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

    
19

    
20
/**
21
 * Creates 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 $taxon
28
 *   A cdm Taxon object
29
 * @return
30
 *   A render array suitable for drupal_render()
31
 *
32
 */
33
function cdm_dataportal_taxon_page_specimens($taxon) {
34

    
35
    $render_array = array();
36
    RenderHints::pushToRenderStack('taxon_page_specimens');
37

    
38
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
39
    $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
40
    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
41

    
42
    $by_associatedtaxon_query_parameters = array(
43
        'relationshipsInvers' => implode(',', $relationship_choice['invers']),
44
        'relationships' => implode(',', $relationship_choice['direct']),
45
    );
46

    
47
    if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
48
        $by_associatedtaxon_query_parameters = array_merge($by_associatedtaxon_query_parameters, $_REQUEST['pager']);
49
    }
50

    
51
    $by_associatedtaxon_query = http_build_query($by_associatedtaxon_query_parameters);
52

    
53
    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
54
        null,
55
        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
56
    );
57

    
58
    $specimensOrObservations = array();
59
    if(isset($pager->records[0])){
60
        $specimensOrObservations =  $pager->records;
61
    }
62

    
63
    // order occurrences by date but types should be on top of the list
64
    $type_specimens = array();
65
    $other_occurrences = array();
66
    foreach ($specimensOrObservations as &$occurrence) {
67
        $typeDesignationsPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $occurrence->uuid);
68
        if (isset($typeDesignationsPager->count) && $typeDesignationsPager->count > 0) {
69
            $type_specimens[] = $occurrence;
70
        } else {
71
            $other_occurrences[] = $occurrence;
72
        }
73
    }
74
    $specimensOrObservations = array_merge($type_specimens, $other_occurrences);
75

    
76
    // Collect media (fieldObjectMedia, derivedUnitMedia) and add as a custom field
77
    // $occurrence->_fieldObjectMedia
78
    foreach ($specimensOrObservations as &$occurrence) {
79
        $occurrence->_fieldObjectMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
80
            $occurrence->uuid,
81
            'fieldObjectMedia',
82
        ));
83
        $occurrence->_derivedUnitMedia = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, array(
84
            $occurrence->uuid,
85
            'derivedUnitMedia',
86
        ));
87
    }
88

    
89
    // --- get map service HTTP query parameters
90
    if (count($specimensOrObservations) > 0) {
91
        $occurrence_queryDto = cdm_ws_get(CDM_WS_GEOSERVICE_OCCURRENCEMAP, $taxon->uuid,  $by_associatedtaxon_query);
92

    
93
        if( isset($occurrence_queryDto->occurrenceQuery) ) {
94
            $occurrence_query = $occurrence_queryDto->occurrenceQuery;
95
            $legend_format_query = null;
96
            $distribution_query = NULL;
97
            $render_array['map'] = compose_map(NULL, $occurrence_query, $distribution_query, $legend_format_query, array());
98
        }
99
    }
100
    if(variable_get('cdm_dataportal_compressed_specimen_derivate_table')){
101

    
102
        //COMPRESSED SPECIMEN DERIVATE TABLE
103
        $associatedFieldUnitsQuery_parameters = array();
104
        if (isset($_REQUEST['pager']) && is_array($_REQUEST['pager'])) {
105
            $associatedFieldUnitsQuery_parameters = array_merge($associatedFieldUnitsQuery_parameters, $_REQUEST['pager']);
106
        }
107

