build(deps): bump the all-java group across 2 directories with 17 updates #1273

Workflow file for this run

	name: CI/CD Pipeline
	on:
	schedule:
	- cron: '00 5 * * *'
	push:
	branches:
	- master
	tags:
	- 'v..*'
	pull_request:
	branches:
	- master

	# Set minimal permissions for all jobs by default
	permissions:
	contents: read

	env:
	JAVA_VERSION: '21'
	JAVA_DISTRIBUTION: 'temurin'
	BLAZECTL_VERSION: v1.2.0
	BLAZECTL_CHECKSUM: c0b2bf0b35c60ff0aa1d66f638d5b8d3a77c506211643932e4132784069cc759


	jobs:
	lint-agent-backend:
	name: Code Format (Agent Backend)
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5.2.0
	with:
	java-version: ${{ env.JAVA_VERSION }}
	distribution: ${{ env.JAVA_DISTRIBUTION }}
	cache: 'maven'

	- uses: actions/cache@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
	with:
	path: \|
	~/.m2/repository
	~/.m2/wrapper
	key: ${{ runner.os }}-maven-agent-${{ hashFiles('agent/backend/pom.xml', '**/pom.xml') }}
	restore-keys: \|
	${{ runner.os }}-maven-agent-${{ hashFiles('agent/backend/pom.xml') }}
	${{ runner.os }}-maven-agent-
	${{ runner.os }}-maven-

	- working-directory: agent/backend
	run: mvn --quiet clean com.spotify.fmt:fmt-maven-plugin:check

	lint-agent-frontend:
	name: Code Format (Agent Frontend)
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
	with:
	fetch-depth: 0

	- uses: actions/setup-node@53b83947a5a98c8d113130e565377fae1a50d02f # v6.3.0
	with:
	node-version: '18'
	cache: 'npm'
	cache-dependency-path: 'agent/frontend/package-lock.json'

	- name: Install dependencies
	working-directory: agent/frontend
	run: npm ci

	- name: Run ESLint
	working-directory: agent/frontend
	run: npm run lint

	lint-server-frontend:
	name: Code Format (Server Frontend)
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- uses: actions/setup-node@53b83947a5a98c8d113130e565377fae1a50d02f # v6.3.0
	with:
	node-version: '18'
	cache: 'npm'
	cache-dependency-path: 'server/frontend/package-lock.json'

	- name: Install dependencies
	working-directory: server/frontend
	run: npm ci

	- name: Run ESLint
	working-directory: server/frontend
	run: npm run lint

	lint-server:
	name: Code Format (Server)
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5.2.0
	with:
	java-version: ${{ env.JAVA_VERSION }}
	distribution: ${{ env.JAVA_DISTRIBUTION }}
	cache: 'maven'

	- uses: actions/cache@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
	with:
	path: \|
	~/.m2/repository
	~/.m2/wrapper
	key: ${{ runner.os }}-maven-server-${{ hashFiles('server/backend/pom.xml', '**/pom.xml') }}
	restore-keys: \|
	${{ runner.os }}-maven-server-${{ hashFiles('server/backend/pom.xml') }}
	${{ runner.os }}-maven-server-
	${{ runner.os }}-maven-

	- working-directory: server/backend
	run: mvn --quiet clean com.spotify.fmt:fmt-maven-plugin:check

	test:
	name: Unit & Integration Tests (Agent)
	runs-on: ubuntu-latest
	needs:
	- lint-agent-backend
	- lint-agent-frontend
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5.2.0
	with:
	java-version: ${{ env.JAVA_VERSION }}
	distribution: ${{ env.JAVA_DISTRIBUTION }}
	cache: 'maven'

	- uses: actions/cache@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
	with:
	path: \|
	~/.m2/repository
	~/.m2/wrapper
	key: ${{ runner.os }}-maven-agent-${{ hashFiles('agent/backend/pom.xml', '**/pom.xml') }}
	restore-keys: \|
	${{ runner.os }}-maven-agent-${{ hashFiles('agent/backend/pom.xml') }}
	${{ runner.os }}-maven-agent-
	${{ runner.os }}-maven-

