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c70b93c3
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Andreas Kohlbecker
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<?php
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| 2 |
f19f47fa
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Andreas Kohlbecker
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/**
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* @file
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| 4 |
bff67f14
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Patric Plitzner
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* Functions for dealing with CDM entities of type SpecimenOrOccurrences
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| 5 |
f19f47fa
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Andreas Kohlbecker
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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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c70b93c3
|
Andreas Kohlbecker
|
*/
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| 19 |
b810158e
|
Patric Plitzner
|
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/**
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| 21 |
30845bda
|
Andreas Kohlbecker
|
* Provides the HTML markup for a specimen page
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*
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* @param $specimen
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*
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| 25 |
b810158e
|
Patric Plitzner
|
* @return string
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| 26 |
30845bda
|
Andreas Kohlbecker
|
* The markup for a specimen page
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| 27 |
b810158e
|
Patric Plitzner
|
*/
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| 28 |
a2acff0a
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Katja Luther
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function render_cdm_specimen_page($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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| 44 |
6eaec849
|
Katja Luther
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'title',
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| 45 |
a2acff0a
|
Katja Luther
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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, $is_specimen_page = false)
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b810158e
|
Patric Plitzner
|
{
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$detail_html = "";
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//link to specimen page
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| 104 |
30845bda
|
Andreas Kohlbecker
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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, $pathToSpecimen, array('attributes' => array('target' => '_blank')));
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25fc25ca
|
Patrick Plitzner
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$detail_html .= "<strong>Specimen summary: $specimenPageLink</strong><br>";
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a7a302a0
|
Patric Plitzner
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}
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b3ac03bf
|
Katja Luther
|
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| 111 |
30845bda
|
Andreas Kohlbecker
|
if($is_specimen_page) {
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if($specimen->citation){
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6a660dc3
|
Patrick Plitzner
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$detail_html .= "<br>".$specimen->citation."<br>";
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b3ac03bf
|
Katja Luther
|
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| 115 |
fdc85125
|
Patric Plitzner
|
}
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| 116 |
b810158e
|
Patric Plitzner
|
}
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| 117 |
c10f70e4
|
Katja Luther
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if ($specimen->preferredStableUri) {
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$stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri, array('attributes' => array('target' => '_blank')));
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| 119 |
907cc9b4
|
Patrick Plitzner
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$detail_html .= create_label("Preferred stable URI") . $stableIdentifierLink . "<br>";
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| 120 |
1cefb4e5
|
Patrick Plitzner
|
}
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| 121 |
c10f70e4
|
Katja Luther
|
if ($is_specimen_page) {
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| 122 |
fdc85125
|
Patric Plitzner
|
// associated taxa
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| 123 |
c10f70e4
|
Katja Luther
|
if ($specimen->associatedTaxa) {
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| 124 |
3dd58832
|
Patric Plitzner
|
$detail_html .= "<br>";
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c10f70e4
|
Katja Luther
|
$detail_html .= create_label("Associated with");
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if (sizeof($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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f37da5d1
|
Patrick Plitzner
|
$detail_html .= l($associatedTaxon->value, path_to_taxon($associatedTaxon->key, "specimens"));//$associatedTaxon->second."<br>";
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| 131 |
c10f70e4
|
Katja Luther
|
}
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| 132 |
fa09fe7d
|
Patrick Plitzner
|
$detail_html .= "<br>";
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| 133 |
fdc85125
|
Patric Plitzner
|
}
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| 134 |
b810158e
|
Patric Plitzner
|
}
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| 135 |
c10f70e4
|
Katja Luther
|
// - type information
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| 136 |
b810158e
|
Patric Plitzner
|
$types = "";
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| 137 |
30845bda
|
Andreas Kohlbecker
|
if (isset($specimen->types)) {
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| 138 |
56d58f9b
|
Patric Plitzner
|
//typed taxa
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| 139 |
30845bda
|
Andreas Kohlbecker
|
foreach ($specimen->types as $typeStatus => $typedTaxa) {
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b0efd824
|
Patrick Plitzner
|
if($specimen->types){
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269e42e0
|
Patrick Plitzner
|
if(empty($typeStatus) || $typeStatus == "_empty_"|| $typeStatus == ""){
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| 142 |
31ab4cf9
|
Patrick Plitzner
|
$detail_html .= "<i>Type for:</i> ";
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269e42e0
|
Patrick Plitzner
|
} else {
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$detail_html .= "<i>".$typeStatus."</i> of ";
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| 145 |
a5b11885
|
Patrick Plitzner
|
}
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| 146 |
b0efd824
|
Patrick Plitzner
|
foreach($typedTaxa as $typedTaxon){
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$detail_html .= $typedTaxon." ";
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| 148 |
b3ac03bf
|
Katja Luther
|
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| 149 |
c10f70e4
|
Katja Luther
|
}
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} else {
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$types .= $typeStatus . " ";
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| 153 |
fdc85125
|
Patric Plitzner
|
}
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| 154 |
b810158e
|
Patric Plitzner
|
}
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| 155 |
|
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}
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| 156 |
30845bda
|
Andreas Kohlbecker
|
$derivateDataDTO = $specimen->derivateDataDTO;
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| 157 |
b810158e
|
Patric Plitzner
|
// - specimen scans
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| 158 |
65a4de51
|
Patrick Plitzner
|
$specimenScans = create_html_links($derivateDataDTO->specimenScans, true);
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| 159 |
b810158e
|
Patric Plitzner
|
// - molecular data
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| 160 |
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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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| 165 |
65a4de51
|
Patrick Plitzner
|
$molecularData .= create_html_link($molecular->providerLink, true);
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| 166 |
2c23b054
|
Patrick Plitzner
|
} else {
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|
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$molecularData .= "[no provider]";
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| 168 |
b810158e
|
Patric Plitzner
|
}
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| 169 |
|
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//contig link
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| 170 |
