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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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*
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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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* Provides the HTML markup for a specimen page
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*
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* @param $specimen
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*
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* @return string
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* The markup for a specimen page
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*/
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function render_cdm_specimen_page($specimen, $is_specimen_page = false)
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{
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$detail_html = "";
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//link to specimen page
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$pathToSpecimen = path_to_specimen($specimen->uuid);
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if (!$is_specimen_page) {
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$specimenPageLink = l($specimen->accessionNumber, $pathToSpecimen, array('attributes' => array('target' => '_blank')));
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$detail_html .= "<strong>$specimenPageLink</strong><br>";
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}
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if($is_specimen_page) {
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if($specimen->citation){
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$detail_html .= "<br>".create_label("Citation") . $specimen->citation . "<br>";
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}
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}
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if($specimen->preferredStableUri){
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$stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri, array('attributes' => array('target' => '_blank')));
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$detail_html .= "<br>".create_label("Preferred stable URI") . $stableIdentifierLink . "<br>";
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}
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if($is_specimen_page){
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// associated taxa
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if($specimen->associatedTaxa){
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$detail_html .= "<br>";
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$detail_html .= create_label("Associated with");
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if(sizeof($specimen->associatedTaxa)>1){
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$detail_html .= "<br>";
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}
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foreach($specimen->associatedTaxa as $associatedTaxon){
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$detail_html .= l($associatedTaxon->second, path_to_taxon($associatedTaxon->first, "specimens"));//$associatedTaxon->second."<br>";
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}
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$detail_html .= "<br>";
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}
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}
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// - type information
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$types = "";
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if (isset($specimen->types)) {
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//typed taxa
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if(sizeof($specimen->types)>1){
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$detail_html .= "<br>";
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}
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foreach ($specimen->types as $typeStatus => $typedTaxa) {
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if($is_specimen_page){
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if($specimen->types){
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$detail_html .= "<i>".$typeStatus."</i>: ";
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foreach($typedTaxa as $typedTaxon){
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$detail_html .= $typedTaxon." ";
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}
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$detail_html .= "<br>";
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}
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}
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else{
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$types .= $typeStatus." ";
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}
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}
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}
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$derivateDataDTO = $specimen->derivateDataDTO;
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// - specimen scans
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$specimenScans = create_html_links($derivateDataDTO->specimenScans, true);
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// - molecular data
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$molecularData = "";
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if ($derivateDataDTO->molecularDataList) {
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foreach ($derivateDataDTO->molecularDataList as $molecular) {
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//provider link
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if (isset($molecular->providerLink)) {
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$molecularData .= create_html_link($molecular->providerLink, true);
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} else {
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$molecularData .= "[no provider]";
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}
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//contig link
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if (isset($molecular->contigFiles)) {
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$molecularData .= "[";
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if (sizeof($molecular->contigFiles) > 0) {
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foreach ($molecular->contigFiles as $contigFile) {
