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Revision a9dc4b35

IDa9dc4b353dbea33629ba384ae3c319f225a03956
Parent 31ab4cf9
Child a0557101

Added by Andreas Kohlbecker about 3 years ago

ref #7658 other relationship reprentation based on DTOs fully implemented

View differences:

modules/cdm_dataportal/includes/taxon.inc
65 65

  
66 66
  // Aggregate misapplied names having the same fullname:
67 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)
68
  //    the duplicates only have different sensu references with detail and appended phrase (see #5647)
69 69
  //  - show only the author team as short citation for the sec reference
70 70
  //  - show the according reference as footnote to this short citation
71 71
  //
......
82 82

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

  
85
          // full name with relation symbol, rel sec as de-dublication key
85
          // full name with relation symbol, rel sec as de-duplication key
86 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 87
          $name_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('name')));
89
          $appended_phrase_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('appendedPhrase')));
90

  
91 88
          $full_name_key = cdm_tagged_text_to_string($taxon_relation->taggedText, array('symbol', 'appendedPhrase'));
89
          $symbol_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('symbol')));
92 90
          $full_name_key = $name_text . ' ' . str_replace($name_text, '', $full_name_key) . ' ' . $symbol_text;
93 91

  
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' => $appended_phrase_text);
120
          }
92
          cdm_taxonRelationships_process_relationship_dto($taxon_relation, $misapplied, $joined_refs, $full_name_key);
121 93

  
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
          }
94
          RenderHints::popFromRenderStack();
145 95
        } else {
146 96
          RenderHints::pushToRenderStack('other_taxon_relationship');
147 97
          // All relationship types except misapplied_name_for and invalid_designation_for.
148 98

  
149 99
          $taxon_relationships_lines[] = cdm_tagged_text_to_markup($taxon_relation->taggedText);
100

  
101
          RenderHints::popFromRenderStack();
150 102
        }
151
        RenderHints::popFromRenderStack();
152 103
      }
153 104
    } // END loop over $taxonRelationshipsDTO->relations
105

  
154 106
  }
155 107

  
156 108
  // Sort the $joined_refs and create footnotes and footnote keys.
......
206 158
      // append the err. sec. if there is any for this MAN
207 159
      if (isset($misapplied_name['relsec_uuids'])) {
208 160
        $relsec_refs_with_fkey = array();
209
        foreach ($misapplied_name['relsec_uuids'] as $relsec_uuid) {
210
          $relsec_refs_with_fkey[$joined_refs[$relsec_uuid]['order_by_key']] = $joined_refs[$relsec_uuid]['markup'];
161
        foreach ($misapplied_name['relsec_uuids'] as $relsec_data) {
162
          if($relsec_data['uuid']) {
163
            $relsec_refs_with_fkey[$relsec_data['prefix'] . $joined_refs[$relsec_data['uuid']]['order_by_key']] = $relsec_data['prefix'] . $joined_refs[$relsec_data['uuid']]['markup'];
164
          }
211 165
        }
212 166
        ksort($relsec_refs_with_fkey);
213 167
        $relsec_refs_with_fkey_markup = join('; ', $relsec_refs_with_fkey);
......
238 192
}
239 193

  
240 194
/**
195
 * @param $taxon_relation
196
 * @param $name_dedup_key
197
 * @param $misapplied
198
 * @param $joined_refs
199

  
200
 */
201
function cdm_taxonRelationships_process_relationship_dto($taxon_relation, &$misapplied, &$joined_refs, $name_dedup_key = null) {
202
  $appended_phrase_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('appendedPhrase')));
203
  // remove/extract appendedPhrase, secReference, relSecReference and add placeholders if needed
204
  tagged_text_extract($taxon_relation->taggedText, 'appendedPhrase');
205
  $sensu_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "secReference", true);
206
  $relsec_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "relSecReference", true);
207

  
208
  if (isset($sensu_tagged_text[1])) {
209
    // for de-duplication everything else needs to be equal except for appendedPhrase + MAN.sec + MAN.secDetail. see #7658#note-21
210
    $name_dedup_key = str_replace(cdm_tagged_text_to_string($sensu_tagged_text), ' ', $name_dedup_key);
211
    $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
212
    $sensu_citation_detail = trim(join(' ', cdm_tagged_text_values($sensu_tagged_text, array('secMicroReference'))));
213
    $sensu_citation_short_markup = cdm_tagged_text_to_markup($sensu_tagged_text);
214
    $sensu_citation_short = cdm_tagged_text_to_string($sensu_tagged_text);
215
    $sensu_uuid = $sensu_tagged_text[0]->entityReference->uuid;
216
    $name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters
217
    $misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => $sensu_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $sensu_citation_detail);
218
    $ref_key = $sensu_uuid . ($sensu_citation_detail ? '#' . $sensu_citation_detail : '');
219
    if (!isset($joined_refs[$ref_key])) {
220
      $joined_refs[$ref_key] = array(
221
        'order_by_key' => $sensu_citation_short,
222
        'markup' => $sensu_citation_short_markup // the footnote key will be appended later
223
      );
224
    }
225
  } else if ($appended_phrase_text) {
226
    // appended phrase without reference
227
    $name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters
228
    $misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => null, 'prefix' => $appended_phrase_text);
229
  }
230

  
231
  if (isset($relsec_tagged_text[1])) {
232
    $appended_phrase_text = array_shift($relsec_tagged_text)->text; // remove first element which contains the "err. sec", this will be added later in this code
233
    $relsec_citation_detail = trim(join(' ', cdm_tagged_text_values($relsec_tagged_text, array('secMicroReference'))));
234
    $relsec_citation_short_markup = cdm_tagged_text_to_markup($relsec_tagged_text);
235
    $relsec_citation_short = cdm_tagged_text_to_string($relsec_tagged_text);
236
    $relsec_uuid = $relsec_tagged_text[0]->entityReference->uuid;
237
    $misapplied[$name_dedup_key]['relsec_uuids'][] = array('uuid' => $relsec_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $relsec_citation_detail);;
238
    $ref_key = $relsec_uuid . ($relsec_citation_detail ? '#' . $relsec_citation_detail : '');
239
    if (!isset($joined_refs[$ref_key])) {
240
      $joined_refs[$ref_key] = array(
241
        'order_by_key' => $relsec_citation_short,
242
        'markup' => $relsec_citation_short_markup // the footnote key will be appended later
243
      );
244
    }
245
  }
246

  
247
  if (!isset($misapplied[$name_dedup_key]['out'])) {
248
    $misapplied[$name_dedup_key]['out'] = cdm_tagged_text_to_markup($taxon_relation->taggedText);
249
  } else {
250
    // We need to add the anchors for all of the other misapplied names not
251
    // being rendered explicitly.
252
    $misapplied[$name_dedup_key]['out'] = uuid_anchor($taxon_relation->taxonUuid, $misapplied[$name_dedup_key]['out']);
253
  }
254
}
255

  
256
/**
241 257
 * Renders a representation of the given taxon relationship.
242 258
 *
243 259
 * According name relationships are also being rendered.

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