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cdm-dataportal / modules / cdm_dataportal / includes / name.inc @ 829d7f26

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<?php
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/**
3
 * @file
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 * Functions for dealing with CDM entities from the package model.name
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 *
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 * @copyright
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 *   (C) 2007-2015 EDIT
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 *   European Distributed Institute of Taxonomy
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 *   http://www.e-taxonomy.eu
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 *
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 *   The contents of this module are subject to the Mozilla
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 *   Public License Version 1.1.
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 * @see http://www.mozilla.org/MPL/MPL-1.1.html
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 *
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 * @author
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 *   - Andreas Kohlbecker <a.kohlbecker@BGBM.org>
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 */
18

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

    
33

    
34
/**
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 * Provides the name render template to be used within the page elements identified the the $renderPath.
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 *
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 * The render templates arrays contains one or more name render templates to be used within the page elements identified the the
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 * renderPath. The renderPath is the key of the subelements whereas the value is the name render template.
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 *
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 * The render paths used for a cdm_dataportal page can be visualized by supplying the HTTP query parameter RENDER_PATH=1.
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 *
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 * It will be tried to find  the best matching default RenderTemplate by stripping the dot separated render path
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 * element by element. If no matching template is found the DEFAULT will be used:
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 *
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 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
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 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
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 * - related_taxon.heterotypicSynonymyGroup.taxon_page_synonymy
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 *
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 * A single render template can be used for multiple render paths. In this case the according key of the render templates
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 * array element should be the list of these render paths concatenated by ONLY a comma character without any whitespace.
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 *
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 * A render template is an associative array. The keys of this array are referring to the keys as defined in the part
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 * definitions array.
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 * @see get_partDefinition($taxonNameType) for more information
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 *
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 * The value of the render template element must be set to TRUE in order to let this part being rendered.
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 * The namePart, nameAuthorPart and referencePart can also hold an associative array with a single
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 * element: array('#uri' => TRUE). The value of the #uri element will be replaced by the according
59
 * links if the parameters $nameLink or $refenceLink are set.
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 *
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 * @param string $render_path
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 *   The render path can consist of multiple dot separated elements
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 *   @see RenderHints::getRenderPath()
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 * @param string $nameLink
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 *   The link path or URL to be used for name parts if a link is forseen in the template
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 *   matching the given $renderPath.
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 * @param string $referenceLink
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 *   The link path ot URL to be used for nomenclatural reference parts if a link is forseen
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 *   in the template matching the given $renderPath.
70
 * @return array
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 *   An associative array, the render template
72
 */
73
function get_nameRenderTemplate($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);
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    // 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 .= theme('cdm_annotations_as_footnotekeys', $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
  if($registration_dto->nameRef){
630
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
631
    cdm_load_tagged_full_title($name);
632
    $render_array['nomenclatural_act']['published_name'] = markup_to_render_array('<div class="published-name">' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</div>', 0);
633
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
634
    $render_array['nomenclatural_act']['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null);
635
    $render_array['nomenclatural_act']['name_relations']['#weight'] = 10;
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($name->uuid))) . '</p>', 40);
640
  }
641
  // typedesignation in detail
642
  if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
643
    $field_unit_uuids = array();
644
    $specimen_type_designation_refs = array();
645
    $name_type_designation_refs = array();
646
    foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {
647
      $tokens = explode("#", $workingset_ref);
648
      $types_in_fieldunit = get_object_vars($obj); // convert into associative array
649

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

    
686
  // citation
687
  if ($with_citation) {
688
    $render_array['citation'] = markup_to_render_array(
689
      "<div class=\"citation nomenclatural_act_citation" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
690
      . "<span class=\"label\">published in: </span>"
691
      . $registration_dto->bibliographicInRefCitationString
692
      . l(custom_icon_font_markup('icon-interal-link-alt-solid', array('class' => array('superscript'))), path_to_reference($registration_dto->citationUuid), array('html' => true))
693
      . "</div>",
694
      $render_array['nomenclatural_act']['#weight'] + 10 );
695
  }
696

    
697
  // registration date and office
698
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto);
699
  if($registration_date_insitute_markup){
700
    $render_array['registration_date_and_institute'] = markup_to_render_array(
701
      $registration_date_insitute_markup . '</p>',
702
      100);
703
  }
704

    
705
  return $render_array;
706
}
707

    
708

    
709
/**
710
 * Composes a compact representation for a registrationDTO object
711
 *
712
 * Registrations which are not yet published are suppressed.
713
 *
714
 * @param $registration_dto
715
 * @param $style string
716
 *   The style of how to compose the 'identifier' and 'registration_date_and_institute' part with the summary
717
 *   - 'citation': Similar to the arrearance of nomenclatural acts in print media
718
 *   - 'list-item' : style suitable for result lists etc
719
 *
720
 * @return array
721
 *    A drupal render array with the elements:
722
 *    - 'registration-metadata' when $style == 'list-item'
723
 *    - 'summary'
724
 * @ingroup compose
725
 */
726
function compose_registration_dto_compact($registration_dto, $style = 'citation', $tag_enclosing_summary = 'p')
727
{
728
  $render_array = array();
729
  $media_link_map = array();
730

    
731
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
732
    return $render_array;
733
  }
734

    
735
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto, 'span');
736
  $itentifier_markup = l($registration_dto->identifier, path_to_registration($registration_dto->identifier), array('attributes' => array('class' => array('identifier'))));
737

