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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 org.apache.commons.lang.StringUtils;
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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.io.berlinModel.in.validation.BerlinModelReferenceImportValidator;
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import eu.etaxonomy.cdm.io.common.ICdmIO;
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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.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.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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/**
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* @author a.mueller
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* @created 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 Logger logger = Logger.getLogger(BerlinModelReferenceImport.class);
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public static final String REFERENCE_NAMESPACE = "Reference";
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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 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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DbSingleAttributeImportMapperBase singleMapper = (DbSingleAttributeImportMapperBase)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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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", "series"),
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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, "RefDepositedAt", "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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public String toString(){return String.valueOf(refCount) ;};
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
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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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boolean success = true;
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initializeMappers(state);
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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 = " 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 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 strSelectIdBase = strSelectId + strIdFrom;
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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
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String strIdQueryFirstPath = strSelectId + strIdFrom ;
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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;
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int recordsPerTransaction = config.getRecordsPerTransaction();
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try{
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//firstPath
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ResultSetPartitioner partitioner = 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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// if (config.getDoReferences() == ALL || config.getDoReferences() == NOMENCLATURAL){
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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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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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// }
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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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return;
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}
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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
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*/
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public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {
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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<Integer, Reference>();
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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, relatedReferences, 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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logger.info("SecUuid changed to: " + config.getSecUuid());
