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Merge branch 'develop' into 10941-remove-custom-guides-navbar #10941
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.env

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APP_IMAGE=gdcc/dataverse:unstable
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POSTGRES_VERSION=16
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POSTGRES_VERSION=17
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DATAVERSE_DB_USER=dataverse
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SOLR_VERSION=9.3.0
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SOLR_VERSION=9.8.0
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SKIP_DEPLOY=0

.github/dependabot.yml

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# Set update schedule for GitHub Actions
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# https://docs.github.com/en/code-security/supply-chain-security/keeping-your-dependencies-updated-automatically/keeping-your-actions-up-to-date-with-dependabot
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version: 2
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updates:
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- package-ecosystem: "github-actions"
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directory: "/"
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schedule:
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# Check for updates to GitHub Actions daily
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interval: "daily"

.github/workflows/codeql.yml

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# For most projects, this workflow file will not need changing; you simply need
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# to commit it to your repository.
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#
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# You may wish to alter this file to override the set of languages analyzed,
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# or to provide custom queries or build logic.
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#
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# ******** NOTE ********
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# We have attempted to detect the languages in your repository. Please check
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# the `language` matrix defined below to confirm you have the correct set of
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# supported CodeQL languages.
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#
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name: "CodeQL Advanced"
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on:
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push:
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branches: [ "develop", "master" ]
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pull_request:
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branches: [ "develop", "master" ]
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schedule:
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- cron: '30 6 * * 4'
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jobs:
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analyze:
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name: Analyze (${{ matrix.language }})
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# Runner size impacts CodeQL analysis time. To learn more, please see:
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# - https://gh.io/recommended-hardware-resources-for-running-codeql
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# - https://gh.io/supported-runners-and-hardware-resources
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# - https://gh.io/using-larger-runners (GitHub.com only)
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# Consider using larger runners or machines with greater resources for possible analysis time improvements.
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runs-on: ${{ (matrix.language == 'swift' && 'macos-latest') || 'ubuntu-latest' }}
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permissions:
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# required for all workflows
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security-events: write
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# required to fetch internal or private CodeQL packs
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packages: read
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# only required for workflows in private repositories
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actions: read
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contents: read
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strategy:
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fail-fast: false
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matrix:
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include:
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- language: actions
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build-mode: none
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- language: java-kotlin
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build-mode: none # This mode only analyzes Java. Set this to 'autobuild' or 'manual' to analyze Kotlin too.
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- language: javascript-typescript
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build-mode: none
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- language: python
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build-mode: none
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# CodeQL supports the following values keywords for 'language': 'actions', 'c-cpp', 'csharp', 'go', 'java-kotlin', 'javascript-typescript', 'python', 'ruby', 'swift'
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# Use `c-cpp` to analyze code written in C, C++ or both
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# Use 'java-kotlin' to analyze code written in Java, Kotlin or both
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# Use 'javascript-typescript' to analyze code written in JavaScript, TypeScript or both
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# To learn more about changing the languages that are analyzed or customizing the build mode for your analysis,
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# see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/customizing-your-advanced-setup-for-code-scanning.
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# If you are analyzing a compiled language, you can modify the 'build-mode' for that language to customize how
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# your codebase is analyzed, see https://docs.github.com/en/code-security/code-scanning/creating-an-advanced-setup-for-code-scanning/codeql-code-scanning-for-compiled-languages
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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# Add any setup steps before running the `github/codeql-action/init` action.
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# This includes steps like installing compilers or runtimes (`actions/setup-node`
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# or others). This is typically only required for manual builds.
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# - name: Setup runtime (example)
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# uses: actions/setup-example@v1
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# Initializes the CodeQL tools for scanning.
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- name: Initialize CodeQL
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uses: github/codeql-action/init@v3
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with:
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languages: ${{ matrix.language }}
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build-mode: ${{ matrix.build-mode }}
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# If you wish to specify custom queries, you can do so here or in a config file.
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# By default, queries listed here will override any specified in a config file.
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# Prefix the list here with "+" to use these queries and those in the config file.
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# For more details on CodeQL's query packs, refer to: https://docs.github.com/en/code-security/code-scanning/automatically-scanning-your-code-for-vulnerabilities-and-errors/configuring-code-scanning#using-queries-in-ql-packs
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# queries: security-extended,security-and-quality
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# If the analyze step fails for one of the languages you are analyzing with
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# "We were unable to automatically build your code", modify the matrix above
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# to set the build mode to "manual" for that language. Then modify this step
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# to build your code.
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# ℹ️ Command-line programs to run using the OS shell.
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# 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
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- if: matrix.build-mode == 'manual'
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shell: bash
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run: |
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echo 'If you are using a "manual" build mode for one or more of the' \
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'languages you are analyzing, replace this with the commands to build' \
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'your code, for example:'
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echo ' make bootstrap'
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echo ' make release'
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exit 1
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- name: Perform CodeQL Analysis
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uses: github/codeql-action/analyze@v3
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with:
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category: "/language:${{matrix.language}}"

