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cdm-dataportal / modules / cdm_dataportal / includes / occurrences.inc @ c10f70e4

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1
<?php
2
/**
3
 * @file
4
 * Functions for dealing with CDM entities of type SpecimenOrOccurrences
5
 *
6
 * @copyright
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 *   (C) 2007-2012 EDIT
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 *   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.
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 * @see http://www.mozilla.org/MPL/MPL-1.1.html
14
 *
15
 * @author
16
 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
17
 */
18

    
19

    
20
/**
21
 * Provides the HTML markup for a specimen page
22
 *
23
 * @param $specimen
24
 *
25
 * @return string
26
 *  The markup for a specimen page
27
 */
28
function render_cdm_specimen_page($specimen, $is_specimen_page = false)
29
{
30
    $detail_html = "";
31
    //link to specimen page
32
    $pathToSpecimen = path_to_specimen($specimen->uuid);
33
    if (!$is_specimen_page) {
34
        $specimenPageLink = l($specimen->accessionNumber, $pathToSpecimen, array('attributes' => array('target' => '_blank')));
35
        $detail_html .= "<strong>$specimenPageLink</strong><br>";
36
    }
37

    
38
    if ($is_specimen_page) {
39
        if ($specimen->citation) {
40
            $detail_html .= "<br>" . create_label("Citation") . $specimen->citation . "<br>";
41
        }
42
    }
43
    if ($specimen->preferredStableUri) {
44
        $stableIdentifierLink = l($specimen->preferredStableUri, $specimen->preferredStableUri, array('attributes' => array('target' => '_blank')));
45
        $detail_html .= create_label("Preferred stable URI") . $stableIdentifierLink . "<br>";
46
    }
47
    if ($is_specimen_page) {
48
        // associated taxa
49
        if ($specimen->associatedTaxa) {
50
            $detail_html .= "<br>";
51
            $detail_html .= create_label("Associated with");
52
            if (sizeof($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
        }
60
    }
61
    // - type information
62
    $types = "";
63
    if (isset($specimen->types)) {
64
        //typed taxa
65
        foreach ($specimen->types as $typeStatus => $typedTaxa) {
66
/* Updated upstream
67
            if($specimen->types){
68
                $detail_html .= "<i>".$typeStatus."</i> of ";
69
                foreach($typedTaxa as $typedTaxon){
70
                    $detail_html .= $typedTaxon." ";
71
                }
72
                $detail_html .= "<br>";
73
*/
74
            if ($is_specimen_page) {
75
                if ($specimen->types) {
76
                    $detail_html .= "<i>" . $typeStatus . "</i>: ";
77
                    foreach ($typedTaxa as $typedTaxon) {
78
                        $detail_html .= $typedTaxon . " ";
79
                    }
80
                    $detail_html .= "<br>";
81
                }
82
            } else {
83
                $types .= $typeStatus . " ";
84

    
85
            }
86
        }
87
    }
88
    $derivateDataDTO = $specimen->derivateDataDTO;
89
    // - specimen scans
90
    $specimenScans = create_html_links($derivateDataDTO->specimenScans, true);
91
    // - molecular data
92
    $molecularData = "";
93
    if ($derivateDataDTO->molecularDataList) {
94
        foreach ($derivateDataDTO->molecularDataList as $molecular) {
95
            //provider link
96
            if (isset($molecular->providerLink)) {
97
                $molecularData .= create_html_link($molecular->providerLink, true);
98
            } else {
99
                $molecularData .= "[no provider]";
100
            }
101
            //contig link
102
            if (isset($molecular->contigFiles)) {
103
                $molecularData .= "[";
104
                if (sizeof($molecular->contigFiles) > 0) {
105
                    foreach ($molecular->contigFiles as $contigFile) {
106
                        if (isset($contigFile->contigLink)) {
107
                            if (isset($contigFile->contigLink->uri) and $contigFile->contigLink->uri != null) {
108
                                $molecularData .= create_html_link($contigFile->contigLink, true) . " ";
109
                            }
110
                        } else {
111
                            $molecularData .= "no contig ";
112
                        }
113
                        //primer links
114
                        if (isset($contigFile->primerLinks)) {
115
                            $molecularData .= create_html_links($contigFile->primerLinks, true);
116
                        }
117
                    }
118
                }
119
                $molecularData = rtrim($molecularData, " ");
120
                $molecularData .= "]";
121
            }
122
            //FIXME separate with comma (remove trailing comma)
123
        }
124
    }
125
    // - detail images
126
    $detailImages = create_html_links($derivateDataDTO->detailImages, true);
127

