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<?php
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/**
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* @file
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* Functions for dealing with CDM entities of type SpecimenOrOccurrences
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* This file contains new functions which are to replace functions in
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* occurrences.inc and should be merged with the latter one.
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*
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* @see http://www.mozilla.org/MPL/MPL-1.1.html
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*
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* @copyright
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* (C) 2007-2021 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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* @author
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* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
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*/
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/**
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* Compose grid of details tabled for a CDM SpecimenOrObservationDTO
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*
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* The resulting render array will contain separate DOM block level elements
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* with header line for the various kind of information like, location,
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* gathering, specimen/observation, DNA, etc.
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*
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*
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* Subordinate derivatives will not be included. For showing the derivation
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* hierarchy see methods like derived_units_sub_tree()
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*
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* compose_hook() implementation
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*
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* @param object $sob_dto
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* the CDM FieldUnitDTO or DerivedUnitDTO to compose
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* the render array for.
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* @param bool $full_details
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* Activates the display of additional data like: annotations, markers, ...
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*
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* @return array
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* The render array for the SpecimenOrObservationDTO
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*
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* @ingroup compose
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*/
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function compose_cdm_specimen_or_observation_dto_details_grid($sob_dto, $full_details = FALSE) {
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$render_array = [];
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if (!$sob_dto) {
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return $render_array;
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}
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if ($sob_dto->type == 'FieldUnit') {
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$render_array['field-unit'] = compose_cdm_field_unit_dto_details($sob_dto, $full_details);
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if (isset($sob_dto->gatheringEvent)) {
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$render_array['gathering'] = compose_cdm_gathering_dto_details($sob_dto->gatheringEvent, $full_details);
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}
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} else {
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if(isset($sob_dto->derivationEvent)){
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$render_array['derivation-event'] = compose_cdm_derivation_event($sob_dto->derivationEvent);
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}
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$render_array['storage'] = compose_cdm_derived_unit_dto_storage_details($sob_dto, $full_details);
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$render_array['type-designations'] = compose_cdm_unit_dto_type_designations($sob_dto, $full_details);
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if($sob_dto->type == 'DnaSample'){
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// FIXME:
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$render_array['dna-sample'] = compose_cdm_derived_unit_dto_sequences($sob_dto, $full_details);
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} else if($sob_dto->type == 'MediaSpecimen' && isset_not_empty($sob_dto->mediaSpecimen)) {
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$render_array['media-specimens'] = cdm_sob_dto_media_table($sob_dto->mediaSpecimen, $sob_dto, 'Media Specimens');
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}
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}
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if(isset_not_empty($sob_dto->determinedNames)){
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$render_array['determinations'] = compose_cdm_sob_dto_determinations($sob_dto, $full_details);
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}
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if(isset_not_empty($sob_dto->listOfMedia)){
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$render_array['media'] = cdm_sob_dto_media_table($sob_dto->listOfMedia, $sob_dto, 'Media');;
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}
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if($full_details){
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// Annotations and Sources
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RenderHints::setAnnotationsAndSourceConfig([
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'sources_as_content' => TRUE,
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'annotations_as_content' => TRUE,
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'link_to_name_used_in_source' => TRUE,
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'link_to_reference' => FALSE,
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'add_footnote_keys' => FALSE,
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'bibliography_aware' => FALSE
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]);
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$annotations_and_sources = handle_annotations_and_sources($sob_dto);
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if ($annotations_and_sources->hasSourceReferences()) {
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$render_array['sources'] = compose_cdm_sob_dto_sources($sob_dto, $annotations_and_sources);
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}
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if(count($annotations_and_sources->getAnnotations()) > 0){
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$render_array['annotations'] = compose_cdm_sob_dto_annotations($sob_dto, $annotations_and_sources);
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}
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// Markers
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$markers = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, [$sob_dto->uuid, 'markers']);
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if(isset_not_empty($markers->records)){
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$render_array['markers'] = compose_cdm_sob_dto_markers($sob_dto, $markers);
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}
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}
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return $render_array;
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}
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/**
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* Data rows with details for a SpecimenOrObservationDTO to be used in a table
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* @param object $sob_dto
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* the CDM SpecimenOrObservationDTO
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* @param bool $full_details
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* Currently unused,
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*
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* @return array
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* The data rows
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*/
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function sob_dto_details_rows($sob_dto, $full_details = FALSE) {
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$table_row_data = [];
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if (isset_not_empty($sob_dto->recordBase)) {
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$label = cdm_term_representation($sob_dto->recordBase);
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if($label == 'Dna Sample'){
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$label == 'DNA Sample';
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}
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$table_row_data[0] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('recordBase'),
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$label);
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}
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if (isset_not_empty($sob_dto->kindOfUnit)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('kindOfUnit'),
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cdm_term_representation($sob_dto->kindOfUnit));
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}
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if (isset_not_empty($sob_dto->preferredStableUri)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('preferredStableUri'),
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cdm_external_uri($sob_dto->preferredStableUri, false));
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}
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if (isset_not_empty($sob_dto->sex)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('sex'),
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cdm_term_representation($sob_dto->sex));
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}
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if (isset_not_empty($sob_dto->lifeStage)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('lifeStage'),
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cdm_term_representation($sob_dto->lifeStage));
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}
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return $table_row_data;
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}
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/**
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* Compose a table of details for a DerivationEventDTO.