.github/workflows/container_app_pr.yml

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if: ${{ github.repository_owner == 'IQSS' }}
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steps:
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# Checkout the pull request code as when merged
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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with:
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ref: 'refs/pull/${{ github.event.client_payload.pull_request.number }}/merge'
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- uses: actions/setup-java@v3
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- uses: actions/setup-java@v4
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with:
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java-version: "17"
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distribution: 'adopt'
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- uses: actions/cache@v3
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- uses: actions/cache@v4
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with:
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path: ~/.m2
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key: ${{ runner.os }}-m2-${{ hashFiles('**/pom.xml') }}
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restore-keys: ${{ runner.os }}-m2
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# Note: Accessing, pushing tags etc. to GHCR will only succeed in upstream because secrets.
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- name: Login to Github Container Registry
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uses: docker/login-action@v2
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ secrets.GHCR_USERNAME }}
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password: ${{ secrets.GHCR_TOKEN }}
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- name: Set up QEMU for multi-arch builds
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uses: docker/setup-qemu-action@v2
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uses: docker/setup-qemu-action@v3
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# Get the image tag from either the command or default to branch name (Not used for now)
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#- name: Get the target tag name
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:ship: [See on GHCR](https://github.com/orgs/gdcc/packages/container). Use by referencing with full name as printed above, mind the registry name.
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# Leave a note when things have gone sideways
90-
- uses: peter-evans/create-or-update-comment@v3
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- uses: peter-evans/create-or-update-comment@v4
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if: ${{ failure() }}
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with:
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issue-number: ${{ github.event.client_payload.pull_request.number }}

.github/workflows/container_app_push.yml

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if: ${{ github.event_name != 'pull_request' && github.ref_name == 'develop' && github.repository_owner == 'IQSS' }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: peter-evans/dockerhub-description@v3
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- uses: actions/checkout@v4
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- uses: peter-evans/dockerhub-description@v4
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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repository: gdcc/dataverse
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short-description: "Dataverse Application Container Image providing the executable"
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readme-filepath: ./src/main/docker/README.md
79-
- uses: peter-evans/dockerhub-description@v3
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- uses: peter-evans/dockerhub-description@v4
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
@@ -126,20 +126,20 @@ jobs:
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# Depending on context, we push to different targets. Login accordingly.
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- if: github.event_name != 'pull_request'
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name: Log in to Docker Hub registry
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uses: docker/login-action@v2
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uses: docker/login-action@v3
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with:
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username: ${{ secrets.DOCKERHUB_USERNAME }}
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password: ${{ secrets.DOCKERHUB_TOKEN }}
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- if: ${{ github.event_name == 'pull_request' }}
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name: Login to Github Container Registry
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uses: docker/login-action@v2
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ secrets.GHCR_USERNAME }}
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password: ${{ secrets.GHCR_TOKEN }}
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- name: Set up QEMU for multi-arch builds
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uses: docker/setup-qemu-action@v2
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uses: docker/setup-qemu-action@v3
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- name: Re-set image tag based on branch (if master)
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if: ${{ github.ref_name == 'master' }}

.github/workflows/container_base_push.yml

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# Configure a remote ARM64 build host in addition to the local AMD64 in two steps.
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- name: Setup SSH agent
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if: ${{ github.event_name != 'schedule' }}
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uses: webfactory/ssh-agent@v0.9.0
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uses: webfactory/ssh-agent@v0.9.1
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with:
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ssh-private-key: ${{ secrets.BUILDER_ARM64_SSH_PRIVATE_KEY }}
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- name: Provide the known hosts key and the builder config

