import java.util.HashSet;
import java.util.Map;
import java.util.Set;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
import org.apache.log4j.Logger;
import org.springframework.stereotype.Component;
import eu.etaxonomy.cdm.common.CdmUtils;
+import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.io.common.DbImportBase;
import eu.etaxonomy.cdm.io.common.IPartitionedIO;
import eu.etaxonomy.cdm.io.common.ImportHelper;
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.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 String pluralString = "names";
+ 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 taxNameString = rs.getString(RedListUtil.TAXNAME);
- String gueltString = rs.getString(RedListUtil.GUELT);
- String rangString = rs.getString(RedListUtil.RANG);
- String ep1String = rs.getString(RedListUtil.EPI1);
- String ep2String = rs.getString(RedListUtil.EPI2);
- String ep3String = rs.getString(RedListUtil.EPI3);
- String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
- String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
- String zusatzString = rs.getString(RedListUtil.ZUSATZ);
- String nonString = rs.getString(RedListUtil.NON);
- String sensuString = rs.getString(RedListUtil.SENSU);
- String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
- String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
- String hybString = rs.getString(RedListUtil.HYB);
+ 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---
- if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
- RedListUtil.logMessage(id, "No name found!", logger);
+ NonViralName<?> name = importName(state, rs, namesToSave);
+
+
+ //--- AUTHORS ---
+ importAuthors(state, rs, name);
+
+ //---TAXON---
+ TaxonBase<?> taxonBase = importTaxon(rs, name, state);
+ if(taxonBase==null){
+ RedListUtil.logMessage(id, "!SERIOUS ERROR! Taxon for name "+name+" could not be created!", logger);
+ return;
}
- Rank rank = makeRank(id, state, rangString);
- BotanicalName name = BotanicalName.NewInstance(rank);
+ //---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);
- //ep1 should always be present
- if(CdmUtils.isBlank(ep1String)){
- RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);
+ //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 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;
+ }
+ ImportHelper.setOriginalSource(clonedTaxon, state.getTransactionalSourceReference(), id, sourceNameSpace);
+ taxaToSave.add(clonedTaxon);
}
- name.setGenusOrUninomial(ep1String);
- if(CdmUtils.isNotBlank(ep2String)){
- name.setSpecificEpithet(ep2String);
+ }
+
+ 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);
+ 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)){
+ taxonBase = Taxon.NewInstance(name, null);
+ taxonBase.setAppendedPhrase(RedListUtil.AUCT);
}
- if(CdmUtils.isNotBlank(ep3String)){
- if(rank==Rank.SUBSPECIES() ||
- rank==Rank.VARIETY()){
- name.setInfraSpecificEpithet(ep3String);
- }
+ else if(gueltString.equals(RedListUtil.GUELT_ACCEPTED_TAXON)){
+ taxonBase = Taxon.NewInstance(name, null);
}
- //nomenclatural status
- if(CdmUtils.isNotBlank(nomZusatzString)){
- NomenclaturalStatusType status = makeNomenclaturalStatus(id, state, nomZusatzString);
- if(status!=null){
- name.addStatus(NomenclaturalStatus.NewInstance(status));
- }
+ else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){
+ taxonBase = Synonym.NewInstance(name, null);
}
- //hybrid
- if(hybString.equals(RedListUtil.HYB_X)){
- name.setBinomHybrid(true);
+ else{
+ RedListUtil.logMessage(id, "Taxon was not created!! Unknown value for "+RedListUtil.GUELT+"!", logger);
+ return null;
}
- else if(hybString.equals(RedListUtil.HYB_XF)){
- name.setTrinomHybrid(true);
+
+ //common name
+ if(taxonBase.isInstanceOf(Taxon.class) && trivialString!=null){
+ Taxon taxon = HibernateProxyHelper.deproxy(taxonBase, Taxon.class);
+ TaxonDescription description = TaxonDescription.NewInstance(taxon);
+ description.addElement(CommonTaxonName.NewInstance(trivialString, Language.GERMAN()));
}
+ //add annotations
+ 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
+ checkTaxonConsistency(id, taxNameString, hybString, epi1String, epi2String, epi3String, taxonBase, state);
+ return taxonBase;
+ }
+
+ private void importAuthors(RedListGefaesspflanzenImportState state, ResultSet rs, NonViralName<?> name) throws SQLException {
+
+ long id = rs.getLong(RedListUtil.NAMNR);
+ String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);
+ String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);
+ 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);
- //--- AUTHORS ---
//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);
}
else if(CdmUtils.isNotBlank(authorKombString)){
- TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorKombString);
+ TeamOrPersonBase<?> authorKomb = (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorKombString);
name.setCombinationAuthorship(authorKomb);
}
//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)){
//this seems to be a convention in the source database: When there is only a single author then only the "AUTOR_BASI" column is used
- TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorBasiString);
+ TeamOrPersonBase<?> authorBasi= (TeamOrPersonBase<?>) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorBasiString);
if(CdmUtils.isBlank(authorKombString)){
name.setCombinationAuthorship(authorBasi);
}
//check authorship consistency
String authorString = rs.getString(RedListUtil.AUTOR);
+ checkNameConsistency(id, nomZusatzString, taxZusatzString, zusatzString, authorString, hybString, name);
+ }
+
+ private NonViralName<?> importName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave) throws SQLException {
+
+ long id = rs.getLong(RedListUtil.NAMNR);
+ String taxNameString = rs.getString(RedListUtil.TAXNAME);
