ERROR Unable to load DLL 'Microsoft.Data.SqlClient.SNI.dll' or one of its dependencies: Access is denied.

Describe the bug
ERROR Unable to load DLL 'Microsoft.Data.SqlClient.SNI.dll' or one of its dependencies: Access is denied.
Exceptions (if any)
'Benchmark.Entities.UserManagement.UserManagementDataContext'.
System.DllNotFoundException: Unable to load DLL 'Microsoft.Data.SqlClient.SNI.dll' or one of its dependencies: Access is denied. (0x80070005 (E_ACCESSDENIED))
at Microsoft.Data.SqlClient.SNINativeMethodWrapper.UnmanagedIsTokenRestricted(IntPtr token, Boolean& isRestricted)
at Microsoft.Data.Win32NativeMethods.IsTokenRestrictedWrapper(IntPtr token)
at Microsoft.Data.ProviderBase.DbConnectionPoolIdentity.GetCurrentNative()
at Microsoft.Data.ProviderBase.DbConnectionPoolIdentity.GetCurrent()
at Microsoft.Data.ProviderBase.DbConnectionPoolGroup.GetConnectionPool(DbConnectionFactory connectionFactory)
at Microsoft.Data.ProviderBase.DbConnectionFactory.GetConnectionPool(DbConnection owningObject, DbConnectionPoolGroup connectionPoolGroup)
at Microsoft.Data.ProviderBase.DbConnectionFactory.TryGetConnection(DbConnection owningConnection, TaskCompletionSource1 retry, DbConnectionOptions userOptions, DbConnectionInternal oldConnection, DbConnectionInternal& connection)    at Microsoft.Data.ProviderBase.DbConnectionInternal.TryOpenConnectionInternal(DbConnection outerConnection, DbConnectionFactory connectionFactory, TaskCompletionSource1 retry, DbConnectionOptions userOptions)
at Microsoft.Data.ProviderBase.DbConnectionClosed.TryOpenConnection(DbConnection outerConnection, DbConnectionFactory connectionFactory, TaskCompletionSource1 retry, DbConnectionOptions userOptions)    at Microsoft.Data.SqlClient.SqlConnection.TryOpen(TaskCompletionSource1 retry, SqlConnectionOverrides overrides)
at Microsoft.Data.SqlClient.SqlConnection.InternalOpenAsync(CancellationToken cancellationToken)
--- End of stack trace from previous location ---
at Microsoft.EntityFrameworkCore.Storage.RelationalConnection.OpenInternalAsync(Boolean errorsExpected, CancellationToken cancellationToken)
at Microsoft.EntityFrameworkCore.Storage.RelationalConnection.OpenInternalAsync(Boolean errorsExpected, CancellationToken cancellationToken)
at Microsoft.EntityFrameworkCore.Storage.RelationalConnection.OpenAsync(CancellationToken cancellationToken, Boolean errorsExpected)
at Microsoft.EntityFrameworkCore.Storage.RelationalCommand.ExecuteReaderAsync(RelationalCommandParameterObject parameterObject, CancellationToken cancellationToken)
at Microsoft.EntityFrameworkCore.Query.Internal.FromSqlQueryingEnumerable1.AsyncEnumerator.InitializeReaderAsync(DbContext _, Boolean result, CancellationToken cancellationToken)    at Microsoft.EntityFrameworkCore.SqlServer.Storage.Internal.SqlServerExecutionStrategy.ExecuteAsync[TState,TResult](TState state, Func4 operation, Func4 verifySucceeded, CancellationToken cancellationToken)    at Microsoft.EntityFrameworkCore.Query.Internal.FromSqlQueryingEnumerable1.AsyncEnumerator.MoveNextAsync()
2021-09-29 13:02:39.7237 ERROR Unable to load DLL 'Microsoft.Data.SqlClient.SNI.dll' or one of its dependencies: Access is denied.
Further technical details
.NET SDK (reflecting any global.json):
Version:   5.0.202
Commit:    db7cc87d51
Runtime Environment:
OS Name:     Windows
OS Version:  10.0.19042
OS Platform: Windows
RID:         win10-x64
Base Path:   C:\Program Files\dotnet\sdk\5.0.202\
Host (useful for support):
Version: 5.0.5
Commit:  2f740adc14
.NET SDKs installed:
1.1.14 [C:\Program Files\dotnet\sdk]
2.1.202 [C:\Program Files\dotnet\sdk]
2.1.523 [C:\Program Files\dotnet\sdk]
2.1.815 [C:\Program Files\dotnet\sdk]
2.2.110 [C:\Program Files\dotnet\sdk]
3.1.201 [C:\Program Files\dotnet\sdk]
3.1.403 [C:\Program Files\dotnet\sdk]
3.1.408 [C:\Program Files\dotnet\sdk]
5.0.201 [C:\Program Files\dotnet\sdk]
5.0.202 [C:\Program Files\dotnet\sdk]
.NET runtimes installed:
Microsoft.AspNetCore.All 2.1.15 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.All]
Microsoft.AspNetCore.All 2.1.17 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.All]
Microsoft.AspNetCore.All 2.1.23 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.All]
Microsoft.AspNetCore.All 2.1.26 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.All]
Microsoft.AspNetCore.All 2.1.27 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.All]
Microsoft.AspNetCore.All 2.2.8 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.All]
Microsoft.AspNetCore.App 2.1.15 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 2.1.17 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 2.1.23 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 2.1.26 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 2.1.27 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 2.2.8 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 3.1.9 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 3.1.13 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 3.1.14 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 5.0.4 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.AspNetCore.App 5.0.5 [C:\Program Files\dotnet\shared\Microsoft.AspNetCore.App]
Microsoft.NETCore.App 1.0.16 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 1.1.13 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 2.0.9 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 2.1.15 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 2.1.17 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 2.1.23 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 2.1.26 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 2.1.27 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 2.2.8 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 3.1.9 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 3.1.13 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 3.1.14 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 5.0.4 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.NETCore.App 5.0.5 [C:\Program Files\dotnet\shared\Microsoft.NETCore.App]
Microsoft.WindowsDesktop.App 3.1.9 [C:\Program Files\dotnet\shared\Microsoft.WindowsDesktop.App]
Microsoft.WindowsDesktop.App 3.1.13 [C:\Program Files\dotnet\shared\Microsoft.WindowsDesktop.App]
Microsoft.WindowsDesktop.App 3.1.14 [C:\Program Files\dotnet\shared\Microsoft.WindowsDesktop.App]
Microsoft.WindowsDesktop.App 5.0.4 [C:\Program Files\dotnet\shared\Microsoft.WindowsDesktop.App]
Microsoft.WindowsDesktop.App 5.0.5 [C:\Program Files\dotnet\shared\Microsoft.WindowsDesktop.App]

Moved to SqlClient.
@ravindragaikwad Please look at existing issues, including closed ones, in this repo for possible solutions. This kind of issue has been discussed a lot before.

@ravindragaikwad this looks more like security issue, but can you tell us what version of Microsoft.Data.SqlClient is being used?

@ravindragaikwad this looks more like security issue, but can you tell us what version of Microsoft.Data.SqlClient is being used?

Hi, its 3.0.1
One thing I would like to point out that I get this error on one of the environments where we have load balancer handling requests. There are 2 IIS servers being used which point to the single shared location on file share. If I use local virtual directories on both the IIS servers this error goes away. But I really want to use a shared location across all IIS servers in the load balancer. Is there any specific step that I need to follow in this case?

@ravindragaikwad from what I know unlike classic ASP.NET, ASP.NET Core applications hosted in IIS run in-place and lock the files that they are running from which means while the app is running the files are locked and you wont be able to access or replace them which, if I understood correctly from your explanation, one server which holds the lock works fine but the other who tries to get access the file fails to do so. This is not Microsoft.Data.SqlClient related/specific issue. I believe if you try to access any other dll or file through IIS from those folders you will get the same exception. IMHO the best solution is to use local virtual directories.

@ravindragaikwad unfortunately I have not found any solid documentation. I know this from different conversations and also I followed some issues at aspnetcore GitHub page. You can open an issue and ask them to clarify this for you or provide a workaround.

Closing this issue as it is external and not related to this driver.


Decomission PoolActionsAddV2.vue

My current understanding is that we're no longer supporting add liquidity for V2 pools, only v2.1 pools.
Component PoolActionsAddV2.vue therefore may be superfluous, please confirm. If so, delete entirely.

done


Invariant Violation: Element type is invalid: expected a string (for built-in components) or a class/function (for composite components) but got: undefined.

I have been through most progressive image loaders, I find this one the most convenient. However, I am finding it difficult to use. What am I doing wrong?
Invariant Violation: Element type is invalid: expected a string (for built-in components) or a class/function (for composite components) but got: undefined. You likely forgot to export your component from the file it's defined in. Check the render method of `Cover`.

import React from 'react'
import ProgressiveImage from 'react-progressive-image-loading';

const Cover = (props) => {
	const CoverStyle = {
		height: "70vh",
		backgroundSize: 'cover',
		backgroundPosition: 'center center'
	}

	return (
		<ProgressiveImage
			preview={props.img_compressed}
			src={props.img}
			render={(src, style) => <img src={src} style={CoverStyle} />}
		/>
	)
};

export default Cover

@exogenesys It seems to be the import that isn't correct. Can you try the following:
import {ProgressiveImage} from 'react-progressive-image-loading';


[op] add back support for scalar type rescale_grad argument for adamw_update/mp_adamw_update

Description
#14171 broke backward compatibility that rescale_grad no longer supports scalar values. This PR adds it back. @szha
Checklist
Essentials
Please feel free to remove inapplicable items for your PR.

[ ] The PR title starts with [MXNET-$JIRA_ID], where $JIRA_ID refers to the relevant JIRA issue created (except PRs with tiny changes)
[x] Changes are complete (i.e. I finished coding on this PR)
[x] All changes have test coverage:
Unit tests are added for small changes to verify correctness (e.g. adding a new operator)
Nightly tests are added for complicated/long-running ones (e.g. changing distributed kvstore)
Build tests will be added for build configuration changes (e.g. adding a new build option with NCCL)
[x] Code is well-documented:
For user-facing API changes, API doc string has been updated.
For new C++ functions in header files, their functionalities and arguments are documented.
For new examples, README.md is added to explain the what the example does, the source of the dataset, expected performance on test set and reference to the original paper if applicable
Check the API doc at http://mxnet-ci-doc.s3-accelerate.dualstack.amazonaws.com/PR-$PR_ID/$BUILD_ID/index.html
[ ] To the my best knowledge, examples are either not affected by this change, or have been fixed to be compatible with this change

Changes

[ ] Feature1, tests, (and when applicable, API doc)
[ ] Feature2, tests, (and when applicable, API doc)

Comments

If this change is a backward incompatible change, why must this change be made.
Interesting edge cases to note here

@mxnet-label-bot add[Operator]


Compatibility issue with babel-runtime generators

Hello,
I'm trying to use a module compiled with babel, which uses generators, from a typescript project.
When trying to import the module, I can see this error in my console:
Uncaught TypeError: Cannot read property 'mark' of undefined
    at vendor.js:22936
    at Number.<anonymous> (vendor.js:23007)
    at c (vendor.js:30809)
    at w.require (vendor.js:30809)
    at Number.<anonymous> (vendor.js:22676)
    at c (vendor.js:30809)
    at w.require (vendor.js:30809)
    at Number.<anonymous> (vendor.js:22210)
    at c (vendor.js:30809)
    at w.require (vendor.js:30809)

Looking at the code:

The original code is the following:
import _regeneratorRuntime from 'babel-runtime/regenerator';

var map = function () {
  var _ref = _asyncToGenerator(_regeneratorRuntime.mark(function _callee2(frames) {
    var _this = this;

     ...

