fix unit test #1626

Workflow file for this run

	name: CI / CD
	on: [push, pull_request]

	jobs:
	get-backend-sha:
	runs-on: ubuntu-latest
	outputs:
	backend_sha: ${{ steps.get-sha.outputs.backend_sha }}
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Checkout submodules
	run: git submodule update --init --recursive

	- name: Get backend sha
	id: get-sha
	run: \|
	echo "backend_sha=$(git rev-parse @:OpenCloning_backend)" >> $GITHUB_OUTPUT

	check-cache:
	runs-on: ubuntu-latest
	needs: get-backend-sha
	outputs:
	cache-hit: ${{ steps.cache-check.outputs.cache-hit }}
	steps:
	- name: Verify backend SHA is not empty
	run: \|
	if [ -z "${{ needs.get-backend-sha.outputs.backend_sha }}" ]; then
	echo "Error: backend_sha is empty"
	exit 1
	fi
	# This step both checks AND saves the cache
	# If there's a cache hit: it restores it
	# If there's no cache hit: it will save any files matching the path at the end of the job
	- name: Check cached venv
	id: cache-check
	uses: actions/cache@v3
	with:
	path: .venv
	key: python-venv-${{ runner.os }}-${{ needs.get-backend-sha.outputs.backend_sha }}

	install-python-dependencies:
	needs: [check-cache, get-backend-sha]
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	if: needs.check-cache.outputs.cache-hit != 'true'
	uses: actions/checkout@v4

	- name: Checkout submodules
	if: needs.check-cache.outputs.cache-hit != 'true'
	run: git submodule update --init --recursive

	- name: Install Python
	if: needs.check-cache.outputs.cache-hit != 'true'
	uses: actions/[email protected]
	with:
	python-version: 3.11

	- name: Create and activate virtual environment
	if: needs.check-cache.outputs.cache-hit != 'true'
	run: \|
	python -m venv .venv
	source .venv/bin/activate

	- name: Install python dependencies
	if: needs.check-cache.outputs.cache-hit != 'true'
	run: \|
	source .venv/bin/activate
	python -m pip install --upgrade pip
	pip install git+https://github.com/manulera/OpenCloning_backend.git@${{ needs.get-backend-sha.outputs.backend_sha }}

	- name: Save venv to cache
	if: needs.check-cache.outputs.cache-hit != 'true'
	uses: actions/cache@v3
	with:
	path: .venv
	key: python-venv-${{ runner.os }}-${{ needs.get-backend-sha.outputs.backend_sha }}

	install-frontend-dependencies:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Cache yarn dependencies
	uses: actions/cache@v3
	id: yarn-cache
	with:
	path: \|
	node_modules
	/home/runner/.cache/Cypress
	key: ${{ runner.os }}-yarn-${{ hashFiles('**/yarn.lock') }}

	- name: Setup Node.js
	if: steps.yarn-cache.outputs.cache-hit != 'true'
	uses: actions/setup-node@v4
	with:
	node-version: "22.17"

	- name: Install frontend dependencies
	if: steps.yarn-cache.outputs.cache-hit != 'true'
	run: corepack enable && yarn install

	cypress-tests:
	name: Run Cypress tests
	needs:
	[
	install-python-dependencies,
	install-frontend-dependencies,
	get-backend-sha,
	]
	runs-on: ubuntu-latest
	env:
	NCBI_API_KEY: ${{ secrets.NCBI_API_KEY }}
	strategy:
	fail-fast: false
	matrix:
	group: [1, 2, 3, 4, "component", "unit-tests"]
	steps:
	- name: Checkout
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	- name: Print git tag
	run: \|
	git describe --tags

	- name: Cache mafft
	id: cache-mafft
	uses: actions/cache@v3
	with:
	path: /usr/bin/mafft
	key: ${{ runner.os }}-mafft

	- name: Install mafft
	if: steps.cache-mafft.outputs.cache-hit != 'true'
	run: \|
	sudo apt-get update
	sudo apt-get install -y mafft

	- name: Download MARS executable
	run: \|
	wget https://github.com/manulera/MARS/releases/download/v0.2/mars-Linux
	chmod +x mars-Linux
	sudo mv mars-Linux /usr/local/bin/mars

	- name: Install Python
	uses: actions/[email protected]
	with:
	python-version: 3.11

	- name: Restore cached venv
	uses: actions/cache@v3
	with:
	path: .venv
	key: python-venv-${{ runner.os }}-${{ needs.get-backend-sha.outputs.backend_sha }}

