Excessive Length of Responses from Mini Gemini

Description:
I've noticed that when interacting with Mini Gemini, the responses tend to be overly long. While the responses contain valuable information, they often include more details than necessary, making it challenging to quickly grasp the main points.
Expected Behavior:
I expect Mini Gemini to provide concise and relevant responses to my queries, focusing on the essential information without unnecessary elaboration.
Actual Behavior:
Currently, the responses from Mini Gemini tend to be verbose, containing additional details that may not always be directly related to the specific query.
Steps to Reproduce:

Interact with Mini Gemini by asking questions or giving commands.
Observe the length and detail of the responses provided.

Impact:
. Long responses make it difficult to quickly extract the required information.
. Reading through lengthy responses can be time-consuming, especially when seeking quick answers or instructions.
. The excessive verbosity may deter users from engaging with Mini Gemini for certain queries or tasks.
Suggestions for Improvement:

Implement a summarization feature to provide concise summaries of long responses.
Offer options for users to specify the level of detail they prefer in responses.
Optimize responses to focus on the most relevant information based on the context of the query.
Provide prompts or guidance to encourage users to ask more specific questions, leading to more targeted responses.

Additional Information:
While detailed responses can be beneficial, it's crucial to strike a balance between thoroughness and readability to enhance the user experience.
Introducing features that allow users to customize or tailor responses to their preferences could improve the overall usability and effectiveness of Mini Gemini.

Thanks for your detailed suggestion! It's really a good idea. We will try them to make the project better.


Implement the option to use a username/password on the site, using .htpassword

Added base64 syntax to custom uploader parser, example syntax for authorization header: Basic $base64:username:password$

ShareX 12.3.0 Changelog

Looks like this idea may be more feasible.

A version of this has been added in Version 2. It doesn't use .htpassword, but I've added a custom login implementation.


Adding message when the script runs successfully

For a while, I thought the script wasn't working correctly because there was no output. This should eliminate that confusion for future users by making it clear that it did run correctly, but found nothing.

Added from fork. Thank you for the PR!


🐛 Bug Report: The avatars commands giving Error: Not Found

👟 Reproduction steps
appwrite avatars --verbose getFlag --code af --destination test.png
👍 Expected behavior
Should download the flag icon and create a new file at the destination path.
👎 Actual Behavior
Throws the below error:
AppwriteException [Error]: Not Found
    at Client.call (/usr/local/lib/node_modules/appwrite-cli/lib/client.js:209:19)
    at process.processTicksAndRejections (node:internal/process/task_queues:95:5)
    at async avatarsGetFlag (/usr/local/lib/node_modules/appwrite-cli/lib/commands/avatars.js:144:22) {
  code: 404,
  response: [Object: null prototype] {
    message: 'Not Found',
    code: 404,
    type: 'general_route_not_found',
    version: '0.10.44'
  }
}

Error Not Found
🎲 Appwrite version
Appwrite CLI v2.0.2
💻 Operating system
macOS v12.6.7
🧱 Your Environment
Using the appwrite CLI v2.0.2 on macbook pro with zsh.
👀 Have you spent some time to check if this issue has been raised before?

[X] I checked and didn't find similar issue

🏢 Have you read the Code of Conduct?

[X] I have read the Code of Conduct

@ra-jeev thanks for raising this issue! 🙏🏼 Looks like there are a few things wrong with how we handle images in the CLI:

The endpoint is included in the path when it shouldn't be:

https://github.com/appwrite/sdk-for-cli/blob/b4619977eb95ca6650aa5291eb6a26d6bfa46eda/lib/commands/avatars.js#L142

The content-type is set to application/json:

https://github.com/appwrite/sdk-for-cli/blob/b4619977eb95ca6650aa5291eb6a26d6bfa46eda/lib/commands/avatars.js#L145

The transformResponse tries to parse the data when it shouldn't:

https://github.com/appwrite/sdk-for-cli/blob/b4619977eb95ca6650aa5291eb6a26d6bfa46eda/lib/client.js#L186

@stnguyen90 Thanks a lot for acknowledging the issue. Glad I was able to notice this bug while playing around with the appwrite CLI (actually I was trying to connect Appwrite CLI to the 1Password CLI, and that is when I noticed it).

Hi, I can work on this if no one's working on this

@adarshjhaa100, are you still interested in working on this?

@stnguyen90 yes I am interested. Just confirming, need to raise PR to the SDK Generator repo right ?

@adarshjhaa100, assigned! Yes, the SDK Generator repo, please.

@stnguyen90 Looks like something's changed. The latest version gives a slightly different issue:

The 1st and 3rd point you've mentioned seems a correct analysis of the issue. I made the change and am able to download the image:

Would like to add something for the 2nd point here. This is a GET request, which has a null request body. So, it seems fair to omit the content-type from request header while fetching avatar. (I presume content-type here is the type of request body, correct me if im wrong)
Given the above analysis, just need to figure out how to handle for images.
Couple of solutions which I can think of:

Probably can use the response header content-type to identify and then apply appropriate transformResponse. But I don't see a way to pull responseHeader in the request config.

I see that responseType of 'arraybuffer' is used for avatars only. So, could use that to change the transformResponse.

Do let me know if either of these seem feasible. I'll raise a PR post that.


comprehensive design + component system

❔ Problem
To ensure consistency and efficiency in the development process and facilitate maintenance scalability, we need a comprehensive design and component system for the native and web app. during the creation process, all decisions should be aligned with the accessibility standards of WCAG 2 (Web Content Accessibility Guidelines).
💡 Proposed solution
Creation of a comprehensive design and component system with assets and guidelines in figma. Components should come from an open source native Angular UI components set, eg. PrimeNG
All design guidelines, principles, and component specifications should be compiled into a comprehensive design system document and stored on Nextcloud (backup/documentation).
↔ Alternatives
none

required guidelines for visual identity

[ ] typography
[ ] colors
[ ] grid system
[ ] Iconography

🧰 required components

[ ] Buttons: Primary/Secondary/Outline/Disabled/Icon button
[ ] Forms: Input fields, Text area, Dropdown/select, Radio buttons, Checkboxes, Switches, Date picker, Time picker
[ ] Navigation: App bar/header, Tabs, Side navigation menu, Breadcrumbs, Pagination
[ ] Modals and Dialogs: Standard modal, Confirmation dialog, Alert dialog, Full-screen modal
[ ] Cards: Feature card, Product card, Image card, Notification card
[ ] Tooltips and Popovers: Tooltip, Popover
[ ] Alerts: Success alert, Error alert, Warning alert, Info alert
[ ] Progress Indicators: Progress bar, Loading spinner
[ ] Typography: Headings (h1 to h6), Body text, Subtitles, Captions
[ ] Icons: Icon set, Icon labels
[ ] Badges: Notification badges, Status badges
[ ] Lists: Ordered lists, Unordered lists, Definition lists
[ ] Tables: Basic table, Data table, Responsive table
[ ] Sliders: Range slider, Single-value slider
[ ] Media Players: Video player, Audio player
[ ] Chips and Tags: Text chips, Filter tags
[ ] Navigation Elements: Back button, Next button, Up arrow
[ ] Search Bar: Basic search bar, Search with filters

related issues: #2338 #2354 #2362

Something we would also like to know is the units. We currently mostly use the absolute px but in a few select places we use relative rem. It's especially a question of how the apps should handle zooming in or out, should e.g. the padding on a button increase with the font size?


Alt+Shift+3 behaves weirdly

Windows Build Number
Microsoft Windows [Version 10.0.19041.985]
WSL Version

[x] WSL 2
[X] WSL 1

Kernel Version
4.4.0
Distro Version
Ubuntu 20.04
Other Software
No response
Repro Steps

Open WSL.
Write anything in the command prompt
Press Ctrl+Shift+3

Expected Behavior
That keyboard shortcut should comment the current line
Actual Behavior
After pressing those keys the command prompt acts weirdly. If you move the cursor to the left and write anything, the text moves backwards. In fact, in order to comment the current line I have to press Ctrl+Alt+3 instead.
Diagnostic Logs
No response

Please note that I only selected WSL1 because I only have WSL1, but it might be worth checking if this happens in WSL2 as well.

That keyboard shortcut should comment the current line

Nothing in WSL would "comment the current line" at the "command prompt" when pressing "Ctrl+Shift+3". Nothing in bash ("the command prompt") would either. This can't even reasonably be punted to console.
What are the repro steps from a clean distro install to manifest "If you move the cursor to the left and write anything, the text moves backwards".

This keyboard shortcut is supposed to comment the current line, according to Daniel Andersson.
https://superuser.com/a/641582/669882

Documented in the bash manual here:
M-# or AltShift3

What are the repro steps from a clean distro install to manifest "If you move the cursor to the left and write anything, the text moves backwards".

Write "qwertyuiop" in the command line
Press ← 5 times.
Press q 10 times.

You will see something like this:

The 'q's overlap the prompt.

Documented in the bash manual here:

Thanks for the reference; very appreciated.
I wasn't able to reproduce here with windows terminal or legacy console. What is the output of echo $TERM. Assuming it returns xterm-256color, I don't have any great guesses on the external variable.

First thing would be to try windows terminal just to get that out of the way. Start WSL from a cmd or powershell prompt inside terminal with wsl.exe or wsl.exe -d [distro-name].
The other usual suspect is something in userspace, although your prompt looks clean as it goes (contrast some highly modded setup). When you tried WSL2, did you do it via an upgrade of your WSL1 distro, or install a new distro? If it was an upgrade, maybe try installing a new distro to start from scratch. For example, if your distro is Ubuntu, install Ubuntu-20.04, or visa-verse. It isn't the distro that matters here, it is just eliminating any local changes vs. a clean install, to the extent that might be applicable.

Alt+Shift+3 seems to insert a bell character instead. Apart from that in the windows terminal everything works as expected.
Running wsl.exe in cmd leads to the same symptoms (the 'q' overlaps the prompt again).
I had Ubuntu-20.04, so I installed Ubuntu. Same problem.
I started to suspect it is just the fault of the cmd, so I run cmd and tried the same without wsl, but this insert the '·' character.
I doubt this is related, but I am using the Spanish keyboard layout:

adrian@DESKTOP-EF8FQ3I:~$ echo $TERM
xterm-256color

Alright. Thanks for trying out a clean install. That was overkill given your scenario, but at least you can say definitively it is not a userspace problem. I should have been quicker on the uptake regarding the meta key-sequence. It isn't a WSL-proper actionable; WSL is consuming the terminal sequence bytes it is getting down the pty (which is why WSL1 v. WSL2 isn't going to make a difference). I can't reproduce "Alt+Shift+3 seems to insert a bell character instead". I get the # comment. For what might be going on there for you, the windows terminal people will have better answers. The sequence you want really is alt-shift-3, not ctrl-shift-3 (the sequence in your OP repro). On Windows Terminal ctrl-shift-3 spawns a new tab, because it is a shortcut for the terminal app itself. Thanks again for pursuing this with all the details.

