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cdm-dataportal / modules / cdm_dataportal / cdm_dataportal.module @ f695daf4

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1
<?php
2
/**
3
 * @file
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 * Module to provide a CDM Dataportal.
5
 *
6
 * @copyright
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 *   (C) 2007-2012 EDIT
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 *   European Distributed Institute of Taxonomy
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 *   http://www.e-taxonomy.eu
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 *
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 *   The contents of this module are subject to the Mozilla
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 *   Public License Version 1.1.
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 * @see http://www.mozilla.org/MPL/MPL-1.1.html
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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

    
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  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/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');
35
  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');
43

    
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  module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
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  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');
48

    
49

    
50
  /* ============================ java script functions ============================= */
51

    
52

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

    
60
    drupal_add_js("
61
          jQuery(document).ready(function() {
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            jQuery.ajax({
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              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() {
67
                    " . $callback . "
68
              }
69
            });
70
          });"
71
    , 'inline');
72
  }
73

    
74
  /**
75
   */
76
  function drupal_add_js_rowToggle($tableId){
77

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

    
85
  /**
86
   * @param unknown_type $link_element_selector
87
   * @param unknown_type $progress_element_selector
88
   */
89
  function _add_js_cdm_ws_progressbar($link_element_selector, $progress_element_selector){
90

    
91
    $callback = "jQuery('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');";
92

    
93
    drupal_add_js_async(variable_get('cdm_webservice_url', '').'js/cdm_ws_progress.js', $callback);
94

    
95
    //   drupal_add_js("
96
    //   	  if (Drupal.jsEnabled) {
97
    //         $(document).ready(function() {
98
    //       		$('" . $link_element_selector . "').cdm_ws_progress('" . $progress_element_selector . "');
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    //         });
100
    //       }", 'inline');
101
    }
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  /**
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   * @todo Please document this function.
105
   * @see http://drupal.org/node/1354
106
   */
107
  function _add_js_treeselector() {
108
    // drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/treeselector.js');
109
    drupal_add_js("
110
        jQuery(document).ready(function() {
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           jQuery('#cdm-taxonomictree-selector-form #edit-val').change(function () {
112
                jQuery('#cdm-taxonomictree-selector-form').submit();
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            });
114

    
115
        });
116
      ",
117
      array(
118
        'type' => 'inline',
119
        'scope' => 'footer'
120
      )
121
    );
122
  }
123

    
124
  function _add_js_openlayers() {
125

    
126
    $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.js';
127
    $proj4js = '/js/map/proj4js-1.1.0/proj4js-compressed.js';
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129
    if(variable_get('cdm_js_devel_mode', FALSE)){
130
      // develooper mode libs
131
  //     $openlayers = '/js/map/OpenLayers-2.13.1/lib/OpenLayers.js';
132
      $openlayers = '/js/map/OpenLayers-2.13.1/OpenLayers.debug.js';
133
      $proj4js = '/js/map/proj4js-1.1.0/proj4js-combined.js';
134
    }
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136
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . $openlayers,
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      array(
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        'type' => 'file',
139
        'weight' => JS_LIBRARY,
140
        'cache' => TRUE,
141
        'preprocess' => FALSE
142
      )
143
    );
144

    
145
    // see https://github.com/proj4js/proj4js
146
    // http://openlayers.org/dev/examples/using-proj4js.html
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    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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        'weight' => JS_LIBRARY,
151
        'cache' => TRUE,
152
      )
153
    );
154

    
155
    // configure the theme
156
    $openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
157
    $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',
160
        'weight' => JS_LIBRARY,
161
        'cache' => TRUE,
162
        'preprocess' => FALSE
163
      ));
164

    
165
    drupal_add_css($openlayers_theme_path . 'style.tidy.css',
166
      array(
167
        'type' => 'file',
168
        'cache' => TRUE,
169
        'preprocess' => FALSE
170
      )
171
    );
172

    
173
  }
174

    
175
  /**
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   * @todo Please document this function.
177
   * @see http://drupal.org/node/1354
178
   */
179
  function _add_js_thickbox() {
180
    // ---- jQuery thickbox:
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    /*
182
    * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
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    * not triggered because of problems with compat-1.0.js' see INSTALL.txt
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    */
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    // drupal_add_js(drupal_get_path('module',
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    // 'cdm_dataportal').'/js/jquery.imagetool.min.js');
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    //
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    // Add a setting for the path to cdm_dataportal module, used to find the path
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    // for the loading animation image in thickbox.
190
    drupal_add_js(array(
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    'cdm_dataportal' => array(
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    'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
193
    )
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    ),
195
    'setting'
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        );
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        drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
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        drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
199
  }
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  /**
202
   * @todo Please document this function.
203
   * @see http://drupal.org/node/1354
204
   */
205
  function _add_js_lightbox($galleryID) {
206
    /*
207
     * Important Notice: The jquery.lightbox-0.5.js has been modified in order to
208
    * allow using the "alt" attribute for captions instead of the "title"
209
    * attribute
210
    */
211
    $lightbox_base_path =  drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';
212
    $lightbox_image_path = base_path() . $lightbox_base_path . '/images/';
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    drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');
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    drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');
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    drupal_add_js('jQuery(document).ready(function() {
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        jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
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          fixedNavigation:  true,
218
          imageLoading:     \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',
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          imageBtnPrev:     \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',
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          imageBtnNext:     \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',
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          imageBtnClose:    \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',
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          imageBlank:       \'' . $lightbox_image_path . 'lightbox-blank.gif\',
223
          adjustToWindow: true
224
        });
225
      });
226
      ', array('type' => 'inline'));
227
  }
228

    
229
  /**
230
   * @todo Please document this function.
231
   * @see http://drupal.org/node/1354
232
   */
233
  function _add_js_footnotes() {
234
    _add_js_domEvent();
235
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
236
  }
237

    
238
  /**
239
   * @todo Please document this function.
240
   * @see http://drupal.org/node/1354
241
   */
242
  function _add_js_cluetip() {
243

    
244
    // TODO replace by
245
    // @see http://www.socialembedded.com/labs/jQuery-Tooltip-Plugin/jQuery-Tooltip-Plugin.html
246
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.min.js');
247
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.dimensions.js');
248
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.hoverIntent.js');
249
    if(variable_get('cdm_js_devel_mode', FALSE)){
250
      drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.js');
251
    }
252
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.css');
253
    drupal_add_js("jQuery(document).ready(function(){
254
        jQuery('.cluetip').css({color: '#0062C2'}).cluetip({
255
          splitTitle: '|',
256
          showTitle: true,
257
          activation: 'hover',
258
          sicky: true,
259
          arrows: true,
260
          dropShadow: false,
261
          cluetipClass: 'rounded'
262
        });
263
      });", array('type' => 'inline'));
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
   * Adds the external javascript file for domEvent.js.
278
   *
279
   * @see drupal_add_js()
280
   */
281
  function _add_js_domEvent() {
282
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
283
  }
284

    
285
  function _add_jquery_ui()
286
  {
287
    drupal_add_css(drupal_get_path('module',
288
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
289
    drupal_add_js(drupal_get_path('module',
290
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
291
      array(
292
        'type' => 'file',
293
        'weight' => JS_LIBRARY,
294
        'cache' => TRUE,
295
        'preprocess' => FALSE
296
      )
297
    );
298
  }
299

    
300
  /**
301
   * Provides the markup for an font awesome icon.
302
   *
303
   * The icons is created in default size without any extra features.
304
   *
305
   * The available icons are listed here http://fontawesome.io/cheatsheet/
306
   * fontawesome icons have much more features than implemented here in this function,
307
   * for spinning icons, fixed width icons, rotation, etc please checkout the
308
   * examples at http://fontawesome.io/examples/
309
   *
310
   * @parameter $icon_name
311
   *  The name of the icon which starts with 'fa-'
312
   *
313
   * @return String
314
   *    the markup for the icon in an <i> tag
315
   *
316
   */
317
  function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
318

    
319

    
320
    //<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
321

    
322
    $font_awesome_css_uri=drupal_get_path('module', 'cdm_dataportal').'/font-awesome/4.5.0/css/font-awesome.min.css';
323
    $font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
324

    
325
    drupal_add_html_head_link(
326
      array(
327
        'href' => $font_awesome_css_uri,
328
        'rel' => 'stylesheet'
329
      )
330
    );
331

    
332
    if($icon_name){
333
      if(!isset($attributes['class'])){
334
        $attributes['class'] = array();
335
      }
336
      $attributes['class'][] = 'fa';
337
      $attributes['class'][] = $icon_name;
338

    
339
      return '<i ' . drupal_attributes($attributes) . '></i>';
340
    }
341

    
342
    return '';
343
  }
344

    
345

    
346
  /* ====================== hook implementations ====================== */
347
  /**
348
   * Implements hook_permission().
349
   *
350
   * Valid permissions for this module.
351
   *
352
   * @return array
353
   *   An array of valid permissions for the portfolio module.
354
   */
355
  function cdm_dataportal_permission() {
356
    return array(
357
      'administer cdm_dataportal' => array(
358
        'title' => t('administer cdm_dataportal'),
359
        'description' => t("TODO Add a description for 'administer cdm_dataportal'"),
360
      ),
361
      'cdm_dataportal view notes' => array(
362
        'title' => t('cdm_dataportal view notes'),
363
        'description' => t("TODO Add a description for 'cdm_dataportal view notes'"),
364
      ),
365
      // TODO Which other permissions are required?
366
      // -> check the WP6 requirements document.
367
    );
368
  }
369

