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Revision 763b610c

ID763b610cafda73d41d185ddb4e44f8baa701c0a2
Parent d27e2b08
Child 8ebd16d6

Added by Andreas Kohlbecker about 5 years ago

fix #5676 displaying the reference titleCache as sensu if authors are missind; also solving other problems

View differences:

modules/cdm_dataportal/includes/taxon.inc
61 61
  $taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT));
62 62

  
63 63
  // Aggregate misapplied names having the same fullname:
64
  //  - deduplicate misapplied names, so that the same name it not shown multiple times in case it
65
  //    the duplicates only have different sensu references/author teams (see #5647)
66
  //  - show the author team as sec reference
67
  //  - show the according reference as footnote to this author team
68
  //  - if the sec reference has no author team it should show instead the title cache
69
  //
70
  // Example:
71
  // "Xenoxylum foobar" sensu Grumbach¹; sensu Lem²
72
  //    1. Novel marsian species, Grumbach, 2022
73
  //    2. Flora solaris, Lem, 2019
64 74
  foreach ($taxonRelationships as $taxonRelation) {
65 75

  
66 76
    if (in_array($taxonRelation->type->uuid, $taxon_relationship_types)) {
67 77

  
68

  
69 78
      if ($taxonRelation->type->uuid == UUID_MISAPPLIED_NAME_FOR || $taxonRelation->type->uuid == UUID_INVALID_DESIGNATION_FOR) {
70 79

  
71 80
        RenderHints::pushToRenderStack('misapplied_name_for'); // TODO the render path string should in future come from $taxonRelation->type->...
72 81

  
73 82
        $name = $taxonRelation->fromTaxon->name->titleCache;
74 83

  
75
        $authorteam = $NULL_AUTHORTEAM;
84
        $sensu_citation_footnote_str = null;
85

  
76 86
        if(isset($taxonRelation->fromTaxon->sec)) {
77
          // taxa not always are have a sec reference (e.g. doubtful taxa)
87
          $sensu_citation_footnote_str = theme('cdm_reference', array('reference' => $taxonRelation->fromTaxon->sec));
78 88
          $authorteam = cdm_ws_get(CDM_WS_REFERENCE_AUTHORTEAM, $taxonRelation->fromTaxon->sec->uuid);
79
          $authorteam = $authorteam->titleCache;
89

  
90
          if(isset($authorteam->titleCache)){
91
            $authorteam_str = $authorteam->titleCache;
92
            if($taxonRelation->fromTaxon->sec->titleCache == $authorteam->titleCache){
93
              // no need for a footnote in case the reference only consists of the author team
94
              $sensu_citation_footnote_str = '';
95
            }
96
          } else {
97
            $authorteam_str = $sensu_citation_footnote_str;
98
            // no need for a footnote in case in case it is used as replacement for missing author teams
99
            $sensu_citation_footnote_str = '';
100
          }
101
        } else {
102
          // taxa not always are have a sec reference (e.g. doubtful taxa)
103
          // use the NULL_AUTHORTEAM in this case
104
          $authorteam_str = $NULL_AUTHORTEAM;
80 105
        }
81 106

  
82 107
        if (!isset($misapplied[$name])) {
......
90 115
        }
91 116

  
92 117
        // Collect all authors for this fullname.
93
        if (isset($authorteam) && $authorteam != $NULL_AUTHORTEAM) {
94
          $misapplied[$name]['authorteam'][$authorteam] = '';
95
          $joinedAuthorTeams[$authorteam] = 'sensu ' . theme('cdm_reference', array('reference' => $taxonRelation->fromTaxon->sec));
118
        if (isset($authorteam_str) && $authorteam_str != $NULL_AUTHORTEAM) {
119
          // prepare entry for the footnote key of the sensu citation footnote
120
          $misapplied[$name]['authorteam'][$authorteam_str] = '';
121
          // map sensu citation footnote to the authorteam string
122
          $joinedAuthorTeams[$authorteam_str] = $sensu_citation_footnote_str;
123

  
96 124
        }
97 125

  
98 126
      }
......
110 138
  // Sort the joinedAuthorTeams and create footnotes and footnotekeys.
111 139
  ksort($joinedAuthorTeams);
112 140
  $author_team_cnt = 0;
113
  foreach ($joinedAuthorTeams as $authorteam => $sensuCitation) {
114
    $footnoteKey = FootnoteManager::addNewFootnote($footnoteListKey, $sensuCitation);
115

  
116
    $sensu = ++$author_team_cnt == 0 ? '' : 'sensu ';
117

  
118
    $joinedAuthorTeams[$authorteam] =  sprintf(
119
        '<span class="sensu">%s%s%s</span>',
120
        $sensu,
121
        ($authorteam != $NULL_AUTHORTEAM ? $authorteam : ''),
122
        theme('cdm_footnote_key', array('footnoteKey' => $footnoteKey))
123
      );
141
  foreach ($joinedAuthorTeams as $authorteam_str => $sensu_citation) {
142
    $footnoteKey = '';
143
    if(!empty($sensu_citation)) {
144
      $footnoteKey = FootnoteManager::addNewFootnote($footnoteListKey, 'sensu ' . $sensu_citation);
145
      $footnoteKey = theme('cdm_footnote_key', array('footnoteKey' => $footnoteKey));
146
    }
147
    $sensu = '';
148
    if($authorteam_str != $NULL_AUTHORTEAM){
149
      $sensu = ++$author_team_cnt == 0 ? '' : 'sensu ' . $authorteam_str;
150
    }
151
    $joinedAuthorTeams[$authorteam_str] = '<span class="sensu">' . $sensu . $footnoteKey .'</span>';
124 152
  }
125 153

  
126 154
  // ---- Generate output ---- //
......
134 162

  
135 163
      if (isset($misapplied_name['authorteam'])) {
136 164
        // Fill authors with the renderedFootnoteKey and sorting 'em.
137
        foreach ($misapplied_name['authorteam'] as $authorteam => &$renderedFootnoteKey) {
138
          $renderedFootnoteKey = $joinedAuthorTeams[$authorteam];
165
        foreach ($misapplied_name['authorteam'] as $authorteam_str => &$renderedFootnoteKey) {
166
          $renderedFootnoteKey = $joinedAuthorTeams[$authorteam_str];
139 167
        }
140 168
        ksort($misapplied_name['authorteam']);
141 169
        $out .= join('; ', $misapplied_name['authorteam']);
......
178 206
 *
179 207
 * According name relationships are also being rendered.
180 208
 *
181
 * @param unknown_type $taxonRelationship
209
 * @param $taxonRelationship
182 210
 * @param boolean $doLinkTaxon
183 211
 *     whether to create a link to the related taxon
184 212
 * @param boolean $inverse

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