Add opentelemetry support

biothings_annotator/application/cli/target.py

@@ -19,6 +19,7 @@
 from biothings_annotator.application.views import build_routes
 from biothings_annotator.application.middleware import build_middleware
 from biothings_annotator.application.exceptions import build_exception_handers
+from biothings_annotator.application.telemetry import instrument_application_telemetry
 
 logging.basicConfig()
 logger = logging.getLogger("sanic-application")
@@ -94,4 +95,5 @@ class Sanic(
             logger.error("Unable to add exception handler %s", exception_handler)
             raise gen_exc
 
+    instrument_application_telemetry(application)
     return application

biothings_annotator/application/configuration/default.json

@@ -7,6 +7,12 @@
             "REQUEST_MAX_SIZE": 100000000,
             "CACHE_MAX_AGE": 604800
         },
+        "opentelemetry": {
+            "OPENTELEMETRY_ENABLED": false,
+            "OPENTELEMETRY_SERVICE_NAME": "biothings-annotator",
+            "OPENTELEMETRY_JAEGER_HOST": "http://localhost", 
+            "OPENTELEMETRY_JAEGER_PORT": 6381
+        },
         "extension": {
             "openapi": {
                 "OAS": true,

biothings_annotator/application/telemetry/__init__.py

@@ -0,0 +1,40 @@
+"""
+Integrates opentelemetry tracing with the biothings-annotator
+web service
+"""
+
+import opentelemetry
+from opentelemetry.exporter.jaeger.thrift import JaegerExporter
+from opentelemetry.sdk.resources import SERVICE_NAME, Resource
+from opentelemetry.sdk.trace import TracerProvider
+from opentelemetry.sdk.trace.export import BatchSpanProcessor
+import sanic
+from tracing import instrument_app
+
+
+def instrument_application_telemetry(application_instance: sanic.Sanic):
+    """
+    Method integrating the opentelemetry into the annotator
+    web service
+    """
+    opentelemetry_configuration = application_instance.config.get("opentelemetry", {})
+    opentelemetry_enabled = opentelemetry_configuration.get("OPENTELEMETRY_ENABLED", False)
+
+    if opentelemetry_enabled:
+        opentelemetry_jaeger_host = opentelemetry_configuration["OPENTELEMETRY_JAEGER_HOST"]
+        opentelemetry_jaeger_port = opentelemetry_configuration["OPENTELEMETRY_JAEGER_PORT"]
+        opentelemetry_service_name = opentelemetry_configuration["OPENTELEMETRY_SERVICE_NAME"]
+
+        jaeger_trace_exporter = JaegerExporter(
+            agent_host_name=opentelemetry_jaeger_host,
+            agent_port=opentelemetry_jaeger_port,
+            udp_split_oversized_batches=True,
+        )
+        service_resource = Resource.create({SERVICE_NAME: opentelemetry_service_name})
+
+        trace_provider = TracerProvider(resource=service_resource)
+        batch_span_processor = BatchSpanProcessor(jaeger_trace_exporter)
+        trace_provider.add_span_processor(batch_span_processor)
+        opentelemetry.trace.set_tracer_provider(trace_provider)
+        tracer = opentelemetry.trace.get_tracer("biothings-annotator")
+        instrument_app(application_instance, tracer)

pyproject.toml

@@ -52,7 +52,13 @@ tests = [
     "sanic-testing >= 24.6.0",
     "pytest-randomly"
 ]
-
+telemetry = [
+    "opentelemetry-api >= 1.28.2",
+    "opentelemetry-sdk >= 1.28.2",
+    "opentelemetry-exporter-otlp >= 1.28.2",
+    "opentelemetry.exporter.jaeger.thrift >= 1.21.0",
+    "opentelemetry-instrumentation >= 0.49b2"
+]
 
 [project.urls]
 "Homepage" = "https://github.com/biothings/biothings_annotator"