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cdm-dataportal / modules / cdm_dataportal / includes / descriptions.inc @ 6722d9a5

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1
<?php
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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 $iModifieable
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 *   cdm instance of an class implementing the interface IModifieable:
12
 *   DescriptionElementBase, StateDate, State
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 *
14
 * @return String
15
 *   localized representations of the modifiers hold by the
16
 *   supplied cdm instance concatenated into one string
17
 */
18
function cdm_modifers_representations($iModifieable, $glue = ', ') {
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  $modifiers_strings = array();
20
  if (isset($iModifieable->modifiers)) {
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    foreach ($iModifieable->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: "feature-toc-item-"
140
 * @param string $fragment
141
 *   Optional parameter to define a url fragment different from the $label,
142
 *   if the $fragment is not defined the $label will be used
143
 * @param boolean $as_first_element
144
 *   Place the new item as fist one. This parameter is ignored when $weight is being set
145
 * @param integer $weight
146
 *   Defines the weight for the ordering the item in the toc list.
147
 *   The item will be placed at the end if weigth is NULL.
148
 */
149
function cdm_toc_list_add_item($label, $class_attribute_suffix, $fragment = NULL, $as_first_element = FALSE, $weight = null) {
150

    
151
  $toc_list_items = &cdm_toc_list();
152

    
153
  if (!$fragment) {
154
    $fragment = $label;
155
  }
156
  $fragment = generalizeString($fragment);
157

    
158
  $class_attributes = 'feature-toc-item-' . $class_attribute_suffix;
159

    
160
  $new_item = toc_list_item(
161
    theme(
162
      'cdm_feature_name',
163
      array('feature_name' => $label)),
164
      array('class' => $class_attributes),
165
      $fragment
166
    );
167

    
168
  if ($weight === null && $as_first_element) {
169
    reset($toc_list_items);
170
    $weight = key($toc_list_items); // returns null for empty arrays
171
    $weight = $weight !== null ? $weight - FEATURE_BLOCK_WEIGHT_INCREMENT : 0;
172
  }
173
  else if($weight === null) {
174
      end($toc_list_items);
175
      $weight = key($toc_list_items); // returns null for empty arrays
176
      $weight = $weight !== null ? $weight + FEATURE_BLOCK_WEIGHT_INCREMENT : 0;
177
  }
178
  $toc_list_items[$weight] = $new_item;
179
  ksort($toc_list_items); // sort so that the last element has always the highest weight
180

    
181
}
182

    
183
/**
184
 * Returns the statically cached table of content items as render array.
185
 *
186
 * @see cdm_toc_list_add_item()
187
 *
188
 * @return array
189
 *   a render array of table of content items suitable for theme_item_list()
190
 */
191
function &cdm_toc_list(){
192
  $toc_list_items = &drupal_static('toc_list_items', array());
193

    
194
  return $toc_list_items;
195
}
196

    
197
/**
198
 * Prepares an empty Drupal block for displaying description elements of a specific CDM Feature.
199
 *
200
 * The block can also be used for pseudo Features like a bibliography. Pseudo features are
201
 * derived from other data on the fly and so not exist as such in the cdm data. For pseudo
202
 * features the $feature can be created using make_pseudo_feature().
203
 *
204
 * @param $feature_name
205
 *   A label describing the feature, usually the localized feature representation.
206
 * @param object $feature
207
 *   The CDM Feature for which the block is created.
208
 * @return object
209
 *   A Drupal block object
210
 */
211
function feature_block($feature_name, $feature) {
212
  $block = new stdclass();
213
  $block->module = 'cdm_dataportal';
214
  $block->region = NULL;
215
  $class_attribute = html_class_attribute_ref($feature);
216
  $block_delta = $feature->class !== 'PseudoFeature' ? $feature_name : $feature->label;
217
  $block->delta = generalizeString($block_delta);
218
  $block->subject = '<a name="' . $block->delta . '"></a><span class="' . $class_attribute . '">'
219
    . theme('cdm_feature_name', array('feature_name' => $feature_name))
220
    . '</span>';
221
  $block->module = "cdm_dataportal-feature";
222
  $block->content = '';
223
  return $block;
224
}
225

    
226

    
227
/**
228
 * Returns a list of a specific type of IdentificationKeys.
229
 *
230
 * The list can be restricted by a taxon.
231
 *
232
 * @param string $type
233
 *   The simple name of the cdm class implementing the interface
234
 *   IdentificationKey, valid values are:
235
 *   PolytomousKey, MediaKey, MultiAccessKey.
236
 * @param string $taxonUuid
237
 *   If given this parameter restrict the listed keys to those which have
238
 *   the taxon identified be this uuid in scope.
239
 *
240
 * @return array
241
 *   List with identification keys.
242
 */
243
function _list_IdentificationKeys($type, $taxonUuid = NULL, $pageSize = NULL, $pageNumber = NULL) {
244
  if (!$type) {
245
    drupal_set_message(t('Type parameter is missing'), 'error');
246
    return;
247
  }
248
  $cdm_ws_pasepath = NULL;
249
  switch ($type) {
250
    case "PolytomousKey":
251
      $cdm_ws_pasepath = CDM_WS_POLYTOMOUSKEY;
252
      break;
253

    
254
    case "MediaKey":
255
      $cdm_ws_pasepath = CDM_WS_MEDIAKEY;
256
      break;
257

    
258
    case "MultiAccessKey":
259
      $cdm_ws_pasepath = CDM_WS_MULTIACCESSKEY;
260
      break;
261

    
262
  }
263

    
264
  if (!$cdm_ws_pasepath) {
265
    drupal_set_message(t('Type parameter is not valid: ') . $type, 'error');
266
  }
267

    
268
  $queryParameters = '';
269
  if (is_numeric($pageSize)) {
270
    $queryParameters = "pageSize=" . $pageSize;
271
  }
272
  else {
273
    $queryParameters = "pageSize=0";
274
  }
275

    
276
  if (is_numeric($pageNumber)) {
277
    $queryParameters = "pageNumber=" . $pageNumber;
278
  }
279
  else {
280
    $queryParameters = "pageNumber=0";
281
  }
282
  $queryParameters = NULL;
283
  if ($taxonUuid) {
284
    $queryParameters = "findByTaxonomicScope=$taxonUuid";
285
  }
286
  $pager = cdm_ws_get($cdm_ws_pasepath, NULL, $queryParameters);
287

    
288
  if (!$pager || $pager->count == 0) {
289
    return array();
290
  }
291
  return $pager->records;
292
}
293

    
294

    
295
/**
296
 * Creates a list item for a table of content, suitable as data element for a themed list
297
 *
298
 * @see theme_list()
299
 *
300
 * @param $label
301
 * @param $http_request_params
302
 * @param $attributes
303
 * @return array
304
 */
305
function toc_list_item($label, $attributes = array(), $fragment = null) {
306

    
307
  // we better cache here since drupal_get_query_parameters has no internal static cache variable
308
  $http_request_params = drupal_static('http_request_params', drupal_get_query_parameters());
309

    
310
  $item =  array(
311
    'data' => l(
312
      $label,
313
      $_GET['q'],
314
      array(
315
        'attributes' => array('class' => array('toc')),
316
        'fragment' => generalizeString($label),
317
        'query' => $http_request_params,
318
      )
319
    ),
320
  );
321
  $item['attributes'] = $attributes;
322
  return $item;
323
}
324

    
325
/**
326
 * Creates the footnotes for the given CDM instance.
327
 *
328
 * Footnotes are created for annotations and original sources whereas the resulting footnote keys depend on the
329
 * parameters $footnote_list_key_suggestion and $is_bibliography_aware, see parameter $footnote_list_key_suggestion
330
 * for more details.
331
 *
332
 * possible keys for
333
 *     - annotation footnotes:
334
 *       - $footnote_list_key_suggestion
335
 *       - RenderHints::getFootnoteListKey().'-annotations'
336
 *     - original source footnotes
337
 *       - "BIBLIOGRAPHY" (when !$is_bibliography_aware && bibliography_settings['enabled'] == 1 )
338
 *       - "BIBLIOGRAPHY-$footnote_list_key_suggestion" (when !$is_bibliography_aware && bibliography_settings['enabled'] == 0 )
339
 *       - $footnote_list_key_suggestion (when $is_bibliography_aware)
340
 *
341
 * @param $descriptionElement
342
 *   A CDM DescriptionElement instance
343
 * @param $separator
344
 *   Optional parameter. The separator string to concatenate the footnote ids, default is ','
345
 * @param $footnote_list_key_suggestion string
346
 *    Optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be determined by the nested
347
 *    method calls by calling RenderHints::getFootnoteListKey(). NOTE: the footnote key for annotations will be set to
348
 *    RenderHints::getFootnoteListKey().'-annotations'. @see cdm_annotations_as_footnotekeys()
349
 *    For original sources the $footnote_list_key_suggestion will be overwritten by original_source_footnote_list_key() when
350
 *    $is_bibliography_aware is set TRUE.
351
 * @$original_source_footnote_tag
352
 *    null will cause original_source_footnote_list_key to use the default
353
 *
354
 * @return String
355
 *   The foot note keys
356
 */
357
function cdm_create_footnotes(
358
    $description_element,
359
    $separator = ',',
360
    $footnote_list_key_suggestion = null,
361
    $do_link_to_reference = FALSE,
362
    $do_link_to_name_used_in_source = FALSE,
363
    $is_bibliography_aware = FALSE
364
  ){
365

    
366
  // Annotations as footnotes.
367
  $footNoteKeys = cdm_annotations_as_footnotekeys($description_element, $footnote_list_key_suggestion);
368

    
369
  // Source references as footnotes.
370

    
371
  if($is_bibliography_aware){
372
    $bibliography_settings = get_bibliography_settings();
373
    $sources_footnote_list_key = original_source_footnote_list_key($footnote_list_key_suggestion);
374
    $original_source_footnote_tag = $bibliography_settings['enabled'] == 1 ? 'div' : null; // null will cause original_source_footnote_list_key to use the default
375
  } else {
376
    $sources_footnote_list_key = $footnote_list_key_suggestion;
377
    $original_source_footnote_tag = NULL;
378
  }
379

    
380
  usort($description_element->sources, 'compare_original_sources');
381
  foreach ($description_element->sources as $source) {
382
    if (_is_original_source_type($source)) {
383
      $fn_key = FootnoteManager::addNewFootnote(
384
        $sources_footnote_list_key,
385
        render_original_source(
386
          $source,
387
          $do_link_to_reference,
388
          $do_link_to_name_used_in_source
389
        ),
390
        $original_source_footnote_tag
391
      );
392
      // Ensure uniqueness of the footnote keys.
393
      cdm_add_footnote_to_array($footNoteKeys, $fn_key);
394
    }
395
  }
396
  // Sort and render footnote keys.
397
  $footnoteKeyListStr = '';
398
  asort($footNoteKeys);
399
  foreach ($footNoteKeys as $footNoteKey) {
400
    try{
401
      $footnoteKeyListStr .= theme('cdm_footnote_key',
402
        array(
403
          'footnoteKey' => $footNoteKey,
404
          'separator' => ($footnoteKeyListStr ? $separator : '')));
405
    } catch (Exception $e) {
406
      drupal_set_message("Exception: " . $e->getMessage(),  'error');
407
    }
408
  }
409
  return $footnoteKeyListStr;
410
}
411

