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.ExtensionType;
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;
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
-import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
-import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
/**
private static final boolean STRICT_TITLE_CHECK = false;
+ private ExtensionType extensionTypeFlor;
+
+ private ExtensionType extensionTypeAtlasIdx;
+
+ private ExtensionType extensionTypeKart;
+
+ private ExtensionType extensionTypeRl2015;
+
+ private ExtensionType extensionTypeEhrd;
+
+ private ExtensionType extensionTypeWissk;
+
public RedListGefaesspflanzenImportNames() {
super(tableName, pluralString);
}
@Override
protected String getIdQuery(RedListGefaesspflanzenImportState state) {
- return "SELECT NAMNR "
+ return "SELECT SEQNUM "
+ "FROM V_TAXATLAS_D20_EXPORT t "
- + " ORDER BY NAMNR";
+ + " ORDER BY SEQNUM";
}
@Override
protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {
String result = " SELECT * "
+ " FROM V_TAXATLAS_D20_EXPORT t "
- + " WHERE t.NAMNR IN (@IDSET)";
+ + " WHERE t.SEQNUM IN (@IDSET)";
result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);
return result;
}
@Override
protected void doInvoke(RedListGefaesspflanzenImportState state) {
+ makeExtensionTypes();
super.doInvoke(state);
}
+ private void makeExtensionTypes() {
+ extensionTypeFlor = ExtensionType.NewInstance(RedListUtil.FLOR, RedListUtil.FLOR, "");
+ extensionTypeAtlasIdx = ExtensionType.NewInstance(RedListUtil.ATLAS_IDX, RedListUtil.ATLAS_IDX, "");
+ extensionTypeKart = ExtensionType.NewInstance(RedListUtil.KART, RedListUtil.KART, "");
+ extensionTypeRl2015 = ExtensionType.NewInstance(RedListUtil.RL2015, RedListUtil.RL2015, "");
+ extensionTypeEhrd = ExtensionType.NewInstance(RedListUtil.EHRD, RedListUtil.EHRD, "");
+ extensionTypeWissk = ExtensionType.NewInstance(RedListUtil.WISSK, RedListUtil.WISSK, "");
+ getTermService().saveOrUpdate(extensionTypeFlor);
+ getTermService().saveOrUpdate(extensionTypeAtlasIdx);
+ getTermService().saveOrUpdate(extensionTypeKart);
+ getTermService().saveOrUpdate(extensionTypeRl2015);
+ getTermService().saveOrUpdate(extensionTypeEhrd);
+ getTermService().saveOrUpdate(extensionTypeWissk);
+ }
+
@Override
public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
ResultSet rs = partitioner.getResultSet();
private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)
throws SQLException {
long id = rs.getLong(RedListUtil.NAMNR);
- String clTaxonString = rs.getString(RedListUtil.CL_TAXON);
+ String relationE = rs.getString(RedListUtil.E);
+ String relationW = rs.getString(RedListUtil.W);
+ String relationK = rs.getString(RedListUtil.K);
+ String relationAW = rs.getString(RedListUtil.AW);
+ String relationAO = rs.getString(RedListUtil.AO);
+ String relationR = rs.getString(RedListUtil.R);
+ String relationO = rs.getString(RedListUtil.O);
+ String relationS = rs.getString(RedListUtil.S);
//---NAME---
NonViralName<?> name = importName(state, rs, namesToSave);
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);
+ RedListUtil.logMessage(id, "!SERIOUS ERROR! Taxon for name "+name+" could not be created!", logger);
return;
}
//---CONCEPT RELATIONSHIPS---
- //checklist
- TaxonBase<?> checklistTaxon = null;
- if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
- checklistTaxon = (TaxonBase<?>) taxonBase.clone();
- if(checklistTaxon.isInstanceOf(Taxon.class)){
- TaxonRelationship relation = HibernateProxyHelper.deproxy(checklistTaxon, Taxon.class).addTaxonRelation(HibernateProxyHelper.deproxy(taxonBase, Taxon.class), TaxonRelationshipType.CONGRUENT_TO(), null, null);
- relation.setDoubtful(true);
- }
-
- ImportHelper.setOriginalSource(checklistTaxon, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
- taxaToSave.add(checklistTaxon);
- }
//E, W, K, AW, AO, R, O, S
- cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_E, taxaToSave, id, state);
- cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_W, taxaToSave, id, state);
- cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_K, taxaToSave, id, state);
- cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_AW, taxaToSave, id, state);
- cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_AO, taxaToSave, id, state);
- cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_R, taxaToSave, id, state);
- cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_O, taxaToSave, id, state);
- cloneTaxon(taxonBase, RedListUtil.CLASSIFICATION_NAMESPACE_S, taxaToSave, id, state);
+ 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);
//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 Taxon cloneTaxon(final TaxonBase<?> gesamtListeTaxon, String sourceNameSpace, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
- Taxon clonedTaxon = null;
+ private void cloneTaxon(final TaxonBase<?> gesamtListeTaxon, String relationString, String sourceNameSpace, Set<TaxonBase> taxaToSave, long id, RedListGefaesspflanzenImportState state){
+ if(CdmUtils.isNotBlank(relationString) && !relationString.equals(".")){
+ 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;
+ 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;
+ }
+ 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 epi1String = rs.getString(RedListUtil.EPI1);
+ String epi2String = rs.getString(RedListUtil.EPI2);
+ String epi3String = rs.getString(RedListUtil.EPI3);
String gueltString = rs.getString(RedListUtil.GUELT);
String trivialString = rs.getString(RedListUtil.TRIVIAL);
String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
taxonBase = Synonym.NewInstance(name, null);
}
else{
+ RedListUtil.logMessage(id, "Taxon was not created!! Unknown value for "+RedListUtil.GUELT+"!", logger);
return null;
}
}
//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);
+ taxonBase.addExtension(florString, extensionTypeFlor);
+ taxonBase.addExtension(atlasIdxString, extensionTypeAtlasIdx);
+ taxonBase.addExtension(kartString, extensionTypeKart);
+ taxonBase.addExtension(rl2015String, extensionTypeRl2015);
+ taxonBase.addExtension(ehrdString, extensionTypeEhrd);
+ taxonBase.addExtension(wisskString, extensionTypeWissk);
//check taxon name consistency
- checkTaxonNameConsistency(id, taxNameString, hybString, taxonBase);
+ checkTaxonConsistency(id, taxNameString, hybString, epi1String, epi2String, epi3String, 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)){
- //TODO: what happens with multiple ex authors??
- String[] kombSplit = authorKombString.split(RedListUtil.EX);
- if(kombSplit.length!=2){
- RedListUtil.logMessage(id, "Multiple ex combination authors found", logger);
- }
- for (int i = 0; i < kombSplit.length; i++) {
- if(i==0){
- //first author is ex author
- TeamOrPersonBase<?> authorKomb = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
- name.setExCombinationAuthorship(authorKomb);
- }
- else{
- TeamOrPersonBase<?> authorKomb = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);
- name.setCombinationAuthorship(authorKomb);
- }
- }
+ // multiple ex authors will be reduced to only the last one
+ // e.g. Almq. ex Sternström ex Dahlst. -> Almq. ex Dahlst.
+ //first author is ex combination author
+ String exAuthorString = RedListUtil.getExAuthorOfExAuthorshipString(authorKombString);
+ TeamOrPersonBase<?> exAuthor = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, exAuthorString);
+ name.setExCombinationAuthorship(exAuthor);
+ //the last author is the combination author
+ String authorString = RedListUtil.getAuthorOfExAuthorshipString(authorKombString);
+ TeamOrPersonBase<?> combAuthor = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorString);
+ name.setCombinationAuthorship(combAuthor);
}
else if(authorKombString.trim().contains(RedListUtil.AUCT)){
RedListUtil.logMessage(id, "AUCT information in "+RedListUtil.AUTOR_KOMB+" column", logger);
}
//basionym author
if(authorBasiString.contains(RedListUtil.EX)){
- String[] basiSplit = authorBasiString.split(RedListUtil.EX);
- for (int i = 0; i < basiSplit.length; i++) {
- if(basiSplit.length!=2){
- RedListUtil.logMessage(id, "Multiple ex basionymn authors found", logger);
- }
- if(i==0){
- TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
- if(CdmUtils.isBlank(authorKombString)){
- name.setExCombinationAuthorship(authorBasi);
- }
- else{
- name.setExBasionymAuthorship(authorBasi);
- }
- }
- else{
- TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);
- if(CdmUtils.isBlank(authorKombString)){
- name.setCombinationAuthorship(authorBasi);
