EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.berlinModel.in;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_ARTICLE;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_BOOK;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_CONFERENCE_PROCEEDINGS;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_DATABASE;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_INFORMAL;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_JOURNAL;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_JOURNAL_VOLUME;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_PART_OF_OTHER_TITLE;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_PRINT_SERIES;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_UNKNOWN;

import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.REF_WEBSITE;

import static eu.etaxonomy.cdm.io.common.ImportHelper.NO_OVERWRITE;

import static eu.etaxonomy.cdm.io.common.ImportHelper.OBLIGATORY;

import static eu.etaxonomy.cdm.io.common.ImportHelper.OVERWRITE;

import java.net.URI;

import java.net.URISyntaxException;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.common.DOI;

import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelReferenceImportValidator;

import eu.etaxonomy.cdm.io.common.ICdmImport;

import eu.etaxonomy.cdm.io.common.IImportConfigurator;

import eu.etaxonomy.cdm.io.common.ImportHelper;

import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;

import eu.etaxonomy.cdm.io.common.Source;

import eu.etaxonomy.cdm.io.common.mapping.CdmAttributeMapperBase;

import eu.etaxonomy.cdm.io.common.mapping.CdmIoMapping;

import eu.etaxonomy.cdm.io.common.mapping.CdmSingleAttributeMapperBase;

import eu.etaxonomy.cdm.io.common.mapping.DbImportExtensionMapper;

import eu.etaxonomy.cdm.io.common.mapping.DbImportMarkerMapper;

import eu.etaxonomy.cdm.io.common.mapping.DbSingleAttributeImportMapperBase;

import eu.etaxonomy.cdm.io.common.mapping.berlinModel.CdmOneToManyMapper;

import eu.etaxonomy.cdm.io.common.mapping.berlinModel.CdmStringMapper;

import eu.etaxonomy.cdm.io.common.mapping.berlinModel.CdmUriMapper;

import eu.etaxonomy.cdm.model.agent.Team;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.common.ExtensionType;

import eu.etaxonomy.cdm.model.common.IdentifiableSource;

import eu.etaxonomy.cdm.model.common.Marker;

import eu.etaxonomy.cdm.model.common.MarkerType;

import eu.etaxonomy.cdm.model.reference.IArticle;

import eu.etaxonomy.cdm.model.reference.IBookSection;

import eu.etaxonomy.cdm.model.reference.IPrintSeries;

import eu.etaxonomy.cdm.model.reference.Reference;

import eu.etaxonomy.cdm.model.reference.ReferenceFactory;

/**

 * @author a.mueller

 * @since 20.03.2008

 */

@Component

public class BerlinModelReferenceImport extends BerlinModelImportBase {

    private static final long serialVersionUID = -3667566958769967591L;

    private static final Logger logger = Logger.getLogger(BerlinModelReferenceImport.class);

	public static final String REFERENCE_NAMESPACE = "Reference";

	private static final String REF_AUTHOR_NAMESPACE = "Reference.refAuthorString";

	public static final UUID REF_DEPOSITED_AT_UUID = UUID.fromString("23ca88c7-ce73-41b2-8ca3-2cb22f013beb");

	public static final UUID REF_SOURCE_UUID = UUID.fromString("d6432582-2216-4b08-b0db-76f6c1013141");

	public static final UUID DATE_STRING_UUID = UUID.fromString("e4130eae-606e-4b0c-be4f-e93dc161be7d");

	public static final UUID IS_PAPER_UUID = UUID.fromString("8a326129-d0d0-4f9d-bbdf-8d86b037c65e");

	private final int modCount = 1000;

	private static final String pluralString = "references";

	private static final String dbTableName = "reference";

	public BerlinModelReferenceImport(){

		super(dbTableName, pluralString);

	}

	protected void initializeMappers(BerlinModelImportState state){

		for (CdmAttributeMapperBase mapper: classMappers){

			if (mapper instanceof DbSingleAttributeImportMapperBase){

				@SuppressWarnings("unchecked")

                DbSingleAttributeImportMapperBase<BerlinModelImportState,Reference> singleMapper =

				        (DbSingleAttributeImportMapperBase<BerlinModelImportState,Reference>)mapper;

				singleMapper.initialize(state, Reference.class);

			}

		}

		return;

