"Cannot load dashboard menu link" Error

I try to set up microk8s on remote server
Other add-on run well, but kubeflow dashboard doesn't.
When I access kubeflow centural dashboard, "Cannot load dashboard menu link" error occur.
I already set SSH tunelling with SOCKS5 proxy in Chrome(Using SwitchyOmega addon)
I don't know why it is happen.
The Error image

When I click recent pipelines, I can go to pipeline section

So I just delete /_/ in URL, so the error is disapperar!

Inspection
inspection-report-20210427_175804.tar.gz

Seems to be same issue as this one: https://github.com/canonical/bundle-kubeflow/issues/344
The answer from @knkski fixed it for me:
https://github.com/canonical/bundle-kubeflow/issues/344#issuecomment-827936799

Seems to be same issue as this one: canonical/bundle-kubeflow#344
The answer from @knkski fixed it for me:
canonical/bundle-kubeflow#344 (comment)

Oh! Thanks to your reply!
It just work!!


Publish gem after was once revoked, and publishes, but returns error

Gem is published. Server still sends back an error mesage.
This is for a very active gem, https://github.com/shakacode/react_on_rails
Using this repo: https://github.com/svenfuchs/gem-release
and this script:
https://github.com/shakacode/react_on_rails/blob/master/rakelib/release.rake#L64
+<EMAIL_ADDRESS>No distRepo provided, done.
cd /Users/justin/shakacode/react-on-rails/react_on_rails && gem release
WARNING:  open-ended dependency on connection_pool (>= 0) is not recommended
  if connection_pool is semantically versioned, use:
    add_runtime_dependency 'connection_pool', '~> 0'
WARNING:  open-ended dependency on rails (>= 3.2) is not recommended
  if rails is semantically versioned, use:
    add_runtime_dependency 'rails', '~> 3.2'
WARNING:  open-ended dependency on addressable (>= 0) is not recommended
  if addressable is semantically versioned, use:
    add_runtime_dependency 'addressable', '~> 0'
WARNING:  open-ended dependency on rspec (>= 0, development) is not recommended
  if rspec is semantically versioned, use:
    add_development_dependency 'rspec', '~> 0'
WARNING:  open-ended dependency on coveralls (>= 0, development) is not recommended
  if coveralls is semantically versioned, use:
    add_development_dependency 'coveralls', '~> 0'
WARNING:  open-ended dependency on generator_spec (>= 0, development) is not recommended
  if generator_spec is semantically versioned, use:
    add_development_dependency 'generator_spec', '~> 0'
WARNING:  open-ended dependency on pry (>= 0, development) is not recommended
  if pry is semantically versioned, use:
    add_development_dependency 'pry', '~> 0'
WARNING:  open-ended dependency on pry-byebug (>= 0, development) is not recommended
  if pry-byebug is semantically versioned, use:
    add_development_dependency 'pry-byebug', '~> 0'
WARNING:  open-ended dependency on pry-stack_explorer (>= 0, development) is not recommended
  if pry-stack_explorer is semantically versioned, use:
    add_development_dependency 'pry-stack_explorer', '~> 0'
WARNING:  open-ended dependency on pry-doc (>= 0, development) is not recommended
  if pry-doc is semantically versioned, use:
    add_development_dependency 'pry-doc', '~> 0'
WARNING:  open-ended dependency on pry-state (>= 0, development) is not recommended
  if pry-state is semantically versioned, use:
    add_development_dependency 'pry-state', '~> 0'
WARNING:  open-ended dependency on pry-toys (>= 0, development) is not recommended
  if pry-toys is semantically versioned, use:
    add_development_dependency 'pry-toys', '~> 0'
WARNING:  open-ended dependency on pry-rescue (>= 0, development) is not recommended
  if pry-rescue is semantically versioned, use:
    add_development_dependency 'pry-rescue', '~> 0'
WARNING:  open-ended dependency on binding_of_caller (>= 0, development) is not recommended
  if binding_of_caller is semantically versioned, use:
    add_development_dependency 'binding_of_caller', '~> 0'
WARNING:  open-ended dependency on awesome_print (>= 0, development) is not recommended
  if awesome_print is semantically versioned, use:
    add_development_dependency 'awesome_print', '~> 0'
WARNING:  open-ended dependency on gem-release (>= 0, development) is not recommended
  if gem-release is semantically versioned, use:
    add_development_dependency 'gem-release', '~> 0'
WARNING:  See http://guides.rubygems.org/specification-reference/ for help
  Successfully built RubyGem
  Name: react_on_rails
  Version: 6.8.2
  File: react_on_rails-6.8.2.gem
Pushing gem to https://rubygems.org...
Successfully registered gem: react_on_rails (6.8.2)
Deleting left over gem file react_on_rails-6.8.2.gem
WARNING:  open-ended dependency on connection_pool (>= 0) is not recommended
  if connection_pool is semantically versioned, use:
    add_runtime_dependency 'connection_pool', '~> 0'
WARNING:  open-ended dependency on rails (>= 3.2) is not recommended
  if rails is semantically versioned, use:
    add_runtime_dependency 'rails', '~> 3.2'
WARNING:  open-ended dependency on addressable (>= 0) is not recommended
  if addressable is semantically versioned, use:
    add_runtime_dependency 'addressable', '~> 0'
WARNING:  open-ended dependency on rspec (>= 0, development) is not recommended
  if rspec is semantically versioned, use:
    add_development_dependency 'rspec', '~> 0'
WARNING:  open-ended dependency on coveralls (>= 0, development) is not recommended
  if coveralls is semantically versioned, use:
    add_development_dependency 'coveralls', '~> 0'
WARNING:  open-ended dependency on generator_spec (>= 0, development) is not recommended
  if generator_spec is semantically versioned, use:
    add_development_dependency 'generator_spec', '~> 0'
WARNING:  open-ended dependency on pry (>= 0, development) is not recommended
  if pry is semantically versioned, use:
    add_development_dependency 'pry', '~> 0'
WARNING:  open-ended dependency on pry-byebug (>= 0, development) is not recommended
  if pry-byebug is semantically versioned, use:
    add_development_dependency 'pry-byebug', '~> 0'
WARNING:  open-ended dependency on pry-stack_explorer (>= 0, development) is not recommended
  if pry-stack_explorer is semantically versioned, use:
    add_development_dependency 'pry-stack_explorer', '~> 0'
WARNING:  open-ended dependency on pry-doc (>= 0, development) is not recommended
  if pry-doc is semantically versioned, use:
    add_development_dependency 'pry-doc', '~> 0'
WARNING:  open-ended dependency on pry-state (>= 0, development) is not recommended
  if pry-state is semantically versioned, use:
    add_development_dependency 'pry-state', '~> 0'
WARNING:  open-ended dependency on pry-toys (>= 0, development) is not recommended
  if pry-toys is semantically versioned, use:
    add_development_dependency 'pry-toys', '~> 0'
WARNING:  open-ended dependency on pry-rescue (>= 0, development) is not recommended
  if pry-rescue is semantically versioned, use:
    add_development_dependency 'pry-rescue', '~> 0'
WARNING:  open-ended dependency on binding_of_caller (>= 0, development) is not recommended
  if binding_of_caller is semantically versioned, use:
    add_development_dependency 'binding_of_caller', '~> 0'
WARNING:  open-ended dependency on awesome_print (>= 0, development) is not recommended
  if awesome_print is semantically versioned, use:
    add_development_dependency 'awesome_print', '~> 0'
WARNING:  open-ended dependency on gem-release (>= 0, development) is not recommended
  if gem-release is semantically versioned, use:
    add_development_dependency 'gem-release', '~> 0'
WARNING:  See http://guides.rubygems.org/specification-reference/ for help
  Successfully built RubyGem
  Name: react_on_rails
  Version: 6.8.2
  File: react_on_rails-6.8.2.gem
Pushing gem to https://rubygems.org...
Repushing of gem versions is not allowed.
Please use `gem yank` to remove bad gem releases.
rake aborted!
Command failed with status (1): [cd /Users/justin/shakacode/react-on-rails/...]
/Users/justin/shakacode/react-on-rails/react_on_rails/rakelib/task_helpers.rb:20:in `block in sh_in_dir'
/Users/justin/shakacode/react-on-rails/react_on_rails/rakelib/task_helpers.rb:20:in `each'
/Users/justin/shakacode/react-on-rails/react_on_rails/rakelib/task_helpers.rb:20:in `sh_in_dir'
/Users/justin/shakacode/react-on-rails/react_on_rails/rakelib/release.rake:64:in `block in <top (required)>'
/Users/justin/.rvm/gems/ruby-2.3.1@react_on_rails/gems/rake-12.0.0/exe/rake:27:in `<top (required)>'
Tasks: TOP => release
(See full trace by running task with --trace)

See #1589 and Issue on RubyGems.

See also https://github.com/rubygems/rubygems.org/issues/1577

In that case, the problem is that release command uses method in_gemspec_dirs which yielded all gem specs it can find. React_on_rails has examples/specs that contains react_on_rails gemspec. Subsequently, the release command is invoked many times.

I found the issue:
find . -name "*.gemspec"
./react_on_rails.gemspec
./spec/dummy/client/node_modules/react-on-rails/react_on_rails.gemspec

That comes from: https://github.com/shakacode/react_on_rails/blob/master/spec/dummy/client/package.json#L36
    "react-on-rails": "file:../../..",

@isolo Any chance that you can take a look at the rake task for the release and delete that extra gemspec? Or maybe delete all gemspecs except the root one? I think the properly crafted find/rm command right here could do the trick.
https://github.com/shakacode/react_on_rails/blob/master/rakelib/release.rake#L29

Moving discussion to React on Rails.

@justin808 I believe your issue should be fixed in v2.0.0.pre.x which gives you more control over this. See https://github.com/svenfuchs/gem-release/pull/64 and the readme.
As far as I understand this scenario is similar to your case. As you can see gem bump would only bump the gem in the top-level directory in this case. gem release uses the same logic for detecting/selecting gems to operate on.
If that does not work, then you can specify gem release react_on_rails in order to make sure only this one gem is used.
I am going to close this here. Please reopen if it doesn't work as expected.


