Package 'laminr'

Get current LaminDB instance

Description

Get the currently connected LaminDB instance

Usage

get_current_lamin_instance(ignore_none = TRUE, silent = FALSE)

Arguments

ignore_none	Whether to ignore the "none/none" virtual instance as a valid instance and return NULL
silent	Whether to suppress messages

Value

The slug of the current LaminDB instance, or NULL invisibly if no instance is found

---

Get current LaminDB settings

Description

Get the current LaminDB settings as an R list

Usage

get_current_lamin_settings(minimal = FALSE, silent = FALSE)

Arguments

minimal	If TRUE, quickly extract a minimal list of important settings instead of converting the complete settings object
silent	Whether to suppress messages

Value

A list of the current LaminDB settings

---

Get current LaminDB user

Description

Get the currently logged in LaminDB user

Usage

get_current_lamin_user(silent = FALSE)

Arguments

silent

Whether to suppress messages

Value

The handle of the current LaminDB user, or NULL invisibly if no user is found

---

Import Python modules

Description

This function can be used to import LaminDB Python modules with additional checks and nicer error messages.

Usage

import_module(module, ...)

Arguments

module

The name of the Python module to import

...

Arguments passed on to require_module options A vector of defined optional dependencies for the module that is being required version A string specifying the version of the module to require source A source for the module requirement, for example ⁠git+https://github.com/owner/module.git⁠ python_version A string defining the Python version to require. Passed to reticulate::py_require(). silent Whether to suppress the message showing what has been required

Details

Python dependencies are set using require_module() before importing the module and used to create an ephemeral environment unless another environment is found (see vignette("versions", package = "reticulate")).

Requirements for the lamindb module can be controlled differently using environment variables, see https://docs.lamin.ai/setup-laminr for details.

Value

An object representing a Python package

See Also

• require_module() and reticulate::py_require() for defining Python dependencies

• vignette("versions", package = "reticulate") for setting the Python environment to use (or online here)

Examples

## Not run: 
# Import lamindb to start interacting with an instance
ln <- import_module("lamindb")

# Import lamindb with optional dependencies
ln <- import_module("lamindb", options = c("dev"))

# Import other LaminDB modules
bt <- import_module("bionty")
pt <- import_module("pertdb")
cc <- import_module("clinicore")

# Import any Python module
np <- import_module("numpy")

## End(Not run)

---

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

## Not run: 
# Import Lamin modules
lc <- import_module("lamin_cli")
ln <- import_module("lamindb")

# Examples of replacing CLI functions with the lamin_cli module

## End(Not run)
## Not run: 
# Connect to a LaminDB instance
lamin_connect(instance)
# ->
lc$connect(instance)

## End(Not run)
## Not run: 
# Disconnect from a LaminDB instance
lamin_disconnect()
# ->
lc$disconnect()

## End(Not run)
## Not run: 
# Log in as a LaminDB user
lamin_login(...)
# ->
lc$login(...)

## End(Not run)
## Not run: 
# Log out of LaminDB
lamin_logout()
# ->
lc$logout()

## End(Not run)
## Not run: 
# Create a new LaminDB instance
lamin_init(...)
# ->
lc$init(...)

## End(Not run)
## Not run: 
# Create a temporary LaminDB instance
lamin_init_temp(...)
# ->
create_temporary_instance()

## End(Not run)
## Not run: 
# Delete a LaminDB entity
lamin_delete(...)
# ->
lc$delete(...)

## End(Not run)
## Not run: 
# Save to a LaminDB instance
lamin_save(...)
# ->
lc$save(...)

## End(Not run)
## Not run: 
# Access Lamin settings
lamin_settings()
# ->
ln$setup$settings
# OR
ln$settings
# Alternatively
get_current_lamin_settings()

## End(Not run)

---

laminr status

Description

Overview of the current status of the laminr package and its dependencies. Can be useful for debugging.

Usage

laminr_status()

Details

Provides information that can be useful for debugging. To run the function when an error occurs, set ⁠options(error = function() { print(laminr::laminr_status() })⁠. Note that this should be used with some caution as it will print the status whenever any error occurs.

Value

A laminr_status object

Examples

laminr_status()

---

Require a Python module

Description

This function can be used to require that Python modules are available for laminr with additional checks and nicer error messages.

Usage

require_module(
  module,
  options = NULL,
  version = NULL,
  source = NULL,
  python_version = NULL,
  silent = FALSE
)

Arguments

module	The name of the Python module to require
options	A vector of defined optional dependencies for the module that is being required
version	A string specifying the version of the module to require
source	A source for the module requirement, for example ⁠git+https://github.com/owner/module.git⁠
python_version	A string defining the Python version to require. Passed to reticulate::py_require().
silent	Whether to suppress the message showing what has been required

Details

Python dependencies are set using reticulate::py_require(). If a connection to Python is already initialized and the requested module is already in the list of requirements then a further call to reticulate::py_require() will not be made to avoid errors/warnings. This means that required versions etc. need to be set before Python is initialized.

Arguments

• Setting options = c("opt1", "opt2") results in "module[opt1,opt2]"

• Setting version = ">=1.0.0" results in "module>=1.0.0"

• Setting source = "my_source" results in "module @ my_source"

• Setting all of the above results in "module[opt1,opt2]>=1.0.0 @ my_source"

Value

The result of reticulate::py_require

See Also

reticulate::py_require()

Examples

## Not run: 
# Require lamindb
require_module("lamindb")

# Require a specific version of lamindb
require_module("lamindb", version = ">=2.0.0")

# Require require lamindb with options
require_module("lamindb", options = c("dev"))

# Require the development version of lamindb from GitHub
require_module("lamindb", source = "git+https://github.com/laminlabs/lamindb.git")

# Require lamindb with a specific Python version
require_module("lamindb", python_version = "3.12")

## End(Not run)

---

Use a temporary LaminDB instance

Description

Create and connect to a temporary LaminDB instance to use for the current session. This function is primarily intended for developers to use during testing and documentation but can also be useful for users to debug issues or create reproducible examples.

Usage

use_temporary_instance(
  name = "laminr-temp",
  modules = NULL,
  add_timestamp = TRUE,
  envir = parent.frame()
)

Arguments

name	A name for the temporary instance
modules	A vector of modules to include (e.g. "bionty")
add_timestamp	Whether to append a time stamp to name to make it unique
envir	An environment passed to withr::defer()

Details

This function creates and connects to a temporary LaminDB instance. A temporary storage folder is created and used to initialize a new instance. An exit handler is registered with withr::defer() that deletes the instance and storage, then reconnects to the previous instance when envir finishes.

Switching to a temporary instance is not possible when another instance is already connected.

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