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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.IImportConfigurator.DO_REFERENCES.ALL;
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import static eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES.CONCEPT_REFERENCES;
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import static eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES.NOMENCLATURAL;
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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.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.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.CdmOneToManyMapper;
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import eu.etaxonomy.cdm.io.berlinModel.CdmStringMapper;
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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.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.IBook;
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import eu.etaxonomy.cdm.model.reference.IBookSection;
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import eu.etaxonomy.cdm.model.reference.IJournal;
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import eu.etaxonomy.cdm.model.reference.IPrintSeries;
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import eu.etaxonomy.cdm.model.reference.ReferenceBase;
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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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/**
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* @author a.mueller
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* @created 20.03.2008
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* @version 1.0
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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 NOM_REFERENCE_NAMESPACE = "NomReference";
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public static final String BIBLIO_REFERENCE_NAMESPACE = "BiblioReference";
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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.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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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();
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}
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protected boolean initializeMappers(BerlinModelImportState state){
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for (CdmAttributeMapperBase mapper: classMappers){
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if (mapper instanceof DbImportExtensionMapper){
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((DbImportExtensionMapper)mapper).initialize(state, ReferenceBase.class);
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}
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}
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return true;
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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 CdmStringMapper("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, "RefSource", "reference source", "source")
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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() {nomRefCount = 0; referenceCount = 0;};
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int nomRefCount;
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int referenceCount;
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public String toString(){return String.valueOf(nomRefCount) + "," +String.valueOf(referenceCount);};
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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 boolean doInvoke(BerlinModelImportState state){
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boolean success = true;
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logger.info("start make " + getPluralString() + " ...");
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success &= 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.RefId as InRefId, InReference.RefCategoryFk as InRefCategoryFk, " +
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" InInReference.RefId as InInRefId, InInReference.RefCategoryFk as InInRefCategoryFk, " +
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" InReference.InRefFk AS InRefInRefFk, InInReference.InRefFk AS InInRefInRefFk, RefSource.RefSource " ;
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String strFrom = " FROM Reference AS InInReference " +
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" RIGHT OUTER JOIN Reference AS InReference ON InInReference.RefId = InReference.InRefFk " +
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" RIGHT OUTER JOIN Reference ON InReference.RefId = dbo.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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//test max number of recursions
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String strQueryTestMaxRecursion = strSelectId + strFrom +
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" AND (Reference.InRefFk is NOT NULL) AND (InReference.InRefFk is NOT NULL) AND (InInReference.InRefFk is NOT NULL) ";
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ResultSet testMaxRecursionResultSet = source.getResultSet(strQueryTestMaxRecursion);
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try {
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if (testMaxRecursionResultSet.next() == true){
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logger.error("Maximum allowed InReference recursions exceeded in Berlin Model. Maximum recursion level is 2.");
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return false;
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}
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} catch (SQLException e1) {
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e1.printStackTrace();
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logger.error("There are references with more then 2 in-reference recursion. Maximum number of allowed recursions is 2. Records will not be stored.");
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success = false;
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}
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String strSelectIdBase = strSelectId + strFrom;
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String strIdQueryNoInRef = strSelectIdBase +
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" AND (Reference.InRefFk is NULL) ";
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String strIdQuery1InRef = strSelectIdBase +
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" AND (Reference.InRefFk is NOT NULL) AND (InReference.InRefFk is NULL) ";
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String strIdQuery2InRefs = strSelectIdBase +
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" AND (Reference.InRefFk is NOT NULL) AND (InReference.InRefFk is NOT NULL) AND (InInReference.InRefFk is NULL) ";