	}

	private Set<Integer> commonNameRefSet = null;

	private void initializeCommonNameRefMap(BerlinModelImportState state) throws SQLException{

	    if (state.getConfig().isEuroMed()){

	        commonNameRefSet = new HashSet<>();

	        String queryStr = "SELECT DISTINCT RefFk "

	                + " FROM emCommonName ";

	        ResultSet rs = state.getConfig().getSource().getResultSet(queryStr);

	        while (rs.next()){

	            commonNameRefSet.add(rs.getInt("RefFk"));

	        }

	    }

	}

	protected static CdmAttributeMapperBase[] classMappers = new CdmAttributeMapperBase[]{

		new CdmStringMapper("edition", "edition"),

		new CdmStringMapper("volume", "volume"),

		new CdmStringMapper("publisher", "publisher"),

		new CdmStringMapper("publicationTown", "placePublished"),

		new CdmStringMapper("isbn", "isbn"),

		new CdmStringMapper("isbn", "isbn"),

		new CdmStringMapper("pageString", "pages"),

		new CdmStringMapper("series", "seriesPart"),

		new CdmStringMapper("issn", "issn"),

		new CdmUriMapper("url", "uri"),

		DbImportExtensionMapper.NewInstance("NomStandard", ExtensionType.NOMENCLATURAL_STANDARD()),

		DbImportExtensionMapper.NewInstance("DateString", DATE_STRING_UUID, "Date String", "Date String", "dates"),

		DbImportExtensionMapper.NewInstance("RefDepositedAt", REF_DEPOSITED_AT_UUID, "Ref. deposited at", "Reference is deposited at", "at"),

		DbImportExtensionMapper.NewInstance("RefSource", REF_SOURCE_UUID, "RefSource", "Reference Source", "source"),

		DbImportMarkerMapper.NewInstance("isPaper", IS_PAPER_UUID, "is paper", "is paper", "paper", false)

	};

	protected static String[] operationalAttributes = new String[]{

		"refId", "refCache", "nomRefCache", "preliminaryFlag", "inRefFk", "title", "nomTitleAbbrev",

		"refAuthorString", "nomAuthorTeamFk",

		"refCategoryFk", "thesisFlag", "informalRefCategory", "idInSource"

	};

	protected static String[] createdAndNotesAttributes = new String[]{

			"created_When", "updated_When", "created_Who", "updated_Who", "notes"

	};

	protected static String[] unclearMappers = new String[]{

			/*"isPaper",*/ "exportDate",

	};

	//TODO isPaper

	//

	//type to count the references nomReferences that have been created and saved

	private class RefCounter{

		RefCounter() {refCount = 0;}

		int refCount;

		@Override

        public String toString(){return String.valueOf(refCount) ;};

	}

	@Override

	protected String getRecordQuery(BerlinModelImportConfigurator config) {

		return null;  //not needed

	}

	@Override

	protected void doInvoke(BerlinModelImportState state){

		logger.info("start make " + getPluralString() + " ...");

		boolean success = true;

		initializeMappers(state);

		try {

            initializeCommonNameRefMap(state);

        } catch (SQLException e1) {

            e1.printStackTrace();

            logger.error("Error in initializeCommonNameRefMap in BerlinModelReferenceimport");

        }

		BerlinModelImportConfigurator config = state.getConfig();

		Source source = config.getSource();

		String strSelectId = " SELECT Reference.RefId as refId ";

		String strSelectFull =

			" SELECT Reference.* ,InReference.RefCategoryFk as InRefCategoryFk, RefSource.RefSource " ;

		String strFrom =  " FROM %s  " +

		    	" LEFT OUTER JOIN Reference as InReference ON InReference.refId = Reference.inRefFk " +

				" LEFT OUTER JOIN RefSource ON Reference.RefSourceFk = RefSource.RefSourceId " +

		    	" WHERE (1=1) ";

		String strWherePartitioned = " AND (Reference.refId IN ("+ ID_LIST_TOKEN + ") ) ";

		String referenceTable = CdmUtils.Nz(state.getConfig().getReferenceIdTable());

		referenceTable = referenceTable.isEmpty() ? " Reference"  : referenceTable + " as Reference ";

		String strIdFrom = String.format(strFrom, referenceTable );

