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<?php
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/**
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 * @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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 */
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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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 */
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33

    
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/**
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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 $renderPath.
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 * @return array
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 *   An associative array, the render template
72
 */
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function get_nameRenderTemplate($render_path, $nameLink = NULL, $referenceLink = NULL) {
74

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

    
78

    
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  if (!isset($default_render_templates)) {
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    $default_render_templates = unserialize(CDM_NAME_RENDER_TEMPLATES_DEFAULT);
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  }
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  if($split_render_templates == NULL) {
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    $render_templates = variable_get(CDM_NAME_RENDER_TEMPLATES, $default_render_templates);
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    // needs to be converted to an array
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    $render_templates = (object_to_array($render_templates));
86

    
87
    // separate render templates which are combined with a comma
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    $split_render_templates = array();
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    foreach($render_templates as $key => $template){
90
      if(strpos($key, ',')){
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        foreach(explode(',', $key) as $path){
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          $split_render_templates[$path] = $template;
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        }
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      } else {
95
        $split_render_templates[$key] = $template;
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      }
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;
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  }
106

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

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

    
127

    
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  // 3. Otherwise get default RenderTemplate from theme.
129
  if (!is_array($template)) {
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    $template = $split_render_templates['#DEFAULT'];
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  }
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  // --- set the link uris to the according template fields if they exist
134
  if(isset($template['nameAuthorPart']) && isset($template['nameAuthorPart']['#uri'])) {
135
    if ($nameLink) {
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      $template['nameAuthorPart']['#uri'] = $nameLink;
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    }
138
    else {
139
      unset($template['nameAuthorPart']['#uri']);
140
    }
141
  }
142

    
143
  if ($nameLink && isset($template['namePart']['#uri'])) {
144
    $template['namePart']['#uri'] = $nameLink;
145
  }
146
  else {
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    unset($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
}
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/**
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 * The part definitions define the specific parts of which a rendered taxon name plus additional information will consist.
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 *
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 * A full taxon name plus additional information can consist of the following elements:
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 *
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 *   - name: the taxon name inclugin rank nbut without author
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 *   - authorTeam:  The authors of a reference, also used in taxon names
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 *   - authors:  The authors of a reference, also used in taxon names
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 *   - reference: the nomenclatural reference,
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 *   - microreference:  Volume, page number etc.
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 *   - status:  The nomenclatural status of a name
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 *   - description: name descriptions like protologues etc ...
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 *
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 * These elements are combined in the part definitions array to from the specific parts to be rendered.
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 * Usually the following parts are formed:
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 *
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 * The name "Lapsana communis L., Sp. Pl.: 811. 1753" shall be an example here:
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 *  - 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.
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 *  - referencePart: the nomencaltural reference (in example: "Sp. Pl. 1753")
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 *  - microreferencePart: usually the page number (in example ": 811.")
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 *  - 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
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 *  - 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
 *    ),
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 *    'BotanicalName' => array(
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 *        'namePart' => array(
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 *            'name' => TRUE,
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 *            'authors' => TRUE,
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 *        ),
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 überall dort falsch, wo ein "in" folgt."
414
    if (isset($renderTemplate['referencePart']['reference'])) {
415
      $microreference = NULL;
416
      if (isset($renderTemplate['referencePart']['microreference'])&& isset($taxonName->nomenclaturalMicroReference)) {
417
        $microreference = $taxonName->nomenclaturalMicroReference;
418
      }
419
      if(count($nomref_tagged_text) == 0 && isset($taxonName->nomenclaturalReference)){
420
        // TODO is this case still relevant? The tagged text should already contain all information!
421
        $citation = cdm_ws_getNomenclaturalReference($taxonName->nomenclaturalReference->uuid, $microreference);
422
        // Find preceding element of the reference.
423
        $precedingKey = get_preceding_contentElementKey('reference', $renderTemplate);
424
        if (str_beginsWith($citation, ", in")) {
425
          $citation = substr($citation, 2);
426
          $separator = ' ';
427
        }
428
        elseif (!str_beginsWith($citation, "in") && $precedingKey == 'authors') {
429
          $separator = ', ';
430
        } else {
431
          $separator = ' ';
432
        }
433
        $referenceArray['#separator'] = $separator;
434
        $referenceArray['#html'] = '<span class="reference">' . $citation . '</span>' . $registration_markup;
435
      } else {
436
        // this ist the case for taxon names
437
        $referenceArray['#html'] = cdm_tagged_text_to_markup($nomref_tagged_text);
438
      }
439