2c23b054
|
Patrick Plitzner
|
if (isset($molecular->contigFiles)) {
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| 171 |
b810158e
|
Patric Plitzner
|
$molecularData .= "[";
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| 172 |
2c23b054
|
Patrick Plitzner
|
if (sizeof($molecular->contigFiles) > 0) {
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| 173 |
b810158e
|
Patric Plitzner
|
foreach ($molecular->contigFiles as $contigFile) {
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| 174 |
2c23b054
|
Patrick Plitzner
|
if (isset($contigFile->contigLink)) {
|
| 175 |
|
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if (isset($contigFile->contigLink->uri) and $contigFile->contigLink->uri != null) {
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| 176 |
|
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$molecularData .= create_html_link($contigFile->contigLink, true) . " ";
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| 177 |
37ab3ddc
|
Patric Plitzner
|
}
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| 178 |
c10f70e4
|
Katja Luther
|
} else {
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| 179 |
2c23b054
|
Patrick Plitzner
|
$molecularData .= "no contig ";
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| 180 |
|
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}
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| 181 |
|
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//primer links
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| 182 |
c10f70e4
|
Katja Luther
|
if (isset($contigFile->primerLinks)) {
|
| 183 |
65a4de51
|
Patrick Plitzner
|
$molecularData .= create_html_links($contigFile->primerLinks, true);
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| 184 |
b810158e
|
Patric Plitzner
|
}
|
| 185 |
|
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}
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| 186 |
|
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}
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| 187 |
5eafa5ff
|
Patric Plitzner
|
$molecularData = rtrim($molecularData, " ");
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| 188 |
b810158e
|
Patric Plitzner
|
$molecularData .= "]";
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| 189 |
|
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}
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| 190 |
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//FIXME separate with comma (remove trailing comma)
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| 191 |
|
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}
|
| 192 |
|
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}
|
| 193 |
|
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// - detail images
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| 194 |
65a4de51
|
Patrick Plitzner
|
$detailImages = create_html_links($derivateDataDTO->detailImages, true);
|
| 195 |
b810158e
|
Patric Plitzner
|
|
| 196 |
|
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if ($types) {
|
| 197 |
c10f70e4
|
Katja Luther
|
$detail_html .= $is_specimen_page ? "<br>" : "";
|
| 198 |
a0bbccce
|
Patrick Plitzner
|
$detail_html .= create_label("Type(s)") . $types . "<br>";
|
| 199 |
b810158e
|
Patric Plitzner
|
}
|
| 200 |
30845bda
|
Andreas Kohlbecker
|
if ($specimenScans and !$is_specimen_page) {
|
| 201 |
3dd58832
|
Patric Plitzner
|
$detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
|
| 202 |
b810158e
|
Patric Plitzner
|
}
|
| 203 |
8d9d64a5
|
Patric Plitzner
|
//specimen scan image gallery
|
| 204 |
c10f70e4
|
Katja Luther
|
if ($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
|
| 205 |
8d9d64a5
|
Patric Plitzner
|
$detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
|
| 206 |
|
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}
|
| 207 |
|
|
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| 208 |
b810158e
|
Patric Plitzner
|
if ($molecularData) {
|
| 209 |
c10f70e4
|
Katja Luther
|
$detail_html .= $is_specimen_page ? "<br>" : "";
|
| 210 |
3dd58832
|
Patric Plitzner
|
$detail_html .= create_label("Molecular Data") . $molecularData . "<br>";
|
| 211 |
b810158e
|
Patric Plitzner
|
}
|
| 212 |
8d9d64a5
|
Patric Plitzner
|
|
| 213 |
30845bda
|
Andreas Kohlbecker
|
if ($detailImages and !$is_specimen_page) {
|
| 214 |
3dd58832
|
Patric Plitzner
|
$detail_html .= create_label("Detail Images") . $detailImages . "<br>";
|
| 215 |
b810158e
|
Patric Plitzner
|
}
|
| 216 |
|
|
|
| 217 |
8d9d64a5
|
Patric Plitzner
|
//detail image gallery
|
| 218 |
c10f70e4
|
Katja Luther
|
if ($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)) {
|
| 219 |
8d9d64a5
|
Patric Plitzner
|
$detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
|
| 220 |
|
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}
|
| 221 |
|
|
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| 222 |
b810158e
|
Patric Plitzner
|
//character data
|
| 223 |
30845bda
|
Andreas Kohlbecker
|
if ($specimen->characterData) {
|
| 224 |
c10f70e4
|
Katja Luther
|
$detail_html .= $is_specimen_page ? "<br>" : "";
|
| 225 |
a442acb8
|
Patric Plitzner
|
$detail_html .= create_label("Character Data");
|
| 226 |
c10f70e4
|
Katja Luther
|
if ($is_specimen_page) {
|
| 227 |
b810158e
|
Patric Plitzner
|
$detail_html .= "<br>";
|
| 228 |
30845bda
|
Andreas Kohlbecker
|
foreach ($specimen->characterData as $characterStatePair) {
|
| 229 |
a442acb8
|
Patric Plitzner
|
$detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second;
|
| 230 |
|
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$detail_html .= "<br>";
|
| 231 |
|
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}
|
| 232 |
c10f70e4
|
Katja Luther
|
} else {
|
| 233 |
|
|
$detail_html .= l("detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
| 234 |
216abf0b
|
Patric Plitzner
|
$detail_html .= "<br>";
|
| 235 |
b810158e
|
Patric Plitzner
|
}
|
| 236 |
|
|
}
|
| 237 |
8d9d64a5
|
Patric Plitzner
|
return $detail_html;
|
| 238 |
|
|
}
|
| 239 |
8c1d6d72
|
Patric Plitzner
|
|
| 240 |
c10f70e4
|
Katja Luther
|
function addImageGallery($galleryName, $imageUuids)
|
| 241 |
|
|
{
|
| 242 |
b5c89485
|
Patric Plitzner
|
$images = array();
|
| 243 |
8d9d64a5
|
Patric Plitzner
|
foreach ($imageUuids as $uuid) {
|
| 244 |
|
|
$images[] = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $uuid);
|
| 245 |
8c1d6d72
|
Patric Plitzner
|
}
|
| 246 |
7cf177d0
|
Patrick Plitzner
|
|
| 247 |
|
|
$gallery_html = '';
|
| 248 |
|
|
if (count($imageUuids) > 0) {
|
| 249 |
|
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
| 250 |
|
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$captionElements = array(
|
| 251 |
|
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'title',
|
| 252 |
|
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'rights',
|
| 253 |
|
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);
|
| 254 |
|
|
$alternativeMediaUris = array();
|
| 255 |
c10f70e4
|
Katja Luther
|
foreach ($images as $image) {
|
| 256 |
|
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$mediaUri = getMediaUri($image);
|
| 257 |
|
|
if ($mediaUri) {
|
| 258 |
|
|
$alternativeMediaUris[] = $mediaUri;
|
| 259 |
|
|
} else {
|
| 260 |
|
|
$alternativeMediaUris[] = path_to_media($image->uuid);
|
| 261 |
|
|
}
|
| 262 |
7cf177d0
|
Patrick Plitzner
|
}
|
| 263 |
|
|
|
| 264 |
6eaec849
|
Katja Luther
|
|
| 265 |
|
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|
| 266 |
a9815578
|
Andreas Kohlbecker
|
$gallery_html = compose_cdm_media_gallerie(array(
|
| 267 |
7cf177d0
|
Patrick Plitzner
|
'mediaList' => $images,
|
| 268 |
|
|
'galleryName' => $galleryName,
|
| 269 |
|
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
| 270 |
|
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
| 271 |
|
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
| 272 |
|
|
'captionElements' => $captionElements,
|
| 273 |
|
|
'mediaLinkType' => 'LIGHTBOX',
|
| 274 |
6eaec849
|
Katja Luther
|
// 'alternativeMediaUri' => $alternativeMediaUris,
|
| 275 |
|
|
'alternativeMediaUri' => NULL,
|
| 276 |
7cf177d0
|
Patrick Plitzner
|
'galleryLinkUri' => NULL,
|
| 277 |
|
|
));
|
| 278 |
|
|
}
|
| 279 |
c10f70e4
|
Katja Luther
|
return "<br>" . create_label($galleryName) . "<br>" . $gallery_html;
|
| 280 |
b810158e
|
Patric Plitzner
|
}
|
| 281 |
|
|
|
| 282 |
c10f70e4
|
Katja Luther
|
function getMediaUri($media)
|
| 283 |
|
|
{
|
| 284 |
|
|
if (isset($media->representations) && sizeof($media->representations) == 1
|
| 285 |
|
|
&& isset($media->representations[0]->parts) &&
|
| 286 |
|
|
sizeof($media->representations[0]->parts) == 1) {
|
| 287 |
|
|
return $media->representations[0]->parts[0]->uri;
|
| 288 |
|
|
}
|
| 289 |
|
|
return null;
|
| 290 |
e2eaa6c7
|
Patrick Plitzner
|
}
|
| 291 |
|
|
|
| 292 |
8d9d64a5
|
Patric Plitzner
|
|
| 293 |
3dd58832
|
Patric Plitzner
|
/**
|
| 294 |
5a079dbf
|
Andreas Kohlbecker
|
* Formats the given string to a label for displaying key-object pairs in HTML
|
| 295 |
3dd58832
|
Patric Plitzner
|
* @return string
|
| 296 |
|
|
*/
|
| 297 |
|
|
function create_label($label)
|
| 298 |
|
|
{
|
| 299 |
c10f70e4
|
Katja Luther
|
return "<span class='specimen_table_label'>" . $label . ": </span>";
|
| 300 |
3dd58832
|
Patric Plitzner
|
}
|
| 301 |
|
|
|
| 302 |
f19f47fa
|
Andreas Kohlbecker
|
/**
|
| 303 |
|
|
* Compose an render array from a CDM DerivedUnitFacade object.
