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cdm-dataportal / modules / cdm_dataportal / cdm_dataportal.module @ 7635cc7d

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<?php
2
/**
3
 * @file
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 * Module to provide a CDM Dataportal.
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 *
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');
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  module_load_include('inc', 'cdm_dataportal', 'includes/common');
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  module_load_include('inc', 'cdm_dataportal', 'includes/name');
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  module_load_include('inc', 'cdm_dataportal', 'includes/taxon');
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  module_load_include('inc', 'cdm_dataportal', 'includes/references');
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  module_load_include('inc', 'cdm_dataportal', 'includes/pages');
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  module_load_include('inc', 'cdm_dataportal', 'includes/media');
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  module_load_include('inc', 'cdm_dataportal', 'includes/maps');
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  module_load_include('inc', 'cdm_dataportal', 'includes/occurrences');
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  module_load_include('inc', 'cdm_dataportal', 'includes/descriptions');
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  module_load_include('inc', 'cdm_dataportal', 'includes/pre-drupal8');
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  module_load_include('inc', 'cdm_dataportal', 'theme/theme_registry');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.common');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.descriptions');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.media');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.occurrence');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.page');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.taxon');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.name');
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  module_load_include('theme', 'cdm_dataportal', 'theme/cdm_dataportal.references');
45

    
46
  module_load_include('php', 'cdm_dataportal', 'classes/footnotemanager');
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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');
50

    
51

    
52
  /* ============================ java script functions ============================= */
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54

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

    
62
    drupal_add_js("
63
          jQuery(document).ready(function() {
64
            jQuery.ajax({
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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() {
69
                    " . $callback . "
70
              }
71
            });
72
          });"
73
    , 'inline');
74
  }
75

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

    
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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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      });
84
      ', array('type' => 'inline'));
85
  }
86

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

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

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

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

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

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

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

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

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

    
149
  function _add_js_openlayers() {
150

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

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

    
170
    // see https://github.com/proj4js/proj4js
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    // http://openlayers.org/dev/examples/using-proj4js.html
172
    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,
176
        'cache' => TRUE,
177
      )
178
    );
179

    
180
    // configure the theme
181
    $openlayers_theme_path = drupal_get_path('module', 'cdm_dataportal') . '/js/map/OpenLayers-2.13.1/theme/default/';
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    $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',
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        'weight' => JS_LIBRARY,
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        'cache' => TRUE,
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        'preprocess' => FALSE
188
      ));
189

    
190
    drupal_add_css($openlayers_theme_path . 'style.tidy.css',
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      array(
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        'type' => 'file',
193
        'cache' => TRUE,
194
        'preprocess' => FALSE
195
      )
196
    );
197

    
198
  }
199

    
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  /**
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   * @todo Please document this function.
202
   * @see http://drupal.org/node/1354
203
   */
204
  function _add_js_thickbox() {
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    // ---- jQuery thickbox:
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    /*
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    * bug: compat-1.0.js && thickbox.js line 237 .trigger("unload") -> event is
208
    * not triggered because of problems with compat-1.0.js' see INSTALL.txt
209
    */
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    // drupal_add_js(drupal_get_path('module',
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    // 'cdm_dataportal').'/js/jquery.imagetool.min.js');
212
    //
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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.
215
    drupal_add_js(array(
216
    'cdm_dataportal' => array(
217
    'cdm_dataportal_path' => base_path() . drupal_get_path('module', 'cdm_dataportal'),
218
    )
219
    ),
220
    'setting'
221
        );
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        drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/thickbox.js');
223
        drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/thickbox/cdm_thickbox.css');
224
  }
225

    
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  /**
227
   * @todo Please document this function.
228
   * @see http://drupal.org/node/1354
229
   */
230
  function _add_js_lightbox($galleryID) {
231
    /*
232
     * Important Notice: The jquery.lightbox-0.5.js has been modified in order to
233
    * allow using the "alt" attribute for captions instead of the "title"
234
    * attribute
235
    */
236
    $lightbox_base_path =  drupal_get_path('module', 'cdm_dataportal') . '/js/jquery-lightbox-0.5';
237
    $lightbox_image_path = base_path() . $lightbox_base_path . '/images/';
238
    drupal_add_js($lightbox_base_path . '/js/jquery.lightbox-0.5.js');
239
    drupal_add_css($lightbox_base_path . '/css/jquery.lightbox-0.5.css');
240
    drupal_add_js('jQuery(document).ready(function() {
241
        jQuery(\'#' . $galleryID . ' a.lightbox\').lightBox({
242
          fixedNavigation:  true,
243
          imageLoading:     \'' . $lightbox_image_path . 'lightbox-ico-loading.gif\',
244
          imageBtnPrev:     \'' . $lightbox_image_path . 'lightbox-btn-prev.gif\',
245
          imageBtnNext:     \'' . $lightbox_image_path . 'lightbox-btn-next.gif\',
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          imageBtnClose:    \'' . $lightbox_image_path . 'lightbox-btn-close.gif\',
247
          imageBlank:       \'' . $lightbox_image_path . 'lightbox-blank.gif\',
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          adjustToWindow: true
249
        });
250
      });
251
      ', array('type' => 'inline'));
252
  }
253

    
254
  /**
255
   * @todo Please document this function.
256
   * @see http://drupal.org/node/1354
257
   */
258
  function _add_js_footnotes() {
259
    _add_js_domEvent();
260
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/footnotes.js');
261
  }
262

    
263
  /**
264
   * @todo Please document this function.
265
   * @see http://drupal.org/node/1354
266
   */
267
  function _add_js_cluetip() {
268

    
269
    // TODO replace by
270
    // @see http://www.socialembedded.com/labs/jQuery-Tooltip-Plugin/jQuery-Tooltip-Plugin.html
271
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.min.js');
272
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.dimensions.js');
273
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.hoverIntent.js');
274
    if(variable_get('cdm_js_devel_mode', FALSE)){
275
      drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.js');
276
    }
277
    drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/js/cluetip/jquery.cluetip.css');
278
    drupal_add_js("jQuery(document).ready(function(){
279
        jQuery('.cluetip').css({color: '#0062C2'}).cluetip({
280
          splitTitle: '|',
281
          showTitle: true,
282
          activation: 'hover',
283
          sicky: true,
284
          arrows: true,
285
          dropShadow: false,
286
          cluetipClass: 'rounded'
287
        });
288
      });",
289
      array(
290
        'type' => 'inline',
291
        'scope' => 'footer'
292
      )
293
    );
294
  }
295

    
296
  /**
297
   * @todo Please document this function.
298
   * @see http://drupal.org/node/1354
299
   */
300
  function _add_js_ahah() {
301

    
302
    _add_js_domEvent(); // requires domEvent.js
303
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/ahah-content.js');
304
  }
305

    
306
/**
307
 * @todo Please document this function.
308
 * @see http://drupal.org/node/1354
309
 */
310
function _add_js_taxonomic_children($jquery_selector) {
311

    
312
  global $base_url;
313

    
314

    
315
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/jquery.cdm.taxonomic_children.js');
316
  
317
  drupal_add_js('jQuery(document).ready(function() {
318
        jQuery(\'' . $jquery_selector . '\').taxonomic_children({
319
          // hoverClass: "fa-rotate-90",
320
          // activeClass: "fa-rotate-90",
321
          classificationUuid: "' . get_current_classification_uuid() . '",
322
          taxonUuid: "' . get_current_taxon_uuid() . '",
323
          cdmWebappBaseUri: "' . variable_get('cdm_webservice_url', '') . '",
324
          proxyBaseUri: "' . $base_url . '",
325
          
326
        });
327
      });
328
      ', array('type' => 'inline'));
329
}
330

    
331
  /**
332
   * Adds the external javascript file for domEvent.js.
333
   *
334
   * @see drupal_add_js()
335
   */
336
  function _add_js_domEvent() {
337
    drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/domEvent.js');
338
  }
339

    
340
  function _add_jquery_ui()
341
  {
342
    drupal_add_css(drupal_get_path('module',
343
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/themes/base/jquery.ui.all.css');
344
    drupal_add_js(drupal_get_path('module',
345
        'cdm_dataportal') . '/js/jquery-ui-1.8.24/ui/jquery-ui.js',
346
      array(
347
        'type' => 'file',
348
        'weight' => JS_LIBRARY,
349
        'cache' => TRUE,
350
        'preprocess' => FALSE
351
      )
352
    );
353
  }
354

    
355
  /**
356
   * Provides the markup for an font awesome icon.
357
   *
358
   * The icons is created in default size without any extra features.
359
   *
360
   * The available icons are listed here http://fontawesome.io/cheatsheet/
361
   * fontawesome icons have much more features than implemented here in this function,
362
   * for spinning icons, fixed width icons, rotation, etc please checkout the
363
   * examples at http://fontawesome.io/examples/
364
   *
365
   * @parameter $icon_name
366
   *  The name of the icon which starts with 'fa-'
367
   *
368
   * @return String
369
   *    the markup for the icon in an <i> tag
370
   *
371
   */
372
  function font_awesome_icon_markup($icon_name = NULL, $attributes = array()){
373

    
374

    
375
    //<link href="//maxcdn.bootstrapcdn.com/font-awesome/4.2.0/css/font-awesome.min.css" rel="stylesheet">
376

    
377
    $font_awesome_css_uri = base_path() . drupal_get_path('module', 'cdm_dataportal').'/fonts/font-awesome-4.6.3/css/font-awesome.min.css';
378
    //$font_awesome_css_uri="//maxcdn.bootstrapcdn.com/font-awesome/4.5.0/css/font-awesome.min.css";
379

    
380
    drupal_add_html_head_link(
381
      array(
382
        'href' => $font_awesome_css_uri,
383
        'rel' => 'stylesheet'
384
      )
385
    );
386

    
387
    if($icon_name){
388
      if(!isset($attributes['class'])){
389
        $attributes['class'] = array();
390
      }
391
      $attributes['class'][] = 'fa';
392
      $attributes['class'][] = $icon_name;
393

    
394
      return '<i ' . drupal_attributes($attributes) . '></i>';
395
    }
396

    
397
    return '';
398
  }
399

    
400

    
401
  /* ====================== hook implementations ====================== */
402
  /**
403
   * Implements hook_permission().
404
   *
405
   * Valid permissions for this module.
406
   *
407
   * @return array
408
   *   An array of valid permissions for the cdm_dataportal module.
409
   */
410
  function cdm_dataportal_permission() {
411
    return array(
412
      'administer cdm_dataportal' => array(
413
        'title' => t('Administer CDM DataPortal settings'),
414
        'description' => t("Access the settings pages specific for the cdm_dataportal module"),
415
      ),
416
      'access cdm content' => array(
417
        'title' => t('Access CDM content'),
418
        'description' => t("Access content (taxa, names, specimens, etc.) served by the CDM web service."),
419
      ),
420
    );
421
  }
422

    
423
/**
424
 * Implements hook_menu().
425
 */
426
function cdm_dataportal_menu() {
427
  $items = array();
428

    
429
  // @see settings.php.
430
  cdm_dataportal_menu_admin($items);
431
  cdm_dataportal_menu_help($items);
432

    
433
  $items['cdm_dataportal/names'] = array(
434
    'page callback' => 'cdm_dataportal_view_names',
435
    'access arguments' => array('access cdm content'),
436
    'type' => MENU_CALLBACK,
437
  );
438

