Skip to content

ARROW-10624: [R] Proactively remove "problems" attributes#9092

New issue

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

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
jonkeane wants to merge 2 commits into from
Closed

ARROW-10624: [R] Proactively remove "problems" attributes #9092

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
ee1efa6
Proactively remove "problems" attributes
jonkeane Jan 4, 2021
94456b4
PR comments, 📰
jonkeane Jan 4, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 4 additions & 2 deletions r/NEWS.md
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -29,17 +29,19 @@

## Enhancements

* Table columns can now be added, replaced, or removed by assigning `<-` with either `$` or `[[`
* Table columns can now be added, replaced, or removed by assigning (`<-`) with either `$` or `[[`
* Column names of Tables and RecordBatches can be renamed by assigning `names()`
* Large string types can now be written to Parquet files
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow-dplyr pipelines.
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow `dplyr` pipelines.
* Option `arrow.skip_nul` (default `FALSE`, as in `base::scan()`) allows conversion of Arrow string (`utf8()`) type data containing embedded nul `\0` characters to R. If set to `TRUE`, nuls will be stripped and a warning is emitted if any are found.

## Bug fixes

* Fixed a performance regression in converting Arrow string types to R that was present in the 2.0.0 release
* C++ functions now trigger garbage collection when needed
* `write_parquet()` can now write RecordBatches
* Reading a Table from a RecordBatchStreamReader containing 0 batches no longer crashes
* `readr`'s `problems` attribute is removed when converting to Arrow RecordBatch and table to prevent large amounts of metadata from accumulating inadvertently [ARROW-10624](https://issues.apache.org/jira/browse/ARROW-10624)

## Packaging and installation

Expand Down
5 changes: 5 additions & 0 deletions r/R/record-batch.R
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -274,6 +274,11 @@ as.data.frame.RecordBatch <- function(x, row.names = NULL, optional = FALSE, ...
}

.serialize_arrow_r_metadata <- function(x) {
assert_is(x, "list")

# drop problems attributes (most likely from readr)
x[["attributes"]][["problems"]] <- NULL

rawToChar(serialize(x, NULL, ascii = TRUE))
}

Expand Down
24 changes: 23 additions & 1 deletion r/tests/testthat/test-metadata.R
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -73,7 +73,9 @@ test_that("Garbage R metadata doesn't break things", {
"Invalid metadata$r",
fixed = TRUE
)
tab$metadata$r <- .serialize_arrow_r_metadata("garbage")
# serialize data like .serialize_arrow_r_metadata does, but don't call that
# directly since it checks to ensure that the data is a list
tab$metadata$r <- rawToChar(serialize("garbage", NULL, ascii = TRUE))
expect_warning(
expect_identical(as.data.frame(tab), example_data[1:6]),
"Invalid metadata$r",
Expand DownExpand Up@@ -134,3 +136,23 @@ test_that("metadata keeps attribute of top level data frame", {
expect_identical(attr(as.data.frame(tab), "foo"), "bar")
expect_identical(as.data.frame(tab), df)
})

test_that("metadata drops readr's problems attribute", {
readr_like <- tibble::tibble(
dbl = 1.1,
not_here = NA_character_
)
attributes(readr_like) <- append(
attributes(readr_like),
list(problems = tibble::tibble(
row = 1L,
col = NA_character_,
expected = "2 columns",
actual = "1 columns",
file = "'test'"
))
)

tab <- Table$create(readr_like)
expect_null(attr(as.data.frame(tab), "problems"))
})
, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
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;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
ARROW-10624: [R] Proactively remove "problems" attributes by jonkeane · Pull Request #9092 · apache/arrow · GitHub
Skip to content
ARROW-10624: [R] Proactively remove "problems" attributes#9092

New issue

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

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jonkeane
wants to merge
2
commits into

from

 Closed


ARROW-10624: [R] Proactively remove "problems" attributes
#9092
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


2 commits


Select commit
Hold shift + click to select a range
ee1efa6

Proactively remove "problems" attributes


jonkeane Jan 4, 2021
94456b4

PR comments, 📰


jonkeane Jan 4, 2021

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


6 changes: 4 additions & 2 deletions
r/NEWS.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -29,17 +29,19 @@

## Enhancements

* Table columns can now be added, replaced, or removed by assigning `<-` with either `$` or `[[`
* Table columns can now be added, replaced, or removed by assigning (`<-`) with either `$` or `[[`
* Column names of Tables and RecordBatches can be renamed by assigning `names()`
* Large string types can now be written to Parquet files
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow-dplyr pipelines.
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow `dplyr` pipelines.
* Option `arrow.skip_nul` (default `FALSE`, as in `base::scan()`) allows conversion of Arrow string (`utf8()`) type data containing embedded nul `\0` characters to R. If set to `TRUE`, nuls will be stripped and a warning is emitted if any are found.

