Revision 1542dee5
Added by Andreas Müller over 8 years ago
cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/faunaEuropaea/FaunaEuropaeaRefImport.java | ||
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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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@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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@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 = startTransaction(); |
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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.setAuthorship(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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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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} |
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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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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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} |
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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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String title = rsTaxRefs.getString("ref_title"); |
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|
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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 = rsTaxRefs.getString("ref_source"); |
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String page = rsTaxRefs.getString("trf_page"); |
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UUID currentTaxonUuid = null; |
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if (resultSetHasColumn(rsTaxRefs, "UUID")){ |
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currentTaxonUuid = UUID.fromString(rsTaxRefs.getString("UUID")); |
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} else { |
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logger.error("Taxon (" + taxonId + ") without UUID ignored"); |
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continue; |
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} |
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|
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fauEuReference = new FaunaEuropaeaReference(); |
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fauEuReference.setTaxonUuid(currentTaxonUuid); |
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fauEuReference.setReferenceId(refId); |
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fauEuReference.setReferenceAuthor(refAuthor); |
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fauEuReference.setReferenceYear(year); |
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fauEuReference.setReferenceTitle(title); |
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fauEuReference.setReferenceSource(refSource); |
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fauEuReference.setPage(page); |
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|
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if (!taxonUuids.contains(currentTaxonUuid)) { |
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taxonUuids.add(currentTaxonUuid); |
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fauEuReferenceTaxon = |
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new FaunaEuropaeaReferenceTaxon(currentTaxonUuid); |
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fauEuTaxonMap.put(currentTaxonUuid, fauEuReferenceTaxon); |
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} else { |
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if (logger.isTraceEnabled()) { |
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logger.trace("Taxon (" + currentTaxonUuid + ") already stored."); |
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//continue; ein Taxon kann mehr als eine Referenz haben |
