EDIT

/**

* Copyright (C) 2017 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.reference.ris.in;

import java.io.ByteArrayInputStream;

import java.io.InputStreamReader;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

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.common.URI;

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

import eu.etaxonomy.cdm.io.common.utils.ImportDeduplicationHelper;

import eu.etaxonomy.cdm.io.reference.ris.in.RisRecordReader.RisValue;

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;

/**

 * @author a.mueller

 * @since 11.05.2017

 */

@Component

public class RisReferenceImport

        extends CdmImportBase<RisReferenceImportConfigurator, RisReferenceImportState>{

    private static final long serialVersionUID = 7022034669942979722L;

    @SuppressWarnings("unused")

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

    @Override

    protected void doInvoke(RisReferenceImportState state) {

        RisReferenceImportConfigurator config = state.getConfig();

        try {

//            new FileReader(file)

            byte[] data = config.getStream();

            ByteArrayInputStream stream = new ByteArrayInputStream(data);

            InputStreamReader reader = new InputStreamReader(stream, "UTF-8");

            RisRecordReader risReader = new RisRecordReader(state, reader);

            Set<Reference> referencesToSave = new HashSet<>();

            Map<RisReferenceTag, List<RisValue>> next = risReader.readRecord();

            while (next != RisRecordReader.EOF){

                Reference ref;

                String location = "";

                try {

                    location = recordLocation(state, next);

                    ref = handleSingleReference(state, next);

                    Reference existingRef = state.getDeduplicationHelper().getExistingReference(ref);

                    if (existingRef == ref){ //reference does not yet exist so the identical reference has been returned

                        state.getDeduplicationHelper().replaceReferenceRelatedData(ref);

                        referencesToSave.add(ref);

                        if (ref.getInReference() != null){

                            referencesToSave.add(ref.getInReference());

                        }

                    }else{

                        //merge ?

                    }

                } catch (Exception e) {

                    String message = "Unexpected exception during RIS Reference Import";

                    state.getResult().addException(e, message, location);

                }

                next = risReader.readRecord();

            }

            getReferenceService().saveOrUpdate(referencesToSave);

            state.getResult().addNewRecords(Reference.class.getSimpleName(), referencesToSave.size());

        } catch (Exception e) {

            String message = "Unexpected exception during RIS Reference Import";

            state.getResult().addException(e, message);

        }

        //unhandled

        Map<RisReferenceTag, Integer> unhandled = state.getUnhandled();

        for (RisReferenceTag tag : unhandled.keySet()){

            String message = "RIS tag %s (%s) not yet handled. n = %d";

            message = String .format(message, tag.name(), tag.getDescription(), unhandled.get(tag));

            state.getResult().addWarning(message);

        }

    }

    private Reference handleSingleReference(RisReferenceImportState state,

            Map<RisReferenceTag, List<RisValue>> record) {

        //type

        ReferenceType type = makeReferenceType(state, record);

        Reference ref = ReferenceFactory.newReference(type);

        Reference inRef = null;

        if (hasInRef(ref)){

            ReferenceType inRefType =

                    type == ReferenceType.Article ? ReferenceType.Journal:

                    type == ReferenceType.BookSection ? ReferenceType.Book :

                        ReferenceType.Generic;

            inRef = ReferenceFactory.newReference(inRefType);

            ref.setInReference(inRef);

        }

        Reference higherRef = (inRef == null) ? ref : inRef;

        //titles

        handleTitle(state, record, ref, inRef, higherRef);

        //authors

        handleAuthors(state, record, ref, inRef);

        //Date

//        RisValue y1 = getSingleValue(state, record, RisReferenceTag.Y1); //Primary Date

        RisValue py = getSingleValue(state, record, RisReferenceTag.PY);

        RisValue da = getSingleValue(state, record, RisReferenceTag.DA);

        Integer year = makeYear(state, py);

        VerbatimTimePeriod date = makeDate(state, da);

        date = assertDateYear(state, year, date, py);

        ref.setDatePublished(date);

