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cdm-dataportal / modules / cdm_dataportal / includes / name.inc @ 67f5eac2

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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 ot 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) {
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    $render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);
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    // needs to be converted to an array
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    $render_templates = (object_to_array($render_templates));
86

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

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

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

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

    
127

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

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

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

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

    
157
  return $template;
158
}
159

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

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

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

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

    
244
}
245

    
246

    
247
/**
248
 * Renders the markup for a CDM TaxonName instance.
249
 *
250
 * The layout of the name representation is configured by the
251
 * part_definitions and render_templates (see get_partDefinition() and
252
 * get_nameRenderTemplate())
253
 *
254
 * @param $taxonName
255
 *    cdm TaxonName instance
256
 * @param $nameLink
257
 *    URI to the taxon, @see path_to_taxon(), must be processed by url() before passing to this method
258
 * @param $refenceLink
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, $nameLink = NULL, $refenceLink = 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
    $taxonName = $taxon_name_or_taxon_base->name;
283
    $is_doubtful = $taxon_name_or_taxon_base->doubtful;
284
    // use the TaxonBase.taggedTitle so we have the secRef
285
    $taggedTitle = $taxon_name_or_taxon_base->taggedTitle;
286
  } else {
287
    // assuming this is a TaxonName
288
    $taxonName = $taxon_name_or_taxon_base;
289
    $taggedTitle = $taxon_name_or_taxon_base->taggedName;
290
  }
291

    
292

    
293
  $renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);
294
  $partDefinition = get_partDefinition($taxonName->nameType);
295

    
296
  // Apply definitions to template.
297
  foreach ($renderTemplate as $part => $uri) {
298

    
299
    if (isset($partDefinition[$part])) {
300
      $renderTemplate[$part] = $partDefinition[$part];
301
    }
302
    if (is_array($uri) && isset($uri['#uri'])) {
303
      $renderTemplate[$part]['#uri'] = $uri['#uri'];
304
    }
305
  }
306

    
307
  $secref_tagged_text = tagged_text_extract_secref($taggedTitle);
308
  $nom_status_tagged_text = tagged_text_extract_nomstatus($taggedTitle);
309
  $appended_phrase_tagged_text = array(); // this is filled later
310

    
311
  normalize_tagged_text($taggedTitle);
312

    
313
  $firstEntryIsValidNamePart =
314
    isset($taggedTitle)
315
    && is_array($taggedTitle)
316
    && isset($taggedTitle[0]->text)
317
    && is_string($taggedTitle[0]->text)
318
    && $taggedTitle[0]->text != ''
319
    && isset($taggedTitle[0]->type)
320
    && $taggedTitle[0]->type == 'name';
321
  $lastAuthorElementString = FALSE;
322

    
323
  $name_encasement = $is_invalid ? '"' : '';
324
  $doubtful_marker = $is_doubtful ? '?&#8239;' : ''; // 	&#8239; =  NARROW NO-BREAK SPACE
325
  $doubtful_marker_markup = '';
326

    
327
  if($doubtful_marker){
328
    $doubtful_marker_markup = '<span class="doubtful">' . $doubtful_marker . '</span>';
329
  }
330

    
331
  // split off all appendedPhrase item  from the end of the array (usually there only should  be one)
332
  while($taggedTitle[count($taggedTitle)-1]->type == "appendedPhrase"){
333
    $appended_phrase_tagged_text[] = array_pop($taggedTitle);
334
  }
335

    
336
  // Got to use second entry as first one, see ToDo comment below ...
337
  if ($firstEntryIsValidNamePart) {
338

    
339
    $taggedName = $taggedTitle;
340
    $hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
341
    $hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
342

    
343

    
344
    if (!(($hasNamePart_with_Authors) || ($hasNameAuthorPart_with_Authors))) {
345
      // Find author and split off from name.
346
      // TODO expecting to find the author as the last element.
347
      /*
348
      if($taggedName[count($taggedName)- 1]->type == 'authors'){
349
        $authorTeam = $taggedName[count($taggedName)- 1]->text;
350
        unset($taggedName[count($taggedName)- 1]);
351
      }
352
      */
353

