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cdm-dataportal / modules / cdm_dataportal / cdm_dataportal.module @ 442f63c3

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1
<?php
2
/**
3
 * @file
4
 * Module to provide a CDM Dataportal.
5
 *
6
 * @copyright
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 *   (C) 2007-2012 EDIT
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 *   European Distributed Institute of Taxonomy
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 *   http://www.e-taxonomy.eu
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 *
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 *   The contents of this module are subject to the Mozilla
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 *   Public License Version 1.1.
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 * @see http://www.mozilla.org/MPL/MPL-1.1.html
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 *
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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');
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  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');
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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');
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  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');
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  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) {
99
    //         $(document).ready(function() {
100
    //       		$('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
101
    //         });
102
    //       }", 'inline');
103
    }
104

    
105
  /**
106
   * @todo Please document this function.
107
   * @see http://drupal.org/node/1354
108
   */
109
  function _add_js_treeselector() {
110
    // drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
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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(
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        '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
        },
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        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)){
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      // 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,
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        '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',
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        'group' => JS_LIBRARY,
177
        'weight' => -1, // before open layers
178
        'cache' => TRUE,
179
      )
180
    );
181

    
182
    // 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',
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    // 'cdm_dataportal').'/js/jquery.imagetool.min.js');
215
    //
216
    // 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');
226
        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
    _add_font_awesome_font();
344

    
345

    
346
    if($icon_name){
347
      if(!isset($attributes['class'])){
348
        $attributes['class'] = array();
349
      }
350
      $attributes['class'][] = 'fa';
351
      $attributes['class'][] = $icon_name;
352

    
353
      return '<i ' . drupal_attributes($attributes) . '></i>';
354
    }
355

    
356
    return '';
357
  }
358

    
359
/**
360
 * Adds the css  containing the font awesome icons to the html header.
361
 */
362
function _add_font_awesome_font()
363
{
364
//<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
365

    
366
  $font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal') . '/fonts/font-awesome-4.6.3/css/font-awesome.min.css';
367
  //$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
368

    
369
  drupal_add_html_head_link(
370
    array(
371
      'href' => $font_awesome_css_uri,
372
      'rel' => 'stylesheet'
373
    )
374
  );
375
}
376

    
377

    
378
/* ====================== hook implementations ====================== */
379
  /**
380
   * Implements hook_permission().
381
   *
382
   * Valid permissions for this module.
383
   *
384
   * @return array
385
   *   An array of valid permissions for the cdm_dataportal module.
386
   */
387
  function cdm_dataportal_permission() {
388
    return array(
389
      'administer cdm_dataportal' => array(
390
        'title' => t('Administer CDM DataPortal settings'),
391
        'description' => t("Access the settings pages specific for the cdm_dataportal module"),
392
      ),
393
      'access cdm content' => array(
394
        'title' => t('Access CDM content'),
395
        'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
396
      ),
397
    );
398
  }
399

    
400
/**
401
 * Implements hook_menu().
402
 */
403
function cdm_dataportal_menu() {
404
  $items = array();
405

    
406
  // @see settings.php.
407
  cdm_dataportal_menu_admin($items);
408
  cdm_dataportal_menu_help($items);
409

    
410
  $items['cdm_dataportal/names'] = array(
411
    'page callback' => 'cdm_dataportal_view_names',
412
    'access arguments' => array('access cdm content'),
413
    'type' => MENU_CALLBACK,
414
  );
415

    
416
  // Optional callback arguments: page.
417
  $items['cdm_dataportal/taxon'] = array(
418
    'page callback' => 'cdm_dataportal_taxon_page_view',
419
    'access arguments' => array('access cdm content'),
420
    'type' => MENU_CALLBACK,
421
    // Expected callback arguments: uuid.
422
  );
423

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

    
431
  $items['cdm_dataportal/named_area'] = array(
432
    'page callback' => 'cdm_dataportal_named_area_page_view',
433
    'access arguments' => array('access cdm content'),
434
    'type' => MENU_CALLBACK,
435
    // Expected callback arguments: uuid.
436
  );
437

    
438
  $items['cdm_dataportal/name'] = array(
439
    'page callback' => 'cdm_dataportal_name_page_view',
440
      /*
441
    'page arguments' => array(
442
       'taxon_name_uuid',
443
       'taxon_to_hide_uuid',
444
       'synonym_uuid' => NULL
445
      ),
446
      */
447
    'access arguments' => array('access cdm content'),
448
    'type' => MENU_CALLBACK,
449
    // Expected callback arguments: uuid.
450
  );
451

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

    
459
  $items['cdm_dataportal/reference/list'] = array(
460
    'page callback' => 'cdm_dataportal_view_reference_list',
461
    'access arguments' => array('access cdm content'),
462
    'type' => MENU_CALLBACK,
463
    // Expected callback arguments: uuid.
464
  );
465

    
466
  $items['cdm_dataportal/media'] = array(
467
    'page callback' => 'cdm_dataportal_view_media',
468
    'access arguments' => array('access cdm content'),
469
    'type' => MENU_CALLBACK,
470
    // Expected callback arguments:
471
    // uuid, mediarepresentation_uuid, part_uuid or part#.
472
  );
473

    
474
  $items['cdm_dataportal/polytomousKey'] = array(
475
    'page callback' => 'cdm_dataportal_view_polytomousKey',
476
    'access arguments' => array('access cdm content'),
477
    'type' => MENU_CALLBACK,
478
    // Expected callback arguments: polytomousKey->uuid.
479
  );
480

    
481
  $items['cdm_dataportal/search'] = array(
482
    'page callback' => 'cdm_dataportal_view_search_advanced',
483
    'access arguments' => array('access cdm content'),
484
    'type' => MENU_CALLBACK,
485
  );
486

    
487
  $items['cdm_dataportal/search/advanced'] = array(
488
    'title' => 'Advanced', // will be passed through t()
489
    'page callback' => 'cdm_dataportal_view_search_advanced',
490
    'access arguments' => array('access cdm content'),
491
    'type' => MENU_DEFAULT_LOCAL_TASK,
492
  );
493

    
494
  $items['cdm_dataportal/search/taxon_by_description'] = array(
495
    'title' => 'By content category', // will be passed through t()
496
    'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
497
    'access arguments' => array('access cdm content'),
498
    'type' => MENU_LOCAL_TASK,
499
  );
500

    
501
  $items['cdm_dataportal/search/results/taxon'] = array(
502
    'page callback' => 'cdm_dataportal_view_search_results_taxon',
503
    'access arguments' => array('access cdm content'),
504
    'type' => MENU_CALLBACK,
505
  );
506
  $items['cdm_dataportal/search/registration'] = array(
507
    'page callback' => 'cdm_dataportal_view_search_registrations_results',
508
    'access arguments' => array('access cdm content'),
509
    'type' => MENU_CALLBACK,
510
  );
511
  // Optional callback arguments: page.
512
  $items['cdm_dataportal/registration'] = array(
513
    'page callback' => 'cdm_dataportal_registration_page_view',
514
    'access arguments' => array('access cdm content'),
515
    'type' => MENU_CALLBACK,
516
    // Expected callback arguments: uuid.
517
  );
518

    
519
  /*
520
   $items['cdm/xml2json'] = array(
521
   'page callback' => 'cdm_view_xml2json',
522
   'access arguments' => array('access cdm content'),
523
   'type' => MENU_CALLBACK,
524
   );
525
   */
526

    
527
  // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
528
  // User configuration of cdm_dataportal.
529
  $items['user/%/cdm_dataportal'] = array(
530
    'title' => 'cdm_dataportal',
531
    'access arguments' => array('access cdm content'),
532
    'page callback' => 'drupal_get_form',
533
    'page arguments' => array('cdm_dataportal_user_form'),
534
    'type' => MENU_LOCAL_TASK,
535
    'weight' => 10,
536
  );
537
  // }
538

    
539
  // 'May not cache' in D5.
540
  $items['cdm_dataportal/name/%'] = array(
541
    // 'page callback' => 'cdm_dataportal_view_name',
542
    'page callback' => 'cdm_dataportal_name_page_view',
543
    'page arguments' => array(2, 3, 4),
544
    'access arguments' => array('access cdm content'),
545
    'type' => MENU_CALLBACK,
546
  );
547

    
548
  // --- Local tasks for Taxon.
549
  // --- tabbed taxon page
550
  if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
551
    $items['cdm_dataportal/taxon/%'] = array(
552
      'title' => cdm_taxonpage_tab_label('General'),
553
      'page callback' => 'cdm_dataportal_taxon_page_view',
554
      'access arguments' => array('access cdm content'),
555
      'type' => MENU_CALLBACK,
556
      'weight' => 1,
557
      'page arguments' => array(2, "description")
558
      , // Expected callback arguments: taxon_uuid.
559
    );
560

    
561
    $items['cdm_dataportal/taxon/%/all'] = array(
562
      'title' => cdm_taxonpage_tab_label('General'),
563
      'page callback' => 'cdm_dataportal_taxon_page_view',
564
      'access arguments' => array('access cdm content'),
565
      'type' => MENU_CALLBACK,
566
      'weight' => 2,
567
      'page arguments' => array(2, "all")
568
      , // Expected callback arguments: taxon_uuid.
569
    );
570

    
571
    $items['cdm_dataportal/taxon/%/description'] = array(
572
      'title' => cdm_taxonpage_tab_label('General'),
573
      'page callback' => 'cdm_dataportal_taxon_page_view',
574
      'access arguments' => array('access cdm content'),
575
      'type' => MENU_DEFAULT_LOCAL_TASK,
576
      'weight' => 2,
577
      'page arguments' => array(2, "description")
578
      , // Expected callback arguments: taxon_uuid.
579
    );
580

