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cdm-dataportal / modules / cdm_dataportal / includes / name.inc @ 1c30a02b

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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
/**
35
 * 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 $renderPath.
70
 * @return array
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 *   An associative array, the render template
72
 */
73
function get_nameRenderTemplate($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) {
83
    $render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);
84
    // needs to be converted to an array
85
    $render_templates = (object_to_array($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){
92
          $split_render_templates[$path] = $template;
93
        }
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);
103
  } 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
114
  // 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;
120
        break;
121
      }
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.
162
 *
163
 * 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
168
 *   - reference: the nomenclatural reference,
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 *   - microreference:  Volume, page number etc.
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 *   - status:  The nomenclatural status of a name
171
 *   - 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),
202
 *        'descriptionPart' => array('description' => TRUE),
203
 *    ),
204
 *    '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 $taxonName
255
 *    cdm TaxonName instance
256
 * @param $name_link
257
 *    URI to the taxon, @see path_to_taxon(), must be processed by url() before passing to this method
258
 * @param $reference_link
259
 *    URI to the reference, @see path_to_reference(), must be processed by url() before passing to this method
260
 * @param $show_annotations
261
 *    turns the display of annotations on
262
 * @param $is_type_designation
263
 *    To indicate that the supplied taxon name is a name type designation.
264
 * @param $skiptags
265
 *    an array of name elements tags like 'name', 'rank' to skip. The name part
266
 *          'authors' will not ber affected by this filter. This part is managed though the render template
267
 *          mechanism.
268
 * @param $is_invalid
269
 *   Indicates that this taxon is invalid. In this case the name part will be shown in double quotes.
270
 *   This is useful when rendering taxon relation ships.
271
 *
272
 * @return string
273
 *  The markup for a taxon name.
274
 *
275
 */
276
function render_taxon_or_name($taxon_name_or_taxon_base, $name_link = NULL, $reference_link = NULL,
277
  $show_annotations = true, $is_type_designation = false, $skiptags = array(), $is_invalid = false) {
278

    
279
  $is_doubtful = false;
280

    
281
  if($taxon_name_or_taxon_base->class == 'Taxon' || $taxon_name_or_taxon_base->class == 'Synonym'){
282
    if(isset($taxon_name_or_taxon_base->name)){
283
      $taxonName = $taxon_name_or_taxon_base->name;
284
    } else {
285
      $taxonName = cdm_ws_get(CDM_WS_TAXON . '/$0/name', array($taxon_name_or_taxon_base->uuid));
286
    }
287
    $is_doubtful = $taxon_name_or_taxon_base->doubtful;
288
    // use the TaxonBase.tagged_title so we have the secRef
289
    $tagged_title = $taxon_name_or_taxon_base->taggedTitle;
290
  } else {
291
    // assuming this is a TaxonName
292
    $taxonName = $taxon_name_or_taxon_base;
293
    if(isset($taxonName->taggedFullTitle)){
294
      $tagged_title = $taxon_name_or_taxon_base->taggedFullTitle;
295
    } else {
296
      $tagged_title = $taxon_name_or_taxon_base->taggedName;
297
    }
298
  }
299

    
300

    
301
  $renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $name_link, $reference_link);
302
  $partDefinition = get_partDefinition($taxonName->nameType);
303

    
304
  // Apply definitions to template.
305
  foreach ($renderTemplate as $part => $uri) {
306

    
307
    if (isset($partDefinition[$part])) {
308
      $renderTemplate[$part] = $partDefinition[$part];
309
    }
310
    if (is_array($uri) && isset($uri['#uri'])) {
311
      $renderTemplate[$part]['#uri'] = $uri['#uri'];
312
    }
313
  }
314

    
315
  $secref_tagged_text = tagged_text_extract_reference_and_detail($tagged_title);
316
  // taxon names will have the nomenclatural reference in the tagged full title:
317
  $nomref_tagged_text = tagged_text_extract_reference($tagged_title);
318
  $nom_status_tagged_text = tagged_text_extract_nomstatus($tagged_title);
319
  $appended_phrase_tagged_text = array(); // this is filled later
320

    
321
  normalize_tagged_text($tagged_title);
322

    
323
  $is_valid_tagged_title =
324
    isset($tagged_title)
325
    && is_array($tagged_title)
326
    && isset($tagged_title[0]->text)
327
    && is_string($tagged_title[0]->text)
328
    && $tagged_title[0]->text != ''
329
    && isset($tagged_title[0]->type);
330
  $lastAuthorElementString = FALSE;
331

    
332
  $name_encasement = $is_invalid ? '"' : '';
333
  $doubtful_marker = $is_doubtful ? '?&#8239;' : ''; // 	&#8239; =  NARROW NO-BREAK SPACE
334
  $doubtful_marker_markup = '';
335

    
336
  if($doubtful_marker){
337
    $doubtful_marker_markup = '<span class="doubtful">' . $doubtful_marker . '</span>';
338
    if($tagged_title[0]->text == '?' ){
339
      // remove the first tagged text element
340
      unset($tagged_title[0]);
341
    }
342
  }
343

    
344
  // split off all appendedPhrase item  from the end of the array (usually there only should  be one)
345
  while($tagged_title[count($tagged_title)-1]->type == "appendedPhrase"){
346
    $appended_phrase_tagged_text[] = array_pop($tagged_title);
347
  }
348

    
349
  // Got to use second entry as first one, see ToDo comment below ...
350
  if ($is_valid_tagged_title) {
351

    
352
    $taggedName = $tagged_title;
353
    $hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
354
    $hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
355

    
356

    
357
    if (!(($hasNamePart_with_Authors) || ($hasNameAuthorPart_with_Authors))) {
358
      // Find author and split off from name.
359
      // TODO expecting to find the author as the last element.
360
      /*
361
      if($taggedName[count($taggedName)- 1]->type == 'authors'){
362
        $authorTeam = $taggedName[count($taggedName)- 1]->text;
363
        unset($taggedName[count($taggedName)- 1]);
364
      }
365
      */
366

    
367
      // Remove all authors.
368
      $taggedNameNew = array();
369
      foreach ($taggedName as $element) {
370
        if ($element->type != 'authors') {
371
          $taggedNameNew[] = $element;
372
        }
373
        else {
374
          $lastAuthorElementString = $element->text;
375
        }
376
      }
377
      $taggedName = $taggedNameNew;
378
      unset($taggedNameNew);
379
    }
380
    $name = '<span class="' . $taxonName->class . '">' . $doubtful_marker_markup . $name_encasement . cdm_tagged_text_to_markup($taggedName, $skiptags) . $name_encasement . '</span>';
381
  }
382
  else {
383
    // use titleCache instead
384
    $name = '<span class="' . $taxonName->class . '_titleCache">' . $doubtful_marker_markup . $name_encasement . $taxonName->titleCache . $name_encasement . '</span>';
385
  }
386

    
387

    
388
  if(isset($appended_phrase_tagged_text[0])){
389
    $name .= ' <span class="appended-phrase">'. cdm_tagged_text_to_markup($appended_phrase_tagged_text) . '</span>';
390
  }
391

    
392
  // Fill name into $renderTemplate.
393
  array_setr('name', $name , $renderTemplate);
394

    
395
  // Fill with authorTeam.
396
  /*
397
  if($authorTeam){
398
    $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
399
    array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
400
  }
401
  */
402

    
403
  // Fill with reference.
404
  if (isset($renderTemplate['referencePart']) && !$is_type_designation) {
405

    
406
    $registrations = cdm_ws_get(CDM_WS_NAME, array($taxonName->uuid, "registrations"));
407
    $registration_markup = render_registrations($registrations);
408

    
409
    // default separator
410
    $separator = '';
411

    
412
    // [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
413
    // Komma nach dem Autornamen ist √ľberall dort falsch, wo ein "in" folgt."
414
    if (isset($renderTemplate['referencePart']['reference'])) {
415
      $microreference = NULL;
416
      if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {
417
        $microreference = $taxonName->nomenclaturalMicroReference;
418
      }
419
      if(count($nomref_tagged_text) == 0 && isset($taxonName->nomenclaturalReference)){
420
        // TODO is this case still relevant? The tagged text should already contain all information!
421
        $citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalReference->uuid, $microreference);
422
        // Find preceding element of the reference.
423
        $precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
424
        if (str_beginsWith($citation, ", in")) {
425
          $citation = substr($citation, 2);
426
          $separator = ' ';
427
        }
428
        elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {
429
          $separator = ', ';
430
        } else {
431
          $separator = ' ';
432
        }
433
        $referenceArray['#separator'] = $separator;
434
        $referenceArray['#html'] = '<span class="reference">' . $citation . '</span>' . $registration_markup;
435
      } else {
436
        // this ist the case for taxon names
437
        $referenceArray['#html'] = cdm_tagged_text_to_markup($nomref_tagged_text);
438
      }
439

