Project

General

Profile

Statistics
| Branch: | Tag: | Revision:

cdm-dataportal / modules / cdm_dataportal / cdm_dataportal.module @ 6e842c77

History | View | Annotate | Download (79 KB)

1
<?php
2
/**
3
 * @file
4
 * Module to provide a CDM Dataportal.
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
 *   - Wouter Addink <w.addink@eti.uva.nl> (migration from Drupal 5 to Drupal7)
18
 */
19

    
20
  module_load_include('php', 'cdm_dataportal', 'node_types');
21
  module_load_include('php', 'cdm_dataportal', 'settings');
22
  module_load_include('php', 'cdm_dataportal', 'help');
23
  module_load_include('php', 'cdm_dataportal', 'cdm_dataportal.search');
24

    
25
  module_load_include('inc', 'cdm_dataportal', 'includes/common');
26
  module_load_include('inc', 'cdm_dataportal', 'includes/name');
27
  module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
28
  module_load_include('inc', 'cdm_dataportal', 'includes/references');
29
  module_load_include('inc', 'cdm_dataportal', 'includes/pages');
30
  module_load_include('inc', 'cdm_dataportal', 'includes/media');
31
  module_load_include('inc', 'cdm_dataportal', 'includes/maps');
32
  module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');
33
  module_load_include('inc', 'cdm_dataportal', 'includes/descriptions');
34
  module_load_include('inc', 'cdm_dataportal', 'includes/pre-drupal8');
35

    
36
  module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');
37
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
38
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
39
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
40
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
41
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
42
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
43
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
44
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
45

    
46
  module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
47
  module_load_include('php', 'cdm_dataportal', 'classes/footnote');
48
  module_load_include('php', 'cdm_dataportal', 'classes/footnotekey');
49
  module_load_include('php', 'cdm_dataportal', 'classes/renderhints');
50

    
51

    
52
  /* ============================ java script functions ============================= */
53

    
54

    
55
  /**
56
  * loads external java script files asynchronously.
57
  *
58
  * @param unknown_type $script_url
59
  */
60
  function drupal_add_js_async($script_url, $callback){
61

    
62
    drupal_add_js("
63
          jQuery(document).ready(function() {
64
            jQuery.ajax({
65
              url: '" . $script_url . "',
66
              dataType: 'script',
67
              cache: true, // otherwise will get fresh copy every page load
68
              success: function() {
69
                    " . $callback . "
70
              }
71
            });
72
          });"
73
    , 'inline');
74
  }
75

    
76
  /**
77
   */
78
  function drupal_add_js_rowToggle($tableId){
79

    
80
      drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/table_modification.js');
81
      drupal_add_js('jQuery(document).ready(function(){
82
          addRowToggle("' . $tableId . '");
83
      });
84
      ', array('type' => 'inline'));
85
  }
86

    
87
  /**
88
   * @param unknown_type $link_element_selector
89
   * @param unknown_type $progress_element_selector
90
   */
91
  function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){
92

    
93
    $callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";
94

    
95
    drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);
96

    
97
    //   drupal_add_js("
98
    //   	  if (Drupal.jsEnabled) {
99
    //         $(document).ready(function() {
100
    //       		$('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
101
    //         });
102
    //       }", 'inline');
103
    }
104

    
105
  /**
106
   * @todo Please document this function.
107
   * @see http://drupal.org/node/1354
108
   */
109
  function _add_js_treeselector() {
110
    // drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
111
    drupal_add_js("
112
        jQuery(document).ready(function() {
113
           jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
114
                jQuery('#cdm-taxonomictree-selector-form').submit();
115
            });
116

    
117
        });
118
      ",
119
      array(
120
        'type' => 'inline',
121
        'scope' => 'footer'
122
      )
123
    );
124
  }
125

    
126
  function _add_js_openlayers() {
127

    
128
    $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';
129
    $proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';
130

    
131
    if(variable_get('cdm_js_devel_mode', FALSE)){
132
      // develooper mode libs
133
  //     $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';
134
      $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';
135
      $proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';
136
    }
137

    
138
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,
139
      array(
140
        'type' => 'file',
141
        'weight' => JS_LIBRARY,
142
        'cache' => TRUE,
143
        'preprocess' => FALSE
144
      )
145
    );
146

    
147
    // see https://github.com/proj4js/proj4js
148
    // http://openlayers.org/dev/examples/using-proj4js.html
149
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $proj4js,
150
      array(
151
        'type' => 'file',
152
        'weight' => JS_LIBRARY,
153
        'cache' => TRUE,
154
      )
155
    );
156

    
157
    // configure the theme
158
    $openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
159
    $openlayers_imp_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/img/dark/';
160
    drupal_add_js('OpenLayers.ImgPath="' . base_path() . $openlayers_imp_path . '";', array(
161
        'type' => 'inline',
162
        'weight' => JS_LIBRARY,
163
        'cache' => TRUE,
164
        'preprocess' => FALSE
165
      ));
166

    
167
    drupal_add_css($openlayers_theme_path . 'style.tidy.css',
168
      array(
169
        'type' => 'file',
170
        'cache' => TRUE,
171
        'preprocess' => FALSE
172
      )
173
    );
174

    
175
  }
176

    
177
  /**
178
   * @todo Please document this function.
179
   * @see http://drupal.org/node/1354
180
   */
181
  function _add_js_thickbox() {
182
    // ---- jQuery thickbox:
183
    /*
184
    * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
185
    * not triggered because of problems with compat-1.0.js' see INSTALL.txt
186
    */
187
    // drupal_add_js(drupal_get_path('module',
188
    // 'cdm_dataportal').'/js/jquery.imagetool.min.js');
189
    //
190
    // Add a setting for the path to cdm_dataportal module, used to find the path
191
    // for the loading animation image in thickbox.
192
    drupal_add_js(array(
193
    'cdm_dataportal' => array(
194
    'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
195
    )
196
    ),
197
    'setting'
198
        );
199
        drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
200
        drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
201
  }
202

    
203
  /**
204
   * @todo Please document this function.
205
   * @see http://drupal.org/node/1354
206
   */
207
  function _add_js_lightbox($galleryID) {
208
    /*
209
     * Important Notice: The jquery.lightbox-0.5.js has been modified in order to
210
    * allow using the "alt" attribute for captions instead of the "title"
211
    * attribute
212
    */
213
    $lightbox_base_path =  drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';
214
    $lightbox_image_path = base_path() . $lightbox_base_path . '/images/';
215
    drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');
216
    drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');
217
    drupal_add_js('jQuery(document).ready(function() {
218
        jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
219
          fixedNavigation:  true,
220
          imageLoading:     \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',
221
          imageBtnPrev:     \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',
222
          imageBtnNext:     \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',
223
          imageBtnClose:    \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',
224
          imageBlank:       \'' . $lightbox_image_path . 'lightbox-blank.gif\',
225
          adjustToWindow: true
226
        });
227
      });
228
      ', array('type' => 'inline'));
229
  }
230

    
231
  /**
232
   * @todo Please document this function.
233
   * @see http://drupal.org/node/1354
234
   */
235
  function _add_js_footnotes() {
236
    _add_js_domEvent();
237
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
238
  }
239

    
240
  /**
241
   * @todo Please document this function.
242
   * @see http://drupal.org/node/1354
243
   */
244
  function _add_js_cluetip() {
245

    
246
    // TODO replace by
247
    // @see http://www.socialembedded.com/labs/jQuery-Tooltip-Plugin/jQuery-Tooltip-Plugin.html
248
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.min.js');
249
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.dimensions.js');
250
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.hoverIntent.js');
251
    if(variable_get('cdm_js_devel_mode', FALSE)){
252
      drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.js');
253
    }
254
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.css');
255
    drupal_add_js("jQuery(document).ready(function(){
256
        jQuery('.cluetip').css({color: '#0062C2'}).cluetip({
257
          splitTitle: '|',
258
          showTitle: true,
259
          activation: 'hover',
260
          sicky: true,
261
          arrows: true,
262
          dropShadow: false,
263
          cluetipClass: 'rounded'
264
        });
265
      });",
266
      array(
267
        'type' => 'inline',
268
        'scope' => 'footer'
269
      )
270
    );
271
  }
272

    
273
  /**
274
   * @todo Please document this function.
275
   * @see http://drupal.org/node/1354
276
   */
277
  function _add_js_ahah() {
278

    
279
    _add_js_domEvent(); // requires domEvent.js
280
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
281
  }
282

    
283
/**
284
 * @todo Please document this function.
285
 * @see http://drupal.org/node/1354
286
 */
287
function _add_js_taxonomic_children($jquery_selector) {
288

    
289
  global $base_url;
290

    
291

    
292
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
293
  
294
  drupal_add_js('jQuery(document).ready(function() {
295
        jQuery(\'' . $jquery_selector . '\').taxonomic_children({
296
          hoverClass: "fa-rotate-90",
297
          activeClass: "fa-rotate-90",
298
          classificationUuid: "' . get_current_classification_uuid() . '",
299
          taxonUuid: "' . get_current_taxon_uuid() . '",
300
          cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
301
          proxyBaseUri: "' . $base_url . '",
302
          
303
        });
304
      });
305
      ', array('type' => 'inline'));
306
}
307

    
308
  /**
309
   * Adds the external javascript file for domEvent.js.
310
   *
311
   * @see drupal_add_js()
312
   */
313
  function _add_js_domEvent() {
314
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
315
  }
316

    
317
  function _add_jquery_ui()
318
  {
319
    drupal_add_css(drupal_get_path('module',
320
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
321
    drupal_add_js(drupal_get_path('module',
322
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
323
      array(
324
        'type' => 'file',
325
        'weight' => JS_LIBRARY,
326
        'cache' => TRUE,
327
        'preprocess' => FALSE
328
      )
329
    );
330
  }
331

