package jalview.fts.service.uniprot;
import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
import com.sun.jersey.api.client.Client;
import com.sun.jersey.api.client.ClientResponse;
import com.sun.jersey.api.client.WebResource;
-import com.sun.jersey.api.client.config.ClientConfig;
import com.sun.jersey.api.client.config.DefaultClientConfig;
public class UniProtFTSRestClient extends FTSRestClient
{
super();
uniprotSearchEndpoint = Cache.getDefault("UNIPROT_DOMAIN",
- DEFAULT_UNIPROT_DOMAIN) + "/uniprot/?";
+ DEFAULT_UNIPROT_DOMAIN) + "/uniprot/";
}
@Override
- public FTSRestResponse executeRequest(FTSRestRequest uniportRestRequest)
+ public FTSRestResponse executeRequest(FTSRestRequest uniprotRestRequest)
throws Exception
{
try
{
- ClientConfig clientConfig = new DefaultClientConfig();
- Client client = Client.create(clientConfig);
-
String wantedFields = getDataColumnsFieldsAsCommaDelimitedString(
- uniportRestRequest.getWantedFields());
- int responseSize = (uniportRestRequest.getResponseSize() == 0)
+ uniprotRestRequest.getWantedFields());
+ int responseSize = (uniprotRestRequest.getResponseSize() == 0)
? getDefaultResponsePageSize()
- : uniportRestRequest.getResponseSize();
+ : uniprotRestRequest.getResponseSize();
- int offSet = uniportRestRequest.getOffSet();
+ int offSet = uniprotRestRequest.getOffSet();
String query;
- if (isAdvancedQuery(uniportRestRequest.getSearchTerm()))
+ if (isAdvancedQuery(uniprotRestRequest.getSearchTerm()))
{
- query = uniportRestRequest.getSearchTerm();
+ query = uniprotRestRequest.getSearchTerm();
}
else
{
- query = uniportRestRequest.getFieldToSearchBy()
+ query = uniprotRestRequest.getFieldToSearchBy()
.equalsIgnoreCase("Search All")
- ? uniportRestRequest.getSearchTerm()
+ ? uniprotRestRequest.getSearchTerm()
+ " or mnemonic:"
- + uniportRestRequest.getSearchTerm()
- : uniportRestRequest.getFieldToSearchBy() + ":"
- + uniportRestRequest.getSearchTerm();
+ + 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 (Jalview.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
+ client = Client.create(new DefaultClientConfig());
+ clientResponseClass = ClientResponse.class;
}
WebResource webResource = null;
.queryParam("sort", "score").queryParam("query", query);
// Execute the REST request
ClientResponse clientResponse = webResource
- .accept(MediaType.TEXT_PLAIN).get(ClientResponse.class);
+ .accept(MediaType.TEXT_PLAIN).get(clientResponseClass);
String uniProtTabDelimittedResponseString = clientResponse
.getEntity(String.class);
// Make redundant objects eligible for garbage collection to conserve
throw new Exception(errorMessage);
}
- int xTotalResults = Integer.valueOf(
- clientResponse.getHeaders().get("X-Total-Results").get(0));
+ int xTotalResults = Jalview.isJS() ? 1
+ : Integer.valueOf(clientResponse.getHeaders()
+ .get("X-Total-Results").get(0));
clientResponse = null;
client = null;
return parseUniprotResponse(uniProtTabDelimittedResponseString,
- uniportRestRequest, xTotalResults);
+ uniprotRestRequest, xTotalResults);
} catch (Exception e)
{
String exceptionMsg = e.getMessage();