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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.berlinModel.out.mapper.DbStringMapper;
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import eu.etaxonomy.cdm.io.berlinModel.out.mapper.DbTimePeriodMapper;
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import eu.etaxonomy.cdm.io.berlinModel.out.mapper.IdMapper;
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import eu.etaxonomy.cdm.io.berlinModel.out.mapper.MethodMapper;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.CdmBase;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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/**
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* @author a.mueller
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* @author e.-m.lee
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* @date 11.02.2010
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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 PesiSourceExport extends PesiExportBase {
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private static final Logger logger = Logger.getLogger(PesiSourceExport.class);
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private static final Class<? extends CdmBase> standardMethodParameter = ReferenceBase.class;
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private static int modCount = 1000;
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private static final String dbTableName = "Source";
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private static final String pluralString = "Sources";
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public PesiSourceExport() {
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super();
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.pesi.out.PesiExportBase#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 boolean 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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// Stores whether this invoke was successful or not.
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boolean success = true ;
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// PESI: Clear the database table Source.
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doDelete(state);
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// Create the database table that hosts state information
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state.createStateTables();
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// CDM: Get the number of all available references.
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// int maxCount = getReferenceService().count(null);
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// logger.error("Total amount of " + maxCount + " " + pluralString + " will be exported.");
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// Get specific mappings: (CDM) Reference -> (PESI) Source
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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 Sources
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// TODO: Store CDM2PESI identifier pairs for later use in other export classes - PesiExportState
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int count = 0;
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int pastCount = 0;
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TransactionStatus txStatus = null;
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List<ReferenceBase> 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 " + pluralString + " (max: " + limit + ") ...");
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while ((list = getReferenceService().list(null, limit, count, null, null)).size() > 0) {
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logger.error("Fetched " + list.size() + " " + pluralString + ". Exporting...");
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for (ReferenceBase<?> reference : list) {
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doCount(count++, modCount, pluralString);
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success &= mapping.invoke(reference);
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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("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 " + pluralString + " (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 success;
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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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return false;
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}
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}
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/**
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* Deletes all entries of database tables related to <code>Source</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 = (PesiExportConfigurator) state.getConfig();
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String sql;
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Source destination = pesiConfig.getDestination();
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// Clear Occurrences
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sql = "DELETE FROM Occurrence";
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destination.setQuery(sql);
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destination.update(sql);
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// Clear Taxa
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sql = "DELETE FROM Taxon";
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destination.setQuery(sql);
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destination.update(sql);
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// Clear Sources
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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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/**
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* Returns the <code>IMIS_Id</code> attribute.
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* @param reference The {@link ReferenceBase Reference}.
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* @return The <code>IMIS_Id</code> attribute.
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* @see MethodMapper
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*/
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@SuppressWarnings("unused")
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private static Integer getIMIS_Id(ReferenceBase<?> reference) {
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// TODO
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// Where is the IMIS_Id from an ERMS import stored in CDM?
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return null;
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}
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/**
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* Returns the <code>SourceCategoryFK</code> attribute.
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* @param reference The {@link ReferenceBase Reference}.
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* @return The <code>SourceCategoryFK</code> attribute.
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* @see MethodMapper
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*/
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@SuppressWarnings("unused")
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private static Integer getSourceCategoryFK(ReferenceBase<?> reference) {
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return PesiTransformer.reference2SourceCategoryFK(reference);
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}
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/**
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* Returns the <code>SourceCategoryCache</code> attribute.
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* @param reference The {@link ReferenceBase Reference}.
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* @return The <code>SourceCategoryCache</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 getSourceCategoryCache(ReferenceBase<?> reference) {
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return PesiTransformer.getSourceCategoryCache(reference);
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}
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/**
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* Returns the <code>Name</code> attribute. The corresponding CDM attribute is <code>title</code>.
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* @param reference The {@link ReferenceBase Reference}.
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* @return The <code>Name</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 getName(ReferenceBase<?> reference) {
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if (reference != null) {
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return reference.getTitle();
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} else {
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return null;
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}
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}
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/**
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* Returns the <code>AuthorString</code> attribute. The corresponding CDM attribute is the <code>titleCache</code> of an <code>authorTeam</code>.
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* @param reference The {@link ReferenceBase Reference}.