    
412

    
413
/**
414
 * Compare callback to be used in usort() to sort render arrays produced by compose_description_element().
415
 *
416
 * @param $a
417
 * @param $b
418
 */
419
function compare_description_element_render_arrays($a, $b){
420
  if ($a['#value'].$a['#value-suffix'] == $b['#value'].$b['#value-suffix']) {
421
    return 0;
422
  }
423
  return ($a['#value'].$a['#value-suffix'] < $b['#value'].$b['#value-suffix']) ? -1 : 1;
424

    
425
}
426

    
427

    
428
/**
429
 * @param $render_array
430
 * @param $element
431
 * @param $feature_block_settings
432
 * @param $element_markup
433
 * @param $footnote_list_key_suggestion
434
 */
435
function compose_description_element($element, $feature_block_settings, $element_markup, $footnote_list_key_suggestion, $prepend_feature_label = FALSE)
436
{
437

    
438
  $render_array = array(
439
    '#type' => 'html_tag',
440
    '#tag' => cdm_feature_block_element_tag_name($feature_block_settings),
441

    
442
    '#attributes' => array(
443
      'class' => array(
444
        'DescriptionElement',
445
        'DescriptionElement-' . $element->class,
446
        html_class_attribute_ref($element)
447
      )
448
    ),
449

    
450
    '#value' => '',
451
    '#value_suffix' => NULL
452

    
453
  );
454

    
455
  $annotations_and_sources = handle_annotations_and_sources(
456
    $element,
457
    handle_annotations_and_sources_config($feature_block_settings),
458
    $element_markup,
459
    $footnote_list_key_suggestion
460
  );
461

    
462
  $timescope_markup = '';
463
  if(isset($element->timeperiod)){
464
    $timescope_markup = ' ' . timePeriodToString($element->timeperiod, true);
465
  }
466

    
467
  // handle the special case were the TextData is used as container for original source with name
468
  // used in source information without any text stored in it.
469
  $names_used_in_source_markup = '';
470
  if (!empty($annotations_and_sources['names_used_in_source']) && empty($element_markup)) {
471
    $names_used_in_source_markup = join(', ', $annotations_and_sources['names_used_in_source']) . ': ';
472
    // remove all <span class="nameUsedInSource">...</span> from all source_references
473
    // these are expected to be at the end of the strings
474
    $pattern = '/ <span class="nameUsedInSource">.*$/';
475
    foreach( $annotations_and_sources['source_references'] as &$source_reference){
476
      $source_reference = preg_replace($pattern , '', $source_reference);
477
    }
478
  }
479

    
480
  $source_references_markup = '';
481
  if (!empty($annotations_and_sources['source_references'])) {
482
    $source_references_markup = '<span class="sources">' . join(' ', $annotations_and_sources['source_references']) . '<span>';
483
  }
484

    
485
  $feature_label = '';
486
  if ($prepend_feature_label) {
487
    $feature_label = '<span class="nested-feature-tree-feature-label">' . $element->feature->representation_L10n . ':</span> ';
488
  }
489
  $content_markup = $names_used_in_source_markup . $element_markup . $timescope_markup . $source_references_markup;
490

    
491
  if(!$content_markup && $feature_block_settings['sources_as_content'] !== 1){
492
    // no textual content? So skip this element completely, even if there could be an footnote key
493
    // see #4379
494
    return null;
495
  }
496

    
497
    $render_array['#value'] = $feature_label . $content_markup;
498
    $render_array['#value_suffix'] = $annotations_and_sources['foot_note_keys'];
499
  return $render_array;
500
}
501

    
502
/**
503
 * Creates a handle_annotations_and_sources configuration array from feature_block_settings.
504
 *
505
 * The handle_annotations_and_sources configuration array is meant to be used for the
506
 * method handle_annotations_and_sources().
507
 *
508
 * @param $feature_block_settings array
509
 *
510
 * @return array
511
 *   The configuration array for handle_annotations_and_sources()
512
 */
513
function handle_annotations_and_sources_config($feature_block_settings){
514

    
515
  $config = $feature_block_settings;
516
  unset($config['sources_as_content_to_bibliography']);
517
  $config['add_footnote_keys'] = 0;
518
  if($feature_block_settings['sources_as_content'] !== 1 || $feature_block_settings['sources_as_content_to_bibliography'] == 1) {
519
    $config['add_footnote_keys'] = 1;
520
  }
521
  $config['bibliography_aware'] = 1;
522

    
523
  return $config;
524
}
525

    
526
  /**
527
   * @param $entity
528
   * @param $config array
529
   *   An associative array to configure the display of the annotations and sources.
530
   *   The array has the following keys
531
   *   - sources_as_content
532
   *   - link_to_name_used_in_source
533
   *   - link_to_reference
534
   *   - add_footnote_keys
535
   *   - bibliography_aware
536
   *   Valid values are 1 or 0.
537
   * @param $inline_text_prefix
538
   *   Only used to decide if the source references should be enclosed in brackets or not when displayed inline.
539
   *   This text will not be included into the response.
540
   * @param $footnote_list_key_suggestion string
541
   *    optional parameter. If this paramter is left empty (null, 0, "") the footnote key will be determined by the nested
542
   *    method calls by calling RenderHints::getFootnoteListKey(). NOTE: the footnore key for annotations will be set to
543
   *    RenderHints::getFootnoteListKey().'-annotations'. @see cdm_annotations_as_footnotekeys()
544
   *
545
   * @return array
546
   *   an associative array with the following elements:
547
   *   - foot_note_keys: all footnote keys as markup
548
   *   - source_references: an array of the source references citations
549
   *   - names used in source: an associative array of the names in source,
550
   *        the name in source strings are de-duplicated
551
   *        !!!NOTE!!!!: this field will most probably be removed soon (TODO)
552
   */
553
  function handle_annotations_and_sources($entity, $config, $inline_text_prefix, $footnote_list_key_suggestion) {
554

    
555
    $annotations_and_sources = array(
556
      'foot_note_keys' => NULL,
557
      'source_references' => array(),
558
      'names_used_in_source' => array()
559
    );
560

    
561
    usort($entity->sources, 'compare_original_sources');
562

    
563
    if ($config['sources_as_content'] == 1) {
564
      foreach ($entity->sources as $source) {
565
        if (_is_original_source_type($source)) {
566
          $reference_citation = render_original_source(
567
            $source,
568
            $config['link_to_reference'] == 1,
569
            $config['link_to_name_used_in_source'] == 1
570
          );
571

    
572
          if ($reference_citation) {
573
            if (empty($inline_text_prefix)) {
574
              $annotations_and_sources['source_references'][] = $reference_citation;
575
            } else {
576
              $annotations_and_sources['source_references'][] = ' (' . $reference_citation . ')';
577
            }
578
          }
579

    
580
          // also put the name in source into the array, these are already included in the $reference_citation but are
581
          // still required to be available separately in some contexts.
582
          $name_in_source_render_array = compose_name_in_source(
583
            $source,
584
            $config['link_to_name_used_in_source'] == 1
585
          );
586

    
587
          if (!empty($name_in_source_render_array)) {
588
            $annotations_and_sources['names_used_in_source'][$name_in_source_render_array['#_plaintext']] = drupal_render($name_in_source_render_array);
589
          }
590
        }
591
      } // END of loop over sources
592

    
593
    // annotations footnotes separate.
594
    $annotations_and_sources['foot_note_keys'] = theme('cdm_annotations_as_footnotekeys',
595
      array(
596
        'cdmBase_list' => $entity,
597
        'footnote_list_key' => $footnote_list_key_suggestion,
598
      )
599
    );
600

    
601
    } // END of references inline
602

    
603
    // footnotes for sources and annotations or put into into bibliography if requested ...
604
    if ($config['add_footnote_keys'] == 1) {
605
        $annotations_and_sources['foot_note_keys'] = cdm_create_footnotes(
606
          $entity, ',',
607
          $footnote_list_key_suggestion,
608
          $config['link_to_reference'] == 1,
609
          $config['link_to_name_used_in_source'] == 1,
610
          !empty($config['bibliography_aware'])
611
        );
612
    }
613

    
614
    return $annotations_and_sources;
615
  }
616

    
617

    
618
  /**
619
   * This method determines the footnote key for original sources to be shown in the bibliography block
620
   *
621
   * The footnote key depends on the value of the 'enabled' value of the bibliography_settings
622
   *    - enabled == 1 -> "BIBLIOGRAPHY"
623
   *    - enabled == 0 -> "BIBLIOGRAPHY-$key_suggestion"
624
   *
625
   * @see get_bibliography_settings() and @see constant BIBLIOGRAPHY_FOOTNOTE_KEY
626
   *
627
   * @param $key_suggestion string
628
   *    optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be retrieved by
629
   *    calling RenderHints::getFootnoteListKey().
630

    
631
   *
632
   * @return string
633
   *  the footnote_list_key
634
   */
635
  function original_source_footnote_list_key($key_suggestion = null) {
636
    if(!$key_suggestion){
637
      $key_suggestion = RenderHints::getFootnoteListKey();
638
    }
639
    $bibliography_settings = get_bibliography_settings();
640
    $footnote_list_key = $bibliography_settings['enabled'] == 1 ? BIBLIOGRAPHY_FOOTNOTE_KEY : BIBLIOGRAPHY_FOOTNOTE_KEY . '-' . $key_suggestion;
641
    return $footnote_list_key;
642
  }
643

    
644
  /**
645
   * Provides the according tag name for the description element markup which fits the  $feature_block_settings['as_list'] value
646
   *
647
   * @param $feature_block_settings
648
   *   A feature_block_settings array, for details, please see get_feature_block_settings($feature_uuid = 'DEFAULT')
649
   */
650
  function cdm_feature_block_element_tag_name($feature_block_settings){
651
    switch ($feature_block_settings['as_list']){
652
      case 'ul':
653
      case 'ol':
654
        return 'li';
655
      case 'div':
656
        if(isset($feature_block_settings['element_tag'])){
657
          return $feature_block_settings['element_tag'];
658
        }
659
        return 'span';
660
      case 'dl':
661
        return 'dd';
662
      default:
663
        return 'div'; // should never happen, throw error instead?
664
    }
665
  }
666

    
667

    
668
/* ==================== COMPOSE FUNCTIONS =============== */
669

    
670
  /**
671
   * Returns a set of feature blocks for a taxon profile from the $mergedFeatureNodes of a given $taxon.
672
   *
673
   * The taxon profile consists of drupal block elements, one for the description elements
674
   * of a specific feature. The structure is defined by specific FeatureTree.
675
   * The chosen FeatureTree is merged with the list of description elements prior to using this method.
676
   *
677
   * The merged nodes can be obtained by making use of the
678
   * function cdm_ws_descriptions_by_featuretree().
679
   *
680
   * @see cdm_ws_descriptions_by_featuretree()
681
   *
682
   * @param $mergedFeatureNodes
683
   *
684
   * @param $taxon
685
   *
686
   * @return array
687
   *  A Drupal render array containing feature blocks and the table of content
688
   *
689
   * @ingroup compose
690
   */
691
  function make_feature_block_list($mergedFeatureNodes, $taxon) {
692

    
693
    $block_list = array();
694

    
695
    $gallery_settings = getGallerySettings(CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME);
696

    
697
    $use_description_features = array(UUID_USE);
698

    
699

    
700
    RenderHints::pushToRenderStack('feature_block');
701
    // Create a drupal block for each feature
702
    $block_weight = - FEATURE_BLOCK_WEIGHT_INCREMENT;
703
    foreach ($mergedFeatureNodes as $feature_node) {
704

