Merge branch 'main' of https://github.com/biothings/bte-server into dev

__test__/integration/controllers/association.test.ts

@@ -2,26 +2,26 @@ import assoc from "../../../src/controllers/association";
 
 describe("Test association module", () => {
   test("By default, should return all associations", async () => {
-    const res = assoc();
+    const res = await assoc();
     expect(res.length).toBeGreaterThan(10);
     expect(res[0]).toHaveProperty("subject");
     expect(res[0]).toHaveProperty("api");
   });
 
   test("If sub specified, should only return associations related to the sub", async () => {
-    const res = assoc("Gene");
+    const res = await assoc("Gene");
     const inputTypes = new Set(res.map(item => item.subject));
     expect(Array.from(inputTypes)).toHaveLength(1);
     expect(Array.from(inputTypes)).toEqual(["Gene"]);
   });
 
   test("If invalid sub specified, should only empty list", async () => {
-    const res = assoc("Gene1");
+    const res = await assoc("Gene1");
     expect(res).toEqual([]);
   });
 
   test("If obj specified, should only return associations related to the obj", async () => {
-    const res = assoc(undefined, "SmallMolecule");
+    const res = await assoc(undefined, "SmallMolecule");
     const outputTypes = new Set(res.map(item => item.object));
     const inputTypes = new Set(res.map(item => item.subject));
     expect(inputTypes.size).toBeGreaterThan(1);
@@ -30,7 +30,7 @@ describe("Test association module", () => {
   });
 
   test("If pred specified, should only return associations related to the pred", async () => {
-    const res = assoc(undefined, undefined, "treats");
+    const res = await assoc(undefined, undefined, "treats");
     const preds = new Set(res.map(item => item.predicate));
     const inputTypes = new Set(res.map(item => item.subject));
     expect(inputTypes.size).toBeGreaterThan(1);
@@ -39,7 +39,7 @@ describe("Test association module", () => {
   });
 
   test("If api specified, should only return associations related to the api", async () => {
-    const res = assoc(undefined, undefined, undefined, undefined, "MyGene.info API");
+    const res = await assoc(undefined, undefined, undefined, undefined, "MyGene.info API");
     const apis = new Set(res.map(item => item.api.name));
     const inputTypes = new Set(res.map(item => item.subject));
     expect(inputTypes.size).toBeGreaterThan(1);
@@ -48,7 +48,7 @@ describe("Test association module", () => {
   });
 
   test("If source specified, should only return associations related to the source", async () => {
-    const res = assoc(undefined, undefined, undefined, undefined, undefined, "infores:disgenet");
+    const res = await assoc(undefined, undefined, undefined, undefined, undefined, "infores:disgenet");
     const sources = new Set(res.map(item => item.provided_by));
     const inputTypes = new Set(res.map(item => item.subject));
     expect(inputTypes.size).toBeGreaterThan(1);
@@ -57,7 +57,7 @@ describe("Test association module", () => {
   });
 
   test("If both sub and obj specified, should only return associations related to both sub and obj", async () => {
-    const res = assoc("Gene", "SmallMolecule");
+    const res = await assoc("Gene", "SmallMolecule");
     const outputTypes = new Set(res.map(item => item.object));
     const inputTypes = new Set(res.map(item => item.subject));
     expect(Array.from(inputTypes)).toHaveLength(1);

package.json

@@ -114,6 +114,7 @@
     "node-cron": "^2.0.3",
     "npm": "^9.9.0",
     "piscina": "^3.2.0",
+    "proper-lockfile": "^4.1.2",
     "ps-node": "^0.1.6",
     "snake-case": "^3.0.4",
     "stream-chunker": "^1.2.8",