[Question] find() working for both language natural name and code

If I understand correctly, currently there are two ways of getting a "language object": either through its code (Language.get('eng')), or via a search over its natural name (langcodes.find('English')).
However, e.g. langcodes.find('eng') returns a LookupError.
What about providing a "unified" function that accepts either, first matching the code and then, if not found, performing the fuzzy search over the natural names?
This would remove the need for third party codes to (re)write such a function into each project. From experience, I know that user-facing code where a "language" parameter is expected will get values in both sets (natural names, codes), no matter how many times your documentation specifies that (say) codes should be provided...
For example, the following would return the same "language object":
langcodes.find('en')
langcodes.find('eng')
langcodes.find('English')
langcodes.find('english')

I definitely understand the use case, and in fact I've encountered this kind of mixed data when parsing fr.wiktionary.org.
There are unfortunate edge cases. Should langcodes.find('pal') return:

Pal, a language of Papua New Guinea with 1200 speakers, whose language code is abw?
Or Middle Persian, otherwise known as Pahlavi, which has no extant speakers but a number of written documents, and whose language code is pal?

Another troubling example is "ron":

The Ron language of Nigeria has 180,000 speakers.
ron is listed in ISO 639-3 as the terminology language code for Romanian, even though I can find no trace of this in modern standards, which use ro or rum.

There are dozens of other examples, though many of them are for moribund languages that will probably never be represented on computers.
I was happy to reduce langcodes.find() to one argument by taking advantage of the fact that Unicode CLDR had eliminated all cross-lingual ambiguity from language names, and this reintroduces some. But if there's a justifiable thing we can do in the face of ambiguity, I'd be happy to implement it.

Hi Rob, thank you for your detailed reply and for providing examples of the difficulties with the approach I proposed.
After your explanation, I think it makes sense not to change how find() function currently works.
Still, maybe a new function, performing the lookup of a given string over both codes and natural names, can be a way to address the use case. Perhaps this new function can return a list of matches, so that the caller can take action depending on whether the list she received back has zero length ("no match found"), one item ("got one language, yay!") or more ("warning! ambiguity!").
Assuming to call this new function "fuzzy_search()" (temporary name, I do not like it):
langcodes.fuzzy_search("asfdasdfassd") => []

langcodes.fuzzy_search("en") => [ ENG ]
langcodes.fuzzy_search("eng") => [ ENG ]
langcodes.fuzzy_search("English") => [ ENG ]
langcodes.fuzzy_search("english") => [ ENG ]

langcodes.fuzzy_search("pal") => [ PAL, ABW ]

In case of ambiguities, the returned list can be even refined depending on the query string:
# ISO code matching the query string first
langcodes.fuzzy_search("pal") => [ PAL, ABW ]

# probably they meant the language, put ABW first
langcodes.fuzzy_search("Pal") => [ ABW, PAL ]
langcodes.fuzzy_search("PAL") => [ ABW, PAL ]

(This "refined" reasoning might be questionable --- it should be checked against the actual ambiguous cases. just thinking aloud...)

At the moment find(), but not get(), returns an error if unexpected content is found. Thus a simple work around for fuzzy search is:
try:     find('foo') except:     get('foo')
In my current use case (where I am expecting language codes, but want to be able to cope if someone puts a language name in instead) it would make more sense to have the order of find and get reversed but get returns anything it doesn't recognise as if it were a valid language for some reason.

After some thought, I don't want to do this. I'd prefer to keep names and codes distinct whenever possible. There are already too many cases where "codes as strings" can be confused with "codes as objects" in the code, and I don't want codes as strings to also be confused with "names as strings".


Adds (optional) JsonSchemaGeneratorSettings to JsonSerializer and JsonDeserializer for custom control over JSON schema generation.

I've encountered issues validating schemas for contracts that rely for example on a JSON converter, or when it is necessary to use a different contract resolver. I dislike having to use JsonConvert.DefaultSettings for this as this can easily be changed mistakenly for other use cases, and thus breaking schema validation.
This PR makes it possible to pass JsonSchemaGeneratorSettings to the JSON (de)serializer.

It looks like @skwasjer hasn't signed our Contributor License Agreement, yet.

The purpose of a CLA is to ensure that the guardian of a project's outputs has the necessary ownership or grants of rights over all contributions to allow them to distribute under the chosen licence.
Wikipedia

You can read and sign our full Contributor License Agreement here.
Once you've signed reply with [clabot:check] to prove it.
Appreciation of efforts,
clabot

[clabot:check]

It looks like @skwasjer hasn't signed our Contributor License Agreement, yet.

The purpose of a CLA is to ensure that the guardian of a project's outputs has the necessary ownership or grants of rights over all contributions to allow them to distribute under the chosen licence.
Wikipedia

You can read and sign our full Contributor License Agreement here.
Once you've signed reply with [clabot:check] to prove it.
Appreciation of efforts,
clabot

[clabot:check]

@confluentinc It looks like @skwasjer just signed our Contributor License Agreement. :+1:
Always at your service,
clabot

thanks! LGTM.


some useful redirects to make first time use a little easier

Added a couple of redirects to the Apache config to send people to where the cgi script lives

I should have used a branch.

Should I expect a new PR from you for this? I'm holding off from building new docker images for now.

I've sent you a tiny new PR: https://github.com/mad-ady/docker-smokeping/pull/3


Support national clouds in search

Description
Please add an informative description that covers that changes made by the pull request and link all relevant issues.
If an SDK is being regenerated based on a new swagger spec, a link to the pull request containing these swagger spec changes has been included above.
All SDK Contribution checklist:

[ ] The pull request does not introduce [breaking changes]
[ ] CHANGELOG is updated for new features, bug fixes or other significant changes.
[ ] I have read the contribution guidelines.

General Guidelines and Best Practices

[ ] Title of the pull request is clear and informative.
[ ] There are a small number of commits, each of which have an informative message. This means that previously merged commits do not appear in the history of the PR. For more information on cleaning up the commits in your PR, see this page.

Testing Guidelines

[ ] Pull request includes test coverage for the included changes.

Does search support Azure Stack?

no - they don't

API change check
APIView has identified API level changes in this PR and created following API reviews.
azure-search-documents


Warn about API key usage/presence when Trusted Publishing is configured

Currently in our Trusted Publishing flow, we don't direct the user to remove/delete API tokens that were previously being used for pushing, potentially leading to the long-lived tokens remaining available for publishing.
As a result, we should do the following:

We should warn (via email) whenever an API key is used for a project where Trusted Publishing is configured, suggesting that the maintainer remove the API token.
We should additionally send a one-time or occasional email (every 1 month?) whenever an API token exists for a project where Trusted Publishing is configured, regardless of whether it's been used fr publishing.
We should update the flow to immediately identify long-lived tokens that are no longer necessary, and prompt the user to remove them.

Should we wait until after trusted publishing has succeeded once to email them? I suspect it would be frustrating to get an email immediately if you're evaluating trusted publishers.

Yes, my thought is that the first bullet above would only happen after a publish event with a trusted publisher, and the second would only happen after some period of time after the publisher was configured.

Instead of prompting to remove old API tokens, I think it would be better to have a project setting that disables uploading via API token, as discussed in https://github.com/pypi/warehouse/issues/14300. Removing all API tokens for a project might not be straightforward, because a user is not able to see a list of outstanding tokens that are scoped to a project since there might be tokens that belong to other users. There also might be tokens scoped to all projects for a user, and some of those projects might not be set up to use Trusted Publishing.
It could still be worthwhile sending an email when an API token is used if Trusted Publishing is enabled, and also if API tokens exist and the project has not disabled publishing with API tokens.
What do y'all think?

Triaging: @facutuesca and I will be working on this next!

We should warn (via email) whenever an API key is used for a project where Trusted Publishing is configured, suggesting that the maintainer remove the API token.

This sounds good to me! We might want to cap this on "once per release," to avoid sending N emails for N files uploaded at a time.

Should we wait until after trusted publishing has succeeded once to email them? I suspect it would be frustrating to get an email immediately if you're evaluating trusted publishers.

Yeah, this makes sense to me -- there's a Release.trusted_published property that we could key on for this.
To summarize, I think we can do this in two parts:

[ ] Email notifications, both on release creation and periodically (30 days to start)
[ ] Form/flow changes, including adding a button/link for users to click to bulk remove any "equivalent" scoped API tokens

If that sounds reasonable to you @di, we'll get started on those 🙂

We might want to put a field on the publisher itself to determine if it's been used or not -- I suspect that would be helpful to identify publishers that were created but never used and might need to be removed.
Otherwise, that all sounds reasonable to me!

Whoops, another thing that @facutuesca and I talked about: in addition to email notifications/flow changes, another thing that PyPI could do here is return an informational message in the successful token exchange. The GitHub Action (or other consuming clients) could then pick that up and render it, similar to how twine will render an informational message from the receiving index.
One downside there is that the message will potentially be "overscoped," i.e. we'll send it to any workflow that does Trusted Publishing, when the people viewing it may not necessarily have permissions to take actions on it (they might be project maintainers but not owners on PyPI, and can't delete existing tokens). So this might not be immediately valuable, but I figured I'd flag it here as well 🙂

I would expect that if the workflow is otherwise successful, the likelihood of the message ever being seen is low, so that might not be worth our effort.

I have some questions to confirm if I'm understanding correctly:

For the 30-day periodic email, who do we want to email? The owner of the project or the owner of the API token? I imagine it's the owner of the token since they are the ones who can take the recommended action (delete the token)

Also, we only care about API tokens scoped only for that single project, correct? Or do we also want to warn about API tokens scoped for all the user's projects?

Finally, for the 30-day periodic email, how do we gather the users who should receive the email? Do we want to iterate over all projects, filter those with a trusted publisher, get their users (owners & maintainers), and then filter those with macaroons scoped to that single project? I'm not sure what's the most efficient way of doing this.

For the 30-day periodic email, who do we want to email? The owner of the project or the owner of the API token? I imagine it's the owner of the token since they are the ones who can take the recommended action (delete the token)

Yep: we want to email the user who can take the action, not other users. Longer term we might want to think about how we can provide all project owners visibility into scoped tokens for their projects, but that has a security dimension that probably needs further thought 🙂

Also, we only care about API tokens scoped only for that single project, correct? Or do we also want to warn about API tokens scoped for all the user's projects?

Correct!

Finally, for the 30-day periodic email, how do we gather the users who should receive the email? Do we want to iterate over all projects, filter those with a trusted publisher, get their users (owners & maintainers), and then filter those with macaroons scoped to that single project? I'm not sure what's the most efficient way of doing this.

We might need to play around with this to build a performant query, but that sounds roughly right. We could also bubble it in the opposite direction (select all macaroons that are registered to trusted publishers, extract their project scopes, and select the projects that have owners with corresponding scoped tokens). But I suspect that'll be less efficient.