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} |
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} |
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|
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if (!referenceIDs.contains(refId)) { |
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|
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|
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referenceIDs.add(refId); |
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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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|
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|
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fauEuTaxonMap.get(currentTaxonUuid).addReference(fauEuReference); |
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|
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|
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|
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if (((i % limit) == 0 && i > 1 ) || i == count) { |
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|
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try { |
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|
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Set<UUID> uuidSet; |
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commitTaxaReferenceRel(taxonUuids, fauEuTaxonMap, |
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referenceUuids, referenceIDs, limit, txStatus, i, |
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taxon); |
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|
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taxonUuids = null; |
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references = null; |
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taxonList = null; |
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fauEuTaxonMap = null; |
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referenceIDs = null; |
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referenceList = null; |
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uuidSet = null; |
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|
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|
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} catch (Exception e) { |
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logger.warn("An exception occurred when creating reference, reference could not be saved."); |
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} |
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} |
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} |
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if (taxonUuids != null){ |
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commitTaxaReferenceRel(taxonUuids, fauEuTaxonMap, |
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referenceUuids, referenceIDs, limit, txStatus, i, |
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taxon); |
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} |
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rsTaxRefs.close(); |
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} catch (SQLException e) { |
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447 |
logger.error("SQLException:" + e); |
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state.setUnsuccessfull(); |
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} |
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taxonUuids = null; |
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references = null; |
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taxonList = null; |
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fauEuTaxonMap = null; |
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referenceIDs = null; |
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referenceList = null; |
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456 |
