avoid race condition during chunk write - #327

Merged
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update
Dec 4, 2018
Merged

avoid race condition during chunk write#327
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update

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@sbalmer

@sbalmersbalmer commented Nov 8, 2018

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When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.

Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.

Fixes#263

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Comment threadzarr/storage.py Outdated
# On windows, rename() can't overwrite files. So
# the file is removed first.
os.remove(new)
os.rename(old, new)

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So this is the case where we would want the pyosreplace package. It's a Windows only backport for os.replace on Python 2.

@alimanfoo

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Just to mention that there are some potential consequences from implementing this PR that we should be aware of, described in #328. I don't think that should stop us from moving ahead with this PR, using os.replace() is clearly a better thing to do under any circumstances, but just something to be aware of.

@sbalmer

sbalmer commented Nov 14, 2018

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@jakirkham I've made a guess at the setup.py changes needed for pyosreplace. I couldn't get environmental markers to work. See previous commit. Could you please have a look at it? And is something else needed?

Comment threadsetup.py Outdated
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Think you had it basically right. Unfortunately there is some lack of clarity about when a colon or semicolon should be used. IIUC it should be a semicolon.

@jakirkhamjakirkham left a comment

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LGTM. Thanks for working on this @sbalmer.

Hopefully the comment above is useful. Am personally fine with how this is. Though if you want to use environment markers instead (or others prefer this), that could be also done, but don't personally think this is critical.

@alimanfoo

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Thanks @sbalmer. Could you add pyosreplace to requirements.txt and requirements_dev.txt, pinned to the latest version in the latter. I guess environment markers are needed in both.

@alimanfooalimanfoo added this to the v2.3 milestone Nov 20, 2018
weatherfrogand others added 6 commits November 21, 2018 13:27
When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.
Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.
Fixeszarr-developers#263
so it's not repeated on every write
Because the env markers didn't work. Just guessing at this point.
@sbalmer

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@alimanfoopyosreplace is now in the requirement files too. I've made a guess at how the env markers should look. If I invert the predicates then pip install -r requirements.txt tries to install the package. Which means I have some confidence it should work.

@jakirkham

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Thanks @sbalmer. LGTM. 😄 Let's see what @alimanfoo thinks. 😉

@jakirkham

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I wonder if we can just drop the try...finally now.

@jakirkhamjakirkham mentioned this pull request Dec 4, 2018
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Many thanks @sbalmer, looks good. Could you add a release note to docs/release.rst.

@alimanfoo

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I wonder if we can just drop the try...finally now.

FWIW I imagine it could still be possible that some failure occurs during the attempt to write to the temporary file (e.g., device gets full or something like that), in which case an exception occurs before the value has been fully written, in which case we'd still want to clean up the temporary file.

@jakirkham

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Good point.

@alimanfoo

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I've resolved conflicts after merging #352 and added a release note. Will merge if CI passes.

@alimanfoo

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@sbalmer apologies I didn't know your full name to include in the release note, you're credited currently just as "sbalmer", happy to leave it that way or add your full name, whichever you prefer.

@alimanfoo
alimanfoo merged commit 94f7a8d into zarr-developers:masterDec 4, 2018
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Thanks @sbalmer 😄

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Thanks @alimanfoo, @jakirkham!

Now we can use mainline again :-)

@sbalmer
sbalmer deleted the atomic-update branch December 6, 2018 13:22
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all
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})();
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try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
Skip to content

avoid race condition during chunk write - #327

Merged
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update
Dec 4, 2018
Merged

avoid race condition during chunk write#327
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update

Conversation

@sbalmer

@sbalmersbalmer commented Nov 8, 2018

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When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.

Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.

Fixes#263

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Comment threadzarr/storage.py Outdated
# On windows, rename() can't overwrite files. So
# the file is removed first.
os.remove(new)
os.rename(old, new)

Copy link
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Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

So this is the case where we would want the pyosreplace package. It's a Windows only backport for os.replace on Python 2.

@alimanfoo

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Just to mention that there are some potential consequences from implementing this PR that we should be aware of, described in #328. I don't think that should stop us from moving ahead with this PR, using os.replace() is clearly a better thing to do under any circumstances, but just something to be aware of.