    
354
      // Remove all authors.
355
      $taggedNameNew = array();
356
      foreach ($taggedName as $element) {
357
        if ($element->type != 'authors') {
358
          $taggedNameNew[] = $element;
359
        }
360
        else {
361
          $lastAuthorElementString = $element->text;
362
        }
363
      }
364
      $taggedName = $taggedNameNew;
365
      unset($taggedNameNew);
366
    }
367
    $name = '<span class="' . $taxonName->class . '">' . $doubtful_marker_markup . $name_encasement . cdm_tagged_text_to_markup($taggedName, $skiptags) . $name_encasement . '</span>';
368
  }
369
  else {
370
    $name = '<span class="' . $taxonName->class . '_titleCache">' . $doubtful_marker_markup . $name_encasement . $taxonName->titleCache . $name_encasement . '</span>';
371
  }
372

    
373

    
374
  if(isset($appended_phrase_tagged_text[0])){
375
    $name .= ' <span class="appended-phrase">'. cdm_tagged_text_to_markup($appended_phrase_tagged_text) . '</span>';
376
  }
377

    
378
  // Fill name into $renderTemplate.
379
  array_setr('name', $name , $renderTemplate);
380

    
381
  // Fill with authorTeam.
382
  /*
383
  if($authorTeam){
384
    $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
385
    array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
386
  }
387
  */
388

    
389
  // Fill with reference.
390
  if (isset($renderTemplate['referencePart']) && !$is_type_designation) {
391

    
392
    $registrations = cdm_ws_get(CDM_WS_NAME, array($taxonName->uuid, "registrations"));
393
    $registration_markup = render_registrations($registrations);
394

    
395
    // default separator
396
    $separator = '';
397

    
398
    // [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
399
    // Komma nach dem Autornamen ist √ľberall dort falsch, wo ein "in" folgt."
400
    if (isset($renderTemplate['referencePart']['reference']) && isset($taxonName->nomenclaturalReference)) {
401
      $microreference = NULL;
402
      if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {
403
        $microreference = $taxonName->nomenclaturalMicroReference;
404
      }
405
      $citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalReference->uuid, $microreference);
406

    
407
      // Find preceding element of the reference.
408
      $precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
409
      if (str_beginsWith($citation, ", in")) {
410
        $citation = substr($citation, 2);
411
        $separator = ' ';
412
      }
413
      elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {
414
        $separator = ', ';
415
      } else {
416
        $separator = ' ';
417
      }
418

    
419

    
420
      $referenceArray['#separator'] = $separator;
421
      $referenceArray['#html'] = '<span class="reference">' . $citation . '</span>' . $registration_markup;
422
      array_setr('reference', $referenceArray, $renderTemplate);
423
    }
424

    
425
    // If authors have been removed from the name part the last named authorteam
426
    // should be added to the reference citation, otherwise, keep the separator
427
    // out of the reference.
428
    if (isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString) {
429
      // If the nomenclaturalReference citation is not included in the
430
      // reference part but display of the microreference
431
      // is wanted, append the microreference to the authorTeam.
432
      $citation = '';
433
      if (!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])) {
434
        $separator = ": ";
435
        $citation = $taxonName->nomenclaturalMicroReference;
436
      }
437
      $referenceArray['#html'] = ' <span class="reference">' . $lastAuthorElementString . $separator . $citation . '</span>';
438
      array_setr('authors', $referenceArray, $renderTemplate);
439
    }
440
  }
441

    
442
  $is_reference_year = false;
443
  if (isset($renderTemplate['referenceYearPart']['reference.year'])) {
444
    if(isset($taxonName->nomenclaturalReference->datePublished)){
445
      $referenceArray['#html'] = ' <span class="reference">' . timePeriodToString($taxonName->nomenclaturalReference->datePublished) . '</span>';
446
      array_setr('reference.year', $referenceArray, $renderTemplate);
447
      $is_reference_year = true;
448
    }
449
  }
450

    
451
  // Fill with status.
452
  if(isset($renderTemplate['statusPart']['status'])){
453
    if (isset($nom_status_tagged_text[0])) {
454
        array_setr('status', '<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, array('postSeparator')) . '</span>', $renderTemplate);
455
    }
456
  }
457

    
458
  if (isset($renderTemplate['secReferencePart'])){
459
    if(isset($secref_tagged_text[1])){
460
      $post_separator_markup = $is_reference_year ? '.': '';
461
      if(isset($nom_status_tagged_text[count($nom_status_tagged_text) - 1]) && ($nom_status_tagged_text[count($nom_status_tagged_text) - 1]->type ==  'postSeparator')){
462
        $post_separator_markup = cdm_tagged_text_to_markup(array($nom_status_tagged_text[count($nom_status_tagged_text) - 1 ]));
463
      };
464
      array_setr('secReference',
465
        $post_separator_markup
466
          . ' <span class="sec_reference">'
467
          . join('', cdm_tagged_text_values($secref_tagged_text))
468
          . '</span>', $renderTemplate);
469
    }
470
  }
471