    
128
    if ($types) {
129
        $detail_html .= $is_specimen_page ? "<br>" : "";
130
        $detail_html .= create_label("Type(s)") . $types . "<br>";
131
    }
132
    if ($specimenScans and !$is_specimen_page) {
133
        $detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
134
    }
135
    //specimen scan image gallery
136
    if ($is_specimen_page and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
137
        $detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
138
    }
139

    
140
    if ($molecularData) {
141
        $detail_html .= $is_specimen_page ? "<br>" : "";
142
        $detail_html .= create_label("Molecular Data") . $molecularData . "<br>";
143
    }
144

    
145
    if ($detailImages and !$is_specimen_page) {
146
        $detail_html .= create_label("Detail Images") . $detailImages . "<br>";
147
    }
148

    
149
    //detail image gallery
150
    if ($is_specimen_page and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)) {
151
        $detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
152
    }
153

    
154
    //character data
155
    if ($specimen->characterData) {
156
        $detail_html .= $is_specimen_page ? "<br>" : "";
157
        $detail_html .= create_label("Character Data");
158
        if ($is_specimen_page) {
159
            $detail_html .= "<br>";
160
            foreach ($specimen->characterData as $characterStatePair) {
161
                $detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second;
162
                $detail_html .= "<br>";
163
            }
164
        } else {
165
            $detail_html .= l("detail page", $pathToSpecimen, array('attributes' => array('target' => '_blank')));
166
            $detail_html .= "<br>";
167
        }
168
    }
169
    return $detail_html;
170
}
171

    
172
function addImageGallery($galleryName, $imageUuids)
173
{
174
    $images = array();
175
    foreach ($imageUuids as $uuid) {
176
        $images[] = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $uuid);
177
    }
178

    
179
    $gallery_html = '';
180
    if (count($imageUuids) > 0) {
181
        $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
182
        $captionElements = array(
183
            'title',
184
            'rights',
185
        );
186
        $alternativeMediaUris = array();
187
        foreach ($images as $image) {
188
            $mediaUri = getMediaUri($image);
189
            if ($mediaUri) {
190
                $alternativeMediaUris[] = $mediaUri;
191
            } else {
192
                $alternativeMediaUris[] = path_to_media($image->uuid);
193
            }
194
        }
195

    
196
        $gallery_html = compose_cdm_media_gallerie(array(
197
            'mediaList' => $images,
198
            'galleryName' => $galleryName,
199
            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
200
            'cols' => $gallery_settings['cdm_dataportal_media_cols'],
201
            'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
202
            'captionElements' => $captionElements,
203
            'mediaLinkType' => 'LIGHTBOX',
204
            'alternativeMediaUri' => $alternativeMediaUris,
205
            'galleryLinkUri' => NULL,
206
        ));
207
    }
208
    return "<br>" . create_label($galleryName) . "<br>" . $gallery_html;
209
}
210

    
211
function getMediaUri($media)
212
{
213
    if (isset($media->representations) && sizeof($media->representations) == 1
214
        && isset($media->representations[0]->parts) &&
215
        sizeof($media->representations[0]->parts) == 1) {
216
        return $media->representations[0]->parts[0]->uri;
217
    }
218
    return null;
219
}
220

    
221

    
222
/**
223
 * Formats the given string to a label for displaying key-object pairs in HTML
224
 * @return string
225
 */
226
function create_label($label)
227
{
228
    return "<span class='specimen_table_label'>" . $label . ": </span>";
229
}
230