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* @return The <code>AuthorString</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 getAuthorString(ReferenceBase<?> reference) {
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String result = null;
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if (reference != null) {
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TeamOrPersonBase team = reference.getAuthorTeam();
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if (team != null) {
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// result = team.getTitleCache();
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result = team.getNomenclaturalTitle();
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} else {
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result = null;
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}
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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>NomRefCache</code> attribute. The corresponding CDM attribute is <code>titleCache</code>.
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* @param reference The {@link ReferenceBase Reference}.
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* @return The <code>NomRefCache</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 getNomRefCache(ReferenceBase<?> reference) {
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if (reference != null) {
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return reference.getTitleCache();
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} else {
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return null;
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}
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}
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/**
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* Returns the <code>Notes</code> attribute.
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* @param reference The {@link ReferenceBase Reference}.
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* @return The <code>Notes</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 getNotes(ReferenceBase<?> reference) {
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// TODO
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return null;
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}
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/**
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* Returns the <code>RefIdInSource</code> attribute.
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* @param reference The {@link ReferenceBase Reference}.
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* @return The <code>RefIdInSource</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 getRefIdInSource(ReferenceBase<?> reference) {
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String result = null;
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if (reference != null) {
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Set<IdentifiableSource> sources = reference.getSources();
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if (sources.size() == 1) {
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result = sources.iterator().next().getIdInSource();
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} else if (sources.size() > 1) {
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logger.warn("Reference has multiple IdentifiableSources: " + reference.getUuid() + " (" + reference.getTitleCache() + ")");
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int count = 1;
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for (IdentifiableSource source : sources) {
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result += source.getIdInSource();
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if (count < sources.size()) {
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result += "; ";
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}
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count++;
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}
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}
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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>OriginalDB</code> attribute. The corresponding CDM attribute is the <code>titleCache</code> of a <code>citation</code>.
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* @param reference The {@link ReferenceBase Reference}.
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* @return The <code>OriginalDB</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 getOriginalDB(ReferenceBase<?> reference) {
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String result = "";
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if (reference != null) {
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Set<IdentifiableSource> sources = reference.getSources();
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if (sources.size() == 1) {
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ReferenceBase citation = sources.iterator().next().getCitation();
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if (citation != null) {
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result = PesiTransformer.databaseString2Abbreviation(citation.getTitleCache()); //or just title
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} else {
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logger.warn("OriginalDB can not be determined because the citation of this source is NULL: " + sources.iterator().next().getUuid());
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}
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} else if (sources.size() > 1) {
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logger.warn("Taxon has multiple IdentifiableSources: " + reference.getUuid() + " (" + reference.getTitleCache() + ")");
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int count = 1;
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for (IdentifiableSource source : sources) {
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ReferenceBase citation = source.getCitation();
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if (citation != null) {
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result += PesiTransformer.databaseString2Abbreviation(citation.getTitleCache());
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if (count < sources.size()) {
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result += "; ";
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}
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count++;
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}
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}
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} else {
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result = null;
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}
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}
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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#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 ! (((PesiExportConfigurator) state.getConfig()).getDoReferences().equals(DO_REFERENCES.ALL));
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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(IdMapper.NewInstance("SourceId"));
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mapping.addMapper(MethodMapper.NewInstance("IMIS_Id", this));
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mapping.addMapper(MethodMapper.NewInstance("SourceCategoryFK", this));
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mapping.addMapper(MethodMapper.NewInstance("SourceCategoryCache", this));
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mapping.addMapper(MethodMapper.NewInstance("Name", this));
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mapping.addMapper(DbStringMapper.NewInstance("referenceAbstract", "Abstract"));
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mapping.addMapper(DbStringMapper.NewInstance("title", "Title"));
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mapping.addMapper(MethodMapper.NewInstance("AuthorString", this));
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mapping.addMapper(DbTimePeriodMapper.NewInstance("datePublished", "RefYear"));
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mapping.addMapper(MethodMapper.NewInstance("NomRefCache", this));
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mapping.addMapper(DbStringMapper.NewInstance("uri", "Link"));
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mapping.addMapper(MethodMapper.NewInstance("Notes", this));
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mapping.addMapper(MethodMapper.NewInstance("RefIdInSource", this));
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mapping.addMapper(MethodMapper.NewInstance("OriginalDB", this));
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return mapping;
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}
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}
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