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/**
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* Copyright (C) 2017 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.reference.ris.in;
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import java.io.ByteArrayInputStream;
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import java.io.InputStreamReader;
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import java.util.ArrayList;
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import java.util.Arrays;
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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 org.apache.log4j.Logger;
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import org.springframework.stereotype.Component;
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import eu.etaxonomy.cdm.common.CdmUtils;
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import eu.etaxonomy.cdm.common.DOI;
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import eu.etaxonomy.cdm.common.URI;
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import eu.etaxonomy.cdm.io.common.CdmImportBase;
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import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper;
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import eu.etaxonomy.cdm.io.reference.ris.in.RisRecordReader.RisValue;
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import eu.etaxonomy.cdm.model.agent.Person;
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import eu.etaxonomy.cdm.model.agent.Team;
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import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
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import eu.etaxonomy.cdm.model.common.Annotation;
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import eu.etaxonomy.cdm.model.common.AnnotationType;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.VerbatimTimePeriod;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
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import eu.etaxonomy.cdm.model.reference.ReferenceType;
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import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
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/**
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* @author a.mueller
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* @since 11.05.2017
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*/
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@Component
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public class RisReferenceImport
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extends CdmImportBase<RisReferenceImportConfigurator, RisReferenceImportState>{
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private static final long serialVersionUID = 7022034669942979722L;
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(RisReferenceImport.class);
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@Override
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protected void doInvoke(RisReferenceImportState state) {
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RisReferenceImportConfigurator config = state.getConfig();
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try {
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// new FileReader(file)
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byte[] data = config.getStream();
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ByteArrayInputStream stream = new ByteArrayInputStream(data);
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InputStreamReader reader = new InputStreamReader(stream, "UTF-8");
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RisRecordReader risReader = new RisRecordReader(state, reader);
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Set<Reference> referencesToSave = new HashSet<>();
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Map<RisReferenceTag, List<RisValue>> next = risReader.readRecord();
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while (next != RisRecordReader.EOF){
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Reference ref;
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String location = "";
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try {
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location = recordLocation(state, next);
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ref = handleSingleReference(state, next);
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Reference existingRef = state.getDeduplicationHelper().getExistingReference(ref);
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if (existingRef == ref){ //reference does not yet exist so the identical reference has been returned
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state.getDeduplicationHelper().replaceReferenceRelatedData(ref);
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referencesToSave.add(ref);
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if (ref.getInReference() != null){
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referencesToSave.add(ref.getInReference());
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}
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}else{
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//merge ?
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}
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} catch (Exception e) {
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String message = "Unexpected exception during RIS Reference Import";
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state.getResult().addException(e, message, location);
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}
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next = risReader.readRecord();
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}
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//TODO handle result counts more generic
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state.getResult().addNewRecords(Reference.class.getSimpleName(), referencesToSave.size());
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for (Reference ref : referencesToSave){
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if (ref.getAuthorship() != null && !ref.getAuthorship().isPersited()){
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TeamOrPersonBase<?> newAuthor = ref.getAuthorship();
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state.getResult().addNewRecord(newAuthor);
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if (newAuthor instanceof Team){
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for (Person member : ((Team)newAuthor).getTeamMembers()){
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if (!member.isPersited()){
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state.getResult().addNewRecord(member);
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}
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}
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}
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}
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}
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getReferenceService().saveOrUpdate(referencesToSave);
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} catch (Exception e) {
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String message = "Unexpected exception during RIS Reference Import";
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state.getResult().addException(e, message);
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}
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//unhandled
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Map<RisReferenceTag, Integer> unhandled = state.getUnhandled();
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for (RisReferenceTag tag : unhandled.keySet()){
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String message = "RIS tag %s (%s) not yet handled. n = %d";
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message = String .format(message, tag.name(), tag.getDescription(), unhandled.get(tag));