    
738
  $tagged_text_options = array();
739
  if(isset($registration_dto->nameRef)){
740
    $tagged_text_options[] = array(
741
      'filter-type' => 'name',
742
      'prefix' => '<span class="registered_name">',
743
      'suffix' => '</span>',
744
    );
745
  } else {
746
    $tagged_text_options[] = array(
747
      'filter-type' => 'name',
748
      'prefix' => '<span class="referenced_typified_name">',
749
      'suffix' => '</span>',
750
    );
751
  }
752
  cdm_tagged_text_add_options($registration_dto->summaryTaggedText, $tagged_text_options);
753
  $taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
754
  foreach ($taggged_text_expanded  as $tagged_text){
755
    if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {
756
      $mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));
757
      if(isset($mediaDTOs[0]->uri)){
758
        $media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';
759
        $tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);
760
        $media_link_map[$media_url_key] =  cdm_external_uri($mediaDTOs[0]->uri, true);
761
      }
762
    }
763
  }
764
  $registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
765
  foreach($media_link_map as $media_url_key => $link){
766
    $registation_markup = str_replace($media_url_key, $link, $registation_markup);
767
  }
768
  if($style == 'citation') {
769
    $registation_markup = $registation_markup . ' ' . $itentifier_markup . ' ' . $registration_date_insitute_markup;
770
  } else {
771
    $render_array['registration-metadata'] = markup_to_render_array('<div class="registration-metadata">' . $itentifier_markup . ' ' . $registration_date_insitute_markup. "</div>", -10);
772
  }
773
  $render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . ' class="registration-summary">' . $registation_markup . '</' . $tag_enclosing_summary . '>', 0);
774

    
775
  return $render_array;
776
}
777

    
778

    
779
/**
780
 * Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.
781
 *
782
 * @param $registration_dto
783
 * @return string
784
 *    The markup or an empty string
785
 */
786
function render_registration_date_and_institute($registration_dto, $enclosing_tag = 'p') {
787
  $registration_date_institute_markup = '';
788
  if ($registration_dto->registrationDate) {
789
    $date_string = format_datetime($registration_dto->registrationDate);
790
    if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {
791
      $registration_date_institute_markup =
792
        t("Registration on @date in @institution", array(
793
          '@date' => $date_string,
794
          '@institution' => $registration_dto->institutionTitleCache,
795
        ));
796
    } else {
797
      $registration_date_institute_markup =
798
        t("Registration on @date", array(
799
          '@date' => $date_string
800
        ));
801
    }
802
    $registration_date_institute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_institute_markup . '</' .$enclosing_tag . '>';
803
  }
804
  return $registration_date_institute_markup;
805
}
806

    
807

    
808
/**
809
 * @param $registrations
810
 * @return string
811
 */
812
function render_registrations($registrations)
813
{
814
  $registration_markup = '';
815
  $registration_markup_array = array();
816
  if ($registrations) {
817
    foreach ($registrations as $reg) {
818
      $registration_markup_array[] = render_registration($reg);
819
    }
820
    $registration_markup = " Registration" . (count($registration_markup_array) > 1 ? 's: ' : ': ')
821
      . join(', ', $registration_markup_array);
822
  }
823
  return $registration_markup;
824
}
825

    
826

    
827
/**
828
 * Renders a registration
829
 *
830
 * TODO replace by compose_registration_dto_compact
831
 * @param $registration
832
 */
833
function render_registration($registration){
834
  $markup = '';
835

    
836
  if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
837
    $office_class_attribute = '';
838
    if(isset($registration->institution->titleCache)){
839
      $office_class_attribute = registration_intitute_class_attribute($registration);
840
    }
841
    $markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, path_to_registration($registration->identifier)) . ', '
842
      .  preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
843
      . '</span>';
844
  }
845
  return $markup;
846
}
847

    
848
/**
849
 * @param $registration
850
 * @return string
851
 */
852
function registration_intitute_class_attribute($registration_dto)
853
{
854
  if(isset($registration_dto->institutionTitleCache)){
855
    $institutionTitleCache = $registration_dto->institutionTitleCache;
856
  } else {
857
    // fall back option to also support cdm entities
858
    $institutionTitleCache = @$registration_dto->institution->titleCache;
859
  }
860
  return $institutionTitleCache ? 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $institutionTitleCache)) : '';
861
}
862

    
863

    
864
/**
865
 * Renders and array of CDM TypeDesignations
866
 *
867
 * @param object $type_designations an array of cdm TypeDesignation entities
868
 *  to render
869
 * @param string $enclosing_tag the tag element type to enclose the whole list
870
 *  of type designation with. By default this DOM element is <ul>
871
 * @param string $element_tag the tag element type to be used for each
872
 *  type designation item.
873
 * @param bool $link_to_specimen_page whether a specimen in type designation element
874
 *  should be a link or not.
875
 *
876
 * @return string The markup.
877
 *
878
 * @InGroup Render
879
 */
880
function render_type_designations($type_designations, $enclosing_tag = 'ul', $element_tag =  'li', $link_to_specimen_page = true) {
881

    
882
  // need to add element to render path since type designations
883
  // need other name render template
884
  RenderHints::pushToRenderStack('typedesignations');
885

    
886
  $out = '<' . $enclosing_tag .' class="typeDesignations">';
887
  $specimen_type_designations = array();
888
  $name_type_designations = array();
889
  $textual_type_designations = array();
890
  $separator = ',';
891

    
892
  foreach ($type_designations as $type_designation) {
893
    switch ($type_designation->class) {
894
      case 'SpecimenTypeDesignation':
895
        $specimen_type_designations[] = $type_designation;
896
        break;
897
      case 'NameTypeDesignation':
898
        $name_type_designations[] = $type_designation;
899
        break;
900
      case 'TextualTypeDesignation':
901
        $textual_type_designations[] = $type_designation;
902
        break;
903
      default:  throw new Exception('Unknown type designation class: ' . $type_designation->class);
904
    }
905
  }
906

    
907
  // NameTypeDesignation ..................................
908
  if(!empty($name_type_designations)){
909
    uksort($name_type_designations, "compare_type_designation_status");
910
    foreach($name_type_designations as $name_type_designation){
911
      if ($name_type_designation->notDesignated) {
912
        $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($name_type_designation) . '">' .  type_designation_status_label_markup($name_type_designation)  . ': '
913
          . t('not designated') . '</'. $element_tag .'>';
914
      }
915
      elseif (isset($name_type_designation->typeName)) {
916
        $link_to_name_page = url(path_to_name($name_type_designation->typeName->uuid));
917
        $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($name_type_designation) . '">' .  type_designation_status_label_markup($name_type_designation) ;
918

