Bump com.google.cloud.tools:jib-maven-plugin from 3.3.2 to 3.4.2 #3450

Workflow file for this run

	# This workflow will build the software and documentation to ensure there are no errors, and also
	# execute the tests.
	#
	# The FHIR server build is separated into three tranches, to minimise overall build time:
	#
	# Tranche 1: ModificationTest, AggregateQueryTest, ExtractTest
	# Tranche 2: ManifestConverterTest, integration tests
	# Tranche 3: All other FHIR server tests, tests from utilities and terminology modules
	#
	# There are a set of performance benchmarks that run and upload their results to a S3 bucket.
	#
	# This workflow also deploys a pre-release version of the software to Docker Hub and Maven Central,
	# if the branch is a release branch (`release/**`).

	name: Test

	on:
	push:
	branches-ignore:
	- gh-pages

	jobs:
	encoders:
	name: Encoders
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Run the verify goal with Maven
	env:
	# If the actor is not Dependabot, we ignore test failures and rely upon the Surefire
	# report action to report them.
	PATHLING_OPTS: ${{ github.actor == 'dependabot[bot]' && '' \|\| '-Dmaven.test.failure.ignore' }}
	run: >-
	mvn --batch-mode verify
	-pl encoders -am
	${{ env.PATHLING_OPTS }}
	timeout-minutes: 20
	- name: Upload encoders test reports
	uses: actions/upload-artifact@v3
	with:
	name: encoders-surefire-reports
	path: encoders/target/surefire-reports
	- name: Upload test coverage report
	uses: actions/upload-artifact@v3
	with:
	name: encoders-coverage
	path: "**/jacoco.xml"
	- name: Upload dump files
	uses: actions/upload-artifact@v3
	with:
	name: encoders-dump-files
	path: \|-
	*/.dump
	*/.dumpstream
	- name: Publish test results
	# If the actor is Dependabot, we need to avoid anything that requires access to secrets.
	if: github.actor != 'dependabot[bot]'
	uses: scacap/action-surefire-report@v1
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: Encoders test report
	fail_on_test_failures: true

	fhir-server-1:
	name: FHIR server (tranche 1)
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Cache test data
	id: cache-test-data
	uses: actions/cache@v3
	with:
	path: fhir-server/src/test/resources/test-data/parquet
	key: ${{ runner.os }}-test-data-${{ hashFiles('fhir-server/src/test/resources/test-data/fhir/.ndjson', 'encoders/src/main//.java', 'encoders/src/main/*/.scala', 'fhir-server/src/main/java/au/csiro/pathling/io/Database.java') }}
	- name: Run the verify goal with Maven
	env:
	# Activate the "tranche 1" test profile. If there is a cache hit on the test data, we
	# don't need to import it.
	PATHLING_PROFILES: testTranche1${{ steps.cache-test-data.outputs.cache-hit && ',!importTestData' \|\| '' }}
	# If the actor is not Dependabot, we ignore test failures and rely upon the Surefire
	# report action to report them.
	PATHLING_OPTS: >-
	-DskipEncodersTests
	-DskipUtilitiesTests
	-DskipTerminologyTests
	-DskipFhirPathTests
	${{ github.actor == 'dependabot[bot]' && '' \|\| '-Dmaven.test.failure.ignore' }}
	run: >-
	mvn --batch-mode verify
	-pl fhir-server -am
	-P${{ env.PATHLING_PROFILES }}
	${{ env.PATHLING_OPTS }}
	timeout-minutes: 30
	- name: Upload fhir-server test reports
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-1-surefire-reports
	path: fhir-server/target/surefire-reports
	- name: Upload test coverage report
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-1-coverage
	path: "**/jacoco.xml"
	- name: Upload timing log
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-1-timing-log
	path: fhir-server/target/timing.log
	- name: Upload dump files
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-1-dump-files
	path: \|-
	*/.dump
	*/.dumpstream
	- name: Publish test results
	# If the actor is Dependabot, we need to avoid anything that requires access to secrets.
	if: github.actor != 'dependabot[bot]'
	uses: scacap/action-surefire-report@v1
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: FHIR server test report 1
	fail_on_test_failures: true

