iOS - Singin - The last link sent to reset your password shows an error

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Action Performed:

Open the app
Enter the login in the signin page
Make it send two password reset links
Use the old or expired link
Ensured appropriate error message is displayed and new link is received in email/sms
Used the latest link and updated password and it worked

Expected Result:
When following the last link we should not see the error of the previous link.
Actual Result:
The last link sent to reset your password shows an error
Workaround:
Unknown
Platform:

Where is this issue occurring?

iOS

Version Number: v1.2.3-0
Reproducible in staging?: Y
Reproducible in production?: Y
Email or phone of affected tester (no customers):
Logs: https://stackoverflow.com/c/expensify/questions/4856
Notes/Photos/Videos:
https://user-images.githubusercontent.com/43996225/191329977-19256be3-2b44-427e-b853-60c19194da33.mp4
Expensify/Expensify Issue URL:
Issue reported by: Applause internal team
Slack conversation:
View all open jobs on GitHub

@kavimuru from the video at around 1:00, it seems like the tester selects the first email that was sent and not the one with the latest validation link (after they tapped Resend link). We will invalidate previous links whenever we generate a new one.
Can you please retest?

Ah, thanks for pointing that out, that was going to be my first question 😅. This doesn't look like a bug provided the second link that we send works as expected.

@kavimuru I see that you removed the DeployBlockerCash label. Does that mean that this is working as expected?

@luacmartins It's happening in production too. So I removed deployblocker label.  Yes, at the timeline 1:00 tapping the invalid link proper error message appears, then again when the latest link is tapped the same error message persistent. But able to set password with 2nd link as in the video.

Ah ok I see what you mean now. I think that's the expected behavior since the error still exists. I do think however that we should clear the error once we click SetPassword. I'm putting up a fix to clear the error on submit here - https://github.com/Expensify/App/pull/11165

Closing this one in favor of https://github.com/Expensify/App/issues/11186


Mantle 0.11.5 does not work on Linux

Reported in the discord:
Run: mantle --version
Outputs: error while loading shared libraries: libssl.so.3: cannot open shared object file: No such file or directory

This seems to just be a user-specific issue. Recommended that they ensure the appropriate openssl version is installed on their system. I could also look into switching to rustls which would remove the need for external dependencies, but it's not clear atm what the pros/cons to that would be.

Closing as won't fix for now, but can be revisited later.

Closing as won't fix for now, but can be revisited later.


Publish/Deployment Doesnt work

I downloaded this repo, restored the npm dependencies and then tried to publish both using VS2017 and
dotnet publish command but none of these works.
Its keeps stuck in publish process for hours, with CPU utilization of 100% where node is taking over 90% resources.

That's strange, just tried it and dotnet publish finished fairly quickly, it runs the vendor bundles then the normal ones.
Do you have dotnet core 2.0.0 installed, or the latest VS2017?

Yes I have dotnet core 2.0 and using latest VS 2017 with latest version of node. I also tried using ASP.Net SPA template and have issues with that as well (though its publish task completes successfully), Please take a look at https://github.com/aspnet/JavaScriptServices/issues/292#issuecomment-329324155

Did increasing the --max-old-space-size=4096 fix the issue at all?

I edited csproj file and updated below under PublishRunWebpack tag:
    <Exec Command="node --max_old_space_size=5048 node_modules/webpack/bin/webpack.js --config webpack.config.vendor.js --env.prod" />
    <Exec Command="node --max_old_space_size=5048 node_modules/webpack/bin/webpack.js --env.prod" />

After this change, with ASP.Net SPA template publish task completes but with aspnetcore-angular2-universal the publish task continue running for hours and never concludes.

Strange, we have synced up on webpack configurations except that we have scss and font-awesome setup here. I'm going to a few other improvements as well (such as switching away from awesome-typescript-loader etc), maybe those would help but still, it should work for either repo!
Do you have a sample repo I could look at to try and investigate?

Its a private repo, should I drop you an email with a sample?

Can you please also confirm the size of files in these folders in your publish directory:
PublishFolder\ClientApp\dist
PublishFolder\wwwroot\dist

Does the size of files in PublishFolder\ClientApp\dist larger than size of files in PublishFolder\wwwroot\dist, if so, can you please explain why is it so?

The server bundle is in client app and the size of that one doesn't matter as there is no "load" on the server, it just contains everything it needs to serialize the app. Wwwroot is the client browser bunde(s).
Problem is it could be a large number of things causing it, I don't have much time as I'm also still dealing with Irma aftermath 😓 My email is<EMAIL_ADDRESS>I can try to take a look sometime if you have a private repo you can invite me to look at.

Thank you so much @MarkPieszak , I really appreciate your quick reply and help despite being affected by Irma.
Regarding the slow publish, I was able to resolve it by upgrading the Node version in Visual Studio 2017 (default is 5.x).  I also upgraded Webpack to the latest version.
Though I am still having the timeout problem, I enabled the log in IIS and found that it was throwing
below error ERROR { Error: Uncaught (in promise): Error: Cannot find module './home/home.module.ngfactory'. when running node on server.
I investigate little further and found that when using Lazy loading and when we do publish the publish process doesn't generate the bundles for the lazy loaded modules.
You can try below to reproduce:

Perform Clean (Build>Clean Solution)
Then perform Publish.

In the Publish directory examine the files in ClientApp\dist, you will notice that the bundles for the lazy loaded modules are missing.
Normally, when we have already debug the application, it generate the bundles in ClientApp\dist and after this if we Publish (without performing Clean Solution) these bundles are copied to publish folder and the app works when deployed on server but its actually using un-optimized Debug build bundles.

which commands does dotnet publish run exactly?  Does it run the webpack production builds (if yes, how does it know what your weback prod commands are) ?  Been trying to figure out just want dotnet publish does!

@naveedahmed1 try the code from the pull request #410
It has the npm dependencies updated to latest, and lazy loading works as expected.

@davidsekar are you sure commenting out resolve: { mainFields: ['main'] }, is the way to ensure server size bundles are created properly with Lazy loading? What about module-map-ngfactory-loader see this angular/universal#741 (comment)
The bundles generated for server side after commenting out resolve: { mainFields: ['main'] } for my project are of size 30 mb. Which is very huge. Also can we make use of @angular-devkit/build-optimizer and CommonsChunkPlugin  to get better optimized bundles for Client as well as Server side builds?
@MarkPieszak mentioned above The server bundle is in client app and the size of that one doesn't matter as there is no "load" on the server, it just contains everything it needs to serialize the app but I think larger the file size more would be the load on the server, deploy it to IIS and monitor CPU and memory utilization for any  server rendered request.

CommonsChunkPlugin - It is really helpful when you have 2 or more asynchronous/lazy loaded modules.

App
-- Module1 (/lazy1) (uses ngx-bootstrap)
-- Module2 (/lazy2) (uses ngx-bootstrap + ng-signalr)
Then using commonchunks plugin would prove useful, It automatically moves ngx-bootstrap to an asynchronous common chunk.
In current repo setup, there is just a single lazy/async loaded module. It doesn't help.
Not sure if adding How To integrate CommonChunksPlugin is part of this repo's direction.

Running webpack bundle analyzer shows that the complete GZipped size of main-client.js is less than 300kb ( which includes complete ngx-bootstrap + momentjs, bootstrap css).

![Visual comparison on various modules imported] (https://davidsekar.com/Content/images/Ext/client-bundle.jpg)
Possible optimizations:
a) Import just the required ngx-bootstrap modules. If you avoid, datepicker module then moment.js will not be added to your bundle.
OR if you need datepicker, then include just the required language locale
https://davidsekar.com/angular/optimize-moment-js-size-using-webpack
b) Remove duplicated bootstrap css styles.
Check the issue #415


Problem with host file

Hi everyone. I wanted to block the porn sites using the host file so I opened the notepad as an administrator, copied the whole text from this link https://raw.githubusercontent.com/StevenBlack/hosts/master/alternates/porn/hosts and saved it in C:\Windows\System32\drivers\etc as hosts file. Now I cannot enter any site at all and the Internet connection seems not to be working at all. If I want to change this HOSTS file back into the blank file it says that I cannot access this file as some other process is currently using it. I restarted the system but the problem still appears. I hope you can help me.

Closing.


Update build.gradle

update to use Android-SpinKit:1.2.0.

Would be great if we get this merged in soon. All builds broken :'(
@maxs15

Please merge it ASAP!!

Yesterday released a new version with the bugfix https://github.com/maxs15/react-native-spinkit/pull/113.
Just update your package.json to "react-native-spinkit": "^1.2.0"

Yesterday released a new version with the bugfix https://github.com/maxs15/react-native-spinkit/pull/113.
But this release isn't in npm yet.


Generalize the build system for Vec128/256 and implement vectorized support for IBM SystemZ

The following PR generalizes the build system and EverCrypt to target several architectures. Building on this addition, this PR also implements support for IBM SystemZ.
Build system
The build system updates are made in several steps.
First, we moved as many macros as possible from evercrypt_targetconfig.h to the configure file, like the ones defining the target architecture.
We also renamed some macros, like BROKEN_INTRINSICS -> COMPILE_INTRINSICS (and applied/removed the proper negations) to make it clear that the macros guarding the code are purely compilation macros. In particular, COMPILE_128 and COMPILE_256 mean that we build the code for targets (potentially) supporting vectors 128/256: the current platform does not necessarily support them, and we may need to do dynamic checks for hardware support before calling the relevant functions.
We removed, whenever possible, the checks of the form EverCrypt.TargetConfig.x64 && ... (* additional dynamic checks for hardware support *), to replace them with more general checks like EverCrypt.TargetConfig.compile_128 && ... (* dynamic checks *)which make the target architectures more abstract. Note that those extract, like before, to code of the form:
#if COMPILE_128
  if ... (* dynamic checks *) {
  ...
}
#endif

128-bit vector support for IBM SystemZ
This PR also adds support for the intrinsics of IBM SystemZ, for the versions >= z13. In order to make it easy to add support for more architectures, we also implemented various testing and debugging utilities for the vectorized functions.
The tests directory now contains a vec128-test.c file which contains very thorough tests for all the 128-bits vectorized functions currently used in Hacl. The tests were designed in order to be easy to debug, so that one can fix his implementations without much effort by looking at the tests output.
We modified the libintvectors.h file so that it is now possible to switch to a debugging mode by providing the proper compiler flags. This mode prints a debugging trace for the vectorized operations, in order to make it easy to understand why a primitive's output is not correct by comparing traces, in case the above test file was not enough. As of now, all the 128-bit functions used in Hacl output useful information when compiling with the debug mode flags.
For future PRs
We leave as future work the addition of test vectors and debugging implementations for the functions which don't have any so far, that is to say the 128-bit functions which are not currently used in Hacl, and the 256-bit functions which I could not test with the machines I had at my disposal.

