Project

General

Profile

Download (48.1 KB) Statistics
| Branch: | Tag: | Revision:
1
<?php
2
/**
3
 * @file
4
 * Page functions.
5
 *
6
 * @copyright
7
 *   (C) 2007-2012 EDIT
8
 *   European Distributed Institute of Taxonomy
9
 *   http://www.e-taxonomy.eu
10
 *
11
 *   The contents of this module are subject to the Mozilla
12
 *   Public License Version 1.1.
13
 * @see http://www.mozilla.org/MPL/MPL-1.1.html
14
 *
15
 * @author
16
 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
17
 */
18

    
19

    
20
/**
21
 * 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 $taxon
28
 *   A cdm Taxon object
29
 * @return
30
 *   A render array suitable for drupal_render()
31
 *
32
 * @ingroup Compose
33
 *
34
 */
35
function compose_cdm_taxon_page_specimens($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,
65
      // $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_TAXONPAGE_TAXON_NODE_SHOW_STATES, 1) && ( $page_part == 'description' || $page_part == 'synonymy' || $page_part == 'all')){
289
    $taxon_nodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, array($taxon->uuid));
290
    $render_array['taxon_node_status'] = compose_taxon_node_status($taxon_nodes);
291
    $render_array['taxon_node_status']['#weight'] = -100;
292
  }
293

    
294
  if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {
295
    $render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);
296
  }
297

    
298
  // --- PAGE PART: DESCRIPTION --- //
299
  if (!taxon_page_tabs_hidden_check('description') && ($page_part == 'description' || $page_part == 'all')) {
300

    
301
    $merged_tree = merged_taxon_feature_tree($taxon);
302

    
303

    
304
    $render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, !$synonymy_as_tab);
305
    $render_array['general']['#weight'] = $weight++;
306
    $render_array['general']['#prefix'] = '<div id="general" class="page-part">';
307
    $render_array['general']['#suffix'] = '</div>';
308
  }
309

    
310
  // --- PAGE PART: IMAGES --- //
311
  if (!taxon_page_tabs_hidden_check('images') && ($page_part == 'images' || $page_part == 'all')) {
312
    $images_html = '<div id="images" class="page-part">';
313
    if ($page_part == 'all') {
314
      $images_html .= '<h2>' . t(cdm_taxonpage_tab_label('Images')) . '</h2>';
315
    }
316
    // Get the image gallery as configured by the admin.
317
    $configured_image_gallery_viewer = variable_get(CDM_MEDIA_GALLERY_VIEWER, CDM_MEDIA_GALLERY_VIEWER_DEFAULT);
318
    if($configured_image_gallery_viewer != 'fsi'){
319
      $images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);
320
    } else {
321
      // the fsi_gallery requires a flash plugin, in case the client browser is not supporting
322
      // flash we also need to provide an the default gallery as alternative
323
      $images_html .= render_taxon_media_gallery($taxon, CDM_MEDIA_GALLERY_VIEWER_DEFAULT, $media);
324
      $images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);
325
    }
326
    $images_html .= '</div>'; // END of <div id="images">
327
    $render_array['images'] = markup_to_render_array($images_html, $weight++);
328
  }
329

    
330
  // --- PAGE PART: SYNONYMY --- //
331
  if (!taxon_page_tabs_hidden_check('synonymy') && (($page_part == 'synonymy' || $page_part == 'all') && $synonymy_as_tab)) {
332
    $synonymy_html = '<div id="synonymy" class="page-part">';
333
    if ($page_part == 'all') {
334
      $synonymy_html .= '<h2>' . t(cdm_taxonpage_tab_label('Synonymy')) . '</h2>';
335
    }
336
    $addAcceptedTaxon = variable_get(CDM_DATAPORTAL_NOMREF_IN_TITLE, CDM_DATAPORTAL_NOMREF_IN_TITLE_DEFAULT);
337

    
338
    $synonym_a = compose_cdm_taxon_page_synonymy($taxon, $addAcceptedTaxon);
339
    $synonymy_html .= drupal_render($synonym_a);
340

    
341
    $synonymy_html .= '</div>';
342
    $render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
343

    
344
  }
345

    
346
  // --- PAGE PART: SPECIMENS --- //
347
  if (!taxon_page_tabs_hidden_check('specimens') && ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all'))) {
348
    $render_array['specimens'] = array(
349
        '#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Specimens')) . '</h2>' : ''),
350
        'content' => compose_cdm_taxon_page_specimens($taxon), // returns render array
351
        '#suffix' => '</div>',
352
    );
353
  }
354

    
355
  // --- PAGE PART: KEYS --- //
356
  if(!taxon_page_tabs_hidden_check('keys')){
357
    if ($identificationKeyCount == 1 && $page_part == 'keys'){
358
      drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));
359
    }
360
    else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {
361
      $keys_html = '<div id="keys" class="page-part">';
362
      if ($page_part == 'all') {
363
        $keys_html .= '<h2>' . t(cdm_taxonpage_tab_label('Keys')) . '</h2>';
364
      }
365
      $keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
366
      $keys_html .= '</div>';
367
      $render_array['keys'] = markup_to_render_array($keys_html, $weight++);
368
    }
369
  }
370

    
371
  // --- PAGE PART: EXPERTS --- //
372

    
373
  if (!taxon_page_tabs_hidden_check('experts') && ($page_part == 'experts' || $page_part == 'all')) {
374
    $render_array['experts'] = array(
375
        '#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Experts')) . '</h2>' : ''),
376
        'content' => compose_cdm_taxon_page_experts($taxon), // returns render array
377
        '#suffix' => '</div>',
378
    );
379
  }
380