I think this way would contradict #15432, right? If we prune macaroons associated with trusted publishers daily, then the list of all macaroons that are registered to trusted publishers won't be an accurate view of all the active trusted publishers

Ah, yep -- that wouldn't work in the presence of #15432. So let's definitely not do that 🙂

For the 30-day periodic email, who do we want to email? The owner of the project or the owner of the API token? I imagine it's the owner of the token since they are the ones who can take the recommended action (delete the token)

We definitely want to email the token owner. I think it wouldn't be unreasonable to also email the other project maintainers at the same time, and tell them there is a token owned by . We definitely should email all maintainers when a token is actually used (and probably say by whom).

Here's the PR for adding the email warnings triggered by a file upload: https://github.com/pypi/warehouse/pull/15453/files

Looking at https://github.com/pypi/warehouse/pull/15453, I'm wondering if this is going to be annoying for users who have a legitimate reason to not do all of their releases via Trusted Publishing (e.g., have some builds on a platform that isn't supported), which might lead to them not wanting to use Trusted Publishing.
I'm thinking we might want this warning to only happen once per API token, as a warning, and not on every usage. This makes things a little more challenging (as we need to maintain state about whether we've warned about a given API token), and makes it a little less likely that the user will take action, but should be a better UX.

I'm wondering if this is going to be annoying for users who have a legitimate reason to not do all of their releases via Trusted Publishing (e.g., have some builds on a platform that isn't supported)

What is the usual workflow in these cases? I would have assumed that given a release version (e.g., 1.0.0), the release would be created by their CI (uploading the files and creating the release on PyPI), and then the user would manually upload the wheels for not-supported platforms under the same (existing) 1.0.0 release version.
In that case, with the current implementation in https://github.com/pypi/warehouse/pull/15453, they would not get a warning since we only warn on API token use during release creation. But the 1.0.0 release is created by their CI (using the Trusted Publisher), so the following file uploads to the same release using the API token should not trigger the email.
Is there another workflow where the release for a project with Trusted Publishing configured is created first by the user manually uploading files?

What is the usual workflow in these cases? I would have assumed that given a release version (e.g., 1.0.0), the release would be created by their CI (uploading the files and creating the release on PyPI), and then the user would manually upload the wheels for not-supported platforms under the same (existing) 1.0.0 release version.

Possibly, but there's no reason it couldn't happen the other way around (my understanding is that for most projects like this, it's basically a race to see which build publishes first, and the behavior probably shouldn't be different depending on which happens first).

since we only warn on API token use during release creation.

I'm thinking this should probably be on file creation, instead. That way, the first upload that uses an API token will always get an email, regardless of whether it's the first file in a release, or the last. (One thing this will help protect against is a compromised API token being used to add additional, possibly malicious files to an existing release without the owners being aware).

@di I think we can close this one as completed (PR here: https://github.com/pypi/warehouse/pull/15641)


Update README.md

Add Harshaan Nihal
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Checkout all the things you've done by placing an x within the square braces below.

Proposed Changes

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[x] I understand opening a PULL REQUEST doesn't mean it will be merged for sure.

closing due to inactivity


multiple threads, workers, bptt questions

Hi!
We try to add a new model to under fairseq/models/. When we set ndatathreads=1, ngpus=1, we observe something strange. We print a forward in the forward function and a backward in backward function of the model. In normal cases, we got one forward followed by one backward. In the error we encounter, there are two backward after the forward. In the second `backward' part, the size of input is changed.
I wonder whether something is mixed in multithread, different workers, or bptt such that it tries to do things simultaneously or compute things twice. Thanks!

Hi @posenhuang, I don't think this should happen if you only train on one GPU. The relevant code is here. Could you try printing a stack trace in your forward and backward with print(debug.traceback()) to check where the second call originates from?

Thanks @jgehring. I did put a debugger but it is hard to trace since it is nested in the nngraph. I'll look into it again.
I think my previous description is not perfectly clear. We have a dummy criterion. In the updateOutput function, we compute both forward and backward operations to save some repeated computations. When the model explicitly calls updateGradInput, we return a previously computed gradInput in the backward'.  The weird thing is that in a rare case, forwardis called once butbackward` is called twice. Hence I was thinking whether there are something smart in pipelining or mixing the codes.
Thanks!

@jgehring, regarding the multi-threads part. If within my model, part of the model is written in c++ with multiple threads and called by the model in lua. Is there anything I should be aware for the multi-thread usages?
For some experiments, I couldn't load the intermediate checkpoints back. I got either *** Error in `/usr/bin/luajit': realloc(): invalid next size: 0x00007effb4076090 *** or Segmentation Fault in loading the checkpoints. Any thoughts? Thanks a lot!

Hey @posenhuang, sorry for the long delay here. Did you resolve this yet or is this still an issue?

I think the issue is related to out of memory usage. I'll close the issue. Thanks for checking!


Pinning Vision Cards lose conditional benefits

Building Terra NV, builder will select her level 10 VC and equip her STMR and properly show 120% MAG on the card. However, after building, if you pin the card the MAG bonus drops to 100%

{"mag":100, "conditional":[{"equipedConditions":["sword"],"mag%":100},{"mag%":20,"exclusiveUnits":["206001905","206001927","206002005","206002027","206002305","206002327","206002405","206002427","206002507","206002517","206002607","206002617"]},{"evokeDamageBoost":{"all":30},"exclusiveUnits":["206001905","206001927","206002005","206002027","206002305","206002327","206002405","206002427","206002507","206002517","206002607","206002617"]}]}
it's as if pinning is causing it to treat the two boosts as separate buffs, and dropping the lesser.


README says script-script

The README demonstrates installing this with cargo install script-script. This is confusing as the project is (now) named rust-script.

Fixed now, thanks for reporting it!


FancyZones - "Send to Back" in layout editor

Description of the new feature / enhancement
When editing multiple levels of window positioning, you can't get to the windows that are beneath the top most levels.  Having a button in that window pane to either minimize or "Send to Back" would allow for editing the windows below the top most levels.
Scenario when this would be used?
When you're using multiple levels  In my use case, I have a 3x3 grid, plus a 3col x 1row setup, plus a 1row x 3col setup, plus a 2+1col x 1row, etc.  So several layers of zones.  I duplicated one of these setups from a monitor with a smaller desktop real estate (1660x1080 rougly, it's a 1920x1080 monitor, but my task bar is snapped to the right of the monitor) over to a full 1080p monitor.  I can't get to the 3x3 grid because they're at the bottom of the stack.
Supporting information
No response

One thought I had about this is that within the layout editor, an option to select a layer number that the user wants to edit.  So layer 1 could be my 3x3 equi-sized zones, layer 2 could be my 3col x 1row zones, etc.  Depending on what layer I have active in that moving modal window, those are the panels that are in the foreground.  Those zones that are not in the selected layer are are visible, ghosted/disabled, and aren't acted on.

The ability to add or delete layers would be added.
Deleted layers would mean that zones are reassigned to the layer above.
Newly added layers disable/ghost all other layers
You can't delete the last layer
"Unlimited" number of layers can be added

If by chance that the user overlaps zones on the same layer.. well... that's a PEBKAC problem.

Can I ask why you are using these 1*3 layers? You can also span windows across multiple zones.

Now that you mention about spanning across multiple zones, and now that I figured out how to do it (Hold CTRL and drag), this suggestion becomes less of a thing.
The only time I'd need something like this is if I usually use a 3x3 setup, and then need to have 12 putty sessions cascaded (Yes, literally 12 for one type of work I do).  But when/if I need that, I can just load that particular profile.....
I'll close this.


Docs: add note to configuration deploy docs

Add note to configuration deploy docs to make explicit that connector
configurations will not be deployed
Testing: make docs, visual inspection

@cawallin @KBP-TDC

looks good! thanks


Fix deprecation errors

sprig.script has been deprecated. It is no longer required and can be safely removed.
PS. I can tell you're not working on this with plugindev ;)

Thanks but I fixed this before seeing your PR.

Oh well!

Wait... you fixed this change to the README already?


Add a delay to make sure newly created file is visible inside the VM

The hack/test-templates.sh test seems to regularly fail for the archlinux template. I'm wondering that maybe the newly created file from the host is simply not yet visible inside the VM when nerdctl tries to stat() it before mounting it into a container.

This attempt did not address the root cause


Update docs on JSON file naming conventions

The JSON files need to be named, based on the convention that is used by by registry. ServiceName+ServiceId. If additional files are created by adopters, it's best to follow the same strategy.

Discovered while working on #496


Feature Request: support '--trim' option in Leaderf rg

By the way, why Leaderf need to support every option of rg respectively but not just give the option to rg? Or add kind of black list for option which need special process.

You can add any option of rg to g:Lf_RgConfig.
Because some options may break the functionality of LeaderF, for example, '--trim' option will make the replacement in Leaderf rg  work incorrectly.

You can add any option of rg to g:Lf_RgConfig.
Because some options may break the functionality of LeaderF, for example, '--trim' option will make the replacement in Leaderf rg  work incorrectly.

Thanks for answer.
By the way, about the g:Lf_RgConfig, Rg also support config file specified by environment variable, can I use that way in Leaderf?
Because some of configuration may be environment relative, and I want to only put environment independent configs in the vimrc.

Thanks for answer.
By the way, about the g:Lf_RgConfig, Rg also support config file specified by environment variable, can I use that way in Leaderf?
Because some of configuration may be environment relative, and I want to only put environment independent configs in the vimrc.

I'm not sure. I think it should work.

I'm not sure. I think it should work.

It didn't work, can rg run from Leaderf get the environment variable export in my bash ?

It didn't work, can rg run from Leaderf get the environment variable export in my bash ?

Can you give me an example that how you use it?

Can you give me an example that how you use it?

Oh, yeah, --no-config is added by default in order not to read configurations from user. Because this can prevent unexpected behavior.
Before, user opened the issue to ask why Leaderf rg does not work well, it turn out to be that rg has read the configurations from ripgreprc.
https://github.com/Yggdroot/LeaderF/blob/25219bf85dcbc1c497d06a85ca9684b130536a31/autoload/leaderf/python/leaderf/rgExpl.py#L303-L305

Oh, yeah, --no-config is added by default in order not to read configurations from user. Because this can prevent unexpected behavior.
Before, user opened the issue to ask why Leaderf rg does not work well, it turn out to be that rg has read the configurations from ripgreprc.
https://github.com/Yggdroot/LeaderF/blob/25219bf85dcbc1c497d06a85ca9684b130536a31/autoload/leaderf/python/leaderf/rgExpl.py#L303-L305

oh, I see. May be those options can be more detailed in documentation, since Leaderf can use rg like in the shell, but indeed there are some limitation on it.

oh, I see. May be those options can be more detailed in documentation, since Leaderf can use rg like in the shell, but indeed there are some limitation on it.

