Project

General

Profile

Statistics
| Branch: | Tag: | Revision:

cdm-dataportal / modules / cdm_dataportal / includes / pages.inc @ 6679207a

History | View | Annotate | Download (48.3 KB)

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_SPECIMEN_LIST_VIEW_MODE, CDM_SPECIMEN_LIST_VIEW_MODE_DEFAULT) == CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_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_SPECIMEN_LIST_VIEW_MODE, CDM_SPECIMEN_LIST_VIEW_MODE_DEFAULT) == CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TABLE)){
94

    
95
        //COMPRESSED SPECIMEN DERIVATE TABLE
96
        $pager_field_units = cdm_ws_page(
97
          cdm_compose_url(CDM_WS_PORTAL_TAXON, [
98
            $taxon->uuid,
99
            'associatedFieldUnits'
100
          ]),
101
          variable_get(CDM_SEARCH_RESULT_PAGE_SIZE, CDM_SEARCH_RESULT_PAGE_SIZE_DEFAULT) * 2,
102
          isset($_REQUEST['pager']['pageNumber']) ? isset($_REQUEST['pager']['pageNumber']) : 0
103
        );
104

    
105
        if (isset($pager_field_units->records[0])) {
106
          $field_unit_uuids = array();
107
          foreach ($pager_field_units->records as $field_unit) {
108
            $field_unit_uuids[] = $field_unit->uuid;
109
          }
110

    
111
          $render_array['derivate_hierarchy_table'] = compose_compressed_specimen_derivate_table($field_unit_uuids);
112
        }
113

    
114
        $render_array['pager'] = markup_to_render_array(
115
            theme('cdm_pager', array(
116
                'pager' => $pager_field_units,
117
                'path' => $_REQUEST['q'],
118
                'parameters' => $_REQUEST
119
            )),
120
            10 // weight
121
        );
122
    }
123
    else if((variable_get(CDM_SPECIMEN_LIST_VIEW_MODE, CDM_SPECIMEN_LIST_VIEW_MODE_DEFAULT) == CDM_SPECIMEN_LIST_VIEW_MODE_OPTION_DERIVATE_TREE)){ // FIXME this seems to be wrong
124
      $render_array['specimen_list'] = compose_specimen_table_top_down($fieldUnitDTOs);
125
      $render_array['specimen_list']['#weight'] = 2;
126
    } else {
127
      $specimen_table = compose_specimens_table_bottom_up($specimensOrObservations);
128

    
129
      $render_array['specimen_list'] = $specimen_table;
130
      $render_array['pager'] = markup_to_render_array(
131
        theme('cdm_pager', array(
132
          'pager' => $pager,
133
          'path' => $_REQUEST['q'],
134
          'parameters' => $_REQUEST,
135
        )),
136
        10 // weight
137
      );
138
    }
139

    
140
    RenderHints::popFromRenderStack();
141
    return $render_array;
142
}
143

    
144
/**
145
 * @return array
146
 *
147
 * TODO move to cdm_dataportal.module or api.module?
148
 */
149
function relationship_filter_query_parameters()
150
{
151
  $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
152
  $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
153
  $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
154

    
155
  $by_associatedtaxon_query_parameters = array(
156
    'relationshipsInvers' => implode(',', $relationship_choice['invers']),
157
    'relationships' => implode(',', $relationship_choice['direct']),
158
  );
159
  return $by_associatedtaxon_query_parameters;
160
}
161

    
162

    
163
function create_html_link($link, $openInExternalWindow=false){
164
    $html = "";
165
    if($link->uri && $link->uri!=""){
166
        $html .= '<a  href="' . $link->uri . '"';
167
        if($openInExternalWindow){
168
            $html .= ' target="_blank"';
169
        }
170
        $html .= '>' . $link->linkText . '</a>';
171
    }
172
    else{
173
        $html .= $link->linkText;
174
    }
175
    return $html;
176
}
177

    
178
/**
179
 * Creates HTML links from the given link list concatenated by default by a comma.
180
 * @param $linkList the list with Link objects having "uri" and "linkText" as members
181
 * @return string the assembled HTML string containing the links
182
 */
183
function create_html_links($linkList, $openInExternalWindow=false, $separator=", ")
184
{
185
    $html = "";
186
    if ($linkList) {
187
        foreach ($linkList as $link) {
188
            $html .= create_html_link($link, $openInExternalWindow).$separator;
189
        }
190
        $html = rtrim($html, $separator);
191
    }
192
    return $html;
193
}
194

    
195
/**
196
 * Composes a taxon page which can consist of multiple parts like
197
 * 'General', 'Synonymy', 'Images', 'Keys'. These parts can be displayed
198
 * as tabs or as sections of a single page.
199
 *
200
 * It is headed by the name of the accepted taxon without author and reference.
201
 *
202
 * @param $taxon
203
 *   The CDM Taxon Instance to compose the page for.
204
 * @param $page_part
205
 *   Name of the part to display, valid values are:
206
 *    - 'description' -  for the general part
207
 *    - 'images'
208
 *    - 'synonymy'
209
 *    - 'keys'
210
 *    - 'all'
211
 *
212
 * @return array
213
 *   A drupal render array
214
 *
215
 * @ingroup compose
216
 */
217
function compose_cdm_taxon_page($taxon, $page_part = 'description') {
218

    
219
  // we better cache here since drupal_get_query_parameters has no internal static cache variable
220
  $http_request_params = drupal_get_query_parameters();
221

    
222
  // add all mandatory js sources
223
  _add_js_footnotes();
224

    
225

    
226
  $render_array = array();
227
  $weight = 0; // the weight for the render array elements
228

    
229
  $tabsToDisplay = variable_get('cdm_taxonpage_tabs_visibility', unserialize(TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT));
230

    
231
  $page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';
232

    
233
  $synonymy_as_tab = variable_get(CDM_SYNONYMY_AS_TAB, CDM_SYNONYMY_AS_TAB_DEFAULT) === 1;
234
  if(!$synonymy_as_tab){
235
    unset($tabsToDisplay["Synonymy"]);
236
    // the synonymy is located in the general part in this case
237
    if($page_part == 'synonymy'){
238
      $page_part = 'description';
239
    }
240
  }
241