|
| 304 |
|
|
*
|
| 305 |
|
|
* compose_hook() implementation
|
| 306 |
235fc94b
|
Andreas Kohlbecker
|
*
|
| 307 |
|
|
* @param object $specimenOrObservation
|
| 308 |
|
|
* the CDM instance of type SpecimenOrObservation to compose
|
| 309 |
|
|
* the render array for
|
| 310 |
|
|
* @param array $derivatives
|
| 311 |
|
|
* the render array which contains the compositions of the derivatives
|
| 312 |
|
|
* of the supplied $specimenOrObservation
|
| 313 |
|
|
*
|
| 314 |
|
|
* @return array
|
| 315 |
|
|
* the supplied render array $derivatives to which the composition of the supplied
|
| 316 |
|
|
* $specimenOrObservation has been added to
|
| 317 |
5b26b91a
|
Andreas Kohlbecker
|
*
|
| 318 |
|
|
* @ingroup compose
|
| 319 |
f19f47fa
|
Andreas Kohlbecker
|
*/
|
| 320 |
|
|
|
| 321 |
a2acff0a
|
Katja Luther
|
function compose_cdm_specimen_or_observation($specimen_or_observation, $isSpecimen_page = false, &$derivatives = null)
|
| 322 |
98262d29
|
Katja Luther
|
{
|
| 323 |
c10f70e4
|
Katja Luther
|
$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
|
| 324 |
|
|
if (!isset($exclude_occurrence_fields)) {
|
| 325 |
|
|
$exclude_occurrence_fields = array(
|
| 326 |
a2acff0a
|
Katja Luther
|
|
| 327 |
c10f70e4
|
Katja Luther
|
'titleCache',
|
| 328 |
|
|
'protectedTitleCache',
|
| 329 |
|
|
'derivedUnitMedia',
|
| 330 |
|
|
'created',
|
| 331 |
|
|
'publish',
|
| 332 |
|
|
'updated',
|
| 333 |
|
|
'class',
|
| 334 |
|
|
'uuid',
|
| 335 |
d3f77ada
|
Katja Luther
|
''
|
| 336 |
c10f70e4
|
Katja Luther
|
);
|
| 337 |
|
|
}
|
| 338 |
a2acff0a
|
Katja Luther
|
if (variable_get('cdm_dataportal_compressed_specimen_derivate_table') || !$isSpecimen_page){
|
| 339 |
|
|
$exclude_occurrence_fields[] = 'derivationEvents';
|
| 340 |
|
|
}
|
| 341 |
f846e7e7
|
Andreas Kohlbecker
|
|
| 342 |
9b9037f3
|
Andreas Kohlbecker
|
|
| 343 |
c10f70e4
|
Katja Luther
|
// only show uuid it the user is logged in
|
| 344 |
e89c1115
|
Katja Luther
|
// if(user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE ) {
|
| 345 |
|
|
// unset($exclude_occurrence_fields[$a_idx]);
|
| 346 |
|
|
// }
|
| 347 |
15b7c460
|
Andreas Kohlbecker
|
|
| 348 |
c10f70e4
|
Katja Luther
|
if (!isset($derivatives)) {
|
| 349 |
|
|
$derivatives = array();
|
| 350 |
|
|
}
|
| 351 |
15b7c460
|
Andreas Kohlbecker
|
|
| 352 |
c10f70e4
|
Katja Luther
|
$descriptions = null;
|
| 353 |
|
|
$derivedFrom = null;
|
| 354 |
|
|
|
| 355 |
|
|
|
| 356 |
|
|
|
| 357 |
a2acff0a
|
Katja Luther
|
if (is_object($specimen_or_observation)) {
|
| 358 |
|
|
|
| 359 |
|
|
// request again for deeper initialization
|
| 360 |
|
|
$specimen_or_observation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimen_or_observation->uuid);
|
| 361 |
|
|
if ($specimen_or_observation->class == 'FieldUnit'){
|
| 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 |
c10f70e4
|
Katja Luther
|
|
| 373 |
a2acff0a
|
Katja Luther
|
$type_label = $specimen_or_observation->class;
|
| 374 |
|
|
RenderHints::setFootnoteListKey($type_label . '-' . $specimen_or_observation->uuid);
|
| 375 |
c10f70e4
|
Katja Luther
|
|
| 376 |
|
|
// collect typeStatus as label
|
| 377 |
a2acff0a
|
Katja Luther
|
if (isset($specimen_or_observation->specimenTypeDesignations)) {
|
| 378 |
c10f70e4
|
Katja Luther
|
$type_status = array();
|
| 379 |
a2acff0a
|
Katja Luther
|
foreach ($specimen_or_observation->specimenTypeDesignations as $typeDesignation) {
|
| 380 |
c10f70e4
|
Katja Luther
|
if (isset($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 |
9b9037f3
|
Andreas Kohlbecker
|
}
|
| 388 |
|
|
|
| 389 |
a2acff0a
|
Katja Luther
|
$title = $type_label . ': ' . $specimen_or_observation->titleCache;
|
| 390 |
c10f70e4
|
Katja Luther
|
|
| 391 |
|
|
$groups = array();
|
| 392 |
a2acff0a
|
Katja Luther
|
|
| 393 |
c10f70e4
|
Katja Luther
|
// --- add initialized fields
|
| 394 |
a2acff0a
|
Katja Luther
|
foreach (get_object_vars($specimen_or_observation) as $field => $value) {
|
| 395 |
c10f70e4
|
Katja Luther
|
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
| 396 |
|
|
switch ($field) {
|
| 397 |
d3f77ada
|
Katja Luther
|
|
| 398 |
c10f70e4
|
Katja Luther
|
/* ---- java.lang.Object --- */
|
| 399 |
|
|
case 'class':
|
| 400 |
|
|
if ($value != '' /* FieldUnit' */) {
|
| 401 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
| 402 |
|
|
}
|
| 403 |
|
|
break;
|
| 404 |
6fbdb943
|
Andreas Kohlbecker
|
|
| 405 |
c10f70e4
|
Katja Luther
|
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 |
4ae6064e
|
Andreas Kohlbecker
|
|
| 413 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 414 |
c10f70e4
|
Katja Luther
|
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'), $dd_elements);
|
| 421 |
|
|
break;
|
| 422 |
|
|
|
| 423 |
|
|
/* ---- SpecimenOrObservationBase --- */
|
| 424 |
|
|
case 'sex':
|
| 425 |
|
|
case 'lifeStage':
|
| 426 |
|
|
case 'kindOfUnit':
|
| 427 |
d3f77ada
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n);
|
| 428 |
c10f70e4
|
Katja Luther
|
break;
|
| 429 |
|
|
|
| 430 |
|
|
case 'definition':
|
| 431 |
|
|
// TODO
|
| 432 |
|
|
break;
|
| 433 |
|
|
|
| 434 |
|
|
case 'preferredStableUri':
|
| 435 |
|
|
|
| 436 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
| 437 |
|
|
break;
|
| 438 |
|
|
|
| 439 |
|
|
case 'specimenTypeDesignations':
|
| 440 |
ddbbdb0b
|
Katja Luther
|
|
| 441 |
|
|
//TODO: better display of details!!
|
| 442 |
c10f70e4
|
Katja Luther
|
@_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 |
4ae6064e
|
Andreas Kohlbecker
|
|
| 466 |
c10f70e4
|
Katja Luther
|
$taxon_name = '';
|
| 467 |
|
|
$name_link = '';
|
| 468 |
|
|
if ($determinationEvent->taxonName) {
|
| 469 |
6eaec849
|
Katja Luther
|
$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 |
c10f70e4
|
Katja Luther
|
}
|
| 476 |
|
|
if ($taxon_name) {
|
| 477 |
|
|
$taxon_html = render_taxon_or_name($taxon_name, $name_link);
|
| 478 |
|
|
$dd_elements[$weight] = $taxon_html;
|
| 479 |
|
|
}
|
| 480 |
|
|
if (isset($determinationEvent->modifier)) {
|
| 481 |
|
|
$dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
|
| 482 |
|
|
}
|
| 483 |
|
|
if ($timeperiod_string) {
|
| 484 |
|
|
$dd_elements[$weight] .= $glue . $timeperiod_string;
|
| 485 |
|
|
}
|
| 486 |
|
|
if (isset($determinationEvent->actor->titleCache)) {
|
| 487 |
|
|
$dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
|
| 488 |
|
|
}
|
| 489 |
|
|
if (isset($determinationEvent->description)) {
|
| 490 |
|
|
$dd_elements[$weight] .= $glue . $determinationEvent->description;
|
| 491 |
|
|
}
|
| 492 |
|
|
}
|
| 493 |
|
|
ksort($dd_elements);
|
| 494 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
|
| 495 |
|
|
break;
|
| 496 |
f846e7e7
|
Andreas Kohlbecker
|
|
| 497 |
c10f70e4
|
Katja Luther
|
case 'descriptions':
|
| 498 |
|
|
$occurrence_featureTree = cdm_get_occurrence_featureTree();
|
| 499 |
|
|
$dd_elements = array();
|
| 500 |
bfb2b81a
|
Andreas Kohlbecker
|
|
| 501 |
c10f70e4
|
Katja Luther
|
foreach ($value as $description) {
|
| 502 |
|
|
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
|
| 503 |
a2acff0a
|
Katja Luther
|
|
| 504 |
|
|
if($description->imageGallery == TRUE) {
|
| 505 |
|
|
continue;
|
| 506 |
|
|
}
|
| 507 |
c10f70e4
|
Katja Luther
|
$elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements);
|
| 508 |
|
|
$description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null));
|
| 509 |
|
|
$dd_elements[] = $description_render_elements;
|
| 510 |
|
|
}
|
| 511 |
6fbdb943
|