## Bug fixes

* Fixed a performance regression in converting Arrow string types to R that was present in the 2.0.0 release
* C++ functions now trigger garbage collection when needed
* `write_parquet()` can now write RecordBatches
* Reading a Table from a RecordBatchStreamReader containing 0 batches no longer crashes
* `readr`'s `problems` attribute is removed when converting to Arrow RecordBatch and table to prevent large amounts of metadata from accumulating inadvertently [ARROW-10624](https://issues.apache.org/jira/browse/ARROW-10624)

## Packaging and installation

Expand Down

5 changes: 5 additions & 0 deletions
r/R/record-batch.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -274,6 +274,11 @@ as.data.frame.RecordBatch <- function(x, row.names = NULL, optional = FALSE, ...
}

.serialize_arrow_r_metadata <- function(x) {
 assert_is(x, "list")

 # drop problems attributes (most likely from readr)
 x[["attributes"]][["problems"]] <- NULL

 rawToChar(serialize(x, NULL, ascii = TRUE))
}

Expand Down

24 changes: 23 additions & 1 deletion
r/tests/testthat/test-metadata.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -73,7 +73,9 @@ test_that("Garbage R metadata doesn't break things", {
 "Invalid metadata$r",
 fixed = TRUE
 )
 tab$metadata$r <- .serialize_arrow_r_metadata("garbage")
 # serialize data like .serialize_arrow_r_metadata does, but don't call that
 # directly since it checks to ensure that the data is a list
 tab$metadata$r <- rawToChar(serialize("garbage", NULL, ascii = TRUE))
 expect_warning(
 expect_identical(as.data.frame(tab), example_data[1:6]),
 "Invalid metadata$r",
Expand DownExpand Up@@ -134,3 +136,23 @@ test_that("metadata keeps attribute of top level data frame", {
 expect_identical(attr(as.data.frame(tab), "foo"), "bar")
 expect_identical(as.data.frame(tab), df)
})

test_that("metadata drops readr's problems attribute", {
 readr_like <- tibble::tibble(
 dbl = 1.1,
 not_here = NA_character_
 )
 attributes(readr_like) <- append(
 attributes(readr_like),
 list(problems = tibble::tibble(
 row = 1L,
 col = NA_character_,
 expected = "2 columns",
 actual = "1 columns",
 file = "'test'"
 ))
 )

 tab <- Table$create(readr_like)
 expect_null(attr(as.data.frame(tab), "problems"))
})

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
ARROW-10624: [R] Proactively remove "problems" attributes by jonkeane · Pull Request #9092 · apache/arrow · GitHub
Skip to content
ARROW-10624: [R] Proactively remove "problems" attributes#9092

New issue

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

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jonkeane
wants to merge
2
commits into

from

 Closed


ARROW-10624: [R] Proactively remove "problems" attributes
#9092
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


2 commits


Select commit
Hold shift + click to select a range
ee1efa6

Proactively remove "problems" attributes


jonkeane Jan 4, 2021
94456b4

PR comments, 📰


jonkeane Jan 4, 2021

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


6 changes: 4 additions & 2 deletions
r/NEWS.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -29,17 +29,19 @@

## Enhancements

* Table columns can now be added, replaced, or removed by assigning `<-` with either `$` or `[[`
* Table columns can now be added, replaced, or removed by assigning (`<-`) with either `$` or `[[`
* Column names of Tables and RecordBatches can be renamed by assigning `names()`
* Large string types can now be written to Parquet files
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow-dplyr pipelines.
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow `dplyr` pipelines.
* Option `arrow.skip_nul` (default `FALSE`, as in `base::scan()`) allows conversion of Arrow string (`utf8()`) type data containing embedded nul `\0` characters to R. If set to `TRUE`, nuls will be stripped and a warning is emitted if any are found.

