Refactor system tests to use the new FTP server and to run in pytest #958

Workflow file for this run

	# Copyright (c) University College London Hospitals NHS Foundation Trust
	#
	# Licensed under the Apache License, Version 2.0 (the "License");
	# you may not use this file except in compliance with the License.
	# You may obtain a copy of the License at
	#
	# http://www.apache.org/licenses/LICENSE-2.0
	#
	# Unless required by applicable law or agreed to in writing, software
	# distributed under the License is distributed on an "AS IS" BASIS,
	# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
	# See the License for the specific language governing permissions and
	# limitations under the License.
	name: pixl-ci

	on:
	push:
	branches:
	- main
	pull_request:
	workflow_dispatch:

	# Only run actions on the most recent push to a branch
	concurrency:
	group: "${{ github.workflow }}-${{ github.head_ref }}"
	cancel-in-progress: true

	jobs:
	lint:
	runs-on: ubuntu-22.04
	timeout-minutes: 5
	steps:
	- name: Checkout
	uses: actions/checkout@v3

	- name: Ensure copyright and license header are present
	run: ./.github/linters/check_headers_exist.sh

	- name: Run pre-commit
	uses: pre-commit/[email protected]
	with:
	extra_args: --all-files

	- name: Validate Docker Compose config file
	working-directory: .
	run: \|
	cp .env.sample .env
	docker compose config --quiet

	hasher-tests:
	runs-on: ubuntu-22.04
	timeout-minutes: 10
	steps:
	- uses: actions/checkout@v3

	- name: Init Python
	uses: actions/setup-python@v4
	with:
	python-version: "3.10"
	cache: "pip"

	- name: Install package
	run: \|
	pip install hasher/[test]

	- name: Run tests
	working-directory: hasher
	run: pytest
	env:
	ENV: test
	AZURE_KEY_VAULT_NAME: test
	AZURE_KEY_VAULT_SECRET_NAME: test

	core-tests:
	runs-on: ubuntu-22.04
	timeout-minutes: 10
	steps:
	- uses: actions/checkout@v3

	- name: Init Python
	uses: actions/setup-python@v4
	with:
	python-version: "3.10"
	cache: "pip"

	- name: Install Python dependencies
	run: \|
	pip install pytest-pixl/ pixl_core/[test]

	- name: Run tests
	working-directory: pixl_core/tests
	run: \|
	pytest
	env:
	ENV: test

	dicom-de-id-tests:
	runs-on: ubuntu-22.04
	timeout-minutes: 10
	steps:
	- uses: actions/checkout@v3

	- name: Init Python
	uses: actions/setup-python@v4
	with:
	python-version: "3.9"
	cache: "pip"

	- name: Install Python dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install -e pixl_core
	pip install -e pytest-pixl
	pip install -e pixl_dcmd[test]

	- name: Run tests
	working-directory: pixl_dcmd
	run: \|
	bin/run-tests.sh
	env:
	ENV: test

	cli-tests:
	runs-on: ubuntu-22.04
	timeout-minutes: 10
	steps:
	- uses: actions/checkout@v3

	- name: Init Python
	uses: actions/setup-python@v4
	with:
	python-version: "3.10"
	cache: "pip"

	- name: Install Python dependencies
	run: \|
	pip install pixl_core/ cli/[test]

	- name: Run tests
	working-directory: cli/tests
	run: \|
	pytest

	ehr-api-tests:
	runs-on: ubuntu-22.04
	timeout-minutes: 30
	steps:
	- uses: actions/checkout@v3

	- uses: docker/setup-buildx-action@v3
	# pre-build and cache the postgres container as installing python3 takes a while, doesn't push
	- name: Cache Docker layers
	uses: actions/cache@v3
	with:
	path: /tmp/.buildx-cache
	key: ${{ runner.os }}-buildx-${{ github.sha }}
	restore-keys: \|
	${{ runner.os }}-buildx-
	- uses: docker/build-push-action@v5
	with:
	context: .
	file: docker/postgres/Dockerfile
	cache-from: type=local,src=/tmp/.buildx-cache
	cache-to: type=local,dest=/tmp/.buildx-cache-new,mode=max
	- # Temp fix
	# https://github.com/docker/build-push-action/issues/252
	# https://github.com/moby/buildkit/issues/1896
	name: Move cache
	run: \|
	rm -rf /tmp/.buildx-cache
	mv /tmp/.buildx-cache-new /tmp/.buildx-cache

	- name: Init Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.10.6
	cache: "pip"

	- name: Install Python dependencies
	run: \|
	pip install pixl_core/ pixl_ehr/[test]

	- name: Run tests
	working-directory: pixl_ehr/tests
	run: \|
	pytest

	imaging-api-tests:
	runs-on: ubuntu-22.04
	timeout-minutes: 10
	steps:
	- uses: actions/checkout@v3

	- name: Init Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.10.6
	cache: "pip"

	- name: Install Python dependencies
	run: \|
	pip install pixl_core/ pixl_imaging/[test]

	- name: Run tests
	working-directory: pixl_imaging/tests
	run: \|
	./run-tests.sh

	system-test:
	if: ${{ ! github.event.pull_request.draft \|\| contains(github.event.pull_request.title, '[force-system-test]') }}
	runs-on: ubuntu-22.04
	timeout-minutes: 30
	steps:
	- uses: actions/checkout@v3
	- name: Prune docker volumes
	# seems like we're getting an error from ftp-server exiting with zero status code
	# this is a workaround that resolves it locally 🤞
	run: \|
	docker volume prune --force

	- uses: docker/setup-buildx-action@v3
	# pre-build and cache the postgres container as installing python3 takes a while, doesn't push
	- name: Cache Docker layers
	uses: actions/cache@v3
	with:
	path: /tmp/.buildx-cache
	key: ${{ runner.os }}-buildx-${{ github.sha }}
	restore-keys: \|
	${{ runner.os }}-buildx-
	- uses: docker/build-push-action@v5
	with:
	context: .
	file: docker/postgres/Dockerfile
	cache-from: type=local,src=/tmp/.buildx-cache
	cache-to: type=local,dest=/tmp/.buildx-cache-new,mode=max
	- # Temp fix
	# https://github.com/docker/build-push-action/issues/252
	# https://github.com/moby/buildkit/issues/1896
	name: Move cache
	run: \|
	rm -rf /tmp/.buildx-cache
	mv /tmp/.buildx-cache-new /tmp/.buildx-cache

	- name: Init Python
	uses: actions/setup-python@v4
	with:
	python-version: 3.10.6
	cache: "pip"

	- name: Install Python dependencies
	run: \|
	pip install pixl_core/
	pip install cli/[test]
	pip install pytest-pixl/

	- name: Build test services
	working-directory: test
	run: \|
	docker compose build

	- name: Build services
	run: \|
	docker compose build

	- name: Run tests
	working-directory: test
	run: \|
	./run-system-test.sh
	echo FINISHED SYSTEM TEST SCRIPT

	- name: Dump ehr-api docker logs for debugging
	if: ${{ always() }}
	run: \|
	docker logs -t system-test-ehr-api-1 2>&1

	- name: Dump imaging-api docker logs for debugging
	if: ${{ always() }}
	run: \|
	docker logs -t system-test-imaging-api-1 2>&1

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Refactor system tests to use the new FTP server and to run in pytest #958

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Refactor system tests to use the new FTP server and to run in pytest #958

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Workflow file for this run