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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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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(HttpServletResponse.SC_UNAUTHORIZED); } | @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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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_UNAUTHORIZED); } | @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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@Test(expected = NotFoundException.class) public void preHandleGet_firecloudLookupFails() throws Exception { mockGetCallWithBearerToken(); Userinfoplus userInfo = new Userinfoplus(); userInfo.setEmail("[email protected]"); when(userInfoService.getUserInfo("foo")).thenReturn(userInfo); when(fireCloudService.getMe()).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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@Test public void preHandleGet_firecloudLookupSucceeds() throws Exception { mockGetCallWithBearerToken(); Userinfoplus userInfo = new Userinfoplus(); userInfo.setEmail("[email protected]"); when(userInfoService.getUserInfo("foo")).thenReturn(userInfo); FirecloudUserInfo fcUserInfo = new FirecloudUserInfo(); fcUserInfo.setUserEmail("[email protected]"); FirecloudMe me = new FirecloudMe(); me.setUserInfo(fcUserInfo); when(fireCloudService.getMe()).thenReturn(me); when(userDao.findUserByUsername("[email protected]")).thenReturn(user); 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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@Test public void preHandleGet_firecloudLookupSucceedsNoUserRecordWrongDomain() throws Exception { mockGetCallWithBearerToken(); Userinfoplus userInfo = new Userinfoplus(); userInfo.setEmail("[email protected]"); when(userInfoService.getUserInfo("foo")).thenReturn(userInfo); FirecloudUserInfo fcUserInfo = new FirecloudUserInfo(); fcUserInfo.setUserEmail("[email protected]"); FirecloudMe me = new FirecloudMe(); me.setUserInfo(fcUserInfo); when(fireCloudService.getMe()).thenReturn(me); when(userDao.findUserByUsername("[email protected]")).thenReturn(null); assertThat(interceptor.preHandle(mockRequest, mockResponse, mockHandler)).isFalse(); verify(mockResponse).sendError(HttpServletResponse.SC_UNAUTHORIZED); } | @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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@Test public void preHandleGet_noUserRecord() throws Exception { workbenchConfig.access.unsafeAllowUserCreationFromGSuiteData = true; mockGetCallWithBearerToken(); mockUserInfoSuccess(); when(userDao.findUserByUsername(eq("[email protected]"))).thenReturn(null); when(devUserRegistrationService.createUser(any())).thenReturn(user); 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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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 freeTierWorkspace = createWorkspace(user, SINGLE_WORKSPACE_TEST_PROJECT); final DbWorkspace userAccountWorkspace = new DbWorkspace(); userAccountWorkspace.setCreator(user); userAccountWorkspace.setWorkspaceNamespace("some other namespace"); userAccountWorkspace.setBillingMigrationStatusEnum(BillingMigrationStatus.NEW); userAccountWorkspace.setBillingAccountName("some other account"); userAccountWorkspace.setBillingStatus(BillingStatus.ACTIVE); workspaceDao.save(userAccountWorkspace); freeTierBillingService.checkFreeTierBillingUsage(); verify(mailService).alertUserFreeTierExpiration(eq(user)); assertSingleWorkspaceTestDbState(user, freeTierWorkspace, BillingStatus.INACTIVE, 100.01); final DbWorkspace retrievedWorkspace = workspaceDao.findOne(userAccountWorkspace.getWorkspaceId()); assertThat(retrievedWorkspace.getBillingStatus()).isEqualTo(BillingStatus.ACTIVE); } | 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 = workspaceCosts.entrySet().stream() .collect( Collectors.groupingBy( e -> e.getKey().getCreator(), Collectors.summingDouble(Entry::getValue))); final Set<DbUser> previouslyExpiredUsers = getExpiredUsersFromDb(); final Set<DbUser> expiredUsers = userCosts.entrySet().stream() .filter(e -> costAboveLimit(e.getKey(), e.getValue())) .map(Entry::getKey) .collect(Collectors.toSet()); final Set<DbUser> newlyExpiredUsers = Sets.difference(expiredUsers, previouslyExpiredUsers); for (final DbUser user : newlyExpiredUsers) { try { mailService.alertUserFreeTierExpiration(user); } catch (final MessagingException e) { logger.log(Level.WARNING, e.getMessage()); } updateFreeTierWorkspacesStatus(user, BillingStatus.INACTIVE); } final Set<DbUser> usersWithNonNullRegistration = userDao.findByFirstRegistrationCompletionTimeNotNull(); final Set<DbUser> usersToThresholdCheck = Sets.difference(usersWithNonNullRegistration, expiredUsers); sendAlertsForCostThresholds(usersToThresholdCheck, previousUserCosts, userCosts); } | FreeTierBillingService { 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 = workspaceCosts.entrySet().stream() .collect( Collectors.groupingBy( e -> e.getKey().getCreator(), Collectors.summingDouble(Entry::getValue))); final Set<DbUser> previouslyExpiredUsers = getExpiredUsersFromDb(); final Set<DbUser> expiredUsers = userCosts.entrySet().stream() .filter(e -> costAboveLimit(e.getKey(), e.getValue())) .map(Entry::getKey) .collect(Collectors.toSet()); final Set<DbUser> newlyExpiredUsers = Sets.difference(expiredUsers, previouslyExpiredUsers); for (final DbUser user : newlyExpiredUsers) { try { mailService.alertUserFreeTierExpiration(user); } catch (final MessagingException e) { logger.log(Level.WARNING, e.getMessage()); } updateFreeTierWorkspacesStatus(user, BillingStatus.INACTIVE); } final Set<DbUser> usersWithNonNullRegistration = userDao.findByFirstRegistrationCompletionTimeNotNull(); final Set<DbUser> usersToThresholdCheck = Sets.difference(usersWithNonNullRegistration, expiredUsers); sendAlertsForCostThresholds(usersToThresholdCheck, previousUserCosts, userCosts); } } | FreeTierBillingService { 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 = workspaceCosts.entrySet().stream() .collect( Collectors.groupingBy( e -> e.getKey().getCreator(), Collectors.summingDouble(Entry::getValue))); final Set<DbUser> previouslyExpiredUsers = getExpiredUsersFromDb(); final Set<DbUser> expiredUsers = userCosts.entrySet().stream() .filter(e -> costAboveLimit(e.getKey(), e.getValue())) .map(Entry::getKey) .collect(Collectors.toSet()); final Set<DbUser> newlyExpiredUsers = Sets.difference(expiredUsers, previouslyExpiredUsers); for (final DbUser user : newlyExpiredUsers) { try { mailService.alertUserFreeTierExpiration(user); } catch (final MessagingException e) { logger.log(Level.WARNING, e.getMessage()); } updateFreeTierWorkspacesStatus(user, BillingStatus.INACTIVE); } final Set<DbUser> usersWithNonNullRegistration = userDao.findByFirstRegistrationCompletionTimeNotNull(); final Set<DbUser> usersToThresholdCheck = Sets.difference(usersWithNonNullRegistration, expiredUsers); sendAlertsForCostThresholds(usersToThresholdCheck, previousUserCosts, userCosts); } @Autowired FreeTierBillingService(
BigQueryService bigQueryService,
Clock clock,
MailService mailService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserServiceAuditor userServiceAuditor,
WorkspaceDao workspaceDao,
WorkspaceFreeTierUsageDao workspaceFreeTierUsageDao); } | FreeTierBillingService { 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 = workspaceCosts.entrySet().stream() .collect( Collectors.groupingBy( e -> e.getKey().getCreator(), Collectors.summingDouble(Entry::getValue))); final Set<DbUser> previouslyExpiredUsers = getExpiredUsersFromDb(); final Set<DbUser> expiredUsers = userCosts.entrySet().stream() .filter(e -> costAboveLimit(e.getKey(), e.getValue())) .map(Entry::getKey) .collect(Collectors.toSet()); final Set<DbUser> newlyExpiredUsers = Sets.difference(expiredUsers, previouslyExpiredUsers); for (final DbUser user : newlyExpiredUsers) { try { mailService.alertUserFreeTierExpiration(user); } catch (final MessagingException e) { logger.log(Level.WARNING, e.getMessage()); } updateFreeTierWorkspacesStatus(user, BillingStatus.INACTIVE); } final Set<DbUser> usersWithNonNullRegistration = userDao.findByFirstRegistrationCompletionTimeNotNull(); final Set<DbUser> usersToThresholdCheck = Sets.difference(usersWithNonNullRegistration, expiredUsers); sendAlertsForCostThresholds(usersToThresholdCheck, previousUserCosts, userCosts); } @Autowired FreeTierBillingService(
BigQueryService bigQueryService,
Clock clock,
MailService mailService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserServiceAuditor userServiceAuditor,
WorkspaceDao workspaceDao,
WorkspaceFreeTierUsageDao workspaceFreeTierUsageDao); double getWorkspaceFreeTierBillingUsage(DbWorkspace dbWorkspace); void checkFreeTierBillingUsage(); @Nullable Double getCachedFreeTierUsage(DbUser user); boolean userHasRemainingFreeTierCredits(DbUser user); double getUserFreeTierDollarLimit(DbUser user); boolean maybeSetDollarLimitOverride(DbUser user, double newDollarLimit); Map<Long, Double> getUserIdToTotalCost(); } | FreeTierBillingService { 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 = workspaceCosts.entrySet().stream() .collect( Collectors.groupingBy( e -> e.getKey().getCreator(), Collectors.summingDouble(Entry::getValue))); final Set<DbUser> previouslyExpiredUsers = getExpiredUsersFromDb(); final Set<DbUser> expiredUsers = userCosts.entrySet().stream() .filter(e -> costAboveLimit(e.getKey(), e.getValue())) .map(Entry::getKey) .collect(Collectors.toSet()); final Set<DbUser> newlyExpiredUsers = Sets.difference(expiredUsers, previouslyExpiredUsers); for (final DbUser user : newlyExpiredUsers) { try { mailService.alertUserFreeTierExpiration(user); } catch (final MessagingException e) { logger.log(Level.WARNING, e.getMessage()); } updateFreeTierWorkspacesStatus(user, BillingStatus.INACTIVE); } final Set<DbUser> usersWithNonNullRegistration = userDao.findByFirstRegistrationCompletionTimeNotNull(); final Set<DbUser> usersToThresholdCheck = Sets.difference(usersWithNonNullRegistration, expiredUsers); sendAlertsForCostThresholds(usersToThresholdCheck, previousUserCosts, userCosts); } @Autowired FreeTierBillingService(
BigQueryService bigQueryService,
Clock clock,
MailService mailService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserServiceAuditor userServiceAuditor,
WorkspaceDao workspaceDao,
WorkspaceFreeTierUsageDao workspaceFreeTierUsageDao); double getWorkspaceFreeTierBillingUsage(DbWorkspace dbWorkspace); void checkFreeTierBillingUsage(); @Nullable Double getCachedFreeTierUsage(DbUser user); boolean userHasRemainingFreeTierCredits(DbUser user); double getUserFreeTierDollarLimit(DbUser user); boolean maybeSetDollarLimitOverride(DbUser user, double newDollarLimit); Map<Long, Double> getUserIdToTotalCost(); } |
@Test public void preHandleGet_noUserRecordAndNoDevRegistration() throws Exception { workbenchConfig.access.unsafeAllowUserCreationFromGSuiteData = false; mockGetCallWithBearerToken(); mockUserInfoSuccess(); when(userDao.findUserByUsername(eq("[email protected]"))).thenReturn(null); assertThat(interceptor.preHandle(mockRequest, mockResponse, mockHandler)).isFalse(); verify(devUserRegistrationService, never()).createUser(any()); } | @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; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 = (HandlerMethod) handler; boolean isAuthRequired = false; ApiOperation apiOp = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp != null) { for (Authorization auth : apiOp.authorizations()) { if (auth.value().equals(authName)) { isAuthRequired = true; break; } } } if (!isAuthRequired) { return true; } String authorizationHeader = request.getHeader(HttpHeaders.AUTHORIZATION); if (authorizationHeader == null || !authorizationHeader.startsWith("Bearer ")) { log.warning("No bearer token found in request"); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } final String token = authorizationHeader.substring("Bearer".length()).trim(); final Userinfoplus userInfo = userInfoService.getUserInfo(token); String userName = userInfo.getEmail(); if (workbenchConfigProvider.get().auth.serviceAccountApiUsers.contains(userName)) { DbUser user = userDao.findUserByUsername(userName); if (user == null) { user = userService.createServiceAccountUser(userName); } SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(user, userInfo, token, UserType.SERVICE_ACCOUNT)); log.log(Level.INFO, "{0} service account in use", userName); return true; } String gsuiteDomainSuffix = "@" + workbenchConfigProvider.get().googleDirectoryService.gSuiteDomain; if (!userName.endsWith(gsuiteDomainSuffix)) { SecurityContextHolder.getContext() .setAuthentication( new UserAuthentication(null, userInfo, token, UserType.SERVICE_ACCOUNT)); userName = fireCloudService.getMe().getUserInfo().getUserEmail(); if (!userName.endsWith(gsuiteDomainSuffix)) { log.info( String.format( "User %s isn't in domain %s, can't access the workbench", userName, gsuiteDomainSuffix)); response.sendError(HttpServletResponse.SC_UNAUTHORIZED); return false; } } DbUser user = userDao.findUserByUsername(userName); if (user == null) { if (workbenchConfigProvider.get().access.unsafeAllowUserCreationFromGSuiteData) { user = devUserRegistrationService.createUser(userInfo); log.info(String.format("Dev user '%s' has been re-created.", user.getUsername())); } else { log.severe(String.format("No User row exists for user '%s'", userName)); return false; } } if (user.getDisabled()) { throw new ForbiddenException( WorkbenchException.errorResponse( "Rejecting request for disabled user account: " + user.getUsername(), ErrorCode.USER_DISABLED)); } SecurityContextHolder.getContext() .setAuthentication(new UserAuthentication(user, userInfo, token, UserType.RESEARCHER)); log.log(Level.INFO, "{0} logged in", userInfo.getEmail()); if (!hasRequiredAuthority(method, user)) { response.sendError(HttpServletResponse.SC_FORBIDDEN); return false; } return true; } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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 fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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 fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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)).thenReturn(userWithAuthorities); Method apiControllerMethod = FakeApiController.class.getMethod("handle"); assertThat(interceptor.hasRequiredAuthority(apiControllerMethod, user)).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 fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | AuthInterceptor extends HandlerInterceptorAdapter { boolean hasRequiredAuthority(HandlerMethod handlerMethod, DbUser user) { return hasRequiredAuthority(InterceptorUtils.getControllerMethod(handlerMethod), user); } @Autowired AuthInterceptor(