Leaving an accept here so that you can merge easily after the next batch of changes...

Leaving an accept here so that you can merge easily after the next batch of changes...

Thanks a lot ! :)

Thanks Benjamin, that's a sensible suggestion.
One thing I mentioned to Son earlier is that we should try to move away from "support" because it's too imprecise. There's actually two notions:

static support at compile-time for generating code for e.g. vec128 or vale -- determined by the configure script, and generating a macro
support at run-time for executing such code determined by a runtime test.

On x64 especially, the two are different notions, so my suggestion was to use "compile" rather than support for the former. So, maybe, EVERCRYPT_CAN_COMPILE_128 and so on, since all of the implementation multiplexing is done at the evercrypt level.

Ok, "support" is kind of standard because it is quite rare to encounter these kind of macros for runtime checks but if you really prefer, that's not a blocker. Call it EVERCRYPT_CAN_COMPILE_VEC128 and we have a deal ;)

Ok, deal! Let me update the code :)

This looks good to me minus this: I'm not sure @karthikbhargavan and/or @polubelova who both worked on libintvector.h will be very happy with the big debug info. They might prefer to leave that sort of debugging to a branch.

This is not blocking for me, but my preference is also not to have debug inside this file

I agree that it is better if libintvector.h doesn't contain debugging related facilities. However I would like to preserve the debugging code on main and not on a quickly forgotten branch, because they took a bit of time to be written, and actually proved quite useful.
Would it be acceptable if libintvector.h contains the following:
#if __has_include("libintvector_debug.h")
#include "libintvector_debug.h"
#endif

Where libintvector_debug.h would be a file only present in lib/c which would be manually copied to gcc-compatible in case we need to debug the vectorized operations? (from there, I can get the switch to work with the appropriate macros).
I might then add a file in tests to use the debugging facilities and make sure they are maintained.

I removed the debug functions from libintvector.h: will put that in the next PR for PowerPC

@victor-dumitrescu would you mind checking that you are now getting the optimized 128-bit versions of the algorithms with the OCaml bindings?

Hi, I think this works as intended. I asked someone with access to a machine to install this as an opam package and indeed 128-bit files are compiled with -m64 -mzarch -mvx -mzvector -march=z13 and are included and pass the tests in the OCaml API.
For reference, this is the output of the configure script:
- ... detected z platform
- ...  supports 128-bit z VSX
-  does not support x64 assembly, disabling Curve64
-  does not support legacy vale stubs
-  does not support 256-bit arithmetic
- ... found ocamlfind in /home/linux1/.opam/tezos_opam_install/bin/ocamlfind
- ... found ctypes in /home/linux1/.opam/tezos_opam_install/lib/ctypes
- ... found ctypes.foreign in /home/linux1/.opam/tezos_opam_install/lib/ctypes
- ... glibc is recent enough for explicit_bzero

excellent! and which algorithms are you calling on Z? are you going through the evercrypt layer for those?

Do you mean specifically in Tezos? Or in the OCaml API in general?

Sorry I meant in Tezos

I think none of the 128-bit algorithms are used either directly or indirectly in Tezos. We use the EverCrypt layer for hashing, HMAC, and Curve25519. Otherwise, we also use Blake2b_256 when possible. We also use NaCl so in theory we could use Poly1305_128 but I don't think that's the case with the current NaCl API.

Ok good to know. Thanks!


make query strings immutable after creation

This PR makes queries read-only from the schedule tab after they are created.
closes #509

This won't be needed any more, but thanks for providing a Plan B :)


swaymsg keybinding.

I searched but didn't find.
I know that I am doing this wrong. Tell me how to do this
exec --no-startup-id swaymsg 'workspace 1:General;exec /$term;workspace 1:General'
Here,
$term is my terminal variable.
Also work spaces are set as variable but I have to mention it's full name to access in swaymsg command.

I don't understand your question.

Suppose,
set $term termite
set $workspace1 "1:General"
Now, if I have to open vim inside termite in specific work space i.e., $workspace1. Then what should I do.
I tried:-
exec --no-startup-id swaymsg 'workspace $workspace1; exec $term -e vim'
but this is not working. I don't know why but due to variables are not working under quotation or something. I just want real way of doing this.

If you just do this at your terminal, what happens:
swaymsg 'workspace test; exec termite'

It goes to workspace test and opens termite.

How about swaymsg 'workspace "1:General"; exec urxvt -e vim' from the terminal?

Sorry for silly questions. I am running Arch Linux under wayland. And I don't know how to load .Xresources under wayland.
Can you please provide some link.


Migrate to AndroidX

Is your feature request related to a problem? Please describe 🙏
AlgoliaSearch is the only external library I need to disable Jetifier. It would be nice if you could release an updated version with AndroidX dependencies.
Describe the solution you'd like 🤔
Please, migrate to AndroidX 🙏

Hello,
We recently released a Kotlin client that is more suited for Android development. It has no dependency on the android framework, avoiding all together the androidx issues.
You can learn more about it by visiting the repository or our documentation.
As we do not plan to update the android client any further, we strongly encourage you to migrate to the Kotlin client.
Thanks

Or just download the code and do the upgrade yourself and reference in your project. thats's what i did, easy.


Get path returns false when not found and when the actual value is false

Consider the following case:
{"isAvailable":false}
If I want to check is is isAvailable is exists then I do $object->get("$.isAvailable") which will return false but this also implies that this field does not exist. Or is there a way to check certain  path exists or not?

Hi @banstola,
This behaviour is defined in the specification of JSONPath [0]. The function would return an array with the results or false. This is also the default behaviour in this library:
$jsonObject = new JsonObject('{ "isAvailable": false }');

$r = $jsonObject->get("$.isAvailable");
var_dump($r);
// Output:
// array(1) {
//   [0] =>
//   bool(false)
// }

$r = $jsonObject->get("$.notThere");
var_dump($r);
// Output:
// bool(false)

As you can see, when the value is there it returns an array with it, and if it is not, it returns false.
From your description I imagine you are using the SmartGet feature [1]. With this feature enabled, there is no way to know whether false is the value the path points to or there is no value pointed to by the path.
[0] http://goessner.net/articles/JsonPath/index.html#e4
[1] https://github.com/Skyscanner/JsonPath-PHP#smartget

Hi,
Thank you for clearing it up. I was using smartGet .


where is the clip function in ndarray module defined?

Environment info
Operating System: macOS
Compiler: clang
Package used (Python/R/Scala/Julia): Python
MXNet version: 0.10.1
Python version and distribution: python-2.7
Error Message:
The import lines tries to import clip function from ndarray module, however, I looked everywhere and no clip function is defined in ndarray.
As I observed the function is implemented in ndarray.cc file, so I wildly guess it's should be provided by _ctypes/ndarray.py, but I can't find any clip function imported from there either.
I'm wondering what did I miss to import the clip function from ndarray module? How should I fix that? (I'm doing this in macOS, didn't confirm the issue in other operating systems.)

here : https://github.com/dmlc/mxnet/blob/master/src/operator/tensor/matrix_op.cc#L442
you can find the line definition of each function in the documentation: http://mxnet.io/api/python/ndarray.html#mxnet.ndarray.clip

try make clean and make

thanks for your help.


[let-properties-opt] Re-factor and simplify the code.

What's in this pull request?

Further improvements of let-properties-opt pass.
Resolved bug number: (SR-1026)

Before merging this pull request to apple/swift repository:

[x ] Test pull request on Swift continuous integration.

Triggering Swift CI
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    Platform     | Comment
    ------------ | -------------
    All supported platforms     | @swift-ci Please smoke test
    OS X platform               | @swift-ci Please smoke test OS X platform
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    Platform     | Comment
    ------------ | -------------
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…ness.
Based on the review of my previous commit, I did some re-factorings.
The code is now simpler and handles more cases. More tests were added.
The overall idea of this rewrite is that the pass basically tries to check if it can
see all possible writes (i.e. initializations) into a given let property. Only if it can be proven
that the pass sees all possible writes and all those initializations are producing
the same constant, statically known value, the pass propagates this constant value
into uses of a property.
SR-1026 and rdar://25303106

@eeckstein Hi Erik! Thanks a lot for your comments on the last patch related to this pass. I tried to incorporate all of your feedback. Do you mind reviewing this improved version?

@swift-ci Please test

@swift-ci Please test


perf: A large number of network IO causes resource to be blocked for a long time

Backgroup

#1529

Under a large number of resources (Ingress >= 10000), retries and updatestatus cause a large amount of network IO consumption, which causes the Controller to block.

Solution
Changes and retries of both CRDs and Ingress resources result in IO requests (updateStatus). The more resources there are, the more network IO, and the api-server is bottlenecked by processing a large number of requests.

Asynchronous IO : When a large number of requests will cause the api-server to be busy, the way the Congroller synchronization IO, will cause the Controller to block in wait for a long time.
Reduce network IO : Assuming that each resource initiates an updateStatus request to the api-server, including IO request for each retry, a large number of requests will increase the pressure on the api-server. Increase the compare of status, there is no need to initiate a request for the same status to be updated

Implementation steps

[ ] Network IO

[ ] Select whether to enable status update through the configuration item.
[ ] Convert the updateStatus implementation to asynchronous IO

[ ] retry

[ ] Optimize the retry policy
[ ]  and limit the number of retries
[ ] ...

SGTM.

Select whether to enable status update through the configuration item.

