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cdm-dataportal / modules / cdm_dataportal / cdm_dataportal.module @ 64cfdac1

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1
<?php
2
/**
3
 * @file
4
 * Module to provide a CDM Dataportal.
5
 *
6
 * @copyright
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 *   (C) 2007-2012 EDIT
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 *   European Distributed Institute of Taxonomy
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 *   http://www.e-taxonomy.eu
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 *
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 *   The contents of this module are subject to the Mozilla
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 *   Public License Version 1.1.
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 * @see http://www.mozilla.org/MPL/MPL-1.1.html
14
 *
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 * @author
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 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
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 *   - Wouter Addink <w.addink@eti.uva.nl> (migration from Drupal 5 to Drupal7)
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 */
19

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

    
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  module_load_include('inc', 'cdm_dataportal', 'includes/common');
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  module_load_include('inc', 'cdm_dataportal', 'includes/agent');
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  module_load_include('inc', 'cdm_dataportal', 'includes/name');
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  module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
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  module_load_include('inc', 'cdm_dataportal', 'includes/taxon-node');
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  module_load_include('inc', 'cdm_dataportal', 'includes/references');
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  module_load_include('inc', 'cdm_dataportal', 'includes/pages');
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  module_load_include('inc', 'cdm_dataportal', 'includes/media');
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  module_load_include('inc', 'cdm_dataportal', 'includes/maps');
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  module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');
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  module_load_include('inc', 'cdm_dataportal', 'includes/descriptions');
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  module_load_include('inc', 'cdm_dataportal', 'includes/pre-drupal8');
37

    
38
  module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');
39
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
41
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
43
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
44
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
45
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
46
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
47

    
48
  module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
49
  module_load_include('php', 'cdm_dataportal', 'classes/footnote');
50
  module_load_include('php', 'cdm_dataportal', 'classes/footnotekey');
51
  module_load_include('php', 'cdm_dataportal', 'classes/renderhints');
52

    
53

    
54
  /* ============================ java script functions ============================= */
55

    
56

    
57
  /**
58
  * loads external java script files asynchronously.
59
  *
60
  * @param unknown_type $script_url
61
  */
62
  function drupal_add_js_async($script_url, $callback){
63

    
64
    drupal_add_js("
65
          jQuery(document).ready(function() {
66
            jQuery.ajax({
67
              url: '" . $script_url . "',
68
              dataType: 'script',
69
              cache: true, // otherwise will get fresh copy every page load
70
              success: function() {
71
                    " . $callback . "
72
              }
73
            });
74
          });"
75
    , 'inline');
76
  }
77

    
78
  /**
79
   */
80
  function drupal_add_js_rowToggle($tableId){
81

    
82
      drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/table_modification.js');
83
      drupal_add_js('jQuery(document).ready(function(){
84
          addRowToggle("' . $tableId . '");
85
      });
86
      ', array('type' => 'inline'));
87
  }
88

    
89
  /**
90
   * @param unknown_type $link_element_selector
91
   * @param unknown_type $progress_element_selector
92
   */
93
  function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){
94

    
95
    $callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";
96

    
97
    drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);
98

    
99
    //   drupal_add_js("
100
    //   	  if (Drupal.jsEnabled) {
101
    //         $(document).ready(function() {
102
    //       		$('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
103
    //         });
104
    //       }", 'inline');
105
    }
106

    
107
  /**
108
   * @todo Please document this function.
109
   * @see http://drupal.org/node/1354
110
   */
111
  function _add_js_treeselector() {
112
    // drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
113
    drupal_add_js("
114
        jQuery(document).ready(function() {
115
           jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
116
                jQuery('#cdm-taxonomictree-selector-form').submit();
117
            });
118

    
119
        });
120
      ",
121
      array(
122
        'type' => 'inline',
123
        'scope' => 'footer'
124
      )
125
    );
126
  }
127

    
128
  function _add_js_resizable_element($selector, $y_axis_only) {
129

    
130
    _add_jquery_ui();
131
    $options = "";
132
    if($y_axis_only) {
133
      $options = "resize: function(event, ui) {
134
        ui.size.width = ui.originalSize.width;
135
        },
136
        handles: \"s\"";
137

    
138
    }
139
    drupal_add_js("
140
          jQuery(document).ready(function() {
141
             jQuery('" . $selector . "').resizable({". $options ."});
142
          });
143
        ",
144
      array(
145
        'type' => 'inline',
146
        'scope' => 'footer'
147
      )
148
    );
149
  }
150

    
151
  function _add_js_openlayers() {
152

    
153
    $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';
154
    $proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';
155

    
156
    if(variable_get('cdm_js_devel_mode', FALSE)){
157
      // develooper mode libs
158
  //     $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';
159
      $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';
160
      $proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';
161
    }
162

    
163
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,
164
      array(
165
        'type' => 'file',
166
        'group' => JS_LIBRARY,
167
        'weight' => 0,
168
        'cache' => TRUE,
169
        'preprocess' => FALSE
170
      )
171
    );
172

    
173

    
174
    // see https://github.com/proj4js/proj4js
175
    // http://openlayers.org/dev/examples/using-proj4js.html
176
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $proj4js,
177
      array(
178
        'type' => 'file',
179
        'group' => JS_LIBRARY,
180
        'weight' => -1, // before open layers
181
        'cache' => TRUE,
182
      )
183
    );
184

    
185
    // configure the theme
186
    $openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
187
    $openlayers_imp_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/img/dark/';
188
    drupal_add_js('OpenLayers.ImgPath="' . base_path() . $openlayers_imp_path . '";', array(
189
        'type' => 'inline',
190
        'group' => JS_LIBRARY,
191
        'weight' => 1, // after openlayers
192
        'cache' => TRUE,
193
        'preprocess' => FALSE
194
      ));
195

    
196
    drupal_add_css($openlayers_theme_path . 'style.tidy.css',
197
      array(
198
        'type' => 'file',
199
        'cache' => TRUE,
200
        'preprocess' => FALSE
201
      )
202
    );
203

    
204
  }
205

    
206
  /**
207
   * @todo Please document this function.
208
   * @see http://drupal.org/node/1354
209
   */
210
  function _add_js_thickbox() {
211
    // ---- jQuery thickbox:
212
    /*
213
    * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
214
    * not triggered because of problems with compat-1.0.js' see INSTALL.txt
215
    */
216
    // drupal_add_js(drupal_get_path('module',
217
    // 'cdm_dataportal').'/js/jquery.imagetool.min.js');
218
    //
219
    // Add a setting for the path to cdm_dataportal module, used to find the path
220
    // for the loading animation image in thickbox.
221
    drupal_add_js(array(
222
    'cdm_dataportal' => array(
223
    'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
224
    )
225
    ),
226
    'setting'
227
        );
228
        drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
229
        drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
230
  }
231

    
232
  /**
233
   * @todo Please document this function.
234
   * @see http://drupal.org/node/1354
235
   */
236
  function _add_js_lightbox($galleryID) {
237
    /*
238
     * Important Notice: The jquery.lightbox-0.5.js has been modified in order to
239
     * allow using the "alt" attribute for captions instead of the "title"
240
     * attribute
241
     */
242
    $lightbox_base_path =  drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';
243
    $lightbox_image_path = base_path() . $lightbox_base_path . '/images/';
244
    drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');
245
    drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');
246
    drupal_add_js('jQuery(document).ready(function() {
247
        jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
248
          fixedNavigation:  true,
249
          imageLoading:     \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',
250
          imageBtnPrev:     \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',
251
          imageBtnNext:     \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',
252
          imageBtnClose:    \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',
253
          imageBlank:       \'' . $lightbox_image_path . 'lightbox-blank.gif\',
254
          adjustToWindow: true
255
        });
256
      });
257
      ', array('type' => 'inline'));
258
  }
259

    
260
  /**
261
   * @todo Please document this function.
262
   * @see http://drupal.org/node/1354
263
   */
264
  function _add_js_footnotes() {
265
    _add_js_domEvent();
266
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
267
  }
268

    
269
  /**
270
   * @todo Please document this function.
271
   * @see http://drupal.org/node/1354
272
   */
273
  function _add_js_ahah() {
274

    
275
    _add_js_domEvent(); // requires domEvent.js
276
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
277
  }
278

    
279
/**
280
 * @todo Please document this function.
281
 * @see http://drupal.org/node/1354
282
 */
283
function _add_js_taxonomic_children($jquery_selector) {
284

    
285
  global $base_url;
286

    
287

    
288
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
289
  
290
  drupal_add_js('jQuery(document).ready(function() {
291
        jQuery(\'' . $jquery_selector . '\').taxonomic_children({
292
          // hoverClass: "fa-rotate-90",
293
          // activeClass: "fa-rotate-90",
294
          classificationUuid: "' . get_current_classification_uuid() . '",
295
          taxonUuid: "' . get_current_taxon_uuid() . '",
296
          cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
297
          proxyBaseUri: "' . $base_url . '",
298
          
299
        });
300
      });
301
      ', array('type' => 'inline'));
302
}
303

    
304
  /**
305
   * Adds the external javascript file for domEvent.js.
306
   *
307
   * @see drupal_add_js()
308
   */
309
  function _add_js_domEvent() {
310
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
311
  }
312

    
313
  function _add_jquery_ui()
314
  {
315
    drupal_add_css(drupal_get_path('module',
316
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
317
    drupal_add_js(drupal_get_path('module',
318
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
319
      array(
320
        'type' => 'file',
321
        'weight' => JS_LIBRARY,
322
        'cache' => TRUE,
323
        'preprocess' => FALSE
324
      )
325
    );
326
  }
327

    
328
  function _add_js_ui_accordion(){
329
    _add_jquery_ui();
330
    drupal_add_js('jQuery(document).ready(function() {
331
        jQuery( "#accordion" ).accordion();
332
      });',
333
      array('type' => 'inline')
334
    );
335
  }
336

    
337

    
338
function _add_js_utis_client($jquery_selector){
339

    
340
  drupal_add_js(drupal_get_path('module',
341
      'cdm_dataportal') . '/js/utis-client/utis-client.js',
342
    array(
343
      'type' => 'file',
344
      'weight' => JS_LIBRARY,
345
      'cache' => TRUE,
346
      'preprocess' => FALSE
347
    )
348
  );
349

    
350
  drupal_add_js('jQuery(document).ready(function() {
351
        jQuery( "' . $jquery_selector . '" ).utis_client(
352
        {
353
          spinnerIcon: \'' . font_awesome_icon_markup('fa-sync', array('class' => array('fa-3x',  'fa-spin'), 'style' => array('opacity: 0.3;'))) . '\',
354
          externalLinkIcon: \'' . font_awesome_icon_markup('fa-external-link-alt') . '\'
355
        });
356
      });',
357
    array('type' => 'inline')
358
  );
359
}
360

    
361
function _add_js_universalviewer($jquery_selector, $manifest_uri){
362

    
363
  $universalviewer_path  = drupal_get_path('module',    'cdm_dataportal') . '/js/universalviewer';
364

    
365
  drupal_add_css($universalviewer_path . '/uv/uv.css');
366
  drupal_add_css($universalviewer_path . '/uv-fix.css');
367

    
368
  // offline.js is all of these dependencies concatenated (jQuery, CoreJS, and JSViews)
369
  drupal_add_js($universalviewer_path . '/uv/lib/offline.js',
370
      array(
371
      'type' => 'file',
372
      'group' => JS_LIBRARY,
373
      'cache' => TRUE,
374
      'preprocess' => FALSE
375
    )
376
  );
377
  drupal_add_js($universalviewer_path . '/uv/helpers.js',
378
    array(
379
      'type' => 'file',
380
      'group' => JS_LIBRARY,
381
      'cache' => TRUE,
382
      'preprocess' => FALSE
383
    )
384
  );
385
  // from UV 3.x documentation:
386
  // "root:
387
  // The path to the uv directory. Use a relative path e.g. root: '../../uv'
388
  // Don't start your path with a / otherwise requirejs will not append .js to
389
  // dependencies and they won't load."
390
  //
391
  // universalviewerPath will be used to build the root config variable.
392
  $iCleanUrlRequest = strpos($_SERVER['REQUEST_URI'], 'q=cdm_dataportal/') === false;
393
  if($iCleanUrlRequest){
394
    $folders_up = preg_replace('/[^\/]+/', '..', $_GET['q']);
395
    $folders_up = preg_replace('/\.\.$/', '', $folders_up);
396
  } else {
397
    $folders_up = '';
398
  }
399
  $basePath = base_path();
400
  $config_file = 'uv-config.json';
401
  drupal_add_js('
402
      console.log(\'jQuery inline: \' + jQuery.fn.jquery);
403
      jQuery(window).on(\'uvLoaded\', function() {
404
        jQuery( "' . $jquery_selector . '" ).jqUniversalviewer(
405
        {
406
          root: \'' . $folders_up . $universalviewer_path . '/uv\',
407
          configUri: \'' . $basePath . $universalviewer_path . '/'. $config_file . '\',
408
          manifestUri: \'' . $manifest_uri . '\'
409
        }
410
        );
411
      });',
412
    array(
413
      'type' => 'inline',
414
      'scope' => 'footer',
415
      'group' => JS_DEFAULT,
416
      'weight' => 0,
417
    )
418
  );
419
  drupal_add_js($universalviewer_path . '/jq-universalviewer.js',
420
    array(
421
      'type' => 'file',
422
      'scope' => 'footer',
423
      'group' => JS_DEFAULT,
424
      'weight' => 10,
425
      'cache' => TRUE,
426
      'preprocess' => FALSE
427
    )
428
  );
429
  // ui.js must be last
430
  drupal_add_js($universalviewer_path . '/uv/uv.js',
431
    array(
432
      'type' => 'file',
433
      'scope' => 'footer',
434
      'group' => 300, // IMPORTANT!
435
      'cache' => TRUE,
436
      'preprocess' => FALSE
437
    )
438
  );
439
}
440