Andreas Kohlbecker
|
|
| 512 |
c10f70e4
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
| 513 |
|
|
break;
|
| 514 |
a2acff0a
|
Katja Luther
|
case '_derivedUnitMedia':
|
| 515 |
|
|
if ($isSpecimen_page){
|
| 516 |
|
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
| 517 |
|
|
$captionElements = array(
|
| 518 |
|
|
'#uri' => t('open media'),
|
| 519 |
|
|
);
|
| 520 |
|
|
$gallery_html = compose_cdm_media_gallerie(array(
|
| 521 |
|
|
'mediaList' => $value,
|
| 522 |
|
|
'galleryName' => $specimen_or_observation->titleCache,
|
| 523 |
|
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
| 524 |
|
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
| 525 |
|
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
| 526 |
|
|
'captionElements' => $captionElements,
|
| 527 |
|
|
'mediaLinkType' => 'LIGHTBOX',
|
| 528 |
|
|
'alternativeMediaUri' => NULL,
|
| 529 |
|
|
'galleryLinkUri' => NULL,
|
| 530 |
|
|
));
|
| 531 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, "Detail Images:" , markup_to_render_array($gallery_html),'',20);
|
| 532 |
a2acff0a
|
Katja Luther
|
}
|
| 533 |
6fbdb943
|
Andreas Kohlbecker
|
|
| 534 |
a2acff0a
|
Katja Luther
|
// $dd_elements[] = markup_to_render_array($gallery_html);
|
| 535 |
|
|
|
| 536 |
|
|
break;
|
| 537 |
c10f70e4
|
Katja Luther
|
case 'sources':
|
| 538 |
4186a152
|
Katja Luther
|
$annotations_and_sources = handle_annotations_and_sources(
|
| 539 |
|
|
$specimen_or_observation,
|
| 540 |
|
|
array(
|
| 541 |
|
|
'sources_as_content' => true,
|
| 542 |
|
|
'link_to_name_used_in_source' => 1,
|
| 543 |
|
|
'link_to_reference' => 0,
|
| 544 |
|
|
'add_footnote_keys' => 0
|
| 545 |
|
|
),
|
| 546 |
|
|
NULL,
|
| 547 |
|
|
''
|
| 548 |
|
|
);
|
| 549 |
|
|
if(!empty($annotations_and_sources['source_references'])){
|
| 550 |
|
|
@_description_list_group_add($groups, t('Sources') . ':', join(', ', $annotations_and_sources['source_references']),'',12 );
|
| 551 |
c10f70e4
|
Katja Luther
|
}
|
| 552 |
|
|
break;
|
| 553 |
|
|
|
| 554 |
|
|
|
| 555 |
|
|
/* ---- DerivedUnitBase --- */
|
| 556 |
|
|
case 'derivedFrom':
|
| 557 |
|
|
$derivedFrom = $value;
|
| 558 |
a2acff0a
|
Katja Luther
|
if ($isSpecimen_page) {
|
| 559 |
|
|
foreach ($derivedFrom->originals as $original) {
|
| 560 |
|
|
$pathToSpecimen = path_to_specimen($original->uuid);
|
| 561 |
|
|
$description = "";
|
| 562 |
|
|
if (isset( $derivedFrom->description) && $derivedFrom->description != ''){
|
| 563 |
|
|
$description = $derivedFrom->description . ": ";
|
| 564 |
|
|
}
|
| 565 |
|
|
|
| 566 |
|
|
$originals[] = markup_to_render_array(l($description . $original->titleCache, $pathToSpecimen, array('attributes' => array('target' => '_blank'))));
|
| 567 |
4186a152
|
Katja Luther
|
if ($original->class == 'FieldUnit'){
|
| 568 |
|
|
$label = t('Field data');
|
| 569 |
|
|
}else{
|
| 570 |
|
|
$label = t('Derived from');
|
| 571 |
|
|
}
|
| 572 |
|
|
@_description_list_group_add($groups, $label . ':',
|
| 573 |
a2acff0a
|
Katja Luther
|
$originals,
|
| 574 |
4186a152
|
Katja Luther
|
'', 13);
|
| 575 |
a2acff0a
|
Katja Luther
|
}
|
| 576 |
|
|
}
|
| 577 |
|
|
break;
|
| 578 |
|
|
case 'derivationEvents':
|
| 579 |
|
|
$derivationEvents = $value;
|
| 580 |
|
|
$derived_units = array();
|
| 581 |
|
|
if ($isSpecimen_page) {
|
| 582 |
|
|
foreach ($derivationEvents as $derivationEvent) {
|
| 583 |
|
|
foreach ($derivationEvent->derivatives as $derived_unit) {
|
| 584 |
|
|
$pathToSpecimen = path_to_specimen($derived_unit->uuid);
|
| 585 |
|
|
$description = "";
|
| 586 |
|
|
if (isset($derived_unit->description) && $derived_unit->description != '') {
|
| 587 |
|
|
$description = $derived_unit->description . ": ";
|
| 588 |
|
|
}
|
| 589 |
|
|
|
| 590 |
|
|
$derived_units[] = markup_to_render_array(l($description . $derived_unit->titleCache, $pathToSpecimen, array('attributes' => array('target' => '_blank'))));
|
| 591 |
|
|
}
|
| 592 |
|
|
} @_description_list_group_add($groups, t('Derivates') . ':',
|
| 593 |
|
|
$derived_units,
|
| 594 |
|
|
'', 100);
|
| 595 |
|
|
|
| 596 |
|
|
}
|
| 597 |
c10f70e4
|
Katja Luther
|
break;
|
| 598 |
|
|
|
| 599 |
|
|
case 'collection':
|
| 600 |
|
|
$sub_dl_groups = array();
|
| 601 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
| 602 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
| 603 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
| 604 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
| 605 |
|
|
// TODO "superCollection"
|
| 606 |
|
|
// TODO may have media
|
| 607 |
|
|
|
| 608 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
| 609 |
|
|
array(
|
| 610 |
|
|
array('#markup' => $value->titleCache),
|
| 611 |
|
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
| 612 |
|
|
)
|
| 613 |
|
|
);
|
| 614 |
|
|
break;
|
| 615 |
|
|
|
| 616 |
|
|
case 'storedUnder':
|
| 617 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
|
| 618 |
|
|
break;
|
| 619 |
|
|
|
| 620 |
|
|
|
| 621 |
|
|
/* ---- Specimen --- */
|
| 622 |
|
|
case 'sequences':
|
| 623 |
|
|
$dd_elements = array();
|
| 624 |
|
|
foreach ($value as $sequence) {
|
| 625 |
|
|
$dd_elements[] = compose_cdm_sequence($sequence);
|
| 626 |
|
|
}
|
| 627 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
| 628 |
|
|
break;
|
| 629 |
|
|
|
| 630 |
|
|
// TODO preservation
|
| 631 |
|
|
// TODO exsiccatum
|
| 632 |
|
|
|
| 633 |
|
|
|
| 634 |
|
|
/* ---- FieldObservation --- */
|
| 635 |
|
|
case 'gatheringEvent':
|
| 636 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache, '', 1);
|
| 637 |
|
|
@_description_list_group_add($groups, t('Gathering date'), timePeriodToString($value->timeperiod), '', 2);
|
| 638 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description, '', 3);
|
| 639 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text, '', 10);
|
| 640 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n, '', 4);
|
| 641 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod,'',5);
|
| 642 |
c10f70e4
|
Katja Luther
|
if (isset($value->absoluteElevation)) {
|
| 643 |
|
|
$min_max_markup = min_max_measure($value, 'absoluteElevation');
|
| 644 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup, '',6);
|
| 645 |
c10f70e4
|
Katja Luther
|
}
|
| 646 |
|
|
if (isset($value->distanceToGround)) {
|
| 647 |
|
|
$min_max_markup = min_max_measure($value, 'distanceToGround');
|
| 648 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup,'',7);
|
| 649 |
c10f70e4
|
Katja Luther
|
}
|
| 650 |
|
|
if (isset($value->distanceToWaterSurface)) {
|
| 651 |
|
|
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface');
|
| 652 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup, '',8);
|
| 653 |
c10f70e4
|
Katja Luther
|
}
|
| 654 |
abe0b021
|
Katja Luther
|
if (isset($value->collectingAreas) && count($value->collectingAreas) > 0) {
|
| 655 |
c10f70e4
|
Katja Luther
|
$area_representations = array();
|
| 656 |
|
|
foreach ($value->collectingAreas as $area) {
|
| 657 |
|
|
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
| 658 |
|
|
}
|
| 659 |
d3f77ada
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
| 660 |
|
|
array(
|
| 661 |
|
|
array('#markup' => implode(', ', $area_representations))
|
| 662 |
abe0b021
|
Katja Luther
|
),'',9
|
| 663 |
d3f77ada
|
Katja Luther
|
);
|
| 664 |
c10f70e4
|
Katja Luther
|
}
|
| 665 |
|
|
if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
|
| 666 |
|
|
$sub_dl_groups = array();
|
| 667 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
