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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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* Creates 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 $taxon
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* A cdm Taxon object
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* @return
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* A render array suitable for drupal_render()
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*
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*/
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function cdm_dataportal_taxon_page_specimens($taxon) {
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$render_array = array();
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RenderHints::pushToRenderStack('taxon_page_specimens');
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$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(',', $relationship_choice['direct']),
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);
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if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
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$by_associatedtaxon_query_parameters = array_merge($by_associatedtaxon_query_parameters, $_REQUEST['pager']);
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}
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$by_associatedtaxon_query = http_build_query($by_associatedtaxon_query_parameters);
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$ws_string = 'specimensOrObservation';
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if (variable_get('cdm_dataportal_specimen_derivate_tree')){
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$ws_string .= "DTOs";
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}else{
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$ws_string .= "s";
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}
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$specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, $ws_string));
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if(!variable_get('cdm_dataportal_specimen_derivate_tree')) {
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$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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}
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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 = $pager->records;
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// }
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// order occurrences by date but types should be on top of the list
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$type_specimens = array();
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$other_occurrences = array();
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foreach ($specimensOrObservations as $occurrence) {
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$typeDesignationsPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $occurrence->uuid);
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if (isset($typeDesignationsPager->count) && $typeDesignationsPager->count > 0) {
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$type_specimens[] = $occurrence;
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} else {
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$other_occurrences[] = $occurrence;
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}
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}
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$specimensOrObservations = array_merge($type_specimens, $other_occurrences);
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// Collect media (fieldObjectMedia, derivedUnitMedia) and add as a custom field
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if (!variable_get('cdm_dataportal_specimen_derivate_tree')) {
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foreach ($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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$occurrence->uuid,
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'derivedUnitMedia',
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));
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}
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}
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// --- get map service HTTP query parameters
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if (count($specimensOrObservations) > 0) {
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$occurrence_queryDto = cdm_ws_get(CDM_WS_GEOSERVICE_OCCURRENCEMAP, $taxon->uuid, $by_associatedtaxon_query);
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$map_visibility = variable_get(SPECIMEN_MAP_VISIBILITY, SPECIMEN_MAP_VISIBILITY_DEFAULT);
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if ($map_visibility == 'always' ||
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variable_get(SPECIMEN_MAP_VISIBILITY, SPECIMEN_MAP_VISIBILITY_DEFAULT) == 'automatic' &&
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(isset($occurrence_queryDto->fieldUnitPoints[0]) || isset($occurrence_queryDto->derivedUnitPoints[0]))) {
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$occurrence_query = $occurrence_queryDto->occurrenceQuery;
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$legend_format_query = null;
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$distribution_query = NULL;
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$render_array['map'] = compose_map('specimens', $occurrence_query, $distribution_query, $legend_format_query, array());
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}
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}
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// -------------------------------------------------------
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if(variable_get('cdm_dataportal_compressed_specimen_derivate_table')){
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//COMPRESSED SPECIMEN DERIVATE TABLE
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$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_specimen_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' => $_REQUEST
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)),
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10 // weight
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);
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}
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else if(variable_get('cdm_dataportal_specimen_derivate_tree')){
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$specimen_table = array(
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'#theme' => 'table',
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'#weight' => 2,
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// prefix attributes and rows with '#' to let it pass toF the theme function,
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// otherwise it is handled as child render array
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'#attributes' => array('class' => 'specimens'),
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'#rows' => array(),
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);
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$specimen_array = compose_specimen_array($specimensOrObservations);
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foreach($specimen_array as $value){
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$renderArray = array(
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'#theme' => 'item_list',
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'#items' => array($value),
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'#type' => 'ul');
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$output = drupal_render($renderArray);
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// $specimen_table['#rows'][] = array(
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// // An array of table rows. collabsible row
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// 'data' => "",
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// 'class' => array('expand_column')
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// );
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$specimen_table['#rows'][] = array(
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// An array of table rows. Every row is an array of cells, or an associative array
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'data' => array($output),
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'class' => array(
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'descriptionElement',
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'descriptionElement_IndividualsAssociation'
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),
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);
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}
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$render_array['specimen_list'] = $specimen_table;
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}
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else{
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//BOTTOM-UP-SPECIMEN-TABLE
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// --- generate the specimen list as table
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$specimen_table = array(
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'#theme' => 'table',
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'#weight' => 2,
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// prefix attributes and rows with '#' to let it pass toF the theme function,
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// otherwise it is handled as child render array
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'#attributes' => array('class' => 'specimens'),
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'#rows' => array(),
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);
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if ($specimensOrObservations) {
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foreach ($specimensOrObservations as $specimenOrObservation) {
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$mediaList = array();
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if (is_array($specimenOrObservation->_fieldObjectMedia)) {
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$mediaList = array_merge($mediaList, $specimenOrObservation->_fieldObjectMedia);
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}
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if (is_array($specimenOrObservation->_derivedUnitMedia)) {
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$mediaList = array_merge($mediaList, $specimenOrObservation->_derivedUnitMedia);
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}
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// typelabel will contain the typeStatus
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$type_label = '';
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$typeDesignationPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $specimenOrObservation->uuid);
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if (isset($typeDesignationPager) and isset($typeDesignationPager->records)) {
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$type_status = array();
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foreach ($typeDesignationPager->records as $typeDesignation) {
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if (isset($typeDesignation->typeStatus->representation_L10n)){
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$type_status[] = $typeDesignation->typeStatus->representation_L10n;
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}
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}
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$type_label = implode(', ', $type_status);
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if($type_label){
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$type_label .= ': ' ;
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}
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}
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// --- Specimen entry as dynamic label:
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// -> Dynabox for the specimenOrObservation
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$gallery_name = $specimenOrObservation->uuid;
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$derived_unit_ws_request = cdm_compose_url(CDM_WS_OCCURRENCE, array( $specimenOrObservation->uuid));
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// --- Render associated media.
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$gallery_html = '';
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if (count($mediaList) > 0) {
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$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
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$captionElements = array(
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'#uri' => t('open media'),
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);
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$gallery_html = compose_cdm_media_gallerie(array(
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'mediaList' => $mediaList,
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'galleryName' => $gallery_name,
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'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
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'cols' => $gallery_settings['cdm_dataportal_media_cols'],
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'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
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'captionElements' => $captionElements,
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'mediaLinkType' => 'LIGHTBOX',
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'alternativeMediaUri' => NULL,
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'galleryLinkUri' => NULL,
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));
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}
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//here we should use the data we already have
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$label_html = cdm_dynabox(
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$specimenOrObservation->uuid,
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$type_label . $specimenOrObservation->titleCache,
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$derived_unit_ws_request,
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'cdm_specimen_or_observation',
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'Click for details',
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array('div', 'div'),
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array(),
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null, // $content_element_selector
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'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').hide(); }', // open_callback
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'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').show(); }' // close_callback
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);
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// --- Render associated media.
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$gallery_html = '';
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if (count($mediaList) > 0) {
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$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
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$captionElements = array(
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'#uri' => t('open media'),
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);
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$gallery_html = compose_cdm_media_gallerie(array(
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'mediaList' => $mediaList,
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'galleryName' => $gallery_name,
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'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
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'cols' => $gallery_settings['cdm_dataportal_media_cols'],
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'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
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'captionElements' => $captionElements,
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'mediaLinkType' => 'LIGHTBOX',
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'alternativeMediaUri' => NULL,
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'galleryLinkUri' => NULL,
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));
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}
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299
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300
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$specimen_table['#rows'][] = array(
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301
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// An array of table rows. Every row is an array of cells, or an associative array
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'data' => array(
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303
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// Each cell can be either a string or an associative array
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$label_html . $gallery_html
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),
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'class' => array(
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'descriptionElement',
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'descriptionElement_IndividualsAssociation'
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),
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);
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311
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}
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312
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}
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313
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314
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$render_array['specimen_list'] = $specimen_table;
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315
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$render_array['pager'] = markup_to_render_array(
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theme('cdm_pager', array(
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317
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'pager' => $pager,
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318
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'path' => $_REQUEST['q'],
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319
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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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324
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RenderHints::popFromRenderStack();
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return $render_array;
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327
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}
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328
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329
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/**
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330
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* Creates the drupal render array for the table showing all derivated which are
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331
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* derive from a common gathering event.
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332
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*
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333
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* @param $field_unit_uuids array
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334
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* An array of uuids for cdm FieldUnit entities.