    
441
  /**
442
   * Provides the markup for an font awesome icon.
443
   *
444
   * The icons is created in default size without any extra features.
445
   *
446
   * The available icons are listed here http://fontawesome.io/cheatsheet/
447
   * fontawesome icons have much more features than implemented here in this function,
448
   * for spinning icons, fixed width icons, rotation, etc please checkout the
449
   * examples at http://fontawesome.io/examples/
450
   *
451
   * @parameter $icon_name
452
   *  The name of the icon which starts with 'fa-'
453
   *
454
   * @return String
455
   *    the markup for the icon in an <i> tag
456
   *
457
   */
458
  function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
459
    _add_font_awesome_font();
460

    
461

    
462
    if($icon_name){
463
      if(!isset($attributes['class'])){
464
        $attributes['class'] = array();
465
      }
466
      $attributes['class'][] = 'fa';
467
      $attributes['class'][] = $icon_name;
468

    
469
      return '<i ' . drupal_attributes($attributes) . '></i>';
470
    }
471

    
472
    return '';
473
  }
474

    
475
/**
476
 * @param string $glyph_name
477
 *   The name of the gloyph (e.g. 'icon-interal-link-alt-solid') for the foll list please
478
 *   refer to modules/cdm_dataportal/fonts/custom-icon-font
479
 * @param array $attributes
480
 * @return string
481
 */
482
  function custom_icon_font_markup($glyph_name = NULL, $attributes = array()){
483
    _add_font_custom_icon_font();
484

    
485

    
486
    if($glyph_name){
487
      if(!isset($attributes['class'])){
488
        $attributes['class'] = array();
489
      }
490
      $attributes['class'][] = $glyph_name;
491

    
492
      return '<i ' . drupal_attributes($attributes) . '></i>';
493
    }
494

    
495
    return '';
496
  }
497

    
498
/**
499
 * Adds the css  containing the font awesome icons to the html header.
500
 */
501
function _add_font_awesome_font()
502
{
503
  // $fa_font_version = 'font-awesome-4.6.3/css/font-awesome.min.css';
504
  $fa_font_version = 'fontawesome-free-5.9.0-web/css/all.css';
505
  $font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/' . $fa_font_version;
506

    
507
  drupal_add_html_head_link(
508
    array(
509
      'href' => $font_awesome_css_uri,
510
      'rel' => 'stylesheet'
511
    )
512
  );
513
}
514

    
515
/**
516
 * Adds the css  containing the font awesome icons to the html header.
517
 */
518
function _add_font_custom_icon_font()
519
{
520

    
521
  $custom_icon_font_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/custom-icon-font/style.css';
522

    
523
  drupal_add_html_head_link(
524
    array(
525
      'href' => $custom_icon_font_css_uri,
526
      'rel' => 'stylesheet'
527
    )
528
  );
529
}
530

    
531
/* ====================== hook implementations ====================== */
532
  /**
533
   * Implements hook_permission().
534
   *
535
   * Valid permissions for this module.
536
   *
537
   * @return array
538
   *   An array of valid permissions for the cdm_dataportal module.
539
   */
540
  function cdm_dataportal_permission() {
541
    return array(
542
      'administer cdm_dataportal' => array(
543
        'title' => t('Administer CDM DataPortal settings'),
544
        'description' => t("Access the settings pages specific for the cdm_dataportal module"),
545
      ),
546
      'access cdm content' => array(
547
        'title' => t('Access CDM content'),
548
        'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
549
      ),
550
    );
551
  }
552

    
553
/**
554
 * Implements hook_menu().
555
 */
556
function cdm_dataportal_menu() {
557
  $items = array();
558

    
559
  // @see settings.php.
560
  cdm_dataportal_menu_admin($items);
561
  cdm_dataportal_menu_help($items);
562

    
563
  $items['cdm_dataportal/names'] = array(
564
    'page callback' => 'cdm_dataportal_view_names',
565
    'access arguments' => array('access cdm content'),
566
    'type' => MENU_CALLBACK,
567
  );
568

    
569
  // Optional callback arguments: page.
570
  $items['cdm_dataportal/taxon'] = array(
571
    'page callback' => 'cdm_dataportal_taxon_page_view',
572
    'access arguments' => array('access cdm content'),
573
    'type' => MENU_CALLBACK,
574
    // Expected callback arguments: uuid.
575
  );
576

    
577
  $items['cdm_dataportal/occurrence'] = array(
578
        'page callback' => 'cdm_dataportal_specimen_page_view',
579
        'access arguments' => array('access cdm content'),
580
        'type' => MENU_CALLBACK,
581
        // Expected callback arguments: uuid.
582
    );
583

    
584
  $items['cdm_dataportal/description'] = array(
585
        'page callback' => 'cdm_dataportal_description_page_view',
586
        'access arguments' => array('access cdm content'),
587
        'type' => MENU_CALLBACK,
588
        // Expected callback arguments: uuid.
589
    );
590

    
591
   $items['cdm_dataportal/specimen/accession_number'] = array(
592
        'page callback' => 'cdm_dataportal_specimen_by_accession_number_page_view',
593
        'access arguments' => array('access cdm content'),
594
        'type' => MENU_CALLBACK,
595
        // Expected callback arguments: accession number.
596
    );
597
  $items['cdm_dataportal/named_area'] = array(
598
    'page callback' => 'cdm_dataportal_named_area_page_view',
599
    'access arguments' => array('access cdm content'),
600
    'type' => MENU_CALLBACK,
601
    // Expected callback arguments: uuid.
602
  );
603

    
604
  $items['cdm_dataportal/name'] = array(
605
    'page callback' => 'cdm_dataportal_name_page_view',
606
      /*
607
    'page arguments' => array(
608
       'taxon_name_uuid',
609
       'taxon_to_hide_uuid',
610
       'synonym_uuid' => NULL
611
      ),
612
      */
613
    'access arguments' => array('access cdm content'),
614
    'type' => MENU_CALLBACK,
615
    // Expected callback arguments: uuid.
616
  );
617

    
618
  $items['cdm_dataportal/reference'] = array(
619
    'page callback' => 'cdm_dataportal_view_reference',
620
    'access arguments' => array('access cdm content'),
621
    'type' => MENU_CALLBACK,
622
    // Expected callback arguments: uuid.
623
  );
624

    
625
  $items['cdm_dataportal/reference/list'] = array(
626
    'page callback' => 'cdm_dataportal_view_reference_list',
627
    'access arguments' => array('access cdm content'),
628
    'type' => MENU_CALLBACK,
629
    // Expected callback arguments: uuid.
630
  );
631

    
632
  $items['cdm_dataportal/media'] = array(
633
    'page callback' => 'cdm_dataportal_view_media',
634
    'access arguments' => array('access cdm content'),
635
    'type' => MENU_CALLBACK,
636
    // Expected callback arguments:
637
    // uuid, mediarepresentation_uuid, part_uuid or part#.
638
  );
639

    
640
  $items['cdm_dataportal/polytomousKey'] = array(
641
    'page callback' => 'cdm_dataportal_view_polytomousKey',
642
    'access arguments' => array('access cdm content'),
643
    'type' => MENU_CALLBACK,
644
    // Expected callback arguments: polytomousKey->uuid.
645
  );
646

    
647
  $items['cdm_dataportal/search'] = array(
648
    'page callback' => 'cdm_dataportal_view_search_advanced',
649
    'access arguments' => array('access cdm content'),
650
    'type' => MENU_CALLBACK,
651
  );
652

    
653
  // Optional callback arguments: page.
654
  $items['cdm_dataportal/registration'] = array(
655
    'page callback' => 'cdm_dataportal_registration_page_view',
656
    'access arguments' => array('access cdm content'),
657
    'type' => MENU_CALLBACK,
658
    // Expected callback arguments: uuid.
659
  );
660

    
661
  // ------------ SEARCH -----------
662
  $items['cdm_dataportal/search/advanced'] = array(
663
    'title' => 'Advanced', // will be passed through t()
664
    'page callback' => 'cdm_dataportal_view_search_advanced',
665
    'access arguments' => array('access cdm content'),
666
    'type' => MENU_DEFAULT_LOCAL_TASK,
667
  );
668
  $items['cdm_dataportal/search/blast'] = array(
669
    'title' => 'Blast', // will be passed through t()
670
    'page callback' => 'cdm_dataportal_view_search_blast',
671
    'access arguments' => array('access cdm content'),
672
    'type' => MENU_LOCAL_TASK,
673
  );
674

    
675
  $items['cdm_dataportal/search/taxon_by_description'] = array(
676
    'title' => 'By content category', // will be passed through t()
677
    'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
678
    'access arguments' => array('access cdm content'),
679
    'type' => MENU_LOCAL_TASK,
680
  );
681
  $items['cdm_dataportal/search/results/taxon'] = array(
682
    'page callback' => 'cdm_dataportal_view_search_results_taxon',
683
    'access arguments' => array('access cdm content'),
684
    'type' => MENU_CALLBACK,
685
  );
686

    
687
  $items['cdm_dataportal/search/results/specimen'] = array(
688
      'page callback' => 'cdm_dataportal_view_search_results_specimen',
689
      'access arguments' => array('access cdm content'),
690
      'type' => MENU_CALLBACK,
691
  );
692

    
693
  /*
694
   * MENU_CALLBACK at cdm_dataportal/registration-search is needed to make the
695
   * tabs in the subordinate paths work, accessing this 'page' will cause the
696
   * MENU_DEFAULT_LOCAL_TASK being displayed
697
   */
698
  $items['cdm_dataportal/registration-search'] = array(
699
    'title' => 'Search', // will be passed through t()
700
    'page callback' => 'cdm_dataportal_view_search_registrations_results',
701
    'page arguments' => array("filter"),
702
    'access arguments' => array('access cdm content'),
703
    'type' => MENU_CALLBACK,
704
  );
705
  /*
706
   * the MENU_DEFAULT_LOCAL_TASK creates a tab for the MENU_CALLBACK
707
   * defined at a higher level of the path (cdm_dataportal/registration-search)
708
   */
709
  $items['cdm_dataportal/registration-search/filter'] = array(
710
    'title' => 'Search', // will be passed through t()
711
    'page callback' => 'cdm_dataportal_view_search_registrations_results',
712
    'page arguments' => array("filter"),
713
    'access arguments' => array('access cdm content'),
714
    'type' => MENU_DEFAULT_LOCAL_TASK,
715
  );
716
  /*
717
   * the MENU_LOCAL_TASK creates another tab
718
   */
719
  $items['cdm_dataportal/registration-search/taxongraph'] = array(
720
    'title' => 'Taxon graph search', // will be passed through t()
721
    'page callback' => 'cdm_dataportal_view_search_registrations_results',
722
    'page arguments' => array("taxongraph"),
723
    'access arguments' => array('access cdm content'),
724
    'type' => MENU_LOCAL_TASK,
725
  );
726

    
727
  // Optional callback arguments: page.
728
  $items['cdm_dataportal/search/agent'] = array(
729
    'page callback' => 'cdm_dataportal_view_search_agent',
730
    'access arguments' => array('access cdm content'),
731
    'type' => MENU_CALLBACK,
732
    // Expected callback arguments: uuid.
733
  );
734

    
735
  // ------------ menu items with variable path elements -----------
736

    
737
  // 'May not cache' in D5.
738
  $items['cdm_dataportal/name/%'] = array(
739
    // 'page callback' => 'cdm_dataportal_view_name',
740
    'page callback' => 'cdm_dataportal_name_page_view',
741
    'page arguments' => array(2, 3, 4, 5),
742
    'access arguments' => array('access cdm content'),
743
    'type' => MENU_CALLBACK,
744
  );
745

    
746
  // --- Local tasks for Taxon.
747
  // --- tabbed taxon page
748
  if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
749
    $items['cdm_dataportal/taxon/%'] = array(
750
      'title' => cdm_taxonpage_tab_label('General'),
751
      'page callback' => 'cdm_dataportal_taxon_page_view',
752
      'access arguments' => array('access cdm content'),
753
      'type' => MENU_CALLBACK,
754
      'weight' => 1,
755
      'page arguments' => array(2, "description")
756
      , // Expected callback arguments: taxon_uuid.
757
    );
758

    
759
    $items['cdm_dataportal/taxon/%/all'] = array(
760
      'title' => cdm_taxonpage_tab_label('General'),
761
      'page callback' => 'cdm_dataportal_taxon_page_view',
762
      'access arguments' => array('access cdm content'),
763
      'type' => MENU_CALLBACK,
764
      'weight' => 2,
765
      'page arguments' => array(2, "all")
766
      , // Expected callback arguments: taxon_uuid.
767
    );
768

    
769
    $items['cdm_dataportal/taxon/%/description'] = array(
770
      'title' => cdm_taxonpage_tab_label('General'),
771
      'page callback' => 'cdm_dataportal_taxon_page_view',
772
      'access arguments' => array('access cdm content'),
773
      'type' => MENU_DEFAULT_LOCAL_TASK,
774
      'weight' => 2,
775
      'page arguments' => array(2, "description")
776
      , // Expected callback arguments: taxon_uuid.
777
    );
778

