Added #truncateNearestWord

There are many occasions that a user may want to truncate a string to a specified length but end at the nearest complete word.
This PR adds truncateNearestWord to do just that.

[x] Implement truncateNearestWord
[x] Add Jasmine tests
[x] Update readme

I also added a test for truncateWords since I couldn't find one.
Any feedback as well as renaming suggestions are always welcome!
@b-ash @akbarry

I think this should just be an option passed to truncateWords. In fact, it'd be sweet if all of these truncation methods were just rolled into truncate and passed as options.

:+1: to adding an option to truncateWords instead. But I'd save refactoring all the truncate methods for another PR (plus that kinda requires a major version bump... at least if we delete the existing truncate* methods).


DBContext Constructor should take IDbContextOptions instead of DbContextOptions

Describe what is not working as expected.
I want to be able to do more mocking but the base class from DbContext is forcing me to use an DbContextOptions instead IDbContextOptions which DbContextOptions is already inheriting.
Forces me to do:
AccountContext(DbContextOptions options) : base(options) { }

But I want to do:
AccountContext(IDbContextOptions options) : base(options) { }

Further technical details
EF Core version: (Microsoft.EntityFrameworkCore" Version="2.0.0"
Database Provider: (Microsoft.EntityFrameworkCore.SqlServer" Version="2.0.0")
Operating system: Windows 10
IDE: Visual Studio 2017 15.3.3

@CubicleJockey While the names are somewhat misleading, IDbContextOptions is not really the contract interface for DbContextOptions. It's only the interface for consuming the options from inside EF Core.
What are your goals for mocking DbContextOptions? Typically, we recommend against creating test doubles for DbContext because it quickly becomes too complex to manage properly. Instead, we would recommend creating your own repository or similar interface and mocking that.


Countdown 60 seconds

Hello.
Is any possible to countdown 60 seconds, and on each second progres circle per 1/60, and when is 60 then stop animation?
Thanks

The answer is "yes" but you need to figure out how to code a countdown timer in JS ;)
And then:
countdownTimer.on('each-second', secondsLeft => {
});

@jensej - here is a simple JS countdown example that I've made for you.

I had an inspiration - here's the full working demo for you.


Design Login Page

@miracle-E @rhedwan Log In and Registration task is done. https://www.figma.com/file/ZiuCDL7seXKfkdzfCHXtkG/Auth_Wiki?node-id=3%3A2


Problem and Solution Facts Don't display correctly on frontend

As a an admin or a Brazilian admin, you can't change the problem or solution fact for the Spanish or Portugese translations of the campaign.
The backend will shows:

Front end shows:

Occurs even if I use TorGuard to come from Brazil OR try to use a fact that exists in prod fact database.

they save correctly in the backend, but the template is pulling the english version, not the translated content


uxn: 1.0-unstable-2024-07-26 -> 1.0-unstable-2024-08-05

Automatic update generated by nixpkgs-update tools. This update was made based on information from passthru.updateScript.
meta.description for uxn is: Assembler and emulator for the Uxn stack machine
meta.homepage for uxn is: https://wiki.xxiivv.com/site/uxn.html
Updates performed

Ran passthru.UpdateScript

To inspect upstream changes
Impact
Checks done

built on NixOS
The tests defined in passthru.tests, if any, passed
found 1.0-unstable-2024-08-05 in filename of file in /nix/store/s5hscvbpmzrvcjil4r56z4viblib629v-uxn-1.0-unstable-2024-08-05

Rebuild report (if merged into master) (click to expand)

2 total rebuild path(s)

2 package rebuild(s)

First fifty rebuilds by attrpath

uxn

Instructions to test this update (click to expand)

Either download from Cachix:
nix-store -r /nix/store/s5hscvbpmzrvcjil4r56z4viblib629v-uxn-1.0-unstable-2024-08-05 \
  --option binary-caches 'https://cache.nixos.org/ https://nix-community.cachix.org/' \
  --option trusted-public-keys '
  nix-community.cachix.org-1:mB9FSh9qf2dCimDSUo8Zy7bkq5CX+/rkCWyvRCYg3Fs=
  cache.nixos.org-1:6NCHdD59X431o0gWypbMrAURkbJ16ZPMQFGspcDShjY=
  '

(The Cachix cache is only trusted for this store-path realization.)
For the Cachix download to work, your user must be in the trusted-users list or you can use sudo since root is effectively trusted.
Or, build yourself:
nix-build -A uxn https://github.com/r-ryantm/nixpkgs/archive/05025aef089b2170b9bc47172cec1ae638c343aa.tar.gz

Or:
nix build github:r-ryantm/nixpkgs/05025aef089b2170b9bc47172cec1ae638c343aa#uxn

After you've downloaded or built it, look at the files and if there are any, run the binaries:
ls -la /nix/store/s5hscvbpmzrvcjil4r56z4viblib629v-uxn-1.0-unstable-2024-08-05
ls -la /nix/store/s5hscvbpmzrvcjil4r56z4viblib629v-uxn-1.0-unstable-2024-08-05/bin

Pre-merge build results
We have automatically built all packages that will get rebuilt due to
this change.
This gives evidence on whether the upgrade will break dependent packages.
Note sometimes packages show up as failed to build independent of the
change, simply because they are already broken on the target branch.
Result of nixpkgs-review run on x86_64-linux 1

2 packages built:

uxn
uxn.projects

Maintainer pings
cc @AndersonTorres for testing.

@NixOS/nixpkgs-merge-bot merge


New package: WiSARD v0.1.0

Registering package: WiSARD
Repository: https://github.com/pedromxavier/WiSARD.jl
Created by: @pedromxavier
Version: v0.1.0
Commit: 8ae820d2cd560b15a366da2fa211a88667331d80
Reviewed by: @pedromxavier
Reference: https://github.com/pedromxavier/WiSARD.jl/commit/8ae820d2cd560b15a366da2fa211a88667331d80#commitcomment-69670805
Description: WiSARD Weightless Neural Network (WNN) Model implemented in Julia Language.

[noblock] May the package be merged now? It's name seems OK in comparison to the conflicting one.

Note that the link to the documentation gives a 404 error: https://pedromxavier.github.com/WiSARD.jl/dev

Thanks @giordano! There is a typo in the url extension... 😅


[Issue]:  Why does the prompt search have duplicate target content?

Do you need to file an issue?

[ ] I have searched the existing issues and this bug is not already filed.
[ ] My model is hosted on OpenAI or Azure. If not, please look at the "model providers" issue and don't file a new one here.
[ ] I believe this is a legitimate bug, not just a question. If this is a question, please use the Discussions area.

Describe the issue
No response
Steps to reproduce
No response
GraphRAG Config Used
# Paste your config here

Logs and screenshots
No response
Additional Information

GraphRAG Version:
Operating System:
Python Version:
Related Issues:

This is an intentional prompt tuning strategy - we have found that LLM performance tends to be better when you repeat content and goals as a "reminder" to reinforce your request. With a large context window, LLMs tend to forget your original request, so we restate it.


Unable to connect to any cluster

After opening Lens I attempt to connect to a cluster and am met with an error

I was able to connect without issue until recently (24 April)
Environment (please complete the following information):

Lens Version: 3.3.1
OS: Windows 10 Pro 64 bit
Installation method (e.g. snap or AppImage in Linux): .exe

Logs:
info: Update for version 3.3.1 is not available (latest version: 3.3.1, downgrade is disallowed).
error: proxy aws exited with code<PHONE_NUMBER>
error: Failed to connect to cluster aws: {"name":"RequestError","message":"Error: ESOCKETTIMEDOUT","cause":{"code":"ESOCKETTIMEDOUT","connect":false},"error":{"code":"ESOCKETTIMEDOUT","connect":false},"options":{"json":true,"timeout":10000,"headers":{"host":"48f07770-379c-4ee7-a8e2-81cc7e81ea29.localhost:49152"},"uri":"http://<IP_ADDRESS>:49152/api-kube/version","simple":true,"resolveWithFullResponse":false,"transform2xxOnly":false}}
(node:20992) UnhandledPromiseRejectionWarning: Error: timeout
    at Timeout.timeoutFunc (C:\Users\Work\AppData\Local\Programs\kontena-lens\resources\app.asar\node_modules\tcp-port-used\index.js:204:25)
    at listOnTimeout (internal/timers.js:531:17)
    at processTimers (internal/timers.js:475:7)
(node:20992) UnhandledPromiseRejectionWarning: Error: timeout
    at Timeout.timeoutFunc (C:\Users\Work\AppData\Local\Programs\kontena-lens\resources\app.asar\node_modules\tcp-port-used\index.js:204:25)
    at listOnTimeout (internal/timers.js:531:17)
    at processTimers (internal/timers.js:475:7)
(node:20992) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). (rejection id: 1)
(node:20992) UnhandledPromiseRejectionWarning: Unhandled promise rejection. This error originated either by throwing inside of an async function without a catch block, or by rejecting a promise which was not handled with .catch(). (rejection id: 1)
(node:20992) [DEP0018] DeprecationWarning: Unhandled promise rejections are deprecated. In the future, promise rejections that are not handled will terminate the Node.js process with a non-zero exit code.
(node:20992) [DEP0018] DeprecationWarning: Unhandled promise rejections are deprecated. In the future, promise rejections that are not handled will terminate the Node.js process with a non-zero exit code.

**Kubeconfig:**
My colleagues are not experiencing the same issue and they have the same config.

**Additional context**
I am able to delete pods and the like via command prompt

@Josh-HouseME is it possible that windows firewall (or similar) blocks the connection?

@jakolehm I have now attempted again with windows virus and threat protection disabled as well as firewall disabled (and no other antiviruses or the like active)
Still experiencing the same issue

@Josh-HouseME does this still happen?

Hi
This does still happen
[cid:bc511fb1-0f2e-4665-831f-808a36f57ac8]
I have been using command line.
Kind Regards,
Josh
[https://support.house.me/support/ImageDisplay?downloadType=uploadedFile&fileName=1540895644403.png&blockId=bc235480bcc800373244af58d0b4d2461faa1b8030da4e5c&zgId=c1e0b4525abb81150b498ee34174141d&mode=view]
HouseME Rentals
W:   www.House.MEhttp://www.house.me/
E:    ask<EMAIL_ADDRESS>Check out our most recent feature on Enterprise Africahttps://enterprise-africa.net/houseme-the-new-way-to-rent-lease-in-sa/

From: Jari Kolehmainen<EMAIL_ADDRESS>Sent: 17 November 2020 14:59
To: lensapp/lens<EMAIL_ADDRESS>Cc: Josh McPetrie<EMAIL_ADDRESS>Mention<EMAIL_ADDRESS>Subject: Re: [lensapp/lens] Unable to connect to any cluster (#323)
@Josh-HouseMEhttps://github.com/Josh-HouseME does this still happen?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHubhttps://github.com/lensapp/lens/issues/323#issuecomment-728910643, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AO24NCZGW4BQ44GVNQ23JGDSQJXR3ANCNFSM4MTQBA2Q.

