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<?php
2

    
3
const BIBLIOGRAPHY_FOOTNOTE_KEY = PSEUDO_FEATURE_BIBLIOGRAPHY;
4

    
5

    
6
/**
7
 * Returns the localized representations of the modifiers hold by the
8
 * supplied cdm instance concatenated into one string.
9
 *
10
 * @param object $is_modifieable
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 *   cdm instance of an class implementing the interface IModifieable:
12
 *   DescriptionElementBase, StateDate, State
13
 *
14
 * @return String
15
 *   localized representations of the modifiers hold by the
16
 *   supplied cdm instance concatenated into one string
17
 */
18
function cdm_modifiers_representations($is_modifieable, $glue = ', ') {
19
  $modifiers_strings = array();
20
  if (isset($is_modifieable->modifiers)) {
21
    foreach ($is_modifieable->modifiers as $modifier) {
22
      $modifiers_strings[] = cdm_term_representation($modifier);
23
    }
24
  }
25
  return implode(', ', $modifiers_strings);
26
}
27

    
28
/**
29
 * Filters the given set of description elements and prefers computed elements over others.
30
 *
31
 * Computed description elements
32
 * are identified by the MarkerType.COMPUTED()
33
 *
34
 * If the given set contains at least one computed element only
35
 * the computed elements are returned.
36
 *
37
 * @param array $description_elements
38
 *   An array of CDM DescriptionElementBase instances
39
 *
40
 * @return array
41
 *   only the computed description elements otherwise all others.
42
 *
43
 * @deprecated this is replaced by the cdmlib DistributionUtil class!!!
44
 */
45
function cdm_description_elements_prefer_computed($description_elements){
46

    
47
  $computed_elements = array();
48
  $other_elements = array();
49

    
50
  if (!empty($description_elements)) {
51
    foreach ($description_elements as $element) {
52
      if (cdm_entity_has_marker($element, UUID_MARKERTYPE_COMPUTED)) {
53
        $computed_elements[] = $element;
54
      }
55
      else {
56
        $other_elements[] = $element;
57
      }
58
    }
59
  }
60

    
61
  if (count($computed_elements) > 0) {
62
    return $computed_elements;
63
  }
64
  else {
65
    return $other_elements;
66
  }
67
}
68

    
69
/**
70
 * Creates a query parameter array based on the setting stored in the drupal variable CDM_DISTRIBUTION_FILTER.
71
 *
72
 * @return array
73
 *   An array with distribution filter query parameters
74
 */
75
function cdm_distribution_filter_query() {
76
  $cdm_distribution_filter = get_array_variable_merged(CDM_DISTRIBUTION_FILTER, CDM_DISTRIBUTION_FILTER_DEFAULT);
77
  $query = array();
78

    
79
  $feature_block_settings = get_feature_block_settings(UUID_DISTRIBUTION);
80
  if($feature_block_settings['sort_elements'] == SORT_HIERARCHICAL){
81
    $query['distributionOrder'] = 'AREA_ORDER';
82
  }
83

    
84
  $query['recipe'] = variable_get(DISTRIBUTION_CONDENSED_RECIPE, DISTRIBUTION_CONDENSED_RECIPE_DEFAULT);
85

    
86

    
87

    
88
  if ($cdm_distribution_filter['filter_rules']['statusOrderPreference']) {
89
    $query['statusOrderPreference'] = 1;
90
  }
91
  if ($cdm_distribution_filter['filter_rules']['subAreaPreference']) {
92
    $query['subAreaPreference'] = 1;
93
  }
94
  if (is_array($cdm_distribution_filter['hiddenAreaMarkerType']) && count($cdm_distribution_filter['hiddenAreaMarkerType']) > 0) {
95
    $query['hiddenAreaMarkerType'] = '';
96
    foreach ($cdm_distribution_filter['hiddenAreaMarkerType'] as $marker_type => $enabled) {
97
      if ($enabled) {
98
        $query['hiddenAreaMarkerType'] .= ($query['hiddenAreaMarkerType'] ? ',' : '') . $marker_type;
99
      }
100
    }
101
  }
102

    
103
  return $query;
104
}
105

    
106
/**
107
 * Merge the fields 'annotations', 'markers', 'sources', 'media' from the source CDM DescriptionElement into  the target.
108
 *
109
 * @param object $target
110
 *   The source CDM DescriptionElement
111
 * @param object $source
112
 *   The target CDM DescriptionElement
113
 */
114
function cdm_merge_description_elements($target, $source) {
115
  static $fields_to_merge = array('annotations', 'markers', 'sources', 'media');
116

    
117
  foreach ($fields_to_merge as $field) {
118
    if (is_array($source->$field)) {
119
      if (!is_array($target->$field)) {
120
        $target->$field = $source->$field;
121
      }
122
      else {
123
        $target->$field = array_merge($target->$field, $source->$field);
124
      }
125
    }
126
  }
127
}
128

    
129
/**
130
 * Adds an entry to the end of the table of content items list
131
 *
132
 * The  table of content items are crated internally by calling
133
 * toc_list_item() the resulting item is added to the statically cached
134
 * list of toc elements
135
 *
136
 * @param string $label
137
 *   The label of toc entry
138
 * @param $class_attribute_suffix
139
 *   The suffix to be appended to the class attribute prefix:
140
 *   "feature-toc-item-"
141
 * @param string $fragment
142
 *   Optional parameter to define a url fragment different from the $label,
143
 *   if the $fragment is not defined the $label will be used
144
 * @param boolean $as_first_element
145
 *   Place the new item as fist one. This parameter is ignored when $weight is
146
 *   being set
147
 * @param integer $weight
148
 *   Defines the weight for the ordering the item in the toc list.
149
 *   The item will be placed at the end if weigth is NULL.
150
 *
151
 * @throws \Exception re-throws exception from theme()
152
 */
153
function cdm_toc_list_add_item($label, $class_attribute_suffix, $fragment = NULL, $as_first_element = FALSE, $weight = null) {
154

    
155
  $toc_list_items = &cdm_toc_list();
156

    
157
  if (!$fragment) {
158
    $fragment = $label;
159
  }
160
  $fragment = generalizeString($fragment);
161

    
162
  $class_attributes = 'feature-toc-item-' . $class_attribute_suffix;
163

    
164
  $new_item = toc_list_item(
165
    theme(
166
      'cdm_feature_name',
167
      array('feature_name' => $label)),
168
      array('class' => $class_attributes),
169
      $fragment
170
    );
171

    
172
  if ($weight === null && $as_first_element) {
173
    reset($toc_list_items);
174
    $weight = key($toc_list_items); // returns null for empty arrays
175
    $weight = $weight !== null ? $weight - FEATURE_BLOCK_WEIGHT_INCREMENT : 0;
176
  }
177
  else if($weight === null) {
178
      end($toc_list_items);
179
      $weight = key($toc_list_items); // returns null for empty arrays
180
      $weight = $weight !== null ? $weight + FEATURE_BLOCK_WEIGHT_INCREMENT : 0;
181
  }
182
  $toc_list_items[$weight] = $new_item;
183
  ksort($toc_list_items); // sort so that the last element has always the highest weight
184

    
185
}
186

    
187
/**
188
 * Returns the statically cached table of content items as render array.
189
 *
190
 * @see cdm_toc_list_add_item()
191
 *
192
 * @return array
193
 *   a render array of table of content items suitable for theme_item_list()
194
 */
195
function &cdm_toc_list(){
196

    
197
  $toc_list_items = &drupal_static('toc_list_items', array());
198

    
199
  return $toc_list_items;
200
}
201

    
202
/**
203
 * Prepares an empty Drupal block for displaying description elements of a
204
 * specific CDM Feature.
205
 *
206
 * The block can also be used for pseudo Features like a bibliography. Pseudo
207
 * features are derived from other data on the fly and so not exist as such in
208
 * the cdm data. For pseudo features the $feature can be created using
209
 * make_pseudo_feature().
210
 *
211
 * @param $feature_name
212
 *   A label describing the feature, usually the localized feature
213
 *   representation.
214
 * @param object $feature
215
 *   The CDM Feature for which the block is created.
216
 *
217
 * @return object
218
 *   A Drupal block object
219
 *
220
 * @throws \Exception re-throws exception from theme()
221
 */
222
function feature_block($feature_name, $feature) {
223
  $block = new stdclass();
224
  $block->module = 'cdm_dataportal';
225
  $block->region = NULL;
226
  $class_attribute = html_class_attribute_ref($feature);
227
  $block_delta = $feature->class !== 'PseudoFeature' ? $feature_name : $feature->label;
228
  $block->delta = generalizeString($block_delta);
229
  $block->subject = '<a name="' . $block->delta . '"></a><span class="' . $class_attribute . '">'
230
    . theme('cdm_feature_name', array('feature_name' => $feature_name))
231
    . '</span>';
232
  $block->module = "cdm_dataportal-feature";
233
  $block->content = '';
234
  return $block;
235
}
236

    
237

    
238
/**
239
 * Returns a list of a specific type of IdentificationKeys.
240
 *
241
 * The list can be restricted by a taxon.
242
 *
243
 * @param string $type
244
 *   The simple name of the cdm class implementing the interface
245
 *   IdentificationKey, valid values are:
246
 *   PolytomousKey, MediaKey, MultiAccessKey.
247
 * @param string $taxonUuid
248
 *   If given this parameter restrict the listed keys to those which have
249
 *   the taxon identified be this uuid in scope.
250
 *
251
 * @return array
252
 *   List with identification keys.
253
 */
254
function _list_IdentificationKeys($type, $taxonUuid = NULL, $pageSize = NULL, $pageNumber = NULL) {
255
  if (!$type) {
256
    drupal_set_message(t('Type parameter is missing'), 'error');
257
    return;
258
  }
259
  $cdm_ws_base_path = NULL;
260
  switch ($type) {
261
    case "PolytomousKey":
262
      $cdm_ws_base_path = CDM_WS_POLYTOMOUSKEY;
263
      break;
264

    
265
    case "MediaKey":
266
      $cdm_ws_base_path = CDM_WS_MEDIAKEY;
267
      break;
268

    
269
    case "MultiAccessKey":
270
      $cdm_ws_base_path = CDM_WS_MULTIACCESSKEY;
271
      break;
272

    
273
  }
274

    
275
  if (!$cdm_ws_base_path) {
276
    drupal_set_message(t('Type parameter is not valid: ') . $type, 'error');
277
  }
278

    
279
  $queryParameters = '';
280
  if (is_numeric($pageSize)) {
281
    $queryParameters = "pageSize=" . $pageSize;
282
  }
283
  else {
284
    $queryParameters = "pageSize=0";
285
  }
286

    
287
  if (is_numeric($pageNumber)) {
288
    $queryParameters = "pageNumber=" . $pageNumber;
289
  }
290
  else {
291
    $queryParameters = "pageNumber=0";
292
  }
293
  $queryParameters = NULL;
294
  if ($taxonUuid) {
295
    $queryParameters = "findByTaxonomicScope=$taxonUuid";
296
  }
297
  $pager = cdm_ws_get($cdm_ws_base_path, NULL, $queryParameters);
298

    
299
  if (!$pager || $pager->count == 0) {
300
    return array();
301
  }
302
  return $pager->records;
303
}
304

    
305

    
306
/**
307
 * Creates a list item for a table of content, suitable as data element for a themed list
308
 *
309
 * @see theme_list()
310
 *
311
 * @param $label
312
 * @param $http_request_params
313
 * @param $attributes
314
 * @return array
315
 */
316
function toc_list_item($label, $attributes = array(), $fragment = null) {
317

    
318
  // we better cache here since drupal_get_query_parameters has no internal static cache variable
319
  $http_request_params = drupal_static('http_request_params', drupal_get_query_parameters());
320

    
321
  $item =  array(
322
    'data' => l(
323
      $label,
324
      $_GET['q'],
325
      array(
326
        'attributes' => array('class' => array('toc')),
327
        'fragment' => generalizeString($label),
328
        'query' => $http_request_params,
329
      )
330
    ),
331
  );
332
  $item['attributes'] = $attributes;
333
  return $item;
334
}
335