    
779
    $items['cdm_dataportal/taxon/%/synonymy'] = array(
780
      'title' => cdm_taxonpage_tab_label('Synonymy'),
781
      'page callback' => 'cdm_dataportal_taxon_page_view',
782
      'access arguments' => array('access cdm content'),
783
      'type' => MENU_LOCAL_TASK,
784
      'weight' => 4,
785
      'page arguments' => array(2, "synonymy", 4)
786
      , // Expected callback arguments: taxon_uuid and ...
787
    );
788
    $items['cdm_dataportal/taxon/%/images'] = array( // Images
789
      'title' => cdm_taxonpage_tab_label('Images'),
790
      'page callback' => 'cdm_dataportal_taxon_page_view',
791
      'access arguments' => array('access cdm content'),
792
      'type' => MENU_LOCAL_TASK,
793
      'weight' => 5,
794
      'page arguments' => array(2, "images")
795
      , // Expected callback arguments: taxon_uuid.
796
    );
797

    
798
    $items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
799
      'title' => cdm_taxonpage_tab_label('Specimens'),
800
      'page callback' => 'cdm_dataportal_taxon_page_view',
801
      'access arguments' => array('access cdm content'),
802
      'type' => MENU_LOCAL_TASK,
803
      'weight' => 6,
804
      'page arguments' => array(2, "specimens")
805
      , // Expected callback arguments: taxon_uuid.
806
    );
807

    
808
    $items['cdm_dataportal/taxon/%/keys'] = array( // Keys
809
      'title' => cdm_taxonpage_tab_label('Keys'),
810
      'page callback' => 'cdm_dataportal_taxon_page_view',
811
      'access arguments' => array('access cdm content'),
812
      'type' => MENU_LOCAL_TASK,
813
      'weight' => 6,
814
      'page arguments' => array(2, "keys")
815
      , // Expected callback arguments: taxon_uuid.
816
    );
817

    
818
    $items['cdm_dataportal/taxon/%/experts'] = array( // Experts
819
      'title' => cdm_taxonpage_tab_label('Experts'),
820
        'page callback' => 'cdm_dataportal_taxon_page_view',
821
        'access arguments' => array('access cdm content'),
822
        'type' => MENU_LOCAL_TASK,
823
        'weight' => 6,
824
        'page arguments' => array(2, "experts")
825
    , // Expected callback arguments: taxon_uuid.
826
    );
827

    
828
    $items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(
829
        'page callback' => 'cdm_dataportal_taxon_autosuggest',
830
        'access arguments' => array('access cdm content'),
831
        'page arguments' => array(3,4,5),
832
        'type' => MENU_CALLBACK
833
    );
834
  }
835

    
836
  // --- refresh link for all cdmnode types
837
  foreach (cdm_get_nodetypes() as $type=>$name) {
838
    $items['cdm_dataportal/' . $name . '/%/refresh'] = array(
839
        'title' => 'Refresh',
840
        'page callback' => 'cdm_dataportal_refresh_node',
841
        'access arguments' => array('administer cdm_dataportal'),
842
        'type' => MENU_LOCAL_TASK,
843
        'weight' => 100,
844
        'page arguments' => array($name, 2)
845
    );
846
  }
847

    
848
  return $items;
849
}
850

    
851
/**
852
 * Implements hook_init().
853
 *
854
 */
855
function cdm_dataportal_init() {
856
  if (!path_is_admin(current_path())) {
857
    //FIXME To add CSS or JS that should be present on all pages, modules
858
    //      should not implement this hook, but declare these files in their .info file.
859
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
860
    // drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
861
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
862
  } else {
863
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');
864
  }
865

    
866
  if(variable_get('cdm_debug_mode', FALSE)){
867
    $file = 'temporary://drupal_debug.txt';
868
    file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
869
  }
870

    
871
  $bibliography_settings = get_bibliography_settings();
872
  $enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
873
  FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
874
}
875

    
876
function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
877

    
878
  $base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
879

    
880
  if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
881
    // force reloading of all and notify user about this special loading
882
    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: ')
883
        . l('Back to tabbed taxon page', $base_path));
884
    $base_path .= '/all';
885
  } else {
886
    drupal_set_message(t('The level 2 cache has been cleared for this page'));
887
  }
888

    
889
  $parameters['cacheL2_refresh'] ='1';
890

    
891

    
892
  drupal_goto($base_path, array('query' => $parameters));
893
}
894

    
895
/**
896
 * Implements hook_requirements($phase)
897
 */
898
function cdm_dataportal_requirements($phase) {
899
    $requirements = array();
900
    if($phase == 'runtime'){
901

    
902
    }
903
    return $requirements;
904
}
905

    
906
/**
907
 * Implements hook_block_info().
908
 */
909
function cdm_dataportal_block_info() {
910

    
911
    // $block[0]["info"] = t("CDM DataPortal DevLinks");
912
    // $block[1]["info"] = t("CDM DataPortal Credits");
913
    $block["2"] = array(
914
        "info" => t("CDM - Search Taxa"),
915
        "cache" => DRUPAL_NO_CACHE
916
      );
917
    // $block[3]["info"] = t("CDM Filters");
918
    $block["4"]["info"] = t("CDM  - Dataportal Print");
919
    $block["keys"]["info"] = t("CDM - Identification keys");
920
    $block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');
921
    $block["classification_breadcrumbs"] =  array(
922
        'info' => t('CDM - Classification breadcrumbs'),
923
        'cache' => DRUPAL_CACHE_PER_PAGE
924
      );
925
    $block["taxonomic_children"] =  array(
926
      'info' => t('CDM - Taxonomic children'),
927
      'cache' => DRUPAL_CACHE_PER_PAGE
928
    );
929
    $block["back_to_search_results"] =  array(
930
      'title' => '<none>',
931
      'info' => t('CDM - Back to search Results'),
932
      'cache' => DRUPAL_CACHE_PER_PAGE,
933
      'visibility' => BLOCK_VISIBILITY_LISTED,
934
      'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!!
935
    );
936
  $block['registrations_search_filter'] =  array(
937
    'title' => 'Filter registrations',
938
    'info' => t('CDM - Registrations search filter'),
939
    'cache' => DRUPAL_CACHE_PER_PAGE,
940
    'visibility' => BLOCK_VISIBILITY_NOTLISTED,
941
    'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!
942
  );
943
  $block['registrations_search_taxongraph'] =  array(
944
    'title' => 'Taxonomic registration search',
945
    'info' => t('CDM - Registrations search by taxon graph'),
946
    'cache' => DRUPAL_CACHE_PER_PAGE,
947
    'visibility' => BLOCK_VISIBILITY_NOTLISTED,
948
    'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!
949
  );
950
  $block['registrations_search'] =  array(
951
    'title' => 'Search',
952
    'info' => t('CDM - Registrations search combining filter and taxon graph search' ),
953
    'cache' => DRUPAL_CACHE_PER_PAGE,
954
    'visibility' => BLOCK_VISIBILITY_NOTLISTED,
955
    'pages' => "cdm_dataportal/registration-search\ncdm_dataportal/registration-search/*", // multiple page paths separated by "\n"!!!
956
  );
957
  $block['utis_search'] =  array(
958
    'title' => 'UTIS Search',
959
    'info' => t('Query the Unified Taxonomic Information Service (UTIS)' ),
960
    'cache' => DRUPAL_CACHE_PER_PAGE,
961
    'visibility' => BLOCK_VISIBILITY_NOTLISTED
962
  );
963
  return $block;
964
}
965

    
966
/**
967
 * Implements hook_block_view().
968
 */
969
function cdm_dataportal_block_view($delta) {
970
  // TODO Rename block deltas (e.g. '2') to readable strings.
971
  switch ($delta) {
972
    // case 'delta-1':
973
    // $block['subject'] = t('Credits');
974
    // $block['content'] = theme('cdm_credits');
975
    // return $block;
976
    case '2':
977
      $block['subject'] = t('Search taxa');
978
      $form = drupal_get_form('cdm_dataportal_search_taxon_form');
979
      $block['content'] = drupal_render($form);
980

    
981
      if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
982
        $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
983
      }
984
      if (variable_get(CDM_SEARCH_BLAST_ENABLED)){
985
          $block['content'] .= '<div>' . l(t('Blast Search'), 'cdm_dataportal/search/blast') . '</div>';
986
      }
987
      return $block;
988
    case '4':
989
      $block['subject'] = '';
990
      $block['content'] = theme('cdm_print_button');
991
      return $block;
992
    case "keys":
993
      $block['subject'] = t('Identification Keys');
994
      $block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
995
      return $block;
996
    case "fundedByEDIT":
997
      // t('Funded by EDIT');
998
      $text = '<none>';
999
      $block['subject'] = $text;
1000
      $img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
1001
      $block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
1002
        'attributes' => array("target" => "EDIT"),
1003
        'absolute' => TRUE,
1004
        'html' => TRUE,
1005
      ));
1006
      return $block;
1007
    case 'classification_breadcrumbs':
1008
      $taxon_uuid = get_current_taxon_uuid();
1009
      $block['subject'] = '<none>';
1010
      $block['content'] = compose_classification_breadcrumbs($taxon_uuid);
1011
      return $block;
1012
    case 'taxonomic_children':
1013
      $taxon_uuid = get_current_taxon_uuid();
1014
      $block['subject'] = '<none>';
1015
      $block['content'] = compose_taxonomic_children($taxon_uuid);
1016
      return $block;
1017
    case 'back_to_search_results':
1018
      $block['subject'] = '<none>';
1019
      if (isset($_SESSION['cdm']['search'])) {
1020
        $block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
1021
      }
1022
      return $block;
1023
    case 'registrations_search_filter':
1024
      $block['subject'] = '<none>';
1025
      $block['content'] = drupal_get_form('cdm_dataportal_search_registration_filter_form'); // see cdm_dataportal_search_registration_filter_form($form, &$form_state)
1026
      return $block;
1027
    case 'registrations_search_taxongraph':
1028
      $block['subject'] = '<none>';
1029
      $block['content'] = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form'); // see cdm_dataportal_search_registration_taxongraph_form($form, &$form_state)
1030
      return $block;
1031
    case 'registrations_search':
1032
      _add_js_ui_accordion();
1033
      _add_font_awesome_font();
1034
      $block['subject'] = '<none>';
1035
      $filter_form = drupal_get_form('cdm_dataportal_search_registration_filter_form');
1036
      $filter_form['#prefix'] = '<div>';
1037
      $filter_form['#suffix'] = '</div>';
1038
      $taxongraph_form = drupal_get_form('cdm_dataportal_search_registration_taxongraph_form');
1039
      $taxongraph_form['#prefix'] = '<div>';
1040
      $taxongraph_form['#suffix'] = '</div>';
1041
      $block['content'] = array(
1042
        'accordion' => array(
1043
          '#markup' => '',
1044
          '#prefix' => '<div id="accordion">',
1045
          '#suffix' => '</div>',
1046
          'content' => array(
1047
            array('#markup' => '<h3>Filter</h3>'),
1048
            $filter_form,
1049
            array('#markup' => '<h3>Taxon graph</h3>'),
1050
            $taxongraph_form,
1051
          )
1052
        )
1053
    );
1054
       return $block;
1055
    case 'utis_search':
1056
      _add_js_utis_client('.utis_client');
1057
      $block['subject'] = '<none>';
1058
      $block['content'] = '<div class="utis_client"></div>';
1059
      return $block;
1060
    default:
1061
      return null;
1062
  }
1063
}
1064

    
1065

    
1066
/**
1067
 * Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
1068
 *
1069
 * @return string
1070
 *   the taxon uuid or NULL
1071
 */
1072
function get_current_taxon_uuid()
1073
{
1074
  static $taxon_uuid;
1075

    
1076
  if(!isset($taxon_uuid)){
1077
    if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
1078
      $taxon_uuid = $_REQUEST['currentTaxon'];
1079
    } else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
1080
      $taxon_uuid = arg(2);
1081
    } else {
1082
      $taxon_uuid = null;
1083
    }
1084
  }
1085

    
1086
  return $taxon_uuid;
1087
}
1088

    
1089
/**
1090
 * Returns the currently classification tree in use.
1091
 *
1092
 * @return string
1093
 *   The uuid of the currently focused classification
1094
 */
1095
function get_current_classification_uuid() {
1096
  if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
1097
    return $_SESSION['cdm']['taxonomictree_uuid'];
1098
  }
1099
  else {
1100
    return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
1101
  }
1102
}
1103

    
1104
/*
1105
 function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
1106
 $_SESSION['cdm'] = NULL;
1107
 if(is_string($cdm_ws_uri_update)){
1108
 $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
1109
 }
1110
 }
1111

    
1112
 function cdm_dataportal_session_validate(){
1113
 if(!isset($_SESSION['cdm']['ws_uri'])){
1114
 $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
1115
 } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
1116
 cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
1117
 }
1118
 }
1119
 */
1120

    
1121
/**
1122
 * creates a  selector form for taxonomic trees.
1123
 *
1124
 * @return array
1125
 *  a drupal form array
1126
 */
1127
function cdm_taxonomictree_selector() {
1128
  _add_js_treeselector();
1129

    
1130
  $form = drupal_get_form('cdm_taxonomictree_selector_form');
1131
  return $form;
1132
}
1133

    
1134
/**
1135
 * @todo Please document this function.
1136
 * @see http://drupal.org/node/1354
1137
 *
1138
 * @deprecated use compose_classification_selector instead
1139
 */
1140
function cdm_taxonomictree_selector_form($form, &$form_state) {
1141

