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cdm-dataportal / modules / cdm_dataportal / includes / taxon.inc @ 23ebb91f

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<?php
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3
/**
4
 * @file
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 * Functions for dealing with CDM entities from the package model.taxon
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 *
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 * @copyright
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 *   (C) 2007-2016 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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 */
19

    
20
/**
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 * @defgroup compose Compose functions
22
 * @{
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 * Functions which are composing Drupal render arrays
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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.
31
 * @}
32
 */
33

    
34
define('TAXON_TYPE_SYNONYM', 'Synonym');
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define('TAXON_TYPE_MISAPPLIEDNAME', 'misapplied-name');
36

    
37
/**
38
 * Returns HTML for misapplied names and invalid designations.
39
 *
40
 * Both relation types are currently treated the same!
41
 *
42
 * @param object taxonRelationships
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 *   A TaxonRelationshipsDTO, see taxon/{uuid}/taxonRelationshipsDTO
44
 *
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 * @param object focusedTaxon
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 *  The taxon being in the focus of the application
47
 *
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 * @return string
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 *    the rendered html
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 */
51
function cdm_taxonRelationships($taxonRelationshipsDTO, $focusedTaxon){
52

    
53
  if (!$taxonRelationshipsDTO || $taxonRelationshipsDTO->size < 1) {
54
    return null;
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  }
56

    
57
  RenderHints::pushToRenderStack('taxon_relationships');
58
  $footnote_list_key = 'taxon_relationships';
59
  RenderHints::setFootnoteListKey($footnote_list_key);
60

    
61
  $misapplied = array();
62
  $joined_refs = array();
63

    
64
  $taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));
65

    
66
  // Aggregate misapplied names having the same fullname:
67
  //  - deduplicate misapplied names, so that the same name it not shown multiple times in case it
68
  //    the duplicates only have different sensu references/author teams (see #5647)
69
  //  - show only the author team as short citation for the sec reference
70
  //  - show the according reference as footnote to this short citation
71
  //
72
  // Example:
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  // "Xenoxylum foobar" sensu Grumbach¹; sensu Lem²
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  //    1. Novel marsian species, Grumbach, 2022
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  //    2. Flora solaris, Lem, 2019
76
  if (isset($taxonRelationshipsDTO->relations[0])) {
77
    foreach($taxonRelationshipsDTO->relations as $taxon_relation){
78

    
79
      if (in_array($taxon_relation->type->uuid, $taxon_relationship_types)) {
80

    
81
        if ($taxon_relation->type->uuid == UUID_MISAPPLIED_NAME_FOR || $taxon_relation->type->uuid == UUID_INVALID_DESIGNATION_FOR) {
82

    
83
          RenderHints::pushToRenderStack('misapplied_name_for'); // TODO the render path string should in future come from $taxonRelation->type->...
84

    
85
          // full name with relation symbol, rel sec as de-dublication key
86
          // the sensu part will be removed from the key below in case it is present
87
          $symbol_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('symbol')));
88
          $name_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('name')));
89
          $appended_phrase_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('appendedPhrase')));
90

    
91
          $full_name_key = cdm_tagged_text_to_string($taxon_relation->taggedText, array('symbol', 'appendedPhrase'));
92
          $full_name_key = $name_text . ' ' . str_replace($name_text, '', $full_name_key) . ' ' . $symbol_text;
93

    
94
          // remove/extract appendedPhrase, secReference, relSecReference and add placeholders if needed
95
          tagged_text_extract($taxon_relation->taggedText, 'appendedPhrase');
96
          $sensu_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "secReference", true);
97
          $relsec_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "relSecReference", true);
98