		String referenceFilter = CdmUtils.Nz(state.getConfig().getReferenceIdTable());

		if (! referenceFilter.isEmpty()){

			referenceFilter = " AND " + referenceFilter + " ";

		}

		referenceFilter = "";  //don't use it for now

		String strIdQueryFirstPath = strSelectId + strIdFrom ;

		String strIdQuerySecondPath = strSelectId + strIdFrom + " AND (Reference.InRefFk is NOT NULL) ";

//		if (config.getDoReferences() == CONCEPT_REFERENCES){

//			strIdQueryNoInRef += " AND ( Reference.refId IN ( SELECT ptRefFk FROM PTaxon) ) " + referenceFilter;

//		}

		String strRecordQuery = strSelectFull + String.format(strFrom, " Reference ") + strWherePartitioned;

		int recordsPerTransaction = config.getRecordsPerTransaction();

		try{

			//firstPath

			ResultSetPartitioner<BerlinModelImportState> partitioner =

			        ResultSetPartitioner.NewInstance(source, strIdQueryFirstPath, strRecordQuery, recordsPerTransaction);

			while (partitioner.nextPartition()){

				partitioner.doPartition(this, state);

			}

			logger.info("end make references without in-references ... " + getSuccessString(success));

			state.setReferenceSecondPath(true);

//			if (config.getDoReferences() == ALL || config.getDoReferences() == NOMENCLATURAL){

			//secondPath

			partitioner = ResultSetPartitioner.NewInstance(source, strIdQuerySecondPath, strRecordQuery, recordsPerTransaction);

			while (partitioner.nextPartition()){

				partitioner.doPartition(this, state);

			}

			logger.info("end make references with no 1 in-reference ... " + getSuccessString(success));

			state.setReferenceSecondPath(false);

//			}

		} catch (SQLException e) {

			logger.error("SQLException:" +  e);

			state.setUnsuccessfull();

			return;

		}

		logger.info("end make " + getPluralString() + " ... " + getSuccessString(success));

		if (! success){

			state.setUnsuccessfull();

		}

		return;

	}

	@Override

	public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {

        deduplicationHelper.restartSession();

	    if (state.isReferenceSecondPath()){

			return doPartitionSecondPath(partitioner, state);

		}

		boolean success = true;

		Map<Integer, Reference> refToSave = new HashMap<>();

		@SuppressWarnings("unchecked")

        Map<String, Reference> relatedReferences = partitioner.getObjectMap(REFERENCE_NAMESPACE);

		BerlinModelImportConfigurator config = state.getConfig();

		try {

			int i = 0;

			RefCounter refCounter  = new RefCounter();

			ResultSet rs = partitioner.getResultSet();

			//for each resultset

			while (rs.next()){

				if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("References handled: " + (i-1) + " in round -" );}

				success &= makeSingleReferenceRecord(rs, state, partitioner, refToSave, relatedReferences, refCounter);

			} // end resultSet

			//for the concept reference a fixed uuid may be needed -> change uuid

			Integer sourceSecId = (Integer)config.getSourceSecId();

			Reference sec = refToSave.get(sourceSecId);

			if (sec != null){

				sec.setUuid(config.getSecUuid());

				logger.info("SecUuid changed to: " + config.getSecUuid());

			}

			//save and store in map

			logger.info("Save references (" + refCounter.refCount + ")");

			getReferenceService().saveOrUpdate(refToSave.values());

//			logger.info("end makeReferences ..." + getSuccessString(success));;

			return success;

		} catch (SQLException e) {

			logger.error("SQLException:" +  e);

			return false;

		}

	}

	/**

	 * Adds the inReference to the according references.

	 * @param partitioner

	 * @param state

	 * @return

	 */

	private boolean doPartitionSecondPath(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, BerlinModelImportState state) {

		boolean success = true;

		Map<Integer, Reference> refToSave = new HashMap<>();

		@SuppressWarnings("unchecked")

        Map<String, Reference> relatedReferencesMap = partitioner.getObjectMap(REFERENCE_NAMESPACE);

		try {

				int i = 0;

				RefCounter refCounter  = new RefCounter();

				ResultSet rs = partitioner.getResultSet();

				//for each resultset

				while (rs.next()){

					if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("References handled: " + (i-1) + " in round -" );}

					Integer refId = rs.getInt("refId");

