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cdm-dataportal / modules / cdm_dataportal / includes / name.inc @ b90ef618

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1
<?php
2
/**
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
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 * 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) {
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;
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        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
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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
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 $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.tagged_title so we have the secRef
285
    $tagged_title = $taxon_name_or_taxon_base->taggedTitle;
286
  } else {
287
    // assuming this is a TaxonName
288
    $taxonName = $taxon_name_or_taxon_base;
289
    if(isset($taxonName->taggedFullTitle)){
290
      $tagged_title = $taxon_name_or_taxon_base->taggedFullTitle;
291
    } else {
292
      $tagged_title = $taxon_name_or_taxon_base->taggedName;
293
    }
294
  }
295

    
296

    
297
  $renderTemplate = get_nameRenderTemplate(RenderHints::getRenderPath(), $nameLink, $refenceLink);
298
  $partDefinition = get_partDefinition($taxonName->nameType);
299

    
300
  // Apply definitions to template.
301
  foreach ($renderTemplate as $part => $uri) {
302

    
303
    if (isset($partDefinition[$part])) {
304
      $renderTemplate[$part] = $partDefinition[$part];
305
    }
306
    if (is_array($uri) && isset($uri['#uri'])) {
307
      $renderTemplate[$part]['#uri'] = $uri['#uri'];
308
    }
309
  }
310

    
311
  $secref_tagged_text = tagged_text_extract_reference_and_detail($tagged_title);
312
  // taxon names will have the nomenclatural reference in the tagged full title:
313
  $nomref_tagged_text = tagged_text_extract_reference($tagged_title);
314
  $nom_status_tagged_text = tagged_text_extract_nomstatus($tagged_title);
315
  $appended_phrase_tagged_text = array(); // this is filled later
316

    
317
  normalize_tagged_text($tagged_title);
318

    
319
  $firstEntryIsValidNamePart =
320
    isset($tagged_title)
321
    && is_array($tagged_title)
322
    && isset($tagged_title[0]->text)
323
    && is_string($tagged_title[0]->text)
324
    && $tagged_title[0]->text != ''
325
    && isset($tagged_title[0]->type)
326
    && $tagged_title[0]->type == 'name';
327
  $lastAuthorElementString = FALSE;
328

    
329
  $name_encasement = $is_invalid ? '"' : '';
330
  $doubtful_marker = $is_doubtful ? '?&#8239;' : ''; // 	&#8239; =  NARROW NO-BREAK SPACE
331
  $doubtful_marker_markup = '';
332

    
333
  if($doubtful_marker){
334
    $doubtful_marker_markup = '<span class="doubtful">' . $doubtful_marker . '</span>';
335
  }
336

    
337
  // split off all appendedPhrase item  from the end of the array (usually there only should  be one)
338
  while($tagged_title[count($tagged_title)-1]->type == "appendedPhrase"){
339
    $appended_phrase_tagged_text[] = array_pop($tagged_title);
340
  }
341

    
342
  // Got to use second entry as first one, see ToDo comment below ...
343
  if ($firstEntryIsValidNamePart) {
344

    
345
    $taggedName = $tagged_title;
346
    $hasNamePart_with_Authors = isset($renderTemplate['namePart']) && isset($renderTemplate['namePart']['authors']);
347
    $hasNameAuthorPart_with_Authors = isset($renderTemplate['nameAuthorPart']) && isset($renderTemplate['nameAuthorPart']['authors']);
348

    
349

    
350
    if (!(($hasNamePart_with_Authors) || ($hasNameAuthorPart_with_Authors))) {
351
      // Find author and split off from name.
352
      // TODO expecting to find the author as the last element.
353
      /*
354
      if($taggedName[count($taggedName)- 1]->type == 'authors'){
355
        $authorTeam = $taggedName[count($taggedName)- 1]->text;
356
        unset($taggedName[count($taggedName)- 1]);
357
      }
358
      */
359

    
360
      // Remove all authors.
361
      $taggedNameNew = array();
362
      foreach ($taggedName as $element) {
363
        if ($element->type != 'authors') {
364
          $taggedNameNew[] = $element;
365
        }
366
        else {
367
          $lastAuthorElementString = $element->text;
368
        }
369
      }
370
      $taggedName = $taggedNameNew;
371
      unset($taggedNameNew);
372
    }
373
    $name = '<span class="' . $taxonName->class . '">' . $doubtful_marker_markup . $name_encasement . cdm_tagged_text_to_markup($taggedName, $skiptags) . $name_encasement . '</span>';
374
  }
375
  else {
376
    $name = '<span class="' . $taxonName->class . '_titleCache">' . $doubtful_marker_markup . $name_encasement . $taxonName->titleCache . $name_encasement . '</span>';
377
  }
378

    
379

    
380
  if(isset($appended_phrase_tagged_text[0])){
381
    $name .= ' <span class="appended-phrase">'. cdm_tagged_text_to_markup($appended_phrase_tagged_text) . '</span>';
382
  }
383

    
384
  // Fill name into $renderTemplate.
385
  array_setr('name', $name , $renderTemplate);
386

    
387
  // Fill with authorTeam.
388
  /*
389
  if($authorTeam){
390
    $authorTeamHtml = ' <span class="authorTeam">'.$authorTeam.'</span>';
391
    array_setr('authorTeam', $authorTeamHtml, $renderTemplate);
392
  }
393
  */
394

    
395
  // Fill with reference.
396
  if (isset($renderTemplate['referencePart']) && !$is_type_designation) {
397

