ARROW-9870: [R] Friendly interface for filesystems (S3)#8351

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ARROW-9870: [R] Friendly interface for filesystems (S3) #8351

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2dbfe8c
Revise dataset vignette to start thinking about UX
nealrichardson Sep 11, 2020
5e85269
More design by wishful thinking
nealrichardson Sep 27, 2020
ac8f7b0
Add SubTreeFileSystem base_fs and base_path properties
nealrichardson Sep 27, 2020
412c544
File writers and open_dataset now accept SubTreeFileSystem as path input
nealrichardson Oct 5, 2020
015c34d
One more
nealrichardson Oct 5, 2020
b85c7b8
File readers now take SubTreeFileSystem
nealrichardson Oct 5, 2020
acfdac0
s3_bucket(), plus docs and assorted fixes
nealrichardson Oct 6, 2020
08f5b5c
doc/namespace
nealrichardson Oct 7, 2020
631dbac
Update write_dataset; fix bad rebase
nealrichardson Oct 8, 2020
9b33d9c
Add ls() method (tested in minio)
nealrichardson Oct 8, 2020
59ba081
Apply suggestions from @bkietz
nealrichardson Oct 8, 2020
a1f02b4
Change copy_files interface (TODO update vignette)
nealrichardson Oct 9, 2020
ed2165c
Docs
nealrichardson Oct 9, 2020
9cae60e
Try to make test robust to windows
nealrichardson Oct 9, 2020
fe737aa
Fine.
nealrichardson Oct 9, 2020
d0a1076
Skip another windows test...
nealrichardson Oct 9, 2020
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4 changes: 4 additions & 0 deletions r/NAMESPACE
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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@
S3method("!=",ArrowObject)
S3method("$",RecordBatch)
S3method("$",Schema)
S3method("$",SubTreeFileSystem)
S3method("$",Table)
S3method("==",ArrowObject)
S3method("[",Array)
Expand DownExpand Up@@ -188,6 +189,7 @@ export(TimestampParser)
export(Type)
export(UnionDataset)
export(arrow_available)
export(arrow_with_s3)
export(binary)
export(bool)
export(boolean)
Expand All@@ -196,6 +198,7 @@ export(cast_options)
export(chunked_array)
export(codec_is_available)
export(contains)
export(copy_files)
export(cpu_count)
export(dataset_factory)
export(date32)
Expand DownExpand Up@@ -249,6 +252,7 @@ export(read_parquet)
export(read_schema)
export(read_tsv_arrow)
export(record_batch)
export(s3_bucket)
export(schema)
export(set_cpu_count)
export(starts_with)
Expand Down
18 changes: 14 additions & 4 deletions r/R/arrow-package.R
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Original file line numberDiff line numberDiff line change
Expand Up@@ -53,18 +53,28 @@

#' Is the C++ Arrow library available?
#'
#' You won't generally need to call this function, but it's here in case it
#' helps for development purposes.
#' You won't generally need to call these function, but they're made available
#' for diagnostic purposes.
#' @return `TRUE` or `FALSE` depending on whether the package was installed
#' with the Arrow C++ library. If `FALSE`, you'll need to install the C++
#' library and then reinstall the R package. See [install_arrow()] for help.
#' with the Arrow C++ library (check with `arrow_available()`) or with S3
#' support enabled (check with `arrow_with_s3()`).
#' @export
#' @examples
#' arrow_available()
#' arrow_with_s3()
#' @seealso If either of these are `FALSE`, see
#' `vignette("install", package = "arrow")` for guidance on reinstalling the
#' package.
arrow_available <- function() {
.Call(`_arrow_available`)
}

#' @rdname arrow_available
#' @export
arrow_with_s3 <- function() {
.Call(`_s3_available`)
}

option_use_threads <- function() {
!is_false(getOption("arrow.use_threads"))
}
Expand Down
12 changes: 12 additions & 0 deletions r/R/arrowExports.R
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8 changes: 3 additions & 5 deletions r/R/csv.R
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Original file line numberDiff line numberDiff line change
Expand Up@@ -77,7 +77,8 @@
#' `col_names`, and the CSV file has a header row that would otherwise be used
#' to idenfity column names, you'll need to add `skip = 1` to skip that row.
#'
#' @param file A character file name or URI, `raw` vector, or an Arrow input stream.
#' @param file A character file name or URI, `raw` vector, an Arrow input stream,
#' or a `FileSystem` with path (`SubTreeFileSystem`).
#' If a file name, a memory-mapped Arrow [InputStream] will be opened and
#' closed when finished; compression will be detected from the file extension
#' and handled automatically. If an input stream is provided, it will be left
Expand DownExpand Up@@ -123,8 +124,6 @@
#' parsing options provided in other arguments (e.g. `delim`, `quote`, etc.).
#' @param convert_options see [file reader options][CsvReadOptions]
#' @param read_options see [file reader options][CsvReadOptions]
#' @param filesystem A [FileSystem] where `file` can be found if it is a
#' string file path; default is the local file system
#' @param as_data_frame Should the function return a `data.frame` (default) or
#' an Arrow [Table]?
#'
Expand DownExpand Up@@ -156,7 +155,6 @@ read_delim_arrow <- function(file,
parse_options = NULL,
convert_options = NULL,
read_options = NULL,
filesystem = NULL,
as_data_frame = TRUE,
timestamp_parsers = NULL) {
if (inherits(schema, "Schema")) {
Expand DownExpand Up@@ -186,7 +184,7 @@ read_delim_arrow <- function(file,
}

if (!inherits(file, "InputStream")) {
file <- make_readable_file(file, filesystem = filesystem)
file <- make_readable_file(file)
on.exit(file$close())
}
reader <- CsvTableReader$create(
Expand Down
3 changes: 0 additions & 3 deletions r/R/dataset-factory.R
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Original file line numberDiff line numberDiff line change
Expand Up@@ -44,9 +44,6 @@ DatasetFactory$create <- function(x,
if (is_list_of(x, "DatasetFactory")) {
return(shared_ptr(DatasetFactory, dataset___UnionDatasetFactory__Make(x)))
}
if (!is.string(x)) {
stop("'x' must be a string or a list of DatasetFactory", call. = FALSE)
}

path_and_fs <- get_path_and_filesystem(x, filesystem)
selector <- FileSelector$create(path_and_fs$path, allow_not_found = FALSE, recursive = TRUE)
Expand Down
9 changes: 3 additions & 6 deletions r/R/dataset-write.R
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Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -27,8 +27,8 @@
#' and `group_by()` operations done on the dataset. `filter()` queries will be
#' applied to restrict written rows.
#' Note that `select()`-ed columns may not be renamed.
#' @param path string pathor URI to a directory to write to (directory will be
#' created if it does not exist)
#' @param path string path, URI, or `SubTreeFileSystem` referencing a directory
#' to write to (directory will be created if it does not exist)
#' @param format file format to write the dataset to. Currently supported
#' formats are "feather" (aka "ipc") and "parquet". Default is to write to the
#' same format as `dataset`.
Expand All@@ -41,8 +41,6 @@
#' will yield `"part-0.feather", ...`.
#' @param hive_style logical: write partition segments as Hive-style
#' (`key1=value1/key2=value2/file.ext`) or as just bare values. Default is `TRUE`.
#' @param filesystem A [FileSystem] where the dataset should be written if it is a
#' string file path; default is the local file system
#' @param ... additional format-specific arguments. For available Parquet
#' options, see [write_parquet()].
#' @return The input `dataset`, invisibly
Expand All@@ -53,7 +51,6 @@ write_dataset <- function(dataset,
partitioning = dplyr::group_vars(dataset),
basename_template = paste0("part-{i}.", as.character(format)),
hive_style = TRUE,
filesystem = NULL,
...) {
if (inherits(dataset, "arrow_dplyr_query")) {
# We can select a subset of columns but we can't rename them
Expand All@@ -79,7 +76,7 @@ write_dataset <- function(dataset,
}
}

path_and_fs <- get_path_and_filesystem(path, filesystem)
path_and_fs <- get_path_and_filesystem(path)
options <- FileWriteOptions$create(format, table = scanner, ...)

dataset___Dataset__Write(options, path_and_fs$fs, path_and_fs$path,
Expand Down
15 changes: 6 additions & 9 deletions r/R/feather.R
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -24,9 +24,8 @@
#' and the version 2 specification, which is the Apache Arrow IPC file format.
#'
#' @param x `data.frame`, [RecordBatch], or [Table]
#' @param sink A string file path, URI, or [OutputStream]
#' @param filesystem A [FileSystem] where `sink` should be written if it is a
#' string file path; default is the local file system
#' @param sink A string file path, URI, or [OutputStream], or path in a file
#' system (`SubTreeFileSystem`)
Comment thread
nealrichardson marked this conversation as resolved.
Outdated
#' @param version integer Feather file version. Version 2 is the current.
#' Version 1 is the more limited legacy format.
#' @param chunk_size For V2 files, the number of rows that each chunk of data
Expand DownExpand Up@@ -54,7 +53,6 @@
#' @include arrow-package.R
write_feather <- function(x,
sink,
filesystem = NULL,
version = 2,
chunk_size = 65536L,
compression = c("default", "lz4", "uncompressed", "zstd"),
Expand DownExpand Up@@ -108,11 +106,10 @@ write_feather <- function(x,
}
assert_is(x, "Table")

if (is.string(sink)) {
sink <- make_output_stream(sink, filesystem)
if (!inherits(sink, "OutputStream")) {
sink <- make_output_stream(sink)
on.exit(sink$close())
}
assert_is(sink, "OutputStream")
ipc___WriteFeather__Table(sink, x, version, chunk_size, compression, compression_level)
invisible(x_out)
}
Expand DownExpand Up@@ -144,9 +141,9 @@ write_feather <- function(x,
#' # Can select columns
#' df <- read_feather(tf, col_select = starts_with("d"))
#' }
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, filesystem = NULL, ...) {
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, ...) {
if (!inherits(file, "RandomAccessFile")) {
file <- make_readable_file(file, filesystem = filesystem)
file <- make_readable_file(file)
on.exit(file$close())
}
reader <- FeatherReader$create(file, ...)
Expand Down
Loading
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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ARROW-9870: [R] Friendly interface for filesystems (S3)#8351

