Feat/bulk methylation templates #65
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# Build JSON-LD on pull requests with data model changes (starts with 'dm/') | |
name: schematic-schema-convert | |
on: | |
pull_request: # default types: opened, synchronize, reopened | |
branches: [main] | |
paths: | |
- 'modules/**' | |
workflow_dispatch: | |
jobs: | |
build: | |
# if: startsWith(github.head_ref, 'dm/') | |
runs-on: ubuntu-latest | |
steps: | |
- name: Install System Dependencies | |
run: | | |
sudo apt-get update | |
sudo apt-get install -y libcurl4-openssl-dev | |
- uses: actions/checkout@v3 | |
with: | |
ref: ${{ github.event.pull_request.head.ref }} | |
persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. | |
fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository | |
- name: Convert schema | |
shell: bash | |
run: | | |
bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install) | |
git clone --depth 1 https://github.com/anngvu/retold.git | |
make | |
- name: Commit files | |
run: | | |
git config user.email "[email protected]" | |
git config user.name "gf-dcc-service" | |
git commit -m "Build jsonld" -a | |
- name: Push changes | |
uses: ad-m/github-push-action@master | |
with: | |
github_token: ${{ secrets.GITHUB_TOKEN }} | |
branch: ${{ github.event.pull_request.head.ref }} | |
# Additionally test PRs | |
test: | |
name: Test with schematic | |
needs: [build] | |
runs-on: ubuntu-22.04 | |
env: | |
SCHEMATIC_SERVICE_ACCT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }} | |
permissions: | |
pull-requests: write | |
strategy: | |
matrix: | |
schematic-version: [23.9.1] | |
steps: | |
- uses: actions/checkout@v3 | |
with: | |
ref: ${{ github.event.pull_request.head.ref }} | |
fetch-depth: 1 | |
- name: Setup schematic | |
id: setup-schematic | |
run: pip3 install schematicpy==${{ matrix.schematic-version }} | |
- name: Test generate googlesheets | |
working-directory: tests/generate | |
continue-on-error: true | |
run: ./basic_templates.sh | |
# TODO Step for test validation of data | |
# TODO Step for test submission of data | |
- name: Create test suite report | |
working-directory: tests | |
continue-on-error: true | |
run: docker run -v $(pwd):/tests rocker/tidyverse R -e "rmarkdown::render('tests/test-suite-report.Rmd')" | |
- name: Report on test suite as PR comment | |
uses: mshick/add-pr-comment@v2 | |
with: | |
message-id: test-suite-report | |
message-path: | | |
tests/test-suite-report.md | |
- name: Upload test artifacts | |
uses: actions/upload-artifact@v3 | |
with: | |
name: test-logs-${{ matrix.schematic-version }} | |
path: tests/**/logs |