@therealkenc Thanks for your support. I reported this bug here as you said: https://github.com/microsoft/terminal/issues/10244

Adrián, I suspect this is a Bash issue. I'm seeing the same issue on Linux with Konsole. When typing Alt+Shift+3, the following bytes are emmited:
0x1B # ESC (alt modifier)
0xC2 # first byte of '·'
0xB7 # second byte of '·'

Note that with the Spanish layout Shift+3 produces the character ·, which is multibyte in UTF-8.
Typing other multibyte characters with the Alt modifier (e.g. Alt+º, Alt+€) also results in invalid characters being printed. So I am certain this is Bash's fault for failing to process multibyte characters preceded by an ESC byte.
Saludos.

I'm seeing the same issue on Linux with Konsole.

Yesterday I was almost going to suggest trying WSLg with gnome-terminal (or konsole, or whatever) and see if it behaves the same. If someone with a Spanish keyboard can confirm or deny, that'd be a decent data point. Or even try other "competing" terminal emulators. I use ttyd now and then, and wsltty has a following. Worth trying before rattling any chains over in the Windows Terminal tracker, anyway.


Query related to AUC and ACC score

Dear Sir,
I noticed one thing that in your experimental results the AUC is greater than Accuracy score. Is it normal to have AUC score greater than Accuracy? Could you please explain this. Thanks

Usually AUC is higher than ACC, no matter if it is binary or multiple classes. I suggest you check literature or do experiments to have a deeper understanding.


Tick values misaligned when updating chart data

Bugs and Questions
Checklist

[ ] not sure This is a victory-native specific issue. (Issues that also appear in victory should be opened here)

[x] I have read through the FAQ and Guides before asking a question

[x] I am using the latest version of victory-native

[x] I have checked to make sure that my versions of react-native and react-native-svg are compatible with this version of victory-native. Read about version requirements

[x] I've searched open issues to make sure I'm not opening a duplicate issue

The Problem
I have an VictoryArea (but happens with all chart types) with two VictoryAxis and everything renders correctly. In my setup the data of the chart can update on the fly (eg.: user choosing a different timespan) and that's when this issue occurs. It seems that there's a rendering issue in the ticks. I don't provide them and let Victory do all the magic, that's when I sometimes end up with this:

https://jmp.sh/uPlhV6p
https://jmp.sh/NLF94cA
Reproduction
Not so easy..  'Sometimes' when the data changes of an existing graphs, the labels are mispositioned
edit: image was not embedding properly, posted links to screenshots

@svenlombaert I believe this was fixed in the latest version of victory-native. The fix involved forcing the key of the label to change on every render to get around some incorrect caching in react-native-svg. Can you let me know which version of victory-native and react-native-svg you're using?

Aha, apparently I was not using the latest version indeed (sorry for the checkmark!). It's resolved indeed!


Investigate and mitigate the affect on block time a single validator can have

There's evidence in the mocha-3 network that a single validator (with less than a third of the voting power) can alter the block intervals of the blocks they produce by changing their local TimeoutCommit.
It is expected that at least 1/3 and as much as 2/3 (depending on how may signatures are present in the commit) of voting power should be required to alter block intervals. The fact that we can get a 3 second block when all but one validator has a TimeoutCommit set to 11 seconds is indicative that validators are continuing to vote on newly arrived proposals even while waiting for TimeoutCommit period from the previous height to pass.
It should be made mandatory that a node respect the full TimeoutCommit period before engaging in round 0 of the following height.

can we close this?


setup-ios.sh fails

Describe the bug
Trying to follow the instructions to setup the forge python environment.
Looks like the script makes an assumption that git-lfs is installed?
Steps to reproduce
Follow instructions and run source ./setup-iOS.sh 3.11
Expected behavior
that it doesn't fail.
Screenshots
No response
Environment

Operating System: Mac OS
Python version: 3.11.6

Logs
$  source ./setup-iOS.sh 3.11
Using /Users/I530566/devel/mine/hamradio/beeware-tutorial/mobile-forge/support as the support folder
Creating Python 3.11 virtual environment for build...
Using /Users/I530566/.pyenv/shims/python3.11 as the build python
Requirement already satisfied: pip in ./venv3.11/lib/python3.11/site-packages (23.2.1)
Collecting pip
  Obtaining dependency information for pip from https://files.pythonhosted.org/packages/d4/55/90db48d85f7689ec6f81c0db0622d704306c5284850383c090e6c7195a5c/pip-24.2-py3-none-any.whl.metadata
  Using cached pip-24.2-py3-none-any.whl.metadata (3.6 kB)
Using cached pip-24.2-py3-none-any.whl (1.8 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 23.2.1
    Uninstalling pip-23.2.1:
      Successfully uninstalled pip-23.2.1
Successfully installed pip-24.2
WARNING: There was an error checking the latest version of pip.
Requirement already satisfied: setuptools in ./venv3.11/lib/python3.11/site-packages (65.5.0)
Collecting setuptools
  Using cached setuptools-75.2.0-py3-none-any.whl.metadata (6.9 kB)
Collecting wheel
  Using cached wheel-0.44.0-py3-none-any.whl.metadata (2.3 kB)
Using cached setuptools-75.2.0-py3-none-any.whl (1.2 MB)
Using cached wheel-0.44.0-py3-none-any.whl (67 kB)
Installing collected packages: wheel, setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 65.5.0
    Uninstalling setuptools-65.5.0:
      Successfully uninstalled setuptools-65.5.0
Successfully installed setuptools-75.2.0 wheel-0.44.0
Obtaining file:///Users/I530566/devel/mine/hamradio/beeware-tutorial/mobile-forge
  Installing build dependencies ... done
  Checking if build backend supports build_editable ... done
  Getting requirements to build editable ... done
  Preparing editable metadata (pyproject.toml) ... done
Collecting crossenv@ git+https://github.com/benfogle/crossenv@c801a526403a06f653939a0c45534d7703f9066f (from mobile-forge==2024.0.0)
  Cloning https://github.com/benfogle/crossenv (to revision c801a526403a06f653939a0c45534d7703f9066f) to /private/var/folders/ly/nghswfcj397gj52vdsczbg580000gn/T/pip-install-p_3mp6hs/crossenv_9aff5e52421e431999adf13e9fdf99e9
  Running command git clone --filter=blob:none --quiet https://github.com/benfogle/crossenv /private/var/folders/ly/nghswfcj397gj52vdsczbg580000gn/T/pip-install-p_3mp6hs/crossenv_9aff5e52421e431999adf13e9fdf99e9
  warning: templates not found in /Users/i530566/.git-template
  git-lfs filter-process: git-lfs: command not found
  fatal: the remote end hung up unexpectedly
  warning: Clone succeeded, but checkout failed.
  You can inspect what was checked out with 'git status'
  and retry with 'git restore --source=HEAD :/'

  error: subprocess-exited-with-error

  × git clone --filter=blob:none --quiet https://github.com/benfogle/crossenv /private/var/folders/ly/nghswfcj397gj52vdsczbg580000gn/T/pip-install-p_3mp6hs/crossenv_9aff5e52421e431999adf13e9fdf99e9 did not run successfully.
  │ exit code: 128
  ╰─> See above for output.

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git clone --filter=blob:none --quiet https://github.com/benfogle/crossenv /private/var/folders/ly/nghswfcj397gj52vdsczbg580000gn/T/pip-install-p_3mp6hs/crossenv_9aff5e52421e431999adf13e9fdf99e9 did not run successfully.
│ exit code: 128
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.

Additional context
No response

Thanks for the report. The problem is in the log you've provided... but it's definitely not obvious, and it's not a requirement that is in the documentation.
The issue is that you need git-lfs installed in order to clone crossenv. The crossenv repo embeds some very large data files that are used for testing; although Mobile Forge doesn't need those files, the clone and checkout performed by an editable install will fail if it can't complete the LFS checkout.
You can get git-lfs from https://git-lfs.comm or from homebrew by running brew install git-lfs. I'll update the docs to reflect this.


ESR Desktop and Mobile App Compatibility

Will defer to @nab-77 on reviewing this, thanks!

@nab-77 Kind reminder to review this, or we can also discuss this further next week as needed.

In the new table its not needed to state "Desktop app v5.0" as the col header describes this. Just go with the version in the cell (e.g. 5.0)


Hellinger distance for Drift Analysis

Hellinger distance: https://en.wikipedia.org/wiki/Hellinger_distance
How to contribute stattest for Drift Analysis: https://github.com/evidentlyai/evidently/wiki/Hacktoberfest

Hi, @emeli-dral I would like to take this,
But I am new to evidently, could you please assign this to me and help me during the progress?
Are there any time constraints you have, do I need to complete it within a short time from assigning it to me?

Hi @Mathanraj-Sharma I already started working on this issue yesterday, forgot to mention it here, @emeli-dral please review this pr, will add tests and example shortly.

Hi @Mathanraj-Sharma!
Thanks for your interest to contribute! We do not have a specific timeline here and will not formally "reserve" issues - though we encourage everyone to post when they start working on the issue so that others can see it (and maybe pick a different test). We will review contributions as they come, on the first come - first reviewed basis.
Note that you can also choose and implement a different statistical test of your choice!

We recently added an example of setting stattests in TestSuites. We are happy to receive PRs to update it with new drift detection methods!


Make docker image tag configurable

Signed-off-by: leonwanghui<EMAIL_ADDRESS>
What this PR does / why we need it:
Which issue this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close that issue when PR gets merged): fixes #
Special notes for your reviewer:
Release note:

@wisererik PTAL


hotkeys do not work with dvorak

Looking at the demo page, pressing Option + B (the counter should be bumped) -- nothing happens. Pressing Option + X (it'd correspond to Option + B if I'd use QWERTY and not Dvorak) -- everything works.
Expected: it says Option + B, I press Option + B, it just works
Real: Press Option + B, nothing happens. Frustrating 🤷♂

What event.key and event.code do you have on B/X presses?
What OS do you use and how did you enable Dvorak there?

Just 'B':
{
"key": "x",
"keyCode": 88,
"which": 88,
"code": "KeyB",
"location": 0,
"altKey": false,
"ctrlKey": false,
"metaKey": false,
"shiftKey": false,
"repeat": false
}
Option+B:
{
"key": "≈",
"keyCode": 88,
"which": 88,
"code": "KeyB",
"location": 0,
"altKey": true,
"ctrlKey": false,
"metaKey": false,
"shiftKey": false,
"repeat": false
}
macOS Sonoma 14.2.1
Dvorak is set up in a standard macOS way.