## Bug fixes

* Fixed a performance regression in converting Arrow string types to R that was present in the 2.0.0 release
* C++ functions now trigger garbage collection when needed
* `write_parquet()` can now write RecordBatches
* Reading a Table from a RecordBatchStreamReader containing 0 batches no longer crashes
* `readr`'s `problems` attribute is removed when converting to Arrow RecordBatch and table to prevent large amounts of metadata from accumulating inadvertently [ARROW-10624](https://issues.apache.org/jira/browse/ARROW-10624)

## Packaging and installation

Expand Down

5 changes: 5 additions & 0 deletions
r/R/record-batch.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -274,6 +274,11 @@ as.data.frame.RecordBatch <- function(x, row.names = NULL, optional = FALSE, ...
}

.serialize_arrow_r_metadata <- function(x) {
 assert_is(x, "list")

 # drop problems attributes (most likely from readr)
 x[["attributes"]][["problems"]] <- NULL

 rawToChar(serialize(x, NULL, ascii = TRUE))
}

Expand Down

24 changes: 23 additions & 1 deletion
r/tests/testthat/test-metadata.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -73,7 +73,9 @@ test_that("Garbage R metadata doesn't break things", {
 "Invalid metadata$r",
 fixed = TRUE
 )
 tab$metadata$r <- .serialize_arrow_r_metadata("garbage")
 # serialize data like .serialize_arrow_r_metadata does, but don't call that
 # directly since it checks to ensure that the data is a list
 tab$metadata$r <- rawToChar(serialize("garbage", NULL, ascii = TRUE))
 expect_warning(
 expect_identical(as.data.frame(tab), example_data[1:6]),
 "Invalid metadata$r",
Expand DownExpand Up@@ -134,3 +136,23 @@ test_that("metadata keeps attribute of top level data frame", {
 expect_identical(attr(as.data.frame(tab), "foo"), "bar")
 expect_identical(as.data.frame(tab), df)
})

test_that("metadata drops readr's problems attribute", {
 readr_like <- tibble::tibble(
 dbl = 1.1,
 not_here = NA_character_
 )
 attributes(readr_like) <- append(
 attributes(readr_like),
 list(problems = tibble::tibble(
 row = 1L,
 col = NA_character_,
 expected = "2 columns",
 actual = "1 columns",
 file = "'test'"
 ))
 )

 tab <- Table$create(readr_like)
 expect_null(attr(as.data.frame(tab), "problems"))
})

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
ARROW-10624: [R] Proactively remove "problems" attributes by jonkeane · Pull Request #9092 · apache/arrow · GitHub
Skip to content
ARROW-10624: [R] Proactively remove "problems" attributes#9092

New issue

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

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jonkeane
wants to merge
2
commits into

from

 Closed


ARROW-10624: [R] Proactively remove "problems" attributes
#9092
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


2 commits


Select commit
Hold shift + click to select a range
ee1efa6

Proactively remove "problems" attributes


jonkeane Jan 4, 2021
94456b4

PR comments, 📰


jonkeane Jan 4, 2021

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


6 changes: 4 additions & 2 deletions
r/NEWS.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -29,17 +29,19 @@

## Enhancements

* Table columns can now be added, replaced, or removed by assigning `<-` with either `$` or `[[`
* Table columns can now be added, replaced, or removed by assigning (`<-`) with either `$` or `[[`
* Column names of Tables and RecordBatches can be renamed by assigning `names()`
* Large string types can now be written to Parquet files
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow-dplyr pipelines.
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow `dplyr` pipelines.
* Option `arrow.skip_nul` (default `FALSE`, as in `base::scan()`) allows conversion of Arrow string (`utf8()`) type data containing embedded nul `\0` characters to R. If set to `TRUE`, nuls will be stripped and a warning is emitted if any are found.

## Bug fixes

* Fixed a performance regression in converting Arrow string types to R that was present in the 2.0.0 release
* C++ functions now trigger garbage collection when needed
* `write_parquet()` can now write RecordBatches
* Reading a Table from a RecordBatchStreamReader containing 0 batches no longer crashes
* `readr`'s `problems` attribute is removed when converting to Arrow RecordBatch and table to prevent large amounts of metadata from accumulating inadvertently [ARROW-10624](https://issues.apache.org/jira/browse/ARROW-10624)

## Packaging and installation

Expand Down

5 changes: 5 additions & 0 deletions
r/R/record-batch.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -274,6 +274,11 @@ as.data.frame.RecordBatch <- function(x, row.names = NULL, optional = FALSE, ...
}

.serialize_arrow_r_metadata <- function(x) {
 assert_is(x, "list")

