Revision 9dc896c9
Added by Andreas Müller almost 7 years ago
| cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/excel/taxa/NormalExplicitImport.java | ||
|---|---|---|
| 52 | 52 |
import eu.etaxonomy.cdm.model.name.NomenclaturalCode; |
| 53 | 53 |
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType; |
| 54 | 54 |
import eu.etaxonomy.cdm.model.name.Rank; |
| 55 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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|
| 55 |
import eu.etaxonomy.cdm.model.name.TaxonName; |
|
| 56 | 56 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
| 57 | 57 |
import eu.etaxonomy.cdm.model.reference.INomenclaturalReference; |
| 58 | 58 |
import eu.etaxonomy.cdm.model.reference.Reference; |
| ... | ... | |
| 327 | 327 |
String childId = taxonDataHolder.getId(); |
| 328 | 328 |
UUID cdmUuid = taxonDataHolder.getCdmUuid(); |
| 329 | 329 |
Taxon acceptedTaxon = null; |
| 330 |
TaxonNameBase<?,?> nameUsedInSource = null;
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|
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TaxonName nameUsedInSource = null; |
|
| 331 | 331 |
TaxonBase<?> taxonBase = null; |
| 332 | 332 |
Taxon parentTaxon = null; |
| 333 | 333 |
|
| ... | ... | |
| 522 | 522 |
* @param taxonDataHolder |
| 523 | 523 |
* @param acceptedTaxon |
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*/ |
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private void handleFeatures(TaxonExcelImportState state, NormalExplicitRow taxonDataHolder, Taxon acceptedTaxon, TaxonNameBase nameUsedInSource) {
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private void handleFeatures(TaxonExcelImportState state, NormalExplicitRow taxonDataHolder, Taxon acceptedTaxon, TaxonName nameUsedInSource) {
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|
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//feature |
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for (UUID featureUuid : taxonDataHolder.getFeatures()){
|
| 528 | 528 |
Feature feature = getFeature(state, featureUuid); |
| ... | ... | |
| 761 | 761 |
private TaxonBase<?> createTaxon(TaxonExcelImportState state, Rank rank, String taxonNameStr, |
| 762 | 762 |
String authorStr, String publishingAutorStr, String basionymAuthor, String reference, String date, String nameStatus, NomenclaturalCode nc) {
|
| 763 | 763 |
TaxonBase<?> taxonBase; |
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INonViralName taxonNameBase = null;
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INonViralName taxonName = null; |
|
| 765 | 765 |
if (nc == NomenclaturalCode.ICVCN){
|
| 766 | 766 |
logger.warn("ICVCN not yet supported");
|
| 767 | 767 |
|
| 768 | 768 |
}else{
|
| 769 | 769 |
//String taxonNameStr = titleCache.substring(0, titleCache.indexOf(authorStr)); |
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taxonNameBase = nc.getNewTaxonNameInstance(rank);
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taxonName = nc.getNewTaxonNameInstance(rank); |
|
| 771 | 771 |
NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance(); |
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taxonNameBase = parser.parseFullName(taxonNameStr, nc, rank);
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taxonName = parser.parseFullName(taxonNameStr, nc, rank); |
|
| 773 | 773 |
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if (! taxonNameBase.getNameCache().equals(taxonNameStr)){
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taxonNameBase.setNameCache(taxonNameStr, true);
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if (! taxonName.getNameCache().equals(taxonNameStr)){
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taxonName.setNameCache(taxonNameStr, true); |
|
| 776 | 776 |
} |
| 777 | 777 |
|
| 778 | 778 |
// Create the author |
| 779 | 779 |
if (StringUtils.isNotBlank(authorStr)) {
|
| 780 | 780 |
try {
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parser.parseAuthors(taxonNameBase, authorStr);
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parser.parseAuthors(taxonName, authorStr); |
|
| 782 | 782 |
} catch (StringNotParsableException e) {
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taxonNameBase.setAuthorshipCache(authorStr);
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taxonName.setAuthorshipCache(authorStr); |
|
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} |
