173 |
7d8ef9fa
|
Patric Plitzner
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}
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else{
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$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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181 |
65a4de51
|
Patrick Plitzner
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* Creates HTML links from the given link list concatenated by default by a comma.
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182 |
7d8ef9fa
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Patric Plitzner
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* @param $linkList the list with Link objects having "uri" and "linkText" as members
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* @return string the assembled HTML string containing the links
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*/
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185 |
65a4de51
|
Patrick Plitzner
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function create_html_links($linkList, $openInExternalWindow=false, $separator=", ")
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186 |
7d8ef9fa
|
Patric Plitzner
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{
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$html = "";
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if ($linkList) {
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foreach ($linkList as $link) {
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190 |
65a4de51
|
Patrick Plitzner
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$html .= create_html_link($link, $openInExternalWindow).$separator;
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191 |
7d8ef9fa
|
Patric Plitzner
|
}
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192 |
65a4de51
|
Patrick Plitzner
|
$html = rtrim($html, $separator);
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193 |
7d8ef9fa
|
Patric Plitzner
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}
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return $html;
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}
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197 |
00a8e4b6
|
Andreas Kohlbecker
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/**
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198 |
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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 $page_part
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* Name of the part to display, valid values are:
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* - 'description' - for the general part
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* - 'images'
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* - 'synonymy'
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* - 'keys'
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* - 'all'
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*
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* @return array
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* A drupal render array
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*
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* @ingroup compose
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*/
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219 |
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function compose_cdm_taxon_page($taxon, $page_part = 'description') {
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221 |
0ae57522
|
Patric Plitzner
|
// we better cache here since drupal_get_query_parameters has no internal static cache variable
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$http_request_params = drupal_get_query_parameters();
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223 |
00a8e4b6
|
Andreas Kohlbecker
|
|
224 |
0ae57522
|
Patric Plitzner
|
// add all mandatory js sources
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225 |
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_add_js_footnotes();
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226 |
00a8e4b6
|
Andreas Kohlbecker
|
|
227 |
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228 |
0ae57522
|
Patric Plitzner
|
$render_array = array();
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229 |
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$weight = 0; // the weight for the render array elements
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230 |
00a8e4b6
|
Andreas Kohlbecker
|
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231 |
0ae57522
|
Patric Plitzner
|
$tabsToDisplay = variable_get('cdm_taxonpage_tabs_visibility', unserialize(TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT));
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232 |
00a8e4b6
|
Andreas Kohlbecker
|
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233 |
0ae57522
|
Patric Plitzner
|
$page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';
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234 |
00a8e4b6
|
Andreas Kohlbecker
|
|
235 |
22383f95
|
Andreas Kohlbecker
|
$synonymy_as_tab = variable_get(CDM_SYNONYMY_AS_TAB, CDM_SYNONYMY_AS_TAB_DEFAULT) === 1;
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236 |
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if(!$synonymy_as_tab){
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237 |
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unset($tabsToDisplay["Synonymy"]);
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238 |
3e6dfbb3
|
Andreas Kohlbecker
|
// the synonymy is located in the general part in this case
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239 |
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if($page_part == 'synonymy'){
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240 |
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$page_part = 'description';
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241 |
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}
|
242 |
22383f95
|
Andreas Kohlbecker
|
}
|
243 |
|
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|
244 |
0ae57522
|
Patric Plitzner
|
$media = _load_media_for_taxon($taxon);
|
245 |
00a8e4b6
|
Andreas Kohlbecker
|
|
246 |
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|
247 |
0ae57522
|
Patric Plitzner
|
if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {
|
248 |
48a6d7e8
|
Andreas Kohlbecker
|
taxon_page_tabs_hidden_add('images');
|
249 |
0ae57522
|
Patric Plitzner
|
}
|
250 |
00a8e4b6
|
Andreas Kohlbecker
|
|
251 |
0ae57522
|
Patric Plitzner
|
// --- GET specimensOrObservations --- //
|
252 |
c10f70e4
|
Katja Luther
|
$specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservationsCount'));
|
253 |
00a8e4b6
|
Andreas Kohlbecker
|
|
254 |
c10f70e4
|
Katja Luther
|
$specimensOrObservationsCount = $specimensOrObservations != null ? $specimensOrObservations->result : 0;
|
255 |
0ae57522
|
Patric Plitzner
|
if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {
|
256 |
48a6d7e8
|
Andreas Kohlbecker
|
taxon_page_tabs_hidden_add('specimens');
|
257 |
0ae57522
|
Patric Plitzner
|
}
|
258 |
00a8e4b6
|
Andreas Kohlbecker
|
|
259 |
0ae57522
|
Patric Plitzner
|
// --- GET polytomousKeys --- //
|
260 |
|
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$polytomousKeysPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, NULL, "findByTaxonomicScope=$taxon->uuid");
|
261 |
|
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$identificationKeyCount = 0;
|
262 |
|
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if ($polytomousKeysPager) {
|
263 |
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$identificationKeyCount += $polytomousKeysPager->count;
|
264 |
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}
|
265 |
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if ($identificationKeyCount == 0 || ($tabsToDisplay["Keys"] == '0')) {
|
266 |
48a6d7e8
|
Andreas Kohlbecker
|
taxon_page_tabs_hidden_add('keys');
|
267 |
0ae57522
|
Patric Plitzner
|
}
|
268 |
092744e1
|
Andreas Kohlbecker
|
|
269 |
22383f95
|
Andreas Kohlbecker
|
// --- GET TaxonNodeAgentRelations --- //
|
270 |
|
|
$current_classification_uuid = get_current_classification_uuid();
|
271 |
|
|
$taxon_node_agent_relations_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
|
272 |
|
|
array(
|
273 |
|
|
$taxon->uuid,
|
274 |
|
|
$current_classification_uuid,
|
275 |
|
|
),
|
276 |
|
|
"pageSize=1&pageIndex=0"// we are only interested into the count so we are fetching only one item, o is not possible!
|
277 |
|
|
);
|
278 |
|
|
if (!$taxon_node_agent_relations_pager || $taxon_node_agent_relations_pager->count == 0){
|
279 |
48a6d7e8
|
Andreas Kohlbecker
|
taxon_page_tabs_hidden_add('experts');
|
280 |
22383f95
|
Andreas Kohlbecker
|
}
|
281 |
7663cd0b
|
Andreas Kohlbecker
|
|
282 |
22383f95
|
Andreas Kohlbecker
|
if (!isset($tabsToDisplay["Synonymy"]) || $tabsToDisplay["Synonymy"] == '0') {
|
283 |
48a6d7e8
|
Andreas Kohlbecker
|
taxon_page_tabs_hidden_add('synonymy');
|
284 |
0ae57522
|
Patric Plitzner
|
}
|
285 |
00a8e4b6
|
Andreas Kohlbecker
|
|
286 |
0ae57522
|
Patric Plitzner
|
// -------------------------------------------- //
|
287 |
00a8e4b6
|
Andreas Kohlbecker
|
|
288 |
fe169cb6
|
Andreas Kohlbecker
|
if(variable_get(CDM_TAXONPAGE_TAXON_NODE_SHOW_STATES, 1) && ( $page_part == 'description' || $page_part == 'synonymy' || $page_part == 'all')){
|
289 |
bd56cbc1
|
Andreas Kohlbecker
|
$taxon_nodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, array($taxon->uuid));
|
290 |
|
|
$render_array['taxon_node_status'] = compose_taxon_node_status($taxon_nodes);
|
291 |
|
|
$render_array['taxon_node_status']['#weight'] = -100;
|
292 |
|
|
}
|
293 |
|
|
|
294 |
0ae57522
|
Patric Plitzner
|
if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {
|
295 |
7272d19c
|
Andreas Kohlbecker
|
$render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);
|
296 |
0ae57522
|
Patric Plitzner
|
}
|
297 |
00a8e4b6
|
Andreas Kohlbecker
|
|
298 |
0ae57522
|
Patric Plitzner
|
// --- PAGE PART: DESCRIPTION --- //
|
299 |
48a6d7e8
|
Andreas Kohlbecker
|
if (!taxon_page_tabs_hidden_check('description') && ($page_part == 'description' || $page_part == 'all')) {
|
300 |
00a8e4b6
|
Andreas Kohlbecker
|
|
301 |
0ae57522
|
Patric Plitzner
|
$merged_tree = merged_taxon_feature_tree($taxon);
|
302 |
00a8e4b6
|
Andreas Kohlbecker
|
|
303 |
7d8ef9fa
|
Patric Plitzner
|
|
304 |
22383f95
|
Andreas Kohlbecker
|
$render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, !$synonymy_as_tab);
|
305 |
0ae57522
|
Patric Plitzner
|
$render_array['general']['#weight'] = $weight++;
|
306 |
|
|
$render_array['general']['#prefix'] = '<div id="general" class="page-part">';
|
307 |
|
|
$render_array['general']['#suffix'] = '</div>';
|
308 |
|
|
}
|
309 |
7d8ef9fa
|
Patric Plitzner
|
|
310 |
0ae57522
|
Patric Plitzner
|
// --- PAGE PART: IMAGES --- //
|
311 |
48a6d7e8
|
Andreas Kohlbecker
|
if (!taxon_page_tabs_hidden_check('images') && ($page_part == 'images' || $page_part == 'all')) {
|
312 |
0ae57522
|
Patric Plitzner
|
$images_html = '<div id="images" class="page-part">';
|
313 |
|
|
if ($page_part == 'all') {
|
314 |
4feeabc7
|
Andreas Kohlbecker
|
$images_html .= '<h2>' . t(cdm_taxonpage_tab_label('Images')) . '</h2>';
|
315 |
7d8ef9fa
|
Patric Plitzner
|
}
|
316 |
0ae57522
|
Patric Plitzner
|
// Get the image gallery as configured by the admin.
