EDIT

/**

* 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.dto;

import java.io.IOException;

import java.io.InputStream;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Hashtable;

import java.util.Iterator;

import java.util.LinkedHashMap;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.TreeMap;

import java.util.UUID;

import javax.servlet.http.HttpServletRequest;

import javax.servlet.http.HttpServletResponse;

import org.apache.lucene.document.Document;

import org.apache.lucene.queryParser.ParseException;

import org.joda.time.DateTime;

import org.joda.time.format.DateTimeFormat;

import org.joda.time.format.DateTimeFormatter;

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

import org.springframework.context.ResourceLoaderAware;

import org.springframework.core.io.Resource;

import org.springframework.core.io.ResourceLoader;

import org.springframework.stereotype.Controller;

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 com.wordnik.swagger.annotations.Api;

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

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

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

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

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

import eu.etaxonomy.cdm.common.DocUtils;

import eu.etaxonomy.cdm.hibernate.search.AcceptedTaxonBridge;

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

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

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

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

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

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

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

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

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

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.persistence.query.OrderHint.SortOrder;

import eu.etaxonomy.cdm.remote.controller.AbstractController;

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

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

import eu.etaxonomy.cdm.remote.dto.namecatalogue.AcceptedNameSearch;

import eu.etaxonomy.cdm.remote.dto.namecatalogue.NameInformation;

import eu.etaxonomy.cdm.remote.dto.namecatalogue.NameSearch;

import eu.etaxonomy.cdm.remote.dto.namecatalogue.TaxonInformation;

import eu.etaxonomy.cdm.remote.view.HtmlView;

/**

 * The controller class for the namespace 'name_catalogue'. This web service namespace

 * is an add-on to the already existing CDM REST API and provides information relating

 * to scientific names as well as taxa present in the underlying datasource.

 *

 * @author c.mathew

 * @version 1.1.0

 * @created 15-Apr-2012

 */

@Controller

@Api("name_catalogue")

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

public class NameCatalogueController extends AbstractController<TaxonNameBase, INameService> implements ResourceLoaderAware {

    private ResourceLoader resourceLoader;

    /** Taxonomic status 'accepted' string */

    public static final String ACCEPTED_NAME_STATUS = "accepted";

    /** Taxonpmic status 'synonym' string */

    public static final String SYNONYM_STATUS = "synonym";

    /** Flag 'doubtful' strings */

    public static final String DOUBTFUL_FLAG = "doubtful";

    /** Base scientific name search type */

    public static final String NAME_SEARCH = "name";

    /** Complete scientific name search type */

    public static final String TITLE_SEARCH = "title";

    /** Default name search type */

    public static final String DEFAULT_SEARCH_TYPE = NAME_SEARCH;

    /** Default max number of hits for the exact name search  */

    public static final String DEFAULT_MAX_NB_FOR_EXACT_SEARCH = "100";

    /** Classifcation 'default' key */

    public static final String CLASSIFICATION_DEFAULT = "default";

    /** Classifcation 'all' key */

    public static final String CLASSIFICATION_ALL = "all";

    /** Classification to include uuids key */

    public static final String INCLUDE_CLUUIDS = "cluuids";

    /** Fuzzy Name Cache search */

    public static final String FUZZY_NAME_CACHE = "name";

    /** Fuzzy Atomised Name search */

    public static final String FUZZY_ATOMISED = "atomised";

    private static final String DWC_DATASET_ID = "http://rs.tdwg.org/dwc/terms/datasetID";

    private static final DateTimeFormatter fmt = DateTimeFormat.forPattern("dd-MM-yyyy");

    @Autowired

    private ITaxonService taxonService;

    @Autowired

    private IClassificationService classificationService;

    @Autowired

    private ICommonService commonService;

    /** Hibernate name search initialisation strategy */

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

            "combinationAuthorship.$",

            "exCombinationAuthorship.$",

            "basionymAuthorship.$",

            "exBasionymAuthorship.$",

            "nameCache",

            "taxonBases",

            "taxonBases.synonymRelations.type.$"});

