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cdm-dataportal / modules / cdm_dataportal / cdm_dataportal.module @ dc69d2dc

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<?php
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// $Id$
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/*
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 * @file
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 * cdm_dataportal
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 *
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 * Copyright (C) 2007 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 file are subject to the Mozilla Public License Version 1.1
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 * See http://www.mozilla.org/MPL/MPL-1.1.html for the full license terms.
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 */
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require_once('node_types.php');
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require_once('settings.php');
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require_once('help.php');
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require_once('theme/cdm_dataportal.common.theme');
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require_once('theme/cdm_dataportal.descriptions.theme');
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require_once('theme/cdm_dataportal.media.theme');
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require_once('theme/cdm_dataportal.occurrence.theme');
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require_once('theme/cdm_dataportal.page.theme');
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require_once('theme/cdm_dataportal.taxon.theme');
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require_once('theme/cdm_dataportal.name.theme');
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require_once('theme/cdm_dataportal.references.theme');
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require_once('classes/footnotemanager.php');
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require_once('classes/footnote.php');
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require_once('classes/footnotekey.php');
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require_once('classes/renderhints.php');
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function _add_js_progressbar(){
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  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/jquery.progressbar/js/jquery.progressbar.js');
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}
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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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    if (Drupal.jsEnabled) {
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      $(document).ready(function() {
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          $('#cdm-taxonomictree-selector-form #edit-val').change(function () {
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              $('#cdm-taxonomictree-selector-form').submit();
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          });
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      });
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    }", 'inline');
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}
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function _add_js_openlayers_map(){
52

    
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  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/OpenLayers/OpenLayers.js', 'core', 'header');
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  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/openlayers_map.js');
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  $gmap_api_key = variable_get('gmap_api_key', 'ABQIAAAAFho6eHAcUOTHLmH9IYHAeBRi_j0U6kJrkFvY4-OX2XYmEAa76BTsyMmEq-tn6nFNtD2UdEGvfhvoCQ');
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  $baseLayers = variable_get('baselayers', array());
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  if(!is_array($baseLayers) || count($baseLayers) == 0){
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    $baseLayers = array('metacarta_vmap0' => 'Metacarta Vmap0', 'PREFERRED' => 'metacarta_vmap0');
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  }
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  $layerNames = '';
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  foreach($baseLayers as $layerName => $layerLabel){
64
    if($layerName == 'PREFERRED'){
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      $preferredLayer = $baseLayers['PREFERRED'];
66
    } else {
67
      $layerNames .= ($layerNames ? ', ': '') . "'$layerName'";
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    }
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  }
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  if( isset($baseLayers['gmap']) || isset($baseLayers['gsat']) || isset($baseLayers['ghyb']) ){
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    drupal_set_html_head('<script src=http://maps.google.com/maps?file=api&amp;v=2&amp;sensor=false&amp;key='.$gmap_api_key.'" type="text/javascript"></script>');
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    drupal_set_html_head('<script src="http://dev.virtualearth.net/mapcontrol/mapcontrol.ashx?v=6.1" type="text/javascript"></script>');
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  }
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76
  drupal_add_js("
77
        if (Drupal.jsEnabled) {
78
          $(document).ready(function() {
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              $('#openlayers_map').cdm_openlayers_map('"
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              .getEDITMapServiceURI()."', {
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                legendPosition: 3,
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                displayWidth: '" . variable_get('cdm_dataportal_geoservice_display_width', false) . "',
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                boundingBox: '" . variable_get('cdm_dataportal_geoservice_bounding_box', false) . "',
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                distributionOpacity: '" . variable_get('cdm_dataportal_geoservice_distributionOpacity', '0.5') . "',
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                legendOpacity: '" . variable_get('cdm_dataportal_geoservice_legendOpacity', '0.5') . "',
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                showLayerSwitcher: " . (variable_get('cdm_dataportal_geoservice_showLayerSwitcher', TRUE) ? 'true':'false') . ",
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                baseLayerNames: [".$layerNames."],
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                defaultBaseLayerName: '".$preferredLayer."',
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            });
90
          });
91
        }", 'inline');
92

    
93
}
94

    
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function get_openlayers_map($width, $occurrenceQuery = false, $distributionQuery = false, $legendFormatQuery = false, $map_caption = false ){
97

    
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  _add_js_openlayers_map();
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100
  $out = '<div id="openlayers">';
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  $out .= '<div id="openlayers_map" class="smallmap"';
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  $out .= ' style="width: ' . $width . 'px; height:'.( $width / 2).'px"';
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  if($occurrenceQuery){
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    //fix $occurrenceQuery
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    $occurrenceQuery .= '&ms=400,350';
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    $occurrenceQuery .= '&l=v%3Aatbi%2Ce_w_0';
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    $occurrenceQuery .= '&legend=0'; //TODO add to cdm service?
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    $out .= ' occurrenceQuery="'.$occurrenceQuery.'"';
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  }
112
  if($distributionQuery){
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    $out .= ' distributionQuery="'.$distributionQuery.'"';
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  }
115
  if($legendFormatQuery){
116
    $out .= ' legendFormatQuery="'.$legendFormatQuery.'"';
117
  }
118
  $out .= '></div></div>';
119

    
120
  // showing map caption
121
  if($map_caption){
122
    $out .= '<div class="distribution_map_caption">' . $map_caption . '</div>' . '<br />'; //FIXME: replace <br> by according css style
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    $out .= '</div>';
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  }
125
  return $out;
126
}
127

    
128
/* ====================== hook implementations ====================== */
129

    
130

    
131
/**
132
 * Implementation of hook_perm()
133
 *
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 * Valid permissions for this module
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 * @return array An array of valid permissions for the portfolio module
136
 */
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function cdm_dataportal_perm() {
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  return array(
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      'administer cdm_dataportal',
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      'cdm_dataportal view notes',
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  //TODO which else permission are required? -> check the WP6 requirements document
142
  );
143
}
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145

    
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/**
147
 * Implementation of hook_menu()
148
 */
149
function cdm_dataportal_menu($may_cache) {
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  $items = array();
151

    
152
  cdm_dataportal_menu_admin($may_cache, $items);
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  cdm_dataportal_menu_help($may_cache, $items);
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155
  if ($may_cache) {
156

    
157
   $items[] = array(
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      'path' => 'cdm_dataportal/names',
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      'callback' => 'cdm_dataportal_view_names',
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      'access' => true,
161
      'type' => MENU_CALLBACK,
162
    );
163
    // optional callback arguments: page
164

    
165
    $items[] = array(
166
      'path' => 'cdm_dataportal/taxon',
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      'callback' => 'cdm_dataportal_taxon_page_view',
168
      'access' => true,
169
      'type' => MENU_CALLBACK,
170
    // expected callback arguments: uuid
171
    );
172

    
173
    $items[] = array(
174
      'path' => 'cdm_dataportal/name',
175
      'callback' => 'cdm_dataportal_name_page_view',
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      'access' => true,
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      'type' => MENU_CALLBACK,
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    // expected callback arguments: uuid
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    );
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181
    $items[] = array(
182
      'path' => 'cdm_dataportal/reference',
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      'callback' => 'cdm_dataportal_view_reference',
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      'access' => true,
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      'type' => MENU_CALLBACK,
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    // expected callback arguments: uuid
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    );
188

    
189
    $items[] = array(
190
      'path' => 'cdm_dataportal/reference/list',
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      'callback' => 'cdm_dataportal_view_reference_list',
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      'access' => true,
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      'type' => MENU_CALLBACK,
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    // expected callback arguments: uuid
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    );
196

    
197
    $items[] = array(
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      'path' => 'cdm_dataportal/media',
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      'callback' => 'cdm_dataportal_view_media',
200
      'access' => true,
201
      'type' => MENU_CALLBACK,
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    // expected callback arguments: uuid, mediarepresentation_uuid, part_uuid or part#
203
    );
204

    
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    $items[] = array(
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      'path' => 'cdm_dataportal/polytomousKey',
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      'callback' => 'cdm_dataportal_view_polytomousKey',
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      'access' => true,
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      'type' => MENU_CALLBACK,
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    // expected callback arguments: polytomousKey->uuid
211
    );
212

    
213
    $items[] = array(
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      'path' => 'cdm_dataportal/search',
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      'callback' => 'cdm_dataportal_view_search_advanced',
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      'access' => true,
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      'type' => MENU_CALLBACK,
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    );
219