    
108
        $by_associatedtaxon_query = http_build_query($associatedFieldUnitsQuery_parameters);
109
        $pagerFieldUnits = cdm_ws_get(CDM_WS_PORTAL_TAXON, array($taxon->uuid, 'associatedFieldUnits'), $by_associatedtaxon_query);
110
        // get icon images
111
        $expand_icon = font_awesome_icon_markup(
112
            'fa-plus-square-o',
113
            array(
114
                'alt'=>'Show details',
115
                'class' => array('expand_icon')
116
            )
117
        );
118
        $collapse_icon = font_awesome_icon_markup(
119
            'fa-minus-square-o',
120
            array(
121
                'alt'=>'Show details',
122
                'class' => array('collapse_icon')
123
            )
124
        );
125
        $detail_image_icon = '<img title="Detail Image" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/detail_image_derivate-16x16-32.png' . '"/>';
126
        $checked_box_icon = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/step_done.gif' . '"/>';
127
        $sequence_icon = '<img title="Molecular Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/sequence_derivate-16x16-32.png' . '"/>';
128
        $character_data_icon = '<img title="Character Data" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/character_data_derivate-16x16-32.png' . '"/>';
129
        if (isset($pagerFieldUnits->records[0])) {
130
            $rowcount = 0;
131
            foreach ($pagerFieldUnits->records as $fieldUnit) {
132
                //get derivate hierarchy for the FieldUnit
133
                $derivateHierarchy = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($fieldUnit->uuid, 'derivateHierarchy'), 'taxonUuid=' . $taxon->uuid);
134
                if($derivateHierarchy){
135
                    //summary row
136
                    $rows[] = array(
137
                        'data' => array(
138
                            array(
139
                                'data' => $expand_icon . $collapse_icon,
140
                                'class' => array('summary_row_cell', 'summary_row_icon', 'expand_column')
141
                            ),
142
                            array(
143
                                'data' => $derivateHierarchy->country,
144
                                'class' => array('summary_row_cell')
145
                            ),
146
                            array(
147
                                'data' => $derivateHierarchy->date,
148
                                'class' => array('summary_row_cell')
149
                            ),
150
                            array(
151
                                'data' => $derivateHierarchy->collection,
152
                                'class' => array('summary_row_cell')
153
                            ),
154
                            array(
155
                                'data' => $derivateHierarchy->herbarium,
156
                                'class' => array('summary_row_cell')
157
                            ),
158
                            array(
159
                                'data' => $derivateHierarchy->hasType? $checked_box_icon:"",
160
                                'class' => array('summary_row_cell', 'summary_row_icon')
161
                            ),
162
                            array(
163
                                'data' => $derivateHierarchy->hasSpecimenScan? $checked_box_icon:"",
164
                                'class' => array('summary_row_cell', 'summary_row_icon')
165
                            ),
166
                            array(
167
                                'data' => ($derivateHierarchy->hasDna? $sequence_icon :"")." "
168
                                    .($derivateHierarchy->hasDetailImage?$detail_image_icon:"")." "
169
                                    .($derivateHierarchy->hasCharacterData?$character_data_icon:""),
170
                                'class' => array('summary_row_cell', 'summary_row_icon')
171
                            )
172
                        ),
173
                        'id' => ('derivate_summary' . $rowcount), // summary row id
174
                        'class' => array('summary_row'),
175
                    );
176

    
177
                    //assemble field unit details
178
                    $detail_html = "";
179
                    // - taxon name
180
                    if (variable_get('cdm_dataportal_compressed_specimen_derivate_table_show_determined_as') && $derivateHierarchy->taxonName) {
181
                        $detail_html .= create_label("Associated with") . $derivateHierarchy->taxonName . "<br>";
182
                    }
183
                    // - protologue
184
                    if ($derivateHierarchy->protologue) {
185
                        //$detail_html .= "<strong>Protologue:</strong> " . $derivateHierarchy->protologue . "<br>"
186
                    }
187
                    // - citation
188
                    if ($derivateHierarchy->citation) {
189
                        $detail_html .= create_label("Citation") . $derivateHierarchy->citation . "<br>";
190
                    }
191
                    //assemble specimen details
192
                    if($derivateHierarchy->preservedSpecimenDTOs){
193
                        foreach($derivateHierarchy->preservedSpecimenDTOs as $preservedSpecimenDTO) {
194
                            $detail_html .= "<br>";
195
                            $detail_html .= compose_cdm_specimen_page_html($preservedSpecimenDTO);
196
                        }
197
                    }
198
                    $detail_html .= "<br>";
199
                    //detail row resp. one BIG detail cell
200
                    $rows[] = array(
201
                        'data' => array(
202
                            array(
203
                                'data' => "", //empty first column
204
                                'class' => array('expand_column')
205
                            ),
206
                            array(
207
                                'data' => $detail_html,
208
                                'colspan' => 7,
209
                            ),
210
                        ),
211
                        'id' => ('derivate_details' . $rowcount),//details row ID
212
                        'class' => array('detail_row'),
213
                    );
214
                    $rowcount++;
215
                }
216
            }
217
        }
218

    
219
        $tableId = "derivate_hierarchy_table";
220
        $derivateHierarchyTable = array(
221
            "#theme" => "table",
222
            "#weight" => 2,
223
            "#header" => array(
224
                array(
225
                    'data' => "",
226
                    'class' => array('expand_column')
227
                ),
228
                "Country", "Date", "Collector + collecting number", "Herbaria", "Type", "Scan", "Derivatives"),
229
            "#rows" => $rows,
230
            "#attributes" => array(
231
                "id" => $tableId,
232
                "border" => 2
233
            )
234
        );
235

    
236
        //add toggle functionality to derivate hierarchy table
237
        drupal_add_js_rowToggle("#".$tableId);
238

    
239
        $render_array['derivate_hierarchy_table'] = $derivateHierarchyTable;
240
        $render_array['pager'] = markup_to_render_array(
241
            theme('cdm_pager', array(
242
                'pager' => $pagerFieldUnits,
243
                'path' => $_REQUEST['q'],
244
                'parameters' => $_REQUEST
245
            )),
246
            10 // weight
247
        );
248
    }
249
    else{
250
        //BOTTOM-UP-SPECIMEN-TABLE
251
        // --- generate the specimen list as table
252
        $specimen_table = array(
253
            '#theme' => 'table',
254
            '#weight' => 2,
255
            // prefix attributes and rows with '#' to let it pass to the theme function,
256
            // otherwise it is handled as child render array
257
            '#attributes' => array('class' => 'specimens'),
258
            '#rows' => array(),
259
        );
260