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 Closed

nealrichardson
wants to merge
16
commits into

from

 Closed


ARROW-9870: [R] Friendly interface for filesystems (S3)
#8351
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16 commits


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2dbfe8c

Revise dataset vignette to start thinking about UX


nealrichardson Sep 11, 2020
5e85269

More design by wishful thinking


nealrichardson Sep 27, 2020
ac8f7b0

Add SubTreeFileSystem base_fs and base_path properties


nealrichardson Sep 27, 2020
412c544

File writers and open_dataset now accept SubTreeFileSystem as path input


nealrichardson Oct 5, 2020
015c34d

One more


nealrichardson Oct 5, 2020
b85c7b8

File readers now take SubTreeFileSystem


nealrichardson Oct 5, 2020
acfdac0

s3_bucket(), plus docs and assorted fixes


nealrichardson Oct 6, 2020
08f5b5c

doc/namespace


nealrichardson Oct 7, 2020
631dbac

Update write_dataset; fix bad rebase


nealrichardson Oct 8, 2020
9b33d9c

Add ls() method (tested in minio)


nealrichardson Oct 8, 2020
59ba081

Apply suggestions from @bkietz


nealrichardson Oct 8, 2020
a1f02b4

Change copy_files interface (TODO update vignette)


nealrichardson Oct 9, 2020
ed2165c

Docs


nealrichardson Oct 9, 2020
9cae60e

Try to make test robust to windows


nealrichardson Oct 9, 2020
fe737aa

Fine.


nealrichardson Oct 9, 2020
d0a1076

Skip another windows test...


nealrichardson Oct 9, 2020

File filter

Filter by extension
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4 changes: 4 additions & 0 deletions
r/NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@
S3method("!=",ArrowObject)
S3method("$",RecordBatch)
S3method("$",Schema)
S3method("$",SubTreeFileSystem)
S3method("$",Table)
S3method("==",ArrowObject)
S3method("[",Array)
Expand DownExpand Up@@ -188,6 +189,7 @@ export(TimestampParser)
export(Type)
export(UnionDataset)
export(arrow_available)
export(arrow_with_s3)
export(binary)
export(bool)
export(boolean)
Expand All@@ -196,6 +198,7 @@ export(cast_options)
export(chunked_array)
export(codec_is_available)
export(contains)
export(copy_files)
export(cpu_count)
export(dataset_factory)
export(date32)
Expand DownExpand Up@@ -249,6 +252,7 @@ export(read_parquet)
export(read_schema)
export(read_tsv_arrow)
export(record_batch)
export(s3_bucket)
export(schema)
export(set_cpu_count)
export(starts_with)
Expand Down

18 changes: 14 additions & 4 deletions
r/R/arrow-package.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -53,18 +53,28 @@

#' Is the C++ Arrow library available?
#'
#' You won't generally need to call this function, but it's here in case it
#' helps for development purposes.
#' You won't generally need to call these function, but they're made available
#' for diagnostic purposes.
#' @return `TRUE` or `FALSE` depending on whether the package was installed
#' with the Arrow C++ library. If `FALSE`, you'll need to install the C++
#' library and then reinstall the R package. See [install_arrow()] for help.
#' with the Arrow C++ library (check with `arrow_available()`) or with S3
#' support enabled (check with `arrow_with_s3()`).
#' @export
#' @examples
#' arrow_available()
#' arrow_with_s3()
#' @seealso If either of these are `FALSE`, see
#' `vignette("install", package = "arrow")` for guidance on reinstalling the
#' package.
arrow_available <- function() {
 .Call(`_arrow_available`)
}

#' @rdname arrow_available
#' @export
arrow_with_s3 <- function() {
 .Call(`_s3_available`)
}

option_use_threads <- function() {
 !is_false(getOption("arrow.use_threads"))
}
Expand Down

12 changes: 12 additions & 0 deletions
r/R/arrowExports.R

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8 changes: 3 additions & 5 deletions
r/R/csv.R

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -77,7 +77,8 @@
#' `col_names`, and the CSV file has a header row that would otherwise be used
#' to idenfity column names, you'll need to add `skip = 1` to skip that row.
#'
#' @param file A character file name or URI, `raw` vector, or an Arrow input stream.
#' @param file A character file name or URI, `raw` vector, an Arrow input stream,
#' or a `FileSystem` with path (`SubTreeFileSystem`).
#' If a file name, a memory-mapped Arrow [InputStream] will be opened and
#' closed when finished; compression will be detected from the file extension
#' and handled automatically. If an input stream is provided, it will be left
Expand DownExpand Up@@ -123,8 +124,6 @@
#' parsing options provided in other arguments (e.g. `delim`, `quote`, etc.).
#' @param convert_options see [file reader options][CsvReadOptions]
#' @param read_options see [file reader options][CsvReadOptions]
#' @param filesystem A [FileSystem] where `file` can be found if it is a
#' string file path; default is the local file system
#' @param as_data_frame Should the function return a `data.frame` (default) or
#' an Arrow [Table]?
#'
Expand DownExpand Up@@ -156,7 +155,6 @@ read_delim_arrow <- function(file,
 parse_options = NULL,
 convert_options = NULL,
 read_options = NULL,
 filesystem = NULL,
 as_data_frame = TRUE,
 timestamp_parsers = NULL) {
 if (inherits(schema, "Schema")) {
Expand DownExpand Up@@ -186,7 +184,7 @@ read_delim_arrow <- function(file,
 }

 if (!inherits(file, "InputStream")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- CsvTableReader$create(
Expand Down

3 changes: 0 additions & 3 deletions
r/R/dataset-factory.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -44,9 +44,6 @@ DatasetFactory$create <- function(x,
 if (is_list_of(x, "DatasetFactory")) {
 return(shared_ptr(DatasetFactory, dataset___UnionDatasetFactory__Make(x)))
 }
 if (!is.string(x)) {
 stop("'x' must be a string or a list of DatasetFactory", call. = FALSE)
 }

 path_and_fs <- get_path_and_filesystem(x, filesystem)
 selector <- FileSelector$create(path_and_fs$path, allow_not_found = FALSE, recursive = TRUE)
Expand Down

9 changes: 3 additions & 6 deletions
r/R/dataset-write.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -27,8 +27,8 @@
#' and `group_by()` operations done on the dataset. `filter()` queries will be
#' applied to restrict written rows.
#' Note that `select()`-ed columns may not be renamed.
#' @param path string pathor URI to a directory to write to (directory will be
#' created if it does not exist)
#' @param path string path, URI, or `SubTreeFileSystem` referencing a directory
#' to write to (directory will be created if it does not exist)
#' @param format file format to write the dataset to. Currently supported
#' formats are "feather" (aka "ipc") and "parquet". Default is to write to the
#' same format as `dataset`.
Expand All@@ -41,8 +41,6 @@
#' will yield `"part-0.feather", ...`.
#' @param hive_style logical: write partition segments as Hive-style
#' (`key1=value1/key2=value2/file.ext`) or as just bare values. Default is `TRUE`.
#' @param filesystem A [FileSystem] where the dataset should be written if it is a
#' string file path; default is the local file system
#' @param ... additional format-specific arguments. For available Parquet
#' options, see [write_parquet()].
#' @return The input `dataset`, invisibly
Expand All@@ -53,7 +51,6 @@ write_dataset <- function(dataset,
 partitioning = dplyr::group_vars(dataset),
 basename_template = paste0("part-{i}.", as.character(format)),
 hive_style = TRUE,
 filesystem = NULL,
 ...) {
 if (inherits(dataset, "arrow_dplyr_query")) {
 # We can select a subset of columns but we can't rename them
Expand All@@ -79,7 +76,7 @@ write_dataset <- function(dataset,
 }
 }

 path_and_fs <- get_path_and_filesystem(path, filesystem)
 path_and_fs <- get_path_and_filesystem(path)
 options <- FileWriteOptions$create(format, table = scanner, ...)

 dataset___Dataset__Write(options, path_and_fs$fs, path_and_fs$path,
Expand Down

15 changes: 6 additions & 9 deletions
r/R/feather.R

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -24,9 +24,8 @@
#' and the version 2 specification, which is the Apache Arrow IPC file format.
#'
#' @param x `data.frame`, [RecordBatch], or [Table]
#' @param sink A string file path, URI, or [OutputStream]
#' @param filesystem A [FileSystem] where `sink` should be written if it is a
#' string file path; default is the local file system
#' @param sink A string file path, URI, or [OutputStream], or path in a file
#' system (`SubTreeFileSystem`)
Comment thread
nealrichardson marked this conversation as resolved.


