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cdm-dataportal / modules / cdm_dataportal / cdm_dataportal.module @ 810710a0

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1
<?php
2
/**
3
 * @file
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 * 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

    
25
  module_load_include('inc', 'cdm_dataportal', 'includes/common');
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  module_load_include('inc', 'cdm_dataportal', 'includes/name');
27
  module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
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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');
35

    
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  module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');
37
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
44
  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
45

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

    
51

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

    
54

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

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

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

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

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

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

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

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

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

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

    
126
  function _add_js_resizable_element($selector, $y_axis_only) {
127

    
128
    _add_jquery_ui();
129
    $options = "";
130
    if($y_axis_only) {
131
      $options = "resize: function(event, ui) {
132
        ui.size.width = ui.originalSize.width;
133
        },
134
        handles: \"s\"";
135

    
136
    }
137
    drupal_add_js("
138
          jQuery(document).ready(function() {
139
             jQuery('" . $selector . "').resizable({". $options ."});
140
          });
141
        ",
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      array(
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        'type' => 'inline',
144
        'scope' => 'footer'
145
      )
146
    );
147
  }
148

    
149
  function _add_js_openlayers() {
150

    
151
    $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';
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    $proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';
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154
    if(variable_get('cdm_js_devel_mode', FALSE)){
155
      // develooper mode libs
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  //     $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';
157
      $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';
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      $proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';
159
    }
160

    
161
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,
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      array(
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        'type' => 'file',
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        'group' => JS_LIBRARY,
165
        'weight' => 0,
166
        'cache' => TRUE,
167
        'preprocess' => FALSE
168
      )
169
    );
170

    
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    // see https://github.com/proj4js/proj4js
172
    // http://openlayers.org/dev/examples/using-proj4js.html
173
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $proj4js,
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      array(
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        'type' => 'file',
176
        'group' => JS_LIBRARY,
177
        'weight' => -1, // before open layers
178
        'cache' => TRUE,
179
      )
180
    );
181

    
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    // configure the theme
183
    $openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
184
    $openlayers_imp_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/img/dark/';
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    drupal_add_js('OpenLayers.ImgPath="' . base_path() . $openlayers_imp_path . '";', array(
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        'type' => 'inline',
187
        'group' => JS_LIBRARY,
188
        'weight' => 1, // after openlayers
189
        'cache' => TRUE,
190
        'preprocess' => FALSE
191
      ));
192

    
193
    drupal_add_css($openlayers_theme_path . 'style.tidy.css',
194
      array(
195
        'type' => 'file',
196
        'cache' => TRUE,
197
        'preprocess' => FALSE
198
      )
199
    );
200

    
201
  }
202

    
203
  /**
204
   * @todo Please document this function.
205
   * @see http://drupal.org/node/1354
206
   */
207
  function _add_js_thickbox() {
208
    // ---- jQuery thickbox:
209
    /*
210
    * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
211
    * not triggered because of problems with compat-1.0.js' see INSTALL.txt
212
    */
213
    // drupal_add_js(drupal_get_path('module',
214
    // 'cdm_dataportal').'/js/jquery.imagetool.min.js');
215
    //
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    // Add a setting for the path to cdm_dataportal module, used to find the path
217
    // for the loading animation image in thickbox.
218
    drupal_add_js(array(
219
    'cdm_dataportal' => array(
220
    'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
221
    )
222
    ),
223
    'setting'
224
        );
225
        drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
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        drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
227
  }
228

    
229
  /**
230
   * @todo Please document this function.
231
   * @see http://drupal.org/node/1354
232
   */
233
  function _add_js_lightbox($galleryID) {
234
    /*
235
     * Important Notice: The jquery.lightbox-0.5.js has been modified in order to
236
     * allow using the "alt" attribute for captions instead of the "title"
237
     * attribute
238
     */
239
    $lightbox_base_path =  drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';
240
    $lightbox_image_path = base_path() . $lightbox_base_path . '/images/';
241
    drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');
242
    drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');
243
    drupal_add_js('jQuery(document).ready(function() {
244
        jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
245
          fixedNavigation:  true,
246
          imageLoading:     \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',
247
          imageBtnPrev:     \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',
248
          imageBtnNext:     \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',
249
          imageBtnClose:    \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',
250
          imageBlank:       \'' . $lightbox_image_path . 'lightbox-blank.gif\',
251
          adjustToWindow: true
252
        });
253
      });
254
      ', array('type' => 'inline'));
255
  }
256

    
257
  /**
258
   * @todo Please document this function.
259
   * @see http://drupal.org/node/1354
260
   */
261
  function _add_js_footnotes() {
262
    _add_js_domEvent();
263
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
264
  }
265

    
266
  /**
267
   * @todo Please document this function.
268
   * @see http://drupal.org/node/1354
269
   */
270
  function _add_js_ahah() {
271

    
272
    _add_js_domEvent(); // requires domEvent.js
273
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
274
  }
275

    
276
/**
277
 * @todo Please document this function.
278
 * @see http://drupal.org/node/1354
279
 */
280
function _add_js_taxonomic_children($jquery_selector) {
281

    
282
  global $base_url;
283

    
284

    
285
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
286
  
287
  drupal_add_js('jQuery(document).ready(function() {
288
        jQuery(\'' . $jquery_selector . '\').taxonomic_children({
289
          // hoverClass: "fa-rotate-90",
290
          // activeClass: "fa-rotate-90",
291
          classificationUuid: "' . get_current_classification_uuid() . '",
292
          taxonUuid: "' . get_current_taxon_uuid() . '",
293
          cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
294
          proxyBaseUri: "' . $base_url . '",
295
          
296
        });
297
      });
298
      ', array('type' => 'inline'));
299
}
300

    
301
  /**
302
   * Adds the external javascript file for domEvent.js.
303
   *
304
   * @see drupal_add_js()
305
   */
306
  function _add_js_domEvent() {
307
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
308
  }
309

    
310
  function _add_jquery_ui()
311
  {
312
    drupal_add_css(drupal_get_path('module',
313
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
314
    drupal_add_js(drupal_get_path('module',
315
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
316
      array(
317
        'type' => 'file',
318
        'weight' => JS_LIBRARY,
319
        'cache' => TRUE,
320
        'preprocess' => FALSE
321
      )
322
    );
323
  }
324

    
325
  /**
326
   * Provides the markup for an font awesome icon.
327
   *
328
   * The icons is created in default size without any extra features.
329
   *
330
   * The available icons are listed here http://fontawesome.io/cheatsheet/
331
   * fontawesome icons have much more features than implemented here in this function,
332
   * for spinning icons, fixed width icons, rotation, etc please checkout the
333
   * examples at http://fontawesome.io/examples/
334
   *
335
   * @parameter $icon_name
336
   *  The name of the icon which starts with 'fa-'
337
   *
338
   * @return String
339
   *    the markup for the icon in an <i> tag
340
   *
341
   */
342
  function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
343

    
344

    
345
    //<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
346

    
347
    $font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal').'/fonts/font-awesome-4.6.3/css/font-awesome.min.css';
348
    //$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
349

    
350
    drupal_add_html_head_link(
351
      array(
352
        'href' => $font_awesome_css_uri,
353
        'rel' => 'stylesheet'
354
      )
355
    );
356

    
357
    if($icon_name){
358
      if(!isset($attributes['class'])){
359
        $attributes['class'] = array();
360
      }
361
      $attributes['class'][] = 'fa';
362
      $attributes['class'][] = $icon_name;
363

    
364
      return '<i ' . drupal_attributes($attributes) . '></i>';
365
    }
366

    
367
    return '';
368
  }
369

    
370

    
371
  /* ====================== hook implementations ====================== */
372
  /**
373
   * Implements hook_permission().
374
   *
375
   * Valid permissions for this module.
376
   *
377
   * @return array
378
   *   An array of valid permissions for the cdm_dataportal module.
379
   */
380
  function cdm_dataportal_permission() {
381
    return array(
382
      'administer cdm_dataportal' => array(
383
        'title' => t('Administer CDM DataPortal settings'),
384
        'description' => t("Access the settings pages specific for the cdm_dataportal module"),
385
      ),
386
      'access cdm content' => array(
387
        'title' => t('Access CDM content'),
388
        'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
389
      ),
390
    );
391
  }
392

    
393
/**
394
 * Implements hook_menu().
395
 */
396
function cdm_dataportal_menu() {
397
  $items = array();
398

    
399
  // @see settings.php.
400
  cdm_dataportal_menu_admin($items);
401
  cdm_dataportal_menu_help($items);
402

    
403
  $items['cdm_dataportal/names'] = array(
404
    'page callback' => 'cdm_dataportal_view_names',
405
    'access arguments' => array('access cdm content'),
406
    'type' => MENU_CALLBACK,
407
  );
408

    
409
  // Optional callback arguments: page.
410
  $items['cdm_dataportal/taxon'] = array(
411
    'page callback' => 'cdm_dataportal_taxon_page_view',
412
    'access arguments' => array('access cdm content'),
413
    'type' => MENU_CALLBACK,
414
    // Expected callback arguments: uuid.
415
  );
416

    
417
  $items['cdm_dataportal/specimen'] = array(
418
      'page callback' => 'cdm_dataportal_specimen_page_view',
419
      'access arguments' => array('access cdm content'),
420
      'type' => MENU_CALLBACK,
421
      // Expected callback arguments: uuid.
422
  );
423

    
424
  $items['cdm_dataportal/named_area'] = array(
425
    'page callback' => 'cdm_dataportal_named_area_page_view',
426
    'access arguments' => array('access cdm content'),
427
    'type' => MENU_CALLBACK,
428
    // Expected callback arguments: uuid.
429
  );
430

    
431
  $items['cdm_dataportal/name'] = array(
432
    'page callback' => 'cdm_dataportal_name_page_view',
433
      /*
434
    'page arguments' => array(
435
       'taxon_name_uuid',
436
       'taxon_to_hide_uuid',
437
       'synonym_uuid' => NULL
438
      ),
439
      */
440
    'access arguments' => array('access cdm content'),
441
    'type' => MENU_CALLBACK,
442
    // Expected callback arguments: uuid.
443
  );
444

    
445
  $items['cdm_dataportal/reference'] = array(
446
    'page callback' => 'cdm_dataportal_view_reference',
447
    'access arguments' => array('access cdm content'),
448
    'type' => MENU_CALLBACK,
449
    // Expected callback arguments: uuid.
450
  );
451

    
452
  $items['cdm_dataportal/reference/list'] = array(
453
    'page callback' => 'cdm_dataportal_view_reference_list',
454
    'access arguments' => array('access cdm content'),
455
    'type' => MENU_CALLBACK,
456
    // Expected callback arguments: uuid.
457
  );
458

