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Apply styler::style_pkg() #778

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merged 7 commits into from
Oct 29, 2024
Merged

Apply styler::style_pkg() #778

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5f66a52
Apply `styler::style_pkg()`
johnkerl Oct 25, 2024
10c6357
devtools::document
johnkerl Oct 25, 2024
1679531
DESCRIPTION NEWS.md
johnkerl Oct 25, 2024
498e8e9
neatens
johnkerl Oct 28, 2024
12609e0
Merge branch 'main' into kerl/styler-style-pkg
johnkerl Oct 29, 2024
bc8f020
Fix incorrect styler formatting
mojaveazure Oct 29, 2024
6d8a8d5
DESCRIPTION and NEWS.md [skip ci]
johnkerl Oct 29, 2024
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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: tiledb
Type: Package
Version: 0.30.2.1
Version: 0.30.2.2
Title: Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays
Authors@R: c(
person("TileDB, Inc.", role = c("aut", "cph")),
Expand Down
1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -4,6 +4,7 @@
* Run `clang-format` on non-autogen C++ source code
* Update unit tests to expect dense current domain
* Support parentheses in query conditions
* memory alloc: Accomodate zero buffer size estimate v2

# tiledb 0.30.2

Expand Down
199 changes: 120 additions & 79 deletions R/Array.R
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,9 @@
#' in case the array should be encryption.
#'
#' @examples
#' \dontshow{ctx <- tiledb_ctx(limitTileDBCores())}
#' \dontshow{
#' ctx <- tiledb_ctx(limitTileDBCores())
#' }
#' \dontrun{
#' pth <- tempdir()
#' dom <- tiledb_domain(dims = c(tiledb_dim("d1", c(1L, 10L), type = "INT32")))
Expand All @@ -38,26 +40,28 @@
#' }
#'
#' @export
tiledb_array_create <- function(uri, schema, encryption_key) { #, ctx = tiledb_get_context()) {
stopifnot("The 'uri' argument must be a string scalar" = !missing(uri) && is.scalar(uri, "character"),
"The 'schema' argument must be a tiledb_array_schema object" = !missing(schema) && is(schema, "tiledb_array_schema"))
if (!missing(encryption_key)) {
## old interface
needreset <- FALSE
config <- oldconfig <- tiledb_config()
if (config["sm.encryption_type"] != "AES_256_GCM" ||
config["sm.encryption_key"] != encryption_key) {
config["sm.encryption_type"] <- "AES_256_GCM"
config["sm.encryption_key"] <- encryption_key
ctx <- tiledb::tiledb_ctx(config)
needreset <- TRUE
}
uri <- libtiledb_array_create(uri, schema@ptr)
if (needreset) ctx <- tiledb::tiledb_ctx(oldconfig)
invisible(uri)
} else {
invisible(libtiledb_array_create(uri, schema@ptr))
tiledb_array_create <- function(uri, schema, encryption_key) { # , ctx = tiledb_get_context()) {
stopifnot(
"The 'uri' argument must be a string scalar" = !missing(uri) && is.scalar(uri, "character"),
"The 'schema' argument must be a tiledb_array_schema object" = !missing(schema) && is(schema, "tiledb_array_schema")
)
if (!missing(encryption_key)) {
## old interface
needreset <- FALSE
config <- oldconfig <- tiledb_config()
if (config["sm.encryption_type"] != "AES_256_GCM" ||
config["sm.encryption_key"] != encryption_key) {
config["sm.encryption_type"] <- "AES_256_GCM"
config["sm.encryption_key"] <- encryption_key
ctx <- tiledb::tiledb_ctx(config)
needreset <- TRUE
}
uri <- libtiledb_array_create(uri, schema@ptr)
if (needreset) ctx <- tiledb::tiledb_ctx(oldconfig)
invisible(uri)
} else {
invisible(libtiledb_array_create(uri, schema@ptr))
}
}

##' Open a TileDB Array
Expand All @@ -68,11 +72,14 @@ tiledb_array_create <- function(uri, schema, encryption_key) { #, ctx = tiledb_g
##' @return The TileDB Array object but opened for reading or writing
##' @importFrom methods .hasSlot
##' @export
tiledb_array_open <- function(arr,
type = if (tiledb_version(TRUE) >= "2.12.0")
c("READ", "WRITE", "DELETE", "MODIFY_EXCLUSIVE")
else
c("READ", "WRITE")) {
tiledb_array_open <- function(
arr,
type = if (tiledb_version(TRUE) >= "2.12.0") {
c("READ", "WRITE", "DELETE", "MODIFY_EXCLUSIVE")
} else {
c("READ", "WRITE")
}
) {
stopifnot("The 'arr' argument must be a tiledb_array object" = .isArray(arr))
type <- match.arg(type)