    
439
  // Optional callback arguments: page.
440
  $items['cdm_dataportal/taxon'] = array(
441
    'page callback' => 'cdm_dataportal_taxon_page_view',
442
    'access arguments' => array('access cdm content'),
443
    'type' => MENU_CALLBACK,
444
    // Expected callback arguments: uuid.
445
  );
446

    
447
   // Optional callback arguments: page.
448
    //FIXME point to view/page method in this module
449
    $items['cdm_dataportal/specimen'] = array(
450
        'page callback' => 'cdm_dataportal_specimen_page_view',
451
        'access arguments' => array('access cdm content'),
452
        'type' => MENU_CALLBACK,
453
        // Expected callback arguments: uuid.
454
    );
455

    
456
  $items['cdm_dataportal/name'] = array(
457
    'page callback' => 'cdm_dataportal_name_page_view',
458
      /*
459
    'page arguments' => array(
460
       'taxon_name_uuid',
461
       'taxon_to_hide_uuid',
462
       'synonym_uuid' => NULL
463
      ),
464
      */
465
    'access arguments' => array('access cdm content'),
466
    'type' => MENU_CALLBACK,
467
    // Expected callback arguments: uuid.
468
  );
469

    
470
  $items['cdm_dataportal/reference'] = array(
471
    'page callback' => 'cdm_dataportal_view_reference',
472
    'access arguments' => array('access cdm content'),
473
    'type' => MENU_CALLBACK,
474
    // Expected callback arguments: uuid.
475
  );
476

    
477
  $items['cdm_dataportal/reference/list'] = array(
478
    'page callback' => 'cdm_dataportal_view_reference_list',
479
    'access arguments' => array('access cdm content'),
480
    'type' => MENU_CALLBACK,
481
    // Expected callback arguments: uuid.
482
  );
483

    
484
  $items['cdm_dataportal/media'] = array(
485
    'page callback' => 'cdm_dataportal_view_media',
486
    'access arguments' => array('access cdm content'),
487
    'type' => MENU_CALLBACK,
488
    // Expected callback arguments:
489
    // uuid, mediarepresentation_uuid, part_uuid or part#.
490
  );
491

    
492
  $items['cdm_dataportal/polytomousKey'] = array(
493
    'page callback' => 'cdm_dataportal_view_polytomousKey',
494
    'access arguments' => array('access cdm content'),
495
    'type' => MENU_CALLBACK,
496
    // Expected callback arguments: polytomousKey->uuid.
497
  );
498

    
499
  $items['cdm_dataportal/search'] = array(
500
    'page callback' => 'cdm_dataportal_view_search_advanced',
501
    'access arguments' => array('access cdm content'),
502
    'type' => MENU_CALLBACK,
503
  );
504

    
505
  $items['cdm_dataportal/search/advanced'] = array(
506
    'title' => 'Advanced', // will be passed through t()
507
    'page callback' => 'cdm_dataportal_view_search_advanced',
508
    'access arguments' => array('access cdm content'),
509
    'type' => MENU_DEFAULT_LOCAL_TASK,
510
  );
511

    
512
  $items['cdm_dataportal/search/taxon_by_description'] = array(
513
    'title' => 'By content category', // will be passed through t()
514
    'page callback' => 'cdm_dataportal_view_search_taxon_by_description',
515
    'access arguments' => array('access cdm content'),
516
    'type' => MENU_LOCAL_TASK,
517
  );
518

    
519
  $items['cdm_dataportal/search/results/taxon'] = array(
520
    'page callback' => 'cdm_dataportal_view_search_results_taxon',
521
    'access arguments' => array('access cdm content'),
522
    'type' => MENU_CALLBACK,
523
  );
524
  /*
525
   $items['cdm/xml2json'] = array(
526
   'page callback' => 'cdm_view_xml2json',
527
   'access arguments' => array('access cdm content'),
528
   'type' => MENU_CALLBACK,
529
   );
530
   */
531

    
532
  // if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
533
  // User configuration of cdm_dataportal.
534
  $items['user/%/cdm_dataportal'] = array(
535
    'title' => 'cdm_dataportal',
536
    'access arguments' => array('access cdm content'),
537
    'page callback' => 'drupal_get_form',
538
    'page arguments' => array('cdm_dataportal_user_form'),
539
    'type' => MENU_LOCAL_TASK,
540
    'weight' => 10,
541
  );
542
  // }
543

    
544
  // 'May not cache' in D5.
545
  $items['cdm_dataportal/name/%'] = array(
546
    // 'page callback' => 'cdm_dataportal_view_name',
547
    'page callback' => 'cdm_dataportal_name_page_view',
548
    'page arguments' => array(2, 3, 4),
549
    'access arguments' => array('access cdm content'),
550
    'type' => MENU_CALLBACK,
551
  );
552

    
553
  // --- Local tasks for Taxon.
554
  // --- tabbed taxon page
555
  if (variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
556
    $items['cdm_dataportal/taxon/%'] = array(
557
      'title' => '@tabname',
558
      'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'General'))),
559
      'page callback' => 'cdm_dataportal_taxon_page_view',
560
      'access arguments' => array('access cdm content'),
561
      'type' => MENU_CALLBACK,
562
      'weight' => 1,
563
      'page arguments' => array(2, "description")
564
      , // Expected callback arguments: taxon_uuid.
565
    );
566

    
567
    $items['cdm_dataportal/taxon/%/all'] = array(
568
      'title' => '@tabname',
569
      'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'General'))),
570
      'page callback' => 'cdm_dataportal_taxon_page_view',
571
      'access arguments' => array('access cdm content'),
572
      'type' => MENU_CALLBACK,
573
      'weight' => 2,
574
      'page arguments' => array(2, "all")
575
      , // Expected callback arguments: taxon_uuid.
576
    );
577

    
578
    $items['cdm_dataportal/taxon/%/description'] = array(
579
      'title' => '@tabname',
580
      'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'General'))),
581
      'page callback' => 'cdm_dataportal_taxon_page_view',
582
      'access arguments' => array('access cdm content'),
583
      'type' => MENU_DEFAULT_LOCAL_TASK,
584
      'weight' => 2,
585
      'page arguments' => array(2, "description")
586
      , // Expected callback arguments: taxon_uuid.
587
    );
588

    
589
    $items['cdm_dataportal/taxon/%/synonymy'] = array(
590
      'title' => '@tabname',
591
      'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Synonymy'))),
592
      'page callback' => 'cdm_dataportal_taxon_page_view',
593
      'access arguments' => array('access cdm content'),
594
      'type' => MENU_LOCAL_TASK,
595
      'weight' => 4,
596
      'page arguments' => array(2, "synonymy", 4)
597
      , // Expected callback arguments: taxon_uuid and ...
598
    );
599
    $items['cdm_dataportal/taxon/%/images'] = array( // Images
600
      'title' => '@tabname',
601
      'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Images'))),
602
      'page callback' => 'cdm_dataportal_taxon_page_view',
603
      'access arguments' => array('access cdm content'),
604
      'type' => MENU_LOCAL_TASK,
605
      'weight' => 5,
606
      'page arguments' => array(2, "images")
607
      , // Expected callback arguments: taxon_uuid.
608
    );
609

    
610
    $items['cdm_dataportal/taxon/%/specimens'] = array( // Specimens
611
      'title' => '@tabname',
612
      'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Specimens'))),
613
      'page callback' => 'cdm_dataportal_taxon_page_view',
614
      'access arguments' => array('access cdm content'),
615
      'type' => MENU_LOCAL_TASK,
616
      'weight' => 6,
617
      'page arguments' => array(2, "specimens")
618
      , // Expected callback arguments: taxon_uuid.
619
    );
620

    
621
    $items['cdm_dataportal/taxon/%/keys'] = array( // Keys
622
      'title' => '@tabname',
623
      'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Keys'))),
624
      'page callback' => 'cdm_dataportal_taxon_page_view',
625
      'access arguments' => array('access cdm content'),
626
      'type' => MENU_LOCAL_TASK,
627
      'weight' => 6,
628
      'page arguments' => array(2, "keys")
629
      , // Expected callback arguments: taxon_uuid.
630
    );
631

    
632
    $items['cdm_dataportal/taxon/%/experts'] = array( // Experts
633
      'title' => '@tabname',
634
      'title arguments' => array('@tabname' => theme('cdm_taxonpage_tab', array('tabname' => 'Experts'))),
635
        'page callback' => 'cdm_dataportal_taxon_page_view',
636
        'access arguments' => array('access cdm content'),
637
        'type' => MENU_LOCAL_TASK,
638
        'weight' => 6,
639
        'page arguments' => array(2, "experts")
640
    , // Expected callback arguments: taxon_uuid.
641
    );
642

    
643
    $items['cdm_dataportal/taxon/autosuggest/%/%/%/'] = array(
644
        'page callback' => 'cdm_dataportal_taxon_autosuggest',
645
        'access arguments' => array('access cdm content'),
646
        'page arguments' => array(3,4,5),
647
        'type' => MENU_CALLBACK
648
    );
649
  }
650

    
651
  // --- refresh link for all cdmnode types
652
  foreach (cdm_get_nodetypes() as $type=>$name) {
653
    $items['cdm_dataportal/' . $name . '/%/refresh'] = array(
654
        'title' => 'Refresh',
655
        'page callback' => 'cdm_dataportal_refresh_node',
656
        'access arguments' => array('administer cdm_dataportal'),
657
        'type' => MENU_LOCAL_TASK,
658
        'weight' => 100,
659
        'page arguments' => array($name, 2)
660
    );
661
  }
662

    
663
  return $items;
664
}
665

    
666
/**
667
 * Implements hook_init().
668
 *
669
 */
670
function cdm_dataportal_init() {
671
  //FIXME To add CSS or JS that should be present on all pages, modules
672
  //      should not implement this hook, but declare these files in their .info file.
673
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal.css');
674
  // drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
675
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal') . '/cdm_dataportal_screen.css', array('type' => 'screen'));
676

    
677
  if(variable_get('cdm_debug_mode', FALSE)){
678
    $file = 'temporary://drupal_debug.txt';
679
    file_put_contents($file, 'CDM DEBUG LOG for ' . $_GET['q']. "\n"); // will overwrite the file
680
  }
681

    
682
  $bibliography_settings = get_bibliography_settings();
683
  $enclosing_tag = $bibliography_settings['enabled'] == 1 ? 'div' : 'span';
684
  FootnoteManager::registerFootnoteSet('BIBLIOGRAPHY', $enclosing_tag, $bibliography_settings['key_format']);
685
}
686

    
687
function cdm_dataportal_refresh_node($cdm_node_name, $uuid, $parameters = array()){
688

    
689
  $base_path = 'cdm_dataportal/' . $cdm_node_name . '/' . $uuid;
690

    
691
  if($cdm_node_name == 'taxon' && variable_get('cdm_dataportal_taxonpage_tabs', 1)){
692
    // force reloading of all and notify user about this special loading
693
    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: ')
694
        . l('Back to tabbed taxon page', $base_path));
695
    $base_path .= '/all';
696
  } else {
697
    drupal_set_message(t('The level 2 cache has been cleared for this page'));
698
  }
699