Karabiner-Elements is installed but it has only simple remappings for external keyboards, nothing that should affect this one.

Can you try to remove this like and check again?

Just 'B':

Is it Dvorak’s B?

Sorry, here it goes:
Dvorak B, QWERTY N:
{
"key": "b",
"keyCode": 66,
"which": 66,
"code": "KeyN",
"location": 0,
"altKey": false,
"ctrlKey": false,
"metaKey": false,
"shiftKey": false,
"repeat": false
}
Dvorak X, QWERTY B
{
"key": "x",
"keyCode": 88,
"which": 88,
"code": "KeyB",
"location": 0,
"altKey": false,
"ctrlKey": false,
"metaKey": false,
"shiftKey": false,
"repeat": false
}

Can you try to remove this like and check again?

not sure I understood correctly. Removed NON_ENGLISH_LAYOUT.test(event.key) && check, started locally (pnpm i && pnpm start) -- no luck

Dvorak B, "key": "b",

Seems like it is not a problem with Dvorak.
Does those h hotkeys in demo works in Dvorak (when you press Dvorak’s h)?

Dvorak B, "key": "b",

Seems like it is not a problem with Dvorak.
Does those h hotkeys in demo works in Dvorak (when you press Dvorak’s h)?

Consecutively pressing 'h' in Dvorak and switching tabs with mouse. Looks like expected behavior:

Hm. Seems like the problem is with Option+B.

Can you show Dvorak’s Option+B event object?
Can you debug those lines to find out why event.code was not used? https://github.com/ai/keyux/blob/main/hotkey.js#L37-L45

Closing since it is rare case and reporter do not respond. We will open it later when we have a real use case.


Added Support for Linux On Power

Hi,
I had added ppc64le(Linux on Power) support on travis-ci in the branch and looks like its been successfully added. I believe it is ready for the final review and merge. The travis ci build logs can be verified from the link below.
https://travis-ci.com/github/ujjwalsh/rubyntlm/builds/207360147
Please have a look.
Regards,
ujjwal

thank you - since this repo is now on gh actions I am closing this.


Cleared formula for resiliency reserve and available memory for VM

I did not get the point of how to calculate resiliency reserve, so I reworked this part and added some example

some changes needed


JIT: replace golang-asm with a thread-safe one (from scratch)

In aarch64, golang-asm is not thread-safe, and the multi-goroutine engine test case actually fails if gorutine num > 1.
We could introduce a mutex in engine.Compile and lock the golang-asm usage, then the test passes, but it's not ideal.
Instead, we should replace golang-asm with a thread-safe, but there's not alternative out there.
That means we have to implement an assembler from scratch.

In anyway, removing golang-asm dependency is good and well aligned with our main goal "zero dependency".

FWIW I totally agree with this change

please make it internal though :) I don't expect we need to support this api for third party use

done with amd64.. now is the time to enjoy arm64!


062- Entra ID B2B

Entra ID(previously Azure AD) and Entra ID B2B challenges and it';s solutions

cancelling


SelectableText should select full sentence on triple-tap

On native desktop and mobile platforms and apps, text selection can be done by dragging to select, double-tapping to select a word, or triple-tapping to select a line or sentence.
Triple-tapping a SelectableText or even text in a TextField should highlight the full sentence. Just as double-tapping selects/highlights the word

@pedromassango

@pedromassangocode

This is similar to https://github.com/flutter/flutter/issues/63576.

@lesliearkorful FYI this is something we've wanted for our app recently so I've started working on it in #80535
Can't predict when it'll be done since it's my first PR and there are many unknowns ;)


egi compatibility

cc @dengemann I have discovered that our code does not properly read binary EGI data from NetStation 5. This is likely due to incompatibility of both our code as well as some issues with EGI's conversion (for example the ECG channel is called u'TR' after the conversion). It also seems that the new files use unicode (as highlighted in the above example). I am going to work on this, but I wanted it documented somewhere so people know. I will explore what the best option is for reading EGI data (I am leaning toward trying to make it so we can read the raw mff files and can avoid dealing with converting the files).

hey @dgwakeman, let me know if you need a hand with this.

@dgwakeman any progress here?

I am in the midst of modifying the EGI code currently, so this would be a great time to tackle this issue again. There has been no response, though, so I'm going to close for now. @dgwakeman feel free to reopen if it's still broken and you can provide samples.

Is there any help we need from EGI? I can be in touch with Don Tucker about this, if necessary.

Matti

On Dec 4, 2015, at 5:06 PM, Eric Larson<EMAIL_ADDRESS>wrote:
I am in the midst of modifying the EGI code currently, so this would be a great time to tackle this issue again. There has been no response, though, so I'm going to close for now. @dgwakeman https://github.com/dgwakeman feel free to reopen if it's still broken and you can provide samples.
—
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@mshamalainen not at the mne-python end yet I don't think. First we'd want to get our hands on a troublesome file and try it with our reader. Then probably look up file specs and see if we can figure out how to fix our reader -- you know, RTM :) Then if that fails, bother other folks.

I'm curious as to the current status of supplying IO support for EGI MFF files? I had started translating the fieldtrip MATLAB code for reading in mff files, but realized it might be more beneficial if these efforts were officially incorporated into MNE. Is this being worked on or planned to be worked on by anyone? If not, I'd be willing to put in the time.

We have support for some EGI files, but not MFF AFAIK.
@SherazKhan you have some Python code to read MFF, right? Any chance you can convert it to an MNE reader in the next week or two?

Just wanted to follow up on this discussion to see if there was any update?

@mattboggess @Eric89GXL Lets do it, @mattboggess do you some sample mff file I can test the reader ?
@Eric89GXL do we have a mff file in testing data ?

No test file. Does anyone have access to a system where they could record a short segment (1 sec?) of data to add to mne-testing-data?

Our EGI person literally broke her back this weekend ... I could do it next year :D
I only have a bunch of very long ones. MFF reader would be very cool!

@jona-sassenhagen may be a segment with multiple events ?

@Mensen do you mind if I share the code you once showed to me? We have a few people who would love to skip the silly conversion step to EGI .raw data.

This is the API I have, please let me know, if you have any-more specific for the IO APIS
`from .io import read_mff_data,read_mff_header,read_mff_events
class mff:
def __init__(self, filename):
    self.filename = filename
    self.hdr = self.get_hdr()

def get_hdr(self):
    return read_mff_header(self.filename)

def get_data(self):
    return read_mff_data(self.filename, 'epoch', 1, self.hdr['nTrials'], self.hdr)

def get_events(self):
    return read_mff_events(self.filename, self.hdr)`

@SherazKhan it should be exposed in the same way as other readers in mne.io; but this is not a problem, we can handle this here. @fraimondo any chance we have silly little mff netstation file to play with?

We have a specific API, most recently worked through here:
https://github.com/mne-tools/mne-python/pull/3754
Basically you need to populate the measurement info in a Neuromag-like way, and provide a function to read arbitrary time segments of the data.

Thanks @Eric89GXL , excellent very detailed, let me work on the API.

I have netstation mff files. But not for the latest net station. In any case, it would be great to be able to read mff files without converting to raw. RAW files don't support non-eeg channels data. I have to go through matlab files. And synthesising the trigger channel for that is painful
Test File Here

@SherazKhan @Eric89GXL  I have a 2 min 45 second recording with multiple events I could share now. This recording does not have any non-EEG channels through the Physio16 nor does it have an associated digitization file, both of which would be nice to support.
I have access to a system and could record something shorter if desired. I also potentially could get access to a longer recording that has Non-EEG channels or record a shorter version with the Physio16 (though this might take more time to acquire since we don't currently plan to use the Physio16).

How big is the file? 1MB is okay but 10 or 100 is probably not, and a shorter file would be better.

Oh no then it's too big (160 MB).

Tomorrow I can edit the file and cut only a few epochs. First thing in the
morning. Need access to and old Mac and a hasp key.

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@fraimondo Were you able to obtain a smaller file?
I recorded a 2.1 MB file today that has multiple events that I could share for testing just in case . It's hard for me to get smaller since we only have high density caps. Notably, it does not contain non-EEG channels and does not have an associated digitization file, though it should be from the latest net station version.

Here's a 2 mb files with a couple of seconds of EEG + PSG data with digital triggers.

Hi guys,
I just starting to use mne, and i have some questions: How can i use the code of SherazKhan to read an egi file directly without the conversion to raw egi, is it possible to do?. Sorry for reopen the thread but i didn't understand if you could solve the problem. I have access to a geodesic Hidrocel, and i can facilitate the data. Thanks.

ping @SherazKhan
any chance to have your help to integrate a good EGI reader in mne-python ?

Same here… I’m in coding mood
On 10 Jan 2017, 21:24 +0100, Alexandre Gramfort<EMAIL_ADDRESS>wrote:

ping @SherazKhan
any chance to have your help to integrate a good EGI reader in mne-python ?
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Sorry Guys for being sparse in my appearances, @ramonapariciog do you have a good sample mff file which can be put into testing dataset ?

@SherazKhan can you make use of this data that @fraimondo posted?
https://www.dropbox.com/s/xqjbtxphkdg26g4/test_data?dl=0
If you can get it working with your reader, we can add it to mne-testing-data. It's a bit unfortunate that it's 50MB, though, so if someone can get a smaller file (~1 sec?) that would be ideal.

Oh wait in a later comment he posted a smaller version
https://www.dropbox.com/s/3awaktm0skdzr64/short_test_data?dl=0

On a related note, is there existing functionality to read in EGI digitization files?


Adding Grafana dashboard

Signed-off-by: Tihomir Surdilovic<EMAIL_ADDRESS>Updated Prometheus and Grafana docker-compose configs to:

enables server metrics
set up automatic prometheus scraping point to temporal server metrics
set up automatic grafana dashboard that can be used out of box
updates the how-to doc to mention this

To test: run ./start then go to http://localhost:3000/ , log in as admin/admin and to go DashBoards->Home and click on the "Temporal" dashboard thats already there

Why build containers instead of using the upstream ones with volumes?

@robholland
managed to disable grafana login -- https://github.com/temporalio/background-checks/pull/19/commits/eb0754b88190d599cbf727827922b33a373ee29a


Camera only opens in portrait mode.

When the camera opens, it is in portrait mode. My application is purely landscape based. When i put a face infornt of camera, the face is rotated by 90 degrees. How would i open the camera in landscape.

@Happily-Hemu thanks for interest on this repo, I just released a new version <IP_ADDRESS> that support landscape mode.

Closing this issue because of inactivity.


groupBy not grouping by a tag created with eval

Full details of your operating system (or distribution) e.g. 64-bit Ubuntu 14.04.

Running InfluxDB/Kapacitor/Chronograf as Docker containers on MacOSX, latest Docker.

The version of Kapacitor you are running

Latest, 1.4.

