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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
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Andreas Kohlbecker
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*/
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19 |
b810158e
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Patric Plitzner
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/**
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21 |
30845bda
|
Andreas Kohlbecker
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* Provides the HTML markup for a specimen page
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*
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* @param $specimen
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*
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25 |
b810158e
|
Patric Plitzner
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* @return string
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26 |
30845bda
|
Andreas Kohlbecker
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* The markup for a specimen page
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27 |
b810158e
|
Patric Plitzner
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*/
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28 |
a2acff0a
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Katja Luther
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function render_cdm_specimen_page($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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6eaec849
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Katja Luther
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'title',
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a2acff0a
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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, $is_specimen_page = false)
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b810158e
|
Patric Plitzner
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{
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$detail_html = "";
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//link to specimen page
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30845bda
|
Andreas Kohlbecker
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$pathToSpecimen = path_to_specimen($specimen->uuid);
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if (!$is_specimen_page) {
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cea59762
|
Andreas Kohlbecker
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$specimenPageLink = l($specimen->accessionNumber, $pathToSpecimen);
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25fc25ca
|
Patrick Plitzner
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$detail_html .= "<strong>Specimen summary: $specimenPageLink</strong><br>";
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a7a302a0
|
Patric Plitzner
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}
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b3ac03bf
|
Katja Luther
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30845bda
|
Andreas Kohlbecker
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if($is_specimen_page) {
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if($specimen->citation){
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6a660dc3
|
Patrick Plitzner
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$detail_html .= "<br>".$specimen->citation."<br>";
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b3ac03bf
|
Katja Luther
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fdc85125
|
Patric Plitzner
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}
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b810158e
|
Patric Plitzner
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}
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c10f70e4
|
Katja Luther
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if ($specimen->preferredStableUri) {
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cea59762
|
Andreas Kohlbecker
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$stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri);
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907cc9b4
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Patrick Plitzner
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$detail_html .= create_label("Preferred stable URI") . $stableIdentifierLink . "<br>";
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1cefb4e5
|
Patrick Plitzner
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}
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c10f70e4
|
Katja Luther
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if ($is_specimen_page) {
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fdc85125
|
Patric Plitzner
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// associated taxa
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c10f70e4
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Katja Luther
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if ($specimen->associatedTaxa) {
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3dd58832
|
Patric Plitzner
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$detail_html .= "<br>";
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c10f70e4
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Katja Luther
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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 $associatedTaxon) {
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f37da5d1
|
Patrick Plitzner
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$detail_html .= l($associatedTaxon->value, path_to_taxon($associatedTaxon->key, "specimens"));//$associatedTaxon->second."<br>";
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131 |
c10f70e4
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Katja Luther
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}
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132 |
fa09fe7d
|
Patrick Plitzner
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$detail_html .= "<br>";
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133 |
fdc85125
|
Patric Plitzner
|
}
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134 |
b810158e
|
Patric Plitzner
|
}
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c10f70e4
|
Katja Luther
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// - type information
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136 |
b810158e
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Patric Plitzner
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$types = "";
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137 |
30845bda
|
Andreas Kohlbecker
|
if (isset($specimen->types)) {
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138 |
56d58f9b
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Patric Plitzner
|
//typed taxa
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139 |
30845bda
|
Andreas Kohlbecker
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foreach ($specimen->types as $typeStatus => $typedTaxa) {
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140 |
b0efd824
|
Patrick Plitzner
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if($specimen->types){
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269e42e0
|
Patrick Plitzner
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if(empty($typeStatus) || $typeStatus == "_empty_"|| $typeStatus == ""){
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31ab4cf9
|
Patrick Plitzner
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$detail_html .= "<i>Type for:</i> ";
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269e42e0
|
Patrick Plitzner
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} else {
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$detail_html .= "<i>".$typeStatus."</i> of ";
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a5b11885
|
Patrick Plitzner
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}
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146 |
b0efd824
|
Patrick Plitzner
|
foreach($typedTaxa as $typedTaxon){
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$detail_html .= $typedTaxon." ";
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148 |
b3ac03bf
|
Katja Luther
|
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149 |
c10f70e4
|
Katja Luther
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}
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} else {
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$types .= $typeStatus . " ";
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153 |
fdc85125
|
Patric Plitzner
|
}
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154 |
b810158e
|
Patric Plitzner
|
}
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}
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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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$molecularData = "";
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if ($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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$molecularData .= "[no provider]";
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168 |
b810158e
|
Patric Plitzner
|
}
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169 |
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//contig link
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2c23b054
|
Patrick Plitzner
|
if (isset($molecular->contigFiles)) {
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b810158e
|
Patric Plitzner
|
$molecularData .= "[";
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2c23b054
|
Patrick Plitzner
|
if (sizeof($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)) {
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if (isset($contigFile->contigLink->uri) and $contigFile->contigLink->uri != null) {
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$molecularData .= create_html_link($contigFile->contigLink, true) . " ";
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177 |
37ab3ddc
|
Patric Plitzner
|
}
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c10f70e4
|
Katja Luther
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} else {
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179 |
2c23b054
|
Patrick Plitzner
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$molecularData .= "no contig ";
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}
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181 |
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//primer links
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c10f70e4
|
Katja Luther
|
if (isset($contigFile->primerLinks)) {
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183 |
65a4de51
|
Patrick Plitzner
|
$molecularData .= create_html_links($contigFile->primerLinks, true);
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184 |
b810158e
|
Patric Plitzner
|
}
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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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//FIXME separate with comma (remove trailing comma)
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}
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}
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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);
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195 |
b810158e
|
Patric Plitzner
|
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196 |
|
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if ($types) {
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197 |
c10f70e4
|
Katja Luther
|
$detail_html .= $is_specimen_page ? "<br>" : "";
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198 |
a0bbccce
|
Patrick Plitzner
|
$detail_html .= create_label("Type(s)") . $types . "<br>";
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199 |
b810158e
|
Patric Plitzner
|
}
|
200 |
30845bda
|
Andreas Kohlbecker
|
if ($specimenScans and !$is_specimen_page) {
|
201 |
3dd58832
|
Patric Plitzner
|
$detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
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202 |
b810158e
|
Patric Plitzner
|
}
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203 |
8d9d64a5
|
Patric Plitzner
|
//specimen scan image gallery
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204 |
c10f70e4
|
Katja Luther
|
if ($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