    
581
    $items['cdm_dataportal/taxon/%/synonymy'] = array(
582
      'title' => cdm_taxonpage_tab_label('Synonymy'),
583
      'page callback' => 'cdm_dataportal_taxon_page_view',
584
      'access arguments' => array('access cdm content'),
585
      'type' => MENU_LOCAL_TASK,
586
      'weight' => 4,
587
      'page arguments' => array(2, "synonymy", 4)
588
      , // Expected callback arguments: taxon_uuid and ...
589
    );
590
    $items['cdm_dataportal/taxon/%/images'] = array( // Images
591
      'title' => cdm_taxonpage_tab_label('Images'),
592
      'page callback' => 'cdm_dataportal_taxon_page_view',
593
      'access arguments' => array('access cdm content'),
594
      'type' => MENU_LOCAL_TASK,
595
      'weight' => 5,
596
      'page arguments' => array(2, "images")
597
      , // Expected callback arguments: taxon_uuid.
598
    );
599

    
600
    $items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
601
      'title' => cdm_taxonpage_tab_label('Specimens'),
602
      'page callback' => 'cdm_dataportal_taxon_page_view',
603
      'access arguments' => array('access cdm content'),
604
      'type' => MENU_LOCAL_TASK,
605
      'weight' => 6,
606
      'page arguments' => array(2, "specimens")
607
      , // Expected callback arguments: taxon_uuid.
608
    );
609

    
610
    $items['cdm_dataportal/taxon/%/keys'] = array( // Keys
611
      'title' => cdm_taxonpage_tab_label('Keys'),
612
      'page callback' => 'cdm_dataportal_taxon_page_view',
613
      'access arguments' => array('access cdm content'),
614
      'type' => MENU_LOCAL_TASK,
615
      'weight' => 6,
616
      'page arguments' => array(2, "keys")
617
      , // Expected callback arguments: taxon_uuid.
618
    );
619

    
620
    $items['cdm_dataportal/taxon/%/experts'] = array( // Experts
621
      'title' => cdm_taxonpage_tab_label('Experts'),
622
        'page callback' => 'cdm_dataportal_taxon_page_view',
623
        'access arguments' => array('access cdm content'),
624
        'type' => MENU_LOCAL_TASK,
625
        'weight' => 6,
626
        'page arguments' => array(2, "experts")
627
    , // Expected callback arguments: taxon_uuid.
628
    );
629

    
630
    $items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(
631
        'page callback' => 'cdm_dataportal_taxon_autosuggest',
632
        'access arguments' => array('access cdm content'),
633
        'page arguments' => array(3,4,5),
634
        'type' => MENU_CALLBACK
635
    );
636
  }
637

    
638
  // --- refresh link for all cdmnode types
639
  foreach (cdm_get_nodetypes() as $type=>$name) {
640
    $items['cdm_dataportal/' . $name . '/%/refresh'] = array(
641
        'title' => 'Refresh',
642
        'page callback' => 'cdm_dataportal_refresh_node',
643
        'access arguments' => array('administer cdm_dataportal'),
644
        'type' => MENU_LOCAL_TASK,
645
        'weight' => 100,
646
        'page arguments' => array($name, 2)
647
    );
648
  }
649

    
650
  return $items;
651
}
652

    
653
/**
654
 * Implements hook_init().
655
 *
656
 */
657
function cdm_dataportal_init() {
658
  if (!path_is_admin(current_path())) {
659
    //FIXME To add CSS or JS that should be present on all pages, modules
660
    //      should not implement this hook, but declare these files in their .info file.
661
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
662
    // drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
663
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
664
  } else {
665
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_settings.css');
666
  }
667

    
668
  if(variable_get('cdm_debug_mode', FALSE)){
669
    $file = 'temporary://drupal_debug.txt';
670
    file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
671
  }
672

    
673
  $bibliography_settings = get_bibliography_settings();
674
  $enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
675
  FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
676
}
677

    
678
function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
679

    
680
  $base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
681

    
682
  if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
683
    // force reloading of all and notify user about this special loading
684
    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: ')
685
        . l('Back to tabbed taxon page', $base_path));
686
    $base_path .= '/all';
687
  } else {
688
    drupal_set_message(t('The level 2 cache has been cleared for this page'));
689
  }
690

    
691
  $parameters['cacheL2_refresh'] ='1';
692

    
693

    
694
  drupal_goto($base_path, array('query' => $parameters));
695
}
696

    
697
/**
698
 * Implements hook_requirements($phase)
699
 */
700
function cdm_dataportal_requirements($phase) {
701
    $requirements = array();
702
    if($phase == 'runtime'){
703

    
704
    }
705
    return $requirements;
706
}
707

    
708

    
709
/**
710
 * The function generate form for own user cdm dataportal configurations.
711
 */
712
function cdm_dataportal_user_form($form, &$form_state) {
713

    
714
  global $user;
715
  $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
716

    
717
  $form['taxon_page_tabs'] = array(
718
      '#type' => 'fieldset',
719
      '#tree' => true,
720
      '#title' => t('Taxon page tabs'),
721
  );
722

    
723
  $form['taxon_page_tabs']['user_defined'] = array(
724
    '#type' => 'checkbox',
725
    '#title' => t('Activate user default configuration'),
726
    '#default_value' => variable_get($checkbox_value, 0),
727
    '#description' => t('Check this if you want configure your own default tab from the below menu.'),
728
  );
729

    
730
  $form['taxon_page_tabs']['default_tab'] = array(
731
    '#type' => 'select',
732
    '#title' => t('Default tab to display'),
733
    '#default_value' => get_default_taxon_tab(TRUE),
734
    '#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
735
    '#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
736
              <strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
737
              to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
738
  );
739

    
740

    
741
  if(false){
742
    $form['developer_options'] = array(
743
        '#type' => 'fieldset',
744
        '#tree' => true,
745
        '#title' => t('Developer options'),
746
    );
747

    
748
    $form['developer_options']['show_render_path'] = array(
749
      '#type' => 'checkbox',
750
      '#title' => t('Display the render path for each taxon name.'),
751
      '#default_value' => variable_get($checkbox_value, 0),
752
      '#description' => t('This option is very helpful if you are editing the !link for taxon names.',
753
        array(
754
            '!link' => l(
755
              'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))
756
            )
757
        ),
758
    );
759
  }
760

    
761
  $form['submit'] = array(
762
    '#type' => 'submit',
763
    '#value' => t('Submit'),
764
  );
765

    
766
  return $form;
767
}
768

    
769
/**
770
 * Form submission handler for user_form().
771
 *
772
 * Submits the user cdm dataportal configurations.
773
 */
774
function cdm_dataportal_user_form_submit($form, &$form_state) {
775
  global $user;
776
  $msg_type = 'status';
777
  $username = $user->name;
778
  $variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
779

    
780
  // FIXME: this is completely wrong, see user_profile_form_submit()
781

    
782
  // it is only possible to change own user settings
783
  if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {
784

    
785
    // DEFAULT_TAXON_TAB
786
    $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
787
    variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);
788
    variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);
789
    if ($form_state['values']['taxon_page_tabs']['user_defined']) {
790
      drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
791
      drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
792
        '!tab' => $variable[variable_get($variable_to_use, 0)],
793
        '!user' => $username,
794
      ))), $msg_type);
795
    }
796
    else {
797
      drupal_set_message(check_plain(t('The user default tab wont be used for
798
        the next taxon site, check the box if you want to use the user default configuration.')));
799
    }
800

    
801
  }
802
  else {
803
    // Problem with the user id => variables wont be saved.
804
    $msg_type = 'warning';
805
    drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
806
  }
807
}
808

    
809
/**
810
 * Implements hook_block_info().
811
 */
812
function cdm_dataportal_block_info() {
813

    
814
    // $block[0]["info"] = t("CDM DataPortal DevLinks");
815
    // $block[1]["info"] = t("CDM DataPortal Credits");
816
    $block["2"] = array(
817
        "info" => t("CDM - Search Taxa"),
818
        "cache" => DRUPAL_NO_CACHE
819
      );
820
    // $block[3]["info"] = t("CDM Filters");
821
    $block["4"]["info"] = t("CDM  - Dataportal Print");
822
    $block["keys"]["info"] = t("CDM - Identification keys");
823
    $block["fundedByEDIT"]["info"] = t('CDM - Powered by EDIT');
824
    $block["classification_breadcrumbs"] =  array(
825
        'info' => t('CDM - Classification breadcrumbs'),
826
        'cache' => DRUPAL_CACHE_PER_PAGE
827
      );
828
    $block["taxonomic_children"] =  array(
829
      'info' => t('CDM - Taxonomic children'),
830
      'cache' => DRUPAL_CACHE_PER_PAGE
831
    );
832
    $block["back_to_search_results"] =  array(
833
      'title' => '<none>',
834
      'info' => t('CDM - Back to search Results'),
835
      'cache' => DRUPAL_CACHE_PER_PAGE,
836
      'visibility' => BLOCK_VISIBILITY_LISTED,
837
      'pages' => "cdm_dataportal/taxon/*", // multiple page paths separated by "\n"!!!
838
    );
839
  $block['registrations_search_filter'] =  array(
840
    'title' => 'Search registrations',
841
    'info' => t('CDM - Registrations search filter'),
842
    'cache' => DRUPAL_CACHE_PER_PAGE,
843
    'visibility' => BLOCK_VISIBILITY_NOTLISTED,
844
    'pages' => "cdm_dataportal/search/registration\ncdm_dataportal/search/registration/*", // multiple page paths separated by "\n"!!!
845
  );
846

    
847
    return $block;
848
}
849

    
850
/**
851
 * Implements hook_block_view().
852
 */
853
function cdm_dataportal_block_view($delta) {
854
  // TODO Rename block deltas (e.g. '2') to readable strings.
855
  switch ($delta) {
856
    // case 'delta-1':
857
    // $block['subject'] = t('Credits');
858
    // $block['content'] = theme('cdm_credits');
859
    // return $block;
860
    case '2':
861
      $block['subject'] = t('Search taxa');
862
      $form = drupal_get_form('cdm_dataportal_search_taxon_form');
863
      $block['content'] = drupal_render($form);
864