    
440

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

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

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

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

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

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

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

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

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

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

    
588

    
589

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

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

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

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

    
628
  // name
629
  if($registration_dto->nameRef){
630
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->nameRef->uuid);
631
    cdm_load_tagged_full_title($name);
632
    $render_array['nomenclatural_act']['published_name'] = markup_to_render_array('<div class="published-name">' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</div>', 0);
633
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
634
    $render_array['nomenclatural_act']['name_relations'] = compose_name_relationships_list($name_relations, $registration_dto->nameRef->uuid, null);
635
    $render_array['nomenclatural_act']['name_relations']['#weight'] = 10;
636
  } else {
637
    // in this case the registration must have a
638
    $name = cdm_ws_get(CDM_WS_PORTAL_NAME, $registration_dto->typifiedNameRef->uuid);
639
    $render_array['typified_name'] = markup_to_render_array('<p class="typified-name">for ' . render_taxon_or_name($name, url(path_to_name($name->uuid))) . '</p>', 40);
640
  }
641
  // typedesignation in detail
642
  if(is_object($registration_dto->orderdTypeDesignationWorkingSets)) {
643
    $field_unit_uuids = array();
644
    $specimen_type_designation_refs = array();
645
    $name_type_designation_refs = array();
646
    foreach ((array)$registration_dto->orderdTypeDesignationWorkingSets as $workingset_ref => $obj) {
647
      $tokens = explode("#", $workingset_ref);
648
      $types_in_fieldunit = get_object_vars($obj); // convert into associative array
649

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

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

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

    
705
  return $render_array;
706
}
707

    
708

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

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

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

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

    
775
  return $render_array;
776
}
777

    
778

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

    
807

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

    
826

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

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

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

    
863

    
864
/**
865
 * Composes the textual representation for the type designation of taxon name identified by the uuid in with a map for the location data.
866
 *
867
 * @param $taxon_name_uuid
868
 * @param $show_specimen_details
869
 * @return array
870
 *    A drupal render array with the following elements:
871
 *    - 'type_designations'
872
 *    - 'map'
873
 *    - 'specimens'
874
 *
875
 * @ingroup compose
876
 */
877
function compose_type_designations($taxon_name_uuid, $show_specimen_details = false)
878
{
879
  $render_array = array(
880
    'type_designations' => array(),
881
    'map' => array(),
882
    );
883
  $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS, $taxon_name_uuid);
884
  if ($type_designations) {
885
    usort($type_designations, 'compare_specimen_type_designation');
886
    $render_array['type_designations'] = markup_to_render_array(
887
      render_type_designations($type_designations, 'div', 'div')
888
    );
889

    
890
    $render_array['map'] = compose_type_designations_map($type_designations);
891
  }
892
  return $render_array;
893
}
894

    
895

    
896
/**
897
 * Composes the TypedEntityReference to name type designations passed as associatve array.
898
 *
899
 * @param $$type_entity_refs array
900
 *   an associative array of name type type => TypedEntityReference for name type designations as
901
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
902
 *
903
 * @ingroup compose
904
 */
905
function compose_name_type_designations($type_entity_refs){
906
  $render_array = array();
907
  $preferredStableUri = '';
908
  foreach($type_entity_refs as $type_status => $name_types){
909
    foreach ($name_types as $name_type){
910
      $type_designation = cdm_ws_get(CDM_WS_TYPEDESIGNATION, array($name_type->uuid, 'preferredUri'));
911
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
912
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
913
      }
914
      $render_array[] = markup_to_render_array('<div class="name_type_designation ' . html_class_attribute_ref($name_type)  . '"><span class="type-status">'. ucfirst($type_status) . "</span>: "
915
        . $name_type->label
916
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
917
        . '</div>');
918
      }
919
  }
920
  return $render_array;
921
}
922

    
923
/**
924
 * Composes the specimen type designations with map from the the $type_entity_refs
925
 *
926
 * @param $type_entity_refs array
927
 *   an associative array of specimen type type => TypedEntityReference for specimen type designations as
928
 *   produced by the eu.etaxonomy.cdm.api.service.name.TypeDesignationSetManager
929
 *
930
 * @param $show_media_specimen
931
 * @return array
932
 *    A drupal render array with the following elements:
933
 *    - 'type_designations'
934
 *    - 'map'
935
 *
936
 * @ingroup compose
937
 *
938
 */
939
function compose_specimen_type_designations($type_entity_refs, $show_media_specimen){
940

    
941
  $render_array = array();
942

    
943
  $type_designation_list = array();
944
  uksort($type_entity_refs, "compare_type_designation_status_labels");
945
  foreach($type_entity_refs as $type_status => $specimen_types){
946
    foreach($specimen_types as $specimen_type){
947

    
948
      $type_designation = cdm_ws_get(CDM_WS_PORTAL_TYPEDESIGNATION, array($specimen_type->uuid));
949
      $type_designation_list[] = $type_designation; // collect for the map
950

    
951
      $derivedUnitFacadeInstance = cdm_ws_get(CDM_WS_PORTAL_DERIVEDUNIT_FACADE, $type_designation->typeSpecimen->uuid);
952
      // the media specimen is not contained in the $type_designation returned by CDM_PORTAL_TYPEDESIGNATION, so we need to fetch it separately
953
      $mediaSpecimen = cdm_ws_get(CDM_WS_PORTAL_OCCURRENCE, array($type_designation->typeSpecimen->uuid, 'mediaSpecimen'));
954

    
955

    
956
      $preferredStableUri = '';
957
      $citation_markup = '';
958
      $media = '';
959