    
99
          if (isset($sensu_tagged_text[1])) {
100
            // for de-dublicationeverything else needs to be equal except for appendedPhrase + MAN.sec + MAN.secDetail. see #7658#note-21
101
            $full_name_key = str_replace(cdm_tagged_text_to_string($sensu_tagged_text), ' ', $full_name_key);
102
            $appended_phrase_text = $appended_phrase_text . array_shift($sensu_tagged_text)->text; // remove first element which contains the "sensu", this will be added later in this code
103
            $sensu_citation_detail = trim(join(' ', cdm_tagged_text_values($sensu_tagged_text, array('secMicroReference'))));
104
            $sensu_citation_short_markup = cdm_tagged_text_to_markup($sensu_tagged_text);
105
            $sensu_citation_short = cdm_tagged_text_to_string($sensu_tagged_text);
106
            $sensu_uuid = $sensu_tagged_text[0]->entityReference->uuid;
107
            $full_name_key = preg_replace('/\s+/', ' ', $full_name_key); // sanitize multiple whitespace characters
108
            $misapplied[$full_name_key]['sensu_uuids'][] = array('uuid' => $sensu_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $sensu_citation_detail);
109
            $ref_key = $sensu_uuid .($sensu_citation_detail ? '#' . $sensu_citation_detail : '');
110
            if (!isset($joined_refs[$ref_key])) {
111
              $joined_refs[$ref_key] = array(
112
                'order_by_key' => $sensu_citation_short,
113
                'markup' => $sensu_citation_short_markup // the footnote key will be appended later
114
              );
115
            }
116
          } else if($appended_phrase_text) {
117
            // appended phrase without reference
118
            $full_name_key = preg_replace('/\s+/', ' ', $full_name_key); // sanitize multiple whitespace characters
119
            $misapplied[$full_name_key]['sensu_uuids'][] = array('uuid' => null, 'prefix' => $appended_phrase_text);
120
          }
121

    
122
          if (isset($relsec_tagged_text[1])) {
123
            array_shift($relsec_tagged_text); // remove first element which contains the "err. sec", this will be added later in this code
124
            $relsec_citation_detail = trim(join(' ', cdm_tagged_text_values($relsec_tagged_text, array('secMicroReference'))));
125
            $relsec_citation_short_markup = cdm_tagged_text_to_markup($relsec_tagged_text);
126
            $relsec_citation_short = cdm_tagged_text_to_string($relsec_tagged_text);
127
            $relsec_uuid = $relsec_tagged_text[0]->entityReference->uuid;
128
            $misapplied[$full_name_key]['relsec_uuids'][] = $relsec_uuid;
129
            $ref_key = $relsec_uuid . ($relsec_citation_detail ? '#' . $relsec_citation_detail : '');
130
            if (!isset($joined_refs[$ref_key])) {
131
              $joined_refs[$ref_key] = array(
132
                'order_by_key' => $relsec_citation_short,
133
                'markup' => $relsec_citation_short_markup // the footnote key will be appended later
134
              );
135
            }
136
          }
137

    
138
          if (!isset($misapplied[$full_name_key]['out'])) {
139
            $misapplied[$full_name_key]['out'] = cdm_tagged_text_to_markup($taxon_relation->taggedText);
140
          } else {
141
            // We need to add the anchors for all of the other misapplied names not
142
            // being rendered explicitly.
143
            $misapplied[$full_name_key]['out'] = uuid_anchor($taxon_relation->taxonUuid, $misapplied[$full_name_key]['out']);
144
          }
145
        } else {
146
          RenderHints::pushToRenderStack('other_taxon_relationship');
147
          // All relationship types except misapplied_name_for and invalid_designation_for.
148
          $taxon_relationships_lines[] = cdm_taxonRelationship($taxon_relation, TRUE, _is_invers_taxonRelationship($taxon_relation, $focusedTaxon));
149
        }
150
        RenderHints::popFromRenderStack();
151
      }
152
    } // END loop over $taxonRelationshipsDTO->relations
153
  }
154

    
155
  // Sort the $joined_refs and create footnotes and footnote keys.
156
  uasort($joined_refs, function($a, $b) {
157
    if ($a['order_by_key'] == $b['order_by_key']) {
158
      return 0;
159
    }
160
    return ($a['order_by_key'] < $b['order_by_key']) ? -1 : 1;
161
  });
162

    
163

    
164
  foreach ($joined_refs as $ref_key => $sensu_strings) {
165
    if(!empty($sensu_strings)) {
166
      $ref_key_tokens = explode('#', $ref_key);
167
      $sensu_uuid = $ref_key_tokens[0];
168
      $sensu_reference = cdm_ws_get(CDM_WS_REFERENCE, $sensu_uuid);
169
      if(!$sensu_reference){
170
        drupal_set_message("Problem fetching sensu reference with uuid " . $sensu_uuid, 'error');
171
      }
172
      if($sensu_strings['order_by_key'] != $sensu_reference->titleCache){
173
        $footnote_key = FootnoteManager::addNewFootnote($footnote_list_key, $sensu_reference->titleCache);
174
        $footnote_key = theme('cdm_footnote_key', array('footnoteKey' => $footnote_key));
175
        $joined_refs[$ref_key]['markup'] = '<span class="sensu">' . $sensu_strings['markup'] . $footnote_key . '</span>';
176
      }
177
    }
178
  }
179

