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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.faunaEuropaea;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.Collection;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Map;
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import java.util.Map.Entry;
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import java.util.Set;
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import java.util.UUID;
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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.IImportConfigurator;
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import eu.etaxonomy.cdm.io.common.ImportHelper;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.model.agent.Team;
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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.OriginalSourceBase;
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import eu.etaxonomy.cdm.model.common.OriginalSourceType;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
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import eu.etaxonomy.cdm.model.description.TextData;
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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.Synonym;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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/**
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* @author a.babadshanjan
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* @created 12.05.2009
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* @version 1.0
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*/
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@Component
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public class FaunaEuropaeaRefImport extends FaunaEuropaeaImportBase {
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private static final Logger logger = Logger.getLogger(FaunaEuropaeaRefImport.class);
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/* Interval for progress info message when retrieving taxa */
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private int modCount = 10000;
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
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*/
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@Override
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protected boolean doCheck(FaunaEuropaeaImportState state) {
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boolean result = true;
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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logger.warn("Checking for References not yet fully implemented");
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result &= checkReferenceStatus(fauEuConfig);
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return result;
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}
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private boolean checkReferenceStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
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boolean result = true;
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// try {
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Source source = fauEuConfig.getSource();
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String sqlStr = "";
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// ResultSet rs = source.getResultSet(sqlStr);
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return result;
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// } catch (SQLException e) {
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// e.printStackTrace();
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// return false;
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// }
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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.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
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*/
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@Override
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protected void doInvoke(FaunaEuropaeaImportState state) {
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/*
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logger.warn("Start RefImport doInvoke");
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ProfilerController.memorySnapshot();
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*/
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List<TaxonBase> taxonList = null;
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List<Reference> referenceList = null;
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Set<UUID> taxonUuids = null;
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Map<Integer, Reference> references = null;
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Map<String,TeamOrPersonBase> authors = null;
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Map<UUID, FaunaEuropaeaReferenceTaxon> fauEuTaxonMap = null;
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Map<Integer, UUID> referenceUuids = new HashMap<Integer, UUID>();
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Set<Integer> referenceIDs = null;
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int limit = state.getConfig().getLimitSave();
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FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
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Source source = fauEuConfig.getSource();
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String namespace = "Reference";
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int i = 0;
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String selectCountTaxRefs =
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" SELECT count(*) ";
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String selectColumnsTaxRefs =
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" SELECT Reference.*, TaxRefs.*, Taxon.UUID ";
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String fromClauseTaxRefs =
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" FROM TaxRefs " +
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" INNER JOIN Reference ON Reference.ref_id = TaxRefs.trf_ref_id " +
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" INNER JOIN Taxon ON TaxRefs.trf_tax_id = Taxon.TAX_ID ";
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String orderClauseTaxRefs =
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" ORDER BY TaxRefs.trf_tax_id";
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String selectCountRefs =
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" SELECT count(*) FROM Reference";
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String selectColumnsRefs =
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" SELECT * FROM Reference order by ref_author";
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String countQueryTaxRefs =
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selectCountTaxRefs + fromClauseTaxRefs;
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String selectQueryTaxRefs =
