Update cats-effect, cats-effect-laws to 2.3.2

Updates

org.typelevel:cats-effect
org.typelevel:cats-effect-laws

from 2.3.0 to 2.3.2.
GitHub Release Notes - Version Diff
I'll automatically update this PR to resolve conflicts as long as you don't change it yourself.
If you'd like to skip this version, you can just close this PR. If you have any feedback, just mention me in the comments below.
Configure Scala Steward for your repository with a .scala-steward.conf file.
Have a fantastic day writing Scala!

Files still referring to the old version number
The following files still refer to the old version number (2.3.0).
You might want to review and update them manually.
project/Dependencies.scala

Ignore future updates
Add this to your .scala-steward.conf file to ignore future updates of this dependency:
updates.ignore = [ { groupId = "org.typelevel" } ]

labels: library-update, semver-patch, old-version-remains

Superseded by #64.


Warn the user when their polymorphic type annotations are imprecise

Consider the following specification:
--------------------- MODULE TestGetXWithRows ---------------------------------
\* @type: { x: a, b } => b;
GetX(r) == r.x
===============================================================================

The type checker infers the type of GetX correctly:
(*
  @type: (({ x: b, b }) => b);
*)
GetX(r) == r["x"]

However, it does not warn the user that their type annotation was imprecise. This does not really affect the behavior of the type checker, as it will always infer the types, and it uses the user annotations only as a guidance. However, it would be nice to tell the user that their annotations do not match the code.

Actually, @shonfeder brought another good point here. It's possible to confuse type variables (of normal kind) with type variables (of row kind).

I have introduced #2108 to deal with kinds.


⚠ Bofrost.at has degraded performance

In 435f5cd, Bofrost.at (https://www.bofrost.at) experienced degraded performance:

HTTP code: 200
Response time: 2636 ms

Resolved: Bofrost.at performance has improved in 3c225ec.


"flutter create ." (for adding web support to plugin) fails on "invalid package name"

Steps to Reproduce
Run "flutter create ." in a plugin directory, where the plugin has specified a valid package name in pubspec.yaml but the folder name contains invalid characters (like '-').
In my case the plugin "mapbox_gl" is contained in a folder called "flutter-mapbox-gl" and calling "flutter create ." inside this folder (to add web support) fails.
Logs
"flutter-mapbox-gl" is not a valid Dart package name.
From the Pubspec format description:
DO use lowercase_with_underscores for package names.
Package names should be all lowercase, with underscores to separate words,
just_like_this.  Use only basic Latin letters and Arabic digits: [a-z0-9_].
Also, make sure the name is a valid Dart identifier -- that it doesn't start
with digits and isn't a reserved word.
Flutter version
I'm running Flutter  v1.12.13+hotfix.6 on channel beta.

I've also tried to pass the plugin's actual name as --project-name, but although the command finishes successfully then, it doesn't do what it should (e.g. it creates a new main.dart file)

@jonahwilliams was recently looking around here.

I'm not able to reproduce this locally. Note that flutter create . must be run within the project directory, unlike flutter create name

I am running flutter create . in the top-level folder that contains pubspec.yaml as well as the android, example, lib etc. folders (I assume this is the project directory?). The issue seems to be that the project directory has a name that differs from the name the plugin specifies in pubspec.yaml and the project directory's name contains characters ('-' in this case) that are invalid for a plugin name.

Are you also providing the --project-name option?

I just tried that again. That e.g. creates a new /lib/main.dart , a new /android/app directory with a new MainActivity and 12 different new ressource/Manifest/etc. files and and also a new /ios/Runner directory with about 30 new files. I'm not sure about iOS but for Android this doesn't seem to be what I want, as an Android implementation of the plugin already exists at the /android directory.

I'm still not able to reproduce this issue. I suspect you are either failing to provide the project-name option correctly or running in the wrong directory.

Steps to reproduce: please use this project stub: https://github.com/londonappbrewery/magic-8-ball-flutter.git
Now to go the project folder and do
flutter create .
As rightly pointed by @m0nac0 flutter keeps taking folder name as project name.
flutter create --projec-name magic_8_ball . works fine.


Testing in VSCode attributes failure to random tests and lines, if failure happened in tearDownAll defined in other library.

Instead, it should be somehow clear that failure happened in tearDownAll.
https://github.com/flutter/flutter/assets/12115586/f24726ba-2ecb-4611-ba5a-32f31d1f6dc9

Thanks for the report @polina-c
Keeping this issue open based on the report and error received.

This is likely related to https://github.com/dart-lang/test/issues/1851. Right now we only have the location of the test that failed, but really we want the location of where that failure happened.

Removed the framework labels since this doesn't seem related to the Flutter framework.
@DanTup Should this be transferred to the VSCode Flutter Plugin tracker?

I thought this was essentially https://github.com/dart-lang/test/issues/1851, but looking again, I think there's a Dart-Code bug here that was slightly masked by the line number of the tearDownAll method in file2 being a location in the test in file1. It seems we're actually recording tearDownAll as being in file1 (the test file), yet using the correct line/col.
I've opened https://github.com/Dart-Code/Dart-Code/issues/4681 for this - I think it should be a simple fix. I'll close this one in favour of that.


polyglot is not working in codespace

I am on windows 11 latest vs code, used anirugu/cpp for creating containers.
I am not able to use the polyglot extension, Can someone check what is wrong? I am having 7.0 as well as the latest preview extension.

I just created a codespace and opened a dib

can you check if the dev container file in my repo has anything different? You can find it here https://github.com/colombod/dotnet-interactive-extension-lab

Thanks, I will check this weekend 😊
From: Diego Colombo @.>
Sent: Wednesday, 28 December, 2022 02:55
To: dotnet/interactive @.>
Cc: Anirudha Gupta @.>; Author @.>
Subject: Re: [dotnet/interactive] polyglot is not working in codespace (Issue #2578)
I just created a codespace and opened a dib
https://user-images.githubusercontent.com/375556/209723680-9775411c-3662-495b-9a59-86d2f2b248a7.png
can you check if the dev container file in my repo has anything different? You can find it here https://github.com/colombod/dotnet-interactive-extension-lab
—
Reply to this email directly, view it on GitHub https://github.com/dotnet/interactive/issues/2578#issuecomment-1366188478 , or unsubscribe https://github.com/notifications/unsubscribe-auth/AIQ5QBKJ7A53QWK6DOSBNBLWPNNBBANCNFSM6AAAAAATIYOVDM .
You are receiving this because you authored the thread.  https://github.com/notifications/beacon/AIQ5QBIJ2PDUNSSWJRO2LXLWPNNBBA5CNFSM6AAAAAATIYOVDOWGG33NNVSW45C7OR4XAZNMJFZXG5LFINXW23LFNZ2KUY3PNVWWK3TUL5UWJTSRNZQ34.gif Message ID: @.*** @.***> >


a simple tripe partern cost very long time

SELECT E {   ?s ?p ?o . }  LIMIT 1
I used the h2 database as the SQL base for vkg. A confusing thing is that all other triples worked fine with solutions quickly returned except when I used the query above, which may take 5~10mins to get one solution or may never stop for the arrival of the solution sometimes.  The table is a bit long with roughly several hundred thousand raws. Is there any way to improve the performance of this sort of query?

Hello,
I found a bug in the tutorial. The number five step is asking to reach the SPARQL endpoint through the following URL (http://localhost:8880/sparql), however the port number is incorrect. It should be port 8080 according to step four of the tutorial. Hence the correct instruction should be

A SPARQL endpoint backed by ontop at URL http://localhost:8080/sparql (assuming default port 8880 is used), which may be accessed using any HTTP client, including SPARQL clients and tools using the standard SPARQL HTTP protocol. For instance, using curl:
curl --request POST
--url http://localhost:8080/sparql
--header 'accept: application/json'
--header 'content-type: application/sparql-query'
--data 'SELECT * { ?s ?p ?o } LIMIT 5'

Instead of:

A SPARQL endpoint backed by ontop at URL http://localhost:8880/sparql (assuming default port 8880 is used), which may be accessed using any HTTP client, including SPARQL clients and tools using the standard SPARQL HTTP protocol. For instance, using curl:
curl --request POST
--url http://localhost:8880/sparql
--header 'accept: application/json'
--header 'content-type: application/sparql-query'
--data 'SELECT * { ?s ?p ?o } LIMIT 5'

The same mistake also exists in the deployment instructions of SPARQL endpoint using Docker.


Fix typo

@changeworld : Thanks for your contribution! The author, @singhkays, has been notified to review your proposed change.


[AutoComplete] onNewRequest does not work

Problem description
onNewRequest function does not work
Versions

Material-UI: 0.14.4
React: 0.14.7
Browser: Chrome 51.0.2704.103

-->

@jackminliu you may want to upgrade Material-ui to the latest one. i.e. 0.15.1

This still doesn't fire on iOS on 0.15.2. I submitted a PR for this a while back, waiting on it to get approved
https://github.com/callemall/material-ui/pull/4291

Duplicate of #4290?

Closed by #4783


Maintain the size of the top information bar on the window at various zooms

Description
Maintain the size of the top information bar on the window at various zooms
What is the purpose of this pull request?

[ ] New feature
[ ] Documentation update
[ ] Bug fix
[ ] Refactor
[ ] Release
[X] Other

Closing this since we'll like have to revisit in a fresh PR


Document how to use EF command line in different environments

There is quite a large matrix of different environments that the EF commands (Migrations and reverse engineering) can be used in. It's very hard for developers to know both what will work and what is the best approach.  We should document this matrix so that somebody can easily ask a question such as, "What do I do if I want to put my EF code into a .NET Standard class library and then use it with a UWP application?"
Initial cut of the matrix is:

Target app platform (.NET Core app, UWP, Xamarin, .NET Framework, none--i.e. .NET Standard class library)
Type of project (Class library, ASP.NET Core, all others)
Development platform (Visual Studio/GUI tooling (use community power tools), Visual Studio/command line (use PMC), Windows/Linux/etc. command line (use dotnet ef)).

We should also make sure that the walkthroughs are consistent with this and point to this information clearly where appropriate.

From triage: Also look at #507, #508, #485, and #481 and consider how to separate the content effectively and how to reference between these areas.

This is a subset of #204


Git Explorer Color Highlight on git diffs does not "refresh" on changes, only highlights on start / restart

Does this issue occur when all extensions are disabled?: Yes

VS Code Version:

Version: 1.63.2
Commit: 899d46d82c4c95423fb7e10e68eba52050e30ba3
Date: 2021-12-15T09:37:28.172Z (1 wk ago)
Electron: 13.5.2
Chromium: 91.0.4472.164
Node.js: 14.16.0
V8: 9.1.269.39-electron.0
OS: Darwin x64 20.6.0

OS Version: MacOS Big Sur 11.6

Steps to Reproduce:

Make a change in on any files that is inside a Git Repository
I don't see the yellow M, or highlight on the Explorer
If I reload VSCode, I now do see the yellow M

Similarly, if I delete the change I just made, the yellow M remains, indicating a diff in git (but there isn't)
If I reload VSCode, it goes away.

Seems like refresh on Explorer is broken, not the Git Diff part, since this feature (the blue bar indicating change in line in file) works perfectly

Let me know if I can help with anything. This feature is very useful for when doing tedious tasks like updating something in 20 files, and saves me from staring at 20 lines of git diff in the command line to figure out if I missed any file.

