benchling-packager

The Benchling Packager is a lambda you can deploy in your own AWS private cloud to process Benchling events in order to create (and link back, if possible) a dedicated Quilt package for every Benchling notebook.

The CloudFormation template is available on open.quiltdata.com.

This repository contains the source code for generating that template. It is open source under the Apache 2.0 license.

Template generation

Requires a recent version of Python 3.

python3 -m venv venv
. ./venv/bin/activate
python3 -m pip install -r requirements.txt
python3 make.py > build/benchling_packager.yaml

Template upload

• setup the Python environment
• generate the template in the build directory
• upload the template to a Quilt package (if you have appropriate permissions)
• open the package URL: https://open.quiltdata.com/b/quilt-example/packages/examples/benchling-packager

Installation

To install and configure the template, see Install.md. Note: this is the file that's distributed as README.md in the package.

Testing for Developers

If you want to modify the actual lambda function, you can run automated tests via:

make test

In order to run these tests, you'll need to set the following environment variables (usually in the .env file, which is auto-included by the Makefile):

• BENCHLING_TENANT: the part before ".benchling.com" in your Benchling URL (e.g. "mycompany" for "mycompany.benchling.com")
• BENCHLING_CLIENT_ID: the client ID for the Benchling API`
• BENCHLING_CLIENT_SECRET_ARN: the ARN of the AWS Secrets Manager secret containing the client secret for the Benchling API
• DST_BUCKET: the name of the S3 bucket (no prefix) where the generated packages should be stored
• PKG_PREFIX: the prefix to use for the generated packages, with a trailing "/" (e.g. "benchling/" to store packages in the "benchling" directory)
• QUILT_CATALOG_DOMAIN: the domain name of your Quilt catalog (if any) where the generated packages can be viewed