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cdm-dataportal / modules / cdm_dataportal / includes / name.inc @ e95b14dd

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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
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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 or URL to be used for name parts if a link is forseen in the template
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 *   matching the given $renderPath.
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 * @param string $referenceLink
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 *   The link path ot URL to be used for nomenclatural reference parts if a link is forseen
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 *   in the template matching the given $renderPath.
70
 * @return array
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 *   An associative array, the render template
72
 */
73
function get_nameRenderTemplate($render_path, $nameLink = NULL, $referenceLink = NULL) {
74

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

    
78

    
79
  if (!isset($default_render_templates)) {
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    $default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);
81
  }
82
  if($split_render_templates == NULL) {
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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
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) {
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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];
111
  }
112

    
113
  // 2. Find best matching default RenderTemplate
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  // by stripping the dot separated render path element by element
115
  // if no matching template is found the DEFAULT will be used.
116
  while (!is_array($template) && strlen($render_path) > 0) {
117
    foreach ($split_render_templates as $path => $t) {
118
      if ($path == $render_path) {
119
        $template = $t;
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        break;
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 $name_link
257
 *    URI to the taxon, @see path_to_taxon(), must be processed by url() before passing to this method
258
 * @param $reference_link
259
 *    URI to the reference, @see path_to_reference(), must be processed by url() before passing to this method
260
 * @param $show_annotations
261
 *    turns the display of annotations on
262
 * @param $is_type_designation
263
 *    To indicate that the supplied taxon name is a name type designation.
264
 * @param $skiptags
265
 *    an array of name elements tags like 'name', 'rank' to skip. The name part
266
 *          'authors' will not ber affected by this filter. This part is managed though the render template
267
 *          mechanism.
268
 * @param $is_invalid
269
 *   Indicates that this taxon is invalid. In this case the name part will be shown in double quotes.
270
 *   This is useful when rendering taxon relation ships.
271
 *
272
 * @return string
273
 *  The markup for a taxon name.
274
 *
275
 */
276
function render_taxon_or_name($taxon_name_or_taxon_base, $name_link = NULL, $reference_link = NULL,
277
  $show_annotations = true, $is_type_designation = false, $skiptags = array(), $is_invalid = false) {
278

    
279
  $is_doubtful = false;
280

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

    
300

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

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

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

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

    
321
  normalize_tagged_text($tagged_title);
322

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

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

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

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

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

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

    
356

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

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

    
387

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

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

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

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

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

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

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

    
439

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

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

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

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

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

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

    
526
          }
527
        }
528
      }
529
    }
530
    array_setr('description', $descriptionHtml, $renderTemplate);
531
  }
532

    
533
  // Render.
534
  $out = '';
535
  if(isset($_REQUEST['RENDER_PATH'])){
536
    // developer option to show the render path with each taxon name
537
    $out .= '<span class="render-path">' . RenderHints::getRenderPath() . '</span>';
538
  }
539
  $out .= '<span class="' . html_class_attribute_ref($taxon_name_or_taxon_base)
540
    . '" data-cdm-ref="/name/' . $taxonName->uuid . '" data-cdm-render-path="' . RenderHints::getRenderPath() .'">';
541

    
542
  foreach ($renderTemplate as $partName => $part) {
543
    $separator = '';
544
    $partHtml = '';
545
    $uri = FALSE;
546
    if (!is_array($part)) {
547
      continue;
548
    }
549
    if (isset($part['#uri']) && is_string($part['#uri'])) {
550
      $uri = $part['#uri'];
551
      unset($part['#uri']);
552
    }
553
    foreach ($part as $key => $content) {
554
      $html = '';
555
      if (is_array($content)) {
556
        $html = $content['#html'];
557
        if(isset($content['#separator'])) {
558
          $separator = $content['#separator'];
559
        }
560
      }
561
      elseif (is_string($content)) {
562
        $html = $content;
563
      }
564
      $partHtml .= '<span class="' . $key . '">' . $html . '</span>';
565
    }
566
    if ($uri) {
567
      // cannot use l() here since the #uri aleady should have been processed through uri() at this point
568
      $out .= $separator . '<a href="' . $uri . '" class="' . $partName . '">' . $partHtml . '</a>';
569

    
570
    }
571
    else {
572
      $out .= $separator . $partHtml;
573
    }
574
  }
575
  $out .= '</span>';
576
  if ($show_annotations) {
577
    // $out .= theme('cdm_annotations_as_footnotekeys', $taxonName);
578
  }
579
  return $out;
580
}
581

    
582

    
583

    
584
/**
585
 * Composes information for a registration from a dto object.
586
 *
587
 * Registrations which are not yet published are suppressed.
588
 *
589
 * @param $registration_dto
590
 * @param $with_citation
591
 *   Whether to show the citation.
592
 *
593
 * @return array
594
 *    A drupal render array with the elements:
595
 *    - 'name'
596
 *    - 'name-relations'
597
 *    - 'specimen_type_designations'
598
 *    - 'name_type_designations'
599
 *    - 'citation'
600
 *    - 'registration_date_and_institute'
601
 * @ingroup compose
602
 */
603
function compose_registration_dto_full($registration_dto, $with_citation = true)
604
{
605
  $render_array = array(
606
    '#prefix' => '<div class="registration">',
607
    '#suffix' => '</div>'
608
  );
609

    
610
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
611
    return $render_array;
612
  }
613

    
614
  $render_array['sub_headline'] = markup_to_render_array(join(", ", registration_types($registration_dto)),-10, '<h3 class="registration_type">' . t('Event: '), '</h3>' );
615
  $render_array['nomenclatural_act'] = array(
616
    '#weight' => 0,
617
    '#prefix' => '<div class="nomenclatural_act">',
618