        //TODO y1 not yet handled

        //Note

        RisValue n1 = getSingleValue(state, record, RisReferenceTag.N1); //Note

        if (n1 != null){

            Annotation annotation = Annotation.NewInstance(n1.value, AnnotationType.EDITORIAL(), Language.DEFAULT());

            ref.addAnnotation(annotation);

        }

        //DOI

        handleDoi(state, record, ref);

        //UR

        RisValue ur = getSingleValue(state, record, RisReferenceTag.UR); //URL

        if (ur != null){

            URI uri;

            try {

                String urStr = ur.value;

                uri = URI.create(urStr);

                ref.setUri(uri);

            } catch (Exception e) {

                String message = "URL could not be recognized: " + ur.value;

                state.getResult().addWarning(message, null, ur.location);

            }

        }

        //Pages

        RisValue sp = getSingleValue(state, record, RisReferenceTag.SP);

        RisValue ep = getSingleValue(state, record, RisReferenceTag.EP);

        String pages = CdmUtils.concat("-", sp != null ? sp.value : null, ep != null ? ep.value : null);

        ref.setPages(pages);

        //Volume

        RisValue vl = getSingleValue(state, record, RisReferenceTag.VL);

        RisValue is = getSingleValue(state, record, RisReferenceTag.IS);

        String vol = (vl == null)? "": vl.value + (is != null ? "("+ is.value + ")": "");

        if (inRef != null && inRef.getType() == ReferenceType.Book){

            inRef.setVolume(vol);

        }else{

            ref.setVolume(vol);

        }

        //Publisher

        RisValue pb = getSingleValue(state, record, RisReferenceTag.PB);

        if (pb != null){

            higherRef.setPublisher(pb.value);

        }

        //CY - Place published

        RisValue cy = getSingleValue(state, record, RisReferenceTag.CY);

        if (cy != null){

            higherRef.setPlacePublished(cy.value);

        }

        //Abstract

        RisValue ab = getSingleValue(state, record, RisReferenceTag.AB);

        RisValue n2 = getSingleValue(state, record, RisReferenceTag.N2);

        RisValue abst = assertEqual(state, "Abstract", ab, n2);

        if (abst != null){

            ref.setReferenceAbstract(abst.value);

        }

        //ISSN/ISBN

        RisValue sn = getSingleValue(state, record, RisReferenceTag.SN);

        if (sn != null){

            if (higherRef.getType() == ReferenceType.Journal){

                higherRef.setIssn(sn.value);

            }else{

                higherRef.setIsbn(sn.value);

            }

        }

        //ID

        RisValue id = getSingleValue(state, record, RisReferenceTag.ID);

        String idStr = id != null? id.value: null;

        String recLoc = recordLocation(state, record);

        ref.addImportSource(idStr, null, state.getConfig().getSourceReference(), recLoc);

        if (inRef != null){

            inRef.addImportSource(idStr, null, state.getConfig().getSourceReference(), recLoc);

        }

        //remove

        record.remove(RisReferenceTag.ER);

        record.remove(RisReferenceTag.TY);

        for (RisReferenceTag tag : record.keySet()){

//            String message = "RIS Tag " + tag.name() +  " not yet handled";

//            state.getResult().addWarning(message, record.get(tag).get(0).location);

            state.addUnhandled(tag);

            //TODO add as annotation or extension

        }

        return ref;

    }

    private void handleDoi(RisReferenceImportState state, Map<RisReferenceTag, List<RisValue>> record, Reference ref) {

        RisValue doiVal = getSingleValue(state, record, RisReferenceTag.DO); //Doi

        if (doiVal != null){

            DOI doi;

            try {

                String doiStr = doiVal.value;

                if (doiStr.toLowerCase().startsWith("doi ")){

                    doiStr = doiStr.substring(4).trim();

                }

                doi = DOI.fromString(doiStr);

                ref.setDoi(doi);