@kamok, sorry for not getting back to you on this until now. I was wondering if you could record a gif (you can use https://gifcap.dev/ for example) of you reproducing the issue as that recording would allow me to learn more about your setup in an attempt to try to reproduce the issue locally in order to get to the bottom of this.

Hey, I'm running into the same issue. Here is a video.
I'm using VS Code 1.64.2 on a MacBook Pro (2021, M1 Pro) and macOS Monterey 12.2.

Sorry @lszomoru, I missed this email completely. I also took some time to make a gif.

I realized I demoed with extensions on, but I did this before and it functions (incorrectly) the same without any extensions.

Also have this issue on 1.64.x, reverting to 1.63.2 fixes it for me.

Well, given that I reported the issue when it was at 16.3.2, I don't think it works for me.

I also have this issue on Windows, version 1.65.2.
Reverting to 1.63.2 on Windows solves this issue.
I performed a set of git commands and recorded on both 1.65.2 and 1.63.2.
My environment:
OS: Windows 10 [10.0.19044.1586]
Git: 2.35.1.windows.2

Please note that I disabled all extensions and I'm using Git Bash as a default terminal.
On VSCode 1.63.2
Version: 1.63.2 (user setup)
Commit: 899d46d82c4c95423fb7e10e68eba52050e30ba3
Date: 2021-12-15T09:40:02.816Z (3 mos ago)
Electron: 13.5.2
Chromium: 91.0.4472.164
Node.js: 14.16.0
V8: 9.1.269.39-electron.0
OS: Windows_NT x64 10.0.19044

Create new file named README.md
Type, Save, Stage and commit
Type again, Note that a blue bar appeared before saving document.
Save, Note that the blue bar disappeared and a green bar appeared.
Stage, Note that the green bar disappeared.
Commit.

On VSCode 1.65.2
Version: 1.65.2 (user setup)
Commit: c722ca6c7eed3d7987c0d5c3df5c45f6b15e77d1
Date: 2022-03-10T14:33:55.248Z (1 wk ago)
Electron: 13.5.2
Chromium: 91.0.4472.164
Node.js: 14.16.0
V8: 9.1.269.39-electron.0
OS: Windows_NT x64 10.0.19044

Create new file named README.md
Type, Save, Stage and commit
Type again, Note that the blue bar does not appeared.
Save, Note that the green bar does not appeared.
If I reopen the file (Ctrl + W and Ctrl + Shift + T), the green bar appeared.
Stage, Note that the green bar does not disappeared.
Reopen the file, the green bar disappeared.
Commit.

Similarly, git diff window also not updated immediately, as shown in below (1.65.2):

@kukdh1, thank you very much for the additional information. I have tried to reproduce the issue without much luck so I was wondering if I could ask you to try couple of things so that we track down the root cause of the issue that you are seeing.

Could you please check if you are able to reproduce the issue in 1.64. Download link are at the top of the release page.
We have made some changes related to file watching so I was wondering if you could collect the file watching logs while you are able to reproduce the problem.

@lszomoru Interestingly, some issues are solved after I removed the VSCode (deleting <HOME>/AppData/Local/Programs/Microsoft VS Code using uninstaller) and installed again.
So, I ran same tests, with uninstalling the VSCode everytime I change the version.
As shown in below (VSCode 1.64.2 and 1.65.2), change bars (blue and green) are appeared correctly as I edit the file.

But still, green bar does not disappear after staging/committing the file (both 1.64.2 and 1.65.2).

When I tested on 1.63.2, log says onWillActivateByEvent:  onFileSystem:git when I staged/committed.
Maybe this event is related to updating git diff?
Below log is collected on 1.63.2:
**** log.ts:289 TRACE CommandService#executeCommand git.stage
log.ts:289 TRACE CommandService#executeCommand setContext
log.ts:289 TRACE CommandService#executeCommand setContext
log.ts:289 TRACE [text file model] resolve() - enter git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
log.ts:289 TRACE [text file model] resolveFromFile() git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
++++ log.ts:289 TRACE onWillActivateByEvent:  onFileSystem:git
++++ log.ts:289 TRACE onWillActivateByEvent:  onFileSystem:git
log.ts:289 TRACE [text file model] resolveFromContent() - enter git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
log.ts:289 TRACE [text file model] doUpdateTextModel() git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
log.ts:289 TRACE [text file model] onModelContentChanged() - enter git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
log.ts:289 TRACE [text file model] onModelContentChanged() - new versionId 3 git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
log.ts:289 TRACE CommandService#executeCommand setContext

**** log.ts:289 TRACE CommandService#executeCommand git.commitStaged
log.ts:289 TRACE CommandService#executeCommand setContext
log.ts:289 TRACE KeybindingService#dispatch . undefined
log.ts:289 TRACE CommandService#executeCommand setContext
log.ts:289 TRACE CommandService#executeCommand setContext
log.ts:289 TRACE [text file model] resolve() - enter git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
log.ts:289 TRACE [text file model] resolveFromFile() git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
++++ log.ts:289 TRACE onWillActivateByEvent:  onFileSystem:git
++++ log.ts:289 TRACE onWillActivateByEvent:  onFileSystem:git
log.ts:289 TRACE [text file model] resolveFromContent() - enter git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
log.ts:289 TRACE [text file model] doUpdateTextModel() git:/d:/git/test/README.md.git?{"path":"d:\\git\\test\\README.md","ref":""}
log.ts:289 TRACE CommandService#executeCommand setContext

Please check below log too, which was collected on 1.64.2:
(This log does not contains onWillActivateByEvent)
**** log.ts:289 TRACE CommandService#executeCommand git.stage
log.ts:289 TRACE CommandService#executeCommand setContext
TRACE [text file model] resolve() - enter file:///d:/git/test/README.md
log.ts:289 TRACE [text file model] resolveFromFile() file:///d:/git/test/README.md
log.ts:289 TRACE KeybindingService#dispatch . undefined
log.ts:289 TRACE [File Watcher (node.js)] [raw] ["change"] globalStorage
log.ts:289 TRACE [File Watcher (node.js)] [CHANGED] c:\Users\kukdh1\AppData\Roaming\Code\User\globalStorage
log.ts:289 TRACE [File Watcher (node.js)] [raw] ["change"] globalStorage
log.ts:289 TRACE [File Watcher (node.js)] [CHANGED] c:\Users\kukdh1\AppData\Roaming\Code\User\globalStorage

**** log.ts:289 TRACE KeybindingService#dispatch Ctrl+Enter scm.acceptInput
log.ts:289 TRACE CommandService#executeCommand scm.acceptInput
log.ts:289 TRACE CommandService#executeCommand _vscode_delegate_cmd_l15cf7oh
log.ts:289 TRACE [File Watcher (node.js)] >> normalized [CHANGED] c:\Users\kukdh1\AppData\Roaming\Code\User\globalStorage
log.ts:295 DEBUG User data changed
log.ts:289 TRACE CommandService#executeCommand setContext

@kukdh1, thank you very much for sharing all these details. The git decorators are being updated through various events, one being the file system events scoped to the .git folder of the folder/workspace. I have just got to the bottom of a similar issue so I was wondering if you could try the following:

Could you please check your user/workspace setting and share the values of the files.watcherExclude.
Could you please invoke the Git: Set Log Level... command to set the log level to Trace
Reproduce the remaining issue, and send me the contents of the Git output channel which you can access by invoking the Git: Show Output Log... command

Could you please check your user/workspace setting and share the values of the files.watcherExclude.

Here is my user settings of files.watcherExclude:

JSON version was little different with the screenshot:
"files.watcherExclude": {
  "*.synctex.*": true,
  "**/__pycache__/**": true,
  "**/.ammonite": true,
  "**/.bloop": true,
  "**/.git/**": true,
  "**/.git/objects/**": false,
  "**/.git/subtree-cache/**": false,
  "**/.metals": true,
  "**/bazel-*/**": true,
  "**/node_modules/**": true,
  "**/node_modules/*/**": false,
  "**/vivado_project/**": true
}

Here is my workspace settings of files.watcherExclude (not changed though).
"files.watcherExclude": {
  "**/.git/objects/**": true,
  "**/.git/subtree-cache/**": true,
  "**/node_modules/*/**": true,
  "**/.hg/store/**": true
}

Git output log

Logs printed after I saved the file.

[2022-03-25T20:30:57.172Z] [debug] [wt] Change: d:\git\test\README.md
[2022-03-25T20:30:57.233Z] [debug] [wt] Change: d:\git\test\README.md
[2022-03-25T20:30:58.300Z] > git symbolic-ref --short HEAD [23ms]
[2022-03-25T20:30:58.331Z] > git for-each-ref --format=%(refname)%00%(upstream:short)%00%(objectname)%00%(upstream:track) refs/heads/master refs/remotes/master [29ms]
[2022-03-25T20:30:58.361Z] > git for-each-ref --sort -committerdate --format %(refname) %(objectname) %(*objectname) [28ms]
[2022-03-25T20:30:58.362Z] > git remote --verbose [27ms]
[2022-03-25T20:30:58.390Z] > git config --get commit.template [25ms]

Logs printed after I staged the file.

[2022-03-25T20:32:14.650Z] git.stage 1
[2022-03-25T20:32:14.650Z] git.stage.scmResources 1
[2022-03-25T20:32:14.679Z] > git add -A -- D:\git\test\README.md [27ms]
[2022-03-25T20:32:14.738Z] > git symbolic-ref --short HEAD [25ms]
[2022-03-25T20:32:14.770Z] > git for-each-ref --format=%(refname)%00%(upstream:short)%00%(objectname)%00%(upstream:track) refs/heads/master refs/remotes/master [30ms]
[2022-03-25T20:32:14.801Z] > git for-each-ref --sort -committerdate --format %(refname) %(objectname) %(*objectname) [29ms]
[2022-03-25T20:32:14.801Z] > git remote --verbose [27ms]
[2022-03-25T20:32:14.830Z] > git config --get commit.template [26ms]

Logs printed after I re-opened the file (to update diff highlights)

[2022-03-25T20:33:37.740Z] > git ls-files --stage -- D:\git\test\README.md [24ms]
[2022-03-25T20:33:37.767Z] > git cat-file -s 3b95c160030f12fd6dfc138e9e1dff143fa1a357 [26ms]

@lszomoru As I noticed that the files.watcherExclude includes whole git directory, I tried with default one by clicking Reset Setting in Settings window:
"files.watcherExclude": {
  "**/.git/objects/**": true,
  "**/.git/subtree-cache/**": true,
  "**/node_modules/*/**": true,
  "**/.hg/store/**": true
}

And I validated that the git highlights are updated correctly (as shown in below, on 1.65.2):

Also, Stage Selected Ranges works well:

Here is the git logs after stage, and last two lines are added:
[2022-03-25T20:54:52.496Z] git.stage 1
[2022-03-25T20:54:52.496Z] git.stage.scmResources 1
[2022-03-25T20:54:52.526Z] > git add -A -- D:\git\test\README.md [25ms]
[2022-03-25T20:54:52.585Z] > git symbolic-ref --short HEAD [24ms]
[2022-03-25T20:54:52.589Z] [debug] [.git] Change: d:\git\test\.git\index
[2022-03-25T20:54:52.615Z] > git for-each-ref --format=%(refname)%00%(upstream:short)%00%(objectname)%00%(upstream:track) refs/heads/master refs/remotes/master [28ms]
[2022-03-25T20:54:52.642Z] > git remote --verbose [24ms]
[2022-03-25T20:54:52.642Z] > git for-each-ref --sort -committerdate --format %(refname) %(objectname) %(*objectname) [26ms]
[2022-03-25T20:54:52.669Z] > git config --get commit.template [24ms]
++++ [2022-03-25T20:54:53.737Z] > git ls-files --stage -- D:\git\test\README.md [25ms]
++++ [2022-03-25T20:54:53.762Z] > git cat-file -s 3b95c160030f12fd6dfc138e9e1dff143fa1a357 [23ms]

I think you can close the issue (I cannot do that as I'm not an author of this issue).
Thank you very much for your help.
For anybody who has same issues:

Try to reinstall VSCode (to remove potential garbage files caused by update).
Reset files.watcherExclude setting to the default.

