Merge pull request #452 from CIMAC-CIDC/add-rna-enrichment-method #979
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: Continuous Integration | |
on: | |
push: | |
branches: ["*"] | |
pull_request: | |
branches: ["*"] | |
jobs: | |
test: | |
strategy: | |
matrix: | |
python-version: [3.8, 3.9] | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v2 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install -r requirements.dev.txt | |
- name: Check code format with black | |
run: | | |
black --check functions main.py --target-version=py37 | |
- name: Test with pytest | |
run: | | |
pytest | |
deploy: | |
runs-on: ubuntu-latest | |
needs: test | |
if: ${{ github.ref == 'refs/heads/master' || github.ref == 'refs/heads/production' }} | |
strategy: | |
matrix: | |
include: | |
- name: ingest_upload | |
topic: uploads | |
timeout: 540 | |
memory: 2048 | |
- name: send_email | |
topic: emails | |
timeout: 60 | |
memory: 512 | |
- name: store_auth0_logs | |
topic: daily_cron | |
timeout: 120 | |
memory: 1024 | |
- name: disable_inactive_users | |
topic: daily_cron | |
timeout: 120 | |
memory: 1024 | |
- name: refresh_download_permissions | |
topic: daily_cron | |
timeout: 120 | |
memory: 1024 | |
- name: vis_preprocessing | |
topic: artifact_upload | |
timeout: 540 | |
memory: 1024 | |
max_instances: 10 | |
- name: derive_files_from_manifest_upload | |
topic: patient_sample_update | |
timeout: 60 | |
memory: 1024 | |
- name: derive_files_from_assay_or_analysis_upload | |
topic: assay_or_analysis_upload_complete | |
timeout: 540 | |
memory: 1024 | |
- name: update_cidc_from_csms | |
topic: csms_trigger | |
timeout: 540 | |
memory: 1024 | |
- name: grant_download_permissions | |
topic: grant_download_perms | |
timeout: 540 | |
memory: 1024 | |
- name: worker | |
topic: worker | |
timeout: 540 | |
memory: 1024 | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Set up Cloud SDK | |
uses: google-github-actions/setup-gcloud@v0 | |
with: | |
project_id: ${{ github.ref == 'refs/heads/production' && 'cidc-dfci' || 'cidc-dfci-staging' }} | |
service_account_key: ${{ github.ref == 'refs/heads/production' && secrets.GCP_SA_KEY_PROD || secrets.GCP_SA_KEY_STAGING }} | |
export_default_credentials: true | |
- name: Deploy ${{ matrix.name }} to Cloud Functions | |
env: | |
ENV_VARS_FILE: ${{ github.ref == 'refs/heads/production' && '.env.prod.yaml' || '.env.staging.yaml' }} | |
run: | | |
gcloud functions deploy ${{ matrix.name }} \ | |
--trigger-topic ${{ matrix.topic }} \ | |
--timeout ${{ matrix.timeout }} \ | |
--memory ${{ matrix.memory }} \ | |
--env-vars-file $ENV_VARS_FILE \ | |
--runtime python37 \ | |
${{ matrix.max_instances && format('--max-instances {0}', matrix.max_instances) || ''}} |