					Integer inRefFk = nullSafeInt(rs, "inRefFk");

					if (inRefFk != null){

						Reference thisRef = relatedReferencesMap.get(String.valueOf(refId));

						Reference inRef = relatedReferencesMap.get(String.valueOf(inRefFk));

						if (thisRef != null){

							if (inRef == null){

								logger.warn("No InRef found for nomRef: " + thisRef.getTitleCache() + "; RefId: " +  refId + "; inRefFK: " +  inRefFk);

							}

							thisRef.setInReference(inRef);

							refToSave.put(refId, thisRef);

							if(!thisRef.isProtectedTitleCache()){

							    thisRef.setTitleCache(null);

							    thisRef.getTitleCache();

							}

						}

						if(inRefFk.equals(0)){

						    logger.warn("InRefFk is 0 for refId "+ refId);

						}

					}

				} // end resultSet

				//save and store in map

				logger.info("Save references (" + refCounter.refCount + ")");

				getReferenceService().saveOrUpdate(refToSave.values());

//			}//end resultSetList

//			logger.info("end makeReferences ..." + getSuccessString(success));;

			return success;

		} catch (SQLException e) {

			logger.error("SQLException:" +  e);

			return false;

		}

	}

	@Override

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {

		String nameSpace;

		Class<?> cdmClass;

		Set<String> idSet;

		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<>();

		try{

			Set<String> teamIdSet = new HashSet<>();

			Set<String> referenceIdSet = new HashSet<>();

			Set<String> teamStringSet = new HashSet<>();

			while (rs.next()){

				handleForeignKey(rs, teamIdSet, "NomAuthorTeamFk");

				handleForeignKey(rs, referenceIdSet, "InRefFk");

				handleForeignKey(rs, teamStringSet, "refAuthorString");

				//TODO only needed in second path but state not available here to check if state is second path

				handleForeignKey(rs, referenceIdSet, "refId");

			}

			Set<String> teamStringSet2 = new HashSet<>();

			for (String teamString : teamStringSet){

			    teamStringSet2.add(teamString.replace("'", "´"));

			}

			//team map

			nameSpace = BerlinModelAuthorTeamImport.NAMESPACE;

			cdmClass = Team.class;

			idSet = teamIdSet;

			@SuppressWarnings("unchecked")

            Map<String, Team> teamMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, teamMap);

            //refAuthor map

            nameSpace = REF_AUTHOR_NAMESPACE;

            cdmClass = Team.class;

            idSet = teamStringSet2;

            @SuppressWarnings("unchecked")

            Map<String, Team> refAuthorMap = (Map<String, Team>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

            result.put(nameSpace, refAuthorMap);

			//reference map

			nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;

			cdmClass = Reference.class;

			idSet = referenceIdSet;

			Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, referenceMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	/**

	 * Handles a single reference record

	 * @param rs

	 * @param state

	 * @param biblioRefToSave

	 * @param nomRefToSave

	 * @param relatedBiblioReferences

	 * @param relatedNomReferences

	 * @param refCounter

	 * @return

	 */

	private boolean makeSingleReferenceRecord(

				ResultSet rs,

				BerlinModelImportState state,

				ResultSetPartitioner<BerlinModelImportState> partitioner,

				Map<Integer, Reference> refToSave,

				Map<String, Reference> relatedReferences,

				RefCounter refCounter){

	    boolean success = true;

		Integer refId = null;

		try {

			Map<String, Object> valueMap = getValueMap(rs);

			Integer categoryFk = (Integer)valueMap.get("refCategoryFk".toLowerCase());

			refId = (Integer)valueMap.get("refId".toLowerCase());

			Boolean thesisFlag = (Boolean)valueMap.get("thesisFlag".toLowerCase());

			Reference reference;

			logger.debug("RefCategoryFk: " + categoryFk);

			if (thesisFlag){

				reference = makeThesis(valueMap);

			}else if (categoryFk == REF_JOURNAL){

				reference = makeJournal(valueMap);

			}else if(categoryFk == REF_BOOK){

				reference = makeBook(valueMap);

			}else if(categoryFk == REF_DATABASE){

				reference = makeDatabase(valueMap);

			}else if(categoryFk == REF_INFORMAL){

				reference = makeInformal(valueMap);

			}else if(categoryFk == REF_WEBSITE){

				reference = makeWebSite(valueMap);

