TileDBCreateOptions

Provides strongly-typed access and default values for platform_config options stored under the “tiledb” \(\rightarrow\) “create” mapping keys.

Intended for internal use only.

Super class

tiledbsoma::MappingBase -> TileDBCreateOptions

Methods

Public methods

• TileDBCreateOptions$new()

• TileDBCreateOptions$cell_tile_orders()

• TileDBCreateOptions$dim_tile()

• TileDBCreateOptions$capacity()

• TileDBCreateOptions$allows_duplicates()

• TileDBCreateOptions$dataframe_dim_zstd_level()

• TileDBCreateOptions$sparse_nd_array_dim_zstd_level()

• TileDBCreateOptions$dense_nd_array_dim_zstd_level()

• TileDBCreateOptions$offsets_filters()

• TileDBCreateOptions$validity_filters()

• TileDBCreateOptions$dim_filters()

• TileDBCreateOptions$attr_filters()

• TileDBCreateOptions$write_X_chunked()

• TileDBCreateOptions$goal_chunk_nnz()

• TileDBCreateOptions$to_list()

• TileDBCreateOptions$clone()

Inherited methods

• tiledbsoma::MappingBase$get()
• tiledbsoma::MappingBase$items()
• tiledbsoma::MappingBase$keys()
• tiledbsoma::MappingBase$length()
• tiledbsoma::MappingBase$print()
• tiledbsoma::MappingBase$remove()
• tiledbsoma::MappingBase$set()
• tiledbsoma::MappingBase$setv()
• tiledbsoma::MappingBase$update()
• tiledbsoma::MappingBase$values()

---

Method new()

Create a TileDBCreateOptions object

Usage

TileDBCreateOptions$new(platform_config = NULL)

Arguments

platform_config

A platform configuration object

---

Method cell_tile_orders()

Returns the cell and tile orders that should be used. If neither cell_order nor tile_order is present, only in this case will we use the default values provided.

Usage

TileDBCreateOptions$cell_tile_orders()

Returns

A two-length character vector with names of “cell_order” and “tile_order”

---

Method dim_tile()

Usage

TileDBCreateOptions$dim_tile(dim_name, default = 2048)

Arguments

dim_name

Name of dimension to get tiling for

default

Default tiling if dim_name is not set

Returns

int

Examples

cfg <- PlatformConfig$new()
cfg$set(
  platform = 'tiledb',
  param = 'create',
  key = 'dims',
  value = list(soma_dim_0 = list(tile = 999))
)
(tdco <- TileDBCreateOptions$new(cfg))
tdco$dim_tile("soma_dim_0")
tdco$dim_tile("soma_dim_1")

---

Method capacity()

Usage

TileDBCreateOptions$capacity()

Returns

int

---

Method allows_duplicates()

Usage

TileDBCreateOptions$allows_duplicates()

Returns

bool

---

Method dataframe_dim_zstd_level()

Usage

TileDBCreateOptions$dataframe_dim_zstd_level()

Returns

int

---

Method sparse_nd_array_dim_zstd_level()

Usage

TileDBCreateOptions$sparse_nd_array_dim_zstd_level()

Returns

int

---

Method dense_nd_array_dim_zstd_level()

Usage

TileDBCreateOptions$dense_nd_array_dim_zstd_level()

Returns

int

---

Method offsets_filters()

Usage

TileDBCreateOptions$offsets_filters(default = list())

Arguments

default

Default offset filters to use if not currently set

Returns

A list of tiledb_filter objects

---

Method validity_filters()

Usage

TileDBCreateOptions$validity_filters(default = list())

Arguments

default

Default validity filters to use if not currently set

Returns

A list of tiledb_filter objects

---

Method dim_filters()

Usage

TileDBCreateOptions$dim_filters(dim_name, default = list())

Arguments

dim_name

Name of dimension to get filters for

default

Default filters to use for if not currently set

Returns

A list of tiledb_filter objects

Examples

filters <- list(
  soma_dim_0 = list(tile = 100, filters = list("RLE")),
  soma_dim_1 = list(tile = 200, filters = list("RLE", list(name = "ZSTD", COMPRESSION_LEVEL = 9)))
)
cfg <- PlatformConfig$new()
cfg$set(platform = 'tiledb', param = 'create', key = 'dims', value = filters)
(tdco <- TileDBCreateOptions$new(cfg))
tdco$dim_filters("soma_dim_0")
tdco$dim_filters("non-existant")

---

Method attr_filters()

Usage

TileDBCreateOptions$attr_filters(attr_name, default = list())

Arguments

attr_name

Name of attribute

default

Default filters to use if not currently set

Returns

A list of tiledb_filter objects

Examples

filters <- list(
  soma_data_a = list(filters = list("RLE")),
  soma_data_b = list(filters = list("RLE", list(name = "ZSTD", COMPRESSION_LEVEL = 9)))
)
cfg <- PlatformConfig$new()
cfg$set(platform = 'tiledb', param = 'create', key = 'attrs', value = filters)
(tdco <- TileDBCreateOptions$new(cfg))
tdco$attr_filters("soma_data_b")
tdco$attr_filters("non-existant")

---

Method write_X_chunked()

Usage

TileDBCreateOptions$write_X_chunked()

Returns

bool

---

Method goal_chunk_nnz()

Usage

TileDBCreateOptions$goal_chunk_nnz()

Returns

int

---

Method to_list()

...

