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Create Reports

Create Reports #1304

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Create Reports

Create Reports #1304

Workflow file for this run

.github/workflows/create_reports.yml at 2737d4c
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: 3.7
- 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: 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: 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"]'