	fhir-server-2:
	name: FHIR server (tranche 2)
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Cache test data
	id: cache-test-data
	uses: actions/cache@v3
	with:
	path: fhir-server/src/test/resources/test-data/parquet
	key: ${{ runner.os }}-test-data-${{ hashFiles('fhir-server/src/test/resources/test-data/fhir/.ndjson', 'encoders/src/main//.java', 'encoders/src/main/*/.scala', 'fhir-server/src/main/java/au/csiro/pathling/io/Database.java') }}
	- name: Run the verify goal with Maven
	env:
	# Activate the "tranche 2" test profile. If there is a cache hit on the test data, we
	# don't need to import it.
	PATHLING_PROFILES: testTranche2${{ steps.cache-test-data.outputs.cache-hit && ',!importTestData' \|\| '' }}
	# If the actor is not Dependabot, we ignore test failures and rely upon the Surefire
	# report action to report them.
	PATHLING_OPTS: >-
	-DskipEncodersTests
	-DskipUtilitiesTests
	-DskipTerminologyTests
	-DskipFhirPathTests
	${{ github.actor == 'dependabot[bot]' && '' \|\| '-Dmaven.test.failure.ignore' }}
	run: >-
	mvn --batch-mode verify
	-pl fhir-server -am
	-P${{ env.PATHLING_PROFILES }}
	${{ env.PATHLING_OPTS }}
	timeout-minutes: 30
	- name: Upload fhir-server test reports
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-2-surefire-reports
	path: fhir-server/target/surefire-reports
	- name: Upload test coverage report
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-2-coverage
	path: "**/jacoco.xml"
	- name: Upload timing log
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-2-timing-log
	path: fhir-server/target/timing.log
	- name: Upload dump files
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-2-dump-files
	path: \|-
	*/.dump
	*/.dumpstream
	- name: Publish test results
	# If the actor is Dependabot, we need to avoid anything that requires access to secrets.
	if: github.actor != 'dependabot[bot]'
	uses: scacap/action-surefire-report@v1
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: FHIR server test report 2
	fail_on_test_failures: true

	# This job builds the FHIR server, and runs all tests that do not fall into tranches 1 or 2.
	fhir-server-3:
	name: FHIR server (tranche 3)
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Cache test data
	id: cache-test-data
	uses: actions/cache@v3
	with:
	path: fhir-server/src/test/resources/test-data/parquet
	key: ${{ runner.os }}-test-data-${{ hashFiles('fhir-server/src/test/resources/test-data/fhir/.ndjson', 'encoders/src/main//.java', 'encoders/src/main/*/.scala', 'fhir-server/src/main/java/au/csiro/pathling/io/Database.java') }}
	- name: Run the verify goal with Maven
	env:
	# Activate the "tranche 3" test profile. If there is a cache hit on the test data, we
	# don't need to import it.
	PATHLING_PROFILES: testTranche3${{ steps.cache-test-data.outputs.cache-hit && ',!importTestData' \|\| '' }}
	# If the actor is not Dependabot, we ignore test failures and rely upon the Surefire
	# report action to report them.
	PATHLING_OPTS: >-
	-DskipEncodersTests
	${{ github.actor == 'dependabot[bot]' && '' \|\| '-Dmaven.test.failure.ignore' }}
	run: >-
	mvn --batch-mode verify
	-pl fhir-server -am
	-P${{ env.PATHLING_PROFILES }}
	${{ env.PATHLING_OPTS }}
	timeout-minutes: 30
	- name: Upload utilities test reports
	uses: actions/upload-artifact@v3
	with:
	name: utilities-surefire-reports
	path: utilities/target/surefire-reports
	- name: Upload terminology test reports
	uses: actions/upload-artifact@v3
	with:
	name: terminology-surefire-reports
	path: terminology/target/surefire-reports
	- name: Upload FHIRPath test reports
	uses: actions/upload-artifact@v3
	with:
	name: fhirpath-surefire-reports
	path: fhirpath/target/surefire-reports
	- name: Upload FHIR server test reports
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-3-surefire-reports
	path: fhir-server/target/surefire-reports
	- name: Upload FHIR server test coverage report
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-3-coverage
	path: "**/jacoco.xml"
	- name: Upload timing log
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-3-timing-log
	path: fhir-server/target/timing.log
	- name: Upload dump files
	uses: actions/upload-artifact@v3
	with:
	name: fhir-server-3-dump-files
	path: \|-
	*/.dump
	*/.dumpstream
	- name: Publish test results
	# If the actor is Dependabot, we need to avoid anything that requires access to secrets.
	if: github.actor != 'dependabot[bot]'
	uses: scacap/action-surefire-report@v1
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: FHIR server test report 3
	fail_on_test_failures: true