|
|
457 |
|
|
458 |
} |
|
459 |
|
|
460 |
private void commitTaxaReferenceRel(Set<UUID> taxonUuids, |
|
461 |
Map<UUID, FaunaEuropaeaReferenceTaxon> fauEuTaxonMap, |
|
462 |
Map<Integer, UUID> referenceUuids, Set<Integer> referenceIDs, |
|
463 |
int limit, TransactionStatus txStatus, int i, Taxon taxon) { |
|
464 |
List<TaxonBase> taxonList; |
|
465 |
List<Reference> referenceList; |
|
466 |
Map<Integer, Reference> references; |
|
467 |
taxonList = getTaxonService().find(taxonUuids); |
|
468 |
//get UUIDs of used references |
|
469 |
Iterator itRefs = referenceIDs.iterator(); |
|
470 |
Set<UUID> uuidSet = new HashSet<UUID>(referenceIDs.size()); |
|
471 |
UUID uuid; |
|
472 |
while (itRefs.hasNext()){ |
|
473 |
uuid = referenceUuids.get(itRefs.next()); |
|
474 |
uuidSet.add(uuid); |
|
475 |
} |
|
476 |
referenceList = getReferenceService().find(uuidSet); |
|
477 |
references = new HashMap<Integer, Reference>(limit); |
|
478 |
for (Reference ref : referenceList){ |
|
479 |
references.put(Integer.valueOf(((OriginalSourceBase)ref.getSources().iterator().next()).getIdInSource()), ref); |
|
480 |
} |
|
481 |
for (TaxonBase taxonBase : taxonList) { |
|
482 |
|
|
483 |
// Create descriptions |
|
484 |
|
|
485 |
if (taxonBase == null) { |
|
486 |
if (logger.isDebugEnabled()) { |
|
487 |
logger.debug("TaxonBase is null "); |
|
488 |
} |
|
489 |
continue; |
|
490 |
} |
|
491 |
boolean isSynonym = taxonBase.isInstanceOf(Synonym.class); |
|
492 |
if (isSynonym) { |
|
493 |
Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class); |
|
494 |
Set<Taxon> acceptedTaxa = syn.getAcceptedTaxa(); |
|
495 |
if (acceptedTaxa.size() > 0) { |
|
496 |
taxon = syn.getAcceptedTaxa().iterator().next(); |
|
497 |
//logger.warn("Synonym (" + taxonBase.getUuid() + ") has accepted taxon" + taxon.getUuid()); |
|
498 |
} else { |
|
499 |
// if (logger.isDebugEnabled()) { |
|
500 |
logger.warn("Synonym (" + taxonBase.getUuid() + ") does not have accepted taxa"); |
|
501 |
// } |
|
502 |
} |
|
503 |
} else { |
|
504 |
taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
505 |
} |
|
506 |
//TODO: statt TaxonDescription TaxonNameDescription und an den Namen anstatt ans Taxon hängen!!! |
|
507 |
if (taxon != null) { |
|
508 |
TaxonNameDescription taxonNameDescription = null; |
|
509 |
Set<TaxonNameDescription> descriptions = taxon.getName().getDescriptions(); |
|
510 |
if (descriptions.size() > 0) { |
|
511 |
taxonNameDescription = descriptions.iterator().next(); |
|
512 |
} else { |
|
513 |
taxonNameDescription = TaxonNameDescription.NewInstance(); |
|
514 |
taxon.getName().addDescription(taxonNameDescription); |
|
515 |
} |
|
516 |
|
|
517 |
|
|
518 |
UUID taxonUuid = taxonBase.getUuid(); |
|
519 |
FaunaEuropaeaReferenceTaxon fauEuHelperTaxon = fauEuTaxonMap.get(taxonUuid); |
|
520 |
Reference<?> citation; |
|
521 |
String microCitation; |
|
522 |
DescriptionElementSource originalSource; |
|
523 |
Synonym syn; |
|
524 |
for (FaunaEuropaeaReference storedReference : fauEuHelperTaxon.getReferences()) { |
|
525 |
|
|
526 |
TextData textData = TextData.NewInstance(Feature.CITATION()); |
|
527 |
|
|
528 |
citation = references.get(storedReference.getReferenceId()); |
|
529 |
microCitation = storedReference.getPage(); |
|
530 |
originalSource = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource, null, null, citation, microCitation, null, null); |
|
531 |
if (isSynonym){ |
|
532 |
syn = CdmBase.deproxy(taxonBase, Synonym.class); |
|
533 |
originalSource.setNameUsedInSource(syn.getName()); |
|
534 |
} |
|
535 |
textData.addSource(originalSource); |
|
536 |
taxonNameDescription.addElement(textData); |
|
537 |
} |
|
538 |
} |
|
539 |
} |
|
540 |
if(logger.isInfoEnabled()) { |
|
541 |
logger.info("i = " + i + " - Transaction committed"); |
|
542 |
} |
|
543 |
|
|
544 |
// save taxa |
|
545 |
getTaxonService().save(taxonList); |
|
546 |
commitTransaction(txStatus); |
|
547 |
|
|
548 |
} |
|
549 |
|
|
550 |
@Override |
|
