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.common.utils;

import java.util.Arrays;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Optional;

import java.util.Set;

import java.util.UUID;

import java.util.function.Predicate;

import org.apache.log4j.Logger;

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

import eu.etaxonomy.cdm.api.service.IService;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

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

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.CdmBase;

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

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

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

import eu.etaxonomy.cdm.model.name.HybridRelationship;

import eu.etaxonomy.cdm.model.name.INonViralName;

import eu.etaxonomy.cdm.model.name.TaxonName;

import eu.etaxonomy.cdm.model.occurrence.Collection;

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

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

import eu.etaxonomy.cdm.strategy.match.DefaultMatchStrategy;

import eu.etaxonomy.cdm.strategy.match.IMatchStrategyEqual;

import eu.etaxonomy.cdm.strategy.match.MatchException;

import eu.etaxonomy.cdm.strategy.match.MatchMode;

/**

 * Helper class for deduplicating authors, references, names, etc.

 * during import.

 *

 * @author a.mueller

 * @since 11.02.2017

 */

public class ImportDeduplicationHelper<STATE extends ImportStateBase> {

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

    private ICdmRepository repository;

    boolean referenceMapIsInitialized = false;

    boolean nameMapIsInitialized = false;

    boolean agentMapIsInitialized = false;

    boolean copyrightMapIsInitialized = false;

    boolean collectionMapIsInitialized = false;

    private Map<String, Set<Reference>> refMap = new HashMap<>();

    private Map<String, Set<Team>> teamMap = new HashMap<>();

    private Map<String, Set<Person>> personMap = new HashMap<>();

    private Map<String, Institution> institutionMap = new HashMap<>();

    //using titleCache

    private Map<String, Set<INonViralName>> nameMap = new HashMap<>();

    private Map<String, Set<Rights>> copyrightMap = new HashMap<>();

    private Map<String, Set<Collection>> collectionMap = new HashMap<>();

    private IMatchStrategyEqual referenceMatcher = DefaultMatchStrategy.NewInstance(Reference.class);

//    private IMatchStrategy collectionMatcher = DefaultMatchStrategy.NewInstance(Collection.class);

    private IMatchStrategyEqual nameMatcher = DefaultMatchStrategy.NewInstance(TaxonName.class);

    private IMatchStrategyEqual personMatcher = DefaultMatchStrategy.NewInstance(Person.class);

    private IMatchStrategyEqual teamMatcher = DefaultMatchStrategy.NewInstance(Team.class);

 // ************************** FACTORY *******************************/

     public static ImportDeduplicationHelper<?> NewInstance(ICdmRepository repository){

         return new ImportDeduplicationHelper<>(repository);

     }

     public static ImportDeduplicationHelper<?> NewStandaloneInstance(){

         return new ImportDeduplicationHelper<>(null);

     }

     /**

      * @param repository

      * @param state not used, only for correct casting of generics

      * @return

      */

     public static <STATE extends ImportStateBase<?,?>> ImportDeduplicationHelper<STATE> NewInstance(ICdmRepository repository, STATE state){

         return new ImportDeduplicationHelper<>(repository);

     }

 // ************************ CONSTRUCTOR *****************************/

     public ImportDeduplicationHelper(ICdmRepository repository) {

         this.repository = repository;

         if (repository == null){

             logger.warn("Repository is null. Deduplication does not work against database");

         }

         try {

             referenceMatcher.setMatchMode("title", MatchMode.EQUAL);

             teamMatcher.setMatchMode("nomenclaturalTitle", MatchMode.EQUAL_OR_SECOND_NULL);

         } catch (MatchException e) {

             throw new RuntimeException(e);  //should not happen

         }

     }

    public ImportDeduplicationHelper() {

        this(null);

    }

    public void restartSession(){

        restartSession(repository, null);

    }

    public void restartSession(ICdmRepository repository, ImportResult importResult){

        if (repository == null){

            return;

        }

        refMap = refreshSetMap(refMap, (IService)repository.getReferenceService(), importResult);

        personMap = refreshSetMap(personMap, (IService)repository.getAgentService(), importResult);

        teamMap = refreshSetMap(teamMap, (IService)repository.getAgentService(), importResult);

        institutionMap = refreshMap(institutionMap, (IService)repository.getAgentService(), importResult);

        nameMap = refreshSetMap(nameMap, (IService)repository.getNameService(), importResult);

        collectionMap = refreshSetMap(collectionMap, (IService)repository.getCollectionService(), importResult);

        //TODO copyright ?

