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package eu.etaxonomy.cdm.io.berlinModel;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Map;
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import org.apache.log4j.Logger;
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import eu.etaxonomy.cdm.api.application.CdmApplicationController;
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import eu.etaxonomy.cdm.api.service.INameService;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator;
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import eu.etaxonomy.cdm.io.common.ImportHelper;
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import eu.etaxonomy.cdm.io.common.MapWrapper;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.name.BotanicalName;
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import eu.etaxonomy.cdm.model.name.CultivarPlantName;
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import eu.etaxonomy.cdm.model.name.NonViralName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.name.ZoologicalName;
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import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
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public class BerlinModelTaxonNameIO extends BerlinModelIOBase {
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameIO.class);
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private static int modCount = 5000;
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public BerlinModelTaxonNameIO(){
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super();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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@Override
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protected boolean doCheck(IImportConfigurator config){
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boolean result = true;
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logger.warn("Checking for TaxonNames not yet implemented");
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//result &= checkArticlesWithoutJournal(bmiConfig);
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//result &= checkPartOfJournal(bmiConfig);
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return result;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
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*/
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@Override
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protected boolean doInvoke(IImportConfigurator config,
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Map<String, MapWrapper<? extends CdmBase>> stores){
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MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)stores.get(ICdmIO.TAXONNAME_STORE);
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MapWrapper<TeamOrPersonBase> authorMap = (MapWrapper<TeamOrPersonBase>)stores.get(ICdmIO.AUTHOR_STORE);
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BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;
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Source source = bmiConfig.getSource();
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String dbAttrName;
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String cdmAttrName;
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boolean success = true ;
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logger.info("start makeTaxonNames ...");
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INameService nameService = config.getCdmAppController().getNameService();
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try {
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//get data from database
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String strQuery =
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"SELECT Name.* , RefDetail.RefDetailId, RefDetail.RefFk, " +
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" RefDetail.FullRefCache, RefDetail.FullNomRefCache, RefDetail.PreliminaryFlag AS RefDetailPrelim, RefDetail.Details, " +
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" RefDetail.SecondarySources, RefDetail.IdInSource, Rank.RankAbbrev, Rank.Rank " +
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" FROM Name LEFT OUTER JOIN RefDetail ON Name.NomRefDetailFk = RefDetail.RefDetailId AND " +
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" Name.NomRefFk = RefDetail.RefFk " +
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" LEFT OUTER JOIN Rank ON Name.RankFk = Rank.rankID " +
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" WHERE (1=1) ";
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//strQuery += " AND RefDetail.PreliminaryFlag = 1 ";
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//strQuery += " AND Name.Created_When > '03.03.2004' ";
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ResultSet rs = source.getResultSet(strQuery) ;
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String namespace = "Name";
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int i = 0;
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//for each reference
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while (rs.next()){
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if ((i++ % modCount) == 0 && i != 1 ){ logger.info("Names handled: " + (i-1));}
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//create TaxonName element
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int nameId = rs.getInt("nameId");
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Object authorFk = rs.getObject("AuthorTeamFk");
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Object exAuthorFk = rs.getObject("ExAuthorTeamFk");
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Object basAuthorFk = rs.getObject("BasAuthorTeamFk");
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Object exBasAuthorFk = rs.getObject("ExBasAuthorTeamFk");
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try {
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boolean useUnknownRank = true;
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Rank rank = BerlinModelTransformer.rankId2Rank(rs, useUnknownRank);
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TaxonNameBase taxonNameBase;
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if (bmiConfig.getNomenclaturalCode() != null){
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taxonNameBase = bmiConfig.getNomenclaturalCode().getNewTaxonNameInstance(rank);
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}else{
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taxonNameBase = NonViralName.NewInstance(rank);
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}
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if (rank == null){
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//TODO rank should never be null or a more sophisticated algorithm has to be implemented for genus/supraGenericName
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logger.warn("Rank is null. Genus epethiton was imported. May be wrong");
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}
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if (rank != null && rank.isSupraGeneric()){
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dbAttrName = "supraGenericName";
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}else{
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dbAttrName = "genus";
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}
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cdmAttrName = "genusOrUninomial";
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success &= ImportHelper.addStringValue(rs, taxonNameBase, dbAttrName, cdmAttrName);
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dbAttrName = "genusSubdivisionEpi";
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cdmAttrName = "infraGenericEpithet";
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success &= ImportHelper.addStringValue(rs, taxonNameBase, dbAttrName, cdmAttrName);
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dbAttrName = "speciesEpi";
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cdmAttrName = "specificEpithet";
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success &= ImportHelper.addStringValue(rs, taxonNameBase, dbAttrName, cdmAttrName);
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dbAttrName = "infraSpeciesEpi";
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cdmAttrName = "infraSpecificEpithet";
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success &= ImportHelper.addStringValue(rs, taxonNameBase, dbAttrName, cdmAttrName);
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dbAttrName = "unnamedNamePhrase";
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cdmAttrName = "appendedPhrase";
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success &= ImportHelper.addStringValue(rs, taxonNameBase, dbAttrName, cdmAttrName);
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dbAttrName = "preliminaryFlag";
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cdmAttrName = "XX" + "protectedTitleCache";
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success &= ImportHelper.addBooleanValue(rs, taxonNameBase, dbAttrName, cdmAttrName);