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selectColumnsTaxRefs + fromClauseTaxRefs + orderClauseTaxRefs;
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String countQueryRefs =
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selectCountRefs;
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String selectQueryRefs =
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selectColumnsRefs;
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if(logger.isInfoEnabled()) { logger.info("Start making References..."); }
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//first add all References to CDM
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processReferences(state, references, authors,
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referenceUuids, limit, fauEuConfig, source, namespace, i,
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countQueryRefs, selectQueryRefs);
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/*
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logger.warn("Start ref taxon relationships");
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ProfilerController.memorySnapshot();
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*/
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//create the relationships between references and taxa
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createTaxonReferenceRel(state, taxonUuids, fauEuTaxonMap,
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referenceUuids, referenceIDs, limit, source,
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countQueryTaxRefs, selectQueryTaxRefs);
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/*
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logger.warn("End RefImport doInvoke");
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ProfilerController.memorySnapshot();
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*/
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if(logger.isInfoEnabled()) { logger.info("End making references ..."); }
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return;
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}
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private void processReferences(FaunaEuropaeaImportState state,
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Map<Integer, Reference> references,
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Map<String, TeamOrPersonBase> authors,
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Map<Integer, UUID> referenceUuids, int limit,
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FaunaEuropaeaImportConfigurator fauEuConfig, Source source,
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String namespace, int i, String countQueryRefs,
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String selectQueryRefs) {
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TransactionStatus txStatus = null;
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int count;
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try {
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ResultSet rsRefs = source.getResultSet(countQueryRefs);
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rsRefs.next();
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count = rsRefs.getInt(1);
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rsRefs = source.getResultSet(selectQueryRefs);
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if (logger.isInfoEnabled()) {
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logger.info("Get all References...");
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logger.info("Number of rows: " + count);
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logger.info("Count Query: " + countQueryRefs);
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logger.info("Select Query: " + selectQueryRefs);
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}
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while (rsRefs.next()){
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int refId = rsRefs.getInt("ref_id");
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String refAuthor = rsRefs.getString("ref_author");
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String year = rsRefs.getString("ref_year");
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String title = rsRefs.getString("ref_title");
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if (year == null){
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try{
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year = String.valueOf((Integer.parseInt(title)));
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}
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catch(Exception ex)
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{
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logger.info("year is empty and " +title + " contains no integer");
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}
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}
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String refSource = rsRefs.getString("ref_source");
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if ((i++ % limit) == 0) {
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txStatus = startTransactionForImports();
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references = new HashMap<Integer,Reference>(limit);
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authors = new HashMap<String,TeamOrPersonBase>(limit);
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if(logger.isInfoEnabled()) {
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logger.info("i = " + i + " - Reference import transaction started");
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}
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}
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Reference<?> reference = null;
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TeamOrPersonBase<Team> author = null;
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//ReferenceFactory refFactory = ReferenceFactory.newInstance();
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reference = ReferenceFactory.newGeneric();
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// reference.setTitleCache(title);
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reference.setTitle(title);
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reference.setDatePublished(ImportHelper.getDatePublished(year));
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if (!authors.containsKey(refAuthor)) {
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if (refAuthor == null) {
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logger.warn("Reference author is null");
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}
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author = Team.NewInstance();
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author.setTitleCache(refAuthor, true);
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authors.put(refAuthor,author);
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if (logger.isTraceEnabled()) {
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logger.trace("Stored author (" + refAuthor + ")");
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}