    
440

    
441
      array_setr('reference', $referenceArray, $renderTemplate);
442
    }
443

    
444
    // If authors have been removed from the name part the last named authorteam
445
    // should be added to the reference citation, otherwise, keep the separator
446
    // out of the reference.
447
    if (isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString) {
448
      // If the nomenclaturalReference citation is not included in the
449
      // reference part but display of the microreference
450
      // is wanted, append the microreference to the authorTeam.
451
      $citation = '';
452
      if (!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])) {
453
        $separator = ": ";
454
        $citation = $taxonName->nomenclaturalMicroReference;
455
      }
456
      $referenceArray['#html'] = ' <span class="reference">' . $lastAuthorElementString . $separator . $citation . '</span>';
457
      array_setr('authors', $referenceArray, $renderTemplate);
458
    }
459
  }
460

    
461
  $is_reference_year = false;
462
  if (isset($renderTemplate['referenceYearPart']['reference.year'])) {
463
    if(isset($taxonName->nomenclaturalReference->datePublished)){
464
      $referenceArray['#html'] = ' <span class="reference">' . timePeriodToString($taxonName->nomenclaturalReference->datePublished) . '</span>';
465
      array_setr('reference.year', $referenceArray, $renderTemplate);
466
      $is_reference_year = true;
467
    }
468
  }
469

    
470
  // Fill with status.
471
  if(isset($renderTemplate['statusPart']['status'])){
472
    if (isset($nom_status_tagged_text[0])) {
473
        $tt_to_markup_options = array('html' => false);
474
        foreach ($nom_status_tagged_text as &$tt){
475
         if($tt->type == 'nomStatus'&& isset($tt->entityReference)) {
476
           $nom_status = cdm_ws_get(CDM_WS_NOMENCLATURALSTATUS, array($tt->entityReference->uuid));
477
           $nom_status_fkey = nomenclatural_status_footnote_markup($nom_status);
478
           $tt->text .= $nom_status_fkey;
479
           $tt_to_markup_options['html'] = true;
480
         }
481
        }
482
        array_setr(
483
          'status',
484
          '<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, array('postSeparator'), 'span', $tt_to_markup_options) . '</span>',
485
          $renderTemplate);
486
    }
487
  }
488

    
489
  if (isset($renderTemplate['secReferencePart'])){
490
    if(isset($secref_tagged_text[1])){
491
      $post_separator_markup = $is_reference_year ? '.': '';
492
      if(isset($nom_status_tagged_text[count($nom_status_tagged_text) - 1]) && ($nom_status_tagged_text[count($nom_status_tagged_text) - 1]->type ==  'postSeparator')){
493
        $post_separator_markup = cdm_tagged_text_to_markup(array($nom_status_tagged_text[count($nom_status_tagged_text) - 1 ]));
494
      };
495
      array_setr('secReference',
496
        $post_separator_markup
497
          . ' <span class="sec_reference">'
498
          . join('', cdm_tagged_text_values($secref_tagged_text))
499
          . '</span>', $renderTemplate);
500
    }
501
  }
502

    
503
  // Fill with protologues etc...
504
  $descriptionHtml = '';
505
  if (array_setr('description', TRUE, $renderTemplate)) {
506
    $descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
507
    if($descriptions){
508
      foreach ($descriptions as $description) {
509
        if (!empty($description)) {
510
          foreach ($description->elements as $description_element) {
511
            $second_citation = '';
512
            if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {
513
              if(isset($description_element->feature) && $description_element->feature->uuid == UUID_ADDITIONAL_PUBLICATION){
514
                $prefix =  '& ';
515
              } else {
516
                $prefix = '';
517
              }
518
              $second_citation = ' [' . $prefix . $description_element->multilanguageText_L10n->text . '].';
519
            }
520
            $descriptionHtml .= $second_citation;
521
            $descriptionHtml .= cdm_description_element_media(
522
                $description_element,
523
                array(
524
                  'application/pdf',
525
                  'image/png',
526
                  'image/jpeg',
527
                  'image/gif',
528
                  'text/html',
529
                )
530
            );
531

    
532
          }
533
        }
534
      }
535
    }
536
    array_setr('description', $descriptionHtml, $renderTemplate);
537
  }
538

    
539
  // Render.
540
  $out = '';
541
  if(isset($_REQUEST['RENDER_PATH'])){
542
    // developer option to show the render path with each taxon name
543
    $out .= '<span class="render-path">' . RenderHints::getRenderPath() . '</span>';
544
  }
545
  $out .= '<span class="' . html_class_attribute_ref($taxon_name_or_taxon_base)
546
    . '" data-cdm-ref="/name/' . $taxonName->uuid . '" data-cdm-render-path="' . RenderHints::getRenderPath() .'">';
547

    
548
  foreach ($renderTemplate as $partName => $part) {
549
    $separator = '';
550
    $partHtml = '';
551
    $uri = FALSE;
552
    if (!is_array($part)) {
553
      continue;
554
    }
555
    if (isset($part['#uri']) && is_string($part['#uri'])) {
556
      $uri = $part['#uri'];
557
      unset($part['#uri']);
558
    }
559
    foreach ($part as $key => $content) {
560
      $html = '';
561
      if (is_array($content)) {
562
        $html = $content['#html'];
563
        if(isset($content['#separator'])) {
564
          $separator = $content['#separator'];
565
        }
566
      }
567
      elseif (is_string($content)) {
568
        $html = $content;
569
      }
570
      $partHtml .= '<span class="' . $key . '">' . $html . '</span>';
571
    }
572
    if ($uri) {
573
      // cannot use l() here since the #uri aleady should have been processed through uri() at this point
574
      $out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';
575

    
576
    }
577
    else {
578
      $out .= $separator . $partHtml;
579
    }
580
  }
581
  $out .= '</span>';
582
  if ($show_annotations) {
583
    // $out .= render_entities_annotations_as_footnote_keys([$taxonName]);
584
  }
585
  return $out;
586
}
587

    
588

    
589

    
590
/**
591
 * Composes information for a registration from a dto object.
592
 *
593
 * Registrations which are not yet published are suppressed.
594
 *
595
 * @param $registration_dto
596
 * @param $with_citation
597
 *   Whether to show the citation.
598
 *
599
 * @return array
600
 *    A drupal render array with the elements:
601
 *    - 'name'
602
 *    - 'name-relations'
603
 *    - 'specimen_type_designations'
604
 *    - 'name_type_designations'
605
 *    - 'citation'
606
 *    - 'registration_date_and_institute'
607
 * @ingroup compose
608
 */
609
function compose_registration_dto_full($registration_dto, $with_citation = true)
610
{
611
  $render_array = array(
612
    '#prefix' => '<div class="registration">',
613
    '#suffix' => '</div>'
614
  );
615

    
616
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
617
    return $render_array;
618
  }
619

    
620
  $render_array['sub_headline'] = markup_to_render_array(join(", ", registration_types($registration_dto)),-10, '<h3 class="registration_type">' . t('Event: '), '</h3>' );
621
  $render_array['nomenclatural_act'] = array(
622
    '#weight' => 0,
623
    '#prefix' => '<div class="nomenclatural_act">',
624

    
625
    '#suffix' => '</div>'
626
  );
627

    
628
  // name
629
  $name_relations = null;
630
  if($registration_dto->nameRef){
631
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
632
    cdm_load_tagged_full_title($name);
633
    $render_array['nomenclatural_act']['published_name'] = markup_to_render_array('<div class="published-name">' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</div>', 0);
634
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
635
    // need to create the name relationships later, so that the foot notes are in correct order, see section // name relations
636
  } else {
637
    // in this case the registration must have a
638
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->typifiedNameRef->uuid);
639
    $render_array['typified_name'] = markup_to_render_array('<p class="typified-name">for ' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</p>', 40);
640
  }
641

    
642
  // typedesignation in detail
643
  if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
644
    $field_unit_uuids = array();
645
    $specimen_type_designation_refs = array();
646
    $name_type_designation_refs = array();
647
    foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {
648
      $tokens = explode("#", $workingset_ref);
649
      $types_in_fieldunit = get_object_vars($obj); // convert into associative array
650

