Revision 763b610c
Added by Andreas Kohlbecker over 7 years ago
| modules/cdm_dataportal/includes/taxon.inc | ||
|---|---|---|
| 61 | 61 |
$taxon_relationship_types = variable_get(CDM_TAXON_RELATIONSHIP_TYPES, unserialize(CDM_TAXON_RELATIONSHIP_TYPES_DEFAULT)); |
| 62 | 62 |
|
| 63 | 63 |
// Aggregate misapplied names having the same fullname: |
| 64 |
// - deduplicate misapplied names, so that the same name it not shown multiple times in case it |
|
| 65 |
// the duplicates only have different sensu references/author teams (see #5647) |
|
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// - show the author team as sec reference |
|
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// - show the according reference as footnote to this author team |
|
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// - if the sec reference has no author team it should show instead the title cache |
|
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// |
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// Example: |
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// "Xenoxylum foobar" sensu Grumbach¹; sensu Lem² |
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// 1. Novel marsian species, Grumbach, 2022 |
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// 2. Flora solaris, Lem, 2019 |
|
| 64 | 74 |
foreach ($taxonRelationships as $taxonRelation) {
|
| 65 | 75 |
|
| 66 | 76 |
if (in_array($taxonRelation->type->uuid, $taxon_relationship_types)) {
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| 67 | 77 |
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| 68 |
|
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| 69 | 78 |
if ($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 = $taxonRelation->fromTaxon->name->titleCache; |
| 74 | 83 |
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$authorteam = $NULL_AUTHORTEAM; |
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$sensu_citation_footnote_str = null; |
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|
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| 76 | 86 |
if(isset($taxonRelation->fromTaxon->sec)) {
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// taxa not always are have a sec reference (e.g. doubtful taxa)
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$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 = $authorteam->titleCache; |
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|
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if(isset($authorteam->titleCache)){
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$authorteam_str = $authorteam->titleCache; |
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if($taxonRelation->fromTaxon->sec->titleCache == $authorteam->titleCache){
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// no need for a footnote in case the reference only consists of the author team |
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$sensu_citation_footnote_str = ''; |
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} |
|
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} else {
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$authorteam_str = $sensu_citation_footnote_str; |
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// no need for a footnote in case in case it is used as replacement for missing author teams |
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$sensu_citation_footnote_str = ''; |
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} |
|
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} else {
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// taxa not always are have a sec reference (e.g. doubtful taxa) |
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// use the NULL_AUTHORTEAM in this case |
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$authorteam_str = $NULL_AUTHORTEAM; |
|
| 80 | 105 |
} |
| 81 | 106 |
|
| 82 | 107 |
if (!isset($misapplied[$name])) {
|
| ... | ... | |
| 90 | 115 |
} |
| 91 | 116 |
|
| 92 | 117 |
// Collect all authors for this fullname. |
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if (isset($authorteam) && $authorteam != $NULL_AUTHORTEAM) {
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$misapplied[$name]['authorteam'][$authorteam] = ''; |
|
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$joinedAuthorTeams[$authorteam] = 'sensu ' . theme('cdm_reference', array('reference' => $taxonRelation->fromTaxon->sec));
|
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if (isset($authorteam_str) && $authorteam_str != $NULL_AUTHORTEAM) {
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// prepare entry for the footnote key of the sensu citation footnote |
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$misapplied[$name]['authorteam'][$authorteam_str] = ''; |
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// map sensu citation footnote to the authorteam string |
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$joinedAuthorTeams[$authorteam_str] = $sensu_citation_footnote_str; |
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|
|
| 96 | 124 |
} |
| 97 | 125 |
|
| 98 | 126 |
} |
| ... | ... | |
| 110 | 138 |
// Sort the joinedAuthorTeams and create footnotes and footnotekeys. |
| 111 | 139 |
ksort($joinedAuthorTeams); |
| 112 | 140 |
$author_team_cnt = 0; |
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foreach ($joinedAuthorTeams as $authorteam => $sensuCitation) {
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$footnoteKey = FootnoteManager::addNewFootnote($footnoteListKey, $sensuCitation);
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|
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$sensu = ++$author_team_cnt == 0 ? '' : 'sensu ';
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$joinedAuthorTeams[$authorteam] = sprintf(
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'<span class="sensu">%s%s%s</span>',
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$sensu,
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($authorteam != $NULL_AUTHORTEAM ? $authorteam : ''),
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theme('cdm_footnote_key', array('footnoteKey' => $footnoteKey))
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);
|
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foreach ($joinedAuthorTeams as $authorteam_str => $sensu_citation) {
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$footnoteKey = '';
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if(!empty($sensu_citation)) {
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$footnoteKey = FootnoteManager::addNewFootnote($footnoteListKey, 'sensu ' . $sensu_citation);
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$footnoteKey = theme('cdm_footnote_key', array('footnoteKey' => $footnoteKey));
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}
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$sensu = '';
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if($authorteam_str != $NULL_AUTHORTEAM){
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$sensu = ++$author_team_cnt == 0 ? '' : 'sensu ' . $authorteam_str;
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}
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$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. |
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foreach ($misapplied_name['authorteam'] as $authorteam => &$renderedFootnoteKey) {
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$renderedFootnoteKey = $joinedAuthorTeams[$authorteam]; |
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foreach ($misapplied_name['authorteam'] as $authorteam_str => &$renderedFootnoteKey) {
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$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 |
* |
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* @param unknown_type $taxonRelationship
|
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* @param $taxonRelationship |
|
| 182 | 210 |
* @param boolean $doLinkTaxon |
| 183 | 211 |
* whether to create a link to the related taxon |
| 184 | 212 |
* @param boolean $inverse |
Also available in: Unified diff
fix #5676 displaying the reference titleCache as sensu if authors are missind; also solving other problems