    
381
  // ------------------ END OF PARTS -------------- //
382

    
383
  // adjust weights of page and toc elements according to the settings
384
  $taxontabs_weights = get_array_variable_merged(CDM_TAXONPAGE_TAB_WEIGHT, CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
385
  foreach($taxontabs_weights as $tab_key => $weight){
386
    if(isset($render_array[$tab_key])){
387
      $render_array[$tab_key]['#weight'] = $weight;
388
    }
389
  }
390

    
391

    
392
  // set up the TOC and pseudo feature blocks for the pages which contain all page parts
393
  if($page_part == 'all' && (!isset( $render_array['general']) || count($render_array['general']) == 0 )) {
394

    
395
    $bibliography_block = make_bibliography_feature_block();
396
    if($bibliography_block){
397
      $render_array['bibliography_block'] = _block_get_renderable_array([$bibliography_block]);
398
      $render_array['bibliography_block']['#weight'] = 100;
399
      cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $render_array['bibliography_block']['#weight']);
400
    }
401

    
402
    $toc_elements = [];
403
    asort($taxontabs_weights);
404
    foreach(array_keys($taxontabs_weights) as $tab_key){
405
      if(isset($render_array[$tab_key])){
406
        if($tab_key != 'general'){
407
          // add entry for page part
408
          $toc_elements[] = array(
409
              'data' => l(t(cdm_taxonpage_tab_label(ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),
410
              'class' => array('page-part-toc-item-' . $tab_key)
411
          );
412
        } else {
413
          // add content of profile part instead
414
          if(isset($render_array['general'])) {
415
            // in case all tabs are shown at once the feature tocs
416
            // should be integrated into the tabs toc as sub list
417
            // and the profile image should be on top of the page
418
            if(isset($render_array['general']['taxon_description_feature_toc'])){;
419
            foreach ($render_array['general']['taxon_description_feature_toc']['#items'] as $profile_toc_item){
420
              $toc_elements[] = $profile_toc_item;
421
            }
422
            unset($render_array['general']['taxon_description_feature_toc']);
423
            }
424
          }
425
        }
426
      }
427
    }
428

    
429
    // move profile image in page structure
430
    if(isset($render_array['general']['taxon_profile_image'])){
431
      $render_array['profile_image'] = $render_array['general']['taxon_profile_image'];
432
      $render_array['profile_image']['#weight'] = -100;
433
      unset($render_array['general']['taxon_profile_image']);
434
    }
435

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

    
446
  }
447

    
448

    
449
  return $render_array;
450
}
451

    
452
/**
453
 * TODO should this function really be a compose function?
454
 *     For a compose function must there always be a theme function with the same name? (ak 8.8.2013)
455
 *
456
 * composes and returns an render array containing the components of the taxon profile tab:
457
 *  - 'taxon_profile_image'
458
 *  - 'taxon_description_feature_toc'
459
 *  - 'taxon_description_features'
460
 *
461
 *
462
 * @param object taxon
463
 * @param object $merged_tree
464
 * @param object media
465
 * @param bool $add_synonymy
466
 *
467
 * @return array
468
 *   A Drupal render array with the following elements:
469
 *     - 'taxon_profile_image'
470
 *     - 'taxon_description_feature_toc'
471
 *     - 'taxon_description_features'
472
 *
473
 * @throws Exception
474
 *
475
 * @ingroup compose
476
 */
477
function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, $add_synonymy) {
478

    
479
  $render_array = array();
480

    
481
  $taxon_profile_image_settings = variable_get(CDM_TAXON_PROFILE_IMAGE, unserialize(CDM_TAXON_PROFILE_IMAGE_DEFAULT));
482

    
483
  $hide_taxon_profile_image = FALSE;
484
  if (variable_get('image_hide_rank', '0') != '0' && isset($taxon->name->rank->uuid)) {
485
    $rankCompare = rank_compare($taxon->name->rank->uuid, variable_get('image_hide_rank', '-99'));
486
    $hide_taxon_profile_image = ($rankCompare > -1);
487
  }
488

    
489
  if ($taxon_profile_image_settings['show'] && !$hide_taxon_profile_image) {
490

    
491
    $representationPart = new stdClass();
492
    $attributes = array();
493
    if (isset($media[0])) {
494
      // due to a bug the portal/taxon/{uuid}/media service only delivers a filtered media object
495
      // which only contains the thumbnail representation even if the height and width filters are not set.
496
      // -->
497
      $preferred_media = cdm_ws_get(CDM_WS_MEDIA, $media[0]->uuid);
498
      $preferred_representations = cdm_preferred_media_representations($preferred_media, array(
499
        'image/jpg',
500
        'image/jpeg',
501
        'image/png',
502
        'image/gif',
503
      ),
504
        $taxon_profile_image_settings['maxextend'],
505
        $taxon_profile_image_settings['maxextend']
506
      );
507
      if(count($preferred_representations) > 0){
508

    
509
        $representation = array_shift($preferred_representations);
510
        $representationPart = $representation->parts[0];
511
        $attributes['alt'] = $representationPart->uri;
512