    
960
      // preferredStableUri
961
      if(isset($type_designation->typeSpecimen->preferredStableUri) && $type_designation->typeSpecimen->preferredStableUri){
962
        $preferredStableUri = $type_designation->typeSpecimen->preferredStableUri;
963
      }
964

    
965
      if($show_media_specimen && $mediaSpecimen){
966
        // compose output
967
        // mediaURI
968
        if(isset($mediaSpecimen->representations[0])) {
969
          $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SPECIMEN_GALLERY_NAME);
970
          $captionElements = array(
971
            '#uri' => t('open media'),
972
            'elements' => array('-none-'),
973
            'sources_as_content' => true
974
          );
975
          $media = compose_cdm_media_gallerie(array(
976
            'mediaList' => array($mediaSpecimen),
977
            'galleryName' => CDM_DATAPORTAL_TYPE_SPECIMEN_GALLERY_NAME . '_' . $specimen_type->uuid,
978
            'maxExtend' => $gallery_settings['cdm_dataportal_media_maxextend'],
979
            'cols' => $gallery_settings['cdm_dataportal_media_cols'],
980
            'captionElements' => $captionElements,
981
          ));
982
        }
983
        // citation and detail
984
        $annotations_and_sources = handle_annotations_and_sources(
985
            $mediaSpecimen,
986
            array(
987
                'sources_as_content' => true,
988
                'link_to_name_used_in_source' => false,
989
                'link_to_reference' => true,
990
                'add_footnote_keys' => false,
991
                'bibliography_aware' => false),
992
            '',
993
            null
994
        );
995
        if(is_array( $annotations_and_sources['source_references'])){
996
          $citation_markup = join(', ', $annotations_and_sources['source_references']);
997
        }
998
      }
999

    
1000
      $specimen_markup = $derivedUnitFacadeInstance->titleCache;
1001
      if(isset($derivedUnitFacadeInstance->specimenLabel) && $derivedUnitFacadeInstance->specimenLabel){
1002
        $specimen_markup = str_replace($derivedUnitFacadeInstance->specimenLabel, l($derivedUnitFacadeInstance->specimenLabel, path_to_specimen($type_designation->typeSpecimen->uuid)), $specimen_markup);
1003
      }
1004

    
1005
      $type_designation_render_array = markup_to_render_array('<div class="specimen_type_designation ' . html_class_attribute_ref($specimen_type)  . '">
1006
          <span class="type-status">' . ucfirst($type_status) . "</span>: "
1007
        . $specimen_markup
1008
        . ($citation_markup ? ' '. $citation_markup : '')
1009
        . ($preferredStableUri ? " ". l($preferredStableUri,  $preferredStableUri) : '')
1010
        . $media
1011
        . '</div>');
1012

    
1013
      $render_array['type_designations'][] = $type_designation_render_array;
1014
    }
1015
  }
1016
  if(count($type_designation_list) > 0 ){
1017
    $render_array['map'] = compose_type_designations_map($type_designation_list);
1018
  } else {
1019
    $render_array['map'] = array();
1020
  }
1021
  return $render_array;
1022
}
1023

    
1024
/**
1025
 * @param $name_rel
1026
 * @param $current_name_uuid
1027
 * @param $current_taxon_uuid
1028
 * @param $suppress_if_current_name_is_source // FIXME UNUSED !!!!
1029
 * @param $show_name_cache_only
1030
 *    The nameCache will be shown instead of the titleCache if this parameter is true.
1031
 * @return null|string
1032
 */
1033
function name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, $show_name_cache_only = false){
1034

    
1035
  $relationship_markup = null;
1036

    
1037
  $current_name_is_toName = $current_name_uuid == $name_rel->toName->uuid;
1038

    
1039
  if($current_name_is_toName){
1040
    $name = $name_rel->fromName;
1041
  } else {
1042
    $name = $name_rel->toName;
1043
  }
1044

    
1045
  cdm_load_tagged_full_title($name);
1046

    
1047
  $highlited_synonym_uuid = isset ($name->taxonBases[0]->uuid) ? $name->taxonBases[0]->uuid : '';
1048
  if(!$show_name_cache_only){
1049
    $relationship_markup = render_taxon_or_name($name,
1050
      url(path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false))
1051
    );
1052
  } else {
1053
    $relationship_markup = l(
1054
      '<span class="' . html_class_attribute_ref($name) . '"">' . $name->nameCache . '</span>',
1055
      path_to_name($name->uuid, $current_taxon_uuid, $highlited_synonym_uuid, false),
1056
      array('html' => true)
1057
    );
1058
  }
1059

