Merge pull request #413 from RTXteam/dkoslicki-patch-2 #534
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| # This workflow is based on GitHub's CI example for Python | |
| name: RTX-KG2 Continous Integration | |
| on: [push, pull_request] | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Export Path | |
| run: | | |
| export PATH=$PATH:~/kg2-build/ | |
| - name: Setup KG2 Build | |
| run: | | |
| git clone https://github.com/RTXteam/RTX-KG2 | |
| cd RTX-KG2 | |
| git checkout $GITHUB_REF_NAME | |
| bash -x ./setup/setup-kg2-build.sh ci | |
| - name: Run Tests | |
| run: | | |
| cd /home/runner/work/RTX-KG2/RTX-KG2/RTX-KG2 | |
| bash -x ./validate/run-validation-tests.sh | |
| bash -x ./build/build-kg2-snakemake.sh all -n ci | |
| bash -x ./build/build-kg2-snakemake.sh all -n ci | |
| bash -x ./build/build-kg2-snakemake.sh all -R_Merge -n ci | |
| bash -x ./build/build-kg2-snakemake.sh all -R_Finish -n ci | |
| bash -x ./build/build-kg2-snakemake.sh all -F -n ci | |
| - name: Test Building One File | |
| run: | | |
| cd /home/runner/work/RTX-KG2/RTX-KG2/RTX-KG2 | |
| bash -x ./extract/extract-mirbase.sh ~/kg2-build/miRNA.dat | |
| ~/kg2-venv/bin/python3 -u convert/mirbase_dat_to_kg_jsonl.py ~/kg2-build/miRNA.dat ~/kg2-build/kg2-mirbase-nodes.jsonl ~/kg2-build/kg2-mirbase-edges.jsonl --test | |
| ~/kg2-venv/bin/python3 -u process/report_stats_on_kg_jsonl.py ~/kg2-build/kg2-mirbase-nodes.jsonl ~/kg2-build/kg2-mirbase-edges.jsonl ~/kg2-build/kg2-mirbase-report.json | |
| cat ~/kg2-build/kg2-mirbase-report.json |