    
370
/**
371
 * Implements hook_menu().
372
 */
373
function cdm_dataportal_menu() {
374
  $items = array();
375

    
376
  // @see settings.php.
377
  cdm_dataportal_menu_admin($items);
378
  cdm_dataportal_menu_help($items);
379

    
380
  $items['cdm_dataportal/names'] = array(
381
    'page callback' => 'cdm_dataportal_view_names',
382
    'access arguments' => array('access content'),
383
    'type' => MENU_CALLBACK,
384
  );
385

    
386
  // Optional callback arguments: page.
387
  $items['cdm_dataportal/taxon'] = array(
388
    'page callback' => 'cdm_dataportal_taxon_page_view',
389
    'access arguments' => array('access content'),
390
    'type' => MENU_CALLBACK,
391
    // Expected callback arguments: uuid.
392
  );
393

    
394
   // Optional callback arguments: page.
395
    //FIXME point to view/page method in this module
396
    $items['cdm_dataportal/specimen'] = array(
397
        'page callback' => 'cdm_dataportal_specimen_page_view',
398
        'access arguments' => array('access content'),
399
        'type' => MENU_CALLBACK,
400
        // Expected callback arguments: uuid.
401
    );
402

    
403
  $items['cdm_dataportal/name'] = array(
404
    'page callback' => 'cdm_dataportal_name_page_view',
405
      /*
406
    'page arguments' => array(
407
       'taxon_name_uuid',
408
       'taxon_to_hide_uuid',
409
       'synonym_uuid' => NULL
410
      ),
411
      */
412
    'access arguments' => array('access content'),
413
    'type' => MENU_CALLBACK,
414
    // Expected callback arguments: uuid.
415
  );
416

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

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

    
431
  $items['cdm_dataportal/media'] = array(
432
    'page callback' => 'cdm_dataportal_view_media',
433
    'access arguments' => array('access content'),
434
    'type' => MENU_CALLBACK,
435
    // Expected callback arguments:
436
    // uuid, mediarepresentation_uuid, part_uuid or part#.
437
  );
438

    
439
  $items['cdm_dataportal/polytomousKey'] = array(
440
    'page callback' => 'cdm_dataportal_view_polytomousKey',
441
    'access arguments' => array('access content'),
442
    'type' => MENU_CALLBACK,
443
    // Expected callback arguments: polytomousKey->uuid.
444
  );
445

    
446
  $items['cdm_dataportal/search'] = array(
447
    'page callback' => 'cdm_dataportal_view_search_advanced',
448
    'access arguments' => array('access content'),
449
    'type' => MENU_CALLBACK,
450
  );
451

    
452
  $items['cdm_dataportal/search/advanced'] = array(
453
    'title' => 'Advanced tt', // will be passed through t()
454
   // 'title arguments' => array('!title' => 'Advanced tt'), // will be passed through t()
455
    'page callback' => 'cdm_dataportal_view_search_advanced',
456
    'access arguments' => array('access content'),
457
    'type' => MENU_DEFAULT_LOCAL_TASK,
458
  );
459

    
460
  $items['cdm_dataportal/search/taxon_by_description'] = array(
461
    'title' => 'By factual data tt', // will be passed through t()
462
    'title arguments' => array('!title' => 'By factual data tt'), // will be passed through t()
463
    'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
464
    'access arguments' => array('access content'),
465
    'type' => MENU_LOCAL_TASK,
466
  );
467

    
468
  $items['cdm_dataportal/search/results/taxon'] = array(
469
    'page callback' => 'cdm_dataportal_view_search_results_taxon',
470
    'access arguments' => array('access content'),
471
    'type' => MENU_CALLBACK,
472
  );
473
  /*
474
   $items['cdm/xml2json'] = array(
475
   'page callback' => 'cdm_view_xml2json',
476
   'access arguments' => array('access content'),
477
   'type' => MENU_CALLBACK,
478
   );
479
   */
480

    
481
  // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
482
  // User configuration of cdm_dataportal.
483
  $items['user/%/cdm_dataportal'] = array(
484
    'title' => 'cdm_dataportal',
485
    'access arguments' => array('access content'),
486
    'page callback' => 'drupal_get_form',
487
    'page arguments' => array('cdm_dataportal_user_form'),
488
    'type' => MENU_LOCAL_TASK,
489
    'weight' => 10,
490
  );
491
  // }
492

    
493
  // 'May not cache' in D5.
494
  $items['cdm_dataportal/name/%'] = array(
495
    // 'page callback' => 'cdm_dataportal_view_name',
496
    'page callback' => 'cdm_dataportal_name_page_view',
497
    'page arguments' => array(2, 3, 4),
498
    'access arguments' => array('access content'),
499
    'type' => MENU_CALLBACK,
500
  );
501

    
502
  // --- Local tasks for Taxon.
503
  // --- tabbed taxon page
504
  if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
505
    $items['cdm_dataportal/taxon/%'] = array(
506
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
507
      'page callback' => 'cdm_dataportal_taxon_page_view',
508
      'access arguments' => array('access content'),
509
      'type' => MENU_CALLBACK,
510
      'weight' => 1,
511
      'page arguments' => array(2, "description")
512
      , // Expected callback arguments: taxon_uuid.
513
    );
514

    
515
    $items['cdm_dataportal/taxon/%/all'] = array(
516
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
517
      'page callback' => 'cdm_dataportal_taxon_page_view',
518
      'access arguments' => array('access content'),
519
      'type' => MENU_CALLBACK,
520
      'weight' => 2,
521
      'page arguments' => array(2, "all")
522
      , // Expected callback arguments: taxon_uuid.
523
    );
524

    
525
    $items['cdm_dataportal/taxon/%/description'] = array(
526
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'General')),
527
      'page callback' => 'cdm_dataportal_taxon_page_view',
528
      'access arguments' => array('access content'),
529
      'type' => MENU_DEFAULT_LOCAL_TASK,
530
      'weight' => 2,
531
      'page arguments' => array(2, "description")
532
      , // Expected callback arguments: taxon_uuid.
533
    );
534

    
535
    $items['cdm_dataportal/taxon/%/synonymy'] = array(
536
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Synonymy')),
537
      'page callback' => 'cdm_dataportal_taxon_page_view',
538
      'access arguments' => array('access content'),
539
      'type' => MENU_LOCAL_TASK,
540
      'weight' => 4,
541
      'page arguments' => array(2, "synonymy", 4)
542
      , // Expected callback arguments: taxon_uuid and ...
543
    );
544
    $items['cdm_dataportal/taxon/%/images'] = array(
545
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Images')),
546
      'page callback' => 'cdm_dataportal_taxon_page_view',
547
      'access arguments' => array('access content'),
548
      'type' => MENU_LOCAL_TASK,
549
      'weight' => 5,
550
      'page arguments' => array(2, "images")
551
      , // Expected callback arguments: taxon_uuid.
552
    );
553

    
554
    $items['cdm_dataportal/taxon/%/specimens'] = array(
555
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Specimens')),
556
      'page callback' => 'cdm_dataportal_taxon_page_view',
557
      'access arguments' => array('access content'),
558
      'type' => MENU_LOCAL_TASK,
559
      'weight' => 6,
560
      'page arguments' => array(2, "specimens")
561
      , // Expected callback arguments: taxon_uuid.
562
    );
563

    
564
    $items['cdm_dataportal/taxon/%/keys'] = array(
565
      'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Keys')),
566
      'page callback' => 'cdm_dataportal_taxon_page_view',
567
      'access arguments' => array('access content'),
568
      'type' => MENU_LOCAL_TASK,
569
      'weight' => 6,
570
      'page arguments' => array(2, "keys")
571
      , // Expected callback arguments: taxon_uuid.
572
    );
573

    
574
    $items['cdm_dataportal/taxon/%/experts'] = array(
575
        'title' => theme('cdm_taxonpage_tab', array('tabname' => 'Experts')),
576
        'page callback' => 'cdm_dataportal_taxon_page_view',
577
        'access arguments' => array('access content'),
578
        'type' => MENU_LOCAL_TASK,
579
        'weight' => 6,
580
        'page arguments' => array(2, "experts")
581
    , // Expected callback arguments: taxon_uuid.
582
    );
583
  }
584

    
585
  // --- refresh link for all cdmnode types
586
  foreach (cdm_get_nodetypes() as $type=>$name) {
587
    $items['cdm_dataportal/' . $name . '/%/refresh'] = array(
588
        'title' => t('Refresh'),
589
        'page callback' => 'cdm_dataportal_refresh_node',
590
        'access arguments' => array('administer cdm_dataportal'),
591
        'type' => MENU_LOCAL_TASK,
592
        'weight' => 100,
593
        'page arguments' => array($name, 2)
594
    );
595
  }
596

    
597
  return $items;
598
}
599

    
600
/**
601
 * Implements hook_init().
602
 *
603
 */
604
function cdm_dataportal_init() {
605
  //FIXME To add CSS or JS that should be present on all pages, modules
606
  //      should not implement this hook, but declare these files in their .info file.
607
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
608
  // drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
609
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
610