Outdated

#' @param version integer Feather file version. Version 2 is the current.
#' Version 1 is the more limited legacy format.
#' @param chunk_size For V2 files, the number of rows that each chunk of data
Expand DownExpand Up@@ -54,7 +53,6 @@
#' @include arrow-package.R
write_feather <- function(x,
 sink,
 filesystem = NULL,
 version = 2,
 chunk_size = 65536L,
 compression = c("default", "lz4", "uncompressed", "zstd"),
Expand DownExpand Up@@ -108,11 +106,10 @@ write_feather <- function(x,
 }
 assert_is(x, "Table")

 if (is.string(sink)) {
 sink <- make_output_stream(sink, filesystem)
 if (!inherits(sink, "OutputStream")) {
 sink <- make_output_stream(sink)
 on.exit(sink$close())
 }
 assert_is(sink, "OutputStream")
 ipc___WriteFeather__Table(sink, x, version, chunk_size, compression, compression_level)
 invisible(x_out)
}
Expand DownExpand Up@@ -144,9 +141,9 @@ write_feather <- function(x,
#' # Can select columns
#' df <- read_feather(tf, col_select = starts_with("d"))
#' }
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, filesystem = NULL, ...) {
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, ...) {
 if (!inherits(file, "RandomAccessFile")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- FeatherReader$create(file, ...)
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
ARROW-9870: [R] Friendly interface for filesystems (S3)#8351

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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 Closed

nealrichardson
wants to merge
16
commits into

from

 Closed


ARROW-9870: [R] Friendly interface for filesystems (S3)
#8351
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Commits

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2dbfe8c

Revise dataset vignette to start thinking about UX


nealrichardson Sep 11, 2020
5e85269

More design by wishful thinking


nealrichardson Sep 27, 2020
ac8f7b0

Add SubTreeFileSystem base_fs and base_path properties


nealrichardson Sep 27, 2020
412c544

File writers and open_dataset now accept SubTreeFileSystem as path input


nealrichardson Oct 5, 2020
015c34d

One more


nealrichardson Oct 5, 2020
b85c7b8

File readers now take SubTreeFileSystem


nealrichardson Oct 5, 2020
acfdac0

s3_bucket(), plus docs and assorted fixes


nealrichardson Oct 6, 2020
08f5b5c

doc/namespace


nealrichardson Oct 7, 2020
631dbac

Update write_dataset; fix bad rebase


nealrichardson Oct 8, 2020
9b33d9c

Add ls() method (tested in minio)


nealrichardson Oct 8, 2020
59ba081

Apply suggestions from @bkietz


nealrichardson Oct 8, 2020
a1f02b4

Change copy_files interface (TODO update vignette)


nealrichardson Oct 9, 2020
ed2165c

Docs


nealrichardson Oct 9, 2020
9cae60e

Try to make test robust to windows


nealrichardson Oct 9, 2020
fe737aa

Fine.


nealrichardson Oct 9, 2020
d0a1076

Skip another windows test...


nealrichardson Oct 9, 2020

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4 changes: 4 additions & 0 deletions
r/NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@
S3method("!=",ArrowObject)
S3method("$",RecordBatch)
S3method("$",Schema)
S3method("$",SubTreeFileSystem)
S3method("$",Table)
S3method("==",ArrowObject)
S3method("[",Array)
Expand DownExpand Up@@ -188,6 +189,7 @@ export(TimestampParser)
export(Type)
export(UnionDataset)
export(arrow_available)
export(arrow_with_s3)
export(binary)
export(bool)
export(boolean)
Expand All@@ -196,6 +198,7 @@ export(cast_options)
export(chunked_array)
export(codec_is_available)
export(contains)
export(copy_files)
export(cpu_count)
export(dataset_factory)
export(date32)
Expand DownExpand Up@@ -249,6 +252,7 @@ export(read_parquet)
export(read_schema)
export(read_tsv_arrow)
export(record_batch)
export(s3_bucket)
export(schema)
export(set_cpu_count)
export(starts_with)
Expand Down

18 changes: 14 additions & 4 deletions
r/R/arrow-package.R

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -53,18 +53,28 @@

#' Is the C++ Arrow library available?
#'
#' You won't generally need to call this function, but it's here in case it
#' helps for development purposes.
#' You won't generally need to call these function, but they're made available
#' for diagnostic purposes.
#' @return `TRUE` or `FALSE` depending on whether the package was installed
#' with the Arrow C++ library. If `FALSE`, you'll need to install the C++
#' library and then reinstall the R package. See [install_arrow()] for help.
#' with the Arrow C++ library (check with `arrow_available()`) or with S3
#' support enabled (check with `arrow_with_s3()`).
#' @export
#' @examples
#' arrow_available()
#' arrow_with_s3()
#' @seealso If either of these are `FALSE`, see
#' `vignette("install", package = "arrow")` for guidance on reinstalling the
#' package.
arrow_available <- function() {
 .Call(`_arrow_available`)
}

#' @rdname arrow_available
#' @export
arrow_with_s3 <- function() {
 .Call(`_s3_available`)
}

option_use_threads <- function() {
 !is_false(getOption("arrow.use_threads"))
}
Expand Down

12 changes: 12 additions & 0 deletions
r/R/arrowExports.R

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8 changes: 3 additions & 5 deletions
r/R/csv.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -77,7 +77,8 @@
#' `col_names`, and the CSV file has a header row that would otherwise be used
#' to idenfity column names, you'll need to add `skip = 1` to skip that row.
#'
#' @param file A character file name or URI, `raw` vector, or an Arrow input stream.
#' @param file A character file name or URI, `raw` vector, an Arrow input stream,
#' or a `FileSystem` with path (`SubTreeFileSystem`).
#' If a file name, a memory-mapped Arrow [InputStream] will be opened and
#' closed when finished; compression will be detected from the file extension
#' and handled automatically. If an input stream is provided, it will be left
Expand DownExpand Up@@ -123,8 +124,6 @@
#' parsing options provided in other arguments (e.g. `delim`, `quote`, etc.).
#' @param convert_options see [file reader options][CsvReadOptions]
#' @param read_options see [file reader options][CsvReadOptions]
#' @param filesystem A [FileSystem] where `file` can be found if it is a
#' string file path; default is the local file system
#' @param as_data_frame Should the function return a `data.frame` (default) or
#' an Arrow [Table]?
#'
Expand DownExpand Up@@ -156,7 +155,6 @@ read_delim_arrow <- function(file,
 parse_options = NULL,
 convert_options = NULL,
 read_options = NULL,
 filesystem = NULL,
 as_data_frame = TRUE,
 timestamp_parsers = NULL) {
 if (inherits(schema, "Schema")) {
Expand DownExpand Up@@ -186,7 +184,7 @@ read_delim_arrow <- function(file,
 }

 if (!inherits(file, "InputStream")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- CsvTableReader$create(
Expand Down

3 changes: 0 additions & 3 deletions
r/R/dataset-factory.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,9 +44,6 @@ DatasetFactory$create <- function(x,
 if (is_list_of(x, "DatasetFactory")) {
 return(shared_ptr(DatasetFactory, dataset___UnionDatasetFactory__Make(x)))
 }
 if (!is.string(x)) {
 stop("'x' must be a string or a list of DatasetFactory", call. = FALSE)
 }

 path_and_fs <- get_path_and_filesystem(x, filesystem)
 selector <- FileSelector$create(path_and_fs$path, allow_not_found = FALSE, recursive = TRUE)
Expand Down

9 changes: 3 additions & 6 deletions
r/R/dataset-write.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,8 +27,8 @@
#' and `group_by()` operations done on the dataset. `filter()` queries will be
#' applied to restrict written rows.
#' Note that `select()`-ed columns may not be renamed.
#' @param path string pathor URI to a directory to write to (directory will be
#' created if it does not exist)
#' @param path string path, URI, or `SubTreeFileSystem` referencing a directory
#' to write to (directory will be created if it does not exist)
#' @param format file format to write the dataset to. Currently supported
#' formats are "feather" (aka "ipc") and "parquet". Default is to write to the
#' same format as `dataset`.
Expand All@@ -41,8 +41,6 @@
#' will yield `"part-0.feather", ...`.
#' @param hive_style logical: write partition segments as Hive-style
#' (`key1=value1/key2=value2/file.ext`) or as just bare values. Default is `TRUE`.
#' @param filesystem A [FileSystem] where the dataset should be written if it is a
#' string file path; default is the local file system
#' @param ... additional format-specific arguments. For available Parquet
#' options, see [write_parquet()].
#' @return The input `dataset`, invisibly
Expand All@@ -53,7 +51,6 @@ write_dataset <- function(dataset,
 partitioning = dplyr::group_vars(dataset),
 basename_template = paste0("part-{i}.", as.character(format)),
 hive_style = TRUE,
 filesystem = NULL,
 ...) {
 if (inherits(dataset, "arrow_dplyr_query")) {
 # We can select a subset of columns but we can't rename them
Expand All@@ -79,7 +76,7 @@ write_dataset <- function(dataset,
 }
 }

 path_and_fs <- get_path_and_filesystem(path, filesystem)
 path_and_fs <- get_path_and_filesystem(path)
 options <- FileWriteOptions$create(format, table = scanner, ...)

 dataset___Dataset__Write(options, path_and_fs$fs, path_and_fs$path,
Expand Down

15 changes: 6 additions & 9 deletions
r/R/feather.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -24,9 +24,8 @@
#' and the version 2 specification, which is the Apache Arrow IPC file format.
#'
#' @param x `data.frame`, [RecordBatch], or [Table]
#' @param sink A string file path, URI, or [OutputStream]
#' @param filesystem A [FileSystem] where `sink` should be written if it is a
#' string file path; default is the local file system
#' @param sink A string file path, URI, or [OutputStream], or path in a file
#' system (`SubTreeFileSystem`)
Comment thread
nealrichardson marked this conversation as resolved.