            } catch (IllegalArgumentException e) {

                String message = "DOI could not be recognized: " + doiVal.value;

                state.getResult().addWarning(message, null, doiVal.location);

            }

        }

    }

    private void handleTitle(RisReferenceImportState state, Map<RisReferenceTag, List<RisValue>> record, Reference ref,

            Reference inRef, Reference higherRef) {

        //Title

        RisValue t1 = getSingleValue(state, record, RisReferenceTag.T1);

        RisValue ti = getSingleValue(state, record, RisReferenceTag.TI);

        RisValue title = assertEqual(state, "title", t1, ti);

        if (title != null){

            ref.setTitle(title.value);

        }

        //Journal title

        RisValue t2 = getSingleValue(state, record, RisReferenceTag.T2); //Secondary Title (journal title, if applicable)

        if (higherRef.getType() == ReferenceType.Journal){

            RisValue jf = getSingleValue(state, record, RisReferenceTag.JF); //Journal/Periodical name: full format. This is an alphanumeric field of up to 255 characters.

            RisValue jo = getSingleValue(state, record, RisReferenceTag.JO); //Journal/Periodical name: full format. This is an alphanumeric field of up to 255 characters.

            RisValue jf_jo = assertEqual(state, "Journal/Periodical name: full format", jf, jo);

            RisValue journalTitle = assertEqual(state, "Journal title", t2, jf_jo);

            if (journalTitle != null){

                higherRef.setTitle(journalTitle.value);

            }

        }else if (t2 != null && inRef != null){

            inRef.setTitle(t2.value);

        }else if (t2 != null){

            String message = "The tag %s ('%s') exists but the reference type usually has no in-reference."

                    + "This part of the title was neglected: %s";

            message = String.format(message, t2.tag.name(), t2.tag.getDescription(), t2.value);

            state.getResult().addWarning(message, null, t2.location);

        }else if (inRef != null){

            String message = "The reference type typically has an inreference but no secondary title (tag T2) was given.";

            state.getResult().addWarning(message, null, (title != null)? title.location : null);

        }

        //ST  (remove as same as TI or T1), not handled otherwise

        RisValue st = getSingleValue(state, record, RisReferenceTag.ST, false); //Short title

        if (st != null && st.value.equals(ref.getTitle())){

            record.remove(RisReferenceTag.ST);

        }

    }

    private void handleAuthors(RisReferenceImportState state, Map<RisReferenceTag, List<RisValue>> record,

            Reference ref, Reference inRef) {

        List<RisValue> authorList = getListValue(record, RisReferenceTag.AU);

        if (!authorList.isEmpty()){

            TeamOrPersonBase<?> author = makeAuthor(state, authorList);

            ref.setAuthorship(author);

        }

        List<RisValue> secondaryAuthorList = getListValue(record, RisReferenceTag.A2);

        if (!secondaryAuthorList.isEmpty()){

            if (inRef != null){

                if (inRef.getType() != ReferenceType.Journal){

                    TeamOrPersonBase<?> secAuthor = makeAuthor(state, secondaryAuthorList);

                    inRef.setAuthorship(secAuthor);

                }else{

                    String message = "The tag %s ('%s') exists but the in-reference type is 'journal' which typically has no author."

                            + "The secondary author(s) was/were neglected: %s";

                    message = String.format(message, RisReferenceTag.AU.name(), RisReferenceTag.AU.getDescription(), secondaryAuthorList.toString());

                    state.getResult().addWarning(message, null, secondaryAuthorList.get(0).location);

                }

            }else{

                String message = "The tag %s ('%s') exists but the reference type usually has no in-reference."

