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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.eflora.centralAfrica.checklist;
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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.api.service.IClassificationService;
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import eu.etaxonomy.cdm.common.CdmUtils;
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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.io.common.TdwgAreaProvider;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMapping;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMarkerMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportObjectCreationMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportTaxIncludedInMapper;
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import eu.etaxonomy.cdm.io.common.mapping.IMappingImport;
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import eu.etaxonomy.cdm.io.eflora.centralAfrica.checklist.validation.CentralAfricaChecklistTaxonImportValidator;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.IBotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
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import eu.etaxonomy.cdm.model.reference.OriginalSourceType;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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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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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.strategy.parser.NonViralNameParserImpl;
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/**
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* @author a.mueller
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* @since 20.02.2010
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*/
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@Component
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public class CentralAfricaChecklistTaxonImport extends CentralAfricaChecklistImportBase<TaxonBase> implements IMappingImport<TaxonBase, CentralAfricaChecklistImportState>{
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private static final Logger logger = Logger.getLogger(CentralAfricaChecklistTaxonImport.class);
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private NonViralNameParserImpl parser = NonViralNameParserImpl.NewInstance();
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private Map<UUID, Taxon> higherTaxonMap;
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private Integer TREE_ID = null;
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private DbImportMapping<?,?> mapping;
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private int modCount = 10000;
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private static final String pluralString = "taxa";
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private static final String dbTableName = "checklist";
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private static final Class cdmTargetClass = TaxonBase.class;
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private static final String strOrderBy = " ORDER BY family, genus, species ";
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public CentralAfricaChecklistTaxonImport(){
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super(pluralString, dbTableName, cdmTargetClass);
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.erms.ErmsImportBase#getIdQuery()
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*/
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@Override
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protected String getIdQuery() {
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String strQuery = " SELECT pk FROM " + dbTableName +
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strOrderBy;
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return strQuery;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.eflora.centralAfrica.checklist.CentralAfricaChecklistImportBase#getMapping()
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*/
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@Override
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protected DbImportMapping getMapping() {
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if (mapping == null){
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mapping = new DbImportMapping();
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mapping.addMapper(DbImportObjectCreationMapper.NewInstance(this, "pk", TAXON_NAMESPACE)); //id + tu_status
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UUID uuidKew = CentralAfricaChecklistTransformer.uuidAcceptedKew;
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mapping.addMapper(DbImportMarkerMapper.NewInstance("accepted kew", uuidKew, "Accepted Kew", "Accepted Kew", "Kew", null));
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UUID uuidGeneva = CentralAfricaChecklistTransformer.uuidAcceptedGeneva;
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mapping.addMapper(DbImportMarkerMapper.NewInstance("accepted geneva", uuidGeneva, "Accepted Geneva", "Accepted Geneva", "Geneva", null));
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UUID uuidItis = CentralAfricaChecklistTransformer.uuidAcceptedItis;
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mapping.addMapper(DbImportMarkerMapper.NewInstance("accepted itis", uuidItis, "Accepted ITIS", "Accepted ITIS", "ITIS", null));
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}
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return mapping;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
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*/
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@Override
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protected String getRecordQuery(CentralAfricaChecklistImportConfigurator config) {
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String strSelect = " SELECT * ";
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String strFrom = " FROM checklist";
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String strWhere = " WHERE ( pk IN (" + ID_LIST_TOKEN + ") )";
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String strRecordQuery = strSelect + strFrom + strWhere + strOrderBy;
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return strRecordQuery;
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}
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@Override
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public boolean doPartition(ResultSetPartitioner partitioner, CentralAfricaChecklistImportState state) {
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higherTaxonMap = new HashMap<UUID, Taxon>();
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Reference genevaReference = getReferenceService().find(state.getConfig().getUuidGenevaReference());
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if (genevaReference == null){
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genevaReference = makeGenevaReference(state);
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getReferenceService().save(genevaReference);
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}
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state.setGenevaReference(genevaReference);
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boolean success = super.doPartition(partitioner, state);
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higherTaxonMap = new HashMap<UUID, Taxon>();
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state.setGenevaReference(null);
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return success;
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}
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, CentralAfricaChecklistImportState state) {
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String nameSpace;
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Class<?> cdmClass;
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Set<String> idSet;