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if (isset($contigFile->contigLink)) {
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if (isset($contigFile->contigLink->uri) and $contigFile->contigLink->uri != null) {
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$molecularData .= create_html_link($contigFile->contigLink, true) . " ";
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}
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}
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else {
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$molecularData .= "no contig ";
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}
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//primer links
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if(isset($contigFile->primerLinks)) {
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$molecularData .= create_html_links($contigFile->primerLinks, true);
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}
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}
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}
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$molecularData = rtrim($molecularData, " ");
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$molecularData .= "]";
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}
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//FIXME separate with comma (remove trailing comma)
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}
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}
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// - detail images
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$detailImages = create_html_links($derivateDataDTO->detailImages, true);
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if ($types) {
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$detail_html .= $is_specimen_page?"<br>":"";
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$detail_html .= create_label("Type(s)") . $types . "<br>";
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}
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if ($specimenScans and !$is_specimen_page) {
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$detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
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}
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//specimen scan image gallery
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if($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
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$detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
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}
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if ($molecularData) {
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$detail_html .= $is_specimen_page?"<br>":"";
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$detail_html .= create_label("Molecular Data") . $molecularData . "<br>";
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}
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if ($detailImages and !$is_specimen_page) {
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$detail_html .= create_label("Detail Images") . $detailImages . "<br>";
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}
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//detail image gallery
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if($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)){
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$detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
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}
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//character data
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if ($specimen->characterData) {
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$detail_html .= $is_specimen_page?"<br>":"";
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$detail_html .= create_label("Character Data");
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if($is_specimen_page) {
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$detail_html .= "<br>";
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foreach ($specimen->characterData as $characterStatePair) {
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$detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second;
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$detail_html .= "<br>";
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}
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}
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else{
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$detail_html .= l("detail page", $pathToSpecimen,array('attributes' => array('target'=>'_blank')));
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$detail_html .= "<br>";
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}
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}
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return $detail_html;
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}
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function addImageGallery($galleryName, $imageUuids){
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$images = array();
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foreach ($imageUuids as $uuid) {
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$images[] = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $uuid);
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}
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$gallery_html = '';
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if (count($imageUuids) > 0) {
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$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
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$captionElements = array(
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'title',
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'rights',
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);
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$alternativeMediaUris = array();
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foreach($images as $image){
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$mediaUri = getMediaUri($image);
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if($mediaUri){
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$alternativeMediaUris[] = $mediaUri;
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}
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else{
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$alternativeMediaUris[] = path_to_media($image->uuid);
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}
