protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException { BasicResponse basicResponse = new BasicResponse(ResultCode.RESULT_DEFAULT); Account account = new Account(); account.fillSelf(request.getParameter(Account.PARAM_ACCOUNT_INFO)); int result = AccountManager.updateAccountInfo(account); if (result != -1) { basicResponse.setResultCode(ResultCode.RESULT_OK); } response.getWriter().println(basicResponse.toJson()); }
@Override public CoverageRecord getCoverage( ExtendedFileInfo file, String chromosome, int start, int end, int zoomLevel) { try { MultivaluedMap<String, String> queryParams = new MultivaluedMapImpl(); queryParams.add("startPos", String.valueOf(start)); queryParams.add("endPos", String.valueOf(end)); queryParams.add("zoomLevel", String.valueOf(zoomLevel)); WebResource resource = getClient() .resource( UriBuilder.fromUri(configuration.getApiRootUri()) .path(file.getHrefCoverage()) .path(chromosome) .build()) .queryParams(queryParams); ClientResponse response = getClient() .resource(resource.getURI()) .accept(MediaType.APPLICATION_XHTML_XML, MediaType.APPLICATION_JSON) .get(ClientResponse.class); switch (response.getClientResponseStatus()) { case OK: String data = response.getEntity(String.class); logger.info(data); CoverageRecord record = mapper.readValue( mapper.readValue(data, JsonNode.class).findPath(RESPONSE).toString(), CoverageRecord.class); logger.info(record.toString()); return record; default: data = response.getEntity(String.class); BasicResponse status = mapper.readValue(data, BasicResponse.class); throw new IllegalArgumentException(status.getResponseStatus().getMessage()); } } catch (BaseSpaceException bs) { throw bs; } catch (Throwable t) { throw new RuntimeException(t); } }
protected String queryVariantsInternal( ExtendedFileInfo file, String chromosome, VariantFetchParams params) { if (file == null || file.getHrefVariants() == null) { throw new IllegalArgumentException( "null VariantFile or hrefVariants property for VariantFile object"); } try { MultivaluedMap<String, String> queryParams = params == null ? new MultivaluedMapImpl() : params.toMap(); WebResource resource = getClient() .resource( UriBuilder.fromUri(configuration.getApiRootUri()) .path(file.getHrefVariants()) .path("variants") .path(chromosome) .build()) .queryParams(queryParams); ClientResponse response = getClient() .resource(resource.getURI()) .accept(MediaType.APPLICATION_XHTML_XML, MediaType.APPLICATION_JSON) .get(ClientResponse.class); switch (response.getClientResponseStatus()) { case OK: return response.getEntity(String.class); default: BasicResponse status = mapper.readValue(response.getEntity(String.class), BasicResponse.class); throw new IllegalArgumentException(status.getResponseStatus().getMessage()); } } catch (BaseSpaceException bs) { throw bs; } catch (IllegalArgumentException iae) { throw iae; } catch (Throwable t) { throw new RuntimeException(t); } }
@Override public CoverageMetaData getCoverageMetaData(ExtendedFileInfo file, String chromosome) { try { WebResource resource = getClient() .resource( UriBuilder.fromUri(configuration.getApiRootUri()) .path(file.getHrefCoverage()) .path(chromosome) .path("meta") .build()); ClientResponse response = getClient() .resource(resource.getURI()) .accept(MediaType.APPLICATION_XHTML_XML, MediaType.APPLICATION_JSON) .get(ClientResponse.class); switch (response.getClientResponseStatus()) { case OK: String data = response.getEntity(String.class); logger.info(data); CoverageMetaData metaData = mapper.readValue( mapper.readValue(data, JsonNode.class).findPath(RESPONSE).toString(), CoverageMetaData.class); logger.info(metaData.toString()); return metaData; default: data = response.getEntity(String.class); BasicResponse status = mapper.readValue(data, BasicResponse.class); throw new IllegalArgumentException(status.getResponseStatus().getMessage()); } } catch (BaseSpaceException bs) { throw bs; } catch (Throwable t) { throw new RuntimeException(t); } }