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}
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//save and store in map
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logger.info("Save references (" + refCounter.refCount + ")");
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getReferenceService().saveOrUpdate(refToSave.values());
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// }//end resultSetList
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// logger.info("end makeReferences ..." + getSuccessString(success));;
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return success;
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} catch (SQLException e) {
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logger.error("SQLException:" + e);
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return false;
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}
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}
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/**
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* Adds the inReference to the according references.
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* @param partitioner
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* @param state
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* @return
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*/
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private boolean doPartitionSecondPath(ResultSetPartitioner partitioner, BerlinModelImportState state) {
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boolean success = true;
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Map<Integer, Reference> refToSave = new HashMap<Integer, Reference>();
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Map<String, Reference> relatedReferencesMap = partitioner.getObjectMap(REFERENCE_NAMESPACE);
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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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Integer refId = rs.getInt("refId");
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Integer inRefFk = rs.getInt("inRefFk");
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if (inRefFk != null){
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Reference<?> thisRef = relatedReferencesMap.get(String.valueOf(refId));
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Reference<?> inRef = relatedReferencesMap.get(String.valueOf(inRefFk));
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if (thisRef != null){
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if (inRef == null){
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logger.warn("No InRef found for nomRef: " + thisRef.getTitleCache() + "; RefId: " + refId + "; inRefFK: " + inRefFk);
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}
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thisRef.setInReference(inRef);
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refToSave.put(refId, thisRef);
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thisRef.setTitleCache(null);
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thisRef.getTitleCache();
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}
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}
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335
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} // end resultSet
|
|
336
|
|
|
337
|
//save and store in map
|
|
338
|
logger.info("Save references (" + refCounter.refCount + ")");
|
|
339
|
getReferenceService().saveOrUpdate(refToSave.values());
|
|
340
|
|
|
341
|
// }//end resultSetList
|
|
342
|
|
|
343
|
// logger.info("end makeReferences ..." + getSuccessString(success));;
|
|
344
|
return success;
|
|
345
|
} catch (SQLException e) {
|
|
346
|
logger.error("SQLException:" + e);
|
|
347
|
return false;
|
|
348
|
}
|
|
349
|
}
|
|
350
|
|
|
351
|
|
|
352
|
|
|
353
|
/* (non-Javadoc)
|
|
354
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
|
|
355
|
*/
|
|
356
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
|
|
357
|
String nameSpace;
|
|
358
|
Class cdmClass;
|
|
359
|
Set<String> idSet;
|
|
360
|
|
|
361
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
362
|
|
|
363
|
try{
|
|
364
|
Set<String> teamIdSet = new HashSet<String>();
|
|
365
|
Set<String> referenceIdSet = new HashSet<String>();
|
|
366
|
|
|
367
|
while (rs.next()){
|
|
368
|
