EDIT

package org.bgbm.biovel.drf.checklist;

import java.net.URI;

import java.net.URISyntaxException;

import java.util.EnumSet;

import java.util.HashMap;

import java.util.Iterator;

import java.util.Map;

import org.apache.http.HttpHost;

import org.apache.http.client.utils.URIBuilder;

import org.bgbm.biovel.drf.client.ServiceProviderInfo;

import org.bgbm.biovel.drf.query.RestClient;

import org.bgbm.biovel.drf.tnr.msg.Classification;

import org.bgbm.biovel.drf.tnr.msg.Query;

import org.bgbm.biovel.drf.tnr.msg.Response;

import org.bgbm.biovel.drf.tnr.msg.Source;

import org.bgbm.biovel.drf.tnr.msg.Synonym;

import org.bgbm.biovel.drf.tnr.msg.Taxon;

import org.bgbm.biovel.drf.tnr.msg.TaxonName;

import org.bgbm.biovel.drf.tnr.msg.TnrMsg;

import org.bgbm.biovel.drf.utils.JSONUtils;

import org.bgbm.biovel.drf.utils.TnrMsgUtils;

import org.json.simple.JSONArray;

import org.json.simple.JSONObject;

public class GBIFBetaBackboneClient extends AggregateChecklistClient<RestClient> {

    /**

     *

     */

    private static final HttpHost HTTP_HOST = new HttpHost("ecat-dev.gbif.org",80);

    public static final String ID = "gbif";

    public static final String LABEL = "GBIF Checklist Bank";

    public static final String URL = "http://ecat-dev.gbif.org/";

    public static final String DATA_AGR_URL = "http://data.gbif.org/tutorial/datauseagreement";

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

    public GBIFBetaBackboneClient() {

        super();

    }

    public GBIFBetaBackboneClient(String checklistInfoJson) throws DRFChecklistException {

        super(checklistInfoJson);

    }

    /**

     * {@inheritDoc}

     */

    @Override

    public void initQueryClient() {

        queryClient = new RestClient(HTTP_HOST);

    }

    @Override

    public ServiceProviderInfo buildServiceProviderInfo()  {

        ServiceProviderInfo checklistInfo = new ServiceProviderInfo(ID,LABEL,URL,DATA_AGR_URL, getSearchModes());

        URIBuilder uriBuilder = new URIBuilder();

        uriBuilder.setScheme("http");

        uriBuilder.setHost(HTTP_HOST.getHostName());

        uriBuilder.setPath("/ws/checklist");

        URI uri;

        try {

            uri = uriBuilder.build();

            System.out.println("buildChecklistMap");

            String responseBody = queryClient.processRESTService(uri);

            JSONObject jsonResponse = JSONUtils.parseJsonToObject(responseBody);

            JSONArray data = (JSONArray) jsonResponse.get("data");

            Iterator<JSONObject> itrResults = data.iterator();

            while(itrResults.hasNext()) {

                JSONObject result = itrResults.next();

                String key = ((Long)result.get("datasetID")).toString();

                String title = (String)result.get("title");

                String url =  "http://ecat-dev.gbif.org/checklist/" + key;

                checklistInfo.addSubChecklist(new ServiceProviderInfo(key, title,  url, DATA_AGR_URL, getSearchModes()));

            }

        } catch (URISyntaxException e) {

            // TODO Auto-generated catch block

            e.printStackTrace();

        } catch (DRFChecklistException e) {

            // TODO Auto-generated catch block

            e.printStackTrace();

        }

        return checklistInfo;

    }

    @Override

    public void resolveScientificNamesExact(TnrMsg tnrMsg) throws DRFChecklistException {

        Query query = singleQueryFrom(tnrMsg);

        Iterator<ServiceProviderInfo> itrKeys = getServiceProviderInfo().getSubChecklists().iterator();

        //http://ecat-dev.gbif.org/ws/usage/?rkey={datasetID}&q={sciName}&pagesize=100&searchType=canonical

        while(itrKeys.hasNext()) {

            ServiceProviderInfo checklistInfo = itrKeys.next();

            //if(checklistInfo.getUse()) {

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

                paramMap.put("rKey", checklistInfo.getId());

                paramMap.put("pageSize", "100");

                paramMap.put("searchType", "canonical");

                URI namesUri = queryClient.buildUriFromQuery(query,

                        "/ws/usage",

                        "q",

                        paramMap);

                String responseBody = queryClient.processRESTService(namesUri);

                updateQueryWithResponse(query,responseBody, paramMap, checklistInfo);

            //}

        }

    }

    @Override

    public int getMaxPageSize() {

        return 10;

    }

    private void updateQueryWithResponse(Query query,

            String response,

            Map<String, String> paramMap,

            ServiceProviderInfo checklistInfo) throws DRFChecklistException {

        JSONObject jsonResponse = JSONUtils.parseJsonToObject(response);

        JSONArray dataArray = (JSONArray)jsonResponse.get("data");

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

        String taxonId = null;

        while (itrNameMsgs.hasNext()) {

            JSONObject data = itrNameMsgs.next();

            Boolean isSynonym = (Boolean)data.get("isSynonym");

