import eu.etaxonomy.cdm.model.common.AnnotationType;
import eu.etaxonomy.cdm.model.common.CdmBase;
import eu.etaxonomy.cdm.model.common.Language;
+import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
import eu.etaxonomy.cdm.model.description.TaxonDescription;
import eu.etaxonomy.cdm.model.name.BotanicalName;
import eu.etaxonomy.cdm.model.name.CultivarPlantName;
+import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
import eu.etaxonomy.cdm.model.name.NonViralName;
import eu.etaxonomy.cdm.model.name.Rank;
+import eu.etaxonomy.cdm.model.name.RankClass;
import eu.etaxonomy.cdm.model.name.TaxonNameBase;
import eu.etaxonomy.cdm.model.taxon.Synonym;
import eu.etaxonomy.cdm.model.taxon.Taxon;
importAuthors(state, rs, name);
//---TAXON---
- TaxonBase<?> taxonBase = importTaxon(rs, name);
+ TaxonBase<?> taxonBase = importTaxon(rs, name, state);
if(taxonBase==null){
RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
return;
}
}
- private TaxonBase<?> importTaxon(ResultSet rs, NonViralName<?> name) throws SQLException {
+ private TaxonBase<?> importTaxon(ResultSet rs, NonViralName<?> name, RedListGefaesspflanzenImportState state) throws SQLException {
long id = rs.getLong(RedListUtil.NAMNR);
String taxNameString = rs.getString(RedListUtil.TAXNAME);
addAnnotation(RedListUtil.WISSK+": "+wisskString, taxonBase);
//check taxon name consistency
- checkTaxonNameConsistency(id, taxNameString, hybString, taxonBase);
+ checkTaxonConsistency(id, taxNameString, hybString, taxonBase, state);
return taxonBase;
}
String zusatzString = rs.getString(RedListUtil.ZUSATZ);
String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
+ String hybString = rs.getString(RedListUtil.HYB);
//combination author
if(authorKombString.contains(RedListUtil.EX)){
//check authorship consistency
String authorString = rs.getString(RedListUtil.AUTOR);
- String authorshipCache = name.getAuthorshipCache();
- checkAuthorShipConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, authorshipCache);
+ checkNameConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, hybString, name);
}
private NonViralName<?> importName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave) throws SQLException {
name.setSpecificEpithet(ep2String);
}
}
- }
- //hybrid
- if(CdmUtils.isNotBlank(hybString)){
- //save hybrid formula
- if(CdmUtils.isNotBlank(formelString)){
- Annotation annotation = Annotation.NewDefaultLanguageInstance(formelString);
- annotation.setAnnotationType(AnnotationType.TECHNICAL());
- name.addAnnotation(annotation);
+ if(CdmUtils.isNotBlank(ep3String)){
+ name.setInfraSpecificEpithet(ep3String);
}
- if(hybString.equals(RedListUtil.HYB_X)){
- name.setBinomHybrid(true);
- if(CdmUtils.isNotBlank(ep3String)){
- name.setInfraSpecificEpithet(ep3String);
- }
- //nomenclatural status
- if(CdmUtils.isNotBlank(nomZusatzString)){
- NomenclaturalStatusType statusType = makeNomenclaturalStatus(id, state, nomZusatzString);
- if(statusType!=null){
- NomenclaturalStatus status = NomenclaturalStatus.NewInstance(statusType);
- //special case for invalid names where the DB entry contains
- //additional information in brackets e.g. "nom. inval. (sine basion.)"
- if(statusType.equals(NomenclaturalStatusType.INVALID())){
- Pattern pattern = Pattern.compile("\\((.*?)\\)");
- Matcher matcher = pattern.matcher(nomZusatzString);
- if (matcher.find()){
- status.setRuleConsidered(matcher.group(1));
- }
+
+ //nomenclatural status
+ if(CdmUtils.isNotBlank(nomZusatzString)){
+ NomenclaturalStatusType statusType = makeNomenclaturalStatus(id, state, nomZusatzString);
+ if(statusType!=null){
+ NomenclaturalStatus status = NomenclaturalStatus.NewInstance(statusType);
+ //special case for invalid names where the DB entry contains
+ //additional information in brackets e.g. "nom. inval. (sine basion.)"
