import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;
import eu.etaxonomy.cdm.model.agent.AgentBase;
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
+import eu.etaxonomy.cdm.model.common.Annotation;
+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;
}
//---CONCEPT RELATIONSHIPS---
+ //E, W, K, AW, AO, R, O, S
+ cloneTaxon(taxonBase, relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxaToSave, id, state);
+ cloneTaxon(taxonBase, relationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxaToSave, id, state);
+ cloneTaxon(taxonBase, relationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxaToSave, id, state);
+ cloneTaxon(taxonBase, relationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxaToSave, id, state);
+ cloneTaxon(taxonBase, relationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxaToSave, id, state);
+ cloneTaxon(taxonBase, relationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxaToSave, id, state);
+ cloneTaxon(taxonBase, relationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxaToSave, id, state);
+ cloneTaxon(taxonBase, relationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxaToSave, id, state);
//checklist
TaxonBase<?> checklistTaxon = null;
if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
ImportHelper.setOriginalSource(checklistTaxon, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
taxaToSave.add(checklistTaxon);
}
- //E, W, K, AW, AO, R, O, S
- addConceptRelation(relationE, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxonBase, checklistTaxon, taxaToSave, id, state);
- addConceptRelation(relationW, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxonBase, checklistTaxon, taxaToSave, id, state);
- addConceptRelation(relationK, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxonBase, checklistTaxon, taxaToSave, id, state);
- addConceptRelation(relationAW, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxonBase, checklistTaxon, taxaToSave, id, state);
- addConceptRelation(relationAO, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxonBase, checklistTaxon, taxaToSave, id, state);
- addConceptRelation(relationR, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxonBase, checklistTaxon, taxaToSave, id, state);
- addConceptRelation(relationO, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxonBase, checklistTaxon, taxaToSave, id, state);
- addConceptRelation(relationS, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxonBase, checklistTaxon, taxaToSave, id, state);
//NOTE: the source has to be added after cloning or otherwise the clone would also get the source
ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);
taxaToSave.add(taxonBase);
}
- private void addConceptRelation(String relationString, String classificationNamespace, TaxonBase<?> gesamtListeTaxon, TaxonBase<?> checkListenTaxon, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
+ private void cloneTaxon(final TaxonBase<?> gesamtListeTaxon, String relationString, String sourceNameSpace, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
- String substring = relationString.substring(relationString.length()-1, relationString.length());
- TaxonRelationshipType taxonRelationshipTypeByKey = new RedListGefaesspflanzenTransformer().getTaxonRelationshipTypeByKey(substring);
- if(taxonRelationshipTypeByKey==null){
- RedListUtil.logMessage(id, "Could not interpret relationship "+relationString+" for taxon "+gesamtListeTaxon.generateTitle(), logger);
- }
- //there is no type "included in" so we have to reverse the direction
- if(substring.equals("<")){
- cloneTaxon(gesamtListeTaxon, checkListenTaxon, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, true, false, state);
- }
- else{
- cloneTaxon(gesamtListeTaxon, checkListenTaxon, taxonRelationshipTypeByKey, taxaToSave, id, classificationNamespace, false, false, state);
- }
- }
- }
-
- /**
- * 1. clone new taxon of gesamtListeTaxon with the same name (in that classification)<br>
- * 2. create concept relationship from clone to gesamtListeTaxon/checklisteTaxon or from its accepted taxon if it is synonym<br>
- *<br>
- * <b>NOTE:</b> the {@link TaxonRelationshipType} passed as parameter is
- * directed <b>from the clone</b> to the taxon.<br>
- * This can be changed with parameter <i>reverseRelation</i>
- * @return cloned taxon
- */
