Package 'R6.tiledb'

Description

Get Array Timestamps

Usage

## S3 method for class 'tiledb_array'
array_timestamps(object, tz = "", ...)

## S3 method for class 'TileDBArray'
array_timestamps(object, tz = "", ...)

Arguments

Value

An object of class array_timestamps that is a list that holds the user supplied temporal timestamps and the time range the array is opened at.

See Also

group_timestamps(), set_tiledb_timestamp()

Description

Close a tiledb::tiledb_array(), tiledb::tiledb_group(), TileDBArray or TileDBGroup object.

Usage

## S3 method for class 'tiledb_array'
close(con, ...)

## S3 method for class 'TileDBArray'
close(con, ...)

## S3 method for class 'tiledb_group'
close(con, ...)

## S3 method for class 'TileDBGroup'
close(con, ...)

Arguments

Value

Invisibly, a logical TRUE on success.

Description

Delete metadata using keys names for a TileDB array or group.

Usage

## S3 method for class 'TileDBArray'
delete_metadata(x, keys, ...)

## S3 method for class 'TileDBGroup'
delete_metadata(x, keys, ...)

## S3 method for class 'tiledb_array'
delete_metadata(x, keys, ...)

## S3 method for class 'tiledb_group'
delete_metadata(x, keys, ...)

## S3 method for class 'character'
delete_metadata(x, keys, ctx = NULL, ...)

Arguments

Details

delete_metadata() works similar to metadata<-() with NULL value but works with a character vector of keys.

The character method requires a valid URI path.

The methods will not alter the mode of the TileDB object; also, the object will be opened temporarily to access the metadata if it is closed.

Value

A logical TRUE, invisibly.

See Also

set_metadata() and metadata().

Description

Create a demo array for UCBAdmissions dataset

Usage

demo_array_UCBAdmissions(uri)

Arguments

Description

Fetch metadata using a list of key-value pairs for a TileDB array or group. Optionally, you can access metadata at specific point in time (time-travelling).

Usage

## S3 method for class 'TileDBArray'
fetch_metadata(x, keys = NULL, timestamp = NULL, ...)

## S3 method for class 'TileDBGroup'
fetch_metadata(x, keys = NULL, timestamp = NULL, ...)

## S3 method for class 'tiledb_array'
fetch_metadata(x, keys = NULL, timestamp = NULL,
  ...)

## S3 method for class 'tiledb_group'
fetch_metadata(x, keys = NULL, timestamp = NULL,
  ...)

## S3 method for class 'character'
fetch_metadata(x, keys = NULL, timestamp = NULL,
  ctx = NULL, ...)

Arguments

Details

fetch_metadata() works similar to metadata() but works with a list of key value pairs and returns a list always.

The character method requires a valid URI path.

The methods will not alter the mode of the TileDB object; also, the object will be opened temporarily to access the metadata if it is closed.

Value

A named list of class tdb_metadata.

See Also

set_metadata() and metadata().

Description

Get Group Timestamps

Usage

## S3 method for class 'tiledb_ctx'
group_timestamps(object, tz = "", ...)

## S3 method for class 'tiledb_group'
group_timestamps(object, tz = "", ...)

## S3 method for class 'tiledb_config'
group_timestamps(object, tz = "", ...)

## S3 method for class 'TileDBGroup'
group_timestamps(object, tz = "", from = c("ctx",
  "cfg"), ...)

Arguments

Value

An object of class group_timestamps that is a list with the time range the group is opened at.

See Also

array_timestamps(), set_tiledb_timestamp()

Description

Get or set a metadata key for a TileDB array or group.