    
651
      if ($tokens[0] == 'NameTypeDesignation') {
652
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
653
          if(!isset($name_type_designation_refs[$type_status])){
654
            $name_type_designation_refs[$type_status]  = $entity_reference_list;
655
          } else {
656
            array_push($name_type_designation_refs[$type_status] ,$entity_reference_list);
657
          }
658
        }
659
      } else if ($tokens[0] == 'FieldUnit'){
660
        $field_unit_uuids[] = $tokens[1];
661
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
662
          if(!isset($specimen_type_designation_refs[$type_status])){
663
            $specimen_type_designation_refs[$type_status] =  $entity_reference_list;
664
          } else {
665
            array_push($specimen_type_designation_refs[$type_status], $entity_reference_list);
666
          }
667
        }
668
      } else {
669
        drupal_set_message("Unimplemented type: " . $tokens[0], 'error');
670
      }
671
    }
672
    // type designations which are in this nomenclatural act.
673
    if (count($name_type_designation_refs) > 0) {
674
      $render_array['nomenclatural_act']['name_type_designations'] = compose_name_type_designations($name_type_designation_refs);
675
      $render_array['nomenclatural_act']['name_type_designations']['#prefix'] = '<p class="name_type_designations">';
676
      $render_array['nomenclatural_act']['name_type_designations']['#suffix'] = '</p>';
677
      $render_array['nomenclatural_act']['name_type_designations']['#weight'] = 20;
678
    }
679
    if (count($field_unit_uuids) > 0) {
680
      $specimen_type_designations_array = compose_specimen_type_designations($specimen_type_designation_refs, true);
681
      $render_array['nomenclatural_act']['specimen_type_designations'] = $specimen_type_designations_array['type_designations'];
682
      $render_array['map'] = $specimen_type_designations_array['map'];
683
      $render_array['map']['#weight'] = $render_array['nomenclatural_act']['#weight'] + 20;
684
    }
685
  }
686

    
687
  // name relations
688
  if($name_relations){
689
    $render_array['nomenclatural_act']['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null);
690
    $render_array['nomenclatural_act']['name_relations']['#weight'] = 10;
691
  }
692

    
693
  // citation
694
  if ($with_citation) {
695
    $render_array['citation'] = markup_to_render_array(
696
      "<div class=\"citation nomenclatural_act_citation" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
697
      . "<span class=\"label\">published in: </span>"
698
      . $registration_dto->bibliographicInRefCitationString
699
      . l(custom_icon_font_markup('icon-interal-link-alt-solid', array('class' => array('superscript'))), path_to_reference($registration_dto->citationUuid), array('html' => true))
700
      . "</div>",
701
      $render_array['nomenclatural_act']['#weight'] + 10 );
702
  }
703

    
704
  $render_array['nomenclatural_act']['footnotes'] = markup_to_render_array(render_footnotes(),100);
705

    
706
  // registration date and office
707
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto);
708
  if($registration_date_insitute_markup){
709
    $render_array['registration_date_and_institute'] = markup_to_render_array(
710
      $registration_date_insitute_markup . '</p>',
711
      100);
712
  }
713

    
714

    
715
  return $render_array;
716
}
717

    
718

    
719
/**
720
 * Composes a compact representation for a registrationDTO object
721
 *
722
 * Registrations which are not yet published are suppressed.
723
 *
724
 * @param $registration_dto
725
 * @param $style string
726
 *   The style of how to compose the 'identifier' and 'registration_date_and_institute' part with the summary
727
 *   - 'citation': Similar to the arrearance of nomenclatural acts in print media
728
 *   - 'list-item' : style suitable for result lists etc
729
 *
730
 * @return array
731
 *    A drupal render array with the elements:
732
 *    - 'registration-metadata' when $style == 'list-item'
733
 *    - 'summary'
734
 * @ingroup compose
735
 */
736
function compose_registration_dto_compact($registration_dto, $style = 'citation', $tag_enclosing_summary = 'p')
737
{
738
  $render_array = array();
739
  $media_link_map = array();
740

    
741
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
742
    return $render_array;
743
  }
744

    
745
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto, 'span');
746
  $itentifier_markup = l($registration_dto->identifier, path_to_registration($registration_dto->identifier), array('attributes' => array('class' => array('identifier'))));
747

    
748
  $tagged_text_options = array();
749
  if(isset($registration_dto->nameRef)){
750
    $tagged_text_options[] = array(
751
      'filter-type' => 'name',
752
      'prefix' => '<span class="registered_name">',
753
      'suffix' => '</span>',
754
    );
755
  } else {
756
    $tagged_text_options[] = array(
757
      'filter-type' => 'name',
758
      'prefix' => '<span class="referenced_typified_name">',
759
      'suffix' => '</span>',
760
    );
761
  }
762
  cdm_tagged_text_add_options($registration_dto->summaryTaggedText, $tagged_text_options);
763
  $taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
764
  foreach ($taggged_text_expanded  as $tagged_text){
765
    if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {
766
      $mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));
767
      if(isset($mediaDTOs[0]->uri)){
768
        $media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';
769
        $tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);
770
        $media_link_map[$media_url_key] =  cdm_external_uri($mediaDTOs[0]->uri, true);
771
      }
772
    }
773
  }
774
  $registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
775
  foreach($media_link_map as $media_url_key => $link){
776
    $registation_markup = str_replace($media_url_key, $link, $registation_markup);
777
  }
778
  if($style == 'citation') {
779
    $registation_markup = $registation_markup . ' ' . $itentifier_markup . ' ' . $registration_date_insitute_markup;
780
  } else {
781
    $render_array['registration-metadata'] = markup_to_render_array('<div class="registration-metadata">' . $itentifier_markup . ' ' . $registration_date_insitute_markup. "</div>", -10);
782
  }
783
  $render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . ' class="registration-summary">' . $registation_markup . '</' . $tag_enclosing_summary . '>', 0);
784

    
785
  return $render_array;
786
}
787

    
788

    
789
/**
790
 * Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.
791
 *
792
 * @param $registration_dto
793
 * @return string
794
 *    The markup or an empty string
795
 */
796
function render_registration_date_and_institute($registration_dto, $enclosing_tag = 'p') {
797
  $registration_date_institute_markup = '';
798
  if ($registration_dto->registrationDate) {
799
    $date_string = format_datetime($registration_dto->registrationDate);
800
    if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {
801
      $registration_date_institute_markup =
802
        t("Registration on @date in @institution", array(
803
          '@date' => $date_string,
804
          '@institution' => $registration_dto->institutionTitleCache,
805
        ));
806
    } else {
807
      $registration_date_institute_markup =
808
        t("Registration on @date", array(
809
          '@date' => $date_string
810
        ));
811
    }
812
    $registration_date_institute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_institute_markup . '</' .$enclosing_tag . '>';
813
  }
814
  return $registration_date_institute_markup;
815
}
816

    
817

    
818
/**
819
 * @param $registrations
820
 * @return string
821
 */
822
function render_registrations($registrations)
823
{
824
  $registration_markup = '';
825
  $registration_markup_array = array();
826
  if ($registrations) {
827
    foreach ($registrations as $reg) {
828
      $registration_markup_array[] = render_registration($reg);
829
    }
830
    $registration_markup = " Registration" . (count($registration_markup_array) > 1 ? 's: ' : ': ')
831
      . join(', ', $registration_markup_array);
832
  }
833
  return $registration_markup;
834
}
835

    
836

    
837
/**
838
 * Renders a registration
839
 *
840
 * TODO replace by compose_registration_dto_compact
841
 * @param $registration
842
 */
843
function render_registration($registration){
844
  $markup = '';
845

    
846
  if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
847
    $office_class_attribute = '';
848
    if(isset($registration->institution->titleCache)){
849
      $office_class_attribute = registration_intitute_class_attribute($registration);
850
    }
851
    $markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, path_to_registration($registration->identifier)) . ', '
852
      .  preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
853
      . '</span>';
854
  }
855
  return $markup;
856
}
857

    
858
/**
859
 * @param $registration
860
 * @return string
861
 */
862
function registration_intitute_class_attribute($registration_dto)
863
{
864
  if(isset($registration_dto->institutionTitleCache)){
865
    $institutionTitleCache = $registration_dto->institutionTitleCache;
866
  } else {
867
    // fall back option to also support cdm entities
868
    $institutionTitleCache = @$registration_dto->institution->titleCache;
869
  }
870
  return $institutionTitleCache ? 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $institutionTitleCache)) : '';
871
}
872

    
873

    
874
/**
875
 * Renders and array of CDM TypeDesignations
876
 *
877
 *  - NameTypeDesignation
878
 *  - SpecimenTypeDesignation
879
 *  - TextualTypeDesignation
880
 *
881
 * @param object $type_designations an array of cdm TypeDesignation entities
882
 *  to render
883
 * @param string $enclosing_tag the tag element type to enclose the whole list
884
 *  of type designation with. By default this DOM element is <ul>
885
 * @param string $element_tag the tag element type to be used for each
886
 *  type designation item.
887
 * @param bool $link_to_specimen_page whether a specimen in type designation element
888
 *  should be a link or not.
889
 *
890
 * @return string The markup.
891
 *
892
 * @InGroup Render
893
 */
894
function render_type_designations($type_designations, $enclosing_tag = 'ul', $element_tag =  'li', $link_to_specimen_page = true) {
895

