import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.name.IBotanicalName;
import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.TaxonName;
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.taxon.Classification;
}else{
nameStr = nameStr.replace(auctStr, "").trim();
}
- IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+ TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
name = state.getDeduplicationHelper().getExistingName(name);
if (name.isProtectedTitleCache()){
taxon.addMisappliedName(misApp, state.getConfig().getSecReference(), null);
}
-
- /**
- * @param col
- * @return
- */
private String getNamespace(CONFIG config) {
return getWorksheetName(config)+"."+ ID_COL;
}
-
- /**
- * @param state
- * @param record
- * @param line
- * @param taxon
- * @param noStr
- */
private void handleSingleSynonym(SimpleExcelTaxonImportState<CONFIG> state, String nameStr,
String line, Taxon taxon, String noStr) {
Rank rank = Rank.SPECIES();
- IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+ TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
name = state.getDeduplicationHelper().getExistingName(name);
if (name.isProtectedTitleCache()){
taxon.addSynonym(synonym, SynonymType.SYNONYM_OF());
}
-
- /**
- * @param state
- * @param line
- * @param record
- * @param taxon
- * @param noStr
- */
private void makeInfraSpecific(SimpleExcelTaxonImportState<CONFIG> state, Map<String, String> record, String line,
TaxonNode speciesNode, String noStr) {
String subSpeciesStr = getValue(record, INFRASPECIFIC);
split = split.replace(" None", "").trim();
}
Rank rank = Rank.SUBSPECIES();
- IBotanicalName name = (IBotanicalName)parser.parseFullName(split.trim(), state.getConfig().getNomenclaturalCode(), rank);
+ TaxonName name = (TaxonName)parser.parseFullName(split.trim(), state.getConfig().getNomenclaturalCode(), rank);
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
name = state.getDeduplicationHelper().getExistingName(name);
if (name.isProtectedTitleCache()){
}
}
- /**
- * @param state
- * @param line
- * @param record
- * @param noStr
- * @return
- */
private TaxonNode makeTaxon(SimpleExcelTaxonImportState<CONFIG> state, String line, Map<String, String> record,
String noStr) {
nameStr = CdmUtils.concat(" ", nameStr, speciesAuthorStr);
Rank rank = Rank.SPECIES();
- IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+ TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
name = state.getDeduplicationHelper().getExistingName(name);
if (name.isProtectedTitleCache()){
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
import eu.etaxonomy.cdm.model.agent.Person;
import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
-import eu.etaxonomy.cdm.model.name.IBotanicalName;
-import eu.etaxonomy.cdm.model.name.INonViralName;
import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
import eu.etaxonomy.cdm.model.name.Rank;
import eu.etaxonomy.cdm.model.name.TaxonName;
isSensuStrictu = true;
taxonStr = taxonStr.substring(0, taxonStr.length() - "s.str.".length() ).trim();
}
- INonViralName name = parser.parseFullName(taxonStr, NomenclaturalCode.ICNAFP, null);
+ TaxonName name = (TaxonName)parser.parseFullName(taxonStr, NomenclaturalCode.ICNAFP, null);
name = replaceNameAuthorsAndReferences(state, name);
if (name.isProtectedTitleCache()){
logger.warn(line + "Name could not be parsed: " + taxonStr);
if (family != null){
familyNode = family.getTaxonNodes().iterator().next();
}else{
- IBotanicalName name = makeFamilyName(state, familyStr);
+ TaxonName name = makeFamilyName(state, familyStr);
name = replaceNameAuthorsAndReferences(state, name);
Reference sec = getSecReference(state);
import eu.etaxonomy.cdm.io.mexico.SimpleExcelTaxonImportState;
import eu.etaxonomy.cdm.model.common.IdentifiableSource;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
-import eu.etaxonomy.cdm.model.name.IBotanicalName;
-import eu.etaxonomy.cdm.model.name.INonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
import eu.etaxonomy.cdm.model.name.TaxonName;
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
}
- protected IBotanicalName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state,