Usage

## S3 method for class 'TileDBArray'
metadata(x, which, ...)

## S3 method for class 'TileDBGroup'
metadata(x, which, ...)

## S3 method for class 'tiledb_array'
metadata(x, which, ...)

## S3 method for class 'tiledb_group'
metadata(x, which, ...)

## S3 method for class 'character'
metadata(x, which, ctx = NULL, ...)

## S3 replacement method for class 'TileDBArray'
metadata(x, which, ...) <- value

## S3 replacement method for class 'TileDBGroup'
metadata(x, which, ...) <- value

## S3 replacement method for class 'tiledb_array'
metadata(x, which, ...) <- value

## S3 replacement method for class 'tiledb_group'
metadata(x, which, ...) <- value

## S3 replacement method for class 'character'
metadata(x, which, ctx = NULL, ...) <- value

Arguments

Details

These functions work similar to attr() and provide access to a single metadata key on an TileDB object. The replacement form (setter) puts a metadata key with the value specified or creates a new metadata with the value given.

The character method is intended for a valid URI path.

The methods will not alter the mode of the TileDB object.

For the extractor the object will be opened temporarily to access the metadata if it is closed.

For the replacement, the object will be opened in write mode temporarily and on exit will revert back to previous mode; in the case where the object is already in write mode then it will be reopened at the same mode in order to flush the metadata on disk.

Value

For the extractor, the key value of the metadata matched, or NULL if no exact match is found.

See Also

For a list of metadata and time-travelling use set_metadata() and fetch_metadata().

Description

Open a URI, tiledb::tiledb_array(), tiledb::tiledb_group(), TileDBArray or TileDBGroup at write mode with an optional timestamp.

Usage

## S3 method for class 'TileDBArray'
open_write(object, timestamp = NULL, ctx = NULL, ...)

## S3 method for class 'tiledb_array'
open_write(object, timestamp = NULL, ctx = NULL,
  ...)

## S3 method for class 'TileDBGroup'
open_write(object, timestamp = NULL, ctx = NULL, ...)

## S3 method for class 'tiledb_group'
open_write(object, timestamp = NULL, ctx = NULL,
  ...)

## S3 method for class 'character'
open_write(object, timestamp = NULL, ctx = NULL, ...)

Arguments

Details

Opening a character string should be a valid URI path for a TileDB resource.

Objects other than a URI character are implicitly closed if found opened and re-opened at write mode.

Note that when using the timestamp argument, the TileDBArray, TileDBGroup and their subclasses will have different timestamps from the returning TileDB object. This is by design, you can not write at timestamp using TileDBArray and TileDBGroup interface only via open_write() method.

Value

An object of class tiledb_array or tiledb_group depending on the method; the object is opened in ⁠‘WRITE’⁠ mode.

Description

These functions will set or unset the parameters of TileDB Config object and return the modified configuration object.

Usage

set_config_params(cfg, keyval)

unset_config_params(cfg, keys)

Arguments

Value

The modified tiledb_config object.

See Also

tiledb::tiledb_config()

Examples

origparams <- c("sm.consolidation.timestamp_start" = "100",
                "sm.consolidation.timestamp_end" = "20000")

# Create a context with a config setting the params above
cfg <- tiledb::tiledb_config(origparams)
ctx <- tiledb::tiledb_ctx(config = cfg)

# Do something with ctx

# Get configs from context
cfg <- tiledb::config(ctx)

# New params
params <-  c("sm.consolidation.timestamp_start" = "100",
             "sm.consolidation.timestamp_end" = "10000")

cfg <- set_config_params(cfg, params)

cfg["sm.consolidation.timestamp_end"] # "10000"

# Update context with modified config object
ctx <- tiledb::tiledb_ctx(config = cfg)


# Reset consolidation timestamps
cfg <- unset_config_params(cfg, names(params))

# check the default values
cfg["sm.consolidation.timestamp_start"] # "0"
cfg["sm.consolidation.timestamp_end"]   # "18446744073709551615"

# Update context with modified config object
ctx <- tiledb::tiledb_ctx(config = cfg)

Description

Set or unset consolidation timestamps to the given configuration object.

Usage

set_consolidation_timestamps(cfg, start_time = NULL, end_time = NULL)

unset_consolidation_timestamps(cfg)

Arguments

Value

The modified tiledb_config object.