    
398
    $registrations = cdm_ws_get(CDM_WS_NAME, array($taxonName->uuid, "registrations"));
399
    $registration_markup = render_registrations($registrations);
400

    
401
    // default separator
402
    $separator = '';
403

    
404
    // [Eckhard]:"Komma nach dem Taxonnamen ist grunsätzlich falsch,
405
    // Komma nach dem Autornamen ist √ľberall dort falsch, wo ein "in" folgt."
406
    if (isset($renderTemplate['referencePart']['reference']) && isset($taxonName->nomenclaturalReference)) {
407
      $microreference = NULL;
408
      if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {
409
        $microreference = $taxonName->nomenclaturalMicroReference;
410
      }
411
      if(count($nomref_tagged_text) == 0){
412
        $citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalReference->uuid, $microreference);
413
        // Find preceding element of the reference.
414
        $precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
415
        if (str_beginsWith($citation, ", in")) {
416
          $citation = substr($citation, 2);
417
          $separator = ' ';
418
        }
419
        elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {
420
          $separator = ', ';
421
        } else {
422
          $separator = ' ';
423
        }
424
        $referenceArray['#separator'] = $separator;
425
        $referenceArray['#html'] = '<span class="reference">' . $citation . '</span>' . $registration_markup;
426
      } else {
427
        // this ist the case for taxon names
428
        $referenceArray['#html'] = cdm_tagged_text_to_markup($nomref_tagged_text);
429
      }
430

    
431

    
432
      array_setr('reference', $referenceArray, $renderTemplate);
433
    }
434

    
435
    // If authors have been removed from the name part the last named authorteam
436
    // should be added to the reference citation, otherwise, keep the separator
437
    // out of the reference.
438
    if (isset($renderTemplate['referencePart']['authors']) && $lastAuthorElementString) {
439
      // If the nomenclaturalReference citation is not included in the
440
      // reference part but display of the microreference
441
      // is wanted, append the microreference to the authorTeam.
442
      $citation = '';
443
      if (!isset($renderTemplate['referencePart']['reference']) && isset($renderTemplate['referencePart']['microreference'])) {
444
        $separator = ": ";
445
        $citation = $taxonName->nomenclaturalMicroReference;
446
      }
447
      $referenceArray['#html'] = ' <span class="reference">' . $lastAuthorElementString . $separator . $citation . '</span>';
448
      array_setr('authors', $referenceArray, $renderTemplate);
449
    }
450
  }
451

    
452
  $is_reference_year = false;
453
  if (isset($renderTemplate['referenceYearPart']['reference.year'])) {
454
    if(isset($taxonName->nomenclaturalReference->datePublished)){
455
      $referenceArray['#html'] = ' <span class="reference">' . timePeriodToString($taxonName->nomenclaturalReference->datePublished) . '</span>';
456
      array_setr('reference.year', $referenceArray, $renderTemplate);
457
      $is_reference_year = true;
458
    }
459
  }
460

    
461
  // Fill with status.
462
  if(isset($renderTemplate['statusPart']['status'])){
463
    if (isset($nom_status_tagged_text[0])) {
464
        $tt_to_markup_options = array('html' => false);
465
        foreach ($nom_status_tagged_text as &$tt){
466
         if($tt->type == 'nomStatus'&& isset($tt->entityReference)) {
467
           $nom_status = cdm_ws_get(CDM_WS_NOMENCLATURALSTATUS, array($tt->entityReference->uuid));
468
           $nom_status_fkey = nomenclatural_status_footnote_markup($nom_status);
469
           $tt->text .= $nom_status_fkey;
470
           $tt_to_markup_options['html'] = true;
471
         }
472
        }
473
        array_setr(
474
          'status',
475
          '<span class="nomenclatural_status">' . cdm_tagged_text_to_markup($nom_status_tagged_text, array('postSeparator'), 'span', $tt_to_markup_options) . '</span>', $renderTemplate);
476
    }
477
  }
478

    
479
  if (isset($renderTemplate['secReferencePart'])){
480
    if(isset($secref_tagged_text[1])){
481
      $post_separator_markup = $is_reference_year ? '.': '';
482
      if(isset($nom_status_tagged_text[count($nom_status_tagged_text) - 1]) && ($nom_status_tagged_text[count($nom_status_tagged_text) - 1]->type ==  'postSeparator')){
483
        $post_separator_markup = cdm_tagged_text_to_markup(array($nom_status_tagged_text[count($nom_status_tagged_text) - 1 ]));
484
      };
485
      array_setr('secReference',
486
        $post_separator_markup
487
          . ' <span class="sec_reference">'
488
          . join('', cdm_tagged_text_values($secref_tagged_text))
489
          . '</span>', $renderTemplate);
490
    }
491
  }
492

    
493
  // Fill with protologues etc...
494
  $descriptionHtml = '';
495
  if (array_setr('description', TRUE, $renderTemplate)) {
496
    $descriptions = cdm_ws_get(CDM_WS_PORTAL_NAME_DESCRIPTIONS, $taxonName->uuid);
497
    foreach ($descriptions as $description) {
498
      if (!empty($description)) {
499
        foreach ($description->elements as $description_element) {
500
          $second_citation = '';
501
          if (isset($description_element->multilanguageText_L10n) && $description_element->multilanguageText_L10n->text) {
502
            $second_citation = '[& ' . $description_element->multilanguageText_L10n->text . '].';
503
          }
504
          $descriptionHtml .= $second_citation;
505
          $descriptionHtml .= cdm_description_element_media(
506
              $description_element,
507
              array(
508
                'application/pdf',
509
                'image/png',
510
                'image/jpeg',
511
                'image/gif',
512
                'text/html',
513
              )
514
          );
515

