EDIT

// $Id$

/**

 * Copyright (C) 2009 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.Collection;

import java.util.EnumSet;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import javax.servlet.http.HttpServletRequest;

import javax.servlet.http.HttpServletResponse;

import org.apache.commons.lang.BooleanUtils;

import org.apache.lucene.queryparser.classic.ParseException;

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

import org.springframework.stereotype.Controller;

import org.springframework.web.bind.WebDataBinder;

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

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

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

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

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

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.TaxaAndNamesSearchMode;

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

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

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

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

import eu.etaxonomy.cdm.api.service.search.LuceneMultiSearchException;

import eu.etaxonomy.cdm.api.service.search.SearchResult;

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.location.NamedArea;

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

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.persistence.query.MatchMode;

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

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

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

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

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

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

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

import io.swagger.annotations.Api;

/**

 * TODO write controller documentation

 *

 * @author a.kohlbecker

 * @date 20.03.2009

 */

@Controller

@Api("taxon")

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

public class TaxonListController extends IdentifiableListController<TaxonBase, ITaxonService> {

    private static final List<String> SIMPLE_TAXON_INIT_STRATEGY = DEFAULT_INIT_STRATEGY;

    protected List<String> getSimpleTaxonInitStrategy() {

        // TODO Auto-generated method stub

        return SIMPLE_TAXON_INIT_STRATEGY;

    }

    /**

     *

     */

    public TaxonListController(){

        super();

        setInitializationStrategy(Arrays.asList(new String[]{"$","name.nomenclaturalReference"}));

    }

    @Override

    @Autowired

    public void setService(ITaxonService service) {

        this.service = service;

    }

    @Autowired

    private IClassificationService classificationService;

    @Autowired

    private ITaxonNodeService taxonNodeService;

    @Autowired

    private ITermService termService;

    @InitBinder

    @Override

    public void initBinder(WebDataBinder binder) {

        super.initBinder(binder);

        binder.registerCustomEditor(DefinedTermBaseList.class, new TermBaseListPropertyEditor<NamedArea>(termService));

        binder.registerCustomEditor(MatchMode.class, new MatchModePropertyEditor());

        binder.registerCustomEditor(Rank.class, new RankPropertyEditor());

    }

    /**

     * Find Taxa, Synonyms, Common Names by name, either globally or in a specific geographic area.

     * <p>

     * URI: <b>taxon&#x002F;search</b>

     *

     * @param query

     *            the string to query for. Since the wildcard character '*'

     *            internally always is appended to the query string, a search

     *            always compares the query string with the beginning of a name.

     *            - <i>required parameter</i>

     * @param treeUuid

     *            the {@link UUID} of a {@link Classification} to which the

     *            search is to be restricted. - <i>optional parameter</i>

     * @param areas

     *            restrict the search to a set of geographic {@link NamedArea}s.

     *            The parameter currently takes a list of TDWG area labels.

     *            - <i>optional parameter</i>

     * @param pageNumber

     *            the number of the page to be returned, the first page has the

     *            pageNumber = 1 - <i>optional parameter</i>

     * @param pageSize

     *            the maximum number of entities returned per page (can be -1

     *            to return all entities in a single page) - <i>optional parameter</i>

     * @param doTaxa

     *            weather to search for instances of {@link Taxon} - <i>optional parameter</i>

     * @param doSynonyms

     *            weather to search for instances of {@link Synonym} - <i>optional parameter</i>

     * @param doTaxaByCommonNames

     *            for instances of {@link Taxon} by a common name used - <i>optional parameter</i>

     * @return a Pager on a list of {@link IdentifiableEntity}s initialized by

     *         the following strategy {@link #SIMPLE_TAXON_INIT_STRATEGY}

     * @throws IOException

     * @throws LuceneMultiSearchException

     * @throws ParseException

     */

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

    public Pager<SearchResult<TaxonBase>> doSearch(

            @RequestParam(value = "query", required = true) String query,

            @RequestParam(value = "tree", required = false) UUID treeUuid,

            @RequestParam(value = "area", required = false) DefinedTermBaseList<NamedArea> areaList,

            @RequestParam(value = "status", required = false) Set<PresenceAbsenceTerm> status,

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

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

            @RequestParam(value = "doTaxa", required = false) Boolean doTaxa,

            @RequestParam(value = "doSynonyms", required = false) Boolean doSynonyms,

            @RequestParam(value = "doMisappliedNames", required = false) Boolean doMisappliedNames,

            @RequestParam(value = "doTaxaByCommonNames", required = false) Boolean doTaxaByCommonNames,

            HttpServletRequest request,

            HttpServletResponse response

            )

             throws IOException, ParseException, LuceneMultiSearchException {

        logger.info("search : " + requestPathAndQuery(request) );