    
705
      $block_weight = $block_weight + FEATURE_BLOCK_WEIGHT_INCREMENT;
706

    
707
      if ((isset($feature_node->descriptionElements['#type']) ||
708
          has_feature_node_description_elements($feature_node)) && $feature_node->term->uuid != UUID_IMAGE) { // skip empty or suppressed features
709

    
710
        RenderHints::pushToRenderStack($feature_node->term->uuid);
711
          
712
        $feature_name = cdm_term_representation($feature_node->term, 'Unnamed Feature');
713
        $feature_block_settings = get_feature_block_settings($feature_node->term->uuid);
714
        
715

    
716
        $block = feature_block($feature_name, $feature_node->term);
717
        $block->content = array();
718
        $block_content_is_empty = TRUE;
719

    
720
        if(array_search($feature_node->term->uuid, $use_description_features) !== false) {
721
          // do not show features which belong to the UseDescriptions, these are
722
          // handled by compose_feature_block_items_use_records() where the according descriptions are
723
          // fetched again separately.
724
          // UseDescriptions are a special feature introduced for palmweb
725
          continue;
726
        }
727

    
728
        /*
729
         * Content/DISTRIBUTION.
730
         */
731
        if ($feature_node->term->uuid == UUID_DISTRIBUTION) {
732
          $block = compose_feature_block_distribution($taxon, $feature_node->descriptionElements, $feature_node->term);
733
          $block_content_is_empty = FALSE;
734
        }
735

    
736
        /*
737
         * Content/COMMON_NAME.
738
         */
739
        else if ($feature_node->term->uuid == UUID_COMMON_NAME) {
740
          $common_names_render_array = compose_feature_block_items_feature_common_name($feature_node->descriptionElements, $feature_node->term);
741
          $block->content[] = $common_names_render_array;
742
          $block_content_is_empty = FALSE;
743
        }
744

    
745
        /*
746
         * Content/Use Description (Use + UseRecord)
747
         */
748
        else if ($feature_node->term->uuid == UUID_USE_RECORD) {
749
          $block->content[] = cdm_block_use_description_content($taxon->uuid, $feature_node->term);
750
          $block_content_is_empty = FALSE;
751
        }
752

    
753
        /*
754
         * Content/ALL OTHER FEATURES.
755
         */
756
        else {
757

    
758
          $media_list = array();
759
          $elements_render_array = array();
760
          $child_elements_render_array = null;
761

    
762
          if (isset($feature_node->descriptionElements[0])) {
763
            $elements_render_array = compose_feature_block_items_generic($feature_node->descriptionElements, $feature_node->term);
764
          }
765

    
766
          // Content/ALL OTHER FEATURES/Subordinate Features
767
          // subordinate features are printed inline in one floating text,
768
          // it is expected hat subordinate features can "contain" TextData,
769
          // Qualitative- and Qualitative- DescriptionElements
770
          if (isset($feature_node->childNodes[0])) {
771
            $child_elements_render_array = compose_feature_block_items_nested($feature_node, $media_list, $feature_block_settings);
772
            $elements_render_array = array_merge($elements_render_array, $child_elements_render_array);
773
          }
774
          $block_content_is_empty = $block_content_is_empty && empty($media_list) && empty($elements_render_array);
775
          if(!$block_content_is_empty){
776
            $block->content[] = compose_feature_block_wrap_elements($elements_render_array, $feature_node->term, $feature_block_settings['glue']);
777
            $block->content[] = compose_feature_media_gallery($feature_node, $media_list, $gallery_settings);
778
            /*
779
             * Footnotes for the feature block
780
             */
781
            $block->content[] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => PSEUDO_FEATURE_BIBLIOGRAPHY . '-' . $feature_node->term->uuid)));
782
            $block->content[] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => $feature_node->term->uuid)));
783
            $block->content[] = markup_to_render_array(theme('cdm_annotation_footnotes', array('footnoteListKey' => $feature_node->term->uuid)));
784
          }
785
        } // END all other features
786

    
787
        // allows modifying the block contents via a the hook_cdm_feature_node_block_content_alter
788
        drupal_alter('cdm_feature_node_block_content', $block->content, $feature_node->term, $feature_node->descriptionElements);
789

    
790
        if(!$block_content_is_empty){ // skip empty block content
791
          $block_list[$block_weight] = $block;
792
          cdm_toc_list_add_item(cdm_term_representation($feature_node->term), $feature_node->term->uuid, null, FALSE, $block_weight);
793
        } // END: skip empty block content
794
      } // END: skip empty or suppressed features
795
      RenderHints::popFromRenderStack();
796
    } // END: creating a block per feature
797

    
798
    RenderHints::popFromRenderStack();
799

    
800
    drupal_alter('cdm_feature_node_blocks', $block_list, $taxon);
801

    
802
    ksort($block_list);
803

    
804
    return  $block_list;
805
  }
806

    
807
/**
808
 * Creates a render array of description elements  held by child nodes of the given feature node.
809
 *
810
 * This function is called recursively!
811
 *
812
 * @param $feature_node
813
 *   The feature node.
814
 * @param array $media_list
815
 *   List of CDM Media entities. All media of subordinate elements should be passed to the main feature.ä
816
 * @param $feature_block_settings
817
 *   The feature block settings.
818
 * @param $main_feature
819
 *  Only used internally in recursive calls.
820
 *
821
 * @return array
822
 *  A Drupal render array
823
 *
824
 * @ingroup compose
825
 */
826
function compose_feature_block_items_nested($feature_node, &$media_list, $feature_block_settings, $main_feature = NULL)
827
{
828

    
829
  if(!$main_feature){
830
    $main_feature = $feature_node->term;
831
  }
832
  /*
833
   * TODO should be configurable, options; YES, NO, AUTOMATIC
834
   * (automatic will only place the label if the first word of the description element text is not the same)
835
   */
836
  $prepend_feature_label = false;
837

    
838
  $render_arrays = array();
839
  foreach ($feature_node->childNodes as $child_node) {
840
    if (isset($child_node->descriptionElements[0])) {
841
      foreach ($child_node->descriptionElements as $element) {
842

    
843
        if (isset($element->media[0])) {
844
          // Append media of subordinate elements to list of main
845
          // feature.
846
          $media_list = array_merge($media_list, $element->media);
847
        }
848

    
849
        $child_node_element = null;
850
        switch ($element->class) {
851
          case 'TextData':
852
            $child_node_element = compose_description_element_text_data($element, $element->feature->uuid, $feature_block_settings, $prepend_feature_label);
853
            break;
854
          case 'CategoricalData':
855
            $child_node_element = compose_description_element_categorical_data($element, $feature_block_settings, $prepend_feature_label);
856
            break;
857
          case 'QuantitativeData':
858
            $child_node_element = compose_description_element_quantitative_data($element, $feature_block_settings, $prepend_feature_label);
859

    
860
        }
861
        if (is_array($child_node_element)) {
862
          $render_arrays[] = $child_node_element;
863
        }
864
      }
865
    }
866

    
867
    if(isset($child_node->childNodes[0])){
868
      $render_arrays = array_merge($render_arrays, compose_feature_block_items_nested($child_node, $media_list, $feature_block_settings, $main_feature ));
869
    }
870
  }
871

    
872
  return $render_arrays;
873
}
874

    
875
  /**
876
   *
877
   * @param $feature_node
878
   *  The merged feature three node which potentially contains media in its description elements.
879
   * @param $media_list
880
   *    Additional media to be merged witht the media contained in the nodes description elements
881
   * @param $gallery_settings
882
   * @return array
883
   *
884
   * @ingroup compose
885
   */
886
  function compose_feature_media_gallery($feature_node, $media_list, $gallery_settings) {
887

    
888
    if (isset($feature_node->descriptionElements)) {
889
      $media_list = array_merge($media_list, cdm_dataportal_media_from_descriptionElements($feature_node->descriptionElements));
890
    }
891

    
892
    $captionElements = array('title', 'rights');
893

    
894
    if (isset($media_list[0]) && isset($gallery_settings['cdm_dataportal_media_maxextend']) && isset($gallery_settings['cdm_dataportal_media_cols'])) {
895
      $gallery = compose_cdm_media_gallerie(array(
896
        'mediaList' => $media_list,
897
        'galleryName' => CDM_DATAPORTAL_DESCRIPTION_GALLERY_NAME . '_' . $feature_node->term->uuid,
898
        'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
899
        'cols' => $gallery_settings['cdm_dataportal_media_cols'],
900
        'captionElements' => $captionElements,
901
      ));
902
      return markup_to_render_array($gallery);
903
    }
904

    
905
    return markup_to_render_array('');
906
  }
907

    
908
  /**
909
   * Composes the distribution feature block for a taxon
910
   *
911
   * @param $taxon
912
   * @param $descriptionElements
913
   *   an associative array with two elements:
914
   *   - '#type': must be 'DTO'
915
   *   - 'DistributionInfoDTO': a CDM DistributionInfoDTO object as returned by the DistributionInfo web service
916
   * @param $feature
917
   *
918
   * @return array
919
   *  A drupal render array
920
   *
921
   * @ingroup compose
922
   */
923
  function compose_feature_block_distribution($taxon, $descriptionElements, $feature) {
924
    $text_data_glue = '';
925
    $text_data_sortOutArray = FALSE;
926
    $text_data_enclosingTag = 'ul';
927
    $text_data_out_array = array();
928

    
929
    $distributionElements = NULL;
930
    $distribution_info_dto = NULL;
931
    $distribution_sortOutArray = FALSE;
932

    
933
    $feature_block_settings = get_feature_block_settings(UUID_DISTRIBUTION);
934

    
935
    // TODO use feature_block_settings instead of DISTRIBUTION_ORDER_MODE
936
    if (variable_get(DISTRIBUTION_ORDER_MODE, DISTRIBUTION_ORDER_MODE_DEFAULT) != 'TREE') {
937
      $distribution_glue = '';
938
      $distribution_enclosingTag = 'dl';
939
    } else {
940
      $distribution_glue = '';
941
      $distribution_enclosingTag = 'ul';
942
    }
943

    
944
    if (!isset($descriptionElements['#type']) || !$descriptionElements['#type'] == 'DTO') {
945
      // skip the DISTRIBUTION section if there is no DTO type element
946
      return array(); // FIXME is it ok to return an empty array?
947
    }
948

    
949
    $block = feature_block(
950
      cdm_term_representation($feature, 'Unnamed Feature'),
951
      $feature
952
    );
953
    $block->content = array();
954

    
955
    // $$descriptionElements['TextData'] is added to to the feature node in merged_taxon_feature_tree()
956
    if (isset($descriptionElements['TextData'])) {
957
      // --- TextData
958
      foreach ($descriptionElements['TextData'] as $text_data_element) {
959
        $text_data_render_array = compose_description_element_text_data($text_data_element, $text_data_element->feature->uuid, $feature_block_settings);
960
        $repr = drupal_render($text_data_render_array);
961

    
962
        if (!array_search($repr, $text_data_out_array)) { // de-duplication !!
963
          $text_data_out_array[] = $repr;
964
          // TODO HINT: sorting in compose_feature_block_wrap_elements will
965
          // not work since this array contains html attributes with uuids
966
          // and what is about cases like the bibliography where
967
          // any content can be prefixed with some foot-note anchors?
968
          $text_data_sortOutArray = TRUE;
969
          $text_data_glue = '<br/> ';
970
          $text_data_enclosingTag = 'p';
971
        }
972
      }
973
    }
974