    
180
  // ---- Generate output ---- //
181
  $out = '<div class="taxon-relationships">';
182
  if (count($misapplied) > 0) {
183
    ksort($misapplied); // order the misapplied by scientific name
184
    $out .= '<ul class="misapplied">';
185

    
186
    // create the list entries per misapplied name
187
    foreach ($misapplied as $misapplied_name) {
188
      $misapplied_name_markup = $misapplied_name['out'];
189
      // all sensu and auct. for this MAN
190
      if (isset($misapplied_name['sensu_uuids'])) {
191
        $sensu_refs_with_fkey = array();
192
        foreach ($misapplied_name['sensu_uuids'] as $sensu_data) {
193
          if($sensu_data['uuid']){
194
            $joined_ref_key = $sensu_data['uuid'] . ($sensu_data['citation_detail'] ? '#' .  $sensu_data['citation_detail'] : '');
195
            $sensu_refs_with_fkey[$sensu_data['prefix'] . $joined_refs[$joined_ref_key]['order_by_key']] = $sensu_data['prefix'] . $joined_refs[$joined_ref_key]['markup'];
196
          } else {
197
            $sensu_refs_with_fkey[$sensu_data['prefix']] = $sensu_data['prefix'];
198
          }
199
        }
200
        ksort($sensu_refs_with_fkey);
201
        $sensu_refs_with_fkey_markup = join('; ', $sensu_refs_with_fkey);
202
        $misapplied_name_markup = str_replace('{PLACEHOLDER_secReference}', $sensu_refs_with_fkey_markup, $misapplied_name_markup);
203
      }
204

    
205
      // append the err. sec. if there is any for this MAN
206
      if (isset($misapplied_name['relsec_uuids'])) {
207
        $relsec_refs_with_fkey = array();
208
        foreach ($misapplied_name['relsec_uuids'] as $relsec_uuid) {
209
          $relsec_refs_with_fkey[$joined_refs[$relsec_uuid]['order_by_key']] = $joined_refs[$relsec_uuid]['markup'];
210
        }
211
        ksort($relsec_refs_with_fkey);
212
        $relsec_refs_with_fkey_markup = join('; ', $relsec_refs_with_fkey);
213
        $misapplied_name_markup = str_replace('{PLACEHOLDER_relSecReference}', ', err. sec. ' . $relsec_refs_with_fkey_markup, $misapplied_name_markup);
214
      }
215
      // final line
216
      $out .= '<li class="synonym"><span class="misapplied">' . $misapplied_name_markup . ' </span></li>';
217
    }
218
    $out .= '</ul>';
219
  }
220

    
221
  if (isset($taxon_relationships_lines) && is_array($taxon_relationships_lines) && count($taxon_relationships_lines) > 0) {
222
    $out .= '<ul class="taxonRelationships">';
223
    foreach ($taxon_relationships_lines as $taxon_relationship_line) {
224
      $out .= '<li class="synonym">' . $taxon_relationship_line . '</li>';
225
    }
226
    $out .= '</ul>';
227
  }
228

    
229
  $footnotes = theme('cdm_footnotes', array('footnoteListKey' => $footnote_list_key, 'enclosingTag' => 'li'));
230
  $footnotes .= theme('cdm_annotation_footnotes', array('footnoteListKey' => $footnote_list_key, 'enclosingTag' => 'li'));
231

    
232
  $out .= '<ul class="footnotes">' . $footnotes . '</ul>';
233
  $out .= '</div>';
234

    
235
  RenderHints::popFromRenderStack();
236
  return $out;
237
}
238

    
239

    
240
/**
241
 * Renders a representation of the given taxon relationship.
242
 *
243
 * According name relationships are also being rendered.
244
 *
245
 * @param $taxonRelationship
246
 * @param boolean $doLinkTaxon
247
 *     whether to create a link to the related taxon
248
 * @param boolean $inverse
249
 *     whether the $taxonRelationship should be treaded as invers relation
250
 *
251
 * @return string
252
 *
253
 */
254
function cdm_taxonRelationship($taxonRelationship, $doLinkTaxon = FALSE, $inverse = FALSE) {
255