    
896
  // need to add element to render path since type designations
897
  // need other name render template
898
  RenderHints::pushToRenderStack('typedesignations');
899

    
900
  $out = '<' . $enclosing_tag .' class="typeDesignations">';
901
  $specimen_type_designations = array();
902
  $name_type_designations = array();
903
  $textual_type_designations = array();
904
  $separator = ',';
905

    
906
  foreach ($type_designations as $type_designation) {
907
    switch ($type_designation->class) {
908
      case 'SpecimenTypeDesignation':
909
        $specimen_type_designations[] = $type_designation;
910
        break;
911
      case 'NameTypeDesignation':
912
        $name_type_designations[] = $type_designation;
913
        break;
914
      case 'TextualTypeDesignation':
915
        $textual_type_designations[] = $type_designation;
916
        break;
917
      default:  throw new Exception('Unknown type designation class: ' . $type_designation->class);
918
    }
919
  }
920

    
921
  // NameTypeDesignation ..................................
922
  if(!empty($name_type_designations)){
923
    usort($name_type_designations, "compare_type_designations_by_status");
924
    foreach($name_type_designations as $name_type_designation){
925
      if ($name_type_designation->notDesignated) {
926
        $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($name_type_designation) . '">' .  type_designation_status_label_markup($name_type_designation)  . ': '
927
          . t('not designated') . '</'. $element_tag .'>';
928
      }
929
      elseif (isset($name_type_designation->typeName)) {
930
        $link_to_name_page = url(path_to_name($name_type_designation->typeName->uuid));
931
        $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($name_type_designation) . '">' .  type_designation_status_label_markup($name_type_designation) ;
932

    
933
        if (!empty($name_type_designation->citation)) {
934
          $out .= type_designation_citation_layout($name_type_designation, $separator); // TODO type_designation_citation_layout() needs most probably to be replaced
935

    
936
        }
937
        $referenceUri = '';
938
        if (isset($name_type_designation->typeName->nomenclaturalReference)) {
939
          $referenceUri = url(path_to_reference($name_type_designation->typeName->nomenclaturalReference->uuid));
940
        }
941
        $out .= ': ' . render_taxon_or_name($name_type_designation->typeName, $link_to_name_page, $referenceUri, TRUE, TRUE);
942
      }
943
      $annotations_and_sources = handle_annotations_and_sources(
944
        $name_type_designation,
945
        typedesignations_annotations_and_sources_config(),
946
        '',
947
        RenderHints::getFootnoteListKey());
948
      $out .= $annotations_and_sources['foot_note_keys'];
949
    }
950
  } // END NameTypeDesignation
951

    
952
  // SpecimenTypeDesignation ...................................
953
  if (!empty($specimen_type_designations)) {
954
    usort($specimen_type_designations, "compare_specimen_type_designation");
955
    foreach ($specimen_type_designations as $specimen_type_designation) {
956
      $type_citation_markup = '';
957

    
958
      if (!empty($specimen_type_designation->citation)) {
959

    
960
        $citation_footnote_str = cdm_reference_markup($specimen_type_designation->citation, null, false, true);
961
        $author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $specimen_type_designation->citation->uuid);
962

    
963
        if (!empty($author_team->titleCache)) {
964
          $year = @timePeriodToString($specimen_type_designation->citation->datePublished, true, 'YYYY');
965
          $authorteam_str = $author_team->titleCache . ($year ? ' ' : '') . $year;
966
          if ($authorteam_str == $specimen_type_designation->citation->titleCache) {
967
            $citation_footnote_str = '';
968
          }
969
        } else {
970
          $authorteam_str = $citation_footnote_str;
971
          // no need for a footnote in case in case it is used as replacement for missing author teams
972
          $citation_footnote_str = '';
973
        }
974

    
975
        // for being registered a typedesignation MUST HAVE a citation, so it is save to handle the
976
        // Registration output in if condition checking if the citation is present
977
        $registration_markup = render_registrations($specimen_type_designation->registrations);
978
        $citation_footnote_str .= ($citation_footnote_str ? ' ' : '') . $registration_markup;
979

    
980
        $footnote_key_markup = '';
981
        if ($citation_footnote_str) {
982
          // footnotes should be rendered in the parent element so we
983
          // are relying on the FootnoteListKey set there
984
          $_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $citation_footnote_str);
985
          $footnote_key_markup = render_footnote_key($_fkey2, $separator, TRUE);
986
        }
987

    
988
        $type_citation_markup .= '&nbsp;(' . t('designated by') . '&nbsp;<span class="typeReference">' . $authorteam_str . '</span>';
989
        if (!empty($specimen_type_designation->citationMicroReference)) {
990
          $type_citation_markup .= ': ' . trim($specimen_type_designation->citationMicroReference);
991
        }
992
        $type_citation_markup .= $footnote_key_markup . ')';
993

    
994
      }
995

    
996

    
997
      $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($specimen_type_designation) . '">';
998
      $out .= type_designation_status_label_markup($specimen_type_designation) . $type_citation_markup;
999

    
1000

    
1001
      $derivedUnitFacadeInstance = null;
1002
      if (isset($specimen_type_designation->typeSpecimen)) {
1003
        $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $specimen_type_designation->typeSpecimen->uuid);
1004
      }
1005

    
1006
      if (!empty($derivedUnitFacadeInstance->titleCache)) {
1007
        $specimen_markup = $derivedUnitFacadeInstance->titleCache;
1008
        if($link_to_specimen_page && isset($derivedUnitFacadeInstance->specimenLabel) && $derivedUnitFacadeInstance->specimenLabel){
1009
          $specimen_markup = str_replace($derivedUnitFacadeInstance->specimenLabel, l($derivedUnitFacadeInstance->specimenLabel, path_to_specimen($specimen_type_designation->typeSpecimen->uuid)), $specimen_markup);
1010
        }
1011
        $annotations_and_sources = handle_annotations_and_sources(
1012
          $derivedUnitFacadeInstance,
1013
          typedesignations_annotations_and_sources_config(),
1014
          '',
1015
          RenderHints::getFootnoteListKey()
1016
        );
1017
        $out .= ': <span class="' . html_class_attribute_ref($specimen_type_designation->typeSpecimen) . '">'
1018
          . $specimen_markup
1019
          . '</span>'; // . ': ' . theme('cdm_specimen', array('specimenTypeDesignation' => $derivedUnitFacadeInstance));
1020
        if(!empty($derivedUnitFacadeInstance->preferredStableUri)){
1021
          $out .= ' ' . l($derivedUnitFacadeInstance->preferredStableUri, $derivedUnitFacadeInstance->preferredStableUri, array('absolute' => true));
1022
        }
1023
        $out .= $annotations_and_sources['foot_note_keys'];
1024
      }
1025
      $out .= '</'. $element_tag .'>';
1026
    }
1027
  } // END Specimen type designations
1028

    
1029
  // TextualTypeDesignation .........................
1030
  usort($textual_type_designations, 'compare_textual_type_designation');
1031
  if(!empty($textual_type_designations)) {
1032
    foreach ($textual_type_designations as $textual_type_designation) {
1033
      $annotations_and_sources = handle_annotations_and_sources(
1034
        $textual_type_designation,
1035
        array(
1036
          // these settings differ from those provided by typedesignations_annotations_and_sources_config()
1037
          // TODO is this by purpose? please document the reason for the difference
1038
          'sources_as_content' => false, // as footnotes
1039
          'link_to_name_used_in_source' => false,
1040
          'link_to_reference' => true,
1041
          'add_footnote_keys' => true,
1042
          'bibliography_aware' => false
1043
        ),
1044
        '',
1045
        RenderHints::getFootnoteListKey() // passing a defined key to avoid a separate annotation footnote key see https://dev.e-taxonomy.eu/redmine/issues/8543
1046
      );
1047
      $encasement =  $textual_type_designation->verbatim ? '"' : '';
1048
      $out .= '<' . $element_tag . ' class="' . html_class_attribute_ref($textual_type_designation) . '">' . type_designation_status_label_markup(null)
1049
        . ': ' .  $encasement . trim($textual_type_designation->text_L10n->text) . $encasement .  $annotations_and_sources['foot_note_keys'] .'</' . $element_tag . '>';
1050
//      if(is_array( $annotations_and_sources['source_references'])){
1051
//        $citation_markup = join(', ', $annotations_and_sources['source_references']);
1052
//      }
1053
//      $out .= $citation_markup;
1054
    }
1055
  }
1056

    
1057
  // Footnotes for citations, collection acronyms.
1058
  // footnotes should be rendered in the parent element so we
1059
  // are relying on the FootnoteListKey set there
1060
  $_fkey = FootnoteManager::addNewFootnote(
1061
    RenderHints::getFootnoteListKey(),
1062
    (isset($derivedUnitFacadeInstance->collection->titleCache) ? $derivedUnitFacadeInstance->collection->titleCache : FALSE)
1063
  );
1064
  $out .= render_footnote_key($_fkey, $separator);
1065
  $out .= '</' . $enclosing_tag .'>';
1066