    
611
  if(variable_get('cdm_debug_mode', FALSE)){
612
    $file = 'temporary://drupal_debug.txt';
613
    file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
614
  }
615

    
616
  $bibliography_settings = get_bibliography_settings();
617
  $enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
618
  FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
619
}
620

    
621
function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
622

    
623
  $base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
624

    
625
  if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
626
    // force reloading of all and notify user about this special loading
627
    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: ')
628
        . l('Back to tabbed taxon page', $base_path));
629
    $base_path .= '/all';
630
  } else {
631
    drupal_set_message(t('The level 2 cache has been cleared for this page'));
632
  }
633

    
634
  $parameters['cacheL2_refresh'] ='1';
635

    
636

    
637
  drupal_goto($base_path, array('query' => $parameters));
638
}
639

    
640
/**
641
 * The function generate form for own user cdm dataportal configurations.
642
 */
643
function cdm_dataportal_user_form($form, &$form_state) {
644

    
645
  global $user;
646
  $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
647

    
648
  $form['taxon_page_tabs'] = array(
649
      '#type' => 'fieldset',
650
      '#tree' => true,
651
      '#title' => t('Taxon page tabs'),
652
  );
653

    
654
  $form['taxon_page_tabs']['user_defined'] = array(
655
    '#type' => 'checkbox',
656
    '#title' => t('Activate user default configuration'),
657
    '#default_value' => variable_get($checkbox_value, 0),
658
    '#description' => t('Check this if you want configure your own default tab from the below menu.'),
659
  );
660

    
661
  $form['taxon_page_tabs']['default_tab'] = array(
662
    '#type' => 'select',
663
    '#title' => t('Default tab to display'),
664
    '#default_value' => get_default_taxon_tab(TRUE),
665
    '#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
666
    '#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
667
              <strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
668
              to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
669
  );
670

    
671

    
672
  if(false){
673
    $form['developer_options'] = array(
674
        '#type' => 'fieldset',
675
        '#tree' => true,
676
        '#title' => t('Developer options'),
677
    );
678

    
679
    $form['developer_options']['show_render_path'] = array(
680
      '#type' => 'checkbox',
681
      '#title' => t('Display the render path for each taxon name.'),
682
      '#default_value' => variable_get($checkbox_value, 0),
683
      '#description' => t('This option is very helpful if you are editing the !link for taxon names.',
684
        array(
685
            '!link' => l(
686
              'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))
687
            )
688
        ),
689
    );
690
  }
691

    
692
  $form['submit'] = array(
693
    '#type' => 'submit',
694
    '#value' => t('Submit'),
695
  );
696

    
697
  return $form;
698
}
699

    
700
/**
701
 * Form submission handler for user_form().
702
 *
703
 * Submits the user cdm dataportal configurations.
704
 */
705
function cdm_dataportal_user_form_submit($form, &$form_state) {
706
  global $user;
707
  $msg_type = 'status';
708
  $username = $user->name;
709
  $variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
710

    
711
  // FIXME: this is completely wrong, see user_profile_form_submit()
712

    
713
  // it is only possible to change own user settings
714
  if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {
715

    
716
    // DEFAULT_TAXON_TAB
717
    $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
718
    variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);
719
    variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);
720
    if ($form_state['values']['taxon_page_tabs']['user_defined']) {
721
      drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
722
      drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
723
        '!tab' => $variable[variable_get($variable_to_use, 0)],
724
        '!user' => $username,
725
      ))), $msg_type);
726
    }
727
    else {
728
      drupal_set_message(check_plain(t('The user default tab wont be used for
729
        the next taxon site, check the box if you want to use the user default configuration.')));
730
    }
731

    
732
  }
733
  else {
734
    // Problem with the user id => variables wont be saved.
735
    $msg_type = 'warning';
736
    drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
737
  }
738
}
739

    
740
/**
741
 * Implements hook_block_info().
742
 */
743
function cdm_dataportal_block_info() {
744

    
745
    // $block[0]["info"] = t("CDM DataPortal DevLinks");
746
    // $block[1]["info"] = t("CDM DataPortal Credits");
747
    $block["2"] = array(
748
        "info" => t("CDM Search Taxa"),
749
        "cache" => DRUPAL_NO_CACHE
750
      );
751
    // $block[3]["info"] = t("CDM Filters");
752
    $block["4"]["info"] = t("CDM Dataportal Print");
753
    $block["keys"]["info"] = t("CDM identification keys");
754
    $block["fundedByEDIT"]["info"] = t('Funded by EDIT');
755
    $block["classification_breadcrumbs"] =  array(
756
        'info' => t('Classification breadcrumbs'),
757
        'cache' => DRUPAL_CACHE_PER_PAGE
758
      );
759

    
760
    return $block;
761
}
762

    
763
/**
764
 * Implements hook_block_view().
765
 */
766
function cdm_dataportal_block_view($delta) {
767
  // TODO Rename block deltas (e.g. '2') to readable strings.
768
  switch ($delta) {
769
    // case 'delta-1':
770
    // $block['subject'] = t('Credits');
771
    // $block['content'] = theme('cdm_credits');
772
    // return $block;
773
    case '2':
774
      $block['subject'] = t('Search taxa');
775
      $form = drupal_get_form('cdm_dataportal_search_taxon_form');
776
      $block['content'] = drupal_render($form);
777

    
778
      if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
779
        $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
780
      }
781
      return $block;
782
    case '4':
783
      $block['subject'] = '';
784
      $block['content'] = theme('cdm_print_button');
785
      return $block;
786
    case "keys":
787
      $block['subject'] = t('Identification Keys');
788
      $block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
789
      return $block;
790
    case "fundedByEDIT":
791
      // t('Funded by EDIT');
792
      $text = '<none>';
793
      $block['subject'] = $text;
794
      $img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
795
      $block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
796
        'attributes' => array("target" => "EDIT"),
797
        'absolute' => TRUE,
798
        'html' => TRUE,
799
      ));
800
      return $block;
801
    case 'classification_breadcrumbs':
802
      if (arg(1) == 'taxon' && is_uuid(arg(2))) {
803
        $block['subject'] = '<none>';
804
        $block['content'] = compose_classification_breadcrumbs(arg(2));
805
        return $block;
806
      }
807
      break;
808
  }
809
}
810

    
811
/*
812
 function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
813
 $_SESSION['cdm'] = NULL;
814
 if(is_string($cdm_ws_uri_update)){
815
 $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
816
 }
817
 }
818

    
819
 function cdm_dataportal_session_validate(){
820
 if(!isset($_SESSION['cdm']['ws_uri'])){
821
 $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
822
 } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
823
 cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
824
 }
825
 }
826
 */
827

    
828
/**
829
 * creates a  selector form for taxonomic trees.
830
 *
831
 * @return a drupal form array
832
 */
833
function cdm_taxonomictree_selector() {
834
  _add_js_treeselector();
835

    
836
  $form = drupal_get_form('cdm_taxonomictree_selector_form');
837
  return $form;
838
}
839

    
840
/**
841
 * @todo Please document this function.
842
 * @see http://drupal.org/node/1354
843
 */
844
function cdm_taxonomictree_selector_form($form, &$form_state) {
845

    
846
  $url = url('cdm_api/setvalue/session', array('query' => NULL));
847
  $form['#action'] = $url;
848

    
849
  $form['var'] = array(
850
    '#weight' => -3,
851
    '#type' => 'hidden',
852
    '#value' => '[cdm][taxonomictree_uuid]',
853
  );
854

    
855
  $destination_array = drupal_get_destination();
856
  $destination = $destination_array['destination'];
857

    
858
  $form['destination'] = array(
859
    '#weight' => -3,
860
    '#type' => 'hidden',
861
    '#value' =>  $destination,
862
  );
863

    
864
  $options = cdm_get_taxontrees_as_options();
865
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
866
  if($taxontree_includes){
867
    $filtered_options = array();
868
    foreach($options as $uuid=>$label){
869
      if(!empty($taxontree_includes[$uuid])){
870
        $filtered_options[$uuid] = $label;
871
      }
872
    }
873
    $options = $filtered_options;
874
  }
875

    
876
  $form['val'] = array(
877
    '#type' => 'select',
878
    '#title' => t('Available classifications'),
879
    '#default_value' => get_current_classification_uuid(),
880
    '#options' => $options,
881
    '#attributes' => array('class' => array('highlite-first-child'))
882
  );
883

    
884
  return $form;
885

    
886
}
887

    
888
/* UNREACHABLE since action of form directly links to view.
889
 function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
890

    
891
 $_SESSION['cdm']['search'] = $form_values;
892
 //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
893
 return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
894
 //$paramstr = compose_url_prameterstr($form_values);
895
 //return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
896
 }
897
 */
898
/* ====================== menu callback functions ====================== */
899
/**
900
 * @todo Please document this function.
901
 * @see http://drupal.org/node/1354
902
 */
903
/*
904
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
905
  static $comment_node_disabled =  0;
906
  static $comment_node_read_only =  1;
907
  static $comment_node_read_write =  2;
908

