Feat/multi query management

HTTPServer.mjs

@@ -17,6 +17,10 @@ import { LoginController } from './controllers/LoginController.mjs';
 import { SessionController } from './controllers/SessionController.mjs';
 import { UserAPIController } from './controllers/UserAPIController.mjs';
 
+// Adapters
+import { TranslatorServicexFEAdapter } from './adapters/TranslatorServicexFEAdapter.mjs';
+import { QueryServicexFEAdapter } from './adapters/QueryServicexFEAdapter.mjs';
+
 export function startServer(config, services) {
 
   const filters = {whitelistRx: /^ara-/}; // TODO: move to config file
@@ -25,15 +29,24 @@ export function startServer(config, services) {
   const authService = services.authService;
   const userService = services.userService;
   const translatorService = services.translatorService;
+  const queryService = services.queryService;
   const demoQueries = config.frontend.cached_queries.filter(e => e.allow_inbound);
+  const translatorServicexFEAdapter = new TranslatorServicexFEAdapter();
+  const queryServicexFEAdapter = new QueryServicexFEAdapter();
   const __root = path.dirname(url.fileURLToPath(import.meta.url));
   const app = express();
   const loginController = new LoginController(config, authService);
-  const queryAPIController = new QueryAPIController(config, translatorService, filters);
+  const queryAPIController = new QueryAPIController(config,
+    translatorService,
+    translatorServicexFEAdapter,
+    queryService,
+    queryServicexFEAdapter,
+    userService,
+    filters);
   const configAPIController = new ConfigAPIController(config);
   const userAPIController = new UserAPIController(config, userService, translatorService);
   const sessionController = new SessionController(config, authService);
-  const API_PATH_PREFIX = '/api/v1';
+  const API_PATH_V1 = '/api/v1';
   const SITE_PATH_PREFIX = '';
   app.use(pinoHttp({logger: logger}));
   app.use(express.json({ limit: config.json_payload_limit }));
@@ -59,8 +72,8 @@ export function startServer(config, services) {
   app.use(sessionController.attachSessionData.bind(sessionController));
 
   // Session status API
-  app.get(`${API_PATH_PREFIX}/session/status`, sessionController.getStatus.bind(sessionController));
-  app.post(`${API_PATH_PREFIX}/session/status`, sessionController.updateStatus.bind(sessionController));
+  app.get(`${API_PATH_V1}/session/status`, sessionController.getStatus.bind(sessionController));
+  app.post(`${API_PATH_V1}/session/status`, sessionController.updateStatus.bind(sessionController));
 
   // Login/logout
   app.get('/oauth2/redir/:provider', loginController.authRedir.bind(loginController));
@@ -75,32 +88,61 @@ export function startServer(config, services) {
    * to explicit user activity (e.g., the FE app needs this at startup regardless of whether there is a user
    * session active). To maintain consistency with the decision that only intentional user activity should count
    * towards updating session last-touch times, we therefore exclude this API from that set. */
-  app.use(`${API_PATH_PREFIX}/config`, configAPIController.getConfig.bind(configAPIController));
+  app.use(`${API_PATH_V1}/config`, configAPIController.getConfig.bind(configAPIController));
 
   /** All routes below this point MUST use one of authenticate[Un]PrivilegedRequest() **/
 
-  // Query routes: unprivileged
-  app.use(`${API_PATH_PREFIX}/query`, sessionController.authenticateUnprivilegedRequest.bind(sessionController));
-  app.post(`${API_PATH_PREFIX}/query`, queryAPIController.submitQuery.bind(queryAPIController));
-  app.get(`${API_PATH_PREFIX}/query/:qid/status`, queryAPIController.getQueryStatus.bind(queryAPIController));
-  app.get(`${API_PATH_PREFIX}/query/:qid/result`, queryAPIController.getQueryResult.bind(queryAPIController));
+  // Submit query route: privileged session
+  app.post(`${API_PATH_V1}/query`,
+    sessionController.authenticatePrivilegedRequest.bind(sessionController),
+    queryAPIController.submitQuery.bind(queryAPIController));
+  // Query request routes: unprivileged session
+  app.get(`${API_PATH_V1}/query/:qid/status`,
+    sessionController.authenticateUnprivilegedRequest.bind(sessionController),
+    queryAPIController.getQueryStatus.bind(queryAPIController));
+  app.get(`${API_PATH_V1}/query/:qid/result`,
+    sessionController.authenticateUnprivilegedRequest.bind(sessionController),
+    queryAPIController.getQueryResult.bind(queryAPIController));
+  // Query callback route: behind hmac
+  app.post(`${API_PATH_V1}/query/update`, queryAPIController.updateQuery.bind(queryAPIController));
 
