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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)
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{
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$specimen_details = compose_cdm_specimen_or_observation($specimen, true);
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//$detail_html .= drupal_render($specimen_details);
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$specimen->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
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$specimen->uuid,
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'fieldObjectMediaDTO',
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));
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$specimen->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
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$specimen->uuid,
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'derivedUnitMedia',
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));
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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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'#uri' => t('open media'),
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);
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if (isset($specimen->fieldObjectMediaDTO) ) {
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$gallery_html = compose_cdm_media_gallerie(array(
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'mediaList' => $specimen->fieldObjectMediaDTO,
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'galleryName' => $specimen->titleCache,
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'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
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'cols' => $gallery_settings['cdm_dataportal_media_cols'],
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'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
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'captionElements' => $captionElements,
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'mediaLinkType' => 'LIGHTBOX',
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'alternativeMediaUri' => NULL,
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'galleryLinkUri' => NULL,
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));
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$specimen_details[] = markup_to_render_array($gallery_html);
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}
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if (isset($specimen->_derivedUnitMedia) ) {
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$gallery_html = compose_cdm_media_gallerie(array(
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'mediaList' => $specimen->_derivedUnitMedia,
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'galleryName' => $specimen->titleCache,
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'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
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'cols' => $gallery_settings['cdm_dataportal_media_cols'],
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'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
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'captionElements' => $captionElements,
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'mediaLinkType' => 'LIGHTBOX',
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'alternativeMediaUri' => NULL,
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'galleryLinkUri' => NULL,
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));
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$specimen_details[] = markup_to_render_array($gallery_html);
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}
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$specimen_array = $specimen_details;
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$output = "";
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foreach($specimen_array as $value){
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$renderArray = array(
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'#theme' => 'item_list',
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'#items' => array($value),
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'#type' => 'ul');
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$output .= drupal_render($renderArray);
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}
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return $output;
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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 $specimen
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*
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* @return string
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* The markup for a specimen page
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*/
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function render_cdm_specimenDTO_page($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>Specimen summary: $specimenPageLink</strong><br>";
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}
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if($is_specimen_page) {
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if($specimen->citation){
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$detail_html .= "<br>".$specimen->citation."<br>";
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}
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}
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if ($specimen->preferredStableUri) {
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$stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri, array('attributes' => array('target' => '_blank')));
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$detail_html .= 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($associatedTaxon->value, path_to_taxon($associatedTaxon->key, "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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foreach ($specimen->types as $typeStatus => $typedTaxa) {
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if($specimen->types){
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if(empty($typeStatus) || $typeStatus == "_empty_"|| $typeStatus == ""){
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$detail_html .= "<i>Type for:</i> ";
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} else {
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$detail_html .= "<i>".$typeStatus."</i> of ";
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}
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foreach($typedTaxa as $typedTaxon){
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$detail_html .= $typedTaxon." ";
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}
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} else {
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$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($contigFile->contigLink, true) . " ";
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}
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} else {
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$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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} 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, $imageUuids)
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{
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$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[] = $mediaUri;
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} else {
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$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' => $alternativeMediaUris,
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'alternativeMediaUri' => NULL,
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'galleryLinkUri' => NULL,
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));
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}
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return "<br>" . create_label($galleryName) . "<br>" . $gallery_html;
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}
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function getMediaUri($media)
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{
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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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* $specimenOrObservation has been added to
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*
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* @ingroup compose
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*/
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function compose_cdm_specimen_or_observation($specimen_or_observation, $isSpecimen_page = false, &$derivatives = null)
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{
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$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
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if (!isset($exclude_occurrence_fields)) {
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$exclude_occurrence_fields = array(
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'titleCache',
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'protectedTitleCache',
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'derivedUnitMedia',
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'created',
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'publish',
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'updated',
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'class',
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'uuid',
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''
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);
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}
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if (variable_get('cdm_dataportal_compressed_specimen_derivate_table') || !$isSpecimen_page){
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$exclude_occurrence_fields[] = 'derivationEvents';
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}
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// only show uuid it the user is logged in
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// if(user_is_logged_in() && ($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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$derivedFrom = null;
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if (is_object($specimen_or_observation)) {
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// request again for deeper initialization
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$specimen_or_observation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimen_or_observation->uuid);
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361
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if ($specimen_or_observation->class == 'FieldUnit'){
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362
|
$specimen_or_observation->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
|
|
363
|
$specimen_or_observation->uuid,
|
|
364
|
'fieldObjectMediaDTO',
|
|
365
|
));
|
|
366
|
}else{
|
|
367
|
$specimen_or_observation->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
|
|
368
|
$specimen_or_observation->uuid,
|
|
369
|
'derivedUnitMedia',
|
|
370
|
));
|
|
371
|
}
|
|
372
|
|
|
373
|
$type_label = $specimen_or_observation->class;
|
|
374
|
RenderHints::setFootnoteListKey($type_label . '-' . $specimen_or_observation->uuid);
|
|
375
|
|
|
376
|
// collect typeStatus as label
|
|
377
|
if (isset($specimen_or_observation->specimenTypeDesignations)) {
|
|
378
|
$type_status = array();
|
|
379
|
foreach ($specimen_or_observation->specimenTypeDesignations as $typeDesignation) {
|
|
380
|
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
|
381
|
$type_status[] = $typeDesignation->typeStatus->representation_L10n;
|
|
382
|
}
|
|
383
|
}
|
|
384
|
if (count($type_status) > 0) {
|
|
385
|
$type_label = implode(', ', $type_status);
|
|
386
|
}
|
|
387
|
}
|
|
388
|
|
|
389
|
$title = $type_label . ': ' . $specimen_or_observation->titleCache;
|
|
390
|
|
|
391
|
$groups = array();
|
|
392
|
|
|
393
|
// --- add initialized fields
|
|
394
|
foreach (get_object_vars($specimen_or_observation) as $field => $value) {
|
|
395
|
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
|
396
|
switch ($field) {
|
|
397
|
|
|
398
|
/* ---- java.lang.Object --- */
|
|
399
|
case 'class':
|
|
400
|
if ($value != '' /* FieldUnit' */) {
|
|
401
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
|
402
|
}
|
|
403
|
break;
|
|
404
|
|
|
405
|
case 'markers':
|
|
406
|
$dd_elements = array();
|
|
407
|
foreach ($value as $marker) {
|
|
408
|
$dd_elements[] = compose_cdm_marker($marker);
|
|
409
|
}
|
|
410
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
|
411
|
break;
|
|
412
|
|
|
413
|
|
|
414
|
case 'annotations':
|
|
415
|
$dd_elements = array();
|
|
416
|
foreach ($value as $annotation) {
|
|
417
|
// TODO respect annotation type filter settings
|
|
418
|
$dd_elements[] = $annotation->text;
|
|
419
|
}
|
|
420
|
@_description_list_group_add($groups, t('Notes'), $dd_elements);
|
|
421
|
break;
|
|
422
|
|
|
423
|
/* ---- SpecimenOrObservationBase --- */
|
|
424
|
case 'sex':
|
|
425
|
case 'lifeStage':
|
|
426
|
case 'kindOfUnit':
|
|
427
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n);
|
|
428
|
break;
|
|
429
|
|
|
430
|
case 'definition':
|
|
431
|
// TODO
|
|
432
|
break;
|
|
433
|
|
|
434
|
case 'preferredStableUri':
|
|
435
|
|
|
436
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
|
437
|
break;
|
|
438
|
|
|
439
|
case 'specimenTypeDesignations':
|
|
440
|
|
|
441
|
//TODO: better display of details!!
