| 1 |
c70b93c3
|
Andreas Kohlbecker
|
<?php
|
| 2 |
f19f47fa
|
Andreas Kohlbecker
|
/**
|
| 3 |
|
|
* @file
|
| 4 |
bff67f14
|
Patric Plitzner
|
* Functions for dealing with CDM entities of type SpecimenOrOccurrences
|
| 5 |
f19f47fa
|
Andreas Kohlbecker
|
*
|
| 6 |
|
|
* @copyright
|
| 7 |
|
|
* (C) 2007-2012 EDIT
|
| 8 |
|
|
* European Distributed Institute of Taxonomy
|
| 9 |
|
|
* http://www.e-taxonomy.eu
|
| 10 |
|
|
*
|
| 11 |
|
|
* The contents of this module are subject to the Mozilla
|
| 12 |
|
|
* Public License Version 1.1.
|
| 13 |
|
|
* @see http://www.mozilla.org/MPL/MPL-1.1.html
|
| 14 |
|
|
*
|
| 15 |
|
|
* @author
|
| 16 |
|
|
* - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
|
| 17 |
c70b93c3
|
Andreas Kohlbecker
|
*/
|
| 18 |
|
|
|
| 19 |
b810158e
|
Patric Plitzner
|
|
| 20 |
|
|
/**
|
| 21 |
30845bda
|
Andreas Kohlbecker
|
* Provides the HTML markup for a specimen page
|
| 22 |
|
|
*
|
| 23 |
|
|
* @param $specimen
|
| 24 |
|
|
*
|
| 25 |
b810158e
|
Patric Plitzner
|
* @return string
|
| 26 |
30845bda
|
Andreas Kohlbecker
|
* The markup for a specimen page
|
| 27 |
b810158e
|
Patric Plitzner
|
*/
|
| 28 |
30845bda
|
Andreas Kohlbecker
|
function render_cdm_specimen_page($specimen, $is_specimen_page = false)
|
| 29 |
b810158e
|
Patric Plitzner
|
{
|
| 30 |
|
|
$detail_html = "";
|
| 31 |
|
|
//link to specimen page
|
| 32 |
30845bda
|
Andreas Kohlbecker
|
$pathToSpecimen = path_to_specimen($specimen->uuid);
|
| 33 |
|
|
if (!$is_specimen_page) {
|
| 34 |
|
|
$specimenPageLink = l($specimen->accessionNumber, $pathToSpecimen, array('attributes' => array('target' => '_blank')));
|
| 35 |
2d6348e5
|
Patrick Plitzner
|
$detail_html .= "<strong>Specimen page: $specimenPageLink</strong><br>";
|
| 36 |
a7a302a0
|
Patric Plitzner
|
}
|
| 37 |
|
|
|
| 38 |
30845bda
|
Andreas Kohlbecker
|
if($is_specimen_page) {
|
| 39 |
|
|
if($specimen->citation){
|
| 40 |
|
|
$detail_html .= "<br>".create_label("Citation") . $specimen->citation . "<br>";
|
| 41 |
fdc85125
|
Patric Plitzner
|
}
|
| 42 |
b810158e
|
Patric Plitzner
|
}
|
| 43 |
30845bda
|
Andreas Kohlbecker
|
if($specimen->preferredStableUri){
|
| 44 |
48b1eaa7
|
Patrick Plitzner
|
$stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri, array('attributes' => array('target' => '_blank')));
|
| 45 |
907cc9b4
|
Patrick Plitzner
|
$detail_html .= create_label("Preferred stable URI") . $stableIdentifierLink . "<br>";
|
| 46 |
1cefb4e5
|
Patrick Plitzner
|
}
|
| 47 |
30845bda
|
Andreas Kohlbecker
|
if($is_specimen_page){
|
| 48 |
fdc85125
|
Patric Plitzner
|
// associated taxa
|
| 49 |
30845bda
|
Andreas Kohlbecker
|
if($specimen->associatedTaxa){
|
| 50 |
3dd58832
|
Patric Plitzner
|
$detail_html .= "<br>";
|
| 51 |
fa09fe7d
|
Patrick Plitzner
|
$detail_html .= create_label("Associated with");
|
| 52 |
|
|
if(sizeof($specimen->associatedTaxa)>1){
|
| 53 |
|
|
$detail_html .= "<br>";
|
| 54 |
|
|
}
|
| 55 |
|
|
foreach($specimen->associatedTaxa as $associatedTaxon){
|
| 56 |
|
|
$detail_html .= l($associatedTaxon->second, path_to_taxon($associatedTaxon->first, "specimens"));//$associatedTaxon->second."<br>";
|
| 57 |
|
|
}
|
| 58 |
|
|
$detail_html .= "<br>";
|
| 59 |
fdc85125
|
Patric Plitzner
|
}
|
| 60 |
b810158e
|
Patric Plitzner
|
}
|
| 61 |
fa09fe7d
|
Patrick Plitzner
|
// - type information
|
| 62 |
b810158e
|
Patric Plitzner
|
$types = "";
|
| 63 |
30845bda
|
Andreas Kohlbecker
|
if (isset($specimen->types)) {
|
| 64 |
56d58f9b
|
Patric Plitzner
|
//typed taxa
|
| 65 |
30845bda
|
Andreas Kohlbecker
|
foreach ($specimen->types as $typeStatus => $typedTaxa) {
|
| 66 |
b0efd824
|
Patrick Plitzner
|
if($specimen->types){
|
| 67 |
a5b11885
|
Patrick Plitzner
|
if($typeStatus == NULL){
|
| 68 |
|
|
$detail_html .= "<i>no type status set:</i> ";
|
| 69 |
|
|
}
|
| 70 |
|
|
else{
|
| 71 |
|
|
$detail_html .= "<i>".$typeStatus."</i> of ";
|
| 72 |
|
|
}
|
| 73 |
b0efd824
|
Patrick Plitzner
|
foreach($typedTaxa as $typedTaxon){
|
| 74 |
|
|
$detail_html .= $typedTaxon." ";
|
| 75 |
fdc85125
|
Patric Plitzner
|
}
|
| 76 |
b0efd824
|
Patrick Plitzner
|
$detail_html .= "<br>";
|
| 77 |
fdc85125
|
Patric Plitzner
|
}
|
| 78 |
b810158e
|
Patric Plitzner
|
}
|
| 79 |
|
|
}
|
| 80 |
30845bda
|
Andreas Kohlbecker
|
$derivateDataDTO = $specimen->derivateDataDTO;
|
| 81 |
b810158e
|
Patric Plitzner
|
// - specimen scans
|
| 82 |
65a4de51
|
Patrick Plitzner
|
$specimenScans = create_html_links($derivateDataDTO->specimenScans, true);
|
| 83 |
b810158e
|
Patric Plitzner
|
// - molecular data
|
| 84 |
|
|
$molecularData = "";
|
| 85 |
|
|
if ($derivateDataDTO->molecularDataList) {
|
| 86 |
|
|
foreach ($derivateDataDTO->molecularDataList as $molecular) {
|
| 87 |
|
|
//provider link
|
| 88 |
|
|
if (isset($molecular->providerLink)) {
|
| 89 |
65a4de51
|
Patrick Plitzner
|
$molecularData .= create_html_link($molecular->providerLink, true);
|
| 90 |
2c23b054
|
Patrick Plitzner
|
} else {
|
| 91 |
|
|