I think this will have a noticeable effect


[BUG] Vulnerability in write handling mechanism leads to ACL deletion risk

Reproduction steps

After pairing, check the ACL as follows:
$ ./chip-tool accesscontrol read acl 1 0
...
[TOO] ACL: 1 entries
[TOO]   [1]: {
[TOO]     Privilege: 5
[TOO]     AuthMode: 2
[TOO]     Subjects: 112233
[TOO]     Targets: null
[TOO]     FabricIndex: 1
[TOO]   }
...

Send a write request with an invalid value:
$ ./chip-tool accesscontrol write acl '[{"privilege":99,"authMode":2,"subjects":[112233],"fabricIndex":1}]' 1 0
...
[TOO] Response Failure: IM Error 0x87 (CONSTRAINT_ERROR)
...

Despite returning a CONSTRAINT_ERROR, all entries are deleted, leaving the ACL list empty and inaccessible.

Bug prevalence
always
GitHub hash of the SDK that was being used
all
Platform
core
Platform Version(s)
No response
Anything else?
Summary

The commands for creating, modifying, and deleting entries are not separated; therefore, users must send a write request to update an entry (e.g., accesscontrol write acl, binding write binding).
Some functions that handle write requests (e.g., WriteAcl, WriteBindingTable, etc.) operate by deleting all existing entries and recreating them based on the user's input.
This approach can introduce unintended vulnerabilities. Specifically, if all ACLs (Access Control Lists) are deleted, it can block access not only for devices within the same fabric but also for the administrator.

Although this issue was mentioned in #36420, I believe the vulnerability in the write command processing structure needs to be addressed, so I'm reopening this issue.
Root Cause Analysis

Key Problem: The WriteAcl function deletes all existing entries first and attempts to recreate them based on user input. If input validation fails during decoding, the process stops, and no entries are restored.
Sequential Logic: Since TLV decoding is processed from start to finish, invalid entries cannot be caught before deletion. This means:

The system deletes all existing entries (ReplaceAll).
It then tries to decode and create new entries.
If decoding fails, the ACL remains empty.

Additional Analysis

The packet captured by Wireshark for the command accesscontrol write acl '[{"privilege":5,"authMode":2,"subjects":[112233],"targets":[],"fabricIndex":1}]' 1 0 looks as follows:

Here, the first TLV structure { 1=<…>, 2=[] } represents ReplaceAll when processed in the code and deletes everything.
The second TLV structure { 1=<…>, 2={…} } represents AppendItem when processed in the code and adds a new entry to the empty list.

⇒ I believe that the structure of the Write request itself is the root cause of this issue.

According to Matter Core Specification:
<IP_ADDRESS>. Administration Guidelines
Administrators SHOULD be careful to avoid inadvertently removing their own administrative access. For example, an Administrator SHOULD change its own administrative access entry by updating the existing entry or by creating a new entry before removing the old entry, and SHOULD NOT remove the old entry before creating any new entry.

However, the current implementation violates this guideline by deleting entries before input validation.

Description
Deleting all entries can isolate a device, blocking access for all users, including administrators. This can lead to severe operational risks in environments requiring secure and consistent access to devices. Without any access, immediate corrective actions are impossible, compromising the reliability and stability of dependent systems.
This vulnerability likely applies to other items such as Bindings, not just ACLs.
Proposed Solutions
If a CONSTRAINT_ERROR is returned due to an invalid value in a Write Request, the existing entries should remain unchanged. While it would be ideal to validate the input before performing the changes, I understand that changing the processing order is challenging because the TLV structure is decoded and processed sequentially from the beginning.
Therefore, I propose one of the following approaches:

Change Write Command Processing:

Record the intent to replace, and after ensuring that there are no errors during decoding, perform the Delete → Create operations.

Introduce explicit commands:

Instead of implicitly handling additions, updates, and deletions with a single write command, provide separate commands like Add, Remove, and Update.
Similar to the Groups cluster has separate add-group and remove-group commands.

Change the structure of the current write command packet.
Other solutions as appropriate.

I think we should seriously consider, at least for ACLs, having the initial "replace" be the first entry in the list, not an empty list, when encoding the write.
Unfortunately, making that change for all list-typed attributes may be dangerous, because at least DefaultOTAProviders was implemented incorrectly on devices until earlier this year and could not handle an initial replace with a nonempty list....

@BoB13-Matter I'm not sure I'm following the "Risk of Overwriting User Data" and "Data Inconsistency Risks" issues you list.
What I am suggesting is that the client always encodes the first ACL entry (which should be one that grants something on the fabric admin privileges) as part of the initial replace, so that we never end up in a state where we lose administrative access.
Yes, this means if there are validation failures later you will end up only accepting a subset of the incoming entries, so some things that should perhaps have access won't.  But it avoids the catastrophic problem of losing access completely.
In terms of using a staging buffer: that could be done, yes.  It's not trivial, and is a bunch of extra code on servers (which are typically constrained devices), so would require some thought/measurement.

@bzbarsky-apple Thank you for clarifying—your explanation makes a lot of sense, and I fully agree that preserving administrative access is the top priority. Your suggested approach seems like a solid solution to address the main risk here.
Would you be open to implementing a patch for this? I think your insights would translate well into a robust fix. Let me know if there’s anything I can do to assist!

Since it has been a week without further updates, I wanted to inform you that I will proceed with requesting a CVE for this issue. This is to ensure the vulnerability is properly documented and tracked for resolution. If there are any updates or additional feedback, please feel free to share them here—I’m happy to coordinate further if needed!

@BoB13-Matter I was on vacation last week, but in any case, I do not believe this is a security vulnerability per se (though it can lead to loss of functionality in some rare power-loss cases).

@BoB13-Matter I'm not in charge of SVEs, so no opinion on that part.

@bzbarsky-apple Thank you for clarifying. Would there be someone in the project responsible for handling such cases that I could coordinate with? Let me know if there’s someone I should reach out to, and thank you again for your time.

@BoB13-Matter I honestly don't know, offhand.


Admin Config -> Session Info missing a data row

Gitea version (or commit ref): 1.0.0 (6aacf4d)
Operating system: Ubuntu 14.04
Database (use [x]):

[ ] PostgreSQL
[X] MySQL
[ ] SQLite

Can you reproduce the bug at https://try.gitea.io:

[ ] Yes (provide example URL)
[X] No (no admin access)
[ ] Not relevant

Description
There is a missing row of data under Admin Panel -> Configuration -> Session Configuration

It seems "session provider" or "provider config" is missing data, hence all rows are shifted up.

No. That's PR will partially resolve #484 not this one.


feat: use yjs as the source-of-truth

This is a major change. Close #331
Before
Previous architecture (detailed in #205) is centered around the browser (yjs <-> browser <-> DB), which is problematic because:

we have two (potential inconsistent) sources of data (yjs and DB)
there can be multiple users/browsers. It's complex to decide which user/browser should push to DB

After
Now we are  changing to Yjs-centered (browser <-> Yjs <-> DB). Yjs is the single source-of-truth.
Details
This PR removes a lot of syncing logic/functions from front-end, notably those addPod, loadRepo, setPodGeo reducers.
TODOs:

[ ] Better indicator to show the syncing status (e.g., synced, offline), prompt user unsynced changes when user leave the page.
[ ] When a user gets disconnected, edits can still be made, but these new edits might be lost. This is a bug. We need to figure out a graceful way to re-sync when Yjs WS re-connects.

This feature is roughly usable. I'm merging this so that people can work on top of this, and avoid merge conflicts, as this PR is too large and touches everything.
Remaining problems: state.pods is now empty. So the following things break and need fixes in the follow-up PRs:

pod.content access, e.g., runtime, parser
pod.result access, e.g., display result, stdout/stderr, images
export .ipynb and markdown
copy & paste

Note: DB schema changed. You need to apply the migration and recreate your docker stack.


Icon request: Plutus

Homepage URL for the brand / app
https://plutus.it/
Logo resources for the icon
https://plutus.it/press-kit
Anything else?
No response

Here you go!
https://github.com/aegis-icons/aegis-icons/blob/master/SVG/Plutus.svg

:question: How to add icon(s) to Aegis?
:star: Support this project by giving a star! Just adding like to this comment is also appreciated.


fix(expect): add missing dependency jest-util

Summary
expect depends on jest-util but doesn't declare it as a dependency.
https://github.com/facebook/jest/blob/045367ad9ca773536a73efdfad019eeb2778ee32/packages/expect/src/asymmetricMatchers.ts#L16
Fixes https://github.com/yarnpkg/berry/runs/6157024113?check_suite_focus=true#step:4:44
Test plan
yarn init -2
yarn add jest@^28

echo "it('should pass', () => { expect(true).toBeTruthy(); });" | tee pass.test.js
yarn jest pass.test.js

@merceyz any idea why it's failing? It's the PnP test

Looks like an issue with the npm registry, you can try re-running it

https://github.com/facebook/jest/releases/tag/v28.0.1


Yaml from WIP

https://issues.apache.org/jira/browse/CAMEL-17304
Work in progress - do not merge - just a way to get feedback

Have merged this


Allow to specify alignment for Card overlay

This PR enhances ContentPosition.overlay to take an alignment argument: .overlay(alignment:)
The alignment is defined as
enum ContentAlignment: CaseIterable {
    case topLeading
    case top
    case topTrailing
    case leading
    case center
    case trailing
    case bottomLeading
    case bottom
    case bottomTrailing
}

The implementation uses the Bootstrap "text alignment" and "vertical alignment" classes.
The following example usage shows all nine cases:
Text(markdown: """
To control the position of the overlay you can specify an alignment using `.overlay(alignment:)`
with one of the following options:
""")

Section {
    for alignment in Card.ContentAlignment.allCases {
        let alignmentName = String(describing: alignment)
        Card(imageName: "/images/photos/dishwasher.jpg") {
            Text(markdown: "`.\(alignmentName)`")
                .foregroundStyle(.white)
                .backgroundColor(.lightGray)

            Link("Back to the homepage", target: "/")
                .linkStyle(.button)
        }
        .contentPosition(.overlay(alignment: alignment))
        .imageOpacity(0.5)
    }
}
.margin(.top, .large)
.columns(3)

@twostraws : I've reworked my solution and documented it in #31.
It uses now .contentPosition(.overlay(alignment: .center)) for centering the overlay. I've added overlay as a static variable to ContentPosition for backward compatibility. But I removed .overlayCenter as this had been included previously "by accident" and was not part of a release.
Let me know whether it needs more rework. I will add a separate PR for IgniteSample later.