- private Taxon cloneTaxon(final TaxonBase<?> gesamtListeTaxon, final TaxonBase<?> checklisteTaxon, TaxonRelationshipType relationFromCloneToTaxon, Set<TaxonBase> taxaToSave, long id, String sourceNameSpace, boolean reverseRelation, boolean doubtful, RedListGefaesspflanzenImportState state){
- Taxon acceptedGesamtListeTaxon = getAcceptedTaxon(gesamtListeTaxon);
- Taxon acceptedChecklistTaxon = getAcceptedTaxon(checklisteTaxon);
- Taxon clonedTaxon = null;
-
- if(gesamtListeTaxon.isInstanceOf(Taxon.class)){
- clonedTaxon = HibernateProxyHelper.deproxy(gesamtListeTaxon.clone(), Taxon.class);
- }
- else if(gesamtListeTaxon.isInstanceOf(Synonym.class)){
- clonedTaxon = Taxon.NewInstance(gesamtListeTaxon.getName(), gesamtListeTaxon.getSec());
- }
- else{
- RedListUtil.logMessage(id, "Taxon base "+gesamtListeTaxon+" is neither taxon nor synonym! Taxon could not be cloned", logger);
- return null;
- }
+ Taxon clonedTaxon = null;
- if(reverseRelation){
- if(acceptedGesamtListeTaxon!=null){
- TaxonRelationship taxonRelation = acceptedGesamtListeTaxon.addTaxonRelation(clonedTaxon, relationFromCloneToTaxon, null, null);
- taxonRelation.setDoubtful(doubtful);
+ if(gesamtListeTaxon.isInstanceOf(Taxon.class)){
+ clonedTaxon = HibernateProxyHelper.deproxy(gesamtListeTaxon.clone(), Taxon.class);
}
- if(acceptedChecklistTaxon!=null) {
- TaxonRelationship taxonRelation = acceptedChecklistTaxon.addTaxonRelation(clonedTaxon, relationFromCloneToTaxon, null, null);
- taxonRelation.setDoubtful(doubtful);
+ else if(gesamtListeTaxon.isInstanceOf(Synonym.class)){
+ clonedTaxon = Taxon.NewInstance(gesamtListeTaxon.getName(), gesamtListeTaxon.getSec());
}
- }
- else {
- if(acceptedGesamtListeTaxon!=null){
- TaxonRelationship taxonRelation = clonedTaxon.addTaxonRelation(acceptedGesamtListeTaxon, relationFromCloneToTaxon, null, null);
- taxonRelation.setDoubtful(doubtful);
- }
- if(acceptedChecklistTaxon!=null) {
- TaxonRelationship taxonRelation = clonedTaxon.addTaxonRelation(acceptedChecklistTaxon, relationFromCloneToTaxon, null, null);
- taxonRelation.setDoubtful(doubtful);
+ else{
+ RedListUtil.logMessage(id, "Taxon base "+gesamtListeTaxon+" is neither taxon nor synonym! Taxon could not be cloned", logger);
+ return;
}
+ ImportHelper.setOriginalSource(clonedTaxon, state.getTransactionalSourceReference(), id, sourceNameSpace);
+ taxaToSave.add(clonedTaxon);
}
-
- ImportHelper.setOriginalSource(clonedTaxon, state.getTransactionalSourceReference(), id, sourceNameSpace);
- taxaToSave.add(clonedTaxon);
- return clonedTaxon;
}
- 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);
String trivialString = rs.getString(RedListUtil.TRIVIAL);
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
String hybString = rs.getString(RedListUtil.HYB);
+ String florString = rs.getString(RedListUtil.FLOR);
+ String atlasIdxString = rs.getString(RedListUtil.ATLAS_IDX);
+ String kartString = rs.getString(RedListUtil.KART);
+ String rl2015String = rs.getString(RedListUtil.RL2015);
+ String ehrdString = rs.getString(RedListUtil.EHRD);
+ String wisskString = rs.getString(RedListUtil.WISSK);
TaxonBase<?> taxonBase = null;
if(authorBasiString.trim().contains(RedListUtil.AUCT)){
description.addElement(CommonTaxonName.NewInstance(trivialString, Language.GERMAN()));
}
+ //add annotations
+ addAnnotation(RedListUtil.FLOR+": "+florString, taxonBase);
+ addAnnotation(RedListUtil.ATLAS_IDX+": "+atlasIdxString, taxonBase);
+ addAnnotation(RedListUtil.KART+": "+kartString, taxonBase);
+ addAnnotation(RedListUtil.RL2015+": "+rl2015String, taxonBase);
+ addAnnotation(RedListUtil.EHRD+": "+ehrdString, taxonBase);
+ addAnnotation(RedListUtil.WISSK+": "+wisskString, taxonBase);
+
//check taxon name consistency
- checkTaxonNameConsistency(id, taxNameString, hybString, taxonBase);
+ checkTaxonConsistency(id, taxNameString, hybString, taxonBase, state);
return taxonBase;
}
+ private void addAnnotation(String string, TaxonBase<?> taxonBase) {
+ if(CdmUtils.isNotBlank(string)){
+ taxonBase.addAnnotation(Annotation.NewInstance(string, AnnotationType.TECHNICAL(), Language.GERMAN()));
+ }
+ }
+
private void importAuthors(RedListGefaesspflanzenImportState state, ResultSet rs, NonViralName<?> name) throws SQLException {
long id = rs.getLong(RedListUtil.NAMNR);
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 {
String ep3String = rs.getString(RedListUtil.EPI3);
String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
