Build failure Could not resolve "@shopify/admin-ui-extensions/extension-points"

Creating an extension with shopify app scaffold extension (selecting "Subscription UI" and "React") ends up with build failures:
Error building extension:  Error: Build failed with 6 errors:
../../node_modules/@shopify/admin-ui-extensions-react/build/esm/extension-api/ContainerApi/index.mjs:1:31: error: Could not resolve "@shopify/admin-ui-extensions/extension-api" (mark it as external to exclude it from the bundle)
../../node_modules/@shopify/admin-ui-extensions-react/build/esm/extension-api/DataApi/index.mjs:1:26: error: Could not resolve "@shopify/admin-ui-extensions/extension-api" (mark it as external to exclude it from the bundle)
../../node_modules/@shopify/admin-ui-extensions-react/build/esm/extension-api/SessionTokenApi/index.mjs:1:34: error: Could not resolve "@shopify/admin-ui-extensions/extension-api" (mark it as external to exclude it from the bundle)
../../node_modules/@shopify/admin-ui-extensions-react/build/esm/extension-api/ToastApi/index.mjs:1:27: error: Could not resolve "@shopify/admin-ui-extensions/extension-api" (mark it as external to exclude it from the bundle)
../../node_modules/@shopify/admin-ui-extensions-react/build/esm/index.mjs:1:14: error: Could not resolve "@shopify/admin-ui-extensions/extension-points" (mark it as external to exclude it from the bundle)
...
    at failureErrorWithLog (/Users/foo/www/playground/subscriptions/node_modules/@shopify/shopify-cli-extensions/node_modules/esbuild/lib/main.js:1475:15)
    at /Users/foo/www/playground/subscriptions/node_modules/@shopify/shopify-cli-extensions/node_modules/esbuild/lib/main.js:1133:28
    at runOnEndCallbacks (/Users/foo/www/playground/subscriptions/node_modules/@shopify/shopify-cli-extensions/node_modules/esbuild/lib/main.js:1051:65)
    at buildResponseToResult (/Users/foo/www/playground/subscriptions/node_modules/@shopify/shopify-cli-extensions/node_modules/esbuild/lib/main.js:1131:7)
    at /Users/foo/www/playground/subscriptions/node_modules/@shopify/shopify-cli-extensions/node_modules/esbuild/lib/main.js:1240:14
    at /Users/foo/www/playground/subscriptions/node_modules/@shopify/shopify-cli-extensions/node_modules/esbuild/lib/main.js:611:9
    at handleIncomingPacket (/Users/foo/www/playground/subscriptions/node_modules/@shopify/shopify-cli-extensions/node_modules/esbuild/lib/main.js:708:9)
    at Socket.readFromStdout (/Users/foo/www/playground/subscriptions/node_modules/@shopify/shopify-cli-extensions/node_modules/esbuild/lib/main.js:578:7)
    at Socket.emit (events.js:400:28)
    at addChunk (internal/streams/readable.js:293:12)

Here's the log excerpt of esbuild with logLevel set to debug:
 > debug: Resolving import "@shopify/admin-ui-extensions/extension-points" in directory "/Users/foo/www/playground/subscriptions/node_modules/@shopify/admin-ui-extensions-react/build/esm" of type "import-statement"
   note: Read 4 entries for directory "/Users/foo/www/playground/subscriptions/node_modules/@shopify/admin-ui-extensions-react/build/esm"
   note: No "browser" map found in directory "/Users/foo/www/playground/subscriptions/node_modules/@shopify/admin-ui-extensions-react/build/esm"
   note: Searching for "@shopify/admin-ui-extensions/extension-points" in "node_modules" directories starting from "/Users/foo/www/playground/subscriptions/node_modules/@shopify/admin-ui-extensions-react/build/esm"
   note:   Parsed package name "@shopify/admin-ui-extensions" and package subpath "./extension-points"
   note:   Checking for a package in the directory "/Users/foo/www/playground/subscriptions/node_modules/@shopify/admin-ui-extensions/extension-points"
   note:   Read 9 entries for directory "/Users/foo/www/playground/subscriptions/node_modules/@shopify"
   note:   The file<EMAIL_ADDRESS>exists
   note:   Read 18 entries for directory "/Users/foo/www/playground/subscriptions/node_modules/@shopify/admin-ui-extensions"
   note:   Looking for "./extension-points" in "exports" map in<EMAIL_ADDRESS>   note:     Checking object path map for "./extension-points"
   note:     The key "./*" matched with "extension-points" left over
   note:     Checking path "extension-points" against target "./*"
   note:       Substituted "extension-points" for "*" in "./*" to get "./extension-points"
   note:     The resolved path "/Users/foo/www/playground/subscriptions/node_modules/@shopify/admin-ui-extensions/extension-points" is exact
   note:     Read 18 entries for directory "/Users/foo/www/playground/subscriptions/node_modules/@shopify/admin-ui-extensions"

Versions
Node: 14.18.2
npm: 6.14.15
@shopify/admin-ui-extensions-react: 1.0.2
@shopify/app: 3.13.1
@shopify/cli: 3.13.1
react: ^17.0.2

@paweltatarczuk the repo for this package lives here - can you please open up an issue there?

Thank you!


Safeguard the caching of Babel transpilations by disallowing .babelrc…

… files.
Also update the version of Babel to pick up a JSON-parsing fix. This was an
issue that was discovered in the course of seeing how reading .babelrc files
would interact badly with Atom's Babel cache.
/cc @sebmck

Yeah, this seems like an appropriate patch. Although I'm not sure how widespread the usage of Babel is in the atom community but this would be a breaking change for those relying on .babelrc files. In the next major all the transformers are going to be optional which means that specifying Babel configuration is going to be critical, not sure if there's some way to specify that currently to the Atom compiler.

There's not that much usage of Babel yet, and I doubt many (if any) use .babelrc files. I can grab all packages and check. If there's no usage of it, I'll :ship: this if that's OK with you @bolinfest?

Sounds great -- thanks @thomasjo!