    
1060
  return $relationship_markup;
1061
}
1062

    
1063

    
1064
/**
1065
 * Composes an inline representation of selected name relationships
1066
 *
1067
 * The output of this function will be usually appended to taxon name representations.
1068
 * Only the following types are displayed: LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR, ORTHOGRAPHIC_VARIANT
1069
 *
1070
 * LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR are displayed as
1071
 * non {titleCache} nec {titleCache} nec {titleCache} whereas the related names
1072
 * are ordered alphabetically.
1073
 *
1074
 * ORTHOGRAPHIC_VARIANT is displayed as 'ort. var. {nameCache}'
1075
 *
1076
 * Related issues:
1077
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1078
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1079
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1080
 *   - https://dev.e-taxonomy.eu/redmine/issues/2001 "[Cichorieae Portal] Name Relationship -> blocking name are not shown"
1081
 *
1082
 * @param $name_relations
1083
 *    The list of CDM NameRelationsips
1084
 * @param $current_name_uuid
1085
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1086
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1087
 * @param $suppress_if_current_name_is_source
1088
 *    The display of the relation will be
1089
 *    suppressed is the current name is on the source of the relation edge.
1090
 *    That is if it is on the from side of the relation. Except for 'blocking name for' which is
1091
 *    an inverse relation. For this relation type the toName is taken in to account.
1092
 * @param $current_taxon_uuid
1093
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1094
 * @return array
1095
 *    A drupal render array
1096
 *
1097
 * @ingroup Compose
1098
 */
1099
function compose_name_relationships_inline($name_relations, $current_name_uuid, $current_taxon_uuid, $suppress_if_current_name_is_source = true) {
1100

    
1101
  RenderHints::pushToRenderStack('homonym');
1102
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1103

    
1104
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_INLINE_TYPES, unserialize(CDM_NAME_RELATIONSHIP_INLINE_TYPES_DEFAULT));
1105
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1106
  foreach ($selected_name_rel_uuids as $uuid){
1107
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1108
    if($uuid != UUID_NAMERELATIONSHIPTYPE_MISSPELLING){
1109
      $name_rel_type_filter['inverse'][$uuid] = $uuid;
1110
    }
1111
  }
1112

    
1113
  $list_prefix = '<span class="name_relationships">[';
1114
  $list_suffix = ']</span>';
1115
  $item_prefix = '<span class="item">';
1116
  $item_suffix = '</span> ';
1117
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1118

    
1119
  // remove the glue space from the last item element which has been added by the $item_suffix = '</span> '
1120
  $items_ctn = count($render_array['list']['items']);
1121
  if($items_ctn){
1122
    $render_array['list']['items'][$items_ctn - 1]['#suffix'] = '</span>';
1123
  }
1124

    
1125
  RenderHints::popFromRenderStack();
1126
  return $render_array;
1127
}
1128

    
1129
/**
1130
 * Composes an list representation of the name relationships.
1131
 *
1132
 * The output of this function will be usually appended to taxon name representations.
1133
 *
1134
 * Related issues:
1135
 *   - https://dev.e-taxonomy.eu/redmine/issues/5697 "Show name conserved against as [non xxx]"
1136
 *   - https://dev.e-taxonomy.eu/redmine/issues/6678 "How to correctly show name relationship "orth. var." in dataportal"
1137
 *   - https://dev.e-taxonomy.eu/redmine/issues/5857
1138
 *
1139
 * @param $name_relations
1140
 *    The list of CDM NameRelationsips
1141
 * @param $current_name_uuid
1142
 *    The Uuid of the name for which the relations are to be rendered, the current name will be hidden when
1143
 *    rendering the relation an only the other name is shown. Parameter is REQUIRED.
1144
 * @param $current_taxon_uuid
1145
 *    The taxon to be omitted from related taxa. This is only used to create links, see path_to_name()
1146
 * @return array
1147
 *    A drupal render array
1148
 *
1149
 * @ingroup Compose
1150
 */
1151
function compose_name_relationships_list($name_relations, $current_name_uuid, $current_taxon_uuid) {
1152

    
1153
  // $ordered_name_relation_type_uuids = array_keys(cdm_terms_by_type_as_option('NameRelationshipType', CDM_ORDER_BY_ORDER_INDEX_ASC));
1154

    
1155
  $key = 'name_relationships';
1156
  RenderHints::pushToRenderStack($key);
1157
  if(!RenderHints::getFootnoteListKey()){
1158
    RenderHints::setFootnoteListKey($key);
1159
  }
1160
  // the render stack element homonyms is being used in the default render templates !!!, see CDM_NAME_RENDER_TEMPLATES_DEFAULT
1161

    
1162
  $selected_name_rel_uuids = variable_get(CDM_NAME_RELATIONSHIP_LIST_TYPES, cdm_vocabulary_as_defaults(UUID_NAME_RELATIONSHIP_TYPE));
1163
  $name_rel_type_filter = array('direct' => array(), 'inverse' => array());
1164
  foreach ($selected_name_rel_uuids as $uuid){
1165
    $name_rel_type_filter['direct'][$uuid] = $uuid;
1166
    $name_rel_type_filter['inverse'][$uuid] = $uuid;
1167
  }
1168

    
1169
  $list_prefix = '<div class="relationships_list name_relationships">';
1170
  $list_suffix = '</div>';
1171
  $item_prefix = '<div class="item">';
1172
  $item_suffix = '</div>';
1173

    
1174
  $render_array = compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid, $list_prefix, $list_suffix, $item_prefix, $item_suffix);
1175