+ if(statusType.equals(NomenclaturalStatusType.INVALID())){
+ Pattern pattern = Pattern.compile("\\((.*?)\\)");
+ Matcher matcher = pattern.matcher(nomZusatzString);
+ if (matcher.find()){
+ status.setRuleConsidered(matcher.group(1));
}
- name.addStatus(status);
}
+ name.addStatus(status);
}
- //hybrid
- if(CdmUtils.isNotBlank(hybString)){
- if(hybString.equals(RedListUtil.HYB_X)){
- name.setBinomHybrid(true);
- }
- else if(hybString.equals(RedListUtil.HYB_G)){
- name.setMonomHybrid(true);
+ }
+ //hybrid
+ if(CdmUtils.isNotBlank(hybString)){
+ //save hybrid formula
+ if(CdmUtils.isNotBlank(formelString)){
+ Annotation annotation = Annotation.NewDefaultLanguageInstance(formelString);
+ annotation.setAnnotationType(AnnotationType.TECHNICAL());
+ name.addAnnotation(annotation);
+ }
+ //more than two hybrids not yet handled by name parser
+ //TODO: use parser when implemented to fully support hybrids
+ if(taxNameString.split(RedListUtil.HYB_SIGN).length>2){
+ name = BotanicalName.NewInstance(rank);
+ name.setTitleCache(taxNameString, true);
+ }
+ else if(hybString.equals(RedListUtil.HYB_X)){
+ name.setBinomHybrid(true);
+ }
+ else if(hybString.equals(RedListUtil.HYB_G)){
+ name.setMonomHybrid(true);
+ }
+ else if(hybString.equals(RedListUtil.HYB_XF)){
+ name.setHybridFormula(true);
+ if(ep1String.contains(RedListUtil.HYB_SIGN)){
+ RedListUtil.logMessage(id, "EPI1 has hybrid signs but with flag: "+RedListUtil.HYB_XF, logger);
}
- else if(hybString.equals(RedListUtil.HYB_XF)){
- name.setHybridFormula(true);
- if(ep1String.contains(RedListUtil.HYB_SIGN)){
- RedListUtil.logMessage(id, "EPI1 has hybrid signs but with flag: "+RedListUtil.HYB_XF, logger);
+ else if(ep2String.contains(RedListUtil.HYB_SIGN)){
+ String[] split = ep2String.split(RedListUtil.HYB_SIGN);
+ String hybridFormula1 = ep1String+" "+split[0].trim();
+ String hybridFormula2 = ep1String+" "+split[1].trim();
+ //check if the specific epithets are from the same genus or not like e.g. EPI2 = pratensis × Lolium multiflorum
+ String[] secondHybrid = split[1].trim().split(" ");
+ if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
+ hybridFormula2 = split[1];
}
- else if(ep2String.contains(RedListUtil.HYB_SIGN)){
- String[] split = ep2String.split(RedListUtil.HYB_SIGN);
- if(split.length!=2){
- RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep2String, logger);
- }
- String hybridFormula1 = ep1String+" "+split[0].trim();
- String hybridFormula2 = ep1String+" "+split[1].trim();
- if(CdmUtils.isNotBlank(ep3String)){
- hybridFormula1 += " "+ep3String;
- hybridFormula2 += " "+ep3String;
- }
- String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
- name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula);
+ if(CdmUtils.isNotBlank(ep3String)){
+ hybridFormula1 += " "+ep3String;
+ hybridFormula2 += " "+ep3String;
}
- else if(ep3String.contains(RedListUtil.HYB_SIGN)){
- String[] split = ep3String.split(RedListUtil.HYB_SIGN);
- if(split.length!=2){
- RedListUtil.logMessage(id, "Multiple hybrid signs found in "+ep3String, logger);
- }
- String hybridFormula1 = ep1String+" "+ep2String+" "+split[0];
- String hybridFormula2 = ep1String+" "+ep2String+" "+split[1];
- String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
- name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula);
- }
- }
- else if(hybString.equals(RedListUtil.HYB_N)){
- name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String+" "+ep2String+" nothosubsp. "+ep3String);
+ String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
+ name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank);
}
- else if(hybString.equals(RedListUtil.HYB_GF)){
- if(ep1String.contains(RedListUtil.HYB_SIGN)){
- name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String);
- }
- else{
- RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
- }
+ else if(ep3String.contains(RedListUtil.HYB_SIGN)){
+ String[] split = ep3String.split(RedListUtil.HYB_SIGN);
+ String hybridFormula1 = ep1String+" "+ep2String+" "+split[0];
+ String hybridFormula2 = ep1String+" "+ep2String+" "+split[1];
+ String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
+ name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank);
}
- else if(hybString.equals(RedListUtil.HYB_XS)){
- //nothing to do
+ }
+ else if(hybString.equals(RedListUtil.HYB_N)){