551 |
protected boolean isIgnore(FaunaEuropaeaImportState state){ |
|
552 |
return (state.getConfig().getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE); |
|
553 |
} |
|
554 |
|
|
555 |
} |
|
1 |
/** |
|
2 |
* Copyright (C) 2007 EDIT |
|
3 |
* European Distributed Institute of Taxonomy |
|
4 |
* http://www.e-taxonomy.eu |
|
5 |
* |
|
6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
8 |
*/ |
|
9 |
|
|
10 |
package eu.etaxonomy.cdm.io.pesi.faunaEuropaea; |
|
11 |
|
|
12 |
import java.sql.ResultSet; |
|
13 |
import java.sql.SQLException; |
|
14 |
import java.util.Collection; |
|
15 |
import java.util.HashMap; |
|
16 |
import java.util.HashSet; |
|
17 |
import java.util.Iterator; |
|
18 |
import java.util.List; |
|
19 |
import java.util.Map; |
|
20 |
import java.util.Map.Entry; |
|
21 |
import java.util.Set; |
|
22 |
import java.util.UUID; |
|
23 |
|
|
24 |
import org.apache.log4j.Logger; |
|
25 |
import org.springframework.stereotype.Component; |
|
26 |
import org.springframework.transaction.TransactionStatus; |
|
27 |
|
|
28 |
import eu.etaxonomy.cdm.io.common.IImportConfigurator; |
|
29 |
import eu.etaxonomy.cdm.io.common.ImportHelper; |
|
30 |
import eu.etaxonomy.cdm.io.common.Source; |
|
31 |
import eu.etaxonomy.cdm.model.agent.Team; |
|
32 |
import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase; |
|
33 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
34 |
import eu.etaxonomy.cdm.model.common.OriginalSourceBase; |
|
35 |
import eu.etaxonomy.cdm.model.common.OriginalSourceType; |
|
36 |
import eu.etaxonomy.cdm.model.description.DescriptionElementSource; |
|
37 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
38 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
39 |
import eu.etaxonomy.cdm.model.description.TextData; |
|
40 |
import eu.etaxonomy.cdm.model.reference.Reference; |
|
41 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
|
42 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
43 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
44 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
45 |
|
|
46 |
|
|
47 |
/** |
|
48 |
* @author a.babadshanjan |
|
49 |
* @created 12.05.2009 |
|
50 |
* @version 1.0 |
|
51 |
*/ |
|
52 |
@Component |
|
53 |
public class FaunaEuropaeaRefImport extends FaunaEuropaeaImportBase { |
|
54 |
private static final long serialVersionUID = -586555645981648177L; |
|
55 |
|
|
56 |
private static final Logger logger = Logger.getLogger(FaunaEuropaeaRefImport.class); |
|
57 |
|
|
58 |
@Override |
|
59 |
protected boolean doCheck(FaunaEuropaeaImportState state) { |
|
60 |
boolean result = true; |
|
61 |
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig(); |
|
62 |
logger.warn("Checking for References not yet fully implemented"); |
|
63 |
// result &= checkReferenceStatus(fauEuConfig); |
|
64 |
|
|
65 |
return result; |
|
66 |
} |
|
67 |
|
|
68 |
@Override |
|
69 |
protected void doInvoke(FaunaEuropaeaImportState state) { |
|
70 |
/* |
|
71 |
logger.warn("Start RefImport doInvoke"); |
|
72 |
ProfilerController.memorySnapshot(); |
|
73 |
*/ |
|
74 |
|
|
75 |
Set<UUID> taxonUuids = null; |
|
76 |
Map<Integer, Reference<?>> references = null; |
|
77 |
Map<String,TeamOrPersonBase<?>> authors = null; |
|
78 |
Map<UUID, FaunaEuropaeaReferenceTaxon> fauEuTaxonMap = null; |
|
79 |
Map<Integer, UUID> referenceUuids = new HashMap<Integer, UUID>(); |
|
80 |
Set<Integer> referenceIDs = null; |
|
81 |
int limit = state.getConfig().getLimitSave(); |
|
82 |
|
|
83 |
FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig(); |
|
84 |
Source source = fauEuConfig.getSource(); |
|
85 |
|
|
86 |
String namespace = "Reference"; |
|
87 |
int i = 0; |
|
88 |
|
|
89 |
String selectCountTaxRefs = |
|
90 |
" SELECT count(*) "; |
|
91 |
|
|
92 |
String selectColumnsTaxRefs = |
|
93 |
" SELECT Reference.*, TaxRefs.*, Taxon.UUID "; |
|
94 |
|
|
95 |
String fromClauseTaxRefs = |
|
96 |
" FROM TaxRefs " + |
|
97 |
" INNER JOIN Reference ON Reference.ref_id = TaxRefs.trf_ref_id " + |
