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fix: workflow yaml #2117

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fix: workflow yaml

fix: workflow yaml #2117

Workflow file for this run

.github/workflows/workflow.yml at 7040343
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 }}
VITE_APP_AUTH0_CLIENT_ID: ${{ secrets.VITE_APP_AUTH0_CLIENT_ID }}
VITE_APP_AUTH0_DOMAIN: ${{ secrets.VITE_APP_AUTH0_DOMAIN }}
VITE_APP_AUTH0_CLIENT_SECRET: ${{ secrets.VITE_APP_AUTH0_CLIENT_SECRET }}
run: |
cp neurosynth-frontend/.env.example neurosynth-frontend/.env.dev && \
docker compose run \
-e "APP_SETTINGS=neurosynth_compose.config.DockerTestConfig" \
-e "AUTH0_CLIENT_ID=${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 "VITE_APP_AUTH0_DOMAIN=${VITE_APP_AUTH0_DOMAIN}" \
-e "VITE_APP_AUTH0_CLIENT_ID=${VITE_APP_AUTH0_CLIENT_ID}" \
-e "VITE_APP_AUTH0_AUDIENCE=https://neurostore.xyz/api/" \
-e "VITE_APP_AUTH0_CLIENT_SECRET=${VITE_APP_AUTH0_CLIENT_SECRET}" \
-e "VITE_APP_ENV=STAGING" \
-e "VITE_APP_NEUROSTORE_API_DOMAIN=http://localhost/api" \
-e "CI=true" \
-e "VITE_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.VITE_APP_AUTH0_CLIENT_ID }}
CYPRESS_auth0ClientSecret: ${{ secrets.VITE_APP_AUTH0_CLIENT_SECRET }}
CYPRESS_: ${{ secrets.VITE_APP_AUTH0_DOMAIN }}
CYPRESS_auth0Audience: https://neurostore.xyz/api/
CYPRESS_RECORD_KEY: ${{ secrets.CYPRESS_RECORD_KEY }}
VITE_APP_AUTH0_AUDIENCE: https://neurostore.xyz/api/
VITE_APP_AUTH0_CLIENT_ID: ${{ secrets.VITE_APP_AUTH0_CLIENT_ID }}
VITE_APP_AUTH0_DOMAIN: ${{ secrets.VITE_APP_AUTH0_DOMAIN }}
VITE_APP_AUTH0_CLIENT_SECRET: ${{ secrets.VITE_APP_AUTH0_CLIENT_SECRET }}
VITE_APP_ENV: STAGING
VITE_APP_NEUROSTORE_API_DOMAIN: ${{ secrets.VITE_APP_NEUROSTORE_API_DOMAIN }}
VITE_APP_NEUROSYNTH_API_DOMAIN: ${{ secrets.VITE_APP_NEUROSYNTH_API_DOMAIN }}
with:
build: npm run build:staging
record: true
start: npm run serve-build
browser: chrome
wait-on: http://localhost:3000
working-directory: /home/runner/work/neurostore/neurostore/compose/neurosynth-frontend