EDIT

// $Id: TaxonController.java 5473 2009-03-25 13:42:07Z a.kohlbecker $

/**

* 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.EnumSet;

import java.util.HashSet;

import java.util.Hashtable;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

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.log4j.Logger;

import org.apache.lucene.queryParser.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.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.IClassificationService;

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

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

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

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

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.pager.Pager;

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

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

import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;

import eu.etaxonomy.cdm.database.UpdatableRoutingDataSource;

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.common.MarkerType;

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

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

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

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

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

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

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

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

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

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

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

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.TaxonRelationship;

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

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

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

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

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

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

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

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

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

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

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

/**

 * The TaxonPortalController class is a Spring MVC Controller.

 * <p>

 * The syntax of the mapped service URIs contains the the {datasource-name} path element.

 * The available {datasource-name}s are defined in a configuration file which

 * is loaded by the {@link UpdatableRoutingDataSource}. If the

 * UpdatableRoutingDataSource is not being used in the actual application

 * context any arbitrary {datasource-name} may be used.

 * <p>

 * Methods mapped at type level, inherited from super classes ({@link BaseController}):

 * <blockquote>

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

 *

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

 * The returned Taxon is initialized by

 * the following strategy {@link #TAXON_INIT_STRATEGY}

 * </blockquote>

 *

 * @author a.kohlbecker

 * @date 20.07.2009

 *

 */

@Controller

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

public class TaxonPortalController extends TaxonController

{

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

    @Autowired

    private INameService nameService;

    @Autowired

    private IDescriptionService descriptionService;

    @Autowired

    private IOccurrenceService occurrenceService;

    @Autowired

    private IClassificationService classificationService;

    @Autowired

    private ITaxonService taxonService;

    @Autowired

    private ITermService termService;

    @Autowired

    private IFeatureTreeService featureTreeService;

    private static final List<String> TAXON_INIT_STRATEGY = Arrays.asList(new String []{

            "$",

            "sources",

            // taxon relations

//            "relationsToThisName.fromTaxon.name",

            // the name

            "name.$",

            "name.nomenclaturalReference.authorTeam",

            "name.nomenclaturalReference.inReference",

            "name.rank.representations",

            "name.status.type.representations",

//            "descriptions" // TODO remove

            });

    private static final List<String> TAXON_WITH_NODES_INIT_STRATEGY = Arrays.asList(new String []{

            "taxonNodes.$",

            "taxonNodes.classification.$",

            "taxonNodes.childNodes.$"

            });

    private static final List<String> SIMPLE_TAXON_INIT_STRATEGY = Arrays.asList(new String []{

            "$",

            // the name

            "name.$",

            "name.rank.representations",

            "name.status.type.representations",

            "name.nomenclaturalReference.authorTeam",

            "name.nomenclaturalReference.inReference",

            "taxonNodes.classification",

            });

    private static final List<String> SYNONYMY_INIT_STRATEGY = Arrays.asList(new String []{

            // initialize homotypical and heterotypical groups; needs synonyms

            "synonymRelations.$",

            "synonymRelations.synonym.$",

            "synonymRelations.synonym.name.status.type.representation",

            "synonymRelations.synonym.name.nomenclaturalReference.authorTeam",

            "synonymRelations.synonym.name.nomenclaturalReference.inReference",

            "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.$",

            "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.$",

            "synonymRelations.synonym.name.combinationAuthorTeam.$",

            "name.typeDesignations",

            "name.homotypicalGroup.$",

            "name.homotypicalGroup.typifiedNames.$",

            "name.homotypicalGroup.typifiedNames.nomenclaturalReference.authorTeam",

            "name.homotypicalGroup.typifiedNames.nomenclaturalReference.inReference",

            "name.homotypicalGroup.typifiedNames.taxonBases.$"

    });

    private static final List<String> SYNONYMY_WITH_NODES_INIT_STRATEGY = Arrays.asList(new String []{