    
516
        }
517
      }
518
    }
519
    array_setr('description', $descriptionHtml, $renderTemplate);
520
  }
521

    
522
  // Render.
523
  $out = '';
524
  if(isset($_REQUEST['RENDER_PATH'])){
525
    // developer option to show the render path with each taxon name
526
    $out .= '<span class="render-path">' . RenderHints::getRenderPath() . '</span>';
527
  }
528
  $out .= '<span class="' . html_class_attribute_ref($taxon_name_or_taxon_base)
529
    . '" data-cdm-ref="/name/' . $taxonName->uuid . '" data-cdm-render-path="' . RenderHints::getRenderPath() .'">';
530

    
531
  foreach ($renderTemplate as $partName => $part) {
532
    $separator = '';
533
    $partHtml = '';
534
    $uri = FALSE;
535
    if (!is_array($part)) {
536
      continue;
537
    }
538
    if (isset($part['#uri']) && is_string($part['#uri'])) {
539
      $uri = $part['#uri'];
540
      unset($part['#uri']);
541
    }
542
    foreach ($part as $key => $content) {
543
      $html = '';
544
      if (is_array($content)) {
545
        $html = $content['#html'];
546
        if(isset($content['#separator'])) {
547
          $separator = $content['#separator'];
548
        }
549
      }
550
      elseif (is_string($content)) {
551
        $html = $content;
552
      }
553
      $partHtml .= '<span class="' . $key . '">' . $html . '</span>';
554
    }
555
    if ($uri) {
556
      // cannot use l() here since the #uri aleady should have been processed through uri() at this point
557
      $out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';
558

    
559
    }
560
    else {
561
      $out .= $separator . $partHtml;
562
    }
563
  }
564
  $out .= '</span>';
565
  if ($show_annotations) {
566
    // $out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
567
  }
568
  return $out;
569
}
570

    
571

    
572

    
573
/**
574
 * Composes information for a registration from a dto object.
575
 *
576
 * Registrations which are not yet published are suppressed.
577
 *
578
 * @param $registration_dto
579
 * @param $with_citation
580
 *   Whether to show the citation.
581
 *
582
 * @return array
583
 *    A drupal render array with the elements:
584
 *    - 'name'
585
 *    - 'name-relations'
586
 *    - 'specimen_type_designations'
587
 *    - 'name_type_designations'
588
 *    - 'citation'
589
 *    - 'registration_date_and_institute'
590
 * @ingroup compose
591
 */
592
function compose_registration_dto_full($registration_dto, $with_citation = true)
593
{
594
  $render_array = array(
595
    '#prefix' => '<div class="registration">',
596
    '#suffix' => '</div>'
597
  );
598

    
599
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
600
    return $render_array;
601
  }
602

    
603
  $render_array['sub_headline'] = markup_to_render_array(ucfirst(join(" & ", registration_types($registration_dto))),false, '<h3 class="regsitration_type">' . t('Event: '), '</h3>' );
604

    
605
  // name and typedesignation in detail
606
  if($registration_dto->nameRef){
607
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
608
    cdm_load_tagged_full_title($name);
609
    $render_array['published_name'] = markup_to_render_array('<p class="published-name">' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</p>', 0);
610
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
611
    $render_array['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null);
612
    $render_array['name_relations']['#weight'] = 10;
613
  } else {
614
    // in this case the registration must have a
615
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->typifiedNameRef->uuid);
616
    $render_array['typified_name'] = markup_to_render_array('<p class="typified-name">for ' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</p>', 40);
617
  }
618
  if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
619
    $field_unit_uuids = array();
620
    $specimen_type_designation_refs = array();
621
    $name_type_designation_refs = array();
622
    foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {
623
      $tokens = explode("#", $workingset_ref);
624
      $types_in_fieldunit = get_object_vars($obj); // convert into associative array
625

    
626
      if ($tokens[0] == 'NameTypeDesignation') {
627
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
628
          if(!isset($name_type_designation_refs[$type_status])){
629
            $name_type_designation_refs[$type_status]  = $entity_reference_list;
630
          } else {
631
            array_push($name_type_designation_refs[$type_status] ,$entity_reference_list);
632
          }
633
        }
634
      } else if ($tokens[0] == 'FieldUnit'){
635
        $field_unit_uuids[] = $tokens[1];
636
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
637
          if(!isset($specimen_type_designation_refs[$type_status])){
638
            $specimen_type_designation_refs[$type_status] =  $entity_reference_list;
639
          } else {
640
            array_push($specimen_type_designation_refs[$type_status], $entity_reference_list);
641
          }
642
        }
643
      } else {
644
        drupal_set_message("Unimplemented type: " . $tokens[0], 'error');
645
      }
646
    }
647
    if (count($name_type_designation_refs) > 0) {
648
      $render_array['name_type_designations'] = compose_name_type_designations($name_type_designation_refs);
649
      $render_array['name_type_designations']['#prefix'] = '<p class="name_type_designations">';
650
      $render_array['name_type_designations']['#suffix'] = '</p>';
651
      $render_array['name_type_designations']['#weight'] = 20;
652
    }
653
    if (count($field_unit_uuids) > 0) {
654
      $render_array['specimen_type_designations'] = compose_specimen_type_designations($specimen_type_designation_refs);
655
    }
656
  }
657

