add jaeger opentelementry

backend/app/main.py

@@ -1,3 +1,5 @@
+import logging
+import os
 from fastapi.responses import RedirectResponse
 from starlette.middleware.cors import CORSMiddleware
 from starlette.middleware.sessions import SessionMiddleware
@@ -46,3 +48,46 @@ def health_check():
 def redirect_root_to_docs():
     """Redirect the route / to /docs"""
     return RedirectResponse(url="/docs")
+
+
+def configure_otel(app):
+    # open telemetry https://github.com/ranking-agent/aragorn/blob/main/src/otel_config.py#L4
+    # https://ncatstranslator.github.io/TranslatorTechnicalDocumentation/deployment-guide/monitoring/
+    # https://github.com/TranslatorSRI/Jaeger-demo
+    if not os.environ.get('NO_JAEGER'):
+        logging.info("starting up jaeger telemetry")
+        import warnings
+        from opentelemetry.instrumentation.fastapi import FastAPIInstrumentor
+        from opentelemetry import trace
+        from opentelemetry.exporter.jaeger.thrift import JaegerExporter
+        from opentelemetry.sdk.resources import SERVICE_NAME as telemetery_service_name_key, Resource
+        from opentelemetry.sdk.trace import TracerProvider
+        from opentelemetry.sdk.trace.export import BatchSpanProcessor
+        from opentelemetry.instrumentation.httpx import HTTPXClientInstrumentor
+
+        service_name = os.environ.get('OTEL_SERVICE_NAME', 'OPENPREDICT')
+        # httpx connections need to be open a little longer by the otel decorators
+        # but some libs display warnings of resource being unclosed.
+        # these supresses such warnings.
+        logging.captureWarnings(capture=True)
+        warnings.filterwarnings("ignore",category=ResourceWarning)
+        trace.set_tracer_provider(
+            TracerProvider(
+                resource=Resource.create({telemetery_service_name_key: service_name})
+            )
+        )
+        jaeger_host = os.environ.get('JAEGER_HOST', 'jaeger-otel-agent.sri')
+        jaeger_port = int(os.environ.get('JAEGER_PORT', '6831'))
+        jaeger_exporter = JaegerExporter(
+            agent_host_name=jaeger_host,
+            agent_port=jaeger_port,
+        )
+        trace.get_tracer_provider().add_span_processor(
+            BatchSpanProcessor(jaeger_exporter)
+        )
+        # tracer = trace.get_tracer(__name__)
+        FastAPIInstrumentor.instrument_app(app, tracer_provider=trace, excluded_urls="docs,openapi.json")
+        HTTPXClientInstrumentor().instrument()
+
+# Configure open telemetry if enabled
+configure_otel(app)

backend/pyproject.toml

@@ -40,6 +40,11 @@ dependencies = [
     # "kgx >=1.6.0",
     "rdflib >=6.1.1",
     "SPARQLWrapper >=1.8.5",
+
+    "opentelemetry-sdk",
+    "opentelemetry-exporter-otlp-proto-http",
+    "opentelemetry-instrumentation-fastapi",
+    "opentelemetry-instrumentation-httpx",
 ]
 
 [project.optional-dependencies]
@@ -121,12 +126,13 @@ itrb-test = "pytest tests/production --server https://collaboratory-api.test.tra
 itrb-prod = "pytest tests/production --server https://collaboratory-api.transltr.io {args}"
 
 
+# OTHER TOOLS
+[tool.hatch.build.targets.wheel]
+packages = ["app"]
+
 [tool.hatch.metadata]
 allow-direct-references = true
 
-
-# OTHER TOOLS
-
 [tool.coverage.run]
 source = ["app"]
 branch = true

docker-compose.override.yml

@@ -13,6 +13,7 @@ services:
       - FRONTEND_URL=http://localhost:19006
       - INSTALL_DEV=true
       - DEV_MODE=true
+      - NO_JAEGER=true
     build:
       context: ./backend
       dockerfile: Dockerfile

docker-compose.prod.yml

@@ -11,6 +11,7 @@ services:
       VIRTUAL_PORT: 80
       VIRTUAL_HOST: api.collaboratory.semanticscience.org
       LETSENCRYPT_HOST: api.collaboratory.semanticscience.org
+      NO_JAEGER: "true"
     volumes:
       - /data/knowledge-collaboratory/ner-models:/data/ner-models
       - /data/knowledge-collaboratory/nanopub-keystore:/data/nanopub-keystore

docker-compose.yml

@@ -9,6 +9,8 @@ services:
         INSTALL_DEV: ${INSTALL_DEV-false}
     env_file:
       - .env
+    environment:
+      - NO_JAEGER=true
     volumes:
       - /data/knowledge-collaboratory/ner-models:/data/ner-models
       - /data/knowledge-collaboratory/nanopub-keystore:/data/nanopub-keystore