@kukdh1, thank you very much for sharing all these details. The git decorators are being updated through various events, one being the file system events scoped to the .git folder of the folder/workspace. I have just got to the bottom of a similar issue so I was wondering if you could try the following:

Could you please check your user/workspace setting and share the values of the files.watcherExclude.
Could you please invoke the Git: Set Log Level... command to set the log level to Trace
Reproduce the remaining issue, and send me the contents of the Git output channel which you can access by invoking the Git: Show Output Log... command

I can happily confirm that I had this in my settings.json for some god awful reason.
    "files.watcherExclude": {
        "**": true
    }

Really not sure where it came from, maybe an extension in the past messed it up(?) Does running VSCode without extensions not reset settings.json(?). But after removing it, the feature works as expected (as it always have for years).
I am closing the issue.


Patch MaterialService.Use2022Materials

Closes #243.
(Do I need to run generate_reflection myself?)

This looks good, though we'll have to regenerate the database. The instructions on how to do so aren't amazing, but you'll need to run generate_reflection yourself.
If you have bash available, there's a script located here but if not, just run the command that's in that script and commit the changed database.

As I'm on Linux, I'm not sure if I'll be able to run generate_reflection very easily.

Provided you have the Rust toolchain installed, it should be straightforward because like I said, there's a script available to build and run it like we need. If that's still not possible, I can just generate it myself, though as a general rule I'd prefer to not push to your branch.

The script tries to locate and run Roblox Studio, which won't work

Ah yes that would be a problem! Sorry, I don't usually run Linux so I didn't think about that. 😓
For the sake of simplicity, I've verified that this affects the database in the intended way and I'll go ahead and merge this without updating it in this PR.


Modify default precision

fix #588
I'm really not sure that this is the right way to solve the issue and I am not sure that it is an issue.
The default precision in based on the value required for that precision; with this PR I modify this concept.

Coverage decreased (-0.04%) to 72.171% when pulling ef23f3096874763fce10ce1c481b037c824a5b6d on lucazulian:timex-to-datetime-truncates-microseconds-588 into 0831edf2dae8060be740330b8cfcaeb8ce1ee762 on bitwalker:master.

Coverage decreased (-0.04%) to 72.171% when pulling ef23f3096874763fce10ce1c481b037c824a5b6d on lucazulian:timex-to-datetime-truncates-microseconds-588 into 0831edf2dae8060be740330b8cfcaeb8ce1ee762 on bitwalker:master.

Can you explain the motivation behind this change? We explicitly want to preserve precision, or match the precision of inputs, in those cases where a precision was not specified or detectable.

The motivation behind this is due to the issue #588, and I'm not sure it's the correct way to solve the issue. This is just an attempt, do you have any suggestion? Or can we close the issue as we don't see the need for an extra precision?

A side note about this pr.  I think this pr would also fix a problem I had.
> Timex.to_datetime({{2017, 1, 1}, {0, 0, 0,0}}) |> Timex.format("{RFC3339z}")
{:ok, "2017-01-01T00:00:00Z"}
> Timex.to_datetime({{2017, 1, 1}, {0, 0, 0,1}}) |> Timex.format("{RFC3339z}")
{:ok, "2017-01-01T00:00:00.000001Z"}

I don't care if the inspect format truncates, but I've also noticed that several of the formatting functions also truncate.  We had an issue where once in awhile elastic search queries would fail sometimes.  It requires that you specify the format of time stamps in its queries and it either accepts a format with milliseconds or without it.
Once every million queries it would fail, and that would occur because the date we were sending to elasticsearch would not have milliseconds because of this truncation.  Luckily the fix was easy in elasticsearch (tell it to try one format, then the other), but I imagine that kind of fix will not always be easy.

@mindreader In your example there, the first date/time had no microseconds (and thus zero precision), while the second one has exactly 1 microsecond (and so requires full precision).
When converting from an Erlang timestamp to an Elxir date/time, we infer the precision based on the precision required to accurately express the input; but Elixir date/times can have values which are more precise than the precision set in the structure itself (i.e. Elixir separates the desired precision from the value, which is then used in printing/etc.).
So in the case of converting an Erlang timestamp (w/ microseconds) to an Elixir date/time and printing it, the results you see are exactly what we'd expect. In the case where an Elixir date/time is the input though, we use the precision defined in the date/time structure itself, rather than infer from the value. You can force zero precision (or full precision), by setting the precision of the DateTime/NaiveDateTime/etc. structure manually (or by providing the precision during construction, if using the Elixir APIs).
@lucazulian The above is why #589 is not a bug, but expected behavior - a microseconds value of 0 is the default value of a zero-precision value (and requires no microsecond precision to express). Your application code should instead force the precision to 6 after constructing the date/time value if that is what is desired in your application.
Since I don't believe this PR is actually addressing a bug, I'm going to close this for now, but I'm open to continuing the discussion if there is still some question around the behavior here.


Correct/Optimize  averageBytesPerRecord estimation (wrong estimation results in OOM)

The Append/Merge handle have a list of records that need to be appended or merged, on a wrong estimation https://github.com/uber/hoodie/blob/master/hoodie-client/src/main/java/com/uber/hoodie/io/HoodieMergeHandle.java#L49 blows up.

@n3nash can you add more details on when the estimation is wrong


SUP no longer supported on Server 2008 R2

We only allow for DPs on Server 2008 R2 per supported config.

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

ID: 0c3e8dd5-a5d0-c96c-841a-21589d58d20b
Version Independent ID: 09984eaa-b26b-bc94-7250-c4e5db8f5f58
Content: Prerequisites for software updates - Configuration Manager
Content Source: sccm/sum/plan-design/prerequisites-for-software-updates.md
Product: configuration-manager
GitHub Login: @aczechowski
Microsoft Alias: aaroncz

@aczechowski Created PR https://github.com/MicrosoftDocs/SCCMDocs-pr/pull/3045 for this issue. Also, I wanted to add a reference to this document, https://docs.microsoft.com/en-us/sccm/core/plan-design/configs/supported-operating-systems-for-site-system-servers#bkmk_2008r2sp1, but wasn't sure the correct path for the link.

Fixed by https://github.com/MicrosoftDocs/SCCMDocs-pr/pull/3045

Thanks @jocasti, closing


Changed slice  method type

I have been using the fs.slice method for almost a year now in my app. and the slice method in the FS interface was returning Promise<void>, which created a small typing issue in the code. This PR changes it from Promise<void> to Promise<string>. In all my testing, this method never returned void, and because JS loads the sliced file to memory, I don't think it will ever return void or any other type other than string. That said, it would be best to test a scenario where the device doesn't have required storage to be able to save the slice in a different directory. In that case, it might break. If I can, I'll test it and update this PR. If anyone else wants to try, let me know.

I will take a look at the native side and merge it or ask for adjustments


Add etcd backup API

Adds the techpreview API for etcd backups as outlined in https://github.com/openshift/enhancements/pull/1370
Adds the following APIs:

backups.config.openshift.io/v1alpha1

Used to configure the schedule and retention policy of periodic backups

etcdbackups.operator.openshift.io/v1alpha1

Triggers a onetime backup of the etcd cluster

/cc @tjungblu @deads2k

Still some TODOs:

Some CEL validation rules
Need to figure out why make update-code-gen-crds isn't generating the openapi schema.

looks pretty good already, @hasbro17! thank you :)

Missing the test suite for the new types. Will update that next.

So I did have malformed yaml but confusingly not where I expected it from the error:
error running generator schemapatch on group backup.openshift.io: could not run schemapatch generator for group/version backup.openshift.io/v1alpha1

That made me think the issue was with backup/v1alpha1/0000_10_01_etcdbackup-TechPreviewNoUpgrade.crd.yaml but it was actually in the testsuite backup/v1alpha1/techpreview.etcdbackup.testsuite.yaml. Should be updated now.

A couple of TODOs for the next update:

Rename the group for the lower level EtcdBackupCRD from backup.openshift.io=> etcdbackups.operator.openshift.io.
Depending on how we want to allow and handle multiple one time EtcdBackup requests, decide if we need an additional EtcdBackup state  e.g Aborted to mark all but the latest (or a singular) EtcdBackup as unfulfilled.

One alternative is to only allow a cluster singleton EtcdBackup CR, which necessitates only one ongoing backup at a time. The drawback of the cluster singleton would be losing the history of previous backup requests i.e Completed EtcdBackup CR objects.

@hasbro17 could you please rebase as well? it's currently impossible for me to create a cluster:

Cluster Bot APP
pull request openshift/api#1482 needs to be rebased to branch master

Rebased and moved out the featuregate into https://github.com/openshift/api/pull/1511
Moved the lower level EtcdBackup CRD from backup.openshift.io to operator.openshift.io
Still adding the cron validation and its unit tests. Also need to sort out why the schema generation isn't running again.

Updated the following for the latest review comments:

Removed EtcdBackupState from EtcdBackup status in favor of defining conditions in the operator
Removed StartTime  and FinishTime  from EtcdBackup status
Other renaming nits for the union members in the Backup config.
Added CEL validation regexes for the Cron and timezone formats.

The cron regex was pared down from the extended version to fit the POSIX variant used by the cronjob. See https://regexr.com/7gcfo for unit tests
I had to construct the timezone regex from scratch but it's passing for all the variants in the tz timezone database that I've tested. See https://regexr.com/7gedh for unit tests.

TODO: Translating the online regex validator unit tests into the API testsuite unit tests.

Made the following update:

Added the integration tests for the regex validations for the schedule and timezone formats (waiting to see that those go green)
Added a Job reference field status.backupJob in the EtcdBackup status so we can reference the backup job associated with that CR
Added basic conditions for the EtcdBackup status: Pending, Completed, Failed, Skipped.

Only last thing remaining is finalizing whether we want the admin's PVC to be created in our "openshift-etcd" namespace or in a separate one https://github.com/openshift/api/pull/1482#discussion_r1245704258
Besides that, this should be good for a final review.

A few comments, but not many.  I think the hardest remaining thing is leaving it possible for a no-opinion zero-value resource to indicate: "take backups stored on a different master every four hours".  We can argue over frequency, but I'll open there.
We don't need that no-opinion behavior now, but we should plan to have it ready a release after we make this feature accessible-by-default.

@deads2k Updated for review comments. All except for allowing the no-option pvcName: "" which we'll target as a follow up. (Unless you meant to add it to the API first).

/lgtm
/approve

Ah, forgot to update the unit tests after making the pvcName field optional. Will update that.

