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cdm-dataportal / modules / cdm_dataportal / includes / pages.inc @ 92e522db

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1
<?php
2
/**
3
 * @file
4
 * Page functions.
5
 *
6
 * @copyright
7
 *   (C) 2007-2012 EDIT
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 *   European Distributed Institute of Taxonomy
9
 *   http://www.e-taxonomy.eu
10
 *
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 *   The contents of this module are subject to the Mozilla
12
 *   Public License Version 1.1.
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 * @see http://www.mozilla.org/MPL/MPL-1.1.html
14
 *
15
 * @author
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 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
17
 */
18

    
19

    
20
/**
21
 * Composes a render array representing the ocurrences associetad with the $taxon.
22
 *
23
 * The resulting render array contains two elements:
24
 *  - 'map': A map showing all point locations of the occurences is availabale
25
 *  - 'specimen_list': the list of occurences prepated as table for theme_table()
26
 *
27
 * @param object $taxon
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 *   A cdm Taxon object
29
 * @return
30
 *   A render array suitable for drupal_render()
31
 *
32
 * @ingroup Compose
33
 *
34
 */
35
function compose_cdm_taxon_page_specimens($taxon) {
36

    
37
    $render_array = array();
38
    RenderHints::pushToRenderStack('taxon_page_specimens');
39

    
40
    $fieldUnitDTOs = null;
41
    $specimensOrObservations = null;
42
    if (variable_get('cdm_dataportal_specimen_derivate_tree')){
43
      // get fieldUnitDTOs
44
      $fieldUnitDTOs = cdm_ws_get(CDM_WS_TAXON_FIELDUNIT_DTOS, array( $taxon->uuid));
45
      $fieldUnitDTOs = order_fieldUnitDtos_by_date_and_type($fieldUnitDTOs);
46
    } else {
47
      // $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservations'));
48
      // extend by associated taxas occurrences
49
      $relationship_filter_query_parameters = relationship_filter_query_parameters();
50

    
51
      if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
52
        $relationship_filter_query_parameters = array_merge($relationship_filter_query_parameters, $_REQUEST['pager']);
53
      }
54
      $by_associatedtaxon_query = http_build_query($relationship_filter_query_parameters);
55
      $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
56
        null,
57
        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
58
      );
59
      $specimensOrObservations = array();
60
      if (isset($pager->records[0])) {
61
        $specimensOrObservations = $pager->records;
62
      }
63
      // cdm_ws_get(CDM_WS_OCCURRENCE_FIELDUNIT_DTO_BY_ASSOCIATEDTAXON,
64
      // null,
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      // $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
66
      // );
67

    
68
      // $specimensOrObservations = array();
69
      // if(isset($pager->records[0])){
70
      //    $specimensOrObservations =  $pager->records;
71
      // }
72
      // Collect media (fieldObjectMedia, derivedUnitMedia) and add as a custom field
73
      foreach ($specimensOrObservations as &$occurrence) {
74
        $occurrence->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
75
          $occurrence->uuid,
76
          'fieldObjectMediaDTO',
77
        ));
78
        $occurrence->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
79
          $occurrence->uuid,
80
          'derivedUnitMedia',
81
        ));
82
      }
83
      $specimensOrObservations = order_specimens_or_observations_by_date_and_type($specimensOrObservations);
84
    }
85

    
86
    // --- get map service HTTP query parameters
87
    if (count($specimensOrObservations) > 0 || $fieldUnitDTOs > 0) {
88
        $render_array['map'] = occurrence_map_query_parameters($taxon);
89
    }
90

    
91
    // -------------------------------------------------------
92

    
93
    if(variable_get('cdm_dataportal_compressed_specimen_derivate_table')){
94

    
95
        //COMPRESSED SPECIMEN DERIVATE TABLE
96
        $associatedFieldUnitsQuery_parameters = array();
97
        if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
98
            $associatedFieldUnitsQuery_parameters = array_merge($associatedFieldUnitsQuery_parameters, $_REQUEST['pager']);
99
        }
100

    
101
        $by_associatedtaxon_query = http_build_query($associatedFieldUnitsQuery_parameters);
102
        $pager_field_units = cdm_ws_get(CDM_WS_PORTAL_TAXON,
103
            array($taxon->uuid, 'associatedFieldUnits'),
104
            $by_associatedtaxon_query . '&pageSize=' . variable_get('cdm_dataportal_compressed_specimen_derivate_table_page_size')
105
        );
106

    
107
        if (isset($pager_field_units->records[0])) {
108
          $field_unit_uuids = array();
109
          foreach ($pager_field_units->records as $field_unit) {
110
            $field_unit_uuids[] = $field_unit->uuid;
111
          }
112

    
113
          $render_array['derivate_hierarchy_table'] = compose_compressed_specimen_derivate_table($field_unit_uuids);
114
        }
115

    
116
        $render_array['pager'] = markup_to_render_array(
117
            theme('cdm_pager', array(
118
                'pager' => $pager_field_units,
119
                'path' => $_REQUEST['q'],
120
                'parameters' => $_REQUEST
121
            )),
122
            10 // weight
123
        );
124
    }
125
    else if(variable_get('cdm_dataportal_specimen_derivate_tree')){
126
      $render_array['specimen_list'] = compose_specimen_table_top_down($fieldUnitDTOs);
127
      $render_array['specimen_list']['#weight'] = 2;
128
    } else {
129
      $specimen_table = compose_specimens_table_bottom_up($specimensOrObservations);
130

    
131
      $render_array['specimen_list'] = $specimen_table;
132
      $render_array['pager'] = markup_to_render_array(
133
        theme('cdm_pager', array(
134
          'pager' => $pager,
135
          'path' => $_REQUEST['q'],
136
          'parameters' => $_REQUEST,
137
        )),
138
        10 // weight
139
      );
140
    }
141

    
142
    RenderHints::popFromRenderStack();
143
    return $render_array;
144
}
145

    
146
/**
147
 * @return array
148
 *
149
 * TODO move to cdm_dataportal.module or api.module?
150
 */
151
function relationship_filter_query_parameters()
152
{
153
  $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
154
  $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
155
  $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
156

    
157
  $by_associatedtaxon_query_parameters = array(
158
    'relationshipsInvers' => implode(',', $relationship_choice['invers']),
159
    'relationships' => implode(',', $relationship_choice['direct']),
160
  );
161
  return $by_associatedtaxon_query_parameters;
162
}
163

    
164

    
165
function create_html_link($link, $openInExternalWindow=false){
166
    $html = "";
167
    if($link->uri && $link->uri!=""){
168
        $html .= '<a  href="' . $link->uri . '"';
169
        if($openInExternalWindow){
170
            $html .= ' target="_blank"';
171
        }
172
        $html .= '>' . $link->linkText . '</a>';
173
    }
174
    else{
175
        $html .= $link->linkText;
176
    }
177
    return $html;
178
}
179