handleForeignKey(rs, teamIdSet, "NomAuthorTeamFk");
|
|
369
|
handleForeignKey(rs, referenceIdSet, "InRefFk");
|
|
370
|
//TODO only needed in second path but state not available here to check if state is second path
|
|
371
|
handleForeignKey(rs, referenceIdSet, "refId");
|
|
372
|
}
|
|
373
|
|
|
374
|
//team map
|
|
375
|
nameSpace = BerlinModelAuthorTeamImport.NAMESPACE;
|
|
376
|
cdmClass = Team.class;
|
|
377
|
idSet = teamIdSet;
|
|
378
|
Map<String, Team> teamMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
379
|
result.put(nameSpace, teamMap);
|
|
380
|
|
|
381
|
//reference map
|
|
382
|
nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;
|
|
383
|
cdmClass = Reference.class;
|
|
384
|
idSet = referenceIdSet;
|
|
385
|
Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
386
|
result.put(nameSpace, referenceMap);
|
|
387
|
|
|
388
|
} catch (SQLException e) {
|
|
389
|
throw new RuntimeException(e);
|
|
390
|
}
|
|
391
|
return result;
|
|
392
|
}
|
|
393
|
|
|
394
|
|
|
395
|
/**
|
|
396
|
* Handles a single reference record
|
|
397
|
* @param rs
|
|
398
|
* @param state
|
|
399
|
* @param biblioRefToSave
|
|
400
|
* @param nomRefToSave
|
|
401
|
* @param relatedBiblioReferences
|
|
402
|
* @param relatedNomReferences
|
|
403
|
* @param refCounter
|
|
404
|
* @return
|
|
405
|
*/
|
|
406
|
private boolean makeSingleReferenceRecord(
|
|
407
|
ResultSet rs,
|
|
408
|
BerlinModelImportState state,
|
|
409
|
ResultSetPartitioner<BerlinModelImportState> partitioner,
|
|
410
|
Map<Integer, Reference> refToSave,
|
|
411
|
Map<String, Reference> relatedReferences,
|
|
412
|
RefCounter refCounter){
|
|
413
|
boolean success = true;
|
|
414
|
|
|
415
|
Integer refId = null;
|
|
416
|
try {
|
|
417
|
Map<String, Object> valueMap = getValueMap(rs);
|
|
418
|
|
|
419
|
Integer categoryFk = (Integer)valueMap.get("refCategoryFk".toLowerCase());
|
|
420
|
refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
421
|
Boolean thesisFlag = (Boolean)valueMap.get("thesisFlag".toLowerCase());
|
|
422
|
|
|
423
|
|
|
424
|
Reference<?> referenceBase;
|
|
425
|
logger.debug("RefCategoryFk: " + categoryFk);
|
|
426
|
|
|
427
|
if (thesisFlag){
|
|
428
|
referenceBase = makeThesis(valueMap);
|
|
429
|
}else if (categoryFk == REF_JOURNAL){
|
|
430
|
referenceBase = makeJournal(valueMap);
|
|
431
|
}else if(categoryFk == REF_BOOK){
|
|
432
|
referenceBase = makeBook(valueMap, refToSave, relatedReferences);
|
|
433
|
}else if(categoryFk == REF_DATABASE){
|
|
434
|
referenceBase = makeDatabase(valueMap);
|
|
435
|
}else if(categoryFk == REF_INFORMAL){
|
|
436
|
referenceBase = makeInformal(valueMap);
|
|
437
|
}else if(categoryFk == REF_WEBSITE){
|
|
438
|
referenceBase = makeWebSite(valueMap);
|
|
439
|
}else if(categoryFk == REF_UNKNOWN){
|
|
440
|
referenceBase = makeUnknown(valueMap);
|
|
441
|
}else if(categoryFk == REF_PRINT_SERIES){
|
|
442
|
referenceBase = makePrintSeries(valueMap);
|
|
443
|
}else if(categoryFk == REF_CONFERENCE_PROCEEDINGS){
|
|
444
|
referenceBase = makeProceedings(valueMap);
|
|
445
|
}else if(categoryFk == REF_ARTICLE){
|
|
446
|
referenceBase = makeArticle(valueMap, refToSave, relatedReferences);
|
|
447
|
}else if(categoryFk == REF_JOURNAL_VOLUME){
|
|
448
|
referenceBase = makeJournalVolume(valueMap);
|
|
449
|
}else if(categoryFk == REF_PART_OF_OTHER_TITLE){
|
|
450
|
referenceBase = makePartOfOtherTitle(valueMap, refToSave, relatedReferences);
|
|
451
|
}else{
|
|
452
|
logger.warn("Unknown categoryFk (" + categoryFk + "). Create 'Generic instead'");
|
|
453
|
referenceBase = ReferenceFactory.newGeneric();
|
|
454
|
success = false;
|
|
455
|
}
|
|
456
|
|
|
457
|
//refYear
|
|
458
|
String refYear = (String)valueMap.get("refYear".toLowerCase());
|
|
459
|
referenceBase.setDatePublished(ImportHelper.getDatePublished(refYear));
|
|
460
|
|
|
461
|
//created, updated, notes
|
|
462
|
doCreatedUpdatedNotes(state, referenceBase, rs);
|
|
463
|
|
|
464
|
//idInSource
|
|
465
|
String idInSource = (String)valueMap.get("IdInSource".toLowerCase());
|
|
466
|
if (isNotBlank(idInSource)){
|
|
467
|
IdentifiableSource source = IdentifiableSource.NewDataImportInstance(idInSource);
|
|
468
|
source.setIdNamespace("import to Berlin Model");
|
|
469
|
referenceBase.addSource(source);
|
|
470
|
}
|
|
471
|
|
|
472
|
//nom&BiblioReference - must be last because a clone is created
|
|
473
|
success &= makeNomAndBiblioReference(rs, state, partitioner, refId, referenceBase, refCounter, refToSave);
