lodestar_start_guide

library(gwangmyeongseong3)

Best practises and hiding passwords and usernames

In this vignette we will be exploring the Lodestar software for sequence annotation and comparative genomics. In the canonical code examples included we will be connecting to a database server that uses a username and password that I would prefer not to be shown in a public-facing technical document. We will therefore have a quick introduction to the r-lib/keyring software.

keyring works out of the box on Windows and MacOS - if you are using a Linux computer please ensure that e.g. libsecret-1-dev has been installed on your system.

# define the objects required for the key ...
keychain_name <- "my_credentials"
kr_service <- "my_service"
kr_username <- "my_username"
kr_password <- "topsecret"

# define the key object - this will be saved in ~/.config/r-keyring
kb <- keyring::backend_file$new()

# create the keyring (this will be placed in the object above)
kb$keyring_create(keychain_name)
#> WARNING: your platform is not supported. Input is not masked!
#> Keyring password:

# and set the username, password and service parameters to be stored
kb$set_with_value(service=kr_service, username=kr_username, password=kr_password, keyring=keychain_name)

# let's see what has been saved in the keychain
kb$keyring_is_locked(keychain_name)
#> [1] FALSE
kb$keyring_list()
#>          keyring num_secrets locked
#> 1       lodestar           1   TRUE
#> 2 my_credentials           1  FALSE
kb$list(keyring = keychain_name, service=kr_service)
#>      service    username
#> 1 my_service my_username

# and show how the password can be extracted again ...
kb$get(keyring = keychain_name, service=kr_service, username=kr_username)
#> [1] "topsecret"

# delete this keyring
kb$keyring_delete(keychain_name)

Using passwords in Lodestar

The Lodestar package provides a simple method to set the passwords that will be used for connecting to one or more databases.

creds <- lodestar_creds(username=kr_username, password=kr_password, service=kr_service, keyring=keychain_name)
#> WARNING: your platform is not supported. Input is not masked!
#> Keyring password:
creds$list(keyring = keychain_name, service=kr_service)
#>      service    username
#> 1 my_service my_username