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335
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*
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336
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* @return array
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337
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* A drupal render array for a table
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338
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*
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339
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* @ingroup compose
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340
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*/
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341
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function compose_specimen_table($field_unit_uuids)
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342
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{
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343
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// get icon images
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344
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$expand_icon = font_awesome_icon_markup(
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345
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'fa-plus-square-o',
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346
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array(
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347
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'alt' => 'Show details',
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348
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'class' => array('expand_icon')
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349
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)
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350
|
);
|
|
351
|
$collapse_icon = font_awesome_icon_markup(
|
|
352
|
'fa-minus-square-o',
|
|
353
|
array(
|
|
354
|
'alt' => 'Show details',
|
|
355
|
'class' => array('collapse_icon')
|
|
356
|
)
|
|
357
|
);
|
|
358
|
$detail_image_icon = '<img title="Detail Image" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/detail_image_derivate-16x16-32.png' . '"/>';
|
|
359
|
$checked_box_icon = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/step_done.gif' . '"/>';
|
|
360
|
$sequence_icon = '<img title="Molecular Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/sequence_derivate-16x16-32.png' . '"/>';
|
|
361
|
$character_data_icon = '<img title="Character Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/character_data_derivate-16x16-32.png' . '"/>';
|
|
362
|
|
|
363
|
$rowcount = 0;
|
|
364
|
$rows = array();
|
|
365
|
|
|
366
|
foreach ($field_unit_uuids as $field_unit_uuid) {
|
|
367
|
|
|
368
|
//get derivate hierarchy for the FieldUnit
|
|
369
|
$derivateHierarchy = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($field_unit_uuid, 'derivateHierarchy'));
|
|
370
|
if ($derivateHierarchy) {
|
|
371
|
//summary row
|
|
372
|
$rows[] = array(
|
|
373
|
'data' => array(
|
|
374
|
array(
|
|
375
|
'data' => $expand_icon . $collapse_icon,
|
|
376
|
'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
|
|
377
|
),
|
|
378
|
array(
|
|
379
|
'data' => $derivateHierarchy->country,
|
|
380
|
'class' => array('summary_row_cell')
|
|
381
|
),
|
|
382
|
array(
|
|
383
|
'data' => $derivateHierarchy->date,
|
|
384
|
'class' => array('summary_row_cell')
|
|
385
|
),
|
|
386
|
array(
|
|
387
|
'data' => $derivateHierarchy->collectingString,
|
|
388
|
'class' => array('summary_row_cell')
|
|
389
|
),
|
|
390
|
@array(
|
|
391
|
'data' => $derivateHierarchy->collection,
|
|
392
|
'class' => array('summary_row_cell')
|
|
393
|
),
|
|
394
|
array(
|
|
395
|
'data' => $derivateHierarchy->hasType ? $checked_box_icon : "",
|
|
396
|
'class' => array('summary_row_cell', 'summary_row_icon')
|
|
397
|
),
|
|
398
|
array(
|
|
399
|
'data' => $derivateHierarchy->hasSpecimenScan ? $checked_box_icon : "",
|
|
400
|
'class' => array('summary_row_cell', 'summary_row_icon')
|
|
401
|
),
|
|
402
|
array(
|
|
403
|
'data' => ($derivateHierarchy->hasDna ? $sequence_icon : "") . " "
|
|
404
|
. ($derivateHierarchy->hasDetailImage ? $detail_image_icon : "") . " "
|
|
405
|
. ($derivateHierarchy->hasCharacterData ? $character_data_icon : ""),
|
|
406
|
'class' => array('summary_row_cell', 'summary_row_icon')
|
|
407
|
)
|
|
408
|
),
|
|
409
|
'id' => 'derivate_summary' . $rowcount, // summary row id
|
|
410
|
'class' => array('summary_row'),
|
|
411
|
);
|
|
412
|
|
|
413
|
//assemble field unit details
|
|
414
|
$detail_html = "";
|
|
415
|
// - citation
|
|
416
|
if ($derivateHierarchy->citation) {
|
|
417
|
$detail_html .= create_label("Citation") . $derivateHierarchy->citation . "<br>";
|
|
418
|
}
|
|
419
|
//assemble specimen details
|
|
420
|
if ($derivateHierarchy->derivates) {
|
|
421
|
foreach ($derivateHierarchy->derivates as $preservedSpecimenDTO) {
|
|
422
|
$detail_html .= "<br>";
|
|
423
|
$detail_html .= render_cdm_specimenDTO_page($preservedSpecimenDTO);
|
|
424
|
}
|
|
425
|
}
|
|
426
|
$detail_html .= "<br>";
|
|
427
|
//detail row resp. one BIG detail cell
|
|
428
|
$rows[] = array(
|
|
429
|
'data' => array(
|
|
430
|
array(
|
|
431
|
'data' => "", //empty first column
|
|
432
|
'class' => array('expand_column')
|
|
433
|
),
|
|
434
|
array(
|
|
435
|
'data' => $detail_html,
|
|
436
|
'colspan' => 7,
|
|
437
|
),
|
|
438
|
),
|
|
439
|
'id' => 'derivate_details' . $rowcount,//details row ID
|
|
440
|
'class' => array('detail_row'),
|
|
441
|
);
|
|
442
|
$rowcount++;
|
|
443
|
}
|
|
444
|
}
|
|
445
|
|
|
446
|
$tableId = "derivate_hierarchy_table";
|
|
447
|
$derivateHierarchyTable = array(
|
|
448
|
"#theme" => "table",
|
|
449
|
"#weight" => 2,
|
|
450
|
"#header" => array(
|
|
451
|
array(
|
|
452
|
'data' => "",
|
|
453
|
'class' => array('expand_column')
|
|
454
|
),
|
|
455
|
"Country", "Date", "Collector + collecting number", "Herbaria", "Type", "Scan", "Derivatives"),
|
|
456
|
"#rows" => $rows,
|
|
457
|
"#attributes" => array(
|
|
458
|
"id" => $tableId,
|
|
459
|
"border" => 2
|
|
460
|
)
|
|
461
|
);
|
|
462
|
|
|
463
|
//add toggle functionality to derivate hierarchy table
|
|
464
|
drupal_add_js_rowToggle("#" . $tableId);
|
|
465
|
|
|
466
|
return $derivateHierarchyTable;
|
|
467
|
}
|
|
468
|
|
|
469
|
function create_html_link($link, $openInExternalWindow=false){
|
|
470
|
$html = "";
|
|
471
|
if($link->uri && $link->uri!=""){
|
|
472
|
$html .= '<a href="' . $link->uri . '"';
|
|
473
|
if($openInExternalWindow){
|
|
474
|
$html .= ' target="_blank"';
|
|
475
|
}
|
|
476
|
$html .= '>' . $link->linkText . '</a>';
|
|
477
|
}
|
|
478
|
else{
|
|
479
|
$html .= $link->linkText;
|
|
480
|
}
|
|
481
|
return $html;
|
|
482
|
}
|
|
483
|
|
|
484
|
/**
|
|
485
|
* Creates HTML links from the given link list concatenated by default by a comma.
|
|
486
|
* @param $linkList the list with Link objects having "uri" and "linkText" as members
|
|
487
|
* @return string the assembled HTML string containing the links
|
|
488
|
*/
|
|
489
|
function create_html_links($linkList, $openInExternalWindow=false, $separator=", ")
|
|
490
|
{
|
|
491
|
$html = "";
|
|
492
|
if ($linkList) {
|
|
493
|
foreach ($linkList as $link) {
|
|
494
|
$html .= create_html_link($link, $openInExternalWindow).$separator;
|
|
495
|
}
|
|
496
|
$html = rtrim($html, $separator);
|
|
497
|
}
|
|
498
|
return $html;
|
|
499
|
}
|
|
500
|
|
|
501
|
/**
|
|
502
|
* Composes a taxon page which can consist of multiple parts like
|
|
503
|
* 'General', 'Synonymy', 'Images', 'Keys'. These parts can be displayed
|
|
504
|
* as tabs or as sections of a single page.
|
|
505
|
*
|
|
506
|
* It is headed by the name of the accepted taxon without author and reference.
|
|
507
|
*
|
|
508
|
* @param $taxon
|
|
509
|
* The CDM Taxon Instance to compose the page for.
|
|
510
|
* @param $page_part
|
|
511
|
* Name of the part to display, valid values are:
|
|
512
|
* - 'description' - for the general part
|
|
513
|
* - 'images'
|
|
514
|
* - 'synonymy'
|
|
515
|
* - 'keys'
|
|
516
|
* - 'all'
|
|
517
|
*
|
|
518
|
* @return array
|
|
519
|
* A drupal render array
|
|
520
|
*
|
|
521
|
* @ingroup compose
|
|
522
|
*/
|
|
523
|
function compose_cdm_taxon_page($taxon, $page_part = 'description') {
|
|
524
|
|
|
525
|
// we better cache here since drupal_get_query_parameters has no internal static cache variable
|
|
526
|
$http_request_params = drupal_get_query_parameters();
|
|
527
|
|
|
528
|
// add all mandatory js sources
|
|
529
|
_add_js_footnotes();
|
|
530
|
|
|
531
|
|
|
532
|
$render_array = array();
|
|
533
|
$weight = 0; // the weight for the render array elements
|
|
534
|
|
|
535
|
$tabsToDisplay = variable_get('cdm_taxonpage_tabs_visibility', unserialize(TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT));
|
|
536
|
|
|
537
|
$page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';
|
|
538
|
|
|
539
|
$synonymy_as_tab = variable_get(CDM_SYNONYMY_AS_TAB, CDM_SYNONYMY_AS_TAB_DEFAULT) === 1;
|
|
540
|
if(!$synonymy_as_tab){
|
|
541
|
unset($tabsToDisplay["Synonymy"]);
|
|
542
|
// the synonymy is located in the general part in this case
|
|
543
|
if($page_part == 'synonymy'){
|
|
544
|
$page_part = 'description';
|
|
545
|
}
|
|
546
|
}
|
|
547
|
|
|
548
|
$media = _load_media_for_taxon($taxon);
|
|
549
|
|
|
550
|
|
|
551
|
if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {
|
|
552
|
taxon_page_tabs_hidden_add('images');
|
|
553
|
}
|
|
554
|
|
|
555
|
// --- GET specimensOrObservations --- //
|
|
556
|
$specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservationsCount'));
|
|
557
|
|
|
558
|
$specimensOrObservationsCount = $specimensOrObservations != null ? $specimensOrObservations->result : 0;
|
|
559
|
if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {
|
|
560
|
taxon_page_tabs_hidden_add('specimens');
|
|
561
|
}
|
|
562
|
|
|
563
|
// --- GET polytomousKeys --- //
|
|
564
|
$polytomousKeysPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, NULL, "findByTaxonomicScope=$taxon->uuid");
|
|
565
|
$identificationKeyCount = 0;
|
|
566
|
if ($polytomousKeysPager) {
|
|
567
|
$identificationKeyCount += $polytomousKeysPager->count;
|
|
568
|
}
|
|
569
|
if ($identificationKeyCount == 0 || ($tabsToDisplay["Keys"] == '0')) {
|
|
570
|
taxon_page_tabs_hidden_add('keys');
|
|
571
|
}
|
|
572
|
|
|
573
|
// --- GET TaxonNodeAgentRelations --- //
|
|
574
|
$current_classification_uuid = get_current_classification_uuid();
|
|
575
|
$taxon_node_agent_relations_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
|
|
576
|
array(
|
|
577
|
$taxon->uuid,
|
|
578
|
$current_classification_uuid,
|
|
579
|
),
|
|
580
|
"pageSize=1&pageIndex=0"// we are only interested into the count so we are fetching only one item, o is not possible!