    
220
    $items[] = array(
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      'path' => 'cdm_dataportal/search/taxon',
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      'callback' => 'cdm_dataportal_view_search_taxon',
223
      'access' => true,
224
      'type' => MENU_CALLBACK,
225
    );
226

    
227
    $items[] = array(
228
      'path' => 'cdm/xml2json',
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      'callback' => 'cdm_view_xml2json',
230
      'access' => true,
231
      'type' => MENU_CALLBACK,
232
    );
233

    
234
  }elseif (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid)) {
235
    //user configuration of cdm_dataportal
236
    $items[] = array('path' => 'user/'.$uid.'/cdm_dataportal',
237
        'title' => t('cdm_dataportal'),
238
        'access' => TRUE,
239
        'callback' => 'drupal_get_form',
240
        'callback arguments' => array('cdm_dataportal_user_form'),
241
        'type' => MENU_LOCAL_TASK,
242
        'weight' => 10,
243
      );
244
  } else {
245
    // may not cache
246
    // --- local tasks for Taxon
247
    $items[] = array(
248
      'path' => 'cdm_dataportal/name/'.arg(2),
249
    //'callback' => 'cdm_dataportal_view_name',
250
      'callback' => 'cdm_dataportal_name_page_view',
251
      'callback arguments' => array(arg(2), arg(3), arg(4)),
252
      'access' => true,
253
      'type' => MENU_CALLBACK,
254
    );
255

    
256
    if(variable_get('cdm_dataportal_taxonpage_tabs', 1)) {
257

    
258
      $items[] = array(
259
      'path' => 'cdm_dataportal/taxon/'.arg(2),
260
      'title' => theme('cdm_taxonpage_tab', 'General'),
261
      'callback' => 'cdm_dataportal_taxon_page_view',
262
      'access' => true,
263
      'type' => MENU_CALLBACK,
264
      'weight' => 1,
265
      'callback arguments' => array(arg(2), "description")
266
      // expected callback arguments: name_uuid
267
      );
268

    
269
      $items[] = array(
270
      'path' => 'cdm_dataportal/taxon/'.arg(2).'/all',
271
      'title' => theme('cdm_taxonpage_tab', 'General'),
272
      'callback' => 'cdm_dataportal_taxon_page_view',
273
      'access' => true,
274
      'type' => MENU_CALLBACK,
275
      'weight' => 2,
276
      'callback arguments' => array(arg(2), "all")
277
      // expected callback arguments: name_uuid
278
      );
279

    
280
      $items[] = array(
281
      'path' => 'cdm_dataportal/taxon/'.arg(2).'/description',
282
      'title' => theme('cdm_taxonpage_tab', 'General'),
283
      'callback' => 'cdm_dataportal_taxon_page_view',
284
      'access' => true,
285
      'type' => MENU_DEFAULT_LOCAL_TASK,
286
      'weight' => 2,
287
      'callback arguments' => array(arg(2), "description")
288
      // expected callback arguments: name_uuid
289
      );
290

    
291
      $items[] = array(
292
      'path' => 'cdm_dataportal/taxon/'.arg(2).'/synonymy',
293
      'title' => theme('cdm_taxonpage_tab', 'Synonymy'),
294
      'callback' => 'cdm_dataportal_taxon_page_view',
295
      'access' => true,
296
      'type' => MENU_LOCAL_TASK,
297
      'weight' => 4,
298
      'callback arguments' => array(arg(2), "synonymy", arg(4))
299
      // expected callback arguments: name_uuid
300
      );
301
      $items[] = array(
302
      'path' => 'cdm_dataportal/taxon/'.arg(2).'/images',
303
      'title' => theme('cdm_taxonpage_tab', 'Images'),
304
      'callback' => 'cdm_dataportal_taxon_page_view',
305
      'access' => true,
306
      'type' => MENU_LOCAL_TASK,
307
      'weight' => 5,
308
      'callback arguments' => array(arg(2), "images")
309
      // expected callback arguments: name_uuid
310
      );
311

    
312
     $items[] = array(
313
     'path' => 'cdm_dataportal/taxon/'.arg(2).'/specimens',
314
     'title' => theme('cdm_taxonpage_tab', 'Specimens'),
315
     'callback' => 'cdm_dataportal_taxon_page_view',
316
     'access' => true,
317
     'type' => MENU_LOCAL_TASK,
318
     'weight' => 6,
319
     'callback arguments' => array(arg(2), "specimens")
320
     // expected callback arguments: name_uuid
321
     );
322

    
323
     $items[] = array(
324
     'path' => 'cdm_dataportal/taxon/'.arg(2).'/keys',
325
     'title' => theme('cdm_taxonpage_tab', 'Keys'),
326
     'callback' => 'cdm_dataportal_taxon_page_view',
327
     'access' => true,
328
     'type' => MENU_LOCAL_TASK,
329
     'weight' => 6,
330
     'callback arguments' => array(arg(2), "keys")
331
     // expected callback arguments: name_uuid
332
     );
333
    }
334
  }
335

    
336
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal.css');
337
  //drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_print.css', 'print');
338
  drupal_add_css(drupal_get_path('module', 'cdm_dataportal').'/cdm_dataportal_screen.css', 'screen');
339

    
340
  return $items;
341

    
342
}
343
/**
344
 * The function generate form for own user cdm dataportal configurations
345
 */
346
function cdm_dataportal_user_form() {
347

    
348
  global $user;
349
    $checkbox_value = 'cdm_dataportal_' .$user->uid . '_default_tab_active';
350

    
351
  $form['check'] = array
352
    (
353
    '#type'            => 'checkbox',
354
    '#title'         => t('Activate user default configuration'),
355
    '#default_value'   => variable_get($checkbox_value, 0),
356
    '#description' => t('Check this if you want configure your own default tab from the below menu.')
357
    );
358

    
359
  $form['cdm_dataportal_user_form'] =  array(
360
      '#type'          => 'select',
361
      '#title'         => t('Default tab to display'),
362
      '#default_value' => get_default_taxon_tab(true),
363
      '#options'       => unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB),
364
      '#description'   => t('<p>Select the default tab to display when visiting a taxon page. Only available if Tabbed Taxon Page is enable.</p>
365
              <strong>Note:</strong> After performing a search and clicking in any synonym, the taxon tab
366
              to be renderized will be the synonymy of the accepted taxon and not the above selected tab.'),
367
  );
368

    
369
  $form['submit'] = array(
370
    '#type' => 'submit',
371
    '#value' => t('Submit')
372
  );
373

    
374
  return $form;
375
}
376

    
377
/**
378
 * The function submit the user cdm dataportal configurations
379
 * @param unknown_type $form
380
 * @param unknown_type $form_values
381
 */
382
function cdm_dataportal_user_form_submit($form, $form_values) {
383
  global $user;
384
  $msg_type = 'status';
385
  $username = $user->name;
386
  $variable_to_use = 'cdm_dataportal_' .$user->uid . '_default_tab';
387

    
388
  //if is the right user the variables are setted
389
  if (arg(0)=='user' && ($uid=arg(1)) && is_numeric($uid) && $user->uid==$uid){
390
    $variable = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
391
    variable_set($variable_to_use . '_active', $form_values['check']);
392
    variable_set($variable_to_use, $form_values['cdm_dataportal_user_form']);
393
    if ($form_values['check']){
394
      drupal_set_message('The user default tab will be used for the next taxon site visit.');
395
      drupal_set_message('The user default tab have been changed to: '
396
            . $variable[variable_get($variable_to_use, 0)]
397
            . ' for the user ' . $username, $msg_type);
398
    }else{
399
      drupal_set_message('The user default tab wont be used for the next taxon site, check the box if you want to use the user default configuration.');
400
    }
401
  //problem with the user id => variables wont be saved
402
  }else{
403
    $msg_type = 'warning';
404
    drupal_set_message('Default tab have not been saved due to user id problems', $msg_type);
405
  }
406
}
407