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if (config.getDoReferences() == CONCEPT_REFERENCES){
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strIdQueryNoInRef += " AND ( Reference.refId IN ( SELECT ptRefFk FROM PTaxon) ) ";
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}
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String strRecordQuery = strSelectFull + strFrom + strWherePartitioned;
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int recordsPerTransaction = config.getRecordsPerTransaction();
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try{
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//NoInRefs
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ResultSetPartitioner partitioner = ResultSetPartitioner.NewInstance(source, strIdQueryNoInRef, 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 in-references ... " + getSuccessString(success));
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if (config.getDoReferences() == ALL || config.getDoReferences() == NOMENCLATURAL){
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//1InRef
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partitioner = ResultSetPartitioner.NewInstance(source, strIdQuery1InRef, 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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//2InRefs
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partitioner = ResultSetPartitioner.NewInstance(source, strIdQuery2InRefs, 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 2 in-reference ... " + getSuccessString(success));
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}
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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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logger.info("end make " + getPluralString() + " ... " + getSuccessString(success));
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return success;
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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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boolean success = true;
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// MapWrapper<ReferenceBase> referenceStore= new MapWrapper<ReferenceBase>(null);
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// MapWrapper<ReferenceBase> nomRefStore= new MapWrapper<ReferenceBase>(null);
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Map<Integer, ReferenceBase> nomRefToSave = new HashMap<Integer, ReferenceBase>();
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Map<Integer, ReferenceBase> biblioRefToSave = new HashMap<Integer, ReferenceBase>();
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Map<String, ReferenceBase> relatedNomReferences = partitioner.getObjectMap(NOM_REFERENCE_NAMESPACE);
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Map<String, ReferenceBase> relatedBiblioReferences = partitioner.getObjectMap(BIBLIO_REFERENCE_NAMESPACE);
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BerlinModelImportConfigurator config = state.getConfig();
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try {
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// //get data from database
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// //strQueryBase += " AND Reference.refId = 1933 " ; //7000000
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//
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// int j = 0;
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// Iterator<ResultSet> resultSetListIterator = resultSetList.listIterator();
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// //for each resultsetlist
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// while (resultSetListIterator.hasNext()){
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int i = 0;
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RefCounter refCounter = new RefCounter();
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// ResultSet rs = resultSetListIterator.next();
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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, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences, 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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ReferenceBase<?> sec = biblioRefToSave.get(sourceSecId);
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if (sec == null){
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sec = nomRefToSave.get(sourceSecId);
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}
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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 nomenclatural references (" + refCounter.nomRefCount + ")");
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getReferenceService().save(nomRefToSave.values());
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logger.info("Save bibliographical references (" + refCounter.referenceCount +")");
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getReferenceService().save(biblioRefToSave.values());
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// j++;
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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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/* (non-Javadoc)
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* @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
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*/
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318
|
public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
|
|
319
|
String nameSpace;
|
|
320
|
Class cdmClass;
|
|
321
|
Set<String> idSet;
|
|
322
|
|
|
323
|
Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
|
|
324
|
|
|
325
|
try{
|
|
326
|
Set<String> teamIdSet = new HashSet<String>();
|
|
327
|
Set<String> referenceIdSet = new HashSet<String>();
|
|
328
|
|
|
329
|
while (rs.next()){
|
|
330
|
handleForeignKey(rs, teamIdSet, "NomAuthorTeamFk");
|
|
331
|
handleForeignKey(rs, referenceIdSet, "InRefFk");
|
|
332
|
}
|
|
333
|
|
|
334
|
//team map
|
|
335
|
nameSpace = BerlinModelAuthorTeamImport.NAMESPACE;
|
|
336
|
cdmClass = Team.class;
|
|
337
|
idSet = teamIdSet;
|
|
338
|
Map<String, Team> teamMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
339
|
result.put(nameSpace, teamMap);
|
|
340
|
|
|
341
|
|
|
342
|
//nom reference map
|
|
343
|
nameSpace = NOM_REFERENCE_NAMESPACE;
|
|
344
|
cdmClass = ReferenceBase.class;
|
|
345
|
idSet = referenceIdSet;
|
|
346
|
Map<String, ReferenceBase> nomRefMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
347
|
result.put(nameSpace, nomRefMap);
|
|
348
|
|
|
349
|
//biblio reference map
|
|
350
|
nameSpace = BIBLIO_REFERENCE_NAMESPACE;
|
|
351
|
cdmClass = ReferenceBase.class;
|
|
352
|
idSet = referenceIdSet;
|
|
353
|
Map<String, ReferenceBase> biblioRefMap = (Map<String, ReferenceBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
