validate: Validate the source database format

In grunwaldlab/oomycetedbtools: Tools for managing the OomyceteDB website and database

Validate the source database format

Description

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

Usage

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.

grunwaldlab/oomycetedbtools documentation built on March 23, 2022, 6:54 a.m.