|
|
442
|
@_description_list_group_add(
|
|
443
|
$groups,
|
|
444
|
cdm_occurrence_field_name_label($field),
|
|
445
|
array(
|
|
446
|
'#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
|
|
447
|
)
|
|
448
|
);
|
|
449
|
break;
|
|
450
|
|
|
451
|
case 'determinations':
|
|
452
|
$dd_elements = array();
|
|
453
|
$glue = ', ';
|
|
454
|
|
|
455
|
foreach ($value as $determinationEvent) {
|
|
456
|
$timeperiod_string = NULL;
|
|
457
|
if (isset($determinationEvent->timeperiod)) {
|
|
458
|
$timeperiod_string = timePeriodToString($determinationEvent->timeperiod);
|
|
459
|
}
|
|
460
|
$weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
|
|
461
|
// check key exists
|
|
462
|
while (array_key_exists($weight, $dd_elements)) {
|
|
463
|
$weight .= '0';
|
|
464
|
}
|
|
465
|
|
|
466
|
$taxon_name = '';
|
|
467
|
$name_link = '';
|
|
468
|
if ($determinationEvent->taxonName) {
|
|
469
|
$taxon_name = cdm_ws_get(CDM_WS_NAME, $determinationEvent->taxonName->uuid);
|
|
470
|
$taxon_name->taggedName = cdm_ws_get(CDM_WS_NAME, array($determinationEvent->taxonName->uuid, "taggedName"));
|
|
471
|
$name_link = path_to_name($determinationEvent->taxonName->uuid);
|
|
472
|
} else if ($determinationEvent->taxon) {
|
|
473
|
$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
|
|
474
|
$name_link = path_to_taxon($determinationEvent->taxon->uuid);
|
|
475
|
}
|
|
476
|
if ($taxon_name) {
|
|
477
|
//$taxon_html = render_taxon_or_name($taxon_name, $name_link);
|
|
478
|
|
|
479
|
$taxon_html = l($taxon_name->titleCache, $name_link, array('attributes' => array('target' => '_blank')));
|
|
480
|
$dd_elements[$weight] = $taxon_html;
|
|
481
|
}
|
|
482
|
if (isset($determinationEvent->modifier)) {
|
|
483
|
$dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
|
|
484
|
}
|
|
485
|
if ($timeperiod_string) {
|
|
486
|
$dd_elements[$weight] .= $glue . $timeperiod_string;
|
|
487
|
}
|
|
488
|
if (isset($determinationEvent->actor->titleCache)) {
|
|
489
|
$dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
|
|
490
|
}
|
|
491
|
if (isset($determinationEvent->description)) {
|
|
492
|
$dd_elements[$weight] .= $glue . $determinationEvent->description;
|
|
493
|
}
|
|
494
|
}
|
|
495
|
ksort($dd_elements);
|
|
496
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
|
|
497
|
break;
|
|
498
|
|
|
499
|
case 'descriptions':
|
|
500
|
$occurrence_featureTree = cdm_get_occurrence_featureTree();
|
|
501
|
$dd_elements = array();
|
|
502
|
|
|
503
|
foreach ($value as $description) {
|
|
504
|
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
|
|
505
|
|
|
506
|
if ($description->imageGallery == TRUE) {
|
|
507
|
continue;
|
|
508
|
}
|
|
509
|
$elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements);
|
|
510
|
$description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null));
|
|
511
|
$dd_elements[] = $description_render_elements;
|
|
512
|
}
|
|
513
|
|
|
514
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
|
515
|
break;
|
|
516
|
case '_derivedUnitMedia':
|
|
517
|
if ($isSpecimen_page) {
|
|
518
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
|
519
|
$captionElements = array(
|
|
520
|
'#uri' => t('open media'),
|
|
521
|
);
|
|
522
|
$gallery_html = compose_cdm_media_gallerie(array(
|
|
523
|
'mediaList' => $value,
|
|
524
|
'galleryName' => $specimen_or_observation->titleCache,
|
|
525
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
|
526
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
|
527
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
|
528
|
'captionElements' => $captionElements,
|
|
529
|
'mediaLinkType' => 'LIGHTBOX',
|
|
530
|
'alternativeMediaUri' => NULL,
|
|
531
|
'galleryLinkUri' => NULL,
|
|
532
|
));
|
|
533
|
@_description_list_group_add($groups, "Detail Images:", markup_to_render_array($gallery_html), '', 20);
|
|
534
|
}
|
|
535
|
|
|
536
|
// $dd_elements[] = markup_to_render_array($gallery_html);
|
|
537
|
|
|
538
|
break;
|
|
539
|
case 'sources':
|
|
540
|
$annotations_and_sources = handle_annotations_and_sources(
|
|
541
|
$specimen_or_observation,
|
|
542
|
array(
|
|
543
|
'sources_as_content' => true,
|
|
544
|
'link_to_name_used_in_source' => 1,
|
|
545
|
'link_to_reference' => 0,
|
|
546
|
'add_footnote_keys' => 0
|
|
547
|
),
|
|
548
|
NULL,
|
|
549
|
''
|
|
550
|
);
|
|
551
|
if (!empty($annotations_and_sources['source_references'])) {
|
|
552
|
@_description_list_group_add($groups, t('Sources') . ':', join(', ', $annotations_and_sources['source_references']), '', 12);
|
|
553
|
}
|
|
554
|
break;
|
|
555
|
|
|
556
|
|
|
557
|
/* ---- DerivedUnitBase --- */
|
|
558
|
case 'derivedFrom':
|
|
559
|
$derivedFrom = $value;
|
|
560
|
if ($isSpecimen_page) {
|
|
561
|
foreach ($derivedFrom->originals as $original) {
|
|
562
|
$pathToSpecimen = path_to_specimen($original->uuid);
|
|
563
|
$description = "";
|
|
564
|
if (isset($derivedFrom->description) && $derivedFrom->description != '') {
|
|
565
|
$description = $derivedFrom->description . ": ";
|
|
566
|
}
|
|
567
|
|
|
568
|