|
317 |
a1f7edc0
|
Andreas Kohlbecker
|
$configured_image_gallery_viewer = variable_get(CDM_MEDIA_GALLERY_VIEWER, CDM_MEDIA_GALLERY_VIEWER_DEFAULT);
|
318 |
|
|
if($configured_image_gallery_viewer != 'fsi'){
|
319 |
|
|
$images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);
|
320 |
|
|
} else {
|
321 |
8f4eb9ce
|
Andreas Kohlbecker
|
// the fsi_gallery requires a flash plugin, in case the client browser is not supporting
|
322 |
|
|
// flash we also need to provide an the default gallery as alternative
|
323 |
a1f7edc0
|
Andreas Kohlbecker
|
$images_html .= render_taxon_media_gallery($taxon, CDM_MEDIA_GALLERY_VIEWER_DEFAULT, $media);
|
324 |
|
|
$images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);
|
325 |
8f4eb9ce
|
Andreas Kohlbecker
|
}
|
326 |
a1f7edc0
|
Andreas Kohlbecker
|
$images_html .= '</div>'; // END of <div id="images">
|
327 |
0ae57522
|
Patric Plitzner
|
$render_array['images'] = markup_to_render_array($images_html, $weight++);
|
328 |
|
|
}
|
329 |
7d8ef9fa
|
Patric Plitzner
|
|
330 |
0ae57522
|
Patric Plitzner
|
// --- PAGE PART: SYNONYMY --- //
|
331 |
48a6d7e8
|
Andreas Kohlbecker
|
if (!taxon_page_tabs_hidden_check('synonymy') && (($page_part == 'synonymy' || $page_part == 'all') && $synonymy_as_tab)) {
|
332 |
0ae57522
|
Patric Plitzner
|
$synonymy_html = '<div id="synonymy" class="page-part">';
|
333 |
|
|
if ($page_part == 'all') {
|
334 |
4feeabc7
|
Andreas Kohlbecker
|
$synonymy_html .= '<h2>' . t(cdm_taxonpage_tab_label('Synonymy')) . '</h2>';
|
335 |
00a8e4b6
|
Andreas Kohlbecker
|
}
|
336 |
aec9ca7d
|
Andreas Kohlbecker
|
$addAcceptedTaxon = variable_get(CDM_DATAPORTAL_NOMREF_IN_TITLE, CDM_DATAPORTAL_NOMREF_IN_TITLE_DEFAULT);
|
337 |
41b4bfc9
|
Andreas Kohlbecker
|
|
338 |
1cda248c
|
Andreas Kohlbecker
|
$synonym_a = compose_cdm_taxon_page_synonymy($taxon, $addAcceptedTaxon);
|
339 |
|
|
$synonymy_html .= drupal_render($synonym_a);
|
340 |
00a8e4b6
|
Andreas Kohlbecker
|
|
341 |
0ae57522
|
Patric Plitzner
|
$synonymy_html .= '</div>';
|
342 |
|
|
$render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
|
343 |
00a8e4b6
|
Andreas Kohlbecker
|
|
344 |
0ae57522
|
Patric Plitzner
|
}
|
345 |
00a8e4b6
|
Andreas Kohlbecker
|
|
346 |
0ae57522
|
Patric Plitzner
|
// --- PAGE PART: SPECIMENS --- //
|
347 |
48a6d7e8
|
Andreas Kohlbecker
|
if (!taxon_page_tabs_hidden_check('specimens') && ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all'))) {
|
348 |
0ae57522
|
Patric Plitzner
|
$render_array['specimens'] = array(
|
349 |
4feeabc7
|
Andreas Kohlbecker
|
'#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Specimens')) . '</h2>' : ''),
|
350 |
02e8615c
|
Andreas Kohlbecker
|
'content' => compose_cdm_taxon_page_specimens($taxon), // returns render array
|
351 |
0ae57522
|
Patric Plitzner
|
'#suffix' => '</div>',
|
352 |
|
|
);
|
353 |
|
|
}
|
354 |
|
|
|
355 |
|
|
// --- PAGE PART: KEYS --- //
|
356 |
48a6d7e8
|
Andreas Kohlbecker
|
if(!taxon_page_tabs_hidden_check('keys')){
|
357 |
|
|
if ($identificationKeyCount == 1 && $page_part == 'keys'){
|
358 |
|
|
drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));
|
359 |
|
|
}
|
360 |
|
|
else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {
|
361 |
|
|
$keys_html = '<div id="keys" class="page-part">';
|
362 |
|
|
if ($page_part == 'all') {
|
363 |
|
|
$keys_html .= '<h2>' . t(cdm_taxonpage_tab_label('Keys')) . '</h2>';
|
364 |
|
|
}
|
365 |
|
|
$keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
|
366 |
|
|
$keys_html .= '</div>';
|
367 |
|
|
$render_array['keys'] = markup_to_render_array($keys_html, $weight++);
|
368 |
0ae57522
|
Patric Plitzner
|
}
|
369 |
|
|
}
|
370 |
|
|
|
371 |
7663cd0b
|
Andreas Kohlbecker
|
// --- PAGE PART: EXPERTS --- //
|
372 |
|
|
|
373 |
48a6d7e8
|
Andreas Kohlbecker
|
if (!taxon_page_tabs_hidden_check('experts') && ($page_part == 'experts' || $page_part == 'all')) {
|
374 |
7663cd0b
|
Andreas Kohlbecker
|
$render_array['experts'] = array(
|
375 |
4feeabc7
|
Andreas Kohlbecker
|
'#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Experts')) . '</h2>' : ''),
|
376 |
7663cd0b
|
Andreas Kohlbecker
|
'content' => compose_cdm_taxon_page_experts($taxon), // returns render array
|
377 |
|
|
'#suffix' => '</div>',
|
378 |
|
|
);
|
379 |
|
|
}
|
380 |
|
|
|
381 |
|
|
// ------------------ END OF PARTS -------------- //
|
382 |
0ae57522
|
Patric Plitzner
|
|
383 |
|
|
// adjust weights of page and toc elements according to the settings
|
384 |
4feeabc7
|
Andreas Kohlbecker
|
$taxontabs_weights = get_array_variable_merged(CDM_TAXONPAGE_TAB_WEIGHT, CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
|
385 |
0ae57522
|
Patric Plitzner
|
foreach($taxontabs_weights as $tab_key => $weight){
|
386 |
|
|
if(isset($render_array[$tab_key])){
|
387 |
|
|
$render_array[$tab_key]['#weight'] = $weight;
|
388 |
|
|
}
|
389 |
|
|
}
|
390 |
|
|
|
391 |
|
|
|
392 |
2203967c
|
Andreas Kohlbecker
|
// set up the TOC and pseudo feature blocks for the pages which contain all page parts
|
393 |
|
|
if($page_part == 'all' && (!isset( $render_array['general']) || count($render_array['general']) == 0 )) {
|
394 |
9b8eb609
|
Andreas Kohlbecker
|
|
395 |
|
|
$bibliography_block = make_bibliography_feature_block();
|
396 |
|
|
if($bibliography_block){
|
397 |
2203967c
|
Andreas Kohlbecker
|
$render_array['bibliography_block'] = _block_get_renderable_array([$bibliography_block]);
|
398 |
9b8eb609
|
Andreas Kohlbecker
|
$render_array['bibliography_block']['#weight'] = 100;
|
399 |
|
|
cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $render_array['bibliography_block']['#weight']);
|
400 |
|
|
}
|
401 |
|
|
|
402 |
aec9ca7d
|
Andreas Kohlbecker
|
$toc_elements = [];
|
403 |
0ae57522
|
Patric Plitzner
|
asort($taxontabs_weights);
|
404 |
|
|
foreach(array_keys($taxontabs_weights) as $tab_key){
|
405 |
|
|
if(isset($render_array[$tab_key])){
|
406 |
|
|
if($tab_key != 'general'){
|
407 |
|
|
// add entry for page part
|
408 |
|
|
$toc_elements[] = array(
|
409 |
4feeabc7
|
Andreas Kohlbecker
|
'data' => l(t(cdm_taxonpage_tab_label(ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),
|
410 |
0ae57522
|
Patric Plitzner
|
'class' => array('page-part-toc-item-' . $tab_key)
|
411 |
|
|
);
|
412 |
|
|
} else {
|
413 |
|
|
// add content of profile part instead
|
414 |
|
|
if(isset($render_array['general'])) {
|
415 |
|
|
// in case all tabs are shown at once the feature tocs
|
416 |
|
|
// should be integrated into the tabs toc as sub list
|
417 |
|
|
// and the profile image should be on top of the page
|
418 |
|
|
if(isset($render_array['general']['taxon_description_feature_toc'])){;
|
419 |
|
|
foreach ($render_array['general']['taxon_description_feature_toc']['#items'] as $profile_toc_item){
|
420 |
|
|
$toc_elements[] = $profile_toc_item;
|
421 |
7d8ef9fa
|
Patric Plitzner
|
}
|
422 |
0ae57522
|
Patric Plitzner
|
unset($render_array['general']['taxon_description_feature_toc']);
|
423 |
|
|
}
|
424 |
|
|
}
|
425 |
7d8ef9fa
|
Patric Plitzner
|
}
|
426 |
0ae57522
|
Patric Plitzner
|
}
|
427 |
|
|
}
|
428 |
7d8ef9fa
|
Patric Plitzner
|
|
429 |
0ae57522
|
Patric Plitzner
|
// move profile image in page structure
|
430 |
|
|
if(isset($render_array['general']['taxon_profile_image'])){
|
431 |
|
|
$render_array['profile_image'] = $render_array['general']['taxon_profile_image'];
|
432 |
|
|
$render_array['profile_image']['#weight'] = -100;
|
433 |
|
|
unset($render_array['general']['taxon_profile_image']);
|
434 |
7d8ef9fa
|
Patric Plitzner
|
}
|
435 |
|
|
|
436 |
0ae57522
|
Patric Plitzner
|
// finally add the table of contents to the render array
|
437 |
|
|
$render_array['toc'] = array(
|
438 |
|
|
'#theme' => 'item_list',
|
439 |
|
|
'#items' => $toc_elements,
|
440 |
|
|
'#title' => t('Content'),
|
441 |
|
|
'#weight' => -101,
|
442 |
|
|
'#suffix' => '</div>',
|
443 |
|
|
'#prefix'=> '<div id="page-toc">'
|
444 |
|
|
);
|
445 |
aec9ca7d
|
Andreas Kohlbecker
|
|
446 |
0ae57522
|
Patric Plitzner
|
}
|
447 |
|
|
|
448 |
7d8ef9fa
|
Patric Plitzner
|
|
449 |
0ae57522
|
Patric Plitzner
|
return $render_array;
|
450 |
00a8e4b6
|
Andreas Kohlbecker
|
}
|
451 |
|
|
|
452 |
1ce9afb7
|
Patric Plitzner
|
/**
|
453 |
22f5e82d
|
Andreas Kohlbecker
|
* TODO should this function really be a compose function?