    
919
        if (!empty($name_type_designation->citation)) {
920
          $out .= type_designation_citation_layout($name_type_designation, $separator); // TODO type_designation_citation_layout() needs most probably to be replaced
921

    
922
        }
923
        $referenceUri = '';
924
        if (isset($name_type_designation->typeName->nomenclaturalReference)) {
925
          $referenceUri = url(path_to_reference($name_type_designation->typeName->nomenclaturalReference->uuid));
926
        }
927
        $out .= ': ' . render_taxon_or_name($name_type_designation->typeName, $link_to_name_page, $referenceUri, TRUE, TRUE);
928
      }
929
    }
930
  } // END NameTypeDesignation
931

    
932
  // SpecimenTypeDesignation ...................................
933
  if (!empty($specimen_type_designations)) {
934
    usort($specimen_type_designations, "compare_specimen_type_designation");
935
    foreach ($specimen_type_designations as $specimen_type_designation) {
936
      $type_citation_markup = '';
937

    
938
      if (!empty($specimen_type_designation->citation)) {
939

    
940
        $citation_footnote_str = theme('cdm_reference', array('reference' => $specimen_type_designation->citation, 'doIconLink' => true));
941
        $author_team = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $specimen_type_designation->citation->uuid);
942

    
943
        if (!empty($author_team->titleCache)) {
944
          $year = @timePeriodToString($specimen_type_designation->citation->datePublished, true, 'YYYY');
945
          $authorteam_str = $author_team->titleCache . ($year ? ' ' : '') . $year;
946
          if ($authorteam_str == $specimen_type_designation->citation->titleCache) {
947
            $citation_footnote_str = '';
948
          }
949
        } else {
950
          $authorteam_str = $citation_footnote_str;
951
          // no need for a footnote in case in case it is used as replacement for missing author teams
952
          $citation_footnote_str = '';
953
        }
954

    
955
        // for being registered a typedesignation MUST HAVE a citation, so it is save to handle the
956
        // Registration output in if condition checking if the citation is present
957
        $registration_markup = render_registrations($specimen_type_designation->registrations);
958
        $citation_footnote_str .= ($citation_footnote_str ? ' ' : '') . $registration_markup;
959

    
960
        $footnote_key_markup = '';
961
        if ($citation_footnote_str) {
962
          // footnotes should be rendered in the parent element so we
963
          // are relying on the FootnoteListKey set there
964
          $_fkey2 = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $citation_footnote_str);
965
          $footnote_key_markup = theme('cdm_footnote_key', array(
966
            'footnoteKey' => $_fkey2,
967
            'separator' => $separator,
968
            'highlightable' => TRUE,
969
            'separator_off' => TRUE,
970
          ));
971

    
972
        }
973

    
974
        $type_citation_markup .= '&nbsp;(' . t('designated by') . '&nbsp;<span class="typeReference">' . $authorteam_str . '</span>';
975
        if (!empty($specimen_type_designation->citationMicroReference)) {
976
          $type_citation_markup .= ': ' . trim($specimen_type_designation->citationMicroReference);
977
        }
978
        $type_citation_markup .= $footnote_key_markup . ')';
979

    
980
      }
981

    
982
      $out .= '<'. $element_tag .' class="' . html_class_attribute_ref($specimen_type_designation) . '">';
983
      $out .= type_designation_status_label_markup($specimen_type_designation) . $type_citation_markup;
984

    
985

    
986
      $derivedUnitFacadeInstance = null;
987
      if (isset($specimen_type_designation->typeSpecimen)) {
988
        $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_DERIVEDUNIT_FACADE, $specimen_type_designation->typeSpecimen->uuid);
989
      }
990

    
991
      if (!empty($derivedUnitFacadeInstance->titleCache)) {
992
        $specimen_markup = $derivedUnitFacadeInstance->titleCache;
993
        if($link_to_specimen_page && isset($derivedUnitFacadeInstance->specimenLabel) && $derivedUnitFacadeInstance->specimenLabel){
994
          $specimen_markup = str_replace($derivedUnitFacadeInstance->specimenLabel, l($derivedUnitFacadeInstance->specimenLabel, path_to_specimen($specimen_type_designation->typeSpecimen->uuid)), $specimen_markup);
995
        }
996
        $out .= ': <span class="' . html_class_attribute_ref($specimen_type_designation->typeSpecimen) . '">'
997
          . $specimen_markup
998
          . '</span>'; // . ': ' . theme('cdm_specimen', array('specimenTypeDesignation' => $derivedUnitFacadeInstance));
999
        if(!empty($derivedUnitFacadeInstance->preferredStableUri)){
1000
          $out .= ' ' . l($derivedUnitFacadeInstance->preferredStableUri, $derivedUnitFacadeInstance->preferredStableUri, array('absolute' => true));
1001
        }
1002
      }
1003

    
1004

    
1005
      $out .= '</'. $element_tag .'>';
1006

    
1007
    }
1008
  } // END Specimen type designations
1009

    
1010
  // TextualTypeDesignation .........................
1011
  if(!empty($textual_type_designations)) {
1012
    foreach ($textual_type_designations as $textual_type_designation) {
1013
      $encasement =  $textual_type_designation->verbatim ? '"' : '';
1014
      $out .= '<' . $element_tag . ' class="' . html_class_attribute_ref($textual_type_designation) . '">' . type_designation_status_label_markup(null)
1015
        . ': ' .  $encasement . $textual_type_designation->text_L10n->text . $encasement . '</' . $element_tag . '>';
1016
      $annotations_and_sources = handle_annotations_and_sources(
1017
        $textual_type_designation,
1018
        array(
1019
          'sources_as_content' => false, // as footnotes
1020
          'link_to_name_used_in_source' => false,
1021
          'link_to_reference' => true,
1022
          'add_footnote_keys' => false,
1023
          'bibliography_aware' => false),
1024
        '',
1025
        RenderHints::getFootnoteListKey() // passing a defined key to avoid separate annotation footnote key see https://dev.e-taxonomy.eu/redmine/issues/8543
1026
      );
1027
      $out .= $annotations_and_sources['foot_note_keys'];
1028
      if(is_array( $annotations_and_sources['source_references'])){
1029
        $citation_markup = join(', ', $annotations_and_sources['source_references']);
1030
      }
1031
    }
1032
  }
1033

