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1
<?php
2
/**
3
 * @file
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 * 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
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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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 */
18

    
19

    
20
/**
21
 * @param $preservedSpecimenDTO
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 * @param $detail_html
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 * @return string
24
 */
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function compose_cdm_specimen_page($specimenUuid)
26
{
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    drupal_set_title("Specimen Details");
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    $preservedSpecimenDTO = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($specimenUuid, 'specimenDerivates'));
29

    
30
    $render_array = array();
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    RenderHints::pushToRenderStack('specimen_page');
32

    
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    $detail_html = compose_cdm_specimen_page_html($preservedSpecimenDTO, true);
34
    $render_array['specimen_html'] = array(
35
        '#markup' => $detail_html
36
    );
37

    
38
    RenderHints::popFromRenderStack();
39
    return $render_array;
40
}
41

    
42
/**
43
 * @param $preservedSpecimenDTO
44
 * @return string
45
 */
46
function compose_cdm_specimen_page_html($preservedSpecimenDTO, $isSpecimenPage = false)
47
{
48
    $detail_html = "";
49
    //link to specimen page
50
    $pathToSpecimen = path_to_specimen($preservedSpecimenDTO->uuid);
51
    if (!$isSpecimenPage) {
52
        $specimenPageLink = l($preservedSpecimenDTO->accessionNumber, $pathToSpecimen, array('attributes' => array('target' => '_blank')));
53
        $detail_html .= "<strong>$specimenPageLink</strong><br>";
54
    }
55

    
56
    if($isSpecimenPage) {
57
        if($preservedSpecimenDTO->citation){
58
            $detail_html .= "<br>".create_label("Citation") . $preservedSpecimenDTO->citation . "<br>";
59
        }
60
    }
61
    if($preservedSpecimenDTO->preferredStableUri){
62
        $detail_html .= "<br>".create_label("Preferred stable URI") . l($preservedSpecimenDTO->preferredStableUri, $preservedSpecimenDTO->preferredStableUri) . "<br>";
63
    }
64
    if($isSpecimenPage){
65
        // associated taxa
66
        if($preservedSpecimenDTO->associatedTaxa){
67
            $detail_html .= "<br>";
68
            $detail_html .= create_label("Associated with");
69
                if(sizeof($preservedSpecimenDTO->associatedTaxa)>1){
70
                    $detail_html .= "<br>";
71
                }
72
            foreach($preservedSpecimenDTO->associatedTaxa as $associatedTaxon){
73
                $detail_html .= l($associatedTaxon->second, path_to_taxon($associatedTaxon->first, "specimens"));//$associatedTaxon->second."<br>";
74
            }
75
        }
76
    }
77
    // - type information
78
    $types = "";
79
    if (isset($preservedSpecimenDTO->types)) {
80
        //typed taxa
81
        if(sizeof($preservedSpecimenDTO->types)>1){
82
            $detail_html .= "<br>";
83
        }
84
        foreach ($preservedSpecimenDTO->types as $typeStatus => $typedTaxa) {
85
            if($isSpecimenPage){
86
                if($preservedSpecimenDTO->types){
87
                    $detail_html .= "<i>".$typeStatus."</i>: ";
88
                    foreach($typedTaxa as $typedTaxon){
89
                        $detail_html .= $typedTaxon." ";
90
                    }
91
                    $detail_html .= "<br>";
92
                }
93
            }
94
            else{
95
                $types .= $typeStatus." ";
96
            }
97
        }
98
    }
99
    $derivateDataDTO = $preservedSpecimenDTO->derivateDataDTO;
100
    // - specimen scans
101
    $specimenScans = create_links($derivateDataDTO->specimenScans);
102
    // - molecular data
103
    $molecularData = "";
104
    if ($derivateDataDTO->molecularDataList) {
105
        foreach ($derivateDataDTO->molecularDataList as $molecular) {
106
            //provider link
107
            if (isset($molecular->providerLink)) {
108
                $molecularData .= create_html_link($molecular->providerLink);
109
            }
110
            //contig link
111
            if (isset($molecular->contigFiles[0])) {//FIXME check if empty
112
                $molecularData .= "[";
113
                if (isset($molecular->contigFiles)) {
114
                    foreach ($molecular->contigFiles as $contigFile) {
115
                        if (isset($contigFile->contigLink)){
116
                            if(isset($contigFile->contigLink->uri) and $contigFile->contigLink->uri!=null) {
117
                               $molecularData .= create_html_link($contigFile->contigLink)." ";
118
                            }
119
                            //primer links
120
                            $molecularData .= create_html_links($contigFile->primerLinks);
121
                        }
122
                    }
123
                } else {
124
                    $molecularData .= "no contig";
125
                }
126
                $molecularData = rtrim($molecularData, " ");
127
                $molecularData .= "]";
128
            }
129
            //FIXME separate with comma (remove trailing comma)
130
        }
131
    }
132
    // - detail images
133
    $detailImages = create_links($derivateDataDTO->detailImages);
134