I M1 have the same prombelm

I use the  latest version


Add policy report integrations to other resource areas

Fix #481 Fix #482 Fix #483
This adds the policy reports column to these resources:

pods
cronjobs
daemonsets
deployments
jobs
statefulsets
ingresses
services

https://github.com/rancher/kubewarden-ui/assets/40806497/226c6d71-3d47-407f-9002-b0bce44a388a
Also fixed an issue on the Dashboard page where the policy server pods and controller version badge not displaying correctly.

Unit tests have been fixed :)


Unable to use newer syntax of typing

Describe the bug
I would like to use generic types such as list[int] instead of from typing import List; List[int].
I do know that the example in the documentation explicitly show that I need to import List from typing, but ever since python 3.9, it is preferred to directly use list as type annotation.
To Reproduce
Create file simple.py
from spock import SpockBuilder, spock

@spock
class BasicConfig:
    most_fancy_parameter: list[int]

def main():
    config = SpockBuilder(BasicConfig, desc="Quick start example").generate()
    print(config)

if __name__ == "__main__":
    main()

Run the script,
python simple.py --BasicConfig.most_fancy_parameter "[128, 128]"

I got:
spock.exceptions._SpockInstantiationError: Spock class `BasicConfig` could not be instantiated -- attrs message: isinstance() argument 2 cannot be a parameterized generic

Environment (please complete the following information):

OS: Mac 10.13
Python version: 3.10
Spock version: 3.0.2

Noted. Will see what it takes to support the basic non typing lib types.
I'm assuming the following basic types:

int
float
str
list
tuple
dict


[libdatachannel][libjuice] Update libdatachannel to 0.14.1 and libjuice to 0.8.4.

Describe the pull request
What does your PR fix?

Nothing, updates libraries.
Which triplets are supported/not supported? Have you updated the CI baseline?

Same triplets as before are supported, I personally tested Windows and Linux triplets.
Does your PR follow the maintainer guide?

Yes.

Yes.
New PR to continue #19268 because I removed my remote branch...

Need to investigate on uwp compilation.
https://github.com/paullouisageneau/libdatachannel/issues/388#issuecomment-890852788

@Nemirtingas ,I tested the feature nettle of libjuice in x86-windows triplet,but it failed,could you take a look:
LINK Pass 1: command "C:\PROGRA~2\MICROS~1\2019\ENTERP~1\VC\Tools\MSVC\1429~1.300\bin\Hostx64\x86\link.exe CMakeFiles\juice.dir\src\addr.c.obj CMakeFiles\juice.dir\src\agent.c.obj CMakeFiles\juice.dir\src\crc32.c.obj CMakeFiles\juice.dir\src\const_time.c.obj CMakeFiles\juice.dir\src\base64.c.obj CMakeFiles\juice.dir\src\hash.c.obj CMakeFiles\juice.dir\src\hmac.c.obj CMakeFiles\juice.dir\src\ice.c.obj CMakeFiles\juice.dir\src\juice.c.obj CMakeFiles\juice.dir\src\log.c.obj CMakeFiles\juice.dir\src\random.c.obj CMakeFiles\juice.dir\src\server.c.obj CMakeFiles\juice.dir\src\stun.c.obj CMakeFiles\juice.dir\src\timestamp.c.obj CMakeFiles\juice.dir\src\turn.c.obj CMakeFiles\juice.dir\src\udp.c.obj /out:juice.dll /implib:juice.lib /pdb:juice.pdb /dll /version:0.8 /machine:X86 /nologo /debug /INCREMENTAL ws2_32.lib bcrypt.lib nettle.lib kernel32.lib user32.lib gdi32.lib winspool.lib shell32.lib ole32.lib oleaut32.lib uuid.lib comdlg32.lib advapi32.lib /MANIFEST /MANIFESTFILE:CMakeFiles\juice.dir/intermediate.manifest CMakeFiles\juice.dir/manifest.res" failed (exit code 1104) with the following output:
LINK : fatal error LNK1104: cannot open file 'nettle.lib'

I fixed it locally, but I have another issue when building libdatachannel, without specifying the library status, cmake should build a static or shared library depending on BUILD_SHARED_LIBS. In tmy case, BUILD_SHARED_LIBS is set to ON but libdatachannel is built statically nonetheless.

Everything should be ok now.

For port libdatachannel and libjuice all features are tested successfully in the following triplet:

x86-windows
x64-windows
x64-windows-static

For port libdatachannel and libjuice all features are tested successfully in the following triplet:
* x86-windows

* x64-windows

* x64-windows-static

I just tested x86-linux, x64-linux, x86-linux-dynamic and x64-linux-dynamic. It compiles just fine.


GraphQL request adding an additional field operationName to curl and generateCode

Expected Behavior
When I generate a request or preview, I expect the GraphQL request to be made exactly how it appears
Actual Behavior
GraphQL request appears to be modified and adds an additional field of operationName
Can be seen from generate preview or code:
e.g.
 curl --request POST \   --url REDACTED \   --header 'Content-Type: application/json' \   --header 'authorization: Bearer REDACTED \   --data '{"query":"query {\n\tgetUserProfile {\n\t\tid\n\t\temail\n\t\tfirstName\n\t\tlastName\n\t\tEULA\n\t\tdisplayName\n\t}\n}\n","operationName":""}' {"errors":[{"message":"Unknown operation named \"\"."}]}
Reproduction Steps

Modify an existing GraphQL query or mutation
Make request or generate code example

Is there an existing issue for this?

[X] I have searched the issue tracker for this problem.

Additional Information
No response
Insomnia Version
2022.7.2
What operating system are you using?
macOS
Operating System Version
13.0.1
Installation method
Download from Insomnia
Last Known Working Insomnia version
No response

Can reproduce this, example generated curl:
curl --request POST \
  --url https://rickandmortyapi.com/graphql \
  --header 'Content-Type: application/json' \
  --data '{"query":"query ($id: ID!) {\n  character(id: $id) {\n    id\n    name\n    status\n    species\n    type\n    gender\n\t}\n}","variables":{"id":1},"operationName":""}'

For the following query:
query ($id: ID!) {
character(id: $id) {
  id
  name
  status
  species
  type
  gender
  }
}

@mchrist13 this should be fixed in the latest 2022.7.5 release
Examples:


It's not clear that caches is a global

Using self.caches throughout to be consistent with addEventListener would be good. Also, maybe explain that self in a service worker is analogous to window in the normal page would be helpful.

Hi!
Thanks for the feedback. I've rewritten the codelab from scratch and believe I have fixed this issue. The code has been updated, and the new guide is now live.
If you find any issues with the new codelab, please let us know!
Thanks!


Improve how we render section index pages.

Instead of using a boring flat list of pages, we now render
modern-looking cards for each subsection.

[APPROVALNOTIFIER] This PR is APPROVED
This pull-request has been approved by: geeknoid
The full list of commands accepted by this bot can be found here.
The pull request process is described here

Needs approval from an approver in each of these files:

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Approvers can indicate their approval by writing /approve in a comment
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Ignore metadata on Markdown import

It’s perfectly legitimate to have metadata (colon-paired values on a line) in Markdown. It would be good, especially for another project of mine, to ignore these.
name:value

Implemented in v1.11.


hosts: Add Host Muting/Unmuting capability

This implements the following:
Muting a host: https://docs.datadoghq.com/api/?lang=console#hosts-mute
Unmuting a host: https://docs.datadoghq.com/api/?lang=console#hosts-unmute
Included with this commit is an integration test for the API.
Signed-off-by: Simarpreet Singh<EMAIL_ADDRESS>

Brilliant, thank you for doing this!


fix(dependencies): Updated sendgrid version to 7.11, added new constr…

…uctor parameters for MailSettings
This pull request is covering latest changes from the https://github.com/sendgrid/sendgrid-php/commit/588c067e074ad37e6ce3c6f6e3b119eeda412e9d

Thanks @antongorodezkiy


fix framing boundaries calculation in case of multiple frames

When more then one framing extras is being used, the boundaries
calcualted incorrectly (old size is not taken into account), which leads
to write attempts beyond vector's buffer, and leads to memory
corruption.

jenkins test this please


Run-time config knobs

Add configuration knobs for .NET Core through runtimeconfig.json or environment variables.
Fixes #15850
Preview links:
Compilation
Debugging and profiling
Globalization
Networking
Threading

@jkotas Could you review please? Some of this you previously reviewed in #12959, but I pulled it out of that PR before it was merged.

LGTM modulo comments.

Thanks for the reviews @jkotas and @Thraka!


Trim cosmic-text's shape run cache

Objective

Fixes https://github.com/bevyengine/bevy/pull/14991. The cosmic-text shape run cache requires manual cleanup for old text that no longer needs to be cached.

Solution

Add a system to trim the cache.
Add an average fps indicator to the text_debug example.

Testing
Tested with cargo run --example text_debug.

No shape run cache: 82fps with ~1fps variance.
Shape run cache no trim: 90-100fps with ~2-4fps variance
Shape run cache trim age = 1: 90-100fps with ~2-8fps variance
Shape run cache trim age = 2: 90-100fps with ~2-4fps variance
Shape run cache trim age = 2000: 80-120fps with ~2-6fps variance

The shape run cache seems to increase average FPS but also increases frame time variance (when there is dynamic text).

Good investigation. Based on those numbers, I think "shape run cache no trim" is my preferred setting here.


Ab/update snapshot class for 5.x

currently page num is omitted from update snapshot class - class to transform old format to new format

Noticed builds are failing - I see Madison resolved it in #140


adds db-cleaner deploy files for db operation needs

PR Template:
Describe your changes

adds extra deployment files that can be leverage for one off aggressive DB operations when needed
initial use case is to drop key tables to allow the migrate command to recreate them with new data types (See https://github.com/project-kessel/inventory-api/pull/220)
These would need to be targeted by saas file before they run so no danger in adding them

Ticket reference (if applicable)
Fixes #
Checklist

[ ] Are the agreed upon acceptance criteria fulfilled?

[ ] Was the 4-eye-principle applied? (async PR review, pairing, ensembling)

[ ] Do your changes have passing automated tests and sufficient observability?

[ ] Are the work steps you introduced repeatable by others, either through automation or documentation?

[ ] If automation is possible but not done due to other constraints, a ticket to the tech debt sprint is added
[ ] An SOP (Standard Operating Procedure) was created

[ ] The Changes were automatically built, tested, and  - if needed, behind a feature flag - deployed to our production environment. (Please check this when the new deployment is done and you could verify it.)

[ ] Are the agreed upon coding/architectural practices applied?

[ ] Are security needs fullfilled? (e.g. no internal URL)

[ ] Is the corresponding Ticket in the right state? (should be on "review" now, put to done when this change made it to production)

[ ] For changes to the public API / code dependencies: Was the whole team (or a sufficient amount of ppl) able to review?

LGTM


Task 1 and 2

Heres my task1 and task2 for firmware 103!

Looks good, just a few comments to be fixed.