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//Details
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dbAttrName = "details";
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cdmAttrName = "nomenclaturalMicroReference";
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success &= ImportHelper.addStringValue(rs, taxonNameBase, dbAttrName, cdmAttrName);
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//nomRef
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success &= makeNomenclaturalReference(bmiConfig, taxonNameBase, nameId, rs, stores);
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//created, notes
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success &= doIdCreatedUpdatedNotes(bmiConfig, taxonNameBase, rs, nameId, namespace);
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//Marker
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boolean flag = true;
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Marker marker = Marker.NewInstance(MarkerType.TO_BE_CHECKED() ,flag);
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taxonNameBase.addMarker(marker);
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//NonViralName
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if (taxonNameBase instanceof NonViralName){
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NonViralName nonViralName = (NonViralName)taxonNameBase;
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//authorTeams
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if (authorMap != null ){
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boolean ignoreNull = config.isIgnoreNull();
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nonViralName.setCombinationAuthorTeam(getAuthorTeam(authorMap, authorFk, nameId, ignoreNull));
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nonViralName.setExCombinationAuthorTeam(getAuthorTeam(authorMap, exAuthorFk, nameId, ignoreNull));
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nonViralName.setBasionymAuthorTeam(getAuthorTeam(authorMap, basAuthorFk, nameId, ignoreNull));
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nonViralName.setExBasionymAuthorTeam(getAuthorTeam(authorMap, exBasAuthorFk, nameId, ignoreNull));
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}
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}//nonviralName
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177
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//zoologicalName
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if (taxonNameBase instanceof ZoologicalName){
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ZoologicalName zooName = (ZoologicalName)taxonNameBase;
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makeZoologialName(rs, zooName, nameId);
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}
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//botanicalName
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else if (taxonNameBase instanceof BotanicalName){
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BotanicalName botName = (BotanicalName)taxonNameBase;
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success &= makeBotanicalNamePart(rs, botName) ;
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}
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189
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190
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//TODO
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//Source_Acc
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//OrthoProjection
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//TODO
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//preliminaryFlag see above
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taxonNameMap.put(nameId, taxonNameBase);
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}
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catch (UnknownCdmTypeException e) {
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logger.warn("Name with id " + nameId + " has unknown rankId " + " and could not be saved.");
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success = false;
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}
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} //while rs.hasNext()
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logger.info(i + " names handled");
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nameService.saveTaxonNameAll(taxonNameMap.objects());
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// makeNameSpecificData(nameMap);
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logger.info("end makeTaxonNames ...");
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return success;
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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return false;
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}
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218
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}
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221
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private boolean makeZoologialName(ResultSet rs, ZoologicalName zooName, int nameId)
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throws SQLException{
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boolean success = true;
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//publicationYear
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String authorTeamYear = rs.getString("authorTeamYear");
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try {
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if (! "".equals(CdmUtils.Nz(authorTeamYear).trim())){
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Integer publicationYear = Integer.valueOf(authorTeamYear.trim());
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zooName.setPublicationYear(publicationYear);
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}
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} catch (NumberFormatException e) {
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logger.warn("authorTeamYear could not be parsed for taxonName: "+ nameId);
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}
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234
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//original publication year
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235
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String basAuthorTeamYear = rs.getString("basAuthorTeamYear");
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try {
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if (! "".equals(CdmUtils.Nz(basAuthorTeamYear).trim())){
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238
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Integer OriginalPublicationYear = Integer.valueOf(basAuthorTeamYear.trim());
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zooName.setOriginalPublicationYear(OriginalPublicationYear);
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}
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} catch (NumberFormatException e) {
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242
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logger.warn("basAuthorTeamYear could not be parsed for taxonName: "+ nameId);
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243
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}
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244
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return success;
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245
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}
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246
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247
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private boolean makeBotanicalNamePart(ResultSet rs, BotanicalName botanicalName){
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248
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boolean success = true;
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249
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String dbAttrName;
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250
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String cdmAttrName;
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251
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252
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dbAttrName = "HybridFormulaFlag";
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253
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cdmAttrName = "isHybridFormula";
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254
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success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
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255
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256
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dbAttrName = "MonomHybFlag";
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257
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cdmAttrName = "isMonomHybrid";