    
1067
  RenderHints::popFromRenderStack();
1068

    
1069
  return $out;
1070
}
1071

    
1072

    
1073
/**
1074
 * Composes the textual representation for the type designation of taxon name identified by the uuid in with a map for the location data.
1075
 *
1076
 * @param $taxon_name_uuid
1077
 * @param $show_specimen_details
1078
 * @return array
1079
 *    A drupal render array with the following elements:
1080
 *    - 'type_designations'
1081
 *    - 'map'
1082
 *    - 'specimens'
1083
 *
1084
 * @ingroup compose
1085
 */
1086
function compose_type_designations($taxon_name_uuid, $show_specimen_details = false)
1087
{
1088
  $render_array = array(
1089
    'type_designations' => array(),
1090
    'map' => array(),
1091
    );
1092
  $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $taxon_name_uuid);
1093
  if ($type_designations) {
1094
    usort($type_designations, 'compare_specimen_type_designation');
1095
    $render_array['type_designations'] = markup_to_render_array(
1096
      render_type_designations($type_designations, 'div', 'div')
1097
    );
1098

    
1099
    $render_array['map'] = compose_type_designations_map($type_designations);
1100
  }
1101
  return $render_array;
1102
}
1103

    
1104

    
1105
/**
1106
 * Composes the TypedEntityReference to name type designations passed as associatve array.
1107
 *
1108
 * @param $type_entity_refs_by_status array
1109
 *   an associative array of name type type => TypedEntityReference for name type designations as
1110
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
1111
 *
1112
 * @ingroup compose
1113
 */
1114
function compose_name_type_designations($type_entity_refs_by_status){
1115
  $render_array = array();
1116
  $preferredStableUri = '';
1117
  foreach($type_entity_refs_by_status as $type_status => $name_type_entityRefs){
1118
    foreach ($name_type_entityRefs as $name_type_entity_ref){
1119
      $type_designation = cdm_ws_get(CDM_WS_TYPEDESIGNATION, array($name_type_entity_ref->uuid, 'preferredUri'));
1120
      $footnote_keys = '';
1121

    
1122
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
1123
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
1124
      }
1125
      // annotations and sources for the $derived_unit_facade_dto
1126
      $annotations_and_sources = handle_annotations_and_sources(
1127
        $name_type_entity_ref,
1128
        typedesignations_annotations_and_sources_config(),
1129
        '',
1130
        RenderHints::getFootnoteListKey()
1131
      );
1132

    
1133
      $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type_entity_ref)  . '"><span class="type-status">'. ucfirst($type_status) . "</span>: "
1134
        . $name_type_entity_ref->label
1135
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
1136
        . $annotations_and_sources['foot_note_keys']
1137
        . '</div>');
1138
      }
1139
  }
1140
  return $render_array;
1141
}
1142

    
1143
/**
1144
 * Composes the specimen type designations with map from the the $type_entity_refs
1145
 *
1146
 * @param $type_entity_refs array
1147
 *   an associative array of specimen type type => TypedEntityReference for specimen type designations as
1148
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
1149
 *
1150
 * @param $show_media_specimen
1151
 * @return array
1152
 *    A drupal render array with the following elements:
1153
 *    - 'type_designations'
1154
 *    - 'map'
1155
 *
1156
 * @ingroup compose
1157
 *
1158
 */
1159
function compose_specimen_type_designations($type_entity_refs, $show_media_specimen){
1160

    
1161
  $render_array = array();
1162

    
1163
  $type_designation_list = array();
1164
  uksort($type_entity_refs, "compare_type_designation_status_labels");
1165
  foreach($type_entity_refs as $type_status => $type_designation_entity_refs){
1166
    foreach($type_designation_entity_refs as $type_designation_entity_ref){
1167

    
1168
      $type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($type_designation_entity_ref->uuid));
1169
      $type_designation_list[] = $type_designation; // collect for the map
1170

    
1171
      $derived_unit_facade_dto = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
1172
      // the media specimen is not contained in the $type_designation returned by CDM_PORTAL_TYPEDESIGNATION, so we need to fetch it separately
1173
      $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
1174

    
1175

    
1176
      $preferredStableUri = '';
1177
      $citation_markup = '';
1178
      $media = '';
1179

    
1180
      // annotations and sources for the $derived_unit_facade_dto
1181
      $annotations_and_sources = handle_annotations_and_sources(
1182
        $derived_unit_facade_dto,
1183
        typedesignations_annotations_and_sources_config(),
1184
        '',
1185
        RenderHints::getFootnoteListKey()
1186
      );
1187
      $source_citations = $annotations_and_sources['source_references'];
1188
      $foot_note_keys = $annotations_and_sources['foot_note_keys'];
1189

    
1190
      // preferredStableUri
1191
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
1192
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
1193
      }
1194

    
1195
      if($show_media_specimen && $mediaSpecimen){
1196
        // compose output
1197
        // mediaURI
1198
        if(isset($mediaSpecimen->representations[0])) {
1199
          $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
1200
          $captionElements = array(
1201
            '#uri' => t('open media'),
1202
            'elements' => array('-none-'),
1203
            'sources_as_content' => true
1204
          );
1205
          $media = compose_cdm_media_gallerie(array(
1206
            'mediaList' => array($mediaSpecimen),
1207
            'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $type_designation_entity_ref->uuid,
1208
            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
1209
            'cols' => $gallery_settings['cdm_dataportal_media_cols'],
1210
            'captionElements' => $captionElements,
1211
          ));
1212
        }
1213
        // citation and detail for the media specimen
1214
        $annotations_and_sources = handle_annotations_and_sources(
1215
          $mediaSpecimen,
1216
          typedesignations_annotations_and_sources_config(),
1217
          '',
1218
          RenderHints::getFootnoteListKey()
1219
        );
1220
        if(is_array( $annotations_and_sources['source_references'])){
1221
          $source_citations = array_merge($source_citations, $annotations_and_sources['source_references']);
1222
        }
1223
        if($annotations_and_sources['foot_note_keys']){
1224
          $foot_note_keys .= ', ' . $annotations_and_sources['foot_note_keys'];
1225
        }
1226
      }
1227

    
1228
      $citation_markup = join(', ', $source_citations);
1229

    
1230
      $specimen_markup = $derived_unit_facade_dto->titleCache;
1231
      if(isset($derived_unit_facade_dto->specimenLabel) && $derived_unit_facade_dto->specimenLabel){
1232
        $specimen_markup = str_replace(
1233
          $derived_unit_facade_dto->specimenLabel,
1234
          l($derived_unit_facade_dto->specimenLabel, path_to_specimen($type_designation->typeSpecimen->uuid)), $specimen_markup);
1235
      }
1236

    
1237
      $type_designation_render_array = markup_to_render_array(
1238
        '<div class="type_designation_entity_ref ' . html_class_attribute_ref($type_designation_entity_ref)  . '">
1239
          <span class="type-status">' . ucfirst($type_status) . "</span>: "
1240
        . $specimen_markup . $foot_note_keys
1241
        . ($citation_markup ? ' '. $citation_markup : '')
1242
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
1243
        . $media
1244
        . '</div>');
1245

    
1246
      $render_array['type_designations'][] = $type_designation_render_array;
1247
    }
1248
  }
1249
  if(count($type_designation_list) > 0 ){
1250
    $render_array['map'] = compose_type_designations_map($type_designation_list);
1251
  } else {
1252
    $render_array['map'] = array();
1253
  }
1254
  return $render_array;
1255
}
1256

    
1257
/**
1258
 * Provides the default configuration for typedesignations which
1259
 * are passed to the handle_annotations_and_sources()
1260
 * function:
1261
 * - 'sources_as_content' => TRUE,
1262
 * - 'link_to_name_used_in_source' => FALSE,
1263
 * - 'link_to_reference' => TRUE,
1264
 * - 'add_footnote_keys' => FALSE,
1265
 * - 'bibliography_aware' => FALSE
1266
 *
1267
 * @return array
1268
 */
1269
function typedesignations_annotations_and_sources_config() {
1270
  static $annotations_and_sources_config = [
1271
    'sources_as_content' => TRUE,
1272
    'link_to_name_used_in_source' => FALSE,
1273
    'link_to_reference' => TRUE,
1274
    'add_footnote_keys' => FALSE,
1275
    'bibliography_aware' => FALSE
1276
  ];
1277
  return $annotations_and_sources_config;
1278
}
1279

    
1280
/**
1281
 * @param $name_rel
1282
 * @param $current_name_uuid
1283
 * @param $current_taxon_uuid
1284
 * @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!
1285
 * @param $show_name_cache_only
1286
 *    The nameCache will be shown instead of the titleCache if this parameter is true.
1287
 * @return null|string
1288
 *    The markup or null
1289
 */
1290
function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $show_name_cache_only = false){
1291