$originals[] = markup_to_render_array(l($description . $original->titleCache, $pathToSpecimen, array('attributes' => array('target' => '_blank'))));
|
|
569
|
if ($original->class == 'FieldUnit') {
|
|
570
|
$label = t('Field data');
|
|
571
|
} else {
|
|
572
|
$label = t('Derived from');
|
|
573
|
}
|
|
574
|
@_description_list_group_add($groups, $label . ':',
|
|
575
|
$originals,
|
|
576
|
'', 13);
|
|
577
|
}
|
|
578
|
}
|
|
579
|
break;
|
|
580
|
case 'derivationEvents':
|
|
581
|
$derivationEvents = $value;
|
|
582
|
$derived_units = array();
|
|
583
|
if ($isSpecimen_page) {
|
|
584
|
foreach ($derivationEvents as $derivationEvent) {
|
|
585
|
foreach ($derivationEvent->derivatives as $derived_unit) {
|
|
586
|
$pathToSpecimen = path_to_specimen($derived_unit->uuid);
|
|
587
|
$description = "";
|
|
588
|
if (isset($derived_unit->description) && $derived_unit->description != '') {
|
|
589
|
$description = $derived_unit->description . ": ";
|
|
590
|
}
|
|
591
|
|
|
592
|
$derived_units[] = markup_to_render_array(l($description . $derived_unit->titleCache, $pathToSpecimen, array('attributes' => array('target' => '_blank'))));
|
|
593
|
}
|
|
594
|
}
|
|
595
|
@_description_list_group_add($groups, t('Derivates') . ':',
|
|
596
|
$derived_units,
|
|
597
|
'', 100);
|
|
598
|
|
|
599
|
}
|
|
600
|
break;
|
|
601
|
|
|
602
|
case 'collection':
|
|
603
|
$sub_dl_groups = array();
|
|
604
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
|
605
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
|
606
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
|
607
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
|
608
|
// TODO "superCollection"
|
|
609
|
// TODO may have media
|
|
610
|
|
|
611
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
612
|
array(
|
|
613
|
array('#markup' => $value->titleCache),
|
|
614
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
615
|
)
|
|
616
|
);
|
|
617
|
break;
|
|
618
|
|
|
619
|
case 'storedUnder':
|
|
620
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
|
|
621
|
break;
|
|
622
|
case 'dnaQuality':
|
|
623
|
$sub_dl_groups = array();
|
|
624
|
|
|
625
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('purificationMethod'), $value->purificationMethod, NULL, 1);
|
|
626
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('ratioOfAbsorbance260_230'), $value->ratioOfAbsorbance260_230, NULL, 2);
|
|
627
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('ratioOfAbsorbance260_280'), $value->ratioOfAbsorbance260_280, NULL, 3);
|
|
628
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('concentration'), $value->concentration, NULL, 4);
|
|
629
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('concentrationUnit'), $value->concentrationUnit, NULL, 4);
|
|
630
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('qualityTerm'), $value->qualityTerm, NULL, 4);
|
|
631
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('qualityCheckDate'), $value->qualityCheckDate, NULL, 4);
|
|
632
|
|
|
633
|
if (is_array($sub_dl_groups) && sizeof($sub_dl_groups)>0) {
|
|
634
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
635
|
array(
|
|
636
|
array('#markup' => $value->titleCache),
|
|
637
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
638
|
)
|
|
639
|
);
|
|
640
|
}
|
|
641
|
break;
|
|
642
|
|
|
643
|
case 'preservation':
|
|
644
|
$sub_dl_groups = array();
|
|
645
|
|
|
646
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('medium'), $value->medium, NULL, 1);
|
|
647
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('temperature'), $value->temperature, NULL, 2);
|
|
648
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('definedMaterialOrMethod'), $value->definedMaterialOrMethod, NULL, 3);
|
|
649
|
|
|
650
|
if (is_array($sub_dl_groups) && sizeof($sub_dl_groups)>0) {
|
|
651
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
652
|
array(
|
|
653
|
array('#markup' => $value->titleCache),
|
|
654
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
655
|
)
|
|
656
|
);
|
|
657
|
}
|
|
658
|
break;
|
|
659
|
|
|
660
|
/* ---- Specimen --- */
|
|
661
|
case 'sequences':
|
|
662
|
$dd_elements = array();
|
|
663
|
foreach ($value as $sequence) {
|
|
664
|
$dd_elements[] = compose_cdm_sequence($sequence);
|
|
665
|
}
|
|
666
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
|
667
|
break;
|
|
668
|
|
|
669
|
// TODO preservation
|
|
670
|
// TODO exsiccatum
|
|
671
|
|
|
672
|
|
|
673
|
/* ---- FieldObservation --- */
|
|
674
|
case 'gatheringEvent':
|
|
675
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache, '', 1);
|
|
676
|
@_description_list_group_add($groups, t('Gathering date'), timePeriodToString($value->timeperiod), '', 2);
|
|
677
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description, '', 3);
|
|
678
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text, '', 10);
|
|
679
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n, '', 4);
|
|
680
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod,'',5);
|
|
681
|
if (isset($value->absoluteElevation)) {
|
|
682
|