    
700
  $parameters['cacheL2_refresh'] ='1';
701

    
702

    
703
  drupal_goto($base_path, array('query' => $parameters));
704
}
705

    
706
/**
707
 * The function generate form for own user cdm dataportal configurations.
708
 */
709
function cdm_dataportal_user_form($form, &$form_state) {
710

    
711
  global $user;
712
  $checkbox_value = 'cdm_dataportal_' . $user->uid . '_default_tab_active';
713

    
714
  $form['taxon_page_tabs'] = array(
715
      '#type' => 'fieldset',
716
      '#tree' => true,
717
      '#title' => t('Taxon page tabs'),
718
  );
719

    
720
  $form['taxon_page_tabs']['user_defined'] = array(
721
    '#type' => 'checkbox',
722
    '#title' => t('Activate user default configuration'),
723
    '#default_value' => variable_get($checkbox_value, 0),
724
    '#description' => t('Check this if you want configure your own default tab from the below menu.'),
725
  );
726

    
727
  $form['taxon_page_tabs']['default_tab'] = array(
728
    '#type' => 'select',
729
    '#title' => t('Default tab to display'),
730
    '#default_value' => get_default_taxon_tab(TRUE),
731
    '#options' => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
732
    '#description' => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
733
              <strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
734
              to be rendered will be the synonymy of the accepted taxon and not the above selected tab.'),
735
  );
736

    
737

    
738
  if(false){
739
    $form['developer_options'] = array(
740
        '#type' => 'fieldset',
741
        '#tree' => true,
742
        '#title' => t('Developer options'),
743
    );
744

    
745
    $form['developer_options']['show_render_path'] = array(
746
      '#type' => 'checkbox',
747
      '#title' => t('Display the render path for each taxon name.'),
748
      '#default_value' => variable_get($checkbox_value, 0),
749
      '#description' => t('This option is very helpful if you are editing the !link for taxon names.',
750
        array(
751
            '!link' => l(
752
              'render template', 'admin/config/cdm_dataportal/settings/layout', array('fragment' => 'edit-cdm-name-render-templates'))
753
            )
754
        ),
755
    );
756
  }
757

    
758
  $form['submit'] = array(
759
    '#type' => 'submit',
760
    '#value' => t('Submit'),
761
  );
762

    
763
  return $form;
764
}
765

    
766
/**
767
 * Form submission handler for user_form().
768
 *
769
 * Submits the user cdm dataportal configurations.
770
 */
771
function cdm_dataportal_user_form_submit($form, &$form_state) {
772
  global $user;
773
  $msg_type = 'status';
774
  $username = $user->name;
775
  $variable_to_use = 'cdm_dataportal_' . $user->uid . '_default_tab';
776

    
777
  // FIXME: this is completely wrong, see user_profile_form_submit()
778

    
779
  // it is only possible to change own user settings
780
  if (arg(0) == 'user' && is_numeric(arg(1)) && $user->uid == arg(1)) {
781

    
782
    // DEFAULT_TAXON_TAB
783
    $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
784
    variable_set($variable_to_use . '_active', $form_state['values']['taxon_page_tabs']['user_defined']);
785
    variable_set($variable_to_use, $form_state['values']['taxon_page_tabs']['default_tab']);
786
    if ($form_state['values']['taxon_page_tabs']['user_defined']) {
787
      drupal_set_message(check_plain(t('The user default tab will be used for the next taxon site visit.')));
788
      drupal_set_message(check_plain(t('The user default tab has been changed to: !tab for the user !user', array(
789
        '!tab' => $variable[variable_get($variable_to_use, 0)],
790
        '!user' => $username,
791
      ))), $msg_type);
792
    }
793
    else {
794
      drupal_set_message(check_plain(t('The user default tab wont be used for
795
        the next taxon site, check the box if you want to use the user default configuration.')));
796
    }
797

    
798
  }
799
  else {
800
    // Problem with the user id => variables wont be saved.
801
    $msg_type = 'warning';
802
    drupal_set_message(check_plain(t('Default tab has not been saved due to user id problems')), $msg_type);
803
  }
804
}
805

    
806
/**
807
 * Implements hook_block_info().
808
 */
809
function cdm_dataportal_block_info() {
810

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

    
837
    return $block;
838
}
839

    
840
/**
841
 * Implements hook_block_view().
842
 */
843
function cdm_dataportal_block_view($delta) {
844
  // TODO Rename block deltas (e.g. '2') to readable strings.
845
  switch ($delta) {
846
    // case 'delta-1':
847
    // $block['subject'] = t('Credits');
848
    // $block['content'] = theme('cdm_credits');
849
    // return $block;
850
    case '2':
851
      $block['subject'] = t('Search taxa');
852
      $form = drupal_get_form('cdm_dataportal_search_taxon_form');
853
      $block['content'] = drupal_render($form);
854

    
855
      if (variable_get('cdm_dataportal_show_advanced_search', 1)) {
856
        $block['content'] .= '<div>' . l(t('Advanced Search'), 'cdm_dataportal/search') . '</div>';
857
      }
858
      return $block;
859
    case '4':
860
      $block['subject'] = '';
861
      $block['content'] = theme('cdm_print_button');
862
      return $block;
863
    case "keys":
864
      $block['subject'] = t('Identification Keys');
865
      $block['content'] = theme('cdm_block_IdentificationKeys', array('taxonUuid' => NULL));
866
      return $block;
867
    case "fundedByEDIT":
868
      // t('Funded by EDIT');
869
      $text = '<none>';
870
      $block['subject'] = $text;
871
      $img_tag = '<img src="' . base_path() . drupal_get_path('module', 'cdm_dataportal') . '/images/powered_by_edit.png' . '" alt="' . $text . '"/>';
872
      $block['content'] = l($img_tag, "http://cybertaxonomy.org/", array(
873
        'attributes' => array("target" => "EDIT"),
874
        'absolute' => TRUE,
875
        'html' => TRUE,
876
      ));
877
      return $block;
878
    case 'classification_breadcrumbs':
879
      $taxon_uuid = get_current_taxon_uuid();
880
      $block['subject'] = '<none>';
881
      $block['content'] = compose_classification_breadcrumbs($taxon_uuid);
882
      return $block;
883
    case 'taxonomic_children':
884
      $taxon_uuid = get_current_taxon_uuid();
885
      $block['subject'] = '<none>';
886
      $block['content'] = compose_taxonomic_children($taxon_uuid);
887
      return $block;
888
    case 'back_to_search_results':
889
      $block['subject'] = '<none>';
890
      if (isset($_SESSION['cdm']['search'])) {
891
        $block['content'] = l(t('Back to search result'), "http://" . $_SERVER['SERVER_NAME'] . $_SESSION['cdm']['last_search']);
892
      }
893
      return $block;
894
    default:
895
      return null;
896
  }
897
}
898

    
899
/**
900
 * Provides the uuid of the taxon for pages with the path ./taxon/{taxon_uuid}
901
 *
902
 * @return string
903
 *   the taxon uuid or NULL
904
 */
905
function get_current_taxon_uuid()
906
{
907
  static $taxon_uuid;
908

    
909
  if(!isset($taxon_uuid)){
910
    if(isset($_REQUEST['currentTaxon']) && is_uuid($_REQUEST['currentTaxon'])) {
911
      $taxon_uuid = $_REQUEST['currentTaxon'];
912
    } else if (arg(1) == 'taxon' && is_uuid(arg(2))) {
913
      $taxon_uuid = arg(2);
914
    } else {
915
      $taxon_uuid = null;
916
    }
917
  }
918

    
919
  return $taxon_uuid;
920
}
921

    
922
/**
923
 * Returns the currently classification tree in use.
924
 *
925
 * @return string
926
 *   The uuid of the currently focused classification
927
 */
928
function get_current_classification_uuid() {
929
  if (isset($_SESSION['cdm']['taxonomictree_uuid']) && is_uuid($_SESSION['cdm']['taxonomictree_uuid'])) {
930
    return $_SESSION['cdm']['taxonomictree_uuid'];
931
  }
932
  else {
933
    return variable_get(CDM_TAXONOMICTREE_UUID, FALSE);
934
  }
935
}
936

    
937
/*
938
 function cdm_dataportal_session_clear($cdm_ws_uri_update = FALSE){
939
 $_SESSION['cdm'] = NULL;
940
 if(is_string($cdm_ws_uri_update)){
941
 $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
942
 }
943
 }
944

    
945
 function cdm_dataportal_session_validate(){
946
 if(!isset($_SESSION['cdm']['ws_uri'])){
947
 $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', FALSE));
948
 } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', FALSE)){
949
 cdm_dataportal_session_clear(variable_get('cdm_webservice_url', FALSE));
950
 }
951
 }
952
 */
953

    
954
/**
955
 * creates a  selector form for taxonomic trees.
956
 *
957
 * @return array
958
 *  a drupal form array
959
 */
960
function cdm_taxonomictree_selector() {
961
  _add_js_treeselector();
962

    
963
  $form = drupal_get_form('cdm_taxonomictree_selector_form');
964
  return $form;
965
}
966

    
967
/**
968
 * @todo Please document this function.
969
 * @see http://drupal.org/node/1354
970
 *
971
 * @deprecated use compose_classification_selector instead
972
 */
973
function cdm_taxonomictree_selector_form($form, &$form_state) {
974

    
975
  $url = url('cdm_api/setvalue/session', array('query' => NULL));
976
  $form['#action'] = $url;
977

    
978
  $form['var'] = array(
979
    '#weight' => -3,
980
    '#type' => 'hidden',
981
    '#value' => '[cdm][taxonomictree_uuid]',
982
  );
983

    
984
  $destination_array = drupal_get_destination();
985
  $destination = $destination_array['destination'];
986

    
987
  $form['destination'] = array(
988
    '#weight' => -3,
989
    '#type' => 'hidden',
990
    '#value' =>  $destination,
991
  );
992

    
993
  $options = cdm_get_taxontrees_as_options();
994
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
995
  if($taxontree_includes){
996
    $filtered_options = array();
997
    foreach($options as $uuid=>$label){
998
      if(!empty($taxontree_includes[$uuid])){
999
        $filtered_options[$uuid] = $label;
1000
      }
1001
    }
1002
    $options = $filtered_options;
1003
  }
1004

    
1005
  $form['val'] = array(
1006
    '#type' => 'select',
1007
    '#title' => t('Available classifications'),
1008
    '#default_value' => get_current_classification_uuid(),
1009
    '#options' => $options,
1010
    '#attributes' => array('class' => array('highlite-first-child')),
1011
  );
1012

    
1013
  return $form;
1014

    
1015
}
1016

    
1017
/**
1018
 *
1019
 * @ingroup compose
1020
 */
1021
function compose_classification_selector() {
1022

    
1023
  $destination_array = drupal_get_destination();
1024
  $destination = $destination_array['destination'];
1025

    
1026
  $options = cdm_get_taxontrees_as_options();
1027
  $items = array();
1028
  $taxontree_includes = variable_get(CDM_TAXONTREE_INCLUDES, null);
1029

    
1030
  $current_classification_uuid = get_current_classification_uuid();
1031

    
1032

    
1033
  foreach($options as $uuid=>$label){
1034
    if(!$taxontree_includes || !empty($taxontree_includes[$uuid])){
1035