Yes, e.g. -I, --no-filename.
rg in the cmdline just print the output, but Leaderf rg needs to use the output for secondary fuzzy filter and jump to the right place of the target file in vim.

Yes, e.g. -I, --no-filename.
rg in the cmdline just print the output, but Leaderf rg needs to use the output for secondary fuzzy filter and jump to the right place of the target file in vim.


Testing Pipelines #2

Your image
supreethkunder/tasklens-dashboard:0.1.1-main-api

Current base image
python:3-slim-bullseye

Refreshed base image
python:3-slim-bullseye

Updated base image
python:alpine

:mag: Vulnerabilities of supreethkunder/tasklens-dashboard:0.1.1-main-api
:package: Image Reference supreethkunder/tasklens-dashboard:0.1.1-main-api

digestsha256:d69cef4552582a4ff240763417b8c55ff01c98469bc54d760867f3876fc7e1ddvulnerabilities
platformlinux/amd64
size89 MB
packages237

:package: Base Image python:3-slim-bullseye

also known as

3.12-slim-bullseye
3.12.3-slim-bullseye
slim-bullseye

digestsha256:11ee4eb9e164c0ff4aeb4eef37163aedc358f57045f394f719b8c130190a440d
vulnerabilities

    expat 2.2.10-2+deb11u5 (deb)
pkg:deb/debian/expat@2.2.10-2+deb11u5?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=2.2.10-2+deb11u5
Fixed versionNot Fixed
Description

An issue was discovered in libexpat before 2.6.3. nextScaffoldPart in xmlparse.c can have an integer overflow for m_groupSize on 32-bit platforms (where UINT_MAX equals SIZE_MAX).

Affected range>=2.2.10-2+deb11u5
Fixed versionNot Fixed
Description

An issue was discovered in libexpat before 2.6.3. dtdCopy in xmlparse.c can have an integer overflow for nDefaultAtts on 32-bit platforms (where UINT_MAX equals SIZE_MAX).

Affected range>=2.2.10-2+deb11u5
Fixed versionNot Fixed
Description

An issue was discovered in libexpat before 2.6.3. xmlparse.c does not reject a negative length for XML_ParseBuffer.

Affected range>=2.2.10-2+deb11u5
Fixed versionNot Fixed
Description

libexpat through 2.6.1 allows an XML Entity Expansion attack when there is isolated use of external parsers (created via XML_ExternalEntityParserCreate).

Affected range>=2.2.10-2+deb11u5
Fixed versionNot Fixed
Description

libexpat through 2.5.0 allows recursive XML Entity Expansion if XML_DTD is undefined at compile time.

Affected range>=2.2.10-2+deb11u5
Fixed versionNot Fixed
Description

expat 2.1.0 and earlier does not properly handle entities expansion unless an application developer uses the XML_SetEntityDeclHandler function, which allows remote attackers to cause a denial of service (resource consumption), send HTTP requests to intranet servers, or read arbitrary files via a crafted XML document, aka an XML External Entity (XXE) issue.  NOTE: it could be argued that because expat already provides the ability to disable external entity expansion, the responsibility for resolving this issue lies with application developers; according to this argument, this entry should be REJECTed, and each affected application would need its own CVE.

    krb5 1.18.3-6+deb11u4 (deb)
pkg:deb/debian/krb5@1.18.3-6+deb11u4?os_distro=bullseye&os_name=debian&os_version=11

Affected range<1.18.3-6+deb11u5
Fixed version1.18.3-6+deb11u5
Description

In MIT Kerberos 5 (aka krb5) before 1.21.3, an attacker can cause invalid memory reads during GSS message token handling by sending message tokens with invalid length fields.

Affected range<1.18.3-6+deb11u5
Fixed version1.18.3-6+deb11u5
Description

In MIT Kerberos 5 (aka krb5) before 1.21.3, an attacker can modify the plaintext Extra Count field of a confidential GSS krb5 wrap token, causing the unwrapped token to appear truncated to the application.

    gnutls28 3.7.1-5+deb11u4 (deb)
pkg:deb/debian/gnutls28@3.7.1-5+deb11u4?os_distro=bullseye&os_name=debian&os_version=11

Affected range<3.7.1-5+deb11u5
Fixed version3.7.1-5+deb11u5
Description

A vulnerability was found in GnuTLS, where a cockpit (which uses gnuTLS) rejects a certificate chain with distributed trust. This issue occurs when validating a certificate chain with cockpit-certificate-ensure. This flaw allows an unauthenticated, remote client or attacker to initiate a denial of service attack.

Affected range<3.7.1-5+deb11u5
Fixed version3.7.1-5+deb11u5
Description

A vulnerability was found in GnuTLS. The response times to malformed ciphertexts in RSA-PSK ClientKeyExchange differ from the response times of ciphertexts with correct PKCS#1 v1.5 padding. This issue may allow a remote attacker to perform a timing side-channel attack in the RSA-PSK key exchange, potentially leading to the leakage of sensitive data. CVE-2024-0553 is designated as an incomplete resolution for CVE-2023-5981.

Affected range<3.7.1-5+deb11u6
Fixed version3.7.1-5+deb11u6
Description

A flaw was found in GnuTLS. The Minerva attack is a cryptographic vulnerability that exploits deterministic behavior in systems like GnuTLS, leading to side-channel leaks. In specific scenarios, such as when using the GNUTLS_PRIVKEY_FLAG_REPRODUCIBLE flag, it can result in a noticeable step in nonce size from 513 to 512 bits, exposing a potential timing side-channel.

Affected range<3.7.1-5+deb11u6
Fixed version3.7.1-5+deb11u6
Description

A flaw has been discovered in GnuTLS where an application crash can be induced when attempting to verify a specially crafted .pem bundle using the "certtool --verify-chain" command.

    systemd 247.3-7+deb11u4 (deb)
pkg:deb/debian/systemd@247.3-7+deb11u4?os_distro=bullseye&os_name=debian&os_version=11

Affected range<247.3-7+deb11u6
Fixed version247.3-7+deb11u6
Description

Certain DNSSEC aspects of the DNS protocol (in RFC 4033, 4034, 4035, 6840, and related RFCs) allow remote attackers to cause a denial of service (CPU consumption) via one or more DNSSEC responses, aka the "KeyTrap" issue. One of the concerns is that, when there is a zone with many DNSKEY and RRSIG records, the protocol specification implies that an algorithm must evaluate all combinations of DNSKEY and RRSIG records.

Affected range<247.3-7+deb11u6
Fixed version247.3-7+deb11u6
Description

A vulnerability was found in systemd-resolved. This issue may allow systemd-resolved to accept records of DNSSEC-signed domains even when they have no signature, allowing man-in-the-middles (or the upstream DNS resolver) to manipulate records.

Affected range<247.3-7+deb11u6
Fixed version247.3-7+deb11u6
Description

The Closest Encloser Proof aspect of the DNS protocol (in RFC 5155 when RFC 9276 guidance is skipped) allows remote attackers to cause a denial of service (CPU consumption for SHA-1 computations) via DNSSEC responses in a random subdomain attack, aka the "NSEC3" issue. The RFC 5155 specification implies that an algorithm must perform thousands of iterations of a hash function in certain situations.

    python-jose 3.3.0 (pypi)
<EMAIL_ADDRESS> Use of a Broken or Risky Cryptographic Algorithm

Affected range<=3.3.0
Fixed versionNot Fixed
CVSS Score7.4
CVSS VectorCVSS:3.1/AV:N/AC:H/PR:N/UI:N/S:U/C:H/I:H/A:N

Description

python-jose through 3.3.0 has algorithm confusion with OpenSSH ECDSA keys and other key formats. This is similar to CVE-2022-29217.

 Uncontrolled Resource Consumption

Affected range<=3.3.0
Fixed versionNot Fixed
CVSS Score5.3
CVSS VectorCVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:N/I:N/A:L

Description

python-jose through 3.3.0 allows attackers to cause a denial of service (resource consumption) during a decode via a crafted JSON Web Encryption (JWE) token with a high compression ratio, aka a "JWT bomb." This is similar to CVE-2024-21319.

    pip 24.2 (pypi)
<EMAIL_ADDRESS> OWASP Top Ten 2017 Category A9 - Using Components with Known Vulnerabilities

Affected range>=0
Fixed versionNot Fixed
CVSS Score7.8
CVSS VectorCVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H

Description

An issue was discovered in pip (all versions) because it installs the version with the highest version number, even if the user had intended to obtain a private package from a private index. This only affects use of the --extra-index-url option, and exploitation requires that the package does not already exist in the public index (and thus the attacker can put the package there with an arbitrary version number).

    setuptools 69.5.1 (pypi)
<EMAIL_ADDRESS> Improper Control of Generation of Code ('Code Injection')

Affected range<70.0.0
Fixed version70.0.0
CVSS Score8.8
CVSS VectorCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H

Description

A vulnerability in the package_index module of pypa/setuptools versions up to 69.1.1 allows for remote code execution via its download functions. These functions, which are used to download packages from URLs provided by users or retrieved from package index servers, are susceptible to code injection. If these functions are exposed to user-controlled inputs, such as package URLs, they can execute arbitrary commands on the system. The issue is fixed in version 70.0.

    pip 24.0 (pypi)
<EMAIL_ADDRESS> OWASP Top Ten 2017 Category A9 - Using Components with Known Vulnerabilities

Affected range>=0
Fixed versionNot Fixed
CVSS Score7.8
CVSS VectorCVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H

Description

An issue was discovered in pip (all versions) because it installs the version with the highest version number, even if the user had intended to obtain a private package from a private index. This only affects use of the --extra-index-url option, and exploitation requires that the package does not already exist in the public index (and thus the attacker can put the package there with an arbitrary version number).

    pcre3 2:8.39-13 (deb)
pkg:deb/debian/pcre3@2:8.39-13?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=2:8.39-13
Fixed versionNot Fixed
Description

libpcre in PCRE before 8.43 allows a subject buffer over-read in JIT when UTF is disabled, and \X or \R has more than one fixed quantifier, a related issue to CVE-2019-20454.

Affected range>=2:8.39-13
Fixed versionNot Fixed
Description

Stack-based buffer overflow in the pcre32_copy_substring function in pcre_get.c in libpcre1 in PCRE 8.40 allows remote attackers to cause a denial of service (WRITE of size 268) or possibly have unspecified other impact via a crafted file.

Affected range>=2:8.39-13
Fixed versionNot Fixed
Description

Stack-based buffer overflow in the pcre32_copy_substring function in pcre_get.c in libpcre1 in PCRE 8.40 allows remote attackers to cause a denial of service (WRITE of size 4) or possibly have unspecified other impact via a crafted file.