    
332
  /**
333
   * Provides the markup for an font awesome icon.
334
   *
335
   * The icons is created in default size without any extra features.
336
   *
337
   * The available icons are listed here http://fontawesome.io/cheatsheet/
338
   * fontawesome icons have much more features than implemented here in this function,
339
   * for spinning icons, fixed width icons, rotation, etc please checkout the
340
   * examples at http://fontawesome.io/examples/
341
   *
342
   * @parameter $icon_name
343
   *  The name of the icon which starts with 'fa-'
344
   *
345
   * @return String
346
   *    the markup for the icon in an <i> tag
347
   *
348
   */
349
  function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
350

    
351

    
352
    //<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
353

    
354
    $font_awesome_css_uri=drupal_get_path('module', 'cdm_dataportal').'/font-awesome/4.5.0/css/font-awesome.min.css';
355
    $font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
356

    
357
    drupal_add_html_head_link(
358
      array(
359
        'href' => $font_awesome_css_uri,
360
        'rel' => 'stylesheet'
361
      )
362
    );
363

    
364
    if($icon_name){
365
      if(!isset($attributes['class'])){
366
        $attributes['class'] = array();
367
      }
368
      $attributes['class'][] = 'fa';
369
      $attributes['class'][] = $icon_name;
370

    
371
      return '<i ' . drupal_attributes($attributes) . '></i>';
372
    }
373

    
374
    return '';
375
  }
376

    
377

    
378
  /* ====================== hook implementations ====================== */
379
  /**
380
   * Implements hook_permission().
381
   *
382
   * Valid permissions for this module.
383
   *
384
   * @return array
385
   *   An array of valid permissions for the portfolio module.
386
   */
387
  function cdm_dataportal_permission() {
388
    return array(
389
      'administer cdm_dataportal' => array(
390
        'title' => t('administer cdm_dataportal'),
391
        'description' => t("TODO Add a description for 'administer cdm_dataportal'"),
392
      ),
393
      'cdm_dataportal view notes' => array(
394
        'title' => t('cdm_dataportal view notes'),
395
        'description' => t("TODO Add a description for 'cdm_dataportal view notes'"),
396
      ),
397
      // TODO Which other permissions are required?
398
      // -> check the WP6 requirements document.
399
    );
400
  }
401

    
402
/**
403
 * Implements hook_menu().
404
 */
405
function cdm_dataportal_menu() {
406
  $items = array();
407

    
408
  // @see settings.php.
409
  cdm_dataportal_menu_admin($items);
410
  cdm_dataportal_menu_help($items);
411

    
412
  $items['cdm_dataportal/names'] = array(
413
    'page callback' => 'cdm_dataportal_view_names',
414
    'access arguments' => array('access content'),
415
    'type' => MENU_CALLBACK,
416
  );
417

    
418
  // Optional callback arguments: page.
419
  $items['cdm_dataportal/taxon'] = array(
420
    'page callback' => 'cdm_dataportal_taxon_page_view',
421
    'access arguments' => array('access content'),
422
    'type' => MENU_CALLBACK,
423
    // Expected callback arguments: uuid.
424
  );
425

    
426
   // Optional callback arguments: page.
427
    //FIXME point to view/page method in this module
428
    $items['cdm_dataportal/specimen'] = array(
429
        'page callback' => 'cdm_dataportal_specimen_page_view',
430
        'access arguments' => array('access content'),
431
        'type' => MENU_CALLBACK,
432
        // Expected callback arguments: uuid.
433
    );
434

    
435
  $items['cdm_dataportal/name'] = array(
436
    'page callback' => 'cdm_dataportal_name_page_view',
437
      /*
438
    'page arguments' => array(
439
       'taxon_name_uuid',
440
       'taxon_to_hide_uuid',
441
       'synonym_uuid' => NULL
442
      ),
443
      */
444
    'access arguments' => array('access content'),
445
    'type' => MENU_CALLBACK,
446
    // Expected callback arguments: uuid.
447
  );
448

    
449
  $items['cdm_dataportal/reference'] = array(
450
    'page callback' => 'cdm_dataportal_view_reference',
451
    'access arguments' => array('access content'),
452
    'type' => MENU_CALLBACK,
453
    // Expected callback arguments: uuid.
454
  );
455

    
456
  $items['cdm_dataportal/reference/list'] = array(
457
    'page callback' => 'cdm_dataportal_view_reference_list',
458
    'access arguments' => array('access content'),
459
    'type' => MENU_CALLBACK,
460
    // Expected callback arguments: uuid.
461
  );
462

    
463
  $items['cdm_dataportal/media'] = array(
464
    'page callback' => 'cdm_dataportal_view_media',
465
    'access arguments' => array('access content'),
466
    'type' => MENU_CALLBACK,
467
    // Expected callback arguments:
468
    // uuid, mediarepresentation_uuid, part_uuid or part#.
469
  );
470

    
471
  $items['cdm_dataportal/polytomousKey'] = array(
472
    'page callback' => 'cdm_dataportal_view_polytomousKey',
473
    'access arguments' => array('access content'),
474
    'type' => MENU_CALLBACK,
475
    // Expected callback arguments: polytomousKey->uuid.
476
  );
477

    
478
  $items['cdm_dataportal/search'] = array(
479
    'page callback' => 'cdm_dataportal_view_search_advanced',
480
    'access arguments' => array('access content'),
481
    'type' => MENU_CALLBACK,
482
  );
483

    
484
  $items['cdm_dataportal/search/advanced'] = array(
485
    'title' => 'Advanced', // will be passed through t()
486
    'page callback' => 'cdm_dataportal_view_search_advanced',
487
    'access arguments' => array('access content'),
488
    'type' => MENU_DEFAULT_LOCAL_TASK,
489
  );
490

    
491
  $items['cdm_dataportal/search/taxon_by_description'] = array(
492
    'title' => 'By factual data', // will be passed through t()
493
    'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
494
    'access arguments' => array('access content'),
495
    'type' => MENU_LOCAL_TASK,
496
  );
497

    
498
  $items['cdm_dataportal/search/results/taxon'] = array(
499
    'page callback' => 'cdm_dataportal_view_search_results_taxon',
500
    'access arguments' => array('access content'),
501
    'type' => MENU_CALLBACK,
502
  );
503
  /*
504
   $items['cdm/xml2json'] = array(
505
   'page callback' => 'cdm_view_xml2json',
506
   'access arguments' => array('access content'),
507
   'type' => MENU_CALLBACK,
508
   );
509
   */
510

    
511
  // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
512
  // User configuration of cdm_dataportal.
513
  $items['user/%/cdm_dataportal'] = array(
514
    'title' => 'cdm_dataportal',
515
    'access arguments' => array('access content'),
516
    'page callback' => 'drupal_get_form',
517
    'page arguments' => array('cdm_dataportal_user_form'),
518
    'type' => MENU_LOCAL_TASK,
519
    'weight' => 10,
520
  );
521
  // }
522

    
523
  // 'May not cache' in D5.
524
  $items['cdm_dataportal/name/%'] = array(
525
    // 'page callback' => 'cdm_dataportal_view_name',
526
    'page callback' => 'cdm_dataportal_name_page_view',
527
    'page arguments' => array(2, 3, 4),
528
    'access arguments' => array('access content'),
529
    'type' => MENU_CALLBACK,
530
  );
531

    
532
  // --- Local tasks for Taxon.
533
  // --- tabbed taxon page
534
  if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
535
    $items['cdm_dataportal/taxon/%'] = array(
536
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
537
      'page callback' => 'cdm_dataportal_taxon_page_view',
538
      'access arguments' => array('access content'),
539
      'type' => MENU_CALLBACK,
540
      'weight' => 1,
541
      'page arguments' => array(2, "description")
542
      , // Expected callback arguments: taxon_uuid.
543
    );
544

    
545
    $items['cdm_dataportal/taxon/%/all'] = array(
546
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
547
      'page callback' => 'cdm_dataportal_taxon_page_view',
548
      'access arguments' => array('access content'),
549
      'type' => MENU_CALLBACK,
550
      'weight' => 2,
551
      'page arguments' => array(2, "all")
552
      , // Expected callback arguments: taxon_uuid.
553
    );
554

    
555
    $items['cdm_dataportal/taxon/%/description'] = array(
556
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
557
      'page callback' => 'cdm_dataportal_taxon_page_view',
558
      'access arguments' => array('access content'),
559
      'type' => MENU_DEFAULT_LOCAL_TASK,
560
      'weight' => 2,
561
      'page arguments' => array(2, "description")
562
      , // Expected callback arguments: taxon_uuid.
563
    );
564

    
565
    $items['cdm_dataportal/taxon/%/synonymy'] = array(
566
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Synonymy')),
567
      'page callback' => 'cdm_dataportal_taxon_page_view',
568
      'access arguments' => array('access content'),
569
      'type' => MENU_LOCAL_TASK,
570
      'weight' => 4,
571
      'page arguments' => array(2, "synonymy", 4)
572
      , // Expected callback arguments: taxon_uuid and ...
573
    );
574
    $items['cdm_dataportal/taxon/%/images'] = array(
575
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Images')),
576
      'page callback' => 'cdm_dataportal_taxon_page_view',
577
      'access arguments' => array('access content'),
578
      'type' => MENU_LOCAL_TASK,
579
      'weight' => 5,
580
      'page arguments' => array(2, "images")
581
      , // Expected callback arguments: taxon_uuid.
582
    );
583

    
584
    $items['cdm_dataportal/taxon/%/specimens'] = array(
585
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Specimens')),
586
      'page callback' => 'cdm_dataportal_taxon_page_view',
587
      'access arguments' => array('access content'),
588
      'type' => MENU_LOCAL_TASK,
589
      'weight' => 6,
590
      'page arguments' => array(2, "specimens")
591
      , // Expected callback arguments: taxon_uuid.
592
    );
593

