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cdm-dataportal / modules / cdm_dataportal / includes / name.inc @ 46a93d1e

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<?php
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/**
3
 * @file
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 * Functions for dealing with CDM entities from the package model.name
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 *
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 * @copyright
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 *   (C) 2007-2015 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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 */
18

    
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/**
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 * @defgroup compose Compose functions
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 * @{
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 * Functions which are composing Drupal render arays
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 *
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 * The cdm_dataportal module needs to compose rather complex render arrays from
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 * the data returned by the CDM REST service. The compose functions are
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 * responsible for creating the render arrays.
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 *
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 * All these functions are also implementations of the compose_hook()
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 * which is used in the proxy_content() function.
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 * @}
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 */
32

    
33

    
34
/**
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 * Provides the name render template to be used within the page elements identified the the $renderPath.
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 *
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 * The render templates arrays contains one or more name render templates to be used within the page elements identified the the
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 * renderPath. The renderPath is the key of the subelements whereas the value is the name render template.
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 *
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 * The render paths used for a cdm_dataportal page can be visualized by supplying the HTTP query parameter RENDER_PATH=1.
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 *
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 * It will be tried to find  the best matching default RenderTemplate by stripping the dot separated render path
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 * element by element. If no matching template is found the DEFAULT will be used:
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 *
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 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
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 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
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 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
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 *
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 * A single render template can be used for multiple render paths. In this case the according key of the render templates
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 * array element should be the list of these render paths concatenated by ONLY a comma character without any whitespace.
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 *
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 * A render template is an associative array. The keys of this array are referring to the keys as defined in the part
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 * definitions array.
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 * @see get_partDefinition($taxonNameType) for more information
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 *
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 * The value of the render template element must be set to TRUE in order to let this part being rendered.
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 * The namePart, nameAuthorPart and referencePart can also hold an associative array with a single
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 * element: array('#uri' => TRUE). The value of the #uri element will be replaced by the according
59
 * links if the parameters $nameLink or $refenceLink are set.
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 *
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 * @param string $render_path
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 *   The render path can consist of multiple dot separated elements
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 *   @see RenderHints::getRenderPath()
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 * @param string $nameLink
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 *   The link path or URL to be used for name parts if a link is forseen in the template
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 *   matching the given $renderPath.
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 * @param string $referenceLink
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 *   The link path ot URL to be used for nomenclatural reference parts if a link is forseen
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 *   in the template matching the given $renderPath.
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 * @return array
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 *   An associative array, the render template
72
 */
73
function get_nameRenderTemplate($render_path, $nameLink = NULL, $referenceLink = NULL) {
74

    
75
  static $default_render_templates = NULL;
76
  static $split_render_templates = NULL;
77

    
78

    
79
  if (!isset($default_render_templates)) {
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    $default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);
81
  }
82
  if($split_render_templates == NULL) {
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    $render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);
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    // needs to be converted to an array
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    $render_templates = (object_to_array($render_templates));
86

    
87
    // separate render templates which are combined with a comma
88
    $split_render_templates = array();
89
    foreach($render_templates as $key => $template){
90
      if(strpos($key, ',')){
91
        foreach(explode(',', $key) as $path){
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          $split_render_templates[$path] = $template;
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        }
94
      } else {
95
        $split_render_templates[$key] = $template;
96
      }
97
    }
98
  }
99

    
100
  // get the base element of the renderPath
101
  if (($separatorPos = strpos($render_path, '.')) > 0) {
102
    $renderPath_base = substr($render_path, 0, $separatorPos);
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  } else {
104
    $renderPath_base = $render_path;
105
  }
106

    
107
  $template = NULL;
108
  // 1. try to find a template using the render path base element
109
  if(array_key_exists($renderPath_base, $split_render_templates)){
110
    $template = (array)$split_render_templates[$renderPath_base];
111
  }
112

    
113
  // 2. Find best matching default RenderTemplate
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  // by stripping the dot separated render path element by element
115
  // if no matching template is found the DEFAULT will be used.
116
  while (!is_array($template) && strlen($render_path) > 0) {
117
    foreach ($split_render_templates as $path => $t) {
118
      if ($path == $render_path) {
119
        $template = $t;
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        break;
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      }
122
    }
123
    // shorten by one element
124
    $render_path = substr($render_path, strrpos($render_path, '.') + 1, strlen($render_path));
125
  }
126

    
127

    
128
  // 3. Otherwise get default RenderTemplate from theme.
129
  if (!is_array($template)) {
130
    $template = $split_render_templates['#DEFAULT'];
131
  }
132

    
133
  // --- set the link uris to the according template fields if they exist
134
  if(isset($template['nameAuthorPart']) && isset($template['nameAuthorPart']['#uri'])) {
135
    if ($nameLink) {
136
      $template['nameAuthorPart']['#uri'] = $nameLink;
137
    }
138
    else {
139
      unset($template['nameAuthorPart']['#uri']);
140
    }
141
  }
142

    
143
  if ($nameLink && isset($template['namePart']['#uri'])) {
144
    $template['namePart']['#uri'] = $nameLink;
145
  }
146
  else {
147
    unset($template['namePart']['#uri']);
148
  }
149

    
150
  if ($referenceLink && isset($template['referencePart']['#uri'])) {
151
    $template['referencePart']['#uri'] = $referenceLink;
152
  }
153
  else {
154
    unset($template['referencePart']['#uri']);
155
  }
156

    
157
  return $template;
158
}
159

    
160
/**
161
 * The part definitions define the specific parts of which a rendered taxon name plus additional information will consist.
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 *
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 * A full taxon name plus additional information can consist of the following elements:
164
 *
165
 *   - name: the taxon name inclugin rank nbut without author
166
 *   - authorTeam:  The authors of a reference, also used in taxon names
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 *   - authors:  The authors of a reference, also used in taxon names
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 *   - reference: the nomenclatural reference,
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 *   - microreference:  Volume, page number etc.
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 *   - status:  The nomenclatural status of a name
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 *   - description: name descriptions like protologues etc ...
172
 *
173
 * These elements are combined in the part definitions array to from the specific parts to be rendered.
174
 * Usually the following parts are formed:
175
 *
176
 * The name "Lapsana communis L., Sp. Pl.: 811. 1753" shall be an example here:
177
 *  - namePart: the name and rank (in example: "Lapsana communis")
178
 *  - authorshipPart: the author (in example: "L.")
179
 *  - nameAuthorPart: the combination of name and author part (in example: "Lapsana communis L.").
180
 *     This is useful for zoological names where the authorshipPart belongs to the name and both should
181
 *     be combined when a link to the taxon is rendered.
182
 *  - referencePart: the nomencaltural reference (in example: "Sp. Pl. 1753")
183
 *  - microreferencePart: usually the page number (in example ": 811.")
184
 *  - statusPart: the nomenclatorical status
185
 *  - descriptionPart:
186
 *
187
 * Each set of parts is dedicated to render a specific TaxonName type, the type names are used as keys for the
188
 * specific parts part definitions:
189
 *
190
 *  - BotanicalName
191
 *  - ZoologicalName
192
 *  - #DEFAULT:  covers ViralNames and general NonViralNames
193
 *
194
 * An example:
195
 * @code
196
 * array(
197
 *    'ZoologicalName' => array(
198
 *        'namePart' => array('name' => TRUE),
199
 *        'referencePart' => array('authorTeam' => TRUE),
200
 *        'microreferencePart' => array('microreference' => TRUE),
201
 *        'statusPart' => array('status' => TRUE),
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 *        'descriptionPart' => array('description' => TRUE),
203
 *    ),
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 *    'BotanicalName' => array(
205
 *        'namePart' => array(
206
 *            'name' => TRUE,
207
 *            'authors' => TRUE,
208
 *        ),
209
 *        'referencePart' => array(
210
 *            'reference' => TRUE,
211
 *            'microreference' => TRUE,
212
 *        ),
213
 *        'statusPart' => array('status' => TRUE),
214
 *        'descriptionPart' => array('description' => TRUE),
215
 *    ),
216
 *  );
217
 * @endcode
218
 *
219
 * @param object $taxonNameType
220
 *    A cdm TaxonNameType entity
221
 *
222
 */
223
function get_partDefinition($taxonNameType) {
224

    
225
  static $default_part_definitions = null;
226
  if (!isset($default_part_definitions)) {
227
    $default_part_definitions= unserialize(CDM_PART_DEFINITIONS_DEFAULT);
228
  }
229

    
230
  static $part_definitions = null;
231
  if (!isset($part_definitions)) {
232
    $part_definitions = object_to_array(variable_get(CDM_PART_DEFINITIONS, $default_part_definitions));
233
  }
234

    
235
  $dtype = nameTypeToDTYPE($taxonNameType);
236
  if (array_key_exists($taxonNameType, $part_definitions)) {
237
    return $part_definitions[$taxonNameType];
238
  } else if (array_key_exists($dtype, $part_definitions)) {
239
    return $part_definitions[$dtype];
240
  } else {
241
    return $part_definitions['#DEFAULT']; // covers ViralNames and general NonViralNames
242
  }
243