See Also

set_config_params()

Examples

cfg <- tiledb::tiledb_config()
cfg <- set_consolidation_timestamps(cfg, as.POSIXct(1), as.POSIXct(1000))
cfg["sm.consolidation.timestamp_start"] # 1000 (ms)

# reset
cfg <- unset_consolidation_timestamps(cfg)
cfg["sm.consolidation.timestamp_start"] # 0

Description

Set or unset group opening start, end timestamps to the given configuration object.

Usage

set_group_timestamps(cfg, start_time = NULL, end_time = NULL)

unset_group_timestamps(cfg)

Arguments

Value

The modified tiledb_config object.

See Also

set_config_params()

Examples

cfg <- tiledb::tiledb_config()
cfg <- set_group_timestamps(cfg, as.POSIXct(1), as.POSIXct(1000))
cfg["sm.group.timestamp_start"] # 1000 (ms)

# reset
cfg <- unset_group_timestamps(cfg)
cfg["sm.group.timestamp_start"] # 0

Description

Set metadata using a list of key-value pairs for a TileDB array or group. Optionally, you can write metadata at specific point in time (time-travelling).

Usage

## S3 method for class 'TileDBArray'
set_metadata(x, keys, timestamp = NULL, ...)

## S3 method for class 'TileDBGroup'
set_metadata(x, keys, timestamp = NULL, ...)

## S3 method for class 'tiledb_array'
set_metadata(x, keys, timestamp = NULL, ...)

## S3 method for class 'tiledb_group'
set_metadata(x, keys, timestamp = NULL, ...)

## S3 method for class 'character'
set_metadata(x, keys, timestamp = NULL, ctx = NULL,
  ...)

Arguments

Details

set_metadata() works similar to metadata<-() but works with a list of key value pairs.

The optional argument timestamp can be used to set metadata at specific point in time.

The character method requires a valid URI path.

The methods will not alter the mode of the TileDB object.

The object will be opened in write mode temporarily and on exit will revert back to previous mode; in the case where the object is already in write mode then it will be reopened at the same mode in order to flush the metadata on disk.

Value

A logical TRUE, invisibly.

See Also

fetch_metadata() and metadata().

Description

Define a list of start,end timestamps intended for opening a TileDB object, either at initialisation or via active field tiledb_timestamp.

Usage

set_tiledb_timestamp(start_time, end_time, tz = "")

Arguments

Value

An list object of class tiledb_timestamp.

See Also

TileDBObject

Examples

# Character input
set_tiledb_timestamp("2025-01-01", "2025-08-01", tz = "UTC")

# Numeric input
set_tiledb_timestamp(1000000, 1000000*4, tz = "UTC")

# Date end point
set_tiledb_timestamp(end_time = as.Date("1990-01-01"), tz = "UTC")

# Default
set_tiledb_timestamp(tz = "Europe/London")

# Invalid: start_time > end_time
# set_tiledb_timestamp(start_time = 1, end_time = 0)
# Error: `start_time` is greater than `end_time`.

Description

Functional interface that initialises a TileDBArrayExp instance and opens an array object at READ or WRITE mode.

Usage

tdb_array(uri, mode = "READ", ctx = NULL, tiledb_timestamp = NULL)

Arguments

Value

A TileDBArrayExp, R6 object.

Active bindings

• ctx : A TileDB Context. See tiledb::tiledb_ctx()

• tiledb_timestamp : A TileDB timestamp range that the resource will be opened at. See set_tiledb_timestamp()

• uri : The URI of the TileDB object

• mode: Get the mode of the object: one of the following: "CLOSED", "READ" or "WRITE"

• object_type : The TileDB object type: "ARRAY","GROUP" or "INVALID"

• object : Access the underlying tiledb::tiledb_array() object. When used before open() method, the underlying array will be initialised at "READ" mode and kept open

