target stringlengths 20 113k | src_fm stringlengths 11 86.3k | src_fm_fc stringlengths 21 86.4k | src_fm_fc_co stringlengths 30 86.4k | src_fm_fc_ms stringlengths 42 86.8k | src_fm_fc_ms_ff stringlengths 43 86.8k |
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@Test public void preHandleOptions_OPTIONS() throws Exception { when(mockRequest.getMethod()).thenReturn(HttpMethods.OPTIONS); assertThat(interceptor.preHandle(mockRequest, mockResponse, mockHandler)).isTrue(); } | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test public void preHandleOptions_publicEndpoint() throws Exception { when(mockHandler.getMethod()).thenReturn(getProfileApiMethod("isUsernameTaken")); when(mockRequest.getMethod()).thenReturn(HttpMethods.GET); assertThat(interceptor.preHandle(mockRequest, mockResponse, mockHandler)).isTrue(); } | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test public void preHandleGet_noAuthorization() throws Exception { when(mockHandler.getMethod()).thenReturn(getTestMethod()); when(mockRequest.getMethod()).thenReturn(HttpMethods.GET); assertThat(interceptor.preHandle(mockRequest, mockResponse, mockHandler)).isFalse(); verify(mockResponse).sendError(HttpServletRespons... | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test public void preHandleGet_nonBearerAuthorization() throws Exception { mockGetCallWithBearerToken(); when(mockRequest.getHeader(HttpHeaders.AUTHORIZATION)).thenReturn("blah"); assertThat(interceptor.preHandle(mockRequest, mockResponse, mockHandler)).isFalse(); verify(mockResponse).sendError(HttpServletResponse.SC_U... | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test(expected = NotFoundException.class) public void preHandleGet_userInfoError() throws Exception { mockGetCallWithBearerToken(); when(userInfoService.getUserInfo("foo")).thenThrow(new NotFoundException()); interceptor.preHandle(mockRequest, mockResponse, mockHandler); } | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test(expected = NotFoundException.class) public void preHandleGet_firecloudLookupFails() throws Exception { mockGetCallWithBearerToken(); Userinfoplus userInfo = new Userinfoplus(); userInfo.setEmail("bob@bad-domain.org"); when(userInfoService.getUserInfo("foo")).thenReturn(userInfo); when(fireCloudService.getMe()).th... | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test public void preHandleGet_firecloudLookupSucceeds() throws Exception { mockGetCallWithBearerToken(); Userinfoplus userInfo = new Userinfoplus(); userInfo.setEmail("bob@bad-domain.org"); when(userInfoService.getUserInfo("foo")).thenReturn(userInfo); FirecloudUserInfo fcUserInfo = new FirecloudUserInfo(); fcUserInfo... | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test public void preHandleGet_firecloudLookupSucceedsNoUserRecordWrongDomain() throws Exception { mockGetCallWithBearerToken(); Userinfoplus userInfo = new Userinfoplus(); userInfo.setEmail("bob@bad-domain.org"); when(userInfoService.getUserInfo("foo")).thenReturn(userInfo); FirecloudUserInfo fcUserInfo = new Fireclou... | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test public void preHandleGet_userInfoSuccess() throws Exception { mockGetCallWithBearerToken(); mockUserInfoSuccess(); assertThat(interceptor.preHandle(mockRequest, mockResponse, mockHandler)).isTrue(); } | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test public void preHandleGet_noUserRecord() throws Exception { workbenchConfig.access.unsafeAllowUserCreationFromGSuiteData = true; mockGetCallWithBearerToken(); mockUserInfoSuccess(); when(userDao.findUserByUsername(eq("bob@fake-domain.org"))).thenReturn(null); when(devUserRegistrationService.createUser(any())).then... | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test public void test_disableOnlyFreeTierWorkspaces() throws MessagingException { workbenchConfig.billing.defaultFreeCreditsDollarLimit = 100.0; doReturn(mockBQTableSingleResult(100.01)).when(bigQueryService).executeQuery(any()); final DbUser user = createUser(SINGLE_WORKSPACE_TEST_USER); final DbWorkspace freeTierWor... | public void checkFreeTierBillingUsage() { final Map<DbUser, Double> previousUserCosts = workspaceFreeTierUsageDao.getUserCostMap(); final Map<DbWorkspace, Double> workspaceCosts = getFreeTierWorkspaceCostsFromBQ(); workspaceCosts.forEach(workspaceFreeTierUsageDao::updateCost); final Map<DbUser, Double> userCosts = work... | FreeTierBillingService { public void checkFreeTierBillingUsage() { final Map<DbUser, Double> previousUserCosts = workspaceFreeTierUsageDao.getUserCostMap(); final Map<DbWorkspace, Double> workspaceCosts = getFreeTierWorkspaceCostsFromBQ(); workspaceCosts.forEach(workspaceFreeTierUsageDao::updateCost); final Map<DbUser,... | FreeTierBillingService { public void checkFreeTierBillingUsage() { final Map<DbUser, Double> previousUserCosts = workspaceFreeTierUsageDao.getUserCostMap(); final Map<DbWorkspace, Double> workspaceCosts = getFreeTierWorkspaceCostsFromBQ(); workspaceCosts.forEach(workspaceFreeTierUsageDao::updateCost); final Map<DbUser,... | FreeTierBillingService { public void checkFreeTierBillingUsage() { final Map<DbUser, Double> previousUserCosts = workspaceFreeTierUsageDao.getUserCostMap(); final Map<DbWorkspace, Double> workspaceCosts = getFreeTierWorkspaceCostsFromBQ(); workspaceCosts.forEach(workspaceFreeTierUsageDao::updateCost); final Map<DbUser,... | FreeTierBillingService { public void checkFreeTierBillingUsage() { final Map<DbUser, Double> previousUserCosts = workspaceFreeTierUsageDao.getUserCostMap(); final Map<DbWorkspace, Double> workspaceCosts = getFreeTierWorkspaceCostsFromBQ(); workspaceCosts.forEach(workspaceFreeTierUsageDao::updateCost); final Map<DbUser,... |
@Test public void preHandleGet_noUserRecordAndNoDevRegistration() throws Exception { workbenchConfig.access.unsafeAllowUserCreationFromGSuiteData = false; mockGetCallWithBearerToken(); mockUserInfoSuccess(); when(userDao.findUserByUsername(eq("bob@fake-domain.org"))).thenReturn(null); assertThat(interceptor.preHandle(m... | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; boolean isAuthRequired = false; ApiO... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... | AuthInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { SecurityContextHolder.clearContext(); if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerM... |
@Test public void authorityCheckPermitsWithNoAnnotation() throws Exception { assertThat(interceptor.hasRequiredAuthority(getTestMethod(), new DbUser())).isTrue(); } | boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudServi... | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudServi... | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudServi... |
@Test public void authorityCheckDeniesWhenUserMissingAuthority() throws Exception { Method apiControllerMethod = FakeController.class.getMethod("handle"); when(userDao.findUserWithAuthorities(USER_ID)).thenReturn(user); assertThat(interceptor.hasRequiredAuthority(apiControllerMethod, user)).isFalse(); } | boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudServi... | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudServi... | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudServi... |
