EDIT

/**

* Copyright (C) 2019 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.descriptive.owl.in;

import java.net.URI;

import java.util.Arrays;

import java.util.Collections;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import com.hp.hpl.jena.rdf.model.Model;

import com.hp.hpl.jena.rdf.model.Resource;

import com.hp.hpl.jena.rdf.model.Statement;

import eu.etaxonomy.cdm.api.application.ICdmRepository;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.io.descriptive.owl.OwlUtil;

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

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

import eu.etaxonomy.cdm.model.description.Character;

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.description.MeasurementUnit;

import eu.etaxonomy.cdm.model.description.State;

import eu.etaxonomy.cdm.model.description.StatisticalMeasure;

import eu.etaxonomy.cdm.model.media.Media;

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

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

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

import eu.etaxonomy.cdm.model.term.DefinedTerm;

import eu.etaxonomy.cdm.model.term.DefinedTermBase;

import eu.etaxonomy.cdm.model.term.Representation;

import eu.etaxonomy.cdm.model.term.TermNode;

import eu.etaxonomy.cdm.model.term.TermType;

import eu.etaxonomy.cdm.model.term.TermVocabulary;

/**

 * @author pplitzner

 * @since May 26, 2019

 */

public class OwlImportUtil {

    static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(OwlImportUtil.class);

    private static void addFeatureProperties(Feature feature, Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        if(termResource.hasProperty(OwlUtil.propFeatureIsCategorical)){

            feature.setSupportsCategoricalData(termResource.getProperty(OwlUtil.propFeatureIsCategorical).getBoolean());

        }

        if(termResource.hasProperty(OwlUtil.propFeatureIsQuantitative)){

            feature.setSupportsQuantitativeData(termResource.getProperty(OwlUtil.propFeatureIsQuantitative).getBoolean());

        }

        // import measurement units

        Set<MeasurementUnit> measurementUnits = new HashSet<>();

        List<Statement> measurementUnitStatements = termResource.listProperties(OwlUtil.propFeatureHasRecommendedMeasurementUnit).toList();

        for (Statement statement : measurementUnitStatements) {

            Resource measurementUnitResource = model.createResource(statement.getObject().toString());

            MeasurementUnit measurementUnit = findTerm(MeasurementUnit.class, measurementUnitResource, repo, model, state);

            if(measurementUnit==null){

                measurementUnit = MeasurementUnit.NewInstance();

                addTermProperties(measurementUnit, measurementUnitResource, repo, model, state);

            }

            measurementUnits.add(measurementUnit);

        }

        measurementUnits.forEach(unit->feature.addRecommendedMeasurementUnit(unit));

        // import modifier TODO: create entire vocabulary if it cannot be found

        Set<TermVocabulary<DefinedTerm>> modifierVocs = new HashSet<>();

        List<Statement> modifierEnumStatements = termResource.listProperties(OwlUtil.propFeatureHasRecommendedModifierEnumeration).toList();

        for (Statement statement : modifierEnumStatements) {

            Resource modifierEnumResource = model.createResource(statement.getObject().toString());

            TermVocabulary modifierVoc = findVocabulary(modifierEnumResource, repo, model, state);

            if(modifierVoc!=null){

                modifierVocs.add(modifierVoc);

            }

        }

        modifierVocs.forEach(modiferVoc->feature.addRecommendedModifierEnumeration(modiferVoc));

        // import statistical measures

        Set<StatisticalMeasure> statisticalMeasures = new HashSet<>();

        List<Statement> statisticalMeasureStatements = termResource.listProperties(OwlUtil.propFeatureHasRecommendedStatisticalMeasure).toList();

        for (Statement statement : statisticalMeasureStatements) {

            Resource statisticalMeasureResource = model.createResource(statement.getObject().toString());

            StatisticalMeasure statisticalMeasure = findTerm(StatisticalMeasure.class, statisticalMeasureResource, repo, model, state);

            if(statisticalMeasure==null){

                statisticalMeasure = StatisticalMeasure.NewInstance();

                addTermProperties(statisticalMeasure, statisticalMeasureResource, repo, model, state);

            }

            statisticalMeasures.add(statisticalMeasure);

        }

        statisticalMeasures.forEach(statisticalMeasure->feature.addRecommendedStatisticalMeasure(statisticalMeasure));