    
244
}
245

    
246

    
247
/**
248
 * Renders the markup for a CDM TaxonName instance.
249
 *
250
 * The layout of the name representation is configured by the
251
 * part_definitions and render_templates (see get_partDefinition() and
252
 * get_nameRenderTemplate())
253
 *
254
 * @param $taxon_name_or_taxon_base
255
 *    A cdm TaxonBase or TaxonName entity
256
 * @param $name_link
257
 *    URI to the taxon, @param $reference_link
258
 *    URI to the reference, @param bool $show_annotations
259
 *    turns the display of annotations on
260
 * @param bool $is_type_designation
261
 *    To indicate that the supplied taxon name is a name type designation.
262
 * @param array $skiptags
263
 *    an array of name elements tags like 'name', 'rank' to skip. The name part
264
 *          'authors' will not ber affected by this filter. This part is managed though the render template
265
 *          mechanism.
266
 * @param bool $is_invalid
267
 *   Indicates that this taxon is invalid. In this case the name part will be shown in double quotes.
268
 *   This is useful when rendering taxon relation ships.
269
 *
270
 * @return string
271
 *  The markup for a taxon name.
272
 * @see path_to_taxon(), must be processed by url() before passing to this method
273
 * @see path_to_reference(), must be processed by url() before passing to this method
274
 */
275
function render_taxon_or_name($taxon_name_or_taxon_base, $name_link = NULL, $reference_link = NULL,
276
  $show_annotations = true, $is_type_designation = false, $skiptags = array(), $is_invalid = false) {
277

    
278
  $is_doubtful = false;
279

    
280
  if($taxon_name_or_taxon_base->class == 'Taxon' || $taxon_name_or_taxon_base->class == 'Synonym'){
281
    if(isset($taxon_name_or_taxon_base->name)){
282
      $taxonName = $taxon_name_or_taxon_base->name;
283
    } else {
284
      $taxonName = cdm_ws_get(CDM_WS_TAXON . '/$0/name', array($taxon_name_or_taxon_base->uuid));
285
    }
286
    $is_doubtful = $taxon_name_or_taxon_base->doubtful;
287
    // use the TaxonBase.tagged_title so we have the secRef
288
    $tagged_title = $taxon_name_or_taxon_base->taggedTitle;
289
  } else {
290
    // assuming this is a TaxonName
291
    $taxonName = $taxon_name_or_taxon_base;
292
    if(isset($taxonName->taggedFullTitle)){
293
      $tagged_title = $taxon_name_or_taxon_base->taggedFullTitle;
294
    } else {
295
      $tagged_title = $taxon_name_or_taxon_base->taggedName;
296
    }
297
  }
298

    
299

    
300
  $renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $name_link, $reference_link);
301
  $partDefinition = get_partDefinition($taxonName->nameType);
302

    
303
  // Apply definitions to template.
304
  foreach ($renderTemplate as $part => $uri) {
305

    
306
    if (isset($partDefinition[$part])) {
307
      $renderTemplate[$part] = $partDefinition[$part];
308
    }
309
    if (is_array($uri) && isset($uri['#uri'])) {
310
      $renderTemplate[$part]['#uri'] = $uri['#uri'];
311
    }
312
  }
313

    
314
  $secref_tagged_text = tagged_text_extract_reference_and_detail($tagged_title);
315
  // taxon names will have the nomenclatural reference in the tagged full title:
316
  $nomref_tagged_text = tagged_text_extract_reference($tagged_title);
317
  $nom_status_tagged_text = tagged_text_extract_nomstatus($tagged_title);
318
  $appended_phrase_tagged_text = array(); // this is filled later
319

    
320
  normalize_tagged_text($tagged_title);
321

    
322
  $is_valid_tagged_title =
323
    isset($tagged_title)
324
    && is_array($tagged_title)
325
    && isset($tagged_title[0]->text)
326
    && is_string($tagged_title[0]->text)
327
    && $tagged_title[0]->text != ''
328
    && isset($tagged_title[0]->type);
329
  $lastAuthorElementString = FALSE;
330

    
331
  $name_encasement = $is_invalid ? '"' : '';
332
  $doubtful_marker = $is_doubtful ? '?&#8239;' : ''; // 	&#8239; =  NARROW NO-BREAK SPACE
333
  $doubtful_marker_markup = '';
334

    
335
  if($doubtful_marker){
336
    $doubtful_marker_markup = '<span class="doubtful">' . $doubtful_marker . '</span>';
337
    if($tagged_title[0]->text == '?' ){
338
      // remove the first tagged text element
339
      unset($tagged_title[0]);
340
    }
341
  }
342

    
343
  // split off all appendedPhrase item  from the end of the array (usually there only should  be one)
344
  while($tagged_title[count($tagged_title)-1]->type == "appendedPhrase"){
345
    $appended_phrase_tagged_text[] = array_pop($tagged_title);
346
  }
347

    
348
  // Got to use second entry as first one, see ToDo comment below ...
349
  if ($is_valid_tagged_title) {
350

    
351
    $taggedName = $tagged_title;
352
    $hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
353
    $hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
354

    
355

    
356
    if (!(($hasNamePart_with_Authors) || ($hasNameAuthorPart_with_Authors))) {
357
      // Find author and split off from name.
358
      // TODO expecting to find the author as the last element.
359
      /*
360
      if($taggedName[count($taggedName)- 1]->type == 'authors'){
361
        $authorTeam = $taggedName[count($taggedName)- 1]->text;
362
        unset($taggedName[count($taggedName)- 1]);
363
      }
364
      */
365

    
366
      // Remove all authors.
367
      $taggedNameNew = array();
368
      foreach ($taggedName as $element) {
369
        if ($element->type != 'authors') {
370
          $taggedNameNew[] = $element;
371
        }
372
        else {
373
          $lastAuthorElementString = $element->text;
374
        }
375
      }
376
      $taggedName = $taggedNameNew;
377
      unset($taggedNameNew);
378
    }
379
    $name = '<span class="' . $taxonName->class . '">' . $doubtful_marker_markup . $name_encasement . cdm_tagged_text_to_markup($taggedName, $skiptags) . $name_encasement . '</span>';
380
  }
381
  else {
382
    // use titleCache instead
383
    $name = '<span class="' . $taxonName->class . '_titleCache">' . $doubtful_marker_markup . $name_encasement . $taxonName->titleCache . $name_encasement . '</span>';
384
  }
385

    
386

    
387
  if(isset($appended_phrase_tagged_text[0])){
388
    $name .= ' <span class="appended-phrase">'. cdm_tagged_text_to_markup($appended_phrase_tagged_text) . '</span>';
389
  }
390

    
391
  // Fill name into $renderTemplate.
392
  array_setr('name', $name , $renderTemplate);
393

    
394
  // Fill with authorTeam.
395
  /*
396
  if($authorTeam){
397
    $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
398
    array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
399
  }
400
  */
401

    
402
  // Fill with reference.
403
  if (isset($renderTemplate['referencePart']) && !$is_type_designation) {
404

    
405
    $registrations = cdm_ws_get(CDM_WS_NAME, array($taxonName->uuid, "registrations"));
406
    $registration_markup = render_registrations($registrations);
407

    
408
    // default separator
409
    $separator = '';
410

    
411
    // [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
412
    // Komma nach dem Autornamen ist √ľberall dort falsch, wo ein "in" folgt."
413
    if (isset($renderTemplate['referencePart']['reference'])) {
414
      $microreference = NULL;
415
      if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalSource->citationMicroReference)) {
416
        $microreference = $taxonName->nomenclaturalSource->citationMicroReference;
417
      }
418
      if(count($nomref_tagged_text) == 0 && isset($taxonName->nomenclaturalSource->citation)){
419
        // TODO is this case still relevant? The tagged text should already contain all information!
420
        $citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalSource->citation->uuid, $microreference);
421
        // Find preceding element of the reference.
422
        $precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
423
        if (str_beginsWith($citation, ", in")) {
424
          $citation = substr($citation, 2);
425
          $separator = ' ';
426
        }
427
        elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {
428
          $separator = ', ';
429
        } else {
430
          $separator = ' ';
431
        }
432
        $referenceArray['#separator'] = $separator;
433
        $referenceArray['#html'] = '<span class="reference">' . $citation . '</span>' . $registration_markup;
434
      } else {
435
        // this ist the case for taxon names
436
        $referenceArray['#html'] = cdm_tagged_text_to_markup($nomref_tagged_text);
437
      }
438

    
439

    
440
      array_setr('reference', $referenceArray, $renderTemplate);
441
    }
442

    
443
    // If authors have been removed from the name part the last named authorteam
444
    // should be added to the reference citation, otherwise, keep the separator
445
    // out of the reference.
446
    if (isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString) {
447
      // If the nomenclaturalReference citation is not included in the
448
      // reference part but display of the microreference
449
      // is wanted, append the microreference to the authorTeam.
450
      $citation = '';
451
      if (!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])) {
452
        $separator = ": ";
453
        $citation = $taxonName->nomenclaturalMicroReference;
454
      }
455
      $referenceArray['#html'] = ' <span class="reference">' . $lastAuthorElementString . $separator . $citation . '</span>';
456
      array_setr('authors', $referenceArray, $renderTemplate);
457
    }
458
  }
459

    
460
  $is_reference_year = false;
461
  if (isset($renderTemplate['referenceYearPart']['reference.year'])) {
462
    if(isset($taxonName->nomenclaturalSource->citation->datePublished)){
463
      $referenceArray['#html'] = ' <span class="reference">' . timePeriodToString($taxonName->nomenclaturalSource->citation->datePublished) . '</span>';
464
      array_setr('reference.year', $referenceArray, $renderTemplate);
465
      $is_reference_year = true;
466
    }
467
  }
468