|
|
581
|
);
|
|
582
|
if (!$taxon_node_agent_relations_pager || $taxon_node_agent_relations_pager->count == 0){
|
|
583
|
taxon_page_tabs_hidden_add('experts');
|
|
584
|
}
|
|
585
|
|
|
586
|
if (!isset($tabsToDisplay["Synonymy"]) || $tabsToDisplay["Synonymy"] == '0') {
|
|
587
|
taxon_page_tabs_hidden_add('synonymy');
|
|
588
|
}
|
|
589
|
|
|
590
|
// -------------------------------------------- //
|
|
591
|
|
|
592
|
if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {
|
|
593
|
$render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);
|
|
594
|
}
|
|
595
|
|
|
596
|
// --- PAGE PART: DESCRIPTION --- //
|
|
597
|
if (!taxon_page_tabs_hidden_check('description') && ($page_part == 'description' || $page_part == 'all')) {
|
|
598
|
|
|
599
|
$merged_tree = merged_taxon_feature_tree($taxon);
|
|
600
|
|
|
601
|
|
|
602
|
$render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, !$synonymy_as_tab);
|
|
603
|
$render_array['general']['#weight'] = $weight++;
|
|
604
|
$render_array['general']['#prefix'] = '<div id="general" class="page-part">';
|
|
605
|
$render_array['general']['#suffix'] = '</div>';
|
|
606
|
}
|
|
607
|
|
|
608
|
// --- PAGE PART: IMAGES --- //
|
|
609
|
if (!taxon_page_tabs_hidden_check('images') && ($page_part == 'images' || $page_part == 'all')) {
|
|
610
|
$images_html = '<div id="images" class="page-part">';
|
|
611
|
if ($page_part == 'all') {
|
|
612
|
$images_html .= '<h2>' . t(cdm_taxonpage_tab_label('Images')) . '</h2>';
|
|
613
|
}
|
|
614
|
// Get the image gallery as configured by the admin.
|
|
615
|
$default_image_gallery = 'default';
|
|
616
|
$configured_image_gallery_viewer = variable_get('image_gallery_viewer', 'default');
|
|
617
|
$taxon_image_gallery = '<div class="error">No image gallery viewer configured</div>';
|
|
618
|
if($configured_image_gallery_viewer == $default_image_gallery || $configured_image_gallery_viewer == 'fsi'){
|
|
619
|
// the fsi_gallery requires a flash plugin, in case the client browser is not supporting
|
|
620
|
// flash we also need to provide an the default gallery as alternative
|
|
621
|
$taxon_image_gallery = '<div id="default-gallery-viewer">' .
|
|
622
|
call_user_func_array('taxon_image_gallery_' . $default_image_gallery, array(
|
|
623
|
$taxon,
|
|
624
|
$media,
|
|
625
|
))
|
|
626
|
. '</div>';
|
|
627
|
}
|
|
628
|
if($configured_image_gallery_viewer == 'fsi'){
|
|
629
|
$taxon_image_gallery .= '<div id="'. $configured_image_gallery_viewer .'-gallery-viewer">' .
|
|
630
|
call_user_func_array('taxon_image_gallery_' . $configured_image_gallery_viewer, array(
|
|
631
|
$taxon,
|
|
632
|
$media,
|
|
633
|
))
|
|
634
|
. '</div>';
|
|
635
|
}
|
|
636
|
$images_html .= $taxon_image_gallery;
|
|
637
|
$images_html .= '</div>';
|
|
638
|
$render_array['images'] = markup_to_render_array($images_html, $weight++);
|
|
639
|
}
|
|
640
|
|
|
641
|
// --- PAGE PART: SYNONYMY --- //
|
|
642
|
if (!taxon_page_tabs_hidden_check('synonymy') && (($page_part == 'synonymy' || $page_part == 'all') && $synonymy_as_tab)) {
|
|
643
|
$synonymy_html = '<div id="synonymy" class="page-part">';
|
|
644
|
if ($page_part == 'all') {
|
|
645
|
$synonymy_html .= '<h2>' . t(cdm_taxonpage_tab_label('Synonymy')) . '</h2>';
|
|
646
|
}
|
|
647
|
$addAcceptedTaxon = variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE);
|
|
648
|
|
|
649
|
$synonym_a = compose_cdm_taxon_page_synonymy($taxon, $addAcceptedTaxon);
|
|
650
|
$synonymy_html .= drupal_render($synonym_a);
|
|
651
|
|
|
652
|
$synonymy_html .= '</div>';
|
|
653
|
$render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
|
|
654
|
|
|
655
|
}
|
|
656
|
|
|
657
|
// --- PAGE PART: SPECIMENS --- //
|
|
658
|
if (!taxon_page_tabs_hidden_check('specimens') && ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all'))) {
|
|
659
|
$render_array['specimens'] = array(
|
|
660
|
'#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Specimens')) . '</h2>' : ''),
|
|
661
|
'content' => cdm_dataportal_taxon_page_specimens($taxon), // returns render array
|
|
662
|
'#suffix' => '</div>',
|
|
663
|
);
|
|
664
|
}
|
|
665
|
|
|
666
|
// --- PAGE PART: KEYS --- //
|
|
667
|
if(!taxon_page_tabs_hidden_check('keys')){
|
|
668
|
if ($identificationKeyCount == 1 && $page_part == 'keys'){
|
|
669
|
drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));
|
|
670
|
}
|
|
671
|
else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {
|
|
672
|
$keys_html = '<div id="keys" class="page-part">';
|
|
673
|
if ($page_part == 'all') {
|
|
674
|
$keys_html .= '<h2>' . t(cdm_taxonpage_tab_label('Keys')) . '</h2>';
|
|
675
|
}
|
|
676
|
$keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
|
|
677
|
$keys_html .= '</div>';
|
|
678
|
$render_array['keys'] = markup_to_render_array($keys_html, $weight++);
|
|
679
|
}
|
|
680
|
}
|
|
681
|
|
|
682
|
// --- PAGE PART: EXPERTS --- //
|
|
683
|
|
|
684
|
if (!taxon_page_tabs_hidden_check('experts') && ($page_part == 'experts' || $page_part == 'all')) {
|
|
685
|
$render_array['experts'] = array(
|
|
686
|
'#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Experts')) . '</h2>' : ''),
|
|
687
|
'content' => compose_cdm_taxon_page_experts($taxon), // returns render array
|
|
688
|
'#suffix' => '</div>',
|
|
689
|
);
|
|
690
|
}
|
|
691
|
|
|
692
|
// ------------------ END OF PARTS -------------- //
|
|
693
|
|
|
694
|
// adjust weights of page and toc elements according to the settings
|
|
695
|
$taxontabs_weights = get_array_variable_merged(CDM_TAXONPAGE_TAB_WEIGHT, CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
|
|
696
|
foreach($taxontabs_weights as $tab_key => $weight){
|
|
697
|
if(isset($render_array[$tab_key])){
|
|
698
|
$render_array[$tab_key]['#weight'] = $weight;
|
|
699
|
}
|
|
700
|
}
|
|
701
|
|
|
702
|
|
|
703
|
// set up the TOC for the pages which contain all pageparts
|
|
704
|
if($page_part == 'all') {
|
|
705
|
|
|
706
|
asort($taxontabs_weights);
|
|
707
|
foreach(array_keys($taxontabs_weights) as $tab_key){
|
|
708
|
if(isset($render_array[$tab_key])){
|
|
709
|
if($tab_key != 'general'){
|
|
710
|
// add entry for page part
|
|
711
|
$toc_elements[] = array(
|
|
712
|
'data' => l(t(cdm_taxonpage_tab_label(ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),
|
|
713
|
'class' => array('page-part-toc-item-' . $tab_key)
|
|
714
|
);
|
|
715
|
} else {
|
|
716
|
// add content of profile part instead
|
|
717
|
if(isset($render_array['general'])) {
|
|
718
|
// in case all tabs are shown at once the feature tocs
|
|
719
|
// should be integrated into the tabs toc as sub list
|
|
720
|
// and the profile image should be on top of the page
|
|
721
|
if(isset($render_array['general']['taxon_description_feature_toc'])){;
|
|
722
|
foreach ($render_array['general']['taxon_description_feature_toc']['#items'] as $profile_toc_item){
|
|
723
|
$toc_elements[] = $profile_toc_item;
|
|
724
|
}
|
|
725
|
unset($render_array['general']['taxon_description_feature_toc']);
|
|
726
|
}
|
|
727
|
}
|
|
728
|
}
|
|
729
|
}
|
|
730
|
}
|
|
731
|
|
|
732
|
// move profile image in page structure
|
|
733
|
if(isset($render_array['general']['taxon_profile_image'])){
|
|
734
|
$render_array['profile_image'] = $render_array['general']['taxon_profile_image'];
|
|
735
|
$render_array['profile_image']['#weight'] = -100;
|
|
736
|
unset($render_array['general']['taxon_profile_image']);
|
|
737
|
}
|
|
738
|
|
|
739
|
// finally add the table of contents to the render array
|
|
740
|
$render_array['toc'] = array(
|
|
741
|
'#theme' => 'item_list',
|
|
742
|
'#items' => $toc_elements,
|
|
743
|
'#title' => t('Content'),
|
|
744
|
'#weight' => -101,
|
|
745
|
'#suffix' => '</div>',
|
|
746
|
'#prefix'=> '<div id="page-toc">'
|
|
747
|
);
|
|
748
|
}
|
|
749
|
|
|
750
|
|
|
751
|
return $render_array;
|
|
752
|
}
|
|
753
|
|
|
754
|
/**
|
|
755
|
* TODO should this function really be a compose function?