        // import categorical enums TODO: create entire vocabulary if it cannot be found

        Set<TermVocabulary<State>> stateVocs = new HashSet<>();

        List<Statement> stateVocStatements = termResource.listProperties(OwlUtil.propFeatureHasSupportedCategoricalEnumeration).toList();

        for (Statement statement : stateVocStatements) {

            Resource stateVocResource = model.createResource(statement.getObject().toString());

            TermVocabulary stateVoc = findVocabulary(stateVocResource, repo, model, state);

            if(stateVoc!=null){

                stateVocs.add(stateVoc);

            }

        }

        stateVocs.forEach(stateVoc->feature.addSupportedCategoricalEnumeration(stateVoc));

    }

    static void addCharacterProperties(Character character, Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        addFeatureProperties(character, termResource, repo, model, state);

        // import property

        if(character.getProperty()!=null){

            Statement propertyStatement = termResource.getProperty(OwlUtil.propCharacterHasProperty);

            Resource propertyResource = model.createResource(propertyStatement.getObject().toString());

            TermNode propertyNode = loadNode(propertyResource, repo, model, state);

            if(propertyNode!=null){

                character.setProperty(propertyNode);

            }

            else{

                logger.error("Property not found for character: "+character);

                return;

            }

        }

        // import structure

        if(character.getStructure()!=null){

            Statement structureStatement = termResource.getProperty(OwlUtil.propCharacterHasStructure);

            Resource structureResource = model.createResource(structureStatement.getObject().toString());

            TermNode structureNode = loadNode(structureResource, repo, model, state);

            if(structureNode!=null){

                character.setStructure(structureNode);

            }

            else{

                logger.error("Structure not found for character: "+character);

                return;

            }

        }

        // import structure modifier

        if(character.getStructureModifier()!=null && termResource.hasProperty(OwlUtil.propCharacterHasStructureModfier)){

            Statement structureModifierStatement = termResource.getProperty(OwlUtil.propCharacterHasStructureModfier);

            Resource structureModifierResource = model.createResource(structureModifierStatement.getObject().toString());

            DefinedTerm structureModifier = findTerm(DefinedTerm.class, structureModifierResource, repo, model, state);

            character.setStructureModifier(structureModifier);

        }

    }

    private static void addTermProperties(DefinedTermBase term, Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        term.setUuid(UUID.fromString(termResource.getProperty(OwlUtil.propUuid).getString()));

        // term URI

        String uriString = termResource.hasProperty(OwlUtil.propUri)?termResource.getProperty(OwlUtil.propUri).getString():null;

        if(CdmUtils.isNotBlank(uriString)){

            term.setUri(URI.create(uriString));

        }

        // symbol

        String symbolString = termResource.hasProperty(OwlUtil.propTermSymbol)?termResource.getProperty(OwlUtil.propTermSymbol).getString():null;

        if(CdmUtils.isNotBlank(symbolString)){

            term.setSymbol(symbolString);

        }

        // symbol2

        String symbol2String = termResource.hasProperty(OwlUtil.propTermSymbol2)?termResource.getProperty(OwlUtil.propTermSymbol2).getString():null;

        if(CdmUtils.isNotBlank(symbol2String)){

            term.setSymbol2(symbol2String);

        }

        // idInVocabulary

        String idInVocabularyString = termResource.hasProperty(OwlUtil.propTermIdInVocabulary)?termResource.getProperty(OwlUtil.propTermIdInVocabulary).getString():null;

        if(CdmUtils.isNotBlank(idInVocabularyString)){

            term.setIdInVocabulary(idInVocabularyString);

        }

        // import representations

        Set<Representation> representations = new HashSet<>();

        termResource.listProperties(OwlUtil.propHasRepresentation).forEachRemaining(r->representations.add(OwlImportUtil.createRepresentation(repo, r, model)));

        if(representations.isEmpty()){

            logger.error("No representations found for term: "+termResource.getProperty(OwlUtil.propUuid));

        }

        representations.forEach(rep->term.addRepresentation(rep));

        // import sources

        Set<IdentifiableSource> sources = new HashSet<>();

        termResource.listProperties(OwlUtil.propTermHasSource).forEachRemaining(sourceStatement->sources.add(OwlImportUtil.createSource(sourceStatement, repo, model)));

        sources.forEach(source->term.addSource(source));