    }

    private <T extends ICdmBase> Map<String, T> refreshMap(Map<String, T> oldMap,

            IService<T> service, ImportResult importResult) {

        Map<String, T> newMap = new HashMap<>();

        for (String key : oldMap.keySet()){

            T old = oldMap.get(key);

            if (old!= null){

                T cdmBase = service.find(old.getUuid());

                if (cdmBase == null){

                    String message = "No cdm object was found for uuid " + old.getUuid() + " of class " + old.getClass().getSimpleName();

                    importResult.addWarning(message);

                }else{

                    newMap.put(key, CdmBase.deproxy(cdmBase));

                }

            }else{

                String message = "Value for key " +  key + " was null in deduplication map";

                importResult.addWarning(message);

            }

        }

        return newMap;

    }

    private <T extends ICdmBase> Map<String, Set<T>> refreshSetMap(Map<String, Set<T>> oldMap,

            IService<T> service, ImportResult importResult) {

        Map<String, Set<T>> newMap = new HashMap<>();

        logger.debug("Start loading map");  //TODO debug only

        //create UUID set

        Set<UUID> uuidSet = new HashSet<>();

        for (String key : oldMap.keySet()){

            Set<T> oldSet = oldMap.get(key);

            for (T item : oldSet){

                UUID uuid = item.getUuid();

                uuidSet.add(uuid);

            }

        }

        //create uuid-item map

        Map<UUID, T> itemMap = new HashMap<>();

        List<T> list = service.find(uuidSet);

        for (T item : list){

            itemMap.put(item.getUuid(), item);

        }

        //refresh

        for (String key : oldMap.keySet()){

            Set<T> oldSet = oldMap.get(key);

            Set<T> newSet = new HashSet<>();

            if (oldSet != null){

                newMap.put(key, newSet);

                for (T item : oldSet){

                    T cdmBase = CdmBase.deproxy(itemMap.get(item.getUuid()));

                    if (cdmBase == null){

                        String message = "No cdm object was found for uuid " + item.getUuid() + " of class " + item.getClass().getSimpleName();

                        importResult.addWarning(message);

                    }else{

                        newSet.add(cdmBase);

                    }

                }

            }else{

                String message = "Value for key " +  key + " was null in deduplication map";

                importResult.addWarning(message);

            }

        }

        return newMap;

    }

//************************ PUTTER / GETTER *****************************/

    //REFERENCES

    private void putReference(String title, Reference ref){

        Set<Reference> refs = refMap.get(title);

        if (refs == null){

            refs = new HashSet<>();

            refMap.put(title, refs);

        }

        refs.add(CdmBase.deproxy(ref));

    }

    private Set<Reference> getReferences(String title){

        return refMap.get(title);

    }

    private Optional<Reference> getMatchingReference(Reference newReference){

        Predicate<Reference> matchFilter = reference ->{

            try {

                return referenceMatcher.invoke(reference, newReference).isSuccessful();

            } catch (MatchException e) {

                throw new RuntimeException(e);

            }

        };

        return Optional.ofNullable(getReferences(newReference.getTitleCache()))

                .orElse(new HashSet<>())

                .stream()

                .filter(matchFilter)

                .findAny();

    }

    // AGENTS

    private void putAgentBase(String title, AgentBase<?> agent){

        if (agent.isInstanceOf(Person.class) ){

            putAgent(title, CdmBase.deproxy(agent, Person.class), personMap);

        }else if (agent.isInstanceOf(Team.class)){

            putAgent(title, CdmBase.deproxy(agent, Team.class), teamMap);

        }else{

//            putAgent(title, CdmBase.deproxy(agent, Institution.class), institutionMap);

            institutionMap.put(title, CdmBase.deproxy(agent, Institution.class));

        }

    }

    //put agent

    private <T extends AgentBase> void putAgent(String title, T agent, Map<String, Set<T>> map){

        Set<T> items = map.get(title);

        if (items == null){

            items = new HashSet<>();

            map.put(title, items);

        }

        items.add(CdmBase.deproxy(agent));

    }

    private Optional<Person> getMatchingPerson(Person newPerson){

        Person newPersonDeproxy = CdmBase.deproxy(newPerson);