|
98 |
" INNER JOIN Taxon ON TaxRefs.trf_tax_id = Taxon.TAX_ID "; |
|
99 |
|
|
100 |
String orderClauseTaxRefs = |
|
101 |
" ORDER BY TaxRefs.trf_tax_id"; |
|
102 |
|
|
103 |
String selectCountRefs = |
|
104 |
" SELECT count(*) FROM Reference"; |
|
105 |
|
|
106 |
String selectColumnsRefs = |
|
107 |
" SELECT * FROM Reference order by ref_author"; |
|
108 |
|
|
109 |
|
|
110 |
String countQueryTaxRefs = |
|
111 |
selectCountTaxRefs + fromClauseTaxRefs; |
|
112 |
|
|
113 |
String selectQueryTaxRefs = |
|
114 |
selectColumnsTaxRefs + fromClauseTaxRefs + orderClauseTaxRefs; |
|
115 |
|
|
116 |
String countQueryRefs = |
|
117 |
selectCountRefs; |
|
118 |
|
|
119 |
String selectQueryRefs = |
|
120 |
selectColumnsRefs; |
|
121 |
|
|
122 |
|
|
123 |
if(logger.isInfoEnabled()) { logger.info("Start making References..."); } |
|
124 |
//first add all References to CDM |
|
125 |
processReferences(state, references, authors, |
|
126 |
referenceUuids, limit, fauEuConfig, source, namespace, i, |
|
127 |
countQueryRefs, selectQueryRefs); |
|
128 |
|
|
129 |
/* |
|
130 |
logger.warn("Start ref taxon relationships"); |
|
131 |
ProfilerController.memorySnapshot(); |
|
132 |
*/ |
|
133 |
//create the relationships between references and taxa |
|
134 |
|
|
135 |
createTaxonReferenceRel(state, taxonUuids, fauEuTaxonMap, |
|
136 |
referenceUuids, referenceIDs, limit, source, |
|
137 |
countQueryTaxRefs, selectQueryTaxRefs); |
|
138 |
|
|
139 |
/* |
|
140 |
logger.warn("End RefImport doInvoke"); |
|
141 |
ProfilerController.memorySnapshot(); |
|
142 |
*/ |
|
143 |
if(logger.isInfoEnabled()) { logger.info("End making references ..."); } |
|
144 |
|
|
145 |
return; |
|
146 |
} |
|
147 |
|
|
148 |
private void processReferences(FaunaEuropaeaImportState state, |
|
149 |
Map<Integer, Reference<?>> references, |
|
150 |
Map<String, TeamOrPersonBase<?>> authors, |
|
151 |
Map<Integer, UUID> referenceUuids, int limit, |
|
152 |
FaunaEuropaeaImportConfigurator fauEuConfig, Source source, |
|
153 |
String namespace, int i, String countQueryRefs, |
|
154 |
String selectQueryRefs) { |
|
155 |
TransactionStatus txStatus = null; |
|
156 |
int count; |
|
157 |
try { |
|
158 |
ResultSet rsRefs = source.getResultSet(countQueryRefs); |
|
159 |
rsRefs.next(); |
|
160 |
count = rsRefs.getInt(1); |
|
161 |
|
|
162 |
rsRefs = source.getResultSet(selectQueryRefs); |
|
163 |
|
|
164 |
if (logger.isInfoEnabled()) { |
|
165 |
logger.info("Get all References..."); |
|
166 |
logger.info("Number of rows: " + count); |
|
167 |
logger.info("Count Query: " + countQueryRefs); |
|
168 |
logger.info("Select Query: " + selectQueryRefs); |
|
169 |
} |
|
170 |
|
|
171 |
while (rsRefs.next()){ |
|
172 |
int refId = rsRefs.getInt("ref_id"); |
|
173 |
String refAuthor = rsRefs.getString("ref_author"); |
|
174 |
String year = rsRefs.getString("ref_year"); |
|
175 |
String title = rsRefs.getString("ref_title"); |
|
176 |
|
|
177 |
if (year == null){ |
|
178 |
try{ |
|
179 |
year = String.valueOf((Integer.parseInt(title))); |
|
180 |
} |
|
181 |
catch(Exception ex) |
|
182 |
{ |
|
183 |
logger.info("year is empty and " +title + " contains no integer"); |
|
184 |
} |
|
185 |
} |
|
186 |
String refSource = rsRefs.getString("ref_source"); |
|
187 |
|
|
188 |
if ((i++ % limit) == 0) { |
|
189 |
|
|
190 |
txStatus = startTransaction(); |
|
191 |
references = new HashMap<Integer,Reference<?>>(limit); |
|
192 |
authors = new HashMap<String,TeamOrPersonBase<?>>(limit); |
|
193 |
|
|
194 |
if(logger.isInfoEnabled()) { |
|
195 |
logger.info("i = " + i + " - Reference import transaction started"); |
|
196 |
} |
|
197 |
} |
|
198 |
|
|
199 |
Reference<?> reference = null; |
|
200 |
TeamOrPersonBase<?> author = null; |
|
201 |
//ReferenceFactory refFactory = ReferenceFactory.newInstance(); |
|
202 |
reference = ReferenceFactory.newGeneric(); |
|
203 |
|
|
204 |
// reference.setTitleCache(title); |
|
205 |
reference.setTitle(title); |
|
206 |