    
1034
  // Footnotes for citations, collection acronym?s.
1035
  // footnotes should be rendered in the parent element so we
1036
  // are relying on the FootnoteListKey set there
1037
  $_fkey = FootnoteManager::addNewFootnote(
1038
    RenderHints::getFootnoteListKey(),
1039
    (isset($derivedUnitFacadeInstance->collection->titleCache) ? $derivedUnitFacadeInstance->collection->titleCache : FALSE)
1040
  );
1041
  $out .= theme('cdm_footnote_key', array('footnoteKey' => $_fkey, 'separator' => $separator));
1042
  $out .= '</' . $enclosing_tag .'>';
1043

    
1044
  RenderHints::popFromRenderStack();
1045

    
1046
  return $out;
1047
}
1048

    
1049

    
1050
/**
1051
 * Composes the textual representation for the type designation of taxon name identified by the uuid in with a map for the location data.
1052
 *
1053
 * @param $taxon_name_uuid
1054
 * @param $show_specimen_details
1055
 * @return array
1056
 *    A drupal render array with the following elements:
1057
 *    - 'type_designations'
1058
 *    - 'map'
1059
 *    - 'specimens'
1060
 *
1061
 * @ingroup compose
1062
 */
1063
function compose_type_designations($taxon_name_uuid, $show_specimen_details = false)
1064
{
1065
  $render_array = array(
1066
    'type_designations' => array(),
1067
    'map' => array(),
1068
    );
1069
  $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $taxon_name_uuid);
1070
  if ($type_designations) {
1071
    usort($type_designations, 'compare_specimen_type_designation');
1072
    $render_array['type_designations'] = markup_to_render_array(
1073
      render_type_designations($type_designations, 'div', 'div')
1074
    );
1075

    
1076
    $render_array['map'] = compose_type_designations_map($type_designations);
1077
  }
1078
  return $render_array;
1079
}
1080

    
1081

    
1082
/**
1083
 * Composes the TypedEntityReference to name type designations passed as associatve array.
1084
 *
1085
 * @param $$type_entity_refs array
1086
 *   an associative array of name type type => TypedEntityReference for name type designations as
1087
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
1088
 *
1089
 * @ingroup compose
1090
 */
1091
function compose_name_type_designations($type_entity_refs){
1092
  $render_array = array();
1093
  $preferredStableUri = '';
1094
  foreach($type_entity_refs as $type_status => $name_types){
1095
    foreach ($name_types as $name_type){
1096
      $type_designation = cdm_ws_get(CDM_WS_TYPEDESIGNATION, array($name_type->uuid, 'preferredUri'));
1097
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
1098
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
1099
      }
1100
      $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type)  . '"><span class="type-status">'. ucfirst($type_status) . "</span>: "
1101
        . $name_type->label
1102
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
1103
        . '</div>');
1104
      }
1105
  }
1106
  return $render_array;
1107
}
1108

    
1109
/**
1110
 * Composes the specimen type designations with map from the the $type_entity_refs
1111
 *
1112
 * @param $type_entity_refs array
1113
 *   an associative array of specimen type type => TypedEntityReference for specimen type designations as
1114
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
1115
 *
1116
 * @param $show_media_specimen
1117
 * @return array
1118
 *    A drupal render array with the following elements:
1119
 *    - 'type_designations'
1120
 *    - 'map'
1121
 *
1122
 * @ingroup compose
1123
 *
1124
 */
1125
function compose_specimen_type_designations($type_entity_refs, $show_media_specimen){
1126

    
1127
  $render_array = array();
1128

    
1129
  $type_designation_list = array();
1130
  uksort($type_entity_refs, "compare_type_designation_status_labels");
1131
  foreach($type_entity_refs as $type_status => $specimen_types){
1132
    foreach($specimen_types as $specimen_type){
1133

    
1134
      $type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($specimen_type->uuid));
1135
      $type_designation_list[] = $type_designation; // collect for the map
1136

    
1137
      $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
1138
      // the media specimen is not contained in the $type_designation returned by CDM_PORTAL_TYPEDESIGNATION, so we need to fetch it separately
1139
      $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
1140

    
1141

    
1142
      $preferredStableUri = '';
1143
      $citation_markup = '';
1144
      $media = '';
1145

    
1146
      // preferredStableUri
1147
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
1148
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
1149
      }
1150

    
1151
      if($show_media_specimen && $mediaSpecimen){
1152
        // compose output
1153
        // mediaURI
1154
        if(isset($mediaSpecimen->representations[0])) {
1155
          $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
1156
          $captionElements = array(
1157
            '#uri' => t('open media'),
1158
            'elements' => array('-none-'),
1159
            'sources_as_content' => true
1160
          );
1161
          $media = compose_cdm_media_gallerie(array(
1162
            'mediaList' => array($mediaSpecimen),
1163
            'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $specimen_type->uuid,
1164
            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
1165
            'cols' => $gallery_settings['cdm_dataportal_media_cols'],
1166
            'captionElements' => $captionElements,
1167
          ));
1168
        }
1169
        // citation and detail
1170
        $annotations_and_sources = handle_annotations_and_sources(
1171
            $mediaSpecimen,
1172
            array(
1173
                'sources_as_content' => true,
1174
                'link_to_name_used_in_source' => false,
1175
                'link_to_reference' => true,
1176
                'add_footnote_keys' => false,
1177
                'bibliography_aware' => false),
1178
            '',
1179
            null
1180
        );
1181
        if(is_array( $annotations_and_sources['source_references'])){
1182
          $citation_markup = join(', ', $annotations_and_sources['source_references']);
1183
        }
1184
      }
1185

