Revision a9dc4b35
Added by Andreas Kohlbecker about 5 years ago
| 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
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| 85 |
// full name with relation symbol, rel sec as de-duplication key
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|
| 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')));
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| 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($sensu_tagged_text[1])) {
|
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// for de-dublicationeverything else needs to be equal except for appendedPhrase + MAN.sec + MAN.secDetail. see #7658#note-21 |
|
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$full_name_key = str_replace(cdm_tagged_text_to_string($sensu_tagged_text), ' ', $full_name_key); |
|
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$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); |
|
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$sensu_uuid = $sensu_tagged_text[0]->entityReference->uuid; |
|
| 107 |
$full_name_key = preg_replace('/\s+/', ' ', $full_name_key); // sanitize multiple whitespace characters
|
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| 108 |
$misapplied[$full_name_key]['sensu_uuids'][] = array('uuid' => $sensu_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $sensu_citation_detail);
|
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$ref_key = $sensu_uuid .($sensu_citation_detail ? '#' . $sensu_citation_detail : ''); |
|
| 110 |
if (!isset($joined_refs[$ref_key])) {
|
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$joined_refs[$ref_key] = array( |
|
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'order_by_key' => $sensu_citation_short, |
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'markup' => $sensu_citation_short_markup // the footnote key will be appended later |
|
| 114 |
); |
|
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} |
|
| 116 |
} else if($appended_phrase_text) {
|
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// appended phrase without reference |
|
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$full_name_key = preg_replace('/\s+/', ' ', $full_name_key); // sanitize multiple whitespace characters
|
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$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, $full_name_key); |
|
| 121 | 93 |
|
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if (isset($relsec_tagged_text[1])) {
|
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//array_shift($relsec_tagged_text); // remove first element which contains the "err. sec", this will be added later in this code |
|
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$relsec_citation_detail = trim(join(' ', cdm_tagged_text_values($relsec_tagged_text, array('secMicroReference'))));
|
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| 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); |
|
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$relsec_uuid = $relsec_tagged_text[0]->entityReference->uuid; |
|
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$misapplied[$full_name_key]['relsec_uuids'][] = $relsec_uuid; |
|
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$ref_key = $relsec_uuid . ($relsec_citation_detail ? '#' . $relsec_citation_detail : ''); |
|
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if (!isset($joined_refs[$ref_key])) {
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$joined_refs[$ref_key] = array( |
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'order_by_key' => $relsec_citation_short, |
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'markup' => $relsec_citation_short_markup // the footnote key will be appended later |
|
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); |
|
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} |
|
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} |
|
| 137 |
|
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if (!isset($misapplied[$full_name_key]['out'])) {
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$misapplied[$full_name_key]['out'] = cdm_tagged_text_to_markup($taxon_relation->taggedText); |
|
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} else {
|
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// We need to add the anchors for all of the other misapplied names not |
|
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// being rendered explicitly. |
|
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$misapplied[$full_name_key]['out'] = uuid_anchor($taxon_relation->taxonUuid, $misapplied[$full_name_key]['out']); |
|
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} |
|
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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 |
|
|
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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 $relsec_uuid) {
|
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$relsec_refs_with_fkey[$joined_refs[$relsec_uuid]['order_by_key']] = $joined_refs[$relsec_uuid]['markup']; |
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foreach ($misapplied_name['relsec_uuids'] as $relsec_data) {
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if($relsec_data['uuid']) {
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$relsec_refs_with_fkey[$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);
|
| ... | ... | |
| 237 | 191 |
return $out; |
| 238 | 192 |
} |
| 239 | 193 |
|
| 194 |
/** |
|
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* @param $taxon_relation |
|
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* @param $name_dedup_key |
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* @param $misapplied |
|
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* @param $joined_refs |
|
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|
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*/ |
|
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function cdm_taxonRelationships_process_relationship_dto($taxon_relation, &$misapplied, &$joined_refs, $name_dedup_key = null) {
|
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$appended_phrase_text = join(' ', cdm_tagged_text_values($taxon_relation->taggedText, array('appendedPhrase')));
|
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// remove/extract appendedPhrase, secReference, relSecReference and add placeholders if needed |
|
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tagged_text_extract($taxon_relation->taggedText, 'appendedPhrase'); |
|
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$sensu_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "secReference", true); |
|
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$relsec_tagged_text = tagged_text_extract_secref($taxon_relation->taggedText, "relSecReference", true); |
|
| 207 |
|
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if (isset($sensu_tagged_text[1])) {
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// for de-duplication everything else needs to be equal except for appendedPhrase + MAN.sec + MAN.secDetail. see #7658#note-21 |
|
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$name_dedup_key = str_replace(cdm_tagged_text_to_string($sensu_tagged_text), ' ', $name_dedup_key); |
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$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'))));
|
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| 213 |
$sensu_citation_short_markup = cdm_tagged_text_to_markup($sensu_tagged_text); |
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$sensu_citation_short = cdm_tagged_text_to_string($sensu_tagged_text); |
|
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$sensu_uuid = $sensu_tagged_text[0]->entityReference->uuid; |
|
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$name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters
|
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$misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => $sensu_uuid, 'prefix' => $appended_phrase_text, 'citation_detail' => $sensu_citation_detail);
|
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$ref_key = $sensu_uuid . ($sensu_citation_detail ? '#' . $sensu_citation_detail : ''); |
|
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if (!isset($joined_refs[$ref_key])) {
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$joined_refs[$ref_key] = array( |
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'order_by_key' => $sensu_citation_short, |
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'markup' => $sensu_citation_short_markup // the footnote key will be appended later |
|
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); |
|
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} |
|
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} else if ($appended_phrase_text) {
|
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// appended phrase without reference |
|
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$name_dedup_key = preg_replace('/\s+/', ' ', $name_dedup_key); // sanitize multiple whitespace characters
|
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$misapplied[$name_dedup_key]['sensu_uuids'][] = array('uuid' => null, 'prefix' => $appended_phrase_text);
|
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| 229 |
} |
|
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|
|
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if (isset($relsec_tagged_text[1])) {
|
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$appended_phrase_text = array_shift($relsec_tagged_text)->text; // remove first element which contains the "err. sec", this will be added later in this code |
|
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$relsec_citation_detail = trim(join(' ', cdm_tagged_text_values($relsec_tagged_text, array('secMicroReference'))));
|
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| 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); |
|
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$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);;
|
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| 238 |
$ref_key = $relsec_uuid . ($relsec_citation_detail ? '#' . $relsec_citation_detail : ''); |
|
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if (!isset($joined_refs[$ref_key])) {
|
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$joined_refs[$ref_key] = array( |
|
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'order_by_key' => $relsec_citation_short, |
|
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'markup' => $relsec_citation_short_markup // the footnote key will be appended later |
|
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); |
|
| 244 |
} |
|
| 245 |
} |
|
| 246 |
|
|
| 247 |
if (!isset($misapplied[$name_dedup_key]['out'])) {
|
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$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']); |
|
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} |
|
| 254 |
} |
|
| 255 |
|
|
| 240 | 256 |
/** |
| 241 | 257 |
* Renders a representation of the given taxon relationship. |
| 242 | 258 |
* |
Also available in: Unified diff
ref #7658 other relationship reprentation based on DTOs fully implemented