Affected range>=2:8.39-13
Fixed versionNot Fixed
Description

In PCRE 8.41, after compiling, a pcretest load test PoC produces a crash overflow in the function match() in pcre_exec.c because of a self-recursive call. NOTE: third parties dispute the relevance of this report, noting that there are options that can be used to limit the amount of stack that is used

Affected range>=2:8.39-13
Fixed versionNot Fixed
Description

In PCRE 8.41, the OP_KETRMAX feature in the match function in pcre_exec.c allows stack exhaustion (uncontrolled recursion) when processing a crafted regular expression.

    sqlite3 3.34.1-3 (deb)
pkg:deb/debian/sqlite3@3.34.1-3?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=3.34.1-3
Fixed versionNot Fixed
Description

SQLite 1.0.12 through 3.39.x before 3.39.2 sometimes allows an array-bounds overflow if billions of bytes are used in a string argument to a C API.

Affected range>=3.34.1-3
Fixed versionNot Fixed
Description

A Memory Leak vulnerability exists in SQLite Project SQLite3 3.35.1 and 3.37.0 via maliciously crafted SQL Queries (made via editing the Database File), it is possible to query a record, and leak subsequent bytes of memory that extend beyond the record, which could let a malicious user obtain sensitive information. NOTE: The developer disputes this as a vulnerability stating that If you give SQLite a corrupted database file and submit a query against the database, it might read parts of the database that you did not intend or expect.

Affected range>=3.34.1-3
Fixed versionNot Fixed
Description

A segmentation fault can occur in the sqlite3.exe command-line component of SQLite 3.36.0 via the idxGetTableInfo function when there is a crafted SQL query. NOTE: the vendor disputes the relevance of this report because a sqlite3.exe user already has full privileges (e.g., is intentionally allowed to execute commands). This report does NOT imply any problem in the SQLite library.

    shadow 1:4.8.1-1 (deb)
pkg:deb/debian/shadow@1:4.8.1-1?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=1:4.8.1-1
Fixed versionNot Fixed
Description

shadow 4.8, in certain circumstances affecting at least Gentoo, Arch Linux, and Void Linux, allows local users to obtain root access because setuid programs are misconfigured. Specifically, this affects shadow 4.8 when compiled using --with-libpam but without explicitly passing --disable-account-tools-setuid, and without a PAM configuration suitable for use with setuid account management tools. This combination leads to account management tools (groupadd, groupdel, groupmod, useradd, userdel, usermod) that can easily be used by unprivileged local users to escalate privileges to root in multiple ways. This issue became much more relevant in approximately December 2019 when an unrelated bug was fixed (i.e., the chmod calls to suidusbins were fixed in the upstream Makefile which is now included in the release version 4.8).

Affected range>=1:4.8.1-1
Fixed versionNot Fixed
Description

shadow: TOCTOU (time-of-check time-of-use) race condition when copying and removing directory trees

Affected range>=1:4.8.1-1
Fixed versionNot Fixed
Description

initscripts in rPath Linux 1 sets insecure permissions for the /var/log/btmp file, which allows local users to obtain sensitive information regarding authentication attempts.  NOTE: because sshd detects the insecure permissions and does not log certain events, this also prevents sshd from logging failed authentication attempts by remote attackers.

    perl 5.32.1-4+deb11u3 (deb)
pkg:deb/debian/perl@5.32.1-4+deb11u3?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=5.32.1-4+deb11u3
Fixed versionNot Fixed
Description

HTTP::Tiny before 0.083, a Perl core module since 5.13.9 and available standalone on CPAN, has an insecure default TLS configuration where users must opt in to verify certificates.

Affected range>=5.32.1-4+deb11u3
Fixed versionNot Fixed
Description

_is_safe in the File::Temp module for Perl does not properly handle symlinks.

    coreutils 8.32-4+b1 (deb)
pkg:deb/debian/coreutils@8.32-4+b1?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=8.32-4
Fixed versionNot Fixed
Description

In GNU Coreutils through 8.29, chown-core.c in chown and chgrp does not prevent replacement of a plain file with a symlink during use of the POSIX "-R -L" options, which allows local users to modify the ownership of arbitrary files by leveraging a race condition.

    libgcrypt20 1.8.7-6 (deb)
pkg:deb/debian/libgcrypt20@1.8.7-6?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=1.8.7-6
Fixed versionNot Fixed
Description

cipher/elgamal.c in Libgcrypt through 1.8.2, when used to encrypt messages directly, improperly encodes plaintexts, which allows attackers to obtain sensitive information by reading ciphertext data (i.e., it does not have semantic security in face of a ciphertext-only attack). The Decisional Diffie-Hellman (DDH) assumption does not hold for Libgcrypt's ElGamal implementation.

    openssl 1.1.1w-0+deb11u1 (deb)
pkg:deb/debian/openssl@1.1.1w-0+deb11u1?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=1.1.1w-0+deb11u1
Fixed versionNot Fixed
Description

OpenSSL 0.9.8i on the Gaisler Research LEON3 SoC on the Xilinx Virtex-II Pro FPGA uses a Fixed Width Exponentiation (FWE) algorithm for certain signature calculations, and does not verify the signature before providing it to a caller, which makes it easier for physically proximate attackers to determine the private key via a modified supply voltage for the microprocessor, related to a "fault-based attack."

    apt 2.2.4 (deb)
pkg:deb/debian/apt@2.2.4?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=2.2.4
Fixed versionNot Fixed
Description

It was found that apt-key in apt, all versions, do not correctly validate gpg keys with the master keyring, leading to a potential man-in-the-middle attack.

    util-linux 2.36.1-8+deb11u2 (deb)
pkg:deb/debian/util-linux@2.36.1-8+deb11u2?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=2.36.1-8+deb11u2
Fixed versionNot Fixed
Description

A flaw was found in the util-linux chfn and chsh utilities when compiled with Readline support. The Readline library uses an "INPUTRC" environment variable to get a path to the library config file. When the library cannot parse the specified file, it prints an error message containing data from the file. This flaw allows an unprivileged user to read root-owned files, potentially leading to privilege escalation. This flaw affects util-linux versions prior to 2.37.4.

    gnupg2 2.2.27-2+deb11u2 (deb)
pkg:deb/debian/gnupg2@2.2.27-2+deb11u2?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=2.2.27-2+deb11u2
Fixed versionNot Fixed
Description

GnuPG can be made to spin on a relatively small input by (for example) crafting a public key with thousands of signatures attached, compressed down to just a few KB.

    tar 1.34+dfsg-1+deb11u1 (deb)
pkg:deb/debian/tar@1.34+dfsg-1+deb11u1?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=1.34+dfsg-1+deb11u1
Fixed versionNot Fixed
Description

Tar 1.15.1 does not properly warn the user when extracting setuid or setgid files, which may allow local users or remote attackers to gain privileges.

    pcre2 10.36-2+deb11u1 (deb)
pkg:deb/debian/pcre2@10.36-2+deb11u1?os_distro=bullseye&os_name=debian&os_version=11

Affected range>=10.36-2+deb11u1
Fixed versionNot Fixed
Description

Integer overflow vulnerability in pcre2test before 10.41 allows attackers to cause a denial of service or other unspecified impacts via negative input.


⚠ Bofrost.de has degraded performance

In 40d0a49, Bofrost.de (https://www.bofrost.de) experienced degraded performance:

HTTP code: 200
Response time: 1357 ms

Resolved: Bofrost.de performance has improved in 3fb3c87 after 312 days, 8 hours, 6 minutes.


Issue converting a http/net request to typhoeus

I'm trying to convert my http/net request to typhoeus and am having trouble with a response error:  Url key and value should be splited by = .
This is the original request:
http = Net::HTTP.new(uri.host, uri.port)
http.use_ssl = true
req = Net::HTTP::Post.new(endpoint, {'Content-Type' => 'application/json; charset=utf-8', 'Authorization' => authorization, 'Host' => host, 'X-TC-Action' => action, 'X-TC-Version' => version, 'X-TC-Timestamp' => timestamp.to_s, 'X-TC-Region' => region })
req.body = params.encode("utf-8")

This is the converted typhoeus request:
req = Typhoeus::Request.new(
  endpoint,
  method: :post,
  body: params.encode("utf-8"),
  params: {'Content-Type' => 'application/json; charset=utf-8', 'Authorization' => authorization, 'Host' => host, 'X-TC-Action' => action, 'X-TC-Version' => version, 'X-TC-Timestamp' => timestamp.to_s, 'X-TC-Region' => region }
)