    
594
    $items['cdm_dataportal/taxon/%/keys'] = array(
595
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Keys')),
596
      'page callback' => 'cdm_dataportal_taxon_page_view',
597
      'access arguments' => array('access content'),
598
      'type' => MENU_LOCAL_TASK,
599
      'weight' => 6,
600
      'page arguments' => array(2, "keys")
601
      , // Expected callback arguments: taxon_uuid.
602
    );
603

    
604
    $items['cdm_dataportal/taxon/%/experts'] = array(
605
        'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Experts')),
606
        'page callback' => 'cdm_dataportal_taxon_page_view',
607
        'access arguments' => array('access content'),
608
        'type' => MENU_LOCAL_TASK,
609
        'weight' => 6,
610
        'page arguments' => array(2, "experts")
611
    , // Expected callback arguments: taxon_uuid.
612
    );
613

    
614
    $items['cdm_dataportal/taxonSearch/autocomplete'] = array(
615
        'page callback' => 'cdm_dataportal_taxon_search_autocomplete',
616
        'access arguments' => array('access taxon search autocomplete'),
617
        'type' => MENU_CALLBACK
618
    );
619
  }
620

    
621
  // --- refresh link for all cdmnode types
622
  foreach (cdm_get_nodetypes() as $type=>$name) {
623
    $items['cdm_dataportal/' . $name . '/%/refresh'] = array(
624
        'title' => t('Refresh'),
625
        'page callback' => 'cdm_dataportal_refresh_node',
626
        'access arguments' => array('administer cdm_dataportal'),
627
        'type' => MENU_LOCAL_TASK,
628
        'weight' => 100,
629
        'page arguments' => array($name, 2)
630
    );
631
  }
632

    
633
  return $items;
634
}
635

    
636
/**
637
 * Implements hook_init().
638
 *
639
 */
640
function cdm_dataportal_init() {
641
  //FIXME To add CSS or JS that should be present on all pages, modules
642
  //      should not implement this hook, but declare these files in their .info file.
643
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
644
  // drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
645
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
646

    
647
  if(variable_get('cdm_debug_mode', FALSE)){
648
    $file = 'temporary://drupal_debug.txt';
649
    file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
650
  }
651

    
652
  $bibliography_settings = get_bibliography_settings();
653
  $enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
654
  FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
655
}
656

    
657
function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
658

    
659
  $base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
660

    
661
  if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
662
    // force reloading of all and notify user about this special loading
663
    drupal_set_message(t('The level 2 cache has been cleared for all tabs of this taxon page at once, please click here to return to the tabbed page: ')
664
        . l('Back to tabbed taxon page', $base_path));
665
    $base_path .= '/all';
666
  } else {
667
    drupal_set_message(t('The level 2 cache has been cleared for this page'));
668
  }
669

    
670
  $parameters['cacheL2_refresh'] ='1';
671

    
672

    
673
  drupal_goto($base_path, array('query' => $parameters));
674
}
675

    
676
/**
677
 * The function generate form for own user cdm dataportal configurations.
678
 */
679
function cdm_dataportal_user_form($form, &$form_state) {
680

    
681
  global $user;
682
  $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
683

    
684
  $form['taxon_page_tabs'] = array(
685
      '#type' => 'fieldset',
686
      '#tree' => true,
687
      '#title' => t('Taxon page tabs'),
688
  );
689

    
690
  $form['taxon_page_tabs']['user_defined'] = array(
691
    '#type' => 'checkbox',
692
    '#title' => t('Activate user default configuration'),
693
    '#default_value' => variable_get($checkbox_value, 0),
694
    '#description' => t('Check this if you want configure your own default tab from the below menu.'),
695
  );
696

    
697
  $form['taxon_page_tabs']['default_tab'] = array(
698
    '#type' => 'select',
699
    '#title' => t('Default tab to display'),
700
    '#default_value' => get_default_taxon_tab(TRUE),
701
    '#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
702
    '#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
703
              <strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
704
              to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
705
  );
706

    
707

    
708
  if(false){
709
    $form['developer_options'] = array(
710
        '#type' => 'fieldset',
711
        '#tree' => true,
712
        '#title' => t('Developer options'),
713
    );
714

    
715
    $form['developer_options']['show_render_path'] = array(
716
      '#type' => 'checkbox',
717
      '#title' => t('Display the render path for each taxon name.'),
718
      '#default_value' => variable_get($checkbox_value, 0),
719
      '#description' => t('This option is very helpful if you are editing the !link for taxon names.',
720
        array(
721
            '!link' => l(
722
              'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))
723
            )
724
        ),
725
    );
726
  }
727

    
728
  $form['submit'] = array(
729
    '#type' => 'submit',
730
    '#value' => t('Submit'),
731
  );
732

    
733
  return $form;
734
}
735

    
736
/**
737
 * Form submission handler for user_form().
738
 *
739
 * Submits the user cdm dataportal configurations.
740
 */
741
function cdm_dataportal_user_form_submit($form, &$form_state) {
742
  global $user;
743
  $msg_type = 'status';
744
  $username = $user->name;
745
  $variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
746

    
747
  // FIXME: this is completely wrong, see user_profile_form_submit()
748

    
749
  // it is only possible to change own user settings
750
  if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {
751

    
752
    // DEFAULT_TAXON_TAB
753
    $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
754
    variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);
755
    variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);
756
    if ($form_state['values']['taxon_page_tabs']['user_defined']) {
757
      drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
758
      drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
759
        '!tab' => $variable[variable_get($variable_to_use, 0)],
760
        '!user' => $username,
761
      ))), $msg_type);
762
    }
763
    else {
764
      drupal_set_message(check_plain(t('The user default tab wont be used for
765
        the next taxon site, check the box if you want to use the user default configuration.')));
766
    }
767

    
768
  }
769
  else {
770
    // Problem with the user id => variables wont be saved.
771
    $msg_type = 'warning';
772
    drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
773
  }
774
}
775

    
776
/**
777
 * Implements hook_block_info().
778
 */
779
function cdm_dataportal_block_info() {
780

    
781
    // $block[0]["info"] = t("CDM DataPortal DevLinks");
782
    // $block[1]["info"] = t("CDM DataPortal Credits");
783
    $block["2"] = array(
784
        "info" => t("CDM Search Taxa"),
785
        "cache" => DRUPAL_NO_CACHE
786
      );
787
    // $block[3]["info"] = t("CDM Filters");
788
    $block["4"]["info"] = t("CDM Dataportal Print");
789
    $block["keys"]["info"] = t("CDM identification keys");
790
    $block["fundedByEDIT"]["info"] = t('Funded by EDIT');
791
    $block["classification_breadcrumbs"] =  array(
792
        'info' => t('Classification breadcrumbs'),
793
        'cache' => DRUPAL_CACHE_PER_PAGE
794
      );
795

    
796
    return $block;
797
}
798

    
799
/**
800
 * Implements hook_block_view().
801
 */
802
function cdm_dataportal_block_view($delta) {
803
  // TODO Rename block deltas (e.g. '2') to readable strings.
804
  switch ($delta) {
805
    // case 'delta-1':
806
    // $block['subject'] = t('Credits');
807
    // $block['content'] = theme('cdm_credits');
808
    // return $block;
809
    case '2':
810
      $block['subject'] = t('Search taxa');
811
      $form = drupal_get_form('cdm_dataportal_search_taxon_form');
812
      $block['content'] = drupal_render($form);
813

    
814
      if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
815
        $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
816
      }
817
      return $block;
818
    case '4':
819
      $block['subject'] = '';
820
      $block['content'] = theme('cdm_print_button');
821
      return $block;
822
    case "keys":
823
      $block['subject'] = t('Identification Keys');
824
      $block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
825
      return $block;
826
    case "fundedByEDIT":
827
      // t('Funded by EDIT');
828
      $text = '<none>';
829
      $block['subject'] = $text;
830
      $img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
831
      $block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
832
        'attributes' => array("target" => "EDIT"),
833
        'absolute' => TRUE,
834
        'html' => TRUE,
835
      ));
836
      return $block;
837
    case 'classification_breadcrumbs':
838
      $taxon_uuid = get_current_taxon_uuid();
839
      $block['subject'] = '<none>';
840
      $block['content'] = compose_classification_breadcrumbs($taxon_uuid);
841
      return $block;
842
    
843
  }
844
}
845

    
846
/**
847
 * Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
848
 *
849
 * @return string
850
 *   the taxon uuid or NULL
851
 */
852
function get_current_taxon_uuid()
853
{
854
  static $taxon_uuid;
855

    
856
  if(!isset($taxon_uuid)){
857
    if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
858
      $taxon_uuid = $_REQUEST['currentTaxon'];
859
    } else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
860
      $taxon_uuid = arg(2);
861
    } else {
862
      $taxon_uuid = null;
863
    }
864
  }
865

    
866
  return $taxon_uuid;
867
}
868

    
869
/**
870
 * Returns the currently classification tree in use.
871
 *
872
 * @return string
873
 *   The uuid of the currently focused classification
874
 */
875
function get_current_classification_uuid() {
876
  if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
877
    return $_SESSION['cdm']['taxonomictree_uuid'];
878
  }
879
  else {
880
    return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
881
  }
882
}
883

    
884
/*
885
 function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
886
 $_SESSION['cdm'] = NULL;
887
 if(is_string($cdm_ws_uri_update)){
888
 $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
889
 }
890
 }
891

    
892
 function cdm_dataportal_session_validate(){
893
 if(!isset($_SESSION['cdm']['ws_uri'])){
894
 $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
895
 } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
896
 cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
897
 }
898
 }
899
 */
900

    
901
/**
902
 * creates a  selector form for taxonomic trees.
903
 *
904
 * @return array
905
 *  a drupal form array
906
 */
907
function cdm_taxonomictree_selector() {
908
  _add_js_treeselector();
909

    
910
  $form = drupal_get_form('cdm_taxonomictree_selector_form');
911
  return $form;
912
}
913