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*
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* compose_hook() implementation
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*
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* @param object $derivation_event_dto
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* the CDM DerivationEventDTO
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* @param bool $full_details
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* Currently unused,
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*
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* @return array
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* The render array for the DerivationEventDTO
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*
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* @ingroup compose
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*/
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function compose_cdm_derivation_event($derivation_event_dto, $full_details = FALSE){
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$details_array = [];
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// $markup = t("Derivation") . ': ';
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$markup = ucfirst(cdm_term_representation($derivation_event_dto->eventType));
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if(isset_not_empty($derivation_event_dto->actor)){
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$details_array[] = $derivation_event_dto->actor;
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}
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if(isset_not_empty($derivation_event_dto->institute)){
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$details_array[] = $derivation_event_dto->institute;
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}
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if(isset_not_empty($derivation_event_dto->timePeriod)){
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$details_array[] = timePeriodToString($derivation_event_dto->timePeriod);
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}
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$details_markup = join(', ', $details_array);
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if($details_markup){
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$markup .= ': ' . $details_markup;
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}
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$render_array = [
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'#type' => 'container',
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'#attributes' => [
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'class' => [
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'derivation-event',
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html_class_attribute_ref($derivation_event_dto)
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],
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'style' => [
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'grid-column-start: span 2'
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]
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],
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'content' => markup_to_render_array($markup)
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];
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return $render_array;
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}
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/**
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* Compose a table of details for a FieldUnitDTO.
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*
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* The resulting DOM block level element will have a header line and details.
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*
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* compose_hook() implementation
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*
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* @param object $fu_dto
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* the CDM FieldUnitDTO
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* @param bool $full_details
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* Currently unused,
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*
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* @return array
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* The render array for the SpecimenOrObservationDTO
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*
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* @ingroup compose
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*/
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function compose_cdm_field_unit_dto_details($fu_dto, $full_details = FALSE) {
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$table_row_data = sob_dto_details_rows($fu_dto, $full_details);
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if (isset_not_empty($fu_dto->individualCount)) {
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$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('individualCount'), $fu_dto->individualCount);
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}
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if (isset_not_empty($fu_dto->definition)) {
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$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('definition'), $fu_dto->definition);
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}
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if (isset_not_empty($fu_dto->fieldNumber)) {
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$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('fieldNumber'), $fu_dto->fieldNumber);
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}
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if (isset_not_empty($fu_dto->primaryCollector)) {
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$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('primaryCollector'), $fu_dto->primaryCollector);
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}
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if (isset_not_empty($fu_dto->fieldNotes)) {
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$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('fieldNotes'), $fu_dto->fieldNotes);
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}
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$heading = $table_row_data[0]['data'][1];
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unset($table_row_data[0]);
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return cdm_sob_dto_table(t($heading), $table_row_data, $fu_dto, 2);
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}
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/**
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* Compose details table for a DerivedUnitDTO.
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*
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* The resulting DOM block level element will have a header line and details.