UserInfoService userInfoService,
FireCloudService fireCloudService,
Provider<WorkbenchConfig> workbenchConfigProvider,
UserDao userDao,
UserService userService,
DevUserRegistrationService devUserRegistrationService); @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@Test public void testPreHandle_getRequest() { boolean result = requestTimeMetricInterceptor.preHandle( mockHttpServletRequest, mockHttpServletResponse, mockHandlerMethod); assertThat(result).isTrue(); verify(mockHttpServletRequest) .setAttribute(attributeKeyCaptor.capture(), attributeValueCaptor.capture()); assertThat(attributeKeyCaptor.getValue()) .isEqualTo(RequestAttribute.START_INSTANT.getKeyName()); Object attrValueObj = attributeValueCaptor.getValue(); assertThat(attrValueObj instanceof Instant).isTrue(); assertThat((Instant) attrValueObj).isEqualTo(START_INSTANT); } | @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 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 true; } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); } | 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 true; } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 true; } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@Test public void testPreHandle_skipsOptionsRequest() { doReturn(HttpMethods.OPTIONS).when(mockHttpServletRequest).getMethod(); boolean result = requestTimeMetricInterceptor.preHandle( mockHttpServletRequest, mockHttpServletResponse, mockHandlerMethod); 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 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 true; } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); } | 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 true; } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 true; } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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 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 true; } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); } | 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 true; } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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 true; } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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, mockModelAndView); verify(mockHttpServletRequest).getAttribute(RequestAttribute.START_INSTANT.getKeyName()); verify(mockLogsBasedMetricService).record(measurementBundleCaptor.capture()); assertThat( measurementBundleCaptor .getValue() .getMeasurements() .get(DistributionMetric.API_METHOD_TIME)) .isEqualTo(DURATION_MILLIS); assertThat(measurementBundleCaptor.getValue().getTags()).hasSize(1); assertThat(measurementBundleCaptor.getValue().getTagValue(MetricLabel.METHOD_NAME).get()) .isEqualTo(METHOD_NAME); } | @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.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@Test public void testPostHandle_skipsOptionsRequest() { doReturn(HttpMethods.OPTIONS).when(mockHttpServletRequest).getMethod(); requestTimeMetricInterceptor.postHandle( mockHttpServletRequest, mockHttpServletResponse, mockHandlerMethod, 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.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@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.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } | 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(); Optional.ofNullable(request.getAttribute(RequestAttribute.START_INSTANT.getKeyName())) .map(obj -> (Instant) obj) .map(start -> Duration.between(start, clock.instant())) .map(Duration::toMillis) .ifPresent( elapsedMillis -> logsBasedMetricService.record( MeasurementBundle.builder() .addMeasurement(DistributionMetric.API_METHOD_TIME, elapsedMillis) .addTag(MetricLabel.METHOD_NAME, methodName) .build())); } RequestTimeMetricInterceptor(LogsBasedMetricService logsBasedMetricService, Clock clock); @Override boolean preHandle(
HttpServletRequest request, HttpServletResponse response, Object handler); @Override void postHandle(
HttpServletRequest request,
HttpServletResponse response,
Object handler,
ModelAndView modelAndView); } |
@Test public void testCloneConceptSetWithNoCdrVersionChange() { DbWorkspace mockDbWorkspace = mockWorkspace(); DbConceptSet fromConceptSet = mockConceptSet(); DbConceptSet copiedConceptSet = conceptSetService.cloneConceptSetAndConceptIds(fromConceptSet, mockDbWorkspace, false); assertNotNull(copiedConceptSet); assertEquals(copiedConceptSet.getConceptIds().size(), 5); assertEquals(copiedConceptSet.getWorkspaceId(), mockDbWorkspace.getWorkspaceId()); } | @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceId(targetWorkspace.getWorkspaceId()) .creationTime(targetWorkspace.getCreationTime()) .lastModifiedTime(targetWorkspace.getLastModifiedTime()) .version(CONCEPT_SET_VERSION) .build(); DbConceptSet dbConceptSetClone = conceptSetMapper.dbModelToDbModel(dbConceptSet, conceptSetContext); if (cdrVersionChanged) { String omopTable = BigQueryTableInfo.getTableName(dbConceptSet.getDomainEnum()); dbConceptSetClone.setParticipantCount( conceptBigQueryService.getParticipantCountForConcepts( dbConceptSet.getDomainEnum(), omopTable, dbConceptSet.getConceptIds())); } return conceptSetDao.save(dbConceptSetClone); } | ConceptSetService { @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceId(targetWorkspace.getWorkspaceId()) .creationTime(targetWorkspace.getCreationTime()) .lastModifiedTime(targetWorkspace.getLastModifiedTime()) .version(CONCEPT_SET_VERSION) .build(); DbConceptSet dbConceptSetClone = conceptSetMapper.dbModelToDbModel(dbConceptSet, conceptSetContext); if (cdrVersionChanged) { String omopTable = BigQueryTableInfo.getTableName(dbConceptSet.getDomainEnum()); dbConceptSetClone.setParticipantCount( conceptBigQueryService.getParticipantCountForConcepts( dbConceptSet.getDomainEnum(), omopTable, dbConceptSet.getConceptIds())); } return conceptSetDao.save(dbConceptSetClone); } } | ConceptSetService { @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceId(targetWorkspace.getWorkspaceId()) .creationTime(targetWorkspace.getCreationTime()) .lastModifiedTime(targetWorkspace.getLastModifiedTime()) .version(CONCEPT_SET_VERSION) .build(); DbConceptSet dbConceptSetClone = conceptSetMapper.dbModelToDbModel(dbConceptSet, conceptSetContext); if (cdrVersionChanged) { String omopTable = BigQueryTableInfo.getTableName(dbConceptSet.getDomainEnum()); dbConceptSetClone.setParticipantCount( conceptBigQueryService.getParticipantCountForConcepts( dbConceptSet.getDomainEnum(), omopTable, dbConceptSet.getConceptIds())); } return conceptSetDao.save(dbConceptSetClone); } @Autowired ConceptSetService(
ConceptSetDao conceptSetDao,
ConceptBigQueryService conceptBigQueryService,
ConceptService conceptService,
CohortBuilderService cohortBuilderService,
ConceptSetMapper conceptSetMapper,
Clock clock,
Provider<WorkbenchConfig> configProvider); } | ConceptSetService { @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceId(targetWorkspace.getWorkspaceId()) .creationTime(targetWorkspace.getCreationTime()) .lastModifiedTime(targetWorkspace.getLastModifiedTime()) .version(CONCEPT_SET_VERSION) .build(); DbConceptSet dbConceptSetClone = conceptSetMapper.dbModelToDbModel(dbConceptSet, conceptSetContext); if (cdrVersionChanged) { String omopTable = BigQueryTableInfo.getTableName(dbConceptSet.getDomainEnum()); dbConceptSetClone.setParticipantCount( conceptBigQueryService.getParticipantCountForConcepts( dbConceptSet.getDomainEnum(), omopTable, dbConceptSet.getConceptIds())); } return conceptSetDao.save(dbConceptSetClone); } @Autowired ConceptSetService(
ConceptSetDao conceptSetDao,
ConceptBigQueryService conceptBigQueryService,
ConceptService conceptService,
CohortBuilderService cohortBuilderService,
ConceptSetMapper conceptSetMapper,
Clock clock,
Provider<WorkbenchConfig> configProvider); ConceptSet copyAndSave(
Long fromConceptSetId, String newConceptSetName, DbUser creator, Long toWorkspaceId); ConceptSet createConceptSet(
CreateConceptSetRequest request, DbUser creator, Long workspaceId); ConceptSet updateConceptSet(Long conceptSetId, ConceptSet conceptSet); ConceptSet updateConceptSetConcepts(Long conceptSetId, UpdateConceptSetRequest request); void delete(Long conceptSetId); ConceptSet getConceptSet(Long conceptSetId); List<ConceptSet> findAll(List<Long> conceptSetIds); List<ConceptSet> findByWorkspaceId(long workspaceId); List<ConceptSet> findByWorkspaceIdAndSurvey(long workspaceId, short surveyId); @Transactional DbConceptSet cloneConceptSetAndConceptIds(
DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged); List<DbConceptSet> getConceptSets(DbWorkspace workspace); } | ConceptSetService { @Transactional public DbConceptSet cloneConceptSetAndConceptIds( DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged) { ConceptSetContext conceptSetContext = new ConceptSetContext.Builder() .name(dbConceptSet.getName()) .creator(targetWorkspace.getCreator()) .workspaceId(targetWorkspace.getWorkspaceId()) .creationTime(targetWorkspace.getCreationTime()) .lastModifiedTime(targetWorkspace.getLastModifiedTime()) .version(CONCEPT_SET_VERSION) .build(); DbConceptSet dbConceptSetClone = conceptSetMapper.dbModelToDbModel(dbConceptSet, conceptSetContext); if (cdrVersionChanged) { String omopTable = BigQueryTableInfo.getTableName(dbConceptSet.getDomainEnum()); dbConceptSetClone.setParticipantCount( conceptBigQueryService.getParticipantCountForConcepts( dbConceptSet.getDomainEnum(), omopTable, dbConceptSet.getConceptIds())); } return conceptSetDao.save(dbConceptSetClone); } @Autowired ConceptSetService(
ConceptSetDao conceptSetDao,
ConceptBigQueryService conceptBigQueryService,
ConceptService conceptService,
CohortBuilderService cohortBuilderService,
ConceptSetMapper conceptSetMapper,
Clock clock,
Provider<WorkbenchConfig> configProvider); ConceptSet copyAndSave(
Long fromConceptSetId, String newConceptSetName, DbUser creator, Long toWorkspaceId); ConceptSet createConceptSet(
CreateConceptSetRequest request, DbUser creator, Long workspaceId); ConceptSet updateConceptSet(Long conceptSetId, ConceptSet conceptSet); ConceptSet updateConceptSetConcepts(Long conceptSetId, UpdateConceptSetRequest request); void delete(Long conceptSetId); ConceptSet getConceptSet(Long conceptSetId); List<ConceptSet> findAll(List<Long> conceptSetIds); List<ConceptSet> findByWorkspaceId(long workspaceId); List<ConceptSet> findByWorkspaceIdAndSurvey(long workspaceId, short surveyId); @Transactional DbConceptSet cloneConceptSetAndConceptIds(
DbConceptSet dbConceptSet, DbWorkspace targetWorkspace, boolean cdrVersionChanged); List<DbConceptSet> getConceptSets(DbWorkspace workspace); @VisibleForTesting static int MAX_CONCEPTS_PER_SET; } |
@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> profileApiProvider,
Provider<BillingApi> billingApiProvider,
Provider<GroupsApi> groupsApiProvider,
Provider<NihApi> nihApiProvider,
@Qualifier(FireCloudConfig.END_USER_WORKSPACE_API)
Provider<WorkspacesApi> endUserWorkspacesApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_WORKSPACE_API)
Provider<WorkspacesApi> serviceAccountWorkspaceApiProvider,
Provider<StatusApi> statusApiProvider,
@Qualifier(FireCloudConfig.END_USER_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> endUserStaticNotebooksApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> serviceAccountStaticNotebooksApiProvider,
FirecloudRetryHandler retryHandler,
@Qualifier(Constants.FIRECLOUD_ADMIN_CREDS)
Provider<ServiceAccountCredentials> fcAdminCredsProvider,
IamCredentialsClient iamCredentialsClient,
HttpTransport httpTransport); } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProvider,
Provider<BillingApi> billingApiProvider,
Provider<GroupsApi> groupsApiProvider,
Provider<NihApi> nihApiProvider,
@Qualifier(FireCloudConfig.END_USER_WORKSPACE_API)
Provider<WorkspacesApi> endUserWorkspacesApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_WORKSPACE_API)
Provider<WorkspacesApi> serviceAccountWorkspaceApiProvider,
Provider<StatusApi> statusApiProvider,
@Qualifier(FireCloudConfig.END_USER_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> endUserStaticNotebooksApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> serviceAccountStaticNotebooksApiProvider,
FirecloudRetryHandler retryHandler,
@Qualifier(Constants.FIRECLOUD_ADMIN_CREDS)
Provider<ServiceAccountCredentials> fcAdminCredsProvider,
IamCredentialsClient iamCredentialsClient,
HttpTransport httpTransport); ApiClient getApiClientWithImpersonation(String userEmail); @Override @VisibleForTesting String getApiBasePath(); @Override boolean getFirecloudStatus(); @Override FirecloudMe getMe(); @Override void registerUser(String contactEmail, String firstName, String lastName); @Override void createAllOfUsBillingProject(String projectName); @Override void deleteBillingProject(String billingProject); @Override FirecloudBillingProjectStatus getBillingProjectStatus(String projectName); @Override void addOwnerToBillingProject(String ownerEmail, String projectName); @Override void removeOwnerFromBillingProject(
String ownerEmailToRemove, String projectName, Optional<String> callerAccessToken); @Override FirecloudWorkspace createWorkspace(String projectName, String workspaceName); @Override FirecloudWorkspace cloneWorkspace(
String fromProject, String fromName, String toProject, String toName); @Override List<FirecloudBillingProjectMembership> getBillingProjectMemberships(); @Override FirecloudWorkspaceACLUpdateResponseList updateWorkspaceACL(
String projectName, String workspaceName, List<FirecloudWorkspaceACLUpdate> aclUpdates); @Override FirecloudWorkspaceACL getWorkspaceAclAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspaceAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspace(String projectName, String workspaceName); @Override Optional<FirecloudWorkspaceResponse> getWorkspace(DbWorkspace dbWorkspace); @Override List<FirecloudWorkspaceResponse> getWorkspaces(); @Override void deleteWorkspace(String projectName, String workspaceName); @Override FirecloudManagedGroupWithMembers getGroup(String groupName); @Override FirecloudManagedGroupWithMembers createGroup(String groupName); @Override void addUserToGroup(String email, String groupName); @Override void removeUserFromGroup(String email, String groupName); @Override boolean isUserMemberOfGroup(String email, String groupName); @Override String staticNotebooksConvert(byte[] notebook); @Override String staticNotebooksConvertAsService(byte[] notebook); @Override FirecloudNihStatus getNihStatus(); @Override void postNihCallback(FirecloudJWTWrapper wrapper); } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProvider,