	# This job builds, tests and scans the FHIR server Docker image.
	docker-image:
	name: Docker image
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Run the verify goal with Maven
	if: github.actor == 'dependabot[bot]'
	env:
	# If the actor is Dependabot we skip the system test, as it requires access to secrets.
	PATHLING_OPTS: >-
	-DskipSurefireTests
	-DskipITs
	-Dpathling.dockerArchitecture=amd64
	run: >-
	mvn --batch-mode verify
	-pl fhir-server -am
	-Pdocker,!importTestData
	${{ env.PATHLING_OPTS }}
	timeout-minutes: 15
	- name: Run the verify goal with Maven
	if: github.actor != 'dependabot[bot]'
	env:
	PATHLING_OPTS: >-
	-DskipSurefireTests
	-Dmaven.test.failure.ignore
	-Dpathling.dockerArchitecture=amd64
	-Dpathling.systemTest.auth.clientSecret=${{ secrets.TEST_CLIENT_SECRET }}
	run: >-
	mvn --batch-mode verify
	-pl fhir-server -am
	-Pdocker,!importTestData
	${{ env.PATHLING_OPTS }}
	timeout-minutes: 15
	- name: Scan Docker image for vulnerabilities
	uses: aquasecurity/trivy-action@master
	env:
	TRIVY_OFFLINE_SCAN: true
	with:
	image-ref: "aehrc/pathling:${{ github.sha }}"
	exit-code: "1"
	ignore-unfixed: true
	security-checks: "vuln"
	severity: CRITICAL
	timeout: 20m
	- name: Publish test results
	# If the actor is Dependabot, we need to avoid anything that requires access to secrets.
	if: github.actor != 'dependabot[bot]'
	uses: scacap/action-surefire-report@v1
	with:
	github_token: ${{ secrets.GITHUB_TOKEN }}
	check_name: Docker image test report
	fail_on_test_failures: true

	benchmark:
	name: Benchmark
	runs-on: ubuntu-latest
	permissions:
	id-token: write
	steps:
	- name: Configure AWS credentials
	uses: aws-actions/configure-aws-credentials@v1
	with:
	role-to-assume: arn:aws:iam::865780493209:role/PathlingBenchmarkUpload
	aws-region: ap-southeast-2
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Cache test data
	id: cache-test-data
	uses: actions/cache@v3
	with:
	path: fhir-server/src/test/resources/test-data/parquet
	key: ${{ runner.os }}-test-data-${{ hashFiles('fhir-server/src/test/resources/test-data/fhir/.ndjson', 'encoders/src/main//.java', 'encoders/src/main/*/.scala', 'fhir-server/src/main/java/au/csiro/pathling/io/Database.java') }}
	- name: Get current time
	id: timestamp
	run: echo "::set-output name=timestamp::$(date +'%Y%m%d%H%M%S')"
	- name: Run the verify goal with Maven
	env:
	# If there is a cache hit on the test data, we don't need to import it. If it is a cache
	# miss, we still need to explicitly activate the `importTestData` profile, otherwise
	# it will be deactivated by `skipTests`.
	PATHLING_PROFILES: runBenchmark,${{ steps.cache-test-data.outputs.cache-hit && '!importTestData' \|\| 'importTestData' }}
	run: >-
	mvn --batch-mode verify
	-pl fhir-server -am
	-P${{ env.PATHLING_PROFILES }}
	-DskipSurefireTests
	timeout-minutes: 20
	- name: Upload benchmark artifact
	uses: actions/upload-artifact@v3
	with:
	name: benchmark-results
	path: "*/jmh-.json"
	- name: Upload benchmark file to S3
	run: aws s3 sync fhir-server/target/benchmark s3://pathling-benchmark/${{ github.ref }}/${{ github.run_id }}/${{ steps.timestamp.outputs.timestamp }}/

	js-client:
	name: JavaScript client
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- uses: actions/setup-node@v3
	with:
	node-version: "16"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Run the verify goal with Maven
	run: >-
	mvn --batch-mode verify
	-pl lib/js -am
	timeout-minutes: 5

	import:
	name: Import lambda
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- uses: actions/setup-node@v3
	with:
	node-version: "16"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Run the verify goal with Maven
	run: \|
	mvn --batch-mode verify \
	-pl lib/import -am
	timeout-minutes: 5
	- name: Upload import lambda
	uses: actions/upload-artifact@v3
	with:
	name: import-lambda
	path: lib/import/target/pathling-import-lambda.zip

