Merge branch 'main' into kg-refactor

biothings · Mar 9, 2024 · 5d1017b · 5d1017b
2 parents 2d3235d + 0b3076f
commit 5d1017b
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Showing 5 changed files with 44 additions and 16 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/config/smartapi_overrides.json b/src/config/smartapi_overrides.json
@@ -2,12 +2,5 @@
   "conf": {
     "only_overrides": false
   },
-  "apis": {
-    "671b45c0301c8624abbd26ae78449ca2": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/orphanet-change/mydisease.info/smartapi.yaml",
-    "b772ebfbfa536bba37764d7fddb11d6f": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/orphanet-change/ncats_rare_source/smartapi.yaml",
-    "326eb1e437303bee27d3cef29227125d": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/orphanet-change/complexportal/smartapi.yaml",
-    "0212611d1c670f9107baf00b77f0889a": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/ctd-batch-query/CTD/smartapi.yaml",
-    "8f08d1446e0bb9c2b323713ce83e2bd3": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/mychem-fda-orphan-edit/mychem.info/openapi_full.yml",
-    "d22b657426375a5295e7da8a303b9893": "https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/v3-biolink-monarch/biolink/openapi.yml"
-  }
+  "apis": {}
 }
diff --git a/src/controllers/cron/update_local_smartapi.js b/src/controllers/cron/update_local_smartapi.js
@@ -63,6 +63,22 @@ 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);
@@ -194,12 +210,13 @@ 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");
@@ -98,8 +99,15 @@ 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 };
-    taskData.req.data.options = {...taskData.req.optoins, metakg: global.metakg?.ops};
+
+    // get otel context
+    const otelData = {};
+    propagation.inject(context.active(), otelData);
+    const { traceparent, tracestate } = otelData;
+
+    const taskData = { req, route, traceparent, tracestate, port: toWorker };
+    taskData.req.data.options = {...taskData.req.data.options, metakg: global.metakg?.ops};
+
     if (job) taskData.job = { jobId: job.id, queueName: job.queue.name };
     const task = pool.run(taskData, { signal: abortController.signal, transferList: [toWorker] });
     if (job) {