package jalview.ws.dbsources;
-import jalview.ws.uimodel.PDBSearchResultPojo;
+import jalview.ws.uimodel.PDBSearchRequest;
+import jalview.ws.uimodel.PDBSearchResponse;
import jalview.ws.uimodel.PDBSummaryListModel;
+import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
+import java.util.ArrayList;
import java.util.Iterator;
+import java.util.List;
-import javax.swing.DefaultListModel;
import javax.ws.rs.core.MediaType;
import org.json.simple.JSONArray;
{
private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
-
public static void main(String[] args)
{
- new PDBRestClient().searchResult("pfam_name", "Lipoc*");
+ PDBSearchRequest request = new PDBSearchRequest();
+ request.setAllowEmptySeq(false);
+ request.setResponseSize(100);
+ request.setSearchTarget("pfam_name");
+ request.setSearchTerm("Lipoc*");
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.MOLECULE_TYPE);
+ wantedFields.add(PDBDocField.PDB_ID);
+ wantedFields.add(PDBDocField.GENUS);
+ wantedFields.add(PDBDocField.GENE_NAME);
+ wantedFields.add(PDBDocField.TITLE);
+ request.setWantedFields(wantedFields);
+ new PDBRestClient().executeRequest(request);
}
- private String executeRestSearch(String qParam,
- String searchTerm)
+ public PDBSearchResponse executeRequest(PDBSearchRequest request)
{
ClientConfig clientConfig = new DefaultClientConfig();
clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
Boolean.TRUE);
Client client = Client.create(clientConfig);
+
+ String query = request.getSearchTarget()
+ + request.getSearchTerm()
+ + ((request.isAllowEmptySeq()) ? ""
+ : " AND molecule_sequence:['' TO *]");
+
+ String wantedFields = getFieldsAsCommaDelimitedString(request
+ .getWantedFields());
+
+ String responseSize = (request.getResponseSize() == 0) ? "200" : String
+ .valueOf(request.getResponseSize());
WebResource webResource = client.resource(pdbSearchEndpoint)
- .queryParam("wt", "json")
-.queryParam("rows", "100")
- .queryParam("q", qParam + ":" + searchTerm);
+ .queryParam("wt", "json").queryParam("fl", wantedFields)
+ .queryParam("rows", responseSize)
+ .queryParam("q", query);
ClientResponse clientResponse = webResource.accept(
MediaType.APPLICATION_JSON).get(ClientResponse.class);
throw new RuntimeException("Failed : HTTP error code : "
+ clientResponse.getStatus());
}
- return responseString;
+ // System.out.println("--------------> " + responseString);
+ return parseResponse(responseString, request.getWantedFields());
}
- public PDBSearchResultPojo searchResult(String qParam,
- String searchTerm)
+ private PDBSearchResponse parseResponse(String jsonResponse,
+ List<PDBDocField> wantedFields)
{
- String jsonResponseString = executeRestSearch(qParam, searchTerm);
- PDBSearchResultPojo searchResult = new PDBSearchResultPojo();
- DefaultListModel<PDBSummaryListModel> result = null;
+ PDBSearchResponse searchResult = new PDBSearchResponse();
+ List<PDBSummaryListModel> result = null;
try
{
JSONParser jsonParser = new JSONParser();
JSONObject jsonObj = (JSONObject) jsonParser
- .parse(jsonResponseString);
+.parse(jsonResponse);
JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
.valueOf(pdbResponse.get("numFound").toString());
if (numFound > 0)
{
- result = new DefaultListModel<PDBSummaryListModel>();
+ result = new ArrayList<PDBSummaryListModel>();
JSONArray docs = (JSONArray) pdbResponse.get("docs");
for (Iterator<JSONObject> docIter = docs.iterator(); docIter
.hasNext();)
{
JSONObject doc = docIter.next();
- if (doc.get("molecule_sequence") != null)
- {
- result.addElement(new PDBSummaryListModel(doc));
- }
+ // if (doc.get("molecule_sequence") != null)
+ // {
+ result.add(new PDBSummaryListModel(doc, wantedFields));
+ // }
}
- searchResult.setItemFound(numFound);
+ searchResult.setItemsFound(numFound);
searchResult.setResponseTime(queryTime);
searchResult.setSearchSummary(result);
}
return searchResult;
}
+ private String getFieldsAsCommaDelimitedString(List<PDBDocField> fields)
+ {
+ String result = "";
+ if (fields != null && !fields.isEmpty())
+ {
+ StringBuilder returnedFields = new StringBuilder();
+ for (PDBDocField field : fields)
+ {
+ returnedFields.append(",").append(field.getCode());
+ }
+ returnedFields.deleteCharAt(0);
+ result = returnedFields.toString();
+ }
+ return result;
+ }
+
+
}