    
135
    if ($types) {
136
        $detail_html .= $isSpecimenPage?"<br>":"";
137
        $detail_html .= create_label("Type(s)") . $types . "<br>";
138
    }
139
    if ($specimenScans and !$isSpecimenPage) {
140
        $detail_html .= create_label("Specimen Scans") . $specimenScans . "<br>";
141
    }
142
    //specimen scan image gallery
143
    if($isSpecimenPage and isset($derivateDataDTO->specimenScanUuids) and !empty($derivateDataDTO->specimenScanUuids)) {
144
        $detail_html .= addImageGallery("Specimen scans", $derivateDataDTO->specimenScanUuids);
145
    }
146

    
147
    if ($molecularData) {
148
        $detail_html .= $isSpecimenPage?"<br>":"";
149
        $detail_html .= create_label("Molecular Data") . $molecularData . "<br>";
150
    }
151

    
152
    if ($detailImages and !$isSpecimenPage) {
153
        $detail_html .= create_label("Detail Images") . $detailImages . "<br>";
154
    }
155

    
156
    //detail image gallery
157
    if($isSpecimenPage and isset($derivateDataDTO->detailImageUuids) and !empty($derivateDataDTO->detailImageUuids)){
158
        $detail_html .= addImageGallery("Detail Images", $derivateDataDTO->detailImageUuids);
159
    }
160

    
161
    //character data
162
    if ($preservedSpecimenDTO->characterData) {
163
        $detail_html .= $isSpecimenPage?"<br>":"";
164
        $detail_html .= create_label("Character Data");
165
        if($isSpecimenPage) {
166
            $detail_html .= "<br>";
167
            foreach ($preservedSpecimenDTO->characterData as $characterStatePair) {
168
                $detail_html .= "<i>" . $characterStatePair->first . "</i>:" . $characterStatePair->second;
169
                $detail_html .= "<br>";
170
            }
171
        }
172
        else{
173
            $detail_html .= l("detail page", $pathToSpecimen,array('attributes' => array('target'=>'_blank')));
174
            $detail_html .= "<br>";
175
        }
176
    }
177
    return $detail_html;
178
}
179

    
180
function addImageGallery($galleryName, $imageUuids){
181
    $images = array();
182
    foreach ($imageUuids as $uuid) {
183
        $images[] = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $uuid);
184
    }
185

    
186
    $gallery_html = '';
187
    if (count($imageUuids) > 0) {
188
        $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
189
        $captionElements = array(
190
            'title',
191
            'rights',
192
        );
193
        $alternativeMediaUris = array();
194
        foreach($images as $image){
195
            $alternativeMediaUris[] = path_to_media($image->uuid);
196
        }
197

    
198
        $gallery_html = theme('cdm_media_gallerie', array(
199
            'mediaList' => $images,
200
            'galleryName' => $galleryName,
201
            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
202
            'cols' => $gallery_settings['cdm_dataportal_media_cols'],
203
            'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
204
            'captionElements' => $captionElements,
205
            'mediaLinkType' => 'LIGHTBOX',
206
            'alternativeMediaUri' => $alternativeMediaUris,
207
            'galleryLinkUri' => NULL,
208
        ));
209
    }
210
    return "<br>".create_label($galleryName)."<br>".$gallery_html;
211
}
212

    
213

    
214
/**
215
 * Formats the given string to a label for displaying key-value pairs in HTML
216
 * @return string
217
 */
218
function create_label($label)
219
{
220
    return "<span class='specimen_table_label'>".$label.": </span>";
221
}
222