    
472
  // Fill with protologues etc...
473
  $descriptionHtml = '';
474
  if (array_setr('description', TRUE, $renderTemplate)) {
475
    $descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
476
    foreach ($descriptions as $description) {
477
      if (!empty($description)) {
478
        foreach ($description->elements as $description_element) {
479
          $second_citation = '';
480
          if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {
481
            $second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';
482
          }
483
          $descriptionHtml .= $second_citation;
484
          $descriptionHtml .= cdm_description_element_media(
485
              $description_element,
486
              array(
487
                'application/pdf',
488
                'image/png',
489
                'image/jpeg',
490
                'image/gif',
491
                'text/html',
492
              )
493
          );
494

    
495
        }
496
      }
497
    }
498
    array_setr('description', $descriptionHtml, $renderTemplate);
499
  }
500

    
501
  // Render.
502
  $out = '';
503
  if(isset($_REQUEST['RENDER_PATH'])){
504
    // developer option to show the render path with each taxon name
505
    $out .= '<span class="render-path">' . RenderHints::getRenderPath() . '</span>';
506
  }
507
  $out .= '<span class="' . html_class_attribute_ref($taxon_name_or_taxon_base)
508
    . '" data-cdm-ref="/name/' . $taxonName->uuid . '" data-cdm-render-path="' . RenderHints::getRenderPath() .'">';
509

    
510
  foreach ($renderTemplate as $partName => $part) {
511
    $separator = '';
512
    $partHtml = '';
513
    $uri = FALSE;
514
    if (!is_array($part)) {
515
      continue;
516
    }
517
    if (isset($part['#uri']) && is_string($part['#uri'])) {
518
      $uri = $part['#uri'];
519
      unset($part['#uri']);
520
    }
521
    foreach ($part as $key => $content) {
522
      $html = '';
523
      if (is_array($content)) {
524
        $html = $content['#html'];
525
        if(isset($content['#separator'])) {
526
          $separator = $content['#separator'];
527
        }
528
      }
529
      elseif (is_string($content)) {
530
        $html = $content;
531
      }
532
      $partHtml .= '<span class="' . $key . '">' . $html . '</span>';
533
    }
534
    if ($uri) {
535
      // cannot use l() here since the #uri aleady should have been processed through uri() at this point
536
      $out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';
537

    
538
    }
539
    else {
540
      $out .= $separator . $partHtml;
541
    }
542
  }
543
  $out .= '</span>';
544
  if ($show_annotations) {
545
    // $out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
546
  }
547
  return $out;
548
}
549

    
550

    
551

    
552
/**
553
 * Composes information for a registration from a dto object.
554
 *
555
 * Registrations which are not yet published are suppressed.
556
 *
557
 * @param $registration_dto
558
 * @param $with_citation
559
 *   Whether to show the citation.
560
 *
561
 * @return array
562
 *    A drupal render array with the elements:
563
 *    - 'name'
564
 *    - 'name-relations'
565
 *    - 'specimen_type_designations'
566
 *    - 'name_type_designations'
567
 *    - 'citation'
568
 *    - 'registration_date_and_institute'
569
 * @ingroup compose
570
 */
571
function compose_registration_dto_full($registration_dto, $with_citation = true)
572
{
573
  $render_array = array();
574

    
575
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
576
    return $render_array;
577
  }
578

    
579
  // name and typedesignation in detail
580
  if($registration_dto->nameRef){
581
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
582
    $render_array['published_name'] = markup_to_render_array('<p class="published-name">' . render_taxon_or_name($name) . '</p>', 0);
583
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
584
    $render_array['name_relations'] = markup_to_render_array(render_name_relationships_of($name_relations, $registration_dto->nameRef->uuid, null, false));
585
    $render_array['name_relations']['#weight'] = 10;
586
  } else {
587
    // in this case the registration must have a
588
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->typifiedNameRef->uuid);
589
    $render_array['typified_name'] = markup_to_render_array('<p class="typified-name">for ' . render_taxon_or_name($name) . '</p>', 40);
590
  }
591
  if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
592
    $field_unit_uuids = array();
593
    $specimen_type_designation_refs = array();
594
    $name_type_designation_refs = array();
595
    foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {
596
      $tokens = explode("#", $workingset_ref);
597
      $types_in_fieldunit = get_object_vars($obj); // convert into associative array
598

