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ehr-api becomes export-api; losing and gaining some features #1435

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ehr-api becomes export-api; losing and gaining some features

ehr-api becomes export-api; losing and gaining some features #1435

Workflow file for this run

.github/workflows/main.yml at 6a997b8
# 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@v4
- 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@v4
- name: Init Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
cache: "pip"
- name: Install Python dependencies
run: |
python -m pip install --upgrade pip
pip install -e pixl_core
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@v4
- name: Init Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
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@v4
- name: Init Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
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@v4
- name: Init Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
cache: "pip"
- name: Install Python dependencies
run: |
pip install -e pixl_core/
pip install -e pytest-pixl/
pip install -e cli/[test]
- name: Run tests
working-directory: cli/tests
run: |
pytest
export-api-tests:
runs-on: ubuntu-22.04
timeout-minutes: 30
steps:
- uses: actions/checkout@v4
- name: Init Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
cache: "pip"
- name: Install Python dependencies
run: |
pip install pytest-pixl/ pixl_core/ pixl_export/[test]
- name: Run tests
working-directory: pixl_export/tests
run: |
pytest
imaging-api-tests:
runs-on: ubuntu-22.04
timeout-minutes: 10
steps:
- uses: actions/checkout@v4
- name: Init Python
uses: actions/setup-python@v5
with:
python-version: "3.11"
cache: "pip"
- name: Install Python dependencies
run: |
pip install pixl_core/ pixl_imaging/[test] pytest-pixl/
- name: Run tests
working-directory: pixl_imaging/tests
run: |
pytest
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@v4
- uses: docker/setup-buildx-action@v3
# pre-build and cache the orthanc-anon image: installing python3 takes a while, doesn't push
- name: Cache Docker layers
uses: actions/cache@v4
with:
path: /tmp/.buildx-cache
key: ${{ runner.os }}-buildx-${{ github.ref }}-${{ github.sha }}
restore-keys: |
${{ runner.os }}-buildx-${{ github.ref }}-
${{ runner.os }}-buildx-
save-always: true
- uses: docker/build-push-action@v5
with:
context: .
file: docker/orthanc-anon/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@v5
with:
python-version: "3.11"
cache: "pip"
- name: Install Python dependencies
# The -e option is required here due to the way the
# code determines the export directory. See issue #318.
run: |
pip install -e pixl_core/
pip install -e pytest-pixl/
pip install -e cli/[test]
- name: Create .secrets.env
run: touch test/.secrets.env
- name: Build test services
working-directory: test
run: |
docker compose build
- name: Build services
run: |
docker compose build
- name: Run tests
working-directory: test
env:
EXPORT_AZ_CLIENT_ID: ${{ secrets.EXPORT_AZ_CLIENT_ID }}
EXPORT_AZ_CLIENT_PASSWORD: ${{ secrets.EXPORT_AZ_CLIENT_PASSWORD }}
EXPORT_AZ_TENANT_ID: ${{ secrets.EXPORT_AZ_TENANT_ID }}
EXPORT_AZ_KEY_VAULT_NAME: ${{ secrets.EXPORT_AZ_KEY_VAULT_NAME }}
HASHER_API_AZ_CLIENT_ID: ${{ secrets.EXPORT_AZ_CLIENT_ID }}
HASHER_API_AZ_CLIENT_PASSWORD: ${{ secrets.EXPORT_AZ_CLIENT_PASSWORD }}
HASHER_API_AZ_TENANT_ID: ${{ secrets.EXPORT_AZ_TENANT_ID }}
HASHER_API_AZ_KEY_VAULT_NAME: ${{ secrets.EXPORT_AZ_KEY_VAULT_NAME }}
run: |
./run-system-test.sh
echo FINISHED SYSTEM TEST SCRIPT
- name: Dump export-api docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-export-api-1 2>&1
- name: Dump orthanc-anon docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-orthanc-anon-1 2>&1
- name: Dump imaging-api docker logs for debugging
if: ${{ failure() }}
run: |
docker logs -t system-test-imaging-api-1 2>&1