| 668 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
| 669 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
| 670 |
|
|
if (isset($value->exactLocation->referenceSystem)) {
|
| 671 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
| 672 |
|
|
}
|
| 673 |
6fbdb943
|
Andreas Kohlbecker
|
|
| 674 |
c10f70e4
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
| 675 |
|
|
array(
|
| 676 |
|
|
array('#markup' => $value->exactLocation->sexagesimalString),
|
| 677 |
|
|
array(
|
| 678 |
|
|
'#theme' => 'description_list',
|
| 679 |
|
|
'#groups' => $sub_dl_groups
|
| 680 |
|
|
),
|
| 681 |
abe0b021
|
Katja Luther
|
),'',11
|
| 682 |
c10f70e4
|
Katja Luther
|
);
|
| 683 |
|
|
}
|
| 684 |
|
|
break;
|
| 685 |
|
|
|
| 686 |
|
|
default:
|
| 687 |
|
|
if (is_object($value) || is_array($value)) {
|
| 688 |
d3f77ada
|
Katja Luther
|
drupal_set_message("Unhandled type in compose_cdm_specimen_or_observation() for field " . $field, "warning");
|
| 689 |
c10f70e4
|
Katja Luther
|
} else {
|
| 690 |
4186a152
|
Katja Luther
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), cdm_occurrence_field_name_label($value));
|
| 691 |
c10f70e4
|
Katja Luther
|
}
|
| 692 |
74ee6b54
|
Andreas Kohlbecker
|
|
| 693 |
c10f70e4
|
Katja Luther
|
}
|
| 694 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 695 |
f846e7e7
|
Andreas Kohlbecker
|
}
|
| 696 |
c10f70e4
|
Katja Luther
|
} // END of loop over $derivedUnitFacade fields
|
| 697 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 698 |
c10f70e4
|
Katja Luther
|
// Extensions
|
| 699 |
a2acff0a
|
Katja Luther
|
$extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $specimen_or_observation->uuid . '/extensions', array($specimen_or_observation->uuid));
|
| 700 |
c10f70e4
|
Katja Luther
|
if ($extensions && count($extensions)) {
|
| 701 |
|
|
|
| 702 |
|
|
$extensions_render_array = compose_extensions($extensions);
|
| 703 |
|
|
@_description_list_group_add($groups, t('Extensions') . ':',
|
| 704 |
|
|
$extensions_render_array,
|
| 705 |
|
|
'', 100);
|
| 706 |
f19f47fa
|
Andreas Kohlbecker
|
}
|
| 707 |
|
|
|
| 708 |
f846e7e7
|
Andreas Kohlbecker
|
|
| 709 |
a2acff0a
|
Katja Luther
|
|
| 710 |
c10f70e4
|
Katja Luther
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
| 711 |
|
|
uasort($groups, 'element_sort');
|
| 712 |
0820cdc0
|
Andreas Kohlbecker
|
|
| 713 |
c10f70e4
|
Katja Luther
|
$occurrence_elements = array(
|
| 714 |
e89c1115
|
Katja Luther
|
// '#title' => $title,
|
| 715 |
c10f70e4
|
Katja Luther
|
'#theme' => 'description_list',
|
| 716 |
|
|
'#groups' => $groups,
|
| 717 |
a2acff0a
|
Katja Luther
|
'#attributes' => array('class' => html_class_attribute_ref($specimen_or_observation)),
|
| 718 |
c10f70e4
|
Katja Luther
|
);
|
| 719 |
a2acff0a
|
Katja Luther
|
|
| 720 |
e89c1115
|
Katja Luther
|
$derivatives[] = drupal_render($occurrence_elements);
|
| 721 |
c10f70e4
|
Katja Luther
|
// all footnotes which has been assembled so far (e.g. from typeDesignations) to here
|
| 722 |
ade2b1f0
|
Katja Luther
|
// $foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
|
| 723 |
|
|
// if (!empty($foonote_li_elements)) {
|
| 724 |
|
|
// $derivatives[] = array(
|
| 725 |
|
|
// '#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>',
|
| 726 |
|
|
// );
|
| 727 |
|
|
// }
|
| 728 |
0820cdc0
|
Andreas Kohlbecker
|
|
| 729 |
c10f70e4
|
Katja Luther
|
// --- recurse into originals
|
| 730 |
a2acff0a
|
Katja Luther
|
if (!isset($derivedFrom) && !$isSpecimen_page) {
|
| 731 |
c10f70e4
|
Katja Luther
|
$derivedFrom = cdm_ws_get(
|
| 732 |
|
|
CDM_WS_OCCURRENCE,
|
| 733 |
a2acff0a
|
Katja Luther
|
array($specimen_or_observation->uuid, 'derivedFrom')
|
| 734 |
c10f70e4
|
Katja Luther
|
);
|
| 735 |
|
|
}
|
| 736 |
a2acff0a
|
Katja Luther
|
if (isset($derivedFrom) && !$isSpecimen_page) {
|
| 737 |
d3f77ada
|
Katja Luther
|
if (isset($derivedFrom->originals)) {
|
| 738 |
|
|
$derived_from_label = t('derived');
|
| 739 |
|
|
$preposition = t('from');
|
| 740 |
|
|
if(isset($derivedFrom->type)){
|
| 741 |
c10f70e4
|
Katja Luther
|
$derived_from_label = $derivedFrom->type->representation_L10n;
|
| 742 |
d3f77ada
|
Katja Luther
|
if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
|
| 743 |
|
|
$preposition = t('of');
|
| 744 |
c10f70e4
|
Katja Luther
|
}
|
| 745 |
|
|
}
|
| 746 |
|
|
if (count($groups) > 0) {
|
| 747 |
|
|
// TODO annotations
|
| 748 |
eeb98da8
|
Andreas Kohlbecker
|
|
| 749 |
c10f70e4
|
Katja Luther
|
// only display the derived from information when the derivative has any element which will be diplayed
|
| 750 |
|
|
$derivatives[] = array(
|
| 751 |
d3f77ada
|
Katja Luther
|
'#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>',
|
| 752 |
c10f70e4
|
Katja Luther
|
);
|
| 753 |
|
|
}
|
| 754 |
d3f77ada
|
Katja Luther
|
foreach ($derivedFrom->originals as $original) {
|
| 755 |
a2acff0a
|
Katja Luther
|
compose_cdm_specimen_or_observation($original, $isSpecimen_page, $derivatives);
|
| 756 |
d3f77ada
|
Katja Luther
|
}
|
| 757 |
c10f70e4
|
Katja Luther
|
}
|
| 758 |
0796d2f9
|
Andreas Kohlbecker
|
}
|
| 759 |
f1f05758
|
Andreas Kohlbecker
|
|
| 760 |
a2acff0a
|
Katja Luther
|
|
| 761 |
|
|
|
| 762 |
|
|
|
| 763 |
c10f70e4
|
Katja Luther
|
} // END of $specimenOrObservation exists
|
| 764 |
c70b93c3
|
Andreas Kohlbecker
|
|
| 765 |
c10f70e4
|
Katja Luther
|
return $derivatives;
|
| 766 |
f1f05758
|
Andreas Kohlbecker
|
}
|
| 767 |
0de9cf51
|
Andreas Kohlbecker
|
|
| 768 |
0820cdc0
|
Andreas Kohlbecker
|
|
| 769 |
0de9cf51
|
Andreas Kohlbecker
|
/**
|
| 770 |
|
|
* Compose an render array from a CDM Sequence object.
|
| 771 |
|
|
*
|
| 772 |
|
|
* compose_hook() implementation
|
| 773 |
|
|
*
|
| 774 |
|
|
* @param object $sequence
|
| 775 |
|
|
* CDM instance of type Sequence
|
| 776 |
|
|
* @return array
|
| 777 |
|
|
* A render array containing the fields of the supplied $sequence
|
| 778 |
5b26b91a
|
Andreas Kohlbecker
|
*
|
| 779 |
|
|
* @ingroup compose
|
| 780 |
0de9cf51
|
Andreas Kohlbecker
|
*/
|
| 781 |
52f57468
|
Katja Luther
|
function compose_cdm_sequence($sequence, $isSpecimenPage = false)
|
| 782 |
c10f70e4
|
Katja Luther
|
{
|
| 783 |
|
|
|
| 784 |
|
|
$exclude_sequence_fields = &drupal_static(__FUNCTION__);
|
| 785 |
|
|
if (!isset($exclude_sequence_fields)) {
|
| 786 |
|
|
$exclude_sequence_fields = array(
|
| 787 |
|
|
'titleCache',
|
| 788 |
|
|
'protectedTitleCache',
|
| 789 |
|
|
'microReference',
|
| 790 |
|
|
'created',
|
| 791 |
|
|
'updated',
|
| 792 |
|
|
'class',
|
| 793 |
|
|
);
|
| 794 |
|
|
}
|
| 795 |
0de9cf51
|
Andreas Kohlbecker
|
|
| 796 |
c10f70e4
|
Katja Luther
|
$groups = array();
|
| 797 |
0de9cf51
|
Andreas Kohlbecker
|
|
| 798 |
c10f70e4
|
Katja Luther
|
// -- retrieve additional data if neesscary
|
| 799 |
|
|
// TODO below call disabled since sequences are not yet supported,
|
| 800 |
|
|
// see #3347 (services and REST service controller for molecular classes implemented)
|
| 801 |
|
|
//
|
| 802 |
|
|
// cdm_load_annotations($sequence);
|
| 803 |
eeb98da8
|
Andreas Kohlbecker
|
|
| 804 |
c10f70e4
|
Katja Luther
|
foreach (get_object_vars($sequence) as $field => $value) {
|
| 805 |
eeb98da8
|
Andreas Kohlbecker
|
|
| 806 |
|
|
|
| 807 |
c10f70e4
|
Katja Luther
|
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
| 808 |
|
|
switch ($field) {
|
| 809 |
0de9cf51
|
Andreas Kohlbecker
|
|
| 810 |
c10f70e4
|
Katja Luther
|
case 'geneticAccessionNumber';
|
| 811 |
52f57468
|
Katja Luther