        Predicate<Person> matchFilter = (person) ->{

            try {

                return personMatcher.invoke(person, newPersonDeproxy).isSuccessful();

            } catch (MatchException e) {

                throw new RuntimeException(e);

            }

        };

        return Optional.ofNullable(getPersons(newPerson.getTitleCache()))

                .orElse(new HashSet<>())

                .stream()

                .filter(matchFilter)

                .findAny();

    }

    private <T extends TeamOrPersonBase<?>> T getTeamOrPerson(T agent){

        T result = agent;

        if (agent.isInstanceOf(Person.class)){

            result = (T)getMatchingPerson(CdmBase.deproxy(agent, Person.class)).orElse(null) ; // personMap.get(title);

        }else if (agent.isInstanceOf(Team.class)) {

            result = (T)getMatchingTeam(CdmBase.deproxy(agent, Team.class)).orElse(null); // teamMap.get(title);

        }

        return result;

    }

    private Optional<Team> getMatchingTeam(Team newTeam){

        Team newTeamDeproxy = CdmBase.deproxy(newTeam);

        Predicate<Team> matchFilter = (team) ->{

            try {

                return teamMatcher.invoke(team, newTeamDeproxy).isSuccessful();

            } catch (MatchException e) {

                throw new RuntimeException(e);

            }

        };

        //TODO better adapt matching strategy

//        newTeam.getNomenclaturalTitle();

        return Optional.ofNullable(getTeams(newTeam.getTitleCache()))

                .orElse(new HashSet<>())

                .stream()

                .filter(matchFilter)

                .findAny();

    }

    private Set<Person> getPersons(String title){

        return personMap.get(title);

    }

    private Set<Team> getTeams(String title){

        return teamMap.get(title);

    }

    //NAMES

    private void putName(String title, INonViralName name){

        Set<INonViralName> names = nameMap.get(title);

        if (names == null){

            names = new HashSet<>();

            nameMap.put(title, names);

        }

        names.add(CdmBase.deproxy(name));

    }

    private Set<INonViralName> getNames(String title){

        return nameMap.get(title);

    }

    private Optional<INonViralName> getMatchingName(INonViralName existing){

        Predicate<INonViralName> matchFilter = name ->{

            try {

                return nameMatcher.invoke(name, existing).isSuccessful();

            } catch (MatchException e) {

                throw new RuntimeException(e);

            }

        };

        return Optional.ofNullable(getNames(existing.getTitleCache()))

                .orElse(new HashSet<>())

                .stream()

                .filter(matchFilter)

                .findAny();

    }

    //COLLECTIONS

    private void putCollection(String title, Collection collection){

        Set<Collection> collections = collectionMap.get(title);

        if (collections == null){

            collections = new HashSet<>();

            collectionMap.put(title, collections);

        }

        collections.add(CdmBase.deproxy(collection));

    }

    private Set<Collection> getCollections(String title){

        return collectionMap.get(title);

    }

    private Optional<Collection> getMatchingCollections(Collection existing){

        Predicate<Collection> matchFilter = collection ->{

//            try {

                //TODO right Collection matching

                if (CdmUtils.nullSafeEqual(collection.getName(), existing.getName())

                        && CdmUtils.nullSafeEqual(collection.getCode(), existing.getCode())){

                    return true;

                }else{

                    return false;

                }

//                return collectionMatcher.invoke(collection, existing);

//            } catch (MatchException e) {

//                throw new RuntimeException(e);

//            }

        };

        return Optional.ofNullable(getCollections(existing.getTitleCache()))

                .orElse(new HashSet<>())

                .stream()

                .filter(matchFilter)

                .findAny();

    }

// **************************** METHODS *****************************/

    /**

     * This method replaces name authors, nomenclatural reference and

     * nomenclatural reference author by existing authors and references

     * if matching authors or references exist. If not, the given authors

     * and references are added to the map of existing entities.