            // initialize homotypical and heterotypical groups; needs synonyms

            "synonymRelations.$",

            "synonymRelations.synonym.$",

            "synonymRelations.synonym.name.status.type.representation",

            "synonymRelations.synonym.name.nomenclaturalReference.authorTeam",

            "synonymRelations.synonym.name.nomenclaturalReference.inReference",

            "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.$",

            "synonymRelations.synonym.name.homotypicalGroup.typifiedNames.taxonBases.$",

            "synonymRelations.synonym.name.combinationAuthorTeam.$",

            "name.homotypicalGroup.$",

            "name.homotypicalGroup.typifiedNames.$",

            "name.homotypicalGroup.typifiedNames.nomenclaturalReference.authorTeam",

            "name.homotypicalGroup.typifiedNames.nomenclaturalReference.inReference",

            "name.homotypicalGroup.typifiedNames.taxonBases.$",

            "taxonNodes.$",

            "taxonNodes.classification.$",

            "taxonNodes.childNodes.$"

    });

    private static final List<String> SIMPLE_TAXON_WITH_NODES_INIT_STRATEGY = Arrays.asList(new String []{

            "*",

            // taxon relations

            "relationsToThisName.fromTaxon.name",

            // the name

            "name.$",

            "name.rank.representations",

            "name.status.type.representations",

            "name.nomenclaturalReference.authorTeam",

            "name.nomenclaturalReference.inReference",

            "taxonNodes.$",

            "taxonNodes.classification.$",

            "taxonNodes.childNodes.$"

            });

    private static final List<String> TAXONRELATIONSHIP_INIT_STRATEGY = Arrays.asList(new String []{

            "$",

            "type.inverseRepresentations",

            "fromTaxon.sec",

            "fromTaxon.name",

            "toTaxon.sec",

            "toTaxon.name"

    });

    private static final List<String> NAMERELATIONSHIP_INIT_STRATEGY = Arrays.asList(new String []{

            "$",

            "type.inverseRepresentations",

            "toName.$",

            "toName.nomenclaturalReference.authorTeam",

            "toName.nomenclaturalReference.inReference",

            "fromName.$",

            "fromName.nomenclaturalReference.authorTeam",

            "fromName.nomenclaturalReference.inReference",

    });

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

            "$",

            "elements.$",

            "elements.stateData.$",

            "elements.sources.citation.authorTeam",

            "elements.sources.nameUsedInSource",

            "elements.multilanguageText",

            "elements.media",

            "elements.modifyingText",

            "elements.modifiers",

            "elements.kindOfUnit",

            "name.$",

            "name.rank.representations",

            "name.status.type.representations",

            "sources.$",

    });

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

            "$",

            "sources.citation.authorTeam",

            "sources.nameUsedInSource",

            "multilanguageText",

            "media",

    });

//	private static final List<String> NAMEDESCRIPTION_INIT_STRATEGY = Arrays.asList(new String []{

//			"uuid",

//			"feature",

//			"elements.$",

//			"elements.multilanguageText",

//			"elements.media",

//	});

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

            "elements.media"

    });

    private static final List<String> TYPEDESIGNATION_INIT_STRATEGY = Arrays.asList(new String []{

            "typeSpecimen.$",

            "citation.authorTeam.$",

            "typeName",

            "typeStatus"

    });

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

            "childNodes.taxon",

    });

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

            "taxonNodes.classification"

    });

    private static final String featureTreeUuidPattern = "^/taxon(?:(?:/)([^/?#&\\.]+))+.*";

    public TaxonPortalController(){

        super();

        setInitializationStrategy(TAXON_INIT_STRATEGY);

    }

    /* (non-Javadoc)

     * @see eu.etaxonomy.cdm.remote.controller.GenericController#setService(eu.etaxonomy.cdm.api.service.IService)

     */

    @Autowired

    @Override

    public void setService(ITaxonService service) {

        this.service = service;

    }

    @InitBinder

    @Override

    public void initBinder(WebDataBinder binder) {

        super.initBinder(binder);

        binder.registerCustomEditor(NamedArea.class, new NamedAreaPropertyEditor());

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

        binder.registerCustomEditor(Class.class, new CdmTypePropertyEditor());

        binder.registerCustomEditor(UuidList.class, new UUIDListPropertyEditor());

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

    }

    /* (non-Javadoc)

     * @see eu.etaxonomy.cdm.remote.controller.BaseController#doGet(javax.servlet.http.HttpServletRequest, javax.servlet.http.HttpServletResponse)

    @Override

    @RequestMapping(method = RequestMethod.GET)

    public TaxonBase doGet(HttpServletRequest request, HttpServletResponse response)throws IOException {

        logger.info("doGet()");

        TaxonBase tb = getCdmBase(request, response, TAXON_INIT_STRATEGY, TaxonBase.class);

        return tb;