Hey Mitchell,
thanks for you reviews, I made the changes but it seems the build is now failing. I think its a lint related issue, is the command to auto-format my code scons lint ?


simulate: fix display of loading message

Model loading was moved to the physics thread sometime back (for good reason). This broke the "loading" message shown in UI because the UI did not a know a model was being loaded until after the fact.
The proposed solution adds optional methods to the Simulate class that set and clear a loading message as part of the UI's model loading state machine.
This works with C++ simulate application and the Python managed viewer. It should not affect the passive viewer.
EDIT: It also moves the loading message for command line based reloads to the left of the screen. Previously it was on the right for command line filenames and the left for UI based reloads (button or drag-n-drop) which is inconsistent.

Can you resync please so the tests pass?
I think you happened to send this right after we broke something but before we fixed it 🙂

For sure, it is done.

@aftersomemath thanks so much ❤

You are welcome!


Incorrect display of data in the cell

ReoGrid 2.0 (from reogrid.net). Windows Forms
Visual Studio 2012. Visual Basic
OS: Windows XP, Windows 7, Windows 10
This error occurs rarely
Type of cells is Text.
The text is written in the cells (letters or comma separated numbers). Everything works well.
At a random time after adding data to the cell (programmatically), for example: "2, 6, 8, 12" or "2; 6; 8; 12", a floating-point number is displayed instead of the entered text (for example: "12290.00"). .
If you save data using the usual Save method, the data is saved correctly ("2, 6, 8, 12" or "2; 6; 8; 12").
If you then restart the project, this error disappears - the data in the cell is displayed correctly.

It looks like the data is parsed as date-time type. A date-time type value saved in memory and might be displayed as a number like 12290.00.
@alexey77777, is there any patterns like 12;34 or 12;34;56 that will also be used to describe a date or time in Russian, Ukraine or even France?

@jingwood,
For Russfa, Ukraine:  DD.MM.(YY)YY HH:MM;SS (04.09.2017 14:49:34 or 04.09.17 14:49)
For France: DD.MM.YYYY HH:MM:SS or DD/MM/YYYY or YYYY-MM-DD  (04.09.2017 14:49:34 or  04.09.2017 14H49, 2017-09-04, 04/09/2017)
:-) ";" not a separator/delimiter.
"," is delimiter in floating-point numbers in CIS.


Consider using fargate over aws batch

cttso-ica-to-pieriandx needs to download a tiny amount of files and really doesn't take any resources.
If we could use AWS fargate over AWS batch, it may save a lot of overhead (and allow us to run pieriandx samlpes in parallel).
This could even mean that the AWS lambda could wait for the fargate jobs to complete before writing their outputs back to the LIMS sheet.

Going one better and moving to step functions in orcabus instead


Make /app image more visible

The image in https://riverside.rocks/app/ looks like it's the actual chat, not just a picture - i say you make it more obvious it's a picture

Good point, thanks!

See commit c1a22d76ae09eac00468377224f5f5b24cbfd2d7. Thanks for the idea!

No problem :P

You can also try a slideshow:
https://www.w3schools.com/howto/tryit.asp?filename=tryhow_js_slideshow


doc: rename createSignVerificationRequest

Changed last function name in uport-js, to match discussion on uport-project/uport-connect#200
createSignVerificationRequest -> createVerificationSignatureRequest
@localredhead -- still having issues building the docs, with the following error on the jsdoc-to-markdown command:
JSDOC_ERROR: The command-line option "template" requires a value.

The jsdoc command succeeds but clobbers the existing docs/ folder again

Going to merge in, to update other libs, lets fix the docs gen in another PR (cc @localredhead @rmw2 )


[1.3] cross-compile for linux kernel 4.9.84 armv7l

Reproduction steps
I follow matter build guide step by step and build success out/host on my linux PC (ubuntu 22.04, x86_x64).
I want to cross-compile matter for my linux device (linux kernel 4.9.84 armv7l), so i config toolchain:
declare -x ARCH="arm"
declare -x CROSS_COMPILE="arm-linux-gnueabihf-"
gn gen out/unified --args='is_debug=true target_os="linux" target_cpu="arm"'
ninja -C out/unified
i get error log:
ninja: Entering directory `out/unified/'
[428/2239] cc obj/BUILD_DIR/gen/include/platform/Linux/dbus/openthread/openthread.introspect.c.o
FAILED: obj/BUILD_DIR/gen/include/platform/Linux/dbus/openthread/openthread.introspect.c.o
arm-linux-gnueabihf-gcc -MMD -MF obj/BUILD_DIR/gen/include/platform/Linux/dbus/openthread/openthread.introspect.c.o.d -O0 -g2 -fno-common -ffunction-sections -fdata-sections -fno-exceptions -fno-unwind-tables -fno-asynchronous-unwind-tables -fPIC -Wall -Werror -Wextra -Wshadow -Wunreachable-code -Wvla -Wformat -Wformat-nonliteral -Wformat-security -Wundef -Wno-deprecated-declarations -Wno-missing-field-initializers -Wno-unknown-warning-option -Wno-unused-parameter -Wno-cast-function-type -Wno-psabi -Wno-maybe-uninitialized -fdiagnostics-color -fno-strict-aliasing -Wno-unreachable-code -I/usr/include/gio-unix-2.0 -I/usr/include/libmount -I/usr/include/blkid -I/usr/include/glib-2.0 -I/usr/lib/x86_64-linux-gnu/glib-2.0/include -std=gnu11  -Igen/include -c gen/include/platform/Linux/dbus/openthread/introspect.c -o obj/BUILD_DIR/gen/include/platform/Linux/dbus/openthread/openthread.introspect.c.o
In file included from /usr/include/glib-2.0/glib/gtypes.h:32,
from /usr/include/glib-2.0/glib/galloca.h:32,
from /usr/include/glib-2.0/glib.h:30,
from /usr/include/glib-2.0/gobject/gbinding.h:28,
from /usr/include/glib-2.0/glib-object.h:22,
from /usr/include/glib-2.0/gio/gioenums.h:28,
from /usr/include/glib-2.0/gio/giotypes.h:28,
from /usr/include/glib-2.0/gio/gio.h:26,
from gen/include/platform/Linux/dbus/openthread/introspect.h:12,
from gen/include/platform/Linux/dbus/openthread/introspect.c:13:
gen/include/platform/Linux/dbus/openthread/introspect.c: In function ‘openthread_io_openthread_border_router_default_init’:
/usr/lib/x86_64-linux-gnu/glib-2.0/include/glibconfig.h:67:33: error: conversion from ‘long long unsigned int’ to ‘guint64’ {aka ‘long unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Werror=overflow]
#define G_GUINT64_CONSTANT(val) (val##UL)
^~~~~~~~~
/usr/include/glib-2.0/glib/gtypes.h:101:21: note: in expansion of macro ‘G_GUINT64_CONSTANT’
#define G_MAXUINT64 G_GUINT64_CONSTANT(0xffffffffffffffff)
^~~~~~~~~~~~~~~~~~
gen/include/platform/Linux/dbus/openthread/introspect.c:1816:67: note: in expansion of macro ‘G_MAXUINT64’
g_param_spec_uint64 ("ext-pan-id", "ExtPanId", "ExtPanId", 0, G_MAXUINT64, 0, G_PARAM_READWRITE | G_PARAM_STATIC_STRINGS));
^~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/glib-2.0/include/glibconfig.h:67:33: error: conversion from ‘long long unsigned int’ to ‘guint64’ {aka ‘long unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Werror=overflow]
#define G_GUINT64_CONSTANT(val) (val##UL)
^~~~~~~~~
/usr/include/glib-2.0/glib/gtypes.h:101:21: note: in expansion of macro ‘G_GUINT64_CONSTANT’
#define G_MAXUINT64 G_GUINT64_CONSTANT(0xffffffffffffffff)
^~~~~~~~~~~~~~~~~~
gen/include/platform/Linux/dbus/openthread/introspect.c:1879:87: note: in expansion of macro ‘G_MAXUINT64’
g_param_spec_uint64 ("extended-address", "ExtendedAddress", "ExtendedAddress", 0, G_MAXUINT64, 0, G_PARAM_READWRITE | G_PARAM_STATIC_STRINGS));
^~~~~~~~~~~
gen/include/platform/Linux/dbus/openthread/introspect.c: At top level:
cc1: error: unrecognized command line option ‘-Wno-unknown-warning-option’ [-Werror]
cc1: all warnings being treated as errors
[441/2239] ACTION //src/controller/data_model:data_model_zapgen_zap_pregen(//build/toolchain/linux:linux_arm_gcc)
ninja: build stopped: subcommand failed.
Bug prevalence
alway
GitHub hash of the SDK that was being used
2b91805ddd2f1c10bf63d1f8d34a409f7517ac29
Platform
other
Platform Version(s)
Linux kernel 4.9.84, armv7l
Type
Test Improvement
Anything else?
No response

I've also got:
/usr/lib/x86_64-linux-gnu/glib-2.0/include/glibconfig.h:67:33: error: conversion from ‘long long unsigned int’ to ‘guint64’ {aka ‘long unsigned int’} changes value from ‘18446744073709551615’ to ‘4294967295’ [-Werror=overflow]
I'm running gn gen out/armhf --args='target_cpu="arm"' followed by ninja -C out/armhf.  I've just run sudo apt-get install gcc-arm-linux-gnueabihf to get past a previous error, but now I get the one above.
Any solution to this...?

Some cross compile support exists for rpi builds.
https://github.com/project-chip/connectedhomeip/blob/master/integrations/docker/images/stage-1/chip-build-crosscompile/README.md#image-description describes how to create a sysroot image for that and maybe you can apply that for your own environment.
Beyond that however, I don't think we can provide SDK developer support for various custom build environments as the combinations are too many.


Color of "regular" text

In my case I have this string that is displayed as a button label.
"Already registered? **Login**"
       let parser = MarkdownParser(font: UIFont.systemFont(ofSize: 17))
        parser.automaticLinkDetectionEnabled = false
        parser.bold.color = UIColor.white
        parser.header.color = UIColor.white

My problem is that "Already registered?" is displayed in blue and "Login" is white as set by bold-attribute. How can the color for regular text be set? Why is it set to blue?

Blue is most likely either your button's tintColor or your button's textLabel textColor.
With that said, might make sense to configure the default color on MarkdownKit.
Keeping this open for now.

Yes - it was the tint-color. I used MardownKit before and there the color can be set in the parser. It would be great if you can adopt it.

👍 this would be a great feature addition

+1 to adding color property for regular text.

Hi, guys,
I vote with all my hands and fingers for this feature. It would be awesome if you could add it.
Thanks in advance and greetings from Berlin

Hi guys, added a PR for this. Just set the color like you would the font, when initializing the parser.


Should we rename "Dolphin*" public API?