|
454 |
|
|
* For a compose function must there always be a theme function with the same name? (ak 8.8.2013)
|
455 |
bf97c2e8
|
Andreas Kohlbecker
|
*
|
456 |
|
|
* composes and returns an render array containing the components of the taxon profile tab:
|
457 |
|
|
* - 'taxon_profile_image'
|
458 |
|
|
* - 'taxon_description_feature_toc'
|
459 |
|
|
* - 'taxon_description_features'
|
460 |
|
|
*
|
461 |
|
|
*
|
462 |
8a1b451e
|
Andreas Kohlbecker
|
* @param object taxon
|
463 |
|
|
* @param object $merged_tree
|
464 |
|
|
* @param object media
|
465 |
|
|
* @param bool $add_synonymy
|
466 |
bf97c2e8
|
Andreas Kohlbecker
|
*
|
467 |
|
|
* @return array
|
468 |
f78fda81
|
Andreas Kohlbecker
|
* A Drupal render array with the following elements:
|
469 |
bf97c2e8
|
Andreas Kohlbecker
|
* - 'taxon_profile_image'
|
470 |
|
|
* - 'taxon_description_feature_toc'
|
471 |
|
|
* - 'taxon_description_features'
|
472 |
|
|
*
|
473 |
8a1b451e
|
Andreas Kohlbecker
|
* @throws Exception
|
474 |
|
|
*
|
475 |
bf97c2e8
|
Andreas Kohlbecker
|
* @ingroup compose
|
476 |
|
|
*/
|
477 |
22383f95
|
Andreas Kohlbecker
|
function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, $add_synonymy) {
|
478 |
bf97c2e8
|
Andreas Kohlbecker
|
|
479 |
0ae57522
|
Patric Plitzner
|
$render_array = array();
|
480 |
|
|
|
481 |
|
|
$taxon_profile_image_settings = variable_get(CDM_TAXON_PROFILE_IMAGE, unserialize(CDM_TAXON_PROFILE_IMAGE_DEFAULT));
|
482 |
|
|
|
483 |
|
|
$hide_taxon_profile_image = FALSE;
|
484 |
|
|
if (variable_get('image_hide_rank', '0') != '0' && isset($taxon->name->rank->uuid)) {
|
485 |
|
|
$rankCompare = rank_compare($taxon->name->rank->uuid, variable_get('image_hide_rank', '-99'));
|
486 |
|
|
$hide_taxon_profile_image = ($rankCompare > -1);
|
487 |
|
|
}
|
488 |
|
|
|
489 |
|
|
if ($taxon_profile_image_settings['show'] && !$hide_taxon_profile_image) {
|
490 |
|
|
|
491 |
|
|
$representationPart = new stdClass();
|
492 |
|
|
$attributes = array();
|
493 |
02faa087
|
Andreas Kohlbecker
|
if (isset($media[0])) {
|
494 |
|
|
// due to a bug the portal/taxon/{uuid}/media service only delivers a filtered media object
|
495 |
|
|
// which only contains the thumbnail representation even if the height and width filters are not set.
|
496 |
673929dd
|
Andreas Kohlbecker
|
// -->
|
497 |
02faa087
|
Andreas Kohlbecker
|
$preferred_media = cdm_ws_get(CDM_WS_MEDIA, $media[0]->uuid);
|
498 |
|
|
$preferred_representations = cdm_preferred_media_representations($preferred_media, array(
|
499 |
|
|
'image/jpg',
|
500 |
|
|
'image/jpeg',
|
501 |
|
|
'image/png',
|
502 |
|
|
'image/gif',
|
503 |
|
|
),
|
504 |
|
|
$taxon_profile_image_settings['maxextend'],
|
505 |
|
|
$taxon_profile_image_settings['maxextend']
|
506 |
|
|
);
|
507 |
|
|
if(count($preferred_representations) > 0){
|
508 |
|
|
|
509 |
|
|
$representation = array_shift($preferred_representations);
|
510 |
|
|
$representationPart = $representation->parts[0];
|
511 |
|
|
$attributes['alt'] = $representationPart->uri;
|
512 |
|
|
|
513 |
|
|
if (!empty($taxon_profile_image_settings['media_uri_query'])) {
|
514 |
|
|
$representationPart->uri = $representationPart->uri
|
515 |
|
|
. (strpos($representationPart->uri, '?') !== FALSE ? '&' : '?')
|
516 |
|
|
. $taxon_profile_image_settings['media_uri_query'];
|
517 |
|
|
}
|
518 |
0ae57522
|
Patric Plitzner
|
}
|
519 |
|
|
}
|
520 |
|
|
else {
|
521 |
9506fd1f
|
Andreas Kohlbecker
|
if ($taxon_profile_image_settings['custom_placeholder_enabled']) {
|
522 |
ca47ea76
|
Andreas Kohlbecker
|
// show placeholder image instead
|
523 |
|
|
if (!empty($taxon_profile_image_settings['custom_placeholder_image_on']) && !empty($taxon_profile_image_settings['custom_placeholder_image_fid'])) {
|
524 |
|
|
// use the user provided image
|
525 |
|
|
$profile_image_file = file_load($taxon_profile_image_settings['custom_placeholder_image_fid']);
|
526 |
|
|
$url = file_create_url($profile_image_file->uri);
|
527 |
|
|
$image_info = image_get_info($profile_image_file->uri);
|
528 |
|
|
$representationPart->width = $image_info['width'];
|
529 |
|
|
$representationPart->height = $image_info['height'];
|
530 |
|
|
$representationPart->uri = $url;
|
531 |
|
|
}
|
532 |
|
|
else {
|
533 |
|
|
// use the hard coded default
|
534 |
|
|
$representationPart->width = 184;
|
535 |
|
|
$representationPart->height = 144;
|
536 |
|
|
$representationPart->uri = base_path() . drupal_get_path('module',
|
537 |
|
|
'cdm_dataportal') . '/images/no_picture.png';
|
538 |
|
|
}
|
539 |
|
|
$attributes['alt'] = "no image available";
|
540 |
0ae57522
|
Patric Plitzner
|
}
|
541 |
|
|
}
|
542 |
|
|
|
543 |
ca47ea76
|
Andreas Kohlbecker
|
if (isset($representationPart->uri)) {
|
544 |
a9815578
|
Andreas Kohlbecker
|
$profile_image = cdm_media_gallerie_image($representationPart, $taxon_profile_image_settings['maxextend'], FALSE, $attributes);
|
545 |
ca47ea76
|
Andreas Kohlbecker
|
// NOTE: style="width:${maxextend}px' is needed for IE8 !!!
|
546 |
84849c31
|
Andreas Kohlbecker
|
$max_extend_with = $taxon_profile_image_settings['maxextend'] . 'px';
|
547 |
062686a1
|
Andreas Kohlbecker
|
$render_array['taxon_profile_image'] = markup_to_render_array('<div id="taxonProfileImage" style="width:' . $max_extend_with . '">' . $profile_image . '</div>',
|
548 |
ca47ea76
|
Andreas Kohlbecker
|
-101);
|
549 |
|
|
}
|
550 |
0ae57522
|
Patric Plitzner
|
}
|
551 |
|
|
|
552 |
22383f95
|
Andreas Kohlbecker
|
if($add_synonymy){
|
553 |
1cda248c
|
Andreas Kohlbecker
|
$synonymy_a = compose_cdm_taxon_page_synonymy($taxon, true);
|
554 |
|
|
$synonymy_a['#weight'] = -102;
|
555 |
aec9ca7d
|
Andreas Kohlbecker
|
$synonymy_a['#prefix'] = '<div id="synonymy">';
|
556 |
|
|
$synonymy_a['#suffix'] = '</div>';
|
557 |
1cda248c
|
Andreas Kohlbecker
|
$render_array['synonymy'] = $synonymy_a;
|
558 |
22383f95
|
Andreas Kohlbecker
|
}
|
559 |
|
|
|
560 |
7ccb6888
|
Andreas Kohlbecker
|
// $pseudo_feature_block_toc_items = array();
|
561 |
0ae57522
|
Patric Plitzner
|
|
562 |
1b756c5f
|
Andreas Kohlbecker
|
// Render the sections for each real feature
|
563 |
|
|
$feature_block_list = make_feature_block_list($merged_tree->root->childNodes, $taxon);
|
564 |
|
|
|
565 |
bf8aea21
|
Andreas Kohlbecker
|
// >>>>>>>>>>>>>>>>>>> PSEUDO FEATURES >>>>>>>>>>>>>>>>>>>
|
566 |
c3a41ddb
|
Andreas Kohlbecker
|
$pseudo_feature_weights = get_array_variable_merged(CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS, CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS_DEFAULT);
|
567 |
0ae57522
|
Patric Plitzner
|
|
568 |
9b8eb609
|
Andreas Kohlbecker
|
// Bibliography
|
569 |
|
|
$bibliography_block = make_bibliography_feature_block();
|
570 |
|
|
if($bibliography_block){
|
571 |
|
|
$feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]] = $bibliography_block;
|
572 |
|
|
cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]);
|
573 |
1b756c5f
|
Andreas Kohlbecker
|
}
|
574 |
|
|
|
575 |
bf8aea21
|
Andreas Kohlbecker
|
// Descriptions (aggregated)
|
576 |
|
|
$descriptionTypes = array();
|
577 |
|
|
$descriptionTypes['descriptionTypes'] = ("AGGREGATED_STRUC_DESC");
|
578 |
|
|
$aggregatedDescriptions = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXON . '/' . $taxon->uuid . '/descriptions', $descriptionTypes);
|
579 |
|
|
if (isset($aggregatedDescriptions) and !empty($aggregatedDescriptions)) {
|
580 |
|
|
// if($feature_block_list) ....TODO
|
581 |
|
|
$feature_description = make_pseudo_feature('Descriptions (aggregated)', PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS);
|
582 |
|
|
$description_item = '';
|
583 |
|
|
foreach ($aggregatedDescriptions as $description) {
|
584 |
92e522db
|
Andreas Kohlbecker
|
$description_item = '<div class="' . html_class_attribute_ref($description) . '">';
|
585 |
2527a83c
|
Andreas Kohlbecker
|
$description_item .= render_description_string(get_root_nodes_for_dataset($description));
|
