laminr (version 0.4.1)

Instance: Instance

Description

Connect to a LaminDB instance using the connect() function. The instance object provides access to the modules and registries of the instance.

Active bindings

is_default

(logical(1))
Whether this is the default instance.

Methods

Public methods

• Instance$new()

• Instance$get_modules()

• Instance$get_module()

• Instance$get_module_names()

• Instance$get_settings()

• Instance$get_api()

• Instance$get_py_lamin()

• Instance$track()

• Instance$finish()

• Instance$print()

• Instance$to_string()

---

Method new()

Creates an instance of this R6 class. This class should not be instantiated directly, but rather by connecting to a LaminDB instance using the connect() function.

Usage

Instance$new(settings, api, schema, is_default, py_lamin)

Arguments

settings

The settings for the instance

api

The API for the instance

schema

The schema for the instance

is_default

Logical, whether this is the default instance

py_lamin

A Python lamindb module object

---

Method get_modules()

Get the modules for the instance.

Usage

Instance$get_modules()

Returns

A list of Module objects.

---

Method get_module()

Get a module by name.

Usage

Instance$get_module(module_name)

Arguments

module_name

The name of the module.

Returns

The Module object.

---

Method get_module_names()

Get the names of the modules. Example: c("core", "bionty").

Usage

Instance$get_module_names()

Returns

A character vector of module names.

---

Method get_settings()

Get instance settings.

Note: This method is intended for internal use only and may be removed in the future.

Usage

Instance$get_settings()

Returns

The settings for the instance.

---

Method get_api()

Get instance API.

Note: This method is intended for internal use only and may be removed in the future.

Usage

Instance$get_api()

Returns

The API for the instance.

---

Method get_py_lamin()

Get the Python lamindb module

Usage

Instance$get_py_lamin(check = FALSE, what = "This functionality")

Arguments

check

Logical, whether to perform checks

what

What the python module is being requested for, used in check messages

Returns

Python lamindb module.

---

Method track()

Start a run with tracked data lineage

Usage

Instance$track(transform = NULL, path = NULL)

Arguments

transform

UID specifying the data transformation

path

Path to the R script or document to track

Details

Calling track() with transform = NULL with return a UID, providing that UID with the same path with start a run

---

Method finish()

Finish a tracked run

Usage

Instance$finish()

---

Method print()

Print an Instance

Usage

Instance$print(style = TRUE)

Arguments

style

Logical, whether the output is styled using ANSI codes

---

Method to_string()

Create a string representation of an Instance

Usage

Instance$to_string(style = FALSE)

Arguments

style

Logical, whether the output is styled using ANSI codes

Returns

A cli::cli_ansi_string if style = TRUE or a character vector

Details

Note that by connecting to an instance via connect(), you receive a "richer" version of the Instance class documented here, providing direct access to all core registries and additional modules. See the vignette on "Package Architecture" for more information: vignette("architecture", package = "laminr").

Examples

if (FALSE) {
# Connect to an instance
db <- connect("laminlabs/cellxgene")

# fetch an artifact
artifact <- db$Artifact$get("MkRm3eUKPwfnAyZMWD9v")

# describe the artifact
artifact$describe()

# view field
artifact$id

# load dataset
artifact$load()
}