    /** Hibernate accepted name search initialisation strategy */

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

            "nameCache",

            "taxonBases",

            "taxonBases.synonymRelations.acceptedTaxon.name.nameCache",

            "taxonBases.synonymRelations.acceptedTaxon.name.rank.titleCache",

            "taxonBases.synonymRelations.acceptedTaxon.taxonNodes.classification",

            "taxonBases.taxonNodes.classification",

            "taxonBases.relationsFromThisTaxon.type.$"});

    /** Hibernate name information initialisation strategy */

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

            "taxonBases",

            "status",

            "nomenclaturalReference.$",

            "combinationAuthorship.$",

            "exCombinationAuthorship.$",

            "basionymAuthorship.$",

            "exBasionymAuthorship.$",

            "relationsToThisName.fromName.$",

            "relationsToThisName.nomenclaturalReference.$",

            "relationsToThisName.type.$",

            "relationsFromThisName.toName.$",

            "relationsFromThisName.nomenclaturalReference.$",

            "relationsFromThisName.type.$"});

    /** Hibernate taxon information initialisation strategy */

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

            "name.titleCache",

            "name.rank.titleCache",

            "sec.updated",

            "sec.titleCache",

            "sources.citation.sources.idNamespace",

            "sources.citation.sources.idInSource",

            "synonymRelations.synonym.name.rank.titleCache",

            "synonymRelations.synonym.sec.updated",

            "synonymRelations.synonym.sec.titleCache",

            "synonymRelations.synonym.sources.citation.sources.idNamespace",

            "synonymRelations.synonym.sources.citation.sources.idInSource",

            "synonymRelations.acceptedTaxon.name.rank.titleCache",

            "synonymRelations.acceptedTaxon.sec.titleCache",

            "synonymRelations.acceptedTaxon.sources.citation.sources.idNamespace",

            "synonymRelations.acceptedTaxon.sources.citation.sources.idInSource",

            "synonymRelations.type.inverseRepresentations",

            "relationsFromThisTaxon.type.inverseRepresentations",

            "relationsFromThisTaxon.toTaxon.name.rank.titleCache",

            "relationsFromThisTaxon.toTaxon.sec.updated",

            "relationsFromThisTaxon.toTaxon.sec.titleCache",

            "relationsFromThisTaxon.toTaxon.sources.citation.sources.idNamespace",

            "relationsFromThisTaxon.toTaxon.sources.citation.sources.idInSource",

            "relationsToThisTaxon.type.inverseRepresentations",

            "relationsToThisTaxon.fromTaxon.name.rank.titleCache",

            "relationsToThisTaxon.fromTaxon.sec.updated",

            "relationsToThisTaxon.fromTaxon.sec.titleCache",

            "relationsToThisTaxon.fromTaxon.sources.citation.sources.idNamespace",

            "relationsToThisTaxon.fromTaxon.sources.citation.sources.idInSource",

            "taxonNodes",

            "taxonNodes.classification" });

    /** Hibernate taxon node initialisation strategy */

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

            "taxon.sec",

            "taxon.name",

            "classification",

            "classification.reference.$",

            "classification.reference.authorship.$" });

    /** Hibernate classification vocabulary initialisation strategy */

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

            "classification",

            "classification.reference.$",

            "classification.reference.authorship.$" });

    /** Hibernate classification vocabulary initialisation strategy */

    private static final List<String> COMMON_INIT_STRATEGY = Arrays.asList(new String[] {});

    public NameCatalogueController() {

        super();

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

    }

    /*

     * (non-Javadoc)

     *

     * @see

     * eu.etaxonomy.cdm.remote.controller.GenericController#setService(eu

     * .etaxonomy.cdm.api.service.IService)

     */

    @Autowired

    @Override

    public void setService(INameService service) {

        this.service = service;

    }

    /**

     * Returns a documentation page for the Name Search API.

     * <p>

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

     *

     * @param request

     * @param response

     * @return Html page describing the Name Search API

     * @throws IOException

     */

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

    public ModelAndView doGetNameSearchDocumentation(

            HttpServletRequest request, HttpServletResponse response)

            throws IOException {

        ModelAndView mv = new ModelAndView();

        // Read apt documentation file.

