Revision c5e6fc74
Added by Andreas Kohlbecker over 8 years ago
| src/main/java/org/bgbm/biovel/drf/checklist/GBIFBackboneClient.java | ||
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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.rest.ServiceProviderInfo; |
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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.tnr.msg.Response; |
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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 GBIFBackboneClient extends AggregateChecklistClient {
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public class GBIFBackboneClient 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("api.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://uat.gbif.org/developer/species"; |
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public static final String DATA_AGR_URL = "http://data.gbif.org/tutorial/datauseagreement"; |
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private static final String MAX_PAGING_LIMIT = "1000"; |
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private static final String VERSION = "v0.9";
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private static final String VERSION = "v1";
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public static final ServiceProviderInfo CINFO = new ServiceProviderInfo(ID,LABEL,ServiceProviderInfo.DEFAULT_SEARCH_MODE,URL,DATA_AGR_URL, VERSION); |
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public static final EnumSet<SearchMode> SEARCH_MODES = EnumSet.of(SearchMode.scientificNameExact); |
| ... | ... | |
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} |
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@Override |
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public HttpHost getHost() {
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// TODO Auto-generated method stub |
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return new HttpHost("api.gbif.org",80);
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public void initQueryClient() {
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queryClient = new RestClient(HTTP_HOST); |
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} |
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|
| ... | ... | |
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URIBuilder uriBuilder = new URIBuilder(); |
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uriBuilder.setScheme("http");
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uriBuilder.setHost(getHost().getHostName());
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uriBuilder.setHost(HTTP_HOST.getHostName());
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uriBuilder.setPath("/" + checklistInfo.getVersion() + "/dataset/search");
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uriBuilder.setParameter("type", "CHECKLIST");
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uriBuilder.setParameter("limit", MAX_PAGING_LIMIT);
|
| ... | ... | |
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uriBuilder.setParameter("offset", Integer.toString(offset));
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uri = uriBuilder.build(); |
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System.out.println("buildChecklistMap");
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String responseBody = processRESTService(uri); |
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String responseBody = queryClient.processRESTService(uri);
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JSONObject jsonResponse = (JSONObject) JSONUtils.parseJsonToObject(responseBody);
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JSONObject jsonResponse = JSONUtils.parseJsonToObject(responseBody); |
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JSONArray results = (JSONArray) jsonResponse.get("results");
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Iterator<JSONObject> itrResults = results.iterator(); |
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while(itrResults.hasNext()) {
|
| ... | ... | |
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paramMap.put("datasetKey", checklistInfo.getId());
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paramMap.put("limit", MAX_PAGING_LIMIT);
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URI namesUri = buildUriFromQuery(query, "/" + CINFO.getVersion() + "/species", "name", paramMap); |
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URI namesUri = queryClient.buildUriFromQuery(query, "/" + CINFO.getVersion() + "/species", "name", paramMap);
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String responseBody = processRESTService(namesUri); |
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String responseBody = queryClient.processRESTService(namesUri);
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updateQueryWithResponse(query,responseBody, paramMap, checklistInfo); |
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} |
| ... | ... | |
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Map<String, String> paramMap, |
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ServiceProviderInfo ci) throws DRFChecklistException {
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JSONObject jsonResponse = (JSONObject) JSONUtils.parseJsonToObject(response);
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JSONObject jsonResponse = JSONUtils.parseJsonToObject(response); |
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JSONArray results = (JSONArray) jsonResponse.get("results");
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if(results != null) {
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| ... | ... | |
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Long key = (Long)res.get("acceptedKey");
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accTaxonId = key.toString(); |
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URI taxonUri = buildUriFromQuery(query, "/" + CINFO.getVersion() + "/species/" + accTaxonId, null); |
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String responseBody = processRESTService(taxonUri); |
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URI taxonUri = queryClient.buildUriFromQuery(query, "/" + CINFO.getVersion() + "/species/" + accTaxonId, null);
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String responseBody = queryClient.processRESTService(taxonUri);
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JSONObject taxon = (JSONObject) JSONUtils.parseJsonToObject(responseBody);
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JSONObject taxon = JSONUtils.parseJsonToObject(responseBody); |
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Taxon accName = generateAccName(taxon); |
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tnrResponse.setTaxon(accName); |
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|
| ... | ... | |
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do {
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paramMap.put("offset", Integer.toString(offset));
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URI synonymsUri = buildUriFromQuery(query, "/" + CINFO.getVersion() + "/species/" + accTaxonId + "/synonyms", paramMap); |
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String synResponse = processRESTService(synonymsUri); |
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URI synonymsUri = queryClient.buildUriFromQuery(query, "/" + CINFO.getVersion() + "/species/" + accTaxonId + "/synonyms", paramMap);
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String synResponse = queryClient.processRESTService(synonymsUri);
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JSONObject pagedSynonyms = (JSONObject) JSONUtils.parseJsonToObject(synResponse);
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JSONObject pagedSynonyms = JSONUtils.parseJsonToObject(synResponse); |
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generateSynonyms(pagedSynonyms, tnrResponse); |
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endOfRecords = (Boolean) pagedSynonyms.get("endOfRecords");
|
| ... | ... | |
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Iterator<JSONObject> itrSynonyms = synonyms.iterator(); |
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while(itrSynonyms.hasNext()) {
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Synonym synonym = new Synonym(); |
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JSONObject synonymjs = (JSONObject) itrSynonyms.next();
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JSONObject synonymjs = itrSynonyms.next(); |
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TaxonName taxonName = new TaxonName(); |
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String resName = (String) synonymjs.get("scientificName");
|
| ... | ... | |
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//Add a comment to this line |
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URIBuilder uriBuilder = new URIBuilder(); |
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uriBuilder.setScheme("http");
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uriBuilder.setHost(getHost().getHostName());
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uriBuilder.setHost(HTTP_HOST.getHostName());
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uriBuilder.setPath("/" + CINFO.getVersion() + "/dataset/" + datasetKey);
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URI uri = uriBuilder.build(); |
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String responseBody = processRESTService(uri); |
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String responseBody = queryClient.processRESTService(uri);
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JSONObject datasetInfo = (JSONObject) JSONUtils.parseJsonToObject(responseBody);
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JSONObject datasetInfo = JSONUtils.parseJsonToObject(responseBody); |
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return (String) datasetInfo.get("title");
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} |
Also available in: Unified diff
separating query protocol implementation from checklist clients