 # drop problems attributes (most likely from readr)
 x[["attributes"]][["problems"]] <- NULL

 rawToChar(serialize(x, NULL, ascii = TRUE))
}

Expand Down

24 changes: 23 additions & 1 deletion
r/tests/testthat/test-metadata.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -73,7 +73,9 @@ test_that("Garbage R metadata doesn't break things", {
 "Invalid metadata$r",
 fixed = TRUE
 )
 tab$metadata$r <- .serialize_arrow_r_metadata("garbage")
 # serialize data like .serialize_arrow_r_metadata does, but don't call that
 # directly since it checks to ensure that the data is a list
 tab$metadata$r <- rawToChar(serialize("garbage", NULL, ascii = TRUE))
 expect_warning(
 expect_identical(as.data.frame(tab), example_data[1:6]),
 "Invalid metadata$r",
Expand DownExpand Up@@ -134,3 +136,23 @@ test_that("metadata keeps attribute of top level data frame", {
 expect_identical(attr(as.data.frame(tab), "foo"), "bar")
 expect_identical(as.data.frame(tab), df)
})

test_that("metadata drops readr's problems attribute", {
 readr_like <- tibble::tibble(
 dbl = 1.1,
 not_here = NA_character_
 )
 attributes(readr_like) <- append(
 attributes(readr_like),
 list(problems = tibble::tibble(
 row = 1L,
 col = NA_character_,
 expected = "2 columns",
 actual = "1 columns",
 file = "'test'"
 ))
 )

 tab <- Table$create(readr_like)
 expect_null(attr(as.data.frame(tab), "problems"))
})

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
ARROW-10624: [R] Proactively remove "problems" attributes by jonkeane · Pull Request #9092 · apache/arrow · GitHub
Skip to content
ARROW-10624: [R] Proactively remove "problems" attributes#9092

New issue

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

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jonkeane
wants to merge
2
commits into

from

 Closed


ARROW-10624: [R] Proactively remove "problems" attributes
#9092
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


2 commits


Select commit
Hold shift + click to select a range
ee1efa6

Proactively remove "problems" attributes


jonkeane Jan 4, 2021
94456b4

PR comments, 📰


jonkeane Jan 4, 2021

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


6 changes: 4 additions & 2 deletions
r/NEWS.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -29,17 +29,19 @@

## Enhancements

* Table columns can now be added, replaced, or removed by assigning `<-` with either `$` or `[[`
* Table columns can now be added, replaced, or removed by assigning (`<-`) with either `$` or `[[`
* Column names of Tables and RecordBatches can be renamed by assigning `names()`
* Large string types can now be written to Parquet files
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow-dplyr pipelines.
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow `dplyr` pipelines.
* Option `arrow.skip_nul` (default `FALSE`, as in `base::scan()`) allows conversion of Arrow string (`utf8()`) type data containing embedded nul `\0` characters to R. If set to `TRUE`, nuls will be stripped and a warning is emitted if any are found.

## Bug fixes

* Fixed a performance regression in converting Arrow string types to R that was present in the 2.0.0 release
* C++ functions now trigger garbage collection when needed
* `write_parquet()` can now write RecordBatches
* Reading a Table from a RecordBatchStreamReader containing 0 batches no longer crashes
* `readr`'s `problems` attribute is removed when converting to Arrow RecordBatch and table to prevent large amounts of metadata from accumulating inadvertently [ARROW-10624](https://issues.apache.org/jira/browse/ARROW-10624)

## Packaging and installation

Expand Down

5 changes: 5 additions & 0 deletions
r/R/record-batch.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -274,6 +274,11 @@ as.data.frame.RecordBatch <- function(x, row.names = NULL, optional = FALSE, ...
}

.serialize_arrow_r_metadata <- function(x) {
 assert_is(x, "list")

 # drop problems attributes (most likely from readr)
 x[["attributes"]][["problems"]] <- NULL

 rawToChar(serialize(x, NULL, ascii = TRUE))
}

Expand Down

24 changes: 23 additions & 1 deletion
r/tests/testthat/test-metadata.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -73,7 +73,9 @@ test_that("Garbage R metadata doesn't break things", {
 "Invalid metadata$r",
 fixed = TRUE
 )
 tab$metadata$r <- .serialize_arrow_r_metadata("garbage")
 # serialize data like .serialize_arrow_r_metadata does, but don't call that
 # directly since it checks to ensure that the data is a list
 tab$metadata$r <- rawToChar(serialize("garbage", NULL, ascii = TRUE))
 expect_warning(
 expect_identical(as.data.frame(tab), example_data[1:6]),
 "Invalid metadata$r",
Expand DownExpand Up@@ -134,3 +136,23 @@ test_that("metadata keeps attribute of top level data frame", {
 expect_identical(attr(as.data.frame(tab), "foo"), "bar")
 expect_identical(as.data.frame(tab), df)
})