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}
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$gallery_html = compose_cdm_media_gallerie(array(
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'mediaList' => $images,
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'galleryName' => $galleryName,
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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' => $alternativeMediaUris,
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'galleryLinkUri' => NULL,
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));
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}
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return "<br>".create_label($galleryName)."<br>".$gallery_html;
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}
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function getMediaUri($media){
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if(isset($media->representations) && sizeof($media->representations)==1
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&& isset($media->representations[0]->parts) &&
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sizeof($media->representations[0]->parts)==1) {
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return $media->representations[0]->parts[0]->uri;
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}
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return null;
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}
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/**
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* Formats the given string to a label for displaying key-object pairs in HTML
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* @return string
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*/
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function create_label($label)
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{
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return "<span class='specimen_table_label'>".$label.": </span>";
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}
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/**
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* Compose an render array from a CDM DerivedUnitFacade object.
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*
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* compose_hook() implementation
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*
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* @param object $specimenOrObservation
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* the CDM instance of type SpecimenOrObservation to compose
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* the render array for
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* @param array $derivatives
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* the render array which contains the compositions of the derivatives
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* of the supplied $specimenOrObservation
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*
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* @return array
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* the supplied render array $derivatives to which the composition of the supplied
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* $specimenOrObservation has been added to
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*
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* @ingroup compose
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*/
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function compose_cdm_specimenOrObservation($specimenOrObservation, &$derivatives = null) {
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$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
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if (!isset($exclude_occurrence_fields)) {
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$exclude_occurrence_fields = array(
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'derivationEvents',
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'titleCache',
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'protectedTitleCache',
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'derivedUnitMedia',
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'created',
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'publish',
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'updated',
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'class',
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'uuid',
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''
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);
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}
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// only show uuid it the user is logged in
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if(user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE ) {
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unset($exclude_occurrence_fields[$a_idx]);
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}
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if (!isset($derivatives)) {
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$derivatives = array();
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}
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$descriptions = null;
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$derivedFrom = null;
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if (is_object($specimenOrObservation)) {
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// request again for deeper initialization
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$specimenOrObservation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);
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$type_label = $specimenOrObservation->class;
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RenderHints::setFootnoteListKey($type_label . '-' . $specimenOrObservation->uuid);
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// collect typeStatus as label
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if (isset($specimenOrObservation->specimenTypeDesignations)) {
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$type_status = array();
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foreach ($specimenOrObservation->specimenTypeDesignations as $typeDesignation) {
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if (isset($typeDesignation->typeStatus->representation_L10n)) {
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$type_status[] = $typeDesignation->typeStatus->representation_L10n;
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}