    
513
        if (!empty($taxon_profile_image_settings['media_uri_query'])) {
514
          $representationPart->uri = $representationPart->uri
515
            . (strpos($representationPart->uri, '?') !== FALSE ? '&' : '?')
516
            . $taxon_profile_image_settings['media_uri_query'];
517
        }
518
      }
519
    }
520
    else {
521
      if ($taxon_profile_image_settings['custom_placeholder_enabled']) {
522
        // show placeholder image instead
523
        if (!empty($taxon_profile_image_settings['custom_placeholder_image_on']) && !empty($taxon_profile_image_settings['custom_placeholder_image_fid'])) {
524
          // use the user provided image
525
          $profile_image_file = file_load($taxon_profile_image_settings['custom_placeholder_image_fid']);
526
          $url = file_create_url($profile_image_file->uri);
527
          $image_info = image_get_info($profile_image_file->uri);
528
          $representationPart->width = $image_info['width'];
529
          $representationPart->height = $image_info['height'];
530
          $representationPart->uri = $url;
531
        }
532
        else {
533
          // use the hard coded default
534
          $representationPart->width = 184;
535
          $representationPart->height = 144;
536
          $representationPart->uri = base_path() . drupal_get_path('module',
537
              'cdm_dataportal') . '/images/no_picture.png';
538
        }
539
        $attributes['alt'] = "no image available";
540
      }
541
    }
542

    
543
    if (isset($representationPart->uri)) {
544
      $profile_image = cdm_media_gallerie_image($representationPart, $taxon_profile_image_settings['maxextend'], FALSE, $attributes);
545
      // NOTE: style="width:${maxextend}px' is needed for IE8 !!!
546
      $max_extend_with = $taxon_profile_image_settings['maxextend'] . 'px';
547
      $render_array['taxon_profile_image'] = markup_to_render_array('<div id="taxonProfileImage" style="width:' . $max_extend_with . '">' . $profile_image . '</div>',
548
        -101);
549
    }
550
  }
551

    
552
  if($add_synonymy){
553
    $synonymy_a = compose_cdm_taxon_page_synonymy($taxon, true);
554
    $synonymy_a['#weight'] = -102;
555
    $synonymy_a['#prefix'] = '<div id="synonymy">';
556
    $synonymy_a['#suffix'] = '</div>';
557
    $render_array['synonymy'] = $synonymy_a;
558
  }
559

    
560
  //  $pseudo_feature_block_toc_items = array();
561

    
562
  // Render the sections for each real feature
563
  $feature_block_list = make_feature_block_list($merged_tree->root->childNodes, $taxon);
564

    
565
  // >>>>>>>>>>>>>>>>>>> PSEUDO FEATURES >>>>>>>>>>>>>>>>>>>
566
  $pseudo_feature_weights = get_array_variable_merged(CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS, CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS_DEFAULT);
567

    
568
  // Bibliography
569
  $bibliography_block = make_bibliography_feature_block();
570
  if($bibliography_block){
571
    $feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]] = $bibliography_block;
572
    cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]);
573
  }
574

    
575
  // Descriptions (aggregated)
576
  $descriptionTypes = array();
577
  $descriptionTypes['descriptionTypes'] = ("AGGREGATED_STRUC_DESC");
578
  $aggregatedDescriptions = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXON . '/' . $taxon->uuid . '/descriptions', $descriptionTypes);
579
  if (isset($aggregatedDescriptions) and !empty($aggregatedDescriptions)) {
580
      // if($feature_block_list) ....TODO
581
      $feature_description = make_pseudo_feature('Descriptions (aggregated)', PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS);
582
      $description_item = '';
583
      foreach ($aggregatedDescriptions as $description) {
584
        $description_item = '<div class="' . html_class_attribute_ref($description) . '">';
585
        $description_item .= render_description_string(get_root_nodes_for_dataset($description));
586
        $description_item .= ' ' . icon_link(path_to_description($description->uuid));
587
        $description_item .= '<div class="content-caption">'. statistical_values_explanation() . '</div>';
588
        $description_item .= '</div>';
589
      }
590
      $description_block = feature_block(t('Descriptions (aggregated)'), $feature_description);
591
      $description_block->content = [];
592
      $description_block->content[] = compose_feature_block_wrap_elements([$description_item], $feature_description);
593

    
594
      $feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]] = $description_block;
595
      cdm_toc_list_add_item('Descriptions (aggregated)', 'aggregation_descriptions', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]);
596

    
597

    
598
  }
599

    
600
  // sort by weight
601
  ksort($feature_block_list);
602
  $render_array['taxon_description_features'] = _block_get_renderable_array($feature_block_list);
603

    
604
/*  // update TOC
605
  if ($pseudo_feature_block_toc_items){
606
    foreach ($pseudo_feature_block_toc_items as $label=>$fragment){
607
      cdm_toc_list_add_item($label, $fragment);
608
    }
609
  }
610
*/
611
  // <<<<<<<<<<<<<<<<<<< PSEUDO FEATURES <<<<<<<<<<<<<<<<<<<
612

    
613
  // create the table of content
614
  $toc = array(
615
      '#theme' => 'item_list',
616
    '#items' => cdm_toc_list(),
617
      '#title' => t('Content'),
618
    '#weight' => -100,                  // move to the top
619
      '#suffix' => '</div>',
620
      '#prefix'=> '<div id="page-toc">'
621
  );
622
  $render_array['taxon_description_feature_toc'] = $toc;
623

    
624
  return $render_array;
625
}
626

    
627
/**
628
 * @return object|\stdclass
629
 */
630
function make_bibliography_feature_block() {
631
  $bibliography_block = null;
632
  $bibliography_settings = get_bibliography_settings();
633
  if ($bibliography_settings['enabled'] == 1) {
634
    $bibliography_markup = FootnoteManager::renderFootnoteList(PSEUDO_FEATURE_BIBLIOGRAPHY, '');
635
    if ($bibliography_markup) {
636
      $feature_bibliography = make_pseudo_feature('Bibliography', PSEUDO_FEATURE_BIBLIOGRAPHY);
637
      $bibliography_item = markup_to_render_array($bibliography_markup);
638
      $bibliography_block = feature_block(t('Bibliography'), $feature_bibliography);
639
      $bibliography_block->content = [];
640
      $bibliography_block->content[] = compose_feature_block_wrap_elements([$bibliography_item], $feature_bibliography);
641
    }
642
  }
643
  return $bibliography_block;
644
}
645