    
619
    '#suffix' => '</div>'
620
  );
621

    
622
  // name
623
  if($registration_dto->nameRef){
624
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
625
    cdm_load_tagged_full_title($name);
626
    $render_array['nomenclatural_act']['published_name'] = markup_to_render_array('<div class="published-name">' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</div>', 0);
627
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
628
    $render_array['nomenclatural_act']['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null);
629
    $render_array['nomenclatural_act']['name_relations']['#weight'] = 10;
630
  } else {
631
    // in this case the registration must have a
632
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->typifiedNameRef->uuid);
633
    $render_array['typified_name'] = markup_to_render_array('<p class="typified-name">for ' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</p>', 40);
634
  }
635
  // typedesignation in detail
636
  if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
637
    $field_unit_uuids = array();
638
    $specimen_type_designation_refs = array();
639
    $name_type_designation_refs = array();
640
    foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {
641
      $tokens = explode("#", $workingset_ref);
642
      $types_in_fieldunit = get_object_vars($obj); // convert into associative array
643

    
644
      if ($tokens[0] == 'NameTypeDesignation') {
645
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
646
          if(!isset($name_type_designation_refs[$type_status])){
647
            $name_type_designation_refs[$type_status]  = $entity_reference_list;
648
          } else {
649
            array_push($name_type_designation_refs[$type_status] ,$entity_reference_list);
650
          }
651
        }
652
      } else if ($tokens[0] == 'FieldUnit'){
653
        $field_unit_uuids[] = $tokens[1];
654
        foreach ($types_in_fieldunit as $type_status => $entity_reference_list) {
655
          if(!isset($specimen_type_designation_refs[$type_status])){
656
            $specimen_type_designation_refs[$type_status] =  $entity_reference_list;
657
          } else {
658
            array_push($specimen_type_designation_refs[$type_status], $entity_reference_list);
659
          }
660
        }
661
      } else {
662
        drupal_set_message("Unimplemented type: " . $tokens[0], 'error');
663
      }
664
    }
665
    // type designations wich are in this nomenclatural act.
666
    if (count($name_type_designation_refs) > 0) {
667
      $render_array['nomenclatural_act']['name_type_designations'] = compose_name_type_designations($name_type_designation_refs);
668
      $render_array['nomenclatural_act']['name_type_designations']['#prefix'] = '<p class="name_type_designations">';
669
      $render_array['nomenclatural_act']['name_type_designations']['#suffix'] = '</p>';
670
      $render_array['nomenclatural_act']['name_type_designations']['#weight'] = 20;
671
    }
672
    if (count($field_unit_uuids) > 0) {
673
      $specimen_type_designations_array = compose_specimen_type_designations($specimen_type_designation_refs, true);
674
      $render_array['nomenclatural_act']['specimen_type_designations'] = $specimen_type_designations_array['type_designations'];
675
      $render_array['map'] = $specimen_type_designations_array['map'];
676
      $render_array['map']['#weight'] = $render_array['nomenclatural_act']['#weight'] + 20;
677
    }
678
  }
679

    
680
  // citation
681
  if ($with_citation) {
682
    $render_array['citation'] = markup_to_render_array(
683
      "<div class=\"citation nomenclatural_act_citation" . html_class_attribute_ref(new TypedEntityReference("Reference", $registration_dto->citationUuid)) . "\">"
684
      . "<span class=\"label\">published in: </span>"
685
      . $registration_dto->bibliographicInRefCitationString
686
      . l(custom_icon_font_markup('icon-interal-link-alt-solid', array('class' => array('superscript'))), path_to_reference($registration_dto->citationUuid), array('html' => true))
687
      . "</div>",
688
      $render_array['nomenclatural_act']['#weight'] + 10 );
689
  }
690

    
691
  // registration date and office
692
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto);
693
  if($registration_date_insitute_markup){
694
    $render_array['registration_date_and_institute'] = markup_to_render_array(
695
      $registration_date_insitute_markup . '</p>',
696
      100);
697
  }
698

    
699
  return $render_array;
700
}
701

    
702

    
703
/**
704
 * Composes a compact representation for a registrationDTO object
705
 *
706
 * Registrations which are not yet published are suppressed.
707
 *
708
 * @param $registration_dto
709
 * @param $style string
710
 *   The style of how to compose the 'identifier' and 'registration_date_and_institute' part with the summary
711
 *   - 'citation': Similar to the arrearance of nomenclatural acts in print media
712
 *   - 'list-item' : style suitable for result lists etc
713
 *
714
 * @return array
715
 *    A drupal render array with the elements:
716
 *    - 'registration-metadata' when $style == 'list-item'
717
 *    - 'summary'
718
 * @ingroup compose
719
 */
720
function compose_registration_dto_compact($registration_dto, $style = 'citation', $tag_enclosing_summary = 'p')
721
{
722
  $render_array = array();
723
  $media_link_map = array();
724

    
725
  if(!(isset($registration_dto->identifier) && $registration_dto->status == 'PUBLISHED')){
726
    return $render_array;
727
  }
728

    
729
  $registration_date_insitute_markup = render_registration_date_and_institute($registration_dto, 'span');
730
  $itentifier_markup = l($registration_dto->identifier, path_to_registration($registration_dto->identifier), array('attributes' => array('class' => array('identifier'))));
731

