ARROW-10386: [R] List column class attributes not preserved in roundtrip by jonkeane · Pull Request #9182 · apache/arrow

jonkeane · 2021-01-13T00:09:24Z

No description provided.

github-actions · 2021-01-13T00:09:50Z

Thanks for opening a pull request!

Could you open an issue for this pull request on JIRA?
https://issues.apache.org/jira/browse/ARROW

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

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

See also:

jonkeane · 2021-01-13T00:11:56Z

@github-actions crossbow submit test-r-version-compatibility

github-actions · 2021-01-13T00:15:25Z

https://issues.apache.org/jira/browse/ARROW-10386

jonkeane · 2021-01-13T00:54:36Z

@github-actions crossbow submit test-r-version-compatibility

github-actions · 2021-01-13T00:55:25Z

Revision: d18222dca3587269aa2abc27ee9033cd352351f4

Submitted crossbow builds: ursa-labs/crossbow @ actions-878

Task	Status
test-r-version-compatibility

…st itself. ARROW-10386.

nealrichardson · 2021-01-13T18:28:19Z

r/R/schema.R

+#'
+#' @section Metadata:
+#'
+#'   Attributes from the `data.frame` are saved alongside tables so that the


"When converting a data.frame to an Arrow Table or RecordBatch, "

nealrichardson · 2021-01-13T18:29:05Z

r/R/schema.R

 #'    Modify or replace by assigning in (`sch$metadata <- new_metadata`).
 #'    All list elements are coerced to string.
+#'
+#' @section Metadata:


This section should either be called something like "R Metadata", or it should start by discussing the key-value metadata more generally.

nealrichardson · 2021-01-13T18:29:45Z

r/R/schema.R

+#'   them when pulled back into R. This metadata is separate from the schema
+#'   (e.g. types of the columns) which is compatible with other Arrow clients.
+#'   The R metadata is only read by R and is ignored by other clients (e.g.
+#'   pyarrow which has its own custom metadata for things like Pandas metadata).


I believe it is Pandas only that stores extra metadata, not pyarrow itself.

nealrichardson · 2021-01-13T18:31:02Z

r/R/schema.R

+#'   object can be reconstructed faithfully in R (e.g. with `as.data.frame()`).
+#'   This metadata can be both at the top-level of the `data.frame` (e.g.
+#'   `attributes(df)`) or at the column (e.g. `attributes(df$col_a)`) or element
+#'   level (e.g. `attributes(df[1, "col_a"])`). For example, this allows for


According to the code, this is only true for list columns (which makes sense because regular vectors can't have attributes on elements)

nealrichardson · 2021-01-13T18:31:35Z

r/R/schema.R

+#'   level (e.g. `attributes(df[1, "col_a"])`). For example, this allows for
+#'   storing `haven` columns in a table and being able to faithfully re-create
+#'   them when pulled back into R. This metadata is separate from the schema
+#'   (e.g. types of the columns) which is compatible with other Arrow clients.


Suggested change

#' (e.g. types of the columns) which is compatible with other Arrow clients.

#' (column names and types), which is compatible with other Arrow clients.

nealrichardson · 2021-01-13T18:32:10Z

r/R/schema.R

+#'   (e.g. types of the columns) which is compatible with other Arrow clients.
+#'   The R metadata is only read by R and is ignored by other clients (e.g.
+#'   pyarrow which has its own custom metadata for things like Pandas metadata).
+#'   This metadata is stored (and can be accessed with) `table$metadata$r`.


Shouldn't say table here, we're in the Schema docs.

Suggested change

#' This metadata is stored (and can be accessed with) `table$metadata$r`.

#' This metadata is stored in `$metadata$r`.

nealrichardson · 2021-01-13T18:32:41Z

r/R/schema.R

+#'   include large amounts of metadata) you can set the option
+#'   `arrow.compress_metadata` to `FALSE`.
+#'
+#'   One exception to storing all metadata: `readr`'s `problems` attribute if it


I don't think this paragraph is necessary.

nealrichardson · 2021-01-13T18:33:34Z

r/R/schema.R

+#'   pyarrow which has its own custom metadata for things like Pandas metadata).
+#'   This metadata is stored (and can be accessed with) `table$metadata$r`.
+#'
+#'   This metadata is saved by serializing R's attribute list structure to a


"Since Schema metadata keys and values must be strings, ..."

nealrichardson · 2021-01-13T18:40:06Z

r/R/schema.R

+#'   serialized string. Because of this, large amounts of metadata can quickly
+#'   increase the size of tables (and therefore the size of tables written to
+#'   parquet or feather files). If the (serialized) metadata exceeds 100Kbs in
+#'   size, it is first compressed before saving. To disable this compression
+#'   (e.g. for tables that are compatible with Arrow versions before 3.0.0 and
+#'   include large amounts of metadata) you can set the option
+#'   `arrow.compress_metadata` to `FALSE`.