@sbalmer

sbalmer commented Nov 14, 2018

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@jakirkham I've made a guess at the setup.py changes needed for pyosreplace. I couldn't get environmental markers to work. See previous commit. Could you please have a look at it? And is something else needed?

Comment threadsetup.py Outdated
@jakirkham

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Think you had it basically right. Unfortunately there is some lack of clarity about when a colon or semicolon should be used. IIUC it should be a semicolon.

@jakirkhamjakirkham left a comment

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LGTM. Thanks for working on this @sbalmer.

Hopefully the comment above is useful. Am personally fine with how this is. Though if you want to use environment markers instead (or others prefer this), that could be also done, but don't personally think this is critical.

@alimanfoo

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Thanks @sbalmer. Could you add pyosreplace to requirements.txt and requirements_dev.txt, pinned to the latest version in the latter. I guess environment markers are needed in both.

@alimanfooalimanfoo added this to the v2.3 milestone Nov 20, 2018
weatherfrogand others added 6 commits November 21, 2018 13:27
When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.
Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.
Fixeszarr-developers#263
so it's not repeated on every write
Because the env markers didn't work. Just guessing at this point.
@sbalmer

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ContributorAuthor

@alimanfoopyosreplace is now in the requirement files too. I've made a guess at how the env markers should look. If I invert the predicates then pip install -r requirements.txt tries to install the package. Which means I have some confidence it should work.

@jakirkham

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Thanks @sbalmer. LGTM. 😄 Let's see what @alimanfoo thinks. 😉

@jakirkham

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I wonder if we can just drop the try...finally now.

@jakirkhamjakirkham mentioned this pull request Dec 4, 2018
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@alimanfooalimanfoo left a comment

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Many thanks @sbalmer, looks good. Could you add a release note to docs/release.rst.

@alimanfoo

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I wonder if we can just drop the try...finally now.

FWIW I imagine it could still be possible that some failure occurs during the attempt to write to the temporary file (e.g., device gets full or something like that), in which case an exception occurs before the value has been fully written, in which case we'd still want to clean up the temporary file.

@jakirkham

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Good point.

@alimanfoo

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I've resolved conflicts after merging #352 and added a release note. Will merge if CI passes.

@alimanfoo

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@sbalmer apologies I didn't know your full name to include in the release note, you're credited currently just as "sbalmer", happy to leave it that way or add your full name, whichever you prefer.

@alimanfoo
alimanfoo merged commit 94f7a8d into zarr-developers:masterDec 4, 2018
@jakirkham

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Thanks @sbalmer 😄

@sbalmer

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Thanks @alimanfoo, @jakirkham!

Now we can use mainline again :-)

@sbalmer
sbalmer deleted the atomic-update branch December 6, 2018 13:22
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@sbalmer@alimanfoo@jakirkham@weatherfrog
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix"); } } catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

avoid race condition during chunk write - #327

Merged
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update
Dec 4, 2018
Merged

avoid race condition during chunk write#327
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update

Conversation

@sbalmer

@sbalmersbalmer commented Nov 8, 2018

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When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.

Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.

Fixes#263

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Comment threadzarr/storage.py Outdated
# On windows, rename() can't overwrite files. So
# the file is removed first.
os.remove(new)
os.rename(old, new)

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

So this is the case where we would want the pyosreplace package. It's a Windows only backport for os.replace on Python 2.

@alimanfoo

Copy link
Copy Markdown
Member

Just to mention that there are some potential consequences from implementing this PR that we should be aware of, described in #328. I don't think that should stop us from moving ahead with this PR, using os.replace() is clearly a better thing to do under any circumstances, but just something to be aware of.

@sbalmer

sbalmer commented Nov 14, 2018

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@jakirkham I've made a guess at the setup.py changes needed for pyosreplace. I couldn't get environmental markers to work. See previous commit. Could you please have a look at it? And is something else needed?

Comment threadsetup.py Outdated
@jakirkham

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Think you had it basically right. Unfortunately there is some lack of clarity about when a colon or semicolon should be used. IIUC it should be a semicolon.

@jakirkhamjakirkham left a comment

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LGTM. Thanks for working on this @sbalmer.