    
658
  // citation
659
  if ($with_citation) {
660
    $render_array['citation'] = markup_to_render_array(
661
      "<p class=\"citation " . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
662
      . l($registration_dto->bibliographicInRefCitationString, path_to_reference($registration_dto->citationUuid))
663
      . "</p>",
664
      50);
665
  }
666

    
667
  // registration date and office
668
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto);
669
  if($registration_date_insitute_markup){
670
    $render_array['registration_date_and_institute'] = markup_to_render_array(
671
      $registration_date_insitute_markup . '</p>',
672
      100);
673
  }
674

    
675
  return $render_array;
676
}
677

    
678

    
679
/**
680
 * Composes a compact representation for a registrationDTO object
681
 *
682
 * Registrations which are not yet published are suppressed.
683
 *
684
 * @param $registration_dto
685
 * @param $style string
686
 *   The style of how to compose the 'identifier' and 'registration_date_and_institute' part with the summary
687
 *   - 'citation': Similar to the arrearance of nomenclatural acts in print media
688
 *   - 'list-item' : style suitable for result lists etc
689
 *
690
 * @return array
691
 *    A drupal render array with the elements:
692
 *    - 'registration-metadata' when $style == 'list-item'
693
 *    - 'summary'
694
 * @ingroup compose
695
 */
696
function compose_registration_dto_compact($registration_dto, $style = 'citation', $tag_enclosing_summary = 'p')
697
{
698
  $render_array = array();
699
  $media_link_map = array();
700

    
701
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
702
    return $render_array;
703
  }
704

    
705
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto, 'span');
706
  $itentifier_markup = l($registration_dto->identifier, path_to_registration($registration_dto->identifier), array('attributes' => array('class' => array('identifier'))));
707

    
708
  $tagged_text_options = array();
709
  if(isset($registration_dto->nameRef)){
710
    $tagged_text_options[] = array(
711
      'filter-type' => 'name',
712
      'prefix' => '<span class="registered_name">',
713
      'suffix' => '</span>',
714
    );
715
  } else {
716
    $tagged_text_options[] = array(
717
      'filter-type' => 'name',
718
      'prefix' => '<span class="referenced_typified_name">',
719
      'suffix' => '</span>',
720
    );
721
  }
722
  cdm_tagged_text_add_options($registration_dto->summaryTaggedText, $tagged_text_options);
723
  $taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
724
  foreach ($taggged_text_expanded  as $tagged_text){
725
    if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {
726
      $mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));
727
      if(isset($mediaDTOs[0]->uri)){
728
        $media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';
729
        $tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);
730
        $media_link_map[$media_url_key] =  cdm_external_uri($mediaDTOs[0]->uri, true);
731
      }
732
    }
733
  }
734
  $registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
735
  foreach($media_link_map as $media_url_key => $link){
736
    $registation_markup = str_replace($media_url_key, $link, $registation_markup);
737
  }
738
  if($style == 'citation') {
739
    $registation_markup = $registation_markup . ' ' . $itentifier_markup . ' ' . $registration_date_insitute_markup;
740
  } else {
741
    $render_array['registration-metadata'] = markup_to_render_array('<div class="registration-metadata">' . $itentifier_markup . ' ' . $registration_date_insitute_markup. "</div>", -10);
742
  }
743
  $render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . ' class="registration-summary">' . $registation_markup . '</' . $tag_enclosing_summary . '>', 0);
744

    
745
  return $render_array;
746
}
747

    
748

    
749
/**
750
 * Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.
751
 *
752
 * @param $registration_dto
753
 * @return string
754
 *    The markup or an empty string
755
 */
756
function render_registration_date_and_institute($registration_dto, $enclosing_tag = 'p') {
757
  $registration_date_institute_markup = '';
758
  if ($registration_dto->registrationDate) {
759
    $date_string = format_datetime($registration_dto->registrationDate);
760
    if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {
761
      $registration_date_institute_markup =
762
        t("Registration on @date in @institution", array(
763
          '@date' => $date_string,
764
          '@institution' => $registration_dto->institutionTitleCache,
765
        ));
766
    } else {
767
      $registration_date_institute_markup =
768
        t("Registration on @date", array(
769
          '@date' => $date_string
770
        ));
771
    }
772
    $registration_date_institute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_institute_markup . '</' .$enclosing_tag . '>';
773
  }
774
  return $registration_date_institute_markup;
775
}
776

    
777

    
778
/**
779
 * @param $registrations
780
 * @return string
781
 */
782
function render_registrations($registrations)
783
{
784
  $registration_markup = '';
785
  $registration_markup_array = array();
786
  if ($registrations) {
787
    foreach ($registrations as $reg) {
788
      $registration_markup_array[] = render_registration($reg);
789
    }
790
    $registration_markup = " Registration" . (count($registration_markup_array) > 1 ? 's: ' : ': ')
791
      . join(', ', $registration_markup_array);
792
  }
793
  return $registration_markup;
794
}
795

    
796

    
797
/**
798
 * Renders a registration
799
 *
800
 * TODO replace by compose_registration_dto_compact
801
 * @param $registration
802
 */
803
function render_registration($registration){
804
  $markup = '';
805

    
806
  if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
807
    $office_class_attribute = '';
808
    if(isset($registration->institution->titleCache)){
809
      $office_class_attribute = registration_intitute_class_attribute($registration);
810
    }
811
    $markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, path_to_registration($registration->identifier)) . ', '
812
      .  preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
813
      . '</span>';
814
  }
815
  return $markup;
816
}
817