+ String rangString = rs.getString(RedListUtil.RANG);
+ String ep1String = rs.getString(RedListUtil.EPI1);
+ String ep2String = rs.getString(RedListUtil.EPI2);
+ 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, 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;
+ }
+ //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.isInfraGenericButNotSpeciesGroup()){
+ name.setInfraGenericEpithet(ep2String);
+ }
+ else{
+ name.setSpecificEpithet(ep2String);
+ }
+ }
+ 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()) || statusType.equals(NomenclaturalStatusType.REJECTED()) ){
+ Pattern pattern = Pattern.compile("\\((.*?)\\)");
+ Matcher matcher = pattern.matcher(nomZusatzString);
+ if (matcher.find()){
+ status.setRuleConsidered(matcher.group(1));
+ }
+ }
+ name.addStatus(status);
+ }
+ }
+ //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(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);
+ }
+ else{
+ 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");
+ }
+ //save hybrid formula
+ if(CdmUtils.isNotBlank(formelString)){
+ Annotation annotation = Annotation.NewDefaultLanguageInstance(formelString);
+ annotation.setAnnotationType(AnnotationType.TECHNICAL());
+ name.addAnnotation(annotation);
+ }
+ }
+ }
+
+ //add source
+ ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);
+
+ namesToSave.add(name);
+ return name;
+ }
+
+ 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(!authorString.equals(authorshipCache)){
- RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
+ 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);
+ }
}
+ else{
+ if(CdmUtils.isNotBlank(authorString) && !authorString.startsWith(authorshipCache)){
+ RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
+ }
+ }
+ }
- //id
- ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);
- state.getNameMap().put(id, name.getUuid());
+ 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;
+ }
- namesToSave.add(name);
+ String nameCache = HibernateProxyHelper.deproxy(taxonBase.getName(), NonViralName.class).getNameCache().trim();
+ taxNameString = taxNameString.trim();
+ taxNameString = taxNameString.replaceAll(" +", " ");
- //---TAXON---
- TaxonBase taxonBase = null;
- if(authorBasiString.trim().contains(RedListUtil.AUCT)){
- taxonBase = Taxon.NewInstance(name, null);
- taxonBase.setAppendedPhrase(RedListUtil.AUCT);
+
+ 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
}
- else if(gueltString.equals(RedListUtil.GUELT_ACCEPTED_TAXON)){
- taxonBase = Taxon.NewInstance(name, null);
+ else if(hybString.equals(RedListUtil.HYB_G)){
+ taxNameString = taxNameString.replace("X ", RedListUtil.HYB_SIGN);
}
- else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){
- taxonBase = Synonym.NewInstance(name, null);
+ else if(hybString.equals(RedListUtil.HYB_GF)){
+ taxNameString = taxNameString.replace(" "+RedListUtil.HYB_SIGN+" ", " "+RedListUtil.HYB_SIGN);
}
- if(taxonBase==null){
- RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
- return;
+ 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);
+ }
}
- //check taxon name consistency
- String nameCache = ((BotanicalName)taxonBase.getName()).getNameCache().trim();
-
- if(taxNameString.endsWith("agg.")){
- taxNameString = taxNameString.replace("agg.", "aggr.");
+ if(taxNameString.endsWith("- Gruppe")){
+ taxNameString = taxNameString.replaceAll("- Gruppe", "species group");
}
- if(hybString.equalsIgnoreCase(RedListUtil.HYB_X)){
- taxNameString = taxNameString.replace("× ", "×");//hybrid sign has no space after it in titleCache for binomial hybrids
+ if(taxNameString.endsWith("- group")){
+ taxNameString = taxNameString.replaceAll("- group", "species group");
}
- if(taxNameString.endsWith(Rank.SPECIESGROUP().toString())){
- taxNameString.replaceAll(Rank.SPECIESGROUP().toString(), "- Gruppe");
- if(!taxNameString.trim().equals(nameCache)){
- taxNameString.replaceAll(Rank.SPECIESGROUP().toString(), "- 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(!taxNameString.trim().equals(nameCache)){
- RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.titleCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
+ if(STRICT_TITLE_CHECK){
+ if(!taxNameString.trim().equals(nameCache)){
+ RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
+ }
}
-
- /*check if taxon/synonym is also in checklist
- * 1. create new taxon with the same name (in the checklist classification)
- * 2. create congruent concept relationship between both
- */
- String clTaxonString = rs.getString(RedListUtil.CL_TAXON);
- if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){
- TaxonBase clone = (TaxonBase) taxonBase.clone();
- clone.setName(name);
- if(taxonBase.isInstanceOf(Taxon.class)){
- TaxonRelationship taxonRelation = ((Taxon) taxonBase).addTaxonRelation((Taxon) clone, TaxonRelationshipType.CONGRUENT_TO(), null, null);
- taxonRelation.setDoubtful(true);//TODO Ist das mit " mit Fragezeichen" gemeint?
+ else{
+ if(!taxNameString.startsWith(nameCache)){
+ RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.nameCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);
}
- ImportHelper.setOriginalSource(clone, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);
- taxaToSave.add(clone);
}
-
- //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 Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr) {
+ private Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr, boolean hasSpecificEpithet) {
Rank rank = null;
try {
- rank = state.getTransformer().getRankByKey(rankStr);
+ if(rankStr.equals("ORA")){
+ //special handling for ORA because of two possibilities
+ if(hasSpecificEpithet){
+ //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);
+ }
} catch (UndefinedTransformerMethodException e) {
e.printStackTrace();
}
BGBM BDI Projects / cdmlib-apps.git / blobdiff