    
261
        if ($specimensOrObservations) {
262

    
263
            foreach ($specimensOrObservations as $specimenOrObservation) {
264

    
265
                $mediaList = array();
266
                if (is_array($specimenOrObservation->_fieldObjectMedia)) {
267
                    $mediaList = array_merge($mediaList, $specimenOrObservation->_fieldObjectMedia);
268
                }
269
                if (is_array($specimenOrObservation->_derivedUnitMedia)) {
270
                    $mediaList = array_merge($mediaList, $specimenOrObservation->_derivedUnitMedia);
271
                }
272

    
273
                // typelabel will contain the typeStatus
274
                $type_label = '';
275
                $typeDesignationPager = cdm_ws_get(CDM_WS_OCCURRENCE . '/$0/specimenTypeDesignations', $specimenOrObservation->uuid);
276
                if (isset($typeDesignationPager) and isset($typeDesignationPager->records)) {
277
                    $type_status = array();
278
                    foreach ($typeDesignationPager->records as $typeDesignation) {
279
                        if (isset($typeDesignation->typeStatus->representation_L10n)){
280
                            $type_status[] = $typeDesignation->typeStatus->representation_L10n;
281
                        }
282
                    }
283
                    $type_label = implode(', ', $type_status);
284
                    if($type_label){
285
                        $type_label .= ': ' ;
286
                    }
287
                }
288

    
289
                // --- Specimen entry as dynamic label:
290
                //     -> Dynabox for the specimenOrObservation
291
                $gallery_name = $specimenOrObservation->uuid;
292

    
293
                $derived_unit_ws_request = cdm_compose_url(CDM_WS_OCCURRENCE, array( $specimenOrObservation->uuid));
294
                $label_html = cdm_dynabox(
295
                  $specimenOrObservation->uuid,
296
                  $type_label . $specimenOrObservation->titleCache,
297
                  $derived_unit_ws_request,
298
                  'cdm_specimenOrObservation',
299
                  'Click for details',
300
                  array('div', 'div'),
301
                  array(),
302
                  null, // $content_element_selector
303
                  'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').hide(); }', // open_callback
304
                  'function(){ jQuery(\'#media_gallery_' . $gallery_name . '\').show(); }' // close_callback
305
                );
306

    
307
                // --- Render associated media.
308
                $gallery_html = '';
309
                if (count($mediaList) > 0) {
310
                    $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
311
                    $captionElements = array(
312
                        '#uri' => t('open media'),
313
                    );
314

    
315
                    $gallery_html = theme('cdm_media_gallerie', array(
316
                        'mediaList' => $mediaList,
317
                        'galleryName' => $gallery_name,
318
                        'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
319
                        'cols' => $gallery_settings['cdm_dataportal_media_cols'],
320
                        'maxRows' => isset($gallery_settings['cdm_dataportal_media_maxRows']) ? isset($gallery_settings['cdm_dataportal_media_maxRows']) : null,
321
                        'captionElements' => $captionElements,
322
                        'mediaLinkType' => 'LIGHTBOX',
323
                        'alternativeMediaUri' => NULL,
324
                        'galleryLinkUri' => NULL,
325
                    ));
326
                }
327

    
328
                $specimen_table['#rows'][] = array(
329
                    // An array of table rows. Every row is an array of cells, or an associative array
330
                    'data' => array(
331
                        // Each cell can be either a string or an associative array
332
                        $label_html . $gallery_html
333
                    ),
334
                    'class' =>  array(
335
                        'descriptionElement',
336
                        'descriptionElement_IndividualsAssociation'
337
                    ),
338
                );
339
            }
340
        }
341

    
342
        $render_array['specimen_list'] = $specimen_table;
343
        $render_array['pager'] = markup_to_render_array(
344
            theme('cdm_pager', array(
345
                'pager' => $pager,
346
                'path' => $_REQUEST['q'],
347
                'parameters' => $_REQUEST,
348
            )),
349
            10 // weight
350
        );
351
    }
352
    RenderHints::popFromRenderStack();
353
    return $render_array;
354
}
355
 
356
function create_html_link($link, $openInExternalWindow=false){
357
    $html = "";
358
    if($link->uri && $link->uri!=""){
359
        $html .= '<a  href="' . $link->uri . '"';
360
        if($openInExternalWindow){
361
            $html .= ' target="_blank"';
362
        }
363
        $html .= '>' . $link->linkText . '</a>';
364
    }
365
    else{
366
        $html .= $link->linkText;
367
    }
368
    return $html;
369
}
370

