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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.berlinModel.in;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_ARTICLE;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_BOOK;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_CONFERENCE_PROCEEDINGS;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_DATABASE;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_INFORMAL;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_JOURNAL;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_JOURNAL_VOLUME;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_PART_OF_OTHER_TITLE;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_PRINT_SERIES;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_UNKNOWN;
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import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_WEBSITE;
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import static eu.etaxonomy.cdm.io.common.ImportHelper.NO_OVERWRITE;
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import static eu.etaxonomy.cdm.io.common.ImportHelper.OBLIGATORY;
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import static eu.etaxonomy.cdm.io.common.ImportHelper.OVERWRITE;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.sql.ResultSet;
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import java.sql.SQLException;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.List;
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import java.util.Map;
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import java.util.Set;
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import java.util.UUID;
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import java.util.regex.Matcher;
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import java.util.regex.Pattern;
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import org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.DOI;
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import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
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import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelReferenceImportValidator;
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import eu.etaxonomy.cdm.io.common.ICdmImport;
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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.ResultSetPartitioner;
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import eu.etaxonomy.cdm.io.common.Source;
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import eu.etaxonomy.cdm.io.common.mapping.CdmAttributeMapperBase;
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import eu.etaxonomy.cdm.io.common.mapping.CdmIoMapping;
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import eu.etaxonomy.cdm.io.common.mapping.CdmSingleAttributeMapperBase;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportExtensionMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbImportMarkerMapper;
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import eu.etaxonomy.cdm.io.common.mapping.DbSingleAttributeImportMapperBase;
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import eu.etaxonomy.cdm.io.common.mapping.berlinModel.CdmOneToManyMapper;
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import eu.etaxonomy.cdm.io.common.mapping.berlinModel.CdmStringMapper;
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import eu.etaxonomy.cdm.io.common.mapping.berlinModel.CdmUriMapper;
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import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper;
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import eu.etaxonomy.cdm.model.agent.Person;
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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.ExtensionType;
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import eu.etaxonomy.cdm.model.common.IdentifiableSource;
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import eu.etaxonomy.cdm.model.common.Identifier;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.reference.IArticle;
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import eu.etaxonomy.cdm.model.reference.IBookSection;
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import eu.etaxonomy.cdm.model.reference.IPrintSeries;
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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.reference.ReferenceType;
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import eu.etaxonomy.cdm.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.model.term.TermVocabulary;
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import eu.etaxonomy.cdm.strategy.cache.agent.PersonDefaultCacheStrategy;
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import eu.etaxonomy.cdm.strategy.cache.agent.TeamDefaultCacheStrategy;
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/**
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* @author a.mueller
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* @since 20.03.2008
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*/
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@Component
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public class BerlinModelReferenceImport extends BerlinModelImportBase {
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private static final long serialVersionUID = -3667566958769967591L;
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private static final Logger logger = Logger.getLogger(BerlinModelReferenceImport.class);
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public static final String REFERENCE_NAMESPACE = "Reference";
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private static final String REF_AUTHOR_NAMESPACE = "Reference.refAuthorString";
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public static final UUID REF_DEPOSITED_AT_UUID = UUID.fromString("23ca88c7-ce73-41b2-8ca3-2cb22f013beb");
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public static final UUID REF_SOURCE_UUID = UUID.fromString("d6432582-2216-4b08-b0db-76f6c1013141");
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public static final UUID DATE_STRING_UUID = UUID.fromString("e4130eae-606e-4b0c-be4f-e93dc161be7d");
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public static final UUID IS_PAPER_UUID = UUID.fromString("8a326129-d0d0-4f9d-bbdf-8d86b037c65e");
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private static ImportDeduplicationHelper<BerlinModelImportState> deduplicationHelper;
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private final int modCount = 1000;
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private static final String pluralString = "references";
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private static final String dbTableName = "reference";
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public BerlinModelReferenceImport(){
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super(dbTableName, pluralString);
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}
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protected void initializeMappers(BerlinModelImportState state){
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for (CdmAttributeMapperBase mapper: classMappers){
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if (mapper instanceof DbSingleAttributeImportMapperBase){
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@SuppressWarnings("unchecked")
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DbSingleAttributeImportMapperBase<BerlinModelImportState,Reference> singleMapper =
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(DbSingleAttributeImportMapperBase<BerlinModelImportState,Reference>)mapper;
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singleMapper.initialize(state, Reference.class);
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}
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}
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return;
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}
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private Set<Integer> commonNameRefSet = null;
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private void initializeCommonNameRefMap(BerlinModelImportState state) throws SQLException{
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if (state.getConfig().isEuroMed()){
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commonNameRefSet = new HashSet<>();
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String queryStr = "SELECT DISTINCT RefFk "
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+ " FROM emCommonName ";
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ResultSet rs = state.getConfig().getSource().getResultSet(queryStr);
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while (rs.next()){
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commonNameRefSet.add(rs.getInt("RefFk"));
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}
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}
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}
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protected static CdmAttributeMapperBase[] classMappers = new CdmAttributeMapperBase[]{
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new CdmStringMapper("edition", "edition"),
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new CdmStringMapper("volume", "volume"),
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new CdmStringMapper("publisher", "publisher"),
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new CdmStringMapper("publicationTown", "placePublished"),
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new CdmStringMapper("isbn", "isbn"),
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new CdmStringMapper("isbn", "isbn"),
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new CdmStringMapper("pageString", "pages"),
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new CdmStringMapper("series", "seriesPart"),
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new CdmStringMapper("issn", "issn"),
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new CdmUriMapper("url", "uri"),
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DbImportExtensionMapper.NewInstance("NomStandard", ExtensionType.NOMENCLATURAL_STANDARD()),
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DbImportExtensionMapper.NewInstance("DateString", DATE_STRING_UUID, "Date String", "Date String", "dates"),
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DbImportExtensionMapper.NewInstance("RefDepositedAt", REF_DEPOSITED_AT_UUID, "Ref. deposited at", "Reference is deposited at", "at"),
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DbImportExtensionMapper.NewInstance("RefSource", REF_SOURCE_UUID, "RefSource", "Reference Source", "source"),
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DbImportMarkerMapper.NewInstance("isPaper", IS_PAPER_UUID, "is paper", "is paper", "paper", false)
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};
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protected static String[] operationalAttributes = new String[]{
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"refId", "refCache", "nomRefCache", "preliminaryFlag", "inRefFk", "title", "nomTitleAbbrev",
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"refAuthorString", "nomAuthorTeamFk",
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"refCategoryFk", "thesisFlag", "informalRefCategory", "idInSource"
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};
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protected static String[] createdAndNotesAttributes = new String[]{
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"created_When", "updated_When", "created_Who", "updated_Who", "notes"
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};
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protected static String[] unclearMappers = new String[]{
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/*"isPaper",*/ "exportDate",
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};
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//TODO isPaper
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//
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//type to count the references nomReferences that have been created and saved
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private class RefCounter{
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RefCounter() {refCount = 0;}
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int refCount;
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int dedupCount;
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@Override
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public String toString(){return String.valueOf(refCount) + "/" + String.valueOf(dedupCount) ;}
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}
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@Override
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protected String getRecordQuery(BerlinModelImportConfigurator config) {
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return null; //not needed
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}
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@Override
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protected void doInvoke(BerlinModelImportState state){
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logger.info("start make " + getPluralString() + " ...");
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deduplicationHelper = ImportDeduplicationHelper.NewInstance(this, state);
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boolean success = true;
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initializeMappers(state);
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try {
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initializeCommonNameRefMap(state);
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} catch (SQLException e1) {
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e1.printStackTrace();
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logger.error("Error in initializeCommonNameRefMap in BerlinModelReferenceimport");
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}
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BerlinModelImportConfigurator config = state.getConfig();
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Source source = config.getSource();
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String strSelectId = " SELECT Reference.RefId as refId ";
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String strSelectFull =
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" SELECT Reference.* ,InReference.RefCategoryFk as InRefCategoryFk, RefSource.RefSource " ;
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String strFrom =
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" FROM %s " +
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" LEFT OUTER JOIN Reference as InReference ON InReference.refId = Reference.inRefFk " +
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" LEFT OUTER JOIN RefSource ON Reference.RefSourceFk = RefSource.RefSourceId " +
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" WHERE (1=1) ";
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String strOrderBy = " ORDER BY InReference.inRefFk, Reference.inRefFk "; //to make in-references available in first run
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String strWherePartitioned = " AND (Reference.refId IN ("+ ID_LIST_TOKEN + ") ) ";
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String referenceTable = CdmUtils.Nz(state.getConfig().getReferenceIdTable());
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referenceTable = referenceTable.isEmpty() ? " Reference" : referenceTable + " as Reference ";