    
646

    
647
/**
648
 * Renders the link which will lead to the specimen detail page
649
 * @param object $specimen
650
 *    the cdm specimen entity which will be linked to
651
 *
652
 * @return string
653
 *     the markup for the link
654
 */
655
function render_cdm_specimen_link($specimen) {
656
  $path = path_to_specimen($specimen->uuid);
657
  $attributes['class'][] = html_class_attribute_ref($specimen);
658
  return $specimen->titleCache.icon_link($path);
659
}
660

    
661
/**
662
 * Returns HTML containing the synonymy for the accepted taxon.
663
 *
664
 * Shows the whole synonymy for the accepted taxon.
665
 * The synonymy list is headed by the complete scientific name
666
 * of the accepted taxon with nomenclatural reference.
667
 *
668
 * @param object $taxon
669
 * @param boolean $add_accepted_taxon
670
 *
671
 * @return array
672
 *  Drupal render array for the synonymy
673
 *
674
 * @throws Exception
675
 *
676
 * @ingroup compose
677
 */
678
function compose_cdm_taxon_page_synonymy($taxon, $add_accepted_taxon) {
679

    
680
  RenderHints::pushToRenderStack('taxon_page_synonymy');
681

    
682
  // footnote key for the homotypic group and accepted taxon,
683
  // both should have the same footnote key
684
  RenderHints::setFootnoteListKey(RenderHints::getRenderPath());
685

    
686
  $synomymie = cdm_ws_get(CDM_WS_PORTAL_TAXON_SYNONYMY, array($taxon->uuid));
687

    
688
  $out = '';
689

    
690
  // Render accepted taxon.
691
  //
692
  // foonotes of the accepted taxon will be rendered in the homotypic group section
693
  // even if there are not synonyms in the homotypic group
694
  // homotypic group and accepted taxon should have the same footnote key
695
  $referenceUri = '';
696
  if ($add_accepted_taxon) {
697
    // remember the last part of the render path
698
    $synonymy_render_path = RenderHints::getRenderPath();
699
    // set new render path for the accepted taxon so
700
    // it can be styled differently via the name render part definitions
701
    RenderHints::pushToRenderStack('accepted_taxon');
702
    $accepted_name = '';
703
    if (variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE, 0)) {
704
      $label = variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL, CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL_DEFAULT);
705
      $accepted_name .= '<div class="secReference"><span class="label">' . t($label) . ':</span> ' . $taxon->sec->titleCache . '</div>';
706
    }
707
    if (isset($taxon->name->nomenclaturalReference)) {
708
      $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
709
    }
710

    
711
    $accepted_name .= '<div class="accepted-name">';
712
    $accepted_name .= render_taxon_or_name($taxon, NULL, $referenceUri);
713

    
714
    $name_relations = cdm_name_relationships_for_taxon($taxon);
715
    $name_relationships = compose_name_relationships_inline($name_relations, $taxon->name->uuid, $taxon->uuid);
716
    // Render relationships of accepted name.
717
    if(isset($name_relationships['list']['items'][0])){
718
      $accepted_name .= ' ' . drupal_render($name_relationships);
719
    }
720

    
721
    // handle annotations of the name and taxon
722
    $special_annotations_array = array();
723
    $special_annotations_array[] = $taxon->name;
724
    $special_annotations_array[] = $taxon;
725
    $accepted_name .= theme('cdm_entities_annotations_as_footnotekeys', array(
726
        'cdmBase_list' => $special_annotations_array,
727
        'footnote_list_key' => $synonymy_render_path . '-annotations')
728
    );
729
    $accepted_name .= '</div>';
730
    RenderHints::popFromRenderStack();
731
  }
732

    
733
  // --- Render homotypic synonymy group
734
  if (!empty($accepted_name)) {
735
    $out .= $accepted_name;
736
  }
737

    
738
  // Render the homotypicSynonymyGroup including the type information.
739
  $out .= theme(
740
    'cdm_homotypicSynonymyGroup',
741
    array(
742
      'synonymList' => $synomymie->homotypicSynonymsByHomotypicGroup,
743
      'accepted_taxon_name_uuid' => $taxon->name->uuid
744
    )
745
  );
746

    
747

    
748
  // Render accepted taxon heterotypic synonymy groups.
749
  if ($synomymie->heterotypicSynonymyGroups) {
750
    foreach ($synomymie->heterotypicSynonymyGroups as $homotypicalGroup) {
751
      $out .= theme('cdm_heterotypicSynonymyGroup', array('homotypicalGroup' => $homotypicalGroup));
752
    }
753
  }
754
  // Render taxon relationships.
755
  if (variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT)) {
756
    $taxonRelationshipsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, $taxon->uuid);
757
    $out .= cdm_taxonRelationships($taxonRelationshipsDTO, $taxon);
758
  }
759

    
760
  RenderHints::popFromRenderStack();
761

    
762
  return markup_to_render_array($out);
763
}
764

    
765

    
766
/**
767
 * composes and returns an render array for the experts associated with the given taxon
768
 *
769
 * @param object taxon
770
 *
771
 * @return array
772
 *   A Drupal render array for a table with the experts
773
 *
774
 * @ingroup compose
775
 */
776
function compose_cdm_taxon_page_experts($taxon){
777

