Integration test for run_dicom_archive_loader.py
#270
Workflow file for this run
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| 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 |