Render lab result HTML as is if it does not conform to the expected f… #1060

Workflow file for this run

.github/workflows/createNewRelease.yaml at 8691ed2

	name: Create New Release
	on:
	workflow_dispatch:
	push:
	branches:
	- main

	# Run all tests before making a release
	jobs:
	# Only make a release if commit contains [RELEASE]
	check-commit-message:
	runs-on: ubuntu-latest
	outputs:
	contains_release: ${{ steps.commit_check.outputs.contains_release }}
	steps:
	- name: Check out code
	uses: actions/checkout@v4
	- name: Check commit message for [RELEASE]
	id: commit_check
	run: \|
	if [[ "${{ github.event.head_commit.message }}" == "[RELEASE]" ]]; then
	echo "contains_release=true" >> $GITHUB_OUTPUT
	else
	echo "contains_release=false" >> $GITHUB_OUTPUT
	fi
	list-containers:
	needs: check-commit-message
	if: ${{ needs.check-commit-message.outputs.contains_release == 'true' }}
	uses: ./.github/workflows/listContainers.yaml

	test-for-release:
	needs:
	- check-commit-message
	- list-containers
	if: ${{ needs.check-commit-message.outputs.contains_release == 'true' }}
	strategy:
	matrix:
	container: ${{fromJson(needs.list-containers.outputs.all-containers)}}
	uses: ./.github/workflows/run-container-workflow.yaml
	with:
	container: ${{ matrix.container }}
	secrets: inherit

	tag-release:
	name: Update phdi init version number
	needs: test-for-release
	permissions:
	contents: write
	outputs:
	version: ${{ steps.get_version.outputs.version }}
	runs-on: ubuntu-22.04
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: "0"
	ref: "main"
	- name: Install poetry and dependencies
	run: \|
	pip install poetry
	# update the version number in the phdi/__init.py__ file
	- name: Get PHDI Version
	id: get_version
	run: \|
	VERSION_WITH_PHDI=$(poetry version)
	echo "version=${VERSION_WITH_PHDI:5}" >> $GITHUB_OUTPUT
	# Create new release tag
	- name: Set up Git user
	run: \|
	git config --local user.email "action@github.com"
	git config --local user.name "GitHub Action"
	- name: Tag Release
	uses: EndBug/latest-tag@latest
	with:
	ref: ${{ steps.get_version.outputs.version }}
	# Generate release notes
	- name: Generate release notes
	id: release_notes
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	run: \|
	latest_release_date=$(gh api "/repos/$GITHUB_REPOSITORY/releases?per_page=1" \| jq ".[0].created_at")
	prs=$(gh pr list --base main --state closed --json title,number,url,closedAt -q ".[] \| select(.closedAt > $latest_release_date) \| select(.title \| contains(\"RELEASE\") \| not)")

	echo "# Release Notes" > release-notes.md
	echo "" >> release-notes.md
	echo "" >> release-notes.md

	while IFS= read -r pr; do
	pr_title=$(echo "$pr" \| jq -r ".title")
	pr_number=$(echo "$pr" \| jq -r ".number")
	pr_url=$(echo "$pr" \| jq -r ".url")
	line_text="- $pr_title ([#$pr_number]($pr_url))"
	echo $line_text >> release-notes.md
	done < <(printf '%s' "$prs")

	# Create new release based upon the latest created tag
	- name: Create Release
	id: create_release
	uses: actions/create-release@v1.1.4
	env:
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	with:
	tag_name: ${{ steps.get_version.outputs.version }}
	release_name: ${{ steps.get_version.outputs.version }}
	body_path: release-notes.md

	release-to-pypi:
	name: Build and publish PHDI to PyPI
	needs: tag-release
	runs-on: ubuntu-latest
	permissions:
	id-token: write
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: "0"
	ref: ${{ needs.tag-release.outputs.version }}
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: "3.x"
	- name: Install pypa/build
	run: >-
	python -m
	pip install
	build
	--user
	- name: Build a binary wheel and a source tarball
	run: >-
	python -m
	build
	--sdist
	--wheel
	--outdir dist/
	.
	- name: Publish distribution 📦 to PyPI
	uses: pypa/gh-action-pypi-publish@release/v1
	with:
	password: ${{ secrets.PYPI_API_TOKEN }}