    
231
/**
232
 * Compose an render array from a CDM DerivedUnitFacade object.
233
 *
234
 * compose_hook() implementation
235
 *
236
 * @param object $specimenOrObservation
237
 *   the CDM instance of type SpecimenOrObservation to compose
238
 *   the render array for
239
 * @param array $derivatives
240
 *   the render array which contains the compositions of the derivatives
241
 *   of the supplied $specimenOrObservation
242
 *
243
 * @return array
244
 *   the supplied render array $derivatives to which the composition of the supplied
245
 *   $specimenOrObservation has been added to
246
 *
247
 * @ingroup compose
248
 */
249
/*<<<<<<< Updated upstream
250
function compose_cdm_specimen_or_observation($specimenOrObservation, &$derivatives = null) {
251

    
252
  $exclude_occurrence_fields = &drupal_static(__FUNCTION__);
253
  if (!isset($exclude_occurrence_fields)) {
254
     $exclude_occurrence_fields = array(
255
        'derivationEvents',
256
        'titleCache',
257
        'protectedTitleCache',
258
        'derivedUnitMedia',
259
        'created',
260
        'publish',
261
        'updated',
262
        'class',
263
        'uuid',
264
       ''
265
    );
266
  }
267

    
268

    
269
  // only show uuid it the user is logged in
270
  if(user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE ) {
271
    unset($exclude_occurrence_fields[$a_idx]);
272
  }
273

    
274
  if (!isset($derivatives)) {
275
    $derivatives = array();
276
  }
277

    
278
  $descriptions = null;
279
  $derivedFrom = null;
280
=======*/
281
function compose_cdm_specimenOrObservation($specimenOrObservation, &$derivatives = null)
282
{
283

    
284
//>>>>>>> Stashed changes
285
    $exclude_occurrence_fields = &drupal_static(__FUNCTION__);
286
    if (!isset($exclude_occurrence_fields)) {
287
        $exclude_occurrence_fields = array(
288
            // 'derivationEvents',
289
            'titleCache',
290
            'protectedTitleCache',
291
            'derivedUnitMedia',
292
            'created',
293
            'publish',
294
            'updated',
295
            'class',
296
            'uuid',
297
            ''
298
        );
299
    }
300

    
301

    
302
    // only show uuid it the user is logged in
303
    if (user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE) {
304
        unset($exclude_occurrence_fields[$a_idx]);
305
    }
306

    
307
    if (!isset($derivatives)) {
308
        $derivatives = array();
309
    }
310

    
311
    $descriptions = null;
312
    $derivedFrom = null;
313
    $derivates = null;
314

    
315
    if (is_object($specimenOrObservation)) {
316

    
317
        // request again for deeper initialization
318
      //  $specimenOrObservation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);
319

    
320

    
321
        $type_label = $specimenOrObservation->recordBase;
322
        RenderHints::setFootnoteListKey($type_label . '-' . $specimenOrObservation->uuid);
323
        /*
324
         * $label_html = cdm_dynabox(
325
                          $specimenOrObservation->uuid,
326
                          $type_label . $specimenOrObservation->titleCache,
327
                          $derived_unit_ws_request, //cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);
328
                          'cdm_specimenOrObservation',
329
                          'Click for details',
330
                          array('div', 'div'),
331
                          array(),
332
                          null, // $content_element_selector
333
                          'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').hide(); }', // open_callback
334
                          'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').show(); }' // close_callback
335
                        );
336

    
337
         */
338
        // collect typeStatus as label
339
        if (isset($specimenOrObservation->specimenTypeDesignations)) {
340
            $type_status = array();
341
            foreach ($specimenOrObservation->specimenTypeDesignations as $typeDesignation) {
342
                if (isset($typeDesignation->typeStatus->representation_L10n)) {
343
                    $type_status[] = $typeDesignation->typeStatus->representation_L10n;
344
                }
345
            }
346
            if (count($type_status) > 0) {
347
                $type_label = implode(', ', $type_status);
348
            }
349
        }
350

    
351
        $title = $type_label . ': ' . $specimenOrObservation->titleCache;
352

    
353
        $groups = array();
354
        // --- add initialized fields
355
        foreach (get_object_vars($specimenOrObservation) as $field => $value) {
356
            if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
357
                switch ($field) {
358
//            case 'recordBasis':
359
//                if ($value != '' /* FieldUnit' */) {
360
//                    @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
361
//                }
362
//                break;
363
                    /* ---- java.lang.Object --- */
364
                    case 'class':
365
                        if ($value != '' /* FieldUnit' */) {
366
                            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
367
                        }
368
                        break;
369