$molecularData .= "[no provider]";
|
| 92 |
b810158e
|
Patric Plitzner
|
}
|
| 93 |
|
|
//contig link
|
| 94 |
2c23b054
|
Patrick Plitzner
|
if (isset($molecular->contigFiles)) {
|
| 95 |
b810158e
|
Patric Plitzner
|
$molecularData .= "[";
|
| 96 |
2c23b054
|
Patrick Plitzner
|
if (sizeof($molecular->contigFiles) > 0) {
|
| 97 |
b810158e
|
Patric Plitzner
|
foreach ($molecular->contigFiles as $contigFile) {
|
| 98 |
2c23b054
|
Patrick Plitzner
|
if (isset($contigFile->contigLink)) {
|
| 99 |
|
|
if (isset($contigFile->contigLink->uri) and $contigFile->contigLink->uri != null) {
|
| 100 |
|
|
$molecularData .= create_html_link($contigFile->contigLink, true) . " ";
|
| 101 |
37ab3ddc
|
Patric Plitzner
|
}
|
| 102 |
2c23b054
|
Patrick Plitzner
|
}
|
| 103 |
|
|
else {
|
| 104 |
|
|
$molecularData .= "no contig ";
|
| 105 |
|
|
}
|
| 106 |
|
|
//primer links
|
| 107 |
|
|
if(isset($contigFile->primerLinks)) {
|
| 108 |
65a4de51
|
Patrick Plitzner
|
$molecularData .= create_html_links($contigFile->primerLinks, true);
|
| 109 |
b810158e
|
Patric Plitzner
|
}
|
| 110 |
|
|
}
|
| 111 |
|
|
}
|
| 112 |
5eafa5ff
|
Patric Plitzner
|
$molecularData = rtrim($molecularData, " ");
|
| 113 |
b810158e
|
Patric Plitzner
|
$molecularData .= "]";
|
| 114 |
|
|
}
|
| 115 |
|
|
//FIXME separate with comma (remove trailing comma)
|
| 116 |
|
|
}
|
| 117 |
|
|
}
|
| 118 |
|
|
// - detail images
|
| 119 |
65a4de51
|
Patrick Plitzner
|
$detailImages = create_html_links($derivateDataDTO->detailImages, true);
|
| 120 |
b810158e
|
Patric Plitzner
|
|
| 121 |
|
|
if ($types) {
|
| 122 |
30845bda
|
Andreas Kohlbecker
|
$detail_html .= $is_specimen_page?"<br>":"";
|
| 123 |
a0bbccce
|
Patrick Plitzner
|
$detail_html .= create_label("Type(s)") . $types . "<br>";
|
| 124 |
b810158e
|
Patric Plitzner
|
}
|
| 125 |
30845bda
|
Andreas Kohlbecker
|
if ($specimenScans and !$is_specimen_page) {
|
| 126 |
3dd58832
|
Patric Plitzner
|
$detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
|
| 127 |
b810158e
|
Patric Plitzner
|
}
|
| 128 |
8d9d64a5
|
Patric Plitzner
|
//specimen scan image gallery
|
| 129 |
30845bda
|
Andreas Kohlbecker
|
if($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
|
| 130 |
8d9d64a5
|
Patric Plitzner
|
$detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
|
| 131 |
|
|
}
|
| 132 |
|
|
|
| 133 |
b810158e
|
Patric Plitzner
|
if ($molecularData) {
|
| 134 |
30845bda
|
Andreas Kohlbecker
|
$detail_html .= $is_specimen_page?"<br>":"";
|
| 135 |
3dd58832
|
Patric Plitzner
|
$detail_html .= create_label("Molecular Data") . $molecularData . "<br>";
|
| 136 |
b810158e
|
Patric Plitzner
|
}
|
| 137 |
8d9d64a5
|
Patric Plitzner
|
|
| 138 |
30845bda
|
Andreas Kohlbecker
|
if ($detailImages and !$is_specimen_page) {
|
| 139 |
3dd58832
|
Patric Plitzner
|
$detail_html .= create_label("Detail Images") . $detailImages . "<br>";
|
| 140 |
b810158e
|
Patric Plitzner
|
}
|
| 141 |
|
|
|
| 142 |
8d9d64a5
|
Patric Plitzner
|
//detail image gallery
|
| 143 |
30845bda
|
Andreas Kohlbecker
|
if($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)){
|
| 144 |
8d9d64a5
|
Patric Plitzner
|
$detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
|
| 145 |
|
|
}
|
| 146 |
|
|
|
| 147 |
b810158e
|
Patric Plitzner
|
//character data
|
| 148 |
30845bda
|
Andreas Kohlbecker
|
if ($specimen->characterData) {
|
| 149 |
|
|
$detail_html .= $is_specimen_page?"<br>":"";
|
| 150 |
a442acb8
|
Patric Plitzner
|
$detail_html .= create_label("Character Data");
|
| 151 |
30845bda
|
Andreas Kohlbecker
|
if($is_specimen_page) {
|
| 152 |
b810158e
|
Patric Plitzner
|
$detail_html .= "<br>";
|
| 153 |
30845bda
|
Andreas Kohlbecker
|
foreach ($specimen->characterData as $characterStatePair) {
|
| 154 |
a442acb8
|
Patric Plitzner
|
$detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second;
|
| 155 |
|
|
$detail_html .= "<br>";
|
| 156 |
|
|
}
|
| 157 |
|
|
}
|
| 158 |
|
|
else{
|
| 159 |
|
|
$detail_html .= l("detail page", $pathToSpecimen,array('attributes' => array('target'=>'_blank')));
|
| 160 |
216abf0b
|
Patric Plitzner
|
$detail_html .= "<br>";
|
| 161 |
b810158e
|
Patric Plitzner
|
}
|
| 162 |
|
|
}
|
| 163 |
8d9d64a5
|
Patric Plitzner
|
return $detail_html;
|
| 164 |
|
|
}
|
| 165 |
8c1d6d72
|
Patric Plitzner
|
|
| 166 |
8d9d64a5
|
Patric Plitzner
|
function addImageGallery($galleryName, $imageUuids){
|
| 167 |
b5c89485
|
Patric Plitzner
|
$images = array();
|
| 168 |
8d9d64a5
|
Patric Plitzner
|
foreach ($imageUuids as $uuid) {
|
| 169 |
|
|
$images[] = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $uuid);
|
| 170 |
8c1d6d72
|
Patric Plitzner
|
}
|
| 171 |
7cf177d0
|
Patrick Plitzner
|
|
| 172 |
|
|
$gallery_html = '';
|
| 173 |
|
|
if (count($imageUuids) > 0) {
|
| 174 |
|
|
$gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
|
| 175 |
|
|
$captionElements = array(
|
| 176 |
|
|
'title',
|
| 177 |
|
|
'rights',
|
| 178 |
|
|
);
|
| 179 |
|
|
$alternativeMediaUris = array();
|
| 180 |