    
180
/**
181
 * Creates HTML links from the given link list concatenated by default by a comma.
182
 * @param $linkList the list with Link objects having "uri" and "linkText" as members
183
 * @return string the assembled HTML string containing the links
184
 */
185
function create_html_links($linkList, $openInExternalWindow=false, $separator=", ")
186
{
187
    $html = "";
188
    if ($linkList) {
189
        foreach ($linkList as $link) {
190
            $html .= create_html_link($link, $openInExternalWindow).$separator;
191
        }
192
        $html = rtrim($html, $separator);
193
    }
194
    return $html;
195
}
196

    
197
/**
198
 * Composes a taxon page which can consist of multiple parts like
199
 * 'General', 'Synonymy', 'Images', 'Keys'. These parts can be displayed
200
 * as tabs or as sections of a single page.
201
 *
202
 * It is headed by the name of the accepted taxon without author and reference.
203
 *
204
 * @param $taxon
205
 *   The CDM Taxon Instance to compose the page for.
206
 * @param $page_part
207
 *   Name of the part to display, valid values are:
208
 *    - 'description' -  for the general part
209
 *    - 'images'
210
 *    - 'synonymy'
211
 *    - 'keys'
212
 *    - 'all'
213
 *
214
 * @return array
215
 *   A drupal render array
216
 *
217
 * @ingroup compose
218
 */
219
function compose_cdm_taxon_page($taxon, $page_part = 'description') {
220

    
221
  // we better cache here since drupal_get_query_parameters has no internal static cache variable
222
  $http_request_params = drupal_get_query_parameters();
223

    
224
  // add all mandatory js sources
225
  _add_js_footnotes();
226

    
227

    
228
  $render_array = array();
229
  $weight = 0; // the weight for the render array elements
230

    
231
  $tabsToDisplay = variable_get('cdm_taxonpage_tabs_visibility', unserialize(TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT));
232

    
233
  $page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';
234

    
235
  $synonymy_as_tab = variable_get(CDM_SYNONYMY_AS_TAB, CDM_SYNONYMY_AS_TAB_DEFAULT) === 1;
236
  if(!$synonymy_as_tab){
237
    unset($tabsToDisplay["Synonymy"]);
238
    // the synonymy is located in the general part in this case
239
    if($page_part == 'synonymy'){
240
      $page_part = 'description';
241
    }
242
  }
243

    
244
  $media = _load_media_for_taxon($taxon);
245

    
246

    
247
  if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {
248
    taxon_page_tabs_hidden_add('images');
249
  }
250

    
251
  // --- GET specimensOrObservations --- //
252
  $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservationsCount'));
253

    
254
  $specimensOrObservationsCount = $specimensOrObservations != null ? $specimensOrObservations->result : 0;
255
  if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {
256
    taxon_page_tabs_hidden_add('specimens');
257
  }
258

    
259
  // --- GET polytomousKeys --- //
260
  $polytomousKeysPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, NULL, "findByTaxonomicScope=$taxon->uuid");
261
  $identificationKeyCount = 0;
262
  if ($polytomousKeysPager) {
263
    $identificationKeyCount += $polytomousKeysPager->count;
264
  }
265
  if ($identificationKeyCount == 0 || ($tabsToDisplay["Keys"] == '0')) {
266
    taxon_page_tabs_hidden_add('keys');
267
  }
268

    
269
  // --- GET TaxonNodeAgentRelations --- //
270
  $current_classification_uuid = get_current_classification_uuid();
271
  $taxon_node_agent_relations_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
272
      array(
273
          $taxon->uuid,
274
          $current_classification_uuid,
275
      ),
276
      "pageSize=1&pageIndex=0"// we are only interested into the count so we are fetching only one item, o is not possible!
277
  );
278
  if (!$taxon_node_agent_relations_pager || $taxon_node_agent_relations_pager->count == 0){
279
      taxon_page_tabs_hidden_add('experts');
280
  }
281

    
282
  if (!isset($tabsToDisplay["Synonymy"]) || $tabsToDisplay["Synonymy"] == '0') {
283
    taxon_page_tabs_hidden_add('synonymy');
284
  }
285

    
286
  // -------------------------------------------- //
287

    
288
  if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {
289
    $render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);
290
  }
291

    
292
  // --- PAGE PART: DESCRIPTION --- //
293
  if (!taxon_page_tabs_hidden_check('description') && ($page_part == 'description' || $page_part == 'all')) {
294

    
295
    $merged_tree = merged_taxon_feature_tree($taxon);
296

    
297

    
298
    $render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, !$synonymy_as_tab);
299
    $render_array['general']['#weight'] = $weight++;
300
    $render_array['general']['#prefix'] = '<div id="general" class="page-part">';
301
    $render_array['general']['#suffix'] = '</div>';
302
  }
303

    
304
  // --- PAGE PART: IMAGES --- //
305
  if (!taxon_page_tabs_hidden_check('images') && ($page_part == 'images' || $page_part == 'all')) {
306
    $images_html = '<div id="images" class="page-part">';
307
    if ($page_part == 'all') {
308
      $images_html .= '<h2>' . t(cdm_taxonpage_tab_label('Images')) . '</h2>';
309
    }
310
    // Get the image gallery as configured by the admin.
311
    $default_image_gallery = 'default';
312
    $configured_image_gallery_viewer = variable_get('image_gallery_viewer', 'default');
313
    $taxon_image_gallery = '<div class="error">No image gallery viewer configured</div>';
314
    if($configured_image_gallery_viewer == $default_image_gallery || $configured_image_gallery_viewer == 'fsi'){
315
      // the fsi_gallery requires a flash plugin, in case the client browser is not supporting
316
      // flash we also need to provide an the default gallery as alternative
317
      $taxon_image_gallery = '<div id="default-gallery-viewer">' .
318
        call_user_func_array('taxon_image_gallery_' . $default_image_gallery, array(
319
          $taxon,
320
          $media,
321
        ))
322
        . '</div>';
323
    }
324
    if($configured_image_gallery_viewer == 'fsi'){
325
      $taxon_image_gallery .= '<div id="'. $configured_image_gallery_viewer .'-gallery-viewer">' .
326
        call_user_func_array('taxon_image_gallery_' . $configured_image_gallery_viewer, array(
327
          $taxon,
328
          $media,
329
        ))
330
       . '</div>';
331
    }
332
    $images_html .= $taxon_image_gallery;
333
    $images_html .= '</div>';
334
    $render_array['images'] = markup_to_render_array($images_html, $weight++);
335
  }
336