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}
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if (count($type_status) > 0) {
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$type_label = implode(', ', $type_status);
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}
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}
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$title = $type_label . ': ' . $specimenOrObservation->titleCache;
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$groups = array();
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// --- add initialized fields
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foreach (get_object_vars($specimenOrObservation) as $field => $value) {
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if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
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switch ($field) {
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305
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/* ---- java.lang.Object --- */
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case 'class':
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if ($value != '' /* FieldUnit' */) {
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
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}
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break;
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312
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case 'markers':
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$dd_elements = array();
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foreach ($value as $marker) {
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$dd_elements[] = compose_cdm_marker($marker);
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}
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
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break;
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320
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321
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case 'annotations':
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$dd_elements = array();
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324
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foreach ($value as $annotation) {
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// TODO respect annotation type filter settings
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$dd_elements[] = $annotation->text;
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}
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@_description_list_group_add($groups, t('Notes'), $dd_elements);
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break;
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330
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331
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/* ---- SpecimenOrObservationBase --- */
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case 'sex':
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case 'lifeStage':
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case 'kindOfUnit':
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n);
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break;
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case 'definition':
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339
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// TODO
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break;
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341
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342
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case 'preferredStableUri':
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343
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@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
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break;
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346
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347
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case 'specimenTypeDesignations':
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@_description_list_group_add(
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$groups,
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cdm_occurrence_field_name_label($field),
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351
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array(
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'#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
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)
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);
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break;
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356
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357
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case 'determinations':
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$dd_elements = array();
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359
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$glue = ', ';
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360
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361
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foreach ($value as $determinationEvent) {
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362
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$timeperiod_string = NULL;
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363
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if (isset($determinationEvent->timeperiod)) {
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$timeperiod_string = timePeriodToString($determinationEvent->timeperiod);
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365
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}
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366
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$weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
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367
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// check key exists
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368
|
while (array_key_exists($weight, $dd_elements)) {
|
|
369
|
$weight .= '0';
|
|
370
|
}
|
|
371
|
|
|
372
|
$taxon_name = '';
|
|
373
|
$name_link = '';
|
|
374
|
if ($determinationEvent->taxonName) {
|
|
375
|
$taxon_name = $determinationEvent->taxonName;
|
|
376
|
} else if ($determinationEvent->taxon) {
|
|
377
|
$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
|
|
378
|
$name_link = path_to_taxon($determinationEvent->taxon->uuid);
|
|
379
|
}
|
|
380
|
if ($taxon_name) {
|
|
381
|
$taxon_html = render_taxon_or_name($taxon_name, $name_link);