    
818
/**
819
 * @param $registration
820
 * @return string
821
 */
822
function registration_intitute_class_attribute($registration_dto)
823
{
824
  if(isset($registration_dto->institutionTitleCache)){
825
    $institutionTitleCache = $registration_dto->institutionTitleCache;
826
  } else {
827
    // fall back option to also support cdm entities
828
    $institutionTitleCache = @$registration_dto->institution->titleCache;
829
  }
830
  return $institutionTitleCache ? 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $institutionTitleCache)) : '';
831
}
832

    
833

    
834
/**
835
 * Composes the TypedEntityReference to name type designations passed as associatve array.
836
 *
837
 * @param $$type_entity_refs array
838
 *   an associative array of name type type => TypedEntityReference for name type designations as
839
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
840
 *
841
 * @ingroup compose
842
 */
843
function compose_name_type_designations($type_entity_refs){
844
  $render_array = array();
845
  $preferredStableUri = '';
846
  foreach($type_entity_refs as $type_status => $name_types){
847
    foreach ($name_types as $name_type){
848
      $type_designation = cdm_ws_get(CDM_TYPEDESIGNATION, array($name_type->uuid, 'preferredUri'));
849
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
850
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
851
      }
852
      $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type)  . '"><span class="type_status">'. ucfirst($type_status) . "</span>: "
853
        . $name_type->label
854
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
855
        . '</div>');
856
      }
857
  }
858
  return $render_array;
859
}
860

    
861
/**
862
 * Composes the TypedEntityReference to specimen type designations passed as associatve array.
863
 *
864
 * @param $type_entity_refs array
865
 *   an associative array of specimen type type => TypedEntityReference for specimen type designations as
866
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
867
 *
868
 * @ingroup compose
869
 */
870
function compose_specimen_type_designations($type_entity_refs){
871

    
872
  $render_array = array();
873

    
874
  foreach($type_entity_refs as $type_status => $specimen_types){
875
    foreach($specimen_types as $specimen_type){
876

    
877
      $type_designation = cdm_ws_get(CDM_TYPEDESIGNATION, array($specimen_type->uuid));
878

    
879
      $preferredStableUri = '';
880
      $citation_markup = '';
881
      $media = '';
882

    
883
      // preferredStableUri
884
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
885
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
886
      }
887

    
888
      $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
889
      if($mediaSpecimen){
890
        // compose output
891
        // mediaURI
892
        if(isset($mediaSpecimen->representations[0])) {
893
          $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
894
          $captionElements = array(
895
            '#uri' => t('open media'),
896
            'elements' => array('-none-'),
897
            'sources_as_content' => true
898
          );
899
          $media = compose_cdm_media_gallerie(array(
900
            'mediaList' => array($mediaSpecimen),
901
            'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $specimen_type->uuid,
902
            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
903
            'cols' => $gallery_settings['cdm_dataportal_media_cols'],
904
            'captionElements' => $captionElements,
905
          ));
906
        }
907
        // citation and detail
908
        $annotations_and_sources = handle_annotations_and_sources(
909
            $mediaSpecimen,
910
            array(
911
                'sources_as_content' => true,
912
                'link_to_name_used_in_source' => false,
913
                'link_to_reference' => true,
914
                'add_footnote_keys' => false,
915
                'bibliography_aware' => false),
916
            '',
917
            null
918
        );
919
        if(is_array( $annotations_and_sources['source_references'])){
920
          $citation_markup = join(', ', $annotations_and_sources['source_references']);
921
        }
922
      }
923

    
924
      $render_array[] = markup_to_render_array('<div class="specimen_type_designation ' . html_class_attribute_ref($specimen_type)  . '">
925
          <span class="type_status">' . ucfirst($type_status) . "</span>: "
926
        . $specimen_type->label
927
        . ($citation_markup ? ' '. $citation_markup : '')
928
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
929
        . $media
930
        . '</div>');
931
    }
932
  }
933
  return $render_array;
934
}
935

    
936
/**
937
 * @param $name_rel
938
 * @param $current_name_uuid
939
 * @param $current_taxon_uuid
940
 * @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!
941
 * @param $show_name_cache_only
942
 *    The nameCache will be shown instead of the titleCache if this parameter is true.
943
 * @return null|string
944
 */
945
function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $show_name_cache_only = false){
946

    
947
  $relationship_markup = null;
948

    
949
  $current_name_is_toName = $current_name_uuid == $name_rel->toName->uuid;
950

    
951
  if($current_name_is_toName){
952
    $name = $name_rel->fromName;
953
  } else {
954
    $name = $name_rel->toName;
955
  }
956

    
957
  cdm_load_tagged_full_title($name);
958

    
959
  $highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';
960
  if(!$show_name_cache_only){
961
    $relationship_markup = render_taxon_or_name($name,
962
      url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false))
963
    );
964
  } else {
965
    $relationship_markup = l(
966
      '<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',
967
      path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false),
968
      array('html' => true)
969
    );
970
  }
971

