- ClientConfig clientConfig = new DefaultClientConfig();
- Client client = Client.create(clientConfig);
-
- String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(uniportRestRequest
- .getWantedFields());
- int responseSize = (uniportRestRequest.getResponseSize() == 0) ? getDefaultResponsePageSize()
- : uniportRestRequest.getResponseSize();
-
- String query = uniportRestRequest.getFieldToSearchBy() + ":"
- + uniportRestRequest.getSearchTerm();
- // + (uniportRestRequest.isAllowUnpublishedEntries() ? ""
- // : " AND status:REL");
- // System.out.println(">>>>> Query : " + query);
- // System.out.println(">>>>> Columns : " + wantedFields);
- WebResource webResource = null;
- webResource = client.resource(UNIPROT_SEARCH_ENDPOINT)
- .queryParam("format", "tab")
- .queryParam("columns", wantedFields)
- .queryParam("limit", String.valueOf(responseSize))
- .queryParam("query", query);
- // Execute the REST request
- ClientResponse clientResponse = webResource
- .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
- String uniProtTabDelimittedResponseString = clientResponse
- .getEntity(String.class);
- // Make redundant objects eligible for garbage collection to conserve
- // memory
- clientResponse = null;
- client = null;
- // System.out.println(">>>>> response : "
- // + uniProtTabDelimittedResponseString);
- return parseUniprotResponse(uniProtTabDelimittedResponseString,
- uniportRestRequest);
+ try
+ {
+ String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
+ uniprotRestRequest.getWantedFields());
+ int responseSize = (uniprotRestRequest.getResponseSize() == 0)
+ ? getDefaultResponsePageSize()
+ : uniprotRestRequest.getResponseSize();
+
+ int offSet = uniprotRestRequest.getOffSet();
+ String query;
+ if (isAdvancedQuery(uniprotRestRequest.getSearchTerm()))
+ {
+ query = uniprotRestRequest.getSearchTerm();
+ }
+ else
+ {
+ query = uniprotRestRequest.getFieldToSearchBy()
+ .equalsIgnoreCase("Search All")
+ ? uniprotRestRequest.getSearchTerm()
+ + " or mnemonic:"
+ + uniprotRestRequest.getSearchTerm()
+ : uniprotRestRequest.getFieldToSearchBy() + ":"
+ + uniprotRestRequest.getSearchTerm();
+ }
+
+ // BH 2018 the trick here is to coerce the classes in Javascript to be
+ // different from the ones in Java yet still allow this to be correct for
+ // Java
+ Client client;
+ Class<ClientResponse> clientResponseClass;
+ if (Platform.isJS())
+ {
+ // JavaScript only -- coerce types to Java types for Java
+ client = (Client) (Object) new jalview.javascript.web.Client();
+ clientResponseClass = (Class<ClientResponse>) (Object) jalview.javascript.web.ClientResponse.class;
+ }
+ else
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ // Java only
+ client = Client.create(new DefaultClientConfig());
+ clientResponseClass = ClientResponse.class;
+ }
+
+ WebResource webResource = null;
+ webResource = client.resource(uniprotSearchEndpoint)
+ .queryParam("format", "tab")
+ .queryParam("columns", wantedFields)
+ .queryParam("limit", String.valueOf(responseSize))
+ .queryParam("offset", String.valueOf(offSet))
+ .queryParam("sort", "score").queryParam("query", query);
+ if (Console.isDebugEnabled())
+ {
+ Console.debug("Uniprot FTS Request: " + webResource.toString());
+ }
+ // Execute the REST request
+ ClientResponse clientResponse = webResource
+ .accept(MediaType.TEXT_PLAIN).get(clientResponseClass);
+ String uniProtTabDelimittedResponseString = clientResponse
+ .getEntity(String.class);
+ // Make redundant objects eligible for garbage collection to conserve
+ // memory
+ // System.out.println(">>>>> response : "
+ // + uniProtTabDelimittedResponseString);
+ if (clientResponse.getStatus() != 200)
+ {
+ String errorMessage = getMessageByHTTPStatusCode(
+ clientResponse.getStatus(), "Uniprot");
+ throw new Exception(errorMessage);
+
+ }
+ int xTotalResults = Platform.isJS() ? 1
+ : Integer.valueOf(clientResponse.getHeaders()
+ .get("X-Total-Results").get(0));
+ clientResponse = null;
+ client = null;
+ return parseUniprotResponse(uniProtTabDelimittedResponseString,
+ uniprotRestRequest, xTotalResults);
+ } catch (Exception e)
+ {
+ String exceptionMsg = e.getMessage();
+ if (exceptionMsg.contains("SocketException"))
+ {
+ // No internet connection
+ throw new Exception(MessageManager.getString(
+ "exception.unable_to_detect_internet_connection"));
+ }
+ else if (exceptionMsg.contains("UnknownHostException"))
+ {
+ // The server 'http://www.uniprot.org' is unreachable
+ throw new Exception(MessageManager.formatMessage(
+ "exception.fts_server_unreachable", "Uniprot"));
+ }
+ else
+ {
+ throw e;
+ }
+ }
+ }