Provider<BillingApi> billingApiProvider,
Provider<GroupsApi> groupsApiProvider,
Provider<NihApi> nihApiProvider,
@Qualifier(FireCloudConfig.END_USER_WORKSPACE_API)
Provider<WorkspacesApi> endUserWorkspacesApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_WORKSPACE_API)
Provider<WorkspacesApi> serviceAccountWorkspaceApiProvider,
Provider<StatusApi> statusApiProvider,
@Qualifier(FireCloudConfig.END_USER_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> endUserStaticNotebooksApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> serviceAccountStaticNotebooksApiProvider,
FirecloudRetryHandler retryHandler,
@Qualifier(Constants.FIRECLOUD_ADMIN_CREDS)
Provider<ServiceAccountCredentials> fcAdminCredsProvider,
IamCredentialsClient iamCredentialsClient,
HttpTransport httpTransport); ApiClient getApiClientWithImpersonation(String userEmail); @Override @VisibleForTesting String getApiBasePath(); @Override boolean getFirecloudStatus(); @Override FirecloudMe getMe(); @Override void registerUser(String contactEmail, String firstName, String lastName); @Override void createAllOfUsBillingProject(String projectName); @Override void deleteBillingProject(String billingProject); @Override FirecloudBillingProjectStatus getBillingProjectStatus(String projectName); @Override void addOwnerToBillingProject(String ownerEmail, String projectName); @Override void removeOwnerFromBillingProject(
String ownerEmailToRemove, String projectName, Optional<String> callerAccessToken); @Override FirecloudWorkspace createWorkspace(String projectName, String workspaceName); @Override FirecloudWorkspace cloneWorkspace(
String fromProject, String fromName, String toProject, String toName); @Override List<FirecloudBillingProjectMembership> getBillingProjectMemberships(); @Override FirecloudWorkspaceACLUpdateResponseList updateWorkspaceACL(
String projectName, String workspaceName, List<FirecloudWorkspaceACLUpdate> aclUpdates); @Override FirecloudWorkspaceACL getWorkspaceAclAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspaceAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspace(String projectName, String workspaceName); @Override Optional<FirecloudWorkspaceResponse> getWorkspace(DbWorkspace dbWorkspace); @Override List<FirecloudWorkspaceResponse> getWorkspaces(); @Override void deleteWorkspace(String projectName, String workspaceName); @Override FirecloudManagedGroupWithMembers getGroup(String groupName); @Override FirecloudManagedGroupWithMembers createGroup(String groupName); @Override void addUserToGroup(String email, String groupName); @Override void removeUserFromGroup(String email, String groupName); @Override boolean isUserMemberOfGroup(String email, String groupName); @Override String staticNotebooksConvert(byte[] notebook); @Override String staticNotebooksConvertAsService(byte[] notebook); @Override FirecloudNihStatus getNihStatus(); @Override void postNihCallback(FirecloudJWTWrapper wrapper); static final List<String> FIRECLOUD_API_OAUTH_SCOPES; static final List<String> FIRECLOUD_WORKSPACE_REQUIRED_FIELDS; } |
@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(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); static final String GAE_CRON_HEADER; } |
@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(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); static final String GAE_CRON_HEADER; } |
@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.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(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); static final String GAE_CRON_HEADER; } |
@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(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(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); static final String GAE_CRON_HEADER; } |
@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(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); } | 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 = AnnotationUtils.findAnnotation(method.getMethod(), ApiOperation.class); if (apiOp == null) { return true; } boolean requireCronHeader = false; for (String tag : apiOp.tags()) { if (CRON_TAG.equals(tag)) { requireCronHeader = true; break; } } boolean hasCronHeader = "true".equals(request.getHeader(GAE_CRON_HEADER)); if (requireCronHeader && !hasCronHeader) { response.sendError( HttpServletResponse.SC_FORBIDDEN, String.format( "cronjob endpoints are only invocable via app engine cronjob, and " + "require the '%s' header", GAE_CRON_HEADER)); return false; } return true; } @Override boolean preHandle(HttpServletRequest request, HttpServletResponse response, Object handler); static final String GAE_CRON_HEADER; } |
@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 static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | QueryParameterValues { @NotNull public static String decorateParameterName(@NotNull String parameterName) { return "@" + parameterName; } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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(parameterName); } | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(parameterName); } } | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(parameterName); } } | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(parameterName); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(parameterName); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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("p0")).isEqualTo(nullString); } | @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(parameterName); } | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(parameterName); } } | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(parameterName); } } | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(parameterName); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | QueryParameterValues { @NotNull public static String buildParameter( @NotNull Map<String, QueryParameterValue> queryParameterValueMap, @NotNull QueryParameterValue queryParameterValue) { String parameterName = "p" + queryParameterValueMap.size(); queryParameterValueMap.put(parameterName, queryParameterValue); return decorateParameterName(parameterName); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | 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); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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(); assertTimeApprox(roundTripOdt.get(), OFFSET_DATE_TIME); } | @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(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | 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(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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(mockWorkspaceService) .getFirecloudUserRoles( mockWorkspace.getWorkspaceNamespace(), mockWorkspace.getFirecloudName()); verify(rdrExportDao, times(1)).save(anyList()); verify(mockRdrApi).exportWorkspaces(Arrays.asList(rdrWorkspace)); } | @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 (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); @Override List<Long> findAllUserIdsToExport(); @Override List<Long> findAllWorkspacesIdsToExport(); @Override void exportUsers(List<Long> userIds); @Override void exportWorkspaces(List<Long> workspaceIds); @Override @VisibleForTesting void updateDbRdrExport(RdrEntity entity, List<Long> idList); } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); @Override List<Long> findAllUserIdsToExport(); @Override List<Long> findAllWorkspacesIdsToExport(); @Override void exportUsers(List<Long> userIds); @Override void exportWorkspaces(List<Long> workspaceIds); @Override @VisibleForTesting void updateDbRdrExport(RdrEntity entity, List<Long> idList); } |
@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 String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | 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 String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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 String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | 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 String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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.ofInstant(i, ZoneOffset.UTC)); } | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofInstant(i, ZoneOffset.UTC)); } } | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofInstant(i, ZoneOffset.UTC)); } } | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofInstant(i, ZoneOffset.UTC)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofInstant(i, ZoneOffset.UTC)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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.ofInstant(i, ZoneOffset.UTC)); } | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofInstant(i, ZoneOffset.UTC)); } } | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofInstant(i, ZoneOffset.UTC)); } } | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofInstant(i, ZoneOffset.UTC)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | QueryParameterValues { public static Optional<OffsetDateTime> timestampQpvToOffsetDateTime( @Nullable QueryParameterValue queryParameterValue) { verifyQpvType(queryParameterValue, StandardSQLTypeName.TIMESTAMP); return Optional.ofNullable(queryParameterValue) .flatMap(QueryParameterValues::timestampQpvToInstant) .map(i -> OffsetDateTime.ofInstant(i, ZoneOffset.UTC)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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("2020-09-17T04:30:15Z"); assertTimeApprox(convertedOdt.get(), expected); assertThat(rowToInsertStringToOffsetTimestamp(null)).isEmpty(); } | 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.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.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.UTC)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | 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.UTC)); } @NotNull static String buildParameter(
@NotNull Map<String, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); } | 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, QueryParameterValue> queryParameterValueMap,
@NotNull QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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 QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T 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 QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@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 QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T 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 QueryParameterValue queryParameterValue); @NotNull static QueryParameterValue instantToQPValue(@Nullable Instant instant); static Optional<Instant> timestampStringToInstant(@Nullable String timestamp); static Optional<Instant> timestampQpvToInstant(@NotNull QueryParameterValue qpv); static void verifyQpvType(
@Nullable QueryParameterValue queryParameterValue, StandardSQLTypeName expectedType); static Optional<OffsetDateTime> timestampQpvToOffsetDateTime(
@Nullable QueryParameterValue queryParameterValue); @NotNull static String replaceNamedParameters(
@NotNull QueryJobConfiguration queryJobConfiguration); @NotNull static String formatQuery(@NotNull String query); @NotNull static String decorateParameterName(@NotNull String parameterName); @Nullable static QueryParameterValue toTimestampQpv(@Nullable OffsetDateTime offsetDateTime); @Nullable static String toInsertRowString(@Nullable OffsetDateTime offsetDateTime); static Optional<OffsetDateTime> rowToInsertStringToOffsetTimestamp(
@Nullable String bqTimeString); @NotNull static QueryParameterValue enumToQpv(@Nullable T enumValue); @Nullable static String enumToString(@Nullable T enumValue); static final DateTimeFormatter QPV_TIMESTAMP_FORMATTER; static final DateTimeFormatter ROW_TO_INSERT_TIMESTAMP_FORMATTER; } |
@Test public void buildCriteriaLookupMapNoSearchParametersException() { SearchRequest searchRequest = new SearchRequest().addIncludesItem(new SearchGroup().addItemsItem(new SearchGroupItem())); try { lookupUtil.buildCriteriaLookupMap(searchRequest); fail("Should have thrown BadRequestException!"); } catch (BadRequestException bre) { assertEquals("Bad Request: search parameters are empty.", bre.getMessage()); } } | 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.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req); } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req); } |
@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); DbCriteria drugNode2 = DbCriteria.builder() .addParentId(drugNode1.getId()) .addDomainId(DomainType.DRUG.toString()) .addType(CriteriaType.RXNORM.toString()) .addConceptId("19069022") .addGroup(false) .addSelectable(true) .build(); saveCriteriaWithPath(drugNode1.getPath(), drugNode2); DbCriteria drugNode3 = DbCriteria.builder() .addParentId(drugNode1.getId()) .addDomainId(DomainType.DRUG.toString()) .addType(CriteriaType.RXNORM.toString()) .addConceptId("1036094") .addGroup(false) .addSelectable(true) .build(); saveCriteriaWithPath(drugNode1.getPath(), drugNode3); jdbcTemplate.execute( "create table cb_criteria_ancestor(ancestor_id integer, descendant_id integer)"); jdbcTemplate.execute( "insert into cb_criteria_ancestor(ancestor_id, descendant_id) values (19069022, 19069022)"); jdbcTemplate.execute( "insert into cb_criteria_ancestor(ancestor_id, descendant_id) values (1036094, 1036094)"); List<Long> childConceptIds = ImmutableList.of(19069022L, 1036094L); SearchParameter searchParameter = new SearchParameter() .domain(DomainType.DRUG.toString()) .type(CriteriaType.ATC.toString()) .group(true) .ancestorData(true) .conceptId(21600002L); SearchRequest searchRequest = new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(searchParameter))); assertEquals( ImmutableMap.of(searchParameter, new HashSet<>(childConceptIds)), lookupUtil.buildCriteriaLookupMap(searchRequest)); jdbcTemplate.execute("drop table cb_criteria_ancestor"); } | 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.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req); } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req); } |