Hopefully the comment above is useful. Am personally fine with how this is. Though if you want to use environment markers instead (or others prefer this), that could be also done, but don't personally think this is critical.

@alimanfoo

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Thanks @sbalmer. Could you add pyosreplace to requirements.txt and requirements_dev.txt, pinned to the latest version in the latter. I guess environment markers are needed in both.

@alimanfooalimanfoo added this to the v2.3 milestone Nov 20, 2018
weatherfrogand others added 6 commits November 21, 2018 13:27
When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.
Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.
Fixeszarr-developers#263
so it's not repeated on every write
Because the env markers didn't work. Just guessing at this point.
@sbalmer

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Copy Markdown
ContributorAuthor

@alimanfoopyosreplace is now in the requirement files too. I've made a guess at how the env markers should look. If I invert the predicates then pip install -r requirements.txt tries to install the package. Which means I have some confidence it should work.

@jakirkham

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Thanks @sbalmer. LGTM. 😄 Let's see what @alimanfoo thinks. 😉

@jakirkham

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I wonder if we can just drop the try...finally now.

@jakirkhamjakirkham mentioned this pull request Dec 4, 2018
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@alimanfooalimanfoo left a comment

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Many thanks @sbalmer, looks good. Could you add a release note to docs/release.rst.

@alimanfoo

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I wonder if we can just drop the try...finally now.

FWIW I imagine it could still be possible that some failure occurs during the attempt to write to the temporary file (e.g., device gets full or something like that), in which case an exception occurs before the value has been fully written, in which case we'd still want to clean up the temporary file.

@jakirkham

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Good point.

@alimanfoo

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I've resolved conflicts after merging #352 and added a release note. Will merge if CI passes.

@alimanfoo

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@sbalmer apologies I didn't know your full name to include in the release note, you're credited currently just as "sbalmer", happy to leave it that way or add your full name, whichever you prefer.

@alimanfoo
alimanfoo merged commit 94f7a8d into zarr-developers:masterDec 4, 2018
@jakirkham

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Thanks @sbalmer 😄

@sbalmer

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Thanks @alimanfoo, @jakirkham!

Now we can use mainline again :-)

@sbalmer
sbalmer deleted the atomic-update branch December 6, 2018 13:22
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@sbalmer@alimanfoo@jakirkham@weatherfrog
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms"); } } catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

avoid race condition during chunk write - #327

Merged
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update
Dec 4, 2018
Merged

avoid race condition during chunk write#327
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update

Conversation

@sbalmer

@sbalmersbalmer commented Nov 8, 2018

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When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.

Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.

Fixes#263

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Comment threadzarr/storage.py Outdated
# On windows, rename() can't overwrite files. So
# the file is removed first.
os.remove(new)
os.rename(old, new)

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

So this is the case where we would want the pyosreplace package. It's a Windows only backport for os.replace on Python 2.

@alimanfoo

Copy link
Copy Markdown
Member

Just to mention that there are some potential consequences from implementing this PR that we should be aware of, described in #328. I don't think that should stop us from moving ahead with this PR, using os.replace() is clearly a better thing to do under any circumstances, but just something to be aware of.

@sbalmer

sbalmer commented Nov 14, 2018

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@jakirkham I've made a guess at the setup.py changes needed for pyosreplace. I couldn't get environmental markers to work. See previous commit. Could you please have a look at it? And is something else needed?

Comment threadsetup.py Outdated
@jakirkham

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Think you had it basically right. Unfortunately there is some lack of clarity about when a colon or semicolon should be used. IIUC it should be a semicolon.

@jakirkhamjakirkham left a comment

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LGTM. Thanks for working on this @sbalmer.

Hopefully the comment above is useful. Am personally fine with how this is. Though if you want to use environment markers instead (or others prefer this), that could be also done, but don't personally think this is critical.

@alimanfoo

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Thanks @sbalmer. Could you add pyosreplace to requirements.txt and requirements_dev.txt, pinned to the latest version in the latter. I guess environment markers are needed in both.