|
|
474
|
|
|
475
|
|
|
476
|
} catch (Exception e) {
|
|
477
|
logger.warn("Reference with BM refId '" + CdmUtils.Nz(refId) + "' threw Exception and could not be saved");
|
|
478
|
e.printStackTrace();
|
|
479
|
success = false;
|
|
480
|
}
|
|
481
|
return success;
|
|
482
|
}
|
|
483
|
|
|
484
|
|
|
485
|
/**
|
|
486
|
* Creates and saves a nom. reference and a biblio. reference after checking necessity
|
|
487
|
* @param rs
|
|
488
|
* @param refId
|
|
489
|
* @param ref
|
|
490
|
* @param refCounter
|
|
491
|
* @param biblioRefToSave
|
|
492
|
* @param nomRefToSave
|
|
493
|
* @param teamMap
|
|
494
|
* @param stores
|
|
495
|
* @return
|
|
496
|
* @throws SQLException
|
|
497
|
*/
|
|
498
|
private boolean makeNomAndBiblioReference(
|
|
499
|
ResultSet rs,
|
|
500
|
BerlinModelImportState state,
|
|
501
|
ResultSetPartitioner partitioner,
|
|
502
|
int refId,
|
|
503
|
Reference<?> ref,
|
|
504
|
RefCounter refCounter,
|
|
505
|
Map<Integer, Reference> refToSave
|
|
506
|
) throws SQLException{
|
|
507
|
|
|
508
|
Map<String, Team> teamMap = partitioner.getObjectMap(BerlinModelAuthorTeamImport.NAMESPACE);
|
|
509
|
|
|
510
|
String refCache = rs.getString("refCache");
|
|
511
|
String nomRefCache = rs.getString("nomRefCache");
|
|
512
|
String title = rs.getString("title");
|
|
513
|
String nomTitleAbbrev = rs.getString("nomTitleAbbrev");
|
|
514
|
boolean isPreliminary = rs.getBoolean("PreliminaryFlag");
|
|
515
|
String refAuthorString = rs.getString("refAuthorString");
|
|
516
|
Integer nomAuthorTeamFk = rs.getInt("NomAuthorTeamFk");
|
|
517
|
String strNomAuthorTeamFk = String.valueOf(nomAuthorTeamFk);
|
|
518
|
TeamOrPersonBase<?> nomAuthor = teamMap.get(strNomAuthorTeamFk);
|
|
519
|
|
|
520
|
Reference<?> sourceReference = state.getTransactionalSourceReference();
|
|
521
|
|
|
522
|
//preliminary
|
|
523
|
if (isPreliminary){
|
|
524
|
ref.setAbbrevTitleCache(nomRefCache, true);
|
|
525
|
ref.setTitleCache(refCache, true);
|
|
526
|
}
|
|
527
|
|
|
528
|
//title/abbrevTitle
|
|
529
|
if (StringUtils.isNotBlank(nomTitleAbbrev)){
|
|
530
|
ref.setAbbrevTitle(nomTitleAbbrev);
|
|
531
|
}
|
|
532
|
if (StringUtils.isNotBlank(title)){
|
|
533
|
ref.setTitle(title);
|
|
534
|
}
|
|
535
|
|
|
536
|
//author
|
|
537
|
TeamOrPersonBase<?> author = getAuthorTeam(refAuthorString , nomAuthor);
|
|
538
|
ref.setAuthorTeam(author);
|
|
539
|
|
|
540
|
//save
|
|
541
|
if (! refToSave.containsKey(refId)){
|
|
542
|
refToSave.put(refId, ref);
|
|
543
|
}else{
|
|
544
|
logger.warn("Duplicate refId in Berlin Model database. Second reference was not imported !!");
|
|
545
|
}
|
|
546
|
refCounter.refCount++;
|
|
547
|
|
|
548
|
//refId
|
|
549
|
ImportHelper.setOriginalSource(ref, sourceReference, refId, REFERENCE_NAMESPACE);
|
|
550
|
|
|
551
|
return true;
|
|
552
|
}
|
|
553
|
|
|
554
|
/**
|
|
555
|
* Copies the created and updated information from the nomReference to the cloned bibliographic reference
|
|
556
|
* @param referenceBase
|
|
557
|
* @param nomReference
|
|
558
|
*/
|
|
559
|
private void copyCreatedUpdated(Reference<?> biblioReference, Reference nomReference) {
|
|
560
|
biblioReference.setCreatedBy(nomReference.getCreatedBy());
|
|
561
|
biblioReference.setCreated(nomReference.getCreated());
|
|
562
|
biblioReference.setUpdatedBy(nomReference.getUpdatedBy());
|
|
563
|
biblioReference.setUpdated(nomReference.getUpdated());
|
|
564
|
|
|
565
|
}
|
|
566
|
|
|
567
|
private Reference<?> makeArticle (Map<String, Object> valueMap, Map<Integer, Reference> refToSave, Map<String, Reference> relatedReferences){
|
|
568
|
|
|
569
|
IArticle article = ReferenceFactory.newArticle();
|
|
570
|
Object inRefFk = valueMap.get("inRefFk".toLowerCase());
|
|
571
|
Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());
|
|
572
|
Integer refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
573
|
|
|
574
|
if (inRefFk != null){
|
|
575
|
if (inRefCategoryFk != REF_JOURNAL){
|
|
576
|
logger.warn("Wrong inrefCategory for Article (refID = " + refId +"). Type must be 'Journal' but was not (RefCategoryFk=" + inRefCategoryFk + "))." +
|
|
577
|
" InReference was added anyway! ");
|
|
578
|
}
|
|
579
|
}else{
|
|
580
|
logger.warn ("Article has no inreference: " + refId);
|
|
581
|
}
|
|
582
|
makeStandardMapper(valueMap, (Reference)article); //url, pages, series, volume
|
|
583
|
return (Reference)article;
|
|
584
|
}
|
|
585
|
|
|
586
|
