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.setFieldToSearchBy("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.getFieldToSearchBy()
  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.getFieldToSortBy() == null || request
  64             .getFieldToSortBy().trim().isEmpty()) ? ""
  65             : (request
  66             .getFieldToSortBy() + (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             request.getAssociatedSequence());
  92   }
  93
  94   private String parseException(String jsonResponse)
  95   {
  96     String errorMessage = "RunTime error";
  97     try
  98     {
  99       JSONParser jsonParser = new JSONParser();
 100       JSONObject jsonObj = (JSONObject) jsonParser.parse(jsonResponse);
 101       JSONObject errorResponse = (JSONObject) jsonObj.get("error");
 102       errorMessage = errorResponse.get("msg").toString();
 103
 104       JSONObject responseHeader = (JSONObject) jsonObj
 105               .get("responseHeader");
 106       errorMessage += responseHeader.get("params").toString();
 107     } catch (ParseException e)
 108     {
 109       e.printStackTrace();
 110     }
 111     return errorMessage;
 112   }
 113
 114   @SuppressWarnings("unchecked")
 115   private PDBSearchResponse parseResponse(String jsonResponse,
 116           List<PDBDocField> wantedFields, String associatedSequence)
 117   {
 118     PDBSearchResponse searchResult = new PDBSearchResponse();
 119     List<PDBResponseSummary> result = null;
 120     try
 121     {
 122       JSONParser jsonParser = new JSONParser();
 123       JSONObject jsonObj = (JSONObject) jsonParser
 124 .parse(jsonResponse);
 125
 126       JSONObject pdbResponse = (JSONObject) jsonObj.get("response");
 127       String queryTime = ((JSONObject) jsonObj.get("responseHeader")).get(
 128               "QTime").toString();
 129       int numFound = Integer
 130               .valueOf(pdbResponse.get("numFound").toString());
 131       if (numFound > 0)
 132       {
 133         result = new ArrayList<PDBResponseSummary>();
 134         JSONArray docs = (JSONArray) pdbResponse.get("docs");
 135         for (Iterator<JSONObject> docIter = docs.iterator(); docIter
 136                 .hasNext();)
 137         {
 138           JSONObject doc = docIter.next();
 139           // if (doc.get("molecule_sequence") != null)
 140           // {
 141           result.add(searchResult.new PDBResponseSummary(doc, wantedFields,
 142                   associatedSequence));
 143           // }
 144         }
 145         searchResult.setItemsFound(numFound);
 146         searchResult.setResponseTime(queryTime);
 147         searchResult.setSearchSummary(result);
 148       }
 149     } catch (ParseException e)
 150     {
 151       e.printStackTrace();
 152     }
 153
 154     return searchResult;
 155   }
 156
 157   private String getFieldsAsCommaDelimitedString(List<PDBDocField> fields)
 158   {
 159     String result = "";
 160     if (fields != null && !fields.isEmpty())
 161     {
 162       StringBuilder returnedFields = new StringBuilder();
 163       for (PDBDocField field : fields)
 164       {
 165         returnedFields.append(",").append(field.getCode());
 166       }
 167       returnedFields.deleteCharAt(0);
 168       result = returnedFields.toString();
 169     }
 170     return result;
 171   }
 172
 173
 174   public enum PDBDocField
 175   {
 176     PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
 177             "Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type",
 178             "molecule_type"), MOLECULE_SEQUENCE("Sequence",
 179             "molecule_sequence"), UNIPROT_FEATURES("Uniprot Features",
 180             "uniprot_features"), PFAM_ACCESSION("PFAM Accession",
 181             "pfam_accession"), INTERPRO_ACCESSION("InterPro Accession",
 182             "interpro_accession"), UNIPROT_ACCESSION("UniProt Accession",
 183             "uniprot_accession"), R_FACTOR("R Factor", "r_factor"), RESOLUTION(
 184             "Resolution", "resolution"), DATA_QUALITY("Data Quality",
 185             "data_quality"), OVERALL_QUALITY("Overall Quality",
 186             "overall_quality"), POLYMER_COUNT("Polymer Count",
 187             "number_of_polymers"), PROTEIN_CHAIN_COUNT(
 188             "Protein Chain Count", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
 189             "Bound Molecule Count", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
 190             "Polymer Residue Count", "number_of_polymer_residues"), UNIPROT_COVERAGE(
 191             "UniProt Coverage", "uniprot_coverage"), GENUS("GENUS", "genus"), GENE_NAME(
 192             "Gene Name", "gene_name"), ALL("ALL", "text");
 193
 194     private String name;
 195
 196     private String code;
 197
 198     PDBDocField(String name, String code)
 199     {
 200       this.name = name;
 201       this.code = code;
 202     }
 203
 204     public String getName()
 205     {
 206       return name;
 207     }
 208
 209     public String getCode()
 210     {
 211       return code;
 212     }
 213
 214     public String toString()
 215     {
 216       return name;
 217     }
 218   }
 219 }