|
|
354
|
result.put(nameSpace, biblioRefMap);
|
|
355
|
|
|
356
|
} catch (SQLException e) {
|
|
357
|
throw new RuntimeException(e);
|
|
358
|
}
|
|
359
|
return result;
|
|
360
|
}
|
|
361
|
|
|
362
|
|
|
363
|
/**
|
|
364
|
* Handles a single reference record
|
|
365
|
* @param rs
|
|
366
|
* @param state
|
|
367
|
* @param biblioRefToSave
|
|
368
|
* @param nomRefToSave
|
|
369
|
* @param relatedBiblioReferences
|
|
370
|
* @param relatedNomReferences
|
|
371
|
* @param refCounter
|
|
372
|
* @return
|
|
373
|
*/
|
|
374
|
private boolean makeSingleReferenceRecord(
|
|
375
|
ResultSet rs,
|
|
376
|
BerlinModelImportState state,
|
|
377
|
ResultSetPartitioner<BerlinModelImportState> partitioner,
|
|
378
|
Map<Integer, ReferenceBase> biblioRefToSave,
|
|
379
|
Map<Integer, ReferenceBase> nomRefToSave,
|
|
380
|
Map<String, ReferenceBase> relatedBiblioReferences,
|
|
381
|
Map<String, ReferenceBase> relatedNomReferences,
|
|
382
|
RefCounter refCounter){
|
|
383
|
boolean success = true;
|
|
384
|
|
|
385
|
Integer refId = null;
|
|
386
|
try {
|
|
387
|
Map<String, Object> valueMap = getValueMap(rs);
|
|
388
|
|
|
389
|
Integer categoryFk = (Integer)valueMap.get("refCategoryFk".toLowerCase());
|
|
390
|
refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
391
|
Boolean thesisFlag = (Boolean)valueMap.get("thesisFlag".toLowerCase());
|
|
392
|
|
|
393
|
|
|
394
|
ReferenceBase<?> referenceBase;
|
|
395
|
logger.debug("RefCategoryFk: " + categoryFk);
|
|
396
|
|
|
397
|
if (thesisFlag){
|
|
398
|
referenceBase = makeThesis(valueMap);
|
|
399
|
}else if (categoryFk == REF_JOURNAL){
|
|
400
|
referenceBase = makeJournal(valueMap);
|
|
401
|
}else if(categoryFk == REF_BOOK){
|
|
402
|
referenceBase = makeBook(valueMap, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences);
|
|
403
|
}else if(categoryFk == REF_DATABASE){
|
|
404
|
referenceBase = makeDatabase(valueMap);
|
|
405
|
}else if(categoryFk == REF_INFORMAL){
|
|
406
|
referenceBase = makeInformal(valueMap);
|
|
407
|
}else if(categoryFk == REF_WEBSITE){
|
|
408
|
referenceBase = makeWebSite(valueMap);
|
|
409
|
}else if(categoryFk == REF_UNKNOWN){
|
|
410
|
referenceBase = makeUnknown(valueMap);
|
|
411
|
}else if(categoryFk == REF_PRINT_SERIES){
|
|
412
|
referenceBase = makePrintSeries(valueMap);
|
|
413
|
}else if(categoryFk == REF_CONFERENCE_PROCEEDINGS){
|
|
414
|
referenceBase = makeProceedings(valueMap);
|
|
415
|
}else if(categoryFk == REF_ARTICLE){
|
|
416
|
referenceBase = makeArticle(valueMap, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences);
|
|
417
|
}else if(categoryFk == REF_JOURNAL_VOLUME){
|
|
418
|
referenceBase = makeJournalVolume(valueMap);
|
|
419
|
}else if(categoryFk == REF_PART_OF_OTHER_TITLE){
|
|
420
|
referenceBase = makePartOfOtherTitle(valueMap, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences);
|
|
421
|
}else{
|
|
422
|
logger.warn("Unknown categoryFk (" + categoryFk + "). Create 'Generic instead'");
|
|
423
|
referenceBase = ReferenceFactory.newGeneric();
|
|
424
|
success = false;
|
|
425
|
}
|
|
426
|
|
|
427
|
//refYear
|
|
428
|
String refYear = (String)valueMap.get("refYear".toLowerCase());
|
|
429
|
referenceBase.setDatePublished(ImportHelper.getDatePublished(refYear));
|
|
430
|
|
|
431
|
//created, updated, notes
|
|
432
|
doCreatedUpdatedNotes(state, referenceBase, rs);
|
|
433
|
|
|
434
|
//isPaper
|
|
435
|
if ((Boolean)valueMap.get("isPaper".toLowerCase())){
|
|
436
|
logger.warn("IsPaper is not yet implemented, but reference " + refId + " is paper");
|
|
437
|
}
|
|
438
|
|
|
439
|
//idInSource
|
|
440
|
String idInSource = (String)valueMap.get("IdInSource".toLowerCase());
|
|
441
|
if (CdmUtils.isNotEmpty(idInSource)){
|
|
442
|
IdentifiableSource source = IdentifiableSource.NewInstance(idInSource);
|
|
443
|
source.setIdNamespace("import to Berlin Model");
|
|
444
|
referenceBase.addSource(source);
|
|
445
|
}
|
|
446
|
|
|
447
|
//nom&BiblioReference - must be last because a clone is created
|
|
448
|
success &= makeNomAndBiblioReference(rs, state, partitioner, refId, referenceBase, refCounter,
|
|
449
|
biblioRefToSave, nomRefToSave );
|
|
450
|
|
|
451
|
|
|
452
|
} catch (Exception e) {
|
|
453
|
logger.warn("Reference with BM refId '" + CdmUtils.Nz(refId) + "' threw Exception and could not be saved");
|
|
454
|
e.printStackTrace();
|
|
455
|
success = false;
|
|
456
|
}
|
|
457
|
return success;
|
|
458
|
}
|
|
459
|
|
|
460
|
|
|
461
|
/**
|
|
462
|
* Creates and saves a nom. reference and a biblio. reference after checking necessity
|
|
463
|
* @param rs
|
|
464
|
* @param refId
|
|
465
|
* @param referenceBase
|
|
466
|
* @param refCounter
|
|
467
|
* @param biblioRefToSave
|
|
468
|
* @param nomRefToSave
|
|
469
|
* @param teamMap
|
|
470
|
* @param stores
|
|
471
|
* @return
|
|
472
|
* @throws SQLException
|
|
473
|
*/
|
|
474
|
private boolean makeNomAndBiblioReference(
|
|
475
|
ResultSet rs,
|
|
476
|
BerlinModelImportState state,
|
|
477
|
ResultSetPartitioner partitioner,
|
|
478
|
int refId,
|
|
479
|
ReferenceBase<?> referenceBase,
|
|
480
|
RefCounter refCounter,
|
|
481
|
Map<Integer, ReferenceBase> biblioRefToSave,
|
|
482
|
Map<Integer, ReferenceBase> nomRefToSave
|
|
483
|
) throws SQLException{
|
|
484
|
|
|
485
|
Map<String, Team> teamMap = partitioner.getObjectMap(BerlinModelAuthorTeamImport.NAMESPACE);
|
|
486
|
|
|
487
|
String refCache = rs.getString("refCache");
|
|
488
|
String nomRefCache = rs.getString("nomRefCache");
|
|
489
|
String title = rs.getString("title");
|
|
490
|
String nomTitleAbbrev = rs.getString("nomTitleAbbrev");
|
|
491
|
boolean isPreliminary = rs.getBoolean("PreliminaryFlag");
|
|
492
|
String refAuthorString = rs.getString("refAuthorString");
|
|
493
|
Integer nomAuthorTeamFk = rs.getInt("NomAuthorTeamFk");
|
|
494
|
String strNomAuthorTeamFk = String.valueOf(nomAuthorTeamFk);
|
|
495
|
TeamOrPersonBase<?> nomAuthor = teamMap.get(strNomAuthorTeamFk);
|
|
496
|
ReferenceBase nomReference = null;
|
|
497
|
|
|
498
|
boolean hasNomRef = false;
|
|
499
|
boolean hasBiblioRef = false;
|
|
500
|
ReferenceBase sourceReference = state.getConfig().getSourceReference();
|
|
501
|
|
|
502
|
//is Nomenclatural Reference
|
|
503
|
if ( (CdmUtils.isNotEmpty(nomRefCache) && isPreliminary) || (CdmUtils.isNotEmpty(nomTitleAbbrev) && ! isPreliminary) ){
|
|
504
|
referenceBase.setTitle(nomTitleAbbrev);
|
|
505
|
TeamOrPersonBase<?> author = getAuthorTeam(refAuthorString , nomAuthor, true);
|
|
506
|
referenceBase.setAuthorTeam(author);
|
|
507
|
//referenceBase.setNomenclaturallyRelevant(true);
|
|
508
|
if (isPreliminary){
|
|
509
|
referenceBase.setTitleCache(nomRefCache, true);
|
|
510
|
}
|
|
511
|
if (! nomRefToSave.containsKey(refId)){
|
|
512
|
if (referenceBase == null){
|
|
513
|
logger.warn("refBase is null");
|
|
514
|
}
|
|
515
|
nomRefToSave.put(refId, referenceBase);
|
|
516
|
}else{
|
|
517
|
logger.warn("Duplicate refId in Berlin Model database. Second reference was not imported !!");
|
|
518
|
}
|
|
519
|
|
|
520
|
// ???
