diff --git a/README.md b/README.md index 756db1a9f..32318c9a4 100644 --- a/README.md +++ b/README.md @@ -33,17 +33,20 @@ - [3. Start the virtual environment](#3-start-the-virtual-environment) - [4. Install `schematic` dependencies](#4-install-schematic-dependencies) - [5. Set up configuration files](#5-set-up-configuration-files) - - [6. Obtain Google credential files](#6-obtain-google-credential-files) + - [6. Obtain Google credential files](#6-obtain-google-credential-files-1) - [7. Set up pre-commit hooks](#7-set-up-pre-commit-hooks) - [8. Verify your setup](#8-verify-your-setup) - [Command Line Usage](#command-line-usage) - [Docker Usage](#docker-usage) - - [Running the REST API](#running-the-rest-api) - - [Example 1: Using the `config.yml` path](#example-1-using-the-configyml-path) - - [Example 2: Use environment variables](#example-2-use-environment-variables) - - [Running `schematic` to Validate Manifests](#running-schematic-to-validate-manifests) - - [Example for macOS/Linux](#example-for-macoslinux) - - [Example for Windows](#example-for-windows) + - [Running the REST API](#running-the-rest-api) + - [Example 1: Using the `config.yml` path](#example-1-using-the-configyml-path) + - [Example 2: Use environment variables](#example-2-use-environment-variables) + - [Running `schematic` to Validate Manifests](#running-schematic-to-validate-manifests) + - [Example for macOS/Linux](#example-for-macoslinux) + - [Example for Windows](#example-for-windows) +- [Exporting OpenTelemetry data from schematic](#exporting-opentelemetry-data-from-schematic) + - [Exporting OpenTelemetry data for SageBionetworks employees](#exporting-opentelemetry-data-for-sagebionetworks-employees) + - [Exporting data locally](#exporting-data-locally) - [Contributors](#contributors) @@ -487,6 +490,67 @@ docker run -v %cd%:/schematic \ -c config.yml validate -mp tests/data/mock_manifests/inValid_Test_Manifest.csv -dt MockComponent -js /schematic/data/example.model.jsonld ``` +# Exporting OpenTelemetry data from schematic +This section is geared towards the SageBionetworks specific deployment of schematic as +an API server running in the Sage specific AWS account. + + +Schematic is setup to produce and export OpenTelemetry data while requests are flowing +through the application code. This may be accomplished by setting a few environment +variables wherever the application is running. Those variables are: + +- `TRACING_EXPORT_FORMAT`: Determines in what format traces will be exported. Supported values: [`otlp`]. +- `LOGGING_EXPORT_FORMAT`: Determines in what format logs will be exported. Supported values: [`otlp`]. +- `TRACING_SERVICE_NAME`: The name of the service to attach for all exported traces. +- `LOGGING_SERVICE_NAME`: The name of the service to attach for all exported logs. +- `DEPLOYMENT_ENVIRONMENT`: The name of the environment to attach for all exported telemetry data. +- `OTEL_EXPORTER_OTLP_ENDPOINT`: The endpoint to export telemetry data to. + +Authentication (Oauth2 client credential exchange): + +Used in cases where an intermediate opentelemetry collector is not, or can not be used. +This option is not preferred over using an intermediate opentelemetry collector, but is +left in the code to show how we may export telemetry data with an authorization header +deried from an oauth2 client credential exchange flow. + +- `TELEMETRY_EXPORTER_CLIENT_ID`: The ID of the client to use when executing the OAuth2.0 "Client Credentials" flow. +- `TELEMETRY_EXPORTER_CLIENT_SECRET`: The Secret of the client to use when executing the OAuth2.0 "Client Credentials" flow. +- `TELEMETRY_EXPORTER_CLIENT_TOKEN_ENDPOINT`: The Token endpoint to use when executing the OAuth2.0 "Client Credentials" flow. +- `TELEMETRY_EXPORTER_CLIENT_AUDIENCE`: The ID of the API server to use when executing the OAuth2.0 "Client Credentials" flow. + +Authentication (Static Bearer token) + +- `OTEL_EXPORTER_OTLP_HEADERS`: Used for developers to set a static Bearer token to be used when exporting telemetry data. + +The above