    
975

    
976
    if ($text_data_out_array && variable_get(DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP, 0)) {
977
      $block->content[] = compose_feature_block_wrap_elements(
978
        $text_data_out_array, $feature, $text_data_glue, $text_data_sortOutArray
979
      );
980
    }
981

    
982
    // --- Distribution map
983
    $distribution_map_query_parameters = NULL;
984

    
985
    $map_visibility = variable_get(DISTRIBUTION_MAP_VISIBILITY, DISTRIBUTION_MAP_VISIBILITY_DEFAULT);
986
    if(variable_get(DISTRIBUTION_MAP_VISIBILITY, DISTRIBUTION_MAP_VISIBILITY_DEFAULT) == 'always' ||
987
        $map_visibility == 'automatic' && isset($descriptionElements['DistributionInfoDTO']->mapUriParams)
988
      )
989
    {
990
      $distribution_map_query_parameters = $descriptionElements['DistributionInfoDTO']->mapUriParams;
991
    }
992
    $map_render_element = compose_distribution_map($distribution_map_query_parameters);
993
    $block->content[] = $map_render_element;
994

    
995
    $dto_out_array = array();
996

    
997
    // --- Condensed Distribution
998
    if(variable_get(DISTRIBUTION_CONDENSED) && isset($descriptionElements['DistributionInfoDTO']->condensedDistribution)){
999
      $condensed_distribution_markup = '<p class="condensed_distribution">';
1000

    
1001
      $isFirst = true;
1002
      if(isset($descriptionElements['DistributionInfoDTO']->condensedDistribution->indigenous[0])){
1003
        foreach($descriptionElements['DistributionInfoDTO']->condensedDistribution->indigenous as $cdItem){
1004
          if(!$isFirst){
1005
            $condensed_distribution_markup .= ' ';
1006
          }
1007
          $condensed_distribution_markup .= '<span class="status_' . $cdItem->status->idInVocabulary . '">'
1008
          . $cdItem->areaStatusLabel . '</span>';
1009
          $isFirst = false;
1010
        }
1011
      }
1012

    
1013
      if(isset($descriptionElements['DistributionInfoDTO']->condensedDistribution->foreign[0])) {
1014
        if(!$isFirst){
1015
          $condensed_distribution_markup .= ' ';
1016
        }
1017
        $isFirst = TRUE;
1018
        $condensed_distribution_markup .= '[';
1019
        foreach ($descriptionElements['DistributionInfoDTO']->condensedDistribution->foreign as $cdItem) {
1020
          if (!$isFirst) {
1021
            $condensed_distribution_markup .= ' ';
1022
          }
1023
          $condensed_distribution_markup .= '<span class="status_' . $cdItem->status->titleCache . '">'
1024
            . $cdItem->areaStatusLabel . '</span>';
1025
          $isFirst = false;
1026
        }
1027
        $condensed_distribution_markup .= ']';
1028
      }
1029

    
1030
      $condensed_distribution_markup .= '&nbsp;' . l(
1031
          font_awesome_icon_markup(
1032
            'fa-info-circle',
1033
            array(
1034
              'alt'=>'help',
1035
              'class' => array('superscript')
1036
            )
1037
          ),
1038
          variable_get(DISTRIBUTION_CONDENSED_INFO_PATH, DISTRIBUTION_CONDENSED_INFO_PATH_DEFAULT) ,
1039
          array('html' => TRUE));
1040
      $condensed_distribution_markup .= '</p>';
1041
      $dto_out_array[] = $condensed_distribution_markup;
1042
    }
1043

    
1044
    // --- tree or list
1045
    if (isset($descriptionElements['DistributionInfoDTO'])) {
1046
      $distribution_info_dto = $descriptionElements['DistributionInfoDTO'];
1047

    
1048
      // --- tree
1049
      if (is_object($distribution_info_dto->tree)) {
1050
        $distribution_tree_render_array = compose_distribution_hierarchy($distribution_info_dto->tree, $feature_block_settings);
1051
        $dto_out_array[] = $distribution_tree_render_array;
1052
      }
1053

    
1054
      // --- sorted element list
1055
      if (is_array($distribution_info_dto->elements) && count($distribution_info_dto->elements) > 0) {
1056
        foreach ($distribution_info_dto->elements as $descriptionElement) {
1057
          if (is_object($descriptionElement->area)) {
1058
            $sortKey = $descriptionElement->area->representation_L10n;
1059
            $distributionElements[$sortKey] = $descriptionElement;
1060
          }
1061
        }
1062
        ksort($distributionElements);
1063
        $distribution_element_render_array = compose_description_elements_distribution($distributionElements);
1064
        $dto_out_array[] = $distribution_element_render_array;
1065

    
1066
      }
1067
      //
1068
      $block->content[] = compose_feature_block_wrap_elements(
1069
        $dto_out_array, $feature, $distribution_glue, $distribution_sortOutArray
1070
      );
1071
    }
1072

    
1073
    // --- TextData at the bottom
1074
    if ($text_data_out_array && !variable_get(DISTRIBUTION_TEXTDATA_DISPLAY_ON_TOP, 0)) {
1075
      $block->content[] = compose_feature_block_wrap_elements(
1076
        $text_data_out_array, $feature, $text_data_glue, $text_data_sortOutArray
1077
      );
1078
    }
1079

    
1080
    $block->content[] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => 'BIBLIOGRAPHY-' . UUID_DISTRIBUTION)));
1081
    $block->content[] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => UUID_DISTRIBUTION)));
1082
    $block->content[] = markup_to_render_array(theme('cdm_annotation_footnotes', array('footnoteListKey' => UUID_DISTRIBUTION)));
1083

    
1084
    return $block;
1085
  }
1086

    
1087

    
1088
  /**
1089
   * Composes a drupal render array for single CDM TextData description element.
1090
   *
1091
   * @param $element
1092
   *    The CDM TextData description element.
1093
   *  @param $feature_uuid
1094
   * @param bool $prepend_feature_label
1095
   *   Used in nested feature trees to put the feature as label in front of the description element text representation.
1096
   *
1097
   * @return array
1098
   *   A drupal render array with the following elements being used:
1099
   *    - #tag: either 'div', 'li', ...
1100
   *    ⁻ #attributes: class attributes
1101
   *    - #value_prefix: (optionally) contains footnote anchors
1102
   *    - #value: contains the textual content
1103
   *    - #value_suffix: (optionally) contains footnote keys
1104
   *
1105
   * @ingroup compose
1106
   */
1107
  function compose_description_element_text_data($element, $feature_uuid, $feature_block_settings, $prepend_feature_label = FALSE) {
1108

    
1109
    $footnote_list_key_suggestion = $feature_uuid;
1110

    
1111
    $element_markup = '';
1112
    if (isset($element->multilanguageText_L10n->text)) {
1113
      // TODO replacement of \n by <br> should be configurable
1114
      $element_markup = str_replace("\n", "<br/>", $element->multilanguageText_L10n->text);
1115
    }
1116

    
1117
    $render_array = compose_description_element($element, $feature_block_settings, $element_markup, $footnote_list_key_suggestion, $prepend_feature_label);
1118

    
1119
    return $render_array;
1120
  }
1121

    
1122

    
1123
/**
1124
 * Theme function to render CDM DescriptionElements of the type TaxonInteraction.
1125
 *
1126
 * @param $element
1127
 *  The CDM TaxonInteraction entity
1128
 *
1129
 * @return
1130
 *  A drupal render array
1131
 *
1132
 * @ingroup compose
1133
 */
1134
function compose_description_element_taxon_interaction($element, $feature_block_settings) {
1135

    
1136
  $out = '';
1137

    
1138

    
1139
  if (isset($element->description_L10n)) {
1140
    $out .=  ' ' . $element->description_L10n;
1141
  }
1142

    
1143
  if(isset($element->taxon2)){
1144
    $out = render_taxon_or_name($element->taxon2, url(path_to_taxon($element->taxon2->uuid)));
1145
  }
1146

    
1147
  $render_array = compose_description_element($element, $feature_block_settings, $out, $element->feature->uuid);
1148

    
1149
  return $render_array;
1150
}
1151

    
1152

    
1153
/**
1154
 * Renders a single instance of the type IndividualsAssociations.
1155
 *
1156
 * @param $element
1157
 *   The CDM IndividualsAssociations entity.
1158
 * @param $feature_block_settings
1159
 *
1160
 * @return array
1161
 *   Drupal render array
1162
 *
1163
 * @ingroup compose
1164
 */
1165
function compose_description_element_individuals_association($element, $feature_block_settings) {
1166

    
1167
  $out = '';
1168

    
1169
  $render_array = compose_cdm_specimen_or_observation($element->associatedSpecimenOrObservation);
1170

    
1171
  if (isset($element->description_L10n)) {
1172
    $out .=  ' ' . $element->description_L10n;
1173
  }
1174

    
1175
  $out .= drupal_render($render_array);
1176

    
1177
  $render_array = compose_description_element($element, $feature_block_settings, $out, $element->feature->uuid);
1178

    
1179
  return $render_array;
1180
}
1181

    
1182
/**
1183
 * Renders a single instance of the type CategoricalData.
1184
 *
1185
 * @param $element
1186
 *  The CDM CategoricalData entity
1187
 *
1188
 * @param $feature_block_settings
1189
 *
1190
 * @param bool $prepend_feature_label
1191
 *   Used in nested feature trees to put the feature as label in front of the description element text representation.
1192
 *
1193
 * @return array
1194
 *   a drupal render array for given CategoricalData element
1195
 *
1196
 * @ingroup compose
1197
 */
1198
function compose_description_element_categorical_data($element, $feature_block_settings, $prepend_feature_label = FALSE) {
1199

    
1200
  $state_data_markup = render_state_data($element);
1201

    
1202
  $render_array = compose_description_element($element, $feature_block_settings, $state_data_markup, $element->feature->uuid, $prepend_feature_label);
1203

    
1204
  return $render_array;
1205
}
1206

    
1207
/**
1208
 * @param $element
1209
 *
1210
 * @return string
1211
 * the markup
1212
 */
1213
function render_state_data($element) {
1214

    
1215
  $state_data_items = [];
1216

    
1217
  if (isset($element->stateData)) {
1218
    foreach ($element->stateData as $state_data) {
1219

    
1220
      $state = NULL;
1221

    
1222
      if (isset($state_data->state)) {
1223
        $state = cdm_term_representation($state_data->state);
1224

    
1225
          $sample_count = 0;
1226
          if (isset($state_data->count)) {
1227
            $sample_count = $state_data->count;
1228
            $state .= ' [' . $state_data->count . ']';
1229
          }
1230
    
1231
          if (isset($state_data->modifyingText_L10n)) {
1232
            $state .= ' ' . $state_data->modifyingText_L10n;
1233
          }
1234
    
1235
          $modifiers_strings = cdm_modifers_representations($state_data);
1236
          $state_data_markup = $state . ($modifiers_strings ? ' ' . $modifiers_strings : '');
1237
          // we could use strip_tags() to reduce the markup to text for the key but this is expensive
1238
          $sort_key = str_pad($sample_count, 6, '0', STR_PAD_LEFT) . '_' . $state_data_markup;
1239
          $state_data_items[$sort_key] = $state_data_markup;
1240
      }
1241

    
1242
    }
1243
    krsort($state_data_items);
1244
    $out = '<span class="' . html_class_attribute_ref($element) . '">' . join(', ', $state_data_items) .  '</span>';
1245
  }
1246
  return $out;
1247
}
1248