@Test public void exportWorkspace_FocusOnUnderservedPopulation() throws ApiException { Set<SpecificPopulationEnum> specificPopulationEnumsSet = new HashSet<SpecificPopulationEnum>(); specificPopulationEnumsSet.add(SpecificPopulationEnum.RACE_AA); mockWorkspace.setSpecificPopulationsEnum(specificPopulationEnumsSet); when(mockWorkspaceDao.findDbWorkspaceByWorkspaceId(1)).thenReturn(mockWorkspace); List<Long> workspaceID = new ArrayList<>(); workspaceID.add(1l); RdrWorkspace rdrWorkspace = toDefaultRdrWorkspace(mockWorkspace); when(rdrMapper.toRdrModel(mockWorkspace)).thenReturn(rdrWorkspace); rdrExportService.exportWorkspaces(workspaceID); verify(mockWorkspaceService) .getFirecloudUserRoles( mockWorkspace.getWorkspaceNamespace(), mockWorkspace.getFirecloudName()); verify(rdrExportDao, times(1)).save(anyList()); rdrWorkspace .getWorkspaceDemographic() .setRaceEthnicity(Arrays.asList(RdrWorkspaceDemographic.RaceEthnicityEnum.AA)); rdrWorkspace.setFocusOnUnderrepresentedPopulations(true); verify(mockRdrApi).exportWorkspaces(Arrays.asList(rdrWorkspace)); } | @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 (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); @Override List<Long> findAllUserIdsToExport(); @Override List<Long> findAllWorkspacesIdsToExport(); @Override void exportUsers(List<Long> userIds); @Override void exportWorkspaces(List<Long> workspaceIds); @Override @VisibleForTesting void updateDbRdrExport(RdrEntity entity, List<Long> idList); } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); @Override List<Long> findAllUserIdsToExport(); @Override List<Long> findAllWorkspacesIdsToExport(); @Override void exportUsers(List<Long> userIds); @Override void exportWorkspaces(List<Long> workspaceIds); @Override @VisibleForTesting void updateDbRdrExport(RdrEntity entity, List<Long> idList); } |
@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); DbCriteria drugNode2 = DbCriteria.builder() .addParentId(drugNode1.getId()) .addDomainId(DomainType.DRUG.toString()) .addType(CriteriaType.RXNORM.toString()) .addConceptId("19069022") .addGroup(false) .addSelectable(true) .build(); saveCriteriaWithPath(drugNode1.getPath(), drugNode2); jdbcTemplate.execute( "create table cb_criteria_ancestor(ancestor_id integer, descendant_id integer)"); jdbcTemplate.execute( "insert into cb_criteria_ancestor(ancestor_id, descendant_id) values (19069022, 19069022)"); jdbcTemplate.execute( "insert into cb_criteria_ancestor(ancestor_id, descendant_id) values (19069022, 1666666)"); List<Long> childConceptIds = ImmutableList.of(1666666L); SearchParameter searchParameter = new SearchParameter() .domain(DomainType.DRUG.toString()) .type(CriteriaType.RXNORM.toString()) .group(true) .ancestorData(true) .conceptId(19069022L); SearchRequest searchRequest = new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(searchParameter))); assertEquals( ImmutableMap.of(searchParameter, new HashSet<>(childConceptIds)), lookupUtil.buildCriteriaLookupMap(searchRequest)); jdbcTemplate.execute("drop table cb_criteria_ancestor"); } | 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.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req); } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req); } |
@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("[CONDITION_rank1]") .build(); saveCriteriaWithPath("0", icd9Parent); DbCriteria icd9Child1 = DbCriteria.builder() .addParentId(icd9Parent.getId()) .addDomainId(DomainType.CONDITION.toString()) .addType(CriteriaType.ICD9CM.toString()) .addGroup(false) .addSelectable(true) .addStandard(false) .addConceptId("44829697") .addSynonyms("[CONDITION_rank1]") .build(); saveCriteriaWithPath(icd9Parent.getPath(), icd9Child1); DbCriteria icd9Child2 = DbCriteria.builder() .addParentId(icd9Parent.getId()) .addDomainId(DomainType.CONDITION.toString()) .addType(CriteriaType.ICD9CM.toString()) .addGroup(false) .addSelectable(true) .addStandard(false) .addConceptId("44835564") .addSynonyms("[CONDITION_rank1]") .build(); saveCriteriaWithPath(icd9Parent.getPath(), icd9Child2); List<Long> childConceptIds = ImmutableList.of(44829697L, 44835564L); SearchParameter searchParameter = new SearchParameter() .domain(DomainType.CONDITION.toString()) .type(CriteriaType.ICD9CM.toString()) .group(true) .standard(false) .ancestorData(false) .conceptId(44829696L); SearchRequest searchRequest = new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(searchParameter))); assertEquals( ImmutableMap.of(searchParameter, new HashSet<>(childConceptIds)), lookupUtil.buildCriteriaLookupMap(searchRequest)); } | 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.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req); } | 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 (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { from(isEmpty()) .test(sgi.getSearchParameters()) .throwException("Bad Request: search parameters are empty."); for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { childrenByAncestor.putIfAbsent(treeKey, Maps.newHashMap()); childrenByAncestor.get(treeKey).putIfAbsent(param.getConceptId(), Sets.newHashSet()); } else { childrenByParentConcept.putIfAbsent(treeKey, Maps.newHashMap()); childrenByParentConcept .get(treeKey) .putIfAbsent(param.getConceptId(), Sets.newHashSet()); } } } } for (CriteriaLookupUtil.FullTreeType treeType : childrenByAncestor.keySet()) { Map<Long, Set<Long>> byParent = childrenByAncestor.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); cbCriteriaDao .findCriteriaAncestors( treeType.domain.toString(), treeType.type.toString(), CriteriaType.ATC.equals(treeType.type), parentConceptIds) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); putLeavesOnParent(byParent, parents, leaves); } for (CriteriaLookupUtil.FullTreeType treeType : childrenByParentConcept.keySet()) { Map<Long, Set<Long>> byParent = childrenByParentConcept.get(treeType); Set<String> parentConceptIds = byParent.keySet().stream().map(c -> c.toString()).collect(Collectors.toSet()); List<DbCriteriaLookup> parents = Lists.newArrayList(); List<DbCriteriaLookup> leaves = Lists.newArrayList(); if (treeType.type.equals(CriteriaType.ICD9CM)) { List<Long> ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> c.getId()) .collect(Collectors.toList()); cbCriteriaDao .findCriteriaLeavesAndParentsByDomainAndTypeAndParentIds( treeType.domain.toString(), treeType.type.toString(), ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } else { String ids = cbCriteriaDao .findCriteriaParentsByDomainAndTypeAndParentConceptIds( treeType.domain.toString(), treeType.type.toString(), treeType.isStandard, parentConceptIds) .stream() .map(c -> String.valueOf(c.getId())) .collect(Collectors.joining(",")); List<Long> longIds = new ArrayList<>(); if (!ids.isEmpty()) { longIds = Stream.of(ids.split(",")).map(Long::parseLong).collect(Collectors.toList()); } cbCriteriaDao .findCriteriaLeavesAndParentsByPath(longIds, ids) .forEach( c -> { if (parentConceptIds.contains(String.valueOf(c.getConceptId()))) { parents.add(c); } else { leaves.add(c); } }); } putLeavesOnParent(byParent, parents, leaves); } Map<SearchParameter, Set<Long>> builder = new HashMap<>(); for (SearchGroup sg : Iterables.concat(req.getIncludes(), req.getExcludes())) { for (SearchGroupItem sgi : sg.getItems()) { for (SearchParameter param : sgi.getSearchParameters()) { if (!param.getGroup() && !param.getAncestorData()) { continue; } CriteriaLookupUtil.FullTreeType treeKey = CriteriaLookupUtil.FullTreeType.fromParam(param); if (param.getAncestorData()) { builder.put(param, childrenByAncestor.get(treeKey).get(param.getConceptId())); } else { builder.put(param, childrenByParentConcept.get(treeKey).get(param.getConceptId())); } } } } return builder; } CriteriaLookupUtil(CBCriteriaDao cbCriteriaDao); Map<SearchParameter, Set<Long>> buildCriteriaLookupMap(SearchRequest req); } |
@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); assertThat(payload.get("scope")).isEqualTo(String.join(" ", SCOPES)); } | @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(GoogleOAuthConstants.TOKEN_SERVER_URL); payload.setIssuer(this.serviceAccountEmail); payload.setSubject(this.userEmail); payload.set("scope", String.join(" ", this.scopes)); return payload; } | 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_TOKEN_DURATION.getSeconds()); payload.setAudience(GoogleOAuthConstants.TOKEN_SERVER_URL); payload.setIssuer(this.serviceAccountEmail); payload.setSubject(this.userEmail); payload.set("scope", String.join(" ", this.scopes)); return payload; } } | 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_TOKEN_DURATION.getSeconds()); payload.setAudience(GoogleOAuthConstants.TOKEN_SERVER_URL); payload.setIssuer(this.serviceAccountEmail); payload.setSubject(this.userEmail); payload.set("scope", String.join(" ", this.scopes)); return payload; } DelegatedUserCredentials(
String serviceAccountEmail,
String userEmail,
List<String> scopes,
IamCredentialsClient credentialsClient,
HttpTransport httpTransport); } | 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_TOKEN_DURATION.getSeconds()); payload.setAudience(GoogleOAuthConstants.TOKEN_SERVER_URL); payload.setIssuer(this.serviceAccountEmail); payload.setSubject(this.userEmail); payload.set("scope", String.join(" ", this.scopes)); return payload; } DelegatedUserCredentials(
String serviceAccountEmail,
String userEmail,
List<String> scopes,
IamCredentialsClient credentialsClient,
HttpTransport httpTransport); @VisibleForTesting void setClock(Clock clock); @VisibleForTesting JsonWebToken.Payload createJwtPayload(); @Override AccessToken refreshAccessToken(); } | 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_TOKEN_DURATION.getSeconds()); payload.setAudience(GoogleOAuthConstants.TOKEN_SERVER_URL); payload.setIssuer(this.serviceAccountEmail); payload.setSubject(this.userEmail); payload.set("scope", String.join(" ", this.scopes)); return payload; } DelegatedUserCredentials(
String serviceAccountEmail,
String userEmail,
List<String> scopes,
IamCredentialsClient credentialsClient,
HttpTransport httpTransport); @VisibleForTesting void setClock(Clock clock); @VisibleForTesting JsonWebToken.Payload createJwtPayload(); @Override AccessToken refreshAccessToken(); static final Duration ACCESS_TOKEN_DURATION; } |
@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); assertThat(cdrQuery.getColumns()).isEqualTo(ImmutableList.of("person_id")); assertThat(cdrQuery.getSql()) .isEqualTo( "select person.person_id person_id\n" + "from `project_id.data_set_id.person` person\n" + "where\n" + "person.person_id in (select person_id\n" + "from `project_id.data_set_id.person` p\n" + "where\n" + "gender_concept_id in unnest(@p0)\n" + ")\n" + "and person.person_id not in unnest(@person_id_blacklist)\n\n" + "order by person.person_id\n"); Map<String, Map<String, Object>> params = getParameters(cdrQuery); Map<String, Object> genderParam = params.get("p0"); Map<String, Object> personIdBlacklistParam = params.get("person_id_blacklist"); assertParameterArray(genderParam, 8507, 8532, 2); assertParameterArray(personIdBlacklistParam, 2L); } | @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } } | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); } | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } |
@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, null); assertThat(cdrQuery.getBigqueryDataset()).isEqualTo(DATA_SET_ID); assertThat(cdrQuery.getBigqueryProject()).isEqualTo(PROJECT_ID); assertThat(cdrQuery.getColumns()) .isEqualTo(ImmutableList.of("person_id", "measurement_concept.concept_name")); assertThat(cdrQuery.getSql()) .isEqualTo( "select inner_results.person_id, " + "measurement_concept.concept_name measurement_concept__concept_name\n" + "from (select measurement.person_id person_id, " + "measurement.measurement_concept_id measurement_measurement_concept_id, " + "measurement.person_id measurement_person_id, " + "measurement.measurement_id measurement_measurement_id\n" + "from `project_id.data_set_id.measurement` measurement\n" + "where\n" + "measurement.person_id in (select person_id\n" + "from `project_id.data_set_id.person` p\n" + "where\n" + "gender_concept_id in unnest(@p0)\n" + ")\n" + "and measurement.person_id not in unnest(@person_id_blacklist)\n" + "\n" + "order by measurement.person_id, measurement.measurement_id\n" + ") inner_results\n" + "LEFT OUTER JOIN `project_id.data_set_id.concept` measurement_concept ON " + "inner_results.measurement_measurement_concept_id = measurement_concept.concept_id\n" + "order by measurement_person_id, measurement_measurement_id"); Map<String, Map<String, Object>> params = getParameters(cdrQuery); Map<String, Object> genderParam = params.get("p0"); Map<String, Object> personIdBlacklistParam = params.get("person_id_blacklist"); assertParameterArray(genderParam, 8507, 8532, 2); assertParameterArray(personIdBlacklistParam, 2L); } | @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } } | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); } | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } | CohortMaterializationService { @VisibleForTesting CdrQuery getCdrQuery( SearchRequest searchRequest, DataTableSpecification dataTableSpecification, @Nullable DbCohortReview cohortReview, @Nullable Set<Long> conceptIds) { DbCdrVersion cdrVersion = CdrVersionContext.getCdrVersion(); CdrQuery cdrQuery = new CdrQuery() .bigqueryDataset(cdrVersion.getBigqueryDataset()) .bigqueryProject(cdrVersion.getBigqueryProject()); List<CohortStatus> statusFilter = dataTableSpecification.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } ParticipantCriteria criteria = getParticipantCriteria(statusFilter, cohortReview, searchRequest); TableQueryAndConfig tableQueryAndConfig = getTableQueryAndConfig(dataTableSpecification.getTableQuery(), conceptIds); cdrQuery.setColumns(tableQueryAndConfig.getTableQuery().getColumns()); if (criteria.getParticipantIdsToInclude() != null && criteria.getParticipantIdsToInclude().isEmpty()) { return cdrQuery; } QueryJobConfiguration jobConfiguration = fieldSetQueryBuilder.getQueryJobConfiguration( criteria, tableQueryAndConfig, dataTableSpecification.getMaxResults()); cdrQuery.setSql(jobConfiguration.getQuery()); ImmutableMap.Builder<String, Object> configurationMap = ImmutableMap.builder(); ImmutableMap.Builder<String, Object> queryConfigurationMap = ImmutableMap.builder(); queryConfigurationMap.put( "queryParameters", jobConfiguration.getNamedParameters().entrySet().stream() .map(TO_QUERY_PARAMETER_MAP) .<Map<String, Object>>toArray()); configurationMap.put("query", queryConfigurationMap.build()); cdrQuery.setConfiguration(configurationMap.build()); return cdrQuery; } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } |
@Test public void testMaterializeAnnotationQueryNoPagination() { FieldSet fieldSet = new FieldSet().annotationQuery(new AnnotationQuery()); MaterializeCohortResponse response = cohortMaterializationService.materializeCohort( cohortReview, SearchRequests.allGenders(), null, 0, makeRequest(fieldSet, 1000)); ImmutableMap<String, Object> p1Map = ImmutableMap.of("person_id", 1L, "review_status", "INCLUDED"); assertResults(response, p1Map); assertThat(response.getNextPageToken()).isNull(); } | 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) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } | 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); } catch (JsonSyntaxException e) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } } | 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); } catch (JsonSyntaxException e) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); } | 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); } catch (JsonSyntaxException e) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } | 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); } catch (JsonSyntaxException e) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } |
@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 = cohortMaterializationService.materializeCohort( cohortReview, SearchRequests.allGenders(), null, 0, request); ImmutableMap<String, Object> p1Map = ImmutableMap.of("person_id", 1L, "review_status", "INCLUDED"); assertResults(response, p1Map); assertThat(response.getNextPageToken()).isNotNull(); request.setPageToken(response.getNextPageToken()); MaterializeCohortResponse response2 = cohortMaterializationService.materializeCohort( cohortReview, SearchRequests.allGenders(), null, 0, request); ImmutableMap<String, Object> p2Map = ImmutableMap.of("person_id", 2L, "review_status", "EXCLUDED"); assertResults(response2, p2Map); assertThat(response2.getNextPageToken()).isNull(); } | 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) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } | 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); } catch (JsonSyntaxException e) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } } | 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); } catch (JsonSyntaxException e) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); } | 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); } catch (JsonSyntaxException e) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } | 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); } catch (JsonSyntaxException e) { throw new BadRequestException("Invalid cohort spec"); } return materializeCohort( cohortReview, searchRequest, conceptIds, Objects.hash(cohortSpec, conceptIds), request); } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } |
@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"); assertResults(response.getResults(), p1Map); } | public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = annotationQueryBuilder.materializeAnnotationQuery( cohortReview, statusFilter, request.getAnnotationQuery(), null, 0L); return new CohortAnnotationsResponse() .results(ImmutableList.copyOf(results.getResults())) .columns(results.getColumns()); } | CohortMaterializationService { public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = annotationQueryBuilder.materializeAnnotationQuery( cohortReview, statusFilter, request.getAnnotationQuery(), null, 0L); return new CohortAnnotationsResponse() .results(ImmutableList.copyOf(results.getResults())) .columns(results.getColumns()); } } | CohortMaterializationService { public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = annotationQueryBuilder.materializeAnnotationQuery( cohortReview, statusFilter, request.getAnnotationQuery(), null, 0L); return new CohortAnnotationsResponse() .results(ImmutableList.copyOf(results.getResults())) .columns(results.getColumns()); } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); } | CohortMaterializationService { public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = annotationQueryBuilder.materializeAnnotationQuery( cohortReview, statusFilter, request.getAnnotationQuery(), null, 0L); return new CohortAnnotationsResponse() .results(ImmutableList.copyOf(results.getResults())) .columns(results.getColumns()); } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } | CohortMaterializationService { public CohortAnnotationsResponse getAnnotations( DbCohortReview cohortReview, CohortAnnotationsRequest request) { List<CohortStatus> statusFilter = request.getStatusFilter(); if (statusFilter == null) { statusFilter = NOT_EXCLUDED; } AnnotationQueryBuilder.AnnotationResults results = annotationQueryBuilder.materializeAnnotationQuery( cohortReview, statusFilter, request.getAnnotationQuery(), null, 0L); return new CohortAnnotationsResponse() .results(ImmutableList.copyOf(results.getResults())) .columns(results.getColumns()); } @Autowired CohortMaterializationService(
FieldSetQueryBuilder fieldSetQueryBuilder,
AnnotationQueryBuilder annotationQueryBuilder,
ParticipantCohortStatusDao participantCohortStatusDao,
CdrBigQuerySchemaConfigService cdrBigQuerySchemaConfigService,
ConceptService conceptService,
Provider<WorkbenchConfig> configProvider); CdrQuery getCdrQuery(
String cohortSpec,
DataTableSpecification dataTableSpecification,
@Nullable DbCohortReview cohortReview,
@Nullable Set<Long> conceptIds); MaterializeCohortResponse materializeCohort(
@Nullable DbCohortReview cohortReview,
String cohortSpec,
@Nullable Set<Long> conceptIds,
MaterializeCohortRequest request); CohortAnnotationsResponse getAnnotations(
DbCohortReview cohortReview, CohortAnnotationsRequest request); } |
@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(1)).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(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); @Override void sendBetaAccessRequestEmail(final String userName); @Override void sendWelcomeEmail(final String contactEmail, final String password, final User user); @Override void sendInstitutionUserInstructions(String contactEmail, String userInstructions); @Override void alertUserFreeTierDollarThreshold(
final DbUser user, double threshold, double currentUsage, double remainingBalance); @Override void alertUserFreeTierExpiration(final DbUser user); @Override void sendBetaAccessCompleteEmail(final String contactEmail, final String username); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); @Override void sendBetaAccessRequestEmail(final String userName); @Override void sendWelcomeEmail(final String contactEmail, final String password, final User user); @Override void sendInstitutionUserInstructions(String contactEmail, String userInstructions); @Override void alertUserFreeTierDollarThreshold(
final DbUser user, double threshold, double currentUsage, double remainingBalance); @Override void alertUserFreeTierExpiration(final DbUser user); @Override void sendBetaAccessCompleteEmail(final String contactEmail, final String username); } |
@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(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); @Override void sendBetaAccessRequestEmail(final String userName); @Override void sendWelcomeEmail(final String contactEmail, final String password, final User user); @Override void sendInstitutionUserInstructions(String contactEmail, String userInstructions); @Override void alertUserFreeTierDollarThreshold(
final DbUser user, double threshold, double currentUsage, double remainingBalance); @Override void alertUserFreeTierExpiration(final DbUser user); @Override void sendBetaAccessCompleteEmail(final String contactEmail, final String username); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); @Override void sendBetaAccessRequestEmail(final String userName); @Override void sendWelcomeEmail(final String contactEmail, final String password, final User user); @Override void sendInstitutionUserInstructions(String contactEmail, String userInstructions); @Override void alertUserFreeTierDollarThreshold(
final DbUser user, double threshold, double currentUsage, double remainingBalance); @Override void alertUserFreeTierExpiration(final DbUser user); @Override void sendBetaAccessCompleteEmail(final String contactEmail, final String username); } |
@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(workspaceIdList); verify(mockRdrApi).exportWorkspaces(Arrays.asList(rdrWorkspace)); workspaceIdList = new ArrayList<>(); workspaceIdList.add(3l); rdrWorkspace = toDefaultRdrWorkspace(mockCreatorWorkspace); when(rdrMapper.toRdrModel(mockCreatorWorkspace)).thenReturn(rdrWorkspace); rdrExportService.exportWorkspaces(workspaceIdList); rdrWorkspace.setCreator( new RdrWorkspaceCreator().userId(2l).familyName("email").givenName("icannothas")); verify(mockRdrApi).exportWorkspaces(Arrays.asList(rdrWorkspace)); } | @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 (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); @Override List<Long> findAllUserIdsToExport(); @Override List<Long> findAllWorkspacesIdsToExport(); @Override void exportUsers(List<Long> userIds); @Override void exportWorkspaces(List<Long> workspaceIds); @Override @VisibleForTesting void updateDbRdrExport(RdrEntity entity, List<Long> idList); } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); @Override List<Long> findAllUserIdsToExport(); @Override List<Long> findAllWorkspacesIdsToExport(); @Override void exportUsers(List<Long> userIds); @Override void exportWorkspaces(List<Long> workspaceIds); @Override @VisibleForTesting void updateDbRdrExport(RdrEntity entity, List<Long> idList); } |
@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(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); @Override void sendBetaAccessRequestEmail(final String userName); @Override void sendWelcomeEmail(final String contactEmail, final String password, final User user); @Override void sendInstitutionUserInstructions(String contactEmail, String userInstructions); @Override void alertUserFreeTierDollarThreshold(
final DbUser user, double threshold, double currentUsage, double remainingBalance); @Override void alertUserFreeTierExpiration(final DbUser user); @Override void sendBetaAccessCompleteEmail(final String contactEmail, final String username); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); @Override void sendBetaAccessRequestEmail(final String userName); @Override void sendWelcomeEmail(final String contactEmail, final String password, final User user); @Override void sendInstitutionUserInstructions(String contactEmail, String userInstructions); @Override void alertUserFreeTierDollarThreshold(
final DbUser user, double threshold, double currentUsage, double remainingBalance); @Override void alertUserFreeTierExpiration(final DbUser user); @Override void sendBetaAccessCompleteEmail(final String contactEmail, final String username); } |
@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(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); @Override void sendBetaAccessRequestEmail(final String userName); @Override void sendWelcomeEmail(final String contactEmail, final String password, final User user); @Override void sendInstitutionUserInstructions(String contactEmail, String userInstructions); @Override void alertUserFreeTierDollarThreshold(
final DbUser user, double threshold, double currentUsage, double remainingBalance); @Override void alertUserFreeTierExpiration(final DbUser user); @Override void sendBetaAccessCompleteEmail(final String contactEmail, final String username); } | 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_RESOURCE, welcomeMessageSubstitutionMap(password, user))) .subject("Your new All of Us Researcher Workbench Account") .fromEmail(workbenchConfigProvider.get().mandrill.fromEmail); sendWithRetries(msg, String.format("Welcome for %s", user.getName())); } @Autowired MailServiceImpl(
Provider<MandrillApi> mandrillApiProvider,
Provider<CloudStorageService> cloudStorageServiceProvider,
Provider<WorkbenchConfig> workbenchConfigProvider); @Override void sendBetaAccessRequestEmail(final String userName); @Override void sendWelcomeEmail(final String contactEmail, final String password, final User user); @Override void sendInstitutionUserInstructions(String contactEmail, String userInstructions); @Override void alertUserFreeTierDollarThreshold(
final DbUser user, double threshold, double currentUsage, double remainingBalance); @Override void alertUserFreeTierExpiration(final DbUser user); @Override void sendBetaAccessCompleteEmail(final String contactEmail, final String username); } |
@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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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_PERSON_ID, "review_status", "EXCLUDED")); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@Test public void testQueryAllStatusesReviewStatusOrder() { saveReviewStatuses(); AnnotationQuery annotationQuery = new AnnotationQuery(); annotationQuery.setOrderBy(ImmutableList.of("review_status")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, annotationQuery, 10, 0), allColumns, ImmutableMap.of("person_id", EXCLUDED_PERSON_ID, "review_status", "EXCLUDED"), 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@Test public void testQueryAllStatusesReviewPersonIdOrderDescending() { saveReviewStatuses(); AnnotationQuery annotationQuery = new AnnotationQuery(); annotationQuery.setOrderBy(ImmutableList.of("DESCENDING(person_id)")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, annotationQuery, 10, 0), allColumns, ImmutableMap.of("person_id", EXCLUDED_PERSON_ID, "review_status", "EXCLUDED"), 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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", "INCLUDED") .put("integer annotation", 123) .put("string annotation", "foo") .put("boolean annotation", true) .put("date annotation", "2017-02-14") .put("enum annotation", "zebra") .build(); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, INCLUDED_ONLY, new AnnotationQuery(), 10, 0), allColumns, expectedResult); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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("integer annotation", 123) .put("string annotation", "foo") .put("boolean annotation", true) .put("date annotation", "2017-02-14") .put("enum annotation", "zebra") .build(); AnnotationQuery annotationQuery = new AnnotationQuery(); annotationQuery.setColumns( ImmutableList.of( "person_id", "integer annotation", "string annotation", "boolean annotation", "date annotation", "enum annotation")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, INCLUDED_ONLY, annotationQuery, 10, 0), annotationQuery.getColumns(), expectedResult); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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( cohortReview, ALL_STATUSES, new AnnotationQuery(), 10, 0), allColumns, expectedResult1, expectedResult2); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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.exportWorkspaces(workspaceID); verify(mockWorkspaceService, never()) .getFirecloudUserRoles( mockDeletedWorkspace.getWorkspaceNamespace(), mockDeletedWorkspace.getFirecloudName()); verify(rdrExportDao, times(1)).save(anyList()); rdrWorkspace.setStatus(RdrWorkspace.StatusEnum.INACTIVE); verify(mockRdrApi).exportWorkspaces(Arrays.asList(rdrWorkspace)); } | @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 (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); @Override List<Long> findAllUserIdsToExport(); @Override List<Long> findAllWorkspacesIdsToExport(); @Override void exportUsers(List<Long> userIds); @Override void exportWorkspaces(List<Long> workspaceIds); @Override @VisibleForTesting void updateDbRdrExport(RdrEntity entity, List<Long> idList); } | 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) .collect(Collectors.toList()); if (!rdrWorkspacesList.isEmpty()) { rdrApiProvider.get().getApiClient().setDebugging(true); rdrApiProvider.get().exportWorkspaces(rdrWorkspacesList); updateDbRdrExport(RdrEntity.WORKSPACE, workspaceIds); } } catch (ApiException ex) { log.severe("Error while sending workspace data to RDR"); } } @Autowired RdrExportServiceImpl(