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Set<String> referenceIdSet = new HashSet<String>();
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
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try{
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while (rs.next()){
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handleForeignKey(rs, referenceIdSet, "source");
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}
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//reference map
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nameSpace = REFERENCE_NAMESPACE;
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cdmClass = Reference.class;
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idSet = referenceIdSet;
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Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, referenceIdSet, nameSpace);
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result.put(REFERENCE_NAMESPACE, referenceMap);
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} catch (SQLException e) {
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throw new RuntimeException(e);
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}
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return result;
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}
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@Override
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public TaxonBase<?> createObject(ResultSet rs, CentralAfricaChecklistImportState state) throws SQLException {
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IBotanicalName speciesName = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
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Reference sec = state.getConfig().getSourceReference();
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getReferenceService().saveOrUpdate(sec);
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String familyString = rs.getString("family");
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String genusString = rs.getString("genus");
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String speciesString = rs.getString("species");
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String authorityString = rs.getString("authority");
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if (logger.isDebugEnabled()){
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System.out.println(familyString + " " + genusString + " " + speciesString);
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}
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Taxon speciesTaxon = Taxon.NewInstance(speciesName, sec);;
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speciesName.setGenusOrUninomial(genusString);
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speciesName.setSpecificEpithet(speciesString);
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parser.handleAuthors(speciesName, CdmUtils.concat(" ", new String[] {"", genusString, speciesString, authorityString}), authorityString);
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//family
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Taxon familyTaxon = null;
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if (StringUtils.isNotBlank(familyString)){
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familyTaxon = getHigherTaxon(state, familyString, null);
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if (familyTaxon == null){
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IBotanicalName familyName = TaxonNameFactory.NewBotanicalInstance(Rank.FAMILY());
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familyName.setGenusOrUninomial(familyString);
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familyTaxon = Taxon.NewInstance(familyName, sec);
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saveHigherTaxon(state, familyTaxon, familyString, null);
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}
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getTaxonService().saveOrUpdate(familyTaxon);
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}
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//genus
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Taxon genusTaxon = getHigherTaxon(state, familyString, genusString);
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if (genusTaxon == null){
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IBotanicalName genusName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
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genusName.setGenusOrUninomial(genusString);
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genusTaxon = Taxon.NewInstance(genusName, sec);
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saveHigherTaxon(state, genusTaxon, familyString, genusString);
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if (familyTaxon != null){
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makeTaxonomicallyIncluded(state, TREE_ID, genusTaxon, familyTaxon, null, null);
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}
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}
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makeTaxonomicallyIncluded(state, TREE_ID, speciesTaxon, genusTaxon, null, null);
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getTaxonService().saveOrUpdate(genusTaxon);
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String sourceString = rs.getString("source");
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String sourceId = rs.getString("source_id");
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Reference sourceRef = state.getRelatedObject(REFERENCE_NAMESPACE, sourceString, Reference.class);
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speciesTaxon.addSource(OriginalSourceType.Import, sourceId, REFERENCE_NAMESPACE, sourceRef, null);
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//geneva id
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Reference genevaReference = state.getGenevaReference();
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Object genevaId = rs.getObject("geneva_ID");
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speciesTaxon.addSource(OriginalSourceType.Import, String.valueOf(genevaId), null, genevaReference, null);
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//distribution
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handleDistribution(rs, speciesTaxon);
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return speciesTaxon;
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}
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private void handleDistribution(ResultSet rs, Taxon speciesTaxon) throws SQLException {
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TaxonDescription description = TaxonDescription.NewInstance(speciesTaxon);
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Boolean isCongo = rs.getBoolean("drc");
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Boolean isBurundi = rs.getBoolean("burundi");
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Boolean isRwanda = rs.getBoolean("rwanda");
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addDistribution(description, isCongo, "ZAI");
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addDistribution(description, isBurundi, "BUR");
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addDistribution(description, isRwanda, "RWA");
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}
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/**
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* @param description
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* @param isCongo
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*/
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private void addDistribution(TaxonDescription description, Boolean exists, String label) {
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if (exists == true){
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NamedArea namedArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(label);