	- name: run python dev server in background
	run: \|
	source .venv/bin/activate
	uvicorn opencloning.main:app &

	- name: check if the server is running
	run: \|
	for i in {1..3}; do
	if curl -s http://127.0.0.1:8000 > /dev/null; then
	echo "Server is up!"
	exit 0
	fi
	echo "Waiting for server... ($i/3)"
	sleep 2
	done
	echo "Server failed to start"
	exit 1

	- name: Restore cached node_modules
	uses: actions/cache@v3
	with:
	path: \|
	node_modules
	/home/runner/.cache/Cypress
	key: ${{ runner.os }}-yarn-${{ hashFiles('**/yarn.lock') }}

	- name: enable corepack
	run: corepack enable

	- name: Cypress run E2E tests
	if: matrix.group != 'component' && matrix.group != 'unit-tests'
	uses: cypress-io/github-action@v6
	env:
	VITE_COVERAGE: "true"
	VITE_LOG_LEVEL: "warn"
	CYPRESS_TEST_GROUP: ${{ matrix.group }}
	with:
	start: yarn start
	install: false

	- name: Cypress run component tests
	if: matrix.group == 'component'
	uses: cypress-io/github-action@v6
	env:
	VITE_COVERAGE: "true"
	VITE_LOG_LEVEL: "warn"
	with:
	component: true
	install: false

	- name: vitest unit tests
	if: matrix.group == 'unit-tests'
	run: yarn vitest run --coverage

	- name: Upload coverage file
	uses: actions/[email protected]
	with:
	name: coverage-${{ matrix.group }}
	path: coverage/coverage-final.json

	- name: Upload screenshots
	uses: actions/[email protected]
	if: failure()
	with:
	name: cypress-screenshots-${{ matrix.group }}
	path: cypress/screenshots

	cypress-gather-coverage:
	needs: cypress-tests
	runs-on: ubuntu-latest
	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Download coverage files
	uses: actions/download-artifact@v4
	with:
	path: coverage
	pattern: coverage*
	- name: list coverage files
	run: \|
	ls coverage

	- name: Merge coverage reports
	run: \|
	for folder in coverage/coverage-*; do
	mv $folder/coverage-final.json $folder.json
	rmdir $folder
	done
	mkdir .nyc_output
	mv coverage/*.json .nyc_output
	rm -rf coverage
	npx nyc report --reporter json --report-dir coverage
	# Remove the absolute path from the coverage file
	sed -i "s\|\"$(pwd)/\|\"\|g" coverage/coverage-final.json

	- name: Upload results to Codecov
	uses: codecov/codecov-action@v4
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	file: coverage/coverage-final.json

	# Update docker image when committing to master branch if tests pass
	push_to_registry:
	name: Push Docker image to Docker Hub
	# Only run if tests pass
	needs: [cypress-tests, cypress-gather-coverage]
	runs-on: ubuntu-latest
	if: github.ref == 'refs/heads/master'
	steps:
	- name: Check out the repo
	uses: actions/checkout@v3

	- name: Log in to Docker Hub
	uses: docker/login-action@f054a8b539a109f9f41c372932f1ae047eff08c9
	with:
	username: ${{ secrets.DOCKER_USERNAME }}
	password: ${{ secrets.DOCKER_PASSWORD }}

	- name: Extract metadata (tags, labels) for Docker
	id: meta
	uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
	with:
	images: manulera/opencloningfrontend

	- name: Build and push Docker image
	uses: docker/[email protected]
	with:
	context: .
	push: true
	tags: manulera/opencloningfrontend:latest
	labels: ${{ steps.meta.outputs.labels }}

	- name: Build and push Docker image
	uses: docker/[email protected]
	with:
	context: .
	push: true
	tags: manulera/opencloningfrontend:latest-baseurl-opencloning
	labels: ${{ steps.meta.outputs.labels }}
	build-args: \|
	BASE_URL=/opencloning/

	- name: Run Trivy vulnerability scanner
	uses: aquasecurity/trivy-action@master
	with:
	image-ref: manulera/opencloningfrontend:latest
	format: 'table'
	exit-code: '0'
	ignore-unfixed: true
	vuln-type: 'os,library'
	severity: 'CRITICAL,HIGH'

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fix unit test #1626

Workflow file

fix unit test #1626

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Workflow file for this run