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Merge remote-tracking branch 'IQSS/develop' into LocallyFAIR
# Conflicts: # src/main/java/edu/harvard/iq/dataverse/api/Access.java # src/main/java/edu/harvard/iq/dataverse/api/Datasets.java
2 parents f8002ff + 5dc8b47 commit 6387e45

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‎.github/workflows/add_bugs_to_project.yml‎

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name: Add bugs to project board
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on:
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issues:
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types:
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- opened
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- labeled
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jobs:
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add-to-project:
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name: Add bug to project
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runs-on: ubuntu-latest
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steps:
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- uses: actions/add-to-project@v1.0.2
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with:
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project-url: https://github.com/orgs/IQSS/projects/34
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github-token: ${{ secrets.ADD_TO_PROJECT_PAT }}
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labeled: "Type: Bug"

‎.github/workflows/container_app_pr.yml‎

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ref: 'refs/pull/${{ github.event.client_payload.pull_request.number }}/merge'
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- uses: actions/setup-java@v5
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with:
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java-version: "17"
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java-version: "21"
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distribution: 'adopt'
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- uses: actions/cache@v5
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with:
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-Dapp.image.tag=${{ env.IMAGE_TAG }}
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-Ddocker.registry=ghcr.io -Ddocker.platforms=${{ env.PLATFORMS }}
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- uses: marocchino/sticky-pull-request-comment@v2
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- uses: marocchino/sticky-pull-request-comment@v3
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with:
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header: registry-push
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hide_and_recreate: true

‎.github/workflows/container_app_push.yml‎

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${{ env.REGISTRY }} -Ddocker.platforms=${{ env.PLATFORMS }}
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-P ct deploy
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- uses: marocchino/sticky-pull-request-comment@v2
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- uses: marocchino/sticky-pull-request-comment@v3
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if: ${{ github.event_name == 'pull_request' }}
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with:
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header: registry-push

‎.github/workflows/container_maintenance.yml‎

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with:
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platforms: ${{ env.PLATFORMS }}
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- name: Setup Trivy binary for vulnerability scanning
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uses: aquasecurity/setup-trivy@v0.2.5
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uses: aquasecurity/setup-trivy@v0.2.6
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with:
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version: v0.63.0
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version: v0.69.3
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# Execute matrix build for the discovered branches
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- name: Execute build matrix script

‎.github/workflows/deploy_beta_testing.yml‎

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- uses: actions/setup-java@v5
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with:
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distribution: 'zulu'
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java-version: '17'
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java-version: '21'
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- name: Enable API Session Auth feature flag
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working-directory: src/main/resources/META-INF
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envs: INPUT_WAR_FILE
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script: |
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APPLICATION_NAME=dataverse-backend
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ASADMIN='/usr/local/payara6/bin/asadmin --user admin'
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ASADMIN='/usr/local/payara7/bin/asadmin --user admin'
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$ASADMIN undeploy $APPLICATION_NAME
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#$ASADMIN stop-domain
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#rm -rf /usr/local/payara6/glassfish/domains/domain1/generated
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#rm -rf /usr/local/payara6/glassfish/domains/domain1/osgi-cache
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#rm -rf /usr/local/payara7/glassfish/domains/domain1/generated
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#rm -rf /usr/local/payara7/glassfish/domains/domain1/osgi-cache
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#$ASADMIN start-domain
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$ASADMIN deploy --name $APPLICATION_NAME $INPUT_WAR_FILE
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#$ASADMIN stop-domain