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state.getResult().addWarning(message);
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}
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}
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private Reference handleSingleReference(RisReferenceImportState state,
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Map<RisReferenceTag, List<RisValue>> record) {
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//type
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ReferenceType type = makeReferenceType(state, record);
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Reference ref = ReferenceFactory.newReference(type);
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Reference inRef = null;
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if (hasInRef(ref)){
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ReferenceType inRefType =
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type == ReferenceType.Article ? ReferenceType.Journal:
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type == ReferenceType.BookSection ? ReferenceType.Book :
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ReferenceType.Generic;
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inRef = ReferenceFactory.newReference(inRefType);
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ref.setInReference(inRef);
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}
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Reference higherRef = (inRef == null) ? ref : inRef;
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//titles
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handleTitle(state, record, ref, inRef, higherRef);
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//authors
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handleAuthors(state, record, ref, inRef);
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//Date
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// RisValue y1 = getSingleValue(state, record, RisReferenceTag.Y1); //Primary Date
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RisValue py = getSingleValue(state, record, RisReferenceTag.PY);
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RisValue da = getSingleValue(state, record, RisReferenceTag.DA);
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Integer year = makeYear(state, py);
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VerbatimTimePeriod date = makeDate(state, da);
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date = assertDateYear(state, year, date, py);
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ref.setDatePublished(date);
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//TODO y1 not yet handled
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//Note
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RisValue n1 = getSingleValue(state, record, RisReferenceTag.N1); //Note
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if (n1 != null){
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Annotation annotation = Annotation.NewInstance(n1.value, AnnotationType.EDITORIAL(), Language.DEFAULT());
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ref.addAnnotation(annotation);
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}
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//DOI
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handleDoi(state, record, ref);
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//UR
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RisValue ur = getSingleValue(state, record, RisReferenceTag.UR); //URL
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if (ur != null){
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URI uri;
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try {
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String urStr = ur.value;
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uri = URI.create(urStr);
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ref.setUri(uri);
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} catch (Exception e) {
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String message = "URL could not be recognized: " + ur.value;
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state.getResult().addWarning(message, null, ur.location);
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}
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}
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//Pages
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RisValue sp = getSingleValue(state, record, RisReferenceTag.SP);
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RisValue ep = getSingleValue(state, record, RisReferenceTag.EP);
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String pages = CdmUtils.concat("-", sp != null ? sp.value : null, ep != null ? ep.value : null);
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ref.setPages(pages);
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//Volume
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RisValue vl = getSingleValue(state, record, RisReferenceTag.VL);
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RisValue is = getSingleValue(state, record, RisReferenceTag.IS);
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String vol = (vl == null)? "": vl.value + (is != null ? "("+ is.value + ")": "");
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if (inRef != null && inRef.getType() == ReferenceType.Book){
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inRef.setVolume(vol);
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}else{
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ref.setVolume(vol);
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}
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//Publisher
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RisValue pb = getSingleValue(state, record, RisReferenceTag.PB);
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if (pb != null){
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higherRef.setPublisher(pb.value);
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}
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//CY - Place published
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RisValue cy = getSingleValue(state, record, RisReferenceTag.CY);
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if (cy != null){
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higherRef.setPlacePublished(cy.value);
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}
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//Abstract
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RisValue ab = getSingleValue(state, record, RisReferenceTag.AB);
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RisValue n2 = getSingleValue(state, record, RisReferenceTag.N2);
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RisValue abst = assertEqual(state, "Abstract", ab, n2);
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if (abst != null){
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ref.setReferenceAbstract(abst.value);
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}
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//ISSN/ISBN
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RisValue sn = getSingleValue(state, record, RisReferenceTag.SN);
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if (sn != null){
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if (higherRef.getType() == ReferenceType.Journal){
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higherRef.setIssn(sn.value);
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}else{
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higherRef.setIsbn(sn.value);
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}
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}
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//ID
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RisValue id = getSingleValue(state, record, RisReferenceTag.ID);
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String idStr = id != null? id.value: null;