    
408
/**
409
 * Implementation of hook_block()
410
 *
411
 * Provides the following blocks:
412
 *  0: list of links useful during development
413
 *
414
 * @param String $op
415
 * @param int $delta
416
 */
417
function cdm_dataportal_block($op='list', $delta=0) {
418
  // listing of blocks, such as on the admin/block page
419
  if ($op == "list") {
420
    //$block[0]["info"] = t("CDM DataPortal DevLinks");
421
    //		$block[1]["info"] = t("CDM DataPortal Credits");
422
    $block[2]["info"] = t("CDM Search Taxa");
423
    //$block[3]["info"] = t("CDM Filters");
424
    $block[4]["info"] = t("CDM Dataportal Print");
425
    $block["keys"]["info"] = t("CDM identification keys");
426
    return $block;
427
  }
428
  else if ($op == 'view') {
429
    switch($delta){
430
      //			case 1:
431
      //				$block['subject'] = t('Credits');
432
      //				$block['content'] = theme('cdm_credits');
433
      //				return $block;
434
      case 2:
435
        $block['subject'] = t('Search taxa');
436
        $block['content'] = drupal_get_form('cdm_dataportal_search_taxon_form');
437
        if (variable_get('cdm_dataportal_show_advanced_search', 1)){
438
            $block['content'] .= '<div>'.l('Advanced Search', '/cdm_dataportal/search').'</div>';
439
        }
440
        return $block;
441
      case 4:
442
        $block['subject'] = t('<none>');
443
        $block['content'] = theme('cdm_print_button');;
444
        return $block;
445
      case "keys":
446
        $block['subject'] = t('Identification Keys');
447
        $block['content'] = theme('cdm_block_IdentificationKeys');
448
        return $block;
449
    }
450
  }
451
}
452

    
453

    
454

    
455
/*
456
 function cdm_dataportal_session_clear($cdm_ws_uri_update = false){
457
 $_SESSION['cdm'] = null;
458
 if(is_string($cdm_ws_uri_update)){
459
 $_SESSION['cdm'] = array('ws_uri'=>$cdm_ws_uri_update);
460
 }
461
 }
462

    
463
 function cdm_dataportal_session_validate(){
464

    
465
 if(!isset($_SESSION['cdm']['ws_uri'])){
466
 $_SESSION['cdm'] = array('ws_uri'=>variable_get('cdm_webservice_url', false));
467
 } else if($_SESSION['cdm']['ws_uri'] != variable_get('cdm_webservice_url', false)){
468
 cdm_dataportal_session_clear(variable_get('cdm_webservice_url', false));
469
 }
470
 }
471
 */
472

    
473
function cdm_dataportal_search_taxon_form($advancedForm = false){
474

    
475
  $preset_query = (isset($_SESSION['cdm']['search']['query']) ? $_SESSION['cdm']['search']['query'] : '');
476
  $preset_doTaxa = (isset($_SESSION['cdm']['search']['doTaxa']) ? 1 : 0);
477
  $preset_doSynonyms = (isset($_SESSION['cdm']['search']['doSynonyms']) ? 1 : 0);
478
  $preset_doTaxaByCommonNames = (isset($_SESSION['cdm']['search']['doTaxaByCommonNames']) ? 1 : 0);
479
  $tdwg_level_select =  (isset($_SESSION['cdm']['search']['tdwg_level_select']) ? $_SESSION['cdm']['search']['tdwg_level_select'] : 2);
480
  $selected_areas =  (isset($_SESSION['cdm']['search']['area']) ? $_SESSION['cdm']['search']['area'] : false);
481

    
482
  $url = 'cdm_dataportal/search/taxon';
483
  $form['#method'] = 'get';
484
  $form['#process'] = array('cdm_dataportal_search_process' => array());
485
  $form['#action'] = url($url, NULL, NULL, true);
486

    
487
  $form['query'] = array(
488
    '#delta' => 0,
489
    '#type' => 'textfield',
490
    '#size' => 20,
491
    '#attributes' => array('title' => t('Enter the name or part of a name you wish to search for. The asterisk  character * can always be used as wildcard')),
492
    '#value' => $preset_query,
493
  );
494

    
495
  $form['search'] = array(
496
      '#delta' => 1,
497
      '#tree' => true,
498
  //'#type' => $advancedForm ? 'fieldset': 'hidden',
499
      '#title' => t('Options')
500
  );
501

    
502
  $form['search']['tree'] = array(
503
    '#delta' => -1,
504
    '#type' => 'hidden',
505
    '#value' => get_taxonomictree_uuid_selected()
506
  );
507

    
508

    
509
  // clean URL get forms breaks if we don't give it a 'q'.
510
  if (!(bool)variable_get('clean_url', '0')) {
511
    $form['search']['q'] = array(
512
      '#delta' => -1,
513
      '#type' => 'hidden',
514
      '#value' => $url,
515
      '#name' => 'q',
516
    );
517
  }
518

    
519
  $form['search']['pageSize'] = array(
520
      '#delta' => -1,
521
      '#type' => 'hidden',
522
      '#value' => variable_get('cdm_dataportal_search_items_on_page', 25)
523
  );
524

    
525
  $form['search']['pageNumber'] = array(
526
      '#delta' => -1,
527
      '#type' => 'hidden',
528
      '#value' => 0
529
  );
530

    
531
  if($advancedForm){
532
    // general search parameters
533
    $form['search']['doTaxa'] = array(
534
      '#delta' => 2,
535
      '#type' => 'checkbox',
536
      '#title' => t('Search for accepted taxa'),
537
      '#value' => $preset_doTaxa
538
    );
539
    $form['search']['doSynonyms'] = array(
540
      '#delta' => 3,
541
      '#type' => 'checkbox',
542
      '#title' => t('Search for synonyms'),
543
      '#value' => $preset_doSynonyms
544
    );
545
    $form['search']['doTaxaByCommonNames'] = array(
546
      '#delta' => 4,
547
      '#type' => 'checkbox',
548
      '#title' => t('Search for common names'),
549
      '#value' => $preset_doTaxaByCommonNames
550
    );
551

    
552
    // Geographic Range
553
    $form['search']['geographic_range'] = array(
554
      '#type' => 'fieldset',
555
      '#delta' => 5,
556
      '#tree' => true,
557
      '#title' => t('Geographic range'),
558
    );
559

    
560
    $form['search']['geographic_range']['tdwg_level_select'] = array(
561
    '#type' => 'radios',
562
    '#title' => t('Select a TDWG distribution level and code'),
563
    '#default_value' => $tdwg_level_select,
564
    '#options' => array(
565
    t('TDWG level-1, i.e. a continent'),
566
    t('TDWG level-2'),
567
    t('TDWG level-3, i.e. a country'),
568
    t('TDWG level-4')
569
    )
570
    );
571
    $tdwg[1] = cdm_ws_get(CDM_WS_TDWG_LEVEL, '1');
572
    $tdwg[2] = cdm_ws_get(CDM_WS_TDWG_LEVEL, '2');
573
    $tdwg[3] = cdm_ws_get(CDM_WS_TDWG_LEVEL, '3');
574
    $tdwg[4] = cdm_ws_get(CDM_WS_TDWG_LEVEL, '4');
575

    
576
    $tdwg_js = '';
577
    foreach($tdwg as $key=>$tdwg_level){
578
      $tdwgOptions = array();
579
      $tdwgOptionsSelected = array();
580
      foreach($tdwg_level as $area){
581
        $representation = $area->representations[0];
582
        $tdwgOptions[$representation->abbreviatedLabel] = $area->representation_L10n;
583
        if(is_array($selected_areas) && in_array($representation->abbreviatedLabel, $selected_areas)){
584
          $tdwgOptionsSelected[] = $representation->abbreviatedLabel; //$area->uuid;
585
        }
586
      }
587
      asort($tdwgOptions);
588
      $form['search']['geographic_range']['tdwg_level_'.$key] = array(
589
        '#type' => 'select',
590
        '#title'         => t('TDWG level').' '.$key,
591
        '#default_value' => $tdwgOptionsSelected,
592
        '#multiple' => TRUE,
593
        '#options' => $tdwgOptions
594
      );
595
      $tdwg_js .= "$('#edit-search-geographic-range-tdwg-level-$key').parent()".($tdwg_level_select + 1 == $key ?  '.show()' : '.hide()'). ";\n";
596
    }
597

