laminr (version 1.2.0)

lamin_cli: Lamin CLI functions

Description

Lamin CLI calls are available from R by importing the lamin_cli Python module using lc <- import_module("lamin_cli"). The previous CLI functions are now deprecated, see examples for how to switch to the new syntax.

Usage

# Import the module instead of using deprecated functions
# lc <- import_module("lamin_cli")
# Deprecated functions
lamin_connect(instance)
lamin_disconnect()
lamin_login(user = NULL, api_key = NULL)
lamin_logout()
lamin_init(storage, name = NULL, db = NULL, modules = NULL)
lamin_init_temp(
  name = "laminr-temp",
  db = NULL,
  modules = NULL,
  add_timestamp = TRUE,
  envir = parent.frame()
)
lamin_delete(instance, force = FALSE)
lamin_save(filepath, key = NULL, description = NULL, registry = NULL)
lamin_settings()

Arguments

instance

Either a slug giving the instance to connect to (<owner>/<name>) or an instance URL (https://lamin.ai/owner/name). For lamin_delete(), the slug for the instance to delete.

user

Handle for the user to login as

api_key

API key for a user

storage

A local directory, AWS S3 bucket or Google Cloud Storage bucket

name

A name for the instance

db

A Postgres database connection URL, use NULL for SQLite

modules

A vector of modules to include (e.g. "bionty")

add_timestamp

Whether to append a timestamp to name to make it unique

envir

An environment passed to withr::defer()

force

Whether to force deletion without asking for confirmation

filepath

Path to the file or folder to save

key

The key for the saved item

description

The description for the saved item

registry

The registry for the saved item

Details

lamin_connect()

Running this will set the LaminDB auto-connect option to True so you auto-connect to instance when importing Python lamindb.

lamin_login()

Depending on the input, one of these commands will be run (in this order):

1. If user is set then lamin login <user>

2. Else if api_key is set then set the LAMIN_API_KEY environment variable temporarily with withr::with_envvar() and run lamin login

3. Else if there is a stored user handle run lamin login <handle>

4. Else if the LAMIN_API_KEY environment variable is set run lamin login

Otherwise, exit with an error

lamin_init_temp()

For lamin_init_temp(), a time stamp is appended to name (if add_timestamp = TRUE) and then a new instance is initialised with lamin_init() using a temporary directory. A lamin_delete() call is registered as an exit handler with withr::defer() to clean up the instance when envir finishes.

The lamin_init_temp() function is mostly for internal use and in most cases users will want lamin_init().

Examples

if (FALSE) {
# Import Lamin modules
lc <- import_module("lamin_cli")
ln <- import_module("lamindb")

# Examples of replacing CLI functions with the lamin_cli module
}
if (FALSE) {
# Connect to a LaminDB instance
lamin_connect(instance)
# ->
lc$connect(instance)
}
if (FALSE) {
# Disconnect from a LaminDB instance
lamin_disconnect()
# ->
lc$disconnect()
}
if (FALSE) {
# Log in as a LaminDB user
lamin_login(...)
# ->
lc$login(...)
}
if (FALSE) {
# Log out of LaminDB
lamin_logout()
# ->
lc$logout()
}
if (FALSE) {
# Create a new LaminDB instance
lamin_init(...)
# ->
lc$init(...)
}
if (FALSE) {
# Create a temporary LaminDB instance
lamin_init_temp(...)
# ->
create_temporary_instance()
}
if (FALSE) {
# Delete a LaminDB entity
lamin_delete(...)
# ->
lc$delete(...)
}
if (FALSE) {
# Save to a LaminDB instance
lamin_save(...)
# ->
lc$save(...)
}
if (FALSE) {
# Access Lamin settings
lamin_settings()
# ->
ln$setup$settings
# OR
ln$settings
# Alternatively
get_current_lamin_settings()
}