ARROW-6532 [R] write_parquet() uses writer properties (general and arrow specific) #5451

romainfrancois · 2019-09-20T09:00:14Z

This adds parameters to write_parquet() to control compression, whether to use dictionary, etc ... on top of the C++ classes parquet::WriterProperties and parquet::ArrowWriterProperties e.g.

write_parquet(tab, file, compression = "gzip", compression_level = 7)

nealrichardson · 2019-09-20T14:58:21Z

Yeah, I'm not sure about this on a few levels. I think the R I want to type to write a compressed Parquet file looks like write_parquet(df, file="file.parquet", compression="snappy"). This should be more naturally exposed to the causal user, without having to create a CompressedOutputStream directly.

I'm also not sure whether this works as intended. The Parquet C++ code seems to have its own compression and writing logic; that may be historical artifact, or it may be meaningful. Maybe we can get away without implementing bindings for those classes--the proof would be a passing test of writing a compressed parquet file and reading it back in. Then again, maybe in principle we should write the Parquet bindings to match the C++ library.

wesm · 2019-09-20T16:24:08Z

It is not a good idea to write a Parquet file into a CompressedOutputStream. Such file will not be readable with read_parquet.

Parquet already compresses data internally.

wesm · 2019-09-20T16:25:55Z

Here's the way we handle it in Python, you'll need to do the same thing in R

https://github.com/apache/arrow/blob/master/python/pyarrow/parquet.py#L363

romainfrancois · 2019-09-24T11:49:23Z

Some progress inspired from the python implementation. write_parquet() gains many parameters:

write_parquet <- function(
  table,
  sink, chunk_size = NULL,
  version = NULL, compression = NULL, use_dictionary = NULL, write_statistics = NULL, data_page_size = NULL,
  properties = ParquetWriterProperties$create(
    version = version,
    compression = compression,
    use_dictionary = use_dictionary,
    write_statistics = write_statistics,
    data_page_size = data_page_size
  ),

  use_deprecated_int96_timestamps = FALSE, coerce_timestamps = NULL, allow_truncated_timestamps = FALSE,
  arrow_properties = ParquetArrowWriterProperties$create(
    use_deprecated_int96_timestamps = use_deprecated_int96_timestamps,
    coerce_timestamps = coerce_timestamps,
    allow_truncated_timestamps = allow_truncated_timestamps
  )
)

that are managed by the classes ParquetWriterProperties and ParquetArrowWriterProperties.

Only simple versions so far, e.g. compression may only be a single string, so we may do:

library(arrow, warn.conflicts = FALSE)

df <- tibble::tibble(x = 1:5)
write_parquet(df, "/tmp/test.parquet", compression = "snappy")
read_parquet("/tmp/test.parquet")
#> # A tibble: 5 x 1
#>       x
#>   <int>
#> 1     1
#> 2     2
#> 3     3
#> 4     4
#> 5     5

but we can't e.g. specify specific variables to handle by such and such compression. This is a good place I think for a tidy select, e.g. something like that:

df <- tibble::tibble(x1 = 1:5, x2 = 1:5, y = 1:5)
write_parquet(df, "/tmp/test.parquet", 
  compression = list(snappy = starts_with("x"))
)

The list in python goes the other way, so if we do something similar it would look like

write_parquet(df, "/tmp/test.parquet", 
  compression = list(x1 = "snappy", x2 = "snappy")
)

perhaps we can have compression = only handle the same type of thing python does, but then come up with some helper function so that we'd have e.g.

write_parquet(df, "/tmp/test.parquet", 
  compression = compression_spec(snappy = starts_with("x"))
)

romainfrancois · 2019-09-25T06:38:22Z

One option we discussed with @nealrichardson was to be able to do e.g.

write_parquet(df, "/tmp/test.parquet", 
  compression = Codec$create("snappy", 5L)
)

But unfortunately, the C++ class arrow::util::Codec does not give a way to swim back to the compression level, so I can't do e.g. compression$level.

Instead, I followed python's lead and we can do this instead:

write_parquet(df, "/tmp/test.parquet", 
  compression = "snappy", 
  compression_level = 5L
)

romainfrancois · 2019-09-25T09:21:54Z

These arguments that are handled by ParquetWriterProperties can now be single values, unnamed vectors of the same length as the number of columns in the table, or named vectors: compression, compression_level, use_dictionary and write_statistics.

nealrichardson · 2019-09-25T17:45:29Z

Taking a look now; FTR Travis says

Missing link or links in documentation object 'write_parquet.Rd':

  ‘to_arrow’

r/R/compression.R

r/R/parquet.R

r/tests/testthat/test-parquet.R

codecov-io · 2019-09-26T16:48:37Z

Codecov Report

Merging #5451 into master will decrease coverage by 11.93%.
The diff coverage is 65.9%.