|
|
521
|
// nomRefToSave.put(refId, referenceBase);
|
|
522
|
hasNomRef = true;
|
|
523
|
nomReference = referenceBase;
|
|
524
|
refCounter.nomRefCount++;
|
|
525
|
}
|
|
526
|
//is bibliographical Reference
|
|
527
|
if ((CdmUtils.isNotEmpty(refCache) && isPreliminary && ! refCache.equalsIgnoreCase(nomRefCache))
|
|
528
|
|| (CdmUtils.isNotEmpty(title) && ! isPreliminary && ! title.equalsIgnoreCase(nomTitleAbbrev))
|
|
529
|
|| hasNomRef == false){
|
|
530
|
if (hasNomRef){
|
|
531
|
referenceBase = (ReferenceBase)referenceBase.clone();
|
|
532
|
copyCreatedUpdated(referenceBase, nomReference);
|
|
533
|
}
|
|
534
|
referenceBase.setTitle(title);
|
|
535
|
TeamOrPersonBase author = getAuthorTeam(refAuthorString , nomAuthor, false);
|
|
536
|
referenceBase.setAuthorTeam(author);
|
|
537
|
referenceBase.setNomenclaturallyRelevant(false);
|
|
538
|
if (isPreliminary){
|
|
539
|
referenceBase.setTitleCache(refCache, true);
|
|
540
|
}
|
|
541
|
if (! biblioRefToSave.containsKey(refId)){
|
|
542
|
biblioRefToSave.put(refId, referenceBase);
|
|
543
|
}else{
|
|
544
|
logger.warn("Duplicate refId in Berlin Model database. Second reference was not imported !!");
|
|
545
|
}
|
|
546
|
hasBiblioRef = true;
|
|
547
|
|
|
548
|
//??
|
|
549
|
//biblioRefToSave.put(refId, referenceBase);
|
|
550
|
refCounter.referenceCount++;
|
|
551
|
}
|
|
552
|
//refId
|
|
553
|
if (hasNomRef){
|
|
554
|
ImportHelper.setOriginalSource(nomReference, sourceReference, refId, NOM_REFERENCE_NAMESPACE);
|
|
555
|
}
|
|
556
|
if (hasBiblioRef){
|
|
557
|
ImportHelper.setOriginalSource(referenceBase, sourceReference, refId, BIBLIO_REFERENCE_NAMESPACE);
|
|
558
|
}
|
|
559
|
|
|
560
|
return true;
|
|
561
|
|
|
562
|
}
|
|
563
|
|
|
564
|
/**
|
|
565
|
* Copies the created and updated information from the nomReference to the cloned bibliographic reference
|
|
566
|
* @param referenceBase
|
|
567
|
* @param nomReference
|
|
568
|
*/
|
|
569
|
private void copyCreatedUpdated(ReferenceBase<?> biblioReference, ReferenceBase nomReference) {
|
|
570
|
biblioReference.setCreatedBy(nomReference.getCreatedBy());
|
|
571
|
biblioReference.setCreated(nomReference.getCreated());
|
|
572
|
biblioReference.setUpdatedBy(nomReference.getUpdatedBy());
|
|
573
|
biblioReference.setUpdated(nomReference.getUpdated());
|
|
574
|
|
|
575
|
}
|
|
576
|
|
|
577
|
private ReferenceBase<?> makeArticle (Map<String, Object> valueMap, Map<Integer, ReferenceBase> biblioRefToSave, Map<Integer, ReferenceBase> nomRefToSave, Map<String, ReferenceBase> relatedBiblioReferences, Map<String, ReferenceBase> relatedNomReferences){
|
|
578
|
|
|
579
|
IArticle article = ReferenceFactory.newArticle();
|
|
580
|
Object inRefFk = valueMap.get("inRefFk".toLowerCase());
|
|
581
|
Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());
|
|
582
|
Integer refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
583
|
|
|
584
|
if (inRefFk != null){
|
|
585
|
if (inRefCategoryFk == REF_JOURNAL){
|
|
586
|
int inRefFkInt = (Integer)inRefFk;
|
|
587
|
if (existsInMapOrToSave(inRefFkInt, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences)){
|
|
588
|
ReferenceBase<?> inJournal = getReferenceFromMaps(inRefFkInt, nomRefToSave, relatedNomReferences);
|
|
589
|
if (inJournal == null){
|
|
590
|
inJournal = getReferenceFromMaps(inRefFkInt, biblioRefToSave, relatedBiblioReferences);
|
|
591
|
logger.info("inJournal (" + inRefFkInt + ") found in referenceStore instead of nomRefStore.");
|
|
592
|
nomRefToSave.put(inRefFkInt, inJournal);
|
|
593
|
}
|
|
594
|
if (inJournal == null){
|
|
595
|
logger.warn("inJournal for " + inRefFkInt + " is null. "+
|
|
596
|
" InReference relation could not be set");
|
|
597
|
//}else if (ReferenceBase.class.isAssignableFrom(inJournal.getClass())){
|
|
598
|
}else if (inJournal.getType().equals(ReferenceType.Journal)){
|
|
599
|
article.setInJournal((IJournal)inJournal);
|
|
600
|
}else{
|
|
601
|
logger.warn("InJournal is not of type journal but of type " + inJournal.getType() +
|
|
602
|
" Inreference relation could not be set");
|
|
603
|
}
|
|
604
|
}else{
|
|
605
|
logger.error("Journal (refId = " + inRefFkInt + " ) for Article (refID = " + refId +") could not be found in nomRefStore. Inconsistency error. ");
|
|
606
|
//success = false;;
|
|
607
|
}
|
|
608
|
}else{
|
|
609
|
logger.warn("Wrong inrefCategory for Article (refID = " + refId +"). Type must be 'Journal' but was not (RefCategoryFk=" + inRefCategoryFk + "))." +
|
|
610
|
" InReference was not added to Article! ");
|
|
611
|
}
|
|
612
|
}
|
|
613
|
makeStandardMapper(valueMap, (ReferenceBase)article); //url, pages, series, volume
|
|
614
|
return (ReferenceBase)article;
|
|
615
|
}
|
|
616
|
|
|
617
|
private ReferenceBase<?> makePartOfOtherTitle (Map<String, Object> valueMap, Map<Integer, ReferenceBase> biblioRefToSave, Map<Integer, ReferenceBase> nomRefToSave, Map<String, ReferenceBase> relatedBiblioReferences, Map<String, ReferenceBase> relatedNomReferences){
|
|
618
|
ReferenceBase<?> result;
|
|
619
|
Object inRefFk = valueMap.get("inRefFk".toLowerCase());
|
|
620
|
Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());
|
|
621
|
Integer refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
622
|
|
|
623
|
if (inRefCategoryFk == null){
|
|
624
|
//null -> error
|
|
625
|