So I can see that fusebox adds a .default after the _regeneratorRuntime.
Is it expected behavior and is there a workaround for this ?
Thanks!
Repro here

There is nothing wrong with it, it's being transpiled by typescript according to the specs. This library doesn't conform to js standards and uses default ( import a from "b" ) where module doesn't export a default module

There is a solution, you should you use that perverted babel plugin to transform this package.
["node_modules/heresy/**", BabelPlugin()]

Thank you for your quick response!
Sorry but I might have not understood the solution.
I tried it without success...

I commented;-)

I tired:
--- fuse.ts	(revision 4812c7e0fb9bd10e5d9ed38af7cc881d524ee763)
+++ fuse.ts	(revision )
@@ -8,13 +8,14 @@
     SVGPlugin(),
     CSSPlugin(),
     WebIndexPlugin({template: './src/index.html'}),
-    ["node_modules/react-error-overlay/**", BabelPlugin({
+    [/react-error-overlay.*\.js/, BabelPlugin({
       config: {
         sourceMaps: true,
         presets: ["react-app"]
       },
     })] as Plugin
-  ]
+  ],
+  debug: true
 });

 fuse.dev();

And I can see the debug output:
16:05:46: BabelPluginClass : Captured lib/index.js
16:05:46: BabelPlugin :
        Configuration: {"sourceMaps":true,"presets":["react-app"]}
16:05:47: BabelPluginClass : Captured lib/overlay.js
16:05:47: BabelPluginClass : Captured lib/effects/unhandledError.js
...

Which indicates that the plugins picks up the files... But still the same error ! 😕

Are you sure that this plugin adds requireExportsInterop?

Ah ok I finally understood what you were getting at.
Unfortunately, the lib I'm trying to use does not provide original (unbabeled) source code so I'm not sure this approach will work.

Then it's your who does something wrong :)
Import * as blabla from

@geowarin I believe 2.2.3-beta.10 solves everything.
useJsNext: ["react", "react-dom"],
polyfillNonStandardDefaultUsage : true,

^^ Add conflicting libraries to useJsNext i tested it myself, works like a charm.

Awesome!
I made it work: diff.
let fuse = new FuseBox({
  useJsNext: ["babel-runtime"],
  polyfillNonStandardDefaultUsage : true,
});

Thank you for taking the time to understand and provide an elegant way of dealing with this issue :heart: .


PRO-2338

Smaller PR today:

Reset expectations some more in the docs.
Moved the automatic inlining of certain require files to an --upgrade-required-files command line option, which will be documented as probably too pre-alpha for most users, at least for now.
Fixed a crash when the upgrader auto-renames a piece module.
The linter can now flag module names ending in -widgets, spot lib/modules, and detect project level folders for legacy core modules which need to be renamed.
The linter engine now supports custom functions for both matching and output purposes.

I think you said there is still one text duplication issue somehow but I can't find it?

(Line numbers have changed)

@boutell It's the other "our A2 example projects"


Extract selected date,month and year to text views

Please help!!!!

A little late, but for future notice:

Set up decorators like in instructions
In decorate override, you have dayView which has getDate() method, which returns date.
Since you cant get day month and year from date directly, you should cast date to calendar:
Calendar calendar =Calendar.getInstance();
calendar.setTime(dayView.getDate());

And from there you can extract day year etc.
Hope it helps someone else stuck here.


Video on Aeon.Co - Cannot Download Its Vimeo Embed

Checklist

[X] I'm reporting a broken site
[X] I've verified that I'm running yt-dlp version 2<IP_ADDRESS>. (update instructions)
[X] I've checked that all provided URLs are alive and playable in a browser
[X] I've checked that all URLs and arguments with special characters are properly quoted or escaped
[X] I've searched the bugtracker for similar issues including closed ones. DO NOT post duplicates
[X] I've read the guidelines for opening an issue
[X] I've read about sharing account credentials and I'm willing to share it if required

Region
United States of America
Description
Aeon uses Vimeo and YouTube embeds.  However, it cannot recognize the Vimeo embed in the page; the page itself does not have a Vimeo link accessible from the player; and digging into the code for the Vimeo player.vimeo.com link fails, as it errors out with:
[vimeo] 639714423: Cannot download embed-only video without embedding URL. Please call yt-dlp with the URL of the page that embeds this video.
Verbose log
[debug] Command-line config: ['-Uv', 'https://aeon.co/videos/a-unique-theatre-performance-explores-what-touch-means-in-an-age-of-lockdown']
[debug] Portable config file: C:\Users\[NAME OMITTED]\bin\EXE\yt-dlp.conf
[debug] Portable config: ['-f', 'mp4', '-o', 'C:\\Users\\[SHORT NAME OMITTED]\\Desktop\\%(duration>%H-%M-%S)s %(title)s.%(ext)s', '--sponsorblock-remove', 'all']
[debug] Encodings: locale cp1252, fs utf-8, out utf-8, err utf-8, pref cp1252
[debug] yt-dlp version 2<IP_ADDRESS> (win_exe)
[debug] Python version 3.8.10 (CPython 64bit) - Windows-10-10.0.19043-SP0
[debug] exe versions: ffmpeg n4.4.1-2-gcc33e73618-20211107 (setts), ffprobe n4.4.1-2-gcc33e73618-20211107
[debug] Optional libraries: Cryptodome, mutagen, sqlite, websockets
[debug] Proxy map: {}
yt-dlp is up to date (2<IP_ADDRESS>)
[debug] [generic] Extracting URL: https://aeon.co/videos/a-unique-theatre-performance-explores-what-touch-means-in-an-age-of-lockdown
[generic] a-unique-theatre-performance-explores-what-touch-means-in-an-age-of-lockdown: Requesting header
WARNING: [generic] Falling back on generic information extractor.
[generic] a-unique-theatre-performance-explores-what-touch-means-in-an-age-of-lockdown: Downloading webpage
[generic] a-unique-theatre-performance-explores-what-touch-means-in-an-age-of-lockdown: Extracting information
[debug] Looking for video embeds
[debug] Identified a JSON LD
[SponsorBlock] SponsorBlock is not supported for Generic
ERROR: [generic] a-unique-theatre-performance-explores-what-touch-means-in-an-age-of-lockdown: Requested format is not available
Traceback (most recent call last):
  File "yt_dlp\YoutubeDL.py", line 1311, in wrapper
  File "yt_dlp\YoutubeDL.py", line 1349, in __extract_info
  File "yt_dlp\YoutubeDL.py", line 1399, in process_ie_result
  File "yt_dlp\YoutubeDL.py", line 2414, in process_video_result
yt_dlp.utils.ExtractorError: [generic] a-unique-theatre-performance-explores-what-touch-means-in-an-age-of-lockdown: Requested format is not available

There is no actual embed in the page. Support for this site will need to be specifically added

digging into the code for the Vimeo player.vimeo.com link fails, as it errors out with:

[vimeo] 639714423: Cannot download embed-only video without embedding URL. Please call yt-dlp with the URL of the page that embeds this video.

For this, you can pass --referer
➤ yt-dlp "https://player.vimeo.com/video/639714423" --referer "https://aeon.co/videos/a-unique-theatre-performance-explores-what-touch-means-in-an-age-of-lockdown"
[vimeo] 639714423: Downloading webpage
[vimeo] 639714423: Downloading akfire_interconnect_quic m3u8 information
WARNING: [vimeo] Ignoring subtitle tracks found in the HLS manifest; if any subtitle tracks are missing, please report this issue on  https://github.com/yt-dlp/yt-dlp . Make sure you are using the latest version; see  https://github.com/yt-dlp/yt-dlp  on how to update. Be sure to call yt-dlp with the --verbose flag and include its complete output.
[vimeo] 639714423: Downloading akfire_interconnect_quic m3u8 information
[vimeo] 639714423: Downloading fastly_skyfire m3u8 information
[vimeo] 639714423: Downloading fastly_skyfire m3u8 information
[vimeo] 639714423: Downloading akfire_interconnect_quic MPD information
[vimeo] 639714423: Downloading akfire_interconnect_quic MPD information
[vimeo] 639714423: Downloading fastly_skyfire MPD information
[vimeo] 639714423: Downloading fastly_skyfire MPD information
[info] 639714423: Downloading 1 format(s): dash-fastly_skyfire-video-ba4204b6
[dashsegments] Total fragments: 189
[download] Destination: Skin Hunger [639714423].mp4

ERROR: Interrupted by user

In a weird moment of serendipity, I worked on this a little bit last night, and managed to download it via referrer -- although what I found was that the downloaded video did not seem to play correctly.  It seemed to have frozen images, then catch up.  I don't know for sure that's the fault of anything -- I don't believe it was related to my machine or hardware -- but just passing that along in the 'for what it's worth' department.

did your download have skipped fragments?

I do not remember seeing any in the report, no.  I will try again this
evening and pay closer attention to that request.
On Mon, Nov 22, 2021 at 12:39 PM pukkandan @.***> wrote:

did your download have skipped fragments?
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https://github.com/yt-dlp/yt-dlp/issues/1653#issuecomment-975812435, or
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It is unlikely to be yt-dlp's issue. But if you encounter it again with no skipped fragments and can check that this does not happen in browser, feel free to open a new bug report for it (with verbose log)


attempt to index a nil value (upvalue 'PlayerJob') on QBCore Framework

It appears that you've made modifications to the code within your script. However, there seems to be an issue in your changes, as the problem is not present in the original code's line 109.

