EDIT

/**

* Copyright (C) 2007 EDIT

* European Distributed Institute of Taxonomy

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

*

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

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

*/

package eu.etaxonomy.cdm.remote.controller;

import java.io.IOException;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import javax.persistence.EntityNotFoundException;

import javax.servlet.http.HttpServletRequest;

import javax.servlet.http.HttpServletResponse;

import org.apache.log4j.Logger;

import org.springframework.beans.factory.annotation.Autowired;

import org.springframework.stereotype.Controller;

import org.springframework.web.bind.WebDataBinder;

import org.springframework.web.bind.annotation.PathVariable;

import org.springframework.web.bind.annotation.RequestMapping;

import org.springframework.web.bind.annotation.RequestMethod;

import org.springframework.web.bind.annotation.RequestParam;

import org.springframework.web.servlet.ModelAndView;

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

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

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

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

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

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

import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;

import eu.etaxonomy.cdm.api.service.config.IncludedTaxonConfiguration;

import eu.etaxonomy.cdm.api.service.dto.FieldUnitDTO;

import eu.etaxonomy.cdm.api.service.dto.IncludedTaxaDTO;

import eu.etaxonomy.cdm.api.service.dto.TaxonRelationshipsDTO;

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.exception.UnpublishedException;

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

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

import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;

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

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

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

import eu.etaxonomy.cdm.model.taxon.Classification;

import eu.etaxonomy.cdm.model.taxon.Synonym;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonBase;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;

import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;

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

import eu.etaxonomy.cdm.persistence.query.OrderHint;

import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder;

import eu.etaxonomy.cdm.remote.controller.util.PagerParameters;

import eu.etaxonomy.cdm.remote.dto.common.StringResultDTO;

import eu.etaxonomy.cdm.remote.editor.TermBasePropertyEditor;

import eu.etaxonomy.cdm.remote.editor.UuidList;

import io.swagger.annotations.Api;

/**

 * TODO write controller documentation

 *

 * @author a.kohlbecker

 * @since 20.07.2009

 *

 */

@Controller

@Api("taxon")

@RequestMapping(value = {"/taxon/{uuid}"})

public class TaxonController extends AbstractIdentifiableController<TaxonBase, ITaxonService>{

    public static final Logger logger = Logger.getLogger(TaxonController.class);

    @Autowired

    private IOccurrenceService occurrenceService;

    @Autowired

    private INameService nameService;

    @Autowired

    private ITaxonNodeService nodeService;

    @Autowired

    private IDescriptionService descriptionService;

    @Autowired

    private ITermService termService;

    protected static final List<String> TAXONNODE_INIT_STRATEGY = Arrays.asList(new String []{

            "taxonNodes.classification","acceptedTaxon.taxonNodes.classification"

    });

    public TaxonController(){

        super();

        setInitializationStrategy(Arrays.asList(new String[]{

                "$",

                "name.nomenclaturalReference"

                }

        ));

    }

    @Override

    @Autowired

    public void setService(ITaxonService service) {

        this.service = service;

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public void initBinder(WebDataBinder binder) {

        super.initBinder(binder);

        binder.registerCustomEditor(MarkerType.class, new TermBasePropertyEditor<>(termService));

    }

    protected List<String> getTaxonDescriptionInitStrategy() {

        return getInitializationStrategy();

    }

    protected List<String> getTaxonDescriptionElementInitStrategy() {

        return getInitializationStrategy();

    }

    @RequestMapping(params="subtree", method = RequestMethod.GET)

    public TaxonBase<?> doGet(@PathVariable("uuid") UUID uuid,

            @RequestParam(value = "subtree", required = true) UUID subtreeUuid,  //if subtree does not exist the base class method is used, therefore required

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        if(request != null) {

            logger.info("doGet() " + requestPathAndQuery(request));

        }

        //TODO do we want to allow Synonyms at all? Maybe needs initialization

        TaxonBase<?> taxonBase = getCdmBaseInstance(uuid, response, TAXONNODE_INIT_STRATEGY);

        //TODO we should move subtree check down to service or persistence

        TaxonNode subtree = getSubtreeOrError(subtreeUuid, nodeService, response);

        taxonBase = checkExistsSubtreeAndAccess(taxonBase, subtree, NO_UNPUBLISHED, response);

        return taxonBase;

    }

    /**

     * Checks if a {@link TaxonBase taxonBase} is public and belongs to a {@link TaxonNode subtree}

     * as accepted taxon or synonym.