    
1142
  $url = url('cdm_api/setvalue/session', array('query' => NULL));
1143
  $form['#action'] = $url;
1144

    
1145
  $form['var'] = array(
1146
    '#weight' => -3,
1147
    '#type' => 'hidden',
1148
    '#value' => '[cdm][taxonomictree_uuid]',
1149
  );
1150

    
1151
  $destination_array = drupal_get_destination();
1152
  $destination = $destination_array['destination'];
1153

    
1154
  $form['destination'] = array(
1155
    '#weight' => -3,
1156
    '#type' => 'hidden',
1157
    '#value' =>  $destination,
1158
  );
1159

    
1160
  $options = cdm_get_taxontrees_as_options();
1161
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1162
  if($taxontree_includes){
1163
    $filtered_options = array();
1164
    foreach($options as $uuid=>$label){
1165
      if(!empty($taxontree_includes[$uuid])){
1166
        $filtered_options[$uuid] = $label;
1167
      }
1168
    }
1169
    $options = $filtered_options;
1170
  }
1171

    
1172
  $form['val'] = array(
1173
    '#type' => 'select',
1174
    '#title' => t('Available classifications'),
1175
    '#default_value' => get_current_classification_uuid(),
1176
    '#options' => $options,
1177
    '#attributes' => array('class' => array('highlite-first-child')),
1178
  );
1179

    
1180
  return $form;
1181

    
1182
}
1183

    
1184
/**
1185
 *
1186
 * @ingroup compose
1187
 */
1188
function compose_classification_selector() {
1189

    
1190
  $destination_array = drupal_get_destination();
1191
  $destination = $destination_array['destination'];
1192

    
1193
  $options = cdm_get_taxontrees_as_options();
1194
  $items = array();
1195
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1196

    
1197
  $current_classification_uuid = get_current_classification_uuid();
1198

    
1199

    
1200
  foreach($options as $uuid=>$label){
1201
    if(!$taxontree_includes || !empty($taxontree_includes[$uuid])){
1202

    
1203
      $class_attributes = '';
1204
      if($current_classification_uuid == $uuid){
1205
        $class_attributes  = array('focused');
1206
      }
1207
      $items[] = array(
1208
        'data' => l($label,
1209
          'cdm_api/setvalue/session',
1210
          array(
1211
            'query' => array(
1212
              'destination' => $destination,
1213
              'val' => $uuid,
1214
              'var' => '[cdm][taxonomictree_uuid]'
1215
            ),
1216
          )
1217
        ),
1218
        'class' => $class_attributes
1219
      );
1220
    }
1221
  }
1222

    
1223
  $render_array = array(
1224
    '#theme' => 'item_list',
1225
    '#type' => 'ul',
1226
    '#items' => $items
1227
  );
1228

    
1229
  return $render_array;
1230
}
1231

    
1232

    
1233
/* UNREACHABLE since action of form directly links to view.
1234
 function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
1235

    
1236
 $_SESSION['cdm']['search'] = $form_values;
1237
 //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
1238
 return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
1239
 //$paramstr = compose_url_prameterstr($form_values);
1240
 //return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
1241
 }
1242
 */
1243
/* ====================== menu callback functions ====================== */
1244
/**
1245
 * @todo Please document this function.
1246
 * @see http://drupal.org/node/1354
1247
 */
1248
/*
1249
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
1250
  static $comment_node_disabled =  0;
1251
  static $comment_node_read_only =  1;
1252
  static $comment_node_read_write =  2;
1253

    
1254
  if ($form_id == 'node_type_form'
1255
   && isset($form['identity']['type'])
1256
   && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
1257
  ) {
1258
    $form['workflow']['comment'] = array(
1259
      '#type' => 'radios',
1260
      '#title' => t('Default comment setting'),
1261
      '#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
1262
      '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
1263
      '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
1264
    );
1265
  }
1266
}
1267
*/
1268

    
1269
/**
1270
 * Displays a list of the known taxonomic names.
1271
 *
1272
 * When the list of taxonomic names is displayed, long lists are split up into
1273
 * multiple pages.
1274
 *
1275
 * TODO: Parameters are still preliminary.
1276
 *
1277
 * @param string $beginsWith
1278
 * @param string $page
1279
 *   Page number to diplay defaults to page 1.
1280
 * @param bool $onlyAccepted
1281
 */
1282
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
1283

    
1284
  $out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
1285

    
1286
  /*
1287
  // FIXME the filter for accepted names will be a form element, thus this
1288
  // widget should be generated via form api preferably as block.
1289
  $out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
1290
  $out .= theme('cdm_dataportal_widget_names_list', $names, $page);
1291
  $out .= theme('cdm_listof_taxa', $taxonPager);
1292
  return $out;
1293
  */
1294
}
1295

    
1296
/**
1297
 * @todo Please document this function.
1298
 * @see http://drupal.org/node/1354
1299
 * @throws Exception
1300
 */
1301
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
1302

    
1303
  cdm_check_valid_portal_page();
1304

    
1305
  return compose_cdm_reference_page($uuid);
1306
}
1307

    
1308
/**
1309
 * Creates a view on a all references contained in the portal.
1310
 *
1311
 * This function is used at the path cdm_dataportal/reference/list
1312
 */
1313
function cdm_dataportal_view_reference_list($pageNumber) {
1314
  $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
1315
  cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
1316
}
1317

    
1318
/**
1319
 * @todo Please document this function.
1320
 * @see http://drupal.org/node/1354
1321
 */
1322
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
1323

    
1324
  cdm_check_valid_portal_page();
1325

    
1326
  $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
1327
  if (!$media) {
1328
    drupal_set_title(t('Media does not exist'), PASS_THROUGH);
1329
    return "";
1330
  }
1331
  return theme('cdm_media_page', array(
1332
    'media' => $media,
1333
    'mediarepresentation_uuid' => $mediarepresentation_uuid,
1334
    'partId' => $part,
1335
    ));
1336
}
1337

    
1338
/**
1339
 * @todo Please document this function.
1340
 * @see http://drupal.org/node/1354
1341
 */
1342
function _load_taxonBase(&$taxonBase) {
1343
  if (isset($taxonBase->uuid)) {
1344
    $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
1345
    $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
1346
    $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
1347
  }
1348
}
1349

    
1350
/**
1351
 * Loads the media associated to the given taxon from the cdm server.
1352
 * The aggregation settings regarding taxon relathionships and
1353
 * taxonnomic childen are taken into account.
1354
 *
1355
 * The media lists are cached in a static variable.
1356
 *
1357
 * @param Taxon $taxon
1358
 *   A CDM Taxon entity
1359
 *
1360
 * @return array
1361
 *   An array of CDM Media entities
1362
 *
1363
 */
1364
  function _load_media_for_taxon($taxon) {
1365

    
1366
  static $media = NULL;
1367

    
1368
  if(!isset($media)) {
1369
    $media = array();
1370
  }
1371
  if (!isset($media[$taxon->uuid])) {
1372

    
1373

    
1374
    $mediaQueryParameters = taxon_media_query_parameters();
1375

    
1376
    $ws_endpoint = NULL;
1377
    if ( $mediaQueryParameters['includeTaxonomicChildren']) {
1378
      $ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1379
    } else {
1380
      $ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1381
    }
1382
    // this parameter is not yet used by the CDM_WS_PORTAL_TAXON_*MEDIA
1383
    // services
1384
    unset($mediaQueryParameters['includeTaxonomicChildren']);
1385

    
1386
    $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1387
        array(
1388
            $taxon->uuid,
1389
        ),
1390
        queryString($mediaQueryParameters)
1391
       );
1392
  }
1393

    
1394
  return $media[$taxon->uuid];
1395
}
1396

    
1397
/**
1398
 *
1399
 * @param Taxon $taxon
1400
 *   A CDM Taxon entitiy
1401
 *
1402
 * @return array
1403
 *   An array of CDM SpecimenOrObservation entities
1404
 *
1405
function _load_occurences_for_taxon($taxon){
1406

    
1407
  static $occurences = NULL;
1408

    
1409
  if(!isset($occurences)) {
1410
    $occurences = array();
1411
  }
1412

    
1413
  if (!isset($occurences[$taxon->uuid])){
1414

    
1415
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1416
    $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1417
    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1418

    
1419
    $by_associatedtaxon_query = http_build_query(array(
1420
        'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1421
        'relationships' => implode(',', $relationship_choice['direct']),
1422
        'pageSize' => null // all hits in one page
1423
    )
1424
    );
1425

    
1426
    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1427
        null,
1428
        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1429
    );
1430

    
1431

    
1432
    if(isset($pager->records[0])){
1433
      $occurences[$taxon->uuid] =  $pager->records;
1434
    }
1435
  }
1436
  return $occurences[$taxon->uuid];
1437
}
1438
 */
1439

    
1440
/**
1441
 * Gets a Drupal variable, string or array and returns it.
1442
 *
1443
 * Similar to the variable_get() function of Drupal, except that this function
1444
 * is able to handle arrays correctly. This function is especially useful
1445
 * when dealing with collections of settings form elements (#tree = TRUE).
1446
 *
1447
 * @param string $variableKey
1448
 *   The Unique key of the Drupal variable in the Drupal variables table.
1449
 * @param string $defaultValueString
1450
 *   A string as for example derived from a CONSTANT.
1451
 *
1452
 * @return mixed
1453
 *   usually an array, depending on the nature of the variable.
1454
 *
1455
 * TODO compare with get_array_variable_merged() duplicate functions?
1456
 * @deprecated rather use get_array_variable_merged() since this function
1457
 * used an array as second parameter
1458
 */
1459
function mixed_variable_get($variableKey, $defaultValueString) {
1460
  $systemDefaults = unserialize($defaultValueString);
1461
  $storedSettings = variable_get($variableKey, array());
1462
  if (is_array($storedSettings)) {
1463
    // TODO better use drupal_array_merge_deep() ?
1464
    $settings = array_merge($systemDefaults, $storedSettings);
1465
  }
1466
  else {
1467
    $settings = $systemDefaults;
1468
  }
1469
  return $settings;
1470
}
1471

    
1472
/**
1473
 * Recursive function to convert an object into an array.
1474
 * also subordinate objects will be converted.
1475
 *
1476
 * @param object $object
1477
 *  the object to be converted
1478
 * @return array
1479
 *  The array
1480
 */
1481
function object_to_array($object) {
1482
  if(is_object($object) || is_array($object)) {
1483
    $array = (array)$object;
1484
    foreach ($array as $key=>$value){
1485
      $array[$key] = object_to_array($value);
1486
    }
1487
    return $array;
1488
  } else {
1489
    return $object;
1490
  }
1491
}
1492

    
1493
/**
1494
 * Searches the $collection for the cdm entitiy given as $element.
1495
 *
1496
 * The elements are compared by their UUID.
1497
 *
1498
 * @param $element
1499
 *  the CDM entitiy to search for
1500
 * @param $collection
1501
 *  the list of CDM entities to search in
1502
 *
1503
 * @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1504
 *
1505
 */
1506
function contains_cdm_entitiy($element, $collection) {
1507
  $result = FALSE;
1508
  foreach ($collection as $a) {
1509
    if ($a->uuid == $element->uuid) {
1510
      $result = TRUE;
1511
    }
1512
  }
1513
  return $result;
1514
}
1515

    
1516
/**
1517
 * Filters the array $entity_list of CDM entities by the list
1518
 * of $excludes. Any element contained in the $excludes will be removed
1519
 * from included int the returned list.
1520
 *
1521
 * If the $entity_list is not an array the $excludes will be returned.
1522
 */
1523
function filter_cdm_entity_list($entity_list, $excludes) {
1524
  if (is_array($entity_list)) {
1525
    $result = $entity_list;
1526
    if ($excludes) {
1527
      foreach ($excludes as $exclude) {
1528
        if (!contains_cdm_entitiy($exclude, $entity_list)) {
1529
          $result[] = $exclude;
1530
        }
1531
      }
1532
    }
1533
  }
1534
  else {
1535
    $result = $excludes;
1536
  }
1537
  return $result;
1538
}
1539

    
1540
/**
1541
 * Wraps the given $html string into a render array suitable for drupal_render()
1542
 *
1543
 * @param $html
1544
 *   the html string, see
1545
 *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1546
 * @param $weight
1547
 *   A positive or negative number (integer or decimal).
1548
 *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1549
 * @param $prefix
1550
 *   Optional markup for the '#prefix' element of the render array
1551
 * @param $suffix
1552
 *   Optional markup for the '#suffix' element of the render array
1553
 *
1554
 * @return array
1555
 *   A render array
1556
 *
1557
 */
1558
function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1559
  $render_array = array(
1560
    '#markup' => $html
1561
      );
1562
  if (is_numeric($weight)) {
1563
    $render_array['#weight'] = $weight;
1564
  }
1565
  if($prefix){
1566
    $render_array['#prefix'] = $prefix;
1567
  }
1568
  if($suffix) {
1569
    $render_array['#suffix'] = $suffix;
1570
  }
1571
  return $render_array;
1572
}
1573

    
1574
/**
1575
 * Loads the subgraph of a given PolytomousKeyNode.
1576
 *
1577
 * Loads the subgraph of the given PolytomousKeyNode recursively from
1578
 * the CDM REST service.
1579
 *
1580
 * @param mixed $polytomousKeyNode
1581
 *   PolytomousKeyNode passed by reference.
1582
 *
1583
 * @return void
1584
 */
1585
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1586

