AutoUpdated #116
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| # This workflow will install R, Rsirius dependencies and test the Rsirius package using testthat | |
| # For more information see: https://github.com/r-lib/actions | |
| name: RTest | |
| on: [workflow_dispatch, workflow_call, pull_request] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 30 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| r-version: ["4.0.0", "4.1.0", "4.2.0", "4.3.0", "4.4.0"] | |
| env: | |
| SIRIUS_USER: ${{ secrets.SIRIUS_USER }} | |
| SIRIUS_PW: ${{ secrets.SIRIUS_PW }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up R ${{ matrix.r-version }} | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.r-version }} | |
| - name: Install Rsirius dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache: false | |
| working-directory: ./client-api_r/generated | |
| - name: Install Rsirius | |
| run: install.packages("/home/runner/work/sirius-client-openAPI/sirius-client-openAPI/client-api_r/generated", repos = NULL, type = "source") | |
| shell: Rscript {0} | |
| - name: Cache Sirius Release | |
| uses: actions/cache@v3 | |
| with: | |
| path: .updater/api/sirius | |
| key: sirius | |
| fail-on-cache-miss: true | |
| - name: Download tomato_small project space | |
| run: wget ${{ secrets.TOMATO_SMALL_DOWNLOAD_LINK }} -O tomato_small.sirius | |
| - name: Change HOME to working directory of runner | |
| run: echo "HOME=/home/runner/work/sirius-client-openAPI" >> $GITHUB_ENV | |
| - name: Run Rest Api | |
| run: bash .updater/api/sirius/bin/sirius REST -p 8080 -s & | |
| - name: Wait for Api to start | |
| run: while ! nc -z localhost 8080; do sleep 0.1; done | |
| - name: Login to SIRIUS | |
| run: | | |
| library(Rsirius) | |
| var_accept_terms <- TRUE | |
| var_account_credentials <- AccountCredentials$new(Sys.getenv('SIRIUS_USER'), Sys.getenv('SIRIUS_PW')) | |
| api_instance <- rsirius_api$new() | |
| api_response <- api_instance$login_and_account_api$Login(var_accept_terms, var_account_credentials) | |
| if (inherits(api_response, "AccountInfo")) { | |
| quit(status=0) | |
| } else { | |
| print('Login failed, aborting...') | |
| quit(status=1) | |
| } | |
| shell: Rscript {0} | |
| - name: Copy tests into Rsirius folder for testing | |
| run: | | |
| mkdir -p client-api_r/generated/tests | |
| cp -r .updater/clientTests/RTests/test client-api_r/generated/tests/testthat | |
| cp .updater/clientTests/RTests/testthat.R client-api_r/generated/tests/testthat.R | |
| # TODO move back after issues are fixed | |
| rm client-api_r/generated/tests/testthat/test_compounds_api.R | |
| - name: Build Rsirius | |
| run: | | |
| R CMD build ./client-api_r/generated | |
| - name: Test Rsirius using testthat | |
| run: | | |
| R CMD check Rsirius_0.9.tar.gz --no-manual |