    
242
  $media = _load_media_for_taxon($taxon);
243

    
244

    
245
  if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {
246
    taxon_page_tabs_hidden_add('images');
247
  }
248

    
249
  // --- GET specimensOrObservations --- //
250
  $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservationsCount'));
251

    
252
  $specimensOrObservationsCount = $specimensOrObservations != null ? $specimensOrObservations->result : 0;
253
  if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {
254
    taxon_page_tabs_hidden_add('specimens');
255
  }
256

    
257
  // --- GET polytomousKeys --- //
258
  $polytomousKeysPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, NULL, "findByTaxonomicScope=$taxon->uuid");
259
  $identificationKeyCount = 0;
260
  if ($polytomousKeysPager) {
261
    $identificationKeyCount += $polytomousKeysPager->count;
262
  }
263
  if ($identificationKeyCount == 0 || ($tabsToDisplay["Keys"] == '0')) {
264
    taxon_page_tabs_hidden_add('keys');
265
  }
266

    
267
  // --- GET TaxonNodeAgentRelations --- //
268
  $current_classification_uuid = get_current_classification_uuid();
269
  $taxon_node_agent_relations_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
270
      array(
271
          $taxon->uuid,
272
          $current_classification_uuid,
273
      ),
274
      "pageSize=1&pageIndex=0"// we are only interested into the count so we are fetching only one item, o is not possible!
275
  );
276
  if (!$taxon_node_agent_relations_pager || $taxon_node_agent_relations_pager->count == 0){
277
      taxon_page_tabs_hidden_add('experts');
278
  }
279

    
280
  if (!isset($tabsToDisplay["Synonymy"]) || $tabsToDisplay["Synonymy"] == '0') {
281
    taxon_page_tabs_hidden_add('synonymy');
282
  }
283

    
284
  // -------------------------------------------- //
285

    
286
  if(variable_get(CDM_TAXONPAGE_TAXON_NODE_SHOW_STATES, 1) && ( $page_part == 'description' || $page_part == 'synonymy' || $page_part == 'all')){
287
    $taxon_nodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, array($taxon->uuid));
288
    $render_array['taxon_node_status'] = compose_taxon_node_status($taxon_nodes);
289
    $render_array['taxon_node_status']['#weight'] = -100;
290
  }
291

    
292
  if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {
293
    $render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);
294
  }
295

    
296
  // --- PAGE PART: DESCRIPTION --- //
297
  if (!taxon_page_tabs_hidden_check('description') && ($page_part == 'description' || $page_part == 'all')) {
298

    
299
    $merged_tree = merged_taxon_feature_tree($taxon);
300

    
301

    
302
    $render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media, !$synonymy_as_tab);
303
    $render_array['general']['#weight'] = $weight++;
304
    $render_array['general']['#prefix'] = '<div id="general" class="page-part">';
305
    $render_array['general']['#suffix'] = '</div>';
306
  }
307

    
308
  // --- PAGE PART: IMAGES --- //
309
  if (!taxon_page_tabs_hidden_check('images') && ($page_part == 'images' || $page_part == 'all')) {
310
    $images_html = '<div id="images" class="page-part">';
311
    if ($page_part == 'all') {
312
      $images_html .= '<h2>' . t(cdm_taxonpage_tab_label('Images')) . '</h2>';
313
    }
314
    // Get the image gallery as configured by the admin.
315
    $configured_image_gallery_viewer = variable_get(CDM_MEDIA_GALLERY_VIEWER, CDM_MEDIA_GALLERY_VIEWER_DEFAULT);
316
    if($configured_image_gallery_viewer != 'fsi'){
317
      $images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);
318
    } else {
319
      // the fsi_gallery requires a flash plugin, in case the client browser is not supporting
320
      // flash we also need to provide an the default gallery as alternative
321
      $images_html .= render_taxon_media_gallery($taxon, CDM_MEDIA_GALLERY_VIEWER_DEFAULT, $media);
322
      $images_html .= render_taxon_media_gallery($taxon, $configured_image_gallery_viewer, $media);
323
    }
324
    $images_html .= '</div>'; // END of <div id="images">
325
    $render_array['images'] = markup_to_render_array($images_html, $weight++);
326
  }
327

    
328
  // --- PAGE PART: SYNONYMY --- //
329
  if (!taxon_page_tabs_hidden_check('synonymy') && (($page_part == 'synonymy' || $page_part == 'all') && $synonymy_as_tab)) {
330
    $synonymy_html = '<div id="synonymy" class="page-part">';
331
    if ($page_part == 'all') {
332
      $synonymy_html .= '<h2>' . t(cdm_taxonpage_tab_label('Synonymy')) . '</h2>';
333
    }
334
    $addAcceptedTaxon = variable_get(CDM_DATAPORTAL_NOMREF_IN_TITLE, CDM_DATAPORTAL_NOMREF_IN_TITLE_DEFAULT);
335

    
336
    $synonym_a = compose_cdm_taxon_page_synonymy($taxon, $addAcceptedTaxon);
337
    $synonymy_html .= drupal_render($synonym_a);
338

    
339
    $synonymy_html .= '</div>';
340
    $render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
341

    
342
  }
343

    
344
  // --- PAGE PART: SPECIMENS --- //
345
  if (!taxon_page_tabs_hidden_check('specimens') && ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all'))) {
346
    $render_array['specimens'] = array(
347
        '#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Specimens')) . '</h2>' : ''),
348
        'content' => compose_cdm_taxon_page_specimens($taxon), // returns render array
349
        '#suffix' => '</div>',
350
    );
351
  }
352

    
353
  // --- PAGE PART: KEYS --- //
354
  if(!taxon_page_tabs_hidden_check('keys')){
355
    if ($identificationKeyCount == 1 && $page_part == 'keys'){
356
      drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));
357
    }
358
    else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {
359
      $keys_html = '<div id="keys" class="page-part">';
360
      if ($page_part == 'all') {
361
        $keys_html .= '<h2>' . t(cdm_taxonpage_tab_label('Keys')) . '</h2>';
362
      }
363
      $keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
364
      $keys_html .= '</div>';
365
      $render_array['keys'] = markup_to_render_array($keys_html, $weight++);
366
    }
367
  }
368