|
|
756
|
* For a compose function must there always be a theme function with the same name? (ak 8.8.2013)
|
|
757
|
*
|
|
758
|
* composes and returns an render array containing the components of the taxon profile tab:
|
|
759
|
* - 'taxon_profile_image'
|
|
760
|
* - 'taxon_description_feature_toc'
|
|
761
|
* - 'taxon_description_features'
|
|
762
|
*
|
|
763
|
*
|
|
764
|
* @param object taxon
|
|
765
|
* @param object $merged_tree
|
|
766
|
* @param object media
|
|
767
|
* @param bool $add_synonymy
|
|
768
|
*
|
|
769
|
* @return array
|
|
770
|
* A Drupal render array with the following elements:
|
|
771
|
* - 'taxon_profile_image'
|
|
772
|
* - 'taxon_description_feature_toc'
|
|
773
|
* - 'taxon_description_features'
|
|
774
|
*
|
|
775
|
* @throws Exception
|
|
776
|
*
|
|
777
|
* @ingroup compose
|
|
778
|
*/
|
|
779
|
function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, $add_synonymy) {
|
|
780
|
|
|
781
|
$render_array = array();
|
|
782
|
|
|
783
|
$taxon_profile_image_settings = variable_get(CDM_TAXON_PROFILE_IMAGE, unserialize(CDM_TAXON_PROFILE_IMAGE_DEFAULT));
|
|
784
|
|
|
785
|
$hide_taxon_profile_image = FALSE;
|
|
786
|
if (variable_get('image_hide_rank', '0') != '0' && isset($taxon->name->rank->uuid)) {
|
|
787
|
$rankCompare = rank_compare($taxon->name->rank->uuid, variable_get('image_hide_rank', '-99'));
|
|
788
|
$hide_taxon_profile_image = ($rankCompare > -1);
|
|
789
|
}
|
|
790
|
|
|
791
|
if ($taxon_profile_image_settings['show'] && !$hide_taxon_profile_image) {
|
|
792
|
|
|
793
|
$representationPart = new stdClass();
|
|
794
|
$attributes = array();
|
|
795
|
if (isset($media[0])) {
|
|
796
|
// due to a bug the portal/taxon/{uuid}/media service only delivers a filtered media object
|
|
797
|
// which only contains the thumbnail representation even if the height and width filters are not set.
|
|
798
|
// -->
|
|
799
|
$preferred_media = cdm_ws_get(CDM_WS_MEDIA, $media[0]->uuid);
|
|
800
|
$preferred_representations = cdm_preferred_media_representations($preferred_media, array(
|
|
801
|
'image/jpg',
|
|
802
|
'image/jpeg',
|
|
803
|
'image/png',
|
|
804
|
'image/gif',
|
|
805
|
),
|
|
806
|
$taxon_profile_image_settings['maxextend'],
|
|
807
|
$taxon_profile_image_settings['maxextend']
|
|
808
|
);
|
|
809
|
if(count($preferred_representations) > 0){
|
|
810
|
|
|
811
|
$representation = array_shift($preferred_representations);
|
|
812
|
$representationPart = $representation->parts[0];
|
|
813
|
$attributes['alt'] = $representationPart->uri;
|
|
814
|
|
|
815
|
if (!empty($taxon_profile_image_settings['media_uri_query'])) {
|
|
816
|
$representationPart->uri = $representationPart->uri
|
|
817
|
. (strpos($representationPart->uri, '?') !== FALSE ? '&' : '?')
|
|
818
|
. $taxon_profile_image_settings['media_uri_query'];
|
|
819
|
}
|
|
820
|
}
|
|
821
|
}
|
|
822
|
else {
|
|
823
|
if ($taxon_profile_image_settings['custom_placeholder_enabled']) {
|
|
824
|
// show placeholder image instead
|
|
825
|
if (!empty($taxon_profile_image_settings['custom_placeholder_image_on']) && !empty($taxon_profile_image_settings['custom_placeholder_image_fid'])) {
|
|
826
|
// use the user provided image
|
|
827
|
$profile_image_file = file_load($taxon_profile_image_settings['custom_placeholder_image_fid']);
|
|
828
|
$url = file_create_url($profile_image_file->uri);
|
|
829
|
$image_info = image_get_info($profile_image_file->uri);
|
|
830
|
$representationPart->width = $image_info['width'];
|
|
831
|
$representationPart->height = $image_info['height'];
|
|
832
|
$representationPart->uri = $url;
|
|
833
|
}
|
|
834
|
else {
|
|
835
|
// use the hard coded default
|
|
836
|
$representationPart->width = 184;
|
|
837
|
$representationPart->height = 144;
|
|
838
|
$representationPart->uri = base_path() . drupal_get_path('module',
|
|
839
|
'cdm_dataportal') . '/images/no_picture.png';
|
|
840
|
}
|
|
841
|
$attributes['alt'] = "no image available";
|
|
842
|
}
|
|
843
|
}
|
|
844
|
|
|
845
|
if (isset($representationPart->uri)) {
|
|
846
|
$profile_image = cdm_media_gallerie_image($representationPart, $taxon_profile_image_settings['maxextend'], FALSE, $attributes);
|
|
847
|
// NOTE: style="width:${maxextend}px' is needed for IE8 !!!
|
|
848
|
$render_array['taxon_profile_image'] = markup_to_render_array('<div id="taxonProfileImage" style="width:' . $taxon_profile_image_settings['maxextend'] . 'px">' . $profile_image . '</div>',
|
|
849
|
-101);
|
|
850
|
}
|
|
851
|
}
|
|
852
|
|
|
853
|
if($add_synonymy){
|
|
854
|
$synonymy_a = compose_cdm_taxon_page_synonymy($taxon, true);
|
|
855
|
$synonymy_a['#weight'] = -102;
|
|
856
|
$render_array['synonymy'] = $synonymy_a;
|
|
857
|
}
|
|
858
|
|
|
859
|
$pseudo_feature_blocks = array();
|
|
860
|
$pseudo_feature_block_toc_items = array();
|
|
861
|
|
|
862
|
|
|
863
|
// Render the sections for each real feature
|
|
864
|
$feature_block_list = make_feature_block_list($merged_tree->root->childNodes, $taxon);
|
|
865
|
|
|
866
|
// Bibliography
|
|
867
|
$bibliography_settings = get_bibliography_settings();
|
|
868
|
if($bibliography_settings['enabled'] == 1){
|
|
869
|
$bibliography_markup = FootnoteManager::renderFootnoteList('BIBLIOGRAPHY', '');
|
|
870
|
if($bibliography_markup) {
|
|
871
|
$feature_bibliography = make_pseudo_feature('Bibliography', 'BIBLIOGRAPHY');
|
|
872
|
$bibliography_block = feature_block(t('Bibliography'), $feature_bibliography);
|
|
873
|
$bibliography_item = markup_to_render_array($bibliography_markup);
|
|
874
|
$bibliography_block->content[] = compose_feature_block_wrap_elements(array($bibliography_item), $feature_bibliography);
|
|
875
|
|
|
876
|
$pseudo_feature_block_toc_items['Bibliography']= 'bibliography';
|
|
877
|
$pseudo_feature_blocks[] = $bibliography_block;
|
|
878
|
}
|
|
879
|
}
|
|
880
|
|
|
881
|
$render_array['taxon_description_features'] = _block_get_renderable_array(
|
|
882
|
array_merge($feature_block_list, $pseudo_feature_blocks)
|
|
883
|
);
|
|
884
|
|
|
885
|
if($pseudo_feature_block_toc_items){
|
|
886
|
foreach ($pseudo_feature_block_toc_items as $label=>$fragment){
|
|
887
|
cdm_toc_list_add_item($label, $fragment);
|
|
888
|
}
|
|
889
|
}
|
|
890
|
|
|
891
|
// create the table of content
|
|
892
|
$toc = array(
|
|
893
|
'#theme' => 'item_list',
|
|
894
|
'#items' => cdm_toc_list(),
|
|
895
|
'#title' => t('Content'),
|
|
896
|
'#weight' => -100, // move to the top
|
|
897
|
'#suffix' => '</div>',
|
|
898
|
'#prefix'=> '<div id="page-toc">'
|
|
899
|
);
|
|
900
|
$render_array['taxon_description_feature_toc'] = $toc;
|
|
901
|
|
|
902
|
return $render_array;
|
|
903
|
}
|
|
904
|
|
|
905
|
|
|
906
|
/**
|
|
907
|
* Returns HTML containing the synonymy for the accepted taxon.