@thomasjo Sounds good to me. I don't really mind what happens, just flagging it just in case it's an issue :blush:

Here's the list of packages that has a .babelrc file in the root of their repo
format
hyperclick
nuclide-arcanist
nuclide-code-format
nuclide-diagnostics-store
nuclide-diagnostics-ui
nuclide-diff-view
nuclide-file-tree
nuclide-file-watcher
nuclide-find-references
nuclide-flow
nuclide-hack
nuclide-hg-repository
nuclide-installer
nuclide-language-hack
nuclide-ocaml
nuclide-quick-open
nuclide-remote-projects
nuclide-type-hint
zephir-ide

@bolinfest I guess we can ignore the nuclide packages from that list?

@thomasjo Yes, all of the nuclide- and hyperclick since that's us, too.

I don't know that much about Babel (yet), so I'm listing the contents of the two remaining .babelrc files;
(1) zephir-ide:
{
  "stage": 0,
  "loose": true,
  "sourceMap": "inline",
  "blacklist": [
    "es6.classes"
  ]
}

(2) format:
{
  "stage": 2,
  "loose": true
}

Would it be problematic for those packages if we ship this PR?

They're very likely using experimental syntax that is enabled via the stage option which would break them.

They're very likely using experimental syntax that is enabled via the stage option which would break them.

We are using stage: 0 by default though. Looks like the only problem for zephir-ide is the blacklisting of es6.classes (unless I'm misunderstanding the implication of stage).

Hold up @sebmck, here are the options that are used in Atom today:
https://github.com/atom/atom/blob/master/src/babel.coffee
So for zephir-ide:

We're already using stage: 0.
I'm not sure about loose: true since the docs say it should take an Array: https://babeljs.io/docs/usage/options/.
We're already using sourceMap: 'inline'.
The different blacklist just means that the generated code will be slightly larger. If ES6 classes are working natively in the version of io.js that is bundled with Atom, then we should include it in the blacklist in https://github.com/atom/atom/blob/master/src/babel.coffee. (I was the one who recently added es6.forOf to that list.)

For  format

stage: 0 means that stage: 2 should be supported
Again, I don't know about loose.

Ah my bad, I talked out of turn. Those other options are fine then.

ES6 classes are working natively in the version of io.js that is bundled with Atom, then we should include it in the blacklis

This will break decorators and class properties which rely on the class desugaring.

@sebmck Ah, good to know about es6.classes. I guess we'll hold off on that then.
@thomasjo It sounds like we're good to go! Without this fix, any file that is bundled in Atom.app with 'use babel' will fail spectacularly and hilariously. (The problem won't manifest in development, however.) This is why we had to introduce https://github.com/facebook/nuclide/commit/6bbe3f440cb0d13dd3815f5c135e8562aab5b6c0 as a stopgap.


Alow Basic Authentication headers

Expected behavior
In order to connect to a Basic Authentication-protected redis server, Jedis would allow to set some specific headers to be added to each request.
Actual behavior
Jedis provides no such option (or I did not find any?).

https://github.com/xetorthio/jedis/blob/master/src/main/java/redis/clients/jedis/JedisPool.java#L91-L94
https://github.com/xetorthio/jedis/blob/1f1e23b26a4aa244ebfdbcbcdf489b630c841884/src/test/java/redis/clients/jedis/tests/utils/JedisURIHelperTest.java#L17-L20

My bad! Thanks!


[Renderer] Fog isn't working

Basically what the title says, here's a video of it on restriction07.
https://github.com/hzqst/MetaHookSv/assets/129798156/ea128aca-9abc-4a45-af7e-08b87cdfeabf
Here's a pic of the same map, but without the renderer active.

My GPU is an RX 570 8gb
And here is what my plugins.lst looks like:
VGUI2Extension.dll
CaptionMod.dll
Renderer.dll
;BulletPhysics.dll
StudioEvents.dll
PrecacheManager.dll
CommunicationDemo.dll
SCModelDownloader.dll
;SteamScreenshots.dll
ThreadGuard.dll
SCCameraFix.dll

Fixed in the latest commit.
https://github.com/hzqst/MetaHookSv/releases/tag/v20240318a


Gateway Disabled: Payfort FORT does not support your store currency at this time.

I have set up the store currency United Arab Emirates dirham (د.إ) please see https://prnt.sc/wbdgui  and for Payfort Sadad – SADAD and Payfort NAPS – NAPS, I am getting this error "Gateway Disabled: Payfort FORT does not support your store currency at this time." Please see https://prnt.sc/wbdnpe
How to resolve this issue

Dear @manojpatial please reach us on<EMAIL_ADDRESS>so we can assist you through the integration.

Hi i also have same issue can u please share the solution

Hello Amazing people, was this resolved ? I'm facing the same problem, since the beginning of the year we are losing sales to that on https://dimitriscoffee.com but I have the currency as (Jordanian Dinar - JOD)
@marabiat can you help buddy ?


Presentation on CNF and Service mesh

Presentation on CNF and Service mesh

We move the document to folder in google drive.


v3 device state

Unit tests for this are currently returning 409 Conflict, so creating as a PR until that is figured out.

=== RUN   TestDeviceList
--- FAIL: TestDeviceList (14.53s)
device_test.go:37: Error updating state: 'Non-2XX response: 409 Conflict'
=== RUN   TestDeviceDelete
--- FAIL: TestDeviceDelete (14.50s)
device_test.go:99: Error updating state: 'Non-2XX response: 409 Conflict'
device_test.go:106: Unexpected error deleting created entry: 'Non-2XX response: 409 Conflict'
FAIL
exit status 1
FAIL	github.com/CyCoreSystems/ari/client/native	29.032s

"409 - Uncontrolled device specified" ref
I would not have figured you had to bind any arbitrary device to ARI in order to get its state, but that appears to be the case.