    
459
  $items['cdm_dataportal/media'] = array(
460
    'page callback' => 'cdm_dataportal_view_media',
461
    'access arguments' => array('access cdm content'),
462
    'type' => MENU_CALLBACK,
463
    // Expected callback arguments:
464
    // uuid, mediarepresentation_uuid, part_uuid or part#.
465
  );
466

    
467
  $items['cdm_dataportal/polytomousKey'] = array(
468
    'page callback' => 'cdm_dataportal_view_polytomousKey',
469
    'access arguments' => array('access cdm content'),
470
    'type' => MENU_CALLBACK,
471
    // Expected callback arguments: polytomousKey->uuid.
472
  );
473

    
474
  $items['cdm_dataportal/search'] = array(
475
    'page callback' => 'cdm_dataportal_view_search_advanced',
476
    'access arguments' => array('access cdm content'),
477
    'type' => MENU_CALLBACK,
478
  );
479

    
480
  $items['cdm_dataportal/search/advanced'] = array(
481
    'title' => 'Advanced', // will be passed through t()
482
    'page callback' => 'cdm_dataportal_view_search_advanced',
483
    'access arguments' => array('access cdm content'),
484
    'type' => MENU_DEFAULT_LOCAL_TASK,
485
  );
486

    
487
  $items['cdm_dataportal/search/taxon_by_description'] = array(
488
    'title' => 'By content category', // will be passed through t()
489
    'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
490
    'access arguments' => array('access cdm content'),
491
    'type' => MENU_LOCAL_TASK,
492
  );
493

    
494
  $items['cdm_dataportal/search/results/taxon'] = array(
495
    'page callback' => 'cdm_dataportal_view_search_results_taxon',
496
    'access arguments' => array('access cdm content'),
497
    'type' => MENU_CALLBACK,
498
  );
499
  $items['cdm_dataportal/search/registration'] = array(
500
    'page callback' => 'cdm_dataportal_view_search_registrations_results',
501
    'access arguments' => array('access cdm content'),
502
    'type' => MENU_CALLBACK,
503
  );
504
  // Optional callback arguments: page.
505
  $items['cdm_dataportal/registration'] = array(
506
    'page callback' => 'cdm_dataportal_registration_page_view',
507
    'access arguments' => array('access cdm content'),
508
    'type' => MENU_CALLBACK,
509
    // Expected callback arguments: uuid.
510
  );
511

    
512
  /*
513
   $items['cdm/xml2json'] = array(
514
   'page callback' => 'cdm_view_xml2json',
515
   'access arguments' => array('access cdm content'),
516
   'type' => MENU_CALLBACK,
517
   );
518
   */
519

    
520
  // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
521
  // User configuration of cdm_dataportal.
522
  $items['user/%/cdm_dataportal'] = array(
523
    'title' => 'cdm_dataportal',
524
    'access arguments' => array('access cdm content'),
525
    'page callback' => 'drupal_get_form',
526
    'page arguments' => array('cdm_dataportal_user_form'),
527
    'type' => MENU_LOCAL_TASK,
528
    'weight' => 10,
529
  );
530
  // }
531

    
532
  // 'May not cache' in D5.
533
  $items['cdm_dataportal/name/%'] = array(
534
    // 'page callback' => 'cdm_dataportal_view_name',
535
    'page callback' => 'cdm_dataportal_name_page_view',
536
    'page arguments' => array(2, 3, 4),
537
    'access arguments' => array('access cdm content'),
538
    'type' => MENU_CALLBACK,
539
  );
540

    
541
  // --- Local tasks for Taxon.
542
  // --- tabbed taxon page
543
  if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
544
    $items['cdm_dataportal/taxon/%'] = array(
545
      'title' => cdm_taxonpage_tab_label('General'),
546
      'page callback' => 'cdm_dataportal_taxon_page_view',
547
      'access arguments' => array('access cdm content'),
548
      'type' => MENU_CALLBACK,
549
      'weight' => 1,
550
      'page arguments' => array(2, "description")
551
      , // Expected callback arguments: taxon_uuid.
552
    );
553

    
554
    $items['cdm_dataportal/taxon/%/all'] = array(
555
      'title' => cdm_taxonpage_tab_label('General'),
556
      'page callback' => 'cdm_dataportal_taxon_page_view',
557
      'access arguments' => array('access cdm content'),
558
      'type' => MENU_CALLBACK,
559
      'weight' => 2,
560
      'page arguments' => array(2, "all")
561
      , // Expected callback arguments: taxon_uuid.
562
    );
563

    
564
    $items['cdm_dataportal/taxon/%/description'] = array(
565
      'title' => cdm_taxonpage_tab_label('General'),
566
      'page callback' => 'cdm_dataportal_taxon_page_view',
567
      'access arguments' => array('access cdm content'),
568
      'type' => MENU_DEFAULT_LOCAL_TASK,
569
      'weight' => 2,
570
      'page arguments' => array(2, "description")
571
      , // Expected callback arguments: taxon_uuid.
572
    );
573

    
574
    $items['cdm_dataportal/taxon/%/synonymy'] = array(
575
      'title' => cdm_taxonpage_tab_label('Synonymy'),
576
      'page callback' => 'cdm_dataportal_taxon_page_view',
577
      'access arguments' => array('access cdm content'),
578
      'type' => MENU_LOCAL_TASK,
579
      'weight' => 4,
580
      'page arguments' => array(2, "synonymy", 4)
581
      , // Expected callback arguments: taxon_uuid and ...
582
    );
583
    $items['cdm_dataportal/taxon/%/images'] = array( // Images
584
      'title' => cdm_taxonpage_tab_label('Images'),
585
      'page callback' => 'cdm_dataportal_taxon_page_view',
586
      'access arguments' => array('access cdm content'),
587
      'type' => MENU_LOCAL_TASK,
588
      'weight' => 5,
589
      'page arguments' => array(2, "images")
590
      , // Expected callback arguments: taxon_uuid.
591
    );
592

    
593
    $items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
594
      'title' => cdm_taxonpage_tab_label('Specimens'),
595
      'page callback' => 'cdm_dataportal_taxon_page_view',
596
      'access arguments' => array('access cdm content'),
597
      'type' => MENU_LOCAL_TASK,
598
      'weight' => 6,
599
      'page arguments' => array(2, "specimens")
600
      , // Expected callback arguments: taxon_uuid.
601
    );
602

    
603
    $items['cdm_dataportal/taxon/%/keys'] = array( // Keys
604
      'title' => cdm_taxonpage_tab_label('Keys'),
605
      'page callback' => 'cdm_dataportal_taxon_page_view',
606
      'access arguments' => array('access cdm content'),
607
      'type' => MENU_LOCAL_TASK,
608
      'weight' => 6,
609
      'page arguments' => array(2, "keys")
610
      , // Expected callback arguments: taxon_uuid.
611
    );
612

    
613
    $items['cdm_dataportal/taxon/%/experts'] = array( // Experts
614
      'title' => cdm_taxonpage_tab_label('Experts'),
615
        'page callback' => 'cdm_dataportal_taxon_page_view',
616
        'access arguments' => array('access cdm content'),
617
        'type' => MENU_LOCAL_TASK,
618
        'weight' => 6,
619
        'page arguments' => array(2, "experts")
620
    , // Expected callback arguments: taxon_uuid.
621
    );
622

    
623
    $items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(
624
        'page callback' => 'cdm_dataportal_taxon_autosuggest',
625
        'access arguments' => array('access cdm content'),
626
        'page arguments' => array(3,4,5),
627
        'type' => MENU_CALLBACK
628
    );
629
  }
630

    
631
  // --- refresh link for all cdmnode types
632
  foreach (cdm_get_nodetypes() as $type=>$name) {
633
    $items['cdm_dataportal/' . $name . '/%/refresh'] = array(
634
        'title' => 'Refresh',
635
        'page callback' => 'cdm_dataportal_refresh_node',
636
        'access arguments' => array('administer cdm_dataportal'),
637
        'type' => MENU_LOCAL_TASK,
638
        'weight' => 100,
639
        'page arguments' => array($name, 2)
640
    );
641
  }
642

    
643
  return $items;
644
}
645

    
646
/**
647
 * Implements hook_init().
648
 *
649
 */
650
function cdm_dataportal_init() {
651
  if (!path_is_admin(current_path())) {
652
    //FIXME To add CSS or JS that should be present on all pages, modules
653
    //      should not implement this hook, but declare these files in their .info file.
654
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
655
    // drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
656
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
657
  } else {
658
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');
659
  }
660

    
661
  if(variable_get('cdm_debug_mode', FALSE)){
662
    $file = 'temporary://drupal_debug.txt';
663
    file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
664
  }
665

    
666
  $bibliography_settings = get_bibliography_settings();
667
  $enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
668
  FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
669
}
670

    
671
function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
672

    
673
  $base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
674

    
675
  if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
676
    // force reloading of all and notify user about this special loading
677
    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: ')
678
        . l('Back to tabbed taxon page', $base_path));
679
    $base_path .= '/all';
680
  } else {
681
    drupal_set_message(t('The level 2 cache has been cleared for this page'));
682
  }
683

    
684
  $parameters['cacheL2_refresh'] ='1';
685

    
686

    
687
  drupal_goto($base_path, array('query' => $parameters));
688
}
689

    
690
/**
691
 * Implements hook_requirements($phase)
692
 */
693
function cdm_dataportal_requirements($phase) {
694
    $requirements = array();
695
    if($phase == 'runtime'){
696

    
697
    }
698
    return $requirements;
699
}
700

    
701

    
702
/**
703
 * The function generate form for own user cdm dataportal configurations.
704
 */
705
function cdm_dataportal_user_form($form, &$form_state) {
706

    
707
  global $user;
708
  $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
709

    
710
  $form['taxon_page_tabs'] = array(
711
      '#type' => 'fieldset',
712
      '#tree' => true,
713
      '#title' => t('Taxon page tabs'),
714
  );
715

    
716
  $form['taxon_page_tabs']['user_defined'] = array(
717
    '#type' => 'checkbox',
718
    '#title' => t('Activate user default configuration'),
719
    '#default_value' => variable_get($checkbox_value, 0),
720
    '#description' => t('Check this if you want configure your own default tab from the below menu.'),
721
  );
722

    
723
  $form['taxon_page_tabs']['default_tab'] = array(
724
    '#type' => 'select',
725
    '#title' => t('Default tab to display'),
726
    '#default_value' => get_default_taxon_tab(TRUE),
727
    '#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
728
    '#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
729
              <strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
730
              to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
731
  );
732

    
733

    
734
  if(false){
735
    $form['developer_options'] = array(
736
        '#type' => 'fieldset',
737
        '#tree' => true,
738
        '#title' => t('Developer options'),
739
    );
740

