Integration test for run_dicom_archive_loader.py
#269
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: ${{ vars.S3_BUCKET_URL }} | |
| BUCKET_NAME: ${{ vars.S3_BUCKET_NAME }} | |
| BUCKET_ACCESS_KEY: ${{ secrets.S3_BUCKET_ACCESS_KEY }} | |
| BUCKET_SECRET_KEY: ${{ secrets.S3_BUCKET_SECRET_KEY }} | |
| jobs: | |
| docker: | |
| name: Docker | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Print variables | |
| run: echo ${{ vars.S3_BUCKET_URL }} ${{ vars.S3_BUCKET_NAME }} | |
| - name: Check out LORIS-MRI | |
| uses: actions/checkout@v4 | |
| - name: Clone the LORIS core repository | |
| run: git clone https://github.com/aces/Loris.git ./test/Loris | |
| - name: Overwrite Raisinbread SQL files | |
| run: cp -f ./test/RB_SQL/*.sql ./test/Loris/raisinbread/RB_files/ | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build Docker database image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| file: ./test/db.Dockerfile | |
| build-args: | | |
| DATABASE_NAME=${{ 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=${{ env.DATABASE_PASSWORD }} | |
| BUCKET_URL=${{ env.BUCKET_URL }} | |
| BUCKET_NAME=${{ env.BUCKET_NAME }} | |
| BUCKET_ACCESS_KEY=${{ env.BUCKET_ACCESS_KEY }} | |
| BUCKET_SECRET_KEY=${{ env.BUCKET_SECRET_KEY }} | |
| tags: loris-mri | |
| load: true | |
| cache-from: type=gha,scope=loris-mri | |
| cache-to: type=gha,mode=max,scope=loris-mri | |
| # TODO: Move as much as possible of this in the MRI dockerfile | |
| - 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 ${{ env.BUCKET_NAME }} /data-imaging -o passwd_file=.passwd-s3fs -o url=${{ env.BUCKET_URL }} -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 |