Release Automation

.github/workflows/create-release-branch.yml

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+name: Create Release Branch
+on:
+  workflow_dispatch:
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+        working-directory: R-package
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+      - name: setup-r
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "4.1.1"
+      - name: Install R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: R-package
+      - name: Source code
+        run: R -e 'source("R/create-release-files.R"); create_release_files(OSF_REPO_LINK = ${{secrets.OSF_REPO_LINK}}, OSF_TOKEN = ${{secrets.OSF_TOKEN}}, github_token = "${{ secrets.ACTION_TOKEN }}")'

.github/workflows/merge-release.yml

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+name: Merge Release 
+
+on:
+  pull_request:
+    types: [closed]
+    branches:
+      - 'release-*'
+
+jobs:
+  upload-dictionaries:
+    defaults:
+      run:
+        shell: bash
+        working-directory: R-package
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v2
+      - name: setup-r
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "4.1.1"
+      - name: Install R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          working-directory: R-package
+      - name: Source code
+        run: R -e 'source("R/osf-interactions.R"); update_osf(OSF_REPO_LINK = ${{secrets.OSF_REPO_LINK}}, OSF_TOKEN = ${{secrets.OSF.TOKEN}})'

release-automation/.Rbuildignore

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+^renv$
+^renv\.lock$
+^.*\.Rproj$
+^\.Rproj\.user$

release-automation/.Rprofile

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+source("renv/activate.R")

release-automation/DESCRIPTION

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+Package: release.automation 
+Type: Package
+Title: Release Automation 
+Version: 2.1.0
+Authors@R: c(
+    person(given = "Yulric", family = "Sequeira", role = c("aut"), email = "[email protected]"),
+    person(given = "Rostyslav", family = "Vyuha", role = c("aut","cre"), email = "[email protected]"))
+Maintainer: Rostyslav Vyuha <[email protected]>
+Description: PHES-ODM
+Depends:
+    R (>= 4.0.3)
+Imports:
+    osfr,
+    magrittr,
+    openxlsx,
+    logger
+License: cc-by-4.0 
+URL: https://github.com/Big-Life-Lab/PHES-ODM
+BugReports: https://github.com/Big-Life-Lab/PHES-ODM/issues
+Encoding: UTF-8
+RoxygenNote: 7.2.3
+Suggests: 
+    testthat (>= 3.0.0)
+Config/testthat/edition: 3

release-automation/NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(create_release_files)