    
223
/**
224
 * Compose an render array from a CDM DerivedUnitFacade object.
225
 *
226
 * compose_hook() implementation
227
 *
228
 * @param object $specimenOrObservation
229
 *   the CDM instance of type SpecimenOrObservation to compose
230
 *   the render array for
231
 * @param array $derivatives
232
 *   the render array which contains the compositions of the derivatives
233
 *   of the supplied $specimenOrObservation
234
 *
235
 * @return array
236
 *   the supplied render array $derivatives to which the composition of the supplied
237
 *   $specimenOrObservation has been added to
238
 *
239
 * @ingroup compose
240
 */
241
function compose_cdm_specimenOrObservation($specimenOrObservation, &$derivatives = null) {
242

    
243
  $exclude_occurrence_fields = &drupal_static(__FUNCTION__);
244
  if (!isset($exclude_occurrence_fields)) {
245
     $exclude_occurrence_fields = array(
246
        'derivationEvents',
247
        'extensions', // TODO ignored for now, how to handle extensions?
248
        'titleCache',
249
        'protectedTitleCache',
250
        'derivedUnitMedia',
251
        'created',
252
        'publish',
253
        'updated',
254
        'class',
255
        'uuid',
256
       ''
257
    );
258
  }
259

    
260

    
261
  // only show uuid it the user is logged in
262
  if(user_is_logged_in() && ($a_idx = array_search('uuid', $exclude_occurrence_fields)) !== FALSE ) {
263
    unset($exclude_occurrence_fields[$a_idx]);
264
  }
265

    
266
  if (!isset($derivatives)) {
267
    $derivatives = array();
268
  }
269

    
270
  $descriptions = null;
271
  $derivedFrom = null;
272

    
273
  if (is_object($specimenOrObservation)) {
274

    
275
    // request again for deeper initialization
276
    $specimenOrObservation = cdm_ws_get("portal/" . CDM_WS_OCCURRENCE, $specimenOrObservation->uuid);
277

    
278

    
279
    $type_label = $specimenOrObservation->class;
280
    RenderHints::setFootnoteListKey($type_label . '-' . $specimenOrObservation->uuid);
281

    
282
    // collect typeStatus as label
283
    if (isset($specimenOrObservation->specimenTypeDesignations)) {
284
      $type_status = array();
285
      foreach ($specimenOrObservation->specimenTypeDesignations as $typeDesignation) {
286
        if (isset($typeDesignation->typeStatus->representation_L10n)){
287
          $type_status[] = $typeDesignation->typeStatus->representation_L10n;
288
        }
289
      }
290
      if (count($type_status) > 0){
291
        $type_label = implode(', ', $type_status);
292
      }
293
    }
294

    
295
    $title = $type_label . ': '. $specimenOrObservation->titleCache;
296

    
297
    $groups = array();
298
    // --- add initialized fields
299
    foreach (get_object_vars($specimenOrObservation) as $field => $value) {
300
      if (!in_array($field, $exclude_occurrence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
301
        switch ($field) {
302

    
303
          /* ---- java.lang.Object --- */
304
          case 'class':
305
            if($value != '' /* FieldUnit' */){
306
              @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
307
            }
308
          break;
309

    
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

    
318

    
319
          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

    
328
          /* ---- SpecimenOrObservationBase --- */
329
          case 'sex':
330
          case 'lifeStage':
331
          case 'kindOfUnit':
332
            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value->representation_L10n);
333
            break;
334

    
335
          case 'definition':
336
            // TODO
337
            break;
338

    
339
          case 'specimenTypeDesignations':
340
            @_description_list_group_add(
341
              $groups,
342
              cdm_occurrence_field_name_label($field),
343
              array(
344
                '#markup'=>theme('cdm_typedesignations', array('typeDesignations' => $value)),
345
              )
346
            );
347
            break;
348

    
349
          case 'determinations':
350
            $dd_elements = array();
351
            $glue = ', ';
352