        Resource resource = resourceLoader.getResource("classpath:eu/etaxonomy/cdm/doc/remote/apt/name-catalogue-default.apt");

        // using input stream as this works for both files in the classes directory

        // as well as files inside jars

        InputStream aptInputStream = resource.getInputStream();

        // Build Html View

        Map<String, String> modelMap = new HashMap<String, String>();

        // Convert Apt to Html

        modelMap.put("html", DocUtils.convertAptToHtml(aptInputStream));

        mv.addAllObjects(modelMap);

        HtmlView hv = new HtmlView();

        mv.setView(hv);

        return mv;

    }

    /**

     * Returns a list of scientific names matching the <code>{query}</code>

     * string pattern. Each of these scientific names is accompanied by a list of

     * name uuids, a list of taxon uuids, a list of accepted taxon uuids, etc.

     * <p>

     * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-default.html">here</a>

     * <p>

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

     *

     * @param queries

     *                The base scientific name pattern(s) to query for. The query can

     *                contain wildcard characters ('*'). The query can be

     *                performed with no wildcard or with the wildcard at the

     *                begin and / or end depending on the search pattern.

     * @param request Http servlet request.

     * @param response Http servlet response.

     * @return a list of {@link NameSearch} objects each corresponding to a

     *         single query. These are built from {@link TaxonNameBase}

     *         entities which are in turn initialized using

     *         the {@link #NAME_SEARCH_INIT_STRATEGY}

     * @throws IOException

     */

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

    public ModelAndView doGetNameSearch(@RequestParam(value = "query", required = true) String[] queries,

            HttpServletRequest request, HttpServletResponse response) throws IOException {

    return doGetNameSearch(queries, DEFAULT_SEARCH_TYPE, DEFAULT_MAX_NB_FOR_EXACT_SEARCH, request, response);

    }

    /**

     * Returns a list of scientific names matching the <code>{query}</code>

     * string pattern. Each of these scientific names is accompanied by a list of

     * name uuids, a list of taxon uuids and a list of accepted taxon uuids.

     * <p>

     * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-default.html">here</a>

     * <p>

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

     *

     * @param query

     *             	The scientific name pattern(s) to query for. The query can

     *             	contain wildcard characters ('*'). The query can be

     *              performed with no wildcard or with the wildcard at the

     *              begin and / or end depending on the search pattern.

     * @param type

     *              The type of name to query. This be either

     *              "name" : scientific name corresponding to 'name cache' in CDM or

     *              "title" : complete name corresponding to 'title cache' in CDM

     * @param hits

     *            	Maximum number of responses to be returned.

     * @param request Http servlet request.

     * @param response Http servlet response.

     * @return a List of {@link NameSearch} objects each corresponding to a

     *         single query. These are built from {@link TaxonNameBase} entities

     *         which are in turn initialized using the {@link #NAME_SEARCH_INIT_STRATEGY}

     * @throws IOException

     */

    @RequestMapping(value = { "" }, method = RequestMethod.GET, params = {"query", "type"})

    public ModelAndView doGetNameSearch(@RequestParam(value = "query", required = true) String[] queries,

            @RequestParam(value = "type", required = false, defaultValue = DEFAULT_SEARCH_TYPE) String searchType,

            @RequestParam(value = "hits", required = false, defaultValue = DEFAULT_MAX_NB_FOR_EXACT_SEARCH) String hits,

            HttpServletRequest request, HttpServletResponse response) throws IOException {

        ModelAndView mv = new ModelAndView();

        List<RemoteResponse> nsList = new ArrayList<RemoteResponse>();

        int h = 100;

        try {

            h = Integer.parseInt(hits);

        } catch(NumberFormatException nfe) {

            ErrorResponse er = new ErrorResponse();

            er.setErrorMessage("hits parameter is not a number");

            mv.addObject(er);

            return mv;

        }

        // search through each query

        for (String query : queries) {

            if(query.equals("")) {

                ErrorResponse er = new ErrorResponse();

                er.setErrorMessage("Empty query field");

                nsList.add(er);

                continue;

            }

            // remove wildcards if any

            String queryWOWildcards = getQueryWithoutWildCards(query);