     *

     * @param state the import state

     * @param name the name with authors and references to replace

     */

    public void replaceAuthorNamesAndNomRef(STATE state,

            INonViralName name) {

        TeamOrPersonBase<?> combAuthor = name.getCombinationAuthorship();

        name.setCombinationAuthorship(getExistingAuthor(state, combAuthor));

        TeamOrPersonBase<?> exAuthor = name.getExCombinationAuthorship();

        name.setExCombinationAuthorship(getExistingAuthor(state, exAuthor));

        TeamOrPersonBase<?> basioAuthor = name.getBasionymAuthorship();

        name.setBasionymAuthorship(getExistingAuthor(state, basioAuthor));

        TeamOrPersonBase<?> exBasioAuthor = name.getExBasionymAuthorship();

        name.setExBasionymAuthorship(getExistingAuthor(state, exBasioAuthor));

        INomenclaturalReference nomRef = name.getNomenclaturalReference();

        if (nomRef != null){

            TeamOrPersonBase<?> refAuthor = nomRef.getAuthorship();

            nomRef.setAuthorship(getExistingAuthor(state, refAuthor));

            Reference existingRef = getExistingReference(state, (Reference)nomRef);

            if (existingRef != null){

                name.setNomenclaturalReference(existingRef);

            }

        }

    }

    /**

     * @param state

     * @param combAuthor

     * @return

     */

    public <T extends TeamOrPersonBase<?>> T getExistingAuthor(STATE state,

            T author) {

        if (author == null){

            return null;

        }else{

            initAgentMap(state);

            initAuthorTitleCaches(author);

            T result = getTeamOrPerson(author);

            if (result == null){

                putAgentBase(author.getTitleCache(), author);

                if (author.isInstanceOf(Team.class)){

                    handleTeam(state, CdmBase.deproxy(author, Team.class));

                }

                result = author;

            }

            return result;

        }

    }

    /**

     * @param author

     */

    private <T extends TeamOrPersonBase<?>> void initAuthorTitleCaches(T author) {

        //more or less copy from CdmPreDataChangeListener

        String nomTitle = author.getNomenclaturalTitle();

        if (author instanceof Team){

            Team team = (Team)author;

            //nomTitle is not necessarily cached when it is created

            team.setNomenclaturalTitle(nomTitle, team.isProtectedNomenclaturalTitleCache());

            String collectorCache = author.getCollectorTitleCache();

            if (! team.isProtectedCollectorTitleCache()){

                team.setCollectorTitleCache(collectorCache, false);

            }

        }else{

            author.setNomenclaturalTitle(nomTitle);

        }

        String titleCache = author.getTitleCache();

        if (! author.isProtectedTitleCache()){

            author.setTitleCache(titleCache, false);

        }

    }

    private void initReferenceCaches(Reference ref) {

        ////TODO better do via matching strategy  (newReference might have caches == null)

        //more or less copy from CdmPreDataChangeListener

        ref.getAbbrevTitleCache();

        ref.getTitleCache();

   }

    public AgentBase<?> getExistingAgent(STATE state,

            AgentBase<?> agent) {

        if (agent == null){

            return null;

        } else if (agent.isInstanceOf(TeamOrPersonBase.class)){

            return getExistingAuthor(state, CdmBase.deproxy(agent, TeamOrPersonBase.class));

        }else{

            initAgentMap(state);

            Institution result = institutionMap.get(agent.getTitleCache());

            if (result == null){

                putAgentBase(agent.getTitleCache(), agent);

                result = CdmBase.deproxy(agent, Institution.class);

            }

            return result;

        }

    }

    @SuppressWarnings("rawtypes")

    private void initAgentMap(STATE state) {

        if (!agentMapIsInitialized && repository != null){

            List<String> propertyPaths = Arrays.asList("");

            List<AgentBase> existingAgents = repository.getAgentService().list(null, null, null, null, propertyPaths);

            for (AgentBase agent : existingAgents){

                putAgentBase(agent.getTitleCache(), CdmBase.deproxy(agent));

            }

            agentMapIsInitialized = true;

        }

    }

    private void handleTeam(STATE state, Team team) {

        List<Person> members = team.getTeamMembers();

        for (int i =0; i< members.size(); i++){

            Person person = CdmBase.deproxy(members.get(i));

            Person existingPerson = getMatchingPerson(person).orElse(null);

            if (existingPerson != null){

                members.set(i, existingPerson);

            }else{

                putAgentBase(person.getTitleCache(), person);

            }

        }

    }

    public Collection getExistingCollection(STATE state, Collection collection) {

        if (collection == null){

            return null;

        }else{

            initCollectionMap(state);

            Collection result = getMatchingCollections(collection).orElse(null);

            if (result == null){

                result = collection;

                putCollection(result.getTitleCache(), result);