    
336
/**
337
 * Compare callback to be used in usort() to sort render arrays produced by
338
 * compose_description_element().
339
 *
340
 * @param $a
341
 * @param $b
342
 *
343
 * @return int Returns < 0 if $a['#value'].$a['#value-suffix'] from is less than
344
 * $b['#value'].$b['#value-suffix'], > 0 if it is greater than $b['#value'].$b['#value-suffix'],
345
 * and 0 if they are equal.
346
 */
347
function compare_description_element_render_arrays($a, $b){
348
  if ($a['#value'].$a['#value-suffix'] == $b['#value'].$b['#value-suffix']) {
349
    return 0;
350
  }
351
  return ($a['#value'].$a['#value-suffix'] < $b['#value'].$b['#value-suffix']) ? -1 : 1;
352

    
353
}
354

    
355

    
356
/**
357
 * @param $element
358
 * @param $feature_block_settings
359
 * @param $element_markup
360
 * @param $footnote_list_key_suggestion
361
 * @param bool $prepend_feature_label
362
 *
363
 * @return array|null
364
 */
365
function compose_description_element($element, $feature_block_settings, $element_markup, $footnote_list_key_suggestion, $prepend_feature_label = FALSE)
366
{
367

    
368
  $render_array = array(
369
    '#type' => 'html_tag',
370
    '#tag' => cdm_feature_block_element_tag_name($feature_block_settings),
371

    
372
    '#attributes' => array(
373
      'class' => array(
374
        'DescriptionElement',
375
        'DescriptionElement-' . $element->class,
376
        html_class_attribute_ref($element)
377
      )
378
    ),
379

    
380
    '#value' => '',
381
    '#value_suffix' => NULL
382

    
383
  );
384

    
385
  $annotations_and_sources = handle_annotations_and_sources(
386
    $element,
387
    handle_annotations_and_sources_config($feature_block_settings),
388
    $element_markup,
389
    $footnote_list_key_suggestion
390
  );
391

    
392
  $timescope_markup = '';
393
  if(isset($element->timeperiod)){
394
    $timescope_markup = ' ' . timePeriodToString($element->timeperiod, true);
395
  }
396

    
397
  // handle the special case were the TextData is used as container for original source with name
398
  // used in source information without any text stored in it.
399
  $names_used_in_source_markup = '';
400
  if (!empty($annotations_and_sources['names_used_in_source']) && empty($element_markup)) {
401
    $names_used_in_source_markup = join(', ', $annotations_and_sources['names_used_in_source']) . ': ';
402
    // remove all <span class="nameUsedInSource">...</span> from all source_references
403
    // these are expected to be at the end of the strings
404
    $pattern = '/ <span class="nameUsedInSource">.*$/';
405
    foreach( $annotations_and_sources['source_references'] as &$source_reference){
406
      $source_reference = preg_replace($pattern , '', $source_reference);
407
    }
408
  }
409

    
410
  $source_references_markup = '';
411
  if (!empty($annotations_and_sources['source_references'])) {
412
    $source_references_markup = '<span class="sources">' . join(' ', $annotations_and_sources['source_references']) . '<span>';
413
  }
414

    
415
  $feature_label = '';
416
  if ($prepend_feature_label) {
417
    $feature_label = '<span class="nested-feature-tree-feature-label">' . $element->feature->representation_L10n . ':</span> ';
418
  }
419
  $content_markup = $names_used_in_source_markup . $element_markup . $timescope_markup . $source_references_markup;
420

    
421
  if(!$content_markup && $feature_block_settings['sources_as_content'] !== 1){
422
    // no textual content? So skip this element completely, even if there could be an footnote key
423
    // see #4379
424
    return null;
425
  }
426

    
427
    $render_array['#value'] = $feature_label . $content_markup;
428
    $render_array['#value_suffix'] = $annotations_and_sources['foot_note_keys'];
429
  return $render_array;
430
}
431

    
432
/**
433
 * Creates a handle_annotations_and_sources configuration array from feature_block_settings.
434
 *
435
 * The handle_annotations_and_sources configuration array is meant to be used for the
436
 * method handle_annotations_and_sources().
437
 *
438
 * @param $feature_block_settings array
439
 *
440
 * @return array
441
 *   The configuration array for handle_annotations_and_sources()
442
 */
443
function handle_annotations_and_sources_config($feature_block_settings){
444

    
445
  $config = $feature_block_settings;
446
  unset($config['sources_as_content_to_bibliography']);
447
  $config['add_footnote_keys'] = 0;
448
  if($feature_block_settings['sources_as_content'] !== 1 || $feature_block_settings['sources_as_content_to_bibliography'] == 1) {
449
    $config['add_footnote_keys'] = 1;
450
  }
451
  $config['bibliography_aware'] = 1;
452

    
453
  return $config;
454
}
455

    
456
/**
457
 * @param $entity
458
 * @param $config array
459
 *   An associative array to configure the display of the annotations and
460
 *   sources. The array has the following keys
461
 *   - sources_as_content
462
 *   - link_to_name_used_in_source
463
 *   - link_to_reference
464
 *   - add_footnote_keys
465
 *   - bibliography_aware
466
 *   Valid values are 1 or 0.
467
 * @param $inline_text_prefix
468
 *   Only used to decide if the source references should be enclosed in
469
 *   brackets or not when displayed inline. This text will not be included into
470
 *   the response.
471
 * @param $footnote_list_key_suggestion string
472
 *    optional parameter. If this paramter is left empty (null, 0, "") the
473
 *   footnote key will be determined by the nested method calls by calling
474
 *   RenderHints::getFootnoteListKey(). NOTE: the footnore key for annotations
475
 *   will be set to RenderHints::getFootnoteListKey().FOOTNOTE_KEY_SUFFIX_ANNOTATIONS.
476
 * @return array
477
 * an associative array with the following elements:
478
 *   - foot_note_keys: all footnote keys as markup
479
 *   - source_references: an array of the source references citations
480
 *   - names used in source: an associative array of the names in source,
481
 *        the name in source strings are de-duplicated
482
 *        !!!NOTE!!!!: this field will most probably be removed soon (TODO)
483
 *
484
 */
485
  function handle_annotations_and_sources($entity, $config, $inline_text_prefix, $footnote_list_key_suggestion) {
486

    
487
    $annotations_and_sources = array(
488
      'foot_note_keys' => NULL,
489
      'source_references' => [],
490
      'names_used_in_source' => []
491
    );
492

    
493
    // some entity types only have single sources:
494
    $sources = cdm_entity_sources_sorted($entity);
495

    
496
    if ($config['sources_as_content'] == 1) {
497
      foreach ($sources as $source) {
498
        if (_is_original_source_type($source)) {
499
          $reference_citation = render_original_source(
500
            $source,
501
            $config['link_to_reference'] == 1,
502
            $config['link_to_name_used_in_source'] == 1
503
          );
504

    
505
          if ($reference_citation) {
506
            if (empty($inline_text_prefix)) {
507
              $annotations_and_sources['source_references'][] = $reference_citation;
508
            } else {
509
              $annotations_and_sources['source_references'][] = ' (' . $reference_citation . ')';
510
            }
511
          }
512

    
513
          // also put the name in source into the array, these are already included in the $reference_citation but are
514
          // still required to be available separately in some contexts.
515
          $name_in_source_render_array = compose_name_in_source(
516
            $source,
517
            $config['link_to_name_used_in_source'] == 1
518
          );
519

    
520
          if (!empty($name_in_source_render_array)) {
521
            $annotations_and_sources['names_used_in_source'][$name_in_source_render_array['#_plaintext']] = drupal_render($name_in_source_render_array);
522
          }
523
        }
524
      } // END of loop over sources
525

    
526
      // annotations footnotes separate from sources
527
      $annotations_and_sources['foot_note_keys'] = render_footnote_keys(
528
        cdm_entity_annotations_as_footnote_keys($entity, $footnote_list_key_suggestion), ', '
529
      );
530

    
531
    } // END of references inline
532

    
533
    // footnotes for sources and annotations or put into into bibliography if requested ...
534
    if ($config['add_footnote_keys'] == 1) {
535
        $annotations_and_sources['foot_note_keys'] = render_entity_footnotes(
536
          $entity, ',',
537
          $footnote_list_key_suggestion,
538
          $config['link_to_reference'] == 1,
539
          $config['link_to_name_used_in_source'] == 1,
540
          !empty($config['bibliography_aware'])
541
        );
542
    }
543

    
544
    return $annotations_and_sources;
545
  }
546

    
547
/**
548
 * Get the source or the sources from a cdm entity and return them ordered by see compare_original_sources()
549
 * (Some entity types only have single sources)
550
 * @param $entity
551
 *
552
 * @return array
553
 */
554
function cdm_entity_sources_sorted($entity) {
555
  if (isset($entity->source) && is_object($entity->source)) {
556
    $sources = [$entity->source];
557
  }
558
  else if (isset($entity->sources)) {
559
    $sources = $entity->sources;
560
  }
561
  else {
562
    $sources = [];
563
  }
564
  usort($sources, 'compare_original_sources');
565
  return $sources;
566
}
567

    
568

    
569
/**
570
   * This method determines the footnote key for original sources to be shown in the bibliography block
571
   *
572
   * The footnote key depends on the value of the 'enabled' value of the bibliography_settings
573
   *    - enabled == 1 -> "BIBLIOGRAPHY"
574
   *    - enabled == 0 -> "BIBLIOGRAPHY-$key_suggestion"
575
   *
576
   * @see get_bibliography_settings() and @see constant BIBLIOGRAPHY_FOOTNOTE_KEY
577
   *
578
   * @param $key_suggestion string
579
   *    optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be retrieved by
580
   *    calling RenderHints::getFootnoteListKey().
581

    
582
   *
583
   * @return string
584
   *  the footnote_list_key
585
   */
586
  function bibliography_footnote_list_key($key_suggestion = null) {
587
    if(!$key_suggestion){
588
      $key_suggestion = RenderHints::getFootnoteListKey();
589
    }
590
    $bibliography_settings = get_bibliography_settings();
591
    $footnote_list_key = $bibliography_settings['enabled'] == 1 ? BIBLIOGRAPHY_FOOTNOTE_KEY : BIBLIOGRAPHY_FOOTNOTE_KEY . '-' . $key_suggestion;
592
    return $footnote_list_key;
593
  }
594

    
595
/**
596
 * Provides the according tag name for the description element markup which
597
 * fits the  $feature_block_settings['as_list'] value
598
 *
599
 * @param $feature_block_settings
600
 *   A feature_block_settings array, for details, please see
601
 *   get_feature_block_settings($feature_uuid = 'DEFAULT')
602
 *
603
 * @return mixed|string
604
 */
605
  function cdm_feature_block_element_tag_name($feature_block_settings){
606
    switch ($feature_block_settings['as_list']){
607
      case 'ul':
608
      case 'ol':
609
        return 'li';
610
      case 'div':
611
        if(isset($feature_block_settings['element_tag'])){
612
          return $feature_block_settings['element_tag'];
613
        }
614
        return 'span';
615
      case 'dl':
616
        return 'dd';
617
      default:
618
        return 'div'; // should never happen, throw error instead?
619
    }
620
  }
621

    
622

    
623
/* ==================== COMPOSE FUNCTIONS =============== */
624

    
625
  /**
626
   * Returns a set of feature blocks for a taxon profile from the $mergedFeatureNodes of a given $taxon.
627
   *
628
   * The taxon profile consists of drupal block elements, one for the description elements
629
   * of a specific feature. The structure is defined by specific FeatureTree.
630
   * The chosen FeatureTree is merged with the list of description elements prior to using this method.
631
   *
632
   * The merged nodes can be obtained by making use of the
633
   * function cdm_ws_descriptions_by_featuretree().
634
   *
635
   * @see cdm_ws_descriptions_by_featuretree()
636
   *
637
   * @param $mergedFeatureNodes
638
   *
639
   * @param $taxon
640
   *
641
   * @return array
642
   *  A Drupal render array containing feature blocks and the table of content
643
   *
644
   * @ingroup compose
645
   */
646
  function make_feature_block_list($mergedFeatureNodes, $taxon) {
647

    
648
    $block_list = array();
649

    
650
    $gallery_settings = getGallerySettings(CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME);
651

