Generate a TileDBArrayExp Object

An enhanced version of TileDBArray with additional methods to operate on the array.

Initialization

A new TileDBArrayExp instance is initialised using the new() method. Alternatively use tdb_array() to create a new instance and open the array at READ mode.

 # uri path
 uri <- tempdir()
 # new instance
 obj <- TileDBArrayExp$new(uri = uri)
 # does array exist at this uri
 obj$exists() # FALSE

 unlink(uri)

Value

An object of class TileDBArrayExp, R6.

Super classes

R6.tiledb::TileDBObject -> R6.tiledb::TileDBArray -> TileDBArrayExp

Active bindings

fragments_object

Access the TileDBFragments instance for this array.

schema_version

Retrieve the schema version for this array.

is_sparse

Check array schema for sparsity.

size

Directory size.

Methods

Public methods

• TileDBArrayExp$create()

• TileDBArrayExp$delete_array()

• TileDBArrayExp$reopen()

• TileDBArrayExp$any_enums()

• TileDBArrayExp$enum_columns()

• TileDBArrayExp$enum_levels()

• TileDBArrayExp$has_enumeration()

• TileDBArrayExp$consolidate()

• TileDBArrayExp$consolidate_async()

• TileDBArrayExp$vacuum()

• TileDBArrayExp$vacuum_async()

• TileDBArrayExp$consolidate_and_vacuum()

• TileDBArrayExp$consolidate_and_vacuum_async()

• TileDBArrayExp$drop_attribute()

• TileDBArrayExp$frag_num()

• TileDBArrayExp$frag_to_vacuum()

• TileDBArrayExp$frag_dump()

• TileDBArrayExp$frag_uris()

• TileDBArrayExp$schema_upgrade()

• TileDBArrayExp$dir_tree()

• TileDBArrayExp$clone()

Inherited methods

• R6.tiledb::TileDBObject$class()
• R6.tiledb::TileDBObject$exists()
• R6.tiledb::TileDBObject$get_metadata()
• R6.tiledb::TileDBObject$initialize()
• R6.tiledb::TileDBObject$is_open()
• R6.tiledb::TileDBObject$set_metadata()
• R6.tiledb::TileDBArray$attributes()
• R6.tiledb::TileDBArray$attrnames()
• R6.tiledb::TileDBArray$close()
• R6.tiledb::TileDBArray$colnames()
• R6.tiledb::TileDBArray$dimensions()
• R6.tiledb::TileDBArray$dimnames()
• R6.tiledb::TileDBArray$open()
• R6.tiledb::TileDBArray$print()
• R6.tiledb::TileDBArray$schema()
• R6.tiledb::TileDBArray$schema_info()
• R6.tiledb::TileDBArray$tiledb_array()

---

Method create()

Create an empty Array with user defined schema.

The array will be opened at the given mode and kept opened; it can be accessed via active field $object.

Usage

TileDBArrayExp$create(sch, mode = "WRITE")

Arguments

sch

A TileDB schema. See constructor tiledb::tiledb_array_schema().

mode

Mode to open: either "READ" or "WRITE" (default).

Returns

The object, invisibly.

---

Method delete_array()

Delete the array.

Usage

TileDBArrayExp$delete_array()

Returns

The object, invisibly.

---

Method reopen()

Close and reopen the TileDB object in a new mode.

Usage

TileDBArrayExp$reopen(mode = c("READ", "WRITE"))

Arguments

mode

New mode to open the object in; choose from: "READ" or "WRITE".

Returns

The object, invisibly.

---

Method any_enums()

Checks array for factors (enumerations).

Usage

TileDBArrayExp$any_enums()

Returns

A boolean. TRUE indicating the array has factors and FALSE otherwise.

---

Method enum_columns()

Retrieve factor columns (attributes).

Usage

TileDBArrayExp$enum_columns()

Returns

A character vector with factor columns (enumeration attributes).

---

Method enum_levels()

Retrieve factor levels for a given attribute.