‎.github/workflows/deploy_to_internal.yml‎

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name: 'Deploy to dataverse-internal.iq.harvard.edu'
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on:
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workflow_dispatch:
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inputs:
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buildlabel:
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description: 'Custom label that will appear after the version number (the equivalent of the old "build number" entry). Leaving it empty will default to the legacy behavior, i.e. " build <branch>-<checksum>".'
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type: string
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required: false
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permissions:
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contents: read
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concurrency:
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group: deploy-to-internal
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cancel-in-progress: false
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v6
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- uses: actions/setup-java@v5
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with:
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distribution: 'zulu'
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java-version: '21'
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- name: Set build number
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run: scripts/installer/custom-build-number "${{ github.event.inputs.buildlabel }}"
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- name: Build application war
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run: mvn package
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- name: Get war file name
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working-directory: target
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run: echo "war_file=$(ls *.war | head -1)">> $GITHUB_ENV
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- name: Upload war artifact
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uses: actions/upload-artifact@v7
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with:
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name: built-app
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path: ./target/${{ env.war_file }}
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deploy-to-payara:
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needs: build
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if: ${{ github.repository_owner == 'IQSS' }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v6
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- name: Download war artifact
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uses: actions/download-artifact@v8
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with:
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name: built-app
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path: ./
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- name: Get war file name
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run: echo "war_file=$(ls *.war | head -1)">> $GITHUB_ENV
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- name: Copy war file to remote instance
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uses: appleboy/scp-action@master
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with:
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host: ${{ secrets.INTERNAL_PAYARA_INSTANCE_HOST }}
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username: ${{ secrets.INTERNAL_PAYARA_INSTANCE_USERNAME }}
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key: ${{ secrets.INTERNAL_PAYARA_INSTANCE_SSH_PRIVATE_KEY }}
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source: './${{ env.war_file }}'
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target: '/home/${{ secrets.INTERNAL_PAYARA_INSTANCE_USERNAME }}'
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overwrite: true
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- name: Execute payara war deployment remotely
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uses: appleboy/ssh-action@v1.2.5
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env:
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INPUT_WAR_FILE: ${{ env.war_file }}
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with:
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host: ${{ secrets.INTERNAL_PAYARA_INSTANCE_HOST }}
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username: ${{ secrets.INTERNAL_PAYARA_INSTANCE_USERNAME }}
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key: ${{ secrets.INTERNAL_PAYARA_INSTANCE_SSH_PRIVATE_KEY }}
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envs: INPUT_WAR_FILE
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script: |
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APPLICATION_NAME=dataverse-backend
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ASADMIN='/usr/local/payara7/bin/asadmin --user admin'
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$ASADMIN undeploy $APPLICATION_NAME
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#$ASADMIN stop-domain
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#$ASADMIN start-domain
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$ASADMIN deploy --name $APPLICATION_NAME $INPUT_WAR_FILE
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#$ASADMIN stop-domain
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#$ASADMIN start-domain

‎.github/workflows/generate_war_file.yml‎

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name: 'Generate dataverse war file'
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on:
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workflow_dispatch:
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inputs:
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buildlabel:
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description: 'Custom label that will appear after the version number (the equivalent of the old "build number" entry). Leaving it empty will default to the legacy behavior, i.e. " build <branch>-<checksum>".'
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type: string
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required: false
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v6
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- uses: actions/setup-java@v5
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with:
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distribution: 'zulu'
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java-version: '21'
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- name: Set build number
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run: scripts/installer/custom-build-number "${{ github.event.inputs.buildlabel }}"
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- name: Build application war
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run: mvn package
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- name: Get war file name
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working-directory: target
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run: echo "war_file=$(ls *.war | head -1)">> $GITHUB_ENV
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- name: Upload war artifact
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uses: actions/upload-artifact@v7
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with:
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name: built-app
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path: ./target/${{ env.war_file }}

‎.github/workflows/maven_unit_test.yml‎

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strategy:
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fail-fast: false
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matrix:
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jdk: [ '17' ]
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jdk: [ '21' ]
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experimental: [false]
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status: ["Stable"]
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continue-on-error: ${{ matrix.experimental }}
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strategy:
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fail-fast: false
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matrix:
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jdk: [ '17' ]
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jdk: [ '21' ]
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experimental: [ false ]
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status: [ "Stable" ]
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#
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- uses: actions/checkout@v6
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- uses: actions/setup-java@v5
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with:
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java-version: '17'
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java-version: '21'
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distribution: temurin
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cache: maven
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‎.github/workflows/spi_release.yml‎

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- uses: actions/checkout@v6
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- uses: actions/setup-java@v5
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with:
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java-version: '17'
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java-version: '21'
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distribution: 'adopt'
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server-id: central
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server-username: MAVEN_USERNAME
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- uses: actions/checkout@v6
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- uses: actions/setup-java@v5
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with:
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java-version: '17'
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java-version: '21'
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distribution: 'adopt'
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- uses: actions/cache@v5
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with:
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- name: Set up Maven Central Repository
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uses: actions/setup-java@v5
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java-version: '17'
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java-version: '21'
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distribution: 'adopt'
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server-id: central
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server-username: MAVEN_USERNAME

‎conf/jhove/jhove.conf‎

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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
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xmlns="http://hul.harvard.edu/ois/xml/ns/jhove/jhoveConfig"
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xsi:schemaLocation="http://hul.harvard.edu/ois/xml/ns/jhove/jhoveConfig
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file:///usr/local/payara6/glassfish/domains/domain1/config/jhoveConfig.xsd">
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file:///usr/local/payara7/glassfish/domains/domain1/config/jhoveConfig.xsd">
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<jhoveHome>/usr/local/src/jhove</jhoveHome>
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<defaultEncoding>utf-8</defaultEncoding>
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<tempDirectory>/tmp</tempDirectory>

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