    
865
      if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
866
        $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
867
      }
868
      return $block;
869
    case '4':
870
      $block['subject'] = '';
871
      $block['content'] = theme('cdm_print_button');
872
      return $block;
873
    case "keys":
874
      $block['subject'] = t('Identification Keys');
875
      $block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
876
      return $block;
877
    case "fundedByEDIT":
878
      // t('Funded by EDIT');
879
      $text = '<none>';
880
      $block['subject'] = $text;
881
      $img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
882
      $block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
883
        'attributes' => array("target" => "EDIT"),
884
        'absolute' => TRUE,
885
        'html' => TRUE,
886
      ));
887
      return $block;
888
    case 'classification_breadcrumbs':
889
      $taxon_uuid = get_current_taxon_uuid();
890
      $block['subject'] = '<none>';
891
      $block['content'] = compose_classification_breadcrumbs($taxon_uuid);
892
      return $block;
893
    case 'taxonomic_children':
894
      $taxon_uuid = get_current_taxon_uuid();
895
      $block['subject'] = '<none>';
896
      $block['content'] = compose_taxonomic_children($taxon_uuid);
897
      return $block;
898
    case 'back_to_search_results':
899
      $block['subject'] = '<none>';
900
      if (isset($_SESSION['cdm']['search'])) {
901
        $block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
902
      }
903
      return $block;
904
    case 'registrations_search_filter':
905
      $block['subject'] = '<none>';
906
      $block['content'] = $form = drupal_get_form('cdm_dataportal_search_registration_form'); // see cdm_dataportal_search_registration_form($form, &$form_state)
907
      return $block;
908
    default:
909
      return null;
910
  }
911
}
912

    
913
/**
914
 * Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
915
 *
916
 * @return string
917
 *   the taxon uuid or NULL
918
 */
919
function get_current_taxon_uuid()
920
{
921
  static $taxon_uuid;
922

    
923
  if(!isset($taxon_uuid)){
924
    if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
925
      $taxon_uuid = $_REQUEST['currentTaxon'];
926
    } else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
927
      $taxon_uuid = arg(2);
928
    } else {
929
      $taxon_uuid = null;
930
    }
931
  }
932

    
933
  return $taxon_uuid;
934
}
935

    
936
/**
937
 * Returns the currently classification tree in use.
938
 *
939
 * @return string
940
 *   The uuid of the currently focused classification
941
 */
942
function get_current_classification_uuid() {
943
  if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
944
    return $_SESSION['cdm']['taxonomictree_uuid'];
945
  }
946
  else {
947
    return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
948
  }
949
}
950

    
951
/*
952
 function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
953
 $_SESSION['cdm'] = NULL;
954
 if(is_string($cdm_ws_uri_update)){
955
 $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
956
 }
957
 }
958

    
959
 function cdm_dataportal_session_validate(){
960
 if(!isset($_SESSION['cdm']['ws_uri'])){
961
 $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
962
 } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
963
 cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
964
 }
965
 }
966
 */
967

    
968
/**
969
 * creates a  selector form for taxonomic trees.
970
 *
971
 * @return array
972
 *  a drupal form array
973
 */
974
function cdm_taxonomictree_selector() {
975
  _add_js_treeselector();
976

    
977
  $form = drupal_get_form('cdm_taxonomictree_selector_form');
978
  return $form;
979
}
980

    
981
/**
982
 * @todo Please document this function.
983
 * @see http://drupal.org/node/1354
984
 *
985
 * @deprecated use compose_classification_selector instead
986
 */
987
function cdm_taxonomictree_selector_form($form, &$form_state) {
988

    
989
  $url = url('cdm_api/setvalue/session', array('query' => NULL));
990
  $form['#action'] = $url;
991

    
992
  $form['var'] = array(
993
    '#weight' => -3,
994
    '#type' => 'hidden',
995
    '#value' => '[cdm][taxonomictree_uuid]',
996
  );
997

    
998
  $destination_array = drupal_get_destination();
999
  $destination = $destination_array['destination'];
1000

    
1001
  $form['destination'] = array(
1002
    '#weight' => -3,
1003
    '#type' => 'hidden',
1004
    '#value' =>  $destination,
1005
  );
1006

    
1007
  $options = cdm_get_taxontrees_as_options();
1008
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1009
  if($taxontree_includes){
1010
    $filtered_options = array();
1011
    foreach($options as $uuid=>$label){
1012
      if(!empty($taxontree_includes[$uuid])){
1013
        $filtered_options[$uuid] = $label;
1014
      }
1015
    }
1016
    $options = $filtered_options;
1017
  }
1018

    
1019
  $form['val'] = array(
1020
    '#type' => 'select',
1021
    '#title' => t('Available classifications'),
1022
    '#default_value' => get_current_classification_uuid(),
1023
    '#options' => $options,
1024
    '#attributes' => array('class' => array('highlite-first-child')),
1025
  );
1026

    
1027
  return $form;
1028

    
1029
}
1030

    
1031
/**
1032
 *
1033
 * @ingroup compose
1034
 */
1035
function compose_classification_selector() {
1036

    
1037
  $destination_array = drupal_get_destination();
1038
  $destination = $destination_array['destination'];
1039

    
1040
  $options = cdm_get_taxontrees_as_options();
1041
  $items = array();
1042
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1043

    
1044
  $current_classification_uuid = get_current_classification_uuid();
1045

    
1046

    
1047
  foreach($options as $uuid=>$label){
1048
    if(!$taxontree_includes || !empty($taxontree_includes[$uuid])){
1049

    
1050
      $class_attributes = '';
1051
      if($current_classification_uuid == $uuid){
1052
        $class_attributes  = array('focused');
1053
      }
1054
      $items[] = array(
1055
        'data' => l($label,
1056
          'cdm_api/setvalue/session',
1057
          array(
1058
            'query' => array(
1059
              'destination' => $destination,
1060
              'val' => $uuid,
1061
              'var' => '[cdm][taxonomictree_uuid]'
1062
            ),
1063
          )
1064
        ),
1065
        'class' => $class_attributes
1066
      );
1067
    }
1068
  }
1069

    
1070
  $render_array = array(
1071
    '#theme' => 'item_list',
1072
    '#type' => 'ul',
1073
    '#items' => $items
1074
  );
1075

    
1076
  return $render_array;
1077
}
1078

    
1079

    
1080
/* UNREACHABLE since action of form directly links to view.
1081
 function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
1082

    
1083
 $_SESSION['cdm']['search'] = $form_values;
1084
 //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
1085
 return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
1086
 //$paramstr = compose_url_prameterstr($form_values);
1087
 //return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
1088
 }
1089
 */
1090
/* ====================== menu callback functions ====================== */
1091
/**
1092
 * @todo Please document this function.
1093
 * @see http://drupal.org/node/1354
1094
 */
1095
/*
1096
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
1097
  static $comment_node_disabled =  0;
1098
  static $comment_node_read_only =  1;
1099
  static $comment_node_read_write =  2;
1100

    
1101
  if ($form_id == 'node_type_form'
1102
   && isset($form['identity']['type'])
1103
   && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
1104
  ) {
1105
    $form['workflow']['comment'] = array(
1106
      '#type' => 'radios',
1107
      '#title' => t('Default comment setting'),
1108
      '#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
1109
      '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
1110
      '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
1111
    );
1112
  }
1113
}
1114
*/
1115

    
1116
/**
1117
 * Displays a list of the known taxonomic names.
1118
 *
1119
 * When the list of taxonomic names is displayed, long lists are split up into
1120
 * multiple pages.
1121
 *
1122
 * TODO: Parameters are still preliminary.
1123
 *
1124
 * @param string $beginsWith
1125
 * @param string $page
1126
 *   Page number to diplay defaults to page 1.
1127
 * @param bool $onlyAccepted
1128
 */
1129
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
1130

    
1131
  $out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
1132

    
1133
  /*
1134
  // FIXME the filter for accepted names will be a form element, thus this
1135
  // widget should be generated via form api preferably as block.
1136
  $out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
1137
  $out .= theme('cdm_dataportal_widget_names_list', $names, $page);
1138
  $out .= theme('cdm_listof_taxa', $taxonPager);
1139
  return $out;
1140
  */
1141
}
1142

    
1143
/**
1144
 * @todo Please document this function.
1145
 * @see http://drupal.org/node/1354
1146
 * @throws Exception
1147
 */
1148
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
1149

    
1150
  cdm_check_valid_portal_page();
1151

    
1152
  return compose_cdm_reference_page($uuid);
1153
}
1154

    
1155
/**
1156
 * Creates a view on a all references contained in the portal.
1157
 *
1158
 * This function is used at the path cdm_dataportal/reference/list
1159
 */
1160
function cdm_dataportal_view_reference_list($pageNumber) {
1161
  $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
1162
  cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
1163
}
1164

    
1165
/**
1166
 * @todo Please document this function.
1167
 * @see http://drupal.org/node/1354
1168
 */
1169
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
1170

    
1171
  cdm_check_valid_portal_page();
1172

    
1173
  $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
1174
  return theme('cdm_media_page', array(
1175
    'media' => $media,
1176
    'mediarepresentation_uuid' => $mediarepresentation_uuid,
1177
    'partId' => $part,
1178
    ));
1179
}
1180

    
1181
/**
1182
 * @todo Please document this function.
1183
 * @see http://drupal.org/node/1354
1184
 */
1185
function _load_taxonBase(&$taxonBase) {
1186
  if (isset($taxonBase->uuid)) {
1187
    $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
1188
    $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
1189
    $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
1190
  }
1191
}
1192

    
1193
/**
1194
 * Loads the media associated to the given taxon from the cdm server.
1195
 * The aggregation settings regarding taxon relathionships and
1196
 * taxonnomic childen are taken into account.
1197
 *
1198
 * The media lists are cached in a static variable.
1199
 *
1200
 * @param Taxon $taxon
1201
 *   A CDM Taxon entitiy
1202
 *
1203
 * @return array
1204
 *   An array of CDM Media entities
1205
 *
1206
 */
1207
function _load_media_for_taxon($taxon) {
1208

    
1209
  static $media = NULL;
1210

    
1211
  if(!isset($media)) {
1212
    $media = array();
1213
  }
1214
  if (!isset($media[$taxon->uuid])) {
1215

    
1216
    // --- GET Images --- //
1217
    $mediaQueryParameters = array(
1218
        "type" => "ImageFile",
1219
    );
1220

    
1221
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1222
    $mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
1223
    $mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
1224

    
1225
    $taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
1226
    $mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
1227
    $mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
1228
    $mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
1229