• 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

• $class()
• $is_open()
• $exists()
• $get_metadata()
• $set_metadata()
• $new()
• $open()
• $close()
• $tiledb_array()
• $schema()
• $schema_info()
• $dimensions()
• $attributes()
• $dimnames()
• $attrnames()
• $colnames()
• $print()
• $create()
• $delete_array()
• $reopen()
• $any_enums()
• $enum_columns()
• $enum_levels()
• $has_enumeration()
• $consolidate()
• $consolidate_async()
• $vacuum()
• $vacuum_async()
• $consolidate_and_vacuum()
• $consolidate_and_vacuum_async()
• $drop_attribute()
• $frag_num()
• $frag_to_vacuum()
• $frag_dump()
• $frag_uris()
• $schema_upgrade()
• $dir_tree()

Examples

## Not run: 
 uri <- tempdir()

 # create demo array on disk
 demo_array_UCBAdmissions(uri)

 arrobj <- tdb_array(uri)

 arrobj$object_type
 #> "ARRAY"

 arrobj$frag_num()
 #> 3

 arrobj$colnames()
 #> "Dept"   "Gender" "Admit"  "Freq"

 arrobj$has_enumeration()
 #> Admit  Freq
 #> TRUE FALSE

## End(Not run)

Description

Given a TileDB schema, it will create an array and instantiate a TileDBArrayExp object. The array will be opened at the given mode and kept opened. It can be accessed via active field ⁠$object⁠.

Usage

tdb_array_create(uri, sch, mode = "WRITE", ctx = NULL)

Arguments

Value

A TileDBArrayExp, R6 object.

Examples

suppressMessages(library(tiledb))

# construct schema
schema <- tiledb_array_schema(
 dom = tiledb_domain(dims = tiledb_dim("id", c(1L, 4L), 4L, "INT32")),
 attrs = tiledb_attr("model", type = "ASCII"))

# uri path
uri <- tempfile()

# create and open array at WRITE mode
arrobj <- tdb_array_create(uri, sch = schema, mode = "WRITE")

arrobj$schema_info()

arrobj$mode # WRITE

Description

Functional interface that initialises a TileDBFragments instance.

Usage

tdb_fragments(uri, ctx = NULL)

Arguments

Value

A TileDBFragments, R6 object.

Active bindings

• uri : The URI of the TileDB object

• fragment_info : Get the TileDB Fragment Info object as returned by tiledb::tiledb_fragment_info.

Methods

Public Methods

• $class()
• $frag_num()
• $frag_uris()
• $reload_finfo()
• $to_vacuum()
• $to_vacuum_num()
• $delete_fragment_range()
• $delete_fragment_list()
• $delete_fragment()
• $get_ifragment()
• $get_first_ifragments()
• $get_last_ifragments()
• $dump()
• $print()

Examples

## Not run: 
uri <- tempdir()
fobj <- demo_array_UCBAdmissions(uri)

# Get metadata information for first fragment
fobj$get_ifragment(1)

## End(Not run)

Description

Functional interface that initialises a TileDBGroupExp instance and opens a group object at READ or WRITE mode.

Usage

tdb_group(uri, mode = "READ", ctx = NULL, tiledb_timestamp = NULL)

Arguments

Value

A TileDBGroupExp, R6 object.

Active bindings

• ctx : A TileDB Context. See tiledb::tiledb_ctx()

• tiledb_timestamp : A TileDB timestamp range that the resource will be opened at. See set_tiledb_timestamp()

• uri : The URI of the TileDB object

• mode: Get the mode of the object: one of the following: "CLOSED", "READ" or "WRITE"

• object_type : The TileDB object type: "ARRAY","GROUP" or "INVALID"

• object : Access the underlying tiledb::tiledb_group() object

• members: Access the list of group members.

• size : Directory size

Methods

Public Methods

• $new()
• $class()
• $is_open()
• $exists()
• $get_metadata()
• $set_metadata()
• $create()
• $open()
• $close()
• $remove()
• $delete()
• $count_members()
• $get_members_df()
• $get_member()
• $set_member()
• $names()
• $member_exists()
• $print()
• $dump()
• $has_non_members()
• $non_members()
• $prune_non_members()
• $delete_group()
• $walk_group()
• $dir_tree()

Examples

## Not run: 
 # uri path
 uri <- tempdir()

 obj <- TileDBGroup$new(uri)

 obj$create()

 obj$close()

 # new instance
 newobj <- tdb_group(uri)

 newobj$is_open() # TRUE

 newobj$mode # "READ"

## End(Not run)

Description

Create a group and instantiate a TileDBGroupExp object. The group will be opened at the given mode and kept opened. It can be accessed via active field ⁠$object⁠.