	- working-directory: agent/backend
	run: mvn --quiet test

	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v5
	with:
	token: ${{ secrets.CODECOV_TOKEN }}
	files: ./agent/backend/target/site/jacoco/jacoco.xml
	flags: agent
	name: agent-coverage
	fail_ci_if_error: false

	test-server:
	name: Unit & Integration Tests (Server)
	runs-on: ubuntu-latest
	needs:
	- lint-server
	- lint-server-frontend
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654 # v5.2.0
	with:
	java-version: ${{ env.JAVA_VERSION }}
	distribution: ${{ env.JAVA_DISTRIBUTION }}
	cache: 'maven'

	- uses: actions/cache@cdf6c1fa76f9f475f3d7449005a359c84ca0f306 # v5.0.3
	with:
	path: \|
	~/.m2/repository
	~/.m2/wrapper
	key: ${{ runner.os }}-maven-server-${{ hashFiles('server/backend/pom.xml', '**/pom.xml') }}
	restore-keys: \|
	${{ runner.os }}-maven-server-${{ hashFiles('server/backend/pom.xml') }}
	${{ runner.os }}-maven-server-
	${{ runner.os }}-maven-

	- working-directory: server/backend
	run: mvn --quiet test

	build-agent-image:
	name: Docker Image Build (Agent)
	runs-on: ubuntu-latest
	needs:
	- lint-agent-backend
	- lint-agent-frontend
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- name: Set up QEMU
	uses: docker/setup-qemu-action@ce360397dd3f832beb865e1373c09c0e9f86d70a # v4.0.0

	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@4d04d5d9486b7bd6fa91e7baf45bbb4f8b9deedd # v4.0.0
	- uses: docker/build-push-action@d08e5c354a6adb9ed34480a06d141179aa583294 # v7.0.0
	name: Build new image
	with:
	context: .
	file: ./agent/Dockerfile
	tags: ghcr.io/bbmri-cz/data-quality-agent:latest
	load: true
	outputs: type=docker,dest=/tmp/agent-image.tar
	cache-from: type=gha
	cache-to: type=gha,mode=max

	- uses: docker/build-push-action@d08e5c354a6adb9ed34480a06d141179aa583294 # v7.0.0
	name: Build new image artifact
	with:
	context: .
	file: ./agent/Dockerfile
	tags: ghcr.io/bbmri-cz/data-quality-agent:latest
	build-args: ARTIFACT_VERSION=${{ github.ref_name }}
	outputs: type=docker,dest=/tmp/agent-image.tar
	cache-from: type=gha

	- name: Upload agent image artifact
	uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
	with:
	name: agent-image
	path: /tmp/agent-image.tar

	test-agent-migration:
	name: Agent DB Migration Test
	runs-on: ubuntu-latest
	needs: build-agent-image
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- run: docker compose up -d quality-agent
	name: Spin up latest stable image

	- name: Run blaze
	run: docker run -d --name blaze -p 8080:8080 samply/blaze:latest

	- name: Wait for Blaze
	run: .github/workflows/scripts/wait-for-url.sh http://localhost:8080/health

	- name: Install Blazectl
	env:
	GH_TOKEN: ${{ github.token }}
	run: .github/workflows/scripts/install-blazectl.sh

	- name: Load Data
	run: blazectl --no-progress --server http://localhost:8080/fhir upload agent/backend/src/test/resources/test_data

	- name: Generate Data Quality Report
	run: .github/workflows/scripts/generate-report.sh

	- run: docker compose down
	name: Down the container

	- name: Download agent image artifact
	uses: actions/download-artifact@70fc10c6e5e1ce46ad2ea6f2b72d43f7d47b13c3 # v8.0.0
	with:
	name: agent-image
	path: /tmp

	- name: Load Docker images
	run: \|
	docker load -i /tmp/agent-image.tar

	- run: docker compose up -d quality-agent
	name: Spin up latest stable image

	- name: Check agent health
	run: \|
	for i in {1..20}; do
	STATUS=$(docker inspect --format='{{.State.Health.Status}}' quality-agent)
	echo "Health status: $STATUS"
	if [ "$STATUS" == "healthy" ]; then
	echo "Container is healthy"
	exit 0
	fi
	sleep 3
	done
	echo "Container is not healthy"
	docker logs quality-agent
	exit 1

