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// $Id$
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/**
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* Copyright (C) 2009 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.out;
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import java.sql.SQLException;
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import java.util.List;
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import java.util.Set;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import org.springframework.transaction.TransactionStatus;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.common.IExportConfigurator.DO_REFERENCES;
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import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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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.TaxonNameBase;
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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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* The export class for additional information linked to {@link eu.etaxonomy.cdm.model.taxon.Taxon Taxa} and {@link eu.etaxonomy.cdm.model.reference.Reference References}.<p>
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* Inserts into DataWarehouse database table <code>AdditionalTaxonSource</code>.
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* @author e.-m.lee
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* @date 23.02.2010
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*
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*/
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@Component
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@SuppressWarnings("unchecked")
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public class PesiAdditionalTaxonSourceExport extends PesiExportBase {
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private static final Logger logger = Logger.getLogger(PesiAdditionalTaxonSourceExport.class);
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private static final Class<? extends CdmBase> standardMethodParameter = Reference.class;
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private static int modCount = 1000;
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private static final String dbTableName = "AdditionalTaxonSource";
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private static final String pluralString = "DescriptionElements";
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private static final String parentPluralString = "Taxa";
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private static boolean sourceUse_AdditionalSource = false;
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private static boolean sourceUse_NomenclaturalReference = false;
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private static boolean sourceUse_SourceOfSynonymy = false;
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private static TaxonNameBase currentTaxonName = null;
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private static String citationMicroReference = null;
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public PesiAdditionalTaxonSourceExport() {
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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.DbExportBase#getStandardMethodParameter()
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*/
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@Override
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public Class<? extends CdmBase> getStandardMethodParameter() {
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return standardMethodParameter;
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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.IoStateBase)
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*/
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@Override
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protected boolean doCheck(PesiExportState state) {
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boolean result = true;
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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.IoStateBase)
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*/
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@Override
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protected void doInvoke(PesiExportState state) {
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try {
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logger.error("*** Started Making " + pluralString + " ...");
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// Get the limit for objects to save within a single transaction.
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// int limit = state.getConfig().getLimitSave();
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int limit = 1000;
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// Stores whether this invoke was successful or not.
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boolean success = true;
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// PESI: Clear the database table Note.
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doDelete(state);
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// CDM: Get the number of all available description elements.
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// int maxCount = getDescriptionService().count(null);
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// logger.error("Total amount of " + maxCount + " " + pluralString + " will be exported.");
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// Get specific mappings: (CDM) DescriptionElement -> (PESI) Note
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PesiExportMapping mapping = getMapping();
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// Initialize the db mapper
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mapping.initialize(state);
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// PESI: Create the Notes
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int count = 0;
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int taxonCount = 0;
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int pastCount = 0;
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TransactionStatus txStatus = null;
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List<TaxonBase> list = null;
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// Start transaction
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txStatus = startTransaction(true);
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logger.error("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
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while ((list = getTaxonService().list(null, limit, taxonCount, null, null)).size() > 0) {
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taxonCount += list.size();
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logger.error("Fetched " + list.size() + " " + parentPluralString + ".");
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logger.error("PHASE 2: Check for SourceUse 'Additional Source'");
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sourceUse_AdditionalSource = true;
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for (TaxonBase taxonBase : list) {
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// Set the current Taxon
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currentTaxonName = taxonBase.getName();
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if (taxonBase.isInstanceOf(Taxon.class)) {
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Taxon taxon = CdmBase.deproxy(taxonBase, Taxon.class);
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// Determine the TaxonDescriptions
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Set<TaxonDescription> taxonDescriptions = taxon.getDescriptions();
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// Determine the DescriptionElements (Citations) for the current Taxon
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for (TaxonDescription taxonDescription : taxonDescriptions) {
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Set<DescriptionElementBase> descriptionElements = taxonDescription.getElements();
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for (DescriptionElementBase descriptionElement : descriptionElements) {
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// According to FaEu Import those DescriptionElementBase elements are of instance TextData
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// There are no other indicators
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if (descriptionElement.isInstanceOf(TextData.class)) {
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Set<DescriptionElementSource> elementSources = descriptionElement.getSources();
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for (DescriptionElementSource elementSource : elementSources) {
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// Set the CitationMicroReference so it is accessible later in getSourceDetail()
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setCitationMicroReference(elementSource.getCitationMicroReference());
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// Get the citation
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Reference reference = elementSource.getCitation();
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// Check whether it was a synonym originally
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TaxonNameBase nameUsedInSource = elementSource.getNameUsedInSource();
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if (nameUsedInSource != null) {
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// It was a synonym originally: Set currentTaxonName to synonym's taxonName
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currentTaxonName = nameUsedInSource;
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}
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// Citations can be empty (null): Is it wrong data or just a normal case?