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String strIdFrom = String.format(strFrom, referenceTable );
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String referenceFilter = CdmUtils.Nz(state.getConfig().getReferenceIdTable());
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if (! referenceFilter.isEmpty()){
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referenceFilter = " AND " + referenceFilter + " ";
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}
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referenceFilter = ""; //don't use it for now, in E+M the tabelle is directly used
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String strIdQueryFirstPath = strSelectId + strIdFrom + strOrderBy ;
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String strIdQuerySecondPath = strSelectId + strIdFrom + " AND (Reference.InRefFk is NOT NULL) ";
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// if (config.getDoReferences() == CONCEPT_REFERENCES){
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// strIdQueryNoInRef += " AND ( Reference.refId IN ( SELECT ptRefFk FROM PTaxon) ) " + referenceFilter;
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// }
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String strRecordQuery = strSelectFull + String.format(strFrom, " Reference ") + strWherePartitioned + strOrderBy;
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int recordsPerTransaction = config.getRecordsPerTransaction();
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try{
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//firstPath
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ResultSetPartitioner<BerlinModelImportState> partitioner =
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ResultSetPartitioner.NewInstance(source, strIdQueryFirstPath, strRecordQuery, recordsPerTransaction);
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while (partitioner.nextPartition()){
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partitioner.doPartition(this, state);
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}
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logger.info("end make references without in-references ... " + getSuccessString(success));
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state.setReferenceSecondPath(true);
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//secondPath
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// partitioner = ResultSetPartitioner.NewInstance(source, strIdQuerySecondPath, strRecordQuery, recordsPerTransaction);
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// while (partitioner.nextPartition()){
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// //currently not used as inRef assignment fully works through sorting of idQuery now, at least in E+M
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// partitioner.doPartition(this, state);
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// }
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// logger.info("end make references with no 1 in-reference ... " + getSuccessString(success));
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state.setReferenceSecondPath(false);
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logger.warn("Parsed book volumes: " + parsedBookVolumes);
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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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return;
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}
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logger.info("end make " + getPluralString() + " ... " + getSuccessString(success));
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if (! success){
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state.setUnsuccessfull();
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}
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deduplicationHelper = null;
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return;
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}
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// not needed, data also in Reference.idInSource
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// private void fillSourceNumberMap(BerlinModelImportState state) throws SQLException {
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// String query = " SELECT * FROM SourceNumber2Ref ";
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// ResultSet rs = state.getConfig().getSource().getResultSet(query);
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// while (rs.next()){
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// String sourceNumber = rs.getString("SourceNumber");
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// int refId = rs.getInt("RefId");
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// if (isNotBlank(sourceNumber)){
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// String oldValue = sourceNumberMap.put(refId, sourceNumber.trim());
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// if (oldValue != null){
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// logger.warn(">1 source number exists for refId: " + refId);
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// }
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// }
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// }
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// }
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@Override
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public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {
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deduplicationHelper.restartSession();
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if (state.isReferenceSecondPath()){
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return doPartitionSecondPath(partitioner, state);
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}
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boolean success = true;
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Map<Integer, Reference> refToSave = new HashMap<>();
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// @SuppressWarnings("unchecked")
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// Map<String, Reference> relatedReferences = partitioner.getObjectMap(REFERENCE_NAMESPACE);
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BerlinModelImportConfigurator config = state.getConfig();
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try {
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int i = 0;
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RefCounter refCounter = new RefCounter();
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ResultSet rs = partitioner.getResultSet();
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//for each resultset
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while (rs.next()){
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if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("References handled: " + (i-1) + " in round -" );}
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success &= makeSingleReferenceRecord(rs, state, partitioner, refToSave, refCounter);
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} // end resultSet
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//for the concept reference a fixed uuid may be needed -> change uuid
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Integer sourceSecId = (Integer)config.getSourceSecId();
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Reference sec = refToSave.get(sourceSecId);
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if (sec != null){
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sec.setUuid(config.getSecUuid());
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322
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logger.info("SecUuid changed to: " + config.getSecUuid());
|
|
323
|
}
|
|
324
|
|
|
325
|
//save and store in map
|
|
326
|
logger.warn("Save references (" + refCounter.toString() + ")"); //set preliminary to warn for printing dedup count
|
|
327
|
|
|
328
|
getReferenceService().saveOrUpdate(refToSave.values());
|
|
329
|
|
|
330
|
// logger.info("end makeReferences ..." + getSuccessString(success));;
|
|
331
|
return success;
|
|
332
|
} catch (SQLException e) {
|
|
333
|
logger.error("SQLException:" + e);
|
|
334
|
return false;
|
|
335
|
}
|
|
336
|
}
|
|
337
|
|
|
338
|
|
|
339
|
|
|
340
|
/**
|
|
341
|
* Adds the inReference to the according references.
|
|
342
|
* @param partitioner
|
|
343
|
* @param state
|
|
344
|
* @return
|
|
345
|
*/
|
|
346
|
private boolean doPartitionSecondPath(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {
|
|
347
|
boolean success = true;
|
|
348
|
|
|
349
|
Map<Integer, Reference> refToSave = new HashMap<>();
|
|
350
|
|
|
351
|
@SuppressWarnings("unchecked")
|
|
352
|
Map<String, Reference> relatedReferencesMap = partitioner.getObjectMap(REFERENCE_NAMESPACE);
|
|
353
|
|
|
354
|
try {
|
|
355
|
int i = 0;
|
|
356
|
RefCounter refCounter = new RefCounter();
|
|
357
|
|
|
358
|
ResultSet rs = partitioner.getResultSet();
|
|
359
|
//for each resultset
|
|
360
|
while (rs.next()){
|
|
361
|
if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("References handled: " + (i-1) + " in round -" );}
|
|
362
|
|
|
363
|
Integer refId = rs.getInt("refId");
|
|
364
|
Integer inRefFk = nullSafeInt(rs, "inRefFk");
|
|
365
|
|
|
366
|
if (inRefFk != null){
|
|
367
|
|
|
368
|
Reference thisRef = relatedReferencesMap.get(String.valueOf(refId));
|
|
369
|
|
|
370
|
Reference inRef = relatedReferencesMap.get(String.valueOf(inRefFk));
|
|
371
|
|
|
372
|
if (thisRef != null){
|
|
373
|
if (inRef == null){
|
|
374
|
logger.warn("No InRef found for nomRef: " + thisRef.getTitleCache() + "; RefId: " + refId + "; inRefFK: " + inRefFk);
|
|
375
|
}
|
|
376
|
thisRef.setInReference(inRef);
|
|
377
|
refToSave.put(refId, thisRef);
|
|
378
|
if(!thisRef.isProtectedTitleCache()){
|
|
379
|
thisRef.setTitleCache(null);
|
|
380
|
thisRef.getTitleCache();
|
|
381
|
}
|
|
382
|
}else{
|
|
383
|
logger.warn("Reference which has an inReference not found in DB. RefId: " + refId);
|
|
384
|
}
|
|
385
|
if(inRefFk.equals(0)){
|
|
386
|
logger.warn("InRefFk is 0 for refId "+ refId);
|
|
387
|
}
|
|
388
|
}
|
|
389
|
|
|
390
|
} // end resultSet
|
|
391
|
|
|
392
|
//save and store in map
|
|
393
|
logger.info("Save in references (" + refCounter.toString() + ")");
|
|
394
|
getReferenceService().saveOrUpdate(refToSave.values());
|
|
395
|
|
|
396
|
// }//end resultSetList
|
|
397
|
|
|
398
|
// logger.info("end makeReferences ..." + getSuccessString(success));;
|
|
399
|
return success;
|
|
400
|
} catch (SQLException e) {
|
|
401
|
logger.error("SQLException:" + e);
|
|
402
|
return false;
|
|
403
|
}
|
|
404
|
}
|
|
405
|
|
|
406
|
|
|
407
|
@Override
|
|
408
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {
|
|
409
|
String nameSpace;
|
|
410
|
Class<?> cdmClass;
|
|
411
|
Set<String> idSet;
|
|
412
|
|
|
413
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();
|
|
414
|
|
|
415
|
try{
|
|
416
|
Set<String> teamIdSet = new HashSet<>();
|
|
417
|
Set<String> referenceIdSet = new HashSet<>();
|
|
418
|
Set<String> teamStringSet = new HashSet<>();
|
|
419
|
|
|
420
|
while (rs.next()){
|
|
421
|
handleForeignKey(rs, teamIdSet, "NomAuthorTeamFk");
|
|
422
|
handleForeignKey(rs, referenceIdSet, "InRefFk");
|
|
423
|
handleForeignKey(rs, teamStringSet, "refAuthorString");
|
|
424
|
//TODO only needed in second path but state not available here to check if state is second path
|
|
425
|
handleForeignKey(rs, referenceIdSet, "refId");
|
|
426
|
}
|
|
427
|
|
|
428
|
Set<String> teamStringSet2 = new HashSet<>();
|
|
429
|
for (String teamString : teamStringSet){
|
|
430
|
teamStringSet2.add(teamString.replace("'", "´"));
|
|
431
|
}
|
|
432
|
|
|
433
|
//team map
|
|
434
|
nameSpace = BerlinModelAuthorTeamImport.NAMESPACE;
|
|
435
|
cdmClass = TeamOrPersonBase.class;
|
|
436
|
idSet = teamIdSet;
|
|
437
|
@SuppressWarnings("unchecked")
|
|
438
|
Map<String, Team> teamMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
439
|
result.put(nameSpace, teamMap);
|
|
440
|
|
|
441
|
//refAuthor map
|
|
442
|
nameSpace = REF_AUTHOR_NAMESPACE;
|
|
443
|
cdmClass = TeamOrPersonBase.class;
|
|
444
|
idSet = teamStringSet2;
|
|
445
|
@SuppressWarnings("unchecked")
|
|
446
|
Map<String, Team> refAuthorMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
447
|
result.put(nameSpace, refAuthorMap);
|
|
448
|
|
|
449
|
//reference map
|
|
450
|
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
|
|
451
|
cdmClass = Reference.class;
|
|
452
|
idSet = referenceIdSet;
|
|
453
|
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
454
|
result.put(nameSpace, referenceMap);
|
|
455
|
|
|
456
|
} catch (SQLException e) {
|
|
457
|
throw new RuntimeException(e);
|
|
458
|
}
|
|
459
|
return result;
|
|
460
|
}
|
|
461
|
|
|
462
|
|
|
463
|
/**
|
|
464
|
* Handles a single reference record
|
|
465
|
* @param rs
|
|
466
|
* @param state
|
|
467
|
* @param biblioRefToSave
|
|
468
|
* @param nomRefToSave
|
|
469
|
* @param relatedBiblioReferences
|
|
470
|
* @param relatedNomReferences
|
|
471
|
* @param refCounter
|
|
472
|
* @return
|
|
473
|
*/
|
|
474
|
private boolean makeSingleReferenceRecord(
|
|
475
|
ResultSet rs,
|
|
476
|
BerlinModelImportState state,
|
|
477
|
ResultSetPartitioner<BerlinModelImportState> partitioner,
|
|
478
|
Map<Integer, Reference> refToSave,
|
|
479
|
RefCounter refCounter){
|
|
480
|
|
|
481
|
boolean success = true;
|
|
482
|
|
|
483
|
Integer refId = null;
|
|
484
|
try {
|
|
485
|
Map<String, Object> valueMap = getValueMap(rs);
|
|
486
|
|
|
487
|
Integer categoryFk = (Integer)valueMap.get("refCategoryFk".toLowerCase());
|
|
488
|
refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
489
|
Boolean thesisFlag = (Boolean)valueMap.get("thesisFlag".toLowerCase());
|
|
490
|
|
|
491
|
|
|
492
|
Reference reference;
|
|
493
|
logger.debug("RefCategoryFk: " + categoryFk);
|
|
494
|
|
|
495
|
if (thesisFlag){
|
|
496
|
reference = makeThesis(valueMap);
|
|
497
|
}else if (categoryFk == REF_JOURNAL){
|
|
498
|
reference = makeJournal(valueMap);
|
|
499
|
}else if(categoryFk == REF_BOOK){
|
|
500
|
reference = makeBook(valueMap);
|
|
501
|
}else if(categoryFk == REF_DATABASE){
|
|
502
|
reference = makeDatabase(valueMap);
|
|
503
|
}else if(categoryFk == REF_INFORMAL){
|
|
504
|
reference = makeInformal(valueMap);
|
|
505
|
}else if(categoryFk == REF_WEBSITE){
|
|
506
|
reference = makeWebSite(valueMap);
|
|
507
|
}else if(categoryFk == REF_UNKNOWN){
|
|
508
|
reference = makeUnknown(valueMap);
|
|
509
|
}else if(categoryFk == REF_PRINT_SERIES){
|
|
510
|
reference = makePrintSeries(valueMap);
|
|
511
|
}else if(categoryFk == REF_CONFERENCE_PROCEEDINGS){
|
|
512
|
reference = makeProceedings(valueMap);
|
|
513
|
}else if(categoryFk == REF_ARTICLE){
|
|
514
|
reference = makeArticle(valueMap);
|
|
515
|
}else if(categoryFk == REF_JOURNAL_VOLUME){
|
|
516
|
reference = makeJournalVolume(valueMap);
|
|
517
|
}else if(categoryFk == REF_PART_OF_OTHER_TITLE){
|
|
518
|
reference = makePartOfOtherTitle(valueMap);
|
|
519
|
}else{
|
|
520
|
logger.warn("Unknown categoryFk (" + categoryFk + "). Create 'Generic instead'");
|
|
521
|
reference = ReferenceFactory.newGeneric();
|
|
522
|
success = false;
|
|
523
|
}
|
|
524
|
|
|
525
|
//refYear
|
|
526
|
String refYear = (String)valueMap.get("refYear".toLowerCase());
|
|
527
|
reference.setDatePublished(ImportHelper.getDatePublished(refYear));
|
|
528
|
|
|
529
|
handleEdition(reference);
|
|
530
|
|
|
531
|
//created, updated, notes
|
|
532
|
doCreatedUpdatedNotes(state, reference, rs);
|
|
533
|
|
|
534
|
//idInSource (import from older source to berlin model)
|
|
535
|
//TODO do we want this being imported? Maybe as alternatvie identifier?