    
1036
      $class_attributes = '';
1037
      if($current_classification_uuid == $uuid){
1038
        $class_attributes  = array('focused');
1039
      }
1040
      $items[] = array(
1041
        'data' => l($label,
1042
          'cdm_api/setvalue/session',
1043
          array(
1044
            'query' => array(
1045
              'destination' => $destination,
1046
              'val' => $uuid,
1047
              'var' => '[cdm][taxonomictree_uuid]'
1048
            ),
1049
          )
1050
        ),
1051
        'class' => $class_attributes
1052
      );
1053
    }
1054
  }
1055

    
1056
  $render_array = array(
1057
    '#theme' => 'item_list',
1058
    '#type' => 'ul',
1059
    '#items' => $items
1060
  );
1061

    
1062
  return $render_array;
1063
}
1064

    
1065

    
1066
/* UNREACHABLE since action of form directly links to view.
1067
 function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
1068

    
1069
 $_SESSION['cdm']['search'] = $form_values;
1070
 //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
1071
 return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
1072
 //$paramstr = compose_url_prameterstr($form_values);
1073
 //return url('/cdm_dataportal/search/taxon/', array('query' => $paramstr));
1074
 }
1075
 */
1076
/* ====================== menu callback functions ====================== */
1077
/**
1078
 * @todo Please document this function.
1079
 * @see http://drupal.org/node/1354
1080
 */
1081
/*
1082
function cdm_dataportal_form_alter(&$form, &$form_state, $form_id) {
1083
  static $comment_node_disabled =  0;
1084
  static $comment_node_read_only =  1;
1085
  static $comment_node_read_write =  2;
1086

    
1087
  if ($form_id == 'node_type_form'
1088
   && isset($form['identity']['type'])
1089
   && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
1090
  ) {
1091
    $form['workflow']['comment'] = array(
1092
      '#type' => 'radios',
1093
      '#title' => t('Default comment setting'),
1094
      '#default_value' => variable_get('comment__' . $node->type . $form['#node_type']->type, $comment_node_disabled),
1095
      '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
1096
      '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
1097
    );
1098
  }
1099
}
1100
*/
1101

    
1102
/**
1103
 * Displays a list of the known taxonomic names.
1104
 *
1105
 * When the list of taxonomic names is displayed, long lists are split up into
1106
 * multiple pages.
1107
 *
1108
 * TODO: Parameters are still preliminary.
1109
 *
1110
 * @param string $beginsWith
1111
 * @param string $page
1112
 *   Page number to diplay defaults to page 1.
1113
 * @param bool $onlyAccepted
1114
 */
1115
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = FALSE) {
1116

    
1117
  $out = t('<h3>Sorry, the name list feature is not yet available in this version of the DataPortal software<h3>');
1118

    
1119
  /*
1120
  // FIXME the filter for accepted names will be a form element, thus this
1121
  // widget should be generated via form api preferably as block.
1122
  $out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
1123
  $out .= theme('cdm_dataportal_widget_names_list', $names, $page);
1124
  $out .= theme('cdm_listof_taxa', $taxonPager);
1125
  return $out;
1126
  */
1127
}
1128

    
1129
/**
1130
 * @todo Please document this function.
1131
 * @see http://drupal.org/node/1354
1132
 */
1133
function cdm_dataportal_view_reference($uuid, $arg2 = NULL) {
1134

    
1135
  cdm_check_valid_portal_page();
1136

    
1137
  $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
1138
  return theme('cdm_reference_page', array('reference' => $reference));
1139
}
1140

    
1141
/**
1142
 * Creates a view on a all references contained in the portal.
1143
 *
1144
 * This function is used at the path cdm_dataportal/reference/list
1145
 */
1146
function cdm_dataportal_view_reference_list($pageNumber) {
1147
  $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
1148
  cdm_reference_pager($referencePager, 'cdm_dataportal/reference/list/');
1149
}
1150

    
1151
/**
1152
 * @todo Please document this function.
1153
 * @see http://drupal.org/node/1354
1154
 */
1155
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = FALSE, $part = 0) {
1156

    
1157
  cdm_check_valid_portal_page();
1158

    
1159
  $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
1160
  return theme('cdm_media_page', array(
1161
    'media' => $media,
1162
    'mediarepresentation_uuid' => $mediarepresentation_uuid,
1163
    'partId' => $part,
1164
    ));
1165
}
1166

    
1167
/**
1168
 * @todo Please document this function.
1169
 * @see http://drupal.org/node/1354
1170
 */
1171
function _load_taxonBase(&$taxonBase) {
1172
  if (isset($taxonBase->uuid)) {
1173
    $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
1174
    $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
1175
    $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
1176
  }
1177
}
1178

    
1179
/**
1180
 * Loads the media associated to the given taxon from the cdm server.
1181
 * The aggregation settings regarding taxon relathionships and
1182
 * taxonnomic childen are taken into account.
1183
 *
1184
 * The media lists are cached in a static variable.
1185
 *
1186
 * @param Taxon $taxon
1187
 *   A CDM Taxon entitiy
1188
 *
1189
 * @return array
1190
 *   An array of CDM Media entities
1191
 *
1192
 */
1193
function _load_media_for_taxon($taxon) {
1194

    
1195
  static $media = NULL;
1196

    
1197
  if(!isset($media)) {
1198
    $media = array();
1199
  }
1200
  if (!isset($media[$taxon->uuid])) {
1201

    
1202
    // --- GET Images --- //
1203
    $mediaQueryParameters = array(
1204
        "type" => "ImageFile",
1205
    );
1206

    
1207
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1208
    $mediaQueryParameters['relationships'] = implode(',', get_selection($relationship_choice['direct']));
1209
    $mediaQueryParameters['relationshipsInvers'] = implode(',', get_selection($relationship_choice['invers']));
1210

    
1211
    $taxon_media_filter_choice = variable_get(CDM_TAXON_MEDIA_FILTER, unserialize(CDM_TAXON_MEDIA_FILTER_DEFAULT));
1212
    $mediaQueryParameters['includeTaxonDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonDescriptions'] != 0;
1213
    $mediaQueryParameters['includeOccurrences'] = (boolean) $taxon_media_filter_choice['includeOccurrences'] != 0;
1214
    $mediaQueryParameters['includeTaxonNameDescriptions'] = (boolean) $taxon_media_filter_choice['includeTaxonNameDescriptions'] != 0;
1215

    
1216
    $ws_endpoint = NULL;
1217
    if ( variable_get('cdm_images_include_children', 0) == 0) {
1218
      $ws_endpoint = CDM_WS_PORTAL_TAXON_MEDIA;
1219
    } else {
1220
      $ws_endpoint = CDM_WS_PORTAL_TAXON_SUBTREE_MEDIA;
1221
    }
1222

    
1223
    $media[$taxon->uuid] = cdm_ws_get($ws_endpoint,
1224
        array(
1225
            $taxon->uuid,
1226
        ),
1227
        queryString($mediaQueryParameters)
1228
       );
1229
  }
1230

    
1231
  return $media[$taxon->uuid];
1232
}
1233

    
1234
/**
1235
 *
1236
 * @param Taxon $taxon
1237
 *   A CDM Taxon entitiy
1238
 *
1239
 * @return array
1240
 *   An array of CDM SpecimenOrObservation entities
1241
 *
1242
function _load_occurences_for_taxon($taxon){
1243

    
1244
  static $occurences = NULL;
1245

    
1246
  if(!isset($occurences)) {
1247
    $occurences = array();
1248
  }
1249

    
1250
  if (!isset($occurences[$taxon->uuid])){
1251

    
1252
    $relationship_choice = variable_get(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS, unserialize(CDM_AGGREGATE_BY_TAXON_RELATIONSHIPS_DEFAULT));
1253
    $relationship_choice['direct'] = get_selection($relationship_choice['direct']);
1254
    $relationship_choice['invers'] = get_selection($relationship_choice['invers']);
1255

    
1256
    $by_associatedtaxon_query = http_build_query(array(
1257
        'relationshipsInvers' => implode(',', $relationship_choice['invers']),
1258
        'relationships' => implode(',', $relationship_choice['direct']),
1259
        'pageSize' => null // all hits in one page
1260
    )
1261
    );
1262

    
1263
    $pager = cdm_ws_get(CDM_WS_OCCURRENCE_BY_ASSOCIATEDTAXON,
1264
        null,
1265
        $by_associatedtaxon_query . '&taxonUuid=' . $taxon->uuid
1266
    );
1267

    
1268

    
1269
    if(isset($pager->records[0])){
1270
      $occurences[$taxon->uuid] =  $pager->records;
1271
    }
1272
  }
1273
  return $occurences[$taxon->uuid];
1274
}
1275
 */
1276

    
1277
/**
1278
 * Gets a Drupal variable, string or array and returns it.
1279
 *
1280
 * Similar to the variable_get() function of Drupal, except that this function
1281
 * is able to handle arrays correctly. This function is especially useful
1282
 * when dealing with collections of settings form elements (#tree = TRUE).
1283
 *
1284
 * @param string $variableKey
1285
 *   The Unique key of the Drupal variable in the Drupal variables table.
1286
 * @param string $defaultValueString
1287
 *   A string as for example derived from a CONSTANT.
1288
 *
1289
 * @return mixed
1290
 *   usually an array, depending on the nature of the variable.
1291
 *
1292
 * TODO compare with get_array_variable_merged() duplicate functions?
1293
 * @deprecated rather use get_array_variable_merged() since this function
1294
 * used an array as second parameter
1295
 */
1296
function mixed_variable_get($variableKey, $defaultValueString) {
1297
  $systemDefaults = unserialize($defaultValueString);
1298
  $storedSettings = variable_get($variableKey, array());
1299
  if (is_array($storedSettings)) {
1300
    // TODO better use drupal_array_merge_deep() ?
1301
    $settings = array_merge($systemDefaults, $storedSettings);
1302
  }
1303
  else {
1304
    $settings = $systemDefaults;
1305
  }
1306
  return $settings;
1307
}
1308

    
1309
/**
1310
 * Recursive function to convert an object into an array.
1311
 * also subordinate objects will be converted.
1312
 *
1313
 * @param object $object
1314
 * @return the array
1315
 */
1316
function convert_to_array($object) {
1317
  if(is_object($object) || is_array($object)) {
1318
    $array = (array)$object;
1319
    foreach ($array as $key=>$value){
1320
      $array[$key] = convert_to_array($value);
1321
    }
1322
    return $array;
1323
  } else {
1324
    return $object;
1325
  }
1326
}
1327

    
1328
/**
1329
 * Searches the $collection for the cdm entitiy given as $element.
1330
 *
1331
 * The elements are compared by their UUID.
1332
 *
1333
 * @param $element
1334
 *  the CDM entitiy to search for
1335
 * @param $collection
1336
 *  the list of CDM entities to search in
1337
 *
1338
 * @return boolean TRUE if the $collection contains the $element, otheriwse FALSE
1339
 *
1340
 */
1341
function contains_cdm_entitiy($element, $collection) {
1342
  $result = FALSE;
1343
  foreach ($collection as $a) {
1344
    if ($a->uuid == $element->uuid) {
1345
      $result = TRUE;
1346
    }
1347
  }
1348
  return $result;
1349
}
1350

