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ARROW-16144: [R] Write compressed data streams (particularly over S3) #13183

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ARROW-16144: [R] Write compressed data streams (particularly over S3) #13183

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boshek
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@boshek boshek commented May 18, 2022

This PR enables reading/writing compressed data streams over s3 and locally and adds some tests to test some of those round trips. For the filesystem path I had to do a little regex on the string for compression detection but any feedback on alternative approaches is very welcome. Previously supplying a file with a compression extension wrote out an uncompressed file. Here is a reprex of the updated writing behaviour:

library(arrow, warn.conflicts = FALSE)
## local
write_csv_arrow(mtcars, file = file)
write_csv_arrow(mtcars, file = comp_file)
file.size(file)
[1] 1303
file.size(comp_file)
[1] 567

## or with s3
dir <- tempfile()
dir.create(dir)
subdir <- file.path(dir, "bucket")
dir.create(subdir)

minio_server <- processx::process$new("minio", args = c("server", dir), supervise = TRUE)
Sys.sleep(2)
stopifnot(minio_server$is_alive())

s3_uri <- "s3://minioadmin:minioadmin@?scheme=http&endpoint_override=localhost%3A9000"
bucket <- s3_bucket(s3_uri)

write_csv_arrow(mtcars, bucket$path("bucket/data.csv.gz"))
write_csv_arrow(mtcars, bucket$path("bucket/data.csv"))

file.size(file.path(subdir, "data.csv.gz"))
[1] 567
file.size(file.path(subdir, "data.csv"))
[1] 1303

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Thanks for opening a pull request!

If this is not a minor PR. Could you open an issue for this pull request on JIRA? https://issues.apache.org/jira/browse/ARROW

Opening JIRAs ahead of time contributes to the Openness of the Apache Arrow project.

Then could you also rename pull request title in the following format?

ARROW-${JIRA_ID}: [${COMPONENT}] ${SUMMARY}

or

MINOR: [${COMPONENT}] ${SUMMARY}

See also:

@boshek boshek changed the title Arrow 16144: [R] Write compressed data streams (particularly over S3) ARROW-16144: [R] Write compressed data streams (particularly over S3) May 18, 2022
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⚠️ Ticket has not been started in JIRA, please click 'Start Progress'.

@boshek boshek marked this pull request as ready for review May 18, 2022 04:57
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This is a nice addition

r/R/io.R Outdated Show resolved Hide resolved
r/R/io.R Outdated Show resolved Hide resolved
r/tests/testthat/test-csv.R Outdated Show resolved Hide resolved
r/tests/testthat/test-s3-minio.R Show resolved Hide resolved
@@ -292,7 +292,7 @@ make_readable_file <- function(file, mmap = TRUE, compression = NULL, filesystem
file
}

make_output_stream <- function(x, filesystem = NULL) {
make_output_stream <- function(x, filesystem = NULL, compression = NULL) {
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One thing to watch out here: sometimes people name their parquet files something.parquet.snappy, but you wouldn't use a CompressedOutputStream for that, you'd pass the compression option to the parquet writer itself. I would guess that the make_readable_file() path handles this already, maybe that can be a model (or maybe it doesn't and needs to).

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So for the parquet.snappy or even snappy.parquet I think it works because "snappy" isn't included here:

arrow/r/R/io.R

Lines 325 to 330 in 3df2e05

switch(tools::file_ext(path),
bz2 = "bz2",
gz = "gzip",
lz4 = "lz4",
zst = "zstd",
"uncompressed"

But if someone tried something like this we do get an error that isn't super informative. I think this is outside this PR so could the resolution here be to open another ticket for this specifically?

library(arrow, warn.conflicts = FALSE)
tf <- tempfile(fileext = ".parquet.gz")
write_parquet(data.frame(x = 1:5), tf, compression = "gzip", compression_level = 5)
read_parquet(tf)
#> Error: file must be a "RandomAccessFile"

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Sure, this fails on master too so ok to make a separate JIRA (please link to it here when you make it).

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boshek and others added 6 commits May 18, 2022 10:18
Co-authored-by: Neal Richardson <neal.p.richardson@gmail.com>
Co-authored-by: Neal Richardson <neal.p.richardson@gmail.com>
Co-authored-by: Neal Richardson <neal.p.richardson@gmail.com>
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ursabot commented May 19, 2022

Benchmark runs are scheduled for baseline = ce4dcbd and contender = d2cbe9e. d2cbe9e is a master commit associated with this PR. Results will be available as each benchmark for each run completes.
Conbench compare runs links:
[Finished ⬇️0.0% ⬆️0.0%] ec2-t3-xlarge-us-east-2
[Failed ⬇️1.29% ⬆️0.0%] test-mac-arm
[Failed ⬇️0.0% ⬆️0.0%] ursa-i9-9960x
[Finished ⬇️0.28% ⬆️0.08%] ursa-thinkcentre-m75q
Buildkite builds:
[Finished] d2cbe9e0 ec2-t3-xlarge-us-east-2
[Failed] d2cbe9e0 test-mac-arm
[Failed] d2cbe9e0 ursa-i9-9960x
[Finished] d2cbe9e0 ursa-thinkcentre-m75q
[Finished] ce4dcbdf ec2-t3-xlarge-us-east-2
[Failed] ce4dcbdf test-mac-arm
[Failed] ce4dcbdf ursa-i9-9960x
[Finished] ce4dcbdf ursa-thinkcentre-m75q
Supported benchmarks:
ec2-t3-xlarge-us-east-2: Supported benchmark langs: Python, R. Runs only benchmarks with cloud = True
test-mac-arm: Supported benchmark langs: C++, Python, R
ursa-i9-9960x: Supported benchmark langs: Python, R, JavaScript
ursa-thinkcentre-m75q: Supported benchmark langs: C++, Java

kou pushed a commit that referenced this pull request Feb 20, 2023
…Hub issue numbers (#34260)