Usage

tdb_group_create(uri, mode = "WRITE", ctx = NULL)

Arguments

Value

A TileDBGroupExp, R6 object.

Examples

# uri path
uri <- tempfile()

# create and open array at WRITE mode
grpobj <- tdb_group_create(uri,mode = "WRITE")

grpobj$mode # WRITE

grpobj$count_members() # 0

Description

Base class for representing a TileDB Array.

Initialization

A new TileDBArray instance is initialized using the new() method:

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

 unlink(uri)

Value

An object of class TileDBArray, R6.

Super class

TileDBObject -> TileDBArray

Active bindings

Methods

Public methods

• TileDBArray$open()

• TileDBArray$close()

• TileDBArray$tiledb_array()

• TileDBArray$schema()

• TileDBArray$schema_info()

• TileDBArray$dimensions()

• TileDBArray$attributes()

• TileDBArray$dimnames()

• TileDBArray$attrnames()

• TileDBArray$colnames()

• TileDBArray$print()

• TileDBArray$clone()

TileDBArray$open()

Open TileDB array object for read or write.

This methods opens the underlying tiledb::tiledb_array() object in the new mode if it is different from the current mode.

When the new mode and current mode is the same, no action is taken. To force close and then open again use reopen() method.

When a time-stamp is specified, it will be effective in "READ" mode only.

Usage

TileDBArray$open(mode = c("READ", "WRITE"))

Arguments

Returns

The object, invisibly.

TileDBArray$close()

Close the object.

Usage

TileDBArray$close()

Returns

The object, invisibly.

TileDBArray$tiledb_array()

Return a tiledb::tiledb_array object.

If a query_type not provided then it will be inherited from class mode; in case the class mode is "CLOSED", then the query type defaults to "READ".

Usage

TileDBArray$tiledb_array(...)

Arguments

Returns

A tiledb::tiledb_array object.

TileDBArray$schema()

Retrieve the array schema as TileDB schema.

Usage

TileDBArray$schema()

Returns

A tiledb::tiledb_array_schema object.

TileDBArray$schema_info()

Retrieve schema information.

Usage

TileDBArray$schema_info()

Returns

A data.frame object with four column schema information: names, types, status and enum.

TileDBArray$dimensions()

Retrieve the array dimensions.

Usage

TileDBArray$dimensions()

Returns

A named list of tiledb::tiledb_dim objects.

TileDBArray$attributes()

Retrieve the array attributes.

Usage

TileDBArray$attributes()

Returns

A list of tiledb::tiledb_attr objects.

TileDBArray$dimnames()

Retrieve dimension names.

Usage

TileDBArray$dimnames()

Returns

A character vector with the array's dimension names.

TileDBArray$attrnames()

Retrieve attribute names.

Usage

TileDBArray$attrnames()

Returns

A character vector with the array's attribute names.

TileDBArray$colnames()

Retrieve the names of all columns, including dimensions and attributes.

Usage

TileDBArray$colnames()

Returns

A character vector with the array's column names.

TileDBArray$print()

Print summary of the array.

Usage

TileDBArray$print()

TileDBArray$clone()

The objects of this class are cloneable with this method.

Usage

TileDBArray$clone(deep = FALSE)

Arguments

Description

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

TileDBObject -> TileDBArray -> TileDBArrayExp

Active bindings

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()

TileDBArrayExp$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

Returns

The object, invisibly.

TileDBArrayExp$delete_array()

Delete the array.

Usage

TileDBArrayExp$delete_array()

Returns

The object, invisibly.

TileDBArrayExp$reopen()

Close and reopen the TileDB object in a new mode.

Usage

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

Arguments

Returns

The object, invisibly.

TileDBArrayExp$any_enums()

Checks array for factors (enumerations).