            // convert first char to upper case

            char[] stringArray = queryWOWildcards.toCharArray();

            stringArray[0] = Character.toUpperCase(stringArray[0]);

            queryWOWildcards = new String(stringArray);

            boolean wc = false;

            if(getMatchModeFromQuery(query) == MatchMode.BEGINNING) {

                wc = true;

            }

            logger.info("doGetNameSearch()" + request.getRequestURI() + " for query \"" + query);

            List<DocumentSearchResult> nameSearchList = new ArrayList<DocumentSearchResult>();

            try {

                nameSearchList = service.findByNameExactSearch(

                        queryWOWildcards,

                        wc,

                        null,

                        false,

                        h);

            } catch (ParseException e) {

                // TODO Auto-generated catch block

                //e.printStackTrace();

                ErrorResponse er = new ErrorResponse();

                er.setErrorMessage("Could not parse name : " + query);

                nsList.add(er);

                continue;

            }

            // if search is successful then get related information , else return error

            if (nameSearchList == null || !nameSearchList.isEmpty()) {

                NameSearch ns = new NameSearch();

                ns.setRequest(query);

                for (DocumentSearchResult searchResult : nameSearchList) {

                    for(Document doc : searchResult.getDocs()) {

                    // we need to retrieve both taxon uuid of name queried and

                    // the corresponding accepted taxa.

                    // reason to return accepted taxa also, is to be able to get from

                    // scientific name to taxon concept in two web service calls.

                    List<String> tbUuidList = new ArrayList<String>();//nvn.getTaxonBases();

                    List<String> accTbUuidList = new ArrayList<String>();

                    String[] tbUuids = doc.getValues("taxonBases.uuid");

                    String[] tbClassNames = doc.getValues("taxonBases.classInfo.name");

                    for(int i=0;i<tbUuids.length;i++) {

                        if(tbClassNames[i].equals("eu.etaxonomy.cdm.model.taxon.Taxon")) {

                            accTbUuidList.add(tbUuids[i]);

                        }

                    }

                    // update name search object

                    ns.addToResponseList(doc.getValues("titleCache")[0],

                            doc.getValues("nameCache")[0],

                            searchResult.getMaxScore(),

                            doc.getValues("uuid")[0].toString(),

                            doc.getValues("taxonBases.uuid"),

                            mergeSynAccTaxonUuids(doc.getValues("taxonBases.accTaxon.uuids")));

                    }

                }

                nsList.add(ns);

            } else {

                ErrorResponse er = new ErrorResponse();

                er.setErrorMessage("No Taxon Name matches : " + query);

                nsList.add(er);

            }

        }

        mv.addObject(nsList);

        return mv;

    }

    /**

     * Returns a documentation page for the Fuzzy Name Search API.

     * <p>

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

     *

     * @param request Http servlet request.

     * @param response Http servlet response.

     * @return Html page describing the Fuzzy Name Search API

     * @throws IOException

     */

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

    public ModelAndView doGetNameFuzzySearchDocumentation(

            HttpServletRequest request, HttpServletResponse response)

            throws IOException {

        ModelAndView mv = new ModelAndView();

        // Read apt documentation file.

        Resource resource = resourceLoader.getResource("classpath:eu/etaxonomy/cdm/doc/remote/apt/name-catalogue-fuzzy.apt");

        // using input stream as this works for both files in the classes directory

        // as well as files inside jars

        InputStream aptInputStream = resource.getInputStream();

        // Build Html View

        Map<String, String> modelMap = new HashMap<String, String>();

        // Convert Apt to Html

        modelMap.put("html", DocUtils.convertAptToHtml(aptInputStream));

        mv.addAllObjects(modelMap);

        HtmlView hv = new HtmlView();

        mv.setView(hv);

        return mv;

    }

    /**

     * Returns a list of scientific names similar to the <code>{query}</code>

     * string pattern. Each of these scientific names is accompanied by a list of

     * name uuids, a list of taxon uuids and a list of accepted taxon uuids.

