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pull-request.yml
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name: pr-test
on: pull_request
jobs:
test:
runs-on: ubuntu-20.04
strategy:
matrix:
infrastructure:
- name: galaxy-base
files: -f docker-compose.yml
exclude_test:
- workflow_example1
- name: galaxy-proxy-prefix
files: -f docker-compose.yml
env: GALAXY_PROXY_PREFIX=/arbitrary_Galaxy-prefix GALAXY_CONFIG_GALAXY_INFRASTRUCTURE_URL=http://localhost/arbitrary_Galaxy-prefix
exclude_test:
- workflow_example1
- name: galaxy-htcondor
files: -f docker-compose.yml -f docker-compose.htcondor.yml
exclude_test:
- workflow_example1
- name: galaxy-slurm
files: -f docker-compose.yml -f docker-compose.slurm.yml
env: SLURM_NODE_COUNT=3
options: --scale slurm_node=3
exclude_test:
- workflow_example1
- name: galaxy-pulsar
files: -f docker-compose.yml -f docker-compose.pulsar.yml
exclude_test:
- workflow_example1
- workflow_mapping_by_sequencing
- workflow_ard
# - name: galaxy-pulsar-mq
# files: -f docker-compose.yml -f docker-compose.pulsar.yml -f docker-compose.pulsar.mq.yml
# exclude_test:
# - workflow_example1
# - workflow_mapping_by_sequencing
- name: galaxy-k8s
files: -f docker-compose.yml -f docker-compose.k8s.yml
exclude_test:
- bioblend
- workflow_ard
- workflow_mapping_by_sequencing
- workflow_example1
- selenium
- name: galaxy-singularity
files: -f docker-compose.yml -f docker-compose.singularity.yml
exclude_test:
- bioblend
- workflow_ard
- workflow_mapping_by_sequencing
- selenium
# - name: galaxy-pulsar-mq-singularity
# files: -f docker-compose.yml -f docker-compose.pulsar.yml -f docker-compose.pulsar.mq.yml -f docker-compose.singularity.yml
# exclude_test:
# - bioblend
# - workflow_ard
# - workflow_mapping_by_sequencing
# - selenium
- name: galaxy-slurm-singularity
files: -f docker-compose.yml -f docker-compose.slurm.yml -f docker-compose.singularity.yml
exclude_test:
- bioblend
- workflow_ard
- workflow_mapping_by_sequencing
- selenium
- name: galaxy-htcondor-singularity
files: -f docker-compose.yml -f docker-compose.htcondor.yml -f docker-compose.singularity.yml
exclude_test:
- bioblend
- workflow_ard
- workflow_mapping_by_sequencing
- selenium
test:
- name: bioblend
files: -f tests/docker-compose.test.yml -f tests/docker-compose.test.bioblend.yml
exit-from: galaxy-bioblend-test
timeout: 60
second_run: "true"
- name: workflow_ard
files: -f tests/docker-compose.test.yml -f tests/docker-compose.test.workflows.yml
exit-from: galaxy-workflow-test
workflow: sklearn/ard/ard.ga
timeout: 60
second_run: "true"
- name: workflow_mapping_by_sequencing
files: -f tests/docker-compose.test.yml -f tests/docker-compose.test.workflows.yml
exit-from: galaxy-workflow-test
workflow: training/variant-analysis/mapping-by-sequencing/mapping_by_sequencing.ga
timeout: 60
- name: workflow_example1
files: -f tests/docker-compose.test.yml -f tests/docker-compose.test.workflows.yml
exit-from: galaxy-workflow-test
workflow: example1/wf3-shed-tools.ga
timeout: 60
- name: selenium
files: -f tests/docker-compose.test.yml -f tests/docker-compose.test.selenium.yml
exit-from: galaxy-selenium-test
timeout: 60
fail-fast: false
steps:
# Self-made `exclude` as Github Actions currently does not support
# exclude/including of dicts in matrices
- name: Check if test should be run
id: run_check
if: contains(matrix.infrastructure.exclude_test, matrix.test.name) != true
run: echo ::set-output name=run::true
- name: Checkout
uses: actions/checkout@v4
- name: Set WORKFLOWS env for worfklows-test