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205 |
8d9d64a5
|
Patric Plitzner
|
$detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
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206 |
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}
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207 |
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208 |
b810158e
|
Patric Plitzner
|
if ($molecularData) {
|
209 |
c10f70e4
|
Katja Luther
|
$detail_html .= $is_specimen_page ? "<br>" : "";
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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") . $detailImages . "<br>";
|
215 |
b810158e
|
Patric Plitzner
|
}
|
216 |
|
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217 |
8d9d64a5
|
Patric Plitzner
|
//detail image gallery
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218 |
c10f70e4
|
Katja Luther
|
if ($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)) {
|
219 |
8d9d64a5
|
Patric Plitzner
|
$detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
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220 |
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}
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221 |
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222 |
b810158e
|
Patric Plitzner
|
//character data
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223 |
30845bda
|
Andreas Kohlbecker
|
if ($specimen->characterData) {
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224 |
c10f70e4
|
Katja Luther
|
$detail_html .= $is_specimen_page ? "<br>" : "";
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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 |
cea59762
|
Andreas Kohlbecker
|
$detail_html .= l("detail page", $pathToSpecimen);
|
234 |
216abf0b
|
Patric Plitzner
|
$detail_html .= "<br>";
|
235 |
b810158e
|
Patric Plitzner
|
}
|
236 |
|
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}
|
237 |
8d9d64a5
|
Patric Plitzner
|
return $detail_html;
|
238 |
|
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}
|
239 |
8c1d6d72
|
Patric Plitzner
|
|
240 |
c10f70e4
|
Katja Luther
|
function addImageGallery($galleryName, $imageUuids)
|
241 |
|
|
{
|
242 |
b5c89485
|
Patric Plitzner
|
$images = array();
|
243 |
8d9d64a5
|
Patric Plitzner
|
foreach ($imageUuids as $uuid) {
|
244 |
|
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$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 |
|
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$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
250 |
|
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$captionElements = array(
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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($image);
|
257 |
|
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if ($mediaUri) {
|
258 |
|
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$alternativeMediaUris[] = $mediaUri;
|
259 |
|
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} else {
|
260 |
|
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$alternativeMediaUris[] = path_to_media($image->uuid);
|
261 |
|
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}
|
262 |
7cf177d0
|
Patrick Plitzner
|
}
|
263 |
|
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|
264 |
6eaec849
|
Katja Luther
|
|
265 |
|
|
|
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 |
|
|
$exclude_occurrence_fields = array(
|
326 |
a2acff0a
|
Katja Luther
|
|
327 |
c10f70e4
|
Katja Luther
|
'titleCache',
|
328 |
|
|
'protectedTitleCache',
|
329 |
|
|
'derivedUnitMedia',
|
330 |
|
|
'created',
|
331 |
|
|
'publish',
|
332 |
|
|
'updated',
|
333 |
|
|
'class',
|
334 |
|
|
'uuid',
|
335 |
d3f77ada
|
Katja Luther
|
''
|
336 |
c10f70e4
|
Katja Luther
|
);
|
337 |
|
|
}
|
338 |
44458b04
|
Andreas Kohlbecker
|
if ((variable_get(CDM_SPECIMEN_LIST_VIEW_MODE, CDM_SPECIMEN_LIST_VIEW_MODE_DEFAULT) == CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TABLE) || !$isSpecimen_page){
|
339 |
a2acff0a
|
Katja Luther
|
$exclude_occurrence_fields[] = 'derivationEvents';
|
340 |
|
|
}
|
341 |
f846e7e7
|
Andreas Kohlbecker
|
|
342 |
9b9037f3
|
Andreas Kohlbecker
|
|
343 |
c10f70e4
|
Katja Luther
|
// only show uuid it the user is logged in
|
344 |
e89c1115
|
Katja Luther
|
// if(user_is_logged_in() && ($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 |
cae389f9
|
Andreas Kohlbecker
|
// WARNING: adding a List<MediaDTO> as $specimen_or_observation->_derivedUnitMedia
|
363 |
a2acff0a
|
Katja Luther
|
$specimen_or_observation->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
|
364 |
|
|
$specimen_or_observation->uuid,
|
365 |
|
|
'fieldObjectMediaDTO',
|
366 |
|
|
));
|
367 |
|
|
}else{
|
368 |
cae389f9
|
Andreas Kohlbecker
|
// WARNING: adding a List<Media> as $specimen_or_observation->_derivedUnitMedia
|
369 |
a2acff0a
|
Katja Luther
|
$specimen_or_observation->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
|
370 |
|
|
$specimen_or_observation->uuid,
|
371 |
|
|
'derivedUnitMedia',
|
372 |
|
|
));
|
373 |
|
|
}
|
374 |
c10f70e4
|
Katja Luther
|
|
375 |
a2acff0a
|
Katja Luther
|
$type_label = $specimen_or_observation->class;
|
376 |
|
|
RenderHints::setFootnoteListKey($type_label . '-' . $specimen_or_observation->uuid);
|
377 |
c10f70e4
|
Katja Luther
|
|
378 |
|
|
// collect typeStatus as label
|
379 |
a2acff0a
|
Katja Luther
|
if (isset($specimen_or_observation->specimenTypeDesignations)) {
|
380 |
c10f70e4
|
Katja Luther
|
$type_status = array();
|
381 |
a2acff0a
|
Katja Luther
|
foreach ($specimen_or_observation->specimenTypeDesignations as $typeDesignation) {
|
382 |
c10f70e4
|
Katja Luther
|
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
383 |
|
|
$type_status[] = $typeDesignation->typeStatus->representation_L10n;
|
384 |
|
|
}
|
385 |
|
|
}
|
386 |
|
|
if (count($type_status) > 0) {
|
387 |
|
|
$type_label = implode(', ', $type_status);
|
388 |
|
|
}
|
389 |
9b9037f3
|
Andreas Kohlbecker
|
}
|
390 |
|
|
|
391 |
a2acff0a
|
Katja Luther
|
$title = $type_label . ': ' . $specimen_or_observation->titleCache;
|
392 |
c10f70e4
|
Katja Luther
|
|
393 |
|
|
$groups = array();
|
394 |
a2acff0a
|
Katja Luther
|
|
395 |
c10f70e4
|
Katja Luther
|
// --- add initialized fields
|
396 |
a2acff0a
|
Katja Luther
|
foreach (get_object_vars($specimen_or_observation) as $field => $value) {
|
397 |
c10f70e4
|
Katja Luther
|
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
398 |
|
|
switch ($field) {
|
399 |
d3f77ada
|
Katja Luther
|
|
400 |
c10f70e4
|
Katja Luther
|
/* ---- java.lang.Object --- */
|
401 |
|
|
case 'class':
|
402 |
|
|
if ($value != '' /* FieldUnit' */) {
|
403 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
404 |
|
|
}
|
405 |
|
|
break;
|
406 |
6fbdb943
|
Andreas Kohlbecker
|
|
407 |
c10f70e4
|
Katja Luther
|
case 'markers':
|
408 |
|
|
$dd_elements = array();
|
409 |
|
|
foreach ($value as $marker) {
|
410 |
|
|
$dd_elements[] = compose_cdm_marker($marker);
|
411 |
|
|
}
|
412 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
413 |
|
|
break;
|
414 |
4ae6064e
|
Andreas Kohlbecker
|
|
415 |
f19f47fa
|
Andreas Kohlbecker
|
|
416 |
c10f70e4
|
Katja Luther
|
case 'annotations':
|
417 |
|
|
$dd_elements = array();
|
418 |
|
|
foreach ($value as $annotation) {
|
419 |
|
|
// TODO respect annotation type filter settings
|
420 |
|
|
$dd_elements[] = $annotation->text;
|
421 |
|
|
}
|
422 |
50caf951
|
Katja Luther
|
@_description_list_group_add($groups, t('Notes:'), $dd_elements);
|
423 |
c10f70e4
|
Katja Luther
|
break;
|
424 |
|
|
|
425 |
|
|
/* ---- SpecimenOrObservationBase --- */
|
426 |
|
|
case 'sex':
|
427 |
|
|
case 'lifeStage':
|
428 |
|
|
case 'kindOfUnit':
|
429 |
d3f77ada
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n);
|
430 |
c10f70e4
|
Katja Luther
|
break;
|
431 |
|
|
|
432 |
|
|
case 'definition':
|
433 |
|
|
// TODO
|
434 |
|
|
break;
|
435 |
|
|
|
436 |
|
|
case 'preferredStableUri':
|
437 |
|
|
|
438 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
439 |
|
|
break;
|
440 |
|
|
|
441 |
|
|
case 'specimenTypeDesignations':
|
442 |
ddbbdb0b
|
Katja Luther
|
|
443 |
|
|
//TODO: better display of details!!
|
444 |
c10f70e4
|
Katja Luther
|
@_description_list_group_add(
|
445 |
|
|
$groups,
|
446 |
|
|
cdm_occurrence_field_name_label($field),
|
447 |
|
|
array(
|
448 |
0c720425
|
Andreas Kohlbecker
|
'#markup' => render_type_designations($value),
|
449 |
c10f70e4
|
Katja Luther
|
)
|
450 |
|
|
);
|
451 |
|
|
break;
|
452 |
|
|
|
453 |
|
|
case 'determinations':
|
454 |
|
|
$dd_elements = array();
|
455 |
|
|
$glue = ', ';
|
456 |
|
|
|
457 |
|
|
foreach ($value as $determinationEvent) {
|
458 |
|
|
$timeperiod_string = NULL;
|
459 |
|
|
if (isset($determinationEvent->timeperiod)) {
|
460 |
|
|
$timeperiod_string = timePeriodToString($determinationEvent->timeperiod);
|
461 |
|
|
}
|
462 |
|
|
$weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
|
463 |
|
|
// check key exists
|
464 |
|
|
while (array_key_exists($weight, $dd_elements)) {
|
465 |
|
|
$weight .= '0';
|
466 |
|
|
}
|
467 |
4ae6064e
|
Andreas Kohlbecker
|
|
468 |
c10f70e4
|
Katja Luther
|
$taxon_name = '';
|
469 |
|
|
$name_link = '';
|
470 |
|
|
if ($determinationEvent->taxonName) {
|
471 |
6eaec849
|
Katja Luther
|
$taxon_name = cdm_ws_get(CDM_WS_NAME, $determinationEvent->taxonName->uuid);
|
472 |
|
|
$taxon_name->taggedName = cdm_ws_get(CDM_WS_NAME, array($determinationEvent->taxonName->uuid, "taggedName"));
|
473 |
|
|
$name_link = path_to_name($determinationEvent->taxonName->uuid);
|
474 |
72d57201
|
Katja Luther
|
} else if ($determinationEvent->taxon) {
|
475 |
|
|
$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
|
476 |
|
|
$name_link = path_to_taxon($determinationEvent->taxon->uuid);
|
477 |
c10f70e4
|
Katja Luther
|
}
|
478 |
|
|
if ($taxon_name) {
|
479 |
4c812e71
|
Katja Luther
|
//$taxon_html = render_taxon_or_name($taxon_name, $name_link);
|
480 |
|
|
|
481 |
cea59762
|
Andreas Kohlbecker
|
$taxon_html = l($taxon_name->titleCache, $name_link);
|
482 |
c10f70e4
|
Katja Luther
|
$dd_elements[$weight] = $taxon_html;
|
483 |
|
|
}
|
484 |
|
|
if (isset($determinationEvent->modifier)) {
|
485 |
|
|
$dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
|
486 |
|
|
}
|
487 |
|
|
if ($timeperiod_string) {
|
488 |
|
|
$dd_elements[$weight] .= $glue . $timeperiod_string;
|
489 |
|
|
}
|
490 |
|
|
if (isset($determinationEvent->actor->titleCache)) {
|
491 |
|
|
$dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
|
492 |
|
|
}
|
493 |
|
|
if (isset($determinationEvent->description)) {
|
494 |
|
|
$dd_elements[$weight] .= $glue . $determinationEvent->description;
|
495 |
|
|
}
|
496 |
|
|
}
|
497 |
|
|
ksort($dd_elements);
|
498 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
|
499 |
|
|
break;
|
500 |
f846e7e7
|
Andreas Kohlbecker
|
|
501 |
c10f70e4
|
Katja Luther
|
case 'descriptions':
|
502 |
|
|
$dd_elements = array();
|
503 |
|
|
foreach ($value as $description) {
|
504 |
|
|
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
|
505 |
a2acff0a
|
Katja Luther
|
|
506 |
72d57201
|
Katja Luther
|
if ($description->imageGallery == TRUE) {
|
507 |
|
|
continue;
|
508 |
|
|
}
|
509 |
2527a83c
|
Andreas Kohlbecker
|
$description_string = render_description_string(get_root_nodes_for_dataset($description));
|
510 |
|
|
$dd_elements[] = markup_to_render_array($description_string);
|
511 |
c10f70e4
|
Katja Luther
|
}
|
512 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
513 |
|
|
break;
|
514 |
a2acff0a
|
Katja Luther
|
case '_derivedUnitMedia':
|
515 |
72d57201
|
Katja Luther
|
if ($isSpecimen_page) {
|
516 |
a2acff0a
|
Katja Luther
|
$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 |
cae389f9
|
Andreas Kohlbecker
|
'mediaList' => $value, // WARNING: this is either a List<Media> or List<MediaDTO>, see above ~line 361
|
522 |
a2acff0a
|
Katja Luther
|
'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' => $captionElements,
|
527 |
|
|
'mediaLinkType' => 'LIGHTBOX',
|
528 |
|
|
'alternativeMediaUri' => NULL,
|
529 |
|
|
'galleryLinkUri' => NULL,
|
530 |
|
|
));
|
531 |
72d57201
|
Katja Luther
|
@_description_list_group_add($groups, "Detail Images:", markup_to_render_array($gallery_html), '', 20);
|
532 |
a2acff0a
|
Katja Luther
|
}
|
533 |
6fbdb943
|
Andreas Kohlbecker
|
|
534 |
72d57201
|
Katja Luther
|
// $dd_elements[] = markup_to_render_array($gallery_html);
|
535 |
a2acff0a
|
Katja Luther
|
|
536 |
|
|
break;
|
537 |
c10f70e4
|
Katja Luther
|
case 'sources':
|
538 |
4186a152
|
Katja Luther
|
$annotations_and_sources = handle_annotations_and_sources(
|
539 |
|
|
$specimen_or_observation,
|
540 |
|
|
array(
|
541 |
|
|
'sources_as_content' => true,
|
542 |
|
