Update #3080
Workflow file for this run
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name: check_dataset | |
# This workflow is triggered on pushes and PRs to the repository. | |
on: | |
pull_request: | |
branches: [master] | |
jobs: | |
AMDirT: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v4 | |
- uses: actions/setup-python@v4 | |
with: | |
python-version: "3.9" | |
architecture: "x64" | |
- name: Install dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install amdirt==1.6.2 | |
pip install jsonschema==4.17.0 | |
- name: Make validation results directory | |
run: mkdir validation/ | |
- name: Add AMDirT validate version | |
run: | | |
echo "$(AMDirT --version)" > validation/validation_results_raw.txt | |
- name: SAMPLES test ancient host-associated metagenome (e.g. microbiomes) | |
if: always() | |
run: | | |
echo "# Samples" >> validation/validation_results_raw.txt | |
echo "## Ancient Metagenome Host Associated" >> validation/validation_results_raw.txt | |
AMDirT validate -s -d -c -i -m --multi_values archive_accession ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples_schema.json &>> validation/validation_results_raw.txt | |
- name: SAMPLES test ancient single microbial genomes (e.g. pathogens) | |
if: always() | |
run: | | |
echo "## Ancient Single Genome Host Associated" >> validation/validation_results_raw.txt | |
AMDirT validate -s -d -c -i -m --multi_values archive_accession ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples_schema.json &>> validation/validation_results_raw.txt | |
- name: SAMPLES test ancient environmental (e.g. sediment) | |
if: always() | |
run: | | |
echo "## Ancient Metagenome Environmental" >> validation/validation_results_raw.txt | |
AMDirT validate -s -d -c -i -m --multi_values archive_accession ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples_schema.json &>> validation/validation_results_raw.txt | |
- name: LIBRARIES test ancient host-associated metagenome (e.g. microbiomes) | |
if: always() | |
run: | | |
echo "# Libraries" >> validation/validation_results_raw.txt | |
echo "## Ancient Metagenome Host Associated" >> validation/validation_results_raw.txt | |
AMDirT validate -s -d -c -m ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries_schema.json &>> validation/validation_results_raw.txt | |
- name: LIBRARIES test ancient host-associated single-genomes (e.g. pathogens) | |
if: always() | |
run: | | |
echo "## Ancient Single Genome Host Associated" >> validation/validation_results_raw.txt | |
AMDirT validate -s -d -c -m ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries_schema.json &>> validation/validation_results_raw.txt | |
- name: LIBRARIES test ancient environmental metagenomes (e.g. sedaDNA) | |
if: always() | |
run: | | |
echo "## Ancient Metagenome Environmental" >> validation/validation_results_raw.txt | |
AMDirT validate -s -d -c -m ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries_schema.json &>> validation/validation_results_raw.txt | |
- name: cleanup validation results from streamlit warnings | |
if: always() | |
run: | | |
grep -v streamlit validation/validation_results_raw.txt > validation/validation_results.txt | |
- uses: actions/upload-artifact@v3 | |
if: always() | |
with: | |
name: results | |
path: validation/validation_results.txt | |
- uses: actions/download-artifact@v3 | |
if: always() | |
with: | |
name: results | |
- name: comment PR | |
if: always() | |
uses: mshick/add-pr-comment@v2 | |
env: | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
with: | |
message-path: validation/validation_results.txt | |
refresh-message-position: true |