    
369
  // --- PAGE PART: EXPERTS --- //
370

    
371
  if (!taxon_page_tabs_hidden_check('experts') && ($page_part == 'experts' || $page_part == 'all')) {
372
    $render_array['experts'] = array(
373
        '#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t(cdm_taxonpage_tab_label('Experts')) . '</h2>' : ''),
374
        'content' => compose_cdm_taxon_page_experts($taxon), // returns render array
375
        '#suffix' => '</div>',
376
    );
377
  }
378

    
379
  // ------------------ END OF PARTS -------------- //
380

    
381
  // adjust weights of page and toc elements according to the settings
382
  $taxontabs_weights = get_array_variable_merged(CDM_TAXONPAGE_TAB_WEIGHT, CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
383
  foreach($taxontabs_weights as $tab_key => $weight){
384
    if(isset($render_array[$tab_key])){
385
      $render_array[$tab_key]['#weight'] = $weight;
386
    }
387
  }
388

    
389

    
390
  // set up the TOC and pseudo feature blocks for the pages which contain all page parts
391
  if($page_part == 'all' && (!isset( $render_array['general']) || count($render_array['general']) == 0 )) {
392

    
393
    $bibliography_block = make_bibliography_feature_block();
394
    if($bibliography_block){
395
      $render_array['bibliography_block'] = _block_get_renderable_array([$bibliography_block]);
396
      $render_array['bibliography_block']['#weight'] = 100;
397
      cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $render_array['bibliography_block']['#weight']);
398
    }
399

    
400
    $toc_elements = [];
401
    asort($taxontabs_weights);
402
    foreach(array_keys($taxontabs_weights) as $tab_key){
403
      if(isset($render_array[$tab_key])){
404
        if($tab_key != 'general'){
405
          // add entry for page part
406
          $toc_elements[] = array(
407
              'data' => l(t(cdm_taxonpage_tab_label(ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),
408
              'class' => array('page-part-toc-item-' . $tab_key)
409
          );
410
        } else {
411
          // add content of profile part instead
412
          if(isset($render_array['general'])) {
413
            // in case all tabs are shown at once the feature tocs
414
            // should be integrated into the tabs toc as sub list
415
            // and the profile image should be on top of the page
416
            if(isset($render_array['general']['taxon_description_feature_toc'])){;
417
            foreach ($render_array['general']['taxon_description_feature_toc']['#items'] as $profile_toc_item){
418
              $toc_elements[] = $profile_toc_item;
419
            }
420
            unset($render_array['general']['taxon_description_feature_toc']);
421
            }
422
          }
423
        }
424
      }
425
    }
426

    
427
    // move profile image in page structure
428
    if(isset($render_array['general']['taxon_profile_image'])){
429
      $render_array['profile_image'] = $render_array['general']['taxon_profile_image'];
430
      $render_array['profile_image']['#weight'] = -100;
431
      unset($render_array['general']['taxon_profile_image']);
432
    }
433

    
434
    // finally add the table of contents to the render array
435
    $render_array['toc'] = array(
436
        '#theme' => 'item_list',
437
        '#items' => $toc_elements,
438
        '#title' => t('Content'),
439
        '#weight' => -101,
440
        '#suffix' => '</div>',
441
        '#prefix'=> '<div id="page-toc">'
442
    );
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
    $synonymy_a['#prefix'] = '<div id="synonymy">';
554
    $synonymy_a['#suffix'] = '</div>';
555
    $render_array['synonymy'] = $synonymy_a;
556
  }
557

    
558
  //  $pseudo_feature_block_toc_items = array();
559

    
560
  // Render the sections for each real feature
561
  $feature_block_list = make_feature_block_list($merged_tree->root->childNodes, $taxon);
562

    
563
  // >>>>>>>>>>>>>>>>>>> PSEUDO FEATURES >>>>>>>>>>>>>>>>>>>
564
  $pseudo_feature_weights = get_array_variable_merged(CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS, CDM_PSEUDO_FEATURE_BLOCK_WEIGHTS_DEFAULT);
565

    
566
  // Bibliography
567
  $bibliography_block = make_bibliography_feature_block();
568
  if($bibliography_block){
569
    $feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]] = $bibliography_block;
570
    cdm_toc_list_add_item('Bibliography', 'bibliography', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_BIBLIOGRAPHY]);
571
  }
572

    
573
  // Descriptions (aggregated)
574
  $descriptionTypes = array();
575
  $descriptionTypes['descriptionTypes'] = ("AGGREGATED_STRUC_DESC");
576
  $aggregatedDescriptions = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXON . '/' . $taxon->uuid . '/descriptions', $descriptionTypes);
577
  if (isset($aggregatedDescriptions) and !empty($aggregatedDescriptions)) {
578
      // if($feature_block_list) ....TODO
579
      $feature_description = make_pseudo_feature('Descriptions (aggregated)', PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS);
580
      $description_item = '';
581
      foreach ($aggregatedDescriptions as $description) {
582
        $description_item = '<div class="' . html_class_attribute_ref($description) . '">';
583
        $description_item .= render_description_string(get_root_nodes_for_dataset($description));
584
        $description_item .= ' ' . icon_link(path_to_description($description->uuid));
585
        $description_item .= '<div class="content-caption">'. statistical_values_explanation() . '</div>';
586
        $description_item .= '</div>';
587
      }
588
      $description_block = feature_block(t('Descriptions (aggregated)'), $feature_description);
589
      $description_block->content = [];
590
      $description_block->content[] = compose_feature_block_wrap_elements([$description_item], $feature_description);
591

    
592
      $feature_block_list[$pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]] = $description_block;
593
      cdm_toc_list_add_item('Descriptions (aggregated)', 'aggregation_descriptions', null, false, $pseudo_feature_weights[PSEUDO_FEATURE_AGGREGATION_DESCRIPTIONS]);
594