Whether you installed it using a pre-built package, or built it from source.

Official Docker container

We are running into an issue with TICKscript and its groupBy behaviour.
We have two sets of measurements, indoor_temperatures and outdoor_temperatures, which we query with a batch.
The queries look as follows:
var out_temp = batch
    |query('SELECT mean(temperature) FROM yyyy')
        .every(10s)
        .period(120d)
        .groupBy(time(1h))
        .fill(0)

var in_temp = batch
    |query('SELECT mean(temperature) FROM xxxx')
        .every(10s)
        .period(120d)
        .groupBy(time(1h))
        .fill(0)

If we HTTP out both of them, they create the following sets of data:
{
  "series": [
    {
      "name": "outdoor_temperatures",
      "columns": [
        "time",
        "mean"
      ],
      "values": [
        [
          "2017-09-20T17:00:00Z",
          0
        ],
        [
          "2017-09-20T18:00:00Z",
          11.5
        ]
        ... the rest
      ]
    }
  ]
}

{
  "series": [
    {
      "name": "indoor_measurements",
      "columns": [
        "time",
        "mean"
      ],
      "values": [
        [
          "2017-09-20T17:00:00Z",
<PHONE_NUMBER>4984
        ],
        [
          "2017-09-20T18:00:00Z",
<PHONE_NUMBER>0949
        ]
        ... the rest
      ]
    }
  ]
}

Now we do a full join of them, which gives us expected results
out_temp
    |join(in_temp)
        .as('out_temp_mean', 'in_temp_mean')
        .tolerance(5m)
        .fill(0)

httpOut:
{
  "series": [
    {
      "name": "outdoor_temperatures",
      "columns": [
        "time",
        "in_temp_mean.mean",
        "out_temp_mean.mean"
      ],
      "values": [
        [
          "2017-09-20T17:00:00Z",
<PHONE_NUMBER>8596,
          0
        ],
        [
          "2017-09-20T18:00:00Z",
<PHONE_NUMBER>0949,
          11.5
        ]
        ... the rest
      ]
    }
  ]
}

Which looks perfect. The issue raises when we want to round the out_temp_mean.mean down and groupBy it
So we go ahead and extend the script
out_temp
    |join(in_temp)
        .as('out_temp_mean', 'in_temp_mean')
        .tolerance(5m)
        .fill(0)
    |eval(lambda: string(floor("out_temp_mean.mean")))
        .as('bucket')
        .tags('bucket')
        .keep('out_temp_mean.mean', 'in_temp_mean.mean')

After which the output STILL looks as it should:
{
  "series": [
    {
      "name": "outdoor_temperatures",
      "columns": [
        "time",
        "in_temp_mean.mean",
        "out_temp_mean.mean",
        "bucket"
      ],
      "values": [
        [
          "2017-09-20T17:00:00Z",
<PHONE_NUMBER>3401,
          0,
          "0"
        ],
        [
          "2017-09-20T18:00:00Z",
<PHONE_NUMBER>0949,
          11.5,
          "11"
        ]
      ]
    }
  ]
}

Now only thing left is to group the values by the new tag bucket:
out_temp
    |join(in_temp)
        .as('out_temp_mean', 'in_temp_mean')
        .tolerance(5m)
        .fill(0)
    |eval(lambda: string(floor("out_temp_mean.mean")))
        .as('bucket')
        .tags('bucket')
        .keep('out_temp_mean.mean', 'in_temp_mean.mean')
    |groupBy('bucket')

After which everything goes awry and we are greeted with series: null
{
  "series": null
}

Is this expected behaviour? A bug? Or something else?

Spend hours debugging this and facing a similar issue the groupBy not grouping by a tag created with eval


Towny commands not working with Gringotts

/t claim doesn't work at all. /t deposit also doesn't work either. Both commands throw "An internal error occurred while attempting to perform this command. /t or any other Towny commands don't give any errors, but the commands also don't work. I'm on a Paperspigot 1.15.2 server with Gringotts 2.11.2-SNAPSHOT. My Towny version is <IP_ADDRESS>. Any help? I can send the Gringotts and Towny config file, along with the full server logs from start-end. All three will be linked in separate Pastebins in the case you ever need it to fix the problem.

I have the same problem


Extract Priority in prependValidator fails on HHVM.

When trying to extract the priority from the validators in prependValidator, the following code is ran -
if (!$this->validators->isEmpty()) {
            $queue = $this->validators->getIterator();
            $queue->setExtractFlags(PriorityQueue::EXTR_PRIORITY);
            $extractedNode = $queue->extract();
            $priority = $extractedNode[0] + 1;
        }

If I dump out $extractedNode with HHVM turned OFF, I get the following output(which is as expected) -
array(2) {
  [0]=>
  int(1)
  [1]=>
  int(9223372036854775807)
}

But with HHVM turned on, I instead get the following -
array(2) {
  ["instance"]=>
  object(stdClass)#6288 (9) {
    ["__CLASS__"]=>
    string(20) "Zend\\Validator\\Regex"
    ["messageTemplates"]=>
    string(8) "Array(3)"
    ["messageVariables"]=>
    string(8) "Array(1)"
    ["pattern"]=>
    string(71) "/^[a-zA-Z0-9.!#$%&'*+\\/=?^_`{|}~-]+@[a-zA-Z0-9-]+(?:\\.[a-zA-Z0-9-]+)*$/"
    ["value"]=>
    NULL
    ["defaultTranslator"]=>
    NULL
    ["defaultTranslatorTextDomain"]=>
    string(7) "default"
    ["messageLength"]=>
    int(-1)
    ["abstractOptions"]=>
    string(8) "Array(7)"
  }
  ["breakChainOnFailure"]=>
  bool(false)
}

This gives an undefined index when trying to define the priority on line 162 in the ValidatorChain.php at $priority = $extractedNode[0] + 1;. Obviously because it hasn't resolved to the priority and appears to instead have just returned the validator?
Actually testing this outside of the ValidatorChain.php I can run the following code with absolutely no issues -
    $priority_queue = new SplPriorityQueue();

	$priority_queue->insert('item',1);
	$priority_queue->insert('item',2);
	$priority_queue->insert('item',3);
	$priority_queue->setExtractFlags(PriorityQueue::EXTR_DATA);
	var_export($priority_queue->extract()); echo "\n";

	$priority_queue->setExtractFlags(PriorityQueue::EXTR_PRIORITY);
	var_export($priority_queue->extract()); echo "\n";

	$priority_queue->setExtractFlags(PriorityQueue::EXTR_BOTH);
	var_export($priority_queue->extract()); echo "\n";

	die();

Which returns -
'item'
array (
  0 => 2,
  1 =><PHONE_NUMBER>854775806,
)
array (
  'data' => 'item',
  'priority' =>
  array (
    0 => 1,
    1 =><PHONE_NUMBER>854775807,
  ),
)

Unsure whether this needed to be submitted as a Zend Framework issue or a HHVM issue as i'm not 100% on what's actually going wrong in the ValidatorChain.
It's also worth noting that I get this error with any Validator that is used and not just the example I have given.

Whilst it's not a permanent fix, this is a workaround that will work on HHVM
public function prependValidator(ValidatorInterface $validator, $breakChainOnFailure = false)
{
    $priority = self::DEFAULT_PRIORITY;

    if (!$this->validators->isEmpty()) {
        $extractedNodes = $this->validators->toArray(PriorityQueue::EXTR_PRIORITY);
		rsort($extractedNodes, SORT_NUMERIC);
	    $priority = $extractedNodes[0] + 1;
    }

    $this->validators->insert(
        array(
            'instance'            => $validator,
            'breakChainOnFailure' => (bool) $breakChainOnFailure,
        ),
        $priority
    );
    return $this;
  }


Calls and SMS

Hey I’m wondering if using this code with a ‘NooElec NESDR Mini’ can allow me to intercept calls and SMS? If not, what kind of radio would I need for this? Will this code allow for it , or does this code just work for displaying the IMSIs?

No. My code only displaying the IMSIs.
Take a look to grgsm_decode (part of gr-gsm).


Get DataFrame data as Pandas DataFrame

A very common use case is for us to use a Pandas DataFrame for data analysis and manipulation for SystemLink data. We should add the ability to request a Pandas.DataFrame directly from a client API for a DataTable by id.

@adamarnesen this work is in progress and will soon raise a PR


What are the limits on external data mash ups?  This document contradicts itself

The Overview section states that:

The integration of the application and Power BI enables data mash-up scenarios that require access to external data sources

however, the Can I do data mash-ups by using external data in the embedded reports? question in the FAQ states that:

No, you can't currently do data mash-ups by using external data in the embedded reports.

Can this please be clarified?
Thanks.

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

ID: 630034c6-dbcc-d365-d58b-36bef4277582
Version Independent ID: ce5941a7-67bb-9c0a-c1ab-230fe8aff69f
Content: Power BI Embedded integration - Finance & Operations | Dynamics 365
Content Source: articles/fin-ops-core/dev-itpro/analytics/power-bi-embedded-integration.md
Service: dynamics-ax-platform
Product: ****
Technology: ****
GitHub Login: @TJVass
Microsoft Alias: tjvass

Thank you for your feedback. @TJVass can you please take a look?

BUG 514878 created to track.

Has there been an update on this?  All I am after is clarification on what is actually possible/supported and what is not.

Removing the FAQ item.


Fix automatic remoting for Windows XR Plugin

Overview
Adds an optional waiting period in the various data providers to ensure that XR is properly initialized before assuming they're properly enabled/disabled.
Previously, data providers would check if their specified loader is the active loader once at initialization, though in some scenarios (like holographic remoting), XR itself isn't initialized until some point later (like when remoting makes a successful connection, which might not be instant).
Now, data providers will wait until an active loader exists before determining their enabled state.
Also fixes a potential null ref in ArticulatedHandDefinition which I noticed during shutdown of remoting when a hand is detected.
Changes

Fixes: https://github.com/microsoft/MixedRealityToolkit-Unity/issues/9682

/azp run


SICPJS: Change spacing between paragraphs

Description

Change spacing between paragraphs to 32px, same as comparison edition.
Changing from line breaks to using margins to control spacing between paragraphs. This gives us more control over how large the spacing will be.

