release: Release a version of the database to the OomyceteDB

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

Release a version of the database to the OomyceteDB

Description

This is an interactive function that walks the user through the steps needed to add a release of OomyceteDB to the oomycetedbdata package. The oomycetedbdata package is the source of the data for the OomyceteDB website, so this will effectively add a release to the website. This function will do the following things:

• Validate that the database is formatted correctly, as described in the database format guide.

• Show the version of the database to be released and any changes to the user for a manual check.

• Upload the release to Github or store/modify a version of the oomycetedbdata package on the local computer for manual upload.

Usage

release(
  database_path = NULL,
  release_path = NULL,
  interactive = TRUE,
  validate = TRUE,
  auto_update = FALSE,
  overwrite = FALSE,
  description = NULL,
  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.
validate	(TRUE/FALSE of length 1) Whether or not to validate the database source before attempting to create a release. It is highly recommended to validate before a release. 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.
overwrite	(TRUE/FALSE of length 1) Whether or not to replace the previous release with this release rather than creating a new one. Default: FALSE.
description	(character of length 1) A description of this release. This will be shown publicly with the release. Default: prompt user.
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.