|
|
| 812 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 2);
|
| 813 |
c10f70e4
|
Katja Luther
|
break;
|
| 814 |
|
|
|
| 815 |
|
|
|
| 816 |
a2acff0a
|
Katja Luther
|
case 'dnaMarker': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
|
| 817 |
|
|
if (isset($value->name)) {
|
| 818 |
c10f70e4
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3);
|
| 819 |
|
|
}
|
| 820 |
|
|
if (isset($value->description)) {
|
| 821 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description'), $value->description, NULL, 4);
|
| 822 |
|
|
}
|
| 823 |
52f57468
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) , $value, NULL, 4);
|
| 824 |
c10f70e4
|
Katja Luther
|
break;
|
| 825 |
a2acff0a
|
Katja Luther
|
|
| 826 |
c10f70e4
|
Katja Luther
|
case 'consensusSequence':
|
| 827 |
|
|
// format in genbank style, force linebreaks after each 70 nucleotites
|
| 828 |
|
|
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
|
| 829 |
52f57468
|
Katja Luther
|
if ($value->length > 0) {
|
| 830 |
|
|
@_description_list_group_add(
|
| 831 |
|
|
$groups,
|
| 832 |
|
|
cdm_occurrence_field_name_label($field),
|
| 833 |
c10f70e4
|
Katja Luther
|
array(
|
| 834 |
52f57468
|
Katja Luther
|
array(
|
| 835 |
|
|
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb') . '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
| 836 |
|
|
'#wrapper_attributes' => array('class' => 'dna-sequence')
|
| 837 |
|
|
)
|
| 838 |
|
|
),
|
| 839 |
|
|
5);
|
| 840 |
|
|
}
|
| 841 |
c10f70e4
|
Katja Luther
|
break;
|
| 842 |
|
|
|
| 843 |
|
|
case 'dnaSample': // FIXME 3.3 implement
|
| 844 |
|
|
break;
|
| 845 |
|
|
case 'singleReads': // FIXME 3.3 implement
|
| 846 |
|
|
break;
|
| 847 |
|
|
case 'contigFile': // FIXME 3.3 implement - Media
|
| 848 |
|
|
break;
|
| 849 |
|
|
case 'pherograms': // FIXME 3.3 implement - Media
|
| 850 |
|
|
break;
|
| 851 |
|
|
case 'haplotype': // FIXME 3.3 implement
|
| 852 |
|
|
break;
|
| 853 |
|
|
case 'dateSequenced': // FIXME 3.3 now in SingelRead
|
| 854 |
|
|
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
| 855 |
|
|
break;
|
| 856 |
|
|
|
| 857 |
|
|
case 'barcode': // boolean
|
| 858 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes' : 'No', NULL, 7);
|
| 859 |
|
|
break;
|
| 860 |
|
|
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
|
| 861 |
|
|
break;
|
| 862 |
|
|
|
| 863 |
|
|
case 'citation':
|
| 864 |
|
|
@_description_list_group_add($groups,
|
| 865 |
|
|
cdm_occurrence_field_name_label($field),
|
| 866 |
|
|
theme('cdm_reference', array('reference' => $value, 'microReference' => $sequence->microReference)),
|
| 867 |
|
|
NULL,
|
| 868 |
|
|
8
|
| 869 |
|
|
);
|
| 870 |
|
|
break;
|
| 871 |
|
|
|
| 872 |
|
|
case 'publishedIn':
|
| 873 |
|
|
@_description_list_group_add($groups,
|
| 874 |
|
|
cdm_occurrence_field_name_label($field),
|
| 875 |
|
|
theme('cdm_reference', array('reference' => $value)),
|
| 876 |
|
|
NULL,
|
| 877 |
|
|
7
|
| 878 |
|
|
);
|
| 879 |
|
|
break;
|
| 880 |
|
|
|
| 881 |
|
|
case 'rights':
|
| 882 |
|
|
array_merge($groups, cdm_rights_as_dl_groups($value));
|
| 883 |
|
|
break;
|
| 884 |
|
|
|
| 885 |
|
|
case 'annotations':
|
| 886 |
|
|
$dd_elements = array();
|
| 887 |
|
|
foreach ($value as $annotation) {
|
| 888 |
|
|
// TODO respect annotation type filter settings
|
| 889 |
|
|
$dd_elements[] = $annotation->text;
|
| 890 |
|
|
}
|
| 891 |
|
|
@_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
|
| 892 |
|
|
break;
|
| 893 |
|
|
|
| 894 |
|
|
case 'markers':
|
| 895 |
|
|
$dd_elements = array();
|
| 896 |
|
|
foreach ($value as $marker) {
|
| 897 |
|
|
$dd_elements[] = compose_cdm_marker($marker);
|
| 898 |
|
|
}
|
| 899 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
|
| 900 |
|
|
break;
|
| 901 |
|
|
|
| 902 |
|
|
case 'chromatograms':
|
| 903 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
| 904 |
|
|
array(
|
| 905 |
|
|
'#markup' => compose_cdm_media_gallerie(array('medialist' => $value)),
|
| 906 |
|
|
),
|
| 907 |
|
|
NULL,
|
| 908 |
|
|
11);
|
| 909 |
|
|
break;
|
| 910 |
|
|
|
| 911 |
|
|
default:
|
| 912 |
|
|
if (is_object($value) || is_array($value)) {
|
| 913 |
|
|
drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
|
| 914 |
|
|
} else {
|
| 915 |
8e15d0fb
|
Katja Luther
|
if (!is_array($value) && strpos($value, 'http:') !== false ){
|
| 916 |
|
|
//make links for urls
|
| 917 |
|
|
$value = l($value, $value, array('attributes' => array('target' => '_blank')));
|
| 918 |
|
|
$value = markup_to_render_array($value);
|
| 919 |
|
|
}
|
| 920 |
|
|
|
| 921 |
58c1a035
|
Katja Luther
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
|
| 922 |
c10f70e4
|
Katja Luther
|
}
|
| 923 |
1b57b3c1
|
Andreas Kohlbecker
|
}
|
| 924 |
c10f70e4
|
Katja Luther
|
}
|
| 925 |
0de9cf51
|
Andreas Kohlbecker
|
}
|
| 926 |
|
|
|
| 927 |
c10f70e4
|
Katja Luther
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
| 928 |
|
|
uasort($groups, 'element_sort');
|
| 929 |
52f57468
|
Katja Luther
|
if ($isSpecimenPage) {
|
| 930 |
|
|
$sequence_elements = array(
|
| 931 |
|
|
'#title' => $sequence->dnaMarker,
|
| 932 |
|
|
'#theme' => 'description_list',
|
| 933 |
|
|
'#groups' => $groups
|
| 934 |
|
|
);
|
| 935 |
|
|
} else{
|
| 936 |
|
|
$sequence_elements = array(
|
| 937 |
|
|
'#title' => $sequence->dnaMarker -> titleCache,
|
| 938 |
|
|
'#theme' => 'description_list',
|
| 939 |
|
|
'#groups' => $groups
|
| 940 |
|
|
);
|
| 941 |
|
|
}
|
| 942 |
0de9cf51
|
Andreas Kohlbecker
|
|
| 943 |
c10f70e4
|
Katja Luther
|
return $sequence_elements;
|
| 944 |
0de9cf51
|
Andreas Kohlbecker
|
}
|
| 945 |
267da0d1
|
Katja Luther
|
/**
|
| 946 |
|
|
* Creates an array from a list of FieldUnitDTOs.
|
| 947 |
|
|
*
|
| 948 |
|
|
*
|
| 949 |
|
|
* @param object $specimenOrObservations
|
| 950 |
|
|
* list of FieldUnitDTOs
|
| 951 |
|
|
* @return array
|
| 952 |
|
|
* An array containing the hierarchy of the field units corresponding to the taxon
|
| 953 |
|
|
*
|
| 954 |
|
|
* @ingroup compose
|
| 955 |
|
|
*/
|
| 956 |
106e1cf9
|
Katja Luther
|
function compose_specimen_array(array $specimenOrObservations){
|
| 957 |
267da0d1
|
Katja Luther
|
$items_specimen = array();
|
| 958 |
|
|
$items = array();
|
| 959 |
276f39f6
|
Katja Luther
|
|
| 960 |
267da0d1
|
Katja Luther
|
//we need one more item to contain the items of one level (fieldunit, derivate data etc.)
|
| 961 |
|
|
foreach ($specimenOrObservations as &$specimenOrObservation) {
|
| 962 |
416bc78f
|
Katja Luther
|
|
| 963 |
|
|
$items['data'] = $specimenOrObservation->listLabel ;
|
| 964 |
106e1cf9
|
Katja Luther
|
$specimen = compose_cdm_specimen_or_observation_tree_entry($specimenOrObservation);
|
| 965 |
267da0d1
|
Katja Luther
|
$children = array();
|
| 966 |
|
|
$child = array();
|
| 967 |
|
|
$child['data'] =$specimen;
|
| 968 |
|
|
// $children[] = create_specimen_array($specimenOrObservation->derivates);
|
| 969 |
|
|
if (isset($specimenOrObservation->derivates) && sizeof($specimenOrObservation->derivates) > 0){
|
| 970 |
106e1cf9
|
Katja Luther
|
$child['children']= compose_specimen_array($specimenOrObservation->derivates);
|
| 971 |
267da0d1
|
Katja Luther
|
}
|
| 972 |
|
|
$children[]=$child;
|
| 973 |
|
|
$items['children'] = $children;
|
| 974 |
|
|
$items_specimen[] = $items;
|
| 975 |
|
|
}
|
| 976 |
|
|
return $items_specimen;
|
| 977 |
|
|
}
|
| 978 |
|
|
|
| 979 |
|
|
|
| 980 |
|
|
/**
|
| 981 |
|
|
* Compose an render array from a CDM DerivedUnitFacade object.