release-automation/R/create-release-branch.R

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+source("R/odm-dictionary-file.R")
+source("R/files.R")
+source("R/logging.R")
+source("R/sets-sheet.R")
+source("R/parts-sheet.R")
+
+#' Create release files
+#'
+#' Creates release files given the user OSF link and auth token.
+#'
+#' @param osf_repo_link The link to the OSF repo.
+#' @param osf_token The OSF token used to authenticate the user.
+#'
+#' @export
+create_release_branch <- function(osf_repo_link, osf_token, github_token) {
+  setup_logging()
+
+  errors <- c()
+  warnings <- c()
+
+  download_dictionary_result <- download_dictionary(osf_token, "dev")
+  warnings <- c(warnings, download_dictionary_result$warnings)
+
+  parse_files_sheet_result <- parse_files_sheet(
+    download_dictionary_result$dictionary
+  )
+  errors <- c(errors, parse_files_sheet_result$errors)
+  warnings <- c(warnings, parse_files_sheet_result$warnings)
+  if (length(errors) == 0) {
+    parsed_github_files <- .get_github_files(
+      parse_files_sheet_result$parsed_files
+    )
+    create_files(
+      parsed_github_files,
+      file.path(getwd(), "..")
+    )
+    # Download previous release dictionary
+    previous_dictionary_download_results <- download_dictionary(
+      osf_token, "current"
+    )
+    files_to_remove_result <-
+      parse_files_sheet(parse_previous_dictionary_result$dictionary)
+    remove_files(
+      .get_github_files(files_to_remove_result$parsed_files),
+      parse_previous_dictionary_result$dictionary
+    )
+
+    # Set git config
+    system('git config user.name "PBL-Bot"')
+    system('git config user.email "[email protected]"')
+    system(glue::glue("git config user.password {github_token}"))
+
+    release_branch_name <- glue::glue(
+      "release-{parse_dictionary_result$dictionary_version}"
+    )
+
+    system(glue::glue("git checkout -b {release_branch_name}"))
+
+    commit_and_push_files(dictionary_version, release_branch_name)
+
+    print("Operation Successful")
+  } else {
+    print(glue::glue(
+      "{length(errors) errors found during the build process. They can be seen
+      in the log file located at {log_file_path}. Aborting operation."
+    ))
+  }
+
+  if (length(warnings) > 0) {
+    print(glue::glue(
+      "{length(warnings) warnings found during the build process. They can be
+      seen in the log file located at {log_file_path}."
+    ))
+  }
+}
+
+#' Remove Files
+#'
+#' Helper function to remove files based on output from validate_and_parse_files_sheet.
+#'
+#' @param files_to_remove List output from validate_and_parse_files_sheet
+#' @param dictionary openxlsx environment object storing the dictionary
+remove_files <- function(files_to_remove, dictionary) {
+  # Loop over files to remove based on fileID
+  for (fileID in names(files_to_remove)) {
+    current_file_info <- files_to_remove[[fileID]]
+    # Skip OSF files
+    if (!"github" %in% current_file_info$destination) {
+      next()
+    }
+
+    # Create full file path
+    file_extension <- switch(current_file_info$file_type,
+      "excel" = ".xlsx",
+      "csv" = ".csv"
+    )
+    file_path <- file.path(
+      "..",
+      current_file_info$github_location,
+      paste0(current_file_info$file_name, file_extension)
+    )
+    # Check if file exists
+    if (file.exists(file_path)) {
+      file.remove(file_path)
+    }
+  }
+}
+
+#' Commit files
+#'
+#' Utility function to add, commit, and push all changes
+#'
+#' @param repo git2r object for repo reference
+#' @param dictionary_version version of the dictionary being deployed
+commit_and_push_files <- function(dictionary_version, branch_name) {
+  # Add all files
+  system("git add --all")
+  # Create commit
+  system(glue::glue('git commit -m "[BOT] release-{dictionary_version}"'))
+  # Push updated branch
+  system(glue::glue("git push origin {branch_name}"))
+}
+
+.get_github_files <- function(parsed_files) {
+  github_files <- list()
+  for (file_id in names(parse_files_sheet_result$parsed_files)) {
+    if (parse_files_sheet_result$parsed_files[[file_id]] == "github") {
+      github_files[[file_id]] <- parse_files_sheet_result$parsed_files[[file_id]]
+    }
+  }
+  return(github_files)
+}

release-automation/R/download-dictionary.R

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+library(magrittr)
+
+source("R/get-latest-version-from-summary-sheet.R")
+
+download_dictionary <- function(osf_token, osf_folder) {
+  osfr::osf_auth(osf_token)
+  repo_files <- osfr::osf_retrieve_node(osf_repo_link) %>%
+    osfr::osf_ls_files()
+  folder_name <- tidyr::if_else(
+    osf_folder == "dev", developer_version_folder, current_version_folder
+  )
+  dictionary_folder <- repo_files[repo_files$name == folder_name, ]
+  dictionary_file <- osfr::osf_ls_files(
+    dictionary_folder,
+    type = "file", pattern = "ODM_dev-dictionary"
+  )
+  download_info <- osfr::osf_download(
+    requested_dictionary,
+    path = dictionary_set_path,
+    conflicts = "overwrite"
+  )
+  return(parse_dictionary(download_info[1, "local_path"]))
+}

release-automation/R/errors.R

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+missing_sheet_id <- "E1"
+missing_sheet_msg <- function(file_id, sheet_name, dictionary_sheets) {
+  return(glue::glue(
+    "Error {missing_sheet_id}: No sheet found with name {sheet_name} when
+    creating file with ID  ", "{file_id}. The following sheets are in the
+    dictionary ", "{paste(dictionary_sheets, collapse = ", ")}."
+  ))
+}
+
+invalid_csv_part_id <- "E2"
+invalid_csv_part_msg <- function(file_id, part_id) {
+  return(glue::glue(
+    "Error {invalid_csv_part_id}: The {part_id} used for the file with ID
+    {file_id} is a set which is only allowed for files with type excel"
+  ))
+}

