From b8c3648231912b43bcf8a814b92cc24796a297e7 Mon Sep 17 00:00:00 2001
From: NeuralFlux <40491005+NeuralFlux@users.noreply.github.com>
Date: Thu, 10 Oct 2024 13:14:49 -0400
Subject: [PATCH 1/5] fix: make otel tracing leaner and synchronous

---
 package.json                               |  2 +-
 src/controllers/opentelemetry.ts           | 14 +++++++++-----
 src/controllers/threading/taskHandler.ts   |  3 +--
 src/controllers/threading/threadHandler.ts |  7 ++++++-
 4 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/package.json b/package.json
index d24b3de..2a7c03e 100644
--- a/package.json
+++ b/package.json
@@ -81,10 +81,10 @@
     "@bull-board/api": "^5.9.1",
     "@bull-board/express": "^5.9.1",
     "@opentelemetry/api": "^1.7.0",
-    "@opentelemetry/auto-instrumentations-node": "^0.44.0",
     "@opentelemetry/exporter-jaeger": "^1.19.0",
     "@opentelemetry/exporter-metrics-otlp-proto": "^0.50.0",
     "@opentelemetry/exporter-trace-otlp-proto": "^0.50.0",
+    "@opentelemetry/instrumentation-http": "^0.53.0",
     "@opentelemetry/resources": "^1.18.1",
     "@opentelemetry/sdk-metrics": "^1.18.1",
     "@opentelemetry/sdk-node": "^0.50.0",
diff --git a/src/controllers/opentelemetry.ts b/src/controllers/opentelemetry.ts
index e05793a..4e5dfa1 100644
--- a/src/controllers/opentelemetry.ts
+++ b/src/controllers/opentelemetry.ts
@@ -1,5 +1,6 @@
 import { NodeSDK } from "@opentelemetry/sdk-node";
-import { getNodeAutoInstrumentations } from "@opentelemetry/auto-instrumentations-node";
+import { SimpleSpanProcessor } from "@opentelemetry/sdk-trace-node";
+import { HttpInstrumentation } from "@opentelemetry/instrumentation-http";
 import { Resource } from "@opentelemetry/resources";
 import Debug from "debug";
 import { OTLPTraceExporter } from '@opentelemetry/exporter-trace-otlp-proto';
@@ -9,17 +10,20 @@ import { ATTR_SERVICE_NAME } from '@opentelemetry/semantic-conventions';
 const jaegerHost = process.env.JAEGER_HOST ?? 'jaeger-otel-collector.sri';
 const jaegerPort = process.env.JAEGER_PORT ?? 4318;
 const jaegerResName = process.env.JAEGER_RES_NAME ?? '/v1/traces';
+const traceExporter = new OTLPTraceExporter({
+  url: `http://${jaegerHost}:${jaegerPort}${jaegerResName}`
+});
 
 debug("Initializing Opentelemetry instrumentation...");
 const sdk = new NodeSDK({
   // metrics, if needed, shall be exported on a different endpoint
-  traceExporter: new OTLPTraceExporter({
-    url: `http://${jaegerHost}:${jaegerPort}${jaegerResName}`
-  }),
-  instrumentations: [getNodeAutoInstrumentations()],
+  // trace a subset of instrumentations to avoid performance overhead
+  instrumentations: [new HttpInstrumentation()],
   resource: new Resource({
     [ATTR_SERVICE_NAME]: "biothings-explorer",
   }),
+  // use simple span processor to avoid losing data when the forked process exits (taskHandler)
+  spanProcessors: [new SimpleSpanProcessor(traceExporter)],
 });
 debug(`OTel URL http://${jaegerHost}:${jaegerPort}${jaegerResName}`);
 sdk.start();
diff --git a/src/controllers/threading/taskHandler.ts b/src/controllers/threading/taskHandler.ts
index 78b2629..4e9705a 100644
--- a/src/controllers/threading/taskHandler.ts
+++ b/src/controllers/threading/taskHandler.ts
@@ -91,14 +91,13 @@ async function runTask({
     });
 
     let activeContext: Context = propagation.extract(context.active(), { traceparent, tracestate });
-    debug(`OTel task ${traceparent} and ${tracestate}`);
+    debug(`OTel task context: ${traceparent} and ${tracestate}`);
     let tracer = trace.getTracer("biothings-explorer-thread")
     span = tracer.startSpan(
       routeNames[route],
       {kind: 1},  // specifies internal span
       activeContext,
     );
-    debug(`OTel span created ${span}`);
   
     span.setAttribute("bte.requestData", JSON.stringify(req.data.queryGraph));
     Telemetry.setOtelSpan(span);
diff --git a/src/controllers/threading/threadHandler.ts b/src/controllers/threading/threadHandler.ts
index e9a595c..894caa8 100644
--- a/src/controllers/threading/threadHandler.ts
+++ b/src/controllers/threading/threadHandler.ts
@@ -1,6 +1,6 @@
 import { MessageChannel, threadId } from "worker_threads";
 import Debug from "debug";
-import { context, propagation } from "@opentelemetry/api";
+import { context, propagation, trace } from "@opentelemetry/api";
 const debug = Debug("bte:biothings-explorer-trapi:threading");
 import path from "path";
 import { redisClient } from "@biothings-explorer/utils";
@@ -221,6 +221,11 @@ export async function runTask(req: Request, res: Response, route: string, useBul
   propagation.inject(context.active(), otelData);
   const { traceparent, tracestate } = otelData;
 