    
595

    
596
  }
597

    
598
  // sort by weight
599
  ksort($feature_block_list);
600
  $render_array['taxon_description_features'] = _block_get_renderable_array($feature_block_list);
601

    
602
/*  // update TOC
603
  if ($pseudo_feature_block_toc_items){
604
    foreach ($pseudo_feature_block_toc_items as $label=>$fragment){
605
      cdm_toc_list_add_item($label, $fragment);
606
    }
607
  }
608
*/
609
  // <<<<<<<<<<<<<<<<<<< PSEUDO FEATURES <<<<<<<<<<<<<<<<<<<
610

    
611
  // create the table of content
612
  $toc = array(
613
      '#theme' => 'item_list',
614
    '#items' => cdm_toc_list(),
615
      '#title' => t('Content'),
616
    '#weight' => -100,                  // move to the top
617
      '#suffix' => '</div>',
618
      '#prefix'=> '<div id="page-toc">'
619
  );
620
  $render_array['taxon_description_feature_toc'] = $toc;
621

    
622
  return $render_array;
623
}
624

    
625
/**
626
 * @return object|\stdclass
627
 */
628
function make_bibliography_feature_block() {
629
  $bibliography_block = null;
630
  $bibliography_settings = get_bibliography_settings();
631
  if ($bibliography_settings['enabled'] == 1) {
632
    $bibliography_markup = FootnoteManager::renderFootnoteList(PSEUDO_FEATURE_BIBLIOGRAPHY, '');
633
    if ($bibliography_markup) {
634
      $feature_bibliography = make_pseudo_feature('Bibliography', PSEUDO_FEATURE_BIBLIOGRAPHY);
635
      $bibliography_item = markup_to_render_array($bibliography_markup);
636
      $bibliography_block = feature_block(t('Bibliography'), $feature_bibliography);
637
      $bibliography_block->content = [];
638
      $bibliography_block->content[] = compose_feature_block_wrap_elements([$bibliography_item], $feature_bibliography);
639
    }
640
  }
641
  return $bibliography_block;
642
}
643

    
644

    
645
/**
646
 * Renders the link which will lead to the specimen detail page
647
 * @param object $specimen
648
 *    the cdm specimen entity which will be linked to
649
 *
650
 * @return string
651
 *     the markup for the link
652
 */
653
function render_cdm_specimen_link($specimen) {
654
  $path = path_to_specimen($specimen->uuid);
655
  $attributes['class'][] = html_class_attribute_ref($specimen);
656
  return $specimen->titleCache.icon_link($path);
657
}
658

    
659
/**
660
 * Returns HTML containing the synonymy for the accepted taxon.
661
 *
662
 * Shows the whole synonymy for the accepted taxon.
663
 * The synonymy list is headed by the complete scientific name
664
 * of the accepted taxon with nomenclatural reference.
665
 *
666
 * @param object $taxon
667
 * @param boolean $add_accepted_taxon
668
 *
669
 * @return array
670
 *  Drupal render array for the synonymy
671
 *
672
 * @throws Exception
673
 *
674
 * @ingroup compose
675
 */
676
function compose_cdm_taxon_page_synonymy($taxon, $add_accepted_taxon) {
677

    
678
  RenderHints::pushToRenderStack('taxon_page_synonymy');
679

    
680
  // footnote key for the homotypic group and accepted taxon,
681
  // both should have the same footnote key
682
  RenderHints::setFootnoteListKey(RenderHints::getRenderPath());
683

    
684
  $synomymie = cdm_ws_get(CDM_WS_PORTAL_TAXON_SYNONYMY, array($taxon->uuid));
685

    
686
  $out = '';
687

    
688
  // Render accepted taxon.
689
  //
690
  // foonotes of the accepted taxon will be rendered in the homotypic group section
691
  // even if there are not synonyms in the homotypic group
692
  // homotypic group and accepted taxon should have the same footnote key
693
  $referenceUri = '';
694
  if ($add_accepted_taxon) {
695
    // set new render path for the accepted taxon so
696
    // it can be styled differently via the name render part definitions
697
    RenderHints::pushToRenderStack('accepted_taxon');
698
    $accepted_name = '';
699
    if (variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE, 0)) {
700
      $label = variable_get(CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL, CDM_SYNONYMY_ACCEPTED_TAXON_SEC_SEPARATE_LABEL_DEFAULT);
701
      $accepted_name .= '<div class="secReference"><span class="label">' . t($label) . ':</span> ' . $taxon->sec->titleCache . '</div>';
702
    }
703
    if (isset($taxon->name->nomenclaturalSource->citation)) {
704
      $referenceUri = url(path_to_reference($taxon->name->nomenclaturalSource->citation->uuid));
705
    }
706

    
707
    $accepted_name .= '<div class="accepted-name">';
708
    $accepted_name .= render_taxon_or_name($taxon, NULL, $referenceUri);
709

    
710
    $name_relations = cdm_name_relationships_for_taxon($taxon);
711
    $name_relationships = compose_name_relationships_inline($name_relations, $taxon->name->uuid, $taxon->uuid);
712
    // Render relationships of accepted name.
713
    if(isset($name_relationships['list']['items'][0])){
714
      $accepted_name .= ' ' . drupal_render($name_relationships);
715
    }
716
    $accepted_name .= render_taxon_and_name_footnotes($taxon);
717
    $accepted_name .= '</div>';
718
    RenderHints::popFromRenderStack();
719
  }
720

    
721
  // --- Render homotypic synonymy group
722
  if (!empty($accepted_name)) {
723
    $out .= $accepted_name;
724
  }
725

    
726
  // Render the homotypicSynonymyGroup including the type information.
727
  $out .= theme(
728
    'cdm_homotypicSynonymyGroup',
729
    array(
730
      'synonymList' => $synomymie->homotypicSynonymsByHomotypicGroup,
731
      'accepted_taxon_name_uuid' => $taxon->name->uuid
732
    )
733
  );
734