Usage

TileDBArrayExp$any_enums()

Returns

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

TileDBArrayExp$enum_columns()

Retrieve factor columns (attributes).

Usage

TileDBArrayExp$enum_columns()

Returns

A character vector with factor columns (enumeration attributes).

TileDBArrayExp$enum_levels()

Retrieve factor levels for a given attribute.

Usage

TileDBArrayExp$enum_levels(x)

Arguments

Returns

A character vector with levels (enumeration values).

TileDBArrayExp$has_enumeration()

Check columns for factors.

Usage

TileDBArrayExp$has_enumeration()

Returns

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

TileDBArrayExp$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

Returns

TRUE, invisibly.

TileDBArrayExp$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

Returns

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

TileDBArrayExp$vacuum()

Clean up consolidated fragments and array metadata.

Usage

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

Arguments

Returns

TRUE, invisibly.

TileDBArrayExp$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

Returns

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

TileDBArrayExp$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

Returns

TRUE, invisibly.

TileDBArrayExp$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

Returns

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

TileDBArrayExp$drop_attribute()

Remove an attribute from array.

Usage

TileDBArrayExp$drop_attribute(x)

Arguments

Returns

The object, invisibly.

TileDBArrayExp$frag_num()

The number of fragments.

Usage

TileDBArrayExp$frag_num()

TileDBArrayExp$frag_to_vacuum()

Consolidated fragments to be removed.

Usage

TileDBArrayExp$frag_to_vacuum(trunc_uri = TRUE)

Arguments

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.

TileDBArrayExp$frag_dump()

Dump to console the commit fragments.

Usage

TileDBArrayExp$frag_dump()

TileDBArrayExp$frag_uris()

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

Usage

TileDBArrayExp$frag_uris(trunc_uri = TRUE)

Arguments

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.

TileDBArrayExp$schema_upgrade()

Upgrade the array to the latest format version.

Usage

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

Arguments

TileDBArrayExp$dir_tree()

Print directory contents.

Usage

TileDBArrayExp$dir_tree(recursive = TRUE)

Arguments

Returns

A character vector with file paths, invisibly.

TileDBArrayExp$clone()

The objects of this class are cloneable with this method.

Usage

TileDBArrayExp$clone(deep = FALSE)

Arguments

Description

A class for working with TileDB Fragments.

Initialization

A new TileDBFragments instance is initialised using the new() method or with the functional interface tdb_fragments().

Value

An object of class TileDBFragments, R6.

Active bindings

Methods

Public methods

• TileDBFragments$new()

• TileDBFragments$class()

• TileDBFragments$frag_num()

• TileDBFragments$frag_uris()

• TileDBFragments$reload_finfo()

• TileDBFragments$to_vacuum()

• TileDBFragments$to_vacuum_num()

• TileDBFragments$delete_fragment_range()

• TileDBFragments$delete_fragment_list()

• TileDBFragments$delete_fragment()

• TileDBFragments$get_ifragment()

• TileDBFragments$get_first_ifragments()

• TileDBFragments$get_last_ifragments()

• TileDBFragments$dump()

• TileDBFragments$print()

TileDBFragments$new()

Create a new TileDBFragments instance.

Usage

TileDBFragments$new(uri, ctx = NULL)

Arguments

TileDBFragments$class()

Print the name of the R6 class.

Usage

TileDBFragments$class()

TileDBFragments$frag_num()

Get the number of fragments.

Usage

TileDBFragments$frag_num()

Returns

A numeric value.

TileDBFragments$frag_uris()

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

Usage

TileDBFragments$frag_uris(trunc_uri = TRUE)

Arguments

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.

TileDBFragments$reload_finfo()

Refresh the TileDB Fragment Info object.

Usage

TileDBFragments$reload_finfo()

Returns

The object, invisibly.

TileDBFragments$to_vacuum()

Consolidated fragments to be removed.

Usage

TileDBFragments$to_vacuum(trunc_uri = TRUE)

Arguments

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.

TileDBFragments$to_vacuum_num()

Return the number of fragments to vacuum

Usage

TileDBFragments$to_vacuum_num()

Returns

A numeric value.

