Merge branch '518-extraction-phase-can-we-make-the-list-of-studies-mo… #2097
Workflow file for this run
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| name: Testing Workflow | |
| on: [workflow_dispatch,push] | |
| jobs: | |
| clean: | |
| strategy: | |
| matrix: | |
| package: ['neurosynth_compose', 'compose_nginx', 'compose_pgsql', 'compose_worker', 'neurostore', 'store_nginx', 'store_pgsql'] | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/delete-package-versions@v5 | |
| with: | |
| package-name: ${{ matrix.package }} | |
| package-type: 'container' | |
| min-versions-to-keep: 10 | |
| delete-only-pre-release-versions: "true" | |
| build_neurosynth_compose: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| working-directory: compose | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - | |
| name: Configuration | |
| run: | | |
| cp .env.example .env | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - | |
| name: Login to GitHub Container Registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - | |
| name: Build and push | |
| uses: docker/bake-action@master | |
| with: | |
| files: docker-compose.yml,docker-compose.dev.yml | |
| push: true | |
| load: false | |
| workdir: compose | |
| set: | | |
| compose.tags=ghcr.io/${{ github.repository_owner }}/neurosynth_compose:${{ hashFiles('**/compose/neurosynth_compose/**') }} | |
| compose.cache-from=type=registry,ref=ghcr.io/${{ github.repository_owner }}/neurosynth_compose:${{ hashFiles('**/compose/neurosynth_compose/**') }} | |
| compose.cache-from=type=gha,scope=cached-compose | |
| compose.cache-to=type=gha,scope=cached-compose,mode=max,ignore-error=true | |
| compose_nginx.tags=ghcr.io/${{ github.repository_owner }}/compose_nginx:${{ hashFiles('**/compose/nginx/**') }} | |
| compose_nginx.cache-from=type=registry,ref=ghcr.io/${{ github.repository_owner }}/compose_nginx:${{ hashFiles('**/compose/nginx/**') }} | |
| compose_nginx.cache-from=type=gha,scope=cached-compose-nginx | |
| compose_nginx.cache-to=type=gha,scope=cached-compose-nginx,mode=max,ignore-error=true | |
| compose_pgsql.tags=ghcr.io/${{ github.repository_owner }}/compose_pgsql:${{ hashFiles('**/compose/postgres/**') }} | |
| compose_pgsql.cache-from=type=registry,ref=ghcr.io/${{ github.repository_owner }}/compose_pgsql:${{ hashFiles('**/compose/postgres/**') }} | |
| compose_pgsql.cache-from=type=gha,scope=cached-compose-pgsql | |
| compose_pgsql.cache-to=type=gha,scope=cached-compose-pgsql,mode=max,ignore-error=true | |
| compose_worker.tags=ghcr.io/${{ github.repository_owner }}/compose_worker:${{ hashFiles('**/compose/neurosynth_compose/**') }} | |
| compose_worker.cache-from=type=registry,ref=ghcr.io/${{ github.repository_owner }}/compose_worker:${{ hashFiles('**/compose/neurosynth_compose/**') }} | |
| compose_worker.cache-from=type=gha,scope=cached-compose-worker | |
| compose_worker.cache-to=type=gha,scope=cached-compose-worker,mode=max,ignore-error=true | |
| build_neurostore: | |
| runs-on: ubuntu-latest | |
| defaults: | |
| run: | |
| working-directory: store | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - | |
| name: Configuration | |
| run: | | |
| cp .env.example .env | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - | |
| name: Login to GitHub Container Registry | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.repository_owner }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - | |
| name: Build and push | |
| uses: docker/bake-action@master | |
| with: | |
| files: docker-compose.yml,docker-compose.dev.yml | |
| push: true | |
| load: false | |
| workdir: store | |
| set: | | |
| neurostore.tags=ghcr.io/${{ github.repository_owner }}/neurostore:${{ hashFiles('**/store/neurostore/**') }} | |
| neurostore.cache-from=type=registry,ref=ghcr.io/${{ github.repository_owner }}/neurostore:${{ hashFiles('**/store/neurostore/**') }} | |
| neurostore.cache-from=type=gha,scope=cached-neurostore | |
| neurostore.cache-to=type=gha,scope=cached-neurostore,mode=max,ignore-error=true | |
| store_nginx.tags=ghcr.io/${{ github.repository_owner }}/store_nginx:${{ hashFiles('**/store/nginx/**') }} | |
| store_nginx.cache-from=type=registry,ref=ghcr.io/${{ github.repository_owner }}/store_nginx:${{ hashFiles('**/store/nginx/**') }} | |
| store_nginx.cache-from=type=gha,scope=cached-store-nginx | |
| store_nginx.cache-to=type=gha,scope=cached-store-nginx,mode=max,ignore-error=true | |
| store_pgsql.tags=ghcr.io/${{ github.repository_owner }}/store_pgsql:${{ hashFiles('**/store/postgres/**') }} | |
| store_pgsql.cache-from=type=registry,ref=ghcr.io/${{ github.repository_owner }}/store_pgsql:${{ hashFiles('**/store/postgres/**') }} | |
| store_pgsql.cache-from=type=gha,scope=cached-store-pgsql | |
| store_pgsql.cache-to=type=gha,scope=cached-store-pgsql,mode=max,ignore-error=true | |
| neurostore_backend_tests: | |
| runs-on: ubuntu-latest | |
| needs: build_neurostore | |
| defaults: | |
| run: | |
| working-directory: store | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - | |
| name: Configuration | |
| run: | | |
| cp .env.example .env | |
| - | |
| name: load images | |
| uses: docker/bake-action@master | |
| with: | |
| files: docker-compose.yml,docker-compose.dev.yml | |
| push: false | |
| load: true | |
| workdir: store | |
| set: | | |
| neurostore.cache-from=type=gha,scope=cached-neurostore | |
| store_nginx.cache-from=type=gha,scope=cached-store-nginx | |
| store_pgsql.cache-from=type=gha,scope=cached-store-pgsql | |
| - | |
| name: spin up backend | |
| run: | | |
| docker network create nginx-proxy | |
| docker compose pull --ignore-buildable | |
| docker compose \ | |
| -f docker-compose.yml \ | |
| -f docker-compose.dev.yml \ | |
| up -d --no-build | |
| - | |
| name: Create Test Database | |
| run: | | |
| until docker compose exec -T \ | |
| store_pgsql pg_isready -U postgres; do sleep 1; done | |
| docker compose exec -T \ | |
| store_pgsql \ | |
| psql -U postgres -c "create database test_db" | |
| - | |
| name: Backend Tests | |
| env: | |
| AUTH0_CLIENT_ID: ${{ secrets.AUTH0_CLIENT_ID }} | |
| AUTH0_CLIENT_SECRET: ${{ secrets.AUTH0_CLIENT_SECRET }} | |
| AUTH0_BASE_URL: ${{ secrets.AUTH0_BASE_URL }} | |
| AUTH0_ACCESS_TOKEN_URL: ${{ secrets.AUTH0_ACCESS_TOKEN_URL }} | |
| AUTH0_AUTH_URL: ${{ secrets.AUTH0_AUTH_URL }} | |
| run: | | |
| docker compose run \ | |
| -e "APP_SETTINGS=neurostore.config.DockerTestConfig" \ | |
| -e "AUTH0_CLIENT_ID=${AUTH0_CLIENT_ID}" \ | |
| -e "AUTH0_CLIENT_SECRET=${AUTH0_CLIENT_SECRET}" \ | |
| -e "AUTH0_BASE_URL=${AUTH0_BASE_URL}" \ | |
| -e "AUTH0_ACCESS_TOKEN_URL=${AUTH0_ACCESS_TOKEN_URL}" \ | |
