Revision 58968197
Added by Andreas Müller over 3 years ago
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTaxonImport.java | ||
|---|---|---|
| 194 | 194 |
String sql = |
| 195 | 195 |
" SELECT id FROM tu WHERE tu_accfinal is NULL" //id of taxa not having accepted taxon |
| 196 | 196 |
+ " UNION SELECT DISTINCT tu_accfinal FROM tu " //fk to accepted taxon (either the accepted taxon or the taxon itself, if accepted) |
| 197 |
+ " UNION SELECT id FROM tu WHERE trim(tu.tu_unacceptreason) like 'misidentification' OR trim(tu.tu_unacceptreason) like 'misidentifications' OR " |
|
| 198 |
+ " tu.tu_unacceptreason like 'misapplied %%name' OR " |
|
| 199 |
+ " tu.tu_unacceptreason like '%%misapplication%%' OR " |
|
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+ " tu.tu_unacceptreason like 'incorrect identification%%'" //Misapplications, see ErmsTransformer.getSynonymRelationTypesByKey |
|
| 197 | 201 |
+ " UNION SELECT syn.id FROM tu syn INNER JOIN tu acc ON syn.tu_accfinal = acc.id WHERE syn.id = acc.tu_parent AND acc.id <> syn.id " //see also ErmsTaxonRelationImport.isAccepted, there are some autonyms being the accepted taxon of there own parents |
| 198 | 202 |
+ " UNION SELECT DISTINCT %s FROM %s " //vernaculars |
| 199 | 203 |
+ " UNION SELECT DISTINCT %s FROM %s " //distributions |
| cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/erms/ErmsTransformer.java | ||
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| 698 | 698 |
|
| 699 | 699 |
//according to SQL script erms300_Match_Relation&Status.sql |
| 700 | 700 |
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| 701 |
unacceptreason = unacceptreason == null? null: unacceptreason.trim(); |
|
| 701 | 702 |
boolean handled = false; |
| 702 |
if (isBlank(unacceptreason)){
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|
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if (unacceptreason == null || isBlank(unacceptreason)){
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|
| 703 | 704 |
handled = true; //no change |
| 704 | 705 |
}else if (unacceptreason.matches("(?i)(synonym|superseded recombination|transferred to .*)")){
|
| 705 | 706 |
handled = true; //no change |
| ... | ... | |
| 713 | 714 |
}else if (unacceptreason.matches("(?i)part.*\\s+synonym.*")){
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| 714 | 715 |
synType = null; |
| 715 | 716 |
taxonRelType = TaxonRelationshipType.PRO_PARTE_SYNONYM_FOR(); |
| 716 |
}else if (unacceptreason.matches("(?i)misapplied.*")){
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|
| 717 |
}else if (unacceptreason.matches("(?i)(misidentifications?|misapplied .*name|.*misapplication.*|incorrect identification)")){
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| 718 |
//see ErmsTaxonImport.getAcceptedTaxaKeys() |
|
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synType = null; |
| 718 | 720 |
taxonRelType = TaxonRelationshipType.MISAPPLIED_NAME_FOR(); |
| 719 | 721 |
}else if (unacceptreason.matches("(?i)(.*jun.*syn.*|\\(synonym\\)|reverted genus transfer)")){
|
Also available in: Unified diff
ref #1444, ref #7976 improve misapplication handling in ERMS import