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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.io.berlinModel.in;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_ACCEPTED;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_PARTIAL_SYN;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_PRO_PARTE_SYN;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_SYNONYM;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_UNRESOLVED;
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import java.lang.reflect.Method;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.commons.lang.StringUtils;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.database.update.DatabaseTypeNotSupportedException;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonImportValidator;
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import eu.etaxonomy.cdm.io.common.IOValidator;
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import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.common.ExtensionType;
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import eu.etaxonomy.cdm.model.common.Language;
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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.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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/**
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* @author a.mueller
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* @since 20.03.2008
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*/
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@Component
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public class BerlinModelTaxonImport extends BerlinModelImportBase {
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private static final long serialVersionUID = -1186364983750790695L;
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private static final Logger logger = Logger.getLogger(BerlinModelTaxonImport.class);
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public static final String NAMESPACE = "Taxon";
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private static final String pluralString = "Taxa";
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private static final String dbTableName = "PTaxon";
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/**
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* How should the publish flag in table PTaxon be interpreted
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* NO_MARKER: No marker is set
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* ONLY_FALSE:
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*/
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public enum PublishMarkerChooser{
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NO_MARKER,
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ONLY_FALSE,
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ONLY_TRUE,
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ALL;
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boolean doMark(boolean value){
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if (value == true){
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return this == ALL || this == ONLY_TRUE;
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}else{
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return this == ALL || this == ONLY_FALSE;
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}
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}
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}
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public BerlinModelTaxonImport(){
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super(dbTableName, pluralString);
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}
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@Override
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protected String getIdQuery(BerlinModelImportState state) {
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String sqlSelect = " SELECT RIdentifier";
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String taxonTable = state.getConfig().getTaxonTable();
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String sqlFrom = String.format(" FROM %s ", taxonTable);
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String sqlWhere = "";
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String sql = sqlSelect + " " + sqlFrom + " " + sqlWhere ;
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return sql;
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}
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@Override
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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String sqlSelect = " SELECT pt.* ";
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String sqlFrom = " FROM PTaxon pt ";
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if (isEuroMed(config) ){
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sqlFrom = " FROM PTaxon AS pt " +
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" INNER JOIN v_cdm_exp_taxaAll AS em ON pt.RIdentifier = em.RIdentifier " +
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" LEFT OUTER JOIN Reference r ON pt.LastScrutinyFk = r.RefId ";
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sqlSelect += " , em.MA, r.RefCache as LastScrutiny ";
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}
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String sqlWhere = " WHERE ( pt.RIdentifier IN (" + ID_LIST_TOKEN + ") )";
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String strRecordQuery =sqlSelect + " " + sqlFrom + " " + sqlWhere ;
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// " SELECT * " +
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// " FROM PTaxon " + state.getConfig().getTaxonTable();
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// " WHERE ( RIdentifier IN (" + ID_LIST_TOKEN + ") )";
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return strRecordQuery;
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}
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private boolean isEuroMed(BerlinModelImportConfigurator config) {
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return config.getTaxonTable().trim().equals("v_cdm_exp_taxaAll");
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}
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@Override
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protected boolean doCheck(BerlinModelImportState state){
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IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonImportValidator();
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return validator.validate(state);
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}
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@Override
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public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
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boolean success = true ;
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BerlinModelImportConfigurator config = state.getConfig();
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Set<TaxonBase> taxaToSave = new HashSet<>();
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Map<String, TaxonName> taxonNameMap = partitioner.getObjectMap(BerlinModelTaxonNameImport.NAMESPACE);
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Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);
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ResultSet rs = partitioner.getResultSet();
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try{
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boolean publishFlagExists = state.getConfig().getSource().checkColumnExists("PTaxon", "PublishFlag");
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boolean isEuroMed = isEuroMed(state.getConfig());
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while (rs.next()){
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// if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("PTaxa handled: " + (i-1));}
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//create TaxonName element
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int taxonId = rs.getInt("RIdentifier");
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int statusFk = rs.getInt("statusFk");