        // add import source

        IdentifiableSource importSource = IdentifiableSource.NewDataImportInstance(termResource.getURI());

        importSource.setCitation(state.getConfig().getSourceReference());

        term.addSource(importSource);

    }

    static <T extends DefinedTermBase> T findTerm(Class<T> clazz, Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        UUID termUuid = UUID.fromString(termResource.getProperty(OwlUtil.propUuid).getString());

        List<T> terms = repo.getTermService().find(clazz, Collections.singleton(termUuid));

        if(!terms.isEmpty()){

            return terms.iterator().next();

        }

        return null;

    }

    private static TermVocabulary findVocabulary(Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        UUID termUuid = UUID.fromString(termResource.getProperty(OwlUtil.propUuid).getString());

        return repo.getVocabularyService().find(termUuid);

    }

    private static TermNode loadNode(Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        UUID uuid = UUID.fromString(termResource.getProperty(OwlUtil.propUuid).getString());

        return repo.getTermNodeService().load(uuid, Arrays.asList(new String[]{"term"}) );

    }

    private static Reference findReference(Resource resource, ICdmRepository repo){

        UUID uuid = UUID.fromString(resource.getProperty(OwlUtil.propUuid).getString());

        return repo.getReferenceService().find(uuid);

    }

    static Media findMedia(Resource resource, ICdmRepository repo){

        UUID uuid = UUID.fromString(resource.getProperty(OwlUtil.propUuid).getString());

        return repo.getMediaService().find(uuid);

    }

    static Feature createFeature(Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        Feature feature = findTerm(Feature.class, termResource, repo, model, state);

        if(feature==null){

            feature = Feature.NewInstance();

            addFeatureProperties(feature, termResource, repo, model, state);

        }

        return feature;

    }

    static State createState(Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        State stateTerm = findTerm(State.class, termResource, repo, model, state);

        if(stateTerm==null){

            stateTerm = State.NewInstance();

        }

        return stateTerm;

    }

    private static Character createCharacter(Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        Character character = findTerm(Character.class, termResource, repo, model, state);

        if(character==null){

            character = Character.NewInstance();

        }

        return character;

    }

    static DefinedTermBase createTerm(Resource termResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        TermType termType = TermType.getByKey(termResource.getProperty(OwlUtil.propType).getString());

        DefinedTermBase term = null;

        // create new term

        if(termType.equals(TermType.Feature)){

            term = createFeature(termResource, repo, model, state);

        }

        else if(termType.equals(TermType.State)){

            term = createState(termResource, repo, model, state);

        }

        else if(termType.equals(TermType.Character)){

            term = createCharacter(termResource, repo, model, state);

        }

        else{

            term = DefinedTerm.NewInstance(termType);

        }

        addTermProperties(term, termResource, repo, model, state);

        return term;

    }

    static IdentifiableSource createSource(Statement sourceStatement, ICdmRepository repo, Model model) {

        Resource sourceResource = model.createResource(sourceStatement.getObject().toString());

        String typeString = sourceResource.getProperty(OwlUtil.propSourceType).getString();

        IdentifiableSource source = IdentifiableSource.NewInstance(OriginalSourceType.getByKey(typeString));

        if(sourceResource.hasProperty(OwlUtil.propSourceIdInSource)){

            String idInSource = sourceResource.getProperty(OwlUtil.propSourceIdInSource).getString();

            source.setIdInSource(idInSource);

        }

        // import citation

        List<Statement> citationStatements = sourceResource.listProperties(OwlUtil.propSourceHasCitation).toList();

        if(citationStatements.size()>1){

            logger.error("More than one citations found for source. Choosing one arbitrarily. - "+sourceResource.toString());

        }

        if(!citationStatements.isEmpty()){

            Statement citationStatement = citationStatements.iterator().next();

            Resource citationResource = model.createResource(citationStatement.getObject().toString());

            Reference reference = findReference(citationResource, repo);

            if(reference==null){

                reference = createReference(citationResource, model);

            }

            source.setCitation(reference);

        }

        return source;

    }

    static Reference createReference(Resource citationResource, Model model){

        String titleString = citationResource.getProperty(OwlUtil.propReferenceTitle).getString();