Python: jinja2 template not working in prompt flow with semantic kernel 1.0.3

Describe the bug
I am using semantic kernel 1.0.3 in Azure machine learning prompt flow and getting below error when using jinja2 template:
Traceback (most recent call last):
File "/usr/local/lib/python3.11/site-packages/semantic_kernel/kernel.py", line 179, in invoke
return await function.invoke(kernel=self, arguments=arguments, metadata=metadata)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/semantic_kernel/functions/kernel_function.py", line 211, in invoke
await stack(function_context)
File "/usr/local/lib/python3.11/site-packages/semantic_kernel/functions/kernel_function_from_prompt.py", line 146, in _invoke_internal
prompt_render_result = await self._render_prompt(context)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/semantic_kernel/functions/kernel_function_from_prompt.py", line 233, in _render_prompt
await stack(prompt_render_context)
File "/usr/local/lib/python3.11/site-packages/semantic_kernel/functions/kernel_function_from_prompt.py", line 245, in inner_render_prompt
context.rendered_prompt = await self.prompt_template.render(context.kernel, context.arguments)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/semantic_kernel/prompt_template/jinja2_prompt_template.py", line 92, in render
{
File "/usr/local/lib/python3.11/site-packages/semantic_kernel/prompt_template/jinja2_prompt_template.py", line 93, in
function.fully_qualified_name.replace("-", ""): create_template_helper_from_function(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.11/site-packages/semantic_kernel/prompt_template/utils/template_function_helpers.py", line 31, in create_template_helper_from_function
nest_asyncio.apply()
File "/usr/local/lib/python3.11/site-packages/nest_asyncio.py", line 19, in apply
_patch_loop(loop)
File "/usr/local/lib/python3.11/site-packages/nest_asyncio.py", line 193, in _patch_loop
raise ValueError('Can't patch loop of type %s' % type(loop))
ValueError: Can't patch loop of type <class 'uvloop.Loop'>
To Reproduce
Steps to reproduce the behavior:

Go to '...'
Click on '....'
Scroll down to '....'
See error

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

OS: [e.g. Windows, Mac]
IDE: Azure machine learning prompt flow
Language: Python
Source: pip 24.0

Additional context
Add any other context about the problem here.

@eavanvalkenburg would you mind taking a look at this?

@rvishwakarma001 please upgrade to 1.0.4 or later, it has upgrade jinja2 templates to use asyncio natively which does not need or use the nest_asyncio and should get you around this error! Please let us know if that helped!

@rvishwakarma001 please upgrade to 1.0.4 or later, it has upgrade jinja2 templates to use asyncio natively which does not need or use the nest_asyncio and should get you around this error! Please let us know if that helped!

@eavanvalkenburg Thanks, it's working now after updated to latest version

@rvishwakarma001 thanks for reporting back! For future reference, at time of writing, handlebars templates use nest_asyncio in order to run the kernel functions in template rendering, which means that the above error throws when using that with other async frameworks like uvloop, anyio or others. Use jinja2 or semantic-kernel templates when you want that.


[BUG][Functional] Abnormal amount of AWS-Authorization-Failure ALARMS

Bug reports which fail to provide the required information will be closed without action.
Required Basic Info

Accelerator Version:  v1.5.0 with CT
Install Type: Clean
Upgrade from version: N/A

Describe the bug
AWS-Authorization-Failure ALARMS are generated because the way the CW ALARMS integrates with SNS is different in the Management account from the other accounts. In the management account the ALARMS action sends a notification to an 'in account' SNS Topic which has a Lambda subscriber. The Lambda relays the notification to the CENTRAL LOG Account. For the other accounts the cw alarms are configured to directly send notifications to the SNS Topics of the CENTRAL LOG Account. Because of this, we can see for each ALARM a warning that states: 'This action sends a message to an SNS topic in a different account. We're unable to verify whether the action is correctly configured.' The side effect is that SecurityHub running in those accounts generates Authorization Failure ALARMS because of this: (For each notification topic) AWSServiceRoleForSecurityHub/securityhub is not authorized to perform: SNS:ListSubscriptionsByTopic on resource: arn:aws:sns:ca-central-1::ASEA-Notification-Ignore because no resource-based policy allows the SNS:ListSubscriptionsByTopic action
Failure Info

What error messages have you identified, if any:  AWSServiceRoleForSecurityHub/securityhub is not authorized to perform: SNS:ListSubscriptionsByTopic on resource: arn:aws:sns:ca-central-1::ASEA-Notification-Ignore because no resource-based policy allows the SNS:ListSubscriptionsByTopic action
What symptoms have you identified, if any: Abnormal amount of AWS-Authorization-Failure ALARMS

Required files

Please provide a copy of your config.json file (sanitize if required)

Steps To Reproduce

Go to '...' Deploy the alarms in ALL accounts instead of just the management account.
Click on '....'
See error

Expected behavior
Modify the resource policies of the notification topics in the LOG account to allow SNS:ListSubscriptionsByTopic or apply the same pattern as in the Management account.
Screenshots
If applicable, add screenshots to help explain your problem.
Additional context
Add any other context about the problem here
config.zip
.

The following resource policy on the topic(s) , adjusted per topic remediate the problem:
{
"Sid": "5-Manual",
"Effect": "Allow",
"Principal": {
"AWS": ""
},
"Action": "sns:ListSubscriptionsByTopic",
"Resource": "arn:aws:sns:ca-central-1:MY-ACCOUNT-ID:ASEA-Notification-High",
"Condition": {
"StringEquals": {
"aws:PrincipalOrgID": "o-MY-ORGANISATION-ID"
},
"StringLike": {
"aws:PrincipalArn": "arn:aws:iam:::role/aws-service-role/securityhub.amazonaws.com/AWSServiceRoleForSecurityHub"
}
}
}

Validated: Add the above resource policy to the existing SNS resource policies on the 4 SNS topics in the log-archive account.  (Obviously updating the resource line and orgid line as required)

@jblaplace ,
Could you clarify the Steps to Reproduce. Looking at your config file, I believe that the steps should say:

modify the config alarms section:
from the default:

"alarms": {
 "default-accounts": ["management"],

to the following:
 "alarms": {
        "default-accounts": [
          "ALL"
        ],

Correct alarms should be set to ALL and not just the management account, so that alarms are deployed in each workload account. Those alarms will try to send SNS using the topics in the log/archive account. That is why security hub will try to access those topics which don't allow sechub from other accounts.
I tried with explicit Principal to the role etc but none of that worked.
I could only get it to work using "*" as the Principal and working with Conditions to narrow down the scope of the caller to being SecHub within the Org.

I've noticed that this issue is present in the CT baseline, but does not exist in the standalone baseline. I'm looking to compare why that is...

yeah, because CT uses account instead of org trails, the CW Alarms also need to be deployed in every account.  SH does nothing in standalone for these rules as its an org trail (and in the org root we added an SNS topic).


