EDIT

package org.cybertaxonomy.utis.checklist;

import java.net.URI;

import java.util.ArrayList;

import java.util.EnumSet;

import java.util.HashMap;

import java.util.Iterator;

import java.util.List;

import java.util.Map;

import org.apache.http.HttpHost;

import org.apache.http.ParseException;

import org.cybertaxonomy.utis.client.ServiceProviderInfo;

import org.cybertaxonomy.utis.query.RestClient;

import org.cybertaxonomy.utis.tnr.msg.Classification;

import org.cybertaxonomy.utis.tnr.msg.NameType;

import org.cybertaxonomy.utis.tnr.msg.Query;

import org.cybertaxonomy.utis.tnr.msg.Response;

import org.cybertaxonomy.utis.tnr.msg.Source;

import org.cybertaxonomy.utis.tnr.msg.Synonym;

import org.cybertaxonomy.utis.tnr.msg.Taxon;

import org.cybertaxonomy.utis.tnr.msg.TaxonName;

import org.cybertaxonomy.utis.tnr.msg.TnrMsg;

import org.cybertaxonomy.utis.utils.IdentifierUtils;

import org.cybertaxonomy.utis.utils.TnrMsgUtils;

import org.gbif.nameparser.NameParser;

import org.json.simple.JSONArray;

import org.json.simple.JSONAware;

import org.json.simple.JSONObject;

import org.json.simple.parser.JSONParser;

public class BgbmEditClient extends AggregateChecklistClient<RestClient> {

    /**

     *

     */

    public static final String ID = "bgbm-cdm-server";

    public static final String LABEL = "Name catalogues served by the BGBM CDM Server";

    public static final String DOC_URL = "http://wp5.e-taxonomy.eu/cdmlib/rest-api-name-catalogue.html";

    public static final String COPYRIGHT_URL = "http://wp5.e-taxonomy.eu/cdmlib/license.html";

    private static final String SERVER_PATH_PREFIX = "/";

    private static final HttpHost HTTP_HOST = new HttpHost("api.cybertaxonomy.org", 80); // new HttpHost("test.e-taxonomy.eu", 80);

    private final Map<String,Query> taxonIdQueryMap = new HashMap<String,Query>();

    private final Map<String,String> taxonIdMatchStringMap = new HashMap<String, String>();

    public static final EnumSet<SearchMode> SEARCH_MODES = EnumSet.of(

            SearchMode.scientificNameExact,

            SearchMode.scientificNameLike,

            SearchMode.findByIdentifier

            );

    public BgbmEditClient() {

        super();

    }

    public BgbmEditClient(String checklistInfoJson) throws DRFChecklistException {

        super(checklistInfoJson);

    }

    @Override

    public void initQueryClient() {

        queryClient = new RestClient(HTTP_HOST);

    }

    @Override

    public ServiceProviderInfo buildServiceProviderInfo() {

        ServiceProviderInfo checklistInfo = new ServiceProviderInfo(ID,LABEL,DOC_URL,COPYRIGHT_URL, getSearchModes());

        checklistInfo.addSubChecklist(new ServiceProviderInfo("col",

                "Catalogue Of Life (EDIT - name catalogue end point)",

                "http://wp5.e-taxonomy.eu/cdmlib/rest-api-name-catalogue.html",

                "http://www.catalogueoflife.org/col/info/copyright", ServiceProviderInfo.DEFAULT_SEARCH_MODE));

        return checklistInfo;

    }

    /**

     * Adds the acceptedTaxonUuids found in the <code>responseBody</code> to the

     * private field <code>taxonIdQueryMap</code>

     * and populates the <code>taxonIdMatchStringMap</code>

     *

     * @param queryList

     * @param responseBodyJson

     * @throws DRFChecklistException

     */

    private void buildTaxonIdMapsFromCatalogueServiceResponse(List<Query> queryList , String responseBody) throws DRFChecklistException {

        JSONArray responseBodyJson = parseResponseBody(responseBody, JSONArray.class);

        if(responseBodyJson.size() != queryList.size()){

            throw new DRFChecklistException("Query and Response lists have different lengths");

        }

        Iterator<JSONObject> itrNameMsgs = responseBodyJson.iterator();

        for (Query query : queryList) {

            JSONArray responseArray = (JSONArray) itrNameMsgs.next().get("response");

            if(responseArray != null) {

                Iterator<JSONObject> resIterator = responseArray.iterator();

                while (resIterator.hasNext()) {

                    JSONObject res = resIterator.next();