    
353
            foreach  ($value as $determinationEvent){
354
                $timeperiod_string = NULL;
355
                if (isset($determinationEvent->timeperiod)) {
356
                    $timeperiod_string = timePeriodToString($determinationEvent->timeperiod);
357
                }
358
                $weight = isset($determinationEvent->preferred) && $determinationEvent->preferred == 1 ? '0' : ($timeperiod_string ? $timeperiod_string : '1');
359
                // check key exists
360
                while (array_key_exists($weight, $dd_elements)) {
361
                    $weight .= '0';
362
                }
363
                if($determinationEvent->taxonName){
364
                    $taxon_name = $determinationEvent->taxonName;
365
                    $name_link = "";
366
                }
367
                else if($determinationEvent->taxon){
368
                    $taxon_name = cdm_ws_get(CDM_WS_TAXON . '/$0/name', $determinationEvent->taxon->uuid);
369
                    $name_link = path_to_taxon($determinationEvent->taxon->uuid);
370
                }
371
                $taxon_html = render_taxon_or_name($taxon_name, $name_link);
372
                $dd_elements[$weight] = $taxon_html;
373
                if (isset($determinationEvent->modifier)) {
374
                    $dd_elements[$weight] .= cdm_term_representation($determinationEvent->modifier);
375
                }
376
                if ($timeperiod_string) {
377
                    $dd_elements[$weight] .= $glue . $timeperiod_string;
378
                }
379
                if (isset($determinationEvent->actor->titleCache)) {
380
                    $dd_elements[$weight] .= $glue . $determinationEvent->actor->titleCache;
381
                }
382
                if (isset($determinationEvent->description)) {
383
                    $dd_elements[$weight] .= $glue . $determinationEvent->description;
384
                }
385
            }
386
            ksort($dd_elements);
387
            @_description_list_group_add($groups, cdm_occurrence_field_name_label('determinations'), $dd_elements);
388
            break;
389

    
390
          case 'descriptions':
391
            $descriptions = $value;
392
            $occurrence_featureTree = cdm_get_occurrence_featureTree();
393
            $dd_elements = array();
394

    
395
            foreach ($value as $description) {
396
              $description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $description->uuid);
397
//               if($description->imageGallery == TRUE) {
398
//                 continue;
399
//               }
400
              $elements_by_feature = _mergeFeatureTreeDescriptions($occurrence_featureTree->root->childNodes, $description->elements);
401
              $description_render_elements = compose_feature_blocks($elements_by_feature, null);
402
              $dd_elements[] = $description_render_elements;
403
            }
404

    
405
            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
406
            break;
407

    
408
          case 'sources':
409
              $dd_elements = array();
410
              foreach ($value as $identifiable_source) {
411
                $dd_elements[] = theme('cdm_OriginalSource', array('source' => $identifiable_source));
412
              }
413
              @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
414
              break;
415

    
416

    
417
          /* ---- DerivedUnitBase --- */
418
          case 'derivedFrom':
419
            $derivedFrom = $value;
420
            break;
421

    
422
          case 'collection':
423
            $sub_dl_groups = array();
424
            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('code'), $value->code, NULL, 1);
425
            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('codeStandard'),  $value->codeStandard, NULL, 2);
426
            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('institute'), $value->institute, NULL, 3);
427
            @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('townOrLocation'), $value->townOrLocation, NULL, 4);
428
            // TODO "superCollection"
429
            // TODO may have media
430

    
431
            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
432
                array(
433
                    array('#markup' => $value->titleCache),
434
                    array('#theme' => 'description_list', '#groups' => $sub_dl_groups)
435
                )
436
            );
437
            break;
438

    
439
            case 'storedUnder':
440
              @_description_list_group_add($groups, cdm_occurrence_field_name_label('storedUnder'), render_taxon_or_name($value));
441
              break;
442

    
443

    
444
            /* ---- Specimen --- */
445
            case 'sequences':
446
              $dd_elements = array();
447
              foreach ($value as $sequence) {
448
                $dd_elements[] = compose_cdm_sequence($sequence);
449
              }
450
              @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements);
451
            break;
452