Expand All @@ -92,9 +99,11 @@ tiledb_array_open <- function(arr,
##' @param timestamp A Datetime object that will be converted to millisecond granularity
##' @return The TileDB Array object but opened for reading or writing
##' @export
tiledb_array_open_at <- function(arr, type=c("READ","WRITE"), timestamp) {
stopifnot("The 'arr' argument must be a tiledb_array object" = .isArray(arr),
"The 'timestamp' argument must be a time object" = inherits(timestamp, "POSIXct"))
tiledb_array_open_at <- function(arr, type = c("READ", "WRITE"), timestamp) {
stopifnot(
"The 'arr' argument must be a tiledb_array object" = .isArray(arr),
"The 'timestamp' argument must be a time object" = inherits(timestamp, "POSIXct")
)
type <- match.arg(type)
ctx <- tiledb_get_context()
if (.hasSlot(arr, "encryption_key") && length(arr@encryption_key) > 0) {
Expand Down Expand Up @@ -123,8 +132,8 @@ tiledb_array_close <- function(arr) {
##' @return A boolean indicating whether the TileDB Array object is open
##' @export
tiledb_array_is_open <- function(arr) {
stopifnot("The 'arr' argument must be a tiledb_array object" = .isArray(arr))
libtiledb_array_is_open(arr@ptr)
stopifnot("The 'arr' argument must be a tiledb_array object" = .isArray(arr))
libtiledb_array_is_open(arr@ptr)
}

##' Check for Homogeneous Domain
Expand All @@ -137,8 +146,10 @@ tiledb_array_is_homogeneous <- function(arr) {
## there is a non-exported call at the C level we could use instead
sch <- schema(arr)
dom <- domain(sch)
domaintype <- sapply(libtiledb_domain_get_dimensions(dom@ptr),
libtiledb_dim_get_datatype)
domaintype <- sapply(
libtiledb_domain_get_dimensions(dom@ptr),
libtiledb_dim_get_datatype
)
n <- length(unique(domaintype))
n == 1
}
Expand All @@ -153,8 +164,10 @@ tiledb_array_is_heterogeneous <- function(arr) {
## there is a non-exported call at the C level we could use instead
sch <- schema(arr)
dom <- domain(sch)
domaintype <- sapply(libtiledb_domain_get_dimensions(dom@ptr),
libtiledb_dim_get_datatype)
domaintype <- sapply(
libtiledb_domain_get_dimensions(dom@ptr),
libtiledb_dim_get_datatype
)
n <- length(unique(domaintype))
n > 1
}
Expand All @@ -167,30 +180,44 @@ tiledb_array_is_heterogeneous <- function(arr) {
##' @param ctx A tiledb_ctx object (optional)
##' @return A boolean indicating success
##' @export
tiledb_array_delete_fragments <- function(arr, ts_start, ts_end, ctx = tiledb_get_context()) {
stopifnot("The 'arr' argument must be a tiledb_array object" = .isArray(arr),
"The 'ts_start' argument must be a time object" = inherits(ts_start, "POSIXct"),
"The 'ts_end' argument must be a time object" = inherits(ts_end, "POSIXct"))
libtiledb_array_delete_fragments(ctx@ptr, arr@ptr, ts_start, ts_end)
invisible(TRUE)
tiledb_array_delete_fragments <- function(
arr,
ts_start,
ts_end,
ctx = tiledb_get_context()
) {
stopifnot(
"The 'arr' argument must be a tiledb_array object" = .isArray(arr),
"The 'ts_start' argument must be a time object" = inherits(ts_start, "POSIXct"),
"The 'ts_end' argument must be a time object" = inherits(ts_end, "POSIXct")
)
libtiledb_array_delete_fragments(ctx@ptr, arr@ptr, ts_start, ts_end)
invisible(TRUE)
}

##' Delete fragments written given by their URIs
##'
##' @param arr A TileDB Array object as for example returned by \code{tiledb_array()}
##' @param arr A TileDB Array object as for example returned by
##' \code{tiledb_array()}
##' @param fragments A character vector with fragment URIs
##' @param ctx A tiledb_ctx object (optional)
##' @return A boolean indicating success
##' @export
tiledb_array_delete_fragments_list <- function(arr, fragments, ctx = tiledb_get_context()) {
stopifnot("The 'arr' argument must be a tiledb_array object" = .isArray(arr),
"The 'fragments' argument must be a character vector" = is.character(fragments))
if (tiledb_version(TRUE) >= "2.18.0") {
libtiledb_array_delete_fragments_list(ctx@ptr, arr@ptr, fragments)
} else {
message("This function is only available with TileDB 2.18.0 or later")
}
invisible(TRUE)
tiledb_array_delete_fragments_list <- function(
arr,
fragments,
ctx = tiledb_get_context()
) {
stopifnot(
"The 'arr' argument must be a tiledb_array object" = .isArray(arr),
"The 'fragments' argument must be a character vector" = is.character(fragments)
)
if (tiledb_version(TRUE) >= "2.18.0") {
libtiledb_array_delete_fragments_list(ctx@ptr, arr@ptr, fragments)
} else {
message("This function is only available with TileDB 2.18.0 or later")
}
invisible(TRUE)
}