    
371
/**
372
 * Creates HTML links from the given link list concatenated by default by a comma.
373
 * @param $linkList the list with Link objects having "uri" and "linkText" as members
374
 * @return string the assembled HTML string containing the links
375
 */
376
function create_html_links($linkList, $openInExternalWindow=false, $separator=", ")
377
{
378
    $html = "";
379
    if ($linkList) {
380
        foreach ($linkList as $link) {
381
            $html .= create_html_link($link, $openInExternalWindow).$separator;
382
        }
383
        $html = rtrim($html, $separator);
384
    }
385
    return $html;
386
}
387

    
388
/**
389
 * Composes a taxon page which can consist of multiple parts like
390
 * 'General', 'Synonymy', 'Images', 'Keys'. These parts can be displayed
391
 * as tabs or as sections of a single page.
392
 *
393
 * It is headed by the name of the accepted taxon without author and reference.
394
 *
395
 * @param $taxon
396
 *   The CDM Taxon Instance to compose the page for.
397
 * @param $page_part
398
 *   Name of the part to display, valid values are:
399
 *    - 'description' -  for the general part
400
 *    - 'images'
401
 *    - 'synonymy'
402
 *    - 'keys'
403
 *    - 'all'
404
 *
405
 * @return array
406
 *   A drupal render array
407
 *
408
 * @ingroup compose
409
 */
410
function compose_cdm_taxon_page($taxon, $page_part = 'description') {
411

    
412
  // we better cache here since drupal_get_query_parameters has no internal static cache variable
413
  $http_request_params = drupal_get_query_parameters();
414

    
415
  // add all mandatory js sources
416
  _add_js_footnotes();
417

    
418

    
419
  $render_array = array();
420
  $weight = 0; // the weight for the render array elements
421

    
422
  $tabsToDisplay = variable_get('cdm_taxonpage_tabs_visibility', unserialize(TAXONPAGE_VISIBILITY_OPTIONS_DEFAULT));
423

    
424
  $page_part = variable_get('cdm_dataportal_taxonpage_tabs', 1) ? $page_part : 'all';
425

    
426
  $media = _load_media_for_taxon($taxon);
427

    
428

    
429
  if (!isset($media[0]) || ($tabsToDisplay["Images"] == '0')) {
430
    taxon_page_tabs_hidden('images');
431
  }
432

    
433
  // --- GET specimensOrObservations --- //
434
  $specimensOrObservations = cdm_ws_get(CDM_WS_TAXON, array( $taxon->uuid, 'specimensOrObservations'));
435

    
436
  $specimensOrObservationsCount = is_array($specimensOrObservations) ? count($specimensOrObservations) : 0;
437
  if ($specimensOrObservationsCount == 0 || ($tabsToDisplay["Specimens"] == '0')) {
438
    taxon_page_tabs_hidden('specimens');
439
  }
440

    
441
  // --- GET polytomousKeys --- //
442
  $polytomousKeysPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, NULL, "findByTaxonomicScope=$taxon->uuid");
443
  $identificationKeyCount = 0;
444
  if ($polytomousKeysPager) {
445
    $identificationKeyCount += $polytomousKeysPager->count;
446
  }
447
  if ($identificationKeyCount == 0 || ($tabsToDisplay["Keys"] == '0')) {
448
    taxon_page_tabs_hidden('keys');
449
  }
450

    
451
    // --- GET TaxonNodeAgentRelations --- //
452
    $current_classification_uuid = get_current_classification_uuid();
453
    $taxon_node_agent_relations_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODEAGENTRELATIONS,
454
        array(
455
            $taxon->uuid,
456
            $current_classification_uuid,
457
        ),
458
        "pageSize=1&pageIndex=0"// we are only interested into the count so we are fetching only one item, o is not possible!
459
    );
460
    if (!$taxon_node_agent_relations_pager || $taxon_node_agent_relations_pager->count == 0){
461
        taxon_page_tabs_hidden('experts');
462
    }
463

    
464
    if ($tabsToDisplay["Synonymy"] == '0') {
465
    taxon_page_tabs_hidden('synonymy');
466
  }
467

    
468
  // -------------------------------------------- //
469

    
470
  if (variable_get('cdm_dataportal_display_is_accepted_for', CDM_DATAPORTAL_DISPLAY_IS_ACCEPTED_FOR) && isset($_REQUEST['acceptedFor'])) {
471
    $render_array['accepted_for'] = markup_to_render_array(cdm_accepted_for($_REQUEST['acceptedFor']), $weight++);
472
  }
473

    
474
  // --- PAGE PART: DESCRIPTION --- //
475
  if ($page_part == 'description' || $page_part == 'all') {
476

    
477
    $merged_tree = merged_taxon_feature_tree($taxon);
478

    
479

    
480
    $render_array['general'] = compose_cdm_taxon_page_profile($taxon, $merged_tree, $media);
481
    $render_array['general']['#weight'] = $weight++;
482
    $render_array['general']['#prefix'] = '<div id="general" class="page-part">';
483
    $render_array['general']['#suffix'] = '</div>';
484
  }
485