$min_max_markup = min_max_measure($value, 'absoluteElevation');
|
|
683
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup, '',6);
|
|
684
|
}
|
|
685
|
if (isset($value->distanceToGround)) {
|
|
686
|
$min_max_markup = min_max_measure($value, 'distanceToGround');
|
|
687
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup,'',7);
|
|
688
|
}
|
|
689
|
if (isset($value->distanceToWaterSurface)) {
|
|
690
|
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface');
|
|
691
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup, '',8);
|
|
692
|
}
|
|
693
|
if (isset($value->collectingAreas) && count($value->collectingAreas) > 0) {
|
|
694
|
$area_representations = array();
|
|
695
|
foreach ($value->collectingAreas as $area) {
|
|
696
|
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
|
697
|
}
|
|
698
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
|
699
|
array(
|
|
700
|
array('#markup' => implode(', ', $area_representations))
|
|
701
|
),'',9
|
|
702
|
);
|
|
703
|
}
|
|
704
|
if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
|
|
705
|
$sub_dl_groups = array();
|
|
706
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
|
707
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
|
708
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
|
709
|
if (isset($value->exactLocation->referenceSystem)) {
|
|
710
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
|
711
|
}
|
|
712
|
|
|
713
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
|
714
|
array(
|
|
715
|
array('#markup' => $value->exactLocation->sexagesimalString),
|
|
716
|
array(
|
|
717
|
'#theme' => 'description_list',
|
|
718
|
'#groups' => $sub_dl_groups
|
|
719
|
),
|
|
720
|
),'',11
|
|
721
|
);
|
|
722
|
}
|
|
723
|
break;
|
|
724
|
|
|
725
|
default:
|
|
726
|
if (is_object($value) || is_array($value)) {
|
|
727
|
drupal_set_message("Unhandled type in compose_cdm_specimen_or_observation() for field " . $field, "warning");
|
|
728
|
} else {
|
|
729
|
if ($field == 'RecordBase' && $value == 'DnaSample') {
|
|
730
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), 'DNA Sample');
|
|
731
|
} else {
|
|
732
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), cdm_occurrence_field_name_label($value));
|
|
733
|
}
|
|
734
|
}
|
|
735
|
|
|
736
|
}
|
|
737
|
|
|
738
|
}
|
|
739
|
} // END of loop over $derivedUnitFacade fields
|
|
740
|
|
|
741
|
// Extensions
|
|
742
|
$extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $specimen_or_observation->uuid . '/extensions', array($specimen_or_observation->uuid));
|
|
743
|
if ($extensions && count($extensions)) {
|
|
744
|
|
|
745
|
$extensions_render_array = compose_extensions($extensions);
|
|
746
|
@_description_list_group_add($groups, t('Extensions') . ':',
|
|
747
|
$extensions_render_array,
|
|
748
|
'', 100);
|
|
749
|
}
|
|
750
|
|
|
751
|
|
|
752
|
|
|
753
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
|
754
|
uasort($groups, 'element_sort');
|
|
755
|
|
|
756
|
$occurrence_elements = array(
|
|
757
|
// '#title' => $title,
|
|
758
|
'#theme' => 'description_list',
|
|
759
|
'#groups' => $groups,
|
|
760
|
'#attributes' => array('class' => html_class_attribute_ref($specimen_or_observation)),
|
|
761
|
);
|
|
762
|
|
|
763
|
$derivatives[] = $occurrence_elements;
|
|
764
|
// all footnotes which has been assembled so far (e.g. from typeDesignations) to here
|
|
765
|
// $foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
|
|
766
|
// if (!empty($foonote_li_elements)) {
|
|
767
|
// $derivatives[] = array(
|
|
768
|
// '#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>',
|
|
769
|
// );
|
|
770
|
// }
|
|
771
|
|
|
772
|
// --- recurse into originals
|
|
773
|
if (!isset($derivedFrom) && !$isSpecimen_page) {
|
|
774
|
$derivedFrom = cdm_ws_get(
|
|
775
|
CDM_WS_OCCURRENCE,
|
|
776
|
array($specimen_or_observation->uuid, 'derivedFrom')
|
|
777
|
);
|
|
778
|
}
|
|
779
|
if (isset($derivedFrom) && !$isSpecimen_page) {
|
|
780
|
if (isset($derivedFrom->originals)) {
|
|
781
|
$derived_from_label = t('derived');
|
|
782
|
$preposition = t('from');
|
|
783
|
if(isset($derivedFrom->type)){
|
|
784
|
$derived_from_label = $derivedFrom->type->representation_L10n;
|
|
785
|
if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
|
|
786
|
$preposition = t('of');
|
|
787
|
}
|
|
788
|
}
|
|
789
|
if (count($groups) > 0) {
|
|
790
|
// TODO annotations
|
|
791
|
|
|
792
|
// only display the derived from information when the derivative has any element which will be diplayed
|
|
793
|
$derivatives[] = array(
|
|
794
|
'#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>',
|
|
795
|
);
|
|
796
|
}
|
|
797
|
foreach ($derivedFrom->originals as $original) {
|
|
798
|
compose_cdm_specimen_or_observation($original, $isSpecimen_page, $derivatives);
|
|
799
|
}
|
|
800
|
}
|
|
801
|
}
|
|
802
|
|
|
803
|
|
|
804
|
|
|
805
|
|
|
806
|
} // END of $specimenOrObservation exists
|
|
807
|
|
|
808
|
return $derivatives;
|
|
809
|
}
|
|
810
|
|
|
811
|
|
|
812
|
/**
|
|
813
|
* Compose an render array from a CDM Sequence object.