    
741
    $form['developer_options']['show_render_path'] = array(
742
      '#type' => 'checkbox',
743
      '#title' => t('Display the render path for each taxon name.'),
744
      '#default_value' => variable_get($checkbox_value, 0),
745
      '#description' => t('This option is very helpful if you are editing the !link for taxon names.',
746
        array(
747
            '!link' => l(
748
              'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))
749
            )
750
        ),
751
    );
752
  }
753

    
754
  $form['submit'] = array(
755
    '#type' => 'submit',
756
    '#value' => t('Submit'),
757
  );
758

    
759
  return $form;
760
}
761

    
762
/**
763
 * Form submission handler for user_form().
764
 *
765
 * Submits the user cdm dataportal configurations.
766
 */
767
function cdm_dataportal_user_form_submit($form, &$form_state) {
768
  global $user;
769
  $msg_type = 'status';
770
  $username = $user->name;
771
  $variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
772

    
773
  // FIXME: this is completely wrong, see user_profile_form_submit()
774

    
775
  // it is only possible to change own user settings
776
  if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {
777

    
778
    // DEFAULT_TAXON_TAB
779
    $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
780
    variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);
781
    variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);
782
    if ($form_state['values']['taxon_page_tabs']['user_defined']) {
783
      drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
784
      drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
785
        '!tab' => $variable[variable_get($variable_to_use, 0)],
786
        '!user' => $username,
787
      ))), $msg_type);
788
    }
789
    else {
790
      drupal_set_message(check_plain(t('The user default tab wont be used for
791
        the next taxon site, check the box if you want to use the user default configuration.')));
792
    }
793

    
794
  }
795
  else {
796
    // Problem with the user id => variables wont be saved.
797
    $msg_type = 'warning';
798
    drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
799
  }
800
}
801

    
802
/**
803
 * Implements hook_block_info().
804
 */
805
function cdm_dataportal_block_info() {
806

    
807
    // $block[0]["info"] = t("CDM DataPortal DevLinks");
808
    // $block[1]["info"] = t("CDM DataPortal Credits");
809
    $block["2"] = array(
810
        "info" => t("CDM - Search Taxa"),
811
        "cache" => DRUPAL_NO_CACHE
812
      );
813
    // $block[3]["info"] = t("CDM Filters");
814
    $block["4"]["info"] = t("CDM  - Dataportal Print");
815
    $block["keys"]["info"] = t("CDM - Identification keys");
816
    $block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');
817
    $block["classification_breadcrumbs"] =  array(
818
        'info' => t('CDM - Classification breadcrumbs'),
819
        'cache' => DRUPAL_CACHE_PER_PAGE
820
      );
821
    $block["taxonomic_children"] =  array(
822
      'info' => t('CDM - Taxonomic children'),
823
      'cache' => DRUPAL_CACHE_PER_PAGE
824
    );
825
    $block["back_to_search_results"] =  array(
826
      'title' => '<none>',
827
      'info' => t('CDM - Back to search Results'),
828
      'cache' => DRUPAL_CACHE_PER_PAGE,
829
      'visibility' => BLOCK_VISIBILITY_LISTED,
830
      'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!!
831
    );
832
  $block['registrations_search_filter'] =  array(
833
    'title' => 'Search registrations',
834
    'info' => t('CDM - Registrations search filter'),
835
    'cache' => DRUPAL_CACHE_PER_PAGE,
836
    'visibility' => BLOCK_VISIBILITY_NOTLISTED,
837
    'pages' => "cdm_dataportal/search/registration\ncdm_dataportal/search/registration/*", // multiple page paths separated by "\n"!!!
838
  );
839

    
840
    return $block;
841
}
842

    
843
/**
844
 * Implements hook_block_view().
845
 */
846
function cdm_dataportal_block_view($delta) {
847
  // TODO Rename block deltas (e.g. '2') to readable strings.
848
  switch ($delta) {
849
    // case 'delta-1':
850
    // $block['subject'] = t('Credits');
851
    // $block['content'] = theme('cdm_credits');
852
    // return $block;
853
    case '2':
854
      $block['subject'] = t('Search taxa');
855
      $form = drupal_get_form('cdm_dataportal_search_taxon_form');
856
      $block['content'] = drupal_render($form);
857

    
858
      if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
859
        $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
860
      }
861
      return $block;
862
    case '4':
863
      $block['subject'] = '';
864
      $block['content'] = theme('cdm_print_button');
865
      return $block;
866
    case "keys":
867
      $block['subject'] = t('Identification Keys');
868
      $block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
869
      return $block;
870
    case "fundedByEDIT":
871
      // t('Funded by EDIT');
872
      $text = '<none>';
873
      $block['subject'] = $text;
874
      $img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
875
      $block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
876
        'attributes' => array("target" => "EDIT"),
877
        'absolute' => TRUE,
878
        'html' => TRUE,
879
      ));
880
      return $block;
881
    case 'classification_breadcrumbs':
882
      $taxon_uuid = get_current_taxon_uuid();
883
      $block['subject'] = '<none>';
884
      $block['content'] = compose_classification_breadcrumbs($taxon_uuid);
885
      return $block;
886
    case 'taxonomic_children':
887
      $taxon_uuid = get_current_taxon_uuid();
888
      $block['subject'] = '<none>';
889
      $block['content'] = compose_taxonomic_children($taxon_uuid);
890
      return $block;
891
    case 'back_to_search_results':
892
      $block['subject'] = '<none>';
893
      if (isset($_SESSION['cdm']['search'])) {
894
        $block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
895
      }
896
      return $block;
897
    case 'registrations_search_filter':
898
      $block['subject'] = '<none>';
899
      $block['content'] = $form = drupal_get_form('cdm_dataportal_search_registration_form'); // see cdm_dataportal_search_registration_form($form, &$form_state)
900
      return $block;
901
    default:
902
      return null;
903
  }
904
}
905

    
906
/**
907
 * Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
908
 *
909
 * @return string
910
 *   the taxon uuid or NULL
911
 */
912
function get_current_taxon_uuid()
913
{
914
  static $taxon_uuid;
915

    
916
  if(!isset($taxon_uuid)){
917
    if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
918
      $taxon_uuid = $_REQUEST['currentTaxon'];
919
    } else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
920
      $taxon_uuid = arg(2);
921
    } else {
922
      $taxon_uuid = null;
923
    }
924
  }
925

    
926
  return $taxon_uuid;
927
}
928

    
929
/**
930
 * Returns the currently classification tree in use.
931
 *
932
 * @return string
933
 *   The uuid of the currently focused classification
934
 */
935
function get_current_classification_uuid() {
936
  if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
937
    return $_SESSION['cdm']['taxonomictree_uuid'];
938
  }
939
  else {
940
    return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
941
  }
942
}
943

    
944
/*
945
 function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
946
 $_SESSION['cdm'] = NULL;
947
 if(is_string($cdm_ws_uri_update)){
948
 $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
949
 }
950
 }
951

    
952
 function cdm_dataportal_session_validate(){
953
 if(!isset($_SESSION['cdm']['ws_uri'])){
954
 $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
955
 } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
956
 cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
957
 }
958
 }
959
 */
960

    
961
/**
962
 * creates a  selector form for taxonomic trees.
963
 *
964
 * @return array
965
 *  a drupal form array
966
 */
967
function cdm_taxonomictree_selector() {
968
  _add_js_treeselector();
969

    
970
  $form = drupal_get_form('cdm_taxonomictree_selector_form');
971
  return $form;
972
}
973

    
974
/**
975
 * @todo Please document this function.
976
 * @see http://drupal.org/node/1354
977
 *
978
 * @deprecated use compose_classification_selector instead
979
 */
980
function cdm_taxonomictree_selector_form($form, &$form_state) {
981

    
982
  $url = url('cdm_api/setvalue/session', array('query' => NULL));
983
  $form['#action'] = $url;
984

    
985
  $form['var'] = array(
986
    '#weight' => -3,
987
    '#type' => 'hidden',
988
    '#value' => '[cdm][taxonomictree_uuid]',
989
  );
990

    
991
  $destination_array = drupal_get_destination();
992
  $destination = $destination_array['destination'];
993

    
994
  $form['destination'] = array(
995
    '#weight' => -3,
996
    '#type' => 'hidden',
997
    '#value' =>  $destination,
998
  );
999

    
1000
  $options = cdm_get_taxontrees_as_options();
1001
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1002
  if($taxontree_includes){
1003
    $filtered_options = array();
1004
    foreach($options as $uuid=>$label){
1005
      if(!empty($taxontree_includes[$uuid])){
1006
        $filtered_options[$uuid] = $label;
1007
      }
1008
    }
1009
    $options = $filtered_options;
1010
  }
1011

    
1012
  $form['val'] = array(
1013
    '#type' => 'select',
1014
    '#title' => t('Available classifications'),
1015
    '#default_value' => get_current_classification_uuid(),
1016
    '#options' => $options,
1017
    '#attributes' => array('class' => array('highlite-first-child')),
1018
  );
1019

    
1020
  return $form;
1021

    
1022
}
1023

    
1024
/**
1025
 *
1026
 * @ingroup compose
1027
 */
1028
function compose_classification_selector() {
1029

    
1030
  $destination_array = drupal_get_destination();
1031
  $destination = $destination_array['destination'];
1032

    
1033
  $options = cdm_get_taxontrees_as_options();
1034
  $items = array();
1035
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1036

    
1037
  $current_classification_uuid = get_current_classification_uuid();
1038

    
1039

    
1040
  foreach($options as $uuid=>$label){
1041
    if(!$taxontree_includes || !empty($taxontree_includes[$uuid])){
1042

    
1043
      $class_attributes = '';
1044
      if($current_classification_uuid == $uuid){
1045
        $class_attributes  = array('focused');
1046
      }
1047
      $items[] = array(
1048
        'data' => l($label,
1049
          'cdm_api/setvalue/session',
1050
          array(
1051
            'query' => array(
1052
              'destination' => $destination,
1053
              'val' => $uuid,
1054
              'var' => '[cdm][taxonomictree_uuid]'
1055
            ),
1056
          )
1057
        ),
1058
        'class' => $class_attributes
1059
      );
1060
    }
1061
  }
1062

    
1063
  $render_array = array(
1064
    '#theme' => 'item_list',
1065
    '#type' => 'ul',
1066
    '#items' => $items
1067
  );
1068

    
1069
  return $render_array;
1070
}
1071

    
1072

    
1073
/* UNREACHABLE since action of form directly links to view.
1074
 function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
1075