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if (reference != null) {
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if (neededValuesNotNull(reference, state)) {
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doCount(count++, modCount, pluralString);
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success &= mapping.invoke(reference);
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}
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}
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}
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}
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}
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}
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}
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}
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sourceUse_AdditionalSource = false;
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logger.error("Exported " + (count - pastCount) + " " + pluralString + ".");
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// Commit transaction
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commitTransaction(txStatus);
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logger.error("Committed transaction.");
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logger.error("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);
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pastCount = count;
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// Start transaction
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txStatus = startTransaction(true);
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logger.error("Started new transaction. Fetching some " + parentPluralString + " first (max: " + limit + ") ...");
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}
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if (list.size() == 0) {
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logger.error("No " + pluralString + " left to fetch.");
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}
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// Commit transaction
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commitTransaction(txStatus);
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logger.error("Committed transaction.");
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logger.error("*** Finished Making " + pluralString + " ..." + getSuccessString(success));
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return;
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} catch (SQLException e) {
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e.printStackTrace();
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logger.error(e.getMessage());
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state.setUnsuccessfull();
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return;
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}
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}
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/**
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* Checks whether needed values for an entity are NULL.
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* @return
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*/
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private boolean neededValuesNotNull(Reference<?> reference, PesiExportState state) {
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boolean result = true;
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if (getSourceFk(reference, state) == null) {
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logger.error("SourceFk is NULL, but is not allowed to be. Therefore no record was written to export database for this reference: " + reference.getUuid());
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result = false;
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}
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if (getSourceUseFk(reference) == null) {
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logger.error("SourceUseFk is NULL, but is not allowed to be. Therefore no record was written to export database for this reference: " + reference.getUuid());
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result = false;
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}
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return result;
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}
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/**
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* Deletes all entries of database tables related to <code>AdditionalTaxonSource</code>.
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* @param state The {@link PesiExportState PesiExportState}.
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* @return Whether the delete operation was successful or not.
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*/
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protected boolean doDelete(PesiExportState state) {
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PesiExportConfigurator pesiConfig = state.getConfig();
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String sql;
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Source destination = pesiConfig.getDestination();
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// Clear AdditionalTaxonSource
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sql = "DELETE FROM " + dbTableName;
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destination.setQuery(sql);
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destination.update(sql);
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return true;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)
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*/
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@Override
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protected boolean isIgnore(PesiExportState state) {
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return ! ( state.getConfig().isDoAdditionalTaxonSource());
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}
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/**
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* Returns the <code>TaxonFk</code> attribute.
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* @param reference The {@link Reference Reference}.
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* @see MethodMapper
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*/
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@SuppressWarnings("unused")
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private static Integer getTaxonFk(Reference<?> reference, PesiExportState state) {
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// Reference parameter isn't needed, but the DbSingleAttributeExportMapperBase throws a type mismatch exception otherwise
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// since it awaits two parameters if one of them is of instance DbExportStateBase.
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Integer result = null;
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if (state != null && currentTaxonName != null) {
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result = state.getDbId(currentTaxonName);
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}
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return result;
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}
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/**
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* Returns the <code>SourceFk</code> attribute.