|
|
foreach($images as $image){
|
| 181 |
e2eaa6c7
|
Patrick Plitzner
|
$mediaUri = getMediaUri($image);
|
| 182 |
|
|
if($mediaUri){
|
| 183 |
|
|
$alternativeMediaUris[] = $mediaUri;
|
| 184 |
|
|
}
|
| 185 |
|
|
else{
|
| 186 |
7cf177d0
|
Patrick Plitzner
|
$alternativeMediaUris[] = path_to_media($image->uuid);
|
| 187 |
e2eaa6c7
|
Patrick Plitzner
|
}
|
| 188 |
7cf177d0
|
Patrick Plitzner
|
}
|
| 189 |
|
|
|
| 190 |
a9815578
|
Andreas Kohlbecker
|
$gallery_html = compose_cdm_media_gallerie(array(
|
| 191 |
7cf177d0
|
Patrick Plitzner
|
'mediaList' => $images,
|
| 192 |
|
|
'galleryName' => $galleryName,
|
| 193 |
|
|
'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
|
| 194 |
|
|
'cols' => $gallery_settings['cdm_dataportal_media_cols'],
|
| 195 |
|
|
'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
|
| 196 |
|
|
'captionElements' => $captionElements,
|
| 197 |
|
|
'mediaLinkType' => 'LIGHTBOX',
|
| 198 |
|
|
'alternativeMediaUri' => $alternativeMediaUris,
|
| 199 |
|
|
'galleryLinkUri' => NULL,
|
| 200 |
|
|
));
|
| 201 |
|
|
}
|
| 202 |
|
|
return "<br>".create_label($galleryName)."<br>".$gallery_html;
|
| 203 |
b810158e
|
Patric Plitzner
|
}
|
| 204 |
|
|
|
| 205 |
e2eaa6c7
|
Patrick Plitzner
|
function getMediaUri($media){
|
| 206 |
|
|
if(isset($media->representations) && sizeof($media->representations)==1
|
| 207 |
|
|
&& isset($media->representations[0]->parts) &&
|
| 208 |
|
|
sizeof($media->representations[0]->parts)==1) {
|
| 209 |
|
|
return $media->representations[0]->parts[0]->uri;
|
| 210 |
|
|
}
|
| 211 |
|
|
return null;
|
| 212 |
|
|
}
|
| 213 |
|
|
|
| 214 |
8d9d64a5
|
Patric Plitzner
|
|
| 215 |
3dd58832
|
Patric Plitzner
|
/**
|
| 216 |
5a079dbf
|
Andreas Kohlbecker
|
* Formats the given string to a label for displaying key-object pairs in HTML
|
| 217 |
3dd58832
|
Patric Plitzner
|
* @return string
|
| 218 |
|
|
*/
|
| 219 |
|
|
function create_label($label)
|
| 220 |
|
|
{
|
| 221 |
|
|
return "<span class='specimen_table_label'>".$label.": </span>";
|
| 222 |
|
|
}
|
| 223 |
|
|
|
| 224 |
f19f47fa
|
Andreas Kohlbecker
|
/**
|
| 225 |
|
|
* Compose an render array from a CDM DerivedUnitFacade object.
|
| 226 |
|
|
*
|
| 227 |
|
|
* compose_hook() implementation
|
| 228 |
235fc94b
|
Andreas Kohlbecker
|
*
|
| 229 |
|
|
* @param object $specimenOrObservation
|
| 230 |
|
|
* the CDM instance of type SpecimenOrObservation to compose
|
| 231 |
|
|
* the render array for
|
| 232 |
|
|
* @param array $derivatives
|
| 233 |
|
|
* the render array which contains the compositions of the derivatives
|
| 234 |
|
|
* of the supplied $specimenOrObservation
|
| 235 |
|
|
*
|
| 236 |
|
|
* @return array
|
| 237 |
|
|
* the supplied render array $derivatives to which the composition of the supplied
|
| 238 |
|
|
* $specimenOrObservation has been added to
|
| 239 |
5b26b91a
|
Andreas Kohlbecker
|
*
|
| 240 |
|
|
* @ingroup compose
|
| 241 |
f19f47fa
|
Andreas Kohlbecker
|
*/
|
| 242 |
bd814ea2
|
Andreas Kohlbecker
|
function compose_cdm_specimen_or_observation($specimenOrObservation, &$derivatives = null) {
|
| 243 |
f846e7e7
|
Andreas Kohlbecker
|
|
| 244 |
eeb98da8
|
Andreas Kohlbecker
|
$exclude_occurrence_fields = &drupal_static(__FUNCTION__);
|
| 245 |
|
|
if (!isset($exclude_occurrence_fields)) {
|
| 246 |
|
|
$exclude_occurrence_fields = array(
|
| 247 |
5b30a682
|
Andreas Kohlbecker
|
'derivationEvents',
|
| 248 |
eeb98da8
|
Andreas Kohlbecker
|
'titleCache',
|
| 249 |
f19f47fa
|
Andreas Kohlbecker
|
'protectedTitleCache',
|
| 250 |
eeb98da8
|
Andreas Kohlbecker
|
'derivedUnitMedia',
|
| 251 |
|
|
'created',
|
| 252 |
f67ffd4e
|
Andreas Kohlbecker
|
'publish',
|
| 253 |
eeb98da8
|
Andreas Kohlbecker
|
'updated',
|
| 254 |
|
|
'class',
|
| 255 |
5b3557f9
|
Andreas Kohlbecker
|
'uuid',
|
| 256 |
f19f47fa
|
Andreas Kohlbecker
|
''
|
| 257 |
eeb98da8
|
Andreas Kohlbecker
|
);
|
| 258 |
|
|
}
|
| 259 |
|
|
|
| 260 |
f846e7e7
|
Andreas Kohlbecker
|
|
| 261 |
98450eb2
|
Andreas Kohlbecker
|
// only show uuid it the user is logged in
|
| 262 |
a67e7364
|
Andreas Kohlbecker
|
if(user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE ) {
|
| 263 |
|
|
unset($exclude_occurrence_fields[$a_idx]);
|
| 264 |
98450eb2
|
Andreas Kohlbecker
|
}
|
| 265 |
9b9037f3
|
Andreas Kohlbecker
|
|
| 266 |
6fbdb943
|
Andreas Kohlbecker
|
if (!isset($derivatives)) {
|
| 267 |
|
|
$derivatives = array();
|
| 268 |
f846e7e7
|
Andreas Kohlbecker
|
}
|
| 269 |
|
|
|
| 270 |
6fbdb943
|
Andreas Kohlbecker
|
$descriptions = null;
|
| 271 |
0796d2f9
|
Andreas Kohlbecker
|
$derivedFrom = null;
|
| 272 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 273 |
6fbdb943
|
Andreas Kohlbecker
|
if (is_object($specimenOrObservation)) {
|
| 274 |
f846e7e7
|
Andreas Kohlbecker
|
|
| 275 |
|
|
// request again for deeper initialization
|
| 276 |
|
|
$specimenOrObservation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);
|
| 277 |
9b9037f3
|
Andreas Kohlbecker
|
|
