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| name: Publish Docker images | ||
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| env: | ||
| REGISTRY: ghcr.io | ||
| IMAGE_NAME: ghcr.io/${{ github.repository }} | ||
| TAG: ${{ github.ref_name }} | ||
| DOCKER_REPOSITORY: ghcr.io/${{ github.repository }} | ||
| GIT_REPO_URL: https://github.com/${{ github.repository }} | ||
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| # production builds | ||
| # - triggered by pushing a tag | ||
| # - builds the current commit | ||
| # - cache is disabled | ||
| # development builds | ||
| # - triggered by workflow_call (in the deploy-qualif workflow) | ||
| # - builds the commit provided in the 'sha' input variable | ||
| # - cache is enabled | ||
| PRODUCTION: ${{ github.event_name == 'push' && '1' || '' }} | ||
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| # id of the git commit to be built | ||
| SHA: ${{ github.event_name == 'push' && github.sha || inputs.sha }} | ||
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| # tag of the resulting docker image | ||
| # - name of the git tag (production builds) | ||
| # - commit id (develpment builds) | ||
| IMAGE_TAG: ${{ github.event_name == 'push' && github.ref_name || inputs.sha }} | ||
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| # boolean: force rebuilding the docker images from scratch | ||
| NO_CACHE: ${{ inputs.no_cache && '1' || '' }} | ||
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| on: | ||
| workflow_dispatch: | ||
| push: | ||
| tags: | ||
| - '*' | ||
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| workflow_call: | ||
| inputs: | ||
| sha: | ||
| description: 'git commit to be built' | ||
| type: string | ||
| required: true | ||
| no_cache: | ||
| description: 'force rebuilding the docker images from scratch' | ||
| type: boolean | ||
| default: false | ||
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| jobs: | ||
| push_to_registry: | ||
| name: Push Docker images to Container registry | ||
| build_images: | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| packages: write | ||
| contents: read | ||
| steps: | ||
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| - name: Set up JDK 17 | ||
| uses: actions/setup-java@v1 | ||
| - name: Check out the repo | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| java-version: 17 | ||
| repository: ${{ env.PRODUCTION && github.repository || 'fli-iam/shanoir-ng' }} | ||
| ref: ${{ env.IMAGE_TAG }} | ||
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| - name: Check out the repo | ||
| uses: actions/checkout@v3 | ||
| - name: Set up JDK 21 | ||
| uses: actions/setup-java@v4 | ||
| with: | ||
| distribution: temurin | ||
| java-version: 21 | ||
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| # maven cache only enabled on development builds | ||
| - name: Set up Maven cache | ||
| uses: actions/cache@v4 | ||
| if: "${{ ! env.production }}" | ||
| with: | ||
| path: ~/.m2/repository | ||
| key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }} | ||
| restore-keys: ${{ runner.os }}-maven- | ||
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| - name: Set up Docker Buildx | ||
| uses: docker/[email protected] | ||
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| - name: Create directory /shanoir-ng-logs | ||
| run: sudo mkdir -m777 /var/log/shanoir-ng-logs | ||
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| - name: Maven build | ||
| run: mvn -f ./shanoir-ng-parent/pom.xml install -DskipTests | ||