| -e "AUTH0_AUTH_URL=${AUTH0_AUTH_URL}" \ | |
| --rm -w /neurostore \ | |
| neurostore \ | |
| bash -c "python -m pytest neurostore/tests && python -m pytest --auth neurostore/tests/test_auth.py" | |
| neurosynth_compose_backend_tests: | |
| runs-on: ubuntu-latest | |
| needs: build_neurosynth_compose | |
| defaults: | |
| run: | |
| working-directory: compose | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - | |
| name: Configuration | |
| run: | | |
| cp .env.example .env | |
| - | |
| name: load images | |
| uses: docker/bake-action@master | |
| with: | |
| files: docker-compose.yml,docker-compose.dev.yml | |
| push: false | |
| load: true | |
| workdir: compose | |
| set: | | |
| compose.cache-from=type=gha,scope=cached-compose | |
| compose_nginx.cache-from=type=gha,scope=cached-compose-nginx | |
| compose_pgsql.cache-from=type=gha,scope=cached-compose-pgsql | |
| compose_worker.cache-from=type=gha,scope=cached-compose-worker | |
| - | |
| name: Spin up backend | |
| run: | | |
| docker network create nginx-proxy | |
| docker compose pull --ignore-buildable | |
| docker compose \ | |
| -f docker-compose.yml \ | |
| -f docker-compose.dev.yml \ | |
| up -d --no-build | |
| - | |
| name: Create Test Database | |
| run: | | |
| until docker compose exec -T \ | |
| compose_pgsql pg_isready -U postgres; do sleep 1; done | |
| docker compose exec -T \ | |
| compose_pgsql \ | |
| psql -U postgres -c "create database test_db" | |
| - | |
| name: Backend Tests | |
| env: | |
| AUTH0_CLIENT_ID: ${{ secrets.AUTH0_CLIENT_ID }} | |
| AUTH0_CLIENT_SECRET: ${{ secrets.AUTH0_CLIENT_SECRET }} | |
| AUTH0_BASE_URL: ${{ secrets.AUTH0_BASE_URL }} | |
| AUTH0_ACCESS_TOKEN_URL: ${{ secrets.AUTH0_ACCESS_TOKEN_URL }} | |
| AUTH0_AUTH_URL: ${{ secrets.AUTH0_AUTH_URL }} | |
| NEUROVAULT_ACCESS_TOKEN: ${{ secrets.NEUROVAULT_ACCESS_TOKEN }} | |
| run: | | |
| docker compose run \ | |
| -e "APP_SETTINGS=neurosynth_compose.config.DockerTestConfig" \ | |
| -e "AUTH0_CLIENT_ID=${AUTH0_CLIENT_ID}" \ | |
| -e "AUTH0_CLIENT_SECRET=${AUTH0_CLIENT_SECRET}" \ | |
| -e "AUTH0_BASE_URL=${AUTH0_BASE_URL}" \ | |
| -e "AUTH0_ACCESS_TOKEN_URL=${AUTH0_ACCESS_TOKEN_URL}" \ | |
| -e "AUTH0_AUTH_URL=${AUTH0_AUTH_URL}" \ | |
| -e "NEUROVAULT_ACCESS_TOKEN=${NEUROVAULT_ACCESS_TOKEN}" \ | |
| --rm -w /compose \ | |
| compose \ | |
| bash -c "python -m pytest neurosynth_compose/tests && python -m pytest --celery neurosynth_compose/tests/api/celery_tests && python -m pytest --auth neurosynth_compose/tests/api/test_auth.py" | |
| style_check: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - | |
| name: run flake8 | |
| run: | | |
| pip install flake8 | |
| cd ./store | |
| flake8 ./neurostore | |
| cd ../compose | |
| flake8 ./neurosynth_compose | |
| neurosynth_compose_JUNIT_tests: | |
| runs-on: ubuntu-latest | |
| needs: build_neurosynth_compose | |
| defaults: | |
| run: | |
| working-directory: compose | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - | |
| name: Configuration | |
| run: | | |
| cp .env.example .env | |
| - | |
| name: load images | |
| uses: docker/bake-action@master | |
| with: | |
| files: docker-compose.yml,docker-compose.dev.yml | |
| push: false | |
| load: true | |
| workdir: compose | |
| set: | | |
| compose.cache-from=type=gha,scope=cached-compose | |
| compose_nginx.cache-from=type=gha,scope=cached-compose-nginx | |