	- name: Generate Data Quality Report
	run: .github/workflows/scripts/generate-report.sh

	- name: Test basic API calls
	run: .github/workflows/scripts/test-api-calls.sh

	build-server-image:
	name: Docker Image Build (Server)
	runs-on: ubuntu-latest
	needs:
	- lint-server
	- lint-server-frontend
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- name: Set up QEMU
	uses: docker/setup-qemu-action@ce360397dd3f832beb865e1373c09c0e9f86d70a # v4.0.0

	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@4d04d5d9486b7bd6fa91e7baf45bbb4f8b9deedd # v4.0.0

	- run: docker compose up -d quality-server \|\| exit 0
	name: Spin up latest stable image


	- uses: docker/build-push-action@d08e5c354a6adb9ed34480a06d141179aa583294 # v7.0.0
	name: Build new image
	with:
	context: .
	file: ./server/Dockerfile
	tags: ghcr.io/bbmri-cz/data-quality-server:latest
	load: true
	outputs: type=docker
	cache-from: type=gha
	cache-to: type=gha,mode=max

	- uses: docker/build-push-action@d08e5c354a6adb9ed34480a06d141179aa583294 # v7.0.0
	name: Build new image artifact
	with:
	context: .
	file: ./server/Dockerfile
	tags: ghcr.io/bbmri-cz/data-quality-server:latest
	build-args: ARTIFACT_VERSION=${{ github.ref_name }}
	outputs: type=docker,dest=/tmp/server-image.tar
	cache-from: type=gha

	- name: Upload server image artifact
	uses: actions/upload-artifact@bbbca2ddaa5d8feaa63e36b76fdaad77386f024f # v7.0.0
	with:
	name: server-image
	path: /tmp/server-image.tar

	test-server-migration:
	name: Server DB Migration Test
	runs-on: ubuntu-latest
	needs: build-server-image
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- run: docker compose up -d quality-server
	name: Spin up latest stable image

	- run: docker compose down
	name: Down the container

	- name: Download agent image artifact
	uses: actions/download-artifact@70fc10c6e5e1ce46ad2ea6f2b72d43f7d47b13c3 # v8.0.0
	with:
	name: server-image
	path: /tmp

	- name: Load Docker images
	run: \|
	docker load -i /tmp/server-image.tar

	- run: docker compose up -d quality-server
	name: Spin up latest stable image

	- name: Check server health
	run: \|
	for i in {1..20}; do
	STATUS=$(docker inspect --format='{{.State.Health.Status}}' quality-server)
	echo "Health status: $STATUS"
	if [ "$STATUS" == "healthy" ]; then
	echo "Container is healthy"
	exit 0
	fi
	sleep 3
	done
	echo "Container is not healthy"
	docker logs quality-server
	exit 1
	docs:
	name: Documentation Build and Deployment
	runs-on: ubuntu-latest
	if: github.ref == 'refs/heads/master'
	env:
	MATOMO_BASE_URL: 'https://matomo.bbmri-eric.eu/'
	MATOMO_SITE_ID: '12'
	permissions:
	contents: read
	pages: write
	id-token: write
	concurrency:
	group: "pages"
	cancel-in-progress: false
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- uses: actions/setup-node@53b83947a5a98c8d113130e565377fae1a50d02f # v6.3.0
	with:
	node-version: '18'
	cache: 'npm'
	cache-dependency-path: 'docs/package-lock.json'

	- name: Install dependencies
	working-directory: docs
	run: npm ci

	- name: Build documentation
	working-directory: docs
	run: npm run build

	- name: Setup Pages
	uses: actions/configure-pages@983d7736d9b0ae728b81ab479565c72886d7745b # v5.0.0

	- name: Upload artifact
	uses: actions/upload-pages-artifact@7b1f4a764d45c48632c6b24a0339c27f5614fb0b # v4.0.0
	with:
	path: docs/.vitepress/dist