| env: | ||
| SHANOIR_URL_HOST: localhost | ||
| SHANOIR_URL_SCHEME: http | ||
| SHANOIR_PREFIX: github | ||
| SHANOIR_ADMIN_EMAIL: [email protected] | ||
| SHANOIR_KEYCLOAK_USER: admin | ||
| SHANOIR_KEYCLOAK_PASSWORD: '&a1A&a1A' | ||
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| - name: Login to GitHub Container Registry | ||
| uses: docker/login-action@v2 | ||
| uses: docker/login-action@v3.0.0 | ||
| with: | ||
| registry: ${{ env.REGISTRY }} | ||
| registry: ${{ env.DOCKER_REPOSITORY }} | ||
| username: ${{ github.actor }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
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| - name: Set up Docker Buildx | ||
| uses: docker/setup-buildx-action@v1 | ||
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| - name: USERS - Build & push Docker image | ||
| uses: docker/build-push-action@v2 | ||
| with: | ||
| context: ./docker-compose/users | ||
| builder: ${{ steps.buildx.outputs.name }} | ||
| push: true | ||
| tags: ${{ env.IMAGE_NAME }}/users:latest, ${{ env.IMAGE_NAME }}/users:${{ env.TAG }} | ||
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| - name: STUDIES - Build & push Docker image | ||
| uses: docker/build-push-action@v2 | ||
| with: | ||
| context: ./docker-compose/studies | ||
| builder: ${{ steps.buildx.outputs.name }} | ||
| push: true | ||
| tags: ${{ env.IMAGE_NAME }}/studies:latest, ${{ env.IMAGE_NAME }}/studies:${{ env.TAG }} | ||
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| - name: IMPORT - Build & push Docker image | ||
| uses: docker/build-push-action@v2 | ||
| with: | ||
| context: ./docker-compose/import | ||
| builder: ${{ steps.buildx.outputs.name }} | ||
| push: true | ||
| tags: ${{ env.IMAGE_NAME }}/import:latest, ${{ env.IMAGE_NAME }}/import:${{ env.TAG }} | ||
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| - name: DATASETS - Build & push Docker image | ||
| uses: docker/build-push-action@v2 | ||
| with: | ||
| context: ./docker-compose/datasets | ||
| builder: ${{ steps.buildx.outputs.name }} | ||
| push: true | ||
| tags: ${{ env.IMAGE_NAME }}/datasets:latest, ${{ env.IMAGE_NAME }}/datasets:${{ env.TAG }} | ||
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| - name: PRECLINICAL - Build & push Docker image | ||
| uses: docker/build-push-action@v2 | ||
| with: | ||
| context: ./docker-compose/preclinical | ||
| builder: ${{ steps.buildx.outputs.name }} | ||
| push: true | ||
| tags: ${{ env.IMAGE_NAME }}/preclinical:latest, ${{ env.IMAGE_NAME }}/preclinical:${{ env.TAG }} | ||
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| - name: NGINX - Build & push Docker image | ||
| uses: docker/build-push-action@v2 | ||
| - name: Generate the docker bake config | ||
| shell: python | ||
| run: | | ||
| import json, os, pathlib, requests, subprocess | ||
| env = os.environ | ||
| # query the sha of the head of the main branch | ||
| MAIN_REPO, MAIN_BRANCH = "fli-iam/shanoir-ng", "develop" | ||
| main_branch_sha = requests.get( | ||
| f"${{ github.api_url }}/repos/{MAIN_REPO}/branches/{MAIN_BRANCH}", | ||
| headers={"Authorization": "Bearer ${{ github.token }}"}, | ||
| ).json().get("commit", {}).get("sha") | ||
| # cache configuration | ||
| # | ||
| # We do not use 'type=gha' because the github actions cache is not | ||
| # able to reliably reuse an existing cache for all images in every | ||
| # build, thus rendering the cache ineffective (this is probably | ||
| # caused by the size limits). | ||
| # | ||
| # Instead we explicitely store the cache in container repository of | ||