    
909
  if ($form_id == 'node_type_form'
910
   && isset($form['identity']['type'])
911
   && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
912
  ) {
913
    $form['workflow']['comment'] = array(
914
      '#type' => 'radios',
915
      '#title' => t('Default comment setting'),
916
      '#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
917
      '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
918
      '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
919
    );
920
  }
921
}
922
*/
923

    
924
/**
925
 * Displays a list of the known taxonomic names.
926
 *
927
 * When the list of taxonomic names is displayed, long lists are split up into
928
 * multiple pages.
929
 *
930
 * TODO: Parameters are still preliminary.
931
 *
932
 * @param string $beginsWith
933
 * @param string $page
934
 *   Page number to diplay defaults to page 1.
935
 * @param bool $onlyAccepted
936
 */
937
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
938

    
939
  $out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
940

    
941
  /*
942
  // FIXME the filter for accepted names will be a form element, thus this
943
  // widget should be generated via form api preferably as block.
944
  $out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
945
  $out .= theme('cdm_dataportal_widget_names_list', $names, $page);
946
  $out .= theme('cdm_listof_taxa', $taxonPager);
947
  return $out;
948
  */
949
}
950

    
951
/**
952
 * @todo Please document this function.
953
 * @see http://drupal.org/node/1354
954
 */
955
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
956

    
957
  cdm_check_valid_portal_page();
958

    
959
  $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
960
  return theme('cdm_reference_page', array('reference' => $reference));
961
}
962

    
963
/**
964
 * Created a view on a all references contained in the portal.
965
 *
966
 * This function is used at the path cdm_dataportal/reference/list
967
 */
968
function cdm_dataportal_view_reference_list($pageNumber) {
969
  $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
970
  return theme('cdm_reference_pager', array(
971
    'referencePager' => $referencePager,
972
    'path' => 'cdm_dataportal/reference/list/',
973
    ));
974
}
975

    
976
/**
977
 * @todo Please document this function.
978
 * @see http://drupal.org/node/1354
979
 */
980
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
981

    
982
  cdm_check_valid_portal_page();
983

    
984
  $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
985
  return theme('cdm_media_page', array(
986
    'media' => $media,
987
    'mediarepresentation_uuid' => $mediarepresentation_uuid,
988
    'partId' => $part,
989
    ));
990
}
991

    
992
/**
993
 * @todo Please document this function.
994
 * @see http://drupal.org/node/1354
995
 */
996
function _load_taxonBase(&$taxonBase) {
997
  if (isset($taxonBase->uuid)) {
998
    $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
999
    $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
1000
    $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
1001
  }
1002
}
1003

    
1004
/**
1005
 * Loads the media associated to the given taxon from the cdm server.
1006
 * The aggregation settings regarding taxon relathionships and
1007
 * taxonnomic childen are taken into account.
1008
 *
1009
 * The media lists are cached in a static variable.
1010
 *
1011
 * @param Taxon $taxon
1012
 *   A CDM Taxon entitiy
1013
 *
1014
 * @return array
1015
 *   An array of CDM Media entities
1016
 *
1017
 */
1018
function _load_media_for_taxon($taxon) {
1019

    
1020
  static $media = NULL;
1021

    
1022
  if(!isset($media)) {
1023
    $media = array();
1024
  }
1025
  if (!isset($media[$taxon->uuid])) {
1026

    
1027
    // --- GET Images --- //
1028
    $mediaQueryParameters = array(
1029
        "type" => "ImageFile",
1030
    );
1031

    
1032
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1033
    $mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
1034
    $mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
1035

    
1036
    $taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
1037
    $mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
1038
    $mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
1039
    $mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
1040

    
1041
    $ws_endpoint = NULL;
1042
    if ( variable_get('cdm_images_include_children', 0) == 0) {
1043
      $ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1044
    } else {
1045
      $ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1046
    }
1047

    
1048
    $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1049
        array(
1050
            $taxon->uuid,
1051
        ),
1052
        queryString($mediaQueryParameters)
1053
       );
1054
  }
1055

    
1056
  return $media[$taxon->uuid];
1057
}
1058

    
1059
/**
1060
 *
1061
 * @param Taxon $taxon
1062
 *   A CDM Taxon entitiy
1063
 *
1064
 * @return array
1065
 *   An array of CDM SpecimenOrObservation entities
1066
 *
1067
function _load_occurences_for_taxon($taxon){
1068

    
1069
  static $occurences = NULL;
1070

    
1071
  if(!isset($occurences)) {
1072
    $occurences = array();
1073
  }
1074

    
1075
  if (!isset($occurences[$taxon->uuid])){
1076

    
1077
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1078
    $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1079
    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1080

    
1081
    $by_associatedtaxon_query = http_build_query(array(
1082
        'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1083
        'relationships' => implode(',', $relationship_choice['direct']),
1084
        'pageSize' => null // all hits in one page
1085
    )
1086
    );
1087

    
1088
    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1089
        null,
1090
        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1091
    );
1092

    
1093

    
1094
    if(isset($pager->records[0])){
1095
      $occurences[$taxon->uuid] =  $pager->records;
1096
    }
1097
  }
1098
  return $occurences[$taxon->uuid];
1099
}
1100
 */
1101

    
1102
/**
1103
 * Gets a Drupal variable, string or array and returns it.
1104
 *
1105
 * Similar to the variable_get() function of Drupal, except that this function
1106
 * is able to handle arrays correctly. This function is especially useful
1107
 * when dealing with collections of settings form elements (#tree = TRUE).
1108
 *
1109
 * @param string $variableKey
1110
 *   The Unique key of the Drupal variable in the Drupal variables table.
1111
 * @param string $defaultValueString
1112
 *   A string as for example derived from a CONSTANT.
1113
 *
1114
 * @return mixed
1115
 *   usually an array, depending on the nature of the variable.
1116
 *
1117
 * TODO compare with get_array_variable_merged() duplicate functions?
1118
 * @deprecated rather use get_array_variable_merged() since this function
1119
 * used an array as second parameter
1120
 */
1121
function mixed_variable_get($variableKey, $defaultValueString) {
1122
  $systemDefaults = unserialize($defaultValueString);
1123
  $storedSettings = variable_get($variableKey, array());
1124
  if (is_array($storedSettings)) {
1125
    // TODO better use drupal_array_merge_deep() ?
1126
    $settings = array_merge($systemDefaults, $storedSettings);
1127
  }
1128
  else {
1129
    $settings = $systemDefaults;
1130
  }
1131
  return $settings;
1132
}
1133

    
1134
/**
1135
 * Recursive function to convert an object into an array.
1136
 * also subordinate objects will be converted.
1137
 *
1138
 * @param object $object
1139
 * @return the array
1140
 */
1141
function convert_to_array($object) {
1142
  if(is_object($object) || is_array($object)) {
1143
    $array = (array)$object;
1144
    foreach ($array as $key=>$value){
1145
      $array[$key] = convert_to_array($value);
1146
    }
1147
    return $array;
1148
  } else {
1149
    return $object;
1150
  }
1151
}
1152

    
1153
/**
1154
 * Searches the $collection for the cdm entitiy given as $element.
1155
 *
1156
 * The elements are compared by their UUID.
1157
 *
1158
 * @param $element
1159
 *  the CDM entitiy to search for
1160
 * @param $collection
1161
 *  the list of CDM entities to search in
1162
 *
1163
 * @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1164
 *
1165
 */
1166
function contains_cdm_entitiy($element, $collection) {
1167
  $result = FALSE;
1168
  foreach ($collection as $a) {
1169
    if ($a->uuid == $element->uuid) {
1170
      $result = TRUE;
1171
    }
1172
  }
1173
  return $result;
1174
}
1175

    
1176
/**
1177
 * Fiters the array $entity_list of CDM entities by the list
1178
 * of $excludes. Any element contained in the $excludes will be removed
1179
 * from included int the retuned list.
1180
 *
1181
 * If the $entity_list is not an array the $excludes will be returned.
1182
 */
1183
function filter_cdm_entity_list($entity_list, $excludes) {
1184
  if (is_array($entity_list)) {
1185
    $result = $entity_list;
1186
    if ($excludes) {
1187
      foreach ($excludes as $exclude) {
1188
        if (!contains_cdm_entitiy($exclude, $entity_list)) {
1189
          $result[] = $exclude;
1190
        }
1191
      }
1192
    }
1193
  }
1194
  else {
1195
    $result = $excludes;
1196
  }
1197
  return $result;
1198
}
1199

    
1200
/**
1201
 * Wraps the given $html string into a render array suitable for drupal_render()
1202
 *
1203
 * @param $html
1204
 *   the html string, see
1205
 *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1206
 * @param $weight
1207
 *   A positive or negative number (integer or decimal).
1208
 *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1209
 * @param $prefix
1210
 *   Optional markup for the '#prefix' element of the render array
1211
 * @param $suffix
1212
 *   Optional markup for the '#suffix' element of the render array
1213
 *
1214
 * @return array
1215
 *   A render array
1216
 *
1217
 */
1218
function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1219
  $render_array = array(
1220
    '#markup' => $html
1221
      );
1222
  if (is_numeric($weight)) {
1223
    $render_array['#weight'] = $weight;
1224
  }
1225
  if($prefix){
1226
    $render_array['#prefix'] = $prefix;
1227
  }
1228
  if($suffix) {
1229
    $render_array['#suffix'] = $suffix;
1230
  }
1231
  return $render_array;
1232
}
1233