[BUG] Directory Entitlement not working without user managment activated

Is there an existing issue for this?

[X] I have searched the existing issues

What version of the Terraform provider are you using?
1.0.0 rc2
What version of the Terraform CLI are you using?
1.7.1
What type of issue are you facing
bug report
Describe the bug
Altough the entitlements are being assigned to the directory, if the user managment is deactivated it still gives an authorization error message.
With the user managment activated it no longer gives the error message.

Expected Behavior
No response
Steps To Reproduce
No response
User's Role Collections
No response
Add screenshots to help explain your problem
No response
Additional context
No response

To be checked if related to #537.

@RCarvalhoSiemens Can you please provide the role collections assigned to the user for:

the setup that works
the setup that raises the error

Hello @lechnerc77, the role collection assigned was the same on both setups, Subaccount Administrator

Fixed with #537 - available with release 1.0.0

Hello @lechnerc77,

@RCarvalhoSiemens: so no global account admin was assigned to the user? In case of user management on directory level. no directory admin role collection was assigned to the user that executed the script?

Global account admin was assigned to the user.

I believe it is not the same problem as in #537 because I  the entitlements are added by terraform although I have the error message mentioned above

@RCarvalhoSiemens : I could not reproduce the issue with what is currently available in  the main branch.
Can you share the Terraform configuration you are using for the overall setup, so that we can give that a shot?

Sure, here you can find attached the file with the provider configuration as well as the directory entitlement part
TF config & directory entitlements.txt

@RCarvalhoSiemens Did another retest with the following configuration using the provider state of main = upcoming release:
resource "btp_directory" "dir_with_features" {
  name        = "my-feat-directory"
  description = "This is a directory with features."
  features    = ["DEFAULT", "ENTITLEMENTS"]
}

resource "btp_directory_entitlement" "alert_notification_service" {
  directory_id = btp_directory.dir_with_features.id
  service_name  = "alert-notification"
  plan_name     = "free"
}

resource "btp_subaccount" "my_project" {
  parent_id = btp_directory.dir_with_features.id
  name      = "Retest entitlement Issue"
  subdomain = "retest-issue-6690"
  region    = var.region
}

The user executing the script is globalaccount and subaccount admin.
No error appears when assigning the entitlement to the directory.


Minor UI improvements

Hi!
Here are a few UI improvements:

Replace some more icons (missed the :book: ones)
Add colored background on code snippets
Wrap text to avoid problems on small devices (long words break the layout)
Display two columns on bottom homepage for medium/large devices

Thanks @willdurand !


Bare Modules Not Being Transformed

I'm not sure if I'm missing something obvious here but I'm migrating a legacy project over to ESM and will eventually be aiming for Typescript.
I'm still using Javascript though and the project builds and runs OK with vite. However using this plugin with Karma the bare module imports for items in node_modules are left intact and aren't transformed.
I've looked at the source and can't see any obvious reason. Logging shows the vite plugin is running.
Should this work? how can I debug this?

Found the issue. The karma config had baseUrl: '' which seemed to be breaking things


Remove 'openimages' endpoint

The 'fulltext' endpoint should be the only entry into this data (and that will become the primary entry point for the ledger with #49.)

Removed and deployed.


Extension install package should handle .Net Framework 4.6 (Preview)

Hi.
While attempting to update from 1.1 to 1.2, the install package complained the required framework was not installed in the system. Since I have had this problem with other packages and I have .Net Framework 4.6 installed on my machine, I decided to take a look.
After extracting the install package to a folder and going through the extension.vsixmanifest I noticed that, to fix this, I only needed to change the dependencies section in the file to
  <Dependencies>
    <Dependency Id="Microsoft.Framework.NDP" DisplayName="Microsoft .NET Framework" Version="[4.5,)" />
    <Dependency Id="Microsoft.VisualStudio.MPF.11.0" DisplayName="Visual Studio MPF 11.0" Version="[11.0]" />
  </Dependencies>

After re-creating the package file, it installed without any further issues.
Please note the Version attributes (for reference, see VSIX Extension Schema 2.0 Reference) and their changed values.
Thanks.

Hi @zmira,
Thanks for pointing out the problem. We will fix for the v1.3 release, which is do to release on Monday.

@zmira, v1.3 has been released. We applied your suggestion. Thank you again.


Launcher Controller Not Working

Hi, Whenever I open a launcher controller i get this

Also A while ago after messing around with a data chip I managed to get it to this screen but I still cant input coords.

It also causes the same problem as i posted in the portable launcher issue

Make sure your using the lastest and click launcher # button to input coords.

There is no option to input the coords

Odd... make sure you using the latest version from here http://www.builtbroken.com/pages/icbm/1.7/downloads.php

Iv been told to make sure about that many many many many! times and I have but this problem still persists I just really want this mod

Whats The Problem?!?

Do i need to download the developer or something?

No from that site you need the ICBM--dev.jar not the -dev-deobf.jar otherwise mc will crash with an exception for sure. Dark will get to adding more content soon. He is busy with other mods and things. I have been busy with voltz and other things as well. The rewrite was because it was over due anyway.
Sent from my iPhone

On Jun 7, 2015, at 9:39 PM, jobensingh<EMAIL_ADDRESS>wrote:
Do i need to download the developer or something?
―
Reply to this email directly or view it on GitHub.

Ok Thanks for the help I hope you guys can fix it soon


optimize: add link of script in document

Ⅰ. Describe what this PR did
Ⅱ. Does this pull request fix one issue?

Ⅲ. Why don't you add test cases (unit test/integration test)?
Ⅳ. Describe how to verify it
Ⅴ. Special notes for reviews

Codecov Report

Merging #2422 into develop will decrease coverage by 0.14%.
The diff coverage is n/a.