    
732
  $tagged_text_options = array();
733
  if(isset($registration_dto->nameRef)){
734
    $tagged_text_options[] = array(
735
      'filter-type' => 'name',
736
      'prefix' => '<span class="registered_name">',
737
      'suffix' => '</span>',
738
    );
739
  } else {
740
    $tagged_text_options[] = array(
741
      'filter-type' => 'name',
742
      'prefix' => '<span class="referenced_typified_name">',
743
      'suffix' => '</span>',
744
    );
745
  }
746
  cdm_tagged_text_add_options($registration_dto->summaryTaggedText, $tagged_text_options);
747
  $taggged_text_expanded = cdm_tagged_text_expand_entity_references($registration_dto->summaryTaggedText);
748
  foreach ($taggged_text_expanded  as $tagged_text){
749
    if(isset($tagged_text->entityReference->type) && $tagged_text->entityReference->type == 'SpecimenTypeDesignation') {
750
      $mediaDTOs = cdm_ws_get('typedesignation/$0/media', array($tagged_text->entityReference->uuid));
751
      if(isset($mediaDTOs[0]->uri)){
752
        $media_url_key = '{link-' . $mediaDTOs[0]->uuid . '}';
753
        $tagged_text->text = str_replace('[icon]', '[icon]' . $media_url_key, $tagged_text->text);
754
        $media_link_map[$media_url_key] =  cdm_external_uri($mediaDTOs[0]->uri, true);
755
      }
756
    }
757
  }
758
  $registation_markup = cdm_tagged_text_to_markup($taggged_text_expanded);
759
  foreach($media_link_map as $media_url_key => $link){
760
    $registation_markup = str_replace($media_url_key, $link, $registation_markup);
761
  }
762
  if($style == 'citation') {
763
    $registation_markup = $registation_markup . ' ' . $itentifier_markup . ' ' . $registration_date_insitute_markup;
764
  } else {
765
    $render_array['registration-metadata'] = markup_to_render_array('<div class="registration-metadata">' . $itentifier_markup . ' ' . $registration_date_insitute_markup. "</div>", -10);
766
  }
767
  $render_array['summary'] = markup_to_render_array('<' . $tag_enclosing_summary . ' class="registration-summary">' . $registation_markup . '</' . $tag_enclosing_summary . '>', 0);
768

    
769
  return $render_array;
770
}
771

    
772

    
773
/**
774
 * Renders the registrationDate and institutionTitleCache of the $registration_dto as markup.
775
 *
776
 * @param $registration_dto
777
 * @return string
778
 *    The markup or an empty string
779
 */
780
function render_registration_date_and_institute($registration_dto, $enclosing_tag = 'p') {
781
  $registration_date_institute_markup = '';
782
  if ($registration_dto->registrationDate) {
783
    $date_string = format_datetime($registration_dto->registrationDate);
784
    if (isset($registration_dto->institutionTitleCache) && $registration_dto->institutionTitleCache) {
785
      $registration_date_institute_markup =
786
        t("Registration on @date in @institution", array(
787
          '@date' => $date_string,
788
          '@institution' => $registration_dto->institutionTitleCache,
789
        ));
790
    } else {
791
      $registration_date_institute_markup =
792
        t("Registration on @date", array(
793
          '@date' => $date_string
794
        ));
795
    }
796
    $registration_date_institute_markup = '<' .$enclosing_tag . ' class="registration-date-and-institute">'. $registration_date_institute_markup . '</' .$enclosing_tag . '>';
797
  }
798
  return $registration_date_institute_markup;
799
}
800

    
801

    
802
/**
803
 * @param $registrations
804
 * @return string
805
 */
806
function render_registrations($registrations)
807
{
808
  $registration_markup = '';
809
  $registration_markup_array = array();
810
  if ($registrations) {
811
    foreach ($registrations as $reg) {
812
      $registration_markup_array[] = render_registration($reg);
813
    }
814
    $registration_markup = " Registration" . (count($registration_markup_array) > 1 ? 's: ' : ': ')
815
      . join(', ', $registration_markup_array);
816
  }
817
  return $registration_markup;
818
}
819

    
820

    
821
/**
822
 * Renders a registration
823
 *
824
 * TODO replace by compose_registration_dto_compact
825
 * @param $registration
826
 */
827
function render_registration($registration){
828
  $markup = '';
829

    
830
  if(isset($registration->identifier) && $registration->status == 'PUBLISHED'){
831
    $office_class_attribute = '';
832
    if(isset($registration->institution->titleCache)){
833
      $office_class_attribute = registration_intitute_class_attribute($registration);
834
    }
835
    $markup = "<span class=\"registration $office_class_attribute\">" . l($registration->identifier, path_to_registration($registration->identifier)) . ', '
836
      .  preg_replace('/^([^T]*)(.*)$/', '${1}', $registration->registrationDate)
837
      . '</span>';
838
  }
839
  return $markup;
840
}
841

    
842
/**
843
 * @param $registration
844
 * @return string
845
 */
846
function registration_intitute_class_attribute($registration_dto)
847
{
848
  if(isset($registration_dto->institutionTitleCache)){
849
    $institutionTitleCache = $registration_dto->institutionTitleCache;
850
  } else {
851
    // fall back option to also support cdm entities
852
    $institutionTitleCache = @$registration_dto->institution->titleCache;
853
  }
854
  return $institutionTitleCache ? 'registration-' . strtolower(preg_replace('/[^a-zA-Z0-9]/', '-', $institutionTitleCache)) : '';
855
}
856

    
857

    
858
/**
859
 * Composes the textual representation for the type designation of taxon name identified by the uuid in with a map for the location data.
860
 *
861
 * @param $taxon_name_uuid
862
 * @param $show_specimen_details
863
 * @return array
864
 *    A drupal render array with the following elements:
865
 *    - 'type_designations'
866
 *    - 'map'
867
 *    - 'specimens'
868
 *
869
 * @ingroup compose
870
 */
871
function compose_type_designations($taxon_name_uuid, $show_specimen_details = false)
872
{
873
  $render_array = array(
874
    'type_designations' => array(),
875
    'map' => array(),
876
    );
877
  $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $taxon_name_uuid);
878
  if ($type_designations) {
879
    usort($type_designations, 'compare_specimen_type_designation');
880
    $render_array['type_designations'] = markup_to_render_array(
881
      theme('cdm_typedesignations', array('typeDesignations' => $type_designations, 'enclosing_tag' => 'div', 'element_tag' => 'div'))
882
    );
883