    
599
      if ($tokens[0] == 'NameTypeDesignation') {
600
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
601
          if(!isset($name_type_designation_refs[$type_status])){
602
            $name_type_designation_refs[$type_status]  = $entity_reference_list;
603
          } else {
604
            array_push($name_type_designation_refs[$type_status] ,$entity_reference_list);
605
          }
606
        }
607
      } else if ($tokens[0] == 'FieldUnit'){
608
        $field_unit_uuids[] = $tokens[1];
609
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
610
          if(!isset($specimen_type_designation_refs[$type_status])){
611
            $specimen_type_designation_refs[$type_status] =  $entity_reference_list;
612
          } else {
613
            array_push($specimen_type_designation_refs[$type_status], $entity_reference_list);
614
          }
615
        }
616
      } else {
617
        drupal_set_message("Unimplemented type: " . $tokens[0], 'error');
618
      }
619
    }
620
    if (count($name_type_designation_refs) > 0) {
621
      $render_array['name_type_designations'] = compose_name_type_designations($name_type_designation_refs);
622
      $render_array['name_type_designations']['#prefix'] = '<p class="name_type_designations">';
623
      $render_array['name_type_designations']['#suffix'] = '</p>';
624
      $render_array['name_type_designations']['#weight'] = 20;
625
    }
626
    if (count($field_unit_uuids) > 0) {
627
      $render_array['specimen_type_designations'] = compose_specimen_type_designations($specimen_type_designation_refs);
628
    }
629
  }
630

    
631
  // citation
632
  if ($with_citation) {
633
    $render_array['citation'] = markup_to_render_array(
634
      "<p class=\"citation " . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
635
      . l($registration_dto->bibliographicInRefCitationString, path_to_reference($registration_dto->citationUuid))
636
      . "</p>",
637
      50);
638
  }
639

    
640
  // registration date and office
641
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto);
642
  if($registration_date_insitute_markup){
643
    $render_array['registration_date_and_institute'] = markup_to_render_array(
644
      $registration_date_insitute_markup . '</p>',
645
      100);
646
  }
647

    
648
  return $render_array;
649
}
650

    
651

    
652
/**
653
 * Composes a compact representation for a registrationDTO object
654
 *
655
 * Registrations which are not yet published are suppressed.
656
 *
657
 * @param $registration_dto
658
 * @param $style string
659
 *   The style of how to compose the 'identifier' and 'registration_date_and_institute' part with the summary
660
 *   - 'citation': Similar to the arrearance of nomenclatural acts in print media
661
 *   - 'list-item' : style suitable for result lists etc
662
 *
663
 * @return array
664
 *    A drupal render array with the elements:
665
 *    - 'registration-metadata' when $style == 'list-item'
666
 *    - 'summary'
667
 * @ingroup compose
668
 */
669
function compose_registration_dto_compact($registration_dto, $style = 'citation', $tag_enclosing_summary = 'p')
670
{
671
  $render_array = array();
672
  $media_link_map = array();
673

    
674
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
675
    return $render_array;
676
  }
677

    
678
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto, 'span');
679
  $itentifier_markup = l($registration_dto->identifier, $registration_dto->identifier, array('attributes' => array('class' => array('identifier'))));
680

    
681
  $tagged_text_options = array();
682
  if(isset($registration_dto->nameRef)){
683
    $tagged_text_options[] = array(
684
      'filter-type' => 'name',
685
      'prefix' => '<span class="registered_name">',
686
      'suffix' => '</span>',
687
    );
688
  } else {
689
    $tagged_text_options[] = array(
690
      'filter-type' => 'name',
691
      'prefix' => '<span class="referenced_typified_name">',
692
      'suffix' => '</span>',
693
    );
694
  }
695
  cdm_tagged_text_add_options($registration_dto->summaryTaggedText, $tagged_text_options);
696
  $taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
697
  foreach ($taggged_text_expanded  as $tagged_text){
698
    if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {
699
      $mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));
700
      if(isset($mediaDTOs[0]->uri)){
701
        $media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';
702
        $tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);
703
        $media_link_map[$media_url_key] =  cdm_external_uri($mediaDTOs[0]->uri, true);
704
      }
705
    }
706
  }
707
  $registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
708
  foreach($media_link_map as $media_url_key => $link){
709
    $registation_markup = str_replace($media_url_key, $link, $registation_markup);
710
  }
711
  if($style == 'citation') {
712
    $registation_markup = $registation_markup . ' ' . $itentifier_markup . ' ' . $registration_date_insitute_markup;
713
  } else {
714
    $render_array['registration-metadata'] = markup_to_render_array('<div class="registration-metadata">' . $itentifier_markup . ' ' . $registration_date_insitute_markup. "</div>", -10);
715
  }
716
  $render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . ' class="registration-summary">' . $registation_markup . '</' . $tag_enclosing_summary . '>', 0);
717

