Create Reports #2147
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| name: Create Reports | |
| on: | |
| schedule: | |
| - cron: "0 0 * * *" | |
| workflow_dispatch: | |
| jobs: | |
| notebooks: | |
| name: "Generate Reports" | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Pull Code | |
| run: | | |
| git clone https://github.com/VirtualFlyBrain/VFB_reporting.git | |
| git clone https://github.com/VirtualFlyBrain/VFB_neo4j.git --branch neo4-2 --single-branch | |
| ln -s ../ ./VFB_reporting/VFB_reporting_results | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install -U pip | |
| python -m pip install -r VFB_reporting/requirements.txt | |
| python -m pip install -r VFB_neo4j/requirements.txt | |
| - name: Run query tools test | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./test/query_tools_test.py | |
| - name: Run report runner | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./report_runner.py | |
| - name: Run comparison | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./comparison.py | |
| - name: Run get catmaid cellTypes | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./get_catmaid_cellTypes.py | |
| - name: Run get catmaid papers | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./get_catmaid_papers.py | |
| - name: Run VFB content report generator | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./VFB_content_report_generator.py | |
| - name: Run ID mapping tables | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./ID_mapping_tables.py | |
| - name: Run individual classification report | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./individual_classification_report.py | |
| - name: Run EM instance-FBbt conflict report | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./Instance_FBbt_conflict_report.py | |
| - name: Run connectome multiple symbol-bearing class report | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./connectome_multi_symbol_class_report.py | |
| - name: Run scRNAseq DataSet report | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| python ./scRNAseq_datasets.py | |
| - name: Create curation files | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH:$PWD/VFB_neo4j/src/ | |
| cd VFB_reporting/src | |
| rm -vf ../VFB_reporting_results/anat_*.tsv | |
| rm -vf ../VFB_reporting_results/anat_*.yaml | |
| ls -lh ../VFB_reporting_results/ | |
| python ./make_curation_records/anat_curation_file_maker.py | |
| - name: Regenerate README | |
| run: | | |
| cat README_header.md VFB_reporting/reports.md > README.md | |
| - name: Clean up | |
| run: | | |
| rm -rfv VFB_reporting | |
| rm -rfv VFB_neo4j | |
| - name: On Completion | |
| run: | | |
| git config --global user.email "support@virtualflybrain.org" | |
| git config --global user.name "gitHub actions" | |
| git add . | |
| git status | |
| - name: Commit changes | |
| uses: EndBug/add-and-commit@v7 | |
| with: | |
| author_name: GitHub Actions | |
| author_email: support@virtualflybrain.org | |
| message: 'Automated report run' | |
| add: '["*.tsv","*.md --force"]' |