    
652
    $use_description_features = array(UUID_USE);
653

    
654

    
655
    RenderHints::pushToRenderStack('feature_block');
656
    // Create a drupal block for each feature
657
    $block_weight = - FEATURE_BLOCK_WEIGHT_INCREMENT;
658
    foreach ($mergedFeatureNodes as $feature_node) {
659

    
660
      $block_weight = $block_weight + FEATURE_BLOCK_WEIGHT_INCREMENT;
661

    
662
      if ((isset($feature_node->descriptionElements['#type']) ||
663
          has_feature_node_description_elements($feature_node)) && $feature_node->term->uuid != UUID_IMAGE) { // skip empty or suppressed features
664

    
665
        RenderHints::pushToRenderStack($feature_node->term->uuid);
666
          
667
        $feature_name = cdm_term_representation($feature_node->term, 'Unnamed Feature');
668
        $feature_block_settings = get_feature_block_settings($feature_node->term->uuid);
669
        
670

    
671
        $block = feature_block($feature_name, $feature_node->term);
672
        $block->content = array();
673
        $block_content_is_empty = TRUE;
674

    
675
        if(array_search($feature_node->term->uuid, $use_description_features) !== false) {
676
          // do not show features which belong to the UseDescriptions, these are
677
          // handled by compose_feature_block_items_use_records() where the according descriptions are
678
          // fetched again separately.
679
          // UseDescriptions are a special feature introduced for palmweb
680
          continue;
681
        }
682

    
683
        /*
684
         * Content/DISTRIBUTION.
685
         */
686
        if ($feature_node->term->uuid == UUID_DISTRIBUTION) {
687
          $block = compose_feature_block_distribution($taxon, $feature_node->descriptionElements, $feature_node->term);
688
          $block_content_is_empty = FALSE;
689
        }
690

    
691
        /*
692
         * Content/COMMON_NAME.
693
         */
694
        else if ($feature_node->term->uuid == UUID_COMMON_NAME) {
695
          $common_names_render_array = compose_feature_block_items_feature_common_name($feature_node->descriptionElements, $feature_node->term);
696
          $block->content[] = $common_names_render_array;
697
          $block_content_is_empty = FALSE;
698
        }
699

    
700
        /*
701
         * Content/Use Description (Use + UseRecord)
702
         */
703
        else if ($feature_node->term->uuid == UUID_USE_RECORD) {
704
          $block->content[] = cdm_block_use_description_content($taxon->uuid, $feature_node->term);
705
          $block_content_is_empty = FALSE;
706
        }
707

    
708
        /*
709
         * Content/ALL OTHER FEATURES.
710
         */
711
        else {
712

    
713
          $media_list = array();
714
          $elements_render_array = array();
715
          $child_elements_render_array = null;
716

    
717
          if (isset($feature_node->descriptionElements[0])) {
718
            $elements_render_array = compose_feature_block_items_generic($feature_node->descriptionElements, $feature_node->term);
719
          }
720

    
721
          // Content/ALL OTHER FEATURES/Subordinate Features
722
          // subordinate features are printed inline in one floating text,
723
          // it is expected hat subordinate features can "contain" TextData,
724
          // Qualitative- and Qualitative- DescriptionElements
725
          if (isset($feature_node->childNodes[0])) {
726
            $child_elements_render_array = compose_feature_block_items_nested($feature_node, $media_list, $feature_block_settings);
727
            $elements_render_array = array_merge($elements_render_array, $child_elements_render_array);
728
          }
729
          $block_content_is_empty = $block_content_is_empty && empty($media_list) && empty($elements_render_array);
730
          if(!$block_content_is_empty){
731
            $block->content[] = compose_feature_block_wrap_elements($elements_render_array, $feature_node->term, $feature_block_settings['glue']);
732
            $block->content[] = compose_feature_media_gallery($feature_node, $media_list, $gallery_settings);
733
            /*
734
             * Footnotes for the feature block
735
             */
736
            $block->content[] = markup_to_render_array(render_footnotes(PSEUDO_FEATURE_BIBLIOGRAPHY . '-' . $feature_node->term->uuid));
737
            $block->content[] = markup_to_render_array(render_footnotes($feature_node->term->uuid));
738
          }
739
        } // END all other features
740

    
741
        // allows modifying the block contents via a the hook_cdm_feature_node_block_content_alter
742
        drupal_alter('cdm_feature_node_block_content', $block->content, $feature_node->term, $feature_node->descriptionElements);
743

    
744
        if(!$block_content_is_empty){ // skip empty block content
745
          $block_list[$block_weight] = $block;
746
          cdm_toc_list_add_item(cdm_term_representation($feature_node->term), $feature_node->term->uuid, null, FALSE, $block_weight);
747
        } // END: skip empty block content
748
      } // END: skip empty or suppressed features
749
      RenderHints::popFromRenderStack();
750
    } // END: creating a block per feature
751

    
752
    RenderHints::popFromRenderStack();
753

    
754
    drupal_alter('cdm_feature_node_blocks', $block_list, $taxon);
755

    
756
    ksort($block_list);
757

    
758
    return  $block_list;
759
  }
760

    
761
/**
762
 * Creates a render array of description elements  held by child nodes of the given feature node.
763
 *
764
 * This function is called recursively!
765
 *
766
 * @param $feature_node
767
 *   The feature node.
768
 * @param array $media_list
769
 *   List of CDM Media entities. All media of subordinate elements should be passed to the main feature.ä
770
 * @param $feature_block_settings
771
 *   The feature block settings.
772
 * @param $main_feature
773
 *  Only used internally in recursive calls.
774
 *
775
 * @return array
776
 *  A Drupal render array
777
 *
778
 * @ingroup compose
779
 */
780
function compose_feature_block_items_nested($feature_node, &$media_list, $feature_block_settings, $main_feature = NULL)
781
{
782

    
783
  if(!$main_feature){
784
    $main_feature = $feature_node->term;
785
  }
786
  /*
787
   * TODO should be configurable, options; YES, NO, AUTOMATIC
788
   * (automatic will only place the label if the first word of the description element text is not the same)
789
   */
790
  $prepend_feature_label = false;
791

    
792
  $render_arrays = array();
793
  foreach ($feature_node->childNodes as $child_node) {
794
    if (isset($child_node->descriptionElements[0])) {
795
      foreach ($child_node->descriptionElements as $element) {
796

    
797
        if (isset($element->media[0])) {
798
          // Append media of subordinate elements to list of main
799
          // feature.
800
          $media_list = array_merge($media_list, $element->media);
801
        }
802

    
803
        $child_node_element = null;
804
        switch ($element->class) {
805
          case 'TextData':
806
            $child_node_element = compose_description_element_text_data($element, $element->feature->uuid, $feature_block_settings, $prepend_feature_label);
807
            break;
808
          case 'CategoricalData':
809
            $child_node_element = compose_description_element_categorical_data($element, $feature_block_settings, $prepend_feature_label);
810
            break;
811
          case 'QuantitativeData':
812
            $child_node_element = compose_description_element_quantitative_data($element, $feature_block_settings, $prepend_feature_label);
813

    
814
        }
815
        if (is_array($child_node_element)) {
816
          $render_arrays[] = $child_node_element;
817
        }
818
      }
819
    }
820

    
821
    if(isset($child_node->childNodes[0])){
822
      $render_arrays = array_merge($render_arrays, compose_feature_block_items_nested($child_node, $media_list, $feature_block_settings, $main_feature ));
823
    }
824
  }
825

    
826
  return $render_arrays;
827
}
828

    
829
  /**
830
   *
831
   * @param $feature_node
832
   *  The merged feature three node which potentially contains media in its description elements.
833
   * @param $media_list
834
   *    Additional media to be merged witht the media contained in the nodes description elements
835
   * @param $gallery_settings
836
   * @return array
837
   *
838
   * @ingroup compose
839
   */
840
  function compose_feature_media_gallery($feature_node, $media_list, $gallery_settings) {
841

    
842
    if (isset($feature_node->descriptionElements)) {
843
      $media_list = array_merge($media_list, cdm_dataportal_media_from_descriptionElements($feature_node->descriptionElements));
844
    }
845

    
846
    $captionElements = array('title', 'rights');
847

    
848
    if (isset($media_list[0]) && isset($gallery_settings['cdm_dataportal_media_maxextend']) && isset($gallery_settings['cdm_dataportal_media_cols'])) {
849
      $gallery = compose_cdm_media_gallerie(array(
850
        'mediaList' => $media_list,
851
        'galleryName' => CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME . '_' . $feature_node->term->uuid,
852
        'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
853
        'cols' => $gallery_settings['cdm_dataportal_media_cols'],
854
        'captionElements' => $captionElements,
855
      ));
856
      return markup_to_render_array($gallery);
857
    }
858

    
859
    return markup_to_render_array('');
860
  }
861

    
862
  /**
863
   * Composes the distribution feature block for a taxon
864
   *
865
   * @param $taxon
866
   * @param $descriptionElements
867
   *   an associative array with two elements:
868
   *   - '#type': must be 'DTO'
869
   *   - 'DistributionInfoDTO': a CDM DistributionInfoDTO object as returned by the DistributionInfo web service
870
   * @param $feature
871
   *
872
   * @return array
873
   *  A drupal render array
874
   *
875
   * @ingroup compose
876
   */
877
  function compose_feature_block_distribution($taxon, $descriptionElements, $feature) {
878
    $text_data_glue = '';
879
    $text_data_sortOutArray = FALSE;
880
    $text_data_enclosingTag = 'ul';
881
    $text_data_out_array = array();
882

    
883
    $distributionElements = NULL;
884
    $distribution_info_dto = NULL;
885
    $distribution_sortOutArray = FALSE;
886

    
887
    $feature_block_settings = get_feature_block_settings(UUID_DISTRIBUTION);
888

    
889
    // TODO use feature_block_settings instead of DISTRIBUTION_ORDER_MODE
890
    if (variable_get(DISTRIBUTION_ORDER_MODE, DISTRIBUTION_ORDER_MODE_DEFAULT) != 'TREE') {
891
      $distribution_glue = '';
892
      $distribution_enclosingTag = 'dl';
893
    } else {
894
      $distribution_glue = '';
895
      $distribution_enclosingTag = 'ul';
896
    }
897

    
898
    if (!isset($descriptionElements['#type']) || !$descriptionElements['#type'] == 'DTO') {
899
      // skip the DISTRIBUTION section if there is no DTO type element
900
      return array(); // FIXME is it ok to return an empty array?
901
    }
902

    
903
    $block = feature_block(
904
      cdm_term_representation($feature, 'Unnamed Feature'),
905
      $feature
906
    );
907
    $block->content = array();
908

    
909
    // $$descriptionElements['TextData'] is added to to the feature node in merged_taxon_feature_tree()
910
    if (isset($descriptionElements['TextData'])) {
911
      // --- TextData
912
      foreach ($descriptionElements['TextData'] as $text_data_element) {
913
        $text_data_render_array = compose_description_element_text_data($text_data_element, $text_data_element->feature->uuid, $feature_block_settings);
914
        $repr = drupal_render($text_data_render_array);
915

    
916
        if (!array_search($repr, $text_data_out_array)) { // de-duplication !!
917
          $text_data_out_array[] = $repr;
918
          // TODO HINT: sorting in compose_feature_block_wrap_elements will
919
          // not work since this array contains html attributes with uuids
920
          // and what is about cases like the bibliography where
921
          // any content can be prefixed with some foot-note anchors?
922
          $text_data_sortOutArray = TRUE;
923
          $text_data_glue = '<br/> ';
924
          $text_data_enclosingTag = 'p';
925
        }
926
      }
927
    }
928

    
929

    
930
    if ($text_data_out_array && variable_get(DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP, 0)) {
931
      $block->content[] = compose_feature_block_wrap_elements(
932
        $text_data_out_array, $feature, $text_data_glue, $text_data_sortOutArray
933
      );
934
    }
935

    
936
    // --- Distribution map
937
    $distribution_map_query_parameters = NULL;
938

    
939
    $map_visibility = variable_get(DISTRIBUTION_MAP_VISIBILITY, DISTRIBUTION_MAP_VISIBILITY_DEFAULT);
940
    if(variable_get(DISTRIBUTION_MAP_VISIBILITY, DISTRIBUTION_MAP_VISIBILITY_DEFAULT) == 'always' ||
941
        $map_visibility == 'automatic' && isset($descriptionElements['DistributionInfoDTO']->mapUriParams)
942
      )
943
    {
944
      $distribution_map_query_parameters = $descriptionElements['DistributionInfoDTO']->mapUriParams;
945
    }
946
    $map_render_element = compose_distribution_map($distribution_map_query_parameters);
947
    $block->content[] = $map_render_element;
948