    
598
    drupal_add_js(
599
    "$(document).ready(function(){
600

    
601
      $(\"input[@name='search[geographic_range][tdwg_level_select]']\").change(
602
        function(event){
603
          var selectId = $(\"input[@name='search[geographic_range][tdwg_level_select]']:checked\").val();
604
          var i;
605
          for(i = 0; i < 4; i++){
606
            if(selectId == i){
607
              $('#edit-search-geographic-range-tdwg-level-' + (i + 1) ).parent().fadeIn('slow');
608
              $('#edit-search-geographic-range-tdwg-level-' + (i + 1)).children().removeAttr('selected');
609
            } else {
610
              $('#edit-search-geographic-range-tdwg-level-' + (i + 1)).parent().fadeOut('slow');
611
              $('#edit-search-geographic-range-tdwg-level-' + (i + 1)).children().removeAttr('selected');
612
            }
613
          }
614
        }
615
      );
616

    
617
      $tdwg_js
618
    });",
619
    'inline');
620

    
621
  } else {
622
    $form['search']['doTaxa'] = array(
623
        '#delta' => -2,
624
        '#type' => 'hidden',
625
        '#value' => 1
626
    );
627
    $form['search']['doSynonyms'] = array(
628
        '#delta' => -3,
629
        '#type' => 'hidden',
630
        '#value' => 1
631
    );
632
    $form['search']['doTaxaByCommonNames'] = array(
633
        '#delta' => -4,
634
        '#type' => 'hidden',
635
        '#value' => 0
636
    );
637
  }
638

    
639
  $form['submit'] = array(
640
    '#delta' => 9,
641
    '#type' => 'submit',
642
    '#name' => '',
643
    '#value' => t('Search')
644
  );
645

    
646
  return $form;
647
}
648

    
649
function cdm_dataportal_search_taxon_form_advanced(){
650
  return cdm_dataportal_search_taxon_form(true);
651
}
652

    
653
function cdm_taxonomictree_selector(){
654
  _add_js_treeselector();
655

    
656
  $out = drupal_get_form('cdm_taxonomictree_selector_form');
657

    
658
  return $out;
659
}
660

    
661

    
662
function cdm_taxonomictree_selector_form(){
663

    
664
  $url = url('cdm_api/setvalue/session', null);
665
  $form['#action'] = $url;
666

    
667
  $form['var'] = array(
668
        '#delta' => -3,
669
        '#type' => 'hidden',
670
        '#value' => '[cdm][taxonomictree_uuid]'
671
        );
672

    
673
        $form['destination'] = array(
674
     '#delta' => -3,
675
     '#type' => 'hidden',
676
     '#value' => substr(drupal_get_destination(), strlen('destination='))
677
        );
678

    
679
        $form['val'] = array(
680
      '#type' => 'select',
681
      '#title'         => t('Available classifications'),
682
      '#default_value' => get_taxonomictree_uuid_selected(),
683
      '#options' => cdm_get_taxontrees_as_options()
684
        );
685

    
686
        return $form;
687

    
688
}
689

    
690
/**
691
 * Implementation #process method call, see form_builder()
692
 * <p>
693
 * Removes Drupal internal form elements from query
694
 * @param $form
695
 * @return unknown_type
696
 */
697
function cdm_dataportal_search_process($form) {
698
  unset($form['form_id']);
699
  unset($form['form_token']);
700
  return $form;
701
}
702

    
703
/**
704
 * Filters $_REQUEST by a list of valid request  parameters and also sets defaults if required.
705
 * returns the processed request parameters submitted by the search form.
706
 */
707
function cdm_dataportal_search_form_request(){
708

    
709

    
710
  $form_params = array();
711
  array_deep_copy($_REQUEST['search'], $form_params);
712
  $form_params['query'] =  trim($_REQUEST['query']);
713

    
714
  // split of  geographic range
715
  if(isset($_REQUEST['search']['geographic_range'])){
716
    $geographicRange = $_REQUEST['search']['geographic_range'];
717
    // remove
718
    unset($form_params['geographic_range']);
719
  }
720

    
721
  // add geographic range
722
  if($geographicRange){
723
    $form_params['tdwg_level_select'] = $geographicRange['tdwg_level_select'];
724
    for($i = 1; $i < 5; $i++){
725
      if(isset($geographicRange['tdwg_level_'.$i])){
726
        $form_params['area'] = $geographicRange['tdwg_level_'.$i];
727
      }
728
    }
729
  }
730

    
731
  // store in session
732
  $_SESSION['cdm']['search'] = $form_params;
733

    
734
  return $form_params;
735
}
736

    
737

    
738
/* UNREACHABLE since action of form directly links to view
739
 function cdm_dataportal_search_taxon_form_submit($form_id, $form_values) {
740

    
741
 $_SESSION['cdm']['search'] = $form_values;
742
 //return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['vernacular']?'1':'0').'/'.$form_values['language'];
743
 return '/cdm_dataportal/search/taxon/'.$form_values['queryString'].'/'.($form_values['onlyAccepted']?'1':'0');
744
 //$paramstr = compose_url_prameterstr($form_values);
745
 //return url('/cdm_dataportal/search/taxon/', $paramstr);
746
 }
747
 */
748
/* ====================== menu callback functions ====================== */
749

    
750

    
751

    
752
function cdm_dataportal_form_alter($form_id, &$form) {
753

    
754
  static $comment_node_disabled =  0;
755
  static $comment_node_read_only =  1;
756
  static $comment_node_read_write =  2;
757

    
758

    
759
  if ($form_id == 'node_type_form'
760
  && isset($form['identity']['type'])
761
  && array_key_exists($form['#node_type']->type, cdm_get_nodetypes())
762
  ) {
763
    $form['workflow']['comment'] = array(
764
      '#type' => 'radios',
765
      '#title' => t('Default comment setting'),
766
      '#default_value' => variable_get('comment_'. $form['#node_type']->type, $comment_node_disabled),
767
      '#options' => array(t('Disabled'), t('Read only'), t('Read/Write')),
768
      '#description' => t('Users with the <em>administer comments</em> permission will be able to override this setting.'),
769
    );
770
  }
771
}
772

    
773

    
774

    
775
function cdm_dataportal_create_gallery_settings_form($form_name, $form_tittle, $collapsed, $form_description = ''){
776
//TODO move into settings.php
777
  $form[$form_name] = array(
778
    '#type' => 'fieldset',
779
    '#title' => t($form_tittle),
780
    '#collapsible' => TRUE,
781
    '#collapsed' => $collapsed,
782
    '#tree' => true,
783
  '#description' => t($form_description),
784
  );
785

    
786
  $default_values = unserialize(CDM_DATAPORTAL_GALLERY_SETTINGS);
787
  $gallery_settings = variable_get($form_name, $default_values);
788
  //$test = variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE);
789

    
790
  if($form_name == CDM_DATAPORTAL_SEARCH_GALLERY_NAME){
791
    /* TODO: why cdm_dataportal_search_items_on_page does not save the value on $test???
792
     $form[$form_name]['cdm_dataportal_search_items_on_page'] = array(
793
     '#type' => 'textfield',
794
     '#title' => t('Search Page Size'),
795
     '#default_value' => $test,
796
     '#description' => t('Number of Names to display per page in search results.')
797
     );
798
     */
799
    $form[$form_name]['cdm_dataportal_show_taxon_thumbnails'] = array(
800
      '#type' => 'checkbox',
801
      '#title' => t('Show media thumbnails for accepted taxa'),
802
      '#default_value' => $gallery_settings['cdm_dataportal_show_taxon_thumbnails'],
803
    );
804

    
805
    $form[$form_name]['cdm_dataportal_show_synonym_thumbnails'] = array(
806
      '#type' => 'checkbox',
807
      '#title' => t('Show media thumbnails for synonyms'),
808
      '#default_value' => $gallery_settings['cdm_dataportal_show_synonym_thumbnails'],
809
      '#description' => t('')
810
    );
811
  }
812

    
813
  //$showCaption = variable_get('cdm_dataportal_findtaxa_show_thumbnail_captions', 0);
814
  $form[$form_name]['cdm_dataportal_show_thumbnail_captions'] = array(
815
    '#type' => 'checkbox',
816
    '#title' => t('Show captions under thumbnails'),
817
    '#default_value' => $gallery_settings['cdm_dataportal_show_thumbnail_captions'],
818
    '#description' => t('')
819
  );
820

    
821
  $form[$form_name]['cdm_dataportal_media_maxextend'] = array(
822
    '#type' => 'textfield',
823
    '#title' => t('Thumbnail size'),
824
    '#default_value' => $gallery_settings['cdm_dataportal_media_maxextend'],
825
    '#description' => t('Select the size of each individual thumbnail.')
826
  );
827