|
'link_to_name_used_in_source' => 1,
|
543 |
|
|
'link_to_reference' => 0,
|
544 |
|
|
'add_footnote_keys' => 0
|
545 |
|
|
),
|
546 |
|
|
NULL,
|
547 |
a067cc04
|
Andreas Kohlbecker
|
RenderHints::getFootnoteListKey()
|
548 |
4186a152
|
Katja Luther
|
);
|
549 |
72d57201
|
Katja Luther
|
if (!empty($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 |
|
|
$description = "";
|
562 |
72d57201
|
Katja Luther
|
if (isset($derivedFrom->description) && $derivedFrom->description != '') {
|
563 |
a2acff0a
|
Katja Luther
|
$description = $derivedFrom->description . ": ";
|
564 |
|
|
}
|
565 |
|
|
|
566 |
cea59762
|
Andreas Kohlbecker
|
$originals[] = markup_to_render_array(l($description . $original->titleCache, $pathToSpecimen));
|
567 |
72d57201
|
Katja Luther
|
if ($original->class == 'FieldUnit') {
|
568 |
4186a152
|
Katja Luther
|
$label = t('Field data');
|
569 |
72d57201
|
Katja Luther
|
} else {
|
570 |
4186a152
|
Katja Luther
|
$label = t('Derived from');
|
571 |
|
|
}
|
572 |
|
|
@_description_list_group_add($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 |
cea59762
|
Andreas Kohlbecker
|
$derived_units[] = markup_to_render_array(l($description . $derived_unit->titleCache, $pathToSpecimen));
|
591 |
72d57201
|
Katja Luther
|
}
|
592 |
|
|
}
|
593 |
|
|
@_description_list_group_add($groups, t('Derivates') . ':',
|
594 |
a2acff0a
|
Katja Luther
|
$derived_units,
|
595 |
72d57201
|
Katja Luther
|
'', 100);
|
596 |
a2acff0a
|
Katja Luther
|
|
597 |
|
|
}
|
598 |
c10f70e4
|
Katja Luther
|
break;
|
599 |
|
|
|
600 |
|
|
case 'collection':
|
601 |
|
|
$sub_dl_groups = array();
|
602 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
603 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
604 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
605 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
606 |
|
|
// TODO "superCollection"
|
607 |
|
|
// TODO may have media
|
608 |
|
|
|
609 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
610 |
|
|
array(
|
611 |
|
|
array('#markup' => $value->titleCache),
|
612 |
|
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
613 |
|
|
)
|
614 |
|
|
);
|
615 |
|
|
break;
|
616 |
|
|
|
617 |
|
|
case 'storedUnder':
|
618 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
|
619 |
|
|
break;
|
620 |
72d57201
|
Katja Luther
|
case 'dnaQuality':
|
621 |
|
|
$sub_dl_groups = array();
|
622 |
|
|
|
623 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('purificationMethod'), $value->purificationMethod, NULL, 1);
|
624 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('ratioOfAbsorbance260_230'), $value->ratioOfAbsorbance260_230, NULL, 2);
|
625 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('ratioOfAbsorbance260_280'), $value->ratioOfAbsorbance260_280, NULL, 3);
|
626 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('concentration'), $value->concentration, NULL, 4);
|
627 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('concentrationUnit'), $value->concentrationUnit, NULL, 4);
|
628 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('qualityTerm'), $value->qualityTerm, NULL, 4);
|
629 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('qualityCheckDate'), $value->qualityCheckDate, NULL, 4);
|
630 |
|
|
|
631 |
|
|
if (is_array($sub_dl_groups) && sizeof($sub_dl_groups)>0) {
|
632 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
633 |
|
|
array(
|
634 |
|
|
array('#markup' => $value->titleCache),
|
635 |
|
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
636 |
|
|
)
|
637 |
|
|
);
|
638 |
|
|
}
|
639 |
|
|
break;
|
640 |
|
|
|
641 |
|
|
case 'preservation':
|
642 |
|
|
$sub_dl_groups = array();
|
643 |
c10f70e4
|
Katja Luther
|
|
644 |
72d57201
|
Katja Luther
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('medium'), $value->medium, NULL, 1);
|
645 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('temperature'), $value->temperature, NULL, 2);
|
646 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('definedMaterialOrMethod'), $value->definedMaterialOrMethod, NULL, 3);
|
647 |
|
|
|
648 |
|
|
if (is_array($sub_dl_groups) && sizeof($sub_dl_groups)>0) {
|
649 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
650 |
|
|
array(
|
651 |
|
|
array('#markup' => $value->titleCache),
|
652 |
|
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
653 |
|
|
)
|
654 |
|
|
);
|
655 |
|
|
}
|
656 |
|
|
break;
|
657 |
c10f70e4
|
Katja Luther
|
|
658 |
|
|
/* ---- Specimen --- */
|
659 |
|
|
case 'sequences':
|
660 |
|
|
$dd_elements = array();
|
661 |
|
|
foreach ($value as $sequence) {
|
662 |
|
|
$dd_elements[] = compose_cdm_sequence($sequence);
|
663 |
|
|
}
|
664 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
665 |
|
|
break;
|
666 |
|
|
|
667 |
|
|
// TODO preservation
|
668 |
|
|
// TODO exsiccatum
|
669 |
|
|
|
670 |
|
|
|
671 |
|
|
/* ---- FieldObservation --- */
|
672 |
|
|
case 'gatheringEvent':
|
673 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache, '', 1);
|
674 |
|
|
@_description_list_group_add($groups, t('Gathering date'), timePeriodToString($value->timeperiod), '', 2);
|
675 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description, '', 3);
|
676 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text, '', 10);
|
677 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n, '', 4);
|
678 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod,'',5);
|
679 |
c10f70e4
|
Katja Luther
|
if (isset($value->absoluteElevation)) {
|
680 |
2f4646e0
|
Andreas Kohlbecker
|
$min_max_markup = statistical_values_from_gathering_event($value, 'absoluteElevation');
|
681 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup, '',6);
|
682 |
c10f70e4
|
Katja Luther
|
}
|
683 |
|
|
if (isset($value->distanceToGround)) {
|
684 |
2f4646e0
|
Andreas Kohlbecker
|
$min_max_markup = statistical_values_from_gathering_event($value, 'distanceToGround');
|
685 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup,'',7);
|
686 |
c10f70e4
|
Katja Luther
|
}
|
687 |
|
|
if (isset($value->distanceToWaterSurface)) {
|
688 |
2f4646e0
|
Andreas Kohlbecker
|
$min_max_markup = statistical_values_from_gathering_event($value, 'distanceToWaterSurface');
|
689 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup, '',8);
|
690 |
c10f70e4
|
Katja Luther
|
}
|
691 |
abe0b021
|
Katja Luther
|
if (isset($value->collectingAreas) && count($value->collectingAreas) > 0) {
|
692 |
c10f70e4
|
Katja Luther
|
$area_representations = array();
|
693 |
|
|
foreach ($value->collectingAreas as $area) {
|
694 |
|
|
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
695 |
|
|
}
|
696 |
d3f77ada
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
697 |
|
|
array(
|
698 |
|
|
array('#markup' => implode(', ', $area_representations))
|
699 |
abe0b021
|
Katja Luther
|
),'',9
|
700 |
d3f77ada
|
Katja Luther
|
);
|
701 |
c10f70e4
|
Katja Luther
|
}
|
702 |
|
|
if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
|
703 |
|
|
$sub_dl_groups = array();
|
704 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
705 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
706 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
707 |
|
|
if (isset($value->exactLocation->referenceSystem)) {
|
708 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
709 |
|
|
}
|
710 |
6fbdb943
|
Andreas Kohlbecker
|
|
711 |
c10f70e4
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
712 |
|
|
array(
|
713 |
|
|
array('#markup' => $value->exactLocation->sexagesimalString),
|
714 |
|
|
array(
|
715 |
|
|
'#theme' => 'description_list',
|
716 |
|
|
'#groups' => $sub_dl_groups
|
717 |
|
|
),
|
718 |
abe0b021
|
Katja Luther
|
),'',11
|
719 |
c10f70e4
|
Katja Luther
|
);
|
720 |
|
|
}
|
721 |
|
|
break;
|
722 |
|
|
|
723 |
|
|
default:
|
724 |
|
|
if (is_object($value) || is_array($value)) {
|
725 |
d3f77ada
|
Katja Luther
|
drupal_set_message("Unhandled type in compose_cdm_specimen_or_observation() for field " . $field, "warning");
|
726 |
c10f70e4
|
Katja Luther
|
} else {
|
727 |
f60b52c4
|
Katja Luther
|
if ($field == 'RecordBase' && $value == 'DnaSample') {
|
728 |
|
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), 'DNA Sample');
|
729 |
|
|
} else {
|
730 |
50caf951
|
Katja Luther
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
731 |
f60b52c4
|
Katja Luther
|
}
|
732 |
c10f70e4
|
Katja Luther
|
}
|
733 |
74ee6b54
|
Andreas Kohlbecker
|
|
734 |
c10f70e4
|
Katja Luther
|
}
|
735 |
f19f47fa
|
Andreas Kohlbecker
|
|
736 |
f846e7e7
|
Andreas Kohlbecker
|
}
|
737 |
c10f70e4
|
Katja Luther
|
} // END of loop over $derivedUnitFacade fields
|
738 |
f19f47fa
|
Andreas Kohlbecker
|
|
739 |
c10f70e4
|
Katja Luther
|
// Extensions
|
740 |
db9c6559
|
Andreas Kohlbecker
|
// TODO: filter by using visible_extensions_sorted()
|
741 |
a2acff0a
|
Katja Luther
|
$extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $specimen_or_observation->uuid . '/extensions', array($specimen_or_observation->uuid));
|
742 |
c10f70e4
|
Katja Luther
|
if ($extensions && count($extensions)) {
|
743 |
|
|
|
744 |
|
|
$extensions_render_array = compose_extensions($extensions);
|
745 |
|
|
@_description_list_group_add($groups, t('Extensions') . ':',
|
746 |
|
|
$extensions_render_array,
|
747 |
|
|
'', 100);
|
748 |
f19f47fa
|
Andreas Kohlbecker
|
}
|
749 |
|
|
|
750 |
f846e7e7
|
Andreas Kohlbecker
|
|
751 |
a2acff0a
|
Katja Luther
|
|
752 |
c10f70e4
|
Katja Luther
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
753 |
|
|
uasort($groups, 'element_sort');
|
754 |
0820cdc0
|
Andreas Kohlbecker
|
|
755 |
c10f70e4
|
Katja Luther
|
$occurrence_elements = array(
|
756 |
e89c1115
|
Katja Luther
|
// '#title' => $title,
|
757 |
c10f70e4
|
Katja Luther
|
'#theme' => 'description_list',
|
758 |
|
|
'#groups' => $groups,
|
759 |
a2acff0a
|
Katja Luther
|
'#attributes' => array('class' => html_class_attribute_ref($specimen_or_observation)),
|
760 |
c10f70e4
|
Katja Luther
|
);
|
761 |
a2acff0a
|
Katja Luther
|
|
762 |
43d01429
|
Andreas Kohlbecker
|
$derivatives[] = $occurrence_elements;
|
763 |
c10f70e4
|
Katja Luther
|
// all footnotes which has been assembled so far (e.g. from typeDesignations) to here
|
764 |
d8069342
|
Andreas Kohlbecker
|
// $foonote_li_elements = render_footnotes(RenderHints::getFootnoteListKey(), 'span');
|
765 |
ade2b1f0
|
Katja Luther
|
// if (!empty($foonote_li_elements)) {
|
766 |
|
|
// $derivatives[] = array(
|
767 |
|
|
// '#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>',
|
768 |
|
|
// );
|
769 |
|
|
// }
|
770 |
0820cdc0
|
Andreas Kohlbecker
|
|
771 |
c10f70e4
|
Katja Luther
|
// --- recurse into originals
|
772 |
a2acff0a
|
Katja Luther
|
if (!isset($derivedFrom) && !$isSpecimen_page) {
|
773 |
c10f70e4
|
Katja Luther
|
$derivedFrom = cdm_ws_get(
|
774 |
|
|
CDM_WS_OCCURRENCE,
|
775 |
a2acff0a
|
Katja Luther
|
array($specimen_or_observation->uuid, 'derivedFrom')
|
776 |
c10f70e4
|
Katja Luther
|
);
|
777 |
|
|
}
|
778 |
a2acff0a
|
Katja Luther
|
if (isset($derivedFrom) && !$isSpecimen_page) {
|
779 |
d3f77ada
|
Katja Luther
|
if (isset($derivedFrom->originals)) {
|
780 |
|
|
$derived_from_label = t('derived');
|
781 |
|
|
$preposition = t('from');
|
782 |
|
|
if(isset($derivedFrom->type)){
|
783 |
c10f70e4
|
Katja Luther
|
$derived_from_label = $derivedFrom->type->representation_L10n;
|
784 |
d3f77ada
|
Katja Luther
|
if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
|
785 |
|
|
$preposition = t('of');
|
786 |
c10f70e4
|
Katja Luther
|
}
|
787 |
|
|
}
|
788 |
|
|
if (count($groups) > 0) {
|
789 |
|
|
// TODO annotations
|
790 |
eeb98da8
|
Andreas Kohlbecker
|
|
791 |
c10f70e4
|
Katja Luther
|
// only display the derived from information when the derivative has any element which will be diplayed
|
792 |
|
|
$derivatives[] = array(
|
793 |
d3f77ada
|
Katja Luther
|
'#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>',
|
794 |
c10f70e4
|
Katja Luther
|
);
|
795 |
|
|
}
|
796 |
d3f77ada
|
Katja Luther
|
foreach ($derivedFrom->originals as $original) {
|
797 |
a2acff0a
|
Katja Luther
|
compose_cdm_specimen_or_observation($original, $isSpecimen_page, $derivatives);
|
798 |
d3f77ada
|
Katja Luther
|
}
|
799 |
c10f70e4
|
Katja Luther
|
}
|
800 |
0796d2f9
|
Andreas Kohlbecker
|
}
|
801 |
f1f05758
|
Andreas Kohlbecker
|
|
802 |
a2acff0a
|
Katja Luther
|
|
803 |
|
|
|
804 |
|
|
|
805 |
c10f70e4
|
Katja Luther
|
} // END of $specimenOrObservation exists
|
806 |
c70b93c3
|
Andreas Kohlbecker
|
|
807 |
c10f70e4
|
Katja Luther
|
return $derivatives;
|
808 |
f1f05758
|
Andreas Kohlbecker
|
}
|
809 |
0de9cf51
|
Andreas Kohlbecker
|
|
810 |
0820cdc0
|
Andreas Kohlbecker
|
|
811 |
0de9cf51
|
Andreas Kohlbecker
|
/**
|
812 |
|
|
* Compose an render array from a CDM Sequence object.