    
469
  // Fill with status.
470
  if(isset($renderTemplate['statusPart']['status'])){
471
    if (isset($nom_status_tagged_text[0])) {
472
        $tt_to_markup_options = array('html' => false);
473
        foreach ($nom_status_tagged_text as &$tt){
474
         if($tt->type == 'nomStatus'&& isset($tt->entityReference)) {
475
           $nom_status = cdm_ws_get(CDM_WS_NOMENCLATURALSTATUS, array($tt->entityReference->uuid));
476
           $nom_status_fkey = handle_nomenclatural_status_as_footnote($nom_status);
477
           $tt->text .= $nom_status_fkey;
478
           $tt_to_markup_options['html'] = true;
479
         }
480
        }
481
        array_setr(
482
          'status',
483
          '<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, array('postSeparator'), 'span', $tt_to_markup_options) . '</span>',
484
          $renderTemplate);
485
    }
486
  }
487

    
488
  if (isset($renderTemplate['secReferencePart'])){
489
    if(isset($secref_tagged_text[1])){
490
      $post_separator_markup = $is_reference_year ? '.': '';
491
      if(isset($nom_status_tagged_text[count($nom_status_tagged_text) - 1]) && ($nom_status_tagged_text[count($nom_status_tagged_text) - 1]->type ==  'postSeparator')){
492
        $post_separator_markup = cdm_tagged_text_to_markup(array($nom_status_tagged_text[count($nom_status_tagged_text) - 1 ]));
493
      };
494
      array_setr('secReference',
495
        $post_separator_markup
496
          . ' <span class="sec_reference">'
497
          . join('', cdm_tagged_text_values($secref_tagged_text))
498
          . '</span>', $renderTemplate);
499
    }
500
  }
501

    
502
  // Fill with protologues etc...
503
  $descriptionHtml = '';
504
  if (array_setr('description', TRUE, $renderTemplate)) {
505
    $descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
506
    if($descriptions){
507
      foreach ($descriptions as $description) {
508
        if (!empty($description)) {
509
          foreach ($description->elements as $description_element) {
510
            $second_citation = '';
511
            if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {
512
              if(isset($description_element->feature) && $description_element->feature->uuid == UUID_ADDITIONAL_PUBLICATION){
513
                $prefix =  '& ';
514
              } else {
515
                $prefix = '';
516
              }
517
              $second_citation = ' [' . $prefix . $description_element->multilanguageText_L10n->text . '].';
518
            }
519
            $descriptionHtml .= $second_citation;
520
            $descriptionHtml .= cdm_description_element_media(
521
                $description_element,
522
                array(
523
                  'application/pdf',
524
                  'image/png',
525
                  'image/jpeg',
526
                  'image/gif',
527
                  'text/html',
528
                )
529
            );
530

    
531
          }
532
        }
533
      }
534
    }
535
    array_setr('description', $descriptionHtml, $renderTemplate);
536
  }
537

    
538
  // Render.
539
  $out = '';
540
  if(isset($_REQUEST['RENDER_PATH'])){
541
    // developer option to show the render path with each taxon name
542
    $out .= '<span class="render-path">' . RenderHints::getRenderPath() . '</span>';
543
  }
544
  $out .= '<span class="' . html_class_attribute_ref($taxon_name_or_taxon_base)
545
    . '" data-cdm-ref="/name/' . $taxonName->uuid . '" data-cdm-render-path="' . RenderHints::getRenderPath() .'">';
546

    
547
  foreach ($renderTemplate as $partName => $part) {
548
    $separator = '';
549
    $partHtml = '';
550
    $uri = FALSE;
551
    if (!is_array($part)) {
552
      continue;
553
    }
554
    if (isset($part['#uri']) && is_string($part['#uri'])) {
555
      $uri = $part['#uri'];
556
      unset($part['#uri']);
557
    }
558
    foreach ($part as $key => $content) {
559
      $html = '';
560
      if (is_array($content)) {
561
        $html = $content['#html'];
562
        if(isset($content['#separator'])) {
563
          $separator = $content['#separator'];
564
        }
565
      }
566
      elseif (is_string($content)) {
567
        $html = $content;
568
      }
569
      $partHtml .= '<span class="' . $key . '">' . $html . '</span>';
570
    }
571
    if ($uri) {
572
      // cannot use l() here since the #uri aleady should have been processed through uri() at this point
573
      $out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';
574

    
575
    }
576
    else {
577
      $out .= $separator . $partHtml;
578
    }
579
  }
580
  $out .= '</span>';
581
  if ($show_annotations) {
582
    // $out .= render_entities_annotations_as_footnote_keys([$taxonName]);
583
  }
584
  return $out;
585
}
586

    
587

    
588

    
589
/**
590
 * Composes information for a registration from a dto object.
591
 *
592
 * Registrations which are not yet published are suppressed.
593
 *
594
 * @param $registration_dto
595
 * @param $with_citation
596
 *   Whether to show the citation.
597
 *
598
 * @return array
599
 *    A drupal render array with the elements:
600
 *    - 'name'
601
 *    - 'name-relations'
602
 *    - 'specimen_type_designations'
603
 *    - 'name_type_designations'
604
 *    - 'citation'
605
 *    - 'registration_date_and_institute'
606
 * @ingroup compose
607
 */
608
function compose_registration_dto_full($registration_dto, $with_citation = true)
609
{
610
  $render_array = array(
611
    '#prefix' => '<div class="registration">',
612
    '#suffix' => '</div>'
613
  );
614

    
615
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
616
    return $render_array;
617
  }
618

    
619
  $render_array['sub_headline'] = markup_to_render_array(join(", ", registration_types($registration_dto)),-10, '<h3 class="registration_type">' . t('Event: '), '</h3>' );
620
  $render_array['nomenclatural_act'] = array(
621
    '#weight' => 0,
622
    '#prefix' => '<div class="nomenclatural_act">',
623

    
624
    '#suffix' => '</div>'
625
  );
626

    
627
  // name
628
  $name_relations = null;
629
  if($registration_dto->nameRef){
630
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
631
    cdm_load_tagged_full_title($name);
632
    $render_array['nomenclatural_act']['published_name'] = markup_to_render_array('<div class="published-name">' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</div>', 0);
633
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
634
    // need to create the name relationships later, so that the foot notes are in correct order, see section // name relations
635
  } else {
636
    // in this case the registration must have a
637
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->typifiedNameRef->uuid);
638
    $render_array['typified_name'] = markup_to_render_array('<p class="typified-name">for ' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</p>', 40);
639
  }
640

    
641
  // typedesignation in detail
642
  if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
643
    $field_unit_uuids = array();
644
    $specimen_type_designation_refs = array();
645
    $name_type_designation_refs = array();
646
    foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {
647
      $tokens = explode("#", $workingset_ref);
648
      $types_in_fieldunit = get_object_vars($obj); // convert into associative array
649

    
650
      if ($tokens[0] == 'NameTypeDesignation') {
651
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
652
          if(!isset($name_type_designation_refs[$type_status])){
653
            $name_type_designation_refs[$type_status]  = $entity_reference_list;
654
          } else {
655
            array_push($name_type_designation_refs[$type_status] ,$entity_reference_list);
656
          }
657
        }
658
      } else if ($tokens[0] == 'FieldUnit'){
659
        $field_unit_uuids[] = $tokens[1];
660
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
661
          if(!isset($specimen_type_designation_refs[$type_status])){
662
            $specimen_type_designation_refs[$type_status] =  $entity_reference_list;
663
          } else {
664
            array_push($specimen_type_designation_refs[$type_status], $entity_reference_list);
665
          }
666
        }
667
      } else {
668
        drupal_set_message("Unimplemented type: " . $tokens[0], 'error');
669
      }
670
    }
671
    // type designations which are in this nomenclatural act.
672
    if (count($name_type_designation_refs) > 0) {
673
      $render_array['nomenclatural_act']['name_type_designations'] = compose_name_type_designations($name_type_designation_refs);
674
      $render_array['nomenclatural_act']['name_type_designations']['#prefix'] = '<p class="name_type_designations">';
675
      $render_array['nomenclatural_act']['name_type_designations']['#suffix'] = '</p>';
676
      $render_array['nomenclatural_act']['name_type_designations']['#weight'] = 20;
677
    }
678
    if (count($field_unit_uuids) > 0) {
679
      $specimen_type_designations_array = compose_specimen_type_designations($specimen_type_designation_refs, true);
680
      $render_array['nomenclatural_act']['specimen_type_designations'] = $specimen_type_designations_array['type_designations'];
681
      $render_array['map'] = $specimen_type_designations_array['map'];
682
      $render_array['map']['#weight'] = $render_array['nomenclatural_act']['#weight'] + 20;
683
    }
684
  }
685

    
686
  // name relations
687
  if($name_relations){
688
    $render_array['nomenclatural_act']['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null);
689
    $render_array['nomenclatural_act']['name_relations']['#weight'] = 10;
690
  }
691

    
692
  // citation
693
  if ($with_citation) {
694
    $render_array['citation'] = markup_to_render_array(
695
      "<div class=\"citation nomenclatural_act_citation" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
696
      . "<span class=\"label\">published in: </span>"
697
      . $registration_dto->bibliographicInRefCitationString
698
      . l(custom_icon_font_markup('icon-interal-link-alt-solid', array('class' => array('superscript'))), path_to_reference($registration_dto->citationUuid), array('html' => true))
699
      . "</div>",
700
      $render_array['nomenclatural_act']['#weight'] + 10 );
701
  }
702

    
703
  $render_array['nomenclatural_act']['footnotes'] = markup_to_render_array(render_footnotes(),100);
704

    
705
  // registration date and office
706
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto);
707
  if($registration_date_insitute_markup){
708
    $render_array['registration_date_and_institute'] = markup_to_render_array(
709
      $registration_date_insitute_markup . '</p>',
710
      100);
711
  }
712