| 278 |
15b7c460
|
Andreas Kohlbecker
|
|
| 279 |
9b9037f3
|
Andreas Kohlbecker
|
$type_label = $specimenOrObservation->class;
|
| 280 |
15b7c460
|
Andreas Kohlbecker
|
RenderHints::setFootnoteListKey($type_label . '-' . $specimenOrObservation->uuid);
|
| 281 |
|
|
|
| 282 |
9b9037f3
|
Andreas Kohlbecker
|
// collect typeStatus as label
|
| 283 |
|
|
if (isset($specimenOrObservation->specimenTypeDesignations)) {
|
| 284 |
|
|
$type_status = array();
|
| 285 |
|
|
foreach ($specimenOrObservation->specimenTypeDesignations as $typeDesignation) {
|
| 286 |
0820cdc0
|
Andreas Kohlbecker
|
if (isset($typeDesignation->typeStatus->representation_L10n)) {
|
| 287 |
9b9037f3
|
Andreas Kohlbecker
|
$type_status[] = $typeDesignation->typeStatus->representation_L10n;
|
| 288 |
|
|
}
|
| 289 |
|
|
}
|
| 290 |
0820cdc0
|
Andreas Kohlbecker
|
if (count($type_status) > 0) {
|
| 291 |
c6787c7d
|
Andreas Kohlbecker
|
$type_label = implode(', ', $type_status);
|
| 292 |
cb7db01d
|
Andreas Kohlbecker
|
}
|
| 293 |
9b9037f3
|
Andreas Kohlbecker
|
}
|
| 294 |
|
|
|
| 295 |
0820cdc0
|
Andreas Kohlbecker
|
$title = $type_label . ': ' . $specimenOrObservation->titleCache;
|
| 296 |
6fbdb943
|
Andreas Kohlbecker
|
|
| 297 |
f846e7e7
|
Andreas Kohlbecker
|
$groups = array();
|
| 298 |
|
|
// --- add initialized fields
|
| 299 |
f19f47fa
|
Andreas Kohlbecker
|
foreach (get_object_vars($specimenOrObservation) as $field => $value) {
|
| 300 |
|
|
if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
| 301 |
6fbdb943
|
Andreas Kohlbecker
|
switch ($field) {
|
| 302 |
|
|
|
| 303 |
|
|
/* ---- java.lang.Object --- */
|
| 304 |
|
|
case 'class':
|
| 305 |
0820cdc0
|
Andreas Kohlbecker
|
if ($value != '' /* FieldUnit' */) {
|
| 306 |
6fbdb943
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
| 307 |
|
|
}
|
| 308 |
0820cdc0
|
Andreas Kohlbecker
|
break;
|
| 309 |
4ae6064e
|
Andreas Kohlbecker
|
|
| 310 |
|
|
case 'markers':
|
| 311 |
|
|
$dd_elements = array();
|
| 312 |
|
|
foreach ($value as $marker) {
|
| 313 |
|
|
$dd_elements[] = compose_cdm_marker($marker);
|
| 314 |
|
|
}
|
| 315 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
| 316 |
|
|
break;
|
| 317 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 318 |
4ae6064e
|
Andreas Kohlbecker
|
|
| 319 |
5b30a682
|
Andreas Kohlbecker
|
case 'annotations':
|
| 320 |
|
|
$dd_elements = array();
|
| 321 |
|
|
foreach ($value as $annotation) {
|
| 322 |
|
|
// TODO respect annotation type filter settings
|
| 323 |
|
|
$dd_elements[] = $annotation->text;
|
| 324 |
|
|
}
|
| 325 |
|
|
@_description_list_group_add($groups, t('Notes'), $dd_elements);
|
| 326 |
|
|
break;
|
| 327 |
eeb98da8
|
Andreas Kohlbecker
|
|
| 328 |
6fbdb943
|
Andreas Kohlbecker
|
/* ---- SpecimenOrObservationBase --- */
|
| 329 |
|
|
case 'sex':
|
| 330 |
|
|
case 'lifeStage':
|
| 331 |
06d6b7fa
|
Andreas Kohlbecker
|
case 'kindOfUnit':
|
| 332 |
6fbdb943
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n);
|
| 333 |
f846e7e7
|
Andreas Kohlbecker
|
break;
|
| 334 |
|
|
|
| 335 |
6fbdb943
|
Andreas Kohlbecker
|
case 'definition':
|
| 336 |
|
|
// TODO
|
| 337 |
|
|
break;
|
| 338 |
|
|
|
| 339 |
a9ed34ad
|
Andreas Kohlbecker
|
case 'preferredStableUri':
|
| 340 |
|
|
|
| 341 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
|
| 342 |
|
|
break;
|
| 343 |
|
|
|
| 344 |
9b9037f3
|
Andreas Kohlbecker
|
case 'specimenTypeDesignations':
|
| 345 |
4c75b2d9
|
Andreas Kohlbecker
|
@_description_list_group_add(
|
| 346 |
|
|
$groups,
|
| 347 |
|
|
cdm_occurrence_field_name_label($field),
|
| 348 |
|
|
array(
|
| 349 |
0820cdc0
|
Andreas Kohlbecker
|
'#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
|
| 350 |
4c75b2d9
|
Andreas Kohlbecker
|
)
|
| 351 |
|
|
);
|
| 352 |
9b9037f3
|
Andreas Kohlbecker
|
break;
|
| 353 |
|
|
|
| 354 |
6fbdb943
|
Andreas Kohlbecker
|
case 'determinations':
|
| 355 |
f19f47fa
|
Andreas Kohlbecker
|
$dd_elements = array();
|
| 356 |
42133a60
|
Andreas Kohlbecker
|
$glue = ', ';
|
| 357 |
9b9037f3
|
Andreas Kohlbecker
|
|
| 358 |
0820cdc0
|
Andreas Kohlbecker
|
foreach ($value as $determinationEvent) {
|
| 359 |
|
|
$timeperiod_string = NULL;
|
| 360 |
|
|
if (isset($determinationEvent->timeperiod)) {
|
| 361 |
|
|
$timeperiod_string = timePeriodToString($determinationEvent->timeperiod);
|
| 362 |
|
|
}
|
| 363 |
|
|
$weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
|
| 364 |
|
|
// check key exists
|
| 365 |
|
|
while (array_key_exists($weight, $dd_elements)) {
|
| 366 |
|
|
$weight .= '0';
|
| 367 |
|
|
}
|
| 368 |
|
|
|
| 369 |
|
|
$taxon_name = '';
|
| 370 |
|
|
$name_link = '';
|
| 371 |
|
|
if ($determinationEvent->taxonName) {
|
| 372 |
|
|
$taxon_name = $determinationEvent->taxonName;
|
| 373 |
|
|
} else if ($determinationEvent->taxon) {
|
| 374 |
|
|
$taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
|
| 375 |
|
|
$name_link = path_to_taxon($determinationEvent->taxon->uuid);
|
| 376 |
|
|
}
|
| 377 |
|
