Revision c5d04eba
Added by Andreas Müller over 2 years ago
| app-import/src/main/java/eu/etaxonomy/cdm/io/bogota/BogotaChecklistTaxonImport.java | ||
|---|---|---|
| 23 | 23 |
import eu.etaxonomy.cdm.model.common.Language; |
| 24 | 24 |
import eu.etaxonomy.cdm.model.name.IBotanicalName; |
| 25 | 25 |
import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.TaxonName; |
|
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
| 27 | 28 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| 28 | 29 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
| ... | ... | |
| 167 | 168 |
}else{
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| 168 | 169 |
nameStr = nameStr.replace(auctStr, "").trim(); |
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} |
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IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
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|
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TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
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|
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name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| 172 | 173 |
name = state.getDeduplicationHelper().getExistingName(name); |
| 173 | 174 |
if (name.isProtectedTitleCache()){
|
| ... | ... | |
| 184 | 185 |
taxon.addMisappliedName(misApp, state.getConfig().getSecReference(), null); |
| 185 | 186 |
} |
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/** |
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* @param col |
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* @return |
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*/ |
|
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private String getNamespace(CONFIG config) {
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| 193 | 189 |
return getWorksheetName(config)+"."+ ID_COL; |
| 194 | 190 |
} |
| 195 | 191 |
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/** |
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* @param state |
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* @param record |
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* @param line |
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* @param taxon |
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* @param noStr |
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*/ |
|
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private void handleSingleSynonym(SimpleExcelTaxonImportState<CONFIG> state, String nameStr, |
| 205 | 193 |
String line, Taxon taxon, String noStr) {
|
| 206 | 194 |
Rank rank = Rank.SPECIES(); |
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IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
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|
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TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
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|
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name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| 209 | 197 |
name = state.getDeduplicationHelper().getExistingName(name); |
| 210 | 198 |
if (name.isProtectedTitleCache()){
|
| ... | ... | |
| 217 | 205 |
taxon.addSynonym(synonym, SynonymType.SYNONYM_OF()); |
| 218 | 206 |
} |
| 219 | 207 |
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/** |
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* @param state |
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* @param line |
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* @param record |
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* @param taxon |
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* @param noStr |
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*/ |
|
| 228 | 208 |
private void makeInfraSpecific(SimpleExcelTaxonImportState<CONFIG> state, Map<String, String> record, String line, |
| 229 | 209 |
TaxonNode speciesNode, String noStr) {
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String subSpeciesStr = getValue(record, INFRASPECIFIC); |
| ... | ... | |
| 235 | 215 |
split = split.replace(" None", "").trim();
|
| 236 | 216 |
} |
| 237 | 217 |
Rank rank = Rank.SUBSPECIES(); |
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IBotanicalName name = (IBotanicalName)parser.parseFullName(split.trim(), state.getConfig().getNomenclaturalCode(), rank);
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TaxonName name = (TaxonName)parser.parseFullName(split.trim(), state.getConfig().getNomenclaturalCode(), rank);
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|
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name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| 240 | 220 |
name = state.getDeduplicationHelper().getExistingName(name); |
| 241 | 221 |
if (name.isProtectedTitleCache()){
|
| ... | ... | |
| 251 | 231 |
} |
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} |
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|
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/** |
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* @param state |
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* @param line |
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* @param record |
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* @param noStr |
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* @return |
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*/ |
|
| 261 | 234 |
private TaxonNode makeTaxon(SimpleExcelTaxonImportState<CONFIG> state, String line, Map<String, String> record, |
| 262 | 235 |
String noStr) {
|
| 263 | 236 |
|
| ... | ... | |
| 272 | 245 |
|
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nameStr = CdmUtils.concat(" ", nameStr, speciesAuthorStr);
|
| 274 | 247 |
Rank rank = Rank.SPECIES(); |
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IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
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TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
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|
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name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null); |
| 277 | 250 |
name = state.getDeduplicationHelper().getExistingName(name); |
| 278 | 251 |
if (name.isProtectedTitleCache()){
|
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