        Reference citation = ReferenceFactory.newGeneric();

        // FIXME setting the UUID leads to org.hibernate.NonUniqueObjectException:

        // A different object with the same identifier value was already associated with the session : [eu.etaxonomy.cdm.model.reference.Reference#12]

//        citation.setUuid(UUID.fromString(citationResource.getProperty(OwlUtil.propUuid).getString()));

        citation.setTitle(titleString);

        return citation;

    }

    static TermVocabulary createVocabulary(Resource vocabularyResource, ICdmRepository repo, Model model, StructureTreeOwlImportState state){

        TermType termType = TermType.getByKey(vocabularyResource.getProperty(OwlUtil.propType).getString());

        // create new vocabulary

        TermVocabulary vocabulary = TermVocabulary.NewInstance(termType);

        vocabulary.setUuid(UUID.fromString(vocabularyResource.getProperty(OwlUtil.propUuid).getString()));

        // voc URI

        String vocUriString = vocabularyResource.hasProperty(OwlUtil.propUri)?vocabularyResource.getProperty(OwlUtil.propUri).getString():null;

        if(CdmUtils.isNotBlank(vocUriString)){

            vocabulary.setUri(URI.create(vocUriString));

        }

        // voc representations

        Set<Representation> vocRepresentations = new HashSet<>();

        vocabularyResource.listProperties(OwlUtil.propHasRepresentation).forEachRemaining(r->vocRepresentations.add(OwlImportUtil.createRepresentation(repo, r, model)));

        if(vocRepresentations.isEmpty()){

            logger.error("No representations found for vocabulary: "+vocabularyResource.getProperty(OwlUtil.propUuid));

        }

        vocRepresentations.forEach(rep->vocabulary.addRepresentation(rep));

        IdentifiableSource importSource = IdentifiableSource.NewDataImportInstance(vocabularyResource.getURI());

        importSource.setCitation(state.getConfig().getSourceReference());

        vocabulary.addSource(importSource);

        return vocabulary;

    }

    static Media createMedia(Resource mediaResource, StructureTreeOwlImportState state){

        URI mediaUri = URI.create(mediaResource.getProperty(OwlUtil.propMediaUri).getString());

        // create new media

        Media media = Media.NewInstance(mediaUri, null, null, null);

        media.setUuid(UUID.fromString(mediaResource.getProperty(OwlUtil.propUuid).getString()));

        if(mediaResource.hasProperty(OwlUtil.propMediaTitle)){

            // TODO: support multiple language titles

            media.putTitle(Language.DEFAULT(), mediaResource.getProperty(OwlUtil.propMediaTitle).getString());

        }

        IdentifiableSource importSource = IdentifiableSource.NewDataImportInstance(mediaResource.getURI());

        importSource.setCitation(state.getConfig().getSourceReference());

        media.addSource(importSource);

        return media;

    }

    static Representation createRepresentation(ICdmRepository repo, Statement repr, Model model) {

        Resource repsentationResource = model.createResource(repr.getObject().toString());

        String languageLabel = repsentationResource.getProperty(OwlUtil.propLanguage).getString();

        UUID languageUuid = UUID.fromString(repsentationResource.getProperty(OwlUtil.propLanguageUuid).getString());

        Language language = Language.getLanguageFromUuid(languageUuid);

        if(language==null){

            language = repo.getTermService().getLanguageByLabel(languageLabel);

        }

        if(language==null){

            language = Language.getDefaultLanguage();

        }

        String abbreviatedLabel = repsentationResource.hasProperty(OwlUtil.propLabelAbbrev)?repsentationResource.getProperty(OwlUtil.propLabelAbbrev).getString():null;

        String plural = repsentationResource.hasProperty(OwlUtil.propLabelPlural)?repsentationResource.getProperty(OwlUtil.propLabelPlural).getString():null;

        String label = repsentationResource.getProperty(OwlUtil.propLabel).getString();

        String description = repsentationResource.hasProperty(OwlUtil.propDescription)?repsentationResource.getProperty(OwlUtil.propDescription).getString():null;

        Representation representation = Representation.NewInstance(description, label, abbreviatedLabel, language);

        representation.setPlural(plural);

        return representation;

    }

}