     * The underlying (Lucene FuzzyQuery) string distance metric used is based on a

     * fail-fast Levenshtein distance algorithm (is aborted if it is discovered that

     * the mimimum distance between the words is greater than some threshold)

     * <p>

     * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-fuzzy.html">here</a>

     * <p>

     * URI: <b>&#x002F;{datasource-name}&#x002F;name_catalogue/fuzzy</b>

     *

     * @param query

     *                The scientific name pattern(s) to query for. Any wildcard characters in the

     *                query are removed.

     * @param accuracy

     *                Similarity measure (between 0 and 1) to impose on the matching algorithm.

     *                Briefly described, this is equivalent to the edit distance between the two words, divided by

     *                the length of the shorter of the compared terms.

     * @param hits

     *            Maximum number of responses to be returned.

     * @param type

     *            The type of fuzzy search to call. This can be either

     *              "name" : fuzzy searches scientific names corresponding to 'name cache' in CDM or

     *              "atomised" : parses the query into atomised elements and fuzzy searches the individual elements in the CDM

     * @param request Http servlet request.

     * @param response Http servlet response.

     * @return a List of {@link NameSearch} objects each corresponding to a

     *         single query. These are built from {@link TaxonNameBase} entities

     *         which are in turn initialized using the {@link #NAME_SEARCH_INIT_STRATEGY}

     * @throws IOException

     */

    @RequestMapping(value = { "fuzzy" }, method = RequestMethod.GET, params = {"query"})

    public ModelAndView doGetNameFuzzySearch(@RequestParam(value = "query", required = true) String[] queries,

            @RequestParam(value = "accuracy", required = false, defaultValue = "0.6") String accuracy,

            @RequestParam(value = "hits", required = false, defaultValue = "10") String hits,

            @RequestParam(value = "type", required = false, defaultValue = FUZZY_NAME_CACHE) String type,

            HttpServletRequest request, HttpServletResponse response) throws IOException {

        ModelAndView mv = new ModelAndView();

        List<RemoteResponse> nsList = new ArrayList<RemoteResponse>();

        float acc = 0.5f;

        int h = 10;

        try {

            acc = Float.parseFloat(accuracy);

            h = Integer.parseInt(hits);

        } catch(NumberFormatException nfe) {

            ErrorResponse er = new ErrorResponse();

            er.setErrorMessage("accuracy or hits parameter is not a number");

            mv.addObject(er);

            return mv;

        }

        if(acc < 0.0 || acc >= 1.0) {

            ErrorResponse er = new ErrorResponse();

            er.setErrorMessage("accuracy should be >= 0.0 and < 1.0");

            mv.addObject(er);

            return mv;

        }

        // search through each query

        for (String query : queries) {

            if(query.equals("")) {

                ErrorResponse er = new ErrorResponse();

                er.setErrorMessage("Empty query field");

                nsList.add(er);

                continue;

            }

            // remove wildcards if any

            String queryWOWildcards = getQueryWithoutWildCards(query);

            // convert first char to upper case

            char[] stringArray = queryWOWildcards.toCharArray();

            stringArray[0] = Character.toUpperCase(stringArray[0]);

            queryWOWildcards = new String(stringArray);

            logger.info("doGetNameSearch()" + request.getRequestURI() + " for query \"" + queryWOWildcards + " with accuracy " + accuracy);

            //List<NonViralName> nameList = new ArrayList<NonViralName>();

            List<DocumentSearchResult> nameSearchList = new ArrayList<DocumentSearchResult>();

            try {

                if(type.equals(FUZZY_ATOMISED)) {

                    nameSearchList = service.findByNameFuzzySearch(

                            queryWOWildcards,

                            acc,

                            null,

                            false,

                            h);

                } else {

                    nameSearchList = service.findByFuzzyNameCacheSearch(

                            queryWOWildcards,

                            acc,

                            null,

                            false,

                            h);

                }

            } catch (ParseException e) {

                // TODO Auto-generated catch block

                //e.printStackTrace();

                ErrorResponse er = new ErrorResponse();

                er.setErrorMessage("Could not parse name : " + queryWOWildcards);

                nsList.add(er);

                continue;

            }

            // if search is successful then get related information , else return error

            if (nameSearchList == null || !nameSearchList.isEmpty()) {

                NameSearch ns = new NameSearch();

                ns.setRequest(query);

                for (DocumentSearchResult searchResult : nameSearchList) {

                    for(Document doc : searchResult.getDocs()) {

                    // we need to retrieve both taxon uuid of name queried and

                    // the corresponding accepted taxa.