|
|
536
|
String idInSource = (String)valueMap.get("IdInSource".toLowerCase());
|
|
537
|
if (isNotBlank(idInSource)){
|
|
538
|
if(!state.getConfig().isDoSourceNumber()){
|
|
539
|
IdentifiableSource source = IdentifiableSource.NewDataImportInstance(idInSource);
|
|
540
|
source.setIdNamespace("import to Berlin Model");
|
|
541
|
reference.addSource(source);
|
|
542
|
}else{
|
|
543
|
makeSourceNumbers(state, idInSource, reference, refId);
|
|
544
|
}
|
|
545
|
}
|
|
546
|
String uuid = null;
|
|
547
|
if (resultSetHasColumn(rs,"UUID")){
|
|
548
|
uuid = rs.getString("UUID");
|
|
549
|
if (uuid != null){
|
|
550
|
reference.setUuid(UUID.fromString(uuid));
|
|
551
|
}
|
|
552
|
}
|
|
553
|
|
|
554
|
//nom&BiblioReference - must be last because a clone is created
|
|
555
|
success &= makeNomAndBiblioReference(rs, state, partitioner, refId, reference, refCounter, refToSave);
|
|
556
|
|
|
557
|
|
|
558
|
} catch (Exception e) {
|
|
559
|
logger.warn("Reference with BM refId '" + CdmUtils.Nz(refId) + "' threw Exception and could not be saved");
|
|
560
|
e.printStackTrace();
|
|
561
|
success = false;
|
|
562
|
}
|
|
563
|
return success;
|
|
564
|
}
|
|
565
|
|
|
566
|
|
|
567
|
/**
|
|
568
|
* @param state
|
|
569
|
* @param idInSource
|
|
570
|
* @param reference
|
|
571
|
* @param refId
|
|
572
|
*/
|
|
573
|
private void makeSourceNumbers(BerlinModelImportState state, String idInSource, Reference reference,
|
|
574
|
Integer refId) {
|
|
575
|
String[] splits = idInSource.split("\\|");
|
|
576
|
for (String split : splits){
|
|
577
|
split = split.trim();
|
|
578
|
UUID uuid = BerlinModelTransformer.uuidEMReferenceSourceNumber;
|
|
579
|
TermVocabulary<DefinedTerm> voc = null; //user defined voc
|
|
580
|
DefinedTerm type = getIdentiferType(state, uuid, "E+M Reference Source Number", "Euro+Med Reference Source Number", "E+M Source Number", voc);
|
|
581
|
Identifier.NewInstance(reference, split, type);
|
|
582
|
}
|
|
583
|
}
|
|
584
|
|
|
585
|
/**
|
|
586
|
* @param reference
|
|
587
|
*/
|
|
588
|
private void handleEdition(Reference reference) {
|
|
589
|
if (reference.getEdition()!= null && reference.getEdition().startsWith("ed. ")){
|
|
590
|
reference.setEdition(reference.getEdition().substring(4));
|
|
591
|
}
|
|
592
|
|
|
593
|
}
|
|
594
|
|
|
595
|
/**
|
|
596
|
* Creates and saves a nom. reference and a biblio. reference after checking necessity
|
|
597
|
* @param rs
|
|
598
|
* @param refId
|
|
599
|
* @param ref
|
|
600
|
* @param refCounter
|
|
601
|
* @param biblioRefToSave
|
|
602
|
* @param nomRefToSave
|
|
603
|
* @param teamMap
|
|
604
|
* @param stores
|
|
605
|
* @return
|
|
606
|
* @throws SQLException
|
|
607
|
*/
|
|
608
|
private boolean makeNomAndBiblioReference(
|
|
609
|
ResultSet rs,
|
|
610
|
BerlinModelImportState state,
|
|
611
|
@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner,
|
|
612
|
int refId,
|
|
613
|
Reference ref,
|
|
614
|
RefCounter refCounter,
|
|
615
|
Map<Integer, Reference> refToSave
|
|
616
|
) throws SQLException{
|
|
617
|
|
|
618
|
@SuppressWarnings("unchecked")
|
|
619
|
Map<String, Team> teamMap = partitioner.getObjectMap(BerlinModelAuthorTeamImport.NAMESPACE);
|
|
620
|
|
|
621
|
String refCache = trim(rs.getString("refCache"));
|
|
622
|
String nomRefCache = trim(rs.getString("nomRefCache"));
|
|
623
|
String title = trim(rs.getString("title"));
|
|
624
|
String nomTitleAbbrev = trim(rs.getString("nomTitleAbbrev"));
|
|
625
|
boolean isPreliminary = rs.getBoolean("PreliminaryFlag");
|
|
626
|
String refAuthorString = trim(rs.getString("refAuthorString"));
|
|
627
|
Integer nomAuthorTeamFk = nullSafeInt(rs, "NomAuthorTeamFk");
|
|
628
|
Integer inRefFk = nullSafeInt(rs, "inRefFk");
|
|
629
|
|
|
630
|
|
|
631
|
TeamOrPersonBase<?> nomAuthor = null;
|
|
632
|
if (nomAuthorTeamFk != null){
|
|
633
|
String strNomAuthorTeamFk = String.valueOf(nomAuthorTeamFk);
|
|
634
|
nomAuthor = teamMap.get(strNomAuthorTeamFk);
|
|
635
|
if (nomAuthor == null){
|
|
636
|
logger.warn("NomAuthor ("+strNomAuthorTeamFk+") not found in teamMap (but it should exist) for " + refId);
|
|
637
|
}
|
|
638
|
}
|
|
639
|
|
|
640
|
Reference sourceReference = state.getTransactionalSourceReference();
|
|
641
|
|
|
642
|
//preliminary
|
|
643
|
if (isPreliminary){
|
|
644
|
ref.setAbbrevTitleCache(nomRefCache, true);
|
|
645
|
ref.setTitleCache(refCache, true);
|
|
646
|
}
|
|
647
|
|
|
648
|
//title/abbrevTitle
|
|
649
|
if (isNotBlank(nomTitleAbbrev)){
|
|
650
|
ref.setAbbrevTitle(nomTitleAbbrev);
|
|
651
|
}
|
|
652
|
if (isNotBlank(title)){
|
|
653
|
ref.setTitle(title);
|
|
654
|
}
|
|
655
|
|
|
656
|
//author
|
|
657
|
TeamOrPersonBase<?> author = getAuthorship(state, refAuthorString, nomAuthor, refId);
|
|
658
|
ref.setAuthorship(author);
|
|
659
|
|
|
660
|
if (ref.getType().equals(ReferenceType.Book)){
|
|
661
|
extraktBookVolume(ref);
|
|
662
|
}
|
|
663
|
|
|
664
|
//inRef
|
|
665
|
Reference inRef = null;
|
|
666
|
if (inRefFk != null){
|
|
667
|
@SuppressWarnings({"unchecked" })
|
|
668
|
Map<String, Reference> relatedReferences = partitioner.getObjectMap(REFERENCE_NAMESPACE);
|
|
669
|
inRef = relatedReferences.get(String.valueOf(inRefFk));
|
|
670
|
if (inRef == null){
|
|
671
|
inRef = refToSave.get(inRefFk);
|
|
672
|
}
|
|
673
|
if (inRef == null){
|
|
674
|
logger.warn("InRef not (yet) found. RefId: " + refId + "; InRef: "+ inRefFk);
|
|
675
|
}else{
|
|
676
|
ref.setInReference(inRef);
|
|
677
|
}
|
|
678
|
}
|
|
679
|
|
|
680
|
Reference result = deduplicateReference(state, ref);
|
|
681
|
if(ref != result){
|
|
682
|
//dedup not possible at this point because inRef exists but is not yet defined
|
|
683
|
if (inRefFk != null && inRef == null){
|
|
684
|
result = ref;
|
|
685
|
logger.warn("Ref has deduplication candidate but inRef is still missing. " + inRef);
|
|
686
|
}else{
|
|
687
|
logger.debug("Reference was deduplicated. RefId: " + refId);
|
|
688
|
//FIXME also check annotations etc. for deduplication
|
|
689
|
refCounter.dedupCount++;
|
|
690
|
}
|
|
691
|
}else{
|
|
692
|
refCounter.refCount++;
|
|
693
|
}
|
|
694
|
|
|
695
|
//save
|
|
696
|
if (! refToSave.containsKey(refId)){
|
|
697
|
refToSave.put(refId, result);
|
|
698
|
}else{
|
|
699
|
//should not happen
|
|
700
|
logger.warn("Duplicate refId in Berlin Model database. Second reference was not imported !!");
|
|
701
|
}
|
|
702
|
|
|
703
|
|
|
704
|
//refId
|
|
705
|
ImportHelper.setOriginalSource(result, sourceReference, refId, REFERENCE_NAMESPACE);
|
|
706
|
|
|
707
|
if (commonNameRefSet != null && commonNameRefSet.contains(refId)){
|
|
708
|
result.addMarker(Marker.NewInstance(MarkerType.COMMON_NAME_REFERENCE(), true));
|
|
709
|
}
|
|
710
|
