edit merge statement #207
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 | |