|
|
382
|
$dd_elements[$weight] = $taxon_html;
|
|
383
|
}
|
|
384
|
if (isset($determinationEvent->modifier)) {
|
|
385
|
$dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
|
|
386
|
}
|
|
387
|
if ($timeperiod_string) {
|
|
388
|
$dd_elements[$weight] .= $glue . $timeperiod_string;
|
|
389
|
}
|
|
390
|
if (isset($determinationEvent->actor->titleCache)) {
|
|
391
|
$dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
|
|
392
|
}
|
|
393
|
if (isset($determinationEvent->description)) {
|
|
394
|
$dd_elements[$weight] .= $glue . $determinationEvent->description;
|
|
395
|
}
|
|
396
|
}
|
|
397
|
ksort($dd_elements);
|
|
398
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
|
|
399
|
break;
|
|
400
|
|
|
401
|
case 'descriptions':
|
|
402
|
$occurrence_featureTree = cdm_get_occurrence_featureTree();
|
|
403
|
$dd_elements = array();
|
|
404
|
|
|
405
|
foreach ($value as $description) {
|
|
406
|
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
|
|
407
|
// if($description->imageGallery == TRUE) {
|
|
408
|
// continue;
|
|
409
|
// }
|
|
410
|
$elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements);
|
|
411
|
$description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null));
|
|
412
|
$dd_elements[] = $description_render_elements;
|
|
413
|
}
|
|
414
|
|
|
415
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
|
416
|
break;
|
|
417
|
|
|
418
|
case 'sources':
|
|
419
|
$dd_elements = array();
|
|
420
|
foreach ($value as $identifiable_source) {
|
|
421
|
$dd_elements[] = theme('cdm_OriginalSource', array('source' => $identifiable_source));
|
|
422
|
}
|
|
423
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
|
424
|
break;
|
|
425
|
|
|
426
|
|
|
427
|
/* ---- DerivedUnitBase --- */
|
|
428
|
case 'derivedFrom':
|
|
429
|
$derivedFrom = $value;
|
|
430
|
break;
|
|
431
|
|
|
432
|
case 'collection':
|
|
433
|
$sub_dl_groups = array();
|
|
434
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
|
435
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
|
436
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
|
437
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
|
438
|
// TODO "superCollection"
|
|
439
|
// TODO may have media
|
|
440
|
|
|
441
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
442
|
array(
|
|
443
|
array('#markup' => $value->titleCache),
|
|
444
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
445
|
)
|
|
446
|
);
|
|
447
|
break;
|
|
448
|
|
|
449
|
case 'storedUnder':
|
|
450
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
|
|
451
|
break;
|
|
452
|
|
|
453
|
|
|
454
|
/* ---- Specimen --- */
|
|
455
|
case 'sequences':
|
|
456
|
$dd_elements = array();
|
|
457
|
foreach ($value as $sequence) {
|
|
458
|
$dd_elements[] = compose_cdm_sequence($sequence);
|
|
459
|
}
|
|
460
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
|
461
|
break;
|
|
462
|
|
|
463
|
// TODO preservation
|
|
464
|
// TODO exsiccatum
|
|
465
|
|
|
466
|
|
|
467
|
/* ---- FieldObservation --- */
|
|
468
|
case 'gatheringEvent':
|
|
469
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache);
|
|
470
|
@_description_list_group_add($groups, t('Gathering time'), timePeriodToString($value->timeperiod));
|
|
471
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
|
|
472
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text);
|
|
473
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n);
|
|
474
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
|
|
475
|
if (isset($value->absoluteElevation)) {
|
|
476
|
$min_max_markup = min_max_measure($value, 'absoluteElevation');
|
|
477
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
|
|
478
|
}
|
|
479
|
if (isset($value->distanceToGround)) {
|
|
480
|
$min_max_markup = min_max_measure($value, 'distanceToGround');
|
|
481
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
|
|
482
|
}
|
|
483
|
if (isset($value->distanceToWaterSurface)) {
|
|
484
|
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface');
|
|
485
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
|
|
486
|
}
|
|
487
|
|
|
488
|
if (isset($value->collectingAreas)) {
|
|
489
|
$area_representations = array();
|
|
490
|
foreach ($value->collectingAreas as $area) {
|
|
491
|
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
|
492
|
}
|
|
493
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
|
494
|
array(
|
|
495
|
array('#markup' => implode(', ', $area_representations))
|
|
496
|
)
|
|
497
|
);
|
|
498
|
}
|
|
499
|
if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
|
|
500
|
$sub_dl_groups = array();
|
|
501
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
|
502
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
|
503
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
|
504
|
if (isset($value->exactLocation->referenceSystem)) {
|
|
505
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
|
506
|
}
|
|
507
|
|
|
508
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
|
509
|
array(
|
|
510
|
array('#markup' => $value->exactLocation->sexagesimalString),
|
|
511
|
array(
|
|
512
|
'#theme' => 'description_list',
|
|
513
|
'#groups' => $sub_dl_groups
|
|
514
|
),
|
|
515
|
)
|
|
516
|
);
|
|
517
|
}
|
|
518
|
break;
|
|
519
|
|
|
520
|
default:
|
|
521
|
if (is_object($value) || is_array($value)) {
|
|
522
|
drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
|
|
523
|
} else {
|
|
524
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
|
525
|
}
|
|
526
|
|
|
527
|
}
|
|
528
|
|
|
529
|
}
|
|
530
|
} // END of loop over $derivedUnitFacade fields
|
|
531
|
|
|
532
|
// Extensions
|
|
533
|
$extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $specimenOrObservation->uuid . '/extensions', array($specimenOrObservation->uuid));
|
|
534
|
if ($extensions && count($extensions)) {
|
|
535
|
|
|
536
|
$extensions_render_array = compose_extensions($extensions);
|
|
537
|
@_description_list_group_add($groups, t('Extensions') . ':',
|
|
538
|
$extensions_render_array,
|
|
539
|
'', 100);
|
|
540
|
}
|
|
541
|
|
|
542
|
|
|
543
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
|
544
|
uasort($groups, 'element_sort');
|
|
545
|
|
|
546
|
$occurrence_elements = array(
|
|
547
|
'#title' => $title,
|
|
548
|
'#theme' => 'description_list',
|
|
549
|
'#groups' => $groups,
|
|
550
|
'#attributes' => array('class' => html_class_attribute_ref($specimenOrObservation)),
|
|
551
|
);
|
|
552
|
$derivatives[] = $occurrence_elements;
|
|
553
|
// all footnotes which has been assembled so far (e.g. from typeDesignations) to here
|
|
554
|
$foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
|
|
555
|
if (!empty($foonote_li_elements)) {
|
|
556
|
$derivatives[] = array(
|
|
557
|
'#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>',
|
|
558
|
);
|
|
559
|
}
|