    
337
  // --- PAGE PART: SYNONYMY --- //
338
  if (!taxon_page_tabs_hidden_check('synonymy') && (($page_part == 'synonymy' || $page_part == 'all') && $synonymy_as_tab)) {
339
    $synonymy_html = '<div id="synonymy" class="page-part">';
340
    if ($page_part == 'all') {
341
      $synonymy_html .= '<h2>' . t(cdm_taxonpage_tab_label('Synonymy')) . '</h2>';
342
    }
343
    $addAcceptedTaxon = variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE);
344

    
345
    $synonym_a = compose_cdm_taxon_page_synonymy($taxon, $addAcceptedTaxon);
346
    $synonymy_html .= drupal_render($synonym_a);
347

    
348
    $synonymy_html .= '</div>';
349
    $render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
350

    
351
  }
352

    
353
  // --- PAGE PART: SPECIMENS --- //
354
  if (!taxon_page_tabs_hidden_check('specimens') && ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all'))) {
355
    $render_array['specimens'] = array(
356
        '#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Specimens')) . '</h2>' : ''),
357
        'content' => compose_cdm_taxon_page_specimens($taxon), // returns render array
358
        '#suffix' => '</div>',
359
    );
360
  }
361

    
362
  // --- PAGE PART: KEYS --- //
363
  if(!taxon_page_tabs_hidden_check('keys')){
364
    if ($identificationKeyCount == 1 && $page_part == 'keys'){
365
      drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));
366
    }
367
    else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {
368
      $keys_html = '<div id="keys" class="page-part">';
369
      if ($page_part == 'all') {
370
        $keys_html .= '<h2>' . t(cdm_taxonpage_tab_label('Keys')) . '</h2>';
371
      }
372
      $keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
373
      $keys_html .= '</div>';
374
      $render_array['keys'] = markup_to_render_array($keys_html, $weight++);
375
    }
376
  }
377

    
378
  // --- PAGE PART: EXPERTS --- //
379

    
380
  if (!taxon_page_tabs_hidden_check('experts') && ($page_part == 'experts' || $page_part == 'all')) {
381
    $render_array['experts'] = array(
382
        '#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Experts')) . '</h2>' : ''),
383
        'content' => compose_cdm_taxon_page_experts($taxon), // returns render array
384
        '#suffix' => '</div>',
385
    );
386
  }
387

    
388
  // ------------------ END OF PARTS -------------- //
389

    
390
  // adjust weights of page and toc elements according to the settings
391
  $taxontabs_weights = get_array_variable_merged(CDM_TAXONPAGE_TAB_WEIGHT, CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
392
  foreach($taxontabs_weights as $tab_key => $weight){
393
    if(isset($render_array[$tab_key])){
394
      $render_array[$tab_key]['#weight'] = $weight;
395
    }
396
  }
397

    
398

    
399
  // set up the TOC for the pages which contain all pageparts
400
  if($page_part == 'all') {
401

    
402
    asort($taxontabs_weights);
403
    foreach(array_keys($taxontabs_weights) as $tab_key){
404
      if(isset($render_array[$tab_key])){
405
        if($tab_key != 'general'){
406
          // add entry for page part
407
          $toc_elements[] = array(
408
              'data' => l(t(cdm_taxonpage_tab_label(ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),
409
              'class' => array('page-part-toc-item-' . $tab_key)
410
          );
411
        } else {
412
          // add content of profile part instead
413
          if(isset($render_array['general'])) {
414
            // in case all tabs are shown at once the feature tocs
415
            // should be integrated into the tabs toc as sub list
416
            // and the profile image should be on top of the page
417
            if(isset($render_array['general']['taxon_description_feature_toc'])){;
418
            foreach ($render_array['general']['taxon_description_feature_toc']['#items'] as $profile_toc_item){
419
              $toc_elements[] = $profile_toc_item;
420
            }
421
            unset($render_array['general']['taxon_description_feature_toc']);
422
            }
423
          }
424
        }
425
      }
426
    }
427

    
428
    // move profile image in page structure
429
    if(isset($render_array['general']['taxon_profile_image'])){
430
      $render_array['profile_image'] = $render_array['general']['taxon_profile_image'];
431
      $render_array['profile_image']['#weight'] = -100;
432
      unset($render_array['general']['taxon_profile_image']);
433
    }
434

    
435
    // finally add the table of contents to the render array
436
    $render_array['toc'] = array(
437
        '#theme' => 'item_list',
438
        '#items' => $toc_elements,
439
        '#title' => t('Content'),
440
        '#weight' => -101,
441
        '#suffix' => '</div>',
442
        '#prefix'=> '<div id="page-toc">'
443
    );
444
  }
445

    
446

    
447
  return $render_array;
448
}
449

    
450
/**
451
 * TODO should this function really be a compose function?
452
 *     For a compose function must there always be a theme function with the same name? (ak 8.8.2013)
453
 *
454
 * composes and returns an render array containing the components of the taxon profile tab:
455
 *  - 'taxon_profile_image'
456
 *  - 'taxon_description_feature_toc'
457
 *  - 'taxon_description_features'
458
 *
459
 *
460
 * @param object taxon
461
 * @param object $merged_tree
462
 * @param object media
463
 * @param bool $add_synonymy
464
 *
465
 * @return array
466
 *   A Drupal render array with the following elements:
467
 *     - 'taxon_profile_image'
468
 *     - 'taxon_description_feature_toc'
469
 *     - 'taxon_description_features'
470
 *
471
 * @throws Exception
472
 *
473
 * @ingroup compose
474
 */
475
function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, $add_synonymy) {
476

    
477
  $render_array = array();
478

    
479
  $taxon_profile_image_settings = variable_get(CDM_TAXON_PROFILE_IMAGE, unserialize(CDM_TAXON_PROFILE_IMAGE_DEFAULT));
480

    
481
  $hide_taxon_profile_image = FALSE;
482
  if (variable_get('image_hide_rank', '0') != '0' && isset($taxon->name->rank->uuid)) {
483
    $rankCompare = rank_compare($taxon->name->rank->uuid, variable_get('image_hide_rank', '-99'));
484
    $hide_taxon_profile_image = ($rankCompare > -1);
485
  }
486

    
487
  if ($taxon_profile_image_settings['show'] && !$hide_taxon_profile_image) {
488

    
489
    $representationPart = new stdClass();
490
    $attributes = array();
491
    if (isset($media[0])) {
492
      // due to a bug the portal/taxon/{uuid}/media service only delivers a filtered media object
493
      // which only contains the thumbnail representation even if the height and width filters are not set.
494
      // -->
495
      $preferred_media = cdm_ws_get(CDM_WS_MEDIA, $media[0]->uuid);
496
      $preferred_representations = cdm_preferred_media_representations($preferred_media, array(
497
        'image/jpg',
498
        'image/jpeg',
499
        'image/png',
500
        'image/gif',
501
      ),
502
        $taxon_profile_image_settings['maxextend'],
503
        $taxon_profile_image_settings['maxextend']
504
      );
505
      if(count($preferred_representations) > 0){
506