private Reference<?> makePartOfOtherTitle (Map<String, Object> valueMap,
|
|
587
|
Map<Integer, Reference> refToSave,
|
|
588
|
Map<String, Reference> relatedReferences){
|
|
589
|
|
|
590
|
Reference<?> result;
|
|
591
|
Object inRefFk = valueMap.get("inRefFk".toLowerCase());
|
|
592
|
Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());
|
|
593
|
Integer refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
594
|
|
|
595
|
if (inRefCategoryFk == null){
|
|
596
|
//null -> error
|
|
597
|
logger.warn("Part-Of-Other-Title has no inRefCategoryFk! RefId = " + refId + ". ReferenceType set to Generic.");
|
|
598
|
result = makeUnknown(valueMap);
|
|
599
|
}else if (inRefFk == null){
|
|
600
|
logger.warn("Part-Of-Other-Title has in in reference: " + refId);
|
|
601
|
result = makeUnknown(valueMap);
|
|
602
|
}else if (inRefCategoryFk == REF_BOOK){
|
|
603
|
//BookSection
|
|
604
|
IBookSection bookSection = ReferenceFactory.newBookSection();
|
|
605
|
result = (Reference<?>)bookSection;
|
|
606
|
}else if (inRefCategoryFk == REF_ARTICLE){
|
|
607
|
//Article
|
|
608
|
//TODO
|
|
609
|
logger.info("Reference (refId = " + refId + ") of type 'part_of_other_title' is part of 'article'." +
|
|
610
|
" There is no specific reference type for such in references yet. Generic reference created instead") ;
|
|
611
|
result = ReferenceFactory.newGeneric();
|
|
612
|
}else if (inRefCategoryFk == REF_JOURNAL){
|
|
613
|
//TODO
|
|
614
|
logger.warn("Reference (refId = " + refId + ") of type 'part_of_other_title' has inReference of type 'journal'." +
|
|
615
|
" This is not allowed! Generic reference created instead") ;
|
|
616
|
result = ReferenceFactory.newGeneric();
|
|
617
|
result.addMarker(Marker.NewInstance(MarkerType.TO_BE_CHECKED(), true));
|
|
618
|
}else{
|
|
619
|
logger.warn("InReference type (catFk = " + inRefCategoryFk + ") of part-of-reference not recognized for refId " + refId + "." +
|
|
620
|
" Create 'Generic' reference instead");
|
|
621
|
result = ReferenceFactory.newGeneric();
|
|
622
|
}
|
|
623
|
makeStandardMapper(valueMap, result); //url, pages
|
|
624
|
return result;
|
|
625
|
}
|
|
626
|
|
|
627
|
|
|
628
|
/**
|
|
629
|
* @param inRefFkInt
|
|
630
|
* @param biblioRefToSave
|
|
631
|
* @param nomRefToSave
|
|
632
|
* @param relatedBiblioReferences
|
|
633
|
* @param relatedNomReferences
|
|
634
|
* @return
|
|
635
|
*/
|
|
636
|
private boolean existsInMapOrToSave(Integer inRefFkInt, Map<Integer, Reference> refToSave, Map<String, Reference> relatedReferences) {
|
|
637
|
boolean result = false;
|
|
638
|
if (inRefFkInt == null){
|
|
639
|
return false;
|
|
640
|
}
|
|
641
|
result |= refToSave.containsKey(inRefFkInt);
|
|
642
|
result |= relatedReferences.containsKey(String.valueOf(inRefFkInt));
|
|
643
|
return result;
|
|
644
|
}
|
|
645
|
|
|
646
|
private Reference<?> makeWebSite(Map<String, Object> valueMap){
|
|
647
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Website'");}
|
|
648
|
Reference<?> webPage = ReferenceFactory.newWebPage();
|
|
649
|
makeStandardMapper(valueMap, webPage); //placePublished, publisher
|
|
650
|
return webPage;
|
|
651
|
}
|
|
652
|
|
|
653
|
private Reference<?> makeUnknown(Map<String, Object> valueMap){
|
|
654
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Unknown'");}
|
|
655
|
Reference<?> generic = ReferenceFactory.newGeneric();
|
|
656
|
// generic.setSeries(series);
|
|
657
|
makeStandardMapper(valueMap, generic); //pages, placePublished, publisher, series, volume
|
|
658
|
return generic;
|
|
659
|
}
|
|
660
|
|
|
661
|
private Reference<?> makeInformal(Map<String, Object> valueMap){
|
|
662
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Informal'");}
|
|
663
|
Reference<?> generic = ReferenceFactory.newGeneric();
|
|
664
|
// informal.setSeries(series);
|
|
665
|
makeStandardMapper(valueMap, generic);//editor, pages, placePublished, publisher, series, volume
|
|
666
|
String informal = (String)valueMap.get("InformalRefCategory".toLowerCase());
|
|
667
|
if (CdmUtils.isNotEmpty(informal) ){
|
|
668
|
generic.addExtension(informal, ExtensionType.INFORMAL_CATEGORY());
|
|
669
|
}
|
|
670
|
return generic;
|
|
671
|
}
|
|
672
|
|
|
673
|
private Reference<?> makeDatabase(Map<String, Object> valueMap){
|
|
674
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Database'");}
|
|
675
|
Reference database = ReferenceFactory.newDatabase();
|
|
676
|
makeStandardMapper(valueMap, database); //?