    
713

    
714
  return $render_array;
715
}
716

    
717

    
718
/**
719
 * Composes a compact representation for a registrationDTO object
720
 *
721
 * Registrations which are not yet published are suppressed.
722
 *
723
 * @param $registration_dto
724
 * @param $style string
725
 *   The style of how to compose the 'identifier' and 'registration_date_and_institute' part with the summary
726
 *   - 'citation': Similar to the arrearance of nomenclatural acts in print media
727
 *   - 'list-item' : style suitable for result lists etc
728
 *
729
 * @return array
730
 *    A drupal render array with the elements:
731
 *    - 'registration-metadata' when $style == 'list-item'
732
 *    - 'summary'
733
 * @ingroup compose
734
 */
735
function compose_registration_dto_compact($registration_dto, $style = 'citation', $tag_enclosing_summary = 'p')
736
{
737
  $render_array = array();
738
  $media_link_map = array();
739

    
740
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
741
    return $render_array;
742
  }
743

    
744
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto, 'span');
745
  $itentifier_markup = l($registration_dto->identifier, path_to_registration($registration_dto->identifier), array('attributes' => array('class' => array('identifier'))));
746

    
747
  $tagged_text_options = array();
748
  if(isset($registration_dto->nameRef)){
749
    $tagged_text_options[] = array(
750
      'filter-type' => 'name',
751
      'prefix' => '<span class="registered_name">',
752
      'suffix' => '</span>',
753
    );
754
  } else {
755
    $tagged_text_options[] = array(
756
      'filter-type' => 'name',
757
      'prefix' => '<span class="referenced_typified_name">',
758
      'suffix' => '</span>',
759
    );
760
  }
761
  cdm_tagged_text_add_options($registration_dto->summaryTaggedText, $tagged_text_options);
762
  $taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
763
  foreach ($taggged_text_expanded  as $tagged_text){
764
    if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {
765
      $mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));
766
      if(isset($mediaDTOs[0]->uri)){
767
        $media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';
768
        $tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);
769
        $media_link_map[$media_url_key] =  cdm_external_uri($mediaDTOs[0]->uri, true);
770
      }
771
    }
772
  }
773
  $registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
774
  foreach($media_link_map as $media_url_key => $link){
775
    $registation_markup = str_replace($media_url_key, $link, $registation_markup);
776
  }
777
  if($style == 'citation') {
778
    $registation_markup = $registation_markup . ' ' . $itentifier_markup . ' ' . $registration_date_insitute_markup;
779
  } else {
780
    $render_array['registration-metadata'] = markup_to_render_array('<div class="registration-metadata">' . $itentifier_markup . ' ' . $registration_date_insitute_markup. "</div>", -10);
781
  }
782
  $render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . ' class="registration-summary">' . $registation_markup . '</' . $tag_enclosing_summary . '>', 0);
783

    
784
  return $render_array;
785
}
786

    
787

    
788
/**
789
 * Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.
790
 *
791
 * @param $registration_dto
792
 * @return string
793
 *    The markup or an empty string
794
 */
795
function render_registration_date_and_institute($registration_dto, $enclosing_tag = 'p') {
796
  $registration_date_institute_markup = '';
797
  if ($registration_dto->registrationDate) {
798
    $date_string = format_datetime($registration_dto->registrationDate);
799
    if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {
800
      $registration_date_institute_markup =
801
        t("Registration on @date in @institution", array(
802
          '@date' => $date_string,
803
          '@institution' => $registration_dto->institutionTitleCache,
804
        ));
805
    } else {
806
      $registration_date_institute_markup =
807
        t("Registration on @date", array(
808
          '@date' => $date_string
809
        ));
810
    }
811
    $registration_date_institute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_institute_markup . '</' .$enclosing_tag . '>';
812
  }
813
  return $registration_date_institute_markup;
814
}
815

    
816

    
817
/**
818
 * @param $registrations
819
 * @return string
820
 */
821
function render_registrations($registrations)
822
{
823
  $registration_markup = '';
824
  $registration_markup_array = array();
825
  if ($registrations) {
826
    foreach ($registrations as $reg) {
827
      $registration_markup_array[] = render_registration($reg);
828
    }
829
    $registration_markup = " Registration" . (count($registration_markup_array) > 1 ? 's: ' : ': ')
830
      . join(', ', $registration_markup_array);
831
  }
832
  return $registration_markup;
833
}
834

    
835

    
836
/**
837
 * Renders a registration
838
 *
839
 * TODO replace by compose_registration_dto_compact
840
 * @param $registration
841
 */
842
function render_registration($registration){
843
  $markup = '';
844

    
845
  if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
846
    $office_class_attribute = '';
847
    if(isset($registration->institution->titleCache)){
848
      $office_class_attribute = registration_intitute_class_attribute($registration);
849
    }
850
    $markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, path_to_registration($registration->identifier)) . ', '
851
      .  preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
852
      . '</span>';
853
  }
854
  return $markup;
855
}
856

    
857
/**
858
 * @param $registration
859
 * @return string
860
 */
861
function registration_intitute_class_attribute($registration_dto)
862
{
863
  if(isset($registration_dto->institutionTitleCache)){
864
    $institutionTitleCache = $registration_dto->institutionTitleCache;
865
  } else {
866
    // fall back option to also support cdm entities
867
    $institutionTitleCache = @$registration_dto->institution->titleCache;
868
  }
869
  return $institutionTitleCache ? 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $institutionTitleCache)) : '';
870
}
871

    
872

    
873
/**
874
 * Renders and array of CDM TypeDesignations
875
 *
876
 *  - NameTypeDesignation
877
 *  - SpecimenTypeDesignation
878
 *  - TextualTypeDesignation
879
 *
880
 * @param object $type_designations an array of cdm TypeDesignation entities
881
 *  to render
882
 * @param string $enclosing_tag the tag element type to enclose the whole list
883
 *  of type designation with. By default this DOM element is <ul>
884
 * @param string $element_tag the tag element type to be used for each
885
 *  type designation item.
886
 * @param bool $link_to_specimen_page whether a specimen in type designation element
887
 *  should be a link or not.
888
 *
889
 * @return string The markup.
890
 *
891
 * @InGroup Render
892
 */
893
function render_type_designations($type_designations, $enclosing_tag = 'ul', $element_tag =  'li', $link_to_specimen_page = true) {
894

    
895
  // need to add element to render path since type designations
896
  // need other name render template
897
  RenderHints::pushToRenderStack('typedesignations');
898

    
899
  $out = '<' . $enclosing_tag .' class="typeDesignations">';
900
  $specimen_type_designations = array();
901
  $name_type_designations = array();
902
  $textual_type_designations = array();
903
  $separator = ',';
904

    
905
  foreach ($type_designations as $type_designation) {
906
    switch ($type_designation->class) {
907
      case 'SpecimenTypeDesignation':
908
        $specimen_type_designations[] = $type_designation;
909
        break;
910
      case 'NameTypeDesignation':
911
        $name_type_designations[] = $type_designation;
912
        break;
913
      case 'TextualTypeDesignation':
914
        $textual_type_designations[] = $type_designation;
915
        break;
916
      default:  throw new Exception('Unknown type designation class: ' . $type_designation->class);
917
    }
918
  }
919

    
920
  // NameTypeDesignation ..................................
921
  if(!empty($name_type_designations)){
922
    usort($name_type_designations, "compare_type_designations_by_status");
923
    foreach($name_type_designations as $name_type_designation){
924
      if ($name_type_designation->notDesignated) {
925
        $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($name_type_designation) . '">' .  type_designation_status_label_markup($name_type_designation)  . ': '
926
          . t('not designated') . '</'. $element_tag .'>';
927
      }
928
      elseif (isset($name_type_designation->typeName)) {
929
        $link_to_name_page = url(path_to_name($name_type_designation->typeName->uuid));
930
        $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($name_type_designation) . '">' .  type_designation_status_label_markup($name_type_designation) ;
931

    
932
        if (!empty($name_type_designation->source->citation)) {
933
          $out .= type_designation_citation_layout($name_type_designation, $separator); // TODO type_designation_citation_layout() needs most probably to be replaced
934

    
935
        }
936
        $referenceUri = '';
937
        if (isset($name_type_designation->typeName->nomenclaturalSource->citation)) {
938
          $referenceUri = url(path_to_reference($name_type_designation->typeName->nomenclaturalSource->citation->uuid));
939
        }
940
        $out .= ': ' . render_taxon_or_name($name_type_designation->typeName, $link_to_name_page, $referenceUri, TRUE, TRUE);
941
      }
942
      $annotations_and_sources = handle_annotations_and_sources(
943
        $name_type_designation,
944
        typedesignations_annotations_and_sources_config(),
945
        '',
946
        RenderHints::getFootnoteListKey());
947
      $out .= $annotations_and_sources['foot_note_keys'];
948
    }
949
  } // END NameTypeDesignation
950

    
951
  // SpecimenTypeDesignation ...................................
952
  if (!empty($specimen_type_designations)) {
953
    usort($specimen_type_designations, "compare_specimen_type_designation");
954
    foreach ($specimen_type_designations as $specimen_type_designation) {
955
      $type_citation_markup = '';
956

    
957
      if (!empty($specimen_type_designation->source->citation)) {
958

    
959
        $citation_footnote_str = cdm_reference_markup($specimen_type_designation->source->citation, null, false, true);
960
        $author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $specimen_type_designation->source->citation->uuid);
961

    
962
        if (!empty($author_team->titleCache)) {
963
          $year = @timePeriodToString($specimen_type_designation->source->citation->datePublished, true, 'YYYY');
964
          $authorteam_str = $author_team->titleCache . ($year ? ' ' : '') . $year;
965
          if ($authorteam_str == $specimen_type_designation->source->citation->titleCache) {
966
            $citation_footnote_str = '';
967
          }
968
        } else {
969
          $authorteam_str = $citation_footnote_str;
970
          // no need for a footnote in case in case it is used as replacement for missing author teams
971
          $citation_footnote_str = '';
972
        }
973