@Test public void authorityCheckPermitsWhenUserHasAuthority() throws Exception { DbUser userWithAuthorities = new DbUser(); Set<Authority> required = new HashSet<>(); required.add(Authority.REVIEW_RESEARCH_PURPOSE); userWithAuthorities.setAuthoritiesEnum(required); when(userDao.findUserWithAuthorities(USER_ID)).thenRet... | boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudServi... | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudServi... | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudServi... |
@Test public void testPreHandle_getRequest() { boolean result = requestTimeMetricInterceptor.preHandle( mockHttpServletRequest, mockHttpServletResponse, mockHandlerMethod); assertThat(result).isTrue(); verify(mockHttpServletRequest) .setAttribute(attributeKeyCaptor.capture(), attributeValueCaptor.capture()); assertThat... | @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return true; } | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... |
@Test public void testPreHandle_skipsOptionsRequest() { doReturn(HttpMethods.OPTIONS).when(mockHttpServletRequest).getMethod(); boolean result = requestTimeMetricInterceptor.preHandle( mockHttpServletRequest, mockHttpServletResponse, mockHandlerMethod); assertThat(result).isTrue(); verify(mockHttpServletRequest, never(... | @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return true; } | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... |
@Test public void testPreHandle_skipsUnsupportedHandler() { boolean result = requestTimeMetricInterceptor.preHandle( mockHttpServletRequest, mockHttpServletResponse, new Object()); assertThat(result).isTrue(); verify(mockHttpServletRequest, never()).setAttribute(anyString(), any()); } | @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return true; } | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle( HttpServletRequest request, HttpServletResponse response, Object handler) { if (shouldSkip(request, handler)) { return true; } request.setAttribute(RequestAttribute.START_INSTANT.toString(), clock.instant()); return tru... |
@Test public void testPostHandle() { doReturn(END_INSTANT).when(mockClock).instant(); doReturn(START_INSTANT) .when(mockHttpServletRequest) .getAttribute(RequestAttribute.START_INSTANT.getKeyName()); requestTimeMetricInterceptor.postHandle( mockHttpServletRequest, mockHttpServletResponse, mockHandlerMethod, mockModelAn... | @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(); Optional.ofNullable(request.getAttribute(RequestAttribute.STAR... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... |
@Test public void testPostHandle_skipsOptionsRequest() { doReturn(HttpMethods.OPTIONS).when(mockHttpServletRequest).getMethod(); requestTimeMetricInterceptor.postHandle( mockHttpServletRequest, mockHttpServletResponse, mockHandlerMethod, mockModelAndView); verify(mockHttpServletRequest, never()).setAttribute(anyString(... | @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(); Optional.ofNullable(request.getAttribute(RequestAttribute.STAR... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... |
@Test public void testPostHandle_skipsUnsupportedHandler() { requestTimeMetricInterceptor.postHandle( mockHttpServletRequest, mockHttpServletResponse, new Object(), mockModelAndView); verify(mockHttpServletRequest, never()).setAttribute(anyString(), any()); verifyZeroInteractions(mockLogsBasedMetricService); } | @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(); Optional.ofNullable(request.getAttribute(RequestAttribute.STAR... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... | RequestTimeMetricInterceptor extends HandlerInterceptorAdapter { @Override public void postHandle( HttpServletRequest request, HttpServletResponse response, Object handler, ModelAndView modelAndView) { if (shouldSkip(request, handler)) { return; } final String methodName = ((HandlerMethod) handler).getMethod().getName(... |
@Test public void testCloneConceptSetWithNoCdrVersionChange() { DbWorkspace mockDbWorkspace = mockWorkspace(); DbConceptSet fromConceptSet = mockConceptSet(); DbConceptSet copiedConceptSet = conceptSetService.cloneConceptSetAndConceptIds(fromConceptSet, mockDbWorkspace, false); assertNotNull(copiedConceptSet); assertEq... | @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceId(targetWorkspace.ge... | ConceptSetService { @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceI... | ConceptSetService { @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceI... | ConceptSetService { @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceI... | ConceptSetService { @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceI... |
@Test(expected = NotFoundException.class) public void testGetMe_throwsNotFound() throws ApiException { when(profileApi.me()).thenThrow(new ApiException(404, "blah")); service.getMe(); } | @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProv... | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProv... | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProv... |
@Test public void preHandleOptions_OPTIONS() throws Exception { when(request.getMethod()).thenReturn(HttpMethods.OPTIONS); assertThat(interceptor.preHandle(request, response, handler)).isTrue(); } | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), Ap... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... |
@Test public void prehandleForCronNoHeader() throws Exception { when(request.getMethod()).thenReturn(HttpMethods.GET); when(handler.getMethod()).thenReturn(OfflineAuditApi.class.getMethod("auditBigQuery")); assertThat(interceptor.preHandle(request, response, handler)).isFalse(); } | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), Ap... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... |
@Test public void prehandleForCronWithBadHeader() throws Exception { when(request.getMethod()).thenReturn(HttpMethods.GET); when(handler.getMethod()).thenReturn(OfflineAuditApi.class.getMethod("auditBigQuery")); when(request.getHeader(CronInterceptor.GAE_CRON_HEADER)).thenReturn("asdf"); assertThat(interceptor.preHandl... | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), Ap... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... |
@Test public void prehandleForCronWithHeader() throws Exception { when(request.getMethod()).thenReturn(HttpMethods.GET); when(handler.getMethod()).thenReturn(OfflineAuditApi.class.getMethod("auditBigQuery")); when(request.getHeader(CronInterceptor.GAE_CRON_HEADER)).thenReturn("true"); assertThat(interceptor.preHandle(r... | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), Ap... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... |
@Test public void prehandleForNonCron() throws Exception { when(request.getMethod()).thenReturn(HttpMethods.GET); when(handler.getMethod()).thenReturn(WorkspacesApi.class.getMethod("getWorkspaces")); assertThat(interceptor.preHandle(request, response, handler)).isTrue(); } | @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), Ap... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... | CronInterceptor extends HandlerInterceptorAdapter { @Override public boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler) throws Exception { if (request.getMethod().equals(HttpMethods.OPTIONS)) { return true; } HandlerMethod method = (HandlerMethod) handler; ApiOperation apiOp = A... |