if: matrix.test.workflow
run: echo "WORKFLOWS=${{ matrix.test.workflow }}" >> $GITHUB_ENV
- name: Build galaxy-container-base
env:
image_name: galaxy-container-base
run: |
docker buildx build \
--output "type=image,name=quay.io/bgruening/$image_name:ci-testing" \
--build-arg IMAGE_TAG=ci-testing \
$image_name
working-directory: ./compose/base-images
- name: Build galaxy-cluster-base
env:
image_name: galaxy-cluster-base
run: |
docker buildx build \
--output "type=image,name=quay.io/bgruening/$image_name:ci-testing" \
--build-arg IMAGE_TAG=ci-testing \
$image_name
working-directory: ./compose/base-images
- name: Run tests for the first time
if: steps.run_check.outputs.run
run: |
export IMAGE_TAG=ci-testing
export COMPOSE_DOCKER_CLI_BUILD=1
export DOCKER_BUILDKIT=1
export ${{ matrix.infrastructure.env }}
export TIMEOUT=${{ matrix.test.timeout }}
docker-compose ${{ matrix.infrastructure.files }} ${{ matrix.test.files }} config
env
for i in {1..4}; do
echo "Running test - try \#$i"
echo "Removing export directory if existent";
sudo rm -rf export
set +e
docker-compose ${{ matrix.infrastructure.files }} ${{ matrix.test.files }} build --build-arg IMAGE_TAG=ci-testing --build-arg GALAXY_REPO=https://github.com/galaxyproject/galaxy
docker-compose ${{ matrix.infrastructure.files }} ${{ matrix.test.files }} up ${{ matrix.infrastructure.options }} --exit-code-from ${{ matrix.test.exit-from }}
test_exit_code=$?
error_exit_codes_count=$(expr $(docker ps -a --filter exited=1 | wc -l) - 1)
docker-compose ${{ matrix.infrastructure.files }} ${{ matrix.test.files }} down
if [ $error_exit_codes_count != 0 ] || [ $test_exit_code != 0 ] ; then
echo "Test failed..";
continue;
else
exit $test_exit_code;
fi
done;
exit 1
shell: bash
working-directory: ./compose
continue-on-error: false
- name: Allow upload-artifact read access
if: failure()
run: sudo chmod -R +r ./compose/export/galaxy/database
- name: Save artifacts for debugging a failed test
uses: actions/upload-artifact@v1
if: failure()
with:
name: ${{ matrix.infrastructure.name }}_${{ matrix.test.name }}_first-run
path: ./compose/export/galaxy/database
- name: Clean up after first run
if: matrix.test.second_run == 'true'
run: |
sudo rm -rf export/postgres
sudo rm -rf export/galaxy/database
working-directory: ./compose
- name: Run tests a second time
if: matrix.test.second_run == 'true' && steps.run_check.run
run: |
export IMAGE_TAG=ci-testing
export COMPOSE_DOCKER_CLI_BUILD=1
export DOCKER_BUILDKIT=1
export ${{ matrix.infrastructure.env }}
export TIMEOUT=${{ matrix.test.timeout }}
for i in {1..4}; do
echo "Running test - try \#$i"
echo "Removing export directory if existent";
sudo rm -rf export
set +e
docker-compose ${{ matrix.infrastructure.files }} ${{ matrix.test.files }} up ${{ matrix.infrastructure.options }} --exit-code-from ${{ matrix.test.exit-from }}
test_exit_code=$?
error_exit_codes_count=$(expr $(docker ps -a --filter exited=1 | wc -l) - 1)
if [ $error_exit_codes_count != 0 ] || [ $test_exit_code != 0 ] ; then
echo "Test failed..";
continue;
else
exit $test_exit_code;
fi
done;
exit 1
shell: bash
working-directory: ./compose
continue-on-error: false
- name: Allow upload-artifact read access
if: failure()
run: sudo chmod -R +r ./compose/export/galaxy/database
- name: Save artifacts for debugging a failed test
uses: actions/upload-artifact@v1
if: failure() && matrix.test.second_run == 'true'
with:
name: ${{ matrix.infrastructure.name }}_${{ matrix.test.name }}_second-run
path: ./compose/export/galaxy/database