    
1249

    
1250
/**
1251
 * Theme function to render CDM DescriptionElements of the type QuantitativeData.
1252
 *
1253
 * The function renders the statisticalValues contained in the QuantitativeData
1254
 * entity according to the following scheme:
1255
 *
1256
 * (ExtremeMin)-Min-Average-Max-(ExtremeMax)
1257
 *
1258
 * All modifiers of these values are appended.
1259
 *
1260
 * If the QuantitativeData is containing more statisticalValues with further
1261
 * statisticalValue types, these additional measures will be appended to the
1262
 * above string separated by whitespace.
1263
 *
1264
 * Special cases;
1265
 * 1. Min==Max: this will be interpreted as Average
1266
 *
1267
 * @param $element
1268
 *  The CDM QuantitativeData entity
1269
 *
1270
 * @param $feature_block_settings
1271
 *
1272
 * @param bool $prepend_feature_label
1273
 *   Used in nested feature trees to put the feature as label in front of the description element text representation.
1274
 *
1275
 *
1276
 * @return array
1277
 *   drupal render array for the given QuantitativeData element
1278
 *
1279
 * @ingroup compose
1280
 */
1281
function compose_description_element_quantitative_data($element, $feature_block_settings, $prepend_feature_label = FALSE) {
1282
  /*
1283
   * - statisticalValues
1284
   *   - value
1285
   *   - modifiers
1286
   *   - type
1287
   * - unit->representation_L10n
1288
   * - modifyingText
1289
   * - modifiers
1290
   * - sources
1291
   */
1292

    
1293
  $out = render_quantitative_statistics($element);
1294

    
1295
  $render_array = compose_description_element($element, $feature_block_settings, $out, $element->feature->uuid, $prepend_feature_label);
1296

    
1297
  return $render_array;
1298
}
1299

    
1300
/**
1301
 * Composes the HTML for quantitative statistics
1302
 * @param $element
1303
 *
1304
 * @return string
1305
 */
1306
function render_quantitative_statistics($element) {
1307
  $out = '';
1308
  $type_representation = NULL;
1309
  $min_max = min_max_array();
1310

    
1311
  $other_values = [];
1312

    
1313
  if (isset($element->statisticalValues)) {
1314
    $out = '<span class=\"' . html_class_attribute_ref($element) . '\">';
1315
    $other_values_markup = [];
1316
    foreach ($element->statisticalValues as $statistical_val) {
1317

    
1318
      // compile the full value string which also may contain modifiers
1319
      if (isset($statistical_val->value)) {
1320
        $statistical_val->_value = $statistical_val->value;
1321
      }
1322
      $val_modifiers_strings = cdm_modifers_representations($statistical_val);
1323
      if ($val_modifiers_strings) {
1324
        $statistical_val->_value = ' ' . $val_modifiers_strings . ' ' . $statistical_val->_value;
1325
      }
1326

    
1327
      // either put into min max array or into $other_values
1328
      // for generic output to be appended to 'min-max' string
1329
      if (array_key_exists(statistical_measure_term2min_max_key($statistical_val->type), $min_max)) {
1330
        $min_max[statistical_measure_term2min_max_key($statistical_val->type)] = $statistical_val;
1331
      }
1332
      else {
1333
        $other_values[] = $statistical_val;
1334
      }
1335
    } // end of loop over statisticalValues
1336

    
1337
    // create markup
1338

    
1339
    $min_max_markup = min_max_markup($min_max);
1340

    
1341

    
1342
    foreach ($other_values as $statistical_val) {
1343
      $statistical_val_type_representation = NULL;
1344
      if (isset($statistical_val->type)) {
1345
        $statistical_val_type_representation = cdm_term_representation($statistical_val->type);
1346
      }
1347

    
1348
      switch (statistical_measure_term2min_max_key($statistical_val->type)){
1349
        case 'SampleSize':
1350
          $value_markup = '<span class="' . html_class_attribute_ref($statistical_val) . ' ' . $statistical_val->type->termType . ' ">'
1351
            . '[' . $statistical_val->_value . ']</span>';
1352
          $type_markup = '';
1353
          break;
1354
        default:
1355
        $value_markup = '<span class="' . html_class_attribute_ref($statistical_val) . ' ' . $statistical_val->type->termType . ' ">'
1356
          . $statistical_val->_value . '</span>';
1357
         $type_markup = ($statistical_val_type_representation ? ' <span class="type">' . $statistical_val_type_representation . '</span>' : '');
1358
      }
1359
      $other_values_markup[] = $value_markup . $type_markup;
1360
    }
1361

    
1362

    
1363
    $out .= $min_max_markup . ' ' . implode($other_values_markup, ', ');
1364
    $out .= '</span>';
1365
  }
1366

    
1367
  if (isset($element->unit)) {
1368
    $out .= ' <span class="unit" title="'
1369
      . cdm_term_representation($element->unit) . '">'
1370
      . cdm_term_representation_abbreviated($element->unit)
1371
      . '</span>';
1372
  }
1373

    
1374
  // modifiers of the description element itself
1375
  $modifier_string = cdm_modifers_representations($element);
1376
  $out .= ($modifier_string ? ' ' . $modifier_string : '');
1377
  if (isset($element->modifyingText_L10n)) {
1378
    $out = $element->modifyingText_L10n . ' ' . $out;
1379
  }
1380
  return $out;
1381
}
1382

    
1383
function statistical_measure_term2min_max_key($term){
1384
  static $uuid2key = [
1385
    UUID_STATISTICALMEASURE_MIN => 'Min',
1386
    UUID_STATISTICALMEASURE_MAX => 'Max',
1387
    UUID_STATISTICALMEASURE_AVERAGE => 'Average',
1388
    UUID_STATISTICALMEASURE_SAMPLESIZE => 'SampleSize',
1389
    UUID_STATISTICALMEASURE_VARIANCE => 'Variance',
1390
    UUID_STATISTICALMEASURE_TYPICALLOWERBOUNDARY => 'TypicalLowerBoundary',
1391
    UUID_STATISTICALMEASURE_TYPICALUPPERBOUNDARY => 'TypicalUpperBoundary',
1392
    UUID_STATISTICALMEASURE_STANDARDDEVIATION => 'StandardDeviation',
1393
    UUID_STATISTICALMEASURE_EXACTVALUE => 'ExactValue',
1394
    UUID_STATISTICALMEASURE_STATISTICALMEASUREUNKNOWNDATA => 'StatisticalMeasureUnknownData'
1395
  ];
1396
  return $uuid2key[$term->uuid];
1397
}
1398

    
1399

    
1400
/**
1401
 * Wraps the render array for the given feature into an enclosing html tag.
1402
 *
1403
 * Optionally the elements can be sorted and glued together by a separator string.
1404
 *
1405
 * @param array $description_element_render_arrays
1406
 *   An list of render arrays. Which are usually are produced by the compose_description_element()
1407
 *   function. The render arrays should be of #type=html_tag, so that they can understand the #attribute property.
1408
 * @param  $feature :
1409
 *  The feature to which the elements given in $elements are belonging to.
1410
 * @param string $glue :
1411
 *  Defaults to empty string.
1412
 * @param bool $sort
1413
 *   Boolean Whether to sort the $elements alphabetically, default is FALSE
1414
 *
1415
 * @return array
1416
 *    A Drupal render array
1417
 *
1418
 * @ingroup compose
1419
 */
1420
  function compose_feature_block_wrap_elements(array $description_element_render_arrays, $feature, $glue = '', $sort = FALSE)
1421
  {
1422

    
1423
    $feature_block_settings = get_feature_block_settings($feature->uuid);
1424
    $enclosing_tag = $feature_block_settings['as_list'];
1425

    
1426
    if ($sort) { // TODO remove parameter and replace by $feature_block_settings['sort_elements']
1427
      usort($description_element_render_arrays, 'compare_description_element_render_arrays');
1428
    }
1429

    
1430
    $is_first = true;
1431
    foreach($description_element_render_arrays as &$element_render_array){
1432
      if(!is_array($element_render_array)){
1433
        $element_render_array = markup_to_render_array($element_render_array);
1434
      }
1435
      $element_render_array['#attributes']['class'][] = "feature-block-element";
1436

    
1437
      // add the glue!
1438
      if(!$is_first) {
1439
        if (isset($element_render_array['#value'])) {
1440
          $element_render_array['#value'] = $glue . $element_render_array['#value'];
1441
        } elseif (isset($element_render_array['#markup'])) {
1442
          $element_render_array['#markup'] = $glue . $element_render_array['#markup'];
1443
        }
1444
      }
1445
      $is_first = false;
1446
    }
1447

    
1448
    $render_array['elements']['children'] = $description_element_render_arrays;
1449

    
1450
    $render_array['elements']['#prefix'] = '<' . $enclosing_tag . ' class="feature-block-elements" id="' . $feature->representation_L10n . '">';
1451
    $render_array['elements']['#suffix'] = '</' . $enclosing_tag . '>';
1452

    
1453
    return $render_array;
1454
  }
1455

    
1456

    
1457
  /* compose nameInSource or originalNameString as markup
1458
   *
1459
   * @param $source
1460
   * @param $do_link_to_name_used_in_source
1461
   * @param $suppress_for_shown_taxon
1462
   *    the nameInSource will be suppressed when it has the same name as the accepted taxon
1463
   *    for which the taxon page is being created, Defaults to TRUE
1464
   *
1465
   * @return array
1466
   *    A Drupal render array with an additional element, the render array is empty
1467
   *    if the source had no name in source information
1468
   *    - #_plaintext: contains the plaintext version of the name (custom element)
1469
   *
1470
   * @ingroup compose
1471
   */
1472
  function compose_name_in_source($source, $do_link_to_name_used_in_source, $suppress_for_shown_taxon = TRUE) {
1473

    
1474
    $plaintext = NULL;
1475
    $markup = NULL;
1476
    $name_in_source_render_array = array();
1477

    
1478
    static $taxon_page_accepted_name = '';
1479
    $taxon_uuid = get_current_taxon_uuid();
1480
    if($suppress_for_shown_taxon && $taxon_uuid && empty($taxon_page_accepted_name)){
1481

    
1482
      $current_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $taxon_uuid);
1483
      $taxon_page_accepted_name = $current_taxon->name->titleCache;
1484
    }
1485

    
1486
    if (isset($source->nameUsedInSource->uuid) && isset($source->nameUsedInSource->titleCache)) {
1487
      // it is a DescriptionElementSource !
1488
      $plaintext = $source->nameUsedInSource->titleCache;
1489
      if($suppress_for_shown_taxon && $taxon_page_accepted_name == $plaintext){
1490
        return $name_in_source_render_array; // SKIP this name
1491
      }
1492
      $markup = render_taxon_or_name($source->nameUsedInSource);
1493
      if ($do_link_to_name_used_in_source) {
1494
        $markup = l(
1495
          $markup,
1496
          path_to_name($source->nameUsedInSource->uuid),
1497
          array(
1498
            'attributes' => array(),
1499
            'absolute' => TRUE,
1500
            'html' => TRUE,
1501
          ));
1502
      }
1503
    }
1504
    else if (isset($source->originalNameString) && !empty($source->originalNameString)) {
1505
      // the name used in source can not be expressed as valid taxon name,
1506
      // so the editor has chosen to put the freetext name into ReferencedEntityBase.originalNameString
1507
      // field
1508
      // using the originalNameString as key to avoid duplicate entries
1509
      $plaintext = $source->originalNameString;
1510
      if($suppress_for_shown_taxon && $taxon_page_accepted_name == $plaintext){
1511
        return $name_in_source_render_array; // SKIP this name
1512
      }
1513
      $markup = $source->originalNameString;
1514
    }
1515