This is really excellent work – thank you!


"Deploy to Heroku" button doesn't work from created repo

Maybe we just remove the "Deploy to Heroku" button for a configured repo? Or somehow check to see if the repo is public before asking if they want the button?

Maybe we just remove the "Deploy to Heroku" button for a configured repo?

I actually like this idea. The original README serves as a primer for getting started with Bullet Train, so it makes sense to me that developers would look at the README and apply any additional configuration (like these deploy buttons) if it's necessary for their use-case, even after the initial setup. We don't necessarily need to have the buttons exist in a new application, as long as we point developers in the right direction.
It may be beneficial to just have solid documentation on how to deploy with each service and link to it in the README too. That would also help to cut down on things to do in bin/configure which would make it quicker/smoother for developers to get setup with a new application.
If we do want the buttons though, I submitted #1614 so developers don't have to write in their repository link.

@andrewculver this should be working now. (Assuming you have your Heroku account connected to your GitHub account.)


Stdin (standard input) for interactive external console programs is not set to the console's in the console/terminal host

Note: #10824  fixed the issue for stdout (standard output).
When invoking external programs, the encoding of their standard input stream should match that of the hosting console, as reflected in [Console]::InputEncoding - just like the standard output encoding is set to [Console]::OutputEncoding (which was always the case in Windows PowerShell, but for PS Core was only recently fixed in #10824).
Note:

This is for the case where stdin is not redirected, where the external program reads input interactively typed by the user; by contrast, when PowerShell pipes input to an external program, the encoding specified in preference variable $OutputEncoding is used.

The problem also exists in Windows PowerShell.

Steps to reproduce
Run the following on Windows, where [Console]::InputEncoding is (still) the OEM code page's encoding by default.
Install dotnet-script for dynamic execution of C# code via an external program.
Run the following and type or paste character ü when prompted:
# Make (BOM-less) UTF8 the input encoding.
[Console]::InputEncoding = [Text.Utf8Encoding]::new($false)

# Execute dotnet-script with ad hoc code that reads bytes
# from stdin.
dotnet-script eval ((@'
  Console.WriteLine("Enter single character 'ü' and press ENTER");
  byte[] buf = new byte[2];
  using (Stream inStream = Console.OpenStandardInput())
  {
    inStream.Read(buf, 0, buf.Length);
  }
  Console.WriteLine("First 2 bytes read (should be 0xC3 0xBC for 'ü'):");
  foreach (byte b in buf) {
    Console.WriteLine("0x" + b.ToString("X"));
  }
'@
) -replace '"', '\"') | Tee-Object -Variable output

$output[-2..-1] | Should -Be '0xC3', '0xBC'

Expected behavior
The test should pass.
That is, the raw bytes read from stdin should reflect the UTF-8 encoding assigned to [Console]::InputEncoding, which is byte sequence 0xC3 0xBC for ü (LATIN SMALL LETTER U WITH DIAERESIS, U+00FC)
Actual behavior
The test fails:
Expected @('0xC3', '0xBC'), but got @('0x0', '0xD').

Curiously, a NUL byte was read instead of the typed character (0xD is just the CR char).
This shows that changing [Console]::InputEncoding had some effect, but not the desired one.
On macOS, changing [Console]::InputEncoding is effectively ignored.
Environment data
PowerShell Core 7.0.0-preview.5

/cc @JamesWTruher @SteveL-MSFT


Inline docs missing for CustomStateCheck

Description
The in-line documentation for CustomStateCheck of the ModuleTemplateSpec is missing. Using our make manifest target it will then translate to a more detailed CRD mainfest. Thus when using kubectl it is more native to work with.
https://github.com/kyma-project/lifecycle-manager/blob/05f85e70640adcb993978d5be971f131f935f9ee/api/v1beta2/moduletemplate_types.go#L115C13-L115C13

Reasons
Possible to use kubectl  explain moduletemplate.spec

How it looks now

Acceptance Criterias
CustomStateCheck should also have a proper description when calling kubectl  explain moduletemplate.spec

Functionality will be removed with Community Modules.
https://github.com/kyma-project/lifecycle-manager/issues/1554


feat: function pointers

A great feature for us at Kakarot, that would reduce step usage by ~5% would be to have a way to have a const-array filled with function pointers, and be able to do something like:
fn execute_opcode(opcode_number: u8){
  let function_ptr = OPCODES[opcode_number];
  return function_ptr();
}

currently we do like
fn execute_opcode(opcode_number: u8){
        if opcode == 0x00 {
            // STOP
            return Result::Ok(self.exec_stop());
        }
        if opcode == 0x01 {
            // ADD
            return self.exec_add();
        }
        if opcode == 0x02 {
            // MUL
            return self.exec_mul();
        }
}

which, when executing thousands of opcodes, can represent a non-marginal part of the computation.

match pattern is more optimized than a sequence of ifs from my xp

match pattern is more optimized than a sequence of ifs from my xp

indeed, looks like its about ~ twice better (40k -> 20k steps in my reference profiling)

as @feltroidprime said - for the specific usecase -
match value {
  0 => self.handle_0(),
  1 => self.handle_1(),
  2 => self.handle_2(),
  3 => self.handle_3(),
  _ => panic!("unsupported"),
}

would be more efficient in the cases you have many opcodes.
function pointers would be a lot more work - and are not planned any time soon (unlike closures which are really close to being released).


Fix autoprefixer invocation

Before this patch enb-autoprefixer always process files with default browserSupport because of incorrect apply with object argument instead of an array.
Because of this we always stepping in this code branch:
https://github.com/postcss/autoprefixer-core/blob/master/lib/autoprefixer.coffee#L24
instead of this:
https://github.com/postcss/autoprefixer-core/blob/master/lib/autoprefixer.coffee#L21
Instead of wrapping arguments in array invocation logic borrowed from grunt-autoprefixer which seems to be closer to official usage recommendation.
Here's results after processing same css file with option browserSupport: "last 8 Chrome versions"
(before/after)
https://yadi.sk/i/x4Fz01G_dgviQ
https://yadi.sk/i/LhLlmbXOdgvi4
Notice that -moz-box-sizing, -webkit-linear-gradient, -ms/moz-user-select props removed and -moz-font-kerning is no longer being added as expected.

Thank you for your contribution! Can you please rebase your PR?

Done!

Thank you for your contribution!

Released in<EMAIL_ADDRESS>


in IOS 11 Restore session between the WKWebview and SFSafariViewController.

Description:
How to restore session between the WKWebview and SFSafariViewController in iOS 11, As I am trying to restore existing cookies for already logged-In user. which I am not able to do in iOS 11.
the earlier version in iOS 9 and iOS 10, I am able to share the cookies between them. but in case of iOS 11, there are new changes from Apple side due to security problem.
Here I found apple developer documents regarding SFSafariViewController:- https://developer.apple.com/documentation/safariservices/sfsafariviewcontroller
Looking for suggestions.
Thanks in advance.

@sharmam-lh did you ever figure out how to implement this? My guess would be to use WKWebView? I need to implement something very similar soon.


cli added config support and validate command

Now, all available commands accept --config which receives a Path. The path can be a .json, .py, or .ini file and the content is returned as a dictionary.
Changes

added logic to handle config path
modified logic that iterates over nodes to handle node.originating_functions is None for config nodes
updated commands.py to load config before building the driver
updated commands from __main__.py for the CLI to handle a new option

How I tested this

added config of each supported format to the examples/cli folder and manually tried them.

Notes
❗ I will add a hamilton validate command then update docs at once

we might want to add support for JSON config from the command line, but Typer doesn't support Union of types for arguments. Would need to add an additional --config-json -cjson to each command and prevent conflicts with --config. Maybe things could be renamed to --config-path and --config when received as JSON string
we could accept argument overload to CLI commands  such as hamilton build key1="true" key2=0 MODULES, but it would be messier to parse and maintain

Checklist

[x] PR has an informative and human-readable title (this will be pulled into the release notes)
[x] Changes are limited to a single goal (no scope creep)
[ ] Code passed the pre-commit check & code is left cleaner/nicer than when first encountered.
[ ] Any change in functionality is tested
[ ] New functions are documented (with a description, list of inputs, and expected output)
[x] Placeholder code is flagged / future TODOs are captured in comments
[ ] Project documentation has been updated if adding/changing functionality.

:rocket: This PR description was created by Ellipsis for commit 42e236d57c03fa914bb46c8c1a2c7a1c41315a6d.

Summary:
This PR enhances the CLI by adding support for configuration files, handling a new case for config nodes, updating the driver building process, handling a new CLI option, improving error handling, and providing a demonstration of the new configuration options.
Key points:

Added support for configuration files in the CLI
Handled a new case where node.originating_functions is None for config nodes
Updated commands.py to load the config before building the driver
Updated commands from __main__.py for the CLI to handle a new option
Improved error handling in logic.py
Added a demonstration of the new configuration options in module_v1.py in the examples/cli directory

Generated with :heart: by ellipsis.dev

Also, can we add config stuff to the README?

I think the CLI is still super experimental. As I work with pre-commit and GitHub actions, new API needs appear and things change frequently.
We should strongly emphasize that user rely on hamilton --help (after all that's why we picked Typer).
Generally speaking, we should probably start adding dates to examples/ to communicate potential deprecation until we automate CI for them. (hopefully the CLI will help)


RecyclableMemoryStreamManager does not ever release the allocated memory

NEST/Elasticsearch.Net version: 7.3.1
RecyclableMemoryStreamManager allocates small memory blocks by request, but the logic of freeing up the allocated memory is never invoked.
MaximumFreeSmallPoolBytes is not set anywhere and has a default value of zero, so the blocks are always returned back to the pool:
https://github.com/elastic/elasticsearch-net/blob/2638c1e9963680abd566b5b599cfb9f5e1045d0f/src/Elasticsearch.Net/Providers/RecyclableMemoryStreamManager.cs#L330
This leads to the growing large objects heap under load.

