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.PDBSearchResponse.PDBResponseSummary;
   6
   7 import java.util.ArrayList;
   8 import java.util.Iterator;
   9 import java.util.List;
  10
  11 import javax.ws.rs.core.MediaType;
  12
  13 import org.json.simple.JSONArray;
  14 import org.json.simple.JSONObject;
  15 import org.json.simple.parser.JSONParser;
  16 import org.json.simple.parser.ParseException;
  17
  18 import com.sun.jersey.api.client.Client;
  19 import com.sun.jersey.api.client.ClientResponse;
  20 import com.sun.jersey.api.client.WebResource;
  21 import com.sun.jersey.api.client.config.ClientConfig;
  22 import com.sun.jersey.api.client.config.DefaultClientConfig;
  23 import com.sun.jersey.api.json.JSONConfiguration;
  24
  25 public class PDBRestClient
  26 {
  27   private String pdbSearchEndpoint = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
  28
  29   public static void main(String[] args)
  30   {
  31     PDBSearchRequest request = new PDBSearchRequest();
  32     request.setAllowEmptySeq(false);
  33     request.setResponseSize(100);
  34     request.setSearchTarget("pfam_name");
  35     request.setSearchTerm("Lipoc*");
  36     List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
  37     wantedFields.add(PDBDocField.MOLECULE_TYPE);
  38     wantedFields.add(PDBDocField.PDB_ID);
  39     wantedFields.add(PDBDocField.GENUS);
  40     wantedFields.add(PDBDocField.GENE_NAME);
  41     wantedFields.add(PDBDocField.TITLE);
  42     request.setWantedFields(wantedFields);
  43     new PDBRestClient().executeRequest(request);
  44   }
  45
  46   public PDBSearchResponse executeRequest(PDBSearchRequest request)
  47   {
  48     ClientConfig clientConfig = new DefaultClientConfig();
  49     clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
  50             Boolean.TRUE);
  51     Client client = Client.create(clientConfig);
  52
  53     String query = request.getSearchTarget()
  54             + request.getSearchTerm()
  55             + ((request.isAllowEmptySeq()) ? ""
  56                     : " AND molecule_sequence:['' TO *]");
  57
  58     String wantedFields = getFieldsAsCommaDelimitedString(request
  59             .getWantedFields());
  60
  61     String responseSize = (request.getResponseSize() == 0) ? "200" : String
  62             .valueOf(request.getResponseSize());
  63     String sortParam = (request.getSortTarget() == null || request
  64             .getSortTarget().trim().isEmpty()) ? ""
  65             : (request
  66             .getSortTarget() + (request.isAscending() ? " asc" : " desc"));
  67
  68     WebResource webResource = client.resource(pdbSearchEndpoint)
  69             .queryParam("wt", "json").queryParam("fl", wantedFields)
  70             .queryParam("rows", responseSize)
  71             .queryParam("q", query)
  72             .queryParam("sort", sortParam);
  73     ClientResponse clientResponse = webResource.accept(
  74             MediaType.APPLICATION_JSON).get(ClientResponse.class);
  75
  76     String responseString = clientResponse.getEntity(String.class);
  77     if (clientResponse.getStatus() != 200)
  78     {
  79       if (clientResponse.getStatus() == 400)
  80       {
  81         throw new RuntimeException(parseException(responseString));
  82       }
  83       else
  84       {
  85       throw new RuntimeException("Failed : HTTP error code : "
  86               + clientResponse.getStatus());
  87       }
  88     }
  89     // System.out.println("--------------> " + responseString);
  90     return parseResponse(responseString, request.getWantedFields());
  91   }
  92
  93   private String parseException(String jsonResponse)
  94   {
  95     String errorMessage = "RunTime error";
  96     try
  97     {
  98       JSONParser jsonParser = new JSONParser();
  99       JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonResponse);
 100       JSONObject errorResponse = (JSONObject) jsonObj.get("error");
 101       errorMessage = errorResponse.get("msg").toString();
 102
 103       JSONObject responseHeader = (JSONObject) jsonObj