    
370
                    case 'markers':
371
                        $dd_elements = array();
372
                        foreach ($value as $marker) {
373
                            $dd_elements[] = compose_cdm_marker($marker);
374
                        }
375
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
376
                        break;
377

    
378

    
379
                    case 'annotations':
380
                        $dd_elements = array();
381
                        foreach ($value as $annotation) {
382
                            // TODO respect annotation type filter settings
383
                            $dd_elements[] = $annotation->text;
384
                        }
385
                        @_description_list_group_add($groups, t('Notes'), $dd_elements);
386
                        break;
387

    
388
                    /* ---- SpecimenOrObservationBase --- */
389
                    case 'sex':
390
                    case 'lifeStage':
391
                    case 'kindOfUnit':
392
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n, NULL, 1);
393
                        break;
394

    
395
                    case 'definition':
396
                        // TODO
397
                        break;
398

    
399
                    case 'preferredStableUri':
400

    
401
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), array(array('#markup' => cdm_external_uri($value, false))));
402
                        break;
403

    
404
                    case 'specimenTypeDesignations':
405
                        @_description_list_group_add(
406
                            $groups,
407
                            cdm_occurrence_field_name_label($field),
408
                            array(
409
                                '#markup' => theme('cdm_typedesignations', array('typeDesignations' => $value)),
410
                            )
411
                        );
412
                        break;
413

    
414
                    case 'determinations':
415
                        $dd_elements = array();
416
                        $glue = ', ';
417

    
418
                        foreach ($value as $determinationEvent) {
419
                            $timeperiod_string = NULL;
420
                            if (isset($determinationEvent->timeperiod)) {
421
                                $timeperiod_string = timePeriodToString($determinationEvent->timeperiod);
422
                            }
423
                            $weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
424
                            // check key exists
425
                            while (array_key_exists($weight, $dd_elements)) {
426
                                $weight .= '0';
427
                            }
428

    
429
                            $taxon_name = '';
430
                            $name_link = '';
431
                            if ($determinationEvent->taxonName) {
432
                                $taxon_name = $determinationEvent->taxonName;
433
                            } else if ($determinationEvent->taxon) {
434
                                $taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
435
                                $name_link = path_to_taxon($determinationEvent->taxon->uuid);
436
                            }
437
                            if ($taxon_name) {
438
                                $taxon_html = render_taxon_or_name($taxon_name, $name_link);
439
                                $dd_elements[$weight] = $taxon_html;
440
                            }
441
                            if (isset($determinationEvent->modifier)) {
442
                                $dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
443
                            }
444
                            if ($timeperiod_string) {
445
                                $dd_elements[$weight] .= $glue . $timeperiod_string;
446
                            }
447
                            if (isset($determinationEvent->actor->titleCache)) {
448
                                $dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
449
                            }
450
                            if (isset($determinationEvent->description)) {
451
                                $dd_elements[$weight] .= $glue . $determinationEvent->description;
452
                            }
453
                        }
454
                        ksort($dd_elements);
455
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
456
                        break;
457

    
458
                    case 'descriptions':
459
                        $occurrence_featureTree = cdm_get_occurrence_featureTree();
460
                        $dd_elements = array();
461

    
462
                        foreach ($value as $description) {
463
                            $description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
464
//               if($description->imageGallery == TRUE) {
465
//                 continue;
466
//               }
467
                            $elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements);
468
                            $description_render_elements = _block_get_renderable_array(make_feature_block_list($elements_by_feature, null));
469
                            $dd_elements[] = $description_render_elements;
470
                            if ($description->isImageGallery) {
471
                                $mediaList = array();
472
                                if (is_array($description->elements)) {
473
                                    $mediaList = $description->elements;
474
                                }
475
                                $gallery_html = '';
476
                                if (count($mediaList) > 0) {
477
                                    $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
478
                                    $captionElements = array(
479
                                        '#uri' => t('open media'),
480
                                    );
481

