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| # Git | ||
| .git | ||
| .gitignore | ||
| .github | ||
| create_permissions.log | ||
| # Logs | ||
| log/* | ||
| # Temp files | ||
| tmp/* | ||
| # Editor temp files | ||
| *.swp | ||
| *.swo | ||
| coverage | ||
| # Ignore generated test data | ||
| test/data/uploaded_ontologies/**/* | ||
| test/data/ontology_files/repo/**/* | ||
| test/log |
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| # Workflow for deploying ontologies_api to stage/prod systems via capistrano. | ||
| # This workflow runs after a successeful execution of the unit test workflow and it | ||
| # can also be triggered manually. | ||
| # | ||
| # Required github secrets: | ||
| # | ||
| # CONFIG_REPO - github repo containing config and customizations for the API. Format 'author/private_config_repo' | ||
| # it is used for getting capistrano deployment configuration for stages on the github actions runner and | ||
| # PRIVATE_CONFIG_REPO env var is constructed from it which is used by capistrano on the remote servers for pulling configs. | ||
| # | ||
| # GH_PAT - github Personal Access Token for accessing PRIVATE_CONFIG_REPO | ||
| # | ||
| # SSH_JUMPHOST - ssh jump/proxy host though which deployments have to though if app servers are hosted on private network. | ||
| # | ||
| # DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/deploy_id_rsa_enc (see miloserdow/capistrano-deploy) | ||
| # this SSH key is used for accessing jump host, UI nodes, and private github repo. | ||
|
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||
| name: Capistrano Deployment | ||
| # Controls when the action will run. | ||
| on: | ||
| # Trigger deployment to staging after unit test action completes | ||
| workflow_run: | ||
| workflows: ["Ruby Unit Tests"] | ||
| types: | ||
| - completed | ||
| branches: [master, develop] | ||
| # Allows running this workflow manually from the Actions tab | ||
| workflow_dispatch: | ||
| branches: [master, develop] | ||
| inputs: | ||
| BRANCH: | ||
| description: 'Branch/tag to deploy' | ||
| default: develop | ||
| required: true | ||
| environment: | ||
| description: 'target environment to deploy to' | ||
| type: choice | ||
| options: | ||
| - staging | ||
| - production | ||
| default: staging | ||
|
|
||
| jobs: | ||
| deploy: | ||
| runs-on: ubuntu-latest | ||
| # run deployment only if "Ruby Unit Tests" workflow completes sucessefully or when manually triggered | ||
| if: ${{ (github.event.workflow_run.conclusion == 'success') || (github.event_name == 'workflow_dispatch') }} | ||
| env: | ||
| BUNDLE_WITHOUT: default #install gems required primarily for the deployment in order to speed this workflow | ||
| PRIVATE_CONFIG_REPO: ${{ format('[email protected]:{0}.git', secrets.CONFIG_REPO) }} | ||
| # Steps represent a sequence of tasks that will be executed as part of the job | ||
| steps: | ||
| - name: set branch/tag and environment to deploy from inputs | ||
| run: | | ||
| # workflow_dispatch default input doesn't get set on push so we need to set defaults | ||
| # via shell parameter expansion | ||
| # https://dev.to/mrmike/github-action-handling-input-default-value-5f2g | ||
| USER_INPUT_BRANCH=${{ inputs.branch }} | ||
| echo "BRANCH=${USER_INPUT_BRANCH:-develop}" >> $GITHUB_ENV | ||
| USER_INPUT_ENVIRONMENT=${{ inputs.environment }} | ||
| echo "TARGET=${USER_INPUT_ENVIRONMENT:-staging}" >> $GITHUB_ENV | ||
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | ||
| - uses: actions/checkout@v3 | ||
| - uses: ruby/setup-ruby@v1 | ||
| with: | ||
| ruby-version: 2.7.6 # Not needed with a .ruby-version file | ||
| bundler-cache: true # runs 'bundle install' and caches installed gems automatically | ||
| - name: get-deployment-config | ||
| uses: actions/checkout@v3 | ||
| with: | ||
| repository: ${{ secrets.CONFIG_REPO }} # repository containing deployment settings | ||