Thank you for raising this we will do another dive into the pool characteristics especially for longer running processes
related: https://github.com/microsoft/Microsoft.IO.RecyclableMemoryStream/issues/75

Opened to https://github.com/elastic/elasticsearch-net/pull/4172 to be able to visualize the characteristics of the memory pool.
Closing this to keep the discussion isolated on the PR. Please don't hesitate to comment there 👍

There is any chance of these fixes get into v6.x? It's happening on release 6.8.1, too :(


Proper call-outs; minor fixes

Added plugins for proper call-outs
Fixed issues introduced by #8 (incorrect nav section).
Several minor fixes which caught my eye (some connected to Mirantis/hmc#364).

Forgot to add markdown-callouts installation to GH actions workflow. Fixed


Business and personal property tax rate results duplicated in Locate

Using http://tryitlive.arcgis.com/liveworklocate/#?app=LOCATE

Search using the default address and drive time
Once results display on the results panel, note that the results listed under "Business Personal Property Tax Rate" are duplicated.

This behavior has been observed both when a webmap and a server config are used.

Can no longer reproduce this with the February 2015 version of the application.


[$250] [Simplified Collect][Tags] Workspace settings - Renaming an enabled tag gets it disabled

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Found when executing PR : https://github.com/Expensify/App/pull/38240
Version Number: 1.4.55-0
Reproducible in staging?: Y
Reproducible in production?: New feature
Email or phone of affected tester (no customers<EMAIL_ADDRESS>Logs: https://stackoverflow.com/c/expensify/questions/4856
Issue reported by: Applause-Internal team
Action Performed:

Go to Workspace settings (Of a collect or Control policy)
Enable tags in "more features"
Go to tag settings by clicking on tag
Enable the tag
Go to tag edit page by clicking on tag name
Edit tag name and Save

Expected Result:
The tag is renamed and stays enabled
Actual Result:
The tag is renamed but becomes disabled
Workaround:
Unknown
Platforms:

Which of our officially supported platforms is this issue occurring on?

[ ] Android: Native
[ ] Android: mWeb Chrome
[ ] iOS: Native
[ ] iOS: mWeb Safari
[x] MacOS: Chrome / Safari
[x] MacOS: Desktop

Screenshots/Videos
https://github.com/Expensify/App/assets/115492554/770a422d-f2be-4363-9d82-d45c5a817a89

View all open jobs on GitHub
Upwork Automation - Do Not Edit

Upwork Job URL: https://www.upwork.com/jobs/~01c36f5b607dcd8cfb
Upwork Job ID:<PHONE_NUMBER>645612544
Last Price Increase: 2024-03-22
Automatic offers:

bernhardoj | Contributor | 0

@stephanieelliott I haven't added the External label as I wasn't 100% sure about this issue. Please take a look and add the label if you agree it's a bug and can be handled by external contributors.
We think this issue might be related to the #collect project.

Proposal
Please re-state the problem that we are trying to solve in this issue.
The tag gets disabled when renaming.
What is the root cause of that problem?
When we rename the tag, we merge the old tag with the new one.
https://github.com/Expensify/App/blob/331106224ba8ca685b2d0f71ce2244b7f7e259df/src/libs/actions/Policy.ts#L3104-L3108
But the old tag is empty because we accessed it incorrectly.
https://github.com/Expensify/App/blob/331106224ba8ca685b2d0f71ce2244b7f7e259df/src/libs/actions/Policy.ts#L3094
What changes do you think we should make in order to solve the problem?

We should get the tag the same way as clearPolicyTagErrors
https://github.com/Expensify/App/blob/331106224ba8ca685b2d0f71ce2244b7f7e259df/src/libs/actions/Policy.ts#L3062-L3064
const oldTag = allPolicyTags?.[`${ONYXKEYS.COLLECTION.POLICY_TAGS}${policyID}`]?.[tagListName]?.tags?.[policyTag.oldName] ?? {};

This is a new feature, not really a blocker, I can take over @arosiclair

@mountiny I have the context of this issue. If we need a C+ here, I would love to take over

@luacmartins Could I take over this issue as a follow-up of this PR as I mentioned above?

Assigning @DylanDylann as C+ and @bernhardoj for implementation of his proposal

PR is ready
cc: @DylanDylann

$250 to @bernhardoj and $250 to @DylanDylann
all yours when the time comes @stephanieelliott

PR is undergoing QA

Just pending payment

Summary here

Summarizing payment on this issue:

Contributor: @bernhardoj $250 PAID via Upwork
Contributor+: @DylanDylann $250 PAID via Upwork

Upwork job is here: https://www.upwork.com/jobs/~01c36f5b607dcd8cfb


Setup CI

Setup basic CI checks to assert the correctness of the implementation.
The same model used in Miden VM will be replicated here, that is:

Run tests
Enforce rustfmt
Reject warnings
Merge first to next

Closed by #4


Docs gen issue in AssertMeasurementProbability: The type of result param is invalid

It is confusing that the type of the result parameter is invalid here and here.
Documentation rendering issue?

Same for Measure() Output (and all entities of type Result?).

@cgranade Are you looking into this, or making sure it gets triaged?

I haven't had the chance to look into it yet, sorry, but wanted to at least make sure it was triaged in the meantime.

My initial thought is that it comes down to the ToMarkdownLink extension method at https://github.com/microsoft/qsharp-compiler/blob/1fd018a6490ca7c0aa42c2f67d7429c85362b187/src/Documentation/DocumentationGenerator/Extensions.cs#L285. It should be an easier fix than I was afraid of, so I'll make a PR for it shortly.

@cgranade Thanks! No rush, I just wanted to make sure someone has an eye on it.

Makes sense! In investigating the fix seems to be pretty straightforward, so I just went on and opened the PR.


Getting a warning message on deployment

Tutorial URL: https://developers.sap.com/tutorials/cap-service-deploy.html
Step 3: Deploy using cf push
Here when we perform the cf push -f gen/db operation we get the below warning
"odata.version='v2' not supported by node runtime, define odata.version='v4' in package.json instead"

From an end user perspective, please include a step to state that this warning might come while push operation.
Best Regards,
Priyanka

Hi Priyanka,
The dev colleagues are still working on a new version and with the next release, this hint will disappear.
Best regards,
Iwona

Thank you for your feedback. The issue seems to be resolved, so I am closing the issue.
If you still have questions, feel free to reopen the issue.


ENH: Wrap PointSet To PointSet Metric and RegistrationMethod

PointSetToPointSetMetric and PointSetToPointSetRegistrationMethod Python wrapping added as requested in ITK Discourse.

PR Checklist

[X] Added Python wrapping to new files (if any) as described in ITK Software Guide Section 9.5

Refer to the ITK Software Guide for
further development details if necessary.

/azp.run

/azp.run *

/azp.run ITK.Linux.Python


Smart charging add a select button to switch from kW to amps in the charging and site curve

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.

if you click on the radio and checkbox once , the hover style do not disappear.

An error occur with some of the transaction and also a spinner need to be added so a user can't click several time as shown in the screenshot.

if you click on the radio and checkbox once , the hover style do not disappear.

An error occur with some of the transaction and also a spinner need to be added so a user can't click several time as shown in the screenshot.

I think, this is a bug of Angular on localhost. I have it everywhere in the Application.

I cannot reproduce the bug with this session and do not understand what really happens there. Maybe we could have a talk tomorrow.


ERROR: store_buffer: Condition ' !p_src ' is true when doing some operations.

Godot version:
3.2.beta.custom_build. 157246ae8
OS/device including version:
Ubuntu 19.10
Issue description:
Using null buffer pointer in fwrite function is Undefinied Behaviour
size_t fwrite(
   const void *buffer,
   size_t size,
   size_t count,
   FILE *stream
);

and this cause this error
ERROR: store_buffer: Condition ' !p_src ' is true.
   At: drivers/unix/file_access_unix.cpp:278.

It can be easily silenced but probably this is not the best solution
Steps to reproduce:

Download "FirstPersonStarter" from Template in Project Manager

https://github.com/godotengine/godot/blob/24e1039eb6fe32115e8d1a62a84965e9be19a2ed/scene/main/http_request.cpp#L358
2.
Import GLTF File Katalog bez nazwy.zip
https://github.com/godotengine/godot/blob/dec10dd776fca2994277faa3a97b13e70317f784/core/io/resource_format_binary.cpp#L1538

I'm also seeing this issue when downloading files with the HTTPRequest node. The download still works, though.

I have the exactly error when I use this plugin: https://github.com/fenix-hub/godot-engine.text-editor

I have the same error. I don't have any plugin and i don't use HTTPRequest but i do have GLTF files imported from blender. (Created from scratch and exported by me with the latest version of blender).
It always happen in the script editor when i have an "error" in my code (ex: when writting an "if" before putting the ":" at the end).
It freeze the whole program for a few minutes... But if godot was started from a terminal, i can do a ctrl+c in it and godot will unfreeze like nothing happened ! Not exiting the program, just unfreezing it.
I use Godot_v3.2.1-stable_x11.64 on Ubuntu 18.04.4 LTS

I also have this problem every time I use http_request to download a file on the android exported version of my game.
The download works correctly, only the debug log is too flooded:

This solved the problem in my case:
$HTTPRequest.download_chunk_size = 65535

This solved the problem in my case:
$HTTPRequest.download_chunk_size = 65535

For reference, this is now the default in 3.3rc: https://github.com/godotengine/godot/pull/42896

This solved the problem in my case:
$HTTPRequest.download_chunk_size = 65535

For reference, this is now the default in 3.3rc: #42896

In 3.3, this doesn't solve the problem.
And although the file is still downloaded successfully, HTTPRequest.get_body_size() returns -1 instead of the actual file size.

HTTPRequest.get_body_size() returns -1 instead of the actual file size.

This is expected with some file hosts such as GitHub because they don't report the body size for files that were generated on-the-fly (such as ZIP archives). In this situation, you will get the body size if you try downloading the same file a second time in a short enough interval.

HTTPRequest.get_body_size() returns -1 instead of the actual file size.