Could you kindly undo the alterations you've made and give it another attempt? If the problem continues to persist, I would appreciate it if you could provide a screenshot of the updated error message, including the updated line number, so that we can understand the issue.


wide and deep code written fully in tensorflow 2.1 throws tensorflow 1 and 2 incompatability error

Hi,
I am writing a code in tensorflow 2.1 with feature_columns but it is giving me errors:
This is the code snippet:
I am keeping the data in pandas dataframe: df
I am defining the feature columns similar to the code snippet below, containing crossed features, categorical features, numerical features:
cat_f1=tf.feature_column.categorical_column_with_vocabulary_list('cat_col_name_1' , df['cat_col_name_1'].unique())
...
num_fn  = tf.feature_column.numeric_column("num_col_name_n")
wide_columns = {cat_f1.key: cat_f1,
...
}
deep_columns = {
...
num_fn.key: num_fn,
}
output_feature = ['label']
And this is how I am defining my input_fn:
def input_fn(df,inner_batch_size=-1,shuffle=False):
input_features=[]
for key ,_ in wide_columns.items():
input_features.append(key)
for key, _ in deep_columns.items():
if '-crossed' in key:
k = key.replace('-crossed','')
keys=[]
keys = k.split('-')
for k in keys:
input_features.append(k)
else:
input_features.append(key)
dataset=tf.data.Dataset.from_tensor_slices((dict(df[input_features]) , df[output_feature].values))
if shuffle ==True:
dataset = dataset.shuffle(100).repeat()
if inner_batch_size>0:
dataset = dataset.batch(inner_batch_size)
return dataset
And the definition of estimator:
model_dir = tempfile.mkdtemp()
optimizer = tf.keras.optimizers.RMSprop(learning_rate=0.001)
estimator = tf.estimator.DNNLinearCombinedClassifier(model_dir = model_dir,
linear_feature_columns = wide_columns ,
dnn_feature_columns=deep_columns,
dnn_hidden_units = [100,50],
dnn_optimizer = optimizer)
and after data preparation, calling the train:
estimator.train(input_fn = lambda: input_fn(train_batch_data,inner_batch_size,shuffle=True) ,steps=10)
metrics = estimator.evaluate(input_fn = lambda: input_fn(val_batch_data,shuffle=False)  , steps = 5)
for key in sorted(metrics):
print ("%s: %s" % (key, results[key]))
This throws the error:
Received a feature column from TensorFlow v1, but this is a TensorFlow v2 Estimator. Please either use v2 feature columns (accessible via tf.feature_column.* in TF 2.x) with this Estimator, or switch to a v1 Estimator for use with v1 feature columns (accessible via tf.compat.v1.estimator.* and tf.compat.v1.feature_column.*, respectively.
What is the problem?

@shnamin
Can you please share the simple standalone code with proper indentation and supporting files or colab link to reproduce the issue in our environment. It helps us in localizing the issue faster. Thanks!

I figured out what the problem was. TF2 requires deep and wide features to be passed as lists, which is a difference between TF2.1 and TF1.X. By passing the list, the error disappears.
There are no examples in TF2.X for wide and deep, and the examples that I found online are for TF1.X and refer to broken links. This causes confusion, I suggest writing a notebook/example for wide and deep in TF2.1 as it is still a popular approach.
Thanks @ravikyram for the great support anyway.

I was passing a dict to them, as is shown in the example.

@shnamin
Glad to know you found the solution. Please, see the link if it helps you. Please,let me know if we can close this issue since it looks to be fixed. Thanks!


Can you please add our VA liveries to the database?

Hi . Love your work and thanks for the effort.
We have a long lived VA Compass Virtual Airlines. I have some liveries for the CSL files. Is it possible to have them included in the next update for the files please? I have included one for the A388 for you.
Best regards
Robert
A388_YMA.dds.zip

Excellent thank you. Ill send them through over a period of time as I need to complete them. I wasn’t sure if you would accept them  ☺  Thanks very much for your help.!
Robert
From: oktal3700 @.>
Reply to: oktal3700/bluebell @.>
Date: Friday, 22 October 2021 at 03:53
To: oktal3700/bluebell @.>
Cc: SonofPicasso @.>, Author @.***>
Subject: Re: [oktal3700/bluebell] Can you please add our VA liveries to the database? (Issue #50)
Yes of course. Send the rest and they will be in the next update.
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Mat good morning.
Question for the texture sizes.
Do they have to be 1024x1024 or will you accept 2048x2048? The higher resolution gives a better look for the AI.
Regards
Robert
From: Robert Grant @.>
Date: Thursday, 28 October 2021 at 08:10
To: oktal3700/bluebell @.>
Subject: Re: [oktal3700/bluebell] Can you please add our VA liveries to the database? (Issue #50)
Thanks for the info and your patience.
Robert
From: oktal3700 @.>
Reply to: oktal3700/bluebell @.>
Date: Thursday, 28 October 2021 at 02:24
To: oktal3700/bluebell @.>
Cc: SonofPicasso @.>, Author @.***>
Subject: Re: [oktal3700/bluebell] Can you please add our VA liveries to the database? (Issue #50)
Hi Robert
Email attachments won't work. You have to go to the GitHub issue page #50 and attach the files to a comment there.
Mat
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They can be any resolution supported by X-Plane, thanks for asking.

And yes, leave the issue open for the extra aircraft, thanks.

Hello again
Attached the first tranche of our VA aircraft. Ive done it up as BB_Compass_VA with all required files to just drop in the Bluebell parent folder. Hope this is OK.
more to come as I complete them
Robert
BB_Compass_VA.zip

did it agin ..ggrrrr silly me

A306_Cargo.dds.zip
Hello again. Could you please replace the dds file in BB_Compass_VA/Airbus/A306/A306_Cargo.dds with the file in the zip file? We have made a couple of adjustments. Thanks again for you great work.

Hi Mat. Another updated dds file for the B738 for BB_Compass_VA please
B738_Sharkfin.dds.zip

All done. Please open a new issue if you have any more updates.


Cannot be deleted the application which created with name having special characters

Description:
As $subject when click on delete icon of an application which has been created with name appended some special characters, an API store error pops up. See attached.
Suggested Labels:
APIM2.2.0
Type/bug
Priority/normal
Sevirity/critical
Affected Product Version:
2.1.0-update5
OS, DB, other environment details and versions:
Steps to reproduce:

Add app with name like (e.g. TomsApp${counterValue})

List and delete the above app

Click on OK won't get delete the app
Note that there were no carbon log for this issue.

API Manager does not allow application names with special characters. Adding such application names was already restricted through UI but it was still possible to add such applications through Store REST API. This issue is now fixed with [1].
The problem reported here is due to application name validation that occurs while removing application; to be more precise an application name that was not validated during creation is being validated at deletion.
[1]. https://github.com/wso2/carbon-apimgt/pull/5046

Closing as this is fixed.


famous-angular breaks angular-breadcrumb

Hi there - first of all thanks for the great tool! :+1:
But - there seems to be a conflict with famous-angular.. when both are used angular-breadcrumb stops working.. i can't really figure out why, but i created a plnkr to demonstrate..
the error occurs, after navigating to the second view.. and then consistently.. i have no idea why ;)
maybe you have an idea ?
http://plnkr.co/edit/wClm2JUizgtSTpkgawvt
i'd be glad for any feedback!

Hi, sorry for the one-year delay :hushed: .
Is the problem still here ? I know nothing about famous-angular, is it still in use ? (the README.md starts with "This integration library is no longer supported by Famo.us"...
The plunker is no longer working.
I close this issue and the associated PR. Feel free to reopen you still need a fix.


On rebuilds: WARNING: Color theme None not found by pygments

Heya, just tried updating myst-parser to sphinx-book-theme==1.0.0rc2,
but now on rebuilds I get 😢 :
WARNING: Color theme None not found by pygments, falling back to tango.
WARNING: Color theme None not found by pygments, falling back to monokai.

Not very informative, but managed to hunt down the warning to:
https://github.com/pydata/pydata-sphinx-theme/blame/0c0d6ca130953ac92ce454ea2d11167d7373e76d/src/pydata_sphinx_theme/__init__.py#L911
I'll leave you guys to deal with upstreaming the problem,
I would also suggest that the warning be changed, to indicate that it's from pydata-sphinx-theme, and even give it a type/subtype to suppress

cc @choldgraf

Good on the whole though cheers 👌

Note, I think it only happens on rebuilds where nothing changes:
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 0 source files that are out of date
updating environment: 0 added, 0 changed, 0 removed
looking for now-outdated files... none found
no targets are out of date.
Writing redirects...
WARNING: Color theme None not found by pygments, falling back to tango.
WARNING: Color theme None not found by pygments, falling back to monokai.
build finished with problems, 2 warnings.

Interesting - I wonder if the pygments themes aren't being added to the build because they are depending on a sphinx event that sometimes does not trigger or something 🤔

@trallard do you have any idea why we would be seeing this error in the book theme?

Not sure - but I can look into this tomorrow.

@trallard did you get a chance to look into this? has it been reported in any other projects that use these pygments stylings?

Yeh not critical, but it is reproducible

Myst-parser is using rc2 at the moment btw: https://myst-parser.readthedocs.io/ 😄

On the pydata theme I wasn't able to reproduce this (ie, by building the docs once, then re-building them immediately, though I did find this bug https://github.com/pydata/pydata-sphinx-theme/issues/1222). I was able to reproduce it on the sphinx-book-theme. So for some reason something different is happening in this theme than in the pydata theme.

Ok so did some hunting and this was reported in https://github.com/pydata/pydata-sphinx-theme/issues/1081
Which resolved by adding accessible-pygments as a full dependency to the theme.

I have the same problem on a simple sphinx-build using pydata-sphinx-theme, but I checked and in my environment I have accessible-pygments...
any news on this? it seems to be also erratic: 5' ago I didn't see it and now it popped out again!

I think this should be fixed now by pydata/pydata-sphinx-theme#1264. Hopefully now nobody ever sees that warning unless they actually request a pygments theme that doesn't exist.


Create CONTRIBUTING.md

@all-contributors please add @ahmetcadirci25  for music

@all-contributors please add @ahmetcadirci25  for code

@all-contributors please add @ahmetcadirci25 for code

@all-contributors please add @ahmetcadirci25 for code

@all-contributors please add @ahmetcadirci25 for code


It doesn't work(on my LinuxMint distro).

System:

4.13.0-37-generic GNU/Linux
Distributor ID: LinuxMint
Release:        18.3
Codename:       sylvia

VSCODE:

Version 1.21.1
Commit 79b44aa704ce542d8ca4a3cc44cfca566e7720f1
Data 2018-03-14T14:46:30.761Z
Shell 1.7.9
Renderer 58.0.3029.110
Nodo 7.9.0
x64

Installed and removed more times, nothing to do, it doesn't work!

@cydside Could you please try again with the latest version (>=11.0.6)?

I can confirm this running on Ubuntu 18.04.

I'm sorry for the late. Updated to 11.0.6, VSCode Version 1.24.1 and it's not working.

Yes.  I just discovered my last comment was ambiguous.  I can confirm the bug ;-)

Thanks for your effort, it's a really useful software. I'm using the online version in the meantime.

This seems to be a clipboard issue.  I'm on it.

Fixed in #9


Create OEMol objects from extended OpenMM topology of #18

We'll need to create OEMol objects from components of an OpenMM Topology as discussed in #18 . Assuming these topologies contain connectivity, element, bond order, and formal charge, this should be possible to do using the basic OEChem primer ingredients such as atom creation, bond creation, assignment of formal charges and so on.
I will raise an issue with OpenEye support to see if it can be done without formal charge provided all of the atoms are explicit.