Outdated

#' @param version integer Feather file version. Version 2 is the current.
#' Version 1 is the more limited legacy format.
#' @param chunk_size For V2 files, the number of rows that each chunk of data
Expand DownExpand Up@@ -54,7 +53,6 @@
#' @include arrow-package.R
write_feather <- function(x,
 sink,
 filesystem = NULL,
 version = 2,
 chunk_size = 65536L,
 compression = c("default", "lz4", "uncompressed", "zstd"),
Expand DownExpand Up@@ -108,11 +106,10 @@ write_feather <- function(x,
 }
 assert_is(x, "Table")

 if (is.string(sink)) {
 sink <- make_output_stream(sink, filesystem)
 if (!inherits(sink, "OutputStream")) {
 sink <- make_output_stream(sink)
 on.exit(sink$close())
 }
 assert_is(sink, "OutputStream")
 ipc___WriteFeather__Table(sink, x, version, chunk_size, compression, compression_level)
 invisible(x_out)
}
Expand DownExpand Up@@ -144,9 +141,9 @@ write_feather <- function(x,
#' # Can select columns
#' df <- read_feather(tf, col_select = starts_with("d"))
#' }
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, filesystem = NULL, ...) {
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, ...) {
 if (!inherits(file, "RandomAccessFile")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- FeatherReader$create(file, ...)
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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ARROW-9870: [R] Friendly interface for filesystems (S3)
#8351
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2dbfe8c

Revise dataset vignette to start thinking about UX


nealrichardson Sep 11, 2020
5e85269

More design by wishful thinking


nealrichardson Sep 27, 2020
ac8f7b0

Add SubTreeFileSystem base_fs and base_path properties


nealrichardson Sep 27, 2020
412c544

File writers and open_dataset now accept SubTreeFileSystem as path input


nealrichardson Oct 5, 2020
015c34d

One more


nealrichardson Oct 5, 2020
b85c7b8

File readers now take SubTreeFileSystem


nealrichardson Oct 5, 2020
acfdac0

s3_bucket(), plus docs and assorted fixes


nealrichardson Oct 6, 2020
08f5b5c

doc/namespace


nealrichardson Oct 7, 2020
631dbac

Update write_dataset; fix bad rebase


nealrichardson Oct 8, 2020
9b33d9c

Add ls() method (tested in minio)


nealrichardson Oct 8, 2020
59ba081

Apply suggestions from @bkietz


nealrichardson Oct 8, 2020
a1f02b4

Change copy_files interface (TODO update vignette)


nealrichardson Oct 9, 2020
ed2165c

Docs


nealrichardson Oct 9, 2020
9cae60e

Try to make test robust to windows


nealrichardson Oct 9, 2020
fe737aa

Fine.


nealrichardson Oct 9, 2020
d0a1076

Skip another windows test...


nealrichardson Oct 9, 2020

File filter

Filter by extension
Filter by extension
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Failed to load comments. 
Loading
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4 changes: 4 additions & 0 deletions
r/NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@
S3method("!=",ArrowObject)
S3method("$",RecordBatch)
S3method("$",Schema)
S3method("$",SubTreeFileSystem)
S3method("$",Table)
S3method("==",ArrowObject)
S3method("[",Array)
Expand DownExpand Up@@ -188,6 +189,7 @@ export(TimestampParser)
export(Type)
export(UnionDataset)
export(arrow_available)
export(arrow_with_s3)
export(binary)
export(bool)
export(boolean)
Expand All@@ -196,6 +198,7 @@ export(cast_options)
export(chunked_array)
export(codec_is_available)
export(contains)
export(copy_files)
export(cpu_count)
export(dataset_factory)
export(date32)
Expand DownExpand Up@@ -249,6 +252,7 @@ export(read_parquet)
export(read_schema)
export(read_tsv_arrow)
export(record_batch)
export(s3_bucket)
export(schema)
export(set_cpu_count)
export(starts_with)
Expand Down

18 changes: 14 additions & 4 deletions
r/R/arrow-package.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -53,18 +53,28 @@

#' Is the C++ Arrow library available?
#'
#' You won't generally need to call this function, but it's here in case it
#' helps for development purposes.
#' You won't generally need to call these function, but they're made available
#' for diagnostic purposes.
#' @return `TRUE` or `FALSE` depending on whether the package was installed
#' with the Arrow C++ library. If `FALSE`, you'll need to install the C++
#' library and then reinstall the R package. See [install_arrow()] for help.
#' with the Arrow C++ library (check with `arrow_available()`) or with S3
#' support enabled (check with `arrow_with_s3()`).
#' @export
#' @examples
#' arrow_available()
#' arrow_with_s3()
#' @seealso If either of these are `FALSE`, see
#' `vignette("install", package = "arrow")` for guidance on reinstalling the
#' package.
arrow_available <- function() {
 .Call(`_arrow_available`)
}

#' @rdname arrow_available
#' @export
arrow_with_s3 <- function() {
 .Call(`_s3_available`)
}

option_use_threads <- function() {
 !is_false(getOption("arrow.use_threads"))
}
Expand Down

12 changes: 12 additions & 0 deletions
r/R/arrowExports.R

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8 changes: 3 additions & 5 deletions
r/R/csv.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -77,7 +77,8 @@
#' `col_names`, and the CSV file has a header row that would otherwise be used
#' to idenfity column names, you'll need to add `skip = 1` to skip that row.
#'
#' @param file A character file name or URI, `raw` vector, or an Arrow input stream.
#' @param file A character file name or URI, `raw` vector, an Arrow input stream,
#' or a `FileSystem` with path (`SubTreeFileSystem`).
#' If a file name, a memory-mapped Arrow [InputStream] will be opened and
#' closed when finished; compression will be detected from the file extension
#' and handled automatically. If an input stream is provided, it will be left
Expand DownExpand Up@@ -123,8 +124,6 @@
#' parsing options provided in other arguments (e.g. `delim`, `quote`, etc.).
#' @param convert_options see [file reader options][CsvReadOptions]
#' @param read_options see [file reader options][CsvReadOptions]
#' @param filesystem A [FileSystem] where `file` can be found if it is a
#' string file path; default is the local file system
#' @param as_data_frame Should the function return a `data.frame` (default) or
#' an Arrow [Table]?
#'
Expand DownExpand Up@@ -156,7 +155,6 @@ read_delim_arrow <- function(file,
 parse_options = NULL,
 convert_options = NULL,
 read_options = NULL,
 filesystem = NULL,
 as_data_frame = TRUE,
 timestamp_parsers = NULL) {
 if (inherits(schema, "Schema")) {
Expand DownExpand Up@@ -186,7 +184,7 @@ read_delim_arrow <- function(file,
 }

 if (!inherits(file, "InputStream")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- CsvTableReader$create(
Expand Down

3 changes: 0 additions & 3 deletions
r/R/dataset-factory.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,9 +44,6 @@ DatasetFactory$create <- function(x,
 if (is_list_of(x, "DatasetFactory")) {
 return(shared_ptr(DatasetFactory, dataset___UnionDatasetFactory__Make(x)))
 }
 if (!is.string(x)) {
 stop("'x' must be a string or a list of DatasetFactory", call. = FALSE)
 }

 path_and_fs <- get_path_and_filesystem(x, filesystem)
 selector <- FileSelector$create(path_and_fs$path, allow_not_found = FALSE, recursive = TRUE)
Expand Down

9 changes: 3 additions & 6 deletions
r/R/dataset-write.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,8 +27,8 @@
#' and `group_by()` operations done on the dataset. `filter()` queries will be
#' applied to restrict written rows.
#' Note that `select()`-ed columns may not be renamed.
#' @param path string pathor URI to a directory to write to (directory will be
#' created if it does not exist)
#' @param path string path, URI, or `SubTreeFileSystem` referencing a directory
#' to write to (directory will be created if it does not exist)
#' @param format file format to write the dataset to. Currently supported
#' formats are "feather" (aka "ipc") and "parquet". Default is to write to the
#' same format as `dataset`.
Expand All@@ -41,8 +41,6 @@
#' will yield `"part-0.feather", ...`.
#' @param hive_style logical: write partition segments as Hive-style
#' (`key1=value1/key2=value2/file.ext`) or as just bare values. Default is `TRUE`.
#' @param filesystem A [FileSystem] where the dataset should be written if it is a
#' string file path; default is the local file system
#' @param ... additional format-specific arguments. For available Parquet
#' options, see [write_parquet()].
#' @return The input `dataset`, invisibly
Expand All@@ -53,7 +51,6 @@ write_dataset <- function(dataset,
 partitioning = dplyr::group_vars(dataset),
 basename_template = paste0("part-{i}.", as.character(format)),
 hive_style = TRUE,
 filesystem = NULL,
 ...) {
 if (inherits(dataset, "arrow_dplyr_query")) {
 # We can select a subset of columns but we can't rename them
Expand All@@ -79,7 +76,7 @@ write_dataset <- function(dataset,
 }
 }

 path_and_fs <- get_path_and_filesystem(path, filesystem)
 path_and_fs <- get_path_and_filesystem(path)
 options <- FileWriteOptions$create(format, table = scanner, ...)

 dataset___Dataset__Write(options, path_and_fs$fs, path_and_fs$path,
Expand Down

15 changes: 6 additions & 9 deletions
r/R/feather.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -24,9 +24,8 @@
#' and the version 2 specification, which is the Apache Arrow IPC file format.
#'
#' @param x `data.frame`, [RecordBatch], or [Table]
#' @param sink A string file path, URI, or [OutputStream]
#' @param filesystem A [FileSystem] where `sink` should be written if it is a
#' string file path; default is the local file system
#' @param sink A string file path, URI, or [OutputStream], or path in a file
#' system (`SubTreeFileSystem`)
Comment thread
nealrichardson marked this conversation as resolved.