    
949
    $dto_out_array = array();
950

    
951
    // --- Condensed Distribution
952
    if(variable_get(DISTRIBUTION_CONDENSED) && isset($descriptionElements['DistributionInfoDTO']->condensedDistribution)){
953
      $condensed_distribution_markup = '<p class="condensed_distribution">';
954

    
955
      $isFirst = true;
956
      if(isset($descriptionElements['DistributionInfoDTO']->condensedDistribution->indigenous[0])){
957
        foreach($descriptionElements['DistributionInfoDTO']->condensedDistribution->indigenous as $cdItem){
958
          if(!$isFirst){
959
            $condensed_distribution_markup .= ' ';
960
          }
961
          $condensed_distribution_markup .= '<span class="status_' . $cdItem->status->idInVocabulary . '">'
962
          . $cdItem->areaStatusLabel . '</span>';
963
          $isFirst = false;
964
        }
965
      }
966

    
967
      if(isset($descriptionElements['DistributionInfoDTO']->condensedDistribution->foreign[0])) {
968
        if(!$isFirst){
969
          $condensed_distribution_markup .= ' ';
970
        }
971
        $isFirst = TRUE;
972
        $condensed_distribution_markup .= '[';
973
        foreach ($descriptionElements['DistributionInfoDTO']->condensedDistribution->foreign as $cdItem) {
974
          if (!$isFirst) {
975
            $condensed_distribution_markup .= ' ';
976
          }
977
          $condensed_distribution_markup .= '<span class="status_' . $cdItem->status->titleCache . '">'
978
            . $cdItem->areaStatusLabel . '</span>';
979
          $isFirst = false;
980
        }
981
        $condensed_distribution_markup .= ']';
982
      }
983

    
984
      $condensed_distribution_markup .= '&nbsp;' . l(
985
          font_awesome_icon_markup(
986
            'fa-info-circle',
987
            array(
988
              'alt'=>'help',
989
              'class' => array('superscript')
990
            )
991
          ),
992
          variable_get(DISTRIBUTION_CONDENSED_INFO_PATH, DISTRIBUTION_CONDENSED_INFO_PATH_DEFAULT) ,
993
          array('html' => TRUE));
994
      $condensed_distribution_markup .= '</p>';
995
      $dto_out_array[] = $condensed_distribution_markup;
996
    }
997

    
998
    // --- tree or list
999
    if (isset($descriptionElements['DistributionInfoDTO'])) {
1000
      $distribution_info_dto = $descriptionElements['DistributionInfoDTO'];
1001

    
1002
      // --- tree
1003
      if (is_object($distribution_info_dto->tree)) {
1004
        $distribution_tree_render_array = compose_distribution_hierarchy($distribution_info_dto->tree, $feature_block_settings);
1005
        $dto_out_array[] = $distribution_tree_render_array;
1006
      }
1007

    
1008
      // --- sorted element list
1009
      if (is_array($distribution_info_dto->elements) && count($distribution_info_dto->elements) > 0) {
1010
        foreach ($distribution_info_dto->elements as $descriptionElement) {
1011
          if (is_object($descriptionElement->area)) {
1012
            $sortKey = $descriptionElement->area->representation_L10n;
1013
            $distributionElements[$sortKey] = $descriptionElement;
1014
          }
1015
        }
1016
        ksort($distributionElements);
1017
        $distribution_element_render_array = compose_description_elements_distribution($distributionElements);
1018
        $dto_out_array[] = $distribution_element_render_array;
1019

    
1020
      }
1021
      //
1022
      $block->content[] = compose_feature_block_wrap_elements(
1023
        $dto_out_array, $feature, $distribution_glue, $distribution_sortOutArray
1024
      );
1025
    }
1026

    
1027
    // --- TextData at the bottom
1028
    if ($text_data_out_array && !variable_get(DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP, 0)) {
1029
      $block->content[] = compose_feature_block_wrap_elements(
1030
        $text_data_out_array, $feature, $text_data_glue, $text_data_sortOutArray
1031
      );
1032
    }
1033

    
1034
    $block->content[] = markup_to_render_array(render_footnotes('BIBLIOGRAPHY-' . UUID_DISTRIBUTION));
1035
    $block->content[] = markup_to_render_array(render_footnotes(UUID_DISTRIBUTION));
1036

    
1037
    return $block;
1038
  }
1039

    
1040

    
1041
  /**
1042
   * Composes a drupal render array for single CDM TextData description element.
1043
   *
1044
   * @param $element
1045
   *    The CDM TextData description element.
1046
   *  @param $feature_uuid
1047
   * @param bool $prepend_feature_label
1048
   *   Used in nested feature trees to put the feature as label in front of the description element text representation.
1049
   *
1050
   * @return array
1051
   *   A drupal render array with the following elements being used:
1052
   *    - #tag: either 'div', 'li', ...
1053
   *    ⁻ #attributes: class attributes
1054
   *    - #value_prefix: (optionally) contains footnote anchors
1055
   *    - #value: contains the textual content
1056
   *    - #value_suffix: (optionally) contains footnote keys
1057
   *
1058
   * @ingroup compose
1059
   */
1060
  function compose_description_element_text_data($element, $feature_uuid, $feature_block_settings, $prepend_feature_label = FALSE) {
1061

    
1062
    $footnote_list_key_suggestion = $feature_uuid;
1063

    
1064
    $element_markup = '';
1065
    if (isset($element->multilanguageText_L10n->text)) {
1066
      // TODO replacement of \n by <br> should be configurable
1067
      $element_markup = str_replace("\n", "<br/>", $element->multilanguageText_L10n->text);
1068
    }
1069

    
1070
    $render_array = compose_description_element($element, $feature_block_settings, $element_markup, $footnote_list_key_suggestion, $prepend_feature_label);
1071

    
1072
    return $render_array;
1073
  }
1074

    
1075

    
1076
/**
1077
 * Theme function to render CDM DescriptionElements of the type TaxonInteraction.
1078
 *
1079
 * @param $element
1080
 *  The CDM TaxonInteraction entity
1081
 *
1082
 * @return
1083
 *  A drupal render array
1084
 *
1085
 * @ingroup compose
1086
 */
1087
function compose_description_element_taxon_interaction($element, $feature_block_settings) {
1088

    
1089
  $out = '';
1090

    
1091

    
1092
  if (isset($element->description_L10n)) {
1093
    $out .=  ' ' . $element->description_L10n;
1094
  }
1095

    
1096
  if(isset($element->taxon2)){
1097
    $out = render_taxon_or_name($element->taxon2, url(path_to_taxon($element->taxon2->uuid)));
1098
  }
1099

    
1100
  $render_array = compose_description_element($element, $feature_block_settings, $out, $element->feature->uuid);
1101

    
1102
  return $render_array;
1103
}
1104

    
1105

    
1106
/**
1107
 * Renders a single instance of the type IndividualsAssociations.
1108
 *
1109
 * @param $element
1110
 *   The CDM IndividualsAssociations entity.
1111
 * @param $feature_block_settings
1112
 *
1113
 * @return array
1114
 *   Drupal render array
1115
 *
1116
 * @ingroup compose
1117
 */
1118
function compose_description_element_individuals_association($element, $feature_block_settings) {
1119

    
1120
  $out = '';
1121

    
1122
  $render_array = compose_cdm_specimen_or_observation($element->associatedSpecimenOrObservation);
1123

    
1124
  if (isset($element->description_L10n)) {
1125
    $out .=  ' ' . $element->description_L10n;
1126
  }
1127

    
1128
  $out .= drupal_render($render_array);
1129

    
1130
  $render_array = compose_description_element($element, $feature_block_settings, $out, $element->feature->uuid);
1131

    
1132
  return $render_array;
1133
}
1134

    
1135
/**
1136
 * Renders a single instance of the type CategoricalData.
1137
 *
1138
 * @param $element
1139
 *  The CDM CategoricalData entity
1140
 *
1141
 * @param $feature_block_settings
1142
 *
1143
 * @param bool $prepend_feature_label
1144
 *   Used in nested feature trees to put the feature as label in front of the description element text representation.
1145
 *
1146
 * @return array
1147
 *   a drupal render array for given CategoricalData element
1148
 *
1149
 * @ingroup compose
1150
 */
1151
function compose_description_element_categorical_data($element, $feature_block_settings, $prepend_feature_label = FALSE) {
1152

    
1153
  $state_data_markup = render_state_data($element);
1154

    
1155
  $render_array = compose_description_element($element, $feature_block_settings, $state_data_markup, $element->feature->uuid, $prepend_feature_label);
1156

    
1157
  return $render_array;
1158
}
1159

    
1160
/**
1161
 * @param $element
1162
 *
1163
 * @return string
1164
 * the markup
1165
 */
1166
function render_state_data($element) {
1167

    
1168
  $state_data_items = [];
1169

    
1170
  $out = '';
1171

    
1172
  if (isset($element->stateData)) {
1173
    foreach ($element->stateData as $state_data) {
1174

    
1175
      $state = NULL;
1176

    
1177
      if (isset($state_data->state)) {
1178
        $state = cdm_term_representation($state_data->state);
1179

    
1180
          $sample_count = 0;
1181
          if (isset($state_data->count)) {
1182
            $sample_count = $state_data->count;
1183
            $state .= ' [' . $state_data->count . ']';
1184
          }
1185
    
1186
          if (isset($state_data->modifyingText_L10n)) {
1187
            $state .= ' ' . $state_data->modifyingText_L10n;
1188
          }
1189
    
1190
          $modifiers_strings = cdm_modifiers_representations($state_data);
1191
          $state_data_markup = $state . ($modifiers_strings ? ' ' . $modifiers_strings : '');
1192
          // we could use strip_tags() to reduce the markup to text for the key but this is expensive
1193
          $sort_key = str_pad($sample_count, 6, '0', STR_PAD_LEFT) . '_' . $state_data_markup;
1194
          $state_data_items[$sort_key] = $state_data_markup;
1195
      }
1196

    
1197
    }
1198
    krsort($state_data_items);
1199
    $out = '<span class="' . html_class_attribute_ref($element) . '">' . join(', ', $state_data_items) .  '</span>';
1200
  }
1201
  return $out;
1202
}
1203

    
1204

    
1205
/**
1206
 * Theme function to render CDM DescriptionElements of the type QuantitativeData.
1207
 *
1208
 * The function renders the statisticalValues contained in the QuantitativeData
1209
 * entity according to the following scheme:
1210
 *
1211
 * (ExtremeMin)-Min-Average-Max-(ExtremeMax)
1212
 *
1213
 * All modifiers of these values are appended.
1214
 *
1215
 * If the QuantitativeData is containing more statisticalValues with further
1216
 * statisticalValue types, these additional measures will be appended to the
1217
 * above string separated by whitespace.
1218
 *
1219
 * Special cases;
1220
 * 1. Min==Max: this will be interpreted as Average
1221
 *
1222
 * @param $element
1223
 *  The CDM QuantitativeData entity
1224
 *
1225
 * @param $feature_block_settings
1226
 *
1227
 * @param bool $prepend_feature_label
1228
 *   Used in nested feature trees to put the feature as label in front of the description element text representation.
1229
 *
1230
 *
1231
 * @return array
1232
 *   drupal render array for the given QuantitativeData element
1233
 *
1234
 * @ingroup compose
1235
 */
1236
function compose_description_element_quantitative_data($element, $feature_block_settings, $prepend_feature_label = FALSE) {
1237
  /*
1238
   * - statisticalValues
1239
   *   - value
1240
   *   - modifiers
1241
   *   - type
1242
   * - unit->representation_L10n
1243
   * - modifyingText
1244
   * - modifiers
1245
   * - sources
1246
   */
1247

    
1248
  $out = render_quantitative_statistics($element);
1249

    
1250
  $render_array = compose_description_element($element, $feature_block_settings, $out, $element->feature->uuid, $prepend_feature_label);
1251