                    JSONArray accTaxonUuidArray = (JSONArray) res.get("acceptedTaxonUuids");

                    String matchingName = res.get("title").toString();

                    Iterator<String> atIterator = accTaxonUuidArray.iterator();

                    while (atIterator.hasNext()) {

                        String acceptedTaxonId = atIterator.next();

                        boolean isAcceptedTaxonMatch = res.get("taxonConceptUuids").toString().contains(acceptedTaxonId);

                        if(!taxonIdQueryMap.containsKey(acceptedTaxonId) || isAcceptedTaxonMatch){

                            // matches for accepted taxa should be preferred here

                            // matches for synomymy or other types should never overwrite

                            // accepted taxon matches

                            taxonIdQueryMap.put(acceptedTaxonId, query);

                            taxonIdMatchStringMap.put(acceptedTaxonId, matchingName);

                        }

                        //System.out.println("Found accepted taxon id : " + accTaxonId);

                    }

                }

            }

        }

    }

    /**

     * Adds the acceptedTaxonUuids found in the <code>responseBody</code> to the

     * private field <code>taxonIdQueryMap</code>

     * and populates the <code>taxonIdMatchStringMap</code>

     *

     * @param queryList

     * @param responseBodyJson

     * @throws DRFChecklistException

     */

    private void addTaxaToTaxonIdMapFromIdentifierServiceResponse(List<Query> queryList , String responseBody) throws DRFChecklistException {

        /*

         * {"class":"DefaultPagerImpl","count":8,"currentIndex":0,"firstRecord":1,"indices":[0],"lastRecord":8,"nextIndex":0,"pageSize":30,"pagesAvailable":1,"prevIndex":0,

            "records":[

                  {

                  "cdmEntity":{

                      "cdmUuid":"0cf5a6fe-b1df-4f4f-85a8-31fef4be2a68",

                      "class":"CdmEntity",

                      "titleCache":"Abies alba Mill. sec. SCHMEIL-FITSCHEN, Flora von Deutschland und angrenzenden Ländern, 89. Aufl"},

                  "class":"FindByIdentifierDTO",

                   "identifier":{"class":"AlternativeIdentifier","identifier":"1","typeLabel":"Florein Identifier","typeUuid":"8b67291e-96e0-4556-8d6a-c94e8750b301"}},{"cdmEntity":{"cdmUuid":"3d256539-d7f7-4dd1-ad7f-cd6e4c141f24","class":"CdmEntity","titleCache":"Abies alba Mill. sec. OBERDORFER, Pflanzensoziologische Exkursionsflora, ed. 7"},"class":"FindByIdentifierDTO","identifier":{"class":"AlternativeIdentifier","identifier":"1","typeLabel":"Florein Identifier","typeUuid":"8b67291e-96e0-4556-8d6a-c94e8750b301"}},{"cdmEntity":{"cdmUuid":"61c2bc4f-a23d-4160-8f14-625b4484fc2f","class":"CdmEntity","titleCache":"Abies alba Mill. sec. HEGI, Illustrierte Flora von Mitteleuropa, Aufl. 2 u. 3"},"class":"FindByIdentifierDTO","identifier":{"class":"AlternativeIdentifier","identifier":"1","typeLabel":"Florein Identifier","typeUuid":"8b67291e-96e0-4556-8d6a-c94e8750b301"}},{"cdmEntity":{"cdmUuid":"7a63f215-0a41-4b7e-9394-bda4521d6ad1","class":"CdmEntity","titleCache":"Abies alba Mill. sec. GREUTER et. al., Med-Checklist bisher Bde. 1, 3 und 4"},"class":"FindByIdentifierDTO","identifier":{"class":"AlternativeIdentifier","identifier":"1","typeLabel":"Florein Identifier","typeUuid":"8b67291e-96e0-4556-8d6a-c94e8750b301"}},{"cdmEntity":{"cdmUuid":"872088a4-95f4-472c-ae79-a29028bb3fbf","class":"CdmEntity","titleCache":"Abies alba Mill. sec. Wisskirchen & Haeupler, 1998"},"class":"FindByIdentifierDTO","identifier":{"class":"AlternativeIdentifier","identifier":"1","typeLabel":"Florein Identifier","typeUuid":"8b67291e-96e0-4556-8d6a-c94e8750b301"}},{"cdmEntity":{"cdmUuid":"90ee17be-d455-4564-949d-9c53e27a6a6f","class":"CdmEntity","titleCache":"Abies alba Mill. sec. TUTIN et al., Flora Europaea"},"class":"FindByIdentifierDTO","identifier":{"class":"AlternativeIdentifier","identifier":"1","typeLabel":"Florein Identifier","typeUuid":"8b67291e-96e0-4556-8d6a-c94e8750b301"}},{"cdmEntity":{"cdmUuid":"b0d35335-63e6-41ab-bdb0-d01851134e9c","class":"CdmEntity","titleCache":"Abies alba Mill. sec. EHRENDORFER, Liste der Gefäßpflanzen Mitteleuropas, 2. Aufl"},"class":"FindByIdentifierDTO","identifier":{"class":"AlternativeIdentifier","identifier":"1","typeLabel":"Florein Identifier","typeUuid":"8b67291e-96e0-4556-8d6a-c94e8750b301"}},{"cdmEntity":{"cdmUuid":"b7a352aa-1f73-41f3-a4e3-b24fc1c2cd5f","class":"CdmEntity","titleCache":"Abies alba Mill. sec. ROTHMALER, 1990"},"class":"FindByIdentifierDTO","identifier":{"class":"AlternativeIdentifier","identifier":"1","typeLabel":"Florein Identifier","typeUuid":"8b67291e-96e0-4556-8d6a-c94e8750b301"}}],"suggestion":""}