    
718
  return $render_array;
719
}
720

    
721

    
722
/**
723
 * Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.
724
 *
725
 * @param $registration_dto
726
 * @return string
727
 *    The markup or an empty string
728
 */
729
function render_registration_date_and_institute($registration_dto, $enclosing_tag = 'p') {
730
  $registration_date_institute_markup = '';
731
  if ($registration_dto->registrationDate) {
732
    $date_string = format_datetime($registration_dto->registrationDate);
733
    if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {
734
      $registration_date_institute_markup =
735
        t("Registration on @date in @institution", array(
736
          '@date' => $date_string,
737
          '@institution' => $registration_dto->institutionTitleCache,
738
        ));
739
    } else {
740
      $registration_date_institute_markup =
741
        t("Registration on @date", array(
742
          '@date' => $date_string
743
        ));
744
    }
745
    $registration_date_institute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_institute_markup . '</' .$enclosing_tag . '>';
746
  }
747
  return $registration_date_institute_markup;
748
}
749

    
750

    
751
/**
752
 * @param $registrations
753
 * @return string
754
 */
755
function render_registrations($registrations)
756
{
757
  $registration_markup = '';
758
  $registration_markup_array = array();
759
  if ($registrations) {
760
    foreach ($registrations as $reg) {
761
      $registration_markup_array[] = render_registration($reg);
762
    }
763
    $registration_markup = " Registration" . (count($registration_markup_array) > 1 ? 's: ' : ': ')
764
      . join(', ', $registration_markup_array);
765
  }
766
  return $registration_markup;
767
}
768

    
769

    
770
/**
771
 * Renders a registration
772
 *
773
 * TODO replace by compose_registration_dto_compact
774
 * @param $registration
775
 */
776
function render_registration($registration){
777
  $markup = '';
778

    
779
  if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
780
    $office_class_attribute = '';
781
    if(isset($registration->institution->titleCache)){
782
      $office_class_attribute = registration_intitute_class_attribute($registration);
783
    }
784
    $markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, $registration->identifier) . ', '
785
      .  preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
786
      . '</span>';
787
  }
788
  return $markup;
789
}
790

    
791
/**
792
 * @param $registration
793
 * @return string
794
 */
795
function registration_intitute_class_attribute($registration_dto)
796
{
797
  if(isset($registration_dto->institutionTitleCache)){
798
    $institutionTitleCache = $registration_dto->institutionTitleCache;
799
  } else {
800
    // fall back option to also support cdm entities
801
    $institutionTitleCache = @$registration_dto->institution->titleCache;
802
  }
803
  return $institutionTitleCache ? 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $institutionTitleCache)) : '';
804
}
805

    
806

    
807
/**
808
 * Composes the TypedEntityReference to name type designations passed as associatve array.
809
 *
810
 * @param $$type_entity_refs array
811
 *   an associative array of name type type => TypedEntityReference for name type designations as
812
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
813
 *
814
 * @ingroup compose
815
 */
816
function compose_name_type_designations($type_entity_refs){
817
  $render_array = array();
818
  $preferredStableUri = '';
819
  foreach($type_entity_refs as $type_status => $name_type){
820
    $type_designation = cdm_ws_get(CDM_TYPEDESIGNATION, array($name_type->uuid, 'preferredUri'));
821
    if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
822
      $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
823
    }
824
    $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type)  . '"><span class="type_status">'. ucfirst($type_status) . "</span>: "
825
      . $name_type->label
826
      . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
827
      . '</div>');
828
  }
829
  return $render_array;
830
}
831