This is expected with some file hosts such as GitHub because they don't report the body size for files that were generated on-the-fly (such as ZIP archives). In this situation, you will get the body size if you try downloading the same file a second time in a short enough interval.

That's generally true, but in my case these are the same specific files of which get_body_size() returns the actual size when exporting with Godot v3.2.3 but not when exporting with v3.3.

@avnerh1 Which platform are you testing this with? The HTML5 HTTPClient has been rewritten to use fetch(), so it's possible that there may be regressions. Please create a new issue with a minimal reproduction project attached.

I got the same error when running on android device via editor. 305c364c13

@avnerh1 Which platform are you testing this with? The HTML5 HTTPClient has been rewritten to use fetch(), so it's possible that there may be regressions. Please create a new issue with a minimal reproduction project attached.

I'm using Win10/Edge.

I'm having this issue on Mac OS X.
The problem occurs in both debug mode (editor) and exported versions.

const endpoint = "https://query1.finance.yahoo.com/v8/finance/chart/AAPL?symbol=AAPL&period1=1614957299&period2=1620054899&useYfid=true&interval=15m&includePrePost=false"
const headers = [
	"user-agent: CustomTrader",
	"Content-Type: application/json",
	"Accept-Encoding: gzip"
]

var http
http = HTTPRequest.new()
http.download_chunk_size = 65535
http.download_file = "user://test.gz"

self.add_child(http)

var result = http.request(endpoint, headers(), true)
assert(result == OK)

result = yield(http, "request_completed")

HTTPRequest.get_body_size() returns -1 instead of the actual file size.

This is expected with some file hosts such as GitHub because they don't report the body size for files that were generated on-the-fly (such as ZIP archives). In this situation, you will get the body size if you try downloading the same file a second time in a short enough interval.

That's generally true, but in my case these are the same specific files of which get_body_size() returns the actual size when exporting with Godot v3.2.3 but not when exporting with v3.3.

I am also having this same problem. It worked in version 3.2.3 and in version 3.3 the function get_body_size () always returns -1 in the same file and server that returned correctly in the version exported with 3.2.3.
Does anyone have any fix or workaround for this? I used this function to show a progress bar.
download_request = HTTPRequest.new()
add_child(download_request)
# download_request.download_chunk_size = 65535;
download_request.download_file = download_destination
download_request.connect("request_completed", self, "_http_request_completed")

func _process(_delta):
  if download_request:
    var size = download_request.get_body_size()
    if size > 0:
      var done = float(download_request.get_downloaded_bytes()) / size

I have full access to the server (AWS) and the file. Is there any configuration that can solve this?
File is a pck with about 20Mb

but progress bar stoped working @dpensky

It's probably not working because the server on the other end is responding with -1 as the content length.
If you could make a small repo to test that it would help narrow down the issue a lot!

Running directly in the editor, and downloading the same file from the same location, everything works perfectly, it only happens when I export to html

Log when running from the EDITOR (this works)
[pck_loader] - Downloading: [https://server.address.com:8080/game_name.pck]
[pck_loader] - 	To: [user://game_name.pck]
[pck_loader] - _http_request_completed(0, 200, [Server: TornadoServer/6.1, Content-Type: application/octet-stream, Date: Fri, 14 May 2021 11:17:39 GMT, Accept-Ranges: bytes, Etag: "0fe59c74512f93f843904cc9a2ff201ffa838967e28a1bd8014258a36a11cc702f50f19ce32a9546575cfa727ef3ac2b59bd9451ff43f67af07f84090c1a6197", Last-Modified: Thu, 13 May 2021 19:58:15 GMT, Content-Length: 15809392], )

Log when running from the HTML EXPORT (this don't work)
[pck_loader] - Downloading: [https://server.address.com:8080/game_name.pck]
[pck_loader] - 	To: [user://game_name.pck]
**ERROR**: Condition "!p_src" is true.
game-lobby.js?v=…2b1d2ad644eabc5:354    At: drivers/unix/file_access_unix.cpp:279:store_buffer() - Condition "!p_src" is true.
game-lobby.js?v=…2b1d2ad644eabc5:354 **ERROR**: Condition "!p_src" is true.
game-lobby.js?v=…2b1d2ad644eabc5:354    At: drivers/unix/file_access_unix.cpp:279:store_buffer() - Condition "!p_src" is true.
[pck_loader] - _http_request_completed(0, 200, [Server: TornadoServer/6.1, Content-Type: application/octet-stream, Date: Fri, 14 May 2021 11:17:39 GMT, Accept-Ranges: bytes, Etag: "0fe59c74512f93f843904cc9a2ff201ffa838967e28a1bd8014258a36a11cc702f50f19ce32a9546575cfa727ef3ac2b59bd9451ff43f67af07f84090c1a6197", Last-Modified: Thu, 13 May 2021 19:58:15 GMT, Content-Length: 15809392], )

Has anyone found solution for this error? Im trying to download files using httprequest node but only sometimes issue is present.

Has anyone found solution for this error? Im trying to download files using httprequest node but only sometimes issue is present.

Which operating system and Godot version are you usign?

Which operating system and Godot version are you using? If this is HTML5, see above.

Im using popos with godot 3.3.2. Error seems to come off at random interval. Tested with filesize less than 1 mb, issue isn't present. Tested with 10mb file issue is present.

Which operating system and Godot version are you using? If this is HTML5, see above.

Im using popos with godot 3.3.2. Error seems to come off at random interval. Tested with filesize less than 1 mb, issue isn't present. Tested with 10mb file issue is present.

Which website are you downloading the file from? Many hosts such as GitHub will not report content lengths unless the file was already recently downloaded. This is because the file is generated on-the-fly, so GitHub doesn't even know the file size until the file is generated.

Mainly itch io and various other sites. Including couple of pictures from wikipedia. Although error is present, file is downloaded.

I noticed that the problem is not consistent. I suspect it has something to do with caching the file by CDN. I will look into it and report back if I find anything useful.

For me the error of httprequet.get_body_size () returning -1 always happens in version 3.3 (and 3.3.2)
This function returns the correct value in version 3.2.3 when downloading the same file, on the same server in the same game

@darcio-studiobluechip which file? Could you provide a sample project?

HTTPRequest.get_body_size() returns -1 instead of the actual file size.

This is expected with some file hosts such as GitHub because they don't report the body size for files that were generated on-the-fly (such as ZIP archives). In this situation, you will get the body size if you try downloading the same file a second time in a short enough interval.

That's generally true, but in my case these are the same specific files of which get_body_size() returns the actual size when exporting with Godot v3.2.3 but not when exporting with v3.3.

I am also having this same problem. It worked in version 3.2.3 and in version 3.3 the function get_body_size () always returns -1 in the same file and server that returned correctly in the version exported with 3.2.3.
Does anyone have any fix or workaround for this? I used this function to show a progress bar.
var download_url = 'https://myawsserver.com/game.pck'
var download_destination = "user://game.pck"
download_request = HTTPRequest.new()
add_child(download_request)
# download_request.download_chunk_size = 65535;
download_request.download_file = download_destination
download_request.connect("request_completed", self, "_http_request_completed")
var error = download_request.request(download_url)

func _process(_delta):
  if download_request:
    var size = download_request.get_body_size()
    if size > 0:
      var done = float(download_request.get_downloaded_bytes()) / size

I have full access to the server (AWS) and the file. Is there any configuration that can solve this?
File is a pck with about 20Mb. File is downloaded correctly, buy progress bar stoped working

My code is the above one.

file is a godot game (only pck)
host is in a amazon instance (s3)
webserver is python tornado
http exported game and files are stored in the same place/server/instance
file is always downloaded correctly
get_body_size works when running from the engine editor

get_body_size also works when running the same code and requesting the same file from the same server on the android exported version of the game

Just switched from v3.2.3 to v3.3.2 and with HTML export the problem immediately showed up again, for every file.
Do we know the root cause of the problem, and what was changed from 3.2 to 3.3 that caused it?

Just switched from v3.2.3 to v3.3.2 and with HTML export the problem immediately showed up again, for every file.
Do we know the root cause of the problem, and what was changed from 3.2 to 3.3 that caused it?

Quoting myself above:

This is likely a regression from #46731 (see also #47597)

The fix is simple:
diff --git a/drivers/unix/file_access_unix.cpp b/drivers/unix/file_access_unix.cpp
index ec23df62d0..6ea55219bb 100644
--- a/drivers/unix/file_access_unix.cpp
+++ b/drivers/unix/file_access_unix.cpp
@@ -264,7 +264,7 @@ void FileAccessUnix::store_8(uint8_t p_dest) {

 void FileAccessUnix::store_buffer(const uint8_t *p_src, uint64_t p_length) {
        ERR_FAIL_COND_MSG(!f, "File must be opened before use.");
-       ERR_FAIL_COND(!p_src);
+       ERR_FAIL_COND(!p_src && p_length > 0);
        ERR_FAIL_COND(fwrite(p_src, 1, p_length, f) != p_length);
 }

Cf. #49394.


Block SequentialQueue on reauthentication

Details
Makes the SequentialQueue work better when we are reauthenticating.
Before: When a request in the SQ needed reauthentication we would call Authenticate and then send the original request into the non-sequential queue (where it would be processed after the SQ empties). That is bad because requests happen out of order.
Request 1 (Fail)
Authenticate
Request 2
Request 3
Request 1

After: The reauthentication logic has been reorganized and calls to Authenticate will block the queue
Request 1 (Fail)
Authenticate
Request 1
Request 2
Request 3

Fixed Issues
https://github.com/Expensify/Expensify/issues/207534
Tests (Build staging version of app)

Go offline via Chrome Dev Tools Network tab

Leave 10 comments on a report
Invalidate the authToken via Preferences

Go back online
Verify by inspecting the Network requests tab in Chrome Dev Tools that each request in the queue is made sequentially and that the first request requiring reauthentication will wait for Authenticate to complete before moving onto the next request in the queue.