   // User routes: privileged
-  app.use(`${API_PATH_PREFIX}/users`, sessionController.authenticatePrivilegedRequest.bind(sessionController));
-  app.get(`${API_PATH_PREFIX}/users/me`, userAPIController.getUser.bind(userAPIController));
-  app.get(`${API_PATH_PREFIX}/users/me/preferences`, userAPIController.getUserPrefs.bind(userAPIController));
-  app.post(`${API_PATH_PREFIX}/users/me/preferences`, userAPIController.updateUserPrefs.bind(userAPIController));
-  app.get(`${API_PATH_PREFIX}/users/me/saves`, userAPIController.getUserSaves.bind(userAPIController));
-  app.post(`${API_PATH_PREFIX}/users/me/saves`, userAPIController.updateUserSaves.bind(userAPIController));
-  app.get(`${API_PATH_PREFIX}/users/me/saves/:save_id`, userAPIController.getUserSaveById.bind(userAPIController));
-  app.put(`${API_PATH_PREFIX}/users/me/saves/:save_id`, userAPIController.updateUserSaveById.bind(userAPIController));
-  app.delete(`${API_PATH_PREFIX}/users/me/saves/:save_id`, userAPIController.deleteUserSaveById.bind(userAPIController));
+  app.use(`${API_PATH_V1}/users`, sessionController.authenticatePrivilegedRequest.bind(sessionController));
+  app.get(`${API_PATH_V1}/users/me`, userAPIController.getUser.bind(userAPIController));
+  app.get(`${API_PATH_V1}/users/me/preferences`, userAPIController.getUserPrefs.bind(userAPIController));
+  app.post(`${API_PATH_V1}/users/me/preferences`, userAPIController.updateUserPrefs.bind(userAPIController));
+  app.use(`${API_PATH_V1}/users`, sessionController.authenticatePrivilegedRequest.bind(sessionController));
+
+  // User queries
+  // Creation of user queries is done on submission. See the /query endpoint
+  app.get(`${API_PATH_V1}/users/me/queries`, userAPIController.getUserQueries.bind(userAPIController));
+  app.post(`${API_PATH_V1}/users/me/queries/:save_id`, userAPIController.updateUserSaveById.bind(userAPIController));
+  app.delete(`${API_PATH_V1}/users/me/queries/:save_id`, userAPIController.deleteUserSaveById.bind(userAPIController));
+
+  // User bookmarks
+  app.get(`${API_PATH_V1}/users/me/bookmarks`, userAPIController.getUserBookmarks.bind(userAPIController));
+  app.post(`${API_PATH_V1}/users/me/bookmarks`, userAPIController.updateUserSaves.bind(userAPIController));
+  app.post(`${API_PATH_V1}/users/me/bookmarks/:save_id`, userAPIController.updateUserSaveById.bind(userAPIController));
+  app.delete(`${API_PATH_V1}/users/me/bookmarks/:save_id`, userAPIController.deleteUserSaveById.bind(userAPIController));
+
+  // User tags
+  app.get(`${API_PATH_V1}/users/me/tags`, userAPIController.getUserTags.bind(userAPIController));
+  app.post(`${API_PATH_V1}/users/me/tags`, userAPIController.updateUserSaves.bind(userAPIController));
+  app.post(`${API_PATH_V1}/users/me/tags/:save_id`, userAPIController.updateUserSaveById.bind(userAPIController));
+  app.delete(`${API_PATH_V1}/users/me/tags/:save_id`, userAPIController.deleteUserSaveById.bind(userAPIController));
+
+  // User saves
+  app.get(`${API_PATH_V1}/users/me/saves`, userAPIController.getUserSaves.bind(userAPIController));
+  app.post(`${API_PATH_V1}/users/me/saves`, userAPIController.updateUserSaves.bind(userAPIController));
+  app.get(`${API_PATH_V1}/users/me/saves/:save_id`, userAPIController.getUserSaveById.bind(userAPIController));
+  app.put(`${API_PATH_V1}/users/me/saves/:save_id`, userAPIController.updateUserSaveById.bind(userAPIController));
+  app.delete(`${API_PATH_V1}/users/me/saves/:save_id`, userAPIController.deleteUserSaveById.bind(userAPIController));
   // workspaces
-  app.get(`${API_PATH_PREFIX}/users/me/workspaces`, userAPIController.getUserWorkspaces.bind(userAPIController));
-  app.get(`${API_PATH_PREFIX}/users/me/workspaces/:ws_id`, userAPIController.getUserWorkspaceById.bind(userAPIController));
-  app.post(`${API_PATH_PREFIX}/users/me/workspaces`, userAPIController.createUserWorkspace.bind(userAPIController));
-  app.put(`${API_PATH_PREFIX}/users/me/workspaces/:ws_id`, userAPIController.updateUserWorkspace.bind(userAPIController));
-  app.delete(`${API_PATH_PREFIX}/users/me/workspaces/:ws_id`, userAPIController.deleteUserWorkspace.bind(userAPIController));
+  app.get(`${API_PATH_V1}/users/me/workspaces`, userAPIController.getUserWorkspaces.bind(userAPIController));
+  app.get(`${API_PATH_V1}/users/me/workspaces/:ws_id`, userAPIController.getUserWorkspaceById.bind(userAPIController));
+  app.post(`${API_PATH_V1}/users/me/workspaces`, userAPIController.createUserWorkspace.bind(userAPIController));
+  app.put(`${API_PATH_V1}/users/me/workspaces/:ws_id`, userAPIController.updateUserWorkspace.bind(userAPIController));
+  app.delete(`${API_PATH_V1}/users/me/workspaces/:ws_id`, userAPIController.deleteUserWorkspace.bind(userAPIController));
 