    
1186
      $specimen_markup = $derivedUnitFacadeInstance->titleCache;
1187
      if(isset($derivedUnitFacadeInstance->specimenLabel) && $derivedUnitFacadeInstance->specimenLabel){
1188
        $specimen_markup = str_replace($derivedUnitFacadeInstance->specimenLabel, l($derivedUnitFacadeInstance->specimenLabel, path_to_specimen($type_designation->typeSpecimen->uuid)), $specimen_markup);
1189
      }
1190

    
1191
      $type_designation_render_array = markup_to_render_array('<div class="specimen_type_designation ' . html_class_attribute_ref($specimen_type)  . '">
1192
          <span class="type-status">' . ucfirst($type_status) . "</span>: "
1193
        . $specimen_markup
1194
        . ($citation_markup ? ' '. $citation_markup : '')
1195
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
1196
        . $media
1197
        . '</div>');
1198

    
1199
      $render_array['type_designations'][] = $type_designation_render_array;
1200
    }
1201
  }
1202
  if(count($type_designation_list) > 0 ){
1203
    $render_array['map'] = compose_type_designations_map($type_designation_list);
1204
  } else {
1205
    $render_array['map'] = array();
1206
  }
1207
  return $render_array;
1208
}
1209

    
1210
/**
1211
 * @param $name_rel
1212
 * @param $current_name_uuid
1213
 * @param $current_taxon_uuid
1214
 * @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!
1215
 * @param $show_name_cache_only
1216
 *    The nameCache will be shown instead of the titleCache if this parameter is true.
1217
 * @return null|string
1218
 */
1219
function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $show_name_cache_only = false){
1220

    
1221
  $relationship_markup = null;
1222

    
1223
  $current_name_is_toName = $current_name_uuid == $name_rel->toName->uuid;
1224

    
1225
  if($current_name_is_toName){
1226
    $name = $name_rel->fromName;
1227
  } else {
1228
    $name = $name_rel->toName;
1229
  }
1230

    
1231
  cdm_load_tagged_full_title($name);
1232

    
1233
  $highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';
1234
  if(!$show_name_cache_only){
1235
    $relationship_markup = render_taxon_or_name($name,
1236
      url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false))
1237
    );
1238
  } else {
1239
    $relationship_markup = l(
1240
      '<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',
1241
      path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false),
1242
      array('html' => true)
1243
    );
1244
  }
1245

    
1246
  return $relationship_markup;
1247
}
1248

    
1249

    
1250
/**
1251
 * Composes an inline representation of selected name relationships
1252
 *
1253
 * The output of this function will be usually appended to taxon name representations.
1254
 * Only the following types are displayed: LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR, ORTHOGRAPHIC_VARIANT
1255
 *
1256
 * LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR are displayed as
1257
 * non {titleCache} nec {titleCache} nec {titleCache} whereas the related names
1258
 * are ordered alphabetically.
1259
 *
1260
 * ORTHOGRAPHIC_VARIANT is displayed as 'ort. var. {nameCache}'
1261
 *
1262
 * Related issues:
1263
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1264
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1265
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1266
 *   - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"
1267
 *
1268
 * @param $name_relations
1269
 *    The list of CDM NameRelationsips
1270
 * @param $current_name_uuid
1271
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1272
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1273
 * @param $suppress_if_current_name_is_source
1274
 *    The display of the relation will be
1275
 *    suppressed is the current name is on the source of the relation edge.
1276
 *    That is if it is on the from side of the relation. Except for 'blocking name for' which is
1277
 *    an inverse relation. For this relation type the toName is taken in to account.
1278
 * @param $current_taxon_uuid
1279
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1280
 * @return array
1281
 *    A drupal render array
1282
 *
1283
 * @ingroup Compose
1284
 */
1285
function compose_name_relationships_inline($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
1286

    
1287
  RenderHints::pushToRenderStack('homonym');
1288
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1289

    
1290
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));
1291
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1292
  foreach ($selected_name_rel_uuids as $uuid){
1293
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1294
    if($uuid != UUID_NAMERELATIONSHIPTYPE_MISSPELLING){
1295
      $name_rel_type_filter['inverse'][$uuid] = $uuid;
1296
    }
1297
  }
1298

    
1299
  $list_prefix = '<span class="name_relationships">[';
1300
  $list_suffix = ']</span>';
1301
  $item_prefix = '<span class="item">';
1302
  $item_suffix = '</span> ';
1303
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1304

    
1305
  // remove the glue space from the last item element which has been added by the $item_suffix = '</span> '
1306
  $items_ctn = count($render_array['list']['items']);
1307
  if($items_ctn){
1308
    $render_array['list']['items'][$items_ctn - 1]['#suffix'] = '</span>';
1309
  }
1310

    
1311
  RenderHints::popFromRenderStack();
1312
  return $render_array;
1313
}
1314

    
1315
/**
1316
 * Composes an list representation of the name relationships.
1317
 *
1318
 * The output of this function will be usually appended to taxon name representations.
1319
 *
1320
 * Related issues:
1321
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1322
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1323
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1324
 *
1325
 * @param $name_relations
1326
 *    The list of CDM NameRelationsips
1327
 * @param $current_name_uuid
1328
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1329
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1330
 * @param $current_taxon_uuid
1331
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1332
 * @return array
1333
 *    A drupal render array
1334
 *
1335
 * @ingroup Compose
1336
 */
1337
function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid) {
1338

    
1339
  // $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));
1340

    
1341
  $key = 'name_relationships';
1342
  RenderHints::pushToRenderStack($key);
1343
  if(!RenderHints::getFootnoteListKey()){
1344
    RenderHints::setFootnoteListKey($key);
1345
  }
1346
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1347

    
1348
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, cdm_vocabulary_as_defaults(UUID_NAME_RELATIONSHIP_TYPE));
1349
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1350
  foreach ($selected_name_rel_uuids as $uuid){
1351
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1352
    $name_rel_type_filter['inverse'][$uuid] = $uuid;
1353
  }
1354