    
453
            // TODO preservation
454
            // TODO exsiccatum
455

    
456

    
457
          /* ---- FieldObservation --- */
458
          case 'gatheringEvent':
459
            @_description_list_group_add($groups, cdm_occurrence_field_name_label('collector'), $value->actor->titleCache);
460
            @_description_list_group_add($groups, t('Gathering time'), timePeriodToString($value->timeperiod));
461
            @_description_list_group_add($groups, cdm_occurrence_field_name_label('description'), $value->description);
462
            @_description_list_group_add($groups, cdm_occurrence_field_name_label('locality'), $value->locality->text);
463
            @_description_list_group_add($groups, cdm_occurrence_field_name_label('country'), $value->country->representation_L10n);
464
            @_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingMethod'), $value->collectingMethod);
465
            if (isset($value->absoluteElevation)) {
466
                $min_max_array = min_max_array();
467
                if(is_numeric($value->absoluteElevation)){
468
                    $min_max_array['Min'] = new stdClass();
469
                    $min_max_array['Min']->_value = $value->absoluteElevation . ' m';
470
                }
471
                if(is_numeric($value->absoluteElevation)){
472
                    $min_max_array['Max'] = new stdClass();
473
                    $min_max_array['Max']->_value = $value->absoluteElevationMax . ' m';
474
                }
475
                $min_max_markup = min_max_markup($min_max_array);
476
                if(isset($value->absoluteElevationError)){
477
                    $min_max_markup .= ' +/-' .  $value->absoluteElevationError . ' m';
478
                }
479
                if(is_string($value->absoluteElevationText)){
480
                    $min_max_markup .= ' ' . $value->absoluteElevationText;
481
                }
482
                @_description_list_group_add($groups, cdm_occurrence_field_name_label('absoluteElevation'), $min_max_markup);
483
            }
484
            if (isset($value->distanceToGround)) {
485
              $min_max_array = min_max_array();
486
              if(is_numeric($value->distanceToGround)){
487
                  $min_max_array['Min'] = new stdClass();
488
                  $min_max_array['Min']->_value = $value->distanceToGround . ' m';
489
              }
490
              if(is_numeric($value->distanceToGround)){
491
                  $min_max_array['Max'] = new stdClass();
492
                  $min_max_array['Max']->_value = $value->distanceToGroundMax . ' m';
493
              }
494
              $min_max_markup = min_max_markup($min_max_array);
495
              if(isset($value->distanceToGroundError)){
496
                  $min_max_markup .= ' +/-' .  $value->distanceToGroundError . ' m';
497
              }
498
              if(is_string($value->distanceToGroundText)){
499
                  $min_max_markup .= ' ' . $value->distanceToGroundText;
500
              }
501
              @_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToGround'), $min_max_markup);
502
            }
503
            if (isset($value->distanceToWaterSurface)) {
504
              $min_max_array = min_max_array();
505
              if(is_numeric($value->distanceToWaterSurface)){
506
                  $min_max_array['Min'] = new stdClass();
507
                  $min_max_array['Min']->_value = $value->distanceToWaterSurface . ' m';
508
              }
509
              if(is_numeric($value->distanceToWaterSurface)){
510
                  $min_max_array['Max'] = new stdClass();
511
                  $min_max_array['Max']->_value = $value->distanceToWaterSurfaceMax . ' m';
512
              }
513
              $min_max_markup = min_max_markup($min_max_array);
514
              if(isset($value->distanceToWaterSurfaceError)){
515
                  $min_max_markup .= ' +/-' .  $value->distanceToWaterSurfaceError . ' m';
516
              }
517
              if(is_string($value->distanceToWaterSurfaceText)){
518
                  $min_max_markup .= ' ' . $value->distanceToWaterSurfaceText;
519
              }
520
              @_description_list_group_add($groups, cdm_occurrence_field_name_label('distanceToWaterSurface'), $min_max_markup);
521
            }
522

    
523
            if (isset($value->collectingAreas)) {
524
              $area_representations = array();
525
              foreach($value->collectingAreas as $area) {
526
                $area_representations[] = $area->representation_L10n;
527
              }
528
              @_description_list_group_add($groups, cdm_occurrence_field_name_label('collectingAreas'), implode(', ', $area_representations));
529
            }
530
            if (isset($value->exactLocation) && $value->exactLocation->sexagesimalString) {
531
              $sub_dl_groups = array();
532
              @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('errorRadius'), $value->exactLocation->errorRadius, ' m', 1);
533
              @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('longitude'), round($value->exactLocation->longitude, 7), '°', 2);
534
              @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('latitude'), round($value->exactLocation->latitude, 7), '°', 3);
535
              if (isset($value->exactLocation->referenceSystem)) {
536
                @_description_list_group_add($sub_dl_groups, cdm_occurrence_field_name_label('referenceSystem'), $value->exactLocation->referenceSystem->representation_L10n, '', 4);
537
              }
538

    
539
              @_description_list_group_add($groups, cdm_occurrence_field_name_label('exactLocation'),
540
                  array(
541
                      array('#markup' => $value->exactLocation->sexagesimalString),
542
                      array(
543
                          '#theme' => 'description_list',
544
                          '#groups' => $sub_dl_groups
545
                      ),
546
                  )
547
              );
548
            }
549
            break;
550