   app.all(['/api', '/api/*'], (req, res) => {
     return res.status(403).send('API action Forbidden');

StartServer.mjs

@@ -7,18 +7,20 @@ import { loadBiolink } from './lib/biolink-model.mjs';
 import { loadChebi } from './lib/chebi.mjs';
 import { loadTrapi } from './lib/trapi.mjs';
 import { TranslatorService } from './services/TranslatorService.mjs';
-import { TranslatorServicexFEAdapter } from './adapters/TranslatorServicexFEAdapter.mjs';
 import { ARSClient } from './lib/ARSClient.mjs';
 import * as httpserver from './HTTPServer.mjs';
 import { AuthService } from './services/AuthService.mjs';
 import { UserService } from './services/UserService.mjs';
+import { QueryService } from './services/QueryService.mjs';
+import { ARSCallbackxQueryServiceAdapter } from './adapters/ARSCallbackxQueryServiceAdapter.mjs';
 
 import { SessionStorePostgres } from './stores/SessionStorePostgres.mjs';
 import { UserStorePostgres } from './stores/UserStorePostgres.mjs';
 import { pg } from './lib/postgres_preamble.mjs';
 import { UserPreferenceStorePostgres } from './stores/UserPreferenceStorePostgres.mjs';
 import { UserSavedDataStorePostgres } from './stores/UserSavedDataStorePostgres.mjs';
 import { UserWorkspaceStorePostgres } from './stores/UserWorkspaceStorePostgres.mjs';
+import { QueryStorePostgres } from './stores/QueryStorePostgres.mjs';
 