Outdated

#' @param version integer Feather file version. Version 2 is the current.
#' Version 1 is the more limited legacy format.
#' @param chunk_size For V2 files, the number of rows that each chunk of data
Expand DownExpand Up@@ -54,7 +53,6 @@
#' @include arrow-package.R
write_feather <- function(x,
 sink,
 filesystem = NULL,
 version = 2,
 chunk_size = 65536L,
 compression = c("default", "lz4", "uncompressed", "zstd"),
Expand DownExpand Up@@ -108,11 +106,10 @@ write_feather <- function(x,
 }
 assert_is(x, "Table")

 if (is.string(sink)) {
 sink <- make_output_stream(sink, filesystem)
 if (!inherits(sink, "OutputStream")) {
 sink <- make_output_stream(sink)
 on.exit(sink$close())
 }
 assert_is(sink, "OutputStream")
 ipc___WriteFeather__Table(sink, x, version, chunk_size, compression, compression_level)
 invisible(x_out)
}
Expand DownExpand Up@@ -144,9 +141,9 @@ write_feather <- function(x,
#' # Can select columns
#' df <- read_feather(tf, col_select = starts_with("d"))
#' }
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, filesystem = NULL, ...) {
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, ...) {
 if (!inherits(file, "RandomAccessFile")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- FeatherReader$create(file, ...)
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

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ARROW-9870: [R] Friendly interface for filesystems (S3)#8351

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ARROW-9870: [R] Friendly interface for filesystems (S3)
#8351
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2dbfe8c

Revise dataset vignette to start thinking about UX


nealrichardson Sep 11, 2020
5e85269

More design by wishful thinking


nealrichardson Sep 27, 2020
ac8f7b0

Add SubTreeFileSystem base_fs and base_path properties


nealrichardson Sep 27, 2020
412c544

File writers and open_dataset now accept SubTreeFileSystem as path input


nealrichardson Oct 5, 2020
015c34d

One more


nealrichardson Oct 5, 2020
b85c7b8

File readers now take SubTreeFileSystem


nealrichardson Oct 5, 2020
acfdac0

s3_bucket(), plus docs and assorted fixes


nealrichardson Oct 6, 2020
08f5b5c

doc/namespace


nealrichardson Oct 7, 2020
631dbac

Update write_dataset; fix bad rebase


nealrichardson Oct 8, 2020
9b33d9c

Add ls() method (tested in minio)


nealrichardson Oct 8, 2020
59ba081

Apply suggestions from @bkietz


nealrichardson Oct 8, 2020
a1f02b4

Change copy_files interface (TODO update vignette)


nealrichardson Oct 9, 2020
ed2165c

Docs


nealrichardson Oct 9, 2020
9cae60e

Try to make test robust to windows


nealrichardson Oct 9, 2020
fe737aa

Fine.


nealrichardson Oct 9, 2020
d0a1076

Skip another windows test...


nealrichardson Oct 9, 2020

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4 changes: 4 additions & 0 deletions
r/NAMESPACE

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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@
S3method("!=",ArrowObject)
S3method("$",RecordBatch)
S3method("$",Schema)
S3method("$",SubTreeFileSystem)
S3method("$",Table)
S3method("==",ArrowObject)
S3method("[",Array)
Expand DownExpand Up@@ -188,6 +189,7 @@ export(TimestampParser)
export(Type)
export(UnionDataset)
export(arrow_available)
export(arrow_with_s3)
export(binary)
export(bool)
export(boolean)
Expand All@@ -196,6 +198,7 @@ export(cast_options)
export(chunked_array)
export(codec_is_available)
export(contains)
export(copy_files)
export(cpu_count)
export(dataset_factory)
export(date32)
Expand DownExpand Up@@ -249,6 +252,7 @@ export(read_parquet)
export(read_schema)
export(read_tsv_arrow)
export(record_batch)
export(s3_bucket)
export(schema)
export(set_cpu_count)
export(starts_with)
Expand Down

18 changes: 14 additions & 4 deletions
r/R/arrow-package.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -53,18 +53,28 @@

#' Is the C++ Arrow library available?
#'
#' You won't generally need to call this function, but it's here in case it
#' helps for development purposes.
#' You won't generally need to call these function, but they're made available
#' for diagnostic purposes.
#' @return `TRUE` or `FALSE` depending on whether the package was installed
#' with the Arrow C++ library. If `FALSE`, you'll need to install the C++
#' library and then reinstall the R package. See [install_arrow()] for help.
#' with the Arrow C++ library (check with `arrow_available()`) or with S3
#' support enabled (check with `arrow_with_s3()`).
#' @export
#' @examples
#' arrow_available()
#' arrow_with_s3()
#' @seealso If either of these are `FALSE`, see
#' `vignette("install", package = "arrow")` for guidance on reinstalling the
#' package.
arrow_available <- function() {
 .Call(`_arrow_available`)
}

#' @rdname arrow_available
#' @export
arrow_with_s3 <- function() {
 .Call(`_s3_available`)
}

option_use_threads <- function() {
 !is_false(getOption("arrow.use_threads"))
}
Expand Down

12 changes: 12 additions & 0 deletions
r/R/arrowExports.R

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8 changes: 3 additions & 5 deletions
r/R/csv.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -77,7 +77,8 @@
#' `col_names`, and the CSV file has a header row that would otherwise be used
#' to idenfity column names, you'll need to add `skip = 1` to skip that row.
#'
#' @param file A character file name or URI, `raw` vector, or an Arrow input stream.
#' @param file A character file name or URI, `raw` vector, an Arrow input stream,
#' or a `FileSystem` with path (`SubTreeFileSystem`).
#' If a file name, a memory-mapped Arrow [InputStream] will be opened and
#' closed when finished; compression will be detected from the file extension
#' and handled automatically. If an input stream is provided, it will be left
Expand DownExpand Up@@ -123,8 +124,6 @@
#' parsing options provided in other arguments (e.g. `delim`, `quote`, etc.).
#' @param convert_options see [file reader options][CsvReadOptions]
#' @param read_options see [file reader options][CsvReadOptions]
#' @param filesystem A [FileSystem] where `file` can be found if it is a
#' string file path; default is the local file system
#' @param as_data_frame Should the function return a `data.frame` (default) or
#' an Arrow [Table]?
#'
Expand DownExpand Up@@ -156,7 +155,6 @@ read_delim_arrow <- function(file,
 parse_options = NULL,
 convert_options = NULL,
 read_options = NULL,
 filesystem = NULL,
 as_data_frame = TRUE,
 timestamp_parsers = NULL) {
 if (inherits(schema, "Schema")) {
Expand DownExpand Up@@ -186,7 +184,7 @@ read_delim_arrow <- function(file,
 }

 if (!inherits(file, "InputStream")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- CsvTableReader$create(
Expand Down

3 changes: 0 additions & 3 deletions
r/R/dataset-factory.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -44,9 +44,6 @@ DatasetFactory$create <- function(x,
 if (is_list_of(x, "DatasetFactory")) {
 return(shared_ptr(DatasetFactory, dataset___UnionDatasetFactory__Make(x)))
 }
 if (!is.string(x)) {
 stop("'x' must be a string or a list of DatasetFactory", call. = FALSE)
 }

 path_and_fs <- get_path_and_filesystem(x, filesystem)
 selector <- FileSelector$create(path_and_fs$path, allow_not_found = FALSE, recursive = TRUE)
Expand Down

9 changes: 3 additions & 6 deletions
r/R/dataset-write.R

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,8 +27,8 @@
#' and `group_by()` operations done on the dataset. `filter()` queries will be
#' applied to restrict written rows.
#' Note that `select()`-ed columns may not be renamed.
#' @param path string pathor URI to a directory to write to (directory will be
#' created if it does not exist)
#' @param path string path, URI, or `SubTreeFileSystem` referencing a directory
#' to write to (directory will be created if it does not exist)
#' @param format file format to write the dataset to. Currently supported
#' formats are "feather" (aka "ipc") and "parquet". Default is to write to the
#' same format as `dataset`.
Expand All@@ -41,8 +41,6 @@
#' will yield `"part-0.feather", ...`.
#' @param hive_style logical: write partition segments as Hive-style
#' (`key1=value1/key2=value2/file.ext`) or as just bare values. Default is `TRUE`.
#' @param filesystem A [FileSystem] where the dataset should be written if it is a
#' string file path; default is the local file system
#' @param ... additional format-specific arguments. For available Parquet
#' options, see [write_parquet()].
#' @return The input `dataset`, invisibly
Expand All@@ -53,7 +51,6 @@ write_dataset <- function(dataset,
 partitioning = dplyr::group_vars(dataset),
 basename_template = paste0("part-{i}.", as.character(format)),
 hive_style = TRUE,
 filesystem = NULL,
 ...) {
 if (inherits(dataset, "arrow_dplyr_query")) {
 # We can select a subset of columns but we can't rename them
Expand All@@ -79,7 +76,7 @@ write_dataset <- function(dataset,
 }
 }

 path_and_fs <- get_path_and_filesystem(path, filesystem)
 path_and_fs <- get_path_and_filesystem(path)
 options <- FileWriteOptions$create(format, table = scanner, ...)

 dataset___Dataset__Write(options, path_and_fs$fs, path_and_fs$path,
Expand Down

15 changes: 6 additions & 9 deletions
r/R/feather.R

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -24,9 +24,8 @@
#' and the version 2 specification, which is the Apache Arrow IPC file format.
#'
#' @param x `data.frame`, [RecordBatch], or [Table]
#' @param sink A string file path, URI, or [OutputStream]
#' @param filesystem A [FileSystem] where `sink` should be written if it is a
#' string file path; default is the local file system
#' @param sink A string file path, URI, or [OutputStream], or path in a file
#' system (`SubTreeFileSystem`)
Comment thread
nealrichardson marked this conversation as resolved.


Outdated

#' @param version integer Feather file version. Version 2 is the current.
#' Version 1 is the more limited legacy format.
#' @param chunk_size For V2 files, the number of rows that each chunk of data
Expand DownExpand Up@@ -54,7 +53,6 @@
#' @include arrow-package.R
write_feather <- function(x,
 sink,
 filesystem = NULL,
 version = 2,
 chunk_size = 65536L,
 compression = c("default", "lz4", "uncompressed", "zstd"),
Expand DownExpand Up@@ -108,11 +106,10 @@ write_feather <- function(x,
 }
 assert_is(x, "Table")

 if (is.string(sink)) {
 sink <- make_output_stream(sink, filesystem)
 if (!inherits(sink, "OutputStream")) {
 sink <- make_output_stream(sink)
 on.exit(sink$close())
 }
 assert_is(sink, "OutputStream")
 ipc___WriteFeather__Table(sink, x, version, chunk_size, compression, compression_level)
 invisible(x_out)
}
Expand DownExpand Up@@ -144,9 +141,9 @@ write_feather <- function(x,
#' # Can select columns
#' df <- read_feather(tf, col_select = starts_with("d"))
#' }
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, filesystem = NULL, ...) {
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, ...) {
 if (!inherits(file, "RandomAccessFile")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- FeatherReader$create(file, ...)
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
ARROW-9870: [R] Friendly interface for filesystems (S3)#8351

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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 Closed

nealrichardson
wants to merge
16
commits into

from

 Closed


ARROW-9870: [R] Friendly interface for filesystems (S3)
#8351
Show file tree
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16 commits