TileDBFragments$delete_fragment_range()

Delete fragments using a time-stamp range.

Usage

TileDBFragments$delete_fragment_range(start_time, end_time)

Arguments

Returns

A logical TRUE, invisibly. Note that if time stamps fall outside fragments' time range no deletion will incur.

TileDBFragments$delete_fragment_list()

Delete fragments using a vector of fragment uris.

Use ⁠$frag_uris(trunc_uri = FALSE)⁠ method to get a data.frame with all fragment uri paths.

Usage

TileDBFragments$delete_fragment_list(frag_uris)

Arguments

Returns

TRUE for successful deletion, invisibly.

TileDBFragments$delete_fragment()

Delete a fragment by index.

Usage

TileDBFragments$delete_fragment(n)

Arguments

Returns

A boolean, invisibly. TRUE for successful deletion and FALSE for no fragment to delete.

TileDBFragments$get_ifragment()

Get a fragment by index.

Usage

TileDBFragments$get_ifragment(fid)

Arguments

Returns

An object of class ifragment.

TileDBFragments$get_first_ifragments()

Get the first n fragments.

Usage

TileDBFragments$get_first_ifragments(n)

Arguments

Returns

An object of class ifragment_list.

TileDBFragments$get_last_ifragments()

Get the last n fragments.

Usage

TileDBFragments$get_last_ifragments(n)

Arguments

Returns

An object of class ifragment_list.

TileDBFragments$dump()

Dump to console the commit fragments.

Usage

TileDBFragments$dump()

TileDBFragments$print()

Print Fragments class.

Usage

TileDBFragments$print()

Description

Base class for representing a TileDB Group.

Initialization

A new TileDBGroup instance is initialized using the new() method:

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

 unlink(uri)

Value

An object of class TileDBGroup, R6.

Super class

TileDBObject -> TileDBGroup

Active bindings

Methods

Public methods

• TileDBGroup$create()

• TileDBGroup$open()

• TileDBGroup$close()

• TileDBGroup$remove()

• TileDBGroup$delete()

• TileDBGroup$count_members()

• TileDBGroup$get_members_df()

• TileDBGroup$get_member()

• TileDBGroup$set_member()

• TileDBGroup$names()

• TileDBGroup$member_exists()

• TileDBGroup$print()

• TileDBGroup$dump()

• TileDBGroup$clone()

TileDBGroup$create()

Create a TileDB Group object at the given URI path.

Usage

TileDBGroup$create(mode = "WRITE")

Arguments

Returns

The object, invisibly.

TileDBGroup$open()

Open TileDB group object in read or write mode.

Usage

TileDBGroup$open(mode = c("READ", "WRITE"))

Arguments

Returns

The object, invisibly.

TileDBGroup$close()

Close the group object.

All instantiated group members will be closed if opened, and before closing the group object.

Usage

TileDBGroup$close()

Returns

The object, invisibly.

TileDBGroup$remove()

Remove member.

Removes an array or group resource from TileDBGroup member list.

Usage

TileDBGroup$remove(name)

Arguments

Returns

The object, invisibly.

TileDBGroup$delete()

Delete member.

Deletes a TileDBGroup's member from disk and removes it from member list.

Usage

TileDBGroup$delete(name)

Arguments

Returns

The object, invisibly.

TileDBGroup$count_members()

Count the number of members in the group.

Usage

TileDBGroup$count_members()

Returns

The number of members in the group.

TileDBGroup$get_members_df()

List group members.

Usage

TileDBGroup$get_members_df(type = c("ALL", "GROUP", "ARRAY"))

Arguments

Returns

A data.frame with columns name, type, and uri.

TileDBGroup$get_member()

Retrieve a group member by name. If the member isn't already open, it is opened in the same mode as the parent.

Usage

TileDBGroup$get_member(name)

Arguments

Returns

A TileDBArray or TileDBGroup.

TileDBGroup$set_member()

Add new member to the group.