Type of change

[x] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update
[ ] Code quality improvements

Checklist

[x] I have tested this code
[ ] I have updated the documentation

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 30.011%

Totals

Change from base Build<PHONE_NUMBER>:
0.0%

Covered Lines:
3196

Relevant Lines:
9805

💛  - Coveralls


Web 116 - Create alternative version of locations page

New page style
Locations static image

Let me know what do you think about rounder corners. I think the page looks better with them.
The images are created from Google maps' static API

Quick one before I dig deeper into the code: the idea behind this ticket is to create an alternative, which is another version of the location page, so we can submit that to the users to see which one they prefer. So I'd suggest to create a pages/03-locations-alt.mustache or something of the likes, together with an location-card-alt.
Aside from that, I was looking on how the the location cards were working, and I've got a couple of questions around them:

Is there any reason for using grid rather than, e.g. floating the image? Given the image is of fixed size, the rest of the text shouldn't be a problem. As it is now, the whole configuration is a bit spread around and seems a bit of a stretch in the use of grid specifically in this instance.
If we use grid shouldn't it be better to use auto in the first column instead of splitting the content precisely at 50%? seems to be able to scale a bit better.
2a. maybe you should have had row templates as well as column templates for what you wanted to achieve.
from an accessibility/usability PoV, I think a link to the actual map would be good, maybe using the image, which due to the way it looks, feels like the natural candidate and as a textual link perhaps?

Currently the heading of one card is closer to the image of the previous card than it's own. This creates the mistaken impression that the previous image is associated with the next heading.
E.g. in the screenshot below, the title "Dublin" looks like it belongs to the map above it, but that's actually for Denver:

The obvious fix would be to add a sufficiently large vertical margin between successive cards. Interestingly, the layout for larger screens (with 2 cards per row) already does this.

Also, some of the map markers aren't pointing to the right place (perhaps they're showing the middle of the postcode area instead of a specific building?).
For example, in the London map half of our 2FA building is visible on the right edge of the image, but map marker is 2 blocks West of there.
Similarly, in New York, it's pointing to the middle of a road but it should be the "WeWork Dumbo Heights" building to the East of there.

@franz899 I think the rounded corners look nice, but it's a new element in our existing design style. So far everything is quite pointy and angular.
However, with @ThePeach's incoming new logo, we'll have something else that's rounded. :-)
So, I suggest we keep the rounded corners for now (to get more feedback), but perhaps consider what else in our UI could/should also be rounded.

I've double checked the map coordinates and I use the same Lat Lon for static and live maps.

Re the map display: I've checked and the link points you to the right place, but the static map is wrong:
static:

live map (opened through the link):

@franz899 I wasn't really doubting that you didn't save the right images, I was just implying that that's apparently a bug on their end... I don't know whether this last commit the best way to deal with it on our end ❓ suggestions? @james-nash?


Pane focus movement does not match alt+direction

Steps to reproduce
Create a vertical split. Then on the left pane, create another vertical split, like so
|_1_|_2_|___3___|
With the focus on pane 3, moveFocus left
Expected behavior
The focus should move to 2
Actual behavior
The focus moves to 1

Thanks! This is a combination of /dup #4692 and #2398, both of which are important and might actually be in conflict. :smile:


Enable interupts and resetting on a pwm timer for synchronization pur…

Enabled interrupts for a pwm timer and possibility to reset the timer for synchronization purposes
Example showing usage can be found at
https://github.com/smeenka/rust-examples/blob/master/nucleo-G070/examples/motors_pwm_interupt.rs
This is a redo of pull request  feature/pwm_with_interrupts, to clean up the history

Note this pull request was created from a brand new fork, to have a request with a clean history.


Workaround issue with fonts.xml parsing

On my stock android parsing failed here
E/Tangram: Error in font.xml parsing: END_TAG expected (position:START_TAG (empty) @219:51 in java.io.InputStreamReader@32d61c)
Seems xmlpullparser does not like this
<font weight="200" style="normal">NotoSansKhmer-VF.ttf
            <axis tag="wdth" stylevalue="100.0" />
            <axis tag="wght" stylevalue="39.0" />
</font>

Rebase and can be merged.


Sails memory leak using sails-postgresql adapter and model.find

Sails version: 1.0
Node version: 8.9.0
NPM version: 5.5.1
DB adapter name: sails-postrgesql
DB adapter version: 1.0.0-12
Operating system: windows 10

Well this is a repost of an issue posted on stackoverflow.  https://stackoverflow.com/questions/48698000/does-v8-node-actually-garbage-collect-during-function-calls-or-is-this-a-sail
SailsJS seems to leak when repeated calling model.find({}). While the code uses populate, without populate it still "leaks" - though much less and it just takes more time to crash.
Github minimal example can be found at: https://github.com/pulli23/memory-leak-sails
To reproduce application must be run with the following options:
I run with the flag: --max-old-space-size=80
Environment variable: node_env=production
Then if using a POST request to localhost:1337/start-runner the runner should start (as found in WorkerController.DoRun() ). - It connects to a postgresql database (database information redacted for obvious reasons).
At my personal setup it runs about 2500 times, each time finding roughly 2000 elements.
After that node will crash reporting heap memory erro.
Increasing the max-old-space-size also dramatically increases the amount of runs, however it still crashes after "some" time.
Using a mock method (as is commented out in the github) it will not crash. And the program keeps running without problem.
The combination of those: Consistent crashing at about the same runcount when calling model.find({}) and not crashing when not using a mock that creates the same result, leads me to believe there's a memory leak in sails or the adapter.

I can't provide more information without any input of a developper. - I'd like to see some activity from your side.

I too have seen this, https://github.com/balderdashy/waterline/issues/1384 was my GitHub issue a while back. I've not solved it yet, I just run 4 threads (4 core CPU) in production with PM2 restarting the threads as they die every few days, which is usually less often than deployments restarting the threads.

@wulfsolter actually, just remembered you posted https://github.com/balderdashy/sails/issues/4264#issuecomment-374081327, and looks like that was slightly after.  Hopefully that means the issue is still fixed for you as well, but if not, please keep me apprised

I think the Model.find() leak is still around.... we're running a read heavy application (~3M rows being read only writing ~5000 daily) but it works, we have deploys more often than running out of RAM and PM2 simply restarts a thread @ 4GB. Sure we lose a few requests, but with most of our clients having less than perfect connectivity our RequestManager() is pretty robust.
Small problems compared to a beautiful framework that makes our lives so much easier :D And there were certainly a few 'death glares' when I did a pres on database migration of MySQL+Mongo -> Postgres with no downtime thanks to the great ORM :D https://wulfsolter.github.io/presentation-mongoToPostgre/#/

@wulfsolter haha no doubt, thanks for the link!
So just to clarify:  the valleys in that chart are where PM2 is restarting the process due to a process crash from running out of heap, and not where the garbage collector runs?

Hi I'm using mongo and I'm having same issue.
I'm using locust to load my api and I can verify that used memory always increase. I'm just doing a simple Model.find()
Help will be appreciated as my app is productive at this moment and my containers are crashing after some time.
Thanks


Replaced white image

Not quite perfect sorry - this still has a black background (should be transparent). I'll prep a new PR.


handle not found

[ ] handle not_found for other entries
[ ] make metrics optional?
[ ] update settings for metrics server to include http server


Stream dies with EOF error every 10 minutes to the second

I have a stream that dies every 10 minutes exactly from when go2rtc launches.  It is a Tuya camera with its stream exposed using the "expose_camera_stream" hacs integration.
Refreshing the webpage brings the stream back up.
As you can see from the logs it happens at precise 10 minute intervals
1/27/2024, 12:32:03 PM	info	go2rtc version 1.8.5 linux/amd64
1/27/2024, 12:32:03 PM	info	[rtsp] listen addr=:8554
1/27/2024, 12:32:03 PM	info	[api] listen addr=:1984
1/27/2024, 12:32:03 PM	info	[webrtc] listen addr=:8555
1/27/2024, 12:42:10 PM	warn	undefined error=EOF url=echo:bash /config/custom_components/expose_camera_stream_source/get_stream.sh camera.xxxxxxx caller=github.com/AlexxIT/go2rtc/internal/streams/producer.go:171
1/27/2024, 12:52:10 PM	warn	undefined error=EOF url=echo:bash /config/custom_components/expose_camera_stream_source/get_stream.sh camera.xxxxxxx caller=github.com/AlexxIT/go2rtc/internal/streams/producer.go:171
1/27/2024, 1:02:11 PM	warn	undefined error=EOF url=echo:bash /config/custom_components/expose_camera_stream_source/get_stream.sh camera.xxxxxxx caller=github.com/AlexxIT/go2rtc/internal/streams/producer.go:171

I have other streams from different cameras that don't exhibit this issue.
Using the Tuya app I can watch the stream indefinitely so it's not Tuya cutting the stream off.

Why do you think Tuya app uses same protocol?

Why do you think Tuya app uses same protocol?

I don't, I'm just putting the info there for you in case it helps with diagnosis.
I considered it could well be Tuya but the stream restarts at 10 minute intervals from when go2rtc first launches so thought it could also be possible its go2rtc somehow.

You do.

Using the Tuya app I can watch the stream indefinitely so it's not Tuya cutting the stream off.

I think Tuya API from Hass integration, that you using, provide link only for 10 minutes. It's usual situation. Nest gives link only for 5 minutes

You do.

Using the Tuya app I can watch the stream indefinitely so it's not Tuya cutting the stream off.

I think Tuya API from Hass integration, that you using, provide link only for 10 minutes. It's usual situation. Nest gives link only for 5 minutes

I see, OK useful info thanks.
It only started happening this past week though, previously it would stay on indefinitely, anyway thanks for the clarification.

@andonevris i have the same EOF that freezes my feed on v1.8.5 but on 1.8.4 it's working absolutely fine all day.

@andonevris i have the same EOF that freezes my feed on v1.8.5 but on 1.8.4 it's working absolutely fine all day.

Thanks for that.  Yeah like I tried to explain this was a recent issue but it was obvious the dev had no interest in this issue and wanted to blame protocols.
In the end I threw the feed into frigate and used a frigate lovelace card, feed stays up all day now.
Useful to know which version broke this though, thank you

@andonevris and now you're blaming the developer for something he didn't do.
I said "I think...". And didn't close this issue or the issue from @oleg-d
I think Tuya breaks connection after 10 minutes all the time. But v1.8.4 can handle auto reconnect, and v1.8.5 don't.


