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#408 cURL issue with HMDB #519

#408 cURL issue with HMDB

#408 cURL issue with HMDB #519

Workflow file for this run

# 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