    
1292
  $relationship_markup = null;
1293

    
1294
  $current_name_is_toName = $current_name_uuid == $name_rel->toName->uuid;
1295

    
1296
  if($current_name_is_toName){
1297
    $name = $name_rel->fromName;
1298
  } else {
1299
    $name = $name_rel->toName;
1300
  }
1301

    
1302
  cdm_load_tagged_full_title($name);
1303

    
1304
  $highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';
1305
  if(!$show_name_cache_only){
1306
    $relationship_markup = render_taxon_or_name($name,
1307
      url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false))
1308
    );
1309
  } else {
1310
    $relationship_markup = l(
1311
      '<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',
1312
      path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false),
1313
      array('html' => true)
1314
    );
1315
  }
1316

    
1317
  return $relationship_markup;
1318
}
1319

    
1320

    
1321
/**
1322
 * Composes an inline representation of selected name relationships
1323
 *
1324
 * The output of this function will be usually appended to taxon name representations.
1325
 * Only the following types are displayed: LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR, ORTHOGRAPHIC_VARIANT
1326
 *
1327
 * LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR are displayed as
1328
 * non {titleCache} nec {titleCache} nec {titleCache} whereas the related names
1329
 * are ordered alphabetically.
1330
 *
1331
 * ORTHOGRAPHIC_VARIANT is displayed as 'ort. var. {nameCache}'
1332
 *
1333
 * Related issues:
1334
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1335
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1336
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1337
 *   - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"
1338
 *
1339
 * @param $name_relations
1340
 *    The list of CDM NameRelationsips
1341
 * @param $current_name_uuid
1342
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1343
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1344
 * @param $suppress_if_current_name_is_source
1345
 *    The display of the relation will be
1346
 *    suppressed is the current name is on the source of the relation edge.
1347
 *    That is if it is on the from side of the relation. Except for 'blocking name for' which is
1348
 *    an inverse relation. For this relation type the toName is taken in to account.
1349
 * @param $current_taxon_uuid
1350
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1351
 * @return array
1352
 *    A drupal render array
1353
 *
1354
 * @ingroup Compose
1355
 */
1356
function compose_name_relationships_inline($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
1357

    
1358
  RenderHints::pushToRenderStack('homonym');
1359
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1360

    
1361
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));
1362
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1363
  foreach ($selected_name_rel_uuids as $uuid){
1364
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1365
    if($uuid != UUID_NAMERELATIONSHIPTYPE_MISSPELLING){
1366
      $name_rel_type_filter['inverse'][$uuid] = $uuid;
1367
    }
1368
  }
1369

    
1370
  $list_prefix = '<span class="name_relationships">[';
1371
  $list_suffix = ']</span>';
1372
  $item_prefix = '<span class="item">';
1373
  $item_suffix = '</span> ';
1374
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1375

    
1376
  // remove the glue space from the last item element which has been added by the $item_suffix = '</span> '
1377
  $items_ctn = count($render_array['list']['items']);
1378
  if($items_ctn){
1379
    $render_array['list']['items'][$items_ctn - 1]['#suffix'] = '</span>';
1380
  }
1381

    
1382
  RenderHints::popFromRenderStack();
1383
  return $render_array;
1384
}
1385

    
1386
/**
1387
 * Composes an list representation of the name relationships.
1388
 *
1389
 * The output of this function will be usually appended to taxon name representations.
1390
 *
1391
 * Related issues:
1392
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1393
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1394
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1395
 *
1396
 * @param $name_relations
1397
 *    The list of CDM NameRelationsips
1398
 * @param $current_name_uuid
1399
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1400
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1401
 * @param $current_taxon_uuid
1402
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1403
 * @return array
1404
 *    A drupal render array
1405
 *
1406
 * @ingroup Compose
1407
 */
1408
function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid) {
1409

    
1410
  // $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));
1411

    
1412
  $key = 'name_relationships';
1413
  RenderHints::pushToRenderStack($key);
1414
  if(RenderHints::isUnsetFootnoteListKey()){
1415
    RenderHints::setFootnoteListKey($key);
1416
  }
1417
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1418

    
1419
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, cdm_vocabulary_as_defaults(UUID_NAME_RELATIONSHIP_TYPE));
1420
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1421
  foreach ($selected_name_rel_uuids as $uuid){
1422
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1423
    $name_rel_type_filter['inverse'][$uuid] = $uuid;
1424
  }
1425

    
1426
  $list_prefix = '<div class="relationships_list name_relationships">';
1427
  $list_suffix = '</div>';
1428
  $item_prefix = '<div class="item">';
1429
  $item_suffix = '</div>';
1430

    
1431
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1432

    
1433
  RenderHints::popFromRenderStack();
1434
  if(RenderHints::getFootnoteListKey() == $key) {
1435
    $render_array['footnotes'] = markup_to_render_array(render_footnotes(RenderHints::getFootnoteListKey()));
1436
    RenderHints::clearFootnoteListKey();
1437
  }
1438
  return $render_array;
1439
}
1440

    
1441
/**
1442
 * @param $name_relations
1443
 * @param $name_rel_type_filter
1444
 *   Associative array with two keys:
1445
 *   - 'direct': the relationship type uuids for the direct direction of the relation edge to be included
1446
 *   - 'inverse': the relationship type uuids for the direct direction of the relation edge to be included
1447
 * @param $current_name_uuid
1448
 * @param $current_taxon_uuid
1449
 * @param $list_prefix
1450
 * @param $list_suffix
1451
 * @param $item_prefix
1452
 * @param $item_suffix
1453
 * @return array
1454
 *
1455
 * @ingroup Compose
1456
 */
1457
function compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid,
1458
                                    $list_prefix, $list_suffix, $item_prefix, $item_suffix)
1459
{
1460
  $non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,
1461
    UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,
1462
    UUID_NAMERELATIONSHIPTYPE_CONSERVED_AGAINST,
1463
    UUID_NAMERELATIONSHIPTYPE_MISSPELLING,
1464
    UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
1465

    
1466
  $render_array = array(
1467
    'list' => array(
1468
      '#prefix' => $list_prefix,
1469
      '#suffix' => $list_suffix,
1470
      'items' => array()
1471
    ),
1472
    'footnotes' => array()
1473
  );
1474

    
1475
  if ($name_relations) {
1476

    
1477
    // remove all relations which are not selected in the settings and
1478
    // separate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs
1479
    // for special handling
1480
    $filtered_name_rels = array();
1481
    $non_nec_name_rels = array();
1482
    $orthographic_variants = array();
1483
    foreach ($name_relations as $name_rel) {
1484
      $rel_type_uuid = $name_rel->type->uuid;
1485
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1486
      if ((!$is_inverse_relation && isset($name_rel_type_filter['direct'][$rel_type_uuid]) && $name_rel_type_filter['direct'][$rel_type_uuid])
1487
        ||($is_inverse_relation && isset($name_rel_type_filter['inverse'][$rel_type_uuid]) && $name_rel_type_filter['inverse'][$rel_type_uuid])) {
1488

    
1489
        if (array_search($rel_type_uuid, $non_nec_name_reltype_uuids) !== false && (
1490
            $current_name_uuid == $name_rel->fromName->uuid && $rel_type_uuid != UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1491
            || $current_name_uuid == $name_rel->toName->uuid && $rel_type_uuid == UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1492
          )
1493
        ){
1494
          $non_nec_name_rels[] = $name_rel;
1495
        } else if (UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $rel_type_uuid) {
1496
          $orthographic_variants[] = $name_rel;
1497
        } else {
1498

    
1499
          $filtered_name_rels[] = $name_rel;
1500
        }
1501
      }
1502
    }
1503
    $name_relations = $filtered_name_rels;
1504

    
1505
    usort($name_relations, 'compare_name_relations_by_term_order_index');
1506

    
1507
    // compose
1508
    foreach ($name_relations as $name_rel) {
1509

    
1510
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1511

    
1512
      $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1513
      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1514

    
1515
      $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1516
      $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1517
      $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
1518
      $relationship_markup = $symbol_markup . $relationship_markup;
1519
      if ($relationship_markup) {
1520
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1521
          null,
1522
          $item_prefix,
1523
          $item_suffix);
1524
      }
1525
    }
1526

    
1527
    // name relationships to be displayed as non nec
1528
    if (count($non_nec_name_rels) > 0) {
1529
      $non_nec_markup = '';
1530
      foreach ($non_nec_name_rels as $name_rel) {
1531
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1532
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1533
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1534
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1535
        $symbol = $non_nec_markup ? ' nec ' : 'non';
1536
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1537
        $non_nec_markup .= $symbol_markup . $relationship_markup;
1538
      }
1539
      if ($non_nec_markup) {
1540
        $render_array['list']['items'][] = markup_to_render_array($non_nec_markup,
1541
          null,
1542
          $item_prefix,
1543
          $item_suffix);
1544
      }
1545
    }
1546