Suggested change

#' serialized string. Because of this, large amounts of metadata can quickly

#' increase the size of tables (and therefore the size of tables written to

#' parquet or feather files). If the (serialized) metadata exceeds 100Kbs in

#' size, it is first compressed before saving. To disable this compression

#' (e.g. for tables that are compatible with Arrow versions before 3.0.0 and

#' include large amounts of metadata) you can set the option

#' `arrow.compress_metadata` to `FALSE`.

#' string. If the serialized metadata exceeds 100Kbs in size, by default

#' it is compressed starting in version 3.0.0. To disable this compression

#' (e.g. for tables that are compatible with Arrow versions before 3.0.0 and

#' include large amounts of metadata), set the option

#' `arrow.compress_metadata` to `FALSE`. Files with compressed metadata

#' are readable by older versions of arrow, but the metadata is dropped.

nealrichardson · 2021-01-13T20:04:49Z

Do we have any backwards compat testing with this feature?

jonkeane · 2021-01-13T20:06:54Z

No, but I'll make a Jira + work on adding one/some

nealrichardson · 2021-01-13T20:21:00Z

Also this deserves a NEWS bullet, including a special mention of sf data.

nealrichardson · 2021-01-13T20:58:02Z

No, but I'll make a Jira + work on adding one/some

TBH I think we need something in this PR since we're up against the release deadline. Don't need the full spectrum of feather/parquet/compression, just pick one, and make sure that we can read a data.frame, likely with a warning about invalid metadata.

jonkeane · 2021-01-13T20:59:33Z

Oops, yeah I just realized I mis-read the notifications on this — I thought this had been merged already. I'll put them here and we can close the (now extraneous) ARROW-11241

jonkeane · 2021-01-13T21:12:56Z

@github-actions crossbow submit test-r-version-compatibility

github-actions · 2021-01-13T21:18:45Z

Revision: a66818d

Submitted crossbow builds: ursa-labs/crossbow @ actions-881

Task	Status
test-r-version-compatibility

jonkeane · 2021-01-13T21:41:58Z

@github-actions crossbow submit test-r-version-compatibility

github-actions · 2021-01-13T21:46:26Z

Revision: 306751f

Submitted crossbow builds: ursa-labs/crossbow @ actions-883

Task	Status
test-r-version-compatibility

jonkeane · 2021-01-13T22:07:16Z

@github-actions crossbow submit test-r-version-compatibility

github-actions · 2021-01-13T22:09:16Z

Revision: fa0041b

Submitted crossbow builds: ursa-labs/crossbow @ actions-884

Task	Status
test-r-version-compatibility

github-actions bot added the Component: R label Jan 13, 2021

jonkeane changed the title ~~[WIP] ARROW-10386: [R] List column class attributes not preserved in roundtrip~~ ARROW-10386: [R] List column class attributes not preserved in roundtrip [WIP] Jan 13, 2021

jonkeane force-pushed the ARROW-10386/List_metadata branch from 039b59e to d18222d Compare January 13, 2021 00:53

romainfrancois and others added 7 commits January 13, 2021 11:43

store metadata for each element of a list column too, not just the li…

05bf857

…st itself. ARROW-10386.

update test

0c6065a

Slight clarification on test

57f05e2

Try some compression

a92ed0d

Oops, attributes must be lists.

95aaa30

Add option for disabling compression

6fd2d35

Updated documentation

5649500

jonkeane force-pushed the ARROW-10386/List_metadata branch from 68d6c47 to 5649500 Compare January 13, 2021 17:46

jonkeane changed the title ~~ARROW-10386: [R] List column class attributes not preserved in roundtrip [WIP]~~ ARROW-10386: [R] List column class attributes not preserved in roundtrip Jan 13, 2021

CI bump

92fa1f3

nealrichardson requested changes Jan 13, 2021

View reviewed changes

github-actions bot added the Component: Parquet label Jan 13, 2021

PR comments

82679fa

nealrichardson mentioned this pull request Jan 13, 2021

ARROW-10386 [R]: List column class attributes not preserved in roundtrip #8549

Closed

nealrichardson approved these changes Jan 13, 2021

View reviewed changes

jonkeane added 2 commits January 13, 2021 15:01

📰

920cfb1

add extra-tests for compressed metadata

a66818d

expect warning for compressed metadata prior to 3.0.0

306751f

backwards compatibility + fixed = TRUE

fa0041b

nealrichardson closed this in 6deb892 Jan 13, 2021

jonkeane deleted the ARROW-10386/List_metadata branch May 5, 2021 12:53

This was referenced Apr 26, 2021

[R] List column class attributes not preserved in roundtrip #26370

Closed

[R] Disable row-level metadata application on datasets #28879

Closed

	#' (e.g. types of the columns) which is compatible with other Arrow clients.
	#' (column names and types), which is compatible with other Arrow clients.

	#' This metadata is stored (and can be accessed with) `table$metadata$r`.
	#' This metadata is stored in `$metadata$r`.

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nealrichardson commented Jan 13, 2021

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