logger.warn("Part-Of-Other-Title has not inRefCategoryFk! RefId = " + refId + ". ReferenceType set to Generic.");
|
|
626
|
result = makeUnknown(valueMap);
|
|
627
|
}else if (inRefCategoryFk == REF_BOOK){
|
|
628
|
//BookSection
|
|
629
|
IBookSection bookSection = ReferenceFactory.newBookSection();
|
|
630
|
result = (ReferenceBase)bookSection;
|
|
631
|
if (inRefFk != null){
|
|
632
|
int inRefFkInt = (Integer)inRefFk;
|
|
633
|
if (existsInMapOrToSave(inRefFkInt, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences)){
|
|
634
|
ReferenceBase<?> inBook = getReferenceFromMaps(inRefFkInt, nomRefToSave, relatedNomReferences);
|
|
635
|
if (inBook == null){
|
|
636
|
inBook = getReferenceFromMaps(inRefFkInt, biblioRefToSave, relatedBiblioReferences);
|
|
637
|
logger.info("inBook (" + inRefFkInt + ") found in referenceStore instead of nomRefStore.");
|
|
638
|
nomRefToSave.put(inRefFkInt, inBook);
|
|
639
|
}
|
|
640
|
if (inBook == null){
|
|
641
|
logger.warn("inBook for " + inRefFkInt + " is null. "+
|
|
642
|
" InReference relation could not be set");;
|
|
643
|
//}else if (Book.class.isAssignableFrom(inBook.getClass())){
|
|
644
|
}else if (inBook.getType().equals(ReferenceType.Book)){
|
|
645
|
bookSection.setInBook((IBook)inBook);
|
|
646
|
//TODO
|
|
647
|
}else{
|
|
648
|
logger.warn("InBook is not of type book but of type " + inBook.getClass().getSimpleName() +
|
|
649
|
" Inreference relation could not be set");
|
|
650
|
}
|
|
651
|
}else{
|
|
652
|
logger.error("Book (refId = " + inRefFkInt + ") for part_of_other_title (refID = " + refId +") could not be found in nomRefStore. Inconsistency error. ");
|
|
653
|
//success = false;
|
|
654
|
}
|
|
655
|
}
|
|
656
|
}else if (inRefCategoryFk == REF_ARTICLE){
|
|
657
|
//Article
|
|
658
|
//TODO
|
|
659
|
logger.warn("Reference (refId = " + refId + ") of type 'part_of_other_title' is part of 'article'." +
|
|
660
|
" This type is not implemented yet. Generic reference created instead") ;
|
|
661
|
result = ReferenceFactory.newGeneric();
|
|
662
|
}else if (inRefCategoryFk == REF_JOURNAL){
|
|
663
|
//TODO
|
|
664
|
logger.warn("Reference (refId = " + refId + ") of type 'part_of_other_title' has inReference of type 'journal'." +
|
|
665
|
" This is not allowed! Generic reference created instead") ;
|
|
666
|
result = ReferenceFactory.newGeneric();
|
|
667
|
result.addMarker(Marker.NewInstance(MarkerType.TO_BE_CHECKED(), true));
|
|
668
|
}else{
|
|
669
|
logger.warn("InReference type (catFk = " + inRefCategoryFk + ") of part-of-reference not recognized for refId " + refId + "." +
|
|
670
|
" Create 'Generic' reference instead");
|
|
671
|
result = ReferenceFactory.newGeneric();
|
|
672
|
}
|
|
673
|
makeStandardMapper(valueMap, result); //url, pages
|
|
674
|
return result;
|
|
675
|
}
|
|
676
|
|
|
677
|
|
|
678
|
/**
|
|
679
|
* @param inRefFkInt
|
|
680
|
* @param biblioRefToSave
|
|
681
|
* @param nomRefToSave
|
|
682
|
* @param relatedBiblioReferences
|
|
683
|
* @param relatedNomReferences
|
|
684
|
* @return
|
|
685
|
*/
|
|
686
|
private boolean existsInMapOrToSave(Integer inRefFkInt, Map<Integer, ReferenceBase> biblioRefToSave, Map<Integer, ReferenceBase> nomRefToSave, Map<String, ReferenceBase> relatedBiblioReferences, Map<String, ReferenceBase> relatedNomReferences) {
|
|
687
|
boolean result = false;
|
|
688
|
if (inRefFkInt == null){
|
|
689
|
return false;
|
|
690
|
}
|
|
691
|
result |= nomRefToSave.containsKey(inRefFkInt);
|
|
692
|
result |= biblioRefToSave.containsKey(inRefFkInt);
|
|
693
|
result |= relatedBiblioReferences.containsKey(String.valueOf(inRefFkInt));
|
|
694
|
result |= relatedNomReferences.containsKey(String.valueOf(inRefFkInt));
|
|
695
|
return result;
|
|
696
|
}
|
|
697
|
|
|
698
|
private ReferenceBase<?> makeWebSite(Map<String, Object> valueMap){
|
|
699
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Website'");}
|
|
700
|
ReferenceBase webPage = ReferenceFactory.newWebPage();
|
|
701
|
makeStandardMapper(valueMap, webPage); //placePublished, publisher
|
|
702
|
return webPage;
|
|
703
|
}
|
|
704
|
|
|
705
|
private ReferenceBase<?> makeUnknown(Map<String, Object> valueMap){
|
|
706
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Unknown'");}
|
|
707
|
ReferenceBase generic = ReferenceFactory.newGeneric();
|
|
708
|
// generic.setSeries(series);
|
|
709
|
makeStandardMapper(valueMap, generic); //pages, placePublished, publisher, series, volume
|
|
710
|
return generic;
|
|
711
|
}
|
|
712
|
|
|
713
|
private ReferenceBase<?> makeInformal(Map<String, Object> valueMap){
|
|
714
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Informal'");}
|
|
715
|
ReferenceBase generic = ReferenceFactory.newGeneric();
|
|
716
|
// informal.setSeries(series);
|
|
717
|
makeStandardMapper(valueMap, generic);//editor, pages, placePublished, publisher, series, volume
|
|
718
|
String informal = (String)valueMap.get("InformalRefCategory".toLowerCase());
|
|
719
|
if (CdmUtils.isNotEmpty(informal) ){
|
|
720
|
generic.addExtension(informal, ExtensionType.INFORMAL_CATEGORY());
|
|
721
|
}
|
|
722
|
return generic;
|
|
723
|
}
|
|
724
|
|
|
725
|
private ReferenceBase<?> makeDatabase(Map<String, Object> valueMap){
|
|
726
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Database'");}
|
|
727
|
ReferenceBase database = ReferenceFactory.newDatabase();
|
|
728
|
makeStandardMapper(valueMap, database); //?
