Revert EmitUnpopulated back to true
in server/server.go
#203
Workflow file for this run
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# Workflow for running the TES compliance suite against Funnel | |
# This includes the following steps: | |
# 1. Build Funnel and store the resulting binary artifact | |
# 2. Install tes-compliance-suite and run against every version of TES simultaneously | |
# 3. start-report-deployment: Send a dispatch to the funnel-compliance repository to generate and publish | |
# the tes-compliance-suite report to https://ohsu-comp-bio.github.io/funnel-compliance/ | |
# Optionally debug via SSH | |
# Ref: https://fleetdm.com/engineering/tips-for-github-actions-usability | |
# | |
# To use this step uncomment and place anywhere in the build steps. The build will pause on this step and | |
# output a ssh address associated with the Github action worker. Helpful for debugging build steps and | |
# and intermediary files/artifacts. | |
# | |
# Example: | |
# Web shell: https://tmate.io/t/q8FU3U9SvmMVxAhMHRyExNhr8 | |
# SSH: ssh q8FU3U9SvmMVxAhMHRyExNhr8@sfo2.tmate.io | |
# | |
# - name: "Debug: Package dependancies for tmate (CentOS)" | |
# run: | | |
# yum install -y xz | |
# ln -s /bin/true /bin/apt-get | |
# | |
# - name: Setup tmate session | |
# uses: mxschmitt/action-tmate@v3 | |
name: Compliance Test | |
on: | |
push: | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
container: quay.io/ohsu-comp-bio/slurm | |
steps: | |
- name: Set up Go 1.x | |
uses: actions/setup-go@v2 | |
with: | |
go-version: ^1.18 | |
- name: Check out code | |
uses: actions/checkout@v2 | |
- name: Build | |
run: make build | |
- name: Store funnel | |
uses: actions/upload-artifact@v2 | |
with: | |
name: funnelBin | |
path: funnel | |
compliance: | |
strategy: | |
fail-fast: false | |
matrix: | |
version: [1.0.0, 1.1.0] | |
db: ["boltdb", "mongodb"] | |
compute: ["local", "slurm"] | |
needs: build | |
runs-on: ubuntu-latest | |
container: | |
image: quay.io/ohsu-comp-bio/slurm | |
options: --hostname slurmctl --cap-add sys_admin | |
steps: | |
# Required to access the 'tests/mongo.config.yml' file | |
# Perhaps uploading it as an artifact would be more efficient? | |
- name: Check out code | |
uses: actions/checkout@v2 | |
- uses: actions/download-artifact@v3 | |
with: | |
name: funnelBin | |
- name: Start Funnel server | |
run: | | |
touch config.yml | |
if [ ${{ matrix.db }} = "mongodb" ]; then | |
make start-mongodb | |
cat `pwd`/tests/mongo.config.yml >> config.yml | |
# Required for Funnel to connect MongoDB | |
echo "172.17.0.1 localhost" >> /etc/hosts | |
elif [ ${{ matrix.compute }} = "slurm" ]; then | |
cat `pwd`/tests/slurm.config.yml >> config.yml | |
cp config.yml /opt/funnel_config.yml | |
# Start Slurm | |
/usr/local/bin/docker-entrypoint.sh | |
fi | |
chmod +x funnel | |
FLAGS="--config `pwd`/config.yml" | |
./funnel server run $FLAGS &> funnel.logs & | |
- uses: actions/checkout@v3 | |
with: | |
repository: lbeckman314/tes-compliance-suite | |
ref: feature/tesv1.1 | |
path: tes-compliance-suite | |
- name: Install TES compliance suite | |
run: | | |
cd tes-compliance-suite | |
/root/.pyenv/shims/python3 -m venv venv | |
source venv/bin/activate | |
pip install -r requirements.txt | |
python setup.py install | |
mkdir reports | |
- name: Test compliance | |
run: | | |
cd tes-compliance-suite | |
source venv/bin/activate | |
tes-compliance-suite report --version "${{ matrix.version }}" --server "http://localhost:8000/" | |
start-report-deployment: | |
needs: compliance | |
runs-on: ubuntu-latest | |
steps: | |
# https://docs.github.com/en/rest/repos/repos?apiVersion=2022-11-28#create-a-repository-dispatch-event | |
- name: Start report generation | |
uses: passeidireto/trigger-external-workflow-action@main | |
env: | |
PAYLOAD_AUTHOR: "Funnel" | |
PAYLOAD_REVISION: "3" | |
with: | |
repository: ohsu-comp-bio/funnel-compliance | |
event: start-report | |
github_pat: ${{ secrets.ACTIONS_TOKEN }} | |