    
1176
  RenderHints::popFromRenderStack();
1177
  $render_array['footnotes'] = markup_to_render_array(theme('cdm_footnotes', array('footnoteListKey' => RenderHints::getFootnoteListKey())));
1178
  if(RenderHints::getFootnoteListKey() == $key) {
1179
    RenderHints::clearFootnoteListKey();
1180
  }
1181
  return $render_array;
1182
}
1183

    
1184
/**
1185
 * @param $name_relations
1186
 * @param $name_rel_type_filter
1187
 *   Associative array with two keys:
1188
 *   - 'direct': the relationship type uuids for the direct direction of the relation edge to be included
1189
 *   - 'inverse': the relationship type uuids for the direct direction of the relation edge to be included
1190
 * @param $current_name_uuid
1191
 * @param $current_taxon_uuid
1192
 * @param $list_prefix
1193
 * @param $list_suffix
1194
 * @param $item_prefix
1195
 * @param $item_suffix
1196
 * @return array
1197
 *
1198
 * @ingroup Compose
1199
 */
1200
function compose_name_relationships($name_relations, $name_rel_type_filter, $current_name_uuid, $current_taxon_uuid,
1201
                                    $list_prefix, $list_suffix, $item_prefix, $item_suffix)
1202
{
1203
  $non_nec_name_reltype_uuids = array(UUID_NAMERELATIONSHIPTYPE_LATER_HOMONYM,
1204
    UUID_NAMERELATIONSHIPTYPE_TREATED_AS_LATER_HOMONYM,
1205
    UUID_NAMERELATIONSHIPTYPE_CONSERVED_AGAINST,
1206
    UUID_NAMERELATIONSHIPTYPE_MISSPELLING,
1207
    UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR);
1208

    
1209
  $render_array = array(
1210
    'list' => array(
1211
      '#prefix' => $list_prefix,
1212
      '#suffix' => $list_suffix,
1213
      'items' => array()
1214
    ),
1215
    'footnotes' => array()
1216
  );
1217

    
1218
  if ($name_relations) {
1219

    
1220
    // remove all relations which are not selected in the settings and
1221
    // separate all LATER_HOMONYM, TREATED_AS_LATER_HOMONYM, BLOCKING_NAME_FOR relations and ORTHOGRAPHIC_VARIANTs
1222
    // for special handling
1223
    $filtered_name_rels = array();
1224
    $non_nec_name_rels = array();
1225
    $orthographic_variants = array();
1226
    foreach ($name_relations as $name_rel) {
1227
      $rel_type_uuid = $name_rel->type->uuid;
1228
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1229
      if ((!$is_inverse_relation && isset($name_rel_type_filter['direct'][$rel_type_uuid]) && $name_rel_type_filter['direct'][$rel_type_uuid])
1230
        ||($is_inverse_relation && isset($name_rel_type_filter['inverse'][$rel_type_uuid]) && $name_rel_type_filter['inverse'][$rel_type_uuid])) {
1231

    
1232
        if (array_search($rel_type_uuid, $non_nec_name_reltype_uuids) !== false && (
1233
            $current_name_uuid == $name_rel->fromName->uuid && $rel_type_uuid != UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1234
            || $current_name_uuid == $name_rel->toName->uuid && $rel_type_uuid == UUID_NAMERELATIONSHIPTYPE_BLOCKING_NAME_FOR
1235
          )
1236
        ){
1237
          $non_nec_name_rels[] = $name_rel;
1238
        } else if (UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT == $rel_type_uuid) {
1239
          $orthographic_variants[] = $name_rel;
1240
        } else {
1241

    
1242
          $filtered_name_rels[] = $name_rel;
1243
        }
1244
      }
1245
    }
1246
    $name_relations = $filtered_name_rels;
1247

    
1248
    usort($name_relations, 'compare_name_relations_by_term_order_index');
1249

    
1250
    // compose
1251
    foreach ($name_relations as $name_rel) {
1252

    
1253
      $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1254

    
1255
      $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1256
      $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1257

    
1258
      $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1259
      $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1260
      $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup . ' ';
1261
      $relationship_markup = $symbol_markup . $relationship_markup;
1262
      if ($relationship_markup) {
1263
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1264
          null,
1265
          $item_prefix,
1266
          $item_suffix);
1267
      }
1268
    }
1269

    
1270
    // name relationships to be displayed as non nec
1271
    if (count($non_nec_name_rels) > 0) {
1272
      $non_nec_markup = '';
1273
      foreach ($non_nec_name_rels as $name_rel) {
1274
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1275
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1276
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid);
1277
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1278
        $symbol = $non_nec_markup ? ' nec ' : 'non';
1279
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1280
        $non_nec_markup .= $symbol_markup . $relationship_markup;
1281
      }
1282
      if ($non_nec_markup) {
1283
        $render_array['list']['items'][] = markup_to_render_array($non_nec_markup,
1284
          null,
1285
          $item_prefix,
1286
          $item_suffix);
1287
      }
1288
    }
1289

    
1290
    // orthographic variants
1291
    if (count($orthographic_variants) > 0) {
1292
      foreach ($orthographic_variants as $name_rel) {
1293