@@             Coverage Diff             @@
##           master    #5451       +/-   ##
===========================================
- Coverage    88.7%   76.76%   -11.94%     
===========================================
  Files         964       59      -905     
  Lines      128215     4330   -123885     
  Branches     1501        0     -1501     
===========================================
- Hits       113731     3324   -110407     
+ Misses      14119     1006    -13113     
+ Partials      365        0      -365

Impacted Files	Coverage Δ
r/R/record-batch.R	`97.36% <ø> (-0.04%)`	⬇️
r/R/field.R	`92.85% <ø> (-0.48%)`	⬇️
r/src/arrow_types.h	`96% <ø> (ø)`	⬆️
r/R/schema.R	`31.25% <ø> (+7.72%)`	⬆️
r/R/type.R	`83.9% <ø> (-0.19%)`	⬇️
r/R/enums.R	`0% <ø> (ø)`	⬆️
r/R/message.R	`75% <ø> (+21.15%)`	⬆️
r/R/array.R	`77.14% <ø> (+4.92%)`	⬆️
r/src/compression.cpp	`85.71% <0%> (-14.29%)`	⬇️
r/R/feather.R	`63.33% <100%> (ø)`	⬆️
... and 928 more

Continue to review full report at Codecov.

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nealrichardson

A few more notes. I'd also like to see better coverage on https://codecov.io/gh/apache/arrow/pull/5451/diff

nealrichardson · 2019-09-26T17:06:35Z

r/R/parquet.R

I'd write this function as

make_valid_version <- function(version, valid_versions = valid_parquet_version) { pq_version <- valid_version[[version]] if (is.null(pq_version)) { stop('"version" should be one of ', oxford_paste(names(valid_versions), "or"), call.=FALSE) } pq_version }

As it stands, make_valid_version(1) won't work, and it seems like it should.

Per the codecov report, this code isn't being exercised.

wfm:

arrow:::make_valid_version("1.0") #> [1] 0 arrow:::make_valid_version("2.0") #> [1] 1 arrow:::make_valid_version(1) #> [1] 0 arrow:::make_valid_version(2) #> [1] 1

^{Created on 2019-09-27 by the reprex package (v0.3.0.9000)}

nealrichardson · 2019-09-26T17:11:38Z

r/R/parquet.R

I'm not sure there's value including properties and arrow_properties in the signature here. I kept them in read_delim_arrow() because there were some properties they expose that aren't mapped to arguments the readr::read_delim signature but that doesn't seem to be the case here. (On reflection, that's probably not the right call there either; if you want lower-level access to those settings, you should probably be doing CsvTableReader$create(...) anyway.

My rationale was that perhaps you'd already have built those objects properties and arrow_properties before.

But I get the point that maybe this could be diverted to using a ParquetFileWriter instance

r/tests/testthat/test-parquet.R

r/tests/testthat/helper-parquet.R

nealrichardson

Some notes on the docs

nealrichardson · 2019-09-26T18:57:56Z

r/R/parquet.R

And not all columns need to be specified, correct?

nealrichardson · 2019-09-26T18:58:50Z

r/R/parquet.R

Does this follow the same conventions as compression? Maybe there should be a paragraph/section in the docs that explains how these parameters work since it's the same/similar.

I've refactored the documentation in @details

r/R/parquet.R

nealrichardson · 2019-09-26T18:59:17Z

r/R/parquet.R

Same, and what are statistics?

I don't know

r/R/parquet.R

… file path for more flexibility

…rrow::WriterProperties to R side

…ties_Builder class skeleton

…perties to write_parquet()

…nstead.

Co-Authored-By: Neal Richardson <[email protected]>

…ch class. Many tests were false positives

nealrichardson

One final style question but otherwise LGTM, happy to merge today regardless of where we land on the whitespace question.

nealrichardson · 2019-09-27T14:58:19Z

r/R/parquet.R

-                         as_data_frame = TRUE,
-                         props = ParquetReaderProperties$create(),
-                         ...) {
+  col_select = NULL,


This is "bad", according to the tidyverse style guide, which I believed we were trying to follow: https://style.tidyverse.org/functions.html#long-lines-1

I can get used to whatever style conventions we decide, just want to make sure we're in agreement.