    
884
    $render_array['map'] = compose_type_designations_map($type_designations);
885
  }
886
  return $render_array;
887
}
888

    
889
/**
890
 * Composes a map with the location points of the passed $type_designations.
891
 *
892
 * @param $type_designations
893
 *
894
 * @return array
895
 *     A drupal render array or an empty array in case there are no point to show.
896
 *
897
 * @ingroup compose
898
 */
899
function compose_type_designations_map($type_designations)
900
{
901
  $points = array();
902
  $map_render_array = array();
903
  foreach ($type_designations as $td) {
904
    if ($td->class == "SpecimenTypeDesignation") {
905
      $derived_unit_facade = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, array($td->typeSpecimen->uuid));
906
      if (isset($derived_unit_facade->exactLocation)) {
907
        $points[] = $derived_unit_facade->exactLocation->latitude . ',' . $derived_unit_facade->exactLocation->longitude;
908
      }
909
    }
910
  }
911

    
912
  if (count($points) > 0) {
913
    // os=1:c/ff0000/10/noLabel&od=1:52.52079,13.57781|-43.46333333333333,172.60355&legend=0
914
    $occurrence_query = 'os=1:c/ff0000/10/noLabel&od=1:' . join('|', $points) . '&legend=0';
915
    // $occurrence_query = 'os=1:c/ff0000/10/noLabel&od=1:52.52079,13.57781|-43.46333333333333,172.60355&legend=0';
916
    $legend_format_query = null;
917
    $distribution_query = NULL;
918
    $map_render_array = compose_map('specimens', $occurrence_query, $distribution_query, $legend_format_query, array());
919
  }
920
  return $map_render_array;
921
}
922

    
923
/**
924
 * Composes the TypedEntityReference to name type designations passed as associatve array.
925
 *
926
 * @param $$type_entity_refs array
927
 *   an associative array of name type type => TypedEntityReference for name type designations as
928
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
929
 *
930
 * @ingroup compose
931
 */
932
function compose_name_type_designations($type_entity_refs){
933
  $render_array = array();
934
  $preferredStableUri = '';
935
  foreach($type_entity_refs as $type_status => $name_types){
936
    foreach ($name_types as $name_type){
937
      $type_designation = cdm_ws_get(CDM_WS_TYPEDESIGNATION, array($name_type->uuid, 'preferredUri'));
938
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
939
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
940
      }
941
      $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type)  . '"><span class="type-status">'. ucfirst($type_status) . "</span>: "
942
        . $name_type->label
943
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
944
        . '</div>');
945
      }
946
  }
947
  return $render_array;
948
}
949

    
950
/**
951
 * Composes the specimen type designations with map from the the $type_entity_refs
952
 *
953
 * @param $type_entity_refs array
954
 *   an associative array of specimen type type => TypedEntityReference for specimen type designations as
955
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
956
 *
957
 * @param $show_media_specimen
958
 * @return array
959
 *    A drupal render array with the following elements:
960
 *    - 'type_designations'
961
 *    - 'map'
962
 *
963
 * @ingroup compose
964
 *
965
 */
966
function compose_specimen_type_designations($type_entity_refs, $show_media_specimen){
967

    
968
  $render_array = array();
969

    
970
  $type_designation_list = array();
971
  uksort($type_entity_refs, "compare_type_designation_status_labels");
972
  foreach($type_entity_refs as $type_status => $specimen_types){
973
    foreach($specimen_types as $specimen_type){
974

    
975
      $type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($specimen_type->uuid));
976
      $type_designation_list[] = $type_designation; // collect for the map
977

    
978
      $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
979
      // the media specimen is not contained in the $type_designation returned by CDM_PORTAL_TYPEDESIGNATION, so we need to fetch it separately
980
      $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
981

    
982

    
983
      $preferredStableUri = '';
984
      $citation_markup = '';
985
      $media = '';
986

    
987
      // preferredStableUri
988
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
989
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
990
      }
991

    
992
      if($show_media_specimen && $mediaSpecimen){
993
        // compose output
994
        // mediaURI
995
        if(isset($mediaSpecimen->representations[0])) {
996
          $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
997
          $captionElements = array(
998
            '#uri' => t('open media'),
999
            'elements' => array('-none-'),
1000
            'sources_as_content' => true
1001
          );
1002
          $media = compose_cdm_media_gallerie(array(
1003
            'mediaList' => array($mediaSpecimen),
1004
            'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $specimen_type->uuid,
1005
            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
1006
            'cols' => $gallery_settings['cdm_dataportal_media_cols'],
1007
            'captionElements' => $captionElements,
1008
          ));
1009
        }
1010
        // citation and detail
1011
        $annotations_and_sources = handle_annotations_and_sources(
1012
            $mediaSpecimen,
1013
            array(
1014
                'sources_as_content' => true,
1015
                'link_to_name_used_in_source' => false,
1016
                'link_to_reference' => true,
1017
                'add_footnote_keys' => false,
1018
                'bibliography_aware' => false),
1019
            '',
1020
            null
1021
        );
1022
        if(is_array( $annotations_and_sources['source_references'])){
1023
          $citation_markup = join(', ', $annotations_and_sources['source_references']);
1024
        }
1025
      }
1026

    
1027
      $specimen_markup = $derivedUnitFacadeInstance->titleCache;
1028
      if(isset($derivedUnitFacadeInstance->specimenLabel) && $derivedUnitFacadeInstance->specimenLabel){
1029
        $specimen_markup = str_replace($derivedUnitFacadeInstance->specimenLabel, l($derivedUnitFacadeInstance->specimenLabel, path_to_specimen($type_designation->typeSpecimen->uuid)), $specimen_markup);
1030
      }
1031

    
1032
      $type_designation_render_array = markup_to_render_array('<div class="specimen_type_designation ' . html_class_attribute_ref($specimen_type)  . '">
1033
          <span class="type-status">' . ucfirst($type_status) . "</span>: "
1034
        . $specimen_markup
1035
        . ($citation_markup ? ' '. $citation_markup : '')
1036
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
1037
        . $media
1038
        . '</div>');
1039