	# Rebuild all containers for the new release
	build-containers-for-release:
	needs:
	- tag-release
	- release-to-pypi
	permissions:
	contents: read
	packages: write
	id-token: write
	uses: ./.github/workflows/buildReleaseContainers.yaml
	with:
	container-tag: ${{ needs.tag-release.outputs.version }}

	# Create updated PHDI docs for the latest release
	generate-and-update-phdi-docs:
	needs:
	- tag-release
	- build-containers-for-release
	permissions:
	contents: write
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: "0"
	ref: ${{ needs.tag-release.outputs.version }}

	- name: Install poetry and dependencies
	run: \|
	pip install poetry
	poetry install

	- name: Set environment variable for pdoc
	run: echo "PDOC_ALLOW_EXEC=1" >> $GITHUB_ENV

	- name: Clear Poetry Cache
	run: \|
	poetry cache clear pypi --all
	poetry cache clear virtualenvs --all

	- name: Generate docs and move to docs branch
	run: \|
	poetry run pdoc ./phdi -o ./docs/${{ needs.tag-release.outputs.version }}/sdk

	- uses: actions/upload-artifact@v3
	with:
	name: phdi-docs
	path: ./docs/${{ needs.tag-release.outputs.version }}/sdk

	# Create updated container docs for the latest release
	generate-and-update-container-docs:
	needs:
	- tag-release
	- list-containers
	- generate-and-update-phdi-docs
	permissions:
	contents: write
	runs-on: ubuntu-latest
	services:
	test-db:
	image: postgres:13-alpine3.16
	env:
	POSTGRES_PASSWORD: pw
	POSTGRES_DB: testdb
	POSTGRES_USER: postgres
	# Set health checks to wait until postgres has started
	options: >-
	--health-cmd pg_isready
	--health-interval 10s
	--health-timeout 5s
	--health-retries 5
	--name testdb
	ports:
	- 5432:5432
	strategy:
	matrix:
	container: ${{fromJson(needs.list-containers.outputs.python-containers)}}
	steps:
	- uses: actions/checkout@v4
	with:
	fetch-depth: "0"
	ref: ${{ needs.tag-release.outputs.version }}

	- name: Update Container Documentation
	env:
	MPI_DBNAME: testdb
	MPI_PASSWORD: pw
	MPI_DB_TYPE: postgres
	MPI_HOST: localhost
	MPI_USER: postgres
	MPI_PORT: 5432
	MPI_PATIENT_TABLE: patient
	MPI_PERSON_TABLE: person
	run: \|
	npm i -g redoc-cli
	CONTAINER=${{ matrix.container }}
	cd $GITHUB_WORKSPACE/containers/$CONTAINER
	cp $GITHUB_WORKSPACE/utils/make_openapi_json.py .
	pip install -r requirements.txt
	python make_openapi_json.py
	redoc-cli build -o $GITHUB_WORKSPACE/docs/${{ needs.tag-release.outputs.version }}/containers/$CONTAINER.html openapi.json

	- uses: actions/upload-artifact@v3
	with:
	name: container-docs
	path: ./docs/${{ needs.tag-release.outputs.version }}/containers

	commit-docs:
	needs:
	- tag-release
	- generate-and-update-phdi-docs
	- generate-and-update-container-docs
	permissions:
	contents: write
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	with:
	ref: docs

	- name: Download phdi docs from artifacts
	uses: actions/download-artifact@v4.1.7
	with:
	name: phdi-docs
	path: ./docs/${{ needs.tag-release.outputs.version }}/sdk

	- name: Download container docs from artifacts
	uses: actions/download-artifact@v4.1.7
	with:
	name: container-docs
	path: ./docs/${{ needs.tag-release.outputs.version }}/containers

	- name: Copy to latest folder
	run: \|
	rm -rf ./docs/latest
	mkdir -p ./docs/latest/sdk
	mkdir -p ./docs/latest/containers
	cp -r ./docs/${{ needs.tag-release.outputs.version }}/sdk/* ./docs/latest/sdk
	cp -r ./docs/${{ needs.tag-release.outputs.version }}/containers/* ./docs/latest/containers

	- name: Commit New Documentation
	uses: EndBug/add-and-commit@v9
	with:
	add: docs
	message: Automated update of docs for ${{ needs.tag-release.outputs.version }} release.

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