|
813 |
|
|
*
|
814 |
|
|
* compose_hook() implementation
|
815 |
|
|
*
|
816 |
|
|
* @param object $sequence
|
817 |
|
|
* CDM instance of type Sequence
|
818 |
|
|
* @return array
|
819 |
|
|
* A render array containing the fields of the supplied $sequence
|
820 |
5b26b91a
|
Andreas Kohlbecker
|
*
|
821 |
|
|
* @ingroup compose
|
822 |
0de9cf51
|
Andreas Kohlbecker
|
*/
|
823 |
52f57468
|
Katja Luther
|
function compose_cdm_sequence($sequence, $isSpecimenPage = false)
|
824 |
c10f70e4
|
Katja Luther
|
{
|
825 |
|
|
|
826 |
|
|
$exclude_sequence_fields = &drupal_static(__FUNCTION__);
|
827 |
|
|
if (!isset($exclude_sequence_fields)) {
|
828 |
|
|
$exclude_sequence_fields = array(
|
829 |
|
|
'titleCache',
|
830 |
|
|
'protectedTitleCache',
|
831 |
|
|
'microReference',
|
832 |
|
|
'created',
|
833 |
|
|
'updated',
|
834 |
|
|
'class',
|
835 |
|
|
);
|
836 |
|
|
}
|
837 |
0de9cf51
|
Andreas Kohlbecker
|
|
838 |
c10f70e4
|
Katja Luther
|
$groups = array();
|
839 |
0de9cf51
|
Andreas Kohlbecker
|
|
840 |
c10f70e4
|
Katja Luther
|
// -- retrieve additional data if neesscary
|
841 |
|
|
// TODO below call disabled since sequences are not yet supported,
|
842 |
|
|
// see #3347 (services and REST service controller for molecular classes implemented)
|
843 |
|
|
//
|
844 |
|
|
// cdm_load_annotations($sequence);
|
845 |
eeb98da8
|
Andreas Kohlbecker
|
|
846 |
c10f70e4
|
Katja Luther
|
foreach (get_object_vars($sequence) as $field => $value) {
|
847 |
eeb98da8
|
Andreas Kohlbecker
|
|
848 |
|
|
|
849 |
c10f70e4
|
Katja Luther
|
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
850 |
|
|
switch ($field) {
|
851 |
0de9cf51
|
Andreas Kohlbecker
|
|
852 |
c10f70e4
|
Katja Luther
|
case 'geneticAccessionNumber';
|
853 |
52f57468
|
Katja Luther
|
|
854 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 2);
|
855 |
c10f70e4
|
Katja Luther
|
break;
|
856 |
|
|
|
857 |
|
|
|
858 |
a2acff0a
|
Katja Luther
|
case 'dnaMarker': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
|
859 |
|
|
if (isset($value->name)) {
|
860 |
c10f70e4
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3);
|
861 |
|
|
}
|
862 |
|
|
if (isset($value->description)) {
|
863 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description'), $value->description, NULL, 4);
|
864 |
|
|
}
|
865 |
52f57468
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) , $value, NULL, 4);
|
866 |
c10f70e4
|
Katja Luther
|
break;
|
867 |
a2acff0a
|
Katja Luther
|
|
868 |
c10f70e4
|
Katja Luther
|
case 'consensusSequence':
|
869 |
|
|
// format in genbank style, force linebreaks after each 70 nucleotites
|
870 |
|
|
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
|
871 |
52f57468
|
Katja Luther
|
if ($value->length > 0) {
|
872 |
|
|
@_description_list_group_add(
|
873 |
|
|
$groups,
|
874 |
|
|
cdm_occurrence_field_name_label($field),
|
875 |
c10f70e4
|
Katja Luther
|
array(
|
876 |
52f57468
|
Katja Luther
|
array(
|
877 |
|
|
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb') . '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
878 |
|
|
'#wrapper_attributes' => array('class' => 'dna-sequence')
|
879 |
|
|
)
|
880 |
|
|
),
|
881 |
|
|
5);
|
882 |
|
|
}
|
883 |
c10f70e4
|
Katja Luther
|
break;
|
884 |
|
|
|
885 |
|
|
case 'dnaSample': // FIXME 3.3 implement
|
886 |
|
|
break;
|
887 |
|
|
case 'singleReads': // FIXME 3.3 implement
|
888 |
|
|
break;
|
889 |
|
|
case 'contigFile': // FIXME 3.3 implement - Media
|
890 |
|
|
break;
|
891 |
|
|
case 'pherograms': // FIXME 3.3 implement - Media
|
892 |
|
|
break;
|
893 |
|
|
case 'haplotype': // FIXME 3.3 implement
|
894 |
|
|
break;
|
895 |
|
|
case 'dateSequenced': // FIXME 3.3 now in SingelRead
|
896 |
|
|
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
897 |
|
|
break;
|
898 |
|
|
|
899 |
|
|
case 'barcode': // boolean
|
900 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes' : 'No', NULL, 7);
|
901 |
|
|
break;
|
902 |
|
|
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
|
903 |
|
|
break;
|
904 |
|
|
|
905 |
|
|
case 'citation':
|
906 |
|
|
@_description_list_group_add($groups,
|
907 |
|
|
cdm_occurrence_field_name_label($field),
|
908 |
e7f3789b
|
Andreas Kohlbecker
|
cdm_reference_markup($value, $sequence->microReference),
|
909 |
c10f70e4
|
Katja Luther
|
NULL,
|
910 |
|
|
8
|
911 |
|
|
);
|
912 |
|
|
break;
|
913 |
|
|
|
914 |
|
|
case 'publishedIn':
|
915 |
|
|
@_description_list_group_add($groups,
|
916 |
|
|
cdm_occurrence_field_name_label($field),
|
917 |
|
|
theme('cdm_reference', array('reference' => $value)),
|
918 |
|
|
NULL,
|
919 |
|
|
7
|
920 |
|
|
);
|
921 |
|
|
break;
|
922 |
|
|
|
923 |
|
|
case 'rights':
|
924 |
|
|
array_merge($groups, cdm_rights_as_dl_groups($value));
|
925 |
|
|
break;
|
926 |
|
|
|
927 |
|
|
case 'annotations':
|
928 |
|
|
$dd_elements = array();
|
929 |
|
|
foreach ($value as $annotation) {
|
930 |
|
|
// TODO respect annotation type filter settings
|
931 |
|
|
$dd_elements[] = $annotation->text;
|
932 |
|
|
}
|
933 |
|
|
@_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
|
934 |
|
|
break;
|
935 |
|
|
|
936 |
|
|
case 'markers':
|
937 |
|
|
$dd_elements = array();
|
938 |
|
|
foreach ($value as $marker) {
|
939 |
|
|
$dd_elements[] = compose_cdm_marker($marker);
|
940 |
|
|
}
|
941 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
|
942 |
|
|
break;
|
943 |
|
|
|
944 |
|
|
case 'chromatograms':
|
945 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
946 |
|
|
array(
|
947 |
|
|
'#markup' => compose_cdm_media_gallerie(array('medialist' => $value)),
|
948 |
|
|
),
|
949 |
|
|
NULL,
|
950 |
|
|
11);
|
951 |
|
|
break;
|
952 |
|
|
|
953 |
|
|
default:
|
954 |
|
|
if (is_object($value) || is_array($value)) {
|
955 |
|
|
drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
|
956 |
|
|
} else {
|
957 |
8e15d0fb
|
Katja Luther
|
if (!is_array($value) && strpos($value, 'http:') !== false ){
|
958 |
|
|
//make links for urls
|
959 |
cea59762
|
Andreas Kohlbecker
|
$value = l($value, $value);
|
960 |
8e15d0fb
|
Katja Luther
|
$value = markup_to_render_array($value);
|
961 |
|
|
}
|
962 |
|
|
|
963 |
58c1a035
|
Katja Luther
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
|
964 |
c10f70e4
|
Katja Luther
|
}
|
965 |
1b57b3c1
|
Andreas Kohlbecker
|
}
|
966 |
c10f70e4
|
Katja Luther
|
}
|
967 |
0de9cf51
|
Andreas Kohlbecker
|
}
|
968 |
|
|
|
969 |
c10f70e4
|
Katja Luther
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
970 |
|
|
uasort($groups, 'element_sort');
|
971 |
52f57468
|
Katja Luther
|
if ($isSpecimenPage) {
|
972 |
|
|
$sequence_elements = array(
|
973 |
|
|
'#title' => $sequence->dnaMarker,
|
974 |
|
|
'#theme' => 'description_list',
|
975 |
|
|
'#groups' => $groups
|
976 |
|
|
);
|
977 |
|
|
} else{
|
978 |
|
|
$sequence_elements = array(
|
979 |
|
|
'#title' => $sequence->dnaMarker -> titleCache,
|
980 |
|
|
'#theme' => 'description_list',
|
981 |
|
|
'#groups' => $groups
|
982 |
|
|
);
|
983 |
|
|
}
|
984 |
0de9cf51
|
Andreas Kohlbecker
|
|
985 |
c10f70e4
|
Katja Luther
|
return $sequence_elements;
|
986 |
0de9cf51
|
Andreas Kohlbecker
|
}
|
987 |
961319fe
|
Andreas Kohlbecker
|
|
988 |
|
|
/**
|
989 |
09762fde
|
Andreas Kohlbecker
|
* Crates an array which can be used in render arrays to be passed to the
|
990 |
|
|
* theme_table() and theme_list().
|
991 |
|
|
*
|
992 |
961319fe
|
Andreas Kohlbecker
|
* @param array $fieldunit_dtos
|
993 |
|
|
* list of FieldUnitDTOs
|
994 |
|
|
*/
|
995 |
|
|
function specimen_render_array_items(array $fieldunit_dtos){
|
996 |
|
|
|
997 |
|
|
$render_array_items = array();
|
998 |
|
|
$items = array();
|
999 |
|
|
|
1000 |
|
|
//we need one more item to contain the items of one level (fieldunit, derivate data etc.)