    
735

    
736
  // Render accepted taxon heterotypic synonymy groups.
737
  if ($synomymie->heterotypicSynonymyGroups) {
738
    foreach ($synomymie->heterotypicSynonymyGroups as $homotypicalGroup) {
739
      $out .= theme('cdm_heterotypicSynonymyGroup', array('homotypicalGroup' => $homotypicalGroup));
740
    }
741
  }
742
  // Render taxon relationships.
743
  if (variable_get(CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS, CDM_DATAPORTAL_DISPLAY_TAXON_RELATIONSHIPS_DEFAULT)) {
744
    $taxonRelationshipsDTO = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS_DTO, $taxon->uuid);
745
    $out .= cdm_taxonRelationships($taxonRelationshipsDTO, $taxon);
746
  }
747

    
748
  RenderHints::popFromRenderStack();
749

    
750
  return markup_to_render_array($out);
751
}
752

    
753
/**
754
 * Provides the default configuration for handle_annotations_and_sources() in the
755
 * synonymy.
756
 *
757
 * @return bool[]
758
 */
759
function synonymy_annotations_and_source_config() {
760
  static $annotations_and_sources_config = null;
761
  if(!$annotations_and_sources_config){
762
    $bibliography_settings = get_bibliography_settings();
763
    $annotations_and_sources_config = [
764
      'sources_as_content' => FALSE,
765
      'link_to_name_used_in_source' => TRUE,
766
      'link_to_reference' => TRUE,
767
      'add_footnote_keys' => TRUE,
768
      'bibliography_aware' => $bibliography_settings['enabled'] == 1
769
    ];
770
  }
771
  return $annotations_and_sources_config;
772
}
773

    
774

    
775
/**
776
 * composes and returns an render array for the experts associated with the given taxon
777
 *
778
 * @param object taxon
779
 *
780
 * @return array
781
 *   A Drupal render array for a table with the experts
782
 *
783
 * @ingroup compose
784
 */
785
function compose_cdm_taxon_page_experts($taxon){
786

    
787
  $render_array = array();
788
  if(!isset($taxon->uuid)){
789
    return $render_array;
790
  }
791

    
792
  $current_classification_uuid = get_current_classification_uuid();
793
  // TODO use cdm_ws_fetchall below but this failes! needs fix!
794
  $taxon_node_agent_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
795
    array(
796
      $taxon->uuid,
797
      $current_classification_uuid
798
    )
799
  );
800

    
801
  $header = array(
802
    array('data' => t('Expert')),
803
    array('data' => t('Role'))
804
  );
805
  $rows = array();
806

    
807

    
808
  foreach($taxon_node_agent_relations->records as $taxon_node_agent_relation){
809

    
810

    
811
    $expert_role_id = $taxon_node_agent_relation->agent->uuid . '-' . $taxon_node_agent_relation->type->uuid;
812
    $expert_details_container_id = 'expert_details_' . $expert_role_id;
813

    
814
    $agent_label_markup = cdm_dynabox(
815
      'expert_' . $expert_role_id,
816
      $taxon_node_agent_relation->agent->titleCache,
817
      // specifying both ends of the relationship will return only one record in the pager
818
      cdm_compose_ws_url(CDM_WS_PORTAL_AGENT,
819
         array($taxon_node_agent_relation->agent->uuid, 'taxonNodeAgentRelations'),
820
        'taxon_uuid=' . $taxon->uuid . '&relType_uuid=' . $taxon_node_agent_relation->type->uuid),
821
      'cdm_taxon_expert',
822
      'Click for details',
823
      array('div', 'div'),
824
      array(), // attributes
825
      '#' . $expert_details_container_id // $content_element_selector
826
    );
827

    
828
    // Expert and Role
829
    $rows[] = array(
830
      'data' => array(
831
        array(
832
          'data' => $agent_label_markup,
833
          'class' => array(html_class_attribute_ref($taxon_node_agent_relation->agent))
834
        ),
835
        array(
836
          'data' => $taxon_node_agent_relation->type->representation_L10n,
837
          'class' => array(html_class_attribute_ref($taxon_node_agent_relation->type))
838
        )
839
      )
840
    );
841
    // Agent details
842
    $rows[] = array(
843
      'data' => array(
844
        array(
845
          'data' => '<!-- expert_details_container -->',
846
          'id' => $expert_details_container_id,
847
          'colspan' => 2
848
        )
849
      )
850
    );
851

    
852
  }
853

    
854

    
855
  $render_array['experts_table'] = array(
856
    '#theme' => 'table',
857
    '#header' => $header,
858
    '#rows' => $rows,
859
  );
860

    
861

    
862
  return $render_array;
863
}
864

    
865

    
866
/**
867
 * Manages the tabs to be hidden in the taxon page.
868
 *
869
 * The tabs are identified by their last menu link path element:
870
 *  - description
871
 *  - synonymy
872
 *  - images
873
 *  - specimens
874
 *  - key
875
 *
876
 * Internally the tabs are stored in a static variable which is
877
 * managed by drupal_static().
878
 *
879
 * @param string $add_tab
880
 *   Optional parameter. The given string will be added to the array of tabs
881
 *
882
 * @return
883
 *   The array of tabs
884
 */
885
function taxon_page_tabs_hidden_add($add_tab = NULL) {
886
  $tabs = &drupal_static('taxon_page_tabs_hidden');
887

    
888
  if(!isset($tabs)){
889
    $tabs = array();
890
  }
891

    
892
  if (isset($add_tab) && !array_key_exists($add_tab, $tabs)) {
893
    $tabs[] = $add_tab;
894
  }
895

    
896
  return $tabs;
897
}
898

    
899
/**
900
 * Manages the tabs to be hidden in the taxon page.
901
 *
902
 * The tabs names are identified by their last menu link path element:
903
 *  - description
904
 *  - synonymy
905
 *  - images
906
 *  - specimens
907
 *  - key
908
 *
909
 * Internally the tabs are stored in a static variable which is
910
 * managed by drupal_static().
911
 *
912
 * @param string $tabname
913
 *   The name of the tab to check
914
 *
915
 * @return boolean
916
 *   True if the tab or section is to be hidden
917
 */
918
function taxon_page_tabs_hidden_check($tabname) {
919

