R_check_all_of_HADES.yml

on: workflow_dispatch

name: R-check-all-of-HADES

jobs:
  R-check-all-of-HADES:
    runs-on: ${{ matrix.config.os }}

    name: ${{ matrix.config.os }} (${{ matrix.config.r }})

    strategy:
      fail-fast: false
      matrix:
        config:
          - {os: macOS-latest, r: 'release'}

    env:
      GITHUB_PAT: ${{ secrets.GH_TOKEN }}
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      RSPM: ${{ matrix.config.rspm }}
      CDM5_ORACLE_CDM_SCHEMA: ${{ secrets.CDM5_ORACLE_CDM_SCHEMA }}
      CDM5_ORACLE_OHDSI_SCHEMA: ${{ secrets.CDM5_ORACLE_OHDSI_SCHEMA }}
      CDM5_ORACLE_PASSWORD: ${{ secrets.CDM5_ORACLE_PASSWORD }}
      CDM5_ORACLE_SERVER: ${{ secrets.CDM5_ORACLE_SERVER }}
      CDM5_ORACLE_USER: ${{ secrets.CDM5_ORACLE_USER }}
      CDM5_POSTGRESQL_CDM_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_CDM_SCHEMA }}
      CDM5_POSTGRESQL_OHDSI_SCHEMA: ${{ secrets.CDM5_POSTGRESQL_OHDSI_SCHEMA }}
      CDM5_POSTGRESQL_PASSWORD: ${{ secrets.CDM5_POSTGRESQL_PASSWORD }}
      CDM5_POSTGRESQL_SERVER: ${{ secrets.CDM5_POSTGRESQL_SERVER }}
      CDM5_POSTGRESQL_USER: ${{ secrets.CDM5_POSTGRESQL_USER }}
      CDM5_SQL_SERVER_CDM_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_CDM_SCHEMA }}
      CDM5_SQL_SERVER_OHDSI_SCHEMA: ${{ secrets.CDM5_SQL_SERVER_OHDSI_SCHEMA }}
      CDM5_SQL_SERVER_PASSWORD: ${{ secrets.CDM5_SQL_SERVER_PASSWORD }}
      CDM5_SQL_SERVER_SERVER: ${{ secrets.CDM5_SQL_SERVER_SERVER }}
      CDM5_SQL_SERVER_USER: ${{ secrets.CDM5_SQL_SERVER_USER }}
      CDM5_REDSHIFT_CDM_SCHEMA: ${{ secrets.CDM5_REDSHIFT_CDM_SCHEMA }}
      CDM5_REDSHIFT_OHDSI_SCHEMA: ${{ secrets.CDM5_REDSHIFT_OHDSI_SCHEMA }}
      CDM5_REDSHIFT_PASSWORD: ${{ secrets.CDM5_REDSHIFT_PASSWORD }}
      CDM5_REDSHIFT_SERVER: ${{ secrets.CDM5_REDSHIFT_SERVER }}
      CDM5_REDSHIFT_USER: ${{ secrets.CDM5_REDSHIFT_USER }}
      CDM5_SPARK_USER: ${{ secrets.CDM5_SPARK_USER }}
      CDM5_SPARK_PASSWORD: ${{ secrets.CDM5_SPARK_PASSWORD }}
      CDM5_SPARK_CONNECTION_STRING: ${{ secrets.CDM5_SPARK_CONNECTION_STRING }}
      WEBAPI_TEST_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_WEBAPI_URL }}
      WEBAPI_TEST_SECURE_WEBAPI_URL: ${{ secrets.WEBAPI_TEST_SECURE_WEBAPI_URL }}
      WEBAPI_TEST_ADMIN_USER_NAME: ${{ secrets.WEBAPI_TEST_ADMIN_USER_NAME }}
      WEBAPI_TEST_ADMIN_USER_PASSWORD: ${{ secrets.WEBAPI_TEST_ADMIN_USER_PASSWORD }}
      STUPID_SECRET: ${{ secrets.STUPID_SECRET }}

    steps:
      - uses: actions/checkout@v3

      - uses: r-lib/actions/setup-r@v2
        with:
          r-version: ${{ matrix.config.r }}

      - uses: r-lib/actions/setup-tinytex@v2

      - uses: r-lib/actions/setup-pandoc@v2
      
      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: |
            any::rcmdcheck 
            any::remotes
          needs: check
      
      - name: Install dependencies of all HADES packages
        run: |
          source(".github/CheckAllOfHadesFunctions.R")
          saveRDS(prepareForRcheck(), "hadesPackages.rds")
        shell: Rscript {0}

      - name: Check all HADES packages
        run: |
          source(".github/CheckAllOfHadesFunctions.R")
          hadesPackages <- readRDS("hadesPackages.rds")
          for (i in seq_len(nrow(hadesPackages)))
            checkPackage(package = hadesPackages$name[i], inCran = hadesPackages$inCran[i])
        shell: Rscript {0}