    
974
        // for being registered a typedesignation MUST HAVE a citation, so it is save to handle the
975
        // Registration output in if condition checking if the citation is present
976
        $registration_markup = render_registrations($specimen_type_designation->registrations);
977
        $citation_footnote_str .= ($citation_footnote_str ? ' ' : '') . $registration_markup;
978

    
979
        $footnote_key_markup = '';
980
        if ($citation_footnote_str) {
981
          // footnotes should be rendered in the parent element so we
982
          // are relying on the FootnoteListKey set there
983
          $_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $citation_footnote_str);
984
          $footnote_key_markup = render_footnote_key($_fkey2, $separator, TRUE);
985
        }
986

    
987
        $type_citation_markup .= '&nbsp;(' . t('designated by') . '&nbsp;<span class="typeReference">' . $authorteam_str . '</span>';
988
        if (!empty($specimen_type_designation->source->citationMicroReference)) {
989
          $type_citation_markup .= ': ' . trim($specimen_type_designation->source->citationMicroReference);
990
        }
991
        $type_citation_markup .= $footnote_key_markup . ')';
992

    
993
      }
994

    
995

    
996
      $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($specimen_type_designation) . '">';
997
      $out .= type_designation_status_label_markup($specimen_type_designation) . $type_citation_markup;
998

    
999

    
1000
      $derivedUnitFacadeInstance = null;
1001
      if (isset($specimen_type_designation->typeSpecimen)) {
1002
        $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $specimen_type_designation->typeSpecimen->uuid);
1003
      }
1004

    
1005
      if (!empty($derivedUnitFacadeInstance->titleCache)) {
1006
        $specimen_markup = $derivedUnitFacadeInstance->titleCache;
1007
        if($link_to_specimen_page && isset($derivedUnitFacadeInstance->specimenLabel) && $derivedUnitFacadeInstance->specimenLabel){
1008
          $specimen_markup = str_replace($derivedUnitFacadeInstance->specimenLabel, l($derivedUnitFacadeInstance->specimenLabel, path_to_specimen($specimen_type_designation->typeSpecimen->uuid)), $specimen_markup);
1009
        }
1010
        $annotations_and_sources = handle_annotations_and_sources(
1011
          $derivedUnitFacadeInstance,
1012
          typedesignations_annotations_and_sources_config(),
1013
          '',
1014
          RenderHints::getFootnoteListKey()
1015
        );
1016
        $out .= ': <span class="' . html_class_attribute_ref($specimen_type_designation->typeSpecimen) . '">'
1017
          . $specimen_markup
1018
          . '</span>'; // . ': ' . theme('cdm_specimen', array('specimenTypeDesignation' => $derivedUnitFacadeInstance));
1019
        if(!empty($derivedUnitFacadeInstance->preferredStableUri)){
1020
          $out .= ' ' . l($derivedUnitFacadeInstance->preferredStableUri, $derivedUnitFacadeInstance->preferredStableUri, array('absolute' => true));
1021
        }
1022
        $out .= $annotations_and_sources['foot_note_keys'];
1023
      }
1024
      $out .= '</'. $element_tag .'>';
1025
    }
1026
  } // END Specimen type designations
1027

    
1028
  // TextualTypeDesignation .........................
1029
  usort($textual_type_designations, 'compare_textual_type_designation');
1030
  if(!empty($textual_type_designations)) {
1031
    foreach ($textual_type_designations as $textual_type_designation) {
1032
      $annotations_and_sources = handle_annotations_and_sources(
1033
        $textual_type_designation,
1034
        array(
1035
          // these settings differ from those provided by typedesignations_annotations_and_sources_config()
1036
          // TODO is this by purpose? please document the reason for the difference
1037
          'sources_as_content' => false, // as footnotes
1038
          'link_to_name_used_in_source' => false,
1039
          'link_to_reference' => true,
1040
          'add_footnote_keys' => true,
1041
          'bibliography_aware' => false
1042
        ),
1043
        '',
1044
        RenderHints::getFootnoteListKey() // passing a defined key to avoid a separate annotation footnote key see https://dev.e-taxonomy.eu/redmine/issues/8543
1045
      );
1046
      $encasement =  $textual_type_designation->verbatim ? '"' : '';
1047
      $out .= '<' . $element_tag . ' class="' . html_class_attribute_ref($textual_type_designation) . '">' . type_designation_status_label_markup(null)
1048
        . ': ' .  $encasement . trim($textual_type_designation->text_L10n->text) . $encasement .  $annotations_and_sources['foot_note_keys'] .'</' . $element_tag . '>';
1049
//      if(is_array( $annotations_and_sources['source_references'])){
1050
//        $citation_markup = join(', ', $annotations_and_sources['source_references']);
1051
//      }
1052
//      $out .= $citation_markup;
1053
    }
1054
  }
1055

    
1056
  // Footnotes for citations, collection acronyms.
1057
  // footnotes should be rendered in the parent element so we
1058
  // are relying on the FootnoteListKey set there
1059
  $_fkey = FootnoteManager::addNewFootnote(
1060
    RenderHints::getFootnoteListKey(),
1061
    (isset($derivedUnitFacadeInstance->collection->titleCache) ? $derivedUnitFacadeInstance->collection->titleCache : FALSE)
1062
  );
1063
  $out .= render_footnote_key($_fkey, $separator);
1064
  $out .= '</' . $enclosing_tag .'>';
1065

    
1066
  RenderHints::popFromRenderStack();
1067

    
1068
  return $out;
1069
}
1070

    
1071

    
1072
/**
1073
 * Composes the textual representation for the type designation of taxon name identified by the uuid in with a map for the location data.
1074
 *
1075
 * @param $taxon_name_uuid
1076
 * @param $show_specimen_details
1077
 * @return array
1078
 *    A drupal render array with the following elements:
1079
 *    - 'type_designations'
1080
 *    - 'map'
1081
 *    - 'specimens'
1082
 *
1083
 * @ingroup compose
1084
 */
1085
function compose_type_designations($taxon_name_uuid, $show_specimen_details = false)
1086
{
1087
  $render_array = array(
1088
    'type_designations' => array(),
1089
    'map' => array(),
1090
    );
1091
  $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $taxon_name_uuid);
1092
  if ($type_designations) {
1093
    usort($type_designations, 'compare_specimen_type_designation');
1094
    $render_array['type_designations'] = markup_to_render_array(
1095
      render_type_designations($type_designations, 'div', 'div')
1096
    );
1097

    
1098
    $render_array['map'] = compose_type_designations_map($type_designations);
1099
  }
1100
  return $render_array;
1101
}
1102

    
1103

    
1104
/**
1105
 * Composes the TypedEntityReference to name type designations passed as associatve array.
1106
 *
1107
 * @param $type_entity_refs_by_status array
1108
 *   an associative array of name type type => TypedEntityReference for name type designations as
1109
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
1110
 *
1111
 * @ingroup compose
1112
 */
1113
function compose_name_type_designations($type_entity_refs_by_status){
1114
  $render_array = array();
1115
  $preferredStableUri = '';
1116
  foreach($type_entity_refs_by_status as $type_status => $name_type_entityRefs){
1117
    foreach ($name_type_entityRefs as $name_type_entity_ref){
1118
      $type_designation = cdm_ws_get(CDM_WS_TYPEDESIGNATION, array($name_type_entity_ref->uuid, 'preferredUri'));
1119
      $footnote_keys = '';
1120

    
1121
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
1122
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
1123
      }
1124
      // annotations and sources for the $derived_unit_facade_dto
1125
      $annotations_and_sources = handle_annotations_and_sources(
1126
        $name_type_entity_ref,
1127
        typedesignations_annotations_and_sources_config(),
1128
        '',
1129
        RenderHints::getFootnoteListKey()
1130
      );
1131

    
1132
      $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type_entity_ref)  . '"><span class="type-status">'. ucfirst($type_status) . "</span>: "
1133
        . $name_type_entity_ref->label
1134
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
1135
        . $annotations_and_sources['foot_note_keys']
1136
        . '</div>');
1137
      }
1138
  }
1139
  return $render_array;
1140
}
1141

    
1142
/**
1143
 * Composes the specimen type designations with map from the the $type_entity_refs
1144
 *
1145
 * @param $type_entity_refs array
1146
 *   an associative array of specimen type type => TypedEntityReference for specimen type designations as
1147
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
1148
 *
1149
 * @param $show_media_specimen
1150
 * @return array
1151
 *    A drupal render array with the following elements:
1152
 *    - 'type_designations'
1153
 *    - 'map'
1154
 *
1155
 * @ingroup compose
1156
 *
1157
 */
1158
function compose_specimen_type_designations($type_entity_refs, $show_media_specimen){
1159

    
1160
  $render_array = array();
1161

    
1162
  $type_designation_list = array();
1163
  uksort($type_entity_refs, "compare_type_designation_status_labels");
1164
  foreach($type_entity_refs as $type_status => $type_designation_entity_refs){
1165
    foreach($type_designation_entity_refs as $type_designation_entity_ref){
1166

    
1167
      $type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($type_designation_entity_ref->uuid));
1168
      $type_designation_list[] = $type_designation; // collect for the map
1169

    
1170
      $derived_unit_facade_dto = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
1171
      // the media specimen is not contained in the $type_designation returned by CDM_PORTAL_TYPEDESIGNATION, so we need to fetch it separately
1172
      $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
1173