    
914
/**
915
 * @todo Please document this function.
916
 * @see http://drupal.org/node/1354
917
 *
918
 * @deprecated use compose_classification_selector instead
919
 */
920
function cdm_taxonomictree_selector_form($form, &$form_state) {
921

    
922
  $url = url('cdm_api/setvalue/session', array('query' => NULL));
923
  $form['#action'] = $url;
924

    
925
  $form['var'] = array(
926
    '#weight' => -3,
927
    '#type' => 'hidden',
928
    '#value' => '[cdm][taxonomictree_uuid]',
929
  );
930

    
931
  $destination_array = drupal_get_destination();
932
  $destination = $destination_array['destination'];
933

    
934
  $form['destination'] = array(
935
    '#weight' => -3,
936
    '#type' => 'hidden',
937
    '#value' =>  $destination,
938
  );
939

    
940
  $options = cdm_get_taxontrees_as_options();
941
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
942
  if($taxontree_includes){
943
    $filtered_options = array();
944
    foreach($options as $uuid=>$label){
945
      if(!empty($taxontree_includes[$uuid])){
946
        $filtered_options[$uuid] = $label;
947
      }
948
    }
949
    $options = $filtered_options;
950
  }
951

    
952
  $form['val'] = array(
953
    '#type' => 'select',
954
    '#title' => t('Available classifications'),
955
    '#default_value' => get_current_classification_uuid(),
956
    '#options' => $options,
957
    '#attributes' => array('class' => array('highlite-first-child')),
958
  );
959

    
960
  return $form;
961

    
962
}
963

    
964
/**
965
 *
966
 * @ingroup compose
967
 */
968
function compose_classification_selector() {
969

    
970
  $destination_array = drupal_get_destination();
971
  $destination = $destination_array['destination'];
972

    
973
  $options = cdm_get_taxontrees_as_options();
974
  $items = array();
975
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
976

    
977
  $current_classification_uuid = get_current_classification_uuid();
978

    
979

    
980
  foreach($options as $uuid=>$label){
981
    if(!$taxontree_includes || !empty($taxontree_includes[$uuid])){
982

    
983
      $class_attributes = '';
984
      if($current_classification_uuid == $uuid){
985
        $class_attributes  = array('focused');
986
      }
987
      $items[] = array(
988
        'data' => l($label,
989
          'cdm_api/setvalue/session',
990
          array(
991
            'query' => array(
992
              'destination' => $destination,
993
              'val' => $uuid,
994
              'var' => '[cdm][taxonomictree_uuid]'
995
            ),
996
          )
997
        ),
998
        'class' => $class_attributes
999
      );
1000
    }
1001
  }
1002

    
1003
  $render_array = array(
1004
    '#theme' => 'item_list',
1005
    '#type' => 'ul',
1006
    '#items' => $items
1007
  );
1008

    
1009
  return $render_array;
1010
}
1011

    
1012

    
1013
/* UNREACHABLE since action of form directly links to view.
1014
 function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
1015

    
1016
 $_SESSION['cdm']['search'] = $form_values;
1017
 //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
1018
 return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
1019
 //$paramstr = compose_url_prameterstr($form_values);
1020
 //return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
1021
 }
1022
 */
1023
/* ====================== menu callback functions ====================== */
1024
/**
1025
 * @todo Please document this function.
1026
 * @see http://drupal.org/node/1354
1027
 */
1028
/*
1029
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
1030
  static $comment_node_disabled =  0;
1031
  static $comment_node_read_only =  1;
1032
  static $comment_node_read_write =  2;
1033

    
1034
  if ($form_id == 'node_type_form'
1035
   && isset($form['identity']['type'])
1036
   && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
1037
  ) {
1038
    $form['workflow']['comment'] = array(
1039
      '#type' => 'radios',
1040
      '#title' => t('Default comment setting'),
1041
      '#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
1042
      '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
1043
      '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
1044
    );
1045
  }
1046
}
1047
*/
1048

    
1049
/**
1050
 * Displays a list of the known taxonomic names.
1051
 *
1052
 * When the list of taxonomic names is displayed, long lists are split up into
1053
 * multiple pages.
1054
 *
1055
 * TODO: Parameters are still preliminary.
1056
 *
1057
 * @param string $beginsWith
1058
 * @param string $page
1059
 *   Page number to diplay defaults to page 1.
1060
 * @param bool $onlyAccepted
1061
 */
1062
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
1063

    
1064
  $out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
1065

    
1066
  /*
1067
  // FIXME the filter for accepted names will be a form element, thus this
1068
  // widget should be generated via form api preferably as block.
1069
  $out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
1070
  $out .= theme('cdm_dataportal_widget_names_list', $names, $page);
1071
  $out .= theme('cdm_listof_taxa', $taxonPager);
1072
  return $out;
1073
  */
1074
}
1075

    
1076
/**
1077
 * @todo Please document this function.
1078
 * @see http://drupal.org/node/1354
1079
 */
1080
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
1081

    
1082
  cdm_check_valid_portal_page();
1083

    
1084
  $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
1085
  return theme('cdm_reference_page', array('reference' => $reference));
1086
}
1087

    
1088
/**
1089
 * Creates a view on a all references contained in the portal.
1090
 *
1091
 * This function is used at the path cdm_dataportal/reference/list
1092
 */
1093
function cdm_dataportal_view_reference_list($pageNumber) {
1094
  $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
1095
  cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
1096
}
1097

    
1098
/**
1099
 * @todo Please document this function.
1100
 * @see http://drupal.org/node/1354
1101
 */
1102
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
1103

    
1104
  cdm_check_valid_portal_page();
1105

    
1106
  $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
1107
  return theme('cdm_media_page', array(
1108
    'media' => $media,
1109
    'mediarepresentation_uuid' => $mediarepresentation_uuid,
1110
    'partId' => $part,
1111
    ));
1112
}
1113

    
1114
/**
1115
 * @todo Please document this function.
1116
 * @see http://drupal.org/node/1354
1117
 */
1118
function _load_taxonBase(&$taxonBase) {
1119
  if (isset($taxonBase->uuid)) {
1120
    $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
1121
    $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
1122
    $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
1123
  }
1124
}
1125

    
1126
/**
1127
 * Loads the media associated to the given taxon from the cdm server.
1128
 * The aggregation settings regarding taxon relathionships and
1129
 * taxonnomic childen are taken into account.
1130
 *
1131
 * The media lists are cached in a static variable.
1132
 *
1133
 * @param Taxon $taxon
1134
 *   A CDM Taxon entitiy
1135
 *
1136
 * @return array
1137
 *   An array of CDM Media entities
1138
 *
1139
 */
1140
function _load_media_for_taxon($taxon) {
1141

    
1142
  static $media = NULL;
1143

    
1144
  if(!isset($media)) {
1145
    $media = array();
1146
  }
1147
  if (!isset($media[$taxon->uuid])) {
1148

    
1149
    // --- GET Images --- //
1150
    $mediaQueryParameters = array(
1151
        "type" => "ImageFile",
1152
    );
1153

    
1154
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1155
    $mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
1156
    $mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
1157

    
1158
    $taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
1159
    $mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
1160
    $mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
1161
    $mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
1162

    
1163
    $ws_endpoint = NULL;
1164
    if ( variable_get('cdm_images_include_children', 0) == 0) {
1165
      $ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1166
    } else {
1167
      $ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1168
    }
1169

    
1170
    $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1171
        array(
1172
            $taxon->uuid,
1173
        ),
1174
        queryString($mediaQueryParameters)
1175
       );
1176
  }
1177

    
1178
  return $media[$taxon->uuid];
1179
}
1180

    
1181
/**
1182
 *
1183
 * @param Taxon $taxon
1184
 *   A CDM Taxon entitiy
1185
 *
1186
 * @return array
1187
 *   An array of CDM SpecimenOrObservation entities
1188
 *
1189
function _load_occurences_for_taxon($taxon){
1190

    
1191
  static $occurences = NULL;
1192

    
1193
  if(!isset($occurences)) {
1194
    $occurences = array();
1195
  }
1196

    
1197
  if (!isset($occurences[$taxon->uuid])){
1198

    
1199
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1200
    $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1201
    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1202

    
1203
    $by_associatedtaxon_query = http_build_query(array(
1204
        'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1205
        'relationships' => implode(',', $relationship_choice['direct']),
1206
        'pageSize' => null // all hits in one page
1207
    )
1208
    );
1209

    
1210
    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1211
        null,
1212
        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1213
    );
1214

    
1215

    
1216
    if(isset($pager->records[0])){
1217
      $occurences[$taxon->uuid] =  $pager->records;
1218
    }
1219
  }
1220
  return $occurences[$taxon->uuid];
1221
}
1222
 */
1223

    
1224
/**
1225
 * Gets a Drupal variable, string or array and returns it.
1226
 *
1227
 * Similar to the variable_get() function of Drupal, except that this function
1228
 * is able to handle arrays correctly. This function is especially useful
1229
 * when dealing with collections of settings form elements (#tree = TRUE).
1230
 *
1231
 * @param string $variableKey
1232
 *   The Unique key of the Drupal variable in the Drupal variables table.
1233
 * @param string $defaultValueString
1234
 *   A string as for example derived from a CONSTANT.
1235
 *
1236
 * @return mixed
1237
 *   usually an array, depending on the nature of the variable.
1238
 *
1239
 * TODO compare with get_array_variable_merged() duplicate functions?
1240
 * @deprecated rather use get_array_variable_merged() since this function
1241
 * used an array as second parameter
1242
 */
1243
function mixed_variable_get($variableKey, $defaultValueString) {
1244
  $systemDefaults = unserialize($defaultValueString);
1245
  $storedSettings = variable_get($variableKey, array());
1246
  if (is_array($storedSettings)) {
1247
    // TODO better use drupal_array_merge_deep() ?
1248
    $settings = array_merge($systemDefaults, $storedSettings);
1249
  }
1250
  else {
1251
    $settings = $systemDefaults;
1252
  }
1253
  return $settings;
1254
}
1255