##' Check for Enumeration (aka Factor aka Dictionary)
Expand All @@ -199,13 +226,13 @@ tiledb_array_delete_fragments_list <- function(arr, fragments, ctx = tiledb_get_
##' @return A boolean indicating if the array has homogeneous domains
##' @export
tiledb_array_has_enumeration <- function(arr) {
stopifnot("The 'arr' argument must be a tiledb_array object" = .isArray(arr))
ctx <- tiledb_get_context()
if (!tiledb_array_is_open(arr)) {
arr <- tiledb_array_open(arr, "READ")
on.exit(tiledb_array_close(arr))
}
return(libtiledb_array_has_enumeration_vector(ctx@ptr, arr@ptr))
stopifnot("The 'arr' argument must be a tiledb_array object" = .isArray(arr))
ctx <- tiledb_get_context()
if (!tiledb_array_is_open(arr)) {
arr <- tiledb_array_open(arr, "READ")
on.exit(tiledb_array_close(arr))
}
return(libtiledb_array_has_enumeration_vector(ctx@ptr, arr@ptr))
}

##' Run an aggregate query on the given (sparse) array and attribute
Expand All @@ -219,27 +246,33 @@ tiledb_array_has_enumeration <- function(arr) {
##' @param nullable A boolean toggle whether the attribute is nullable
##' @return The value of the aggregation
##' @export
tiledb_array_apply_aggregate <- function(array, attrname,
operation = c("Count", "NullCount", "Min", "Max",
"Mean", "Sum"),
nullable = TRUE) {
stopifnot("The 'array' argument must be a TileDB Array object" = is(array, "tiledb_array"),
"The 'array' must be a sparse TileDB Array" = is.sparse(schema(array)),
"The 'attrname' argument must be character" = is.character(attrname),
"The 'operation' argument must be character" = is.character(operation),
"The 'nullable' argument must be logical" = is.logical(nullable))
tiledb_array_apply_aggregate <- function(
array,
attrname,
operation = c("Count", "NullCount", "Min", "Max", "Mean", "Sum"),
nullable = TRUE
) {
stopifnot(
"The 'array' argument must be a TileDB Array object" = is(array, "tiledb_array"),
"The 'array' must be a sparse TileDB Array" = is.sparse(schema(array)),
"The 'attrname' argument must be character" = is.character(attrname),
"The 'operation' argument must be character" = is.character(operation),
"The 'nullable' argument must be logical" = is.logical(nullable)
)

operation <- match.arg(operation)
operation <- match.arg(operation)

if (tiledb_array_is_open(array))
array <- tiledb_array_close(array)
if (tiledb_array_is_open(array)) {
array <- tiledb_array_close(array)
}

query <- tiledb_query(array, "READ")
query <- tiledb_query(array, "READ")

if (! tiledb_query_get_layout(query) %in% c("UNORDERED", "GLOBAL_ORDER"))
query <- tiledb_query_set_layout(query, "UNORDERED")
if (!tiledb_query_get_layout(query) %in% c("UNORDERED", "GLOBAL_ORDER")) {
query <- tiledb_query_set_layout(query, "UNORDERED")
}

libtiledb_query_apply_aggregate(query@ptr, attrname, operation, nullable)
libtiledb_query_apply_aggregate(query@ptr, attrname, operation, nullable)
}

##' Upgrade an Array to the current TileDB Array Schema Format
Expand All @@ -249,10 +282,18 @@ tiledb_array_apply_aggregate <- function(array, attrname,
##' @param ctx A tiledb_ctx object (optional)
##' @return Nothing is returned as the function is invoked for its side effect
##' @export
tiledb_array_upgrade_version <- function(array, config = NULL, ctx = tiledb_get_context()) {
stopifnot("The 'array' argument must be a TileDB Array object" = is(array, "tiledb_array"),
"The 'config' argument must be NULL or a TileDB Config" =
is.null(config) || is(config, "tiledb_config"))
libtiledb_array_upgrade_version(ctx@ptr, array@ptr, array@uri,
if (is.null(config)) NULL else config@ptr)
tiledb_array_upgrade_version <- function(
array,
config = NULL,
ctx = tiledb_get_context()
) {
stopifnot(
"The 'array' argument must be a TileDB Array object" = is(array, "tiledb_array"),
"The 'config' argument must be NULL or a TileDB Config" =
is.null(config) || is(config, "tiledb_config")
)
libtiledb_array_upgrade_version(
ctx@ptr, array@ptr, array@uri,
if (is.null(config)) NULL else config@ptr
)
}
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