|
|
711
|
return true;
|
|
712
|
}
|
|
713
|
|
|
714
|
/**
|
|
715
|
* @param string
|
|
716
|
* @return
|
|
717
|
*/
|
|
718
|
private String trim(String string) {
|
|
719
|
if (string == null){
|
|
720
|
return null;
|
|
721
|
}else{
|
|
722
|
return string.trim();
|
|
723
|
}
|
|
724
|
}
|
|
725
|
|
|
726
|
/**
|
|
727
|
* Copies the created and updated information from the nomReference to the cloned bibliographic reference
|
|
728
|
* @param referenceBase
|
|
729
|
* @param nomReference
|
|
730
|
*/
|
|
731
|
private void copyCreatedUpdated(Reference biblioReference, Reference nomReference) {
|
|
732
|
biblioReference.setCreatedBy(nomReference.getCreatedBy());
|
|
733
|
biblioReference.setCreated(nomReference.getCreated());
|
|
734
|
biblioReference.setUpdatedBy(nomReference.getUpdatedBy());
|
|
735
|
biblioReference.setUpdated(nomReference.getUpdated());
|
|
736
|
|
|
737
|
}
|
|
738
|
|
|
739
|
private Reference makeArticle (Map<String, Object> valueMap){
|
|
740
|
|
|
741
|
IArticle article = ReferenceFactory.newArticle();
|
|
742
|
Object inRefFk = valueMap.get("inRefFk".toLowerCase());
|
|
743
|
Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());
|
|
744
|
Integer refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
745
|
|
|
746
|
if (inRefFk != null){
|
|
747
|
if (inRefCategoryFk != REF_JOURNAL){
|
|
748
|
logger.warn("Wrong inrefCategory for Article (refID = " + refId +"). Type must be 'Journal' but was not (RefCategoryFk=" + inRefCategoryFk + "))." +
|
|
749
|
" InReference was added anyway! ");
|
|
750
|
}
|
|
751
|
}else{
|
|
752
|
logger.warn ("Article has no inreference: " + refId);
|
|
753
|
}
|
|
754
|
makeStandardMapper(valueMap, (Reference)article); //url, pages, series, volume
|
|
755
|
String url = (String)valueMap.get("url");
|
|
756
|
if (url != null && url.contains("dx.doi.org")){
|
|
757
|
article.setDoi(DOI.fromString(url));
|
|
758
|
article.setUri(null);
|
|
759
|
}
|
|
760
|
return (Reference)article;
|
|
761
|
}
|
|
762
|
|
|
763
|
private Reference makePartOfOtherTitle (Map<String, Object> valueMap){
|
|
764
|
|
|
765
|
Reference result;
|
|
766
|
Object inRefFk = valueMap.get("inRefFk".toLowerCase());
|
|
767
|
Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());
|
|
768
|
Integer refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
769
|
|
|
770
|
if (inRefCategoryFk == null){
|
|
771
|
//null -> error
|
|
772
|
logger.warn("Part-Of-Other-Title has no inRefCategoryFk! RefId = " + refId + ". ReferenceType set to Generic.");
|
|
773
|
result = makeUnknown(valueMap);
|
|
774
|
}else if (inRefFk == null){
|
|
775
|
//TODO is this correct ??
|
|
776
|
logger.warn("Part-Of-Other-Title has no in reference: " + refId);
|
|
777
|
result = makeUnknown(valueMap);
|
|
778
|
}else if (inRefCategoryFk == REF_BOOK){
|
|
779
|
//BookSection
|
|
780
|
IBookSection bookSection = ReferenceFactory.newBookSection();
|
|
781
|
result = (Reference)bookSection;
|
|
782
|
}else if (inRefCategoryFk == REF_ARTICLE){
|
|
783
|
//Article
|
|
784
|
logger.info("Reference (refId = " + refId + ") of type 'part_of_other_title' is part of 'article'." +
|
|
785
|
" We use the section reference type for such in references now.") ;
|
|
786
|
result = ReferenceFactory.newSection();
|
|
787
|
}else if (inRefCategoryFk == REF_JOURNAL){
|
|
788
|
//TODO
|
|
789
|
logger.warn("Reference (refId = " + refId + ") of type 'part_of_other_title' has inReference of type 'journal'." +
|
|
790
|
" This is not allowed! Generic reference created instead") ;
|
|
791
|
result = ReferenceFactory.newGeneric();
|
|
792
|
result.addMarker(Marker.NewInstance(MarkerType.TO_BE_CHECKED(), true));
|
|
793
|
}else if (inRefCategoryFk == REF_PART_OF_OTHER_TITLE){
|
|
794
|
logger.info("Reference (refId = " + refId + ") of type 'part_of_other_title' has inReference 'part of other title'." +
|
|
795
|
" This is allowed, but may be true only for specific cases (e.g. parts of book chapters). You may want to check if this is correct") ;
|
|
796
|
result = ReferenceFactory.newSection();
|
|
797
|
}else{
|
|
798
|
logger.warn("InReference type (catFk = " + inRefCategoryFk + ") of part-of-reference not recognized for refId " + refId + "." +
|
|
799
|
" Create 'Generic' reference instead");
|
|
800
|
result = ReferenceFactory.newGeneric();
|
|
801
|
}
|
|
802
|
makeStandardMapper(valueMap, result); //url, pages
|
|
803
|
return result;
|
|
804
|
}
|
|
805
|
|
|
806
|
|
|
807
|
/**
|
|
808
|
* @param inRefFkInt
|
|
809
|
* @param biblioRefToSave
|
|
810
|
* @param nomRefToSave
|
|
811
|
* @param relatedBiblioReferences
|
|
812
|
* @param relatedNomReferences
|
|
813
|
* @return
|
|
814
|
*/
|
|
815
|
private boolean existsInMapOrToSave(Integer inRefFkInt, Map<Integer, Reference> refToSave, Map<String, Reference> relatedReferences) {
|
|
816
|
boolean result = false;
|
|
817
|
if (inRefFkInt == null){
|
|
818
|
return false;
|
|
819
|
}
|
|
820
|
result |= refToSave.containsKey(inRefFkInt);
|
|
821
|
result |= relatedReferences.containsKey(String.valueOf(inRefFkInt));
|
|
822
|
return result;
|
|
823
|
}
|
|
824
|
|
|
825
|
private Reference makeWebSite(Map<String, Object> valueMap){
|
|
826
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Website'");}
|
|
827
|
Reference webPage = ReferenceFactory.newWebPage();
|
|
828
|
makeStandardMapper(valueMap, webPage); //placePublished, publisher
|
|
829
|
return webPage;
|
|
830
|
}
|
|
831
|
|
|
832
|
private Reference makeUnknown(Map<String, Object> valueMap){
|
|
833
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Unknown'");}
|
|
834
|
Reference generic = ReferenceFactory.newGeneric();
|
|
835
|
// generic.setSeries(series);
|
|
836
|
makeStandardMapper(valueMap, generic); //pages, placePublished, publisher, series, volume
|
|
837
|
return generic;
|
|
838
|
}
|
|
839
|
|
|
840
|
private Reference makeInformal(Map<String, Object> valueMap){
|
|
841
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Informal'");}
|
|
842
|
Reference generic = ReferenceFactory.newGeneric();
|
|
843
|
// informal.setSeries(series);
|
|
844
|
makeStandardMapper(valueMap, generic);//editor, pages, placePublished, publisher, series, volume
|
|
845
|
String informal = (String)valueMap.get("InformalRefCategory".toLowerCase());
|
|
846
|
if (isNotBlank(informal) ){
|
|
847
|
generic.addExtension(informal, ExtensionType.INFORMAL_CATEGORY());
|
|
848
|
}
|
|
849
|
return generic;
|
|
850
|
}
|
|
851
|
|
|
852
|
private Reference makeDatabase(Map<String, Object> valueMap){
|
|
853
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Database'");}
|
|
854
|
Reference database = ReferenceFactory.newDatabase();
|
|
855
|
makeStandardMapper(valueMap, database); //?