@Test public void testDecorateParameterName() { assertThat(decorateParameterName("foo")).isEqualTo("@foo"); } | @NotNull public static String decorateParameterName(@NotNull String parameterName) { return "@" + parameterName; } | QueryParameterValues { @NotNull public static String decorateParameterName(@NotNull String parameterName) { return "@" + parameterName; } } | QueryParameterValues { @NotNull public static String decorateParameterName(@NotNull String parameterName) { return "@" + parameterName; } } | QueryParameterValues { @NotNull public static String decorateParameterName(@NotNull String parameterName) { return "@" + parameterName; } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull stat... | QueryParameterValues { @NotNull public static String decorateParameterName(@NotNull String parameterName) { return "@" + parameterName; } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull stat... |
@Test public void testBuildParameter() { final QueryParameterValue newParameter = QueryParameterValue.int64(42); final String parameter = buildParameter(PARAM_MAP, newParameter); assertThat(parameter).isEqualTo("@p2"); assertThat(PARAM_MAP.get("p2")).isEqualTo(newParameter); } | @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(par... | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return de... | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return de... | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return de... | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return de... |
@Test public void testBuildParameter_emptyMap_nullQpv() { PARAM_MAP.clear(); final QueryParameterValue nullString = QueryParameterValue.string(null); final String parameterName = buildParameter(PARAM_MAP, nullString); assertThat(parameterName).isEqualTo("@p0"); assertThat(PARAM_MAP).hasSize(1); assertThat(PARAM_MAP.get... | @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(par... | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return de... | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return de... | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return de... | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return de... |
@Test public void testInstantToQpvValue_nullInput() { final QueryParameterValue qpv = instantToQPValue(null); assertThat(qpv.getType()).isEqualTo(StandardSQLTypeName.TIMESTAMP); assertThat(qpv.getValue()).isNull(); } | @NotNull public static QueryParameterValue instantToQPValue(@Nullable Instant instant) { final Long epochMicros = Optional.ofNullable(instant) .map(Instant::toEpochMilli) .map(milli -> milli * MICROSECONDS_IN_MILLISECOND) .orElse(null); return QueryParameterValue.timestamp(epochMicros); } | QueryParameterValues { @NotNull public static QueryParameterValue instantToQPValue(@Nullable Instant instant) { final Long epochMicros = Optional.ofNullable(instant) .map(Instant::toEpochMilli) .map(milli -> milli * MICROSECONDS_IN_MILLISECOND) .orElse(null); return QueryParameterValue.timestamp(epochMicros); } } | QueryParameterValues { @NotNull public static QueryParameterValue instantToQPValue(@Nullable Instant instant) { final Long epochMicros = Optional.ofNullable(instant) .map(Instant::toEpochMilli) .map(milli -> milli * MICROSECONDS_IN_MILLISECOND) .orElse(null); return QueryParameterValue.timestamp(epochMicros); } } | QueryParameterValues { @NotNull public static QueryParameterValue instantToQPValue(@Nullable Instant instant) { final Long epochMicros = Optional.ofNullable(instant) .map(Instant::toEpochMilli) .map(milli -> milli * MICROSECONDS_IN_MILLISECOND) .orElse(null); return QueryParameterValue.timestamp(epochMicros); } @NotNu... | QueryParameterValues { @NotNull public static QueryParameterValue instantToQPValue(@Nullable Instant instant) { final Long epochMicros = Optional.ofNullable(instant) .map(Instant::toEpochMilli) .map(milli -> milli * MICROSECONDS_IN_MILLISECOND) .orElse(null); return QueryParameterValue.timestamp(epochMicros); } @NotNu... |
@Test public void testToTimestampQpv() { final QueryParameterValue qpv = toTimestampQpv(OFFSET_DATE_TIME); assertThat(qpv).isNotNull(); assertThat(qpv.getType()).isEqualTo(StandardSQLTypeName.TIMESTAMP); final Optional<OffsetDateTime> roundTripOdt = timestampQpvToOffsetDateTime(qpv); assertThat(roundTripOdt).isPresent(... | @Nullable public static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime) { final String arg = Optional.ofNullable(offsetDateTime).map(QPV_TIMESTAMP_FORMATTER::format).orElse(null); return QueryParameterValue.timestamp(arg); } | QueryParameterValues { @Nullable public static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime) { final String arg = Optional.ofNullable(offsetDateTime).map(QPV_TIMESTAMP_FORMATTER::format).orElse(null); return QueryParameterValue.timestamp(arg); } } | QueryParameterValues { @Nullable public static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime) { final String arg = Optional.ofNullable(offsetDateTime).map(QPV_TIMESTAMP_FORMATTER::format).orElse(null); return QueryParameterValue.timestamp(arg); } } | QueryParameterValues { @Nullable public static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime) { final String arg = Optional.ofNullable(offsetDateTime).map(QPV_TIMESTAMP_FORMATTER::format).orElse(null); return QueryParameterValue.timestamp(arg); } @NotNull static String buildParameter(
... | QueryParameterValues { @Nullable public static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime) { final String arg = Optional.ofNullable(offsetDateTime).map(QPV_TIMESTAMP_FORMATTER::format).orElse(null); return QueryParameterValue.timestamp(arg); } @NotNull static String buildParameter(
... |
@Test public void exportWorkspace() throws ApiException { List<Long> workspaceID = new ArrayList<>(); workspaceID.add(1l); RdrWorkspace rdrWorkspace = toDefaultRdrWorkspace(mockWorkspace); when(rdrMapper.toRdrModel(mockWorkspace)).thenReturn(rdrWorkspace); rdrExportService.exportWorkspaces(workspaceID); verify(mockWork... | @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull) .collect(Collectors.toList()); if (!rdrWorkspaces... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... |
@Test public void testTimestampQpvToInstant_nullQpvValue() { assertThat(timestampQpvToInstant(QueryParameterValue.timestamp((String) null))).isEmpty(); } | public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } | QueryParameterValues { public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } } | QueryParameterValues { public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } } | QueryParameterValues { public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } @NotNull static Str... | QueryParameterValues { public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } @NotNull static Str... |
@Test(expected = IllegalArgumentException.class) public void testTimestampQpvToInstant_wrongQpvType() { timestampQpvToInstant(QueryParameterValue.bool(false)); } | public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } | QueryParameterValues { public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } } | QueryParameterValues { public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } } | QueryParameterValues { public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } @NotNull static Str... | QueryParameterValues { public static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv) { verifyQpvType(qpv, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(qpv.getValue()) .map(s -> ZonedDateTime.parse(s, QPV_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } @NotNull static Str... |