            }else{

                if(logger.isDebugEnabled()) {

                    logger.debug("Matches");

                 }

            }

            return result;

        }

    }

    private void initCollectionMap(STATE state) {

        if (!collectionMapIsInitialized && repository != null){

            List<String> propertyPaths = Arrays.asList("");

            List<Collection> existingCollections = repository.getCollectionService().list(null, null, null, null, propertyPaths);

            for (Collection collection : existingCollections){

                putCollection(collection.getTitleCache(), collection);

            }

            collectionMapIsInitialized = true;

        }

    }

   public Reference getExistingReference(STATE state, Reference ref) {

       if (ref == null){

           return null;

       }else{

           initRerenceMap(state);

           initReferenceCaches(ref);

           Reference result = getMatchingReference(ref).orElse(null);

           if (result == null){

               result = ref;

               Reference inRef = result.getInReference();

               if (inRef != null){

                   result.setInReference(getExistingReference(state, result.getInReference()));

               }

               putReference(result.getTitleCache(), result);

           }else{

               if(logger.isDebugEnabled()) {

                   logger.debug("Matches");

                }

           }

           return result;

       }

   }

   private void initRerenceMap(STATE state) {

       if (!referenceMapIsInitialized && repository != null){

           List<String> propertyPaths = Arrays.asList("");

           List<Reference> existingReferences = repository.getReferenceService().list(null, null, null, null, propertyPaths);

           for (Reference ref : existingReferences){

               putReference(ref.getTitleCache(), ref);

           }

           referenceMapIsInitialized = true;

       }

   }

   public <NAME extends INonViralName> NAME getExistingName(STATE state, NAME name) {

       if (name == null){

           return null;

       }else{

           initNameMap(state);

           @SuppressWarnings("unchecked")

           NAME result = (NAME)getMatchingName(name).orElse(null);

           if (result == null){

               result = name;

               Set<HybridRelationship> parentRelations = result.getHybridChildRelations();

               for (HybridRelationship rel : parentRelations){

                   INonViralName parent = rel.getParentName();

                   if (parent != null){

                       rel.setParentName(getExistingName(state, parent));

                   }

               }

               putName(result.getTitleCache(), result);

           }else{

               if(logger.isDebugEnabled()) {

                   logger.debug("Matches");

                }

           }

           return result;

       }

   }

   private void initNameMap(STATE state) {

       if (!nameMapIsInitialized && repository != null){

           List<String> propertyPaths = Arrays.asList("");

           List<TaxonName> existingNames = repository.getNameService().list(null, null, null, null, propertyPaths);

           for (TaxonName name : existingNames){

               putName(name.getTitleCache(), name);

           }

          nameMapIsInitialized = true;

       }

   }

   public Rights getExistingCopyright(STATE state,

           Rights right) {

       if (right == null || !RightsType.COPYRIGHT().equals(right.getType())){

           return null;

       }else{

           initCopyrightMap(state);

           String key = makeCopyrightKey(right);

           Set<Rights> set = copyrightMap.get(key);

           if (set == null || set.isEmpty()){

               putCopyright(key, right);

               return right;

           }else if (set.size()>1){

               //TODO

               logger.warn("More than 1 matching copyright not yet handled for key: " + key);

           }

           return set.iterator().next();

       }

   }

    private void initCopyrightMap(STATE state) {

        if (!copyrightMapIsInitialized && repository != null){

            List<String> propertyPaths = Arrays.asList("");

            List<Rights> existingRights = repository.getRightsService().list(null, null, null, null, propertyPaths);

            for (Rights right : existingRights){

                if (RightsType.COPYRIGHT().equals(right.getType())){

                    putCopyright(makeCopyrightKey(right), right);

                }

            }

            copyrightMapIsInitialized = true;

        }

    }

    private void putCopyright(String key, Rights right) {

        Set<Rights> rights = copyrightMap.get(key);

        if (rights == null){

            rights = new HashSet<>();

            copyrightMap.put(key, rights);

        }

        rights.add(CdmBase.deproxy(right));

    }

    private String makeCopyrightKey(Rights right) {

        if (right.getAgent() != null){

            return right.getAgent().getTitleCache();

        }else if (right.getText() != null){

            return right.getText();

        }else {

            logger.warn("Key for copyright could not be created: " + right);

            return right.getUuid().toString();

        }

    }

}