.github/workflows/copy_labels.yml

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name: Copy labels from issue to pull request
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on:
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pull_request:
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types: [opened]
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jobs:
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copy-labels:
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runs-on: ubuntu-latest
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name: Copy labels from linked issues
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steps:
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- name: copy-labels
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uses: michalvankodev/copy-issue-labels@v1.3.0
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/deploy_beta_testing.yml

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branches:
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- develop
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concurrency:
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group: deploy-beta-testing
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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@v3
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- uses: actions/checkout@v4
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- uses: actions/setup-java@v3
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- uses: actions/setup-java@v4
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with:
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distribution: 'zulu'
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java-version: '17'
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run: echo "war_file=$(ls *.war | head -1)">> $GITHUB_ENV
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- name: Upload war artifact
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uses: actions/upload-artifact@v3
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uses: actions/upload-artifact@v4
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with:
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name: built-app
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path: ./target/${{ env.war_file }}
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Download war artifact
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uses: actions/download-artifact@v3
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uses: actions/download-artifact@v4
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with:
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name: built-app
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path: ./
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overwrite: true
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- name: Execute payara war deployment remotely
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uses: appleboy/ssh-action@v1.0.0
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uses: appleboy/ssh-action@v1.2.2
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env:
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INPUT_WAR_FILE: ${{ env.war_file }}
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with:

.github/workflows/guides_build_sphinx.yml

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docs:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: OdumInstitute/sphinx-action@master
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- uses: actions/checkout@v4
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- uses: uncch-rdmc/sphinx-action@master
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with:
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docs-folder: "doc/sphinx-guides/"

.github/workflows/maven_unit_test.yml

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steps:
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# TODO: As part of #10618 change to setup-maven custom action
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# Basic setup chores
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- uses: actions/checkout@v3
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- uses: actions/checkout@v4
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- name: Set up JDK ${{ matrix.jdk }}
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uses: actions/setup-java@v3
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uses: actions/setup-java@v4
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with:
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java-version: ${{ matrix.jdk }}
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distribution: temurin
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# Upload the built war file. For download, it will be wrapped in a ZIP by GitHub.
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# See also https://github.com/actions/upload-artifact#zipped-artifact-downloads
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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with:
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name: dataverse-java${{ matrix.jdk }}.war
6363
path: target/dataverse*.war
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- run: |
6868
tar -cvf java-builddir.tar target
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tar -cvf java-m2-selection.tar ~/.m2/repository/io/gdcc/dataverse-*
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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with:
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name: java-artifacts
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path: |
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steps:
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# TODO: As part of #10618 change to setup-maven custom action
100100
# Basic setup chores
101-
- uses: actions/checkout@v3
101+
- uses: actions/checkout@v4
102102
- name: Set up JDK ${{ matrix.jdk }}
103-
uses: actions/setup-java@v3
103+
uses: actions/setup-java@v4
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with:
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java-version: ${{ matrix.jdk }}
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distribution: temurin
107107
cache: maven
108108

109109
# Get the build output from the unit test job
110-
- uses: actions/download-artifact@v3
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- uses: actions/download-artifact@v4
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with:
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name: java-artifacts
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- run: |
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120120
# Wrap up and send to coverage job
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- run: tar -cvf java-reportdir.tar target/site
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- uses: actions/upload-artifact@v3
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- uses: actions/upload-artifact@v4
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with:
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name: java-reportdir
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path: java-reportdir.tar
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steps:
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# TODO: As part of #10618 change to setup-maven custom action
134134
# Basic setup chores
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- uses: actions/checkout@v3
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- uses: actions/setup-java@v3
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- uses: actions/checkout@v4
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- uses: actions/setup-java@v4
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with:
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java-version: '17'
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distribution: temurin
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cache: maven
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# Get the build output from the integration test job
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- uses: actions/download-artifact@v3
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- uses: actions/download-artifact@v4
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with:
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name: java-reportdir
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- run: tar -xvf java-reportdir.tar

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