    
778
  $render_array = array();
779
  if(!isset($taxon->uuid)){
780
    return $render_array;
781
  }
782

    
783
  $current_classification_uuid = get_current_classification_uuid();
784
  // TODO use cdm_ws_fetchall below but this failes! needs fix!
785
  $taxon_node_agent_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
786
    array(
787
      $taxon->uuid,
788
      $current_classification_uuid
789
    )
790
  );
791

    
792
  $header = array(
793
    array('data' => t('Expert')),
794
    array('data' => t('Role'))
795
  );
796
  $rows = array();
797

    
798

    
799
  foreach($taxon_node_agent_relations->records as $taxon_node_agent_relation){
800

    
801

    
802
    $expert_role_id = $taxon_node_agent_relation->agent->uuid . '-' . $taxon_node_agent_relation->type->uuid;
803
    $expert_details_container_id = 'expert_details_' . $expert_role_id;
804

    
805
    $agent_label_markup = cdm_dynabox(
806
      'expert_' . $expert_role_id,
807
      $taxon_node_agent_relation->agent->titleCache,
808
      // specifying both ends of the relationship will return only one record in the pager
809
      cdm_compose_url(CDM_WS_PORTAL_AGENT,
810
         array($taxon_node_agent_relation->agent->uuid, 'taxonNodeAgentRelations'),
811
        'taxon_uuid=' . $taxon->uuid . '&relType_uuid=' . $taxon_node_agent_relation->type->uuid),
812
      'cdm_taxon_expert',
813
      'Click for details',
814
      array('div', 'div'),
815
      array(), // attributes
816
      '#' . $expert_details_container_id // $content_element_selector
817
    );
818

    
819
    // Expert and Role
820
    $rows[] = array(
821
      'data' => array(
822
        array(
823
          'data' => $agent_label_markup,
824
          'class' => array(html_class_attribute_ref($taxon_node_agent_relation->agent))
825
        ),
826
        array(
827
          'data' => $taxon_node_agent_relation->type->representation_L10n,
828
          'class' => array(html_class_attribute_ref($taxon_node_agent_relation->type))
829
        )
830
      )
831
    );
832
    // Agent details
833
    $rows[] = array(
834
      'data' => array(
835
        array(
836
          'data' => '<!-- expert_details_container -->',
837
          'id' => $expert_details_container_id,
838
          'colspan' => 2
839
        )
840
      )
841
    );
842

    
843
  }
844

    
845

    
846
  $render_array['experts_table'] = array(
847
    '#theme' => 'table',
848
    '#header' => $header,
849
    '#rows' => $rows,
850
  );
851

    
852

    
853
  return $render_array;
854
}
855

    
856

    
857
/**
858
 * Manages the tabs to be hidden in the taxon page.
859
 *
860
 * The tabs are identified by their last menu link path element:
861
 *  - description
862
 *  - synonymy
863
 *  - images
864
 *  - specimens
865
 *  - key
866
 *
867
 * Internally the tabs are stored in a static variable which is
868
 * managed by drupal_static().
869
 *
870
 * @param string $add_tab
871
 *   Optional parameter. The given string will be added to the array of tabs
872
 *
873
 * @return
874
 *   The array of tabs
875
 */
876
function taxon_page_tabs_hidden_add($add_tab = NULL) {
877
  $tabs = &drupal_static('taxon_page_tabs_hidden');
878

    
879
  if(!isset($tabs)){
880
    $tabs = array();
881
  }
882

    
883
  if (isset($add_tab) && !array_key_exists($add_tab, $tabs)) {
884
    $tabs[] = $add_tab;
885
  }
886

    
887
  return $tabs;
888
}
889

    
890
/**
891
 * Manages the tabs to be hidden in the taxon page.
892
 *
893
 * The tabs names are identified by their last menu link path element:
894
 *  - description
895
 *  - synonymy
896
 *  - images
897
 *  - specimens
898
 *  - key
899
 *
900
 * Internally the tabs are stored in a static variable which is
901
 * managed by drupal_static().
902
 *
903
 * @param string $tabname
904
 *   The name of the tab to check
905
 *
906
 * @return boolean
907
 *   True if the tab or section is to be hidden
908
 */
909
function taxon_page_tabs_hidden_check($tabname) {
910

    
911
  $tabs = &drupal_static('taxon_page_tabs_hidden');
912

    
913
  if(!isset($tabs)){
914
    $tabs = array();
915
  }
916

    
917
  return array_search($tabname, $tabs) !== FALSE;
918
}
919

    
920
/**
921
 * Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
922
 *
923
 *  - Removes the tabs to be hidden, @see taxon_page_tabs_hidden_add()
924
 *  - Renames tabs according to the settings // TODO (this will replace the theme_cdm_taxonpage_tab() function !!!)
925
 *
926
 * @param array $variables
927
 *   The variables array
928
 */
929
function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {
930

    
931
  $hidden_tabs = taxon_page_tabs_hidden_add();
932

    
933
  if (!variable_get(CDM_SEARCH_BLAST_ENABLED)) {
934
      if (is_array($variables['primary'])) {
935
          foreach ($variables['primary'] as $key => &$element) {
936
              if ($element['#link']['path'] == 'cdm_dataportal/search/blast') {
937
                  // remove the tab
938
                  unset($variables['primary'][$key]);
939
              }
940

    
941
          }
942
      }
943
  }
944
  if (is_array($variables['primary'])) {
945
    foreach ($variables['primary'] as $key => &$element) {
946