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*
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* compose_hook() implementation
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*
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* @param object $du_dto
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* the CDM DerivedUnitDTO
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* @param bool $full_details
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* Currently unused,
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*
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* @return array
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* The render array for the DerivedUnitDTO
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*
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* @ingroup compose
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*/
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function compose_cdm_derived_unit_dto_storage_details($du_dto, $full_details = FALSE) {
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$table_row_data = sob_dto_details_rows($du_dto, $full_details);
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if (isset($du_dto->accessionNumber)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('accessionNumber'),
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$du_dto->accessionNumber);
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}
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if (isset($du_dto->collection)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('collection'),
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render_collection_dto($du_dto->collection));
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}
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if (isset($du_dto->storedUnder)) {
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$taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($du_dto->storedUnder->uuid));
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('storedUnder'),
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render_taxon_or_name($taxon_name, path_to_name($taxon_name->uuid)));
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}
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if (isset($du_dto->exsiccatum)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('exsiccatum'),
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$du_dto->exsiccatum);
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}
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if (isset($du_dto->catalogNumber)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('catalogNumber'),
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$du_dto->catalogNumber);
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}
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if (isset($du_dto->barcode)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('barcode'),
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$du_dto->barcode);
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}
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292
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if (isset($du_dto->preservationMethod)) {
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293
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('preservationMethod'),
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$du_dto->preservationMethod);
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}
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297
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298
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/* TODO
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300
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('medium'), $value->medium, NULL, 1);
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301
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('temperature'), $value->temperature, NULL, 2);
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@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('definedMaterialOrMethod'), $value->definedMaterialOrMethod, NULL, 3);
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*/
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if (isset_not_empty($du_dto->characterData)) {
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$table_row_data[] = cdm_sob_dto_table_row(
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cdm_occurrence_field_name_label('characterData'),
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icon_link(path_to_specimen($du_dto->uuid), '', FALSE), false);
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}
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310
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$heading = $table_row_data[0]['data'][1];
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unset($table_row_data[0]);
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return cdm_sob_dto_table(t($heading), $table_row_data, $du_dto, 1);
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}
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/**
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317
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* Compose an render array from a CDM GatheringDTO.
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318
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*
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319
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* The resulting DOM block level element will have a header line and details.
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320
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*
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321
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* compose_hook() implementation
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322
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*
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323
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* @param object $gathering_dto
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324
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* the CDM GatheringDTO object
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325
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* @param bool $full_details
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326
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* Currently unused,
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327
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*
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328
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* @return array
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329
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* The render array for the GatheringDTO
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330
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*
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331
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* @ingroup compose
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332
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*/
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333
|
function compose_cdm_gathering_dto_details($gathering_dto, $full_details = FALSE) {
|
|
334
|
|
|
335
|
$table_row_data = [];
|
|
336
|
if (isset_not_empty($gathering_dto->date)) {
|
|
337
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('date'),
|
|
338
|
partialToDate($gathering_dto->date));
|
|
339
|
}
|
|
340
|
if (isset_not_empty($gathering_dto->collector)) {
|
|
341
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('collector'),
|
|
342
|
$gathering_dto->collector);
|
|
343
|
}
|
|
344
|
if (isset_not_empty($gathering_dto->description)) {
|
|
345
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('description'),
|
|
346
|
$gathering_dto->description);
|
|
347
|
}
|
|
348
|
if (isset_not_empty($gathering_dto->locality)) {
|
|
349
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('locality'),
|
|
350
|
$gathering_dto->locality);
|
|
351
|
}
|
|
352
|
if (isset_not_empty($gathering_dto->country)) {
|
|
353
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('country'),
|
|
354
|
$gathering_dto->country);
|
|
355
|
}
|
|
356
|
if (isset_not_empty($gathering_dto->collectingMethod)) {
|
|
357
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('collectingMethod'),
|
|
358
|
$gathering_dto->collectingMethod);
|
|
359
|
}
|
|
360
|
if (isset($gathering_dto->exactLocation)) {
|
|
361
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('exactLocation'),
|
|
362
|
render_point($gathering_dto->exactLocation));
|
|
363
|
}
|
|
364
|
if (isset($gathering_dto->absoluteElevation)) {
|
|
365
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('absoluteElevation'),
|
|
366
|
statistical_values_from_gathering_event($gathering_dto, 'absoluteElevation'));
|
|
367
|
}
|
|
368
|
if (isset($gathering_dto->distanceToGround) && $gathering_dto->distanceToGround > 0) {
|
|
369
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('distanceToGround'),
|
|
370
|
statistical_values_from_gathering_event($gathering_dto, 'distanceToGround'));
|
|
371
|
}
|
|
372
|
if (isset($gathering_dto->distanceToWaterSurface) && $gathering_dto->distanceToWaterSurface > 0) {
|
|
373
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('distanceToWaterSurface'),
|
|
374
|
statistical_values_from_gathering_event($gathering_dto, 'distanceToWaterSurface'));
|
|
375
|
}
|
|
376
|
if (isset_not_empty($gathering_dto->collectingAreas)) {
|
|
377
|
$area_representations = [];
|
|
378
|
foreach ($gathering_dto->collectingAreas as $area) {
|
|
379
|
// $area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
|
380
|
$area_representations[] = $area;
|
|
381
|
}
|
|
382
|
if (!empty($area_representations)) {
|
|
383
|
$table_row_data[] = cdm_sob_dto_table_row(cdm_occurrence_field_name_label('collectingAreas'),
|
|
384
|
implode(', ', $area_representations)
|
|
385
|
);
|
|
386
|
}
|
|
387
|
}
|
|
388
|
|
|
389
|
return cdm_sob_dto_table(t("Gathering & Location"), $table_row_data, $gathering_dto, 1);
|
|
390
|
}
|
|
391
|
|
|
392
|
/**
|
|
393
|
* Compose an render array from the SpecimenOrObservationDTO.determinedNames.