@@              Coverage Diff              @@
##             develop    #2422      +/-   ##
=============================================
- Coverage      51.81%   51.67%   -0.15%
  Complexity      2698     2698
=============================================
  Files            517      517
  Lines          16764    16744      -20
  Branches        2028     1989      -39
=============================================
- Hits            8686     8652      -34
+ Misses          7269     7260       -9
- Partials         809      832      +23

Impacted Files
Coverage Δ
Complexity Δ

...obuf/convertor/BranchRegisterRequestConvertor.java
90.47% <0%> (-9.53%)
3% <0%> (ø)

...otobuf/convertor/BranchReportRequestConvertor.java
90.9% <0%> (-9.1%)
3% <0%> (ø)

...obuf/convertor/BranchRollbackRequestConvertor.java
92% <0%> (-8%)
3% <0%> (ø)

...otobuf/convertor/GlobalBeginResponseConvertor.java
92.59% <0%> (-7.41%)
3% <0%> (ø)

...otobuf/convertor/GlobalStatusRequestConvertor.java
93.75% <0%> (-6.25%)
3% <0%> (ø)

...otobuf/convertor/GlobalCommitRequestConvertor.java
93.75% <0%> (-6.25%)
3% <0%> (ø)

...obuf/convertor/GlobalRollbackRequestConvertor.java
93.75% <0%> (-6.25%)
3% <0%> (ø)

...protobuf/convertor/RegisterTMRequestConvertor.java
94.73% <0%> (-5.27%)
3% <0%> (ø)

...protobuf/convertor/RegisterRMRequestConvertor.java
90.47% <0%> (-4.77%)
3% <0%> (ø)

...tobuf/convertor/BranchReportResponseConvertor.java
95.45% <0%> (-4.55%)
3% <0%> (ø)

... and 22 more


Document In Mysql cdc and mongodb

Describe the bug(Please use English)
A clear and concise description of what the bug is.
mysql cdc description:

and code:

mongodb doc:

Closed by #1751.


Proposal to add smart study management system in python

Hi! @strivedi4u
I want to add a Smart Study Management System in python to this repo under hacktoberfest 2024 which will do following tasks.
Smart Study Assistant

Task Management
Notes Management
Flashcards
Text Summarization
Study Material Recommendations
Exit
please assign me this task so that i can create a pull request.

@strivedi4u done! Kindly review my pull request.

@strivedi4u On the official site it is showing that this repository is excluded from Hacktoberfest 2024.
Please look into it.

https://github.com/strivedi4u/hacktoberfest24_projects
please contribute on this repo

@strivedi4u okayy!


FileHandle: create invalid handle properly on Windows

Use the FileHandle(handle:closeOnDealloc:) initializer rather than
passing the fd as -1 which causes a failure in the C runtime due to an
invalid fd being passed to _get_ofshandle.

CC: @jakepetroules @millenomi

@swift-ci please test


replace gravatar with static image

Is there any way to do it?

I'll look into implementing a nice way to configure this. For now you can provide your own layouts/partials/sidebar.html, just copy the theme one with the following change:
- {{ with .Site.Params.gravatarHash }}{{ end }}
+

Thank your very much zyro. One question though, where should I put the image? I mean, in which folder?

It should go in your /static folder.

Thanks. However, the problem is that it works so far only for the first/home page. Once I click somewhere else (e.g. in some blog post) it cannot find the image.
See for yourself what I mean:
http://drpaneas.github.io  (image working)
http://drpaneas.github.io/about/ (image not working)

Make sure the src starts with a /, or better yet with {{ .Site.BaseUrl }}

Now it's working. You rock \m/

Cool, glad it's sorted.


Lossless Cutting (with Speedchange!)

Referencing #399
I believe I have solved it! Speeding up and slowing down of videos is also possible. With help from @Fir121
After testing, I hope you can add this into auto-editor main cli, with --lossless flag and warning.
Code
import numpy as np
import time
import re
import sys
import json
import os
import concurrent.futures as multi

def cleanup_pre():
	for file in os.listdir():
		for unwanted in ["_segment", "_stripped"]:
			if unwanted in file.lower():
				os.remove(file)

def cleanup_post():
	for file in os.listdir():
		for unwanted in ["_segment"]:
			if unwanted in file.lower():
				os.remove(file)

def get_fps(input_file):
	info = os.popen(f'ffprobe -i "{input_file}" 2>&1').read()
	match = re.search(r'\s([\d\.]*)\sfps', info)
	if match:
		return float(match.group(1))
	return 0.0

def get_keyframe_interval(input_file):
	"""
	Get average keyframe interval
	"""

	start_time_to_read = 1
	max_seconds_to_read = 5
	info = os.popen(f"""
	ffprobe -read_intervals {start_time_to_read}%+{max_seconds_to_read} -select_streams v -show_entries frame=pts_time -of csv=p=0 -skip_frame nokey -v 0 -hide_banner -i {input_file}
	""").read()

	keyframe_time_points = np.array(info.split("\n"))
	keyframe_time_points = keyframe_time_points[
		(keyframe_time_points != "")
	]
	keyframe_time_points = keyframe_time_points.astype(np.float32)
	keyframe_interval = np.round(np.mean(np.diff(keyframe_time_points))).astype(int)
	return keyframe_interval

def process_json(input_file, fps, json):
	extension = os.path.splitext(input_file)[1]
	cmd = []
	with open('_segments.txt', 'w') as f:
		sounded_chunks = json["v"][0]
		for segment_number, sounded_chunk in enumerate(sounded_chunks):
			segment_file_name = f"_segment{segment_number}{extension}"

			f.write(f'file {segment_file_name}\n')

			offset_time = sounded_chunk["offset"] / fps
			start_time = sounded_chunk["start"] / fps
			speed = sounded_chunk["speed"]
			duration = (sounded_chunk["dur"]/speed) / fps

			cmd.append(f"""
			ffmpeg -hide_banner -loglevel error \
			-itsoffset {-(offset_time)} \
			-t {start_time + duration} \
			{(
				f"-itsscale {1/speed}"
				if speed==1
				else ""
			)} \
			-i "{input_file}" \
			-ss 0 \
			{(
				"-c:a copy"
				if speed==1
				else f"-af volume=0 -af atempo={speed}"
			)} \
			-c:v copy \
			{segment_file_name} \
			""")
			# didn't use -shortest \

		with multi.ProcessPoolExecutor() as executor:
			executor.map(os.system, cmd)

def combine_segments(input_file):
	os.system(f"""
	ffmpeg -y -hide_banner -loglevel error \
	-f concat -safe 0 \
	-i _segments.txt \
	-c copy \
	"{os.path.splitext(input_file)[0]}_STRIPPED{os.path.splitext(input_file)[1]}"
	""")