|
|
908
|
*
|
|
909
|
* Shows the whole synonymy for the accepted taxon.
|
|
910
|
* The synonymy list is headed by the complete scientific name
|
|
911
|
* of the accepted taxon with nomenclatural reference.
|
|
912
|
*
|
|
913
|
* @param object $taxon
|
|
914
|
* @param boolean $add_accepted_taxon
|
|
915
|
*
|
|
916
|
* @return array
|
|
917
|
* Drupal render array for the synonymy
|
|
918
|
*
|
|
919
|
* @throws Exception
|
|
920
|
*
|
|
921
|
* @ingroup compose
|
|
922
|
*/
|
|
923
|
function compose_cdm_taxon_page_synonymy($taxon, $add_accepted_taxon) {
|
|
924
|
|
|
925
|
RenderHints::pushToRenderStack('taxon_page_synonymy');
|
|
926
|
|
|
927
|
// footnote key for the homotypic group and accepted taxon,
|
|
928
|
// both should have the same footnote key
|
|
929
|
RenderHints::setFootnoteListKey(RenderHints::getRenderPath());
|
|
930
|
|
|
931
|
$synomymie = cdm_ws_get(CDM_WS_PORTAL_TAXON_SYNONYMY, array($taxon->uuid));
|
|
932
|
|
|
933
|
$out = '';
|
|
934
|
|
|
935
|
// Render accepted taxon.
|
|
936
|
//
|
|
937
|
// foonotes of the accepted taxon will be rendered in the homotypic group section
|
|
938
|
// even if there are not synonyms in the homotypic group
|
|
939
|
// homotypic group and accepted taxon should have the same footnote key
|
|
940
|
$referenceUri = '';
|
|
941
|
if ($add_accepted_taxon) {
|
|
942
|
// remember the last part of the render path
|
|
943
|
$synonymy_render_path = RenderHints::getRenderPath();
|
|
944
|
// set new render path for the accepted taxon so
|
|
945
|
// it can be styled differently via the name render part definitions
|
|
946
|
RenderHints::pushToRenderStack('accepted_taxon');
|
|
947
|
$accepted_name = '';
|
|
948
|
if (variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE, 0)) {
|
|
949
|
$label = variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL, CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL_DEFAULT);
|
|
950
|
$accepted_name .= '<div class="secReference"><span class="label">' . t($label) . ':</span> ' . $taxon->sec->titleCache . '</div>';
|
|
951
|
}
|
|
952
|
if (isset($taxon->name->nomenclaturalReference)) {
|
|
953
|
$referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
|
|
954
|
}
|
|
955
|
|
|
956
|
$accepted_name .= '<div class="accepted-name">';
|
|
957
|
$accepted_name .= render_taxon_or_name($taxon, NULL, $referenceUri);
|
|
958
|
|
|
959
|
$name_relations = cdm_name_relationships_for_taxon($taxon);
|
|
960
|
$name_relationships = compose_name_relationships_inline($name_relations, $taxon->name->uuid, $taxon->uuid);
|
|
961
|
// Render relationships of accepted name.
|
|
962
|
if(isset($name_relationships['list']['items'][0])){
|
|
963
|
$accepted_name .= ' ' . drupal_render($name_relationships);
|
|
964
|
}
|
|
965
|
|
|
966
|
// handle annotations of the name and taxon
|
|
967
|
$special_annotations_array = array();
|
|
968
|
$special_annotations_array[] = $taxon->name;
|
|
969
|
$special_annotations_array[] = $taxon;
|
|
970
|
$accepted_name .= theme('cdm_annotations_as_footnotekeys', array(
|
|
971
|
'cdmBase_list' => $special_annotations_array,
|
|
972
|
'footnote_list_key' => $synonymy_render_path . '-annotations')
|
|
973
|
);
|
|
974
|
$accepted_name .= '</div>';
|
|
975
|
RenderHints::popFromRenderStack();
|
|
976
|
}
|
|
977
|
|
|
978
|
// --- Render homotypic synonymy group
|
|
979
|
if (!empty($accepted_name)) {
|
|
980
|
$out .= $accepted_name;
|
|
981
|
}
|
|
982
|
|
|
983
|
// Render the homotypicSynonymyGroup including the type information.
|
|
984
|
$out .= theme(
|
|
985
|
'cdm_homotypicSynonymyGroup',
|
|
986
|
array(
|
|
987
|
'synonymList' => $synomymie->homotypicSynonymsByHomotypicGroup,
|
|
988
|
'accepted_taxon_name_uuid' => $taxon->name->uuid
|
|
989
|
)
|
|
990
|
);
|
|
991
|
|
|
992
|
|
|
993
|
// Render accepted taxon heterotypic synonymy groups.
|
|
994
|
if ($synomymie->heterotypicSynonymyGroups) {
|
|
995
|
foreach ($synomymie->heterotypicSynonymyGroups as $homotypicalGroup) {
|
|
996
|
$out .= theme('cdm_heterotypicSynonymyGroup', array('homotypicalGroup' => $homotypicalGroup));
|
|
997
|
}
|
|
998
|
}
|
|
999
|
// Render taxon relationships.
|
|
1000
|
if (variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT)) {
|
|
1001
|
$taxonRelationshipsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, $taxon->uuid);
|
|
1002
|
$out .= cdm_taxonRelationships($taxonRelationshipsDTO, $taxon);
|
|
1003
|
}
|
|
1004
|
|
|
1005
|
RenderHints::popFromRenderStack();
|
|
1006
|
|
|
1007
|
return markup_to_render_array($out);
|
|
1008
|
}
|
|
1009
|
|
|
1010
|
|
|
1011
|
/**
|
|
1012
|
* composes and returns an render array for the experts associated with the given taxon
|
|
1013
|
*
|
|
1014
|
* @param object taxon
|
|
1015
|
*
|
|
1016
|
* @return array
|
|
1017
|
* A Drupal render array for a table with the experts
|
|
1018
|
*
|
|
1019
|
* @ingroup compose
|
|
1020
|
*/
|
|
1021
|
function compose_cdm_taxon_page_experts($taxon){
|
|
1022
|
|
|
1023
|
$render_array = array();
|
|
1024
|
if(!isset($taxon->uuid)){
|
|
1025
|
return $render_array;
|
|
1026
|
}
|
|
1027
|
|
|
1028
|
$current_classification_uuid = get_current_classification_uuid();
|
|
1029
|
// TODO use cdm_ws_fetchall below but this failes! needs fix!
|
|
1030
|
$taxon_node_agent_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
|
|
1031
|
array(
|
|
1032
|
$taxon->uuid,
|
|
1033
|
$current_classification_uuid
|
|
1034
|
)
|
|
1035
|
);
|
|
1036
|
|
|
1037
|
$header = array(
|
|
1038
|
array('data' => t('Expert')),
|
|
1039
|
array('data' => t('Role'))
|
|
1040
|
);
|
|
1041
|
$rows = array();
|
|
1042
|
|
|
1043
|
|
|
1044
|
foreach($taxon_node_agent_relations->records as $taxon_node_agent_relation){
|
|
1045
|
|
|
1046
|
|
|
1047
|
$expert_role_id = $taxon_node_agent_relation->agent->uuid . '-' . $taxon_node_agent_relation->type->uuid;
|
|
1048
|
$expert_details_container_id = 'expert_details_' . $expert_role_id;
|
|
1049
|
|
|
1050
|
$agent_label_markup = cdm_dynabox(
|
|
1051
|
'expert_' . $expert_role_id,
|
|
1052
|
$taxon_node_agent_relation->agent->titleCache,
|
|
1053
|
// specifying both ends of the relationship will return only one record in the pager
|
|
1054
|
cdm_compose_url(CDM_WS_PORTAL_AGENT,
|
|
1055
|
array($taxon_node_agent_relation->agent->uuid, 'taxonNodeAgentRelations'),
|
|
1056
|
'taxon_uuid=' . $taxon->uuid . '&relType_uuid=' . $taxon_node_agent_relation->type->uuid),
|
|
1057
|
'cdm_taxon_expert',
|
|
1058
|
'Click for details',
|
|
1059
|
array('div', 'div'),
|
|
1060
|
array(), // attributes
|
|
1061
|
'#' . $expert_details_container_id // $content_element_selector
|
|
1062
|
);
|
|
1063
|
|
|
1064
|
// Expert and Role
|
|
1065
|
$rows[] = array(
|
|
1066
|
'data' => array(
|
|
1067
|
array(
|
|
1068
|
'data' => $agent_label_markup,
|
|
1069
|
'class' => array(html_class_attribute_ref($taxon_node_agent_relation->agent))
|
|
1070
|
),
|
|
1071
|
array(
|
|
1072
|
'data' => $taxon_node_agent_relation->type->representation_L10n,
|
|
1073
|
'class' => array(html_class_attribute_ref($taxon_node_agent_relation->type))
|
|
1074
|
)
|
|
1075
|
)
|
|
1076
|
);
|
|
1077
|
// Agent details
|
|
1078
|
$rows[] = array(
|
|
1079
|
'data' => array(
|
|
1080
|
array(
|
|
1081
|
'data' => '<!-- expert_details_container -->',
|
|
1082
|
'id' => $expert_details_container_id,
|
|
1083
|
'colspan' => 2
|
|
1084
|
)
|
|
1085
|
)
|
|
1086
|
);
|
|
1087
|
|
|
1088
|
}
|
|
1089
|
|
|
1090
|
|
|
1091
|
$render_array['experts_table'] = array(
|
|
1092
|
'#theme' => 'table',
|
|
1093
|
'#header' => $header,
|
|
1094
|
'#rows' => $rows,
|
|
1095
|
);
|
|
1096
|
|
|
1097
|
|
|
1098
|
return $render_array;
|
|
1099
|
}
|
|
1100
|
|
|
1101
|
|
|
1102
|
/**
|
|
1103
|
* Manages the tabs to be hidden in the taxon page.