|
|
677
|
return database;
|
|
678
|
}
|
|
679
|
|
|
680
|
private Reference<?> makeJournal(Map<String, Object> valueMap){
|
|
681
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Journal'");}
|
|
682
|
Reference journal = ReferenceFactory.newJournal();
|
|
683
|
|
|
684
|
Set<String> omitAttributes = new HashSet<String>();
|
|
685
|
String series = "series";
|
|
686
|
// omitAttributes.add(series);
|
|
687
|
|
|
688
|
makeStandardMapper(valueMap, journal, omitAttributes); //issn,placePublished,publisher
|
|
689
|
// if (valueMap.get(series) != null){
|
|
690
|
// logger.warn("Series not yet implemented for journal!");
|
|
691
|
// }
|
|
692
|
return journal;
|
|
693
|
}
|
|
694
|
|
|
695
|
private Reference<?> makeBook(
|
|
696
|
Map<String, Object> valueMap,
|
|
697
|
Map<Integer, Reference> refToSave,
|
|
698
|
Map<String, Reference> relatedReferences){
|
|
699
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Book'");}
|
|
700
|
Reference<?> book = ReferenceFactory.newBook();
|
|
701
|
Integer refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
702
|
|
|
703
|
//Set bookAttributes = new String[]{"edition", "isbn", "pages","publicationTown","publisher","volume"};
|
|
704
|
|
|
705
|
Set<String> omitAttributes = new HashSet<String>();
|
|
706
|
String attrSeries = "series";
|
|
707
|
// omitAttributes.add(attrSeries);
|
|
708
|
|
|
709
|
makeStandardMapper(valueMap, book, omitAttributes);
|
|
710
|
|
|
711
|
//Series (as String)
|
|
712
|
IPrintSeries printSeries = null;
|
|
713
|
if (valueMap.get(attrSeries) != null){
|
|
714
|
String series = (String)valueMap.get("title".toLowerCase());
|
|
715
|
if (series == null){
|
|
716
|
String nomTitle = (String)valueMap.get("nomTitleAbbrev".toLowerCase());
|
|
717
|
series = nomTitle;
|
|
718
|
}
|
|
719
|
printSeries = ReferenceFactory.newPrintSeries(series);
|
|
720
|
logger.info("Implementation of printSeries is preliminary");
|
|
721
|
}
|
|
722
|
//Series (as Reference)
|
|
723
|
if (book.getInSeries() != null && printSeries != null){
|
|
724
|
logger.warn("Book has series string and inSeries reference. Can not take both. Series string neglected");
|
|
725
|
}else{
|
|
726
|
book.setInSeries(printSeries);
|
|
727
|
}
|
|
728
|
book.setEditor(null);
|
|
729
|
return book;
|
|
730
|
|
|
731
|
}
|
|
732
|
|
|
733
|
/**
|
|
734
|
* Returns the requested object if it exists in one of both maps. Prefers the refToSaveMap in ambigious cases.
|
|
735
|
* @param inRefFkInt
|
|
736
|
* @param nomRefToSave
|
|
737
|
* @param relatedNomReferences
|
|
738
|
* @return
|
|
739
|
*/
|
|
740
|
private Reference<?> getReferenceFromMaps(
|
|
741
|
int inRefFkInt,
|
|
742
|
Map<Integer, Reference> refToSaveMap,
|
|
743
|
Map<String, Reference> relatedRefMap) {
|
|
744
|
Reference<?> result = null;
|
|
745
|
result = refToSaveMap.get(inRefFkInt);
|
|
746
|
if (result == null){
|
|
747
|
result = relatedRefMap.get(String.valueOf(inRefFkInt));
|
|
748
|
}
|
|
749
|
return result;
|
|
750
|
}
|
|
751
|
|
|
752
|
private Reference<?> makePrintSeries(Map<String, Object> valueMap){
|
|
753
|
if (logger.isDebugEnabled()){logger.debug("RefType 'PrintSeries'");}
|
|
754
|
Reference<?> printSeries = ReferenceFactory.newPrintSeries();
|
|
755
|
makeStandardMapper(valueMap, printSeries, null);
|
|
756
|
return printSeries;
|
|
757
|
}
|
|
758
|
|
|
759
|
private Reference<?> makeProceedings(Map<String, Object> valueMap){
|
|
760
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Proceedings'");}