    
1256
/**
1257
 * Recursive function to convert an object into an array.
1258
 * also subordinate objects will be converted.
1259
 *
1260
 * @param object $object
1261
 * @return the array
1262
 */
1263
function convert_to_array($object) {
1264
  if(is_object($object) || is_array($object)) {
1265
    $array = (array)$object;
1266
    foreach ($array as $key=>$value){
1267
      $array[$key] = convert_to_array($value);
1268
    }
1269
    return $array;
1270
  } else {
1271
    return $object;
1272
  }
1273
}
1274

    
1275
/**
1276
 * Searches the $collection for the cdm entitiy given as $element.
1277
 *
1278
 * The elements are compared by their UUID.
1279
 *
1280
 * @param $element
1281
 *  the CDM entitiy to search for
1282
 * @param $collection
1283
 *  the list of CDM entities to search in
1284
 *
1285
 * @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1286
 *
1287
 */
1288
function contains_cdm_entitiy($element, $collection) {
1289
  $result = FALSE;
1290
  foreach ($collection as $a) {
1291
    if ($a->uuid == $element->uuid) {
1292
      $result = TRUE;
1293
    }
1294
  }
1295
  return $result;
1296
}
1297

    
1298
/**
1299
 * Fiters the array $entity_list of CDM entities by the list
1300
 * of $excludes. Any element contained in the $excludes will be removed
1301
 * from included int the retuned list.
1302
 *
1303
 * If the $entity_list is not an array the $excludes will be returned.
1304
 */
1305
function filter_cdm_entity_list($entity_list, $excludes) {
1306
  if (is_array($entity_list)) {
1307
    $result = $entity_list;
1308
    if ($excludes) {
1309
      foreach ($excludes as $exclude) {
1310
        if (!contains_cdm_entitiy($exclude, $entity_list)) {
1311
          $result[] = $exclude;
1312
        }
1313
      }
1314
    }
1315
  }
1316
  else {
1317
    $result = $excludes;
1318
  }
1319
  return $result;
1320
}
1321

    
1322
/**
1323
 * Wraps the given $html string into a render array suitable for drupal_render()
1324
 *
1325
 * @param $html
1326
 *   the html string, see
1327
 *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1328
 * @param $weight
1329
 *   A positive or negative number (integer or decimal).
1330
 *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1331
 * @param $prefix
1332
 *   Optional markup for the '#prefix' element of the render array
1333
 * @param $suffix
1334
 *   Optional markup for the '#suffix' element of the render array
1335
 *
1336
 * @return array
1337
 *   A render array
1338
 *
1339
 */
1340
function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1341
  $render_array = array(
1342
    '#markup' => $html
1343
      );
1344
  if (is_numeric($weight)) {
1345
    $render_array['#weight'] = $weight;
1346
  }
1347
  if($prefix){
1348
    $render_array['#prefix'] = $prefix;
1349
  }
1350
  if($suffix) {
1351
    $render_array['#suffix'] = $suffix;
1352
  }
1353
  return $render_array;
1354
}
1355

    
1356
/**
1357
 * Loads the subgraph of a given PolytomousKeyNode.
1358
 *
1359
 * Loads the subgraph of the given PolytomousKeyNode recursively from
1360
 * the CDM REST service.
1361
 *
1362
 * @param mixed $polytomousKeyNode
1363
 *   PolytomousKeyNode passed by reference.
1364
 *
1365
 * @return void
1366
 */
1367
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1368

    
1369
  if (!$polytomousKeyNode) {
1370
    return;
1371
  }
1372
  if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1373
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1374
    return;
1375
  }
1376
  if (!is_uuid($polytomousKeyNode->uuid)) {
1377
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1378
    return;
1379
  }
1380

    
1381
  $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1382

    
1383
  if (!$polytomousKeyNode) {
1384
    // drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1385
    return;
1386
  }
1387

    
1388
  // Load children.
1389
  foreach ($polytomousKeyNode->children as &$childNode) {
1390
    _load_polytomousKeySubGraph($childNode);
1391
  }
1392

    
1393
  // Load subkey.
1394
  $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1395

    
1396
  // Load taxon.
1397
  $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1398
  _load_taxonBase($polytomousKeyNode->taxon);
1399
  return;
1400
}
1401

    
1402
/**
1403
 * @todo Please document this function.
1404
 * @see http://drupal.org/node/1354
1405
 */
1406
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1407

    
1408
  cdm_check_valid_portal_page();
1409

    
1410
  $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1411

    
1412
  $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1413
  if (is_array($sourcePager->records)) {
1414
    $polytomousKey->sources = $sourcePager->records;
1415
    // $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1416
  }
1417

    
1418
  $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1419
  if (is_array($annotationPager->records)) {
1420
    $polytomousKey->annotations = $annotationPager->records;
1421
  }
1422

    
1423
  _load_polytomousKeySubGraph($polytomousKey->root);
1424
  return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1425
}
1426

    
1427
/**
1428
 * Creates a taxon page view or a chapter of it.
1429
 *
1430
 * The taxon page gives detailed information on a taxon, it shows:
1431
 *  - Taxon name.
1432
 *  - Full list of synonyms homotypic synonyms on top, followed by the
1433
 *    heterotypic and finally followed by misapplied names.
1434
 *    The list is ordered historically.
1435
 *  - All description associated with the taxon.
1436
 *
1437
 * @param string $uuid
1438
 * @param string $chapter
1439
 *   Name of the part to display, valid values are:
1440
 *   'description', 'images', 'synonymy', 'specimens', 'all'.
1441
 *
1442
 * @return unknown_type
1443
 */
1444
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
1445

    
1446
  cdm_check_valid_taxon_page($chapter);
1447
  cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1448
  // show a warning in case the javascript development mode is anabled
1449
  if(variable_get('cdm_js_devel_mode', FALSE)) {
1450
    drupal_set_message(t('The !url1 is enabled.
1451
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1452
          '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1453
    )),
1454
    'warning'
1455
        );
1456
  }
1457

    
1458
  // Display the page for the taxon defined by $uuid.
1459
  // set_last_taxon_page_tab(arg(3));
1460
  $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter, $synonym_uuid);
1461
  if (!empty($taxonpage)) {
1462
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1463
    return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1464
  }
1465
  else {
1466
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1467
    return '';
1468
  }
1469
}
1470

    
1471
/**
1472
 * This function will genreate the taxon page part ($chapter) and returns a taxonpage object
1473
 * which has two fields, one for the page title and one for the content. Later on in the
1474
 * process chain the value contained in these fields will be passed to the cdm_node_show()
1475
 * function as the function parameters $title and $content.
1476
 *
1477
 * @param string $uuid
1478
 *   the uuid of the taxon to show
1479
 * @param string $chapter
1480
 *   Name of the part to display, valid values are:
1481
 *   'description', 'images', 'synonymy', 'all'.
1482
 *
1483
 * @return taxonpage object with the following fields:
1484
 *   - title : the title of the page
1485
 *   - content: the content of the page
1486
 *
1487
 */
1488
function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1489
  // Taxon object.
1490
  $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1491
  if (empty($taxon)) {
1492
    drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1493
    return FALSE;
1494
  }
1495
  $taxonpage = new stdClass();
1496

    
1497
  $taxonpage->title = theme('cdm_taxon_page_title', array(
1498
    'taxon' => $taxon
1499
  ));
1500

    
1501
  // Check if the taxon id contained in the currently selected tree.
1502
  $taxon_in_current_classification = taxon_in_current_classification($uuid);
1503

    
1504
  if (!$taxon_in_current_classification) {
1505
    $classifications = get_classifications_for_taxon($taxon);
1506
    RenderHints::pushToRenderStack('not_in_current_classification');
1507
    $taxon_name_markup = render_taxon_or_name($taxon);
1508

    
1509
    if (count($classifications) == 0) {
1510
      drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
1511
        array(
1512
        '!taxonname' => $taxon_name_markup,
1513
        )
1514
      ), 'warning');
1515
    }
1516
    else {
1517
      $trees = '';
1518
      foreach ($classifications as $classification) {
1519
        if (isset($classification->titleCache)) {
1520
          $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1521
        }
1522
      }
1523

    
1524
      drupal_set_message(format_plural(count($trees),
1525
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in this one: !trees',
1526
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1527
          array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1528
        ) ,
1529
        'warning');
1530
    }
1531
    RenderHints::popFromRenderStack();
1532
  }
1533

    
1534
  // Render the taxon page.
1535
  $render_array = compose_cdm_taxon_page($taxon, $chapter);
1536
  $taxonpage->content = drupal_render($render_array);
1537

    
1538
  return $taxonpage;
1539
}
1540

    
1541
/**
1542
 * Creates a specimen page view.
1543
 * @param string $uuid the UUID of the specimen
1544
 * @return array|string
1545
 */
1546
function cdm_dataportal_specimen_page_view($uuid) {
1547

    
1548
    //cdm_check_valid_taxon_page($chapter);
1549
    //cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1550
    // show a warning in case the javascript development mode is anabled
1551
    if(variable_get('cdm_js_devel_mode', FALSE)) {
1552
        drupal_set_message(t('The !url1 is enabled.
1553
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1554
            '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1555
        )),
1556
            'warning'
1557
        );
1558
    }
1559

    
1560
    // Display the page for the specimen defined by $uuid.
1561
    $specimenpage = cdm_dataportal_specimen_view($uuid);
1562
    if (!empty($specimenpage)) {
1563
        return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
1564
    }
1565
    else {
1566
        return '';
1567
    }
1568
}
1569