@alimanfooalimanfoo added this to the v2.3 milestone Nov 20, 2018
weatherfrogand others added 6 commits November 21, 2018 13:27
When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.
Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.
Fixeszarr-developers#263
so it's not repeated on every write
Because the env markers didn't work. Just guessing at this point.
@sbalmer

Copy link
Copy Markdown
ContributorAuthor

@alimanfoopyosreplace is now in the requirement files too. I've made a guess at how the env markers should look. If I invert the predicates then pip install -r requirements.txt tries to install the package. Which means I have some confidence it should work.

@jakirkham

Copy link
Copy Markdown
Member

Thanks @sbalmer. LGTM. 😄 Let's see what @alimanfoo thinks. 😉

@jakirkham

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I wonder if we can just drop the try...finally now.

@jakirkhamjakirkham mentioned this pull request Dec 4, 2018
7 tasks

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Many thanks @sbalmer, looks good. Could you add a release note to docs/release.rst.

@alimanfoo

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I wonder if we can just drop the try...finally now.

FWIW I imagine it could still be possible that some failure occurs during the attempt to write to the temporary file (e.g., device gets full or something like that), in which case an exception occurs before the value has been fully written, in which case we'd still want to clean up the temporary file.

@jakirkham

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Good point.

@alimanfoo

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I've resolved conflicts after merging #352 and added a release note. Will merge if CI passes.

@alimanfoo

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Member

@sbalmer apologies I didn't know your full name to include in the release note, you're credited currently just as "sbalmer", happy to leave it that way or add your full name, whichever you prefer.

@alimanfoo
alimanfoo merged commit 94f7a8d into zarr-developers:masterDec 4, 2018
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Thanks @sbalmer 😄

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Thanks @alimanfoo, @jakirkham!

Now we can use mainline again :-)

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sbalmer deleted the atomic-update branch December 6, 2018 13:22
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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links"); } } catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); } })(); (function(){ try { var __m = "youtube.com"; var __re = new RegExp('^' + "youtube\\.com" + '
Skip to content

avoid race condition during chunk write - #327

Merged
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update
Dec 4, 2018
Merged

avoid race condition during chunk write#327
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update

Conversation

@sbalmer

@sbalmersbalmer commented Nov 8, 2018

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When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.

Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.

Fixes#263

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Comment threadzarr/storage.py Outdated
# On windows, rename() can't overwrite files. So
# the file is removed first.
os.remove(new)
os.rename(old, new)

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So this is the case where we would want the pyosreplace package. It's a Windows only backport for os.replace on Python 2.

@alimanfoo

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Just to mention that there are some potential consequences from implementing this PR that we should be aware of, described in #328. I don't think that should stop us from moving ahead with this PR, using os.replace() is clearly a better thing to do under any circumstances, but just something to be aware of.

@sbalmer

sbalmer commented Nov 14, 2018

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@jakirkham I've made a guess at the setup.py changes needed for pyosreplace. I couldn't get environmental markers to work. See previous commit. Could you please have a look at it? And is something else needed?

Comment threadsetup.py Outdated
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Think you had it basically right. Unfortunately there is some lack of clarity about when a colon or semicolon should be used. IIUC it should be a semicolon.

@jakirkhamjakirkham left a comment

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LGTM. Thanks for working on this @sbalmer.

Hopefully the comment above is useful. Am personally fine with how this is. Though if you want to use environment markers instead (or others prefer this), that could be also done, but don't personally think this is critical.

@alimanfoo

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Thanks @sbalmer. Could you add pyosreplace to requirements.txt and requirements_dev.txt, pinned to the latest version in the latter. I guess environment markers are needed in both.

@alimanfooalimanfoo added this to the v2.3 milestone Nov 20, 2018
weatherfrogand others added 6 commits November 21, 2018 13:27
When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.
Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.
Fixeszarr-developers#263
so it's not repeated on every write
Because the env markers didn't work. Just guessing at this point.
@sbalmer

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@alimanfoopyosreplace is now in the requirement files too. I've made a guess at how the env markers should look. If I invert the predicates then pip install -r requirements.txt tries to install the package. Which means I have some confidence it should work.

@jakirkham

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Thanks @sbalmer. LGTM. 😄 Let's see what @alimanfoo thinks. 😉

@jakirkham

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I wonder if we can just drop the try...finally now.

@jakirkhamjakirkham mentioned this pull request Dec 4, 2018
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Many thanks @sbalmer, looks good. Could you add a release note to docs/release.rst.

