Skip to content

Validate annotations #2393

Validate annotations

Validate annotations #2393

Workflow file for this run

# This workflow will install Python dependencies and run the included validation script.
name: Validate annotations
on:
push:
paths:
- 'annotated-projects/**'
- 'validate.py'
pull_request:
branches: [ master ]
paths:
- 'annotated-projects/**'
- 'validate.py'
schedule:
- cron: '0 0 * * *'
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 "$FILELIST"
if grep -q '^validate.py' "$FILELIST"; then
echo "Validating all projects (script changed)"
python validate.py -v
else
projects=$(cat "$FILELIST" | grep '^annotated-projects' | cut -d/ -f 2)
echo "Validating projects:" $projects
python validate.py -v $projects
fi
fi
# mage_tab_validation:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v2
# - name: Setup conda
# uses: s-weigand/setup-conda@v1
# with:
# update-conda: true
# conda-channels: anaconda, bioconda, conda-forge
# - name: Install perl-atlas-modules
# run: conda create -n perl-atlas -c ebi-gene-expression-group -c bioconda perl-atlas-modules perl-graphviz
# - name: Validate General MAGE-TAB
# run: |
# . /usr/share/miniconda/bin/activate /usr/share/miniconda/envs/perl-atlas
# perl simple_validate_magetab.pl
# - name: Archive production artifacts
# uses: actions/upload-artifact@v2
# with:
# name: sdrf-picture
# path: graph_file_sdrf.png
# retention-days: 5
# mage_tab_expression_atlas_validations:
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v2
# - name: Setup conda
# uses: s-weigand/setup-conda@v1
# with:
# update-conda: true
# conda-channels: anaconda, bioconda, conda-forge
# - name: Install perl-atlas-modules
# run: conda create -n perl-atlas -c ebi-gene-expression-group perl-atlas-modules
# - name: Validate Expression Atlas MAGE-TAB
# id: atlas
# run: |
# . /usr/share/miniconda/bin/activate /usr/share/miniconda/envs/perl-atlas
# perl validate_magetab.pl -i annotated-projects/PXD000288/PXD000288.idf.tsv -x -c -v
# RSPEC_RESULT=$?
# exit 0