|
1001 |
|
|
foreach ($fieldunit_dtos as &$fieldunit_dto) {
|
1002 |
|
|
|
1003 |
|
|
$items['data'] = $fieldunit_dto->listLabel ;
|
1004 |
|
|
$specimen = compose_cdm_specimen_or_observation_tree_entry($fieldunit_dto);
|
1005 |
|
|
$children = array();
|
1006 |
|
|
$child = array();
|
1007 |
|
|
$child['data'] =$specimen;
|
1008 |
|
|
// $children[] = create_specimen_array($specimenOrObservation->derivates);
|
1009 |
|
|
if (isset($fieldunit_dto->derivates) && sizeof($fieldunit_dto->derivates) > 0){
|
1010 |
|
|
$child['children']= specimen_render_array_items($fieldunit_dto->derivates);
|
1011 |
|
|
}
|
1012 |
|
|
$children[]=$child;
|
1013 |
|
|
$items['children'] = $children;
|
1014 |
|
|
$render_array_items[] = $items;
|
1015 |
|
|
}
|
1016 |
|
|
return $render_array_items;
|
1017 |
|
|
}
|
1018 |
|
|
|
1019 |
|
|
/**
|
1020 |
|
|
* Creates the drupal render array for the table showing all derivatives which
|
1021 |
|
|
* stem from a common gathering event.
|
1022 |
|
|
*
|
1023 |
|
|
* @param $field_unit_uuids array
|
1024 |
|
|
* An array of uuids for cdm FieldUnit entities.
|
1025 |
|
|
*
|
1026 |
|
|
* @return array
|
1027 |
|
|
* A drupal render array for a table
|
1028 |
|
|
*
|
1029 |
|
|
* @ingroup compose
|
1030 |
|
|
*/
|
1031 |
|
|
|
1032 |
|
|
function compose_compressed_specimen_derivate_table($field_unit_uuids) {
|
1033 |
|
|
|
1034 |
|
|
// prepare font icons
|
1035 |
|
|
$expand_icon = font_awesome_icon_markup(
|
1036 |
|
|
'fa-plus-square-o',
|
1037 |
|
|
array(
|
1038 |
|
|
'alt' => 'Show details',
|
1039 |
|
|
'class' => array('expand_icon')
|
1040 |
|
|
)
|
1041 |
|
|
);
|
1042 |
|
|
$collapse_icon = font_awesome_icon_markup(
|
1043 |
|
|
'fa-minus-square-o',
|
1044 |
|
|
array(
|
1045 |
|
|
'alt' => 'Show details',
|
1046 |
|
|
'class' => array('collapse_icon')
|
1047 |
|
|
)
|
1048 |
|
|
);
|
1049 |
|
|
$detail_image_icon = '<img title="Detail Image" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/detail_image_derivate-16x16-32.png' . '"/>';
|
1050 |
|
|
$checked_box_icon = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/step_done.gif' . '"/>';
|
1051 |
|
|
$sequence_icon = '<img title="Molecular Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/sequence_derivate-16x16-32.png' . '"/>';
|
1052 |
|
|
$character_data_icon = '<img title="Character Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/character_data_derivate-16x16-32.png' . '"/>';
|
1053 |
|
|
|
1054 |
|
|
$rowcount = 0;
|
1055 |
|
|
$rows = array();
|
1056 |
|
|
|
1057 |
|
|
foreach ($field_unit_uuids as $field_unit_uuid) {
|
1058 |
|
|
|
1059 |
|
|
//get derivate hierarchy for the FieldUnit
|
1060 |
|
|
$derivateHierarchy = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($field_unit_uuid, 'derivateHierarchy'));
|
1061 |
|
|
if ($derivateHierarchy) {
|
1062 |
|
|
//summary row
|
1063 |
|
|
$rows[] = array(
|
1064 |
|
|
'data' => array(
|
1065 |
|
|
array(
|
1066 |
|
|
'data' => $expand_icon . $collapse_icon,
|
1067 |
|
|
'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
|
1068 |
|
|
),
|
1069 |
|
|
array(
|
1070 |
|
|
'data' => $derivateHierarchy->country,
|
1071 |
|
|
'class' => array('summary_row_cell')
|
1072 |
|
|
),
|
1073 |
|
|
array(
|
1074 |
|
|
'data' => $derivateHierarchy->date,
|
1075 |
|
|
'class' => array('summary_row_cell')
|
1076 |
|
|
),
|
1077 |
|
|
array(
|
1078 |
|
|
'data' => $derivateHierarchy->collectingString,
|
1079 |
|
|
'class' => array('summary_row_cell')
|
1080 |
|
|
),
|
1081 |
|
|
@array(
|
1082 |
|
|
'data' => $derivateHierarchy->collection,
|
1083 |
|
|
'class' => array('summary_row_cell')
|
1084 |
|
|
),
|
1085 |
|
|
array(
|
1086 |
|
|
'data' => $derivateHierarchy->hasType ? $checked_box_icon : "",
|
1087 |
|
|
'class' => array('summary_row_cell', 'summary_row_icon')
|
1088 |
|
|
),
|
1089 |
|
|
array(
|
1090 |
|
|
'data' => $derivateHierarchy->hasSpecimenScan ? $checked_box_icon : "",
|
1091 |
|
|
'class' => array('summary_row_cell', 'summary_row_icon')
|
1092 |
|
|
),
|
1093 |
|
|
array(
|
1094 |
|
|
'data' => ($derivateHierarchy->hasDna ? $sequence_icon : "") . " "
|
1095 |
|
|
. ($derivateHierarchy->hasDetailImage ? $detail_image_icon : "") . " "
|
1096 |
|
|
. ($derivateHierarchy->hasCharacterData ? $character_data_icon : ""),
|
1097 |
|
|
'class' => array('summary_row_cell', 'summary_row_icon')
|
1098 |
|
|
)
|
1099 |
|
|
),
|
1100 |
|
|
'id' => 'derivate_summary' . $rowcount, // summary row id
|
1101 |
|
|
'class' => array('summary_row'),
|
1102 |
|
|
);
|
1103 |
|
|
|
1104 |
|
|
//assemble field unit details
|
1105 |
|
|
$detail_html = "";
|
1106 |
|
|
// - citation
|
1107 |
|
|
if ($derivateHierarchy->citation) {
|
1108 |
|
|
$detail_html .= create_label("Citation") . $derivateHierarchy->citation . "<br>";
|
1109 |
|
|
}
|
1110 |
|
|
//assemble specimen details
|
1111 |
|
|
if ($derivateHierarchy->derivates) {
|
1112 |
|
|
foreach ($derivateHierarchy->derivates as $preservedSpecimenDTO) {
|
1113 |
|
|
$detail_html .= "<br>";
|
1114 |
|
|
$detail_html .= render_cdm_specimenDTO_page($preservedSpecimenDTO);
|
1115 |
|
|
}
|
1116 |
|
|
}
|
1117 |
|
|
$detail_html .= "<br>";
|
1118 |
|
|
//detail row resp. one BIG detail cell
|
1119 |
|
|
$rows[] = array(
|
1120 |
|
|
'data' => array(
|
1121 |
|
|
array(
|
1122 |
|
|
'data' => "", //empty first column
|
1123 |
|
|
'class' => array('expand_column')
|
1124 |
|
|
),
|
1125 |
|
|
array(
|
1126 |
|
|
'data' => $detail_html,
|
1127 |
|
|
'colspan' => 7,
|
1128 |
|
|
),
|
1129 |
|
|
),
|
1130 |
|
|
'id' => 'derivate_details' . $rowcount,//details row ID
|
1131 |
|
|
'class' => array('detail_row'),
|
1132 |
|
|
);
|
1133 |
|
|
$rowcount++;
|
1134 |
|
|
}
|
1135 |
|
|
}
|
1136 |
|
|
|
1137 |
|
|
$tableId = "derivate_hierarchy_table";
|
1138 |
|
|
$derivateHierarchyTable = array(
|
1139 |
|
|
"#theme" => "table",
|
1140 |
|
|
"#weight" => 2,
|
1141 |
|
|
"#header" => array(
|
1142 |
|
|
array(
|
1143 |
|
|
'data' => "",
|
1144 |
|
|
'class' => array('expand_column')
|
1145 |
|
|
),
|
1146 |
|
|
"Country", "Date", "Collector + collecting number", "Herbaria", "Type", "Scan", "Derivatives"),
|
1147 |
|
|
"#rows" => $rows,
|
1148 |
|
|
"#attributes" => array(
|
1149 |
|
|
"id" => $tableId,
|
1150 |
|
|
"border" => 2
|
1151 |
|
|
)
|
1152 |
|
|
);
|
1153 |
|
|
|
1154 |
|
|
//add toggle functionality to derivate hierarchy table
|
1155 |
|
|
drupal_add_js_rowToggle("#" . $tableId);
|
1156 |
|
|
|
1157 |
|
|
return $derivateHierarchyTable;
|
1158 |
|
|
}
|
1159 |
|
|
|
1160 |
267da0d1
|
Katja Luther
|
/**
|
1161 |
09762fde
|
Andreas Kohlbecker
|
* Composes the view on specimens and occurrences as derivate tree
|
1162 |
|
|
* starting from the field unit including all derivatives.
