LEfSe Lambda Analysis

Setup

Prerequisites

1. Install pre-commit for code quality checks:

   pip install pre-commit
   pre-commit install

Build and Deploy

1. Build Docker image locally:

   docker build -t lefse-lambda .

2. Login to AWS ECR:

   aws ecr get-login-password --region ap-southeast-1 | docker login --username AWS --password-stdin 256056681342.dkr.ecr.ap-southeast-1.amazonaws.com

3. Build and push to ECR:

   docker buildx build \
     --platform linux/amd64 \
     --provenance=false \
     --push \
     -t 256056681342.dkr.ecr.ap-southeast-1.amazonaws.com/iomics/analyses/lefse-lambda:latest \
     .

4. Update Lambda function: ENV options include: dev, staging, prod

   aws lambda update-function-code \
      --function-name lefseAnalysisLambda \
      --region ap-southeast-1 \
      --image-uri 256056681342.dkr.ecr.ap-southeast-1.amazonaws.com/iomics/analyses/lefse-lambda:latest
   
   aws lambda update-function-configuration \
      --function-name lefseAnalysisLambda \
      --region ap-southeast-1 \
      --environment Variables="{ENV=dev,API_KEY=/dev/data_access/API_KEY,PORTAL_API_URL=https://test-data-access.iomics.io/api/v1/external}"

Local Testing

1. Build local test image:

   docker build -t lambda-built-manual-local .

2. Run locally:

   docker run -p 9000:8080 lambda-built-manual-local

3. Test with sample request:

   curl -XPOST "http://localhost:9000/2015-03-31/functions/function/invocations" \
     -d '{
       "workspace_id": "402eae8f-55ad-427b-9724-bf569c11a4a2",
       "analysis_id": "63f9546d-f467-41ed-a9ba-