|
if ($taxon_name) {
|
| 378 |
63c3ac73
|
Andreas Kohlbecker
|
$taxon_html = render_taxon_or_name($taxon_name, $name_link);
|
| 379 |
3dd58832
|
Patric Plitzner
|
$dd_elements[$weight] = $taxon_html;
|
| 380 |
0820cdc0
|
Andreas Kohlbecker
|
}
|
| 381 |
|
|
if (isset($determinationEvent->modifier)) {
|
| 382 |
|
|
$dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
|
| 383 |
|
|
}
|
| 384 |
|
|
if ($timeperiod_string) {
|
| 385 |
|
|
$dd_elements[$weight] .= $glue . $timeperiod_string;
|
| 386 |
|
|
}
|
| 387 |
|
|
if (isset($determinationEvent->actor->titleCache)) {
|
| 388 |
|
|
$dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
|
| 389 |
|
|
}
|
| 390 |
|
|
if (isset($determinationEvent->description)) {
|
| 391 |
|
|
$dd_elements[$weight] .= $glue . $determinationEvent->description;
|
| 392 |
|
|
}
|
| 393 |
1b04a204
|
Andreas Kohlbecker
|
}
|
| 394 |
9b9037f3
|
Andreas Kohlbecker
|
ksort($dd_elements);
|
| 395 |
f19f47fa
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
|
| 396 |
1b04a204
|
Andreas Kohlbecker
|
break;
|
| 397 |
f846e7e7
|
Andreas Kohlbecker
|
|
| 398 |
f19f47fa
|
Andreas Kohlbecker
|
case 'descriptions':
|
| 399 |
bfb2b81a
|
Andreas Kohlbecker
|
$occurrence_featureTree = cdm_get_occurrence_featureTree();
|
| 400 |
|
|
$dd_elements = array();
|
| 401 |
|
|
|
| 402 |
a7a96336
|
Andreas Kohlbecker
|
foreach ($value as $description) {
|
| 403 |
bfb2b81a
|
Andreas Kohlbecker
|
$description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
|
| 404 |
a67e7364
|
Andreas Kohlbecker
|
// if($description->imageGallery == TRUE) {
|
| 405 |
|
|
// continue;
|
| 406 |
|
|
// }
|
| 407 |
fae36a2a
|
Andreas Kohlbecker
|
$elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements);
|
| 408 |
1b756c5f
|
Andreas Kohlbecker
|
$description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null));
|
| 409 |
9b9037f3
|
Andreas Kohlbecker
|
$dd_elements[] = $description_render_elements;
|
| 410 |
bfb2b81a
|
Andreas Kohlbecker
|
}
|
| 411 |
|
|
|
| 412 |
f19f47fa
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
| 413 |
6fbdb943
|
Andreas Kohlbecker
|
break;
|
| 414 |
|
|
|
| 415 |
f846e7e7
|
Andreas Kohlbecker
|
case 'sources':
|
| 416 |
0820cdc0
|
Andreas Kohlbecker
|
$dd_elements = array();
|
| 417 |
|
|
foreach ($value as $identifiable_source) {
|
| 418 |
|
|
$dd_elements[] = theme('cdm_OriginalSource', array('source' => $identifiable_source));
|
| 419 |
|
|
}
|
| 420 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
| 421 |
|
|
break;
|
| 422 |
0796d2f9
|
Andreas Kohlbecker
|
|
| 423 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 424 |
0796d2f9
|
Andreas Kohlbecker
|
/* ---- DerivedUnitBase --- */
|
| 425 |
|
|
case 'derivedFrom':
|
| 426 |
|
|
$derivedFrom = $value;
|
| 427 |
f19f47fa
|
Andreas Kohlbecker
|
break;
|
| 428 |
6fbdb943
|
Andreas Kohlbecker
|
|
| 429 |
|
|
case 'collection':
|
| 430 |
|
|
$sub_dl_groups = array();
|
| 431 |
f19f47fa
|
Andreas Kohlbecker
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
|
| 432 |
0820cdc0
|
Andreas Kohlbecker
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
|
| 433 |
964c2f69
|
Andreas Kohlbecker
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
|
| 434 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
|
| 435 |
6fbdb943
|
Andreas Kohlbecker
|
// TODO "superCollection"
|
| 436 |
|
|
// TODO may have media
|
| 437 |
|
|
|
| 438 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
| 439 |
0820cdc0
|
Andreas Kohlbecker
|
array(
|
| 440 |
|
|
array('#markup' => $value->titleCache),
|
| 441 |
|
|
array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
|
| 442 |
|
|
)
|
| 443 |
f19f47fa
|
Andreas Kohlbecker
|
);
|
| 444 |
6fbdb943
|
Andreas Kohlbecker
|
break;
|
| 445 |
|
|
|
| 446 |
0820cdc0
|
Andreas Kohlbecker
|
case 'storedUnder':
|
| 447 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
|
| 448 |
|
|
break;
|
| 449 |
6fbdb943
|
Andreas Kohlbecker
|
|
| 450 |
|
|
|
| 451 |
0820cdc0
|
Andreas Kohlbecker
|
/* ---- Specimen --- */
|
| 452 |
|
|
case 'sequences':
|
| 453 |
|
|
$dd_elements = array();
|
| 454 |
|
|
foreach ($value as $sequence) {
|
| 455 |
|
|
$dd_elements[] = compose_cdm_sequence($sequence);
|
| 456 |
|
|
}
|
| 457 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
|
| 458 |
0de9cf51
|
Andreas Kohlbecker
|
break;
|
| 459 |
|
|
|
| 460 |
0820cdc0
|
Andreas Kohlbecker
|
// TODO preservation
|
| 461 |
|
|
// TODO exsiccatum
|
| 462 |
6fbdb943
|
Andreas Kohlbecker
|
|
| 463 |
|
|
|
| 464 |
|
|
/* ---- FieldObservation --- */
|
| 465 |
|
|
case 'gatheringEvent':
|
| 466 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache);
|
| 467 |
7aedf624
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, t('Gathering time'), timePeriodToString($value->timeperiod));
|
| 468 |
f19f47fa
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
|
| 469 |
5b30a682
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text);
|
| 470 |
6fbdb943