Regarding the formal charge, we can use OEAssignFormalCharges ( http://docs.eyesopen.com/toolkits/python/oechemtk/OEChemFunctions/OEAssignFormalCharges.html ) with this additional info:

"Sets the formal charge property of an atom, based upon a simplistic valence model. This function assumes that the bond orders and implicit hydrogen counts have been set on a molecule. For example, this function will place a single positive charge on a neutral four-valent nitrogen. Note that this function only modifies neutral atoms, with zero formal charge. This preserves any formal charges previously assigned, but requires the charge to be reset to zero in order to force a reassignment."

There are more details on the valence model here:
https://docs.eyesopen.com/toolkits/python/oechemtk/valence.html#openeye-valence-models


Makefile target for rebar3 shell

The rebar3 shell was no longer working.
I created a special config file sys-debug.config for use with the shell. It is similar to the sys.config used for releases, but does not use environment variables. I also had to add the schema_dirs configuration for riak_core to make it work.
Besides the make shell target, I also added a make auto target for a shell which automatically compiles and reloads the code when it is changed on disk (see https://github.com/vans163/rebar3_auto).

Got two errors when trying on other machines:
1.
 ===> Failed to boot riak_core for reason {bad_return,
                                                     {{riak_core_app,start,
                                                       [normal,[]]},
                                                      {'EXIT',
                                                       {{function_clause,
                                                         [{orddict,fetch,
<EMAIL_ADDRESS>                                                            [{nonode@nohost,
                                                              [{{riak_core,
                                                                 bucket_types},
                                                                [true,false]},

Deleting the data* folders from the antidote directory fixed that problem.
2.

Erlang Distribution failed, falling back to nonode@nohost. Verify that epmd is running and try again.

Running epmd & before make shell fixed this.

I am not sure if there is a nice way to handle these problems in the Makefile.

:+1:, thanks @peterzeller


CAMEL-21107 - Camel-Kubernetes: Add ability to add annotation to crea…

…te resources operation - Namespaces
Description

Target

[x] I checked that the commit is targeting the correct branch (note that Camel 3 uses camel-3.x, whereas Camel 4 uses the main branch)

Tracking

[x] If this is a large change, bug fix, or code improvement, I checked there is a JIRA issue filed for the change (usually before you start working on it).

Apache Camel coding standards and style

[x] I checked that each commit in the pull request has a meaningful subject line and body.

[x] I have run mvn clean install -DskipTests locally from root folder and I have committed all auto-generated changes.

/component-tests kubernetes


Add more granular tests for CI

This adds a test directory with a few different cases that test different modes of 3DThesis.
This is a draft PR until the following are complete:

[ ] CI actually uses the tests (I don't know the best way to implement a test suite for C++)

We use googletest in a lot of cases; I know some projects that use boost. Let me know if you want me to add a test harness

Examples are moved and the readme is updated. Due to removing TestInputs, I also removed the default behavior for 3DThesis run without command line arguments. It will now just throw an error that it can't read the input file (Jamie gave the okay on that).


Font flash in Firefox in dev mode

Since updating from v5 to v6 we have noticed that adding or removing a global style will cause the fonts to flash, but only in Firefox and only in dev mode. You can see in the screen recording below that when the contents of the <style> tag are modified the web font gets requested again.
Is this a known issue? I can see some historical issues relating to font flash but not v6 related. Should we avoid changing global styles on React state changes?
Here's a simple reproduction:
https://github.com/keeganstreet/sc6-ff-font-flash/blob/main/src/App.js
https://github.com/styled-components/styled-components/assets/513363/d946fc29-eb70-42fa-98ab-a3b84d70f211

Hi @keeganstreet,
I encountered a similar issue with the font-face in globalStyles.
To address this, I moved all my font-face declarations to index.css, which successfully resolved the problem.


[BUG] Unreliable page routing for documentation website

Describe the bug
There is some funny routing going on for the documentation website which sometimes causes the page to be not found.
To Reproduce
Steps to reproduce the behavior:

Visit the homepage of the repo - https://github.com/AmruthPillai/Reactive-Resume
Scroll down to"Build from Source" section, click on Source Code hyperlink
Click on either "Docker" or "Local Build"
See Page Not Found error

Expected behavior
The page should load.
Desktop (please complete the following information):

OS: Windows 10
Browser: Firefox 98.0 (64-bit)
Version: 98.0 (64-bit)

Additional context
I noticed that the URL when getting referred from GitHub's README is "https://docs.rxresu.me/source-code". However, if you just add "/" at the end of the URL ("https://docs.rxresu.me/source-code/"), then the "Docker" and "Local Build" hyperlinks are updated properly.
TL:DR; "https://docs.rxresu.me/source-code" and "https://docs.rxresu.me/source-code/" are rendering different HTML content.

Thank you for raising this issue and bringing this to light, this has been fixed now :)


Not working :/

This looks like a fantastic little module but I can't seem to get it working.  I'm using Browserify normally as my bundler (not webpack for local dev) with ES6 React components.  Here is my config:
module.exports = {
    title: 'SpotHero React Components',
    rootDir: './',
    components: 'frontend/src/js/components/**/*.jsx',
    styleguideDir: './spothero/static/main/uniform/docs-react'
};

If I run the build script and nothing else, the resulting HTML page shows this error:
Error: HtmlWebpackPlugin: Unable to read HTML template "./src/templates/index.html"

If I try to run the server for local dev I just get:
Cannot GET /

When I look at my Terminal window I see this:
[185] ./~/react-styleguidist/~/css-loader?modules&importLoaders=1&localIdentName=[name]__[local]___[hash:base64:5]!./~/react-styleguidist/~/postcss-loader!./~/react-styleguidist/~/sanitize.css/dist/sanitize.css 2.17 kB {0} [built]
  [186] ./~/react-styleguidist/~/style-loader/addStyles.js 6.09 kB {0} [built]
  [187] ./~/react-styleguidist/src/styles.css 1.25 kB {0} [built]

ERROR in ./frontend/src/js/components/breadcrumbs/Breadcrumbs.jsx
Module parse failed: /Users/mprzybylski/Work/SpotHero/SpotHero-Django/frontend/src/js/components/breadcrumbs/Breadcrumbs.jsx Line 1: Unexpected token
You may need an appropriate loader to handle this file type.
| import React, {Component, PropTypes} from 'react';
|
| class Breadcrumbs extends Component {
 @ ./~/react-styleguidist/loaders/styleguide.loader.js! 3:139-253

Over and over for all my components that its trying to parse.
Any ideas what I'm doing wrong?  Really appreciate any help you could offer.

Sure, I forget to add .jsx extension.

I'm not familiar with Webpack but is this something I should do myself extending the config or needs to be added to the project by you?

You can do something like this but I’ll add .jsx support soon.


Disable new version check

I vote for this.  I already have SickRage set to autoupdate.
I don't want to see an update notification everytime I open ShowsRage.

Yes, I understand the need for this feature.
I don't know if I'll manage to include it the next version, but it will definitely make it in the following one in the worst case.

Cool. As long as it's in the pipeline.
I can be patient.

I just implemented this.
It will be available in version 1.3 (version 1.2 is being deployed to test users and will be available in a couple of days).


Acceptance Testing Tour causes second test to fail

I am trying to test my ember-shepherd tour using an acceptance test. The first test I have is the "happy path" i.e. it tests that the tour works from start to finish if all expected things happen (user clicks on the correct buttons, API responds successfully etc.).  The second test is designed to verify that the tour ends if there is an API error during the tour.  I use the waitFor() ember test-helper function to make the test waits for the first tooltip in the tour to appear.
Individually the tests pass but, when run together, whichever test runs second fails. The waitFor() times out waiting for the tour to start.
When running the tests in the browser I use pauseTest() to pause at the start of the test.  When I do this for the failing test I see that:

the tour starts,
the modal overlay is rendered (as I'm running the tour in modal mode)
but the initial tool tip is never displayed.

Has anyone seen tests on the ember-shepherd tour interfere with one another? Is there something I should be resetting between tests?
Thanks.

@BitBrit are you doing anything differently than we do in our internal tests? https://github.com/shipshapecode/ember-shepherd/blob/master/tests/acceptance/ember-shepherd-test.js

Depending on how granular I go, yes.
Here are a few things I notice:

I don't start the tour in my test, I visit a route which starts the tour.
I don't call tour.complete() after each test. The idea here is that the test completes itself via successful completion of the tour, cancelling, or correct handling of errors.
Side Note: Line 25 awaits a promise but https://github.com/shipshapecode/ember-shepherd/blob/9058708218169cc3a27f5cfa63a1d304caa540cf/addon/services/tour.js#L291 does not seem to return promise. This is the same for Line 9 in the test when tour.start() is called.
My test had a few more steps in it than yours. Not that that should matter as everything is torn down and reestablished for each test, right?

Other than that, our tests look similar. My tests and yours both visit a url (the same URL) and then run assertions on what happens.

@BitBrit without seeing and being able to debug the tests, I am afraid I cannot be much help. I would recommend trying to do similar await and such as we do in our tests, and to ensure the tour is completed after each test. I suspect that the test is not done tearing down when you transition routes.

Ok thanks for the response. At least your response tells me that you haven't heard of this before and so there are no obvious fixes.

@BitBrit the TL;DR here is you just have to make sure the tour is completed and totally torn down. I would do an extra tour.complete or tour.cancel etc in afterEach just to be totally sure.


Rate-limit workflow reconcilliation

Provide a knob that we can use to rate limit reconciliations - reducing CPU usage and allow other workflows to get prioritised.

Fix for this is out on https://github.com/argoproj/argo/releases/tag/v2.12.3

Fix for this is out on https://github.com/argoproj/argo/releases/tag/v2.12.3


Discovered today that GO:0004674 protein serine/threonine  kinase activity has 2 RHEAs (EC:<IP_ADDRESS>, . creating separate terms. and remove rheas from base term.

Discovered today that GO:0004674 protein serine/threonine  kinase activity has 2 RHEAs (EC:<IP_ADDRESS>, . creating separate terms. and remove rheas from base term.
+id: GO:0106310
+name: protein serine kinase activity
+[Term]
+id: GO:0106311
+name: protein threonine kinase activity
have already done same for protein serine/threonine phosphatase activity for a different ticket.
Originally posted by @hdrabkin in https://github.com/geneontology/go-ontology/issues/19152#issuecomment-696953523

I was just about to request a merge of a term that one of our users  has used (quite correctly).

I was going to request this for a number of reasons.

Short term reason, a  serine/threonine protein kinas has specificity for serine or threonine residues , depending on context. I did not ire this as 2 indemendent activities and I though that GO didn't eaither. But it seems that recently
separate terms were added for serine and threonine kinases. Do you have an exampe of a kinase that  phosphorylates only serie or only threonine.

This will make it very difficult to make consistent, and specific annotations becasue, cdc for exxampele phosphorylates seringes in some proteins, threonines in csome proteins and serine and threonines in some protiens. I ask GO to seriusly consider if we really want this specificity in the MF ontology. Muuch better would be the ability to specify the modified residue on the target protein, rather than bake the residue into the kinse term (I know that we specify functoions for teh histine modifiers right now but this seems more of  a special case because many of the modifiers are histone residue specific. Kinases are are more prolific and this would  make the curaton very challenging.

regardless of the ansewer  to 1, I still don't think we should have this specificity at the process level....

