README for KBase orcidlink utils

This repo contains standalone utilities for the orcidlink service. They are run in a "lightweight" container based on Alpine Linux 3.18 and Python 3.12.

At present there is only one useful script, database-maintenance.py, which removes expired linking sessions from the orclink database.

All maintenance tasks are run against the orcidlink service's management api using a KBase auth token with the "orcidlink_admin" role.

Using Locally

To run with docker:

docker build . -t kbase/kbase-orcidlink-utils 

An example of running database maintenance against CI:

KBASE_AUTH_TOKEN=TOKEN_HERE \
KBASE_ENDPOINT=https://ci.kbase.us/services/  \
docker run -e KBASE_AUTH_TOKEN -e KBASE_ENDPOINT \
kbase/kbase-orcidlink-utils python src/database-maintenance.py

or using docker compose, which is handy for development:

KBASE_AUTH_TOKEN=TOKEN_HERE \
KBASE_ENDPOINT=https://ci.kbase.us/services/  \
docker compose run --rm utils python src/database-maintenance.py

Deploy Image

The image containing the utils is built by a GitHub Action in the GitHub repo. Images will be built for pull requests, PR merge to main, manually, and when a release is created. The release build will have a name like ghcr.io/kbase/kbase-orcidlink-utils:v1.2.3.

Deployment Requirements

The following environment variables must be set:

• KBASE_AUTH_TOKEN must be set to a KBase auth token (preferably a service token) with the custom role ORCIDLINK_MANAGER

• KBASE_ENDPOINT must be set to the KBase services base URL for the given deployment environment; e.g. for ci it should be https://ci.kbase.us/services/. Note that the utils are not sensitive to the terminal forward slash / as some KBase services are.