     * If not the according {@link HttpStatusMessage http messages} are send to response.

     * <BR>

     * Not (yet) checked is the relation to a subtree via a concept relationship.

     * @param taxonBase

     * @param includeUnpublished

     * @param response

     * @return

     * @throws IOException

     */

    protected <S extends TaxonBase<?>> S checkExistsSubtreeAndAccess(S taxonBase,

            TaxonNode subtree, boolean includeUnpublished,

            HttpServletResponse response) throws IOException {

        taxonBase = checkExistsAndAccess(taxonBase, NO_UNPUBLISHED, response);

        if (subtree == null){

            return taxonBase;

        }else if(taxonBase != null){

            //TODO synonyms maybe can not be initialized

            Taxon taxon = taxonBase.isInstanceOf(Synonym.class)?

                    CdmBase.deproxy(taxonBase, Synonym.class).getAcceptedTaxon():

                    CdmBase.deproxy(taxonBase, Taxon.class);

            //check if taxon has any node that is a descendant of subtree

            for (TaxonNode taxonNode :taxon.getTaxonNodes()){

                if (subtree.isAncestor(taxonNode)){

                    return taxonBase;

                }

            }

            HttpStatusMessage.ACCESS_DENIED.send(response);

        }

        return null;

    }

    /**

     * Get the accepted {@link Taxon} for a given

     * {@link TaxonBase} entity identified by the <code>{taxon-uuid}</code>.

     * <p>

     * URI: <b>&#x002F;{datasource-name}&#x002F;taxon&#x002F;{taxon-uuid}&#x002F;accepted</b>

     *

     * @param request

     * @param response

     * @return a set on a list of {@link Taxon} entities which are initialized

     *         using the following initialization strategy:

     *         {@link #DEFAULT_INIT_STRATEGY}

     * @throws IOException

     */

    @RequestMapping(value = "accepted", method = RequestMethod.GET)

    public Taxon doGetAcceptedFor(

            @PathVariable("uuid") UUID uuid,

            @RequestParam(value = "classificationFilter", required = false) UUID classification_uuid,

            HttpServletRequest request,

            HttpServletResponse response)

            throws IOException {

        if(request != null){

            logger.info("doGetAcceptedFor() " + requestPathAndQuery(request));

        }

        try {

            boolean includeUnpublished = NO_UNPUBLISHED;

            Taxon result = service.findAcceptedTaxonFor(uuid, classification_uuid, includeUnpublished, getInitializationStrategy());

            result = checkExistsAndAccess(result, includeUnpublished, response);

            return result;

        } catch (EntityNotFoundException e){

            HttpStatusMessage.UUID_NOT_FOUND.send(response, e.getMessage());

        } catch (UnpublishedException e) {

            HttpStatusMessage.ACCESS_DENIED.send(response, e.getMessage());

        }

        return null;

    }

    @RequestMapping(value = "classifications", method = RequestMethod.GET)

    public List<Classification> doGetClassifications(

            @PathVariable("uuid") UUID uuid,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        boolean includeUnpublished = NO_UNPUBLISHED;

        logger.info("doGetClassifications(): " + request.getRequestURI());

        TaxonBase<?> taxonBase = service.load(uuid);

        taxonBase = checkExistsAndAccess(taxonBase, includeUnpublished, response);

        return service.listClassifications(taxonBase, null, null, getInitializationStrategy());

    }

    @RequestMapping(value = "taxonNodes", method = RequestMethod.GET)

    public Set<TaxonNode>  doGetTaxonNodes(

            @PathVariable("uuid") UUID taxonUuid,

            @RequestParam(value = "subtree", required = false) UUID subtreeUuid,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        logger.info("doGetTaxonNodes" + requestPathAndQuery(request));

        TaxonBase<?> taxonBase;

        if (subtreeUuid != null){

            taxonBase = doGet(taxonUuid, subtreeUuid, request, response);

        }else{

            taxonBase = service.load(taxonUuid, NO_UNPUBLISHED, TAXONNODE_INIT_STRATEGY);

        }

        if(taxonBase instanceof Taxon){

            return ((Taxon)taxonBase).getTaxonNodes();

        } else {

            HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);

            return null;