                    // reason to return accepted taxa also, is to be able to get from

                    // scientific name to taxon concept in two web service calls.

                    List<String> tbUuidList = new ArrayList<String>();//nvn.getTaxonBases();

                    List<String> accTbUuidList = new ArrayList<String>();

                    String[] tbUuids = doc.getValues("taxonBases.uuid");

                    String[] tbClassNames = doc.getValues("taxonBases.classInfo.name");

                    for(int i=0;i<tbUuids.length;i++) {

                        if(tbClassNames[i].equals("eu.etaxonomy.cdm.model.taxon.Taxon")) {

                            accTbUuidList.add(tbUuids[i]);

                        }

                    }

                    // update name search object

                    ns.addToResponseList(doc.getValues("titleCache")[0],

                            doc.getValues("nameCache")[0],

                            searchResult.getMaxScore(),

                            doc.getValues("uuid")[0].toString(),

                            doc.getValues("taxonBases.uuid"),

                            mergeSynAccTaxonUuids(doc.getValues("taxonBases.accTaxon.uuids")));

                    }

                }

                nsList.add(ns);

            } else {

                ErrorResponse er = new ErrorResponse();

                er.setErrorMessage("No Taxon Name matches : " + query + ", for given accuracy");

                nsList.add(er);

            }

        }

        mv.addObject(nsList);

        return mv;

    }

    private String[] mergeSynAccTaxonUuids(String[] accTaxonUuids) {

        List<String> accTaxonUuidList = new ArrayList<String>();

        for(String accTaxonUuid : accTaxonUuids) {

            for(String uuidListAsString : accTaxonUuid.split(AcceptedTaxonBridge.ACCEPTED_TAXON_UUID_LIST_SEP)) {

                accTaxonUuidList.add(uuidListAsString);

            }

        }

        return accTaxonUuidList.toArray(new String[0]);

    }

    /**

     * Returns a documentation page for the Name Information API.

     * <p>

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

     *

     * @param request Http servlet request.

     * @param response Http servlet response.

     * @return Html page describing the Name Information API

     * @throws IOException

     */

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

    public ModelAndView doGetNameInformationDocumentation(

            HttpServletRequest request, HttpServletResponse response)

            throws IOException {

        ModelAndView mv = new ModelAndView();

        // Read apt documentation file.

        Resource resource = resourceLoader.getResource("classpath:eu/etaxonomy/cdm/doc/remote/apt/name-catalogue-name-info.apt");

        // using input stream as this works for both files in the classes directory

        // as well as files inside jars

        InputStream aptInputStream = resource.getInputStream();

        // Build Html View

        Map<String, String> modelMap = new HashMap<String, String>();

        // Convert Apt to Html

        modelMap.put("html", DocUtils.convertAptToHtml(aptInputStream));

        mv.addAllObjects(modelMap);

        HtmlView hv = new HtmlView();

        mv.setView(hv);

        return mv;

    }

    /**

     * Returns information related to the scientific name matching the given

     * <code>{nameUuid}</code>. The information includes the name string,

     * relationships, rank, list of related lsids / taxon uuids, etc.

     * <p>

     * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-name-info.html">here</a>

     * <p>

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

     *

     * @param nameUuids uuid(s) of the scientific name to search for.

     * @param request Http servlet request.

     * @param response Http servlet response.