Use Debug.Log for Ruffles

Perhaps it's a good idea to make RufflesTransport change the log handlers of Ruffles (e.g. https://github.com/MidLevel/Ruffles/blob/master/Ruffles/Utils/Logging.cs#L19) so that Unity logging is used. Console.WriteLine is not really visible in Unity and so important messages might get missed (like if the connection failed because of time difference)

The latest version of Ruffles auto hooks into Unity logs. I will update the version the trabsport uses. (https://github.com/MidLevel/Ruffles/blob/master/Ruffles/Utils/Logging.cs#L59)


Unverified Contract Bug Fix / Update

Replaced Mutex with Lock
Increased performance
Fixed the bug that was putting the bot into infinite loops

Deployed already to test. works nicely.


fix(@angular/cli): remove unneeded dependencies

When I have tried to install npm install @angular/core@latest but it is doesn't update. Please give me solutions.
<EMAIL_ADDRESS>/var/www/html/loyalty-dapp
├── UNMET PEER DEPENDENCY<EMAIL_ADDRESS>invalid
├── UNMET PEER DEPENDENCY<EMAIL_ADDRESS>└── UNMET PEER DEPENDENCY<EMAIL_ADDRESS>npm WARN optional SKIPPING OPTIONAL DEPENDENCY<EMAIL_ADDRESS>(node_modules/chokidar/node_modules/fsevents):
npm WARN notsup SKIPPING OPTIONAL DEPENDENCY: Unsupported platform for<EMAIL_ADDRESS>wanted {"os":"darwin","arch":"any"} (current: {"os":"linux","arch":"x64"})
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.
npm WARN<EMAIL_ADDRESS>requires a peer of<EMAIL_ADDRESS>but none was installed.


mj-section is full width i OWA

When using OWA (Outlook Web App) the mj-section is 100% width instead of the default 600px - I can see, that this is not an issue in the mailgun-example but I have not tested to see if e.g. the templates from zurb have the same issue or not. Any idea if this can be solved?

Hi there,
They are displayed in a 600px on my outlook account, but in mobile view see #40 for more informations about it
Can you share a screenshot about it please ?

Hey @iRyusa
I have already read that issue, but as I see it only covers responsive columns, my issue is about the total width of the email. I have attached a screenshot with the result of your Underwater template in OWA in IE11 - the width is 100% (here ~1300px) instead of 600px.

.

Oh sorry, I thought OWA was exactly the same as current outlook " https://outlook.live.com/owa/ "

yup - those who dislike older versions of IE have never tried to make markup for emails. I hope a solution can be found :)

@kila03 I was wondering where did you get this OWA version ?

@iRyusa It is my work account - guess it is part of Microsoft Office Web Apps in Microsoft Office 365.

I don't know what to do about this issue, I didn't find any information about conditionnal comment for this specific outlook version.

The only solution I have seen is the mailgun example, which, in short, just uses 3 columns instead of only 1. I have not yet seen any disadvantages with this technique, but unfortunately I have not access to e.g. litmus to test it more widely.

Hi, thought I would add this since I have a client which uses OWA webmail (and so does all her customers apparently). It's a bit hacky but the following seems to fix the width to 600px in OWA whilst maintaining the mobile element, be it a little off centre on desktop if you have a 600px full width image. If there is no 600px width, the email width will be one third width of the window. From what kila03 suggests the best approach is a 3 column wrapper table. Thing is with OWA, if you double-click the email it opens a new window where the email is rendered to the 600px width. So many email clients seem to strip out any styles too, but the below got the best results but does require more widespread testing as I don't have access to Litmus.
With the below email, the email content would stretch to fill the width of the window and the banner image would remain at 600px width. The '.container' class has a width of 600px applied to it, under the 480px breakpoint the width is declared as 320px. Feel free to test further.

Hey @RJRandell79, thanks for investigating this issue and providing feedback!
We'd need more tests to confidently go down this route, no way for you to test in Litmus or Email On Acid? Here's an MJML template you can use for testing: https://mjml.io/try-it-live/ryfYFW1ix

Also getting this issue on Outlook desktop (not sure which version but all my office mates that use it show the same issue)
It's interesting to note that this is not the case with the outlook web client (outlook.com)


Matrix Addition

Any types of programming languages are accepted.

Please assign me this issue under Hacktoberfest!

Hello Soumyadeep can you please assign me this issue?

Hey @SoumyadeepMukherjee ..Please assign this to me under hacktoberfest.


coroutine support (qcoro)

have you seen this project
https://github.com/danvratil/qcoro
and how can this ease the reimplementation QSqlQueryModel  , QSqlTableModel  ,QSqlRelationalTableModel

Yes, I've seen, without almost rewriting QtSql there's not magical way to turn sync into async code, coroutines also need special handling.


Cluster setup fail - germination cleanup code for R

Hi - happy Wednesday!
Thanks for developing this software. I am trying to run the Germination assay. Preprocessing of the images went great in ImageJ, and I have the project on in R-studio, but when I run the R code for cleanup_germination_data - I get the following error.
Error in makePSOCKcluster(names = spec, ...) :
  Cluster setup failed. 7 of 7 workers failed to connect.

Do you know what could be causing the issue? I am attaching my sessionInfo() below:
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS  10.16

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] rlang_0.4.10      RcppRoll_0.3.0    zoo_1.8-8         data.table_1.12.8 doParallel_1.0.16 iterators_1.0.12  foreach_1.5.0
[8] dplyr_1.0.0       pacman_0.5.1

loaded via a namespace (and not attached):
 [1] Rcpp_<IP_ADDRESS>     rstudioapi_0.11  magrittr_1.5     tidyselect_1.1.0 lattice_0.20-41  R6_2.4.1         tools_4.0.0
 [8] grid_4.0.0       packrat_0.5.0    ellipsis_0.3.1   tibble_3.0.1     lifecycle_0.2.0  crayon_1.3.4     purrr_0.3.4
[15] vctrs_0.3.0      codetools_0.2-16 glue_1.4.1       compiler_4.0.0   pillar_1.4.4     generics_0.0.2   pkgconfig_2.0.3

Hi, and a merry Wednesday to you too!
I have a hunch that it may be related to this bug in R. Could you please try running it on R 4.1.2?

Great! I'll add it to the troubleshooting table.


Bug: QuickDic crashes when I alternate the translation

Steps:

Open QuickDic (English - Spanish in my case)
Press the X button

I also noticed that when I press the flag button, I only see the "dictionary manger button" and not the 3 differ dictionaries I have. Maybe the bug is that QD doesn't manage them correctly.
It didn't happen before, I'm using v. 5.3.9 on Android 6.0.1

5.3.9 is/was not a fully stable version, but can't really mark it as such in F-droid.
5.4.0 has been released since a while and F-Droid shows it as successfully built, I don't know why it hasn't appeared yet, but either way I expect this is already fixed, just need to wait for the new version.


Rework CachedMetricMetadataAPI

Adds in concept of Stale (by default disabled) whereupon if the cache entry is older than that a background fetch request will be enqueued.
Any request for a metric key where a fetch is already in progress and the cache item has expired will wait for that fetch to come back (instead of issuing it's own synchronous call).
Added some more logging.

R: @Nathan-Fenner || @DanielNi || @syamp

I've made some notes where I think there are some race conditions or cleanup to be done. I haven't finished over it, but I think it might be possible to make this a bit simpler by changing the structure to be:
CacheData map[MetricKey]Data
where Data stores the fields and the time that they were updated, and nothing else.
CacheStatus map[MetricKey]Status
CacheArrival map[MetricKey] <-chan struct{}
where Status is one of Absent (zero-value), Stored (for metrics with CacheData), Enqueued (for metrics that may or may not have CacheData but are awaiting a request to update them) and InFlight (for metrics that may or may not have a stored value but have an in-flight request).
To synchronize waits for InFlight requests, receive on a member of the CacheArrival map (which is protected by the same mutex as CacheStatus).
When a request comes in, we check the cache:

If fresh, return from CacheData and do nothing
If not expired but not fresh, return from CacheData but update CacheStatus to Enqueued (unless it's already InFlight, in which case, do nothing).
If expired, update CacheStatus to InFlight and run it yourself and return the result.

In particular, there should be functions:
PromoteToQueue (fast) : locks the maps, checks if it's not InFlight, and then sets it to Enqueued.
PromoteToFlight (blocks until done with request): locks the maps, checks if it's not InFlight:

If it's not InFlight, set it to be InFlight, make a channel, set it for CacheArrival on that key, then unlock the mutex. Launch the request and when you're done, store it in CacheData, and close the synchronizing chan. Lastly, as a convenience, return the value.
If it already was InFlight, get the chan instance from CacheArrival for this metric, unlock the mutex, and wait on the channel. Then lock, read CacheData, unlock, and return the result.

AFAICT there aren't any race conditions, certain methods just require the lock to be in a specific state.
This is ideally focused around the least number of "global" locks - hence the only ones are getAllTagsCacheMutex for protecting insertion to getAllTagsCache and queueMutex for protecting the queue. Everything else simply requires the item's lock.
As a side note, we can't use channels here because we can have n threads all waiting on the same GetAllTags request.
Any specific reason you prefer the poll method (like you described, where you have a process polling for which metrics need an update) over a push method (by pushing jobs onto a queue)? Also, any specific reason for splitting things out into three maps instead of just one?

I see some things that are still race conditions:
func (c *CachedMetricMetadataAPI) GetAllTags(metricKey api.MetricKey, context metadata.Context) ([]api.TagSet, error) {
 	defer context.Profiler.Record("CachedMetricMetadataAPI_GetAllTags")()

 	// Get the cached result for this metric.
	item, ok := c.getAllTagsCache[metricKey]

Map access isn't threadsafe- need to acquire a lock before reading (it's not atomic, so you can get garbage data or a panic).

As a side note, we can't use channels here because we can have n threads all waiting on the same GetAllTags request.

I was suggesting waiting for a to channel close (which lots of things can listen to) instead of actually using a received value.

Any specific reason you prefer the poll method (like you described, where you have a process polling for which metrics need an update) over a push method (by pushing jobs onto a queue)?

In this case, I think it just makes things simpler, because it means the map that holds item status functions as a queue (so you don't need to keep them in sync- marking something as "needs to be updated" is equivalent to adding it to the "queue").

Also, any specific reason for splitting things out into three maps instead of just one?

It's probably better to combine them together. You could get away with only using one lock (though in principle, two locks, one for CacheData and one for the other two, would suffice).

Map access isn't threadsafe- need to acquire a lock before reading (it's not atomic, so you can get garbage data or a panic).

Ah, nice catch - I've updated that.

I was suggesting waiting for a to channel close (which lots of things can listen to) instead of actually using a received value.

Gotcha, I do like the explicitness of a sync.WaitGroup though.

In this case, I think it just makes things simpler, because it means the map that holds item status functions as a queue (so you don't need to keep them in sync- marking something as "needs to be updated" is equivalent to adding it to the "queue").

It's probably better to combine them together. You could get away with only using one lock (though in principle, two locks, one for CacheData and one for the other two, would suffice).

So the downside of that approach is that to check the status of any individual item you need to lock the entire "table", whereas by only locking on the original write to make sure the item exists and then all other operations are locked on a per-item basis. It does improve the queue approach (instead of having a channel you pull functions from), but we're doing many people reads than updates.

LGTM


FCC doc in another language Bengali

I have added the doc in localise form .I added it in Bengali . I added the Bengali directory & translating docs into bengali language .
hope all love this.