reference.setDatePublished(ImportHelper.getDatePublished(year)); |
|
207 |
|
|
208 |
if (!authors.containsKey(refAuthor)) { |
|
209 |
if (refAuthor == null) { |
|
210 |
logger.warn("Reference author is null"); |
|
211 |
} |
|
212 |
author = Team.NewInstance(); |
|
213 |
author.setTitleCache(refAuthor, true); |
|
214 |
authors.put(refAuthor,author); |
|
215 |
if (logger.isTraceEnabled()) { |
|
216 |
logger.trace("Stored author (" + refAuthor + ")"); |
|
217 |
} |
|
218 |
//} |
|
219 |
|
|
220 |
} else { |
|
221 |
author = authors.get(refAuthor); |
|
222 |
if (logger.isDebugEnabled()) { |
|
223 |
logger.debug("Not imported author with duplicated aut_id (" + refId + |
|
224 |
") " + refAuthor); |
|
225 |
} |
|
226 |
} |
|
227 |
|
|
228 |
reference.setAuthorship(author); |
|
229 |
|
|
230 |
ImportHelper.setOriginalSource(reference, fauEuConfig.getSourceReference(), refId, namespace); |
|
231 |
ImportHelper.setOriginalSource(author, fauEuConfig.getSourceReference(), refId, namespace); |
|
232 |
|
|
233 |
// Store reference |
|
234 |
|
|
235 |
|
|
236 |
if (!references.containsKey(refId)) { |
|
237 |
|
|
238 |
if (reference == null) { |
|
239 |
logger.warn("Reference is null"); |
|
240 |
} |
|
241 |
references.put(refId, reference); |
|
242 |
if (logger.isTraceEnabled()) { |
|
243 |
logger.trace("Stored reference (" + refAuthor + ")"); |
|
244 |
} |
|
245 |
} else { |
|
246 |
if (logger.isDebugEnabled()) { |
|
247 |
logger.debug("Duplicated reference (" + refId + ", " + refAuthor + ")"); |
|
248 |
} |
|
249 |
//continue; |
|
250 |
} |
|
251 |
|
|
252 |
if (((i % limit) == 0 && i > 1 ) || i == count ) { |
|
253 |
|
|
254 |
commitReferences(references, authors, referenceUuids, i, |
|
255 |
txStatus); |
|
256 |
references= null; |
|
257 |
authors = null; |
|
258 |
} |
|
259 |
|
|
260 |
|
|
261 |
|
|
262 |
} |
|
263 |
if (references != null){ |
|
264 |
commitReferences(references, authors, referenceUuids, i, txStatus); |
|
265 |
references= null; |
|
266 |
authors = null; |
|
267 |
} |
|
268 |
}catch(SQLException e) { |
|
269 |
logger.error("SQLException:" + e); |
|
270 |
state.setUnsuccessfull(); |
|
271 |
} |
|
272 |
|
|
273 |
} |
|
274 |
|
|
275 |
private void commitReferences(Map<Integer, Reference<?>> references, |
|
276 |
Map<String, TeamOrPersonBase<?>> authors, |
|
277 |
Map<Integer, UUID> referenceUuids, int i, TransactionStatus txStatus) { |
|
278 |
Map <UUID, Reference> referenceMap =getReferenceService().save((Collection)references.values()); |
|
279 |
logger.info("i = " + i + " - references saved"); |
|
280 |
|
|
281 |
Iterator<Entry<UUID, Reference>> it = referenceMap.entrySet().iterator(); |
|
282 |
while (it.hasNext()){ |
|
283 |
Reference<?> ref = it.next().getValue(); |
|
284 |
int refID = Integer.valueOf((ref.getSources().iterator().next()).getIdInSource()); |
|
285 |
UUID uuid = ref.getUuid(); |
|
286 |
referenceUuids.put(refID, uuid); |
|
287 |
} |
|
288 |
|
|
289 |
getAgentService().save((Collection)authors.values()); |
|
290 |
commitTransaction(txStatus); |
|
291 |
} |
|
292 |
|
|
293 |
private void createTaxonReferenceRel(FaunaEuropaeaImportState state, |
|
294 |
Set<UUID> taxonUuids, |
|
295 |
Map<UUID, FaunaEuropaeaReferenceTaxon> fauEuTaxonMap, |
|
296 |
Map<Integer, UUID> referenceUuids, Set<Integer> referenceIDs, |
|
297 |
int limit, Source source, String countQueryTaxRefs, |
|
298 |
String selectQueryTaxRefs) { |
|
299 |
|
|
300 |
TransactionStatus txStatus = null; |
|
301 |
int i; |
|
302 |
int count; |
|
303 |
Taxon taxon = null; |
|
304 |
i = 0; |
|
305 |
try{ |
|
306 |
ResultSet rsTaxRefs = source.getResultSet(countQueryTaxRefs); |
|
307 |
rsTaxRefs.next(); |
|
308 |
count = rsTaxRefs.getInt(1); |
|
309 |
|
|
310 |
rsTaxRefs = source.getResultSet(selectQueryTaxRefs); |
|
311 |
|
|
312 |
logger.info("Start taxon reference-relationships"); |
|
313 |
FaunaEuropaeaReference fauEuReference; |
|
314 |
FaunaEuropaeaReferenceTaxon fauEuReferenceTaxon; |
|
315 |
while (rsTaxRefs.next()) { |