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//}
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} else {
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author = authors.get(refAuthor);
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if (logger.isDebugEnabled()) {
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logger.debug("Not imported author with duplicated aut_id (" + refId +
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") " + refAuthor);
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}
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}
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reference.setAuthorTeam(author);
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ImportHelper.setOriginalSource(reference, fauEuConfig.getSourceReference(), refId, namespace);
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ImportHelper.setOriginalSource(author, fauEuConfig.getSourceReference(), refId, namespace);
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// Store reference
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if (!references.containsKey(refId)) {
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if (reference == null) {
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logger.warn("Reference is null");
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}
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references.put(refId, reference);
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if (logger.isTraceEnabled()) {
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logger.trace("Stored reference (" + refAuthor + ")");
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}
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} else {
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if (logger.isDebugEnabled()) {
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logger.debug("Duplicated reference (" + refId + ", " + refAuthor + ")");
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}
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//continue;
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}
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if (((i % limit) == 0 && i > 1 ) || i == count ) {
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commitReferences(references, authors, referenceUuids, i,
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txStatus);
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references= null;
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authors = null;
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}
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}
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rsRefs = null;
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if (references != null){
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commitReferences(references, authors, referenceUuids, i, txStatus);
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references= null;
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authors = null;
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}
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}catch(SQLException e) {
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logger.error("SQLException:" + e);
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state.setUnsuccessfull();
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}
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references = null;
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authors = null;
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}
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private void commitReferences(Map<Integer, Reference> references,
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Map<String, TeamOrPersonBase> authors,
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Map<Integer, UUID> referenceUuids, int i, TransactionStatus txStatus) {
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Map <UUID, Reference> referenceMap =getReferenceService().save(references.values());
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logger.info("i = " + i + " - references saved");
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Iterator<Entry<UUID, Reference>> it = referenceMap.entrySet().iterator();
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while (it.hasNext()){
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Reference ref = it.next().getValue();
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int refID = Integer.valueOf(((OriginalSourceBase)ref.getSources().iterator().next()).getIdInSource());
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UUID uuid = ref.getUuid();
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referenceUuids.put(refID, uuid);
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}
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getAgentService().save((Collection)authors.values());
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commitTransaction(txStatus);
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}
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private void createTaxonReferenceRel(FaunaEuropaeaImportState state,
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Set<UUID> taxonUuids,
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Map<UUID, FaunaEuropaeaReferenceTaxon> fauEuTaxonMap,
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Map<Integer, UUID> referenceUuids, Set<Integer> referenceIDs,
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int limit, Source source, String countQueryTaxRefs,
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String selectQueryTaxRefs) {
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TransactionStatus txStatus = null;
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List<TaxonBase> taxonList;
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List<Reference> referenceList;
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Map<Integer, Reference> references;
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Map<String, TeamOrPersonBase> authors;
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int i;
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int count;
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Taxon taxon = null;
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i = 0;
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try{
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ResultSet rsTaxRefs = source.getResultSet(countQueryTaxRefs);
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rsTaxRefs.next();
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count = rsTaxRefs.getInt(1);
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rsTaxRefs = source.getResultSet(selectQueryTaxRefs);
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logger.info("Start taxon reference-relationships");
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FaunaEuropaeaReference fauEuReference;
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FaunaEuropaeaReferenceTaxon fauEuReferenceTaxon;
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while (rsTaxRefs.next()) {
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345