|
| 982 |
|
|
*
|
| 983 |
|
|
* compose_hook() implementation
|
| 984 |
|
|
*
|
| 985 |
|
|
* @param object $specimenOrObservation
|
| 986 |
|
|
* the CDM instance of type SpecimenOrObservation to compose
|
| 987 |
|
|
* the render array for
|
| 988 |
|
|
* @param array $derivatives
|
| 989 |
|
|
* the render array which contains the compositions of the derivatives
|
| 990 |
|
|
* of the supplied $specimenOrObservation
|
| 991 |
|
|
*
|
| 992 |
|
|
* @return array
|
| 993 |
|
|
* the supplied render array $derivatives to which the composition of the supplied
|
| 994 |
|
|
* $specimenOrObservation has been added to
|
| 995 |
|
|
*
|
| 996 |
|
|
* @ingroup compose
|
| 997 |
|
|
*/
|
| 998 |
|
|
|
| 999 |
58c1a035
|
Katja Luther
|
function compose_cdm_specimen_or_observation_tree_entry($specimen_or_observation)
|
| 1000 |
267da0d1
|
Katja Luther
|
{
|
| 1001 |
|
|
$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
|
| 1002 |
|
|
if (!isset($exclude_occurrence_fields)) {
|
| 1003 |
|
|
$exclude_occurrence_fields = array(
|
| 1004 |
|
|
'type',
|
| 1005 |
|
|
'taxonRelatedDerivedUnits',
|
| 1006 |
7965ef92
|
Katja Luther
|
'label',
|
| 1007 |
267da0d1
|
Katja Luther
|
'titleCache',
|
| 1008 |
7965ef92
|
Katja Luther
|
'listLabel',
|
| 1009 |
267da0d1
|
Katja Luther
|
'protectedTitleCache',
|
| 1010 |
|
|
'class',
|
| 1011 |
|
|
'uuid',
|
| 1012 |
ddbbdb0b
|
Katja Luther
|
'derivates',
|
| 1013 |
|
|
'collection'
|
| 1014 |
267da0d1
|
Katja Luther
|
);
|
| 1015 |
|
|
}
|
| 1016 |
|
|
$items = array();
|
| 1017 |
|
|
|
| 1018 |
|
|
// only show uuid it the user is logged in
|
| 1019 |
|
|
if (user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE) {
|
| 1020 |
|
|
// unset($exclude_occurrence_fields[$a_idx]);
|
| 1021 |
|
|
}
|
| 1022 |
|
|
|
| 1023 |
|
|
|
| 1024 |
58c1a035
|
Katja Luther
|
if (is_object($specimen_or_observation)) {
|
| 1025 |
267da0d1
|
Katja Luther
|
|
| 1026 |
58c1a035
|
Katja Luther
|
$type_label = $specimen_or_observation->recordBase;
|
| 1027 |
|
|
RenderHints::setFootnoteListKey($type_label . '-' . $specimen_or_observation->uuid);
|
| 1028 |
267da0d1
|
Katja Luther
|
|
| 1029 |
|
|
// collect typeStatus as label
|
| 1030 |
58c1a035
|
Katja Luther
|
if (isset($specimen_or_observation->specimenTypeDesignations)) {
|
| 1031 |
267da0d1
|
Katja Luther
|
$type_status = array();
|
| 1032 |
58c1a035
|
Katja Luther
|
foreach ($specimen_or_observation->specimenTypeDesignations as $typeDesignation) {
|
| 1033 |
267da0d1
|
Katja Luther
|
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
| 1034 |
|
|
$type_status[] = $typeDesignation->typeStatus->representation_L10n;
|
| 1035 |
|
|
}
|
| 1036 |
|
|
}
|
| 1037 |
|
|
if (count($type_status) > 0) {
|
| 1038 |
|
|
$type_label = implode(', ', $type_status);
|
| 1039 |
|
|
}
|
| 1040 |
|
|
}
|
| 1041 |
|
|
|
| 1042 |
6eaec849
|
Katja Luther
|
if (isset($typeDesignation)){
|
| 1043 |
|
|
$title = $type_label . ' for: ' . $typeDesignation->typifiedNames;
|
| 1044 |
|
|
}else{
|
| 1045 |
|
|
$title = $type_label;
|
| 1046 |
|
|
}
|
| 1047 |
|
|
|
| 1048 |
7965ef92
|
Katja Luther
|
$items['data'] = $title;
|
| 1049 |
267da0d1
|
Katja Luther
|
|
| 1050 |
|
|
$groups = array();
|
| 1051 |
|
|
$items['children'] = $groups;
|
| 1052 |
|
|
$children_items = array();
|
| 1053 |
|
|
// --- add initialized fields
|
| 1054 |
58c1a035
|
Katja Luther
|
foreach (get_object_vars($specimen_or_observation) as $field => $value) {
|
| 1055 |
267da0d1
|
Katja Luther
|
$child_item = array();
|
| 1056 |
|
|
|
| 1057 |
|
|
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
| 1058 |
|
|
switch ($field) {
|
| 1059 |
|
|
|
| 1060 |
|
|
/* ---- SpecimenOrObservationBase --- */
|
| 1061 |
a2acff0a
|
Katja Luther
|
case 'derivationEvent':
|
| 1062 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1);
|
| 1063 |
|
|
break;
|
| 1064 |
267da0d1
|
Katja Luther
|
case 'kindOfUnit':
|
| 1065 |
52f57468
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1);
|
| 1066 |
267da0d1
|
Katja Luther
|
break;
|
| 1067 |
|
|
|
| 1068 |
|
|
|
| 1069 |
|
|
case 'preferredStableUri':
|
| 1070 |
|
|
|
| 1071 |
7965ef92
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
| 1072 |
267da0d1
|
Katja Luther
|
break;
|
| 1073 |
|
|
|
| 1074 |
|
|
case 'specimenTypeDesignations':
|
| 1075 |
f1239704
|
Katja Luther
|
@_description_list_group_add(
|
| 1076 |
|
|
$groups,
|
| 1077 |
267da0d1
|
Katja Luther
|
cdm_occurrence_field_name_label($field),
|
| 1078 |
|
|
array(
|
| 1079 |
|
|
'#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
|
| 1080 |
|
|
)
|
| 1081 |
|
|
);
|
| 1082 |
|
|
break;
|
| 1083 |
|
|
|
| 1084 |
|
|
|
| 1085 |
f1239704
|
Katja Luther
|
|
| 1086 |
7965ef92
|
Katja Luther
|
case 'listOfMedia':
|
| 1087 |
|
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
| 1088 |
6eaec849
|
Katja Luther
|
|
| 1089 |
7965ef92
|
Katja Luther
|
$captionElements = array(
|
| 1090 |
6eaec849
|
Katja Luther
|
'title',
|
| 1091 |
7965ef92
|
Katja Luther
|
'#uri' => t('open media'),
|
| 1092 |
|
|
);
|
| 1093 |
|
|
$gallery_html = compose_cdm_media_gallerie(array(
|
| 1094 |
|
|
'mediaList' => $value,
|
| 1095 |
58c1a035
|
Katja Luther
|
'galleryName' => $specimen_or_observation->label,
|
| 1096 |
7965ef92
|
Katja Luther
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
| 1097 |
|
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
| 1098 |
|
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
| 1099 |
|
|
'captionElements' => $captionElements,
|
| 1100 |
|
|
'mediaLinkType' => 'LIGHTBOX',
|
| 1101 |
|
|
'alternativeMediaUri' => NULL,
|
| 1102 |
|
|
'galleryLinkUri' => NULL,
|
| 1103 |
6eaec849
|
Katja Luther
|
'showCaption' => true
|
| 1104 |
7965ef92
|
Katja Luther
|
));
|
| 1105 |
|
|
|
| 1106 |
276f39f6
|
Katja Luther
|
//@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $gallery_html);
|
| 1107 |
7965ef92
|
Katja Luther
|
break;
|
| 1108 |
267da0d1
|
Katja Luther
|
|
| 1109 |
|
|
|
| 1110 |
|
|
|
| 1111 |
|
|
/* ---- DerivedUnitBase --- */
|
| 1112 |
|
|
|
| 1113 |
1083804e
|
Andreas Kohlbecker
|
|
| 1114 |
a2acff0a
|
Katja Luther
|
case 'collectionDTO':
|
| 1115 |
7965ef92
|
Katja Luther
|
|
| 1116 |
267da0d1
|
Katja Luther
|
$sub_dl_groups = array();
|
| 1117 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
| 1118 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
| 1119 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
| 1120 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
| 1121 |
|
|
// TODO "superCollection"
|
| 1122 |
|
|
// TODO may have media
|
| 1123 |
|
|
|
| 1124 |
a2acff0a
|
Katja Luther
|
@_description_list_group_add($groups, 'Collection',
|
| 1125 |
267da0d1
|
Katja Luther
|
array(
|
| 1126 |
|
|
array('#markup' => $value->titleCache),
|
| 1127 |
|
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
| 1128 |
|
|
)
|
| 1129 |
|
|
);
|
| 1130 |
7965ef92
|
Katja Luther
|
|
| 1131 |
267da0d1
|
Katja Luther
|
break;
|
| 1132 |
|
|
|
| 1133 |
|
|
|
| 1134 |
|
|
|
| 1135 |
|
|
|
| 1136 |
|
|
/* ---- Specimen --- */
|
| 1137 |
|
|
case 'sequences':
|
| 1138 |
|
|