/lgtm


show loading bar when checking for entries

Shows a loading bar when fetching my tools/workflows, instead of showing blank or showing the alert that they have no tools/workflows/

This type of change can just reuse the refreshMessage variable.  Just set the refreshMessage to something truthy before the usersService call and finalize with something non-truthy


creating resizable-panel component with breakpoint 5%, 50%, 90%

creating resizable-panel component with breakpoint 5%, 50%, 90% to sit next to a example leaflet map
ticket number: https://apps.nrs.gov.bc.ca/int/jira/browse/WFPREV-68.
This PR implements a resizable panel under map page. with an embedded Leaflet map. The panel can be resized to preset viewport widths (5%, 50%, and 90%) and the map automatically adjusts its layout to fit the new dimensions.
this resizable component can be resued inside other components if needed.

this is just a stub component without meaningful contents

Components also require stories

Storybooks added, and ng-content added


upgrade django + wagtail

update to newer version of wagtail
update to newer version of django
update to newer version of python

testing / review
public site

[x] home page
[x] blog (list, individual pages, pagination)
[x] events (list, individual event pages)
[x] project pages (lists, individual pages)
[x] people (lists, individual profile pages)
[x] content pages and landing pages
[x] search

editing in wagtail
test editing existing content and adding new:

[x] content page
[x] landing page
[x] blog post
[x] event
[x] project; update grants and members
[x] profile
[x] adding new image (upload and associate with something)

PUBLIC SITE
Home page: carousel images are not showing up in Chrome, Firefox, or Safari; i checked to make sure there was a photo selected and that the post was featured but still no photos
Blog posts: alt text showing up where images should be
Events: no images on event card or on actual individual event page
Project Pages: some images show up and some don't (this is true of the thumbnails and of the images on the event page); interestingly, all of the ones that do NOT show up appear to be current projects (for example, Healing, Water & Art, whereas photos are working for past projects. In the cases that photos are not showing up, alt text is shown on the project description page.
People: Older photos show up whereas newer ones don't. On the list, missing images show as blue boxes; on staff profile pages, alt text is shown rather than the image.
Content pages / landing pages: Issue again is images. The landing page for "research" should have an image of PUL but it does not. Images on the other landing pages are fine. Most pages don't have photos but I noticed the Creative Commons license on the project charters page was alt text.

PUBLIC SITE:
Events were in a slightly different order. On the test site, the African Language Tech postdoc deadline came before the MARBAS one. On our current site, it's the opposite. Note the deadline is the same for both of them. Otherwise fine.

Okay, I think it's good! Occasionally a little trial and error was involved (as it is on the actual site) but I got everything to work. I tried out photos, links, PDFs, etc.

testing completed successfully! 🎉


BUG: INSTALL script fails

Description
INSTALL script fails:
remote: Enumerating objects: 285, done.
remote: Counting objects: 100% (285/285), done.
remote: Compressing objects: 100% (184/184), done.
remote: Total 285 (delta 79), reused 217 (delta 64), pack-reused 0
Receiving objects: 100% (285/285), 180.79 KiB | 1.08 MiB/s, done.
Resolving deltas: 100% (79/79), done.
From https://github.com/plume-oss/plume
 * branch            develop    -> FETCH_HEAD
 * [new branch]      develop    -> origin/develop
HEAD is now at e396ed7 :white_check_mark: CPG-generator/query-language integration testing setup (#39)

FAILURE: Build failed with an exception.

What went wrong:
Task 'oneJar' not found in root project 'plume'. Some candidates are: 'jar'.

Gradle version 6.7
Mac OS X Big Sur
OpenJDK Version 14.0.1
Steps to reproduce

Clone the Repo
Execute the INSTALL script

P.S.
Is the INSTALL script even needed?
I could run the TinkerGraph example, although the XML file only contained a single Meta-Node :
<?xml version="1.0" ?><graphml xmlns="http://graphml.graphdrawing.org/xmlns" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://graphml.graphdrawing.org/xmlns http://graphml.graphdrawing.org/xmlns/1.1/graphml.xsd%22%3E<key id="labelV" for="node" attr.name="labelV" attr.type="string"></key><key id="language" for="node" attr.name="language" attr.type="string"></key><key id="version" for="node" attr.name="version" attr.type="string"></key><key id="labelE" for="edge" attr.name="labelE" attr.type="string"></key><graph id="G" edgedefault="directed"><node id="306760763"><data key="labelV">META_DATA</data><data key="language">Java</data><data key="version">Java</data></node></graph></graphml>%

Oh yeah this is quite an old artifact from before Plume had releases. I'll get rid of it. I'm busy looking into the single metanode bug now.

"although the XML file only contained a single Meta-Node" - this is linked to the following issue: https://github.com/plume-oss/plume/issues/91


Update install.sh

Updates plex download links to point to official releases

open config/app.jsonl: no such file or directory
Can you change the script to make a directory called config inside plex. The app.jsonl and instruction_template.jsonl should live inside there.

Thank you @thetechnocrat-dev. Changes incorporated


The dropdown menu ⋮ to remove a GitHub connection is not being shown

I want to remove a GitHub connection I've made but the button for this step is not there.
Screenshot used in docs:

My screenshot:

No ⋮ button found

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

ID: db555e9d-f86e-be8e-be13-d9d10e1b54d0
Version Independent ID: 21327f5a-4731-3004-86bf-05954134119e
Content: Add or remove GitHub repositories - Azure Boards
Content Source: docs/boards/github/add-remove-repositories.md
Product: devops
Technology: devops-agile
GitHub Login: @KathrynEE
Microsoft Alias: kaelli

@NicolasDue - Thank you for your inquiry. Could you check that you are a member of the Project Administrators group for your project? It may be that you were when you added the repo but it has since changed. If that isn't the issue, then I recommend that you report your issue on our Developer Community page.  They may be able to help you troubleshoot further.


fuzzy matching script

uploading some Python code for doing curated name fuzzy matching

@cgmeyer , thanks for creating the script. Please find a suggestion on line 18 - 21. The absolute path will not work for others. Please consider the following
import os

# Get the absolute path of the current script
script_path = os.path.abspath(__file__)

# Get the directory containing the script
script_directory = os.path.dirname(script_path)

print("Directory of the script:", script_directory)


build process broke/changed

My "rebuild from scratch" script no longer works.
; ./config
Configuring OpenSSL version 3.0.0-alpha13-dev for target linux-x86_64
Using os-specific seed configuration
Creating configdata.pm
Running configdata.pm
Creating Makefile

**********************************************************************
{banner elided}
**********************************************************************
; make -s update tags build_generated
./util/libcrypto.num: No new symbols added
./util/libcrypto.num: 899 symbols are without ordinal number
./util/libssl.num: No new symbols added
./util/libssl.num: 23 symbols are without ordinal number
; make doc-nits
Detected changed: doc/build.info
/usr/bin/perl configdata.pm -r
Configuring OpenSSL version 3.0.0-alpha13-dev for target linux-x86_64
Using os-specific seed configuration
Creating configdata.pm
Running configdata.pm
Creating Makefile

{banner elided}
**************************************************
***                                            ***
***   Please run the same make command again   ***
***                                            ***
**************************************************
Makefile:4090: recipe for target 'configdata.pm' failed
make: *** [configdata.pm] Error 1
        exit 2
;

I assume something from #14292, #14269 changed things.  If I combine the two make commands into one it seems to work:
; ./config
Configuring OpenSSL version 3.0.0-alpha13-dev for target linux-x86_64
Using os-specific seed configuration
Creating configdata.pm
Running configdata.pm
Creating Makefile

{banner}
; make -s update tags build_generated doc-nits
./util/libcrypto.num: No new symbols added
./util/libcrypto.num: 899 symbols are without ordinal number
./util/libssl.num: No new symbols added
./util/libssl.num: 23 symbols are without ordinal number
;

I can work around this (pity, I've been using this script for years), but it seems the change introduced some dependency error?

Try with #14309


Changing config file is triggering Webpack, but not updating compiled CSS

When changing my tailwind.js file it triggers the Webpack build, however nothing is updated in the final app.css file. It used to work perfectly, not sure if this is a change in Tailwind or something else.
package.json:
{
    "private": true,
    "scripts": {
        "dev": "npm run development",
        "development": "cross-env NODE_ENV=development node_modules/webpack/bin/webpack.js --progress --hide-modules --config=node_modules/laravel-mix/setup/webpack.config.js",
        "watch": "npm run development -- --watch",
        "watch-poll": "npm run watch -- --watch-poll",
        "hot": "cross-env NODE_ENV=development node_modules/webpack-dev-server/bin/webpack-dev-server.js --inline --hot --config=node_modules/laravel-mix/setup/webpack.config.js",
        "prod": "npm run production",
        "production": "cross-env NODE_ENV=production node_modules/webpack/bin/webpack.js --no-progress --hide-modules --config=node_modules/laravel-mix/setup/webpack.config.js"
    },
    "devDependencies": {
        "cross-env": "^5.2.0",
        "laravel-mix": "^2.0",
        "tailwindcss": "^0.6.3"
    }
}

webpack.mix.js:
let mix = require('laravel-mix')
let tailwindcss = require('tailwindcss')

mix
    .js('resources/assets/js/app.js', 'public/js')
    .sass('resources/assets/sass/app.scss', 'public/css')
    .version()
    .options({
        processCssUrls: false,
        postCss: [tailwindcss('tailwind.js')]
    })

Lame — confirmed, will fix.

Fixed in 0.6.4 which is now available 🤙

Can confirm it works now on 0.6.4!

Was there a regression on this? Somehow this doesn't work anymore and I swear I had it working before. 🤔

Can you create a project that reproduces the issue?

I've been working with Bedrock's WordPress starter theme, Sage that comes with Laravel Mix, but I'm currently failing at isolating the problem. When I start a blank project and add the same dependencies with the same versions, it works. I made sure it's not a caching issue by looking at the built css to make sure the values aren't reflected in the file itself 🤔 . I'll try to isolate it and I'll update here... might just be a random dependency conflicting.

Ugh, found it, a change I made myself and had completely forgot and overlooked. I was loading my config with const tailwindconfig = require('./tailwind.config.js'); to edit it some values inside my webpack.mix.js file because I wanted to change some values according to another package and passing it as an object to the plugin...
    processCssUrls: false,
    postCss: [
        tailwindcss(tailwindconfig),
        postcssCustomProperties()
    ],
});

...instead of passing a string path directly 🤦 . I totally get why it wasn't working! I apologize for the random pings, but if someone gets the same problem, at least it will be documented here I guess!


Coding on the terminal?

Hey I was wondering if you could use the windows terminal as a code editor just as I saw on the release video?

The code editor shown in the video was Vim. Any text-based code editor will work.


Improve location info for syntax errors.

Patch is ready for review.

@zherczeg Please rebase after #4818 .

@zherczeg please rebase


Invocation-level fault tolerance guarantees

Hi people! I am aware that Github issues might not be the right place to ask questions, but Slack won't send an invitation to my email.
Does someone know if OpenWhisk provides any fault tolerance guarantees on the invocation level? For example, if some component on the critical path of an invocation or a worker node fails during the execution of a request, will OpenWhisk try to reexecute the failed invocation, or this is left to the user to handle?
Thanks.

Hi,
Sorry the slack invitation isn't woking for you.
To answer the question, OpenWhisk offers an "at most once" instead of an "at least once" execution model.  So if there is a failure during the execution of a request, the execution will not be automatically retried by OpenWhisk.  If a user wants to ensure that a request will be executed at least once, they have to track their open requests externally and resubmit requests that haven't completed within some time threshold they think is reasonable.