    }

     */

    @RequestMapping(method = RequestMethod.GET,

            value = {"/portal/taxon/find"}) //TODO map to path /*/portal/taxon/

    public Pager<IdentifiableEntity> doFind(

            @RequestParam(value = "query", required = false) 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("doFind : " + 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(SIMPLE_TAXON_INIT_STRATEGY);

        config.setNamedAreas(areas);

        if(treeUuid != null){

            Classification classification = classificationService.find(treeUuid);

            config.setClassification(classification);

        }

        return service.findTaxaAndNames(config);

    }

    /**

     * <b>NOTE and TODO</b>: this method is a direct copy of the same method in {@link TaxonListController},

     * refactorting needed to avoid method dublication

     * <p>

     * 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 value must be a list of comma separated NamedArea uuids

     *            - <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={"/portal/taxon/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<PresenceAbsenceTermBase<?>> 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, SIMPLE_TAXON_INIT_STRATEGY);

    }

    /**

     * @param clazz

     * @param queryString

     * @param treeUuid

     * @param languages

     * @param features one or more feature uuids

     * @param pageNumber

     * @param pageSize

     * @param request

     * @param response

     * @return

     * @throws IOException

     * @throws ParseException

     */

    @SuppressWarnings("rawtypes")

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

    public Pager<SearchResult<TaxonBase>> dofindByDescriptionElementFullText(

            @RequestParam(value = "clazz", required = false) Class 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), SIMPLE_TAXON_INIT_STRATEGY);

        return pager;

    }

    /**

     * Get the synonymy for a taxon identified by the <code>{taxon-uuid}</code>.

     * The synonymy consists

     * of two parts: The group of homotypic synonyms of the taxon and the

     * heterotypic synonymy groups of the taxon. The synonymy is ordered

     * historically by the type designations and by the publication date of the

     * nomenclatural reference

     * <p>

     * URI:

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

     *

     *

     * @param request

     * @param response

     * @return a Map with to entries which are mapped by the following keys:

     *         "homotypicSynonymsByHomotypicGroup", "heterotypicSynonymyGroups",

     *         containing lists of {@link Synonym}s which are initialized using the

     *         following initialization strategy: {@link #SYNONYMY_INIT_STRATEGY}

     *

     * @throws IOException

     */

    @RequestMapping(

            value = {"synonymy"},

            method = RequestMethod.GET)

    public ModelAndView doGetSynonymy(@PathVariable("uuid") UUID uuid,

            HttpServletRequest request, HttpServletResponse response)throws IOException {

        if(request != null){

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

        }

        ModelAndView mv = new ModelAndView();

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

        Map<String, List<?>> synonymy = new Hashtable<String, List<?>>();

        //new

        List<List<Synonym>> synonymyGroups = service.getSynonymsByHomotypicGroup(taxon, SYNONYMY_INIT_STRATEGY);

        synonymy.put("homotypicSynonymsByHomotypicGroup", synonymyGroups.get(0));

        synonymyGroups.remove(0);

        synonymy.put("heterotypicSynonymyGroups", synonymyGroups);

        //old

//        synonymy.put("homotypicSynonymsByHomotypicGroup", service.getHomotypicSynonymsByHomotypicGroup(taxon, SYNONYMY_INIT_STRATEGY));

//        synonymy.put("heterotypicSynonymyGroups", service.getHeterotypicSynonymyGroups(taxon, SYNONYMY_INIT_STRATEGY));

        mv.addObject(synonymy);

        return mv;

    }

    /**

     * Get the list of {@link TaxonRelationship}s for the given

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

     * <p>

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

     *

     * @param request

     * @param response

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

     *         using the following initialization strategy:

     *         {@link #TAXONRELATIONSHIP_INIT_STRATEGY}

     * @throws IOException

     */

    @RequestMapping(

            value = {"taxonRelationships"},

            method = RequestMethod.GET)

    public List<TaxonRelationship> doGetTaxonRelations(@PathVariable("uuid") UUID uuid,

            HttpServletRequest request, HttpServletResponse response)throws IOException {

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

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

        List<TaxonRelationship> toRelationships = service.listToTaxonRelationships(taxon, null, null, null, null, TAXONRELATIONSHIP_INIT_STRATEGY);

        List<TaxonRelationship> fromRelationships = service.listFromTaxonRelationships(taxon, null, null, null, null, TAXONRELATIONSHIP_INIT_STRATEGY);