|
|
814
|
*
|
|
815
|
* compose_hook() implementation
|
|
816
|
*
|
|
817
|
* @param object $sequence
|
|
818
|
* CDM instance of type Sequence
|
|
819
|
* @return array
|
|
820
|
* A render array containing the fields of the supplied $sequence
|
|
821
|
*
|
|
822
|
* @ingroup compose
|
|
823
|
*/
|
|
824
|
function compose_cdm_sequence($sequence, $isSpecimenPage = false)
|
|
825
|
{
|
|
826
|
|
|
827
|
$exclude_sequence_fields = &drupal_static(__FUNCTION__);
|
|
828
|
if (!isset($exclude_sequence_fields)) {
|
|
829
|
$exclude_sequence_fields = array(
|
|
830
|
'titleCache',
|
|
831
|
'protectedTitleCache',
|
|
832
|
'microReference',
|
|
833
|
'created',
|
|
834
|
'updated',
|
|
835
|
'class',
|
|
836
|
);
|
|
837
|
}
|
|
838
|
|
|
839
|
$groups = array();
|
|
840
|
|
|
841
|
// -- retrieve additional data if neesscary
|
|
842
|
// TODO below call disabled since sequences are not yet supported,
|
|
843
|
// see #3347 (services and REST service controller for molecular classes implemented)
|
|
844
|
//
|
|
845
|
// cdm_load_annotations($sequence);
|
|
846
|
|
|
847
|
foreach (get_object_vars($sequence) as $field => $value) {
|
|
848
|
|
|
849
|
|
|
850
|
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
|
851
|
switch ($field) {
|
|
852
|
|
|
853
|
case 'geneticAccessionNumber';
|
|
854
|
|
|
855
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 2);
|
|
856
|
break;
|
|
857
|
|
|
858
|
|
|
859
|
case 'dnaMarker': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
|
|
860
|
if (isset($value->name)) {
|
|
861
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3);
|
|
862
|
}
|
|
863
|
if (isset($value->description)) {
|
|
864
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description'), $value->description, NULL, 4);
|
|
865
|
}
|
|
866
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) , $value, NULL, 4);
|
|
867
|
break;
|
|
868
|
|
|
869
|
case 'consensusSequence':
|
|
870
|
// format in genbank style, force linebreaks after each 70 nucleotites
|
|
871
|
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
|
|
872
|
if ($value->length > 0) {
|
|
873
|
@_description_list_group_add(
|
|
874
|
$groups,
|
|
875
|
cdm_occurrence_field_name_label($field),
|
|
876
|
array(
|
|
877
|
array(
|
|
878
|
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb') . '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
|
879
|
'#wrapper_attributes' => array('class' => 'dna-sequence')
|
|
880
|
)
|
|
881
|
),
|
|
882
|
5);
|
|
883
|
}
|
|
884
|
break;
|
|
885
|
|
|
886
|
case 'dnaSample': // FIXME 3.3 implement
|
|
887
|
break;
|
|
888
|
case 'singleReads': // FIXME 3.3 implement
|
|
889
|
break;
|
|
890
|
case 'contigFile': // FIXME 3.3 implement - Media
|
|
891
|
break;
|
|
892
|
case 'pherograms': // FIXME 3.3 implement - Media
|
|
893
|
break;
|
|
894
|
case 'haplotype': // FIXME 3.3 implement
|
|
895
|
break;
|
|
896
|
case 'dateSequenced': // FIXME 3.3 now in SingelRead
|
|
897
|
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
|
898
|
break;
|
|
899
|
|
|
900
|
case 'barcode': // boolean
|
|
901
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes' : 'No', NULL, 7);
|
|
902
|
break;
|
|
903
|
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
|
|
904
|
break;
|
|
905
|
|
|
906
|
case 'citation':
|
|
907
|
@_description_list_group_add($groups,
|
|
908
|
cdm_occurrence_field_name_label($field),
|
|
909
|
theme('cdm_reference', array('reference' => $value, 'microReference' => $sequence->microReference)),
|
|
910
|
NULL,
|
|
911
|
8
|
|
912
|
);
|
|
913
|
break;
|
|
914
|
|
|
915
|
case 'publishedIn':
|
|
916
|
@_description_list_group_add($groups,
|
|
917
|
cdm_occurrence_field_name_label($field),
|
|
918
|
theme('cdm_reference', array('reference' => $value)),
|
|
919
|
NULL,
|
|
920
|
7
|
|
921
|
);
|
|
922
|
break;
|
|
923
|
|
|
924
|
case 'rights':
|
|
925
|
array_merge($groups, cdm_rights_as_dl_groups($value));
|
|
926
|
break;
|
|
927
|
|
|
928
|
case 'annotations':
|
|
929
|
$dd_elements = array();
|
|
930
|
foreach ($value as $annotation) {
|
|
931
|
// TODO respect annotation type filter settings
|
|
932
|
$dd_elements[] = $annotation->text;
|
|
933
|
}
|
|
934
|
@_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
|
|
935
|
break;
|
|
936
|
|
|
937
|
case 'markers':
|
|
938
|
$dd_elements = array();
|
|
939
|
foreach ($value as $marker) {
|
|
940
|
$dd_elements[] = compose_cdm_marker($marker);
|
|
941
|
}
|
|
942
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
|
|
943
|
break;
|
|
944
|
|
|
945
|
case 'chromatograms':
|
|
946
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
|
947
|
array(
|
|
948
|
'#markup' => compose_cdm_media_gallerie(array('medialist' => $value)),
|
|
949
|
),
|
|
950
|
NULL,
|
|
951
|
11);
|
|
952
|
break;
|
|
953
|
|
|
954
|
default:
|
|
955
|
if (is_object($value) || is_array($value)) {
|
|
956
|
drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
|
|
957
|
} else {
|
|
958
|
if (!is_array($value) && strpos($value, 'http:') !== false ){
|
|
959
|
//make links for urls
|
|
960
|
$value = l($value, $value, array('attributes' => array('target' => '_blank')));
|
|
961
|
$value = markup_to_render_array($value);
|
|
962
|
}
|
|
963
|
|
|
964
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
|
|
965
|
}
|
|
966
|
}
|
|
967
|
}
|
|
968
|
}
|
|
969
|
|
|
970
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
|
971
|
uasort($groups, 'element_sort');
|
|
972
|
if ($isSpecimenPage) {
|
|
973
|
$sequence_elements = array(
|
|
974
|
'#title' => $sequence->dnaMarker,
|
|
975
|
'#theme' => 'description_list',
|
|
976
|
'#groups' => $groups
|
|
977
|
);
|
|
978
|
} else{
|
|
979
|
$sequence_elements = array(
|
|
980
|
'#title' => $sequence->dnaMarker -> titleCache,
|
|
981
|
'#theme' => 'description_list',
|
|
982
|
'#groups' => $groups
|
|
983
|
);
|
|
984
|
}
|
|
985
|
|
|
986
|
return $sequence_elements;
|
|
987
|
}
|
|
988
|
/**
|
|
989
|
* Creates an array from a list of FieldUnitDTOs.