586 |
92e522db
|
Andreas Kohlbecker
|
$description_item .= ' ' . icon_link(path_to_description($description->uuid));
|
587 |
cd3ea2e8
|
Andreas Kohlbecker
|
$description_item .= '<div class="content-caption">'. statistical_values_explanation() . '</div>';
|
588 |
92e522db
|
Andreas Kohlbecker
|
$description_item .= '</div>';
|
589 |
bf8aea21
|
Andreas Kohlbecker
|
}
|
590 |
|
|
$description_block = feature_block(t('Descriptions (aggregated)'), $feature_description);
|
591 |
|
|
$description_block->content = [];
|
592 |
|
|
$description_block->content[] = compose_feature_block_wrap_elements([$description_item], $feature_description);
|
593 |
e170a53e
|
Patrick Plitzner
|
|
594 |
c3a41ddb
|
Andreas Kohlbecker
|
$feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]] = $description_block;
|
595 |
089fb6ea
|
Andreas Kohlbecker
|
cdm_toc_list_add_item('Descriptions (aggregated)', 'aggregation_descriptions', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]);
|
596 |
c3a41ddb
|
Andreas Kohlbecker
|
|
597 |
0ae57522
|
Patric Plitzner
|
|
598 |
bf8aea21
|
Andreas Kohlbecker
|
}
|
599 |
9d88232c
|
Patrick Plitzner
|
|
600 |
c3a41ddb
|
Andreas Kohlbecker
|
// sort by weight
|
601 |
|
|
ksort($feature_block_list);
|
602 |
|
|
$render_array['taxon_description_features'] = _block_get_renderable_array($feature_block_list);
|
603 |
|
|
|
604 |
|
|
/* // update TOC
|
605 |
bf8aea21
|
Andreas Kohlbecker
|
if ($pseudo_feature_block_toc_items){
|
606 |
1b756c5f
|
Andreas Kohlbecker
|
foreach ($pseudo_feature_block_toc_items as $label=>$fragment){
|
607 |
|
|
cdm_toc_list_add_item($label, $fragment);
|
608 |
|
|
}
|
609 |
0ae57522
|
Patric Plitzner
|
}
|
610 |
c3a41ddb
|
Andreas Kohlbecker
|
*/
|
611 |
bf8aea21
|
Andreas Kohlbecker
|
// <<<<<<<<<<<<<<<<<<< PSEUDO FEATURES <<<<<<<<<<<<<<<<<<<
|
612 |
|
|
|
613 |
0ae57522
|
Patric Plitzner
|
// create the table of content
|
614 |
|
|
$toc = array(
|
615 |
|
|
'#theme' => 'item_list',
|
616 |
|
|
'#items' => cdm_toc_list(),
|
617 |
|
|
'#title' => t('Content'),
|
618 |
|
|
'#weight' => -100, // move to the top
|
619 |
|
|
'#suffix' => '</div>',
|
620 |
|
|
'#prefix'=> '<div id="page-toc">'
|
621 |
|
|
);
|
622 |
|
|
$render_array['taxon_description_feature_toc'] = $toc;
|
623 |
|
|
|
624 |
|
|
return $render_array;
|
625 |
bf97c2e8
|
Andreas Kohlbecker
|
}
|
626 |
|
|
|
627 |
9b8eb609
|
Andreas Kohlbecker
|
/**
|
628 |
|
|
* @return object|\stdclass
|
629 |
|
|
*/
|
630 |
|
|
function make_bibliography_feature_block() {
|
631 |
|
|
$bibliography_block = null;
|
632 |
|
|
$bibliography_settings = get_bibliography_settings();
|
633 |
|
|
if ($bibliography_settings['enabled'] == 1) {
|
634 |
|
|
$bibliography_markup = FootnoteManager::renderFootnoteList(PSEUDO_FEATURE_BIBLIOGRAPHY, '');
|
635 |
|
|
if ($bibliography_markup) {
|
636 |
|
|
$feature_bibliography = make_pseudo_feature('Bibliography', PSEUDO_FEATURE_BIBLIOGRAPHY);
|
637 |
|
|
$bibliography_item = markup_to_render_array($bibliography_markup);
|
638 |
|
|
$bibliography_block = feature_block(t('Bibliography'), $feature_bibliography);
|
639 |
|
|
$bibliography_block->content = [];
|
640 |
|
|
$bibliography_block->content[] = compose_feature_block_wrap_elements([$bibliography_item], $feature_bibliography);
|
641 |
|
|
}
|
642 |
|
|
}
|
643 |
|
|
return $bibliography_block;
|
644 |
|
|
}
|
645 |
|
|
|
646 |
a38c0718
|
Patrick Plitzner
|
|
647 |
67ce7111
|
Patrick Plitzner
|
/**
|
648 |
|
|
* Renders the link which will lead to the specimen detail page
|
649 |
55236f7f
|
Andreas Kohlbecker
|
* @param object $specimen
|
650 |
|
|
* the cdm specimen entity which will be linked to
|
651 |
67ce7111
|
Patrick Plitzner
|
*
|
652 |
55236f7f
|
Andreas Kohlbecker
|
* @return string
|
653 |
|
|
* the markup for the link
|
654 |
67ce7111
|
Patrick Plitzner
|
*/
|
655 |
|
|
function render_cdm_specimen_link($specimen) {
|
656 |
|
|
$path = path_to_specimen($specimen->uuid);
|
657 |
|
|
$attributes['class'][] = html_class_attribute_ref($specimen);
|
658 |
ab025781
|
Andreas Kohlbecker
|
return $specimen->titleCache.icon_link($path);
|
659 |
67ce7111
|
Patrick Plitzner
|
}
|
660 |
|
|
|
661 |
57dabcba
|
Andreas Kohlbecker
|
/**
|
662 |
|
|
* Returns HTML containing the synonymy for the accepted taxon.
|
663 |
|
|
*
|
664 |
|
|
* Shows the whole synonymy for the accepted taxon.
|
665 |
|
|
* The synonymy list is headed by the complete scientific name
|
666 |
|
|
* of the accepted taxon with nomenclatural reference.
|
667 |
|
|
*
|
668 |
|
|
* @param object $taxon
|
669 |
|
|
* @param boolean $add_accepted_taxon
|
670 |
|
|
*
|
671 |
|
|
* @return array
|
672 |
|
|
* Drupal render array for the synonymy
|
673 |
|
|
*
|
674 |
|
|
* @throws Exception
|
675 |
|
|
*
|
676 |
|
|
* @ingroup compose
|
677 |
|
|
*/
|
678 |
|
|
function compose_cdm_taxon_page_synonymy($taxon, $add_accepted_taxon) {
|
679 |
|
|
|
680 |
|
|
RenderHints::pushToRenderStack('taxon_page_synonymy');
|
681 |
|
|
|
682 |
|
|
// footnote key for the homotypic group and accepted taxon,
|
683 |
|
|
// both should have the same footnote key
|
684 |
|
|
RenderHints::setFootnoteListKey(RenderHints::getRenderPath());
|
685 |
|
|
|
686 |
|
|
$synomymie = cdm_ws_get(CDM_WS_PORTAL_TAXON_SYNONYMY, array($taxon->uuid));
|
687 |
|
|
|
688 |
|
|
$out = '';
|
689 |
|
|
|
690 |
|
|
// Render accepted taxon.
|
691 |
|
|
//
|
692 |
|
|
// foonotes of the accepted taxon will be rendered in the homotypic group section
|
693 |
|
|
// even if there are not synonyms in the homotypic group
|
694 |
|
|
// homotypic group and accepted taxon should have the same footnote key
|
695 |
|
|
$referenceUri = '';
|
696 |
|
|
if ($add_accepted_taxon) {
|
697 |
|
|
// remember the last part of the render path
|
698 |
|
|
$synonymy_render_path = RenderHints::getRenderPath();
|
699 |
|
|
// set new render path for the accepted taxon so
|
700 |
|
|
// it can be styled differently via the name render part definitions
|
701 |
|
|
RenderHints::pushToRenderStack('accepted_taxon');
|
702 |
|
|
$accepted_name = '';
|
703 |
|
|
if (variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE, 0)) {
|
704 |
|
|
$label = variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL, CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL_DEFAULT);
|
705 |
|
|
$accepted_name .= '<div class="secReference"><span class="label">' . t($label) . ':</span> ' . $taxon->sec->titleCache . '</div>';
|
706 |
|
|
}
|
707 |
|
|
if (isset($taxon->name->nomenclaturalReference)) {
|
708 |
|
|
$referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
|
709 |
|
|
}
|
710 |
|
|
|
711 |
|
|
$accepted_name .= '<div class="accepted-name">';
|
712 |
|
|
$accepted_name .= render_taxon_or_name($taxon, NULL, $referenceUri);
|
713 |
|
|
|
714 |
|
|
$name_relations = cdm_name_relationships_for_taxon($taxon);
|
715 |
|
|
$name_relationships = compose_name_relationships_inline($name_relations, $taxon->name->uuid, $taxon->uuid);
|
716 |
|
|
// Render relationships of accepted name.
|
717 |
|
|
if(isset($name_relationships['list']['items'][0])){
|
718 |
|
|
$accepted_name .= ' ' . drupal_render($name_relationships);
|
719 |
|
|
}
|
720 |
|
|
|
721 |
|
|
// handle annotations of the name and taxon
|
722 |
|
|
$special_annotations_array = array();
|
723 |
|
|
$special_annotations_array[] = $taxon->name;
|
724 |
|
|
$special_annotations_array[] = $taxon;
|
725 |
d0be436a
|
Andreas Kohlbecker
|
$accepted_name .= cdm_entities_annotations_as_footnotekeys($special_annotations_array, $synonymy_render_path . '-annotations');
|
726 |
57dabcba
|
Andreas Kohlbecker
|
$accepted_name .= '</div>';
|
727 |
|
|
RenderHints::popFromRenderStack();
|
728 |
|
|
}
|
729 |
|
|
|
730 |
|
|
// --- Render homotypic synonymy group
|
731 |
|
|
if (!empty($accepted_name)) {
|
732 |
|
|
$out .= $accepted_name;
|
733 |
|
|
}
|
734 |
|
|
|
735 |
|
|
// Render the homotypicSynonymyGroup including the type information.