    
551
          default:
552
            if(is_object($value) || is_array($value)){
553
              drupal_set_message("Unhandled type in compose_cdm_specimenOrObservation() for field " . $field, "warning");
554
            } else {
555
              _description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value);
556
            }
557

    
558
        }
559

    
560
      }
561
    } // END of loop over $derivedUnitFacade fields
562

    
563

    
564
    // template_preprocess_description_list() is not worting by weight so we do it right here
565
    uasort($groups, 'element_sort');
566

    
567
    $occurrence_elements = array(
568
        '#title' => $title,
569
        '#theme' => 'description_list',
570
        '#groups' => $groups,
571
        '#attributes' => array('class' => html_class_attribute_ref($specimenOrObservation)),
572
    );
573
    $derivatives[] = $occurrence_elements;
574
    // all footnotes which has been assembled so far (e.g. from typeDesignations) to here
575
    $foonote_li_elements = theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey(), 'enclosingTag' => 'span'));
576
    if (!empty($foonote_li_elements)) {
577
      $derivatives[] =  array(
578
          '#markup' =>  '<div class="footnotes">' . $foonote_li_elements . '</div>',
579
      );
580
    }
581

    
582
    // --- recurse into originals
583
    if (!isset($derivedFrom)) {
584
      $derivedFrom = cdm_ws_get(
585
          CDM_WS_OCCURRENCE,
586
          array($specimenOrObservation->uuid, 'derivedFrom')
587
        );
588
    }
589

    
590
    if (isset($derivedFrom)) {
591
      if (isset($derivedFrom->originals)) {
592
        $derived_from_label = t('derived');
593
        $preposition = t('from');
594
        if(isset($derivedFrom->type)){
595
          $derived_from_label = $derivedFrom->type->representation_L10n;
596
          if($derivedFrom->type->uuid == UUID_DERIVATIONEVENTTYPE_ACCESSIONING){
597
            $preposition = t('of');
598
          }
599
        }
600
        if (count($groups) > 0) {
601
          // TODO  annotations
602

    
603
          // only display the derived from information when the derivative has any element which will be diplayed
604
          $derivatives[] = array(
605
              '#markup' => '<div class="derived_from">' . $derived_from_label . ' ' . $preposition . ': </div>',
606
          );
607
        }
608
        foreach ($derivedFrom->originals as $original) {
609
          compose_cdm_specimenOrObservation($original, $derivatives);
610
        }
611
      }
612
    }
613

    
614
  } // END of $specimenOrObservation exists
615

    
616
  return $derivatives;
617
}
618

    
619
/**
620
 * Compose an render array from a CDM Sequence object.
621
 *
622
 * compose_hook() implementation
623
 *
624
 * @param object $sequence
625
 *   CDM instance of type Sequence
626
 * @return array
627
 *   A render array containing the fields of the supplied $sequence
628
 *
629
 * @ingroup compose
630
 */
631
function compose_cdm_sequence($sequence) {
632

    
633
  $exclude_sequence_fields = &drupal_static(__FUNCTION__);
634
  if (!isset($exclude_sequence_fields)) {
635
    $exclude_sequence_fields = array(
636
      'titleCache',
637
      'protectedTitleCache',
638
      'microReference',
639
      'created',
640
      'updated',
641
      'class',
642
    );
643
  }
644

    
645
  $groups = array();
646

    
647
  // -- retrieve additional data if neesscary
648
  // TODO below call disabled since sequences are not yet supported,
649
  //      see  #3347 (services and REST service controller for molecular classes implemented)
650
  //
651
  // cdm_load_annotations($sequence);
652

    
653
  foreach (get_object_vars($sequence) as $field => $value) {
654

    
655

    
656
    if (!in_array($field, $exclude_sequence_fields) && ($value && (!is_object($value) || isset($value->class)))) {
657
      switch ($field) {
658

    
659
        case 'geneticAccessionNumber';
660
          $dd_elements = array();
661
          foreach ($value as $accession) {
662
            if (isset($accession->uri) ){
663
              $dd_elements[] = l($accession->accessionNumber, $accession->uri);
664
            } else {
665
              $dd_elements[] = $accession->accessionNumber;
666
            }
667
          }
668
          @_description_list_group_add($groups, cdm_occurrence_field_name_label($field),  $dd_elements, NULL, 1);
669
          break;
670