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I wonder if we can just drop the try...finally now.

FWIW I imagine it could still be possible that some failure occurs during the attempt to write to the temporary file (e.g., device gets full or something like that), in which case an exception occurs before the value has been fully written, in which case we'd still want to clean up the temporary file.

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Good point.

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I've resolved conflicts after merging #352 and added a release note. Will merge if CI passes.

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@sbalmer apologies I didn't know your full name to include in the release note, you're credited currently just as "sbalmer", happy to leave it that way or add your full name, whichever you prefer.

@alimanfoo
alimanfoo merged commit 94f7a8d into zarr-developers:masterDec 4, 2018
@jakirkham

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Thanks @sbalmer 😄

@sbalmer

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Thanks @alimanfoo, @jakirkham!

Now we can use mainline again :-)

@sbalmer
sbalmer deleted the atomic-update branch December 6, 2018 13:22
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@sbalmer@alimanfoo@jakirkham@weatherfrog
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default"); } } catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

avoid race condition during chunk write - #327

Merged
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update
Dec 4, 2018
Merged

avoid race condition during chunk write#327
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update

Conversation

@sbalmer

@sbalmersbalmer commented Nov 8, 2018

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When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.

Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.

Fixes#263

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Comment threadzarr/storage.py Outdated
# On windows, rename() can't overwrite files. So
# the file is removed first.
os.remove(new)
os.rename(old, new)

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Choose a reason for hiding this comment

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So this is the case where we would want the pyosreplace package. It's a Windows only backport for os.replace on Python 2.

@alimanfoo

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Just to mention that there are some potential consequences from implementing this PR that we should be aware of, described in #328. I don't think that should stop us from moving ahead with this PR, using os.replace() is clearly a better thing to do under any circumstances, but just something to be aware of.

@sbalmer

sbalmer commented Nov 14, 2018

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@jakirkham I've made a guess at the setup.py changes needed for pyosreplace. I couldn't get environmental markers to work. See previous commit. Could you please have a look at it? And is something else needed?

Comment threadsetup.py Outdated
@jakirkham

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Think you had it basically right. Unfortunately there is some lack of clarity about when a colon or semicolon should be used. IIUC it should be a semicolon.

@jakirkhamjakirkham left a comment

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LGTM. Thanks for working on this @sbalmer.

Hopefully the comment above is useful. Am personally fine with how this is. Though if you want to use environment markers instead (or others prefer this), that could be also done, but don't personally think this is critical.

@alimanfoo

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Thanks @sbalmer. Could you add pyosreplace to requirements.txt and requirements_dev.txt, pinned to the latest version in the latter. I guess environment markers are needed in both.

@alimanfooalimanfoo added this to the v2.3 milestone Nov 20, 2018
weatherfrogand others added 6 commits November 21, 2018 13:27
When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.
Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.
Fixeszarr-developers#263
so it's not repeated on every write
Because the env markers didn't work. Just guessing at this point.
@sbalmer

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ContributorAuthor

@alimanfoopyosreplace is now in the requirement files too. I've made a guess at how the env markers should look. If I invert the predicates then pip install -r requirements.txt tries to install the package. Which means I have some confidence it should work.

@jakirkham

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Thanks @sbalmer. LGTM. 😄 Let's see what @alimanfoo thinks. 😉

@jakirkham

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I wonder if we can just drop the try...finally now.

@jakirkhamjakirkham mentioned this pull request Dec 4, 2018
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Many thanks @sbalmer, looks good. Could you add a release note to docs/release.rst.

@alimanfoo

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I wonder if we can just drop the try...finally now.

FWIW I imagine it could still be possible that some failure occurs during the attempt to write to the temporary file (e.g., device gets full or something like that), in which case an exception occurs before the value has been fully written, in which case we'd still want to clean up the temporary file.

@jakirkham

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Good point.

@alimanfoo

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I've resolved conflicts after merging #352 and added a release note. Will merge if CI passes.

@alimanfoo

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@sbalmer apologies I didn't know your full name to include in the release note, you're credited currently just as "sbalmer", happy to leave it that way or add your full name, whichever you prefer.