| compose_pgsql.cache-from=type=gha,scope=cached-compose-pgsql | |
| compose_worker.cache-from=type=gha,scope=cached-compose-worker | |
| - | |
| name: Spin up backend | |
| run: | | |
| docker network create nginx-proxy | |
| docker compose pull --ignore-buildable | |
| docker compose \ | |
| -f docker-compose.yml \ | |
| -f docker-compose.dev.yml \ | |
| up -d --no-build | |
| - | |
| name: Create Test Database | |
| run: | | |
| until docker compose exec -T \ | |
| compose_pgsql pg_isready -U postgres; do sleep 1; done | |
| docker compose exec -T \ | |
| compose_pgsql \ | |
| psql -U postgres -c "create database test_db" | |
| - | |
| name: Frontend Jest Unit Tests | |
| env: | |
| AUTH0_CLIENT_ID: ${{ secrets.AUTH0_CLIENT_ID }} | |
| AUTH0_CLIENT_SECRET: ${{ secrets.AUTH0_CLIENT_SECRET }} | |
| AUTH0_BASE_URL: ${{ secrets.AUTH0_BASE_URL }} | |
| AUTH0_ACCESS_TOKEN_URL: ${{ secrets.AUTH0_ACCESS_TOKEN_URL }} | |
| AUTH0_AUTH_URL: ${{ secrets.AUTH0_AUTH_URL }} | |
| REACT_APP_AUTH0_CLIENT_ID: ${{ secrets.REACT_APP_AUTH0_CLIENT_ID }} | |
| REACT_APP_AUTH0_DOMAIN: ${{ secrets.REACT_APP_AUTH0_DOMAIN }} | |
| REACT_APP_AUTH0_CLIENT_SECRET: ${{ secrets.REACT_APP_AUTH0_CLIENT_SECRET }} | |
| run: | | |
| cp neurosynth-frontend/.env.example neurosynth-frontend/.env.dev && \ | |
| docker compose run \ | |
| -e "APP_SETTINGS=neurosynth_compose.config.DockerTestConfig" \ | |
| -e "AUTH0_CLIENT_ID=${AUTH0_CLIENT_ID}" \ | |
| -e "AUTH0_CLIENT_SECRET=${AUTH0_CLIENT_SECRET}" \ | |
| -e "AUTH0_BASE_URL=${AUTH0_BASE_URL}" \ | |
| -e "AUTH0_ACCESS_TOKEN_URL=${AUTH0_ACCESS_TOKEN_URL}" \ | |
| -e "AUTH0_AUTH_URL=${AUTH0_AUTH_URL}" \ | |
| -e "REACT_APP_AUTH0_DOMAIN=${REACT_APP_AUTH0_DOMAIN}" \ | |
| -e "REACT_APP_AUTH0_CLIENT_ID=${REACT_APP_AUTH0_CLIENT_ID}" \ | |
| -e "REACT_APP_AUTH0_AUDIENCE=localhost" \ | |
| -e "REACT_APP_AUTH0_CLIENT_SECRET=${REACT_APP_AUTH0_CLIENT_SECRET}" \ | |
| -e "REACT_APP_ENV=DEV" \ | |
| -e "REACT_APP_NEUROSTORE_API_DOMAIN=http://localhost/api" \ | |
| -e "CI=true" \ | |
| -e "REACT_APP_NEUROSYNTH_API_DOMAIN=http://localhost:81/api" \ | |
| --rm -w /compose/neurosynth-frontend \ | |
| compose \ | |
| bash -c "cd /compose/neurosynth-frontend && \ | |
| npm install && npm run test" | |
| neurosynth_compose_cypress_tests: | |
| runs-on: ubuntu-latest | |
| needs: | |
| - build_neurosynth_compose | |
| - build_neurostore | |
| steps: | |
| - | |
| name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - | |
| name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - | |
| name: Configuration | |
| run: | | |
| cp compose/.env.example compose/.env | |
| cp store/.env.example store/.env | |
| - | |
| name: load compose images | |
| uses: docker/bake-action@master | |
| with: | |
| files: docker-compose.yml,docker-compose.dev.yml | |
| push: false | |
| load: true | |
| workdir: compose | |
| set: | | |
| compose.cache-from=type=gha,scope=cached-compose | |
| compose_nginx.cache-from=type=gha,scope=cached-compose-nginx | |
| compose_pgsql.cache-from=type=gha,scope=cached-compose-pgsql | |
| compose_worker.cache-from=type=gha,scope=cached-compose-worker | |
| - | |
| name: load store images | |
| uses: docker/bake-action@master | |
| with: | |
| files: docker-compose.yml,docker-compose.dev.yml | |
| push: false | |
| load: true | |
