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Add dedicated seqr sync module to db layers #3679

Add dedicated seqr sync module to db layers

Add dedicated seqr sync module to db layers #3679

Workflow file for this run

name: Unittests
on: push
jobs:
run-unittests:
# Run on merge to main, where the commit name starts with "Bump version:" (for bump2version)
# if: "startsWith(github.event.head_commit.message, 'Bump version:')"
runs-on: ubuntu-latest
env:
DOCKER_BUILDKIT: 1
BUILDKIT_PROGRESS: plain
CLOUDSDK_CORE_DISABLE_PROMPTS: 1
# used for generating API
SM_DOCKER: samplemetadata:dev
defaults:
run:
shell: bash -eo pipefail -l {0}
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: "3.11"
- uses: actions/setup-java@v4
with:
distribution: "temurin" # See 'Supported distributions' for available options
java-version: "17"
- name: Setup build env
run: |
set -euxo pipefail
pip install --no-deps -r requirements-dev.txt
# openapi-generator
wget https://repo1.maven.org/maven2/org/openapitools/openapi-generator-cli/5.3.0/openapi-generator-cli-5.3.0.jar -O openapi-generator-cli.jar
# liquibase connector
pushd db/
wget https://repo1.maven.org/maven2/org/mariadb/jdbc/mariadb-java-client/3.0.3/mariadb-java-client-3.0.3.jar
popd
# liquibase
VERSION=4.28.0
curl -L https://github.com/liquibase/liquibase/releases/download/v${VERSION}/liquibase-${VERSION}.zip --output liquibase-${VERSION}.zip
unzip -o -d liquibase liquibase-${VERSION}.zip
echo "$(pwd)/liquibase" >> $GITHUB_PATH
- name: "build image"
run: |
docker build \
--build-arg SM_ENVIRONMENT=local \
--tag $SM_DOCKER \
-f deploy/api/Dockerfile \
.
- name: "build deployable API"
run: |
export OPENAPI_COMMAND="java -jar openapi-generator-cli.jar"
python regenerate_api.py
pip install .
- name: "Run unit tests"
id: runtests
run: |
coverage run -m unittest discover -p 'test*.py' -s '.'
rc=$?
coverage xml
echo "rc=$rc" >> $GITHUB_OUTPUT
- name: "Upload coverage report"
uses: codecov/codecov-action@v4
with:
files: ./coverage.xml
token: ${{ secrets.CODECOV_TOKEN }}
- name: "build web front-end"
run: |
set -eo pipefail
pushd web
# installs package-lock, not what it thinks it should be
npm ci
npm run build
rc=$?
echo "web_rc=$rc" >> $GITHUB_OUTPUT
# eventually run web front-end tests
popd
- name: Fail if unit tests are not passing
if: ${{ steps.runtests.outputs.rc != 0}}
uses: actions/github-script@v6
with:
script: |
core.setFailed('Unittests failed with rc = ${{ steps.runtests.outputs.rc }}')
- name: Fail if web build fails
if: ${{ steps.runtests.outputs.rc != 0}}
uses: actions/github-script@v6
with:
script: |
core.setFailed('Web failed to build with rc = ${{ steps.runtests.outputs.web_rc }}')