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Hold shift + click to select a range
2dbfe8c

Revise dataset vignette to start thinking about UX


nealrichardson Sep 11, 2020
5e85269

More design by wishful thinking


nealrichardson Sep 27, 2020
ac8f7b0

Add SubTreeFileSystem base_fs and base_path properties


nealrichardson Sep 27, 2020
412c544

File writers and open_dataset now accept SubTreeFileSystem as path input


nealrichardson Oct 5, 2020
015c34d

One more


nealrichardson Oct 5, 2020
b85c7b8

File readers now take SubTreeFileSystem


nealrichardson Oct 5, 2020
acfdac0

s3_bucket(), plus docs and assorted fixes


nealrichardson Oct 6, 2020
08f5b5c

doc/namespace


nealrichardson Oct 7, 2020
631dbac

Update write_dataset; fix bad rebase


nealrichardson Oct 8, 2020
9b33d9c

Add ls() method (tested in minio)


nealrichardson Oct 8, 2020
59ba081

Apply suggestions from @bkietz


nealrichardson Oct 8, 2020
a1f02b4

Change copy_files interface (TODO update vignette)


nealrichardson Oct 9, 2020
ed2165c

Docs


nealrichardson Oct 9, 2020
9cae60e

Try to make test robust to windows


nealrichardson Oct 9, 2020
fe737aa

Fine.


nealrichardson Oct 9, 2020
d0a1076

Skip another windows test...


nealrichardson Oct 9, 2020

File filter

Filter by extension
Filter by extension
Conversations

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4 changes: 4 additions & 0 deletions
r/NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@
S3method("!=",ArrowObject)
S3method("$",RecordBatch)
S3method("$",Schema)
S3method("$",SubTreeFileSystem)
S3method("$",Table)
S3method("==",ArrowObject)
S3method("[",Array)
Expand DownExpand Up@@ -188,6 +189,7 @@ export(TimestampParser)
export(Type)
export(UnionDataset)
export(arrow_available)
export(arrow_with_s3)
export(binary)
export(bool)
export(boolean)
Expand All@@ -196,6 +198,7 @@ export(cast_options)
export(chunked_array)
export(codec_is_available)
export(contains)
export(copy_files)
export(cpu_count)
export(dataset_factory)
export(date32)
Expand DownExpand Up@@ -249,6 +252,7 @@ export(read_parquet)
export(read_schema)
export(read_tsv_arrow)
export(record_batch)
export(s3_bucket)
export(schema)
export(set_cpu_count)
export(starts_with)
Expand Down

18 changes: 14 additions & 4 deletions
r/R/arrow-package.R

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -53,18 +53,28 @@

#' Is the C++ Arrow library available?
#'
#' You won't generally need to call this function, but it's here in case it
#' helps for development purposes.
#' You won't generally need to call these function, but they're made available
#' for diagnostic purposes.
#' @return `TRUE` or `FALSE` depending on whether the package was installed
#' with the Arrow C++ library. If `FALSE`, you'll need to install the C++
#' library and then reinstall the R package. See [install_arrow()] for help.
#' with the Arrow C++ library (check with `arrow_available()`) or with S3
#' support enabled (check with `arrow_with_s3()`).
#' @export
#' @examples
#' arrow_available()
#' arrow_with_s3()
#' @seealso If either of these are `FALSE`, see
#' `vignette("install", package = "arrow")` for guidance on reinstalling the
#' package.
arrow_available <- function() {
 .Call(`_arrow_available`)
}

#' @rdname arrow_available
#' @export
arrow_with_s3 <- function() {
 .Call(`_s3_available`)
}

option_use_threads <- function() {
 !is_false(getOption("arrow.use_threads"))
}
Expand Down

12 changes: 12 additions & 0 deletions
r/R/arrowExports.R

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8 changes: 3 additions & 5 deletions
r/R/csv.R

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -77,7 +77,8 @@
#' `col_names`, and the CSV file has a header row that would otherwise be used
#' to idenfity column names, you'll need to add `skip = 1` to skip that row.
#'
#' @param file A character file name or URI, `raw` vector, or an Arrow input stream.
#' @param file A character file name or URI, `raw` vector, an Arrow input stream,
#' or a `FileSystem` with path (`SubTreeFileSystem`).
#' If a file name, a memory-mapped Arrow [InputStream] will be opened and
#' closed when finished; compression will be detected from the file extension
#' and handled automatically. If an input stream is provided, it will be left
Expand DownExpand Up@@ -123,8 +124,6 @@
#' parsing options provided in other arguments (e.g. `delim`, `quote`, etc.).
#' @param convert_options see [file reader options][CsvReadOptions]
#' @param read_options see [file reader options][CsvReadOptions]
#' @param filesystem A [FileSystem] where `file` can be found if it is a
#' string file path; default is the local file system
#' @param as_data_frame Should the function return a `data.frame` (default) or
#' an Arrow [Table]?
#'
Expand DownExpand Up@@ -156,7 +155,6 @@ read_delim_arrow <- function(file,
 parse_options = NULL,
 convert_options = NULL,
 read_options = NULL,
 filesystem = NULL,
 as_data_frame = TRUE,
 timestamp_parsers = NULL) {
 if (inherits(schema, "Schema")) {
Expand DownExpand Up@@ -186,7 +184,7 @@ read_delim_arrow <- function(file,
 }

 if (!inherits(file, "InputStream")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- CsvTableReader$create(
Expand Down

3 changes: 0 additions & 3 deletions
r/R/dataset-factory.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -44,9 +44,6 @@ DatasetFactory$create <- function(x,
 if (is_list_of(x, "DatasetFactory")) {
 return(shared_ptr(DatasetFactory, dataset___UnionDatasetFactory__Make(x)))
 }
 if (!is.string(x)) {
 stop("'x' must be a string or a list of DatasetFactory", call. = FALSE)
 }

 path_and_fs <- get_path_and_filesystem(x, filesystem)
 selector <- FileSelector$create(path_and_fs$path, allow_not_found = FALSE, recursive = TRUE)
Expand Down

9 changes: 3 additions & 6 deletions
r/R/dataset-write.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,8 +27,8 @@
#' and `group_by()` operations done on the dataset. `filter()` queries will be
#' applied to restrict written rows.
#' Note that `select()`-ed columns may not be renamed.
#' @param path string pathor URI to a directory to write to (directory will be
#' created if it does not exist)
#' @param path string path, URI, or `SubTreeFileSystem` referencing a directory
#' to write to (directory will be created if it does not exist)
#' @param format file format to write the dataset to. Currently supported
#' formats are "feather" (aka "ipc") and "parquet". Default is to write to the
#' same format as `dataset`.
Expand All@@ -41,8 +41,6 @@
#' will yield `"part-0.feather", ...`.
#' @param hive_style logical: write partition segments as Hive-style
#' (`key1=value1/key2=value2/file.ext`) or as just bare values. Default is `TRUE`.
#' @param filesystem A [FileSystem] where the dataset should be written if it is a
#' string file path; default is the local file system
#' @param ... additional format-specific arguments. For available Parquet
#' options, see [write_parquet()].
#' @return The input `dataset`, invisibly
Expand All@@ -53,7 +51,6 @@ write_dataset <- function(dataset,
 partitioning = dplyr::group_vars(dataset),
 basename_template = paste0("part-{i}.", as.character(format)),
 hive_style = TRUE,
 filesystem = NULL,
 ...) {
 if (inherits(dataset, "arrow_dplyr_query")) {
 # We can select a subset of columns but we can't rename them
Expand All@@ -79,7 +76,7 @@ write_dataset <- function(dataset,
 }
 }

 path_and_fs <- get_path_and_filesystem(path, filesystem)
 path_and_fs <- get_path_and_filesystem(path)
 options <- FileWriteOptions$create(format, table = scanner, ...)

 dataset___Dataset__Write(options, path_and_fs$fs, path_and_fs$path,
Expand Down

15 changes: 6 additions & 9 deletions
r/R/feather.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -24,9 +24,8 @@
#' and the version 2 specification, which is the Apache Arrow IPC file format.
#'
#' @param x `data.frame`, [RecordBatch], or [Table]
#' @param sink A string file path, URI, or [OutputStream]
#' @param filesystem A [FileSystem] where `sink` should be written if it is a
#' string file path; default is the local file system
#' @param sink A string file path, URI, or [OutputStream], or path in a file
#' system (`SubTreeFileSystem`)
Comment thread
nealrichardson marked this conversation as resolved.


Outdated

#' @param version integer Feather file version. Version 2 is the current.
#' Version 1 is the more limited legacy format.
#' @param chunk_size For V2 files, the number of rows that each chunk of data
Expand DownExpand Up@@ -54,7 +53,6 @@
#' @include arrow-package.R
write_feather <- function(x,
 sink,
 filesystem = NULL,
 version = 2,
 chunk_size = 65536L,
 compression = c("default", "lz4", "uncompressed", "zstd"),
Expand DownExpand Up@@ -108,11 +106,10 @@ write_feather <- function(x,
 }
 assert_is(x, "Table")

 if (is.string(sink)) {
 sink <- make_output_stream(sink, filesystem)
 if (!inherits(sink, "OutputStream")) {
 sink <- make_output_stream(sink)
 on.exit(sink$close())
 }
 assert_is(sink, "OutputStream")
 ipc___WriteFeather__Table(sink, x, version, chunk_size, compression, compression_level)
 invisible(x_out)
}
Expand DownExpand Up@@ -144,9 +141,9 @@ write_feather <- function(x,
#' # Can select columns
#' df <- read_feather(tf, col_select = starts_with("d"))
#' }
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, filesystem = NULL, ...) {
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, ...) {
 if (!inherits(file, "RandomAccessFile")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- FeatherReader$create(file, ...)
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
ARROW-9870: [R] Friendly interface for filesystems (S3)#8351

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Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

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privacy statement. We’ll occasionally send you account related emails.