def process_file(input_file):
	fps_val = get_fps(input_file)
	keyframe_interval = get_keyframe_interval(input_file)
	print(keyframe_interval)

	if fps_val <= 0.0:
		print(f'Unable to determine FPS of {input_file}')
		return

	os.system(f'auto-editor "{input_file}" --edit "audio:threshold=30%,mincut={max([1, 1 + keyframe_interval])}s" --margin "{max([1, 1 + keyframe_interval])}s" --export json')
	json_file = os.path.splitext(input_file)[0] + '_ALTERED.json'
	with open(json_file) as f:
		json_data = json.load(f)
	process_json(input_file, fps_val, json_data)
	os.remove(json_file)
	combine_segments(input_file)

def iterate_files():
	for input_file in sys.argv[1:]:
		process_file(input_file)

def main():
	cleanup_pre()

	start_time = time.time()
	iterate_files()
	print("--- %s seconds ---" % (time.time() - start_time))

	cleanup_post()

if __name__ == "__main__":
	main()

Execution
python main.py input.mp4

Any comments/suggestions?
If not, I'll close this issue to keep your repo clean.

I'm intrigued by the feature and I'm interested in turning this into a PR request.

Great!

I've used ffprobe to automatically get the keyframe interval. I've set the margin using this as a fail-safe for inaccurate keyframe trimming.

I'm not able to get the exact cuts like what I achieve with 'detect silent parts' with LosslessCut and cutting out those parts.
https://github.com/mifi/lossless-cut/issues/1334

I'll still accept a PR but I don't care enough about this feature to implement this myself.


Rendering table for selected/all data structures

I am defining all possible errors of my API in the Data structures section as follows (corresponding to Json-api):
# Data Structures

## ERR_USER_NOT_ALLOWED (object)
- id: 2
- links
    - about: http://docs.offisy.apiary.io/#reference/errors/ERR_USER_NOT_ALLOWED
- status: 403
- code: ERR_USER_NOT_ALLOWED
- title: User not allowed
- detail: You are not allowed to do this action.

## ERR_USER_NOT_FOUND (object)
- id: 3
- links
    - about: http://docs.offisy.apiary.io/#reference/errors/ERR_USER_NOT_FOUND
- status: 404
- code: ERR_USER_NOT_FOUND
- title: User not found
- detail: A user with the given user_id was not found

## ERR_COMPANY_NOT_FOUND (object)
- id: 4
- links
    - about: http://docs.offisy.apiary.io/#reference/errors/ERR_COMPANY_NOT_FOUND
- status: 404
- code: ERR_COMPANY_NOT_FOUND
- title: Company not found
- detail: A company with the given company_id was not found

## ERR_USER_ALREADY_EXISTS (object)
- id: 5
- links
    - about: http://docs.offisy.apiary.io/#reference/errors/ERR_USER_ALREADY_EXISTS
- status: 409
- code: ERR_USER_ALREADY_EXISTS
- title: User already exists
- detail: A user with the given email address<EMAIL_ADDRESS>already exists

## ERR_COMPANY_ALREADY_EXISTS (object)
- id: 6
- links
    - about: http://docs.offisy.apiary.io/#reference/errors/ERR_COMPANY_ALREADY_EXISTS
- status: 409
- code: ERR_COMPANY_ALREADY_EXISTS
- title: Company already exists
- detail: A company with the given name and address already exists

There are also other data structures defined besides the errors. As I would like to reference them via links->about, I am looking for a way to partially render those data structures in a table in a "errors" group inside the documentation, or to at least render all data structures somewhere in the documentation.
How can this be achieved currently?

I use a manual table as a workaround for now, like that:

| Id | Error-Code | Status                     | Title                  | Detail                                                   |
|----|------------|----------------------------|------------------------|----------------------------------------------------------|
| 2  | 403        | ERR_USER_NOT_ALLOWED       | User not allowed       | You are not allowed to do this action.                   |
| 3  | 404        | ERR_USER_NOT_FOUND         | User not found         | A user with the given user_id was not found              |
| 4  | 404        | ERR_COMPANY_NOT_FOUND      | Company not found      | A company with the given company_id was not found        |
| 5  | 409        | ERR_USER_ALREADY_EXISTS    | User already exists    | A user with the given email address already exists       |
| 6  | 409        | ERR_COMPANY_ALREADY_EXISTS | Company already exists | A company with the given name and address already exists |

but this is not very DRY.

Hey @Perni1984 the Data Structures rendering is planned and on its way.

Also I have started playing with JSON API error here https://github.com/apiaryio/datapool/blob/zdne/datapool-origin/jsonapi-error.apib

@zdne: nice.

I am closing this issue and waiting for rendering of data structures to be implemented in Apiary.


Added resume to the navbar

Sir kindly review and if something is wrong please suggest changes.

Fix the bug in the mobile view please

sir I was not able to push the changes as it was showing some error so I searched and then used -f with the push command so it is showing forced push. So is there any error regarding this?

sir I was not able to push the changes as it was showing some error so I searched and then used -f with the push command so it is showing forced push. So is there any error regarding this?

Now it's fine, actually, when you gave the PR, I made some changes to your commit to make the code more readable, so at times Git shows such errors.


Will the updates clears the custom internal cache for "premium" tier API magement service.

Will the updates clears the custom internal cache for "premium" tier API magement service.

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

ID: e16fb185-c6ea-affe-5fbf-f385af4ec293
Version Independent ID: 824c6f91-8f82-8f15-7034-a427b28e11f0
Content: Upcoming Breaking Changes in Azure API Management
Content Source: articles/api-management/breaking-changes/overview.md
Service: api-management
GitHub Login: @adrianhall
Microsoft Alias: adhal

@AnandKatta
Thanks for your feedback! We will investigate and update as appropriate.

@AnandKatta Yes, internal cache is available in all tiers (except Consumption tier) and the behavior is same including premium tier. Note: the cache is shared across all the units, and restarting a specific unit only affects keys stored in that unit.
Due to volatile nature, we recommend using external cache in API Management. I hope this helps and let us know if any questions.