    
1234
/**
1235
 * Loads the subgraph of a given PolytomousKeyNode.
1236
 *
1237
 * Loads the subgraph of the given PolytomousKeyNode recursively from
1238
 * the CDM REST service.
1239
 *
1240
 * @param mixed $polytomousKeyNode
1241
 *   PolytomousKeyNode passed by reference.
1242
 *
1243
 * @return void
1244
 */
1245
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1246

    
1247
  if (!$polytomousKeyNode) {
1248
    return;
1249
  }
1250
  if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1251
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1252
    return;
1253
  }
1254
  if (!is_uuid($polytomousKeyNode->uuid)) {
1255
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1256
    return;
1257
  }
1258

    
1259
  $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1260

    
1261
  if (!$polytomousKeyNode) {
1262
    // drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1263
    return;
1264
  }
1265

    
1266
  // Load children.
1267
  foreach ($polytomousKeyNode->children as &$childNode) {
1268
    _load_polytomousKeySubGraph($childNode);
1269
  }
1270

    
1271
  // Load subkey.
1272
  $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1273

    
1274
  // Load taxon.
1275
  $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1276
  _load_taxonBase($polytomousKeyNode->taxon);
1277
  return;
1278
}
1279

    
1280
/**
1281
 * @todo Please document this function.
1282
 * @see http://drupal.org/node/1354
1283
 */
1284
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1285

    
1286
  cdm_check_valid_portal_page();
1287

    
1288
  $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1289

    
1290
  $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1291
  if (is_array($sourcePager->records)) {
1292
    $polytomousKey->sources = $sourcePager->records;
1293
    // $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1294
  }
1295

    
1296
  $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1297
  if (is_array($annotationPager->records)) {
1298
    $polytomousKey->annotations = $annotationPager->records;
1299
  }
1300

    
1301
  _load_polytomousKeySubGraph($polytomousKey->root);
1302
  return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1303
}
1304

    
1305
/**
1306
 * Creates a taxon page view or a chapter of it.
1307
 *
1308
 * The taxon page gives detailed information on a taxon, it shows:
1309
 *  - Taxon name.
1310
 *  - Full list of synonyms homotypic synonyms on top, followed by the
1311
 *    heterotypic and finally followed by misapplied names.
1312
 *    The list is ordered historically.
1313
 *  - All description associated with the taxon.
1314
 *
1315
 * @param string $uuid
1316
 * @param string $chapter
1317
 *   Name of the part to display, valid values are:
1318
 *   'description', 'images', 'synonymy', 'specimens', 'all'.
1319
 *
1320
 * @return unknown_type
1321
 */
1322
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all', $synonym_uuid = NULL) {
1323

    
1324
  cdm_check_valid_taxon_page($chapter);
1325
  cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1326
  // show a warning in case the javascript development mode is anabled
1327
  if(variable_get('cdm_js_devel_mode', FALSE)) {
1328
    drupal_set_message(t('The !url1 is enabled.
1329
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1330
          '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1331
    )),
1332
    'warning'
1333
        );
1334
  }
1335

    
1336
  // Display the page for the taxon defined by $uuid.
1337
  // set_last_taxon_page_tab(arg(3));
1338
  $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter, $synonym_uuid);
1339
  if (!empty($taxonpage)) {
1340
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1341
    return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1342
  }
1343
  else {
1344
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1345
    return '';
1346
  }
1347
}
1348

    
1349
/**
1350
 * This function will genreate the taxon page part ($chapter) and returns a taxonpage object
1351
 * which has two fields, one for the page title and one for the content. Later on in the
1352
 * process chain the value contained in these fields will be passed to the cdm_node_show()
1353
 * function as the function parameters $title and $content.
1354
 *
1355
 * @param string $uuid
1356
 *   the uuid of the taxon to show
1357
 * @param string $chapter
1358
 *   Name of the part to display, valid values are:
1359
 *   'description', 'images', 'synonymy', 'all'.
1360
 *
1361
 * @return taxonpage object with the following fields:
1362
 *   - title : the title of the page
1363
 *   - content: the content of the page
1364
 *
1365
 */
1366
function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1367
  // Taxon object.
1368
  $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1369
  if (empty($taxon)) {
1370
    drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1371
    return FALSE;
1372
  }
1373
  $taxonpage = new stdClass();
1374

    
1375
  $taxonpage->title = theme('cdm_taxon_page_title', array(
1376
    'taxon' => $taxon
1377
  ));
1378

    
1379
  // Check if the taxon id contained in the currently selected tree.
1380
  $taxon_in_current_classification = taxon_in_current_classification($uuid);
1381

    
1382
  if (!$taxon_in_current_classification) {
1383
    $classifications = get_classifications_for_taxon($taxon);
1384
    RenderHints::pushToRenderStack('not_in_current_classification');
1385
    $taxon_name_markup = render_taxon_or_name($taxon);
1386

    
1387
    if (count($classifications) == 0) {
1388
      drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
1389
        array(
1390
        '!taxonname' => $taxon_name_markup,
1391
        )
1392
      ), 'warning');
1393
    }
1394
    else {
1395
      $trees = '';
1396
      foreach ($classifications as $classification) {
1397
        if (isset($classification->titleCache)) {
1398
          $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1399
        }
1400
      }
1401

    
1402
      drupal_set_message(format_plural(count($trees),
1403
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in this one: !trees',
1404
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1405
          array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1406
        ) ,
1407
        'warning');
1408
    }
1409
    RenderHints::popFromRenderStack();
1410
  }
1411

    
1412
  // Render the taxon page.
1413
  $render_array = compose_cdm_taxon_page($taxon, $chapter);
1414
  $taxonpage->content = drupal_render($render_array);
1415

    
1416
  return $taxonpage;
1417
}
1418

    
1419
/**
1420
 * Creates a specimen page view.
1421
 * @param string $uuid the UUID of the specimen
1422
 * @return array|string
1423
 */
1424
function cdm_dataportal_specimen_page_view($uuid) {
1425

    
1426
    //cdm_check_valid_taxon_page($chapter);
1427
    //cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1428
    // show a warning in case the javascript development mode is anabled
1429
    if(variable_get('cdm_js_devel_mode', FALSE)) {
1430
        drupal_set_message(t('The !url1 is enabled.
1431
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1432
            '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1433
        )),
1434
            'warning'
1435
        );
1436
    }
1437

    
1438
    // Display the page for the specimen defined by $uuid.
1439
    $specimenpage = cdm_dataportal_specimen_view($uuid);
1440
    if (!empty($specimenpage)) {
1441
        return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
1442
    }
1443
    else {
1444
        return '';
1445
    }
1446
}
1447

    
1448
/**
1449
 *
1450
 * Creates a specimen view.
1451
 * @param string $uuid the UUID of the specimen
1452
 * @return array|string
1453
 */
1454
function cdm_dataportal_specimen_view($uuid) {
1455
    $specimen = cdm_ws_get(CDM_WS_OCCURRENCE, $uuid);
1456
    if (empty($specimen)) {
1457
        drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1458
        return FALSE;
1459
    }
1460
    $specimenpage = new stdClass();
1461

    
1462
    $specimenpage->title = theme('cdm_specimen_page_title', array(
1463
        'specimen' => $specimen
1464
    ));
1465

    
1466
    // Render the specimen page.
1467
    $render_array = compose_cdm_specimen_page($uuid);
1468
    $specimenpage->content = drupal_render($render_array);
1469

    
1470
    return $specimenpage;
1471
}
1472

    
1473
/**
1474
 * Returns a name page as a Drupal node ready to be renderized by Drupal.
1475
 *
1476
 * The node page shows the taxon name title and the list of taxon related
1477
 * with such taxon. Name on the tree already in use.
1478
 *
1479
 * @param UUID $taxon_name_uuid
1480
 *   The uuid of the CDM TaxonNameBase to show a name page for
1481
 * @param UUID $taxon_to_hide_uuid
1482
 *   A taxon which should not be displayed in the taxon list
1483
 * @param UUID $highlite_synonym_uuid
1484
 *   Optinal parameter wich takes another taxon uuid, if given the
1485
 *   target taxon pages will show the syonymy tab where the taxon
1486
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1487
 *   in case it is found on this page.
1488
 *
1489
 * @return mixed
1490
 *   The formatted name page as node.
1491
 */
1492
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
1493

    
1494
  cdm_check_valid_portal_page();
1495

    
1496
  $taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
1497
  if (!empty($taxonname_page)) {
1498
    return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
1499
  }
1500
  else {
1501
    return '';
1502
  }
1503
}
1504