|
|
990
|
*
|
|
991
|
*
|
|
992
|
* @param object $specimenOrObservations
|
|
993
|
* list of FieldUnitDTOs
|
|
994
|
* @return array
|
|
995
|
* An array containing the hierarchy of the field units corresponding to the taxon
|
|
996
|
*
|
|
997
|
* @ingroup compose
|
|
998
|
*/
|
|
999
|
function compose_specimen_array(array $specimenOrObservations){
|
|
1000
|
$items_specimen = array();
|
|
1001
|
$items = array();
|
|
1002
|
|
|
1003
|
//we need one more item to contain the items of one level (fieldunit, derivate data etc.)
|
|
1004
|
foreach ($specimenOrObservations as &$specimenOrObservation) {
|
|
1005
|
|
|
1006
|
$items['data'] = $specimenOrObservation->listLabel ;
|
|
1007
|
$specimen = compose_cdm_specimen_or_observation_tree_entry($specimenOrObservation);
|
|
1008
|
$children = array();
|
|
1009
|
$child = array();
|
|
1010
|
$child['data'] =$specimen;
|
|
1011
|
// $children[] = create_specimen_array($specimenOrObservation->derivates);
|
|
1012
|
if (isset($specimenOrObservation->derivates) && sizeof($specimenOrObservation->derivates) > 0){
|
|
1013
|
$child['children']= compose_specimen_array($specimenOrObservation->derivates);
|
|
1014
|
}
|
|
1015
|
$children[]=$child;
|
|
1016
|
$items['children'] = $children;
|
|
1017
|
$items_specimen[] = $items;
|
|
1018
|
}
|
|
1019
|
return $items_specimen;
|
|
1020
|
}
|
|
1021
|
|
|
1022
|
|
|
1023
|
/**
|
|
1024
|
* Compose an render array from a CDM DerivedUnitFacade object.
|
|
1025
|
*
|
|
1026
|
* compose_hook() implementation
|
|
1027
|
*
|
|
1028
|
* @param object $specimenOrObservation
|
|
1029
|
* the CDM instance of type SpecimenOrObservation to compose
|
|
1030
|
* the render array for
|
|
1031
|
* @param array $derivatives
|
|
1032
|
* the render array which contains the compositions of the derivatives
|
|
1033
|
* of the supplied $specimenOrObservation
|
|
1034
|
*
|
|
1035
|
* @return array
|
|
1036
|
* the supplied render array $derivatives to which the composition of the supplied
|
|
1037
|
* $specimenOrObservation has been added to
|
|
1038
|
*
|
|
1039
|
* @ingroup compose
|
|
1040
|
*/
|
|
1041
|
|
|
1042
|
function compose_cdm_specimen_or_observation_tree_entry($specimen_or_observation)
|
|
1043
|
{
|
|
1044
|
$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
|
|
1045
|
if (!isset($exclude_occurrence_fields)) {
|
|
1046
|
$exclude_occurrence_fields = array(
|
|
1047
|
'type',
|
|
1048
|
'taxonRelatedDerivedUnits',
|
|
1049
|
'label',
|
|
1050
|
'titleCache',
|
|
1051
|
'listLabel',
|
|
1052
|
'protectedTitleCache',
|
|
1053
|
'class',
|
|
1054
|
'uuid',
|
|
1055
|
'derivates',
|
|
1056
|
'collection'
|
|
1057
|
);
|
|
1058
|
}
|
|
1059
|
$items = array();
|
|
1060
|
|
|
1061
|
// only show uuid it the user is logged in
|
|
1062
|
if (user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE) {
|
|
1063
|
// unset($exclude_occurrence_fields[$a_idx]);
|
|
1064
|
}
|
|
1065
|
|
|
1066
|
|
|
1067
|
if (is_object($specimen_or_observation)) {
|
|
1068
|
|
|
1069
|
$type_label = $specimen_or_observation->recordBase;
|
|
1070
|
RenderHints::setFootnoteListKey($type_label . '-' . $specimen_or_observation->uuid);
|
|
1071
|
|
|
1072
|
// collect typeStatus as label
|
|
1073
|
if (isset($specimen_or_observation->specimenTypeDesignations)) {
|
|
1074
|
$type_status = array();
|
|
1075
|
foreach ($specimen_or_observation->specimenTypeDesignations as $typeDesignation) {
|
|
1076
|
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
|
1077
|
$type_status[] = $typeDesignation->typeStatus->representation_L10n;
|
|
1078
|
}
|
|
1079
|
}
|
|
1080
|
if (count($type_status) > 0) {
|
|
1081
|
$type_label = implode(', ', $type_status);
|
|
1082
|
}
|
|
1083
|
}
|
|
1084
|
|
|
1085
|
if (isset($typeDesignation->typifiedNames)){
|
|
1086
|
$title = $type_label . ' for: ' . $typeDesignation->typifiedNames;
|
|
1087
|
}else{
|
|
1088
|
$title = $type_label;
|
|
1089
|
}
|
|
1090
|
|
|
1091
|
$items['data'] = $title;
|
|
1092
|
|
|
1093
|
$groups = array();
|
|
1094
|
$items['children'] = $groups;
|
|
1095
|
$children_items = array();
|
|
1096
|
// --- add initialized fields
|
|
1097
|
foreach (get_object_vars($specimen_or_observation) as $field => $value) {
|
|
1098
|
$child_item = array();
|
|
1099
|
|
|
1100
|
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
|
1101
|
switch ($field) {
|
|
1102
|
|
|
1103
|
/* ---- SpecimenOrObservationBase --- */
|
|
1104
|
case 'derivationEvent':
|
|
1105
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1);
|
|
1106
|
break;
|
|
1107
|
case 'kindOfUnit':
|
|
1108
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1);
|
|
1109
|
break;
|
|
1110
|
case 'accessionNumber':
|
|
1111
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 0);
|
|
1112
|
break;
|
|
1113
|
|
|
1114
|
case 'preferredStableUri':
|
|
1115
|
|
|
1116
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
|
1117
|
break;
|
|
1118
|
|
|
1119
|
case 'specimenTypeDesignations':
|
|
1120
|
@_description_list_group_add(
|
|
1121
|
$groups,
|
|
1122
|
cdm_occurrence_field_name_label($field),
|
|
1123
|
array(
|
|
1124
|
'#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
|
|
1125
|
)
|
|
1126
|
);
|
|
1127
|
break;
|
|
1128
|
|
|
1129
|
|
|
1130
|
|
|