        List<TaxonRelationship> allRelationships = new ArrayList<TaxonRelationship>(toRelationships.size() + fromRelationships.size());

        allRelationships.addAll(toRelationships);

        allRelationships.addAll(fromRelationships);

        return allRelationships;

    }

    /**

     * Get the list of {@link NameRelationship}s of the Name associated with the

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

     * <p>

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

     *

     * @param request

     * @param response

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

     *         using the following initialization strategy:

     *         {@link #NAMERELATIONSHIP_INIT_STRATEGY}

     * @throws IOException

     */

    @RequestMapping(

            value = {"toNameRelationships"},

            method = RequestMethod.GET)

    public List<NameRelationship> doGetToNameRelations(@PathVariable("uuid") UUID uuid,

            HttpServletRequest request, HttpServletResponse response)throws IOException {

        logger.info("doGetNameRelations()" + request.getRequestURI());

        TaxonBase taxonBase = getCdmBaseInstance(TaxonBase.class, uuid, response, (List<String>)null);

        List<NameRelationship> list = nameService.listNameRelationships(taxonBase.getName(), Direction.relatedTo, null, null, 0, null, NAMERELATIONSHIP_INIT_STRATEGY);

        //List<NameRelationship> list = nameService.listToNameRelationships(taxonBase.getName(), null, null, null, null, NAMERELATIONSHIP_INIT_STRATEGY);

        return list;

    }

    /**

     * Get the list of {@link NameRelationship}s of the Name associated with the

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

     * <p>

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

     *

     * @param request

     * @param response

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

     *         using the following initialization strategy:

     *         {@link #NAMERELATIONSHIP_INIT_STRATEGY}

     * @throws IOException

     */

    @RequestMapping(

            value = {"fromNameRelationships"},

            method = RequestMethod.GET)

    public List<NameRelationship> doGetFromNameRelations(@PathVariable("uuid") UUID uuid,

            HttpServletRequest request, HttpServletResponse response)throws IOException {

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

        TaxonBase taxonbase = getCdmBaseInstance(TaxonBase.class, uuid, response, SIMPLE_TAXON_INIT_STRATEGY);

        List<NameRelationship> list = nameService.listNameRelationships(taxonbase.getName(), Direction.relatedFrom, null, null, 0, null, NAMERELATIONSHIP_INIT_STRATEGY);

        //List<NameRelationship> list = nameService.listFromNameRelationships(taxonbase.getName(), null, null, null, null, NAMERELATIONSHIP_INIT_STRATEGY);

        return list;

    }

    @Override

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

    public Set<TaxonNode>  doGetTaxonNodes(

            @PathVariable("uuid") UUID uuid,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

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

        TaxonBase taxon = service.load(uuid, TAXONNODE_INIT_STRATEGY);

        if(taxon instanceof Taxon){

            return ((Taxon)taxon).getTaxonNodes();

        } else {

            HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);

            return null;

        }

    }

    /**

     * 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 List<TaxonDescription> doGetDescriptions(

            @PathVariable("uuid") UUID uuid,

            @RequestParam(value = "markerTypes", required = false) UuidList markerTypeUUIDs,

            HttpServletRequest request,

            HttpServletResponse response)throws IOException {

        if(request != null){

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

        }

        List<DefinedTermBase> markerTypeTerms = null;

        Set<UUID> sMarkerTypeUUIDs = null;

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

            sMarkerTypeUUIDs = new HashSet<UUID>(markerTypeUUIDs);

            markerTypeTerms = termService.find(sMarkerTypeUUIDs);

        } else if(markerTypeUUIDs != null && markerTypeUUIDs.isEmpty()){

            markerTypeTerms = new ArrayList<DefinedTermBase>();

        }

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

        List<TaxonDescription> descriptions = new ArrayList<TaxonDescription>();

        if (markerTypeTerms != null) {

            for (DefinedTermBase markerTypeTerm : markerTypeTerms) {

                markerTypes.add((MarkerType)markerTypeTerm);

            }

        }

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

        if (markerTypeTerms == null) {

            Pager<TaxonDescription> p = descriptionService.pageTaxonDescriptions(t, null, null, null, null, TAXONDESCRIPTION_INIT_STRATEGY);

            descriptions = p.getRecords();

        }

        else if (markerTypeTerms != null && markerTypeTerms.isEmpty()) {

            descriptions = descriptionService.listTaxonDescriptions(t, null, null, markerTypes, null, null, TAXONDESCRIPTION_INIT_STRATEGY);

        }

        else {

            descriptions = descriptionService.listTaxonDescriptions(t, null, null, markerTypes, null, null, TAXONDESCRIPTION_INIT_STRATEGY);

            /*for (TaxonDescription description: descriptions) {

                for (IdentifiableSource source :description.getSources()) {

                    if (source.getOriginalNameString() != null) {

                        description.