|
736 |
|
|
$out .= theme(
|
737 |
|
|
'cdm_homotypicSynonymyGroup',
|
738 |
|
|
array(
|
739 |
|
|
'synonymList' => $synomymie->homotypicSynonymsByHomotypicGroup,
|
740 |
|
|
'accepted_taxon_name_uuid' => $taxon->name->uuid
|
741 |
|
|
)
|
742 |
|
|
);
|
743 |
|
|
|
744 |
|
|
|
745 |
|
|
// Render accepted taxon heterotypic synonymy groups.
|
746 |
|
|
if ($synomymie->heterotypicSynonymyGroups) {
|
747 |
|
|
foreach ($synomymie->heterotypicSynonymyGroups as $homotypicalGroup) {
|
748 |
|
|
$out .= theme('cdm_heterotypicSynonymyGroup', array('homotypicalGroup' => $homotypicalGroup));
|
749 |
|
|
}
|
750 |
|
|
}
|
751 |
|
|
// Render taxon relationships.
|
752 |
|
|
if (variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT)) {
|
753 |
|
|
$taxonRelationshipsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, $taxon->uuid);
|
754 |
|
|
$out .= cdm_taxonRelationships($taxonRelationshipsDTO, $taxon);
|
755 |
|
|
}
|
756 |
|
|
|
757 |
|
|
RenderHints::popFromRenderStack();
|
758 |
|
|
|
759 |
|
|
return markup_to_render_array($out);
|
760 |
|
|
}
|
761 |
|
|
|
762 |
|
|
|
763 |
f9a3d0f6
|
Andreas Kohlbecker
|
/**
|
764 |
|
|
* composes and returns an render array for the experts associated with the given taxon
|
765 |
|
|
*
|
766 |
8a1b451e
|
Andreas Kohlbecker
|
* @param object taxon
|
767 |
f9a3d0f6
|
Andreas Kohlbecker
|
*
|
768 |
|
|
* @return array
|
769 |
|
|
* A Drupal render array for a table with the experts
|
770 |
|
|
*
|
771 |
|
|
* @ingroup compose
|
772 |
|
|
*/
|
773 |
7663cd0b
|
Andreas Kohlbecker
|
function compose_cdm_taxon_page_experts($taxon){
|
774 |
|
|
|
775 |
|
|
$render_array = array();
|
776 |
|
|
if(!isset($taxon->uuid)){
|
777 |
|
|
return $render_array;
|
778 |
|
|
}
|
779 |
|
|
|
780 |
|
|
$current_classification_uuid = get_current_classification_uuid();
|
781 |
|
|
// TODO use cdm_ws_fetchall below but this failes! needs fix!
|
782 |
|
|
$taxon_node_agent_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
|
783 |
|
|
array(
|
784 |
|
|
$taxon->uuid,
|
785 |
|
|
$current_classification_uuid
|
786 |
|
|
)
|
787 |
|
|
);
|
788 |
|
|
|
789 |
|
|
$header = array(
|
790 |
|
|
array('data' => t('Expert')),
|
791 |
|
|
array('data' => t('Role'))
|
792 |
|
|
);
|
793 |
|
|
$rows = array();
|
794 |
|
|
|
795 |
|
|
|
796 |
|
|
foreach($taxon_node_agent_relations->records as $taxon_node_agent_relation){
|
797 |
|
|
|
798 |
d9763fd3
|
Andreas Kohlbecker
|
|
799 |
|
|
$expert_role_id = $taxon_node_agent_relation->agent->uuid . '-' . $taxon_node_agent_relation->type->uuid;
|
800 |
|
|
$expert_details_container_id = 'expert_details_' . $expert_role_id;
|
801 |
|
|
|
802 |
|
|
$agent_label_markup = cdm_dynabox(
|
803 |
|
|
'expert_' . $expert_role_id,
|
804 |
|
|
$taxon_node_agent_relation->agent->titleCache,
|
805 |
|
|
// specifying both ends of the relationship will return only one record in the pager
|
806 |
|
|
cdm_compose_url(CDM_WS_PORTAL_AGENT,
|
807 |
|
|
array($taxon_node_agent_relation->agent->uuid, 'taxonNodeAgentRelations'),
|
808 |
|
|
'taxon_uuid=' . $taxon->uuid . '&relType_uuid=' . $taxon_node_agent_relation->type->uuid),
|
809 |
|
|
'cdm_taxon_expert',
|
810 |
|
|
'Click for details',
|
811 |
|
|
array('div', 'div'),
|
812 |
|
|
array(), // attributes
|
813 |
cea412e7
|
Andreas Kohlbecker
|
'#' . $expert_details_container_id // $content_element_selector
|
814 |
d9763fd3
|
Andreas Kohlbecker
|
);
|
815 |
|
|
|
816 |
|
|
// Expert and Role
|
817 |
|
|
$rows[] = array(
|
818 |
|
|
'data' => array(
|
819 |
|
|
array(
|
820 |
|
|
'data' => $agent_label_markup,
|
821 |
|
|
'class' => array(html_class_attribute_ref($taxon_node_agent_relation->agent))
|
822 |
7663cd0b
|
Andreas Kohlbecker
|
),
|
823 |
d9763fd3
|
Andreas Kohlbecker
|
array(
|
824 |
|
|
'data' => $taxon_node_agent_relation->type->representation_L10n,
|
825 |
|
|
'class' => array(html_class_attribute_ref($taxon_node_agent_relation->type))
|
826 |
|
|
)
|
827 |
|
|
)
|
828 |
|
|
);
|
829 |
|
|
// Agent details
|
830 |
|
|
$rows[] = array(
|
831 |
|
|
'data' => array(
|
832 |
|
|
array(
|
833 |
|
|
'data' => '<!-- expert_details_container -->',
|
834 |
|
|
'id' => $expert_details_container_id,
|
835 |
|
|
'colspan' => 2
|
836 |
|
|
)
|
837 |
|
|
)
|
838 |
7663cd0b
|
Andreas Kohlbecker
|
);
|
839 |
d9763fd3
|
Andreas Kohlbecker
|
|
840 |
7663cd0b
|
Andreas Kohlbecker
|
}
|
841 |
|
|
|
842 |
|
|
|
843 |
|
|
$render_array['experts_table'] = array(
|
844 |
|
|
'#theme' => 'table',
|
845 |
|
|
'#header' => $header,
|
846 |
|
|
'#rows' => $rows,
|
847 |
|
|
);
|
848 |
|
|
|
849 |
|
|
|
850 |
|
|
return $render_array;
|
851 |
|
|
}
|
852 |
|
|
|
853 |
bf97c2e8
|
Andreas Kohlbecker
|
|
854 |
3f259ca3
|
Andreas Kohlbecker
|
/**
|
855 |
7663cd0b
|
Andreas Kohlbecker
|
* Manages the tabs to be hidden in the taxon page.
|
856 |
3f259ca3
|
Andreas Kohlbecker
|
*
|
857 |
|
|
* The tabs are identified by their last menu link path element:
|
858 |
|
|
* - description
|
859 |
|
|
* - synonymy
|
860 |
|
|
* - images
|
861 |
|
|
* - specimens
|
862 |
|
|
* - key
|
863 |
|
|
*
|
864 |
|
|
* Internally the tabs are stored in a static variable which is
|
865 |
|
|
* managed by drupal_static().
|
866 |
|
|
*
|
867 |
|
|
* @param string $add_tab
|
868 |
7663cd0b
|
Andreas Kohlbecker
|
* Optional parameter. The given string will be added to the array of tabs
|
869 |
3f259ca3
|
Andreas Kohlbecker
|
*
|
870 |
|
|
* @return
|
871 |
|
|
* The array of tabs
|
872 |
|
|
*/
|
873 |
48a6d7e8
|
Andreas Kohlbecker
|
function taxon_page_tabs_hidden_add($add_tab = NULL) {
|
874 |
|
|
$tabs = &drupal_static('taxon_page_tabs_hidden');
|
875 |
3f259ca3
|
Andreas Kohlbecker
|
|
876 |
0ae57522
|
Patric Plitzner
|
if(!isset($tabs)){
|
877 |
|
|
$tabs = array();
|
878 |
|
|
}
|
879 |
3f259ca3
|
Andreas Kohlbecker
|
|
880 |
0ae57522
|
Patric Plitzner
|
if (isset($add_tab) && !array_key_exists($add_tab, $tabs)) {
|
881 |
|
|
$tabs[] = $add_tab;
|
882 |
|
|
}
|
883 |
3f259ca3
|
Andreas Kohlbecker
|
|
884 |
0ae57522
|
Patric Plitzner
|
return $tabs;
|
885 |
3f259ca3
|
Andreas Kohlbecker
|
}
|
886 |
|
|
|
887 |
48a6d7e8
|
Andreas Kohlbecker
|
/**
|
888 |
|
|
* Manages the tabs to be hidden in the taxon page.
|
889 |
|
|
*
|
890 |
|
|
* The tabs names are identified by their last menu link path element:
|
891 |
|
|
* - description
|
892 |
|
|
* - synonymy
|
893 |
|
|
* - images
|
894 |
|
|
* - specimens
|
895 |
|
|
* - key
|
896 |
|
|
*
|
897 |
|
|
* Internally the tabs are stored in a static variable which is
|
898 |
|
|
* managed by drupal_static().
|
899 |
|
|
*
|
900 |
|
|
* @param string $tabname
|
901 |
|
|
* The name of the tab to check
|
902 |
|
|
*
|
903 |
|
|
* @return boolean
|
904 |
|
|
* True if the tab or section is to be hidden
|
905 |
|
|
*/
|
906 |
|
|
function taxon_page_tabs_hidden_check($tabname) {
|
907 |
|
|
|
908 |
|
|
$tabs = &drupal_static('taxon_page_tabs_hidden');
|
909 |
|
|
|
910 |
|
|
if(!isset($tabs)){
|
911 |
|
|
$tabs = array();
|
912 |
|
|
}
|
913 |
|
|
|
914 |
|
|
return array_search($tabname, $tabs) !== FALSE;
|
915 |
|
|
}
|
916 |
|
|
|
917 |
3f259ca3
|
Andreas Kohlbecker
|
/**
|
918 |
|
|
* Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
|
919 |
|
|
*
|
920 |
48a6d7e8
|
Andreas Kohlbecker
|
* - Removes the tabs to be hidden, @see taxon_page_tabs_hidden_add()
|
921 |
9438ad3a
|
Andreas Kohlbecker
|
* - Renames tabs according to the settings // TODO (this will replace the theme_cdm_taxonpage_tab() function !!!)