        }

    }

    /**

    *

    * See also {@link AgentController#doGetTaxonNodeAgentRelations(UUID, UUID, Integer, Integer, HttpServletRequest, HttpServletResponse)}

    *

    * @param uuid

    * @param classificationUuid

    * @param pageNumber

    * @param pageSize

    * @param request

    * @param response

    * @return

    * @throws IOException

    *

    */

    @RequestMapping(value = "taxonNodeAgentRelations/{classification_uuid}", method = RequestMethod.GET)

    public Pager<TaxonNodeAgentRelation>  doGetTaxonNodeAgentRelations(

            @PathVariable("uuid") UUID uuid,

            @PathVariable("classification_uuid") UUID classificationUuid,

            @RequestParam(value = "relType_uuid" , required = false) UUID relTypeUuid,

            @RequestParam(value = "pageNumber", required = false) Integer pageNumber,

            @RequestParam(value = "pageSize", required = false) Integer pageSize,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);

        pagerParams.normalizeAndValidate(response);

        Pager<TaxonNodeAgentRelation> pager = nodeService.pageTaxonNodeAgentRelations(uuid, classificationUuid,

                null, null, relTypeUuid, pagerParams.getPageSize(), pagerParams.getPageIndex(), null);

        return pager;

    }

    @RequestMapping(value = "specimensOrObservationsCount", method = RequestMethod.GET)

    public StringResultDTO doCountSpecimensOrObservations(

            @PathVariable("uuid") UUID uuid,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        logger.info("doListSpecimensOrObservations() - " + request.getRequestURI());

        List<OrderHint> orderHints = new ArrayList<>();

        orderHints.add(new OrderHint("titleCache", SortOrder.DESCENDING));

        FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();

        config.setAssociatedTaxonUuid(uuid);

        long countSpecimen = occurrenceService.countOccurrences(config);

        return new StringResultDTO(String.valueOf(countSpecimen));

    }

    @RequestMapping(value = "specimensOrObservationDTOs", method = RequestMethod.GET)

    public ModelAndView doListSpecimensOrObservationDTOs(

            @PathVariable("uuid") UUID uuid,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        logger.info("doListSpecimensOrObservations() - " + request.getRequestURI());

        ModelAndView mv = new ModelAndView();

        List<FieldUnitDTO> fieldUnitDtos = occurrenceService.findFieldUnitDTOByAssociatedTaxon(null, uuid);

           // List<SpecimenOrObservationBase<?>> specimensOrObservations = occurrenceService.listByAssociatedTaxon(null, null, (Taxon)tb, null, null, null, orderHints, null);

        mv.addObject(fieldUnitDtos);

        return mv;

    }

    @RequestMapping(value = "specimensOrObservations", method = RequestMethod.GET)

    public ModelAndView doListSpecimensOrObservations(

            @PathVariable("uuid") UUID uuid,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        logger.info("doListSpecimensOrObservations() - " + request.getRequestURI());

        ModelAndView mv = new ModelAndView();

        TaxonBase<?> tb = service.load(uuid);

        List<OrderHint> orderHints = new ArrayList<>();

        orderHints.add(new OrderHint("titleCache", SortOrder.DESCENDING));

        if(tb instanceof Taxon){

            List<SpecimenOrObservationBase<?>> specimensOrObservations = occurrenceService.listByAssociatedTaxon(null, null, (Taxon)tb, null, null, null, orderHints, null);

            mv.addObject(specimensOrObservations);

        } else {

            HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);

            return null;

        }

        return mv;

    }

    @RequestMapping(value = "associatedFieldUnits", method = RequestMethod.GET)

    public Pager<SpecimenOrObservationBase> doGetFieldUnits(

            @PathVariable("uuid") UUID uuid,

            @RequestParam(value = "maxDepth", required = false) Integer maxDepth,

            @RequestParam(value = "pageNumber", required = false) Integer pageNumber,

            @RequestParam(value = "pageSize", required = false) Integer pageSize,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        logger.info("doGetFieldUnits() - " + request.getRequestURI());

        TaxonBase<?> taxonBase = service.load(uuid);

        taxonBase = checkExistsAndAccess(taxonBase, NO_UNPUBLISHED, response);

        List<OrderHint> orderHints = new ArrayList<>();

        orderHints.add(new OrderHint("titleCache", SortOrder.ASCENDING));

        if(taxonBase instanceof Taxon){

            PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);

            pagerParams.normalizeAndValidate(response);

            return occurrenceService.pageFieldUnitsByAssociatedTaxon(null, (Taxon) taxonBase, null, pagerParams.getPageSize(), pagerParams.getPageIndex(), orderHints, null);

