src/jalview/ws/dbsources/PDBRestClient.java

   1 package jalview.ws.dbsources;
   2
   3 import jalview.ws.uimodel.PDBSearchResultPojo;
   4 import jalview.ws.uimodel.PDBSummaryListModel;
   5
   6 import java.util.Iterator;
   7
   8 import javax.swing.DefaultListModel;
   9 import javax.ws.rs.core.MediaType;
  10
  11 import org.json.simple.JSONArray;
  12 import org.json.simple.JSONObject;
  13 import org.json.simple.parser.JSONParser;
  14 import org.json.simple.parser.ParseException;
  15
  16 import com.sun.jersey.api.client.Client;
  17 import com.sun.jersey.api.client.ClientResponse;
  18 import com.sun.jersey.api.client.WebResource;
  19 import com.sun.jersey.api.client.config.ClientConfig;
  20 import com.sun.jersey.api.client.config.DefaultClientConfig;
  21 import com.sun.jersey.api.json.JSONConfiguration;
  22
  23 public class PDBRestClient
  24 {
  25   private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
  26
  27
  28   public static void main(String[] args)
  29   {
  30     new PDBRestClient().searchResult("pfam_name", "Lipoc*");
  31   }
  32
  33   private String executeRestSearch(String qParam,
  34           String searchTerm)
  35   {
  36     ClientConfig clientConfig = new DefaultClientConfig();
  37     clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
  38             Boolean.TRUE);
  39     Client client = Client.create(clientConfig);
  40     WebResource webResource = client.resource(pdbSearchEndpoint)
  41             .queryParam("wt", "json")
  42             .queryParam("q", qParam + ":" + searchTerm);
  43     ClientResponse clientResponse = webResource.accept(
  44             MediaType.APPLICATION_JSON).get(ClientResponse.class);
  45
  46     String responseString = clientResponse.getEntity(String.class);
  47     if (clientResponse.getStatus() != 200)
  48     {
  49       throw new RuntimeException("Failed : HTTP error code : "
  50               + clientResponse.getStatus());
  51     }
  52     return responseString;
  53   }
  54
  55   public PDBSearchResultPojo searchResult(String qParam,
  56           String searchTerm)
  57   {
  58     String jsonResponseString = executeRestSearch(qParam, searchTerm);
  59     PDBSearchResultPojo searchResult = new PDBSearchResultPojo();
  60     DefaultListModel<PDBSummaryListModel> result = null;
  61     try
  62     {
  63       JSONParser jsonParser = new JSONParser();
  64       JSONObject jsonObj = (JSONObject) jsonParser
  65               .parse(jsonResponseString);
  66
  67       JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
  68       String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
  69               "QTime").toString();
  70       int numFound = Integer
  71               .valueOf(pdbResponse.get("numFound").toString());
  72       if (numFound > 0)
  73       {
  74         result = new DefaultListModel<PDBSummaryListModel>();
  75         JSONArray docs = (JSONArray) pdbResponse.get("docs");
  76         for (Iterator<JSONObject> docIter = docs.iterator(); docIter
  77                 .hasNext();)
  78         {
  79           JSONObject doc = docIter.next();
  80           if (doc.get("molecule_sequence") != null)
  81           {
  82             result.addElement(new PDBSummaryListModel(doc));
  83           }
  84         }
  85         searchResult.setItemFound(numFound);
  86         searchResult.setResponseTime(queryTime);
  87         searchResult.setSearchSummary(result);
  88       }
  89     } catch (ParseException e)
  90     {
  91       e.printStackTrace();
  92     }
  93
  94     return searchResult;
  95   }
  96
  97 }