[ ] Verify that no errors appear in the JS console

PR Review Checklist

PR Reviewer Checklist

[ ] I verified the correct issue is linked in the ### Fixed Issues section above
[ ] I verified testing steps are clear and they cover the changes made in this PR

[ ] I verified the steps for local testing are in the Tests section
[ ] I verified the steps for Staging and/or Production testing are in the QA steps section
[ ] I verified the steps cover any possible failure scenarios (i.e. verify an input displays the correct error message if the entered data is not correct)
[ ] I turned off my network connection and tested it while offline to ensure it matches the expected behavior (i.e. verify the default avatar icon is displayed if app is offline)

[ ] I checked that screenshots or videos are included for tests on all platforms
[ ] I verified tests pass on all platforms & I tested again on:

[ ] iOS / native
[ ] Android / native
[ ] iOS / Safari
[ ] Android / Chrome
[ ] MacOS / Chrome
[ ] MacOS / Desktop

[ ] I verified there are no console errors (if there’s a console error not related to the PR, report it or open an issue for it to be fixed)
[ ] I verified proper code patterns were followed (see Reviewing the code)

[ ] I verified that any callback methods that were added or modified are named for what the method does and never what callback they handle (i.e. toggleReport and not onIconClick).
[ ] I verified that comments were added to code that is not self explanatory
[ ] I verified that any new or modified comments were clear, correct English, and explained “why” the code was doing something instead of only explaining “what” the code was doing.
[ ] I verified any copy / text shown in the product was added in all src/languages/* files
[ ] I verified any copy / text that was added to the app is correct English and approved by marketing by tagging the marketing team on the original GH to get the correct copy.
[ ] I verified proper file naming conventions were followed for any new files or renamed files. All non-platform specific files are named after what they export and are not named “index.js”. All platform-specific files are named for the platform the code supports as outlined in the README.
[ ] I verified the JSDocs style guidelines (in STYLE.md) were followed

[ ] If a new code pattern is added I verified it was agreed to be used by multiple Expensify engineers
[ ] I verified that this PR follows the guidelines as stated in the Review Guidelines
[ ] I verified all code is DRY (the PR doesn't include any logic written more than once, with the exception of tests)
[ ] I verified any variables that can be defined as constants (ie. in CONST.js or at the top of the file that uses the constant) are defined as such
[ ] If a new component is created I verified that:

[ ] A similar component doesn't exist in the codebase
[ ] All props are defined accurately and each prop has a /** comment above it */
[ ] Any functional components have the displayName property
[ ] The file is named correctly
[ ] The component has a clear name that is non-ambiguous and the purpose of the component can be inferred from the name alone
[ ] The only data being stored in the state is data necessary for rendering and nothing else
[ ] For Class Components, any internal methods passed to components event handlers are bound to this properly so there are no scoping issues (i.e. for onClick={this.submit} the method this.submit should be bound to this in the constructor)
[ ] Any internal methods bound to this are necessary to be bound (i.e. avoid this.submit = this.submit.bind(this); if this.submit is never passed to a component event handler like onClick)
[ ] All JSX used for rendering exists in the render method
[ ] The component has the minimum amount of code necessary for its purpose and it is broken down into smaller components in order to separate concerns and functions

[ ] If a new CSS style is added I verified that:

[ ] A similar style doesn’t already exist
[ ] The style can’t be created with an existing StyleUtils function (i.e. StyleUtils.getBackgroundAndBorderStyle(themeColors.componentBG)

[ ] If the PR modifies a generic component, I tested and verified that those changes do not break usages of that component in the rest of the App (i.e. if a shared library or component like Avatar is modified, I verified that Avatar is working as expected in all cases)
[ ] If the PR modifies a component related to any of the existing Storybook stories, I tested and verified all stories for that component are still working as expected.

QA Steps

[ ] Verify that no errors appear in the JS console

Screenshots

Web

Mobile Web

Desktop

iOS

Android

@tgolen This PR got a little out of hand - but I think in a good way.
So many things that were bugging me about the Network code feel pretty nice now with the middleware idea applied.
Here's the basic idea...

Network.post() passes requests to the queues

The queues call Request.process() which calls HttpUtils.xhr() with middlewares applied

Each middleware returns a promise and passes the response to the next middleware

The order is important and we have:

Logging - Logs the request details (this cleaned up all circular dependencies with Log)
Recheck connection - Not sure how much we need the stuff in this file, but figured I'd leave it for now.
Reauthentication - Handles reauthentication
Retry - Handles request retry logic

One thing that is still bugging me about this (but will be fixed shortly) is that I've got a isFromSequentialQueue argument getting passed to the middleware. This is necessary because I haven't yet forced all network requests that can be persisted directly into the sequential queue. Once we do that we can just look at the request object and see if it's "persistable", but for now, isFromSequentialQueue is the only  way to tell if it was called from the sequential queue or not.

Ok ready for review now.
Gonna add another reviewer here since the changes are pretty extensive (though a lot of this is just reorganizing).
I am open to splitting this stuff up into several PRs, but would have to think about how to do it.

Gonna merge since we have a couple of approvals.
@tylerkaraszewski let me know if you have any thoughts about my response here.

🚀 Cherry-picked to staging by @sketchydroide in version: 1.1.57-8 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
success ✅

🕸 web 🕸
success ✅

@Expensify/applauseleads please QA this PR and check it off on the deploy checklist if it passes.

🚀 Deployed to production by @chiragsalian in version: 1.1.57-17 🚀

platform
result

🤖 android 🤖
success ✅

🖥 desktop 🖥
success ✅

🍎 iOS 🍎
success ✅

🕸 web 🕸
success ✅


Added name to index

Added name to index for first contribution.

added a space in between your last list item, otherwise good to pass


riboWaltz on galaxy.eu fails to run

Hi Fabio,
I am trying to run riboWaltz on galaxy.eu.  The transcriptome-mapped.bam file was generated by RNA STAR, using the built-in index and hg38 on the Galaxy server, and gencode.v43.basic.annotation.gtf.gz, which I uploaded into Galaxy directly from the database. I used the same gtf for riboWaltz.  RiboWaltz failed to run, with the following error message:
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
The "phase" metadata column contains non-NA values for features of type
stop_codon. This information was ignored.
Error in (function (x)  : attempt to apply non-function
If I understand correctly from your feedback on previous issues, the "The "phase" metadata column contains non-NA values for features of type stop_codon." is just a warning, and should not cause the failure. But I cannot figure out what the last line, "Error in (function (x)  : attempt to apply non-function" may refer to, although I suppose it indicates the error causing the failure.
Your help would be greatly appreciated,
Thank you very much,
Beata
I am copying here the command line from Galaxy:
ln -s /data/dnb08/galaxy_db/files/2/9/8/dataset_2989d96b-5e2d-4547-8700-b4e45121c568.dat ls180_1'.bam' && Rscript '/opt/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/ribowaltz_process/6d4c94373bba/ribowaltz_process/ribowaltz.R' -b . -g '/data/dnb08/galaxy_db/files/e/1/0/dataset_e10dfbb5-19e4-49cf-a8eb-29ea41fa2295.dat' --refseq_sep '' --params_duplicate_filterting '[{"extremity": "both", "keep": "shortest"}]' --params_peridiocity_filterting '[{"periodicity_threshold": 50}]' --params_psite_additional '[{"flanking": 6, "use_start": true, "psite_extrimity": "auto", "cl": 99}]' --params_coverage_additional '[{"psites_per_region": true, "min_overlap": 1, "start_nts": 0, "stop_nts": 0}]' --psite_info_rdata '/data/jwd02f/main/060/770/60770492/outputs/galaxy_dataset_e1178f2c-57e6-4162-b986-bea0a3ca3aaa.dat' --codon_coverage_info '/data/jwd02f/main/060/770/60770492/outputs/galaxy_dataset_32b21edf-1c05-4f7e-82e1-a1b5e8f81f6d.dat' --cds_coverage_info '/data/jwd02f/main/060/770/60770492/outputs/galaxy_dataset_a6016f82-a5e0-45d6-be7d-587c497ef070.dat' && cd plots && for i in /.pdf; do mv $i ${i///-}; done;

Hi Beata,
thank you for using riboWaltz.
As you correctly reported, the message about the stop_codon is just a warning and can be ignored.
About the error, I cannot really answer you. It's not clear to me which function of riboWaltz is arising the issue. In any case I'm not even sure I knew about riboWaltz being available in the Galaxy environment, and I'm not able to find it. Maybe it's because I'm not registered. Just to be sure could you please send me a link or an indication about where/how to find the tool in Galaxy.eu? I can try and test it to see if it works fine or not.
Best
Fabio

Hi Fabio,
Thanks for the quick response.  If you look at the Galaxy tools (https://usegalaxy-eu.github.io/tools.html), in the RNA Analysis folder, at the very end are some riboseq tools, including riboWaltz.  It is not available at usegalaxy.org, if that's the one you checked - I am using galaxy.eu.
Thank you for looking into it,
Cheers,
Beata

Feladó: fabiolauria @.>
Elküldve: 2023. június 14., szerda 16:19
Címzett: LabTranslationalArchitectomics/riboWaltz @.>
Másolatot kap: Scholtz Beáta @.>; Author @.>
Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi Beata,
thank you for using riboWaltz.
As you correctly reported, the message about the stop_codon is just a warning and can be ignored.
About the error, I cannot really answer you. It's not clear to me which function of riboWaltz is arising the issue. In any case I'm not even sure I knew about riboWaltz being available in the Galaxy environment, and I'm not able to find it. Maybe it's because I'm not registered. Just to be sure could you please send me a link or an indication about where/how to find the tool in Galaxy.eu? I can try and test it to see if it works fine or not.
Best
Fabio
—
Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1591313052, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPMHVWRPJUV7SPGYRRDXLHB7RANCNFSM6AAAAAAZGAQMXQ.
You are receiving this because you authored the thread.Message ID: @.***>

This is the link to my Galaxy History, if that helps:
url: https://usegalaxy.eu/u/scholtz/h/ribowaltz-trial https://usegalaxy.eu/u/scholtz/h/ribowaltz-trial
Cheers,
Beata