| workdir: store | |
| set: | | |
| neurostore.cache-from=type=gha,scope=cached-neurostore | |
| store_nginx.cache-from=type=gha,scope=cached-store-nginx | |
| store_pgsql.cache-from=type=gha,scope=cached-store-pgsql | |
| - | |
| name: Spin up compose backend | |
| run: | | |
| cd compose | |
| docker network create nginx-proxy | |
| docker compose pull --ignore-buildable | |
| docker compose \ | |
| -f docker-compose.yml \ | |
| -f docker-compose.dev.yml \ | |
| up -d --no-build | |
| - | |
| name: Spin up store backend | |
| run: | | |
| cd store | |
| docker compose pull --ignore-buildable | |
| docker compose \ | |
| -f docker-compose.yml \ | |
| -f docker-compose.dev.yml \ | |
| up -d --no-build | |
| - | |
| name: Create Compose Database | |
| run: | | |
| cd compose | |
| until docker compose exec -T \ | |
| compose_pgsql pg_isready -U postgres; do sleep 1; done | |
| docker compose exec -T \ | |
| compose_pgsql \ | |
| psql -U postgres -c "create database compose" | |
| - | |
| name: Create Store Database | |
| run: | | |
| cd store | |
| until docker compose exec -T \ | |
| store_pgsql pg_isready -U postgres; do sleep 1; done | |
| docker compose exec -T \ | |
| store_pgsql \ | |
| psql -U postgres -c "create database neurostore" | |
| - | |
| name: Initialize Compose Database | |
| run: | | |
| cd compose | |
| docker compose exec -T compose \ | |
| bash -c \ | |
| "flask db merge heads && \ | |
| flask db stamp head && \ | |
| flask db migrate && \ | |
| flask db upgrade" | |
| - | |
| name: Initialize Store Database | |
| run: | | |
| cd store | |
| docker compose exec -T neurostore \ | |
| bash -c \ | |
| "flask db merge heads && \ | |
| flask db stamp head && \ | |
| flask db migrate && \ | |
| flask db upgrade" | |
| - | |
| name: Ingest data into Store | |
| run: | | |
| cd store | |
| docker compose exec -T neurostore bash -c "flask ingest-neurosynth --max-rows 100" | |
| - | |
| name: Ingest data into Compose | |
| run: | | |
| cd compose | |
| ipaddr=$(docker inspect neurostore | python3 -c "import sys, json; print(json.load(sys.stdin)[0]['NetworkSettings']['Networks']['nginx-proxy']['IPAddress'])") | |
| docker compose exec -T compose bash -c "flask create-meta-analyses --n-studysets 1 --neurostore-url http://${ipaddr}:8000" | |
| - | |
| name: Frontend Cypress E2E Tests | |
| uses: cypress-io/github-action@v6 | |
| env: | |
| CYPRESS_auth0ClientId: ${{ secrets.REACT_APP_AUTH0_CLIENT_ID }} | |
| CYPRESS_auth0ClientSecret: ${{ secrets.REACT_APP_AUTH0_CLIENT_SECRET }} | |
| CYPRESS_auth0Domain: ${{ secrets.REACT_APP_AUTH0_DOMAIN }} | |
| CYPRESS_auth0Audience: localhost | |
| REACT_APP_AUTH0_AUDIENCE: localhost | |
| REACT_APP_AUTH0_CLIENT_ID: ${{ secrets.REACT_APP_AUTH0_CLIENT_ID }} | |
| REACT_APP_AUTH0_DOMAIN: ${{ secrets.REACT_APP_AUTH0_DOMAIN }} | |
| REACT_APP_AUTH0_CLIENT_SECRET: ${{ secrets.REACT_APP_AUTH0_CLIENT_SECRET }} | |
| REACT_APP_ENV: DEV | |
| REACT_APP_NEUROSTORE_API_DOMAIN: ${{ secrets.REACT_APP_NEUROSTORE_API_DOMAIN }} | |
| REACT_APP_NEUROSYNTH_API_DOMAIN: ${{ secrets.REACT_APP_NEUROSYNTH_API_DOMAIN }} | |
| with: | |
| build: npm run build:dev | |
| start: npm run start-ci:dev | |
| browser: chrome | |
| wait-on: http://localhost:3000 | |
| working-directory: /home/runner/work/neurostore/neurostore/compose/neurosynth-frontend |