			}else if(categoryFk == REF_UNKNOWN){

				reference = makeUnknown(valueMap);

			}else if(categoryFk == REF_PRINT_SERIES){

				reference = makePrintSeries(valueMap);

			}else if(categoryFk == REF_CONFERENCE_PROCEEDINGS){

				reference = makeProceedings(valueMap);

			}else if(categoryFk == REF_ARTICLE){

				reference = makeArticle(valueMap);

			}else if(categoryFk == REF_JOURNAL_VOLUME){

				reference = makeJournalVolume(valueMap);

			}else if(categoryFk == REF_PART_OF_OTHER_TITLE){

				reference = makePartOfOtherTitle(valueMap);

			}else{

				logger.warn("Unknown categoryFk (" + categoryFk + "). Create 'Generic instead'");

				reference = ReferenceFactory.newGeneric();

				success = false;

			}

			//refYear

			String refYear = (String)valueMap.get("refYear".toLowerCase());

			reference.setDatePublished(ImportHelper.getDatePublished(refYear));

			//created, updated, notes

			doCreatedUpdatedNotes(state, reference, rs);

			//idInSource

			String idInSource = (String)valueMap.get("IdInSource".toLowerCase());

			if (isNotBlank(idInSource)){

				IdentifiableSource source = IdentifiableSource.NewDataImportInstance(idInSource);

				source.setIdNamespace("import to Berlin Model");

				reference.addSource(source);

			}

			//nom&BiblioReference  - must be last because a clone is created

			success &= makeNomAndBiblioReference(rs, state, partitioner, refId, reference, refCounter, refToSave);

		} catch (Exception e) {

			logger.warn("Reference with BM refId '" + CdmUtils.Nz(refId) +  "' threw Exception and could not be saved");

			e.printStackTrace();

			success = false;

		}

		return success;

	}

	/**

	 * Creates and saves a nom. reference and a biblio. reference after checking necessity

	 * @param rs

	 * @param refId

	 * @param ref

	 * @param refCounter

	 * @param biblioRefToSave

	 * @param nomRefToSave

	 * @param teamMap

	 * @param stores

	 * @return

	 * @throws SQLException

	 */

	private boolean makeNomAndBiblioReference(

				ResultSet rs,

				BerlinModelImportState state,

				@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner,

				int refId,

				Reference ref,

				RefCounter refCounter,

				Map<Integer, Reference> refToSave

				) throws SQLException{

		@SuppressWarnings("unchecked")

        Map<String, Team> teamMap = partitioner.getObjectMap(BerlinModelAuthorTeamImport.NAMESPACE);

		String refCache = rs.getString("refCache");

		String nomRefCache = rs.getString("nomRefCache");

		String title = rs.getString("title");

		String nomTitleAbbrev = rs.getString("nomTitleAbbrev");

		boolean isPreliminary = rs.getBoolean("PreliminaryFlag");

		String refAuthorString = rs.getString("refAuthorString");

		Integer nomAuthorTeamFk = rs.getInt("NomAuthorTeamFk");

		String strNomAuthorTeamFk = String.valueOf(nomAuthorTeamFk);

		TeamOrPersonBase<?> nomAuthor = teamMap.get(strNomAuthorTeamFk);

		Reference sourceReference = state.getTransactionalSourceReference();

		//preliminary

		if (isPreliminary){

			ref.setAbbrevTitleCache(nomRefCache, true);

			ref.setTitleCache(refCache, true);

		}

		//title/abbrevTitle

		if (isNotBlank(nomTitleAbbrev)){

			ref.setAbbrevTitle(nomTitleAbbrev);

		}

		if (isNotBlank(title)){

			ref.setTitle(title);

		}

		//author

		TeamOrPersonBase<?> author = getAuthorship(state, refAuthorString, nomAuthor);

		ref.setAuthorship(author);

		//save

		if (! refToSave.containsKey(refId)){

			refToSave.put(refId, ref);

		}else{

			logger.warn("Duplicate refId in Berlin Model database. Second reference was not imported !!");

		}

		refCounter.refCount++;

		//refId

		ImportHelper.setOriginalSource(ref, sourceReference, refId, REFERENCE_NAMESPACE);

		if (commonNameRefSet != null && commonNameRefSet.contains(refId)){

            ref.addMarker(Marker.NewInstance(MarkerType.COMMON_NAME_REFERENCE(), true));