    
972
  return $relationship_markup;
973
}
974

    
975

    
976
/**
977
 * Composes an inline representation of selected name relationships
978
 *
979
 * The output of this function will be usually appended to taxon name representations.
980
 * Only the following types are displayed: LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR, ORTHOGRAPHIC_VARIANT
981
 *
982
 * LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR are displayed as
983
 * non {titleCache} nec {titleCache} nec {titleCache} whereas the related names
984
 * are ordered alphabetically.
985
 *
986
 * ORTHOGRAPHIC_VARIANT is displayed as 'ort. var. {nameCache}'
987
 *
988
 * Related issues:
989
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
990
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
991
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
992
 *   - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"
993
 *
994
 * @param $name_relations
995
 *    The list of CDM NameRelationsips
996
 * @param $current_name_uuid
997
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
998
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
999
 * @param $suppress_if_current_name_is_source
1000
 *    The display of the relation will be
1001
 *    suppressed is the current name is on the source of the relation edge.
1002
 *    That is if it is on the from side of the relation. Except for 'blocking name for' which is
1003
 *    an inverse relation. For this relation type the toName is taken in to account.
1004
 * @param $current_taxon_uuid
1005
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1006
 * @return array
1007
 *    A drupal render array
1008
 *
1009
 * @ingroup Compose
1010
 */
1011
function compose_name_relationships_inline($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
1012

    
1013
  RenderHints::pushToRenderStack('homonym');
1014
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1015

    
1016
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));
1017
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1018
  foreach ($selected_name_rel_uuids as $uuid){
1019
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1020
    if($uuid != UUID_NAMERELATIONSHIPTYPE_MISSPELLING){
1021
      $name_rel_type_filter['inverse'][$uuid] = $uuid;
1022
    }
1023
  }
1024

    
1025
  $list_prefix = '<span class="name_relationships">[';
1026
  $list_suffix = ']</span>';
1027
  $item_prefix = '<span class="item">';
1028
  $item_suffix = '</span> ';
1029
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1030

    
1031
  // remove the glue space from the last item element which has been added by the $item_suffix = '</span> '
1032
  $items_ctn = count($render_array['list']['items']);
1033
  if($items_ctn){
1034
    $render_array['list']['items'][$items_ctn - 1]['#suffix'] = '</span>';
1035
  }
1036

    
1037
  RenderHints::popFromRenderStack();
1038
  return $render_array;
1039
}
1040

    
1041
/**
1042
 * Composes an list representation of the name relationships.
1043
 *
1044
 * The output of this function will be usually appended to taxon name representations.
1045
 *
1046
 * Related issues:
1047
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1048
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1049
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1050
 *
1051
 * @param $name_relations
1052
 *    The list of CDM NameRelationsips
1053
 * @param $current_name_uuid
1054
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1055
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1056
 * @param $current_taxon_uuid
1057
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1058
 * @return array
1059
 *    A drupal render array
1060
 *
1061
 * @ingroup Compose
1062
 */
1063
function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid) {
1064

    
1065
  // $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));
1066

    
1067
  $key = 'name_relationships';
1068
  RenderHints::pushToRenderStack($key);
1069
  if(!RenderHints::getFootnoteListKey()){
1070
    RenderHints::setFootnoteListKey($key);
1071
  }
1072
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1073

    
1074
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, unserialize(CDM_NAME_RELATIONSHIP_LIST_TYPES_DEFAULT));
1075
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1076
  foreach ($selected_name_rel_uuids as $uuid){
1077
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1078
    $name_rel_type_filter['inverse'][$uuid] = $uuid;
1079
  }
1080

    
1081
  $list_prefix = '<div class="relationships_list name_relationships">';
1082
  $list_suffix = '</div>';
1083
  $item_prefix = '<div class="item">';
1084
  $item_suffix = '</div>';
1085

    
1086
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1087

    
1088
  RenderHints::popFromRenderStack();
1089
  $render_array['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));
1090
  if(RenderHints::getFootnoteListKey() == $key) {
1091
    RenderHints::clearFootnoteListKey();
1092
  }
1093
  return $render_array;
1094
}
1095

    
1096
/**
1097
 * @param $name_relations
1098
 * @param $name_rel_type_filter
1099
 *   Associative array with two keys:
1100
 *   - 'direct': the relationship type uuids for the direct direction of the relation edge to be included
1101
 *   - 'inverse': the relationship type uuids for the direct direction of the relation edge to be included
1102
 * @param $current_name_uuid
1103
 * @param $current_taxon_uuid
1104
 * @param $list_prefix
1105
 * @param $list_suffix
1106
 * @param $item_prefix
1107
 * @param $item_suffix
1108
 * @return array
1109
 *
1110
 * @ingroup Compose
1111
 */
1112
function compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid,
1113
                                    $list_prefix, $list_suffix, $item_prefix, $item_suffix)
1114
{
1115
  $non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,
1116
    UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,
1117
    UUID_NAMERELATIONSHIPTYPE_CONSERVED_AGAINST,
1118
    UUID_NAMERELATIONSHIPTYPE_MISSPELLING,
1119
    UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
1120

    
1121
  $render_array = array(
1122
    'list' => array(
1123
      '#prefix' => $list_prefix,
1124
      '#suffix' => $list_suffix,
1125
      'items' => array()
1126
    ),
1127
    'footnotes' => array()
1128
  );
1129

    
1130
  if ($name_relations) {
1131

    
1132
    // remove all relations which are not selected in the settings and
1133
    // separate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs
1134
    // for special handling
1135
    $filtered_name_rels = array();
1136
    $non_nec_name_rels = array();
1137
    $orthographic_variants = array();
1138
    foreach ($name_relations as $name_rel) {
1139
      $rel_type_uuid = $name_rel->type->uuid;
1140
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1141
      if ((!$is_inverse_relation && isset($name_rel_type_filter['direct'][$rel_type_uuid]) && $name_rel_type_filter['direct'][$rel_type_uuid])
1142
        ||($is_inverse_relation && isset($name_rel_type_filter['inverse'][$rel_type_uuid]) && $name_rel_type_filter['inverse'][$rel_type_uuid])) {
1143