        }else{

            return null;

        }

    }

    @RequestMapping(value = "taggedName", method = RequestMethod.GET)

    public ModelAndView doGetTaggedName(

            @PathVariable("uuid") UUID uuid,

            HttpServletRequest request) {

        logger.info("doGetDescriptionElementsByType() - " + request.getRequestURI());

        ModelAndView mv = new ModelAndView();

        TaxonBase<?> tb = service.load(uuid, NO_UNPUBLISHED, Arrays.asList(new String[] {"name"}));

        mv.addObject(nameService.getTaggedName(tb.getName().getUuid()));

        return mv;

    }

    /**

     * This webservice endpoint returns all taxa which are congruent or included in the taxon represented by the given taxon uuid.

     * The result also returns the path to these taxa represented by the uuids of the taxon relationships types and doubtful information.

     * If classificationUuids is set only taxa of classifications are returned which are included in the given classifications.

     * Also the path to these taxa may not include taxa from other classifications.

     *

     * @param taxonUUIDString

     * @param classificationStringList

     * @param includeDoubtful

     * @param onlyCongruent

     * @param response

     * @param request

     * @return

     * @throws IOException

     */

    @RequestMapping(value = { "includedTaxa" }, method = { RequestMethod.GET })

    public IncludedTaxaDTO doGetIncludedTaxa(

            @PathVariable("uuid") UUID uuid,

            @RequestParam(value="classificationFilter", required=false) final List<String> classificationStringList,

            @RequestParam(value="includeDoubtful", required=false) final boolean includeDoubtful,

            @RequestParam(value="onlyCongruent", required=false) final boolean onlyCongruent,

            HttpServletResponse response,

            HttpServletRequest request) throws IOException {

        if(request != null){

            logger.info("doGetIncludedTaxa()" + requestPathAndQuery(request));

        }

        List<UUID> classificationFilter = null;

        if( classificationStringList != null ){

            classificationFilter = new ArrayList<>();

            for(String classString :classificationStringList){

                classificationFilter.add(UUID.fromString(classString));

            }

        }

        IncludedTaxonConfiguration configuration =

                new IncludedTaxonConfiguration(classificationFilter, includeDoubtful, onlyCongruent);

        IncludedTaxaDTO listIncludedTaxa = service.listIncludedTaxa(uuid, configuration);

        return listIncludedTaxa;

    }

    // TODO ================================================================================ //

    // move all description and descriptionElement related methods into the according

    // Description Controllers

    /**

     * Get the list of {@link TaxonDescription}s of the

     * {@link Taxon} instance identified by the <code>{taxon-uuid}</code>.

     * <p>

     * URI: <b>&#x002F;{datasource-name}&#x002F;portal&#x002F;taxon&#x002F;{taxon-uuid}&#x002F;descriptions</b>

     *

     * @param request

     * @param response

     * @return a List of {@link TaxonDescription} entities which are initialized

     *         using the following initialization strategy:

     *         {@link #TAXONDESCRIPTION_INIT_STRATEGY}

     * @throws IOException

     */

    @RequestMapping(

            value = {"descriptions"},

            method = RequestMethod.GET)

    public Pager<TaxonDescription> doGetDescriptions(

            @PathVariable("uuid") UUID uuid,

            @RequestParam(value = "markerTypes", required = false) List<MarkerType> markerTypes,

            HttpServletRequest request,

            HttpServletResponse response)throws IOException {

        if(request != null){

            logger.info("doGetDescriptions()" + requestPathAndQuery(request));

        }

        Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);

        taxon = checkExistsAndAccess(taxon, NO_UNPUBLISHED, response);

        Set<MarkerType> markerTypesSet = new HashSet<>();

        if (markerTypes != null) {

            markerTypesSet.addAll(markerTypes);

        }

        Pager<TaxonDescription> p = descriptionService.pageTaxonDescriptions(taxon, null, null, markerTypesSet, null, null, getTaxonDescriptionInitStrategy());

        return p;