|
316 |
|
|
317 |
|
|
318 |
if ((i++ % limit) == 0) { |
|
319 |
|
|
320 |
txStatus = startTransaction(); |
|
321 |
taxonUuids = new HashSet<UUID>(limit); |
|
322 |
referenceIDs = new HashSet<Integer>(limit); |
|
323 |
fauEuTaxonMap = new HashMap<UUID, FaunaEuropaeaReferenceTaxon>(limit); |
|
324 |
|
|
325 |
if(logger.isInfoEnabled()) { |
|
326 |
logger.info("i = " + i + " - Reference import transaction started"); |
|
327 |
} |
|
328 |
} |
|
329 |
|
|
330 |
|
|
331 |
int taxonId = rsTaxRefs.getInt("trf_tax_id"); |
|
332 |
int refId = rsTaxRefs.getInt("ref_id"); |
|
333 |
String refAuthor = rsTaxRefs.getString("ref_author"); |
|
334 |
String year = rsTaxRefs.getString("ref_year"); |
|
335 |
String title = rsTaxRefs.getString("ref_title"); |
|
336 |
|
|
337 |
if (year == null){ |
|
338 |
try{ |
|
339 |
year = String.valueOf((Integer.parseInt(title))); |
|
340 |
} |
|
341 |
catch(Exception ex) |
|
342 |
{ |
|
343 |
logger.info("year is empty and " +title + " contains no integer"); |
|
344 |
} |
|
345 |
} |
|
346 |
String refSource = rsTaxRefs.getString("ref_source"); |
|
347 |
String page = rsTaxRefs.getString("trf_page"); |
|
348 |
UUID currentTaxonUuid = null; |
|
349 |
if (resultSetHasColumn(rsTaxRefs, "UUID")){ |
|
350 |
currentTaxonUuid = UUID.fromString(rsTaxRefs.getString("UUID")); |
|
351 |
} else { |
|
352 |
logger.error("Taxon (" + taxonId + ") without UUID ignored"); |
|
353 |
continue; |
|
354 |
} |
|
355 |
|
|
356 |
fauEuReference = new FaunaEuropaeaReference(); |
|
357 |
fauEuReference.setTaxonUuid(currentTaxonUuid); |
|
358 |
fauEuReference.setReferenceId(refId); |
|
359 |
fauEuReference.setReferenceAuthor(refAuthor); |
|
360 |
fauEuReference.setReferenceYear(year); |
|
361 |
fauEuReference.setReferenceTitle(title); |
|
362 |
fauEuReference.setReferenceSource(refSource); |
|
363 |
fauEuReference.setPage(page); |
|
364 |
|
|
365 |
if (!taxonUuids.contains(currentTaxonUuid)) { |
|
366 |
taxonUuids.add(currentTaxonUuid); |
|
367 |
fauEuReferenceTaxon = |
|
368 |
new FaunaEuropaeaReferenceTaxon(currentTaxonUuid); |
|
369 |
fauEuTaxonMap.put(currentTaxonUuid, fauEuReferenceTaxon); |
|
370 |
} else { |
|
371 |
if (logger.isTraceEnabled()) { |
|
372 |
logger.trace("Taxon (" + currentTaxonUuid + ") already stored."); |
|
373 |
//continue; ein Taxon kann mehr als eine Referenz haben |
|
374 |
} |
|
375 |
} |
|
376 |
|
|
377 |
if (!referenceIDs.contains(refId)) { |
|
378 |
|
|
379 |
|
|
380 |
referenceIDs.add(refId); |
|
381 |
if (logger.isTraceEnabled()) { |
|
382 |
logger.trace("Stored reference (" + refAuthor + ")"); |
|
383 |
} |
|
384 |
} else { |
|
385 |
if (logger.isDebugEnabled()) { |
|
386 |
logger.debug("Duplicated reference (" + refId + ", " + refAuthor + ")"); |
|
387 |
} |
|
388 |
//continue; |
|
389 |
} |
|
390 |
|
|
391 |
fauEuTaxonMap.get(currentTaxonUuid).addReference(fauEuReference); |
|
392 |
|
|
393 |
if (((i % limit) == 0 && i > 1 ) || i == count) { |
|
394 |
|
|
395 |
try { |
|
396 |
commitTaxaReferenceRel(taxonUuids, fauEuTaxonMap, |
|
397 |
referenceUuids, referenceIDs, limit, txStatus, i, |
|
398 |
taxon); |
|
399 |
|
|
400 |
taxonUuids = null; |
|
401 |
|
|
402 |
fauEuTaxonMap = null; |
|
403 |
referenceIDs = null; |
|
404 |
|
|
405 |
} catch (Exception e) { |
|
406 |
logger.warn("An exception occurred when creating reference, reference could not be saved."); |
|
407 |
} |
|
408 |
} |
|
409 |
} |
|
410 |
if (taxonUuids != null){ |
|
411 |
commitTaxaReferenceRel(taxonUuids, fauEuTaxonMap, |
|
412 |
referenceUuids, referenceIDs, limit, txStatus, i, |
|
413 |
taxon); |
|
414 |
} |
|
415 |
rsTaxRefs.close(); |
|
416 |
} catch (SQLException e) { |
|
417 |
logger.error("SQLException:" + e); |
|
418 |
state.setUnsuccessfull(); |
|
419 |
} |
|
420 |
taxonUuids = null; |
|
421 |
|
|
422 |
fauEuTaxonMap = null; |
|
423 |
referenceIDs = null; |
|
424 |
|
|
425 |
} |
|
426 |
|
|
427 |
private void commitTaxaReferenceRel(Set<UUID> taxonUuids, |
|
428 |