    
1230
    $ws_endpoint = NULL;
1231
    if ( variable_get('cdm_images_include_children', 0) == 0) {
1232
      $ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1233
    } else {
1234
      $ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1235
    }
1236

    
1237
    $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1238
        array(
1239
            $taxon->uuid,
1240
        ),
1241
        queryString($mediaQueryParameters)
1242
       );
1243
  }
1244

    
1245
  return $media[$taxon->uuid];
1246
}
1247

    
1248
/**
1249
 *
1250
 * @param Taxon $taxon
1251
 *   A CDM Taxon entitiy
1252
 *
1253
 * @return array
1254
 *   An array of CDM SpecimenOrObservation entities
1255
 *
1256
function _load_occurences_for_taxon($taxon){
1257

    
1258
  static $occurences = NULL;
1259

    
1260
  if(!isset($occurences)) {
1261
    $occurences = array();
1262
  }
1263

    
1264
  if (!isset($occurences[$taxon->uuid])){
1265

    
1266
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1267
    $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1268
    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1269

    
1270
    $by_associatedtaxon_query = http_build_query(array(
1271
        'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1272
        'relationships' => implode(',', $relationship_choice['direct']),
1273
        'pageSize' => null // all hits in one page
1274
    )
1275
    );
1276

    
1277
    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1278
        null,
1279
        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1280
    );
1281

    
1282

    
1283
    if(isset($pager->records[0])){
1284
      $occurences[$taxon->uuid] =  $pager->records;
1285
    }
1286
  }
1287
  return $occurences[$taxon->uuid];
1288
}
1289
 */
1290

    
1291
/**
1292
 * Gets a Drupal variable, string or array and returns it.
1293
 *
1294
 * Similar to the variable_get() function of Drupal, except that this function
1295
 * is able to handle arrays correctly. This function is especially useful
1296
 * when dealing with collections of settings form elements (#tree = TRUE).
1297
 *
1298
 * @param string $variableKey
1299
 *   The Unique key of the Drupal variable in the Drupal variables table.
1300
 * @param string $defaultValueString
1301
 *   A string as for example derived from a CONSTANT.
1302
 *
1303
 * @return mixed
1304
 *   usually an array, depending on the nature of the variable.
1305
 *
1306
 * TODO compare with get_array_variable_merged() duplicate functions?
1307
 * @deprecated rather use get_array_variable_merged() since this function
1308
 * used an array as second parameter
1309
 */
1310
function mixed_variable_get($variableKey, $defaultValueString) {
1311
  $systemDefaults = unserialize($defaultValueString);
1312
  $storedSettings = variable_get($variableKey, array());
1313
  if (is_array($storedSettings)) {
1314
    // TODO better use drupal_array_merge_deep() ?
1315
    $settings = array_merge($systemDefaults, $storedSettings);
1316
  }
1317
  else {
1318
    $settings = $systemDefaults;
1319
  }
1320
  return $settings;
1321
}
1322

    
1323
/**
1324
 * Recursive function to convert an object into an array.
1325
 * also subordinate objects will be converted.
1326
 *
1327
 * @param object $object
1328
 *  the object to be converted
1329
 * @return array
1330
 *  The array
1331
 */
1332
function object_to_array($object) {
1333
  if(is_object($object) || is_array($object)) {
1334
    $array = (array)$object;
1335
    foreach ($array as $key=>$value){
1336
      $array[$key] = object_to_array($value);
1337
    }
1338
    return $array;
1339
  } else {
1340
    return $object;
1341
  }
1342
}
1343

    
1344
/**
1345
 * Searches the $collection for the cdm entitiy given as $element.
1346
 *
1347
 * The elements are compared by their UUID.
1348
 *
1349
 * @param $element
1350
 *  the CDM entitiy to search for
1351
 * @param $collection
1352
 *  the list of CDM entities to search in
1353
 *
1354
 * @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1355
 *
1356
 */
1357
function contains_cdm_entitiy($element, $collection) {
1358
  $result = FALSE;
1359
  foreach ($collection as $a) {
1360
    if ($a->uuid == $element->uuid) {
1361
      $result = TRUE;
1362
    }
1363
  }
1364
  return $result;
1365
}
1366

    
1367
/**
1368
 * Fiters the array $entity_list of CDM entities by the list
1369
 * of $excludes. Any element contained in the $excludes will be removed
1370
 * from included int the retuned list.
1371
 *
1372
 * If the $entity_list is not an array the $excludes will be returned.
1373
 */
1374
function filter_cdm_entity_list($entity_list, $excludes) {
1375
  if (is_array($entity_list)) {
1376
    $result = $entity_list;
1377
    if ($excludes) {
1378
      foreach ($excludes as $exclude) {
1379
        if (!contains_cdm_entitiy($exclude, $entity_list)) {
1380
          $result[] = $exclude;
1381
        }
1382
      }
1383
    }
1384
  }
1385
  else {
1386
    $result = $excludes;
1387
  }
1388
  return $result;
1389
}
1390

    
1391
/**
1392
 * Wraps the given $html string into a render array suitable for drupal_render()
1393
 *
1394
 * @param $html
1395
 *   the html string, see
1396
 *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1397
 * @param $weight
1398
 *   A positive or negative number (integer or decimal).
1399
 *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1400
 * @param $prefix
1401
 *   Optional markup for the '#prefix' element of the render array
1402
 * @param $suffix
1403
 *   Optional markup for the '#suffix' element of the render array
1404
 *
1405
 * @return array
1406
 *   A render array
1407
 *
1408
 */
1409
function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1410
  $render_array = array(
1411
    '#markup' => $html
1412
      );
1413
  if (is_numeric($weight)) {
1414
    $render_array['#weight'] = $weight;
1415
  }
1416
  if($prefix){
1417
    $render_array['#prefix'] = $prefix;
1418
  }
1419
  if($suffix) {
1420
    $render_array['#suffix'] = $suffix;
1421
  }
1422
  return $render_array;
1423
}
1424

    
1425
/**
1426
 * Loads the subgraph of a given PolytomousKeyNode.
1427
 *
1428
 * Loads the subgraph of the given PolytomousKeyNode recursively from
1429
 * the CDM REST service.
1430
 *
1431
 * @param mixed $polytomousKeyNode
1432
 *   PolytomousKeyNode passed by reference.
1433
 *
1434
 * @return void
1435
 */
1436
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1437

    
1438
  if (!$polytomousKeyNode) {
1439
    return;
1440
  }
1441
  if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1442
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1443
    return;
1444
  }
1445
  if (!is_uuid($polytomousKeyNode->uuid)) {
1446
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1447
    return;
1448
  }
1449

    
1450
  $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1451

    
1452
  if (!$polytomousKeyNode) {
1453
    // drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1454
    return;
1455
  }
1456

    
1457
  // Load children.
1458
  foreach ($polytomousKeyNode->children as &$childNode) {
1459
    _load_polytomousKeySubGraph($childNode);
1460
  }
1461

    
1462
  // Load subkey.
1463
  $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1464

    
1465
  // Load taxon.
1466
  $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1467
  _load_taxonBase($polytomousKeyNode->taxon);
1468
  return;
1469
}
1470

    
1471
/**
1472
 * @todo Please document this function.
1473
 * @see http://drupal.org/node/1354
1474
 */
1475
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1476

    
1477
  cdm_check_valid_portal_page();
1478

    
1479
  $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1480

    
1481
  $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1482
  if (is_array($sourcePager->records)) {
1483
    $polytomousKey->sources = $sourcePager->records;
1484
    // $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1485
  }
1486

    
1487
  $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1488
  if (is_array($annotationPager->records)) {
1489
    $polytomousKey->annotations = $annotationPager->records;
1490
  }
1491

    
1492
  _load_polytomousKeySubGraph($polytomousKey->root);
1493
  return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1494
}
1495

    
1496
/**
1497
 * Creates a taxon page view or a chapter of it.
1498
 *
1499
 * The taxon page gives detailed information on a taxon, it shows:
1500
 *  - Taxon name.
1501
 *  - Full list of synonyms homotypic synonyms on top, followed by the
1502
 *    heterotypic and finally followed by misapplied names.
1503
 *    The list is ordered historically.
1504
 *  - All description associated with the taxon.
1505
 *
1506
 * @param string $uuid
1507
 * @param string $chapter
1508
 *   Name of the part to display, valid values are:
1509
 *   'description', 'images', 'synonymy', 'specimens', 'all'.
1510
 *
1511
 * @return string
1512
 */
1513
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
1514

    
1515
  cdm_check_valid_taxon_page($chapter);
1516
  cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1517
  // show a warning in case the javascript development mode is anabled
1518
  if(variable_get('cdm_js_devel_mode', FALSE)) {
1519
    drupal_set_message(t('The !url1 is enabled.
1520
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1521
          '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1522
    )),
1523
    'warning'
1524
        );
1525
  }
1526

    
1527
  // Display the page for the taxon defined by $uuid.
1528
  // set_last_taxon_page_tab(arg(3));
1529
  $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
1530
  if (!empty($taxonpage)) {
1531
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1532
    return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1533
  }
1534
  else {
1535
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1536
    return '';
1537
  }
1538
}
1539

    
1540
/**
1541
 * This function will genreate the taxon page part ($chapter) and returns a taxonpage object
1542
 * which has two fields, one for the page title and one for the content. Later on in the
1543
 * process chain the value contained in these fields will be passed to the cdm_node_show()
1544
 * function as the function parameters $title and $content.
1545
 *
1546
 * @param string $uuid
1547
 *   the uuid of the taxon to show
1548
 * @param string $chapter
1549
 *   Name of the part to display, valid values are:
1550
 *   'description', 'images', 'synonymy', 'all'.
1551
 *
1552
 * @return object with the following fields:
1553
 *   - title : the title of the page
1554
 *   - content: the content of the page
1555
 *
1556
 * @throws Exception
1557
 *
1558
 */
1559
function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1560
  // Taxon object.
1561
  $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1562
  if (empty($taxon)) {
1563
    drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1564
    return null;
1565
  }
1566
  $taxonpage = new stdClass();
1567

    
1568
  $taxonpage->title = theme('cdm_taxon_page_title', array(
1569
    'taxon' => $taxon
1570
  ));
1571