    
1505
/**
1506
 * View function for a TaxonNameBase page.
1507
 *
1508
 * The name page lists all taxa for which the name specified by the
1509
 * $taxon_name_uuid is being used. I case there is only one name the
1510
 * page automatically redirects ti the according taxon page. Otherwise
1511
 * the list of names is displayed.
1512
 *
1513
 * The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
1514
 * list of taxa. This is useful for example when referencing from a taxon
1515
 * to the name page and the referring taxon should not be repeaded in the
1516
 * name page.
1517
 *
1518
 *
1519
 * @param UUID $taxon_name_uuid
1520
 *   The uuid of the CDM TaxonNameBase to show a name page for
1521
 * @param UUID $taxon_to_hide_uuid
1522
 *   A taxon which should not be displayed in the taxon list
1523
 * @param UUID $highlite_synonym_uuid
1524
 *   Optinal parameter wich takes another taxon uuid, if given the
1525
 *   target taxon pages will show the syonymy tab where the taxon
1526
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1527
 *   in case it is found on this page.
1528
 *
1529
 * @return object
1530
 *   An object with two fields:
1531
 *     - title: the page title
1532
 *     - content: the page content
1533
 */
1534
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
1535
  // Getting the full taxonname object from the server.
1536
  $taxon_name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
1537
  if (!$taxon_name) {
1538
    drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
1539
    return FALSE;
1540
  }
1541
  // Searching for all the taxa connected with the taxon name on the tree
1542
  // in use.
1543
  $name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
1544
  $request_params = array();
1545
  $request_params['query'] = $name_cache;
1546
  $request_params['tree'] = get_current_classification_uuid();
1547
  $request_params['doTaxa'] = 1;
1548
  $request_params['doSynonyms'] = 1;
1549
  $request_params['doTaxaByCommonNames'] = 0;
1550
  $request_params['matchMode'] = "EXACT";
1551
  $taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
1552

    
1553
  // Removing the name where we come from.
1554
  foreach ($taxon_pager->records as $k => &$taxon) {
1555
    if ($taxon->uuid == $taxon_to_hide_uuid) {
1556
      unset($taxon_pager->records[$k]);
1557
    }
1558
  }
1559
  // Show the taxa list or go to the singular taxon.
1560
  if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
1561
    $singleTaxon = array_pop($taxon_pager->records);
1562
    if ($singleTaxon->class != "Taxon") {
1563
      // It is a Synonym -> look for the accepted.
1564
      $accepted_taxa = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid, get_current_classification_uuid()));
1565
      if (!empty($highlite_synonym_uuid)) {
1566
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1567
      }
1568
      else {
1569
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxa[0]->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
1570
      }
1571
    }
1572
    else {
1573
      // It is an accepted taxon.
1574
      if (!empty($highlite_synonym_uuid)) {
1575
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1576
      }
1577
      else {
1578
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
1579
      }
1580
    }
1581
  }
1582
  else {// More than one taxa case.
1583
    $taxon_name_page = new stdClass();
1584
    $taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
1585
    if ($taxon_pager->records) {
1586
      $taxon_name_page->content = theme_cdm_list_of_taxa($taxon_pager->records, FALSE);
1587
    }
1588
    else {
1589
      $taxon_name_page->content = 'This name has no taxa';
1590
    }
1591
    return $taxon_name_page;
1592
  }
1593
}
1594

    
1595
/**
1596
 * Creates a page with the advance search form.
1597
 *
1598
 * NOTE: The advance search form allows searching for taxa.
1599
 */
1600
function cdm_dataportal_view_search_advanced() {
1601
  drupal_set_title(t('Advanced search'), PASS_THROUGH);
1602
  return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
1603
}
1604

    
1605
/**
1606
 * Creates a page with the search form for searching by taxon descriptions.
1607
 */
1608
function cdm_dataportal_view_search_taxon_by_description() {
1609
  drupal_set_title(t('Search by factual data'), PASS_THROUGH);
1610
  return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
1611
}
1612

    
1613
/**
1614
 * Executes the search and generates the result list of taxa.
1615
 */
1616
function cdm_dataportal_view_search_results_taxon() {
1617

    
1618
  $taxonPager = cdm_dataportal_search_execute();
1619

    
1620
  $showThumbnails = do_showThumbnails();
1621

    
1622
  $setSessionUri = url('cdm_api/setvalue/session', array(
1623
      'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
1624
  ));
1625

    
1626
  drupal_add_js('jQuery(document).ready(function() {
1627

    
1628
      // init
1629
      if(' . $showThumbnails . ' == 1){
1630
          jQuery(\'.media_gallery\').show(20);
1631
      } else {
1632
          jQuery(\'.media_gallery\').hide(20);
1633
      }
1634

    
1635
      // add change handler
1636
      jQuery(\'#showThumbnails input.showThumbnails\').change(
1637
      function(event){
1638
        var state = 0;
1639
        if(jQuery(this).is(\':checked\')){
1640
          jQuery(\'.media_gallery\').show(20);
1641
          state = 1;
1642
        } else {
1643
          jQuery(\'.media_gallery\').hide(20);
1644
        }
1645
        // store state in session variable
1646
        var uri = \'' . $setSessionUri . '\' + state;
1647
        jQuery.get(uri);
1648
      });
1649
  });',
1650
  array('type' => "inline", 'scope' => JS_DEFAULT));
1651

    
1652
  drupal_set_title(t('Search results'), PASS_THROUGH);
1653

    
1654
  return theme('cdm_search_results', array(
1655
    'pager' => $taxonPager,
1656
    'path' => 'cdm_dataportal/search/results/taxon',
1657
    ));
1658
}
1659

    
1660
/**
1661
 * Provides the standart image wich indicated a loading process
1662
 *
1663
 * @return string
1664
 *  The img html tag
1665
 */
1666
function loading_image_html() {
1667
  return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
1668
    . '/images/loading_circle_grey_16.gif" style="display:none;">';
1669
}
1670

    
1671
/**
1672
 * Returns the state of the the showThumbnails flag set in the
1673
 * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
1674
 *
1675
 * @return boolean
1676
 *    returns 1 if the flag is set
1677
 */
1678
function do_showThumbnails() {
1679
  static $showThumbnails = null;
1680

    
1681
  if($showThumbnails == null) {
1682
    $showThumbnails = 0;
1683
    if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
1684
      $showThumbnails = 0;
1685
      $search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
1686
      $showThumbnails = is_array($search_gallery_settings)
1687
        && isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
1688
        && (
1689
            $search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
1690
            $search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
1691
            $search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
1692
            )
1693
         ? 1 : 0;
1694

    
1695
       drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
1696
    }
1697
    $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
1698
    if (!is_numeric($showThumbnails)) {
1699
      $showThumbnails = 1;
1700
    }
1701
  }
1702

    
1703
  return $showThumbnails;
1704
}
1705

    
1706
/**
1707
 * View which transforms XML output from a given webservice endpoint into JSON.
1708
 */
1709
/*
1710
 function cdm_view_xml2json(){
1711
 $file = arg(2);
1712
 $datastr = file_get_contents(variable_get('cdm_webservice_url', '').$file);
1713
 return  xml2json::transformXmlStringToJson($datastr);
1714
 }
1715
 */
1716

    
1717
/* ====================== other functions ====================== */
1718
/**
1719
 * Creates a URL to the taxon page specified by the $uuid parameter.
1720
 *
1721
 * The URL will be prepended with a path element to a specific taxon page tab.
1722
 *
1723
 * This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
1724
 * be set globally in the administrative settings or individually in the user
1725
 * profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
1726
 * the last portal will stay on this last tab.
1727
 *
1728
 * A third option is offerered by the $page_tab parameter which allows overwriting this
1729
 * internal mechanism by a specific value.
1730
 *
1731
 * @param string $uuid
1732
 *   The UUID of the taxon.
1733
 * @param string $page_tab
1734
 *   Overwriting the preset mechanism by defining specific value for the
1735
 *   taxon page tab.
1736
 *
1737
 * @return string
1738
 *   The created URL.
1739
 */
1740
function path_to_taxon($uuid, $page_tab = FALSE) {
1741

    
1742
  $tab = get_default_taxon_tab();
1743
  $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
1744

    
1745
  if (!$uuid) {
1746
    return FALSE;
1747
  }
1748

    
1749
  if ($page_tab) {
1750
    return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
1751
  }
1752
  elseif (!$tab || strtolower($tab) == 'general') {
1753
    return 'cdm_dataportal/taxon/' . $uuid;
1754
  }
1755
  elseif (get_last_taxon_page_tab() &&   $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
1756
    return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
1757
  }
1758
  else {
1759
    return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
1760
  }
1761
}
1762

    
1763
function path_to_specimen($uuid) {
1764

    
1765
    if (!$uuid) {
1766
        return FALSE;
1767
    }
1768
    else {
1769
        return 'cdm_dataportal/specimen/' . $uuid;
1770
    }
1771
}
1772

    
1773
/**
1774
 * Creates a URL to show a synonmy in the according taxon page.
1775
 *
1776
 * The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
1777
 * The resulting URI will include query parameters to highlight the synonym, and to optionally display
1778
 * the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
1779
 * include the sysnonym uuid as fragment in order to let the browser scroll to the according location
1780
 * in the page
1781
 *
1782
 * @param string $synonymUuid
1783
 *    The uuid of the synonym
1784
 * @param string $acceptedUuid
1785
 *    The uuid of the according accepted taxon
1786
 * @return string
1787
 *    The URL to show a synonmy in the according taxon page
1788
 */
1789
function uri_to_synonym($synonymUuid, $acceptedUuid) {
1790
  $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
1791
  return url($acceptedPath, array(
1792
      'query' => array(
1793
        // highlite the synony in the synonymy
1794
        'highlite' => $synonymUuid,
1795
        // the taxon page is refered from a synonym and the synonym can optionally be named in the page title
1796
        // see theme_taxon_page_title()
1797
        'acceptedFor' => $synonymUuid
1798
      ),
1799
      'fragment' => $synonymUuid
1800
  ));
1801