configuration will work when the application is running locally, in a +container, running in AWS, or running via CLI. The important part is that the +environment variables are set before the code executes, as the configuration is setup +when the code runs. + +## Exporting OpenTelemetry data for SageBionetworks employees +The DPE (Data Processing & Engineering) team is responsible for maintaining and giving +out the above sensitive information. Please reach out to the DPE team if a new ID/Secret +is needed in order to export telemetry data in a new environment, or locally during +development. + +### Exporting data locally +In order to conserve the number of monthly token requests that can be made the following +process should be followed instead of setting the `TELEMETRY_EXPORTER_CLIENT_*` +environment variables above. + +1) Request access to a unique client ID/Secret that identifies you from DPE. +2) Retrieve a token that must be refreshed every 24 hours via cURL. The specific values will be given when the token is requested. Example: +``` +curl --request POST \ + --url https://TOKEN_URL.us.auth0.com/oauth/token \ + --header 'content-type: application/json' \ + --data '{"client_id":"...","client_secret":"...","audience":"...","grant_type":"client_credentials"}' +``` +3) Set an environment variable in your `.env` file like: `OTEL_EXPORTER_OTLP_HEADERS=Authorization=Bearer ey...` + +If you fail to create a new access token after 24 hours you will see HTTP 403 JWT +Expired messages when the application attempts to export telemetry data. + # Contributors Main contributors and developers: diff --git a/env.example b/env.example index 8b88f00fd..f1f56a8a4 100644 --- a/env.example +++ b/env.example @@ -13,6 +13,15 @@ SERVICE_ACCOUNT_CREDS='Provide service account creds' # LOGGING_SERVICE_NAME=schematic-api ## Other examples: dev, staging, prod # DEPLOYMENT_ENVIRONMENT=local +# OTEL_EXPORTER_OTLP_ENDPOINT=https://..../telemetry +## Opentelemetry authentication +# TELEMETRY_EXPORTER_CLIENT_ID=... +# TELEMETRY_EXPORTER_CLIENT_SECRET-... +# TELEMETRY_EXPORTER_CLIENT_TOKEN_ENDPOINT=... +# TELEMETRY_EXPORTER_CLIENT_AUDIENCE=... +## Alternative Opentelemetry authentication: Sets a static Authorization header to use for all requests. Used when developing locally +# OTEL_EXPORTER_OTLP_HEADERS=Authorization=Bearer ey... + # Used during integration test run to determine if files will be output for manual # inspection. These tests cannot fully finish all validation via code. 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"3.20.2" +version = "3.21.0" description = "Backport of pathlib-compatible object wrapper for zip files" optional = false -python-versions = ">=3.8" +python-versions = ">=3.9" files = [ - {file = "zipp-3.20.2-py3-none-any.whl", hash = "sha256:a817ac80d6cf4b23bf7f2828b7cabf326f15a001bea8b1f9b49631780ba28350"}, - {file = "zipp-3.20.2.tar.gz", hash = "sha256:bc9eb26f4506fda01b81bcde0ca78103b6e62f991b381fec825435c836edbc29"}, + {file = "zipp-3.21.0-py3-none-any.whl", hash = "sha256:ac1bbe05fd2991f160ebce24ffbac5f6d11d83dc90891255885223d42b3cd931"}, + {file = "zipp-3.21.0.tar.gz", hash = "sha256:2c9958f6430a2040341a52eb608ed6dd93ef4392e02ffe219417c1b28b5dd1f4"}, ] [package.extras] @@ -4920,10 +4897,10 @@ test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", type = ["pytest-mypy"] [extras] -api = ["Flask", "Flask-Cors", "Jinja2", "connexion", "opentelemetry-api", "opentelemetry-exporter-otlp-proto-grpc", "opentelemetry-instrumentation-flask", "opentelemetry-sdk", "pyopenssl"] +api = ["Flask", "Flask-Cors", "Jinja2", "connexion", "opentelemetry-api", "opentelemetry-exporter-otlp-proto-http", "opentelemetry-instrumentation-flask", "opentelemetry-sdk", "pyopenssl", "requests-oauth2client"] aws = ["uWSGI"] [metadata] lock-version = "2.0" python-versions = ">=3.9.0,<3.11" -content-hash = "dae73881beabf04e3a742f695e99b965bca94e2ac4d8dd4719ae650247b407ec" +content-hash = "e6a9548ab006a486b1f64fecfd32177821b373ad8b6a4528e79a38449cfe8065" diff --git a/pyproject.toml