    
482
                                    $gallery_html = compose_cdm_media_gallerie(array(
483
                                        'mediaList' => $mediaList,
484
                                        'galleryName' => $gallery_name,
485
                                        'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
486
                                        'cols' => $gallery_settings['cdm_dataportal_media_cols'],
487
                                        'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
488
                                        'captionElements' => $captionElements,
489
                                        'mediaLinkType' => 'LIGHTBOX',
490
                                        'alternativeMediaUri' => NULL,
491
                                        'galleryLinkUri' => NULL,
492
                                    ));
493
                                }
494

    
495
                            }
496
                        }
497

    
498
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
499
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $gallery_html);
500
                        break;
501

    
502
                    case 'sources':
503
                        $dd_elements = array();
504
                        foreach ($value as $identifiable_source) {
505
                            $dd_elements[] = theme('cdm_OriginalSource', array('source' => $identifiable_source));
506
                        }
507
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
508
                        break;
509

    
510

    
511
                    /* ---- DerivedUnitBase --- */
512
                    case 'derivedFrom':
513
                        $derivedFrom = $value;
514
                        break;
515

    
516
                    case 'collection':
517
                        $sub_dl_groups = array();
518
                        @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
519
                        @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'), $value->codeStandard, NULL, 2);
520
                        @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
521
                        @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
522
                        // TODO "superCollection"
523
                        // TODO may have media
524

    
525
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
526
                            array(
527
                                array('#markup' => $value->titleCache),
528
                                array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
529
                            )
530
                        );
531
                        break;
532

    
533
                    case 'storedUnder':
534
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
535
                        break;
536

    
537

    
538
                    /* ---- Specimen --- */
539
                    case 'sequences':
540
                        $dd_elements = array();
541
                        foreach ($value as $sequence) {
542
                            $dd_elements[] = compose_cdm_sequence($sequence);
543
                        }
544
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
545
                        break;
546

    
547
                    // TODO preservation
548
                    // TODO exsiccatum
549

    
550

    
551
                    /* ---- FieldObservation --- */
552
                    case 'gatheringEvent':
553
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache);
554
                        @_description_list_group_add($groups, t('Gathering time'), timePeriodToString($value->timeperiod));
555
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
556
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text);
557
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n);
558
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
559
                        if (isset($value->absoluteElevation)) {
560
                            $min_max_markup = min_max_measure($value, 'absoluteElevation');
561
                            @_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
562
                        }
563
                        if (isset($value->distanceToGround)) {
564
                            $min_max_markup = min_max_measure($value, 'distanceToGround');
565
                            @_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
566
                        }
567
                        if (isset($value->distanceToWaterSurface)) {
568
                            $min_max_markup = min_max_measure($value, 'distanceToWaterSurface');
569
                            @_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
570
                        }
571

    
572
                        if (isset($value->collectingAreas)) {
573
                            $area_representations = array();
574
                            foreach ($value->collectingAreas as $area) {
575
                                $area_representations[] = l($area->representation_L10n, path_to_named_area($area->uuid));
576
                            }
577
                            if (!empty($area_representations))
578
                                @_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'),
579
                                    array(
580
                                        array('#markup' => implode(', ', $area_representations))
581
                                    )
582
                                );
583
                        }
584
                        if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
585
                            $sub_dl_groups = array();
586
                            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
587
                            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
588
                            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
589
                            if (isset($value->exactLocation->referenceSystem)) {
590
                                @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
591
                            }
592

    
593
                            @_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
594
                                array(
595
                                    array('#markup' => $value->exactLocation->sexagesimalString),
596
                                    array(
597
                                        '#theme' => 'description_list',
598
                                        '#groups' => $sub_dl_groups
599
                                    ),
600
                                )
601
                            );
602
                        }
603
                        break;
604

    
605
                    /* ---- DerivationEvent --- */
606
                    case 'derivationEvents':
607
                        @_description_list_group_add($groups, t('Association type'), $value->description);
608
                        break;
609
                    case 'preservedSpecimenDTOs':
610
                        $derivates = $value;
611
                        break;
612
                    case 'derivates':
613
                        $derivates = $value;
614
                        break;
615

    
616
                    default:
617
                        if (is_object($value) || is_array($value)) {
618
                            drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
619
                        } else {
620
                            _description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
621
                        }
622