@Test public void testTimestampQpvToOffsetDateTime() { final Optional<OffsetDateTime> offsetDateTime = timestampQpvToOffsetDateTime(TIMESTAMP_QPV); assertTimeApprox(offsetDateTime.get().toInstant(), INSTANT); } | public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofIn... | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i... | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i... | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i... | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i... |
@Test public void testTimestampQpvToOffset_nullInput() { assertThat(timestampQpvToOffsetDateTime(null)).isEmpty(); } | public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofIn... | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i... | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i... | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i... | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i... |
@Test public void testRowToInsertStringToOffsetTimestamp() { final String timestampString = "2020-09-17 04:30:15.000000"; final Optional<OffsetDateTime> convertedOdt = rowToInsertStringToOffsetTimestamp(timestampString); assertThat(convertedOdt).isPresent(); final OffsetDateTime expected = OffsetDateTime.parse("2020-09... | public static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp( @Nullable String bqTimeString) { return Optional.ofNullable(bqTimeString) .filter(s -> s.length() > 0) .map(ROW_TO_INSERT_TIMESTAMP_FORMATTER::parse) .map(LocalDateTime::from) .map(ldt -> OffsetDateTime.of(ldt, ZoneOffset.UTC)); } | QueryParameterValues { public static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp( @Nullable String bqTimeString) { return Optional.ofNullable(bqTimeString) .filter(s -> s.length() > 0) .map(ROW_TO_INSERT_TIMESTAMP_FORMATTER::parse) .map(LocalDateTime::from) .map(ldt -> OffsetDateTime.of(ldt, ZoneOffset.... | QueryParameterValues { public static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp( @Nullable String bqTimeString) { return Optional.ofNullable(bqTimeString) .filter(s -> s.length() > 0) .map(ROW_TO_INSERT_TIMESTAMP_FORMATTER::parse) .map(LocalDateTime::from) .map(ldt -> OffsetDateTime.of(ldt, ZoneOffset.... | QueryParameterValues { public static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp( @Nullable String bqTimeString) { return Optional.ofNullable(bqTimeString) .filter(s -> s.length() > 0) .map(ROW_TO_INSERT_TIMESTAMP_FORMATTER::parse) .map(LocalDateTime::from) .map(ldt -> OffsetDateTime.of(ldt, ZoneOffset.... | QueryParameterValues { public static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp( @Nullable String bqTimeString) { return Optional.ofNullable(bqTimeString) .filter(s -> s.length() > 0) .map(ROW_TO_INSERT_TIMESTAMP_FORMATTER::parse) .map(LocalDateTime::from) .map(ldt -> OffsetDateTime.of(ldt, ZoneOffset.... |
@Test public void testTimestampStringToInstant_nullInput() { assertThat(timestampStringToInstant(null)).isEmpty(); } | public static Optional<Instant> timestampStringToInstant(@Nullable String timestamp) { return Optional.ofNullable(timestamp) .map(s -> ZonedDateTime.parse(s, ROW_TO_INSERT_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } | QueryParameterValues { public static Optional<Instant> timestampStringToInstant(@Nullable String timestamp) { return Optional.ofNullable(timestamp) .map(s -> ZonedDateTime.parse(s, ROW_TO_INSERT_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } } | QueryParameterValues { public static Optional<Instant> timestampStringToInstant(@Nullable String timestamp) { return Optional.ofNullable(timestamp) .map(s -> ZonedDateTime.parse(s, ROW_TO_INSERT_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } } | QueryParameterValues { public static Optional<Instant> timestampStringToInstant(@Nullable String timestamp) { return Optional.ofNullable(timestamp) .map(s -> ZonedDateTime.parse(s, ROW_TO_INSERT_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } @NotNull static String buildParameter(
@NotNull Map<String, Qu... | QueryParameterValues { public static Optional<Instant> timestampStringToInstant(@Nullable String timestamp) { return Optional.ofNullable(timestamp) .map(s -> ZonedDateTime.parse(s, ROW_TO_INSERT_TIMESTAMP_FORMATTER)) .map(ZonedDateTime::toInstant); } @NotNull static String buildParameter(
@NotNull Map<String, Qu... |
@Test public void testEnumToQpv() { final QueryParameterValue qpv = enumToQpv(WorkspaceAccessLevel.READER); assertThat(qpv.getType()).isEqualTo(StandardSQLTypeName.STRING); assertThat(qpv.getValue()).isEqualTo("READER"); } | @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } | QueryParameterValues { @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } } | QueryParameterValues { @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } } | QueryParameterValues { @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParam... | QueryParameterValues { @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParam... |
@Test public void testEnumToQpv_nullInput() { final QueryParameterValue qpv = enumToQpv(null); assertThat(qpv.getType()).isEqualTo(StandardSQLTypeName.STRING); assertThat(qpv.getValue()).isNull(); } | @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } | QueryParameterValues { @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } } | QueryParameterValues { @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } } | QueryParameterValues { @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParam... | QueryParameterValues { @NotNull public static <T extends Enum<T>> QueryParameterValue enumToQpv(@Nullable T enumValue) { return QueryParameterValue.string(enumToString(enumValue)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParam... |
@Test public void buildCriteriaLookupMapNoSearchParametersException() { SearchRequest searchRequest = new SearchRequest().addIncludesItem(new SearchGroup().addItemsItem(new SearchGroupItem())); try { lookupUtil.buildCriteriaLookupMap(searchRequest); fail("Should have thrown BadRequestException!"); } catch (BadRequestEx... | public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGroup sg : Iterables.co... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... |
@Test public void buildCriteriaLookupMapDrugCriteria_ATC() { DbCriteria drugNode1 = DbCriteria.builder() .addParentId(99999) .addDomainId(DomainType.DRUG.toString()) .addType(CriteriaType.ATC.toString()) .addConceptId("21600002") .addGroup(true) .addSelectable(true) .build(); saveCriteriaWithPath("0", drugNode1); DbCri... | public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGroup sg : Iterables.co... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... |
@Test public void exportWorkspace_FocusOnUnderservedPopulation() throws ApiException { Set<SpecificPopulationEnum> specificPopulationEnumsSet = new HashSet<SpecificPopulationEnum>(); specificPopulationEnumsSet.add(SpecificPopulationEnum.RACE_AA); mockWorkspace.setSpecificPopulationsEnum(specificPopulationEnumsSet); whe... | @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull) .collect(Collectors.toList()); if (!rdrWorkspaces... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... |