    
947
      // 1. Remove the tabs to be hidden
948
      foreach ($hidden_tabs as $tab) {
949
        if ($element['#link']['path'] == 'cdm_dataportal/taxon/%/' . $tab) {
950
          // remove the tab
951
          unset($variables['primary'][$key]);
952
        }
953
      }
954
    }
955
  }
956
}
957

    
958

    
959

    
960
/**
961
 * Implements the hook_preprocess_HOOK() for theme_menu_local_task()
962
 *
963
 *
964
 * @param array $variables
965
 *   An associative array containing:
966
 *     - element: A render element containing:
967
 *          #link: A menu link array with 'title', 'href', and 'localized_options' keys.
968
 *          #active: A boolean indicating whether the local task is active.
969
 *
970
 */
971
function cdm_dataportal_preprocess_menu_local_task(&$variables) {
972

    
973
  $link = $variables['element']['#link'];
974
  if (preg_match('/cdm_dataportal\/.*\/refresh$/', $link['href'])) {
975
    $link['title'] = '<img class="refresh" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/view-refresh.png' . '" alt="' . check_plain($link['title']) . '" title="' . check_plain($link['title']) . '"/>';
976
    $link['localized_options']['html'] = TRUE;
977

    
978
    $variables['element']['#link'] = $link;
979
  }
980
}
981

    
982
/* =================== block composition ===================== */
983

    
984
/**
985
 * Composes and returns an render array for the classification breadcrumbs of the given taxon.
986
 *
987
 * @param taxon
988
 *
989
 * @return array
990
 *   A Drupal render array for a table with the experts
991
 *
992
 * @ingroup compose
993
 */
994
function compose_classification_breadcrumbs($taxon_uuid) {
995

    
996
  _add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');
997

    
998
  $render_array = array();
999

    
1000
  $render_array['#theme'] = 'item_list';
1001
  $render_array['#type'] = 'ul';
1002
  $render_array['#attributes'] = array(
1003
    'id' => 'classification-breadcrumbs',
1004
    'class' => 'breadcrumbs inline',
1005
  );
1006

    
1007
  $items = array();
1008

    
1009
  $parent_taxon_nodes = null;
1010
  if($taxon_uuid){
1011
    $parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
1012
  }
1013

    
1014
  $classifications = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
1015
  // find current classification in list
1016
  $classification = null;
1017
  $current_classification_uuid = get_current_classification_uuid();
1018
  foreach ($classifications as $classification){
1019
    if($classification->uuid == $current_classification_uuid){
1020
      break;
1021
    }
1022
  }
1023

    
1024
  $node_name = '';
1025
  if(count($classifications) > 1 ){
1026
    // need to add the current classification as first label
1027

    
1028
    $label = $classification->titleCache;
1029
    if(strlen($label) > 20){
1030
      $label = substr($label, 0, strpos($label, ' ', 15)) . '...';
1031
    }
1032
    $node_name = font_awesome_icon_markup('fa-th-list')  . ' ' . l($label, '#', array(
1033
      'attributes' => array(
1034
        'class' => 'taxonomic-children-button classification-chooser',
1035
        'data-destination-uri' => drupal_get_destination(),
1036
        'data-cdm-align-with' => array('prev')
1037
      ),
1038
      'html' => true
1039
    ));
1040
  }
1041

    
1042
  $rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
1043

    
1044
  $rank_separator = '<span> '
1045
    . font_awesome_icon_markup('fa-chevron-right')
1046
    . ' </span>';
1047
  $more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');
1048
  $more_children_label = '...';
1049

    
1050
  $items[] = $node_name;
1051

    
1052
  $more_children_for = null;
1053
  if($parent_taxon_nodes){
1054
    foreach ($parent_taxon_nodes as $node) {
1055

    
1056
      $is_first_item = count($items) == 0;
1057
      $is_last_item = count($items) == count($parent_taxon_nodes);
1058
      $node_name = cdm_dataportal_shortname_of($node);
1059
      $path = path_to_taxon($node->taxonUuid);
1060

    
1061
      if($node->taxonomicChildrenCount > 0) {
1062
        $more_children_for = $node->taxonUuid;
1063
      } else {
1064
        $more_children_for = null;
1065
      }
1066

    
1067
      // 'fa-sitemap'
1068

    
1069
      $items[] =
1070
        ($is_first_item ? '' : ' ')
1071
        . $rank_separator
1072
        . l(
1073
          '<span class="' . html_class_attribute_ref($node) . '">' . $node_name . '</span>',
1074
          $path,
1075
          array(
1076
            'attributes' => array(
1077
              'class' => array('taxonomic-children-button'),
1078
              'data-cdm-taxon-uuid' => array($node->taxonUuid),
1079
              'data-cdm-classification-mode' => array('siblings'),
1080
              'data-cdm-align-with' => array('prev')
1081
            ),
1082
            'html' => true
1083
          )
1084
        );
1085
      }
1086
    }
1087

    
1088
  // add more button to the end
1089
  if(!$parent_taxon_nodes) {
1090
    // not taxon focused yet, adding button to make  the root nodes available
1091
    $items[] = '<span>'
1092
      . $more_children_icon . '&nbsp;' .
1093
      '<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
1094
      . '" data-rank-limit-uuid="' . $rank_limit_uuid . '" data-cdm-align-with="prev"> ' . $more_children_label . '<span>'
1095
      . '</span>';
1096
  } else if($more_children_for){
1097
    // last parent item has child taxon nodes
1098
    $items[] = ' <span>'
1099
      . $more_children_icon . '&nbsp;' .
1100
      '<span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
1101
      . '" data-cdm-classification-mode="children" data-cdm-align-with="prev"> ' . $more_children_label . '</span>'
1102
      . '</span>';
1103