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String recLoc = recordLocation(state, record);
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ref.addImportSource(idStr, null, state.getConfig().getSourceReference(), recLoc);
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if (inRef != null){
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inRef.addImportSource(idStr, null, state.getConfig().getSourceReference(), recLoc);
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}
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//remove
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record.remove(RisReferenceTag.ER);
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record.remove(RisReferenceTag.TY);
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for (RisReferenceTag tag : record.keySet()){
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// String message = "RIS Tag " + tag.name() + " not yet handled";
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// state.getResult().addWarning(message, record.get(tag).get(0).location);
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state.addUnhandled(tag);
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//TODO add as annotation or extension
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}
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return ref;
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}
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private void handleDoi(RisReferenceImportState state, Map<RisReferenceTag, List<RisValue>> record, Reference ref) {
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RisValue doiVal = getSingleValue(state, record, RisReferenceTag.DO); //Doi
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if (doiVal != null){
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DOI doi;
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try {
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String doiStr = doiVal.value;
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if (doiStr.toLowerCase().startsWith("doi ")){
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doiStr = doiStr.substring(4).trim();
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}
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doi = DOI.fromString(doiStr);
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ref.setDoi(doi);
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} catch (IllegalArgumentException e) {
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String message = "DOI could not be recognized: " + doiVal.value;
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state.getResult().addWarning(message, null, doiVal.location);
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}
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}
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}
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private void handleTitle(RisReferenceImportState state, Map<RisReferenceTag, List<RisValue>> record, Reference ref,
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Reference inRef, Reference higherRef) {
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//Title
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RisValue t1 = getSingleValue(state, record, RisReferenceTag.T1);
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RisValue ti = getSingleValue(state, record, RisReferenceTag.TI);
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RisValue title = assertEqual(state, "title", t1, ti);
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if (title != null){
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ref.setTitle(title.value);
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}
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//Journal title
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RisValue t2 = getSingleValue(state, record, RisReferenceTag.T2); //Secondary Title (journal title, if applicable)
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if (higherRef.getType() == ReferenceType.Journal){
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RisValue jf = getSingleValue(state, record, RisReferenceTag.JF); //Journal/Periodical name: full format. This is an alphanumeric field of up to 255 characters.
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RisValue jo = getSingleValue(state, record, RisReferenceTag.JO); //Journal/Periodical name: full format. This is an alphanumeric field of up to 255 characters.
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RisValue jf_jo = assertEqual(state, "Journal/Periodical name: full format", jf, jo);
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RisValue journalTitle = assertEqual(state, "Journal title", t2, jf_jo);
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if (journalTitle != null){
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higherRef.setTitle(journalTitle.value);
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}
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}else if (t2 != null && inRef != null){
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inRef.setTitle(t2.value);
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}else if (t2 != null){
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String message = "The tag %s ('%s') exists but the reference type usually has no in-reference."
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+ "This part of the title was neglected: %s";
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message = String.format(message, t2.tag.name(), t2.tag.getDescription(), t2.value);
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state.getResult().addWarning(message, null, t2.location);
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}else if (inRef != null){
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String message = "The reference type typically has an inreference but no secondary title (tag T2) was given.";
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state.getResult().addWarning(message, null, (title != null)? title.location : null);
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}
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//ST (remove as same as TI or T1), not handled otherwise
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RisValue st = getSingleValue(state, record, RisReferenceTag.ST, false); //Short title
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if (st != null && st.value.equals(ref.getTitle())){
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record.remove(RisReferenceTag.ST);
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}
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}
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private void handleAuthors(RisReferenceImportState state, Map<RisReferenceTag, List<RisValue>> record,
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Reference ref, Reference inRef) {
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List<RisValue> authorList = getListValue(record, RisReferenceTag.AU);
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if (!authorList.isEmpty()){
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TeamOrPersonBase<?> author = makeAuthor(state, authorList, record);
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ref.setAuthorship(author);
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}
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List<RisValue> secondaryAuthorList = getListValue(record, RisReferenceTag.A2);
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if (!secondaryAuthorList.isEmpty()){
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if (inRef != null){
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if (inRef.getType() != ReferenceType.Journal){
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TeamOrPersonBase<?> secAuthor = makeAuthor(state, secondaryAuthorList, record);
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inRef.setAuthorship(secAuthor);
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}else{
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String message = "The tag %s ('%s') exists but the in-reference type is 'journal' which typically has no author."