    
1587
  if (!$polytomousKeyNode) {
1588
    return;
1589
  }
1590
  if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1591
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1592
    return;
1593
  }
1594
  if (!is_uuid($polytomousKeyNode->uuid)) {
1595
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1596
    return;
1597
  }
1598

    
1599
  $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1600

    
1601
  if (!$polytomousKeyNode) {
1602
    // drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1603
    return;
1604
  }
1605

    
1606
  // Load children.
1607
  foreach ($polytomousKeyNode->children as &$childNode) {
1608
    _load_polytomousKeySubGraph($childNode);
1609
  }
1610

    
1611
  // Load subkey.
1612
  $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1613

    
1614
  // Load taxon.
1615
  $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1616
  _load_taxonBase($polytomousKeyNode->taxon);
1617
  return;
1618
}
1619

    
1620
/**
1621
 * @todo Please document this function.
1622
 * @see http://drupal.org/node/1354
1623
 */
1624
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1625

    
1626
  cdm_check_valid_portal_page();
1627

    
1628
  $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1629
  if (!$polytomousKey) {
1630
    drupal_set_title(t('Polytomous key does not exist'), PASS_THROUGH);
1631
    return "";
1632
  }
1633

    
1634
  $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1635
  if (is_array($sourcePager->records)) {
1636
    $polytomousKey->sources = $sourcePager->records;
1637
    // $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1638
  }
1639

    
1640
  $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1641
  if (is_array($annotationPager->records)) {
1642
    $polytomousKey->annotations = $annotationPager->records;
1643
  }
1644

    
1645
  _load_polytomousKeySubGraph($polytomousKey->root);
1646
  return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1647
}
1648

    
1649
/**
1650
 * Creates a taxon page view or a chapter of it.
1651
 *
1652
 * The taxon page gives detailed information on a taxon, it shows:
1653
 *  - Taxon name.
1654
 *  - Full list of synonyms homotypic synonyms on top, followed by the
1655
 *    heterotypic and finally followed by misapplied names.
1656
 *    The list is ordered historically.
1657
 *  - All description associated with the taxon.
1658
 *
1659
 * @param string $uuid
1660
 * @param string $chapter
1661
 *   Name of the part to display, valid values are:
1662
 *   'description', 'images', 'synonymy', 'specimens', 'all'.
1663
 *
1664
 * @return string
1665
 */
1666
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
1667

    
1668
  cdm_check_valid_taxon_page($chapter);
1669
  cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1670

    
1671

    
1672
  // Display the page for the taxon defined by $uuid.
1673
  // set_last_taxon_page_tab(arg(3));
1674
  $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
1675
  if (!empty($taxonpage)) {
1676
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1677
    return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1678
  }
1679
  else {
1680
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1681
    return '';
1682
  }
1683
}
1684

    
1685
/**
1686
 * This function will generate the taxon page part ($chapter) and returns a taxonpage object
1687
 * which has two fields, one for the page title and one for the content. Later on in the
1688
 * process chain the value contained in these fields will be passed to the cdm_node_show()
1689
 * function as the function parameters $title and $content.
1690
 *
1691
 * @param string $uuid
1692
 *   the uuid of the taxon to show
1693
 * @param string $chapter
1694
 *   Name of the part to display, valid values are:
1695
 *   'description', 'images', 'synonymy', 'all'.
1696
 *
1697
 * @return object with the following fields:
1698
 *   - title : the title of the page
1699
 *   - content: the content of the page
1700
 *
1701
 * @throws Exception
1702
 *
1703
 */
1704
function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1705
  // Taxon object.
1706
  $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1707
  if (empty($taxon)) {
1708
    drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1709
    return null;
1710
  }
1711
  $taxonpage = new stdClass();
1712

    
1713
  $taxonpage->title = theme('cdm_taxon_page_title', array(
1714
    'taxon' => $taxon
1715
  ));
1716

    
1717
  // Check if the taxon id contained in the currently selected tree.
1718
  $taxon_in_current_classification = taxon_in_current_classification($uuid);
1719

    
1720
  if (!$taxon_in_current_classification) {
1721
    $classifications = get_classifications_for_taxon($taxon);
1722
    RenderHints::pushToRenderStack('not_in_current_classification');
1723
    $taxon_name_markup = render_taxon_or_name($taxon);
1724

    
1725
    if (count($classifications) == 0) {
1726
      drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
1727
        array(
1728
        '!taxonname' => $taxon_name_markup,
1729
        )
1730
      ), 'warning');
1731
    }
1732
    else {
1733
      $trees = '';
1734
      foreach ($classifications as $classification) {
1735
        if (isset($classification->titleCache)) {
1736
          $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1737
        }
1738
      }
1739

    
1740
      drupal_set_message(format_plural(count($trees),
1741
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in this one: !trees',
1742
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1743
          array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1744
        ) ,
1745
        'warning');
1746
    }
1747
    RenderHints::popFromRenderStack();
1748
  }
1749

    
1750
  // Render the taxon page.
1751
  $render_array = compose_cdm_taxon_page($taxon, $chapter);
1752
  $taxonpage->content = drupal_render($render_array);
1753

    
1754
  return $taxonpage;
1755
}
1756

    
1757

    
1758
function cdm_dataportal_specimen_by_accession_number_page_view($accession_number)
1759
{
1760
  cdm_check_valid_portal_page();
1761

    
1762
  $specimenpage = specimen_by_accession_number_view($accession_number);
1763

    
1764
  if (!empty($specimenpage)) {
1765
    return cdm_node_show_simulate($specimenpage->content);
1766
  }
1767
  else {
1768
    return '';
1769
  }
1770

    
1771

    
1772
}
1773

    
1774
/**
1775
 * Creates a specimen page view.
1776
 * @param string $uuid the UUID of the specimen
1777
 * @return array|string
1778
 */
1779
function cdm_dataportal_specimen_page_view($uuid) {
1780

    
1781
    cdm_check_valid_portal_page();
1782
    $specimenpage = cdm_dataportal_specimen_view($uuid);
1783
    if (!empty($specimenpage)) {
1784
        return cdm_node_show_simulate($specimenpage->content);
1785
    }
1786
    else {
1787
        return '';
1788
    }
1789
}
1790

    
1791

    
1792
/**
1793
 * Creates a specimen page view.
1794
 * @param string $uuid the UUID of the specimen
1795
 * @return object
1796
 *  The page object with the following fields:
1797
 *   - 'title': the page title
1798
 *   - 'content' : the page content rendered as markup
1799
 */
1800
function specimen_by_accession_number_view($accession_number = null) {
1801

    
1802
  $field_unit_dto = cdm_ws_get(CDM_WS_OCCURRENCE_ACCESSION_NUMBER, null, 'accessionNumber=' . $accession_number);
1803

    
1804
  // Display the page for the specimen defined by $uuid.
1805
  if (isset($field_unit_dto)){
1806
    $dto_array = array($field_unit_dto);
1807
    $specimen_array = specimen_render_array_items($dto_array);
1808
    $specimen_table = array(
1809
      '#theme' => 'table',
1810
      '#weight' => 2,
1811
      // prefix attributes and rows with '#' to let it pass toF the theme function,
1812
      // otherwise it is handled as child render array
1813
      '#attributes' => array('class' => 'specimens'),
1814
      '#rows' => array(),
1815
      '#prefix' => '<div id="specimens">',
1816
      '#suffix' => '</div>',
1817
    );
1818
    foreach($specimen_array as $value){
1819
      $renderArray = array(
1820
        '#theme' => 'item_list',
1821
        '#items' => array($value),
1822
        '#type' => 'ul');
1823
      $output = drupal_render($renderArray);
1824
      $specimen_table['#rows'][] = array(
1825
        // An array of table rows. Every row is an array of cells, or an associative array
1826
        'data' => array($output),
1827
        'class' =>  array(
1828
          'descriptionElement',
1829
          'descriptionElement_IndividualsAssociation'
1830
        ),
1831
      );
1832

    
1833

    
1834
    }
1835
    $specimenpage = new stdClass();
1836

    
1837
    $specimenpage->title = theme('theme_cdm_specimen_dto_page_title', array(
1838
      'specimen' => $field_unit_dto
1839
    ));
1840

    
1841
     $render_array['markup'] = $specimen_table;
1842
     $specimenpage->content = drupal_render($render_array);
1843
  }
1844

    
1845
  return $specimenpage;
1846
}
1847

    
1848

    
1849
/**
1850
 *
1851
 * Creates a specimen view.
1852
 * @param string $uuid the UUID of the specimen
1853
 * @return object
1854
 *    Page object with the fields
1855
 *    - title
1856
 *    - content
1857
 */
1858
function cdm_dataportal_specimen_view($uuid) {
1859
    //TODO: get the derivateDTO and don't call the webservice a second time in compose_cdm_specimen_page
1860
    $specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, $uuid);
1861
    if (empty($specimen)) {
1862
        drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1863
        return FALSE;
1864
    }
1865
    $specimenpage = new stdClass();
1866

    
1867
    $specimenpage->title = specimen_page_title($specimen);
1868

    
1869
    // Render the specimen page.
1870
    $render_array = compose_cdm_specimen_page($specimen);
1871
    $specimenpage->content = drupal_render($render_array);
1872

    
1873
    return $specimenpage;
1874
}
1875

    
1876
/**
1877
 *
1878
 * Creates a description view.
1879
 *
1880
 * @param string $uuid the UUID of the description
1881
 * @param null $descriptive_dataset_uuid the uuid of the data set which defines
1882
 * the display of the description detail page
1883
 *
1884
 * @return object Page object with the fields
1885
 * Page object with the fields
1886
 * - title
1887
 * - content
1888
 */
1889
function cdm_dataportal_description_view($uuid, $descriptive_dataset_uuid = NULL) {
1890
    $description = cdm_ws_get(CDM_WS_PORTAL_DESCRIPTION, $uuid);
1891
    $description_page = new stdClass();
1892
    if (empty($description)) {
1893
      $description_page->title = t('Description does not exist');
1894
      drupal_set_title($description_page->title, PASS_THROUGH); // not necessary if correctly implemented as drupal node
1895
      $description_page->content = "";
1896

    
1897
    } else {
1898
      $description_page->title = $description->titleCache;
1899
      drupal_set_title($description_page->title); // not necessary if correctly implemented as drupal node
1900

    
1901
      // Render the description page.
1902
      $render_array = compose_description_table($description->uuid, $descriptive_dataset_uuid);
1903
      if($render_array['title']){
1904
        $page_title = strip_tags($render_array['title']['#markup']);
1905
        drupal_set_title($page_title);
1906
        unset($render_array['title']);
1907
      }
1908
      $description_page->content = drupal_render($render_array);
1909
    }
1910

    
1911
    return $description_page;
1912
}
1913

    
1914
function cdm_dataportal_description_page_view($uuid, $descriptive_dataset_uuid = NULL) {
1915

    
1916
  cdm_check_valid_portal_page();
1917
  $descriptionpage = cdm_dataportal_description_view($uuid, $descriptive_dataset_uuid);
1918
  if (!empty($descriptionpage)) {
1919
    return cdm_node_show_simulate($descriptionpage->content);
1920
  }
1921
  else {
1922
    return NULL;
1923
  }
1924
}
1925

    
1926
/**
1927
 *
1928
 * Creates a named area view.
1929
 * @param string $uuid the UUID of the specimen
1930
 *  * @return object
1931
 *   An object with two fields:
1932
 *     - title: the page title
1933
 *     - content: the page content
1934
 */
1935

    
1936
function cdm_dataportal_named_area_view($uuid) {
1937
  $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid);
1938
  if (empty($named_area) || $named_area->class !== 'NamedArea') {
1939
    drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
1940
    return null;
1941
  }
1942
  $named_area_page = new stdClass();
1943

    
1944
  $named_area_page->title = $named_area->representation_L10n;
1945

    
1946
  // Render the specimen page.
1947
  $render_array = compose_cdm_named_area_page($uuid);
1948
  $named_area_page->content = drupal_render($render_array);
1949

    
1950
  return $named_area_page;
1951
}
1952

    
1953
function cdm_dataportal_named_area_page_view($uuid) {
1954

    
1955
  cdm_check_valid_portal_page();
1956

    
1957
  $named_area_page = cdm_dataportal_named_area_view($uuid);
1958
  if (!empty($named_area_page)) {
1959
    return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content);
1960
  }
1961
  else {
1962
    return '';
1963
  }
1964

    
1965

    
1966
}
1967

    
1968
/**
1969
 * Returns a name page as a Drupal node ready to be renderized by Drupal.
1970
 *
1971
 * The node page shows the taxon name title and the list of taxon related
1972
 * with such taxon. Name on the tree already in use.
1973
 *
1974
 * @param string $taxon_name_uuid
1975
 *   The uuid of the CDM TaxonName to show a name page for
1976
 * @param string $taxon_to_hide_uuid
1977
 *   A taxon which should not be displayed in the taxon list
1978
 * @param $redirect_to_taxon
1979
 *   Automatically redirect to the related taxon if there is only one
1980
 *   accepted taxon for this name.
1981
 * @param string $highlite_synonym_uuid
1982
 *   Optinal parameter wich takes another taxon uuid, if given the
1983
 *   target taxon pages will show the syonymy tab where the taxon
1984
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1985
 *   in case it is found on this page.
1986
 *
1987
 * @return mixed
1988
 *   The formatted name page as node.
1989
 */
1990
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL, $redirect_to_taxon = false) {
1991