	python-api:
	name: Python API
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Set up Python 3.8
	uses: actions/setup-python@v4
	id: pythoninstall
	with:
	python-version: 3.8
	- name: Cache Python packages
	uses: actions/cache@v3
	id: pythoncache
	with:
	path: /home/runner/.cache/pip
	key: ${{ runner.os }}-pip-${{ hashFiles('lib/python/requirements/dev.txt', 'lib/python/requirements/package.txt') }}
	- name: Run the install goal with Maven
	env:
	# If the actor is not Dependabot, we ignore test failures and rely upon the Surefire
	# report action to report them.
	PATHLING_OPTS: >-
	-DskipEncodersTests
	-DskipUtilitiesTests
	-DskipTerminologyTests
	-DskipFhirPathTests
	${{ github.actor == 'dependabot[bot]' && '' \|\| '-Dmaven.test.failure.ignore' }}
	PYSPARK_PYTHON: ${{ steps.pythoninstall.outputs.python-path }}
	PYSPARK_DRIVER_PYTHON: ${{ steps.pythoninstall.outputs.python-path }}
	run: >-
	mvn --batch-mode install
	-pl lib/python -am
	${{ env.PATHLING_OPTS }}
	timeout-minutes: 30
	- name: Upload library API test reports
	uses: actions/upload-artifact@v3
	with:
	name: library-api-surefire-reports
	path: library-api/target/surefire-reports
	- name: Upload library API test coverage report
	uses: actions/upload-artifact@v3
	with:
	name: library-api-coverage
	path: "**/jacoco.xml"
	- name: Upload Python API test coverage report
	uses: actions/upload-artifact@v3
	with:
	name: python-api-coverage
	path: lib/python/**/coverage.xml

	R-api:
	name: R API
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Get R package installation location
	run: echo "R_PACKAGES=$(Rscript -e 'cat(.libPaths(), sep="\n")' \| head -n 1)" >> $GITHUB_ENV
	- name: Cache R packages
	uses: actions/cache@v2
	with:
	path: ${{ env.R_PACKAGES }}
	key: r-packages-${{ runner.os }}-${{ hashFiles('lib/R/DESCRIPTION.src') }}
	restore-keys: r-packages-${{ runner.os }}-
	- name: Extract Spark version
	working-directory: lib/R
	run: echo "SPARK_VERSION=$(mvn help:evaluate -Dexpression=pathling.Rapi.sparkVersion -q -DforceStdout)" >> $GITHUB_ENV
	- name: Extract Hadoop version
	working-directory: lib/R
	run: echo "HADOOP_VERSION=$(mvn help:evaluate -Dexpression=pathling.Rapi.hadoopVersion -q -DforceStdout)" >> $GITHUB_ENV
	- name: Cache Spark
	id: cache-spark
	uses: actions/cache@v2
	with:
	path: /home/runner/spark/spark-${{ env.SPARK_VERSION }}-bin-hadoop${{ env.HADOOP_VERSION }}
	key: spark-${{ env.SPARK_VERSION }}-bin-hadoop${{ env.HADOOP_VERSION }}
	- name: Install Pandoc
	uses: r-lib/actions/setup-pandoc@v2
	- name: Install R
	uses: r-lib/actions/setup-r@v2
	with:
	r-version: "4.1.3"
	use-public-rspm: true
	- name: Install texlive and libcurl
	run: sudo apt-get install -y texlive-latex-base texlive-fonts-extra libcurl4-openssl-dev
	- name: Run the install goal with Maven
	env:
	# If the actor is not Dependabot, we ignore test failures and rely upon the Surefire
	# report action to report them.
	R_KEEP_PKG_SOURCE: yes
	PATHLING_OPTS: >-
	-DskipEncodersTests
	-DskipUtilitiesTests
	-DskipTerminologyTests
	-DskipFhirPathTests
	-DskipLibraryApiTests
	${{ github.actor == 'dependabot[bot]' && '' \|\| '-Dmaven.test.failure.ignore' }}
	run: >-
	mvn --batch-mode install
	-pl lib/R -am -Pdocs
	${{ env.PATHLING_OPTS }}
	timeout-minutes: 60
	- name: Upload package as artifact
	uses: actions/upload-artifact@v2
	with:
	name: r-package
	path: lib/R/target/pathling_*.tar.gz