Usage

TileDBCreateOptions$to_list(build_filters = TRUE)

Arguments

build_filters

Build filters into tiledb_filter objects. If set to FALSE, JSON strings are created instead of filter objects.

Returns

The 'create options' as a list

---

Method clone()

The objects of this class are cloneable with this method.

Usage

TileDBCreateOptions$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `TileDBCreateOptions$dim_tile`
## ------------------------------------------------

cfg <- PlatformConfig$new()
cfg$set(
  platform = 'tiledb',
  param = 'create',
  key = 'dims',
  value = list(soma_dim_0 = list(tile = 999))
)
(tdco <- TileDBCreateOptions$new(cfg))
#> <TileDBCreateOptions>
#>   dims: list(soma_dim_0 = list(tile = 999))
#>   tile_order: ROW_MAJOR
#>   cell_order: ROW_MAJOR
#>   capacity: 1e+05
#>   allows_duplicates: FALSE
#>   dataframe_dim_zstd_level: 3
#>   sparse_nd_array_dim_zstd_level: 3
#>   dense_nd_array_dim_zstd_level: 3
#>   offsets_filters: list("DOUBLE_DELTA", "BIT_WIDTH_REDUCTION", "ZSTD")
#>   write_X_chunked: TRUE
#>   goal_chunk_nnz: 2e+08
tdco$dim_tile("soma_dim_0")
#> [1] 999
tdco$dim_tile("soma_dim_1")
#> [1] 2048


## ------------------------------------------------
## Method `TileDBCreateOptions$dim_filters`
## ------------------------------------------------

filters <- list(
  soma_dim_0 = list(tile = 100, filters = list("RLE")),
  soma_dim_1 = list(tile = 200, filters = list("RLE", list(name = "ZSTD", COMPRESSION_LEVEL = 9)))
)
cfg <- PlatformConfig$new()
cfg$set(platform = 'tiledb', param = 'create', key = 'dims', value = filters)
(tdco <- TileDBCreateOptions$new(cfg))
#> <TileDBCreateOptions>
#>   dims: list(soma_dim_0 = list(tile = 100, filters = list("RLE")), soma_dim_1 = list(tile = 200, filters = list("RLE", list(name = "ZSTD", COMPRESSION_LEVEL = 9))))
#>   tile_order: ROW_MAJOR
#>   cell_order: ROW_MAJOR
#>   capacity: 1e+05
#>   allows_duplicates: FALSE
#>   dataframe_dim_zstd_level: 3
#>   sparse_nd_array_dim_zstd_level: 3
#>   dense_nd_array_dim_zstd_level: 3
#>   offsets_filters: list("DOUBLE_DELTA", "BIT_WIDTH_REDUCTION", "ZSTD")
#>   write_X_chunked: TRUE
#>   goal_chunk_nnz: 2e+08
tdco$dim_filters("soma_dim_0")
#> [[1]]
#> tiledb_filter_set_option(tiledb_filter("RLE"),"COMPRESSION_LEVEL",-1) 
#> 
tdco$dim_filters("non-existant")
#> list()


## ------------------------------------------------
## Method `TileDBCreateOptions$attr_filters`
## ------------------------------------------------

filters <- list(
  soma_data_a = list(filters = list("RLE")),
  soma_data_b = list(filters = list("RLE", list(name = "ZSTD", COMPRESSION_LEVEL = 9)))
)
cfg <- PlatformConfig$new()
cfg$set(platform = 'tiledb', param = 'create', key = 'attrs', value = filters)
(tdco <- TileDBCreateOptions$new(cfg))
#> <TileDBCreateOptions>
#>   attrs: list(soma_data_a = list(filters = list("RLE")), soma_data_b = list(filters = list("RLE", list(name = "ZSTD", COMPRESSION_LEVEL = 9))))
#>   tile_order: ROW_MAJOR
#>   cell_order: ROW_MAJOR
#>   capacity: 1e+05
#>   allows_duplicates: FALSE
#>   dataframe_dim_zstd_level: 3
#>   sparse_nd_array_dim_zstd_level: 3
#>   dense_nd_array_dim_zstd_level: 3
#>   offsets_filters: list("DOUBLE_DELTA", "BIT_WIDTH_REDUCTION", "ZSTD")
#>   write_X_chunked: TRUE
#>   goal_chunk_nnz: 2e+08
tdco$attr_filters("soma_data_b")
#> [[1]]
#> tiledb_filter_set_option(tiledb_filter("RLE"),"COMPRESSION_LEVEL",-1) 
#> 
#> [[2]]
#> tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",9) 
#> 
tdco$attr_filters("non-existant")
#> list()