import com.sun.jersey.api.client.WebResource;
import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
-import com.sun.jersey.api.json.JSONConfiguration;
+
/**
* A rest client for querying the Search endpoing of the PDB REST API
*/
public class PDBRestClient
{
- private static String PDB_SEARCH_ENDPOINT = "http://wwwdev.ebi.ac.uk/pdbe/search/pdb/select?";
+ public static final String PDB_SEARCH_ENDPOINT = "http://www.ebi.ac.uk/pdbe/search/pdb/select?";
private static int DEFAULT_RESPONSE_SIZE = 200;
* @param pdbRestRequest
* the PDBRestRequest instance to be processed
* @return the pdbResponse object for the given request
+ * @throws Exception
*/
public PDBRestResponse executeRequest(PDBRestRequest pdbRestRequest)
+ throws Exception
{
- ClientConfig clientConfig = new DefaultClientConfig();
- clientConfig.getFeatures().put(JSONConfiguration.FEATURE_POJO_MAPPING,
- Boolean.TRUE);
- Client client = Client.create(clientConfig);
-
- String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
- .getWantedFields());
- int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
- : pdbRestRequest.getResponseSize();
- String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
- .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
- .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
- : " desc"));
-
- // Build request parameters for the REST Request
- WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
- .queryParam("wt", "json").queryParam("fl", wantedFields)
- .queryParam("rows", String.valueOf(responseSize))
- .queryParam("q", pdbRestRequest.getQuery())
- .queryParam("sort", sortParam);
-
- // Execute the REST request
- ClientResponse clientResponse = webResource.accept(
- MediaType.APPLICATION_JSON).get(ClientResponse.class);
-
- // Get the JSON string from the response object
- String responseString = clientResponse.getEntity(String.class);
-
- // Check the response status and report exception if one occurs
- if (clientResponse.getStatus() != 200)
+ try
+ {
+ ClientConfig clientConfig = new DefaultClientConfig();
+ Client client = Client.create(clientConfig);
+
+ String wantedFields = getPDBDocFieldsAsCommaDelimitedString(pdbRestRequest
+ .getWantedFields());
+ int responseSize = (pdbRestRequest.getResponseSize() == 0) ? DEFAULT_RESPONSE_SIZE
+ : pdbRestRequest.getResponseSize();
+ String sortParam = (pdbRestRequest.getFieldToSortBy() == null || pdbRestRequest
+ .getFieldToSortBy().trim().isEmpty()) ? "" : (pdbRestRequest
+ .getFieldToSortBy() + (pdbRestRequest.isAscending() ? " asc"
+ : " desc"));
+ // Build request parameters for the REST Request
+ WebResource webResource = client.resource(PDB_SEARCH_ENDPOINT)
+ .queryParam("wt", "json").queryParam("fl", wantedFields)
+ .queryParam("rows", String.valueOf(responseSize))
+ .queryParam("q", pdbRestRequest.getQuery())
+ .queryParam("sort", sortParam);
+
+ // Execute the REST request
+ ClientResponse clientResponse = webResource.accept(
+ MediaType.APPLICATION_JSON).get(ClientResponse.class);
+
+ // Get the JSON string from the response object
+ String responseString = clientResponse.getEntity(String.class);
+
+ // Check the response status and report exception if one occurs
+ if (clientResponse.getStatus() != 200)
+ {
+ String errorMessage = "";
+ if (clientResponse.getStatus() == 400)
+ {
+ errorMessage = parseJsonExceptionString(responseString);
+ throw new Exception(errorMessage);
+ }
+ else
+ {
+ errorMessage = getMessageByHTTPStatusCode(clientResponse
+ .getStatus());
+ throw new Exception(errorMessage);
+ }
+ }
+
+ // Make redundant objects eligible for garbage collection to conserve
+ // memory
+ clientResponse = null;
+ client = null;
+
+ // Process the response and return the result to the caller.
+ return parsePDBJsonResponse(responseString, pdbRestRequest);
+ } catch (Exception e)
{
- String errorMessage = "";
- if (clientResponse.getStatus() == 400)
+ String exceptionMsg = e.getMessage();
+ if (exceptionMsg.contains("SocketException"))
{
- errorMessage = parseJsonExceptionString(responseString);
- throw new RuntimeException(errorMessage);
+ throw new Exception(
+ "Jalview is unable to detect an internet connection");
+ // No internet connection
+ }
+ else if (exceptionMsg.contains("UnknownHostException"))
+ {
+ throw new Exception(
+ "Jalview is unable to reach the host server \'www.ebi.ac.uk\'. "
+ + "\nPlease ensure that you are connected to the internet and try again.");
+ // The server 'www.ebi.ac.uk' is unreachable
}
else
{
- errorMessage = "Failed : HTTP error code : "
- + clientResponse.getStatus();
- throw new RuntimeException(errorMessage);
+ throw e;
}
}
+ }
- // Make redundant objects eligible for garbage collection to conserve
- // memory
- clientResponse = null;
- client = null;
-
- // Process the response and return the result to the caller.
- return parsePDBJsonResponse(responseString, pdbRestRequest);
+ public String getMessageByHTTPStatusCode(int code)
+ {
+ String message = "";
+ switch (code)
+ {
+ case 410:
+ message = "PDB Rest Service no longer exists!";
+ break;
+ case 403:
+ case 404:
+ message = "The requested resource could not be found";
+ break;
+ case 408:
+ case 409:
+ case 500:
+ case 501:
+ case 502:
+ case 503:
+ case 504:
+ case 505:
+ message = "There seems to be an error from the PDB Rest API server.";
+ break;
+
+ default:
+ break;
+ }
+ return message;
}
/**
* table. The PDB Id serves as a unique identifier for a given row in the
* summary table
*
- * @param wantedFeilds
+ * @param wantedFields
* the available table columns in no particular order
* @return the pdb id field column index
*/
public static int getPDBIdColumIndex(
- Collection<PDBDocField> wantedFeilds, boolean hasRefSeq)
+ Collection<PDBDocField> wantedFields, boolean hasRefSeq)
{
// If a reference sequence is attached then start counting from 1 else
// start from zero
- int pdbFeildIndexCounter = hasRefSeq ? 1 : 0;
+ int pdbFieldIndexCounter = hasRefSeq ? 1 : 0;
- for (PDBDocField feild : wantedFeilds)
+ for (PDBDocField field : wantedFields)
{
- if (feild.equals(PDBDocField.PDB_ID))
+ if (field.equals(PDBDocField.PDB_ID))
{
break; // Once PDB Id index is determined exit iteration
}
- ++pdbFeildIndexCounter;
+ ++pdbFieldIndexCounter;
}
- return pdbFeildIndexCounter;
+ return pdbFieldIndexCounter;
}
/**