        }

		return true;

	}

	/**

	 * Copies the created and updated information from the nomReference to the cloned bibliographic reference

	 * @param referenceBase

	 * @param nomReference

	 */

	private void copyCreatedUpdated(Reference biblioReference, Reference nomReference) {

		biblioReference.setCreatedBy(nomReference.getCreatedBy());

		biblioReference.setCreated(nomReference.getCreated());

		biblioReference.setUpdatedBy(nomReference.getUpdatedBy());

		biblioReference.setUpdated(nomReference.getUpdated());

	}

	private Reference makeArticle (Map<String, Object> valueMap){

		IArticle article = ReferenceFactory.newArticle();

		Object inRefFk = valueMap.get("inRefFk".toLowerCase());

		Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());

		Integer refId = (Integer)valueMap.get("refId".toLowerCase());

		if (inRefFk != null){

			if (inRefCategoryFk != REF_JOURNAL){

				logger.warn("Wrong inrefCategory for Article (refID = " + refId +"). Type must be 'Journal' but was not (RefCategoryFk=" + inRefCategoryFk + "))." +

					" InReference was added anyway! ");

			}

		}else{

			logger.warn ("Article has no inreference: " + refId);

		}

		makeStandardMapper(valueMap, (Reference)article); //url, pages, series, volume

		String url = (String)valueMap.get("url");

		if (url != null && url.contains("dx.doi.org")){

		    article.setDoi(DOI.fromString(url));

		    article.setUri(null);

		}

		return (Reference)article;

	}

	private Reference makePartOfOtherTitle (Map<String, Object> valueMap){

		Reference result;

		Object inRefFk = valueMap.get("inRefFk".toLowerCase());

		Integer inRefCategoryFk = (Integer)valueMap.get("inRefCategoryFk".toLowerCase());

		Integer refId = (Integer)valueMap.get("refId".toLowerCase());

		if (inRefCategoryFk == null){

			//null -> error

			logger.warn("Part-Of-Other-Title has no inRefCategoryFk! RefId = " + refId + ". ReferenceType set to Generic.");

			result = makeUnknown(valueMap);

		}else if (inRefFk == null){

			//TODO is this correct ??

			logger.warn("Part-Of-Other-Title has no in reference: " + refId);

			result = makeUnknown(valueMap);

		}else if (inRefCategoryFk == REF_BOOK){

			//BookSection

			IBookSection bookSection = ReferenceFactory.newBookSection();

			result = (Reference)bookSection;

		}else if (inRefCategoryFk == REF_ARTICLE){

			//Article

			logger.info("Reference (refId = " + refId + ") of type 'part_of_other_title' is part of 'article'." +

					" We use the section reference type for such in references now.") ;

			result = ReferenceFactory.newSection();

		}else if (inRefCategoryFk == REF_JOURNAL){

			//TODO

			logger.warn("Reference (refId = " + refId + ") of type 'part_of_other_title' has inReference of type 'journal'." +

					" This is not allowed! Generic reference created instead") ;

			result = ReferenceFactory.newGeneric();

			result.addMarker(Marker.NewInstance(MarkerType.TO_BE_CHECKED(), true));

		}else if (inRefCategoryFk == REF_PART_OF_OTHER_TITLE){

			logger.info("Reference (refId = " + refId + ") of type 'part_of_other_title' has inReference 'part of other title'." +

					" This is allowed, but may be true only for specific cases (e.g. parts of book chapters). You may want to check if this is correct") ;

			result = ReferenceFactory.newSection();

		}else{

			logger.warn("InReference type (catFk = " + inRefCategoryFk + ") of part-of-reference not recognized for refId " + refId + "." +

				" Create 'Generic' reference instead");

			result = ReferenceFactory.newGeneric();

		}

		makeStandardMapper(valueMap, result); //url, pages

		return result;

	}

	/**

	 * @param inRefFkInt

	 * @param biblioRefToSave

	 * @param nomRefToSave

	 * @param relatedBiblioReferences

	 * @param relatedNomReferences

	 * @return

	 */

	private boolean existsInMapOrToSave(Integer inRefFkInt, Map<Integer, Reference> refToSave, Map<String, Reference> relatedReferences) {

		boolean result = false;

		if (inRefFkInt == null){

			return false;