release-automation/R/files.R

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+files_sheet_metadata <- list(
+  file_name = list(
+    name = "name"
+  ),
+  file_ID = list(
+    name = "fileID"
+  ),
+  file_type = list(
+    name = "fileType",
+    categories = list(
+      excel = "excel",
+      csv = "csv"
+    )
+  ),
+  part_ID = list(
+    name = "partID"
+  ),
+  add_headers = list(
+    name = "addHeaders"
+  ),
+  destinations = list(
+    name = "destinations",
+    categories = list(
+      osf = "osf",
+      github = "github"
+    )
+  ),
+  osf_locations = list(
+    name = "osfLocation"
+  ),
+  github_location = list(
+    name = "githubLocation"
+  )
+)
+
+create_files <- function(files_to_create, dictionary, write_dir) {
+  # Loop over files to extract based on fileID
+  for (file_id in names(files_to_create)) {
+    current_file_info <- files_to_create[[file_id]]
+
+    # Create a write directory based on destination and saving location
+    current_file_dir <- file.path(
+      write_dir,
+      current_file_info$github_location
+    )
+    dir.create(current_file_dir,
+      showWarnings = FALSE,
+      recursive = TRUE
+    )
+
+    if (current_file_info$file_type == "excel") {
+      # Use parts as names of sheets to extract
+      sheets_to_copy <- current_file_info$sheet_names
+      excel_file <- openxlsx::copyWorkbook(dictionary)
+      all_dictionary_sheets <- names(dictionary)
+      for (sheet_name in all_dictionary_sheets) {
+        if (!(sheet_name %in% sheets_to_copy)) {
+          openxlsx::removeWorksheet(excel_file, sheet_name)
+        }
+      }
+
+      if (!is.null(current_file_info$add_headers)) {
+        for (sheet_to_copy in sheets_to_copy) {
+          worksheet <- openxlsx::readWorkbook(excel_file, sheet_to_copy)
+          openxlsx::writeData(
+            excel_file,
+            sheet_to_copy,
+            .add_headers(worksheet, current_file_info$add_headers)
+          )
+        }
+      }
+
+      # Save the workbook in the appropriate directory
+      openxlsx::saveWorkbook(excel_file,
+        file = file.path(
+          current_file_dir,
+          glue::glue("{current_file_info$file_name}.xlsx")
+        ),
+        overwrite = TRUE
+      )
+    } else if (current_file_info$file_type == "csv") {
+      sheet_name <- current_file_info$sheet_names[1]
+      csv_file <-
+        openxlsx::readWorkbook(dictionary, sheet_name)
+      if (!is.null(current_file_info$add_headers)) {
+        csv_file <- .add_headers(csv_file, current_file_info$add_headers)
+      }
+
+      write.csv(csv_file,
+        file = file.path(
+          current_file_dir,
+          glue::glue(
+            "{current_file_info$file_name}.csv"
+          )
+        ),
+        row.names = FALSE
+      )
+    }
+  }
+}
+
+.add_headers <- function(df, headers) {
+  df <-
+    rbind(colnames(df), df)
+  if (length(colnames(df)) > length(headers)) {
+    length_to_append <-
+      length(colnames(df)) - length(headers)
+    headers <- c(headers, rep("", length_to_append))
+  } else if (length(colnames(df)) < length(headers)) {
+    length_to_append <-
+      length(headers) - length(colnames(df))
+    for (col_counter in 1:length_to_append) {
+      df <- cbind(df, "")
+    }
+  }
+  colnames(df) <- headers
+  return(df)
+}

release-automation/R/get-latest-version-from-summary-sheet.R

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+get_latest_version_from_summary_sheet <- function(summary_sheet) {
+  return(
+    summary_sheet[[1]]
+    %>% .[!is.na(.)]
+      %>% .[length(.)]
+  )
+}

release-automation/R/logging.R

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+log_file_path <- file.path(getwd(), "log")
+
+#' Sets up logging
+setup_logging <- function() {
+  file.remove(log_file_path)
+  logger::log_appender(logger::appender_file(log_file_path))
+}