    
486
  // --- PAGE PART: IMAGES --- //
487
  if (array_search('images', taxon_page_tabs_hidden()) === FALSE && ($page_part == 'images' || $page_part == 'all')) {
488
    $images_html = '<div id="images" class="page-part">';
489
    if ($page_part == 'all') {
490
      $images_html .= '<h2>' . t('Images') . '</h2>';
491
    }
492
    // Get the image gallery as configured by the admin.
493
    $default_image_gallery = 'default';
494
    $configured_image_gallery_viewer = variable_get('image_gallery_viewer', 'default');
495
    if($configured_image_gallery_viewer == $default_image_gallery || $configured_image_gallery_viewer == 'fsi'){
496
      // the fsi_gallery requires a flash plugin, in case the client browser is not supporting
497
      // flash we also need to provide an the default gallery as alternative
498
      $taxon_image_gallery = '<div id="default-gallery-viewer">' .
499
        call_user_func_array('taxon_image_gallery_' . $default_image_gallery, array(
500
          $taxon,
501
          $media,
502
        ))
503
        . '</div>';
504
    }
505
    if($configured_image_gallery_viewer == 'fsi'){
506
      $taxon_image_gallery .= '<div id="'. $configured_image_gallery_viewer .'-gallery-viewer">' .
507
        call_user_func_array('taxon_image_gallery_' . $configured_image_gallery_viewer, array(
508
          $taxon,
509
          $media,
510
        ))
511
       . '</div>';
512
    }
513
    $images_html .= $taxon_image_gallery;
514
    $images_html .= '</div>';
515
    $render_array['images'] = markup_to_render_array($images_html, $weight++);
516
  }
517

    
518
  // --- PAGE PART: SYNONYMY --- //
519
  if (($page_part == 'synonymy' || $page_part == 'all')) {
520
    $synonymy_html = '<div id="synonymy" class="page-part">';
521
    if ($page_part == 'all') {
522
      $synonymy_html .= '<h2>' . t('Synonymy') . '</h2>';
523
    }
524
    $addAcceptedTaxon = variable_get('cdm_dataportal_nomref_in_title', CDM_DATAPORTAL_NOMREF_IN_TITLE);
525

    
526
    $synonymy_html .= theme('cdm_taxon_page_synonymy', array('taxon' => $taxon, 'addAcceptedTaxon' => $addAcceptedTaxon));
527

    
528
    $synonymy_html .= '</div>';
529
    $render_array['synonymy'] = markup_to_render_array($synonymy_html, $weight++);
530

    
531
  }
532

    
533
  // --- PAGE PART: SPECIMENS --- //
534
  if ($specimensOrObservationsCount > 0 && ($page_part == 'specimens' || $page_part == 'all')) {
535
    $render_array['specimens'] = array(
536
        '#prefix' => '<div id="specimens" class="page-part">' . ($page_part == 'all' ? '<h2>' . t('Specimens') . '</h2>' : ''),
537
        'content' => cdm_dataportal_taxon_page_specimens($taxon), // returns render array
538
        '#suffix' => '</div>',
539
    );
540
  }
541

    
542
  // --- PAGE PART: KEYS --- //
543
  if ($identificationKeyCount == 1 && $page_part == 'keys'){
544
    drupal_goto(path_to_key($polytomousKeysPager->records[0]->class, $polytomousKeysPager->records[0]->uuid));
545
  }
546
  else if ($identificationKeyCount > 0 && ($page_part == 'keys' || $page_part == 'all')) {
547
    $keys_html = '<div id="keys" class="page-part">';
548
    if ($page_part == 'all') {
549
      $keys_html .= '<h2>' . t('Keys') . '</h2>';
550
    }
551
    $keys_html .= theme('cdm_block_IdentificationKeys', array('taxonUuid' => $taxon->uuid));
552
    $keys_html .= '</div>';
553
    $render_array['keys'] = markup_to_render_array($keys_html, $weight++);
554
  }
555

    
556
  // --- PAGE PART: EXPERTS --- //
557

    
558
  if (array_search('experts', taxon_page_tabs_hidden()) === FALSE && ($page_part == 'experts' || $page_part == 'all')) {
559
    $render_array['experts'] = array(
560
        '#prefix' => '<div id="experts" class="page-part">' . ($page_part == 'all' ? '<h2>' . t('Experts') . '</h2>' : ''),
561
        'content' => compose_cdm_taxon_page_experts($taxon), // returns render array
562
        '#suffix' => '</div>',
563
    );
564
  }
565