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* @param reference The {@link Reference Reference}.
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* @return The <code>SourceFk</code> attribute.
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* @see MethodMapper
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*/
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private static Integer getSourceFk(Reference<?> reference, PesiExportState state) {
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Integer result = null;
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if (state != null && reference != null) {
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result = state.getDbId(reference);
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}
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return result;
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}
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/**
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* Returns the <code>SourceUseFk</code> attribute.
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* @param reference The {@link Reference Reference}.
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* @return The <code>SourceUseFk</code> attribute.
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* @see MethodMapper
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*/
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private static Integer getSourceUseFk(Reference<?> reference) {
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// TODO
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Integer result = null;
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if (sourceUse_AdditionalSource) {
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result = PesiTransformer.sourceUseIdSourceUseId(3);
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} else if (sourceUse_SourceOfSynonymy) {
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result = PesiTransformer.sourceUseIdSourceUseId(4);
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} else if (sourceUse_NomenclaturalReference) {
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result = PesiTransformer.sourceUseIdSourceUseId(8);
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}
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return result;
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}
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/**
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* Returns the <code>SourceUseCache</code> attribute.
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* @param reference The {@link Reference Reference}.
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* @return The <code>SourceUseCache</code> attribute.
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* @see MethodMapper
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*/
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@SuppressWarnings("unused")
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private static String getSourceUseCache(Reference<?> reference) {
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// TODO
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String result = null;
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if (sourceUse_AdditionalSource) {
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result = PesiTransformer.sourceUseId2SourceUseCache(3);
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} else if (sourceUse_SourceOfSynonymy) {
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result = PesiTransformer.sourceUseId2SourceUseCache(4);
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} else if (sourceUse_NomenclaturalReference) {
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result = PesiTransformer.sourceUseId2SourceUseCache(8);
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}
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return result;
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}
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/**
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* Returns the <code>SourceNameCache</code> attribute.
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* @param reference The {@link Reference Reference}.
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* @return The <code>SourceNameCache</code> attribute.
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* @see MethodMapper
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*/
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@SuppressWarnings("unused")
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private static String getSourceNameCache(Reference<?> reference) {
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String result = null;
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if (reference != null) {
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result = reference.getTitle();
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}
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return result;
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}
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/**
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* Returns the <code>SourceDetail</code> attribute.
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* @param reference The {@link Reference Reference}.
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* @return The <code>SourceDetail</code> attribute.
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* @see MethodMapper
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*/
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@SuppressWarnings("unused")
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private static String getSourceDetail(Reference<?> reference) {
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return PesiAdditionalTaxonSourceExport.citationMicroReference;
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}
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/**
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* @param citationMicroReference the citationMicroReference to set
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*/
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public static void setCitationMicroReference(String citationMicroReference) {
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PesiAdditionalTaxonSourceExport.citationMicroReference = citationMicroReference;
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}
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/**
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* Returns the CDM to PESI specific export mappings.
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* @return The {@link PesiExportMapping PesiExportMapping}.
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*/
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private PesiExportMapping getMapping() {
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PesiExportMapping mapping = new PesiExportMapping(dbTableName);
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mapping.addMapper(MethodMapper.NewInstance("TaxonFk", this.getClass(), "getTaxonFk", standardMethodParameter, PesiExportState.class));
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mapping.addMapper(MethodMapper.NewInstance("SourceFk", this.getClass(), "getSourceFk", standardMethodParameter, PesiExportState.class));
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mapping.addMapper(MethodMapper.NewInstance("SourceUseFk", this));
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mapping.addMapper(MethodMapper.NewInstance("SourceUseCache", this));
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mapping.addMapper(MethodMapper.NewInstance("SourceNameCache", this));
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mapping.addMapper(MethodMapper.NewInstance("SourceDetail", this));
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return mapping;
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}
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}
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