+  // add req dest to root span name as HTTP instrumentation doesn't do it automatically
+  const activeContext = context.active();
+  const rootSpan = trace.getSpan(activeContext);
+  rootSpan.updateName(`${req.method} ${req.originalUrl}`);
+
   const taskInfo: TaskInfo = {
     data: {
       route,

From 677886ccd47a3b455484c448a5dfb362ea442307 Mon Sep 17 00:00:00 2001
From: NeuralFlux <40491005+NeuralFlux@users.noreply.github.com>
Date: Thu, 10 Oct 2024 13:44:44 -0400
Subject: [PATCH 2/5] chore: ignore ts lint error

---
 src/controllers/opentelemetry.ts | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/controllers/opentelemetry.ts b/src/controllers/opentelemetry.ts
index 4e5dfa1..252b286 100644
--- a/src/controllers/opentelemetry.ts
+++ b/src/controllers/opentelemetry.ts
@@ -23,6 +23,7 @@ const sdk = new NodeSDK({
     [ATTR_SERVICE_NAME]: "biothings-explorer",
   }),
   // use simple span processor to avoid losing data when the forked process exits (taskHandler)
+  // @ts-ignore - fix from MetinSeylan/Nestjs-OpenTelemetry#63
   spanProcessors: [new SimpleSpanProcessor(traceExporter)],
 });
 debug(`OTel URL http://${jaegerHost}:${jaegerPort}${jaegerResName}`);

From daac52bc50358bba542810f0538ae5779ce12ccd Mon Sep 17 00:00:00 2001
From: NeuralFlux <40491005+NeuralFlux@users.noreply.github.com>
Date: Thu, 10 Oct 2024 13:57:56 -0400
Subject: [PATCH 3/5] fix: update root span only if it exists

---
 src/controllers/threading/threadHandler.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/controllers/threading/threadHandler.ts b/src/controllers/threading/threadHandler.ts
index 894caa8..5a8a771 100644
--- a/src/controllers/threading/threadHandler.ts
+++ b/src/controllers/threading/threadHandler.ts
@@ -224,7 +224,7 @@ export async function runTask(req: Request, res: Response, route: string, useBul
   // add req dest to root span name as HTTP instrumentation doesn't do it automatically
   const activeContext = context.active();
   const rootSpan = trace.getSpan(activeContext);
-  rootSpan.updateName(`${req.method} ${req.originalUrl}`);
+  if (rootSpan != undefined) rootSpan.updateName(`${req.method} ${req.originalUrl}`);
 
   const taskInfo: TaskInfo = {
     data: {

From 08aefaabf08440bf1b34dd7d7959cd258a0f2edc Mon Sep 17 00:00:00 2001
From: NeuralFlux <40491005+NeuralFlux@users.noreply.github.com>
Date: Thu, 10 Oct 2024 14:01:10 -0400
Subject: [PATCH 4/5] chore: add type hints to otel vars

---
 src/controllers/threading/taskHandler.ts   | 4 ++--
 src/controllers/threading/threadHandler.ts | 6 +++---
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/controllers/threading/taskHandler.ts b/src/controllers/threading/taskHandler.ts
index 4e9705a..1a42dbd 100644
--- a/src/controllers/threading/taskHandler.ts
+++ b/src/controllers/threading/taskHandler.ts
@@ -14,7 +14,7 @@ import { tasks } from "../../routes/index";
 import { getQueryQueue } from "../async/asyncquery_queue";
 import * as Sentry from "@sentry/node";
 import { ProfilingIntegration } from "@sentry/profiling-node";
-import { Span, trace, context, propagation, Context } from "@opentelemetry/api";
+import { Span, trace, context, propagation, Context, Tracer } from "@opentelemetry/api";
 import { Telemetry } from "@biothings-explorer/utils";
 import { InnerTaskData } from "@biothings-explorer/types";
 
@@ -92,7 +92,7 @@ async function runTask({
 
     let activeContext: Context = propagation.extract(context.active(), { traceparent, tracestate });
     debug(`OTel task context: ${traceparent} and ${tracestate}`);
-    let tracer = trace.getTracer("biothings-explorer-thread")
+    let tracer: Tracer = trace.getTracer("biothings-explorer-thread")
     span = tracer.startSpan(
       routeNames[route],
       {kind: 1},  // specifies internal span
diff --git a/src/controllers/threading/threadHandler.ts b/src/controllers/threading/threadHandler.ts
index 5a8a771..c23e69c 100644
--- a/src/controllers/threading/threadHandler.ts
+++ b/src/controllers/threading/threadHandler.ts
@@ -1,6 +1,6 @@
 import { MessageChannel, threadId } from "worker_threads";
 import Debug from "debug";
-import { context, propagation, trace } from "@opentelemetry/api";
+import { context, propagation, trace, Context, Span } from "@opentelemetry/api";
 const debug = Debug("bte:biothings-explorer-trapi:threading");
 import path from "path";
 import { redisClient } from "@biothings-explorer/utils";
@@ -222,8 +222,8 @@ export async function runTask(req: Request, res: Response, route: string, useBul
   const { traceparent, tracestate } = otelData;
 