    
1570
/**
1571
 *
1572
 * Creates a specimen view.
1573
 * @param string $uuid the UUID of the specimen
1574
 * @return array|string
1575
 */
1576
function cdm_dataportal_specimen_view($uuid) {
1577
    $specimen = cdm_ws_get(CDM_WS_OCCURRENCE, $uuid);
1578
    if (empty($specimen)) {
1579
        drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1580
        return FALSE;
1581
    }
1582
    $specimenpage = new stdClass();
1583

    
1584
    $specimenpage->title = theme('cdm_specimen_page_title', array(
1585
        'specimen' => $specimen
1586
    ));
1587

    
1588
    // Render the specimen page.
1589
    $render_array = compose_cdm_specimen_page($uuid);
1590
    $specimenpage->content = drupal_render($render_array);
1591

    
1592
    return $specimenpage;
1593
}
1594

    
1595
/**
1596
 * Returns a name page as a Drupal node ready to be renderized by Drupal.
1597
 *
1598
 * The node page shows the taxon name title and the list of taxon related
1599
 * with such taxon. Name on the tree already in use.
1600
 *
1601
 * @param UUID $taxon_name_uuid
1602
 *   The uuid of the CDM TaxonNameBase to show a name page for
1603
 * @param UUID $taxon_to_hide_uuid
1604
 *   A taxon which should not be displayed in the taxon list
1605
 * @param UUID $highlite_synonym_uuid
1606
 *   Optinal parameter wich takes another taxon uuid, if given the
1607
 *   target taxon pages will show the syonymy tab where the taxon
1608
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1609
 *   in case it is found on this page.
1610
 *
1611
 * @return mixed
1612
 *   The formatted name page as node.
1613
 */
1614
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
1615

    
1616
  cdm_check_valid_portal_page();
1617

    
1618
  $taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
1619
  if (!empty($taxonname_page)) {
1620
    return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
1621
  }
1622
  else {
1623
    return '';
1624
  }
1625
}
1626

    
1627
/**
1628
 * View function for a TaxonNameBase page.
1629
 *
1630
 * The name page lists all taxa for which the name specified by the
1631
 * $taxon_name_uuid is being used. I case there is only one name the
1632
 * page automatically redirects ti the according taxon page. Otherwise
1633
 * the list of names is displayed.
1634
 *
1635
 * The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
1636
 * list of taxa. This is useful for example when referencing from a taxon
1637
 * to the name page and the referring taxon should not be repeaded in the
1638
 * name page.
1639
 *
1640
 *
1641
 * @param UUID $taxon_name_uuid
1642
 *   The uuid of the CDM TaxonNameBase to show a name page for
1643
 * @param UUID $taxon_to_hide_uuid
1644
 *   A taxon which should not be displayed in the taxon list
1645
 * @param UUID $highlite_synonym_uuid
1646
 *   Optinal parameter wich takes another taxon uuid, if given the
1647
 *   target taxon pages will show the syonymy tab where the taxon
1648
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1649
 *   in case it is found on this page.
1650
 *
1651
 * @return object
1652
 *   An object with two fields:
1653
 *     - title: the page title
1654
 *     - content: the page content
1655
 */
1656
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
1657
  // Getting the full taxonname object from the server.
1658
  $taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
1659
  if (!$taxon_name) {
1660
    drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
1661
    return FALSE;
1662
  }
1663
  // Searching for all the taxa connected with the taxon name on the tree
1664
  // in use.
1665
  $name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
1666
  $request_params = array();
1667
  $request_params['query'] = $name_cache;
1668
  $request_params['tree'] = get_current_classification_uuid();
1669
  $request_params['doTaxa'] = 1;
1670
  $request_params['doSynonyms'] = 1;
1671
  $request_params['doTaxaByCommonNames'] = 0;
1672
  $request_params['matchMode'] = "EXACT";
1673
  $taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
1674

    
1675
  // Removing the name where we came from.
1676
  foreach ($taxon_pager->records as $k => &$taxon) {
1677
    if ($taxon->uuid == $taxon_to_hide_uuid) {
1678
      unset($taxon_pager->records[$k]);
1679
    }
1680
  }
1681
  // Show the taxa list or go to the singular taxon.
1682
  if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
1683
    $singleTaxon = array_pop($taxon_pager->records);
1684
    if ($singleTaxon->class != "Taxon") {
1685
      // It is a Synonym -> look for the accepted.
1686
      $accepted_taxa = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid, get_current_classification_uuid()));
1687
      if (!empty($highlite_synonym_uuid)) {
1688
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1689
      }
1690
      else {
1691
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
1692
      }
1693
    }
1694
    else {
1695
      // It is an accepted taxon.
1696
      if (!empty($highlite_synonym_uuid)) {
1697
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1698
      }
1699
      else {
1700
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
1701
      }
1702
    }
1703
  }
1704
  else {// More than one taxa case.
1705
    $taxon_name_page = new stdClass();
1706
    $taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
1707
    if ($taxon_pager->records) {
1708
      $taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
1709
    }
1710
    else {
1711
      $taxon_name_page->content = 'This name has no taxa';
1712
    }
1713
    return $taxon_name_page;
1714
  }
1715
}
1716

    
1717
/**
1718
 * Creates a page with the advance search form.
1719
 *
1720
 * NOTE: The advance search form allows searching for taxa.
1721
 */
1722
function cdm_dataportal_view_search_advanced() {
1723
  drupal_set_title(t('Advanced search'), PASS_THROUGH);
1724
  return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
1725
}
1726

    
1727
/**
1728
 * Creates a page with the search form for searching by taxon descriptions.
1729
 */
1730
function cdm_dataportal_view_search_taxon_by_description() {
1731
  drupal_set_title(t('Search by factual data'), PASS_THROUGH);
1732
  return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
1733
}
1734

    
1735
/**
1736
 * Executes the search and generates the result list of taxa.
1737
 */
1738
function cdm_dataportal_view_search_results_taxon() {
1739

    
1740
  $taxonPager = cdm_dataportal_search_execute();
1741

    
1742
  $showThumbnails = do_showThumbnails();
1743

    
1744
  $setSessionUri = url('cdm_api/setvalue/session', array(
1745
      'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
1746
  ));
1747

    
1748
  drupal_add_js('jQuery(document).ready(function() {
1749

    
1750
      // init
1751
      if(' . $showThumbnails . ' == 1){
1752
          jQuery(\'.media_gallery\').show(20);
1753
      } else {
1754
          jQuery(\'.media_gallery\').hide(20);
1755
      }
1756

    
1757
      // add change handler
1758
      jQuery(\'#showThumbnails input.showThumbnails\').change(
1759
      function(event){
1760
        var state = 0;
1761
        if(jQuery(this).is(\':checked\')){
1762
          jQuery(\'.media_gallery\').show(20);
1763
          state = 1;
1764
        } else {
1765
          jQuery(\'.media_gallery\').hide(20);
1766
        }
1767
        // store state in session variable
1768
        var uri = \'' . $setSessionUri . '\' + state;
1769
        jQuery.get(uri);
1770
      });
1771
  });',
1772
  array('type' => "inline", 'scope' => JS_DEFAULT));
1773

    
1774
  drupal_set_title(t('Search results'), PASS_THROUGH);
1775

    
1776
  return theme('cdm_search_results', array(
1777
    'pager' => $taxonPager,
1778
    'path' => 'cdm_dataportal/search/results/taxon',
1779
    ));
1780
}
1781

    
1782
/**
1783
 * Provides the standart image wich indicated a loading process
1784
 *
1785
 * @return string
1786
 *  The img html tag
1787
 */
1788
function loading_image_html() {
1789
  return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
1790
    . '/images/loading_circle_grey_16.gif" style="display:none;">';
1791
}
1792

    
1793
/**
1794
 * Returns the state of the the showThumbnails flag set in the
1795
 * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
1796
 *
1797
 * @return boolean
1798
 *    returns 1 if the flag is set
1799
 */
1800
function do_showThumbnails() {
1801
  static $showThumbnails = null;
1802

    
1803
  if($showThumbnails == null) {
1804
    $showThumbnails = 0;
1805
    if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
1806
      $showThumbnails = 0;
1807
      $search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
1808
      $showThumbnails = is_array($search_gallery_settings)
1809
        && isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
1810
        && (
1811
            $search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
1812
            $search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
1813
            $search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
1814
            )
1815
         ? 1 : 0;
1816

    
1817
       drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
1818
    }
1819
    $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
1820
    if (!is_numeric($showThumbnails)) {
1821
      $showThumbnails = 1;
1822
    }
1823
  }
1824

    
1825
  return $showThumbnails;
1826
}
1827

    
1828

    
1829
/* ====================== other functions ====================== */
1830
/**
1831
 * Creates a URL to the taxon page specified by the $uuid parameter.
1832
 *
1833
 * The URL will be prepended with a path element to a specific taxon page tab.
1834
 *
1835
 * This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
1836
 * be set globally in the administrative settings or individually in the user
1837
 * profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
1838
 * the last portal will stay on this last tab.
1839
 *
1840
 * A third option is offerered by the $page_tab parameter which allows overwriting this
1841
 * internal mechanism by a specific value.
1842
 *
1843
 * @param string $uuid
1844
 *   The UUID of the taxon.
1845
 * @param string $page_tab
1846
 *   Overwriting the preset mechanism by defining specific value for the
1847
 *   taxon page tab.
1848
 *
1849
 * @return string
1850
 *   The created URL.
1851
 */
1852
function path_to_taxon($uuid, $page_tab = FALSE) {
1853

    
1854
  $tab = get_default_taxon_tab();
1855
  $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
1856

    
1857
  if (!$uuid) {
1858
    return FALSE;
1859
  }
1860

    
1861
  if ($page_tab) {
1862
    return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
1863
  }
1864
  elseif (!$tab || strtolower($tab) == 'general') {
1865
    return 'cdm_dataportal/taxon/' . $uuid;
1866
  }
1867
  elseif (get_last_taxon_page_tab() &&   $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
1868
    return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
1869
  }
1870
  else {
1871
    return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
1872
  }
1873
}
1874