@dgrove-oss
It seems this invitation button does not work as expected.
https://openwhisk.apache.org/slack.html
The action was running on bluemix and it seems it is no longer valid.
$ curl -X GET<EMAIL_ADDRESS>-k
404 Not Found: Requested route ('21ef035.api-gw.mybluemix.net') does not exist.

https://github.com/apache/openwhisk-slackinvite
Do you have any idea about it?
Maybe we need to deploy it on another cloud?
If we can't use bluemix anymore, I would look for another one.

@style95 -- IBM Cloud withdrew API gateway support and the action was also probably running on a really old node.js version that is no longer supported.  Definitely is not working now.
We either need to host it somewhere else, or look for a more direct way of adding people to Slack.  It was a cute demo to use an OpenWhisk function, but there may be simpler ways to do it.

@dgrove-oss Any quick fix on getting the slack invite link working? I am interested in joining the OpenWhisk Slack community.

@Abhishekghosh1998 -- the most expedient thing would be to send an email to me<EMAIL_ADDRESS>with your email and I will invite you to join directly from Slack.

should we replace the instructions with "send email to the dev list to get an invitation"?


CB does not display correctly in HTML when select CB

Keep in mind, this occurs on HTML only

fixed


Core calc

The core calculation module for complex mathematical operations.
This module includes calculation module with the supporting unit tests.
The following operations are supported

Addition ( + )
Subtraction ( - )
Multiplication ( * )
Division ( / )
Exponent ( ** )
Bitwise And ( & )
Bitwise Or ( | )
Bitwise Xor ( ^ )

Use

evalExp(String)

to perform expression evaluation.
Example :

evalExp('6 * (3 + 4)')

gives

42

Use this to run the tests
mocha coreCalc.test.js

Great work Man 🥳


feat(storage): add redis storage

This PR is based on #2!
The storage based on JSON like aiogram.
TODO: think about context.TODO(), maybe we can add a new argument ctx into each storage method?
But anyway telebot doesn't support context.Context "flow" :-(

Oh, I found out that for the numbers json.Unmarshal always returns float64.
Even if we use decoder.UseNumbers(), we can return only int64 or float64, not int32, int16 etc, so we can't return the initial type for the integers or floats.
The solution might be storing the type of the variable as well as the value just like:
{
  "inputName": {"type": "string", "value": "Peter"},
  "inputAge":  {"type": "int", "value": 21}
}

But then we don't even need to store the state data in JSON I think.

The solution might be storing the type of the variable as well as the value just like:

Seems that will be so hard and even impossible for some custom types I think.
Seems the only one easy way to solve it - encode the value via "encoding/gob" and let the "GetData" method accept "to interface{}" argument and not return the value like
GetData(chatId, userId int64, key string, to interface{}) error

and the client code will look like
var age int
if err := state.Get("age", &age); err != nil {
  return err
}
fmt.Println(age) // 21

It needs to change the Context and Storage interface, but I don't see any other type-safe solution.

Here is the example of letting the "GetData" save the data to "to interface{}" argument: https://github.com/vitaliy-ukiru/fsm-telebot/pull/4

TODO: think about context.TODO(), maybe we can add a new argument ctx into each storage method?

good idea, I think can add the WithContext(context.Context) fsm.Context method to fsm.Context, default sets context.Background, or (and) embed context.Context

TODO: think about context.TODO(), maybe we can add a new argument ctx into each storage method?

good idea, I think can add the WithContext(context.Context) fsm.Context method to fsm.Context, default sets context.Background, or (and) embed context.Context

if you mean to put the client's context into the fsm.Context as a field of the fsmContext structure, then don't know, what if the client wants to control every Set and Get with his own contexts

I don't want "FSMContext" to always require context, this will make interface more complex. I want it to be light version of access to storage.

but it's the usual way in Go, isn't it? :)


Publicly available list of the workshops' secretaries.

This could probably be integrated into the info panel on the main page.
Remark: this is a feature request from Ákos Blaskovics.

We will need the workshop pages soon, I'd add there if not urgent.


Whitelist asset registeraddress

New user's address registration requires whitelist asset. Zero fee for the transaction.

FYI I'm removing the exception throws from whitelist.cpp.
On Tue, 16 Apr 2019 at 12:59, Nikos Kostoulas<EMAIL_ADDRESS>wrote:

@nkostoulas requested changes on this pull request.
By the way do the exceptions in whitelist crash the node? Does that mean
that if someone sends a transaction with invalid address it will cause the
node to crash?
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https://github.com/commerceblock/ocean/pull/110#pullrequestreview-227147113,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AEDzvOyCjISWJGX_z_kno_4TdsK5iqTxks5vhbssgaJpZM4cyCF0
.

I've kept some throws but simplified them into one basic category (std::invalid_argument), and handled where necessary.


Nerve httpd collector

Implement reporting metrics from apache running inside docker containers discoverable via nerve config.
A majority of services may not have httpd status from them and hence this collector will cache 404 responses for 1 hour and not collect from the services for that time duration.  This avoids spamming unrelated services with server-status requests.

+1 lgtm!

My comment about the new WithValue interface is more a personal preference than a big issue, so if both you and @tiras-j like that more, feel free to go ahead.
+1


[WIP] Add Filtering

Using the ManageIQ::API::Common::ErrorDocument and dropping our copy as it is shared with Filter & Topological-Inventory API.
Updated Application Controller to support Filtering of requests via the filter parameter leveraging ManageIQ::API::Common::Filter
Updated the OpenAPI 3.0.0 Specification to know about the filter parameter, generated via an update
to the openapi:generate rake task.

TODO:

Spec tests

/cc @gmcculloug  @lindgrenj6 here is the PR for adding Filtering to the sources-api using the common libraries used by Topological-Inventory API.  The relevant commits for you to look at are: https://github.com/ManageIQ/sources-api/pull/13/commits/82297f2e951e53d057ac17d8007a362709e10bc0 and https://github.com/ManageIQ/sources-api/pull/13/commits/c77b75135b037d127b7e9ca4060d86208da6dc40

/cc @agrare @gtanzillo here you go, filtering enabled and workin' like a champ.  Just need to add spec tests just to show filtering is enabled before I un-wip.


Provide filter in jobs page

cleaning old issues,  @fanyangCS please help to evaluate whether this is still an issue, thanks.

As there may be a lot of jobs in job list, a filter is helpful to find interested one. Currently, there is a search box, and can search in any column. But it's not so intuitive, and friendly. It's better to provide some filters, like My jobs, Running, Failed as so on. So that user can get them with one click.

https://github.com/Microsoft/pai/pull/2111

Artboards

Test case:

Job lists rendered fine, could go into details page
Paginator works fine
Filters
a. All filters works fine
b. Filtered label displayed in the label, with (+n) when multiple
c. Change the filters will reset the pagination
d. Clear filter (cross icon at the right of the filter bar)
Ordered by Name / Date Modified / User / Duration / Vrtual Cluster / Status
"Stop" button
a. For simple job, right of the row.
b. For multiple jobs at the top bar.
"New" button, linked to submit job page.
The filter state will persist after browser close and open.
The initial filter:to recover the initial filter: run window.localStorage.removeItem("pai-job-filter") in console.
a. If user is admin, default no filtered.
b. If not, default filtered user's jobs.


window.performance.mark becomes undefined after timer install

I have noticed the following behavior in the browser:
import { useFakeTimers } from 'sinon';

console.log('1', window.performance.mark) // '1', function mark() { ... }
clock = useFakeTimers();
console.log('2', window.performance.mark) // '2', undefined

window.performance became a function after calling useFakeTimers. I believe that the issue is coming from this line:
https://github.com/sinonjs/lolex/blob/c08ff362a47e9786bc62da6c37175838bb7bd21e/src/lolex-src.js#L406-L408
One simple workaround is the following:
-clock = useFakeTimers();
+clock = useFakeTimers({
+  toFake: ["setTimeout", "clearTimeout", "setImmediate", "clearImmediate","setInterval", + "clearInterval", "Date"]
+});

I had to do some digging, the error on my side was coming from this line: https://github.com/facebook/react/blob/v16.0.0/src/renderers/shared/fiber/ReactDebugFiberPerf.js#L81.

Verified. Here is the test with a browserified transpiled output that can be copy-pasted directly into Chrome for verification. Tested with master (6476935).
test.js.txt
transpiled.js.txt

@oliviertassinari wanna take a shot at a PR at this? Otherwise I can probably take a stab

@benjamingr I'm already pretty busy with Material-UI. Sorry, it's not a priority for me.

@oliviertassinari no need to justify or apologize - it's entirely fine if it's not a priority for you - I was merely offering :)

@fatso83 I still can't assign myself to issues by the way :D I'll take a stab next week hopefully

Is there anyone working at this issue at the moment? :-)

sorry, completely forgot about it - can take a look early next week

Thank you very much!

This temporary solution did not work for me using:

<EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS>
However, @oliviertassinari's workaround did work for me.

Going to tackle this now

I added a test case as:

describe("issue #136", function () {
    if (performancePresent) {
        it("should clear performance.mark after uninstall", function () {
            var oldMark = performance.mark;
            var clock = lolex.install();
            assert.same(performance.mark, oldMark);
            clock.uninstall();
            assert.same(performance.mark, oldMark);
        });
    }
});

but it passed without any changes - what am I not understanding?

I created pull request, #160. If there is someone who has admin permissions, please review my PR.


2024-10-18_01-35-23_master-next_aws-cli

Automatically created.

Successfully created backport PR for kirkstone-next:

#10033

Successfully created backport PR for scarthgap-next:

#10034

Successfully created backport PR for styhead-next:

#10035


Use Yarn and update dependencies

Adam and I are off tomorrow so I'd rather wait to merge these changes in case they create any unexpected issue.
I'll merge next week when I have some time but please feel free to merge it any time before @avclarke.


python311Packages.openant: 2017-02-11 -> 1.2.1

Description of changes
Diff: https://github.com/Tigge/openant/compare/ed89281e37f65d768641e87356cef38877952397...v1.2.1

Things done

Built on platform(s)

[x] x86_64-linux
[ ] aarch64-linux
[ ] x86_64-darwin
[ ] aarch64-darwin

[ ] For non-Linux: Is sandbox = true set in nix.conf? (See Nix manual)
[x] Tested, as applicable:

NixOS test(s) (look inside nixos/tests)
and/or package tests
or, for functions and "core" functionality, tests in lib/tests or pkgs/test
made sure NixOS tests are linked to the relevant packages

[ ] Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
[ ] Tested basic functionality of all binary files (usually in ./result/bin/)
23.11 Release Notes (or backporting 23.05 Release notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.


Remove process_currencies

Fixes #59
@siddharth-krishna could you add use of https://github.com/olejandro/times-ireland-model_gams for comparison in this PR?

@olejandro, sure. Do you mean replace MaREI-EPMG/times-ireland-model_gams with olejandro/times-ireland-model_gams in our CI for the benchmark "Ireland"? Or maybe add a new benchmark "Ireland latest" with olejandro/times-ireland-model_gams as the ground truth (and MaREI-EPMG/times-ireland-model as the input?).

@olejandro, sure. Do you mean replace MaREI-EPMG/times-ireland-model_gams with olejandro/times-ireland-model_gams in our CI for the benchmark "Ireland"? Or maybe add a new benchmark "Ireland latest" with olejandro/times-ireland-model_gams as the ground truth (and MaREI-EPMG/times-ireland-model as the input?).

