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Revert EmitUnpopulated back to true in server/server.go #203

Revert EmitUnpopulated back to true in server/server.go

Revert EmitUnpopulated back to true in server/server.go #203

# 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 }}