    
1294
        $is_inverse_relation = $current_name_uuid == $name_rel->toName->uuid;
1295
        $rel_footnote_key_markup = name_relationship_footnote_markup($name_rel);
1296
        $relationship_markup = name_relationship_markup($name_rel, $current_name_uuid, $current_taxon_uuid, TRUE);
1297
        $nomref_footnote_key_markup = nomenclatural_reference_footnote_key_markup($name_rel->toName);
1298
        $label = cdm_relationship_type_term_abbreviated_label($name_rel->type, $is_inverse_relation);
1299
        $symbol = cdm_relationship_type_term_symbol($name_rel->type, $is_inverse_relation);
1300
        $symbol_markup = '<span class="symbol" title="' . $label . '">' . $symbol . '</span>' . $rel_footnote_key_markup .  ' ';
1301
        $relationship_markup = $symbol_markup . $relationship_markup . $nomref_footnote_key_markup;
1302
      }
1303
      if ($relationship_markup) {
1304
        $render_array['list']['items'][] = markup_to_render_array($relationship_markup,
1305
          null,
1306
          $item_prefix,
1307
          $item_suffix);
1308
      }
1309
    }
1310
  }
1311
  return $render_array;
1312
}
1313

    
1314
/**
1315
 * @param $name_rel
1316
 * @return string
1317
 */
1318
function name_relationship_footnote_markup($name_rel)
1319
{
1320
  $footnote_markup = '';
1321
  $footnote_key_markup = '';
1322
  if (isset($name_rel->ruleConsidered) && $name_rel->ruleConsidered) {
1323
    $footnote_markup = '<span class="rule_considered">' . $name_rel->ruleConsidered . '</span> ';
1324
  }
1325
  if (isset($name_rel->citation)) {
1326
    $footnote_markup .= '<span class="reference">' . $name_rel->citation->titleCache . '</span>';
1327
  }
1328
  if (isset($name_rel->citationMicroReference) && $name_rel->citationMicroReference) {
1329
    $footnote_markup .= (isset($name_rel->citation) ? ':' : '') . '<span class="reference_detail">' . $name_rel->citationMicroReference . '</span>';
1330
  }
1331
  if ($footnote_markup) {
1332
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1333
    $footnote_key_markup = theme('cdm_footnote_key', array(
1334
      'footnoteKey' => $fnkey,
1335
      'separator' => ',',
1336
      'highlightable' => TRUE,
1337
      'separator_off' => TRUE,
1338
    ));
1339
  }
1340
  return $footnote_key_markup;
1341
}
1342

    
1343
/**
1344
 * @param $nom_status
1345
 * @return string
1346
 */
1347
function nomenclatural_status_footnote_markup($nom_status)
1348
{
1349
  // NomenclaturalStatus is a subclass of ReferencedEntityBase
1350
  // and has the same structure as TaxonNameRelationship
1351
  return name_relationship_footnote_markup($nom_status);
1352
}
1353

    
1354
/**
1355
 * @param $name
1356
 * @return string
1357
 */
1358
function nomenclatural_reference_footnote_key_markup($name)
1359
{
1360
  $footnote_markup = '';
1361
  $footnote_key_markup = '';
1362
  if (isset($name->nomenclaturalReference) && $name->nomenclaturalReference) {
1363
    $footnote_markup .= '<span class="reference">' . $name->nomenclaturalReference->titleCache . '</span>';
1364
  }
1365
  if (isset($name->nomenclaturalMicroReference)) {
1366
    $footnote_markup .= ($footnote_key_markup ? ':' : '') . '<span class="reference_detail">' . $name->nomenclaturalMicroReference . '</span>';
1367
  }
1368
  if ($footnote_markup) {
1369
    $fnkey = FootnoteManager::addNewFootnote(RenderHints::getFootnoteListKey(), $footnote_markup);
1370
    $footnote_key_markup = theme('cdm_footnote_key', array(
1371
      'footnoteKey' => $fnkey,
1372
      'separator' => ',',
1373
      'highlightable' => TRUE,
1374
      'separator_off' => TRUE,
1375
    ));
1376
  }
1377
  return $footnote_key_markup;
1378
}
1379

    
1380

    
1381
/**
1382
 * @param $taxon
1383
 * @return array
1384
 */
1385
function cdm_name_relationships_for_taxon($taxon)
1386
{
1387
  $from_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_FROM_NAMERELATIONS, $taxon->uuid);
1388
  $to_name_relations = cdm_ws_get(CDM_WS_PORTAL_TAXON_TO_NAMERELATIONS, $taxon->uuid);
1389
  $name_relations = array_merge($from_name_relations, $to_name_relations);
1390
  return $name_relations;
1391
}
1392

    
1393

    
1394
/**
1395
 * Recursively searches the array for the $key and sets the given value.
1396
 *
1397
 * @param mixed $key
1398
 *   Key to search for.
1399
 * @param mixed $value
1400
 *   Value to set.'
1401
 * @param array $array
1402
 *   Array to search in.
1403
 *
1404
 * @return bool
1405
 *   True if the key has been found.
1406
 */
1407
function &array_setr($key, $value, array &$array) {
1408
  $res = NULL;
1409
  foreach ($array as $k => &$v) {
1410
    if ($key == $k) {
1411
      $v = $value;
1412
      return $array;
1413
    }
1414
    elseif (is_array($v)) {
1415
      $innerArray = array_setr($key, $value, $v);
1416
      if ($innerArray) {
1417
        return $array;
1418
      }
1419
    }
1420
  }
1421
  return $res;
1422
}
1423