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Distribution distribution = Distribution.NewInstance(namedArea, PresenceAbsenceTerm.PRESENT());
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description.addElement(distribution);
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}
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}
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private void saveHigherTaxon(CentralAfricaChecklistImportState state, Taxon higherTaxon, String family, String genus) {
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String higherName = normalizeHigherTaxonName(family, genus);
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UUID uuid = higherTaxon.getUuid();
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state.putHigherTaxon(higherName, uuid);
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higherTaxonMap.put(uuid, higherTaxon);
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}
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private Taxon getHigherTaxon(CentralAfricaChecklistImportState state, String family, String genus) {
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String higherName = normalizeHigherTaxonName(family, genus);
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UUID uuid = state.getHigherTaxon(higherName);
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Taxon taxon = null;
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if (uuid != null){
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taxon = higherTaxonMap.get(uuid);
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if (taxon == null){
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taxon = CdmBase.deproxy(getTaxonService().find(uuid), Taxon.class);
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}
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}
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return taxon;
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}
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/**
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* @param family
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* @param genus
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*/
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private String normalizeHigherTaxonName(String family, String genus) {
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return (CdmUtils.Nz(family) + "-" + CdmUtils.Nz(genus)).trim();
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}
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// private boolean makeTaxonomicallyIncluded(CentralAfricaChecklistImportState state, Taxon parent, Taxon child, Reference citation, String microCitation){
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// Reference sec = child.getSec();
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// UUID uuid = state.getTreeUuid(sec);
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// Classification tree;
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// tree = state.getTree(sec);
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//
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// if (tree == null){
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// tree = makeTreeMemSave(state, sec);
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// }
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// TaxonNode childNode;
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// if (parent != null){
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// childNode = tree.addParentChild(parent, child, citation, microCitation);
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// }else{
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// childNode = tree.addChildTaxon(child, citation, microCitation, null);
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// }
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// return (childNode != null);
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// }
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//TODO use Mapper
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private boolean makeTaxonomicallyIncluded(CentralAfricaChecklistImportState state, Integer treeRefFk, Taxon child, Taxon parent, Reference citation, String microCitation){
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String treeKey;
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UUID treeUuid;
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if (treeRefFk == null){
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treeKey = "1"; // there is only one tree and it gets the map key '1'
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treeUuid = state.getConfig().getClassificationUuid();
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}else{
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treeKey =String.valueOf(treeRefFk);
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treeUuid = state.getTreeUuidByTreeKey(treeKey);
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}
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Classification tree = (Classification)state.getRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey);
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if (tree == null){
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IClassificationService service = state.getCurrentIO().getClassificationService();
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tree = service.find(treeUuid);
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if (tree == null){
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String treeName = state.getConfig().getClassificationName();
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tree = Classification.NewInstance(treeName);
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tree.setUuid(treeUuid);
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//FIXME tree reference
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//tree.setReference(ref);
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service.save(tree);
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}
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state.addRelatedObject(DbImportTaxIncludedInMapper.TAXONOMIC_TREE_NAMESPACE, treeKey, tree);
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}
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TaxonNode childNode = tree.addParentChild(parent, child, citation, microCitation);
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return (childNode != null);
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}
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private Reference makeGenevaReference(CentralAfricaChecklistImportState state) {
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Reference result = ReferenceFactory.newDatabase();
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result.setTitleCache(state.getConfig().getGenevaReferenceTitle(), true);
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result.setUuid(state.getConfig().getUuidGenevaReference());
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return result;
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}
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@Override
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protected boolean doCheck(CentralAfricaChecklistImportState state){
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IOValidator<CentralAfricaChecklistImportState> validator = new CentralAfricaChecklistTaxonImportValidator();
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return validator.validate(state);
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}
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@Override
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protected boolean isIgnore(CentralAfricaChecklistImportState state){
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return ! state.getConfig().isDoTaxa();
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}
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}
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