The SOMA Object Base Class

Base class to implement shared functionality across the SOMAArrayBase and SOMACollectionBase classes. (lifecycle: maturing)

See also

Derived classes: SOMAArrayBase, SOMACollectionBase

Active bindings

platform_config

Platform configuration

context

SOMAContext context object for TileDB operations

tiledbsoma_ctx

SOMATileDBContext

tiledb_timestamp

Time that object was opened at

uri

The URI of the TileDB object

soma_type

The SOMA object type

.tiledb_timestamp_range

Time range for libtiledbsoma

Methods

Public methods

• SOMAObject$new()

• SOMAObject$is_open()

• SOMAObject$class()

• SOMAObject$mode()

• SOMAObject$reopen()

• SOMAObject$exists()

• SOMAObject$get_metadata()

• SOMAObject$set_metadata()

• SOMAObject$print()

• SOMAObject$clone()

---

Method new()

Create a new SOMA object. (lifecycle: maturing)

Usage

SOMAObject$new(
  uri,
  ...,
  platform_config = NULL,
  tiledbsoma_ctx = NULL,
  tiledb_timestamp = NULL,
  context = NULL
)

Arguments

uri

URI for the SOMA object

...

Ignored

platform_config

Optional platform configuration

tiledbsoma_ctx

Optional (DEPRECATED) TileDB SOMA context

tiledb_timestamp

Optional timestamp (POSIXct) to open the object at

context

Optional SOMAContext object used for TileDB operations. If a context is not provided, then the default context will be used. Call set_default_context once before other SOMA operations to configure the default context.

---

Method is_open()

Determine if the object is open for reading or writing

Usage

SOMAObject$is_open()

Returns

TRUE if the object is open, otherwise FALSE

---

Method class()

Print the name of the R6 class

Usage

SOMAObject$class()

Returns

The name of the R6 class

---

Method mode()

Get the mode of the object

Usage

SOMAObject$mode()

Returns

The mode of the object, one of:

• “CLOSED”

• “READ”

• “WRITE”

• “DELETE”

---

Method reopen()

Close and reopen the TileDB object in a new mode

Usage

SOMAObject$reopen(mode, tiledb_timestamp = NULL)

Arguments

mode

New mode to open the object in; choose from:

• “READ”

• “WRITE”

• “DELETE”

tiledb_timestamp

Optional Datetime (POSIXct) with TileDB timestamp

Returns

Invisibly returns self opened in mode

---

Method exists()

Check if the object exists. (lifecycle: maturing)

Usage

SOMAObject$exists()

Returns

TRUE if the object exists, otherwise FALSE

---

Method get_metadata()

Retrieve metadata. (lifecycle: maturing)

Usage

SOMAObject$get_metadata(key = NULL)

Arguments

key

The name of the metadata attribute to retrieve is not NULL.

Returns

A list of metadata values.

---

Method set_metadata()

Add list of metadata. (lifecycle: maturing)

Usage

SOMAObject$set_metadata(metadata)

Arguments

metadata

Named list of metadata to add

Returns

Invisibly returns self

---

Method print()

Print-friendly representation of the object

Usage

SOMAObject$print()

Returns

Invisibly returns self

---

Method clone()

The objects of this class are cloneable with this method.

Usage

SOMAObject$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.