src/config/index.ts

@@ -86,14 +86,14 @@ export default class Config {
     });
     this.app.use("/", fastLimiter);
     this.app.use("/v1/query", medLimiter);
-    this.app.use("/v1/team/:team_name/query", medLimiter);
-    this.app.use("/v1/team/:smartapiID/query", fastLimiter);
+    this.app.use("/v1/team/:teamName/query", medLimiter);
+    this.app.use("/v1/team/:smartAPIID/query", fastLimiter);
     this.app.use("/v1/meta_knowledge_graph", fastLimiter);
     this.app.use("/v1/team/:teamName/meta_knowledge_graph", fastLimiter);
-    this.app.use("/v1/smartapi/:smartapiID/meta_knowledge_graph", fastLimiter);
+    this.app.use("/v1/smartapi/:smartAPIID/meta_knowledge_graph", fastLimiter);
     this.app.use("/v1/asyncquery", fastLimiter);
     this.app.use("/v1/team/:teamName/asyncquery", fastLimiter);
-    this.app.use("/v1/smartapi/:smartapiID/asyncquery", fastLimiter);
+    this.app.use("/v1/smartapi/:smartAPIID/asyncquery", fastLimiter);
     this.app.use("/queues", fastLimiter);
   }
 

src/controllers/association.ts

@@ -22,21 +22,21 @@ export interface AssocResult {
   };
 }
 
-export default function (
+export default async function (
   sub: string = undefined,
   obj: string = undefined,
   pred: string = undefined,
   component: string = undefined,
   api: string = undefined,
   source: string = undefined,
-): AssocResult[] {
+): Promise<AssocResult[]> {
   const smartapi_specs = path.resolve(__dirname, "../../data/smartapi_specs.json");
   debug(`smartapi specs loaded: ${smartapi_specs}`);
   const predicates = path.resolve(__dirname, "../../data/predicates.json");
   debug(`predicates endpoints loaded, ${predicates}`);
   const kg = new meta_kg(smartapi_specs, predicates);
   debug("metakg initialized");
-  kg.constructMetaKGSync(true, {});
+  await kg.constructMetaKGWithFileLock(true, {});
   debug(`metakg loaded: ${kg.ops.length} ops`);
   const associations: AssocResult[] = [];
   const filtered_res = kg.filter({

src/controllers/async/asyncquery_queue.ts

@@ -79,7 +79,7 @@ export function getQueryQueue(name: string): BullQueue {
               workflow: [
                 {
                   id:
-                    job.data.route.includes(":smartapi_id") || job.data.route.includes(":team_name")
+                    job.data.route.includes(":smartAPIID") || job.data.route.includes(":teamName")
                       ? "lookup"
                       : "lookup_and_score",
                 },

src/controllers/cron/update_local_smartapi.ts

@@ -12,8 +12,9 @@ import SMARTAPI_EXCLUSIONS from "../../config/smartapi_exclusions";
 import getSmartApiOverrideConfig from "../../config/smartapi_overrides";
 import { SmartApiOverrides } from "../../types";
 import apiList from "../../config/api_list";
-import MetaKG, { SmartAPISpec } from "@biothings-explorer/smartapi-kg";
-import { redisClient } from "@biothings-explorer/utils";
+import MetaKG from "@biothings-explorer/smartapi-kg";
+import { lockWithActionAsync, redisClient } from "@biothings-explorer/utils";
+import { setTimeout } from "timers/promises";
 
 const userAgent = `BTE/${process.env.NODE_ENV === "production" ? "prod" : "dev"} Node/${process.version} ${
   process.platform
@@ -325,17 +326,42 @@ async function updateSmartAPISpecs() {
     delete obj._score;
   });
 
-  await fs.writeFile(localFilePath, JSON.stringify({ hits: hits }));
+  await lockWithActionAsync([localFilePath], async () => {
+    await fs.writeFile(localFilePath, JSON.stringify({ hits: hits }));
+  }, debug)
+
   const predicatesInfo = await getOpsFromPredicatesEndpoints(res.data.hits);
-  await fs.writeFile(predicatesFilePath, JSON.stringify(predicatesInfo));
+  await lockWithActionAsync([predicatesFilePath], async () => {
+    await fs.writeFile(predicatesFilePath, JSON.stringify(predicatesInfo));
+  }, debug);
 