    
1252
  return $render_array;
1253
}
1254

    
1255
/**
1256
 * Composes the HTML for quantitative statistics
1257
 * @param $element
1258
 *
1259
 * @return string
1260
 */
1261
function render_quantitative_statistics($element) {
1262

    
1263
  $out = '';
1264
  $type_representation = NULL;
1265
  $min_max = statistical_values_array();
1266
  $sample_size_markup = null;
1267

    
1268
  if (isset($element->statisticalValues)) {
1269
    $out = '<span class=\"' . html_class_attribute_ref($element) . '\">';
1270
    $other_values_markup = [];
1271
    foreach ($element->statisticalValues as $statistical_val) {
1272

    
1273
      // compile the full value string which also may contain modifiers
1274
      if (isset($statistical_val->value)) {
1275
        $statistical_val->_value = $statistical_val->value;
1276
      }
1277
      $val_modifiers_strings = cdm_modifiers_representations($statistical_val);
1278
      if ($val_modifiers_strings) {
1279
        $statistical_val->_value = ' ' . $val_modifiers_strings . ' ' . $statistical_val->_value;
1280
      }
1281

    
1282
      // either put into min max array or into $other_values
1283
      // for generic output to be appended to 'min-max' string
1284
      if (array_key_exists(statistical_measure_term2min_max_key($statistical_val->type), $min_max)) {
1285
        $min_max[statistical_measure_term2min_max_key($statistical_val->type)] = $statistical_val;
1286
      }
1287
      else {
1288
        drupal_set_message("Unsupported statistical value type: " . $statistical_val->type->uuid, "error");
1289
      }
1290
    } // end of loop over statisticalValues
1291

    
1292
    // create markup
1293
    $unit = null;
1294
    if (isset($element->unit)) {
1295
      $unit = ' <span class="unit" title="'
1296
        . cdm_term_representation($element->unit) . '">'
1297
        . cdm_term_representation_abbreviated($element->unit)
1298
        . '</span>';
1299
    }
1300
    $min_max_markup = statistical_values($min_max, $unit);
1301
    $out .= $min_max_markup . '</span>';
1302
  }
1303

    
1304
  if($sample_size_markup){
1305
    $out .= ' ' . $sample_size_markup;
1306

    
1307
  }
1308

    
1309
  // modifiers of the description element itself
1310
  $modifier_string = cdm_modifiers_representations($element);
1311
  $out .= ($modifier_string ? ' ' . $modifier_string : '');
1312
  if (isset($element->modifyingText_L10n)) {
1313
    $out = $element->modifyingText_L10n . ' ' . $out;
1314
  }
1315
  return $out;
1316
}
1317

    
1318
function statistical_measure_term2min_max_key($term){
1319
  static $uuid2key = [
1320
    UUID_STATISTICALMEASURE_MIN => 'Min',
1321
    UUID_STATISTICALMEASURE_MAX => 'Max',
1322
    UUID_STATISTICALMEASURE_AVERAGE => 'Average',
1323
    UUID_STATISTICALMEASURE_SAMPLESIZE => 'SampleSize',
1324
    UUID_STATISTICALMEASURE_VARIANCE => 'Variance',
1325
    UUID_STATISTICALMEASURE_TYPICALLOWERBOUNDARY => 'TypicalLowerBoundary',
1326
    UUID_STATISTICALMEASURE_TYPICALUPPERBOUNDARY => 'TypicalUpperBoundary',
1327
    UUID_STATISTICALMEASURE_STANDARDDEVIATION => 'StandardDeviation',
1328
    UUID_STATISTICALMEASURE_EXACTVALUE => 'ExactValue',
1329
    UUID_STATISTICALMEASURE_STATISTICALMEASUREUNKNOWNDATA => 'StatisticalMeasureUnknownData'
1330
  ];
1331
  return $uuid2key[$term->uuid];
1332
}
1333

    
1334

    
1335
/**
1336
 * Wraps the render array for the given feature into an enclosing html tag.
1337
 *
1338
 * Optionally the elements can be sorted and glued together by a separator string.
1339
 *
1340
 * @param array $description_element_render_arrays
1341
 *   An list of render arrays. Which are usually are produced by the compose_description_element()
1342
 *   function. The render arrays should be of #type=html_tag, so that they can understand the #attribute property.
1343
 * @param  $feature :
1344
 *  The feature to which the elements given in $elements are belonging to.
1345
 * @param string $glue :
1346
 *  Defaults to empty string.
1347
 * @param bool $sort
1348
 *   Boolean Whether to sort the $elements alphabetically, default is FALSE
1349
 *
1350
 * @return array
1351
 *    A Drupal render array
1352
 *
1353
 * @ingroup compose
1354
 */
1355
  function compose_feature_block_wrap_elements(array $description_element_render_arrays, $feature, $glue = '', $sort = FALSE)
1356
  {
1357

    
1358
    $feature_block_settings = get_feature_block_settings($feature->uuid);
1359
    $enclosing_tag = $feature_block_settings['as_list'];
1360

    
1361
    if ($sort) { // TODO remove parameter and replace by $feature_block_settings['sort_elements']
1362
      usort($description_element_render_arrays, 'compare_description_element_render_arrays');
1363
    }
1364

    
1365
    $is_first = true;
1366
    foreach($description_element_render_arrays as &$element_render_array){
1367
      if(!is_array($element_render_array)){
1368
        $element_render_array = markup_to_render_array($element_render_array);
1369
      }
1370
      $element_render_array['#attributes']['class'][] = "feature-block-element";
1371

    
1372
      // add the glue!
1373
      if(!$is_first) {
1374
        if (isset($element_render_array['#value'])) {
1375
          $element_render_array['#value'] = $glue . $element_render_array['#value'];
1376
        } elseif (isset($element_render_array['#markup'])) {
1377
          $element_render_array['#markup'] = $glue . $element_render_array['#markup'];
1378
        }
1379
      }
1380
      $is_first = false;
1381
    }
1382

    
1383
    $render_array['elements']['children'] = $description_element_render_arrays;
1384

    
1385
    $render_array['elements']['#prefix'] = '<' . $enclosing_tag . ' class="feature-block-elements" id="' . $feature->representation_L10n . '">';
1386
    $render_array['elements']['#suffix'] = '</' . $enclosing_tag . '>';
1387

    
1388
    return $render_array;
1389
  }
1390

    
1391

    
1392
  /* compose nameInSource or originalNameString as markup
1393
   *
1394
   * @param $source
1395
   * @param $do_link_to_name_used_in_source
1396
   * @param $suppress_for_shown_taxon
1397
   *    the nameInSource will be suppressed when it has the same name as the accepted taxon
1398
   *    for which the taxon page is being created, Defaults to TRUE
1399
   *
1400
   * @return array
1401
   *    A Drupal render array with an additional element, the render array is empty
1402
   *    if the source had no name in source information
1403
   *    - #_plaintext: contains the plaintext version of the name (custom element)
1404
   *
1405
   * @ingroup compose
1406
   */
1407
  function compose_name_in_source($source, $do_link_to_name_used_in_source, $suppress_for_shown_taxon = TRUE) {
1408

    
1409
    $plaintext = NULL;
1410
    $markup = NULL;
1411
    $name_in_source_render_array = array();
1412

    
1413
    static $taxon_page_accepted_name = '';
1414
    $taxon_uuid = get_current_taxon_uuid();
1415
    if($suppress_for_shown_taxon && $taxon_uuid && empty($taxon_page_accepted_name)){
1416

    
1417
      $current_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $taxon_uuid);
1418
      $taxon_page_accepted_name = $current_taxon->name->titleCache;
1419
    }
1420

    
1421
    if (isset($source->nameUsedInSource->uuid) && isset($source->nameUsedInSource->titleCache)) {
1422
      // it is a DescriptionElementSource !
1423
      $plaintext = $source->nameUsedInSource->titleCache;
1424
      if($suppress_for_shown_taxon && $taxon_page_accepted_name == $plaintext){
1425
        return $name_in_source_render_array; // SKIP this name
1426
      }
1427
      $markup = render_taxon_or_name($source->nameUsedInSource);
1428
      if ($do_link_to_name_used_in_source) {
1429
        $markup = l(
1430
          $markup,
1431
          path_to_name($source->nameUsedInSource->uuid),
1432
          array(
1433
            'attributes' => array(),
1434
            'absolute' => TRUE,
1435
            'html' => TRUE,
1436
          ));
1437
      }
1438
    }
1439
    else if (isset($source->originalNameString) && !empty($source->originalNameString)) {
1440
      // the name used in source can not be expressed as valid taxon name,
1441
      // so the editor has chosen to put the freetext name into ReferencedEntityBase.originalNameString
1442
      // field
1443
      // using the originalNameString as key to avoid duplicate entries
1444
      $plaintext = $source->originalNameString;
1445
      if($suppress_for_shown_taxon && $taxon_page_accepted_name == $plaintext){
1446
        return $name_in_source_render_array; // SKIP this name
1447
      }
1448
      $markup = $source->originalNameString;
1449
    }
1450

    
1451
    if ($plaintext) { // checks if we have any content
1452
      $name_in_source_render_array = markup_to_render_array($markup);
1453
      $name_in_source_render_array['#_plaintext'] = $plaintext;
1454
    }
1455

    
1456
    return $name_in_source_render_array;
1457
  }
1458

    
1459

    
1460

    
1461
  /**
1462
   * Return HTML for a list of description elements.
1463
   *
1464
   * Usually these are of a specific feature type.
1465
   *
1466
   * @param $description_elements
1467
   *   array of descriptionElements which belong to the same feature.
1468
   *   These descriptions elements of a Description must be ordered by the chosen feature tree by
1469
   *   calling the function _mergeFeatureTreeDescriptions().
1470
   *   @see _mergeFeatureTreeDescriptions()
1471
   *
1472
   * @param  $feature_uuid
1473
   *
1474
   * @return
1475
   *    A drupal render array for the $descriptionElements, may be an empty array if the textual content was empty.
1476
   *    Footnote key or anchors are not considered to be textual content.
1477
   *
1478
   * @ingroup compose
1479
   */
1480
  function compose_feature_block_items_generic($description_elements, $feature) {
1481

    
1482
    $elements_out_array = array();
1483
    $distribution_tree = null;
1484

    
1485
    /*
1486
     * $feature_block_has_content will be set true if at least one of the
1487
     * $descriptionElements contains some text which makes up some content
1488
     * for the feature block. Footnote keys are not considered
1489
     * to be content in this sense.
1490
     */
1491
    $feature_block_has_content = false;
1492

    
1493
    if (is_array($description_elements)) {
1494
      foreach ($description_elements as $description_element) {
1495
          /* decide based on the description element class
1496
           *
1497
           * Features handled here:
1498
           * all except DISTRIBUTION, COMMON_NAME, USES, IMAGES,
1499
           *
1500
           * TODO provide api_hook as extension point for this?
1501
           */
1502
        $feature_block_settings = get_feature_block_settings($description_element->feature->uuid);
1503
        switch ($description_element->class) {
1504
          case 'TextData':
1505
            $elements_out_array[] = compose_description_element_text_data($description_element, $description_element->feature->uuid, $feature_block_settings);
1506
            break;
1507
          case 'CategoricalData':
1508
            $elements_out_array[] = compose_description_element_categorical_data($description_element, $feature_block_settings);
1509
            break;
1510
          case 'QuantitativeData':
1511
            $elements_out_array[] = compose_description_element_quantitative_data($description_element, $feature_block_settings);
1512
            break;
1513
          case 'IndividualsAssociation':
1514
            $elements_out_array[] = compose_description_element_individuals_association($description_element, $feature_block_settings);
1515
            break;
1516
          case 'TaxonInteraction':
1517
            $elements_out_array[] = compose_description_element_taxon_interaction($description_element, $feature_block_settings);
1518
            break;
1519
          case 'CommonTaxonName':
1520
            $elements_out_array[] = compose_description_element_common_taxon_name($description_element, $feature_block_settings);
1521
            break;
1522
          case 'Uses':
1523
            /* IGNORE Uses classes, these are handled completely in compose_feature_block_items_use_records()  */
1524
            break;
1525
          default:
1526
            $feature_block_has_content = true;
1527
            $elements_out_array[] = markup_to_render_array('<li>No method for rendering unknown description class: ' . $description_element->class . '</li>');
1528
        }
1529
        $elements_out_array_last_item = $elements_out_array[count($elements_out_array) - 1];
1530
        // considering not empty as long as the last item added is a render array
1531
        $feature_block_has_content = $feature_block_has_content || !empty($elements_out_array_last_item['#type']);
1532
      }
1533