    
1355
  $list_prefix = '<div class="relationships_list name_relationships">';
1356
  $list_suffix = '</div>';
1357
  $item_prefix = '<div class="item">';
1358
  $item_suffix = '</div>';
1359

    
1360
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1361

    
1362
  RenderHints::popFromRenderStack();
1363
  $render_array['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));
1364
  if(RenderHints::getFootnoteListKey() == $key) {
1365
    RenderHints::clearFootnoteListKey();
1366
  }
1367
  return $render_array;
1368
}
1369

    
1370
/**
1371
 * @param $name_relations
1372
 * @param $name_rel_type_filter
1373
 *   Associative array with two keys:
1374
 *   - 'direct': the relationship type uuids for the direct direction of the relation edge to be included
1375
 *   - 'inverse': the relationship type uuids for the direct direction of the relation edge to be included
1376
 * @param $current_name_uuid
1377
 * @param $current_taxon_uuid
1378
 * @param $list_prefix
1379
 * @param $list_suffix
1380
 * @param $item_prefix
1381
 * @param $item_suffix
1382
 * @return array
1383
 *
1384
 * @ingroup Compose
1385
 */
1386
function compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid,
1387
                                    $list_prefix, $list_suffix, $item_prefix, $item_suffix)
1388
{
1389
  $non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,
1390
    UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,
1391
    UUID_NAMERELATIONSHIPTYPE_CONSERVED_AGAINST,
1392
    UUID_NAMERELATIONSHIPTYPE_MISSPELLING,
1393
    UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
1394

    
1395
  $render_array = array(
1396
    'list' => array(
1397
      '#prefix' => $list_prefix,
1398
      '#suffix' => $list_suffix,
1399
      'items' => array()
1400
    ),
1401
    'footnotes' => array()
1402
  );
1403

    
1404
  if ($name_relations) {
1405

    
1406
    // remove all relations which are not selected in the settings and
1407
    // separate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs
1408
    // for special handling
1409
    $filtered_name_rels = array();
1410
    $non_nec_name_rels = array();
1411
    $orthographic_variants = array();
1412
    foreach ($name_relations as $name_rel) {
1413
      $rel_type_uuid = $name_rel->type->uuid;
1414
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1415
      if ((!$is_inverse_relation && isset($name_rel_type_filter['direct'][$rel_type_uuid]) && $name_rel_type_filter['direct'][$rel_type_uuid])
1416
        ||($is_inverse_relation && isset($name_rel_type_filter['inverse'][$rel_type_uuid]) && $name_rel_type_filter['inverse'][$rel_type_uuid])) {
1417

    
1418
        if (array_search($rel_type_uuid, $non_nec_name_reltype_uuids) !== false && (
1419
            $current_name_uuid == $name_rel->fromName->uuid && $rel_type_uuid != UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1420
            || $current_name_uuid == $name_rel->toName->uuid && $rel_type_uuid == UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1421
          )
1422
        ){
1423
          $non_nec_name_rels[] = $name_rel;
1424
        } else if (UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $rel_type_uuid) {
1425
          $orthographic_variants[] = $name_rel;
1426
        } else {
1427

    
1428
          $filtered_name_rels[] = $name_rel;
1429
        }
1430
      }
1431
    }
1432
    $name_relations = $filtered_name_rels;
1433

    
1434
    usort($name_relations, 'compare_name_relations_by_term_order_index');
1435

    
1436
    // compose
1437
    foreach ($name_relations as $name_rel) {
1438

    
1439
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1440

    
1441
      $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1442
      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1443

    
1444
      $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1445
      $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1446
      $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
1447
      $relationship_markup = $symbol_markup . $relationship_markup;
1448
      if ($relationship_markup) {
1449
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1450
          null,
1451
          $item_prefix,
1452
          $item_suffix);
1453
      }
1454
    }
1455

    
1456
    // name relationships to be displayed as non nec
1457
    if (count($non_nec_name_rels) > 0) {
1458
      $non_nec_markup = '';
1459
      foreach ($non_nec_name_rels as $name_rel) {
1460
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1461
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1462
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1463
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1464
        $symbol = $non_nec_markup ? ' nec ' : 'non';
1465
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1466
        $non_nec_markup .= $symbol_markup . $relationship_markup;
1467
      }
1468
      if ($non_nec_markup) {
1469
        $render_array['list']['items'][] = markup_to_render_array($non_nec_markup,
1470
          null,
1471
          $item_prefix,
1472
          $item_suffix);
1473
      }
1474
    }
1475

    
1476
    // orthographic variants
1477
    if (count($orthographic_variants) > 0) {
1478
      foreach ($orthographic_variants as $name_rel) {
1479

    
1480
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1481
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1482
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, TRUE);
1483
        $nomref_footnote_key_markup = nomenclatural_reference_footnote_key_markup($name_rel->toName);
1484
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1485
        $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1486
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1487
        $relationship_markup = $symbol_markup . $relationship_markup . $nomref_footnote_key_markup;
1488
      }
1489
      if ($relationship_markup) {
1490
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1491
          null,
1492
          $item_prefix,
1493
          $item_suffix);
1494
      }
1495
    }
1496
  }
1497
  return $render_array;
1498
}
1499

    
1500
/**
1501
 * @param $name_rel
1502
 * @return string
1503
 */
1504
function name_relationship_footnote_markup($name_rel)
1505
{
1506
  $footnote_markup = '';
1507
  $footnote_key_markup = '';
1508
  if (isset($name_rel->ruleConsidered) && $name_rel->ruleConsidered) {
1509
    $footnote_markup = '<span class="rule_considered">' . $name_rel->ruleConsidered . '</span> ';
1510
  }
1511
  if (isset($name_rel->citation)) {
1512
    $footnote_markup .= '<span class="reference">' . $name_rel->citation->titleCache . '</span>';
1513
  }
1514
  if (isset($name_rel->citationMicroReference) && $name_rel->citationMicroReference) {
1515
    $footnote_markup .= (isset($name_rel->citation) ? ':' : '') . '<span class="reference_detail">' . $name_rel->citationMicroReference . '</span>';
1516
  }
1517
  if ($footnote_markup) {
1518
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1519
    $footnote_key_markup = theme('cdm_footnote_key', array(
1520
      'footnoteKey' => $fnkey,
1521
      'separator' => ',',
1522
      'highlightable' => TRUE,
1523
      'separator_off' => TRUE,
1524
    ));
1525
  }
1526
  return $footnote_key_markup;
1527
}
1528