   // Create a new metakg
   const metakg = new MetaKG();
-  metakg.constructMetaKGSync(true, { predicates: predicatesInfo, smartapiSpecs: { hits: hits as any }, apiList });
+  await metakg.constructMetaKGWithFileLock(true, { predicates: predicatesInfo, smartapiSpecs: { hits: hits as any }, apiList });
   global.metakg = metakg;
-  global.smartapi = { hits };
+  global.smartapi = { hits };  // hits is an array, but smartapi must be a dict
 };
 
+async function loadGlobalMetaKGReadOnly() {
+  await setTimeout(30000);
+  const localFilePath = path.resolve(__dirname, "../../../data/smartapi_specs.json");
+  const predicatesFilePath = path.resolve(__dirname, "../../../data/predicates.json");
+
+  const metakg = new MetaKG(localFilePath, predicatesFilePath);
+  await metakg.constructMetaKGWithFileLock(true, { apiList });
+  global.metakg = metakg;
+
+  global.smartapi = await lockWithActionAsync(
+    [localFilePath],
+    async () => {
+      const file = await fs.readFile(localFilePath, 'utf-8');
+      const hits = JSON.parse(file);
+      return hits;
+    },
+    debug
+  );
+}
+
 async function getAPIOverrides(data: { total?: number; hits: any }, overrides: SmartApiOverrides) {
   // if only_overrides is enabled, only overridden apis are used
   if (overrides.config.only_overrides) {
@@ -422,12 +448,35 @@ export default function manageSmartApi() {
       process.env.INSTANCE_ID && process.env.INSTANCE_ID === "0", // Only one PM2 cluster instance should sync
     ].every(condition => condition);
 
+  /*
+  We schedule 2 cron jobs, one for non-syncing processes and one for the syncing process.
+  The non-syncing processes will only read from the local copy of the SmartAPI specs
+  after a 30 second timeout each time.
+  Whereas the syncing process will update the local copy of the SmartAPI specs.
+  We also run them once initially.
+  */
   if (!should_sync) {
-    debug(`SmartAPI sync disabled, server process ${process.pid} disabling smartapi updates.`);
+    debug(`Server process ${process.pid} disabling smartapi updates. SmartAPI files will be read from but not written to.`);
+    cron.schedule("*/10 * * * *", async () => {
+      debug(`Reading from SmartAPI specs now at ${new Date().toUTCString()}!`);
+      try {
+        await loadGlobalMetaKGReadOnly();
+        debug("Reading local copy of SmartAPI specs successful.");
+      } catch (err) {
+        debug(`Reading local copy of SmartAPI specs failed! The error message is ${err.toString()}`);
+      }
+    });
+
+    loadGlobalMetaKGReadOnly()
+      .then(() => {
+      debug("Reading local copy of SmartAPI specs successful.");
+      })
+      .catch(err => {
+      debug(`Reading local copy of SmartAPI specs failed! The error message is ${err.toString()}`);
+      });
     return;
   }
 
-  // Otherwise, schedule sync!
   cron.schedule("*/10 * * * *", async () => {
     debug(`Updating local copy of SmartAPI specs now at ${new Date().toUTCString()}!`);
     try {
@@ -438,7 +487,6 @@ export default function manageSmartApi() {
     }
   });
 
-  // Run at start once
   debug(`Running initial update of SmartAPI specs now at ${new Date().toUTCString()}`);
   updateSmartAPISpecs()
     .then(() => {
@@ -447,4 +495,4 @@ export default function manageSmartApi() {
     .catch(err => {
       debug(`Updating local copy of SmartAPI specs failed! The error message is ${err.toString()}`);
     });
-}
+}

src/controllers/meta_knowledge_graph.ts

@@ -1,10 +1,12 @@
 import meta_kg, { KGQualifiersObject } from "@biothings-explorer/smartapi-kg";
 import { snakeCase } from "snake-case";
+import lockfile from "proper-lockfile";
 import path from "path";
 import PredicatesLoadingError from "../utils/errors/predicates_error";
 const debug = require("debug")("bte:biothings-explorer-trapi:metakg");
 import apiList from "../config/api_list";
 import { supportedLookups } from "@biothings-explorer/query_graph_handler";
+import MetaKG from "@biothings-explorer/smartapi-kg";
 