|
1163 |
267da0d1
|
Katja Luther
|
*
|
1164 |
09762fde
|
Andreas Kohlbecker
|
* @see DM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TREE
|
1165 |
267da0d1
|
Katja Luther
|
*
|
1166 |
ca7468b6
|
Andreas Kohlbecker
|
* @param object $fieldunit_dtos
|
1167 |
267da0d1
|
Katja Luther
|
* list of FieldUnitDTOs
|
1168 |
|
|
* @return array
|
1169 |
09762fde
|
Andreas Kohlbecker
|
* The Drupal render array
|
1170 |
267da0d1
|
Katja Luther
|
*
|
1171 |
|
|
* @ingroup compose
|
1172 |
|
|
*/
|
1173 |
961319fe
|
Andreas Kohlbecker
|
function compose_specimen_table_top_down(array $fieldunit_dtos){
|
1174 |
276f39f6
|
Katja Luther
|
|
1175 |
961319fe
|
Andreas Kohlbecker
|
$specimen_render_array_items = specimen_render_array_items($fieldunit_dtos);
|
1176 |
|
|
|
1177 |
|
|
// add icons
|
1178 |
|
|
$expand_icon = font_awesome_icon_markup(
|
1179 |
|
|
'fa-plus-square-o',
|
1180 |
|
|
array(
|
1181 |
|
|
'alt' => 'Show details',
|
1182 |
|
|
'class' => array('expand_icon')
|
1183 |
|
|
)
|
1184 |
|
|
);
|
1185 |
|
|
$collapse_icon = font_awesome_icon_markup(
|
1186 |
|
|
'fa-minus-square-o',
|
1187 |
|
|
array(
|
1188 |
|
|
'alt' => 'Show details',
|
1189 |
|
|
'class' => array('collapse_icon')
|
1190 |
|
|
)
|
1191 |
|
|
);
|
1192 |
|
|
$tableId = "specimen_tree_table";
|
1193 |
|
|
$specimen_table = array(
|
1194 |
|
|
'#theme' => 'table',
|
1195 |
|
|
// prefix attributes and rows with '#' to let it pass toF the theme function,
|
1196 |
|
|
// otherwise it is handled as child render array
|
1197 |
|
|
'#attributes' => array(
|
1198 |
09762fde
|
Andreas Kohlbecker
|
'class' => 'specimens ' . CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TREE ,
|
1199 |
961319fe
|
Andreas Kohlbecker
|
'id' => $tableId
|
1200 |
|
|
),
|
1201 |
|
|
'#rows' => array(),
|
1202 |
|
|
);
|
1203 |
|
|
$rowcount = 0;
|
1204 |
|
|
foreach($specimen_render_array_items as $value){
|
1205 |
|
|
$renderArray = array(
|
1206 |
|
|
'#theme' => 'item_list',
|
1207 |
|
|
'#items' => $value['children'],
|
1208 |
|
|
'#type' => 'ul');
|
1209 |
|
|
$output = drupal_render($renderArray);
|
1210 |
|
|
|
1211 |
|
|
$specimen_table['#rows'][] = array(
|
1212 |
|
|
'data' =>array(
|
1213 |
|
|
array(
|
1214 |
|
|
'data' => $expand_icon . $collapse_icon,
|
1215 |
|
|
'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
|
1216 |
|
|
),
|
1217 |
|
|
$value['data']
|
1218 |
|
|
),
|
1219 |
|
|
'id' => 'label' . $rowcount, // summary row id
|
1220 |
|
|
'class' => array('summary_row'),
|
1221 |
|
|
);
|
1222 |
|
|
$specimen_table['#rows'][] = array(
|
1223 |
|
|
'data' => array(
|
1224 |
|
|
array(
|
1225 |
|
|
'data' => "", //empty first column
|
1226 |
|
|
'class' => array('expand_column')
|
1227 |
|
|
),
|
1228 |
|
|
array(
|
1229 |
|
|
'data' => $output
|
1230 |
|
|
|
1231 |
|
|
)
|
1232 |
|
|
),
|
1233 |
|
|
'class' => array('detail_row')
|
1234 |
|
|
// 'class' => array(
|
1235 |
|
|
// 'descriptionElement',
|
1236 |
|
|
// 'descriptionElement_IndividualsAssociation'
|
1237 |
|
|
// ),
|
1238 |
|
|
);
|
1239 |
|
|
$rowcount++;
|
1240 |
|
|
|
1241 |
|
|
}
|
1242 |
|
|
drupal_add_js_rowToggle("#".$tableId);
|
1243 |
|
|
|
1244 |
|
|
return $specimen_table;
|
1245 |
267da0d1
|
Katja Luther
|
}
|
1246 |
|
|
|
1247 |
|
|
|
1248 |
|
|
/**
|
1249 |
|
|
* Compose an render array from a CDM DerivedUnitFacade object.
|
1250 |
|
|
*
|
1251 |
|
|
* compose_hook() implementation
|
1252 |
|
|
*
|
1253 |
|
|
* @param object $specimenOrObservation
|
1254 |
|
|
* the CDM instance of type SpecimenOrObservation to compose
|
1255 |
|
|
* the render array for
|
1256 |
|
|
* @param array $derivatives
|
1257 |
|
|
* the render array which contains the compositions of the derivatives
|
1258 |
|
|
* of the supplied $specimenOrObservation
|
1259 |
|
|
*
|
1260 |
|
|
* @return array
|
1261 |
|
|
* the supplied render array $derivatives to which the composition of the supplied
|
1262 |
|
|
* $specimenOrObservation has been added to
|
1263 |
|
|
*
|
1264 |
|
|
* @ingroup compose
|
1265 |
|
|
*/
|
1266 |
|
|
|
1267 |
58c1a035
|
Katja Luther
|
function compose_cdm_specimen_or_observation_tree_entry($specimen_or_observation)
|
1268 |
267da0d1
|
Katja Luther
|
{
|
1269 |
|
|
$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
|
1270 |
|
|
if (!isset($exclude_occurrence_fields)) {
|
1271 |
|
|
$exclude_occurrence_fields = array(
|
1272 |
|
|
'type',
|
1273 |
|
|
'taxonRelatedDerivedUnits',
|
1274 |
7965ef92
|
Katja Luther
|
'label',
|
1275 |
267da0d1
|
Katja Luther
|
'titleCache',
|
1276 |
7965ef92
|
Katja Luther
|
'listLabel',
|
1277 |
267da0d1
|
Katja Luther
|
'protectedTitleCache',
|
1278 |
|
|
'class',
|
1279 |
|
|
'uuid',
|
1280 |
ddbbdb0b
|
Katja Luther
|
'derivates',
|
1281 |
|
|
'collection'
|
1282 |
267da0d1
|
Katja Luther
|
);
|
1283 |
|
|
}
|
1284 |
|
|
$items = array();
|
1285 |
|
|
|
1286 |
|
|
// only show uuid it the user is logged in
|
1287 |
|
|
if (user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE) {
|
1288 |
|
|
// unset($exclude_occurrence_fields[$a_idx]);
|
1289 |
|
|
}
|
1290 |
|
|
|
1291 |
|
|
|
1292 |
58c1a035
|
Katja Luther
|
if (is_object($specimen_or_observation)) {
|
1293 |
267da0d1
|
Katja Luther
|
|
1294 |
58c1a035
|
Katja Luther
|
$type_label = $specimen_or_observation->recordBase;
|
1295 |
|
|
RenderHints::setFootnoteListKey($type_label . '-' . $specimen_or_observation->uuid);
|
1296 |
267da0d1
|
Katja Luther
|
|
1297 |
|
|
// collect typeStatus as label
|
1298 |
58c1a035
|
Katja Luther
|
if (isset($specimen_or_observation->specimenTypeDesignations)) {
|
1299 |
267da0d1
|
Katja Luther
|
$type_status = array();
|
1300 |
58c1a035
|
Katja Luther
|
foreach ($specimen_or_observation->specimenTypeDesignations as $typeDesignation) {
|
1301 |
267da0d1
|
Katja Luther
|
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
1302 |
|
|
$type_status[] = $typeDesignation->typeStatus->representation_L10n;
|
1303 |
|
|
}
|
1304 |
|
|
}
|
1305 |
|
|
if (count($type_status) > 0) {
|
1306 |
|
|
$type_label = implode(', ', $type_status);
|
1307 |
0557d51a
|
Andreas Kohlbecker
|
}
|
1308 |
267da0d1
|
Katja Luther
|
}
|
1309 |
|
|
|
1310 |
0557d51a
|
Andreas Kohlbecker
|
if (isset($typeDesignation->typifiedNames)){
|
1311 |
6eaec849
|
Katja Luther
|
$title = $type_label . ' for: ' . $typeDesignation->typifiedNames;
|
1312 |
|
|
}else{
|
1313 |
|
|
$title = $type_label;
|
1314 |
|
|
}
|
1315 |
|
|
|
1316 |
7965ef92
|
Katja Luther
|
$items['data'] = $title;
|
1317 |
267da0d1
|
Katja Luther
|
|
1318 |
|
|
$groups = array();
|
1319 |
|
|
$items['children'] = $groups;
|
1320 |
|
|
$children_items = array();
|
1321 |
|
|
// --- add initialized fields
|
1322 |
58c1a035
|
Katja Luther
|
foreach (get_object_vars($specimen_or_observation) as $field => $value) {
|
1323 |
267da0d1
|
Katja Luther
|
$child_item = array();
|
1324 |
|
|
|
1325 |
|
|
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
1326 |
|
|
switch ($field) {
|
1327 |
|
|
|
1328 |
|
|
/* ---- SpecimenOrObservationBase --- */
|
1329 |
a2acff0a
|
Katja Luther
|
case 'derivationEvent':
|
1330 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1);
|
1331 |
|
|
break;
|
1332 |
267da0d1
|
Katja Luther
|
case 'kindOfUnit':
|
1333 |
52f57468
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 1);
|
1334 |
267da0d1
|
Katja Luther
|
break;
|
1335 |
72d57201
|
Katja Luther
|
case 'accessionNumber':
|
1336 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 0);
|
1337 |
|
|
break;
|
1338 |
267da0d1
|
Katja Luther
|
|
1339 |
|
|
case 'preferredStableUri':
|
1340 |
|
|
|
1341 |
7965ef92
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
1342 |
267da0d1
|
Katja Luther
|
break;
|
1343 |
|
|
|
1344 |
|
|
case 'specimenTypeDesignations':
|
1345 |
f1239704
|
Katja Luther
|
@_description_list_group_add(
|
1346 |
|
|
$groups,
|
1347 |
267da0d1
|
Katja Luther
|
cdm_occurrence_field_name_label($field),
|
1348 |
|
|
array(
|
1349 |
0c720425
|
Andreas Kohlbecker
|
'#markup' => render_type_designations($value),
|
1350 |
267da0d1
|
Katja Luther
|
)
|
1351 |
|
|
);
|
1352 |
|
|
break;
|
1353 |
|
|
|
1354 |
|
|
|
1355 |
f1239704
|
Katja Luther
|
|
1356 |
7965ef92
|
Katja Luther
|
case 'listOfMedia':
|
1357 |
|
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
1358 |
6eaec849
|
Katja Luther
|
|
1359 |
7965ef92
|
Katja Luther
|
$captionElements = array(
|
1360 |
6eaec849
|
Katja Luther
|
'title',
|
1361 |
7965ef92
|
Katja Luther
|
'#uri' => t('open media'),
|
1362 |
|
|
);
|
1363 |
|
|
$gallery_html = compose_cdm_media_gallerie(array(
|
1364 |
|
|
'mediaList' => $value,
|
1365 |
72d57201
|
Katja Luther
|
'galleryName' => $specimen_or_observation->uuid,
|
1366 |
7965ef92
|
Katja Luther
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
1367 |
|
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
1368 |
|
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
1369 |
|
|
'captionElements' => $captionElements,
|
1370 |
|
|
'mediaLinkType' => 'LIGHTBOX',
|
1371 |
|
|
'alternativeMediaUri' => NULL,
|
1372 |
|
|
'galleryLinkUri' => NULL,
|
1373 |
6eaec849
|
Katja Luther
|
'showCaption' => true
|
1374 |
7965ef92
|
Katja Luther
|
));
|
1375 |
|
|
|
1376 |
276f39f6
|
Katja Luther
|
//@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $gallery_html);
|
1377 |
7965ef92
|
Katja Luther
|
break;
|
1378 |
267da0d1
|
