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refactor: Clean up DB sessions consistently #2229

refactor: Clean up DB sessions consistently

refactor: Clean up DB sessions consistently #2229

Workflow file for this run

name: CI
on:
pull_request_target:
types: [assigned, opened, synchronize, reopened]
push:
branches:
- main
env:
GCS_PROJECT: qc-oss-mamba-org-quetz-dev
GCS_TOKEN: /home/runner/gcs/token.json
GCS_TOKEN_CONTENT: ${{ secrets.gcs_token_content }}
jobs:
test_quetz:
# timeout for the whole job
timeout-minutes: 10
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
test_database: ["sqlite", "postgres"]
db_init: ["use-migrations", "create-tables"]
services:
postgres:
image: postgres
env:
POSTGRES_PASSWORD: mysecretpassword
POSTGRES_USER: postgres
POSTGRES_DB: postgres
ports:
- 5432/tcp
# Set health checks to wait until postgres has started
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
redis:
image: redis
options: >-
--health-cmd "redis-cli ping"
--health-interval 10s
--health-timeout 5s
--health-retries 5
ports:
- 6379:6379
steps:
- uses: actions/checkout@v2
with:
ref: ${{ github.event.pull_request.head.sha }}
- name: write gcs token file
run: |
mkdir $(dirname "${GCS_TOKEN}")
echo "${GCS_TOKEN_CONTENT}" > "${GCS_TOKEN}"
- name: install mamba
uses: mamba-org/setup-micromamba@v1
with:
environment-file: environment.yml
- name: test quetz
shell: bash -l -eo pipefail {0}
env:
TEST_DB_BACKEND: ${{ matrix.test_database }}
QUETZ_TEST_DBINIT: ${{ matrix.db_init }}
POSTGRES_HOST: localhost
POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }}
S3_ACCESS_KEY: ${{ secrets.s3_access_key }}
S3_SECRET_KEY: ${{ secrets.s3_secret_key }}
S3_ENDPOINT: https://s3.sbg.cloud.ovh.net/
S3_REGION: sbg
S3_BUCKET_NAME: quetz
run: |
# install dev dependencies
pip install -e .[all,dev]
pip install redis rq
pip install pytest-github-actions-annotate-failures
- name: Testing server
shell: bash -l -eo pipefail {0}
# timeout for the step
timeout-minutes: 5
env:
TEST_DB_BACKEND: ${{ matrix.test_database }}
QUETZ_TEST_DBINIT: ${{ matrix.db_init }}
POSTGRES_HOST: localhost
POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }}
S3_ACCESS_KEY: ${{ secrets.s3_access_key }}
S3_SECRET_KEY: ${{ secrets.s3_secret_key }}
S3_ENDPOINT: https://s3.sbg.cloud.ovh.net/
S3_REGION: sbg
S3_BUCKET_NAME: quetz
run: |
if [ "$TEST_DB_BACKEND" == "postgres" ]; then
export QUETZ_TEST_DATABASE="postgresql://postgres:mysecretpassword@${POSTGRES_HOST}:${POSTGRES_PORT}/postgres"
echo "Running with postgres"
fi
if [ "$QUETZ_TEST_DBINIT" == "use-migrations" ]; then
echo "Using migrations"
fi
export QUETZ_IS_TEST=1
pytest -v ./quetz/tests/ --cov-config=pyproject.toml --cov=. --cov-report=xml --capture=no
- name: Test the plugins
shell: bash -l -eo pipefail {0}
env:
TEST_DB_BACKEND: ${{ matrix.test_database }}
QUETZ_TEST_DBINIT: ${{ matrix.db_init }}
POSTGRES_HOST: localhost
POSTGRES_PORT: ${{ job.services.postgres.ports[5432] }}
S3_ACCESS_KEY: ${{ secrets.s3_access_key }}
S3_SECRET_KEY: ${{ secrets.s3_secret_key }}
S3_ENDPOINT: https://s3.sbg.cloud.ovh.net/
S3_REGION: sbg
S3_BUCKET_NAME: quetz
run: |
if [ "$TEST_DB_BACKEND" == "postgres" ]; then
export QUETZ_TEST_DATABASE="postgresql://postgres:mysecretpassword@${POSTGRES_HOST}:${POSTGRES_PORT}/postgres"
echo "Running with postgres"
fi
# add micromamba to path
export PATH=$(dirname $MAMBA_EXE):$PATH
echo "adding micromamba to path: $MAMBA_EXE"
pip install --no-deps git+https://[email protected]/regro/libcflib@master
for f in ./plugins/quetz_*
do
echo "::group::Testing plugin ${f}"
quetz plugin install $f
# We want to test all the plugins, regardless of whether one fails
set +e
pytest -v $f
pytest_exit_code=$?
set -e
echo "::endgroup::"
if [ $pytest_exit_code -ne 0 ]; then
echo "::error::Tests for plugin $f failed!"
tests_failed="true"
fi
done
if [ "$tests_failed" == "true" ]; then
echo "::error::Some plugin tests failed!"
exit 1
fi
- uses: codecov/codecov-action@v1
with:
verbose: true
file: ./coverage.xml
test_release:
runs-on: ubuntu-latest
permissions:
contents: write
steps:
- uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: "3.10"
- name: install missing dependency
run: pip install ipython_genutils
- name: Get branch name
id: branch-name
uses: tj-actions/branch-names@eee8675bd61ec38bcfbfedd504d8473292ba649e
- name: Check Release
uses: jupyter-server/jupyter_releaser/.github/actions/check-release@v2
with:
token: ${{ secrets.GITHUB_TOKEN }}