 interface PredicateInfo {
   predicate: string;
@@ -31,16 +33,17 @@ export default class MetaKnowledgeGraphHandler {
     const smartapi_specs = path.resolve(__dirname, "../../data/smartapi_specs.json");
     const predicates = path.resolve(__dirname, "../../data/predicates.json");
     const kg = new meta_kg(smartapi_specs, predicates);
+
     try {
       if (smartAPIID !== undefined) {
         debug(`Constructing with SmartAPI ID ${smartAPIID}`);
-        kg.constructMetaKGSync(false, { apiList, smartAPIID: smartAPIID });
+        await kg.constructMetaKGWithFileLock(false, { apiList, smartAPIID: smartAPIID });
       } else if (teamName !== undefined) {
         debug(`Constructing with team ${teamName}`);
-        kg.constructMetaKGSync(false, { apiList, teamName: teamName });
+        await kg.constructMetaKGWithFileLock(false, { apiList, teamName: teamName });
       } else {
         debug(`Constructing with default`);
-        kg.constructMetaKGSync(true, { apiList });
+        await kg.constructMetaKGWithFileLock(true, { apiList });
       }
       if (kg.ops.length === 0) {
         debug(`Found 0 operations`);
@@ -86,10 +89,13 @@ export default class MetaKnowledgeGraphHandler {
   }
 
   async getKG(
+    metakg: MetaKG = undefined,
     smartAPIID: string = this.smartAPIID,
     teamName: string = this.teamName,
   ): Promise<{ nodes: {}; edges: any[] }> {
-    const kg = await this._loadMetaKG(smartAPIID, teamName);
+    // read metakg from files if not globally defined
+    const kg = metakg ?? await this._loadMetaKG(smartAPIID, teamName);
+
     let knowledge_graph = {
       nodes: {},
       edges: [],

src/controllers/threading/threadHandler.ts

@@ -226,11 +226,11 @@ export async function runTask(req: Request, res: Response, route: string, useBul
       route,
       queryGraph: (req.body as TrapiQuery)?.message?.query_graph,
       workflow: (req.body as TrapiQuery)?.workflow,
+      smartAPIID: req.params.smartAPIID,
+      teamName: req.params.teamName,
       options: {
         logLevel: (req.body as TrapiQuery).log_level || (req.query.log_level as string),
         submitter: (req.body as TrapiQuery).submitter,
-        smartAPIID: req.params.smartapi_id,
-        teamName: req.params.team_name,
         ...req.query,
       },
       params: req.params,

src/routes/bullboard.ts

@@ -23,8 +23,8 @@ class BullBoardPage {
     }
     const queues = {
       "/v1/asynquery": getQueryQueue("bte_query_queue"),
-      "/v1/smartapi/{smartapi_id}/asyncquery": getQueryQueue("bte_query_queue_by_api"),
-      "/v1/team/{team_name}/asyncquery": getQueryQueue("bte_query_queue_by_team"),
+      "/v1/smartapi/{smartAPIID}/asyncquery": getQueryQueue("bte_query_queue_by_api"),
+      "/v1/team/{teamName}/asyncquery": getQueryQueue("bte_query_queue_by_team"),
       "/v1/query": getQueryQueue("bte_sync_query_queue"),
     };
 

