Update graph-tests.yml #8
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| name: download-neo4j | |
| on: [push] | |
| jobs: | |
| job_1: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: '3.10' | |
| - name: Download Neo4j | |
| run: | | |
| curl -fsSL https://debian.neo4j.com/neotechnology.gpg.key |sudo gpg --dearmor -o /usr/share/keyrings/neo4j.gpg | |
| echo "deb [signed-by=/usr/share/keyrings/neo4j.gpg] https://debian.neo4j.com stable 4.1" | sudo tee -a /etc/apt/sources.list.d/neo4j.list | |
| sudo apt update | |
| sudo apt install neo4j | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements-tests.txt | |
| - name: Download OSF files #osf -p 6jtc9 fetch Datasets/Datasets.zip Datasets.zip; unzip Datasets.zip; | |
| run: | | |
| echo 'Downloading OSF data...'; | |
| osf -p 6jtc9 fetch Datasets/Petagraph_datasets.zip Petagraph_datasets.zip; | |
| unzip Petagraph_datasets.zip; rm Petagraph_datasets.zip; | |
| osf -p 6jtc9 fetch reduced_csvs_github_actions.zip reduced_csvs_github_actions.zip; | |
| unzip reduced_csvs_github_actions.zip; rm reduced_csvs_github_actions.zip; | |
| echo 'Finished Downloading and unzipping....'; | |
| ls data; | |
| - name: Build Petagraph | |
| run: | | |
| sudo chmod 777 -R /var/lib/neo4j/; sudo chmod 777 -R /etc/neo4j; | |
| sudo chmod 777 -R /var/log/neo4j/; sudo chmod 777 -R /var/run/neo4j | |
| mv reduced_csvs_github_actions/C*.csv /var/lib/neo4j/import/; | |
| rm -rf /var/lib/neo4j/data/databases/* | |
| rm -rf /var/lib/neo4j/data/transactions/* | |
| cd /var/lib/neo4j/ | |
| export HEAP_SIZE=1G; echo heapsize set to: $HEAP_SIZE | |
| neo4j-admin import --verbose --nodes=Concept="import/CUIs.csv" --relationships="import/CUI-CUIs.csv" --nodes=Code="import/CODEs.csv" --relationships=CODE="import/CUI-CODEs.csv" --skip-bad-relationships --skip-duplicate-nodes | |
| echo 'starting database...' | |
| neo4j start | |
| - name: Run tests # cat /etc/neo4j/neo4j.conf , echo 'test string' > .github/graph_test_logs/logfile.txt | |
| run: | | |
| python3 tests/Petagraph_ingestion_test_auto.py | |
| - name: Upload Artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: QC Report | |
| path: .github/graph_test_logs/logfile.txt | |