1131
|
case 'listOfMedia':
|
|
1132
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
|
1133
|
|
|
1134
|
$captionElements = array(
|
|
1135
|
'title',
|
|
1136
|
'#uri' => t('open media'),
|
|
1137
|
);
|
|
1138
|
$gallery_html = compose_cdm_media_gallerie(array(
|
|
1139
|
'mediaList' => $value,
|
|
1140
|
'galleryName' => $specimen_or_observation->uuid,
|
|
1141
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
|
1142
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
|
1143
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
|
1144
|
'captionElements' => $captionElements,
|
|
1145
|
'mediaLinkType' => 'LIGHTBOX',
|
|
1146
|
'alternativeMediaUri' => NULL,
|
|
1147
|
'galleryLinkUri' => NULL,
|
|
1148
|
'showCaption' => true
|
|
1149
|
));
|
|
1150
|
|
|
1151
|
//@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $gallery_html);
|
|
1152
|
break;
|
|
1153
|
|
|
1154
|
|
|
1155
|
|
|
1156
|
/* ---- DerivedUnitBase --- */
|
|
1157
|
|
|
1158
|
|
|
1159
|
case 'collectionDTO':
|
|
1160
|
|
|
1161
|
$sub_dl_groups = array();
|
|
1162
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
|
1163
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
|
1164
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
|
1165
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
|
1166
|
// TODO "superCollection"
|
|
1167
|
// TODO may have media
|
|
1168
|
|
|
1169
|
@_description_list_group_add($groups, 'Collection',
|
|
1170
|
array(
|
|
1171
|
array('#markup' => $value->titleCache),
|
|
1172
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
|
1173
|
)
|
|
1174
|
);
|
|
1175
|
|
|
1176
|
break;
|
|
1177
|
|
|
1178
|
|
|
1179
|
|
|
1180
|
|
|
1181
|
/* ---- Specimen --- */
|
|
1182
|
case 'sequences':
|
|
1183
|
$dd_elements = array();
|
|
1184
|
foreach ($value as $sequence) {
|
|
1185
|
$dd_elements[] = compose_cdm_sequence($sequence, true);
|
|
1186
|
$dd_elements[] = "";
|
|
1187
|
}
|
|
1188
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements,'', 100);
|
|
1189
|
break;
|
|
1190
|
|
|
1191
|
// TODO preservation
|
|
1192
|
// TODO exsiccatum
|
|
1193
|
|
|
1194
|
|
|
1195
|
/* ---- FieldObservation --- */
|
|
1196
|
case 'gatheringEvent':
|
|
1197
|
|
|
1198
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->collector);
|
|
1199
|
@_description_list_group_add($groups, t('Gathering date'), timePeriodToString($value->timeperiod));
|
|
1200
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
|
|
1201
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality, '', 10);
|
|
1202
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country);
|
|
1203
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
|
|
1204
|
if (isset($value->absoluteElevation)) {
|
|
1205
|
$min_max_markup = min_max_measure($value, 'absoluteElevation');
|
|
1206
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
|
|
1207
|
}
|
|
1208
|
if (isset($value->distanceToGround) && $value->distanceToGround >0) {
|
|
1209
|
$min_max_markup = min_max_measure($value, 'distanceToGround');
|
|
1210
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
|
|
1211
|
}
|
|
1212
|
if (isset($value->distanceToWaterSurface) && $value->distanceToWaterSurface > 0) {
|
|
1213
|
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface');
|
|
1214
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
|
|
1215
|
}
|
|
1216
|
|
|
1217
|
if (isset($value->collectingAreas)) {
|
|
1218
|
$area_representations = array();
|
|
1219
|
foreach ($value->collectingAreas as $area) {
|
|
1220
|
// $area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
|
1221
|
$area_representations[] = $area;
|
|
1222
|
}
|
|
1223
|
if (!empty($area_representations))
|
|
1224
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
|
1225
|
array(
|
|
1226
|
array('#markup' => implode(', ', $area_representations))
|
|
1227
|
)
|
|
1228
|
);
|
|
1229
|
}
|
|
1230
|
if (isset($value->exactLocation) ) {
|
|
1231
|
$sub_dl_groups = array();
|
|
1232
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
|
1233
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
|
1234
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
|
1235
|
if (isset($value->exactLocation->referenceSystem)) {
|
|
1236
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
|
1237
|
}
|
|
1238
|
if ( isSet($value->exactLocation->sexagesimalString)){
|
|
1239
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
|
1240
|
array(
|
|
1241
|
array('#markup' => $value->exactLocation->sexagesimalString),
|
|
1242
|
array(
|
|
1243
|
'#theme' => 'description_list',
|
|
1244
|
'#groups' => $sub_dl_groups
|
|
1245
|
),
|
|
1246
|
), '', 11
|
|
1247
|
);
|
|
1248
|
}
|
|
1249
|
}
|
|
1250
|
|
|
1251
|
break;
|
|
1252
|
|
|
1253
|
/* ---- DerivationEvent --- */
|
|
1254
|
case 'derivationEvents':
|
|
1255
|
//@_description_list_group_add($groups, t('Association type'), $value->description);
|
|
1256
|
break;
|
|
1257
|
case 'determinedNames':
|
|
1258
|
$dd_elements = array();
|
|
1259
|
foreach ($value as $name) {
|
|
1260
|
$taxon_name = cdm_ws_get(CDM_WS_NAME, $name->key);
|
|
1261
|
$taxon_name->taggedName = cdm_ws_get(CDM_WS_NAME, array($name->key, "taggedName"));
|
|
1262
|
$name_link = path_to_name($name->key);
|
|