    
566
  // ------------------ END OF PARTS -------------- //
567

    
568
  // adjust weights of page and toc elements according to the settings
569
  $taxontabs_weights = get_array_variable_merged('cdm_taxonpage_tabs_weight', CDM_TAXONPAGE_TAB_WEIGHT_DEFAULT);
570
  foreach($taxontabs_weights as $tab_key => $weight){
571
    if(isset($render_array[$tab_key])){
572
      $render_array[$tab_key]['#weight'] = $weight;
573
    }
574
  }
575

    
576

    
577
  // set up the TOC for the pages which contain all pageparts
578
  if($page_part == 'all') {
579

    
580
    asort($taxontabs_weights);
581
    foreach(array_keys($taxontabs_weights) as $tab_key){
582
      if(isset($render_array[$tab_key])){
583
        if($tab_key != 'general'){
584
          // add entry for page part
585
          $toc_elements[] = array(
586
              'data' => l(t('@tab-name', array('@tab-name' => ucfirst($tab_key))), $_GET['q'], array('fragment' => $tab_key, 'query' => $http_request_params)),
587
              'class' => array('page-part-toc-item-' . $tab_key)
588
          );
589
        } else {
590
          // add content of profile part instead
591
          if(isset($render_array['general'])) {
592
            // in case all tabs are shown at once the feature tocs
593
            // should be integrated into the tabs toc as sub list
594
            // and the profile image should be on top of the page
595
            if(isset($render_array['general']['taxon_description_feature_toc'])){;
596
            foreach ($render_array['general']['taxon_description_feature_toc']['#items'] as $profile_toc_item){
597
              $toc_elements[] = $profile_toc_item;
598
            }
599
            unset($render_array['general']['taxon_description_feature_toc']);
600
            }
601
          }
602
        }
603
      }
604
    }
605

    
606
    // move profile image in page structure
607
    if(isset($render_array['general']['taxon_profile_image'])){
608
      $render_array['profile_image'] = $render_array['general']['taxon_profile_image'];
609
      $render_array['profile_image']['#weight'] = -100;
610
      unset($render_array['general']['taxon_profile_image']);
611
    }
612

    
613
    // finally add the table of contents to the render array
614
    $render_array['toc'] = array(
615
        '#theme' => 'item_list',
616
        '#items' => $toc_elements,
617
        '#title' => t('Content'),
618
        '#weight' => -101,
619
        '#suffix' => '</div>',
620
        '#prefix'=> '<div id="page-toc">'
621
    );
622
  }
623

    
624

    
625
  return $render_array;
626
}
627

    
628
/**
629
 * TODO should this function really be a compose function?
630
 *     For a compose function must there always be a theme function with the same name? (ak 8.8.2013)
631
 *
632
 * composes and returns an render array containing the components of the taxon profile tab:
633
 *  - 'taxon_profile_image'
634
 *  - 'taxon_description_feature_toc'
635
 *  - 'taxon_description_features'
636
 *
637
 *
638
 * @param taxon
639
 * @param mergedTrees
640
 * @param media
641
 *
642
 * @return array
643
 *   A Drupal render array with the following elements:
644
 *     - 'taxon_profile_image'
645
 *     - 'taxon_description_feature_toc'
646
 *     - 'taxon_description_features'
647
 *
648
 * @ingroup compose
649
 */
650
function compose_cdm_taxon_page_profile($taxon, $merged_tree, $media) {
651

    
652
  $render_array = array();
653

    
654
  $taxon_profile_image_settings = variable_get(CDM_TAXON_PROFILE_IMAGE, unserialize(CDM_TAXON_PROFILE_IMAGE_DEFAULT));
655

    
656
  $hide_taxon_profile_image = FALSE;
657
  if (variable_get('image_hide_rank', '0') != '0' && isset($taxon->name->rank->uuid)) {
658
    $rankCompare = rank_compare($taxon->name->rank->uuid, variable_get('image_hide_rank', '-99'));
659
    $hide_taxon_profile_image = ($rankCompare > -1);
660
  }
661

    
662
  if ($taxon_profile_image_settings['show'] && !$hide_taxon_profile_image) {
663

    
664
    $representationPart = new stdClass();
665
    $attributes = array();
666
    if (isset($media[0]->representations[0]->parts[0])) {
667
      $representationPart = $media[0]->representations[0]->parts[0];
668
      $attributes['alt'] = $representationPart->uri;
669

    
670
      if (!empty($taxon_profile_image_settings['media_uri_query'])) {
671
        $representationPart->uri = $representationPart->uri
672
          . (strpos($representationPart->uri, '?') !== FALSE ? '&' : '?')
673
          . $taxon_profile_image_settings['media_uri_query'];
674
      }
675
    }
676
    else {
677
      if ($taxon_profile_image_settings['custom_placeholder_enabled']) {
678
        // show placeholder image instead
679
        if (!empty($taxon_profile_image_settings['custom_placeholder_image_on']) && !empty($taxon_profile_image_settings['custom_placeholder_image_fid'])) {
680
          // use the user provided image
681
          $profile_image_file = file_load($taxon_profile_image_settings['custom_placeholder_image_fid']);
682
          $url = file_create_url($profile_image_file->uri);
683
          $image_info = image_get_info($profile_image_file->uri);
684
          $representationPart->width = $image_info['width'];
685
          $representationPart->height = $image_info['height'];
686
          $representationPart->uri = $url;
687
        }
688
        else {
689
          // use the hard coded default
690
          $representationPart->width = 184;
691
          $representationPart->height = 144;
692
          $representationPart->uri = base_path() . drupal_get_path('module',
693
              'cdm_dataportal') . '/images/no_picture.png';
694
        }
695
        $attributes['alt'] = "no image available";
696
      }
697
    }
698