    
1351
/**
1352
 * Fiters the array $entity_list of CDM entities by the list
1353
 * of $excludes. Any element contained in the $excludes will be removed
1354
 * from included int the retuned list.
1355
 *
1356
 * If the $entity_list is not an array the $excludes will be returned.
1357
 */
1358
function filter_cdm_entity_list($entity_list, $excludes) {
1359
  if (is_array($entity_list)) {
1360
    $result = $entity_list;
1361
    if ($excludes) {
1362
      foreach ($excludes as $exclude) {
1363
        if (!contains_cdm_entitiy($exclude, $entity_list)) {
1364
          $result[] = $exclude;
1365
        }
1366
      }
1367
    }
1368
  }
1369
  else {
1370
    $result = $excludes;
1371
  }
1372
  return $result;
1373
}
1374

    
1375
/**
1376
 * Wraps the given $html string into a render array suitable for drupal_render()
1377
 *
1378
 * @param $html
1379
 *   the html string, see
1380
 *   http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#markup
1381
 * @param $weight
1382
 *   A positive or negative number (integer or decimal).
1383
 *   see http://api.drupal.org/api/drupal/developer!topics!forms_api_reference.html/7#weightval
1384
 * @param $prefix
1385
 *   Optional markup for the '#prefix' element of the render array
1386
 * @param $suffix
1387
 *   Optional markup for the '#suffix' element of the render array
1388
 *
1389
 * @return array
1390
 *   A render array
1391
 *
1392
 */
1393
function markup_to_render_array($html, $weight = FALSE, $prefix = NULL, $suffix = NULL) {
1394
  $render_array = array(
1395
    '#markup' => $html
1396
      );
1397
  if (is_numeric($weight)) {
1398
    $render_array['#weight'] = $weight;
1399
  }
1400
  if($prefix){
1401
    $render_array['#prefix'] = $prefix;
1402
  }
1403
  if($suffix) {
1404
    $render_array['#suffix'] = $suffix;
1405
  }
1406
  return $render_array;
1407
}
1408

    
1409
/**
1410
 * Loads the subgraph of a given PolytomousKeyNode.
1411
 *
1412
 * Loads the subgraph of the given PolytomousKeyNode recursively from
1413
 * the CDM REST service.
1414
 *
1415
 * @param mixed $polytomousKeyNode
1416
 *   PolytomousKeyNode passed by reference.
1417
 *
1418
 * @return void
1419
 */
1420
function _load_polytomousKeySubGraph(&$polytomousKeyNode) {
1421

    
1422
  if (!$polytomousKeyNode) {
1423
    return;
1424
  }
1425
  if ($polytomousKeyNode->class != "PolytomousKeyNode") {
1426
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1427
    return;
1428
  }
1429
  if (!is_uuid($polytomousKeyNode->uuid)) {
1430
    drupal_set_message('_load_polytomousKeySubGraph(): ' . t('invalid type given.'), 'error');
1431
    return;
1432
  }
1433

    
1434
  $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
1435

    
1436
  if (!$polytomousKeyNode) {
1437
    // drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
1438
    return;
1439
  }
1440

    
1441
  // Load children.
1442
  foreach ($polytomousKeyNode->children as &$childNode) {
1443
    _load_polytomousKeySubGraph($childNode);
1444
  }
1445

    
1446
  // Load subkey.
1447
  $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
1448

    
1449
  // Load taxon.
1450
  $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
1451
  _load_taxonBase($polytomousKeyNode->taxon);
1452
  return;
1453
}
1454

    
1455
/**
1456
 * @todo Please document this function.
1457
 * @see http://drupal.org/node/1354
1458
 */
1459
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid) {
1460

    
1461
  cdm_check_valid_portal_page();
1462

    
1463
  $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
1464

    
1465
  $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1466
  if (is_array($sourcePager->records)) {
1467
    $polytomousKey->sources = $sourcePager->records;
1468
    // $polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'sources'));
1469
  }
1470

    
1471
  $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, 'annotations'));
1472
  if (is_array($annotationPager->records)) {
1473
    $polytomousKey->annotations = $annotationPager->records;
1474
  }
1475

    
1476
  _load_polytomousKeySubGraph($polytomousKey->root);
1477
  return theme('cdm_polytomousKey_page', array('polytomousKey' => $polytomousKey));
1478
}
1479

    
1480
/**
1481
 * Creates a taxon page view or a chapter of it.
1482
 *
1483
 * The taxon page gives detailed information on a taxon, it shows:
1484
 *  - Taxon name.
1485
 *  - Full list of synonyms homotypic synonyms on top, followed by the
1486
 *    heterotypic and finally followed by misapplied names.
1487
 *    The list is ordered historically.
1488
 *  - All description associated with the taxon.
1489
 *
1490
 * @param string $uuid
1491
 * @param string $chapter
1492
 *   Name of the part to display, valid values are:
1493
 *   'description', 'images', 'synonymy', 'specimens', 'all'.
1494
 *
1495
 * @return string
1496
 */
1497
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all') {
1498

    
1499
  cdm_check_valid_taxon_page($chapter);
1500
  cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1501
  // show a warning in case the javascript development mode is anabled
1502
  if(variable_get('cdm_js_devel_mode', FALSE)) {
1503
    drupal_set_message(t('The !url1 is enabled.
1504
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1505
          '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1506
    )),
1507
    'warning'
1508
        );
1509
  }
1510

    
1511
  // Display the page for the taxon defined by $uuid.
1512
  // set_last_taxon_page_tab(arg(3));
1513
  $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter);
1514
  if (!empty($taxonpage)) {
1515
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid);
1516
    return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title, $taxonpage->content);
1517
  }
1518
  else {
1519
    cdm_dd("END OF TAXON PAGE [" . $chapter . "] " . $uuid . ' !!! PAGE IS EMPTY !!!');
1520
    return '';
1521
  }
1522
}
1523

    
1524
/**
1525
 * This function will genreate the taxon page part ($chapter) and returns a taxonpage object
1526
 * which has two fields, one for the page title and one for the content. Later on in the
1527
 * process chain the value contained in these fields will be passed to the cdm_node_show()
1528
 * function as the function parameters $title and $content.
1529
 *
1530
 * @param string $uuid
1531
 *   the uuid of the taxon to show
1532
 * @param string $chapter
1533
 *   Name of the part to display, valid values are:
1534
 *   'description', 'images', 'synonymy', 'all'.
1535
 *
1536
 * @return object with the following fields:
1537
 *   - title : the title of the page
1538
 *   - content: the content of the page
1539
 *
1540
 */
1541
function cdm_dataportal_taxon_view($uuid, $chapter = 'all') {
1542
  // Taxon object.
1543
  $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1544
  if (empty($taxon)) {
1545
    drupal_set_title(t('Taxon does not exist'), PASS_THROUGH);
1546
    return FALSE;
1547
  }
1548
  $taxonpage = new stdClass();
1549

    
1550
  $taxonpage->title = theme('cdm_taxon_page_title', array(
1551
    'taxon' => $taxon
1552
  ));
1553

    
1554
  // Check if the taxon id contained in the currently selected tree.
1555
  $taxon_in_current_classification = taxon_in_current_classification($uuid);
1556

    
1557
  if (!$taxon_in_current_classification) {
1558
    $classifications = get_classifications_for_taxon($taxon);
1559
    RenderHints::pushToRenderStack('not_in_current_classification');
1560
    $taxon_name_markup = render_taxon_or_name($taxon);
1561

    
1562
    if (count($classifications) == 0) {
1563
      drupal_set_message(t('This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification.',
1564
        array(
1565
        '!taxonname' => $taxon_name_markup,
1566
        )
1567
      ), 'warning');
1568
    }
1569
    else {
1570
      $trees = '';
1571
      foreach ($classifications as $classification) {
1572
        if (isset($classification->titleCache)) {
1573
          $trees .= ($trees ? ', ' : '') . '<strong>' . $classification->titleCache . '</strong>';
1574
        }
1575
      }
1576

    
1577
      drupal_set_message(format_plural(count($trees),
1578
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in this one: !trees',
1579
          'This concept of the taxon !taxonname is not contained as an accepted taxon in the currently chosen classification, but in one of these: !trees',
1580
          array('!taxonname' => $taxon_name_markup, '!trees' => $trees)
1581
        ) ,
1582
        'warning');
1583
    }
1584
    RenderHints::popFromRenderStack();
1585
  }
1586

    
1587
  // Render the taxon page.
1588
  $render_array = compose_cdm_taxon_page($taxon, $chapter);
1589
  $taxonpage->content = drupal_render($render_array);
1590

    
1591
  return $taxonpage;
1592
}
1593

    
1594
/**
1595
 * Creates a specimen page view.
1596
 * @param string $uuid the UUID of the specimen
1597
 * @return array|string
1598
 */
1599
function cdm_dataportal_specimen_page_view($uuid) {
1600

    
1601
    //cdm_check_valid_taxon_page($chapter);
1602
    //cdm_dd("START OF TAXON PAGE [" . $chapter . "] " . $uuid . ' for ' . $_GET['q']);
1603
    // show a warning in case the javascript development mode is anabled
1604
    if(variable_get('cdm_js_devel_mode', FALSE)) {
1605
        drupal_set_message(t('The !url1 is enabled.
1606
        WARNING: this is a performance penalty and must be turned off on production websites.', array(
1607
            '!url1' => l('java-script development mode', 'admin/config/cdm_dataportal/settings', array('fragment' => 'edit-cdm-js-devel-mode'))
1608
        )),
1609
            'warning'
1610
        );
1611
    }
1612

    
1613
    // Display the page for the specimen defined by $uuid.
1614
    $specimenpage = cdm_dataportal_specimen_view($uuid);
1615
    if (!empty($specimenpage)) {
1616
        return cdm_node_show(NODETYPE_TAXON, $uuid, $specimenpage->title, $specimenpage->content);
1617
    }
1618
    else {
1619
        return '';
1620
    }
1621
}
1622

    
1623
/**
1624
 *
1625
 * Creates a specimen view.
1626
 * @param string $uuid the UUID of the specimen
1627
 * @return array|string
1628
 */
1629
function cdm_dataportal_specimen_view($uuid) {
1630
    $specimen = cdm_ws_get(CDM_WS_OCCURRENCE, $uuid);
1631
    if (empty($specimen)) {
1632
        drupal_set_title(t('Specimen does not exist'), PASS_THROUGH);
1633
        return FALSE;
1634
    }
1635
    $specimenpage = new stdClass();
1636

    
1637
    $specimenpage->title = theme('cdm_specimen_page_title', array(
1638
        'specimen' => $specimen
1639
    ));
1640

    
1641
    // Render the specimen page.
1642
    $render_array = compose_cdm_specimen_page($uuid);
1643
    $specimenpage->content = drupal_render($render_array);
1644

    
1645
    return $specimenpage;
1646
}
1647

    
1648
/**
1649
 * Returns a name page as a Drupal node ready to be renderized by Drupal.
1650
 *
1651
 * The node page shows the taxon name title and the list of taxon related
1652
 * with such taxon. Name on the tree already in use.
1653
 *
1654
 * @param UUID $taxon_name_uuid
1655
 *   The uuid of the CDM TaxonNameBase to show a name page for
1656
 * @param UUID $taxon_to_hide_uuid
1657
 *   A taxon which should not be displayed in the taxon list
1658
 * @param UUID $highlite_synonym_uuid
1659
 *   Optinal parameter wich takes another taxon uuid, if given the
1660
 *   target taxon pages will show the syonymy tab where the taxon
1661
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1662
 *   in case it is found on this page.
1663
 *
1664
 * @return mixed
1665
 *   The formatted name page as node.
1666
 */
1667
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = NULL) {
1668