    
1516
    if ($plaintext) { // checks if we have any content
1517
      $name_in_source_render_array = markup_to_render_array($markup);
1518
      $name_in_source_render_array['#_plaintext'] = $plaintext;
1519
    }
1520

    
1521
    return $name_in_source_render_array;
1522
  }
1523

    
1524

    
1525

    
1526
  /**
1527
   * Return HTML for a list of description elements.
1528
   *
1529
   * Usually these are of a specific feature type.
1530
   *
1531
   * @param $description_elements
1532
   *   array of descriptionElements which belong to the same feature.
1533
   *   These descriptions elements of a Description must be ordered by the chosen feature tree by
1534
   *   calling the function _mergeFeatureTreeDescriptions().
1535
   *   @see _mergeFeatureTreeDescriptions()
1536
   *
1537
   * @param  $feature_uuid
1538
   *
1539
   * @return
1540
   *    A drupal render array for the $descriptionElements, may be an empty array if the textual content was empty.
1541
   *    Footnote key or anchors are not considered to be textual content.
1542
   *
1543
   * @ingroup compose
1544
   */
1545
  function compose_feature_block_items_generic($description_elements, $feature) {
1546

    
1547
    $elements_out_array = array();
1548
    $distribution_tree = null;
1549

    
1550
    /*
1551
     * $feature_block_has_content will be set true if at least one of the
1552
     * $descriptionElements contains some text which makes up some content
1553
     * for the feature block. Footnote keys are not considered
1554
     * to be content in this sense.
1555
     */
1556
    $feature_block_has_content = false;
1557

    
1558
    if (is_array($description_elements)) {
1559
      foreach ($description_elements as $description_element) {
1560
          /* decide based on the description element class
1561
           *
1562
           * Features handled here:
1563
           * all except DISTRIBUTION, COMMON_NAME, USES, IMAGES,
1564
           *
1565
           * TODO provide api_hook as extension point for this?
1566
           */
1567
        $feature_block_settings = get_feature_block_settings($description_element->feature->uuid);
1568
        switch ($description_element->class) {
1569
          case 'TextData':
1570
            $elements_out_array[] = compose_description_element_text_data($description_element, $description_element->feature->uuid, $feature_block_settings);
1571
            break;
1572
          case 'CategoricalData':
1573
            $elements_out_array[] = compose_description_element_categorical_data($description_element, $feature_block_settings);
1574
            break;
1575
          case 'QuantitativeData':
1576
            $elements_out_array[] = compose_description_element_quantitative_data($description_element, $feature_block_settings);
1577
            break;
1578
          case 'IndividualsAssociation':
1579
            $elements_out_array[] = compose_description_element_individuals_association($description_element, $feature_block_settings);
1580
            break;
1581
          case 'TaxonInteraction':
1582
            $elements_out_array[] = compose_description_element_taxon_interaction($description_element, $feature_block_settings);
1583
            break;
1584
          case 'CommonTaxonName':
1585
            $elements_out_array[] = compose_description_element_common_taxon_name($description_element, $feature_block_settings);
1586
            break;
1587
          case 'Uses':
1588
            /* IGNORE Uses classes, these are handled completely in compose_feature_block_items_use_records()  */
1589
            break;
1590
          default:
1591
            $feature_block_has_content = true;
1592
            $elements_out_array[] = markup_to_render_array('<li>No method for rendering unknown description class: ' . $description_element->class . '</li>');
1593
        }
1594
        $elements_out_array_last_item = $elements_out_array[count($elements_out_array) - 1];
1595
        // considering not empty as long as the last item added is a render array
1596
        $feature_block_has_content = $feature_block_has_content || !empty($elements_out_array_last_item['#type']);
1597
      }
1598

    
1599
      // If feature = CITATION sort the list of sources.
1600
      // This is ONLY for FLORA MALESIANA and FLORE d'AFRIQUE CENTRALE.
1601
      if (isset($description_element) && $description_element->feature->uuid == UUID_CITATION) {
1602
        sort($elements_out_array);
1603
      }
1604
    }
1605

    
1606
    // sanitize: remove empty and NULL items from the render array
1607
    $tmp_out_array = $elements_out_array;
1608
    $elements_out_array = array();
1609
    foreach($tmp_out_array as $item){
1610
      if(is_array($item) && count($item) > 0){
1611
        $elements_out_array[] = $item;
1612
      }
1613
    }
1614

    
1615
    return $elements_out_array;
1616
  }
1617

    
1618
/**
1619
 * Composes block of common names for the given DescriptionElements $elements which must be of the feature CommonName
1620
 *
1621
 * @parameter $elements
1622
 *  an array of CDM DescriptionElements either of type CommonName or TextData
1623
 * @parameter $feature
1624
 *  the common feature of all $elements, must be CommonName
1625
 *
1626
 * @return
1627
 *   A drupal render array
1628
 *
1629
 * @ingroup compose
1630
 */
1631
function compose_feature_block_items_feature_common_name($elements, $feature, $weight = FALSE) {
1632

    
1633
  $common_name_out = '';
1634
  $common_name_feature_elements = array();
1635
  $textData_commonNames = array();
1636

    
1637
  $footnote_key_suggestion = 'common-names-feature-block';
1638

    
1639
  $feature_block_settings = get_feature_block_settings(UUID_COMMON_NAME);
1640

    
1641
  if (is_array($elements)) {
1642
    foreach ($elements as $element) {
1643

    
1644
      if ($element->class == 'CommonTaxonName') {
1645

    
1646
        // common name without a language or area, should not happen but is possible
1647
        $language_area_key = '';
1648
        if (isset($element->language->representation_L10n)) {
1649
          $language_area_key .= $element->language->representation_L10n ;
1650
        }
1651
        if(isset($element->area->titleCache) && strlen($element->area->titleCache) > 0){
1652
          $language_area_key .= ($language_area_key ? ' '  : '') . '(' . $element->area->titleCache . ')';
1653
        }
1654
        if($language_area_key){
1655
          $language_area_key = '<span class="language-area-label">' . $language_area_key . '<span class="separator">: </span></span>';
1656
        }
1657

    
1658
        if(isset($common_names[$language_area_key][$element->name])) {
1659
          // same name already exists for language and area combination, se we merge the description elements
1660
          cdm_merge_description_elements($common_names[$language_area_key][$element->name], $element);
1661
        } else{
1662
          // otherwise add as new entry
1663
          $common_names[$language_area_key][$element->name] = $element;
1664
        }
1665

    
1666
      }
1667
      elseif ($element->class == 'TextData') {
1668
        $textData_commonNames[] = $element;
1669
      }
1670
    }
1671
  }
1672
  // Handling common names.
1673
  if (isset($common_names) && count($common_names) > 0) {
1674
    // Sorting the array based on the key (language, + area if set).
1675
    // Comment @WA there are common names without a language, so this sorting
1676
    // can give strange results.
1677
    ksort($common_names);
1678

    
1679
    // loop over set of elements per language area
1680
    foreach ($common_names as $language_area_key => $elements) {
1681
      ksort($elements); // sort names alphabetically
1682
      $per_language_area_out = array();
1683

    
1684
      foreach ($elements as $element) {
1685
        $common_name_render_array = compose_description_element_common_taxon_name($element, $feature_block_settings, $footnote_key_suggestion);
1686
        $common_name_markup = drupal_render($common_name_render_array);
1687
        // IMPORTANT!
1688
        // during the above drupal_render the theme_html_tag function is executed, which adds a "\n" character to the end of the markup
1689
        // this is an error and the trailing whitespace needs to be removed
1690
        if(str_endsWith($common_name_markup, "\n")){
1691
          $common_name_markup = substr($common_name_markup, 0, strlen($common_name_markup) - 1);
1692
        }
1693
        $per_language_area_out[] = $common_name_markup;
1694
      }
1695

    
1696
      $common_name_feature_elements[] = $language_area_key . join(', ', $per_language_area_out);
1697
    } // End of loop over set of elements per language area
1698

    
1699

    
1700
    $common_name_feature_elements_render_array = compose_feature_block_wrap_elements(
1701
      $common_name_feature_elements, $feature, '; ', FALSE
1702
    );
1703
    $common_name_out .= drupal_render($common_name_feature_elements_render_array); // FIXME should this be a render array instead?
1704

    
1705
  }
1706

    
1707
  // Handling commons names as text data.
1708
  $text_data_out = array();
1709

    
1710
  foreach ($textData_commonNames as $text_data_element) {
1711
    /* footnotes are not handled correctly in compose_description_element_text_data,
1712
       need to set 'common-names-feature-block' as $footnote_key_suggestion */
1713
    RenderHints::setFootnoteListKey($footnote_key_suggestion);
1714
    $text_data_render_array = compose_description_element_text_data($text_data_element, $text_data_element->feature->uuid, $feature_block_settings);
1715
    $text_data_out[] = drupal_render($text_data_render_array);
1716
  }
1717

    
1718
  $common_name_out_text_data = compose_feature_block_wrap_elements(
1719
    $text_data_out, $feature
1720
  );
1721

    
1722
  $footnotes = theme('cdm_footnotes', array('footnoteListKey' => 'BIBLIOGRAPHY-' . $footnote_key_suggestion));
1723
  $footnotes .= theme('cdm_footnotes', array('footnoteListKey' => $footnote_key_suggestion)); // FIXME is this needed at all?
1724
  $footnotes .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $footnote_key_suggestion));
1725

    
1726
  return  markup_to_render_array(  // FIXME markup_to_render_array should no longer be needed
1727
    '<div class="common-taxon-name">' . $common_name_out . '</div>'
1728
    .'<div class="text-data">' . drupal_render($common_name_out_text_data) . '</div>'
1729
    .$footnotes,
1730
    $weight
1731
  );
1732
}
1733

    
1734
/**
1735
 * Renders a single instance of the type CommonTaxonName.
1736
 *
1737
 * @param $element
1738
 *   The CDM CommonTaxonName entity.
1739
 * @param $feature_block_settings
1740
 *
1741
 * @param $footnote_key_suggestion
1742
 *
1743
 * @param $element_tag_name
1744
 *
1745
 * @return array
1746
 *   Drupal render array
1747
 *
1748
 * @ingroup compose
1749
 */
1750
function compose_description_element_common_taxon_name($element, $feature_block_settings, $footnote_key_suggestion = NULL)
1751
{
1752

    
1753
  if(!$footnote_key_suggestion) {
1754
    $footnote_key_suggestion = $element->feature->uuid;
1755
  }
1756

    
1757
  $name = '';
1758
  if(isset($element->name)){
1759
    $name = $element->name;
1760
  }
1761

    
1762

    
1763
  return compose_description_element($element, $feature_block_settings, $name, $footnote_key_suggestion);
1764
}
1765

    
1766
/**
1767
 * Composes the render array for a CDM Distribution description element
1768
 *
1769
 * @param array $description_elements
1770
 *   Array of CDM Distribution instances
1771
 * @param $enclosingTag
1772
 *   The html tag to be use for the enclosing element
1773
 *
1774
 * @return array
1775
 *   A Drupal render array
1776
 *
1777
 * @ingroup compose
1778
 */
1779
function compose_description_elements_distribution($description_elements){
1780