DolphinEventBus -> RemotingEventBus
DolphinModel -> Model
DolphinController -> Controller
DolphinAction -> Action

Idea:
DolphinEventBus -> RemotingEventBus
DolphinModel -> RemotingModel
DolphinController -> RemotingController
DolphinAction -> RemotingAction
@blackdrag what do you thing


Properly check exceptions in raylib

Right now, some exceptions are only exposed if we use the value. For example, if you do the following in scripts/shell.py.
>>> ray.put(10 ** 100)
>>> ray.get(ray.put(10 ** 100))
-1L
>>> ref = ray.put(10 ** 100)
---------------------------------------------------------------------------
error                                     Traceback (most recent call last)
error: serialization: long overflow

Also, if you start a regular python shell,
>>> import ray
>>> ray.serialization.serialize(ray.worker.global_worker.handle, 1)
(<capsule object "obj" at 0x106ed9db0>, [])
>>> x = ray.serialization.serialize(ray.worker.global_worker.handle, 1)
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
TypeError: must be a 'worker' capsule

The first example works now and the second is outdated.


fix(helm): update init containers to include extra env vars

SUMMARY

The init containers in the helm chart do not get the same environment variables as the other pods. This causes issues when the init containers attempt to ping the database, and the database variables are overridden in environment variables.
BEFORE/AFTER SCREENSHOTS OR ANIMATED GIF

TESTING INSTRUCTIONS

Add env vars to values.yaml, extraEnvRaw, or extraEnv example:

extraEnvRaw:
  # Load DB password from other secret (e.g. for zalando operator)
  - name: DB_PASS
    valueFrom:
      secretKeyRef:
        name: superset.superset-postgres.credentials.postgresql.acid.zalan.do
        key: password

extraEnv:
  GUNICORN_TIMEOUT: 300

Run helm template superset .

Verify changes, in this case deployment.yaml, shortened for readability.

With no values in envFromRaw or extraEnv:
# Source: superset/templates/deployment.yaml
[...]
      initContainers:
      - command:
        - /bin/sh
        - -c
        - dockerize -wait "tcp://$DB_HOST:$DB_PORT" -timeout 120s
        envFrom:
        - secretRef:
            name: 'superset-test-env'
        image: 'apache/superset:dockerize'
        imagePullPolicy: 'IfNotPresent'
        name: wait-for-postgres
      containers:
[...]

With no values in envFromRaw, but GUNICORN_TIMEOUT set in extraEnv:
# Source: superset/templates/deployment.yaml
[...]
      initContainers:
      - command:
        - /bin/sh
        - -c
        - dockerize -wait "tcp://$DB_HOST:$DB_PORT" -timeout 120s
        envFrom:
        - secretRef:
            name: 'superset-test-env'
        image: 'apache/superset:dockerize'
        imagePullPolicy: 'IfNotPresent'
        name: wait-for-postgres
        env:
          - name: "GUNICORN_TIMEOUT"
            value: "300"
      containers:
[...]

With DB_PASS set in envFromRaw, no values set in extraEnv:
[...]
      initContainers:
      - command:
        - /bin/sh
        - -c
        - dockerize -wait "tcp://$DB_HOST:$DB_PORT" -timeout 120s
        envFrom:
        - secretRef:
            name: 'superset-test-env'
        image: 'apache/superset:dockerize'
        imagePullPolicy: 'IfNotPresent'
        name: wait-for-postgres
        env:
          - name: DB_PASS
            valueFrom:
              secretKeyRef:
                key: password
                name: superset.superset-postgres.credentials.postgresql.acid.zalan.do
      containers:
[...]

With both DB_PASS and GUNICORN_TIMEOUT set:
[...]
      initContainers:
      - command:
        - /bin/sh
        - -c
        - dockerize -wait "tcp://$DB_HOST:$DB_PORT" -timeout 120s
        envFrom:
        - secretRef:
            name: 'superset-test-env'
        image: 'apache/superset:dockerize'
        imagePullPolicy: 'IfNotPresent'
        name: wait-for-postgres
        env:
          - name: "GUNICORN_TIMEOUT"
            value: "300"
          - name: DB_PASS
            valueFrom:
              secretKeyRef:
                key: password
                name: superset.superset-postgres.credentials.postgresql.acid.zalan.do

      containers:
[...]

ADDITIONAL INFORMATION

[x] Has associated issue: Fixes #24805
[ ] Required feature flags:
[ ] Changes UI
[ ] Includes DB Migration (follow approval process in SIP-59)

[ ] Migration is atomic, supports rollback & is backwards-compatible
[ ] Confirm DB migration upgrade and downgrade tested
[ ] Runtime estimates and downtime expectations provided

[ ] Introduces new feature or API
[ ] Removes existing feature or API

This should be good to go now. Let me know if you need any further changes.

Any updates on this one?

I resolved the conflict on the Chart.yaml, however the README will need to be rebuilt as well.

Is there any interest in rekindling this, or shall we close it? I'd love to see the linked issue closed by this PR or the other one.

Actually, I'll just close this in favor of https://github.com/apache/superset/pull/27226 which seems closer to merging. Thanks for the contribution @luthes and feel free to reopen this if you want to get it across the finish line.


Adding auto generate license file from WAR file

@ciaranRoche / @dimitraz if you are happy w/ the location, let's get this merged!

@lgriffin feel free to review too :-)

This looks good and is a great starting point certainly for the work in front of us. I'd suggest merging this as a good system of record. I do have some suggestions to have us more compliant with the wider MW teams which would be a good follow on PR:

Use of the canonical names: https://github.com/bucharest-gold/license-reporter/blob/master/lib/utils/resources/default-canonical-names.json

Use of the official metadata: https://github.com/bucharest-gold/license-reporter/blob/master/lib/utils/resources/default-unified-list.json e.g. official URL for the remote URL and also the approved flag. If something is NOT approved it should be a red flag :)

Add a distribution tag per license. This seems to be what EAP do for their Java based XML file.

<license>
    <name>Eclipse Public License, Version 1.0</name>
    <url>http://repository.jboss.org/licenses/epl-1.0.txt</url>
    <distribution>repo</distribution>
</license>

Everything else structurally looks perfect and this almost matches the official EAP XML structure save for the 3 suggestions above :)

I think there is some MW plugin that might actually address 1) and 2) - I can follow up on that one, but when I started this (September) not much was there, to actually generate the lib.

Add a distribution tag per license.

what's the valid/allowed values?   The generated XML file can be easily tweaked via a little plugin I wrote: https://github.com/aerogear/aerogear-jar-resource-bundle/blob/master/src/main/resources/META-INF/licenses.xml.vm

All of the valid licenses are in the files I linked. All the metadata we default to is there as well. Ping me off this if I'm not answering your question :P

This looks good and is a great starting point certainly for the work in front of us

going to rebase and merge this

@lgriffin @pb82 I've applied a few changes:

we do not include our own JARs (they are composing the server), the licenses.xml just contains non aerogear dependencies
We are not checking them in, since that is out of data, aspa. Instead we copy the SERVER licenses into the distribution folder
adding LICENSE.txt to the distribtion as well


Explain support

Codecov Report

Merging #9 into master will increase coverage by 2.41%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master       #9      +/-   ##
==========================================
+ Coverage   26.07%   28.48%   +2.41%
==========================================
  Files          18       18
  Lines        1162     1197      +35
==========================================
+ Hits          303      341      +38
+ Misses        841      837       -4
- Partials       18       19       +1

Impacted Files
Coverage Δ

find.go
34.65% <100%> (+34.65%)
:arrow_up:

db.go
16.43% <0%> (+1.4%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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Crash while running in de background

Describe the bug
While the app is running in the background, the app sometimes crashes. Current running version: 0.23.3. These crashes are already in the SDK for multiple versions. Version 0.19.8 seems to be the most stable one, but since that version is quite outdated we would like to update the SDK.
Crash happens in the update func of the MXRoomSummaryMO. Log:
2022-05-04 14:50:03.005492+0200 xxx[1478:811419] [error] fault: Fetching generated an error AND a result: Error Domain=NSCocoaErrorDomain Code=256 "The file “RoomSummaryStore.sqlite” couldn’t be opened." UserInfo={NSFilePath=/var/mobile/Containers/Data/Application/C78AC27B-A062-431D-A363-ED70E7C6A577/Library/Caches/MXCoreDataRoomSummaryStore/@app102399:logging-tst.xxx.eu/RoomSummaryStore.sqlite, NSSQLiteErrorDomain=23} 2022-05-04 14:50:03.005650+0200 xxx[1478:813433]  [MXSyncResponseFileStore] saveMetaData: Remove file CoreData: fault: Fetching generated an error AND a result: Error Domain=NSCocoaErrorDomain Code=256 "The file “RoomSummaryStore.sqlite” couldn’t be opened." UserInfo={NSFilePath=/var/mobile/Containers/Data/Application/C78AC27B-A062-431D-A363-ED70E7C6A577/Library/Caches/MXCoreDataRoomSummaryStore/@app102399:logging-tst.xxx.eu/RoomSummaryStore.sqlite, NSSQLiteErrorDomain=23} 2022-05-04 14:50:03.005810+0200 xxx[1478:810171]  [MXRestClient] tokenProviderHandler: 1478-503D9CE5-0449-4F9F-AD32-D10E76EDA7AA success token (null), 0 2022-05-04 14:50:03.006367+0200 xxx[1478:766799]  [MXHTTPClient] #640 - GET _matrix/client/r0/sync 2022-05-04 14:50:03.007345+0200 xxx[1478:811419] [error] CoreData: Fetching generated an error AND a result: Error Domain=NSCocoaErrorDomain Code=256 "The file “RoomSummaryStore.sqlite” couldn’t be opened." UserInfo={NSFilePath=/var/mobile/Containers/Data/Application/C78AC27B-A062-431D-A363-ED70E7C6A577/Library/Caches/MXCoreDataRoomSummaryStore/@app102399:logging-tst.xxx.eu/RoomSummaryStore.sqlite, NSSQLiteErrorDomain=23} 2022-05-04 14:50:03.009165+0200 xxx[1478:811419] 🚨 [MXCoreDataRoomSummaryStore] fetchSummary failed: Error Domain=NSCocoaErrorDomain Code=256 "The file “RoomSummaryStore.sqlite” couldn’t be opened." UserInfo={NSFilePath=/var/mobile/Containers/Data/Application/C78AC27B-A062-431D-A363-ED70E7C6A577/Library/Caches/MXCoreDataRoomSummaryStore/@app102399:logging-tst.xxx.eu/RoomSummaryStore.sqlite, NSSQLiteErrorDomain=23} 2022-05-04 14:50:03.010283+0200 xxx[1478:766799] [logging] API call with unopened database connection pointer 2022-05-04 14:50:03.010329+0200 xxx[1478:766799] [logging] misuse at line 173833 of [d24547a13b] 2022-05-04 14:50:03.010449+0200 xxx[1478:766799] [error] error: SQLCore dispatchRequest: exception handling request: <NSSQLGenerateObjectIDRequestContext: 0x282a9d0a0> , authorization denied with userInfo of {     NSFilePath = "/var/mobile/Containers/Data/Application/C78AC27B-A062-431D-A363-ED70E7C6A577/Library/Caches/MXCoreDataRoomSummaryStore/@app102399:logging-tst.xxx.eu/RoomSummaryStore.sqlite";     NSSQLiteErrorDomain = 23; } CoreData: error: SQLCore dispatchRequest: exception handling request: <NSSQLGenerateObjectIDRequestContext: 0x282a9d0a0> , authorization denied with userInfo of {     NSFilePath = "/var/mobile/Containers/Data/Application/C78AC27B-A062-431D-A363-ED70E7C6A577/Library/Caches/MXCoreDataRoomSummaryStore/@app102399:logging-tst.xxx.eu/RoomSummaryStore.sqlite";     NSSQLiteErrorDomain = 23; } 2022-05-04 14:50:03.010777+0200 xxx[1478:766799] [logging] API call with unopened database connection pointer 2022-05-04 14:50:03.010803+0200 xxx[1478:766799] [logging] misuse at line 173833 of [d24547a13b] 2022-05-04 14:50:03.010883+0200 xxx[1478:766799] [error] error: SQLCore dispatchRequest: exception handling request: <NSSQLGenerateObjectIDRequestContext: 0x282a9d0a0> , authorization denied with userInfo of {     NSFilePath = "/var/mobile/Containers/Data/Application/C78AC27B-A062-431D-A363-ED70E7C6A577/Library/Caches/MXCoreDataRoomSummaryStore/@app102399:logging-tst.xxx.eu/RoomSummaryStore.sqlite";     NSSQLiteErrorDomain = 23; } CoreData: error: SQLCore dispatchRequest: exception handling request: <NSSQLGenerateObjectIDRequestContext: 0x282a9d0a0> , authorization denied with userInfo of {     NSFilePath = "/var/mobile/Containers/Data/Application/C78AC27B-A062-431D-A363-ED70E7C6A577/Library/Caches/MXCoreDataRoomSummaryStore/@app102399:logging-tst.xxx.eu/RoomSummaryStore.sqlite";     NSSQLiteErrorDomain = 23; }
To Reproduce
Steps to reproduce the behavior:

Make sure the app is running in the background

Expected behavior
Not to crash. :)
Screenshots

Device info:

Device: Doesn't matter
OS: Tested on iOS 14 & iOS 15
Version 0.23.3

This happened to me when I updated the SDK to the latest version and ran the app over the previous one.
I simply deleted the app and run it again it didn't happen. But it might happen to the production users if we push an app store update :(

The existing users of your app, has the permission set already to NSFileProtectionComplete in your previous release. So you have to programmatically reset to disable the permission level of the core data files.
This is not the case for Element iOS app as it has the default NSFileProtectionCompleteUntilFirstUserAuthentication and works without any crash.
I guess you can try changing your local MatrixSDK repository.

@toshanmugaraj I don't want to disable to file protection, as it's a security requirement. Any way the MatrixSDK is able to run with the NSFileProtectionComplete entitlement?


Feature/search by instance name

Adds search by instance feature

Hi @PhillipsOwen I have pushed up a change to Augusts branch feature/search-by-instance-name that will rebuild the app whenever gulp sees a change to the apsviz.json file. Gulp will need to run in the docker container as well if it is not already a part of it. Thank you let me know if you have any questions.


Added some test attributes

Unashamedly taken from a previous project

Looks like code I wrote at some stage. :D
I wanted to use @herecydev's nuget package but it's a little behind due to xunit changes and foo. Would still rather wait for the official package than steal it. :D

Cmon @herecydev. WTB: New update

That's no problem :D

Check 2.0.0-rc1 and report any problems. Not promising anything. Need some help with it, not totally convinced it's playing ball.

@herecydev, I'll check it out tomorrow and report back / help fix anything I come across

Replaced by #13


errors with external-secrets operator

Discussed in https://github.com/external-secrets/external-secrets/discussions/1474

Originally posted by marcus1aleksand August 17, 2022
I deployed the secrets-operator helm-chart to a new cluster and I am seeing the following error:
"Failed to get API Group-Resources"
Also I noticed that the webhook opaque secret is empty. Would anybody have an idea on what t could be causing that?

hi @marcus1aleksand ! We would need more information on how you're trying to install it. This message normally relates to CRDs not installed.

Thanks for getting back to me, Gustavo. I checked for that, the CRDs are installed. I noticed that during the init process, there's an API call to the kubernetes service <IP_ADDRESS>/api and that is failing. I wonder if there's something wrong with this new cluster.

The issue may be closed. The problem was created because of missing firewall rules.


Import issues

Hi,
I followed the installation instructions as presented in the readme:

However, I now can't import midi_writer in the same way the readme suggests:

This is the error:

How can I fix it?

Howdy @lara-arikan - it has been a while since I've worked on this package. I should probably publish it to PyPI to make things easier. Are you using a venv of some kind? What version of Python?


LOOP-1489: therapy settings insulin model

This adds Insulin Model settings editing to Therapy Settings.
Note also: consider turning off whitespace changes when reviewing https://github.com/tidepool-org/LoopKit/pull/170/files#diff-8f27638a59e9ef8908cb88e1c92b68c2
LW PR: https://github.com/tidepool-org/LoopWorkspace/pull/182

@novalegra @mpangburn this is now reconciled with dev and ready for review.  Thanks!

@novalegra Yep... when I merged with your code I accidentally took my Codable implementation and not yours, which was different enough to make the tests fail.  I reverted my implementation and restored yours... can you please review that change?  Thanks, and sorry for the mishap!


read.maf , output truncation

Hi, I am trying to read in a maf file with more than 500 samples using read.maf, but my getSampleSummary has only 34 samples . Am I missing any option to read in large maf files?
Command
Please post your commands and the output (errors or any unexpected output)

Session info
Run sessionInfo() and post the output below

Hi,
How did you generate your maf file? Also can you run below commands and check you can actually see all 500+ samples?
maf = data.table::fread(file = "my.maf")
maf[,.N,Tumor_Sample_Barcode]

Hi,
Sorry for the delay in response from my end.
when I read the maf file using
maf_parse = data.table::fread(file = "my.maf")
maf_parse[,.N,Tumor_Sample_Barcode]
I see all the samples listed but when I read the maf using read.maf as below , I am getting the error as below.

maf_parse_read = read.maf(maf = maf_parse)
-Validating
--Removed 5013 duplicated variants
Error: vector memory exhausted (limit reached?)

Hi,
Do you still see the missing samples issue with removeDuplicatedVariants = FALSE in read.maf?

Hi,
The missing sample issue was resolved,
Thanks for yourr suggestion.


How to define and import my own targetClass in ScriptModuleUtils.findAssignableClass?

In the GroovyModuleLoaderExample.java :
Class callable = ScriptModuleUtils.findAssignableClass(scriptModule, Callable.class);
If we define our own targetClass ,for example:
Class transfer = ScriptModuleUtils.findAssignableClass(scriptModule, ITransfer.class);
error happends:
Caused by: java.lang.NoClassDefFoundError: com/demo/ITransfer
I notice that in JBossModuleUtils.java, NICOBAR_CORE_DEPENDENCY_SPEC has been created by adding pathFilter. Of course ,if we add "com/demo" in pathFilter, it work. But, obvious, it shouldn't do so.
Is there any other way to make it work? that is, make JBossModuleClassLoader import my own interface?

got it:
public ScriptModuleLoader.Builder addAppPackages(@Nullable java.util.Set incomingPaths)
Specify a set of packages to make available from the application classloader as runtime dependencies for all scripts loaded by this script module.

Thanks, glad you were able to find the interface for adding your own application packages!


Route is undefined after post(), put(), save()

Hi mgonto, could you tell me what am I doing wrong here?  When calling save() or post() the request is good but responseAlarm.route is undefined, so if I try to update the object later the request url is wrong.  I noticed that responseAlarm.parentResource is populated with the route among other properties.
var Alarms =  Restangular.service('alarms');
var newAlarm = Alarms.one();
newAlarm.name = 'test';
newAlarm.save().then(function(responseAlarm) { // post request is ok
responseAlarm.put();  // leads to PUT alarms/undefined/34  (34 is the last inserted id)
});
Thanks in advance!

Running into this as well. Though on older code it seems to work fine? Odd.

Running into this as well. Though on older code it seems to work fine? Odd.

Actually when user tries to pass undefined value as a operation param this should be treated as a implementation error. Further fixes to be carried on here -> #1010

Using Accounts.one() is a wrong way of creating a new object. One is meant for query building where you plan to get/delete/put some additional details.
From docs:
var baseAccounts = Restangular.all('accounts');

var newAccount = {name: "Gonto's account"};

// POST /accounts
baseAccounts.post(newAccount);

Why should you need to POST to your API to create something new? In my app this is highly inconvenient, I need a simple way to have a local-only instance that can be saved later. Not sure why this was closed as it's completely valid.

I second @OrganicPanda 's lament. It is ugly to have to post explicitly and then save. I was hoping to have save to be universal method. Can we have an @mgonto comment on this?


Winget cli always installing to AMD64 binary in Arm64 Windows

Brief description of your issue
I'm trying to upgrade GoLang.Go package in Arm64 Windows from 1.21.1 to 1.21.3.
But, Winget cli staring download to AMD64 binary. Arm64 definition exists in Winget-pkg repository.
https://github.com/microsoft/winget-pkgs/blob/master/manifests/g/GoLang/Go/1.21.3/GoLang.Go.installer.yaml

Steps to reproduce
winget upgrade upgrade --all
in Arm64 Windows(22H2).
winget cli version is 1.6.2771
Expected behavior
Install Golang.Go Arm64 binary.
Actual behavior
Winget cli trying to install GoLang.Go AMD 64 binary.
Environment
Windows: Windows.Desktop v10.0.22621.2428
システム アーキテクチャ: Arm64
パッケージ: Microsoft.DesktopAppInstaller v1.21.2771.0

Thank you comment.
I tried to upgrade repro 1.21.3, but not repro.... I'll re-open this issue. Please close this issue currently.
golang_upgrade.txt


Messages caught by AutoMod don't show which word was profane

Describe the bug
When AutoMod catches a message in a channel when using WebChat, the message is shown for approval and the questionable phrase is highlighted. This is not the case in Chatterino though. Instead, it just shows the entire message without any phrase highlighting.
To reproduce
Enable AutoMod in your channel, open chat windows in both Chatterino and WebChat and on another account, type a phrase (along with other text for better clarity) that would typically get caught based on your AutoMod rulesets and compare the results.
Screenshots
Chatterino: https://i.imgur.com/TBqNNqV.png
WebChat: https://i.imgur.com/P2H7HGZ.png
Chatterino version
Chatterino 2.1.7 (commit 845c8fa63)
Operating system
Windows 10
Additional information
This would be especially useful when moderating channels with foreign languages when AutoMod still catches messages.

The automod endpoint currently only returns the message in question, it's id and what type triggered the bot. We can't know what caused it.

Could this be revisted after discovering @flags?

Could this be revisted after discovering @flags?

Could you elaborate?

Could this be revisted after discovering @flags?

Could you elaborate?

The undocumented* flags IRC tag includes automod flags/detections in a message.
* I described flags in  chatterino/chatterino2#1772 in more detail.

Could this be revisted after discovering @flags?

Could you elaborate?

The undocumented* flags IRC tag includes automod flags/detections in a message.