    
1174

    
1175
      $preferredStableUri = '';
1176
      $citation_markup = '';
1177
      $media = '';
1178

    
1179
      // annotations and sources for the $derived_unit_facade_dto
1180
      $annotations_and_sources = handle_annotations_and_sources(
1181
        $derived_unit_facade_dto,
1182
        typedesignations_annotations_and_sources_config(),
1183
        '',
1184
        RenderHints::getFootnoteListKey()
1185
      );
1186
      $source_citations = $annotations_and_sources['source_references'];
1187
      $foot_note_keys = $annotations_and_sources['foot_note_keys'];
1188

    
1189
      // preferredStableUri
1190
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
1191
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
1192
      }
1193

    
1194
      if($show_media_specimen && $mediaSpecimen){
1195
        // compose output
1196
        // mediaURI
1197
        if(isset($mediaSpecimen->representations[0])) {
1198
          $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
1199
          $captionElements = array(
1200
            '#uri' => t('open media'),
1201
            'elements' => array('-none-'),
1202
            'sources_as_content' => true
1203
          );
1204
          $media = compose_cdm_media_gallerie(array(
1205
            'mediaList' => array($mediaSpecimen),
1206
            'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $type_designation_entity_ref->uuid,
1207
            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
1208
            'cols' => $gallery_settings['cdm_dataportal_media_cols'],
1209
            'captionElements' => $captionElements,
1210
          ));
1211
        }
1212
        // citation and detail for the media specimen
1213
        $annotations_and_sources = handle_annotations_and_sources(
1214
          $mediaSpecimen,
1215
          typedesignations_annotations_and_sources_config(),
1216
          '',
1217
          RenderHints::getFootnoteListKey()
1218
        );
1219
        if(is_array( $annotations_and_sources['source_references'])){
1220
          $source_citations = array_merge($source_citations, $annotations_and_sources['source_references']);
1221
        }
1222
        if($annotations_and_sources['foot_note_keys']){
1223
          $foot_note_keys .= ', ' . $annotations_and_sources['foot_note_keys'];
1224
        }
1225
      }
1226

    
1227
      $citation_markup = join(', ', $source_citations);
1228

    
1229
      $specimen_markup = $derived_unit_facade_dto->titleCache;
1230
      if(isset($derived_unit_facade_dto->specimenLabel) && $derived_unit_facade_dto->specimenLabel){
1231
        $specimen_markup = str_replace(
1232
          $derived_unit_facade_dto->specimenLabel,
1233
          l($derived_unit_facade_dto->specimenLabel, path_to_specimen($type_designation->typeSpecimen->uuid)), $specimen_markup);
1234
      }
1235

    
1236
      $type_designation_render_array = markup_to_render_array(
1237
        '<div class="type_designation_entity_ref ' . html_class_attribute_ref($type_designation_entity_ref)  . '">
1238
          <span class="type-status">' . ucfirst($type_status) . "</span>: "
1239
        . $specimen_markup . $foot_note_keys
1240
        . ($citation_markup ? ' '. $citation_markup : '')
1241
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
1242
        . $media
1243
        . '</div>');
1244

    
1245
      $render_array['type_designations'][] = $type_designation_render_array;
1246
    }
1247
  }
1248
  if(count($type_designation_list) > 0 ){
1249
    $render_array['map'] = compose_type_designations_map($type_designation_list);
1250
  } else {
1251
    $render_array['map'] = array();
1252
  }
1253
  return $render_array;
1254
}
1255

    
1256
/**
1257
 * Provides the default configuration for typedesignations which
1258
 * are passed to the handle_annotations_and_sources()
1259
 * function:
1260
 * - 'sources_as_content' => TRUE,
1261
 * - 'link_to_name_used_in_source' => FALSE,
1262
 * - 'link_to_reference' => TRUE,
1263
 * - 'add_footnote_keys' => FALSE,
1264
 * - 'bibliography_aware' => FALSE
1265
 *
1266
 * @return array
1267
 */
1268
function typedesignations_annotations_and_sources_config() {
1269
  static $annotations_and_sources_config = [
1270
    'sources_as_content' => TRUE,
1271
    'link_to_name_used_in_source' => FALSE,
1272
    'link_to_reference' => TRUE,
1273
    'add_footnote_keys' => FALSE,
1274
    'bibliography_aware' => FALSE
1275
  ];
1276
  return $annotations_and_sources_config;
1277
}
1278

    
1279
/**
1280
 * @param $name_rel
1281
 * @param $current_name_uuid
1282
 * @param $current_taxon_uuid
1283
 * @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!
1284
 * @param $show_name_cache_only
1285
 *    The nameCache will be shown instead of the titleCache if this parameter is true.
1286
 * @return null|string
1287
 *    The markup or null
1288
 */
1289
function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $show_name_cache_only = false){
1290

    
1291
  $relationship_markup = null;
1292

    
1293
  $current_name_is_toName = $current_name_uuid == $name_rel->toName->uuid;
1294

    
1295
  if($current_name_is_toName){
1296
    $name = $name_rel->fromName;
1297
  } else {
1298
    $name = $name_rel->toName;
1299
  }
1300

    
1301
  cdm_load_tagged_full_title($name);
1302

    
1303
  $highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';
1304
  if(!$show_name_cache_only){
1305
    $relationship_markup = render_taxon_or_name($name,
1306
      url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false))
1307
    );
1308
  } else {
1309
    $relationship_markup = l(
1310
      '<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',
1311
      path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false),
1312
      array('html' => true)
1313
    );
1314
  }
1315

    
1316
  return $relationship_markup;
1317
}
1318

    
1319

    
1320
/**
1321
 * Composes an inline representation of selected name relationships
1322
 *
1323
 * The output of this function will be usually appended to taxon name representations.
1324
 * Only the following types are displayed: LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR, ORTHOGRAPHIC_VARIANT
1325
 *
1326
 * LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR are displayed as
1327
 * non {titleCache} nec {titleCache} nec {titleCache} whereas the related names
1328
 * are ordered alphabetically.
1329
 *
1330
 * ORTHOGRAPHIC_VARIANT is displayed as 'ort. var. {nameCache}'
1331
 *
1332
 * Related issues:
1333
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1334
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1335
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1336
 *   - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"
1337
 *
1338
 * @param $name_relations
1339
 *    The list of CDM NameRelationsips
1340
 * @param $current_name_uuid
1341
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1342
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1343
 * @param $suppress_if_current_name_is_source
1344
 *    The display of the relation will be
1345
 *    suppressed is the current name is on the source of the relation edge.
1346
 *    That is if it is on the from side of the relation. Except for 'blocking name for' which is
1347
 *    an inverse relation. For this relation type the toName is taken in to account.
1348
 * @param $current_taxon_uuid
1349
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1350
 * @return array
1351
 *    A drupal render array
1352
 *
1353
 * @ingroup Compose
1354
 */
1355
function compose_name_relationships_inline($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
1356

    
1357
  RenderHints::pushToRenderStack('homonym');
1358
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1359

    
1360
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));
1361
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1362
  foreach ($selected_name_rel_uuids as $uuid){
1363
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1364
    if($uuid != UUID_NAMERELATIONSHIPTYPE_MISSPELLING){
1365
      $name_rel_type_filter['inverse'][$uuid] = $uuid;
1366
    }
1367
  }
1368

    
1369
  $list_prefix = '<span class="name_relationships">[';
1370
  $list_suffix = ']</span>';
1371
  $item_prefix = '<span class="item">';
1372
  $item_suffix = '</span> ';
1373
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1374

    
1375
  // remove the glue space from the last item element which has been added by the $item_suffix = '</span> '
1376
  $items_ctn = count($render_array['list']['items']);
1377
  if($items_ctn){
1378
    $render_array['list']['items'][$items_ctn - 1]['#suffix'] = '</span>';
1379
  }
1380

    
1381
  RenderHints::popFromRenderStack();
1382
  return $render_array;
1383
}
1384

    
1385
/**
1386
 * Composes an list representation of the name relationships.
1387
 *
1388
 * The output of this function will be usually appended to taxon name representations.
1389
 *
1390
 * Related issues:
1391
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1392
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1393
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1394
 *
1395
 * @param $name_relations
1396
 *    The list of CDM NameRelationsips
1397
 * @param $current_name_uuid
1398
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1399
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1400
 * @param $current_taxon_uuid
1401
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1402
 * @return array
1403
 *    A drupal render array
1404
 *
1405
 * @ingroup Compose
1406
 */
1407
function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid) {
1408

    
1409
  // $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));
1410

    
1411
  $key = 'name_relationships';
1412
  RenderHints::pushToRenderStack($key);
1413
  if(RenderHints::isUnsetFootnoteListKey()){
1414
    RenderHints::setFootnoteListKey($key);
1415
  }
1416
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1417

    
1418
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, cdm_vocabulary_as_defaults(UUID_NAME_RELATIONSHIP_TYPE));
1419
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1420
  foreach ($selected_name_rel_uuids as $uuid){
1421
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1422
    $name_rel_type_filter['inverse'][$uuid] = $uuid;
1423
  }
1424

    
1425
  $list_prefix = '<div class="relationships_list name_relationships">';
1426
  $list_suffix = '</div>';
1427
  $item_prefix = '<div class="item">';
1428
  $item_suffix = '</div>';
1429

    
1430
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1431

    
1432
  RenderHints::popFromRenderStack();
1433
  if(RenderHints::getFootnoteListKey() == $key) {
1434
    $render_array['footnotes'] = markup_to_render_array(render_footnotes(RenderHints::getFootnoteListKey()));
1435
    RenderHints::clearFootnoteListKey();
1436
  }
1437
  return $render_array;
1438
}
1439