|
922 |
3f259ca3
|
Andreas Kohlbecker
|
*
|
923 |
|
|
* @param array $variables
|
924 |
|
|
* The variables array
|
925 |
|
|
*/
|
926 |
|
|
function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {
|
927 |
|
|
|
928 |
48a6d7e8
|
Andreas Kohlbecker
|
$hidden_tabs = taxon_page_tabs_hidden_add();
|
929 |
3f259ca3
|
Andreas Kohlbecker
|
|
930 |
868be375
|
Katja Luther
|
if (!variable_get(CDM_SEARCH_BLAST_ENABLED)) {
|
931 |
6f6f79f6
|
Katja Luther
|
if (is_array($variables['primary'])) {
|
932 |
|
|
foreach ($variables['primary'] as $key => &$element) {
|
933 |
|
|
if ($element['#link']['path'] == 'cdm_dataportal/search/blast') {
|
934 |
|
|
// remove the tab
|
935 |
|
|
unset($variables['primary'][$key]);
|
936 |
|
|
}
|
937 |
868be375
|
Katja Luther
|
|
938 |
6f6f79f6
|
Katja Luther
|
}
|
939 |
868be375
|
Katja Luther
|
}
|
940 |
|
|
}
|
941 |
0ae57522
|
Patric Plitzner
|
if (is_array($variables['primary'])) {
|
942 |
|
|
foreach ($variables['primary'] as $key => &$element) {
|
943 |
6f1a217c
|
Andreas Kohlbecker
|
|
944 |
0ae57522
|
Patric Plitzner
|
// 1. Remove the tabs to be hidden
|
945 |
|
|
foreach ($hidden_tabs as $tab) {
|
946 |
|
|
if ($element['#link']['path'] == 'cdm_dataportal/taxon/%/' . $tab) {
|
947 |
|
|
// remove the tab
|
948 |
|
|
unset($variables['primary'][$key]);
|
949 |
9438ad3a
|
Andreas Kohlbecker
|
}
|
950 |
0ae57522
|
Patric Plitzner
|
}
|
951 |
3f259ca3
|
Andreas Kohlbecker
|
}
|
952 |
0ae57522
|
Patric Plitzner
|
}
|
953 |
6f1a217c
|
Andreas Kohlbecker
|
}
|
954 |
|
|
|
955 |
|
|
|
956 |
|
|
|
957 |
|
|
/**
|
958 |
|
|
* Implements the hook_preprocess_HOOK() for theme_menu_local_task()
|
959 |
|
|
*
|
960 |
|
|
*
|
961 |
|
|
* @param array $variables
|
962 |
|
|
* An associative array containing:
|
963 |
|
|
* - element: A render element containing:
|
964 |
|
|
* #link: A menu link array with 'title', 'href', and 'localized_options' keys.
|
965 |
|
|
* #active: A boolean indicating whether the local task is active.
|
966 |
|
|
*
|
967 |
|
|
*/
|
968 |
|
|
function cdm_dataportal_preprocess_menu_local_task(&$variables) {
|
969 |
|
|
|
970 |
0ae57522
|
Patric Plitzner
|
$link = $variables['element']['#link'];
|
971 |
|
|
if (preg_match('/cdm_dataportal\/.*\/refresh$/', $link['href'])) {
|
972 |
|
|
$link['title'] = '<img class="refresh" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/view-refresh.png' . '" alt="' . check_plain($link['title']) . '" title="' . check_plain($link['title']) . '"/>';
|
973 |
|
|
$link['localized_options']['html'] = TRUE;
|
974 |
6f1a217c
|
Andreas Kohlbecker
|
|
975 |
0ae57522
|
Patric Plitzner
|
$variables['element']['#link'] = $link;
|
976 |
|
|
}
|
977 |
f19f47fa
|
Andreas Kohlbecker
|
}
|
978 |
f9a3d0f6
|
Andreas Kohlbecker
|
|
979 |
|
|
/* =================== block composition ===================== */
|
980 |
|
|
|
981 |
|
|
/**
|
982 |
23ad16a1
|
Andreas Kohlbecker
|
* Composes and returns an render array for the classification breadcrumbs of the given taxon.
|
983 |
f9a3d0f6
|
Andreas Kohlbecker
|
*
|
984 |
|
|
* @param taxon
|
985 |
|
|
*
|
986 |
|
|
* @return array
|
987 |
|
|
* A Drupal render array for a table with the experts
|
988 |
|
|
*
|
989 |
|
|
* @ingroup compose
|
990 |
|
|
*/
|
991 |
|
|
function compose_classification_breadcrumbs($taxon_uuid) {
|
992 |
|
|
|
993 |
b0adfd32
|
Andreas Kohlbecker
|
_add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');
|
994 |
d0d23caa
|
Andreas Kohlbecker
|
|
995 |
f9a3d0f6
|
Andreas Kohlbecker
|
$render_array = array();
|
996 |
|
|
|
997 |
|
|
$render_array['#theme'] = 'item_list';
|
998 |
|
|
$render_array['#type'] = 'ul';
|
999 |
|
|
$render_array['#attributes'] = array(
|
1000 |
|
|
'id' => 'classification-breadcrumbs',
|
1001 |
|
|
'class' => 'breadcrumbs inline',
|
1002 |
|
|
);
|
1003 |
|
|
|
1004 |
|
|
$items = array();
|
1005 |
|
|
|
1006 |
38da4e54
|
Andreas Kohlbecker
|
$parent_taxon_nodes = null;
|
1007 |
|
|
if($taxon_uuid){
|
1008 |
|
|
$parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
|
1009 |
|
|
}
|
1010 |
f9a3d0f6
|
Andreas Kohlbecker
|
|
1011 |
38da4e54
|
Andreas Kohlbecker
|
$classifications = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
|
1012 |
|
|
// find current classification in list
|
1013 |
|
|
$classification = null;
|
1014 |
|
|
$current_classification_uuid = get_current_classification_uuid();
|
1015 |
|
|
foreach ($classifications as $classification){
|
1016 |
|
|
if($classification->uuid == $current_classification_uuid){
|
1017 |
|
|
break;
|
1018 |
b0adfd32
|
Andreas Kohlbecker
|
}
|
1019 |
38da4e54
|
Andreas Kohlbecker
|
}
|
1020 |
b0adfd32
|
Andreas Kohlbecker
|
|
1021 |
38da4e54
|
Andreas Kohlbecker
|
$node_name = '';
|
1022 |
|
|
if(count($classifications) > 1 ){
|
1023 |
|
|
// need to add the current classification as first label
|
1024 |
0af3ce28
|
Andreas Kohlbecker
|
|
1025 |
|
|
$label = $classification->titleCache;
|
1026 |
|
|
if(strlen($label) > 20){
|
1027 |
|
|
$label = substr($label, 0, strpos($label, ' ', 15)) . '...';
|
1028 |
|
|
}
|
1029 |
|
|
$node_name = font_awesome_icon_markup('fa-th-list') . ' ' . l($label, '#', array(
|
1030 |
|
|
'attributes' => array(
|
1031 |
|
|
'class' => 'taxonomic-children-button classification-chooser',
|
1032 |
|
|
'data-destination-uri' => drupal_get_destination(),
|
1033 |
|
|
'data-cdm-align-with' => array('prev')
|
1034 |
|
|
),
|
1035 |
|
|
'html' => true
|
1036 |
|
|
));
|
1037 |
f9a3d0f6
|
Andreas Kohlbecker
|
}
|
1038 |
b0adfd32
|
Andreas Kohlbecker
|
|
1039 |
38da4e54
|
Andreas Kohlbecker
|
$rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
|
1040 |
0af3ce28
|
Andreas Kohlbecker
|
|
1041 |
|
|
$rank_separator = '<span> '
|
1042 |
38da4e54
|
Andreas Kohlbecker
|
. font_awesome_icon_markup('fa-chevron-right')
|
1043 |
|
|
. ' </span>';
|
1044 |
0af3ce28
|
Andreas Kohlbecker
|
$more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');
|
1045 |
69fb3dbb
|
Andreas Kohlbecker
|
$more_children_label = '...';
|
1046 |
38da4e54
|
Andreas Kohlbecker
|
|
1047 |
0af3ce28
|
Andreas Kohlbecker
|
$items[] = $node_name;
|
1048 |
38da4e54
|
Andreas Kohlbecker
|
|
1049 |
0af3ce28
|
Andreas Kohlbecker
|
$more_children_for = null;
|
1050 |
e3235962
|
Andreas Kohlbecker
|
if($parent_taxon_nodes){
|
1051 |
0af3ce28
|
Andreas Kohlbecker
|
foreach ($parent_taxon_nodes as $node) {
|
1052 |
38da4e54
|
Andreas Kohlbecker
|
|
1053 |
|
|
$is_first_item = count($items) == 0;
|
1054 |
0af3ce28
|
Andreas Kohlbecker
|
$is_last_item = count($items) == count($parent_taxon_nodes);
|
1055 |
38da4e54
|
Andreas Kohlbecker
|
$node_name = cdm_dataportal_shortname_of($node);
|
1056 |
|
|
$path = path_to_taxon($node->taxonUuid);
|
1057 |
|
|
|
1058 |
0af3ce28
|
Andreas Kohlbecker
|
if($node->taxonomicChildrenCount > 0) {
|
1059 |
|
|
$more_children_for = $node->taxonUuid;
|
1060 |
|
|
} else {
|
1061 |
|
|
$more_children_for = null;
|
1062 |
38da4e54
|
Andreas Kohlbecker
|
}
|
1063 |
|
|
|
1064 |
0af3ce28
|
Andreas Kohlbecker
|
// 'fa-sitemap'
|
1065 |
|
|
|
1066 |
38da4e54
|
Andreas Kohlbecker
|
$items[] =
|
1067 |
0af3ce28
|
Andreas Kohlbecker
|
($is_first_item ? '' : ' ')
|
1068 |
|
|
. $rank_separator
|
1069 |
|
|
. l(
|
1070 |
4b3be949
|
Andreas Kohlbecker
|
'<span class="' . html_class_attribute_ref($node) . '">' . $node_name . '</span>',
|
1071 |
0af3ce28
|
Andreas Kohlbecker
|
$path,
|
1072 |
|
|
array(
|
1073 |
|
|
'attributes' => array(
|
1074 |
|
|
'class' => array('taxonomic-children-button'),
|
1075 |
|
|
'data-cdm-taxon-uuid' => array($node->taxonUuid),
|
1076 |
|
|
'data-cdm-classification-mode' => array('siblings'),
|
1077 |
|
|
'data-cdm-align-with' => array('prev')
|
1078 |
4b3be949
|
Andreas Kohlbecker
|
),
|
1079 |
|
|
'html' => true
|
1080 |
0af3ce28
|
Andreas Kohlbecker
|
)
|
1081 |
|
|
);
|
1082 |
|
|
}
|
1083 |
38da4e54
|
Andreas Kohlbecker
|
}
|
1084 |
0af3ce28
|
Andreas Kohlbecker
|
|
1085 |
|
|
// add more button to the end
|
1086 |
|
|
if(!$parent_taxon_nodes) {
|
1087 |
|
|
// not taxon focused yet, adding button to make the root nodes available
|
1088 |
69fb3dbb
|
Andreas Kohlbecker
|
$items[] = '<span>'
|
1089 |
|
|
. $more_children_icon . ' ' .