                    }

                }

            }*/

        }

        return descriptions;

    }

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

    public List<TaxonDescription> doGetUseDescriptions(

            @PathVariable("uuid") UUID uuid,

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

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

        //ModelAndView mv = new ModelAndView();

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

       //MarkerType useMarkerType = (MarkerType) markerTypeService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f059"));

        MarkerType useMarkerType = (MarkerType) termService.find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f039"));

       //find(UUID.fromString("2e6e42d9-e92a-41f4-899b-03c0ac64f059"));

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

       markerTypes.add(useMarkerType);

       List<TaxonDescription> descriptionElements = descriptionService.listTaxonDescriptions(t, null, null, markerTypes, null, null, TAXONDESCRIPTION_INIT_STRATEGY);

        //getDescriptionElements(description, features, type, pageSize, pageNumber, propertyPaths)  load(uuid);

        /*if(!(description instanceof TaxonDescription)){

            HttpStatusMessage.UUID_REFERENCES_WRONG_TYPE.send(response);

            // will terminate thread

        }*/

        //boolean hasStructuredData = service.        hasStructuredData(description);

        //mv.addObject(hasStructuredData);

        return descriptionElements;

    }

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

    public ModelAndView doGetDescriptionElementsByType(

            @PathVariable("uuid") UUID uuid,

            @PathVariable("classSimpleName") String classSimpleName,

            @RequestParam(value = "markerTypes", required = false) UuidList markerTypeUUIDs,

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

            HttpServletRequest request,

            HttpServletResponse response) throws IOException {

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

        ModelAndView mv = new ModelAndView();

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

        List<DescriptionElementBase> elements;

        int count = 0;

        List<String> initStrategy = doCount ? null : DESCRIPTION_ELEMENT_INIT_STRATEGY;

        List<TaxonDescription> taxonDescriptions = doGetDescriptions(uuid, markerTypeUUIDs, request, response);

        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.fromString(e.getLocalizedMessage()).send(response);

        }

        if(doCount){

            mv.addObject(count);

        } else {

            mv.addObject(allElements);

        }

        return mv;

    }

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

//	public ModelAndView doGetSpecimens(

//			@PathVariable("uuid") UUID uuid,

//			HttpServletRequest request,

//			HttpServletResponse response) throws IOException, ClassNotFoundException {

//		logger.info("doGetSpecimens() - " + request.getRequestURI());

//

//		ModelAndView mv = new ModelAndView();

//

//		List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();

//

//		// find speciemens in the TaxonDescriptions

//		List<TaxonDescription> taxonDescriptions = doGetDescriptions(uuid, request, response);

//		if (taxonDescriptions != null) {

//

//			for (TaxonDescription description : taxonDescriptions) {

//				derivedUnitFacadeList.addAll( occurrenceService.listDerivedUnitFacades(description, null) );

//			}

//		}

//		// TODO find speciemens in the NameDescriptions ??

//

//		// TODO also find type specimens

//

//		mv.addObject(derivedUnitFacadeList);

//

//		return mv;

//	}

    /**

     * Get the {@link Media} attached to the {@link Taxon} instance

     * identified by the <code>{taxon-uuid}</code>.

     *

     * Usage /{datasource-name}/portal/taxon/{taxon-

     * uuid}/media/{mime type

     * list}/{size}[,[widthOrDuration}][,{height}]/

     *

     * Whereas

     * <ul>

     * <li><b>{mime type list}</b>: a comma separated list of mime types, in the

     * order of preference. The forward slashes contained in the mime types must

     * be replaced by a colon. Regular expressions can be used. Each media

     * associated with this given taxon is being searched whereas the first

     * matching mime type matching a representation always rules.</li>

     * <li><b>{size},{widthOrDuration},{height}</b>: <i>not jet implemented</i>

     * valid values are an integer or the asterisk '*' as a wildcard</li>