|
|
394
|
*
|
|
395
|
* The resulting DOM block level element will have a header line and details.
|
|
396
|
*
|
|
397
|
* compose_hook() implementation
|
|
398
|
*
|
|
399
|
* @param object $sob_dto
|
|
400
|
* the CDM SpecimenOrObservationDTO
|
|
401
|
* @param bool $full_details
|
|
402
|
* Currently unused,
|
|
403
|
*
|
|
404
|
* @return array
|
|
405
|
* The render array for the SpecimenOrObservationDTO.determinedNames
|
|
406
|
*
|
|
407
|
* @ingroup compose
|
|
408
|
*/
|
|
409
|
function compose_cdm_sob_dto_determinations($sob_dto, $full_details = FALSE) {
|
|
410
|
|
|
411
|
$table_row_data = [];
|
|
412
|
|
|
413
|
foreach ($sob_dto->determinations as $det_event) {
|
|
414
|
// FIXME use $det_event->determination->taggedText instead of loading the entity
|
|
415
|
if($det_event->determination->type == "TaxonName") {
|
|
416
|
$link_path = path_to_name($det_event->determination->uuid);
|
|
417
|
$taxon_or_name = cdm_ws_get(CDM_WS_PORTAL_NAME, [$det_event->determination->uuid]);
|
|
418
|
} else {
|
|
419
|
$link_path = path_to_taxon($det_event->determination->uuid);
|
|
420
|
$taxon_or_name = cdm_ws_get(CDM_WS_PORTAL_TAXON, [$det_event->determination->uuid]);
|
|
421
|
}
|
|
422
|
$timeperiod_string = NULL;
|
|
423
|
if (isset($det_eventEvent->timeperiod)) {
|
|
424
|
$timeperiod_string = timePeriodToString($det_event->timeperiod);
|
|
425
|
}
|
|
426
|
$markup = $det_event->determination->taggedText;
|
|
427
|
if (isset($determinationEvent->modifier)) {
|
|
428
|
$markup .= cdm_term_representation($determinationEvent->modifier);
|
|
429
|
}
|
|
430
|
if ($timeperiod_string) {
|
|
431
|
$markup .= ' ' . $timeperiod_string;
|
|
432
|
}
|
|
433
|
if (isset($determinationEvent->actor->titleCache)) {
|
|
434
|
$markup .= ' ' . $determinationEvent->actor->titleCache;
|
|
435
|
}
|
|
436
|
// FXIME not yet supported by the DTO!
|
|
437
|
if (isset($determinationEvent->description)) {
|
|
438
|
$markup .= ' ' . $determinationEvent->description;
|
|
439
|
}
|
|
440
|
$row = cdm_sob_dto_table_row(NULL, render_taxon_or_name($taxon_or_name, $link_path));
|
|
441
|
$row['#weight'] = isset_numerical($det_event->isPreferred) ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
|
|
442
|
$table_row_data[] = $row;
|
|
443
|
}
|
|
444
|
|
|
445
|
$label = count($table_row_data) > 1 ? t("Identifications") : t("Identification");
|
|
446
|
return cdm_sob_dto_table($label, $table_row_data, $sob_dto, 1);
|
|
447
|
}
|
|
448
|
|
|
449
|
/**
|
|
450
|
* Compose an render array from the SpecimenOrObservationDTO.determinedNames.