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258
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success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
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259
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260
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dbAttrName = "BinomHybFlag";
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261
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cdmAttrName = "isBinomHybrid";
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262
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success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
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263
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264
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dbAttrName = "TrinomHybFlag";
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265
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cdmAttrName = "isTrinomHybrid";
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266
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success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
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267
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268
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if (botanicalName instanceof CultivarPlantName){
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269
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//TODO
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270
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//CultivarGroupName
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271
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//CultivarName
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272
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}
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273
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return success;
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274
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}
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275
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276
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277
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private boolean makeNomenclaturalReference(IImportConfigurator config, TaxonNameBase taxonNameBase,
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278
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int nameId, ResultSet rs, Map<String, MapWrapper<? extends CdmBase>> stores)
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279
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throws SQLException{
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280
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MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);
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281
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MapWrapper<ReferenceBase> nomRefMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.NOMREF_STORE);
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282
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MapWrapper<ReferenceBase> refDetailMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REF_DETAIL_STORE);
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283
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MapWrapper<ReferenceBase> nomRefDetailMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.NOMREF_DETAIL_STORE);
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284
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285
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Object nomRefFk = rs.getObject("NomRefFk");
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286
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int nomRefDetailFk = rs.getInt("NomRefDetailFk");
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287
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boolean refDetailPrelim = rs.getBoolean("RefDetailPrelim");
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288
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289
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boolean success = true;
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290
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//nomenclatural Reference
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291
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if (referenceMap != null){
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292
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if (nomRefFk != null){
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293
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int nomRefFkInt = (Integer)nomRefFk;
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294
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295
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//get nomRef
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296
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ReferenceBase nomReference = nomRefDetailMap.get(nomRefDetailFk);
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297
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if (nomReference == null){
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298
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nomReference = refDetailMap.get(nomRefDetailFk);
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299
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}
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300
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if (nomReference == null){
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301
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nomReference = nomRefMap.get(nomRefFkInt);
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302
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}if (nomReference == null){
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303
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nomReference = referenceMap.get(nomRefFkInt);
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304
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}
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305
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306
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//setNomRef
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307
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if (nomReference == null ){
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308
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//TODO
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309
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if (! config.isIgnoreNull()){logger.warn("Nomenclatural reference (nomRefFk = " + nomRefFkInt + ") for TaxonName (nameId = " + nameId + ")"+
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310
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" was not found in reference store. Nomenclatural reference was not set!!");}
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311
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}else if (! INomenclaturalReference.class.isAssignableFrom(nomReference.getClass())){
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312
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logger.error("Nomenclatural reference (nomRefFk = " + nomRefFkInt + ") for TaxonName (nameId = " + nameId + ")"+
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313
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" is not assignable from INomenclaturalReference. Relation was not set!! (Class = " + nomReference.getClass()+ ")");
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314
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}else{
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315
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nomReference.setNomenclaturallyRelevant(true);
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316
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taxonNameBase.setNomenclaturalReference((INomenclaturalReference)nomReference);
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317
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}
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318
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}
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319
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}
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320
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return success;
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|
321
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}
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|
322
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|
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323
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private static TeamOrPersonBase getAuthorTeam(MapWrapper<TeamOrPersonBase> authorMap, Object teamIdObject, int nameId, boolean ignoreNull){
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|