@Test public void buildCriteriaLookupMapDrugCriteria_RXNORM() { DbCriteria drugNode1 = DbCriteria.builder() .addParentId(99999) .addDomainId(DomainType.DRUG.toString()) .addType(CriteriaType.ATC.toString()) .addConceptId("21600002") .addGroup(true) .addSelectable(true) .build(); saveCriteriaWithPath("0", drugNode1); Db... | public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGroup sg : Iterables.co... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... |
@Test public void buildCriteriaLookupMapConditionICD9Criteria() { DbCriteria icd9Parent = DbCriteria.builder() .addParentId(0) .addDomainId(DomainType.CONDITION.toString()) .addType(CriteriaType.ICD9CM.toString()) .addGroup(true) .addSelectable(true) .addStandard(false) .addConceptId("44829696") .addSynonyms("[CONDITIO... | public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGroup sg : Iterables.co... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... | CriteriaLookupUtil { public Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req) { Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByAncestor = Maps.newHashMap(); Map<CriteriaLookupUtil.FullTreeType, Map<Long, Set<Long>>> childrenByParentConcept = Maps.newHashMap(); for (SearchGr... |
@Test public void testClaims() { JsonWebToken.Payload payload = delegatedCredentials.createJwtPayload(); assertThat(payload.getAudience()).isEqualTo(GoogleOAuthConstants.TOKEN_SERVER_URL); assertThat(payload.getIssuer()).isEqualTo(SERVICE_ACCOUNT_EMAIL); assertThat(payload.getSubject()).isEqualTo(USER_EMAIL); assertTha... | @VisibleForTesting public JsonWebToken.Payload createJwtPayload() { JsonWebToken.Payload payload = new JsonWebToken.Payload(); payload.setIssuedAtTimeSeconds(Instant.now().getEpochSecond()); payload.setExpirationTimeSeconds( Instant.now().getEpochSecond() + ACCESS_TOKEN_DURATION.getSeconds()); payload.setAudience(Googl... | DelegatedUserCredentials extends OAuth2Credentials { @VisibleForTesting public JsonWebToken.Payload createJwtPayload() { JsonWebToken.Payload payload = new JsonWebToken.Payload(); payload.setIssuedAtTimeSeconds(Instant.now().getEpochSecond()); payload.setExpirationTimeSeconds( Instant.now().getEpochSecond() + ACCESS_TO... | DelegatedUserCredentials extends OAuth2Credentials { @VisibleForTesting public JsonWebToken.Payload createJwtPayload() { JsonWebToken.Payload payload = new JsonWebToken.Payload(); payload.setIssuedAtTimeSeconds(Instant.now().getEpochSecond()); payload.setExpirationTimeSeconds( Instant.now().getEpochSecond() + ACCESS_TO... | DelegatedUserCredentials extends OAuth2Credentials { @VisibleForTesting public JsonWebToken.Payload createJwtPayload() { JsonWebToken.Payload payload = new JsonWebToken.Payload(); payload.setIssuedAtTimeSeconds(Instant.now().getEpochSecond()); payload.setExpirationTimeSeconds( Instant.now().getEpochSecond() + ACCESS_TO... | DelegatedUserCredentials extends OAuth2Credentials { @VisibleForTesting public JsonWebToken.Payload createJwtPayload() { JsonWebToken.Payload payload = new JsonWebToken.Payload(); payload.setIssuedAtTimeSeconds(Instant.now().getEpochSecond()); payload.setExpirationTimeSeconds( Instant.now().getEpochSecond() + ACCESS_TO... |
@Test public void testGetCdrQueryNoTableQuery() { CdrQuery cdrQuery = cohortMaterializationService.getCdrQuery( SearchRequests.allGenders(), new DataTableSpecification(), cohortReview, null); assertThat(cdrQuery.getBigqueryDataset()).isEqualTo(DATA_SET_ID); assertThat(cdrQuery.getBigqueryProject()).isEqualTo(PROJECT_ID... | @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBig... | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bi... | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bi... | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bi... | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bi... |
@Test public void testGetCdrQueryWithTableQuery() { CdrQuery cdrQuery = cohortMaterializationService.getCdrQuery( SearchRequests.allGenders(), new DataTableSpecification() .tableQuery( new TableQuery() .tableName("measurement") .columns( ImmutableList.of("person_id", "measurement_concept.concept_name"))), cohortReview,... | @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBig... | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bi... | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bi... | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bi... | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bi... |
@Test public void testMaterializeAnnotationQueryNoPagination() { FieldSet fieldSet = new FieldSet().annotationQuery(new AnnotationQuery()); MaterializeCohortResponse response = cohortMaterializationService.materializeCohort( cohortReview, SearchRequests.allGenders(), null, 0, makeRequest(fieldSet, 1000)); ImmutableMap<... | public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catch (JsonSyntaxException e) { thr... | CohortMaterializationService { public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catc... | CohortMaterializationService { public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catc... | CohortMaterializationService { public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catc... | CohortMaterializationService { public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catc... |
@Test public void testMaterializeAnnotationQueryWithPagination() { FieldSet fieldSet = new FieldSet().annotationQuery(new AnnotationQuery()); MaterializeCohortRequest request = makeRequest(fieldSet, 1) .statusFilter(ImmutableList.of(CohortStatus.INCLUDED, CohortStatus.EXCLUDED)); MaterializeCohortResponse response = co... | public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catch (JsonSyntaxException e) { thr... | CohortMaterializationService { public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catc... | CohortMaterializationService { public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catc... | CohortMaterializationService { public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catc... | CohortMaterializationService { public MaterializeCohortResponse materializeCohort( @Nullable DbCohortReview cohortReview, String cohortSpec, @Nullable Set<Long> conceptIds, MaterializeCohortRequest request) { SearchRequest searchRequest; try { searchRequest = new Gson().fromJson(cohortSpec, SearchRequest.class); } catc... |
@Test public void testGetAnnotations() { CohortAnnotationsResponse response = cohortMaterializationService.getAnnotations( cohortReview, new CohortAnnotationsRequest().annotationQuery(new AnnotationQuery())); ImmutableMap<String, Object> p1Map = ImmutableMap.of("person_id", 1L, "review_status", "INCLUDED"); assertResul... | public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = annotationQueryBuilder.materializeA... | CohortMaterializationService { public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = anno... | CohortMaterializationService { public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = anno... | CohortMaterializationService { public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = anno... | CohortMaterializationService { public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = anno... |