b/pyproject.toml index 849b5eb09..5751cf41e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -73,11 +73,12 @@ asyncio = "^3.4.3" PyJWT = "^2.9.0" opentelemetry-api = {version = ">=1.21.0", optional = true} opentelemetry-sdk = {version = ">=1.21.0", optional = true} -opentelemetry-exporter-otlp-proto-grpc = {version="^1.0.0", optional = true} -opentelemetry-instrumentation-flask = {version=">=0.48b0 ", optional = true} +opentelemetry-exporter-otlp-proto-http = {version="^1.0.0", optional = true} +opentelemetry-instrumentation-flask = {version=">=0.48b0", optional = true} +requests-oauth2client = {version=">=1.6.0", optional = true} [tool.poetry.extras] -api = ["connexion", "Flask", "Flask-Cors", "Jinja2", "pyopenssl", "opentelemetry-api", "opentelemetry-sdk", "opentelemetry-exporter-otlp-proto-grpc", "opentelemetry-instrumentation-flask"] +api = ["connexion", "Flask", "Flask-Cors", "Jinja2", "pyopenssl", "opentelemetry-api", "opentelemetry-sdk", "opentelemetry-exporter-otlp-proto-http", "opentelemetry-instrumentation-flask", "requests-oauth2client"] aws = ["uWSGI"] [tool.poetry.group.dev.dependencies] diff --git a/schematic/__init__.py b/schematic/__init__.py index 8b5e924b1..718feb6a3 100644 --- a/schematic/__init__.py +++ b/schematic/__init__.py @@ -1,30 +1,20 @@ import logging import os -import time from typing import Dict, List -import pkg_resources +import requests from opentelemetry import trace from opentelemetry._logs import set_logger_provider -from opentelemetry.exporter.otlp.proto.grpc._log_exporter import OTLPLogExporter -from opentelemetry.exporter.otlp.proto.grpc.trace_exporter import OTLPSpanExporter +from opentelemetry.exporter.otlp.proto.http._log_exporter import OTLPLogExporter +from opentelemetry.exporter.otlp.proto.http.trace_exporter import OTLPSpanExporter from opentelemetry.instrumentation.flask import FlaskInstrumentor from opentelemetry.sdk._logs import LoggerProvider, LoggingHandler from opentelemetry.sdk._logs.export import BatchLogRecordProcessor -from opentelemetry.sdk.resources import ( - DEPLOYMENT_ENVIRONMENT, - SERVICE_NAME, - SERVICE_VERSION, - Resource, -) +from opentelemetry.sdk.resources import DEPLOYMENT_ENVIRONMENT, SERVICE_NAME, Resource from opentelemetry.sdk.trace import TracerProvider -from opentelemetry.sdk.trace.export import ( - BatchSpanProcessor, - ConsoleSpanExporter, - SimpleSpanProcessor, - Span, -) +from opentelemetry.sdk.trace.export import BatchSpanProcessor, Span from opentelemetry.sdk.trace.sampling import ALWAYS_OFF +from requests_oauth2client import OAuth2Client, OAuth2ClientCredentialsAuth from synapseclient import Synapse from werkzeug import Request @@ -36,36 +26,81 @@ logger = logging.getLogger(__name__) -# borrowed from: https://github.com/Sage-Bionetworks/synapsePythonClient/blob/develop/tests/integration/conftest.py -class FileSpanExporter(ConsoleSpanExporter): - """Create an exporter for OTEL data to a file.""" +def create_telemetry_session() -> requests.Session: + """ + Create a requests session with authorization enabled if environment variables are set. + If no environment variables are set, the session will be created without authorization. + + Returns: + requests.Session: A session object with authorization enabled if environment + variables are set. If no environment variables are set, the session will be + created without authorization. If no telemetry export format is set, None + will be returned. + """ + tracing_export = os.environ.get("TRACING_EXPORT_FORMAT", None) + logging_export = os.environ.get("LOGGING_EXPORT_FORMAT", None) + if not (tracing_export or logging_export): + return None + + session = requests.Session() + static_otlp_headers = os.environ.get("OTEL_EXPORTER_OTLP_HEADERS", None) + if static_otlp_headers: + logger.info( + "Using static OTLP headers set in environment variable `OTEL_EXPORTER_OTLP_HEADERS`." + ) + return session + + client_id = os.environ.get("TELEMETRY_EXPORTER_CLIENT_ID", None) + client_secret = os.environ.get("TELEMETRY_EXPORTER_CLIENT_SECRET", None) + client_token_endpoint = os.environ.get( + "TELEMETRY_EXPORTER_CLIENT_TOKEN_ENDPOINT", None + ) + client_audience = os.environ.get("TELEMETRY_EXPORTER_CLIENT_AUDIENCE", None) + if ( + not client_id + or not client_secret + or not client_token_endpoint + or not client_audience + ): + logger.warning( + "No client_id, client_secret, client_audience, or token_endpoint provided for telemetry exporter. Telemetry data will be sent without authentication." + ) + return session + + oauth2client = OAuth2Client( + token_endpoint=client_token_endpoint, + client_id=client_id, + client_secret=client_secret, + ) - def __init__(self, file_path: str) -> None: - """Init with a path.""" - self.file_path = file_path + auth = OAuth2ClientCredentialsAuth(client=oauth2client, audience=client_audience) + session.auth = auth - def export(self, spans: List[Span]) -> None: - """Export the spans to the file.""" - with open(self.file_path, "a", encoding="utf-8") as f: - for span in spans: - span_json_one_line = span.to_json().replace("\n", "") + "\n" - f.write(span_json_one_line) + return session -def set_up_tracing() -> None: - """Set up tracing for the API.""" +def set_up_tracing(session: requests.Session) -> None: + """Set up tracing for the API. + Args: + session: requests.Session object to use for exporting telemetry data. If + the exporter is set to OTLP, this session will be used to send the data. + If the exporter is set to file, this session will be ignored. + """ tracing_export = os.environ.get("TRACING_EXPORT_FORMAT", None) if tracing_export is not None and tracing_export: Synapse.enable_open_telemetry(True) tracing_service_name = os.environ.get("TRACING_SERVICE_NAME", "schematic-api") deployment_environment = os.environ.get("DEPLOYMENT_ENVIRONMENT", "") - package_version = pkg_resources.get_distribution("schematicpy").version trace.set_tracer_provider( TracerProvider( resource=Resource( attributes={ SERVICE_NAME: tracing_service_name, - SERVICE_VERSION: package_version, + # TODO: Revisit this portion later on. As of 11/12/2024 when + # deploying this to ECS or running within a docker container, + # the package version errors out with the following error: + # importlib.metadata.PackageNotFoundError: No package metadata was found for schematicpy + # SERVICE_VERSION: package_version, DEPLOYMENT_ENVIRONMENT: deployment_environment, } ) @@ -76,20 +111,13 @@ def set_up_tracing() -> None: ) if tracing_export == "otlp": - trace.get_tracer_provider().add_span_processor( - BatchSpanProcessor(OTLPSpanExporter()) - ) - elif tracing_export == "file": - timestamp_millis = int(time.time() * 1000) - file_name = f"otel_spans_integration_testing_{timestamp_millis}.ndjson" - file_path = os.path.join(os.path.dirname(os.path.abspath(__file__)), file_name) - processor = SimpleSpanProcessor(FileSpanExporter(file_path)) - trace.get_tracer_provider().add_span_processor(processor) + exporter = OTLPSpanExporter(session=session) + trace.get_tracer_provider().add_span_processor(BatchSpanProcessor(exporter)) else: trace.set_tracer_provider(TracerProvider(sampler=ALWAYS_OFF)) -def set_up_logging() -> None: +def set_up_logging(session: requests.Session) -> None: """Set up logging to export to OTLP.""" logging_export = os.environ.get("LOGGING_EXPORT_FORMAT", None) logging_service_name = os.environ.get("LOGGING_SERVICE_NAME", "schematic-api") @@ -105,7 +133,7 @@ def set_up_logging() -> None: logger_provider = LoggerProvider(resource=resource) set_logger_provider(logger_provider=logger_provider) - exporter = OTLPLogExporter() + exporter = OTLPLogExporter(session=session) logger_provider.add_log_record_processor(BatchLogRecordProcessor(exporter)) handler = LoggingHandler(level=logging.NOTSET, logger_provider=logger_provider) logging.getLogger().addHandler(handler) @@ -150,5 +178,6 @@ def response_hook(span: Span, status: str, response_headers: List) -> None: pass -set_up_tracing() -set_up_logging() +request_session = create_telemetry_session() +set_up_tracing(session=request_session) +set_up_logging(session=request_session)