Replace 🙏, seems some bugs were fixed, since I had generated the original files


Obisidan 1.0.0: Button color only visible by hovering

With Obsidian 1 (also with Installer-Version: v1.0.0), the button color went away. When I hover, I can see it.
This can be seen in every theme (tested: obsidianite, its, minimal and standard theme.

fixed in #0.4.18

It works! Thank you very much!


[DOC] skpro tutorial introduction notebook

work in progress

Codecov Report
Patch coverage has no change and project coverage change: -1.99% :warning:

Comparison is base (721549c) 71.38% compared to head (34dcc74) 69.39%.

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #75      +/-   ##
==========================================
- Coverage   71.38%   69.39%   -1.99%
==========================================
  Files          92       92
  Lines        4945     4944       -1
  Branches      897      897
==========================================
- Hits         3530     3431      -99
- Misses       1180     1284     +104
+ Partials      235      229       -6

see 5 files with indirect coverage changes

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


Does it support Deta Space micros?

Hi! Just tried your library by following your instructions with using Deta Space
But I cannot save the changes when I inputted the URL in the Endpoint URL box:

What should I do?

hey ... you have to add /interactions to public routes

Oh it works now! I've just registered the command on the dashboard
But it is making this error now... How do I fix it?

Can you share some logs? You can join our discord server for more help
https://discord.gg/a67HbpfTk8

It is now fixed with help from the Discord guild! Thanks 🙏🏻!


[HW] Siraj Din

Name: Siraj-din Umeya
Email<EMAIL_ADDRESS>Linkedin Profile: https://www.linkedin.com/in/siraj-din-umeya/
Attach the homework step I screenshots below:

Hey Siraj, great job! Congrats! Here is your badge! https://api.badgr.io/public/assertions/x00zNmr3QtCBP0Yrj0TXrg


Retry 500 errors from gh release

See this example release run: ci link.
Upload failed with the following output.
+ gh release upload v0.3.0 cargo-marker-x86_64-unknown-linux-gnu.tar.gz cargo-marker-x86_64-unknown-linux-gnu.zip cargo-marker-x86_64-unknown-linux-gnu.sha256 --clobber
HTTP 502: Server Error (https://api.github.com/repos/Veetaha/marker/releases/assets/125294025)
Error: Process completed with exit code 1.

I suggest using exponential backoff to retry the gh release operation when it fails.
Here is an example bash function that we use to retry any network operations.

Thanks for the report! Fixed in 1.16.1.


Veracode Static Dynamic upload fail

File to import: veracode/veracode.Sample_Static_and_Dynamic.xml
Issue: DD reports Server Error (500)
Logs:
Internal Server Error: /product/2/import_scan_results
Traceback (most recent call last):
  File "/usr/local/lib/python2.7/site-packages/django/core/handlers/exception.py", line 41, in inner
    response = get_response(request)
  File "/usr/local/lib/python2.7/site-packages/django/core/handlers/base.py", line 249, in _legacy_get_response
    response = self._get_response(request)
  File "/usr/local/lib/python2.7/site-packages/django/core/handlers/base.py", line 187, in _get_response
    response = self.process_exception_by_middleware(e, request)
  File "/usr/local/lib/python2.7/site-packages/django/core/handlers/base.py", line 185, in _get_response
    response = wrapped_callback(request, *callback_args, **callback_kwargs)
  File "/usr/local/lib/python2.7/site-packages/django/contrib/auth/decorators.py", line 23, in _wrapped_view
    return view_func(request, *args, **kwargs)
  File "./dojo/product/views.py", line 382, in import_scan_results_prod
    return import_scan_results(request, pid=pid)
  File "/usr/local/lib/python2.7/site-packages/django/contrib/auth/decorators.py", line 23, in _wrapped_view
    return view_func(request, *args, **kwargs)
  File "./dojo/engagement/views.py", line 519, in import_scan_results
    parser = import_parser_factory(file, t)
  File "./dojo/tools/factory.py", line 69, in import_parser_factory
    parser = VeracodeXMLParser(file, test)
  File "./dojo/tools/veracode/parser.py", line 59, in __init__
    dupe_key = sev + flaw.attrib['cweid'] + flaw.attrib['module'] + flaw.attrib['type'] + flaw.attrib['line'] + flaw.attrib['issueid']
KeyError: 'line'

why is it marked as closed? the issue still exists

hello, @wheelq make a pull on the dev branch it is fixed in dev branch. Master branch is still not updated it will take some time to merge dev branch to master.

hello, @wheelq make a pull on the dev branch it is

Thanks, I already did, but dev needs some hacks (python tool not found etc). Thanks, will try and hopefully it works :)


[REVIEW]

GitHub Profile Link
https://github.com/abrahamalen

very nice profile i would just suggest minor changes just center the first header with your name and the activity stats and i have made a PR with those incase you might want to add them

very nice profile i would just suggest minor changes just center the first header with your name and the activity stats and i have made a PR with those incase you might want to add them

@AmrMonier Hey thanks for the changes


Get rid of unarchived directory

Checklist

[ ] I've read and followed the Contribution Guidelines
[ ] step.yml and README.md is updated with the changes (if needed)

Version

Requires a MAJOR version update
Context

We currently start to use this step and found out that the content land in the directory $extra_to_path/unarchived.
We thought this is a strange behaviour to "create an additionally directoy within the "extract_to_path" input".
So I thought it make sense to simply remove this extra directoy. 🙃
Changes

Copy only contents from the downloaded and extract zip archive to the extract_to_path input. Not the whole unarchived directoy.

Investigation details

Decisions

It is not so obvious by using this step, declaring the extra_to_path path but content wil land in extra_to_path/unarchived. Its more obvious that the content land directoy into extra_to_path.

@viktorbenei @godrei can you have a look pleas 🙏.
Sorry for mention you, but I saw you in the commit history 🙃

Stale. Seems no one is interested in this 🤷


Diagrams do not work

If I use a diagram, it does not work.
The diagram is created in 'src/static/img', but it is not moved/copied to 'site'.
It might be a bigger issue. It seems nothing is copied from static.
I also think that there should be 2 dirs :

'src' for adoc files
'static' for user css/icons/images

and diagrams should go in a temp dir, like .adbook-cache.

As I’m also using zola, I would recommend their structure.
https://www.getzola.org/documentation/getting-started/directory-structure/

I appreciate your dive ❤
includes in book.ron has to be added:
// files copied to `site` directory
includes: [
    "static/img",
],

I changed it to be commented out by default (#b7959b4). Also I need to write better doc!

Regarding the structure, adbook basically copies src/ to site/, converting .adoc files to .html files. User can opt in other files in src/ with the includes attribute. It has some explicity, but it lacks the free of user project structure.
So I'm considering to support symlinks [^1] in addition to the current just-copy model.
For example, if src/img refers to static/images, the latter directory is copied to site/img.
[^1]: (Shortcuts on Windows?)

Or copy attribute in book.ron might be better:
copy: [
     ("static", "site/static"),
]

I'll support it today or next weekend.

Ooh it looks like Zola's public/* is mixin of content/* and static/*. Cool!
So I'm considering to add user-defined build actions like this..
build_actins: [
    ConvertAsciiDocToSite("src/*"),
    Copy("static/*", "site/"),
]

..so that user gets both full control and explicity.

That would be awesome.
You could use submodules, and copy them.
It could be more generic for build.
build_actions : [
    BuildAndCopy("asciidoctor", "src/*", "site/"),
    BuildAndCopy("sass", "sass/*", "site/css/"),
    Copy("static/fonts", "site/"),
    Copy("submodudes/myawesometheme/img/*", "site/images/"),

With a select few backend, or have build commands.
build_commands : [
    "asciidoctor" : "asciidoctor -r asciidoctor-diagram ...",
    "sass" : "...",
]

However, it is much more work.


Allow tables with same name in different schemas in Blackhole

Minor bug fix in BlackHoleConnector
BlackholeConnector cannot have tables with same table names in different
schemas.
This is because originally BlackHoleConnector only supports default
schema so it use the table name string to identify table. When creating
schema was supported in 4e522f355ed7f0711d877e2259e489a8ebf626b9, the
table identity should be updated to use SchemaTableName.
Extracted from: https://github.com/prestodb/presto/pull/12457

@kokosing please fix the cmt msg so that it says what the commit does. I edited the PR title with my suggestion for the cmt title.

@findepi

please fix the cmt msg so that it says what the commit does. I edited the PR title with my suggestion for the cmt title.

I assume "cmt msg" actually means "cmt title".
For the commit title, there is always the tradeoff of making commit title too long (50 characters) vs. make things clear in commit title :)


AttributeError: 'Central' object has no attribute 'auto'

Cannot use raw packets capabilities.

Thanks for reporting this issue, can you provide at least a minimal working example in order to reproduce it ? It looks like some old code has not been updated (this auto attribute was used some time ago and has been reworked to provide a synchronous packet processing feature).

Allright, I see what the issue is. It seems our documentation is not up-to-date with the latest features we implemented in WHAD: this auto() method originally implemented only in BLE connectors has been moved into the WhadDeviceConnector class in order to generalize this behaviour to all connectors (and domains).
Therefore, instead of calling auto(), you must use the enable_synchronous() method as shown below:
# Old code: central.auto(False)
# Replaced with the following to disable automatic PDU processing (synchronous mode):
central.enable_synchronous(True)

# To re-enable automatic PDU processing:
central.enable_synchronous(False)

I've updated the documentation in branch bugfix/issue-82 to reflect these changes in the API. If this solution works for you, please let me know.

Hi, I guess that works thanks.
However I gave up into trying raw packets sending since I encountered the same butterfly-related issues (discussed with Romain a while ago).
Thank you again, I will close this.


Funnotate job running for over 2 hrs!  AHRD problem?

I have submitted a funnotate job on LIS and it has been running the AHRD for over 2 hours now. The job ID is P3Q6Z and I submitted 6 fna sequences with 23582 total base pairs.
So I am wondering if there is something wrong with the AHRD pipeline because it has never taken this long before.

It runs quickly on the development VM, can I restart the production one and have you try again?

The log file reports inability to create a temporary file at some point in the past, but it may not be related to this job.

I restarted it from the same upload (597). The new job is L4G1W, it completed in the usual time.
https://funnotate.legumeinfo.org/?job=L4G1W

Thanks @svengato I ran another job independently and it also worked fine. Sounds like it may have been a transient issue but let us know if it happens to you again @jd-campbell and thanks for reporting it. I'll leave the issue open for now but go ahead and close it if things seems to be working fine to you too.

Any update on this?

Fwiw, I used the tool maybe 20 times on Monday successfully. It ran quickly for the sequences I was testing -- up to a dozen or so, of nucleotide gene sequence. I think it's OK to close this issue if you'd like, @svengato


Issue revoking an access token

Description:
Is there a way to revokke a token as there is a way to renew the token using the renewToken method?
OAuth Provider (Twitter, Github, ..):
AirService
OAuth Version:

[ ] Version 1
[x] Version 2

OS (Please fill the version) :

[x] iOS :
[ ] OSX :
[ ] TVOS :
[ ] WatchOS  :

Installation method:

[ ] Carthage
[x ] CocoaPods
[ ] Manually

Library version:

[x ] head
[ ] v1.0.0
[ ] v0.6
[ ] other: (Please fill in the version you are using.)