    
1802
}
1803

    
1804
/**
1805
 * Compses the drupal path to the key identified by the uuid.
1806
 *
1807
 * @param string $keyType
1808
 *    the key typer corresponds to the specific class of the CDM
1809
 *    IdentificationKey. Possible values are
1810
 *      -PolytomousKey
1811
 *      -MultimediaKey
1812
 *      - ...
1813
 * @param UUID $keyUuid
1814
 *   The UUID of the key
1815
 */
1816
function path_to_key($keyType, $keyUuid) {
1817
  if (!$keyUuid || !$keyType) {
1818
    return FALSE;
1819
  }
1820
  $keyType{0} = strtolower($keyType{0});
1821
  return "cdm_dataportal/" . $keyType . "/$keyUuid";
1822
}
1823

    
1824
/**
1825
 * @todo Please document this function.
1826
 * @see http://drupal.org/node/1354
1827
 */
1828
function path_to_reference($uuid) {
1829
  if (!$uuid) {
1830
    return FALSE;
1831
  }
1832
  return 'cdm_dataportal/reference/' . $uuid;
1833
}
1834

    
1835
/**
1836
 * Creates the path to a cdm_dataportal taxon name page.
1837
 *
1838
 * @param UUID $taxon_name_uuid
1839
 *   The uuid of the CDM TaxonNameBase to show a name page for
1840
 * @param UUID $taxon_to_hide_uuid
1841
 *   A taxon which should not be displayed in the taxon list
1842
 * @param UUID $highlite_synonym_uuid
1843
 *   Optinal parameter wich takes another taxon uuid, if given the
1844
 *   target taxon pages will show the syonymy tab where the taxon
1845
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1846
 *   in case it is found on this page.
1847
 *
1848
 * @return a URI path element as string
1849
 */
1850
function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid  = NULL) {
1851
  $res = FALSE;
1852
  if ($name_uuid) {
1853
    $res = 'cdm_dataportal/name/' . $name_uuid;
1854
  }
1855
  if($taxon_to_hide_uuid){
1856
    $res .= '/' . $taxon_to_hide_uuid;
1857
    if($synonym_uuid){
1858
      $res .= '/' . $synonym_uuid;
1859
    }
1860
  }
1861
  return $res;
1862
}
1863

    
1864
/**
1865
 * @todo Please document this function.
1866
 * @see http://drupal.org/node/1354
1867
 */
1868
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
1869
  if (!$uuid) {
1870
    return FALSE;
1871
  }
1872
  $out = 'cdm_dataportal/media/' . $uuid;
1873
  if ($representaion_uuid) {
1874
    $out .= '/' . $representaion_uuid;
1875
    if ($partId !== FALSE) {
1876
      $out .= '/' . $partId;
1877
    }
1878
  }
1879
  return $out;
1880
}
1881

    
1882
/**
1883
 * Compares thisRank with thatRank.
1884
 *
1885
 * Returns a negative integer, zero, or a positive integer
1886
 * as the of thisRank is higher than, equal to, or lower than thatRank.
1887
 * e.g:
1888
 * <ul>
1889
 * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
1890
 * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
1891
 * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
1892
 * </ul>
1893
 * <p>
1894
 * This compare logic of the underlying webservice is the
1895
 * <b>inverse logic</b> of the the one implemented in
1896
 * java.lang.Comparable#compareTo(java.lang.Object)
1897
 *
1898
 * @param $thisRankUuid
1899
 * @param $thatRankUuid
1900
 *
1901
 * @return int
1902
 *   A negative integer, zero, or a positive integer
1903
 *   as the thisRank is lower than, equal to, or higher than thatRank.
1904
 */
1905
function rank_compare($thisRankUuid, $thatRankUuid) {
1906
  $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
1907
  return $result->Integer;
1908
}
1909

    
1910
/**
1911
 * Composes an HTML element class attribute value composed of
1912
 * the shortname of the cdm class and the uuid of the entity.
1913
 * This class attribute should be used whereever an cdm-entity is rendered.
1914
 *
1915
 * These according class selectors in css must be escaped, eg:
1916
 *    .cdm\:TextData
1917
 *
1918
 * @param $cdmEntity
1919
 */
1920
function html_class_attribute_ref($cdmEntity) {
1921

    
1922
  if (is_cdm_entity($cdmEntity)) {
1923
    return "cdm:" . $cdmEntity->class . " uuid:" . $cdmEntity->uuid;
1924
  }
1925
}
1926

    
1927

    
1928
/**
1929
 * Creates a short taxonname.
1930
 *
1931
 * The short name is created by using the taggedTitle field of
1932
 * NameSTO or NameTO instances.
1933
 * If the taggedTitle if empty the fullname will be returned.
1934
 *
1935
 * @param unknown_type $name
1936
 *   Name or TreeNode.
1937
 *
1938
 * @return string
1939
 */
1940
function cdm_dataportal_shortname_of($name) {
1941
  $nameStr = '';
1942

    
1943
  normalize_tagged_text($name->taggedTitle);
1944

    
1945
  // Get all tagged text tokens of the scientific name.
1946
  foreach ($name->taggedTitle as $tagtxt) {
1947
    if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
1948
      $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
1949
    }
1950
  }
1951
  $nameStr = trim($nameStr);
1952

    
1953
  if ($nameStr) {
1954

    
1955
    // Do not return short names for these.
1956
    if ($name->unplaced || $name->excluded) {
1957
      return $nameStr;
1958
    }
1959

    
1960
    /*
1961
    1st capture group (^[a-zA-Z]): First letter of uninomial.
1962
    Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
1963
    Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
1964
    but only matching if no '(' or '.' in second word of name,        ( \x2E = '.')
1965
    OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$             (\x22= '"', \x2D='-', \xD7='×' )
1966
    */
1967
    $pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
1968
    if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
1969
      return $matches[1][0] . "." . $matches[3][0];
1970
    }
1971
    else {
1972
      return $nameStr;
1973
    }
1974
  }
1975
  else {
1976
    return $name->titleCache;
1977
  }
1978
}
1979

    
1980
/**
1981
 * Check if a taxon is accepted by the current taxonomic tree.
1982
 *
1983
 * @param mixed $taxon
1984
 *   The Taxon obkect to check.
1985
 *
1986
 * @return bool
1987
 *   Returns TRUE if $taxon is accepted, FALSE otherwise.
1988
 */
1989
function _cdm_dataportal_acceptedByCurrentView($taxon) {
1990

    
1991
  $defaultTreeUuid = get_current_classification_uuid();
1992

    
1993
  if (isset($taxon->taxonNodes)) {
1994
    $taxonNodes = $taxon->taxonNodes;
1995
  }
1996
  else {
1997
    $taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
1998
  }
1999

    
2000
  if ($taxon->class == "Taxon" && isset($taxonNodes)) {
2001
    foreach ($taxonNodes as $node) {
2002
      if (isset($node->classification)){
2003
        if(is_object($node->classification)) {
2004
          if ($node->classification->uuid == $defaultTreeUuid) {
2005
            return TRUE;
2006
          }
2007
        }
2008
        else {
2009
          if ($node->classification == $defaultTreeUuid) {
2010
            return TRUE;
2011
          }
2012
        }
2013
      }
2014
    }
2015
  }
2016

    
2017
  return FALSE;
2018
}
2019

    
2020
/**
2021
 * Checks is the source has one of the given types.
2022
 *
2023
 * @param object $source
2024
 *   The original source entity
2025
 * @param array $types
2026
 *   An array of elementd of the OriginalSourceType enumeration
2027
 *   If not set the default will be used which is:
2028
 *    - Lineage
2029
 *    - PrimaryMediaSource
2030
 *    - PrimaryTaxonomicSource
2031
 *    - Unknown
2032
 *    - Other
2033
 * @return boolean
2034
 */
2035
  function _is_original_source_type($source, $types = null) {
2036
    // this is the default
2037
    // maybe this should also be put into the settings
2038
    static $default = array(
2039
      OriginalSourceType::Lineage,
2040
      OriginalSourceType::PrimaryMediaSource,
2041
      OriginalSourceType::PrimaryTaxonomicSource,
2042
      OriginalSourceType::Unknown,
2043
      OriginalSourceType::Other,
2044
    );
2045

    
2046
    if(!$types){
2047
      $types = $default;
2048
    }
2049
    return isset($source->type) && in_array($source->type, $types);
2050
  }
2051

    
2052
/**
2053
 * @todo Please document this function.
2054
 * @see http://drupal.org/node/1354
2055
 */
2056
function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
2057
  return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
2058
}
2059

    
2060

    
2061
/**
2062
 * Collects all the media from a list of description elements.
2063
 *
2064
 * @param array $descriptionElements
2065
 *   The description elements from which to collect the media.
2066
 *
2067
 * @return array
2068
 *   The output with all the collected media.
2069
 */
2070
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2071