|
1090 |
|
|
'<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
|
1091 |
53c705d4
|
Andreas Kohlbecker
|
. '" data-rank-limit-uuid="' . $rank_limit_uuid . '" data-cdm-align-with="prev"> ' . $more_children_label . '<span>'
|
1092 |
69fb3dbb
|
Andreas Kohlbecker
|
. '</span>';
|
1093 |
0af3ce28
|
Andreas Kohlbecker
|
} else if($more_children_for){
|
1094 |
|
|
// last parent item has child taxon nodes
|
1095 |
69fb3dbb
|
Andreas Kohlbecker
|
$items[] = ' <span>'
|
1096 |
|
|
. $more_children_icon . ' ' .
|
1097 |
|
|
'<span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
|
1098 |
53c705d4
|
Andreas Kohlbecker
|
. '" data-cdm-classification-mode="children" data-cdm-align-with="prev"> ' . $more_children_label . '</span>'
|
1099 |
69fb3dbb
|
Andreas Kohlbecker
|
. '</span>';
|
1100 |
0af3ce28
|
Andreas Kohlbecker
|
|
1101 |
e3235962
|
Andreas Kohlbecker
|
}
|
1102 |
b0adfd32
|
Andreas Kohlbecker
|
|
1103 |
30845bda
|
Andreas Kohlbecker
|
$render_array['#items'] = $items;
|
1104 |
0af3ce28
|
Andreas Kohlbecker
|
|
1105 |
30845bda
|
Andreas Kohlbecker
|
return $render_array;
|
1106 |
|
|
}
|
1107 |
0af3ce28
|
Andreas Kohlbecker
|
|
1108 |
69fb3dbb
|
Andreas Kohlbecker
|
|
1109 |
30845bda
|
Andreas Kohlbecker
|
/**
|
1110 |
|
|
* @param $specimen_uuid
|
1111 |
|
|
* @return array
|
1112 |
|
|
* The drupal render array for the page
|
1113 |
|
|
*
|
1114 |
|
|
* @ingroup compose
|
1115 |
|
|
*/
|
1116 |
e89c1115
|
Katja Luther
|
function compose_cdm_specimen_page($specimen_uuid)
|
1117 |
30845bda
|
Andreas Kohlbecker
|
{
|
1118 |
|
|
drupal_set_title("Specimen Details");
|
1119 |
|
|
RenderHints::pushToRenderStack('specimen_page');
|
1120 |
f9a3d0f6
|
Andreas Kohlbecker
|
|
1121 |
78a42a9b
|
Katja Luther
|
$specimen_table = array(
|
1122 |
|
|
'#theme' => 'table',
|
1123 |
|
|
'#weight' => 2,
|
1124 |
2527a83c
|
Andreas Kohlbecker
|
// prefix attributes and rows with '#' to let it pass to the theme function,
|
1125 |
78a42a9b
|
Katja Luther
|
// otherwise it is handled as child render array
|
1126 |
489f7610
|
Katja Luther
|
|
1127 |
|
|
'#attributes' => array('class' => 'specimens'),
|
1128 |
78a42a9b
|
Katja Luther
|
'#rows' => array(),
|
1129 |
93fb962c
|
Katja Luther
|
'#prefix' => '<div id="specimens">',
|
1130 |
|
|
'#suffix' => '</div>',
|
1131 |
|
|
|
1132 |
489f7610
|
Katja Luther
|
|
1133 |
78a42a9b
|
Katja Luther
|
);
|
1134 |
|
|
$specimen = compose_cdm_specimen_or_observation($specimen_uuid, true);
|
1135 |
44f44469
|
Andreas Kohlbecker
|
/*
|
1136 |
961319fe
|
Andreas Kohlbecker
|
$render_array = array(
|
1137 |
78a42a9b
|
Katja Luther
|
'#theme' => 'item_list',
|
1138 |
|
|
'#items' => array($specimen),
|
1139 |
|
|
'#type' => 'ul');
|
1140 |
961319fe
|
Andreas Kohlbecker
|
$output = drupal_render($render_array);
|
1141 |
44f44469
|
Andreas Kohlbecker
|
*/
|
1142 |
78a42a9b
|
Katja Luther
|
$specimen_table['#rows'][] = array(
|
1143 |
|
|
// An array of table rows. Every row is an array of cells, or an associative array
|
1144 |
961319fe
|
Andreas Kohlbecker
|
'data' => $specimen,
|
1145 |
78a42a9b
|
Katja Luther
|
'class' => array(
|
1146 |
|
|
'descriptionElement',
|
1147 |
|
|
'descriptionElement_IndividualsAssociation'
|
1148 |
|
|
),
|
1149 |
|
|
);
|
1150 |
e89c1115
|
Katja Luther
|
|
1151 |
|
|
|
1152 |
78a42a9b
|
Katja Luther
|
// $detail_html = compose_cdm_specimen_or_observation($specimen_uuid, true);
|
1153 |
93fb962c
|
Katja Luther
|
// $render_array['markup'] = array(
|
1154 |
|
|
// '#prefix' => '<div id="specimens" class="page">',
|
1155 |
|
|
// 'content' => $specimen_table,
|
1156 |
|
|
// '#suffix' => '</div>',
|
1157 |
|
|
// );
|
1158 |
2527a83c
|
Andreas Kohlbecker
|
$render_array['specimen_table'] = $specimen_table;
|
1159 |
e89c1115
|
Katja Luther
|
|
1160 |
30845bda
|
Andreas Kohlbecker
|
RenderHints::popFromRenderStack();
|
1161 |
961319fe
|
Andreas Kohlbecker
|
return $specimen; // $render_array;
|
1162 |
30845bda
|
Andreas Kohlbecker
|
}
|
1163 |
f9a3d0f6
|
Andreas Kohlbecker
|
|
1164 |
30845bda
|
Andreas Kohlbecker
|
/**
|
1165 |
|
|
* @param $named_area_uuid
|
1166 |
|
|
* @return array
|
1167 |
|
|
* The drupal render array for the page
|
1168 |
|
|
*
|
1169 |
|
|
* @ingroup compose
|
1170 |
|
|
*/
|
1171 |
|
|
function compose_cdm_named_area_page($named_area_uuid)
|
1172 |
|
|
{
|
1173 |
|
|
|
1174 |
|
|
$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid));
|
1175 |
|
|
|
1176 |
|
|
$render_array = array();
|
1177 |
|
|
RenderHints::pushToRenderStack('named_area_page');
|
1178 |
|
|
|
1179 |
|
|
$groups = array();
|
1180 |
|
|
@_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);
|
1181 |
|
|
@_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);
|
1182 |
|
|
if(isset($named_area->level)) {
|
1183 |
|
|
@_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);
|
1184 |
|
|
}
|
1185 |
|
|
|
1186 |
|
|
$name_area_details_elements = array(
|
1187 |
|
|
// '#title' => $title,
|
1188 |
|
|
'#theme' => 'description_list',
|
1189 |
|
|
'#groups' => $groups,
|
1190 |
|
|
'#attributes' => array('class' => html_class_attribute_ref($named_area)),
|
1191 |
|
|
);
|
1192 |
|
|
|
1193 |
|
|
$render_array[] = $name_area_details_elements;
|
1194 |
|
|
|
1195 |
|
|
RenderHints::popFromRenderStack();
|
1196 |
|
|
return $render_array;
|
1197 |
f9a3d0f6
|
Andreas Kohlbecker
|
}
|
1198 |
4feeabc7
|
Andreas Kohlbecker
|
|
1199 |
57dabcba
|
Andreas Kohlbecker
|
|
1200 |
|
|
/**
|
1201 |
|
|
* Returns a drupal render array for a single reference page.
|
1202 |
|
|
*
|
1203 |
|
|
* Composes a page with all data on a single reference.
|
1204 |
|
|
*
|
1205 |
|
|
* @param string $uuid
|
1206 |
|
|
* An uuid for a cdm reference.
|
1207 |
|
|
*
|
1208 |
|
|
* @return array
|
1209 |
|
|
* A drupal render array
|
1210 |
|
|
*
|
1211 |
|
|
* @throws Exception
|
1212 |
|
|
*
|
1213 |
|
|
* @ingroup compose
|
1214 |
|
|
*/
|
1215 |
|
|
function compose_cdm_reference_page($uuid) {
|
1216 |
|
|
|
1217 |
|
|
$pathelement = "reference_page";
|
1218 |
|
|
RenderHints::pushToRenderStack($pathelement);
|
1219 |
|
|
$reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
|
1220 |
4d9660ef
|
Andreas Kohlbecker
|
if (!$reference) {
|
1221 |
|
|
drupal_set_title(t('Reference does not exist'), PASS_THROUGH);
|
1222 |
de017852
|
Andreas Kohlbecker
|
return "";
|
1223 |
4d9660ef
|
Andreas Kohlbecker
|
}
|
1224 |
57dabcba
|
Andreas Kohlbecker
|
if (isset($reference->titleCache)) {
|
1225 |
|
|
drupal_set_title($reference->titleCache, PASS_THROUGH);
|
1226 |
|
|
}
|
1227 |
|
|
|
1228 |
|
|
$field_order = array(
|
1229 |
|
|
"title",
|
1230 |
|
|
"abbrevTitle",
|
1231 |
|
|
// "titleCache" abbrevTitleCache
|
1232 |
|
|
// "citation",
|
1233 |
|
|
"authorship",
|
1234 |
|
|
"editor",
|
1235 |
|
|
"publisher",
|
1236 |
|
|
"placePublished",
|
1237 |
|
|
"datePublished",
|
1238 |
|
|
"year",
|
1239 |
|
|
"edition",// Class Book.