    
828
  if($form_name != CDM_DATAPORTAL_MEDIA_GALLERY_NAME){
829
     $form[$form_name]['cdm_dataportal_media_cols'] = array(
830
        '#type' => 'textfield',
831
        '#title' => t('Number of columns'),
832
        '#default_value' => $gallery_settings['cdm_dataportal_media_cols'],
833
        '#description' => t('Group the thumbnails in columns: select how many columns should the gallery display.')
834
     );
835
  }
836

    
837
  if($form_name == CDM_DATAPORTAL_SEARCH_GALLERY_NAME){
838
    $form[$form_name]['cdm_dataportal_media_maxRows'] = array(
839
      '#type' => 'textfield',
840
      '#title' => t('Maximum number of rows'),
841
      '#default_value' => $gallery_settings['cdm_dataportal_media_maxRows'],
842
      '#description' => t('You can group the thumbnails in rows, select in how many rows should be the thumbnails grouped.<br>
843
                           <b>Note:</b> If you want an unlimited number of rows please set to 0')
844
    );
845
  }
846

    
847
  return $form;
848
}
849

    
850

    
851
/**
852
 * Displays a list of the known taxonomic names. Long lists are split up into multiple pages
853
 *
854
 * TODO: parameters are still preliminar
855
 * @param String $page page number to diplay defaults to page 1
856
 * @param boolean $hide_unaccepted whether to hide nams which are not accepted by the current view
857
 */
858
function cdm_dataportal_view_names($beginsWith = 'A', $page = 1, $onlyAccepted = false ){
859

    
860
  $request_params  = array(
861
    'q' => $beginsWith,
862
  //'sec' = '',
863
  //'higherTaxa' => getFiters(),
864
  // 'matchAnywhere' => false, // default is false
865
    'page' => $page,
866
    'onlyAccepted' => $onlyAccepted,
867
    'pagesize' => 20  /*$_SESSION['cdm']['namelist_pagesize'] */);
868

    
869
  $taxonPager = cdm_ws_find(CDM_WS_PORTAL_TAXON_FIND, $request_params);
870
  /*
871
   * FIXME the filter for accepted names will be a form element, thus this widget
872
   * should be generated via form api preferably as block
873
   */
874
  //$out  = theme('cdm_dataportal_widget_filter_accepted', $onlyAccepted);
875
  //$out .= theme('cdm_dataportal_widget_names_list', $names, $page);
876
  $out .= theme('cdm_listof_taxa', $taxonPager);
877
  return $out;
878
}
879

    
880
function cdm_dataportal_view_reference($uuid, $arg2 = null){
881
  $reference = cdm_ws_get(CDM_WS_REFERENCE, $uuid);
882
  return theme('cdm_reference_page', $reference);
883
}
884

    
885
function cdm_dataportal_view_reference_list($pageNumber){
886
  $referencePager = cdm_ws_page(CDM_WS_REFERENCE, variable_get('cdm_dataportal_search_items_on_page', CDM_DATAPORTAL_SEARCH_ITEMS_ON_PAGE), $pageNumber);
887
  return theme('cdm_reference_pager', $referencePager, 'cdm_dataportal/reference/list/');
888
}
889

    
890
function cdm_dataportal_view_media($mediaUuid, $mediarepresentation_uuid = false, $part = 0){
891
  $media = cdm_ws_get(CDM_WS_PORTAL_MEDIA, $mediaUuid);
892
  return theme('cdm_media_page', $media, $mediarepresentation_uuid, $part);
893
}
894

    
895
function _load_taxonBase(&$taxonBase){
896
  if(isset($taxonBase->uuid)){
897
      $taxonBase->name = cdm_ws_get(CDM_WS_TAXON, array($taxonBase->uuid, "name"));
898
      $taxonBase->name->taggedName = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "taggedName"));
899
      $taxonBase->name->nomenclaturalReference = cdm_ws_get(CDM_WS_NAME, array($taxonBase->name->uuid, "nomenclaturalReference"));
900
    }
901
}
902

    
903
/**
904
 * similar to the variable_get() function of Drupal, except of thst this function
905
 * is able to handle arrays correctly. This function is especially useful
906
 * when dealing with collections of setting form elemens (#tree = true)
907
 *
908
 * @param String $variableKey
909
 * @param String $defaultValueString a sting as for example derived from a CONSTANT
910
 * @return mixed, usually an array
911
 */
912
function mixed_variable_get($variableKey, $defaultValueString){
913
    $systemDefaults = unserialize($defaultValueString);
914
    $storedSettings = variable_get($variableKey, array());
915
    if(is_array($storedSettings)){
916
      $settings =  array_merge($systemDefaults, $storedSettings);
917
    } else {
918
      $settings = $systemDefaults;
919
    }
920
    return $settings;
921
}
922

    
923
/**
924
 * Loads the subgraph of the given PolytomousKeyNode recursively from the cdm REST service.
925
 * @param PolytomousKeyNode $polytomousKeyNode passed by reference
926
 * @return nothing
927
 */
928
function _load_polytomousKeySubGraph(&$polytomousKeyNode){
929

    
930
  if(!$polytomousKeyNode){
931
    return;
932
  }
933
  if($polytomousKeyNode->class != "PolytomousKeyNode"){
934
    drupal_set_message("_load_polytomousKeySubGraph() invalid type given.", "error");
935
    return;
936
  }
937
  if(!is_uuid($polytomousKeyNode->uuid)){
938
    drupal_set_message("_load_polytomousKeySubGraph() invalid type given.", "error");
939
    return;
940
  }
941

    
942
  $polytomousKeyNode = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, $polytomousKeyNode->uuid);
943

    
944
  if(!$polytomousKeyNode){
945
    //drupal_set_message("_load_polytomousKeyChildNodes() : could not load polytomousKeyNode", "error");
946
    return;
947
  }
948

    
949
  // load children
950
  foreach($polytomousKeyNode->children as &$childNode){
951
    _load_polytomousKeySubGraph($childNode);
952
  }
953

    
954
  // load subkey
955
  $polytomousKeyNode->subkey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "subkey"));
956

    
957
  // load taxon
958
  $polytomousKeyNode->taxon = cdm_ws_get(CDM_WS_POLYTOMOUSKEY_NODE, array($polytomousKeyNode->uuid, "taxon"));
959
  _load_taxonBase($polytomousKeyNode->taxon);
960
  return;
961
}
962

    
963
function cdm_dataportal_view_polytomousKey($polytomousKeyUuid){
964
  $polytomousKey = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, $polytomousKeyUuid);
965

    
966
  $sourcePager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, "sources"));
967
  if(is_array($sourcePager->records)){
968
    $polytomousKey->sources =  $sourcePager->records;
969
    //$polytomousKey->sources->citation = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, "sources"));
970
  }
971

    
972
  $annotationPager = cdm_ws_get(CDM_WS_POLYTOMOUSKEY, array($polytomousKeyUuid, "annotations"));
973
  if(is_array($annotationPager->records)){
974
    $polytomousKey->annotations = $annotationPager->records;
975
  }
976

    
977
  _load_polytomousKeySubGraph($polytomousKey->root);
978
  return theme('cdm_polytomousKey_page', $polytomousKey);
979
}
980

    
981
/**
982
 * The taxon page gives detailed information on a taxon, it shows:
983
 *  - Taxon name
984
 *  - Full list of synonyms homotypic synonyms on top, followed by the
985
 *    heterotypic and finally followed by misapplied names.
986
 *    The list is ordered historically.
987
 *  - All description associated with the taxon.
988
 *
989
 * @param $uuid
990
 * @param $chapter name of the part to display,
991
 *         valid values are: 'description', 'images', 'synonymy', 'specimens', 'all'
992
 * @return unknown_type
993
 */
994
function cdm_dataportal_taxon_page_view($uuid, $chapter = 'all', $synonym_uuid = null){
995
  // display the page for the taxon defined by $uuid
996
  set_last_taxon_page_tab(arg(3));
997
  $taxonpage = cdm_dataportal_taxon_view($uuid, $chapter, $synonym_uuid);
998
  return cdm_node_show(NODETYPE_TAXON, $uuid, $taxonpage->title , $taxonpage->content);
999
}
1000