|
|
451
|
*
|
|
452
|
* The resulting DOM block level element will have a header line and details.
|
|
453
|
*
|
|
454
|
* compose_hook() implementation
|
|
455
|
*
|
|
456
|
* @param \AnnotationsAndSources $annotations_and_sources
|
|
457
|
* see
|
|
458
|
*
|
|
459
|
* @return array
|
|
460
|
* The render array for the SpecimenOrObservationDTO.determinedNames
|
|
461
|
*
|
|
462
|
* @ingroup compose
|
|
463
|
*/
|
|
464
|
function compose_cdm_sob_dto_sources($sob_dto, $annotations_and_sources) {
|
|
465
|
|
|
466
|
$table_row_data = [];
|
|
467
|
|
|
468
|
foreach ($annotations_and_sources->getSourceReferences() as $source_ref) {
|
|
469
|
$table_row_data[] = cdm_sob_dto_table_row(NULL, $source_ref);
|
|
470
|
}
|
|
471
|
|
|
472
|
$label = count($table_row_data) > 1 ? t("Sources") : t("Source");
|
|
473
|
return cdm_sob_dto_table($label, $table_row_data, $sob_dto, 1);
|
|
474
|
}
|
|
475
|
|
|
476
|
/**
|
|
477
|
* @param $sob_dto
|
|
478
|
* @param \AnnotationsAndSources $annotations_and_sources
|
|
479
|
*
|
|
480
|
* @return array|null
|
|
481
|
*/
|
|
482
|
function compose_cdm_sob_dto_annotations($sob_dto, $annotations_and_sources) {
|
|
483
|
|
|
484
|
$table_row_data = [];
|
|
485
|
|
|
486
|
foreach ($annotations_and_sources->getAnnotations() as $annotation_text) {
|
|
487
|
$table_row_data[] = cdm_sob_dto_table_row(NULL, $annotation_text);
|
|
488
|
}
|
|
489
|
|
|
490
|
$label = count($table_row_data) > 1 ? t("Annotations") : t("Annotation");
|
|
491
|
return cdm_sob_dto_table($label, $table_row_data, $sob_dto, 1);
|
|
492
|
}
|
|
493
|
|
|
494
|
function compose_cdm_sob_dto_markers($sob_dto, $markers) {
|
|
495
|
|
|
496
|
$table_row_data = [];
|
|
497
|
foreach ($markers->records as $marker) {
|
|
498
|
$table_row_data[] = cdm_sob_dto_table_row($marker->markerType->representation_L10n, ($marker->flag !== TRUE ? t('yes') : t('no')));
|
|
499
|
}
|
|
500
|
|
|
501
|
$label = count($table_row_data) > 1 ? t("Markers") : t("Marker");
|
|
502
|
return cdm_sob_dto_table($label, $table_row_data, $sob_dto, 1);
|
|
503
|
}
|
|
504
|
|
|
505
|
/**
|
|
506
|
* Compose an render array from the DerivedUnitDTO.specimenTypeDesignations.
|
|
507
|
*
|
|
508
|
* The resulting DOM block level element will have a header line and details.