    
1144
        if (array_search($rel_type_uuid, $non_nec_name_reltype_uuids) !== false && (
1145
            $current_name_uuid == $name_rel->fromName->uuid && $rel_type_uuid != UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1146
            || $current_name_uuid == $name_rel->toName->uuid && $rel_type_uuid == UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1147
          )
1148
        ){
1149
          $non_nec_name_rels[] = $name_rel;
1150
        } else if (UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $rel_type_uuid) {
1151
          $orthographic_variants[] = $name_rel;
1152
        } else {
1153

    
1154
          $filtered_name_rels[] = $name_rel;
1155
        }
1156
      }
1157
    }
1158
    $name_relations = $filtered_name_rels;
1159

    
1160
    usort($name_relations, 'compare_name_relations_by_term_order_index');
1161

    
1162
    // compose
1163
    foreach ($name_relations as $name_rel) {
1164

    
1165
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1166

    
1167
      $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1168
      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1169

    
1170
      $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1171
      $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1172
      $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
1173
      $relationship_markup = $symbol_markup . $relationship_markup;
1174
      if ($relationship_markup) {
1175
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1176
          null,
1177
          $item_prefix,
1178
          $item_suffix);
1179
      }
1180
    }
1181

    
1182
    // name relationships to be displayed as non nec
1183
    if (count($non_nec_name_rels) > 0) {
1184
      $non_nec_markup = '';
1185
      foreach ($non_nec_name_rels as $name_rel) {
1186
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1187
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1188
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1189
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1190
        $symbol = $non_nec_markup ? ' nec ' : 'non';
1191
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1192
        $non_nec_markup .= $symbol_markup . $relationship_markup;
1193
      }
1194
      if ($non_nec_markup) {
1195
        $render_array['list']['items'][] = markup_to_render_array($non_nec_markup,
1196
          null,
1197
          $item_prefix,
1198
          $item_suffix);
1199
      }
1200
    }
1201

    
1202
    // orthographic variants
1203
    if (count($orthographic_variants) > 0) {
1204
      foreach ($orthographic_variants as $name_rel) {
1205

    
1206
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1207
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1208
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, TRUE);
1209
        $nomref_footnote_key_markup = nomenclatural_reference_footnote_key_markup($name_rel->toName);
1210
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1211
        $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1212
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1213
        $relationship_markup = $symbol_markup . $relationship_markup . $nomref_footnote_key_markup;
1214
      }
1215
      if ($relationship_markup) {
1216
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1217
          null,
1218
          $item_prefix,
1219
          $item_suffix);
1220
      }
1221
    }
1222
  }
1223
  return $render_array;
1224
}
1225

    
1226
/**
1227
 * @param $name_rel
1228
 * @return string
1229
 */
1230
function name_relationship_footnote_markup($name_rel)
1231
{
1232
  $footnote_markup = '';
1233
  $footnote_key_markup = '';
1234
  if (isset($name_rel->ruleConsidered) && $name_rel->ruleConsidered) {
1235
    $footnote_markup = '<span class="rule_considered">' . $name_rel->ruleConsidered . '</span> ';
1236
  }
1237
  if (isset($name_rel->citation)) {
1238
    $footnote_markup .= '<span class="reference">' . $name_rel->citation->titleCache . '</span>';
1239
  }
1240
  if (isset($name_rel->citationMicroReference) && $name_rel->citationMicroReference) {
1241
    $footnote_markup .= (isset($name_rel->citation) ? ':' : '') . '<span class="reference_detail">' . $name_rel->citationMicroReference . '</span>';
1242
  }
1243
  if ($footnote_markup) {
1244
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1245
    $footnote_key_markup = theme('cdm_footnote_key', array(
1246
      'footnoteKey' => $fnkey,
1247
      'separator' => ',',
1248
      'highlightable' => TRUE,
1249
      'separator_off' => TRUE,
1250
    ));
1251
  }
1252
  return $footnote_key_markup;
1253
}
1254

    
1255
/**
1256
 * @param $nom_status
1257
 * @return string
1258
 */
1259
function nomenclatural_status_footnote_markup($nom_status)
1260
{
1261
  // NomenclaturalStatus is a subclass of ReferencedEntityBase
1262
  // and has the same structure as TaxonNameRelationship
1263
  return name_relationship_footnote_markup($nom_status);
1264
}
1265

    
1266
/**
1267
 * @param $name
1268
 * @return string
1269
 */
1270
function nomenclatural_reference_footnote_key_markup($name)
1271
{
1272
  $footnote_markup = '';
1273
  $footnote_key_markup = '';
1274
  if (isset($name->nomenclaturalReference) && $name->nomenclaturalReference) {
1275
    $footnote_markup .= '<span class="reference">' . $name->nomenclaturalReference->titleCache . '</span>';
1276
  }
1277
  if (isset($name->nomenclaturalMicroReference)) {
1278
    $footnote_markup .= ($footnote_key_markup ? ':' : '') . '<span class="reference_detail">' . $name->nomenclaturalMicroReference . '</span>';
1279
  }
1280
  if ($footnote_markup) {
1281
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1282
    $footnote_key_markup = theme('cdm_footnote_key', array(
1283
      'footnoteKey' => $fnkey,
1284
      'separator' => ',',
1285
      'highlightable' => TRUE,
1286
      'separator_off' => TRUE,
1287
    ));
1288
  }
1289
  return $footnote_key_markup;
1290
}
1291