    
1534
      // If feature = CITATION sort the list of sources.
1535
      // This is ONLY for FLORA MALESIANA and FLORE d'AFRIQUE CENTRALE.
1536
      if (isset($description_element) && $description_element->feature->uuid == UUID_CITATION) {
1537
        sort($elements_out_array);
1538
      }
1539
    }
1540

    
1541
    // sanitize: remove empty and NULL items from the render array
1542
    $tmp_out_array = $elements_out_array;
1543
    $elements_out_array = array();
1544
    foreach($tmp_out_array as $item){
1545
      if(is_array($item) && count($item) > 0){
1546
        $elements_out_array[] = $item;
1547
      }
1548
    }
1549

    
1550
    return $elements_out_array;
1551
  }
1552

    
1553
/**
1554
 * Composes block of common names for the given DescriptionElements $elements which must be of the feature CommonName
1555
 *
1556
 * @parameter $elements
1557
 *  an array of CDM DescriptionElements either of type CommonName or TextData
1558
 * @parameter $feature
1559
 *  the common feature of all $elements, must be CommonName
1560
 *
1561
 * @return
1562
 *   A drupal render array
1563
 *
1564
 * @ingroup compose
1565
 */
1566
function compose_feature_block_items_feature_common_name($elements, $feature, $weight = FALSE) {
1567

    
1568
  $common_name_out = '';
1569
  $common_name_feature_elements = array();
1570
  $textData_commonNames = array();
1571

    
1572
  $footnote_key_suggestion = 'common-names-feature-block';
1573

    
1574
  $feature_block_settings = get_feature_block_settings(UUID_COMMON_NAME);
1575

    
1576
  if (is_array($elements)) {
1577
    foreach ($elements as $element) {
1578

    
1579
      if ($element->class == 'CommonTaxonName') {
1580

    
1581
        // common name without a language or area, should not happen but is possible
1582
        $language_area_key = '';
1583
        if (isset($element->language->representation_L10n)) {
1584
          $language_area_key .= $element->language->representation_L10n ;
1585
        }
1586
        if(isset($element->area->titleCache) && strlen($element->area->titleCache) > 0){
1587
          $language_area_key .= ($language_area_key ? ' '  : '') . '(' . $element->area->titleCache . ')';
1588
        }
1589
        if($language_area_key){
1590
          $language_area_key = '<span class="language-area-label">' . $language_area_key . '<span class="separator">: </span></span>';
1591
        }
1592

    
1593
        if(isset($common_names[$language_area_key][$element->name])) {
1594
          // same name already exists for language and area combination, se we merge the description elements
1595
          cdm_merge_description_elements($common_names[$language_area_key][$element->name], $element);
1596
        } else{
1597
          // otherwise add as new entry
1598
          $common_names[$language_area_key][$element->name] = $element;
1599
        }
1600

    
1601
      }
1602
      elseif ($element->class == 'TextData') {
1603
        $textData_commonNames[] = $element;
1604
      }
1605
    }
1606
  }
1607
  // Handling common names.
1608
  if (isset($common_names) && count($common_names) > 0) {
1609
    // Sorting the array based on the key (language, + area if set).
1610
    // Comment @WA there are common names without a language, so this sorting
1611
    // can give strange results.
1612
    ksort($common_names);
1613

    
1614
    // loop over set of elements per language area
1615
    foreach ($common_names as $language_area_key => $elements) {
1616
      ksort($elements); // sort names alphabetically
1617
      $per_language_area_out = array();
1618

    
1619
      foreach ($elements as $element) {
1620
        $common_name_render_array = compose_description_element_common_taxon_name($element, $feature_block_settings, $footnote_key_suggestion);
1621
        $common_name_markup = drupal_render($common_name_render_array);
1622
        // IMPORTANT!
1623
        // during the above drupal_render the theme_html_tag function is executed, which adds a "\n" character to the end of the markup
1624
        // this is an error and the trailing whitespace needs to be removed
1625
        if(str_endsWith($common_name_markup, "\n")){
1626
          $common_name_markup = substr($common_name_markup, 0, strlen($common_name_markup) - 1);
1627
        }
1628
        $per_language_area_out[] = $common_name_markup;
1629
      }
1630

    
1631
      $common_name_feature_elements[] = $language_area_key . join(', ', $per_language_area_out);
1632
    } // End of loop over set of elements per language area
1633

    
1634

    
1635
    $common_name_feature_elements_render_array = compose_feature_block_wrap_elements(
1636
      $common_name_feature_elements, $feature, '; ', FALSE
1637
    );
1638
    $common_name_out .= drupal_render($common_name_feature_elements_render_array); // FIXME should this be a render array instead?
1639

    
1640
  }
1641

    
1642
  // Handling commons names as text data.
1643
  $text_data_out = array();
1644

    
1645
  foreach ($textData_commonNames as $text_data_element) {
1646
    /* footnotes are not handled correctly in compose_description_element_text_data,
1647
       need to set 'common-names-feature-block' as $footnote_key_suggestion */
1648
    RenderHints::setFootnoteListKey($footnote_key_suggestion);
1649
    $text_data_render_array = compose_description_element_text_data($text_data_element, $text_data_element->feature->uuid, $feature_block_settings);
1650
    $text_data_out[] = drupal_render($text_data_render_array);
1651
  }
1652

    
1653
  $common_name_out_text_data = compose_feature_block_wrap_elements(
1654
    $text_data_out, $feature
1655
  );
1656

    
1657
  $footnotes = render_footnotes('BIBLIOGRAPHY-' . $footnote_key_suggestion);
1658
  $footnotes .= render_footnotes($footnote_key_suggestion);
1659

    
1660
  return  markup_to_render_array(  // FIXME markup_to_render_array should no longer be needed
1661
    '<div class="common-taxon-name">' . $common_name_out . '</div>'
1662
    .'<div class="text-data">' . drupal_render($common_name_out_text_data) . '</div>'
1663
    .$footnotes,
1664
    $weight
1665
  );
1666
}
1667

    
1668
/**
1669
 * Renders a single instance of the type CommonTaxonName.
1670
 *
1671
 * @param $element
1672
 *   The CDM CommonTaxonName entity.
1673
 * @param $feature_block_settings
1674
 *
1675
 * @param $footnote_key_suggestion
1676
 *
1677
 * @param $element_tag_name
1678
 *
1679
 * @return array
1680
 *   Drupal render array
1681
 *
1682
 * @ingroup compose
1683
 */
1684
function compose_description_element_common_taxon_name($element, $feature_block_settings, $footnote_key_suggestion = NULL)
1685
{
1686

    
1687
  if(!$footnote_key_suggestion) {
1688
    $footnote_key_suggestion = $element->feature->uuid;
1689
  }
1690

    
1691
  $name = '';
1692
  if(isset($element->name)){
1693
    $name = $element->name;
1694
  }
1695

    
1696

    
1697
  return compose_description_element($element, $feature_block_settings, $name, $footnote_key_suggestion);
1698
}
1699

    
1700
/**
1701
 * Composes the render array for a CDM Distribution description element
1702
 *
1703
 * @param array $description_elements
1704
 *   Array of CDM Distribution instances
1705
 * @param $enclosingTag
1706
 *   The html tag to be use for the enclosing element
1707
 *
1708
 * @return array
1709
 *   A Drupal render array
1710
 *
1711
 * @ingroup compose
1712
 */
1713
function compose_description_elements_distribution($description_elements){
1714

    
1715
  $markup_array = array();
1716
  RenderHints::pushToRenderStack('descriptionElementDistribution');
1717
  RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);
1718

    
1719
  $feature_block_settings = get_feature_block_settings(UUID_DISTRIBUTION);
1720
  $enclosingTag = cdm_feature_block_element_tag_name($feature_block_settings);
1721

    
1722
  foreach ($description_elements as $description_element) {
1723
    $annotations_and_sources = handle_annotations_and_sources(
1724
      $description_element,
1725
      handle_annotations_and_sources_config($feature_block_settings),
1726
      $description_element->area->representation_L10n,
1727
      UUID_DISTRIBUTION
1728
    );
1729

    
1730

    
1731
    $status = distribution_status_label_and_markup([$description_element]);
1732

    
1733
    $out = '';
1734
    $out .= '<' . $enclosingTag . ' class="descriptionElement descriptionElement-' . $description_element->uuid
1735
      . ' " title="' . $status['label']. '">'
1736
      . $description_element->area->representation_L10n
1737
      . $status['markup'];
1738
    if(!empty($annotations_and_sources['source_references'])){
1739
      $out .= ' ' . join(' ', $annotations_and_sources['source_references'] );
1740
    }
1741
    $out .= $annotations_and_sources['foot_note_keys']   . '</' . $enclosingTag . '>';
1742
    $markup_array[] = $out;
1743
  }
1744

    
1745
  RenderHints::popFromRenderStack();
1746
  return markup_to_render_array(join('<span class="separator">' . $feature_block_settings['glue'] . '</span>', $markup_array));
1747
}
1748

    
1749
  /**
1750
   * @param array $distribution_status
1751
   * @return array an array with following keys
1752
   *   - 'label': the plain text status label
1753
   *   - 'markup': markup for the status
1754
   */
1755
  function distribution_status_label_and_markup(array $distribution_status, $status_glue = '&#8210; ') {
1756

    
1757
    $status_markup = '';
1758
    $status_label = '';
1759

    
1760
    foreach($distribution_status as $status) {
1761
      $status_label .= ($status_label ? $status_glue : '') . $status->representation_L10n;
1762
      $status_markup .=  '<span class="distributionStatus"> '
1763
        . ($status_markup ? $status_glue : '')
1764
        . '<span class="distributionStatus-' . $status->idInVocabulary . '">'
1765
        .  $status->representation_L10n
1766
        . '</span></span>';
1767

    
1768
    };
1769
    return ['label' => $status_label, 'markup' => $status_markup];
1770
  }
1771

    
1772

    
1773
  /**
1774
   * Provides the merged feature tree for a taxon profile page.
1775
   *
1776
   * The merging of the profile feature tree is actually done in
1777
   * _mergeFeatureTreeDescriptions(). See this method  for details
1778
   * on the structure of the merged tree.
1779
   *
1780
   * This method provides a hook which can be used to modify the
1781
   * merged feature tree after it has been created, see
1782
   * hook_merged_taxon_feature_tree_alter()
1783
   *
1784
   * @param $taxon
1785
   *    A CDM Taxon instance
1786
   *
1787
   * @return object
1788
   *    The merged feature tree
1789
   *
1790
   */
1791
  function merged_taxon_feature_tree($taxon) {
1792

    
1793
    // 1. fetch descriptions_by_featuretree but exclude the distribution feature
1794
    $merged_tree = cdm_ws_descriptions_by_featuretree(get_profile_feature_tree(), $taxon->uuid, array(UUID_DISTRIBUTION));
1795

    
1796

    
1797
    // 2. find the distribution feature node
1798
    $distribution_node =& cdm_feature_tree_find_node($merged_tree->root->childNodes, UUID_DISTRIBUTION);
1799

    
1800
    if ($distribution_node) {
1801
      // 3. get the distributionInfoDTO
1802
      $query_parameters = cdm_distribution_filter_query();
1803
      $query_parameters['part'] = array('mapUriParams');
1804
      if(variable_get(DISTRIBUTION_CONDENSED)){
1805
        $query_parameters['part'][] = 'condensedDistribution';
1806
      }
1807
      if (variable_get(DISTRIBUTION_ORDER_MODE, DISTRIBUTION_ORDER_MODE_DEFAULT) == 'TREE') {
1808
        $query_parameters['part'][] = 'tree';
1809
      }
1810
      else {
1811
        $query_parameters['part'][] = 'elements';
1812
      }
1813
      $query_parameters['omitLevels'] = array();
1814
      foreach(variable_get(DISTRIBUTION_TREE_OMIT_LEVELS, array()) as $uuid){
1815
        if(is_uuid($uuid)){
1816
          $query_parameters['omitLevels'][] = $uuid;
1817
        }
1818
      }
1819
      $customStatusColorsJson = variable_get(DISTRIBUTION_STATUS_COLORS, NULL);
1820
      if ($customStatusColorsJson) {
1821
        $query_parameters['statusColors'] = $customStatusColorsJson;
1822
      }
1823