|
|
856
|
return database;
|
|
857
|
}
|
|
858
|
|
|
859
|
private Reference makeJournal(Map<String, Object> valueMap){
|
|
860
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Journal'");}
|
|
861
|
Reference journal = ReferenceFactory.newJournal();
|
|
862
|
|
|
863
|
Set<String> omitAttributes = new HashSet<>();
|
|
864
|
String series = "series";
|
|
865
|
// omitAttributes.add(series);
|
|
866
|
|
|
867
|
makeStandardMapper(valueMap, journal, omitAttributes); //issn,placePublished,publisher
|
|
868
|
// if (valueMap.get(series) != null){
|
|
869
|
// logger.warn("Series not yet implemented for journal!");
|
|
870
|
// }
|
|
871
|
return journal;
|
|
872
|
}
|
|
873
|
|
|
874
|
private Reference makeBook(
|
|
875
|
Map<String, Object> valueMap){
|
|
876
|
|
|
877
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Book'");}
|
|
878
|
Reference book = ReferenceFactory.newBook();
|
|
879
|
// Integer refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
880
|
|
|
881
|
//Set bookAttributes = new String[]{"edition", "isbn", "pages","publicationTown","publisher","volume"};
|
|
882
|
|
|
883
|
Set<String> omitAttributes = new HashSet<>();
|
|
884
|
String attrSeries = "series";
|
|
885
|
// omitAttributes.add(attrSeries);
|
|
886
|
|
|
887
|
makeStandardMapper(valueMap, book, omitAttributes);
|
|
888
|
|
|
889
|
//Series (as String)
|
|
890
|
IPrintSeries printSeries = null;
|
|
891
|
if (valueMap.get(attrSeries) != null){
|
|
892
|
String series = (String)valueMap.get("title".toLowerCase());
|
|
893
|
if (series == null){
|
|
894
|
String nomTitle = (String)valueMap.get("nomTitleAbbrev".toLowerCase());
|
|
895
|
series = nomTitle;
|
|
896
|
}
|
|
897
|
printSeries = ReferenceFactory.newPrintSeries(series);
|
|
898
|
logger.info("Implementation of printSeries is preliminary");
|
|
899
|
}
|
|
900
|
//Series (as Reference)
|
|
901
|
if (book.getInSeries() != null && printSeries != null){
|
|
902
|
logger.warn("Book has series string and inSeries reference. Can not take both. Series string neglected");
|
|
903
|
}else{
|
|
904
|
book.setInSeries(printSeries);
|
|
905
|
}
|
|
906
|
book.setEditor(null);
|
|
907
|
|
|
908
|
return book;
|
|
909
|
|
|
910
|
}
|
|
911
|
|
|
912
|
|
|
913
|
int parsedBookVolumes = 0;
|
|
914
|
private void extraktBookVolume(Reference book) {
|
|
915
|
if (isExtractBookVolumeCandidate(book)){
|
|
916
|
String patternStr = "(.{2,})\\s(\\d{1,2})";
|
|
917
|
int groupIndex = 2;
|
|
918
|
Pattern pattern = Pattern.compile(patternStr);
|
|
919
|
|
|
920
|
String abbrevCache = book.getAbbrevTitleCache();
|
|
921
|
String titleCache = book.getTitleCache();
|
|
922
|
String vol = null;
|
|
923
|
String volFull = null;
|
|
924
|
String abbrev = book.getAbbrevTitle();
|
|
925
|
if (isNotBlank(abbrev)){
|
|
926
|
Matcher matcher = pattern.matcher(abbrev);
|
|
927
|
if (matcher.matches()){
|
|
928
|
vol = matcher.group(groupIndex);
|
|
929
|
abbrev = matcher.group(1);
|
|
930
|
}
|
|
931
|
}
|
|
932
|
|
|
933
|
String full = book.getTitle();
|
|
934
|
if (isNotBlank(full)){
|
|
935
|
Matcher matcher = pattern.matcher(full);
|
|
936
|
if (matcher.matches()){
|
|
937
|
volFull = matcher.group(groupIndex);
|
|
938
|
full = matcher.group(1);
|
|
939
|
}
|
|
940
|
}
|
|
941
|
if (vol != null && volFull != null){
|
|
942
|
if (!vol.equals(volFull)){
|
|
943
|
return;
|
|
944
|
}
|
|
945
|
}else if (vol == null && volFull == null){
|
|
946
|
return;
|
|
947
|
}else if (vol == null){
|
|
948
|
if (isNotBlank(abbrev)){
|
|
949
|
return;
|
|
950
|
}else{
|
|
951
|
vol = volFull;
|
|
952
|
}
|
|
953
|
}else if (volFull == null){
|
|
954
|
if (isNotBlank(full)){
|
|
955
|
return;
|
|
956
|
}
|
|
957
|
}else{
|
|
958
|
logger.warn("Should not happen");
|
|
959
|
}
|
|
960
|
book.setVolume(vol);
|
|
961
|
book.setAbbrevTitle(abbrev);
|
|
962
|
book.setTitle(full);
|
|
963
|
if (!book.getAbbrevTitleCache().equals(abbrevCache)){
|
|
964
|
logger.warn("Abbrev title cache for parsed book volume does not match: " + book.getAbbrevTitleCache() + " <-> "+abbrevCache);
|
|
965
|
}else if (!book.getTitleCache().equals(titleCache)){
|
|
966
|
logger.warn("Title cache for parsed book volume does not match: " + book.getTitleCache() + " <-> "+titleCache);
|
|
967
|
}else{
|
|
968
|
// System.out.println(titleCache);
|
|
969
|
// System.out.println(abbrevCache);
|
|
970
|
parsedBookVolumes++;
|
|
971
|
}
|
|
972
|
}else{
|
|
973
|
return;
|
|
974
|
}
|
|
975
|
}
|
|
976
|
|
|
977
|
/**
|
|
978
|
* @param book
|
|
979
|
* @return
|
|
980
|
*/
|
|
981
|
private boolean isExtractBookVolumeCandidate(Reference book) {
|
|
982
|
if (isNotBlank(book.getVolume()) || isNotBlank(book.getEdition()) || isNotBlank(book.getSeriesPart())){
|
|
983
|
return false;
|
|
984
|
}
|
|
985
|
if (!checkExtractBookVolumeTitle(book.getAbbrevTitle())){
|
|
986
|
return false;
|
|
987
|
}
|
|
988
|
if (!checkExtractBookVolumeTitle(book.getTitle())){
|
|
989
|
return false;
|
|
990
|
}
|
|
991
|
return true;
|
|
992
|
}
|
|
993
|
|
|
994
|
/**
|
|
995
|
* @param abbrevTitle
|
|
996
|
* @return
|
|
997
|
*/
|
|
998
|
private boolean checkExtractBookVolumeTitle(String title) {
|
|
999
|
if (title == null){
|
|
1000
|
return true;
|
|
1001
|
}
|
|
1002
|
if (title.contains(",") || title.contains("ed.") || title.contains("Ed.")|| title.contains("Suppl")
|
|
1003
|
|| title.contains("Ser.")|| title.contains("ser.")) {
|
|
1004
|
return false;
|
|
1005
|
}
|
|
1006
|
return true;
|
|
1007
|
}
|
|
1008
|
|
|
1009
|
/**
|
|
1010
|
* Returns the requested object if it exists in one of both maps. Prefers the refToSaveMap in ambigious cases.
|
|
1011
|
* @param inRefFkInt
|
|
1012
|
* @param nomRefToSave
|
|
1013
|
* @param relatedNomReferences
|
|
1014
|
* @return
|
|
1015
|
*/
|
|
1016
|
private Reference getReferenceFromMaps(
|
|
1017
|
int inRefFkInt,
|
|
1018
|
Map<Integer, Reference> refToSaveMap,
|
|
1019
|
Map<String, Reference> relatedRefMap) {
|
|
1020
|
Reference result = null;
|
|
1021
|
result = refToSaveMap.get(inRefFkInt);
|
|
1022
|
if (result == null){
|
|
1023
|
result = relatedRefMap.get(String.valueOf(inRefFkInt));
|
|
1024
|
}
|
|
1025
|
return result;
|
|
1026
|
}
|
|
1027
|
|
|
1028
|
private Reference makePrintSeries(Map<String, Object> valueMap){
|
|
1029
|
if (logger.isDebugEnabled()){logger.debug("RefType 'PrintSeries'");}
|
|
1030
|
Reference printSeries = ReferenceFactory.newPrintSeries();
|
|
1031
|
makeStandardMapper(valueMap, printSeries, null);
|
|
1032
|
return printSeries;
|
|
1033
|
}
|
|
1034
|
|
|
1035
|
private Reference makeProceedings(Map<String, Object> valueMap){
|
|
1036
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Proceedings'");}
|
|
1037
|
Reference proceedings = ReferenceFactory.newProceedings();
|
|
1038
|
makeStandardMapper(valueMap, proceedings, null);
|
|
1039
|
return proceedings;
|
|
1040
|
}
|
|
1041
|
|
|
1042
|
private Reference makeThesis(Map<String, Object> valueMap){
|
|
1043
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Thesis'");}
|
|
1044
|
Reference thesis = ReferenceFactory.newThesis();
|
|
1045
|
makeStandardMapper(valueMap, thesis, null);
|
|
1046
|
return thesis;
|
|
1047
|
}
|
|
1048
|
|
|
1049
|
|
|
1050
|
private Reference makeJournalVolume(Map<String, Object> valueMap){
|
|
1051
|
if (logger.isDebugEnabled()){logger.debug("RefType 'JournalVolume'");}
|
|
1052
|
//Proceedings proceedings = Proceedings.NewInstance();
|
|
1053
|
Reference journalVolume = ReferenceFactory.newGeneric();
|
|
1054
|
makeStandardMapper(valueMap, journalVolume, null);
|
|
1055
|
logger.warn("Journal volumes not yet implemented. Generic created instead but with errors");
|
|
1056
|
return journalVolume;
|
|
1057
|
}
|
|
1058
|
|
|
1059
|
private boolean makeStandardMapper(Map<String, Object> valueMap, Reference ref){
|
|
1060
|
return makeStandardMapper(valueMap, ref, null);
|
|
1061
|
}
|
|
1062
|
|
|
1063
|
|
|
1064
|