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int nameFk = rs.getInt("PTNameFk");
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int refFkInt = rs.getInt("PTRefFk");
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String doubtful = rs.getString("DoubtfulFlag");
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String uuid = null;
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if (resultSetHasColumn(rs,"UUID")){
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uuid = rs.getString("UUID");
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}
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TaxonName taxonName = null;
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taxonName = taxonNameMap.get(String.valueOf(nameFk));
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Reference reference = null;
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String refFk = String.valueOf(refFkInt);
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reference = refMap.get(refFk);
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if(! config.isIgnoreNull()){
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if (taxonName == null ){
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logger.warn("TaxonName belonging to taxon (RIdentifier = " + taxonId + ") could not be found in store. Taxon will not be imported");
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success = false;
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continue; //next taxon
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}else if (reference == null ){
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logger.warn("Reference belonging to taxon could not be found in store. Taxon will not be imported");
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success = false;
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continue; //next taxon
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}
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}
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TaxonBase<?> taxonBase;
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Synonym synonym;
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Taxon taxon;
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try {
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logger.debug(statusFk);
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if (statusFk == T_STATUS_ACCEPTED || statusFk == T_STATUS_UNRESOLVED ){
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taxon = Taxon.NewInstance(taxonName, reference);
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taxonBase = taxon;
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if (statusFk == T_STATUS_UNRESOLVED){
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taxon.setTaxonStatusUnknown(true);
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}
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}else if (statusFk == T_STATUS_SYNONYM || statusFk == T_STATUS_PRO_PARTE_SYN || statusFk == T_STATUS_PARTIAL_SYN){
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synonym = Synonym.NewInstance(taxonName, reference);
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taxonBase = synonym;
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if (statusFk == T_STATUS_PRO_PARTE_SYN){
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synonym.setProParte(true);
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}
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if (statusFk == T_STATUS_PARTIAL_SYN){
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synonym.setPartial(true);
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}
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}else{
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logger.warn("TaxonStatus " + statusFk + " not yet implemented. Taxon (RIdentifier = " + taxonId + ") left out.");
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success = false;
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continue;
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}
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if (uuid != null){
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taxonBase.setUuid(UUID.fromString(uuid));
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}
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//doubtful
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if (doubtful.equals("a")){
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taxonBase.setDoubtful(false);
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}else if(doubtful.equals("d")){
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taxonBase.setDoubtful(true);
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}else if(doubtful.equals("i")){
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taxonBase.setDoubtful(false);
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logger.warn("Doubtful = i (inactivated) does not exist in CDM. Doubtful set to false. RIdentifier: " + taxonId);
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}
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//detail
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String detail = rs.getString("Detail");
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if (isNotBlank(detail)){
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ExtensionType detailExtensionType = getExtensionType(state, BerlinModelTransformer.DETAIL_EXT_UUID, "micro reference","micro reference","micro ref.");
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Extension.NewInstance(taxonBase, detail, detailExtensionType);
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}
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//idInSource
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String idInSource = rs.getString("IdInSource");
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if (isNotBlank(idInSource)){
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ExtensionType detailExtensionType = getExtensionType(state, BerlinModelTransformer.ID_IN_SOURCE_EXT_UUID, "Berlin Model IdInSource","Berlin Model IdInSource","BM source id");
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Extension.NewInstance(taxonBase, idInSource, detailExtensionType);
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}
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//namePhrase
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String namePhrase = rs.getString("NamePhrase");
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if (StringUtils.isNotBlank(namePhrase)){
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taxonBase.setAppendedPhrase(namePhrase);
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}
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//useNameCache
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Boolean useNameCacheFlag = rs.getBoolean("UseNameCacheFlag");
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if (useNameCacheFlag){
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taxonBase.setUseNameCache(true);
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}
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//publisheFlag
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if (publishFlagExists){
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Boolean publishFlag = rs.getBoolean("PublishFlag");
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Boolean misapplied = false;
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if (isEuroMed){
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misapplied = rs.getBoolean("MA");
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}
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if ( ! misapplied){
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taxonBase.setPublish(publishFlag);
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}
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}
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//
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if (resultSetHasColumn(rs, "LastScrutiny")){
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String lastScrutiny = rs.getString("LastScrutiny");
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//TODO strange, why not Extension last scrutiny? To match PESI? Is there a difference
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//to LastScrutinyFK and SpeciesExpertFK?
