compose-runner 0.8.4

A package for running neurosynth-compose analyses

compose-runner

Python package to execute meta-analyses created using neurosynth compose and NiMARE as the meta-analysis execution engine.

AWS Deployment

This repository includes an AWS CDK application that turns compose-runner into a serverless batch pipeline using Step Functions, AWS Lambda, and ECS Fargate. The deployed architecture works like this:

• ComposeRunnerSubmit (Lambda Function URL) accepts HTTP requests, validates the meta-analysis payload, and starts a Step Functions execution. The response is immediate and returns both a durable job_id (the execution ARN) and the artifact_prefix used for S3 and log correlation.
• A Standard state machine runs a single Fargate task (compose_runner.ecs_task) and waits for completion. The container downloads inputs, executes the meta-analysis on up to 4 vCPU / 30 GiB of memory, uploads artifacts to S3, and writes metadata.json into the same prefix.
• ComposeRunnerStatus (Lambda Function URL) wraps DescribeExecution, merges metadata from S3, and exposes a simple status endpoint suitable for polling.
• ComposeRunnerLogPoller streams the ECS CloudWatch Logs for a given artifact_prefix, while ComposeRunnerResultsFetcher returns presigned URLs for stored artifacts.

1. Create a virtual environment and install the CDK dependencies:

   cd infra/cdk
   python -m venv .venv
   source .venv/bin/activate
   pip install -r requirements.txt
   

2. (One-time per account/region) bootstrap the CDK environment:

   cdk bootstrap
   

3. Deploy the stack (supplying the compose-runner version you want baked into the images):

   cdk deploy \
     -c composeRunnerVersion=$(hatch version) \
     -c resultsPrefix=compose-runner/results \
     -c taskCpu=4096 \
     -c taskMemoryMiB=30720
   

   Pass -c resultsBucketName=<bucket> to use an existing S3 bucket, or omit it to let the stack create and retain a dedicated bucket. Additional knobs:

• -c stateMachineTimeoutSeconds=32400 to control the max wall clock per run
• -c submitTimeoutSeconds / -c statusTimeoutSeconds / -c pollTimeoutSeconds to tune Lambda timeouts
• -c taskEphemeralStorageGiB if the default 21 GiB scratch volume is insufficient

The deployment builds both the Lambda image (aws_lambda/Dockerfile) and the Fargate task image (Dockerfile), provisions the Step Functions state machine, and configures a public VPC so each task has outbound internet access. The CloudFormation outputs list the HTTPS endpoints for submission, status, logs, and artifact retrieval, alongside the Step Functions ARN.