Map<UUID, FaunaEuropaeaReferenceTaxon> fauEuTaxonMap, |
|
429 |
Map<Integer, UUID> referenceUuids, Set<Integer> referenceIDs, |
|
430 |
int limit, TransactionStatus txStatus, int i, Taxon taxon) { |
|
431 |
List<TaxonBase> taxonList; |
|
432 |
List<Reference> referenceList; |
|
433 |
Map<Integer, Reference> references; |
|
434 |
taxonList = getTaxonService().find(taxonUuids); |
|
435 |
//get UUIDs of used references |
|
436 |
Iterator<?> itRefs = referenceIDs.iterator(); |
|
437 |
Set<UUID> uuidSet = new HashSet<UUID>(referenceIDs.size()); |
|
438 |
UUID uuid; |
|
439 |
while (itRefs.hasNext()){ |
|
440 |
uuid = referenceUuids.get(itRefs.next()); |
|
441 |
uuidSet.add(uuid); |
|
442 |
} |
|
443 |
referenceList = getReferenceService().find(uuidSet); |
|
444 |
references = new HashMap<Integer, Reference>(limit); |
|
445 |
for (Reference<?> ref : referenceList){ |
|
446 |
references.put(Integer.valueOf(((OriginalSourceBase)ref.getSources().iterator().next()).getIdInSource()), ref); |
|
447 |
} |
|
448 |
for (TaxonBase<?> taxonBase : taxonList) { |
|
449 |
|
|
450 |
// Create descriptions |
|
451 |
|
|
452 |
if (taxonBase == null) { |
|
453 |
if (logger.isDebugEnabled()) { |
|
454 |
logger.debug("TaxonBase is null "); |
|
455 |
} |
|
456 |
continue; |
|
457 |
} |
|
458 |
boolean isSynonym = taxonBase.isInstanceOf(Synonym.class); |
|
459 |
if (isSynonym) { |
|
460 |
Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class); |
|
461 |
Set<Taxon> acceptedTaxa = syn.getAcceptedTaxa(); |
|
462 |
if (acceptedTaxa.size() > 0) { |
|
463 |
taxon = syn.getAcceptedTaxa().iterator().next(); |
|
464 |
//logger.warn("Synonym (" + taxonBase.getUuid() + ") has accepted taxon" + taxon.getUuid()); |
|
465 |
} else { |
|
466 |
// if (logger.isDebugEnabled()) { |
|
467 |
logger.warn("Synonym (" + taxonBase.getUuid() + ") does not have accepted taxa"); |
|
468 |
// } |
|
469 |
} |
|
470 |
} else { |
|
471 |
taxon = CdmBase.deproxy(taxonBase, Taxon.class); |
|
472 |
} |
|
473 |
|
|
474 |
if (taxon != null) { |
|
475 |
TaxonDescription taxonDescription; |
|
476 |
Set<TaxonDescription> descriptions = taxon.getDescriptions(); |
|
477 |
if (descriptions.size() > 0) { |
|
478 |
taxonDescription = descriptions.iterator().next(); |
|
479 |
} else { |
|
480 |
taxonDescription = TaxonDescription.NewInstance(); |
|
481 |
taxon.addDescription(taxonDescription); |
|
482 |
} |
|
483 |
|
|
484 |
|
|
485 |
UUID taxonUuid = taxonBase.getUuid(); |
|
486 |
FaunaEuropaeaReferenceTaxon fauEuHelperTaxon = fauEuTaxonMap.get(taxonUuid); |
|
487 |
Reference<?> citation; |
|
488 |
String microCitation; |
|
489 |
DescriptionElementSource originalSource; |
|
490 |
Synonym syn; |
|
491 |
for (FaunaEuropaeaReference storedReference : fauEuHelperTaxon.getReferences()) { |
|
492 |
|
|
493 |
TextData textData = TextData.NewInstance(Feature.CITATION()); |
|
494 |
|
|
495 |
citation = references.get(storedReference.getReferenceId()); |
|
496 |
microCitation = storedReference.getPage(); |
|
497 |
originalSource = DescriptionElementSource.NewInstance(OriginalSourceType.PrimaryTaxonomicSource, null, null, citation, microCitation, null, null); |
|
498 |
if (isSynonym){ |
|
499 |
syn = CdmBase.deproxy(taxonBase, Synonym.class); |
|
500 |
originalSource.setNameUsedInSource(syn.getName()); |
|
501 |
} |
|
502 |
textData.addSource(originalSource); |
|
503 |
taxonDescription.addElement(textData); |
|
504 |
} |
|
505 |
} |
|
506 |
} |
|
507 |
if(logger.isInfoEnabled()) { |
|
508 |
logger.info("i = " + i + " - Transaction committed"); |
|
509 |
} |
|
510 |
|
|
511 |
// save taxa |
|
512 |
getTaxonService().save(taxonList); |
|
513 |
commitTransaction(txStatus); |
|
514 |
|
|
515 |
} |
|
516 |
|
|
517 |
@Override |
|
518 |
protected boolean isIgnore(FaunaEuropaeaImportState state){ |
|
519 |
return (state.getConfig().getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE); |
|
520 |
} |
|
521 |
|
|
522 |
} |
Also available in: Unified diff
Import references as taxon descriptions in FauEu