Clock clock,
Provider<RdrApi> rdrApiProvider,
RdrExportDao rdrExportDao,
RdrMapper rdrMapper,
WorkspaceDao workspaceDao,
InstitutionService institutionService,
WorkspaceService workspaceService,
UserDao userDao,
VerifiedInstitutionalAffiliationDao verifiedInstitutionalAffiliationDao); @Override List<Long> findAllUserIdsToExport(); @Override List<Long> findAllWorkspacesIdsToExport(); @Override void exportUsers(List<Long> userIds); @Override void exportWorkspaces(List<Long> workspaceIds); @Override @VisibleForTesting void updateDbRdrExport(RdrEntity entity, List<Long> idList); } |
@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( cohortReview, ALL_STATUSES, new AnnotationQuery(), 1, 0), allColumns, expectedResult1); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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.materializeAnnotationQuery( cohortReview, ALL_STATUSES, new AnnotationQuery(), 1, 1), allColumns, expectedResult2); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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 AnnotationQuery(); annotationQuery.setOrderBy(ImmutableList.of("DESCENDING(integer annotation)", "person_id")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, annotationQuery, 10, 0), allColumns, expectedResult2, expectedResult1); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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(); annotationQuery.setOrderBy(ImmutableList.of("boolean annotation", "person_id")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, annotationQuery, 10, 0), allColumns, expectedResult2, expectedResult1); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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 AnnotationQuery(); annotationQuery.setOrderBy(ImmutableList.of("DESCENDING(date annotation)", "person_id")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, annotationQuery, 10, 0), allColumns, expectedResult2, expectedResult1); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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(); annotationQuery.setOrderBy(ImmutableList.of("string annotation", "person_id")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, annotationQuery, 10, 0), allColumns, expectedResult2, expectedResult1); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@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(); annotationQuery.setOrderBy(ImmutableList.of("enum annotation", "person_id")); assertResults( annotationQueryBuilder.materializeAnnotationQuery( cohortReview, ALL_STATUSES, annotationQuery, 10, 0), allColumns, expectedResult2, expectedResult1); } | 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, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); } | 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"); } Map<String, DbCohortAnnotationDefinition> annotationDefinitions = null; List<String> columns = annotationQuery.getColumns(); if (columns == null || columns.isEmpty()) { columns = new ArrayList<>(); columns.add(PERSON_ID_COLUMN); columns.add(REVIEW_STATUS_COLUMN); annotationDefinitions = getAnnotationDefinitions(cohortReview); columns.addAll( annotationDefinitions.values().stream() .map(DbCohortAnnotationDefinition::getColumnName) .collect(Collectors.toList())); annotationQuery.setColumns(columns); } List<String> orderBy = annotationQuery.getOrderBy(); if (orderBy == null || orderBy.isEmpty()) { annotationQuery.setOrderBy(ImmutableList.of(PERSON_ID_COLUMN)); } ImmutableMap.Builder<String, Object> parameters = ImmutableMap.builder(); String sql = getSql( cohortReview, statusFilter, annotationQuery, limit, offset, annotationDefinitions, parameters); Iterable<Map<String, Object>> results = namedParameterJdbcTemplate.query( sql, parameters.build(), new RowMapper<Map<String, Object>>() { @Override public Map<String, Object> mapRow(ResultSet rs, int rowNum) throws SQLException { ImmutableMap.Builder<String, Object> result = ImmutableMap.builder(); List<String> columns = annotationQuery.getColumns(); for (int i = 0; i < columns.size(); i++) { Object obj = rs.getObject(i + 1); if (obj != null) { String column = columns.get(i); if (column.equals(REVIEW_STATUS_COLUMN)) { result.put( column, DbStorageEnums.cohortStatusFromStorage(((Number) obj).shortValue()) .name()); } else if (obj instanceof java.sql.Date) { result.put(column, DATE_FORMAT.format((java.sql.Date) obj)); } else { result.put(column, obj); } } } return result.build(); } }); return new AnnotationResults(results, annotationQuery.getColumns()); } @Autowired AnnotationQueryBuilder(
NamedParameterJdbcTemplate namedParameterJdbcTemplate,
CohortAnnotationDefinitionDao cohortAnnotationDefinitionDao); AnnotationResults materializeAnnotationQuery(
DbCohortReview cohortReview,
List<CohortStatus> statusFilter,
AnnotationQuery annotationQuery,
Integer limit,
long offset); static final String PERSON_ID_COLUMN; static final String REVIEW_STATUS_COLUMN; static final ImmutableSet<String> RESERVED_COLUMNS; static final String DESCENDING_PREFIX; } |
@Test public void testRandomizeVariant() { VariantContext randomizedVariant = randomizeVcf.randomizeVariant(variantContext); assertThat(randomizedVariant.getGenotypes().size()).isEqualTo(2); assertThat(randomizedVariant.getGenotypes().getSampleNames()) .isEqualTo(new HashSet<>(sampleNames)); randomizedVariant.getGenotypes().stream() .flatMap(genotype -> genotype.getAlleles().stream()) .forEach( allele -> assertThat( variantContext.getAlleles().stream() .anyMatch(vcAllele -> vcAllele.basesMatch(allele))) .isTrue()); } | @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream() .map(name -> randomizeGenotype(variant, variant.getGenotype(0), name)) .collect(Collectors.toList()); GenotypesContext randomizedGenotypesContext = GenotypesContext.create(new ArrayList<>(randomizedGenotypes)); variantContextBuilder.genotypes(randomizedGenotypesContext); return variantContextBuilder.make(); } | RandomizeVcf extends VariantWalker { @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream() .map(name -> randomizeGenotype(variant, variant.getGenotype(0), name)) .collect(Collectors.toList()); GenotypesContext randomizedGenotypesContext = GenotypesContext.create(new ArrayList<>(randomizedGenotypes)); variantContextBuilder.genotypes(randomizedGenotypesContext); return variantContextBuilder.make(); } } | RandomizeVcf extends VariantWalker { @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream() .map(name -> randomizeGenotype(variant, variant.getGenotype(0), name)) .collect(Collectors.toList()); GenotypesContext randomizedGenotypesContext = GenotypesContext.create(new ArrayList<>(randomizedGenotypes)); variantContextBuilder.genotypes(randomizedGenotypesContext); return variantContextBuilder.make(); } RandomizeVcf(); @VisibleForTesting protected RandomizeVcf(List<String> sampleNames, Random random); } | RandomizeVcf extends VariantWalker { @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream() .map(name -> randomizeGenotype(variant, variant.getGenotype(0), name)) .collect(Collectors.toList()); GenotypesContext randomizedGenotypesContext = GenotypesContext.create(new ArrayList<>(randomizedGenotypes)); variantContextBuilder.genotypes(randomizedGenotypesContext); return variantContextBuilder.make(); } RandomizeVcf(); @VisibleForTesting protected RandomizeVcf(List<String> sampleNames, Random random); static void main(String[] argv); @Override void apply(
VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext); @Override void onTraversalStart(); @Override void closeTool(); } | RandomizeVcf extends VariantWalker { @VisibleForTesting protected VariantContext randomizeVariant(VariantContext variant) { VariantContextBuilder variantContextBuilder = new VariantContextBuilder(variant); variantContextBuilder.alleles(variant.getAlleles()); List<Genotype> randomizedGenotypes = this.sampleNames.stream() .map(name -> randomizeGenotype(variant, variant.getGenotype(0), name)) .collect(Collectors.toList()); GenotypesContext randomizedGenotypesContext = GenotypesContext.create(new ArrayList<>(randomizedGenotypes)); variantContextBuilder.genotypes(randomizedGenotypesContext); return variantContextBuilder.make(); } RandomizeVcf(); @VisibleForTesting protected RandomizeVcf(List<String> sampleNames, Random random); static void main(String[] argv); @Override void apply(
VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext); @Override void onTraversalStart(); @Override void closeTool(); } |
@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.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(1)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(0)); } else { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(1)); } } else { if (genotypeTypeIndex < .0145) { alleles.add(Allele.NO_CALL); alleles.add(Allele.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8095) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getReference()); } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getAlternateAllele(0)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getReference()); } else { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(0)); } } return alleles; } | 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(Allele.NO_CALL); alleles.add(Allele.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(1)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(0)); } else { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(1)); } } else { if (genotypeTypeIndex < .0145) { alleles.add(Allele.NO_CALL); alleles.add(Allele.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8095) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getReference()); } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getAlternateAllele(0)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getReference()); } else { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(0)); } } return alleles; } } | 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(Allele.NO_CALL); alleles.add(Allele.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(1)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(0)); } else { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(1)); } } else { if (genotypeTypeIndex < .0145) { alleles.add(Allele.NO_CALL); alleles.add(Allele.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8095) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getReference()); } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getAlternateAllele(0)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getReference()); } else { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(0)); } } return alleles; } RandomizeVcf(); @VisibleForTesting protected RandomizeVcf(List<String> sampleNames, Random random); } | 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(Allele.NO_CALL); alleles.add(Allele.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(1)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(0)); } else { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(1)); } } else { if (genotypeTypeIndex < .0145) { alleles.add(Allele.NO_CALL); alleles.add(Allele.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8095) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getReference()); } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getAlternateAllele(0)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getReference()); } else { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(0)); } } return alleles; } RandomizeVcf(); @VisibleForTesting protected RandomizeVcf(List<String> sampleNames, Random random); static void main(String[] argv); @Override void apply(
VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext); @Override void onTraversalStart(); @Override void closeTool(); } | 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(Allele.NO_CALL); alleles.add(Allele.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(1)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(0)); } else { alleles.add(variantContext.getAlternateAllele(1)); alleles.add(variantContext.getAlternateAllele(1)); } } else { if (genotypeTypeIndex < .0145) { alleles.add(Allele.NO_CALL); alleles.add(Allele.NO_CALL); return alleles; } else if (genotypeTypeIndex < .8095) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getReference()); } else if (genotypeTypeIndex < .8654) { alleles.add(variantContext.getReference()); alleles.add(variantContext.getAlternateAllele(0)); } else if (genotypeTypeIndex < .9268) { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getReference()); } else { alleles.add(variantContext.getAlternateAllele(0)); alleles.add(variantContext.getAlternateAllele(0)); } } return alleles; } RandomizeVcf(); @VisibleForTesting protected RandomizeVcf(List<String> sampleNames, Random random); static void main(String[] argv); @Override void apply(
VariantContext variant,
ReadsContext readsContext,
ReferenceContext referenceContext,
FeatureContext featureContext); @Override void onTraversalStart(); @Override void closeTool(); } |
@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(
Provider<ShibbolethApi> shibbolethApiProvider,
ShibbolethRetryHandler shibbolethRetryHandler); } | ShibbolethServiceImpl implements ShibbolethService { @Override public void updateShibbolethToken(String jwt) { ShibbolethApi shibbolethApi = shibbolethApiProvider.get(); shibbolethRetryHandler.run( (context) -> { shibbolethApi.postShibbolethToken(jwt); return null; }); } @Autowired ShibbolethServiceImpl(
