1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740
|
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License. You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing,
# software distributed under the License is distributed on an
# "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
# KIND, either express or implied. See the License for the
# specific language governing permissions and limitations
# under the License.
#' @include arrow-object.R
#' @title FileSystem entry info
#' @usage NULL
#' @format NULL
#'
#' @section Methods:
#'
#' - `base_name()` : The file base name (component after the last directory
#' separator).
#' - `extension()` : The file extension
#'
#' @section Active bindings:
#'
#' - `$type`: The file type
#' - `$path`: The full file path in the filesystem
#' - `$size`: The size in bytes, if available. Only regular files are
#' guaranteed to have a size.
#' - `$mtime`: The time of last modification, if available.
#'
#' @rdname FileInfo
#' @export
FileInfo <- R6Class(
"FileInfo",
inherit = ArrowObject,
public = list(
base_name = function() fs___FileInfo__base_name(self),
extension = function() fs___FileInfo__extension(self)
),
active = list(
type = function(type) {
if (missing(type)) {
fs___FileInfo__type(self)
} else {
fs___FileInfo__set_type(self, type)
}
},
path = function(path) {
if (missing(path)) {
fs___FileInfo__path(self)
} else {
invisible(fs___FileInfo__set_path(self))
}
},
size = function(size) {
if (missing(size)) {
fs___FileInfo__size(self)
} else {
invisible(fs___FileInfo__set_size(self, size))
}
},
mtime = function(time) {
if (missing(time)) {
fs___FileInfo__mtime(self)
} else {
if (!inherits(time, "POSIXct") && length(time) == 1L) {
abort("invalid time")
}
invisible(fs___FileInfo__set_mtime(self, time))
}
}
)
)
#' @title file selector
#' @format NULL
#'
#' @section Factory:
#'
#' The `$create()` factory method instantiates a `FileSelector` given the 3 fields
#' described below.
#'
#' @section Fields:
#'
#' - `base_dir`: The directory in which to select files. If the path exists but
#' doesn't point to a directory, this should be an error.
#' - `allow_not_found`: The behavior if `base_dir` doesn't exist in the
#' filesystem. If `FALSE`, an error is returned. If `TRUE`, an empty
#' selection is returned
#' - `recursive`: Whether to recurse into subdirectories.
#'
#' @rdname FileSelector
#' @export
FileSelector <- R6Class(
"FileSelector",
inherit = ArrowObject,
active = list(
base_dir = function() fs___FileSelector__base_dir(self),
allow_not_found = function() fs___FileSelector__allow_not_found(self),
recursive = function() fs___FileSelector__recursive(self)
)
)
FileSelector$create <- function(base_dir, allow_not_found = FALSE, recursive = FALSE) {
fs___FileSelector__create(clean_path_rel(base_dir), allow_not_found, recursive)
}
#' @title FileSystem classes
#' @description `FileSystem` is an abstract file system API,
#' `LocalFileSystem` is an implementation accessing files
#' on the local machine. `SubTreeFileSystem` is an implementation that delegates
#' to another implementation after prepending a fixed base path
#'
#' @section Factory:
#'
#' `LocalFileSystem$create()` returns the object and takes no arguments.
#'
#' `SubTreeFileSystem$create()` takes the following arguments:
#'
#' - `base_path`, a string path
#' - `base_fs`, a `FileSystem` object
#'
#' `S3FileSystem$create()` optionally takes arguments:
#'
#' - `anonymous`: logical, default `FALSE`. If true, will not attempt to look up
#' credentials using standard AWS configuration methods.
#' - `access_key`, `secret_key`: authentication credentials. If one is provided,
#' the other must be as well. If both are provided, they will override any
#' AWS configuration set at the environment level.
#' - `session_token`: optional string for authentication along with
#' `access_key` and `secret_key`
#' - `role_arn`: string AWS ARN of an AccessRole. If provided instead of `access_key` and
#' `secret_key`, temporary credentials will be fetched by assuming this role.
#' - `session_name`: optional string identifier for the assumed role session.
#' - `external_id`: optional unique string identifier that might be required
#' when you assume a role in another account.
#' - `load_frequency`: integer, frequency (in seconds) with which temporary
#' credentials from an assumed role session will be refreshed. Default is
#' 900 (i.e. 15 minutes)
#' - `region`: AWS region to connect to. If omitted, the AWS library will
#' provide a sensible default based on client configuration, falling back
#' to "us-east-1" if no other alternatives are found.
