benchling-packager

This repository generates a CloudFormation template for processing Benchling events in order create (and link, if possible) a Quilt package for every Benchling notebook.

The code in this repository 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