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package org.bgbm.biovel.drf.checklist;
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import java.net.URI;
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import java.net.URISyntaxException;
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import java.util.EnumSet;
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import java.util.HashMap;
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import java.util.Iterator;
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import java.util.Map;
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import org.apache.http.HttpHost;
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import org.apache.http.client.utils.URIBuilder;
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import org.bgbm.biovel.drf.client.ServiceProviderInfo;
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import org.bgbm.biovel.drf.query.RestClient;
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import org.bgbm.biovel.drf.tnr.msg.Classification;
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import org.bgbm.biovel.drf.tnr.msg.Query;
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import org.bgbm.biovel.drf.tnr.msg.Response;
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import org.bgbm.biovel.drf.tnr.msg.Source;
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import org.bgbm.biovel.drf.tnr.msg.Synonym;
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import org.bgbm.biovel.drf.tnr.msg.Taxon;
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import org.bgbm.biovel.drf.tnr.msg.TaxonName;
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import org.bgbm.biovel.drf.tnr.msg.TnrMsg;
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import org.bgbm.biovel.drf.utils.JSONUtils;
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import org.bgbm.biovel.drf.utils.TnrMsgUtils;
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import org.json.simple.JSONArray;
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import org.json.simple.JSONObject;
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public class GBIFBetaBackboneClient extends AggregateChecklistClient<RestClient> {
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/**
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*
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*/
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private static final HttpHost HTTP_HOST = new HttpHost("ecat-dev.gbif.org",80);
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public static final String ID = "gbif";
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public static final String LABEL = "GBIF Checklist Bank";
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public static final String URL = "http://ecat-dev.gbif.org/";
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public static final String DATA_AGR_URL = "http://data.gbif.org/tutorial/datauseagreement";
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public static final EnumSet<SearchMode> SEARCH_MODES = EnumSet.of(SearchMode.scientificNameExact);
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public GBIFBetaBackboneClient() {
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super();
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}
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public GBIFBetaBackboneClient(String checklistInfoJson) throws DRFChecklistException {
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super(checklistInfoJson);
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}
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/**
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* {@inheritDoc}
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*/
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@Override
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public void initQueryClient() {
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queryClient = new RestClient(HTTP_HOST);
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}
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@Override
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public ServiceProviderInfo buildServiceProviderInfo() {
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ServiceProviderInfo checklistInfo = new ServiceProviderInfo(ID,LABEL,URL,DATA_AGR_URL, getSearchModes());
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URIBuilder uriBuilder = new URIBuilder();
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uriBuilder.setScheme("http");
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uriBuilder.setHost(HTTP_HOST.getHostName());
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uriBuilder.setPath("/ws/checklist");
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URI uri;
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try {
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uri = uriBuilder.build();
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System.out.println("buildChecklistMap");
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String responseBody = queryClient.get(uri);
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JSONObject jsonResponse = JSONUtils.parseJsonToObject(responseBody);
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JSONArray data = (JSONArray) jsonResponse.get("data");
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Iterator<JSONObject> itrResults = data.iterator();
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while(itrResults.hasNext()) {
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JSONObject result = itrResults.next();
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String key = ((Long)result.get("datasetID")).toString();
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String title = (String)result.get("title");
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String url = "http://ecat-dev.gbif.org/checklist/" + key;
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checklistInfo.addSubChecklist(new ServiceProviderInfo(key, title, url, DATA_AGR_URL, getSearchModes()));
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}
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} catch (URISyntaxException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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} catch (DRFChecklistException e) {
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// TODO Auto-generated catch block
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e.printStackTrace();
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}
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return checklistInfo;
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}
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@Override
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public void resolveScientificNamesExact(TnrMsg tnrMsg) throws DRFChecklistException {
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Query query = singleQueryFrom(tnrMsg);
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Iterator<ServiceProviderInfo> itrKeys = getServiceProviderInfo().getSubChecklists().iterator();
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//http://ecat-dev.gbif.org/ws/usage/?rkey={datasetID}&q={sciName}&pagesize=100&searchType=canonical
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while(itrKeys.hasNext()) {
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ServiceProviderInfo checklistInfo = itrKeys.next();
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//if(checklistInfo.getUse()) {
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Map<String, String> paramMap = new HashMap<String, String>();
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paramMap.put("rKey", checklistInfo.getId());
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paramMap.put("pageSize", "100");
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paramMap.put("searchType", "canonical");
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URI namesUri = queryClient.buildUriFromQuery(query,
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"/ws/usage",
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"q",
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paramMap);
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String responseBody = queryClient.get(namesUri);
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updateQueryWithResponse(query,responseBody, paramMap, checklistInfo);
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//}
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}
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}
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private void updateQueryWithResponse(Query query,
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String response,
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Map<String, String> paramMap,
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ServiceProviderInfo checklistInfo) throws DRFChecklistException {
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JSONObject jsonResponse = JSONUtils.parseJsonToObject(response);
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JSONArray dataArray = (JSONArray)jsonResponse.get("data");
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Iterator<JSONObject> itrNameMsgs = dataArray.iterator();
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String taxonId = null;
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while (itrNameMsgs.hasNext()) {
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JSONObject data = itrNameMsgs.next();
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Boolean isSynonym = (Boolean)data.get("isSynonym");
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String taxonomicStatus = (String)data.get("taxonomicStatus");
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String rank = (String)data.get("rank");
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if(rank == null || isSynonym == null){
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continue;
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}
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if(!isSynonym.booleanValue() || (taxonomicStatus != null && taxonomicStatus.equals("Accepted"))) {