    
256
  // Validate object.
257
  if (!(isset($taxonRelationship->toTaxon) && isset($taxonRelationship->fromTaxon) && isset($taxonRelationship->type))) {
258
    return null;
259
  }
260

    
261
  $taxonRelationType = $taxonRelationship->type;
262

    
263
  if ($inverse) {
264
    $toTaxon = $taxonRelationship->fromTaxon;
265
    $relsign = $taxonRelationType->inverseSymbol;
266
    $reltype_representation = $taxonRelationType->inverseRepresentation_L10n;
267
  }
268
  else {
269
    $toTaxon = $taxonRelationship->toTaxon;
270
    $relsign = $taxonRelationType->symbol;
271
    $reltype_representation = $taxonRelationType->representation_L10n;
272
  }
273

    
274
  return cdm_related_taxon($toTaxon, NULL, $relsign, $reltype_representation, $taxonRelationship->doubtful, $doLinkTaxon);
275
}
276

    
277
/**
278
 * Renders a representation of the given taxon relationship.
279
 *
280
 * According name relationships are also being rendered.
281
 *
282
 * @param $taxon
283
 *  The CDM TaxonBase entity
284
 * @param $reltype_uuid
285
 *  The UUID of the TaxonRelationshipType
286
 * @param $relsign
287
 *  Optional. Can be  used to override the internal decision strategy on finding a suitable icon for the relationship
288
 * @param $reltype_representation
289
 *   Optional: Defines the value for the title attribute of the html element enclosing the relsign
290
 * @param $doubtful
291
 *   TODO
292
 * @param $doLinkTaxon
293
 *   The taxon will be rendered as clickable link when true.
294
 *
295
 * @return string
296
 *   Markup for the taxon relationship.
297
 *
298
 * @throws Exception
299
 */
300
function cdm_related_taxon($taxon, $reltype_uuid = NULL, $relsign = NULL, $reltype_representation = NULL, $doubtful=false, $doLinkTaxon = FALSE) {
301
  static $relsign_homo = '≡';
302
  static $relsign_hetero = '=';
303
  static $relsign_invalid = '&ndash;';
304
  static $nom_status_invalid_type_uuids =  array(
305
    UUID_NOMENCLATURALSTATUS_TYPE_INVALID,
306
    UUID_NOMENCLATURALSTATUS_TYPE_NUDUM,
307
    UUID_NOMENCLATURALSTATUS_TYPE_COMBINATIONINVALID,
308
    UUID_NOMENCLATURALSTATUS_TYPE_PROVISIONAL
309
  );
310

    
311
  // 'taxonRelationships';
312
  $footnoteListKey = NULL;
313

    
314
  $skip_tags = array();
315

    
316
  $is_invalid = false;
317

    
318
  if (!$relsign) {
319

    
320
    switch ($reltype_uuid) {
321
      case UUID_HETEROTYPIC_SYNONYM_OF:
322
      case UUID_SYNONYM_OF:
323
        $relsign = $relsign_hetero;
324
        break;
325

    
326
      case UUID_HOMOTYPIC_SYNONYM_OF:
327
        $relsign = $relsign_homo;
328
        break;
329

    
330
      case UUID_MISAPPLIED_NAME_FOR:
331
      case UUID_INVALID_DESIGNATION_FOR:
332
        $skip_tags[] = 'authors';
333
        $is_invalid = true;
334
        $relsign = $relsign_invalid;
335

    
336
        break;
337

    
338
      default:
339
        $relsign = $relsign_invalid;
340
    }
341

    
342
  }
343

    
344
  if($doubtful) {
345
    $relsign = '?' . $relsign;
346
  }
347

    
348
  /*
349
  Names with status invalid or nudum are to be displayed with the
350
  $relsign_invalid, these names appear at the end of all names in their
351
  homotypic group (ordered correctly by the java cdm_lib).
352
  */
353
  if (isset($taxon->name->status) && is_array($taxon->name->status)) {
354
    foreach ($taxon->name->status as $status) {
355
      if (in_array($status->type->uuid , $nom_status_invalid_type_uuids)) {
356
        $relsign = $relsign_invalid;
357
        break;
358
      }
359
    }
360
  }
361