Hi @sayantanHack
Thanks for your PR.
I understand you would like to add documentation translation for Bengali. This PR is a good start. I would encourage you to make more substantial translations for rest of the docs and then open a fresh PR.
Unfortunately we find the current state of this PR, not enough to justify a merge.
Thanks for your understanding.
Happy contributing.


Capture the expected payload type in commands

Implements inference and enforcement of the payload type for LexicalCommand, as discussed in point 2. in #2536.

Closes #2536

Thanks for looking into this @PAkerstrand!

I keep getting these types of failures in the test suite, and it's usually on Windows and composition. Not sure whether it's coincidence or if I've accidentally introduced some errors? Not sure how I could introduce connection refused errors though.

This seems to be the core issue of the failed runs, we get an EMFILE-error emitted. Might be some file descriptor leakage somewhere?

@thegreatercurve - the author let me know he is on vacation for the next 3 weeks - can you take this over and see if we need to make any changes or if we can merge it as-is?

@thegreatercurve - the author let me know he is on vacation for the next 3 weeks - can you take this over and see if we need to make any changes or if we can merge it as-is?
The CI failure is the Windows thing I fixed and should pass on rebase (or we can ignore that signal and merge as-is if you're good)

Correct ☝🏼
I’m completely OK with you pushing any changes required to get this merged. I am somewhat around to be able to respond, but won’t be coding for the next few weeks


ValueError from None and build_api_error

Hello,
I recently answered a post on stackoverflow about a strange behaviour of your API
(http://stackoverflow.com/questions/37638359/api-coinbase-valueerror-from-get-buy-price/37646769#37646769).
There seems to be an internal error (build_api_error seems to confirm my assertion) under some conditions (which I can't reproduce because I'm not the author of the post).
I suspect that's something related to a network connectivity problem that causes a null JSON file.
It's why the code throws a raise ValueError(errmsg("Expecting value", s, err.value)) from None error.
It also seems quite related to that other issue: https://github.com/coinbase/coinbase-python/issues/15
I hope it will help :)

Hey @aclarembeau, thanks for the report!
Closing in favor of the more general issue, which is that the library should improve its error handling for these cases.


chore(main): release 0.1.45

:robot: I have created a release beep boop
0.1.45 (2024-05-30)
Features

Run: Run pipelines with the debugger ready to be used (a67d0fe)
Run: Run pipelines with the debugger ready to be used (#157) (754c21b)
Run: Run pipelines with the debugger ready to be used (#157) (6863173)

Bug Fixes

Cli: no error is thrown when workspace doesn't exist (#153) (fbbec07)
Cli: no error is thrown when workspace doesn't exist (#153) (cefc69c)

Miscellaneous

deps: bump docker from 7.0.0 to 7.1.0 (#156) (e6cc226)
deps: bump docker from 7.0.0 to 7.1.0 (#156) (377fca6)

This PR was generated with Release Please. See documentation.

:robot: Release is at https://github.com/BLSQ/openhexa-sdk-python/releases/tag/0.1.45 :sunflower:


observable.deps() is not working.

hello , i would like to ask about why observable.deps() is not working , i have tried as
Bacon.spy(function (obs) {
console.log(obs.deps());
});
In console i got error that deps() is not a function ?
And another this in would like to ask is that
what is the current status about following discussion
https://github.com/baconjs/bacon.js/issues/273
Do we have such visualizing tool for debugging already ?
Many Thanks in advance.

Hi,
The deps() method had been removed and was accessible by .desc.deps().
I restored the method to the API and it's once again available in version 0.7.88.

The introspection features were undocumented. I added a section to the readme: https://github.com/baconjs/bacon.js/#introspection-and-metadata

i have read your in one of your comment on
"On the other hand, now there shouldn't be a need to subscribe, as you'll get all the events through your newEvent handler anyway."
https://github.com/baconjs/bacon.js/issues/273
Could you please explain me what are  {newObservable, newEvent} , and how can i use them ?
Actually i would like to log all observables (eventstream + property) to create dependency graph in chrome dev tool extension ,
Do we already have such extension ?
Best Regards
Waqas Abbas

That was probly just speculation; there's no "newEvent handler" concept in Bacon as we speak. For debug tools it would be useful to have a mechanism for snooping events without forcing a subscription on the observable. Could be implemented into the Dispatcher quite easily if there's pull for the feature.
The dep graph thing would be cool and I dont think we have that yet. Go ahead! I'll do my best to help.

wa-sunlab<EMAIL_ADDRESS>kirjoitti 7.10.2016 kello 15.56:
i have read your in o one of your comment on
"On the other hand, now there shouldn't be a need to subscribe, as you'll get all the events through your newEvent handler anyway."
#273
Could you please explain me what are {newObservable, newEvent} , and how can i use them ?
Actually i would like to log all observables (eventstream + property) to create dependency graph in chrome dev tool extension ,
Do we already have such extension ?
Best Regards
Waqas Abbas
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub, or mute the thread.

Hello,
Thanks for your offer to help.
Yes i will need your help to develop some debugging tool.
I am using .spy to log observable values , when i try following code
http://jsfiddle.net/123xLwdd/
Why i am not getting values of my 3rd Observer which is made by "zip" of first two.
Thanks
Best Regards
Waqas

That's because Bacon.fromArray is a synchronous source and emits its value only once. See https://github.com/baconjs/bacon.js/wiki/FAQ#why-isnt-my-subscriber-called

If you use a "real" stream, it'll work. Try with Bacon.sequentially, for instance. See http://jsfiddle.net/rmojenv9/


Take a lot of seconds to show the last contacts messages on dashboard

Take a lot of seconds to show the last contacts messages on dashboard.

Looks like it's fixed now.


[BP-1.10][FLINK-18902][rest] Allow request serving while the REST handlers are shutting down

Backport of #13131 to release-1.10.

Travis has passed. Merging this PR now.

Manually merged via fd7b3719616435cd2aebf65929dbc193a53e68f3


Integrating Germline and MHC into AIRR data model

Trying to capture an email discussion that grew out of the Common Repository Working Group and has been on the back burner with all of us for some time... How do we annotate AIRR-seq data sets with Germline and MHC information?
This is somewhat related to #157 and #258 but I am starting a new thread/conversation specifically for this...

Excuse me if I miss out some of the earlier discussion.
I do not think this will be useful unless people run a genotyping tool on their sequence annotations, e.g. Tigger, IgDiscover, or partis (which has it built in). But doing so will greatly improve the annotation quality anyway.
For OGRDB, this is how we document gene usage today:
We defined a standardised format for a genotype and provided a tool that will create that format from the commonly used inference tools. That’s detailed here: https://github.com/airr-community/ogrdbstats
Here’s a sample file in that format: https://github.com/airr-community/ogrdbstats/blob/master/example_ogrdbstats_genotype.csv
Here’s what a genotype looks like in OGRDB (the genotype is the final table on the page) https://ogrdb.airr-community.org/genotype/14
OGRDB will return information on genes, iven the IMGT name. You can find the API definition and a test harness here: https://ogrdb.airr-community.org/api/
It could take years for an ontology to be defined, but you could implement the above today, and move to ontology when it's available.
Best wishes
William

It could take years for an ontology to be defined, but you could implement the above today, and move to ontology when it's available.

Sorry, I used much too strong of language - I agree with you, we don't want to wait for an ontology, but we should apply some rigor to how describe the terms in the standard so that we have a mechanism to look thing up (e.g. in OGRDB or similar).
The AIRR Ontology approach (from the Ontovoc subgroup) provides the mechanism - there is a information provider (e.g. OGRDB) and an ID (e.g. a gene name) - and that is what I meant to suggest we try to do... What we want to be able to do (IMHO) is be able to swap out information providers and still use the same ID and get a definition for that ID.
I agree we don't need a formal ontology to get started...

My thoughts on this:

I agree that we should not wait for a proper ontology, but that we can borough a lot from what we have learned with ontologies, and I am quite convinced that we also need to do this. In the end the biology of Ig/TCR loci has a certain complexity and we need a representation that must be able to capture this.

Do we think that this is only useful when it is used with a subject-specific germline reference set? IMO the answer to this is "no", i.e., it is also useful for any other annotation but in this case the reference needs to move from the subject level to the rearrangement level.

Regarding @bcorrie's question "[...] the problem is agreeing what XXXX and GENELABELFORXXXX are. Are we using GERMLINE:airr1-1, GERMLINE:X07448, GERMLINE:IGHV1-2*01 ?", we need to distinguish between:
a. the abstract concept of a certain IGHV gene, which
b. has the local ID airr1-1 and
c. has the label (=gene symbol) IGHV1-2*01 and
d. could have a PID (PURL, IRI, DOI, HANDLE, whatever flavor you like). We
need to distinguish this from
e. observations (=instances) of this concept, e.g., the sequence with the
Genbank ID X07448.
To simplify things a bit, we can assume for now that the local ID is actually a global ID (but not a full-fleged PID), so that it will always refer to the same concept in different repositories, so that the CURIEs would work even without proper PIDs.
Long story short, IMO we should use GERMLINE:airr1-1.

Sorry Christian, would you mind expanding on '...the reference needs to move from the subject level to the rearrangement level'? Thanks.

Sorry Christian, would you mind expanding on '...the reference needs to move from the subject level to the rearrangement level'?

Sure, sorry for being fuzzy: If we want to annotate the comprehensive germline gene set of an individual, then this should be done in the Subject object, as it should not change between observations.
However, if we do not have subject-specific germline gene set (i.e. annotating against the default database), then the linkage to the records of the database has to happen on the level of the Rearrangement. There are some other fringe cases (chimeric/transgenic animals) where this approach would be required.
If having the references on both level was the idea the whole time and I just didn't realize it, then you can ignore this comment.

OK, thanks, I understand. I'd say that, at the subject level, the information provided is an inferred genotype (or subject-specific germline set, if you prefer). At the rearrangement level, it's expressing ambiguity in the annotation (there will be fewer cases of ambiguity if the subject-specific germline set is available, but there will still be some).
A further point to consider, in the case of subject-specific germline sets, is how to handle novel inferences, i.e. those sequences assigned to an inferred gene that is not part of the reference set at the time the inference is made, Both how these should be labelled at the time of annotation, and whether any update or review is required should the reference set be extended subsequently. I;d be happy to demomstrate how this is addressed in OGRDB today, if that's of interest.

OK, thanks, I understand. I'd say that, at the subject level, the information provided is an inferred genotype (or subject-specific germline set, if you prefer). At the rearrangement level, it's expressing ambiguity in the annotation (there will be fewer cases of ambiguity if the subject-specific germline set is available, but there will still be some).