    
1292

    
1293
/**
1294
 * @param $taxon
1295
 * @return array
1296
 */
1297
function cdm_name_relationships_for_taxon($taxon)
1298
{
1299
  $from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
1300
  $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
1301
  $name_relations = array_merge($from_name_relations, $to_name_relations);
1302
  return $name_relations;
1303
}
1304

    
1305

    
1306
/**
1307
 * Recursively searches the array for the $key and sets the given value.
1308
 *
1309
 * @param mixed $key
1310
 *   Key to search for.
1311
 * @param mixed $value
1312
 *   Value to set.'
1313
 * @param array $array
1314
 *   Array to search in.
1315
 *
1316
 * @return bool
1317
 *   True if the key has been found.
1318
 */
1319
function &array_setr($key, $value, array &$array) {
1320
  $res = NULL;
1321
  foreach ($array as $k => &$v) {
1322
    if ($key == $k) {
1323
      $v = $value;
1324
      return $array;
1325
    }
1326
    elseif (is_array($v)) {
1327
      $innerArray = array_setr($key, $value, $v);
1328
      if ($innerArray) {
1329
        return $array;
1330
      }
1331
    }
1332
  }
1333
  return $res;
1334
}
1335

    
1336
/**
1337
 * @todo Please document this function.
1338
 * @see http://drupal.org/node/1354
1339
 */
1340
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
1341
  $res = NULL;
1342
  $precedingElement = NULL;
1343
  foreach ($renderTemplate as &$part) {
1344
    foreach ($part as $key => &$element) {
1345
      if ($key == $contentElementKey) {
1346
        return $precedingElement;
1347
      }
1348
      $precedingElement = $element;
1349
    }
1350
  }
1351
  return $res;
1352
}
1353

    
1354
/**
1355
 * @todo Please document this function.
1356
 * @see http://drupal.org/node/1354
1357
 */
1358
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
1359
  $res = NULL;
1360
  $precedingKey = NULL;
1361
  foreach ($renderTemplate as &$part) {
1362
    if (is_array($part)) {
1363
      foreach ($part as $key => &$element) {
1364
        if ($key == $contentElementKey) {
1365
          return $precedingKey;
1366
        }
1367
        if (!str_beginsWith($key, '#')) {
1368
          $precedingKey = $key;
1369
        }
1370
      }
1371
    }
1372
  }
1373
  return $res;
1374
}
1375

    
1376
function nameTypeToDTYPE($dtype){
1377
  static $nameTypeLabelMap = array(
1378
    "ICNB" => "BacterialName",
1379
    "ICNAFP" => "BotanicalName",
1380
    "ICNCP" => "CultivarPlantName",
1381
    "ICZN" => "ZoologicalName",
1382
    "ICVCN" => "ViralName",
1383
    "Any taxon name" => "TaxonName",
1384
    "NonViral" => "TaxonName",
1385
    "Fungus" => "BotanicalName",
1386
    "Plant" => "BotanicalName",
1387
    "Algae" => "BotanicalName",
1388
  );
1389
  return $nameTypeLabelMap[$dtype];
1390

    
1391
}
1392

    
1393

    
1394
function compare_name_relations_by_term_order_index($name_rel1, $name_rel2){
1395
  return compare_terms_by_order_index($name_rel1->type, $name_rel2->type);
1396
}
1397

    
1398
/**
1399
 * Provides an array with the different registration types covered by the passed registration.
1400
 *
1401
 * The labels in the returned array are translatable.
1402
 *
1403
 * See also https://dev.e-taxonomy.eu/redmine/issues/8016
1404
 *
1405
 * @param $registration_dto
1406
 * @return array
1407
 *    An array of the labels describing the different registration types covered by the passed registration.
1408
 */
1409
function registration_types($registration_dto){
1410
  $reg_type_labels = array();
1411
  if(isset($registration_dto->nameRef)){
1412
    $reg_type_labels[] = t("new name");
1413
    $reg_type_labels[] = t("new taxon");
1414
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
1415
    foreach($name_relations as $name_rel){
1416
      if(isset($name_rel->type->uuid)){
1417
        $name_is_from_name = $registration_dto->nameRef->uuid == $name_rel->fromName->uuid;
1418
        switch($name_rel->type->uuid) {
1419
          case UUID_NAMERELATIONSHIPTYPE_BASIONYM:
1420
            if(!$name_is_from_name){
1421
              $reg_type_labels[] = t("new combination");
1422
            }
1423
            break;
1424
          case UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM:
1425
            if(!$name_is_from_name) {
1426
              $reg_type_labels[] = t("new name");
1427
            }
1428
            break;
1429
          case UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME:
1430
            if(!$name_is_from_name) {
1431
              $reg_type_labels[] = t("validation");
1432
            }
1433
            break;
1434
          case UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT:
1435
            if(!$name_is_from_name) {
1436
              $reg_type_labels[] = t("orthographical correction");
1437
            }break;
1438
          default:
1439
            // NOTHING
1440
        }
1441
      }
1442
    }
1443
  }
1444
  if(isset($registration_dto->orderdTypeDesignationWorkingSets)){
1445
    $reg_type_labels[] = t("new nomeclatural type");
1446
  }
1447
  return $reg_type_labels;
1448
}
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