    
1040
      $render_array['type_designations'][] = $type_designation_render_array;
1041
    }
1042
  }
1043
  if(count($type_designation_list) > 0 ){
1044
    $render_array['map'] = compose_type_designations_map($type_designation_list);
1045
  } else {
1046
    $render_array['map'] = array();
1047
  }
1048
  return $render_array;
1049
}
1050

    
1051
/**
1052
 * @param $name_rel
1053
 * @param $current_name_uuid
1054
 * @param $current_taxon_uuid
1055
 * @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!
1056
 * @param $show_name_cache_only
1057
 *    The nameCache will be shown instead of the titleCache if this parameter is true.
1058
 * @return null|string
1059
 */
1060
function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $show_name_cache_only = false){
1061

    
1062
  $relationship_markup = null;
1063

    
1064
  $current_name_is_toName = $current_name_uuid == $name_rel->toName->uuid;
1065

    
1066
  if($current_name_is_toName){
1067
    $name = $name_rel->fromName;
1068
  } else {
1069
    $name = $name_rel->toName;
1070
  }
1071

    
1072
  cdm_load_tagged_full_title($name);
1073

    
1074
  $highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';
1075
  if(!$show_name_cache_only){
1076
    $relationship_markup = render_taxon_or_name($name,
1077
      url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false))
1078
    );
1079
  } else {
1080
    $relationship_markup = l(
1081
      '<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',
1082
      path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false),
1083
      array('html' => true)
1084
    );
1085
  }
1086

    
1087
  return $relationship_markup;
1088
}
1089

    
1090

    
1091
/**
1092
 * Composes an inline representation of selected name relationships
1093
 *
1094
 * The output of this function will be usually appended to taxon name representations.
1095
 * Only the following types are displayed: LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR, ORTHOGRAPHIC_VARIANT
1096
 *
1097
 * LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR are displayed as
1098
 * non {titleCache} nec {titleCache} nec {titleCache} whereas the related names
1099
 * are ordered alphabetically.
1100
 *
1101
 * ORTHOGRAPHIC_VARIANT is displayed as 'ort. var. {nameCache}'
1102
 *
1103
 * Related issues:
1104
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1105
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1106
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1107
 *   - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"
1108
 *
1109
 * @param $name_relations
1110
 *    The list of CDM NameRelationsips
1111
 * @param $current_name_uuid
1112
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1113
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1114
 * @param $suppress_if_current_name_is_source
1115
 *    The display of the relation will be
1116
 *    suppressed is the current name is on the source of the relation edge.
1117
 *    That is if it is on the from side of the relation. Except for 'blocking name for' which is
1118
 *    an inverse relation. For this relation type the toName is taken in to account.
1119
 * @param $current_taxon_uuid
1120
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1121
 * @return array
1122
 *    A drupal render array
1123
 *
1124
 * @ingroup Compose
1125
 */
1126
function compose_name_relationships_inline($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
1127

    
1128
  RenderHints::pushToRenderStack('homonym');
1129
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1130

    
1131
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));
1132
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1133
  foreach ($selected_name_rel_uuids as $uuid){
1134
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1135
    if($uuid != UUID_NAMERELATIONSHIPTYPE_MISSPELLING){
1136
      $name_rel_type_filter['inverse'][$uuid] = $uuid;
1137
    }
1138
  }
1139

    
1140
  $list_prefix = '<span class="name_relationships">[';
1141
  $list_suffix = ']</span>';
1142
  $item_prefix = '<span class="item">';
1143
  $item_suffix = '</span> ';
1144
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1145

    
1146
  // remove the glue space from the last item element which has been added by the $item_suffix = '</span> '
1147
  $items_ctn = count($render_array['list']['items']);
1148
  if($items_ctn){
1149
    $render_array['list']['items'][$items_ctn - 1]['#suffix'] = '</span>';
1150
  }
1151

    
1152
  RenderHints::popFromRenderStack();
1153
  return $render_array;
1154
}
1155

    
1156
/**
1157
 * Composes an list representation of the name relationships.
1158
 *
1159
 * The output of this function will be usually appended to taxon name representations.
1160
 *
1161
 * Related issues:
1162
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1163
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1164
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1165
 *
1166
 * @param $name_relations
1167
 *    The list of CDM NameRelationsips
1168
 * @param $current_name_uuid
1169
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1170
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1171
 * @param $current_taxon_uuid
1172
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1173
 * @return array
1174
 *    A drupal render array
1175
 *
1176
 * @ingroup Compose
1177
 */
1178
function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid) {
1179

    
1180
  // $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));
1181

    
1182
  $key = 'name_relationships';
1183
  RenderHints::pushToRenderStack($key);
1184
  if(!RenderHints::getFootnoteListKey()){
1185
    RenderHints::setFootnoteListKey($key);
1186
  }
1187
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1188

    
1189
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, cdm_vocabulary_as_defaults(UUID_NAME_RELATIONSHIP_TYPE));
1190
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1191
  foreach ($selected_name_rel_uuids as $uuid){
1192
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1193
    $name_rel_type_filter['inverse'][$uuid] = $uuid;
1194
  }
1195

    
1196
  $list_prefix = '<div class="relationships_list name_relationships">';
1197
  $list_suffix = '</div>';
1198
  $item_prefix = '<div class="item">';
1199
  $item_suffix = '</div>';
1200

    
1201
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1202

    
1203
  RenderHints::popFromRenderStack();
1204
  $render_array['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));
1205
  if(RenderHints::getFootnoteListKey() == $key) {
1206
    RenderHints::clearFootnoteListKey();
1207
  }
1208
  return $render_array;
1209
}
1210