    
1669
  cdm_check_valid_portal_page();
1670

    
1671
  $taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
1672
  if (!empty($taxonname_page)) {
1673
    return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title, $taxonname_page->content);
1674
  }
1675
  else {
1676
    return '';
1677
  }
1678
}
1679

    
1680
/**
1681
 * View function for a TaxonNameBase page.
1682
 *
1683
 * The name page lists all taxa for which the name specified by the
1684
 * $taxon_name_uuid is being used. I case there is only one name the
1685
 * page automatically redirects ti the according taxon page. Otherwise
1686
 * the list of names is displayed.
1687
 *
1688
 * The parameter $taxon_to_hide_uuid allows to exclude a taxon from the
1689
 * list of taxa. This is useful for example when referencing from a taxon
1690
 * to the name page and the referring taxon should not be repeaded in the
1691
 * name page.
1692
 *
1693
 *
1694
 * @param UUID $taxon_name_uuid
1695
 *   The uuid of the CDM TaxonNameBase to show a name page for
1696
 * @param UUID $taxon_to_hide_uuid
1697
 *   A taxon which should not be displayed in the taxon list
1698
 * @param UUID $highlite_synonym_uuid
1699
 *   Optinal parameter wich takes another taxon uuid, if given the
1700
 *   target taxon pages will show the syonymy tab where the taxon
1701
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
1702
 *   in case it is found on this page.
1703
 *
1704
 * @return object
1705
 *   An object with two fields:
1706
 *     - title: the page title
1707
 *     - content: the page content
1708
 */
1709
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $highlite_synonym_uuid = NULL) {
1710
  // Getting the full taxonname object from the server.
1711
  $taxon_name = cdm_ws_get(CDM_WS_PORTAL_NAME, array($taxon_name_uuid));
1712
  if (!$taxon_name) {
1713
    drupal_set_title(t('Taxon name does not exist'), PASS_THROUGH);
1714
    return FALSE;
1715
  }
1716
  // Searching for all the taxa connected with the taxon name on the tree
1717
  // in use.
1718
  $name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
1719
  $request_params = array();
1720
  $request_params['query'] = $name_cache;
1721
  $request_params['tree'] = get_current_classification_uuid();
1722
  $request_params['doTaxa'] = 1;
1723
  $request_params['doSynonyms'] = 1;
1724
  $request_params['doTaxaByCommonNames'] = 0;
1725
  $request_params['matchMode'] = "EXACT";
1726
  $taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, NULL, queryString($request_params));
1727

    
1728
  // Removing the name where we came from.
1729
  foreach ($taxon_pager->records as $k => &$taxon) {
1730
    if ($taxon->uuid == $taxon_to_hide_uuid) {
1731
      unset($taxon_pager->records[$k]);
1732
    }
1733
  }
1734
  // Show the taxa list or go to the singular taxon.
1735
  if (sizeof($taxon_pager->records) == 1) {// Single taxon case.
1736
    $singleTaxon = array_pop($taxon_pager->records);
1737
    if ($singleTaxon->class != "Taxon") {
1738
      // It is a Synonym -> look for the accepted.
1739
      $accepted_taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid), 'classificationFilter=' . get_current_classification_uuid());
1740
      if (!empty($highlite_synonym_uuid)) {
1741
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1742
      }
1743
      else {
1744
        drupal_goto('cdm_dataportal/taxon/' . $accepted_taxon->uuid . '/synonymy', array('query' => array('highlite' => $singleTaxon->uuid)));
1745
      }
1746
    }
1747
    else {
1748
      // It is an accepted taxon.
1749
      if (!empty($highlite_synonym_uuid)) {
1750
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', array('query' => array('highlite' => $highlite_synonym_uuid)));
1751
      }
1752
      else {
1753
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
1754
      }
1755
    }
1756
  }
1757
  else {// More than one taxa case.
1758
    $taxon_name_page = new stdClass();
1759
    $taxon_name_page->title = theme('cdm_name_page_title', array('taxon_name' => $taxon_name));
1760
    if ($taxon_pager->records) {
1761
      $taxon_name_page->content = compose_list_of_taxa($taxon_pager->records);
1762
    }
1763
    else {
1764
      $taxon_name_page->content = 'This name has no taxa';
1765
    }
1766
    return $taxon_name_page;
1767
  }
1768
}
1769

    
1770
/**
1771
 * Creates a page with the advance search form.
1772
 *
1773
 * NOTE: The advance search form allows searching for taxa.
1774
 */
1775
function cdm_dataportal_view_search_advanced() {
1776
  drupal_set_title(t('Advanced search'), PASS_THROUGH);
1777
  return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
1778
}
1779

    
1780
/**
1781
 * Creates a page with the search form for searching by taxon descriptions.
1782
 */
1783
function cdm_dataportal_view_search_taxon_by_description() {
1784
  drupal_set_title(t('Search by factual data'), PASS_THROUGH);
1785
  return drupal_get_form('cdm_dataportal_search_taxon_by_description_form');
1786
}
1787

    
1788
/**
1789
 * Executes the search and generates the result list of taxa.
1790
 */
1791
function cdm_dataportal_view_search_results_taxon() {
1792

    
1793
  $taxonPager = cdm_dataportal_search_execute();
1794

    
1795
  $showThumbnails = do_showThumbnails();
1796

    
1797
  $setSessionUri = url('cdm_api/setvalue/session', array(
1798
      'query' => array('var' => '[pageoption][searchtaxa][showThumbnails]', 'val' => ''),
1799
  ));
1800

    
1801
  drupal_add_js('jQuery(document).ready(function() {
1802

    
1803
      // init
1804
      if(' . $showThumbnails . ' == 1){
1805
          jQuery(\'.media_gallery\').show(20);
1806
      } else {
1807
          jQuery(\'.media_gallery\').hide(20);
1808
      }
1809

    
1810
      // add change handler
1811
      jQuery(\'#showThumbnails input.showThumbnails\').change(
1812
      function(event){
1813
        var state = 0;
1814
        if(jQuery(this).is(\':checked\')){
1815
          jQuery(\'.media_gallery\').show(20);
1816
          state = 1;
1817
        } else {
1818
          jQuery(\'.media_gallery\').hide(20);
1819
        }
1820
        // store state in session variable
1821
        var uri = \'' . $setSessionUri . '\' + state;
1822
        jQuery.get(uri);
1823
      });
1824
  });',
1825
  array('type' => "inline", 'scope' => JS_DEFAULT));
1826

    
1827
  drupal_set_title(t('Search results'), PASS_THROUGH);
1828

    
1829
  return theme('cdm_search_results', array(
1830
    'pager' => $taxonPager,
1831
    'path' => 'cdm_dataportal/search/results/taxon',
1832
    ));
1833
}
1834

    
1835
/**
1836
 * Provides the standart image wich indicated a loading process
1837
 *
1838
 * @return string
1839
 *  The img html tag
1840
 */
1841
function loading_image_html() {
1842
  return '<img class="loading" src="' . base_path() . drupal_get_path('module', 'cdm_dataportal')
1843
    . '/images/loading_circle_grey_16.gif" style="display:none;">';
1844
}
1845

    
1846
/**
1847
 * Returns the state of the the showThumbnails flag set in the
1848
 * users session ($_SESSION['pageoption']['searchtaxa']['showThumbnails']).
1849
 *
1850
 * @return boolean
1851
 *    returns 1 if the flag is set
1852
 */
1853
function do_showThumbnails() {
1854
  static $showThumbnails = null;
1855

    
1856
  if($showThumbnails == null) {
1857
    $showThumbnails = 0;
1858
    if (!isset($_SESSION['pageoption']['searchtaxa']['showThumbnails'])) {
1859
      $showThumbnails = 0;
1860
      $search_gallery_settings = variable_get(CDM_DATAPORTAL_SEARCH_GALLERY_NAME, null);
1861
      $showThumbnails = is_array($search_gallery_settings)
1862
        && isset($search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'])
1863
        && (
1864
            $search_gallery_settings['cdm_dataportal_show_taxon_thumbnails'] +
1865
            $search_gallery_settings['cdm_dataportal_show_synonym_thumbnails'] +
1866
            $search_gallery_settings['cdm_dataportal_show_thumbnail_captions'] > 0
1867
            )
1868
         ? 1 : 0;
1869

    
1870
       drupal_array_set_nested_value($_SESSION, array('pageoption', 'searchtaxa', 'showThumbnails'), $showThumbnails);
1871
    }
1872
    $showThumbnails = $_SESSION['pageoption']['searchtaxa']['showThumbnails'];
1873
    if (!is_numeric($showThumbnails)) {
1874
      $showThumbnails = 1;
1875
    }
1876
  }
1877

    
1878
  return $showThumbnails;
1879
}
1880

    
1881

    
1882
/* ====================== other functions ====================== */
1883
/**
1884
 * Creates a URL to the taxon page specified by the $uuid parameter.
1885
 *
1886
 * The URL will be prepended with a path element to a specific taxon page tab.
1887
 *
1888
 * This tab is either taken from the CDM_DATAPORTAL_DEFAULT_TAXON_TAB which can
1889
 * be set globally in the administrative settings or individually in the user
1890
 * profile. If the CDM_DATAPORTAL_DEFAULT_TAXON_TAB value is set to LAST_VISITED_TAB
1891
 * the last portal will stay on this last tab.
1892
 *
1893
 * A third option is offerered by the $page_tab parameter which allows overwriting this
1894
 * internal mechanism by a specific value.
1895
 *
1896
 * @param string $uuid
1897
 *   The UUID of the taxon.
1898
 * @param string $page_tab
1899
 *   Overwriting the preset mechanism by defining specific value for the
1900
 *   taxon page tab.
1901
 *
1902
 * @return string
1903
 *   The created URL.
1904
 */
1905
function path_to_taxon($uuid, $page_tab = FALSE) {
1906

    
1907
  $tab = get_default_taxon_tab();
1908
  $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
1909

    
1910
  if (!$uuid) {
1911
    return FALSE;
1912
  }
1913

    
1914
  if ($page_tab) {
1915
    return 'cdm_dataportal/taxon/' . $uuid . '/' . $page_tab;
1916
  }
1917
  elseif (!$tab || strtolower($tab) == 'general') {
1918
    return 'cdm_dataportal/taxon/' . $uuid;
1919
  }
1920
  elseif (get_last_taxon_page_tab() &&   $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]) {
1921
    return 'cdm_dataportal/taxon/' . $uuid . '/' . get_last_taxon_page_tab();
1922
  }
1923
  else {
1924
    return 'cdm_dataportal/taxon/' . $uuid . '/' . strtolower($tab);
1925
  }
1926
}
1927

    
1928
function path_to_specimen($uuid) {
1929

    
1930
    if (!$uuid) {
1931
        return FALSE;
1932
    }
1933
    else {
1934
        return 'cdm_dataportal/specimen/' . $uuid;
1935
    }
1936
}
1937