    
1529
/**
1530
 * @param $nom_status
1531
 * @return string
1532
 */
1533
function nomenclatural_status_footnote_markup($nom_status)
1534
{
1535
  // NomenclaturalStatus is a subclass of ReferencedEntityBase
1536
  // and has the same structure as TaxonNameRelationship
1537
  return name_relationship_footnote_markup($nom_status);
1538
}
1539

    
1540
/**
1541
 * @param $name
1542
 * @return string
1543
 */
1544
function nomenclatural_reference_footnote_key_markup($name)
1545
{
1546
  $footnote_markup = '';
1547
  $footnote_key_markup = '';
1548
  if (isset($name->nomenclaturalReference) && $name->nomenclaturalReference) {
1549
    $footnote_markup .= '<span class="reference">' . $name->nomenclaturalReference->titleCache . '</span>';
1550
  }
1551
  if (isset($name->nomenclaturalMicroReference)) {
1552
    $footnote_markup .= ($footnote_key_markup ? ':' : '') . '<span class="reference_detail">' . $name->nomenclaturalMicroReference . '</span>';
1553
  }
1554
  if ($footnote_markup) {
1555
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1556
    $footnote_key_markup = theme('cdm_footnote_key', array(
1557
      'footnoteKey' => $fnkey,
1558
      'separator' => ',',
1559
      'highlightable' => TRUE,
1560
      'separator_off' => TRUE,
1561
    ));
1562
  }
1563
  return $footnote_key_markup;
1564
}
1565

    
1566

    
1567
/**
1568
 * @param $taxon
1569
 * @return array
1570
 */
1571
function cdm_name_relationships_for_taxon($taxon)
1572
{
1573
  $from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
1574
  $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
1575
  $name_relations = array_merge($from_name_relations, $to_name_relations);
1576
  return $name_relations;
1577
}
1578

    
1579

    
1580
/**
1581
 * Recursively searches the array for the $key and sets the given value.
1582
 *
1583
 * @param mixed $key
1584
 *   Key to search for.
1585
 * @param mixed $value
1586
 *   Value to set.'
1587
 * @param array $array
1588
 *   Array to search in.
1589
 *
1590
 * @return bool
1591
 *   True if the key has been found.
1592
 */
1593
function &array_setr($key, $value, array &$array) {
1594
  $res = NULL;
1595
  foreach ($array as $k => &$v) {
1596
    if ($key == $k) {
1597
      $v = $value;
1598
      return $array;
1599
    }
1600
    elseif (is_array($v)) {
1601
      $innerArray = array_setr($key, $value, $v);
1602
      if ($innerArray) {
1603
        return $array;
1604
      }
1605
    }
1606
  }
1607
  return $res;
1608
}
1609

    
1610
/**
1611
 * @todo Please document this function.
1612
 * @see http://drupal.org/node/1354
1613
 */
1614
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
1615
  $res = NULL;
1616
  $precedingElement = NULL;
1617
  foreach ($renderTemplate as &$part) {
1618
    foreach ($part as $key => &$element) {
1619
      if ($key == $contentElementKey) {
1620
        return $precedingElement;
1621
      }
1622
      $precedingElement = $element;
1623
    }
1624
  }
1625
  return $res;
1626
}
1627

    
1628
/**
1629
 * @todo Please document this function.
1630
 * @see http://drupal.org/node/1354
1631
 */
1632
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
1633
  $res = NULL;
1634
  $precedingKey = NULL;
1635
  foreach ($renderTemplate as &$part) {
1636
    if (is_array($part)) {
1637
      foreach ($part as $key => &$element) {
1638
        if ($key == $contentElementKey) {
1639
          return $precedingKey;
1640
        }
1641
        if (!str_beginsWith($key, '#')) {
1642
          $precedingKey = $key;
1643
        }
1644
      }
1645
    }
1646
  }
1647
  return $res;
1648
}
1649

    
1650
function nameTypeToDTYPE($dtype){
1651
  static $nameTypeLabelMap = array(
1652
    "ICNB" => "BacterialName",
1653
    "ICNAFP" => "BotanicalName",
1654
    "ICNCP" => "CultivarPlantName",
1655
    "ICZN" => "ZoologicalName",
1656
    "ICVCN" => "ViralName",
1657
    "Any taxon name" => "TaxonName",
1658
    "NonViral" => "TaxonName",
1659
    "Fungus" => "BotanicalName",
1660
    "Plant" => "BotanicalName",
1661
    "Algae" => "BotanicalName",
1662
  );
1663
  return $nameTypeLabelMap[$dtype];
1664

    
1665
}
1666

    
1667

    
1668
function compare_name_relations_by_term_order_index($name_rel1, $name_rel2){
1669
  return compare_terms_by_order_index($name_rel1->type, $name_rel2->type);
1670
}
1671