    
1875
function path_to_specimen($uuid) {
1876

    
1877
    if (!$uuid) {
1878
        return FALSE;
1879
    }
1880
    else {
1881
        return 'cdm_dataportal/specimen/' . $uuid;
1882
    }
1883
}
1884

    
1885
/**
1886
 * Creates a URL to show a synonmy in the according taxon page.
1887
 *
1888
 * The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
1889
 * The resulting URI will include query parameters to highlight the synonym, and to optionally display
1890
 * the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
1891
 * include the sysnonym uuid as fragment in order to let the browser scroll to the according location
1892
 * in the page
1893
 *
1894
 * @param string $synonymUuid
1895
 *    The uuid of the synonym
1896
 * @param string $acceptedUuid
1897
 *    The uuid of the according accepted taxon
1898
 * @return string
1899
 *    The URL to show a synonmy in the according taxon page
1900
 */
1901
function uri_to_synonym($synonymUuid, $acceptedUuid) {
1902
  $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
1903
  return url($acceptedPath, array(
1904
      'query' => array(
1905
        // highlite the synony in the synonymy
1906
        'highlite' => $synonymUuid,
1907
        // the taxon page is refered from a synonym and the synonym can optionally be named in the page title
1908
        // see theme_taxon_page_title()
1909
        'acceptedFor' => $synonymUuid
1910
      ),
1911
      'fragment' => $synonymUuid
1912
  ));
1913

    
1914
}
1915

    
1916
/**
1917
 * Compses the drupal path to the key identified by the uuid.
1918
 *
1919
 * @param string $keyType
1920
 *    the key typer corresponds to the specific class of the CDM
1921
 *    IdentificationKey. Possible values are
1922
 *      -PolytomousKey
1923
 *      -MultimediaKey
1924
 *      - ...
1925
 * @param UUID $keyUuid
1926
 *   The UUID of the key
1927
 */
1928
function path_to_key($keyType, $keyUuid) {
1929
  if (!$keyUuid || !$keyType) {
1930
    return FALSE;
1931
  }
1932
  $keyType{0} = strtolower($keyType{0});
1933
  return "cdm_dataportal/" . $keyType . "/$keyUuid";
1934
}
1935

    
1936
/**
1937
 * @todo Please document this function.
1938
 * @see http://drupal.org/node/1354
1939
 */
1940
function path_to_reference($uuid) {
1941
  if (!$uuid) {
1942
    return FALSE;
1943
  }
1944
  return 'cdm_dataportal/reference/' . $uuid;
1945
}
1946

    
1947
/**
1948
 * Creates the path to a cdm_dataportal taxon name page.
1949
 *
1950
 * @param UUID $taxon_name_uuid
1951
 *   The uuid of the CDM TaxonNameBase to show a name page for
1952
 * @param UUID $taxon_to_hide_uuid
1953
 *   A taxon which should not be displayed in the taxon list
1954
 * @param UUID $highlite_synonym_uuid
1955
 *   Optinal parameter wich takes another taxon uuid, if given the
1956
 *   target taxon pages will show the syonymy tab where the taxon
1957
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1958
 *   in case it is found on this page.
1959
 *
1960
 * @return a URI path element as string
1961
 */
1962
function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid  = NULL) {
1963
  $res = FALSE;
1964
  if ($name_uuid) {
1965
    $res = 'cdm_dataportal/name/' . $name_uuid;
1966
  }
1967
  if($taxon_to_hide_uuid){
1968
    $res .= '/' . $taxon_to_hide_uuid;
1969
    if($synonym_uuid){
1970
      $res .= '/' . $synonym_uuid;
1971
    }
1972
  }
1973
  return $res;
1974
}
1975

    
1976
/**
1977
 * @todo Please document this function.
1978
 * @see http://drupal.org/node/1354
1979
 */
1980
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
1981
  if (!$uuid) {
1982
    return FALSE;
1983
  }
1984
  $out = 'cdm_dataportal/media/' . $uuid;
1985
  if ($representaion_uuid) {
1986
    $out .= '/' . $representaion_uuid;
1987
    if ($partId !== FALSE) {
1988
      $out .= '/' . $partId;
1989
    }
1990
  }
1991
  return $out;
1992
}
1993

    
1994
/**
1995
 * Compares thisRank with thatRank.
1996
 *
1997
 * Returns a negative integer, zero, or a positive integer
1998
 * as the of thisRank is higher than, equal to, or lower than thatRank.
1999
 * e.g:
2000
 * <ul>
2001
 * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
2002
 * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
2003
 * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
2004
 * </ul>
2005
 * <p>
2006
 * This compare logic of the underlying webservice is the
2007
 * <b>inverse logic</b> of the the one implemented in
2008
 * java.lang.Comparable#compareTo(java.lang.Object)
2009
 *
2010
 * @param $thisRankUuid
2011
 * @param $thatRankUuid
2012
 *
2013
 * @return int
2014
 *   A negative integer, zero, or a positive integer
2015
 *   as the thisRank is lower than, equal to, or higher than thatRank.
2016
 */
2017
function rank_compare($thisRankUuid, $thatRankUuid) {
2018
  $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
2019
  return $result->Integer;
2020
}
2021

    
2022
/**
2023
 * Composes an HTML element class attribute value composed of
2024
 * the shortname of the cdm class and the uuid of the entity.
2025
 * This class attribute should be used whereever an cdm-entity is rendered.
2026
 *
2027
 * These according class selectors in css must be escaped, eg:
2028
 *    .cdm\:TextData
2029
 *
2030
 * @param $cdmEntity
2031
 */
2032
function html_class_attribute_ref($cdmEntity) {
2033

    
2034
  if (is_cdm_entity($cdmEntity)) {
2035
    return "cdm:" . $cdmEntity->class . " uuid:" . $cdmEntity->uuid;
2036
  }
2037
}
2038

    
2039

    
2040
/**
2041
 * Creates a short taxonname.
2042
 *
2043
 * The short name is created by using the taggedTitle field of
2044
 * NameSTO or NameTO instances.
2045
 * If the taggedTitle if empty the fullname will be returned.
2046
 *
2047
 * @param unknown_type $name
2048
 *   Name or TreeNode.
2049
 *
2050
 * @return string
2051
 */
2052
function cdm_dataportal_shortname_of($name) {
2053
  $nameStr = '';
2054

    
2055
  normalize_tagged_text($name->taggedTitle);
2056

    
2057
  // Get all tagged text tokens of the scientific name.
2058
  foreach ($name->taggedTitle as $tagtxt) {
2059
    if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
2060
      $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
2061
    }
2062
  }
2063
  $nameStr = trim($nameStr);
2064

    
2065
  if ($nameStr) {
2066

    
2067
    // Do not return short names for these.
2068
    if ($name->unplaced || $name->excluded) {
2069
      return $nameStr;
2070
    }
2071

    
2072
    /*
2073
    1st capture group (^[a-zA-Z]): First letter of uninomial.
2074
    Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
2075
    Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
2076
    but only matching if no '(' or '.' in second word of name,        ( \x2E = '.')
2077
    OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$             (\x22= '"', \x2D='-', \xD7='×' )
2078
    */
2079
    $pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
2080
    if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
2081
      return $matches[1][0] . "." . $matches[3][0];
2082
    }
2083
    else {
2084
      return $nameStr;
2085
    }
2086
  }
2087
  else {
2088
    return $name->titleCache;
2089
  }
2090
}
2091

    
2092
/**
2093
 * Check if a taxon is accepted by the current taxonomic tree.
2094
 *
2095
 * @param mixed $taxon
2096
 *   The Taxon obkect to check.
2097
 *
2098
 * @return bool
2099
 *   Returns TRUE if $taxon is accepted, FALSE otherwise.
2100
 */
2101
function _cdm_dataportal_acceptedByCurrentView($taxon) {
2102

    
2103
  $defaultTreeUuid = get_current_classification_uuid();
2104

    
2105
  if (isset($taxon->taxonNodes)) {
2106
    $taxonNodes = $taxon->taxonNodes;
2107
  }
2108
  else {
2109
    $taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
2110
  }
2111

    
2112
  if ($taxon->class == "Taxon" && isset($taxonNodes)) {
2113
    foreach ($taxonNodes as $node) {
2114
      if (isset($node->classification)){
2115
        if(is_object($node->classification)) {
2116
          if ($node->classification->uuid == $defaultTreeUuid) {
2117
            return TRUE;
2118
          }
2119
        }
2120
        else {
2121
          if ($node->classification == $defaultTreeUuid) {
2122
            return TRUE;
2123
          }
2124
        }
2125
      }
2126
    }
2127
  }
2128

    
2129
  return FALSE;
2130
}
2131

    
2132
/**
2133
 * Checks is the source has one of the given types.
2134
 *
2135
 * @param object $source
2136
 *   The original source entity
2137
 * @param array $types
2138
 *   An array of elementd of the OriginalSourceType enumeration
2139
 *   If not set the default will be used which is:
2140
 *    - Lineage
2141
 *    - PrimaryMediaSource
2142
 *    - PrimaryTaxonomicSource
2143
 *    - Unknown
2144
 *    - Other
2145
 * @return boolean
2146
 */
2147
  function _is_original_source_type($source, $types = null) {
2148
    // this is the default
2149
    // maybe this should also be put into the settings
2150
    static $default = array(
2151
      OriginalSourceType::Lineage,
2152
      OriginalSourceType::PrimaryMediaSource,
2153
      OriginalSourceType::PrimaryTaxonomicSource,
2154
      OriginalSourceType::Unknown,
2155
      OriginalSourceType::Other,
2156
    );
2157

    
2158
    if(!$types){
2159
      $types = $default;
2160
    }
2161
    return isset($source->type) && in_array($source->type, $types);
2162
  }
2163

    
2164
/**
2165
 * @todo Please document this function.
2166
 * @see http://drupal.org/node/1354
2167
 */
2168
function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
2169
  return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
2170
}
2171