| token: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT | ||
| path: deploy_config | ||
| - name: copy-deployment-config | ||
| run: cp -r deploy_config/ontologies_api/* . | ||
| # add ssh hostkey so that capistrano doesn't complain | ||
| - name: Add jumphost's hostkey to Known Hosts | ||
| run: | | ||
| mkdir -p ~/.ssh | ||
| ssh-keyscan -H ${{ secrets.SSH_JUMPHOST }} > ~/.ssh/known_hosts | ||
| shell: bash | ||
| - uses: miloserdow/capistrano-deploy@master | ||
| with: | ||
| target: ${{ env.TARGET }} # which environment to deploy | ||
| deploy_key: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project |
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| name: Docker Image CI | ||
|
|
||
| on: | ||
| release: | ||
| types: [published] | ||
|
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||
| jobs: | ||
| push_to_registry: | ||
| name: Push Docker image to Docker Hub | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - name: Check out the repo | ||
| uses: actions/checkout@v3 | ||
|
|
||
| - name: Set up QEMU | ||
| uses: docker/setup-qemu-action@v2 | ||
|
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||
| - name: Set up Docker Buildx | ||
| uses: docker/setup-buildx-action@v2 | ||
|
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||
| - name: Log in to Docker Hub | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| username: ${{ secrets.DOCKERHUB_USERNAME }} | ||
| password: ${{ secrets.DOCKERHUB_TOKEN }} | ||
|
|
||
| - name: Extract metadata (tags, labels) for Docker | ||
| id: meta | ||
| uses: docker/metadata-action@v4 | ||
| with: | ||
| images: bioportal/ontologies_api | ||
|
|
||
| - name: Build and push Docker image | ||
| uses: docker/build-push-action@v4 | ||
| with: | ||
| context: . | ||
| platforms: linux/amd64,linux/arm64 | ||
| build-args: | | ||
| RUBY_VERSION=2.7 | ||
| push: true | ||
| tags: ${{ steps.meta.outputs.tags }} | ||
| labels: ${{ steps.meta.outputs.labels }} |
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| FROM ruby:2.6 | ||
| ARG RUBY_VERSION | ||
| ARG DISTRO_NAME=bullseye | ||
|
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||
| RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends openjdk-11-jre-headless raptor2-utils wait-for-it | ||
| FROM ruby:$RUBY_VERSION-$DISTRO_NAME | ||
|
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||
| RUN apt-get update -yqq && apt-get install -yqq --no-install-recommends \ | ||
| openjdk-11-jre-headless \ | ||
| raptor2-utils \ | ||
| && rm -rf /var/lib/apt/lists/* | ||
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| # The Gemfile Caching Trick | ||
| # we install gems before copying the code in its own layer so that gems would not have to get | ||
| # installed every single time code is updated | ||
| RUN mkdir -p /srv/ontoportal/ontologies_api | ||
| RUN mkdir -p /srv/ontoportal/bundle | ||
| COPY Gemfile* /srv/ontoportal/ontologies_api/ | ||
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| WORKDIR /srv/ontoportal/ontologies_api | ||
| RUN gem install bundler -v "$(grep -A 1 "BUNDLED WITH" Gemfile.lock | tail -n 1)" | ||
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| RUN gem update --system | ||
| RUN gem install bundler | ||
| ENV BUNDLE_PATH=/srv/ontoportal/bundle | ||
| RUN bundle install | ||
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| COPY . /srv/ontoportal/ontologies_api | ||
| RUN cp /srv/ontoportal/ontologies_api/config/environments/config.rb.sample /srv/ontoportal/ontologies_api/config/environments/development.rb | ||
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| EXPOSE 9393 | ||
| CMD ["bundle","exec","rackup","-p","9393","--host","0.0.0.0"] | ||
| CMD ["bundle", "exec", "rackup", "-p", "9393", "--host", "0.0.0.0"] |
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