src/jalview/fts/service/threedbeacons/TDBeaconsFTSRestClient.java

   1 package jalview.fts.service.threedbeacons;
   2
   3 import java.net.URI;
   4 import java.util.ArrayList;
   5 import java.util.Collection;
   6 import java.util.Iterator;
   7 import java.util.List;
   8 import java.util.Map;
   9
  10 import javax.ws.rs.core.MediaType;
  11
  12 import org.json.simple.parser.ParseException;
  13
  14 import com.sun.jersey.api.client.Client;
  15 import com.sun.jersey.api.client.ClientResponse;
  16 import com.sun.jersey.api.client.WebResource;
  17 import com.sun.jersey.api.client.config.DefaultClientConfig;
  18
  19 import jalview.datamodel.SequenceI;
  20 import jalview.fts.api.FTSData;
  21 import jalview.fts.api.FTSDataColumnI;
  22 import jalview.fts.api.FTSRestClientI;
  23 import jalview.fts.core.FTSRestClient;
  24 import jalview.fts.core.FTSRestRequest;
  25 import jalview.fts.core.FTSRestResponse;
  26 import jalview.fts.service.pdb.PDBFTSRestClient;
  27 import jalview.util.JSONUtils;
  28 import jalview.util.MessageManager;
  29 import jalview.util.Platform;
  30
  31 public class TDBeaconsFTSRestClient extends FTSRestClient
  32 {
  33   private static final String DEFAULT_THREEDBEACONS_DOMAIN =
  34           "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/";
  35
  36   private static FTSRestClientI instance = null;
  37
  38   @SuppressWarnings("unchecked")
  39   @Override
  40   public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
  41           throws Exception
  42   {
  43     try
  44     {
  45       // Removed wantedFields, sortParam & facetPivot from PDBFTSRClient
  46       String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
  47               tdbRestRequest.getWantedFields());
  48       int responseSize = (tdbRestRequest.getResponseSize() == 0)
  49               ? getDefaultResponsePageSize()
  50               : tdbRestRequest.getResponseSize();
  51
  52       String query = tdbRestRequest.getFieldToSearchBy()
  53               + tdbRestRequest.getSearchTerm();
  54       Client client;
  55       Class<ClientResponse> clientResponseClass;
  56       if (Platform.isJS())
  57       {
  58         // JavaScript only
  59         client = (Client) (Object) new jalview.javascript.web.Client();
  60         clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
  61       }
  62       else
  63       /**
  64        * Java only
  65        * @j2sIgnore
  66        */
  67       {
  68         client = Client.create(new DefaultClientConfig());
  69         clientResponseClass = ClientResponse.class;
  70       }
  71       WebResource webResource;
  72       webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN)
  73               .queryParam("P",query);
  74       URI uri = webResource.getURI();
  75
  76       System.out.println(uri);
  77
  78       // Execute the REST request
  79       ClientResponse clientResponse = webResource
  80               .accept(MediaType.APPLICATION_JSON).get(clientResponseClass);
  81
  82       // Get the JSON string from the response object or directly from the
  83       // client (JavaScript)
  84       Map<String, Object> jsonObj = null;
  85       String responseString = null;
  86
  87       System.out.println("query >>>>>>> " + tdbRestRequest.toString());
  88
  89       // Check the response status and report exception if one occurs
  90       int responseStatus = clientResponse.getStatus();
  91       switch (responseStatus)
  92       {
  93       // if succesful
  94       case 200:
  95         if (Platform.isJS())
  96         {
  97           jsonObj = clientResponse.getEntity(Map.class);
  98         }
  99         else
 100         {
 101           responseString = clientResponse.getEntity(String.class);
 102         }
 103         break;
 104       case 400:
 105         throw new Exception(parseJsonExceptionString(responseString));
 106       default:
 107         throw new Exception(
 108                 getMessageByHTTPStatusCode(responseStatus, "3DBeacons"));
 109       }
 110       // Process the response and return the result to the caller.