    
1211
/**
1212
 * @param $name_relations
1213
 * @param $name_rel_type_filter
1214
 *   Associative array with two keys:
1215
 *   - 'direct': the relationship type uuids for the direct direction of the relation edge to be included
1216
 *   - 'inverse': the relationship type uuids for the direct direction of the relation edge to be included
1217
 * @param $current_name_uuid
1218
 * @param $current_taxon_uuid
1219
 * @param $list_prefix
1220
 * @param $list_suffix
1221
 * @param $item_prefix
1222
 * @param $item_suffix
1223
 * @return array
1224
 *
1225
 * @ingroup Compose
1226
 */
1227
function compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid,
1228
                                    $list_prefix, $list_suffix, $item_prefix, $item_suffix)
1229
{
1230
  $non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,
1231
    UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,
1232
    UUID_NAMERELATIONSHIPTYPE_CONSERVED_AGAINST,
1233
    UUID_NAMERELATIONSHIPTYPE_MISSPELLING,
1234
    UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
1235

    
1236
  $render_array = array(
1237
    'list' => array(
1238
      '#prefix' => $list_prefix,
1239
      '#suffix' => $list_suffix,
1240
      'items' => array()
1241
    ),
1242
    'footnotes' => array()
1243
  );
1244

    
1245
  if ($name_relations) {
1246

    
1247
    // remove all relations which are not selected in the settings and
1248
    // separate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs
1249
    // for special handling
1250
    $filtered_name_rels = array();
1251
    $non_nec_name_rels = array();
1252
    $orthographic_variants = array();
1253
    foreach ($name_relations as $name_rel) {
1254
      $rel_type_uuid = $name_rel->type->uuid;
1255
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1256
      if ((!$is_inverse_relation && isset($name_rel_type_filter['direct'][$rel_type_uuid]) && $name_rel_type_filter['direct'][$rel_type_uuid])
1257
        ||($is_inverse_relation && isset($name_rel_type_filter['inverse'][$rel_type_uuid]) && $name_rel_type_filter['inverse'][$rel_type_uuid])) {
1258

    
1259
        if (array_search($rel_type_uuid, $non_nec_name_reltype_uuids) !== false && (
1260
            $current_name_uuid == $name_rel->fromName->uuid && $rel_type_uuid != UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1261
            || $current_name_uuid == $name_rel->toName->uuid && $rel_type_uuid == UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1262
          )
1263
        ){
1264
          $non_nec_name_rels[] = $name_rel;
1265
        } else if (UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $rel_type_uuid) {
1266
          $orthographic_variants[] = $name_rel;
1267
        } else {
1268

    
1269
          $filtered_name_rels[] = $name_rel;
1270
        }
1271
      }
1272
    }
1273
    $name_relations = $filtered_name_rels;
1274

    
1275
    usort($name_relations, 'compare_name_relations_by_term_order_index');
1276

    
1277
    // compose
1278
    foreach ($name_relations as $name_rel) {
1279

    
1280
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1281

    
1282
      $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1283
      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1284

    
1285
      $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1286
      $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1287
      $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
1288
      $relationship_markup = $symbol_markup . $relationship_markup;
1289
      if ($relationship_markup) {
1290
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1291
          null,
1292
          $item_prefix,
1293
          $item_suffix);
1294
      }
1295
    }
1296

    
1297
    // name relationships to be displayed as non nec
1298
    if (count($non_nec_name_rels) > 0) {
1299
      $non_nec_markup = '';
1300
      foreach ($non_nec_name_rels as $name_rel) {
1301
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1302
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1303
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1304
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1305
        $symbol = $non_nec_markup ? ' nec ' : 'non';
1306
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1307
        $non_nec_markup .= $symbol_markup . $relationship_markup;
1308
      }
1309
      if ($non_nec_markup) {
1310
        $render_array['list']['items'][] = markup_to_render_array($non_nec_markup,
1311
          null,
1312
          $item_prefix,
1313
          $item_suffix);
1314
      }
1315
    }
1316

    
1317
    // orthographic variants
1318
    if (count($orthographic_variants) > 0) {
1319
      foreach ($orthographic_variants as $name_rel) {
1320

    
1321
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1322
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1323
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, TRUE);
1324
        $nomref_footnote_key_markup = nomenclatural_reference_footnote_key_markup($name_rel->toName);
1325
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1326
        $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1327
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1328
        $relationship_markup = $symbol_markup . $relationship_markup . $nomref_footnote_key_markup;
1329
      }
1330
      if ($relationship_markup) {
1331
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1332
          null,
1333
          $item_prefix,
1334
          $item_suffix);
1335
      }
1336
    }
1337
  }
1338
  return $render_array;
1339
}
1340

    
1341
/**
1342
 * @param $name_rel
1343
 * @return string
1344
 */
1345
function name_relationship_footnote_markup($name_rel)
1346
{
1347
  $footnote_markup = '';
1348
  $footnote_key_markup = '';
1349
  if (isset($name_rel->ruleConsidered) && $name_rel->ruleConsidered) {
1350
    $footnote_markup = '<span class="rule_considered">' . $name_rel->ruleConsidered . '</span> ';
1351
  }
1352
  if (isset($name_rel->citation)) {
1353
    $footnote_markup .= '<span class="reference">' . $name_rel->citation->titleCache . '</span>';
1354
  }
1355
  if (isset($name_rel->citationMicroReference) && $name_rel->citationMicroReference) {
1356
    $footnote_markup .= (isset($name_rel->citation) ? ':' : '') . '<span class="reference_detail">' . $name_rel->citationMicroReference . '</span>';
1357
  }
1358
  if ($footnote_markup) {
1359
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1360
    $footnote_key_markup = theme('cdm_footnote_key', array(
1361
      'footnoteKey' => $fnkey,
1362
      'separator' => ',',
1363
      'highlightable' => TRUE,
1364
      'separator_off' => TRUE,
1365
    ));
1366
  }
1367
  return $footnote_key_markup;
1368
}
1369