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+ "The secondary author(s) was/were neglected: %s";
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message = String.format(message, RisReferenceTag.AU.name(), RisReferenceTag.AU.getDescription(), secondaryAuthorList.toString());
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state.getResult().addWarning(message, null, secondaryAuthorList.get(0).location);
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}
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}else{
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String message = "The tag %s ('%s') exists but the reference type usually has no in-reference."
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+ "The secondary author(s) was/were neglected: %s";
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message = String.format(message, RisReferenceTag.AU.name(), RisReferenceTag.AU.getDescription(), secondaryAuthorList.toString());
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state.getResult().addWarning(message, null, secondaryAuthorList.get(0).location);
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}
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}
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}
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private boolean hasInRef(Reference ref) {
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return ref.getType() == ReferenceType.BookSection || ref.getType() == ReferenceType.Article ;
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}
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private String recordLocation(RisReferenceImportState state,
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Map<RisReferenceTag, List<RisValue>> record) {
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RisValue typeTag = this.getSingleValue(state, record, RisReferenceTag.TY, false);
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RisValue erTag = this.getSingleValue(state, record, RisReferenceTag.ER, false);
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String start = typeTag == null ? "??" : typeTag.location;
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String end = erTag == null ? "??" : erTag.location;
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String result = CdmUtils.concat(" - ", start, end);
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return result;
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}
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private VerbatimTimePeriod assertDateYear(RisReferenceImportState state, Integer year, VerbatimTimePeriod date, RisValue py) {
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if (year == null && date == null){
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return null;
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}else if (year == null){
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return date;
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}else if (date == null){
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return TimePeriodParser.parseStringVerbatim(String.valueOf(year));
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}else{
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if (!year.equals(date.getStartYear())){
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if (date.getStartYear() == null){
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date.setStartYear(year);
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}else if (isNotBlank(date.getFreeText())){
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date.setStartYear(year); //does this happen at all?
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String message = "Year 'PY' and date 'DA' are not consistent. PY is neglected.";
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state.getResult().addWarning(message, null, py.location);
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return date;
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}else{
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String message = "Year 'PY' and date 'DA' are not consistent. DA is used for freetext and PY is used for (start) year.";
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state.getResult().addWarning(message, null, py.location);
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return date;
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}
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}
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return date;
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}
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}
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379
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/**
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* If val1 and val2 are both <code>not null</code> and not equal a warning is logged.