        */

        if(queryList.size() > 1){

            throw new DRFChecklistException("Only single Querys are supported");

        }

        Query query = queryList.get(0);

        JSONObject jsonPager = parseResponseBody(responseBody, JSONObject.class);

        JSONArray jsonRecords = (JSONArray) jsonPager.get("records");

        Iterator<JSONObject> resIterator = jsonRecords.iterator();

        while (resIterator.hasNext()) {

            JSONObject record = resIterator.next();

            JSONObject cdmEntity = (JSONObject) record.get("cdmEntity");

            String uuid = cdmEntity.get("cdmUuid").toString();

            taxonIdQueryMap.put(uuid, query);

        }

    }

    private void addTaxonToTaxonIdMap(List<Query> queryList , String responseBody) throws DRFChecklistException {

        if(queryList.size() > 1){

            throw new DRFChecklistException("Only single Querys are supported");

        }

        Query query = queryList.get(0);

        JSONObject cdmEntity = parseResponseBody(responseBody, JSONObject.class);

        String uuid = cdmEntity.get("uuid").toString();

        taxonIdQueryMap.put(uuid, query);

    }

    /**

     * @param responseBody

     * @return

     * @throws DRFChecklistException

     */

    private <T extends JSONAware> T parseResponseBody(String responseBody, Class<T> jsonType) throws DRFChecklistException {

        // TODO use Jackson instead? it is much faster!

        JSONParser parser = new JSONParser();

        Object obj;

        try {

            obj = parser.parse(responseBody);

        } catch (ParseException e) {

            logger.error("parseResponseBody() - ", e);

            throw new DRFChecklistException(e);

        } catch (org.json.simple.parser.ParseException e) {

            logger.error("parseResponseBody() - ", e);

            throw new DRFChecklistException(e);

        }

        if(jsonType.isAssignableFrom(obj.getClass())){

            return jsonType.cast(obj);

        } else {

            throw new DRFChecklistException("parseResponseBody() - deserialized responseBody is not of type " + jsonType ) ;

        }

    }

    private Taxon generateAccName(JSONObject taxon) {

        Taxon accTaxon = new Taxon();

        TaxonName taxonName = new TaxonName();

        String resName = (String) taxon.get("name");

        taxonName.setFullName(resName);

        NameParser ecatParser = new NameParser();

        String nameCanonical = ecatParser.parseToCanonical(resName);

        taxonName.setCanonicalName(nameCanonical);

        taxonName.setRank((String) taxon.get("rank"));

        String lsid = (String) taxon.get("lsid");

        JSONObject scrutinyjs = (JSONObject)taxon.get("taxonomicScrutiny");

        String accordingTo = (String) scrutinyjs.get("accordingTo");

        String modified = (String) scrutinyjs.get("modified");

        accTaxon.setTaxonName(taxonName);

        accTaxon.setTaxonomicStatus((String)taxon.get("taxonStatus"));

        accTaxon.setAccordingTo(accordingTo);

        accTaxon.setIdentifier(lsid);