src/routes/index.ts

@@ -52,9 +52,9 @@ export const tasks: TaskByRoute = {
   asyncquery_v1_by_team: (taskInfo: TaskInfo) => V1AsyncQueryByTeam.task(taskInfo),
   // load MetaKG from global
   meta_knowledge_graph_v1: (taskInfo: TaskInfo) => V1MetaKG.task(taskInfo),
+  meta_knowledge_graph_v1_by_team: (taskInfo: TaskInfo) => V1MetaKGByTeam.task(taskInfo),
+  meta_knowledge_graph_v1_by_api: (taskInfo: TaskInfo) => V1MetaKGByAPI.task(taskInfo),
   // Not threaded due to being lightweight/speed being higher priority
   // performance: (taskInfo: TaskInfo) => Performance.task(taskInfo),
   // metakg: (taskInfo: TaskInfo) => MetaKG.task(taskInfo),
-  // meta_knowledge_graph_v1_by_api: (taskInfo: TaskInfo) => V1MetaKGByAPI.task(taskInfo),
-  // meta_knowledge_graph_v1_by_team: (taskInfo: TaskInfo) => V1MetaKGByTeam.task(taskInfo),
 };

src/routes/metakg.ts

@@ -18,7 +18,7 @@ class MetaKG {
           if (req.query.provided_by !== undefined) {
             source = utils.removeQuotesFromQuery(req.query.provided_by as string);
           }
-          const assocs = assoc(
+          const assocs = await assoc(
             req.query.subject as string,
             req.query.object as string,
             req.query.predicate as string,

src/routes/v1/asyncquery_v1_by_api.ts

@@ -20,12 +20,12 @@ import { BteRoute } from "../../types";
 class V1AsyncQueryByAPI implements BteRoute {
   setRoutes(app: Express) {
     app
-      .route("/v1/smartapi/:smartapi_id/asyncquery")
+      .route("/v1/smartapi/:smartAPIID/asyncquery")
       .post(swaggerValidation.validate, async (req: Request, res: Response, next: NextFunction) => {
         const queueData: QueueData = {
           route: req.route.path,
           queryGraph: req.body?.message.query_graph,
-          smartAPIID: req.params.smartapi_id,
+          smartAPIID: req.params.smartAPIID,
           workflow: req.body?.workflow,
           callback_url: req.body?.callback,
           options: {

src/routes/v1/asyncquery_v1_by_team.ts

@@ -21,12 +21,12 @@ import { QueueData, TaskInfo } from "@biothings-explorer/types";
 class V1AsyncQueryByTeam implements BteRoute {
   setRoutes(app: Express) {
     app
-      .route("/v1/team/:team_name/asyncquery")
+      .route("/v1/team/:teamName/asyncquery")
       .post(swaggerValidation.validate, (async (req: Request, res: Response, next: NextFunction) => {
         const queueData: QueueData = {
           route: req.route.path,
           queryGraph: req.body?.message.query_graph,
-          teamName: req.params.team_name,
+          teamName: req.params.teamName,
           workflow: req.body?.workflow,
           callback_url: req.body?.callback,
           options: {

src/routes/v1/meta_knowledge_graph_v1.ts

@@ -5,6 +5,8 @@ import * as utils from "../../utils/common";
 import { runTask, taskResponse, taskError } from "../../controllers/threading/threadHandler";
 import { Express, NextFunction, Request, Response, RequestHandler } from "express";
 
+import MetaKnowledgeGraph from "@biothings-explorer/smartapi-kg";
+
 class MetaKG {
   setRoutes(app: Express) {
     app
@@ -23,15 +25,12 @@ class MetaKG {
 
   async task(taskInfo: TaskInfo) {
     try {
-      let kg = undefined;
-
-      // read metakg from files if not globally defined
-      if(!taskInfo.data.options.metakg) {
-        const metaKGHandler = new handler(undefined);
-        kg = await metaKGHandler.getKG(); 
-      } else {
-        kg = taskInfo.data.options.metakg;
-      }
+      const metaKGHandler = new handler(undefined);
+      let metakg = undefined;
+      // initialize MetaKG only if ops are provided because handler logic is built upon that
+      if (taskInfo.data.options.metakg !== undefined)
+        metakg = new MetaKnowledgeGraph(undefined, undefined, taskInfo.data.options.metakg);
+      const kg = await metaKGHandler.getKG(metakg);
       // response.logs = utils.filterForLogLevel(response.logs, options.logLevel);
       return taskResponse(kg);
     } catch (error) {