    
1076
 $_SESSION['cdm']['search'] = $form_values;
1077
 //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
1078
 return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
1079
 //$paramstr = compose_url_prameterstr($form_values);
1080
 //return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
1081
 }
1082
 */
1083
/* ====================== menu callback functions ====================== */
1084
/**
1085
 * @todo Please document this function.
1086
 * @see http://drupal.org/node/1354
1087
 */
1088
/*
1089
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
1090
  static $comment_node_disabled =  0;
1091
  static $comment_node_read_only =  1;
1092
  static $comment_node_read_write =  2;
1093

    
1094
  if ($form_id == 'node_type_form'
1095
   && isset($form['identity']['type'])
1096
   && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
1097
  ) {
1098
    $form['workflow']['comment'] = array(
1099
      '#type' => 'radios',
1100
      '#title' => t('Default comment setting'),
1101
      '#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
1102
      '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
1103
      '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
1104
    );
1105
  }
1106
}
1107
*/
1108

    
1109
/**
1110
 * Displays a list of the known taxonomic names.
1111
 *
1112
 * When the list of taxonomic names is displayed, long lists are split up into
1113
 * multiple pages.
1114
 *
1115
 * TODO: Parameters are still preliminary.
1116
 *
1117
 * @param string $beginsWith
1118
 * @param string $page
1119
 *   Page number to diplay defaults to page 1.
1120
 * @param bool $onlyAccepted
1121
 */
1122
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
1123

    
1124
  $out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
1125

    
1126
  /*
1127
  // FIXME the filter for accepted names will be a form element, thus this
1128
  // widget should be generated via form api preferably as block.
1129
  $out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
1130
  $out .= theme('cdm_dataportal_widget_names_list', $names, $page);
1131
  $out .= theme('cdm_listof_taxa', $taxonPager);
1132
  return $out;
1133
  */
1134
}
1135

    
1136
/**
1137
 * @todo Please document this function.
1138
 * @see http://drupal.org/node/1354
1139
 */
1140
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
1141

    
1142
  cdm_check_valid_portal_page();
1143

    
1144
  return compose_cdm_reference_page($uuid);
1145
}
1146

    
1147
/**
1148
 * Creates a view on a all references contained in the portal.
1149
 *
1150
 * This function is used at the path cdm_dataportal/reference/list
1151
 */
1152
function cdm_dataportal_view_reference_list($pageNumber) {
1153
  $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
1154
  cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
1155
}
1156

    
1157
/**
1158
 * @todo Please document this function.
1159
 * @see http://drupal.org/node/1354
1160
 */
1161
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
1162

    
1163
  cdm_check_valid_portal_page();
1164

    
1165
  $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
1166
  return theme('cdm_media_page', array(
1167
    'media' => $media,
1168
    'mediarepresentation_uuid' => $mediarepresentation_uuid,
1169
    'partId' => $part,
1170
    ));
1171
}
1172

    
1173
/**
1174
 * @todo Please document this function.
1175
 * @see http://drupal.org/node/1354
1176
 */
1177
function _load_taxonBase(&$taxonBase) {
1178
  if (isset($taxonBase->uuid)) {
1179
    $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
1180
    $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
1181
    $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
1182
  }
1183
}
1184

    
1185
/**
1186
 * Loads the media associated to the given taxon from the cdm server.
1187
 * The aggregation settings regarding taxon relathionships and
1188
 * taxonnomic childen are taken into account.
1189
 *
1190
 * The media lists are cached in a static variable.
1191
 *
1192
 * @param Taxon $taxon
1193
 *   A CDM Taxon entitiy
1194
 *
1195
 * @return array
1196
 *   An array of CDM Media entities
1197
 *
1198
 */
1199
function _load_media_for_taxon($taxon) {
1200

    
1201
  static $media = NULL;
1202

    
1203
  if(!isset($media)) {
1204
    $media = array();
1205
  }
1206
  if (!isset($media[$taxon->uuid])) {
1207

    
1208
    // --- GET Images --- //
1209
    $mediaQueryParameters = array(
1210
        "type" => "ImageFile",
1211
    );
1212

    
1213
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1214
    $mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
1215
    $mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
1216

    
1217
    $taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
1218
    $mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
1219
    $mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
1220
    $mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
1221

    
1222
    $ws_endpoint = NULL;
1223
    if ( variable_get('cdm_images_include_children', 0) == 0) {
1224
      $ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1225
    } else {
1226
      $ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1227
    }
1228

    
1229
    $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1230
        array(
1231
            $taxon->uuid,
1232
        ),
1233
        queryString($mediaQueryParameters)
1234
       );
1235
  }
1236

    
1237
  return $media[$taxon->uuid];
1238
}
1239

    
1240
/**
1241
 *
1242
 * @param Taxon $taxon
1243
 *   A CDM Taxon entitiy
1244
 *
1245
 * @return array
1246
 *   An array of CDM SpecimenOrObservation entities
1247
 *
1248
function _load_occurences_for_taxon($taxon){
1249

    
1250
  static $occurences = NULL;
1251

    
1252
  if(!isset($occurences)) {
1253
    $occurences = array();
1254
  }
1255

    
1256
  if (!isset($occurences[$taxon->uuid])){
1257

    
1258
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1259
    $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1260
    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1261

    
1262
    $by_associatedtaxon_query = http_build_query(array(
1263
        'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1264
        'relationships' => implode(',', $relationship_choice['direct']),
1265
        'pageSize' => null // all hits in one page
1266
    )
1267
    );
1268

    
1269
    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1270
        null,
1271
        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1272
    );
1273

    
1274

    
1275
    if(isset($pager->records[0])){
1276
      $occurences[$taxon->uuid] =  $pager->records;
1277
    }
1278
  }
1279
  return $occurences[$taxon->uuid];
1280
}
1281
 */
1282

    
1283
/**
1284
 * Gets a Drupal variable, string or array and returns it.
1285
 *
1286
 * Similar to the variable_get() function of Drupal, except that this function
1287
 * is able to handle arrays correctly. This function is especially useful
1288
 * when dealing with collections of settings form elements (#tree = TRUE).
1289
 *
1290
 * @param string $variableKey
1291
 *   The Unique key of the Drupal variable in the Drupal variables table.
1292
 * @param string $defaultValueString
1293
 *   A string as for example derived from a CONSTANT.
1294
 *
1295
 * @return mixed
1296
 *   usually an array, depending on the nature of the variable.
1297
 *
1298
 * TODO compare with get_array_variable_merged() duplicate functions?
1299
 * @deprecated rather use get_array_variable_merged() since this function
1300
 * used an array as second parameter
1301
 */
1302
function mixed_variable_get($variableKey, $defaultValueString) {
1303
  $systemDefaults = unserialize($defaultValueString);
1304
  $storedSettings = variable_get($variableKey, array());
1305
  if (is_array($storedSettings)) {
1306
    // TODO better use drupal_array_merge_deep() ?
1307
    $settings = array_merge($systemDefaults, $storedSettings);
1308
  }
1309
  else {
1310
    $settings = $systemDefaults;
1311
  }
1312
  return $settings;
1313
}
1314

    
1315
/**
1316
 * Recursive function to convert an object into an array.
1317
 * also subordinate objects will be converted.
1318
 *
1319
 * @param object $object
1320
 *  the object to be converted
1321
 * @return array
1322
 *  The array
1323
 */
1324
function object_to_array($object) {
1325
  if(is_object($object) || is_array($object)) {
1326
    $array = (array)$object;
1327
    foreach ($array as $key=>$value){
1328
      $array[$key] = object_to_array($value);
1329
    }
1330
    return $array;
1331
  } else {
1332
    return $object;
1333
  }
1334
}
1335

    
1336
/**
1337
 * Searches the $collection for the cdm entitiy given as $element.
1338
 *
1339
 * The elements are compared by their UUID.
1340
 *
1341
 * @param $element
1342
 *  the CDM entitiy to search for
1343
 * @param $collection
1344
 *  the list of CDM entities to search in
1345
 *
1346
 * @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1347
 *
1348
 */
1349
function contains_cdm_entitiy($element, $collection) {
1350
  $result = FALSE;
1351
  foreach ($collection as $a) {
1352
    if ($a->uuid == $element->uuid) {
1353
      $result = TRUE;
1354
    }
1355
  }
1356
  return $result;
1357
}
1358

    
1359
/**
1360
 * Fiters the array $entity_list of CDM entities by the list
1361
 * of $excludes. Any element contained in the $excludes will be removed
1362
 * from included int the retuned list.
1363
 *
1364
 * If the $entity_list is not an array the $excludes will be returned.
1365
 */
1366
function filter_cdm_entity_list($entity_list, $excludes) {
1367
  if (is_array($entity_list)) {
1368
    $result = $entity_list;
1369
    if ($excludes) {
1370
      foreach ($excludes as $exclude) {
1371
        if (!contains_cdm_entitiy($exclude, $entity_list)) {
1372
          $result[] = $exclude;
1373
        }
1374
      }
1375
    }
1376
  }
1377
  else {
1378
    $result = $excludes;
1379
  }
1380
  return $result;
1381
}
1382

    
1383
/**
1384
 * Wraps the given $html string into a render array suitable for drupal_render()
1385
 *
1386
 * @param $html
1387
 *   the html string, see
1388
 *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1389
 * @param $weight
1390
 *   A positive or negative number (integer or decimal).
1391
 *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1392
 * @param $prefix
1393
 *   Optional markup for the '#prefix' element of the render array
1394
 * @param $suffix
1395
 *   Optional markup for the '#suffix' element of the render array
1396
 *
1397
 * @return array
1398
 *   A render array
1399
 *
1400
 */
1401
function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1402
  $render_array = array(
1403
    '#markup' => $html
1404
      );
1405
  if (is_numeric($weight)) {
1406
    $render_array['#weight'] = $weight;
1407
  }
1408
  if($prefix){
1409
    $render_array['#prefix'] = $prefix;
1410
  }
1411
  if($suffix) {
1412
    $render_array['#suffix'] = $suffix;
1413
  }
1414
  return $render_array;
1415
}
1416

    
1417
/**
1418
 * Loads the subgraph of a given PolytomousKeyNode.
1419
 *
1420
 * Loads the subgraph of the given PolytomousKeyNode recursively from
1421
 * the CDM REST service.
1422
 *
1423
 * @param mixed $polytomousKeyNode
1424
 *   PolytomousKeyNode passed by reference.
1425
 *
1426
 * @return void
1427
 */
1428
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1429

    
1430
  if (!$polytomousKeyNode) {
1431
    return;
1432
  }
1433
  if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1434
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1435
    return;
1436
  }
1437
  if (!is_uuid($polytomousKeyNode->uuid)) {
1438
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1439
    return;
1440
  }
1441

