create smartapi test files

src/controllers/cron/index.ts

@@ -1,7 +1,9 @@
 import smartapiCron from "./update_local_smartapi";
+import testCron from "./test_smartapi";
 import cacheClearCron from "./clear_edge_cache";
 
 export default function scheduleCronJobs() {
  smartapiCron();
  cacheClearCron();
+ testCron();
 }

src/controllers/cron/test_smartapi.ts

@@ -0,0 +1,132 @@
+import MetaKG, { SmartAPIKGOperationObject, TestExampleObject } from "@biothings-explorer/smartapi-kg";
+import { QEdge2APIEdgeHandler, QEdge } from "@biothings-explorer/query_graph_handler";
+import CallAPI from "@biothings-explorer/call-apis";
+import { Telemetry, redisClient } from "@biothings-explorer/utils";
+import Debug from "debug";
+const debug = Debug("bte:biothings-explorer-trapi:cron");
+import cron from "node-cron";
+import path from "path";
+import { stdout } from "process";
+import { spanStatusfromHttpCode } from "@sentry/node";
+const smartAPIPath = path.resolve(
+ __dirname,
+ process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/smartapi_specs.json` : "../../../data/smartapi_specs.json",
+);
+const predicatesPath = path.resolve(
+ __dirname,
+ process.env.STATIC_PATH ? `${process.env.STATIC_PATH}/data/predicates.json` : "../../../data/predicates.json",
+);
+
+interface OpError {
+ op: string;
+ issue: Error;
+}
+
+function generateEdge(op: SmartAPIKGOperationObject, ex: TestExampleObject) {
+ return {
+ subject: {
+ categories: [op.association.input_type],
+ ids: [ex.qInput],
+ id: "n0"
+ },
+ object: {
+ categories: [op.association.output_type],
+ ids: [ex.oneOutput],
+ id: "n1"
+ },
+ predicates: ["biolink:" + op.association.predicate],
+ id: "e01",
+ frozen: true,
+ };
+}
+
+function generateId(op: SmartAPIKGOperationObject, ex: TestExampleObject) {
+ return `${op.association.api_name} [${ex.qInput}-${op.association.predicate}-${ex.oneOutput}]`;
+}
+
+async function runTests(debug = false): Promise<{errors: OpError[], opsCount: number }> {
+ let errors = [];
+ let opsCount = 0;
+ const metakg: MetaKG = global.metakg ? global.metakg : new MetaKG(smartAPIPath, predicatesPath);
+ if (!global.metakg) {
+ metakg.constructMetaKGSync(false);
+ }
+ const ops = metakg.ops;
+ for (const op of ops) { 
+ if (op.testExamples && op.testExamples.length > 0) {
+ opsCount++;
+ }
+ }
+ if (debug) console.log(`Operation Count: ${opsCount}`);
+ let curCount = 0;
+ let errCount = 0;
+ for (const op of ops) {
+ if (op.testExamples && op.testExamples.length > 0) {
+ curCount++;
+ for (const example of op.testExamples) {
+ try {
+ const newMeta = new MetaKG(undefined, undefined, [op]);
+ const edge = new QEdge(generateEdge(op, example));
+ edge.subject.setEquivalentIDs({ [example.qInput]: { primaryID: example.qInput, equivalentIDs: [example.qInput], label: example.qInput, labelAliases: [], primaryTypes: [op.association.input_type], semanticTypes: [op.association.input_type] }})
+ const edgeConverter = new QEdge2APIEdgeHandler([edge], newMeta);
+ const APIEdges = await edgeConverter.convert([edge]);
+ const executor = new CallAPI(APIEdges, {}, redisClient);
+ const records = await executor.query(false, {});
+ if (records.filter(r => r.object.original === example.oneOutput).length <= 0) {
+ errors.push({ op: generateId(op, example), issue: new Error("Record is missing") });
+ errCount++;
+ }
+ } catch (error) {
+ errors.push({ op: generateId(op, example), issue: error });
+ errCount++;
+ }
+ }
+ if (debug) stdout.write("\r\r\r\r\r\r\r\r\r\r\r" + curCount.toString().padStart(4, '0') + " (" + errCount.toString().padStart(4, '0') + ")");
+ }
+ }
+ if (debug) console.log("");
+
+ return { errors, opsCount }
+}
+
+export default function testSmartApi() {
+ // Env set in manual sync script
+ const sync_and_exit = process.env.SYNC_AND_EXIT === "true";
+ if (sync_and_exit) {
+ console.log("Testing SmartAPI specs with subsequent exit...");
+ runTests(true).then(data => {
+ if (data.errors.length === 0) {
+ console.log(`Testing SmartAPI specs successful. ${data.opsCount} operations tested.`);
+ }
+ else {
+ console.log(`Testing SmartAPI specs failed. ${data.errors.length} operations failed.`);
+ data.errors.forEach(err => {
+ console.log(`${err.op}: ${err.issue.message}${err.issue.message = "Record is missing" ? "" : "\n"+err.issue.stack}`);
+ });
+ }
+ process.exit(0);
+ })
+ return;
+ }
+
+ cron.schedule("0 0 * * *", async () => {
+ debug(`Testing SmartAPI specs now at ${new Date().toUTCString()}!`);
+ const span = Telemetry.startSpan({ description: "smartapiTest" });
+ try {
+ const results = await runTests(false);
+ if (results.errors.length === 0) {
+ debug(`Testing SmartAPI specs successful. ${results.opsCount} operations tested.`);
+ }
+ else {
+ debug(`Testing SmartAPI specs failed. ${results.errors.length} operations failed (${results.opsCount} tested).`);
+ results.errors.forEach(err => {
+ debug(`${err.op}: ${err.issue.message}${err.issue.message = "Record is missing" ? "" : "\n"+err.issue.stack}`);
+ Telemetry.captureException(err.issue);
+ });
+ }
+ } catch (err) {
+ debug(`Testing SmartAPI specs failed! The error message is ${err.toString()}`);
+ }
+ span.finish();
+ });
+}