private boolean makeStandardMapper(Map<String, Object> valueMap, CdmBase cdmBase, Set<String> omitAttributes){
|
|
1065
|
boolean result = true;
|
|
1066
|
for (CdmAttributeMapperBase mapper : classMappers){
|
|
1067
|
if (mapper instanceof CdmSingleAttributeMapperBase){
|
|
1068
|
result &= makeStandardSingleMapper(valueMap, cdmBase, (CdmSingleAttributeMapperBase)mapper, omitAttributes);
|
|
1069
|
}else if (mapper instanceof CdmOneToManyMapper){
|
|
1070
|
result &= makeMultipleValueAddMapper(valueMap, cdmBase, (CdmOneToManyMapper)mapper, omitAttributes);
|
|
1071
|
}else{
|
|
1072
|
logger.error("Unknown mapper type");
|
|
1073
|
result = false;
|
|
1074
|
}
|
|
1075
|
}
|
|
1076
|
return result;
|
|
1077
|
}
|
|
1078
|
|
|
1079
|
private boolean makeStandardSingleMapper(Map<String, Object> valueMap, CdmBase cdmBase, CdmSingleAttributeMapperBase mapper, Set<String> omitAttributes){
|
|
1080
|
boolean result = true;
|
|
1081
|
if (omitAttributes == null){
|
|
1082
|
omitAttributes = new HashSet<>();
|
|
1083
|
}
|
|
1084
|
if (mapper instanceof DbImportExtensionMapper){
|
|
1085
|
result &= ((DbImportExtensionMapper)mapper).invoke(valueMap, cdmBase);
|
|
1086
|
}else if (mapper instanceof DbImportMarkerMapper){
|
|
1087
|
result &= ((DbImportMarkerMapper)mapper).invoke(valueMap, cdmBase);
|
|
1088
|
}else{
|
|
1089
|
String sourceAttribute = mapper.getSourceAttributeList().get(0).toLowerCase();
|
|
1090
|
Object value = valueMap.get(sourceAttribute);
|
|
1091
|
if (mapper instanceof CdmUriMapper && value != null){
|
|
1092
|
try {
|
|
1093
|
value = new URI (value.toString());
|
|
1094
|
} catch (URISyntaxException e) {
|
|
1095
|
logger.error("URI syntax exception: " + value.toString());
|
|
1096
|
value = null;
|
|
1097
|
}
|
|
1098
|
}
|
|
1099
|
if (value != null){
|
|
1100
|
String destinationAttribute = mapper.getDestinationAttribute();
|
|
1101
|
if (! omitAttributes.contains(destinationAttribute)){
|
|
1102
|
result &= ImportHelper.addValue(value, cdmBase, destinationAttribute, mapper.getTypeClass(), OVERWRITE, OBLIGATORY);
|
|
1103
|
}
|
|
1104
|
}
|
|
1105
|
}
|
|
1106
|
return result;
|
|
1107
|
}
|
|
1108
|
|
|
1109
|
|
|
1110
|
private boolean makeMultipleValueAddMapper(Map<String, Object> valueMap, CdmBase cdmBase, CdmOneToManyMapper<CdmBase, CdmBase, CdmSingleAttributeMapperBase> mapper, Set<String> omitAttributes){
|
|
1111
|
if (omitAttributes == null){
|
|
1112
|
omitAttributes = new HashSet<>();
|
|
1113
|
}
|
|
1114
|
boolean result = true;
|
|
1115
|
String destinationAttribute = mapper.getSingleAttributeName();
|
|
1116
|
List<Object> sourceValues = new ArrayList<>();
|
|
1117
|
List<Class> classes = new ArrayList<>();
|
|
1118
|
for (CdmSingleAttributeMapperBase singleMapper : mapper.getSingleMappers()){
|
|
1119
|
String sourceAttribute = singleMapper.getSourceAttribute();
|
|
1120
|
Object value = valueMap.get(sourceAttribute);
|
|
1121
|
sourceValues.add(value);
|
|
1122
|
Class<?> clazz = singleMapper.getTypeClass();
|
|
1123
|
classes.add(clazz);
|
|
1124
|
}
|
|
1125
|
|
|
1126
|
result &= ImportHelper.addMultipleValues(sourceValues, cdmBase, destinationAttribute, classes, NO_OVERWRITE, OBLIGATORY);
|
|
1127
|
return result;
|
|
1128
|
}
|
|
1129
|
|
|
1130
|
|
|
1131
|
private TeamOrPersonBase<?> getAuthorship(BerlinModelImportState state, String refAuthorString,
|
|
1132
|
TeamOrPersonBase<?> nomAuthor, Integer refId){
|
|
1133
|
|
|
1134
|
TeamOrPersonBase<?> result;
|
|
1135
|
if (nomAuthor != null){
|
|
1136
|
result = nomAuthor;
|
|
1137
|
if (isNotBlank(refAuthorString) && !nomAuthor.getTitleCache().equals(refAuthorString)){
|
|
1138
|
boolean isSimilar = handleSimilarAuthors(state, refAuthorString, nomAuthor, refId);
|
|
1139
|
if (! isSimilar){
|
|
1140
|
String message = "refAuthorString differs from nomAuthor.titleCache: " + refAuthorString
|
|
1141
|
+ " <-> " + nomAuthor.getTitleCache() + "; RefId: " + refId;
|
|
1142
|
logger.warn(message);
|
|
1143
|
}
|
|
1144
|
}
|
|
1145
|
} else if (isNotBlank(refAuthorString)){//only RefAuthorString exists
|
|
1146
|
refAuthorString = refAuthorString.trim();
|
|
1147
|
//TODO match with existing Persons/Teams
|
|
1148
|
TeamOrPersonBase<?> author = state.getRelatedObject(REF_AUTHOR_NAMESPACE, refAuthorString, TeamOrPersonBase.class);
|
|
1149
|
if (author == null){
|
|
1150
|
if (!BerlinModelAuthorTeamImport.hasTeamSeparator(refAuthorString)){
|
|
1151
|
author = makePerson(refAuthorString, false, refId);
|
|
1152
|
}else{
|
|
1153
|
author = makeTeam(state, refAuthorString, refId);
|
|
1154
|
}
|
|
1155
|
state.addRelatedObject(REF_AUTHOR_NAMESPACE, refAuthorString, author);
|
|
1156
|
result = deduplicatePersonOrTeam(state, author);
|
|
1157
|
|
|
1158
|
if (result != author){
|
|
1159
|
logger.debug("RefAuthorString author deduplicated " + author);
|
|
1160
|
}else{
|
|
1161
|
if (!importSourceExists(author, refAuthorString, REF_AUTHOR_NAMESPACE, state.getTransactionalSourceReference() )){
|
|
1162
|
author.addImportSource(refAuthorString, REF_AUTHOR_NAMESPACE, state.getTransactionalSourceReference(), null);
|
|
1163
|
}
|
|
1164
|
}
|
|
1165
|
}else{
|
|
1166
|
logger.debug("RefAuthor loaded from map");
|
|
1167
|
}
|
|
1168
|
result = author;
|
|
1169
|
}else{
|
|
1170
|
result = null;
|
|
1171
|
}
|
|
1172
|
|
|
1173
|
return result;
|
|
1174
|
}
|
|
1175
|
|
|
1176
|
|
|
1177
|
/**
|
|
1178
|
* @param state
|
|
1179
|
* @param refAuthorString
|
|
1180
|
* @param refId
|
|
1181
|
* @return
|
|
1182
|
*/
|
|
1183
|
private TeamOrPersonBase<?> makeTeam(BerlinModelImportState state, String refAuthorString, Integer refId) {
|
|
1184
|
Team team = Team.NewInstance();
|
|
1185
|
boolean hasDedupMember = false;
|
|
1186
|
if (containsEdOrColon(refAuthorString)){
|
|
1187
|
team.setTitleCache(refAuthorString, true);
|
|
1188
|
}else{
|
|
1189
|
String[] refAuthorTeams = BerlinModelAuthorTeamImport.splitTeam(refAuthorString);
|
|
1190
|
boolean lastWasInitials = false;
|
|
1191
|
for (int i = 0; i< refAuthorTeams.length ;i++){
|
|
1192
|
if (lastWasInitials){
|
|
1193
|
lastWasInitials = false;
|
|
1194
|
continue;
|
|
1195
|
}
|
|
1196
|
String fullTeam = refAuthorTeams[i].trim();
|
|
1197
|
String initials = null;
|
|
1198
|
if (refAuthorTeams.length > i+1){
|
|
1199
|
String nextSplit = refAuthorTeams[i+1].trim();
|
|
1200
|
if (isInitial(nextSplit)){
|
|
1201
|
lastWasInitials = true;
|
|
1202
|
initials = nextSplit;
|
|
1203
|
}
|
|
1204
|
}
|
|
1205
|
Person member = makePerson(fullTeam, isNotBlank(initials), refId);
|
|
1206
|
|
|
1207
|
if (initials != null){
|
|
1208
|
if (member.getInitials() != null){
|
|
1209
|
logger.warn("Initials already set: " + refId);
|
|
1210
|
}else if (!member.isProtectedTitleCache()){
|
|
1211
|
member.setInitials(initials);
|
|
1212
|
}else {
|
|
1213
|
member.setTitleCache(member.getTitleCache() + ", " + initials, true);
|
|
1214
|
}
|
|
1215
|
}
|
|
1216
|
|
|
1217
|
if (i == refAuthorTeams.length -1 && BerlinModelAuthorTeamImport.isEtAl(member)){
|
|
1218
|
team.setHasMoreMembers(true);
|
|
1219
|
}else{
|
|
1220
|
Person dedupMember = deduplicatePersonOrTeam(state, member);
|
|
1221
|
if (dedupMember != member){
|
|
1222
|
hasDedupMember = true;
|
|
1223
|
}else{
|
|
1224
|
if (!importSourceExists(member, refAuthorString, REF_AUTHOR_NAMESPACE, state.getTransactionalSourceReference())){
|
|
1225
|
member.addImportSource(refAuthorString, REF_AUTHOR_NAMESPACE, state.getTransactionalSourceReference(), null);
|
|
1226
|
}
|
|
1227
|
}
|
|
1228
|
|
|
1229
|
team.addTeamMember(dedupMember);
|
|
1230
|
}
|
|
1231
|
}
|
|
1232
|
}
|
|
1233
|
|
|
1234
|
TeamOrPersonBase<?> result = team;
|
|
1235
|
if (team.getTeamMembers().size() == 1 && !team.isHasMoreMembers()){
|
|
1236
|
Person person = team.getTeamMembers().get(0);
|
|
1237
|
checkPerson(person, refAuthorString, hasDedupMember, refId);
|
|
1238
|
result = person;
|
|
1239
