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python-app.yml
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name: OMERO
on:
push:
pull_request:
jobs:
test:
name: Run integration tests against OMERO
runs-on: ubuntu-latest
steps:
- name: Checkout omero-test-infra
uses: actions/checkout@main
with:
repository: ome/omero-test-infra
path: .omero
- name: Launch OMERO test database
run: .omero/compose up -d
env:
ROOTPASS: omero
POSTGRES_IMAGE: postgres
POSTGRES_VERSION: 10
POSTGRES_PASSWORD: postgres
OMERO_SERVER_IMAGE: openmicroscopy/omero-server
OMERO_SERVER_VERSION: 5
OMERO_SERVER_TCP: "4063:"
OMERO_SERVER_SSL: "4064:"
OMERO_WEB_IMAGE: openmicroscopy/omero-web-standalone
OMERO_WEB_VERSION: 5
OMERO_WEB_PORT: "4080:"
BUILD_IMAGE: adoptopenjdk:11-jdk-hotspot-bionic
- name: checkout arc_omero
uses: actions/checkout@v3
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.9"
cache: 'pip' # caching pip dependencies
- name: Build arc_omero
run: |
wget https://downloads.openmicroscopy.org/bio-formats/7.2.0/artifacts/bftools.zip
unzip bftools.zip
pip install --upgrade pip
pip install "omero-cli-transfer @ git+https://github.com/MicheleBortol/omero-cli-transfer.git@omero_arc_importer"
pip install ".[dev]"
- name: Import datasets
run: |
export PATH=$(pwd)/bftools:$PATH
omero login --user root --password omero localhost
omero transfer prepare --plugin arc_omero test/data/arcs/Resolve/assays/ResolveMolecularCartography/dataset
omero transfer unpack --folder test/data/arcs/Resolve/assays/ResolveMolecularCartography/dataset
- name: Run tests
run: |
pip install pytest
pytest -v
- name: Checkout omero-test-infra
uses: actions/checkout@main
with:
repository: ome/omero-test-infra
path: .omero
- name: Stop OMERO test database
run: .omero/compose down