Each time a enzyme phosphorylates only one or the other not both at the same time.

Above edited for clarity.
Imagine how challenging it would be if I had to specify serine or threonine or both for all of these kinase activities. It would look  silly.....it's a single  activity.

The kinase is a serine/threonine protein kinase. I don't think we should follow the Rhea split here. Form the GO perspective a) it does not add anything biologically  b) it makes curation harder. We would want to know the specific residue (possibly as an extension?)  but just whether it is a threonine or threonine is not useful on its own.
At PomBase we  currently capture this information (modified residue)  as follows:

Capture the modification information on the modified gene product
(for example:

Bear in mind that this is the modification data for just one of the hundreds of proteins phosphorylated on serines and threonines  by cdc2. Imagine the work involved in capturing these as  a serine or threonine kinase. If we used serine kinase and threonine kinase on the gene pages  consistently  (i.e cdc2 above)

On the modified product , if the modification is connected to a particular causal relation we will request a PRO ID to represent the modification   (ideally the modified form would be represented more succinctly (cut12-T75,T78)

I urge you to merge these into a single term for serine/threonine  (whether the processes should be in GO at all is a separate issue. At PomBAse we don't really use these terms for annotation if we can make the kinase annotation as we can in this case)
Does this make sense?
@thomaspd
@pgaudet
@cmungall
@dr

Each time a enzyme phosphorylates only one or the other not both at the same time.

Yes, but the definitions could cover this? Phosphorylates a threonine or a serine?
So now we would need to make 2 annotations for all of those cdc2 substrates:
cyclin-dependent protein serine/threonine kinase activity
 phosphorylates clp1 involved in negative regulation of exit from mitosis during mitotic metaphase
would need to become
cyclin-dependent protein serine kinase activity
 phosphorylates clp1 involved in negative regulation of exit from mitosis during mitotic metaphase
AND
cyclin-dependent protein threonine kinase activity
 phosphorylates clp1 involved in negative regulation of exit from mitosis during mitotic metaphase
x 200
can we be pragmatic in this case  please... we discussed this historically and always decided that this should be a single term, so why change now?

Each time a enzyme phosphorylates only one or the other not both at the same time.

Yes, but the definitions could cover this? Phosphorylates a threonine or a serine?

Yes - I thought the GO classes were not 'instance level'. I thought those terms existed because there were examples of kinases that specifically phosphorylated Ser OR Thr. I thought a normal Ser/Thr kinase should have been annotated to GO:0004674 protein serine/threonine kinase activity.
I agree all BPs should be merged/obsoleted.
Will check with @thomaspd
Pascale

I thought those terms existed because there were examples of kinases that specifically phosphorylated Ser OR Thr.

Oh, I did not know that. Which ones are they? and how would we know? We don't know all of the physiological substrates of any kinase?

Yes it is a rule; Because we will use them for logical defs you can't have two of them per one term. Annotating to the parent is not a problem.

Can't we just not map this term to RHEA, just map to protein kinase? We don't map to CHEBI for example in situations where we need to be pragmatic about the effects on GO annotation.
Personally, I think we could capture residue specificity differently across the board if we want to do it in a scalable way, but that is a discussion for another day.

Annotating to the parent is not a problem.

This isn't a problem in that we can do it, but it is a problem in that people will not know when they should deepen.
But if we use the parent then the term we use won't have a logical definition by Rhea route.
Presumably, a logical definition can still be crafter via another route for this term. Rhea for reaction + CHEBI for substrate?

@amorgat can you help ??

'his isn't a problem in that we can do it, but it is a problem in that people will not know when they should deepen.'
Won't they know when reading the paper? If the paper talks about phosphorylating a ser residue, then that is the reaction being used.

his isn't a problem in that we can do it, but it is a problem in that people will not know when they should deepen.'
Won't they know when reading the paper? If the paper talks about phosphorylating a ser residue, then that is the reaction being used.

It just isn't practical to do this and we discussed in the past why  a serine/threonine  protein phosphatase would not be split into 2 term. I will look for the old discussion.
This is a problem if there are proteins that phosphorylate only serines or only threonines. Has anyone got an example of this?  but even so I think we could still use the serine/threonine term.

I can't find the old discussion. Too many tickets with serine/threonine... ;)

Does the ticket you seek pre-date RHEA?

Probably but the point was that from a curational and biological point of view it did not make sense to split these in GO. This fact doesn't change because we are using Rhea.  It would be an inordinate amount of work, and additional complication, for no discernable advantage to  users?

I can't find the old discussion.

could be #18460

Yes thank you @mah11 !
Case argued excellently by @deustp01  and supported by me and @srengel
and it seemed to be agreed that it wasn't necessary to follow Rhea here.

Similar situation for protein phosphatases:
So we only show IEAs if they are more specific and not covered. by EXP annotation
Here we get the individual phosphatase terms.

Sowe would require
MAP kinase serine phosphatase
and MAP kinase protein phosphatase
which would be bonkers.
My interim solution is to filter these annotations as they don't add value.

You can see the inconsistencies here already:

I note that UniProt has annotated or UniProtKB:G4NH08 GSK1, Magnaporthe oryzae to the serine RHEA based on the paper that only looked at ser 8 (The publication used to reference  the ser residue reaction for the kinase appears to have been made because the paper only looks at ser 8; They make target mutants (HAT1) but not a thr 8). I don't know how many instances there are in the UniProt set.

but that is all they tested?  (we have bazillions of examples like this).
we would annotate as a
serine/threonine-protein kinase phosphorylation  HAT1-S8
as a  substrate.

corrected above comment

Exactly that is ALL they were concerned with in the paper; they only looked at phosphorylation of ser 8 of hat by the kinase; and yes one could do input /output unphosphorylated HAT1 Ser8/phosphorylated Hat1 ser8 (PRO id names if pro had them for this species).

Just in case they are needed, I've created the following terms in PRO:

unphosphorylated HAT1 Ser8 = PR:000050462 = "histone acetyltransferase type B catalytic subunit unphosphorylated 1 (rice blastfungus)"
phosphorylated Hat1 ser8   = PR:000050463 = "histone acetyltransferase type B catalytic subunit phosphorylated 1 (rice blastfungus)"

Note that the names are based on UniProtKB names, but these are MoHAT1 given in the paper PMID:30776962.

We'll talk about this with @amorgat next week - if you are available Anne ?

@cmungall It would be nice to be aligned with Uniprot in terms of annotation practices. Are they adding both Rheas for S/T kinases ?

@pgaudet

It would be nice to be aligned with Uniprot in terms of annotation practices. Are they adding both Rheas for S/T kinases ?

I compared the annotations to the two Rheas (just looking at the SwissProt subset):

https://www.uniprot.org/uniprot/?query=annotation:(type:"catalytic activity" rhea:46608)&fil=reviewed%3Ayes
https://www.uniprot.org/uniprot/?query=annotation:(type:"catalytic activity" rhea:17989)&fil=reviewed%3Ayes

G4NH08 + Q9Y2I7 + Q9Z1T6 : only in RHEA:17989
Q9VZI2 : only in RHEA:46608
3602 proteins in both lists
So it seems like SP have been consistent in always annotating to both. It's not clear if the minor discrepancy is intentional or accidental. Also not clear if the consistency is due to annotation to a different system like GO and then propagating to Rhea, and if there are rules for curators moving forward.

I really really hope we don't do this (in fact I can't see a way to easily do this sustainably for all of the serine/threonine protein kinases we have already captured).
These are the 380 rows (substrates+residues) of a single kinase cyclin-dependent protein serine/threonine  kinase  cdc2
https://docs.google.com/spreadsheets/d/1wrmpbjdUcbyempnLhZ2x2pxmoW28iacv68Cv4jDu8zI/edit?usp=sharing
As you can see cdc2 phosphorylates most proteins promiscuously on both serine and threonine. We have  a number of protein kinases with a lot of substrate data now (47 kinases have numerous substrates, most including serine and threonine residues). I don't expect any serine/threonine kinase to phosphorylate only serine or threonine....
Protein kinases phosphorylate a consensus  "motif" so the CDK family motif is Cdk1 consensus sequence (S/T*-P, or S/T*-P-x-K/R, where x represents any amino acid and the asterisk indicates the site of phosphorylation). The S/T may switch between species  but the site is biologically equivalent. It is the context  (site) that is biologically interesting here not the specific residue.
It would be a lot of work to split these (indeed the terms do not even exist for cyclin dependent/ MAPK/MAPKKK etc).
So for  fission yeast we would continue to annotate to  serine/threonine term because it would be too much work to change. I am happy to reannotate anything, but if there is value in doing so.
I don't see how we could possibly keep these annotations internally consistent.

Uploading mods_single_kinase.txt…

mods_single_kinase.txt

@ValWood - agreed. Curious as to the Rhea/SIB strategy, how they maintain consistency; perhaps Rhea could be persuaded to have a grouping here.
We will of course keep S/T groupings in GO.
I think the options are:

Rhea creates a S/T grouping and we have a equivalence mapping
GO keeps S/T grouping but makes two subclasses each with 1:1 mappings; we may have a do-not-annotate tag on the subclasses and have the rule we always roll up
We define the GO S/T class using OWL unionOf of the two Rheas, and we categorize these mappings as narrow rather than equivalent

My preference is for 1. I don't think anyone would be in favor of 2 but I list to be exhaustive.
Seems likely we may end up with 3. We have discussed elsewhere the need to stratify our mappings and make it explicit whether a mapping is exact/narrow/broad/related. E..g metalloendopeptidases and EC

I like 1 or 3.

Hi
sorry for the late reply, I think Anne is pretty occupied so I take the liberty of butting in.
Most annotations in UniProt now to the two Rhea reactions
ATP + L-seryl-[protein] = ADP + H+ + O-phospho-L-seryl-[protein]
ATP + L-threonyl-[protein] = ADP + H+ + O-phospho-L-threonyl-[protein]
will have been created based on their mapping to EC numbers and EC number annotations in UniProt. Curators annotating to Rhea now are now in theory free to add one or the other based on the experimental evidence of which sites in the known targets have been tested. We would expect them to annotate those sites in the target proteins too as part of their normal work, so enzyme and target should be consistent, and we use the same ChEBIs in our list of PTMs too at https://www.uniprot.org/docs/ptmlist, e.g.
ID   Phosphoserine
AC   PTM-0253
FT   MOD_RES
...
KW   Phosphoprotein.
DR   ChEBI; CHEBI:83421.
DR   RESID; AA0037.
DR   PSI-MOD; MOD:00046.
DR   Unimod; 21.
//
ID   Phosphothreonine
AC   PTM-0254
FT   MOD_RES
...
DR   ChEBI; CHEBI:61977.
DR   RESID; AA0038.
DR   PSI-MOD; MOD:00047.
DR   Unimod; 21.
//
So for any given modified residue you should be able to link it to the corresponding Rheas and eventually enzymes.
I think number 3 may be the best solution, given the weight of legacy data on both sides, but @amorgat will have her say on Rhea!
All the best, Alan

On GO call, with @amorgat
Rhea represents reactions. GO wants to keep the S/T term, so we're leaning towards @cmungall 's solution 3 https://github.com/geneontology/go-ontology/issues/20114#issuecomment-713063804

Ask Rhea for a grouping term
@amorgat
@kaxelsen
Can it be done?