    
1572
  // Check if the taxon id contained in the currently selected tree.
1573
  $taxon_in_current_classification = taxon_in_current_classification($uuid);
1574

    
1575
  if (!$taxon_in_current_classification) {
1576
    $classifications = get_classifications_for_taxon($taxon);
1577
    RenderHints::pushToRenderStack('not_in_current_classification');
1578
    $taxon_name_markup = render_taxon_or_name($taxon);
1579

    
1580
    if (count($classifications) == 0) {
1581
      drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
1582
        array(
1583
        '!taxonname' => $taxon_name_markup,
1584
        )
1585
      ), 'warning');
1586
    }
1587
    else {
1588
      $trees = '';
1589
      foreach ($classifications as $classification) {
1590
        if (isset($classification->titleCache)) {
1591
          $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1592
        }
1593
      }
1594

    
1595
      drupal_set_message(format_plural(count($trees),
1596
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in this one: !trees',
1597
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1598
          array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1599
        ) ,
1600
        'warning');
1601
    }
1602
    RenderHints::popFromRenderStack();
1603
  }
1604

    
1605
  // Render the taxon page.
1606
  $render_array = compose_cdm_taxon_page($taxon, $chapter);
1607
  $taxonpage->content = drupal_render($render_array);
1608

    
1609
  return $taxonpage;
1610
}
1611

    
1612
/**
1613
 * Creates a specimen page view.
1614
 * @param string $uuid the UUID of the specimen
1615
 * @return array|string
1616
 */
1617
function cdm_dataportal_specimen_page_view($uuid) {
1618

    
1619
    //cdm_check_valid_taxon_page($chapter);
1620
    //cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1621
    // show a warning in case the javascript development mode is anabled
1622
    if(variable_get('cdm_js_devel_mode', FALSE)) {
1623
        drupal_set_message(t('The !url1 is enabled.
1624
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1625
            '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1626
        )),
1627
            'warning'
1628
        );
1629
    }
1630

    
1631
    // Display the page for the specimen defined by $uuid.
1632
    $specimenpage = cdm_dataportal_specimen_view($uuid);
1633
    if (!empty($specimenpage)) {
1634
        return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
1635
    }
1636
    else {
1637
        return '';
1638
    }
1639
}
1640

    
1641
/**
1642
 *
1643
 * Creates a specimen view.
1644
 * @param string $uuid the UUID of the specimen
1645
 * @return array|string
1646
 */
1647
function cdm_dataportal_specimen_view($uuid) {
1648
    $specimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, $uuid);
1649
    if (empty($specimen)) {
1650
        drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1651
        return FALSE;
1652
    }
1653
    $specimenpage = new stdClass();
1654

    
1655
    $specimenpage->title = theme('cdm_specimen_page_title', array(
1656
        'specimen' => $specimen
1657
    ));
1658

    
1659
    // Render the specimen page.
1660
    $render_array = compose_cdm_specimen_page($uuid);
1661
    $specimenpage->content = drupal_render($render_array);
1662

    
1663
    return $specimenpage;
1664
}
1665

    
1666
/**
1667
 *
1668
 * Creates a named area view.
1669
 * @param string $uuid the UUID of the specimen
1670
 *  * @return object
1671
 *   An object with two fields:
1672
 *     - title: the page title
1673
 *     - content: the page content
1674
 */
1675

    
1676
function cdm_dataportal_named_area_view($uuid) {
1677
  $named_area = cdm_ws_get(CDM_WS_PORTAL_TERM, $uuid);
1678
  if (empty($named_area) || $named_area->class !== 'NamedArea') {
1679
    drupal_set_title(t('Named area does not exist'), PASS_THROUGH);
1680
    return FALSE;
1681
  }
1682
  $named_area_page = new stdClass();
1683

    
1684
  $named_area_page->title = $named_area->representation_L10n;
1685

    
1686
  // Render the specimen page.
1687
  $render_array = compose_cdm_named_area_page($uuid);
1688
  $named_area_page->content = drupal_render($render_array);
1689

    
1690
  return $named_area_page;
1691
}
1692

    
1693
function cdm_dataportal_named_area_page_view($uuid) {
1694

    
1695
  cdm_check_valid_portal_page();
1696

    
1697
  $named_area_page = cdm_dataportal_named_area_view($uuid);
1698
  if (!empty($named_area_page)) {
1699
    return cdm_node_show(NODETYPE_NAME, $uuid, $named_area_page->title, $named_area_page->content);
1700
  }
1701
  else {
1702
    return '';
1703
  }
1704

    
1705

    
1706
}
1707

    
1708
/**
1709
 * Returns a name page as a Drupal node ready to be renderized by Drupal.
1710
 *
1711
 * The node page shows the taxon name title and the list of taxon related
1712
 * with such taxon. Name on the tree already in use.
1713
 *
1714
 * @param UUID $taxon_name_uuid
1715
 *   The uuid of the CDM TaxonName to show a name page for
1716
 * @param UUID $taxon_to_hide_uuid
1717
 *   A taxon which should not be displayed in the taxon list
1718
 * @param UUID $highlite_synonym_uuid
1719
 *   Optinal parameter wich takes another taxon uuid, if given the
1720
 *   target taxon pages will show the syonymy tab where the taxon
1721
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1722
 *   in case it is found on this page.
1723
 *
1724
 * @return mixed
1725
 *   The formatted name page as node.
1726
 */
1727
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
1728

    
1729
  cdm_check_valid_portal_page();
1730

    
1731
  $taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
1732
  if (!empty($taxonname_page)) {
1733
    return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
1734
  }
1735
  else {
1736
    return '';
1737
  }
1738
}
1739

    
1740
/**
1741
 * View function for a TaxonName page.
1742
 *
1743
 * The name page lists all taxa for which the name specified by the
1744
 * $taxon_name_uuid is being used. I case there is only one name the
1745
 * page automatically redirects ti the according taxon page. Otherwise
1746
 * the list of names is displayed.
1747
 *
1748
 * The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
1749
 * list of taxa. This is useful for example when referencing from a taxon
1750
 * to the name page and the referring taxon should not be repeaded in the
1751
 * name page.
1752
 *
1753
 *
1754
 * @param UUID $taxon_name_uuid
1755
 *   The uuid of the CDM TaxonName to show a name page for
1756
 * @param UUID $taxon_to_hide_uuid
1757
 *   A taxon which should not be displayed in the taxon list
1758
 * @param UUID $highlite_synonym_uuid
1759
 *   Optinal parameter wich takes another taxon uuid, if given the
1760
 *   target taxon pages will show the syonymy tab where the taxon
1761
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1762
 *   in case it is found on this page.
1763
 *
1764
 * @return object
1765
 *   An object with two fields:
1766
 *     - title: the page title
1767
 *     - content: the page content
1768
 */
1769
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
1770
  // Getting the full taxonname object from the server.
1771
  $taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
1772
  if (!$taxon_name) {
1773
    drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
1774
    return FALSE;
1775
  }
1776
  // Searching for all the taxa connected with the taxon name on the tree
1777
  // in use.
1778
  $name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
1779
  $request_params = array();
1780
  $request_params['query'] = $name_cache;
1781
  $request_params['tree'] = get_current_classification_uuid();
1782
  $request_params['doTaxa'] = 1;
1783
  $request_params['doSynonyms'] = 1;
1784
  $request_params['doTaxaByCommonNames'] = 0;
1785
  $request_params['matchMode'] = "EXACT";
1786
  $taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
1787

    
1788
  // Removing the name where we came from.
1789
  foreach ($taxon_pager->records as $k => &$taxon) {
1790
    if ($taxon->uuid == $taxon_to_hide_uuid) {
1791
      unset($taxon_pager->records[$k]);
1792
    }
1793
  }
1794
  // Show the taxa list or go to the singular taxon.
1795
  if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
1796
    $singleTaxon = array_pop($taxon_pager->records);
1797
    if ($singleTaxon->class != "Taxon") {
1798
      // It is a Synonym -> look for the accepted.
1799
      $accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid());
1800
      if (!empty($highlite_synonym_uuid)) {
1801
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1802
      }
1803
      else {
1804
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
1805
      }
1806
    }
1807
    else {
1808
      // It is an accepted taxon.
1809
      if (!empty($highlite_synonym_uuid)) {
1810
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1811
      }
1812
      else {
1813
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
1814
      }
1815
    }
1816
  }
1817
  else {// More than one taxa case.
1818
    $taxon_name_page = new stdClass();
1819
    $taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
1820
    if ($taxon_pager->records) {
1821
      $taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
1822
    }
1823
    else {
1824
      $taxon_name_page->content = 'This name is not assigned to a taxon.';
1825
    }
1826
    return $taxon_name_page;
1827
  }
1828
}
1829

    
1830
/**
1831
 * Returns a registration page as a Drupal node to be rendered by Drupal.
1832
 *
1833
 * @param string  $registration_identifier_encoded
1834
 *   The persistent identifier of the registration urlencoded.
1835
 * @return mixed
1836
 *   The formatted registration page as node.
1837
 */
1838
function cdm_dataportal_registration_page_view($registration_identifier_encoded) {
1839

    
1840
  cdm_check_valid_portal_page("/\/cdm_dataportal\/registration\/.*$/");
1841
  $registration_page = cdm_dataportal_registration_view($registration_identifier_encoded);
1842
  return cdm_node_show_simulate($registration_page);
1843
}
1844

    
1845
function cdm_dataportal_registration_view($registration_identifier_encoded) {
1846

    
1847
  $registration_identifier = urldecode($registration_identifier_encoded);
1848

    
1849

    
1850

    
1851
  $render_array = array();
1852
  $registration_dto = cdm_ws_get("registrationDTO/identifier/" . $registration_identifier_encoded);
1853
  if($registration_dto){
1854
    drupal_set_title(t('Registration') . ' ' . $registration_identifier, PASS_THROUGH);
1855

