Add setup + dependencies and barebones metrics.py

Author: nss10

bin/_common_setup.sh

@@ -7,7 +7,7 @@ set -e
 CURRENT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
 
 # Source the environment variables from the metrics setup script
-# source "${CURRENT_DIR}/setup_prometheus"
+source "${CURRENT_DIR}/setup_prometheus"
 
 echo "installing dependencies with 'poetry install -vv'..."
 poetry install -vv

bin/setup_prometheus

@@ -0,0 +1,33 @@
+#!/usr/bin/env bash
+# Prepares the prometheus_multiproc_dir folder to store the metrics from separate workers (per PID)
+#
+# This script is called by:
+#   Dockerfile & run.py
+#     - So local runs setup necessary environment vars and folders for prometheus metrics
+#   Test framework in conftest
+#     - So test runs setup necessary environment vars and folders for prometheus metrics
+
+# Usage:
+#   ./setup_prometheus [DIR] [true]
+
+# Default directory if no argument is provided
+DIR=${1:-/var/tmp/prometheus_metrics}
+
+# Determine whether to wipe the directory (default is to wipe)
+SETUP_DIR=${2:-true}
+
+set -ex
+
+if [[ "$SETUP_DIR" == "true" ]]; then
+    echo "setting up $PROMETHEUS_MULTIPROC_DIR. clearing existing files, ensuring it exists, chmod 755"
+    rm -Rf "$DIR"
+    mkdir -p "$DIR"
+    chmod 755 "$DIR"
+fi
+
+if id -u nginx &>/dev/null; then
+    chown "$(id -u nginx)":"$(id -g nginx)" "$DIR"
+fi
+
+export PROMETHEUS_MULTIPROC_DIR="$DIR"
+echo "PROMETHEUS_MULTIPROC_DIR is $PROMETHEUS_MULTIPROC_DIR"

docs/metrics.md

@@ -0,0 +1,11 @@
+## Metrics
+
+Metrics can be exposed at a `/metrics` endpoint compatible with Prometheus scraping and visualize in Prometheus or
+Graphana, etc.
+
+The metrics are defined in `gen3workflow/metrics.py` as follows:
+
+* **gen3_workflow_api_requests_total**:  API requests for made to Gen3-Workflow service.
+* ** **More metrics yet to be decided** **
+
+You can [run Prometheus locally](https://github.com/prometheus/prometheus) if you want to test or visualize these.

gen3workflow/app.py

@@ -8,6 +8,7 @@
 
 from gen3workflow import logger
 from gen3workflow.config import config
+from gen3workflow.metrics import Metrics
 from gen3workflow.routes.ga4gh_tes import router as ga4gh_tes_router
 from gen3workflow.routes.s3 import router as s3_router
 from gen3workflow.routes.storage import router as storage_router
@@ -54,6 +55,16 @@ def get_app(httpx_client=None) -> FastAPI:
             logger=get_logger("gen3workflow.gen3authz", log_level=log_level),
         )
 
+    logger.info(
+        f"Setting up Metrics with ENABLE_PROMETHEUS_METRICS flag set to {config['ENABLE_PROMETHEUS_METRICS']}"
+    )
+    app.metrics = Metrics(
+        enabled=config["ENABLE_PROMETHEUS_METRICS"],
+        prometheus_dir=config["PROMETHEUS_MULTIPROC_DIR"],
+    )
+    if app.metrics.enabled:
+        app.include_router("/metrics", app.metrics.get_asgi_app())
+
     return app
 
 

gen3workflow/config.py

@@ -61,6 +61,11 @@ def validate_top_level_configs(self) -> None:
                 "DB_CONNECTION_STRING": {"type": "string"},
                 "TASK_IMAGE_WHITELIST": {"type": "array", "items": {"type": "string"}},
                 "TES_SERVER_URL": {"type": "string"},
+                "ENABLE_PROMETHEUS_METRICS": {"type": "boolean", "default": False},
+                "PROMETHEUS_MULTIPROC_DIR": {
+                    "type": "string",
+                    "default": "/var/tmp/prometheus_metrics",
+                },
             },
         }
         validate(instance=self, schema=schema)

gen3workflow/metrics.py

@@ -0,0 +1,12 @@
+from typing import Any, Dict
+
+from cdispyutils.metrics import BaseMetrics
+
+from gen3workflow.config import config
+
+
+class Metrics(BaseMetrics):
+    def __init__(self, prometheus_dir: str, enabled: bool = True) -> None:
+        super().__init__(
+            prometheus_dir=config["PROMETHEUS_MULTIPROC_DIR"], enabled=enabled
+        )

poetry.lock

@@ -25,6 +25,7 @@ httpx = "<1"
 jsonschema = "<5"
 sqlalchemy = { extras = ["asyncio"], version = "<3" }
 uvicorn = "<1"
+cdispyutils = "^2.4.0"
 
 [tool.poetry.dev-dependencies]
 freezegun = "<2"