    
1424
/**
1425
 * @todo Please document this function.
1426
 * @see http://drupal.org/node/1354
1427
 */
1428
function &get_preceding_contentElement($contentElementKey, array &$renderTemplate) {
1429
  $res = NULL;
1430
  $precedingElement = NULL;
1431
  foreach ($renderTemplate as &$part) {
1432
    foreach ($part as $key => &$element) {
1433
      if ($key == $contentElementKey) {
1434
        return $precedingElement;
1435
      }
1436
      $precedingElement = $element;
1437
    }
1438
  }
1439
  return $res;
1440
}
1441

    
1442
/**
1443
 * @todo Please document this function.
1444
 * @see http://drupal.org/node/1354
1445
 */
1446
function &get_preceding_contentElementKey($contentElementKey, array &$renderTemplate) {
1447
  $res = NULL;
1448
  $precedingKey = NULL;
1449
  foreach ($renderTemplate as &$part) {
1450
    if (is_array($part)) {
1451
      foreach ($part as $key => &$element) {
1452
        if ($key == $contentElementKey) {
1453
          return $precedingKey;
1454
        }
1455
        if (!str_beginsWith($key, '#')) {
1456
          $precedingKey = $key;
1457
        }
1458
      }
1459
    }
1460
  }
1461
  return $res;
1462
}
1463

    
1464
function nameTypeToDTYPE($dtype){
1465
  static $nameTypeLabelMap = array(
1466
    "ICNB" => "BacterialName",
1467
    "ICNAFP" => "BotanicalName",
1468
    "ICNCP" => "CultivarPlantName",
1469
    "ICZN" => "ZoologicalName",
1470
    "ICVCN" => "ViralName",
1471
    "Any taxon name" => "TaxonName",
1472
    "NonViral" => "TaxonName",
1473
    "Fungus" => "BotanicalName",
1474
    "Plant" => "BotanicalName",
1475
    "Algae" => "BotanicalName",
1476
  );
1477
  return $nameTypeLabelMap[$dtype];
1478

    
1479
}
1480

    
1481

    
1482
function compare_name_relations_by_term_order_index($name_rel1, $name_rel2){
1483
  return compare_terms_by_order_index($name_rel1->type, $name_rel2->type);
1484
}
1485

    
1486
/**
1487
 * Provides an array with the different registration types covered by the passed registration.
1488
 *
1489
 * The labels in the returned array are translatable.
1490
 *
1491
 * See also https://dev.e-taxonomy.eu/redmine/issues/8016
1492
 *
1493
 * @param $registration_dto
1494
 * @return array
1495
 *    An array of the labels describing the different registration types covered by the passed registration.
1496
 */
1497
function registration_types($registration_dto){
1498
  $reg_type_labels = array();
1499
  if(isset($registration_dto->nameRef)){
1500
    $reg_type_labels["name"] = t("new name");
1501
    $reg_type_labels["taxon"] = t("new taxon");
1502
    $name_relations = cdm_ws_fetch_all(str_replace("$0", $registration_dto->nameRef->uuid, CDM_WS_PORTAL_NAME_NAME_RELATIONS));
1503
    $is_new_combination = true;
1504
    foreach($name_relations as $name_rel){
1505
      if(isset($name_rel->type->uuid)){
1506
        $name_is_from_name = $registration_dto->nameRef->uuid == $name_rel->fromName->uuid;
1507
        switch($name_rel->type->uuid) {
1508
          case UUID_NAMERELATIONSHIPTYPE_BASIONYM:
1509
            if(!$name_is_from_name){
1510
              $reg_type_labels["basionym"] = t("new combination");
1511
              $is_new_combination = true;
1512
            }
1513
            break;
1514
          case UUID_NAMERELATIONSHIPTYPE_REPLACED_SYNONYM:
1515
            if(!$name_is_from_name) {
1516
              $is_new_combination = true;
1517
            }
1518
            break;
1519
          case UUID_NAMERELATIONSHIPTYPE_VALIDATED_BY_NAME:
1520
            if(!$name_is_from_name) {
1521
              $reg_type_labels["validation"] = t("validation");
1522
            }
1523
            break;
1524
          case UUID_NAMERELATIONSHIPTYPE_ORTHOGRAPHIC_VARIANT:
1525
            if(!$name_is_from_name) {
1526
              $reg_type_labels["orth_var"] = t("orthographical correction");
1527
            }break;
1528
          default:
1529
            // NOTHING
1530
        }
1531
      }
1532
    }
1533
    if($is_new_combination){
1534
      unset($reg_type_labels["taxon"]);
1535
    }
1536
  }
1537
  if(isset($registration_dto->orderdTypeDesignationWorkingSets)){
1538
    $reg_type_labels[] = t("new nomenclatural type");
1539
  }
1540
  return $reg_type_labels;
1541
}
1542

