fixes #303
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python application | |
| on: | |
| push: | |
| branches: '**' | |
| tags: '**' | |
| pull_request: | |
| branches: '**' | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.10 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: "3.7" | |
| - name: Start databases | |
| run: | | |
| docker run -d --name db -p 7474:7474 -p 7687:7687 --env=NEO4J_AUTH=neo4j/test --env=NEOREADONLY=false --env=NEO4J_dbms_read__only=false --env=NEO4J_dbms_memory_heap_maxSize=1G --volume=$(pwd)/src/:/import/ virtualflybrain/vfb-prod:kb-v4-2 | |
| docker run -d --name pdb -p 7475:7474 -p 7688:7687 --env=NEO4J_AUTH=neo4j/test --env=NEOREADONLY=false --env=NEO4J_dbms_read__only=false --env=NEO4J_dbms_memory_heap_maxSize=1G --env=NEO4J_HEAP_MEMORY=2560 --volume=$(pwd)/src/:/import/ virtualflybrain/docker-vfb-neo4j-productiondb | |
| sleep 60s | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8 | |
| continue-on-error: true | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Install VFBconnect | |
| run: | | |
| git clone https://github.com/VirtualFlyBrain/VFB_connect.git | |
| pip install -r VFB_connect/requirements.txt | |
| - name: KB checks | |
| timeout-minutes: 960 | |
| run: | | |
| echo -e "KB check:" | |
| sleep 190 | |
| export LANDING_PAGE="http://localhost:7474/browser/" | |
| Test () { export http_status=$(curl -s -i -u neo4j:test $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "200" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; } | |
| Test || : | |
| sleep 30 | |
| curl -sSf -u neo4j:test "$LANDING_PAGE" | |
| - name: PDB checks | |
| timeout-minutes: 960 | |
| run: | | |
| echo -e "PDB check:" | |
| export LANDING_PAGE="http://localhost:7475/browser/" | |
| Test () { export http_status=$(curl -s -i -u neo4j:test $LANDING_PAGE | grep HTTP/1.1 | awk {'print $2'}); echo "Returned status \"$http_status\""; if [ "$http_status" != "200" ]; then echo "Waiting for docker to finish building..."; iterations=$((iterations+1)); if [ "$iterations" != "200" ]; then sleep 1; Test; fi; else echo "$(date) - connected successfully"; fi; } | |
| Test || : | |
| sleep 30 | |
| curl -sSf -u neo4j:test "$LANDING_PAGE" | |
| - name: KB startup log | |
| if: always() | |
| run: | | |
| echo -e "KB log" | |
| docker logs db | |
| - name: PDB startup log | |
| if: always() | |
| run: | | |
| echo -e "PDB log" | |
| docker logs pdb | |
| - name: Run KB_tools_test | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH":/"$(pwd)/VFB_connect/src | |
| cd src | |
| python -m uk.ac.ebi.vfb.neo4j.test.KB_tools_test | |
| - name: Run neo_tools_tests | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH":/"$(pwd)/VFB_connect/src | |
| cd src | |
| python -m uk.ac.ebi.vfb.neo4j.test.neo_tools_tests | |
| - name: Run feature_tools_tests | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH":/"$(pwd)/VFB_connect/src | |
| cd src | |
| python -m uk.ac.ebi.vfb.neo4j.flybase2neo.test.feature_tools_tests | |
| - name: Run pub_tools_tests | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH":/"$(pwd)/VFB_connect/src | |
| cd src | |
| python -m uk.ac.ebi.vfb.neo4j.flybase2neo.test.pub_tools_tests | |
| - name: Run flybase2neo expression_runner test | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH":/"$(pwd)/VFB_connect/src | |
| export IMPORT=$(pwd)/src/ | |
| cd src | |
| python -m uk.ac.ebi.vfb.neo4j.flybase2neo.expression_runner --test http://localhost:7475 neo4j test $IMPORT | |
| - name: Run flybase2neo add_refs_for_anat | |
| run: | | |
| export PYTHONPATH=$PYTHONPATH":/"$(pwd)/VFB_connect/src | |
| cd src | |
| python -m uk.ac.ebi.vfb.neo4j.flybase2neo.add_refs_for_anat http://localhost:7475 neo4j test | |