test_that("metadata drops readr's problems attribute", {
 readr_like <- tibble::tibble(
 dbl = 1.1,
 not_here = NA_character_
 )
 attributes(readr_like) <- append(
 attributes(readr_like),
 list(problems = tibble::tibble(
 row = 1L,
 col = NA_character_,
 expected = "2 columns",
 actual = "1 columns",
 file = "'test'"
 ))
 )

 tab <- Table$create(readr_like)
 expect_null(attr(as.data.frame(tab), "problems"))
})

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
ARROW-10624: [R] Proactively remove "problems" attributes by jonkeane · Pull Request #9092 · apache/arrow · GitHub
Skip to content
ARROW-10624: [R] Proactively remove "problems" attributes#9092

New issue

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

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jonkeane
wants to merge
2
commits into

from

 Closed


ARROW-10624: [R] Proactively remove "problems" attributes
#9092
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


2 commits


Select commit
Hold shift + click to select a range
ee1efa6

Proactively remove "problems" attributes


jonkeane Jan 4, 2021
94456b4

PR comments, 📰


jonkeane Jan 4, 2021

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


6 changes: 4 additions & 2 deletions
r/NEWS.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -29,17 +29,19 @@

## Enhancements

* Table columns can now be added, replaced, or removed by assigning `<-` with either `$` or `[[`
* Table columns can now be added, replaced, or removed by assigning (`<-`) with either `$` or `[[`
* Column names of Tables and RecordBatches can be renamed by assigning `names()`
* Large string types can now be written to Parquet files
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow-dplyr pipelines.
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow `dplyr` pipelines.
* Option `arrow.skip_nul` (default `FALSE`, as in `base::scan()`) allows conversion of Arrow string (`utf8()`) type data containing embedded nul `\0` characters to R. If set to `TRUE`, nuls will be stripped and a warning is emitted if any are found.

## Bug fixes

* Fixed a performance regression in converting Arrow string types to R that was present in the 2.0.0 release
* C++ functions now trigger garbage collection when needed
* `write_parquet()` can now write RecordBatches
* Reading a Table from a RecordBatchStreamReader containing 0 batches no longer crashes
* `readr`'s `problems` attribute is removed when converting to Arrow RecordBatch and table to prevent large amounts of metadata from accumulating inadvertently [ARROW-10624](https://issues.apache.org/jira/browse/ARROW-10624)

## Packaging and installation

Expand Down

5 changes: 5 additions & 0 deletions
r/R/record-batch.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -274,6 +274,11 @@ as.data.frame.RecordBatch <- function(x, row.names = NULL, optional = FALSE, ...
}

.serialize_arrow_r_metadata <- function(x) {
 assert_is(x, "list")

 # drop problems attributes (most likely from readr)
 x[["attributes"]][["problems"]] <- NULL

 rawToChar(serialize(x, NULL, ascii = TRUE))
}

Expand Down

24 changes: 23 additions & 1 deletion
r/tests/testthat/test-metadata.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -73,7 +73,9 @@ test_that("Garbage R metadata doesn't break things", {
 "Invalid metadata$r",
 fixed = TRUE
 )
 tab$metadata$r <- .serialize_arrow_r_metadata("garbage")
 # serialize data like .serialize_arrow_r_metadata does, but don't call that
 # directly since it checks to ensure that the data is a list
 tab$metadata$r <- rawToChar(serialize("garbage", NULL, ascii = TRUE))
 expect_warning(
 expect_identical(as.data.frame(tab), example_data[1:6]),
 "Invalid metadata$r",
Expand DownExpand Up@@ -134,3 +136,23 @@ test_that("metadata keeps attribute of top level data frame", {
 expect_identical(attr(as.data.frame(tab), "foo"), "bar")
 expect_identical(as.data.frame(tab), df)
})

test_that("metadata drops readr's problems attribute", {
 readr_like <- tibble::tibble(
 dbl = 1.1,
 not_here = NA_character_
 )
 attributes(readr_like) <- append(
 attributes(readr_like),
 list(problems = tibble::tibble(
 row = 1L,
 col = NA_character_,
 expected = "2 columns",
 actual = "1 columns",
 file = "'test'"
 ))
 )

 tab <- Table$create(readr_like)
 expect_null(attr(as.data.frame(tab), "problems"))
})

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
})();
ARROW-10624: [R] Proactively remove "problems" attributes by jonkeane · Pull Request #9092 · apache/arrow · GitHub
Skip to content
ARROW-10624: [R] Proactively remove "problems" attributes#9092

New issue

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

 Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and
privacy statement. We’ll occasionally send you account related emails.