+ protected TaxonName makeFamilyName(SimpleExcelTaxonImportState<CONFIG> state,
String famStr) {
TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
famStr = famStr.substring(0,1).toUpperCase() + famStr.substring(1).toLowerCase();
return name;
}
- protected <NAME extends INonViralName> NAME replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, NAME name) {
- NAME result = state.getDeduplicationHelper().getExistingName(name);
+ protected TaxonName replaceNameAuthorsAndReferences(SimpleExcelTaxonImportState<CONFIG> state, TaxonName name) {
+ TaxonName result = state.getDeduplicationHelper().getExistingName(name);
state.getDeduplicationHelper().replaceAuthorNamesAndNomRef(result);
return result;
}
import eu.etaxonomy.cdm.model.description.State;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.location.NamedArea;
-import eu.etaxonomy.cdm.model.name.IBotanicalName;
import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.TaxonName;
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.taxon.Classification;
nameStr = nameStr.substring(0, nameStr.length() - "s.str.".length() ).trim();
}
Rank rank = isSubSpecies ? Rank.SUBSPECIES() : Rank.SPECIES();
- IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+ TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
if (name.isProtectedTitleCache()){
logger.warn(line + "Name could not be parsed: " + nameStr);
}
return CdmUtils.concat(" ", new String[]{genusStr, speciesStr, speciesAuthorStr});
}
- /**
- * @param state
- * @param record
- * @param genusStr
- * @return
- */
private TaxonNode makeGenusNode(SimpleExcelTaxonImportState<CONFIG> state,
Map<String, String> record, String genusStr) {
- IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
+ TaxonName name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
name.setGenusOrUninomial(genusStr);
name = replaceNameAuthorsAndReferences(state, name);
Taxon genus = Taxon.NewInstance(name, getSecReference(state));
return genusNode;
}
- /**
- * @param state
- * @param parentStr
- * @return
- */
private TaxonNode getParent(SimpleExcelTaxonImportState<CONFIG> state, String parentStr) {
Taxon taxon = state.getHigherTaxon(parentStr);
return taxon == null ? null : taxon.getTaxonNodes().iterator().next();
}
- /**
- * @param record
- * @param state
- * @return
- */
private TaxonNode getFamilyTaxon(Map<String, String> record, SimpleExcelTaxonImportState<CONFIG> state) {
String familyStr = getValue(record, "Family");
if (familyStr == null){
if (family != null){
familyNode = family.getTaxonNodes().iterator().next();
}else{
- IBotanicalName name = makeFamilyName(state, familyStr);
+ TaxonName name = makeFamilyName(state, familyStr);
name = replaceNameAuthorsAndReferences(state, name);
Reference sec = getSecReference(state);
if (group != null){
groupNode = group.getTaxonNodes().iterator().next();
}else{
- IBotanicalName name = makeFamilyName(state, groupStr);
+ TaxonName name = makeFamilyName(state, groupStr);
name = replaceNameAuthorsAndReferences(state, name);
Reference sec = getSecReference(state);
classification.setUuid(state.getConfig().getClassificationUuid());
classification.getRootNode().setUuid(rootUuid);
- IBotanicalName plantaeName = TaxonNameFactory.NewBotanicalInstance(Rank.KINGDOM());
+ TaxonName plantaeName = TaxonNameFactory.NewBotanicalInstance(Rank.KINGDOM());
plantaeName.setGenusOrUninomial("Plantae");
plantaeName = replaceNameAuthorsAndReferences(state, plantaeName);
return rootNode;
}
- /**
- * @param desc
- * @param string
- * @param uuidUserDefinedAnnotationTypeVocabulary
- */
private void handleDistribution(SimpleExcelTaxonImportState<CONFIG> state,
TaxonDescription desc, String key, UUID uuid, String line, String id) {
Map<String, String> record = state.getOriginalRecord();
nameStr = normalizeNameStr(nameStr);
Rank rank = Rank.SPECIES();
- IBotanicalName name = (IBotanicalName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
+ TaxonName name = (TaxonName)parser.parseFullName(nameStr, state.getConfig().getNomenclaturalCode(), rank);
name.addImportSource(noStr, getNamespace(state.getConfig()), getSourceCitation(state), null);
name = state.getDeduplicationHelper().getExistingName(name);
if (name.isProtectedTitleCache()){