    
920
  $tabs = &drupal_static('taxon_page_tabs_hidden');
921

    
922
  if(!isset($tabs)){
923
    $tabs = array();
924
  }
925

    
926
  return array_search($tabname, $tabs) !== FALSE;
927
}
928

    
929
/**
930
 * Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
931
 *
932
 *  - Removes the tabs to be hidden, @see taxon_page_tabs_hidden_add()
933
 *  - Renames tabs according to the settings // TODO (this will replace the theme_cdm_taxonpage_tab() function !!!)
934
 *
935
 * @param array $variables
936
 *   The variables array
937
 */
938
function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {
939

    
940
  $hidden_tabs = taxon_page_tabs_hidden_add();
941

    
942
  if (!variable_get(CDM_SEARCH_BLAST_ENABLED)) {
943
      if (is_array($variables['primary'])) {
944
          foreach ($variables['primary'] as $key => &$element) {
945
              if ($element['#link']['path'] == 'cdm_dataportal/search/blast') {
946
                  // remove the tab
947
                  unset($variables['primary'][$key]);
948
              }
949

    
950
          }
951
      }
952
  }
953
  if (is_array($variables['primary'])) {
954
    foreach ($variables['primary'] as $key => &$element) {
955

    
956
      // 1. Remove the tabs to be hidden
957
      foreach ($hidden_tabs as $tab) {
958
        if ($element['#link']['path'] == 'cdm_dataportal/taxon/%/' . $tab) {
959
          // remove the tab
960
          unset($variables['primary'][$key]);
961
        }
962
      }
963
    }
964
  }
965
}
966

    
967

    
968

    
969
/**
970
 * Implements the hook_preprocess_HOOK() for theme_menu_local_task()
971
 *
972
 *
973
 * @param array $variables
974
 *   An associative array containing:
975
 *     - element: A render element containing:
976
 *          #link: A menu link array with 'title', 'href', and 'localized_options' keys.
977
 *          #active: A boolean indicating whether the local task is active.
978
 *
979
 */
980
function cdm_dataportal_preprocess_menu_local_task(&$variables) {
981

    
982
  $link = $variables['element']['#link'];
983
  if (preg_match('/cdm_dataportal\/.*\/refresh$/', $link['href'])) {
984
    $link['title'] = '<img class="refresh" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/view-refresh.png' . '" alt="' . check_plain($link['title']) . '" title="' . check_plain($link['title']) . '"/>';
985
    $link['localized_options']['html'] = TRUE;
986

    
987
    $variables['element']['#link'] = $link;
988
  }
989
}
990

    
991
/* =================== block composition ===================== */
992

    
993
/**
994
 * Composes and returns an render array for the classification breadcrumbs of the given taxon.
995
 *
996
 * @param taxon
997
 *
998
 * @return array
999
 *   A Drupal render array for a table with the experts
1000
 *
1001
 * @ingroup compose
1002
 */
1003
function compose_classification_breadcrumbs($taxon_uuid) {
1004

    
1005
  _add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');
1006

    
1007
  $render_array = array();
1008

    
1009
  $render_array['#theme'] = 'item_list';
1010
  $render_array['#type'] = 'ul';
1011
  $render_array['#attributes'] = array(
1012
    'id' => 'classification-breadcrumbs',
1013
    'class' => 'breadcrumbs inline',
1014
  );
1015

    
1016
  $items = array();
1017

    
1018
  $parent_taxon_nodes = null;
1019
  if($taxon_uuid){
1020
    $parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
1021
  }
1022

    
1023
  $classifications = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
1024
  // find current classification in list
1025
  $classification = null;
1026
  $current_classification_uuid = get_current_classification_uuid();
1027
  foreach ($classifications as $classification){
1028
    if($classification->uuid == $current_classification_uuid){
1029
      break;
1030
    }
1031
  }
1032

    
1033
  $node_name = '';
1034
  if(count($classifications) > 1 ){
1035
    // need to add the current classification as first label
1036

    
1037
    $label = $classification->titleCache;
1038
    if(strlen($label) > 20){
1039
      $label = substr($label, 0, strpos($label, ' ', 15)) . '...';
1040
    }
1041
    $node_name = font_awesome_icon_markup('fa-th-list')  . ' ' . l($label, '#', array(
1042
      'attributes' => array(
1043
        'class' => 'taxonomic-children-button classification-chooser',
1044
        'data-destination-uri' => drupal_get_destination(),
1045
        'data-cdm-align-with' => array('prev')
1046
      ),
1047
      'html' => true
1048
    ));
1049
  }
1050

    
1051
  $rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
1052

    
1053
  $rank_separator = '<span> '
1054
    . font_awesome_icon_markup('fa-chevron-right')
1055
    . ' </span>';
1056
  $more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');
1057
  $more_children_label = '...';
1058

    
1059
  $items[] = $node_name;
1060

    
1061
  $more_children_for = null;
1062
  if($parent_taxon_nodes){
1063
    foreach ($parent_taxon_nodes as $node) {
1064

    
1065
      $is_first_item = count($items) == 0;
1066
      $is_last_item = count($items) == count($parent_taxon_nodes);
1067
      $node_name = cdm_dataportal_shortname_of($node);
1068
      $path = path_to_taxon($node->taxonUuid);
1069

    
1070
      if($node->taxonomicChildrenCount > 0) {
1071
        $more_children_for = $node->taxonUuid;
1072
      } else {
1073
        $more_children_for = null;
1074
      }
1075

    
1076
      // 'fa-sitemap'
1077

    
1078
      $items[] =
1079
        ($is_first_item ? '' : ' ')
1080
        . $rank_separator
1081
        . l(
1082
          '<span class="' . html_class_attribute_ref($node) . '">' . $node_name . '</span>',
1083
          $path,
1084
          array(
1085
            'attributes' => array(
1086
              'class' => array('taxonomic-children-button'),
1087
              'data-cdm-taxon-uuid' => array($node->taxonUuid),
1088
              'data-cdm-classification-mode' => array('siblings'),
1089
              'data-cdm-align-with' => array('prev')
1090
            ),
1091
            'html' => true
1092
          )
1093
        );
1094
      }
1095
    }
1096