@alimanfoo
alimanfoo merged commit 94f7a8d into zarr-developers:masterDec 4, 2018
@jakirkham

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Thanks @sbalmer 😄

@sbalmer

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Thanks @alimanfoo, @jakirkham!

Now we can use mainline again :-)

@sbalmer
sbalmer deleted the atomic-update branch December 6, 2018 13:22
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4 participants

@sbalmer@alimanfoo@jakirkham@weatherfrog
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers"); } } catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); } })(); (function(){ try { var __m = "*"; var __re = new RegExp('^' + ".*" + '
Skip to content

avoid race condition during chunk write - #327

Merged
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update
Dec 4, 2018
Merged

avoid race condition during chunk write#327
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update

Conversation

@sbalmer

@sbalmersbalmer commented Nov 8, 2018

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When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.

Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.

Fixes#263

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Comment threadzarr/storage.py Outdated
# On windows, rename() can't overwrite files. So
# the file is removed first.
os.remove(new)
os.rename(old, new)

Copy link
Copy Markdown
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

So this is the case where we would want the pyosreplace package. It's a Windows only backport for os.replace on Python 2.

@alimanfoo

Copy link
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Member

Just to mention that there are some potential consequences from implementing this PR that we should be aware of, described in #328. I don't think that should stop us from moving ahead with this PR, using os.replace() is clearly a better thing to do under any circumstances, but just something to be aware of.

@sbalmer

sbalmer commented Nov 14, 2018

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@jakirkham I've made a guess at the setup.py changes needed for pyosreplace. I couldn't get environmental markers to work. See previous commit. Could you please have a look at it? And is something else needed?

Comment threadsetup.py Outdated
@jakirkham

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Think you had it basically right. Unfortunately there is some lack of clarity about when a colon or semicolon should be used. IIUC it should be a semicolon.

@jakirkhamjakirkham left a comment

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LGTM. Thanks for working on this @sbalmer.

Hopefully the comment above is useful. Am personally fine with how this is. Though if you want to use environment markers instead (or others prefer this), that could be also done, but don't personally think this is critical.

@alimanfoo

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Thanks @sbalmer. Could you add pyosreplace to requirements.txt and requirements_dev.txt, pinned to the latest version in the latter. I guess environment markers are needed in both.

@alimanfooalimanfoo added this to the v2.3 milestone Nov 20, 2018
weatherfrogand others added 6 commits November 21, 2018 13:27
When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.
Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.
Fixeszarr-developers#263
so it's not repeated on every write
Because the env markers didn't work. Just guessing at this point.
@sbalmer

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Copy Markdown
ContributorAuthor

@alimanfoopyosreplace is now in the requirement files too. I've made a guess at how the env markers should look. If I invert the predicates then pip install -r requirements.txt tries to install the package. Which means I have some confidence it should work.

@jakirkham

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Thanks @sbalmer. LGTM. 😄 Let's see what @alimanfoo thinks. 😉

@jakirkham

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I wonder if we can just drop the try...finally now.

@jakirkhamjakirkham mentioned this pull request Dec 4, 2018
7 tasks

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Many thanks @sbalmer, looks good. Could you add a release note to docs/release.rst.

@alimanfoo

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I wonder if we can just drop the try...finally now.

FWIW I imagine it could still be possible that some failure occurs during the attempt to write to the temporary file (e.g., device gets full or something like that), in which case an exception occurs before the value has been fully written, in which case we'd still want to clean up the temporary file.

@jakirkham

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Good point.

@alimanfoo

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I've resolved conflicts after merging #352 and added a release note. Will merge if CI passes.

@alimanfoo

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@sbalmer apologies I didn't know your full name to include in the release note, you're credited currently just as "sbalmer", happy to leave it that way or add your full name, whichever you prefer.

@alimanfoo
alimanfoo merged commit 94f7a8d into zarr-developers:masterDec 4, 2018
@jakirkham

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Thanks @sbalmer 😄

@sbalmer

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Thanks @alimanfoo, @jakirkham!