     * @return a List of {@link NameInformation} objects each corresponding to a

     *         single name uuid. These are built from {@link TaxonNameBase} entities

     *         which are in turn initialized using the {@link #NAME_INFORMATION_INIT_STRATEGY}

     * @throws IOException

     */

    @RequestMapping(value = { "name" }, method = RequestMethod.GET, params = {"nameUuid"})

    public ModelAndView doGetNameInformation(@RequestParam(value = "nameUuid", required = true) String[] nameUuids,

            HttpServletRequest request, HttpServletResponse response) throws IOException {

        ModelAndView mv = new ModelAndView();

        List<RemoteResponse> niList = new ArrayList<RemoteResponse>();

        // loop through each name uuid

        for (String nameUuid : nameUuids) {

            logger.info("doGetNameInformation()" + request.getRequestURI() + " for name uuid \""

                    + nameUuid + "\"");

            // find name by uuid

            NonViralName nvn = service.findNameByUuid(UUID.fromString(nameUuid),

                        NAME_INFORMATION_INIT_STRATEGY);

            // if search is successful then get related information, else return error

            if (nvn != null) {

                NameInformation ni = new NameInformation();

                ni.setRequest(nameUuid);

                Reference ref = (Reference) nvn.getNomenclaturalReference();

                String citation = "";

                String citation_details = "";

                if (ref != null) {

                    citation = ref.getTitleCache();

                }

                // update name information object

                ni.setResponse(nvn.getTitleCache(), nvn.getNameCache(), nvn.getRank().getTitleCache(),

                        nvn.getStatus(), citation, nvn.getRelationsFromThisName(),

                        nvn.getRelationsToThisName(), nvn.getTaxonBases());

                niList.add(ni);

            } else {

                ErrorResponse re = new ErrorResponse();

                if(isValid(nameUuid)) {

                    re.setErrorMessage("No Name for given UUID : " + nameUuid);

                } else {

                    re.setErrorMessage(nameUuid + " not a valid UUID");

                }

                niList.add(re);

            }

        }

        mv.addObject(niList);

        return mv;

    }

    /**

     * Returns a documentation page for the Taxon Information API.

     * <p>

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

     *

     * @param request Http servlet request.

     * @param response Http servlet response.

     * @return Html page describing the Taxon Information API

     * @throws IOException

     */

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

    public ModelAndView doGetTaxonInformation(

            HttpServletRequest request, HttpServletResponse response)

            throws IOException {

        ModelAndView mv = new ModelAndView();

        // Read apt documentation file.

        Resource resource = resourceLoader.getResource("classpath:eu/etaxonomy/cdm/doc/remote/apt/name-catalogue-taxon-info.apt");

        // using input stream as this works for both files in the classes directory

        // as well as files inside jars

        InputStream aptInputStream = resource.getInputStream();

        // Build Html View

        Map<String, String> modelMap = new HashMap<String, String>();

        // Convert Apt to Html

        modelMap.put("html", DocUtils.convertAptToHtml(aptInputStream));

        mv.addAllObjects(modelMap);

        HtmlView hv = new HtmlView();

        mv.setView(hv);

        return mv;

    }

    /**

     * Returns information related to the taxon matching the given

     * <code>{taxonUuid}</code>. The information includes the name cache, title cache

     * relationship type, taxonomic status, information , etc.

     * <p>

     * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-taxon-info.html">here</a>

     * <p>

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

     *

     * @param taxonUuid

     *                 The taxon uuid to query for. The classification returned corresponds

     *                 to the first in the alphabetically sorted list of classifications

     *                 currently available in the database.

     *

     * @param request Http servlet request.

     * @param response Http servlet response.

     * @return a List of {@link TaxonInformation} objects each corresponding to a

     *         single query. These are built from {@TaxonBase} entities which are

     *         in turn initialized using the {@link #TAXON_INFORMATION_INIT_STRATEGY}

     * @throws IOException

     */

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

//    public ModelAndView doGetTaxonInformation(

//            @RequestParam(value = "taxonUuid", required = true) String[] taxonUuids,

//            HttpServletRequest request, HttpServletResponse response) throws IOException {

//        return doGetTaxonInformation(taxonUuids,CLASSIFICATION_DEFAULT, new String[]{},request, response);

//    }

    /**

     * Returns information related to the taxon matching the given

     * <code>{taxonUuid}</code>. The information includes the name cache, title cache

     * relationship type, taxonomic status, information , etc.

     * <p>

     * Endpoint documentation can be found <a href="{@docRoot}/../remote/name-catalogue-taxon-info.html">here</a>

     * <p>

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

     *

     * @param taxonUuid

     *                 The taxon uuid to query for.