|
|
1104
|
*
|
|
1105
|
* The tabs are identified by their last menu link path element:
|
|
1106
|
* - description
|
|
1107
|
* - synonymy
|
|
1108
|
* - images
|
|
1109
|
* - specimens
|
|
1110
|
* - key
|
|
1111
|
*
|
|
1112
|
* Internally the tabs are stored in a static variable which is
|
|
1113
|
* managed by drupal_static().
|
|
1114
|
*
|
|
1115
|
* @param string $add_tab
|
|
1116
|
* Optional parameter. The given string will be added to the array of tabs
|
|
1117
|
*
|
|
1118
|
* @return
|
|
1119
|
* The array of tabs
|
|
1120
|
*/
|
|
1121
|
function taxon_page_tabs_hidden_add($add_tab = NULL) {
|
|
1122
|
$tabs = &drupal_static('taxon_page_tabs_hidden');
|
|
1123
|
|
|
1124
|
if(!isset($tabs)){
|
|
1125
|
$tabs = array();
|
|
1126
|
}
|
|
1127
|
|
|
1128
|
if (isset($add_tab) && !array_key_exists($add_tab, $tabs)) {
|
|
1129
|
$tabs[] = $add_tab;
|
|
1130
|
}
|
|
1131
|
|
|
1132
|
return $tabs;
|
|
1133
|
}
|
|
1134
|
|
|
1135
|
/**
|
|
1136
|
* Manages the tabs to be hidden in the taxon page.
|
|
1137
|
*
|
|
1138
|
* The tabs names are identified by their last menu link path element:
|
|
1139
|
* - description
|
|
1140
|
* - synonymy
|
|
1141
|
* - images
|
|
1142
|
* - specimens
|
|
1143
|
* - key
|
|
1144
|
*
|
|
1145
|
* Internally the tabs are stored in a static variable which is
|
|
1146
|
* managed by drupal_static().
|
|
1147
|
*
|
|
1148
|
* @param string $tabname
|
|
1149
|
* The name of the tab to check
|
|
1150
|
*
|
|
1151
|
* @return boolean
|
|
1152
|
* True if the tab or section is to be hidden
|
|
1153
|
*/
|
|
1154
|
function taxon_page_tabs_hidden_check($tabname) {
|
|
1155
|
|
|
1156
|
$tabs = &drupal_static('taxon_page_tabs_hidden');
|
|
1157
|
|
|
1158
|
if(!isset($tabs)){
|
|
1159
|
$tabs = array();
|
|
1160
|
}
|
|
1161
|
|
|
1162
|
return array_search($tabname, $tabs) !== FALSE;
|
|
1163
|
}
|
|
1164
|
|
|
1165
|
/**
|
|
1166
|
* Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
|
|
1167
|
*
|
|
1168
|
* - Removes the tabs to be hidden, @see taxon_page_tabs_hidden_add()
|
|
1169
|
* - Renames tabs according to the settings // TODO (this will replace the theme_cdm_taxonpage_tab() function !!!)
|
|
1170
|
*
|
|
1171
|
* @param array $variables
|
|
1172
|
* The variables array
|
|
1173
|
*/
|
|
1174
|
function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {
|
|
1175
|
|
|
1176
|
$hidden_tabs = taxon_page_tabs_hidden_add();
|
|
1177
|
|
|
1178
|
if (!variable_get(CDM_SEARCH_BLAST_ENABLED)) {
|
|
1179
|
if (is_array($variables['primary'])) {
|
|
1180
|
foreach ($variables['primary'] as $key => &$element) {
|
|
1181
|
if ($element['#link']['path'] == 'cdm_dataportal/search/blast') {
|
|
1182
|
// remove the tab
|
|
1183
|
unset($variables['primary'][$key]);
|
|
1184
|
}
|
|
1185
|
|
|
1186
|
}
|
|
1187
|
}
|
|
1188
|
}
|
|
1189
|
if (is_array($variables['primary'])) {
|
|
1190
|
foreach ($variables['primary'] as $key => &$element) {
|
|
1191
|
|
|
1192
|
// 1. Remove the tabs to be hidden
|
|
1193
|
foreach ($hidden_tabs as $tab) {
|
|
1194
|
if ($element['#link']['path'] == 'cdm_dataportal/taxon/%/' . $tab) {
|
|
1195
|
// remove the tab
|
|
1196
|
unset($variables['primary'][$key]);
|
|
1197
|
}
|
|
1198
|
}
|
|
1199
|
}
|
|
1200
|
}
|
|
1201
|
}
|
|
1202
|
|
|
1203
|
|
|
1204
|
|
|
1205
|
/**
|
|
1206
|
* Implements the hook_preprocess_HOOK() for theme_menu_local_task()
|
|
1207
|
*
|
|
1208
|
*
|
|
1209
|
* @param array $variables
|
|
1210
|
* An associative array containing:
|
|
1211
|
* - element: A render element containing:
|
|
1212
|
* #link: A menu link array with 'title', 'href', and 'localized_options' keys.
|
|
1213
|
* #active: A boolean indicating whether the local task is active.
|
|
1214
|
*
|
|
1215
|
*/
|
|
1216
|
function cdm_dataportal_preprocess_menu_local_task(&$variables) {
|
|
1217
|
|
|
1218
|
$link = $variables['element']['#link'];
|
|
1219
|
if (preg_match('/cdm_dataportal\/.*\/refresh$/', $link['href'])) {
|
|
1220
|
$link['title'] = '<img class="refresh" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/view-refresh.png' . '" alt="' . check_plain($link['title']) . '" title="' . check_plain($link['title']) . '"/>';
|
|
1221
|
$link['localized_options']['html'] = TRUE;
|
|
1222
|
|
|
1223
|
$variables['element']['#link'] = $link;
|
|
1224
|
}
|
|
1225
|
}
|
|
1226
|
|
|
1227
|
/* =================== block composition ===================== */
|
|
1228
|
|
|
1229
|
/**
|
|
1230
|
* Composes and returns an render array for the classification breadcrumbs of the given taxon.