|
560
|
|
|
561
|
// --- recurse into originals
|
|
562
|
if (!isset($derivedFrom)) {
|
|
563
|
$derivedFrom = cdm_ws_get(
|
|
564
|
CDM_WS_OCCURRENCE,
|
|
565
|
array($specimenOrObservation->uuid, 'derivedFrom')
|
|
566
|
);
|
|
567
|
}
|
|
568
|
|
|
569
|
if (isset($derivedFrom)) {
|
|
570
|
if (isset($derivedFrom->originals)) {
|
|
571
|
$derived_from_label = t('derived');
|
|
572
|
$preposition = t('from');
|
|
573
|
if(isset($derivedFrom->type)){
|
|
574
|
$derived_from_label = $derivedFrom->type->representation_L10n;
|
|
575
|
if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
|
|
576
|
$preposition = t('of');
|
|
577
|
}
|
|
578
|
}
|
|
579
|
if (count($groups) > 0) {
|
|
580
|
// TODO annotations
|
|
581
|
|
|
582
|
// only display the derived from information when the derivative has any element which will be diplayed
|
|
583
|
$derivatives[] = array(
|
|
584
|
'#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>',
|
|
585
|
);
|
|
586
|
}
|
|
587
|
foreach ($derivedFrom->originals as $original) {
|
|
588
|
compose_cdm_specimenOrObservation($original, $derivatives);
|
|
589
|
}
|
|
590
|
}
|
|
591
|
}
|
|
592
|
|
|
593
|
} // END of $specimenOrObservation exists
|
|
594
|
|
|
595
|
return $derivatives;
|
|
596
|
}
|
|
597
|
|
|
598
|
|
|
599
|
/**
|
|
600
|
* Compose an render array from a CDM Sequence object.
|
|
601
|
*
|
|
602
|
* compose_hook() implementation
|
|
603
|
*
|
|
604
|
* @param object $sequence
|
|
605
|
* CDM instance of type Sequence
|
|
606
|
* @return array
|
|
607
|
* A render array containing the fields of the supplied $sequence
|
|
608
|
*
|
|
609
|
* @ingroup compose
|
|
610
|
*/
|
|
611
|
function compose_cdm_sequence($sequence) {
|
|
612
|
|
|
613
|
$exclude_sequence_fields = &drupal_static(__FUNCTION__);
|
|
614
|
if (!isset($exclude_sequence_fields)) {
|
|
615
|
$exclude_sequence_fields = array(
|
|
616
|
'titleCache',
|
|
617
|
'protectedTitleCache',
|
|
618
|
'microReference',
|
|
619
|
'created',
|
|
620
|
'updated',
|
|
621
|
'class',
|
|
622
|
);
|
|
623
|
}
|
|
624
|
|
|
625
|
$groups = array();
|
|
626
|
|
|
627
|
// -- retrieve additional data if neesscary
|
|
628
|
// TODO below call disabled since sequences are not yet supported,
|
|
629
|
// see #3347 (services and REST service controller for molecular classes implemented)
|
|
630
|
//
|
|
631
|
// cdm_load_annotations($sequence);
|
|
632
|
|
|
633
|
foreach (get_object_vars($sequence) as $field => $value) {
|
|
634
|
|
|
635
|
|
|
636
|
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
|
637
|
switch ($field) {
|
|
638
|
|
|
639
|
case 'geneticAccessionNumber';
|
|
640
|
$dd_elements = array();
|
|
641
|
foreach ($value as $accession) {
|
|
642
|
if (isset($accession->uri) ){
|
|
643
|
$dd_elements[] = l($accession->accessionNumber, $accession->uri);
|
|
644
|
} else {
|
|
645
|
$dd_elements[] = $accession->accessionNumber;
|
|
646
|
}
|
|
647
|
}
|
|
648
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 1);
|
|
649
|
break;
|
|
650
|
|
|
651
|
|
|
652
|
case 'locus': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
|
|
653
|
if (isset($value->name)) {
|
|
654
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3);
|
|
655
|
}
|
|
656
|
if (isset($value->description)) {
|
|
657
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description') , $value->description, NULL, 4);
|
|
658
|
}
|
|
659
|
break;
|
|
660
|
|
|
661
|
case 'consensusSequence':
|
|
662
|
// format in genbank style, force linebreaks after each 70 nucleotites
|
|
663
|
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
|
|
664
|
@_description_list_group_add(
|
|
665
|
$groups,
|
|
666
|
cdm_occurrence_field_name_label($field),
|
|
667
|
array(
|
|
668
|
array(
|
|
669
|
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb'). '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
|
670
|
'#wrapper_attributes' => array('class'=>'dna-sequence')
|
|
671
|
)
|
|
672
|
),
|
|
673
|
5);
|
|
674
|
break;
|
|
675
|
|
|
676
|
case 'dnaSample': // FIXME 3.3 implement
|
|
677
|
break;
|
|
678
|
case 'singleReads': // FIXME 3.3 implement
|
|
679
|
break;
|
|
680
|
case 'contigFile': // FIXME 3.3 implement - Media
|
|
681
|
break;
|
|
682
|
case 'pherograms': // FIXME 3.3 implement - Media
|
|
683
|
break;
|
|
684
|
case 'haplotype': // FIXME 3.3 implement
|
|
685
|
break;
|
|
686
|
case 'dateSequenced': // FIXME 3.3 now in SingelRead
|
|
687
|
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
|
688
|
break;
|
|
689
|
|
|
690
|
case 'barcode': // boolean
|
|
691
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes': 'No', NULL, 7);
|
|
692
|
break;
|
|
693
|
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
|
|
694
|
break;
|
|
695
|
|
|
696
|
case 'citation':
|
|
697
|
@_description_list_group_add($groups,
|
|
698
|
cdm_occurrence_field_name_label($field),
|
|
699
|
theme('cdm_reference', array('reference' =>$value, 'microReference' => $sequence->microReference)),
|
|
700
|
NULL,
|
|
701
|
8
|
|
702
|
);
|
|
703
|
break;
|
|
704
|
|
|
705
|
case 'publishedIn':
|
|
706
|
@_description_list_group_add($groups,
|
|
707
|
cdm_occurrence_field_name_label($field),
|
|
708
|
theme('cdm_reference', array('reference'=>$value)),
|
|
709
|
NULL,
|
|
710
|
7
|
|
711
|
);
|
|
712
|
break;
|
|
713
|
|
|
714
|
case 'rights':
|
|
715
|
array_merge($groups, cdm_rights_as_dl_groups($value));
|
|
716
|
break;
|
|
717
|
|
|
718
|
case 'annotations':
|
|
719
|
$dd_elements = array();
|
|
720
|
foreach ($value as $annotation) {
|
|
721
|
// TODO respect annotation type filter settings
|
|
722
|
$dd_elements[] = $annotation->text;
|
|
723
|
}
|
|
724
|
@_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
|
|
725
|
break;
|
|
726
|
|
|
727
|
case 'markers':
|
|
728
|
$dd_elements = array();
|
|
729
|
foreach ($value as $marker) {
|
|
730
|
$dd_elements[] = compose_cdm_marker($marker);
|
|
731
|
}
|
|
732
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
|
|
733
|
break;
|
|
734
|
|
|
735
|
case 'chromatograms':
|
|
736
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
737
|
array(
|
|
738
|
'#markup'=>compose_cdm_media_gallerie(array('medialist'=>$value)),
|
|
739
|
),
|
|
740
|
NULL,
|
|
741
|
11);
|
|
742
|
break;
|
|
743
|
|
|
744
|
default:
|
|
745
|
if(is_object($value) || is_array($value)){
|
|
746
|
drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
|
|
747
|
} else {
|
|
748
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
|
|
749
|
}
|
|
750
|
}
|
|
751
|
}
|
|
752
|
}
|
|
753
|
|
|
754
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
|
755
|
uasort($groups, 'element_sort');
|
|
756
|
|
|
757
|
$sequence_elements = array(
|
|
758
|
'#theme' => 'description_list',
|
|
759
|
'#groups' => $groups
|
|
760
|
);
|
|
761
|
|
|
762
|
return $sequence_elements;
|
|
763
|
}
|
|
764
|
|
|
765
|
|