 
 // Load the config asap as basically everything depends on it
@@ -48,8 +50,7 @@ const TRANSLATOR_SERVICE = (function (config) {
     config.ars_endpoint.post_uri,
     config.ars_endpoint.retain_uri,
     config.ars_endpoint.use_ars_merging);
-  const outputAdapter = new TranslatorServicexFEAdapter();
-  return new TranslatorService(queryClient, outputAdapter);
+  return new TranslatorService(queryClient);
 })(SERVER_CONFIG);
 
 // Bootstrap the auth service
@@ -83,10 +84,20 @@ const USER_SERVICE = (function (config) {
   );
 })(SERVER_CONFIG);
 
+const QUERY_SERVICE = (function (config) {
+  const dbPool = new pg.Pool({
+    ...config.storage.pg,
+    password: config.secrets.pg.password,
+    ssl: config.db_conn.ssl
+  });
+  return new QueryService(new QueryStorePostgres(dbPool),
+                          new ARSCallbackxQueryServiceAdapter());
+})(SERVER_CONFIG);
 logger.info(SERVER_CONFIG, "Server configuration");
 
 httpserver.startServer(SERVER_CONFIG, {
   translatorService: TRANSLATOR_SERVICE,
   authService: AUTH_SERVICE,
-  userService: USER_SERVICE
+  userService: USER_SERVICE,
+  queryService: QUERY_SERVICE
 });

adapters/ARSCallbackxQueryServiceAdapter.mjs

@@ -0,0 +1,43 @@
+export { ARSCallbackxQueryServiceAdapter };
+import { logger } from '../lib/logger.mjs';
+import * as cmn from '../lib/common.mjs';
+
+class ARSCallbackxQueryServiceAdapter {
+  processQueryUpdate(queryUpdate) {
+    const eventType = cmn.jsonGet(queryUpdate, 'event_type');
+    const update = {
+      pk: cmn.jsonGet(queryUpdate, 'pk'),
+      timestamp: cmn.jsonGet(queryUpdate, 'timestamp'),
+      status: null,
+      aras: []
+    };
+    switch (eventType) {
+      case _UPDATE_EVENT.MV_AVAILABLE:
+        update.aras = cmn.jsonGet(queryUpdate, 'merged_versions_list').map(idAraPair => idAraPair[1]);
+        update.aras.reverse();
+        if (cmn.jsonGet(queryUpdate, 'complete')) {
+          update.status = cmn.QUERY_STATUS.COMPLETE;
+        } else {
+          update.status = cmn.QUERY_STATUS.RUNNING;
+        }
+        break;
+      case _UPDATE_EVENT.MV_BEGUN:
+      case _UPDATE_EVENT.ARA_COMPLETE:
+        break; // We can ignore these events for now
+      case _UPDATE_EVENT.ERROR:
+        logger.error(`Received ARS callback error for query with PK ${update.pk}: ${queryUpdate.message}`);
+        update.status = cmn.QUERY_STATUS.ERROR;
+        break;
+      default:
+        throw new Error(`Unknown ARS callback event type: ${eventType}`);
+    }
+    return update;
+  }
+}
+
+const _UPDATE_EVENT = Object.freeze({
+  MV_AVAILABLE: 'merged_version_available',
+  MV_BEGUN: 'merged_version_begun',
+  ARA_COMPLETE: 'ara_response_complete',
+  ERROR: 'ars_error'
+});

adapters/QueryServicexFEAdapter.mjs

@@ -0,0 +1,23 @@
+'use strict';
+export { QueryServicexFEAdapter };
+
+class QueryServicexFEAdapter {
+
+  querySubmitToFE(queryModel) {
+    return {
+      status: 'success',
+      data: queryModel.pk
+    }
+  }
+
+  queryStatusToFE(queryModel) {
+    return {
+      status: queryModel.status,
+      data: {
+        qid: queryModel.pk,
+        aras: queryModel.metadata.aras,
+        timestamp: queryModel.time_updated
+      }
+    };
+  }
+}