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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.pesi.indexFungorum;
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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 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.io.common.ResultSetPartitioner;
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import eu.etaxonomy.cdm.io.pesi.out.PesiTransformer;
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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.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.reference.Reference;
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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 27.02.2012
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*/
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@Component
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public class IndexFungorumDistributionImport extends IndexFungorumImportBase {
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private static final long serialVersionUID = -815842161276543719L;
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private static final Logger logger = Logger.getLogger(IndexFungorumDistributionImport.class);
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private static final String pluralString = "distributions";
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private static final String dbTableName = "[tblPESIfungi]";
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public IndexFungorumDistributionImport(){
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super(pluralString, dbTableName);
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}
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@Override
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protected String getIdQuery() {
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String result = " SELECT PreferredNameIFnumber FROM " + getTableName() +
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" ORDER BY PreferredNameIFnumber ";
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return result;
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}
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@Override
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protected String getRecordQuery(IndexFungorumImportConfigurator config) {
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String strRecordQuery =
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" SELECT distribution.* " +
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" FROM tblPESIfungi AS distribution " +
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" WHERE ( distribution.PreferredNameIFnumber IN (" + ID_LIST_TOKEN + ") )" +
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"";
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return strRecordQuery;
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}
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@Override
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public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner,
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IndexFungorumImportState state) {
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boolean success = true;
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// Reference sourceReference = state.getRelatedObject(NAMESPACE_REFERENCE, SOURCE_REFERENCE, Reference.class);
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ResultSet rs = partitioner.getResultSet();
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try {
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//column names that do not hold distribution information
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Set<String> excludedColumns = new HashSet<>();
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excludedColumns.add("PreferredName");
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excludedColumns.add("PreferredNameIFnumber");
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excludedColumns.add("PreferredNameFDCnumber");
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PresenceAbsenceTerm status = PresenceAbsenceTerm.PRESENT();
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MarkerType noLastActionMarkerType = getNoLastActionMarkerType(state);
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while (rs.next()){
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//get taxon description
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Integer id = rs.getInt("PreferredNameIFnumber");
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Taxon taxon = state.getRelatedObject(NAMESPACE_SPECIES, String.valueOf(id), Taxon.class);
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Reference ref = null;
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if (taxon == null){
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logger.debug("taxon is null for id " + id);
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} else{
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TaxonDescription description = getTaxonDescription(taxon, ref, false, true);
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//handle single distributions
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int count = rs.getMetaData().getColumnCount();
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for (int i=1; i <= count; i++ ){
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String colName = rs.getMetaData().getColumnName(i);
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//exclude non distribution columns
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if (! excludedColumns.contains(colName)){
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String distributionValue = rs.getString(i);
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if (StringUtils.isNotBlank(distributionValue)){
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//create distribution for existing occurrences
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if (! distributionValue.equals("X")){
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logger.warn("Unexpected distribution value '" + distributionValue + "' for area " + colName);
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}
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NamedArea area = state.getTransformer().getNamedAreaByKey(colName);
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Distribution distribution = Distribution.NewInstance(area, status);
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description.addElement(distribution);
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//no last action
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distribution.addMarker(Marker.NewInstance(noLastActionMarkerType, true));
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}
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}
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}
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getTaxonService().saveOrUpdate(taxon);
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}
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//save
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}
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} catch (Exception e) {
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e.printStackTrace();
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logger.error(e.getMessage());
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state.setSuccess(false);
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success = false;
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}
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return success;
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}
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private Taxon getParentTaxon(IndexFungorumImportState state, ResultSet rs) throws SQLException {
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Integer genusId = rs.getInt("PreferredNameFDCnumber");
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Taxon taxon = state.getRelatedObject(NAMESPACE_GENERA, String.valueOf(genusId), Taxon.class);
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if (taxon == null){
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logger.warn("Taxon not found for " + genusId);
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}
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return taxon;
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}
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@Override
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public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, IndexFungorumImportState state) {
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String nameSpace;
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Set<String> idSet;
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Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
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try{
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Set<String> taxonIdSet = new HashSet<>();
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while (rs.next()){
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handleForeignKey(rs, taxonIdSet, "PreferredNameIFnumber" );
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}
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//taxon map
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nameSpace = NAMESPACE_SPECIES;
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idSet = taxonIdSet;
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@SuppressWarnings({ "rawtypes" })
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Map<String, TaxonBase> taxonMap = getCommonService().getSourcedObjectsByIdInSourceC(TaxonBase.class, idSet, nameSpace);
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result.put(nameSpace, taxonMap);
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//sourceReference
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Reference sourceReference = getReferenceService().find(PesiTransformer.uuidSourceRefIndexFungorum);
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Map<String, Reference> referenceMap = new HashMap<>();
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referenceMap.put(SOURCE_REFERENCE, sourceReference);
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result.put(NAMESPACE_REFERENCE, 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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protected boolean doCheck(IndexFungorumImportState state){
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return true;
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}
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@Override
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protected boolean isIgnore(IndexFungorumImportState state){
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return ! state.getConfig().isDoOccurrence();
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}
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}
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