#' - `endpoint_override`: If non-empty, override region with a connect string
#' such as "localhost:9000". This is useful for connecting to file systems
#' that emulate S3.
#' - `scheme`: S3 connection transport (default "https")
#' - `proxy_options`: optional string, URI of a proxy to use when connecting
#' to S3
#' - `background_writes`: logical, whether `OutputStream` writes will be issued
#' in the background, without blocking (default `TRUE`)
#' - `allow_bucket_creation`: logical, if TRUE, the filesystem will create
#' buckets if `$CreateDir()` is called on the bucket level (default `FALSE`).
#' - `allow_bucket_deletion`: logical, if TRUE, the filesystem will delete
#' buckets if`$DeleteDir()` is called on the bucket level (default `FALSE`).
#' - `check_directory_existence_before_creation`: logical, check if directory
#' already exists or not before creation. Helpful for cloud storage operations
#' where object mutation operations are rate limited or existing directories
#' are read-only. (default `FALSE`).
#' - `request_timeout`: Socket read time on Windows and macOS in seconds. If
#' negative, the AWS SDK default (typically 3 seconds).
#' - `connect_timeout`: Socket connection timeout in seconds. If negative, AWS
#' SDK default is used (typically 1 second).
#'
#' `GcsFileSystem$create()` optionally takes arguments:
#'
#' - `anonymous`: logical, default `FALSE`. If true, will not attempt to look up
#' credentials using standard GCS configuration methods.
#' - `access_token`: optional string for authentication. Should be provided along
#' with `expiration`
#' - `expiration`: `POSIXct`. optional datetime representing point at which
#' `access_token` will expire.
#' - `json_credentials`: optional string for authentication. Either a string
#' containing JSON credentials or a path to their location on the filesystem.
#' If a path to credentials is given, the file should be UTF-8 encoded.
#' - `endpoint_override`: if non-empty, will connect to provided host name / port,
#' such as "localhost:9001", instead of default GCS ones. This is primarily useful
#' for testing purposes.
#' - `scheme`: connection transport (default "https")
#' - `default_bucket_location`: the default location (or "region") to create new
#' buckets in.
#' - `retry_limit_seconds`: the maximum amount of time to spend retrying if
#' the filesystem encounters errors. Default is 15 seconds.
#' - `default_metadata`: default metadata to write in new objects.
#' - `project_id`: the project to use for creating buckets.
#'
#' @section Methods:
#'
#' - `path(x)`: Create a `SubTreeFileSystem` from the current `FileSystem`
#' rooted at the specified path `x`.
#' - `cd(x)`: Create a `SubTreeFileSystem` from the current `FileSystem`
#' rooted at the specified path `x`.
#' - `ls(path, ...)`: List files or objects at the given path or from the root
#' of the `FileSystem` if `path` is not provided. Additional arguments passed
#' to `FileSelector$create`, see [FileSelector][FileSelector].
#' - `$GetFileInfo(x)`: `x` may be a [FileSelector][FileSelector] or a character
#' vector of paths. Returns a list of [FileInfo][FileInfo]
#' - `$CreateDir(path, recursive = TRUE)`: Create a directory and subdirectories.
#' - `$DeleteDir(path)`: Delete a directory and its contents, recursively.
#' - `$DeleteDirContents(path)`: Delete a directory's contents, recursively.
#' Like `$DeleteDir()`,
#' but doesn't delete the directory itself. Passing an empty path (`""`) will
#' wipe the entire filesystem tree.
#' - `$DeleteFile(path)` : Delete a file.
#' - `$DeleteFiles(paths)` : Delete many files. The default implementation
#' issues individual delete operations in sequence.
#' - `$Move(src, dest)`: Move / rename a file or directory. If the destination
#' exists:
#' if it is a non-empty directory, an error is returned
#' otherwise, if it has the same type as the source, it is replaced
#' otherwise, behavior is unspecified (implementation-dependent).
#' - `$CopyFile(src, dest)`: Copy a file. If the destination exists and is a
#' directory, an error is returned. Otherwise, it is replaced.
#' - `$OpenInputStream(path)`: Open an [input stream][InputStream] for
#' sequential reading.
#' - `$OpenInputFile(path)`: Open an [input file][RandomAccessFile] for random
#' access reading.