        JSONObject sourcejs = (JSONObject)taxon.get("source");

        String sourceUrl = (String) sourcejs.get("url");

        String sourceDatasetID =  (String) sourcejs.get("datasetID");

        String sourceDatasetName = (String) sourcejs.get("datasetName");

        String sourceName = "";

        Source source = new Source();

        source.setIdentifier(sourceDatasetID);

        source.setDatasetName(sourceDatasetName);

        source.setName(sourceName);

        source.setUrl(sourceUrl);

        accTaxon.getSources().add(source);

        JSONObject classification =(JSONObject)taxon.get("classification");

        if(classification != null) {

            Classification c = new Classification();

            c.setKingdom((String) classification.get("Kingdom"));

            c.setPhylum((String) classification.get("Phylum"));

            c.setClazz((String) classification.get("Class"));

            c.setOrder((String) classification.get("Order"));

            c.setFamily((String) classification.get("Family"));

            c.setGenus((String) classification.get("Genus"));

            accTaxon.setClassification(c);

        }

        return accTaxon;

    }

    private void generateSynonyms(JSONArray relatedTaxa, Response tnrResponse) {

        Iterator<JSONObject> itrSynonyms = relatedTaxa.iterator();

        while(itrSynonyms.hasNext()) {

            JSONObject synonymjs = itrSynonyms.next();

            String status = (String) synonymjs.get("taxonStatus");

            if(status != null && status.equals("synonym")) {

                Synonym synonym = new Synonym();

                TaxonName taxonName = new TaxonName();

                String resName = (String) synonymjs.get("name");

                taxonName.setFullName(resName);

                NameParser ecatParser = new NameParser();

                String nameCanonical = ecatParser.parseToCanonical(resName);

                taxonName.setCanonicalName(nameCanonical);

                synonym.setTaxonomicStatus((String)synonymjs.get("taxonStatus"));

                taxonName.setRank((String) synonymjs.get("rank"));

                synonym.setTaxonName(taxonName);

                JSONObject scrutinyjs = (JSONObject)synonymjs.get("taxonomicScrutiny"); // TODO this will change in future releases of the service

                synonym.setAccordingTo((String) scrutinyjs.get("accordingTo"));

                JSONObject sourcejs = (JSONObject)synonymjs.get("source");

                String sourceUrl = (String) sourcejs.get("url");

                String sourceDatasetID =  (String) sourcejs.get("datasetID");

                String sourceDatasetName = (String) sourcejs.get("datasetName");

                String sourceName = "";

                Source source = new Source();

                source.setIdentifier(sourceDatasetID);

                source.setDatasetName(sourceDatasetName);

                source.setName(sourceName);

                source.setUrl(sourceUrl);

                synonym.getSources().add(source);

                tnrResponse.getSynonym().add(synonym);

            }

        }

    }

    @Override

    public void resolveScientificNamesExact(TnrMsg tnrMsg) throws DRFChecklistException {

        List<Query> queryList = tnrMsg.getQuery();

        // selecting one request as representative, only

        // the search mode and addSynonmy flag are important

        // for the further usage of the request object

        Query.Request request = queryList.get(0).getRequest();

        for (ServiceProviderInfo checklistInfo : getServiceProviderInfo().getSubChecklists()) {

            URI namesUri = queryClient.buildUriFromQueryList(queryList,

                    SERVER_PATH_PREFIX + checklistInfo.getId() + "/name_catalogue.json",

                    "query",

                    "*", null);

            String searchResponseBody = queryClient.get(namesUri);

            buildTaxonIdMapsFromCatalogueServiceResponse(queryList, searchResponseBody);

            List<String> taxonIdList = new ArrayList<String>(taxonIdQueryMap.keySet());

            if(taxonIdList.size() > 0) {

                URI taxonUri = queryClient.buildUriFromQueryStringList(taxonIdList,

                        SERVER_PATH_PREFIX + checklistInfo.getId() + "/name_catalogue/taxon.json",

                        "taxonUuid",

                        null);

                String taxonResponseBody = queryClient.get(taxonUri);

                updateQueriesWithResponse(taxonResponseBody, checklistInfo, request);

            }

        }

    }

    @Override

    public void resolveScientificNamesLike(TnrMsg tnrMsg) throws DRFChecklistException {

        // delegate to resolveScientificNamesExact, since the like search mode is handled in buildUriFromQueryList

        resolveScientificNamesExact(tnrMsg);