    
1001
/**
1002
 * @param $uuid
1003
 * @param $chapter name of the part to display,
1004
 *         valid values are: 'description', 'images', 'synonymy', 'all'
1005
 * @return unknown_type
1006
 */
1007
function cdm_dataportal_taxon_view($uuid, $chapter = 'all', $synonym_uuid = null){
1008
  $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON, $uuid);
1009
  if(!$taxon){
1010
    drupal_set_title(t('Taxon does not exist'));
1011
    return false;
1012
  }
1013

    
1014
  $taxonpage->title = theme('cdm_taxon_page_title', $taxon, $uuid, $synonym_uuid);
1015

    
1016
  // check if the taxon id contained in the currently selected tree
1017
  $taxon_in_current_tree = taxon_in_current_tree($uuid);
1018
  $taxon_nodes = cdm_ws_get(CDM_WS_PORTAL_TAXON_TAXONNODES, $uuid);
1019
  if(!$taxon_in_current_tree){
1020
    if(count($taxon_nodes) == 0){
1021
      drupal_set_message('This concept of the taxon '.theme('cdm_taxonName', $taxon->name).' is not contained any classification.'
1022
      ,'warning');
1023
    } else {
1024
      $trees = '';
1025
      foreach($taxon_nodes as $node){
1026
        $trees .= ($trees?', ':'').'<strong>'.$node->classification->titleCache.'</strong>';
1027

    
1028
      }
1029
      drupal_set_message('This concept of the taxon '.theme('cdm_taxonName', $taxon->name).' is not contained in the currently chosen classification, but in '
1030
      .(count($taxon_nodes) > 1? ' one of these: ' : ' this one: ') . $trees
1031
      , 'warning');
1032
    }
1033
  }
1034

    
1035
  // render the taxon page
1036
  $taxonpage->content = theme('cdm_taxon_page', $taxon, $chapter);
1037

    
1038
  return $taxonpage;
1039
}
1040

    
1041
/**
1042
 * The function returns a name page as a drupal node ready to be renderized by drupal.
1043
 * The node page show the taxon name title and the list of taxon related with such taxon
1044
 * name on the tree already in used.
1045
 * @param $taxon_name_uuid A taxon name uuid
1046
 * @return The formatted name page as node
1047
 */
1048
function cdm_dataportal_name_page_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = null){
1049
  $taxonname_page = cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid);
1050
  return cdm_node_show(NODETYPE_NAME, $taxon_name_uuid, $taxonname_page->title , $taxonname_page->content);
1051
}
1052

    
1053
/**
1054
 * The function genates a object ready to be transformated to a node
1055
 * in order to show as a drupal node
1056
 * @param $taxon_name_uuid
1057
 * @return the object with the page content and title
1058
 */
1059
function cdm_dataportal_name_view($taxon_name_uuid, $taxon_to_hide_uuid, $synonym_uuid = null){
1060
  //getting the full taxonname object from the server
1061
  $taxon_name = cdm_ws_get(CDM_WS_NAME, array($taxon_name_uuid));
1062
  if(!$taxon_name){
1063
    drupal_set_title(t('Taxon name does not exist'));
1064
    return false;
1065
  }
1066
  //searching for all the taxa connected with the taxon name on the tree in used
1067
  $name_cache = cdm_ws_get(CDM_WS_NAME_NAMECAHE, array($taxon_name_uuid));
1068
  $request_params = array();
1069
  $request_params['query'] = $name_cache;
1070
  $request_params['tree'] = get_taxonomictree_uuid_selected();
1071
  $request_params['doTaxa'] = 1;
1072
  $request_params['doSynonyms'] = 1;
1073
  $request_params['doTaxaByCommonNames'] = 0;
1074
  $request_params['matchMode'] = "EXACT";
1075
  $taxon_pager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, null, queryString($request_params));
1076

    
1077
  //removing the name where we come from and
1078
  foreach($taxon_pager->records as $k=>&$taxon){
1079
    if($taxon->uuid == $taxon_to_hide_uuid){
1080
      unset($taxon_pager->records[$k]);
1081
    }
1082
  }
1083
  //show the taxa list or go to the singular taxon
1084
  if (sizeof($taxon_pager->records) == 1){ //sigle taxon case
1085
    reset($taxon_pager->records);
1086
    $singleTaxon = $taxon_pager->records[0];
1087
    if($singleTaxon->class != "Taxon"){
1088
      // it is a Synonym -> look for the accepted
1089
      $taxon = cdm_ws_get(CDM_WS_PORTAL_TAXON_ACCEPTED, array($singleTaxon->uuid, get_taxonomictree_uuid_selected()));
1090
      if($synonym_uuid){
1091
        drupal_goto('cdm_dataportal/taxon/' . $taxon[0]->uuid . '/synonymy', 'highlite=' . $synonym_uuid);
1092
      }else {
1093
        drupal_goto('cdm_dataportal/taxon/' . $taxon[0]->uuid . '/synonymy', 'highlite=' . $singleTaxon->uuid);
1094
      }
1095
    }else{
1096
      // it is an accepted taxon 
1097
      if($synonym_uuid){
1098
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid . '/synonymy', 'highlite=' . $synonym_uuid);
1099
      }else{
1100
        drupal_goto('cdm_dataportal/taxon/' . $singleTaxon->uuid);
1101
      }
1102
    }
1103
  }else{ //more than one taxa case
1104
    $taxon_name_page->title = theme('cdm_name_page_title', $taxon_name);
1105
    if($taxon_pager->records){
1106
      $taxon_name_page->content = theme_cdm_list_of_taxa($taxon_pager->records, false);
1107
    }else{
1108
      $taxon_name_page->content = 'This name has no taxa';
1109
    }
1110
    return $taxon_name_page;
1111
  }
1112
}
1113

    
1114
function cdm_dataportal_view_search_advanced(){
1115

    
1116
  drupal_set_title(t('Advanced search'));
1117

    
1118
  $searchForm = cdm_dataportal_search_taxon_form(true);
1119

    
1120
  return drupal_get_form('cdm_dataportal_search_taxon_form_advanced');
1121

    
1122
}
1123

    
1124
/**
1125
 *
1126
 * future extensions to meet palmweb mockup requirements:
1127
 *  - habitat
1128
 *  - uses
1129
 *  - conservation status
1130
 *  - locality / tdwg region
1131
 */
1132
function cdm_dataportal_view_search_taxon(){
1133

    
1134
  $_SESSION['cdm']['last_search'] = $_SERVER['REQUEST_URI'];
1135

    
1136
  $request_params = cdm_dataportal_search_form_request();
1137
  $taxonPager = cdm_ws_get(CDM_WS_PORTAL_TAXON_FIND, null, queryString($request_params));
1138

    
1139
  $search_params = $_REQUEST;
1140
  unset($search_params['q']);
1141
  return theme('cdm_search_results', $taxonPager, 'cdm_dataportal/search/taxon', $search_params);
1142
}
1143

    
1144

    
1145
function cdm_view_xml2json(){
1146
  $file = arg(2);
1147
  $datastr = get_content(variable_get('cdm_webservice_url', '').$file);
1148
  return  xml2json::transformXmlStringToJson($datastr);
1149
}
1150

    
1151
/* ====================== other functions ====================== */
1152

    
1153

    
1154
/**
1155
 * Enter description here...
1156
 *
1157
 * @param String $uuid the UUID of the taxon
1158
 * @return the URL
1159
 */
1160
function path_to_taxon($uuid, $no_tab = false){
1161
  $tab = get_default_taxon_tab();
1162
  $values = unserialize(CDM_DATAPORTAL_DEFAULT_TAXON_TAB);
1163

    
1164
  if(!$uuid) return false;
1165

    
1166
  if (!$tab){
1167
    return 'cdm_dataportal/taxon/'.$uuid;
1168
  }else if(get_last_taxon_page_tab() &&  $tab == $values[CDM_DATAPORTAL_LAST_VISITED_TAB_ARRAY_INDEX]){
1169
    return 'cdm_dataportal/taxon/'.$uuid . '/' . get_last_taxon_page_tab();
1170
  } else {
1171
    return 'cdm_dataportal/taxon/'.$uuid . '/' . strtolower($tab);
1172
  }
1173
}
1174

    
1175
function path_to_key($keyType, $keyUuid){
1176
  if(!$keyUuid || !$keyType) return false;
1177
  $keyType{0} = strtolower($keyType{0});
1178
  return "cdm_dataportal/".$keyType."/$keyUuid";
1179
}
1180

    
1181
function path_to_reference($uuid){
1182
  if(!$uuid) return false;
1183
  return 'cdm_dataportal/reference/'.$uuid;
1184
}
1185