 111       return parseTDBeaconsJsonResponse(responseString, jsonObj, tdbRestRequest);
 112     } catch (Exception e)
 113     {
 114       String exceptionMsg = e.getMessage();
 115       if (exceptionMsg.contains("SocketException"))
 116       {
 117         // No internet connection
 118         throw new Exception(MessageManager.getString(
 119                 "exception.unable_to_detect_internet_connection"));
 120       }
 121       else if (exceptionMsg.contains("UnknownHostException"))
 122       {
 123         // The server is unreachable
 124         throw new Exception(MessageManager.formatMessage(
 125                 "exception.fts_server_unreachable", "3DB Hub"));
 126       }
 127       else
 128       {
 129         throw e;
 130       }
 131     }
 132
 133   }
 134
 135   public static FTSRestResponse parseTDBeaconsJsonResponse(
 136           String tdbJsonResponseString, FTSRestRequest tdbRestRequest)
 137   {
 138     return parseTDBeaconsJsonResponse(tdbJsonResponseString,
 139             (Map<String, Object>) null, tdbRestRequest);
 140   }
 141
 142   @SuppressWarnings("unchecked")
 143   public static FTSRestResponse parseTDBeaconsJsonResponse(String tdbJsonResponseString,
 144           Map<String, Object> jsonObj, FTSRestRequest tdbRestRequest)
 145   {
 146     FTSRestResponse searchResult = new FTSRestResponse();
 147     //searchResult.setNumberOfItemsFound(1);
 148     List<FTSData> result = null;
 149
 150     try
 151     {
 152       if (jsonObj == null)
 153       {
 154         jsonObj = (Map<String, Object>) JSONUtils.parse(tdbJsonResponseString);
 155       }
 156       Map<String, Object> tdbEntry = (Map<String, Object>) jsonObj.get("uniprot_entry");
 157       //String seqLength = tdbEntry.get("sequence_length").toString();
 158       int seqLength = Integer.valueOf(tdbEntry.get("sequence_length").toString());
 159
 160       // tdbStructures is the list of found structures
 161 //      Map<String, Object> tdbStructures = (Map<String, Object>) jsonObj.get("structures");
 162       Object[] structures = (Object[]) jsonObj.get("structures");
 163       String accessName = ((Map<String, Object>) jsonObj.get("uniprot_entry"))
 164               .get("ac").toString();
 165       // this is to be modified
 166       int numFound = structures.length;
 167 //      if (numFound > 0)
 168 //      {
 169 //
 170 //        result = new ArrayList<>();
 171 //        List<String> models;
 172 //        //= ((Map<String, Object>) jsonObj.get("structures"))
 173 //                //.get("model_identifier").toString();
 174 //        for (Iterator<String> modelsIter = models.iterator(); modelsIter.hasNext();)
 175 //                .hasNext();)
 176 //        {
 177 //          Map<String, Object> doc = (Map<String, Object>) docIter.next();
 178 //          result.add(getFTSData(doc, tdbRestRequest));
 179 //        }
 180         searchResult.setNumberOfItemsFound(numFound);
 181         // searchResult.setAccessionName(accessName); ?usefulness?
 182 //        searchResult.setSearchSummary(result);
 183 //
 184 //      }
 185     } catch (ParseException e)
 186     {
 187       e.printStackTrace();
 188     }
 189     return searchResult;
 190   }
 191
 192 //  private static FTSData getFTSData(Map<String, Object> doc,
 193 //          FTSRestRequest tdbRestRequest)
 194 //  {
 195 //    String primaryKey = null;
 196 //
 197 //    Object[] summaryRowData;
 198 //
 199 //    Collection<FTSDataColumnI> displayFields = tdbRestRequest.getWantedFields();
 200 //    int colCounter = 0;
 201 //    summaryRowData = new Object[displayFields.size() + 1];
 202 //
 203 //    return null;
 204 //  }
 205
 206   private String parseJsonExceptionString(String jsonErrorString)
 207   {
 208     // TODO Auto-generated method stub
 209     return null;
 210   }
 211
 212   @Override
 213   public String getColumnDataConfigFileName()
 214   {
 215     // TODO Auto-generated method stub
 216     return null;
 217   }
 218
 219   public static FTSRestClientI getInstance()
 220   {
 221     if (instance == null)
 222     {
 223       instance = new TDBeaconsFTSRestClient();
 224     }
 225     return instance;
 226   }
 227
 228   private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
 229
 230   public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
 231   {
 232     if (allDefaultDisplayedStructureDataColumns == null
 233             || allDefaultDisplayedStructureDataColumns.isEmpty())
 234     {
 235       allDefaultDisplayedStructureDataColumns = new ArrayList<>();
 236       allDefaultDisplayedStructureDataColumns
 237               .addAll(super.getAllDefaultDisplayedFTSDataColumns());
 238     }
 239     return allDefaultDisplayedStructureDataColumns;
 240   }
 241
 242 }