    
1856
    $render_array = compose_registation_dto($registration_dto);
1857

    
1858
    if(is_object($registration_dto->orderdTypeDesignationWorkingSets)){
1859
      $field_unit_uuids = array();
1860
      foreach((array)$registration_dto->orderdTypeDesignationWorkingSets as $field_unit_ref => $obj){
1861
        $tokens = explode("#", $field_unit_ref);
1862
        $field_unit_uuids[] = $tokens[1];
1863
      }
1864
      $render_array['specimen_table'] = compose_specimen_table($field_unit_uuids);
1865
    }
1866

    
1867
  } else {
1868
    drupal_set_title(t('Registration not found'), PASS_THROUGH);
1869
    $render_array['error'] = markup_to_render_array("A registration with the identifier  " . $registration_identifier . " does not exist.");
1870
  }
1871

    
1872
  return $render_array ;
1873
}
1874

    
1875
/**
1876
 * Composes information for a registation from a dtp object
1877
 *
1878
 * @param $registration_dto
1879
 *
1880
 * @return array
1881
 *    A drupal render array
1882
 *
1883
 * @ingroup compose
1884
 */
1885
function compose_registation_dto($registration_dto, $with_citation = true, $with_identifier = false)
1886
{
1887
  $render_array = array();
1888
  $media_link_map = array();
1889
  if($registration_dto->registrationDate){
1890
    if(isset($registration_dto->institutionTitleCache)){
1891
      $registration_date_insitute_markup =
1892
        t("Registration at @date in @institution", array(
1893
          '@date' => $registration_dto->registrationDate,
1894
          '@institution' => $registration_dto->institutionTitleCache,
1895
        ));
1896
    } else {
1897
      $registration_date_insitute_markup =
1898
        t("Registration at @date", array(
1899
          '@date' => $registration_dto->registrationDate
1900
        ));
1901
    }
1902
    $render_array['publication_date_and_office'] = markup_to_render_array($registration_date_insitute_markup);
1903
  }
1904
  $taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
1905
  foreach ($taggged_text_expanded  as $tagged_text){
1906
    if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {
1907
      $mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));
1908
      if(isset($mediaDTOs[0]->uri)){
1909
          $media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';
1910
          $tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);
1911
          $media_link_map[$media_url_key] =  cdm_external_uri($mediaDTOs[0]->uri, true);
1912
      }
1913
    }
1914
  }
1915
  $registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
1916
  foreach($media_link_map as $media_url_key => $link){
1917
    $registation_markup = str_replace($media_url_key, $link, $registation_markup);
1918
  }
1919
  if($with_identifier){
1920
    $registation_markup .= " " . l ($registration_dto->identifier, $registration_dto->identifier);
1921
  }
1922
  $render_array['summary'] = markup_to_render_array("<div>" . $registation_markup . "</div>");
1923

    
1924
  if ($with_citation) {
1925
    $render_array['citation'] = markup_to_render_array("<div class=\"" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
1926
      . l($registration_dto->bibliographicCitationString, path_to_reference($registration_dto->citationUuid))
1927
      . "</br>&nbsp;</div>");
1928
  }
1929

    
1930
  return $render_array;
1931
}
1932

    
1933

    
1934
/**
1935
 * Creates a page with the advance search form.
1936
 *
1937
 * NOTE: The advance search form allows searching for taxa.
1938
 */
1939
function cdm_dataportal_view_search_advanced() {
1940
  drupal_set_title(t('Advanced search'), PASS_THROUGH);
1941
  return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
1942
}
1943

    
1944
/**
1945
 * Creates a page with the search form for searching by taxon descriptions.
1946
 */
1947
function cdm_dataportal_view_search_taxon_by_description() {
1948
  drupal_set_title(t('Search by factual data'), PASS_THROUGH);
1949
  return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
1950
}
1951

    
1952
/**
1953
 * Executes the search and generates the result list of taxa.
1954
 */
1955
function cdm_dataportal_view_search_results_taxon() {
1956

    
1957
  $taxonPager = cdm_dataportal_search_taxon_execute();
1958

    
1959
  $showThumbnails = do_showThumbnails();
1960

    
1961
  $setSessionUri = url('cdm_api/setvalue/session', array(
1962
      'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
1963
  ));
1964

    
1965
  drupal_add_js('jQuery(document).ready(function() {
1966

    
1967
      // init
1968
      if(' . $showThumbnails . ' == 1){
1969
          jQuery(\'.media_gallery\').show(20);
1970
      } else {
1971
          jQuery(\'.media_gallery\').hide(20);
1972
      }
1973

    
1974
      // add change handler
1975
      jQuery(\'#showThumbnails input.showThumbnails\').change(
1976
      function(event){
1977
        var state = 0;
1978
        if(jQuery(this).is(\':checked\')){
1979
          jQuery(\'.media_gallery\').show(20);
1980
          state = 1;
1981
        } else {
1982
          jQuery(\'.media_gallery\').hide(20);
1983
        }
1984
        // store state in session variable
1985
        var uri = \'' . $setSessionUri . '\' + state;
1986
        jQuery.get(uri);
1987
      });
1988
  });',
1989
  array('type' => "inline", 'scope' => JS_DEFAULT));
1990

    
1991
  drupal_set_title(t('Search results'), PASS_THROUGH);
1992

    
1993
  return theme('cdm_search_taxa_results', array(
1994
    'pager' => $taxonPager,
1995
    'path' => 'cdm_dataportal/search/results/taxon',
1996
    ));
1997
}
1998

    
1999
/**
2000
 * Executes the search for registrations and generates the result list..
2001
 */
2002
function cdm_dataportal_view_search_registrations_results() {
2003

    
2004
  $block = block_load('cdm_dataportal', 'registrations_search_filter');
2005
  $render_array = _block_get_renderable_array(_block_render_blocks(array($block)));
2006

    
2007
  $registration_pager = cdm_dataportal_search_registrations_execute();
2008

    
2009
  drupal_set_title(t('Search registrations'), PASS_THROUGH);
2010

    
2011
  $registrations_pager_array = compose_registrations_search_results($registration_pager);
2012

    
2013
  $render_array = array_merge($render_array, $registrations_pager_array);
2014

    
2015
  return $render_array;
2016
}
2017

    
2018

    
2019
/**
2020
 * Provides the standart image wich indicated a loading process
2021
 *
2022
 * @return string
2023
 *  The img html tag
2024
 */
2025
function loading_image_html() {
2026
  return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
2027
    . '/images/loading_circle_grey_16.gif" style="display:none;">';
2028
}
2029

    
2030
/**
2031
 * Returns the state of the the showThumbnails flag set in the
2032
 * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
2033
 *
2034
 * @return boolean
2035
 *    returns 1 if the flag is set
2036
 */
2037
function do_showThumbnails() {
2038
  static $showThumbnails = null;
2039

    
2040
  if($showThumbnails == null) {
2041
    $showThumbnails = 0;
2042
    if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
2043
      $showThumbnails = 0;
2044
      $search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
2045
      $showThumbnails = is_array($search_gallery_settings)
2046
        && isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
2047
        && (
2048
            $search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
2049
            $search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
2050
            $search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
2051
            )
2052
         ? 1 : 0;
2053

    
2054
       drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
2055
    }
2056
    $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
2057
    if (!is_numeric($showThumbnails)) {
2058
      $showThumbnails = 1;
2059
    }
2060
  }
2061

    
2062
  return $showThumbnails;
2063
}
2064

    
2065

    
2066

    
2067
/* ====================== other functions ====================== */
2068
/**
2069
 * Creates a URL to the taxon page specified by the $uuid parameter.
2070
 *
2071
 * The URL will be prepended with a path element to a specific taxon page tab.
2072
 *
2073
 * This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
2074
 * be set globally in the administrative settings or individually in the user
2075
 * profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
2076
 * the last portal will stay on this last tab.
2077
 *
2078
 * A third option is offerered by the $page_tab parameter which allows overwriting this
2079
 * internal mechanism by a specific value.
2080
 *
2081
 * @param string $uuid
2082
 *   The UUID of the taxon.
2083
 * @param string $page_tab
2084
 *   Overwriting the preset mechanism by defining specific value for the
2085
 *   taxon page tab.
2086
 *
2087
 * @return string
2088
 *   The created URL.
2089
 */
2090
function path_to_taxon($uuid, $page_tab = FALSE) {
2091

    
2092
  $tab = get_default_taxon_tab();
2093
  $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
2094

    
2095
  if (!$uuid) {
2096
    return FALSE;
2097
  }
2098

    
2099
  if ($page_tab) {
2100
    return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
2101
  }
2102
  elseif (!$tab || strtolower($tab) == 'general') {
2103
    return 'cdm_dataportal/taxon/' . $uuid;
2104
  }
2105
  elseif (get_last_taxon_page_tab() &&   $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
2106
    return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
2107
  }
2108
  else {
2109
    return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
2110
  }
2111
}
2112

    
2113
function path_to_specimen($uuid) {
2114

    
2115
    if (!$uuid) {
2116
        return FALSE;
2117
    }
2118
    else {
2119
        return 'cdm_dataportal/specimen/' . $uuid;
2120
    }
2121
}
2122

    
2123
function path_to_named_area($uuid) {
2124

    
2125
  if (!$uuid) {
2126
    return FALSE;
2127
  }
2128
  else {
2129
    return 'cdm_dataportal/named_area/' . $uuid;
2130
  }
2131
}
2132

    
2133
/**
2134
 * Creates a URL to show a synonmy in the according taxon page.
2135
 *
2136
 * The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
2137
 * The resulting URI will include query parameters to highlight the synonym, and to optionally display
2138
 * the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
2139
 * include the sysnonym uuid as fragment in order to let the browser scroll to the according location
2140
 * in the page
2141
 *
2142
 * @param string $synonymUuid
2143
 *    The uuid of the synonym
2144
 * @param string $acceptedUuid
2145
 *    The uuid of the according accepted taxon
2146
 * @return string
2147
 *    The URL to show a synonmy in the according taxon page
2148
 */
2149
function uri_to_synonym($synonymUuid, $acceptedUuid) {
2150
  $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
2151
  return url($acceptedPath, array(
2152
      'query' => array(
2153
        // highlite the synony in the synonymy
2154
        'highlite' => $synonymUuid,
2155
        // the taxon page is refered from a synonym and the synonym can optionally be named in the page title
2156
        // see theme_taxon_page_title()
2157
        'acceptedFor' => $synonymUuid
2158
      ),
2159
      'fragment' => $synonymUuid
2160
  ));
2161