    
1938
/**
1939
 * Creates a URL to show a synonmy in the according taxon page.
1940
 *
1941
 * The URL will point to the synonymy tab of the taxon page of the accepted taxon given as parameter $acceptedUuid.
1942
 * The resulting URI will include query parameters to highlight the synonym, and to optionally display
1943
 * the accepted taxons name in aform like "Foo bar is accepted taxon for Ree doo". The URI will also
1944
 * include the sysnonym uuid as fragment in order to let the browser scroll to the according location
1945
 * in the page
1946
 *
1947
 * @param string $synonymUuid
1948
 *    The uuid of the synonym
1949
 * @param string $acceptedUuid
1950
 *    The uuid of the according accepted taxon
1951
 * @return string
1952
 *    The URL to show a synonmy in the according taxon page
1953
 */
1954
function uri_to_synonym($synonymUuid, $acceptedUuid) {
1955
  $acceptedPath = path_to_taxon($acceptedUuid, "synonymy");
1956
  return url($acceptedPath, array(
1957
      'query' => array(
1958
        // highlite the synony in the synonymy
1959
        'highlite' => $synonymUuid,
1960
        // the taxon page is refered from a synonym and the synonym can optionally be named in the page title
1961
        // see theme_taxon_page_title()
1962
        'acceptedFor' => $synonymUuid
1963
      ),
1964
      'fragment' => $synonymUuid
1965
  ));
1966

    
1967
}
1968

    
1969
/**
1970
 * Compses the drupal path to the key identified by the uuid.
1971
 *
1972
 * @param string $keyType
1973
 *    the key typer corresponds to the specific class of the CDM
1974
 *    IdentificationKey. Possible values are
1975
 *      -PolytomousKey
1976
 *      -MultimediaKey
1977
 *      - ...
1978
 * @param UUID $keyUuid
1979
 *   The UUID of the key
1980
 */
1981
function path_to_key($keyType, $keyUuid) {
1982
  if (!$keyUuid || !$keyType) {
1983
    return FALSE;
1984
  }
1985
  $keyType{0} = strtolower($keyType{0});
1986
  return "cdm_dataportal/" . $keyType . "/$keyUuid";
1987
}
1988

    
1989
/**
1990
 * @todo Please document this function.
1991
 * @see http://drupal.org/node/1354
1992
 */
1993
function path_to_reference($uuid) {
1994
  if (!$uuid) {
1995
    return FALSE;
1996
  }
1997
  return 'cdm_dataportal/reference/' . $uuid;
1998
}
1999

    
2000
/**
2001
 * Creates the path to a cdm_dataportal taxon name page.
2002
 *
2003
 * @param UUID $taxon_name_uuid
2004
 *   The uuid of the CDM TaxonNameBase to show a name page for
2005
 * @param UUID $taxon_to_hide_uuid
2006
 *   A taxon which should not be displayed in the taxon list
2007
 * @param UUID $highlite_synonym_uuid
2008
 *   Optinal parameter wich takes another taxon uuid, if given the
2009
 *   target taxon pages will show the syonymy tab where the taxon
2010
 *   refenrenced by the $highlite_synonym_uuid will be highlighted
2011
 *   in case it is found on this page.
2012
 *
2013
 * @return a URI path element as string
2014
 */
2015
function path_to_name($name_uuid, $taxon_to_hide_uuid = NULL, $synonym_uuid  = NULL) {
2016
  $res = FALSE;
2017
  if ($name_uuid) {
2018
    $res = 'cdm_dataportal/name/' . $name_uuid;
2019
  }
2020
  if($taxon_to_hide_uuid){
2021
    $res .= '/' . $taxon_to_hide_uuid;
2022
    if($synonym_uuid){
2023
      $res .= '/' . $synonym_uuid;
2024
    }
2025
  }
2026
  return $res;
2027
}
2028

    
2029
/**
2030
 * @todo Please document this function.
2031
 * @see http://drupal.org/node/1354
2032
 */
2033
function path_to_media($uuid, $representaion_uuid = FALSE, $partId = FALSE) {
2034
  if (!$uuid) {
2035
    return FALSE;
2036
  }
2037
  $out = 'cdm_dataportal/media/' . $uuid;
2038
  if ($representaion_uuid) {
2039
    $out .= '/' . $representaion_uuid;
2040
    if ($partId !== FALSE) {
2041
      $out .= '/' . $partId;
2042
    }
2043
  }
2044
  return $out;
2045
}
2046

    
2047
/**
2048
 * Compares thisRank with thatRank.
2049
 *
2050
 * Returns a negative integer, zero, or a positive integer
2051
 * as the of thisRank is higher than, equal to, or lower than thatRank.
2052
 * e.g:
2053
 * <ul>
2054
 * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
2055
 * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
2056
 * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
2057
 * </ul>
2058
 * <p>
2059
 * This compare logic of the underlying webservice is the
2060
 * <b>inverse logic</b> of the the one implemented in
2061
 * java.lang.Comparable#compareTo(java.lang.Object)
2062
 *
2063
 * @param $thisRankUuid
2064
 * @param $thatRankUuid
2065
 *
2066
 * @return int
2067
 *   A negative integer, zero, or a positive integer
2068
 *   as the thisRank is lower than, equal to, or higher than thatRank.
2069
 */
2070
function rank_compare($thisRankUuid, $thatRankUuid) {
2071
  $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
2072
  return $result->Integer;
2073
}
2074

    
2075
/**
2076
 * Composes an HTML element class attribute value composed of
2077
 * the shortname of the cdm class and the uuid of the entity.
2078
 * This class attribute should be used whereever an cdm-entity is rendered.
2079
 *
2080
 * These according class selectors in css must be escaped, eg:
2081
 *    .cdm\:TextData
2082
 *
2083
 * @param $cdmEntity
2084
 */
2085
function html_class_attribute_ref($cdmEntity) {
2086

    
2087
  if (is_cdm_entity($cdmEntity)) {
2088
    return "cdm:" . $cdmEntity->class . " uuid:" . $cdmEntity->uuid;
2089
  }
2090
}
2091

    
2092

    
2093
/**
2094
 * Creates a short taxonname.
2095
 *
2096
 * The short name is created by using the taggedTitle field of
2097
 * NameSTO or NameTO instances.
2098
 * If the taggedTitle if empty the fullname will be returned.
2099
 *
2100
 * @param unknown_type $name
2101
 *   Name or TreeNode.
2102
 *
2103
 * @return string
2104
 */
2105
function cdm_dataportal_shortname_of($name) {
2106
  $nameStr = '';
2107

    
2108
  normalize_tagged_text($name->taggedTitle);
2109

    
2110
  // Get all tagged text tokens of the scientific name.
2111
  foreach ($name->taggedTitle as $tagtxt) {
2112
    if ($tagtxt->type == 'name' || $tagtxt->type == 'rank') {
2113
      $nameStr .= ($nameStr ? ' ' : '') . $tagtxt->text;
2114
    }
2115
  }
2116
  $nameStr = trim($nameStr);
2117

    
2118
  if ($nameStr) {
2119

    
2120
    // Do not return short names for these.
2121
    if ($name->unplaced || $name->excluded) {
2122
      return $nameStr;
2123
    }
2124

    
2125
    /*
2126
    1st capture group (^[a-zA-Z]): First letter of uninomial.
2127
    Second capture group ([\p{L}]+): remaining letters of uninomial ([\p{L} = an UTF-8 letter).
2128
    Third capture group (\s+[^(\x2E]+\s+.+$|\s+[a-zA-Z]+$): letters of name,
2129
    but only matching if no '(' or '.' in second word of name,        ( \x2E = '.')
2130
    OR only one specific epithet \s+[\p{L}\x22\x2D\xD7]+$             (\x22= '"', \x2D='-', \xD7='×' )
2131
    */
2132
    $pattern = '/(^[a-zA-Z])([\p{L}]+)(\s+[^(\x2E]+\s+.+$|\s+[\p{L}\x22\x2D\xD7]+$)/u';
2133
    if (preg_match($pattern, $nameStr, $matches, PREG_OFFSET_CAPTURE)) {
2134
      return $matches[1][0] . "." . $matches[3][0];
2135
    }
2136
    else {
2137
      return $nameStr;
2138
    }
2139
  }
2140
  else {
2141
    return $name->titleCache;
2142
  }
2143
}
2144

    
2145
/**
2146
 * Check if a taxon is accepted by the current taxonomic tree.
2147
 *
2148
 * @param mixed $taxon
2149
 *   The Taxon obkect to check.
2150
 *
2151
 * @return bool
2152
 *   Returns TRUE if $taxon is accepted, FALSE otherwise.
2153
 */
2154
function _cdm_dataportal_acceptedByCurrentView($taxon) {
2155

    
2156
  $defaultTreeUuid = get_current_classification_uuid();
2157

    
2158
  if (isset($taxon->taxonNodes)) {
2159
    $taxonNodes = $taxon->taxonNodes;
2160
  }
2161
  else {
2162
    $taxonNodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $taxon->uuid);
2163
  }
2164

    
2165
  if ($taxon->class == "Taxon" && isset($taxonNodes)) {
2166
    foreach ($taxonNodes as $node) {
2167
      if (isset($node->classification)){
2168
        if(is_object($node->classification)) {
2169
          if ($node->classification->uuid == $defaultTreeUuid) {
2170
            return TRUE;
2171
          }
2172
        }
2173
        else {
2174
          if ($node->classification == $defaultTreeUuid) {
2175
            return TRUE;
2176
          }
2177
        }
2178
      }
2179
    }
2180
  }
2181

    
2182
  return FALSE;
2183
}
2184

    
2185
/**
2186
 * Checks is the source has one of the given types.
2187
 *
2188
 * @param object $source
2189
 *   The original source entity
2190
 * @param array $types
2191
 *   An array of elementd of the OriginalSourceType enumeration
2192
 *   If not set the default will be used which is:
2193
 *    - Lineage
2194
 *    - PrimaryMediaSource
2195
 *    - PrimaryTaxonomicSource
2196
 *    - Unknown
2197
 *    - Other
2198
 * @return boolean
2199
 */
2200
  function _is_original_source_type($source, $types = null) {
2201
    // this is the default
2202
    // maybe this should also be put into the settings
2203
    static $default = array(
2204
      OriginalSourceType::Lineage,
2205
      OriginalSourceType::PrimaryMediaSource,
2206
      OriginalSourceType::PrimaryTaxonomicSource,
2207
      OriginalSourceType::Unknown,
2208
      OriginalSourceType::Other,
2209
    );
2210

    
2211
    if(!$types){
2212
      $types = $default;
2213
    }
2214
    return isset($source->type) && in_array($source->type, $types);
2215
  }
2216

    
2217
/**
2218
 * @todo Please document this function.
2219
 * @see http://drupal.org/node/1354
2220
 */
2221
function _is_invers_taxonRelationship($taxonRelationship, $focusedTaxon) {
2222
  return $taxonRelationship->toTaxon->uuid == $focusedTaxon->uuid;
2223
}
2224

    
2225

    
2226
/**
2227
 * Collects all the media from a list of description elements.
2228
 *
2229
 * @param array $descriptionElements
2230
 *   The description elements from which to collect the media.
2231
 *
2232
 * @return array
2233
 *   The output with all the collected media.
2234
 */
2235
function cdm_dataportal_media_from_descriptionElements($descriptionElements) {
2236