This doesn't need to be annotated at the rearrangement level does it. That is, there isn't a different germline set that is used for each rearrangement is there? Isn't this a feature of the DataProcessing object. That is, a specific annotation tool uses a specific germline set to produce a set of rearrangement annotations.
I can see three levels where one would have a germline set:

At the subject level, either inferred genotype or sequenced
At the sample level, inferred genotype from the annotations for that sample using an inference tool
At the data processing level, denoting the germline set used for that annotation, assuming that if one used either the subject or sample level genotype the annotation would be "higher quality" than if one used a general germline database.

@bcorrie

This doesn't need to be annotated at the rearrangement level does it? That is, there isn't a different germline set that is used for each rearrangement is there?

No, there should not be different germline sets for a Subject as... well... it's in the genes :wink: Therefore I don't think that we need an additional reference on the Sample level, as this should always be the same.
However, if the Subject-specific genotype record is not available, users will search against a reference database (annotated in DataProcessing) that likely will contain more than two alleles for some of the genes and might change over time (in contrast to the Subject record, which I assume is stable). In this situation you do not only want to know what DB you blasted against, but also the result for each Rearrangement, which requires stable identifiers and unfortunately gene symbols haven't been stable in the past. Therefore we need a link to a stable record of the reference gene.

No, there should not be different germline sets for a Subject as... well... it's in the genes 😉 Therefore I don't think that we need an additional reference on the Sample level, as this should always be the same.

The reason I suggested that this might be useful is that it is my understanding that tools that infer germlines are often applied at the repertoire level, with a genotype and haplotype often attached to a repertoire/sample. I believe that is what VDJbase stores. So is it wrong to store this at the sample/repertoire level if that is an analysis that has been performed for that repertoire? Does the AIRR Community take the "high road" and not allow genotype to be stored for a repertoire (as an analysis output), but instead ensure that an inferred genotype is linked with the subject only?

As it’s an inference, my vote would be to store it with the repertoire that it was inferred from, and this is indeed what we do in VDJbase. It wouldn’t, perhaps, be too surprising to find some variation in the inferences for some of the less frequently expressed genes.
For reproducability, it would be good to store also the reference set that was used to do the initial annotation before the genotype was inferred,

If I was to envision such a process, I would likely store the original germline used for annotation (e.g. IMGT) in the DataProcessing object (e.g. data_processing.germline_database = "IMGT 2020-06-23" for a given SampleProcessing. In this object I would likely include in the DataProcessing that I used Tigger to infer a germline for the repertoire (e.g. data_processing.software_versions = "..., Tigger/x.y"). It probably makes sense that the inferred germline gets stored in the DataProcessing object from which it was inferred. (e.g. data_processing.inferred_germline = "XXX").
If I was then to rerun an annotation tool for that SampleProcessing using the inferred germline, I would create a second DataProcessing object for the repertoire, record the germline for annotation as the inferred germline (e.g. data_processing.germline_database = "XXX"). One might want to store the inferred germline for this data processing as well (e.g. data_processing.inferred_germline = "XXX")? In this way you could tell that the germline used for annotation was the inferred germline.
If one was to then infer the germline for a subject, based on one or more inferred germlines from multiple repertoires from the subject, it would make sense to have an inferred germline at the subject level (e.g. subject.germline = "XXX + YYY" where YYY might be added information for the subject germline that was found in another repertoire from that subject??? In this case, since it is possible for a subjects germline to be inferred or not inferred, we might need track whether the subject's germline was inferred or not (e.g. subject.germline_process = ["inferred"|"sequenced"|???])
In this model, we really only need three new fields:

data_processing.inferred_germline
sample.germline
sample.germline_process
We of course also need a mechanism to store a germline XXX 8-)

Does that make sense as a starting point? Can you poke holes in my thinking??? 8-)

Hi Brian,
I think it's a good approach, but here are a couple of things to consider:
It's certainly useful to store the date on which the reference set was downloaded from IMGT, and many people do, but I am not sure that there is a way of retrieving the set as it was on that day. For full information, it would be better to store the set itself (which is not that large, for a particular species and locus). This may get more important in the future, if people start to use sets published from various sources - until we get a good, referencable, solution.
For the source of the genotype or haplotype - given the different methods available, - it might be better to record the sequencing method rather than 'inferred' or 'genomic' as there can be inference involved in the 'genmoic' methods. Examples could be:

Repertoire sequencing
Long read next-generation genomic sequencing
Short read next-generation genomic sequencing
Sanger sequencing of genomic material

For full information, it would be better to store the set itself

Fully agree, just that this potentially infringes IMGT IP (as per Art. 7 (2) a 96/9/EC) under their current license. So the three possibilities would be:

IMGT starts providing referenceable versions of their database
IMGT licenses under CC-BY (i.e., with NC-ND restrictions)
Use a third-party non-for-profit service to performs regular snapshots from IMGT and create references to these snapshots (something like perma.cc)

For the source of the genotype or haplotype - given the different methods available, - it might be better to record the sequencing method rather than 'inferred' or 'genomic' as there can be inference involved in the 'genomic' methods.

Also agreed. I am wondering whether we a) could reuse some of the existing vocabulary for sequencing methods and b) should actually annotate both, sequencing and data processing.

It would not take very long to set up a github repo that snapshotted the IMGT reference set regularly, and baselined copies on each change. I think this would be allowed under their current CC-BY-NC-ND licence, provided similar terms were applied to the result.

For the source of the genotype or haplotype - given the different methods available, - it might be better to record the sequencing method rather than 'inferred' or 'genomic' as there can be inference involved in the 'genmoic' methods. Examples could be:

Repertoire sequencing
Long read next-generation genomic sequencing
Short read next-generation genomic sequencing
Sanger sequencing of genomic material

@williamdlees do you have any suggestions for the controlled vocabulary for this? Currently have the following:
            enum:
                - sequenced
                - inferred

If we really want to boil it down we could use
derived from:

genomic sequencing
repertoire sequencing

Changed this here: https://github.com/airr-community/airr-standards/pull/438/commits/61a232a3d0746b1eef77486cd235997da76279e9

All, there is some active discussion around this in the pull request here: #438
If you are interested you might want to review/comment.


Regex group support

For some regex use cases, a user may need to go beyond just knowing whether there was a match and actually extract the strings that matched. An example implementation of this is Python regex grouping.
As a specific example use case, this could be a possible alternative to the implementation envisioned for #2092. Instead of using functions to split/slice desired fields, and re-join back into a string, a regex approach in Python could look like:
$ python
>>> import re
>>> query='www.brimsecurity.com'
>>> m = re.search(r'(\w+\.\w+)$', query)
>>> print(m.group(1))
brimsecurity.com

A community zync user inquired about this functionality. In their own words:

Do you have any idea how we can use Zed to extract a substring based on a regular expression ? Suppose I need to extract the street number out of a postal address, or maybe  extract a particular pieces of a URL, or parse a special text field in a CSV file.
Would it be possible to enhance the split function using a regular expression pattern split(s: string, <pattern>) -> [string] and returning an array of matching substrings? Perhaps something similar to TCL regexp ?switches? exp string ?matchVar? ?subMatch1 ... subMatchN??

Verified in Zed commit e9624c3.
Performing the Zed equivalent of the Python example shown in the opening text of this issue:
$ zq -version
Version: v1.2.0-85-ge9624c3b

$ echo '{"query": "www.brimdata.io"}' | zq -z 'yield regexp("(\\w+\\.\\w+)$", query)' -
["brimdata.io","brimdata.io"]

A more sophisticated example is shown in the regexp() docs.
Notice how we had to escape the backslashes, which is because the regexp is passed to the function as a string. #4148 has been opened to track a possible improvement on this.
Thanks @mattnibs!


Support for more chat types

This adds more chat types, notably group, supergroup, and channel, with their respective slots. Given the new things introduced in #10, message processing was broken, and this fixes it.
This also fixes an exported symbol duplication and an initarg name in message.lisp, introduced in #10.

OK, closer-mop-reliant initialization is there. @svetlyak40wt, I've added a 0.3.2 entry to a changelog, is that the right course of action? Should I push a v0.3.2 Git tag too then?

Imports fixed!

Cool! Thank you!


Add guidance doc

@skamalas

CLA is valid!

Coverage remained the same at 88.274% when pulling 01d5e3d3ba694226fbab97c4946dfb60d8eab88d on guide into ee84b3cde3c95cae5680041a0a13bae6a5e5c1af on master.

👍

Maybe also add a link from the Readme to the guide?


Hi @mcavdar,

          Hi @mcavdar,

Thanks for your responses.
Since i am  using deepdive 0.8, Bazaar parser is doing document parsing process.So that i could start CoreNLP as a service in this version.  After exporting a variable called DEEPDIVE_NUM_PROCESSES=1 the parser can successfully running on  all the documents without any errors.
Thanks @mcavdar
Originally posted by @Balachandar-R in https://github.com/HazyResearch/deepdive/issues/655#issuecomment-324877700

Hello author, how did you solve the problem that the database table generated after the deepdive do sentences instruction is executed


chore(master): release 1.0.2

:robot: I have created a release beep boop
1.0.2 (2023-02-11)
Bug Fixes

player: resolve issue with player.stop being ignored (eacab59)

This PR was generated with Release Please. See documentation.

:robot: Release is at https://github.com/ooliver1/mafic/releases/tag/v1.0.2 :sunflower:


Allow custom path for stack definitions

TODO

[x] add a main field to sst.json pointing to the index file (defaults to "lib/index.js")
[x] add a test with custom main field. Similar to this test - https://github.com/serverless-stack/serverless-stack/tree/master/packages/cli/test/config
[x] document the main field here - https://docs.serverless-stack.com/installation#project-config

Released in v0.35.0


IEN-734 Create test report 4

Created four test cases for Report 4. It includes hard coded data in a separate file as well.
The tests mainly cover the adding and removing of milestones for applicants. I had to include a delete function for each test so that Report 5 would not fail.

I see the issue, also, need to reformat the tests using the functions Cory created for 5.


Data profiling as per data type

Is your feature request related to a problem? Please describe.
Current data profiling integration doesn't distinguish between VARCHAR, Integer and other data type. Even if data type is VARCHAR, profiler provides sum, average and aggregated vales
Describe the solution you'd like
Profiling tab should provide data according to data type such as data such as Sum, Average etc not valid for strings (varchar) while few others few others such as lower or upper case not valid for numeric values.
Describe alternatives you've considered
Written python script to generate report based on data type
Additional context
Attached screen-capture for varchar columns
Add any

other context or screenshots about the feature request here.

same as https://github.com/open-metadata/OpenMetadata/issues/11951

duplicate of #11951


Bug for sign in on mobile rendering

if you  set the mobile view , the sign up button overlay the sign in button, it looks like this

if U are agree I would like to work with this

Thanks for reporting. Please do work on it :)

do U have any discord chanel for support ?

That is actually not a bad idea. Create one now https://discord.gg/zgK3tHjz

Maybe related: on mobile the footer is cut off after "Terms & Conditions".

Fixed