@Test(expected = MessagingException.class) public void testSendWelcomeEmail_throwsMessagingException() throws MessagingException, ApiException { when(msgStatus.getRejectReason()).thenReturn("this was rejected"); User user = createUser(); service.sendWelcomeEmail(CONTACT_EMAIL, PASSWORD, user); verify(mandrillApi, times... | @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOURCE, welcomeMessageSubstitutionMap(passwor... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... |
@Test(expected = MessagingException.class) public void testSendWelcomeEmail_throwsApiException() throws MessagingException, ApiException { doThrow(ApiException.class).when(mandrillApi).send(any()); User user = createUser(); service.sendWelcomeEmail(CONTACT_EMAIL, PASSWORD, user); verify(mandrillApi, times(3)).send(any(... | @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOURCE, welcomeMessageSubstitutionMap(passwor... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... |
@Test public void exportWorkspace_CreatorInformation() throws ApiException { List<Long> workspaceIdList = new ArrayList<>(); workspaceIdList.add(1l); RdrWorkspace rdrWorkspace = toDefaultRdrWorkspace(mockWorkspace); when(rdrMapper.toRdrModel(mockWorkspace)).thenReturn(rdrWorkspace); rdrExportService.exportWorkspaces(wo... | @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull) .collect(Collectors.toList()); if (!rdrWorkspaces... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... |
@Test(expected = MessagingException.class) public void testSendWelcomeEmail_invalidEmail() throws MessagingException { User user = createUser(); service.sendWelcomeEmail("Nota valid email", PASSWORD, user); } | @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOURCE, welcomeMessageSubstitutionMap(passwor... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... |
@Test public void testSendWelcomeEmail() throws MessagingException, ApiException { User user = createUser(); service.sendWelcomeEmail(CONTACT_EMAIL, PASSWORD, user); verify(mandrillApi, times(1)).send(any(MandrillApiKeyAndMessage.class)); } | @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOURCE, welcomeMessageSubstitutionMap(passwor... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... | MailServiceImpl implements MailService { @Override public void sendWelcomeEmail(final String contactEmail, final String password, final User user) throws MessagingException { final MandrillMessage msg = new MandrillMessage() .to(Collections.singletonList(validatedRecipient(contactEmail))) .html(buildHtml(WELCOME_RESOUR... |
@Test public void testQueryEmptyReview() { assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, INCLUDED_ONLY, new AnnotationQuery(), 10, 0), allColumns); } | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryOneIncluded() { saveReviewStatuses(); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, INCLUDED_ONLY, new AnnotationQuery(), 10, 0), allColumns, ImmutableMap.of("person_id", INCLUDED_PERSON_ID, "review_status", "INCLUDED")); } | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllStatuses() { saveReviewStatuses(); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, new AnnotationQuery(), 10, 0), allColumns, ImmutableMap.of("person_id", INCLUDED_PERSON_ID, "review_status", "INCLUDED"), ImmutableMap.of("person_id", EXCLUDED_P... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllStatusesReviewStatusOrder() { saveReviewStatuses(); AnnotationQuery annotationQuery = new AnnotationQuery(); annotationQuery.setOrderBy(ImmutableList.of("review_status")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, annotationQuery, 10, 0),... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllStatusesReviewPersonIdOrderDescending() { saveReviewStatuses(); AnnotationQuery annotationQuery = new AnnotationQuery(); annotationQuery.setOrderBy(ImmutableList.of("DESCENDING(person_id)")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, anno... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryIncludedWithAnnotations() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); ImmutableMap<String, Object> expectedResult = ImmutableMap.<String, Object>builder() .put("person_id", INCLUDED_PERSON_ID) .put("review_status", "IN... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryIncludedWithAnnotationsNoReviewStatus() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); ImmutableMap<String, Object> expectedResult = ImmutableMap.<String, Object>builder() .put("person_id", INCLUDED_PERSON_ID) .put("integ... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllWithAnnotations() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); saveAnnotations(EXCLUDED_PERSON_ID, 456, null, false, "2017-02-15", "aardvark"); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohort... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void exportWorkspace_DeletedWorkspace() throws ApiException { List<Long> workspaceID = new ArrayList<>(); workspaceID.add(2l); RdrWorkspace rdrWorkspace = toDefaultRdrWorkspace(mockDeletedWorkspace); when(rdrMapper.toRdrModel(mockDeletedWorkspace)).thenReturn(rdrWorkspace); rdrExportService.exportWorkspace... | @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull) .collect(Collectors.toList()); if (!rdrWorkspaces... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... | RdrExportServiceImpl implements RdrExportService { @Override public void exportWorkspaces(List<Long> workspaceIds) { List<RdrWorkspace> rdrWorkspacesList; try { rdrWorkspacesList = workspaceIds.stream() .map( workspaceId -> toRdrWorkspace(workspaceDao.findDbWorkspaceByWorkspaceId(workspaceId))) .filter(Objects::nonNull... |
@Test public void testQueryAllWithAnnotationsLimit1() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); saveAnnotations(EXCLUDED_PERSON_ID, 456, null, false, "2017-02-15", "aardvark"); assertResults( annotationQueryBuilder.materializeAnnotationQuery( ... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllWithAnnotationsLimit1Offset1() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); saveAnnotations(EXCLUDED_PERSON_ID, 456, null, false, "2017-02-15", "aardvark"); assertResults( annotationQueryBuilder.materializeAnnotation... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllWithAnnotationsOrderByIntegerDescending() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); saveAnnotations(EXCLUDED_PERSON_ID, 456, null, false, "2017-02-15", "aardvark"); AnnotationQuery annotationQuery = new Annotation... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllWithAnnotationsOrderByBoolean() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); saveAnnotations(EXCLUDED_PERSON_ID, 456, null, false, "2017-02-15", "aardvark"); AnnotationQuery annotationQuery = new AnnotationQuery(); a... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllWithAnnotationsOrderByDateDescending() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); saveAnnotations(EXCLUDED_PERSON_ID, 456, null, false, "2017-02-15", "aardvark"); AnnotationQuery annotationQuery = new AnnotationQue... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllWithAnnotationsOrderByString() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); saveAnnotations(EXCLUDED_PERSON_ID, 456, null, false, "2017-02-15", "aardvark"); AnnotationQuery annotationQuery = new AnnotationQuery(); an... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testQueryAllWithAnnotationsOrderByEnum() throws Exception { saveReviewStatuses(); saveAnnotations(INCLUDED_PERSON_ID, 123, "foo", true, "2017-02-14", "zebra"); saveAnnotations(EXCLUDED_PERSON_ID, 456, null, false, "2017-02-15", "aardvark"); AnnotationQuery annotationQuery = new AnnotationQuery(); anno... | public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); } Map<String, DbCohortAnn... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... | AnnotationQueryBuilder { public AnnotationResults materializeAnnotationQuery( DbCohortReview cohortReview, List<CohortStatus> statusFilter, AnnotationQuery annotationQuery, Integer limit, long offset) { if (statusFilter == null || statusFilter.isEmpty()) { throw new BadRequestException("statusFilter cannot be empty"); ... |