1263
|
|
|
1264
|
//$taxon_html = render_taxon_or_name($taxon_name, $name_link);
|
|
1265
|
$taxon_html = l($taxon_name->titleCache, $name_link, array('attributes' => array('target' => '_blank')));
|
|
1266
|
$dd_elements[] = $taxon_html;
|
|
1267
|
}
|
|
1268
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label("Identification(s)"), $dd_elements,'', 100);
|
|
1269
|
break;
|
|
1270
|
|
|
1271
|
|
|
1272
|
default:
|
|
1273
|
if (is_object($value) || is_array($value)) {
|
|
1274
|
drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
|
|
1275
|
} else {
|
|
1276
|
if ($field == 'recordBase' && $value == 'Dna Sample'){
|
|
1277
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), 'DNA Sample');
|
|
1278
|
}else{
|
|
1279
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
|
1280
|
}
|
|
1281
|
|
|
1282
|
}
|
|
1283
|
|
|
1284
|
}
|
|
1285
|
|
|
1286
|
|
|
1287
|
}
|
|
1288
|
} // END of loop over $derivedUnitFacade fields
|
|
1289
|
|
|
1290
|
|
|
1291
|
|
|
1292
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
|
1293
|
uasort($groups, 'element_sort');
|
|
1294
|
|
|
1295
|
$occurrence_elements = array(
|
|
1296
|
// '#title' => $title,
|
|
1297
|
'#theme' => 'description_list',
|
|
1298
|
'#groups' => $groups,
|
|
1299
|
'#attributes' => array('class' => html_class_attribute_ref($specimen_or_observation)),
|
|
1300
|
);
|
|
1301
|
$output = drupal_render($occurrence_elements);
|
|
1302
|
if (isset($gallery_html)){
|
|
1303
|
$output .= $gallery_html;
|
|
1304
|
}
|
|
1305
|
$pathToSpecimen = path_to_specimen($specimen_or_observation->uuid);
|
|
1306
|
$output .= l("Detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
|
1307
|
} // END of $specimenOrObservation exists
|
|
1308
|
|
|
1309
|
return $output;
|
|
1310
|
}
|
|
1311
|
|
|
1312
|
function compose_table_of_blast_result(array $data){
|
|
1313
|
// get icon images
|
|
1314
|
$expand_icon = font_awesome_icon_markup(
|
|
1315
|
'fa-plus-square-o',
|
|
1316
|
array(
|
|
1317
|
'alt' => 'Show details',
|
|
1318
|
'class' => array('expand_icon')
|
|
1319
|
)
|
|
1320
|
);
|
|
1321
|
$collapse_icon = font_awesome_icon_markup(
|
|
1322
|
'fa-minus-square-o',
|
|
1323
|
array(
|
|
1324
|
'alt' => 'Show details',
|
|
1325
|
'class' => array('collapse_icon')
|
|
1326
|
)
|
|
1327
|
);
|
|
1328
|
//$detail_image_icon = '<img title="Detail Image" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/detail_image_derivate-16x16-32.png' . '"/>';
|
|
1329
|
$rowcount = 0;
|
|
1330
|
$rows = array();
|
|
1331
|
|
|
1332
|
foreach ($data as $row_data){
|
|
1333
|
$pathToSpecimen = path_to_specimen_by_accession_number($row_data['id']);
|
|
1334
|
$specimenPageLink = l($row_data['id'], $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
|
1335
|
$ncbiLink = l($row_data['id'], 'https://www.ncbi.nlm.nih.gov/nuccore/'.$row_data['id'].'?report=graph', array('attributes' => array('target' => '_blank')));
|
|
1336
|
$rows[] = array(
|
|
1337
|
'data' => array(
|
|
1338
|
array(
|
|
1339
|
'data' => $expand_icon . $collapse_icon,
|
|
1340
|
'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
|
|
1341
|
),
|
|
1342
|
array(
|
|
1343
|
'data' => $row_data['def'],
|
|
1344
|
),
|
|
1345
|
array(
|
|
1346
|
'data' => $specimenPageLink,
|
|
1347
|
),
|
|
1348
|
array(
|
|
1349
|
'data' => $row_data['hsp_align_length'],
|
|
1350
|
),
|
|
1351
|
array(
|
|
1352
|
'data' => $ncbiLink,
|
|
1353
|
),
|
|
1354
|
array(
|
|
1355
|
'data' => $row_data['hsp_identity']/$row_data['hsp_align_length']*100,
|
|
1356
|
)
|
|
1357
|
),
|
|
1358
|
'id' => 'blast_summary' . $rowcount, // summary row id
|
|
1359
|
'class' => array('summary_row'),
|
|
1360
|
);
|
|
1361
|
$detail_html = "";
|
|
1362
|
|
|
1363
|
$detail_html .= create_label("Details") . $row_data["hsp_align_length"] . "<br>";
|
|
1364
|
|
|
1365
|
|
|
1366
|
$detail_html .= "<br>";
|
|
1367
|
$detail_html .= $row_data["hsp_midline"];
|
|
1368
|
|
|
1369
|
//$detail_html .= "<br>";
|
|
1370
|
|
|
1371
|
$rows[] = array(
|
|
1372
|
'data' => array(
|
|
1373
|
array(
|
|
1374
|
'data' => "", //empty first column
|
|
1375
|
'class' => array('expand_column')
|
|
1376
|
),
|
|
1377
|
array(
|
|
1378
|
'data' => $detail_html,
|
|
1379
|
'colspan' => 5,
|
|
1380
|
),
|
|
1381
|
),
|
|
1382
|
'id' => 'blast_detail' . $rowcount,//details row ID
|
|
1383
|
'class' => array('detail_row'),
|
|
1384
|
);
|
|
1385
|
$rowcount++;
|
|
1386
|
}
|
|
1387
|
|
|
1388
|
$tableId = "blast_result_table";
|
|
1389
|
$blast_result_table = array(
|
|
1390
|
"#theme" => "table",
|
|
1391
|
"#weight" => 2,
|
|
1392
|
"#header" => array(
|
|
1393
|
array(
|
|
1394
|
'data' => "",
|
|
1395
|
'class' => array('expand_column')
|
|
1396
|
),
|
|
1397
|
"Name", "Accession Number", "Align Length", "NCBI", "% Identity"),
|
|
1398
|
"#rows" => $rows,
|
|
1399
|
"#attributes" => array(
|
|
1400
|
"id" => $tableId,
|
|
1401
|
"border" => 2
|
|
1402
|
)
|
|
1403
|
);
|
|
1404
|
|
|
1405
|
drupal_add_js_rowToggle("#".$tableId);
|
|
1406
|
|
|
1407
|
$render_array[$tableId] = $blast_result_table;
|
|
1408
|
$out = drupal_render($render_array);
|
|
1409
|
//$blast_result_page-> content = drupal_render($render_array);
|
|
1410
|
return $out;
|
|
1411
|
}
|
|
1412
|
|