SQC

SQC (Structure Quality Control) is a validation service replicating the PDB standalone validation server.

First setup

To set up your system for development, create a Python virtual environment and install PDM:

$ python -m venv venv
$ source venv/bin/activate
$ python -m pip install pdm

Once you have PDM installed, you can install all of SQC's dependencies:

pdm install -G:all

Local development

To create a locally running instance of SQC, you can utilize docker compose:

docker compose up

After the images are fetched and built (building MolProbity can take up to an hour), the MinIO instance will be available at localhost:9000 and accessible using the SQCLib library.

Deployment

To deploy SQC, first make sure you're still in the virtual environment:

$ source venv/bin/activate

If you have already installed all the dependencies and want to deploy SQC using the default configuration, you can run the deployment playbook using the following command:

$ ansible-playbook --inventory ansible/inventory/ ansible/deploy-sqc.yaml --ask-vault-pass

You will be prompted for the password to the Ansible vault before continuing.

You do NOT have to tear down SQC to redeploy a new version, but if it's necessary, it's a similar process:

$ ansible-playbook --inventory ansible/inventory/ ansible/teardown-sqc.yaml --ask-vault-pass

Configuration

To edit SQC's deploy configuration, see the metacentrum inventory file.

Management

To access the MinIO management server, visit MinIO management in a browser.