Xcode version:

[x ] 8.0 (Swift 3.0)
[ ] 8.0 (Swift 2.3)
[ ] 7.3.1
[ ] other: (Please fill in the version you are using.)
[ ] objective c

https://github.com/OAuthSwift/OAuthSwift/wiki/OAuth-2.0-Token-Revocation
I think there is no universal way to do it
So you must look into your api provider documentation if there is an URL for that


Cleaned up

items still keep disappearing from the page on scroll and resize

Thanks for the pull request. I have to close it for now as I'm not actively maintaining this component. Any bugs should be reported in issues 👍


Refactor to support asynchronous calls. Switching to aiohttp instead of requests

Made a refactor to support asynchronous api calls. Haven't tested all the endpoints, only the one I need (episodesByFeedId).

Oops.. i missed this PR and just found the email deep in my inbox.
Can you fix the conflicts please and I'll happily merge this in 🙏 Thanks so much for your contribution!

@ becutandavid this could be a valuable change. Will you have a chance to fix the conflicts?

Ah, I forgot about this PR. I'll fix the conflicts by the end of the week.

Tests passing. This is a breaking change, maybe play with it a little before deciding to merge.
I needed async support back when I made the pull request, and when I went over it againt now I have mixed feelings about forcing everyone to make async requests :)

@becutandavid
This looks great, although I am also concerned with the folks using the library who aren't ready to handle the change. Perhaps you can consider a design that would elegantly allow non async users to run the async code.
import asyncio

def run_async(func):
    """Helper function to run coroutine in a new event loop."""
    return asyncio.new_event_loop().run_until_complete(func)

async def async_function():
    # Your async code here
    pass

# Users can call your async function like this:
run_async(async_function())

I think something like this could be implemented through a configuration option during podcastindex.init() or something.
@SarvagyaVaish this will break peoples code if they update without reading the diff.

Thanks, Davids! @becutandavid @dbellotti
David Galevski, I really appreciate the work you put into this refactor! As David Bellotti mentioned, and you identified as well, I don't think this PR is ready as is to merge because of the backwards incompatibility. I think a wrapper approach is better.
Closing for now :)


Put distinct types of template in distinct config files

The merging of contact, host, and service templates into a single file is confusing. This is aggravated by having distinct nagios_templates, nagios_hosttemplates, They should ideally be split to three distinct files for maximum comprehensibility and correspondence with the original data bags.

IMO it shouldn't matter.  If your wrapper passes spec tests, who cares how the config stanza are broken up?

Anyone trying to draw links between the data bags they write, and the resulgint configuration files the data resides in, can be confused by the inconsistency. This is actually a longstanding problem with the original default published nagios "templates.cfg", and this is a good opportunity to eliminate the confusion.
If it's welcome, I'd be happy to submit patches for it.

I personally don't care, so feel free to move the configuration into another file as you want.

@nkadel-skyhook a pr would be great.
I'm going to start a custom resource rewrite and we'll look at doing it exactly this way for simplicity.

Hi @nkadel-skyhook,
You're welcome to submit a PR to add this functionality but for most people when a configuration file is managed by Chef they aren't too phased what it looks like because the config is in their config management system.
I'm going to close this for now, again PR welcome if you wish to tidy up the files.
Stephen


bcbio vardict java error : Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1

Hi,
I have been running the process below for almost 3 days. It went without a problem until this step. I did not change anythin in the configuration related to mutation calling but I dont know why do I get this error?
[2016-04-02T01:59Z] Genotyping with VarDict: Inference
[2016-04-02T02:07Z] tabix index syn3-14_35012924_51408901-raw.vcf.gz
[2016-04-02T02:07Z] Annotate with dbSNP
[2016-04-02T02:12Z] Sort BED file : deneme1_tumor
[2016-04-02T02:12Z] Remove high depth regions
[2016-04-02T02:12Z] Genotyping with VarDict: Inference
[2016-04-02T02:13Z] tabix index syn3-15_0_20219201-raw.vcf.gz
[2016-04-02T02:13Z] Annotate with dbSNP
[2016-04-02T02:13Z] tabix index syn3-14_101336909_107349540-raw.vcf.gz
[2016-04-02T02:13Z] Annotate with dbSNP
[2016-04-02T02:14Z] Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
[2016-04-02T02:14Z] 	at java.lang.String.charAt(String.java:658)
[2016-04-02T02:14Z] 	at com.astrazeneca.vardict.VarDict.parseSAM(VarDict.java:1896)
[2016-04-02T02:14Z] 	at com.astrazeneca.vardict.VarDict.toVars(VarDict.java:2552)
[2016-04-02T02:14Z] 	at com.astrazeneca.vardict.VarDict.somaticNotParallel(VarDict.java:354)
[2016-04-02T02:14Z] 	at com.astrazeneca.vardict.VarDict.nonAmpVardict(VarDict.java:249)
[2016-04-02T02:14Z] 	at com.astrazeneca.vardict.VarDict.start(VarDict.java:65)
[2016-04-02T02:14Z] 	at com.astrazeneca.vardict.Main.run(Main.java:134)
[2016-04-02T02:14Z] 	at com.astrazeneca.vardict.Main.main(Main.java:25)
[2016-04-02T02:18Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
    _do_run(cmd, checks, log_stdout)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; unset R_HOME && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && export VAR_DICT_OPTS='-Xms750m -Xmx3000m -XX:+UseSerialGC -Djava.io.tmpdir=/home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/tx/tmpMW1qbw' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -f 0.1 -N deneme1_tumor -b "/home/ec2-user/puppey/icgc_data/try1/real_deneme/work/prealign/deneme1_tumor/tumor.bam|/home/ec2-user/puppey/icgc_data/try1/real_deneme/work/prealign/denem1_normal/normal.bam" -c 1 -S 2 -E 3 -g 4 -Q 10 /home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/syn3-14_51409528_70891309-raw-regions-glimit-regionlimit.bed | testsomatic.R | var2vcf_paired.pl -P 0.9 -m 4.25 -f 0.1  -M  -N "deneme1_tumor|denem1_normal" | bcftools filter -m '+' -s 'REJECT' -e 'STATUS !~ ".*Somatic"' 2> /dev/null | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vardict.depth_freq_filter(x, 0, "False")' | sed 's/\\.*Somatic\\/Somatic/' | sed 's/REJECT,Description=".*">/REJECT,Description="Not Somatic via VarDict">/' | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.freebayes.call_somatic(x)' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' |  awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/bin/vcfstreamsort | bgzip -c > /home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/tx/tmpMW1qbw/syn3-14_51409528_70891309-raw.vcf.gz
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
	at java.lang.String.charAt(String.java:658)
	at com.astrazeneca.vardict.VarDict.parseSAM(VarDict.java:1896)
	at com.astrazeneca.vardict.VarDict.toVars(VarDict.java:2552)
	at com.astrazeneca.vardict.VarDict.somaticNotParallel(VarDict.java:354)
	at com.astrazeneca.vardict.VarDict.nonAmpVardict(VarDict.java:249)
	at com.astrazeneca.vardict.VarDict.start(VarDict.java:65)
	at com.astrazeneca.vardict.Main.run(Main.java:134)
	at com.astrazeneca.vardict.Main.main(Main.java:25)
' returned non-zero exit status 1
[2016-04-02T02:18Z] Sort BED file : deneme1_tumor
[2016-04-02T02:18Z] Remove high depth regions
[2016-04-02T02:18Z] Genotyping with VarDict: Inference

my configuration file
details:
- algorithm:
    #bam_sort: coordinate
    aligner: false
    mark_duplicates: false
    realign: false
    recalibrate: false
    variantcaller: [vardict, mutect, freebayes, varscan, mutect2]
    indelcaller: pindel
    ensemble:
        numpass: 2
  analysis: variant2
  description: denem1_normal
  files:
  - /home/ec2-user/puppey/icgc_data/try1/real_deneme/input/normal.bam
  genome_build: GRCh37
  metadata:
    batch: syn3
    phenotype: normal
- algorithm:
    #bam_sort: coordinate
    aligner: false
    mark_duplicates: false
    realign: false
    recalibrate: false
    variantcaller: [vardict, mutect, freebayes, varscan, mutect2]
    indelcaller: pindel
    ensemble:
        numpass: 2
  analysis: variant2
  description: deneme1_tumor
  files:
  - /home/ec2-user/puppey/icgc_data/try1/real_deneme/input/tumor.bam
  genome_build: GRCh37
  metadata:
    batch: syn3
    phenotype: tumor
fc_date: '2016-03-24'
fc_name: real_deneme
upload:
  dir: ../final

Tunc;
Sorry about the analysis problems. What version of vardict-java are you currently running with (it should be listed in provenance/programs.txt)? There were some issues like this in earlier versions that I believe are fixed with version 1.4.5. If you have an older version you can update with:
bcbio_nextgen.py upgrade --tools

hope this helps explain the problem.

Brad;
I am afraid my vardict version is 1.4.5 but i will still update the system. Also, when i check the output, there were mutations called from chr 1 to 15. So it might have been failed somewhere. Should I also ask the same question to vardictjava github account?
Thank you very much,
Tunc.
[ec2-user@ip-172-31-57-166 provenance]$ cat programs.txt
bamtools,2.4.0
bcbio-nextgen,0.9.6
bcbio-variation,0.2.6
bcftools,1.3
bedtools,2.24.0
biobambam,2.0.25
bioconductor-bubbletree,2.1.5
bowtie2,2.2.7
bwa,0.7.13
chanjo,
cnvkit,0.7.9
cufflinks,2.2.1
cutadapt,1.9.1
fastqc,0.11.4
featurecounts,1.4.4
freebayes,1.0.2
gatk,3.5-0-g36282e4
gatk-framework,3.4.46
gemini,0.18.3
grabix,0.1.6
htseq,0.6.1p1
lumpy-sv,0.2.12
manta,0.29.3
metasv,0.4.0
mutect,1.1.7
novoalign,3.03.02
novosort,V3.00.02
oncofuse,1.1.0
phylowgs,20150714
picard,1.141
platypus-variant,0.8.1
qualimap,2.1.3
rna-star,
rtg-tools,3.6
sambamba,0.5.9
samblaster,0.1.22
samtools,1.3
scalpel,0.5.1
snpeff,4.2
vardict,2016.02.19
vardict-java,1.4.5
variant-effect-predictor,83
varscan,2.4.0
vcflib,1.0.0_rc0
vt,2015.11.10
wham,<IP_ADDRESS>

Hi @mortunco, did you align these files previously with bwa and perform any kind of Gatk realignment/recalibration? Gatk realignment often produces alignments with improper CIGAR strings that VarDict chokes on. It might be best to align the raw data with bwa for VarDict and not do any Gatk steps.
Apologies for all the problems, looks like you're hitting all the edge cases.

Dear @mjafin ;
I am using aligned file which came from ICGC. I dont think I have an access to raw fastq files though. To prove I don't do extra recalibration, you may want to check my configuration file.
And I do think so that I am the unluckiest person alive.
I am willing to do everything you say. Thank you for your help,
Best,
Tunc.