    
2162
}
2163

    
2164
/**
2165
 * Composes the drupal path to the key identified by the uuid.
2166
 *
2167
 * @param string $keyType
2168
 *    the key typer corresponds to the specific class of the CDM
2169
 *    IdentificationKey. Possible values are
2170
 *      -PolytomousKey
2171
 *      -MultimediaKey
2172
 *      - ...
2173
 * @param string $keyUuid
2174
 *   The UUID of the key
2175
 */
2176
function path_to_key($keyType, $keyUuid) {
2177
  if (!$keyUuid || !$keyType) {
2178
    return FALSE;
2179
  }
2180
  $keyType{0} = strtolower($keyType{0});
2181
  return "cdm_dataportal/" . $keyType . "/$keyUuid";
2182
}
2183

    
2184
/**
2185
 * Composes the drupal path to the reference identified by the uuid.
2186
 *
2187
 * @param $uuid string String representation of the registration entity uuid.
2188
 *
2189
 * @return string
2190
 *  The drupal path
2191
 *
2192
 */
2193
function path_to_reference($uuid) {
2194
  if (!$uuid) {
2195
    return FALSE;
2196
  }
2197
  return 'cdm_dataportal/reference/' . $uuid;
2198
}
2199

    
2200
/**
2201
 * Composes the drupal path to the reference identified by the uuid.
2202
 *
2203
 * @param string $identifier
2204
 *  The persistent identifier of the registration entity (Registration.identifier).
2205
 * @return string
2206
 *  The drupal path
2207
 */
2208
function path_to_registration($identifier) {
2209

    
2210
  return 'cdm_dataportal/registration/' . urlencode($identifier);
2211
}
2212

    
2213
/**
2214
 * Creates the path to a cdm_dataportal taxon name page.
2215
 *
2216
 * @param string $taxon_name_uuid
2217
 *   The uuid as string of the CDM TaxonName to show a name page for
2218
 * @param string $taxon_to_hide_uuid
2219
 *   The uuid as string of a taxon which should not be displayed in the taxon list
2220
 * @param string $highlite_synonym_uuid
2221
 *   Optional parameter which takes another taxon uuid, if given the
2222
 *   target taxon pages will show the synonymy tab where the taxon
2223
 *   referenced by the $highlite_synonym_uuid will be highlighted
2224
 *   in case it is found on this page.
2225
 *
2226
 * @return string
2227
 *  URI path element as string
2228
 */
2229
function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid  = NULL) {
2230
  $res = FALSE;
2231
  if ($name_uuid) {
2232
    $res = 'cdm_dataportal/name/' . $name_uuid;
2233
  }
2234
  if($taxon_to_hide_uuid){
2235
    $res .= '/' . $taxon_to_hide_uuid;
2236
    if($synonym_uuid){
2237
      $res .= '/' . $synonym_uuid;
2238
    }
2239
  }
2240
  return $res;
2241
}
2242

    
2243
/**
2244
 * Composes the drupal path to the media entity identified by the uuid.
2245
 *
2246
 * @param string $uuid
2247
 *  The persistent identifier of the entity entity
2248
 * @return string
2249
 *  The drupal path
2250
 */
2251
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
2252
  if (!$uuid) {
2253
    return FALSE;
2254
  }
2255
  $out = 'cdm_dataportal/media/' . $uuid;
2256
  if ($representaion_uuid) {
2257
    $out .= '/' . $representaion_uuid;
2258
    if (is_numeric($partId)) {
2259
      $out .= '/' . $partId;
2260
    }
2261
  }
2262
  return $out;
2263
}
2264

    
2265
/**
2266
 * Compares thisRank with thatRank.
2267
 *
2268
 * Returns a negative integer, zero, or a positive integer
2269
 * as the of thisRank is higher than, equal to, or lower than thatRank.
2270
 * e.g:
2271
 * <ul>
2272
 * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
2273
 * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
2274
 * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
2275
 * </ul>
2276
 * <p>
2277
 * This compare logic of the underlying webservice is the
2278
 * <b>inverse logic</b> of the the one implemented in
2279
 * java.lang.Comparable#compareTo(java.lang.Object)
2280
 *
2281
 * @param $thisRankUuid
2282
 * @param $thatRankUuid
2283
 *
2284
 * @return int
2285
 *   A negative integer, zero, or a positive integer
2286
 *   as the thisRank is lower than, equal to, or higher than thatRank.
2287
 */
2288
function rank_compare($thisRankUuid, $thatRankUuid) {
2289
  $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
2290
  return $result->Integer;
2291
}
2292

    
2293
/**
2294
 * Composes an HTML element class attribute value composed of
2295
 * the short-name of the cdm class and the uuid of the entity.
2296
 * This class attribute should be used wherever an cdm-entity is rendered.
2297
 *
2298
 * In case of Taxon entities or TaxonNodeDTOs the secReference is also added
2299
 * to the class attributes as 'sec_uuid:<uuid>'. In case of TaxonNodeDTOs the
2300
 * Taxon uuid is added also as taxon_uuid:<uuid>
2301
 *
2302
 * These according class selectors in css must be escaped, eg:
2303
 *    .cdm\:TextData
2304
 *
2305
 * @param $cdm_entity
2306
 *    A CDM entity, TaxonNodeDTO or TypedEntityReference
2307
 */
2308
function html_class_attribute_ref($cdm_entity) {
2309

    
2310
  $attributes = '';
2311
  if (is_cdm_entity($cdm_entity)) {
2312
    $attributes =  "cdm:" . $cdm_entity->class . " uuid:" . $cdm_entity->uuid;
2313
  } else if($cdm_entity->class == 'TypedEntityReference') {
2314
    $attributes =  "cdm:" . $cdm_entity->type . " uuid:" . $cdm_entity->uuid;
2315
  }
2316
  if($cdm_entity->class == 'TaxonNodeDto'){
2317
    $attributes .= " taxon_uuid:"  . $cdm_entity->taxonUuid . " sec_uuid:"  . $cdm_entity->secUuid;;
2318
  }
2319
  if($cdm_entity->class == 'Taxon' && isset($cdm_entity->sec->uuid)){
2320
    $attributes .= " sec_uuid:"  . $cdm_entity->sec->uuid;
2321
  }
2322
  return $attributes;
2323
}
2324

    
2325

    
2326
/**
2327
 * Creates a short version of a taxonname.
2328
 *
2329
 * The short name is created by using the taggedTitle field of
2330
 * TaxonNodeDTO instances.
2331
 * If the taggedTitle if empty the fullname will be returned.
2332
 *
2333
 * @param object $taxonNodeDTO
2334
 *   A TaxonNodeDTO object
2335
 *
2336
 * @return string
2337
 */
2338
function cdm_dataportal_shortname_of($taxonNodeDTO) {
2339

    
2340
  $nameStr = '';
2341

    
2342
  normalize_tagged_text($taxonNodeDTO->taggedTitle);
2343

    
2344
  // Get all tagged text tokens of the scientific name.
2345
  foreach ($taxonNodeDTO->taggedTitle as $tagtxt) {
2346
    if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
2347
      $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
2348
    }
2349
  }
2350
  $nameStr = trim($nameStr);
2351

    
2352
  if ($nameStr) {
2353

    
2354
    // Do not return short names for these.
2355
    if ($taxonNodeDTO->unplaced || $taxonNodeDTO->excluded) {
2356
      return $nameStr;
2357
    }
2358

    
2359
    /*
2360
    1st capture group (^[a-zA-Z]): First letter of uninomial.
2361
    Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
2362
    Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
2363
    but only matching if no '(' or '.' in second word of name,        ( \x2E = '.')
2364
    OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$             (\x22= '"', \x2D='-', \xD7='×' )
2365
    */
2366
    $pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
2367
    if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
2368
      return $matches[1][0] . "." . $matches[3][0];
2369
    }
2370
    else {
2371
      return $nameStr;
2372
    }
2373
  }
2374
  else {
2375
    return $taxonNodeDTO->titleCache;
2376
  }
2377
}
2378

    
2379
/**
2380
 * Check if a taxon is accepted by the current taxonomic tree.
2381
 *
2382
 * @param mixed $taxon
2383
 *   The Taxon obkect to check.
2384
 *
2385
 * @return bool
2386
 *   Returns TRUE if $taxon is accepted, FALSE otherwise.
2387
 */
2388
function _cdm_dataportal_acceptedByCurrentView($taxon) {
2389

    
2390
  $defaultTreeUuid = get_current_classification_uuid();
2391

    
2392
  if (isset($taxon->taxonNodes)) {
2393
    $taxonNodes = $taxon->taxonNodes;
2394
  }
2395
  else {
2396
    $taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
2397
  }
2398

    
2399
  if ($taxon->class == "Taxon" && isset($taxonNodes)) {
2400
    foreach ($taxonNodes as $node) {
2401
      if (isset($node->classification)){
2402
        if(is_object($node->classification)) {
2403
          if ($node->classification->uuid == $defaultTreeUuid) {
2404
            return TRUE;
2405
          }
2406
        }
2407
        else {
2408
          if ($node->classification == $defaultTreeUuid) {
2409
            return TRUE;
2410
          }
2411
        }
2412
      }
2413
    }
2414
  }
2415

    
2416
  return FALSE;
2417
}
2418

    
2419
/**
2420
 * Checks is the source has one of the given types.
2421
 *
2422
 * @param object $source
2423
 *   The original source entity
2424
 * @param array $types
2425
 *   An array of elementd of the OriginalSourceType enumeration
2426
 *   If not set the default will be used which is:
2427
 *    - Lineage
2428
 *    - PrimaryMediaSource
2429
 *    - PrimaryTaxonomicSource
2430
 *    - Unknown
2431
 *    - Other
2432
 * @return boolean
2433
 */
2434
  function _is_original_source_type($source, $types = null) {
2435
    // this is the default
2436
    // maybe this should also be put into the settings
2437
    static $default = array(
2438
      OriginalSourceType::Lineage,
2439
      OriginalSourceType::PrimaryMediaSource,
2440
      OriginalSourceType::PrimaryTaxonomicSource,
2441
      OriginalSourceType::Unknown,
2442
      OriginalSourceType::Other,
2443
    );
2444