324
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if (teamIdObject == null){
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325
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return null;
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|
326
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}else {
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327
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int teamId = (Integer)teamIdObject;
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328
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TeamOrPersonBase author = authorMap.get(teamId);
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329
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if (author == null){
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330
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//TODO
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331
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if (!ignoreNull){ logger.warn("AuthorTeam (teamId = " + teamId + ") for TaxonName (nameId = " + nameId + ")"+
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332
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" was not found in authorTeam store. Relation was not set!!");}
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333
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return null;
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|
334
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// }else if(teamId == 0){ //casus El Salvador
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|
335
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// //do nothing
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|
336
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// return null;
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|
337
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}else{
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338
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return author;
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|
339
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}
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|
340
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}
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|
341
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}
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|
342
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|
|
343
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/* (non-Javadoc)
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344
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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345
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*/
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346
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protected boolean isIgnore(IImportConfigurator config){
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347
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return ! config.isDoTaxonNames();
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348
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}
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349
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350
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351
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//FOR FUTURE USE , DONT DELETE
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352
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// new CdmStringMapper("nameId", "nameId"),
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353
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// new CdmStringMapper("rankFk", "rankFk"),
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354
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// new CdmStringMapper("nameCache", "nameCache"),
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355
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// new CdmStringMapper("unnamedNamePhrase", "unnamedNamePhrase"),
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356
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// new CdmStringMapper("fullNameCache", "fullNameCache"),
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357
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// new CdmStringMapper("preliminaryFlag", "preliminaryFlag"),
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358
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// new CdmStringMapper("supragenericName", "supragenericName"),
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359
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// new CdmStringMapper("genus", "genus"),
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360
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// new CdmStringMapper("genusSubdivisionEpi", "genusSubdivisionEpi"),
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361
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// new CdmStringMapper("speciesEpi", "speciesEpi"),
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362
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// new CdmStringMapper("infraSpeciesEpi", "infraSpeciesEpi"),
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363
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// new CdmStringMapper("authorTeamFk", "authorTeamFk"),
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364
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// new CdmStringMapper("exAuthorTeamFk", "exAuthorTeamFk"),
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365
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// new CdmStringMapper("basAuthorTeamFk", "basAuthorTeamFk"),
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366
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// new CdmStringMapper("exBasAuthorTeamFk", "exBasAuthorTeamFk"),
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367
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// new CdmStringMapper("hybridFormulaFlag", "hybridFormulaFlag"),
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368
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// new CdmStringMapper("monomHybFlag", "monomHybFlag"),
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369
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// new CdmStringMapper("binomHybFlag", "binomHybFlag"),
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370
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// new CdmStringMapper("trinomHybFlag", "trinomHybFlag"),
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371
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// new CdmStringMapper("cultivarGroupName", "cultivarGroupName"),
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372
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// new CdmStringMapper("cultivarName", "cultivarName"),
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373
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// new CdmStringMapper("nomRefFk", "nomRefFk"),
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374
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// new CdmStringMapper("nomRefDetailFk", "nomRefDetailFk"),
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375
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// new CdmStringMapper("nameSourceRefFk", "nameSourceRefFk"),
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376
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// new CdmStringMapper("source_Acc", "source_Acc"),
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377
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// new CdmStringMapper("created_When", "created_When"),
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378
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// new CdmStringMapper("created_Who", "created_Who"),
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379
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// new CdmStringMapper("notes", "notes"),
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380
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// new CdmStringMapper("parsingComments", "parsingComments"),
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381
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// new CdmStringMapper("oldNomRefFk", "oldNomRefFk"),
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382
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// new CdmStringMapper("oldNomRefDetailFk", "oldNomRefDetailFk"),
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383
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// new CdmStringMapper("updated_Who", "updated_Who"),
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384
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// new CdmStringMapper("orthoProjection", "orthoProjection"),
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385
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386
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387
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}
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