String hybString = rs.getString(RedListUtil.HYB);
+ String formelString = rs.getString(RedListUtil.FORMEL);
if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
RedListUtil.logMessage(id, "No name found!", logger);
}
+ NonViralName<?> name = null;
Rank rank = makeRank(id, state, rangString, ep3String!=null);
- NonViralName<?> name = BotanicalName.NewInstance(rank);
+ //cultivar
+ if(rank!= null && rank.equals(Rank.CULTIVAR())){
+ CultivarPlantName cultivar = CultivarPlantName.NewInstance(rank);
+ cultivar.setGenusOrUninomial(ep1String);
+ cultivar.setSpecificEpithet(ep2String);
+ cultivar.setCultivarName(ep3String);
+ name = cultivar;
+ }
+ //botanical names
+ else{
+ name = BotanicalName.NewInstance(rank);
- //ep1 should always be present
- if(CdmUtils.isBlank(ep1String)){
- RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
- }
- name.setGenusOrUninomial(ep1String);
- if(CdmUtils.isNotBlank(ep2String)){
- if(rank!=null && rank.isInfraGeneric()){
- name.setInfraGenericEpithet(ep2String);
- }
- else{
- name.setSpecificEpithet(ep2String);
+ //ep1 should always be present
+ if(CdmUtils.isBlank(ep1String)){
+ RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
}
- }
- 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));
- }
+ name.setGenusOrUninomial(ep1String);
+ if(CdmUtils.isNotBlank(ep2String)){
+ if(rank!=null && rank.isInfraGenericButNotSpeciesGroup()){
+ name.setInfraGenericEpithet(ep2String);
+ }
+ else{
+ name.setSpecificEpithet(ep2String);
}
- name.addStatus(status);
}
- }
- //hybrid
- if(CdmUtils.isNotBlank(hybString)){
- if(hybString.equals(RedListUtil.HYB_X)){
- name.setBinomHybrid(true);
+ if(CdmUtils.isNotBlank(ep3String)){
+ name.setInfraSpecificEpithet(ep3String);
}
- else if(hybString.equals(RedListUtil.HYB_G)){
- name.setMonomHybrid(true);
+
+
+ //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);
+ }
}
- 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);
+ //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(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);
+ 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(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];
+ }
+ if(CdmUtils.isNotBlank(ep3String)){
+ hybridFormula1 += " "+ep3String;
+ hybridFormula2 += " "+ep3String;
+ }
+ String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
+ name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank);
}
- String hybridFormula1 = ep1String+" "+split[0].trim();
- String hybridFormula2 = ep1String+" "+split[1].trim();
- if(CdmUtils.isNotBlank(ep3String)){
- hybridFormula1 += " "+ep3String;
- hybridFormula2 += " "+ep3String;
+ 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);
}
- String fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
- name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula);
}
- 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);
+ 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{
+ RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, 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);
- }
- else if(hybString.equals(RedListUtil.HYB_GF)){
- if(ep1String.contains(RedListUtil.HYB_SIGN)){
- name = NonViralNameParserImpl.NewInstance().parseFullName(ep1String);
+ else if(hybString.equals(RedListUtil.HYB_XS)){
+ //nothing to do
}
else{
- RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
+ logger.error("HYB value "+hybString+" not yet handled");
}
}
- else{
- logger.error("HYB value "+hybString+" not yet handled");
- }
}
//add source
ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);
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, "");
}
}
}
else{
- if(!authorString.startsWith(authorshipCache)){
+ if(CdmUtils.isNotBlank(authorString) && !authorString.startsWith(authorshipCache)){
RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
}
}
}
- 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", 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(taxNameString.endsWith("aggr.")){
- taxNameString = taxNameString.replaceFirst(" ", " (");
- taxNameString = taxNameString.replace(" aggr.", ") 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.replaceAll("- group", "species group");
}
- if(taxNameString.endsWith("species group")){
- taxNameString = taxNameString.replaceFirst(" ", " (");
- taxNameString = taxNameString.replace(" species group", ") species 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