    
1442
  $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1443

    
1444
  if (!$polytomousKeyNode) {
1445
    // drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1446
    return;
1447
  }
1448

    
1449
  // Load children.
1450
  foreach ($polytomousKeyNode->children as &$childNode) {
1451
    _load_polytomousKeySubGraph($childNode);
1452
  }
1453

    
1454
  // Load subkey.
1455
  $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1456

    
1457
  // Load taxon.
1458
  $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1459
  _load_taxonBase($polytomousKeyNode->taxon);
1460
  return;
1461
}
1462

    
1463
/**
1464
 * @todo Please document this function.
1465
 * @see http://drupal.org/node/1354
1466
 */
1467
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1468

    
1469
  cdm_check_valid_portal_page();
1470

    
1471
  $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1472

    
1473
  $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1474
  if (is_array($sourcePager->records)) {
1475
    $polytomousKey->sources = $sourcePager->records;
1476
    // $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1477
  }
1478

    
1479
  $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1480
  if (is_array($annotationPager->records)) {
1481
    $polytomousKey->annotations = $annotationPager->records;
1482
  }
1483

    
1484
  _load_polytomousKeySubGraph($polytomousKey->root);
1485
  return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1486
}
1487

    
1488
/**
1489
 * Creates a taxon page view or a chapter of it.
1490
 *
1491
 * The taxon page gives detailed information on a taxon, it shows:
1492
 *  - Taxon name.
1493
 *  - Full list of synonyms homotypic synonyms on top, followed by the
1494
 *    heterotypic and finally followed by misapplied names.
1495
 *    The list is ordered historically.
1496
 *  - All description associated with the taxon.
1497
 *
1498
 * @param string $uuid
1499
 * @param string $chapter
1500
 *   Name of the part to display, valid values are:
1501
 *   'description', 'images', 'synonymy', 'specimens', 'all'.
1502
 *
1503
 * @return string
1504
 */
1505
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
1506

    
1507
  cdm_check_valid_taxon_page($chapter);
1508
  cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1509
  // show a warning in case the javascript development mode is anabled
1510
  if(variable_get('cdm_js_devel_mode', FALSE)) {
1511
    drupal_set_message(t('The !url1 is enabled.
1512
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1513
          '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1514
    )),
1515
    'warning'
1516
        );
1517
  }
1518

    
1519
  // Display the page for the taxon defined by $uuid.
1520
  // set_last_taxon_page_tab(arg(3));
1521
  $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
1522
  if (!empty($taxonpage)) {
1523
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1524
    return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1525
  }
1526
  else {
1527
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1528
    return '';
1529
  }
1530
}
1531

    
1532
/**
1533
 * This function will genreate the taxon page part ($chapter) and returns a taxonpage object
1534
 * which has two fields, one for the page title and one for the content. Later on in the
1535
 * process chain the value contained in these fields will be passed to the cdm_node_show()
1536
 * function as the function parameters $title and $content.
1537
 *
1538
 * @param string $uuid
1539
 *   the uuid of the taxon to show
1540
 * @param string $chapter
1541
 *   Name of the part to display, valid values are:
1542
 *   'description', 'images', 'synonymy', 'all'.
1543
 *
1544
 * @return object with the following fields:
1545
 *   - title : the title of the page
1546
 *   - content: the content of the page
1547
 *
1548
 */
1549
function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1550
  // Taxon object.
1551
  $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1552
  if (empty($taxon)) {
1553
    drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1554
    return FALSE;
1555
  }
1556
  $taxonpage = new stdClass();
1557

    
1558
  $taxonpage->title = theme('cdm_taxon_page_title', array(
1559
    'taxon' => $taxon
1560
  ));
1561

    
1562
  // Check if the taxon id contained in the currently selected tree.
1563
  $taxon_in_current_classification = taxon_in_current_classification($uuid);
1564

    
1565
  if (!$taxon_in_current_classification) {
1566
    $classifications = get_classifications_for_taxon($taxon);
1567
    RenderHints::pushToRenderStack('not_in_current_classification');
1568
    $taxon_name_markup = render_taxon_or_name($taxon);
1569

    
1570
    if (count($classifications) == 0) {
1571
      drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
1572
        array(
1573
        '!taxonname' => $taxon_name_markup,
1574
        )
1575
      ), 'warning');
1576
    }
1577
    else {
1578
      $trees = '';
1579
      foreach ($classifications as $classification) {
1580
        if (isset($classification->titleCache)) {
1581
          $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1582
        }
1583
      }
1584

    
1585
      drupal_set_message(format_plural(count($trees),
1586
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in this one: !trees',
1587
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1588
          array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1589
        ) ,
1590
        'warning');
1591
    }
1592
    RenderHints::popFromRenderStack();
1593
  }
1594

    
1595
  // Render the taxon page.
1596
  $render_array = compose_cdm_taxon_page($taxon, $chapter);
1597
  $taxonpage->content = drupal_render($render_array);
1598

    
1599
  return $taxonpage;
1600
}
1601

    
1602
/**
1603
 * Creates a specimen page view.
1604
 * @param string $uuid the UUID of the specimen
1605
 * @return array|string
1606
 */
1607
function cdm_dataportal_specimen_page_view($uuid) {
1608

    
1609
    //cdm_check_valid_taxon_page($chapter);
1610
    //cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1611
    // show a warning in case the javascript development mode is anabled
1612
    if(variable_get('cdm_js_devel_mode', FALSE)) {
1613
        drupal_set_message(t('The !url1 is enabled.
1614
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1615
            '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1616
        )),
1617
            'warning'
1618
        );
1619
    }
1620

    
1621
    // Display the page for the specimen defined by $uuid.
1622
    $specimenpage = cdm_dataportal_specimen_view($uuid);
1623
    if (!empty($specimenpage)) {
1624
        return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
1625
    }
1626
    else {
1627
        return '';
1628
    }
1629
}
1630

    
1631
/**
1632
 *
1633
 * Creates a specimen view.
1634
 * @param string $uuid the UUID of the specimen
1635
 * @return array|string
1636
 */
1637
function cdm_dataportal_specimen_view($uuid) {
1638
    $specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, $uuid);
1639
    if (empty($specimen)) {
1640
        drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1641
        return FALSE;
1642
    }
1643
    $specimenpage = new stdClass();
1644

    
1645
    $specimenpage->title = theme('cdm_specimen_page_title', array(
1646
        'specimen' => $specimen
1647
    ));
1648

    
1649
    // Render the specimen page.
1650
    $render_array = compose_cdm_specimen_page($uuid);
1651
    $specimenpage->content = drupal_render($render_array);
1652

    
1653
    return $specimenpage;
1654
}
1655

    
1656
/**
1657
 *
1658
 * Creates a named area view.
1659
 * @param string $uuid the UUID of the specimen
1660
 *  * @return object
1661
 *   An object with two fields:
1662
 *     - title: the page title
1663
 *     - content: the page content
1664
 */
1665

    
1666
function cdm_dataportal_named_area_view($uuid) {
1667
  $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid);
1668
  if (empty($named_area) || $named_area->class !== 'NamedArea') {
1669
    drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
1670
    return FALSE;
1671
  }
1672
  $named_area_page = new stdClass();
1673

    
1674
  $named_area_page->title = $named_area->representation_L10n;
1675

    
1676
  // Render the specimen page.
1677
  $render_array = compose_cdm_named_area_page($uuid);
1678
  $named_area_page->content = drupal_render($render_array);
1679

    
1680
  return $named_area_page;
1681
}
1682

    
1683
function cdm_dataportal_named_area_page_view($uuid) {
1684

    
1685
  cdm_check_valid_portal_page();
1686

    
1687
  $named_area_page = cdm_dataportal_named_area_view($uuid);
1688
  if (!empty($named_area_page)) {
1689
    return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content);
1690
  }
1691
  else {
1692
    return '';
1693
  }
1694

    
1695

    
1696
}
1697

    
1698
/**
1699
 * Returns a name page as a Drupal node ready to be renderized by Drupal.
1700
 *
1701
 * The node page shows the taxon name title and the list of taxon related
1702
 * with such taxon. Name on the tree already in use.
1703
 *
1704
 * @param UUID $taxon_name_uuid
1705
 *   The uuid of the CDM TaxonName to show a name page for
1706
 * @param UUID $taxon_to_hide_uuid
1707
 *   A taxon which should not be displayed in the taxon list
1708
 * @param UUID $highlite_synonym_uuid
1709
 *   Optinal parameter wich takes another taxon uuid, if given the
1710
 *   target taxon pages will show the syonymy tab where the taxon
1711
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1712
 *   in case it is found on this page.
1713
 *
1714
 * @return mixed
1715
 *   The formatted name page as node.
1716
 */
1717
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
1718

    
1719
  cdm_check_valid_portal_page();
1720

    
1721
  $taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
1722
  if (!empty($taxonname_page)) {
1723
    return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
1724
  }
1725
  else {
1726
    return '';
1727
  }
1728
}
1729

    
1730
/**
1731
 * View function for a TaxonName page.
1732
 *
1733
 * The name page lists all taxa for which the name specified by the
1734
 * $taxon_name_uuid is being used. I case there is only one name the
1735
 * page automatically redirects ti the according taxon page. Otherwise
1736
 * the list of names is displayed.
1737
 *
1738
 * The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
1739
 * list of taxa. This is useful for example when referencing from a taxon
1740
 * to the name page and the referring taxon should not be repeaded in the
1741
 * name page.
1742
 *
1743
 *
1744
 * @param UUID $taxon_name_uuid
1745
 *   The uuid of the CDM TaxonName to show a name page for
1746
 * @param UUID $taxon_to_hide_uuid
1747
 *   A taxon which should not be displayed in the taxon list
1748
 * @param UUID $highlite_synonym_uuid
1749
 *   Optinal parameter wich takes another taxon uuid, if given the
1750
 *   target taxon pages will show the syonymy tab where the taxon
1751
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1752
 *   in case it is found on this page.
1753
 *
1754
 * @return object
1755
 *   An object with two fields:
1756
 *     - title: the page title
1757
 *     - content: the page content
1758
 */
1759
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
1760
  // Getting the full taxonname object from the server.
1761
  $taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
1762
  if (!$taxon_name) {
1763
    drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
1764
    return FALSE;
1765
  }
1766
  // Searching for all the taxa connected with the taxon name on the tree
1767
  // in use.
1768
  $name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
1769
  $request_params = array();
1770
  $request_params['query'] = $name_cache;
1771
  $request_params['tree'] = get_current_classification_uuid();
1772
  $request_params['doTaxa'] = 1;
1773
  $request_params['doSynonyms'] = 1;
1774
  $request_params['doTaxaByCommonNames'] = 0;
1775
  $request_params['matchMode'] = "EXACT";
1776
  $taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
1777

