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.ResultSetPartitioner;
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.CdmBase;
import eu.etaxonomy.cdm.model.name.BotanicalName;
+import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
+import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
import eu.etaxonomy.cdm.model.name.Rank;
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;
/**
*
@Component
@SuppressWarnings("serial")
public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {
+
private static final Logger logger = Logger.getLogger(RedListGefaesspflanzenImportNames.class);
private static final String tableName = "Rote Liste Gefäßpflanzen";
private static final String pluralString = "names";
- private static final String NAME_NAMESPACE = "name";
-
public RedListGefaesspflanzenImportNames() {
super(tableName, pluralString);
}
public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {
ResultSet rs = partitioner.getResultSet();
Set<TaxonNameBase> namesToSave = new HashSet<TaxonNameBase>();
+ Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
try {
while (rs.next()){
- makeSingleName(state, rs, namesToSave);
+ makeSingleNameAndTaxon(state, rs, namesToSave, taxaToSave);
}
} catch (SQLException e) {
}
getNameService().saveOrUpdate(namesToSave);
+ getTaxonService().saveOrUpdate(taxaToSave);
return true;
}
- private void makeSingleName(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave)
+ private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)
throws SQLException {
- long id = rs.getLong("NAMNR");
- String taxNameString = rs.getString("TAXNAME");
- String rangString = rs.getString("RANG");
- String ep1String = rs.getString("EPI1");
- String ep2String = rs.getString("EPI2");
- String ep3String = rs.getString("EPI3");
- String nomZusatzString = rs.getString("NOM_ZUSATZ");
- String zusatzString = rs.getString("ZUSATZ");
- String authorKombString = rs.getString("AUTOR_KOMB");
- String authorBasiString = rs.getString("AUTOR_BASI");
-
+ 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 zusatzString = rs.getString(RedListUtil.ZUSATZ);
+ String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
+ String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
+
+ //---NAME---
if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){
- logger.error("NAMNR: "+id+" No name found!");
+ RedListUtil.logMessage(id, "No name found!", logger);
}
-
- Rank rank = makeRank(state, rangString);
+ Rank rank = makeRank(id, state, rangString);
+ if(rank==null){
+ RedListUtil.logMessage(id, "Rank could not be resolved.", logger);
+ }
BotanicalName 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(rank==Rank.SPECIES()){
- name.setGenusOrUninomial(ep1String);
+ if(!CdmUtils.isBlank(ep2String)){
+ name.setSpecificEpithet(ep2String);
+ }
+ if(!CdmUtils.isBlank(ep3String)){
+ if(rank==Rank.SUBSPECIES() ||
+ rank==Rank.VARIETY()){
+ name.setInfraSpecificEpithet(ep3String);
+ }
+ }
+ //nomenclatural status
+ NomenclaturalStatusType status = makeNomenclaturalStatus(id, state, nomZusatzString);
+ if(status!=null){
+ name.addStatus(NomenclaturalStatus.NewInstance(status));
}
- //add author
- TeamOrPersonBase authorKomb = HibernateProxyHelper.deproxy(getAgentService().load(state.getAuthorMap().get(authorKombString)), TeamOrPersonBase.class);
- name.setCombinationAuthorship(authorKomb);
- TeamOrPersonBase authorBasi = HibernateProxyHelper.deproxy(getAgentService().load(state.getAuthorMap().get(authorBasiString)), TeamOrPersonBase.class);
- name.setBasionymAuthorship(authorBasi);
+
+ //--- 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);
+ }
+ }
+ }
+ else if(authorKombString.trim().equals(RedListUtil.AUCT)){
+ RedListUtil.logMessage(id, "AUCT information in "+RedListUtil.AUTOR_KOMB+" column", logger);
+ }
+ else if(!CdmUtils.isBlank(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);
+ }
+ }
+ }
+ }
+ else if(authorBasiString.trim().equals(RedListUtil.AUCT)){
+ name.setAppendedPhrase(authorBasiString);
+ }
+ else if(!CdmUtils.isBlank(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);
+ if(CdmUtils.isBlank(authorKombString)){
+ name.setCombinationAuthorship(authorBasi);
+ }
+ else{
+ name.setBasionymAuthorship(authorBasi);
+ }
+ }
//check authorship consistency
- String authorString = rs.getString("AUTOR");
- if(!authorString.equals(name.getAuthorshipCache())){
- logger.warn("Authorship inconsisten! Name-AuthorhshipCache: +"+name.getAuthorshipCache()+" Column AUTOR: "+authorString);
+ String authorString = rs.getString(RedListUtil.AUTOR);
+ String authorshipCache = name.getAuthorshipCache();
+
+ if(!CdmUtils.isBlank(zusatzString)){
+ authorString = authorString.replace(", "+zusatzString, "");
+ }
+// if(CdmUtils.isBlank(authorKombString) && !CdmUtils.isBlank(authorBasiString)){
+// authorString = "("+authorString+")";
+// }
+ if(authorString.equals(RedListUtil.AUCT)){
+ authorString = "";
+ }
+ if(!authorString.equals(authorshipCache)){
+ RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);
}
//id
- ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, NAME_NAMESPACE);
+ ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);
+ state.getNameMap().put(id, name.getUuid());
namesToSave.add(name);
+
+ //---TAXON---
+ TaxonBase taxonBase = null;
+ if(gueltString.equals(RedListUtil.GUELT_ACCEPTED_TAXON) || (name.getAppendedPhrase()!=null && name.getAppendedPhrase().equals(RedListUtil.AUCT))){
+ taxonBase = Taxon.NewInstance(name, null);
+ }
+ else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){
+ taxonBase = Synonym.NewInstance(name, null);
+ }
+ if(taxonBase==null){
+ RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);
+ return;
+ }
+
+ taxaToSave.add(taxonBase);
+
+ //id
+ ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_NAMESPACE);
+ state.getTaxonMap().put(id, taxonBase.getUuid());
}
- private Rank makeRank(RedListGefaesspflanzenImportState state, String rankStr) {
+ private Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr) {
Rank rank = null;
try {
rank = state.getTransformer().getRankByKey(rankStr);
e.printStackTrace();
}
if(rank==null){
- logger.error(rankStr+" could not be associated to a known rank.");
+ RedListUtil.logMessage(id, rankStr+" could not be associated to a known rank.", logger);
}
return rank;
}
+ private NomenclaturalStatusType makeNomenclaturalStatus(long id, RedListGefaesspflanzenImportState state, String nomZusatzString) {
+ NomenclaturalStatusType status = null;
+ try {
+ status = state.getTransformer().getNomenclaturalStatusByKey(nomZusatzString);
+ } catch (UndefinedTransformerMethodException e) {
+ e.printStackTrace();
+ }
+ if(status==null){
+ RedListUtil.logMessage(id, nomZusatzString+" could not be associated to a known nomenclatural status.", logger);
+ }
+ return status;
+ }
+
@Override
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,
RedListGefaesspflanzenImportState state) {
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
-// Map<Long, AgentBase<?>> authorKombMap = new HashMap<>();
-// Map<Long, AgentBase<?>> authorBasiMap = new HashMap<>();
-//
-// //load authors
-// for(Entry<Long, UUID> entry:state.getAuthorKombMap().entrySet()){
-// authorKombMap.put(entry.getKey(), getAgentService().load(entry.getValue()));
-// }
-// for(Entry<Long, UUID> entry:state.getAuthorBasiMap().entrySet()){
-// authorBasiMap.put(entry.getKey(), getAgentService().load(entry.getValue()));
-// }
-// try {
-// while (rs.next()){
-// long id = rs.getLong("NAMNR");
-// }
-// } catch (SQLException e) {
-// e.printStackTrace();
-// }
-//
-// //Authors
-// Set<UUID> uuidSet = new HashSet<>();
-// for (String authorStr : authorKombSet){
-// UUID uuid = state.getAuthorUuid(authorStr);
-// uuidSet.add(uuid);
-// }
-// List<TeamOrPersonBase<?>> authors = (List)getAgentService().find(uuidSet);
-// Map<UUID, TeamOrPersonBase<?>> authorUuidMap = new HashMap<>();
-// for (TeamOrPersonBase<?> author : authors){
-// authorUuidMap.put(author.getUuid(), author);
-// }
-//
-// for (String authorStr : authorKombSet){
-// UUID uuid = state.getAuthorUuid(authorStr);
-// TeamOrPersonBase<?> author = authorUuidMap.get(uuid);
-// authorMap.put(authorStr, author);
-// }
-// result.put(AUTHOR_NAMESPACE, authorMap);
-//
-// //reference map
-// String nameSpace = REFERENCE_NAMESPACE;
-// Class<?> cdmClass = Reference.class;
-// Set<String> idSet = referenceIdSet;
-// Map<String, Reference<?>> referenceMap = (Map<String, Reference<?>>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
-// result.put(nameSpace, referenceMap);
-//
-// //secundum
-// UUID secUuid = state.getConfig().getSecUuid();
-// Reference<?> secRef = getReferenceService().find(secUuid);
-// referenceMap.put(secUuid.toString(), secRef);
+ Map<String, AgentBase<?>> authorMap = new HashMap<String, AgentBase<?>>();
+
+ try {
+ while (rs.next()){
+ String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);
+
+ if(authorKombString.contains(RedListUtil.EX)){
+ String[] kombSplit = authorKombString.split(RedListUtil.EX);
+ for (int i = 0; i < kombSplit.length; i++) {
+ if(!authorMap.containsKey(kombSplit[i])){
+ authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i])));
+ }
+ }
+ }
+ else if(!CdmUtils.isBlank(authorKombString) && !authorMap.containsKey(authorKombString)){
+ authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString)));
+ }
+
+ String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);
+ //basionym author
+ if(authorBasiString.contains(RedListUtil.EX)){
+ String[] basiSplit = authorBasiString.split(RedListUtil.EX);
+ for (int i = 0; i < basiSplit.length; i++) {
+ if(!authorMap.containsKey(basiSplit[i])){
+ authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i])));
+ }
+ }
+ }
+ else if(!CdmUtils.isBlank(authorBasiString) && !authorMap.containsKey(authorBasiString)){
+ authorMap.put(authorBasiString, getAgentService().load(state.getAuthorMap().get(authorBasiString)));
+ }
+ }
+ } catch (SQLException e) {
+ e.printStackTrace();
+ }
+ result.put(RedListUtil.AUTHOR_NAMESPACE, authorMap);
return result;
}
BGBM BDI Projects / cdmlib-apps.git / blobdiff