    
1992
  cdm_check_valid_portal_page();
1993

    
1994
  $taxonname_page = cdm_dataportal_name_view(
1995
    is_uuid($taxon_name_uuid) ? $taxon_name_uuid : null,
1996
    is_uuid($taxon_to_hide_uuid) ? $taxon_to_hide_uuid : null,
1997
    $redirect_to_taxon == 'redirect_to_taxon',
1998
    is_uuid($synonym_uuid) ? $synonym_uuid : null);
1999
  if (!empty($taxonname_page)) {
2000
    return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
2001
  }
2002
  else {
2003
    return '';
2004
  }
2005
}
2006

    
2007
/**
2008
 * View function for a TaxonName page.
2009
 *
2010
 * The name page lists all taxa for which the name specified by the
2011
 * $taxon_name_uuid is being used. I case there is only one name the
2012
 * page automatically redirects ti the according taxon page. Otherwise
2013
 * the list of names is displayed.
2014
 *
2015
 * The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
2016
 * list of taxa. This is useful for example when referencing from a taxon
2017
 * to the name page and the referring taxon should not be repeaded in the
2018
 * name page.
2019
 *
2020
 *
2021
 * @param string $taxon_name_uuid
2022
 *   The uuid of the CDM TaxonName to show a name page for
2023
 * @param string $taxon_to_hide_uuid
2024
 *   A taxon which should not be displayed in the taxon list
2025
 * @param $redirect_to_taxon
2026
 *   Automatically redirect to the related taxon if there is only one
2027
 *   accepted taxon for this name.
2028
 * @param string $highlite_synonym_uuid
2029
 *   Optional parameter which takes another taxon uuid, if given the
2030
 *   target taxon pages will show the synonymy tab where the taxon
2031
 *   referenced by the $highlite_synonym_uuid will be highlighted
2032
 *   in case it is found on this page.
2033
 *
2034
 * @return object|boolean
2035
 *   An object with two fields:
2036
 *     - title: the page title
2037
 *     - content: the page content
2038
 *   or FALSE
2039
 *
2040
 */
2041
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $redirect_to_taxon, $highlite_synonym_uuid = NULL) {
2042
  // Getting the full taxonname object from the server.
2043
  $taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
2044
  if (!$taxon_name) {
2045
    drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
2046
    return FALSE;
2047
  }
2048
  cdm_load_tagged_full_title($taxon_name);
2049
  // Searching for all the taxa connected with the taxon name on the tree
2050
  // in use.
2051
  $name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
2052
  $restrictions = array(new Restriction("name.titleCache","EXACT", array($name->titleCache), 'AND'));
2053
  $init_strategy = array(
2054
    "name.titleCache",
2055
    "name.nomenclaturalReference.authorship",
2056
    "name.nomenclaturalReference.inReference.authorship",
2057
    "name.nomenclaturalReference.inReference.inReference.authorship",
2058
    "name.nomenclaturalReference.inReference.inReference.inReference.authorship"
2059
  );
2060
  $taxa = cdm_ws_fetch_all_by_restriction("Taxon", NULL, $restrictions, $init_strategy);
2061

    
2062
  // Removing the name where we came from.
2063
  foreach ($taxa as $k => &$taxon) {
2064
    if ($taxon->uuid == $taxon_to_hide_uuid) {
2065
      unset($taxa[$k]);
2066
    }
2067
  }
2068
  // Show the taxa list or go to the singular taxon.
2069
  if (sizeof($taxa) == 1 && $redirect_to_taxon) {
2070
    // redirect to the taxon if there is only one.
2071
    $singleTaxon = array_pop($taxa);
2072
    if ($singleTaxon->class != "Taxon") {
2073
      // It is a Synonym -> look for the accepted.
2074
      $accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid());
2075
      if (!empty($highlite_synonym_uuid)) {
2076
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
2077
      }
2078
      else {
2079
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
2080
      }
2081
    }
2082
    else {
2083
      // It is an accepted taxon.
2084
      if (!empty($highlite_synonym_uuid)) {
2085
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
2086
      }
2087
      else {
2088
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
2089
      }
2090
    }
2091
  }
2092
  else {
2093
    // display the name page content
2094
    $taxon_name_page = new stdClass();
2095
    $taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
2096
    $content = array();
2097

    
2098
    RenderHints::pushToRenderStack('name_page');
2099
    RenderHints::setFootnoteListKey('name_page');
2100
    $content['taxon_name'] = markup_to_render_array(render_taxon_or_name($taxon_name), null, '<div class="name-page-name">', '</div>');
2101

    
2102

    
2103
    // name relationships
2104
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $taxon_name->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
2105
    if(count($name_relations) > 0){
2106
      $content['name_relationships'] = compose_name_relationships_list($name_relations, $taxon_name->uuid, null);
2107
    }
2108

    
2109
    // type designations
2110
    $type_designations_render_array = compose_type_designations($taxon_name->uuid);
2111
    $content = array_merge($content, $type_designations_render_array);
2112
    // registrations
2113
    $registrationDTOs= cdm_ws_fetch_all(CDM_WS_REGISTRATION_DTO,  array('nameUuid' => $taxon_name_uuid));
2114
    if(isset($registrationDTOs) && count($registrationDTOs ) > 0 ){
2115
      $content['registrations'][] = markup_to_render_array('<h2>' . t("Registrations") . '</h2>') ;
2116
      foreach ($registrationDTOs as $regDTO){
2117
        $content['registrations'][] = compose_registration_dto_compact($regDTO);
2118
      }
2119
    }
2120

    
2121

    
2122
    // related taxa
2123
    $show_taxa_section = variable_get(CDM_NAME_PAGE_SECTION_TAXA, CDM_NAME_PAGE_SECTION_TAXA_DEFAULT);
2124
    if($show_taxa_section){
2125
      if ($taxa) {
2126
        $content['related_taxa_header'] = markup_to_render_array("<h2>Taxa for this name</h2>");
2127
        $content['related_taxa'] = compose_list_of_taxa($taxa);
2128
      }
2129
      else {
2130
        $content['related_taxa'] = markup_to_render_array('This name is not assigned to a taxon.', null, '<div class="no-taxon-message">', '</div>');
2131
      }
2132
    }
2133

    
2134
    $content['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));
2135

    
2136
    $taxon_name_page->content = $content;
2137
    RenderHints::popFromRenderStack();
2138
    RenderHints::clearFootnoteListKey();
2139
    return $taxon_name_page;
2140
  }
2141
}
2142

    
2143

    
2144
/**
2145
 * Returns a registration page as a Drupal node to be rendered by Drupal.
2146
 *
2147
 * @param string  $registration_identifier_encoded
2148
 *   The persistent identifier of the registration urlencoded.
2149
 * @return mixed
2150
 *   The formatted registration page as node.
2151
 */
2152
function cdm_dataportal_registration_page_view($registration_identifier_encoded) {
2153

    
2154
  cdm_check_valid_portal_page("/\/cdm_dataportal\/registration\/.*$/");
2155
  $registration_page = cdm_dataportal_registration_view($registration_identifier_encoded);
2156
  return cdm_node_show_simulate($registration_page);
2157
}
2158

    
2159
/**
2160
 * @param $registration_identifier_encoded
2161
 * @return array
2162
 *   The drupal render array for the registration view.
2163
 */
2164
function cdm_dataportal_registration_view($registration_identifier_encoded) {
2165

    
2166
  $registration_identifier = urldecode($registration_identifier_encoded);
2167

    
2168
  RenderHints::pushToRenderStack('registration_page');
2169
  RenderHints::setFootnoteListKey('registration_page');
2170

    
2171
  $render_array = array();
2172
  $registration_dto = cdm_ws_get(CDM_WS_REGISTRATION_DTO_BY_IDENTIFIER . $registration_identifier_encoded);
2173
  if($registration_dto){
2174

    
2175
    drupal_set_title(t('Registration Id:') . ' ' . $registration_identifier, PASS_THROUGH);
2176
    $render_array = compose_registration_dto_full($registration_dto, true);
2177

    
2178
  } else {
2179
    $status_text = cdm_ws_get(CDM_WS_REGISTRATION_STATUS_BY_IDENTIFIER, array($registration_identifier));
2180
    if(isset($status_text->String)) {
2181
      $status_text = strtolower($status_text->String);
2182
      if($status_text == 'preparation' || $status_text == 'curation'){
2183
        $status_text = 'in ' . $status_text;
2184
      }
2185
      drupal_set_title(t('Registration ' . $status_text), PASS_THROUGH);
2186
      //$status_message;
2187
      drupal_set_message("A registration with the identifier  " . $registration_identifier . " is " . $status_text, "status");
2188
    } else {
2189
      drupal_set_title(t('Registration not found'), PASS_THROUGH);
2190
      drupal_set_message("A registration with the identifier  " . $registration_identifier . " does not exist", "warning");
2191
    }
2192
  }
2193

    
2194
  $render_array = array(
2195
    '#prefix' => '<div id="registration">',
2196
    'registration' => $render_array,
2197
    '#suffix' => '</div>',
2198
  );
2199

    
2200
  RenderHints::popFromRenderStack();
2201
  RenderHints::clearFootnoteListKey();
2202

    
2203
  return $render_array ;
2204
}
2205

    
2206

    
2207
/**
2208
 * Creates a page with the advance search form.
2209
 *
2210
 * NOTE: The advance search form allows searching for taxa.
2211
 */
2212
function cdm_dataportal_view_search_advanced() {
2213
  drupal_set_title(t('Advanced search'), PASS_THROUGH);
2214
  return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
2215
}
2216

    
2217
/**
2218
 * Creates a page with the blast search form.
2219
 *
2220
 * NOTE: The advance search form allows searching for specimen in blast DB.
2221
 */
2222
function cdm_dataportal_view_search_blast() {
2223
    drupal_set_title(t('Blast search'), PASS_THROUGH);
2224
    return drupal_get_form('cdm_dataportal_search_blast_form');
2225
}
2226

    
2227
/**
2228
 * Creates a page with the search form for searching by taxon descriptions.
2229
 */
2230
function cdm_dataportal_view_search_taxon_by_description() {
2231
  drupal_set_title(t('Search by factual data'), PASS_THROUGH);
2232
  return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
2233
}
2234

    
2235
/**
2236
 * Executes the search and generates the result list of taxa.
2237
 */
2238
function cdm_dataportal_view_search_results_taxon() {
2239

    
2240
  $taxonPager = cdm_dataportal_search_taxon_execute();
2241

    
2242
  $showThumbnails = do_showThumbnails();
2243

    
2244
  $setSessionUri = url('cdm_api/setvalue/session', array(
2245
      'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
2246
  ));
2247

    
2248
  drupal_add_js('jQuery(document).ready(function() {
2249

    
2250
      // init
2251
      if(' . $showThumbnails . ' == 1){
2252
          jQuery(\'.media_gallery\').show(20);
2253
      } else {
2254
          jQuery(\'.media_gallery\').hide(20);
2255
      }
2256

    
2257
      // add change handler
2258
      jQuery(\'#showThumbnails input.showThumbnails\').change(
2259
      function(event){
2260
        var state = 0;
2261
        if(jQuery(this).is(\':checked\')){
2262
          jQuery(\'.media_gallery\').show(20);
2263
          state = 1;
2264
        } else {
2265
          jQuery(\'.media_gallery\').hide(20);
2266
        }
2267
        // store state in session variable
2268
        var uri = \'' . $setSessionUri . '\' + state;
2269
        jQuery.get(uri);
2270
      });
2271
  });',
2272
  array('type' => "inline", 'scope' => JS_DEFAULT));
2273

    
2274
  drupal_set_title(t('Search results'), PASS_THROUGH);
2275

    
2276
  return theme('cdm_search_taxa_results', array(
2277
    'pager' => $taxonPager,
2278
    'path' => 'cdm_dataportal/search/results/taxon',
2279
    ));
2280
}
2281

    
2282
/**
2283
 * Executes the blast search and generates the result list of specimen.
2284
 */
2285
function cdm_dataportal_view_search_results_specimen() {
2286

    
2287
    $specimenPager = cdm_dataportal_search_blast_execute();
2288

    
2289
    return theme('cdm_search_specimen_results', array(
2290
        'pager' => $specimenPager,
2291
        'path' => 'cdm_dataportal/search/results/specimen',
2292
    ));
2293
}
2294

    
2295

    
2296
/**
2297
 * Executes the search for registrations and generates the result list..
2298
 */
2299
function cdm_dataportal_view_search_registrations_results($mode = 'filter') {
2300

    
2301
  switch($mode ){
2302
    case 'taxongraph':
2303
      $block = block_load('cdm_dataportal', 'registrations_search_taxongraph');
2304
      $registration_pager = cdm_dataportal_search_registrations_taxongraph_execute();
2305
      break;
2306
    case 'filter':
2307
    default:
2308
      $block = block_load('cdm_dataportal', 'registrations_search_filter');
2309
      $registration_pager = cdm_dataportal_search_registrations_filter_execute();
2310
  }
2311
  $block->title = null;
2312

    
2313
  drupal_set_title(t('Search registrations'), PASS_THROUGH);
2314

    
2315
  $render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
2316
  $registrations_pager_array = compose_search_results($registration_pager, new RegistrationDTOComposeHandler());
2317
  $render_array = array_merge($render_array, $registrations_pager_array);
2318

    
2319
  return $render_array;
2320
}
2321

    
2322
/**
2323
 * Executes the search for registrations and generates the result list..
2324
 */
2325
function cdm_dataportal_view_search_agent() {
2326