    
1440
/**
1441
 * @param $name_relations
1442
 * @param $name_rel_type_filter
1443
 *   Associative array with two keys:
1444
 *   - 'direct': the relationship type uuids for the direct direction of the relation edge to be included
1445
 *   - 'inverse': the relationship type uuids for the direct direction of the relation edge to be included
1446
 * @param $current_name_uuid
1447
 * @param $current_taxon_uuid
1448
 * @param $list_prefix
1449
 * @param $list_suffix
1450
 * @param $item_prefix
1451
 * @param $item_suffix
1452
 * @return array
1453
 *
1454
 * @ingroup Compose
1455
 */
1456
function compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid,
1457
                                    $list_prefix, $list_suffix, $item_prefix, $item_suffix)
1458
{
1459
  $non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,
1460
    UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,
1461
    UUID_NAMERELATIONSHIPTYPE_CONSERVED_AGAINST,
1462
    UUID_NAMERELATIONSHIPTYPE_MISSPELLING,
1463
    UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
1464

    
1465
  $render_array = array(
1466
    'list' => array(
1467
      '#prefix' => $list_prefix,
1468
      '#suffix' => $list_suffix,
1469
      'items' => array()
1470
    ),
1471
    'footnotes' => array()
1472
  );
1473

    
1474
  if ($name_relations) {
1475

    
1476
    // remove all relations which are not selected in the settings and
1477
    // separate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs
1478
    // for special handling
1479
    $filtered_name_rels = array();
1480
    $non_nec_name_rels = array();
1481
    $orthographic_variants = array();
1482
    foreach ($name_relations as $name_rel) {
1483
      $rel_type_uuid = $name_rel->type->uuid;
1484
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1485
      if ((!$is_inverse_relation && isset($name_rel_type_filter['direct'][$rel_type_uuid]) && $name_rel_type_filter['direct'][$rel_type_uuid])
1486
        ||($is_inverse_relation && isset($name_rel_type_filter['inverse'][$rel_type_uuid]) && $name_rel_type_filter['inverse'][$rel_type_uuid])) {
1487

    
1488
        if (array_search($rel_type_uuid, $non_nec_name_reltype_uuids) !== false && (
1489
            $current_name_uuid == $name_rel->fromName->uuid && $rel_type_uuid != UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1490
            || $current_name_uuid == $name_rel->toName->uuid && $rel_type_uuid == UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1491
          )
1492
        ){
1493
          $non_nec_name_rels[] = $name_rel;
1494
        } else if (UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $rel_type_uuid) {
1495
          $orthographic_variants[] = $name_rel;
1496
        } else {
1497

    
1498
          $filtered_name_rels[] = $name_rel;
1499
        }
1500
      }
1501
    }
1502
    $name_relations = $filtered_name_rels;
1503

    
1504
    usort($name_relations, 'compare_name_relations_by_term_order_index');
1505

    
1506
    // compose
1507
    foreach ($name_relations as $name_rel) {
1508

    
1509
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1510

    
1511
      $rel_footnote_key_markup = handle_name_relationship_as_footnote($name_rel);
1512
      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1513

    
1514
      $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1515
      $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1516
      $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
1517
      $relationship_markup = $symbol_markup . $relationship_markup;
1518
      if ($relationship_markup) {
1519
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1520
          null,
1521
          $item_prefix,
1522
          $item_suffix);
1523
      }
1524
    }
1525

    
1526
    // name relationships to be displayed as non nec
1527
    if (count($non_nec_name_rels) > 0) {
1528
      $non_nec_markup = '';
1529
      foreach ($non_nec_name_rels as $name_rel) {
1530
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1531
        $rel_footnote_key_markup = handle_name_relationship_as_footnote($name_rel);
1532
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1533
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1534
        $symbol = $non_nec_markup ? ' nec ' : 'non';
1535
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1536
        $non_nec_markup .= $symbol_markup . $relationship_markup;
1537
      }
1538
      if ($non_nec_markup) {
1539
        $render_array['list']['items'][] = markup_to_render_array($non_nec_markup,
1540
          null,
1541
          $item_prefix,
1542
          $item_suffix);
1543
      }
1544
    }
1545

    
1546
    // orthographic variants
1547
    if (count($orthographic_variants) > 0) {
1548
      foreach ($orthographic_variants as $name_rel) {
1549

    
1550
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1551
        $rel_footnote_key_markup = handle_name_relationship_as_footnote($name_rel);
1552
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, TRUE);
1553
        $nomref_footnote_key_markup = handle_nomenclatural_reference_as_footnote($name_rel->toName);
1554
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1555
        $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1556
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1557
        $relationship_markup = $symbol_markup . $relationship_markup . $nomref_footnote_key_markup;
1558
      }
1559
      if (isset($relationship_markup) && $relationship_markup) {
1560
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1561
          null,
1562
          $item_prefix,
1563
          $item_suffix);
1564
      }
1565
    }
1566
  }
1567
  return $render_array;
1568
}
1569

    
1570

    
1571

    
1572
/**
1573
 * @param $taxon
1574
 * @return array
1575
 */
1576
function cdm_name_relationships_for_taxon($taxon)
1577
{
1578
  $from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
1579
  $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
1580
  $name_relations = array_merge($from_name_relations, $to_name_relations);
1581
  return $name_relations;
1582
}
1583

    
1584

    
1585
/**
1586
 * Recursively searches the array for the $key and sets the given value.
1587
 *
1588
 * @param mixed $key
1589
 *   Key to search for.
1590
 * @param mixed $value
1591
 *   Value to set.'
1592
 * @param array $array
1593
 *   Array to search in.
1594
 *
1595
 * @return bool
1596
 *   True if the key has been found.
1597
 */
1598
function &array_setr($key, $value, array &$array) {
1599
  $res = NULL;
1600
  foreach ($array as $k => &$v) {
1601
    if ($key == $k) {
1602
      $v = $value;
1603
      return $array;
1604
    }
1605
    elseif (is_array($v)) {
1606
      $innerArray = array_setr($key, $value, $v);
1607
      if ($innerArray) {
1608
        return $array;
1609
      }
1610
    }
1611
  }
1612
  return $res;
1613
}
1614

    
1615
/**
1616
 * @todo Please document this function.
1617
 * @see http://drupal.org/node/1354
1618
 */
1619
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
1620
  $res = NULL;
1621
  $precedingElement = NULL;
1622
  foreach ($renderTemplate as &$part) {
1623
    foreach ($part as $key => &$element) {
1624
      if ($key == $contentElementKey) {
1625
        return $precedingElement;
1626
      }
1627
      $precedingElement = $element;
1628
    }
1629
  }
1630
  return $res;
1631
}
1632

    
1633
/**
1634
 * @todo Please document this function.
1635
 * @see http://drupal.org/node/1354
1636
 */
1637
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
1638
  $res = NULL;
1639
  $precedingKey = NULL;
1640
  foreach ($renderTemplate as &$part) {
1641
    if (is_array($part)) {
1642
      foreach ($part as $key => &$element) {
1643
        if ($key == $contentElementKey) {
1644
          return $precedingKey;
1645
        }
1646
        if (!str_beginsWith($key, '#')) {
1647
          $precedingKey = $key;
1648
        }
1649
      }
1650
    }
1651
  }
1652
  return $res;
1653
}
1654

    
1655
function nameTypeToDTYPE($dtype){
1656
  static $nameTypeLabelMap = array(
1657
    "ICNB" => "BacterialName",
1658
    "ICNAFP" => "BotanicalName",
1659
    "ICNCP" => "CultivarPlantName",
1660
    "ICZN" => "ZoologicalName",
1661
    "ICVCN" => "ViralName",
1662
    "Any taxon name" => "TaxonName",
1663
    "NonViral" => "TaxonName",
1664
    "Fungus" => "BotanicalName",
1665
    "Plant" => "BotanicalName",
1666
    "Algae" => "BotanicalName",
1667
  );
1668
  return $nameTypeLabelMap[$dtype];
1669

    
1670
}
1671

    
1672

    
1673
function compare_name_relations_by_term_order_index($name_rel1, $name_rel2){
1674
  return compare_terms_by_order_index($name_rel1->type, $name_rel2->type);
1675
}
1676

    
1677
/**
1678
 * Provides an array with the different registration types covered by the passed registration.
1679
 *
1680
 * The labels in the returned array are translatable.
1681
 *
1682
 * See also https://dev.e-taxonomy.eu/redmine/issues/8016
1683
 *
1684
 * @param $registration_dto
1685
 * @return array
1686
 *    An array of the labels describing the different registration types covered by the passed registration.
1687
 */
1688
function registration_types($registration_dto){
1689
  $reg_type_labels = array();
1690
  if(isset($registration_dto->nameRef)){
1691
    $reg_type_labels["name"] = t("new name");
1692
    $reg_type_labels["taxon"] = t("new taxon");
1693
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
1694
    $is_new_combination = true;
1695
    foreach($name_relations as $name_rel){
1696
      if(isset($name_rel->type->uuid)){
1697
        $name_is_from_name = $registration_dto->nameRef->uuid == $name_rel->fromName->uuid;
1698
        switch($name_rel->type->uuid) {
1699
          case UUID_NAMERELATIONSHIPTYPE_BASIONYM:
1700
            if(!$name_is_from_name){
1701
              $reg_type_labels["basionym"] = t("new combination");
1702
              $is_new_combination = true;
1703
            }
1704
            break;
1705
          case UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM:
1706
            if(!$name_is_from_name) {
1707
              $is_new_combination = true;
1708
            }
1709
            break;
1710
          case UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME:
1711
            if(!$name_is_from_name) {
1712
              $reg_type_labels["validation"] = t("validation");
1713
            }
1714
            break;
1715
          case UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT:
1716
            if(!$name_is_from_name) {
1717
              $reg_type_labels["orth_var"] = t("orthographical correction");
1718
            }break;
1719
          default:
1720
            // NOTHING
1721
        }
1722
      }
1723
    }
1724
    if($is_new_combination){
1725
      unset($reg_type_labels["taxon"]);
1726
    }
1727
  }
1728
  if(isset($registration_dto->orderdTypeDesignationWorkingSets)){
1729
    $reg_type_labels[] = t("new nomenclatural type");
1730
  }
1731
  return $reg_type_labels;
1732
}
1733