@Test public void testRandomizeVariant() { VariantContext randomizedVariant = randomizeVcf.randomizeVariant(variantContext); assertThat(randomizedVariant.getGenotypes().size()).isEqualTo(2); assertThat(randomizedVariant.getGenotypes().getSampleNames()) .isEqualTo(new HashSet<>(sampleNames)); randomizedVariant.getGenoty... | @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream() .map(name -> randomizeGenotype(vari... | RandomizeVcf extends VariantWalker { @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream(... | RandomizeVcf extends VariantWalker { @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream(... | RandomizeVcf extends VariantWalker { @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream(... | RandomizeVcf extends VariantWalker { @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream(... |
@Test public void testRandomizeAlleles() { List<Allele> alleles = randomizeVcf.randomizeAlleles(variantContext); assertThat(alleles.size()).isEqualTo(2); alleles.forEach(allele -> assertThat(variantContext.getAlleles()).contains(allele)); } | @VisibleForTesting protected List<Allele> randomizeAlleles(VariantContext variantContext) { List<Allele> alleles = new ArrayList<>(); double genotypeTypeIndex = random.nextDouble(); if (variantContext.getAlternateAlleles().size() == 2) { if (genotypeTypeIndex < .8240) { alleles.add(Allele.NO_CALL); alleles.add(Allele.N... | RandomizeVcf extends VariantWalker { @VisibleForTesting protected List<Allele> randomizeAlleles(VariantContext variantContext) { List<Allele> alleles = new ArrayList<>(); double genotypeTypeIndex = random.nextDouble(); if (variantContext.getAlternateAlleles().size() == 2) { if (genotypeTypeIndex < .8240) { alleles.add(... | RandomizeVcf extends VariantWalker { @VisibleForTesting protected List<Allele> randomizeAlleles(VariantContext variantContext) { List<Allele> alleles = new ArrayList<>(); double genotypeTypeIndex = random.nextDouble(); if (variantContext.getAlternateAlleles().size() == 2) { if (genotypeTypeIndex < .8240) { alleles.add(... | RandomizeVcf extends VariantWalker { @VisibleForTesting protected List<Allele> randomizeAlleles(VariantContext variantContext) { List<Allele> alleles = new ArrayList<>(); double genotypeTypeIndex = random.nextDouble(); if (variantContext.getAlternateAlleles().size() == 2) { if (genotypeTypeIndex < .8240) { alleles.add(... | RandomizeVcf extends VariantWalker { @VisibleForTesting protected List<Allele> randomizeAlleles(VariantContext variantContext) { List<Allele> alleles = new ArrayList<>(); double genotypeTypeIndex = random.nextDouble(); if (variantContext.getAlternateAlleles().size() == 2) { if (genotypeTypeIndex < .8240) { alleles.add(... |
@Test public void testUpdateShibbolethToken() throws Exception { shibbolethService.updateShibbolethToken("asdf"); verify(shibbolethApi, times(1)).postShibbolethToken("asdf"); } | @Override public void updateShibbolethToken(String jwt) { ShibbolethApi shibbolethApi = shibbolethApiProvider.get(); shibbolethRetryHandler.run( (context) -> { shibbolethApi.postShibbolethToken(jwt); return null; }); } | ShibbolethServiceImpl implements ShibbolethService { @Override public void updateShibbolethToken(String jwt) { ShibbolethApi shibbolethApi = shibbolethApiProvider.get(); shibbolethRetryHandler.run( (context) -> { shibbolethApi.postShibbolethToken(jwt); return null; }); } } | ShibbolethServiceImpl implements ShibbolethService { @Override public void updateShibbolethToken(String jwt) { ShibbolethApi shibbolethApi = shibbolethApiProvider.get(); shibbolethRetryHandler.run( (context) -> { shibbolethApi.postShibbolethToken(jwt); return null; }); } @Autowired ShibbolethServiceImpl(
Provide... | ShibbolethServiceImpl implements ShibbolethService { @Override public void updateShibbolethToken(String jwt) { ShibbolethApi shibbolethApi = shibbolethApiProvider.get(); shibbolethRetryHandler.run( (context) -> { shibbolethApi.postShibbolethToken(jwt); return null; }); } @Autowired ShibbolethServiceImpl(
Provide... | ShibbolethServiceImpl implements ShibbolethService { @Override public void updateShibbolethToken(String jwt) { ShibbolethApi shibbolethApi = shibbolethApiProvider.get(); shibbolethRetryHandler.run( (context) -> { shibbolethApi.postShibbolethToken(jwt); return null; }); } @Autowired ShibbolethServiceImpl(
Provide... |
@Test(expected = GatewayTimeoutException.class) public void convertNotebookException() throws Exception { ApiException cause = new ApiException(new SocketTimeoutException()); ExceptionUtils.convertNotebookException(cause); } | public static WorkbenchException convertNotebookException( org.pmiops.workbench.notebooks.ApiException e) { if (isSocketTimeoutException(e.getCause())) { throw new GatewayTimeoutException(); } throw codeToException(e.getCode()); } | ExceptionUtils { public static WorkbenchException convertNotebookException( org.pmiops.workbench.notebooks.ApiException e) { if (isSocketTimeoutException(e.getCause())) { throw new GatewayTimeoutException(); } throw codeToException(e.getCode()); } } | ExceptionUtils { public static WorkbenchException convertNotebookException( org.pmiops.workbench.notebooks.ApiException e) { if (isSocketTimeoutException(e.getCause())) { throw new GatewayTimeoutException(); } throw codeToException(e.getCode()); } private ExceptionUtils(); } | ExceptionUtils { public static WorkbenchException convertNotebookException( org.pmiops.workbench.notebooks.ApiException e) { if (isSocketTimeoutException(e.getCause())) { throw new GatewayTimeoutException(); } throw codeToException(e.getCode()); } private ExceptionUtils(); static boolean isGoogleServiceUnavailableExce... | ExceptionUtils { public static WorkbenchException convertNotebookException( org.pmiops.workbench.notebooks.ApiException e) { if (isSocketTimeoutException(e.getCause())) { throw new GatewayTimeoutException(); } throw codeToException(e.getCode()); } private ExceptionUtils(); static boolean isGoogleServiceUnavailableExce... |
@Test public void buildDemoChartAggregationAgeGenderRace() { AggregationBuilder actualBuilder = AggregationUtils.buildDemoChartAggregation( GenderOrSexType.GENDER, AgeType.AGE, RANGE_18_44); assertThat(actualBuilder.getName()).isEqualTo(DATE + RANGE_18_44); assertThat(actualBuilder.getType()).isEqualTo("date_range"); a... | public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != null) ? ElasticUtils... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... |
@Test public void buildDemoChartAggregationAgeSexAtBirthRace() { AggregationBuilder actualBuilder = AggregationUtils.buildDemoChartAggregation( GenderOrSexType.SEX_AT_BIRTH, AgeType.AGE, RANGE_18_44); assertThat(actualBuilder.getName()).isEqualTo(DATE + RANGE_18_44); assertThat(actualBuilder.getType()).isEqualTo("date_... | public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != null) ? ElasticUtils... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... |
