OMERO

Merge branch 'main' into ontop #1

	# Install and test and OMERO plugin e.g. a Web app, a CLI plugin or a library
	#
	# This workflow will install omero-test-infra, start an OMERO environment
	# including database, server and web deployment, configure the OMERO plugin
	# and run integration tests.
	#
	# 1. Set up the stage variable depending on the plugin. Supported stages
	# are: app, cli, scripts, lib, srv
	#
	# 2. Adjust the cron schedule as necessary

	name: OMERO
	on:
	push:
	pull_request:
	schedule:
	- cron: '0 0 * * 0'

	jobs:
	test:
	name: Run integration tests against OMERO
	runs-on: ubuntu-latest
	env:
	STAGE: app
	NOCLEAN: true
	VERBOSE: true
	steps:
	- uses: actions/checkout@v4
	- name: Checkout omero-test-infra
	uses: actions/checkout@master
	with:
	repository: ome/omero-test-infra
	path: .omero
	ref: ${{ secrets.OMERO_TEST_INFRA_REF }}
	- name: Install java
	run: sudo apt install default-jdk -y
	- name: Install omero-py
	run: utils/install_omero-py.sh
	- name: ontop-cli
	run: utils/install_ontop.sh
	- name: patch portmapping
	run: cp utils/portmapping.patch .omero && cd .omero && patch -p1 < portmapping.patch && git diff
	- name: check python
	run: $(which python) --version
	- name: start omero
	run: .omero/docker dev start_up
	- name: check processes
	run: ps ax \| grep docker
	- name: test omero web
	run: wget http://localhost:14080 && ls -lrt
	- name: Launch omero, insert data and launch ontop
	run: bash utils/omero-ontop.sh
	- name: pytest
	run: pytest

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