    
832
/**
833
 * Composes the TypedEntityReference to specimen type designations passed as associatve array.
834
 *
835
 * @param $type_entity_refs array
836
 *   an associative array of specimen type type => TypedEntityReference for specimen type designations as
837
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
838
 *
839
 * @ingroup compose
840
 */
841
function compose_specimen_type_designations($type_entity_refs){
842

    
843
  $render_array = array();
844

    
845
  foreach($type_entity_refs as $type_status => $specimen_types){
846
    foreach($specimen_types as $specimen_type){
847

    
848
      $type_designation = cdm_ws_get(CDM_TYPEDESIGNATION, array($specimen_type->uuid));
849

    
850
      $preferredStableUri = '';
851
      $citation_markup = '';
852
      $media = '';
853

    
854
      // preferredStableUri
855
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
856
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
857
      }
858

    
859
      $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
860
      if($mediaSpecimen){
861
        // compose output
862
        // mediaURI
863
        if(isset($mediaSpecimen->representations[0])) {
864
          $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
865
          $captionElements = array(
866
            '#uri' => t('open media'),
867
            'elements' => array('-none-'),
868
            'sources_as_content' => true
869
          );
870
          $media = compose_cdm_media_gallerie(array(
871
            'mediaList' => array($mediaSpecimen),
872
            'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $specimen_type->uuid,
873
            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
874
            'cols' => $gallery_settings['cdm_dataportal_media_cols'],
875
            'captionElements' => $captionElements,
876
          ));
877
        }
878
        // citation and detail
879
        $annotations_and_sources = handle_annotations_and_sources(
880
            $mediaSpecimen,
881
            array(
882
                'sources_as_content' => true,
883
                'link_to_name_used_in_source' => false,
884
                'link_to_reference' => true,
885
                'add_footnote_keys' => false,
886
                'bibliography_aware' => false),
887
            '',
888
            null
889
        );
890
        if(is_array( $annotations_and_sources['source_references'])){
891
          $citation_markup = join(', ', $annotations_and_sources['source_references']);
892
        }
893
      }
894

    
895
      $render_array[] = markup_to_render_array('<div class="specimen_type_designation ' . html_class_attribute_ref($specimen_type)  . '">
896
          <span class="type_status">' . ucfirst($type_status) . "</span>: "
897
        . $specimen_type->label
898
        . ($citation_markup ? ' '. $citation_markup : '')
899
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
900
        . $media
901
        . '</div>');
902
    }
903
  }
904
  return $render_array;
905
}
906

    
907
/**
908
 * Renders the name relationships.
909
 *
910
 * @param $name_relations
911
 *    The list of CDM NameRelationsips
912
 * @param $current_name_uuid
913
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
914
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
915
 * @param $suppress_if_current_name_is_source
916
 *    The display of the relation will be
917
 *    suppressed is the current name is on the source of the relation edge.
918
 *    That is if it is on the from side of the relation. Except for 'blocking name for' which is
919
 *    an inverse relation. For this relation type the toName is taken in to account.
920
 * @param $current_taxon_uuid
921
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
922
 * @return String
923
 *    The markup for the name relationships
924
 */
925
function render_name_relationships_of($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
926

    
927
  static $inverse_name_rels_uuids = array(UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
928

    
929
  RenderHints::pushToRenderStack('homonym');
930
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
931

    
932
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_TYPES, unserialize(CDM_NAME_RELATIONSHIP_TYPES_DEFAULT));
933

    
934
  $relations_array = array();
935

    
936
  if ($name_relations) {
937
    foreach ($name_relations as $name_rel) {
938
      if (!(isset($selected_name_rel_uuids[$name_rel->type->uuid]) && $selected_name_rel_uuids[$name_rel->type->uuid])) {
939
        // skip if not selected in the settings
940
        continue;
941
      }
942
      $is_inverse_relation = array_search($name_rel->type->uuid, $inverse_name_rels_uuids) !== false;
943
      $is_current_name_to_name = $current_name_uuid == $name_rel->toName->uuid;
944
      $is_current_name_from_name = $current_name_uuid == $name_rel->fromName->uuid;
945
      $relationship_markup = null;
946