    
1104
  }
1105

    
1106
  $render_array['#items'] = $items;
1107

    
1108
  return $render_array;
1109
}
1110

    
1111

    
1112
/**
1113
 * @param $specimen_uuid
1114
 * @return array
1115
 *    The drupal render array for the page
1116
 *
1117
 * @ingroup compose
1118
 */
1119
function compose_cdm_specimen_page($specimen_uuid)
1120
{
1121
  drupal_set_title("Specimen Details");
1122
  RenderHints::pushToRenderStack('specimen_page');
1123

    
1124
  $specimen_table = array(
1125
      '#theme' => 'table',
1126
      '#weight' => 2,
1127
      // prefix attributes and rows with '#' to let it pass to the theme function,
1128
      // otherwise it is handled as child render array
1129

    
1130
    '#attributes' => array('class' => 'specimens'),
1131
      '#rows' => array(),
1132
      '#prefix' => '<div id="specimens">',
1133
      '#suffix' => '</div>',
1134

    
1135

    
1136
  );
1137
  $specimen = compose_cdm_specimen_or_observation($specimen_uuid, true);
1138
  /*
1139
  $render_array = array(
1140
          '#theme' => 'item_list',
1141
          '#items' => array($specimen),
1142
          '#type' => 'ul');
1143
  $output = drupal_render($render_array);
1144
 */
1145
  $specimen_table['#rows'][] = array(
1146
          // An array of table rows. Every row is an array of cells, or an associative array
1147
          'data' => $specimen,
1148
          'class' =>  array(
1149
              'descriptionElement',
1150
              'descriptionElement_IndividualsAssociation'
1151
          ),
1152
  );
1153

    
1154

    
1155
 // $detail_html = compose_cdm_specimen_or_observation($specimen_uuid, true);
1156
//    $render_array['markup'] = array(
1157
//        '#prefix' => '<div id="specimens" class="page">',
1158
//        'content' => $specimen_table,
1159
//        '#suffix' => '</div>',
1160
//    );
1161
  $render_array['specimen_table'] =  $specimen_table;
1162

    
1163
  RenderHints::popFromRenderStack();
1164
  return $specimen; // $render_array;
1165
}
1166

    
1167
/**
1168
 * @param $named_area_uuid
1169
 * @return array
1170
 *    The drupal render array for the page
1171
 *
1172
 * @ingroup compose
1173
 */
1174
function compose_cdm_named_area_page($named_area_uuid)
1175
{
1176

    
1177
  $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid));
1178

    
1179
  $render_array = array();
1180
  RenderHints::pushToRenderStack('named_area_page');
1181

    
1182
  $groups = array();
1183
  @_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);
1184
  @_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);
1185
  if(isset($named_area->level)) {
1186
    @_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);
1187
  }
1188

    
1189
  $name_area_details_elements = array(
1190
   // '#title' => $title,
1191
    '#theme' => 'description_list',
1192
    '#groups' => $groups,
1193
    '#attributes' => array('class' => html_class_attribute_ref($named_area)),
1194
  );
1195

    
1196
  $render_array[] = $name_area_details_elements;
1197

    
1198
  RenderHints::popFromRenderStack();
1199
  return $render_array;
1200
}
1201

    
1202

    
1203
/**
1204
 * Returns a drupal render array for a single reference page.
1205
 *
1206
 * Composes a page with all data on a single reference.
1207
 *
1208
 * @param string $uuid
1209
 *   An uuid for a cdm reference.
1210
 *
1211
 * @return array
1212
 *  A drupal render array
1213
 *
1214
 * @throws Exception
1215
 *
1216
 * @ingroup compose
1217
 */
1218
function compose_cdm_reference_page($uuid) {
1219

    
1220
  $pathelement = "reference_page";
1221
  RenderHints::pushToRenderStack($pathelement);
1222
  $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
1223
  if (!$reference) {
1224
    drupal_set_title(t('Reference does not exist'), PASS_THROUGH);
1225
    return "";
1226
  }
1227
  if (isset($reference->titleCache)) {
1228
    drupal_set_title($reference->titleCache, PASS_THROUGH);
1229
  }
1230

    
1231
  $field_order = array(
1232
    "title",
1233
    "abbrevTitle",
1234
    // "titleCache" abbrevTitleCache
1235
    // "citation",
1236
    "authorship",
1237
    "editor",
1238
    "publisher",
1239
    "placePublished",
1240
    "datePublished",
1241
    "year",
1242
    "edition",// Class Book.
1243
    "volume",// Class Article.
1244
    "seriesPart",
1245
    "inReference",
1246
    "nomRefBase", // Class BookSection, Book, Article.
1247
    "pages",// Class Article.
1248
    "series",// Class Article, PrintSeries.
1249
    "school",// Class Thesis.
1250
    "institution",// Class Report.
1251
    "organization",// Class Proceedings.
1252
    "nextVersion",
1253
    "previousVersion",
1254
    "isbn",// Class Book.
1255
    "issn",// Class Journal.
1256
    "doi",
1257
    "uri"
1258
  );
1259

    
1260
  $table_rows = array();
1261

    
1262
  if (!isset($reference->authorship)) {
1263
    $authorship = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid);
1264
    $reference->authorship = isset($authorship->titleCache) ? $authorship->titleCache : '';
1265
  }
1266

    
1267
  if (!isset($reference->inReference)) {
1268
    $reference->inReference = cdm_ws_get(CDM_WS_REFERENCE, array(
1269
      $reference->uuid,
1270
      "inReference",
1271
    ));
1272
  }
1273