    }

    @Override

    public void resolveVernacularNamesExact(TnrMsg tnrMsg) throws DRFChecklistException {

        // TODO Auto-generated method stub

    }

    @Override

    public void resolveVernacularNamesLike(TnrMsg tnrMsg) throws DRFChecklistException {

        // TODO Auto-generated method stub

    }

    @Override

    public void findByIdentifier(TnrMsg tnrMsg) throws DRFChecklistException {

        List<Query> queryList = tnrMsg.getQuery();

        if(queryList.size() > 1){

            throw new DRFChecklistException("Only single Querys are supported");

        }

        Query.Request request = queryList.get(0).getRequest();

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

        findByIdentifierParameters.put("includeEntity", "1");

        String identifier = request.getQueryString();

        for (ServiceProviderInfo checklistInfo : getServiceProviderInfo().getSubChecklists()) {

            // taxon/findByIdentifier.json?identifier=1&includeEntity=1

            if(IdentifierUtils.checkLSID(identifier)){

                URI namesUri = queryClient.buildUriFromQueryList(queryList,

                        SERVER_PATH_PREFIX + checklistInfo.getId() + "/authority/metadata.do",

                        "lsid",

                        null,

                        null );

                String responseBody = queryClient.get(namesUri);

                addTaxonToTaxonIdMap(queryList, responseBody);

            } else {

                URI namesUri = queryClient.buildUriFromQueryList(queryList,

                        SERVER_PATH_PREFIX + checklistInfo.getId() + "/taxon/findByIdentifier.json",

                        "identifier",

                        null, // like search for identifiers not supported by this client

                        findByIdentifierParameters );

                String responseBody = queryClient.get(namesUri);

                addTaxaToTaxonIdMapFromIdentifierServiceResponse(queryList, responseBody);

            }

            List<String> taxonIdList = new ArrayList<String>(taxonIdQueryMap.keySet());

            if(taxonIdList.size() > 0) {

                URI taxonUri = queryClient.buildUriFromQueryStringList(taxonIdList,

                        SERVER_PATH_PREFIX + checklistInfo.getId() + "/name_catalogue/taxon.json",

                        "taxonUuid",

                        null);

                String taxonResponseBody = queryClient.get(taxonUri);

                updateQueriesWithResponse(taxonResponseBody, checklistInfo, request);

            }

        }

    }

    private void updateQueriesWithResponse(String responseBody, ServiceProviderInfo ci, Query.Request request) throws DRFChecklistException {

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

            return;

        }

        JSONArray responseBodyJson = parseResponseBody(responseBody, JSONArray.class);

        Iterator<JSONObject> itrTaxonMsgs = responseBodyJson.iterator();

        int i = -1;

        while(itrTaxonMsgs.hasNext()) {

            i++;

            JSONObject taxonInfo = itrTaxonMsgs.next();

            JSONObject taxonResponse = (JSONObject) taxonInfo.get("response");

            JSONObject taxon = (JSONObject) taxonResponse.get("taxon");

            JSONArray relatedTaxa = (JSONArray) taxonResponse.get("relatedTaxa");

            JSONObject taxonRequest = (JSONObject) taxonInfo.get("request");

            String taxonUuid = (String) taxonRequest.get("taxonUuid");

            if(taxon != null) {

                Response tnrResponse = TnrMsgUtils.tnrResponseFor(ci);

                String matchingName = taxonIdMatchStringMap.get(taxonUuid);

                if(matchingName != null){

                    tnrResponse.setMatchingNameString(matchingName);

                    tnrResponse.setMatchingNameType(matchingName.equals(taxon.get("name").toString()) ? NameType.TAXON : NameType.SYNONYM);

                }

                Taxon accName = generateAccName(taxon);

                tnrResponse.setTaxon(accName);

                if(request.isAddSynonymy()){

                    generateSynonyms(relatedTaxa, tnrResponse);

                }

                Query query = taxonIdQueryMap.get(taxonUuid);

                if(query != null) {

                    query.getResponse().add(tnrResponse);

                }

            }

        }

    }

    @Override

    public EnumSet<SearchMode> getSearchModes() {

        return SEARCH_MODES ;

    }

    @Override

    public boolean isSupportedIdentifier(String value) {

        // return IdentifierUtils.checkLSID(value) || IdentifierUtils.checkUUID(value);

        return value != null;

    }

}