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n);
|
| 471 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
|
| 472 |
74ee6b54
|
Andreas Kohlbecker
|
if (isset($value->absoluteElevation)) {
|
| 473 |
5a079dbf
|
Andreas Kohlbecker
|
$min_max_markup = min_max_measure($value, 'absoluteElevation');
|
| 474 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
|
| 475 |
74ee6b54
|
Andreas Kohlbecker
|
}
|
| 476 |
|
|
if (isset($value->distanceToGround)) {
|
| 477 |
5a079dbf
|
Andreas Kohlbecker
|
$min_max_markup = min_max_measure($value, 'distanceToGround');
|
| 478 |
74ee6b54
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
|
| 479 |
|
|
}
|
| 480 |
|
|
if (isset($value->distanceToWaterSurface)) {
|
| 481 |
5a079dbf
|
Andreas Kohlbecker
|
$min_max_markup = min_max_measure($value, 'distanceToWaterSurface');
|
| 482 |
74ee6b54
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
|
| 483 |
|
|
}
|
| 484 |
|
|
|
| 485 |
2228f46b
|
Andreas Kohlbecker
|
if (isset($value->collectingAreas) && count($value->collectingAreas) > 0) {
|
| 486 |
6fbdb943
|
Andreas Kohlbecker
|
$area_representations = array();
|
| 487 |
0820cdc0
|
Andreas Kohlbecker
|
foreach ($value->collectingAreas as $area) {
|
| 488 |
30845bda
|
Andreas Kohlbecker
|
$area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
|
| 489 |
6fbdb943
|
Andreas Kohlbecker
|
}
|
| 490 |
30845bda
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
|
| 491 |
|
|
array(
|
| 492 |
|
|
array('#markup' => implode(', ', $area_representations))
|
| 493 |
|
|
)
|
| 494 |
|
|
);
|
| 495 |
6fbdb943
|
Andreas Kohlbecker
|
}
|
| 496 |
c08f7882
|
Andreas Kohlbecker
|
if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
|
| 497 |
6fbdb943
|
Andreas Kohlbecker
|
$sub_dl_groups = array();
|
| 498 |
f19f47fa
|
Andreas Kohlbecker
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
|
| 499 |
9abfeeb1
|
Andreas Kohlbecker
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
|
| 500 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
|
| 501 |
6fbdb943
|
Andreas Kohlbecker
|
if (isset($value->exactLocation->referenceSystem)) {
|
| 502 |
|
|
@_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
|
| 503 |
|
|
}
|
| 504 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 505 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
|
| 506 |
0820cdc0
|
Andreas Kohlbecker
|
array(
|
| 507 |
|
|
array('#markup' => $value->exactLocation->sexagesimalString),
|
| 508 |
f19f47fa
|
Andreas Kohlbecker
|
array(
|
| 509 |
0820cdc0
|
Andreas Kohlbecker
|
'#theme' => 'description_list',
|
| 510 |
|
|
'#groups' => $sub_dl_groups
|
| 511 |
|
|
),
|
| 512 |
|
|
)
|
| 513 |
6fbdb943
|
Andreas Kohlbecker
|
);
|
| 514 |
f19f47fa
|
Andreas Kohlbecker
|
}
|
| 515 |
|
|
break;
|
| 516 |
|
|
|
| 517 |
f846e7e7
|
Andreas Kohlbecker
|
default:
|
| 518 |
0820cdc0
|
Andreas Kohlbecker
|
if (is_object($value) || is_array($value)) {
|
| 519 |
bd814ea2
|
Andreas Kohlbecker
|
drupal_set_message("Unhandled type in compose_cdm_specimen_or_observation() for field " . $field, "warning");
|
| 520 |
f846e7e7
|
Andreas Kohlbecker
|
} else {
|
| 521 |
|
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
|
| 522 |
|
|
}
|
| 523 |
f19f47fa
|
Andreas Kohlbecker
|
|
| 524 |
|
|
}
|
| 525 |
|
|
|
| 526 |
|
|
}
|
| 527 |
f846e7e7
|
Andreas Kohlbecker
|
} // END of loop over $derivedUnitFacade fields
|
| 528 |
|
|
|
| 529 |
0820cdc0
|
Andreas Kohlbecker
|
// Extensions
|
| 530 |
|
|
$extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $specimenOrObservation->uuid . '/extensions', array($specimenOrObservation->uuid));
|
| 531 |
|
|
if ($extensions && count($extensions)) {
|
| 532 |
|
|
|
| 533 |
|
|
$extensions_render_array = compose_extensions($extensions);
|
| 534 |
|
|
@_description_list_group_add($groups, t('Extensions') . ':',
|
| 535 |
|
|
$extensions_render_array,
|
| 536 |
|
|
'', 100);
|
| 537 |
|
|
}
|
| 538 |
|
|
|
| 539 |
f846e7e7
|
Andreas Kohlbecker
|
|
| 540 |
eeb98da8
|
Andreas Kohlbecker
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
| 541 |
|
|
uasort($groups, 'element_sort');
|
| 542 |
|
|
|
| 543 |
f846e7e7
|
Andreas Kohlbecker
|
$occurrence_elements = array(
|
| 544 |
f19f47fa
|
Andreas Kohlbecker
|
'#title' => $title,
|
| 545 |
|
|
'#theme' => 'description_list',
|
| 546 |
6fbdb943
|
Andreas Kohlbecker
|
'#groups' => $groups,
|
| 547 |
f19f47fa
|
Andreas Kohlbecker
|
'#attributes' => array('class' => html_class_attribute_ref($specimenOrObservation)),
|
| 548 |
f846e7e7
|
Andreas Kohlbecker
|
);
|
| 549 |
|
|
$derivatives[] = $occurrence_elements;
|
| 550 |
c9d996cd
|
Andreas Kohlbecker
|
// all footnotes which has been assembled so far (e.g. from typeDesignations) to here
|
| 551 |
15b7c460
|
Andreas Kohlbecker
|
$foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
|
| 552 |
c9d996cd
|
Andreas Kohlbecker
|
if (!empty($foonote_li_elements)) {
|
| 553 |
|
|
$derivatives[] = array(
|
| 554 |
5dd1c644
|
Andreas Kohlbecker
|