Usage

TileDBArrayExp$enum_levels(x)

Arguments

x

An attribute name.

Returns

A character vector with levels (enumeration values).

---

Method has_enumeration()

Check columns for factors.

Usage

TileDBArrayExp$has_enumeration()

Returns

A logical vector indicating which column (attribute) is encoded as factor (enumeration).

---

Method consolidate()

Consolidates the fragments of the array into a single fragment.

Usage

TileDBArrayExp$consolidate(mode = c("fragments", "commits", "fragment_meta",
  "array_meta"), cfg = NULL, start_time = NULL, end_time = NULL)

Arguments

mode

The consolidate mode, one of the following:

• "fragments": - consolidate all fragments (default)

• "commits": - consolidate all commit files

• "fragment_meta": - consolidate only fragment metadata footers to a single file

• "array_meta": - consolidate array metadata only

cfg

A configuration object tiledb::tiledb_config() to set parameters for the consolidation. When NULL (default) the configuration parameters will be retrieved from object's context.

start_time, end_time

Optional time stamp values. A date time objects of class POSIXt. If not provided, the default values from configuration object will be used.

Returns

TRUE, invisibly.

---

Method consolidate_async()

Consolidate fragments of the array into a single fragment asynchronously.

The consolidation will run in a separate R process in a clean environment.

Note this function requires the mirai package.

Usage

TileDBArrayExp$consolidate_async(mode = c("fragments", "commits",
  "fragment_meta", "array_meta"), cfg = NULL, start_time = NULL,
  end_time = NULL)

Arguments

mode

The consolidate mode, one of the following:

• "fragments": - consolidate all fragments (default)

• "commits": - consolidate all commit files

• "fragment_meta": - consolidate only fragment metadata footers to a single file

• "array_meta": - consolidate array metadata only

cfg

A configuration object tiledb::tiledb_config() to set parameters for the consolidation. When NULL (default) the configuration parameters will be retrieved from object's context.

start_time, end_time

Optional time stamp values. A date time objects of class POSIXt. If not provided, the default values from configuration object will be used.

Returns

This function will return a mirai::mirai() object immediately. When it is resolved, it returns TRUE indicating consolidation success.

---

Method vacuum()

Clean up consolidated fragments and array metadata.

Usage

TileDBArrayExp$vacuum(mode = c("fragments", "commits", "fragment_meta",
  "array_meta"), cfg = NULL)

Arguments

mode

The vacuum mode, one of the following:

• "fragments": - vacuum all fragments (default)

• "commits": - vacuum all commit files

• "fragment_meta": - vacuum only fragment metadata footers to a single file

• "array_meta": - vacuum array metadata only

cfg

A configuration object tiledb::tiledb_config() to set parameters for the vacuum. When NULL (default) the configuration parameters will be retrieved from object's context.

Returns

TRUE, invisibly.

---

Method vacuum_async()

Asynchronously clean up consolidated fragments and array metadata.

The clean up will run in a separate R process in a clean environment.

Note this function requires the mirai package.

Usage

TileDBArrayExp$vacuum_async(mode = c("fragments", "commits", "fragment_meta",
  "array_meta"), cfg = NULL)

Arguments

mode

The vacuum mode, one of the following:

• "fragments": - vacuum all fragments (default)

• "commits": - vacuum all commit files

• "fragment_meta": - vacuum only fragment metadata footers to a single file

• "array_meta": - vacuum array metadata only

cfg

A configuration object tiledb::tiledb_config() to set parameters for the vacuum process. When NULL (default) the configuration parameters will be retrieved from object's context.

Returns

This function will return a mirai::mirai() object immediately. When it is resolved, it returns TRUE indicating vacuum success.

---

Method consolidate_and_vacuum()

Consolidates and vacuums the fragments.