    
1824
      $distribution_info_dto = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION_DISTRIBUTION_INFO_FOR, $taxon->uuid, queryString($query_parameters));
1825
      // 4. get distribution TextData is there are any
1826
      $distribution_text_data = cdm_ws_fetch_all(CDM_WS_DESCRIPTIONELEMENT_BY_TAXON,
1827
        array(
1828
          'taxon' => $taxon->uuid,
1829
          'type' => 'TextData',
1830
          'features' => UUID_DISTRIBUTION
1831
        )
1832
      );
1833

    
1834
      // 5. put all distribution data into the distribution feature node
1835
      if ($distribution_text_data //if text data exists
1836
        || ($distribution_info_dto && isset($distribution_info_dto->tree) && $distribution_info_dto->tree->rootElement->numberOfChildren > 0) // OR if tree element has distribution elements
1837
        || ($distribution_info_dto && !empty($distribution_info_dto->elements))
1838
      ) { // OR if DTO has distribution elements
1839
        $distribution_node->descriptionElements = array('#type' => 'DTO');
1840
        if ($distribution_text_data) {
1841
          $distribution_node->descriptionElements['TextData'] = $distribution_text_data;
1842
        }
1843
        if ($distribution_info_dto) {
1844
          $distribution_node->descriptionElements['DistributionInfoDTO'] = $distribution_info_dto;
1845
        }
1846
      }
1847
    }
1848

    
1849
    // allows modifying the merged tree via a the hook_cdm_feature_node_block_content_alter
1850
    drupal_alter('merged_taxon_feature_tree', $taxon, $merged_tree);
1851

    
1852
    return $merged_tree;
1853
  }
1854

    
1855
  /**
1856
   * @param $distribution_tree
1857
   *  A tree cdm TreeNode items. A TreeNode item has a NamedArea as nodeId
1858
   *  and Distribution items as data array. Per data array some Distributions may
1859
   *  be with status information, others only with sources, others with both.
1860
   *  Each node may also have subordinate node items in the children field.
1861
   *  TreeNode:
1862
   *   - array data
1863
   *   - array children
1864
   *   - int numberOfChildren
1865
   *   - stdClass nodeId
1866
   *
1867
   * @param $feature_block_settings
1868
   *
1869
   * @return array
1870
   * @throws \Exception
1871
   */
1872
  function compose_distribution_hierarchy($distribution_tree, $feature_block_settings){
1873

    
1874
    static $hierarchy_style;
1875
    // TODO expose $hierarchy_style to administration or provide a hook
1876
    if( !isset($hierarchy_style)){
1877
      $hierarchy_style = get_array_variable_merged(DISTRIBUTION_HIERARCHY_STYLE, DISTRIBUTION_HIERARCHY_STYLE_DEFAULT);
1878
    }
1879

    
1880
    $render_array = array();
1881

    
1882
    RenderHints::pushToRenderStack('descriptionElementDistribution');
1883
    RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);
1884

    
1885
    // Returning NULL if there are no description elements.
1886
    if ($distribution_tree == null) {
1887
      return $render_array;
1888
    }
1889
    // for now we are not using a render array internally to avoid performance problems
1890
    $markup = '';
1891
    if (isset($distribution_tree->rootElement->children)) {
1892
      $tree_nodes = $distribution_tree->rootElement->children;
1893
      _compose_distribution_hierarchy($tree_nodes, $feature_block_settings, $markup, $hierarchy_style);
1894
    }
1895

    
1896
    $render_array['distribution_hierarchy'] = markup_to_render_array(
1897
      $markup,
1898
      0,
1899
      '<div id="distribution_hierarchy" class="distribution_hierarchy">',
1900
      '</div>'
1901
    );
1902

    
1903
    RenderHints::popFromRenderStack();
1904

    
1905
    return $render_array;
1906
  }
1907

    
1908
/**
1909
 * this function should produce markup as the
1910
 * compose_description_elements_distribution() function.
1911
 *
1912
 * @param array $tree_nodes
1913
 *  An array of cdm TreeNode items. A TreeNode item has a NamedArea as nodeId
1914
 *  and Distribution items as data array. Per data array some Distributions may
1915
 *  be with status information, others only with sources, others with both.
1916
 *  TreeNode:
1917
 *   - array data
1918
 *   - array children
1919
 *   - int numberOfChildren
1920
 *   - stdClass nodeId
1921
 * @param array $feature_block_settings
1922
 * @param $markup
1923
 * @param $hierarchy_style
1924
 * @param int $level_index
1925
 *
1926
 * @throws \Exception
1927
 *
1928
 * @see compose_description_elements_distribution()
1929
 * @see compose_distribution_hierarchy()
1930
 *
1931
 */
1932
  function _compose_distribution_hierarchy(array $tree_nodes, array $feature_block_settings, &$markup, $hierarchy_style, $level_index = -1){
1933

    
1934
    $level_index++;
1935
    static $enclosingTag = "span";
1936

    
1937
    $level_style = array_shift($hierarchy_style);
1938
    if(count($hierarchy_style) == 0){
1939
      // lowest defined level style will be reused for all following levels
1940
      $hierarchy_style[] = $level_style;
1941
    }
1942

    
1943
    $node_index = -1;
1944
    $per_node_markup = array();
1945

    
1946
    foreach ($tree_nodes as $node){
1947

    
1948
      $per_node_markup[++$node_index] = '';
1949
      $label = $node->nodeId->representation_L10n;
1950

    
1951
      $distributions = $node->data;
1952
      $distribution_uuids = array();
1953
      $distribution_aggregate = NULL;
1954
      $status = ['label' => '', 'markup' => ''];
1955

    
1956
      foreach($distributions as $distribution){
1957
        $distribution_uuids[] = $distribution->uuid;
1958
        // if there is more than one distribution we aggregate the sources and
1959
        // annotations into a synthetic distribution so that the footnote keys
1960
        // can be rendered consistently
1961
        if(!$distribution_aggregate) {
1962
          $distribution_aggregate = $distribution;
1963
          if(isset($distribution->status)){
1964
            $distribution_aggregate->status = [$distribution->status];
1965
          } else {
1966
            $distribution_aggregate->status = [];
1967
          }
1968
          if(!isset($distribution_aggregate->sources[0])){
1969
            $distribution_aggregate->sources = array();
1970
          }
1971
          if(!isset($distribution_aggregate->annotations[0])){
1972
            $distribution_aggregate->annotations = array();
1973
          }
1974
        } else {
1975
          if(isset($distribution->status)){
1976
            $distribution_aggregate->status[] = $distribution->status;
1977
          }
1978
          if(isset($distribution->sources[0])) {
1979
            $distribution_aggregate->sources = array_merge($distribution_aggregate->sources,
1980
              $distribution->sources);
1981
          }
1982
          if(isset($distribution->annotations[0])) {
1983
            $distribution_aggregate->annotations = array_merge($distribution_aggregate->annotations,
1984
              $distribution->annotations);
1985
          }
1986
        }
1987
      }
1988

    
1989
      $annotations_and_sources =  null;
1990
      if($distribution_aggregate) {
1991
        $annotations_and_sources = handle_annotations_and_sources(
1992
          $distribution_aggregate,
1993
          handle_annotations_and_sources_config($feature_block_settings),
1994
          $label,
1995
          UUID_DISTRIBUTION
1996
        );
1997

    
1998
        $status = distribution_status_label_and_markup($distribution_aggregate->status, $level_style['status_glue']);
1999
      }
2000

    
2001
      $per_node_markup[$node_index] .= '<' . $enclosingTag . ' class="descriptionElement'
2002
        . join(' descriptionElement-', $distribution_uuids)
2003
        . ' level_index_' . $level_index
2004
        . ' " title="' . $status['label'] . '">'
2005
        . '<span class="area_label">' . $label
2006
        . $level_style['label_suffix'] . '</span>'
2007
        . $status['markup']
2008
      ;
2009

    
2010
      if(isset($annotations_and_sources)){
2011
        if(!empty($annotations_and_sources['source_references'])){
2012
          $per_node_markup[$node_index] .= ' ' . join(', ' , $annotations_and_sources['source_references']);
2013
        }
2014
        if($annotations_and_sources['foot_note_keys']) {
2015
          $per_node_markup[$node_index] .= $annotations_and_sources['foot_note_keys'];
2016
        }
2017
      }
2018

    
2019
      if(isset($node->children[0])){
2020
        _compose_distribution_hierarchy(
2021
          $node->children,
2022
          $feature_block_settings,
2023
          $per_node_markup[$node_index],
2024
          $hierarchy_style,
2025
          $level_index
2026
        );
2027
      }
2028

    
2029
      $per_node_markup[$node_index] .= '</' . $enclosingTag . '>';
2030
    }
2031
    $markup .= $level_style['item_group_prefix']  . join( $level_style['item_glue'], $per_node_markup) . $level_style['item_group_postfix'];
2032
  }
2033

    
2034

    
2035
/**
2036
 * Provides the content for a block of Uses Descriptions for a given taxon.
2037
 *
2038
 * Fetches the list of TaxonDescriptions tagged with the MARKERTYPE_USE
2039
 * and passes them to the theme function theme_cdm_UseDescription().
2040
 *
2041
 * @param string $taxon_uuid
2042
 *   The uuid of the Taxon
2043
 *
2044
 * @return array
2045
 *   A drupal render array
2046
 */
2047
function cdm_block_use_description_content($taxon_uuid, $feature) {
2048

    
2049
  $use_description_content = array();
2050

    
2051
  if (is_uuid($taxon_uuid )) {
2052
    $markerTypes = array();
2053
    $markerTypes['markerTypes'] = UUID_MARKERTYPE_USE;
2054
    $useDescriptions = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXON . '/' . $taxon_uuid . '/descriptions', $markerTypes);
2055
    if (!empty($useDescriptions)) {
2056
      $use_description_content = compose_feature_block_items_use_records($useDescriptions, $taxon_uuid, $feature);
2057
    }
2058
  }
2059

    
2060
  return $use_description_content;
2061
}
2062

    
2063
/**
2064
 * Creates a trunk of a feature object which can be used to build pseudo feature blocks like the Bibliography.
2065
 *
2066
 * @param $representation_L10n
2067
 * @param String $pseudo_feature_key
2068
 *    Will be set as uuid but should be one of 'BIBLIOGRAPHY', ... more to come. See also get_feature_block_settings()
2069
 *
2070
 * @return object
2071
 *  The feature object
2072
 */
2073
function make_pseudo_feature($representation_L10n, $pseudo_feature_key = null){
2074
  $feature = new stdClass;
2075
  $feature->representation_L10n = $representation_L10n;
2076
  $feature->uuid = NULL; // $pseudo_feature_key;
2077
  $feature->label = $pseudo_feature_key;
2078
  $feature->class = 'PseudoFeature';
2079

    
2080
  return $feature;
2081

    
2082
}
2083

    
2084
/**
2085
 * @param $root_nodes, for obtaining the  root nodes from a description you can
2086
 * use the function get_root_nodes_for_dataset($description);
2087
 *
2088
 * @return string
2089
 */
2090
function render_description_string($root_nodes, &$item_cnt = 0) {
2091

    
2092
  $out = '';
2093

    
2094
  $description_strings= [];
2095
  if (!empty($root_nodes)) {
2096
    foreach ($root_nodes as $root_node) {
2097
      if(isset($root_node->descriptionElements)) {
2098
        foreach ($root_node->descriptionElements as $element) {
2099
          $feature_label = $element->feature->representation_L10n;
2100
          if($item_cnt == 0){
2101
            $feature_label = ucfirst($feature_label);
2102
          }
2103
          switch ($element->class) {
2104
            case 'CategoricalData':
2105
              $state_data = render_state_data($element);
2106
              if (!empty($state_data)) {
2107
                if(is_suppress_state_present_display($element, $root_node)){
2108
                  $description_strings[] = '<span class="'. html_class_attribute_ref($element) .'"><span class="label">' . $feature_label . '</span>: '  . '</span>';
2109
                } else {
2110
                  $description_strings[] = '<span class="'. html_class_attribute_ref($element) .'"><span class="label">' . $feature_label . '</span>: ' . $state_data . '</span>;' ;
2111
                }
2112
              }
2113
              break;
2114
            case 'QuantitativeData':
2115
              $description_strings[] = '<span class="'. html_class_attribute_ref($element) .'"><span class="label">' . $feature_label . '</span>: ' . render_quantitative_statistics($element) . '</span>;';
2116
              break;
2117
          }
2118
        }
2119
        $item_cnt++;
2120
      }
2121