    
1097
  // add more button to the end
1098
  if(!$parent_taxon_nodes) {
1099
    // not taxon focused yet, adding button to make  the root nodes available
1100
    $items[] = '<span>'
1101
      . $more_children_icon . '&nbsp;' .
1102
      '<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
1103
      . '" data-rank-limit-uuid="' . $rank_limit_uuid . '" data-cdm-align-with="prev"> ' . $more_children_label . '<span>'
1104
      . '</span>';
1105
  } else if($more_children_for){
1106
    // last parent item has child taxon nodes
1107
    $items[] = ' <span>'
1108
      . $more_children_icon . '&nbsp;' .
1109
      '<span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
1110
      . '" data-cdm-classification-mode="children" data-cdm-align-with="prev"> ' . $more_children_label . '</span>'
1111
      . '</span>';
1112

    
1113
  }
1114

    
1115
  $render_array['#items'] = $items;
1116

    
1117
  return $render_array;
1118
}
1119

    
1120

    
1121
/**
1122
 * @param $specimen_uuid
1123
 * @return array
1124
 *    The drupal render array for the page
1125
 *
1126
 * @ingroup compose
1127
 */
1128
function compose_cdm_specimen_page($specimen_uuid)
1129
{
1130
  drupal_set_title("Specimen Details");
1131
  RenderHints::pushToRenderStack('specimen_page');
1132

    
1133
  $specimen_table = array(
1134
      '#theme' => 'table',
1135
      '#weight' => 2,
1136
      // prefix attributes and rows with '#' to let it pass to the theme function,
1137
      // otherwise it is handled as child render array
1138

    
1139
    '#attributes' => array('class' => 'specimens'),
1140
      '#rows' => array(),
1141
      '#prefix' => '<div id="specimens">',
1142
      '#suffix' => '</div>',
1143

    
1144

    
1145
  );
1146
  $specimen = compose_cdm_specimen_or_observation($specimen_uuid, true);
1147
  /*
1148
  $render_array = array(
1149
          '#theme' => 'item_list',
1150
          '#items' => array($specimen),
1151
          '#type' => 'ul');
1152
  $output = drupal_render($render_array);
1153
 */
1154
  $specimen_table['#rows'][] = array(
1155
          // An array of table rows. Every row is an array of cells, or an associative array
1156
          'data' => $specimen,
1157
          'class' =>  array(
1158
              'descriptionElement',
1159
              'descriptionElement_IndividualsAssociation'
1160
          ),
1161
  );
1162

    
1163

    
1164
 // $detail_html = compose_cdm_specimen_or_observation($specimen_uuid, true);
1165
//    $render_array['markup'] = array(
1166
//        '#prefix' => '<div id="specimens" class="page">',
1167
//        'content' => $specimen_table,
1168
//        '#suffix' => '</div>',
1169
//    );
1170
  $render_array['specimen_table'] =  $specimen_table;
1171

    
1172
  RenderHints::popFromRenderStack();
1173
  return $specimen; // $render_array;
1174
}
1175

    
1176
/**
1177
 * @param $named_area_uuid
1178
 * @return array
1179
 *    The drupal render array for the page
1180
 *
1181
 * @ingroup compose
1182
 */
1183
function compose_cdm_named_area_page($named_area_uuid)
1184
{
1185

    
1186
  $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, array($named_area_uuid));
1187

    
1188
  $render_array = array();
1189
  RenderHints::pushToRenderStack('named_area_page');
1190

    
1191
  $groups = array();
1192
  @_description_list_group_add($groups, t('Name') . ':', $named_area->representation_L10n);
1193
  @_description_list_group_add($groups, t('IdInVocabulary') . ':', $named_area->idInVocabulary);
1194
  if(isset($named_area->level)) {
1195
    @_description_list_group_add($groups, t('Level') . ':', $named_area->level->representation_L10n);
1196
  }
1197

    
1198
  $name_area_details_elements = array(
1199
   // '#title' => $title,
1200
    '#theme' => 'description_list',
1201
    '#groups' => $groups,
1202
    '#attributes' => array('class' => html_class_attribute_ref($named_area)),
1203
  );
1204

    
1205
  $render_array[] = $name_area_details_elements;
1206

    
1207
  RenderHints::popFromRenderStack();
1208
  return $render_array;
1209
}
1210

    
1211

    
1212
/**
1213
 * Returns a drupal render array for a single reference page.
1214
 *
1215
 * Composes a page with all data on a single reference.
1216
 *
1217
 * @param string $uuid
1218
 *   An uuid for a cdm reference.
1219
 *
1220
 * @return array
1221
 *  A drupal render array
1222
 *
1223
 * @throws Exception
1224
 *
1225
 * @ingroup compose
1226
 */
1227
function compose_cdm_reference_page($uuid) {
1228

    
1229
  $pathelement = "reference_page";
1230
  RenderHints::pushToRenderStack($pathelement);
1231
  $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
1232
  if (!$reference) {
1233
    drupal_set_title(t('Reference does not exist'), PASS_THROUGH);
1234
    return "";
1235
  }
1236
  if (isset($reference->titleCache)) {
1237
    drupal_set_title($reference->titleCache, PASS_THROUGH);
1238
  }
1239

    
1240
  $field_order = array(
1241
    "title",
1242
    "abbrevTitle",
1243
    // "titleCache" abbrevTitleCache
1244
    // "citation",
1245
    "authorship",
1246
    "editor",
1247
    "publisher",
1248
    "placePublished",
1249
    "datePublished",
1250
    "year",
1251
    "edition",// Class Book.
1252
    "volume",// Class Article.
1253
    "seriesPart",
1254
    "inReference",
1255
    "nomRefBase", // Class BookSection, Book, Article.
1256
    "pages",// Class Article.
1257
    "series",// Class Article, PrintSeries.
1258
    "school",// Class Thesis.
1259
    "institution",// Class Report.
1260
    "organization",// Class Proceedings.
1261
    "nextVersion",
1262
    "previousVersion",
1263
    "isbn",// Class Book.
1264
    "issn",// Class Journal.
1265
    "doi",
1266
    "uri"
1267
  );
1268