    
1186
function path_to_name($name_uuid){
1187
  $res = false;
1188
  if($name_uuid){
1189
   $res = 'cdm_dataportal/name/'.$name_uuid;
1190
  }
1191
  return $res;
1192
}
1193

    
1194
function path_to_media($uuid, $representaion_uuid = false, $partId = false){
1195
  if(!$uuid) return false;
1196
  $out = 'cdm_dataportal/media/'.$uuid;
1197
  if($representaion_uuid){
1198
    $out .= '/'.$representaion_uuid;
1199
    if($partId !== false){
1200
      $out .= '/'.$partId;
1201
    }
1202
  }
1203
  return $out;
1204
}
1205

    
1206
/**
1207
 * Compares thisRank with thatRank.
1208
 * Returns a negative integer, zero, or a positive integer
1209
 * as the of thisRank is higher than, equal to, or lower than thatRank.
1210
 * e.g:
1211
 * <ul>
1212
 * <li>rank_compare({species_uuid}, {genus_uuid}) = -1</li>
1213
 * <li>rank_compare({genus_uuid}, {genus_uuid}) = 0</li>
1214
 * <li>rank_compare({genus_uuid}, {tribus_uuid}) = 1</li>
1215
 * </ul>
1216
 * <p>
1217
 * This compare logic of the underlying webservice is the
1218
 * <b>inverse logic</b> of the the one implemented in
1219
 * java.lang.Comparable#compareTo(java.lang.Object)
1220
 * @param $thisRankUuid
1221
 * @param $thatRankUuid
1222
 * @return  a negative integer, zero, or a positive integer
1223
 * as the thisRank is lower than, equal to, or higher than thatRank
1224
 */
1225
function rank_compare($thisRankUuid, $thatRankUuid){
1226
  $result = cdm_ws_get(CDM_WS_TERM_COMPARE, array($thisRankUuid, $thatRankUuid));
1227
  return $result->Integer;
1228
}
1229

    
1230
/**
1231
 * Composes an HTML element class attribute value composed of
1232
 * the shortname of the cdm class and the uuid of the entity.
1233
 * This class attribute should be used whereever an cdm-entity is rendered.
1234
 *
1235
 * These according class selectors in css must be escaped, eg:
1236
 *    .cdm\:TextData
1237
 *
1238
 * @param $cdmEntity
1239
 */
1240
function html_class_atttibute_ref($cdmEntity){
1241

    
1242
  if(is_cdm_entity($cdmEntity)) {
1243
    return "cdm:".$cdmEntity->class." uuid:".$cdmEntity->uuid;
1244
  }
1245
}
1246

    
1247
function theme_cdm_uri_to_synonym($synonymUuid, $acceptedUuid, $pagePart = null){
1248
  $acceptedPath = path_to_taxon($acceptedUuid, true);
1249
  return url($acceptedPath.($pagePart ? '/'.$pagePart : ''), 'highlite='.$synonymUuid.'&acceptedFor='.$synonymUuid, $synonymUuid);
1250
}
1251

    
1252
/**
1253
 * Preprocess the taggedName to normalize newly introduced tagtypes like hybridSign, separator, .. more?
1254
 *
1255
 * @param unknown_type $taggedTextList
1256
 */
1257
function normalize_TaggedName(&$taggedTextList){
1258

    
1259
    if(is_array($taggedTextList)) {
1260

    
1261
      // first pass: rename
1262
      for($i = 0; $i < count($taggedTextList); $i++){
1263

    
1264
        if($taggedTextList[$i]->type == "hybridSign"){
1265
          $taggedTextList[$i]->type = "name";
1266
        }
1267

    
1268
      }
1269

    
1270
      // second pass: resolve separators
1271
      $taggedNameListNew = array();
1272
      for($i = 0; $i < count($taggedTextList); $i++){
1273

    
1274
        if($i + 1 < count($taggedTextList) && $taggedTextList[$i + 1]->type == "separator" ) {
1275

    
1276
          if($taggedTextList[$i]->type == $taggedTextList[$i + 2]->type){
1277
            $taggedName = $taggedTextList[$i];
1278
            $taggedName->text = $taggedName->text . $taggedTextList[$i + 1]->text . $taggedTextList[$i + 2]->text;
1279
            $taggedNameListNew[] = $taggedName;
1280
            ++$i;
1281
            ++$i;
1282
          }
1283
        } else {
1284
          $taggedNameListNew[] = $taggedTextList[$i];
1285
        }
1286
	  }
1287
	   $taggedTextList = $taggedNameListNew;
1288
    }
1289
}
1290

    
1291
/**
1292
 * Creates a short taxonname by using the taggename field of NameSTO or NameTO instances.
1293
 * If the taggename if empty the fullname will be returned.
1294
 *
1295
 * @param unknown_type $Name or TreeNode
1296
 * @return string
1297
 */
1298
function cdm_dataportal_shortname_of($name){
1299
  $nameStr = '';
1300

    
1301
  normalize_TaggedName($name->taggedTitle);
1302

    
1303
  // get all tagged text tokens of the scientific name
1304
  foreach($name->taggedTitle as $tagtxt){
1305
    if($tagtxt->type == 'name' || $tagtxt->type == 'rank'){
1306
      $nameStr .= ($nameStr ? ' ' : '').$tagtxt->text;
1307
    }
1308
  }
1309
  $nameStr = trim($nameStr);
1310
  if($nameStr){
1311
    // do not return short names for these
1312
    //if (stristr(strtolower($nameStr), 'incertae sedis') !== FALSE ||
1313
    //	stristr(strtolower($nameStr), 'nomina excludenda') !== FALSE) {
1314
    if ($name->unplaced || $name->excluded){
1315
      return $nameStr;
1316
    }
1317
    if($pos = stripos($nameStr, ' ')){
1318
      return substr($nameStr, 0, 1).'. '.substr($nameStr, $pos);
1319
    } else {
1320
      return $nameStr;
1321
    }
1322
  } else {
1323
    return $name->titleCache;
1324
  }
1325
}
1326

    
1327

    
1328
/**
1329
 * Check if a taxon is accepted by the current taxonomic tree
1330
 *
1331
 * @param Taxon $taxon
1332
 * @return true if $taxon is accepted, false otherwise
1333
 */
1334

    
1335
function _cdm_dataportal_acceptedByCurrentView($taxon){
1336

    
1337
  $defaultTreeUuid = get_taxonomictree_uuid_selected();
1338
  if($taxon->class == "Taxon" && isset($taxon->taxonNodes)){
1339
    foreach($taxon->taxonNodes as $node){
1340
      if($node->classification == $defaultTreeUuid) {
1341
        return true;
1342
      }
1343
    }
1344
  }
1345
  return false;
1346
}
1347

    
1348
/**@Deprecated
1349
 *
1350
 */
1351
function compose_url_prameterstr($parameters = array(), $parentPropertyName = false){
1352
  $pstr = '';
1353
  foreach($parameters as $key=>$value){
1354
    if(is_array($value)){
1355

    
1356
    } else {
1357
      $pstr .= ($pstr ? '&' :'').$key.'='.urlencode($value);
1358
    }
1359
  }
1360
  return $pstr;
1361
}
1362

    
1363
/**
1364
 * workaround for missing original source type, idNamespace is always set in these cases
1365
 * @param unknown_type $source
1366
 * @return unknown_type
1367
 */
1368
function _is_original_source_type($source){
1369
  return !$source->idNamespace && strlen($source->idNamespace) == 0;
1370
}
1371

    
1372

    
1373

    
1374
/**
1375
 * The function read the metadata info such title or artist of a media file. The
1376
 * function tries at first to get all the info from the file metadata and if it is
1377
 * not avaible look at the media file info stored at the database.
1378
 * @param $media The media file
1379
 * @return array The array with the avilable specified metadata info.
1380
 * TODO rename to read_media_metadata() and move to *.module
1381
 */
1382
function cdm_read_media_metadata($media){
1383

    
1384
  $metadata_caption = array('title' => '',           //media_metadata and media
1385
                              'artist' => '',          //media_metadata and media
1386
                              'rights',                //media_metadata and media
1387
                              'location',              //media_metadata
1388
                              'filename' => '',        //media
1389
                              'mediacreated' => '',    //media
1390
                              'description' => '');    //media
1391