                        + "The secondary author(s) was/were neglected: %s";

                message = String.format(message, RisReferenceTag.AU.name(), RisReferenceTag.AU.getDescription(), secondaryAuthorList.toString());

                state.getResult().addWarning(message, null, secondaryAuthorList.get(0).location);

            }

        }

    }

    private boolean hasInRef(Reference ref) {

        return ref.getType() == ReferenceType.BookSection || ref.getType() == ReferenceType.Article ;

    }

    private String recordLocation(RisReferenceImportState state,

            Map<RisReferenceTag, List<RisValue>> record) {

        RisValue typeTag = this.getSingleValue(state, record, RisReferenceTag.TY, false);

        RisValue erTag = this.getSingleValue(state, record, RisReferenceTag.ER, false);

        String start = typeTag == null ? "??" : typeTag.location;

        String end = erTag == null ? "??" : erTag.location;

        String result = "line " + CdmUtils.concat(" - ", start, end);

        return result;

    }

    private VerbatimTimePeriod assertDateYear(RisReferenceImportState state, Integer year, VerbatimTimePeriod date, RisValue py) {

        if (year == null && date == null){

            return null;

        }else if (year == null){

            return date;

        }else if (date == null){

            return TimePeriodParser.parseStringVerbatim(String.valueOf(year));

        }else{

            if  (!year.equals(date.getStartYear())){

                if (date.getStartYear() == null){

                    date.setStartYear(year);

                }else if (isNotBlank(date.getFreeText())){

                    date.setStartYear(year);  //does this happen at all?

                    String message = "Year 'PY' and date 'DA' are not consistent. PY is neglected.";

                    state.getResult().addWarning(message, null, py.location);

                    return date;

                }else{

                    String message = "Year 'PY' and date 'DA' are not consistent. DA is used for freetext and PY is used for (start) year.";

                    state.getResult().addWarning(message, null, py.location);

                    return date;

                }

            }

            return date;

        }

    }

    /**

     * If val1 and val2 are both <code>not null</code> and not equal a warning is logged.

     * @return val1 if val1 is not null, val2 otherwise

     */

    private RisValue assertEqual(RisReferenceImportState state, String meaning, RisValue val1, RisValue val2) {

        if (val1 != null && val2 != null && !val1.value.equals(val2.value)){

            String message = "The tags '%s' and '%s' are not equal but have a similar meaning ('%s'). "

                    + "%s was used and %s neglected";

            message = String.format(message, val1.tag.name(), val2.tag.name(), meaning , val1.tag.name(), val2.tag.name());

            state.getResult().addWarning(message, null, val1.location);

        }

        return val1 != null ? val1 : val2;

    }

    private VerbatimTimePeriod makeDate(RisReferenceImportState state, RisValue da) {

        if (da == null){

            return null;

        }

        if (! da.value.matches("([0-9]{4})?(\\/([0-9]{2})?(\\/([0-9]{2})?(\\/.*)?)?)?")){

            String message = "Tag '%s' has incorrect format. Only exactly 'dddd/dd/dd/any text' is allowed (where d is a digit), but was '%s'";

            message = String.format(message, da.tag.name(), da.value);

            state.getResult().addWarning(message, null, da.location);

            return null;

        }

        String[] split = da.value.split("/");

        VerbatimTimePeriod tp = VerbatimTimePeriod.NewVerbatimInstance();

        if (split.length > 0 && isNotBlank(split[0])){

            tp.setStartYear(Integer.valueOf(split[0]));

        }

        if (split.length > 1 && isNotBlank(split[1])){

            tp.setStartMonth(Integer.valueOf(split[1]));

        }

        if (split.length > 2 && isNotBlank(split[2])){

            tp.setStartDay(Integer.valueOf(split[2]));

        }

        if (split.length > 3 && isNotBlank(split[3])){

            List<String> other = Arrays.asList(split).subList(3, split.length);

            String otherStr = CdmUtils.concat("/", other.toArray(new String[other.size()]));

            tp.setFreeText(tp.toString() + " " + otherStr);

        }

        return tp;

    }

    private Integer makeYear(RisReferenceImportState state, RisValue py) {

        if (py == null){

            return null;

        }

        if (py.value.matches("[0-9]{4}")){

            return Integer.valueOf(py.value);