     * @param classification

     *                 [Optional] String representing the taxonomic classification to use for

     *                 building the classification tree. Defaults to the first in the alphabetically

     *                 sorted list of classifications currently available in the database.

     * @param include

     *                 Array of data types to be included in addition to the normal response

     *

     * @param request Http servlet request.

     * @param response Http servlet response.

     * @return a List of {@link TaxonInformation} objects each corresponding to a

     *         single query. These are built from {@TaxonBase} entities which are

     *         in turn initialized using the {@link #TAXON_INFORMATION_INIT_STRATEGY}

     * @throws IOException

     */

    @RequestMapping(value = { "taxon" }, method = RequestMethod.GET, params = {"taxonUuid"})

    public ModelAndView doGetTaxonInformation(

            @RequestParam(value = "taxonUuid", required = true) String[] taxonUuids,

            @RequestParam(value = "classification", required = false, defaultValue = CLASSIFICATION_DEFAULT) String classificationType,

            @RequestParam(value = "include", required = false, defaultValue = "") String[] includes,

            HttpServletRequest request, HttpServletResponse response) throws IOException {

        ModelAndView mv = new ModelAndView();

        List<RemoteResponse> tiList = new ArrayList<RemoteResponse>();

        // loop through each name uuid

        for (String taxonUuid : taxonUuids) {

            logger.info("doGetTaxonInformation()" + request.getRequestURI() + " for taxon uuid \""

                    + taxonUuid);

            // find name by uuid

            TaxonBase tb = taxonService.findTaxonByUuid(UUID.fromString(taxonUuid),

                    TAXON_INFORMATION_INIT_STRATEGY);

            // if search is successful then get related information, else return error

            if (tb != null) {

                TaxonInformation ti = new TaxonInformation();

                ti.setRequest(taxonUuid);

                // check if result (taxon base) is a taxon or synonym

                if (tb.isInstanceOf(Taxon.class)) {

                    Taxon taxon = (Taxon) tb;

                    // build classification map

                    boolean includeUuids = Arrays.asList(includes).contains(INCLUDE_CLUUIDS);

                    Map classificationMap = getClassification(taxon, classificationType, includeUuids);

                    logger.info("taxon uuid " + taxon.getUuid().toString() + " original hash code : " + System.identityHashCode(taxon) + ", name class " + taxon.getName().getClass().getName());

                    // update taxon information object with taxon related data

                    NonViralName nvn = CdmBase.deproxy(taxon.getName(),NonViralName.class);

                    String secTitle = "" ;

                    String modified = "";

                    if(taxon.getSec() != null) {

                        secTitle = taxon.getSec().getTitleCache();

                        DateTime dt = taxon.getUpdated();

                        modified = fmt.print(dt);

                    }

                    Set<IdentifiableSource> sources = taxon.getSources();

                    String[] didname = getDatasetIdName(sources);

                    ti.setResponseTaxon(tb.getTitleCache(),

                            nvn.getTitleCache(),

                            nvn.getRank().getTitleCache(),

                            ACCEPTED_NAME_STATUS,

                            buildFlagMap(tb),

                            classificationMap,

                            "",

                            didname[0],

                            didname[1],

                            secTitle,

                            modified,

                            taxon.getLsid().toString());

                    Set<SynonymRelationship> synRelationships = taxon.getSynonymRelations();

                    // add synonyms (if exists) to taxon information object

                    for (SynonymRelationship sr : synRelationships) {

                        Synonym syn = sr.getSynonym();

                        String uuid = syn.getUuid().toString();

                        String title = syn.getTitleCache();

                        TaxonNameBase synnvn = syn.getName();

                        String name = synnvn.getTitleCache();

                        String rank = (synnvn.getRank() == null)? "" : synnvn.getRank().getTitleCache();

                        String status = SYNONYM_STATUS;

                        String relLabel = sr.getType()

                                .getInverseRepresentation(Language.DEFAULT())

                                .getLabel();

                        secTitle = "" ;

                        modified = "";

                        if(syn.getSec() != null) {

                            secTitle = syn.getSec().getTitleCache();

                            DateTime dt = syn.getUpdated();

                            modified = fmt.print(dt);

                        }