    
1370
/**
1371
 * @param $nom_status
1372
 * @return string
1373
 */
1374
function nomenclatural_status_footnote_markup($nom_status)
1375
{
1376
  // NomenclaturalStatus is a subclass of ReferencedEntityBase
1377
  // and has the same structure as TaxonNameRelationship
1378
  return name_relationship_footnote_markup($nom_status);
1379
}
1380

    
1381
/**
1382
 * @param $name
1383
 * @return string
1384
 */
1385
function nomenclatural_reference_footnote_key_markup($name)
1386
{
1387
  $footnote_markup = '';
1388
  $footnote_key_markup = '';
1389
  if (isset($name->nomenclaturalReference) && $name->nomenclaturalReference) {
1390
    $footnote_markup .= '<span class="reference">' . $name->nomenclaturalReference->titleCache . '</span>';
1391
  }
1392
  if (isset($name->nomenclaturalMicroReference)) {
1393
    $footnote_markup .= ($footnote_key_markup ? ':' : '') . '<span class="reference_detail">' . $name->nomenclaturalMicroReference . '</span>';
1394
  }
1395
  if ($footnote_markup) {
1396
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1397
    $footnote_key_markup = theme('cdm_footnote_key', array(
1398
      'footnoteKey' => $fnkey,
1399
      'separator' => ',',
1400
      'highlightable' => TRUE,
1401
      'separator_off' => TRUE,
1402
    ));
1403
  }
1404
  return $footnote_key_markup;
1405
}
1406

    
1407

    
1408
/**
1409
 * @param $taxon
1410
 * @return array
1411
 */
1412
function cdm_name_relationships_for_taxon($taxon)
1413
{
1414
  $from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
1415
  $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
1416
  $name_relations = array_merge($from_name_relations, $to_name_relations);
1417
  return $name_relations;
1418
}
1419

    
1420

    
1421
/**
1422
 * Recursively searches the array for the $key and sets the given value.
1423
 *
1424
 * @param mixed $key
1425
 *   Key to search for.
1426
 * @param mixed $value
1427
 *   Value to set.'
1428
 * @param array $array
1429
 *   Array to search in.
1430
 *
1431
 * @return bool
1432
 *   True if the key has been found.
1433
 */
1434
function &array_setr($key, $value, array &$array) {
1435
  $res = NULL;
1436
  foreach ($array as $k => &$v) {
1437
    if ($key == $k) {
1438
      $v = $value;
1439
      return $array;
1440
    }
1441
    elseif (is_array($v)) {
1442
      $innerArray = array_setr($key, $value, $v);
1443
      if ($innerArray) {
1444
        return $array;
1445
      }
1446
    }
1447
  }
1448
  return $res;
1449
}
1450

    
1451
/**
1452
 * @todo Please document this function.
1453
 * @see http://drupal.org/node/1354
1454
 */
1455
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
1456
  $res = NULL;
1457
  $precedingElement = NULL;
1458
  foreach ($renderTemplate as &$part) {
1459
    foreach ($part as $key => &$element) {
1460
      if ($key == $contentElementKey) {
1461
        return $precedingElement;
1462
      }
1463
      $precedingElement = $element;
1464
    }
1465
  }
1466
  return $res;
1467
}
1468

    
1469
/**
1470
 * @todo Please document this function.
1471
 * @see http://drupal.org/node/1354
1472
 */
1473
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
1474
  $res = NULL;
1475
  $precedingKey = NULL;
1476
  foreach ($renderTemplate as &$part) {
1477
    if (is_array($part)) {
1478
      foreach ($part as $key => &$element) {
1479
        if ($key == $contentElementKey) {
1480
          return $precedingKey;
1481
        }
1482
        if (!str_beginsWith($key, '#')) {
1483
          $precedingKey = $key;
1484
        }
1485
      }
1486
    }
1487
  }
1488
  return $res;
1489
}
1490

    
1491
function nameTypeToDTYPE($dtype){
1492
  static $nameTypeLabelMap = array(
1493
    "ICNB" => "BacterialName",
1494
    "ICNAFP" => "BotanicalName",
1495
    "ICNCP" => "CultivarPlantName",
1496
    "ICZN" => "ZoologicalName",
1497
    "ICVCN" => "ViralName",
1498
    "Any taxon name" => "TaxonName",
1499
    "NonViral" => "TaxonName",
1500
    "Fungus" => "BotanicalName",
1501
    "Plant" => "BotanicalName",
1502
    "Algae" => "BotanicalName",
1503
  );
1504
  return $nameTypeLabelMap[$dtype];
1505

    
1506
}
1507

    
1508

    
1509
function compare_name_relations_by_term_order_index($name_rel1, $name_rel2){
1510
  return compare_terms_by_order_index($name_rel1->type, $name_rel2->type);
1511
}
1512