    
1274
  foreach ($field_order as $fieldname) {
1275

    
1276
    if (isset($reference->$fieldname)) {
1277

    
1278
      if ($fieldname == "datePublished") {
1279
        $period = $reference->$fieldname;
1280
        $datePublished = timePeriodToString($period);
1281
        if (isset($datePublished) && $datePublished != '') {
1282
          $table_rows[] = array(
1283
            t("Date published"),
1284
            $datePublished,
1285
          );
1286
        }
1287
      }
1288
      elseif ($fieldname == "doi" && is_object($reference->doi)) {
1289
        $table_rows[] = array(
1290
          t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1291
          cdm_doi($reference->doi, false)
1292
        );
1293
      }
1294
      elseif ($fieldname == "uri" && isset($reference->uri) && $reference->uri) {
1295
        $table_rows[] = array(
1296
          t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1297
          cdm_external_uri($reference->uri, false)
1298
        );
1299
      }
1300
      elseif (is_object($reference->$fieldname)) {
1301
        if ($fieldname == "authorship") {
1302
          $dump = $reference->$fieldname;
1303
          $teammembers = "teamMembers";
1304
          $team = $dump->$teammembers;
1305
          $nameArray = array();
1306

    
1307
          foreach ($team as $member) {
1308
            if (strlen($member->lastname) > 0) {
1309
              $nname = $member->lastname;
1310
              $name = $nname;
1311
              if (strlen($member->firstname) > 0) {
1312
                $vname = $member->firstname;
1313
                $name = $vname . " " . $nname;
1314
              }
1315
              $nameArray[] = $name;
1316
            }
1317
            else {
1318
              if (strlen($member->titleCache) > 0) {
1319
                $nameArray[] = $member->titleCache;
1320
              }
1321
            }
1322
          }
1323
          $value = join($nameArray, ", ");
1324
        }
1325
        elseif ($fieldname == "inReference") {
1326
          $type = $reference->$fieldname->type;
1327
          $value = l($reference->$fieldname->titleCache, path_to_reference($reference->$fieldname->uuid));
1328
          switch ($type) {
1329
            case "Book":
1330
              $fieldname = "in book";
1331
              break;
1332
            case "Journal":
1333
              $fieldname = "in journal";
1334
              break;
1335
            case "Proceedings":
1336
              $fieldname = "in proceedings";
1337
              break;
1338
          }
1339
        }
1340
        else {
1341
          $value = $reference->$fieldname->titleCache;
1342
        }
1343

    
1344

    
1345
        if (isset($value) && $value != '') {
1346
          $table_rows[] = array(
1347
            t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1348
            $value,
1349
          );
1350
        }
1351

    
1352
      }
1353
      else {
1354
        if (isset($reference->$fieldname) && $reference->$fieldname != '') {
1355
          $table_rows[] = array(
1356
            t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1357
            $reference->$fieldname,
1358
          );
1359
        }
1360
      }
1361
    }
1362
  }
1363

    
1364
  $out = theme_table(array(
1365
    'header' => array(),
1366
    'rows' => $table_rows,
1367
    'attributes' => array(
1368
      'class' => html_class_attribute_ref($reference)
1369
    ),
1370
    'caption' => NULL,
1371
    'colgroups' => NULL,
1372
    'sticky' => NULL,
1373
    'empty' => NULL,
1374
  ));
1375

    
1376
  if(isset($reference->referenceAbstract)){
1377
    $out .= '<h2 class="block-title">Abstract</h2><div class="abstract">' . $reference->referenceAbstract . '</div>';
1378
  }
1379

    
1380

    
1381
  // Annotations below the table
1382
  $annotations = cdm_fetch_visible_annotations($reference);
1383
  $out .= cdm_annotations($annotations);
1384

    
1385
  $registration_working_set = cdm_ws_get("registrationWorkingSetDTO", array($uuid));
1386
  if($registration_working_set && count($registration_working_set->registrationDTOs) > 0){
1387
    $out .= "<h3>Nomenclatural acts:</h3><div class=\"cdm-item-list registration-item-list\">";
1388
    foreach($registration_working_set->registrationDTOs as $registration_dto){
1389
      if($registration_dto->status == "PUBLISHED"){
1390
        $registration_render_a = compose_registration_dto_compact($registration_dto, 'citation');
1391
        $registration_render_a["#prefix"] = "<div class=\"item item-registration\">";
1392
        $registration_render_a["#suffix"] = "</div>";
1393
        $out .= drupal_render($registration_render_a);
1394
      }
1395
    }
1396
    $out .= "</div>";
1397
  }
1398

    
1399
  RenderHints::popFromRenderStack();
1400

    
1401
  return markup_to_render_array($out);
1402
}
1403

    
1404
/**
1405
 * Provides the the label string for taxon page tabs.
1406
 *
1407
 * The $tabname as passed to the method will be returned if no override
1408
 * label is configured in the settings.
1409
 */
1410
function cdm_taxonpage_tab_label($tabname) {
1411
  static $taxon_tabs_labels = null;
1412
  if($taxon_tabs_labels == null){
1413
    $taxon_tabs_labels = get_array_variable_merged(CDM_TAXONPAGE_TAB_LABELS, CDM_TAXONPAGE_TAB_LABELS_DEFAULT);
1414
  }
1415
  $tabname_key = strtolower($tabname);
1416
  if(isset($taxon_tabs_labels[$tabname_key]) && $taxon_tabs_labels[$tabname_key]){
1417
    return $taxon_tabs_labels[$tabname_key];
1418
  }
1419
  return $tabname;
1420
}
(8-8/13)