@pgaudet, sorry but we will not create the parent reaction with Ser/Thr residues. This not the scope of Rhea. Similarly we don't create reactions with NAD(H) nor NADP(H).
As mentioned earlier by @alanbridge, UniProt entries with the EC <IP_ADDRESS> enzyme are annotated with
RHEA:17989 ATP + L-seryl-[protein] = ADP + H+ + O-phospho-L-seryl-[protein]
RHEA:46608 ATP + L-threonyl-[protein] = ADP + H+ + O-phospho-L-threonyl-[protein]
Note that these 2 reactions are linked to several EC numbers (see https://www.rhea-db.org/rhea/?query=ec%3A<IP_ADDRESS>&columns=%2Crhea-id%2Cequation%2Cenzyme-class%2Cuniprot%2Cgo).
This is typically a case where UniProt/Rhea have different annotation guidelines compared to GO. In these cases the 1:1 mapping will not be possible.

Thanks for the clarification @amorgat

Some further questions for @amorgat , but more curiosity-driven so not urgent.
There is a lot of proteins annotated to both, with high overlap:

ID
num proteins

RHEA:46608
395357

RHEA:17989
386066

both
387135

RHEA:46608 only
8280

RHEA:17989 only
8

this is the RHEA:17989-only set:

id
label

uniprot:G4NH08
Glycogen synthase kinase 1

uniprot:Q3S406
Glycogen synthase kinase 1

uniprot:P42336
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform

uniprot:P42337
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform

uniprot:Q9Y2I7
1-phosphatidylinositol 3-phosphate 5-kinase

uniprot:Q9Z1T6
1-phosphatidylinositol 3-phosphate 5-kinase

uniprot:P32871
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform

uniprot:A0A0G2K344
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform

to what extent are these differences biologically meaningful? I assume that many of the annotations come from transference from EC, where the annotations are auto-rolled down.

@cmungall, as your question concerns UniProt annotations, I forwarded it to @sylvainpoux. Below his answer:
Classical Ser/Thr protein kinases mediate 2 reactions: the Ser protein kinase activity (RHEA:17989) and the Thr protein kinase activity (RHEA:46608)
Most proteins are able to phosphorylate both Ser and Thr and we add both reactions by default (there are bunch of EC numbers).
BUT there might be cases where the situation is not that clear and where only one reaction is observed.
We have only few cases in Swiss-Prot (10 entries, corresponding to 4 protein coding genes):

1 case for rhea:46608 and NO rhea:17989
This case might be dubious and adding the other reaction might be considered

9 entries with rhea:17989 and NO rhea:46608 (corresponding to 3 protein coding genes)

The second case is more interesting because it concerns proteins with different kinase activities (lipid and glycogen kinases) that also have Ser-protein kinase activity. But these proteins are not classical members of the Ser/Thr protein-kinase activity and for these cases, it would be daring to add the other reaction because we clearly don’t have enough evidence.

Discussing with @thomaspd
Indeed that PIK example is interesting - we could keep/modify the Ser kinase activity, but in this case it cannot be a child of Ser/Thr kinase, as it would be a TPV, since it doesn't have the Thr activity.

Maybe too little coffe.
If ser/ thr  means either why not? Does the  ser/thr kinase term d mean that something annotated can use either or it's a grouping term (I don't know of any one gene product that can use either?)?

Ah ok - the definition or Ser/thr kinase seems to state otherwise?
"Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate."

Looking at the EC:<IP_ADDRESS>, it says neither but has all sorts of synonyms.
https://enzyme.expasy.org/EC/<IP_ADDRESS>

Hi @pgaudet,
"it cannot be a child of Ser/Thr kinase, as it would be a TPV, since it doesn't have the Thr activity."
Actually, we don't know. We know that there is Ser kinase activity but we have NO evidence that it has Thr kinase activity, as it is not a member of the classical family.
Sylvain

And I think the text def should say OR, not AND

Decision on ontology call:

[ ] obsolete GO:0106310 protein serine kinase activity
[ ]  obsolete GO:0106311 protein threonine kinase activity

@pgaudet Could you please add a little more text about the rationale for the obsoletions for posterity and ease of reference? It made sense during the call today but my memory of that may fade.  Thanks.

The reason for obsoletion is that GO represents molecular functions at the level of specificity of known enzymes, and these terms represent specific substrates. I've added this to the documentation for creating new terms, http://wiki.geneontology.org/index.php/Principles_for_creating_a_GO_term#Out_of_scope
Thanks, Pascale

[x] merged 'GO:0106311 protein threonine kinase activity' into 'GO:0004674 protein serine/threonine kinase activity'
[x] moved 'GO:0106310 protein serine kinase activity' directly under 'GO:0004672 protein kinase activity'
[x] added comment on 'GO:0106310 protein serine kinase activity' "Note that this term is to annotate proteins the specifically phosphorylate a serine residue on a protein. An example is human PIKFYVE (UniProt:Q9Y2I7). For dual specificity protein kinases, use 'protein serine/threonine kinase activity' ; GO:0004712."

@pgaudet Just checking: should EC:<IP_ADDRESS> (Non-specific serine/threonine protein kinase) be an xref on 'GO:0004674 protein serine/threonine kinase activity'?
That EC is present as the reference for lots of the synonyms on GO:0004674, but doesn't appear as an xref (looking at the latest go-basic.obo).  Intentional?

It does look like an omission. I added the xref.

@pgaudet
Just noticed that the go-edit.obo file lists the EC xref twice on GO:0004674 - I guess one should be removed:
id: GO:0004674
name: protein serine/threonine kinase activity
namespace: molecular_function
alt_id: GO:0004695
alt_id: GO:0004696
alt_id: GO:0004700
alt_id: GO:0106311
def: "Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate."


Add Brotli static compression "mode"

Is your feature request related to a problem? Please describe.
Right now Drogon will brotli compress on the fly if type isn't a binary and content-length is greater then 1024bytes.
I'd like to have assets already compressed with brotli and serve them, which is where Brotli shines.
Describe the solution you'd like
Be able to configure drogon, to serve brotli statically compressed files ( you compress assets ahead of time on the server, ideally at build )
A solution could be:
any request to /path/to/asset.[js|css|html] will be rewrite into /path/to/asset.[js|css|html].br
based on include or exclude rules sets in config.json :
"brotli": {
  "use": true, \\ default to false
  "static": true, \\ default to false
  "include": "*.js, *.css, *.html",
  "exclude": "content-to-not-compress.html"  \\ you might want this for different purposes,
  \\ ie. avoid BREACH attack on compressed content
}

Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
https://sites.google.com/site/powturbo/home/web-compression
http://breachattack.com/#mitigations
Further reading
https://csswizardry.com/2020/04/real-world-effectiveness-of-brotli/

Actually, there is a similar configuration option in Drogon config file:
        //br_static: If it is set to true, when the client requests a static file, drogon first finds the compressed
        //file with the extension ".br" in the same path and send the compressed file to the client.
        //The default value of br_static is true.
        "br_static": true,

Actually, there is a similar configuration option in Drogon config file:
        //br_static: If it is set to true, when the client requests a static file, drogon first finds the compressed
        //file with the extension ".br" in the same path and send the compressed file to the client.
        //The default value of br_static is true.
        "br_static": true,

Oh gosh... 🤦🏽  getting old how could I miss that!
that's much better then my solution, great!
Much appreciated @an-tao 🙏🏽

Oh gosh... 🤦🏽  getting old how could I miss that!
that's much better then my solution, great!
Much appreciated @an-tao 🙏🏽

So if I understand correctly br_static is indipendent of use_brotli value ?
or you need to have both set to true ?

So if I understand correctly br_static is indipendent of use_brotli value ?
or you need to have both set to true ?

So if I understand correctly br_static is indipendent of use_brotli value ?
or you need to have both set to true ?

Yes, br_static is indipendent of use_brotli.

So if I understand correctly br_static is indipendent of use_brotli value ?
or you need to have both set to true ?

Yes, br_static is indipendent of use_brotli.

Is this stated in the docs already? should we add something in the like:
Drogon supports out of the box brotli statically compressed files if it finds next to asset.[js|css|html] the corresponding brotli compressed file asset.[js|css|html].br
and if you want to dynamically compress using brotli  you'll set use_brotli to true.
also users that don't use brotli don't want that extra check to see if there's sibling brotli compressed file, and might want to know they should set br_static false ....
I personally think that br_static and use_brotli could be renamed in brotli_static and  brotli_dynamic that would make it less ambigous to human interpretations....

Is this stated in the docs already? should we add something in the like:
Drogon supports out of the box brotli statically compressed files if it finds next to asset.[js|css|html] the corresponding brotli compressed file asset.[js|css|html].br
and if you want to dynamically compress using brotli  you'll set use_brotli to true.
also users that don't use brotli don't want that extra check to see if there's sibling brotli compressed file, and might want to know they should set br_static false ....
I personally think that br_static and use_brotli could be renamed in brotli_static and  brotli_dynamic that would make it less ambigous to human interpretations....

Is this stated in the docs already?
Should we add something in the like:

Drogon supports out of the box brotli statically compressed files if it finds next to asset.[js|css|html] the corresponding brotli >compressed file asset.[js|css|html].br
and if you want to dynamically compress using brotli  you'll set use_brotli to true.
also users that don't use brotli don't want that extra check to see if there's a sibling brotli compressed file,
and might want to know they should set br_static to false

would you like to make a PR to https://github.com/an-tao/drogon-docs? thanks so much.

I personally think that br_static and use_brotli could be renamed to brotli_static and brotli_dynamic that would make it less ambigous to human interpretations....

Yes, that's more clear, but the change breaks version compatibility, old users would get errors after updating.

Is this stated in the docs already?
Should we add something in the like:

Drogon supports out of the box brotli statically compressed files if it finds next to asset.[js|css|html] the corresponding brotli >compressed file asset.[js|css|html].br
and if you want to dynamically compress using brotli  you'll set use_brotli to true.
also users that don't use brotli don't want that extra check to see if there's a sibling brotli compressed file,
and might want to know they should set br_static to false

would you like to make a PR to https://github.com/an-tao/drogon-docs? thanks so much.

I personally think that br_static and use_brotli could be renamed to brotli_static and brotli_dynamic that would make it less ambigous to human interpretations....

Yes, that's more clear, but the change breaks version compatibility, old users would get errors after updating.

ok perfect. here's the pull
I added in chapter 15 since I didn't saw any obvious fitting place.

ok perfect. here's the pull
I added in chapter 15 since I didn't saw any obvious fitting place.

Thanks so much for the patch. I will close this as the documentation was already updated and merged. If there’s need for more discussion, please continue in the official Drogon chat.

Thanks so much for the patch. I will close this as the documentation was already updated and merged. If there’s need for more discussion, please continue in the official Drogon chat.