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Number taxonIDNumber = (Number)data.get("taxonID");
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taxonId = taxonIDNumber.toString();
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}
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if(isSynonym.booleanValue()) {
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Number taxonIDNumber = (Number)data.get("higherTaxonID");
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taxonId = taxonIDNumber.toString();
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}
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Response tnrResponse = TnrMsgUtils.tnrResponseFor(checklistInfo);
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URI taxonUri = queryClient.buildUriFromQuery(query, "/ws/usage/" + taxonId, null);
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String responseBody = queryClient.get(taxonUri);
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JSONObject res = JSONUtils.parseJsonToObject(responseBody);
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JSONObject jsonAccName = (JSONObject)res.get("data");
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Taxon accName = generateAccName(jsonAccName);
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tnrResponse.setTaxon(accName);
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if(query != null) {
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query.getResponse().add(tnrResponse);
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}
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JSONArray synonyms = (JSONArray) jsonAccName.get("synonyms");
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if(synonyms != null) {
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Iterator iterator = synonyms.iterator();
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System.out.println("Synonms");
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String synTaxonId = null;
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while (iterator.hasNext()) {
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JSONObject syn = (JSONObject)iterator.next();
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Number synIdNumber = (Number) syn.get("taxonID");
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synTaxonId = String.valueOf(synIdNumber);
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URI synonymsUri = queryClient.buildUriFromQuery(query, "/ws/usage/" + synTaxonId, null);
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String synResponse = queryClient.get(synonymsUri);
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JSONObject synonym = JSONUtils.parseJsonToObject(synResponse);
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generateSynonyms((JSONObject)synonym.get("data"), tnrResponse);
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}
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}
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}
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}
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private Taxon generateAccName(JSONObject taxon) {
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Taxon accTaxon = new Taxon();
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TaxonName taxonName = new TaxonName();
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String resName = (String) taxon.get("scientificName");
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taxonName.setFullName(resName);
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taxonName.setCanonicalName((String) taxon.get("canonicalName"));
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taxonName.setRank((String) taxon.get("rank"));
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accTaxon.setTaxonName(taxonName);
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accTaxon.setTaxonomicStatus((String)taxon.get("taxonomicStatus"));
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accTaxon.setAccordingTo((String)taxon.get("accordingTo"));
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//FIXME : To fill in
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String sourceUrl = "";
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Number datasetIDNumber = (Number)taxon.get("datasetID");
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String sourceDatasetID = datasetIDNumber.toString();
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String sourceDatasetName = (String)taxon.get("datasetName");
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String sourceName = ""; // TODO
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Source source = new Source();
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source.setIdentifier(sourceDatasetID);
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source.setDatasetName(sourceDatasetName);
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source.setName(sourceName);
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source.setUrl(sourceUrl);
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accTaxon.getSources().add(source);
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Classification c = new Classification();
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c.setKingdom((String) taxon.get("kingdom"));
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c.setPhylum((String) taxon.get("phylum"));
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c.setClazz((String) taxon.get("class"));
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c.setOrder((String) taxon.get("order"));
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c.setFamily((String) taxon.get("family"));
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c.setGenus((String) taxon.get("genus"));
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accTaxon.setClassification(c);
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return accTaxon;
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}
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private void generateSynonyms(JSONObject synonym, Response tnrResponse) {
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Synonym syn = new Synonym();
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TaxonName taxonName = new TaxonName();
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String resName = (String) synonym.get("scientificName");
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taxonName.setFullName(resName);
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taxonName.setCanonicalName((String) synonym.get("canonicalName"));
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taxonName.setRank((String) synonym.get("rank"));
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syn.setTaxonName(taxonName);
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syn.setTaxonomicStatus((String) synonym.get("taxonomicStatus"));
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syn.setAccordingTo((String) synonym.get("accordingTo"));
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//FIXME : To fill in
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String sourceUrl = "";
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Number datasetIDNumber = (Number) synonym.get("datasetID");
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String sourceDatasetID = datasetIDNumber.toString();
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String sourceDatasetName = (String) synonym.get("datasetName");
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String sourceName = (String) synonym.get("accordingTo"); ;
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Source source = new Source();
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source.setIdentifier(sourceDatasetID);
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source.setDatasetName(sourceDatasetName);
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source.setName(sourceName);
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source.setUrl(sourceUrl);
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syn.getSources().add(source);
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tnrResponse.getSynonym().add(syn);
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}
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@Override
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public void resolveScientificNamesLike(TnrMsg tnrMsg) throws DRFChecklistException {
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// TODO Auto-generated method stub
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}
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@Override
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public void resolveVernacularNamesExact(TnrMsg tnrMsg) throws DRFChecklistException {
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// TODO Auto-generated method stub
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}
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@Override
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public EnumSet<SearchMode> getSearchModes() {
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return SEARCH_MODES;
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}
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@Override
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public void resolveVernacularNamesLike(TnrMsg tnrMsg) throws DRFChecklistException {
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// TODO Auto-generated method stub
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}
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@Override
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public boolean isSupportedIdentifier(String value) {
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return value != null;
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}
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@Override
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public void findByIdentifier(TnrMsg tnrMsg) throws DRFChecklistException {
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// TODO Auto-generated method stub
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}
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}
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