    
1513
/**
1514
 * Provides an array with the different registration types covered by the passed registration.
1515
 *
1516
 * The labels in the returned array are translatable.
1517
 *
1518
 * See also https://dev.e-taxonomy.eu/redmine/issues/8016
1519
 *
1520
 * @param $registration_dto
1521
 * @return array
1522
 *    An array of the labels describing the different registration types covered by the passed registration.
1523
 */
1524
function registration_types($registration_dto){
1525
  $reg_type_labels = array();
1526
  if(isset($registration_dto->nameRef)){
1527
    $reg_type_labels["name"] = t("new name");
1528
    $reg_type_labels["taxon"] = t("new taxon");
1529
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
1530
    $is_new_combination = true;
1531
    foreach($name_relations as $name_rel){
1532
      if(isset($name_rel->type->uuid)){
1533
        $name_is_from_name = $registration_dto->nameRef->uuid == $name_rel->fromName->uuid;
1534
        switch($name_rel->type->uuid) {
1535
          case UUID_NAMERELATIONSHIPTYPE_BASIONYM:
1536
            if(!$name_is_from_name){
1537
              $reg_type_labels["basionym"] = t("new combination");
1538
              $is_new_combination = true;
1539
            }
1540
            break;
1541
          case UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM:
1542
            if(!$name_is_from_name) {
1543
              $is_new_combination = true;
1544
            }
1545
            break;
1546
          case UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME:
1547
            if(!$name_is_from_name) {
1548
              $reg_type_labels["validation"] = t("validation");
1549
            }
1550
            break;
1551
          case UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT:
1552
            if(!$name_is_from_name) {
1553
              $reg_type_labels["orth_var"] = t("orthographical correction");
1554
            }break;
1555
          default:
1556
            // NOTHING
1557
        }
1558
      }
1559
    }
1560
    if($is_new_combination){
1561
      unset($reg_type_labels["taxon"]);
1562
    }
1563
  }
1564
  if(isset($registration_dto->orderdTypeDesignationWorkingSets)){
1565
    $reg_type_labels[] = t("new nomenclatural type");
1566
  }
1567
  return $reg_type_labels;
1568
}
1569

    
1570
/**
1571
 * Collects and deduplicates the type designations associated with the passes synonyms.
1572
 *
1573
 * @param $synonymy_group
1574
 *    An array containing a homotypic or heterotypic group of names.
1575
 * @param $accepted_taxon_name_uuid
1576
 *    The uuid of the accepted taxon name. Optional parameter which is required when composing
1577
 *    the information for the homotypic group. In this case the accepted taxon is not included
1578
 *    in the $synonymy_group and must therefor passed in this second parameter.
1579
 *
1580
 * @return array
1581
 *    The type designations
1582
 */
1583
function type_designations_for_synonymy_group($synonymy_group, $accepted_taxon_name_uuid = null)
1584
{
1585
  if (count($synonymy_group) > 0) {
1586
    $name_uuid = array_pop($synonymy_group)->name->uuid;
1587
  } else {
1588
    $name_uuid = $accepted_taxon_name_uuid;
1589
  }
1590
  if ($name_uuid) {
1591
   $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS_IN_HOMOTYPICAL_GROUP, $name_uuid);
1592
    if ($type_designations) {
1593
      return $type_designations;
1594
    }
1595
  }
1596

    
1597
  return array();
1598
}
1599

    
1600

    
1601
/**
1602
 * Compares the status of two SpecimenTypeDesignations
1603
 *
1604
 * @param object $a
1605
 *   A SpecimenTypeDesignation.
1606
 * @param object $b
1607
 *   SpecimenTypeDesignation.
1608
 */
1609
function compare_specimen_type_designation($a, $b) {
1610

    
1611
  $type_status_order = type_status_order();
1612

    
1613

    
1614
  $aQuantifier = FALSE;
1615
  $bQuantifier = FALSE;
1616
  if (isset($a->typeStatus->titleCache) && isset($b->typeStatus->titleCache)) {
1617
    $aQuantifier = array_search($a->typeStatus->titleCache, $type_status_order);
1618
    $bQuantifier = array_search($b->typeStatus->titleCache, $type_status_order);
1619
  }
1620
  if ($aQuantifier == $bQuantifier) {
1621
    // Sort alphabetically.
1622
    $a_text =  isset($a->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $a->typeSpecimen->titleCache) : '';
1623
    $b_text =  isset($b->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $b->typeSpecimen->titleCache) : '';
1624
    return strcasecmp($a_text, $b_text);
1625
  }
1626
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1627
}
1628

    
1629
/**
1630
 * Compares the status of two SpecimenTypeDesignations
1631
 *
1632
 * @param object $a
1633
 *   A TypeDesignationStatusBase.
1634
 * @param object $b
1635
 *   TypeDesignationStatusBase.
1636
 */
1637
function compare_type_designation_status($a, $b) {
1638

    
1639
  $type_status_order = type_status_order();
1640

    
1641

    
1642
  $aQuantifier = FALSE;
1643
  $bQuantifier = FALSE;
1644
  if (isset($a->label) && isset($b->label)) {
1645
    $aQuantifier = array_search($a->label, $type_status_order);
1646
    $bQuantifier = array_search($b->label, $type_status_order);
1647
  }
1648
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1649
}
1650

    
1651

    
1652
/**
1653
 * Compares two SpecimenTypeDesignation status labels
1654
 *
1655
 * @param string $a
1656
 *   A TypeDesignationStatus label.
1657
 * @param string $b
1658
 *   A TypeDesignationStatus label.
1659
 */
1660
function compare_type_designation_status_labels($a, $b) {
1661

    
1662
  $type_status_order = type_status_order();
1663

    
1664

    
1665
  $aQuantifier = FALSE;
1666
  $bQuantifier = FALSE;
1667
  if (isset($a) && isset($b)) {
1668
    $aQuantifier = array_search($a, $type_status_order);
1669
    $bQuantifier = array_search($b, $type_status_order);
1670
  }
1671
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1672
}
1673

    
1674
/**
1675
 * @return array
1676
 */
1677
function type_status_order()
1678
{
1679
  /*
1680
    This is the desired sort order as of now: Holotype Isotype Lectotype
1681
    Isolectotype Syntype.
1682
    TODO Basically, what we are trying to do is, we define
1683
    an ordered array of TypeDesignation-states and use the index of this array
1684
    for comparison. This array has to be filled with the cdm- TypeDesignation
1685
    states and the order should be parameterisable inside the dataportal.
1686
    */
1687
  // Make that static for now.
1688
  $type_status_order = array(
1689
    'Epitype',
1690
    'Holotype',
1691
    'Isotype',
1692
    'Lectotype',
1693
    'Isolectotype',
1694
    'Syntype',
1695
    'Paratype'
1696
  );
1697
  return $type_status_order;
1698
}
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