mirror of
https://github.com/Novartis/cellxgene-gateway.git
synced 2026-09-15 12:47:59 +08:00
added start scripts for flask, gunicorn and uwsgi
This commit is contained in:
Alok Saldanha
3
env_example
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3
env_example
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export CELLXGENE_LOCATION=$(pwd)/.venv/bin/cellxgene
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export CELLXGENE_DATA=../cellxgene_data
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export GATEWAY_IP=127.0.0.1
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@@ -1,6 +0,0 @@
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export CELLXGENE_LOCATION=$(pwd)/.cellxgene-gateway/bin/cellxgene
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export CELLXGENE_DATA=../cellxgene_data
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export GATEWAY_IP=127.0.0.1
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#Once these are set, you run like a normal Flask app
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cellxgene-gateway
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41
start_flask.sh
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41
start_flask.sh
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#!/bin/bash
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# start_gunicorn.sh - Start Cellxgene Gateway with Gunicorn
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#
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# PREREQUISITES:
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# - Gunicorn installed (included with cellxgene 1.3.0, or: pip install gunicorn)
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# - Virtual environment activated or .venv present
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# - .env file with CELLXGENE_LOCATION and CELLXGENE_DATA (or CELLXGENE_BUCKET)
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#
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# USAGE:
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# ./start_gunicorn.sh
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# Exit on error
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set -e
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# Get the directory where this script is located
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SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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# Source environment variables
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echo "Loading environment variables..."
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if [ -f "$SCRIPT_DIR/.env" ]; then
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source "$SCRIPT_DIR/.env"
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else
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echo "Error: .env file not found at $SCRIPT_DIR/.env"
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echo "Please create it with required environment variables"
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exit 1
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fi
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# Verify required environment variables
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if [ -z "$CELLXGENE_LOCATION" ]; then
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echo "Error: CELLXGENE_LOCATION not set"
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exit 1
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fi
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if [ -z "$CELLXGENE_DATA" ] && [ -z "$CELLXGENE_BUCKET" ]; then
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echo "Error: Either CELLXGENE_DATA or CELLXGENE_BUCKET must be set"
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exit 1
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fi
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cellxgene-gateway
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91
start_gunicorn.sh
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91
start_gunicorn.sh
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#!/bin/bash
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# start_gunicorn.sh - Start Cellxgene Gateway with Gunicorn
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#
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# PREREQUISITES:
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# - Gunicorn installed (included with cellxgene 1.3.0, or: pip install gunicorn)
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# - Virtual environment activated or .venv present
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# - .env file with CELLXGENE_LOCATION and CELLXGENE_DATA (or CELLXGENE_BUCKET)
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#
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# USAGE:
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# ./start_gunicorn.sh
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# Exit on error
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set -e
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# Get the directory where this script is located
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SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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# Source environment variables
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echo "Loading environment variables..."
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if [ -f "$SCRIPT_DIR/.env" ]; then
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source "$SCRIPT_DIR/.env"
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else
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echo "Error: .env file not found at $SCRIPT_DIR/.env"
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echo "Please create it with required environment variables"
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exit 1
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fi
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# Verify required environment variables
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if [ -z "$CELLXGENE_LOCATION" ]; then
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echo "Error: CELLXGENE_LOCATION not set"
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exit 1
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fi
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if [ -z "$CELLXGENE_DATA" ] && [ -z "$CELLXGENE_BUCKET" ]; then
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echo "Error: Either CELLXGENE_DATA or CELLXGENE_BUCKET must be set"
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exit 1
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fi
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# Gunicorn configuration
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# WARNING: Multi-worker mode has cache synchronization issues (see plans/002-shared-cache-implementation.md)
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# Each worker maintains its own in-memory cache, causing 404s for static assets when different
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# workers handle requests for the same dataset. Use GUNICORN_WORKERS=1 until shared cache is implemented.
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WORKERS=${GUNICORN_WORKERS:-1}
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BIND=${GATEWAY_IP:-0.0.0.0}:${GATEWAY_PORT:-5005}
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TIMEOUT=${GUNICORN_TIMEOUT:-120}
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WORKER_CLASS=${GUNICORN_WORKER_CLASS:-sync}
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KEEPALIVE=${GUNICORN_KEEPALIVE:-5}
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LOG_LEVEL=${GUNICORN_LOG_LEVEL:-info}
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# Production optimization: enable backed mode to reduce memory usage
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export GATEWAY_ENABLE_BACKED_MODE=${GATEWAY_ENABLE_BACKED_MODE:-true}
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# Check if gunicorn is installed
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if ! command -v gunicorn &> /dev/null; then
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echo "Error: gunicorn not found. Install with: pip install gunicorn"
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exit 1
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fi
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# Display configuration
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echo "Starting Cellxgene Gateway with Gunicorn..."
