[MRI] Check if CenterID and MRI_Alias are defined before going further #364
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Integration tests | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - 'main' | |
| - '*-release' | |
| env: | |
| DATABASE_NAME: TestDatabase | |
| DATABASE_USERNAME: TestUsername | |
| DATABASE_PASSWORD: TestPassword | |
| BUCKET_URL: https://ace-minio-1.loris.ca:9000 | |
| BUCKET_NAME: loris-rb-data | |
| # NOTE: These are read-only keys on public data. | |
| # Ideally, we would like to hide these keys. However, both GitHub variables and GitHub secrets | |
| # are not accessible from pull requests from forks. Since we want to run integration tests on | |
| # pull requests, we define these variables here. | |
| BUCKET_ACCESS_KEY: lorisadmin-ro | |
| BUCKET_SECRET_KEY: Tn=qP3LupmXnMuc | |
| jobs: | |
| docker: | |
| name: Docker | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out LORIS-MRI | |
| uses: actions/checkout@v4 | |
| - name: Clone the LORIS core repository | |
| run: git clone https://github.com/aces/Loris.git ./test/Loris | |
| - name: Overwrite Raisinbread SQL files | |
| run: cp -f ./test/RB_SQL/*.sql ./test/Loris/raisinbread/RB_files/ | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build Docker database image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| file: ./test/db.Dockerfile | |
| build-args: | | |
| DATABASE_NAME=${{ env.DATABASE_NAME }} | |
| DATABASE_USER=${{ env.DATABASE_USERNAME }} | |
| DATABASE_PASS=${{ env.DATABASE_PASSWORD }} | |
| tags: loris-db | |
| load: true | |
| cache-from: type=gha,scope=loris-db | |
| cache-to: type=gha,scope=loris-db | |
| - name: Build Docker MRI image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| file: ./test/mri.Dockerfile | |
| build-args: | | |
| DATABASE_NAME=${{ env.DATABASE_NAME }} | |
| DATABASE_USER=${{ env.DATABASE_USERNAME }} | |
| DATABASE_PASS=${{ env.DATABASE_PASSWORD }} | |
| tags: loris-mri | |
| load: true | |
| cache-from: type=gha,scope=loris-mri | |
| cache-to: type=gha,mode=max,scope=loris-mri | |
| # NOTE: Ideally, we would like to mount the S3 bucket in the Docker image, but since it | |
| # interacts with the kernel to add a file system, it is hard to do so. | |
| - name: Mount imaging files S3 bucket | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y s3fs fuse kmod | |
| sudo modprobe fuse | |
| sudo mkdir /data-imaging | |
| touch .passwd-s3fs | |
| chmod 600 .passwd-s3fs | |
| echo ${{ env.BUCKET_ACCESS_KEY }}:${{ env.BUCKET_SECRET_KEY }} > .passwd-s3fs | |
| sudo s3fs ${{ env.BUCKET_NAME }} /data-imaging -o url=${{ env.BUCKET_URL }} -o passwd_file=.passwd-s3fs -o use_path_request_style -o allow_other | |
| - name: Run integration tests | |
| run: docker compose --file ./test/docker-compose.yml run mri pytest python/tests/integration |