|
}else{
|
|
1240
|
checkTeam(team, refAuthorString, refId);
|
|
1241
|
result = team;
|
|
1242
|
}
|
|
1243
|
|
|
1244
|
return result;
|
|
1245
|
}
|
|
1246
|
|
|
1247
|
/**
|
|
1248
|
* @param team
|
|
1249
|
* @param refAuthorString
|
|
1250
|
* @param refId
|
|
1251
|
*/
|
|
1252
|
private static void checkTeam(Team team, String refAuthorString, Integer refId) {
|
|
1253
|
TeamDefaultCacheStrategy formatter = (TeamDefaultCacheStrategy) team.getCacheStrategy();
|
|
1254
|
formatter.setEtAlPosition(100);
|
|
1255
|
if (formatter.getTitleCache(team).equals(refAuthorString)){
|
|
1256
|
team.setProtectedTitleCache(false);
|
|
1257
|
}else if(formatter.getTitleCache(team).replace(" & ", ", ").equals(refAuthorString.replace(" & ", ", ").replace(" ,", ","))){
|
|
1258
|
//also accept teams with ', ' as final member separator as not protected
|
|
1259
|
team.setProtectedTitleCache(false);
|
|
1260
|
}else if(formatter.getFullTitle(team).replace(" & ", ", ").equals(refAuthorString.replace(" & ", ", "))){
|
|
1261
|
//.. or teams with initials first
|
|
1262
|
team.setProtectedTitleCache(false);
|
|
1263
|
}else if (containsEdOrColon(refAuthorString)){
|
|
1264
|
//nothing to do, it is expected to be protected
|
|
1265
|
|
|
1266
|
}else{
|
|
1267
|
team.setTitleCache(refAuthorString, true);
|
|
1268
|
logger.warn("Creation of titleCache for team with members did not (fully) work: " + refAuthorString + " <-> " + formatter.getTitleCache(team)+ " : " + refId);
|
|
1269
|
}
|
|
1270
|
|
|
1271
|
}
|
|
1272
|
|
|
1273
|
/**
|
|
1274
|
* @param hasDedupMember
|
|
1275
|
* @param result
|
|
1276
|
* @return
|
|
1277
|
*/
|
|
1278
|
private static void checkPerson(Person person, String refAuthorString, boolean hasDedupMember, Integer refId) {
|
|
1279
|
PersonDefaultCacheStrategy formatter = (PersonDefaultCacheStrategy) person.getCacheStrategy();
|
|
1280
|
|
|
1281
|
String oldTitleCache = person.getTitleCache();
|
|
1282
|
boolean oldTitleCacheProtected = person.isProtectedTitleCache();
|
|
1283
|
|
|
1284
|
if (! oldTitleCache.equals(refAuthorString)){
|
|
1285
|
logger.error("Old titleCache does not equal refAuthorString this should not happen. "+ oldTitleCache + " <-> " + refAuthorString + "; refId = " + refId);
|
|
1286
|
}
|
|
1287
|
|
|
1288
|
boolean protect = true;
|
|
1289
|
person.setProtectedTitleCache(false);
|
|
1290
|
if (refAuthorString.equals(formatter.getTitleCache(person))){
|
|
1291
|
protect = false;
|
|
1292
|
}else if(formatter.getFullTitle(person).equals(refAuthorString)){
|
|
1293
|
//.. or teams with initials first
|
|
1294
|
protect = false;
|
|
1295
|
}else{
|
|
1296
|
//keep protected, see below
|
|
1297
|
}
|
|
1298
|
|
|
1299
|
if (hasDedupMember){
|
|
1300
|
//restore
|
|
1301
|
//TODO maybe even do not use dedup for testing
|
|
1302
|
person.setTitleCache(oldTitleCache, oldTitleCacheProtected);
|
|
1303
|
if (protect != oldTitleCacheProtected){
|
|
1304
|
logger.warn("Deduplicated person protection requirement unclear for "+refAuthorString+". New:"+protect+"/Old:"+oldTitleCacheProtected+"; RefId: " + refId);
|
|
1305
|
}
|
|
1306
|
}else{
|
|
1307
|
if (protect){
|
|
1308
|
logger.warn("Creation of titleCache for person (converted from team) with members did not (fully) work: " + refAuthorString + " <-> " + formatter.getTitleCache(person)+ " : " + refId);
|
|
1309
|
person.setTitleCache(refAuthorString, protect);
|
|
1310
|
}else{
|
|
1311
|
//keep unprotected
|
|
1312
|
}
|
|
1313
|
}
|
|
1314
|
}
|
|
1315
|
|
|
1316
|
/**
|
|
1317
|
* @param refAuthorString
|
|
1318
|
* @return
|
|
1319
|
*/
|
|
1320
|
private static boolean containsEdOrColon(String str) {
|
|
1321
|
if (str.contains(" ed.") || str.contains(" Ed.") || str.contains("(ed.")
|
|
1322
|
|| str.contains("[ed.") || str.contains("(Eds)") || str.contains("(Eds.)") ||
|
|
1323
|
str.contains("(eds.)") || str.contains(":")|| str.contains(";") || str.contains("Publ. & Inform. Directorate")
|
|
1324
|
|| str.contains("Anonymous [Department of Botany, Faculty of Science, FER-ZPR, University of Zagreb]")
|
|
1325
|
|| str.contains("Davis, P. H. (Güner, A. & al.)")){
|
|
1326
|
return true;
|
|
1327
|
}else{
|
|
1328
|
return false;
|
|
1329
|
}
|
|
1330
|
}
|
|
1331
|
|
|
1332
|
/**
|
|
1333
|
* @param nextSplit
|
|
1334
|
* @return
|
|
1335
|
*/
|
|
1336
|
private static boolean isInitial(String str) {
|
|
1337
|
if (str == null){
|
|
1338
|
return false;
|
|
1339
|
}
|
|
1340
|
boolean matches = str.trim().matches("(\\p{javaUpperCase}|Yu|Ya|Th|Ch|Lj|Sz|Dz|Sh|Ju|R. M. da S)\\.?"
|
|
1341
|
+ "(\\s*[-\\s]\\s*(\\p{javaUpperCase}|Yu|Ja|Kh|Tz|Ya|Th|Ju)\\.?)*(\\s+(van|von|de|de la|del|da|van der))?");
|
|
1342
|
return matches;
|
|
1343
|
}
|
|
1344
|
|
|
1345
|
private <T extends TeamOrPersonBase<?>> T deduplicatePersonOrTeam(BerlinModelImportState state,T author) {
|
|
1346
|
T result = deduplicationHelper.getExistingAuthor(state, author);
|
|
1347
|
return result;
|
|
1348
|
}
|
|
1349
|
|
|
1350
|
private Reference deduplicateReference(BerlinModelImportState state,Reference ref) {
|
|
1351
|
Reference result = deduplicationHelper.getExistingReference(state, ref);
|
|
1352
|
return result;
|
|
1353
|
}
|
|
1354
|
|
|
1355
|
private static Person makePerson(String full, boolean followedByInitial, Integer refId) {
|
|
1356
|
Person person = Person.NewInstance();
|
|
1357
|
person.setTitleCache(full, true);
|
|
1358
|
if (!full.matches(".*[\\s\\.].*")){
|
|
1359
|
person.setFamilyName(full);
|
|
1360
|
person.setProtectedTitleCache(false);
|
|
1361
|
}else{
|
|
1362
|
parsePerson(person, full, true, followedByInitial);
|
|
1363
|
}
|
|
1364
|
|
|
1365
|
if ((full.length() <= 2 && !full.matches("(Li|Bo|Em|Ay|Ma)")) || (full.length() == 3 && full.endsWith(".") && !full.equals("al.")) ){
|
|
1366
|
logger.warn("Unexpected short nom author name part: " + full + "; " + refId);
|
|
1367
|
}
|
|
1368
|
|
|
1369
|
return person;
|
|
1370
|
}
|
|
1371
|
|
|
1372
|
private static void parsePerson(Person person, String str, boolean preliminary, boolean followedByInitial) {
|
|
1373
|
String capWord = "\\p{javaUpperCase}\\p{javaLowerCase}{2,}";
|
|
1374
|
String famStart = "(Le |D'|'t |Mc|Mac|Des |d'|Du |De |Al-)";
|
|
1375
|
String regEx = "((\\p{javaUpperCase}|Ya|Th|Ju|Kh|An)\\.([\\s-]\\p{javaUpperCase}\\.)*(\\s(de|del|da|von|van|van der|v.|af|zu|von M. Und L.))?\\s)("
|
|
1376
|
+ famStart + "?" + capWord + "((-| y | i | é | de | de la )" + capWord + ")?)";
|
|
1377
|
Matcher matcher = Pattern.compile(regEx).matcher(str);
|
|
1378
|
if (matcher.matches()){
|
|
1379
|
person.setProtectedTitleCache(false);
|
|
1380
|
String familyName = matcher.group(6).trim();
|
|
1381
|
person.setFamilyName(familyName);
|
|
1382
|
person.setInitials(matcher.group(1).trim());
|
|
1383
|
}else{
|
|
1384
|
String regEx2 = "("+ capWord + "\\s" + capWord + "|Le Sueur|Beck von Mannagetta|Di Martino|Galán de Mera|Van Der Maesen|Farga i Arquimbau|Perez de Paz|Borzatti de Loewenstern|Lo Giudice|Perez de Paz)";
|
|
1385
|
Matcher matcher2 = Pattern.compile(regEx2).matcher(str);
|
|
1386
|
if (followedByInitial && matcher2.matches()){
|
|
1387
|
person.setFamilyName(str);
|
|
1388
|
person.setProtectedTitleCache(false);
|
|
1389
|
}else{
|
|
1390
|
person.setTitleCache(str, preliminary);
|
|
1391
|
}
|
|
1392
|
}
|
|
1393
|
}
|
|
1394
|
|
|
1395
|
/**
|
|
1396
|
* @param state
|
|
1397
|
* @param refAuthorString
|
|
1398
|
* @param nomAuthor
|
|
1399
|
* @return
|
|
1400
|
*/
|
|
1401
|
private static boolean handleSimilarAuthors(BerlinModelImportState state, String refAuthorString,
|
|
1402
|
TeamOrPersonBase<?> nomAuthor, int refId) {
|
|
1403
|
String nomTitle = nomAuthor.getTitleCache();
|
|
1404
|
|
|
1405
|
if (refAuthorString.equals(nomAuthor.getNomenclaturalTitle())){
|
|
1406
|
//nomTitle equal
|
|
1407
|
return true;
|
|
1408
|
}else{
|
|
1409
|
if (refAuthorString.replace(" & ", ", ").equals(nomTitle.replace(" & ", ", "))){