    
1269
  $table_rows = array();
1270

    
1271
  if (!isset($reference->authorship)) {
1272
    $authorship = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $reference->uuid);
1273
    $reference->authorship = isset($authorship->titleCache) ? $authorship->titleCache : '';
1274
  }
1275

    
1276
  if (!isset($reference->inReference)) {
1277
    $reference->inReference = cdm_ws_get(CDM_WS_REFERENCE, array(
1278
      $reference->uuid,
1279
      "inReference",
1280
    ));
1281
  }
1282

    
1283
  foreach ($field_order as $fieldname) {
1284

    
1285
    if (isset($reference->$fieldname)) {
1286

    
1287
      if ($fieldname == "datePublished") {
1288
        $period = $reference->$fieldname;
1289
        $datePublished = timePeriodToString($period);
1290
        if (isset($datePublished) && $datePublished != '') {
1291
          $table_rows[] = array(
1292
            t("Date published"),
1293
            $datePublished,
1294
          );
1295
        }
1296
      }
1297
      elseif ($fieldname == "doi" && is_object($reference->doi)) {
1298
        $table_rows[] = array(
1299
          t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1300
          cdm_doi($reference->doi, false)
1301
        );
1302
      }
1303
      elseif ($fieldname == "uri" && isset($reference->uri) && $reference->uri) {
1304
        $table_rows[] = array(
1305
          t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1306
          cdm_external_uri($reference->uri, false)
1307
        );
1308
      }
1309
      elseif (is_object($reference->$fieldname)) {
1310
        if ($fieldname == "authorship") {
1311
          $dump = $reference->$fieldname;
1312
          $teammembers = "teamMembers";
1313
          $team = $dump->$teammembers;
1314
          $nameArray = array();
1315

    
1316
          foreach ($team as $member) {
1317
            if (strlen($member->lastname) > 0) {
1318
              $nname = $member->lastname;
1319
              $name = $nname;
1320
              if (strlen($member->firstname) > 0) {
1321
                $vname = $member->firstname;
1322
                $name = $vname . " " . $nname;
1323
              }
1324
              $nameArray[] = $name;
1325
            }
1326
            else {
1327
              if (strlen($member->titleCache) > 0) {
1328
                $nameArray[] = $member->titleCache;
1329
              }
1330
            }
1331
          }
1332
          $value = join($nameArray, ", ");
1333
        }
1334
        elseif ($fieldname == "inReference") {
1335
          $type = $reference->$fieldname->type;
1336
          $value = l($reference->$fieldname->titleCache, path_to_reference($reference->$fieldname->uuid));
1337
          switch ($type) {
1338
            case "Book":
1339
              $fieldname = "in book";
1340
              break;
1341
            case "Journal":
1342
              $fieldname = "in journal";
1343
              break;
1344
            case "Proceedings":
1345
              $fieldname = "in proceedings";
1346
              break;
1347
          }
1348
        }
1349
        else {
1350
          $value = $reference->$fieldname->titleCache;
1351
        }
1352

    
1353

    
1354
        if (isset($value) && $value != '') {
1355
          $table_rows[] = array(
1356
            t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1357
            $value,
1358
          );
1359
        }
1360

    
1361
      }
1362
      else {
1363
        if (isset($reference->$fieldname) && $reference->$fieldname != '') {
1364
          $table_rows[] = array(
1365
            t('@fieldname', array('@fieldname' => ucfirst(strtolower($fieldname)))),
1366
            $reference->$fieldname,
1367
          );
1368
        }
1369
      }
1370
    }
1371
  }
1372

    
1373
  $out = theme_table(array(
1374
    'header' => array(),
1375
    'rows' => $table_rows,
1376
    'attributes' => array(
1377
      'class' => html_class_attribute_ref($reference)
1378
    ),
1379
    'caption' => NULL,
1380
    'colgroups' => NULL,
1381
    'sticky' => NULL,
1382
    'empty' => NULL,
1383
  ));
1384

    
1385
  if(isset($reference->referenceAbstract)){
1386
    $out .= '<h2 class="block-title">Abstract</h2><div class="abstract">' . $reference->referenceAbstract . '</div>';
1387
  }
1388

    
1389

    
1390
  // Annotations below the table
1391
  $annotations = cdm_fetch_visible_annotations($reference);
1392
  $out .= cdm_annotations($annotations);
1393

    
1394
  $registration_working_set = cdm_ws_get("registrationWorkingSetDTO", array($uuid));
1395
  if($registration_working_set && count($registration_working_set->registrationDTOs) > 0){
1396
    $out .= "<h3>Nomenclatural acts:</h3><div class=\"cdm-item-list registration-item-list\">";
1397
    foreach($registration_working_set->registrationDTOs as $registration_dto){
1398
      if($registration_dto->status == "PUBLISHED"){
1399
        $registration_render_a = compose_registration_dto_compact($registration_dto, 'citation');
1400
        $registration_render_a["#prefix"] = "<div class=\"item item-registration\">";
1401
        $registration_render_a["#suffix"] = "</div>";
1402
        $out .= drupal_render($registration_render_a);
1403
      }
1404
    }
1405
    $out .= "</div>";
1406
  }
1407

    
1408
  RenderHints::popFromRenderStack();
1409

    
1410
  return markup_to_render_array($out);
1411
}
1412

    
1413
/**
1414
 * Provides the the label string for taxon page tabs.
1415
 *
1416
 * The $tabname as passed to the method will be returned if no override
1417
 * label is configured in the settings.
1418
 */
1419
function cdm_taxonpage_tab_label($tabname) {
1420
  static $taxon_tabs_labels = null;
1421
  if($taxon_tabs_labels == null){
1422
    $taxon_tabs_labels = get_array_variable_merged(CDM_TAXONPAGE_TAB_LABELS, CDM_TAXONPAGE_TAB_LABELS_DEFAULT);
1423
  }
1424
  $tabname_key = strtolower($tabname);
1425
  if(isset($taxon_tabs_labels[$tabname_key]) && $taxon_tabs_labels[$tabname_key]){
1426
    return $taxon_tabs_labels[$tabname_key];
1427
  }
1428
  return $tabname;
1429
}
Add picture from clipboard (Maximum size: 40 MB)