I described flags in #1772 in more detail.

since the message was caught by automod, it hasn't been sent over irc yet so there is no flags tag to inspect

The automod endpoint currently only returns the message in question, it's id and what type triggered the bot. We can't know what caused it.

now, on automod_rejected under chat_moderator_actions, one can inspect args to get the problematic phrase & reason
example (phrase is shit, reason is profanity): {"type":"MESSAGE","data":{"topic":"chat_moderator_actions.493418343.53482260","message":"{\"type\":\"moderation_action\",\"data\":{\"type\":\"chat_login_moderation\",\"moderation_action\":\"automod_rejected\",\"args\":[\"ogprodigy\",\"shit\",\"profanity\"],\"created_by\":\"\",\"created_by_user_id\":\"\",\"created_at\":\"\",\"msg_id\":\"44ede2ad-c88e-4038-baee-1ae049437fff\",\"target_user_id\":\"53888434\",\"target_user_login\":\"ogprodigy\",\"from_automod\":false}}"}}
(note: this is only present for moderators & not even the user who sent the offending message)


hideNavBar does not work

Version
Tell us which versions you are using:

react-native-router-flux v3.37.0
react-native v0.39.2

Expected behaviour
For the NavBar to completely disappear from the screen.
Actual behaviour
When using hideNavBar prop, it does not go away and just shows a blank navbar at the top with no functionality.
Steps to reproduce

Create a scene with hideNavBar and component scene

My config:
<Scene key="analytics" component={AnalyticView} direction="vertical" navigationBarStyle={{ backgroundColor: 'transparent' }} hideNavBar={true}/>

can you try :
<Router showNavigationBar={false}>
.........
</Router>

Same issue as reported.
 didn't work either

Same issue as reported.


crash with { clamp: true }

🐛 Bug Report
adding { clamp: true } to spring options caused rangeValue.replace is not a function error
To Reproduce
  const props = useSpring({
    opacity: 1,
    from: { opacity: 0 },
    clamp: true,
    config: { friction: 220 },
    onRest: () => console.log('done fading'),
  })

  return (
    <animated.div style={props}>Fading In</animated.div>
  )

creates this call stack
client.js?path=/__webpack_hmr&reload=true&overlay=false:95 [HMR] connected
web.js:1851 Uncaught TypeError: rangeValue.replace is not a function
    at web.js:1851
    at Array.map (<anonymous>)
    at createStringInterpolator (web.js:1851)
    at web.js:941
    at Array.reduce (<anonymous>)
    at Controller.diff (web.js:922)
    at web.js:822
    at Array.forEach (<anonymous>)
    at Controller.start (web.js:800)
    at web.js:1092
    at Array.map (<anonymous>)
    at web.js:1087
    at mountMemo (react-dom.development.js:15666)
    at Object.useMemo (react-dom.development.js:15888)
    at useMemo (react.development.js:1592)
    at wrappedHook (react-hot-loader.development.js:2728)
    at useSprings (web.js:1079)
    at useSpring (web.js:1136)
    at Testimonials (Testimonials.js:43)
    at renderWithHooks (react-dom.development.js:15105)
    at mountIndeterminateComponent (react-dom.development.js:17339)
    at beginWork$1 (react-dom.development.js:18483)
    at HTMLUnknownElement.callCallback (react-dom.development.js:348)
    at Object.invokeGuardedCallbackDev (react-dom.development.js:398)
    at invokeGuardedCallback (react-dom.development.js:455)
    at beginWork$$1 (react-dom.development.js:23214)
    at performUnitOfWork (react-dom.development.js:22205)
    at workLoopSync (react-dom.development.js:22182)
    at renderRoot (react-dom.development.js:21875)
    at runRootCallback (react-dom.development.js:21551)
    at react-dom.development.js:11354
    at unstable_runWithPriority (scheduler.development.js:643)
    at runWithPriority$2 (react-dom.development.js:11306)
    at flushSyncCallbackQueueImpl (react-dom.development.js:11350)
    at flushSyncCallbackQueue (react-dom.development.js:11339)
    at scheduleUpdateOnFiber (react-dom.development.js:21428)
    at Object.enqueueSetState (react-dom.development.js:13101)
    at JSONStore../node_modules/react/cjs/react.development.js.Component.setState (react.development.js:325)
    at JSONStore._this.handleMittEvent (json-store.js:1)
    at mitt.es.js:58
    at Array.map (<anonymous>)
    at Object.emit (mitt.es.js:58)
    at r.<anonymous> (socketIo.js:20)
    at r.emit (index.js:83)
    at r.onevent (index.js:83)
    at r.onpacket (index.js:83)
    at r.<anonymous> (index.js:83)
    at r.emit (index.js:83)
    at r.ondecoded (index.js:83)
    at a.<anonymous> (index.js:83)
(anonymous) @ web.js:1851
createStringInterpolator @ web.js:1851
(anonymous) @ web.js:941
diff @ web.js:922
(anonymous) @ web.js:822
start @ web.js:800
(anonymous) @ web.js:1092
(anonymous) @ web.js:1087
mountMemo @ react-dom.development.js:15666
useMemo @ react-dom.development.js:15888
useMemo @ react.development.js:1592
wrappedHook @ react-hot-loader.development.js:2728
useSprings @ web.js:1079
useSpring @ web.js:1136
Testimonials @ Testimonials.js:43
renderWithHooks @ react-dom.development.js:15105
mountIndeterminateComponent @ react-dom.development.js:17339
beginWork$1 @ react-dom.development.js:18483
callCallback @ react-dom.development.js:348
invokeGuardedCallbackDev @ react-dom.development.js:398
invokeGuardedCallback @ react-dom.development.js:455
beginWork$$1 @ react-dom.development.js:23214
performUnitOfWork @ react-dom.development.js:22205
workLoopSync @ react-dom.development.js:22182
renderRoot @ react-dom.development.js:21875
runRootCallback @ react-dom.development.js:21551
(anonymous) @ react-dom.development.js:11354
unstable_runWithPriority @ scheduler.development.js:643
runWithPriority$2 @ react-dom.development.js:11306
flushSyncCallbackQueueImpl @ react-dom.development.js:11350
flushSyncCallbackQueue @ react-dom.development.js:11339
scheduleUpdateOnFiber @ react-dom.development.js:21428
enqueueSetState @ react-dom.development.js:13101
./node_modules/react/cjs/react.development.js.Component.setState @ react.development.js:325
JSONStore._this.handleMittEvent @ json-store.js:1
(anonymous) @ mitt.es.js:58
emit @ mitt.es.js:58
(anonymous) @ socketIo.js:20
r.emit @ index.js:83
r.onevent @ index.js:83
r.onpacket @ index.js:83
(anonymous) @ index.js:83
r.emit @ index.js:83
r.ondecoded @ index.js:83
(anonymous) @ index.js:83
r.emit @ index.js:83
a.add @ index.js:83
r.ondata @ index.js:83
(anonymous) @ index.js:83
r.emit @ index.js:83
r.onPacket @ index.js:83
(anonymous) @ index.js:83
r.emit @ index.js:83
r.onPacket @ index.js:83
r.onData @ index.js:83
ws.onmessage @ index.js:83
Show 26 more frames

If I comment out the clamp option, the animations works.
Expected behavior
Should not crash
Environment

react-spring v8.0.27
react v16.9.0

Can you make a small repro of this? 👍

OK, let me try v9, if it still happens I'll do a repro

Hi Alec,
Just wanted to let you know that the problem was that I was using clamp outside of the config object, when i put it inside the config object all worked fine.
Also, when I moved to v9, the crash went away, even if clamp was outside of the config object
Cheers!
Steve


Add new package for maps api

The maps-api package we originally designed outside, included as a new package.

@rjimenezda It looks like now, without 'declare module' it builds AND also runs all tests correctly.
The only missing piece I found is being able to reference one external type (eg. a Class) as a Type for a variable. See https://github.com/CartoDB/toolkit/issues/3


Release version metric

PR Description
Exposing web3singer_version metric so it can be displayed on a grafana dashboard.
Fixed Issue(s)

Fixes #480
Documentation

[ ] I thought about documentation and added the doc-change-required label to this PR if updates are required.

Changelog

[ ] I thought about adding a changelog entry, and added one if I deemed necessary.

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


update COMPAS_AGS

update COMPAS_AGS.ags2
add comments to examples

Nice update @duchaoyu! It takes out the weird dependences on "from compas_bi_ags" and it is well documented, look forward to test the examples.

@duchaoyu @ricardoavelino Since this pull request is now obsolete and will be updated, I will close it.


Append querystring to package binary download to bust CDN cache

Partial fix for https://github.com/NuGet/NuGetGallery/issues/3168
Forwards query string parameters to the package binary CDN download so
we fetch a fresh cache version from the CDN.
@scottbommarito @skofman1 @ryuyu

LGTM

Looks good.


Change acquireTokenSilent to ssoSilent

Purpose

I tested the method acquireTokenSilent of msal and if I change the informations with B2C edit profile inside this project I don't have the  new value on claims of token. If I use ssoSilent method of msal object this work fine.
Does this introduce a breaking change?

[ ] Yes
[x] No

Pull Request Type
What kind of change does this Pull Request introduce?

[x] Bugfix
[ ] Feature
[ ] Code style update (formatting, local variables)
[ ] Refactoring (no functional changes, no api changes)
[ ] Documentation content changes
[ ] Other... Please describe:

How to Test

Get the code

git clone [repo-address]
cd [repo-name]
git checkout [branch-name]
npm install

Test the code

Create a B2C Edit flow and add a button that call instance.loginPopup( uri_editprofile)
What to Check
Verify that the following are valid
Verify that the claims of access token as the same with the claim modified in B2C EditProfile mask
Other Information

@dandresini thank you very much for the PR! And you are right, ssoSilent is the better choice when implementing profile edit user flow. Unfortunately, we won't be able to accept this as this sample is meant to work with Azure AD only. For a B2C sample with msal-react, please see.


Devel

Description
Checklist/ToDo's

[ x] Added documentation?
[x ] Added release note entry? (  docs/release-notes.md )
[x ] Tested?

With commit 9df66400abbbb715aa998b3866e713cf876093e5 in devel tree I fixed the DigitalOcean DNS provider. I switch to  community.digitalocean.digital_ocean_domain_record it's indeed better. Thanks for the hint.


extend: supplying the #43 issue for list processes

extend #104 (by @Horaddrim)

Codecov Report

Merging #105 into master will increase coverage by 0.17%.
The diff coverage is 72.72%.

@@            Coverage Diff             @@
##           master     #105      +/-   ##
==========================================
+ Coverage   61.78%   61.96%   +0.17%
==========================================
  Files           5        5
  Lines         662      673      +11
==========================================
+ Hits          409      417       +8
- Misses        220      222       +2
- Partials       33       34       +1

Impacted Files
Coverage Δ

provision/docker.go
62.67% <72.72%> (+0.84%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update f44bf7e...c9f983d. Read the comment docs.


Improvement: Check if Server URLs are valid on login

If you enter (by accident) a blank in the server URL like "https://foo.bar. com" it will drop a DNS error.
It would be more customer friendly, to check if the url is a valid RFC URL.
Just a #wish .