        }else{

            String message = "Tag '%s' has incorrect format. Only exactly 4 digits are allowed, but was '%s'";

            message = String.format(message, py.tag.name(), py.value);

            state.getResult().addWarning(message, null, py.location);

            return null;

        }

    }

    private TeamOrPersonBase<?> makeAuthor(RisReferenceImportState state, List<RisValue> list) {

        if (list.size() == 1){

            return makePerson(state, list.get(0));

        }else{

            Team team = Team.NewInstance();

            for (RisValue value : list){

                team.addTeamMember(makePerson(state, value));

            }

            return team;

        }

    }

    private Person makePerson(RisReferenceImportState state, RisValue risValue) {

        Person person = Person.NewInstance();

        String[] split = risValue.value.split(",");

        if (split.length >= 1){

            person.setFamilyName(split[0].trim());

        }

        if (split.length >= 2){

            String givenNameOrInitial = split[1].trim();

            if (givenNameOrInitial.matches("[A-Za-z]\\.(\\s*[A-Za-z]\\.)*")){

                person.setInitials(givenNameOrInitial);

            }else{

                person.setGivenName(givenNameOrInitial);

            }

        }

        if (split.length >= 3){

            person.setSuffix(split[2].trim());

        }

        return person;

    }

    /**

     * Returns the single value for the given tag

     * and removes the tag from the record.

     * If more than 1 value exists this is logged

     * as a warning.

     */

    private RisValue getSingleValue(RisReferenceImportState state,

            Map<RisReferenceTag, List<RisValue>> record,

            RisReferenceTag tag) {

        return getSingleValue(state, record, tag, true);

    }

    /**

     * Returns the single value for the given tag

     * and removes the tag from the record.

     * If more than 1 value exists this is logged

     * as a warning.

     */

    private RisValue getSingleValue(RisReferenceImportState state,

            Map<RisReferenceTag, List<RisValue>> record,

            RisReferenceTag tag, boolean remove) {

        List<RisValue> list = record.get(tag);

        if (list == null){

            return null;

        }

        assertSingle(state, list, tag);

        if (remove){

            record.remove(tag);

        }

        return list.get(0);

    }

    private List<RisValue> getListValue(Map<RisReferenceTag, List<RisValue>> record,

            RisReferenceTag tag) {

        List<RisValue> list = record.get(tag);

        record.remove(tag);

        if (list == null){

            list = new ArrayList<>();

        }

        return list;

    }

    private void assertSingle(RisReferenceImportState state, List<RisValue> list, RisReferenceTag tag) {

        if (list.size() > 1){

            String message = "There is more than 1 tag '%s' but only 1 tag is supported by RIS format or"

                    + " by the current import implementation.";

            message = String.format(message, tag.name());

            state.getResult().addWarning(message, null, list.get(0).location + "ff");

        }else if (list.isEmpty()){

            state.getResult().addError("A tag list was empty. This should not happen and is a programming code error");

        }

    }

    private ReferenceType makeReferenceType(RisReferenceImportState state,

            Map<RisReferenceTag, List<RisValue>> record) {

        RisReferenceTag tyTag = RisReferenceTag.TY;

        RisValue value = this.getSingleValue(state, record, tyTag, false);

        String typeStr = value.value;

        RisRecordType type = RisRecordType.valueOf(typeStr);

        ReferenceType cdmType = type.getCdmReferenceType();

        return cdmType;

    }

    @Override

    public ImportDeduplicationHelper createDeduplicationHelper(RisReferenceImportState state){

        ImportDeduplicationHelper result = super.createDeduplicationHelper(state);

        result.setMaxCountFullLoad(state.getConfig().getDeduplicationMaxCountForFullLoad());

        return result;

    }

    @Override

    protected boolean doCheck(RisReferenceImportState state) {

        return true;

    }

    @Override

    protected boolean isIgnore(RisReferenceImportState state) {

        return false;

    }

}