Feladó: Scholtz Beáta @.>
Elküldve: 2023. június 14., szerda 16:27
Címzett: LabTranslationalArchitectomics/riboWaltz @.>
Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
Hi Fabio,
Thanks for the quick response.  If you look at the Galaxy tools (https://usegalaxy-eu.github.io/tools.html), in the RNA Analysis folder, at the very end are some riboseq tools, including riboWaltz.  It is not available at usegalaxy.org, if that's the one you checked - I am using galaxy.eu.
Thank you for looking into it,
Cheers,
Beata

Feladó: fabiolauria @.>
Elküldve: 2023. június 14., szerda 16:19
Címzett: LabTranslationalArchitectomics/riboWaltz @.>
Másolatot kap: Scholtz Beáta @.>; Author @.>
Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi Beata,
thank you for using riboWaltz.
As you correctly reported, the message about the stop_codon is just a warning and can be ignored.
About the error, I cannot really answer you. It's not clear to me which function of riboWaltz is arising the issue. In any case I'm not even sure I knew about riboWaltz being available in the Galaxy environment, and I'm not able to find it. Maybe it's because I'm not registered. Just to be sure could you please send me a link or an indication about where/how to find the tool in Galaxy.eu? I can try and test it to see if it works fine or not.
Best
Fabio
—
Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1591313052, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPMHVWRPJUV7SPGYRRDXLHB7RANCNFSM6AAAAAAZGAQMXQ.
You are receiving this because you authored the thread.Message ID: @.***>

Hi there,
thanks for the links (and sorry, I found the link to riboWaltz 30 sec after I sent my reply).
Your history is a bit strange because after the alignment step (44), it jumps directly at the inclusion P-site-related info to your data structure (step 45, based on step 44 and the GTF file from step 40). I cannot understand when (if) the P-site has been computed. Is it called internally? Where you trying to perform a specific step on the pipeline when you got the error?
BTW it seems the error occurred while reading the GTF, even if I cannot understand the aim of this step. I'll check with my own data to be sure everything is still working off-line. I hope your history won't be delated too soon so I will have a chance to take a better look after this.
Best
Fabio

Hi Fabio,
Steps 45-49 are supposed to be the output files from riboWaltz, not sequential steps in the pipeline.  When calling up riboWaltz from the Tools section, all I had to provide for the program were the bam file and the gtf file (screenshot attached). I will leave the history available for you.
Cheers,
Beata

Feladó: fabiolauria @.>
Elküldve: 2023. június 14., szerda 16:48
Címzett: LabTranslationalArchitectomics/riboWaltz @.>
Másolatot kap: Scholtz Beáta @.>; Author @.>
Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi there,
thanks for the links (and sorry, I found the link to riboWaltz 30 sec after I sent my reply).
Your history is a bit strange because after the alignment step (44), it jumps directly at the inclusion P-site-related info to your data structure (step 45, based on step 44 and the GTF file from step 40). I cannot understand when (if) the P-site has been computed. Is it called internally? Where you trying to perform a specific step on the pipeline when you got the error?
BTW it seems the error occurred while reading the GTF, even if I cannot understand the aim of this step. I'll check with my own data to be sure everything is still working off-line. I hope your history won't be delated too soon so I will have a chance to take a better look after this.
Best
Fabio
—
Reply to this email directly, view it on GitHubhttps://github.com/LabTranslationalArchitectomics/riboWaltz/issues/71#issuecomment-1591377777, or unsubscribehttps://github.com/notifications/unsubscribe-auth/BAR7MPOTYA7ONWK7HMQM43LXLHFKPANCNFSM6AAAAAAZGAQMXQ.
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Hi Beata,
I tried most of my functions and I was not able to replicate the error you mentioned and everything works with data from our lab.
There are two options: either something is going on with your data or the Galaxy implementation somehow introduced some bugs. Either way, it would be nice to understand which function throws the error, but if you just list the inputs at the beginning of the process and everything is run automatically, debugging is a bit hard.
Could you try to find out at which step you get the error? It would be useful for investigating this issue with some indications and criteria.
Best,
Fabio

Hi Fabio,
Thank you very much for testing. I will try and contact the Galaxy Support team about the issue, maybe something went wrong with the wrapper.  Unfortunately I cannot test the analysis steps in Galaxy, everything runs kinda hidden in the wrapper, but maybe they can see where it gets stuck.  The data is really nothing fancy, human cell line, it worked with ribotaper on galaxy.eu (although I used the HISAT2-aligned files for that), and the P-site graphs for some selected genes looked as expected, good triplet periodicity.
I will get back to you with the answer (hopefully some really simple issue).
Thanks again,
Beata

Feladó: fabiolauria @.>
Elküldve: 2023. június 19., hétfő 18:17
Címzett: LabTranslationalArchitectomics/riboWaltz @.>
Másolatot kap: Scholtz Beáta @.>; Author @.>
Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi Beata,
I tried most of my functions and I was not able to replicate the error you mentioned and everything works with data from our lab.
There are two options: either something is going on with your data or the Galaxy implementation somehow introduced some bugs. Either way, it would be nice to understand which function throws the error, but if you just list the inputs at the beginning of the process and everything is run automatically, debugging is a bit hard.
Could you try to find out at which step you get the error? It would be useful for investigating this issue with some indications and criteria.
Best,
Fabio
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Thank you Beata.
Let me know how it is going.
I'll keep this issue open for a while to have your feedbacks.
Best
Fabio

Will do so, thank you!
Beata

Feladó: fabiolauria @.>
Elküldve: 2023. június 20., kedd 8:23
Címzett: LabTranslationalArchitectomics/riboWaltz @.>
Másolatot kap: Scholtz Beáta @.>; Author @.>
Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
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Thank you Beata.
Let me know how it is going.
I'll keep this issue open for a while to have your feedbacks.
Best
Fabio
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@scholtzb , have you managed to solve the issue? I'm trying to run RiboWlatz on Galaxy.eu as well, and hit the same error as you. Thanks!

Dear Nathalie,
Thank you for getting back to me - no, I haven't received any help so far, I'm stuck...
Do you have any suggestions what I could try?
Cheers,
Beata

Feladó: Nathalie Lailler @.>
Elküldve: 2023. szeptember 3., vasárnap 14:45
Címzett: LabTranslationalArchitectomics/riboWaltz @.>
Másolatot kap: Scholtz Beáta @.>; Mention @.>
Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
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@scholtzbhttps://github.com/scholtzb , have you managed to solve the issue? I'm trying to run RiboWlatz on Galaxy.eu as well, and hit the same error as you. Thanks!
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Hi Beata, I haven't managed to make it work with Galaxy so I ran it as command line.
@scholtzb

Hi Nathalie,
So, if I understand correctly, it is not possible to know at this point which step causes the problem with ribowaltz with Galaxy.eu, right?

Feladó: Nathalie Lailler @.>
Elküldve: 2023. szeptember 17., vasárnap 11:14
Címzett: LabTranslationalArchitectomics/riboWaltz @.>
Másolatot kap: Scholtz Beáta @.>; Mention @.>
Tárgy: Re: [LabTranslationalArchitectomics/riboWaltz] riboWaltz on galaxy.eu fails to run (Issue #71)
FIGYELEM: Ez a levél külső feladótól származik. Ne kattintson semmire a levélben, és ne nyissa meg a csatolmányt, amennyiben a küldő e-mail címét nem ismeri fel!
Hi Beata, I haven't managed to make it work with Galaxy so I ran it as command line.
@scholtzbhttps://github.com/scholtzb
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Questions about dataset object

Hi, @zhiqwang
Can you, please, explain what happens here?
https://github.com/zhiqwang/crnn.pytorch/blob/master/datasets/dataset.py#L53
After this batch target will always be 1D array, but according to the documentation you need to return batch-wise 2D array.
For example, if you input ([2], [3, 4]), you will return [2, 3, 4]

Hi, @skurzhanskyi
target can also be a tensor of size (sum(target_lengths)), the master branch of the documentation is clear. In this case, the targets are assumed to be un-padded and concatenated within 1 dimension.
Also remarked in this documentation:

In order to use CuDNN, targets must be in concatenated format.

Oh, thanks. I see, so we get information about which number belongs to which example from target_lengths.
Just one more question: how data changes when here you stack?
I understand your explanation of keep_ratio parameter, but it seems that images have already fix dimension due to Transform

After Transform, the image's shape can also be arbitrary, for example, suppose your image's width is bigger than height, when you set transforms.Resize(32),  then image will be rescaled to (32, 32 * width / height).
You can refer torchvision's documentation here and the code snippet here.

Thanks a lot for the explanation.


Cant install extension - Regresion

VSCode Version: 1.3
OS Version: ubuntu 14.04 LTS
Node.js Version: 6.2.2

Hi there, I can't install extension in VSCode 1.3 I just updated my editor to 1.3 and want to install a theme
ext install theme-dracula
I click the little green buttons to install the theme but nothing happens. I opened the Dev Tool and the following error appears.
shell.ts:416 Cannot read property 'call' of undefined: TypeError: Cannot read property 'call' of undefined,    at e.onCommonRequest (/opt/VSCode-linux-x64/resources/app/out/vs/code/node/sharedProcessMain.js:6:20045),    at e.onMessage (/opt/VSCode-linux-x64/resources/app/out/vs/code/node/sharedProcessMain.js:6:19889),    at /opt/VSCode-linux-x64/resources/app/out/vs/code/node/sharedProcessMain.js:6:19697,    at Socket.<anonymous> (/opt/VSCode-linux-x64/resources/app/out/vs/code/node/sharedProcessMain.js:6:23456),    at emitOne (events.js:90:13),    at Socket.emit (events.js:182:7),    at readableAddChunk (_stream_readable.js:153:18),    at Socket.Readable.push (_stream_readable.js:111:10),    at Pipe.onread (net.js:531:20)

Hope this can help!

dup of https://github.com/Microsoft/vscode/issues/8859


Add cachebuster to Pages

Add a page in the admin of b1 app and add a link that points to it.
Go to the public site and view the page.
Go to admin and edit the page
View the page again

On step 4, the changes you made will not show up.  It's loading a .html file from S3 and that file is cached.  I think we just need a cachebuster query param with the last modified date like page123.html?ts=20210927225347.

You are genius!


Improve make develop and update dev deps

@flands I also updated the read me to mention code based config options and merged all config options in a single table. LMK if you think we shouldn't do that.