|
|
509
|
*
|
|
510
|
* compose_hook() implementation
|
|
511
|
*
|
|
512
|
* @param object $unit_dto
|
|
513
|
* the CDM DerivedUnitDTO
|
|
514
|
* @param bool $full_details
|
|
515
|
* Currently unused,
|
|
516
|
*
|
|
517
|
* @return array
|
|
518
|
* The render array for the SpecimenOrObservationDTO.determinedNames
|
|
519
|
*
|
|
520
|
* @ingroup compose
|
|
521
|
*/
|
|
522
|
function compose_cdm_unit_dto_type_designations($unit_dto, $full_details = FALSE) {
|
|
523
|
|
|
524
|
$table_row_data = [];
|
|
525
|
|
|
526
|
if (isset_not_empty($unit_dto->specimenTypeDesignations)) {
|
|
527
|
$table_row_data[] = cdm_sob_dto_table_row(
|
|
528
|
NULL,
|
|
529
|
render_specimen_typedesignation_dto($unit_dto->specimenTypeDesignations));
|
|
530
|
}
|
|
531
|
|
|
532
|
return cdm_sob_dto_table(t('Type designations'), $table_row_data, $unit_dto, 5, 2);
|
|
533
|
}
|
|
534
|
|
|
535
|
/**
|
|
536
|
* @param $listOfMedia
|
|
537
|
* @param $sob_dto
|
|
538
|
* @param $heading
|
|
539
|
*
|
|
540
|
* @return array|null
|
|
541
|
*/
|
|
542
|
function cdm_sob_dto_media_table(array $listOfMedia, $sob_dto, $heading) {
|
|
543
|
$table_row_data = [];
|
|
544
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
|
545
|
$captionElements = array(
|
|
546
|
'title',
|
|
547
|
'#uri' => t('open media'),
|
|
548
|
);
|
|
549
|
$gallery_markup = compose_cdm_media_gallerie(array(
|
|
550
|
'mediaList' => $listOfMedia,
|
|
551
|
'galleryName' => $sob_dto->uuid,
|
|
552
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
|
553
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
|
554
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
|
555
|
'captionElements' => $captionElements,
|
|
556
|
'mediaLinkType' => 'LIGHTBOX',
|
|
557
|
'alternativeMediaUri' => NULL,
|
|
558
|
'galleryLinkUri' => NULL,
|
|
559
|
'showCaption' => true
|
|
560
|
));
|
|
561
|
$table_row_data[] = cdm_sob_dto_table_row(NULL, $gallery_markup);
|
|
562
|
$grid_col_span = count($listOfMedia) > 1 ? 2 : NULL;
|
|
563
|
return cdm_sob_dto_table(t($heading), $table_row_data, $sob_dto, 20, $grid_col_span);
|
|
564
|
}
|
|
565
|
|
|
566
|
/**
|
|
567
|
* Compose an render array from the DerivedUnitDTO.sequences.
|
|
568
|
*
|
|
569
|
* The resulting DOM block level element will have a header line and details.
|
|
570
|
*
|
|
571
|
* compose_hook() implementation
|
|
572
|
*
|
|
573
|
* @param object $unit_dto
|
|
574
|
* the CDM DerivedUnitDTO
|
|
575
|
* @param bool $full_details
|
|
576
|
* Currently unused,
|
|
577
|
*
|
|
578
|
* @return array
|
|
579
|
* The render array for the DerivedUnitDTO.sequences.
|
|
580
|
*
|
|
581
|
* @ingroup compose
|
|
582
|
*
|
|
583
|
* TODO see #3347 (services and REST service controller for molecular classes implemented)
|
|
584
|
*/
|
|
585
|
function compose_cdm_derived_unit_dto_sequences($unit_dto, $full_details = FALSE) {
|
|
586
|
|
|
587
|
$table_row_data = [];
|
|
588
|
if(isset_not_empty($unit_dto->sequences)){
|
|
589
|
foreach ($unit_dto->sequences as $sequence) {
|
|
590
|
if (isset($sequence->geneticAccessionNumber)) {
|
|
591
|
$table_row_data[] = cdm_sob_dto_table_row(
|
|
592
|
cdm_occurrence_field_name_label('geneticAccessionNumber'),
|
|
593
|
$sequence->geneticAccessionNumber);
|
|
594
|
}
|
|
595
|
// TODO ....
|
|
596
|
}
|
|
597
|
}
|
|
598
|
|
|
599
|
/* TODO
|
|
600
|
case 'dnaQuality':
|
|
601
|
$sub_dl_groups = array();
|
|
602
|
|
|
603
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('purificationMethod'), $value->purificationMethod, NULL, 1);
|
|
604
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('ratioOfAbsorbance260_230'), $value->ratioOfAbsorbance260_230, NULL, 2);
|
|
605
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('ratioOfAbsorbance260_280'), $value->ratioOfAbsorbance260_280, NULL, 3);
|
|
606
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('concentration'), $value->concentration, NULL, 4);
|
|
607
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('concentrationUnit'), $value->concentrationUnit, NULL, 4);
|
|
608
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('qualityTerm'), $value->qualityTerm, NULL, 4);
|
|
609
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('qualityCheckDate'), $value->qualityCheckDate, NULL, 4);
|
|
610
|
|
|
611
|
if (is_array($sub_dl_groups) && sizeof($sub_dl_groups)>0) {
|
|
612
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
613
|
array(
|
|
614
|
array('#markup' => $value->titleCache),
|
|
615
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
616
|
)
|
|
617
|
);
|
|
618
|
}
|
|
619
|
break;
|
|
620
|
*/
|
|
621
|
|
|
622
|
return cdm_sob_dto_table(t('Storage'), $table_row_data, $unit_dto, 1);
|
|
623
|
}
|
|
624
|
|
|
625
|
/**
|
|
626
|
* Creates a form array for showing details of SpecimenOrObservationDTO in a
|
|
627
|
* tabular form with heading.