Provider<ShibbolethApi> shibbolethApiProvider,
ShibbolethRetryHandler shibbolethRetryHandler); @Override void updateShibbolethToken(String jwt); } | ShibbolethServiceImpl implements ShibbolethService { @Override public void updateShibbolethToken(String jwt) { ShibbolethApi shibbolethApi = shibbolethApiProvider.get(); shibbolethRetryHandler.run( (context) -> { shibbolethApi.postShibbolethToken(jwt); return null; }); } @Autowired ShibbolethServiceImpl(
Provider<ShibbolethApi> shibbolethApiProvider,
ShibbolethRetryHandler shibbolethRetryHandler); @Override void updateShibbolethToken(String jwt); } |
@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 isGoogleServiceUnavailableException(IOException e); static boolean isGoogleConflictException(IOException e); static WorkbenchException convertGoogleIOException(IOException e); static boolean isSocketTimeoutException(Throwable e); static WorkbenchException convertFirecloudException(ApiException e); static WorkbenchException convertNotebookException(
org.pmiops.workbench.notebooks.ApiException e); static WorkbenchException convertLeonardoException(
org.pmiops.workbench.leonardo.ApiException e); static WorkbenchException convertShibbolethException(
org.pmiops.workbench.shibboleth.ApiException e); static boolean isServiceUnavailable(int code); } | 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 isGoogleServiceUnavailableException(IOException e); static boolean isGoogleConflictException(IOException e); static WorkbenchException convertGoogleIOException(IOException e); static boolean isSocketTimeoutException(Throwable e); static WorkbenchException convertFirecloudException(ApiException e); static WorkbenchException convertNotebookException(
org.pmiops.workbench.notebooks.ApiException e); static WorkbenchException convertLeonardoException(
org.pmiops.workbench.leonardo.ApiException e); static WorkbenchException convertShibbolethException(
org.pmiops.workbench.shibboleth.ApiException e); static boolean isServiceUnavailable(int code); } |
@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"); assertThat(actualBuilder.getSubAggregations().size()).isEqualTo(1); AggregationBuilder genderBuilder = actualBuilder.getSubAggregations().iterator().next(); assertThat(genderBuilder.getName()).isEqualTo(GENDER_OR_SEX + RANGE_18_44); assertThat(genderBuilder.getType()).isEqualTo("terms"); assertThat(genderBuilder.getSubAggregations().size()).isEqualTo(1); AggregationBuilder raceBuilder = genderBuilder.getSubAggregations().iterator().next(); assertThat(raceBuilder.getName()).isEqualTo(RACE + RANGE_18_44); assertThat(raceBuilder.getType()).isEqualTo("terms"); assertThat(raceBuilder.getSubAggregations().isEmpty()).isTrue(); } | 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.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } static AggregationBuilder buildDemoChartAggregation(
GenderOrSexType genderOrSexType, AgeType ageType, String ageRange); static List<DemoChartInfo> unwrapDemoChartBuckets(
SearchResponse searchResponse, String... ageRanges); } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } static AggregationBuilder buildDemoChartAggregation(
GenderOrSexType genderOrSexType, AgeType ageType, String ageRange); static List<DemoChartInfo> unwrapDemoChartBuckets(
SearchResponse searchResponse, String... ageRanges); static final String RANGE_18_44; static final String RANGE_45_64; static final String RANGE_GT_65; static final String DATE; static final String GENDER_OR_SEX; static final String RACE; } |
@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_range"); assertThat(actualBuilder.getSubAggregations().size()).isEqualTo(1); AggregationBuilder genderBuilder = actualBuilder.getSubAggregations().iterator().next(); assertThat(genderBuilder.getName()).isEqualTo(GENDER_OR_SEX + RANGE_18_44); assertThat(genderBuilder.getType()).isEqualTo("terms"); assertThat(genderBuilder.getSubAggregations().size()).isEqualTo(1); AggregationBuilder raceBuilder = genderBuilder.getSubAggregations().iterator().next(); assertThat(raceBuilder.getName()).isEqualTo(RACE + RANGE_18_44); assertThat(raceBuilder.getType()).isEqualTo("terms"); assertThat(raceBuilder.getSubAggregations().isEmpty()).isTrue(); } | 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.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } static AggregationBuilder buildDemoChartAggregation(
GenderOrSexType genderOrSexType, AgeType ageType, String ageRange); static List<DemoChartInfo> unwrapDemoChartBuckets(
SearchResponse searchResponse, String... ageRanges); } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } static AggregationBuilder buildDemoChartAggregation(
GenderOrSexType genderOrSexType, AgeType ageType, String ageRange); static List<DemoChartInfo> unwrapDemoChartBuckets(
SearchResponse searchResponse, String... ageRanges); static final String RANGE_18_44; static final String RANGE_45_64; static final String RANGE_GT_65; static final String DATE; static final String GENDER_OR_SEX; static final String RACE; } |
@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()).isEqualTo("range"); assertThat(actualBuilder.getSubAggregations().size()).isEqualTo(1); AggregationBuilder genderBuilder = actualBuilder.getSubAggregations().iterator().next(); assertThat(genderBuilder.getName()).isEqualTo(GENDER_OR_SEX + RANGE_18_44); assertThat(genderBuilder.getType()).isEqualTo("terms"); assertThat(genderBuilder.getSubAggregations().size()).isEqualTo(1); AggregationBuilder raceBuilder = genderBuilder.getSubAggregations().iterator().next(); assertThat(raceBuilder.getName()).isEqualTo(RACE + RANGE_18_44); assertThat(raceBuilder.getType()).isEqualTo("terms"); assertThat(raceBuilder.getSubAggregations().isEmpty()).isTrue(); } | 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.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } static AggregationBuilder buildDemoChartAggregation(
GenderOrSexType genderOrSexType, AgeType ageType, String ageRange); static List<DemoChartInfo> unwrapDemoChartBuckets(
SearchResponse searchResponse, String... ageRanges); } | 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 != null) ? ElasticUtils.todayMinusYears(hi + 1) : null; LocalDate endDate = ElasticUtils.todayMinusYears(lo); boolean isGender = GenderOrSexType.GENDER.equals(genderOrSexType); boolean isAgeAtConsent = AgeType.AGE_AT_CONSENT.equals(ageType); TermsAggregationBuilder termsAggregationBuilder = AggregationBuilders.terms(GENDER_OR_SEX + ageRange) .field(isGender ? "gender_concept_name" : "sex_at_birth_concept_name") .order(BucketOrder.key(true)) .subAggregation( AggregationBuilders.terms(RACE + ageRange) .field("race_concept_name") .order(BucketOrder.key(true)) .minDocCount(1)); return AgeType.AGE.equals(ageType) ? AggregationBuilders.dateRange(DATE + ageRange) .field("birth_datetime") .format("yyyy-MM-dd") .addRange((startDate == null) ? null : startDate.toString(), endDate.toString()) .subAggregation(termsAggregationBuilder) : AggregationBuilders.range(DATE + ageRange) .field(isAgeAtConsent ? "age_at_consent" : "age_at_cdr") .addRange(new Double(lo), new Double(hi)) .subAggregation(termsAggregationBuilder); } static AggregationBuilder buildDemoChartAggregation(
GenderOrSexType genderOrSexType, AgeType ageType, String ageRange); static List<DemoChartInfo> unwrapDemoChartBuckets(
SearchResponse searchResponse, String... ageRanges); static final String RANGE_18_44; static final String RANGE_45_64; static final String RANGE_GT_65; static final String DATE; static final String GENDER_OR_SEX; static final String RACE; } |
@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")); assertThat(resp) .isEqualTo( singleNestedQuery( ImmutableList.of("has_ehr_data", "has_physical_measurement_data"), QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of("772")))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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> profileApiProvider,
Provider<BillingApi> billingApiProvider,
Provider<GroupsApi> groupsApiProvider,
Provider<NihApi> nihApiProvider,
@Qualifier(FireCloudConfig.END_USER_WORKSPACE_API)
Provider<WorkspacesApi> endUserWorkspacesApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_WORKSPACE_API)
Provider<WorkspacesApi> serviceAccountWorkspaceApiProvider,
Provider<StatusApi> statusApiProvider,
@Qualifier(FireCloudConfig.END_USER_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> endUserStaticNotebooksApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> serviceAccountStaticNotebooksApiProvider,
FirecloudRetryHandler retryHandler,
@Qualifier(Constants.FIRECLOUD_ADMIN_CREDS)
Provider<ServiceAccountCredentials> fcAdminCredsProvider,
IamCredentialsClient iamCredentialsClient,
HttpTransport httpTransport); } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProvider,
Provider<BillingApi> billingApiProvider,
Provider<GroupsApi> groupsApiProvider,
Provider<NihApi> nihApiProvider,
@Qualifier(FireCloudConfig.END_USER_WORKSPACE_API)
Provider<WorkspacesApi> endUserWorkspacesApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_WORKSPACE_API)
Provider<WorkspacesApi> serviceAccountWorkspaceApiProvider,
Provider<StatusApi> statusApiProvider,
@Qualifier(FireCloudConfig.END_USER_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> endUserStaticNotebooksApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> serviceAccountStaticNotebooksApiProvider,
FirecloudRetryHandler retryHandler,
@Qualifier(Constants.FIRECLOUD_ADMIN_CREDS)
Provider<ServiceAccountCredentials> fcAdminCredsProvider,
IamCredentialsClient iamCredentialsClient,
HttpTransport httpTransport); ApiClient getApiClientWithImpersonation(String userEmail); @Override @VisibleForTesting String getApiBasePath(); @Override boolean getFirecloudStatus(); @Override FirecloudMe getMe(); @Override void registerUser(String contactEmail, String firstName, String lastName); @Override void createAllOfUsBillingProject(String projectName); @Override void deleteBillingProject(String billingProject); @Override FirecloudBillingProjectStatus getBillingProjectStatus(String projectName); @Override void addOwnerToBillingProject(String ownerEmail, String projectName); @Override void removeOwnerFromBillingProject(
String ownerEmailToRemove, String projectName, Optional<String> callerAccessToken); @Override FirecloudWorkspace createWorkspace(String projectName, String workspaceName); @Override FirecloudWorkspace cloneWorkspace(
String fromProject, String fromName, String toProject, String toName); @Override List<FirecloudBillingProjectMembership> getBillingProjectMemberships(); @Override FirecloudWorkspaceACLUpdateResponseList updateWorkspaceACL(
String projectName, String workspaceName, List<FirecloudWorkspaceACLUpdate> aclUpdates); @Override FirecloudWorkspaceACL getWorkspaceAclAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspaceAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspace(String projectName, String workspaceName); @Override Optional<FirecloudWorkspaceResponse> getWorkspace(DbWorkspace dbWorkspace); @Override List<FirecloudWorkspaceResponse> getWorkspaces(); @Override void deleteWorkspace(String projectName, String workspaceName); @Override FirecloudManagedGroupWithMembers getGroup(String groupName); @Override FirecloudManagedGroupWithMembers createGroup(String groupName); @Override void addUserToGroup(String email, String groupName); @Override void removeUserFromGroup(String email, String groupName); @Override boolean isUserMemberOfGroup(String email, String groupName); @Override String staticNotebooksConvert(byte[] notebook); @Override String staticNotebooksConvertAsService(byte[] notebook); @Override FirecloudNihStatus getNihStatus(); @Override void postNihCallback(FirecloudJWTWrapper wrapper); } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProvider,
Provider<BillingApi> billingApiProvider,
Provider<GroupsApi> groupsApiProvider,
Provider<NihApi> nihApiProvider,
@Qualifier(FireCloudConfig.END_USER_WORKSPACE_API)
Provider<WorkspacesApi> endUserWorkspacesApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_WORKSPACE_API)
Provider<WorkspacesApi> serviceAccountWorkspaceApiProvider,
Provider<StatusApi> statusApiProvider,
@Qualifier(FireCloudConfig.END_USER_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> endUserStaticNotebooksApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> serviceAccountStaticNotebooksApiProvider,
FirecloudRetryHandler retryHandler,
@Qualifier(Constants.FIRECLOUD_ADMIN_CREDS)
Provider<ServiceAccountCredentials> fcAdminCredsProvider,
IamCredentialsClient iamCredentialsClient,
HttpTransport httpTransport); ApiClient getApiClientWithImpersonation(String userEmail); @Override @VisibleForTesting String getApiBasePath(); @Override boolean getFirecloudStatus(); @Override FirecloudMe getMe(); @Override void registerUser(String contactEmail, String firstName, String lastName); @Override void createAllOfUsBillingProject(String projectName); @Override void deleteBillingProject(String billingProject); @Override FirecloudBillingProjectStatus getBillingProjectStatus(String projectName); @Override void addOwnerToBillingProject(String ownerEmail, String projectName); @Override void removeOwnerFromBillingProject(
String ownerEmailToRemove, String projectName, Optional<String> callerAccessToken); @Override FirecloudWorkspace createWorkspace(String projectName, String workspaceName); @Override FirecloudWorkspace cloneWorkspace(
String fromProject, String fromName, String toProject, String toName); @Override List<FirecloudBillingProjectMembership> getBillingProjectMemberships(); @Override FirecloudWorkspaceACLUpdateResponseList updateWorkspaceACL(
String projectName, String workspaceName, List<FirecloudWorkspaceACLUpdate> aclUpdates); @Override FirecloudWorkspaceACL getWorkspaceAclAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspaceAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspace(String projectName, String workspaceName); @Override Optional<FirecloudWorkspaceResponse> getWorkspace(DbWorkspace dbWorkspace); @Override List<FirecloudWorkspaceResponse> getWorkspaces(); @Override void deleteWorkspace(String projectName, String workspaceName); @Override FirecloudManagedGroupWithMembers getGroup(String groupName); @Override FirecloudManagedGroupWithMembers createGroup(String groupName); @Override void addUserToGroup(String email, String groupName); @Override void removeUserFromGroup(String email, String groupName); @Override boolean isUserMemberOfGroup(String email, String groupName); @Override String staticNotebooksConvert(byte[] notebook); @Override String staticNotebooksConvertAsService(byte[] notebook); @Override FirecloudNihStatus getNihStatus(); @Override void postNihCallback(FirecloudJWTWrapper wrapper); static final List<String> FIRECLOUD_API_OAUTH_SCOPES; static final List<String> FIRECLOUD_WORKSPACE_REQUIRED_FIELDS; } |
