Definition of Data acquisition method in the specification [DO NOT MERGE] #2465
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# This workflow will install Python dependencies and run the included validation script. | |
name: Validate annotations | |
on: | |
push: | |
branches: [ master, dev ] | |
paths: | |
- 'annotated-projects/**' | |
pull_request: | |
branches: [ master, dev ] | |
paths: | |
- 'annotated-projects/**' | |
jobs: | |
sdrf_proteomics_validations: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v2 | |
with: | |
fetch-depth: 0 | |
- name: Set up Python 3.8 | |
uses: actions/setup-python@v2 | |
with: | |
python-version: 3.8 | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install wheel | |
pip install git+https://github.com/bigbio/sdrf-pipelines | |
- name: Get a list of changed files | |
if: github.event_name != 'schedule' | |
id: getfiles | |
run: | | |
export OUTFILE=$HOME/filelist.txt | |
if [ "${{ github.event_name }}" == pull_request ]; then | |
echo 'Changed files:' | |
git diff-tree --no-commit-id --name-only -r origin/${{ github.event.pull_request.base.ref }} ${{ github.sha }} | tee "$OUTFILE" | |
else | |
# push | |
if [ "${{ github.event.before }}" == "0000000000000000000000000000000000000000" ]; then | |
parent="origin/master" # compare with master as a last resort | |
else | |
parent="${{ github.event.before }}" | |
fi | |
git diff-tree --no-commit-id --name-only -r "$parent" ${{ github.sha }} | tee "$OUTFILE" | |
fi | |
- name: Run validation | |
run: | | |
if [ ${{ github.event_name }} == "schedule" ]; then | |
echo "Validating all projects (schedule)" | |
python validate.py -v | |
else | |
export FILELIST=$HOME/filelist.txt | |
cat "$FILELIST" | grep "*sdrf.tsv" | while read line; do echo "Changed file: $line"; parse_sdrf validate-sdrf --sdrf_file $line --skip_factor_validation --skip_experimental_design_validation --use_ols_cache_only; done | |
fi | |