    
1734
/**
1735
 * Collects and deduplicates the type designations associated with the passes synonyms.
1736
 *
1737
 * @param $synonymy_group
1738
 *    An array containing a homotypic or heterotypic group of names.
1739
 * @param $accepted_taxon_name_uuid
1740
 *    The uuid of the accepted taxon name. Optional parameter which is required when composing
1741
 *    the information for the homotypic group. In this case the accepted taxon is not included
1742
 *    in the $synonymy_group and must therefor passed in this second parameter.
1743
 *
1744
 * @return array
1745
 *    The type designations
1746
 */
1747
function type_designations_for_synonymy_group($synonymy_group, $accepted_taxon_name_uuid = null)
1748
{
1749
  if (count($synonymy_group) > 0) {
1750
    $name_uuid = array_pop($synonymy_group)->name->uuid;
1751
  } else {
1752
    $name_uuid = $accepted_taxon_name_uuid;
1753
  }
1754
  if ($name_uuid) {
1755
   $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS_IN_HOMOTYPICAL_GROUP, $name_uuid);
1756
    if ($type_designations) {
1757
      return $type_designations;
1758
    }
1759
  }
1760

    
1761
  return array();
1762
}
1763

    
1764

    
1765
/**
1766
 * Compares two SpecimenTypeDesignations
1767
 *
1768
 * @param object $a
1769
 *   A SpecimenTypeDesignation.
1770
 * @param object $b
1771
 *   SpecimenTypeDesignation.
1772
 */
1773
function compare_specimen_type_designation($a, $b) {
1774

    
1775
  $cmp_by_status = compare_type_designations_by_status($a,$b);
1776
  if($cmp_by_status !== 0){
1777
    return $cmp_by_status;
1778
  }
1779

    
1780
  $aQuantifier = FALSE;
1781
  $bQuantifier = FALSE;
1782
  if ($aQuantifier == $bQuantifier) {
1783
    // Sort alphabetically.
1784
    $a_text =  isset($a->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $a->typeSpecimen->titleCache) : '';
1785
    $b_text =  isset($b->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $b->typeSpecimen->titleCache) : '';
1786
    return strcasecmp($a_text, $b_text);
1787
  }
1788
  return ($aQuantifier < $bQuantifier) ? -1 : (($aQuantifier > $bQuantifier) ? 1 : 0);
1789
}
1790

    
1791
/**
1792
 * Compares the status of two TypeDesignations
1793
 *
1794
 * @param object $a
1795
 *   A TypeDesignation
1796
 * @param object $b
1797
 *   TypeDesignation
1798
 */
1799
function compare_type_designations_by_status($a, $b) {
1800
  $status_a = isset($a->typeStatus) ? $a->typeStatus : null;
1801
  $status_b = isset($b->typeStatus) ? $b->typeStatus : null;
1802
  return compare_type_designation_status($status_a, $status_b);
1803
}
1804

    
1805
/**
1806
 * Compares two TypeDesignationStatusBase
1807
 *
1808
 * @param object $a
1809
 *   A TypeDesignationStatusBase.
1810
 * @param object $b
1811
 *   TypeDesignationStatusBase.
1812
 */
1813
function compare_type_designation_status($a, $b) {
1814
  $type_status_order = type_status_order();
1815
  $aQuantifier = FALSE;
1816
  $bQuantifier = FALSE;
1817
  if (isset($a->label) && isset($b->label)) {
1818
    $aQuantifier = array_search($a->label, $type_status_order);
1819
    $bQuantifier = array_search($b->label, $type_status_order);
1820
  }
1821
  return ($aQuantifier < $bQuantifier) ? -1 : (($aQuantifier > $bQuantifier) ? 1 : 0);
1822
}
1823

    
1824
/**
1825
 * Compares the two TextualTypeDesignations
1826
 *
1827
 * @param object $a
1828
 *   A TextualTypeDesignations.
1829
 * @param object $b
1830
 *   TextualTypeDesignations.
1831
 */
1832
function compare_textual_type_designation($a, $b) {
1833

    
1834
  $cmp_by_status = compare_type_designations_by_status($a,$b);
1835
  if($cmp_by_status !== 0){
1836
    return $cmp_by_status;
1837
  }
1838

    
1839
  $aQuantifier = FALSE;
1840
  $bQuantifier = FALSE;
1841
  if ($aQuantifier == $bQuantifier) {
1842
    // Sort alphabetically.
1843
    $a_text =  isset($a->text_L10n->text) ? $a->text_L10n->text : '';
1844
    $b_text =  isset($b->text_L10n->text) ? $b->text_L10n->text : '';
1845
    return strcasecmp($a_text, $b_text);
1846
  }
1847
  return ($aQuantifier < $bQuantifier) ? -1 : (($aQuantifier > $bQuantifier) ? 1 : 0);
1848
}
1849

    
1850

    
1851
/**
1852
 * Compares two SpecimenTypeDesignation status labels
1853
 *
1854
 * @param string $a
1855
 *   A TypeDesignationStatus label.
1856
 * @param string $b
1857
 *   A TypeDesignationStatus label.
1858
 */
1859
function compare_type_designation_status_labels($a, $b) {
1860

    
1861
  $type_status_order = type_status_order();
1862

    
1863
  $aQuantifier = FALSE;
1864
  $bQuantifier = FALSE;
1865
  if (isset($a) && isset($b)) {
1866
    $aQuantifier = array_search($a, $type_status_order);
1867
    $bQuantifier = array_search($b, $type_status_order);
1868
  }
1869
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1870
}
1871

    
1872
/**
1873
 * @return array
1874
 */
1875
function type_status_order()
1876
{
1877
  /*
1878
    This is the desired sort order as of now: Holotype Isotype Lectotype
1879
    Isolectotype Syntype.
1880
    TODO Basically, what we are trying to do is, we define
1881
    an ordered array of TypeDesignation-states and use the index of this array
1882
    for comparison. This array has to be filled with the cdm- TypeDesignation
1883
    states and the order should be parameterisable inside the dataportal.
1884
    */
1885
  // Make that static for now.
1886
  $type_status_order = array(
1887
    'Epitype',
1888
    'Holotype',
1889
    'Isotype',
1890
    'Lectotype',
1891
    'Isolectotype',
1892
    'Syntype',
1893
    'Paratype'
1894
  );
1895
  return $type_status_order;
1896
}
1897

    
1898
/**
1899
 * Return HTML for the lectotype citation with the correct layout.
1900
 *
1901
 * This function prints the lectotype citation with the correct layout.
1902
 * Lectotypes are renderized in the synonymy tab of a taxon if they exist.
1903
 *
1904
 * @param mixed $typeDesignation
1905
 *   Object containing the lectotype citation to print.
1906
 *
1907
 * @return string
1908
 *   Valid html string.
1909
 */
1910
function type_designation_citation_layout($typeDesignation, $footnote_separator = ',') {
1911
  $res = '';
1912
  $citation = $typeDesignation->source->citation;
1913
  $pages = $typeDesignation->source->citationMicroReference;
1914
  if(isset($typeDesignation->typeStatus->uuid) && isset($typeDesignation->typeStatus->representation_L10n)) {
1915
    if ( $typeDesignation->typeStatus->uuid == UUID_NTD_ORIGINAL_DESIGNATION || $typeDesignation->typeStatus->uuid == UUID_NTD_MONOTYPY) {
1916
      $res = ' (' . $typeDesignation->typeStatus->representation_L10n . ')';
1917
      return $res;
1918
    }
1919
  }
1920

    
1921
  if ($citation) {
1922
    // $type = $typeDesignation_citation->type;
1923
    $year = isset($citation->datePublished->start) ? substr($citation->datePublished->start, 0, 4) : '';
1924
    $author = isset($citation->authorship->titleCache) ? $citation->authorship->titleCache : '';
1925
    $res .= ' (designated by ';
1926
    $res .= $author;
1927
    $res .= ($year ? ' ' . $year : '');
1928
    $res .= ($pages ? ': ' . $pages : '');
1929
    // $res .= ')';
1930

    
1931
    // footnotes should be rendered in the parent element so we
1932
    // are relying on the FootnoteListKey set there
1933
    $fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $citation->titleCache);
1934
    $res .= render_footnote_key($fkey_typeDesignation, $footnote_separator,TRUE) . ')';
1935
  }
1936
  return $res;
1937
}
1938

    
1939
/**
1940
 * Creates markup for the status of a type designation. In case the status or its representation is missing the label will be set to "Type"
1941
 *
1942
 * @param $type_designation
1943
 * @return string
1944
 */
1945
function type_designation_status_label_markup($type_designation)
1946
{
1947
  return '<span class="type-status">'
1948
    . ((isset($type_designation->typeStatus->representation_L10n)) ? ucfirst($type_designation->typeStatus->representation_L10n) : t('Type')) . '</span>'
1949
    ;
1950
}
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