    
671

    
672
        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.
673
          if (isset($value->name)) {
674
            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field),  $value->name, NULL, 3);
675
          }
676
          if (isset($value->description)) {
677
            @_description_list_group_add($groups, cdm_occurrence_field_name_label($field) . ' ' . t('description') , $value->description, NULL, 4);
678
          }
679
          break;
680

    
681
        case 'consensusSequence':
682
          // format in genbank style, force linebreaks after each 70 nucleotites
683
          // see also http://stackoverflow.com/questions/499137/css-how-can-i-force-a-long-string-without-any-blank-to-be-wrapped-in-xul-and
684
          @_description_list_group_add(
685
            $groups,
686
            cdm_occurrence_field_name_label($field),
687
            array(
688
              array(
689
                '#markup' => '<div class="sequence-length">' . $value->length . ' ' . t('pb'). '</div><div>' . wordwrap($value->string, 70, '</br>', TRUE) . '</div>',
690
                '#wrapper_attributes' => array('class'=>'dna-sequence')
691
                )
692
              ),
693
            5);
694
          break;
695

    
696
         case 'dnaSample': // FIXME 3.3 implement
697
            break;
698
        case 'singleReads': // FIXME 3.3 implement
699
          break;
700
        case 'contigFile': // FIXME 3.3 implement - Media
701
            break;
702
        case 'pherograms': // FIXME 3.3 implement - Media
703
          break;
704
        case 'haplotype': // FIXME 3.3 implement
705
            break;
706
        case 'dateSequenced': // FIXME 3.3 now in SingelRead
707
          @_description_list_group_add($groups, t('Sequencing date'),  timePeriodToString($value), NULL, 6);
708
          break;
709

    
710
        case 'barcode': // boolean
711
          @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value ? 'Yes': 'No', NULL, 7);
712
          break;
713
        case 'barcodeSequencePart': // FIXME 3.3 implement, compose sequence
714
            break;
715

    
716
        case 'citation':
717
          @_description_list_group_add($groups,
718
            cdm_occurrence_field_name_label($field),
719
            theme('cdm_reference', array('reference' =>$value, 'microReference' => $sequence->microReference)),
720
            NULL,
721
            8
722
          );
723
          break;
724

    
725
        case 'publishedIn':
726
          @_description_list_group_add($groups,
727
            cdm_occurrence_field_name_label($field),
728
            theme('cdm_reference', array('reference'=>$value)),
729
            NULL,
730
            7
731
          );
732

    
733
        case 'rights':
734
          array_merge($groups, cdm_rights_as_dl_groups($value));
735
        break;
736

    
737
        case 'annotations':
738
          $dd_elements = array();
739
          foreach ($value as $annotation) {
740
            // TODO respect annotation type filter settings
741
            $dd_elements[] = $annotation->text;
742
          }
743
          @_description_list_group_add($groups, t('Notes'), $dd_elements, NULL, 9);
744
          break;
745

    
746
        case 'markers':
747
          $dd_elements = array();
748
          foreach ($value as $marker) {
749
            $dd_elements[] = compose_cdm_marker($marker);
750
          }
751
          @_description_list_group_add($groups, cdm_occurrence_field_name_label($field), $dd_elements, NULL, 10);
752
          break;
753

    
754
        case 'chromatograms':
755
          @_description_list_group_add($groups, cdm_occurrence_field_name_label($field),
756
              array(
757
                  '#markup'=>theme('cdm_media_gallerie', array('medialist'=>$value)),
758
              ),
759
              NULL,
760
              11);
761
          break;
762

    
763
        default:
764
          if(is_object($value) || is_array($value)){
765
            drupal_set_message("Unhandled type in compose_cdm_sequence() for field " . $field, "warning");
766
          } else {
767
            _description_list_group_add($groups, cdm_occurrence_field_name_label($field), $value, NULL, 20);
768
          }
769
      }
770
    }
771
  }
772

    
773
  // template_preprocess_description_list() is not worting by weight so we do it right here
774
  uasort($groups, 'element_sort');
775

    
776
  $sequence_elements = array(
777
      '#theme' => 'description_list',
778
      '#groups' => $groups
779
  );
780

    
781
  return $sequence_elements;
782
}
783

    
784

    
(6-6/10)