    
2072
  $outArrayOfMedia = array();
2073

    
2074
  // Avoiding a warning box in Drupal for Flora Malesiana.
2075
  if (isset($descriptionElements) && is_array($descriptionElements)) {
2076
    foreach ($descriptionElements as $descriptionElement) {
2077
      if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2078
        foreach ($descriptionElement->media as $media) {
2079
          if (is_object($media)) {
2080
            $outArrayOfMedia[] = $media;
2081
          }
2082
        }
2083
      }
2084
    }
2085
  }
2086
  return $outArrayOfMedia;
2087
}
2088

    
2089
/**
2090
 * @todo Please document this function.
2091
 * @see http://drupal.org/node/1354
2092
 *
2093
 * @param array $cdm_entities
2094
 *   An array of CdmBase instances or a single instance.
2095
 * @param string $footnote_list_key_suggestion
2096
 *
2097
 * @return unknown
2098
 */
2099
function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
2100

    
2101
   static $annotations_types_filter = null;
2102
   if(!$annotations_types_filter) {
2103
     $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
2104
   }
2105

    
2106
  $footNoteKeys = array();
2107

    
2108
  // Is argument cdmBase an array?
2109
  if (!is_array($cdm_entities)) {
2110
    $cdmBase_array = array();
2111
    $cdmBase_array[] = $cdm_entities;
2112
  }
2113
  else {
2114
    $cdmBase_array = $cdm_entities;
2115
  }
2116

    
2117
  // Getting the key for the footnotemanager.
2118
  if (isset($footnote_list_key_suggestion)) {
2119
    $footnote_list_key = $footnote_list_key_suggestion;
2120
  }
2121
  else {
2122
    $footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2123
  }
2124

    
2125
  // Adding the footnotes keys.
2126
  foreach ($cdmBase_array as $cdmBase_element) {
2127
    $annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
2128
    if (is_array($annotations)) {
2129
      foreach ($annotations as $annotation) {
2130
        $footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2131
      }
2132
    }
2133
  }
2134

    
2135
  return $footNoteKeys;
2136
}
2137

    
2138

    
2139
/**
2140
 * Creates a CDM Dynabox.
2141
 *
2142
 * @param string $dynabox_id
2143
 *   a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2144
 * @param string $label
2145
 *   The clickable text to show.
2146
 * @param string $content_url
2147
 *   The cdm REST service request url wich will deliver the content to be shown
2148
 *   once the dynabox toggles open.
2149
 * @param string $theme
2150
 *   The theme to be used for rendering the cdm REST service response with is
2151
 *   returned from the $content_url.
2152
 * @param string $link_alt_text
2153
 *   The value for the alt attribute of the dynabox link.
2154
 * @param array $enclosingtags
2155
 *   An array with two elements: $enclosingtags[0] will be used for the dynabox
2156
 *   element itself, $enclosingtags[1] is the tag to be used for the
2157
 *   dynabox_content (optional)
2158
 * @param array $attributes
2159
 * @param $content_element_selector
2160
 *   Optional jQuery selector which can be used to reference a dom element which should
2161
 *   be used as container for the content to be shown. The dynabox-<dynabox id>-content
2162
 *  element will be placed in this container.
2163
 *
2164
 * @param string $open_callback
2165
 *   optional javascript call back function to be triggered after toggling the box to
2166
 *   the open state.
2167
 * @param string $close_callback
2168
 *   optional javascript call back function to be triggered after toggling the box to
2169
 *   the closed state.
2170
 * @return string Returns HTML for a dynabox.
2171
 * Returns HTML for a dynabox.
2172
 */
2173
function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2174
                     $enclosingtags = array('li', 'ul'), $attributes = array(),
2175
                     $content_element_selector = null,
2176
                     $open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2177
  $out = '';
2178

    
2179
  // check for plain class attribute string
2180
  $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2181

    
2182
  if(!array_key_exists('class', $attributes)) {
2183
    $attributes['class'] = array();
2184
  }
2185
  $attributes['id'][] = 'dynabox-' . $dynabox_id;
2186
  $dynabox_attributes = drupal_attributes($attributes);
2187

    
2188

    
2189
  _add_js_domEvent(); // requires domEvent.js
2190
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2191
  drupal_add_js("
2192
  jQuery(document).ready(
2193
      function() {
2194
        dynabox('". $dynabox_id ."',
2195
          {
2196
            open_callback: " . $open_callback .",
2197
            close_callback: " . $close_callback .
2198
            ($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2199
          }
2200
        );
2201
      }
2202
   );",
2203
   array(
2204
    'type'=>'inline',
2205
    'scope'=>'footer'
2206
    )
2207
  );
2208

    
2209

    
2210
  $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2211
  $out .= '<!-- dynabox for ' . $content_url . ' -->';
2212
  $out .= '<' . $enclosingtags[0] . ' ' .  $dynabox_attributes. '><a href="' . $cdm_proxy_url . '" class="label" alt="' . t($link_alt_text) . '">' . $label . '</a>';
2213
  $out .= '  <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2214
  $out .= '    <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2215
  $out .= '    </' . $enclosingtags[1] . '>';
2216
  $out .= '  </' . $enclosingtags[0] . '>';
2217
  $out .= '<!-- dynabox end -->';
2218
  return $out;
2219
}
2220

    
2221
/**
2222
 * Checks whether a feature has any description elements.
2223
 *
2224
 * @param mixed $featureNode
2225
 *   A feature node as produced by the function _mergeFeatureTreeDescriptions().
2226
 *
2227
 * @see _mergeFeatureTreeDescriptions()
2228
 *
2229
 * @return bool
2230
 *   Returns TRUE if the given $featureNode or any of its subordinate nodes
2231
 *   contains at least one non empty TextData or at least one DescriptionElement
2232
 *   of an other type. A TextData element holding a multilanguageText or a
2233
 *   source reference is considered to be not empty.
2234
 *
2235
 * @TODO this function may have become obsolete by the new method of detecting empty blocks,
2236
 *       see $block_content_is_not_empty in compose_feature_blocks() and
2237
 *       $feature_block_has_content in compose_feature_block_items_generic
2238
 */
2239
function has_feature_node_description_elements($featureNode) {
2240

    
2241
  if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2242
    if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2243
      foreach ($featureNode->descriptionElements as $descriptionElement) {
2244
        if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
2245
          && $descriptionElement->multilanguageText_L10n->text != ''
2246
          || isset($descriptionElement->sources[0])
2247
          || isset($descriptionElement->media[0]) ) {
2248
          return TRUE;
2249
        }
2250
      }
2251
    }
2252
  }
2253
  else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2254
    foreach ($featureNode->childNodes as $child) {
2255
      if (has_feature_node_description_elements($child)) {
2256
        return TRUE;
2257
      }
2258
    }
2259
  }
2260
  return FALSE;
2261
}
2262

    
2263
/**
2264
 * Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
2265
 *
2266
 * @param $chapter
2267
 *   The taxon page chapter or part
2268
 */
2269
function cdm_check_valid_taxon_page($chapter){
2270
  static $taxon_tabs = null;
2271

    
2272
  cdm_check_valid_portal_page();
2273

    
2274
  if($taxon_tabs == null){
2275
    $taxon_tabs = array('all', 'description');
2276
    foreach(get_taxon_tabs_list() as $tab){
2277
      $taxon_tabs[] = strtolower($tab);
2278
    }
2279
  }
2280

    
2281
  if(!in_array($chapter, $taxon_tabs)){
2282
    // oops this is not a valid chapter name
2283
    http_send_status(404); // 404 = Not Found
2284
  }
2285

    
2286
}
2287

    
2288
/**
2289
 * Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise
2290
 *
2291
 * @param $chapter
2292
 *   The taxon page chapter or part
2293
 */
2294
function cdm_check_valid_portal_page(){
2295
  $ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
2296
  if(preg_match($ends_with_file_suffix_pattern, $_GET['q'])){
2297
    // oops this urls ends with a file_suffix and thus does not refer to a portal page
2298
    http_send_status(404); // 404 = Not Found
2299
    exit('HTTP 404');
2300
  }
2301
}
2302

    
2303
/**
2304
 * Generates the diff of the texts and presents it in a HTML diff viewer.
2305
 *
2306
 * @param $text_a
2307
 * @param $text_b
2308
 * @return string
2309
 */
2310
function diff_viewer($text_a, $text_b) {
2311

    
2312
  static $diff_viewer_count = 0;
2313

    
2314
  $element_id = 'part_definitions_diff_' . $diff_viewer_count++;
2315

    
2316
  // http://code.stephenmorley.org/php/diff-implementation/
2317
  module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
2318
  drupal_add_css(drupal_get_path('module',
2319
      'cdm_dataportal') . '/css/diff.css');
2320
  _add_jquery_ui();
2321
  drupal_add_js(
2322
    'jQuery(document).ready( function(){
2323
        jQuery(\'#' . $element_id . '\').accordion({
2324
        collapsible: true,
2325
        active: false,
2326
        fillSpace: true,
2327
        }).children(\'div\').css({ \'height\': \'auto\' });
2328
        jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
2329
     });'
2330
    , array(
2331
    'type' => 'inline',
2332
    'scope' => 'footer'
2333
  ));
2334

    
2335
  $diff = Diff::compare($text_a,
2336
    $text_b);
2337
  $diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
2338
    . Diff::toTable($diff, '', '')
2339
    . '</div></div>';
2340
  return $diff_viewer_markup;
2341
}
2342

    
2343

    
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