test.yml

# 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