|
|
761
|
Reference<?> proceedings = ReferenceFactory.newProceedings();
|
|
762
|
makeStandardMapper(valueMap, proceedings, null);
|
|
763
|
return proceedings;
|
|
764
|
}
|
|
765
|
|
|
766
|
private Reference<?> makeThesis(Map<String, Object> valueMap){
|
|
767
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Thesis'");}
|
|
768
|
Reference<?> thesis = ReferenceFactory.newThesis();
|
|
769
|
makeStandardMapper(valueMap, thesis, null);
|
|
770
|
return thesis;
|
|
771
|
}
|
|
772
|
|
|
773
|
|
|
774
|
private Reference<?> makeJournalVolume(Map<String, Object> valueMap){
|
|
775
|
if (logger.isDebugEnabled()){logger.debug("RefType 'JournalVolume'");}
|
|
776
|
//Proceedings proceedings = Proceedings.NewInstance();
|
|
777
|
Reference<?> journalVolume = ReferenceFactory.newGeneric();
|
|
778
|
makeStandardMapper(valueMap, journalVolume, null);
|
|
779
|
logger.warn("Journal volumes not yet implemented. Generic created instead but with errors");
|
|
780
|
return journalVolume;
|
|
781
|
}
|
|
782
|
|
|
783
|
private boolean makeStandardMapper(Map<String, Object> valueMap, Reference<?> ref){
|
|
784
|
return makeStandardMapper(valueMap, ref, null);
|
|
785
|
}
|
|
786
|
|
|
787
|
|
|
788
|
private boolean makeStandardMapper(Map<String, Object> valueMap, CdmBase cdmBase, Set<String> omitAttributes){
|
|
789
|
boolean result = true;
|
|
790
|
for (CdmAttributeMapperBase mapper : classMappers){
|
|
791
|
if (mapper instanceof CdmSingleAttributeMapperBase){
|
|
792
|
result &= makeStandardSingleMapper(valueMap, cdmBase, (CdmSingleAttributeMapperBase)mapper, omitAttributes);
|
|
793
|
}else if (mapper instanceof CdmOneToManyMapper){
|
|
794
|
result &= makeMultipleValueAddMapper(valueMap, cdmBase, (CdmOneToManyMapper)mapper, omitAttributes);
|
|
795
|
}else{
|
|
796
|
logger.error("Unknown mapper type");
|
|
797
|
result = false;
|
|
798
|
}
|
|
799
|
}
|
|
800
|
return result;
|
|
801
|
}
|
|
802
|
|
|
803
|
private boolean makeStandardSingleMapper(Map<String, Object> valueMap, CdmBase cdmBase, CdmSingleAttributeMapperBase mapper, Set<String> omitAttributes){
|
|
804
|
boolean result = true;
|
|
805
|
if (omitAttributes == null){
|
|
806
|
omitAttributes = new HashSet<String>();
|
|
807
|
}
|
|
808
|
if (mapper instanceof DbImportExtensionMapper){
|
|
809
|
result &= ((DbImportExtensionMapper)mapper).invoke(valueMap, cdmBase);
|
|
810
|
}else if (mapper instanceof DbImportMarkerMapper){
|
|
811
|
result &= ((DbImportMarkerMapper)mapper).invoke(valueMap, cdmBase);
|
|
812
|
}else{
|
|
813
|
String sourceAttribute = mapper.getSourceAttributeList().get(0).toLowerCase();
|
|
814
|
Object value = valueMap.get(sourceAttribute);
|
|
815
|
if (mapper instanceof CdmUriMapper && value != null){
|
|
816
|
try {
|
|
817
|
value = new URI (value.toString());
|
|
818
|
} catch (URISyntaxException e) {
|
|
819
|
logger.error("URI syntax exception: " + value.toString());
|
|
820
|
value = null;
|
|
821
|
}
|
|
822
|
}
|
|
823
|
if (value != null){
|
|
824
|
String destinationAttribute = mapper.getDestinationAttribute();
|
|
825
|
if (! omitAttributes.contains(destinationAttribute)){
|
|
826
|
result &= ImportHelper.addValue(value, cdmBase, destinationAttribute, mapper.getTypeClass(), OVERWRITE, OBLIGATORY);
|
|
827
|
}
|
|
828
|
}
|
|
829
|
}
|
|
830
|
return result;
|
|
831
|
}
|
|
832
|
|
|
833
|
|
|
834
|
private boolean makeMultipleValueAddMapper(Map<String, Object> valueMap, CdmBase cdmBase, CdmOneToManyMapper<CdmBase, CdmBase, CdmSingleAttributeMapperBase> mapper, Set<String> omitAttributes){