    
2445
    if(!$types){
2446
      $types = $default;
2447
    }
2448
    return isset($source->type) && in_array($source->type, $types);
2449
  }
2450

    
2451
/**
2452
 * Collects all the media from a list of description elements.
2453
 *
2454
 * @param array $descriptionElements
2455
 *   The description elements from which to collect the media.
2456
 *
2457
 * @return array
2458
 *   The output with all the collected media.
2459
 */
2460
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2461

    
2462
  $outArrayOfMedia = array();
2463

    
2464
  // Avoiding a warning box in Drupal for Flora Malesiana.
2465
  if (isset($descriptionElements) && is_array($descriptionElements)) {
2466
    foreach ($descriptionElements as $descriptionElement) {
2467
      if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2468
        foreach ($descriptionElement->media as $media) {
2469
          if (is_object($media)) {
2470
            $outArrayOfMedia[] = $media;
2471
          }
2472
        }
2473
      }
2474
    }
2475
  }
2476
  return $outArrayOfMedia;
2477
}
2478

    
2479
/**
2480
 * @todo Please document this function.
2481
 * @see http://drupal.org/node/1354
2482
 *
2483
 * @param array $cdm_entities
2484
 *   An array of CdmBase instances or a single instance.
2485
 * @param string $footnote_list_key_suggestion
2486
 *
2487
 * @return unknown
2488
 */
2489
function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
2490

    
2491
   static $annotations_types_filter = null;
2492
   if(!$annotations_types_filter) {
2493
     $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
2494
   }
2495

    
2496
  $footNoteKeys = array();
2497

    
2498
  // Is argument cdmBase an array?
2499
  if (!is_array($cdm_entities)) {
2500
    $cdmBase_array = array();
2501
    $cdmBase_array[] = $cdm_entities;
2502
  }
2503
  else {
2504
    $cdmBase_array = $cdm_entities;
2505
  }
2506

    
2507
  // Getting the key for the footnotemanager.
2508
  if (isset($footnote_list_key_suggestion)) {
2509
    $footnote_list_key = $footnote_list_key_suggestion;
2510
  }
2511
  else {
2512
    $footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2513
  }
2514

    
2515
  // Adding the footnotes keys.
2516
  foreach ($cdmBase_array as $cdmBase_element) {
2517
    $annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
2518
    if (is_array($annotations)) {
2519
      foreach ($annotations as $annotation) {
2520
        $footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2521
      }
2522
    }
2523
  }
2524

    
2525
  return $footNoteKeys;
2526
}
2527

    
2528

    
2529
/**
2530
 * Creates a CDM Dynabox.
2531
 *
2532
 * @param string $dynabox_id
2533
 *   a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2534
 * @param string $label
2535
 *   The clickable text to show.
2536
 * @param string $content_url
2537
 *   The cdm REST service request url wich will deliver the content to be shown
2538
 *   once the dynabox toggles open.
2539
 * @param string $theme
2540
 *   The theme to be used for rendering the cdm REST service response with is
2541
 *   returned from the $content_url.
2542
 * @param string $link_alt_text
2543
 *   The value for the alt attribute of the dynabox link.
2544
 * @param array $enclosingtags
2545
 *   An array with two elements: $enclosingtags[0] will be used for the dynabox
2546
 *   element itself, $enclosingtags[1] is the tag to be used for the
2547
 *   dynabox_content (optional)
2548
 * @param array $attributes
2549
 * @param $content_element_selector
2550
 *   Optional jQuery selector which can be used to reference a dom element which should
2551
 *   be used as container for the content to be shown. The dynabox-<dynabox id>-content
2552
 *  element will be placed in this container.
2553
 *
2554
 * @param string $open_callback
2555
 *   optional javascript call back function to be triggered after toggling the box to
2556
 *   the open state.
2557
 * @param string $close_callback
2558
 *   optional javascript call back function to be triggered after toggling the box to
2559
 *   the closed state.
2560
 * @return string Returns HTML for a dynabox.
2561
 * Returns HTML for a dynabox.
2562
 */
2563
function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2564
                     $enclosingtags = array('li', 'ul'), $attributes = array(),
2565
                     $content_element_selector = null,
2566
                     $open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2567
  $out = '';
2568

    
2569
  // check for plain class attribute string
2570
  $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2571

    
2572
  if(!array_key_exists('class', $attributes)) {
2573
    $attributes['class'] = array();
2574
  }
2575
  $attributes['id'][] = 'dynabox-' . $dynabox_id;
2576
  $dynabox_attributes = drupal_attributes($attributes);
2577

    
2578

    
2579
  _add_js_domEvent(); // requires domEvent.js
2580
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2581
  drupal_add_js("
2582
  jQuery(document).ready(
2583
      function() {
2584
        dynabox('". $dynabox_id ."',
2585
          {
2586
            open_callback: " . $open_callback .",
2587
            close_callback: " . $close_callback .
2588
            ($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2589
          }
2590
        );
2591
      }
2592
   );",
2593
   array(
2594
    'type'=>'inline',
2595
    'scope'=>'footer'
2596
    )
2597
  );
2598

    
2599

    
2600
  $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2601
  $out .= '<!-- dynabox for ' . $content_url . ' -->';
2602
  $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>';
2603
  $out .= '  <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2604
  $out .= '    <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2605
  $out .= '    </' . $enclosingtags[1] . '>';
2606
  $out .= '  </' . $enclosingtags[0] . '>';
2607
  $out .= '<!-- dynabox end -->';
2608
  return $out;
2609
}
2610

    
2611
/**
2612
 * Checks whether a feature has any description elements.
2613
 *
2614
 * @param mixed $featureNode
2615
 *   A feature node as produced by the function _mergeFeatureTreeDescriptions().
2616
 *
2617
 * @see _mergeFeatureTreeDescriptions()
2618
 *
2619
 * @return bool
2620
 *   Returns TRUE if the given $featureNode or any of its subordinate nodes
2621
 *   contains at least one non empty TextData or at least one DescriptionElement
2622
 *   of an other type. A TextData element holding a multilanguageText or a
2623
 *   source reference is considered to be not empty.
2624
 *
2625
 * @TODO this function may have become obsolete by the new method of detecting empty blocks,
2626
 *       see $block_content_is_not_empty in make_feature_block_list() and
2627
 *       $feature_block_has_content in compose_feature_block_items_generic
2628
 */
2629
function has_feature_node_description_elements($featureNode) {
2630

    
2631
  if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2632
    if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2633
      foreach ($featureNode->descriptionElements as $descriptionElement) {
2634
        if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
2635
          && $descriptionElement->multilanguageText_L10n->text != ''
2636
          || isset($descriptionElement->sources[0])
2637
          || isset($descriptionElement->media[0]) ) {
2638
          return TRUE;
2639
        }
2640
      }
2641
    }
2642
  }
2643
  else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2644
    foreach ($featureNode->childNodes as $child) {
2645
      if (has_feature_node_description_elements($child)) {
2646
        return TRUE;
2647
      }
2648
    }
2649
  }
2650
  return FALSE;
2651
}
2652

    
2653
/**
2654
 * Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
2655
 *
2656
 * @param $chapter
2657
 *   The taxon page chapter or part
2658
 */
2659
function cdm_check_valid_taxon_page($chapter){
2660
  static $taxon_tabs = null;
2661

    
2662
  cdm_check_valid_portal_page();
2663

    
2664
  if($taxon_tabs == null){
2665
    $taxon_tabs = array('all', 'description');
2666
    foreach(get_taxon_tabs_list() as $tab){
2667
      $taxon_tabs[] = strtolower($tab);
2668
    }
2669
  }
2670

    
2671
  if(!in_array($chapter, $taxon_tabs)){
2672
    // oops this is not a valid chapter name
2673
    http_response_code(404); // 404 = Not Found
2674
  }
2675

    
2676
}
2677

    
2678
/**
2679
 * Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise.
2680
 * The test applied by default it a check for the query parameter 'q' ending with a file suffix like '*.*'
2681
 *
2682
 * @param $preg_pattern
2683
 *   Optional regular expression pattern to be used in preg_match().
2684
 */
2685
function cdm_check_valid_portal_page($preg_pattern = null){
2686
  $ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
2687
  if($preg_pattern === null){
2688
    $preg_pattern = $ends_with_file_suffix_pattern;
2689
  }
2690
  if(preg_match($preg_pattern, $_GET['q'])){
2691
    // oops this urls ends with a file_suffix and thus does not refer to a portal page
2692
    http_response_code(404); // 404 = Not Found
2693
    exit('HTTP 404');
2694
  }
2695
}
2696

    
2697
/**
2698
 * Generates the diff of the texts and presents it in a HTML diff viewer.
2699
 *
2700
 * @param $text_a
2701
 * @param $text_b
2702
 * @return string
2703
 */
2704
function diff_viewer($text_a, $text_b) {
2705

    
2706
  static $diff_viewer_count = 0;
2707

    
2708
  $element_id = 'part_definitions_diff_' . $diff_viewer_count++;
2709

    
2710
  // http://code.stephenmorley.org/php/diff-implementation/
2711
  module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
2712
  drupal_add_css(drupal_get_path('module',
2713
      'cdm_dataportal') . '/css/diff.css');
2714
  _add_jquery_ui();
2715
  drupal_add_js(
2716
    'jQuery(document).ready( function(){
2717
        jQuery(\'#' . $element_id . '\').accordion({
2718
        collapsible: true,
2719
        active: false,
2720
        fillSpace: true,
2721
        }).children(\'div\').css({ \'height\': \'auto\' });
2722
        jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
2723
     });'
2724
    , array(
2725
    'type' => 'inline',
2726
    'scope' => 'footer'
2727
  ));
2728

    
2729
  $diff = Diff::compare($text_a,
2730
    $text_b);
2731
  $diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
2732
    . Diff::toTable($diff, '', '')
2733
    . '</div></div>';
2734
  return $diff_viewer_markup;
2735
}
2736

    
2737

    
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