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echo "Configuration:"
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echo " Data source: ${CELLXGENE_DATA:-$CELLXGENE_BUCKET}"
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echo " Binding to: $BIND"
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echo " Workers: $WORKERS"
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echo " Worker class: $WORKER_CLASS"
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echo " Timeout: ${TIMEOUT}s"
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echo " Keepalive: ${KEEPALIVE}s"
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echo " Log level: $LOG_LEVEL"
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echo " Backed mode: ${GATEWAY_ENABLE_BACKED_MODE}"
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echo ""
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cd "$SCRIPT_DIR"
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# Start Gunicorn with optimized settings
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# Additional options you can add via environment variables:
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# - GUNICORN_MAX_REQUESTS: Restart worker after N requests (prevents memory leaks)
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# - GUNICORN_MAX_REQUESTS_JITTER: Add randomness to max-requests
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gunicorn cellxgene_gateway.gateway:app \
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--workers "$WORKERS" \
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--worker-class "$WORKER_CLASS" \
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--bind "$BIND" \
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--timeout "$TIMEOUT" \
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--keep-alive "$KEEPALIVE" \
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--access-logfile - \
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--error-logfile - \
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--log-level "$LOG_LEVEL" \
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--preload \
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${GUNICORN_MAX_REQUESTS:+--max-requests "$GUNICORN_MAX_REQUESTS"} \
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${GUNICORN_MAX_REQUESTS_JITTER:+--max-requests-jitter "$GUNICORN_MAX_REQUESTS_JITTER"} \
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"$@"
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88
start_uwsgi.sh
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88
start_uwsgi.sh
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@@ -0,0 +1,88 @@
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#!/bin/bash
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# start_uwsgi.sh - Start Cellxgene Gateway with uWSGI
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#
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# PREREQUISITES:
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# - uWSGI installed (pip install uwsgi)
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# - Virtual environment activated or .venv present
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# - .env file with CELLXGENE_LOCATION and CELLXGENE_DATA (or CELLXGENE_BUCKET)
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#
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# USAGE:
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# ./start_uwsgi.sh
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# Exit on error
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set -e
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# Get the directory where this script is located
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SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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# Source environment variables
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echo "Loading environment variables..."
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if [ -f "$SCRIPT_DIR/.env" ]; then
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source "$SCRIPT_DIR/.env"
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else
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echo "Error: .env file not found at $SCRIPT_DIR/.env"
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echo "Please create it with required environment variables"
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exit 1
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fi
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# Verify required environment variables
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if [ -z "$CELLXGENE_LOCATION" ]; then
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echo "Error: CELLXGENE_LOCATION not set"
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exit 1
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fi
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if [ -z "$CELLXGENE_DATA" ] && [ -z "$CELLXGENE_BUCKET" ]; then
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echo "Error: Either CELLXGENE_DATA or CELLXGENE_BUCKET must be set"
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exit 1
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fi
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# uWSGI configuration
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# WARNING: Multi-worker mode has cache synchronization issues (see plans/002-shared-cache-implementation.md)
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# Each worker maintains its own in-memory cache, causing 404s for static assets when different
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# workers handle requests for the same dataset. Use UWSGI_WORKERS=1 until shared cache is implemented.
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WORKERS=${UWSGI_WORKERS:-1}
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HOST=${GATEWAY_IP:-0.0.0.0}
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PORT=${GATEWAY_PORT:-5005}
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TIMEOUT=${UWSGI_TIMEOUT:-120}
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THREADS=${UWSGI_THREADS:-1}
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# Production optimization: enable backed mode to reduce memory usage
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export GATEWAY_ENABLE_BACKED_MODE=${GATEWAY_ENABLE_BACKED_MODE:-true}
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# Check if uwsgi is installed
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if ! command -v uwsgi &> /dev/null; then
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echo "Error: uwsgi not found. Install with: pip install uwsgi"
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exit 1
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fi
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# Display configuration
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echo "Starting Cellxgene Gateway with uWSGI..."
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echo "Configuration:"
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echo " Data source: ${CELLXGENE_DATA:-$CELLXGENE_BUCKET}"
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echo " Binding to: $HOST:$PORT"
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echo " Workers: $WORKERS"
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echo " Threads: $THREADS"
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echo " Timeout: ${TIMEOUT}s"
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echo " Backed mode: ${GATEWAY_ENABLE_BACKED_MODE}"
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echo ""
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cd "$SCRIPT_DIR"
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# Start uWSGI with optimized settings
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# Additional options you can add via environment variables:
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# - UWSGI_MAX_REQUESTS: Restart worker after N requests (prevents memory leaks)
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exec uwsgi \
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--http "$HOST:$PORT" \
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--module cellxgene_gateway.gateway:app \
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--workers "$WORKERS" \
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--threads "$THREADS" \
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--harakiri "$TIMEOUT" \
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--master \
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--enable-threads \
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--single-interpreter \
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--need-app \
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--die-on-term \
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--log-x-forwarded-for \
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${UWSGI_MAX_REQUESTS:+--max-requests "$UWSGI_MAX_REQUESTS"} \
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"$@"
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