    
947
      if($is_current_name_to_name && ($suppress_if_current_name_is_source && $is_inverse_relation || !$suppress_if_current_name_is_source)){
948
        $highlited_synonym_uuid = isset ($name_rel->fromName->taxonBases[0]->uuid) ? $name_rel->fromName->taxonBases[0]->uuid : '';
949
        $relationship_markup = render_taxon_or_name($name_rel->fromName,
950
          url(path_to_name($name_rel->fromName->uuid, $current_taxon_uuid, $highlited_synonym_uuid))
951
        );
952
      } else if($is_current_name_from_name && ($suppress_if_current_name_is_source && !$is_inverse_relation || !$suppress_if_current_name_is_source)){
953
        $highlited_synonym_uuid = isset ($name_rel->toName->taxonBases[0]->uuid) ? $name_rel->toName->taxonBases[0]->uuid : '';
954
        $relationship_markup = render_taxon_or_name($name_rel->toName,
955
          url(path_to_name($name_rel->toName->uuid, $current_taxon_uuid, $highlited_synonym_uuid))
956
        );
957
      }
958
        
959
      if($relationship_markup){
960
        if (count($relations_array)) {
961
          // lat: "non nec" == german: "weder noch"
962
          $relations_array [] = 'nec ' . $relationship_markup;
963
        } else {
964
          $relations_array [] = 'non ' . $relationship_markup;
965
        }
966
      }
967

    
968
    }
969
  }
970

    
971
  RenderHints::popFromRenderStack();
972
  return (count($relations_array) ?'<div class="name-relationships">[' . trim(join(" ", $relations_array)) . ']</div>' : '');
973
}
974

    
975
/**
976
 * @param $taxon
977
 * @return array
978
 */
979
function cdm_name_relationships_for_taxon($taxon)
980
{
981
  $from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
982
  $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
983
  $name_relations = array_merge($from_name_relations, $to_name_relations);
984
  return $name_relations;
985
}
986

    
987

    
988
/**
989
 * Recursively searches the array for the $key and sets the given value.
990
 *
991
 * @param mixed $key
992
 *   Key to search for.
993
 * @param mixed $value
994
 *   Value to set.'
995
 * @param array $array
996
 *   Array to search in.
997
 *
998
 * @return bool
999
 *   True if the key has been found.
1000
 */
1001
function &array_setr($key, $value, array &$array) {
1002
  $res = NULL;
1003
  foreach ($array as $k => &$v) {
1004
    if ($key == $k) {
1005
      $v = $value;
1006
      return $array;
1007
    }
1008
    elseif (is_array($v)) {
1009
      $innerArray = array_setr($key, $value, $v);
1010
      if ($innerArray) {
1011
        return $array;
1012
      }
1013
    }
1014
  }
1015
  return $res;
1016
}
1017

    
1018
/**
1019
 * @todo Please document this function.
1020
 * @see http://drupal.org/node/1354
1021
 */
1022
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
1023
  $res = NULL;
1024
  $precedingElement = NULL;
1025
  foreach ($renderTemplate as &$part) {
1026
    foreach ($part as $key => &$element) {
1027
      if ($key == $contentElementKey) {
1028
        return $precedingElement;
1029
      }
1030
      $precedingElement = $element;
1031
    }
1032
  }
1033
  return $res;
1034
}
1035

    
1036
/**
1037
 * @todo Please document this function.
1038
 * @see http://drupal.org/node/1354
1039
 */
1040
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
1041
  $res = NULL;
1042
  $precedingKey = NULL;
1043
  foreach ($renderTemplate as &$part) {
1044
    if (is_array($part)) {
1045
      foreach ($part as $key => &$element) {
1046
        if ($key == $contentElementKey) {
1047
          return $precedingKey;
1048
        }
1049
        if (!str_beginsWith($key, '#')) {
1050
          $precedingKey = $key;
1051
        }
1052
      }
1053
    }
1054
  }
1055
  return $res;
1056
}
1057

    
1058
function nameTypeToDTYPE($dtype){
1059
  static $nameTypeLabelMap = array(
1060
    "ICNB" => "BacterialName",
1061
    "ICNAFP" => "BotanicalName",
1062
    "ICNCP" => "CultivarPlantName",
1063
    "ICZN" => "ZoologicalName",
1064
    "ICVCN" => "ViralName",
1065
    "Any taxon name" => "TaxonName",
1066
    "NonViral" => "TaxonName",
1067
    "Fungus" => "BotanicalName",
1068
    "Plant" => "BotanicalName",
1069
    "Algae" => "BotanicalName",
1070
  );
1071
  return $nameTypeLabelMap[$dtype];
1072

    
1073
}
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