    
507
        $representation = array_shift($preferred_representations);
508
        $representationPart = $representation->parts[0];
509
        $attributes['alt'] = $representationPart->uri;
510

    
511
        if (!empty($taxon_profile_image_settings['media_uri_query'])) {
512
          $representationPart->uri = $representationPart->uri
513
            . (strpos($representationPart->uri, '?') !== FALSE ? '&' : '?')
514
            . $taxon_profile_image_settings['media_uri_query'];
515
        }
516
      }
517
    }
518
    else {
519
      if ($taxon_profile_image_settings['custom_placeholder_enabled']) {
520
        // show placeholder image instead
521
        if (!empty($taxon_profile_image_settings['custom_placeholder_image_on']) && !empty($taxon_profile_image_settings['custom_placeholder_image_fid'])) {
522
          // use the user provided image
523
          $profile_image_file = file_load($taxon_profile_image_settings['custom_placeholder_image_fid']);
524
          $url = file_create_url($profile_image_file->uri);
525
          $image_info = image_get_info($profile_image_file->uri);
526
          $representationPart->width = $image_info['width'];
527
          $representationPart->height = $image_info['height'];
528
          $representationPart->uri = $url;
529
        }
530
        else {
531
          // use the hard coded default
532
          $representationPart->width = 184;
533
          $representationPart->height = 144;
534
          $representationPart->uri = base_path() . drupal_get_path('module',
535
              'cdm_dataportal') . '/images/no_picture.png';
536
        }
537
        $attributes['alt'] = "no image available";
538
      }
539
    }
540

    
541
    if (isset($representationPart->uri)) {
542
      $profile_image = cdm_media_gallerie_image($representationPart, $taxon_profile_image_settings['maxextend'], FALSE, $attributes);
543
      // NOTE: style="width:${maxextend}px' is needed for IE8 !!!
544
      $max_extend_with = $taxon_profile_image_settings['maxextend'] . 'px';
545
      $render_array['taxon_profile_image'] = markup_to_render_array('<div id="taxonProfileImage" style="width:' . $max_extend_with . '">' . $profile_image . '</div>',
546
        -101);
547
    }
548
  }
549

    
550
  if($add_synonymy){
551
    $synonymy_a = compose_cdm_taxon_page_synonymy($taxon, true);
552
    $synonymy_a['#weight'] = -102;
553
    $render_array['synonymy'] = $synonymy_a;
554
  }
555

    
556
//  $pseudo_feature_block_toc_items = array();
557

    
558

    
559
  // Render the sections for each real feature
560
  $feature_block_list = make_feature_block_list($merged_tree->root->childNodes, $taxon);
561

    
562
  // >>>>>>>>>>>>>>>>>>> PSEUDO FEATURES >>>>>>>>>>>>>>>>>>>
563
  $pseudo_feature_weights = get_array_variable_merged(CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS, CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS_DEFAULT);
564
  // Bibliography
565
  $bibliography_settings = get_bibliography_settings();
566
  if($bibliography_settings['enabled'] == 1){
567
    $bibliography_markup = FootnoteManager::renderFootnoteList(PSEUDO_FEATURE_BIBLIOGRAPHY, '');
568
    if($bibliography_markup) {
569
      $feature_bibliography = make_pseudo_feature('Bibliography', PSEUDO_FEATURE_BIBLIOGRAPHY);
570
      $bibliography_item = markup_to_render_array($bibliography_markup);
571
      $bibliography_block = feature_block(t('Bibliography'), $feature_bibliography);
572
      $bibliography_block->content = array();
573
      $bibliography_block->content[] = compose_feature_block_wrap_elements(array($bibliography_item), $feature_bibliography);
574

    
575
      $feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]] = $bibliography_block;
576
      cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]);
577
    }
578
  }
579

    
580
  // Descriptions (aggregated)
581
  $descriptionTypes = array();
582
  $descriptionTypes['descriptionTypes'] = ("AGGREGATED_STRUC_DESC");
583
  $aggregatedDescriptions = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXON . '/' . $taxon->uuid . '/descriptions', $descriptionTypes);
584
  if (isset($aggregatedDescriptions) and !empty($aggregatedDescriptions)) {
585
      // if($feature_block_list) ....TODO
586
      $feature_description = make_pseudo_feature('Descriptions (aggregated)', PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS);
587
      $description_item = '';
588
      foreach ($aggregatedDescriptions as $description) {
589
        $description_item = '<div class="' . html_class_attribute_ref($description) . '">';
590
        $description_item .= render_description_string($description, get_root_nodes_for_dataset($description));
591
        $description_item .= ' ' . icon_link(path_to_description($description->uuid));
592
        $description_item .= '<div class="content-caption">'. t('Bracketed numbers denote sample size') . '</div>';
593
        $description_item .= '</div>';
594
      }
595
      $description_block = feature_block(t('Descriptions (aggregated)'), $feature_description);
596
      $description_block->content = [];
597
      $description_block->content[] = compose_feature_block_wrap_elements([$description_item], $feature_description);
598

    
599
      $feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]] = $description_block;
600
      cdm_toc_list_add_item('Descriptions (aggregated)', 'aggregation_descriptions', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]);
601

    
602

    
603
  }
604

    
605
  // sort by weight
606
  ksort($feature_block_list);
607
  $render_array['taxon_description_features'] = _block_get_renderable_array($feature_block_list);
608

    
609
/*  // update TOC
610
  if ($pseudo_feature_block_toc_items){
611
    foreach ($pseudo_feature_block_toc_items as $label=>$fragment){
612
      cdm_toc_list_add_item($label, $fragment);
613
    }
614
  }
615
*/
616
  // <<<<<<<<<<<<<<<<<<< PSEUDO FEATURES <<<<<<<<<<<<<<<<<<<
617

    
618
  // create the table of content
619
  $toc = array(
620
      '#theme' => 'item_list',
621
    '#items' => cdm_toc_list(),
622
      '#title' => t('Content'),
623
    '#weight' => -100,                  // move to the top
624
      '#suffix' => '</div>',
625
      '#prefix'=> '<div id="page-toc">'
626
  );
627
  $render_array['taxon_description_feature_toc'] = $toc;
628

    
629
  return $render_array;
630
}
631

    
632

    
633
/**
634
 * Renders the link which will lead to the specimen detail page
635
 * @param object $specimen
636
 *    the cdm specimen entity which will be linked to
637
 *
638
 * @return string
639
 *     the markup for the link
640
 */
641
function render_cdm_specimen_link($specimen) {
642
  $path = path_to_specimen($specimen->uuid);
643
  $attributes['class'][] = html_class_attribute_ref($specimen);
644
  return $specimen->titleCache.icon_link($path);
645
}
646

