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perf: containerize the app and enabe gh actions to publish image
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,70 @@ | ||
| # Workflow derived from https://github.com/r-lib/actions/tree/master/examples | ||
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | ||
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| name: Create Github release and generate Docker image | ||
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| on: | ||
| push: | ||
| branches: | ||
| - 'master' | ||
| tags: | ||
| - 'v*' | ||
| env: | ||
| REGISTRY: ghcr.io | ||
| IMAGE_PATH: ghcr.io/${{ github.repository }} | ||
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| jobs: | ||
| tagging: | ||
| runs-on: ubuntu-latest | ||
| outputs: | ||
| tag: ${{steps.tag_version.outputs.new_tag}} | ||
| steps: | ||
| - uses: actions/checkout@v3 | ||
| with: | ||
| fetch-depth: '0' | ||
| - name: Bump version and push tag | ||
| id: tag_version | ||
| uses: mathieudutour/[email protected] | ||
| with: | ||
| github_token: ${{ secrets.GITHUB_TOKEN }} | ||
| custom_release_rules: fix:patch:Bug Fixes,chore:patch:Chores,feat:minor:Features,perf:Major:Performance | ||
| - name: Create a GitHub release | ||
| uses: ncipollo/release-action@v1 | ||
| with: | ||
| tag: ${{ steps.tag_version.outputs.new_tag }} | ||
| name: Release ${{ steps.tag_version.outputs.new_tag }} | ||
| body: ${{ steps.tag_version.outputs.changelog }} | ||
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| build-and-push-image: | ||
| needs: tagging | ||
| runs-on: ubuntu-latest | ||
| permissions: | ||
| contents: read | ||
| packages: write | ||
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| steps: | ||
| - name: Checkout repository | ||
| uses: actions/checkout@v3 | ||
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| - name: Log in to the Container registry | ||
| uses: docker/[email protected] | ||
| if: github.event_name == 'push' | ||
| with: | ||
| registry: ${{ env.REGISTRY }} | ||
| username: ${{ github.actor }} | ||
| password: ${{ secrets.GITHUB_TOKEN }} | ||
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| - name: Extract metadata (tags, labels) for Docker | ||
| id: meta | ||
| uses: docker/[email protected] | ||
| with: | ||
| images: ${{ env.IMAGE_PATH }} | ||
| tags: ${{ needs.tagging.outputs.tag}} | ||
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| - name: Build and push Docker image | ||
| uses: docker/[email protected] | ||
| with: | ||
| context: . | ||
| push: true | ||
| tags: ${{ steps.meta.outputs.tags}} | ||
| labels: ${{ steps.meta.outputs.labels }} |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,19 @@ | ||
| FROM sagebionetworks/shiny-base:release-1.0 | ||
| # This is the expected application installation folder | ||
| WORKDIR /srv/shiny-server/app | ||
| COPY --chown=shiny ./ ./ | ||
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| # Set up Python and install the Synapse Python client | ||
| RUN Rscript -e "install.packages('reticulate', repos='http://cran.rstudio.com/', verbose=FALSE)" | ||
| RUN Rscript -e "library(reticulate); install_miniconda(); py_discover_config(); py_install(c('synapseclient', 'pandas'), pip = TRUE, pip_ignore_installed=TRUE)" | ||
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| # By default the log level is TRACE. We bump up one level to DEBUG to make the logs a bit less verbose | ||
| ENV SHINY_LOG_LEVEL=DEBUG | ||
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| # set up r packages via renv. Use binary lib matching the shiny-base ubuntu version | ||
| # to speed up installatioon. | ||
| RUN Rscript -e 'renv::restore(repos="https://packagemanager.rstudio.com/all/__linux__/jammy/latest"); renv::install("./")' | ||
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| # running that script, to pass a configuration env var to Shiny | ||
| RUN chmod +x dccvalidator_PEC_startup.sh | ||
| CMD ["./dccvalidator_PEC_startup.sh"] |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,11 @@ | ||
| #!/usr/bin/bash | ||
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| # Pass environment variable to Shiny | ||
| echo "" >> .Renviron | ||
| echo APP_REDIRECT_URL=$APP_REDIRECT_URL >> .Renviron | ||
| echo R_CONFIG_ACTIVE=$R_CONFIG_ACTIVE >> .Renviron | ||
| echo client_id=$client_id >> .Renviron | ||
| echo client_name=$client_name >> .Renviron | ||
| echo client_secret=$client_secret >> .Renviron | ||
| # Now run the base start-up script | ||
| ./startup.sh |
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@@ -151,7 +151,6 @@ amp-ad: | |
| contact_email: "[email protected]" | ||
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| pec: | ||
| app_url: "https://shinypro.synapse.org/users/danlu/dccvalidator/" | ||
| parent: "syn21763123" | ||
| path_to_markdown: "inst/using-the-dccvalidator-pec.Rmd" | ||
| study_table: "syn20968992" | ||
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