    
623
                }
624

    
625
/*
626
 *
627
          default:
628
            if (is_object($value) || is_array($value)) {
629
              drupal_set_message("Unhandled type in compose_cdm_specimen_or_observation() for field " . $field, "warning");
630
            } else {
631
              _description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
632
*/
633
// Stashed changes
634
            }
635
        } // END of loop over $derivedUnitFacade fields
636

    
637
        // Extensions
638
        $extensions = cdm_ws_fetch_all(CDM_WS_PORTAL_OCCURRENCE . '/' . $specimenOrObservation->uuid . '/extensions', array($specimenOrObservation->uuid));
639
        if ($extensions && count($extensions)) {
640

    
641
            $extensions_render_array = compose_extensions($extensions);
642
            @_description_list_group_add($groups, t('Extensions') . ':',
643
                $extensions_render_array,
644
                '', 100);
645
        }
646

    
647

    
648
        // template_preprocess_description_list() is not worting by weight so we do it right here
649
        uasort($groups, 'element_sort');
650

    
651
        $occurrence_elements = array(
652
            '#title' => $title,
653
            '#theme' => 'description_list',
654
            '#groups' => $groups,
655
            '#attributes' => array('class' => html_class_attribute_ref($specimenOrObservation)),
656
        );
657
        $derivatives[] = $occurrence_elements;
658
        // all footnotes which has been assembled so far (e.g. from typeDesignations) to here
659
        $foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
660
        if (!empty($foonote_li_elements)) {
661
            $derivatives[] = array(
662
                '#markup' => '<div class="footnotes">' . $foonote_li_elements . '</div>',
663
            );
664
        }
665

    
666
        // --- recurse into originals
667
        if (!isset($derivedFrom)) {
668
            $derivedFrom = cdm_ws_get(
669
                CDM_WS_OCCURRENCE,
670
                array($specimenOrObservation->uuid, 'derivedFrom')
671
            );
672
        }
673

    
674
        if (isset($derivates)) {
675
            if (isset($derivedFrom->originals)) {
676
                $derived_from_label = t('derivated');
677
                // $preposition = t('from');
678
                if (isset($derivedFrom->type)) {
679
                    $derived_from_label = $derivedFrom->type->representation_L10n;
680
                    if (isset($derivedFrom->description)) {
681
                        $derived_from_label = $derivedFrom->description;
682
                    }
683
                    //  if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
684
                    //  $preposition = t('of');
685
                    // }
686
                }
687
                if (count($groups) > 0) {
688
                    // TODO  annotations
689

    
690
                    // only display the derived from information when the derivative has any element which will be diplayed
691
                    $derivatives[] = array(
692
                        '#markup' => '<div class="derived_from">' . $derived_from_label . ': </div>',//' ' . $preposition . ': </div>',
693
                    );
694
                }
695
                // foreach ($derivedFrom->originals as $original) {
696

    
697

    
698

    
699
            }
700
        }
701
/*<<<<<<< Updated upstream
702
        foreach ($derivedFrom->originals as $original) {
703
          compose_cdm_specimen_or_observation($original, $derivatives);
704
=======*/
705
        if (isset($derivates )) {
706

    
707
            foreach ($derivates as $derivate){
708
                compose_cdm_specimenOrObservation($derivate, $derivatives);
709
            }
710
//>>>>>>> Stashed changes
711
        }
712

    
713
    } // END of $specimenOrObservation exists
714

    
715
    return $derivatives;
716
}
717

    
718

    
719
/**
720
 * Compose an render array from a CDM Sequence object.
721
 *
722
 * compose_hook() implementation
723
 *
724
 * @param object $sequence
725
 *   CDM instance of type Sequence
726
 * @return array
727
 *   A render array containing the fields of the supplied $sequence
728
 *
729
 * @ingroup compose
730
 */
731
function compose_cdm_sequence($sequence)
732
{
733

    
734
    $exclude_sequence_fields = &drupal_static(__FUNCTION__);
735
    if (!isset($exclude_sequence_fields)) {
736
        $exclude_sequence_fields = array(
737
            'titleCache',
738
            'protectedTitleCache',
739
            'microReference',
740
            'created',
741
            'updated',
742
            'class',
743
        );
744
    }
745