This is the typhoeus object after making the request:
=> #<Typhoeus::Request:0x00007ff861942a80
 @base_url="https://tmt.na-siliconvalley.tencentcloudapi.com",
 @hydra=
  #<Typhoeus::Hydra:0x00007ff85b00eb40
   @max_concurrency=200,
   @memory={},
   @multi=
    #<Ethon::Multi:0x00007ff85b00ea00
     @easy_handles=[],
     @fd_excep=#<Ethon::Curl::FDSet:0x00007ff85b00e1e0>,
     @fd_read=#<Ethon::Curl::FDSet:0x00007ff85b00e438>,
     @fd_write=#<Ethon::Curl::FDSet:0x00007ff85b00e2a8>,
     @handle=#<FFI::AutoPointer address=0x00007ff847f3c780>,
     @max_fd=#<FFI::MemoryPointer address=0x00007ff863e3f190 size=4>,
     @running_count=0,
     @timeout=#<FFI::MemoryPointer address=0x00007ff863c6e2a0 size=8>,
     @timeval=#<Ethon::Curl::Timeval:0x00007ff85b00e528>>,
   @options={},
   @queued_requests=[]>,
 @on_complete=[],
 @on_headers=[],
 @on_progress=[],
 @on_success=[],
 @options=
  {:method=>:post,
   :body=>"{\"ProjectId\":0,\"SourceText\":\"I am a boy\",\"Source\":\"en\",\"Target\":\"zh\"}",
   :params=>
    {"Content-Type"=>"application/json; charset=utf-8",
     "Authorization"=>
      "TC3-HMAC-SHA256 Credential=AKIDymLfjXYaEhvtHQL7ex2q6JL7A2YopZ9V/2019-10-14/tmt/tc3_request, SignedHeaders=content-type;host, Signature=191c0f66c0562b403e4252c227ba77d9488e68a7e0594d5bcd90b711a8309773",
     "Host"=>"tmt.na-siliconvalley.tencentcloudapi.com",
     "X-TC-Action"=>"TextTranslate",
     "X-TC-Version"=>"2018-03-21",
     "X-TC-Timestamp"=>"1571037888",
     "X-TC-Region"=>"na-siliconvalley"},
   :headers=>{"User-Agent"=>"Typhoeus - https://github.com/typhoeus/typhoeus", "Expect"=>""},
   :maxredirs=>50},
 @original_options=
  {:method=>:post,
   :body=>"{\"ProjectId\":0,\"SourceText\":\"I am a boy\",\"Source\":\"en\",\"Target\":\"zh\"}",
   :params=>
    {"Content-Type"=>"application/json; charset=utf-8",
     "Authorization"=>
      "TC3-HMAC-SHA256 Credential=AKIDymLfjXYaEhvtHQL7ex2q6JL7A2YopZ9V/2019-10-14/tmt/tc3_request, SignedHeaders=content-type;host, Signature=191c0f66c0562b403e4252c227ba77d9488e68a7e0594d5bcd90b711a8309773",
     "Host"=>"tmt.na-siliconvalley.tencentcloudapi.com",
     "X-TC-Action"=>"TextTranslate",
     "X-TC-Version"=>"2018-03-21",
     "X-TC-Timestamp"=>"1571037888",
     "X-TC-Region"=>"na-siliconvalley"}},
 @response=
  #<Typhoeus::Response:0x00007ff857216068
   @options=
    {:httpauth_avail=>0,
     :total_time=>0.666025,
     :starttransfer_time=>0.0,
     :appconnect_time=>0.512197,
     :pretransfer_time=>0.512308,
     :connect_time=>0.190879,
     :namelookup_time=>0.039239,
     :redirect_time=>0.0,
     :effective_url=>
      "https://tmt.na-siliconvalley.tencentcloudapi.com?Content-Type=application%2Fjson%3B%20charset%3Dutf-8&Authorization=TC3-HMAC-SHA256%20Credential%3DAKIDymLfjXYaEhvtHQL7ex2q6JL7A2YopZ9V%2F2019-10-14%2Ftmt%2Ftc3_request%2C%20SignedHeaders%3Dcontent-type%3Bhost%2C%20Signature%3D191c0f66c0562b403e4252c227ba77d9488e68a7e0594d5bcd90b711a8309773&Host=tmt.na-siliconvalley.tencentcloudapi.com&X-TC-Action=TextTranslate&X-TC-Version=2018-03-21&X-TC-Timestamp=1571037888&X-TC-Region=na-siliconvalley",
     :primary_ip=>"<IP_ADDRESS>",
     :response_code=>200,
     :request_size=>721,
     :redirect_count=>0,
     :return_code=>:ok,
     :response_headers=>"HTTP/1.1 200 OK\r\nServer: nginx\r\nDate: Mon, 14 Oct 2019 07:25:27 GMT\r\nContent-Type: application/json\r\nContent-Length: 157\r\nConnection: close\r\n\r\n",
     :response_body=>
      "{\"Response\":{\"Error\":{\"Code\":\"InvalidParameter\",\"Message\":\"Url key and value should be splited by `=`.\"},\"RequestId\":\"a141b417-6d34-471f-b1e5-f5cfde81cfc9\"}}",
     :debug_info=>#<Ethon::Easy::DebugInfo:0x00007ff8574fc660 @messages=[]>},
   @request=#<Typhoeus::Request:0x00007ff861942a80 ...>>>

What is the best way to debug this issue?  The error Url key and value doesn't make a lot of sense to me.
EDIT:
My guess the issue is because the authorization variable in the request is a string with keys and values within it:
authorization = (algorithm + ' Credential=' + ENV['TENCENT_SECRET_ID'] + '/' + credential_scope + ', ' + 'SignedHeaders=' + signed_headers + ', ' + 'Signature=' + signature)
But nevertheless, the net/http request I was originally using works..

Ah, the correct request is:
req = Typhoeus::Request.new(
  endpoint,
  method: :post,
  body: params.encode("utf-8"),
  headers: {'Content-Type' => 'application/json; charset=utf-8', 'Authorization' => authorization, 'Host' => host, 'X-TC-Action' => action, 'X-TC-Version' => version, 'X-TC-Timestamp' => timestamp.to_s, 'X-TC-Region' => region }
)


Flutter inspector not opening...

It just shows this dialogue when I try opening flutter inspector...

Hey @,
This issue tracker is used for tracking bugs and feature requests for the flutter framework, engine and the flutter tool.
Since this is an error/bug with the intelliJ plugin, please close this issue and open it here instead.
Thanks


client: add GET /downloads path

Issue: https://github.com/moov-io/ofac/issues/36

Codecov Report

Merging #46 into master will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master      #46   +/-   ##
=======================================
  Coverage   58.29%   58.29%
=======================================
  Files          15       15
  Lines        1151     1151
=======================================
  Hits          671      671
  Misses        383      383
  Partials       97       97


fix(onyx-145): update the search input field when scrolling through options using keyboard arrows

The type of this PR is: Fix
This PR solves ONYX-145
Description
https://github.com/artsy/force/assets/3934579/83a5e67c-f937-47ed-a2ea-9d194159be08

LGTM


[0364] Remove MCB from codebase

Context
MCB code
Changes proposed in this pull request
Removed MCB from codebase, It has served it purpose and now it can finally be laid to rest.
Guidance to review
Was there more to be delete?
Checklist

[ ] Make sure all information from the Trello card is in here
[ ] Attach to Trello card
[ ] Rebased master
[ ] Cleaned commit history
[ ] Tested by running locally

 Remove MCB from codebase


Revert "Revert 1 juliana micheal patch 1"

Reverts Oluwasetemi/altschool-opensource-names#539

Your name is not in the PR.
File changes says zero.
confirm your name on this url


[Task] - Choose and install a CSS-Framework

Goal
We need a design-framework, which fits our needs.
Description
I´d suggest TailwindCSS, but can be choosen by the first person who deals with styling.

Done


New Features

Change log

Added inspirational quotes to the dashboard
Added player count gauge to dashboard
Added motels to the character page
Added character edits to panel log
Added Panel logs view
Player search Banned or not banned
Bug fixing
Back button for character page
Ability for staff to remove players tattoos

@ExpDev07 bunch of cool new features and some bug fixes

Awesome, nice work


Secure Graylog - SSL proxy and anonymization of PII

Our server logs can contain sensitive information. Graylog should be tightly secured behind an SSL proxy. We also need to anonymize IP addresses to protect the privacy of our users.

I added SSL and set up a Graylog extractor to mask the last octet of all logged IPs.


Adding Weight Conversion

Hey I made Weight Conversion Project Which Is Very Good!
This Project is very Helpfull,
I Make This Project With the help of HTML, CSS & JavaScript,
The CSS & JavaScript Code are Available in very well mannered! & Easy to understand!

@kalashvasaniya The name of the extension appears to be "Height Conversion" where as you have mentioned it to be "Weight Conversion Tool" please make the necessary changes in the manifest file.

@kalashvasaniya The name of the extension appears to be "Height Conversion" where as you have mentioned it to be "Weight Conversion Tool" please make the necessary changes in the manifest file.

Okk sorry I will

@kalashvasaniya The name of the extension appears to be "Height Conversion" where as you have mentioned it to be "Weight Conversion Tool" please make the necessary changes in the manifest file.

Done :)


Which statement is correct ?

[Enter feedback here]
Hi,
There are two contradictory statements Which is correct?

You may use an Enterprise Gateway with Azure SQL DB. However, you may not use SSO or oAuth2 to authenticate in those scenarios.

For paginated reports, Azure SQL Database and Azure Analysis Services currently can't be accessed via a Power BI data gateway.

If both are correct, the difference between the assumptions cannot be read from the description, so the difference needs to be clarified.
Thanks

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 40a5444a-ce6c-9a0c-3e84-832e67b75d47
Version Independent ID: df2623ba-2917-faf6-0077-e9d182a9e96c
Content: Supported data sources for Power BI paginated reports - Power BI
Content Source: powerbi-docs/paginated-reports/paginated-reports-data-sources.md
Service: powerbi
Sub-service: report-builder
GitHub Login: @onegoodsausage
Microsoft Alias: andremi

Thanks for your comment, @ryoma-nagata - sorry for the confusion. We’ve forwarded your feedback to the writer, who should respond to this thread shortly. Thanks!

Hi, @ryoma-nagata -- thanks for asking! We've updated the article. The change should be published this afternoon.

Thank you for your help.


Cursor (blit?) regression in 2.0.16

Describe the bug
TL;DR: https://github.com/pyglet/pyglet/pull/1109 may have done something weird to blending in 2.0.16
I'm filing this on behalf of a Discord user I'm guiding through getting diagnostic info. Discord discussion here.
Expected Behavior

Actual Behavior

Reproduction Code & Image
How to Reproduce
Image:

import pyglet

win = pyglet.window.Window()
image = pyglet.image.load('cursor.png')

@win.event
def on_draw():
    win.clear()
    image.get_texture().blit(5,5)

pyglet.app.run()

System Info

Windows 10 64-bit

full python -m pyglet.info

This should be resolved with the latest PR.


⚠ Shadow Does Streams has degraded performance

In 298f2f9, Shadow Does Streams (https://stream.everythingbagel.me) experienced degraded performance:

HTTP code: 200
Response time: 7744 ms

Resolved: Shadow Does Streams performance has improved in ebf98e9 after 28 minutes.


Setting clipRect makes MathJax time out

PhantomJS Version
2.1.1
Reproducing the problem
I'm trying to get MathJax to render the math on the html page before PhantomJS renders the html into png. The relevant code is shown below, where ./test.html is some html file which contains math and imports MathJax.
Symptom Cases
I've tried setting clipRect in two ways. The results I got for .png and .pdf formats are below.
page.clipRect = {...} (deprecated)
PNG: works perfectly
PDF: program hangs
page.set('clipRect', {...}) (recommended)
PNG: times out
PDF:  times out
PhantomJS renders perfectly fine when clipRect is not being set.
Operating system
Windows
Phantom type
Binary
Code
`var page = require('webpage').create();
var system = require('system');
var fs = require('fs');
page.open('./test.html', function () {
page.onAlert = function (msg) {
if (msg === "MathJax Done") {
page.clipRect={
top:    10,
left:   10,
width:  400,
height: 500
}
page.render('example.png');
} else if (msg === "MathJax Timeout") {
  console.log("Timed out waiting for MathJax");
} else {console.log(msg)}
phantom.exit();

};
page.evaluate(function () {
MathJax.Hub.Queue(
["Typeset",MathJax.Hub],
[alert,'MathJax Done']
);
setTimeout(function () {alert("MathJax Timeout")},10000);  // timeout after 10 seconds
});
});`

Closing, same problem as: https://github.com/ariya/phantomjs/issues/10465


fixed build errors for iOS target under Xcode 8.2

Some of the *.swift files aren't included to the iOS target

That's small details, but anyway very helpful to craft a great product. Thanks a lot!