Rewrite the Jira issue numbers to the GitHub issue numbers, so that the GitHub issue numbers are automatically linked to the issues by pkgdown's auto-linking feature.

Issue numbers have been rewritten based on the following correspondence.
Also, the pkgdown settings have been changed and updated to link to GitHub.

I generated the Changelog page using the `pkgdown::build_news()` function and verified that the links work correctly.

---
ARROW-6338	#5198
ARROW-6364	#5201
ARROW-6323	#5169
ARROW-6278	#5141
ARROW-6360	#5329
ARROW-6533	#5450
ARROW-6348	#5223
ARROW-6337	#5399
ARROW-10850	#9128
ARROW-10624	#9092
ARROW-10386	#8549
ARROW-6994	#23308
ARROW-12774	#10320
ARROW-12670	#10287
ARROW-16828	#13484
ARROW-14989	#13482
ARROW-16977	#13514
ARROW-13404	#10999
ARROW-16887	#13601
ARROW-15906	#13206
ARROW-15280	#13171
ARROW-16144	#13183
ARROW-16511	#13105
ARROW-16085	#13088
ARROW-16715	#13555
ARROW-16268	#13550
ARROW-16700	#13518
ARROW-16807	#13583
ARROW-16871	#13517
ARROW-16415	#13190
ARROW-14821	#12154
ARROW-16439	#13174
ARROW-16394	#13118
ARROW-16516	#13163
ARROW-16395	#13627
ARROW-14848	#12589
ARROW-16407	#13196
ARROW-16653	#13506
ARROW-14575	#13160
ARROW-15271	#13170
ARROW-16703	#13650
ARROW-16444	#13397
ARROW-15016	#13541
ARROW-16776	#13563
ARROW-15622	#13090
ARROW-18131	#14484
ARROW-18305	#14581
ARROW-18285	#14615
* Closes: #33631

Authored-by: SHIMA Tatsuya <ts1s1andn@gmail.com>
Signed-off-by: Sutou Kouhei <kou@clear-code.com>
fatemehp pushed a commit to fatemehp/arrow that referenced this pull request Feb 24, 2023
…to GitHub issue numbers (apache#34260)

Rewrite the Jira issue numbers to the GitHub issue numbers, so that the GitHub issue numbers are automatically linked to the issues by pkgdown's auto-linking feature.

Issue numbers have been rewritten based on the following correspondence.
Also, the pkgdown settings have been changed and updated to link to GitHub.

I generated the Changelog page using the `pkgdown::build_news()` function and verified that the links work correctly.

---
ARROW-6338	apache#5198
ARROW-6364	apache#5201
ARROW-6323	apache#5169
ARROW-6278	apache#5141
ARROW-6360	apache#5329
ARROW-6533	apache#5450
ARROW-6348	apache#5223
ARROW-6337	apache#5399
ARROW-10850	apache#9128
ARROW-10624	apache#9092
ARROW-10386	apache#8549
ARROW-6994	apache#23308
ARROW-12774	apache#10320
ARROW-12670	apache#10287
ARROW-16828	apache#13484
ARROW-14989	apache#13482
ARROW-16977	apache#13514
ARROW-13404	apache#10999
ARROW-16887	apache#13601
ARROW-15906	apache#13206
ARROW-15280	apache#13171
ARROW-16144	apache#13183
ARROW-16511	apache#13105
ARROW-16085	apache#13088
ARROW-16715	apache#13555
ARROW-16268	apache#13550
ARROW-16700	apache#13518
ARROW-16807	apache#13583
ARROW-16871	apache#13517
ARROW-16415	apache#13190
ARROW-14821	apache#12154
ARROW-16439	apache#13174
ARROW-16394	apache#13118
ARROW-16516	apache#13163
ARROW-16395	apache#13627
ARROW-14848	apache#12589
ARROW-16407	apache#13196
ARROW-16653	apache#13506
ARROW-14575	apache#13160
ARROW-15271	apache#13170
ARROW-16703	apache#13650
ARROW-16444	apache#13397
ARROW-15016	apache#13541
ARROW-16776	apache#13563
ARROW-15622	apache#13090
ARROW-18131	apache#14484
ARROW-18305	apache#14581
ARROW-18285	apache#14615
* Closes: apache#33631

Authored-by: SHIMA Tatsuya <ts1s1andn@gmail.com>
Signed-off-by: Sutou Kouhei <kou@clear-code.com>
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