#' - `$OpenOutputStream(path)`: Open an [output stream][OutputStream] for
#' sequential writing.
#' - `$OpenAppendStream(path)`: Open an [output stream][OutputStream] for
#' appending.
#'
#' @section Active bindings:
#'
#' - `$type_name`: string filesystem type name, such as "local", "s3", etc.
#' - `$region`: string AWS region, for `S3FileSystem` and `SubTreeFileSystem`
#' containing a `S3FileSystem`
#' - `$base_fs`: for `SubTreeFileSystem`, the `FileSystem` it contains
#' - `$base_path`: for `SubTreeFileSystem`, the path in `$base_fs` which is considered
#' root in this `SubTreeFileSystem`.
#' - `$options`: for `GcsFileSystem`, the options used to create the
#' `GcsFileSystem` instance as a `list`
#'
#' @section Notes:
#'
#' On S3FileSystem, `$CreateDir()` on a top-level directory creates a new bucket.
#' When S3FileSystem creates new buckets (assuming allow_bucket_creation is TRUE),
#' it does not pass any non-default settings. In AWS S3, the bucket and all
#' objects will be not publicly visible, and will have no bucket policies
#' and no resource tags. To have more control over how buckets are created,
#' use a different API to create them.
#'
#' On S3FileSystem, output is only produced for fatal errors or when printing
#' return values. For troubleshooting, the log level can be set using the
#' environment variable `ARROW_S3_LOG_LEVEL` (e.g.,
#' `Sys.setenv("ARROW_S3_LOG_LEVEL"="DEBUG")`). The log level must be set prior
#' to running any code that interacts with S3. Possible values include 'FATAL'
#' (the default), 'ERROR', 'WARN', 'INFO', 'DEBUG' (recommended), 'TRACE', and
#' 'OFF'.
#'
#' @usage NULL
#' @format NULL
#' @docType class
#'
#' @rdname FileSystem
#' @name FileSystem
#' @export
FileSystem <- R6Class(
"FileSystem",
inherit = ArrowObject,
public = list(
GetFileInfo = function(x) {
if (inherits(x, "FileSelector")) {
fs___FileSystem__GetTargetInfos_FileSelector(self, x)
} else if (is.character(x)) {
fs___FileSystem__GetTargetInfos_Paths(self, clean_path_rel(x))
} else {
abort("incompatible type for FileSystem$GetFileInfo()")
}
},
CreateDir = function(path, recursive = TRUE) {
fs___FileSystem__CreateDir(self, clean_path_rel(path), isTRUE(recursive))
},
DeleteDir = function(path) {
fs___FileSystem__DeleteDir(self, clean_path_rel(path))
},
DeleteDirContents = function(path) {
fs___FileSystem__DeleteDirContents(self, clean_path_rel(path))
},
DeleteFile = function(path) {
fs___FileSystem__DeleteFile(self, clean_path_rel(path))
},
DeleteFiles = function(paths) {
fs___FileSystem__DeleteFiles(self, clean_path_rel(paths))
},
Move = function(src, dest) {
fs___FileSystem__Move(self, clean_path_rel(src), clean_path_rel(dest))
},
CopyFile = function(src, dest) {
fs___FileSystem__CopyFile(self, clean_path_rel(src), clean_path_rel(dest))
},
OpenInputStream = function(path) {
fs___FileSystem__OpenInputStream(self, clean_path_rel(path))
},
OpenInputFile = function(path) {
fs___FileSystem__OpenInputFile(self, clean_path_rel(path))
},
OpenOutputStream = function(path) {
fs___FileSystem__OpenOutputStream(self, clean_path_rel(path))
},
OpenAppendStream = function(path) {
fs___FileSystem__OpenAppendStream(self, clean_path_rel(path))
},
# Friendlier R user interface
path = function(x) SubTreeFileSystem$create(x, self),
cd = function(x) SubTreeFileSystem$create(x, self),
ls = function(path = "", ...) {
selector <- FileSelector$create(path, ...) # ... for recursive = TRUE
infos <- self$GetFileInfo(selector)
map_chr(infos, ~ .$path)
# TODO: add full.names argument like base::dir() (default right now is TRUE)
# TODO: see fs package for glob/regexp filtering
# TODO: verbose method that shows other attributes as df
# TODO: print methods for FileInfo, SubTreeFileSystem, S3FileSystem
}
),
active = list(
type_name = function() fs___FileSystem__type_name(self),
url_scheme = function() {
fs_type_name <- self$type_name
if (identical(fs_type_name, "subtree")) {
# Recurse
return(self$base_fs$url_scheme)
}
# Some type_names are the url scheme but others aren't
type_map <- list(
local = "file",
gcs = "gs"
)