    
2122
      // recurse child nodes
2123
      $child_markup = render_description_string($root_node->childNodes, $item_cnt);
2124
      if($child_markup){
2125
        $description_strings[] = $child_markup;
2126
      }
2127
    }
2128
    if(count($description_strings) > 0){
2129
      // remove last semicolon
2130
      $description_strings[count($description_strings) - 1] = preg_replace('/;$/', '', $description_strings[count($description_strings) - 1]);
2131
    }
2132
    $out  = join($description_strings,  ' ');
2133
  }
2134
  return $out;
2135
}
2136

    
2137
/**
2138
 * Compose a description as a table of Feature<->State
2139
 *
2140
 * @param $description_uuid
2141
 *
2142
 * @return array
2143
 *    The drupal render array for the page
2144
 *
2145
 * @ingroup compose
2146
 */
2147
function  compose_description_table($description_uuid, $descriptive_dataset_uuid = NULL) {
2148

    
2149
  RenderHints::pushToRenderStack('description_table');
2150

    
2151
  $render_array = [];
2152

    
2153
  $description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, [$description_uuid]);
2154
  $dataSet = NULL;
2155
  // dataset passed as parameter
2156
  if ($descriptive_dataset_uuid != NULL) {
2157
    foreach ($description->descriptiveDataSets as $set) {
2158
      if ($set->uuid == $descriptive_dataset_uuid) {
2159
        $dataSet = $set;
2160
        break;
2161
      }
2162
    }
2163
  }
2164

    
2165
  if(!empty($description->descriptiveDataSets)) {
2166
    // only one dataset present
2167
    if (!isset($dataSet) && sizeof($description->descriptiveDataSets) == 1) {
2168
      foreach ($description->descriptiveDataSets as $dataSet) {
2169
        break;
2170
      }
2171
    }
2172

    
2173
    // generate description title
2174
    RenderHints::pushToRenderStack('title');
2175
    if (isset($dataSet)) {
2176

    
2177
      $described_entity_title = NULL;
2178
      if(isset($description->describedSpecimenOrObservation)){
2179
        $described_entity_title = $description->describedSpecimenOrObservation->titleCache;
2180
      } else if($description->taxon) {
2181
          $described_entity_title = render_taxon_or_name($description->taxon);
2182
      }
2183
      $title = 'Descriptive Data ' . $dataSet->titleCache .
2184
        ($described_entity_title ? ' for ' . $described_entity_title : '');
2185
    }
2186
    $render_array['title'] = markup_to_render_array($title, null, '<h3 class="title">', '</h3>');
2187
    RenderHints::popFromRenderStack();
2188
    // END of --- generate description title
2189

    
2190
    if (isset($description->types)) {
2191
      foreach ($description->types as $type) {
2192
        if ($type == 'CLONE_FOR_SOURCE') {
2193
          $render_array['source'] = markup_to_render_array("Aggregation source from " . $description->created, null, '<div class="date-created">', '</div>');
2194
          break;
2195
        }
2196
      }
2197
    }
2198
  }
2199
  // multiple datasets present see #8714 "Show multiple datasets per description as list of links"
2200
  else {
2201
    $items = [];
2202
    foreach ($description->descriptiveDataSets as $dataSet) {
2203
      $path = path_to_description($description->uuid, $dataSet->uuid);
2204
      $attributes['class'][] = html_class_attribute_ref($description);
2205
      $items[] = [
2206
        'data' => $dataSet->titleCache . icon_link($path),
2207
      ];
2208
    }
2209
    $render_array['description_elements'] = [
2210
      '#title' => 'Available data sets for description',
2211
      '#theme' => 'item_list',
2212
      '#type' => 'ul',
2213
      '#items' => $items,
2214
    ];
2215
  }
2216

    
2217
  $described_entities = [];
2218
  if (isset($description->describedSpecimenOrObservation)) {
2219
    $decr_entitiy = '<span class="label">Specimen:</span> ' . render_cdm_specimen_link($description->describedSpecimenOrObservation);
2220
    $described_entities['specimen'] = markup_to_render_array($decr_entitiy, null, '<div>', '</div>');
2221
  }
2222
  if (isset($description->taxon)) {
2223
    $decr_entitiy = '<span class="label">Taxon:</span> ' . render_taxon_or_name($description->taxon, url(path_to_taxon($description->taxon->uuid)));
2224
    $described_entities['taxon'] = markup_to_render_array($decr_entitiy, null, '<div>', '</div>');
2225
  }
2226

    
2227
  if(count($described_entities)){
2228
    $render_array['described_entities'] = $described_entities;
2229
    $render_array['described_entities']['#prefix'] = '<div class="described-entities">';
2230
    $render_array['described_entities']['#suffix'] = '</div>';
2231
  }
2232

    
2233

    
2234
  $root_nodes = get_root_nodes_for_dataset($description);
2235

    
2236

    
2237
  $rows = [];
2238
  $rows = description_element_table_rows($root_nodes, $rows);
2239

    
2240
  // --- create headers
2241
  $header = [0 => [], 1 => []];
2242

    
2243
  foreach($rows as $row) {
2244
    if(array_search('Character', $row['class']) && array_search('Character', $header[0]) === false){
2245
      $header[0][] = 'Character';
2246
    } elseif (array_search('Feature', $row['class']) && array_search('Feature', $header[0]) === false){
2247
      $header[0][] = 'Feature';
2248
    }
2249
    if(array_search('has_state', $row['class']) && array_search('States', $header[1]) === false){
2250
      $header[1][] = 'States';
2251
    } elseif (array_search('has_values', $row['class']) && array_search('Values', $header[1]) === false){
2252
      $header[1][] = 'Values';
2253
    }
2254
  }
2255
  asort($header[0]);
2256
  asort($header[1]);
2257
  $header[0] = join('/', $header[0]);
2258
  $header[1] = join('/', $header[1]);
2259

    
2260
  // ---
2261

    
2262
  if (!empty($rows)) {
2263
    $render_array['table'] = markup_to_render_array(theme('table', [
2264
      'header' => $header,
2265
      'rows' => $rows,
2266
      'caption' => statistical_values_explanation(),
2267
      'title' => "Table"
2268
    ]));
2269
  }
2270

    
2271
  // --- sources
2272
  if (isset($description->sources) and !empty($description->sources)) {
2273
    $items = [];
2274
    foreach ($description->sources as $source) {
2275
      if ($source->type == 'Aggregation' and isset($source->cdmSource)){
2276
        $cdm_source_entity = $source->cdmSource;
2277
        switch($cdm_source_entity->class){
2278
          case 'Taxon':
2279
            $source_link_markup = render_taxon_or_name($cdm_source_entity) . icon_link(path_to_taxon($cdm_source_entity->uuid, false));
2280
            break;
2281
          case 'TaxonDescription':
2282
          case 'NameDescription':
2283
          case 'SpecimenDescription':
2284
            $source_link_markup = render_cdm_entity_link($cdm_source_entity);
2285
            break;
2286
          default:
2287
            $source_link_markup = '<span class="error">Unhandled CdmSource</span>';
2288
        }
2289
        $items[$cdm_source_entity->titleCache] = [
2290
          'data' => $source_link_markup
2291
        ];
2292
      }
2293
    }
2294
    ksort($items);
2295
    $render_array['sources'] = [
2296
      '#title' => 'Sources',
2297
      '#theme' => 'item_list',
2298
      '#type' => 'ul',
2299
      '#items' => $items,
2300
      '#attributes' => ['class' => 'sources']
2301
    ];
2302
    $render_array['#prefix'] = '<div class="description-table">';
2303
    $render_array['#suffix'] = '</div>';
2304
  }
2305

    
2306
  RenderHints::popFromRenderStack();
2307

    
2308
  return $render_array;
2309
}
2310

    
2311
/**
2312
 * For a given description returns the root nodes according to the
2313
 *corresponding term tree. The term tree is determined as follow:
2314
 * 1. If description is part of a descriptive data set the term tree of that
2315
 *    data set is used (FIXME handle multiple term trees)
2316
 * 2. Otherwise the portal taxon profile tree is used
2317
 * @param $description
2318
 *
2319
 * @return array
2320
 */
2321
function get_root_nodes_for_dataset($description) {
2322
  if (!empty($description->descriptiveDataSets)) {
2323
    foreach ($description->descriptiveDataSets as $dataSet) {
2324
      break;// FIXME handle multiple term trees
2325
    }
2326
    $tree = cdm_ws_get(CDM_WS_TERMTREE, $dataSet->descriptiveSystem->uuid);
2327
    $root_nodes = _mergeFeatureTreeDescriptions($tree->root->childNodes, $description->elements);
2328
  }
2329
  else {
2330
    $root_nodes = _mergeFeatureTreeDescriptions(get_profile_feature_tree()->root->childNodes, $description->elements);
2331
  }
2332
  return $root_nodes;
2333
}
2334

    
2335
/**
2336
 * Recursively creates an array of row items to be used in theme_table.
2337
 *
2338
 * The array items will have am element 'class' with information on the
2339
 * nature of the DescriptionElement ('has_values' | 'has_state') and on the
2340
 * type of the FeatureNode ('Feature' | 'Character')
2341
 *
2342
 * @param array $root_nodes
2343
 * @param array $row_items
2344
 * @param int $level
2345
 *     the depth in the hierarchy
2346
 *
2347
 * @return array
2348
 *  An array of row items to be used in theme_table
2349
 *
2350
 *
2351
 */
2352
function description_element_table_rows($root_nodes, $row_items, $level = 0) {
2353

    
2354
  $indent_string = '&nbsp;&nbsp;&nbsp;';
2355
  foreach ($root_nodes as $root_node) {
2356
    if(isset($root_node->descriptionElements)) {
2357
      foreach ($root_node->descriptionElements as $element) {
2358
        $level_indent = str_pad('', $level * strlen($indent_string), $indent_string);
2359
        switch ($element->class) {
2360
          case 'QuantitativeData':
2361
            $row_items[] = [
2362
              'data' => [
2363
                [
2364
                  'data' => markup_to_render_array($level_indent . $element->feature->representation_L10n),
2365
                  'class' => ['level_' . $level]
2366
                ],
2367
                render_quantitative_statistics($element)
2368
              ],
2369
              'class' => ['level_' . $level, 'has_values', $element->feature->class]
2370
            ];
2371
            break;
2372
          case 'CategoricalData':
2373
            default:
2374
            if (!empty($element->stateData)) {
2375
              $supress_state_display = is_suppress_state_present_display($element, $root_node);
2376
              if(!$supress_state_display){
2377
                $state_cell = render_state_data($element);
2378
              } else {
2379
                $state_cell = "<span> </span>";
2380
              }
2381
              $row_items[] = [
2382
                'data' => [
2383
                  [
2384
                    'data' => markup_to_render_array($level_indent . $element->feature->representation_L10n),
2385
                    'class' => ['level_' . $level]
2386
                  ],
2387
                  $state_cell,
2388
                ],
2389
                'class' => ['level_' . $level, 'has_state', $element->feature->class]
2390
              ];
2391
            }
2392
            break;
2393
        }
2394
      }
2395
    }
2396
    // recurse child nodes
2397
    $row_items = description_element_table_rows($root_node->childNodes, $row_items, $level + 1);
2398
  }
2399
  return $row_items;
2400
}
2401

    
2402
/**
2403
 * @param $element
2404
 * @param $root_node
2405
 *
2406
 * @return bool
2407
 */
2408
function is_suppress_state_present_display($element, $root_node) {
2409
  return count($element->stateData) == 1 & $element->stateData[0]->state->representation_L10n == 'present' && is_array($root_node->childNodes);
2410
}
2411

    
2412

    
2413

    
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