        Set<NamedArea> areaSet = null;

        if(areaList != null){

            areaSet = new HashSet<NamedArea>(areaList.size());

            areaSet.addAll(areaList);

            TaxonListController.includeAllSubAreas(areaSet, termService);

        }

        PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);

        pagerParams.normalizeAndValidate(response);

        // TODO change type of do* parameters  to TaxaAndNamesSearchMode

        EnumSet<TaxaAndNamesSearchMode> searchModes = EnumSet.noneOf(TaxaAndNamesSearchMode.class);

        if(BooleanUtils.toBoolean(doTaxa)) {

            searchModes.add(TaxaAndNamesSearchMode.doTaxa);

        }

        if(BooleanUtils.toBoolean(doSynonyms)) {

            searchModes.add(TaxaAndNamesSearchMode.doSynonyms);

        }

        if(BooleanUtils.toBoolean(doMisappliedNames)) {

            searchModes.add(TaxaAndNamesSearchMode.doMisappliedNames);

        }

        if(BooleanUtils.toBoolean(doTaxaByCommonNames)) {

            searchModes.add(TaxaAndNamesSearchMode.doTaxaByCommonNames);

        }

        Classification classification = null;

        if(treeUuid != null){

            classification = classificationService.find(treeUuid);

        }

        return service.findTaxaAndNamesByFullText(searchModes, query,

                classification, areaSet, status, null,

                false, pagerParams.getPageSize(), pagerParams.getPageIndex(),

                OrderHint.NOMENCLATURAL_SORT_ORDER.asList(), getSimpleTaxonInitStrategy());

    }

    /**

     * Find Taxa, Synonyms, Common Names by name, either globally or in a specific geographic area.

     * <p>

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

     *

     * @param query

     *            the string to query for. Since the wildcard character '*'

     *            internally always is appended to the query string, a search

     *            always compares the query string with the beginning of a name.

     *            - <i>required parameter</i>

     * @param treeUuid

     *            the {@link UUID} of a {@link Classification} to which the

     *            search is to be restricted. - <i>optional parameter</i>

     * @param areas

     *            restrict the search to a set of geographic {@link NamedArea}s.

     *            The parameter currently takes a list of TDWG area labels.

     *            - <i>optional parameter</i>

     * @param pageNumber

     *            the number of the page to be returned, the first page has the

     *            pageNumber = 1 - <i>optional parameter</i>

     * @param pageSize

     *            the maximum number of entities returned per page (can be -1

     *            to return all entities in a single page) - <i>optional parameter</i>

     * @param doTaxa

     *            weather to search for instances of {@link Taxon} - <i>optional parameter</i>

     * @param doSynonyms

     *            weather to search for instances of {@link Synonym} - <i>optional parameter</i>

     * @param doTaxaByCommonNames

     *            for instances of {@link Taxon} by a common name used - <i>optional parameter</i>

     * @param matchMode

     *           valid values are "EXACT", "BEGINNING", "ANYWHERE", "END" (case sensitive !!!)

     * @return a Pager on a list of {@link IdentifiableEntity}s initialized by

     *         the following strategy {@link #SIMPLE_TAXON_INIT_STRATEGY}

     * @throws IOException

     */

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

    public Pager<IdentifiableEntity> doFind(

            @RequestParam(value = "query", required = true) String query,

            @RequestParam(value = "tree", required = false) UUID treeUuid,

            @RequestParam(value = "area", required = false) Set<NamedArea> areas,

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

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

            @RequestParam(value = "doTaxa", required = false) Boolean doTaxa,

            @RequestParam(value = "doSynonyms", required = false) Boolean doSynonyms,

            @RequestParam(value = "doMisappliedNames", required = false) Boolean doMisappliedNames,

            @RequestParam(value = "doTaxaByCommonNames", required = false) Boolean doTaxaByCommonNames,

            @RequestParam(value = "matchMode", required = false) MatchMode matchMode,

            HttpServletRequest request,

            HttpServletResponse response

            )

             throws IOException {

        logger.info("find : " + request.getRequestURI() + "?" + request.getQueryString() );

        PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);

        pagerParams.normalizeAndValidate(response);

        IFindTaxaAndNamesConfigurator config = new FindTaxaAndNamesConfiguratorImpl();

        config.setPageNumber(pagerParams.getPageIndex());

        config.setPageSize(pagerParams.getPageSize());

        config.setTitleSearchString(query);

        config.setDoTaxa(doTaxa!= null ? doTaxa : Boolean.FALSE );

        config.setDoSynonyms(doSynonyms != null ? doSynonyms : Boolean.FALSE );

        config.setDoMisappliedNames(doMisappliedNames != null ? doMisappliedNames : Boolean.FALSE);

        config.setDoTaxaByCommonNames(doTaxaByCommonNames != null ? doTaxaByCommonNames : Boolean.FALSE );

        config.setMatchMode(matchMode != null ? matchMode : MatchMode.BEGINNING);

        config.setTaxonPropertyPath(getSimpleTaxonInitStrategy());

        config.setNamedAreas(areas);

        if(treeUuid != null){

            Classification classification = classificationService.find(treeUuid);

            config.setClassification(classification);

        }

        return service.findTaxaAndNames(config);

    }

    /**

     * @param clazz

     * @param queryString

     * @param treeUuid TODO unimplemented in TaxonServiceImpl !!!!