    
362
  // Now rendering starts ..
363
  RenderHints::pushToRenderStack('related_taxon');
364

    
365
  if (isset($taxon->name->nomenclaturalReference)) {
366
    $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
367
  }
368
  $taxonUri = '';
369
  if ($doLinkTaxon) {
370
    $taxonUri = url(path_to_taxon($taxon->uuid, "synonymy"));
371
  }
372
  // Printing the taxonName and the handling the special case of annotations.
373
  if (!isset($referenceUri)) {
374
    $referenceUri = FALSE;
375
  }
376
  $out_taxon_part = render_taxon_or_name($taxon, $taxonUri, $referenceUri, TRUE, FALSE, $skip_tags, $is_invalid);
377
  $taxon_footnotes = theme('cdm_annotations_as_footnotekeys',
378
    array('cdmBase_list' => array(
379
      $taxon->name,
380
      $taxon,
381
    ),
382
      'footnote_list_key' => $footnoteListKey)
383
  );
384

    
385
  $homonyms = cdm_name_relationships_of($taxon);
386

    
387
  $out = '<span class="relation_sign" title="' . $reltype_representation . '">' . $relsign . '</span>'
388
    . $out_taxon_part . $taxon_footnotes . ' '  . $homonyms;
389

    
390
  $out = uuid_anchor($taxon->uuid, $out);
391

    
392
  RenderHints::popFromRenderStack();
393

    
394
  return $out;
395
}
396

    
397

    
398
/**
399
 * Creates markup for a taxon which is the accepted of another one
400
 *
401
 * @param $accepted_for_uuid
402
 *   The uuid of the accepted taxon
403
 */
404
function cdm_accepted_for($accepted_for_uuid) {
405

    
406
  if(!is_uuid($accepted_for_uuid)){
407
    return '';
408
  }
409

    
410
  RenderHints::pushToRenderStack('acceptedFor');
411
  $out = '';
412

    
413
  $synonym = cdm_ws_get(CDM_WS_PORTAL_TAXON, $accepted_for_uuid);
414
  if ($synonym) {
415
    $out .= '<span class="acceptedFor">';
416
    $out .= t('is accepted for ');
417
    if (isset($synonym->name->nomenclaturalReference)) {
418
      $referenceUri = url(path_to_reference($synonym->name->nomenclaturalReference->uuid));
419
    }
420
    $out .= render_taxon_or_name($synonym->name, NULL, $referenceUri);
421
    $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $synonym));
422
    $out .= '</span>';
423
  }
424
  RenderHints::popFromRenderStack();
425
  return $out;
426
}
427

    
428
/**
429
 * Compose function for a list of taxa.
430
 *
431
 * This function is for used to:
432
 *
433
 * 1. Display search results
434
 * 2. List the taxa for a taxon name in the name page.
435
 *
436
 * @param $taxon_list array
437
 *   The list of CDM Taxon entities. e.g. The records array as contained in a pager object.
438
 * @param $freetext_search_results array
439
 * @param $show_classification boolean
440
 *
441
 * @ingroup compose
442
 *
443
 */
444
function compose_list_of_taxa($taxon_list, $freetext_search_results = array(), $show_classification = false) {
445

    
446
  $unclassified_snippet = '<span class="unclassified">' . t('unclassified') . '</span>';
447

    
448
  RenderHints::pushToRenderStack('list_of_taxa');
449

    
450
  $gallery_settings = getGallerySettings(CDM_DATAPORTAL_SEARCH_GALLERY_NAME);
451

    
452
  $showMedia_taxa = $gallery_settings['cdm_dataportal_show_taxon_thumbnails'];
453
  $showMedia_synonyms = $gallery_settings['cdm_dataportal_show_synonym_thumbnails'];
454
  $searched_in_classification = cdm_dataportal_searched_in_classification();
455
  $searched_in_classification_uuid = null;
456
  if(isset($searched_in_classification->uuid)){
457
    $searched_in_classification_uuid = $searched_in_classification->uuid;
458
  }
459