    
1392
  //getting the media metadata
1393
  $media_metadata = cdm_ws_get(CDM_WS_MEDIA_METADATA, array($media->uuid));
1394
  $media_metadata_aux = (array) $media_metadata;
1395

    
1396
  //filename
1397
  if(isset($media->representations[0]->parts[0]->uri)){
1398
    $fileUri = $media->representations[0]->parts[0]->uri;
1399
    $filename = substr($fileUri, strrpos($fileUri, "/")+1);
1400
    $metadata_caption['filename'] = $filename;
1401
  }
1402
  else{
1403
      $metadata_caption['filename'] = '';
1404
  }
1405

    
1406
  //title
1407
  if ($media_metadata->ObjectName) {
1408
    $metadata_caption['title'] = $media_metadata->ObjectName;
1409
  } else if ($media_metadata_aux['Object Name']){
1410
    $metadata_caption['title'] = $media_metadata_aux['Object Name'];
1411
  } else if ($media->title_L10n){
1412
    $metadata_caption['title'] = $media->title_L10n;
1413
  } else if ($media->titleCache){
1414
    $metadata_caption['title'] = $media->titleCache;
1415
  }
1416

    
1417
  // append description to title
1418
  if ($media->description_L10n) {
1419
    $metadata_caption['title'] .= '<span class="media-description">' . $media->description_L10n . '<span>';
1420
  }
1421

    
1422
  //artist
1423
  if ($media_metadata->Artist){
1424
   $metadata_caption['artist'] = ($media_metadata->Artist ? ''.$media_metadata->Artist : '');
1425
  }
1426
  elseif ($media->artist->titleCache){
1427
   $metadata_caption['artist'] = $media->artist->titleCache;
1428
  }
1429

    
1430
  //copyright
1431
  $metadata_caption['rights'] = array('copyright' => array('agentNames' => array()),
1432
                                      'license' => array('agentNames' => array(), 'types' => array(), 'abbreviatedTexts' => array(), 'uris' => array()));
1433
  if ($media_metadata->Copyright)
1434
  $metadata_caption['rights']['copyright']['agentNames'][] = $media_metadata->Copyright;
1435
  elseif ($media->rights){
1436
    foreach($media->rights as $right){
1437
      switch($right->term->uuid){
1438
        case UUID_RIGHTS_LICENCE:
1439
          $metadata_caption['rights']['license']['agentNames'][] = ($right->agent ? ''.$right->agent->firstname.' '.$right->agent->lastname : '');
1440
          $metadata_caption['rights']['license']['types'][] = ($right->representation_L10n ? ''.$right->representation_L10n : '');
1441
          $metadata_caption['rights']['license']['abbreviatedTexts'][] = ($right->abbreviatedText ? ''.$right->abbreviatedText : '');
1442
          $metadata_caption['rights']['license']['uris'][] = ($right->uri ? ''.$right->uri : '');
1443
          break;
1444
        case UUID_RIGHTS_COPYRIGHT:
1445
          $metadata_caption['rights']['copyright']['agentNames'][] = $right->agent->firstname . ' ' . $right->agent->lastname;
1446
          break;
1447
      }
1448
    }
1449
  } else {
1450
    $metadata_caption['rights']['agentNames'][] = '';
1451
  }
1452

    
1453
  //filling the description (though there is no description in the db???)
1454
  //$metadata_caption['description'] = $media->description_L10n;
1455

    
1456
  //location
1457
  $metadata_caption['location'] = array();
1458
  $metadata_caption['location']['sublocation'] = $media_metadata->Sublocation;
1459
  $metadata_caption['location']['city'] = $media_metadata->City;
1460
  $metadata_caption['location']['province'] = $media_metadata->Province;
1461
  $metadata_caption['location']['country'] = $media_metadata->Country;
1462

    
1463
  /*
1464
   //creation date
1465
   if($media_metadata["Modify Date"])
1466
   $metadata_caption['mediacreated'] = $media_metadata["Modify Date"];
1467
   else
1468
   $metadata_caption['mediacreated'] = $media->created;
1469
   */
1470
  //returned value
1471
  return $metadata_caption;
1472
}
1473

    
1474
/**
1475
 * This function collects all the media from a list of description elements
1476
 * and return them as an Array.
1477
 *
1478
 * @param $descriptionElementes The description elements
1479
 * @return Array The output with all the media
1480
 */
1481
function cdm_dataportal_media_from_descriptionElements($descriptionElements){
1482
  //variables
1483
  $outArrayOfMedia = array(); //return value
1484
  //implementation
1485
  if(is_array($descriptionElements)){//avoiding warning box in drupal for flora malesiana
1486
    foreach($descriptionElements as $descriptionElement){
1487
      if(is_array($descriptionElement->media)){
1488
        foreach($descriptionElement->media as $media){
1489
          if(is_object($media)){
1490
            $outArrayOfMedia[] = $media;
1491
          }
1492
        }
1493
      }
1494
    }
1495
  }
1496
  return $outArrayOfMedia;
1497
}
1498

    
1499
function cdm_annotations_as_footnotekeys($cdmBase, $footnote_list_key = null){
1500
  $footNoteKeys = array();
1501
  //is argument cdmBase an array?
1502
  if (!is_array($cdmBase)){
1503
    $cdmBase_array = array();
1504
    $cdmBase_array[] = $cdmBase;
1505
  }else{
1506
    $cdmBase_array = $cdmBase;
1507
  }
1508
  //getting the key for the footnotemanager
1509
  if( $footnote_list_key ){
1510
    $footnoteListKey = $footnote_list_key;
1511
  }else{
1512
    $footnoteListKey = RenderHints::getFootnoteListKey() . '-annotations';
1513
  }
1514
  //adding the footnotes keys
1515
  foreach($cdmBase_array as $cdmBase_element){
1516
    $annotations = cdm_ws_getAnnotationsFor($cdmBase_element, variable_get('annotations_types_as_footnotes', unserialize(ANNOTATIONS_TYPES_AS_FOOTNOTES_DEFAULT)));
1517
    if(is_array($annotations)){
1518
      foreach($annotations as $annotation){
1519
          $footNoteKeys[] = FootnoteManager::addNewFootnote($footnoteListKey, $annotation->text);
1520
      }
1521
    }
1522
  }
1523
  return $footNoteKeys;
1524
}
1525

    
1526
function cdm_dynabox($label, $content_url, $theme, $link_alt_text, $enclosingtags = array('li', 'ul')){
1527

    
1528
  drupal_add_js(drupal_get_path('module', 'cdm_dataportal').'/js/cdm_dynabox.js');
1529

    
1530
  $cdm_proxy_url = url('cdm_api/proxy/'.urlencode($content_url)."/$theme");
1531
  $out .= '<'. $enclosingtags[0]. ' class="dynabox"><a href="'.$content_url.'" class="label" alt="'.t($link_alt_text).'">'.$label.'</a>';
1532
  $out .= '<'. $enclosingtags[1]. ' class="dynabox_content" title="'.$cdm_proxy_url.'"><'. $enclosingtags[0]. '><img class="loading" src="'.drupal_get_path('module', 'cdm_dataportal').'/images/loading_circle_grey_16.gif" style="display:none;"></'. $enclosingtags[0]. '></'. $enclosingtags[1]. '>';
1533
  $out .= '</'. $enclosingtags[0]. '>';
1534
  return $out;
1535
}
1536

    
1537
/**
1538
 * returns true if the given $featureNode or any of its subordinate nodes contains
1539
 * at least one non empty TextData or at leas one DescriptionElement of an other type.
1540
 *
1541
 * @param unknown_type $featureNode A heature node as produced by the function _mergeFeatureTreeDescriptions()
1542
 */
1543
function hasFeatureNodeDescriptionElements($featureNode) {
1544

    
1545
  if(is_array($featureNode->descriptionElements) && count($featureNode->descriptionElements) > 0) {
1546
    foreach ($featureNode->descriptionElements as $descriptionElement) {
1547
      if($descriptionElement->class != "TextData" || $descriptionElement->multilanguageText_L10n->text){
1548
        return true;
1549
      }
1550
    }
1551
  } else if(is_array($featureNode->children)) {
1552
    foreach ($featureNode->children as $child) {
1553
      if(hasFeatureNodeDescriptionElements($child)){
1554
        return true;
1555
      }
1556
    }
1557
  }
1558
  return false;
1559
}
1560

    
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