Usage

TileDBGroup$set_member(object, name = NULL, relative = NULL)

Arguments

Returns

The object, invisibly.

TileDBGroup$names()

Retrieve the members' names.

Usage

TileDBGroup$names()

Returns

A character vector of member names.

TileDBGroup$member_exists()

Check if a member exists.

Usage

TileDBGroup$member_exists(name)

Arguments

Returns

A logical value.

TileDBGroup$print()

Print summary of the group.

Usage

TileDBGroup$print()

TileDBGroup$dump()

Dump the TileDB Group structure to string.

Usage

TileDBGroup$dump(title = "TileDB Directory", recursive = TRUE)

Arguments

Returns

A character string, invisibly.

TileDBGroup$clone()

The objects of this class are cloneable with this method.

Usage

TileDBGroup$clone(deep = FALSE)

Arguments

Description

An enhanced version of TileDBGroup with additional methods to operate on the group.

Initialization

A new TileDBGroupExp instance is initialised using the new() method. Alternatively use tdb_group() to create a new instance and open the group at READ mode.

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

 unlink(uri)

Value

An object of class TileDBGroupExp, R6.

Super classes

TileDBObject -> TileDBGroup -> TileDBGroupExp

Active bindings

Methods

Public methods

• TileDBGroupExp$has_non_members()

• TileDBGroupExp$non_members()

• TileDBGroupExp$prune_non_members()

• TileDBGroupExp$delete_group()

• TileDBGroupExp$walk_group()

• TileDBGroupExp$dir_tree()

• TileDBGroupExp$clone()

TileDBGroupExp$has_non_members()

Checks for non group members at group's uri path.

This function compares the TileDB resources at group's uri path to its members to determine if there are any non member.

Usage

TileDBGroupExp$has_non_members()

Returns

TRUE for having non members, FALSE otherwise.

TileDBGroupExp$non_members()

List TileDB resources which are not members at group's uri path.

This function compares the TileDB resources at group's uri path to its members and returns a data.frame with non members object type and uri path.

Usage

TileDBGroupExp$non_members()

Returns

An object of class data.frame with columns TYPE and URI of non member TileDB resources.

TileDBGroupExp$prune_non_members()

Delete TileDB resources which are not members.

Usage

TileDBGroupExp$prune_non_members()

Returns

An character vector of deleted uri paths.

TileDBGroupExp$delete_group()

Delete written data from Group.

This function deletes all written data from a tiledb_group object, i.e., the folder will not be consider as a TileDB Group after the operation. Any other data will not be deleted unless we set recursive = TRUE.

Usage

TileDBGroupExp$delete_group(recursive = FALSE)

Arguments

Returns

The object, invisibly.

TileDBGroupExp$walk_group()

List all TileDB resources at group's uri path.

Usage

TileDBGroupExp$walk_group(order = c("pre", "post"))

Arguments

Returns

An object of class data.frame with columns TYPE and URI with all TileDB resources under group's uri path.

TileDBGroupExp$dir_tree()

Print directory contents.

Usage

TileDBGroupExp$dir_tree(recursive = TRUE)

Arguments

Returns

A character vector with file paths, invisibly.

TileDBGroupExp$clone()

The objects of this class are cloneable with this method.

Usage

TileDBGroupExp$clone(deep = FALSE)

Arguments

Description

A modified version of fs::dir_tree() to work with TileDB VFS.

Usage

vfs_dir_tree(uri, recursive = TRUE, vfs = NULL)

Arguments

Value

A character vector with file paths, invisibly.

Examples

## Not run: 
# URI path
uri <- tempfile()

# Demo array
demo_array_UCBAdmissions(uri)

# Array instance
arrobj <- tdb_array(uri)

# Print directory contents
arrobj$dir_tree()

## End(Not run)

Description

VFS Directory Size

Usage

vfs_size(uri, vfs = NULL)

Arguments

Value

The size of the directory.

Examples

## Not run: 
# URI path
uri <- tempfile()

# Demo array
demo_UCBAdmissions_array(uri)

# Directory size
vfs_size(uri)

## End(Not run)