	- name: Deploy to GitHub Pages
	id: deployment
	uses: actions/deploy-pages@d6db90164ac5ed86f2b6aed7e0febac5b3c0c03e # v4.0.5

	build:
	name: Agent Image Publishing
	runs-on: ubuntu-latest
	needs:
	- integration-test
	- otel-metrics-push-test
	permissions:
	packages: write
	contents: read
	id-token: write
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- name: Install Cosign
	uses: sigstore/cosign-installer@faadad0cce49287aee09b3a48701e75088a2c6ad # v4.0.0

	- name: Download agent image artifact
	uses: actions/download-artifact@70fc10c6e5e1ce46ad2ea6f2b72d43f7d47b13c3 # v8.0.0
	with:
	name: agent-image
	path: /tmp

	- name: Load Docker image
	run: docker load -i /tmp/agent-image.tar

	- id: meta
	uses: docker/metadata-action@030e881283bb7a6894de51c315a6bfe6a94e05cf # v6.0.0
	with:
	images: ghcr.io/${{ github.repository_owner }}/data-quality-agent
	tags: \|
	type=sha
	type=raw,value=${{ github.head_ref }},event=pr
	type=semver,pattern={{version}}
	type=semver,pattern={{major}}.{{minor}}
	type=semver,pattern={{major}}
	type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'master') }}

	- uses: docker/login-action@b45d80f862d83dbcd57f89517bcf500b2ab88fb2 # v4.0.0
	with:
	registry: ghcr.io
	username: ${{ github.repository_owner }}
	password: ${{ secrets.GITHUB_TOKEN }}

	- name: Tag and push images
	env:
	TAGS: ${{ steps.meta.outputs.tags }}
	run: \|
	LOADED_IMAGE="ghcr.io/bbmri-cz/data-quality-agent:latest"
	# Tag and push each generated tag
	echo "$TAGS" \| while read -r tag; do
	if [ -n "$tag" ]; then
	echo "Tagging and pushing: $tag"
	docker tag "$LOADED_IMAGE" "$tag"
	docker push "$tag"
	fi
	done

	- name: Sign images with Cosign
	env:
	TAGS: ${{ steps.meta.outputs.tags }}
	run: \|
	# Sign each pushed image
	echo "$TAGS" \| while read -r tag; do
	if [ -n "$tag" ]; then
	echo "Signing: $tag"
	cosign sign --yes "$tag"
	fi
	done

	publish-server-image:
	name: Server Image Publishing
	runs-on: ubuntu-latest
	needs:
	- integration-test
	- otel-metrics-push-test
	permissions:
	packages: write
	contents: read
	id-token: write
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- name: Install Cosign
	uses: sigstore/cosign-installer@faadad0cce49287aee09b3a48701e75088a2c6ad # v4.0.0

	- name: Download server image artifact
	uses: actions/download-artifact@70fc10c6e5e1ce46ad2ea6f2b72d43f7d47b13c3 # v8.0.0
	with:
	name: server-image
	path: /tmp

	- name: Load Docker image
	run: docker load -i /tmp/server-image.tar

	- id: meta
	uses: docker/metadata-action@030e881283bb7a6894de51c315a6bfe6a94e05cf # v6.0.0
	with:
	images: ghcr.io/${{ github.repository_owner }}/data-quality-server
	tags: \|
	type=sha
	type=raw,value=${{ github.head_ref }},event=pr
	type=semver,pattern={{version}}
	type=semver,pattern={{major}}
	type=semver,pattern={{major}}.{{minor}}
	type=raw,value=latest,enable=${{ github.ref == format('refs/heads/{0}', 'master') }}

	- uses: docker/login-action@b45d80f862d83dbcd57f89517bcf500b2ab88fb2 # v4.0.0
	with:
	registry: ghcr.io
	username: ${{ github.repository_owner }}
	password: ${{ secrets.GITHUB_TOKEN }}

	- name: Tag and push images
	env:
	TAGS: ${{ steps.meta.outputs.tags }}
	run: \|
	LOADED_IMAGE="ghcr.io/bbmri-cz/data-quality-server:latest"
	# Tag and push each generated tag
	echo "$TAGS" \| while read -r tag; do
	if [ -n "$tag" ]; then
	echo "Tagging and pushing: $tag"
	docker tag "$LOADED_IMAGE" "$tag"
	docker push "$tag"
	fi
	done