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if ((i++ % limit) == 0) {
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txStatus = startTransaction();
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taxonUuids = new HashSet<UUID>(limit);
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referenceIDs = new HashSet<Integer>(limit);
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authors = new HashMap<String,TeamOrPersonBase>(limit);
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fauEuTaxonMap = new HashMap<UUID, FaunaEuropaeaReferenceTaxon>(limit);
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if(logger.isInfoEnabled()) {
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logger.info("i = " + i + " - Reference import transaction started");
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}
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357
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}
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358
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359
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360
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int taxonId = rsTaxRefs.getInt("trf_tax_id");
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int refId = rsTaxRefs.getInt("ref_id");
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String refAuthor = rsTaxRefs.getString("ref_author");
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String year = rsTaxRefs.getString("ref_year");
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364
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String title = rsTaxRefs.getString("ref_title");
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365
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366
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if (year == null){
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367
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try{
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368
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year = String.valueOf((Integer.parseInt(title)));
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369
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}
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catch(Exception ex)
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{
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372
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logger.info("year is empty and " +title + " contains no integer");
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373
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}
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374
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}
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375
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String refSource = rsTaxRefs.getString("ref_source");
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String page = rsTaxRefs.getString("trf_page");
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377
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UUID currentTaxonUuid = null;
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378
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if (resultSetHasColumn(rsTaxRefs, "UUID")){
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currentTaxonUuid = UUID.fromString(rsTaxRefs.getString("UUID"));
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380
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} else {
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381
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logger.error("Taxon (" + taxonId + ") without UUID ignored");
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382
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continue;
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383
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}
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384
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385
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fauEuReference = new FaunaEuropaeaReference();
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386
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fauEuReference.setTaxonUuid(currentTaxonUuid);
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387
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fauEuReference.setReferenceId(refId);
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fauEuReference.setReferenceAuthor(refAuthor);
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389
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fauEuReference.setReferenceYear(year);
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390
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fauEuReference.setReferenceTitle(title);
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391
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fauEuReference.setReferenceSource(refSource);
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392
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fauEuReference.setPage(page);
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393
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394
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if (!taxonUuids.contains(currentTaxonUuid)) {
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395
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taxonUuids.add(currentTaxonUuid);
|
396
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fauEuReferenceTaxon =
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397
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new FaunaEuropaeaReferenceTaxon(currentTaxonUuid);
|
398
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fauEuTaxonMap.put(currentTaxonUuid, fauEuReferenceTaxon);
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399
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} else {
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400
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if (logger.isTraceEnabled()) {
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401
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logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
|
402
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//continue; ein Taxon kann mehr als eine Referenz haben
|
403
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}
|
404
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}
|
405
|
|
406
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if (!referenceIDs.contains(refId)) {
|
407
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408
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409
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referenceIDs.add(refId);
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410
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if (logger.isTraceEnabled()) {
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411
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logger.trace("Stored reference (" + refAuthor + ")");
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412
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}