+ name = NonViralNameParserImpl.NewInstance().parseFullName(taxNameString, NomenclaturalCode.ICNAFP, rank);
+ }
+ else if(hybString.equals(RedListUtil.HYB_GF)){
+ if(ep1String.contains(RedListUtil.HYB_SIGN)){
+ name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String, NomenclaturalCode.ICNAFP, rank);
}
else{
- logger.error("HYB value "+hybString+" not yet handled");
+ RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
}
}
+ else if(hybString.equals(RedListUtil.HYB_XS)){
+ //nothing to do
+ }
else{
logger.error("HYB value "+hybString+" not yet handled");
}
return name;
}
- private void checkAuthorShipConsistency(long id, String nomZusatzString, String taxZusatzString,
- String zusatzString, String authorString, String authorshipCache) {
+ private void checkNameConsistency(long id, String nomZusatzString, String taxZusatzString,
+ String zusatzString, String authorString, String hybString, NonViralName<?> name) {
+ String authorshipCache = name.getAuthorshipCache();
+ //FIXME: remove split length check when name parser can parse multiple hybrid parents
+ if(hybString.equals(RedListUtil.HYB_XF) && name.getTitleCache().split(RedListUtil.HYB_SIGN).length==2){
+ if(name.getHybridChildRelations().isEmpty()){
+ RedListUtil.logMessage(id, "Hybrid formula but no hybrid child relations: "+name.getTitleCache(), logger);
+ return;
+ }
+ return;
+ }
+
if(CdmUtils.isNotBlank(zusatzString)){
authorString = authorString.replace(", "+zusatzString, "");
}
}
}
- private void checkTaxonNameConsistency(long id, String taxNameString, String hybString, TaxonBase<?> taxonBase) {
- if(hybString.equals(RedListUtil.HYB_XF)){
- if(HibernateProxyHelper.deproxy(taxonBase.getName(),NonViralName.class).getHybridChildRelations().isEmpty()){
- RedListUtil.logMessage(id, "Hybrid name but no hybrid child relations: "+taxonBase.getTitleCache(), logger);
- return;
- }
- return;
- }
-
-
+ private void checkTaxonConsistency(long id, String taxNameString, String hybString, TaxonBase<?> taxonBase, RedListGefaesspflanzenImportState state) {
String nameCache = HibernateProxyHelper.deproxy(taxonBase.getName(), NonViralName.class).getNameCache().trim();
taxNameString = taxNameString.trim();
- taxNameString.replaceAll(" +", " ");
+ taxNameString = taxNameString.replaceAll(" +", " ");
if(taxNameString.endsWith("agg.")){
taxNameString = taxNameString.replace("agg.", "aggr.");
}
- if(hybString.equals(RedListUtil.HYB_X)){
+ if(hybString.equals(RedListUtil.HYB_X) || hybString.equals(RedListUtil.HYB_N)){
taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN+" ", " "+RedListUtil.HYB_SIGN);//hybrid sign has no space after it in titleCache for binomial hybrids
taxNameString = taxNameString.replace(" x ", " "+RedListUtil.HYB_SIGN);//in some cases a standard 'x' is used
}
taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN, " x");
}
- if(taxNameString.endsWith("- Gruppe")){String a ="Festuca ×xx Lolium <-> Festuca ×× Lolium";
+ if(taxNameString.endsWith("- Gruppe")){
taxNameString = taxNameString.replaceAll("- Gruppe", "species group");
}
if(taxNameString.endsWith("- group")){
}
taxNameString = taxNameString.replace("[ranglos]", "[unranked]");
+ if(taxonBase.getName().getRank()!=null){
+ if(taxonBase.getName().getRank().equals(Rank.PROLES())){
+ taxNameString = taxNameString.replace("proles", "prol.");
+ }
+ else if(taxonBase.getName().getRank().equals(state.getRank(RedListUtil.uuidRankCollectionSpecies))){
+ taxNameString = taxNameString.replace("\"Sammelart\"", "\"Coll. Species\"");
+ }
+ }
if(STRICT_TITLE_CHECK){
if(!taxNameString.trim().equals(nameCache)){
- RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.titleCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
+ RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
}
}
else{
if(!taxNameString.startsWith(nameCache)){
- RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.titleCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
+ RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
}
}
}
return Rank.UNRANKED_INFRAGENERIC();
}
}
+ else if(rankStr.equals("SAM")){
+ return getRank(state, RedListUtil.uuidRankCollectionSpecies, "Collective Species", "Collective Species", "\"Coll. Species\"", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.SpeciesGroup);
+ }
else{
rank = state.getTransformer().getRankByKey(rankStr);
}
BGBM BDI Projects / cdmlib-apps.git / blobdiff