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| Original file line number | Diff line number | Diff line change |
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| # Workflow to deploy NCBO Cron to stage/prod systems | ||
| # | ||
| # Required github secrets: | ||
| # | ||
| # CONFIG_REPO - github repo containing config and customizations for NCBO_CRON. 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 API hosts 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 API nodes live on private network. | ||
| # SSH_JUMPHOST_USER - username to use to connect to the ssh jump/proxy. | ||
| # | ||
| # DEPLOY_ENC_KEY - key for decrypting deploymnet ssh key residing in config/ | ||
| # this SSH key is used for accessing jump host, API nodes, and private github repo. | ||
|
|
||
| name: Capistrano Deployment | ||
| # Controls when the action will run. | ||
| on: | ||
| push: | ||
| branches: | ||
| - stage | ||
| - development | ||
| # Allows running this workflow manually from the Actions tab | ||
| workflow_dispatch: | ||
| inputs: | ||
| BRANCH: | ||
| description: "Branch/tag to deploy" | ||
| type: choice | ||
| options: | ||
| - stage | ||
| - development | ||
| - master | ||
| default: stage | ||
| required: true | ||
| environment: | ||
| description: "target environment to deploy to" | ||
| type: choice | ||
| options: | ||
| - staging | ||
| - test | ||
| - agroportal | ||
| default: stage | ||
| jobs: | ||
| deploy: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| BUNDLE_WITHOUT: default #install gems required primarely for deployment in order to speed up workflow | ||
| PRIVATE_CONFIG_REPO: ${{ format('[email protected]:{0}.git', secrets.CONFIG_REPO) }} | ||
| # Steps represent a sequence of tasks that will be executed as part of the job | ||
| steps: | ||
| - name: set branch/tag and environment to deploy from inputs | ||
| run: | | ||
| # workflow_dispatch default input doesn't get set on push so we need to set defaults | ||
| # via shell parameter expansion | ||
| USER_INPUT_BRANCH="${{ inputs.branch || github.head_ref || 'master' }}" | ||
| echo "BRANCH=${USER_INPUT_BRANCH}" >> $GITHUB_ENV | ||
| USER_INPUT_ENVIRONMENT=${{ inputs.environment }} | ||
| echo "TARGET=${USER_INPUT_ENVIRONMENT:-test}" >> $GITHUB_ENV | ||
| CONFIG_REPO=${{ secrets.CONFIG_REPO }} | ||
| GH_PAT=${{ secrets.GH_PAT }} | ||
| echo "PRIVATE_CONFIG_REPO=https://${GH_PAT}@github.com/${CONFIG_REPO}" >> $GITHUB_ENV | ||
| echo "SSH_JUMPHOST=${{ secrets.SSH_JUMPHOST }}" >> $GITHUB_ENV | ||
| echo "SSH_JUMPHOST_USER=${{ secrets.SSH_JUMPHOST_USER }}" >> $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: 2.7.8 # 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: ${{ secrets.GH_PAT }} # `GH_PAT` is a secret that contains your PAT | ||
| path: deploy_config | ||
| - name: copy-deployment-config | ||
| run: cp -r deploy_config/ncbo_cron/${{ inputs.environment }}/* . | ||
| # add ssh hostkey so that capistrano doesn't complain | ||
| - name: Add jumphost's hostkey to Known Hosts | ||
| run: | | ||
| mkdir -p ~/.ssh | ||
| echo "${{ secrets.SSH_JUMPHOST }}" | ||
| 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: ${{ secrets.DEPLOY_ENC_KEY }} # Name of the variable configured in Settings/Secrets of your github project |
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| #!/usr/bin/env ruby | ||
|
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| require 'fileutils' | ||
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| # Usage: ruby migrate_and_extract.rb <source_folder> <target_folder> | ||
| # Check if the correct number of arguments are provided | ||
| if ARGV.size != 2 | ||
| puts "Usage: #{$PROGRAM_NAME} <source_folder> <target_folder>" | ||
| exit 1 | ||
| end | ||
|
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| source_folder = ARGV[0] | ||
| target_folder = ARGV[1] | ||
| processed_dir = File.join(target_folder, 'processed_files') | ||
|
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| # Create the target directory if it doesn't exist | ||
| FileUtils.mkdir_p(processed_dir) | ||
|
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| # Find all files in the source folder and process them | ||
| Dir.glob(File.join(source_folder, '**', '*')).select { |file| File.file?(file) }.each do |file| | ||
| puts "Processing file: #{file}" | ||
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| # Define the new filename with .n3 extension | ||
| filename = File.basename(file) | ||
| new_file = File.join(processed_dir, "#{filename}.n3") | ||
|
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| # Copy the original file to the target folder with .n3 extension | ||
| FileUtils.cp(file, new_file) | ||
| puts "Copied to: #{new_file}" | ||
|
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| # Extract the first line and remove the "## GRAPH " prefix, then save it to .graph file | ||
| graph_file = "#{new_file}.graph" | ||
| first_line = File.open(file, &:readline).sub(/^## GRAPH /, '').strip | ||
| File.write(graph_file, first_line) | ||
| puts "Extracted graph URI to: #{graph_file}" | ||
|
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| # Remove the first line from the copied .n3 file | ||
| File.write(new_file, File.readlines(new_file).drop(1).join) | ||
| puts "Removed the first line from: #{new_file}" | ||
| end | ||
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| puts "Migration and extraction complete." |
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