    
1547
    // orthographic variants
1548
    if (count($orthographic_variants) > 0) {
1549
      foreach ($orthographic_variants as $name_rel) {
1550

    
1551
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1552
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1553
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, TRUE);
1554
        $nomref_footnote_key_markup = nomenclatural_reference_footnote_key_markup($name_rel->toName);
1555
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1556
        $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1557
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1558
        $relationship_markup = $symbol_markup . $relationship_markup . $nomref_footnote_key_markup;
1559
      }
1560
      if (isset($relationship_markup) && $relationship_markup) {
1561
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1562
          null,
1563
          $item_prefix,
1564
          $item_suffix);
1565
      }
1566
    }
1567
  }
1568
  return $render_array;
1569
}
1570

    
1571
/**
1572
 * @param $name_rel
1573
 * @return string
1574
 */
1575
function name_relationship_footnote_markup($name_rel)
1576
{
1577
  $footnote_markup = '';
1578
  $footnote_key_markup = '';
1579
  if (isset($name_rel->ruleConsidered) && $name_rel->ruleConsidered) {
1580
    $footnote_markup = '<span class="rule_considered">' . $name_rel->ruleConsidered . '</span> ';
1581
  }
1582
  if (isset($name_rel->citation)) {
1583
    $footnote_markup .= '<span class="reference">' . $name_rel->citation->titleCache . '</span>';
1584
  }
1585
  if (isset($name_rel->citationMicroReference) && $name_rel->citationMicroReference) {
1586
    $footnote_markup .= (isset($name_rel->citation) ? ':' : '') . ' <span class="reference_detail">' . $name_rel->citationMicroReference . '</span>';
1587
  }
1588
  if ($footnote_markup) {
1589
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1590
    $footnote_key_markup = render_footnote_key($fnkey,',',TRUE);
1591
  }
1592
  return $footnote_key_markup;
1593
}
1594

    
1595
/**
1596
 * @param $nom_status
1597
 * @return string
1598
 */
1599
function nomenclatural_status_footnote_markup($nom_status)
1600
{
1601
  // NomenclaturalStatus is a subclass of ReferencedEntityBase
1602
  // and has the same structure as TaxonNameRelationship
1603
  return name_relationship_footnote_markup($nom_status);
1604
}
1605

    
1606
/**
1607
 * @param $name
1608
 * @return string
1609
 */
1610
function nomenclatural_reference_footnote_key_markup($name)
1611
{
1612
  $footnote_markup = '';
1613
  $footnote_key_markup = '';
1614
  if (isset($name->nomenclaturalReference) && $name->nomenclaturalReference) {
1615
    $footnote_markup .= '<span class="reference">' . $name->nomenclaturalReference->titleCache . '</span>';
1616
  }
1617
  if (isset($name->nomenclaturalMicroReference)) {
1618
    $footnote_markup .= ($footnote_key_markup ? ':' : '') . '<span class="reference_detail">' . $name->nomenclaturalMicroReference . '</span>';
1619
  }
1620
  if ($footnote_markup) {
1621
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1622
    $footnote_key_markup = render_footnote_key($fnkey, ',',TRUE);
1623
  }
1624
  return $footnote_key_markup;
1625
}
1626

    
1627

    
1628
/**
1629
 * @param $taxon
1630
 * @return array
1631
 */
1632
function cdm_name_relationships_for_taxon($taxon)
1633
{
1634
  $from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
1635
  $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
1636
  $name_relations = array_merge($from_name_relations, $to_name_relations);
1637
  return $name_relations;
1638
}
1639

    
1640

    
1641
/**
1642
 * Recursively searches the array for the $key and sets the given value.
1643
 *
1644
 * @param mixed $key
1645
 *   Key to search for.
1646
 * @param mixed $value
1647
 *   Value to set.'
1648
 * @param array $array
1649
 *   Array to search in.
1650
 *
1651
 * @return bool
1652
 *   True if the key has been found.
1653
 */
1654
function &array_setr($key, $value, array &$array) {
1655
  $res = NULL;
1656
  foreach ($array as $k => &$v) {
1657
    if ($key == $k) {
1658
      $v = $value;
1659
      return $array;
1660
    }
1661
    elseif (is_array($v)) {
1662
      $innerArray = array_setr($key, $value, $v);
1663
      if ($innerArray) {
1664
        return $array;
1665
      }
1666
    }
1667
  }
1668
  return $res;
1669
}
1670

    
1671
/**
1672
 * @todo Please document this function.
1673
 * @see http://drupal.org/node/1354
1674
 */
1675
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
1676
  $res = NULL;
1677
  $precedingElement = NULL;
1678
  foreach ($renderTemplate as &$part) {
1679
    foreach ($part as $key => &$element) {
1680
      if ($key == $contentElementKey) {
1681
        return $precedingElement;
1682
      }
1683
      $precedingElement = $element;
1684
    }
1685
  }
1686
  return $res;
1687
}
1688

    
1689
/**
1690
 * @todo Please document this function.
1691
 * @see http://drupal.org/node/1354
1692
 */
1693
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
1694
  $res = NULL;
1695
  $precedingKey = NULL;
1696
  foreach ($renderTemplate as &$part) {
1697
    if (is_array($part)) {
1698
      foreach ($part as $key => &$element) {
1699
        if ($key == $contentElementKey) {
1700
          return $precedingKey;
1701
        }
1702
        if (!str_beginsWith($key, '#')) {
1703
          $precedingKey = $key;
1704
        }
1705
      }
1706
    }
1707
  }
1708
  return $res;
1709
}
1710

    
1711
function nameTypeToDTYPE($dtype){
1712
  static $nameTypeLabelMap = array(
1713
    "ICNB" => "BacterialName",
1714
    "ICNAFP" => "BotanicalName",
1715
    "ICNCP" => "CultivarPlantName",
1716
    "ICZN" => "ZoologicalName",
1717
    "ICVCN" => "ViralName",
1718
    "Any taxon name" => "TaxonName",
1719
    "NonViral" => "TaxonName",
1720
    "Fungus" => "BotanicalName",
1721
    "Plant" => "BotanicalName",
1722
    "Algae" => "BotanicalName",
1723
  );
1724
  return $nameTypeLabelMap[$dtype];
1725

    
1726
}
1727

    
1728

    
1729
function compare_name_relations_by_term_order_index($name_rel1, $name_rel2){
1730
  return compare_terms_by_order_index($name_rel1->type, $name_rel2->type);
1731
}
1732

    
1733
/**
1734
 * Provides an array with the different registration types covered by the passed registration.
1735
 *
1736
 * The labels in the returned array are translatable.
1737
 *
1738
 * See also https://dev.e-taxonomy.eu/redmine/issues/8016
1739
 *
1740
 * @param $registration_dto
1741
 * @return array
1742
 *    An array of the labels describing the different registration types covered by the passed registration.
1743
 */
1744
function registration_types($registration_dto){
1745
  $reg_type_labels = array();
1746
  if(isset($registration_dto->nameRef)){
1747
    $reg_type_labels["name"] = t("new name");
1748
    $reg_type_labels["taxon"] = t("new taxon");
1749
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
1750
    $is_new_combination = true;
1751
    foreach($name_relations as $name_rel){
1752
      if(isset($name_rel->type->uuid)){
1753
        $name_is_from_name = $registration_dto->nameRef->uuid == $name_rel->fromName->uuid;
1754
        switch($name_rel->type->uuid) {
1755
          case UUID_NAMERELATIONSHIPTYPE_BASIONYM:
1756
            if(!$name_is_from_name){
1757
              $reg_type_labels["basionym"] = t("new combination");
1758
              $is_new_combination = true;
1759
            }
1760
            break;
1761
          case UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM:
1762
            if(!$name_is_from_name) {
1763
              $is_new_combination = true;
1764
            }
1765
            break;
1766
          case UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME:
1767
            if(!$name_is_from_name) {
1768
              $reg_type_labels["validation"] = t("validation");
1769
            }
1770
            break;
1771
          case UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT:
1772
            if(!$name_is_from_name) {
1773
              $reg_type_labels["orth_var"] = t("orthographical correction");
1774
            }break;
1775
          default:
1776
            // NOTHING
1777
        }
1778
      }
1779
    }
1780
    if($is_new_combination){
1781
      unset($reg_type_labels["taxon"]);
1782
    }
1783
  }
1784
  if(isset($registration_dto->orderdTypeDesignationWorkingSets)){
1785
    $reg_type_labels[] = t("new nomenclatural type");
1786
  }
1787
  return $reg_type_labels;
1788
}
1789