| # the project ('type=registry'), under the tag 'cache' | ||
| # - we pull the cache (cache_from) before development builds of any | ||
| # branch when inputs.no_cache is false | ||
| # - we push the cache (cache_to) after development builds of the | ||
| # main branch only | ||
| # - we never use the cache on production builds | ||
| # | ||
| # The image is exported in the OCI format ('image-manifest=true') | ||
| # to avoid a "failed to solve: not found" error when pushing to the | ||
| # github container registry. | ||
| enable_cache_from = not env['PRODUCTION'] and not env['NO_CACHE'] | ||
| enable_cache_to = not env['PRODUCTION'] and ( | ||
| main_branch_sha == env['IMAGE_TAG'] == env['SHA']) | ||
| print(f"{enable_cache_from = }\n{enable_cache_to = }\n") | ||
| def cache_arg(enabled: bool, image: str, extra=""): | ||
| return [f"type=registry,image-manifest=true,ref={env['DOCKER_REPOSITORY']}/{image}:cache{extra}" | ||
| ] if enabled else [] | ||
| # extract the list of images to be built from the docker-compose config | ||
| images = json.loads(subprocess.check_output( | ||
| ["docker", "buildx", "bake", "--print", "-f", "docker-compose-dev.yml"]) | ||
| )["group"]["default"]["targets"] | ||
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| # override the bake config (add cache config + set tags & labels) | ||
| pathlib.Path("docker-bake.json").write_text(json.dumps({ | ||
| #"group": { "default": { "targets": ["database"] }}, # TODO: remove | ||
| "target": { | ||
| image: { | ||
| "cache-from": cache_arg(enable_cache_from, image), | ||
| "cache-to": cache_arg(enable_cache_to, image, ",mode=max"), | ||
| "tags": [f"{env['DOCKER_REPOSITORY']}/{image}:{env['IMAGE_TAG']}"], | ||
| "labels": { | ||
| "org.opencontainers.image.url": env['GIT_REPO_URL'], | ||
| "org.opencontainers.image.source": env['GIT_REPO_URL'], | ||
| "org.opencontainers.image.version": env['IMAGE_TAG'], | ||
| "org.opencontainers.image.revision": env['SHA'], | ||
| }, | ||
| } for image in images }})) | ||
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| - name: Maven build | ||
| run: mvn -f ./shanoir-ng-parent/pom.xml install -DskipTests | ||
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| - name: Build docker images | ||
| uses: docker/bake-action@v5 | ||
| with: | ||
| context: ./docker-compose/nginx | ||
| builder: ${{ steps.buildx.outputs.name }} | ||
| files: | | ||
| docker-compose-dev.yml | ||
| docker-bake.json | ||
| push: true | ||
| tags: ${{ env.IMAGE_NAME }}/nginx:latest, ${{ env.IMAGE_NAME }}/nginx:${{ env.TAG }} | ||
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| Original file line number | Diff line number | Diff line change |
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| In alphabetic order: | ||
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| Alexandre Abadie, Anthony Baire, Elise Bannier, Emmanuel Barbier, Christian Barillot, Marjolaine Bodin, Olivier Commowick, Isabelle Corouge, Yao Chi, Pierre-Henri Dauvergne, Jean-Côme Douteau, Michel Dojat, Quentin Duché, Alae Es-Saki, Inès Fakhfakh, Adrien Férial, Bernard Gibaud, Justine Guillaumont, Malo Gaubert, Wefa Hakem, Guewen Hubert, Michael Kain, Khalil Kessa, Romain Lahaxe, Julien Lamy, Julien Louis, Simon Loury, Camille Maumet, Arthur Masson, Youenn Merel, Olivier Montignon, Aneta Morawin, Farid Ouhmich, Alexandre Pron, Guillaume Renard, Mathieu Simon, Arnaud Touboulic, Laurent Vallet, Nicolas Wiest Daessle. | ||