    
746
    $groups = array();
747

    
748
    // -- retrieve additional data if neesscary
749
    // TODO below call disabled since sequences are not yet supported,
750
    //      see  #3347 (services and REST service controller for molecular classes implemented)
751
    //
752
    // cdm_load_annotations($sequence);
753

    
754
    foreach (get_object_vars($sequence) as $field => $value) {
755

    
756

    
757
        if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
758
            switch ($field) {
759

    
760
                case 'geneticAccessionNumber';
761
                    $dd_elements = array();
762
                    foreach ($value as $accession) {
763
                        if (isset($accession->uri)) {
764
                            $dd_elements[] = l($accession->accessionNumber, $accession->uri);
765
                        } else {
766
                            $dd_elements[] = $accession->accessionNumber;
767
                        }
768
                    }
769
                    @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 2);
770
                    break;
771

    
772

    
773
                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.
774
                    if (isset($value->name)) {
775
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->name, NULL, 3);
776
                    }
777
                    if (isset($value->description)) {
778
                        @_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description'), $value->description, NULL, 4);
779
                    }
780
                    break;
781

    
782
                case 'consensusSequence':
783
                    // format in genbank style, force linebreaks after each 70 nucleotites
784
                    // see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
785
                    @_description_list_group_add(
786
                        $groups,
787
                        cdm_occurrence_field_name_label($field),
788
                        array(
789
                            array(
790
                                '#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb') . '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
791
                                '#wrapper_attributes' => array('class' => 'dna-sequence')
792
                            )
793
                        ),
794
                        5);
795
                    break;
796

    
797
                case 'dnaSample': // FIXME 3.3 implement
798
                    break;
799
                case 'singleReads': // FIXME 3.3 implement
800
                    break;
801
                case 'contigFile': // FIXME 3.3 implement - Media
802
                    break;
803
                case 'pherograms': // FIXME 3.3 implement - Media
804
                    break;
805
                case 'haplotype': // FIXME 3.3 implement
806
                    break;
807
                case 'dateSequenced': // FIXME 3.3 now in SingelRead
808
                    @_description_list_group_add($groups, t('Sequencing date'), timePeriodToString($value), NULL, 6);
809
                    break;
810

    
811
                case 'barcode': // boolean
812
                    @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes' : 'No', NULL, 7);
813
                    break;
814
                case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
815
                    break;
816

    
817
                case 'citation':
818
                    @_description_list_group_add($groups,
819
                        cdm_occurrence_field_name_label($field),
820
                        theme('cdm_reference', array('reference' => $value, 'microReference' => $sequence->microReference)),
821
                        NULL,
822
                        8
823
                    );
824
                    break;
825

    
826
                case 'publishedIn':
827
                    @_description_list_group_add($groups,
828
                        cdm_occurrence_field_name_label($field),
829
                        theme('cdm_reference', array('reference' => $value)),
830
                        NULL,
831
                        7
832
                    );
833
                    break;
834

    
835
                case 'rights':
836
                    array_merge($groups, cdm_rights_as_dl_groups($value));
837
                    break;
838

    
839
                case 'annotations':
840
                    $dd_elements = array();
841
                    foreach ($value as $annotation) {
842
                        // TODO respect annotation type filter settings
843
                        $dd_elements[] = $annotation->text;
844
                    }
845
                    @_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
846
                    break;
847

    
848
                case 'markers':
849
                    $dd_elements = array();
850
                    foreach ($value as $marker) {
851
                        $dd_elements[] = compose_cdm_marker($marker);
852
                    }
853
                    @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
854
                    break;
855

    
856
                case 'chromatograms':
857
                    @_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
858
                        array(
859
                            '#markup' => compose_cdm_media_gallerie(array('medialist' => $value)),
860
                        ),
861
                        NULL,
862
                        11);
863
                    break;
864

    
865
                default:
866
                    if (is_object($value) || is_array($value)) {
867
                        drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
868
                    } else {
869
                        _description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
870
                    }
871
            }
872
        }
873
    }
874

    
875
    // template_preprocess_description_list() is not worting by weight so we do it right here
876
    uasort($groups, 'element_sort');
877

    
878
    $sequence_elements = array(
879
        '#theme' => 'description_list',
880
        '#groups' => $groups
881
    );
882

    
883
    return $sequence_elements;
884
}
885

    
886

    
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