    
1781
  $markup_array = array();
1782
  RenderHints::pushToRenderStack('descriptionElementDistribution');
1783
  RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);
1784

    
1785
  $feature_block_settings = get_feature_block_settings(UUID_DISTRIBUTION);
1786
  $enclosingTag = cdm_feature_block_element_tag_name($feature_block_settings);
1787

    
1788
  foreach ($description_elements as $description_element) {
1789
    $annotations_and_sources = handle_annotations_and_sources(
1790
      $description_element,
1791
      handle_annotations_and_sources_config($feature_block_settings),
1792
      $description_element->area->representation_L10n,
1793
      UUID_DISTRIBUTION
1794
    );
1795

    
1796

    
1797
    list($status_label, $status_markup) = distribution_status_label_and_markup($description_element);
1798

    
1799
    $out = '';
1800
    $out .= '<' . $enclosingTag . ' class="descriptionElement descriptionElement-' . $description_element->uuid
1801
      . ' " title="' . $status_label. '">'
1802
      . $description_element->area->representation_L10n
1803
      . $status_markup;
1804
    if(!empty($annotations_and_sources['source_references'])){
1805
      $out .= ' ' . join(' ', $annotations_and_sources['source_references'] );
1806
    }
1807
    $out .= $annotations_and_sources['foot_note_keys']   . '</' . $enclosingTag . '>';
1808
    $markup_array[] = $out;
1809
  }
1810

    
1811
  RenderHints::popFromRenderStack();
1812
  return markup_to_render_array(join('<span class="separator">' . $feature_block_settings['glue'] . '</span>', $markup_array));
1813
}
1814

    
1815
  /**
1816
   * @param $descriptionElement
1817
   * @return array
1818
   */
1819
  function distribution_status_label_and_markup($descriptionElement, $status_glue = '&#8210; ') {
1820
    $status_markup = '';
1821
    $status_label = '';
1822

    
1823
    if (isset($descriptionElement->status)) {
1824
      $status_label = $descriptionElement->status->representation_L10n;
1825
      $status_markup =  '<span class="distributionStatus"> '
1826
        . $status_glue
1827
        . '<span class="distributionStatus-' . $descriptionElement->status->idInVocabulary . '">'
1828
        . $status_label
1829
        . '</span></span>';
1830

    
1831
    };
1832
    return array($status_label, $status_markup);
1833
  }
1834

    
1835

    
1836
  /**
1837
   * Provides the merged feature tree for a taxon profile page.
1838
   *
1839
   * The merging of the profile feature tree is actually done in
1840
   * _mergeFeatureTreeDescriptions(). See this method  for details
1841
   * on the structure of the merged tree.
1842
   *
1843
   * This method provides a hook which can be used to modify the
1844
   * merged feature tree after it has been created, see
1845
   * hook_merged_taxon_feature_tree_alter()
1846
   *
1847
   * @param $taxon
1848
   *    A CDM Taxon instance
1849
   *
1850
   * @return object
1851
   *    The merged feature tree
1852
   *
1853
   */
1854
  function merged_taxon_feature_tree($taxon) {
1855

    
1856
    // 1. fetch descriptions_by_featuretree but exclude the distribution feature
1857
    $merged_tree = cdm_ws_descriptions_by_featuretree(get_profile_feature_tree(), $taxon->uuid, array(UUID_DISTRIBUTION));
1858

    
1859

    
1860
    // 2. find the distribution feature node
1861
    $distribution_node =& cdm_feature_tree_find_node($merged_tree->root->childNodes, UUID_DISTRIBUTION);
1862

    
1863
    if ($distribution_node) {
1864
      // 3. get the distributionInfoDTO
1865
      $query_parameters = cdm_distribution_filter_query();
1866
      $query_parameters['part'] = array('mapUriParams');
1867
      if(variable_get(DISTRIBUTION_CONDENSED)){
1868
        $query_parameters['part'][] = 'condensedDistribution';
1869
      }
1870
      if (variable_get(DISTRIBUTION_ORDER_MODE, DISTRIBUTION_ORDER_MODE_DEFAULT) == 'TREE') {
1871
        $query_parameters['part'][] = 'tree';
1872
      }
1873
      else {
1874
        $query_parameters['part'][] = 'elements';
1875
      }
1876
      $query_parameters['omitLevels'] = array();
1877
      foreach(variable_get(DISTRIBUTION_TREE_OMIT_LEVELS, array()) as $uuid){
1878
        if(is_uuid($uuid)){
1879
          $query_parameters['omitLevels'][] = $uuid;
1880
        }
1881
      }
1882
      $customStatusColorsJson = variable_get(DISTRIBUTION_STATUS_COLORS, NULL);
1883
      if ($customStatusColorsJson) {
1884
        $query_parameters['statusColors'] = $customStatusColorsJson;
1885
      }
1886

    
1887
      $distribution_info_dto = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION_DISTRIBUTION_INFO_FOR, $taxon->uuid, queryString($query_parameters));
1888
      // 4. get distribution TextData is there are any
1889
      $distribution_text_data = cdm_ws_fetch_all(CDM_WS_DESCRIPTIONELEMENT_BY_TAXON,
1890
        array(
1891
          'taxon' => $taxon->uuid,
1892
          'type' => 'TextData',
1893
          'features' => UUID_DISTRIBUTION
1894
        )
1895
      );
1896

    
1897
      // 5. put all distribution data into the distribution feature node
1898
      if ($distribution_text_data //if text data exists
1899
        || ($distribution_info_dto && isset($distribution_info_dto->tree) && $distribution_info_dto->tree->rootElement->numberOfChildren > 0) // OR if tree element has distribution elements
1900
        || ($distribution_info_dto && !empty($distribution_info_dto->elements))
1901
      ) { // OR if DTO has distribution elements
1902
        $distribution_node->descriptionElements = array('#type' => 'DTO');
1903
        if ($distribution_text_data) {
1904
          $distribution_node->descriptionElements['TextData'] = $distribution_text_data;
1905
        }
1906
        if ($distribution_info_dto) {
1907
          $distribution_node->descriptionElements['DistributionInfoDTO'] = $distribution_info_dto;
1908
        }
1909
      }
1910
    }
1911

    
1912
    // allows modifying the merged tree via a the hook_cdm_feature_node_block_content_alter
1913
    drupal_alter('merged_taxon_feature_tree', $taxon, $merged_tree);
1914

    
1915
    return $merged_tree;
1916
  }
1917

    
1918

    
1919
  function compose_distribution_hierarchy($distribution_tree, $feature_block_settings){
1920

    
1921
    static $hierarchy_style;
1922
    // TODO expose $hierarchy_style to administration or provide a hook
1923
    if( !isset($hierarchy_style)){
1924
      $hierarchy_style = get_array_variable_merged(DISTRIBUTION_HIERARCHY_STYLE, DISTRIBUTION_HIERARCHY_STYLE_DEFAULT);
1925
    }
1926

    
1927
    $render_array = array();
1928

    
1929
    RenderHints::pushToRenderStack('descriptionElementDistribution');
1930
    RenderHints::setFootnoteListKey(UUID_DISTRIBUTION);
1931

    
1932
    // Returning NULL if there are no description elements.
1933
    if ($distribution_tree == null) {
1934
      return $render_array;
1935
    }
1936
    // for now we are not using a render array internally to avoid performance problems
1937
    $markup = '';
1938
    if (isset($distribution_tree->rootElement->children)) {
1939
      $tree_nodes = $distribution_tree->rootElement->children;
1940
      _compose_distribution_hierarchy($tree_nodes, $feature_block_settings, $markup, $hierarchy_style);
1941
    }
1942

    
1943
    $render_array['distribution_hierarchy'] = markup_to_render_array(
1944
      $markup,
1945
      0,
1946
      '<div id="distribution_hierarchy" class="distribution_hierarchy">',
1947
      '</div>'
1948
    );
1949

    
1950
    RenderHints::popFromRenderStack();
1951

    
1952
    return $render_array;
1953
  }
1954

    
1955
  /**
1956
   * this function should produce markup as the compose_description_elements_distribution()
1957
   * function.
1958
   *
1959
   * @see compose_description_elements_distribution()
1960
   *
1961
   * @param $distribution_tree
1962
   * @param $feature_block_settings
1963
   * @param $tree_nodes
1964
   * @param $markup
1965
   * @param $hierarchy_style
1966
   */
1967
  function _compose_distribution_hierarchy($tree_nodes, $feature_block_settings, &$markup, $hierarchy_style, $level_index = -1){
1968

    
1969
    $level_index++;
1970
    static $enclosingTag = "span";
1971

    
1972
    $level_style = array_shift($hierarchy_style);
1973
    if(count($hierarchy_style) == 0){
1974
      // lowest defined level style will be reused for all following levels
1975
      $hierarchy_style[] = $level_style;
1976
    }
1977

    
1978
    $node_index = -1;
1979
    $per_node_markup = array();
1980
    foreach ($tree_nodes as $node){
1981

    
1982
      $per_node_markup[++$node_index] = '';
1983

    
1984
      $label = $node->nodeId->representation_L10n;
1985

    
1986
      $distributions = $node->data;
1987
      $distribution_uuids = array();
1988
      $distribution_aggregate = NULL;
1989
        foreach($distributions as $distribution){
1990

    
1991
          $distribution_uuids[] = $distribution->uuid;
1992

    
1993
          // if there is more than one distribution we aggregate the sources and
1994
          // annotations into a synthetic distribution so that the footnote keys
1995
          // can be rendered consistently
1996
          if(!$distribution_aggregate) {
1997
            $distribution_aggregate = $distribution;
1998
            if(!isset($distribution_aggregate->sources[0])){
1999
              $distribution_aggregate->sources = array();
2000
            }
2001
            if(!isset($distribution_aggregate->annotations[0])){
2002
              $distribution_aggregate->annotations = array();
2003
            }
2004
          } else {
2005
            if(isset($distribution->sources[0])) {
2006
              $distribution_aggregate->sources = array_merge($distribution_aggregate->sources,
2007
                $distribution->sources);
2008
            }
2009
            if(isset($distribution->annotations[0])) {
2010
              $distribution_aggregate->annotations = array_merge($distribution_aggregate->annotations,
2011
                $distribution->annotations);
2012
            }
2013
          }
2014
        }
2015

    
2016
      $status_label= '';
2017
      $status_markup = '';
2018
      $annotations_and_sources =  null;
2019
      if($distribution_aggregate) {
2020
        $annotations_and_sources = handle_annotations_and_sources(
2021
          $distribution_aggregate,
2022
          handle_annotations_and_sources_config($feature_block_settings),
2023
          $label,
2024
          UUID_DISTRIBUTION
2025
        );
2026

    
2027
        list($status_label, $status_markup) = distribution_status_label_and_markup($distribution, $level_style['status_glue']);
2028
      }
2029

    
2030
      $per_node_markup[$node_index] .= '<' . $enclosingTag . ' class="descriptionElement'
2031
        . join(' descriptionElement-', $distribution_uuids)
2032
        . ' level_index_' . $level_index
2033
        . ' " title="' . $status_label . '">'
2034
        . '<span class="area_label">' . $label
2035
        . $level_style['label_suffix'] . '</span>'
2036
        . $status_markup
2037
      ;
2038

    
2039
      if(isset($annotations_and_sources)){
2040
        if(!empty($annotations_and_sources['source_references'])){
2041
          $per_node_markup[$node_index] .= ' ' . join(', ' , $annotations_and_sources['source_references']);
2042
        }
2043
        if($annotations_and_sources['foot_note_keys']) {
2044
          $per_node_markup[$node_index] .= $annotations_and_sources['foot_note_keys'];
2045
        }
2046
      }
2047

