2a. Test Main FrEDI Data #47
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| ### https://github.com/actions/upload-artifact | |
| ### https://github.blog/changelog/2021-11-10-github-actions-input-types-for-manual-workflows/ | |
| ### https://docs.github.com/en/actions/using-workflows/caching-dependencies-to-speed-up-workflows | |
| ### https://github.com/r-lib/actions/tree/v2/setup-r-dependencies | |
| ### https://docs.github.com/en/actions/using-jobs/using-conditions-to-control-job-execution | |
| ### https://github.com/marketplace/actions/download-workflow-artifact | |
| ### https://docs.github.com/en/actions/writing-workflows/choosing-what-your-workflow-does/storing-and-sharing-data-from-a-workflow | |
| ### For uploading artifacts: | |
| ### "path:" is the output path where Pandoc will write the compiled PDF. | |
| ### Note, this should be the same directory as the input paper.md | |
| name: 2a. Test Main FrEDI Data | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| workflow_id: | |
| type: string | |
| description: Enter the run ID for the workflow from which to retrieve the main FrEDI Data | |
| fredi_branch: | |
| type: string | |
| description: Which FrEDI Package branch do you want to use? | |
| default: "main" | |
| gen_test: | |
| type: choice | |
| description: Run general tests on main FrEDI data? | |
| required: true | |
| options: | |
| - no | |
| - yes | |
| figures: | |
| type: choice | |
| description: Create scaled impact figures from main FrEDI data? | |
| required: true | |
| options: | |
| - no | |
| - yes | |
| sector: | |
| type: string | |
| description: Which sectors do you want to run? | |
| default: "all" | |
| jobs: | |
| # download: | |
| # runs-on: ubuntu-latest | |
| # # needs: install | |
| # env: | |
| # GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| # steps: | |
| # ### Download tmp_sysdata.rda from 1. Compile Main FrEDI Data run | |
| # - name: Download all artifacts | |
| # id: download-artifact | |
| # uses: actions/download-artifact@v4 | |
| # with: | |
| # github-token: ${{ secrets.GITHUB_TOKEN }} | |
| # # github-token: ${{ GITHUB_PAT }} | |
| # run-id: ${{ inputs.workflow_id }} | |
| # path: ./data | |
| # - run: | | |
| # pwd | |
| # ls -R ./data/Data | |
| test_data: | |
| runs-on: ubuntu-latest | |
| # needs: download | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| name: Process Data | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| # echo "$${{ github.ref_name }} ${{ inputs.workflow_id }} ${{ inputs.fredi_branch }} ${{ inputs.gen_test }} ${{ inputs.figures }}" | |
| - name: Send input status | |
| run: | | |
| echo "$${{ github.ref_name }} ${{ inputs.fredi_branch }} ${{ inputs.gen_test }} ${{ inputs.figures }}" | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Setup R package dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache: true | |
| cache-version: 1 | |
| packages: | | |
| any::tidyverse | |
| any::ggpubr | |
| any::openxlsx | |
| any::devtools | |
| any::admisc | |
| any::zoo | |
| - name: Install FrEDI | |
| run: | | |
| Rscript -e ' | |
| devtools::install_github( | |
| repo = "https://github.com/USEPA/FrEDI", | |
| ref = "${{ github.event.inputs.fredi_branch }}", | |
| dependencies = FALSE, | |
| upgrade = "never", | |
| force = TRUE, | |
| type = "source" | |
| )' | |
| ### Download tmp_sysdata.rda from 1. Compile Main FrEDI Data run | |
| - name: Download all artifacts | |
| id: download-artifact | |
| uses: actions/download-artifact@v4 | |
| with: | |
| github-token: ${{ secrets.GITHUB_TOKEN }} | |
| # github-token: ${{ GITHUB_PAT }} | |
| run-id: ${{ inputs.workflow_id }} | |
| path: ./data | |
| # - run: | | |
| # pwd | |
| # ls -R ./data/Data | |
| - name: Run Tests on Main FrEDI Data | |
| run: | | |
| Rscript -e ' | |
| ### Libraries | |
| require(tidyverse) | |
| require(devtools) | |
| ### Arguments | |
| doGenTests <- "${{ inputs.gen_test }}" %in% c("true", "yes") | |
| doFigures <- "${{ inputs.figures }}" %in% c("true", "yes") | |
| doTests <- doGenTests | doFigures | |
| sectors0 <- "${{ inputs.sector }}" | |
| ### Directories for project, scripts, data, and artifacts | |
| projectDir <- "." | |
| ### Load all code | |
| projectDir |> devtools::load_all() | |
| ### Create directory for outputs | |
| ### - Filename for general tests | |
| ### - Filename for list of tests | |
| outDir <- projectDir |> file.path("data_tests") | |
| doOutDir <- !(outDir |> dir.exists()) | |
| if(doOutDir) outDir |> dir.create() | |
| ### Output paths | |
| testFile <- "configTestResults" |> paste0(".", "xlsx") | |
| listFile <- "testList" |> paste0(".", "rda") | |
| listPath <- outDir |> file.path(listFile) | |
| ### Load Scripts | |
| scriptDir <- projectDir |> file.path("scripts") | |
| scriptName <- c("testFrediData") |> paste0(".", "R") | |
| scriptPath <- scriptDir |> file.path(scriptName) | |
| scriptPath |> source() | |
| # for(path_i in scriptPath){path_i |> source()} | |
| ### Load Data | |
| dataDir <- projectDir |> file.path("data") | |
| artDir <- dataDir |> file.path("Data") | |
| # getwd() |> print() | |
| # "." |> list.files() |> print(); | |
| # dataDir |> list.files() |> print(); | |
| # artDir |> list.files() |> print(); | |
| ### Artifact paths | |
| artName <- "tmp_sysdata.rda" | |
| artPath <- artDir |> file.path(artName) | |
| artExists <- artPath |> file.exists() | |
| artExists |> print() | |
| ### Whether to run the test | |
| runTests <- doTests & artExists | |
| ### Modify sectors | |
| sectors0 |> print() | |
| sectors0 <- sectors0 |> trimws() | |
| sectors0 <- sectors0 |> str_replace_all(" ", "") | |
| sectors0 <- sectors0 |> trimws() | |
| sectors0 <- sectors0 |> str_split(pattern=",") |> unlist() | |
| sectors0 |> print() | |
| ### Run general test | |
| if(runTests) { | |
| ### Load data | |
| artPath |> load() | |
| ### Run tests | |
| testList <- projectDir |> testFrediData( | |
| dataList = rDataList , ### List with data (e.g., rDataList) | |
| general = doGenTests, ### Whether to run the general test | |
| figures = doFigures , ### Whether to create scaled impact figures | |
| sectors = sectors0 , ### Which sector to run | |
| outDir = outDir , ### Where to save output files | |
| testFile = testFile ### Name of Excel file for testing results | |
| ) ### End testFrediData | |
| ### Save data | |
| testList |> save(file=listPath) | |
| outDir |> list.files() |> print() | |
| } ### End if(doTests) | |
| ' | |
| - name: Upload Tests | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: Tests | |
| path: | | |
| ./data_tests/* | |