Merge branch 'main' into biolink-4-update

biothings · Mar 7, 2024 · fd578fe · fd578fe
2 parents 3bba1fe + 0b3076f
commit fd578fe
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Showing 4 changed files with 42 additions and 7 deletions.
diff --git a/src/config/apis.js b/src/config/apis.js
@@ -7,9 +7,7 @@ exports.API_LIST = {
  // also accessible by v1/team/Service Provider/ endpoints and by api-specific endpoints
  {
  id: "d22b657426375a5295e7da8a303b9893",
- name: "BioLink API",
- // also known as Monarch: https://monarchinitiative.org/
- // NOT the same as the Biolink-model
+ name: "Monarch API",
  },
  {
  id: "0212611d1c670f9107baf00b77f0889a",
@@ -72,6 +70,14 @@ exports.API_LIST = {
  id: "1f47552dabd67351d4c625adb0a10d00",
  name: "BioThings EBIgene2phenotype API",
  },
+ {
+ id: "f1b8f64c316a01d1722f0fb842499fe5",
+ name: "BioThings FooDB API",
+ },
+ {
+ id: "895ec14a3650ec7ad85959a2d1554e2f",
+ name: "BioThings FoodData Central API",
+ },
  {
  id: "cc857d5b7c8b7609b5bbb38ff990bfff",
  name: "BioThings GO Biological Process API",
@@ -112,6 +118,10 @@ exports.API_LIST = {
  id: "b772ebfbfa536bba37764d7fddb11d6f",
  name: "BioThings RARe-SOURCE API",
  },
+ {
+ id: "1138c3297e8e403b6ac10cff5609b319",
+ name: "BioThings repoDB API",
+ },
  {
  id: "03283cc2b21c077be6794e1704b1d230",
  name: "BioThings Rhea API",

diff --git a/src/controllers/cron/update_local_smartapi.js b/src/controllers/cron/update_local_smartapi.js
@@ -61,6 +61,22 @@ const getServerFromSpec = spec => {
  return sorted_servers[0].url;
 };
 
+const sortObject = object => {
+ if (Array.isArray(object)) {
+ return object.sort();
+ } 
+
+ // apparently typeof null is object
+ if (typeof object === 'object' && object !== null) {
+ return Object.keys(object).sort().reduce((acc, key) => {
+ acc[key] = sortObject(object[key]);
+ return acc;
+ }, {});
+ }
+
+ return object;
+}
+
 const getTRAPIWithPredicatesEndpoint = specs => {
  const trapi = [];
  let excluded_list = config.EXCLUDE_LIST.map(api => api.id);
@@ -192,12 +208,13 @@ const getOpsFromEndpoint = async metadata => {
 
 const getOpsFromPredicatesEndpoints = async specs => {
  const metadatas = getTRAPIWithPredicatesEndpoint(specs);
+ metadatas.sort((a, b) => a.association.smartapi.id.localeCompare(b.association.smartapi.id));
  let res = [];
  debug(`Now caching predicates from ${metadatas.length} TRAPI APIs`);
  await Promise.allSettled(metadatas.map(metadata => getOpsFromEndpoint(metadata))).then(results => {
  results.map(rec => {
  if (rec.status === "fulfilled" && rec.value) {
- res.push(rec.value);
+ res.push(sortObject(rec.value));
  }
  });
  });

diff --git a/src/controllers/threading/taskHandler.js b/src/controllers/threading/taskHandler.js
@@ -44,7 +44,7 @@ try {
  debug(error);
 }
 
-const runTask = async ({ req, route, port, job: { jobId, queueName } = {} }) => {
+const runTask = async ({ req, route, traceparent, tracestate, port, job: { jobId, queueName } = {} }) => {
  debug(`Worker thread ${threadId} beginning ${workerData.queue} task.`);
 
  global.SCHEMA_VERSION = "1.4.0";
@@ -81,7 +81,7 @@ const runTask = async ({ req, route, port, job: { jobId, queueName } = {} }) =>
  scope.setSpan(transaction);
  });
 
- span = opentelemetry.trace.getTracer('biothings-explorer-thread').startSpan(routeNames[route])
+ span = opentelemetry.trace.getTracer('biothings-explorer-thread').startSpan(routeNames[route], undefined, opentelemetry.propagation.extract(opentelemetry.context.active(), {traceparent, tracestate}))
  span.setAttribute("bte.requestData", JSON.stringify(req.data.queryGraph));
  Telemetry.setOtelSpan(span);
  } catch (error) {

diff --git a/src/controllers/threading/threadHandler.js b/src/controllers/threading/threadHandler.js
@@ -1,4 +1,5 @@
 const { MessageChannel, threadId } = require("worker_threads");
+const { context, propagation, trace } = require("@opentelemetry/api");
 const debug = require("debug")("bte:biothings-explorer-trapi:threading");
 const path = require("path");
 // const taskHandler = require("./taskHandler");
@@ -98,7 +99,14 @@ const queueTaskToWorkers = async (pool, req, route, job) => {
  let WorkerThreadID;
  const abortController = new AbortController();
  const { port1: toWorker, port2: fromWorker } = new MessageChannel();
- const taskData = { req, route, port: toWorker };
+
+ // get otel context
+ const otelData = {};
+ propagation.inject(context.active(), otelData);
+ const { traceparent, tracestate } = otelData;
+
+
+ const taskData = { req, route, traceparent, tracestate, port: toWorker };
  if (job) taskData.job = { jobId: job.id, queueName: job.queue.name };
  const task = pool.run(taskData, { signal: abortController.signal, transferList: [toWorker] });
  if (job) {