|
|
628
|
*
|
|
629
|
* @param $table_heading
|
|
630
|
* @param array $table_row_data
|
|
631
|
* @param $sob_dto
|
|
632
|
* @param $weight
|
|
633
|
* The weight determining the order of the drupal render element
|
|
634
|
* @param $grid_col_span
|
|
635
|
* The number of grid colums the table should
|
|
636
|
*
|
|
637
|
* @return array|null
|
|
638
|
*/
|
|
639
|
function cdm_sob_dto_table($table_heading, array $table_row_data, $sob_dto, $weight = NULL, $grid_col_span = 1) {
|
|
640
|
|
|
641
|
if (count($table_row_data) > 0) {
|
|
642
|
$wrapper_style = '';
|
|
643
|
if($grid_col_span > 1){
|
|
644
|
$wrapper_style = ' style="grid-column-start: span ' . $grid_col_span. ';"';
|
|
645
|
}
|
|
646
|
$sob_table = [
|
|
647
|
'#theme' => 'table',
|
|
648
|
'#prefix' => '<div class="table-wrapper"' . $wrapper_style . '>',
|
|
649
|
'#suffix' => '</div>',
|
|
650
|
'#header' => [
|
|
651
|
[
|
|
652
|
'data' => $table_heading,
|
|
653
|
'colspan' => 2,
|
|
654
|
],
|
|
655
|
],
|
|
656
|
"#rows" => $table_row_data,
|
|
657
|
"#attributes" => [
|
|
658
|
"class" => [
|
|
659
|
'details-table',
|
|
660
|
'details-table-' . normalize_to_class_attribute($table_heading),
|
|
661
|
html_class_attribute_ref($sob_dto)
|
|
662
|
],
|
|
663
|
],
|
|
664
|
];
|
|
665
|
if ($weight) {
|
|
666
|
$sob_table['#weight'] = $weight;
|
|
667
|
}
|
|
668
|
return $sob_table;
|
|
669
|
}
|
|
670
|
return NULL;
|
|
671
|
}
|
|
672
|
|
|
673
|
function cdm_sob_dto_table_row($label, $value) {
|
|
674
|
if ($value) {
|
|
675
|
if($label) {
|
|
676
|
return [
|
|
677
|
'data' => [
|
|
678
|
[
|
|
679
|
'data' => str_replace(':', '', $label),
|
|
680
|
'class' => [
|
|
681
|
'label',
|
|
682
|
],
|
|
683
|
],
|
|
684
|
$value,
|
|
685
|
],
|
|
686
|
'no_striping' => TRUE,
|
|
687
|
];
|
|
688
|
} else {
|
|
689
|
// value spanning two columns
|
|
690
|
return [
|
|
691
|
'data' => [
|
|
692
|
[
|
|
693
|
'data' => $value,
|
|
694
|
'colspan' => 2,
|
|
695
|
]
|
|
696
|
],
|
|
697
|
'no_striping' => TRUE,
|
|
698
|
];
|
|
699
|
}
|
|
700
|
}
|
|
701
|
return NULL;
|
|
702
|
}
|
|
703
|
|
|
704
|
|
|
705
|
|
|
706
|
/**
|
|
707
|
* Compose an render array from a CDD SpecimenOrObservation entity.
|
|
708
|
*
|
|
709
|
* compose_hook() implementation
|
|
710
|
*
|
|
711
|
* @param object $sob_dto
|
|
712
|
* the CDM FieldUnit or DerivedUnit to compose
|
|
713
|
* the render array for.
