#387 finishing up the different edge types #472
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 |