    
2237
  $outArrayOfMedia = array();
2238

    
2239
  // Avoiding a warning box in Drupal for Flora Malesiana.
2240
  if (isset($descriptionElements) && is_array($descriptionElements)) {
2241
    foreach ($descriptionElements as $descriptionElement) {
2242
      if (isset($descriptionElement->media) && is_array($descriptionElement->media)) {
2243
        foreach ($descriptionElement->media as $media) {
2244
          if (is_object($media)) {
2245
            $outArrayOfMedia[] = $media;
2246
          }
2247
        }
2248
      }
2249
    }
2250
  }
2251
  return $outArrayOfMedia;
2252
}
2253

    
2254
/**
2255
 * @todo Please document this function.
2256
 * @see http://drupal.org/node/1354
2257
 *
2258
 * @param array $cdm_entities
2259
 *   An array of CdmBase instances or a single instance.
2260
 * @param string $footnote_list_key_suggestion
2261
 *
2262
 * @return unknown
2263
 */
2264
function cdm_annotations_as_footnotekeys($cdm_entities, $footnote_list_key_suggestion = NULL) {
2265

    
2266
   static $annotations_types_filter = null;
2267
   if(!$annotations_types_filter) {
2268
     $annotations_types_filter = unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT);
2269
   }
2270

    
2271
  $footNoteKeys = array();
2272

    
2273
  // Is argument cdmBase an array?
2274
  if (!is_array($cdm_entities)) {
2275
    $cdmBase_array = array();
2276
    $cdmBase_array[] = $cdm_entities;
2277
  }
2278
  else {
2279
    $cdmBase_array = $cdm_entities;
2280
  }
2281

    
2282
  // Getting the key for the footnotemanager.
2283
  if (isset($footnote_list_key_suggestion)) {
2284
    $footnote_list_key = $footnote_list_key_suggestion;
2285
  }
2286
  else {
2287
    $footnote_list_key = RenderHints::getFootnoteListKey() . '-annotations';
2288
  }
2289

    
2290
  // Adding the footnotes keys.
2291
  foreach ($cdmBase_array as $cdmBase_element) {
2292
    $annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', $annotations_types_filter));
2293
    if (is_array($annotations)) {
2294
      foreach ($annotations as $annotation) {
2295
        $footNoteKeys[] = FootnoteManager::addNewFootnote($footnote_list_key, $annotation->text);
2296
      }
2297
    }
2298
  }
2299

    
2300
  return $footNoteKeys;
2301
}
2302

    
2303

    
2304
/**
2305
 * Creates a CDM Dynabox.
2306
 *
2307
 * @param string $dynabox_id
2308
 *   a uninque name for tha dynabox, using a cdm entity uuid as id is good practice.
2309
 * @param string $label
2310
 *   The clickable text to show.
2311
 * @param string $content_url
2312
 *   The cdm REST service request url wich will deliver the content to be shown
2313
 *   once the dynabox toggles open.
2314
 * @param string $theme
2315
 *   The theme to be used for rendering the cdm REST service response with is
2316
 *   returned from the $content_url.
2317
 * @param string $link_alt_text
2318
 *   The value for the alt attribute of the dynabox link.
2319
 * @param array $enclosingtags
2320
 *   An array with two elements: $enclosingtags[0] will be used for the dynabox
2321
 *   element itself, $enclosingtags[1] is the tag to be used for the
2322
 *   dynabox_content (optional)
2323
 * @param array $attributes
2324
 * @param $content_element_selector
2325
 *   Optional jQuery selector which can be used to reference a dom element which should
2326
 *   be used as container for the content to be shown. The dynabox-<dynabox id>-content
2327
 *  element will be placed in this container.
2328
 *
2329
 * @param string $open_callback
2330
 *   optional javascript call back function to be triggered after toggling the box to
2331
 *   the open state.
2332
 * @param string $close_callback
2333
 *   optional javascript call back function to be triggered after toggling the box to
2334
 *   the closed state.
2335
 * @return string Returns HTML for a dynabox.
2336
 * Returns HTML for a dynabox.
2337
 */
2338
function cdm_dynabox($dynabox_id, $label, $content_url, $theme, $link_alt_text,
2339
                     $enclosingtags = array('li', 'ul'), $attributes = array(),
2340
                     $content_element_selector = null,
2341
                     $open_callback = 'function(){}', $close_callback = 'function(){}' ) {
2342
  $out = '';
2343

    
2344
  // check for plain class attribute string
2345
  $dynabox_id = preg_replace('/[^a-zA-Z0-9\-]/', '', $dynabox_id);
2346

    
2347
  if(!array_key_exists('class', $attributes)) {
2348
    $attributes['class'] = array();
2349
  }
2350
  $attributes['id'][] = 'dynabox-' . $dynabox_id;
2351
  $dynabox_attributes = drupal_attributes($attributes);
2352

    
2353

    
2354
  _add_js_domEvent(); // requires domEvent.js
2355
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal') . '/js/cdm_dynabox.js');
2356
  drupal_add_js("
2357
  jQuery(document).ready(
2358
      function() {
2359
        dynabox('". $dynabox_id ."',
2360
          {
2361
            open_callback: " . $open_callback .",
2362
            close_callback: " . $close_callback .
2363
            ($content_element_selector ? ",\n content_container_selector: '" . $content_element_selector . "'" : "") . "
2364
          }
2365
        );
2366
      }
2367
   );",
2368
   array(
2369
    'type'=>'inline',
2370
    'scope'=>'footer'
2371
    )
2372
  );
2373

    
2374

    
2375
  $cdm_proxy_url = url('cdm_api/proxy/' . urlencode($content_url) . "/$theme");
2376
  $out .= '<!-- dynabox for ' . $content_url . ' -->';
2377
  $out .= '<' . $enclosingtags[0] . ' ' .  $dynabox_attributes. '><a href="' . $cdm_proxy_url . '" class="label" alt="' . t('@link-alt-text', array('@link-alt-text' => $link_alt_text)) . '">' . $label . '</a>';
2378
  $out .= '  <' . $enclosingtags[1] . ' id="dynabox-' . $dynabox_id . '-content">';
2379
  $out .= '    <' . $enclosingtags[0] . ' class="dynabox-content-inner">' . loading_image_html() . '</' . $enclosingtags[0] . '>';
2380
  $out .= '    </' . $enclosingtags[1] . '>';
2381
  $out .= '  </' . $enclosingtags[0] . '>';
2382
  $out .= '<!-- dynabox end -->';
2383
  return $out;
2384
}
2385

    
2386
/**
2387
 * Checks whether a feature has any description elements.
2388
 *
2389
 * @param mixed $featureNode
2390
 *   A feature node as produced by the function _mergeFeatureTreeDescriptions().
2391
 *
2392
 * @see _mergeFeatureTreeDescriptions()
2393
 *
2394
 * @return bool
2395
 *   Returns TRUE if the given $featureNode or any of its subordinate nodes
2396
 *   contains at least one non empty TextData or at least one DescriptionElement
2397
 *   of an other type. A TextData element holding a multilanguageText or a
2398
 *   source reference is considered to be not empty.
2399
 *
2400
 * @TODO this function may have become obsolete by the new method of detecting empty blocks,
2401
 *       see $block_content_is_not_empty in compose_feature_blocks() and
2402
 *       $feature_block_has_content in compose_feature_block_items_generic
2403
 */
2404
function has_feature_node_description_elements($featureNode) {
2405

    
2406
  if (isset($featureNode->descriptionElements) && is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
2407
    if(!isset($featureNode->descriptionElements['#type'])){ // #type is used to identify e.g. DTO elements: '#type' => 'DTO'
2408
      foreach ($featureNode->descriptionElements as $descriptionElement) {
2409
        if ($descriptionElement->class != "TextData" || isset($descriptionElement->multilanguageText_L10n->text)
2410
          && $descriptionElement->multilanguageText_L10n->text != ''
2411
          || isset($descriptionElement->sources[0])
2412
          || isset($descriptionElement->media[0]) ) {
2413
          return TRUE;
2414
        }
2415
      }
2416
    }
2417
  }
2418
  else if (isset($featureNode->childNodes) && is_array($featureNode->childNodes)) {
2419
    foreach ($featureNode->childNodes as $child) {
2420
      if (has_feature_node_description_elements($child)) {
2421
        return TRUE;
2422
      }
2423
    }
2424
  }
2425
  return FALSE;
2426
}
2427

    
2428
/**
2429
 * Checks if the current page is a valid taxon portal page and responds with HTTP status 404 (not found) otherwise
2430
 *
2431
 * @param $chapter
2432
 *   The taxon page chapter or part
2433
 */
2434
function cdm_check_valid_taxon_page($chapter){
2435
  static $taxon_tabs = null;
2436

    
2437
  cdm_check_valid_portal_page();
2438

    
2439
  if($taxon_tabs == null){
2440
    $taxon_tabs = array('all', 'description');
2441
    foreach(get_taxon_tabs_list() as $tab){
2442
      $taxon_tabs[] = strtolower($tab);
2443
    }
2444
  }
2445

    
2446
  if(!in_array($chapter, $taxon_tabs)){
2447
    // oops this is not a valid chapter name
2448
    http_response_code(404); // 404 = Not Found
2449
  }
2450

    
2451
}
2452

    
2453
/**
2454
 * Checks if the current page is a valid portal page and responds with HTTP status 404 (not found) otherwise
2455
 *
2456
 * @param $chapter
2457
 *   The taxon page chapter or part
2458
 */
2459
function cdm_check_valid_portal_page(){
2460
  $ends_with_file_suffix_pattern = '/\/[^\.\/]*[\.][^\.\/]*$/';
2461
  if(preg_match($ends_with_file_suffix_pattern, $_GET['q'])){
2462
    // oops this urls ends with a file_suffix and thus does not refer to a portal page
2463
    http_response_code(404); // 404 = Not Found
2464
    exit('HTTP 404');
2465
  }
2466
}
2467

    
2468
/**
2469
 * Generates the diff of the texts and presents it in a HTML diff viewer.
2470
 *
2471
 * @param $text_a
2472
 * @param $text_b
2473
 * @return string
2474
 */
2475
function diff_viewer($text_a, $text_b) {
2476

    
2477
  static $diff_viewer_count = 0;
2478

    
2479
  $element_id = 'part_definitions_diff_' . $diff_viewer_count++;
2480

    
2481
  // http://code.stephenmorley.org/php/diff-implementation/
2482
  module_load_include('php', 'cdm_dataportal', 'lib/class.Diff');
2483
  drupal_add_css(drupal_get_path('module',
2484
      'cdm_dataportal') . '/css/diff.css');
2485
  _add_jquery_ui();
2486
  drupal_add_js(
2487
    'jQuery(document).ready( function(){
2488
        jQuery(\'#' . $element_id . '\').accordion({
2489
        collapsible: true,
2490
        active: false,
2491
        fillSpace: true,
2492
        }).children(\'div\').css({ \'height\': \'auto\' });
2493
        jQuery(\'#' . $element_id . ' table.diff\').prepend(\'<thead><tr><th>Default</th><th>User defined<th></th><tr></thead>\');
2494
     });'
2495
    , array(
2496
    'type' => 'inline',
2497
    'scope' => 'footer'
2498
  ));
2499

    
2500
  $diff = Diff::compare($text_a,
2501
    $text_b);
2502
  $diff_viewer_markup = '<div id="' . $element_id . '"><h3>View Diff</h3><div>'
2503
    . Diff::toTable($diff, '', '')
2504
    . '</div></div>';
2505
  return $diff_viewer_markup;
2506
}
2507

    
2508

    
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