Katja Luther
|
|
1379 |
|
|
|
1380 |
|
|
|
1381 |
|
|
/* ---- DerivedUnitBase --- */
|
1382 |
|
|
|
1383 |
1083804e
|
Andreas Kohlbecker
|
|
1384 |
a2acff0a
|
Katja Luther
|
case 'collectionDTO':
|
1385 |
7965ef92
|
Katja Luther
|
|
1386 |
267da0d1
|
Katja Luther
|
$sub_dl_groups = array();
|
1387 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
1388 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
1389 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
1390 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
1391 |
|
|
// TODO "superCollection"
|
1392 |
|
|
// TODO may have media
|
1393 |
|
|
|
1394 |
a2acff0a
|
Katja Luther
|
@_description_list_group_add($groups, 'Collection',
|
1395 |
267da0d1
|
Katja Luther
|
array(
|
1396 |
|
|
array('#markup' => $value->titleCache),
|
1397 |
|
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
1398 |
|
|
)
|
1399 |
|
|
);
|
1400 |
7965ef92
|
Katja Luther
|
|
1401 |
267da0d1
|
Katja Luther
|
break;
|
1402 |
|
|
|
1403 |
|
|
|
1404 |
|
|
|
1405 |
|
|
|
1406 |
|
|
/* ---- Specimen --- */
|
1407 |
|
|
case 'sequences':
|
1408 |
|
|
$dd_elements = array();
|
1409 |
|
|
foreach ($value as $sequence) {
|
1410 |
52f57468
|
Katja Luther
|
$dd_elements[] = compose_cdm_sequence($sequence, true);
|
1411 |
|
|
$dd_elements[] = "";
|
1412 |
267da0d1
|
Katja Luther
|
}
|
1413 |
a0f26798
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements,'', 100);
|
1414 |
267da0d1
|
Katja Luther
|
break;
|
1415 |
|
|
|
1416 |
|
|
// TODO preservation
|
1417 |
|
|
// TODO exsiccatum
|
1418 |
|
|
|
1419 |
|
|
|
1420 |
|
|
/* ---- FieldObservation --- */
|
1421 |
|
|
case 'gatheringEvent':
|
1422 |
|
|
|
1423 |
52f57468
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->collector);
|
1424 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, t('Gathering date'), timePeriodToString($value->timeperiod));
|
1425 |
267da0d1
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
|
1426 |
abe0b021
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality, '', 10);
|
1427 |
52f57468
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country);
|
1428 |
267da0d1
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
|
1429 |
|
|
if (isset($value->absoluteElevation)) {
|
1430 |
2f4646e0
|
Andreas Kohlbecker
|
$min_max_markup = statistical_values_from_gathering_event($value, 'absoluteElevation');
|
1431 |
267da0d1
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
|
1432 |
|
|
}
|
1433 |
276f39f6
|
Katja Luther
|
if (isset($value->distanceToGround) && $value->distanceToGround >0) {
|
1434 |
2f4646e0
|
Andreas Kohlbecker
|
$min_max_markup = statistical_values_from_gathering_event($value, 'distanceToGround');
|
1435 |
267da0d1
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
|
1436 |
|
|
}
|
1437 |
276f39f6
|
Katja Luther
|
if (isset($value->distanceToWaterSurface) && $value->distanceToWaterSurface > 0) {
|
1438 |
2f4646e0
|
Andreas Kohlbecker
|
$min_max_markup = statistical_values_from_gathering_event($value, 'distanceToWaterSurface');
|
1439 |
267da0d1
|
Katja Luther
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
|
1440 |
|
|
}
|
1441 |
|
|
|
1442 |
|
|
if (isset($value->collectingAreas)) {
|
1443 |
|
|
$area_representations = array();
|
1444 |
|
|
foreach ($value->collectingAreas as $area) {
|
1445 |
52f57468
|
Katja Luther
|
// $area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
1446 |
|
|
$area_representations[] = $area;
|
1447 |
267da0d1
|
Katja Luther
|
}
|
1448 |
|
|
if (!empty($area_representations))
|
1449 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
1450 |
|
|
array(
|
1451 |
|
|
array('#markup' => implode(', ', $area_representations))
|
1452 |
|
|
)
|
1453 |
|
|
);
|
1454 |
|
|
}
|
1455 |
106e1cf9
|
Katja Luther
|
if (isset($value->exactLocation) ) {
|
1456 |
267da0d1
|
Katja Luther
|
$sub_dl_groups = array();
|
1457 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
1458 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
1459 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
1460 |
|
|
if (isset($value->exactLocation->referenceSystem)) {
|
1461 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
1462 |
|
|
}
|
1463 |
106e1cf9
|
Katja Luther
|
if ( isSet($value->exactLocation->sexagesimalString)){
|
1464 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
1465 |
267da0d1
|
Katja Luther
|
array(
|
1466 |
106e1cf9
|
Katja Luther
|
array('#markup' => $value->exactLocation->sexagesimalString),
|
1467 |
|
|
array(
|
1468 |
|
|
'#theme' => 'description_list',
|
1469 |
|
|
'#groups' => $sub_dl_groups
|
1470 |
|
|
),
|
1471 |
abe0b021
|
Katja Luther
|
), '', 11
|
1472 |
106e1cf9
|
Katja Luther
|
);
|
1473 |
|
|
}
|
1474 |
267da0d1
|
Katja Luther
|
}
|
1475 |
|
|
|
1476 |
|
|
break;
|
1477 |
|
|
|
1478 |
|
|
/* ---- DerivationEvent --- */
|
1479 |
|
|
case 'derivationEvents':
|
1480 |
|
|
//@_description_list_group_add($groups, t('Association type'), $value->description);
|
1481 |
|
|
break;
|
1482 |
72d57201
|
Katja Luther
|
case 'determinedNames':
|
1483 |
|
|
$dd_elements = array();
|
1484 |
|
|
foreach ($value as $name) {
|
1485 |
|
|
$taxon_name = cdm_ws_get(CDM_WS_NAME, $name->key);
|
1486 |
|
|
$taxon_name->taggedName = cdm_ws_get(CDM_WS_NAME, array($name->key, "taggedName"));
|
1487 |
|
|
$name_link = path_to_name($name->key);
|
1488 |
|
|
|
1489 |
|
|
//$taxon_html = render_taxon_or_name($taxon_name, $name_link);
|
1490 |
cea59762
|
Andreas Kohlbecker
|
$taxon_html = l($taxon_name->titleCache, $name_link);
|
1491 |
72d57201
|
Katja Luther
|
$dd_elements[] = $taxon_html;
|
1492 |
|
|
}
|
1493 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label("Identification(s)"), $dd_elements,'', 100);
|
1494 |
|
|
break;
|
1495 |
267da0d1
|
Katja Luther
|
|
1496 |
|
|
|
1497 |
|
|
default:
|
1498 |
|
|
if (is_object($value) || is_array($value)) {
|
1499 |
52f57468
|
Katja Luther
|
drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
|
1500 |
267da0d1
|
Katja Luther
|
} else {
|
1501 |
f60b52c4
|
Katja Luther
|
if ($field == 'recordBase' && $value == 'Dna Sample'){
|
1502 |
|
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), 'DNA Sample');
|
1503 |
|
|
}else{
|
1504 |
|
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
1505 |
|
|
}
|
1506 |
267da0d1
|
Katja Luther
|
}
|
1507 |
|
|
}
|
1508 |
|
|
}
|
1509 |
|
|
} // END of loop over $derivedUnitFacade fields
|
1510 |
|
|
|
1511 |
|
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
1512 |
|
|
uasort($groups, 'element_sort');
|
1513 |
|
|
$occurrence_elements = array(
|
1514 |
|
|
// '#title' => $title,
|
1515 |
|
|
'#theme' => 'description_list',
|
1516 |
|
|
'#groups' => $groups,
|
1517 |
58c1a035
|
Katja Luther
|
'#attributes' => array('class' => html_class_attribute_ref($specimen_or_observation)),
|
1518 |
267da0d1
|
Katja Luther
|
);
|
1519 |
|
|
$output = drupal_render($occurrence_elements);
|
1520 |
106e1cf9
|
Katja Luther
|
if (isset($gallery_html)){
|
1521 |
|
|
$output .= $gallery_html;
|
1522 |
|
|
}
|
1523 |
a2acff0a
|
Katja Luther
|
$pathToSpecimen = path_to_specimen($specimen_or_observation->uuid);
|
1524 |
cea59762
|
Andreas Kohlbecker
|
$output .= l("Detail page", $pathToSpecimen);
|
1525 |
267da0d1
|
Katja Luther
|
} // END of $specimenOrObservation exists
|
1526 |
|
|
|
1527 |
|
|
return $output;
|
1528 |
|
|
}
|
1529 |
1083804e
|
Andreas Kohlbecker
|
|
1530 |
6eaec849
|
Katja Luther
|
function compose_table_of_blast_result(array $data){
|
1531 |
72d57201
|
Katja Luther
|
// get icon images
|
1532 |
|
|
$expand_icon = font_awesome_icon_markup(
|
1533 |
|
|
'fa-plus-square-o',
|
1534 |
|
|
array(
|
1535 |
|
|
'alt' => 'Show details',
|
1536 |
|
|
'class' => array('expand_icon')
|
1537 |
|
|
)
|
1538 |
|
|
);
|
1539 |
|
|
$collapse_icon = font_awesome_icon_markup(
|
1540 |
|
|
'fa-minus-square-o',
|
1541 |
|
|
array(
|
1542 |
|
|
'alt' => 'Show details',
|
1543 |
|
|
'class' => array('collapse_icon')
|
1544 |
|
|
)
|
1545 |
|
|
);
|
1546 |
|
|
//$detail_image_icon = '<img title="Detail Image" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/detail_image_derivate-16x16-32.png' . '"/>';
|
1547 |
|
|
$rowcount = 0;
|
1548 |
|
|
$rows = array();
|
1549 |
6eaec849
|
Katja Luther
|
|
1550 |
|
|
foreach ($data as $row_data){
|
1551 |
|
|
$pathToSpecimen = path_to_specimen_by_accession_number($row_data['id']);
|
1552 |
cea59762
|
Andreas Kohlbecker
|
$specimenPageLink = l($row_data['id'], $pathToSpecimen);
|
1553 |
|
|
$ncbiLink = l($row_data['id'], 'https://www.ncbi.nlm.nih.gov/nuccore/'.$row_data['id'].'?report=graph');
|
1554 |
6eaec849
|
Katja Luther
|
$rows[] = array(
|
1555 |
|
|
'data' => array(
|
1556 |
72d57201
|
Katja Luther
|
array(
|
1557 |
|
|
'data' => $expand_icon . $collapse_icon,
|
1558 |
|
|
'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
|
1559 |
|
|
),
|
1560 |
6eaec849
|
Katja Luther
|
array(
|
1561 |
|
|
'data' => $row_data['def'],
|
1562 |
|
|
),
|
1563 |
|
|
array(
|
1564 |
|
|
'data' => $specimenPageLink,
|
1565 |
|
|
),
|
1566 |
|
|
array(
|
1567 |
|
|
'data' => $row_data['hsp_align_length'],
|
1568 |
|
|
),
|
1569 |
|
|
array(
|
1570 |
ce347d23
|
Katja Luther
|
'data' => $ncbiLink,
|
1571 |
72d57201
|
Katja Luther
|
),
|
1572 |
|
|
array(
|
1573 |
|
|
'data' => $row_data['hsp_identity']/$row_data['hsp_align_length']*100,