|
|
729
|
return database;
|
|
730
|
}
|
|
731
|
|
|
732
|
private ReferenceBase<?> makeJournal(Map<String, Object> valueMap){
|
|
733
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Journal'");}
|
|
734
|
ReferenceBase journal = ReferenceFactory.newJournal();
|
|
735
|
|
|
736
|
Set<String> omitAttributes = new HashSet<String>();
|
|
737
|
String series = "series";
|
|
738
|
// omitAttributes.add(series);
|
|
739
|
|
|
740
|
makeStandardMapper(valueMap, journal, omitAttributes); //issn,placePublished,publisher
|
|
741
|
// if (valueMap.get(series) != null){
|
|
742
|
// logger.warn("Series not yet implemented for journal!");
|
|
743
|
// }
|
|
744
|
return journal;
|
|
745
|
}
|
|
746
|
|
|
747
|
private ReferenceBase<?> makeBook(
|
|
748
|
Map<String, Object> valueMap,
|
|
749
|
Map<Integer, ReferenceBase> biblioRefToSave,
|
|
750
|
Map<Integer, ReferenceBase> nomRefToSave,
|
|
751
|
Map<String, ReferenceBase> relatedBiblioReferences,
|
|
752
|
Map<String, ReferenceBase> relatedNomReferences){
|
|
753
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Book'");}
|
|
754
|
ReferenceBase book = ReferenceFactory.newBook();
|
|
755
|
Integer refId = (Integer)valueMap.get("refId".toLowerCase());
|
|
756
|
|
|
757
|
//Set bookAttributes = new String[]{"edition", "isbn", "pages","publicationTown","publisher","volume"};
|
|
758
|
|
|
759
|
Set<String> omitAttributes = new HashSet<String>();
|
|
760
|
String attrSeries = "series";
|
|
761
|
// omitAttributes.add(attrSeries);
|
|
762
|
|
|
763
|
makeStandardMapper(valueMap, book, omitAttributes);
|
|
764
|
|
|
765
|
//Series (as String)
|
|
766
|
IPrintSeries printSeries = null;
|
|
767
|
if (valueMap.get(attrSeries) != null){
|
|
768
|
String series = (String)valueMap.get("title".toLowerCase());
|
|
769
|
if (series == null){
|
|
770
|
String nomTitle = (String)valueMap.get("nomTitleAbbrev".toLowerCase());
|
|
771
|
series = nomTitle;
|
|
772
|
}
|
|
773
|
printSeries = ReferenceFactory.newPrintSeries(series);
|
|
774
|
logger.info("Implementation of printSeries is preliminary");
|
|
775
|
}
|
|
776
|
Object inRefFk = valueMap.get("inRefFk".toLowerCase());
|
|
777
|
//Series (as Reference)
|
|
778
|
if (inRefFk != null){
|
|
779
|
int inRefFkInt = (Integer)inRefFk;
|
|
780
|
if (existsInMapOrToSave(inRefFkInt, biblioRefToSave, nomRefToSave, relatedBiblioReferences, relatedNomReferences)){
|
|
781
|
ReferenceBase<?> inSeries = getReferenceFromMaps(inRefFkInt, nomRefToSave, relatedNomReferences);
|
|
782
|
if (inSeries == null){
|
|
783
|
inSeries = getReferenceFromMaps(inRefFkInt, biblioRefToSave, relatedBiblioReferences);
|
|
784
|
logger.info("inSeries (" + inRefFkInt + ") found in referenceStore instead of nomRefStore.");
|
|
785
|
nomRefToSave.put(inRefFkInt, inSeries);
|
|
786
|
}
|
|
787
|
if (inSeries == null){
|
|
788
|
logger.warn("inSeries for " + inRefFkInt + " is null. "+
|
|
789
|
" InReference relation could not be set");;
|
|
790
|
//}else if (PrintSeries.class.isAssignableFrom(inSeries.getClass())){
|
|
791
|
}else if (inSeries.getType().equals(ReferenceType.PrintSeries)){
|
|
792
|
book.setInSeries((IPrintSeries)inSeries);
|
|
793
|
//TODO
|
|
794
|
}else{
|
|
795
|
logger.warn("inSeries is not of type PrintSeries but of type " + inSeries.getType().getMessage() +
|
|
796
|
". In-reference relation could not be set for refId " + refId + " and inRefFk " + inRefFk);
|
|
797
|
}
|
|
798
|
}else{
|
|
799
|
logger.error("PrintSeries (refId = " + inRefFkInt + ") for book (refID = " + refId +") could not be found in nomRefStore. Inconsistency error. ");
|
|
800
|
//success = false;
|
|
801
|
}
|
|
802
|
}
|
|
803
|
if (book.getInSeries() != null && printSeries != null){
|
|
804
|
logger.warn("Book has series string and inSeries reference. Can not take both. Series string neglected");
|
|
805
|
}else{
|
|
806
|
book.setInSeries(printSeries);
|
|
807
|
}
|
|
808
|
book.setEditor(null);
|
|
809
|
return book;
|
|
810
|
|
|
811
|
}
|
|
812
|
|
|
813
|
/**
|
|
814
|
* Returns the requested object if it exists in one of both maps. Prefers the refToSaveMap in ambigious cases.