	- name: Sign images with Cosign
	env:
	TAGS: ${{ steps.meta.outputs.tags }}
	run: \|
	# Sign each pushed image
	echo "$TAGS" \| while read -r tag; do
	if [ -n "$tag" ]; then
	echo "Signing: $tag"
	cosign sign --yes "$tag"
	fi
	done

	integration-test:
	name: System Test
	runs-on: ubuntu-latest
	needs:
	- build-agent-image
	- build-server-image
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- name: Set up Docker Buildx
	uses: docker/setup-buildx-action@4d04d5d9486b7bd6fa91e7baf45bbb4f8b9deedd # v4.0.0

	- name: Download agent image artifact
	uses: actions/download-artifact@70fc10c6e5e1ce46ad2ea6f2b72d43f7d47b13c3 # v8.0.0
	with:
	name: agent-image
	path: /tmp

	- name: Download server image artifact
	uses: actions/download-artifact@70fc10c6e5e1ce46ad2ea6f2b72d43f7d47b13c3 # v8.0.0
	with:
	name: server-image
	path: /tmp

	- name: Run blaze
	run: docker run -d --name blaze -p 8080:8080 samply/blaze:latest

	- name: Wait for Blaze
	run: .github/workflows/scripts/wait-for-url.sh http://localhost:8080/health

	- name: Install Blazectl
	env:
	GH_TOKEN: ${{ github.token }}
	run: .github/workflows/scripts/install-blazectl.sh

	- name: Load Data
	run: blazectl --no-progress --server http://localhost:8080/fhir upload agent/backend/src/test/resources/test_data

	- name: Load Docker images
	run: \|
	docker load -i /tmp/agent-image.tar
	docker load -i /tmp/server-image.tar

	- name: Docker Compose Up
	run: docker compose -f compose.yaml -f .github/compose.override.yaml up -d

	- name: Check agent health
	run: \|
	for i in {1..20}; do
	STATUS=$(docker inspect --format='{{.State.Health.Status}}' quality-agent)
	echo "Health status: $STATUS"
	if [ "$STATUS" == "healthy" ]; then
	echo "Container is healthy"
	exit 0
	fi
	sleep 3
	done
	echo "Container is not healthy"
	docker logs quality-agent
	exit 1

	- name: Check server health
	run: \|
	for i in {1..20}; do
	STATUS=$(docker inspect --format='{{.State.Health.Status}}' quality-server)
	echo "Health status: $STATUS"
	if [ "$STATUS" == "healthy" ]; then
	echo "Container is healthy"
	exit 0
	fi
	sleep 3
	done
	echo "Container is not healthy"
	docker logs quality-server
	exit 1

	- name: Check OIDC server health
	run: .github/workflows/scripts/wait-for-url.sh http://localhost:4011/.well-known/openid-configuration

	- name: Test Agent and Server Interaction
	run: .github/workflows/scripts/system-test-interaction.sh

	otel-metrics-push-test:
	name: OTEL Metrics Push Test
	runs-on: ubuntu-latest
	needs:
	- build-agent-image
	steps:
	- uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2

	- name: Download agent image artifact
	uses: actions/download-artifact@70fc10c6e5e1ce46ad2ea6f2b72d43f7d47b13c3 # v8.0.0
	with:
	name: agent-image
	path: /tmp

	- name: Load agent image
	run: docker load -i /tmp/agent-image.tar

	- name: Docker Compose Up (Agent + OTEL Collector)
	run: docker compose -f compose.yaml -f .github/compose.otel.override.yaml up -d quality-agent otel-collector

	- name: Wait for agent health endpoint
	run: .github/workflows/scripts/wait-for-url.sh http://localhost:8081/api/health

	- name: Trigger a few requests for application metrics
	run: \|
	for i in {1..5}; do
	curl -fsS http://localhost:8081/api/health >/dev/null
	sleep 1
	done

	- name: Validate OTEL metrics push
	run: bash .github/workflows/scripts/validate-otel-metrics-push.sh

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build(deps): bump the all-java group across 2 directories with 17 updates #1273

Workflow file

build(deps): bump the all-java group across 2 directories with 17 updates #1273

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Workflow file for this run