    
647
/**
648
 * Returns HTML containing the synonymy for the accepted taxon.
649
 *
650
 * Shows the whole synonymy for the accepted taxon.
651
 * The synonymy list is headed by the complete scientific name
652
 * of the accepted taxon with nomenclatural reference.
653
 *
654
 * @param object $taxon
655
 * @param boolean $add_accepted_taxon
656
 *
657
 * @return array
658
 *  Drupal render array for the synonymy
659
 *
660
 * @throws Exception
661
 *
662
 * @ingroup compose
663
 */
664
function compose_cdm_taxon_page_synonymy($taxon, $add_accepted_taxon) {
665

    
666
  RenderHints::pushToRenderStack('taxon_page_synonymy');
667

    
668
  // footnote key for the homotypic group and accepted taxon,
669
  // both should have the same footnote key
670
  RenderHints::setFootnoteListKey(RenderHints::getRenderPath());
671

    
672
  $synomymie = cdm_ws_get(CDM_WS_PORTAL_TAXON_SYNONYMY, array($taxon->uuid));
673

    
674
  $out = '';
675

    
676
  // Render accepted taxon.
677
  //
678
  // foonotes of the accepted taxon will be rendered in the homotypic group section
679
  // even if there are not synonyms in the homotypic group
680
  // homotypic group and accepted taxon should have the same footnote key
681
  $referenceUri = '';
682
  if ($add_accepted_taxon) {
683
    // remember the last part of the render path
684
    $synonymy_render_path = RenderHints::getRenderPath();
685
    // set new render path for the accepted taxon so
686
    // it can be styled differently via the name render part definitions
687
    RenderHints::pushToRenderStack('accepted_taxon');
688
    $accepted_name = '';
689
    if (variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE, 0)) {
690
      $label = variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL, CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL_DEFAULT);
691
      $accepted_name .= '<div class="secReference"><span class="label">' . t($label) . ':</span> ' . $taxon->sec->titleCache . '</div>';
692
    }
693
    if (isset($taxon->name->nomenclaturalReference)) {
694
      $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
695
    }
696

    
697
    $accepted_name .= '<div class="accepted-name">';
698
    $accepted_name .= render_taxon_or_name($taxon, NULL, $referenceUri);
699

    
700
    $name_relations = cdm_name_relationships_for_taxon($taxon);
701
    $name_relationships = compose_name_relationships_inline($name_relations, $taxon->name->uuid, $taxon->uuid);
702
    // Render relationships of accepted name.
703
    if(isset($name_relationships['list']['items'][0])){
704
      $accepted_name .= ' ' . drupal_render($name_relationships);
705
    }
706

    
707
    // handle annotations of the name and taxon
708
    $special_annotations_array = array();
709
    $special_annotations_array[] = $taxon->name;
710
    $special_annotations_array[] = $taxon;
711
    $accepted_name .= theme('cdm_annotations_as_footnotekeys', array(
712
        'cdmBase_list' => $special_annotations_array,
713
        'footnote_list_key' => $synonymy_render_path . '-annotations')
714
    );
715
    $accepted_name .= '</div>';
716
    RenderHints::popFromRenderStack();
717
  }
718

    
719
  // --- Render homotypic synonymy group
720
  if (!empty($accepted_name)) {
721
    $out .= $accepted_name;
722
  }
723

    
724
  // Render the homotypicSynonymyGroup including the type information.
725
  $out .= theme(
726
    'cdm_homotypicSynonymyGroup',
727
    array(
728
      'synonymList' => $synomymie->homotypicSynonymsByHomotypicGroup,
729
      'accepted_taxon_name_uuid' => $taxon->name->uuid
730
    )
731
  );
732

    
733

    
734
  // Render accepted taxon heterotypic synonymy groups.
735
  if ($synomymie->heterotypicSynonymyGroups) {
736
    foreach ($synomymie->heterotypicSynonymyGroups as $homotypicalGroup) {
737
      $out .= theme('cdm_heterotypicSynonymyGroup', array('homotypicalGroup' => $homotypicalGroup));
738
    }
739
  }
740
  // Render taxon relationships.
741
  if (variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT)) {
742
    $taxonRelationshipsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, $taxon->uuid);
743
    $out .= cdm_taxonRelationships($taxonRelationshipsDTO, $taxon);
744
  }
745

    
746
  RenderHints::popFromRenderStack();
747

    
748
  return markup_to_render_array($out);
749
}
750

    
751

    
752
/**
753
 * composes and returns an render array for the experts associated with the given taxon
754
 *
755
 * @param object taxon
756
 *
757
 * @return array
758
 *   A Drupal render array for a table with the experts
759
 *
760
 * @ingroup compose
761
 */
762
function compose_cdm_taxon_page_experts($taxon){
763

    
764
  $render_array = array();
765
  if(!isset($taxon->uuid)){
766
    return $render_array;
767
  }
768

    
769
  $current_classification_uuid = get_current_classification_uuid();
770
  // TODO use cdm_ws_fetchall below but this failes! needs fix!
771
  $taxon_node_agent_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
772
    array(
773
      $taxon->uuid,
774
      $current_classification_uuid
775
    )
776
  );
777

    
778
  $header = array(
779
    array('data' => t('Expert')),
780
    array('data' => t('Role'))
781
  );
782
  $rows = array();
783

    
784

    
785
  foreach($taxon_node_agent_relations->records as $taxon_node_agent_relation){
786

    
787

    
788
    $expert_role_id = $taxon_node_agent_relation->agent->uuid . '-' . $taxon_node_agent_relation->type->uuid;
789
    $expert_details_container_id = 'expert_details_' . $expert_role_id;
790

    
791
    $agent_label_markup = cdm_dynabox(
792
      'expert_' . $expert_role_id,
793
      $taxon_node_agent_relation->agent->titleCache,
794
      // specifying both ends of the relationship will return only one record in the pager
795
      cdm_compose_url(CDM_WS_PORTAL_AGENT,
796
         array($taxon_node_agent_relation->agent->uuid, 'taxonNodeAgentRelations'),
797
        'taxon_uuid=' . $taxon->uuid . '&relType_uuid=' . $taxon_node_agent_relation->type->uuid),
798
      'cdm_taxon_expert',
799
      'Click for details',
800
      array('div', 'div'),
801
      array(), // attributes
802
      '#' . $expert_details_container_id // $content_element_selector
803
    );
804