    
1778
  // Removing the name where we came from.
1779
  foreach ($taxon_pager->records as $k => &$taxon) {
1780
    if ($taxon->uuid == $taxon_to_hide_uuid) {
1781
      unset($taxon_pager->records[$k]);
1782
    }
1783
  }
1784
  // Show the taxa list or go to the singular taxon.
1785
  if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
1786
    $singleTaxon = array_pop($taxon_pager->records);
1787
    if ($singleTaxon->class != "Taxon") {
1788
      // It is a Synonym -> look for the accepted.
1789
      $accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid());
1790
      if (!empty($highlite_synonym_uuid)) {
1791
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1792
      }
1793
      else {
1794
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
1795
      }
1796
    }
1797
    else {
1798
      // It is an accepted taxon.
1799
      if (!empty($highlite_synonym_uuid)) {
1800
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1801
      }
1802
      else {
1803
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
1804
      }
1805
    }
1806
  }
1807
  else {// More than one taxa case.
1808
    $taxon_name_page = new stdClass();
1809
    $taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
1810
    if ($taxon_pager->records) {
1811
      $taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
1812
    }
1813
    else {
1814
      $taxon_name_page->content = 'This name is not assigned to a taxon.';
1815
    }
1816
    return $taxon_name_page;
1817
  }
1818
}
1819

    
1820
/**
1821
 * Returns a registration page as a Drupal node to be rendered by Drupal.
1822
 *
1823
 * @param string  $registration_identifier_encoded
1824
 *   The persistent identifier of the registration urlencoded.
1825
 * @return mixed
1826
 *   The formatted registration page as node.
1827
 */
1828
function cdm_dataportal_registration_page_view($registration_identifier_encoded) {
1829

    
1830
  cdm_check_valid_portal_page("/\/cdm_dataportal\/registration\/.*$/");
1831
  $registration_page = cdm_dataportal_registration_view($registration_identifier_encoded);
1832
  return cdm_node_show_simulate($registration_page);
1833
}
1834

    
1835
function cdm_dataportal_registration_view($registration_identifier_encoded) {
1836

    
1837
  $registration_identifier = urldecode($registration_identifier_encoded);
1838

    
1839

    
1840

    
1841
  $render_array = array();
1842
  $registration_dto = cdm_ws_get("registrationDTO/identifier/" . $registration_identifier_encoded);
1843
  if($registration_dto){
1844
    drupal_set_title(t('Registration') . ' ' . $registration_identifier, PASS_THROUGH);
1845

    
1846
    $render_array = compose_registation_dto($registration_dto);
1847

    
1848
    if(is_object($registration_dto->orderdTypeDesignationWorkingSets)){
1849
      $field_unit_uuids = array();
1850
      foreach((array)$registration_dto->orderdTypeDesignationWorkingSets as $field_unit_ref => $obj){
1851
        $tokens = explode("#", $field_unit_ref);
1852
        $field_unit_uuids[] = $tokens[1];
1853
      }
1854
      $render_array['specimen_table'] = compose_derivate_hierarchy_table($field_unit_uuids);
1855
    }
1856

    
1857
  } else {
1858
    drupal_set_title(t('Registration not found'), PASS_THROUGH);
1859
    $render_array['error'] = markup_to_render_array("A registration with the identifier  " . $registration_identifier . " does not exist.");
1860
  }
1861

    
1862
  return $render_array ;
1863
}
1864

    
1865
/**
1866
 * Composes information for a registation from a dtp object
1867
 *
1868
 * @param $registration_dto
1869
 *
1870
 * @return array
1871
 *    A drupal render array
1872
 *
1873
 * @ingroup compose
1874
 */
1875
function compose_registation_dto($registration_dto, $with_citation = true, $with_identifier = false)
1876
{
1877
  $render_array = array();
1878
  if ($with_citation) {
1879
    $render_array['citation'] = markup_to_render_array("<div class=\"" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
1880
      . l($registration_dto->bibliographicCitationString, path_to_reference($registration_dto->citationUuid))
1881
      . "</br>&nbsp;</div>");
1882
  }
1883
  $registation_markup = cdm_tagged_text_to_markup($registration_dto->summaryTaggedText);
1884
  if($with_identifier){
1885
    $registation_markup .= " " . l ($registration_dto->identifier, $registration_dto->identifier);
1886
  }
1887
  $render_array['summary'] = markup_to_render_array("<div>" . $registation_markup . "</div>");
1888
  return $render_array;
1889
}
1890

    
1891

    
1892
/**
1893
 * Creates a page with the advance search form.
1894
 *
1895
 * NOTE: The advance search form allows searching for taxa.
1896
 */
1897
function cdm_dataportal_view_search_advanced() {
1898
  drupal_set_title(t('Advanced search'), PASS_THROUGH);
1899
  return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
1900
}
1901

    
1902
/**
1903
 * Creates a page with the search form for searching by taxon descriptions.
1904
 */
1905
function cdm_dataportal_view_search_taxon_by_description() {
1906
  drupal_set_title(t('Search by factual data'), PASS_THROUGH);
1907
  return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
1908
}
1909

    
1910
/**
1911
 * Executes the search and generates the result list of taxa.
1912
 */
1913
function cdm_dataportal_view_search_results_taxon() {
1914

    
1915
  $taxonPager = cdm_dataportal_search_taxon_execute();
1916

    
1917
  $showThumbnails = do_showThumbnails();
1918

    
1919
  $setSessionUri = url('cdm_api/setvalue/session', array(
1920
      'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
1921
  ));
1922

    
1923
  drupal_add_js('jQuery(document).ready(function() {
1924

    
1925
      // init
1926
      if(' . $showThumbnails . ' == 1){
1927
          jQuery(\'.media_gallery\').show(20);
1928
      } else {
1929
          jQuery(\'.media_gallery\').hide(20);
1930
      }
1931

    
1932
      // add change handler
1933
      jQuery(\'#showThumbnails input.showThumbnails\').change(
1934
      function(event){
1935
        var state = 0;
1936
        if(jQuery(this).is(\':checked\')){
1937
          jQuery(\'.media_gallery\').show(20);
1938
          state = 1;
1939
        } else {
1940
          jQuery(\'.media_gallery\').hide(20);
1941
        }
1942
        // store state in session variable
1943
        var uri = \'' . $setSessionUri . '\' + state;
1944
        jQuery.get(uri);
1945
      });
1946
  });',
1947
  array('type' => "inline", 'scope' => JS_DEFAULT));
1948

    
1949
  drupal_set_title(t('Search results'), PASS_THROUGH);
1950

    
1951
  return theme('cdm_search_taxa_results', array(
1952
    'pager' => $taxonPager,
1953
    'path' => 'cdm_dataportal/search/results/taxon',
1954
    ));
1955
}
1956

    
1957
/**
1958
 * Executes the search for registrations and generates the result list..
1959
 */
1960
function cdm_dataportal_view_search_registrations_results() {
1961

    
1962
  $block = block_load('cdm_dataportal', 'registrations_search_filter');
1963
  $render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
1964

    
1965
  $registration_pager = cdm_dataportal_search_registrations_execute();
1966

    
1967
  drupal_set_title(t('Search registrations'), PASS_THROUGH);
1968

    
1969
  $registrations_pager_array = compose_registrations_search_results($registration_pager);
1970

    
1971
  $render_array = array_merge($render_array, $registrations_pager_array);
1972

    
1973
  return $render_array;
1974
}
1975

    
1976

    
1977
/**
1978
 * Provides the standart image wich indicated a loading process
1979
 *
1980
 * @return string
1981
 *  The img html tag
1982
 */
1983
function loading_image_html() {
1984
  return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
1985
    . '/images/loading_circle_grey_16.gif" style="display:none;">';
1986
}
1987

    
1988
/**
1989
 * Returns the state of the the showThumbnails flag set in the
1990
 * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
1991
 *
1992
 * @return boolean
1993
 *    returns 1 if the flag is set
1994
 */
1995
function do_showThumbnails() {
1996
  static $showThumbnails = null;
1997

    
1998
  if($showThumbnails == null) {
1999
    $showThumbnails = 0;
2000
    if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
2001
      $showThumbnails = 0;
2002
      $search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
2003
      $showThumbnails = is_array($search_gallery_settings)
2004
        && isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
2005
        && (
2006
            $search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
2007
            $search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
2008
            $search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
2009
            )
2010
         ? 1 : 0;
2011

    
2012
       drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
2013
    }
2014
    $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
2015
    if (!is_numeric($showThumbnails)) {
2016
      $showThumbnails = 1;
2017
    }
2018
  }
2019

    
2020
  return $showThumbnails;
2021
}
2022

    
2023

    
2024

    
2025
/* ====================== other functions ====================== */
2026
/**
2027
 * Creates a URL to the taxon page specified by the $uuid parameter.
2028
 *
2029
 * The URL will be prepended with a path element to a specific taxon page tab.
2030
 *
2031
 * This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
2032
 * be set globally in the administrative settings or individually in the user
2033
 * profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
2034
 * the last portal will stay on this last tab.
2035
 *
2036
 * A third option is offerered by the $page_tab parameter which allows overwriting this
2037
 * internal mechanism by a specific value.
2038
 *
2039
 * @param string $uuid
2040
 *   The UUID of the taxon.
2041
 * @param string $page_tab
2042
 *   Overwriting the preset mechanism by defining specific value for the
2043
 *   taxon page tab.
2044
 *
2045
 * @return string
2046
 *   The created URL.
2047
 */
2048
function path_to_taxon($uuid, $page_tab = FALSE) {
2049

    
2050
  $tab = get_default_taxon_tab();
2051
  $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
2052

    
2053
  if (!$uuid) {
2054
    return FALSE;
2055
  }
2056

    
2057
  if ($page_tab) {
2058
    return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
2059
  }
2060
  elseif (!$tab || strtolower($tab) == 'general') {
2061
    return 'cdm_dataportal/taxon/' . $uuid;
2062
  }
2063
  elseif (get_last_taxon_page_tab() &&   $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
2064
    return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
2065
  }
2066
  else {
2067
    return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
2068
  }
2069
}
2070

    
2071
function path_to_specimen($uuid) {
2072

    
2073
    if (!$uuid) {
2074
        return FALSE;
2075
    }
2076
    else {
2077
        return 'cdm_dataportal/specimen/' . $uuid;
2078
    }
2079
}
2080

    
2081
function path_to_named_area($uuid) {
2082

    
2083
  if (!$uuid) {
2084
    return FALSE;
2085
  }
2086
  else {
2087
    return 'cdm_dataportal/named_area/' . $uuid;
2088
  }
2089
}
2090