Yes! On the version 2 we are checking if the server URL is valid.
Thanks for opening this issue.


Add a production deployment checklist

https://github.com/keystonejs/keystone-5/issues/1511

My solution is cleaner, I think, since it allows configuring any Express
setting and avoids having hardcoded options in the Keystone ctor for
specific ones.
On Fri, Oct 11, 2019 at 9:48 AM sarneaud<EMAIL_ADDRESS>wrote:

@sarneaud commented on this pull request.
In docs/guides/production.md
https://github.com/keystonejs/keystone-5/pull/1758#discussion_r333767189
:

+javascript +const app = express(); +app.set('trust proxy', 1); // behind one reverse proxy +app.use(keystoneMiddlewares); +

Thanks, I just pushed an update, but I'll take a look at your PR to see if
it's a better option.
—
You are receiving this because you commented.
Reply to this email directly, view it on GitHub
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or unsubscribe
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.

What do you mean? My PR doesn't wrap the API, it just passes all settings along to each middleware's Express instance.

@sarneaud Approved :) Thanks!


Update get_currencies query params. Fix bug with transparency.

@TaylorFacen 👋
This PR:

Adds missing query params for get_currencies as described in the doco:
Fixes a bug with include_transparency, where even an argument of False is rejected by Nomics for a free plan with the following error:

Your plan does not allow you to access transparency information. See https://p.nomics.com/pricing for more information.

In this case, Nomics expects no argument be provided at all.

ping @TaylorFacen  :)

Thanks @samkillin ! This is now pushed up to pypi and available in nomics-python 3.2.0


Mobile- Footer Image in Confirmation email off center

Expected behavior
When clients place an order, if they look at this via Mobile the footer should be centered
Actual behavior
Love it Guarantee----- It is not centered and is off to the right

Steps to reproduce behavior
Place an Order via buy now or join
Use an email address you can access
View the order confirmation email you receive on mobile, you will see the footer is off center to the right an you have to scroll to see the whole image.

This is ready for QA.

This looks good on iphone and samsung now


[DDMD] Make it possible to automatically convert outbuffer.c/outbuffer.h to D

Work around https://issues.dlang.org/show_bug.cgi?id=11837 which I had previously worked around in the manually-written outbuffer.d
Move constructor and destructor definitions into the header.  D is not capable of generating these (especially the no-args ctor) and they therefore always need to be defined on the C++ side, even if the rest of OutBuffer's functions are implemented in D.
Fix a char* vs ubyte* mistmatch (they are the same in C++ but not in D)
Remove the unused align method

I don't think the freebsd64 failure is related.

@braddr Is the farm-2 freebsd64 box's hdd full?

Looks good.

Auto-merge toggled on

Thanks!


memleaks in X509_REQ_to_X509, and X509_REQ_to_X509 not completely.

When I loop with X509_REQ_to_X509, memory grows infinite,
And I see extension assign not finished.
Any plan on it.
X509 *X509_REQ_to_X509(X509_REQ *r, int days, EVP_PKEY *pkey)
	{
	X509 *ret=NULL;
	X509_CINF *xi=NULL;
	X509_NAME *xn;

	if ((ret=X509_new()) == NULL)
		{
		X509err(X509_F_X509_REQ_TO_X509,ERR_R_MALLOC_FAILURE);
		goto err;
		}

	/* duplicate the request */
	xi=ret->cert_info;

	if (sk_X509_ATTRIBUTE_num(r->req_info->attributes) != 0)
		{
		if ((xi->version=M_ASN1_INTEGER_new()) == NULL) goto err;
		if (!ASN1_INTEGER_set(xi->version,2)) goto err;
/*		xi->extensions=ri->attributes; <- bad, should not ever be done
		ri->attributes=NULL; */
		}

	xn=X509_REQ_get_subject_name(r);
	if (X509_set_subject_name(ret,X509_NAME_dup(xn)) == 0)
		goto err;
	if (X509_set_issuer_name(ret,X509_NAME_dup(xn)) == 0)
		goto err;

	if (X509_gmtime_adj(xi->validity->notBefore,0) == NULL)
		goto err;
	if (X509_gmtime_adj(xi->validity->notAfter,(long)60*60*24*days) == NULL)
		goto err;

	X509_set_pubkey(ret,X509_REQ_get_pubkey(r));

	if (!X509_sign(ret,pkey,EVP_md5()))
		goto err;
	if (0)
		{
err:
		X509_free(ret);
		ret=NULL;
		}
	return(ret);
	}

@zhaozg do you still have a problem with this? - No comments on this since Oct 2014

@richsalz what should be the next steps with this issue? does the proposed code need to be reviewed? What should we do when something like this happens?

It's a bug/PR that nobody has looked at recently.  We got lots of those, sadly.

Hi,
I dig this one a bit.
X509_REQ_to_X50O is leaking by calling X509_NAME_dup,
because X509_set_subject/issuer_name is also doing the same.
Moreover, IMHO, req_main is not using memleaks test harness, that why it is unseen.
I will try to fix it on my repo, before submitting a PR.

This got fixed by #933. Closing.

Backport to 1.0.2 branch is waiting for commit , see PR #999


Push custom video buffer

Hello,
I'm looking for a way to push to the library a custom video buffer, is that possible?
Here is an example :

Use case example :

stream the GoPro video with RTMP
stream DJI video with RTMP
stream local video with RTMP...
stream any external video stream on an RTMP stream

Is there a way to do it?
If yes, with filters?
Thanks :)

Hello you can try like this:
https://github.com/pedroSG94/rtmp-rtsp-stream-client-java/issues/1033
RtspClient and RtmpClient have a the same usage.

No,
Actually it is not supported.

Thanks @pedroSG94 for your reponse !


New taxon constraint: membrane-bound organelles only in eukaryotes

currently no TC:
[Term]
id: GO:0043227
name: membrane-bounded organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators]
subset: gosubset_prok
synonym: "membrane-enclosed organelle" EXACT []
xref: NIF_Subcellular:sao414196390
is_a: GO:0043226 ! organelle

Here is an example of an IBA from PAINT to E coli that I think is wrong:
http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P00722
(While we're at it, is there any reason why we would annotate directly to an abstract grouping like intracellular-membrane bound organelle?)
Evidence breakdown:

with experimental broken down by species:

Hi Chris,
I agree that it makes sense to add the "only in Eukaryota" taxon constraint to the term 'membrane bounded organelle'. As it says in the Wikipedia page for Archaea (https://en.wikipedia.org/wiki/Archaea):

These microbes (archaea; singular archaeon) are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells.

I was most of the way through this, when I noticed that this term is currently part of the prokaryotic subset:

[Term]
id: GO:0043227
name: membrane-bounded organelle
namespace: cellular_component
def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators]
subset: gosubset_prok
synonym: "membrane-enclosed organelle" EXACT []
xref: NIF_Subcellular:sao414196390
is_a: GO:0043226 ! organelle

so I'd like to include @jimhu-tamu in this discussion since it seems inconsistent to have a taxon constraint that excludes prokaryotes on a term that is in the prokaryotic subset. Jim, any objections to removing this term from the 'membrane bounded organelle' form the prokaryotic subset? It seems like a mistake.

@cmungall - I was also wondering why the annotation to the 'membrane bounded organelle' even shows up in AmiGO. When I look at the current GAF for this family, either in PAINT or directly at the GAF in the SVN repository, I don't see this term at all. Here is what is propagated to the top of the clade that includes beta-galactosidase:

and grepping the GAF directly doesn't find the GO ID for this term (GO:0043227) at all
~/Documents/PAINTcuration/GO-paint/PTHR10066 $ cut -f 5 PTHR10066.gaf | sort -u
!gaf-version: 2.0
GO:0004553
GO:0004565
GO:0004566
GO:0004567
GO:0005764
GO:0005829
GO:0005990
GO:0006027
GO:0006516
GO:0009341
GO:0019391
GO:0046355

Hi @cmungall
I sometimes annotate to 'membrane-enclosed organelle' when there are plants in the clade and annotations to both chloroplast and mitochondrion. I find this informative but I agree it's not the most informative term.

Pascale

@krchristie - it was in ftp://ftp.pantherdb.org/paint/presubmission/gene_association.paint_ecocyc.gaf.gz until recently. It's gone now (and I also note that this has switched from UniProt IDs to EcoGene IDs). Should be fixed in the next amigo load within a week.

Kind of odd that this has recently changed. The curation on this family isn't new.

My mistake. this is actually do to the switch in source from svn to panther

$ curl -L http://www.geneontology.org/gene-associations/gene_association.ecocyc.gz | gzip -dc | grep lacZ | grep  GO:0043231
UniProtKB       P00722  lacZ            GO:0043231      GO_REF:0000033  IBA     PANTHER:PTN000007197    C       beta-galactosidase      lacZ|b0344|ECK0341      protein taxon:83333     20141113        GO_CENTRAL                PR:P00722

So EcoCyc slurped this in from PAINT, don't know when, and we get it from them (PAINTs are not loaded in amigo other than paint_other, we get annotations from MODs etc)

@krchristie
I reannotated the tree (but I forgot to update the date in the Google doc). The delay from curation to integration has been very long, it's hard to know where we are at !

@pgaudet I was looking at the SVN log for dates, so it didn't matter what the date in the Google doc was. Leaving out all the touch up and rollbacks of touchback, that just leaves these two commits below.
------------------------------------------------------------------------
r28032 | pgaudet | 2015-08-19 05:07:38 -0700 (Wed, 19 Aug 2015) | 1 line

new PAINT annotations
------------------------------------------------------------------------

------------------------------------------------------------------------
r21583 | huaiyumi | 2014-11-14 10:57:46 -0800 (Fri, 14 Nov 2014) | 1 line

New annotation PTHR10066
------------------------------------------------------------------------

The GO definition of organelle from GO:0043226

Organized structure of distinctive morphology and function. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton, and prokaryotic structures such as anammoxosomes and pirellulosomes. Excludes the plasma membrane

Based on that, I would consider bacterial thylakoids to be organelles, but interestingly, GO:0009579 ! thylakoid specifically excludes them from being considered organelles. Others include:

Magnetosomes PMID: 26884433
Gas vacuoles/vesicles

Looking for more literature and other examples (posted a question on twitter!), but I would hesitate on adding this constraint. Despite wikipedia, to me the fundamental divide is whether the genome is in a nucleus, which is the linguistic root of the "kary" part of prokaryote and eukaryote.