|
1240 |
|
|
"volume",// Class Article.
|
1241 |
|
|
"seriesPart",
|
1242 |
|
|
"inReference",
|
1243 |
|
|
"nomRefBase", // Class BookSection, Book, Article.
|
1244 |
|
|
"pages",// Class Article.
|
1245 |
|
|
"series",// Class Article, PrintSeries.
|
1246 |
|
|
"school",// Class Thesis.
|
1247 |
|
|
"institution",// Class Report.
|
1248 |
|
|
"organization",// Class Proceedings.
|
1249 |
|
|
"nextVersion",
|
1250 |
|
|
"previousVersion",
|
1251 |
|
|
"isbn",// Class Book.
|
1252 |
|
|
"issn",// Class Journal.
|
1253 |
|
|
"doi",
|
1254 |
|
|
"uri"
|
1255 |
|
|
);
|
1256 |
|
|
|
1257 |
|
|
$table_rows = array();
|
1258 |
|
|
|
1259 |
|
|
if (!isset($reference->authorship)) {
|
1260 |
|
|
$authorship = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid);
|
1261 |
|
|
$reference->authorship = isset($authorship->titleCache) ? $authorship->titleCache : '';
|
1262 |
|
|
}
|
1263 |
|
|
|
1264 |
|
|
if (!isset($reference->inReference)) {
|
1265 |
|
|
$reference->inReference = cdm_ws_get(CDM_WS_REFERENCE, array(
|
1266 |
|
|
$reference->uuid,
|
1267 |
|
|
"inReference",
|
1268 |
|
|
));
|
1269 |
|
|
}
|
1270 |
|
|
|
1271 |
|
|
foreach ($field_order as $fieldname) {
|
1272 |
|
|
|
1273 |
|
|
if (isset($reference->$fieldname)) {
|
1274 |
|
|
|
1275 |
|
|
if ($fieldname == "datePublished") {
|
1276 |
|
|
$period = $reference->$fieldname;
|
1277 |
|
|
$datePublished = timePeriodToString($period);
|
1278 |
|
|
if (isset($datePublished) && $datePublished != '') {
|
1279 |
|
|
$table_rows[] = array(
|
1280 |
|
|
t("Date published"),
|
1281 |
|
|
$datePublished,
|
1282 |
|
|
);
|
1283 |
|
|
}
|
1284 |
|
|
}
|
1285 |
|
|
elseif ($fieldname == "doi" && is_object($reference->doi)) {
|
1286 |
|
|
$table_rows[] = array(
|
1287 |
|
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
1288 |
|
|
cdm_doi($reference->doi, false)
|
1289 |
|
|
);
|
1290 |
|
|
}
|
1291 |
|
|
elseif ($fieldname == "uri" && isset($reference->uri) && $reference->uri) {
|
1292 |
|
|
$table_rows[] = array(
|
1293 |
|
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
1294 |
|
|
cdm_external_uri($reference->uri, false)
|
1295 |
|
|
);
|
1296 |
|
|
}
|
1297 |
|
|
elseif (is_object($reference->$fieldname)) {
|
1298 |
|
|
if ($fieldname == "authorship") {
|
1299 |
|
|
$dump = $reference->$fieldname;
|
1300 |
|
|
$teammembers = "teamMembers";
|
1301 |
|
|
$team = $dump->$teammembers;
|
1302 |
|
|
$nameArray = array();
|
1303 |
|
|
|
1304 |
|
|
foreach ($team as $member) {
|
1305 |
|
|
if (strlen($member->lastname) > 0) {
|
1306 |
|
|
$nname = $member->lastname;
|
1307 |
|
|
$name = $nname;
|
1308 |
|
|
if (strlen($member->firstname) > 0) {
|
1309 |
|
|
$vname = $member->firstname;
|
1310 |
|
|
$name = $vname . " " . $nname;
|
1311 |
|
|
}
|
1312 |
|
|
$nameArray[] = $name;
|
1313 |
|
|
}
|
1314 |
|
|
else {
|
1315 |
|
|
if (strlen($member->titleCache) > 0) {
|
1316 |
|
|
$nameArray[] = $member->titleCache;
|
1317 |
|
|
}
|
1318 |
|
|
}
|
1319 |
|
|
}
|
1320 |
|
|
$value = join($nameArray, ", ");
|
1321 |
|
|
}
|
1322 |
|
|
elseif ($fieldname == "inReference") {
|
1323 |
|
|
$type = $reference->$fieldname->type;
|
1324 |
|
|
$value = l($reference->$fieldname->titleCache, path_to_reference($reference->$fieldname->uuid));
|
1325 |
|
|
switch ($type) {
|
1326 |
|
|
case "Book":
|
1327 |
|
|
$fieldname = "in book";
|
1328 |
|
|
break;
|
1329 |
|
|
case "Journal":
|
1330 |
|
|
$fieldname = "in journal";
|
1331 |
|
|
break;
|
1332 |
|
|
case "Proceedings":
|
1333 |
|
|
$fieldname = "in proceedings";
|
1334 |
|
|
break;
|
1335 |
|
|
}
|
1336 |
|
|
}
|
1337 |
|
|
else {
|
1338 |
|
|
$value = $reference->$fieldname->titleCache;
|
1339 |
|
|
}
|
1340 |
|
|
|
1341 |
|
|
|
1342 |
|
|
if (isset($value) && $value != '') {
|
1343 |
|
|
$table_rows[] = array(
|
1344 |
|
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
1345 |
|
|
$value,
|
1346 |
|
|
);
|
1347 |
|
|
}
|
1348 |
|
|
|
1349 |
|
|
}
|
1350 |
|
|
else {
|
1351 |
|
|
if (isset($reference->$fieldname) && $reference->$fieldname != '') {
|
1352 |
|
|
$table_rows[] = array(
|
1353 |
|
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
1354 |
|
|
$reference->$fieldname,
|
1355 |
|
|
);
|
1356 |
|
|
}
|
1357 |
|
|
}
|
1358 |
|
|
}
|
1359 |
|
|
}
|
1360 |
|
|
|
1361 |
|
|
$out = theme_table(array(
|
1362 |
|
|
'header' => array(),
|
1363 |
|
|
'rows' => $table_rows,
|
1364 |
|
|
'attributes' => array(
|
1365 |
|
|
'class' => html_class_attribute_ref($reference)
|
1366 |
|
|
),
|
1367 |
|
|
'caption' => NULL,
|
1368 |
|
|
'colgroups' => NULL,
|
1369 |
|
|
'sticky' => NULL,
|
1370 |
|
|
'empty' => NULL,
|
1371 |
|
|
));
|
1372 |
|
|
|
1373 |
|
|
if(isset($reference->referenceAbstract)){
|
1374 |
|
|
$out .= '<h2 class="block-title">Abstract</h2><div class="abstract">' . $reference->referenceAbstract . '</div>';
|
1375 |
|
|
}
|
1376 |
|
|
|
1377 |
|
|
|
1378 |
|
|
// Annotations below the table
|
1379 |
|
|
$annotations = cdm_fetch_visible_annotations($reference);
|
1380 |
e9cc637a
|
Andreas Kohlbecker
|
$out .= cdm_annotations($annotations);
|
1381 |
57dabcba
|
Andreas Kohlbecker
|
|
1382 |
|
|
$registration_working_set = cdm_ws_get("registrationWorkingSetDTO", array($uuid));
|
1383 |
|
|
if($registration_working_set && count($registration_working_set->registrationDTOs) > 0){
|
1384 |
|
|
$out .= "<h3>Nomenclatural acts:</h3><div class=\"cdm-item-list registration-item-list\">";
|
1385 |
|
|
foreach($registration_working_set->registrationDTOs as $registration_dto){
|
1386 |
|
|
if($registration_dto->status == "PUBLISHED"){
|
1387 |
|
|
$registration_render_a = compose_registration_dto_compact($registration_dto, 'citation');
|
1388 |
|
|
$registration_render_a["#prefix"] = "<div class=\"item item-registration\">";
|
1389 |
|
|
$registration_render_a["#suffix"] = "</div>";
|
1390 |
|
|
$out .= drupal_render($registration_render_a);
|
1391 |
|
|
}
|
1392 |
|
|
}
|
1393 |
|
|
$out .= "</div>";
|
1394 |
|
|
}
|
1395 |
|
|
|
1396 |
|
|
RenderHints::popFromRenderStack();
|
1397 |
|
|
|
1398 |
|
|
return markup_to_render_array($out);
|
1399 |
|
|
}
|
1400 |
|
|
|
1401 |
4feeabc7
|
Andreas Kohlbecker
|
/**
|
1402 |
|
|
* Provides the the label string for taxon page tabs.
|
1403 |
|
|
*
|
1404 |
|
|
* The $tabname as passed to the method will be returned if no override
|
1405 |
|
|
* label is configured in the settings.
|
1406 |
|
|
*/
|
1407 |
|
|
function cdm_taxonpage_tab_label($tabname) {
|
1408 |
|
|
static $taxon_tabs_labels = null;
|
1409 |
|
|
if($taxon_tabs_labels == null){
|
1410 |
|
|
$taxon_tabs_labels = get_array_variable_merged(CDM_TAXONPAGE_TAB_LABELS, CDM_TAXONPAGE_TAB_LABELS_DEFAULT);
|
1411 |
|
|
}
|
1412 |
|
|
$tabname_key = strtolower($tabname);
|
1413 |
|
|
if(isset($taxon_tabs_labels[$tabname_key]) && $taxon_tabs_labels[$tabname_key]){
|
1414 |
|
|
return $taxon_tabs_labels[$tabname_key];
|
1415 |
|
|
}
|
1416 |
|
|
return $tabname;
|
1417 |
|
|
}
|