Better indication that content is still downloading (page looks broken on first access)

When accessing content that was uploaded from LBRY on spee.ch for the first time, the video looks like it's broken because playback does not start immediately during download (I could have sworn it used to, maybe something broke here recently). If you refresh the page and the download has completed, it will then play.

Fix included with https://github.com/lbryio/spee.ch/issues/593


fix: move types to be first entry in package.json exports

"types" - can be used by typing systems to resolve the typing file for the given export. This condition should always be included first.

https://nodejs.org/api/packages.html#community-conditions-definitions
<EMAIL_ADDRESS>

Just FYI, this won't be released until the next release PR is pushed through. Not sure when that will be. If this is something you need now or you think it's pressing I can do a version only release to get the package.json out in a v10.4.1 release.

That’s ok. I don’t need it, but thank you. I am just working on this bug: https://github.com/denoland/deno/issues/17279


Nova v4.18.0

Nova will now disable the resource table row buttons instead of hiding them.
When using this package icons are still hidden. Is it possible to match the blade views from the new version?

Seems the behaviour changed again in version 4.19.0

Any news on this?

Any news on that? How to fix it? Would like to use this but i can because no icons...

Published version 3.4.0, that bumps laravel/nova version to latest (4.20.2).

@KasparRosin thank you!


remove the old .so file from build area when installing GPU implementation via pip

While investigating something else I found that the behaviour of pip install . has changed - it builds the library in a local build directory before copying it to site-packages.   This was not being rebuilt after changing the code.
This change to setup.py cleans the existing library, so it is rebuilt every time.

I've moved these changes to a bugfix release on main v0.7.2. I'll also merge them into devel from the branch where I'm drafting the release, and close this PR.

Codecov Report
Attention: Patch coverage is 0% with 7 lines in your changes missing coverage. Please review.

Project coverage is 76.77%. Comparing base (1245081) to head (b35afaa).
Report is 11 commits behind head on devel.

Files with missing lines
Patch %
Lines

setup.py
0.00%
7 Missing :warning:

Additional details and impacted files
@@            Coverage Diff             @@
##            devel     #243      +/-   ##
==========================================
- Coverage   76.82%   76.77%   -0.06%
==========================================
  Files          55       55
  Lines        9477     9484       +7
==========================================
  Hits         7281     7281
- Misses       2196     2203       +7

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


a

Hi @vccarneiro
Was this issue resolved? I could not find it when I came to look for it.
Thanks

Sorry Sagnik,
I had to move forward rather then wait. I tried a couple of things both with the example data and my own data. It seems that every time I include samples (SRA) to be downloaded, it works fine. For the ARATH, I removed the dummy data (1 and 2) and it worked.
For my genome, I am also struggling to getting it running with online data.
I wonder if you could help me figure it out or if I should download the data myself to run it.
Here is the .error file
-bash-4.2$ less FINDER_marmorkrebs.error
cat: /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round1_SJ.out.tab: No such file or directory
cat: /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round2_SJ.out.tab: No such file or directory
mv: cannot stat <80><98>/omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_final_Unmapped.out.mate1<80><99>: No such file or directory
mv: cannot stat <80><98>/omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_final_Unmapped.out.mate2<80><99>: No such file or directory
mv: cannot stat <80><98>/omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_final_Log.final.out<80><99>: No such file or directory
cat: /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round3_SJ.out.tab: No such file or directory
samtools index: "/omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
samtools index: "/omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_final.sortedByCoord.out.bam" is in a format that cannot be usefully indexed
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
Can not open /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_final.sortedByCoord.out.bam.
mv: cannot stat <80><98>/omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/assemblies_psiclass_modified/combined/psiclass_output_sample_0.gtf<80><99>: No such file or directory
mv: cannot stat <80><98>/omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/assemblies_psiclass_modified/combined/psiclass_output_sample_1.gtf<80><99>: No such file or directory
mv: cannot stat <80><98>/omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/assemblies_psiclass_modified/combined/psiclass_output_vote.gtf<80><99>: No such file or directory
Traceback (most recent call last):
File "/omics/groups/OE0033/internal/vitor/projects/finder/finder", line 675, in
main()

File "/omics/groups/OE0033/internal/vitor/projects/finder/finder", line 636, in main
orchestrateGeneModelPrediction(options,logger_proxy,logging_mutex)

File "/omics/groups/OE0033/internal/vitor/projects/finder/finder", line 449, in orchestrateGeneModelPrediction
findTranscriptsInEachSampleNotReportedInCombinedAnnotations(options,logger_proxy,logging_mutex)

File "/omics/groups/OE0033/internal/vitor/projects/finder/scripts/findTranscriptsInEachSampleNotReportedInCombinedAnnotations.py", line 17, in findTranscriptsInEachSampleNotReportedInCombinedAnnotations
combined_transcript_info=readAllTranscriptsFromGTFFileInParallel([combined_gtf_filename,"combined","combined"])[0]

File "/omics/groups/OE0033/internal/vitor/projects/finder/scripts/fileReadWriteOperations.py", line 279, in readAllTranscriptsFromGTFFileInParallel
fhr=open(gtf_filename,"r")

FileNotFoundError: [Errno 2] No such file or directory: '/omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/assemblies_psiclass_modified/combined/combined.gtf'
FINDER_marmorkrebs.error (END)
Best wishes and thanks for your help,
Vitor.

Dr. Vitor Coutinho
Epigenetics Division / A130
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-3804
fax:      +49 6221 42-3804
<EMAIL_ADDRESS>www.dkfz.dehttp://www.dkfz.de/
@.***
Management Board: Prof. Dr. med. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537
From: Sagnik Banerjee @.>
Reply-To: sagnikbanerjee15/Finder @.>
Date: Saturday, 27. November 2021 at 14:29
To: sagnikbanerjee15/Finder @.>
Cc: "Coutinho, Vitor" @.>, Mention @.***>
Subject: Re: [sagnikbanerjee15/Finder] a (Issue #38)
Hi @vccarneirohttps://github.com/vccarneiro
Was this issue resolved? I could not find it when I came to look for it.
Thanks
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com/sagnikbanerjee15/Finder/issues/38#issuecomment-980618466, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWRJXHUID57L426XAN7IJBDUODMKJANCNFSM5IS2BISA.
Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Actually, I noticed that the missing alignments are from the data I have it on my cluster already, and not the one online as I mentioned.

Dr. Vitor Coutinho
Epigenetics Division / A130
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-3804
fax:      +49 6221 42-3804
<EMAIL_ADDRESS>www.dkfz.dehttp://www.dkfz.de/
@.***
Management Board: Prof. Dr. med. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537
From: Sagnik Banerjee @.>
Reply-To: sagnikbanerjee15/Finder @.>
Date: Saturday, 27. November 2021 at 14:29
To: sagnikbanerjee15/Finder @.>
Cc: "Coutinho, Vitor" @.>, Mention @.***>
Subject: Re: [sagnikbanerjee15/Finder] a (Issue #38)
Hi @vccarneirohttps://github.com/vccarneiro
Was this issue resolved? I could not find it when I came to look for it.
Thanks
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com/sagnikbanerjee15/Finder/issues/38#issuecomment-980618466, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWRJXHUID57L426XAN7IJBDUODMKJANCNFSM5IS2BISA.
Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