    
1672
/**
1673
 * Provides an array with the different registration types covered by the passed registration.
1674
 *
1675
 * The labels in the returned array are translatable.
1676
 *
1677
 * See also https://dev.e-taxonomy.eu/redmine/issues/8016
1678
 *
1679
 * @param $registration_dto
1680
 * @return array
1681
 *    An array of the labels describing the different registration types covered by the passed registration.
1682
 */
1683
function registration_types($registration_dto){
1684
  $reg_type_labels = array();
1685
  if(isset($registration_dto->nameRef)){
1686
    $reg_type_labels["name"] = t("new name");
1687
    $reg_type_labels["taxon"] = t("new taxon");
1688
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
1689
    $is_new_combination = true;
1690
    foreach($name_relations as $name_rel){
1691
      if(isset($name_rel->type->uuid)){
1692
        $name_is_from_name = $registration_dto->nameRef->uuid == $name_rel->fromName->uuid;
1693
        switch($name_rel->type->uuid) {
1694
          case UUID_NAMERELATIONSHIPTYPE_BASIONYM:
1695
            if(!$name_is_from_name){
1696
              $reg_type_labels["basionym"] = t("new combination");
1697
              $is_new_combination = true;
1698
            }
1699
            break;
1700
          case UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM:
1701
            if(!$name_is_from_name) {
1702
              $is_new_combination = true;
1703
            }
1704
            break;
1705
          case UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME:
1706
            if(!$name_is_from_name) {
1707
              $reg_type_labels["validation"] = t("validation");
1708
            }
1709
            break;
1710
          case UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT:
1711
            if(!$name_is_from_name) {
1712
              $reg_type_labels["orth_var"] = t("orthographical correction");
1713
            }break;
1714
          default:
1715
            // NOTHING
1716
        }
1717
      }
1718
    }
1719
    if($is_new_combination){
1720
      unset($reg_type_labels["taxon"]);
1721
    }
1722
  }
1723
  if(isset($registration_dto->orderdTypeDesignationWorkingSets)){
1724
    $reg_type_labels[] = t("new nomenclatural type");
1725
  }
1726
  return $reg_type_labels;
1727
}
1728

    
1729
/**
1730
 * Collects and deduplicates the type designations associated with the passes synonyms.
1731
 *
1732
 * @param $synonymy_group
1733
 *    An array containing a homotypic or heterotypic group of names.
1734
 * @param $accepted_taxon_name_uuid
1735
 *    The uuid of the accepted taxon name. Optional parameter which is required when composing
1736
 *    the information for the homotypic group. In this case the accepted taxon is not included
1737
 *    in the $synonymy_group and must therefor passed in this second parameter.
1738
 *
1739
 * @return array
1740
 *    The type designations
1741
 */
1742
function type_designations_for_synonymy_group($synonymy_group, $accepted_taxon_name_uuid = null)
1743
{
1744
  if (count($synonymy_group) > 0) {
1745
    $name_uuid = array_pop($synonymy_group)->name->uuid;
1746
  } else {
1747
    $name_uuid = $accepted_taxon_name_uuid;
1748
  }
1749
  if ($name_uuid) {
1750
   $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS_IN_HOMOTYPICAL_GROUP, $name_uuid);
1751
    if ($type_designations) {
1752
      return $type_designations;
1753
    }
1754
  }
1755

    
1756
  return array();
1757
}
1758

    
1759

    
1760
/**
1761
 * Compares the status of two SpecimenTypeDesignations
1762
 *
1763
 * @param object $a
1764
 *   A SpecimenTypeDesignation.
1765
 * @param object $b
1766
 *   SpecimenTypeDesignation.
1767
 */
1768
function compare_specimen_type_designation($a, $b) {
1769

    
1770
  $type_status_order = type_status_order();
1771

    
1772

    
1773
  $aQuantifier = FALSE;
1774
  $bQuantifier = FALSE;
1775
  if (isset($a->typeStatus->titleCache) && isset($b->typeStatus->titleCache)) {
1776
    $aQuantifier = array_search($a->typeStatus->titleCache, $type_status_order);
1777
    $bQuantifier = array_search($b->typeStatus->titleCache, $type_status_order);
1778
  }
1779
  if ($aQuantifier == $bQuantifier) {
1780
    // Sort alphabetically.
1781
    $a_text =  isset($a->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $a->typeSpecimen->titleCache) : '';
1782
    $b_text =  isset($b->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $b->typeSpecimen->titleCache) : '';
1783
    return strcasecmp($a_text, $b_text);
1784
  }
1785
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1786
}
1787

    
1788
/**
1789
 * Compares the status of two SpecimenTypeDesignations
1790
 *
1791
 * @param object $a
1792
 *   A TypeDesignationStatusBase.
1793
 * @param object $b
1794
 *   TypeDesignationStatusBase.
1795
 */
1796
function compare_type_designation_status($a, $b) {
1797

    
1798
  $type_status_order = type_status_order();
1799

    
1800

    
1801
  $aQuantifier = FALSE;
1802
  $bQuantifier = FALSE;
1803
  if (isset($a->label) && isset($b->label)) {
1804
    $aQuantifier = array_search($a->label, $type_status_order);
1805
    $bQuantifier = array_search($b->label, $type_status_order);
1806
  }
1807
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1808
}
1809

    
1810

    
1811
/**
1812
 * Compares two SpecimenTypeDesignation status labels
1813
 *
1814
 * @param string $a
1815
 *   A TypeDesignationStatus label.
1816
 * @param string $b
1817
 *   A TypeDesignationStatus label.
1818
 */
1819
function compare_type_designation_status_labels($a, $b) {
1820

    
1821
  $type_status_order = type_status_order();
1822

    
1823

    
1824
  $aQuantifier = FALSE;
1825
  $bQuantifier = FALSE;
1826
  if (isset($a) && isset($b)) {
1827
    $aQuantifier = array_search($a, $type_status_order);
1828
    $bQuantifier = array_search($b, $type_status_order);
1829
  }
1830
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1831
}
1832

    
1833
/**
1834
 * @return array
1835
 */
1836
function type_status_order()
1837
{
1838
  /*
1839
    This is the desired sort order as of now: Holotype Isotype Lectotype
1840
    Isolectotype Syntype.
1841
    TODO Basically, what we are trying to do is, we define
1842
    an ordered array of TypeDesignation-states and use the index of this array
1843
    for comparison. This array has to be filled with the cdm- TypeDesignation
1844
    states and the order should be parameterisable inside the dataportal.
1845
    */
1846
  // Make that static for now.
1847
  $type_status_order = array(
1848
    'Epitype',
1849
    'Holotype',
1850
    'Isotype',
1851
    'Lectotype',
1852
    'Isolectotype',
1853
    'Syntype',
1854
    'Paratype'
1855
  );
1856
  return $type_status_order;
1857
}
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