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if (isNotBlank(lastScrutiny)){
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ExtensionType extensionTypeSpeciesExpert = getExtensionType(state, BerlinModelTransformer.uuidSpeciesExpertName, "Species Expert", "Species Expert", "Species Expert");
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taxonBase.addExtension(lastScrutiny, extensionTypeSpeciesExpert);
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ExtensionType extensionTypeExpert = getExtensionType(state, BerlinModelTransformer.uuidExpertName, "Expert", "Expert for a taxonomic group", "Expert");
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taxonBase.addExtension(lastScrutiny, extensionTypeExpert);
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}
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}
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//
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if (resultSetHasColumn(rs, "IsExcludedMarker")){
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boolean isExcluded = rs.getBoolean("IsExcludedMarker");
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if (isExcluded){
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String extension = rs.getString("IsExcludedExtension");
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String valueless = "not accepted: taxonomically valueless local or singular biotype";
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String provisional = "provisional: probably a taxonomically valueless local or singular biotype";
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MarkerType markerType = null;
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if (valueless.equals(extension)){
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markerType = getMarkerType(state, BerlinModelTransformer.uuidTaxonomicallyValueless, "taxonomically valueless", valueless, "valueless");
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}else if (provisional.equals(extension)){
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markerType = getMarkerType(state, BerlinModelTransformer.uuidProbablyTaxonomicallyValueless, "probably taxonomically valueless", provisional, "provisional");
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}
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if (markerType != null){
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taxonBase.addMarker(Marker.NewInstance(markerType, true));
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}else{
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logger.warn("IsExcludedExtension not regonized for taxon " + taxonId + "; " + extension);
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}
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}
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}
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288
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289
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//Notes
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boolean excludeNotes = state.getConfig().isTaxonNoteAsFeature() && taxonBase.isInstanceOf(Taxon.class);
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doIdCreatedUpdatedNotes(state, taxonBase, rs, taxonId, NAMESPACE, false, excludeNotes);
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if (excludeNotes){
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makeTaxonomicNote(state, CdmBase.deproxy(taxonBase, Taxon.class), rs.getString("Notes"));
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}
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295
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//external url
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if (config.getMakeUrlForTaxon() != null){
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Method urlMethod = config.getMakeUrlForTaxon();
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urlMethod.invoke(null, taxonBase, rs);
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}
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301
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partitioner.startDoSave();
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taxaToSave.add(taxonBase);
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} catch (Exception e) {
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logger.warn("An exception (" +e.getMessage()+") occurred when creating taxon with id " + taxonId + ". Taxon could not be saved.");
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success = false;
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}
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}
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} catch (DatabaseTypeNotSupportedException e) {
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logger.error("MethodNotSupportedException:" + e);
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return false;
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} catch (Exception e) {
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logger.error("SQLException:" + e);
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return false;
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}
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316
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317
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// logger.info( i + " names handled");
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getTaxonService().save(taxaToSave);
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return success;
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321
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}
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322
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323
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/**
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* @param state
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325
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* @param taxonBase
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326
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* @param notes
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*/
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private void makeTaxonomicNote(BerlinModelImportState state, Taxon taxon, String notes) {
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if (isNotBlank(notes)){
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TaxonDescription desc = getTaxonDescription(taxon, false, true);
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desc.setDefault(true); //hard coded for Salvador, not used elsewhere as far as I can see
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TextData textData = TextData.NewInstance(Feature.NOTES() , notes, Language.SPANISH_CASTILIAN(), null);
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desc.addElement(textData);
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}
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335
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}
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336
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337
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
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339
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String nameSpace;
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340
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Class<?> cdmClass;
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341
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Set<String> idSet;
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342
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
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343
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344
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try{
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345
|
Set<String> nameIdSet = new HashSet<>();
|
|
346
|
Set<String> referenceIdSet = new HashSet<>();
|
|
347
|
while (rs.next()){
|
|
348
|
handleForeignKey(rs, nameIdSet, "PTNameFk");
|
|
349
|
handleForeignKey(rs, referenceIdSet, "PTRefFk");
|
|
350
|
}
|
|
351
|
|
|
352
|
//name map
|
|
353
|
nameSpace = BerlinModelTaxonNameImport.NAMESPACE;
|
|
354
|
cdmClass = TaxonName.class;
|
|
355
|
idSet = nameIdSet;
|
|
356
|
Map<String, Person> nameMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
357
|
result.put(nameSpace, nameMap);
|
|
358
|
|
|
359
|
//reference map
|
|
360
|
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
|
|
361
|
cdmClass = Reference.class;
|
|
362
|
idSet = referenceIdSet;
|
|
363
|
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
364
|
result.put(nameSpace, referenceMap);
|
|
365
|
|
|
366
|
} catch (SQLException e) {
|
|
367
|
throw new RuntimeException(e);
|
|
368
|
}
|
|
369
|
return result;
|
|
370
|
}
|
|
371
|
|
|
372
|
@Override
|
|
373
|
protected String getTableName() {
|
|
374
|
return dbTableName;
|
|
375
|
}
|
|
376
|
|
|
377
|
@Override
|
|
378
|
public String getPluralString() {
|
|
379
|
return pluralString;
|
|
380
|
}
|
|
381
|
|
|
382
|
@Override
|
|
383
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
384
|
return ! state.getConfig().isDoTaxa();
|
|
385
|
}
|
|
386
|
|
|
387
|
|
|
388
|
|
|
389
|
}
|