[feature] add multi-select capability

I primarily listen to music thorough my playlists, and it's a real pain to have to add tracks one at a time. Perhaps something like long-press on a track to initiate a multi-select would be feasible?
Alternatively, if this already exists, I couldn't seem to get it to trigger.

Hi @taiyoko,
Thanks for your feedback.
Odeon used to allow multi-selection from the list of all tracks, but this has been changed to single popup menu due to not playing very well with tabs.
Creating playlists this way is terrible since, I can't deny it. In fact, playlist management in the app is kinda... basic, to say the least.
Here is my suggestion: I could implement a new screen accessible from the "Playlists" tab, allowing you to create/edit a playlist.
This new screen would allow you to:

rename the playlist
reorder tracks in the playlist
remove tracks from the playlist
search tracks by name and add them to the playlist
save all changes to the playlist at once.

IMHO searching and selecting is more user-friendly compared to multi-selection in a list of 200+ tracks.
Tell me what do you think about it.

Hi @taiyoko,
Thanks for your feedback.
Odeon used to allow multi-selection from the list of all tracks, but this has been changed to single popup menu due to not playing very well with tabs.
Creating playlists this way is terrible since, I can't deny it. In fact, playlist management in the app is kinda... basic, to say the least.
Here is my suggestion: I could implement a new screen accessible from the "Playlists" tab, allowing you to create/edit a playlist.
This new screen would allow you to:

rename the playlist
reorder tracks in the playlist
remove tracks from the playlist
search tracks by name and add them to the playlist
save all changes to the playlist at once.

IMHO searching and selecting is more user-friendly compared to multi-selection in a list of 200+ tracks.
Tell me what do you think about it.


undefined method `inline_edit' for #RailsAdmin::Config::Fields::Types::HasManyAssociation:0x00000006766a50

I have found interesting error:
My code in rails_admin.rb file is this:
  config.model Category do
    edit do
      field :speeches do
        inline_add false
        inline_edit false
      end
    end
  end

When I open my rails_admin panel it shows me this:
 NoMethodError in RailsAdmin::MainController#dashboard
 undefined method `inline_edit' for #<RailsAdmin::Config::Fields::Types::HasManyAssociation:0x00000006766a50> Did you mean? inline_add

However, if I remove inline_edit it works.
Inline edit exists in has_many association, it could be called when user double-clicks to models name and editing modal appears.

@SuperMasterBlasterLaser the has_many association in rails_admin simply does not feature a inline_edit option. its currently limited to has_one and belongs_to.
so this is not a bug. ;)

see https://github.com/sferik/rails_admin/blob/master/lib/rails_admin/config/fields/types/has_many_association.rb#L20

@thedanielhanke But when I double click on name of my model, edit modal appears.

@SuperMasterBlasterLaser ah cool. even nested_form false does not help in this case. that might indeed be a bug. :+1:
maybe you might want to rephrase this issues title to point on beein unable to disable this.

@thedanielhanke Updated my question as you asked.

👍

I have the same problem.
Doble click show modal form to edit.
I mark nested_form false but nothing change.

Dup of #1911.


Fix example in README

As reported in #214 the example in README is wrong. This pull request fixes just that issue.

Can this be merged now? I am not really sure what the state is after approving it but before merging.


Add feature-freeze configuration option

Closes https://github.com/channable/hoff/issues/243
This adds a configuration option, called featureFreezePeriod.
In the configured feature freeze period:

Normal merge commands are blocked;
Instead, merge hotfix commands are allowed;
merge and (tag | deploy) becomes merge hotfix and (tag | deploy)
Using merge hotfix outside of the configured feature freeze period is not allowed.

A few choices I made here:

The default on Friday suffix is not necessary during a feature freeze, to keep it simple;
For the retry command, neither on Friday nor hotfix is necessary to specify;
The feature freeze period is configured globally, not per project.

@OpsBotPrime merge

Failed to rebase, please rebase manually using
git fetch && git rebase --interactive --autosquash origin/master riscky/feature-freeze-feature

@OpsBotPrime retry

Only approved PRs with failed builds can be retried..

@OpsBotPrime merge

Rebased as 74ab82f7b4d03929408f3428e922bd0e66ada414, waiting for CI …


[main] 3D rendering of labels has wrong colors (mostly label 1, brown)

🐛 Bug Report
3D rendering of labels is broken, label colors are not displayed properly:

Git bisect points to ca2d186e1e908a19c5a34c932215ebc86afed88d
0.4.18 and 0.4.19rc3 are both fine.
💡 Steps to Reproduce
Script:
import napari
from skimage import data
from scipy import ndimage as ndi

blobs = data.binary_blobs(length=128, volume_fraction=0.1, n_dim=3)
labeled = ndi.label(blobs)[0]
viewer = napari.Viewer()
viewer.add_labels(labeled, name='blob ID')
viewer.dims.ndisplay = 3

Or use the super new Balls 3D sample!
💡 Expected Behavior
The 3D labels should still use the proper label colors.
🌎 Environment
napari: 0.5.0a2.dev520+gec90e5c3c
Platform: macOS-13.3.1-arm64-arm-64bit
System: MacOS 13.3.1
Python: 3.11.7 | packaged by conda-forge | (main, Dec 15 2023, 08:41:36) [Clang 16.0.6 ]
Qt: 6.6.0
PyQt6:
NumPy: 1.26.3
SciPy: 1.11.4
Dask: 2023.12.1
VisPy: 0.14.1
magicgui: 0.8.1
superqt: 0.6.1
in-n-out: 0.1.9
app-model: 0.2.4
npe2: 0.7.3
OpenGL:

GL version:  2.1 Metal - 83.1
MAX_TEXTURE_SIZE: 16384

Screens:

screen 1: resolution 1680x1050, scale 2.0

Settings path:

/Users/piotrsobolewski/Library/Application Support/napari/napari-dev_a1eb8b76ba95fa16ad06e26097b46b8455dfbf0b/settings.yaml
Plugins:
ERROR:npe2.manifest.schema:napari.manifest -> 'napari_animation' could not be imported: The name field in the manifest ('napari-animation') must match the package name ('napari_animation')
napari: 0.5.0a2.dev495+gd507dd64e (81 contributions)
napari-console: 0.0.9 (0 contributions)
napari-svg: 0.1.10 (2 contributions)

💡 Additional Context
No response

Looks like an issue with interpolation and it does look like interpolation was removed from labels during the refactor, as far as I can tell.