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* @return val1 if val1 is not null, val2 otherwise
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*/
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private RisValue assertEqual(RisReferenceImportState state, String meaning, RisValue val1, RisValue val2) {
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if (val1 != null && val2 != null && !val1.value.equals(val2.value)){
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String message = "The tags '%s' and '%s' are not equal but have a similar meaning ('%s'). "
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+ "%s was used and %s neglected";
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message = String.format(message, val1.tag.name(), val2.tag.name(), meaning , val1.tag.name(), val2.tag.name());
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state.getResult().addWarning(message, null, val1.location);
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}
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return val1 != null ? val1 : val2;
|
391
|
}
|
392
|
|
393
|
private VerbatimTimePeriod makeDate(RisReferenceImportState state, RisValue da) {
|
394
|
if (da == null){
|
395
|
return null;
|
396
|
}
|
397
|
if (! da.value.matches("([0-9]{4})?(\\/([0-9]{2})?(\\/([0-9]{2})?(\\/.*)?)?)?")){
|
398
|
String message = "Tag '%s' has incorrect format. Only exactly 'dddd/dd/dd/any text' is allowed (where d is a digit), but was '%s'";
|
399
|
message = String.format(message, da.tag.name(), da.value);
|
400
|
state.getResult().addWarning(message, null, da.location);
|
401
|
return null;
|
402
|
}
|
403
|
String[] split = da.value.split("/");
|
404
|
VerbatimTimePeriod tp = VerbatimTimePeriod.NewVerbatimInstance();
|
405
|
if (split.length > 0 && isNotBlank(split[0])){
|
406
|
tp.setStartYear(Integer.valueOf(split[0]));
|
407
|
}
|
408
|
if (split.length > 1 && isNotBlank(split[1])){
|
409
|
tp.setStartMonth(Integer.valueOf(split[1]));
|
410
|
}
|
411
|
if (split.length > 2 && isNotBlank(split[2])){
|
412
|
tp.setStartDay(Integer.valueOf(split[2]));
|
413
|
}
|
414
|
if (split.length > 3 && isNotBlank(split[3])){
|
415
|
List<String> other = Arrays.asList(split).subList(3, split.length);
|
416
|
String otherStr = CdmUtils.concat("/", other.toArray(new String[other.size()]));
|
417
|
tp.setFreeText(tp.toString() + " " + otherStr);
|
418
|
}
|
419
|
return tp;
|
420
|
}
|
421
|
|
422
|
private Integer makeYear(RisReferenceImportState state, RisValue py) {
|
423
|
if (py == null){
|
424
|
return null;
|
425
|
}
|
426
|
if (py.value.matches("[0-9]{4}")){
|
427
|
return Integer.valueOf(py.value);
|
428
|
}else{
|
429
|
String message = "Tag '%s' has incorrect format. Only exactly 4 digits are allowed, but was '%s'";
|
430
|
message = String.format(message, py.tag.name(), py.value);
|
431
|
state.getResult().addWarning(message, null, py.location);
|
432
|
return null;
|
433
|
}
|
434
|
}
|
435
|
|
436
|
private TeamOrPersonBase<?> makeAuthor(RisReferenceImportState state, List<RisValue> list, Map<RisReferenceTag, List<RisValue>> record) {
|
437
|
if (list.size() == 1){
|
438
|
return makePerson(state, list.get(0), record);
|
439
|
}else{
|
440
|
Team team = Team.NewInstance();
|
441
|
|
442
|
for (RisValue value : list){
|
443
|
team.addTeamMember(makePerson(state, value, record));
|
444
|
}
|
445
|
|
446
|
//source
|
447
|
String recordLocation = recordLocation(state, record);
|
448
|
team.addImportSource(null, null, state.getConfig().getSourceReference(), recordLocation);
|
449
|
|
450
|
return team;
|
451
|
}
|
452
|
}
|
453
|
|
454
|
private Person makePerson(RisReferenceImportState state, RisValue risValue, Map<RisReferenceTag, List<RisValue>> record) {
|
455
|
Person person = Person.NewInstance();
|
456
|
String[] split = risValue.value.split(",");
|
457
|
if (split.length >= 1){
|
458
|
person.setFamilyName(split[0].trim());
|
459
|
}
|
460
|
if (split.length >= 2){
|
461
|
String givenNameOrInitial = split[1].trim();
|
462
|
if (givenNameOrInitial.matches("[A-Za-z]\\.(\\s*[A-Za-z]\\.)*")){
|
463
|
person.setInitials(givenNameOrInitial);
|
464
|
}else{
|
465
|
person.setGivenName(givenNameOrInitial);
|
466
|
}
|
467
|
}
|
468
|
if (split.length >= 3){
|
469
|
person.setSuffix(split[2].trim());
|
470
|
}
|
471
|
|
472
|
//source
|
473
|
String recordLocation = recordLocation(state, record);
|
474
|
person.addImportSource(null, null, state.getConfig().getSourceReference(), recordLocation);
|
475
|
|
476
|
return person;
|
477
|
}
|
478
|
|
479
|
/**
|
480
|
* Returns the single value for the given tag
|
481
|
* and removes the tag from the record.
