Validate the source database format — validate • oomycetedbtools

Check that the database spreadsheet does not have any issues that would cause problems when hosting the website.

validate(
  database_path = NULL,
  release_path = NULL,
  interactive = TRUE,
  auto_update = FALSE,
  stop_on_fail = FALSE,
  verbose = TRUE,
  google_user = NULL,
  google_pass = NULL,
  github_user = NULL,
  github_pass = NULL,
  config_path = find_config("oomycetedbtools_config.yml")
)

Arguments

database_path	(`character` of length 1) The file path or URL to the spreadsheet with the sequence and taxonomy data, formatted as described in the database format guide. Default: `NULL`, prompt user if needed.
release_path	(`character` of length 1) The file path or URL to the git/github repository the releases are stored in. Default: `NULL`, prompt user if needed.
interactive	(`TRUE`/`FALSE` of length 1) Whether or not to prompt the user. This function is designed to be interactive, so `TRUE` is recommended. Default: `TRUE`.
auto_update	(`TRUE`/`FALSE` of length 1) Whether or not to allow automated edits to the source database specified by `database_path`. Before any edits are made, a backup of the file will be made in the same location prefixed with ".backup_". Default: `FALSE`.
stop_on_fail	(`TRUE`/`FALSE` of length 1) Whether or not to stop the validation on the fist failed check. Even when `FALSE`, some checks will stop the validation when they fail. Default: `FALSE`.
verbose	(`TRUE`/`FALSE` of length 1) Print extra information.
google_user	(`character` of length 1) A Google Drive user ID with read/write permissions for the database folder. Required if `database_path` is a URL to a Google spreadsheet. Default: `NULL`, prompt user if needed.
google_pass	(`character` of length 1) The password associated with the `google_user` option. Required if `database_path` is a URL to a Google spreadsheet. Default: `NULL`, prompt user if needed.
github_user	(`character` of length 1) A Github user ID with read/write permissions for the `oomycetedbdata` repository. Required if `release_path` is a URL to a Github repository. Default: `NULL`, prompt user if needed.
github_pass	(`character` of length 1) The password associated with the `github_user` option. Required if `release_path` is a URL to a Github repository. Default: `NULL`, prompt user if needed.
config_path	(`character` of length 1) The file path to a configuration file with defaults for these parameters.