Usage

TileDBArrayExp$consolidate_and_vacuum(mode = c("fragments", "commits",
  "fragment_meta", "array_meta"), cfg = NULL, start_time = NULL,
  end_time = NULL)

Arguments

mode

The consolidate and vacuum mode, one of the following:

• "fragments": - consolidate all fragments (default)

• "commits": - consolidate all commit files

• "fragment_meta": - consolidate only fragment metadata footers to a single file

• "array_meta": - consolidate array metadata only

cfg

A configuration object tiledb::tiledb_config() to set parameters for the consolidation and vacuum. When NULL (default) the configuration parameters will be retrieved from object's context.

start_time, end_time

Optional time stamp values. A date time objects of class POSIXt. If not provided, the default values from configuration object will be used.

Returns

TRUE, invisibly.

---

Method consolidate_and_vacuum_async()

Consolidate and vacuum fragments asynchronously.

The consolidation and vacuum will run in a separate R process in a clean environment.

Note this function requires the mirai package.

Usage

TileDBArrayExp$consolidate_and_vacuum_async(mode = c("fragments", "commits",
  "fragment_meta", "array_meta"), cfg = NULL, start_time = NULL,
  end_time = NULL)

Arguments

mode

The consolidate and vacuum mode, one of the following:

• "fragments": - consolidate all fragments (default)

• "commits": - consolidate all commit files

• "fragment_meta": - consolidate only fragment metadata footers to a single file

• "array_meta": - consolidate array metadata only

cfg

A configuration object tiledb::tiledb_config() to set parameters for the consolidation and vacuum. When NULL (default) the configuration parameters will be retrieved from object's context.

start_time, end_time

Optional time stamp values. A date time objects of class POSIXt. If not provided, the default values from configuration object will be used.

Returns

This function will return a mirai::mirai() object immediately. When it is resolved, it returns TRUE indicating consolidation success.

---

Method drop_attribute()

Remove an attribute from array.

Usage

TileDBArrayExp$drop_attribute(x)

Arguments

x

An attribute name.

Returns

The object, invisibly.

---

Method frag_num()

The number of fragments.

Usage

TileDBArrayExp$frag_num()

---

Method frag_to_vacuum()

Consolidated fragments to be removed.

Usage

TileDBArrayExp$frag_to_vacuum(trunc_uri = TRUE)

Arguments

trunc_uri

TRUE to truncate uri path.

Returns

An object of class data.frame with four columns:

• Fragment: the fragment index (starts at 1)

• start_timestamp: fragment's start time stamp

• end_timestamp: fragment's end time stamp

• URI: fragment's truncated uri path (fragment name) when trunc_uri = TRUE (default), otherwise the full uri path

Note that the return object will be of class data.table if the package is found in your system.

---

Method frag_dump()

Dump to console the commit fragments.

Usage

TileDBArrayExp$frag_dump()

---

Method frag_uris()

Return a data.frame with time stamps and fragments uris.

Usage

TileDBArrayExp$frag_uris(trunc_uri = TRUE)

Arguments

trunc_uri

TRUE to truncate uri path.

Returns

An object of class data.frame with four columns:

• Fragment: the fragment index (start at 1)

• start_timestamp: start time-stamp of when fragment was written

• end_timestamp: end time-stamp of when fragment was written

• URI: fragment's truncated uri path (fragment name) when trunc_uri = TRUE (default), otherwise the full uri path

Note that the return object will be of class data.table if the package is found in your system.

---

Method schema_upgrade()

Upgrade the array to the latest format version.

Usage

TileDBArrayExp$schema_upgrade(cfg = NULL, ctx = NULL)

Arguments

cfg

A configuration object tiledb::tiledb_config().

ctx

Optional tiledb::tiledb_ctx() object. By default, object's context is used.

---

Method dir_tree()

Print directory contents.

Usage

TileDBArrayExp$dir_tree(recursive = TRUE)

Arguments

recursive

Should it recurse fully? Defaults to TRUE.

Returns

A character vector with file paths, invisibly.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

TileDBArrayExp$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.