    
1790
/**
1791
 * Collects and deduplicates the type designations associated with the passes synonyms.
1792
 *
1793
 * @param $synonymy_group
1794
 *    An array containing a homotypic or heterotypic group of names.
1795
 * @param $accepted_taxon_name_uuid
1796
 *    The uuid of the accepted taxon name. Optional parameter which is required when composing
1797
 *    the information for the homotypic group. In this case the accepted taxon is not included
1798
 *    in the $synonymy_group and must therefor passed in this second parameter.
1799
 *
1800
 * @return array
1801
 *    The type designations
1802
 */
1803
function type_designations_for_synonymy_group($synonymy_group, $accepted_taxon_name_uuid = null)
1804
{
1805
  if (count($synonymy_group) > 0) {
1806
    $name_uuid = array_pop($synonymy_group)->name->uuid;
1807
  } else {
1808
    $name_uuid = $accepted_taxon_name_uuid;
1809
  }
1810
  if ($name_uuid) {
1811
   $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS_IN_HOMOTYPICAL_GROUP, $name_uuid);
1812
    if ($type_designations) {
1813
      return $type_designations;
1814
    }
1815
  }
1816

    
1817
  return array();
1818
}
1819

    
1820

    
1821
/**
1822
 * Compares two SpecimenTypeDesignations
1823
 *
1824
 * @param object $a
1825
 *   A SpecimenTypeDesignation.
1826
 * @param object $b
1827
 *   SpecimenTypeDesignation.
1828
 */
1829
function compare_specimen_type_designation($a, $b) {
1830

    
1831
  $cmp_by_status = compare_type_designations_by_status($a,$b);
1832
  if($cmp_by_status !== 0){
1833
    return $cmp_by_status;
1834
  }
1835

    
1836
  $aQuantifier = FALSE;
1837
  $bQuantifier = FALSE;
1838
  if ($aQuantifier == $bQuantifier) {
1839
    // Sort alphabetically.
1840
    $a_text =  isset($a->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $a->typeSpecimen->titleCache) : '';
1841
    $b_text =  isset($b->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $b->typeSpecimen->titleCache) : '';
1842
    return strcasecmp($a_text, $b_text);
1843
  }
1844
  return ($aQuantifier < $bQuantifier) ? -1 : (($aQuantifier > $bQuantifier) ? 1 : 0);
1845
}
1846

    
1847
/**
1848
 * Compares the status of two TypeDesignations
1849
 *
1850
 * @param object $a
1851
 *   A TypeDesignation
1852
 * @param object $b
1853
 *   TypeDesignation
1854
 */
1855
function compare_type_designations_by_status($a, $b) {
1856
  $status_a = isset($a->typeStatus) ? $a->typeStatus : null;
1857
  $status_b = isset($b->typeStatus) ? $b->typeStatus : null;
1858
  return compare_type_designation_status($status_a, $status_b);
1859
}
1860

    
1861
/**
1862
 * Compares two TypeDesignationStatusBase
1863
 *
1864
 * @param object $a
1865
 *   A TypeDesignationStatusBase.
1866
 * @param object $b
1867
 *   TypeDesignationStatusBase.
1868
 */
1869
function compare_type_designation_status($a, $b) {
1870
  $type_status_order = type_status_order();
1871
  $aQuantifier = FALSE;
1872
  $bQuantifier = FALSE;
1873
  if (isset($a->label) && isset($b->label)) {
1874
    $aQuantifier = array_search($a->label, $type_status_order);
1875
    $bQuantifier = array_search($b->label, $type_status_order);
1876
  }
1877
  return ($aQuantifier < $bQuantifier) ? -1 : (($aQuantifier > $bQuantifier) ? 1 : 0);
1878
}
1879

    
1880
/**
1881
 * Compares the two TextualTypeDesignations
1882
 *
1883
 * @param object $a
1884
 *   A TextualTypeDesignations.
1885
 * @param object $b
1886
 *   TextualTypeDesignations.
1887
 */
1888
function compare_textual_type_designation($a, $b) {
1889

    
1890
  $cmp_by_status = compare_type_designations_by_status($a,$b);
1891
  if($cmp_by_status !== 0){
1892
    return $cmp_by_status;
1893
  }
1894

    
1895
  $aQuantifier = FALSE;
1896
  $bQuantifier = FALSE;
1897
  if ($aQuantifier == $bQuantifier) {
1898
    // Sort alphabetically.
1899
    $a_text =  isset($a->text_L10n->text) ? $a->text_L10n->text : '';
1900
    $b_text =  isset($b->text_L10n->text) ? $b->text_L10n->text : '';
1901
    return strcasecmp($a_text, $b_text);
1902
  }
1903
  return ($aQuantifier < $bQuantifier) ? -1 : (($aQuantifier > $bQuantifier) ? 1 : 0);
1904
}
1905

    
1906

    
1907
/**
1908
 * Compares two SpecimenTypeDesignation status labels
1909
 *
1910
 * @param string $a
1911
 *   A TypeDesignationStatus label.
1912
 * @param string $b
1913
 *   A TypeDesignationStatus label.
1914
 */
1915
function compare_type_designation_status_labels($a, $b) {
1916

    
1917
  $type_status_order = type_status_order();
1918

    
1919
  $aQuantifier = FALSE;
1920
  $bQuantifier = FALSE;
1921
  if (isset($a) && isset($b)) {
1922
    $aQuantifier = array_search($a, $type_status_order);
1923
    $bQuantifier = array_search($b, $type_status_order);
1924
  }
1925
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1926
}
1927

    
1928
/**
1929
 * @return array
1930
 */
1931
function type_status_order()
1932
{
1933
  /*
1934
    This is the desired sort order as of now: Holotype Isotype Lectotype
1935
    Isolectotype Syntype.
1936
    TODO Basically, what we are trying to do is, we define
1937
    an ordered array of TypeDesignation-states and use the index of this array
1938
    for comparison. This array has to be filled with the cdm- TypeDesignation
1939
    states and the order should be parameterisable inside the dataportal.
1940
    */
1941
  // Make that static for now.
1942
  $type_status_order = array(
1943
    'Epitype',
1944
    'Holotype',
1945
    'Isotype',
1946
    'Lectotype',
1947
    'Isolectotype',
1948
    'Syntype',
1949
    'Paratype'
1950
  );
1951
  return $type_status_order;
1952
}
1953

    
1954
/**
1955
 * Return HTML for the lectotype citation with the correct layout.
1956
 *
1957
 * This function prints the lectotype citation with the correct layout.
1958
 * Lectotypes are renderized in the synonymy tab of a taxon if they exist.
1959
 *
1960
 * @param mixed $typeDesignation
1961
 *   Object containing the lectotype citation to print.
1962
 *
1963
 * @return string
1964
 *   Valid html string.
1965
 */
1966
function type_designation_citation_layout($typeDesignation, $footnote_separator = ',') {
1967
  $res = '';
1968
  $citation = $typeDesignation->citation;
1969
  $pages = $typeDesignation->citationMicroReference;
1970
  if(isset($typeDesignation->typeStatus->uuid) && isset($typeDesignation->typeStatus->representation_L10n)) {
1971
    if ( $typeDesignation->typeStatus->uuid == UUID_NTD_ORIGINAL_DESIGNATION || $typeDesignation->typeStatus->uuid == UUID_NTD_MONOTYPY) {
1972
      $res = ' (' . $typeDesignation->typeStatus->representation_L10n . ')';
1973
      return $res;
1974
    }
1975
  }
1976

    
1977
  if ($citation) {
1978
    // $type = $typeDesignation_citation->type;
1979
    $year = isset($citation->datePublished->start) ? substr($citation->datePublished->start, 0, 4) : '';
1980
    $author = isset($citation->authorship->titleCache) ? $citation->authorship->titleCache : '';
1981
    $res .= ' (designated by ';
1982
    $res .= $author;
1983
    $res .= ($year ? ' ' . $year : '');
1984
    $res .= ($pages ? ': ' . $pages : '');
1985
    // $res .= ')';
1986

    
1987
    // footnotes should be rendered in the parent element so we
1988
    // are relying on the FootnoteListKey set there
1989
    $fkey_typeDesignation = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $typeDesignation->citation->titleCache);
1990
    $res .= render_footnote_key($fkey_typeDesignation, $footnote_separator,TRUE) . ')';
1991
  }
1992
  return $res;
1993
}
1994

    
1995
/**
1996
 * 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"
1997
 *
1998
 * @param $type_designation
1999
 * @return string
2000
 */
2001
function type_designation_status_label_markup($type_designation)
2002
{
2003
  return '<span class="type-status">'
2004
    . ((isset($type_designation->typeStatus->representation_L10n)) ? ucfirst($type_designation->typeStatus->representation_L10n) : t('Type')) . '</span>'
2005
    ;
2006
}
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