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 import java.util.Objects;
  10
  11 import javax.ws.rs.core.MediaType;
  12
  13 import org.json.simple.parser.ParseException;
  14
  15 import com.sun.jersey.api.client.Client;
  16 import com.sun.jersey.api.client.ClientResponse;
  17 import com.sun.jersey.api.client.WebResource;
  18 import com.sun.jersey.api.client.config.DefaultClientConfig;
  19
  20 import jalview.datamodel.SequenceI;
  21 import jalview.fts.api.FTSData;
  22 import jalview.fts.api.FTSDataColumnI;
  23 import jalview.fts.api.FTSRestClientI;
  24 import jalview.fts.core.FTSRestClient;
  25 import jalview.fts.core.FTSRestRequest;
  26 import jalview.fts.core.FTSRestResponse;
  27 import jalview.fts.service.pdb.PDBFTSRestClient;
  28 import jalview.util.JSONUtils;
  29 import jalview.util.MessageManager;
  30 import jalview.util.Platform;
  31
  32 public class TDBeaconsFTSRestClient extends FTSRestClient
  33 {
  34   private static final String DEFAULT_THREEDBEACONS_DOMAIN =
  35           "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons-hub-api/uniprot/";
  36
  37   private static FTSRestClientI instance = null;
  38
  39   protected TDBeaconsFTSRestClient()
  40   {
  41   }
  42
  43   @SuppressWarnings("unchecked")
  44   @Override
  45   public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
  46           throws Exception
  47   {
  48     try
  49     {
  50       // Removed wantedFields, sortParam & facetPivot from PDBFTSRClient
  51       String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
  52               tdbRestRequest.getWantedFields());
  53       int responseSize = (tdbRestRequest.getResponseSize() == 0)
  54               ? getDefaultResponsePageSize()
  55               : tdbRestRequest.getResponseSize();
  56       //int offSet = pdbRestRequest.getOffSet();
  57
  58       String query = tdbRestRequest.getFieldToSearchBy()
  59               + tdbRestRequest.getSearchTerm();
  60       Client client;
  61       Class<ClientResponse> clientResponseClass;
  62       if (Platform.isJS())
  63       {
  64         // JavaScript only
  65         client = (Client) (Object) new jalview.javascript.web.Client();
  66         clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
  67       }
  68       else
  69       /**
  70        * Java only
  71        * @j2sIgnore
  72        */
  73       {
  74         client = Client.create(new DefaultClientConfig());
  75         clientResponseClass = ClientResponse.class;
  76       }
  77       WebResource webResource;
  78       webResource = client.resource(DEFAULT_THREEDBEACONS_DOMAIN).path(query);
  79       URI uri = webResource.getURI();
  80 //              .queryParam("P", query);
  81 //              .queryParam("rows", String.valueOf(responseSize))
  82 //              .queryParam("P",query);
  83 //      URI uri = webResource.getURI();
  84       System.out.println(uri.toString());
  85
  86       // Execute the REST request
  87       ClientResponse clientResponse = webResource
  88               .accept(MediaType.APPLICATION_JSON).get(clientResponseClass);
  89
  90       // Get the JSON string from the response object or directly from the
  91       // client (JavaScript)
  92       Map<String, Object> jsonObj = null;
  93       String responseString = null;
  94
  95       //System.out.println("query >>>>>>> " + tdbRestRequest.toString());
  96
  97       // Check the response status and report exception if one occurs
  98       int responseStatus = clientResponse.getStatus();
  99       switch (responseStatus)
 100       {
 101       // if succesful
 102       case 200:
 103         if (Platform.isJS())
 104         {
 105           jsonObj = clientResponse.getEntity(Map.class);
 106         }
 107         else
 108         {
 109           responseString = clientResponse.getEntity(String.class);
 110         }
 111         break;
 112       case 400:
 113         throw new Exception(parseJsonExceptionString(responseString));
 114       default:
 115         throw new Exception(
 116                 getMessageByHTTPStatusCode(responseStatus, "3DBeacons"));
 117       }
 118       // Process the response and return the result to the caller.