|
|
815
|
* @param inRefFkInt
|
|
816
|
* @param nomRefToSave
|
|
817
|
* @param relatedNomReferences
|
|
818
|
* @return
|
|
819
|
*/
|
|
820
|
private ReferenceBase<?> getReferenceFromMaps(
|
|
821
|
int inRefFkInt,
|
|
822
|
Map<Integer, ReferenceBase> refToSaveMap,
|
|
823
|
Map<String, ReferenceBase> relatedRefMap) {
|
|
824
|
ReferenceBase result = null;
|
|
825
|
result = refToSaveMap.get(inRefFkInt);
|
|
826
|
if (result == null){
|
|
827
|
result = relatedRefMap.get(String.valueOf(inRefFkInt));
|
|
828
|
}
|
|
829
|
return result;
|
|
830
|
}
|
|
831
|
|
|
832
|
private ReferenceBase<?> makePrintSeries(Map<String, Object> valueMap){
|
|
833
|
if (logger.isDebugEnabled()){logger.debug("RefType 'PrintSeries'");}
|
|
834
|
ReferenceBase printSeries = ReferenceFactory.newPrintSeries();
|
|
835
|
makeStandardMapper(valueMap, printSeries, null);
|
|
836
|
return printSeries;
|
|
837
|
}
|
|
838
|
|
|
839
|
private ReferenceBase<?> makeProceedings(Map<String, Object> valueMap){
|
|
840
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Proceedings'");}
|
|
841
|
ReferenceBase proceedings = ReferenceFactory.newProceedings();
|
|
842
|
makeStandardMapper(valueMap, proceedings, null);
|
|
843
|
return proceedings;
|
|
844
|
}
|
|
845
|
|
|
846
|
private ReferenceBase<?> makeThesis(Map<String, Object> valueMap){
|
|
847
|
if (logger.isDebugEnabled()){logger.debug("RefType 'Thesis'");}
|
|
848
|
ReferenceBase thesis = ReferenceFactory.newThesis();
|
|
849
|
makeStandardMapper(valueMap, thesis, null);
|
|
850
|
return thesis;
|
|
851
|
}
|
|
852
|
|
|
853
|
|
|
854
|
private ReferenceBase<?> makeJournalVolume(Map<String, Object> valueMap){
|
|
855
|
if (logger.isDebugEnabled()){logger.debug("RefType 'JournalVolume'");}
|
|
856
|
//Proceedings proceedings = Proceedings.NewInstance();
|
|
857
|
ReferenceBase journalVolume = ReferenceFactory.newGeneric();
|
|
858
|
makeStandardMapper(valueMap, journalVolume, null);
|
|
859
|
logger.warn("Journal volumes not yet implemented. Generic created instead but with errors");
|
|
860
|
return journalVolume;
|
|
861
|
}
|
|
862
|
|
|
863
|
private boolean makeStandardMapper(Map<String, Object> valueMap, ReferenceBase<?> ref){
|
|
864
|
return makeStandardMapper(valueMap, ref, null);
|
|
865
|
}
|
|
866
|
|
|
867
|
|
|
868
|
private boolean makeStandardMapper(Map<String, Object> valueMap, CdmBase cdmBase, Set<String> omitAttributes){
|
|
869
|
boolean result = true;
|
|
870
|
for (CdmAttributeMapperBase mapper : classMappers){
|
|
871
|
if (mapper instanceof CdmSingleAttributeMapperBase){
|
|
872
|
result &= makeStandardSingleMapper(valueMap, cdmBase, (CdmSingleAttributeMapperBase)mapper, omitAttributes);
|
|
873
|
}else if (mapper instanceof CdmOneToManyMapper){
|
|
874
|
result &= makeMultipleValueAddMapper(valueMap, cdmBase, (CdmOneToManyMapper)mapper, omitAttributes);
|
|
875
|
}else{
|
|
876
|
logger.error("Unknown mapper type");
|
|
877
|
result = false;
|
|
878
|
}
|
|
879
|
}
|
|
880
|
return result;
|
|
881
|
}
|
|
882
|
|
|
883
|
private boolean makeStandardSingleMapper(Map<String, Object> valueMap, CdmBase cdmBase, CdmSingleAttributeMapperBase mapper, Set<String> omitAttributes){
|
|
884
|
boolean result = true;
|
|
885
|
if (omitAttributes == null){
|
|
886
|
omitAttributes = new HashSet<String>();
|
|
887
|
}
|
|
888
|
if (mapper instanceof DbImportExtensionMapper){
|
|
889
|
result &= ((DbImportExtensionMapper)mapper).invoke(valueMap, cdmBase);
|
|
890
|
}else{
|
|
891
|
String sourceAttribute = mapper.getSourceAttributeList().get(0).toLowerCase();
|
|
892
|
Object value = valueMap.get(sourceAttribute);
|
|
893
|
if (value != null){
|
|
894
|
String destinationAttribute = mapper.getDestinationAttribute();
|
|
895
|
if (! omitAttributes.contains(destinationAttribute)){
|
|
896
|
result &= ImportHelper.addValue(value, cdmBase, destinationAttribute, mapper.getTypeClass(), OVERWRITE, OBLIGATORY);
|
|
897
|
}
|
|
898
|
}
|
|
899
|
}
|
|
900
|
return result;
|
|
901
|
}
|
|
902
|
|
|
903
|
|
|
904
|
private boolean makeMultipleValueAddMapper(Map<String, Object> valueMap, CdmBase cdmBase, CdmOneToManyMapper<CdmBase, CdmBase, CdmSingleAttributeMapperBase> mapper, Set<String> omitAttributes){
|
|
905
|
if (omitAttributes == null){
|
|
906
|
omitAttributes = new HashSet<String>();
|
|
907
|
}
|
|
908
|
boolean result = true;
|
|
909
|