type_map[[fs_type_name]] %||% fs_type_name
}
)
)
FileSystem$from_uri <- function(uri) {
assert_that(is.string(uri))
fs___FileSystemFromUri(uri)
}
get_paths_and_filesystem <- function(x, filesystem = NULL) {
# Wrapper around FileSystem$from_uri that handles local paths
# and an optional explicit filesystem
if (inherits(x, "SubTreeFileSystem")) {
return(list(fs = x$base_fs, path = x$base_path))
}
assert_that(is.character(x))
are_urls <- are_urls(x)
if (any(are_urls)) {
if (!all(are_urls)) {
stop("Vectors of mixed paths and URIs are not supported", call. = FALSE)
}
if (!is.null(filesystem)) {
# Stop? Can't have URL (which yields a fs) and another fs
}
x <- lapply(x, FileSystem$from_uri)
if (length(unique(map(x, ~ class(.$fs)))) > 1) {
stop(
"Vectors of URIs for different file systems are not supported",
call. = FALSE
)
}
fs <- x[[1]]$fs
path <- map_chr(x, ~ .$path) # singular name "path" used for compatibility
} else {
fs <- filesystem %||% LocalFileSystem$create()
if (inherits(fs, "LocalFileSystem")) {
path <- clean_path_abs(x)
} else {
path <- clean_path_rel(x)
}
}
list(
fs = fs,
path = path
)
}
# variant of the above function that asserts that x is either a scalar string
# or a SubTreeFileSystem
get_path_and_filesystem <- function(x, filesystem = NULL) {
assert_that(is.string(x) || inherits(x, "SubTreeFileSystem"))
get_paths_and_filesystem(x, filesystem)
}
is_url <- function(x) is.string(x) && grepl("://", x)
is_http_url <- function(x) is_url(x) && grepl("^http", x)
are_urls <- function(x) if (!is.character(x)) FALSE else grepl("://", x)
#' @usage NULL
#' @format NULL
#' @rdname FileSystem
#' @export
LocalFileSystem <- R6Class("LocalFileSystem", inherit = FileSystem)
LocalFileSystem$create <- function() {
# from_uri needs a non-empty path, so just use a placeholder of /_
FileSystem$from_uri("file:///_")$fs
}
#' @usage NULL
#' @format NULL
#' @rdname FileSystem
#' @importFrom utils modifyList
#' @export
S3FileSystem <- R6Class(
"S3FileSystem",
inherit = FileSystem,
active = list(
region = function() fs___S3FileSystem__region(self)
)
)
S3FileSystem$create <- function(anonymous = FALSE, ...) {
args <- list2(...)
if (anonymous) {
invalid_args <- intersect(
c(
"access_key",
"secret_key",
"session_token",
"role_arn",
"session_name",
"external_id",
"load_frequency",
"allow_bucket_creation",
"allow_bucket_deletion",
"check_directory_existence_before_creation"
),
names(args)
)
if (length(invalid_args)) {
stop("Cannot specify ", oxford_paste(invalid_args), " when anonymous = TRUE", call. = FALSE)
}
} else {
keys_present <- length(intersect(c("access_key", "secret_key"), names(args)))
if (keys_present == 1) {
stop("Key authentication requires both access_key and secret_key", call. = FALSE)
}
if ("session_token" %in% names(args) && keys_present != 2) {
stop(
"In order to initialize a session with temporary credentials, ",
"both secret_key and access_key must be provided ",
"in addition to session_token.",
call. = FALSE
)
}
arn <- "role_arn" %in% names(args)
if (keys_present == 2 && arn) {
stop("Cannot provide both key authentication and role_arn", call. = FALSE)
}
arn_extras <- intersect(c("session_name", "external_id", "load_frequency"), names(args))
if (length(arn_extras) > 0 && !arn) {
stop("Cannot specify ", oxford_paste(arn_extras), " without providing a role_arn string", call. = FALSE)
}
}
args <- c(modifyList(default_s3_options, args), anonymous = anonymous)
exec(fs___S3FileSystem__create, !!!args)
}
default_s3_options <- list(
access_key = "",
secret_key = "",
session_token = "",
role_arn = "",
session_name = "",
external_id = "",
load_frequency = 900L,
region = "",
endpoint_override = "",
scheme = "",
proxy_options = "",
background_writes = TRUE,
allow_bucket_creation = FALSE,
allow_bucket_deletion = FALSE,
check_directory_existence_before_creation = FALSE,
connect_timeout = -1,
request_timeout = -1
)
#' Connect to an AWS S3 bucket
#'
#' `s3_bucket()` is a convenience function to create an `S3FileSystem` object
#' that automatically detects the bucket's AWS region and holding onto the its
#' relative path.