|
|
1231
|
*
|
|
1232
|
* @param taxon
|
|
1233
|
*
|
|
1234
|
* @return array
|
|
1235
|
* A Drupal render array for a table with the experts
|
|
1236
|
*
|
|
1237
|
* @ingroup compose
|
|
1238
|
*/
|
|
1239
|
function compose_classification_breadcrumbs($taxon_uuid) {
|
|
1240
|
|
|
1241
|
_add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');
|
|
1242
|
|
|
1243
|
$render_array = array();
|
|
1244
|
|
|
1245
|
$render_array['#theme'] = 'item_list';
|
|
1246
|
$render_array['#type'] = 'ul';
|
|
1247
|
$render_array['#attributes'] = array(
|
|
1248
|
'id' => 'classification-breadcrumbs',
|
|
1249
|
'class' => 'breadcrumbs inline',
|
|
1250
|
);
|
|
1251
|
|
|
1252
|
$items = array();
|
|
1253
|
|
|
1254
|
$parent_taxon_nodes = null;
|
|
1255
|
if($taxon_uuid){
|
|
1256
|
$parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
|
|
1257
|
}
|
|
1258
|
|
|
1259
|
$classifications = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
|
|
1260
|
// find current classification in list
|
|
1261
|
$classification = null;
|
|
1262
|
$current_classification_uuid = get_current_classification_uuid();
|
|
1263
|
foreach ($classifications as $classification){
|
|
1264
|
if($classification->uuid == $current_classification_uuid){
|
|
1265
|
break;
|
|
1266
|
}
|
|
1267
|
}
|
|
1268
|
|
|
1269
|
$node_name = '';
|
|
1270
|
if(count($classifications) > 1 ){
|
|
1271
|
// need to add the current classification as first label
|
|
1272
|
|
|
1273
|
$label = $classification->titleCache;
|
|
1274
|
if(strlen($label) > 20){
|
|
1275
|
$label = substr($label, 0, strpos($label, ' ', 15)) . '...';
|
|
1276
|
}
|
|
1277
|
$node_name = font_awesome_icon_markup('fa-th-list') . ' ' . l($label, '#', array(
|
|
1278
|
'attributes' => array(
|
|
1279
|
'class' => 'taxonomic-children-button classification-chooser',
|
|
1280
|
'data-destination-uri' => drupal_get_destination(),
|
|
1281
|
'data-cdm-align-with' => array('prev')
|
|
1282
|
),
|
|
1283
|
'html' => true
|
|
1284
|
));
|
|
1285
|
}
|
|
1286
|
|
|
1287
|
$rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
|
|
1288
|
|
|
1289
|
$rank_separator = '<span> '
|
|
1290
|
. font_awesome_icon_markup('fa-chevron-right')
|
|
1291
|
. ' </span>';
|
|
1292
|
$more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');
|
|
1293
|
$more_children_label = '...';
|
|
1294
|
|
|
1295
|
$items[] = $node_name;
|
|
1296
|
|
|
1297
|
$more_children_for = null;
|
|
1298
|
if($parent_taxon_nodes){
|
|
1299
|
foreach ($parent_taxon_nodes as $node) {
|
|
1300
|
|
|
1301
|
$is_first_item = count($items) == 0;
|
|
1302
|
$is_last_item = count($items) == count($parent_taxon_nodes);
|
|
1303
|
$node_name = cdm_dataportal_shortname_of($node);
|
|
1304
|
$path = path_to_taxon($node->taxonUuid);
|
|
1305
|
|
|
1306
|
if($node->taxonomicChildrenCount > 0) {
|
|
1307
|
$more_children_for = $node->taxonUuid;
|
|
1308
|
} else {
|
|
1309
|
$more_children_for = null;
|
|
1310
|
}
|
|
1311
|
|
|
1312
|
// 'fa-sitemap'
|
|
1313
|
|
|
1314
|
$items[] =
|
|
1315
|
($is_first_item ? '' : ' ')
|
|
1316
|
. $rank_separator
|
|
1317
|
. l(
|
|
1318
|
'<span class="' . html_class_attribute_ref($node) . '">' . $node_name . '</span>',
|
|
1319
|
$path,
|
|
1320
|
array(
|
|
1321
|
'attributes' => array(
|
|
1322
|
'class' => array('taxonomic-children-button'),
|
|
1323
|
'data-cdm-taxon-uuid' => array($node->taxonUuid),
|
|
1324
|
'data-cdm-classification-mode' => array('siblings'),
|
|
1325
|
'data-cdm-align-with' => array('prev')
|
|
1326
|
),
|
|
1327
|
'html' => true
|
|
1328
|
)
|
|
1329
|
);
|
|
1330
|
}
|
|
1331
|
}
|
|
1332
|
|
|
1333
|
// add more button to the end
|
|
1334
|
if(!$parent_taxon_nodes) {
|
|
1335
|
// not taxon focused yet, adding button to make the root nodes available
|
|
1336
|
$items[] = '<span>'
|
|
1337
|
. $more_children_icon . ' ' .
|
|
1338
|
'<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
|
|
1339
|
. '" data-rank-limit-uuid="' . $rank_limit_uuid . '" data-cdm-align-with="prev"> ' . $more_children_label . '<span>'
|
|
1340
|
. '</span>';
|
|
1341
|
} else if($more_children_for){
|
|
1342
|
// last parent item has child taxon nodes
|
|
1343
|
$items[] = ' <span>'
|
|
1344
|
. $more_children_icon . ' ' .
|
|
1345
|
'<span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
|
|
1346
|
. '" data-cdm-classification-mode="children" data-cdm-align-with="prev"> ' . $more_children_label . '</span>'
|
|
1347
|
. '</span>';
|
|
1348
|
|
|
1349
|
}
|
|
1350
|
|
|
1351
|
$render_array['#items'] = $items;
|
|
1352
|
|
|
1353
|
return $render_array;
|
|
1354
|
}
|
|
1355
|
|
|
1356
|
|
|
1357
|
/**
|
|
1358
|
* @param $specimen_uuid
|
|
1359
|
* @return array
|
|
1360
|
* The drupal render array for the page
|
|
1361
|
*
|
|
1362
|
* @ingroup compose
|
|
1363
|
*/
|
|
1364
|
function compose_cdm_specimen_page($specimen_uuid)
|
|
1365
|
{
|
|
1366
|
drupal_set_title("Specimen Details");
|
|
1367
|
$render_array = array();
|
|
1368
|
RenderHints::pushToRenderStack('specimen_page');
|
|
1369
|
|
|
1370
|
$specimen_table = array(
|
|
1371
|
'#theme' => 'table',
|
|
1372
|
'#weight' => 2,
|
|
1373
|
// prefix attributes and rows with '#' to let it pass toF the theme function,
|
|
1374
|
// otherwise it is handled as child render array
|
|
1375
|
|
|
1376
|
'#attributes' => array('class' => 'specimens'),
|
|
1377
|
'#rows' => array(),
|
|
1378
|
'#prefix' => '<div id="specimens">',
|
|
1379
|
'#suffix' => '</div>',
|
|
1380
|
|
|
1381
|
|
|
1382
|
);
|
|
1383
|
$specimen = compose_cdm_specimen_or_observation($specimen_uuid, true);
|
|
1384
|
$renderArray = array(
|
|
1385
|
'#theme' => 'item_list',
|
|
1386
|
'#items' => array($specimen),
|
|
1387
|
'#type' => 'ul');
|
|
1388
|
$output = drupal_render($renderArray);
|
|
1389
|
|
|
1390
|
$specimen_table['#rows'][] = array(
|
|
1391
|
// An array of table rows. Every row is an array of cells, or an associative array
|
|
1392
|
'data' => array($output),
|
|
1393
|
'class' => array(
|
|
1394
|
'descriptionElement',
|
|
1395
|
'descriptionElement_IndividualsAssociation'
|
|
1396
|
),
|
|
1397
|
|
|
1398
|
);
|
|
1399
|
|
|
1400
|
|
|
1401
|
// $detail_html = compose_cdm_specimen_or_observation($specimen_uuid, true);
|
|
1402
|
// $render_array['markup'] = array(
|
|
1403
|
// '#prefix' => '<div id="specimens" class="page">',
|
|
1404
|
// 'content' => $specimen_table,
|
|
1405
|
// '#suffix' => '</div>',
|
|
1406
|
// );
|
|
1407
|
$render_array['markup'] = $specimen_table;
|
|
1408
|
|
|
1409
|
RenderHints::popFromRenderStack();
|
|
1410
|
return $render_array;
|
|
1411
|
}
|
|
1412
|
|
|
1413
|
/**
|
|
1414
|
* @param $named_area_uuid
|
|
1415
|
* @return array
|
|
1416
|
* The drupal render array for the page
|
|
1417
|
*
|
|
1418
|
* @ingroup compose
|
|
1419
|
*/
|
|
1420
|
function compose_cdm_named_area_page($named_area_uuid)
|
|
1421
|
{
|
|
1422
|
|
|
1423
|
$named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid));
|
|
1424
|
|
|
1425
|
$render_array = array();
|
|
1426
|
RenderHints::pushToRenderStack('named_area_page');
|
|
1427
|
|
|
1428
|
$groups = array();
|
|
1429
|
@_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);
|
|
1430
|
@_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);
|
|
1431
|
if(isset($named_area->level)) {
|
|
1432
|
@_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);
|
|
1433
|
}
|
|
1434
|
|
|
1435
|
$name_area_details_elements = array(
|
|
1436
|
// '#title' => $title,
|
|
1437
|
'#theme' => 'description_list',
|
|
1438
|
'#groups' => $groups,
|
|
1439
|
'#attributes' => array('class' => html_class_attribute_ref($named_area)),
|
|
1440
|
);
|
|
1441
|
|
|
1442
|
$render_array[] = $name_area_details_elements;
|
|
1443
|
|
|
1444
|
RenderHints::popFromRenderStack();
|
|
1445
|
return $render_array;
|
|
1446
|
}
|
|
1447
|
|
|
1448
|
|
|
1449
|
/**
|
|
1450
|
* Returns a drupal render array for a single reference page.
|
|
1451
|
*
|
|
1452
|
* Composes a page with all data on a single reference.
|
|
1453
|
*
|
|
1454
|
* @param string $uuid
|
|
1455
|
* An uuid for a cdm reference.
|
|
1456
|
*
|
|
1457
|
* @return array
|
|
1458
|
* A drupal render array
|
|
1459
|
*
|
|
1460
|
* @throws Exception
|
|
1461
|
*
|
|
1462
|
* @ingroup compose
|
|
1463
|
*/
|
|
1464
|
function compose_cdm_reference_page($uuid) {
|
|
1465
|
|
|
1466
|
$pathelement = "reference_page";
|
|
1467
|
RenderHints::pushToRenderStack($pathelement);
|
|
1468
|
$reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
|
|
1469
|
if (isset($reference->titleCache)) {
|
|
1470
|
drupal_set_title($reference->titleCache, PASS_THROUGH);
|
|
1471
|
}
|
|
1472
|
|
|
1473
|
$field_order = array(
|
|
1474
|
"title",
|
|
1475
|
"abbrevTitle",
|
|
1476
|
// "titleCache" abbrevTitleCache
|
|
1477
|
// "citation",
|
|
1478
|
"authorship",
|
|
1479
|
"editor",
|
|
1480
|
"publisher",
|
|
1481
|
"placePublished",
|
|
1482
|
"datePublished",
|
|
1483
|
"year",
|
|
1484
|
"edition",// Class Book.