|
|
714
|
*
|
|
715
|
* @return array
|
|
716
|
* the supplied render array $derivatives to which the composition of the supplied
|
|
717
|
* $specimenOrObservation has been added to
|
|
718
|
*
|
|
719
|
* @ingroup compose
|
|
720
|
*/
|
|
721
|
function compose_cdm_specimen_or_observation_new($sob_dto)
|
|
722
|
{
|
|
723
|
|
|
724
|
$render_array = [];
|
|
725
|
if (is_object($sob_dto)) {
|
|
726
|
|
|
727
|
/*** 95% no longer needed
|
|
728
|
if ($sob_dto->class == 'FieldUnit'){
|
|
729
|
// WARNING: adding a List<MediaDTO> as $specimen_or_observation->_derivedUnitMedia
|
|
730
|
$sob_dto->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
|
|
731
|
$sob_dto->uuid,
|
|
732
|
'fieldObjectMediaDTO',
|
|
733
|
));
|
|
734
|
}else{
|
|
735
|
// WARNING: adding a List<Media> as $specimen_or_observation->_derivedUnitMedia
|
|
736
|
$sob_dto->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
|
|
737
|
$sob_dto->uuid,
|
|
738
|
'derivedUnitMedia',
|
|
739
|
));
|
|
740
|
}
|
|
741
|
******/
|
|
742
|
|
|
743
|
RenderHints::pushToRenderStack('specimen_or_observation');
|
|
744
|
$footnote_list_key = $sob_dto->type . '-' . $sob_dto->uuid;
|
|
745
|
RenderHints::setFootnoteListKey($footnote_list_key);
|
|
746
|
|
|
747
|
$render_array['sob_details_grid'] = [
|
|
748
|
'#type' => 'container',
|
|
749
|
'#attributes' => [
|
|
750
|
'class' => 'derived-unit-details-grid'
|
|
751
|
],
|
|
752
|
'children' => compose_cdm_specimen_or_observation_dto_details_grid($sob_dto, true)
|
|
753
|
];;
|
|
754
|
|
|
755
|
$derivation_tree_roots = cdm_ws_get(CDM_WS_OCCURRENCE_FIELD_UNIT_DTOS, [$sob_dto->uuid]);
|
|
756
|
$render_array['derivation_tree_header'] = markup_to_render_array("<h3>Derivation tree</h3>");
|
|
757
|
$derivationTreeComposer = new DerivationTreeComposer($derivation_tree_roots);
|
|
758
|
$derivationTreeComposer->setWithDetails(false);
|
|
759
|
$derivationTreeComposer->setFocusedUnitUuid($sob_dto->uuid);
|
|
760
|
$render_array['derivation_tree'] = $derivationTreeComposer->compose();
|
|
761
|
|
|
762
|
/* TODO
|
|
763
|
case 'definition':
|
|
764
|
|
|
765
|
case 'annotations':
|
|
766
|
$dd_elements = array();
|
|
767
|
foreach ($value as $annotation) {
|
|
768
|
// TODO respect annotation type filter settings
|
|
769
|
$dd_elements[] = $annotation->text;
|
|
770
|
}
|
|
771
|
break;
|
|
772
|
|
|
773
|
|
|
774
|
|
|
775
|
/** TODO
|
|
776
|
|
|
777
|
|
|
778
|
case 'determinations':
|
|
779
|
$dd_elements = array();
|
|
780
|
$glue = ', ';
|
|
781
|
|
|
782
|
foreach ($value as $determinationEvent) {
|
|
783
|
|
|
784
|
break;
|
|
785
|
*/
|
|
786
|
|
|
787
|
/* TODO Extensions
|
|
788
|
// TODO: filter by using visible_extensions_sorted()
|
|
789
|
// TODO: treat as top level element, see https://dev.e-taxonomy.eu/redmine/issues/2985#note-23
|
|
790
|
$extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $sob_dto->uuid . '/extensions', array($sob_dto->uuid));
|
|
791
|
if ($extensions && count($extensions)) {
|
|
792
|
|
|
793
|
$extensions_render_array = compose_extensions($extensions);
|
|
794
|
@_description_list_group_add($groups, t('Extensions') . ':',
|
|
795
|
$extensions_render_array,
|
|
796
|
'', 100);
|
|
797
|
}
|
|
798
|
*/
|
|
799
|
|
|
800
|
$render_array['footnotes'] = markup_to_render_array(render_footnotes($footnote_list_key));
|
|
801
|
|
|
802
|
|
|
803
|
} // END of $specimenOrObservation exists
|
|
804
|
|
|
805
|
return $render_array;
|
|
806
|
}
|
|
807
|
|