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| Inclusion of authors of research articles dealing with Shanoir [[1], [2]](https://www.zotero.org/google-docs/?Uc9jGd), [Inria BIL ](https://team.inria.fr/bilv2/fr/software/) (shanoir, shanoir-ng, qtshanoir, shanoirtk, shanoir-uploader, shanoir-uploader-ofsep) as well as all contributors to the Github code repositories shanoir-ng, shanoir-downloader, shanoir-deploy on January 7 th 2025, sorted by surname in alphabetical order. | ||
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| [1] C. Barillot et al., “Shanoir: Applying the Software as a Service Distribution Model to Manage Brain Imaging Research Repositories,” Front. ICT, vol. 3, Dec. 2016, doi: 10.3389/fict.2016.00025. | ||
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| [2] M. Kain et al., “Small Animal Shanoir (SAS) A Cloud-Based Solution for Managing Preclinical MR Brain Imaging Studies,” Front. Neuroinformatics, vol. 14, p. 20, May 2020, doi: 10.3389/fninf.2020.00020. | ||
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| Contributions detailed following [https://allcontributors.org/docs/en/emoji-key](https://allcontributors.org/docs/en/emoji-key) | ||
| All possible contributions ordered: | ||
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| 🔊 ♿️ 🐛 📝 💼 💻 🖋 🔣 📖 🎨 💡 📋 💵 🔍 🤔 🚇 🚧 🧑🏫 📦 🔌 📆 📣 💬 🔬 👀 🛡️ 🔧 🌍 ⚠️ ✅ 📢 📓 📹 | ||
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| |Contributor | Contribution(s) | | ||
| |----------------------|----------------------------------------------------------------------------------------------------- | | ||
| |Alexandre Abadie | | | ||
| |Anthony Baire | ♿️ 🐛 💻 📖 🤔 🚇 🚧 🧑🏫 📦 🔌 💬 👀 🛡️ 🔧 ⚠️ ✅ | | ||
| |Elise Bannier | ♿️ 🐛 🖋 🔣 📖 💵 🔍 🤔 📆 📣 🔧 ✅ 📓 | | ||
| |Emmanuel Barbier | | | ||
| |Christian Barillot | | | ||
| |Marjolaine Bodin | | | ||
| |Olivier Commowick | | | ||
| |Isabelle Corouge | | | ||
| |Yao Chi | | | ||
| |Pierre-Henri Dauvergne| ♿️ 🐛 💻 📖 📋 🚧 🧑🏫 🔌 💬 👀 ⚠️ ✅ 📓 | | ||
| |Jean Côme Douteau | ♿️ 🐛 📝 💻 🖋 📖 📋 🤔 🚇 🚧 🧑🏫 📦 🔌 📣 💬 👀 🛡️ 🔧 ⚠️ ✅ 📢 📓 | | ||
| |Michel Dojat | | | ||
| |Quentin Duché | 🐛 💻 📖 💡 🤔 🧑🏫 👀 🔧 📢 📓 | | ||
| |Alae Es-Saki | | | ||
| |Inès Fakhfakh | | | ||
| |Adrien Férial | | | ||
| |Bernard Gibaud | | | ||
| |Justine Guillaumont | | | ||
| |Malo Gaubert | 🐛 💻 📖 💡 🤔 🧑🏫 👀 🔧 📢 📓 | | ||
| |Wefa Hakem | | | ||
| |Guewen Hubert | ♿️ 🐛 💻 📖 📋 🚧 🧑🏫 🔌 💬 👀 ⚠️ ✅ 📓 | | ||
| |Michael Kain | ♿️ 🐛 📝 💻 🖋 🔣 📖 🎨 💡 📋 🔍 🤔 🚇 🚧 🧑🏫 📦 🔌 📆 📣 💬 🔬 👀 🛡️ 🔧 ⚠️ ✅ 📢 📓 | | ||
| |Khalil Kessa | | | ||
| |Romain Lahaxe | | | ||
| |Julien Lamy | | | ||
| |Julien Louis | ♿️ 🐛 💻 🖋 📖 🎨 💡 📋 🤔 🚇 🚧 🧑🏫 📦 💬 👀 🛡️ 🔧 ⚠️ ✅ 📢 📓 | | ||
| |Simon Loury | | | ||
| |Camille Maumet | ♿️ 🐛 🖋 🔣 📖 📋 🤔 🔌 📆 📣 💬 👀 🛡️ 🔧 📢 📓 | | ||
| |Arthur Masson | | | ||
| |Youenn Merel | ♿️ 🐛 💻 🖋 📖 💡 📋 🤔 🚇 🚧 🧑🏫 📦 🔌 💬 👀 🛡️ 🔧 ⚠️ ✅ 📢 📓 📹 | | ||
| |Olivier Montignon | | | ||
| |Aneta Morawin | | | ||
| |Farid Ouhmich | | | ||
| |Alexandre Pron | ♿️ 🐛 💻 📖 🔌 ⚠️ ✅ 📓 | | ||
| |Guillaume Renard | | | ||
| |Mathieu Simon | | | ||
| |Arnaud Touboulic | | | ||
| |Laurent Vallet | ♿️ 🐛 💻 🖋 📖 💡 📋 🤔 🚧 🧑🏫 📦 🔌 💬 👀 🔧 ⚠️ 📓| | ||
| |Nicolas Wiest Daessle | | | ||
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| # Fundings | ||
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| This page lists the funding that has contributed to the development of Shanoir and its software ecosystem. | ||
| | Funding | | ||
| |: ----------------------------------------------------:| | ||
| | _Technological development program_ of Inria | | ||
| | Brittany region council | | ||
| | _Investments for the Future program_: ANR-11-INBS-006 | |
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