    
805
    // Expert and Role
806
    $rows[] = array(
807
      'data' => array(
808
        array(
809
          'data' => $agent_label_markup,
810
          'class' => array(html_class_attribute_ref($taxon_node_agent_relation->agent))
811
        ),
812
        array(
813
          'data' => $taxon_node_agent_relation->type->representation_L10n,
814
          'class' => array(html_class_attribute_ref($taxon_node_agent_relation->type))
815
        )
816
      )
817
    );
818
    // Agent details
819
    $rows[] = array(
820
      'data' => array(
821
        array(
822
          'data' => '<!-- expert_details_container -->',
823
          'id' => $expert_details_container_id,
824
          'colspan' => 2
825
        )
826
      )
827
    );
828

    
829
  }
830

    
831

    
832
  $render_array['experts_table'] = array(
833
    '#theme' => 'table',
834
    '#header' => $header,
835
    '#rows' => $rows,
836
  );
837

    
838

    
839
  return $render_array;
840
}
841

    
842

    
843
/**
844
 * Manages the tabs to be hidden in the taxon page.
845
 *
846
 * The tabs are identified by their last menu link path element:
847
 *  - description
848
 *  - synonymy
849
 *  - images
850
 *  - specimens
851
 *  - key
852
 *
853
 * Internally the tabs are stored in a static variable which is
854
 * managed by drupal_static().
855
 *
856
 * @param string $add_tab
857
 *   Optional parameter. The given string will be added to the array of tabs
858
 *
859
 * @return
860
 *   The array of tabs
861
 */
862
function taxon_page_tabs_hidden_add($add_tab = NULL) {
863
  $tabs = &drupal_static('taxon_page_tabs_hidden');
864

    
865
  if(!isset($tabs)){
866
    $tabs = array();
867
  }
868

    
869
  if (isset($add_tab) && !array_key_exists($add_tab, $tabs)) {
870
    $tabs[] = $add_tab;
871
  }
872

    
873
  return $tabs;
874
}
875

    
876
/**
877
 * Manages the tabs to be hidden in the taxon page.
878
 *
879
 * The tabs names are identified by their last menu link path element:
880
 *  - description
881
 *  - synonymy
882
 *  - images
883
 *  - specimens
884
 *  - key
885
 *
886
 * Internally the tabs are stored in a static variable which is
887
 * managed by drupal_static().
888
 *
889
 * @param string $tabname
890
 *   The name of the tab to check
891
 *
892
 * @return boolean
893
 *   True if the tab or section is to be hidden
894
 */
895
function taxon_page_tabs_hidden_check($tabname) {
896

    
897
  $tabs = &drupal_static('taxon_page_tabs_hidden');
898

    
899
  if(!isset($tabs)){
900
    $tabs = array();
901
  }
902

    
903
  return array_search($tabname, $tabs) !== FALSE;
904
}
905

    
906
/**
907
 * Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
908
 *
909
 *  - Removes the tabs to be hidden, @see taxon_page_tabs_hidden_add()
910
 *  - Renames tabs according to the settings // TODO (this will replace the theme_cdm_taxonpage_tab() function !!!)
911
 *
912
 * @param array $variables
913
 *   The variables array
914
 */
915
function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {
916

    
917
  $hidden_tabs = taxon_page_tabs_hidden_add();
918

    
919
  if (!variable_get(CDM_SEARCH_BLAST_ENABLED)) {
920
      if (is_array($variables['primary'])) {
921
          foreach ($variables['primary'] as $key => &$element) {
922
              if ($element['#link']['path'] == 'cdm_dataportal/search/blast') {
923
                  // remove the tab
924
                  unset($variables['primary'][$key]);
925
              }
926

    
927
          }
928
      }
929
  }
930
  if (is_array($variables['primary'])) {
931
    foreach ($variables['primary'] as $key => &$element) {
932

    
933
      // 1. Remove the tabs to be hidden
934
      foreach ($hidden_tabs as $tab) {
935
        if ($element['#link']['path'] == 'cdm_dataportal/taxon/%/' . $tab) {
936
          // remove the tab
937
          unset($variables['primary'][$key]);
938
        }
939
      }
940
    }
941
  }
942
}
943

    
944

    
945

    
946
/**
947
 * Implements the hook_preprocess_HOOK() for theme_menu_local_task()
948
 *
949
 *
950
 * @param array $variables
951
 *   An associative array containing:
952
 *     - element: A render element containing:
953
 *          #link: A menu link array with 'title', 'href', and 'localized_options' keys.
954
 *          #active: A boolean indicating whether the local task is active.
955
 *
956
 */
957
function cdm_dataportal_preprocess_menu_local_task(&$variables) {
958

    
959
  $link = $variables['element']['#link'];
960
  if (preg_match('/cdm_dataportal\/.*\/refresh$/', $link['href'])) {
961
    $link['title'] = '<img class="refresh" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/view-refresh.png' . '" alt="' . check_plain($link['title']) . '" title="' . check_plain($link['title']) . '"/>';
962
    $link['localized_options']['html'] = TRUE;
963

    
964
    $variables['element']['#link'] = $link;
965
  }
966
}
967

    
968
/* =================== block composition ===================== */
969

    
970
/**
971
 * Composes and returns an render array for the classification breadcrumbs of the given taxon.
972
 *
973
 * @param taxon
974
 *
975
 * @return array
976
 *   A Drupal render array for a table with the experts
977
 *
978
 * @ingroup compose
979
 */
980
function compose_classification_breadcrumbs($taxon_uuid) {
981

    
982
  _add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');
983

    
984
  $render_array = array();
985

    
986
  $render_array['#theme'] = 'item_list';
987
  $render_array['#type'] = 'ul';
988
  $render_array['#attributes'] = array(
989
    'id' => 'classification-breadcrumbs',
990
    'class' => 'breadcrumbs inline',
991
  );
992

    
993
  $items = array();
994

    
995
  $parent_taxon_nodes = null;
996
  if($taxon_uuid){
997
    $parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
998
  }
999

    
1000
  $classifications = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
1001
  // find current classification in list
1002
  $classification = null;
1003
  $current_classification_uuid = get_current_classification_uuid();
1004
  foreach ($classifications as $classification){
1005
    if($classification->uuid == $current_classification_uuid){
1006
      break;
1007
    }
1008
  }
1009

    
1010
  $node_name = '';
1011
  if(count($classifications) > 1 ){
1012
    // need to add the current classification as first label
1013

    
1014
    $label = $classification->titleCache;
1015
    if(strlen($label) > 20){
1016
      $label = substr($label, 0, strpos($label, ' ', 15)) . '...';
1017
    }
1018
    $node_name = font_awesome_icon_markup('fa-th-list')  . ' ' . l($label, '#', array(
1019
      'attributes' => array(
1020
        'class' => 'taxonomic-children-button classification-chooser',
1021
        'data-destination-uri' => drupal_get_destination(),
1022
        'data-cdm-align-with' => array('prev')
1023
      ),
1024
      'html' => true
1025
    ));
1026
  }
1027