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Sign in
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 Closed

nealrichardson
wants to merge
16
commits into

from

 Closed


ARROW-9870: [R] Friendly interface for filesystems (S3)
#8351
Show file tree
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Commits

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2dbfe8c

Revise dataset vignette to start thinking about UX


nealrichardson Sep 11, 2020
5e85269

More design by wishful thinking


nealrichardson Sep 27, 2020
ac8f7b0

Add SubTreeFileSystem base_fs and base_path properties


nealrichardson Sep 27, 2020
412c544

File writers and open_dataset now accept SubTreeFileSystem as path input


nealrichardson Oct 5, 2020
015c34d

One more


nealrichardson Oct 5, 2020
b85c7b8

File readers now take SubTreeFileSystem


nealrichardson Oct 5, 2020
acfdac0

s3_bucket(), plus docs and assorted fixes


nealrichardson Oct 6, 2020
08f5b5c

doc/namespace


nealrichardson Oct 7, 2020
631dbac

Update write_dataset; fix bad rebase


nealrichardson Oct 8, 2020
9b33d9c

Add ls() method (tested in minio)


nealrichardson Oct 8, 2020
59ba081

Apply suggestions from @bkietz


nealrichardson Oct 8, 2020
a1f02b4

Change copy_files interface (TODO update vignette)


nealrichardson Oct 9, 2020
ed2165c

Docs


nealrichardson Oct 9, 2020
9cae60e

Try to make test robust to windows


nealrichardson Oct 9, 2020
fe737aa

Fine.


nealrichardson Oct 9, 2020
d0a1076

Skip another windows test...


nealrichardson Oct 9, 2020

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4 changes: 4 additions & 0 deletions
r/NAMESPACE

View file


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Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@
S3method("!=",ArrowObject)
S3method("$",RecordBatch)
S3method("$",Schema)
S3method("$",SubTreeFileSystem)
S3method("$",Table)
S3method("==",ArrowObject)
S3method("[",Array)
Expand DownExpand Up@@ -188,6 +189,7 @@ export(TimestampParser)
export(Type)
export(UnionDataset)
export(arrow_available)
export(arrow_with_s3)
export(binary)
export(bool)
export(boolean)
Expand All@@ -196,6 +198,7 @@ export(cast_options)
export(chunked_array)
export(codec_is_available)
export(contains)
export(copy_files)
export(cpu_count)
export(dataset_factory)
export(date32)
Expand DownExpand Up@@ -249,6 +252,7 @@ export(read_parquet)
export(read_schema)
export(read_tsv_arrow)
export(record_batch)
export(s3_bucket)
export(schema)
export(set_cpu_count)
export(starts_with)
Expand Down

18 changes: 14 additions & 4 deletions
r/R/arrow-package.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -53,18 +53,28 @@

#' Is the C++ Arrow library available?
#'
#' You won't generally need to call this function, but it's here in case it
#' helps for development purposes.
#' You won't generally need to call these function, but they're made available
#' for diagnostic purposes.
#' @return `TRUE` or `FALSE` depending on whether the package was installed
#' with the Arrow C++ library. If `FALSE`, you'll need to install the C++
#' library and then reinstall the R package. See [install_arrow()] for help.
#' with the Arrow C++ library (check with `arrow_available()`) or with S3
#' support enabled (check with `arrow_with_s3()`).
#' @export
#' @examples
#' arrow_available()
#' arrow_with_s3()
#' @seealso If either of these are `FALSE`, see
#' `vignette("install", package = "arrow")` for guidance on reinstalling the
#' package.
arrow_available <- function() {
 .Call(`_arrow_available`)
}

#' @rdname arrow_available
#' @export
arrow_with_s3 <- function() {
 .Call(`_s3_available`)
}

option_use_threads <- function() {
 !is_false(getOption("arrow.use_threads"))
}
Expand Down

12 changes: 12 additions & 0 deletions
r/R/arrowExports.R

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8 changes: 3 additions & 5 deletions
r/R/csv.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -77,7 +77,8 @@
#' `col_names`, and the CSV file has a header row that would otherwise be used
#' to idenfity column names, you'll need to add `skip = 1` to skip that row.
#'
#' @param file A character file name or URI, `raw` vector, or an Arrow input stream.
#' @param file A character file name or URI, `raw` vector, an Arrow input stream,
#' or a `FileSystem` with path (`SubTreeFileSystem`).
#' If a file name, a memory-mapped Arrow [InputStream] will be opened and
#' closed when finished; compression will be detected from the file extension
#' and handled automatically. If an input stream is provided, it will be left
Expand DownExpand Up@@ -123,8 +124,6 @@
#' parsing options provided in other arguments (e.g. `delim`, `quote`, etc.).
#' @param convert_options see [file reader options][CsvReadOptions]
#' @param read_options see [file reader options][CsvReadOptions]
#' @param filesystem A [FileSystem] where `file` can be found if it is a
#' string file path; default is the local file system
#' @param as_data_frame Should the function return a `data.frame` (default) or
#' an Arrow [Table]?
#'
Expand DownExpand Up@@ -156,7 +155,6 @@ read_delim_arrow <- function(file,
 parse_options = NULL,
 convert_options = NULL,
 read_options = NULL,
 filesystem = NULL,
 as_data_frame = TRUE,
 timestamp_parsers = NULL) {
 if (inherits(schema, "Schema")) {
Expand DownExpand Up@@ -186,7 +184,7 @@ read_delim_arrow <- function(file,
 }

 if (!inherits(file, "InputStream")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- CsvTableReader$create(
Expand Down

3 changes: 0 additions & 3 deletions
r/R/dataset-factory.R

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Original file line numberDiff line numberDiff line change
Expand Up@@ -44,9 +44,6 @@ DatasetFactory$create <- function(x,
 if (is_list_of(x, "DatasetFactory")) {
 return(shared_ptr(DatasetFactory, dataset___UnionDatasetFactory__Make(x)))
 }
 if (!is.string(x)) {
 stop("'x' must be a string or a list of DatasetFactory", call. = FALSE)
 }

 path_and_fs <- get_path_and_filesystem(x, filesystem)
 selector <- FileSelector$create(path_and_fs$path, allow_not_found = FALSE, recursive = TRUE)
Expand Down

9 changes: 3 additions & 6 deletions
r/R/dataset-write.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,8 +27,8 @@
#' and `group_by()` operations done on the dataset. `filter()` queries will be
#' applied to restrict written rows.
#' Note that `select()`-ed columns may not be renamed.
#' @param path string pathor URI to a directory to write to (directory will be
#' created if it does not exist)
#' @param path string path, URI, or `SubTreeFileSystem` referencing a directory
#' to write to (directory will be created if it does not exist)
#' @param format file format to write the dataset to. Currently supported
#' formats are "feather" (aka "ipc") and "parquet". Default is to write to the
#' same format as `dataset`.
Expand All@@ -41,8 +41,6 @@
#' will yield `"part-0.feather", ...`.
#' @param hive_style logical: write partition segments as Hive-style
#' (`key1=value1/key2=value2/file.ext`) or as just bare values. Default is `TRUE`.
#' @param filesystem A [FileSystem] where the dataset should be written if it is a
#' string file path; default is the local file system
#' @param ... additional format-specific arguments. For available Parquet
#' options, see [write_parquet()].
#' @return The input `dataset`, invisibly
Expand All@@ -53,7 +51,6 @@ write_dataset <- function(dataset,
 partitioning = dplyr::group_vars(dataset),
 basename_template = paste0("part-{i}.", as.character(format)),
 hive_style = TRUE,
 filesystem = NULL,
 ...) {
 if (inherits(dataset, "arrow_dplyr_query")) {
 # We can select a subset of columns but we can't rename them
Expand All@@ -79,7 +76,7 @@ write_dataset <- function(dataset,
 }
 }

 path_and_fs <- get_path_and_filesystem(path, filesystem)
 path_and_fs <- get_path_and_filesystem(path)
 options <- FileWriteOptions$create(format, table = scanner, ...)

 dataset___Dataset__Write(options, path_and_fs$fs, path_and_fs$path,
Expand Down

15 changes: 6 additions & 9 deletions
r/R/feather.R

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Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -24,9 +24,8 @@
#' and the version 2 specification, which is the Apache Arrow IPC file format.
#'
#' @param x `data.frame`, [RecordBatch], or [Table]
#' @param sink A string file path, URI, or [OutputStream]
#' @param filesystem A [FileSystem] where `sink` should be written if it is a
#' string file path; default is the local file system
#' @param sink A string file path, URI, or [OutputStream], or path in a file
#' system (`SubTreeFileSystem`)
Comment thread
nealrichardson marked this conversation as resolved.