|
|
835
|
if (omitAttributes == null){
|
|
836
|
omitAttributes = new HashSet<String>();
|
|
837
|
}
|
|
838
|
boolean result = true;
|
|
839
|
String destinationAttribute = mapper.getSingleAttributeName();
|
|
840
|
List<Object> sourceValues = new ArrayList<Object>();
|
|
841
|
List<Class> classes = new ArrayList<Class>();
|
|
842
|
for (CdmSingleAttributeMapperBase singleMapper : mapper.getSingleMappers()){
|
|
843
|
String sourceAttribute = singleMapper.getSourceAttribute();
|
|
844
|
Object value = valueMap.get(sourceAttribute);
|
|
845
|
sourceValues.add(value);
|
|
846
|
Class<?> clazz = singleMapper.getTypeClass();
|
|
847
|
classes.add(clazz);
|
|
848
|
}
|
|
849
|
|
|
850
|
result &= ImportHelper.addMultipleValues(sourceValues, cdmBase, destinationAttribute, classes, NO_OVERWRITE, OBLIGATORY);
|
|
851
|
return result;
|
|
852
|
}
|
|
853
|
|
|
854
|
|
|
855
|
private static TeamOrPersonBase<?> getAuthorTeam(String authorString, TeamOrPersonBase<?> nomAuthor){
|
|
856
|
TeamOrPersonBase<?> result;
|
|
857
|
if (nomAuthor != null){
|
|
858
|
result = nomAuthor;
|
|
859
|
} else if (StringUtils.isNotBlank(authorString)){
|
|
860
|
//FIXME check for existing team / persons
|
|
861
|
TeamOrPersonBase<?> team = Team.NewInstance();
|
|
862
|
team.setNomenclaturalTitle(authorString);
|
|
863
|
team.setTitleCache(authorString, true);
|
|
864
|
team.setNomenclaturalTitle(authorString);
|
|
865
|
result = team;
|
|
866
|
}else{
|
|
867
|
result = null;
|
|
868
|
}
|
|
869
|
|
|
870
|
return result;
|
|
871
|
}
|
|
872
|
|
|
873
|
|
|
874
|
/**
|
|
875
|
* @param lowerCase
|
|
876
|
* @param config
|
|
877
|
* @return
|
|
878
|
*/
|
|
879
|
public Set<String> getObligatoryAttributes(boolean lowerCase, BerlinModelImportConfigurator config){
|
|
880
|
Set<String> result = new HashSet<String>();
|
|
881
|
Class<ICdmIO>[] ioClassList = config.getIoClassList();
|
|
882
|
logger.warn("getObligatoryAttributes has been commented because it still needs to be adapted to the new package structure");
|
|
883
|
result.addAll(Arrays.asList(unclearMappers));
|
|
884
|
result.addAll(Arrays.asList(createdAndNotesAttributes));
|
|
885
|
result.addAll(Arrays.asList(operationalAttributes));
|
|
886
|
CdmIoMapping mapping = new CdmIoMapping();
|
|
887
|
for (CdmAttributeMapperBase mapper : classMappers){
|
|
888
|
mapping.addMapper(mapper);
|
|
889
|
}
|
|
890
|
result.addAll(mapping.getSourceAttributes());
|
|
891
|
if (lowerCase){
|
|
892
|
Set<String> lowerCaseResult = new HashSet<String>();
|
|
893
|
for (String str : result){
|
|
894
|
if (str != null){lowerCaseResult.add(str.toLowerCase());}
|
|
895
|
}
|
|
896
|
result = lowerCaseResult;
|
|
897
|
}
|
|
898
|
return result;
|
|
899
|
}
|
|
900
|
|
|
901
|
/* (non-Javadoc)
|
|
902
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
|
|
903
|
*/
|
|
904
|
@Override
|
|
905
|
protected boolean doCheck(BerlinModelImportState state){
|
|
906
|
BerlinModelReferenceImportValidator validator = new BerlinModelReferenceImportValidator();
|
|
907
|
return validator.validate(state, this);
|
|
908
|
}
|
|
909
|
|
|
910
|
|
|
911
|
/* (non-Javadoc)
|
|
912
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
913
|
*/
|
|
914
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
915
|
return (state.getConfig().getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
|
|
916
|
}
|
|
917
|
|
|
918
|
|
|
919
|
|
|
920
|
|
|
921
|
}
|