            String taxonomicStatus = (String)data.get("taxonomicStatus");

            String rank = (String)data.get("rank");

            if(rank == null || isSynonym == null){

                continue;

            }

            if(!isSynonym.booleanValue() ||  (taxonomicStatus != null && taxonomicStatus.equals("Accepted"))) {

                Number taxonIDNumber = (Number)data.get("taxonID");

                taxonId = taxonIDNumber.toString();

            }

            if(isSynonym.booleanValue()) {

                Number taxonIDNumber = (Number)data.get("higherTaxonID");

                taxonId = taxonIDNumber.toString();

            }

            Response tnrResponse = TnrMsgUtils.tnrResponseFor(checklistInfo);

            URI taxonUri = queryClient.buildUriFromQuery(query, "/ws/usage/" + taxonId, null);

            String responseBody = queryClient.processRESTService(taxonUri);

            JSONObject res = JSONUtils.parseJsonToObject(responseBody);

            JSONObject jsonAccName = (JSONObject)res.get("data");

            Taxon accName = generateAccName(jsonAccName);

            tnrResponse.setTaxon(accName);

            if(query != null) {

                query.getResponse().add(tnrResponse);

            }

            JSONArray synonyms = (JSONArray) jsonAccName.get("synonyms");

            if(synonyms != null) {

                Iterator iterator = synonyms.iterator();

                System.out.println("Synonms");

                String synTaxonId = null;

                while (iterator.hasNext()) {

                    JSONObject syn = (JSONObject)iterator.next();

                    Number synIdNumber = (Number) syn.get("taxonID");

                    synTaxonId = String.valueOf(synIdNumber);

                    URI synonymsUri = queryClient.buildUriFromQuery(query, "/ws/usage/" + synTaxonId, null);

                    String synResponse = queryClient.processRESTService(synonymsUri);

                    JSONObject synonym = JSONUtils.parseJsonToObject(synResponse);

                    generateSynonyms((JSONObject)synonym.get("data"), tnrResponse);

                }

            }

        }

    }

    private Taxon generateAccName(JSONObject taxon) {

        Taxon accTaxon = new Taxon();

        TaxonName taxonName = new TaxonName();

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

        taxonName.setFullName(resName);

        taxonName.setCanonicalName((String) taxon.get("canonicalName"));

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

        accTaxon.setTaxonName(taxonName);

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

        accTaxon.setAccordingTo((String)taxon.get("accordingTo"));

        //FIXME : To fill in

        String sourceUrl = "";

        Number datasetIDNumber = (Number)taxon.get("datasetID");

        String sourceDatasetID = datasetIDNumber.toString();

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

        String sourceName = ""; // TODO

        Source source = new Source();

        source.setIdentifier(sourceDatasetID);

        source.setDatasetName(sourceDatasetName);

        source.setName(sourceName);

        source.setUrl(sourceUrl);

        accTaxon.getSources().add(source);

        Classification c = new Classification();

        c.setKingdom((String) taxon.get("kingdom"));

        c.setPhylum((String) taxon.get("phylum"));

        c.setClazz((String) taxon.get("class"));

        c.setOrder((String) taxon.get("order"));

        c.setFamily((String) taxon.get("family"));

        c.setGenus((String) taxon.get("genus"));

        accTaxon.setClassification(c);

        return accTaxon;

    }

    private void generateSynonyms(JSONObject synonym, Response tnrResponse) {

        Synonym syn = new Synonym();

        TaxonName taxonName = new TaxonName();

        String resName = (String) synonym.get("scientificName");

        taxonName.setFullName(resName);

        taxonName.setCanonicalName((String) synonym.get("canonicalName"));

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

        syn.setTaxonName(taxonName);

        syn.setTaxonomicStatus((String) synonym.get("taxonomicStatus"));

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

        //FIXME : To fill in

        String sourceUrl = "";

        Number datasetIDNumber = (Number) synonym.get("datasetID");

        String sourceDatasetID = datasetIDNumber.toString();

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

        String sourceName = (String) synonym.get("accordingTo");		;

        Source source = new Source();

        source.setIdentifier(sourceDatasetID);

        source.setDatasetName(sourceDatasetName);

        source.setName(sourceName);

        source.setUrl(sourceUrl);

        syn.getSources().add(source);

        tnrResponse.getSynonym().add(syn);

    }

    @Override

    public void resolveScientificNamesLike(TnrMsg tnrMsg) throws DRFChecklistException {

        // TODO Auto-generated method stub

    }

    @Override

    public void resolveVernacularNamesExact(TnrMsg tnrMsg) throws DRFChecklistException {

        // TODO Auto-generated method stub

    }

    @Override

    public EnumSet<SearchMode> getSearchModes() {

        return SEARCH_MODES;

    }

    @Override

    public void resolveVernacularNamesLike(TnrMsg tnrMsg) throws DRFChecklistException {

        // TODO Auto-generated method stub

    }

    @Override

    public boolean isSupportedIdentifier(String value) {

        return value != null;

    }

    @Override

    public void findByIdentifier(TnrMsg tnrMsg) throws DRFChecklistException {

        // TODO Auto-generated method stub

    }

}