'#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>',
|
| 555 |
c9d996cd
|
Andreas Kohlbecker
|
);
|
| 556 |
|
|
}
|
| 557 |
f846e7e7
|
Andreas Kohlbecker
|
|
| 558 |
|
|
// --- recurse into originals
|
| 559 |
0796d2f9
|
Andreas Kohlbecker
|
if (!isset($derivedFrom)) {
|
| 560 |
|
|
$derivedFrom = cdm_ws_get(
|
| 561 |
6fbdb943
|
Andreas Kohlbecker
|
CDM_WS_OCCURRENCE,
|
| 562 |
|
|
array($specimenOrObservation->uuid, 'derivedFrom')
|
| 563 |
|
|
);
|
| 564 |
|
|
}
|
| 565 |
|
|
|
| 566 |
0796d2f9
|
Andreas Kohlbecker
|
if (isset($derivedFrom)) {
|
| 567 |
|
|
if (isset($derivedFrom->originals)) {
|
| 568 |
|
|
$derived_from_label = t('derived');
|
| 569 |
6644c262
|
Andreas Kohlbecker
|
$preposition = t('from');
|
| 570 |
0796d2f9
|
Andreas Kohlbecker
|
if(isset($derivedFrom->type)){
|
| 571 |
0de9cf51
|
Andreas Kohlbecker
|
$derived_from_label = $derivedFrom->type->representation_L10n;
|
| 572 |
6644c262
|
Andreas Kohlbecker
|
if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
|
| 573 |
|
|
$preposition = t('of');
|
| 574 |
|
|
}
|
| 575 |
0796d2f9
|
Andreas Kohlbecker
|
}
|
| 576 |
4554da02
|
Andreas Kohlbecker
|
if (count($groups) > 0) {
|
| 577 |
eeb98da8
|
Andreas Kohlbecker
|
// TODO annotations
|
| 578 |
|
|
|
| 579 |
4554da02
|
Andreas Kohlbecker
|
// only display the derived from information when the derivative has any element which will be diplayed
|
| 580 |
|
|
$derivatives[] = array(
|
| 581 |
6644c262
|
Andreas Kohlbecker
|
'#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>',
|
| 582 |
4554da02
|
Andreas Kohlbecker
|
);
|
| 583 |
|
|
}
|
| 584 |
0796d2f9
|
Andreas Kohlbecker
|
foreach ($derivedFrom->originals as $original) {
|
| 585 |
bd814ea2
|
Andreas Kohlbecker
|
compose_cdm_specimen_or_observation($original, $derivatives);
|
| 586 |
0796d2f9
|
Andreas Kohlbecker
|
}
|
| 587 |
f846e7e7
|
Andreas Kohlbecker
|
}
|
| 588 |
|
|
}
|
| 589 |
f1f05758
|
Andreas Kohlbecker
|
|
| 590 |
f846e7e7
|
Andreas Kohlbecker
|
} // END of $specimenOrObservation exists
|
| 591 |
c70b93c3
|
Andreas Kohlbecker
|
|
| 592 |
f846e7e7
|
Andreas Kohlbecker
|
return $derivatives;
|
| 593 |
f1f05758
|
Andreas Kohlbecker
|
}
|
| 594 |
0de9cf51
|
Andreas Kohlbecker
|
|
| 595 |
0820cdc0
|
Andreas Kohlbecker
|
|
| 596 |
0de9cf51
|
Andreas Kohlbecker
|
/**
|
| 597 |
|
|
* Compose an render array from a CDM Sequence object.
|
| 598 |
|
|
*
|
| 599 |
|
|
* compose_hook() implementation
|
| 600 |
|
|
*
|
| 601 |
|
|
* @param object $sequence
|
| 602 |
|
|
* CDM instance of type Sequence
|
| 603 |
|
|
* @return array
|
| 604 |
|
|
* A render array containing the fields of the supplied $sequence
|
| 605 |
5b26b91a
|
Andreas Kohlbecker
|
*
|
| 606 |
|
|
* @ingroup compose
|
| 607 |
0de9cf51
|
Andreas Kohlbecker
|
*/
|
| 608 |
|
|
function compose_cdm_sequence($sequence) {
|
| 609 |
|
|
|
| 610 |
eeb98da8
|
Andreas Kohlbecker
|
$exclude_sequence_fields = &drupal_static(__FUNCTION__);
|
| 611 |
|
|
if (!isset($exclude_sequence_fields)) {
|
| 612 |
|
|
$exclude_sequence_fields = array(
|
| 613 |
0de9cf51
|
Andreas Kohlbecker
|
'titleCache',
|
| 614 |
|
|
'protectedTitleCache',
|
| 615 |
|
|
'microReference',
|
| 616 |
|
|
'created',
|
| 617 |
|
|
'updated',
|
| 618 |
|
|
'class',
|
| 619 |
eeb98da8
|
Andreas Kohlbecker
|
);
|
| 620 |
|
|
}
|
| 621 |
0de9cf51
|
Andreas Kohlbecker
|
|
| 622 |
|
|
$groups = array();
|
| 623 |
|
|
|
| 624 |
eeb98da8
|
Andreas Kohlbecker
|
// -- retrieve additional data if neesscary
|
| 625 |
1083804e
|
Andreas Kohlbecker
|
// TODO below call disabled since sequences are not yet supported,
|
| 626 |
a950f2f9
|
Andreas Kohlbecker
|
// see #3347 (services and REST service controller for molecular classes implemented)
|
| 627 |
|
|
//
|
| 628 |
|
|
// cdm_load_annotations($sequence);
|
| 629 |
eeb98da8
|
Andreas Kohlbecker
|
|
| 630 |
0de9cf51
|
Andreas Kohlbecker
|
foreach (get_object_vars($sequence) as $field => $value) {
|
| 631 |
eeb98da8
|
Andreas Kohlbecker
|
|
| 632 |
|
|
|
| 633 |
|
|
if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
|
| 634 |
0de9cf51
|
Andreas Kohlbecker
|
switch ($field) {
|
| 635 |
|
|
|
| 636 |
1083804e
|
Andreas Kohlbecker
|
case 'geneticAccessionNumber';
|
| 637 |
1b57b3c1
|
Andreas Kohlbecker
|
$dd_elements = array();
|
| 638 |
|
|
foreach ($value as $accession) {
|
| 639 |
|
|
if (isset($accession->uri) ){
|
| 640 |
|
|
$dd_elements[] = l($accession->accessionNumber, $accession->uri);
|
| 641 |
|
|
} else {
|
| 642 |
|
|
$dd_elements[] = $accession->accessionNumber;
|
| 643 |
|
|
}
|
| 644 |
0de9cf51
|
Andreas Kohlbecker
|
}
|
| 645 |
1b57b3c1
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 1);
|
| 646 |
0de9cf51
|
Andreas Kohlbecker
|
break;
|
| 647 |
|
|
|
| 648 |
|
|
|
| 649 |
1083804e
|
Andreas Kohlbecker
|
case 'locus': // FIXME 3.3 now dnaMarker (DefinedTerm) if multiple amplifications where used to build this consensus sequence it may be the super set of the markers used in amplification.
