//protologue
for (String protologue : taxonDataHolder.getProtologues()){
TextData textData = TextData.NewInstance(Feature.PROTOLOGUE());
- this.getNameDescription(taxonBase.getName()).addElement(textData);
+ this.getNameDescription(taxonBase.getName(), state).addElement(textData);
URI uri;
try {
uri = new URI(protologue);
textData.addMedia(Media.NewInstance(uri, null, null, null));
+
} catch (URISyntaxException e) {
String warning = "URISyntaxException when trying to convert to URI: " + protologue;
logger.error(warning);
if (parentTaxon != null) {
//Taxon taxon = (Taxon)state.getTaxonBase(childId);
- Reference sourceRef = state.getConfig().getSourceReference();
+ // Reference sourceRef = state.getConfig().getSourceReference();
String microCitation = null;
Taxon childTaxon = taxon;
- makeParent(state, parentTaxon, childTaxon, sourceRef, microCitation);
+ makeParent(state, parentTaxon, childTaxon, null, microCitation);
getTaxonService().saveOrUpdate(childTaxon);
state.putTaxon(parentId, parentTaxon);
} else {
if (parentTaxon != null) {
Taxon taxon = (Taxon)state.getTaxonBase(childId);
- Reference sourceRef = state.getConfig().getSourceReference();
+ // Reference sourceRef = state.getConfig().getSourceReference();
String microCitation = null;
Taxon childTaxon = taxon;
- makeParent(state, parentTaxon, childTaxon, sourceRef, microCitation);
+ makeParent(state, parentTaxon, childTaxon, null, microCitation);
getTaxonService().saveOrUpdate(parentTaxon);
state.putTaxon(parentId, parentTaxon);
} else {
if (StringUtils.isNotBlank(reference)) {
String pub = CdmUtils.concat(" ", reference, state.getCurrentRow().getCollation());
String[] split = pub.split(":");
-
- INomenclaturalReference ref = parser.parseReferenceTitle(reference, date, true);
+ pub = split[0];
+ INomenclaturalReference ref = parser.parseReferenceTitle(pub, date, true);
if (split.length > 1){
String detail = split[split.length-1];
taxonName.setNomenclaturalMicroReference(detail.trim());
- pub = pub.substring(0, pub.length() - detail.length() - 1).trim();
+
}
- ref.setAbbrevTitle(pub);
+ // ref.setAbbrevTitle(pub);
if (ref.getAuthorship() == null){
}
//Create the taxon
- Reference sec = state.getConfig().getSourceReference();
+ //Reference sec = state.getConfig().getSourceReference();
// Create the status
nameStatus = CdmUtils.Nz(nameStatus).trim().toLowerCase();
if (validMarkers.contains(nameStatus)){
- taxonBase = Taxon.NewInstance(taxonName, sec);
+ taxonBase = Taxon.NewInstance(taxonName, null);
}else if (synonymMarkers.contains(nameStatus)){
- taxonBase = Synonym.NewInstance(taxonName, sec);
+ taxonBase = Synonym.NewInstance(taxonName, null);
}else {
- Taxon taxon = Taxon.NewInstance(taxonName, sec);
+ Taxon taxon = Taxon.NewInstance(taxonName, null);
if (nameStatusMarkers.contains(nameStatus)){
if (nameStatus.equals(NOM_ILLEG)){
taxonName.addStatus(NomenclaturalStatusType.ILLEGITIMATE(), null, null);
}
taxonBase = taxon;
}
- taxonBase.getName().addSource(OriginalSourceType.Import, null,"TaxonName" ,null, null);
- taxonBase.addSource(OriginalSourceType.Import, null,"TaxonName" ,null, null);
+ taxonBase.getName().addSource(OriginalSourceType.Import, null,"TaxonName" ,state.getConfig().getSourceReference(), null);
+ taxonBase.addSource(OriginalSourceType.Import, null,"TaxonName" ,state.getConfig().getSourceReference(), null);
return taxonBase;
}
//TODO implementation must be improved when matching of taxon names with existing names is implemented
//=> the assumption that the only description is the description added by this import
//is wrong then
- private TaxonNameDescription getNameDescription(TaxonName name) {
+ private TaxonNameDescription getNameDescription(TaxonName name, TaxonExcelImportState state) {
Set<TaxonNameDescription> descriptions = name.getDescriptions();
if (descriptions.size()>1){
throw new IllegalStateException("Implementation does not yet support names with multiple descriptions");
}else if (descriptions.size()==1){
return descriptions.iterator().next();
}else{
- return TaxonNameDescription.NewInstance(name);
+ TaxonNameDescription desc = TaxonNameDescription.NewInstance(name);
+ desc.addSource(OriginalSourceType.Import, null, "NameDescription", state.getConfig().getSourceReference(), null);
+ return desc;
}
}
if (cdmBase.isInstanceOf(LanguageString.class)){
return cdmRepository.getTermService().saveLanguageData(CdmBase.deproxy(cdmBase, LanguageString.class));
}else if (cdmBase.isInstanceOf(SpecimenOrObservationBase.class)){
- return cdmRepository.getOccurrenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class));
+ SpecimenOrObservationBase specimen = CdmBase.deproxy(cdmBase, SpecimenOrObservationBase.class);
+
+ return cdmRepository.getOccurrenceService().saveOrUpdate(specimen);
}else if (cdmBase.isInstanceOf(Reference.class)){
return cdmRepository.getReferenceService().saveOrUpdate(CdmBase.deproxy(cdmBase, Reference.class));
}else if (cdmBase.isInstanceOf(Classification.class)){
}else if (cdmBase.isInstanceOf(Collection.class)){
return cdmRepository.getCollectionService().saveOrUpdate(CdmBase.deproxy(cdmBase, Collection.class));
}else if (cdmBase.isInstanceOf(DescriptionBase.class)){
- return cdmRepository.getDescriptionService().saveOrUpdate(CdmBase.deproxy(cdmBase, DescriptionBase.class));
+ DescriptionBase description = CdmBase.deproxy(cdmBase, DescriptionBase.class);
+
+ return cdmRepository.getDescriptionService().saveOrUpdate(description);
}else if (cdmBase.isInstanceOf(TaxonBase.class)){
return cdmRepository.getTaxonService().saveOrUpdate(CdmBase.deproxy(cdmBase, TaxonBase.class));
}else if (cdmBase.isInstanceOf(TaxonName.class)){
if (!existsInClassification(taxon,state.getClassification(), state)){
if(config.isMoveNewTaxaToDefaultClassification()){
//check if node exists in default classification
- if (!existsInClassification(taxon, state.getDefaultClassification(), state)){
- addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification());
+ if (!existsInClassification(taxon, state.getDefaultClassification(true), state)){
+ addParentTaxon(taxon, state, preferredFlag, state.getDefaultClassification(true));
}
- }
- else {
+ }else{
//add non-existing taxon to current classification
addParentTaxon(taxon, state, preferredFlag, state.getClassification());
}
+
}
}
BGBM BDI Projects / cdmlib.git / commitdiff