"Onnxruntime is required, please check requirements are installed."

Installed ONNX Runtime and still get this error.

My mistake I was running only "pip install -r requirements.txt" in the folder.
"D:\ComfyUI\ComfyUI\custom_nodes\ComfyUI-WD14-Tagger"
What fixed it was running the full path to the python file in python_emebeded along with "-s -m pip install -r requirements.txt"
Example : running this in ComfyUI-WD14-Tagger folder. "D:\ComfyUI\python_embeded\python.exe -s -m pip install -r requirements.txt"


Update README.md

@Pulkit0076  Can you please sign CLA. Thanks!

@Pulkit0076 Can you please sign CLA. Thanks!

@gbaned already done :)

Why did you delete the file?

Why did you delete the file?
Actually it was having some errors, so I updated and deleted the file that was having a error

There cannot be an error from a README file.

There cannot be an error from a README file.

I meant to say in first file , I made a mistake so I updated it and deleted the error commit ( file )

Your first commit is spam.


Sort

Add a Sort primitive to the collections package that uses Yaroslavskiy's algorithm (the dual-pivot QuickSort that is used in Java 7).

I have a few comments.

Directly using a Seq interface instead of generics is a real performance hit. The same code with generics performed more than 2 times better in my tests (where I was sorting big Arrays).
The function shouldn't be partial. The only error sources are out of bounds accesses and we know those won't happen (unless the Seq is lying about its size but I don't think we should handle this case).
_swap can use the "Pony way": a = b = a.

Thanks for looking into the performance @Praetonus!

I have a comment on this:

Using the Seq interface requires a fair number of methods to be provided by a container.
The only methods that a container needs to provide is size, update and ```apply`` so perhaps using the minimal interface would be more appropriate.

@lukecheeseman pointed out that when we have Vector, it won't be compatible with Seq, but I added a separate ticket to cover that, so we can merge this one.


fetching contacts in new thread (Android)

description:
added a new thread for fetching contacts on Android, because it takes some time and makes the main thread irresponsible for user interactions
the reason for this PR:
I have ~350 contacts and it takes 5-7 seconds to fetch it with few keys (displayName, givenName, thumbnailImageData, phoneNumbers, instantMessageAddresses).
Alternative proposition:
As I understood, the main time eater is thumbnailImageData. So maybe it will be faster if to give links to the thumbnail in this look "content://com.android.contacts/contacts/527/photo"? (add new key 'thumbnailUri')

Hi, thank you for the pull request, sorry it took long to review it.
Actually,  the @ReactMethod is already running on a user thread. You can see it if you add a log call in the native code. An example logcat line starts with: 02-21 14:10:41.026 10452-10494/com.clubs ...
Notice the 10452-10494 numbers - the first number is the main thread id, and the second is the thread id that the logcat is printing from. If they are different - then we are on a user thread.
Loading many contacts takes many seconds, but it is most likely not related to any ANR, since we're not on the UI thread. But it looks like the app is stuck.
I think that the best was to tackle this is by displaying a wait spinner on the JS side, or split the contacts list to 20 for example, and after displaying them - fetch the rest.
Both options are JS logic.


kube-solo halts unexpectedly

While using kube-solo v0.6.4 (and earlier versions), I often see the k8s api become unresponsive. All I can tell is that the VM has halted. If I click the "Up" menu item, kube-solo starts up as if nothing were wrong.
This happens often and easily--my test case is running the workflow-v2.0.0-e2e chart on top of Deis workflow-v2.0.0. Let me know if there are any logs I can provide. I have also tried configuring with 4GB of RAM allocated to kube-solo instead of the default 2GB, but same results.

@mboersma can you provide the exact steps, so I can try to reproduce it. thanks

@rimusz here's what I do:

Install latest kube-solo
Delete /etc/exports
Go through kube-solo initial setup (allocate 4GB RAM, 30GB disk)
Install the workflow-v2.0.0 chart
Install the workflow-v2.0.0-e2e chart and let the tests run

Reliably, somewhere in the middle of the test run there will be an unexpected error, or the suite will just stall. Looking at kube-solo shows that the k8s API no longer answers because the VM is halted.
This is also reproducible through normal Deis Workflow usage for me, without running tests. I'm not able to keep the instance running for more than 20-30 minutes max without this occurring. Usually starting up the VM again makes everything available, but the problem will recur.
Any specific logs or other info I can add?

@AntonioMeireles ping, any ideas why the corectl could crash after running for 30 min, I'm not able to reproduce it yet.

humm. this doesn't seem a deterministic issue here too.
@mboersma - for context and to try to scope this issue - OS X version/RAM & hw version ?(not an hackintosh, right ?) . do you get anything in the system logs (command-space > console > search for corectl)  ? thanks!

I'll try again with v0.6.6 and add more detail here if I can reproduce the issue.

It did happen to me again with v0.6.6 of kube-solo, following the steps I described above. At the start of the workflow-e2e tests, the VM apparently halted. The console app had this:
6/15/16 9:07:31.956 AM sudo[1782]:     matt : TTY=ttys001 ; PWD=/Users/matt/kube-solo ; USER=root ; COMMAND=/Applications/Kube-Solo.app/Contents/Resources/bin/corectl load settings/k8solo-01.toml
6/15/16 9:07:33.216 AM InternetSharing[1787]: corectl: com.apple.NetworkSharing.broadcast-0 has been started
6/15/16 9:07:33.217 AM InternetSharing[1787]: corectl: com.apple.NetworkSharing.broadcast-0 (idle) has been stopped
6/15/16 9:07:33.752 AM InternetSharing[1787]: corectl: com.apple.NetworkSharing.broadcast-1 has been started
6/15/16 9:08:30.000 AM kernel[0]: process corectl[1794] caught causing excessive wakeups. Observed wakeups rate (per sec): 785; Maximum permitted wakeups rate (per sec): 150; Observation period: 300 seconds; Task lifetime number of wakeups: 45012
6/15/16 9:08:34.477 AM spindump[774]: Saved wakeups_resource.diag report for corectl version ??? (???) to /Library/Logs/DiagnosticReports/corectl_2016-06-15-090834_gradishar.wakeups_resource.diag
6/15/16 9:25:58.122 AM InternetSharing[1787]: corectl: com.apple.NetworkSharing.broadcast-1 (idle) has been stopped
6/15/16 9:26:14.024 AM sudo[3917]:     matt : TTY=ttys003 ; PWD=/Users/matt/kube-solo ; USER=root ; COMMAND=/Applications/Kube-Solo.app/Contents/Resources/bin/corectl load settings/k8solo-01.toml
6/15/16 9:26:14.130 AM InternetSharing[1787]: corectl: com.apple.NetworkSharing.broadcast-2 has been started
6/15/16 9:26:14.130 AM InternetSharing[1787]: corectl: com.apple.NetworkSharing.broadcast-2 (idle) has been stopped
6/15/16 9:26:14.480 AM InternetSharing[1787]: corectl: com.apple.NetworkSharing.broadcast-3 has been started

The 9:25 has been stopped message seems to correspond with the VM halting, after which I chose the "Up" menu item in kube-solo to bring it up again.
Macintosh is MacBook Pro retina 13", late 2013, 2.8 GhZ Core i7, 16GB RAM, OS X El Capitan 10.11.5.

@mboersma please try the latest v0.8.0 it is based on the latest corectl v0.7.x with a separate server daemon and client.

I haven't seen this happen with the new separate corectl. I'll keep an eye out. Thanks @rimusz!

awesome


WebExtensions, Firefox 79

Story
As a WebExtensions developer, I want to be informed about the latest API changes and read up-to-date reference docs.
Acceptance criteria
The following bugs are dev-doc-complete, BCD is updated, an entry to Firefox release notes is added, experimental features page is updated, the content has been reviewed as needed.

[ ] WebExtension API to 'warm up' a tab

@caitmuenster and @kewisch can you let us know about the changes to document for Firefox 79 in WebExtensions land?
Also, given Richard isn't contracting with you anymore, who will document/review docs from your side in the future? Thanks!

Hey @Elchi3! It looks like we only have one bug tagged dev-doc-needed for the WebExtensions API: https://mzl.la/2VXsOwV
I had talked with @chrisdavidmills about how to handle documentation updates/approvals without Richard. If we maintain a low volume of changes, can @wbamberg or some of the other MDN writers help us out with the writing? Our engineers are happy to review documentation updates. I can also help out where I can but my technical knowledge is fairly limited.

If we maintain a low volume of changes, can @wbamberg or some of the other MDN writers help us out with the writing?

Yes. We did this for 78 and it was fine for me. Also I asked for and got helpful review feedback from the engineering team for the 78 updates.
If it gets to be more than a few days' work in each release, we'd need to talk about how to resource it.

Thanks @caitmuenster!
I haven't looked at the one DDN we have for Fx79. I guess "API" is quite an overloaded term, so maybe "WebExtension API to 'warm up' a tab" isn't about an entire new API that would require a many new pages, etc. If Will is fine to do this work this time around, then let's do this.
Also, I don't know how and when the WebExtension team tags bugs "dev-doc-needed". Sometimes they get added quite late in the cycle, but maybe 79 really is a light cycle and we only have this one change to the public APIs :)

If it gets to be more than a few days' work in each release, we'd need to talk about how to resource it.

Exactly this is the situation that we will probably face sooner or later.

@Elchi3, what schedule would you prefer? I can certainly help coordinate with the engineers.

@caitmuenster We plan our sprints at the end of every month (or rather at the end of every Firefox cycle).
So, last week, I collected all ddn items for Fx79 (including this issue). For the next round, I would file user stories and plan time in the week of July 20 (and it would take into account all items for Fx80). If the Fx80 bugs aren't tagged by then, I would miss them for the initial docs planning for the Fx80 cycle.
Does that make sense? Happy to talk this through some more if needed.

Quick update: we just added a dev-doc-needed for this bug.
Sorry @Elchi3 I will respond more fully to your comment in a little bit.

Quick update: we just added a dev-doc-needed for this bug.

More info also here https://blog.mozilla.org/addons/2020/07/09/changes-to-storage-sync-in-firefox-79/
(we can reference this post from the Fx79 hacks blog on July 28)

This bug now also shows up as ddn for Fx79: https://bugzilla.mozilla.org/show_bug.cgi?id=1634615

The storage.sync DDNs are done:
https://bugzilla.mozilla.org/show_bug.cgi?id=1637166#c7
The tabs.warmup() one is waiting for engineering review, but if I don't have it by the time I'm back in the "office" I'll close that one too.

I got a review from Tomislav for the warmup() one https://bugzilla.mozilla.org/show_bug.cgi?id=1402256), so closing that too.

Awesome, thank you @wbamberg! I think that wraps WebExtensions up for 79.


Feature/tdtm doc update

Critical Changes
Changes
Updated readme and change log to provide clearer description of tdtm work.
Issues Closed

@coriobriensfdo @Szandor72 Re-created PR #1240.  Apologies, but will need to review again.


Use usleep instead of sleep/nanosleep on Mbed OS.

