Fds 1301 cross manifest validation #710
Workflow file for this run
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| name: shiny-deploy | |
| on: | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| shiny-deploy: | |
| runs-on: ubuntu-latest | |
| container: rocker/rstudio:4.1.2 | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| DCA_SCHEMATIC_API_TYPE: rest | |
| DCA_API_HOST: "https://schematic-dev.api.sagebionetworks.org" | |
| steps: | |
| - name: Install System Dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev libpng-dev libxml2-dev | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }} | |
| name: Install python | |
| run: | | |
| sudo apt-get install -y pip python3.8-venv | |
| - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }} | |
| name: Set up virtual environment | |
| # When shinyapps.io supports python 3.9+ split this into two steps | |
| # to install schematic from pypi or github | |
| shell: bash | |
| run: | | |
| python3 -m venv .venv | |
| chmod 755 .venv/bin/activate | |
| source .venv/bin/activate | |
| - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }} | |
| name: Install schematicpy | |
| shell: bash | |
| run: | | |
| source .venv/bin/activate | |
| pip install schematicpy==23.1.1 | |
| # https://github.com/actions/setup-python/blob/main/docs/advanced-usage.md#caching-packages | |
| # For the future, look at poetry install | |
| # - uses: actions/checkout@v3 | |
| # - name: Install poetry | |
| # run: pipx install poetry | |
| # - uses: actions/setup-python@v4 | |
| # with: | |
| # python-version: '3.9' | |
| # cache: 'poetry' | |
| # - run: poetry install | |
| # - run: poetry run pytest | |
| # | |
| - name: Set Configurations for Schematic | |
| # write out configuration files using github secrets | |
| if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }} | |
| shell: bash | |
| run: | | |
| echo "${{ secrets.SCHEMATIC_SYNAPSE_CONFIG }}" > .synapseConfig | |
| - name: Save service account credentials for Schematic | |
| if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }} | |
| id: create-json | |
| uses: jsdaniell/[email protected] | |
| with: | |
| name: 'schematic_service_account_creds.json' | |
| json: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }} | |
| - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }} | |
| name: Set Configurations for Data Model | |
| shell: bash | |
| run: | | |
| source .venv/bin/activate | |
| # download the data models and create config.json | |
| python3 .github/config_schema.py \ | |
| -c schematic_config.yml \ | |
| --service_repo 'Sage-Bionetworks/schematic' \ | |
| --overwrite | |
| - if: ${{env.DCA_SCHEMATIC_API_TYPE == 'reticulate' }} | |
| name: zip virtual env | |
| shell: bash | |
| # ShinyApps has a limit of 7000 files, far exceeded by the many Python dependencies | |
| # that this app' has. As a workaround we zip the virtual environment and later | |
| # unzip it in 'global.R' | |
| run: | | |
| zip -rm .venv.zip .venv | |
| - uses: r-lib/actions/setup-renv@v2 | |
| - name: shinyapps.io R pkg hack | |
| # Delete files that makes shinyapps.io treat this like a golem app | |
| shell: bash | |
| run: | | |
| cp R/* functions/ | |
| rm -r R/ DESCRIPTION NAMESPACE | |
| - name: Write R environmental variables | |
| shell: bash | |
| run: | | |
| echo 'DCA_CLIENT_ID="${{ secrets.OAUTH_CLIENT_ID }}"' >> .Renviron | |
| echo 'DCA_CLIENT_SECRET="${{ secrets.OAUTH_CLIENT_SECRET }}"' >> .Renviron | |
| echo 'DCA_SCHEMATIC_API_TYPE="${{ env.DCA_SCHEMATIC_API_TYPE }}"' >> .Renviron | |
| echo 'DCA_API_HOST="${{ env.DCA_API_HOST }}"' >> .Renviron | |
| echo 'DCA_SYNAPSE_PROJECT_API=TRUE' >> .Renviron | |
| echo 'DCA_DCC_CONFIG="https://raw.githubusercontent.com/Sage-Bionetworks/data_curator_config/shinyapps-io/dcc_config.csv"' >> .Renviron | |
| echo 'GITHUB_PAT="${{ secrets.GITHUB_TOKEN }}"' >> .Renviron | |
| - name: Authorize and deploy app | |
| shell: Rscript {0} | |
| run: | | |
| renv::restore() | |
| install.packages("rsconnect") | |
| repo <- Sys.getenv("GITHUB_REPOSITORY") | |
| appName <- strsplit(repo, "/")[[1]][2] | |
| refName <- Sys.getenv("GITHUB_REF_NAME") | |
| # if tag is v*.*.*, deploy to prod, if main to staging, otherwise to test | |
| if (grepl("v[0-9]+.[0-9]+.[0-9]+", refName)) { | |
| message("Deploying release version of app") | |
| } else if (refName %in% c("main")) { | |
| appName <- paste(appName, "staging", sep = "-") | |
| message("Deploying staging version of app") | |
| } else { | |
| appName <- paste(appName, "testing1", sep = "-") | |
| message("Deploying testing version of app") | |
| } | |
| message(sprintf("Deploying to %s instance.", appName)) | |
| rsConnectUser <- "${{ secrets.RSCONNECT_USER }}" | |
| rsConnectToken <- "${{ secrets.RSCONNECT_TOKEN }}" | |
| rsConnectSecret <- "${{ secrets.RSCONNECT_SECRET }}" | |
| rsconnect::setAccountInfo(rsConnectUser, rsConnectToken, rsConnectSecret) | |
| # Set app URL for OAuth | |
| appUrl <- sprintf("https://%s.shinyapps.io/%s", rsConnectUser, appName) | |
| renviron <- readLines(".Renviron") | |
| renviron <- c(renviron, sprintf("DCA_APP_URL=%s", appUrl)) | |
| writeLines(renviron, ".Renviron") | |
| # Get app names. If app exists, configure then deploy. Otherwise | |
| # deploy then configure. | |
| apps <- rsconnect::applications()$name | |
| if (appName %in% apps) { | |
| rsconnect::configureApp(appName = appName, size = "xxxlarge", logLevel = "verbose") | |
| rsconnect::deployApp(appName = appName) | |
| } else { | |
| rsconnect::deployApp(appName = appName) | |
| rsconnect::configureApp(appName = appName, size = "xxxlarge", logLevel = "verbose") | |
| } |