src/jalview/ws/dbsources/PDBRestClient.java

   1 package jalview.ws.dbsources;
   2
   3 import jalview.ws.uimodel.PDBSearchRequest;
   4 import jalview.ws.uimodel.PDBSearchResponse;
   5 import jalview.ws.uimodel.PDBSummaryListModel;
   6 import jalview.ws.uimodel.PDBSummaryListModel.PDBDocField;
   7
   8 import java.util.ArrayList;
   9 import java.util.Iterator;
  10 import java.util.List;
  11
  12 import javax.ws.rs.core.MediaType;
  13
  14 import org.json.simple.JSONArray;
  15 import org.json.simple.JSONObject;
  16 import org.json.simple.parser.JSONParser;
  17 import org.json.simple.parser.ParseException;
  18
  19 import com.sun.jersey.api.client.Client;
  20 import com.sun.jersey.api.client.ClientResponse;
  21 import com.sun.jersey.api.client.WebResource;
  22 import com.sun.jersey.api.client.config.ClientConfig;
  23 import com.sun.jersey.api.client.config.DefaultClientConfig;
  24 import com.sun.jersey.api.json.JSONConfiguration;
  25
  26 public class PDBRestClient
  27 {
  28   private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
  29
  30   public static void main(String[] args)
  31   {
  32     PDBSearchRequest request = new PDBSearchRequest();
  33     request.setAllowEmptySeq(false);
  34     request.setResponseSize(100);
  35     request.setSearchTarget("pfam_name");
  36     request.setSearchTerm("Lipoc*");
  37     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  38     wantedFields.add(PDBDocField.MOLECULE_TYPE);
  39     wantedFields.add(PDBDocField.PDB_ID);
  40     wantedFields.add(PDBDocField.GENUS);
  41     wantedFields.add(PDBDocField.GENE_NAME);
  42     wantedFields.add(PDBDocField.TITLE);
  43     request.setWantedFields(wantedFields);
  44     new PDBRestClient().executeRequest(request);
  45   }
  46
  47   public PDBSearchResponse executeRequest(PDBSearchRequest request)
  48   {
  49     ClientConfig clientConfig = new DefaultClientConfig();
  50     clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
  51             Boolean.TRUE);
  52     Client client = Client.create(clientConfig);
  53
  54     String query = request.getSearchTarget()
  55             + request.getSearchTerm()
  56             + ((request.isAllowEmptySeq()) ? ""
  57                     : " AND molecule_sequence:['' TO *]");
  58
  59     String wantedFields = getFieldsAsCommaDelimitedString(request
  60             .getWantedFields());
  61
  62     String responseSize = (request.getResponseSize() == 0) ? "200" : String
  63             .valueOf(request.getResponseSize());
  64     WebResource webResource = client.resource(pdbSearchEndpoint)
  65             .queryParam("wt", "json").queryParam("fl", wantedFields)
  66             .queryParam("rows", responseSize)
  67             .queryParam("q", query);
  68     ClientResponse clientResponse = webResource.accept(
  69             MediaType.APPLICATION_JSON).get(ClientResponse.class);
  70
  71     String responseString = clientResponse.getEntity(String.class);
  72     if (clientResponse.getStatus() != 200)
  73     {
  74       throw new RuntimeException("Failed : HTTP error code : "
  75               + clientResponse.getStatus());
  76     }
  77     // System.out.println("--------------> " + responseString);
  78     return parseResponse(responseString, request.getWantedFields());
  79   }
  80
  81   private PDBSearchResponse parseResponse(String jsonResponse,
  82           List<PDBDocField> wantedFields)
  83   {
  84     PDBSearchResponse searchResult = new PDBSearchResponse();
  85     List<PDBSummaryListModel> result = null;
  86     try
  87     {
  88       JSONParser jsonParser = new JSONParser();
  89       JSONObject jsonObj = (JSONObject) jsonParser
  90 .parse(jsonResponse);
  91
  92       JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
  93       String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
  94               "QTime").toString();
  95       int numFound = Integer
  96               .valueOf(pdbResponse.get("numFound").toString());
  97       if (numFound > 0)
  98       {
  99         result = new ArrayList<PDBSummaryListModel>();
 100         JSONArray docs = (JSONArray) pdbResponse.get("docs");
 101         for (Iterator<JSONObject> docIter = docs.iterator(); docIter
 102                 .hasNext();)
 103         {
 104           JSONObject doc = docIter.next();
 105           // if (doc.get("molecule_sequence") != null)
 106           // {
 107           result.add(new PDBSummaryListModel(doc, wantedFields));
 108           // }
 109         }
 110         searchResult.setItemsFound(numFound);
 111         searchResult.setResponseTime(queryTime);
 112         searchResult.setSearchSummary(result);
 113       }
 114     } catch (ParseException e)
 115     {
 116       e.printStackTrace();
 117     }
 118
 119     return searchResult;
 120   }
 121
 122   private String getFieldsAsCommaDelimitedString(List<PDBDocField> fields)
 123   {
 124     String result = "";
 125     if (fields != null && !fields.isEmpty())
 126     {
 127       StringBuilder returnedFields = new StringBuilder();
 128       for (PDBDocField field : fields)
 129       {
 130         returnedFields.append(",").append(field.getCode());
 131       }
 132       returnedFields.deleteCharAt(0);
 133       result = returnedFields.toString();
 134     }
 135     return result;
 136   }
 137
 138
 139 }