    
2172

    
2173
/**
2174
 * Collects all the media from a list of description elements.
2175
 *
2176
 * @param array $descriptionElements
2177
 *   The description elements from which to collect the media.
2178
 *
2179
 * @return array
2180
 *   The output with all the collected media.
2181
 */
2182
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2183

    
2184
  $outArrayOfMedia = array();
2185

    
2186
  // Avoiding a warning box in Drupal for Flora Malesiana.
2187
  if (isset($descriptionElements) && is_array($descriptionElements)) {
2188
    foreach ($descriptionElements as $descriptionElement) {
2189
      if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2190
        foreach ($descriptionElement->media as $media) {
2191
          if (is_object($media)) {
2192
            $outArrayOfMedia[] = $media;
2193
          }
2194
        }
2195
      }
2196
    }
2197
  }
2198
  return $outArrayOfMedia;
2199
}
2200

    
2201
/**
2202
 * @todo Please document this function.
2203
 * @see http://drupal.org/node/1354
2204
 *
2205
 * @param array $cdm_entities
2206
 *   An array of CdmBase instances or a single instance.
2207
 * @param string $footnote_list_key_suggestion
2208
 *
2209
 * @return unknown
2210
 */
2211
function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
2212

    
2213
   static $annotations_types_filter = null;
2214
   if(!$annotations_types_filter) {
2215
     $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
2216
   }
2217

    
2218
  $footNoteKeys = array();
2219

    
2220
  // Is argument cdmBase an array?
2221
  if (!is_array($cdm_entities)) {
2222
    $cdmBase_array = array();
2223
    $cdmBase_array[] = $cdm_entities;
2224
  }
2225
  else {
2226
    $cdmBase_array = $cdm_entities;
2227
  }
2228

    
2229
  // Getting the key for the footnotemanager.
2230
  if (isset($footnote_list_key_suggestion)) {
2231
    $footnote_list_key = $footnote_list_key_suggestion;
2232
  }
2233
  else {
2234
    $footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2235
  }
2236

    
2237
  // Adding the footnotes keys.
2238
  foreach ($cdmBase_array as $cdmBase_element) {
2239
    $annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
2240
    if (is_array($annotations)) {
2241
      foreach ($annotations as $annotation) {
2242
        $footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2243
      }
2244
    }
2245
  }
2246

    
2247
  return $footNoteKeys;
2248
}
2249

    
2250

    
2251
/**
2252
 * Creates a CDM Dynabox.
2253
 *
2254
 * @param string $dynabox_id
2255
 *   a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2256
 * @param string $label
2257
 *   The clickable text to show.
2258
 * @param string $content_url
2259
 *   The cdm REST service request url wich will deliver the content to be shown
2260
 *   once the dynabox toggles open.
2261
 * @param string $theme
2262
 *   The theme to be used for rendering the cdm REST service response with is
2263
 *   returned from the $content_url.
2264
 * @param string $link_alt_text
2265
 *   The value for the alt attribute of the dynabox link.
2266
 * @param array $enclosingtags
2267
 *   An array with two elements: $enclosingtags[0] will be used for the dynabox
2268
 *   element itself, $enclosingtags[1] is the tag to be used for the
2269
 *   dynabox_content (optional)
2270
 * @param array $attributes
2271
 * @param $content_element_selector
2272
 *   Optional jQuery selector which can be used to reference a dom element which should
2273
 *   be used as container for the content to be shown. The dynabox-<dynabox id>-content
2274
 *  element will be placed in this container.
2275
 *
2276
 * @param string $open_callback
2277
 *   optional javascript call back function to be triggered after toggling the box to
2278
 *   the open state.
2279
 * @param string $close_callback
2280
 *   optional javascript call back function to be triggered after toggling the box to
2281
 *   the closed state.
2282
 * @return string Returns HTML for a dynabox.
2283
 * Returns HTML for a dynabox.
2284
 */
2285
function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2286
                     $enclosingtags = array('li', 'ul'), $attributes = array(),
2287
                     $content_element_selector = null,
2288
                     $open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2289
  $out = '';
2290

    
2291
  // check for plain class attribute string
2292
  $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2293

    
2294
  if(!array_key_exists('class', $attributes)) {
2295
    $attributes['class'] = array();
2296
  }
2297
  $attributes['id'][] = 'dynabox-' . $dynabox_id;
2298
  $dynabox_attributes = drupal_attributes($attributes);
2299

    
2300

    
2301
  _add_js_domEvent(); // requires domEvent.js
2302
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2303
  drupal_add_js("
2304
  jQuery(document).ready(
2305
      function() {
2306
        dynabox('". $dynabox_id ."',
2307
          {
2308
            open_callback: " . $open_callback .",
2309
            close_callback: " . $close_callback .
2310
            ($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2311
          }
2312
        );
2313
      }
2314
   );",
2315
   array(
2316
    'type'=>'inline',
2317
    'scope'=>'footer'
2318
    )
2319
  );
2320

    
2321

    
2322
  $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2323
  $out .= '<!-- dynabox for ' . $content_url . ' -->';
2324
  $out .= '<' . $enclosingtags[0] . ' ' .  $dynabox_attributes. '><a href="' . $cdm_proxy_url . '" class="label" alt="' . t($link_alt_text) . '">' . $label . '</a>';
2325
  $out .= '  <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2326
  $out .= '    <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2327
  $out .= '    </' . $enclosingtags[1] . '>';
2328
  $out .= '  </' . $enclosingtags[0] . '>';
2329
  $out .= '<!-- dynabox end -->';
2330
  return $out;
2331
}
2332

    
2333
/**
2334
 * Checks whether a feature has any description elements.
2335
 *
2336
 * @param mixed $featureNode
2337
 *   A feature node as produced by the function _mergeFeatureTreeDescriptions().
2338
 *
2339
 * @see _mergeFeatureTreeDescriptions()
2340
 *
2341
 * @return bool
2342
 *   Returns TRUE if the given $featureNode or any of its subordinate nodes
2343
 *   contains at least one non empty TextData or at least one DescriptionElement
2344
 *   of an other type. A TextData element holding a multilanguageText or a
2345
 *   source reference is considered to be not empty.
2346
 *
2347
 * @TODO this function may have become obsolete by the new method of detecting empty blocks,
2348
 *       see $block_content_is_not_empty in compose_feature_blocks() and
2349
 *       $feature_block_has_content in compose_feature_block_items_generic
2350
 */
2351
function has_feature_node_description_elements($featureNode) {
2352

    
2353
  if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2354
    if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2355
      foreach ($featureNode->descriptionElements as $descriptionElement) {
2356
        if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
2357
          && $descriptionElement->multilanguageText_L10n->text != ''
2358
          || isset($descriptionElement->sources[0])
2359
          || isset($descriptionElement->media[0]) ) {
2360
          return TRUE;
2361
        }
2362
      }
2363
    }
2364
  }
2365
  else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2366
    foreach ($featureNode->childNodes as $child) {
2367
      if (has_feature_node_description_elements($child)) {
2368
        return TRUE;
2369
      }
2370
    }
2371
  }
2372
  return FALSE;
2373
}
2374

    
2375
/**
2376
 * Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
2377
 *
2378
 * @param $chapter
2379
 *   The taxon page chapter or part
2380
 */
2381
function cdm_check_valid_taxon_page($chapter){
2382
  static $taxon_tabs = null;
2383

    
2384
  cdm_check_valid_portal_page();
2385

    
2386
  if($taxon_tabs == null){
2387
    $taxon_tabs = array('all', 'description');
2388
    foreach(get_taxon_tabs_list() as $tab){
2389
      $taxon_tabs[] = strtolower($tab);
2390
    }
2391
  }
2392

    
2393
  if(!in_array($chapter, $taxon_tabs)){
2394
    // oops this is not a valid chapter name
2395
    http_response_code(404); // 404 = Not Found
2396
  }
2397

    
2398
}
2399

    
2400
/**
2401
 * Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise
2402
 *
2403
 * @param $chapter
2404
 *   The taxon page chapter or part
2405
 */
2406
function cdm_check_valid_portal_page(){
2407
  $ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
2408
  if(preg_match($ends_with_file_suffix_pattern, $_GET['q'])){
2409
    // oops this urls ends with a file_suffix and thus does not refer to a portal page
2410
    http_response_code(404); // 404 = Not Found
2411
    exit('HTTP 404');
2412
  }
2413
}
2414

    
2415
/**
2416
 * Generates the diff of the texts and presents it in a HTML diff viewer.
2417
 *
2418
 * @param $text_a
2419
 * @param $text_b
2420
 * @return string
2421
 */
2422
function diff_viewer($text_a, $text_b) {
2423

    
2424
  static $diff_viewer_count = 0;
2425

    
2426
  $element_id = 'part_definitions_diff_' . $diff_viewer_count++;
2427

    
2428
  // http://code.stephenmorley.org/php/diff-implementation/
2429
  module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
2430
  drupal_add_css(drupal_get_path('module',
2431
      'cdm_dataportal') . '/css/diff.css');
2432
  _add_jquery_ui();
2433
  drupal_add_js(
2434
    'jQuery(document).ready( function(){
2435
        jQuery(\'#' . $element_id . '\').accordion({
2436
        collapsible: true,
2437
        active: false,
2438
        fillSpace: true,
2439
        }).children(\'div\').css({ \'height\': \'auto\' });
2440
        jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
2441
     });'
2442
    , array(
2443
    'type' => 'inline',
2444
    'scope' => 'footer'
2445
  ));
2446

    
2447
  $diff = Diff::compare($text_a,
2448
    $text_b);
2449
  $diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
2450
    . Diff::toTable($diff, '', '')
2451
    . '</div></div>';
2452
  return $diff_viewer_markup;
2453
}
2454

    
2455

    
Add picture from clipboard (Maximum size: 40 MB)