    }

    @RequestMapping(value = "descriptions/elementsByType/{classSimpleName}", method = RequestMethod.GET)

    public ModelAndView doGetDescriptionElementsByType(

            @PathVariable("uuid") UUID uuid,

            @PathVariable("classSimpleName") String classSimpleName,

            @RequestParam(value = "markerTypes", required = false) List<MarkerType> markerTypes,

            @RequestParam(value = "count", required = false, defaultValue = "false") Boolean doCount,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        logger.info("doGetDescriptionElementsByType() - " + requestPathAndQuery(request));

        boolean includeUnpublished = NO_UNPUBLISHED;

        ModelAndView mv = new ModelAndView();

        List<DescriptionElementBase> allElements = new ArrayList<>();

        List<DescriptionElementBase> elements;

        int count = 0;

        List<String> initStrategy = doCount ? null : getTaxonDescriptionElementInitStrategy();

        Taxon taxon = getCdmBaseInstance(Taxon.class, uuid, response, (List<String>)null);

        taxon = checkExistsAndAccess(taxon, includeUnpublished, response);

        Set<MarkerType> markerTypesSet = new HashSet<>();

        if (markerTypes == null) {

            markerTypesSet.addAll(markerTypes);

        }

        List<TaxonDescription> taxonDescriptions = descriptionService.listTaxonDescriptions(

                taxon, null, null, markerTypesSet, null, null, null);

        try {

            Class type;

            type = Class.forName("eu.etaxonomy.cdm.model.description."

                    + classSimpleName);

            if (taxonDescriptions != null) {

                for (TaxonDescription description : taxonDescriptions) {

                    elements = descriptionService.listDescriptionElements(description, null, type, null, 0, initStrategy);

                    allElements.addAll(elements);

                    count += elements.size();

                }

            }

        } catch (ClassNotFoundException e) {

            HttpStatusMessage.create(e.getLocalizedMessage(), 400).send(response);

        }

        if(doCount){

            mv.addObject(count);

        } else {

            mv.addObject(allElements);

        }

        return mv;

    }

    @RequestMapping(value = "taxonRelationshipsDTO", method = RequestMethod.GET)

    public TaxonRelationshipsDTO doGetTaxonRelationshipsDTO(

            @PathVariable("uuid") UUID taxonUuid,

            @RequestParam(value = "directTypes", required = false) UuidList directTypeUuids,

            @RequestParam(value = "inversTypes", required = false) UuidList inversTypeUuids,

            @RequestParam(value = "direction", required = false) Direction direction,

            @RequestParam(value="groupMisapplications", required=false, defaultValue="false") final boolean groupMisapplications,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

        boolean includeUnpublished = NO_UNPUBLISHED;

        logger.info("doGetTaxonRelationshipDTOs(): " + request.getRequestURI());

        TaxonBase<?> taxonBase = service.load(taxonUuid);

        checkExistsAccessType(taxonBase, includeUnpublished, Taxon.class, response);

        Set<TaxonRelationshipType> directTypes = getTermsByUuidSet(TaxonRelationshipType.class, directTypeUuids);

        Set<TaxonRelationshipType> inversTypes = getTermsByUuidSet(TaxonRelationshipType.class, inversTypeUuids);

//        Set<TaxonRelationshipType> inversTypes = null;

//        if (directTypeUuids != null && !directTypeUuids.isEmpty()){

//            types = new HashSet<>();

//            List<TaxonRelationshipType> typeList = termService.find(TaxonRelationshipType.class, new HashSet<>(directTypeUuids));

//            types.addAll(typeList);

//            //TODO should we handle missing uuids as error response

////            HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);

//        }

//        boolean deduplicateMisapplications = true;

        Integer pageSize = null;

        Integer pageNumber = null;

        return service.listTaxonRelationships(taxonUuid, directTypes, inversTypes, direction, groupMisapplications,

                includeUnpublished, pageSize, pageNumber);

    }

    /**

     * @param directTypeUuids

     * @return

     */

    protected <T extends DefinedTermBase<T>> Set<T> getTermsByUuidSet(Class<T> clazz, UuidList directTypeUuids) {

        Set<T> directTypes = null;

        if (directTypeUuids != null && !directTypeUuids.isEmpty()){

            directTypes = new HashSet<>();

            List<T> typeList = termService.find(clazz, new HashSet<>(directTypeUuids));

            directTypes.addAll(typeList);

            //TODO should we handle missing uuids as error response

//            HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);

        }

        return directTypes;

    }

    // TODO ================================================================================ //

}