		}

		result |= refToSave.containsKey(inRefFkInt);

		result |= relatedReferences.containsKey(String.valueOf(inRefFkInt));

		return result;

	}

	private Reference makeWebSite(Map<String, Object> valueMap){

		if (logger.isDebugEnabled()){logger.debug("RefType 'Website'");}

		Reference webPage = ReferenceFactory.newWebPage();

		makeStandardMapper(valueMap, webPage); //placePublished, publisher

		return webPage;

	}

	private Reference makeUnknown(Map<String, Object> valueMap){

		if (logger.isDebugEnabled()){logger.debug("RefType 'Unknown'");}

		Reference generic = ReferenceFactory.newGeneric();

//		generic.setSeries(series);

		makeStandardMapper(valueMap, generic); //pages, placePublished, publisher, series, volume

		return generic;

	}

	private Reference makeInformal(Map<String, Object> valueMap){

		if (logger.isDebugEnabled()){logger.debug("RefType 'Informal'");}

		Reference generic = ReferenceFactory.newGeneric();

//		informal.setSeries(series);

		makeStandardMapper(valueMap, generic);//editor, pages, placePublished, publisher, series, volume

		String informal = (String)valueMap.get("InformalRefCategory".toLowerCase());

		if (isNotBlank(informal) ){

			generic.addExtension(informal, ExtensionType.INFORMAL_CATEGORY());

		}

		return generic;

	}

	private Reference makeDatabase(Map<String, Object> valueMap){

		if (logger.isDebugEnabled()){logger.debug("RefType 'Database'");}

		Reference database =  ReferenceFactory.newDatabase();

		makeStandardMapper(valueMap, database); //?

		return database;

	}

	private Reference makeJournal(Map<String, Object> valueMap){

		if (logger.isDebugEnabled()){logger.debug("RefType 'Journal'");}

		Reference journal = ReferenceFactory.newJournal();

		Set<String> omitAttributes = new HashSet<>();

		String series = "series";

//		omitAttributes.add(series);

		makeStandardMapper(valueMap, journal, omitAttributes); //issn,placePublished,publisher

//		if (valueMap.get(series) != null){

//			logger.warn("Series not yet implemented for journal!");

//		}

		return journal;

	}

	private Reference makeBook(

				Map<String, Object> valueMap){

		if (logger.isDebugEnabled()){logger.debug("RefType 'Book'");}

		Reference book = ReferenceFactory.newBook();

		Integer refId = (Integer)valueMap.get("refId".toLowerCase());

		//Set bookAttributes = new String[]{"edition", "isbn", "pages","publicationTown","publisher","volume"};

		Set<String> omitAttributes = new HashSet<>();

		String attrSeries = "series";

//		omitAttributes.add(attrSeries);

		makeStandardMapper(valueMap, book, omitAttributes);

		//Series (as String)

		IPrintSeries printSeries = null;

		if (valueMap.get(attrSeries) != null){

			String series = (String)valueMap.get("title".toLowerCase());

			if (series == null){

				String nomTitle = (String)valueMap.get("nomTitleAbbrev".toLowerCase());

				series = nomTitle;

			}

			printSeries = ReferenceFactory.newPrintSeries(series);

			logger.info("Implementation of printSeries is preliminary");

		}

		//Series (as Reference)

		if (book.getInSeries() != null && printSeries != null){

			logger.warn("Book has series string and inSeries reference. Can not take both. Series string neglected");

		}else{

			book.setInSeries(printSeries);

		}

		book.setEditor(null);

		return book;

	}

	/**

	 * Returns the requested object if it exists in one of both maps. Prefers the refToSaveMap in ambigious cases.

	 * @param inRefFkInt

	 * @param nomRefToSave

	 * @param relatedNomReferences

	 * @return

	 */

	private Reference getReferenceFromMaps(

			int inRefFkInt,

			Map<Integer, Reference> refToSaveMap,

			Map<String, Reference> relatedRefMap) {

		Reference result = null;

		result = refToSaveMap.get(inRefFkInt);

		if (result == null){

			result = relatedRefMap.get(String.valueOf(inRefFkInt));

		}

		return result;

	}

	private Reference makePrintSeries(Map<String, Object> valueMap){