Outdated

#' @param version integer Feather file version. Version 2 is the current.
#' Version 1 is the more limited legacy format.
#' @param chunk_size For V2 files, the number of rows that each chunk of data
Expand DownExpand Up@@ -54,7 +53,6 @@
#' @include arrow-package.R
write_feather <- function(x,
 sink,
 filesystem = NULL,
 version = 2,
 chunk_size = 65536L,
 compression = c("default", "lz4", "uncompressed", "zstd"),
Expand DownExpand Up@@ -108,11 +106,10 @@ write_feather <- function(x,
 }
 assert_is(x, "Table")

 if (is.string(sink)) {
 sink <- make_output_stream(sink, filesystem)
 if (!inherits(sink, "OutputStream")) {
 sink <- make_output_stream(sink)
 on.exit(sink$close())
 }
 assert_is(sink, "OutputStream")
 ipc___WriteFeather__Table(sink, x, version, chunk_size, compression, compression_level)
 invisible(x_out)
}
Expand DownExpand Up@@ -144,9 +141,9 @@ write_feather <- function(x,
#' # Can select columns
#' df <- read_feather(tf, col_select = starts_with("d"))
#' }
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, filesystem = NULL, ...) {
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, ...) {
 if (!inherits(file, "RandomAccessFile")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- FeatherReader$create(file, ...)
Expand Down
Loading

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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ARROW-9870: [R] Friendly interface for filesystems (S3)
#8351
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2dbfe8c

Revise dataset vignette to start thinking about UX


nealrichardson Sep 11, 2020
5e85269

More design by wishful thinking


nealrichardson Sep 27, 2020
ac8f7b0

Add SubTreeFileSystem base_fs and base_path properties


nealrichardson Sep 27, 2020
412c544

File writers and open_dataset now accept SubTreeFileSystem as path input


nealrichardson Oct 5, 2020
015c34d

One more


nealrichardson Oct 5, 2020
b85c7b8

File readers now take SubTreeFileSystem


nealrichardson Oct 5, 2020
acfdac0

s3_bucket(), plus docs and assorted fixes


nealrichardson Oct 6, 2020
08f5b5c

doc/namespace


nealrichardson Oct 7, 2020
631dbac

Update write_dataset; fix bad rebase


nealrichardson Oct 8, 2020
9b33d9c

Add ls() method (tested in minio)


nealrichardson Oct 8, 2020
59ba081

Apply suggestions from @bkietz


nealrichardson Oct 8, 2020
a1f02b4

Change copy_files interface (TODO update vignette)


nealrichardson Oct 9, 2020
ed2165c

Docs


nealrichardson Oct 9, 2020
9cae60e

Try to make test robust to windows


nealrichardson Oct 9, 2020
fe737aa

Fine.


nealrichardson Oct 9, 2020
d0a1076

Skip another windows test...


nealrichardson Oct 9, 2020

File filter

Filter by extension
Filter by extension
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4 changes: 4 additions & 0 deletions
r/NAMESPACE

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -3,6 +3,7 @@
S3method("!=",ArrowObject)
S3method("$",RecordBatch)
S3method("$",Schema)
S3method("$",SubTreeFileSystem)
S3method("$",Table)
S3method("==",ArrowObject)
S3method("[",Array)
Expand DownExpand Up@@ -188,6 +189,7 @@ export(TimestampParser)
export(Type)
export(UnionDataset)
export(arrow_available)
export(arrow_with_s3)
export(binary)
export(bool)
export(boolean)
Expand All@@ -196,6 +198,7 @@ export(cast_options)
export(chunked_array)
export(codec_is_available)
export(contains)
export(copy_files)
export(cpu_count)
export(dataset_factory)
export(date32)
Expand DownExpand Up@@ -249,6 +252,7 @@ export(read_parquet)
export(read_schema)
export(read_tsv_arrow)
export(record_batch)
export(s3_bucket)
export(schema)
export(set_cpu_count)
export(starts_with)
Expand Down

18 changes: 14 additions & 4 deletions
r/R/arrow-package.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -53,18 +53,28 @@

#' Is the C++ Arrow library available?
#'
#' You won't generally need to call this function, but it's here in case it
#' helps for development purposes.
#' You won't generally need to call these function, but they're made available
#' for diagnostic purposes.
#' @return `TRUE` or `FALSE` depending on whether the package was installed
#' with the Arrow C++ library. If `FALSE`, you'll need to install the C++
#' library and then reinstall the R package. See [install_arrow()] for help.
#' with the Arrow C++ library (check with `arrow_available()`) or with S3
#' support enabled (check with `arrow_with_s3()`).
#' @export
#' @examples
#' arrow_available()
#' arrow_with_s3()
#' @seealso If either of these are `FALSE`, see
#' `vignette("install", package = "arrow")` for guidance on reinstalling the
#' package.
arrow_available <- function() {
 .Call(`_arrow_available`)
}

#' @rdname arrow_available
#' @export
arrow_with_s3 <- function() {
 .Call(`_s3_available`)
}

option_use_threads <- function() {
 !is_false(getOption("arrow.use_threads"))
}
Expand Down

12 changes: 12 additions & 0 deletions
r/R/arrowExports.R

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8 changes: 3 additions & 5 deletions
r/R/csv.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -77,7 +77,8 @@
#' `col_names`, and the CSV file has a header row that would otherwise be used
#' to idenfity column names, you'll need to add `skip = 1` to skip that row.
#'
#' @param file A character file name or URI, `raw` vector, or an Arrow input stream.
#' @param file A character file name or URI, `raw` vector, an Arrow input stream,
#' or a `FileSystem` with path (`SubTreeFileSystem`).
#' If a file name, a memory-mapped Arrow [InputStream] will be opened and
#' closed when finished; compression will be detected from the file extension
#' and handled automatically. If an input stream is provided, it will be left
Expand DownExpand Up@@ -123,8 +124,6 @@
#' parsing options provided in other arguments (e.g. `delim`, `quote`, etc.).
#' @param convert_options see [file reader options][CsvReadOptions]
#' @param read_options see [file reader options][CsvReadOptions]
#' @param filesystem A [FileSystem] where `file` can be found if it is a
#' string file path; default is the local file system
#' @param as_data_frame Should the function return a `data.frame` (default) or
#' an Arrow [Table]?
#'
Expand DownExpand Up@@ -156,7 +155,6 @@ read_delim_arrow <- function(file,
 parse_options = NULL,
 convert_options = NULL,
 read_options = NULL,
 filesystem = NULL,
 as_data_frame = TRUE,
 timestamp_parsers = NULL) {
 if (inherits(schema, "Schema")) {
Expand DownExpand Up@@ -186,7 +184,7 @@ read_delim_arrow <- function(file,
 }

 if (!inherits(file, "InputStream")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- CsvTableReader$create(
Expand Down

3 changes: 0 additions & 3 deletions
r/R/dataset-factory.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -44,9 +44,6 @@ DatasetFactory$create <- function(x,
 if (is_list_of(x, "DatasetFactory")) {
 return(shared_ptr(DatasetFactory, dataset___UnionDatasetFactory__Make(x)))
 }
 if (!is.string(x)) {
 stop("'x' must be a string or a list of DatasetFactory", call. = FALSE)
 }

 path_and_fs <- get_path_and_filesystem(x, filesystem)
 selector <- FileSelector$create(path_and_fs$path, allow_not_found = FALSE, recursive = TRUE)
Expand Down

9 changes: 3 additions & 6 deletions
r/R/dataset-write.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -27,8 +27,8 @@
#' and `group_by()` operations done on the dataset. `filter()` queries will be
#' applied to restrict written rows.
#' Note that `select()`-ed columns may not be renamed.
#' @param path string pathor URI to a directory to write to (directory will be
#' created if it does not exist)
#' @param path string path, URI, or `SubTreeFileSystem` referencing a directory
#' to write to (directory will be created if it does not exist)
#' @param format file format to write the dataset to. Currently supported
#' formats are "feather" (aka "ipc") and "parquet". Default is to write to the
#' same format as `dataset`.
Expand All@@ -41,8 +41,6 @@
#' will yield `"part-0.feather", ...`.
#' @param hive_style logical: write partition segments as Hive-style
#' (`key1=value1/key2=value2/file.ext`) or as just bare values. Default is `TRUE`.
#' @param filesystem A [FileSystem] where the dataset should be written if it is a
#' string file path; default is the local file system
#' @param ... additional format-specific arguments. For available Parquet
#' options, see [write_parquet()].
#' @return The input `dataset`, invisibly
Expand All@@ -53,7 +51,6 @@ write_dataset <- function(dataset,
 partitioning = dplyr::group_vars(dataset),
 basename_template = paste0("part-{i}.", as.character(format)),
 hive_style = TRUE,
 filesystem = NULL,
 ...) {
 if (inherits(dataset, "arrow_dplyr_query")) {
 # We can select a subset of columns but we can't rename them
Expand All@@ -79,7 +76,7 @@ write_dataset <- function(dataset,
 }
 }

 path_and_fs <- get_path_and_filesystem(path, filesystem)
 path_and_fs <- get_path_and_filesystem(path)
 options <- FileWriteOptions$create(format, table = scanner, ...)

 dataset___Dataset__Write(options, path_and_fs$fs, path_and_fs$path,
Expand Down

15 changes: 6 additions & 9 deletions
r/R/feather.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -24,9 +24,8 @@
#' and the version 2 specification, which is the Apache Arrow IPC file format.
#'
#' @param x `data.frame`, [RecordBatch], or [Table]
#' @param sink A string file path, URI, or [OutputStream]
#' @param filesystem A [FileSystem] where `sink` should be written if it is a
#' string file path; default is the local file system
#' @param sink A string file path, URI, or [OutputStream], or path in a file
#' system (`SubTreeFileSystem`)
Comment thread
nealrichardson marked this conversation as resolved.


Outdated

#' @param version integer Feather file version. Version 2 is the current.
#' Version 1 is the more limited legacy format.
#' @param chunk_size For V2 files, the number of rows that each chunk of data
Expand DownExpand Up@@ -54,7 +53,6 @@
#' @include arrow-package.R
write_feather <- function(x,
 sink,
 filesystem = NULL,
 version = 2,
 chunk_size = 65536L,
 compression = c("default", "lz4", "uncompressed", "zstd"),
Expand DownExpand Up@@ -108,11 +106,10 @@ write_feather <- function(x,
 }
 assert_is(x, "Table")

 if (is.string(sink)) {
 sink <- make_output_stream(sink, filesystem)
 if (!inherits(sink, "OutputStream")) {
 sink <- make_output_stream(sink)
 on.exit(sink$close())
 }
 assert_is(sink, "OutputStream")
 ipc___WriteFeather__Table(sink, x, version, chunk_size, compression, compression_level)
 invisible(x_out)
}
Expand DownExpand Up@@ -144,9 +141,9 @@ write_feather <- function(x,
#' # Can select columns
#' df <- read_feather(tf, col_select = starts_with("d"))
#' }
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, filesystem = NULL, ...) {
read_feather <- function(file, col_select = NULL, as_data_frame = TRUE, ...) {
 if (!inherits(file, "RandomAccessFile")) {
 file <- make_readable_file(file, filesystem = filesystem)
 file <- make_readable_file(file)
 on.exit(file$close())
 }
 reader <- FeatherReader$create(file, ...)
Expand Down
Loading