@Test public void buildDemoChartAggregationAgeAtConsentGenderRace() { AggregationBuilder actualBuilder = AggregationUtils.buildDemoChartAggregation( GenderOrSexType.GENDER, AgeType.AGE_AT_CONSENT, RANGE_18_44); assertThat(actualBuilder.getName()).isEqualTo(DATE + RANGE_18_44); assertThat(actualBuilder.getType()).isEqua... | public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != null) ? ElasticUtils... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... | AggregationUtils { public static AggregationBuilder buildDemoChartAggregation( GenderOrSexType genderOrSexType, AgeType ageType, String ageRange) { String[] ages = ageRange.split("-"); Integer lo = Integer.valueOf(ages[0]); Integer hi = (ages.length > 1) ? Integer.valueOf(ages[1]) : null; LocalDate startDate = (hi != n... |
@Test public void testLeafQuery() { QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(leafParam2))) .addDataFiltersItem("has_ehr_data") .addDataFiltersItem("has_physical_measurement_data... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test(expected = ForbiddenException.class) public void testGetMe_throwsForbidden() throws ApiException { when(profileApi.me()).thenThrow(new ApiException(403, "blah")); service.getMe(); } | @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProv... | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProv... | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProv... |
@Test public void testParentConceptQuery() { QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem() .addSearchParametersItem( new SearchParameter() .conceptId(21600002L) .domain(DomainType.DRUG.toString()) .type(Cr... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testICD9Query() { QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem() .addSearchParametersItem( new SearchParameter() .value("001") .conceptId(771L) .domain(DomainType.CONDITION.toString()) .ty... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testICD9AndSnomedQuery() { QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem() .addSearchParametersItem( new SearchParameter() .value("001") .conceptId(771L) .domain(DomainType.CONDITION.toStri... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testPPIAnswerQuery() { Attribute attr = new Attribute().name(AttrName.NUM).operator(Operator.EQUAL).addOperandsItem("1"); QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem() .addSearchParameter... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testPPIAnswerQueryCat() { Attribute attr = new Attribute().name(AttrName.CAT).operator(Operator.IN).addOperandsItem("1"); QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem() .addSearchParameter... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testAgeAtEventModifierQuery() { QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem() .addSearchParametersItem(leafParam2) .addModifiersItem( new Modifier() .name(ModifierType.AGE_AT_EVENT) .oper... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testDateModifierQuery() { QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem() .addSearchParametersItem(leafParam2) .addModifiersItem( new Modifier() .name(ModifierType.EVENT_DATE) .operator(Ope... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testVisitsModifierQuery() { QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem() .addSearchParametersItem(leafParam2) .addModifiersItem( new Modifier() .name(ModifierType.ENCOUNTERS) .operator(O... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testNumOfOccurrencesModifierQuery() { QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem() .addSearchParametersItem(leafParam2) .addModifiersItem( new Modifier() .name(ModifierType.NUM_OF_OCCURR... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testHeightAnyQuery() { String conceptId = "903133"; SearchParameter heightAnyParam = new SearchParameter() .conceptId(Long.parseLong(conceptId)) .domain(DomainType.PHYSICAL_MEASUREMENT.toString()) .type(CriteriaType.PPI.toString()) .standard(false) .ancestorData(false) .group(false); QueryBuilder resp... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test(expected = UnauthorizedException.class) public void testGetMe_throwsUnauthorized() throws ApiException { when(profileApi.me()).thenThrow(new ApiException(401, "blah")); service.getMe(); } | @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProv... | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProv... | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProv... |
@Test public void testHeightEqualQuery() { Attribute attr = new Attribute().name(AttrName.NUM).operator(Operator.EQUAL).operands(ImmutableList.of("1")); Object left = Float.parseFloat(attr.getOperands().get(0)); Object right = Float.parseFloat(attr.getOperands().get(0)); String conceptId = "903133"; SearchParameter hei... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testWeightBetweenQuery() { Attribute attr = new Attribute() .name(AttrName.NUM) .operator(Operator.BETWEEN) .operands(ImmutableList.of("1", "2")); Object left = Float.parseFloat(attr.getOperands().get(0)); Object right = Float.parseFloat(attr.getOperands().get(1)); String conceptId = "903121"; SearchP... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testGenderQuery() { String conceptId = "8507"; SearchParameter genderParam = new SearchParameter() .conceptId(Long.parseLong(conceptId)) .domain(DomainType.PERSON.toString()) .type(CriteriaType.GENDER.toString()) .standard(true) .ancestorData(false) .group(false); QueryBuilder resp = ElasticFilters.fr... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testGenderExcludeQuery() { String conceptId = "8507"; SearchParameter genderParam = new SearchParameter() .conceptId(Long.parseLong(conceptId)) .domain(DomainType.PERSON.toString()) .type(CriteriaType.GENDER.toString()) .group(false) .ancestorData(false) .standard(true); QueryBuilder resp = ElasticFil... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testGenderIncludeAndExcludeQuery() { String conceptId = "8507"; SearchParameter genderParam = new SearchParameter() .conceptId(Long.parseLong(conceptId)) .domain(DomainType.PERSON.toString()) .type(CriteriaType.GENDER.toString()) .group(false) .ancestorData(false) .standard(true); QueryBuilder resp = ... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
@Test public void testRaceQuery() { String conceptId = "8515"; SearchParameter raceParam = new SearchParameter() .conceptId(Long.parseLong(conceptId)) .domain(DomainType.PERSON.toString()) .type(CriteriaType.RACE.toString()) .group(false) .ancestorData(false) .standard(true); QueryBuilder resp = ElasticFilters.fromCoho... | public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); } | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... | ElasticFilters { public static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequest req) { ElasticFilters f = new ElasticFilters(cbCriteriaDao); return f.process(req); } private ElasticFilters(CBCriteriaDao cbCriteriaDao); static QueryBuilder fromCohortSearch(CBCriteriaDao cbCriteriaDao, SearchRequ... |
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