Problem
nanosleep is not available on Mbed OS and sleep as a different semantic compared to POSIX (not tie to newlib).
Some unit tests actively use this feature which cause a compilation error.
Change overview
In unit tests, use usleep instead of nanosleep or sleep when compiled for Mbed OS.
Testing

How was this tested? (at least one bullet point required)

Existing unit tests.

I use usleep everywhere, everything seems fine.

@pan- See review comments?

@bzbarsky-apple Hi, @pan- is on holiday so I take over this PR. I changed the casting according to your comments


Login button has changed. Please contact support.

Running from a Synology NAS, receive the following:
Opening browser
Login button has changed. Please contact support.
I've tried multiple times on multiple days, with no luck.
This is the same issue as #27 , but that one was closed by accident it seems.
I have a full linux vm that is running https://github.com/loblab/noip-renew, that seems to still be working properly.

Hi,
I have tested both latest debian and alpine variants and both ran successfully.
That error can also occur if, for example, NOIP requires you to complete a captcha or you have NOIP set to another language that is not English. Is any of this your case? Have you tried access your NOIP account page and log in only using your username and password?

I quickly popped it onto a test Ubuntu VM, and it worked perfectly, but for some reason, i can't get it to run properly on my Synology... what am I missing here?

I ssh'd into the NAS and ran the exact same command that ran perfectly on my ubuntu VM, and it gave me the same error as before...

Unfortunately, I don't know what it could be and I am unable to reproduce this.  I will close this until further new developments.

Hi, just because I was facing the same issue on my Synology... In my case the problem was the Pi-hole.


native_pdf_renderer:: convert pdf into image issue.

Describe the bug
A clear and concise description of what the bug is.
Image is not the view of pdf file.
One page sample pdf.
PDF Bookmark Sample.pdf
To Reproduce
Testing on iOS ipadOS 14
    final document = await PdfDocument.openFile(filePath);
    final page = await document.getPage(1);
    final pageImage = await page.render(width: page.width, height: page.height);
    await page.close();
    ....

Results;

Expected behavior
A clear and concise description of what you expected to happen.
Screenshots
If applicable, add screenshots to help explain your problem.
original Pdf View

Smartphone (please complete the following information):

Device:ipad
OS: ipadOS 14
Version : 14

Additional context
Add any other context about the problem here.

@CellCS you can set backgroundColor


Dual versions for parallel

Hi @andrewdalpino,
To resolve #305 is it suitable to dual-require parallel versions 1.3 and 2.2, and let Composer choose the right one based on your PHP version?

Hey thanks @27pchrisl this could very well be a solution but we may have to make some changes to the code itself. See the failed test here https://github.com/RubixML/ML/actions/runs/9035283567/job/24858504227?pr=332 and let me know what you think. Thanks again!

Hiya @andrewdalpino, I created an Amp2 class that the package user can use if they have the v2 of parallel. Essentially a clone of Amp but implementing the newer interface.

I could implement a common abstract class, but it would only really abstract away the constructor and the __toString method, so I have created them completely separately.

Unfortuantely we don't have the resources to support this at this time. Will look to upgrading to Amp Parallel 2.2 in ML 3.0. Thank you!


[WIP] Bloom filter Quick Implementation

What is the context for this pull request?

Tracking Issue: If you expect any subjective discussions around this pull request, please consider opening a tracking issue and link to the PR. Write N/A, if this pull request is self-contained.
Parent Issue: Link to the issue that captures the overall plan. Write N/A, if this is a stand-alone pull request with a tracking issue OR self-contained pull request.
Dependencies: Links to issues you depend on for this pull request to work. Write N/A, if no dependencies.

Issue 1
Issue 2

What changes were proposed in this pull request?

Does this PR introduce any user-facing change?

How was this patch tested?

@thugsatbay Could you add BFFilterIndexRule to apply BF index & measure the performance? (for e2e prototype)
I wonder file-level BF & filtering files would be beneficial if we use parquet dictionary filter.
https://medium.com/analytics-vidhya/spark-parquet-file-cac4af92981d
https://www.slideshare.net/RyanBlue3/parquet-performance-tuning-the-missing-guide
So .. it might be good to measure the perf using dictionary filter & compare with BF..
cc @imback82


Breaking Change: Split wiredep-cli into its own module

Yeah, what the title says. Reasons for this:

This repowould be more focused on wiredep itself
The cli is a thin wrapper anyway
It would be helpful to know if anyone even uses that

Done in https://github.com/taptapship/wiredep-cli


Supporting e-Entity from browser

Our collegue works on integrating FREME services in his authoring environment. From the browser he calls e-Translate and e-Entity. E-Translate seems to work well, but with e-Entity he gets an error related to CORS. This only happens when requesting text\html as output. When asking for e.g. JSON, it works. The input is also text\html.
A discussion about this can be found here.

See als CORS support in Spring

CORS should be already support by all FREME services.
@pheyvaer do you have any info on the differences in the response headers from the call with text/html and requests with other formats?

This is what Chrome tells us about the request:
#General
Remote Address:<IP_ADDRESS>:80
Request URL:http://api-dev.freme-project.eu/current/e-entity/freme-ner/documents?informat=text%2Fhtml&outformat=text%2Fhtml&language=en&dataset=dbpedia&mode=all
Request Method:OPTIONS
Status Code:400 Bad Request

#Response Headers
Access-Control-Allow-Headers:x-requested-with, content-type
Access-Control-Allow-Methods:POST, GET, OPTIONS, DELETE
Access-Control-Allow-Origin:*
Access-Control-Max-Age:3600
Connection:close
Date:Wed, 04 Nov 2015 11:35:33 GMT
Server:Apache-Coyote/1.1
Transfer-Encoding:chunked

#Request Headers
Accept:*/*
Accept-Encoding:gzip, deflate, sdch
Accept-Language:en-US,en;q=0.8,nl;q=0.6
Access-Control-Request-Headers:accept, content-type
Access-Control-Request-Method:POST
Cache-Control:no-cache
Connection:keep-alive
Host:api-dev.freme-project.eu
Origin:http://localhost
Pragma:no-cache
Referer:http://localhost/pages/contents
User-Agent:Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/46.0.2490.80 Safari/537.36

#Query String Parameters
informat:text/html
outformat:text/html
language:en
dataset:dbpedia
mode:all

In order to do CORS OPTIONS should be supported, but it is not.

This can be reproduced also from Documentation page. set informat=text and outformat=text (from dropdowns) and it gives an error.
header says that there is 400 error, but body that 500.
Headers
{
  "date": "Wed, 04 Nov 2015 11:58:03 GMT",
  "via": "1.1 QUIGON",
  "x-content-type-options": "nosniff",
  "access-control-max-age": "3600",
  "proxy-connection": "Keep-Alive",
  "connection": "Keep-Alive",
  "content-length": "229",
  "x-xss-protection": "1; mode=block",
  "pragma": "no-cache",
  "server": "Apache-Coyote/1.1",
  "x-frame-options": "DENY",
  "access-control-allow-methods": "POST, GET, OPTIONS, DELETE",
  "content-type": "application/json;charset=UTF-8",
  "access-control-allow-origin": "*",
  "cache-control": "no-cache, no-store, max-age=0, must-revalidate",
  "access-control-allow-headers": "x-requested-with, content-type",
  "expires": "0"
}

Body*

{
  "exception": "eu.freme.broker.exception.BadRequestException",
  "path": "/e-entity/freme-ner/documents",
  "message": "HTTP 500 Internal Server Error",
  "error": "Bad Request",
  "status": 400,
  "timestamp":<PHONE_NUMBER>088
}

There is filter implemented for support for CORS
see https://github.com/freme-project/Broker/blob/master/src/main/java/eu/freme/broker/tools/CORSFilter.java#L41-L46
Maybe @jnehring knows more about this.

I could not reproduce the problems. Which call exactly did your colleague do? Can he share the Javascript that he used?
@pheyvaer wrote

In order to do CORS OPTIONS should be supported, but it is not.

The response you posted has one line saying Access-Control-Allow-Methods:POST, GET, OPTIONS, DELETE. I think this says that this request supports OPTIONS for CORS.
@andish wrote

This can be reproduced also from Documentation page. set informat=text and outformat=text (from dropdowns) and it gives an error.

Which API call did you try? We do not support outformat=text, when this is an option for outformat in the api documentation then it is a mistake.
@m1ci wrote

There is filter implemented for support for CORS
see https://github.com/freme-project/Broker/blob/master/src/main/java/eu/freme/broker/tools/CORSFilter.java#L41-L46

This is the part of the broker that enables CORS for FREME. It adds these 4 lines the the header of every HTTP response:
Access-Control-Allow-Headers:x-requested-with, content-type
Access-Control-Allow-Methods:POST, GET, OPTIONS, DELETE
Access-Control-Allow-Origin:*
Access-Control-Max-Age:3600

I tried Post to /e-entity/freme-ner/documents. and there is a lot of formats in outformat dropdown

I raised https://github.com/freme-project/Documentation/issues/134 to remove outformat=text in POT /e-entity/freme-ner/documents

The OPTIONS-part doesn't work using this javascript
$.ajax({
    method: 'POST',
    headers: {'Content-Type': 'text/html', Accept: 'text/html'},
    data: encodeURIComponent('
Paris the city.
'),
    url: 'http://api-dev.freme-project.eu/current/e-entity/freme-ner/documents?informat=text%2Fhtml&outformat=text%2Fhtml&language=en&dataset=dbpedia&mode=all'
})

but it does using this javascript
$.ajax({
    method: 'POST',
    headers: {'Content-Type': 'text/html', Accept: 'text/n3'},
    data: encodeURIComponent('
Paris the city.
'),
    url: 'http://api-dev.freme-project.eu/current/e-entity/freme-ner/documents?informat=html&outformat=html&language=en&dataset=dbpedia&mode=all'
})

However, the actual POST fails with the second javascript because of the wrong parameters. As soon as one of the informat or outformat parameters has text/html, OPTIONS fails when used in the browser.

Tested in Chrome, jQuery 1.10

I could reproduce the bug. The first code example produced "Response for preflight has invalid HTTP status code 400" on Google Chromes JS console.
I fixed a bug: The e-Internationalization filter performs some input validation on the pre-flight request and throws "400 - bad request" because there is no post body in the pre-flight request. So I disabled e-Internationalization filter for all OPTIONS requests. Now I can run your code example without errors.
I installed the patch on freme-dev. @bjdmeest please try again.

Works like a charm, thanks!

The bug shown by https://github.com/freme-project/Broker/issues/131#issuecomment-153731180 is back

I will fix the bug.

I could not reproduce the bug. When I executed your jQuery I got back "bad request". "html" is not a valid value for "informat". it should be "text/html". Can you please check again if the bug is really a CORS issue?
Here is the HTML I used to check this - I added .txt to the extension so I can attach it to the GitHub.
cors-bug.html.txt

Hmm, indeed, it might have been related to https://github.com/freme-project/e-services/issues/12, apologies for the duplicate issue, I consider this fixed now, thanks!