More info (progress.log)
bash-4.2$ less progress.log
AMtype BAM SortedByCoordinate  --outFilterMultimapNmax 500  --outFilterMismatchNmax 5   --alignIntronMin 20   --alignIntronMax 10000  --limitBAMsortRAM<PHONE_NUMBER>00  --alignEndsType Local  --outSAMprimaryFlag AllBestScore  --outFilterScoreMinOverLread 0.90  --outFilterMatchNminOverLread 0.90  --outSJfilterOverhangMin 8 8 8 8  --outSAMattributes NH HI AS nM NM MD jM jI XS  --outReadsUnmapped Fastx  --outSAMattrRGline ID:1  --outFileNamePrefix /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round1_ --outSJfilterCountUniqueMin 1 1 1 1  --outSJfilterCountTotalMin 1 1 1 1  --alignSJoverhangMin 12  --alignSJDBoverhangMin 8  --readFilesIn /omics/groups/OE0033/internal/vitor/Sequences/Marmorkrebs/Transcriptomes/AS-327974-LR-42085_1.fastq  /omics/groups/OE0033/internal/vitor/Sequences/Marmorkrebs/Transcriptomes/AS-327974-LR-42085_2.fastq  > /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round1.output 2> /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round1.error
2021-11-27 13:45:54,161 - finder -   INFO - STAR Round1 run for AS-327974-LR-42085 completed
2021-11-27 13:45:54,164 - finder -   INFO - Running command STAR  --runThreadN 50 --genomeDir /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/star_index_without_transcriptome --outSAMtype BAM SortedByCoordinate  --outFilterMultimapNmax 500  --outFilterMismatchNmax 5   --alignIntronMin 20   --alignIntronMax 10000  --limitBAMsortRAM<PHONE_NUMBER>00  --alignEndsType Local  --outSAMprimaryFlag AllBestScore  --outFilterScoreMinOverLread 0.90  --outFilterMatchNminOverLread 0.90  --outSJfilterOverhangMin 8 8 8 8  --outSAMattributes NH HI AS nM NM MD jM jI XS  --outReadsUnmapped Fastx  --outSAMattrRGline ID:1  --outFileNamePrefix /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round1_ --outSJfilterCountUniqueMin 1 1 1 1  --outSJfilterCountTotalMin 1 1 1 1  --alignSJoverhangMin 12  --alignSJDBoverhangMin 8  --readFilesIn /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/raw_data_downloaded_from_NCBI/SRR6906024_1.fastq  /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/raw_data_downloaded_from_NCBI/SRR6906024_2.fastq  > /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round1.output 2> /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round1.error
2021-11-27 14:59:03,663 - finder -   INFO - STAR Round1 run for SRR6906024 completed
2021-11-27 14:59:03,664 - finder -   INFO - Mapping of reads for round1 completed for Hepatopancreas_
2021-11-27 14:59:05,890 - finder -   INFO - Selecting high confidence junctions after round1 mapping completed for Hepatopancreas_
2021-11-27 14:59:05,893 - finder -   INFO - Running command STAR  --runThreadN 50 --genomeDir /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/star_index_without_transcriptome --outSAMtype BAM SortedByCoordinate  --outFilterMultimapNmax 500  --outFilterMismatchNmax 5   --alignIntronMin 20   --alignIntronMax 10000  --limitBAMsortRAM<PHONE_NUMBER>00 --alignEndsType Local  --outSAMprimaryFlag AllBestScore  --outFilterScoreMinOverLread 0.90  --outFilterMatchNminOverLread 0.90  --outSJfilterOverhangMin 8 8 8 8  --outSAMattributes NH HI AS nM NM MD jM jI XS  --outReadsUnmapped Fastx  --outSAMattrRGline ID:2  --sjdbFileChrStartEnd /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/Hepatopancreas__round1_SJ.out.tab  --outFileNamePrefix /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round2_ --outSJfilterCountUniqueMin 1 1 1 1  --outSJfilterCountTotalMin 1 1 1 1  --alignSJoverhangMin 1000  --alignSJDBoverhangMin 8  --readFilesIn /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round1_Unmapped.out.mate1  /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round1_Unmapped.out.mate2 > /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round2.output 2> /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/AS-327974-LR-42085_round2.error
2021-11-27 14:59:05,947 - finder -   INFO - STAR Round2 run for AS-327974-LR-42085 completed
2021-11-27 14:59:05,950 - finder -   INFO - Running command STAR  --runThreadN 50 --genomeDir /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/star_index_without_transcriptome --outSAMtype BAM SortedByCoordinate  --outFilterMultimapNmax 500  --outFilterMismatchNmax 5   --alignIntronMin 20   --alignIntronMax 10000  --limitBAMsortRAM<PHONE_NUMBER>00 --alignEndsType Local  --outSAMprimaryFlag AllBestScore  --outFilterScoreMinOverLread 0.90  --outFilterMatchNminOverLread 0.90  --outSJfilterOverhangMin 8 8 8 8  --outSAMattributes NH HI AS nM NM MD jM jI XS  --outReadsUnmapped Fastx  --outSAMattrRGline ID:2  --sjdbFileChrStartEnd /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/Hepatopancreas__round1_SJ.out.tab  --outFileNamePrefix /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round2_ --outSJfilterCountUniqueMin 1 1 1 1  --outSJfilterCountTotalMin 1 1 1 1  --alignSJoverhangMin 1000  --alignSJDBoverhangMin 8  --readFilesIn /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round1_Unmapped.out.mate1  /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round1_Unmapped.out.mate2 > /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round2.output 2> /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round2.error
2021-11-27 15:44:55,704 - finder -   INFO - STAR Round2 run for SRR6906024 completed
2021-11-27 15:44:55,709 - finder -   INFO - Mapping of reads for round2 completed for Hepatopancreas_
2021-11-27 15:44:55,852 - finder -   INFO - Selecting high confidence junctions after round2 mapping completed for Hepatopancreas_
2021-11-27 15:44:55,854 - finder -   INFO - Mapping rate in round2 Hepatopancreas_ AS-327974-LR-42085 0.0
2021-11-27 15:44:55,858 - finder -   INFO - Mapping rate in round2 Hepatopancreas_ SRR6906024 0.706984333290216
2021-11-27 15:44:55,858 - finder -   INFO - Resorting to alignment with relaxed parameters for these runs due to poor mapping AS-327974-LR-42085
2021-11-27 15:44:55,996 - finder -   INFO - STAR relaxed alignment run for AS-327974-LR-42085 completed
2021-11-27 15:44:55,999 - finder -   INFO - Running command STAR  --runThreadN 50 --genomeDir /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/star_index_without_transcriptome --outSAMtype BAM SortedByCoordinate  --outFilterMultimapNmax 500  --outFilterMismatchNmax 5   --alignIntronMin 10000   --alignIntronMax 100000000  --limitBAMsortRAM<PHONE_NUMBER>00 --alignEndsType Local  --outSAMprimaryFlag AllBestScore  --outFilterScoreMinOverLread 0.90  --outFilterMatchNminOverLread 0.90  --outSJfilterOverhangMin 8 8 8 8  --outSAMattributes NH HI AS nM NM MD jM jI XS  --outReadsUnmapped Fastx  --outSAMattrRGline ID:3  --outFileNamePrefix /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round3_ --outSJfilterCountUniqueMin 3 3 3 3  --outSJfilterCountTotalMin 5 5 5 5  --alignSJoverhangMin 8  --readFilesIn /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round2_Unmapped.out.mate1 /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round2_Unmapped.out.mate2 > /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round3.output 2> /omics/groups/OE0033/internal/vitor/projects/finder/marmorkrebs/FINDER_marmorkrebs/alignments/SRR6906024_round3.error
2021-11-27 17:42:29,961 - finder -   INFO - STAR Round3 run for SRR6906024 completed
2021-11-27 17:42:29,962 - finder -   INFO - Mapping of reads for round3 completed for Hepatopancreas_
2021-11-27 17:42:30,199 - finder -   INFO - Selecting high confidence junctions after round3 mapping completed for Hepatopancreas_
2021-11-27 17:42:30,486 - finder -   INFO - Mapping with OLego for micro-exon detection skipped for SRR6906024 due to huge number of reads
2021-11-27 17:42:30,486 - finder -   INFO - Mapping with OLego for micro-exon detection completed for Hepatopancreas_
2021-11-27 17:59:33,603 - finder -   INFO - Merging of alignments from all rounds of mapping completed for Hepatopancreas_
2021-11-27 17:59:33,603 - finder -   INFO - Mapping of all runs completed for Hepatopancreas_
2021-11-27 21:36:21,512 - finder -   INFO - Information collection about alignments completed
2021-11-27 22:37:31,607 - finder -   INFO - Generation of assemblies with PsiCLASS completed

Dr. Vitor Coutinho
Epigenetics Division / A130
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-3804
fax:      +49 6221 42-3804
<EMAIL_ADDRESS>www.dkfz.dehttp://www.dkfz.de/
@.***
Management Board: Prof. Dr. med. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537
From: Sagnik Banerjee @.>
Reply-To: sagnikbanerjee15/Finder @.>
Date: Saturday, 27. November 2021 at 14:29
To: sagnikbanerjee15/Finder @.>
Cc: "Coutinho, Vitor" @.>, Mention @.***>
Subject: Re: [sagnikbanerjee15/Finder] a (Issue #38)
Hi @vccarneirohttps://github.com/vccarneiro
Was this issue resolved? I could not find it when I came to look for it.
Thanks
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com/sagnikbanerjee15/Finder/issues/38#issuecomment-980618466, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWRJXHUID57L426XAN7IJBDUODMKJANCNFSM5IS2BISA.
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Hello @vccarneiro,
So sorry for the late reply. I was busy with some other stuff last week. Could you please send me the metadata.csv file? You can attach it here or email me at<EMAIL_ADDRESS>We will get this done!
Thanks.

No problem.
Here it goes!

Dr. Vitor Coutinho
Epigenetics Division / A130
German Cancer Research Center (DKFZ)
Foundation under Public Law
Im Neuenheimer Feld 580
69120 Heidelberg
Germany
phone: +49 6221 42-3804
fax:      +49 6221 42-3804
<EMAIL_ADDRESS>www.dkfz.dehttp://www.dkfz.de/
@.***
Management Board: Prof. Dr. med. Michael Baumann, Ursula Weyrich
VAT-ID No.: DE143293537
From: Sagnik Banerjee @.>
Reply-To: sagnikbanerjee15/Finder @.>
Date: Sunday, 28. November 2021 at 14:36
To: sagnikbanerjee15/Finder @.>
Cc: "Coutinho, Vitor" @.>, Mention @.***>
Subject: Re: [sagnikbanerjee15/Finder] a (Issue #38)
Hello @vccarneirohttps://github.com/vccarneiro,
So sorry for the late reply. I was busy with some other stuff last week. Could you please send me the metadata.csv file? You can attach it here or email me at<EMAIL_ADDRESS>We will get this done!
Thanks.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com/sagnikbanerjee15/Finder/issues/38#issuecomment-981086857, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWRJXHVXRQV42RQUS4WGGLLUOIV5BANCNFSM5IS2BISA.
Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

Hi @vccarneiro,
I could not find the attachment. Could you please try again?
Thanks.

Dear Sagnik, you may close this issue. I solved the problem by figuring out that my Illumina fastqs were paired-end seq and the discrimination was "_R1" and "_R2". I renamed the samples to simply _1 and _2 and everything is running now.
All the best,
Vitor.

Hello @vccarneiro,
Thank you for reporting this. Please let me know if you need any further assistance.
Thank you.


[BrokenLinksH2] Fix path in link

Removed broken link and text line 155, this behavior is no longer available in the Windows Community Toolkit

Docs Build status updates of commit 362cbe3:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

docs/animations/Offset.md
:white_check_mark:Succeeded
View

For more details, please refer to the build report.
Note: Broken links written as relative paths are included in the above build report. For broken links written as absolute paths or external URLs, see the broken link report.
For any questions, please:Try searching the docs.microsoft.com contributor guidesPost your question in the Docs support channel

Global effort to fix broken links
@michael-hawker - The Content & Learning team is fixing broken links on docs.microsoft.com for the rest of H2. This effort will eliminate potential accessibility, security, and usability issues. This PR includes only link fixes and does not change other content. Please review within five business days and merge, or comment in the PR with any changes you'd like to see. Thanks!


Refactor routes

[x] Moved route configs to page folders
[x] Extracted paths to one centralized file

Closes #41


fix: Don't use a csv.Reader when parsing scan result and network lists

Checklist:

[ ] The readme and documentation has been updated or does not need to be updated
[ ] This change has been communicated with the team if needed
[ ] I have linked to the original issue
[ ] I have added tests to cover my changes
[ ] This PR does not need notes or I've added them below
[ ] This PR does not need extra testing from our release testing process or I've added a 'tests' section below

https://plantiga.slack.com/archives/CDS48MFBP/p1641503760031600?thread_ts=1641497255.012600&cid=CDS48MFBP

what is the purpose of this change?

The slack thread I linked gives context, @dsludwig was concerned that using the CSV reader with LazyQuotes might still be risky with quotes, and that the CSV reader may be overkill for the task.

If you want to use LazyQuotes instead, I'm fine with that, but we need to check its behaviour to make sure it wouldn't strip quotes unexpectedly (e.g. if the SSID was "My Great Network").

@ahollist I checked it with the unit tests I added in #2, and LazyQuotes is enough to fix the problem. I think we can go with that instead.
Do you mind rebasing this to be just setting up CI for this repo?

This is superceded by #3 and #2


add reflash function in job list of ui

In GitLab by @sokril on Mar 26, 2020, 07:56

In GitLab by @sokril on Mar 26, 2020, 07:57
assigned to @liyanq528