|
|
1410
|
//nomTitle equal except for "&"
|
|
1411
|
return true;
|
|
1412
|
}
|
|
1413
|
String nomFullTitle = nomAuthor.getFullTitle();
|
|
1414
|
if (refAuthorString.replace(" & ", ", ").equals(nomFullTitle.replace(" & ", ", "))){
|
|
1415
|
return true;
|
|
1416
|
}
|
|
1417
|
|
|
1418
|
if (nomAuthor.isInstanceOf(Person.class)){
|
|
1419
|
Person person = CdmBase.deproxy(nomAuthor, Person.class);
|
|
1420
|
|
|
1421
|
//refAuthor has initials behind, nom Author in front // the other way round is handled in firstIsFullNameOfInitialName
|
|
1422
|
if (refAuthorString.contains(",") && !nomTitle.contains(",") ){
|
|
1423
|
String[] splits = refAuthorString.split(",");
|
|
1424
|
if (splits.length == 2){
|
|
1425
|
String newMatch = splits[1].trim() + " " + splits[0].trim();
|
|
1426
|
if (newMatch.equals(nomTitle)){
|
|
1427
|
if (isBlank(person.getFamilyName())){
|
|
1428
|
person.setFamilyName(splits[0].trim());
|
|
1429
|
}
|
|
1430
|
if (isBlank(person.getInitials())){
|
|
1431
|
person.setInitials(splits[1].trim());
|
|
1432
|
}
|
|
1433
|
return true;
|
|
1434
|
}
|
|
1435
|
}
|
|
1436
|
}
|
|
1437
|
|
|
1438
|
if (refAuthorIsFamilyAuthorOfNomAuthor(state, refAuthorString, person)){
|
|
1439
|
return true;
|
|
1440
|
}
|
|
1441
|
|
|
1442
|
if (firstIsFullNameOfInitialName(state, refAuthorString, person, refId)){
|
|
1443
|
return true;
|
|
1444
|
}
|
|
1445
|
}
|
|
1446
|
|
|
1447
|
}
|
|
1448
|
return false;
|
|
1449
|
}
|
|
1450
|
|
|
1451
|
/**
|
|
1452
|
* @param state
|
|
1453
|
* @param refAuthorString
|
|
1454
|
* @param person
|
|
1455
|
* @return
|
|
1456
|
*/
|
|
1457
|
private static boolean refAuthorIsFamilyAuthorOfNomAuthor(BerlinModelImportState state, String refAuthorString,
|
|
1458
|
Person person) {
|
|
1459
|
if (refAuthorString.equals(person.getFamilyName())){
|
|
1460
|
return true;
|
|
1461
|
}else{
|
|
1462
|
return false;
|
|
1463
|
}
|
|
1464
|
}
|
|
1465
|
|
|
1466
|
/**
|
|
1467
|
* @param state
|
|
1468
|
* @param refAuthorString
|
|
1469
|
* @param nomAuthor
|
|
1470
|
* @return
|
|
1471
|
*/
|
|
1472
|
private static boolean firstIsFullNameOfInitialName(BerlinModelImportState state, String fullName,
|
|
1473
|
Person initialAuthor, int refId) {
|
|
1474
|
String initialName = initialAuthor.getTitleCache();
|
|
1475
|
|
|
1476
|
String[] fullSplits = fullName.split(",");
|
|
1477
|
String[] initialSplits = initialName.split(",");
|
|
1478
|
|
|
1479
|
if (fullSplits.length == 2 && initialSplits.length == 2){
|
|
1480
|
String[] fullGivenName = fullSplits[1].trim().split(" ");
|
|
1481
|
String[] initialsGivenName = initialSplits[1].trim().split(" ");
|
|
1482
|
boolean result = compareFamilyAndInitials(fullSplits[0], initialSplits[0], fullGivenName, initialsGivenName);
|
|
1483
|
if (result){
|
|
1484
|
setGivenName(state, fullSplits[1], initialAuthor, refId);
|
|
1485
|
}
|
|
1486
|
return result;
|
|
1487
|
}else if (fullSplits.length == 1 && initialSplits.length == 2){
|
|
1488
|
String[] fullSingleSplits = fullName.split(" ");
|
|
1489
|
String fullFamily = fullSingleSplits[fullSingleSplits.length-1];
|
|
1490
|
String[] fullGivenName = Arrays.copyOfRange(fullSingleSplits, 0, fullSingleSplits.length-1);
|
|
1491
|
String[] initialsGivenName = initialSplits[1].trim().split(" ");
|
|
1492
|
boolean result = compareFamilyAndInitials(fullFamily, initialSplits[0], fullGivenName, initialsGivenName);
|
|
1493
|
if (result){
|
|
1494
|
if(hasAtLeastOneFullName(fullGivenName)){
|
|
1495
|
setGivenName(state, CdmUtils.concat(" ", fullGivenName), initialAuthor, refId);
|
|
1496
|
}
|
|
1497
|
}
|
|
1498
|
return result;
|
|
1499
|
}else if (fullSplits.length == 1 && initialAuthor.getInitials() == null){
|
|
1500
|
//don't if this will be implemented, initialAuthors with only nomencl.Author set
|
|
1501
|
}
|
|
1502
|
|
|
1503
|
return false;
|
|
1504
|
}
|
|
1505
|
|
|
1506
|
/**
|
|
1507
|
* @param fullGivenName
|
|
1508
|
* @return
|
|
1509
|
*/
|
|
1510
|
private static boolean hasAtLeastOneFullName(String[] fullGivenName) {
|
|
1511
|
for (String singleName : fullGivenName){
|
|
1512
|
if (!singleName.endsWith(".") && singleName.length() > 2 && !singleName.matches("(von|van)") ){
|
|
1513
|
return true;
|
|
1514
|
}
|
|
1515
|
}
|
|
1516
|
return false;
|
|
1517
|
}
|
|
1518
|
|
|
1519
|
/**
|
|
1520
|
* @param state
|
|
1521
|
* @param string
|
|
1522
|
* @param initialAuthor
|
|
1523
|
*/
|
|
1524
|
private static void setGivenName(BerlinModelImportState state, String givenName, Person person, int refId) {
|
|
1525
|
givenName = givenName.trim();
|
|
1526
|
if(person.getGivenName() == null || person.getGivenName().equals(givenName)){
|
|
1527
|
person.setGivenName(givenName);
|
|
1528
|
}else{
|
|
1529
|
logger.warn("RefAuthor given name and existing given name differ: " + givenName + " <-> " + person.getGivenName() + "; RefId + " + refId);
|
|
1530
|
}
|
|
1531
|
}
|
|
1532
|
|
|
1533
|
/**
|
|
1534
|
* @param fullGivenName
|
|
1535
|
* @param initialsGivenName
|
|
1536
|
*/
|
|
1537
|
protected static boolean compareFamilyAndInitials(String fullFamilyName, String initialsFamilyName,
|
|
1538
|
String[] fullGivenName, String[] initialsGivenName) {
|
|
1539
|
if (!fullFamilyName.equals(initialsFamilyName)){
|
|
1540
|
return false;
|
|
1541
|
}
|
|
1542
|
if (fullGivenName.length == initialsGivenName.length){
|
|
1543
|
for (int i =0; i< fullGivenName.length ; i++){
|
|
1544
|
if (fullGivenName[i].length() == 0 //comma ending not allowed
|
|
1545
|
|| initialsGivenName[i].length() != 2 //only K. or similar allowed
|
|
1546
|
|| fullGivenName[i].length() < initialsGivenName[i].length() //fullFirstName must be longer than abbrev Name
|
|
1547
|
|| !initialsGivenName[i].endsWith(".") //initials must end with "."
|
|
1548
|
|| !fullGivenName[i].startsWith(initialsGivenName[i].replace(".", ""))){ //start with same letter
|
|
1549
|
if (fullGivenName[i].matches("(von|van|de|zu)") && fullGivenName[i].equals(initialsGivenName[i])){
|
|
1550
|
continue;
|
|
1551
|
}else{
|
|
1552
|
return false;
|
|
1553
|
}
|
|
1554
|
}
|
|
1555
|
}
|
|
1556
|
return true;
|
|
1557
|
}else{
|
|
1558
|
return false;
|
|
1559
|
}
|
|
1560
|
}
|
|
1561
|
|
|
1562
|
/**
|
|
1563
|
* @param lowerCase
|
|
1564
|
* @param config
|
|
1565
|
* @return
|
|
1566
|
*/
|
|
1567
|
public Set<String> getObligatoryAttributes(boolean lowerCase, BerlinModelImportConfigurator config){
|
|
1568
|
Set<String> result = new HashSet<>();
|
|
1569
|
Class<ICdmImport>[] ioClassList = config.getIoClassList();
|
|
1570
|
logger.warn("getObligatoryAttributes has been commented because it still needs to be adapted to the new package structure");
|
|
1571
|
result.addAll(Arrays.asList(unclearMappers));
|
|
1572
|
result.addAll(Arrays.asList(createdAndNotesAttributes));
|
|
1573
|
result.addAll(Arrays.asList(operationalAttributes));
|
|
1574
|
CdmIoMapping mapping = new CdmIoMapping();
|
|
1575
|
for (CdmAttributeMapperBase mapper : classMappers){
|
|
1576
|
mapping.addMapper(mapper);
|
|
1577
|
}
|
|
1578
|
result.addAll(mapping.getSourceAttributes());
|
|
1579
|
if (lowerCase){
|
|
1580
|
Set<String> lowerCaseResult = new HashSet<>();
|
|
1581
|
for (String str : result){
|
|
1582
|
if (str != null){lowerCaseResult.add(str.toLowerCase());}
|
|
1583
|
}
|
|
1584
|
result = lowerCaseResult;
|
|
1585
|
}
|
|
1586
|
return result;
|
|
1587
|
}
|
|
1588
|
|
|
1589
|
@Override
|
|
1590
|
protected boolean doCheck(BerlinModelImportState state){
|
|
1591
|
BerlinModelReferenceImportValidator validator = new BerlinModelReferenceImportValidator();
|
|
1592
|
return validator.validate(state, this);
|
|
1593
|
}
|
|
1594
|
|
|
1595
|
@Override
|
|
1596
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
1597
|
return (state.getConfig().getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
|
|
1598
|
}
|
|
1599
|
|
|
1600
|
}
|