    
460
  // .. Well, for sure not as performant as before, but better than nothing.
461
  $synonym_uuids = array();
462
  $misappied_uuids = array();
463
  foreach ($taxon_list as $taxon) {
464
    if ($taxon->class == "Synonym") {
465
      if (!array_key_exists($taxon->uuid, $synonym_uuids)) {
466
        $synonym_uuids[$taxon->uuid] = $taxon->uuid;
467
      }
468
    }
469
    elseif (!_cdm_dataportal_acceptedByCurrentView($taxon)) {
470
      // Assuming that it is a misappied name, will be further examined below.
471
      $misappied_uuids[$taxon->uuid] = $taxon->uuid;
472
    }
473
  }
474

    
475
  // Batch service not jet implemented:
476
  // $table_of_accepted = cdm_ws_property(CDM_WS_PORTAL_TAXON_ACCEPTED,
477
  // join(',', $synonym_uuids));
478
  // thus ...
479
  $table_of_accepted = array();
480

    
481
  foreach ($synonym_uuids as $relatedUuid) {
482
    $classification_filter = '';
483
    if($searched_in_classification_uuid){
484
      $classification_filter = 'classificationFilter=' . $searched_in_classification_uuid;
485
    }
486
    $table_of_accepted[$relatedUuid] = cdm_ws_get(
487
      CDM_WS_PORTAL_TAXON_ACCEPTED,
488
      array($relatedUuid),
489
      $classification_filter
490
    );
491
  }
492

    
493
  foreach ($misappied_uuids as $relatedUuid) {
494
    $taxonRelations = cdm_ws_get(CDM_WS_PORTAL_TAXON_RELATIONS, array(
495
      $relatedUuid,
496
    ));
497
    foreach ($taxonRelations as $relation) {
498
      if ($relation->type->uuid == UUID_MISAPPLIED_NAME_FOR && _cdm_dataportal_acceptedByCurrentView($relation->toTaxon)) {
499
        $table_of_accepted[$relatedUuid][] = $relation->toTaxon;
500
      }
501
    }
502
  }
503

    
504
  $out = '<div class="cdm-item-list" style="background-image: none;">';
505
  $itemCnt = -1;
506
  foreach ($taxon_list as $taxon) {
507
    $itemCnt++;
508
    if (isset($table_of_accepted[$taxon->uuid])) {
509
      // Its a synonym or misapplied name.
510
      $is_synonym = isset($synonym_uuids[$taxon->uuid]); //TODO better use the $taxon->class attribute?
511
      $taxon_type = $is_synonym ? TAXON_TYPE_SYNONYM :TAXON_TYPE_MISAPPLIEDNAME;
512

    
513
      $acceptedTaxa = $table_of_accepted[$taxon->uuid];
514

    
515
      if (!is_array($acceptedTaxa)) {
516
        $acceptedTaxa = array($acceptedTaxa);
517
      }
518

    
519
      foreach ($acceptedTaxa as $acceptedTaxon) {
520
        if (is_object($acceptedTaxon)) {
521