    
2091
/**
2092
 * Creates a URL to show a synonmy in the according taxon page.
2093
 *
2094
 * The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
2095
 * The resulting URI will include query parameters to highlight the synonym, and to optionally display
2096
 * the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
2097
 * include the sysnonym uuid as fragment in order to let the browser scroll to the according location
2098
 * in the page
2099
 *
2100
 * @param string $synonymUuid
2101
 *    The uuid of the synonym
2102
 * @param string $acceptedUuid
2103
 *    The uuid of the according accepted taxon
2104
 * @return string
2105
 *    The URL to show a synonmy in the according taxon page
2106
 */
2107
function uri_to_synonym($synonymUuid, $acceptedUuid) {
2108
  $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
2109
  return url($acceptedPath, array(
2110
      'query' => array(
2111
        // highlite the synony in the synonymy
2112
        'highlite' => $synonymUuid,
2113
        // the taxon page is refered from a synonym and the synonym can optionally be named in the page title
2114
        // see theme_taxon_page_title()
2115
        'acceptedFor' => $synonymUuid
2116
      ),
2117
      'fragment' => $synonymUuid
2118
  ));
2119

    
2120
}
2121

    
2122
/**
2123
 * Composes the drupal path to the key identified by the uuid.
2124
 *
2125
 * @param string $keyType
2126
 *    the key typer corresponds to the specific class of the CDM
2127
 *    IdentificationKey. Possible values are
2128
 *      -PolytomousKey
2129
 *      -MultimediaKey
2130
 *      - ...
2131
 * @param string $keyUuid
2132
 *   The UUID of the key
2133
 */
2134
function path_to_key($keyType, $keyUuid) {
2135
  if (!$keyUuid || !$keyType) {
2136
    return FALSE;
2137
  }
2138
  $keyType{0} = strtolower($keyType{0});
2139
  return "cdm_dataportal/" . $keyType . "/$keyUuid";
2140
}
2141

    
2142
/**
2143
 * Composes the drupal path to the reference identified by the uuid.
2144
 *
2145
 * @param $uuid string String representation of the registration entity uuid.
2146
 *
2147
 * @return string
2148
 *  The drupal path
2149
 *
2150
 */
2151
function path_to_reference($uuid) {
2152
  if (!$uuid) {
2153
    return FALSE;
2154
  }
2155
  return 'cdm_dataportal/reference/' . $uuid;
2156
}
2157

    
2158
/**
2159
 * Composes the drupal path to the reference identified by the uuid.
2160
 *
2161
 * @param string $identifier
2162
 *  The persistent identifier of the registration entity (Registration.identifier).
2163
 * @return string
2164
 *  The drupal path
2165
 */
2166
function path_to_registration($identifier) {
2167

    
2168
  return 'cdm_dataportal/registration/' . urlencode($identifier);
2169
}
2170

    
2171
/**
2172
 * Creates the path to a cdm_dataportal taxon name page.
2173
 *
2174
 * @param string $taxon_name_uuid
2175
 *   The uuid as string of the CDM TaxonName to show a name page for
2176
 * @param string $taxon_to_hide_uuid
2177
 *   The uuid as string of a taxon which should not be displayed in the taxon list
2178
 * @param string $highlite_synonym_uuid
2179
 *   Optional parameter which takes another taxon uuid, if given the
2180
 *   target taxon pages will show the synonymy tab where the taxon
2181
 *   referenced by the $highlite_synonym_uuid will be highlighted
2182
 *   in case it is found on this page.
2183
 *
2184
 * @return string
2185
 *  URI path element as string
2186
 */
2187
function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid  = NULL) {
2188
  $res = FALSE;
2189
  if ($name_uuid) {
2190
    $res = 'cdm_dataportal/name/' . $name_uuid;
2191
  }
2192
  if($taxon_to_hide_uuid){
2193
    $res .= '/' . $taxon_to_hide_uuid;
2194
    if($synonym_uuid){
2195
      $res .= '/' . $synonym_uuid;
2196
    }
2197
  }
2198
  return $res;
2199
}
2200

    
2201
/**
2202
 * Composes the drupal path to the media entity identified by the uuid.
2203
 *
2204
 * @param string $uuid
2205
 *  The persistent identifier of the entity entity
2206
 * @return string
2207
 *  The drupal path
2208
 */
2209
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
2210
  if (!$uuid) {
2211
    return FALSE;
2212
  }
2213
  $out = 'cdm_dataportal/media/' . $uuid;
2214
  if ($representaion_uuid) {
2215
    $out .= '/' . $representaion_uuid;
2216
    if (is_numeric($partId)) {
2217
      $out .= '/' . $partId;
2218
    }
2219
  }
2220
  return $out;
2221
}
2222

    
2223
/**
2224
 * Compares thisRank with thatRank.
2225
 *
2226
 * Returns a negative integer, zero, or a positive integer
2227
 * as the of thisRank is higher than, equal to, or lower than thatRank.
2228
 * e.g:
2229
 * <ul>
2230
 * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
2231
 * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
2232
 * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
2233
 * </ul>
2234
 * <p>
2235
 * This compare logic of the underlying webservice is the
2236
 * <b>inverse logic</b> of the the one implemented in
2237
 * java.lang.Comparable#compareTo(java.lang.Object)
2238
 *
2239
 * @param $thisRankUuid
2240
 * @param $thatRankUuid
2241
 *
2242
 * @return int
2243
 *   A negative integer, zero, or a positive integer
2244
 *   as the thisRank is lower than, equal to, or higher than thatRank.
2245
 */
2246
function rank_compare($thisRankUuid, $thatRankUuid) {
2247
  $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
2248
  return $result->Integer;
2249
}
2250

    
2251
/**
2252
 * Composes an HTML element class attribute value composed of
2253
 * the short-name of the cdm class and the uuid of the entity.
2254
 * This class attribute should be used wherever an cdm-entity is rendered.
2255
 *
2256
 * In case of Taxon entities or TaxonNodeDTOs the secReference is also added
2257
 * to the class attributes as 'sec_uuid:<uuid>'. In case of TaxonNodeDTOs the
2258
 * Taxon uuid is added also as taxon_uuid:<uuid>
2259
 *
2260
 * These according class selectors in css must be escaped, eg:
2261
 *    .cdm\:TextData
2262
 *
2263
 * @param $cdm_entity
2264
 *    A CDM entity, TaxonNodeDTO or TypedEntityReference
2265
 */
2266
function html_class_attribute_ref($cdm_entity) {
2267

    
2268
  $attributes = '';
2269
  if (is_cdm_entity($cdm_entity)) {
2270
    $attributes =  "cdm:" . $cdm_entity->class . " uuid:" . $cdm_entity->uuid;
2271
  } else if($cdm_entity->class == 'TypedEntityReference') {
2272
    $attributes =  "cdm:" . $cdm_entity->type . " uuid:" . $cdm_entity->uuid;
2273
  }
2274
  if($cdm_entity->class == 'TaxonNodeDto'){
2275
    $attributes .= " taxon_uuid:"  . $cdm_entity->taxonUuid . " sec_uuid:"  . $cdm_entity->secUuid;;
2276
  }
2277
  if($cdm_entity->class == 'Taxon' && isset($cdm_entity->sec->uuid)){
2278
    $attributes .= " sec_uuid:"  . $cdm_entity->sec->uuid;
2279
  }
2280
  return $attributes;
2281
}
2282

    
2283

    
2284
/**
2285
 * Creates a short version of a taxonname.
2286
 *
2287
 * The short name is created by using the taggedTitle field of
2288
 * TaxonNodeDTO instances.
2289
 * If the taggedTitle if empty the fullname will be returned.
2290
 *
2291
 * @param object $taxonNodeDTO
2292
 *   A TaxonNodeDTO object
2293
 *
2294
 * @return string
2295
 */
2296
function cdm_dataportal_shortname_of($taxonNodeDTO) {
2297

    
2298
  $nameStr = '';
2299

    
2300
  normalize_tagged_text($taxonNodeDTO->taggedTitle);
2301

    
2302
  // Get all tagged text tokens of the scientific name.
2303
  foreach ($taxonNodeDTO->taggedTitle as $tagtxt) {
2304
    if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
2305
      $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
2306
    }
2307
  }
2308
  $nameStr = trim($nameStr);
2309

    
2310
  if ($nameStr) {
2311

    
2312
    // Do not return short names for these.
2313
    if ($taxonNodeDTO->unplaced || $taxonNodeDTO->excluded) {
2314
      return $nameStr;
2315
    }
2316

    
2317
    /*
2318
    1st capture group (^[a-zA-Z]): First letter of uninomial.
2319
    Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
2320
    Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
2321
    but only matching if no '(' or '.' in second word of name,        ( \x2E = '.')
2322
    OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$             (\x22= '"', \x2D='-', \xD7='×' )
2323
    */
2324
    $pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
2325
    if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
2326
      return $matches[1][0] . "." . $matches[3][0];
2327
    }
2328
    else {
2329
      return $nameStr;
2330
    }
2331
  }
2332
  else {
2333
    return $taxonNodeDTO->titleCache;
2334
  }
2335
}
2336

    
2337
/**
2338
 * Check if a taxon is accepted by the current taxonomic tree.
2339
 *
2340
 * @param mixed $taxon
2341
 *   The Taxon obkect to check.
2342
 *
2343
 * @return bool
2344
 *   Returns TRUE if $taxon is accepted, FALSE otherwise.
2345
 */
2346
function _cdm_dataportal_acceptedByCurrentView($taxon) {
2347

    
2348
  $defaultTreeUuid = get_current_classification_uuid();
2349

    
2350
  if (isset($taxon->taxonNodes)) {
2351
    $taxonNodes = $taxon->taxonNodes;
2352
  }
2353
  else {
2354
    $taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
2355
  }
2356

    
2357
  if ($taxon->class == "Taxon" && isset($taxonNodes)) {
2358
    foreach ($taxonNodes as $node) {
2359
      if (isset($node->classification)){
2360
        if(is_object($node->classification)) {
2361
          if ($node->classification->uuid == $defaultTreeUuid) {
2362
            return TRUE;
2363
          }
2364
        }
2365
        else {
2366
          if ($node->classification == $defaultTreeUuid) {
2367
            return TRUE;
2368
          }
2369
        }
2370
      }
2371
    }
2372
  }
2373