 104               .get("responseHeader");
 105       errorMessage += responseHeader.get("params").toString();
 106     } catch (ParseException e)
 107     {
 108       e.printStackTrace();
 109     }
 110     return errorMessage;
 111   }
 112
 113   @SuppressWarnings("unchecked")
 114   private PDBSearchResponse parseResponse(String jsonResponse,
 115           List<PDBDocField> wantedFields)
 116   {
 117     PDBSearchResponse searchResult = new PDBSearchResponse();
 118     List<PDBResponseSummary> result = null;
 119     try
 120     {
 121       JSONParser jsonParser = new JSONParser();
 122       JSONObject jsonObj = (JSONObject) jsonParser
 123 .parse(jsonResponse);
 124
 125       JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
 126       String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
 127               "QTime").toString();
 128       int numFound = Integer
 129               .valueOf(pdbResponse.get("numFound").toString());
 130       if (numFound > 0)
 131       {
 132         result = new ArrayList<PDBResponseSummary>();
 133         JSONArray docs = (JSONArray) pdbResponse.get("docs");
 134         for (Iterator<JSONObject> docIter = docs.iterator(); docIter
 135                 .hasNext();)
 136         {
 137           JSONObject doc = docIter.next();
 138           // if (doc.get("molecule_sequence") != null)
 139           // {
 140           result.add(searchResult.new PDBResponseSummary(doc, wantedFields));
 141           // }
 142         }
 143         searchResult.setItemsFound(numFound);
 144         searchResult.setResponseTime(queryTime);
 145         searchResult.setSearchSummary(result);
 146       }
 147     } catch (ParseException e)
 148     {
 149       e.printStackTrace();
 150     }
 151
 152     return searchResult;
 153   }
 154
 155   private String getFieldsAsCommaDelimitedString(List<PDBDocField> fields)
 156   {
 157     String result = "";
 158     if (fields != null && !fields.isEmpty())
 159     {
 160       StringBuilder returnedFields = new StringBuilder();
 161       for (PDBDocField field : fields)
 162       {
 163         returnedFields.append(",").append(field.getCode());
 164       }
 165       returnedFields.deleteCharAt(0);
 166       result = returnedFields.toString();
 167     }
 168     return result;
 169   }
 170
 171
 172   public enum PDBDocField
 173   {
 174     PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
 175             "Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type",
 176             "molecule_type"), MOLECULE_SEQUENCE("Sequence",
 177             "molecule_sequence"), UNIPROT_FEATURES("Uniprot Features",
 178             "uniprot_features"), PFAM_ACCESSION("PFAM Accession",
 179             "pfam_accession"), INTERPRO_ACCESSION("InterPro Accession",
 180             "interpro_accession"), UNIPROT_ACCESSION("UniProt Accession",
 181             "uniprot_accession"), R_FACTOR("R Factor", "r_factor"), RESOLUTION(
 182             "Resolution", "resolution"), DATA_QUALITY("Data Quality",
 183             "data_quality"), OVERALL_QUALITY("Overall Quality",
 184             "overall_quality"), POLYMER_COUNT("Polymer Count",
 185             "number_of_polymers"), PROTEIN_CHAIN_COUNT(
 186             "Protein Chain Count", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
 187             "Bound Molecule Count", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
 188             "Polymer Residue Count", "number_of_polymer_residues"), UNIPROT_COVERAGE(
 189             "UniProt Coverage", "uniprot_coverage"), GENUS("GENUS", "genus"), GENE_NAME(
 190             "Gene Name", "gene_name"), ALL("ALL", "text");
 191
 192     private String name;
 193
 194     private String code;
 195
 196     PDBDocField(String name, String code)
 197     {
 198       this.name = name;
 199       this.code = code;
 200     }
 201
 202     public String getName()
 203     {
 204       return name;
 205     }
 206
 207     public String getCode()
 208     {
 209       return code;
 210     }
 211
 212     public String toString()
 213     {
 214       return name;
 215     }
 216   }
 217 }