ECDC_update_PR_fork #17
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| name: ECDC_update_PR_fork | |
| # This example workflow is meant to depict steps needed to get the model-output data | |
| # from your_organization data GitHub repository and open a pull request to upload data | |
| # to european-modelling-hubs/RespiCast-SyndromicIndicators hub-repository | |
| # A good starting point for a better understandig of how GitHub actions work | |
| # is this: https://docs.github.com/en/actions/quickstart | |
| # N.B. | |
| # 1. This workflow should be placed under the .github/workflows folder of your FORKED REPO !! | |
| # 2. Since the current workflow pulls data directly from the upstream hub (european-modelling-hubs/RespiCast-SyndromicIndicators), | |
| # you do not need to sync the forked repo! | |
| ## TODO: secrets & tokens! | |
| # Firts step is to define di events that can trigger this workflow | |
| on: | |
| workflow_run: | |
| workflows: [Generate_RespiCast_Forecasts] | |
| types: | |
| - completed | |
| # Or you can manually trigger the workflow | |
| workflow_dispatch: | |
| jobs: | |
| create_PR_job: | |
| runs-on: ubuntu-latest | |
| steps: | |
| # Step 1: Checkout your forked repository - main branch - | |
| # --------------------------------------------------- | |
| - name: checkout forked repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: 'main' | |
| token: ${{secrets.Secret_PUSH_ACCESS_RespiCast}} | |
| #this might raise a problem | |
| repository: 'ECDC-modelling-team/RespiCast-SyndromicIndicators' | |
| path: './destination-repo/' | |
| # Step 2: Checkout the model data repository - main branch - | |
| # This is the repository where the model output data reside | |
| # In this example data repo is https://github.com/your_organization/modeloutput-data-repo | |
| # ----------------------------------------------------------------------------- | |
| - name: checkout data repository | |
| uses: actions/checkout@v3 | |
| with: | |
| ref: 'main' # the git branch to work on | |
| token: ${{ secrets.Secret_PUSH_ACCESS_RespiCast}} #this token will need to be the math modelling one (might need to create a new one) | |
| repository: 'EU-ECDC/ECDC-Mathematical-Models' | |
| path: './source-repo/' # Relative path under $GITHUB_WORKSPACE to place the repository | |
| # Step 3?: Set the default remote repository to use when querying the GitHub API for the locally cloned repository. | |
| - run: | | |
| cd ./destination-repo/ | |
| gh repo set-default european-modelling-hubs/RespiCast-SyndromicIndicators | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.Secret_PUSH_ACCESS_RespiCast}} #this is probably the correct one (but will need to save the secrets locally) | |
| # Step 4: Pull directly from main branch of the upstream repository, | |
| # so you do not have to sync and the workflow is not part of the PR | |
| - run: | | |
| cd ./destination-repo/ | |
| git config --global user.name "ECDC-modelling-team" #update | |
| git config --global user.email "[email protected]" #update | |
| git remote add upstream https://github.com/european-modelling-hubs/RespiCast-SyndromicIndicators.git | |
| git fetch --all | |
| git checkout -b pr-new-branch upstream/main | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.Secret_PUSH_ACCESS_RespiCast }} #same as for step3 | |
| # Step 5: Calculate Wednesday's date of the current week | |
| - name: Calculate Wednesday's date | |
| id: calculate_wednesday | |
| run: | | |
| # Get the current day of the week (1=Monday, ..., 7=Sunday) | |
| weekday=$(date +%u) | |
| # Calculate how many days to add or subtract to get to Wednesday (3) | |
| offset=$((3 - weekday)) | |
| # Calculate the date of the Wednesday (if offset is negative, subtract days) | |
| wednesday_date=$(date -d "$offset days" +%Y-%m-%d) | |
| echo "Wednesday's date is $wednesday_date" | |
| # Set the output | |
| echo "::set-output name=wednesday_date::$wednesday_date" | |
| # Step 6: make a copy of the needed files from data repository | |
| - name: Copy model-output file | |
| run: | | |
| wednesday_date=${{ steps.calculate_wednesday.outputs.wednesday_date }} | |
| cp ./source-repo/Forecasting-hubs_models/model_output/Syndromic_indicators/${wednesday_date}-ECDC-soca_simplex.csv \ | |
| ./destination-repo/model-output/ECDC-soca_simplex/ | |
| cp ./source-repo/Forecasting-hubs_models/model_output/Syndromic_indicators/${wednesday_date}-ECDC-SARIMA.csv \ | |
| ./destination-repo/model-output/ECDC-SARIMA/ | |
| #cp ./data-repo/archive/yyyy-mm-dd-TeamName-ModelName.csv ./model-output/ECDC | |
| # Step 7?: commit changes to the new brach! This step is needed in order | |
| # to succesfully open the subsequent pull request | |
| - run: | | |
| cd ./destination-repo/ | |
| wednesday_date=${{ steps.calculate_wednesday.outputs.wednesday_date }} | |
| git add ./model-output/ECDC-soca_simplex/${wednesday_date}-ECDC-soca_simplex.csv | |
| git add ./model-output/ECDC-SARIMA/${wednesday_date}-ECDC-SARIMA.csv | |
| git commit -m "AutoSubmitPR" | |
| git push -u origin pr-new-branch | |
| # Step 8: Finally, open the pull request from local pr-new-branch to the main branch | |
| # secrets.MY_PAT_SECRET is a repository secret you have to create in your forked repository | |
| # containing a valid PERSONAL ACCESS TOKEN for YourGitHubUserName. | |
| # Without this secret the pr create fails with "Resource not accessible by integration" error | |
| - name: Open the pull requests | |
| run: | | |
| cd ./destination-repo/ | |
| gh pr create --head ECDC-modelling-team:pr-new-branch --base main --title 'PR Title' --body 'PR Body' | |
| env: | |
| GH_TOKEN: ${{ secrets.MY_PAT_SECRET }} #Probably largely the same token (?) - one for respicast, one for modelling repo. |