| 785 | 785 |
} |
| 786 | 786 |
if (StringUtils.isNotBlank(reference)) {
|
| 787 | 787 |
|
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INomenclaturalReference ref = parser.parseReferenceTitle(reference, date, true); |
| 789 | 789 |
if (ref.getAuthorship() == null){
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ref.setAuthorship(taxonNameBase.getCombinationAuthorship());
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ref.setAuthorship(taxonName.getCombinationAuthorship()); |
|
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} |
| 792 | 792 |
|
| 793 | 793 |
if (ref.getAbbrevTitle() == null && !ref.isOfType(ReferenceType.Article)) {
|
| ... | ... | |
| 797 | 797 |
|
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ref.setProtectedTitleCache(false); |
| 799 | 799 |
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taxonNameBase.setNomenclaturalReference(ref);
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taxonNameBase.setNomenclaturalMicroReference(state.getCurrentRow().getCollation());
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taxonName.setNomenclaturalReference(ref); |
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taxonName.setNomenclaturalMicroReference(state.getCurrentRow().getCollation()); |
|
| 802 | 802 |
} |
| 803 | 803 |
} |
| 804 | 804 |
|
| ... | ... | |
| 807 | 807 |
// Create the status |
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nameStatus = CdmUtils.Nz(nameStatus).trim().toLowerCase(); |
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if (validMarkers.contains(nameStatus)){
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taxonBase = Taxon.NewInstance(taxonNameBase, sec);
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taxonBase = Taxon.NewInstance(taxonName, sec); |
|
| 811 | 811 |
}else if (synonymMarkers.contains(nameStatus)){
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taxonBase = Synonym.NewInstance(taxonNameBase, sec);
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taxonBase = Synonym.NewInstance(taxonName, sec); |
|
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}else {
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Taxon taxon = Taxon.NewInstance(taxonNameBase, sec);
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Taxon taxon = Taxon.NewInstance(taxonName, sec); |
|
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if (nameStatusMarkers.contains(nameStatus)){
|
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if (nameStatus.equals(NOM_ILLEG)){
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taxonNameBase.addStatus(NomenclaturalStatusType.ILLEGITIMATE(), null, null);
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taxonName.addStatus(NomenclaturalStatusType.ILLEGITIMATE(), null, null); |
|
| 818 | 818 |
} else if (nameStatus.equals(NOM_REJ)){
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taxonNameBase.addStatus(NomenclaturalStatusType.REJECTED(), null, null);
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taxonName.addStatus(NomenclaturalStatusType.REJECTED(), null, null); |
|
| 820 | 820 |
} else if (nameStatus.equals(NOM_CONS)){
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taxonNameBase.addStatus(NomenclaturalStatusType.CONSERVED(), null, null);
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taxonName.addStatus(NomenclaturalStatusType.CONSERVED(), null, null); |
|
| 822 | 822 |
} |
| 823 | 823 |
}else{
|
| 824 | 824 |
taxon.setTaxonStatusUnknown(true); |
| ... | ... | |
| 838 | 838 |
//TODO implementation must be improved when matching of taxon names with existing names is implemented |
| 839 | 839 |
//=> the assumption that the only description is the description added by this import |
| 840 | 840 |
//is wrong then |
| 841 |
private TaxonNameDescription getNameDescription(TaxonNameBase<?,?> name) {
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private TaxonNameDescription getNameDescription(TaxonName<?,?> name) {
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| 842 | 842 |
Set<TaxonNameDescription> descriptions = name.getDescriptions(); |
| 843 | 843 |
if (descriptions.size()>1){
|
| 844 | 844 |
throw new IllegalStateException("Implementation does not yet support names with multiple descriptions");
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Also available in: Unified diff
fix #6368 rename table and class TaxonNameBase