    
699
    if (isset($representationPart->uri)) {
700
      $profile_image = theme('cdm_media_gallerie_image', array(
701
        'mediaRepresentationPart' => $representationPart,
702
        'maxExtend' => $taxon_profile_image_settings['maxextend'],
703
        'addPassePartout' => FALSE,
704
        'attributes' => $attributes,
705
      ));
706
      // NOTE: style="width:${maxextend}px' is needed for IE8 !!!
707
      $render_array['taxon_profile_image'] = markup_to_render_array('<div id="taxonProfileImage" style="width:' . $taxon_profile_image_settings['maxextend'] . 'px">' . $profile_image . '</div>',
708
        -101);
709
    }
710
  }
711

    
712

    
713
  // Render the sections for each feature
714
  $render_array['taxon_description_features'] = compose_feature_blocks($merged_tree->root->childNodes, $taxon);
715

    
716
  $bibliography_settings = get_bibliography_settings();
717
  if($bibliography_settings['enabled'] == 1){
718
    $bibliography_block = feature_block(t('Bibliography'));
719
    $bibliography_block->content = FootnoteManager::renderFootnoteList('BIBLIOGRAPHY', '');
720

    
721
    if(!empty($bibliography_block->content)){
722
      $render_array['taxon_description_bibliography'] =  markup_to_render_array(
723
        theme('block',
724
          array(
725
            'elements' => array(
726
              '#block' => $bibliography_block,
727
              '#children' => $bibliography_block->content,
728
            )
729
          )
730
        ),
731
        100 // weight
732
      );
733
      cdm_toc_list_add_item('Bibliography', 'bibliography');
734
    }
735

    
736
  }
737

    
738
  // create the table of content
739
  $toc = array(
740
      '#theme' => 'item_list',
741
    '#items' => cdm_toc_list(),
742
      '#title' => t('Content'),
743
    '#weight' => -100,                  // move to the top
744
      '#suffix' => '</div>',
745
      '#prefix'=> '<div id="page-toc">'
746
  );
747
  $render_array['taxon_description_feature_toc'] = $toc;
748

    
749
  return $render_array;
750
}
751

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

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

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

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

    
784

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

    
787

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

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

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

    
829
  }
830

    
831

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

    
838

    
839
  return $render_array;
840
}
841

    
842

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

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

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

    
873
  return $tabs;
874
}
875

    
876
/**
877
 * Implements the hook_preprocess_HOOK() for theme_menu_local_tasks()
878
 *
879
 *  - Removes the tabs to be hidden, @see taxon_page_tabs_hidden()
880
 *  - Renames tabs according to the settings // TODO (this will replace the theme_cdm_taxonpage_tab() function !!!)
881
 *
882
 * @param array $variables
883
 *   The variables array
884
 */
885
function cdm_dataportal_preprocess_menu_local_tasks(&$variables) {
886

    
887
  $hidden_tabs = taxon_page_tabs_hidden();
888

    
889
  if (is_array($variables['primary'])) {
890
    foreach ($variables['primary'] as $key => &$element) {
891

    
892
      // 1. Remove the tabs to be hidden
893
      foreach ($hidden_tabs as $tab) {
894
        if ($element['#link']['path'] == 'cdm_dataportal/taxon/%/' . $tab) {
895
          // remove the tab
896
          unset($variables['primary'][$key]);
897
        }
898
      }
899
    }
900
  }
901
}
902

    
903

    
904

    
905
/**
906
 * Implements the hook_preprocess_HOOK() for theme_menu_local_task()
907
 *
908
 *
909
 * @param array $variables
910
 *   An associative array containing:
911
 *     - element: A render element containing:
912
 *          #link: A menu link array with 'title', 'href', and 'localized_options' keys.
913
 *          #active: A boolean indicating whether the local task is active.
914
 *
915
 */
916
function cdm_dataportal_preprocess_menu_local_task(&$variables) {
917

    
918
  $link = $variables['element']['#link'];
919
  if (preg_match('/cdm_dataportal\/.*\/refresh$/', $link['href'])) {
920
    $link['title'] = '<img class="refresh" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/view-refresh.png' . '" alt="' . check_plain($link['title']) . '" title="' . check_plain($link['title']) . '"/>';
921
    $link['localized_options']['html'] = TRUE;
922