     * @param languages

     * @param pageNumber

     * @param pageSize

     * @param request

     * @param response

     * @return

     * @throws IOException

     * @throws ParseException

     */

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

    public Pager<SearchResult<TaxonBase>> dofindByDescriptionElementFullText(

            @RequestParam(value = "clazz", required = false) Class<? extends DescriptionElementBase> clazz,

            @RequestParam(value = "query", required = true) String queryString,

            @RequestParam(value = "tree", required = false) UUID treeUuid,

            @RequestParam(value = "features", required = false) UuidList featureUuids,

            @RequestParam(value = "languages", required = false) List<Language> languages,

            @RequestParam(value = "hl", required = false) Boolean highlighting,

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

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

            HttpServletRequest request,

            HttpServletResponse response

            )

             throws IOException, ParseException {

         logger.info("findByDescriptionElementFullText : " + requestPathAndQuery(request) );

         PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);

         pagerParams.normalizeAndValidate(response);

         if(highlighting == null){

             highlighting = false;

         }

         Classification classification = null;

        if(treeUuid != null){

            classification = classificationService.find(treeUuid);

        }

        List<Feature> features = null;

        if(featureUuids != null){

            features = new ArrayList<Feature>(featureUuids.size());

            for(UUID uuid : featureUuids){

                features.add((Feature) termService.find(uuid));

            }

        }

        Pager<SearchResult<TaxonBase>> pager = service.findByDescriptionElementFullText(

                clazz, queryString, classification, features, languages, highlighting,

                pagerParams.getPageSize(), pagerParams.getPageIndex(),

                ((List<OrderHint>)null), getSimpleTaxonInitStrategy());

        return pager;

    }

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

    public Pager<SearchResult<TaxonBase>> dofindByFullText(

            @RequestParam(value = "clazz", required = false) Class<? extends TaxonBase> clazz,

            @RequestParam(value = "query", required = true) String queryString,

            @RequestParam(value = "tree", required = false) UUID treeUuid,

            @RequestParam(value = "languages", required = false) List<Language> languages,

            @RequestParam(value = "hl", required = false) Boolean highlighting,

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

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

            HttpServletRequest request,

            HttpServletResponse response

            )

             throws IOException, ParseException {

         logger.info("findByFullText : " + requestPathAndQuery(request)  );

         PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);

         pagerParams.normalizeAndValidate(response);

         if(highlighting == null){

             highlighting = false;

         }

         Classification classification = null;

        if(treeUuid != null){

            classification = classificationService.find(treeUuid);

        }

        Pager<SearchResult<TaxonBase>> pager = service.findByFullText(clazz, queryString, classification, languages,

                highlighting, pagerParams.getPageSize(), pagerParams.getPageIndex(), ((List<OrderHint>)  null),

                initializationStrategy);

        return pager;

    }

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

    public Pager<SearchResult<TaxonBase>> dofindByEverythingFullText(

            @RequestParam(value = "clazz", required = false) Class<? extends TaxonBase> clazz,

            @RequestParam(value = "query", required = true) String queryString,

            @RequestParam(value = "tree", required = false) UUID treeUuid,

            @RequestParam(value = "languages", required = false) List<Language> languages,

            @RequestParam(value = "hl", required = false) Boolean highlighting,

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

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

            HttpServletRequest request,

            HttpServletResponse response

            )

             throws IOException, ParseException, LuceneMultiSearchException {

         logger.info("findByEverythingFullText : " + requestPathAndQuery(request) );

         PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber);

         pagerParams.normalizeAndValidate(response);

         if(highlighting == null){

             highlighting = false;

         }

         Classification classification = null;

        if(treeUuid != null){

            classification = classificationService.find(treeUuid);

        }

        Pager<SearchResult<TaxonBase>> pager = service.findByEverythingFullText(

                queryString, classification, languages, highlighting,

                pagerParams.getPageSize(), pagerParams.getPageIndex(),

                ((List<OrderHint>)null), initializationStrategy);

        return pager;