|
1574 |
6eaec849
|
Katja Luther
|
)
|
1575 |
72d57201
|
Katja Luther
|
),
|
1576 |
|
|
'id' => 'blast_summary' . $rowcount, // summary row id
|
1577 |
|
|
'class' => array('summary_row'),
|
1578 |
|
|
);
|
1579 |
|
|
$detail_html = "";
|
1580 |
|
|
|
1581 |
|
|
$detail_html .= create_label("Details") . $row_data["hsp_align_length"] . "<br>";
|
1582 |
|
|
|
1583 |
|
|
|
1584 |
|
|
$detail_html .= "<br>";
|
1585 |
|
|
$detail_html .= $row_data["hsp_midline"];
|
1586 |
|
|
|
1587 |
|
|
//$detail_html .= "<br>";
|
1588 |
|
|
|
1589 |
|
|
$rows[] = array(
|
1590 |
|
|
'data' => array(
|
1591 |
|
|
array(
|
1592 |
|
|
'data' => "", //empty first column
|
1593 |
|
|
'class' => array('expand_column')
|
1594 |
|
|
),
|
1595 |
|
|
array(
|
1596 |
|
|
'data' => $detail_html,
|
1597 |
|
|
'colspan' => 5,
|
1598 |
|
|
),
|
1599 |
|
|
),
|
1600 |
|
|
'id' => 'blast_detail' . $rowcount,//details row ID
|
1601 |
|
|
'class' => array('detail_row'),
|
1602 |
6eaec849
|
Katja Luther
|
);
|
1603 |
72d57201
|
Katja Luther
|
$rowcount++;
|
1604 |
6eaec849
|
Katja Luther
|
}
|
1605 |
72d57201
|
Katja Luther
|
|
1606 |
6eaec849
|
Katja Luther
|
$tableId = "blast_result_table";
|
1607 |
|
|
$blast_result_table = array(
|
1608 |
|
|
"#theme" => "table",
|
1609 |
|
|
"#weight" => 2,
|
1610 |
|
|
"#header" => array(
|
1611 |
72d57201
|
Katja Luther
|
array(
|
1612 |
|
|
'data' => "",
|
1613 |
|
|
'class' => array('expand_column')
|
1614 |
|
|
),
|
1615 |
ce347d23
|
Katja Luther
|
"Name", "Accession Number", "Align Length", "NCBI", "% Identity"),
|
1616 |
6eaec849
|
Katja Luther
|
"#rows" => $rows,
|
1617 |
|
|
"#attributes" => array(
|
1618 |
|
|
"id" => $tableId,
|
1619 |
|
|
"border" => 2
|
1620 |
|
|
)
|
1621 |
|
|
);
|
1622 |
|
|
|
1623 |
|
|
drupal_add_js_rowToggle("#".$tableId);
|
1624 |
|
|
|
1625 |
72d57201
|
Katja Luther
|
$render_array[$tableId] = $blast_result_table;
|
1626 |
6eaec849
|
Katja Luther
|
$out = drupal_render($render_array);
|
1627 |
|
|
//$blast_result_page-> content = drupal_render($render_array);
|
1628 |
|
|
return $out;
|
1629 |
|
|
}
|
1630 |
|
|
|
1631 |
ca7468b6
|
Andreas Kohlbecker
|
|
1632 |
|
|
/**
|
1633 |
|
|
* Composes a BOTTOM-UP-SPECIMEN-TABLE
|
1634 |
|
|
* @param $specimensOrObservations
|
1635 |
|
|
* @return array
|
1636 |
|
|
* A drupal render array with the following keys:
|
1637 |
|
|
* - 'specimen_list'
|
1638 |
|
|
* - 'pager'
|
1639 |
|
|
*
|
1640 |
|
|
* @ingroup Compose
|
1641 |
|
|
*/
|
1642 |
|
|
function compose_specimens_table_bottom_up($specimensOrObservations)
|
1643 |
|
|
{
|
1644 |
|
|
|
1645 |
|
|
// --- generate the specimen list as table
|
1646 |
|
|
$specimen_table = array(
|
1647 |
|
|
'#theme' => 'table',
|
1648 |
|
|
'#weight' => 2,
|
1649 |
|
|
// prefix attributes and rows with '#' to let it pass toF the theme function,
|
1650 |
|
|
// otherwise it is handled as child render array
|
1651 |
09762fde
|
Andreas Kohlbecker
|
'#attributes' => array('class' => 'specimens '),
|
1652 |
ca7468b6
|
Andreas Kohlbecker
|
'#rows' => array(),
|
1653 |
|
|
);
|
1654 |
|
|
|
1655 |
|
|
if ($specimensOrObservations) {
|
1656 |
|
|
|
1657 |
|
|
foreach ($specimensOrObservations as $specimenOrObservation) {
|
1658 |
|
|
|
1659 |
|
|
$mediaList = array();
|
1660 |
|
|
if (is_array($specimenOrObservation->_fieldObjectMedia)) {
|
1661 |
|
|
$mediaList = array_merge($mediaList, $specimenOrObservation->_fieldObjectMedia);
|
1662 |
|
|
}
|
1663 |
|
|
if (is_array($specimenOrObservation->_derivedUnitMedia)) {
|
1664 |
|
|
$mediaList = array_merge($mediaList, $specimenOrObservation->_derivedUnitMedia);
|
1665 |
|
|
}
|
1666 |
|
|
|
1667 |
|
|
|
1668 |
|
|
// typelabel will contain the typeStatus
|
1669 |
|
|
$type_label = '';
|
1670 |
|
|
$typeDesignationPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $specimenOrObservation->uuid);
|
1671 |
|
|
if (isset($typeDesignationPager) and isset($typeDesignationPager->records)) {
|
1672 |
|
|
$type_status = array();
|
1673 |
|
|
foreach ($typeDesignationPager->records as $typeDesignation) {
|
1674 |
|
|
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
1675 |
|
|
$type_status[] = $typeDesignation->typeStatus->representation_L10n;
|
1676 |
|
|
}
|
1677 |
|
|
}
|
1678 |
|
|
$type_label = implode(', ', $type_status);
|
1679 |
|
|
if ($type_label) {
|
1680 |
|
|
$type_label .= ': ';
|
1681 |
|
|
}
|
1682 |
|
|
}
|
1683 |
|
|
|
1684 |
|
|
// --- Specimen entry as dynamic label:
|
1685 |
|
|
// -> Dynabox for the specimenOrObservation
|
1686 |
|
|
$gallery_name = $specimenOrObservation->uuid;
|
1687 |
|
|
|
1688 |
44458b04
|
Andreas Kohlbecker
|
$derived_unit_ws_request = cdm_compose_ws_url(CDM_WS_OCCURRENCE, array($specimenOrObservation->uuid));
|
1689 |
ca7468b6
|
Andreas Kohlbecker
|
// --- Render associated media.
|
1690 |
|
|
$gallery_html = '';
|
1691 |
|
|
if (count($mediaList) > 0) {
|
1692 |
|
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
1693 |
|
|
$captionElements = array(
|
1694 |
|
|
'#uri' => t('open media'),
|
1695 |
|
|
);
|
1696 |
|
|
|
1697 |
|
|
$gallery_html = compose_cdm_media_gallerie(array(
|
1698 |
|
|
'mediaList' => $mediaList,
|
1699 |
|
|
'galleryName' => $gallery_name,
|
1700 |
|
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
1701 |
|
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
1702 |
|
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
1703 |
|
|
'captionElements' => $captionElements,
|
1704 |
|
|
'mediaLinkType' => 'LIGHTBOX',
|
1705 |
|
|
'alternativeMediaUri' => NULL,
|
1706 |
|
|
'galleryLinkUri' => NULL,
|
1707 |
|
|
));
|
1708 |
|
|
}
|
1709 |
|
|
//here we should use the data we already have
|
1710 |
|
|
$label_html = cdm_dynabox(
|
1711 |
|
|
$specimenOrObservation->uuid,
|
1712 |
|
|
$type_label . $specimenOrObservation->titleCache,
|
1713 |
|
|
$derived_unit_ws_request,
|
1714 |
|
|
'cdm_specimen_or_observation',
|
1715 |
|
|
'Click for details',
|
1716 |
|
|
array('div', 'div'),
|
1717 |
|
|
array(),
|
1718 |
|
|
null, // $content_element_selector
|
1719 |
|
|
'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').hide(); }', // open_callback
|
1720 |
|
|
'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').show(); }' // close_callback
|
1721 |
|
|
);
|
1722 |
|
|
|
1723 |
|
|
// --- Render associated media.
|
1724 |
|
|
$gallery_html = '';
|
1725 |
|
|
if (count($mediaList) > 0) {
|
1726 |
|
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
1727 |
|
|
$captionElements = array(
|
1728 |
|
|
'#uri' => t('open media'),
|
1729 |
|
|
);
|
1730 |
|
|
|
1731 |
|
|
$gallery_html = compose_cdm_media_gallerie(array(
|
1732 |
|
|
'mediaList' => $mediaList,
|
1733 |
|
|
'galleryName' => $gallery_name,
|
1734 |
|
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
1735 |
|
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
1736 |
|
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
1737 |
|
|
'captionElements' => $captionElements,
|
1738 |
|
|
'mediaLinkType' => 'LIGHTBOX',
|
1739 |
|
|
'alternativeMediaUri' => NULL,
|
1740 |
|
|
'galleryLinkUri' => NULL,
|
1741 |
|
|
));
|
1742 |
|
|
}
|
1743 |
|
|
|
1744 |
|
|
$specimen_table['#rows'][] = array(
|
1745 |
|
|
// An array of table rows. Every row is an array of cells, or an associative array
|
1746 |
|
|
'data' => array(
|
1747 |
|
|
// Each cell can be either a string or an associative array
|
1748 |
|
|
$label_html . $gallery_html
|
1749 |
|
|
),
|
1750 |
|
|
'class' => array(
|
1751 |
|
|
'descriptionElement',
|
1752 |
|
|
'descriptionElement_IndividualsAssociation'
|
1753 |
|
|
),
|
1754 |
|
|
);
|
1755 |
|
|
}
|
1756 |
|
|
}
|
1757 |
|
|
|
1758 |
|
|
return $specimen_table;
|
1759 |
|
|
}
|
1760 |
|
|
|
1761 |
961319fe
|
Andreas Kohlbecker
|
|
1762 |
|
|
/**
|
1763 |
|
|
* Orders occurrences by date but types should be on top of the list.
|
1764 |
|
|
*
|
1765 |
|
|
* @param $specimensOrObservations_or_fieldUnitDTO
|
1766 |
|
|
*
|
1767 |
|
|
* @return array
|
1768 |
|
|
*/
|
1769 |
|
|
function order_specimens_or_observations_by_date_and_type($specimensOrObservations)
|
1770 |
|
|
{
|
1771 |
|
|
// order occurrences by date but types should be on top of the list
|
1772 |
|
|
$type_specimens = array();
|
1773 |
|
|
$other_occurrences = array();
|
1774 |
|
|
foreach ($specimensOrObservations as &$occurrence) {
|
1775 |
|
|
$typeDesignationsPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $occurrence->uuid);
|
1776 |
|
|
if (isset($typeDesignationsPager->count) && $typeDesignationsPager->count > 0) {
|
1777 |
|
|
$type_specimens[] = $occurrence;
|
1778 |
|
|
} else {
|
1779 |
|
|
$other_occurrences[] = $occurrence;
|
1780 |
|
|
}
|
1781 |
|
|
}
|
1782 |
|
|
$specimensOrObservations = array_merge($type_specimens, $other_occurrences);
|
1783 |
|
|
return $specimensOrObservations;
|
1784 |
|
|
}
|
1785 |
|
|
|
1786 |
|
|
/**
|
1787 |
|
|
* Orders FieldUnitDTOs by date but types should be on top of the list.
|
1788 |
|
|
*
|
1789 |
|
|
* Delegates internally to order_specimens_or_observations_by_date_and_type()
|
1790 |
|
|
*
|
1791 |
|
|
* @param $fieldUnitDTOs
|
1792 |
|
|
*
|
1793 |
|
|
* @return array
|
1794 |
|
|
*/
|
1795 |
|
|
function order_fieldUnitDtos_by_date_and_type($fieldUnitDTOs)
|
1796 |
|
|
{
|
1797 |
|
|
return order_specimens_or_observations_by_date_and_type($fieldUnitDTOs);
|
1798 |
|
|
}
|