    
1543
/**
1544
 * Collects and deduplicates the type designations associated with the passes synonyms.
1545
 *
1546
 * @param $synonymy_group
1547
 *    An array containing a homotypic or heterotypic group of names.
1548
 * @param $accepted_taxon_name_uuid
1549
 *    The uuid of the accepted taxon name. Optional parameter which is required when composing
1550
 *    the information for the homotypic group. In this case the accepted taxon is not included
1551
 *    in the $synonymy_group and must therefor passed in this second parameter.
1552
 *
1553
 * @return array
1554
 *    The type designations
1555
 */
1556
function type_designations_for_synonymy_group($synonymy_group, $accepted_taxon_name_uuid = null)
1557
{
1558
  if (count($synonymy_group) > 0) {
1559
    $name_uuid = array_pop($synonymy_group)->name->uuid;
1560
  } else {
1561
    $name_uuid = $accepted_taxon_name_uuid;
1562
  }
1563
  if ($name_uuid) {
1564
   $type_designations = cdm_ws_get(CDM_WS_PORTAL_NAME_TYPEDESIGNATIONS_IN_HOMOTYPICAL_GROUP, $name_uuid);
1565
    if ($type_designations) {
1566
      return $type_designations;
1567
    }
1568
  }
1569

    
1570
  return array();
1571
}
1572

    
1573

    
1574
/**
1575
 * Compares the status of two SpecimenTypeDesignations
1576
 *
1577
 * @param object $a
1578
 *   A SpecimenTypeDesignation.
1579
 * @param object $b
1580
 *   SpecimenTypeDesignation.
1581
 */
1582
function compare_specimen_type_designation($a, $b) {
1583

    
1584
  $type_status_order = type_status_order();
1585

    
1586

    
1587
  $aQuantifier = FALSE;
1588
  $bQuantifier = FALSE;
1589
  if (isset($a->typeStatus->titleCache) && isset($b->typeStatus->titleCache)) {
1590
    $aQuantifier = array_search($a->typeStatus->titleCache, $type_status_order);
1591
    $bQuantifier = array_search($b->typeStatus->titleCache, $type_status_order);
1592
  }
1593
  if ($aQuantifier == $bQuantifier) {
1594
    // Sort alphabetically.
1595
    $a_text =  isset($a->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $a->typeSpecimen->titleCache) : '';
1596
    $b_text =  isset($b->typeSpecimen->titleCache) ? preg_replace('/[\[\]\"]/', '', $b->typeSpecimen->titleCache) : '';
1597
    return strcasecmp($a_text, $b_text);
1598
  }
1599
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1600
}
1601

    
1602
/**
1603
 * Compares the status of two SpecimenTypeDesignations
1604
 *
1605
 * @param object $a
1606
 *   A TypeDesignationStatusBase.
1607
 * @param object $b
1608
 *   TypeDesignationStatusBase.
1609
 */
1610
function compare_type_designation_status($a, $b) {
1611

    
1612
  $type_status_order = type_status_order();
1613

    
1614

    
1615
  $aQuantifier = FALSE;
1616
  $bQuantifier = FALSE;
1617
  if (isset($a->label) && isset($b->label)) {
1618
    $aQuantifier = array_search($a->label, $type_status_order);
1619
    $bQuantifier = array_search($b->label, $type_status_order);
1620
  }
1621
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1622
}
1623

    
1624

    
1625
/**
1626
 * Compares two SpecimenTypeDesignation status labels
1627
 *
1628
 * @param string $a
1629
 *   A TypeDesignationStatus label.
1630
 * @param string $b
1631
 *   A TypeDesignationStatus label.
1632
 */
1633
function compare_type_designation_status_labels($a, $b) {
1634

    
1635
  $type_status_order = type_status_order();
1636

    
1637

    
1638
  $aQuantifier = FALSE;
1639
  $bQuantifier = FALSE;
1640
  if (isset($a) && isset($b)) {
1641
    $aQuantifier = array_search($a, $type_status_order);
1642
    $bQuantifier = array_search($b, $type_status_order);
1643
  }
1644
  return ($aQuantifier < $bQuantifier) ? -1 : 1;
1645
}
1646

    
1647
/**
1648
 * @return array
1649
 */
1650
function type_status_order()
1651
{
1652
  /*
1653
    This is the desired sort order as of now: Holotype Isotype Lectotype
1654
    Isolectotype Syntype.
1655
    TODO Basically, what we are trying to do is, we define
1656
    an ordered array of TypeDesignation-states and use the index of this array
1657
    for comparison. This array has to be filled with the cdm- TypeDesignation
1658
    states and the order should be parameterisable inside the dataportal.
1659
    */
1660
  // Make that static for now.
1661
  $type_status_order = array(
1662
    'Epitype',
1663
    'Holotype',
1664
    'Isotype',
1665
    'Lectotype',
1666
    'Isolectotype',
1667
    'Syntype',
1668
    'Paratype'
1669
  );
1670
  return $type_status_order;
1671
}
(6-6/13)