    
2327
  $render_array = [];
2328
  $title = isset($_REQUEST['class']) && $_REQUEST['class'] ? $_REQUEST['class'] : 'Persons & Teams';
2329
  drupal_set_title(t($title), PASS_THROUGH);
2330
  // TODO $block = block_load('cdm_dataportal', 'search_agent_filter');
2331
  // $block->title = null;
2332
  // $render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
2333
  $pager = cdm_dataportal_search_agent_execute();
2334
  $pager_render_array = compose_search_results($pager, new AgentComposeHandler());
2335
  $render_array = array_merge($render_array, $pager_render_array);
2336
  return $render_array;
2337
}
2338

    
2339

    
2340
/**
2341
 * Provides the standard image which indicated a loading process
2342
 *
2343
 * @return string
2344
 *  The img html tag
2345
 */
2346
function loading_image_html() {
2347
  return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
2348
    . '/images/loading_circle_grey_16.gif" style="display:none;">';
2349
}
2350

    
2351
/**
2352
 * Returns the state of the the showThumbnails flag set in the
2353
 * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
2354
 *
2355
 * @return boolean
2356
 *    returns 1 if the flag is set
2357
 */
2358
function do_showThumbnails() {
2359
  static $showThumbnails = null;
2360

    
2361
  if($showThumbnails == null) {
2362
    $showThumbnails = 0;
2363
    if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
2364
      $showThumbnails = 0;
2365
      $search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
2366
      $showThumbnails = is_array($search_gallery_settings)
2367
        && isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
2368
        && (
2369
            $search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
2370
            $search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
2371
            $search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
2372
            )
2373
         ? 1 : 0;
2374

    
2375
       drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
2376
    }
2377
    $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
2378
    if (!is_numeric($showThumbnails)) {
2379
      $showThumbnails = 1;
2380
    }
2381
  }
2382

    
2383
  return $showThumbnails;
2384
}
2385

    
2386

    
2387

    
2388
/* ====================== other functions ====================== */
2389
/**
2390
 * Creates a URL to the taxon page specified by the $uuid parameter.
2391
 *
2392
 * The URL will be prepended with a path element to a specific taxon page tab.
2393
 *
2394
 * This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
2395
 * be set globally in the administrative settings or individually in the user
2396
 * profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
2397
 * the last portal will stay on this last tab.
2398
 *
2399
 * A third option is offerered by the $page_tab parameter which allows overwriting this
2400
 * internal mechanism by a specific value.
2401
 *
2402
 * @param string $uuid
2403
 *   The UUID of the taxon.
2404
 * @param string $page_tab
2405
 *   Overwriting the preset mechanism by defining specific value for the
2406
 *   taxon page tab.
2407
 * @return string
2408
 *   The created URL.
2409
 */
2410
function path_to_taxon($uuid, $page_tab = FALSE) {
2411

    
2412
  $tab = get_default_taxon_tab();
2413
  $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
2414

    
2415
  if (!$uuid) {
2416
    return FALSE;
2417
  }
2418

    
2419
  if ($page_tab) {
2420
    $url = 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
2421
  }
2422
  elseif (!$tab || strtolower($tab) == 'general') {
2423
    $url = 'cdm_dataportal/taxon/' . $uuid;
2424
  }
2425
  elseif (get_last_taxon_page_tab() &&   $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
2426
    $url = 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
2427
  }
2428
  else {
2429
    $url = 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
2430
  }
2431
  return $url;
2432
}
2433

    
2434
function path_to_description($uuid, $descriptive_dataset_uuid = NULL) {
2435

    
2436
    if (!$uuid) {
2437
        return FALSE;
2438
    }
2439
    else {
2440
      return 'cdm_dataportal/description/' . $uuid
2441
        . (is_uuid($descriptive_dataset_uuid) ? '/' . $descriptive_dataset_uuid : '');
2442
    }
2443
}
2444

    
2445
function path_to_specimen($uuid) {
2446

    
2447
    if (!$uuid) {
2448
        return FALSE;
2449
    }
2450
    else {
2451
        return 'cdm_dataportal/occurrence/' . $uuid;
2452
    }
2453
}
2454

    
2455
function path_to_specimen_by_accession_number($accession_number) {
2456

    
2457
    if (!$accession_number) {
2458
        return FALSE;
2459
    }
2460
    else {
2461
        return 'cdm_dataportal/specimen/accession_number/' . $accession_number;
2462
    }
2463
}
2464

    
2465
function path_to_named_area($uuid) {
2466

    
2467
  if (!$uuid) {
2468
    return FALSE;
2469
  }
2470
  else {
2471
    return 'cdm_dataportal/named_area/' . $uuid;
2472
  }
2473
}
2474

    
2475
/**
2476
 * Creates a URL to show a synonmy in the according taxon page.
2477
 *
2478
 * The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
2479
 * The resulting URI will include query parameters to highlight the synonym, and to optionally display
2480
 * the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
2481
 * include the sysnonym uuid as fragment in order to let the browser scroll to the according location
2482
 * in the page
2483
 *
2484
 * @param string $synonymUuid
2485
 *    The uuid of the synonym
2486
 * @param string $acceptedUuid
2487
 *    The uuid of the according accepted taxon
2488
 * @return string
2489
 *    The URL to show a synonmy in the according taxon page
2490
 */
2491
function uri_to_synonym($synonymUuid, $acceptedUuid) {
2492
  $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
2493
  return url($acceptedPath, array(
2494
      'query' => array(
2495
        // highlite the synony in the synonymy
2496
        'highlite' => $synonymUuid,
2497
        // the taxon page is refered from a synonym and the synonym can optionally be named in the page title
2498
        // see theme_taxon_page_title()
2499
        'acceptedFor' => $synonymUuid
2500
      ),
2501
      'fragment' => $synonymUuid
2502
  ));
2503

    
2504
}
2505

    
2506
/**
2507
 * Composes the drupal path to the key identified by the uuid.
2508
 *
2509
 * @param string $keyType
2510
 *    the key typer corresponds to the specific class of the CDM
2511
 *    IdentificationKey. Possible values are
2512
 *      -PolytomousKey
2513
 *      -MultimediaKey
2514
 *      - ...
2515
 * @param string $keyUuid
2516
 *   The UUID of the key
2517
 */
2518
function path_to_key($keyType, $keyUuid) {
2519
  if (!$keyUuid || !$keyType) {
2520
    return FALSE;
2521
  }
2522
  $keyType{0} = strtolower($keyType{0});
2523
  return "cdm_dataportal/" . $keyType . "/$keyUuid";
2524
}
2525

    
2526
/**
2527
 * Composes the drupal path to the reference identified by the uuid.
2528
 *
2529
 * @param $uuid string String representation of the registration entity uuid.
2530
 *
2531
 * @return string
2532
 *  The drupal path
2533
 *
2534
 */
2535
function path_to_reference($uuid) {
2536
  if (!$uuid) {
2537
    return FALSE;
2538
  }
2539
  return 'cdm_dataportal/reference/' . $uuid;
2540
}
2541

    
2542
/**
2543
 * Composes the drupal path to the reference identified by the uuid.
2544
 *
2545
 * @param string $identifier
2546
 *  The persistent identifier of the registration entity (Registration.identifier).
2547
 * @return string
2548
 *  The drupal path
2549
 */
2550
function path_to_registration($identifier) {
2551

    
2552
  if(variable_get(CDM_REGISTRATION_PRESISTENT_IDENTIFIER_AS_LINK)){
2553
    return $identifier;
2554
  } else {
2555
    return 'cdm_dataportal/registration/' . urlencode($identifier);
2556
  }
2557
}
2558

    
2559
/**
2560
 * Creates the path to a cdm_dataportal taxon name page.
2561
 *
2562
 * @param string $taxon_name_uuid
2563
 *   The uuid as string of the CDM TaxonName to show a name page for
2564
 * @param string $taxon_to_hide_uuid
2565
 *   The uuid as string of a taxon which should not be displayed in the taxon list
2566
 * @param string $highlited_synonym_uuid
2567
 *   Optional parameter which takes another taxon uuid, if given the
2568
 *   target taxon pages will show the synonymy tab where the taxon
2569
 *   referenced by the $highlite_synonym_uuid will be highlighted
2570
 *   in case it is found on this page.
2571
 * @param $redirect_to_taxon
2572
 *   If true, the name page will redirect to the related taxon if there is a single one
2573
 *   for this name only.
2574
 *
2575
 * @return string
2576
 *  URI path element as string
2577
 */
2578
function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $highlited_synonym_uuid  = NULL, $redirect_to_taxon = false) {
2579
  $res = FALSE;
2580
  if ($name_uuid) {
2581
    $res = 'cdm_dataportal/name/' . $name_uuid .
2582
    '/' . (is_uuid($taxon_to_hide_uuid) ? $taxon_to_hide_uuid : "null") .
2583
    '/' . (is_uuid($highlited_synonym_uuid) ? $highlited_synonym_uuid : "null") .
2584
    '/' . ($redirect_to_taxon || variable_get(CDM_NAME_PAGE_AUTOREDIRECT, 0) ? "redirect_to_taxon" : "");
2585
  }
2586

    
2587
  return $res;
2588
}
2589

    
2590
/**
2591
 * Composes the drupal path to the media entity identified by the uuid.
2592
 *
2593
 * @param string $uuid
2594
 *  The persistent identifier of the entity entity
2595
 * @return string
2596
 *  The drupal path
2597
 */
2598
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
2599
  if (!$uuid) {
2600
    return FALSE;
2601
  }
2602
  $out = 'cdm_dataportal/media/' . $uuid;
2603
  if ($representaion_uuid) {
2604
    $out .= '/' . $representaion_uuid;
2605
    if (is_numeric($partId)) {
2606
      $out .= '/' . $partId;
2607
    }
2608
  }
2609
  return $out;
2610
}
2611

    
2612
/**
2613
 * Compares thisRank with thatRank.
2614
 *
2615
 * Returns a negative integer, zero, or a positive integer
2616
 * as the of thisRank is higher than, equal to, or lower than thatRank.
2617
 * e.g:
2618
 * <ul>
2619
 * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
2620
 * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
2621
 * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
2622
 * </ul>
2623
 * <p>
2624
 * This compare logic of the underlying webservice is the
2625
 * <b>inverse logic</b> of the the one implemented in
2626
 * java.lang.Comparable#compareTo(java.lang.Object)
2627
 *
2628
 * @param $thisRankUuid
2629
 * @param $thatRankUuid
2630
 *
2631
 * @return int
2632
 *   A negative integer, zero, or a positive integer
2633
 *   as the thisRank is lower than, equal to, or higher than thatRank.
2634
 */
2635
function rank_compare($thisRankUuid, $thatRankUuid) {
2636
  $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
2637
  return $result->Integer;
2638
}
2639

    
2640
/**
2641
 * Creates a short version of a taxonname.
2642
 *
2643
 * The short name is created by using the taggedTitle field of
2644
 * TaxonNodeDTO instances.
2645
 * If the taggedTitle if empty the fullname will be returned.
2646
 *
2647
 * @param object $taxonNodeDTO
2648
 *   A TaxonNodeDTO object
2649
 *
2650
 * @return string
2651
 */
2652
function cdm_dataportal_shortname_of($taxonNodeDTO) {
2653

    
2654
  $nameStr = '';
2655

    
2656
  normalize_tagged_text($taxonNodeDTO->taggedTitle);
2657

    
2658
  // Get all tagged text tokens of the scientific name.
2659
  foreach ($taxonNodeDTO->taggedTitle as $tagtxt) {
2660
    if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
2661
      $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
2662
    }
2663
  }
2664
  $nameStr = trim($nameStr);
2665

    
2666
  if ($nameStr) {
2667
    if(isset($taxonNodeDTO->nodeStatus->symbol)){
2668
      $nameStr = $taxonNodeDTO->nodeStatus->symbol . ' ' . $nameStr;
2669
    }
2670
    // Do not return short names for these.
2671
    if ($taxonNodeDTO->unplaced || $taxonNodeDTO->excluded) {
2672
      return $nameStr;
2673
    }
2674

    
2675
    /*
2676
    1st capture group (^[a-zA-Z]): First letter of uninomial.
2677
    Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
2678
    Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
2679
    but only matching if no '(' or '.' in second word of name,        ( \x2E = '.')
2680
    OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$             (\x22= '"', \x2D='-', \xD7='×' )
2681
    */
2682
    $pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
2683
    if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
2684
      return $matches[1][0] . "." . $matches[3][0];
2685
    }
2686
    else {
2687
      return $nameStr;
2688
    }
2689
  }
2690
  else {
2691
    return $taxonNodeDTO->titleCache;
2692
  }
2693
}
2694

    
2695
/**
2696
 * Check if a taxon is accepted by the current taxonomic tree.
2697
 *
2698
 * @param mixed $taxon
2699
 *   The Taxon obkect to check.
2700
 *
2701
 * @return bool
2702
 *   Returns TRUE if $taxon is accepted, FALSE otherwise.
2703
 */
2704
function _cdm_dataportal_acceptedByCurrentView($taxon) {
2705

    
2706
  $defaultTreeUuid = get_current_classification_uuid();
2707

    
2708
  if (isset($taxon->taxonNodes)) {
2709
    $taxonNodes = $taxon->taxonNodes;
2710
  }
2711
  else {
2712
    $taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
2713
  }
2714

    
2715
  if ($taxon->class == "Taxon" && isset($taxonNodes)) {
2716
    foreach ($taxonNodes as $node) {
2717
      if (isset($node->classificationUUID)){
2718
        if ($node->classificationUUID == $defaultTreeUuid) {
2719
          return TRUE;
2720
        }
2721
      }
2722
      else {
2723
        if ($node->classification == $defaultTreeUuid) {
2724
          return TRUE;
2725
        }
2726
      }
2727
    }
2728
  }
2729