    
522
          $taxonUri = uri_to_synonym($taxon->uuid, $acceptedTaxon->uuid);
523
          $referenceUri = '';
524
          if (isset($acceptedTaxon->name->nomenclaturalReference)) {
525
            $referenceUri = url(path_to_reference($acceptedTaxon->name->nomenclaturalReference->uuid));
526
          }
527
          $taxon_or_name = $is_synonym ? $taxon->name : $taxon;
528
          // $taxon_or_name this is a trick to suppress the sec reference for synonyms
529
          // supplying the name will cause render_taxon_or_name() to not show the sec reference
530
          $out .= "<div class=\"item " . $taxon_type . "\">" . render_taxon_or_name($taxon_or_name, $taxonUri, $referenceUri);
531
          if($taxon_type == TAXON_TYPE_MISAPPLIEDNAME && is_object($taxon->sec)){
532
            if(isset($taxon->sec->authorship)){
533
              $authorship = $taxon->sec->authorship->titleCache;
534
            } else {
535
              $authorship = $taxon->sec->titleCache;
536
            }
537
            $out .=  ' sensu ' . $authorship;
538
          }
539
          if ($show_classification) {
540
            $classifications = get_classifications_for_taxon($taxon);
541
            $classification_titles = array();
542
            foreach ($classifications as $classification) {
543
              if (isset($classification->titleCache)) {
544
                $classification_titles[] = $classification->titleCache;
545
              }
546
            }
547
            if (count($classification_titles) == 0) {
548
              $classification_titles[] = $unclassified_snippet;
549
            }
550
            $out .= '<span class="classifications"><span class="separator"> : </span>' . implode(', ', $classification_titles) . '</span>';
551
          }
552
          $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));
553
          if ($showMedia_synonyms) {
554
            $out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $acceptedTaxon));
555
          }
556
        }
557
      }
558
    }
559
    else {
560
      // Its a Taxon.
561
      $taxonUri = url(path_to_taxon($taxon->uuid));
562
      $referenceUri = '';
563
      if (isset($taxon->name->nomenclaturalReference)) {
564
        $referenceUri = url(path_to_reference($taxon->name->nomenclaturalReference->uuid));
565
      }
566
      $out .= '<div class="item Taxon">' . render_taxon_or_name($taxon, $taxonUri, $referenceUri);
567
      if ($show_classification) {
568
        $classifications = get_classifications_for_taxon($taxon);
569
        $classification_titles = array();
570
        foreach ($classifications as $classification) {
571
          if (isset($classification->titleCache)) {
572
            $classification_titles[] = $classification->titleCache;
573
          }
574
        }
575
        if(count($classification_titles) == 0){
576
          $classification_titles[] = $unclassified_snippet;
577
        }
578
        $out .= '<span class="classifications"><span class="separator"> : </span>' . implode(', ', $classification_titles) . '</span>';
579
      }
580
      $out .= theme('cdm_annotations_as_footnotekeys', array('cdmBase_list' => $taxon));
581

    
582
      if ($showMedia_taxa) {
583
        $out .= theme('cdm_taxon_list_thumbnails', array('taxon' => $taxon));
584
      }
585
    }
586

    
587
    /*
588
     * the score field will be empty in case of MultiTermQueries like
589
     * WildcardQueries, since these are  constant score by default
590
     * since Lucene 2.9
591
     */
592
    if(isset($freetext_search_results[$itemCnt]) && $freetext_search_results[$itemCnt]->score && $freetext_search_results[$itemCnt]->maxScore){
593
      $percentage =  ( $freetext_search_results[$itemCnt]->score / $freetext_search_results[$itemCnt]->maxScore ) * 100;
594
      $out .= '<div class="score-bar"><div class="score-bar-indicator" style="width:' . $percentage .'% "></div></div>';
595
      $out .= '<div class="score-bar-value">' . number_format($percentage, 2) .'%</div>';
596
    }
597

    
598
    // Render highlighted fragments, these are made available by free text
599
    // searches.
600
    if (isset($freetext_search_results[$itemCnt]->fieldHighlightMap)) {
601
      $field_fragments = (array) $freetext_search_results[$itemCnt]->fieldHighlightMap;
602
      if (count($field_fragments) > 0) {
603
        $fragments_out = '';
604
        foreach ($field_fragments as $fieldName => $fragments) {
605
          $fragments_out .= '... <span class="' . $fieldName. '">' . filter_xss(join(" ... ", $fragments), array('b') ) . '</span>';
606
        }
607
        $out .= '<div class="fragment_highlight">' . $fragments_out . ' ...</div>';
608
      }
609
    }
610

    
611
    $out .= '</div>';
612
  }
613

    
614
  $out .= '</div>';
615
  RenderHints::popFromRenderStack();
616

    
617
  return markup_to_render_array($out); // TODO create render array of all list items in function
618
}
619

    
620

    
621
/**
622
 * Compose function for the taxonomic children
623
 *
624
 * @param $taxon_uuid
625
 *    The uuuid of the taxon to compose the list of taxonomic children for
626
 * @return
627
 *   A drupal render array.
628
 *
629
 * @ingroup compose
630
 */
631
function compose_taxonomic_children($taxon_uuid){
632

    
633
  $render_array = array();
634
  
635
  if($taxon_uuid) {
636
    $children = cdm_ws_get(CDM_WS_PORTAL_TAXONOMY_CHILDNODES_OF_TAXON, array(
637
      get_current_classification_uuid(),
638
      $taxon_uuid
639
      ));
640
    if($children){
641
      $taxonomic_children = theme('cdm_taxontree', array('tree' => $children));
642
      $render_array = markup_to_render_array($taxonomic_children);
643
    }
644
  }
645
  return $render_array;
646
}
647

    
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