Already on GitHub?
Sign in
to your account

 Closed

jonkeane
wants to merge
2
commits into

from

 Closed


ARROW-10624: [R] Proactively remove "problems" attributes
#9092
Show file tree
Hide file tree
 Changes from all commits
Commits

Show all changes


2 commits


Select commit
Hold shift + click to select a range
ee1efa6

Proactively remove "problems" attributes


jonkeane Jan 4, 2021
94456b4

PR comments, 📰


jonkeane Jan 4, 2021

File filter

Filter by extension
Filter by extension
Conversations

Failed to load comments. 
Loading
Jump to

Jump to file


Failed to load files. 
Loading
 Diff view

 Diff view


6 changes: 4 additions & 2 deletions
r/NEWS.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -29,17 +29,19 @@

## Enhancements

* Table columns can now be added, replaced, or removed by assigning `<-` with either `$` or `[[`
* Table columns can now be added, replaced, or removed by assigning (`<-`) with either `$` or `[[`
* Column names of Tables and RecordBatches can be renamed by assigning `names()`
* Large string types can now be written to Parquet files
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow-dplyr pipelines.
* The [pronouns `.data` and `.env`](https://rlang.r-lib.org/reference/tidyeval-data.html) are now fully supported in Arrow `dplyr` pipelines.
* Option `arrow.skip_nul` (default `FALSE`, as in `base::scan()`) allows conversion of Arrow string (`utf8()`) type data containing embedded nul `\0` characters to R. If set to `TRUE`, nuls will be stripped and a warning is emitted if any are found.

## Bug fixes

* Fixed a performance regression in converting Arrow string types to R that was present in the 2.0.0 release
* C++ functions now trigger garbage collection when needed
* `write_parquet()` can now write RecordBatches
* Reading a Table from a RecordBatchStreamReader containing 0 batches no longer crashes
* `readr`'s `problems` attribute is removed when converting to Arrow RecordBatch and table to prevent large amounts of metadata from accumulating inadvertently [ARROW-10624](https://issues.apache.org/jira/browse/ARROW-10624)

## Packaging and installation

Expand Down

5 changes: 5 additions & 0 deletions
r/R/record-batch.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -274,6 +274,11 @@ as.data.frame.RecordBatch <- function(x, row.names = NULL, optional = FALSE, ...
}

.serialize_arrow_r_metadata <- function(x) {
 assert_is(x, "list")

 # drop problems attributes (most likely from readr)
 x[["attributes"]][["problems"]] <- NULL

 rawToChar(serialize(x, NULL, ascii = TRUE))
}

Expand Down

24 changes: 23 additions & 1 deletion
r/tests/testthat/test-metadata.R

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -73,7 +73,9 @@ test_that("Garbage R metadata doesn't break things", {
 "Invalid metadata$r",
 fixed = TRUE
 )
 tab$metadata$r <- .serialize_arrow_r_metadata("garbage")
 # serialize data like .serialize_arrow_r_metadata does, but don't call that
 # directly since it checks to ensure that the data is a list
 tab$metadata$r <- rawToChar(serialize("garbage", NULL, ascii = TRUE))
 expect_warning(
 expect_identical(as.data.frame(tab), example_data[1:6]),
 "Invalid metadata$r",
Expand DownExpand Up@@ -134,3 +136,23 @@ test_that("metadata keeps attribute of top level data frame", {
 expect_identical(attr(as.data.frame(tab), "foo"), "bar")
 expect_identical(as.data.frame(tab), df)
})

test_that("metadata drops readr's problems attribute", {
 readr_like <- tibble::tibble(
 dbl = 1.1,
 not_here = NA_character_
 )
 attributes(readr_like) <- append(
 attributes(readr_like),
 list(problems = tibble::tibble(
 row = 1L,
 col = NA_character_,
 expected = "2 columns",
 actual = "1 columns",
 file = "'test'"
 ))
 )

 tab <- Table$create(readr_like)
 expect_null(attr(as.data.frame(tab), "problems"))
})