    }

    /**

     * @param areaSet

     */

    static public void includeAllSubAreas(Set<NamedArea> areaSet, ITermService termService) {

        Collection<NamedArea> tmpAreas = new HashSet<NamedArea>(areaSet);

        // expand all areas to include also the sub areas

        Pager<NamedArea> pager = null;

        while(true){

            pager = termService.getIncludes(tmpAreas, 1000, null, null);

            if(pager.getCount() == 0){

                break;

            }

            tmpAreas = pager.getRecords();

            tmpAreas.removeAll(areaSet);

            areaSet.addAll(tmpAreas);

        }

    }

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

    public TaxonBase doFindBestMatchingTaxon(

            @RequestParam(value = "query", required = true) String taxonName,

            HttpServletRequest request,

            HttpServletResponse response)throws IOException {

        logger.info("doFindBestMatchingTaxon : " + requestPathAndQuery(request) );

        Taxon bestMatchingTaxon =  service.findBestMatchingTaxon(taxonName);

        return bestMatchingTaxon;

    }

    /**

     * list IdentifiableEntity objects by identifiers

     *

     * @param type

     * @param identifierType

     * @param identifier

     * @param pageNumber

     * @param pageSize

     * @param matchMode

     * @param request

     * @param response

     * @return

     * @see IdentifiableListController#doFindByIdentifier(Class, String, String, Integer, Integer, MatchMode, Boolean, HttpServletRequest, HttpServletResponse)

     * @throws IOException

     */

    @RequestMapping(method = RequestMethod.GET, value={"findByIdentifier"}, params={"subtree"})

    public <T extends TaxonBase>  Pager<FindByIdentifierDTO<T>> doFindByIdentifier(

            @RequestParam(value = "class", required = false) Class<T> type,

            @RequestParam(value = "identifierType", required = false) UUID identifierType,

            @RequestParam(value = "identifier", required = false) String identifier,

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

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

            @RequestParam(value = "matchMode", required = false) MatchMode matchMode,

            @RequestParam(value = "includeEntity", required = false, defaultValue="true") Boolean includeEntity, //TODO true only for debuging

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

            HttpServletRequest request,

            HttpServletResponse response

            )

             throws IOException {

        DefinedTerm definedTerm = null;

        if(identifierType != null){

            definedTerm = CdmBase.deproxy(termService.find(identifierType), DefinedTerm.class);

        }

        TaxonNode subTree;

        Classification cl = classificationService.load(subtreeUuid);

        if (cl != null){

            subTree = cl.getRootNode();

        }else{

            subTree = taxonNodeService.find(subtreeUuid);

        }

        logger.info("doFindByIdentifier [subtreeUuid]  : " + request.getRequestURI() + "?" + request.getQueryString() );

        PagerParameters pagerParams = new PagerParameters(pageSize, pageNumber).normalizeAndValidate(response);

        matchMode = matchMode != null ? matchMode : MatchMode.EXACT;

        return service.findByIdentifier(type, identifier, definedTerm , subTree, matchMode, includeEntity, pagerParams.getPageSize(), pagerParams.getPageIndex(), initializationStrategy);

    }

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

    public Pager<TaxonBase> doFindByNameParts(

            @RequestParam(value = "genusOrUninomial", required = false) String genusOrUninomial,

            @RequestParam(value = "infragenericEpithet", required = false) String infragenericEpithet,

            @RequestParam(value = "specificEpithet", required = false) String specificEpithet,

            @RequestParam(value = "infraspecificEpithet", required = false) String infraspecificEpithet,

            @RequestParam(value = "authorship", required = false) String authorship,

            @RequestParam(value = "rankUuid", required = false) UUID rankUuid,

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

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

            HttpServletRequest request,

            HttpServletResponse response)throws IOException {

        logger.info("doFindByNameParts : " + requestPathAndQuery(request) );

        if (genusOrUninomial == null && infragenericEpithet == null && specificEpithet == null && infraspecificEpithet == null){

            response.sendError(404 , "At least 1 name part must be defined " );

            return null;

        }

        Rank rank = null;

        if (rankUuid != null){

             rank = findRank(rankUuid);

        }

        Pager<TaxonBase> result = service.findTaxaByName(null, genusOrUninomial, infragenericEpithet, specificEpithet, infraspecificEpithet, authorship, rank, pageSize, pageNumber);

        return result;

    }

    private Rank findRank(UUID rankUuid) {

        Rank rank = null;

        if(rankUuid != null){

            DefinedTermBase<?> definedTermBase =  termService.find(rankUuid);

            if(definedTermBase instanceof Rank){

                rank = (Rank) definedTermBase;

            } else {

               throw new IllegalArgumentException("DefinedTermBase is not a Rank");

            }

        }

        return rank;

    }

}