#'
#' @param bucket string S3 bucket name or path
#' @param ... Additional connection options, passed to `S3FileSystem$create()`
#'
#' @details By default, \code{\link{s3_bucket}} and other
#' \code{\link{S3FileSystem}} functions only produce output for fatal errors
#' or when printing their return values. When troubleshooting problems, it may
#' be useful to increase the log level. See the Notes section in
#' \code{\link{S3FileSystem}} for more information or see Examples below.
#'
#' @return A `SubTreeFileSystem` containing an `S3FileSystem` and the bucket's
#' relative path. Note that this function's success does not guarantee that you
#' are authorized to access the bucket's contents.
#' @examplesIf FALSE
#' bucket <- s3_bucket("arrow-datasets")
#'
#' @examplesIf FALSE
#' # Turn on debug logging. The following line of code should be run in a fresh
#' # R session prior to any calls to `s3_bucket()` (or other S3 functions)
#' Sys.setenv("ARROW_S3_LOG_LEVEL" = "DEBUG")
#' bucket <- s3_bucket("arrow-datasets")
#'
#' @export
s3_bucket <- function(bucket, ...) {
assert_that(is.string(bucket))
args <- list2(...)
# If user specifies args, they must specify region as arg, env var, or config
if (length(args) == 0) {
# Use FileSystemFromUri to detect the bucket's region
if (!is_url(bucket)) {
bucket <- paste0("s3://", bucket)
}
fs_and_path <- FileSystem$from_uri(bucket)
fs <- fs_and_path$fs
} else {
# If there are no additional S3Options, we can use that filesystem
fs <- exec(S3FileSystem$create, !!!args)
}
# Return a subtree pointing at that bucket path
SubTreeFileSystem$create(bucket, fs)
}
#' Connect to a Google Cloud Storage (GCS) bucket
#'
#' `gs_bucket()` is a convenience function to create an `GcsFileSystem` object
#' that holds onto its relative path
#'
#' @param bucket string GCS bucket name or path
#' @param ... Additional connection options, passed to `GcsFileSystem$create()`
#' @return A `SubTreeFileSystem` containing an `GcsFileSystem` and the bucket's
#' relative path. Note that this function's success does not guarantee that you
#' are authorized to access the bucket's contents.
#' @examplesIf FALSE
#' bucket <- gs_bucket("arrow-datasets")
#' @export
gs_bucket <- function(bucket, ...) {
assert_that(is.string(bucket))
args <- list2(...)
fs <- exec(GcsFileSystem$create, !!!args)
SubTreeFileSystem$create(bucket, fs)
}
#' @usage NULL
#' @format NULL
#' @rdname FileSystem
#' @export
GcsFileSystem <- R6Class(
"GcsFileSystem",
inherit = FileSystem,
active = list(
options = function() {
out <- fs___GcsFileSystem__options(self)
# Convert from nanoseconds to POSIXct w/ UTC tz
if ("expiration" %in% names(out)) {
out$expiration <- as.POSIXct(
out$expiration / 1000000000,
origin = "1970-01-01",
tz = "UTC"
)
}
out
}
)
)
GcsFileSystem$create <- function(anonymous = FALSE, retry_limit_seconds = 15, ...) {
# The default retry limit in C++ is 15 minutes, but that is experienced as
# hanging in an interactive context, so default is set here to 15 seconds.
options <- list(...)