    
923
    $variables['element']['#link'] = $link;
924
  }
925
}
926

    
927
/* =================== block composition ===================== */
928

    
929
/**
930
 * Composes and returns an render array for the classification breadcrumbs of the given taxon.
931
 *
932
 * @param taxon
933
 *
934
 * @return array
935
 *   A Drupal render array for a table with the experts
936
 *
937
 * @ingroup compose
938
 */
939
function compose_classification_breadcrumbs($taxon_uuid) {
940

    
941
  _add_js_taxonomic_children('#classification-breadcrumbs .taxonomic-children-button');
942

    
943
  $render_array = array();
944

    
945
  $render_array['#theme'] = 'item_list';
946
  $render_array['#type'] = 'ul';
947
  $render_array['#attributes'] = array(
948
    'id' => 'classification-breadcrumbs',
949
    'class' => 'breadcrumbs inline',
950
  );
951

    
952
  $items = array();
953

    
954
  $parent_taxon_nodes = null;
955
  if($taxon_uuid){
956
    $parent_taxon_nodes = cdm_ws_taxonomy_pathFromRoot($taxon_uuid);
957
  }
958

    
959
  $classifications = cdm_ws_fetch_all(CDM_WS_PORTAL_TAXONOMY);
960
  // find current classification in list
961
  $classification = null;
962
  $current_classification_uuid = get_current_classification_uuid();
963
  foreach ($classifications as $classification){
964
    if($classification->uuid == $current_classification_uuid){
965
      break;
966
    }
967
  }
968

    
969
  $node_name = '';
970
  if(count($classifications) > 1 ){
971
    // need to add the current classification as first label
972

    
973
    $label = $classification->titleCache;
974
    if(strlen($label) > 20){
975
      $label = substr($label, 0, strpos($label, ' ', 15)) . '...';
976
    }
977
    $node_name = font_awesome_icon_markup('fa-th-list')  . ' ' . l($label, '#', array(
978
      'attributes' => array(
979
        'class' => 'taxonomic-children-button classification-chooser',
980
        'data-destination-uri' => drupal_get_destination(),
981
        'data-cdm-align-with' => array('prev')
982
      ),
983
      'html' => true
984
    ));
985
  }
986

    
987
  $rank_limit_uuid = variable_get(TAXONTREE_RANKLIMIT, TAXONTREE_RANKLIMIT_DEFAULT);
988

    
989
  $rank_separator = '<span> '
990
    . font_awesome_icon_markup('fa-chevron-right')
991
    . ' </span>';
992
  $more_children_icon = font_awesome_icon_markup('fa-sitemap fa-rotate-270');
993

    
994
  $items[] = $node_name;
995

    
996
  $more_children_for = null;
997
  if($parent_taxon_nodes){
998
    foreach ($parent_taxon_nodes as $node) {
999

    
1000
      $is_first_item = count($items) == 0;
1001
      $is_last_item = count($items) == count($parent_taxon_nodes);
1002
      $node_name = cdm_dataportal_shortname_of($node);
1003
      $path = path_to_taxon($node->taxonUuid);
1004

    
1005
      if($node->taxonomicChildrenCount > 0) {
1006
        $more_children_for = $node->taxonUuid;
1007
      } else {
1008
        $more_children_for = null;
1009
      }
1010

    
1011
      // 'fa-sitemap'
1012

    
1013
      $items[] =
1014
        ($is_first_item ? '' : ' ')
1015
        . $rank_separator
1016
        . l(
1017
          $node_name,
1018
          $path,
1019
          array(
1020
            'attributes' => array(
1021
              'class' => array('taxonomic-children-button'),
1022
              'data-cdm-taxon-uuid' => array($node->taxonUuid),
1023
              'data-cdm-classification-mode' => array('siblings'),
1024
              'data-cdm-align-with' => array('prev')
1025
            )
1026
          )
1027
        );
1028
      }
1029
    }
1030

    
1031
  // add more button to the end
1032
  if(!$parent_taxon_nodes) {
1033
    // not taxon focused yet, adding button to make  the root nodes available
1034
    $items[] = '<span class="taxonomic-children-button" data-classification-uuid="' . $current_classification_uuid
1035
      . '" data-rank-limit-uuid="' . $rank_limit_uuid . '" > '
1036
      . $more_children_icon
1037
      . '&nbsp;</span>';
1038
  } else if($more_children_for){
1039
    // last parent item has child taxon nodes
1040
    $items[] = ' <span class="taxonomic-children-button" data-cdm-taxon-uuid="' .$more_children_for
1041
      . '" data-cdm-classification-mode="children" >'
1042
      . $more_children_icon
1043
      . '&nbsp;</span>';
1044

    
1045
  }
1046

    
1047

    
1048

    
1049
  $render_array['#items'] = $items;
1050

    
1051
  return $render_array;
1052

    
1053
}
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