    
2730
  return FALSE;
2731
}
2732

    
2733
/**
2734
 * Checks is the source has one of the given types.
2735
 *
2736
 * @param object $source
2737
 *   The original source entity
2738
 * @param array $types
2739
 *   An array of element of the OriginalSourceType enumeration
2740
 *   If not set the default will be used which is:
2741
 *    - Lineage
2742
 *    - PrimaryMediaSource
2743
 *    - PrimaryTaxonomicSource
2744
 *    - Unknown
2745
 *    - Other
2746
 * @return boolean
2747
 */
2748
  function _is_original_source_type($source, $types = null) {
2749
    // this is the default
2750
    // maybe this should also be put into the settings
2751
    static $default = array(
2752
      OriginalSourceType::Lineage,
2753
      OriginalSourceType::PrimaryMediaSource,
2754
      OriginalSourceType::PrimaryTaxonomicSource,
2755
      OriginalSourceType::Unknown,
2756
      OriginalSourceType::Other,
2757
      OriginalSourceType::Aggregation
2758
    );
2759

    
2760
    if(!$types){
2761
      $types = $default;
2762
    }
2763
    return isset($source->type) && in_array($source->type, $types);
2764
  }
2765

    
2766
/**
2767
 * Collects all the media from a list of description elements.
2768
 *
2769
 * @param array $descriptionElements
2770
 *   The description elements from which to collect the media.
2771
 *
2772
 * @return array
2773
 *   The output with all the collected media.
2774
 */
2775
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2776

    
2777
  $outArrayOfMedia = array();
2778

    
2779
  // Avoiding a warning box in Drupal for Flora Malesiana.
2780
  if (isset($descriptionElements) && is_array($descriptionElements)) {
2781
    foreach ($descriptionElements as $descriptionElement) {
2782
      if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2783
        foreach ($descriptionElement->media as $media) {
2784
          if (is_object($media)) {
2785
            $outArrayOfMedia[] = $media;
2786
          }
2787
        }
2788
      }
2789
    }
2790
  }
2791
  return $outArrayOfMedia;
2792
}
2793

    
2794
/**
2795
 * Fetches the list of visible annotations for each of the cdm entities and returns the footnote keys for them.
2796
 *
2797
 * The footnotes are passed to the FootnoteManager in order to store the annotations and to create the footnote keys.
2798
 *
2799
 * @see cdm_fetch_visible_annotations()
2800
 *
2801
 * @param array $cdm_entities
2802
 *   An array of CdmBase instances or a single instance.
2803
 * @param $footnote_list_key_suggestion string
2804
 *    optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be determined be set to
2805
 *    RenderHints::getFootnoteListKey().'-annotations' otherwise the supplied key will be used.
2806
 *
2807
 * @return array of footnote keys
2808
 */
2809
function cdm_annotations_as_footnotekeys(array $cdm_entities, $footnote_list_key_suggestion = NULL) {
2810

    
2811
  $foot_note_keys = array();
2812

    
2813
  // Is argument cdmBase an array?
2814
  if (!is_array($cdm_entities)) {
2815
    $enties = array();
2816
    $enties[] = $cdm_entities;
2817
  }
2818
  else {
2819
    $enties = $cdm_entities;
2820
  }
2821

    
2822
  // Getting the key for the footnotemanager.
2823
  if (isset($footnote_list_key_suggestion)) {
2824
    $footnote_list_key = $footnote_list_key_suggestion;
2825
  }
2826
  else {
2827
    $footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2828
  }
2829

    
2830
  // Adding the footnotes keys.
2831
  foreach ($enties as $cdm_entity) {
2832
    $annotations = cdm_fetch_visible_annotations($cdm_entity);
2833
    if (is_array($annotations)) {
2834
      foreach ($annotations as $annotation) {
2835
        $foot_note_keys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2836
      }
2837
    }
2838
  }
2839

    
2840
  return $foot_note_keys;
2841
}
2842

    
2843
/**
2844
 * Fetches the list of visible annotations for each of the cdm entities and returns the footnote keys for them.
2845
 *
2846
 * The footnotes are passed to the FootnoteManager in order to store the annotations and to create the footnote keys.
2847
 *
2848
 * @see cdm_fetch_visible_annotations()
2849
 *
2850
 * @param array $cdm_entities
2851
 *   An array of CdmBase instances or a single instance.
2852
 * @param $footnote_list_key_suggestion string
2853
 *    optional parameter. If this parameter is left empty (null, 0, "") the footnote key will be determined be set to
2854
 *    RenderHints::getFootnoteListKey().'-annotations' otherwise the supplied key will be used.
2855
 *
2856
 * @return array of footnote keys
2857
 */
2858
function cdm_entity_annotations_as_footnotekeys($cdm_entity, $footnote_list_key_suggestion = NULL) {
2859

    
2860
  $foot_note_keys = array();
2861

    
2862
  // Getting the key for the footnotemanager.
2863
  if (isset($footnote_list_key_suggestion)) {
2864
    $footnote_list_key = $footnote_list_key_suggestion;
2865
  } else {
2866
    $footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2867
  }
2868

    
2869
  // Adding the footnotes keys.
2870
  $annotations = cdm_fetch_visible_annotations($cdm_entity);
2871
  if (is_array($annotations)) {
2872
    foreach ($annotations as $annotation) {
2873
      $foot_note_keys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2874
    }
2875
  }
2876

    
2877
  return $foot_note_keys;
2878
}
2879

    
2880

    
2881
/**
2882
 * Creates a CDM Dynabox.
2883
 *
2884
 * @param string $dynabox_id
2885
 *   a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2886
 * @param string $label
2887
 *   The clickable text to show.
2888
 * @param string $content_url
2889
 *   The cdm REST service request url wich will deliver the content to be shown
2890
 *   once the dynabox toggles open.
2891
 * @param string $theme
2892
 *   The theme to be used for rendering the cdm REST service response with is
2893
 *   returned from the $content_url.
2894
 * @param string $link_alt_text
2895
 *   The value for the alt attribute of the dynabox link.
2896
 * @param array $enclosingtags
2897
 *   An array with two elements: $enclosingtags[0] will be used for the dynabox
2898
 *   element itself, $enclosingtags[1] is the tag to be used for the
2899
 *   dynabox_content (optional)
2900
 * @param array $attributes
2901
 * @param $content_element_selector
2902
 *   Optional jQuery selector which can be used to reference a dom element which should
2903
 *   be used as container for the content to be shown. The dynabox-<dynabox id>-content
2904
 *  element will be placed in this container.
2905
 *
2906
 * @param string $open_callback
2907
 *   optional javascript call back function to be triggered after toggling the box to
2908
 *   the open state.
2909
 * @param string $close_callback
2910
 *   optional javascript call back function to be triggered after toggling the box to
2911
 *   the closed state.
2912
 * @return string Returns HTML for a dynabox.
2913
 * Returns HTML for a dynabox.
2914
 */
2915
function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2916
                     $enclosingtags = array('li', 'ul'), $attributes = array(),
2917
                     $content_element_selector = null,
2918
                     $open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2919
  $out = '';
2920

    
2921
  // check for plain class attribute string
2922
  $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2923

    
2924
  if(!array_key_exists('class', $attributes)) {
2925
    $attributes['class'] = array();
2926
  }
2927
  $attributes['id'][] = 'dynabox-' . $dynabox_id;
2928
  $dynabox_attributes = drupal_attributes($attributes);
2929

    
2930

    
2931
  _add_js_domEvent(); // requires domEvent.js
2932
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2933
  drupal_add_js("
2934
  jQuery(document).ready(
2935
      function() {
2936
        dynabox('". $dynabox_id ."',
2937
          {
2938
            open_callback: " . $open_callback .",
2939
            close_callback: " . $close_callback .
2940
            ($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2941
          }
2942
        );
2943
      }
2944
   );",
2945
   array(
2946
    'type'=>'inline',
2947
    'scope'=>'footer'
2948
    )
2949
  );
2950

    
2951

    
2952
  $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2953
  $out .= '<!-- dynabox for ' . $content_url . ' -->';
2954
  $out .= '<' . $enclosingtags[0] . ' ' .  $dynabox_attributes. '><a href="' . $cdm_proxy_url . '" class="label" alt="' . t('@link-alt-text', array('@link-alt-text' => $link_alt_text)) . '">' . $label . '</a>';
2955
  $out .= '  <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2956
  $out .= '    <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2957
  $out .= '    </' . $enclosingtags[1] . '>';
2958
  $out .= '  </' . $enclosingtags[0] . '>';
2959
  $out .= '<!-- dynabox end -->';
2960
  return $out;
2961
}
2962

    
2963
/**
2964
 * Checks whether a feature has any description elements.
2965
 *
2966
 * @param mixed $featureNode
2967
 *   A feature node as produced by the function _mergeFeatureTreeDescriptions().
2968
 *
2969
 * @see _mergeFeatureTreeDescriptions()
2970
 *
2971
 * @return bool
2972
 *   Returns TRUE if the given $featureNode or any of its subordinate nodes
2973
 *   contains at least one non empty TextData or at least one DescriptionElement
2974
 *   of an other type. A TextData element holding a multilanguageText or a
2975
 *   source reference is considered to be not empty.
2976
 *
2977
 * @TODO this function may have become obsolete by the new method of detecting empty blocks,
2978
 *       see $block_content_is_not_empty in make_feature_block_list() and
2979
 *       $feature_block_has_content in compose_feature_block_items_generic
2980
 */
2981
function has_feature_node_description_elements($featureNode) {
2982

    
2983
  if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2984
    if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2985
      foreach ($featureNode->descriptionElements as $descriptionElement) {
2986
        if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
2987
          && $descriptionElement->multilanguageText_L10n->text != ''
2988
          || isset($descriptionElement->sources[0])
2989
          || isset($descriptionElement->media[0]) ) {
2990
          return TRUE;
2991
        }
2992
      }
2993
    }
2994
  }
2995
  else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2996
    foreach ($featureNode->childNodes as $child) {
2997
      if (has_feature_node_description_elements($child)) {
2998
        return TRUE;
2999
      }
3000
    }
3001
  }
3002
  return FALSE;
3003
}
3004

    
3005
/**
3006
 * Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
3007
 *
3008
 * @param $chapter
3009
 *   The taxon page chapter or part
3010
 */
3011
function cdm_check_valid_taxon_page($chapter){
3012
  static $taxon_tabs = null;
3013

    
3014
  cdm_check_valid_portal_page();
3015

    
3016
  if($taxon_tabs == null){
3017
    $taxon_tabs = array('all', 'description');
3018
    foreach(get_taxon_tabs_list() as $tab){
3019
      $taxon_tabs[] = strtolower($tab);
3020
    }
3021
  }
3022

    
3023
  if(!in_array($chapter, $taxon_tabs)){
3024
    // oops this is not a valid chapter name
3025
    http_response_code(404); // 404 = Not Found
3026
  }
3027

    
3028
}
3029

    
3030
function check_js_devel_mode_disabled() {
3031
  if(variable_get('cdm_js_devel_mode', FALSE)) {
3032
    drupal_set_message(t('The !url1 is enabled.
3033
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
3034
      '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
3035
    )),
3036
      'warning'
3037
    );
3038
  }
3039
}
3040

    
3041
/**
3042
 * Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise.
3043
 * The test applied by default it a check for the query parameter 'q' ending with a file suffix like '*.*'
3044
 *
3045
 * @param $preg_pattern
3046
 *   Optional regular expression pattern to be used in preg_match().
3047
 */
3048
function cdm_check_valid_portal_page($preg_pattern = null){
3049
  $ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
3050
  if($preg_pattern === null){
3051
    $preg_pattern = $ends_with_file_suffix_pattern;
3052
  }
3053
  if(preg_match($preg_pattern, $_GET['q'])){
3054
    // oops this urls ends with a file_suffix and thus does not refer to a portal page
3055
    http_response_code(404); // 404 = Not Found
3056
    exit('HTTP 404');
3057
  }
3058
  check_js_devel_mode_disabled();
3059
}
3060

    
3061
/**
3062
 * Generates the diff of the texts and presents it in a HTML diff viewer.
3063
 *
3064
 * @param $text_a
3065
 * @param $text_b
3066
 * @return string
3067
 */
3068
function diff_viewer($text_a, $text_b) {
3069

    
3070
  static $diff_viewer_count = 0;
3071

    
3072
  $element_id = 'part_definitions_diff_' . $diff_viewer_count++;
3073

    
3074
  // http://code.stephenmorley.org/php/diff-implementation/
3075
  module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
3076
  drupal_add_css(drupal_get_path('module',
3077
      'cdm_dataportal') . '/css/diff.css');
3078
  _add_jquery_ui();
3079
  drupal_add_js(
3080
    'jQuery(document).ready( function(){
3081
        jQuery(\'#' . $element_id . '\').accordion({
3082
        collapsible: true,
3083
        active: false,
3084
        fillSpace: true,
3085
        }).children(\'div\').css({ \'height\': \'auto\' });
3086
        jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
3087
     });'
3088
    , array(
3089
    'type' => 'inline',
3090
    'scope' => 'footer'
3091
  ));
3092

    
3093
  $diff = Diff::compare($text_a,
3094
    $text_b);
3095
  $diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
3096
    . Diff::toTable($diff, '', '')
3097
    . '</div></div>';
3098
  return $diff_viewer_markup;
3099
}
3100

    
3101

    
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