# Validate options
if (isTRUE(anonymous)) {
invalid_args <- intersect(
c("access_token", "expiration", "json_credentials"),
names(options)
)
if (length(invalid_args)) {
stop(
"Cannot specify ",
oxford_paste(invalid_args),
" when anonymous = TRUE",
call. = FALSE
)
}
} else {
token_args <- intersect(c("access_token", "expiration"), names(options))
if (!is.null(options[["json_credentials"]]) && length(token_args) > 0) {
stop("Cannot provide access_token with json_credentials", call. = FALSE)
} else if (length(token_args) == 1) {
stop("token auth requires both 'access_token' and 'expiration'", call. = FALSE)
}
}
valid_opts <- c(
"access_token",
"expiration",
"json_credentials",
"endpoint_override",
"scheme",
"default_bucket_location",
"default_metadata",
"project_id"
)
invalid_opts <- setdiff(names(options), valid_opts)
if (length(invalid_opts)) {
stop(
"Invalid options for GcsFileSystem: ",
oxford_paste(invalid_opts),
call. = FALSE
)
}
# Stop if expiration isn't a POSIXct
if ("expiration" %in% names(options) && !inherits(options$expiration, "POSIXct")) {
stop(
paste(
"Option 'expiration' must be of class POSIXct, not",
class(options$expiration)[[1]]
),
call. = FALSE
)
}
options$retry_limit_seconds <- retry_limit_seconds
# Handle reading json_credentials from the filesystem
if ("json_credentials" %in% names(options) && file.exists(options[["json_credentials"]])) {
options[["json_credentials"]] <- paste(read_file_utf8(options[["json_credentials"]]), collapse = "\n")
}
fs___GcsFileSystem__Make(anonymous, options)
}
#' @usage NULL
#' @format NULL
#' @rdname FileSystem
#' @export
SubTreeFileSystem <- R6Class(
"SubTreeFileSystem",
inherit = FileSystem,
public = list(
print = function(...) {
cat(
"SubTreeFileSystem: ",
self$url_scheme,
"://",
self$base_path,
"\n",
sep = ""
)
invisible(self)
}
),
active = list(
base_fs = function() {
fs___SubTreeFileSystem__base_fs(self)
},
base_path = function() fs___SubTreeFileSystem__base_path(self)
)
)
SubTreeFileSystem$create <- function(base_path, base_fs = NULL) {
fs_and_path <- get_path_and_filesystem(base_path, base_fs)
fs___SubTreeFileSystem__create(fs_and_path$path, fs_and_path$fs)
}
#' @export
`$.SubTreeFileSystem` <- function(x, name, ...) {
# This is to allow delegating methods/properties to the base_fs
assert_that(is.string(name))
if (name %in% ls(envir = x)) {
get(name, x)
} else if (name %in% ls(envir = x$base_fs)) {
get(name, x$base_fs)
} else {
NULL
}
}
#' Copy files between FileSystems
#'
#' @param from A string path to a local directory or file, a URI, or a
#' `SubTreeFileSystem`. Files will be copied recursively from this path.
#' @param to A string path to a local directory or file, a URI, or a
#' `SubTreeFileSystem`. Directories will be created as necessary
#' @param chunk_size The maximum size of block to read before flushing
#' to the destination file. A larger chunk_size will use more memory while
#' copying but may help accommodate high latency FileSystems.
#' @return Nothing: called for side effects in the file system
#' @export
#' @examplesIf FALSE
#' # Copy an S3 bucket's files to a local directory:
#' copy_files("s3://your-bucket-name", "local-directory")
#' # Using a FileSystem object
#' copy_files(s3_bucket("your-bucket-name"), "local-directory")
#' # Or go the other way, from local to S3
#' copy_files("local-directory", s3_bucket("your-bucket-name"))
copy_files <- function(from, to, chunk_size = 1024L * 1024L) {
from <- get_path_and_filesystem(from)
to <- get_path_and_filesystem(to)
invisible(fs___CopyFiles(
from$fs,
FileSelector$create(from$path, recursive = TRUE),
to$fs,
to$path,
chunk_size,
option_use_threads()
))
}
clean_path_abs <- function(path) {
# Make sure we have a valid, absolute, forward-slashed path for passing to Arrow
enc2utf8(normalizePath(path, winslash = "/", mustWork = FALSE))
}
clean_path_rel <- function(path) {
# Make sure all path separators are "/", not "\" as on Windows
path_sep <- ifelse(tolower(Sys.info()[["sysname"]]) == "windows", "\\\\", "/")
gsub(path_sep, "/", path)
}
read_file_utf8 <- function(file) {
res <- readBin(file, "raw", n = file.size(file))
res <- rawToChar(res)
Encoding(res) <- "UTF-8"
res
}
|