	site:
	name: Site
	runs-on: ubuntu-latest
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Set up Helm
	uses: azure/setup-helm@v3
	with:
	version: 3.13.2
	- uses: actions/setup-node@v3
	with:
	node-version: "16"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|-
	${{ runner.os }}-maven-
	- name: Extract Spark version
	working-directory: lib/R
	run: echo "SPARK_VERSION=$(mvn help:evaluate -Dexpression=pathling.Rapi.sparkVersion -q -DforceStdout)" >> $GITHUB_ENV
	- name: Extract Hadoop version
	working-directory: lib/R
	run: echo "HADOOP_VERSION=$(mvn help:evaluate -Dexpression=pathling.Rapi.hadoopVersion -q -DforceStdout)" >> $GITHUB_ENV
	- name: Cache Spark
	id: cache-spark
	uses: actions/cache@v2
	with:
	path: /home/runner/spark/spark-${{ env.SPARK_VERSION }}-bin-hadoop${{ env.HADOOP_VERSION }}
	key: spark-${{ env.SPARK_VERSION }}-bin-hadoop${{ env.HADOOP_VERSION }}
	- name: Install Pandoc
	uses: r-lib/actions/setup-pandoc@v2
	- name: Install R
	uses: r-lib/actions/setup-r@v2
	with:
	r-version: "4.1.3"
	use-public-rspm: true
	- name: Install texlive and libcurl
	run: sudo apt-get install -y texlive-latex-base texlive-fonts-extra libcurl4-openssl-dev
	- name: Run the verify goal with Maven
	env:
	R_KEEP_PKG_SOURCE: yes
	run: >-
	mvn --batch-mode verify
	-pl site -am
	-Pdocs
	-DskipTests
	timeout-minutes: 45

	upload-coverage:
	name: Upload coverage
	runs-on: ubuntu-latest
	needs: [ encoders, fhir-server-1, fhir-server-2, fhir-server-3, python-api ]
	if: github.actor != 'dependabot[bot]'
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	- name: Download encoders coverage report
	uses: actions/download-artifact@v3
	with:
	name: encoders-coverage
	path: encoders-coverage
	- name: Download library API coverage report
	uses: actions/download-artifact@v3
	with:
	name: library-api-coverage
	path: library-api-coverage
	- name: Download Python API coverage report
	uses: actions/download-artifact@v3
	with:
	name: python-api-coverage
	path: python-api-coverage
	- name: Download FHIR server coverage report 1
	uses: actions/download-artifact@v3
	with:
	name: fhir-server-1-coverage
	path: fhir-server-1-coverage
	- name: Download FHIR server coverage report 2
	uses: actions/download-artifact@v3
	with:
	name: fhir-server-2-coverage
	path: fhir-server-2-coverage
	- name: Download FHIR server coverage report 3
	uses: actions/download-artifact@v3
	with:
	name: fhir-server-3-coverage
	path: fhir-server-3-coverage
	- name: Upload coverage to Codecov
	uses: codecov/codecov-action@v2

	deploy-pre-release:
	name: Pre-release deployment
	needs: [ encoders, fhir-server-1, fhir-server-2, fhir-server-3, docker-image ]
	runs-on: ubuntu-latest
	# If the branch starts with "release/", we deploy pre-release packages.
	if: startsWith(github.ref, 'refs/heads/release/')
	steps:
	- name: Checkout code
	uses: actions/checkout@v3
	with:
	# This is required so that git-commit-id-plugin can find the latest tag.
	fetch-depth: 0
	- name: Set up JDK
	uses: actions/setup-java@v2
	with:
	java-version: 11
	distribution: "zulu"
	- name: Cache local Maven repository
	uses: actions/cache@v3
	with:
	path: ~/.m2/repository
	key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
	restore-keys: \|
	${{ runner.os }}-maven-
	- name: Login to Docker Hub
	uses: docker/login-action@v1
	with:
	username: ${{ secrets.DOCKER_USERNAME }}
	password: ${{ secrets.DOCKER_PASSWORD }}
	- name: Install GPG key
	run: \|
	cat <(echo -e "${{ secrets.GPG_KEY }}") \| gpg --batch --import
	gpg --list-secret-keys --keyid-format LONG
	- name: Configure Maven settings
	uses: s4u/maven-settings-action@v2.6.0
	with:
	servers: \|
	[{
	"id": "ossrh",
	"username": "${{ secrets.OSSRH_USERNAME }}",
	"password": "${{ secrets.OSSRH_PASSWORD }}"
	}]
	- name: Run the deploy goal with Maven
	run: \|
	TAG=$(echo '${{ github.ref }}' \| sed 's/refs\/heads\/release\///')
	mvn --batch-mode deploy \
	-pl fhir-server,library-api,library-runtime -am \
	-PmavenPreRelease,dockerPreRelease,docs \
	-Dpathling.fhirServerDockerTag=$TAG \
	-DskipTests -DskipScalaDocs \
	-Dgpg.passphrase="${{ secrets.GPG_PASSPHRASE }}"
	timeout-minutes: 30

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Bump com.google.cloud.tools:jib-maven-plugin from 3.3.2 to 3.4.2 #3450

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Bump com.google.cloud.tools:jib-maven-plugin from 3.3.2 to 3.4.2 #3450

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