|
482
|
* If more than 1 value exists this is logged
|
483
|
* as a warning.
|
484
|
*/
|
485
|
private RisValue getSingleValue(RisReferenceImportState state,
|
486
|
Map<RisReferenceTag, List<RisValue>> record,
|
487
|
RisReferenceTag tag) {
|
488
|
return getSingleValue(state, record, tag, true);
|
489
|
}
|
490
|
|
491
|
/**
|
492
|
* Returns the single value for the given tag
|
493
|
* and removes the tag from the record.
|
494
|
* If more than 1 value exists this is logged
|
495
|
* as a warning.
|
496
|
*/
|
497
|
private RisValue getSingleValue(RisReferenceImportState state,
|
498
|
Map<RisReferenceTag, List<RisValue>> record,
|
499
|
RisReferenceTag tag, boolean remove) {
|
500
|
|
501
|
List<RisValue> list = record.get(tag);
|
502
|
if (list == null){
|
503
|
return null;
|
504
|
}
|
505
|
assertSingle(state, list, tag);
|
506
|
if (remove){
|
507
|
record.remove(tag);
|
508
|
}
|
509
|
return list.get(0);
|
510
|
}
|
511
|
|
512
|
private List<RisValue> getListValue(Map<RisReferenceTag, List<RisValue>> record,
|
513
|
RisReferenceTag tag) {
|
514
|
|
515
|
List<RisValue> list = record.get(tag);
|
516
|
record.remove(tag);
|
517
|
if (list == null){
|
518
|
list = new ArrayList<>();
|
519
|
}
|
520
|
return list;
|
521
|
}
|
522
|
|
523
|
private void assertSingle(RisReferenceImportState state, List<RisValue> list, RisReferenceTag tag) {
|
524
|
if (list.size() > 1){
|
525
|
String message = "There is more than 1 tag '%s' but only 1 tag is supported by RIS format or"
|
526
|
+ " by the current import implementation.";
|
527
|
message = String.format(message, tag.name());
|
528
|
state.getResult().addWarning(message, null, list.get(0).location + "ff");
|
529
|
}else if (list.isEmpty()){
|
530
|
state.getResult().addError("A tag list was empty. This should not happen and is a programming code error");
|
531
|
}
|
532
|
}
|
533
|
|
534
|
private ReferenceType makeReferenceType(RisReferenceImportState state,
|
535
|
Map<RisReferenceTag, List<RisValue>> record) {
|
536
|
RisReferenceTag tyTag = RisReferenceTag.TY;
|
537
|
RisValue value = this.getSingleValue(state, record, tyTag, false);
|
538
|
String typeStr = value.value;
|
539
|
RisRecordType type = RisRecordType.valueOf(typeStr);
|
540
|
ReferenceType cdmType = type.getCdmReferenceType();
|
541
|
return cdmType;
|
542
|
}
|
543
|
|
544
|
@Override
|
545
|
public ImportDeduplicationHelper createDeduplicationHelper(RisReferenceImportState state){
|
546
|
ImportDeduplicationHelper result = super.createDeduplicationHelper(state);
|
547
|
result.setMaxCountFullLoad(state.getConfig().getDeduplicationMaxCountForFullLoad());
|
548
|
return result;
|
549
|
}
|
550
|
|
551
|
@Override
|
552
|
protected boolean doCheck(RisReferenceImportState state) {
|
553
|
return true;
|
554
|
}
|
555
|
|
556
|
@Override
|
557
|
protected boolean isIgnore(RisReferenceImportState state) {
|
558
|
return false;
|
559
|
}
|
560
|
}
|