    
1028
  $rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
1029

    
1030
  $rank_separator = '<span> '
1031
    . font_awesome_icon_markup('fa-chevron-right')
1032
    . ' </span>';
1033
  $more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');
1034
  $more_children_label = '...';
1035

    
1036
  $items[] = $node_name;
1037

    
1038
  $more_children_for = null;
1039
  if($parent_taxon_nodes){
1040
    foreach ($parent_taxon_nodes as $node) {
1041

    
1042
      $is_first_item = count($items) == 0;
1043
      $is_last_item = count($items) == count($parent_taxon_nodes);
1044
      $node_name = cdm_dataportal_shortname_of($node);
1045
      $path = path_to_taxon($node->taxonUuid);
1046

    
1047
      if($node->taxonomicChildrenCount > 0) {
1048
        $more_children_for = $node->taxonUuid;
1049
      } else {
1050
        $more_children_for = null;
1051
      }
1052

    
1053
      // 'fa-sitemap'
1054

    
1055
      $items[] =
1056
        ($is_first_item ? '' : ' ')
1057
        . $rank_separator
1058
        . l(
1059
          '<span class="' . html_class_attribute_ref($node) . '">' . $node_name . '</span>',
1060
          $path,
1061
          array(
1062
            'attributes' => array(
1063
              'class' => array('taxonomic-children-button'),
1064
              'data-cdm-taxon-uuid' => array($node->taxonUuid),
1065
              'data-cdm-classification-mode' => array('siblings'),
1066
              'data-cdm-align-with' => array('prev')
1067
            ),
1068
            'html' => true
1069
          )
1070
        );
1071
      }
1072
    }
1073

    
1074
  // add more button to the end
1075
  if(!$parent_taxon_nodes) {
1076
    // not taxon focused yet, adding button to make  the root nodes available
1077
    $items[] = '<span>'
1078
      . $more_children_icon . '&nbsp;' .
1079
      '<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
1080
      . '" data-rank-limit-uuid="' . $rank_limit_uuid . '" data-cdm-align-with="prev"> ' . $more_children_label . '<span>'
1081
      . '</span>';
1082
  } else if($more_children_for){
1083
    // last parent item has child taxon nodes
1084
    $items[] = ' <span>'
1085
      . $more_children_icon . '&nbsp;' .
1086
      '<span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
1087
      . '" data-cdm-classification-mode="children" data-cdm-align-with="prev"> ' . $more_children_label . '</span>'
1088
      . '</span>';
1089

    
1090
  }
1091

    
1092
  $render_array['#items'] = $items;
1093

    
1094
  return $render_array;
1095
}
1096

    
1097

    
1098
/**
1099
 * @param $specimen_uuid
1100
 * @return array
1101
 *    The drupal render array for the page
1102
 *
1103
 * @ingroup compose
1104
 */
1105
function compose_cdm_specimen_page($specimen_uuid)
1106
{
1107
  drupal_set_title("Specimen Details");
1108
  RenderHints::pushToRenderStack('specimen_page');
1109

    
1110
  $specimen_table = array(
1111
      '#theme' => 'table',
1112
      '#weight' => 2,
1113
      // prefix attributes and rows with '#' to let it pass toF the theme function,
1114
      // otherwise it is handled as child render array
1115

    
1116
    '#attributes' => array('class' => 'specimens'),
1117
      '#rows' => array(),
1118
      '#prefix' => '<div id="specimens">',
1119
      '#suffix' => '</div>',
1120

    
1121

    
1122
  );
1123
  $specimen = compose_cdm_specimen_or_observation($specimen_uuid, true);
1124
  $render_array = array(
1125
          '#theme' => 'item_list',
1126
          '#items' => array($specimen),
1127
          '#type' => 'ul');
1128
  $output = drupal_render($render_array);
1129

    
1130
  $specimen_table['#rows'][] = array(
1131
          // An array of table rows. Every row is an array of cells, or an associative array
1132
          'data' => $specimen,
1133
          'class' =>  array(
1134
              'descriptionElement',
1135
              'descriptionElement_IndividualsAssociation'
1136
          ),
1137
  );
1138

    
1139

    
1140
 // $detail_html = compose_cdm_specimen_or_observation($specimen_uuid, true);
1141
//    $render_array['markup'] = array(
1142
//        '#prefix' => '<div id="specimens" class="page">',
1143
//        'content' => $specimen_table,
1144
//        '#suffix' => '</div>',
1145
//    );
1146
    $render_array['specimen_table'] =  $specimen_table;
1147

    
1148
  RenderHints::popFromRenderStack();
1149
  return $specimen; // $render_array;
1150
}
1151

    
1152
/**
1153
 * @param $named_area_uuid
1154
 * @return array
1155
 *    The drupal render array for the page
1156
 *
1157
 * @ingroup compose
1158
 */
1159
function compose_cdm_named_area_page($named_area_uuid)
1160
{
1161

    
1162
  $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid));
1163

    
1164
  $render_array = array();
1165
  RenderHints::pushToRenderStack('named_area_page');
1166

    
1167
  $groups = array();
1168
  @_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);
1169
  @_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);
1170
  if(isset($named_area->level)) {
1171
    @_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);
1172
  }
1173

    
1174
  $name_area_details_elements = array(
1175
   // '#title' => $title,
1176
    '#theme' => 'description_list',
1177
    '#groups' => $groups,
1178
    '#attributes' => array('class' => html_class_attribute_ref($named_area)),
1179
  );
1180

    
1181
  $render_array[] = $name_area_details_elements;
1182

    
1183
  RenderHints::popFromRenderStack();
1184
  return $render_array;
1185
}
1186

    
1187

    
1188
/**
1189
 * Returns a drupal render array for a single reference page.
1190
 *
1191
 * Composes a page with all data on a single reference.
1192
 *
1193
 * @param string $uuid
1194
 *   An uuid for a cdm reference.
1195
 *
1196
 * @return array
1197
 *  A drupal render array
1198
 *
1199
 * @throws Exception
1200
 *
1201
 * @ingroup compose
1202
 */
1203
function compose_cdm_reference_page($uuid) {
1204

    
1205
  $pathelement = "reference_page";
1206
  RenderHints::pushToRenderStack($pathelement);
1207
  $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
1208
  if (!$reference) {
1209
    drupal_set_title(t('Reference does not exist'), PASS_THROUGH);
1210
    return "";
1211
  }
1212
  if (isset($reference->titleCache)) {
1213
    drupal_set_title($reference->titleCache, PASS_THROUGH);
1214
  }
1215