I'll setup my Rstudio to obey the style, perhaps we should use styler:: once in a while to do that automatically.

wesm · 2019-09-27T17:44:32Z

Can you update the PR description to reflect what is actually in the PR (since writing a Parquet file into a CompressedOutputStream isn't recommendable -- you would have to decompress the entire file first to be able to read any part of it)

The ability to preserve categorical values was introduced in #5077 as the convention of storing a special `ARROW:schema` key in the metadata. To invoke this, we need to call `ArrowWriterProperties::store_schema()`. The R binding is already ready for this, but calls `store_schema()` only conditionally and uses `parquet___default_arrow_writer_properties()` by default. Though I don't see the motivation to implement as such in #5451, considering [the Python binding always calls `store_schema()`](https://github.com/apache/arrow/blob/dbe708c7527a4aa6b63df7722cd57db4e0bd2dc7/python/pyarrow/_parquet.pyx#L1269), I guess the R code can do the same. Closes #6135 from yutannihilation/ARROW-7045_preserve_factor_in_parquet and squashes the following commits: 9227e7e <Hiroaki Yutani> Fix test 4d8bb46 <Hiroaki Yutani> Remove default_arrow_writer_properties() dfd08cb <Hiroaki Yutani> Add failing tests Authored-by: Hiroaki Yutani <[email protected]> Signed-off-by: Neal Richardson <[email protected]>

romainfrancois requested a review from nealrichardson September 20, 2019 09:00

fsaintjacques added the Component: R label Sep 20, 2019

romainfrancois force-pushed the ARROW-6532/write_parquet_compression branch from d85b6fc to aa2833e Compare September 24, 2019 11:26

nealrichardson requested changes Sep 25, 2019

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nealrichardson requested changes Sep 26, 2019

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nealrichardson reviewed Sep 26, 2019

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romainfrancois added 16 commits September 27, 2019 15:57

Make write_parquet() generic, internal impl using streams rather than…

9ed32b6

… file path for more flexibility

passing down the right stream

aa34095

lint

0e09ac8

Exposing classes parquet::arrow::ArrowWriterProperties and parquet::a…

1b84ad4

…rrow::WriterProperties to R side

+ ParquetWriterProperties$create() and associated ParquetWriterProper…

09ea0ad

…ties_Builder class skeleton

Expose options from ParquetWriterProperties and ParquetArrowWriterPro…

fa8990b

…perties to write_parquet()

lint

b8337e1

+ compression_level= in write_parquet()

2dd2cb9

document()

1e3b5b6

More flexible compression= and compression_level=

2f2ae00

More flexible arguments use_dictionary= and write_statistics=

4055f67

using make_valid_time_unit()

1166264

Remove $default() methods and use $create() wityh default arguments i…

738ea6e

…nstead.

using assert_that()

72caaab

align arguments following tidyverse style guide

7f1c184

==.Table

d318a66

romainfrancois and others added 14 commits September 27, 2019 15:57

add test helper so that we actually can test parquet roundtrip

6c4f003

Remove the _ from builder classes

86d9ff4

M%ake compression_from_name() vectorized

004cf90

define and use internal make_valid_version() function

9bee8de

suggestsions from @nealrichardson

1fdcc0b

abstract various ParquetWriterPropertiesBuilder$set_*() methods

00cc214

wrong length for use_dictionary and write_statistics

5ade52d

Test ==.Table

c5549de

added all.equal.Object() that uses ==

66c51fd

Update r/R/parquet.R

45ec63b

Co-Authored-By: Neal Richardson <[email protected]>

Move read_parquet() and write_parquet() to top of the file

56dac33

rework documentation for write_parquet()

ecd9218

implement ==.Object that calls $Equals instead of implementing for ea…

9aff79b

…ch class. Many tests were false positives

rename arguments to x and sink

50555f8

romainfrancois force-pushed the ARROW-6532/write_parquet_compression branch from 354d263 to 50555f8 Compare September 27, 2019 14:04

test make_valid_version()

413dd41

nealrichardson approved these changes Sep 27, 2019

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romainfrancois changed the title ~~ARROW-6532 [R] Write parquet files with compression~~ ARROW-6532 [R] write_parquet() uses writer properties (general and arrow specific) Sep 27, 2019

nealrichardson closed this in cf9df14 Sep 27, 2019

yutannihilation mentioned this pull request Jan 7, 2020

ARROW-7045: [R] Preserve factor in Parquet roundtrip #6135

Closed

asfimport mentioned this pull request Sep 30, 2019

[R] Write parquet files with compression #22896

Closed

ARROW-6532 [R] write_parquet() uses writer properties (general and arrow specific) #5451

ARROW-6532 [R] write_parquet() uses writer properties (general and arrow specific) #5451

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