Lamin CLI functions — lamin

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):

If user is set then lamin login <user>
Else if api_key is set then set the LAMIN_API_KEY environment variable temporarily with withr::with_envvar() and run lamin login
Else if there is a stored user handle run lamin login <handle>
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) { # \dontrun{
# Import Lamin modules
lc <- import_module("lamin_cli")
ln <- import_module("lamindb")

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