    
2374
  return FALSE;
2375
}
2376

    
2377
/**
2378
 * Checks is the source has one of the given types.
2379
 *
2380
 * @param object $source
2381
 *   The original source entity
2382
 * @param array $types
2383
 *   An array of elementd of the OriginalSourceType enumeration
2384
 *   If not set the default will be used which is:
2385
 *    - Lineage
2386
 *    - PrimaryMediaSource
2387
 *    - PrimaryTaxonomicSource
2388
 *    - Unknown
2389
 *    - Other
2390
 * @return boolean
2391
 */
2392
  function _is_original_source_type($source, $types = null) {
2393
    // this is the default
2394
    // maybe this should also be put into the settings
2395
    static $default = array(
2396
      OriginalSourceType::Lineage,
2397
      OriginalSourceType::PrimaryMediaSource,
2398
      OriginalSourceType::PrimaryTaxonomicSource,
2399
      OriginalSourceType::Unknown,
2400
      OriginalSourceType::Other,
2401
    );
2402

    
2403
    if(!$types){
2404
      $types = $default;
2405
    }
2406
    return isset($source->type) && in_array($source->type, $types);
2407
  }
2408

    
2409
/**
2410
 * @todo Please document this function.
2411
 * @see http://drupal.org/node/1354
2412
 */
2413
function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
2414
  return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
2415
}
2416

    
2417

    
2418
/**
2419
 * Collects all the media from a list of description elements.
2420
 *
2421
 * @param array $descriptionElements
2422
 *   The description elements from which to collect the media.
2423
 *
2424
 * @return array
2425
 *   The output with all the collected media.
2426
 */
2427
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2428

    
2429
  $outArrayOfMedia = array();
2430

    
2431
  // Avoiding a warning box in Drupal for Flora Malesiana.
2432
  if (isset($descriptionElements) && is_array($descriptionElements)) {
2433
    foreach ($descriptionElements as $descriptionElement) {
2434
      if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2435
        foreach ($descriptionElement->media as $media) {
2436
          if (is_object($media)) {
2437
            $outArrayOfMedia[] = $media;
2438
          }
2439
        }
2440
      }
2441
    }
2442
  }
2443
  return $outArrayOfMedia;
2444
}
2445

    
2446
/**
2447
 * @todo Please document this function.
2448
 * @see http://drupal.org/node/1354
2449
 *
2450
 * @param array $cdm_entities
2451
 *   An array of CdmBase instances or a single instance.
2452
 * @param string $footnote_list_key_suggestion
2453
 *
2454
 * @return unknown
2455
 */
2456
function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
2457

    
2458
   static $annotations_types_filter = null;
2459
   if(!$annotations_types_filter) {
2460
     $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
2461
   }
2462

    
2463
  $footNoteKeys = array();
2464

    
2465
  // Is argument cdmBase an array?
2466
  if (!is_array($cdm_entities)) {
2467
    $cdmBase_array = array();
2468
    $cdmBase_array[] = $cdm_entities;
2469
  }
2470
  else {
2471
    $cdmBase_array = $cdm_entities;
2472
  }
2473

    
2474
  // Getting the key for the footnotemanager.
2475
  if (isset($footnote_list_key_suggestion)) {
2476
    $footnote_list_key = $footnote_list_key_suggestion;
2477
  }
2478
  else {
2479
    $footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2480
  }
2481

    
2482
  // Adding the footnotes keys.
2483
  foreach ($cdmBase_array as $cdmBase_element) {
2484
    $annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
2485
    if (is_array($annotations)) {
2486
      foreach ($annotations as $annotation) {
2487
        $footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2488
      }
2489
    }
2490
  }
2491

    
2492
  return $footNoteKeys;
2493
}
2494

    
2495

    
2496
/**
2497
 * Creates a CDM Dynabox.
2498
 *
2499
 * @param string $dynabox_id
2500
 *   a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2501
 * @param string $label
2502
 *   The clickable text to show.
2503
 * @param string $content_url
2504
 *   The cdm REST service request url wich will deliver the content to be shown
2505
 *   once the dynabox toggles open.
2506
 * @param string $theme
2507
 *   The theme to be used for rendering the cdm REST service response with is
2508
 *   returned from the $content_url.
2509
 * @param string $link_alt_text
2510
 *   The value for the alt attribute of the dynabox link.
2511
 * @param array $enclosingtags
2512
 *   An array with two elements: $enclosingtags[0] will be used for the dynabox
2513
 *   element itself, $enclosingtags[1] is the tag to be used for the
2514
 *   dynabox_content (optional)
2515
 * @param array $attributes
2516
 * @param $content_element_selector
2517
 *   Optional jQuery selector which can be used to reference a dom element which should
2518
 *   be used as container for the content to be shown. The dynabox-<dynabox id>-content
2519
 *  element will be placed in this container.
2520
 *
2521
 * @param string $open_callback
2522
 *   optional javascript call back function to be triggered after toggling the box to
2523
 *   the open state.
2524
 * @param string $close_callback
2525
 *   optional javascript call back function to be triggered after toggling the box to
2526
 *   the closed state.
2527
 * @return string Returns HTML for a dynabox.
2528
 * Returns HTML for a dynabox.
2529
 */
2530
function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2531
                     $enclosingtags = array('li', 'ul'), $attributes = array(),
2532
                     $content_element_selector = null,
2533
                     $open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2534
  $out = '';
2535

    
2536
  // check for plain class attribute string
2537
  $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2538

    
2539
  if(!array_key_exists('class', $attributes)) {
2540
    $attributes['class'] = array();
2541
  }
2542
  $attributes['id'][] = 'dynabox-' . $dynabox_id;
2543
  $dynabox_attributes = drupal_attributes($attributes);
2544

    
2545

    
2546
  _add_js_domEvent(); // requires domEvent.js
2547
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2548
  drupal_add_js("
2549
  jQuery(document).ready(
2550
      function() {
2551
        dynabox('". $dynabox_id ."',
2552
          {
2553
            open_callback: " . $open_callback .",
2554
            close_callback: " . $close_callback .
2555
            ($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2556
          }
2557
        );
2558
      }
2559
   );",
2560
   array(
2561
    'type'=>'inline',
2562
    'scope'=>'footer'
2563
    )
2564
  );
2565

    
2566

    
2567
  $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2568
  $out .= '<!-- dynabox for ' . $content_url . ' -->';
2569
  $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>';
2570
  $out .= '  <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2571
  $out .= '    <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2572
  $out .= '    </' . $enclosingtags[1] . '>';
2573
  $out .= '  </' . $enclosingtags[0] . '>';
2574
  $out .= '<!-- dynabox end -->';
2575
  return $out;
2576
}
2577

    
2578
/**
2579
 * Checks whether a feature has any description elements.
2580
 *
2581
 * @param mixed $featureNode
2582
 *   A feature node as produced by the function _mergeFeatureTreeDescriptions().
2583
 *
2584
 * @see _mergeFeatureTreeDescriptions()
2585
 *
2586
 * @return bool
2587
 *   Returns TRUE if the given $featureNode or any of its subordinate nodes
2588
 *   contains at least one non empty TextData or at least one DescriptionElement
2589
 *   of an other type. A TextData element holding a multilanguageText or a
2590
 *   source reference is considered to be not empty.
2591
 *
2592
 * @TODO this function may have become obsolete by the new method of detecting empty blocks,
2593
 *       see $block_content_is_not_empty in make_feature_block_list() and
2594
 *       $feature_block_has_content in compose_feature_block_items_generic
2595
 */
2596
function has_feature_node_description_elements($featureNode) {
2597

    
2598
  if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2599
    if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2600
      foreach ($featureNode->descriptionElements as $descriptionElement) {
2601
        if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
2602
          && $descriptionElement->multilanguageText_L10n->text != ''
2603
          || isset($descriptionElement->sources[0])
2604
          || isset($descriptionElement->media[0]) ) {
2605
          return TRUE;
2606
        }
2607
      }
2608
    }
2609
  }
2610
  else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2611
    foreach ($featureNode->childNodes as $child) {
2612
      if (has_feature_node_description_elements($child)) {
2613
        return TRUE;
2614
      }
2615
    }
2616
  }
2617
  return FALSE;
2618
}
2619

    
2620
/**
2621
 * Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
2622
 *
2623
 * @param $chapter
2624
 *   The taxon page chapter or part
2625
 */
2626
function cdm_check_valid_taxon_page($chapter){
2627
  static $taxon_tabs = null;
2628

    
2629
  cdm_check_valid_portal_page();
2630

    
2631
  if($taxon_tabs == null){
2632
    $taxon_tabs = array('all', 'description');
2633
    foreach(get_taxon_tabs_list() as $tab){
2634
      $taxon_tabs[] = strtolower($tab);
2635
    }
2636
  }
2637

    
2638
  if(!in_array($chapter, $taxon_tabs)){
2639
    // oops this is not a valid chapter name
2640
    http_response_code(404); // 404 = Not Found
2641
  }
2642

    
2643
}
2644

    
2645
/**
2646
 * Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise.
2647
 * The test applied by default it a check for the query parameter 'q' ending with a file suffix like '*.*'
2648
 *
2649
 * @param $preg_pattern
2650
 *   Optional regular expression pattern to be used in preg_match().
2651
 */
2652
function cdm_check_valid_portal_page($preg_pattern = null){
2653
  $ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
2654
  if($preg_pattern === null){
2655
    $preg_pattern = $ends_with_file_suffix_pattern;
2656
  }
2657
  if(preg_match($preg_pattern, $_GET['q'])){
2658
    // oops this urls ends with a file_suffix and thus does not refer to a portal page
2659
    http_response_code(404); // 404 = Not Found
2660
    exit('HTTP 404');
2661
  }
2662
}
2663

    
2664
/**
2665
 * Generates the diff of the texts and presents it in a HTML diff viewer.
2666
 *
2667
 * @param $text_a
2668
 * @param $text_b
2669
 * @return string
2670
 */
2671
function diff_viewer($text_a, $text_b) {
2672

    
2673
  static $diff_viewer_count = 0;
2674

    
2675
  $element_id = 'part_definitions_diff_' . $diff_viewer_count++;
2676

    
2677
  // http://code.stephenmorley.org/php/diff-implementation/
2678
  module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
2679
  drupal_add_css(drupal_get_path('module',
2680
      'cdm_dataportal') . '/css/diff.css');
2681
  _add_jquery_ui();
2682
  drupal_add_js(
2683
    'jQuery(document).ready( function(){
2684
        jQuery(\'#' . $element_id . '\').accordion({
2685
        collapsible: true,
2686
        active: false,
2687
        fillSpace: true,
2688
        }).children(\'div\').css({ \'height\': \'auto\' });
2689
        jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
2690
     });'
2691
    , array(
2692
    'type' => 'inline',
2693
    'scope' => 'footer'
2694
  ));
2695

    
2696
  $diff = Diff::compare($text_a,
2697
    $text_b);
2698
  $diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
2699
    . Diff::toTable($diff, '', '')
2700
    . '</div></div>';
2701
  return $diff_viewer_markup;
2702
}
2703

    
2704

    
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