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413
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} else {
|
414
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if (logger.isDebugEnabled()) {
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415
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logger.debug("Duplicated reference (" + refId + ", " + refAuthor + ")");
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416
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}
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417
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//continue;
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418
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}
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419
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420
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421
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fauEuTaxonMap.get(currentTaxonUuid).addReference(fauEuReference);
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422
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423
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|
424
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|
425
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|
426
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if (((i % limit) == 0 && i > 1 ) || i == count) {
|
427
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428
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try {
|
429
|
|
430
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Set<UUID> uuidSet;
|
431
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commitTaxaReferenceRel(taxonUuids, fauEuTaxonMap,
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432
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referenceUuids, referenceIDs, limit, txStatus, i,
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433
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taxon);
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434
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435
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taxonUuids = null;
|
436
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references = null;
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437
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taxonList = null;
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438
|
fauEuTaxonMap = null;
|
439
|
referenceIDs = null;
|
440
|
referenceList = null;
|
441
|
uuidSet = null;
|
442
|
|
443
|
|
444
|
} catch (Exception e) {
|
445
|
logger.warn("An exception occurred when creating reference, reference could not be saved.");
|
446
|
}
|
447
|
}
|
448
|
}
|
449
|
if (taxonUuids != null){
|
450
|
commitTaxaReferenceRel(taxonUuids, fauEuTaxonMap,
|
451
|
referenceUuids, referenceIDs, limit, txStatus, i,
|
452
|
taxon);
|
453
|
}
|
454
|
rsTaxRefs.close();
|
455
|
} catch (SQLException e) {
|
456
|
logger.error("SQLException:" + e);
|
457
|
state.setUnsuccessfull();
|
458
|
}
|
459
|
taxonUuids = null;
|
460
|
references = null;
|
461
|
taxonList = null;
|
462
|
fauEuTaxonMap = null;
|
463
|
referenceIDs = null;
|
464
|
referenceList = null;
|
465
|
|
466
|
|
467
|
}
|
468
|
|
469
|
private void commitTaxaReferenceRel(Set<UUID> taxonUuids,
|
470
|
Map<UUID, FaunaEuropaeaReferenceTaxon> fauEuTaxonMap,
|
471
|
Map<Integer, UUID> referenceUuids, Set<Integer> referenceIDs,
|
472
|
int limit, TransactionStatus txStatus, int i, Taxon taxon) {
|
473
|
List<TaxonBase> taxonList;
|
474
|
List<Reference> referenceList;
|
475
|
Map<Integer, Reference> references;
|
476
|
taxonList = getTaxonService().find(taxonUuids);
|
477
|
//get UUIDs of used references
|
478
|
Iterator itRefs = referenceIDs.iterator();
|
479
|
Set<UUID> uuidSet = new HashSet<UUID>(referenceIDs.size());
|
480
|
UUID uuid;
|
481
|
while (itRefs.hasNext()){
|
482
|
uuid = referenceUuids.get(itRefs.next());
|
483
|
uuidSet.add(uuid);
|
484
|
}
|
485
|
referenceList = getReferenceService().find(uuidSet);
|
486
|
references = new HashMap<Integer, Reference>(limit);
|
487
|
for (Reference ref : referenceList){
|
488
|
references.put(Integer.valueOf(((OriginalSourceBase)ref.getSources().iterator().next()).getIdInSource()), ref);
|
489
|
}
|
490
|
for (TaxonBase taxonBase : taxonList) {
|
491
|
|
492
|
// Create descriptions
|
493
|
|
494
|
if (taxonBase == null) {
|
495
|
if (logger.isDebugEnabled()) {
|
496
|
logger.debug("TaxonBase is null ");
|
497
|
}
|
498
|
continue;
|
499
|
}
|
500
|
boolean isSynonym = taxonBase.isInstanceOf(Synonym.class);
|
501
|
if (isSynonym) {
|
502
|
Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);
|
503
|
Set<Taxon> acceptedTaxa = syn.getAcceptedTaxa();
|
504
|
if (acceptedTaxa.size() > 0) {
|
505
|
taxon = syn.getAcceptedTaxa().iterator().next();
|
506
|
logger.warn("Synonym (" + taxonBase.getUuid() + ") has accepted taxon" + taxon.getUuid());
|
507
|
} else {
|
508
|
// if (logger.isDebugEnabled()) {
|
509
|
logger.warn("Synonym (" + taxonBase.getUuid() + ") does not have accepted taxa");
|
510
|
// }
|
511
|
}
|
512
|
} else {
|
513
|
taxon = CdmBase.deproxy(taxonBase, Taxon.class);
|
514
|
}
|
515
|
//TODO: statt TaxonDescription TaxonNameDescription und an den Namen anstatt ans Taxon hängen!!!
|
516
|
if (taxon != null) {
|
517
|
TaxonNameDescription taxonNameDescription = null;
|
518
|
Set<TaxonNameDescription> descriptions = taxon.getName().getDescriptions();
|
519
|
if (descriptions.size() > 0) {
|
520
|
taxonNameDescription = descriptions.iterator().next();
|
521
|
} else {
|
522
|
taxonNameDescription = TaxonNameDescription.NewInstance();
|
523
|
taxon.getName().addDescription(taxonNameDescription);
|
524
|
}
|
525
|
|
526
|
|
527
|
UUID taxonUuid = taxonBase.getUuid();
|
528
|
FaunaEuropaeaReferenceTaxon fauEuHelperTaxon = fauEuTaxonMap.get(taxonUuid);
|
529
|
Reference<?> citation;
|
530
|
String microCitation;
|
531
|
DescriptionElementSource originalSource;
|
532
|
Synonym syn;
|
533
|
for (FaunaEuropaeaReference storedReference : fauEuHelperTaxon.getReferences()) {
|
534
|
|
535
|
TextData textData = TextData.NewInstance(Feature.CITATION());
|
536
|
|
537
|
citation = references.get(storedReference.getReferenceId());
|
538
|
microCitation = storedReference.getPage();
|
539
|
originalSource = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource, null, null, citation, microCitation, null, null);
|
540
|
if (isSynonym){
|
541
|
syn = CdmBase.deproxy(taxonBase, Synonym.class);
|
542
|
originalSource.setNameUsedInSource(syn.getName());
|
543
|
}
|
544
|
textData.addSource(originalSource);
|
545
|
taxonNameDescription.addElement(textData);
|
546
|
}
|
547
|
}
|
548
|
}
|
549
|
if(logger.isInfoEnabled()) {
|
550
|
logger.info("i = " + i + " - Transaction committed");
|
551
|
}
|
552
|
|
553
|
// save taxa
|
554
|
getTaxonService().save(taxonList);
|
555
|
commitTransaction(txStatus);
|
556
|
|
557
|
}
|
558
|
|
559
|
|
560
|
|
561
|
|
562
|
|
563
|
|
564
|
/* (non-Javadoc)
|
565
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
566
|
*/
|
567
|
protected boolean isIgnore(FaunaEuropaeaImportState state){
|
568
|
return (state.getConfig().getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
|
569
|
}
|
570
|
|
571
|
}
|