|
|
1485
|
"volume",// Class Article.
|
|
1486
|
"seriesPart",
|
|
1487
|
"inReference",
|
|
1488
|
"nomRefBase", // Class BookSection, Book, Article.
|
|
1489
|
"pages",// Class Article.
|
|
1490
|
"series",// Class Article, PrintSeries.
|
|
1491
|
"school",// Class Thesis.
|
|
1492
|
"institution",// Class Report.
|
|
1493
|
"organization",// Class Proceedings.
|
|
1494
|
"nextVersion",
|
|
1495
|
"previousVersion",
|
|
1496
|
"isbn",// Class Book.
|
|
1497
|
"issn",// Class Journal.
|
|
1498
|
"doi",
|
|
1499
|
"uri"
|
|
1500
|
);
|
|
1501
|
|
|
1502
|
$table_rows = array();
|
|
1503
|
|
|
1504
|
if (!isset($reference->authorship)) {
|
|
1505
|
$authorship = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid);
|
|
1506
|
$reference->authorship = isset($authorship->titleCache) ? $authorship->titleCache : '';
|
|
1507
|
}
|
|
1508
|
|
|
1509
|
if (!isset($reference->inReference)) {
|
|
1510
|
$reference->inReference = cdm_ws_get(CDM_WS_REFERENCE, array(
|
|
1511
|
$reference->uuid,
|
|
1512
|
"inReference",
|
|
1513
|
));
|
|
1514
|
}
|
|
1515
|
|
|
1516
|
foreach ($field_order as $fieldname) {
|
|
1517
|
|
|
1518
|
if (isset($reference->$fieldname)) {
|
|
1519
|
|
|
1520
|
if ($fieldname == "datePublished") {
|
|
1521
|
$period = $reference->$fieldname;
|
|
1522
|
$datePublished = timePeriodToString($period);
|
|
1523
|
if (isset($datePublished) && $datePublished != '') {
|
|
1524
|
$table_rows[] = array(
|
|
1525
|
t("Date published"),
|
|
1526
|
$datePublished,
|
|
1527
|
);
|
|
1528
|
}
|
|
1529
|
}
|
|
1530
|
elseif ($fieldname == "doi" && is_object($reference->doi)) {
|
|
1531
|
$table_rows[] = array(
|
|
1532
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
|
1533
|
cdm_doi($reference->doi, false)
|
|
1534
|
);
|
|
1535
|
}
|
|
1536
|
elseif ($fieldname == "uri" && isset($reference->uri) && $reference->uri) {
|
|
1537
|
$table_rows[] = array(
|
|
1538
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
|
1539
|
cdm_external_uri($reference->uri, false)
|
|
1540
|
);
|
|
1541
|
}
|
|
1542
|
elseif (is_object($reference->$fieldname)) {
|
|
1543
|
if ($fieldname == "authorship") {
|
|
1544
|
$dump = $reference->$fieldname;
|
|
1545
|
$teammembers = "teamMembers";
|
|
1546
|
$team = $dump->$teammembers;
|
|
1547
|
$nameArray = array();
|
|
1548
|
|
|
1549
|
foreach ($team as $member) {
|
|
1550
|
if (strlen($member->lastname) > 0) {
|
|
1551
|
$nname = $member->lastname;
|
|
1552
|
$name = $nname;
|
|
1553
|
if (strlen($member->firstname) > 0) {
|
|
1554
|
$vname = $member->firstname;
|
|
1555
|
$name = $vname . " " . $nname;
|
|
1556
|
}
|
|
1557
|
$nameArray[] = $name;
|
|
1558
|
}
|
|
1559
|
else {
|
|
1560
|
if (strlen($member->titleCache) > 0) {
|
|
1561
|
$nameArray[] = $member->titleCache;
|
|
1562
|
}
|
|
1563
|
}
|
|
1564
|
}
|
|
1565
|
$value = join($nameArray, ", ");
|
|
1566
|
}
|
|
1567
|
elseif ($fieldname == "inReference") {
|
|
1568
|
$type = $reference->$fieldname->type;
|
|
1569
|
$value = l($reference->$fieldname->titleCache, path_to_reference($reference->$fieldname->uuid));
|
|
1570
|
switch ($type) {
|
|
1571
|
case "Book":
|
|
1572
|
$fieldname = "in book";
|
|
1573
|
break;
|
|
1574
|
case "Journal":
|
|
1575
|
$fieldname = "in journal";
|
|
1576
|
break;
|
|
1577
|
case "Proceedings":
|
|
1578
|
$fieldname = "in proceedings";
|
|
1579
|
break;
|
|
1580
|
}
|
|
1581
|
}
|
|
1582
|
else {
|
|
1583
|
$value = $reference->$fieldname->titleCache;
|
|
1584
|
}
|
|
1585
|
|
|
1586
|
|
|
1587
|
if (isset($value) && $value != '') {
|
|
1588
|
$table_rows[] = array(
|
|
1589
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
|
1590
|
$value,
|
|
1591
|
);
|
|
1592
|
}
|
|
1593
|
|
|
1594
|
}
|
|
1595
|
else {
|
|
1596
|
if (isset($reference->$fieldname) && $reference->$fieldname != '') {
|
|
1597
|
$table_rows[] = array(
|
|
1598
|
t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
|
|
1599
|
$reference->$fieldname,
|
|
1600
|
);
|
|
1601
|
}
|
|
1602
|
}
|
|
1603
|
}
|
|
1604
|
}
|
|
1605
|
|
|
1606
|
$out = theme_table(array(
|
|
1607
|
'header' => array(),
|
|
1608
|
'rows' => $table_rows,
|
|
1609
|
'attributes' => array(
|
|
1610
|
'class' => html_class_attribute_ref($reference)
|
|
1611
|
),
|
|
1612
|
'caption' => NULL,
|
|
1613
|
'colgroups' => NULL,
|
|
1614
|
'sticky' => NULL,
|
|
1615
|
'empty' => NULL,
|
|
1616
|
));
|
|
1617
|
|
|
1618
|
if(isset($reference->referenceAbstract)){
|
|
1619
|
$out .= '<h2 class="block-title">Abstract</h2><div class="abstract">' . $reference->referenceAbstract . '</div>';
|
|
1620
|
}
|
|
1621
|
|
|
1622
|
|
|
1623
|
// Annotations below the table
|
|
1624
|
$annotations = cdm_fetch_visible_annotations($reference);
|
|
1625
|
$out .= theme("cdm_annotations", array('annotations' => $annotations));
|
|
1626
|
|
|
1627
|
$registration_working_set = cdm_ws_get("registrationWorkingSetDTO", array($uuid));
|
|
1628
|
if($registration_working_set && count($registration_working_set->registrationDTOs) > 0){
|
|
1629
|
$out .= "<h3>Nomenclatural acts:</h3><div class=\"cdm-item-list registration-item-list\">";
|
|
1630
|
foreach($registration_working_set->registrationDTOs as $registration_dto){
|
|
1631
|
if($registration_dto->status == "PUBLISHED"){
|
|
1632
|
$registration_render_a = compose_registration_dto_compact($registration_dto, 'citation');
|
|
1633
|
$registration_render_a["#prefix"] = "<div class=\"item item-registration\">";
|
|
1634
|
$registration_render_a["#suffix"] = "</div>";
|
|
1635
|
$out .= drupal_render($registration_render_a);
|
|
1636
|
}
|
|
1637
|
}
|
|
1638
|
$out .= "</div>";
|
|
1639
|
}
|
|
1640
|
|
|
1641
|
RenderHints::popFromRenderStack();
|
|
1642
|
|
|
1643
|
return markup_to_render_array($out);
|
|
1644
|
}
|
|
1645
|
|
|
1646
|
/**
|
|
1647
|
* Provides the the label string for taxon page tabs.
|
|
1648
|
*
|
|
1649
|
* The $tabname as passed to the method will be returned if no override
|
|
1650
|
* label is configured in the settings.
|
|
1651
|
*/
|
|
1652
|
function cdm_taxonpage_tab_label($tabname) {
|
|
1653
|
static $taxon_tabs_labels = null;
|
|
1654
|
if($taxon_tabs_labels == null){
|
|
1655
|
$taxon_tabs_labels = get_array_variable_merged(CDM_TAXONPAGE_TAB_LABELS, CDM_TAXONPAGE_TAB_LABELS_DEFAULT);
|
|
1656
|
}
|
|
1657
|
$tabname_key = strtolower($tabname);
|
|
1658
|
if(isset($taxon_tabs_labels[$tabname_key]) && $taxon_tabs_labels[$tabname_key]){
|
|
1659
|
return $taxon_tabs_labels[$tabname_key];
|
|
1660
|
}
|
|
1661
|
return $tabname;
|
|
1662
|
}
|