@krchristie the examples I gave are membrane-bound. The point of going back to the organelle definition is to ask when a membrane-bound compartment with a specialized function is or is not an organelle.
There are a few more here: https://www.ncbi.nlm.nih.gov/pubmed/23615191/

"The traditional view of biology divides living organisms into two major groups, the eukaryotes and the prokaryotes, the former having membrane-bound organelles, the latter lacking them. However, recent research has revealed that this view is blatantly in error"
thats me told!
Discussion here, but it doesn't really add anything to the Saier paper:
https://biology.stackexchange.com/questions/54872/why-is-it-said-that-bacteria-have-no-membrane-bound-organelles-when-they-often
OK, so clearly my original request is too strict (though I'm sure we could contort definitions to make it such that we exclude proks). But it's interesting that the only MBO in proks in GO is one that is in error (albeit an error that was fixed at source yet is sticking around). It shows the gaps we would have to fill to improve GO for microbial biology.
Poor microbes are not served well by any biological terminology:
http://bioportal.bioontology.org/search?utf8=✓&query=ammoxosome&button=
Although we don't have a use case for adding these right now, I'm still keen to add them. If someone can send me the Saier paper I may try and make a start on a PR if I get a chance (I don't seem to have institutional access)

@jimhu-tamu - Thanks for the clarification. You had cited the definition of the organelle term, so I misunderstood what you were checking on.
thylakoids - I see the comment you refer to on the top level term:

A thylakoid is not considered an organelle, but some thylakoids are part of organelles.

However, I also see that we have a term for 'bacterial thylakoid', which is a type of
'intracellular non-membrane-bounded organelle'.

Is this the correct classification of a bacterial thylakoid?
This comment may been to be deleted or revised to be accurate.

gas vesicle - We have a term for this. It is also classified as a 'intracellular non-membrane-bounded organelle', but that seems fine based on the definition.
magnetosome - I don't see a term for this. If needed, you can request it.
@cmungall

Discussion here, but it doesn't really add anything to the Saier paper:
https://biology.stackexchange.com/questions/54872/why-is-it-said-that-bacteria-have-no-membrane-bound-organelles-when-they-often

This discussion doesn't add anything new for me, so I'm pretty sure we're handling eubacterial, archaeal, and eukaryotic flagella appropriately in GO, both with respect to the fact that they have completely different structures from each other, and also with respect to the fact that only the eukaryotic flagella (aka cilia) have a membrane bounded portion, though the organelle itself is not considered to be membrane bound as it is not fully enclosed by membrane. With input from Jim to confirm, I've already removed a term that got inappropriately added to GO referring to the cytosolic compartment of the bacterial flagellum.

OK, so clearly my original request is too strict (though I'm sure we could contort definitions to make it such that we exclude proks). But it's interesting that the only MBO in proks in GO is one that is in error (albeit an error that was fixed at source yet is sticking around). It shows the gaps we would have to fill to improve GO for microbial biology.

By "the only MBO in proks in GO is one that is in error", are you referring to flagella? Paola and I have fixed many errors with the way GO handled these. Please let me know if you see any more.
However, this isn't the only MBO in proks that is handled in GO. We already have these:

acidocalsisome - conserved from bacteria to humans (https://www.ncbi.nlm.nih.gov/pubmed/15738951)
pirellulosome - a bacterial specific MBO (could possibly add a taxon constraint to this term, though it is indicated to be in two phyla, and I haven't looked to see if there is an appropriate grouping term)

It seems that we already have information that contradicts the idea that it is appropriate to add the 'only in Eukaryota" taxon constraint to the term "membrane-bounded organelle" (GO:0043227).
The only two action items I see still active in this ticket are:

[ ] possible corrections related to 'thylakoid'
[ ] possible addition of a taxon constraint to 'pirellulosome'

me:

But it's interesting that the only MBO in proks in GO is one that is in error

sorry, my mistake, we have other prok MBOs already that appear to be fine, sorry for confusion caused.

acidocalsisome - conserved from bacteria to humans (https://www.ncbi.nlm.nih.gov/pubmed/15738951)

interesting. We only have bacterial annotation on this so far: http://amigo.geneontology.org/amigo/term/GO:0020022
the paper talks about similarity to GO:0042827 ! platelet dense granule.
Ruiz, F. A., Lea, C. R., Oldfield, E. & Docampo, R. Human platelet dense granules contain polyphosphate and are similar to acidocalcisomes of bacteria and unicellular eukaryotes. J. Biol. Chem. 279, 44250–44267 (2004).
Shows that human platelet dense granules have morphological and structural similarities to acidocalcisomes, and contain polyphosphate that was released on thrombin stimulation.
I think we should be clear in GO about distinctions between identity, evolutionary relationships and mere structural or functional relationships. Would we use the term "acidocalcisome" for human gene products? It seems not, we'd use the existing dense granule term. It seems some kind of  TC is warranted for acidocalcisome.
Anyway, I think the ticket can be closed. We can open new tickets for new TRs or TCs

From both the acidocalcisome paper I mentioned earlier, and this newer one:
Docampo R, Huang G. Acidocalcisomes of eukaryotes. Curr Opin Cell Biol. 2016
Aug;41:66-72. doi: 10.1016/j.ceb.2016.04.007. Epub 2016 Apr 25. Review. PubMed
PMID: 27125677
it is pretty clear that people do refer to acidocalcisomes of eukaryotes, so I don't think any TC is warranted here. It might even be that 'platelet dense granules' could be considered a specialized type of acidocalcisome, but I don't feel the need to read enough to be sure. I'll just leave it as is.
I will close this ticket and open new ones for the couple bacterial issues I mentioned earlier.


Issue with Direct Connect Component

Direct connect is getiing disabled if we add Gateway LB with centralised or decentralised model.

This is by design - not all service combinations are available for now.


✨ Terminal Cursor Style, Width, Blinking

Currently the integrated terminal in CodeEdit uses the block cursor and users have no ability to change this.
In Terminal settings, users should be able to set the cursor to either Block, Underline, or Vertical Bar and additionally toggle whether or not it blinks like so...
https://user-images.githubusercontent.com/806104/196791402-ea79b149-f079-4f91-aca6-d806c571eeb0.mp4

@austincondiff Can you please add more details :)

@prasoonmhwr ✅ Done. Would you like me to assign this one to you?

@prasoonmhwr ✅ Done. Would you like me to assign this one to you?

Yes please, I would love to work on this :)

@austincondiff may i know which file i can find this code

@prasoonmhwr We are using SwiftTerm. It is implemented in CodeEditModules/TerminalEmulator/src.

@austincondiff if I am making any changes in TerminalPreferences file it throws an error Thread 1: EXC_BAD_ACCESS (code=EXC_I386_GPFLT) , here is the screenshot of my changes

@prasoonmhwr I don't exactly know why an error is thrown here but may I suggest using an enum for cursorStyle? This can be implemented like the public var shell: TerminalShell.

Hey Guys,
I am using this terminal.cursorStyleChanged(source: terminal.getTerminal(), newStyle: SwiftTerm.CursorStyle.blinkUnderline) to update the cursor but this is not working in swiftTerm, any ideas? I even wrote to SwiftTerm Q&A but no reply yet.

@prasoonmhwr I see your issue, https://github.com/migueldeicaza/SwiftTerm/issues/264. Hopefully they get back to you soon. I will look through their code and if anything jumps out at me I will let you know.

@prasoonmhwr I found it posted in their API documentation here.

@austincondiff there is no reply in that issue and I have tried this TerminalOptions as well but no luck, what should we do now.

https://user-images.githubusercontent.com/25121427/223324870-7d7f439f-aac3-4bc2-9e2f-c7e80efc590e.mov


Refactor testing

Coverage increased (+0.7%) to 65.086% when pulling c671370351b64c5ae31d08bc0db69ed72a7a2ad2 on refactorTesting into 2795d5613d4eb3e20213523fd64987977397c164 on master.


[Question] Unit tests and mock UserManager

I'm migrating from oidc-client to oidc-client-ts and having trouble to adjust my unit tests.
Method under test:
public onUserExpired(callback: () => void) {
   this.userManager.events.addAccessTokenExpired(callback);
}

I want to verify that my registered callback is invoked upon access token expiration.
Previous test code:
it('registers callback for event: addAccessTokenExpired', async () => {
      // Arrange
      let addAccessTokenExpired!: () => void;
      mockUserManager.events = {
        addAccessTokenExpired: (callback: any) => (addAccessTokenExpired = callback),
      } as any;
      const authService = new AuthService(mockUserManager);

      // Act
      const mockCallback = jest.fn();
      authService.onUserExpired(mockCallback);
      addAccessTokenExpired();

      expect(mockCallback).toBeCalledTimes(1);
    });

New adjusted test code:
it('registers callback for event: addAccessTokenExpired', async () => {
      // Arrange
      const mockUserManager = new UserManager({
          authority: 'authority',
          redirect_uri: 'http://test.com',
          client_id: 'app',
          monitorSession: true,
          accessTokenExpiringNotificationTimeInSeconds: 60
       }) as Mock<UserManager>;

      let addAccessTokenExpired!: () => void;
      mockUserManager.events.addAccessTokenExpired = (callback: any) => (addAccessTokenExpired = callback) as any;
      const authService = new AuthService(mockUserManager);

      // Act
      const mockCallback = jest.fn();
      authService.onUserExpired(mockCallback);
      addAccessTokenExpired();

      expect(mockCallback).toBeCalledTimes(1);
    });

but mockUserManager.events is undefined.

I guess you need to mock events then too

When I look att the source code for UserManager, it looks like events is initialized, so shouldn't need to mock it?
https://github.com/authts/oidc-client-ts/blob/main/src/UserManager.ts#L91

That code is in the constructor. Is the constructor called when mocked?


Determine what APIs are available for service point validation

Rudimentary analysis with Charles shows that, as long as the UUID is well-formed, the calendar module will perform no further validation.  Although there should be no real use case that would cause this issue to arise, it is still an unhandled input error.  The current module allows creating/editing/retrieving calendars for service points that do not exist.

This will significantly impact the permissions decided on (#5) as certain ones will need to be required for service points (    inventory-storage.service-points.collection.get?)

Yes, there should be validation for service point existence with a fail and no DB alteration if the test fails.


OpenSSL Version Error

I packaged my apk file and uploaded it but the google play store is saying this
"Security alert
Your app is statically linking against a version of OpenSSL that has multiple security vulnerabilities. You should update OpenSSL as soon as possible. Please see the alerts page for more information."

we've also experienced this. it's an issue with the crosswalk webview using outdated openssl version :+1:

@felixhammerl Did you resolve this manually / file an issue with them?
@clelland fyi.

We've updated to Crosswalk 11, which addresses the problem.  This will be included in the next release of cca (coming soon!).
Until that release, see XWALK-3217 for possible workarounds.

Just to clarify, does cca v0.5.1 address this problem or do we need to still use the workaround for this?


Xamarin Studio 5.9.2 support

Can you update the add in to support XS 5.9.2 and nuget 2.8.5?

Version 0.8 of the addin supports Xamarin Studio 5.9.2.
You can download the MonoDevelop.PackageManagement.Extensions_0.8.mpack directly from GitHub.
I have also created a separate addin repository which you can add to the Xamarin Studio's Add-in Manager:
http://lastexitcode.com/monodevelop-addins/5.0/main.mrep

Unfortunately the addin seems to fail to build on the main MonoDevelop addins gallery so I am unable to publish it there currently.

thanks!


Update managed-disks-overview.md fixes #113369

removes one of the double "own"

@KimiaTahvildari Thanks for the typo fix!