$dd_elements = array();
|
| 1139 |
|
|
foreach ($value as $sequence) {
|
| 1140 |
52f57468
|
Katja Luther
|
$dd_elements[] = compose_cdm_sequence($sequence, true);
|
| 1141 |
|
|
$dd_elements[] = "";
|
| 1142 |
267da0d1
|
Katja Luther
|
}
|
| 1143 |
a0f26798
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements,'', 100);
|
| 1144 |
267da0d1
|
Katja Luther
|
break;
|
| 1145 |
|
|
|
| 1146 |
|
|
// TODO preservation
|
| 1147 |
|
|
// TODO exsiccatum
|
| 1148 |
|
|
|
| 1149 |
|
|
|
| 1150 |
|
|
/* ---- FieldObservation --- */
|
| 1151 |
|
|
case 'gatheringEvent':
|
| 1152 |
|
|
|
| 1153 |
52f57468
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->collector);
|
| 1154 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, t('Gathering date'), timePeriodToString($value->timeperiod));
|
| 1155 |
267da0d1
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
|
| 1156 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality, '', 10);
|
| 1157 |
52f57468
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country);
|
| 1158 |
267da0d1
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
|
| 1159 |
|
|
if (isset($value->absoluteElevation)) {
|
| 1160 |
|
|
$min_max_markup = min_max_measure($value, 'absoluteElevation');
|
| 1161 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
|
| 1162 |
|
|
}
|
| 1163 |
276f39f6
|
Katja Luther
|
if (isset($value->distanceToGround) && $value->distanceToGround >0) {
|
| 1164 |
267da0d1
|
Katja Luther
|
$min_max_markup = min_max_measure($value, 'distanceToGround');
|
| 1165 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
|
| 1166 |
|
|
}
|
| 1167 |
276f39f6
|
Katja Luther
|
if (isset($value->distanceToWaterSurface) && $value->distanceToWaterSurface > 0) {
|
| 1168 |
267da0d1
|
Katja Luther
|
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface');
|
| 1169 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
|
| 1170 |
|
|
}
|
| 1171 |
|
|
|
| 1172 |
|
|
if (isset($value->collectingAreas)) {
|
| 1173 |
|
|
$area_representations = array();
|
| 1174 |
|
|
foreach ($value->collectingAreas as $area) {
|
| 1175 |
52f57468
|
Katja Luther
|
// $area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
| 1176 |
|
|
$area_representations[] = $area;
|
| 1177 |
267da0d1
|
Katja Luther
|
}
|
| 1178 |
|
|
if (!empty($area_representations))
|
| 1179 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
| 1180 |
|
|
array(
|
| 1181 |
|
|
array('#markup' => implode(', ', $area_representations))
|
| 1182 |
|
|
)
|
| 1183 |
|
|
);
|
| 1184 |
|
|
}
|
| 1185 |
106e1cf9
|
Katja Luther
|
if (isset($value->exactLocation) ) {
|
| 1186 |
267da0d1
|
Katja Luther
|
$sub_dl_groups = array();
|
| 1187 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
| 1188 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
| 1189 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
| 1190 |
|
|
if (isset($value->exactLocation->referenceSystem)) {
|
| 1191 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
| 1192 |
|
|
}
|
| 1193 |
106e1cf9
|
Katja Luther
|
if ( isSet($value->exactLocation->sexagesimalString)){
|
| 1194 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
| 1195 |
267da0d1
|
Katja Luther
|
array(
|
| 1196 |
106e1cf9
|
Katja Luther
|
array('#markup' => $value->exactLocation->sexagesimalString),
|
| 1197 |
|
|
array(
|
| 1198 |
|
|
'#theme' => 'description_list',
|
| 1199 |
|
|
'#groups' => $sub_dl_groups
|
| 1200 |
|
|
),
|
| 1201 |
abe0b021
|
Katja Luther
|
), '', 11
|
| 1202 |
106e1cf9
|
Katja Luther
|
);
|
| 1203 |
|
|
}
|
| 1204 |
267da0d1
|
Katja Luther
|
}
|
| 1205 |
|
|
|
| 1206 |
|
|
break;
|
| 1207 |
|
|
|
| 1208 |
|
|
/* ---- DerivationEvent --- */
|
| 1209 |
|
|
case 'derivationEvents':
|
| 1210 |
|
|
//@_description_list_group_add($groups, t('Association type'), $value->description);
|
| 1211 |
|
|
break;
|
| 1212 |
|
|
|
| 1213 |
|
|
|
| 1214 |
|
|
default:
|
| 1215 |
|
|
if (is_object($value) || is_array($value)) {
|
| 1216 |
52f57468
|
Katja Luther
|
drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
|
| 1217 |
267da0d1
|
Katja Luther
|
} else {
|
| 1218 |
|
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
| 1219 |
|
|
}
|
| 1220 |
|
|
|
| 1221 |
|
|
}
|
| 1222 |
|
|
|
| 1223 |
|
|
|
| 1224 |
|
|
}
|
| 1225 |
|
|
} // END of loop over $derivedUnitFacade fields
|
| 1226 |
|
|
|
| 1227 |
|
|
|
| 1228 |
|
|
|
| 1229 |
|
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
| 1230 |
|
|
uasort($groups, 'element_sort');
|
| 1231 |
|
|
|
| 1232 |
|
|
$occurrence_elements = array(
|
| 1233 |
|
|
// '#title' => $title,
|
| 1234 |
|
|
'#theme' => 'description_list',
|
| 1235 |
|
|
'#groups' => $groups,
|
| 1236 |
58c1a035
|
Katja Luther
|
'#attributes' => array('class' => html_class_attribute_ref($specimen_or_observation)),
|
| 1237 |
267da0d1
|
Katja Luther
|
);
|
| 1238 |
|
|
$output = drupal_render($occurrence_elements);
|
| 1239 |
106e1cf9
|
Katja Luther
|
if (isset($gallery_html)){
|
| 1240 |
|
|
$output .= $gallery_html;
|
| 1241 |
|
|
}
|
| 1242 |
a2acff0a
|
Katja Luther
|
$pathToSpecimen = path_to_specimen($specimen_or_observation->uuid);
|
| 1243 |
|
|
$output .= l("detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
| 1244 |
267da0d1
|
Katja Luther
|
} // END of $specimenOrObservation exists
|
| 1245 |
|
|
|
| 1246 |
|
|
return $output;
|
| 1247 |
|
|
}
|
| 1248 |
1083804e
|
Andreas Kohlbecker
|
|
| 1249 |
6eaec849
|
Katja Luther
|
function compose_table_of_blast_result(array $data){
|
| 1250 |
|
|
|
| 1251 |
|
|
foreach ($data as $row_data){
|
| 1252 |
|
|
$pathToSpecimen = path_to_specimen_by_accession_number($row_data['id']);
|
| 1253 |
|
|
$specimenPageLink = l($row_data['id'], $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
| 1254 |
|
|
|
| 1255 |
|
|
$rows[] = array(
|
| 1256 |
|
|
'data' => array(
|
| 1257 |
|
|
array(
|
| 1258 |
|
|
'data' => $row_data['def'],
|
| 1259 |
|
|
),
|
| 1260 |
|
|
array(
|
| 1261 |
|
|
'data' => $specimenPageLink,
|
| 1262 |
|
|
),
|
| 1263 |
|
|
array(
|
| 1264 |
|
|
'data' => $row_data['hsp_align_length'],
|
| 1265 |
|
|
),
|
| 1266 |
|
|
// array(
|
| 1267 |
|
|
// 'data' => $row_data['midline'],
|
| 1268 |
|
|
// ),
|
| 1269 |
|
|
array(
|
| 1270 |
|
|
'data' => $row_data['hsp_evalue'],
|
| 1271 |
|
|
)
|
| 1272 |
|
|
)
|
| 1273 |
|
|
);
|
| 1274 |
|
|
}
|
| 1275 |
|
|
$tableId = "blast_result_table";
|
| 1276 |
|
|
$blast_result_table = array(
|
| 1277 |
|
|
"#theme" => "table",
|
| 1278 |
|
|
"#weight" => 2,
|
| 1279 |
|
|
"#header" => array(
|
| 1280 |
|
|
"Name", "id", "Align Length", "e Value"),
|
| 1281 |
|
|
"#rows" => $rows,
|
| 1282 |
|
|
"#attributes" => array(
|
| 1283 |
|
|
"id" => $tableId,
|
| 1284 |
|
|
"border" => 2
|
| 1285 |
|
|
)
|
| 1286 |
|
|
);
|
| 1287 |
|
|
|
| 1288 |
|
|
drupal_add_js_rowToggle("#".$tableId);
|
| 1289 |
|
|
|
| 1290 |
|
|
$render_array['content'] = $blast_result_table;
|
| 1291 |
|
|
$out = drupal_render($render_array);
|
| 1292 |
|
|
//$blast_result_page-> content = drupal_render($render_array);
|
| 1293 |
|
|
return $out;
|
| 1294 |
|
|
}
|
| 1295 |
|
|
|
| 1296 |
|
|
|