Now we can use mainline again :-)

@sbalmer
sbalmer deleted the atomic-update branch December 6, 2018 13:22
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4 participants

@sbalmer@alimanfoo@jakirkham@weatherfrog
, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode"); } } catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); } })(); })();
Skip to content

avoid race condition during chunk write - #327

Merged
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update
Dec 4, 2018
Merged

avoid race condition during chunk write#327
alimanfoo merged 8 commits into
zarr-developers:masterfrom
meteotest:atomic-update

Conversation

@sbalmer

@sbalmersbalmer commented Nov 8, 2018

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When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.

Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.

Fixes#263

TODO:

  • Add unit tests and/or doctests in docstrings
  • Add docstrings and API docs for any new/modified user-facing classes and functions
  • New/modified features documented in docs/tutorial.rst
  • Changes documented in docs/release.rst
  • Docs build locally (e.g., run tox -e docs)
  • AppVeyor and Travis CI passes
  • Test coverage is 100% (Coveralls passes)

Comment threadzarr/storage.py Outdated
# On windows, rename() can't overwrite files. So
# the file is removed first.
os.remove(new)
os.rename(old, new)

Copy link
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Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

So this is the case where we would want the pyosreplace package. It's a Windows only backport for os.replace on Python 2.

@alimanfoo

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Member

Just to mention that there are some potential consequences from implementing this PR that we should be aware of, described in #328. I don't think that should stop us from moving ahead with this PR, using os.replace() is clearly a better thing to do under any circumstances, but just something to be aware of.

@sbalmer

sbalmer commented Nov 14, 2018

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@jakirkham I've made a guess at the setup.py changes needed for pyosreplace. I couldn't get environmental markers to work. See previous commit. Could you please have a look at it? And is something else needed?

Comment threadsetup.py Outdated
@jakirkham

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Think you had it basically right. Unfortunately there is some lack of clarity about when a colon or semicolon should be used. IIUC it should be a semicolon.

@jakirkhamjakirkham left a comment

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LGTM. Thanks for working on this @sbalmer.

Hopefully the comment above is useful. Am personally fine with how this is. Though if you want to use environment markers instead (or others prefer this), that could be also done, but don't personally think this is critical.

@alimanfoo

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Thanks @sbalmer. Could you add pyosreplace to requirements.txt and requirements_dev.txt, pinned to the latest version in the latter. I guess environment markers are needed in both.

@alimanfooalimanfoo added this to the v2.3 milestone Nov 20, 2018
weatherfrogand others added 6 commits November 21, 2018 13:27
When the chunk file is first removed before the new version
is moved into place, racing reads may encounter a missing chunk.
Using rename() or replace() without remove() avoids the issue
on Posix-Systems as the methods are atomic. The fallback of
remove() -> rename() is included for Windows pre Python 3.3.
Fixeszarr-developers#263
so it's not repeated on every write
Because the env markers didn't work. Just guessing at this point.
@sbalmer

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@alimanfoopyosreplace is now in the requirement files too. I've made a guess at how the env markers should look. If I invert the predicates then pip install -r requirements.txt tries to install the package. Which means I have some confidence it should work.

@jakirkham

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Thanks @sbalmer. LGTM. 😄 Let's see what @alimanfoo thinks. 😉

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I wonder if we can just drop the try...finally now.

@jakirkhamjakirkham mentioned this pull request Dec 4, 2018
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Many thanks @sbalmer, looks good. Could you add a release note to docs/release.rst.

@alimanfoo

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I wonder if we can just drop the try...finally now.

FWIW I imagine it could still be possible that some failure occurs during the attempt to write to the temporary file (e.g., device gets full or something like that), in which case an exception occurs before the value has been fully written, in which case we'd still want to clean up the temporary file.

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Good point.

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I've resolved conflicts after merging #352 and added a release note. Will merge if CI passes.

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@sbalmer apologies I didn't know your full name to include in the release note, you're credited currently just as "sbalmer", happy to leave it that way or add your full name, whichever you prefer.

@alimanfoo
alimanfoo merged commit 94f7a8d into zarr-developers:masterDec 4, 2018
@jakirkham

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Thanks @sbalmer 😄

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Thanks @alimanfoo, @jakirkham!

Now we can use mainline again :-)

@sbalmer
sbalmer deleted the atomic-update branch December 6, 2018 13:22
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4 participants

@sbalmer@alimanfoo@jakirkham@weatherfrog