@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(CriteriaType.ATC.toString()) .ancestorData(true) .standard(true) .group(true))))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery( "events.concept_id", ImmutableList.of("21600002", "21600009")))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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()) .type(CriteriaType.ICD9CM.toString()) .group(true) .ancestorData(false) .standard(false))))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery( "events.source_concept_id", ImmutableList.of("771", "772", "773")))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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.toString()) .type(CriteriaType.ICD9CM.toString()) .group(false) .ancestorData(false) .standard(false)) .addSearchParametersItem( new SearchParameter() .conceptId(477L) .domain(DomainType.CONDITION.toString()) .type(CriteriaType.SNOMED.toString()) .group(false) .ancestorData(false) .standard(true))))); BoolQueryBuilder source = QueryBuilders.boolQuery(); source.filter(QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of("771"))); BoolQueryBuilder standard = QueryBuilders.boolQuery(); standard.filter(QueryBuilders.termsQuery("events.concept_id", ImmutableList.of("477"))); QueryBuilder expected = QueryBuilders.boolQuery() .filter( QueryBuilders.boolQuery() .should( QueryBuilders.functionScoreQuery( QueryBuilders.nestedQuery( "events", QueryBuilders.constantScoreQuery(source), ScoreMode.Total)) .setMinScore(1)) .should( QueryBuilders.functionScoreQuery( QueryBuilders.nestedQuery( "events", QueryBuilders.constantScoreQuery(standard), ScoreMode.Total)) .setMinScore(1))); assertThat(resp).isEqualTo(expected); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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() .addSearchParametersItem( new SearchParameter() .domain(DomainType.SURVEY.toString()) .type(CriteriaType.PPI.toString()) .subtype(CriteriaSubType.ANSWER.toString()) .conceptId(7771L) .group(false) .ancestorData(false) .standard(false) .addAttributesItem(attr))))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of("7771")), QueryBuilders.rangeQuery("events.value_as_number").gte(1.0F).lte(1.0F))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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() .addSearchParametersItem( new SearchParameter() .domain(DomainType.SURVEY.toString()) .type(CriteriaType.PPI.toString()) .subtype(CriteriaSubType.ANSWER.toString()) .conceptId(777L) .group(false) .ancestorData(false) .standard(false) .addAttributesItem(attr))))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of("777")), QueryBuilders.termsQuery( "events.value_as_source_concept_id", ImmutableList.of("1")))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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) .operator(Operator.GREATER_THAN_OR_EQUAL_TO) .addOperandsItem("18"))))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of("772")), QueryBuilders.rangeQuery("events.age_at_start").gte(18))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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(Operator.BETWEEN) .addOperandsItem("12/25/1988") .addOperandsItem("12/27/1988"))))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of("772")), QueryBuilders.rangeQuery("events.start_date").gte("12/25/1988").lte("12/27/1988"))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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(Operator.IN) .addOperandsItem("123"))))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of("772")), QueryBuilders.termsQuery("events.visit_concept_id", ImmutableList.of("123")))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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_OCCURRENCES) .operator(Operator.GREATER_THAN_OR_EQUAL_TO) .addOperandsItem("13"))))); assertThat(resp) .isEqualTo( singleNestedQueryOccurrences( NO_DATA_FILTERS, 13, QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of("772")))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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 = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem( new SearchGroupItem().addSearchParametersItem(heightAnyParam)))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of(conceptId)))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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> profileApiProvider,
Provider<BillingApi> billingApiProvider,
Provider<GroupsApi> groupsApiProvider,
Provider<NihApi> nihApiProvider,
@Qualifier(FireCloudConfig.END_USER_WORKSPACE_API)
Provider<WorkspacesApi> endUserWorkspacesApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_WORKSPACE_API)
Provider<WorkspacesApi> serviceAccountWorkspaceApiProvider,
Provider<StatusApi> statusApiProvider,
@Qualifier(FireCloudConfig.END_USER_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> endUserStaticNotebooksApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> serviceAccountStaticNotebooksApiProvider,
FirecloudRetryHandler retryHandler,
@Qualifier(Constants.FIRECLOUD_ADMIN_CREDS)
Provider<ServiceAccountCredentials> fcAdminCredsProvider,
IamCredentialsClient iamCredentialsClient,
HttpTransport httpTransport); } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProvider,
Provider<BillingApi> billingApiProvider,
Provider<GroupsApi> groupsApiProvider,
Provider<NihApi> nihApiProvider,
@Qualifier(FireCloudConfig.END_USER_WORKSPACE_API)
Provider<WorkspacesApi> endUserWorkspacesApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_WORKSPACE_API)
Provider<WorkspacesApi> serviceAccountWorkspaceApiProvider,
Provider<StatusApi> statusApiProvider,
@Qualifier(FireCloudConfig.END_USER_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> endUserStaticNotebooksApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> serviceAccountStaticNotebooksApiProvider,
FirecloudRetryHandler retryHandler,
@Qualifier(Constants.FIRECLOUD_ADMIN_CREDS)
Provider<ServiceAccountCredentials> fcAdminCredsProvider,
IamCredentialsClient iamCredentialsClient,
HttpTransport httpTransport); ApiClient getApiClientWithImpersonation(String userEmail); @Override @VisibleForTesting String getApiBasePath(); @Override boolean getFirecloudStatus(); @Override FirecloudMe getMe(); @Override void registerUser(String contactEmail, String firstName, String lastName); @Override void createAllOfUsBillingProject(String projectName); @Override void deleteBillingProject(String billingProject); @Override FirecloudBillingProjectStatus getBillingProjectStatus(String projectName); @Override void addOwnerToBillingProject(String ownerEmail, String projectName); @Override void removeOwnerFromBillingProject(
String ownerEmailToRemove, String projectName, Optional<String> callerAccessToken); @Override FirecloudWorkspace createWorkspace(String projectName, String workspaceName); @Override FirecloudWorkspace cloneWorkspace(
String fromProject, String fromName, String toProject, String toName); @Override List<FirecloudBillingProjectMembership> getBillingProjectMemberships(); @Override FirecloudWorkspaceACLUpdateResponseList updateWorkspaceACL(
String projectName, String workspaceName, List<FirecloudWorkspaceACLUpdate> aclUpdates); @Override FirecloudWorkspaceACL getWorkspaceAclAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspaceAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspace(String projectName, String workspaceName); @Override Optional<FirecloudWorkspaceResponse> getWorkspace(DbWorkspace dbWorkspace); @Override List<FirecloudWorkspaceResponse> getWorkspaces(); @Override void deleteWorkspace(String projectName, String workspaceName); @Override FirecloudManagedGroupWithMembers getGroup(String groupName); @Override FirecloudManagedGroupWithMembers createGroup(String groupName); @Override void addUserToGroup(String email, String groupName); @Override void removeUserFromGroup(String email, String groupName); @Override boolean isUserMemberOfGroup(String email, String groupName); @Override String staticNotebooksConvert(byte[] notebook); @Override String staticNotebooksConvertAsService(byte[] notebook); @Override FirecloudNihStatus getNihStatus(); @Override void postNihCallback(FirecloudJWTWrapper wrapper); } | FireCloudServiceImpl implements FireCloudService { @Override public FirecloudMe getMe() { ProfileApi profileApi = profileApiProvider.get(); return retryHandler.run((context) -> profileApi.me()); } @Autowired FireCloudServiceImpl(
Provider<WorkbenchConfig> configProvider,
Provider<ProfileApi> profileApiProvider,
Provider<BillingApi> billingApiProvider,
Provider<GroupsApi> groupsApiProvider,
Provider<NihApi> nihApiProvider,
@Qualifier(FireCloudConfig.END_USER_WORKSPACE_API)
Provider<WorkspacesApi> endUserWorkspacesApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_WORKSPACE_API)
Provider<WorkspacesApi> serviceAccountWorkspaceApiProvider,
Provider<StatusApi> statusApiProvider,
@Qualifier(FireCloudConfig.END_USER_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> endUserStaticNotebooksApiProvider,
@Qualifier(FireCloudConfig.SERVICE_ACCOUNT_STATIC_NOTEBOOKS_API)
Provider<StaticNotebooksApi> serviceAccountStaticNotebooksApiProvider,
FirecloudRetryHandler retryHandler,
@Qualifier(Constants.FIRECLOUD_ADMIN_CREDS)
Provider<ServiceAccountCredentials> fcAdminCredsProvider,
IamCredentialsClient iamCredentialsClient,
HttpTransport httpTransport); ApiClient getApiClientWithImpersonation(String userEmail); @Override @VisibleForTesting String getApiBasePath(); @Override boolean getFirecloudStatus(); @Override FirecloudMe getMe(); @Override void registerUser(String contactEmail, String firstName, String lastName); @Override void createAllOfUsBillingProject(String projectName); @Override void deleteBillingProject(String billingProject); @Override FirecloudBillingProjectStatus getBillingProjectStatus(String projectName); @Override void addOwnerToBillingProject(String ownerEmail, String projectName); @Override void removeOwnerFromBillingProject(
String ownerEmailToRemove, String projectName, Optional<String> callerAccessToken); @Override FirecloudWorkspace createWorkspace(String projectName, String workspaceName); @Override FirecloudWorkspace cloneWorkspace(
String fromProject, String fromName, String toProject, String toName); @Override List<FirecloudBillingProjectMembership> getBillingProjectMemberships(); @Override FirecloudWorkspaceACLUpdateResponseList updateWorkspaceACL(
String projectName, String workspaceName, List<FirecloudWorkspaceACLUpdate> aclUpdates); @Override FirecloudWorkspaceACL getWorkspaceAclAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspaceAsService(String projectName, String workspaceName); @Override FirecloudWorkspaceResponse getWorkspace(String projectName, String workspaceName); @Override Optional<FirecloudWorkspaceResponse> getWorkspace(DbWorkspace dbWorkspace); @Override List<FirecloudWorkspaceResponse> getWorkspaces(); @Override void deleteWorkspace(String projectName, String workspaceName); @Override FirecloudManagedGroupWithMembers getGroup(String groupName); @Override FirecloudManagedGroupWithMembers createGroup(String groupName); @Override void addUserToGroup(String email, String groupName); @Override void removeUserFromGroup(String email, String groupName); @Override boolean isUserMemberOfGroup(String email, String groupName); @Override String staticNotebooksConvert(byte[] notebook); @Override String staticNotebooksConvertAsService(byte[] notebook); @Override FirecloudNihStatus getNihStatus(); @Override void postNihCallback(FirecloudJWTWrapper wrapper); static final List<String> FIRECLOUD_API_OAUTH_SCOPES; static final List<String> FIRECLOUD_WORKSPACE_REQUIRED_FIELDS; } |
@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 heightParam = new SearchParameter() .conceptId(Long.parseLong(conceptId)) .domain(DomainType.PHYSICAL_MEASUREMENT.toString()) .type(CriteriaType.PPI.toString()) .group(false) .ancestorData(false) .standard(false) .addAttributesItem(attr); QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(heightParam)))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of(conceptId)), QueryBuilders.rangeQuery("events.value_as_number").gte(left).lte(right))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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"; SearchParameter weightParam = new SearchParameter() .conceptId(Long.parseLong(conceptId)) .domain(DomainType.PHYSICAL_MEASUREMENT.toString()) .type(CriteriaType.PPI.toString()) .standard(false) .ancestorData(false) .group(false) .addAttributesItem(attr); QueryBuilder resp = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(weightParam)))); assertThat(resp) .isEqualTo( singleNestedQuery( NO_DATA_FILTERS, QueryBuilders.termsQuery("events.source_concept_id", ImmutableList.of(conceptId)), QueryBuilders.rangeQuery("events.value_as_number").gte(left).lte(right))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(genderParam)))); assertThat(resp) .isEqualTo( nonNestedQuery( QueryBuilders.termsQuery("gender_concept_id", ImmutableList.of(conceptId)))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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 = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addExcludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(genderParam)))); assertThat(resp) .isEqualTo( nonNestedQuery( QueryBuilders.termsQuery("gender_concept_id", ImmutableList.of(conceptId)))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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 = ElasticFilters.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(genderParam))) .addExcludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(genderParam)))); assertThat(resp) .isEqualTo( nonNestedMustNotQuery( QueryBuilders.termsQuery("gender_concept_id", ImmutableList.of(conceptId)))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
@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.fromCohortSearch( cbCriteriaDao, new SearchRequest() .addIncludesItem( new SearchGroup() .addItemsItem(new SearchGroupItem().addSearchParametersItem(raceParam)))); assertThat(resp) .isEqualTo( nonNestedQuery( QueryBuilders.termsQuery("race_concept_id", ImmutableList.of(conceptId)))); } | 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, SearchRequest req); } | 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, SearchRequest req); } |
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