|
| 650 |
1b57b3c1
|
Andreas Kohlbecker
|
if (isset($value->name)) {
|
| 651 |
2196c738
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3);
|
| 652 |
1b57b3c1
|
Andreas Kohlbecker
|
}
|
| 653 |
|
|
if (isset($value->description)) {
|
| 654 |
2196c738
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description') , $value->description, NULL, 4);
|
| 655 |
1b57b3c1
|
Andreas Kohlbecker
|
}
|
| 656 |
|
|
break;
|
| 657 |
|
|
|
| 658 |
1083804e
|
Andreas Kohlbecker
|
case 'consensusSequence':
|
| 659 |
0de9cf51
|
Andreas Kohlbecker
|
// format in genbank style, force linebreaks after each 70 nucleotites
|
| 660 |
|
|
// see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
|
| 661 |
|
|
@_description_list_group_add(
|
| 662 |
|
|
$groups,
|
| 663 |
|
|
cdm_occurrence_field_name_label($field),
|
| 664 |
|
|
array(
|
| 665 |
|
|
array(
|
| 666 |
1083804e
|
Andreas Kohlbecker
|
'#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb'). '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
|
| 667 |
0de9cf51
|
Andreas Kohlbecker
|
'#wrapper_attributes' => array('class'=>'dna-sequence')
|
| 668 |
|
|
)
|
| 669 |
|
|
),
|
| 670 |
2196c738
|
Andreas Kohlbecker
|
5);
|
| 671 |
0de9cf51
|
Andreas Kohlbecker
|
break;
|
| 672 |
|
|
|
| 673 |
1083804e
|
Andreas Kohlbecker
|
case 'dnaSample': // FIXME 3.3 implement
|
| 674 |
|
|
break;
|
| 675 |
|
|
case 'singleReads': // FIXME 3.3 implement
|
| 676 |
|
|
break;
|
| 677 |
|
|
case 'contigFile': // FIXME 3.3 implement - Media
|
| 678 |
|
|
break;
|
| 679 |
|
|
case 'pherograms': // FIXME 3.3 implement - Media
|
| 680 |
|
|
break;
|
| 681 |
|
|
case 'haplotype': // FIXME 3.3 implement
|
| 682 |
|
|
break;
|
| 683 |
|
|
case 'dateSequenced': // FIXME 3.3 now in SingelRead
|
| 684 |
2196c738
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
|
| 685 |
0de9cf51
|
Andreas Kohlbecker
|
break;
|
| 686 |
|
|
|
| 687 |
|
|
case 'barcode': // boolean
|
| 688 |
2196c738
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes': 'No', NULL, 7);
|
| 689 |
0de9cf51
|
Andreas Kohlbecker
|
break;
|
| 690 |
1083804e
|
Andreas Kohlbecker
|
case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
|
| 691 |
|
|
break;
|
| 692 |
0de9cf51
|
Andreas Kohlbecker
|
|
| 693 |
|
|
case 'citation':
|
| 694 |
|
|
@_description_list_group_add($groups,
|
| 695 |
|
|
cdm_occurrence_field_name_label($field),
|
| 696 |
1b57b3c1
|
Andreas Kohlbecker
|
theme('cdm_reference', array('reference' =>$value, 'microReference' => $sequence->microReference)),
|
| 697 |
0de9cf51
|
Andreas Kohlbecker
|
NULL,
|
| 698 |
2196c738
|
Andreas Kohlbecker
|
8
|
| 699 |
0de9cf51
|
Andreas Kohlbecker
|
);
|
| 700 |
|
|
break;
|
| 701 |
|
|
|
| 702 |
1b57b3c1
|
Andreas Kohlbecker
|
case 'publishedIn':
|
| 703 |
|
|
@_description_list_group_add($groups,
|
| 704 |
|
|
cdm_occurrence_field_name_label($field),
|
| 705 |
|
|
theme('cdm_reference', array('reference'=>$value)),
|
| 706 |
|
|
NULL,
|
| 707 |
|
|
7
|
| 708 |
|
|
);
|
| 709 |
daef68e9
|
Andreas Kohlbecker
|
break;
|
| 710 |
eeb98da8
|
Andreas Kohlbecker
|
|
| 711 |
|
|
case 'rights':
|
| 712 |
|
|
array_merge($groups, cdm_rights_as_dl_groups($value));
|
| 713 |
daef68e9
|
Andreas Kohlbecker
|
break;
|
| 714 |
eeb98da8
|
Andreas Kohlbecker
|
|
| 715 |
|
|
case 'annotations':
|
| 716 |
|
|
$dd_elements = array();
|
| 717 |
|
|
foreach ($value as $annotation) {
|
| 718 |
|
|
// TODO respect annotation type filter settings
|
| 719 |
|
|
$dd_elements[] = $annotation->text;
|
| 720 |
|
|
}
|
| 721 |
|
|
@_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
|
| 722 |
1b57b3c1
|
Andreas Kohlbecker
|
break;
|
| 723 |
|
|
|
| 724 |
4ae6064e
|
Andreas Kohlbecker
|
case 'markers':
|
| 725 |
|
|
$dd_elements = array();
|
| 726 |
|
|
foreach ($value as $marker) {
|
| 727 |
|
|
$dd_elements[] = compose_cdm_marker($marker);
|
| 728 |
|
|
}
|
| 729 |
|
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
|
| 730 |
|
|
break;
|
| 731 |
|
|
|
| 732 |
0de9cf51
|
Andreas Kohlbecker
|
case 'chromatograms':
|
| 733 |
1b57b3c1
|
Andreas Kohlbecker
|
@_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
|
| 734 |
0de9cf51
|
Andreas Kohlbecker
|
array(
|
| 735 |
a9815578
|
Andreas Kohlbecker
|
'#markup'=>compose_cdm_media_gallerie(array('medialist'=>$value)),
|
| 736 |
2196c738
|
Andreas Kohlbecker
|
),
|
| 737 |
|
|
NULL,
|
| 738 |
4ae6064e
|
Andreas Kohlbecker
|
11);
|
| 739 |
0de9cf51
|
Andreas Kohlbecker
|
break;
|
| 740 |
|
|
|
| 741 |
|
|
default:
|
| 742 |
|
|
if(is_object($value) || is_array($value)){
|
| 743 |
|
|
drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
|
| 744 |
|
|
} else {
|
| 745 |
eeb98da8
|
Andreas Kohlbecker
|
_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
|
| 746 |
0de9cf51
|
Andreas Kohlbecker
|
}
|
| 747 |
|
|
}
|
| 748 |
|
|
}
|
| 749 |
|
|
}
|
| 750 |
|
|
|
| 751 |
eeb98da8
|
Andreas Kohlbecker
|
// template_preprocess_description_list() is not worting by weight so we do it right here
|
| 752 |
|
|
uasort($groups, 'element_sort');
|
| 753 |
|
|
|
| 754 |
0de9cf51
|
Andreas Kohlbecker
|
$sequence_elements = array(
|
| 755 |
|
|
'#theme' => 'description_list',
|
| 756 |
|
|
'#groups' => $groups
|
| 757 |
|
|
);
|
| 758 |
|
|
|
| 759 |
|
|
return $sequence_elements;
|
| 760 |
|
|
}
|
| 761 |
1083804e
|
Andreas Kohlbecker
|
|