    
2048
      if(isset($node->children[0])){
2049
        _compose_distribution_hierarchy(
2050
          $node->children,
2051
          $feature_block_settings,
2052
          $per_node_markup[$node_index],
2053
          $hierarchy_style,
2054
          $level_index
2055
        );
2056
      }
2057

    
2058
      $per_node_markup[$node_index] .= '</' . $enclosingTag . '>';
2059
    }
2060
    $markup .= $level_style['item_group_prefix']  . join( $level_style['item_glue'], $per_node_markup) . $level_style['item_group_postfix'];
2061
  }
2062

    
2063

    
2064
/**
2065
 * Provides the content for a block of Uses Descriptions for a given taxon.
2066
 *
2067
 * Fetches the list of TaxonDescriptions tagged with the MARKERTYPE_USE
2068
 * and passes them to the theme function theme_cdm_UseDescription().
2069
 *
2070
 * @param string $taxon_uuid
2071
 *   The uuid of the Taxon
2072
 *
2073
 * @return array
2074
 *   A drupal render array
2075
 */
2076
function cdm_block_use_description_content($taxon_uuid, $feature) {
2077

    
2078
  $use_description_content = array();
2079

    
2080
  if (is_uuid($taxon_uuid )) {
2081
    $markerTypes = array();
2082
    $markerTypes['markerTypes'] = UUID_MARKERTYPE_USE;
2083
    $useDescriptions = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXON . '/' . $taxon_uuid . '/descriptions', $markerTypes);
2084
    if (!empty($useDescriptions)) {
2085
      $use_description_content = compose_feature_block_items_use_records($useDescriptions, $taxon_uuid, $feature);
2086
    }
2087
  }
2088

    
2089
  return $use_description_content;
2090
}
2091

    
2092
/**
2093
 * Creates a trunk of a feature object which can be used to build pseudo feature blocks like the Bibliography.
2094
 *
2095
 * @param $representation_L10n
2096
 * @param String $pseudo_feature_key
2097
 *    Will be set as uuid but should be one of 'BIBLIOGRAPHY', ... more to come. See also get_feature_block_settings()
2098
 *
2099
 * @return object
2100
 *  The feature object
2101
 */
2102
function make_pseudo_feature($representation_L10n, $pseudo_feature_key = null){
2103
  $feature = new stdClass;
2104
  $feature->representation_L10n = $representation_L10n;
2105
  $feature->uuid = NULL; // $pseudo_feature_key;
2106
  $feature->label = $pseudo_feature_key;
2107
  $feature->class = 'PseudoFeature';
2108

    
2109
  return $feature;
2110

    
2111
}
2112

    
2113

    
2114
/**
2115
 * Renders the description and adds a link to the description detail page
2116
 *
2117
 * @param object $description
2118
 *     the cdm description entity which will be linked to
2119
 *
2120
 * @param bool $show_description_elements
2121
 *     if True the description elements will be rendered
2122
 * @param $descriptive_dataset_uuid
2123
 *     the data set which should be passed to the description detail page
2124
 *
2125
 * @return string the markup for the description
2126
 */
2127
function render_cdm_description($description, $show_description_elements = False, $descriptive_dataset_uuid = NULL) {
2128

    
2129
  $out = '<span class="' . html_class_attribute_ref($description) . '">' . $description->titleCache . '</span>';
2130
  $path_to_description = path_to_description($description->uuid, $descriptive_dataset_uuid);
2131
  if($show_description_elements){
2132
    $out = render_description_string($description, get_root_nodes_for_dataset($description));
2133
  }
2134
  $out .= icon_link($path_to_description);
2135

    
2136
  return $out;
2137
}
2138

    
2139
/**
2140
 * @param $description
2141
 * @param $root_nodes
2142
 *
2143
 * @return string
2144
 */
2145
function render_description_string($description, $root_nodes) {
2146
  $descriptionString = '';
2147
  if (!empty($root_nodes)) {
2148
    foreach ($root_nodes as $root_node) {
2149
      if(isset($root_node->descriptionElements)) {
2150
        foreach ($root_node->descriptionElements as $element) {
2151
          switch ($element->class) {
2152
            case 'CategoricalData':
2153
              $state_data = render_state_data($element);
2154
              if (!empty($state_data)) {
2155
                $descriptionString .= '<i>' . $element->feature->representation_L10n . '</i>: ' . $state_data . "; ";
2156
              }
2157
              break;
2158
            case 'QuantitativeData':
2159
              $descriptionString .= '<i>' . $element->feature->representation_L10n . '</i>: ' . render_quantitative_statistics($element) . "; ";
2160
              break;
2161
          }
2162
        }
2163
      }
2164
      // recurse child nodes
2165
      $descriptionString .= render_description_string($description, $root_node->childNodes);
2166
    }
2167
  }
2168
  return $descriptionString;
2169
}
2170

    
2171
/**
2172
 * Compose a description as a table of Feature<->State
2173
 *
2174
 * @param $description_uuid
2175
 *
2176
 * @return array
2177
 *    The drupal render array for the page
2178
 *
2179
 * @ingroup compose
2180
 */
2181
function  compose_description_table($description_uuid, $descriptive_dataset_uuid = NULL) {
2182

    
2183
  RenderHints::pushToRenderStack('description_table');
2184

    
2185
  $render_array = [];
2186

    
2187
  $description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, [$description_uuid]);
2188
  $dataSet = NULL;
2189
  // dataset passed as parameter
2190
  if ($descriptive_dataset_uuid != NULL) {
2191
    foreach ($description->descriptiveDataSets as $set) {
2192
      if ($set->uuid == $descriptive_dataset_uuid) {
2193
        $dataSet = $set;
2194
        break;
2195
      }
2196
    }
2197
  }
2198

    
2199
  if(!empty($description->descriptiveDataSets)) {
2200
    // only one dataset present
2201
    if (!isset($dataSet) && sizeof($description->descriptiveDataSets) == 1) {
2202
      foreach ($description->descriptiveDataSets as $dataSet) {
2203
        break;
2204
      }
2205
    }
2206

    
2207
    // generate description title
2208
    RenderHints::pushToRenderStack('title');
2209
    if (isset($dataSet)) {
2210

    
2211
      $described_entity_title = NULL;
2212
      if(isset($description->describedSpecimenOrObservation)){
2213
        $described_entity_title = $description->describedSpecimenOrObservation->titleCache;
2214
      } else if($description->taxon) {
2215
          $described_entity_title = render_taxon_or_name($description->taxon);
2216
      }
2217
      $title = 'Descriptive Data ' . $dataSet->titleCache .
2218
        ($described_entity_title ? ' for ' . $described_entity_title : '');
2219
      }
2220
      $render_array['title'] = markup_to_render_array($title, null, '<h3 class="title">', '</h3>');
2221
    RenderHints::popFromRenderStack();
2222

    
2223
      if (isset($description->types)) {
2224
        foreach ($description->types as $type) {
2225
          if ($type == 'CLONE_FOR_SOURCE') {
2226
            $render_array['source'] = markup_to_render_array("Aggregation source from " . $description->created . '<br><br>');
2227
            break;
2228
          }
2229
        }
2230
      }
2231
    }
2232
    // multiple datasets present see #8714 "Show multiple datasets per description as list of links"
2233
    else {
2234
      $items = [];
2235
      foreach ($description->descriptiveDataSets as $dataSet) {
2236
        $path = path_to_description($description->uuid, $dataSet->uuid);
2237
        $attributes['class'][] = html_class_attribute_ref($description);
2238
        $items[] = [
2239
          'data' => $dataSet->titleCache . icon_link($path),
2240
        ];
2241
      }
2242
      $render_array['description_elements'] = [
2243
        '#title' => 'Available data sets for description',
2244
        '#theme' => 'item_list',
2245
        '#type' => 'ul',
2246
        '#items' => $items,
2247
      ];
2248
    }
2249

    
2250

    
2251
  if (isset($description->describedSpecimenOrObservation)) {
2252
    $render_array['specimen'] = markup_to_render_array("<b>Specimen</b><br>");
2253
    $render_array['specimen_link'] = markup_to_render_array(render_cdm_specimen_link($description->describedSpecimenOrObservation));
2254
  }
2255
  if (isset($description->taxon)) {
2256
    $render_array['taxon'] = markup_to_render_array("<b>Taxon</b><br>");
2257
    $render_array['taxon_link'] = markup_to_render_array(render_taxon_or_name($description->taxon, path_to_taxon($description->taxon->uuid)));
2258
  }
2259

    
2260
  $root_nodes = get_root_nodes_for_dataset($description);
2261

    
2262
  $header = ['Feature/Character', 'State'];
2263

    
2264
  $rows = [];
2265
  $rows = compose_description_element_rows($root_nodes, $rows);
2266

    
2267
  if (!empty($rows)) {
2268
    $render_array[] = markup_to_render_array(theme('table', [
2269
      'header' => $header,
2270
      'rows' => $rows,
2271
      'caption' => "Bracketed numbers denote sample size.",
2272
      'title' => "Table"
2273
    ]));
2274
  }
2275

    
2276
  if (isset($description->sources) and !empty($description->sources)) {
2277
    $items = [];
2278
    foreach ($description->sources as $source) {
2279
      if ($source->type == 'Aggregation' and isset($source->cdmSource)){
2280
        $cdm_source_entity = $source->cdmSource;
2281
        switch($cdm_source_entity->class){
2282
          case 'Taxon':
2283
            $source_link_markup = render_taxon_or_name($cdm_source_entity) . icon_link(path_to_taxon($cdm_source_entity->uuid, false), generalizeString(PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS));
2284
            break;
2285
          case 'TaxonDescription':
2286
          case 'SpecimenDescription':
2287
          case 'NameDescription':
2288
            $source_link_markup = render_cdm_description($cdm_source_entity);
2289
            break;
2290
          default:
2291
            $source_link_markup = '<span class="error">unhandled CdmSource</span>';
2292
        }
2293
        $items[] = [
2294
          'data' => $source_link_markup
2295
        ];
2296
      }
2297
    }
2298
    $render_array[] = [
2299
      '#title' => 'Sources',
2300
      '#theme' => 'item_list',
2301
      '#type' => 'ul',
2302
      '#items' => $items,
2303
    ];
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
 * @param $root_nodes
2337
 * @param $rows
2338
 *
2339
 * @return array
2340
 */
2341
function compose_description_element_rows($root_nodes, $rows) {
2342
  foreach ($root_nodes as $root_node) {
2343
    if(isset($root_node->descriptionElements)) {
2344
      foreach ($root_node->descriptionElements as $element) {
2345
        switch ($element->class) {
2346
          case 'CategoricalData':
2347
            if (!empty($element->stateData)) {
2348
              $rows[] = [
2349
                $element->feature->representation_L10n,
2350
                render_state_data($element),
2351
              ];
2352
            }
2353
            break;
2354
          case 'QuantitativeData':
2355
            $rows[] = [
2356
              $element->feature->representation_L10n,
2357
              render_quantitative_statistics($element),
2358
            ];
2359
            break;
2360
        }
2361
      }
2362
    }
2363
    // recurse child nodes
2364
    $rows = compose_description_element_rows($root_node->childNodes, $rows);
2365
  }
2366
  return $rows;
2367
}
2368

    
2369

    
2370

    
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