   // add req dest to root span name as HTTP instrumentation doesn't do it automatically
-  const activeContext = context.active();
-  const rootSpan = trace.getSpan(activeContext);
+  const activeContext: Context = context.active();
+  const rootSpan: Span = trace.getSpan(activeContext);
   if (rootSpan != undefined) rootSpan.updateName(`${req.method} ${req.originalUrl}`);
 
   const taskInfo: TaskInfo = {

From 0d30d9b56d6188223874edf93e48d3401c6e0d5f Mon Sep 17 00:00:00 2001
From: NeuralFlux <40491005+NeuralFlux@users.noreply.github.com>
Date: Thu, 10 Oct 2024 17:50:59 -0400
Subject: [PATCH 5/5] fix: switch to BatchSpanProcessor and flush spans when
 thread exits

---
 src/controllers/opentelemetry.ts         | 15 +++++++++++----
 src/controllers/threading/taskHandler.ts |  2 ++
 2 files changed, 13 insertions(+), 4 deletions(-)

diff --git a/src/controllers/opentelemetry.ts b/src/controllers/opentelemetry.ts
index 252b286..77b81e3 100644
--- a/src/controllers/opentelemetry.ts
+++ b/src/controllers/opentelemetry.ts
@@ -1,5 +1,5 @@
 import { NodeSDK } from "@opentelemetry/sdk-node";
-import { SimpleSpanProcessor } from "@opentelemetry/sdk-trace-node";
+import { BatchSpanProcessor } from "@opentelemetry/sdk-trace-node";
 import { HttpInstrumentation } from "@opentelemetry/instrumentation-http";
 import { Resource } from "@opentelemetry/resources";
 import Debug from "debug";
@@ -10,9 +10,11 @@ import { ATTR_SERVICE_NAME } from '@opentelemetry/semantic-conventions';
 const jaegerHost = process.env.JAEGER_HOST ?? 'jaeger-otel-collector.sri';
 const jaegerPort = process.env.JAEGER_PORT ?? 4318;
 const jaegerResName = process.env.JAEGER_RES_NAME ?? '/v1/traces';
+
 const traceExporter = new OTLPTraceExporter({
   url: `http://${jaegerHost}:${jaegerPort}${jaegerResName}`
 });
+const spanProcessor = new BatchSpanProcessor(traceExporter);
 
 debug("Initializing Opentelemetry instrumentation...");
 const sdk = new NodeSDK({
@@ -22,10 +24,15 @@ const sdk = new NodeSDK({
   resource: new Resource({
     [ATTR_SERVICE_NAME]: "biothings-explorer",
   }),
-  // use simple span processor to avoid losing data when the forked process exits (taskHandler)
-  // @ts-ignore - fix from MetinSeylan/Nestjs-OpenTelemetry#63
-  spanProcessors: [new SimpleSpanProcessor(traceExporter)],
+  // @ts-ignore because MetinSeylan/Nestjs-OpenTelemetry#63
+  spanProcessors: [spanProcessor],
 });
 debug(`OTel URL http://${jaegerHost}:${jaegerPort}${jaegerResName}`);
 sdk.start();
 debug("Opentelemetry instrumentation initialized.");
+
+export async function flushRemainingSpans(): Promise<void> {
+  // avoid losing any spans in the buffer when taskHandler exits
+  debug("Flushing remaining spans...");
+  await spanProcessor.forceFlush();
+}
diff --git a/src/controllers/threading/taskHandler.ts b/src/controllers/threading/taskHandler.ts
index 1a42dbd..b22ae41 100644
--- a/src/controllers/threading/taskHandler.ts
+++ b/src/controllers/threading/taskHandler.ts
@@ -17,6 +17,7 @@ import { ProfilingIntegration } from "@sentry/profiling-node";
 import { Span, trace, context, propagation, Context, Tracer } from "@opentelemetry/api";
 import { Telemetry } from "@biothings-explorer/utils";
 import { InnerTaskData } from "@biothings-explorer/types";
+import { flushRemainingSpans } from "../opentelemetry";
 
 // use SENTRY_DSN environment variable
 try {
@@ -113,6 +114,7 @@ async function runTask({
     transaction.finish();
     span.end();
     Telemetry.removeOtelSpan();
+    await flushRemainingSpans();
   } catch (error) {
     debug("Sentry/OpenTelemetry transaction finish error. This does not affect execution.");
     debug(error);