- }
- else{
- name.setBasionymAuthorship(authorBasi);
- }
- }
+ TeamOrPersonBase<?> authorExBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, RedListUtil.getExAuthorOfExAuthorshipString(authorBasiString));
+ if(CdmUtils.isBlank(authorKombString)){
+ name.setExCombinationAuthorship(authorExBasi);
+ }
+ else{
+ name.setExBasionymAuthorship(authorExBasi);
+ }
+ TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, RedListUtil.getAuthorOfExAuthorshipString(authorBasiString));
+ if(CdmUtils.isBlank(authorKombString)){
+ name.setCombinationAuthorship(authorBasi);
+ }
+ else{
+ name.setBasionymAuthorship(authorBasi);
}
}
else if(CdmUtils.isNotBlank(authorBasiString)){
//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 {
RedListUtil.logMessage(id, "No name found!", logger);
}
- Rank rank = makeRank(id, state, rangString, ep3String!=null);
- NonViralName<?> name = BotanicalName.NewInstance(rank);
-
- //ep1 should always be present
- if(CdmUtils.isBlank(ep1String)){
- RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
+ NonViralName<?> name = null;
+ Rank rank = makeRank(id, state, rangString, CdmUtils.isNotBlank(ep3String));
+ //cultivar
+ if(rank!= null && rank.equals(Rank.CULTIVAR())){
+ CultivarPlantName cultivar = CultivarPlantName.NewInstance(rank);
+ cultivar.setGenusOrUninomial(ep1String);
+ cultivar.setSpecificEpithet(ep2String);
+ cultivar.setCultivarName(ep3String);
+ name = cultivar;
}
- name.setGenusOrUninomial(ep1String);
- if(CdmUtils.isNotBlank(ep2String)){
- if(rank!=null && rank.isInfraGeneric()){
- name.setInfraGenericEpithet(ep2String);
- }
- else{
- name.setSpecificEpithet(ep2String);
+ //botanical names
+ else{
+ name = BotanicalName.NewInstance(rank);
+
+ //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)){
- //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);
- }
- 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()) || statusType.equals(NomenclaturalStatusType.REJECTED()) ){
+ 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)){
+ //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(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_G)){
+ name.setMonomHybrid(true);
+ }
+ else if(hybString.equals(RedListUtil.HYB_XF) || hybString.equals(RedListUtil.HYB_XU)){
+ name.setHybridFormula(true);
+ String fullFormula = buildHybridFormula(ep1String, ep2String, ep3String, rank);
+ name = NonViralNameParserImpl.NewInstance().parseFullName(fullFormula, NomenclaturalCode.ICNAFP, rank);
+ }
+ 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);
}
- String hybridFormula1 = ep1String+" "+split[0].trim();
- String hybridFormula2 = ep1String+" "+split[1].trim();
- if(CdmUtils.isNotBlank(ep3String)){
- hybridFormula1 += " "+ep3String;
- hybridFormula2 += " "+ep3String;
+ else{
+ RedListUtil.logMessage(id, "HYB is "+hybString+" but "+RedListUtil.HYB+" does not contain "+RedListUtil.HYB_SIGN, logger);
}
- 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);
- }
- 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");
+ }
+ //save hybrid formula
+ if(CdmUtils.isNotBlank(formelString)){
+ Annotation annotation = Annotation.NewDefaultLanguageInstance(formelString);
+ annotation.setAnnotationType(AnnotationType.TECHNICAL());
+ name.addAnnotation(annotation);
}
- }
- else if(hybString.equals(RedListUtil.HYB_XS)){
- //nothing to do
- }
- 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 String buildHybridFormula(String ep1String, String ep2String, String ep3String, Rank rank) {
+ String fullFormula = null;
+ if(ep1String.contains(RedListUtil.HYB_SIGN)){
+ fullFormula = ep1String;
+ }
+ 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 genus is mentioned in EP2 or not
+ String[] secondHybrid = split[1].trim().split(" ");
+ //check if the genus is abbreviated like e.g. Centaurea jacea × C. decipiens
+ if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
+ hybridFormula2 = ep1String+" "+split[1].trim().substring(3);
+ }
+ else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
+ hybridFormula2 = split[1].trim();
+ }
+ if(CdmUtils.isNotBlank(ep3String)){
+ hybridFormula1 += " "+rank.getAbbreviation()+" "+ep3String;
+ hybridFormula2 += " "+rank.getAbbreviation()+" "+ep3String;
+ }
+ fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
+ }
+ else if(ep3String.contains(RedListUtil.HYB_SIGN)){
+ String[] split = ep3String.split(RedListUtil.HYB_SIGN);
+ String hybridFormula1 = ep1String+" "+ep2String+" "+rank.getAbbreviation()+" "+split[0].trim();
+ String hybridFormula2 = ep1String+" "+ep2String+" "+rank.getAbbreviation()+" "+split[1].trim();
+ //check if the genus is mentioned in EP3 or not
+ String[] secondHybrid = split[1].trim().split(" ");
+ //check if the genus is abbreviated like e.g. Centaurea jacea jacea × C. jacea subsp. decipiens
+ if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z]\\.")){
+ hybridFormula2 = ep1String+" "+split[1].trim().substring(3);
+ }
+ else if(secondHybrid.length>1 && secondHybrid[0].matches("[A-Z].*")){
+ hybridFormula2 = split[1].trim();
+ }
+ fullFormula = hybridFormula1+" "+RedListUtil.HYB_SIGN+" "+hybridFormula2;
+ }
+ return fullFormula;
+ }
+
+ 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, "");
}
if(authorString.equals(RedListUtil.AUCT)){
authorString = "";
}
+ if(!STRICT_TITLE_CHECK && authorString.matches(".*ex.*ex.*")){
+ return;
+ }
if(STRICT_TITLE_CHECK){
if(!authorString.equals(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;
- }
+ private void checkTaxonConsistency(long id, String taxNameString, String hybString, String epi1String, String epi2String, String epi3String, TaxonBase<?> taxonBase, RedListGefaesspflanzenImportState state) {
+ if(taxNameString.split(RedListUtil.HYB_SIGN).length>2){
+ RedListUtil.logInfoMessage(id, "multiple hybrid signs. No name check for "+taxNameString, logger);
return;
}
-
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))
+ && nameCache.matches(".*\\s"+RedListUtil.HYB_SIGN+"\\w.*")){
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("X ", RedListUtil.HYB_SIGN);
}
else if(hybString.equals(RedListUtil.HYB_GF)){
- taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN, " x");
+ taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN+" ", " "+RedListUtil.HYB_SIGN);
+ }
+ else if(hybString.equals(RedListUtil.HYB_XF)){
+ nameCache = taxonBase.getName().getTitleCache();
+ if(nameCache.contains("sec")){
+ nameCache = nameCache.substring(0, nameCache.indexOf("sec"));
+ }
+ if(!STRICT_TITLE_CHECK){
+ taxNameString = buildHybridFormula(epi1String, epi2String, epi3String, taxonBase.getName().getRank());
+ }
+ if(taxNameString.split(RedListUtil.HYB_SIGN).length==1){
+ taxNameString = taxNameString.replace(RedListUtil.HYB_SIGN+" ", RedListUtil.HYB_SIGN);
+ }
}
- 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("agg.", "aggr.");
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);
}
}
}
if(rankStr.equals("ORA")){
//special handling for ORA because of two possibilities
if(hasSpecificEpithet){
- return Rank.UNRANKED_INFRASPECIFIC();
+ //re-load term because the representation was changed before
+ return (Rank) getTermService().load(Rank.uuidInfraspecificTaxon);
}
else{
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 if(rankStr.equals("SPR")){
+ return getRank(state, RedListUtil.uuidRankSubproles, "Subproles", "Subproles", "subproles", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
+ }
+ else if(rankStr.equals("MOD")){
+ return getRank(state, RedListUtil.uuidRankModification, "Modification", "Modification", "modificatio", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
+ }
+ else if(rankStr.equals("LUS")){
+ return getRank(state, RedListUtil.uuidRankLusus, "Lusus", "Lusus", "lusus", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
+ }
+ else if(rankStr.equals("SPI")){
+ return getRank(state, RedListUtil.uuidRankSubspeciesPrincipes, "Subspecies principes", "Subspecies principes", "subsp. princ.", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
+ }
+ else if(rankStr.equals("KMB")){
+ return getRank(state, RedListUtil.uuidRankCombination, "Combination", "Combination", "", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
+ }
+ else if(rankStr.equals("'FO")){
+ return getRank(state, RedListUtil.uuidRankForme, "Forme'", "Forme'", "", (OrderedTermVocabulary<Rank>) Rank.GENUS().getVocabulary(), null, RankClass.Infraspecific);
+ }
else{
rank = state.getTransformer().getRankByKey(rankStr);
}
BGBM BDI Projects / cdmlib-apps.git / blobdiff