@mortunco for testing purposes, could you do another run of bcbio on the sample that failed where you disable all the other variant callers except Vardict (to speed things up) and set
aligner: bwa

If these are whole genomes the alignment can take a long time unfortunately so you may want to throw all the cpu cores you can get at the alignment process.
If you still get the error then the next step (if you're still game) would be to narrow down to the exact region it's failing in and extracting the reads there with Samtools so we can take a look. In the above command
set -o pipefail; unset R_HOME && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && export VAR_DICT_OPTS='-Xms750m -Xmx3000m -XX:+UseSerialGC -Djava.io.tmpdir=/home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/tx/tmpMW1qbw' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -f 0.1 -N deneme1_tumor -b "/home/ec2-user/puppey/icgc_data/try1/real_deneme/work/prealign/deneme1_tumor/tumor.bam|/home/ec2-user/puppey/icgc_data/try1/real_deneme/work/prealign/denem1_normal/normal.bam" -c 1 -S 2 -E 3 -g 4 -Q 10 /home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/syn3-14_51409528_70891309-raw-regions-glimit-regionlimit.bed | testsomatic.R | var2vcf_paired.pl -P 0.9 -m 4.25 -f 0.1  -M  -N "deneme1_tumor|denem1_normal" | bcftools filter -m '+' -s 'REJECT' -e 'STATUS !~ ".*Somatic"' 2> /dev/null | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vardict.depth_freq_filter(x, 0, "False")' | sed 's/\\.*Somatic\\/Somatic/' | sed 's/REJECT,Description=".*">/REJECT,Description="Not Somatic via VarDict">/' | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.freebayes.call_somatic(x)' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' |  awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/bin/vcfstreamsort | bgzip -c > /home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/tx/tmpMW1qbw/syn3-14_51409528_70891309-raw.vcf.gz

this file /home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/syn3-14_51409528_70891309-raw-regions-glimit-regionlimit.bed controls the region and you could split it further to understand where the failure happens. I know this is asking a lot,

@mjafin I will perform everything you say, I just need time. I will report you asap.
Thank you very much!
Tunc.

@mjafin;
I got the same error during variant calling. Actually from the same exact region. I posted the bed file here so that we can go deeper.
So whats next ? :)
Best,
Tunc.
[2016-04-05T18:03Z] Uncaught exception occurred
Traceback (most recent call last):
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 21, in run
    _do_run(cmd, checks, log_stdout)
  File "/usr/local/share/bcbio/anaconda/lib/python2.7/site-packages/bcbio/provenance/do.py", line 95, in _do_run
    raise subprocess.CalledProcessError(exitcode, error_msg)
CalledProcessError: Command 'set -o pipefail; unset R_HOME && export PATH=/usr/local/share/bcbio/anaconda/bin:$PATH && export VAR_DICT_OPTS='-Xms750m -Xmx3000m -XX:+UseSerialGC -Djava.io.tmpdir=/home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/tx/tmpl6DQlr' && vardict-java -G /usr/local/share/bcbio/genomes/Hsapiens/GRCh37/seq/GRCh37.fa -f 0.1 -N deneme1_tumor -b "/home/ec2-user/puppey/icgc_data/try1/real_deneme/work/prealign/deneme1_tumor/tumor.bam|/home/ec2-user/puppey/icgc_data/try1/real_deneme/work/prealign/denem1_normal/normal.bam" -c 1 -S 2 -E 3 -g 4 -Q 10 /home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/syn3-14_51409528_70891309-raw-regions-glimit-regionlimit.bed | testsomatic.R | var2vcf_paired.pl -P 0.9 -m 4.25 -f 0.1  -M  -N "deneme1_tumor|denem1_normal" | bcftools filter -m '+' -s 'REJECT' -e 'STATUS !~ ".*Somatic"' 2> /dev/null | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.vardict.depth_freq_filter(x, 0, "False")' | sed 's/\\.*Somatic\\/Somatic/' | sed 's/REJECT,Description=".*">/REJECT,Description="Not Somatic via VarDict">/' | /usr/local/share/bcbio/anaconda/bin/py -x 'bcbio.variation.freebayes.call_somatic(x)' | awk -F$'\t' -v OFS='\t' '{if ($0 !~ /^#/) gsub(/[KMRYSWBVHDX]/, "N", $4) } {print}' |  awk -F$'\t' -v OFS='\t' '$1!~/^#/ && $4 == $5 {next} {print}' | /usr/local/bin/vcfstreamsort | bgzip -c > /home/ec2-user/puppey/icgc_data/try1/real_deneme/work/vardict/14/tx/tmpl6DQlr/syn3-14_51409528_70891309-raw.vcf.gz
Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: -1
	at java.lang.String.charAt(String.java:658)
	at com.astrazeneca.vardict.VarDict.parseSAM(VarDict.java:1896)
	at com.astrazeneca.vardict.VarDict.toVars(VarDict.java:2552)
	at com.astrazeneca.vardict.VarDict.somaticNotParallel(VarDict.java:354)
	at com.astrazeneca.vardict.VarDict.nonAmpVardict(VarDict.java:249)
	at com.astrazeneca.vardict.VarDict.start(VarDict.java:65)
	at com.astrazeneca.vardict.Main.run(Main.java:134)
	at com.astrazeneca.vardict.Main.main(Main.java:25)
' returned non-zero exit status 1

This is the content of the bed file.
[ec2-user@ip-172-31-57-166 14]$ cat syn3-14_51409528_70891309-raw-regions-glimit-regionlimit.bed
14	51409544	52409544
14	52409294	53409294
14	53409044	54409044
14	54408794	55408794
14	55408544	56408544
14	56408294	56909026
14	56909341	57909341
14	57909091	58909091
14	58908841	59429219
14	59429518	59545313
14	59545595	60545595
14	60545345	61079110
14	61079399	61525316
14	61525666	62525666
14	62525416	63525416
14	63525166	64525166
14	64524916	65360429
14	65360833	65361550
14	65361857	65363235
14	65363519	66363519
14	66363269	67363269
14	67363019	68363019
14	68362769	68603328
14	68603725	69603725
14	69603475	70603475
14	70603225	70891282

This is the configuration file that I used for this analysis. I shared just to be sure that we are on the same page.
details:
- algorithm:
    aligner: bwa
    aligner: false
    mark_duplicates: false
    realign: false
    recalibrate: false
    variantcaller: [vardict]
    indelcaller: #pindel
    ensemble:
        numpass: 2
  analysis: variant2
  description: denem1_normal
  files:
  - /home/ec2-user/puppey/icgc_data/try1/real_deneme/input/normal.bam
  genome_build: GRCh37
  metadata:
    batch: syn3
    phenotype: normal
- algorithm:
    aligner: bwa
    aligner: false
    mark_duplicates: false
    realign: false
    recalibrate: false
    variantcaller: [vardict]
    indelcaller: #pindel
    ensemble:
        numpass: 2
  analysis: variant2
  description: deneme1_tumor
  files:
  - /home/ec2-user/puppey/icgc_data/try1/real_deneme/input/tumor.bam
  genome_build: GRCh37
  metadata:
    batch: syn3
    phenotype: tumor
fc_date: '2016-03-24'
fc_name: real_deneme
upload:
  dir: ../final

Hi @mortunco, you have now aligner set twice in your configuration file, with false as the last entry. Was the data aligned or did it skip right to variant calling? Could you remove the aligner: false line and retry once more. If after realigning the data you get this error then I would suggest splitting the bed file in half recursively until you identify the offending region and then extracting the reads there for us

Oh my god that totally missed that one. I am sorry. I will inform you when its done.

FWIW I'm seeing the same error running VarDict 1.4.5 outside of bcbio.  I modified the VarDict source to spit out the read name and cigar string of the read it was processing when the exception occurred, and in my case the read's cigar started with an insertion operator (e.g. 2I98M).  That's technically valid SAM - it's just unusual, but VarDict seems to assume that that won't be the case.
I'm not sure how much flexibility you have in the bcbio workflow, but if you can avoid running GATK Indel Realigner or soft-clip insertions at the starts of ends of reads in your BAM file before feeding it in, I believe it should work.

Thanks for chiming in @tfenne, this points to Gatk Indel Realigner once again being the culprit here. As VarDict performs indel realignment intrinsically we'd recommend running it on non-Gatk modified BAM files where possible. @zhongwulai has implemented a lot of checking and fixing of improper and odd CIGARs as special cases in VarDict but clearly the 2I98M case isn't there.

Miika, Tim and Tunc -- thanks for debugging this. It would be great to have a fix for this in VarDict and I'll continue the thread in AstraZeneca-NGS/VarDictJava#34


Adm::Mship::Role::Delete (Old 249)

In gitlab by @A-Lawrence on Aug 31, 2015, 01:08
Allow roles to be deleted.
When this happens, any associated permissions and assignments should be deleted too!
(Check that it's not already a DELETE action on the foreign key).

In gitlab by @A-Lawrence on Aug 31, 2015, 01:14
Made some more permission & role modifications.
Roles can now be modified.  When modified the attached permissions are also correctly modified - resolves issue #488505 (248).
Roles can be deleted.  When deleted, the eventDeleted model is called and the attached accounts and permissions are desync'd.  Resolves issue #249.
When roles are updated, if default is set to 1, the OLD default is removed.
ÔåÆ <>
ALawrence66 - 2015-02-21T20:54:20.550796+00:00


Add TOWER: TowerToken

[x] I understand that token listing is not required to use the Polygon Wallet with a token.

Token Name: Tower Token
Token Symbol: TOWER
Decimals: 18
Polygon Address: 0x2bC07124D8dAc638E290f401046Ad584546BC47b
Ethereum Address: 0x1C9922314ED1415c95b9FD453c3818fd41867d0B
Logo URI: https://crazydefenseheroes.com/static/media/logo-tower.2bca4bdd.svg
Project Name: Tower Token
Project Summary: The TOWER Token is a utility token for the TOWER Platform that comprises the token, the Free-to-Play games in the Crazy Kings franchise and the blockchain game.
Project Contact<EMAIL_ADDRESS>Project Website: https://crazydefenseheroes.com/
Mainnet/Testnet:
Additonal Notes: Mapped with https://mapper.polygon.technology/ in mainnet and testnet
For testnet latest tower address: 0xbb2c9203c8d0c169638c6391da2828f0278231af

Included in AllTokens v1.2.0.


Escape single quotes in filenames

This is a quick fix - the point is to prevent syntax errors in the generated cache file when the filename contains a single quote.
Not sure what effect this will have on the ResourceWatcher::calculateHashOfFile() method.

Updated the initial PR: made sure quotes are escaped for both absolute & relative paths and added tests


compatibility angular 9 Ivy

I looks like directives like *isDesktop/*isMobile ... doesn't work with ivy.
Doesn't work with :
"angularCompilerOptions": {
"enableIvy": true
}
Works only when I set enableIvy to false

Hello we created a new nx workspace to keep some ngx libs up to date.
We added also the ngx-responsive lib, it should work out of the box you have only to change the import path.
We migrate it also to ng12, if you like please have a look
https://github.com/lanthings/ngx-components
npm i --save @lanthings/ngx-responsive


fix: updates dependencies

What
fix: updates dependencies

:tada: This PR is included in version 0.11.2 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Consider Unpublishing nickreese/elderjs from npm registry?

When searching www.npmjs.com for "elderjs" the top result (due to being an "exact match") is nickreese/elderjs ie. 3 files that haven't been changed in 2 years, where the javascript just prints "This is a placeholder" to the console, and the total size of all the files is less than 1KB.
Noticing this I thought I'd suggest considering unregistering / unpublishing this package from the npm registry to avoid this issue.
I don't think it's much of a problem, and I don't even know if it's fooled anyone before (I would have likely followed the directions in the online docs to discover the package, and was just searching around on npm registry website on this occasion as it gave a quick answer to something I was curious about) but I perhaps it might be a minor annoyance to someone and it possibly is somewhat ironic for the proper version of the SEO first framework to not be the top result on the major package registry's search engine.

@nat42 done.