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Definition of Data acquisition method in the specification [DO NOT MERGE] #2462

Definition of Data acquisition method in the specification [DO NOT MERGE]

Definition of Data acquisition method in the specification [DO NOT MERGE] #2462

Workflow file for this run

# 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