    
1216
  $field_order = array(
1217
    "title",
1218
    "abbrevTitle",
1219
    // "titleCache" abbrevTitleCache
1220
    // "citation",
1221
    "authorship",
1222
    "editor",
1223
    "publisher",
1224
    "placePublished",
1225
    "datePublished",
1226
    "year",
1227
    "edition",// Class Book.
1228
    "volume",// Class Article.
1229
    "seriesPart",
1230
    "inReference",
1231
    "nomRefBase", // Class BookSection, Book, Article.
1232
    "pages",// Class Article.
1233
    "series",// Class Article, PrintSeries.
1234
    "school",// Class Thesis.
1235
    "institution",// Class Report.
1236
    "organization",// Class Proceedings.
1237
    "nextVersion",
1238
    "previousVersion",
1239
    "isbn",// Class Book.
1240
    "issn",// Class Journal.
1241
    "doi",
1242
    "uri"
1243
  );
1244

    
1245
  $table_rows = array();
1246

    
1247
  if (!isset($reference->authorship)) {
1248
    $authorship = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid);
1249
    $reference->authorship = isset($authorship->titleCache) ? $authorship->titleCache : '';
1250
  }
1251

    
1252
  if (!isset($reference->inReference)) {
1253
    $reference->inReference = cdm_ws_get(CDM_WS_REFERENCE, array(
1254
      $reference->uuid,
1255
      "inReference",
1256
    ));
1257
  }
1258

    
1259
  foreach ($field_order as $fieldname) {
1260

    
1261
    if (isset($reference->$fieldname)) {
1262

    
1263
      if ($fieldname == "datePublished") {
1264
        $period = $reference->$fieldname;
1265
        $datePublished = timePeriodToString($period);
1266
        if (isset($datePublished) && $datePublished != '') {
1267
          $table_rows[] = array(
1268
            t("Date published"),
1269
            $datePublished,
1270
          );
1271
        }
1272
      }
1273
      elseif ($fieldname == "doi" && is_object($reference->doi)) {
1274
        $table_rows[] = array(
1275
          t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1276
          cdm_doi($reference->doi, false)
1277
        );
1278
      }
1279
      elseif ($fieldname == "uri" && isset($reference->uri) && $reference->uri) {
1280
        $table_rows[] = array(
1281
          t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1282
          cdm_external_uri($reference->uri, false)
1283
        );
1284
      }
1285
      elseif (is_object($reference->$fieldname)) {
1286
        if ($fieldname == "authorship") {
1287
          $dump = $reference->$fieldname;
1288
          $teammembers = "teamMembers";
1289
          $team = $dump->$teammembers;
1290
          $nameArray = array();
1291

    
1292
          foreach ($team as $member) {
1293
            if (strlen($member->lastname) > 0) {
1294
              $nname = $member->lastname;
1295
              $name = $nname;
1296
              if (strlen($member->firstname) > 0) {
1297
                $vname = $member->firstname;
1298
                $name = $vname . " " . $nname;
1299
              }
1300
              $nameArray[] = $name;
1301
            }
1302
            else {
1303
              if (strlen($member->titleCache) > 0) {
1304
                $nameArray[] = $member->titleCache;
1305
              }
1306
            }
1307
          }
1308
          $value = join($nameArray, ", ");
1309
        }
1310
        elseif ($fieldname == "inReference") {
1311
          $type = $reference->$fieldname->type;
1312
          $value = l($reference->$fieldname->titleCache, path_to_reference($reference->$fieldname->uuid));
1313
          switch ($type) {
1314
            case "Book":
1315
              $fieldname = "in book";
1316
              break;
1317
            case "Journal":
1318
              $fieldname = "in journal";
1319
              break;
1320
            case "Proceedings":
1321
              $fieldname = "in proceedings";
1322
              break;
1323
          }
1324
        }
1325
        else {
1326
          $value = $reference->$fieldname->titleCache;
1327
        }
1328

    
1329

    
1330
        if (isset($value) && $value != '') {
1331
          $table_rows[] = array(
1332
            t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1333
            $value,
1334
          );
1335
        }
1336

    
1337
      }
1338
      else {
1339
        if (isset($reference->$fieldname) && $reference->$fieldname != '') {
1340
          $table_rows[] = array(
1341
            t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1342
            $reference->$fieldname,
1343
          );
1344
        }
1345
      }
1346
    }
1347
  }
1348

    
1349
  $out = theme_table(array(
1350
    'header' => array(),
1351
    'rows' => $table_rows,
1352
    'attributes' => array(
1353
      'class' => html_class_attribute_ref($reference)
1354
    ),
1355
    'caption' => NULL,
1356
    'colgroups' => NULL,
1357
    'sticky' => NULL,
1358
    'empty' => NULL,
1359
  ));
1360

    
1361
  if(isset($reference->referenceAbstract)){
1362
    $out .= '<h2 class="block-title">Abstract</h2><div class="abstract">' . $reference->referenceAbstract . '</div>';
1363
  }
1364

    
1365

    
1366
  // Annotations below the table
1367
  $annotations = cdm_fetch_visible_annotations($reference);
1368
  $out .= theme("cdm_annotations", array('annotations' => $annotations));
1369

    
1370
  $registration_working_set = cdm_ws_get("registrationWorkingSetDTO", array($uuid));
1371
  if($registration_working_set && count($registration_working_set->registrationDTOs) > 0){
1372
    $out .= "<h3>Nomenclatural acts:</h3><div class=\"cdm-item-list registration-item-list\">";
1373
    foreach($registration_working_set->registrationDTOs as $registration_dto){
1374
      if($registration_dto->status == "PUBLISHED"){
1375
        $registration_render_a = compose_registration_dto_compact($registration_dto, 'citation');
1376
        $registration_render_a["#prefix"] = "<div class=\"item item-registration\">";
1377
        $registration_render_a["#suffix"] = "</div>";
1378
        $out .= drupal_render($registration_render_a);
1379
      }
1380
    }
1381
    $out .= "</div>";
1382
  }
1383

    
1384
  RenderHints::popFromRenderStack();
1385

    
1386
  return markup_to_render_array($out);
1387
}
1388

    
1389
/**
1390
 * Provides the the label string for taxon page tabs.
1391
 *
1392
 * The $tabname as passed to the method will be returned if no override
1393
 * label is configured in the settings.
1394
 */
1395
function cdm_taxonpage_tab_label($tabname) {
1396
  static $taxon_tabs_labels = null;
1397
  if($taxon_tabs_labels == null){
1398
    $taxon_tabs_labels = get_array_variable_merged(CDM_TAXONPAGE_TAB_LABELS, CDM_TAXONPAGE_TAB_LABELS_DEFAULT);
1399
  }
1400
  $tabname_key = strtolower($tabname);
1401
  if(isset($taxon_tabs_labels[$tabname_key]) && $taxon_tabs_labels[$tabname_key]){
1402
    return $taxon_tabs_labels[$tabname_key];
1403
  }
1404
  return $tabname;
1405
}
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