String destinationAttribute = mapper.getSingleAttributeName();
|
|
910
|
List<Object> sourceValues = new ArrayList<Object>();
|
|
911
|
List<Class> classes = new ArrayList<Class>();
|
|
912
|
for (CdmSingleAttributeMapperBase singleMapper : mapper.getSingleMappers()){
|
|
913
|
String sourceAttribute = singleMapper.getSourceAttribute();
|
|
914
|
Object value = valueMap.get(sourceAttribute);
|
|
915
|
sourceValues.add(value);
|
|
916
|
Class<?> clazz = singleMapper.getTypeClass();
|
|
917
|
classes.add(clazz);
|
|
918
|
}
|
|
919
|
|
|
920
|
result &= ImportHelper.addMultipleValues(sourceValues, cdmBase, destinationAttribute, classes, NO_OVERWRITE, OBLIGATORY);
|
|
921
|
// //only for testing
|
|
922
|
// if (cdmBase instanceof PublicationBase){
|
|
923
|
// PublicationBase pub = ((PublicationBase)cdmBase);
|
|
924
|
// pub.addPublisher("A new publisher for " + pub.getTitleCache(), "A nice place");
|
|
925
|
// }
|
|
926
|
return result;
|
|
927
|
}
|
|
928
|
|
|
929
|
|
|
930
|
private static TeamOrPersonBase<?> getAuthorTeam(String authorString, TeamOrPersonBase<?> nomAuthor, boolean preferNomeclaturalAuthor){
|
|
931
|
TeamOrPersonBase<?> result;
|
|
932
|
if (preferNomeclaturalAuthor){
|
|
933
|
if (nomAuthor != null){
|
|
934
|
result = nomAuthor;
|
|
935
|
}else{
|
|
936
|
if (CdmUtils.isEmpty(authorString)){
|
|
937
|
result = null;
|
|
938
|
}else{
|
|
939
|
TeamOrPersonBase<?> team = Team.NewInstance();
|
|
940
|
//TODO which one to use??
|
|
941
|
team.setNomenclaturalTitle(authorString);
|
|
942
|
team.setTitleCache(authorString, true);
|
|
943
|
result = team;
|
|
944
|
}
|
|
945
|
}
|
|
946
|
}else{ //prefer bibliographic
|
|
947
|
if (CdmUtils.isNotEmpty(authorString)){
|
|
948
|
TeamOrPersonBase<?> team = Team.NewInstance();
|
|
949
|
//TODO which one to use??
|
|
950
|
team.setNomenclaturalTitle(authorString);
|
|
951
|
team.setTitleCache(authorString, true);
|
|
952
|
result = team;
|
|
953
|
}else{
|
|
954
|
result = nomAuthor;
|
|
955
|
}
|
|
956
|
}
|
|
957
|
return result;
|
|
958
|
}
|
|
959
|
|
|
960
|
|
|
961
|
/**
|
|
962
|
* @param lowerCase
|
|
963
|
* @param config
|
|
964
|
* @return
|
|
965
|
*/
|
|
966
|
public Set<String> getObligatoryAttributes(boolean lowerCase, BerlinModelImportConfigurator config){
|
|
967
|
Set<String> result = new HashSet<String>();
|
|
968
|
Class<ICdmIO>[] ioClassList = config.getIoClassList();
|
|
969
|
logger.warn("getObligatoryAttributes has been commented because it still needs to be adapted to the new package structure");
|
|
970
|
result.addAll(Arrays.asList(unclearMappers));
|
|
971
|
result.addAll(Arrays.asList(createdAndNotesAttributes));
|
|
972
|
result.addAll(Arrays.asList(operationalAttributes));
|
|
973
|
CdmIoMapping mapping = new CdmIoMapping();
|
|
974
|
for (CdmAttributeMapperBase mapper : classMappers){
|
|
975
|
mapping.addMapper(mapper);
|
|
976
|
}
|
|
977
|
result.addAll(mapping.getSourceAttributes());
|
|
978
|
if (lowerCase){
|
|
979
|
Set<String> lowerCaseResult = new HashSet<String>();
|
|
980
|
for (String str : result){
|
|
981
|
if (str != null){lowerCaseResult.add(str.toLowerCase());}
|
|
982
|
}
|
|
983
|
result = lowerCaseResult;
|
|
984
|
}
|
|
985
|
return result;
|
|
986
|
}
|
|
987
|
|
|
988
|
/* (non-Javadoc)
|
|
989
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
|
|
990
|
*/
|
|
991
|
@Override
|
|
992
|
protected boolean doCheck(BerlinModelImportState state){
|
|
993
|
BerlinModelReferenceImportValidator validator = new BerlinModelReferenceImportValidator();
|
|
994
|
return validator.validate(state, this);
|
|
995
|
}
|
|
996
|
|
|
997
|
|
|
998
|
/* (non-Javadoc)
|
|
999
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
|
|
1000
|
*/
|
|
1001
|
@Override
|
|
1002
|
protected String getTableName() {
|
|
1003
|
return dbTableName;
|
|
1004
|
}
|
|
1005
|
|
|
1006
|
/* (non-Javadoc)
|
|
1007
|
* @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
|
|
1008
|
*/
|
|
1009
|
@Override
|
|
1010
|
public String getPluralString() {
|
|
1011
|
return pluralString;
|
|
1012
|
}
|
|
1013
|
|
|
1014
|
/* (non-Javadoc)
|
|
1015
|
* @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
|
|
1016
|
*/
|
|
1017
|
protected boolean isIgnore(BerlinModelImportState state){
|
|
1018
|
return (state.getConfig().getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
|
|
1019
|
}
|
|
1020
|
|
|
1021
|
|
|
1022
|
|
|
1023
|
|
|
1024
|
}
|