 119       return parseTDBeaconsJsonResponse(responseString, jsonObj, tdbRestRequest);
 120     } catch (Exception e)
 121     {
 122       String exceptionMsg = e.getMessage();
 123       if (exceptionMsg.contains("SocketException"))
 124       {
 125         // No internet connection
 126         throw new Exception(MessageManager.getString(
 127                 "exception.unable_to_detect_internet_connection"));
 128       }
 129       else if (exceptionMsg.contains("UnknownHostException"))
 130       {
 131         // The server is unreachable
 132         throw new Exception(MessageManager.formatMessage(
 133                 "exception.fts_server_unreachable", "3DB Hub"));
 134       }
 135       else
 136       {
 137         throw e;
 138       }
 139     }
 140
 141   }
 142
 143   public String setSearchTerm(String term) {
 144     return term;
 145   }
 146
 147   public static FTSRestResponse parseTDBeaconsJsonResponse(
 148           String tdbJsonResponseString, FTSRestRequest tdbRestRequest)
 149   {
 150     return parseTDBeaconsJsonResponse(tdbJsonResponseString,
 151             (Map<String, Object>) null, tdbRestRequest);
 152   }
 153
 154   @SuppressWarnings("unchecked")
 155   public static FTSRestResponse parseTDBeaconsJsonResponse(String tdbJsonResponseString,
 156           Map<String, Object> jsonObj, FTSRestRequest tdbRestRequest)
 157   {
 158     FTSRestResponse searchResult = new FTSRestResponse();
 159     //searchResult.setNumberOfItemsFound(1);
 160     List<FTSData> result = null;
 161
 162     try
 163     {
 164       if (jsonObj == null)
 165       {
 166         jsonObj = (Map<String, Object>) JSONUtils.parse(tdbJsonResponseString);
 167       }
 168       //Map<String, Object> tdbResponse = (Map<String, Object>) jsonObj.get("structures");
 169       //String seqLength = tdbEntry.get("sequence_length").toString();
 170       //int seqLength = Integer.valueOf(tdbEntry.get("sequence_length").toString());
 171
 172       Long seqLength = (Long) ((Map<String, Object>) jsonObj.get("uniprot_entry")).get("sequence_length");
 173       result = new ArrayList<>();
 174       List<Object> structures = (List<Object>) jsonObj.get("structures");
 175       int numFound = 0;
 176       for (Iterator<Object> strucIter = structures.iterator(); strucIter
 177               .hasNext();)
 178       {
 179         Map<String, Object> structure = (Map<String, Object>) strucIter.next();
 180         result.add(getFTSData(structure, tdbRestRequest));
 181         numFound++;
 182       }
 183         searchResult.setNumberOfItemsFound(numFound);
 184         searchResult.setSearchSummary(result);
 185         searchResult.setSequenceLength(seqLength);
 186
 187     } catch (ParseException e)
 188     {
 189       e.printStackTrace();
 190     }
 191     return searchResult;
 192   }
 193
 194 private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
 195           FTSRestRequest tdbRequest)
 196   {
 197     // TODO Auto-generated method stub
 198     String primaryKey = null;
 199     Object[] summaryRowData;
 200     Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
 201     int colCounter = 0;
 202     summaryRowData = new Object[displayFields.size()];
 203     for (FTSDataColumnI field : displayFields) {
 204       String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " "
 205               : tdbJsonStructure.get(field.getCode()).toString();
 206       if (field.isPrimaryKeyColumn())
 207       {
 208         primaryKey = fieldData;
 209         summaryRowData[colCounter++] = primaryKey;
 210       }
 211       else if (fieldData == null || fieldData.isEmpty())
 212       {
 213         summaryRowData[colCounter++] = null;
 214       }
 215       else
 216       {
 217         try
 218         {
 219           summaryRowData[colCounter++] = (field.getDataType()
 220                   .getDataTypeClass() == Integer.class)
 221                           ? Integer.valueOf(fieldData)
 222                           : (field.getDataType()
 223                                   .getDataTypeClass() == Double.class)
 224                                           ? Double.valueOf(fieldData)
 225                                           : fieldData;
 226         } catch (Exception e)
 227         {
 228           e.printStackTrace();
 229           System.out.println("offending value:" + fieldData);
 230         }
 231       }
 232     }
 233     final String primaryKey1 = primaryKey;
 234     final Object[] summaryRowData1 = summaryRowData;
 235
 236     return new FTSData()
 237     {
 238
 239       @Override
 240       public Object[] getSummaryData()
 241       {
 242         return summaryRowData1;
 243       }
 244
 245       @Override
 246       public Object getPrimaryKey()
 247       {
 248         return primaryKey1;
 249       }
 250
 251       /**
 252        * Returns a string representation of this object;
 253        */
 254       @Override
 255       public String toString()
 256       {
 257         StringBuilder summaryFieldValues = new StringBuilder();
 258         for (Object summaryField : summaryRowData1)
 259         {
 260           summaryFieldValues.append(
 261                   summaryField == null ? " " : summaryField.toString())
 262                   .append("\t");
 263         }
 264         return summaryFieldValues.toString();
 265       }
 266
 267       /**
 268        * Returns hash code value for this object
 269        */
 270       @Override
 271       public int hashCode()
 272       {
 273         return Objects.hash(primaryKey1, this.toString());
 274       }
 275
 276       @Override
 277       public boolean equals(Object that)
 278       {
 279         return this.toString().equals(that.toString());
 280       }
 281     };
 282   }
 283
 284 //  private static FTSData getFTSData(Map<String, Object> doc,
 285 //          FTSRestRequest tdbRestRequest)
 286 //  {
 287 //    String primaryKey = null;
 288 //
 289 //    Object[] summaryRowData;
 290 //
 291 //    Collection<FTSDataColumnI> displayFields = tdbRestRequest.getWantedFields();
 292 //    int colCounter = 0;
 293 //    summaryRowData = new Object[displayFields.size() + 1];
 294 //
 295 //    return null;
 296 //  }
 297
 298   private String parseJsonExceptionString(String jsonErrorString)
 299   {
 300     // TODO Auto-generated method stub
 301     return null;
 302   }
 303
 304   @Override
 305   public String getColumnDataConfigFileName()
 306   {
 307     return "/fts/tdbeacons_data_columns.txt";
 308   }
 309
 310   public static FTSRestClientI getInstance()
 311   {
 312     if (instance == null)
 313     {
 314       instance = new TDBeaconsFTSRestClient();
 315     }
 316     return instance;
 317   }
 318
 319   private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
 320
 321   public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
 322   {
 323     if (allDefaultDisplayedStructureDataColumns == null
 324             || allDefaultDisplayedStructureDataColumns.isEmpty())
 325     {
 326       allDefaultDisplayedStructureDataColumns = new ArrayList<>();
 327       allDefaultDisplayedStructureDataColumns
 328               .addAll(super.getAllDefaultDisplayedFTSDataColumns());
 329     }
 330     return allDefaultDisplayedStructureDataColumns;
 331   }
 332
 333 }