Gah, thanks for the report @psobolewskiPhD! I had noticed but it's one of those things where I was like "hmmm probably something weird with my install env, will investigate later". 😅 Hopefully not too hard to fix. Great to have discovered it before the next rc.


Guys.. all fixed after 2 days and neo4j auth disabled etc and STILL get a py2neo.packages.httpstream.http.ClientError: 401 Unauthorized

about to jump off a cliff
everythings cool.. mongo.. rep set.. neo desktop uip.. browser up.. db started..  auth disabled on neo4j conf ...   but still mongo-connector can't hook to the neo browser and dump my rep set in there
any clues guys ??
leveridge@leveridge-PowerEdge-R710:~$ mongo-connector -m localhost:27017 -t http://localhost:7474/db/data -d neo4j_doc_manager
Logging to /home/leveridge/mongo-connector.log.
.. in the log..
py2neo.packages.httpstream.http.ClientError: 401 Unauthorized
its crazy.. no darn reason.
using py3 and still have py2 also of course as it uses some libs from there..  but installed mongo-connector via pip3 and neo4j-doc-manager via pip3  all coolio
set the neo conf to false on the authentication.. thats cool..  re-started instance.. all cool. and STILL mongo connect cant connect to my neo
welcome ANY clues thanks
mongo 4.4 .. yep Rep set all coolio in the mongo conf.. its happy .    py3 good..  neo is 4.1
.. log file.. from mongo-connect
Traceback (most recent call last):
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 258, in get
response = self.__base.get(headers=headers, redirect_limit=redirect_limit, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/packages/httpstream/http.py", line 966, in get
return self.__get_or_head("GET", if_modified_since, headers, redirect_limit, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/packages/httpstream/http.py", line 943, in __get_or_head
return rq.submit(redirect_limit=redirect_limit, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/packages/httpstream/http.py", line 452, in submit
return Response.wrap(http, uri, self, rs, **response_kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/packages/httpstream/http.py", line 489, in wrap
raise inst
py2neo.packages.httpstream.http.ClientError: 401 Unauthorized
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/util.py", line 33, in wrapped
return f(*args, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/doc_managers/neo4j_doc_manager.py", line 78, in bulk_upsert
tx = self.graph.cypher.begin()
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 661, in cypher
metadata = self.resource.metadata
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 213, in metadata
self.get()
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 261, in get
raise Unauthorized(self.uri.string)
py2neo.error.Unauthorized: http://localhost:7474/db/data/
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/oplog_manager.py", line 668, in do_dump
upsert_all(dm)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/oplog_manager.py", line 651, in upsert_all
dm.bulk_upsert(docs_to_dump(from_coll), mapped_ns, long_ts)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/util.py", line 44, in wrapped
raise new_type(str(exc_value)).with_traceback(exc_tb)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/util.py", line 33, in wrapped
return f(*args, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/doc_managers/neo4j_doc_manager.py", line 78, in bulk_upsert
tx = self.graph.cypher.begin()
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 661, in cypher
metadata = self.resource.metadata
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 213, in metadata
self.get()
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 261, in get
raise Unauthorized(self.uri.string)
mongo_connector.doc_managers.error_handler.Neo4jOperationFailed: http://localhost:7474/db/data/
2020-10-22 11:41:02,865 [ERROR] mongo_connector.oplog_manager:723 - OplogThread: Failed during dump collection cannot recover! Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True, replicaset='replica01'), 'local'), 'oplog.rs')
2020-10-22 11:41:03,855 [ERROR] mongo_connector.connector:411 - MongoConnector: OplogThread <OplogThread(Thread-2, started<PHONE_NUMBER>44352)> unexpectedly stopped! Shutting down

turned off ie true the neo4j conf dbms  and set the ENV variables to  'neo4j' and 'password' set in my database in neo4j desktop (which has same name as replicaset  'replica01'   ..
try mongo-connector again and now i get a py2neo '404'
"2020-10-22 14:55:18,169 [ALWAYS] mongo_connector.connector:50 - Starting mongo-connector version: 3.1.1
2020-10-22 14:55:18,170 [ALWAYS] mongo_connector.connector:50 - Python version: 3.6.9 (default, Oct  8 2020, 12:12:24)
[GCC 8.4.0]
2020-10-22 14:55:18,171 [ALWAYS] mongo_connector.connector:50 - Platform: Linux-4.15.0-122-generic-x86_64-with-Ubuntu-18.04-bionic
2020-10-22 14:55:18,171 [ALWAYS] mongo_connector.connector:50 - pymongo version: 3.11.0
2020-10-22 14:55:18,179 [ALWAYS] mongo_connector.connector:50 - Source MongoDB version: 4.4.1
2020-10-22 14:55:18,180 [ALWAYS] mongo_connector.connector:50 - Target DocManager: mongo_connector.doc_managers.neo4j_doc_manager version: unknown
2020-10-22 14:55:18,223 [CRITICAL] mongo_connector.oplog_manager:714 - Exception during collection dump
Traceback (most recent call last):
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 258, in get
response = self.__base.get(headers=headers, redirect_limit=redirect_limit, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/packages/httpstream/http.py", line 966, in get
return self.__get_or_head("GET", if_modified_since, headers, redirect_limit, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/packages/httpstream/http.py", line 943, in __get_or_head
return rq.submit(redirect_limit=redirect_limit, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/packages/httpstream/http.py", line 452, in submit
return Response.wrap(http, uri, self, rs, **response_kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/packages/httpstream/http.py", line 489, in wrap
raise inst
py2neo.packages.httpstream.http.ClientError: 404 Not Found
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/util.py", line 33, in wrapped
return f(*args, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/doc_managers/neo4j_doc_manager.py", line 78, in bulk_upsert
tx = self.graph.cypher.begin()
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 661, in cypher
metadata = self.resource.metadata
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 213, in metadata
self.get()
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 267, in get
raise_from(self.error_class(message, **content), error)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/util.py", line 235, in raise_from
raise exception
py2neo.error.GraphError: HTTP GET returned response 404
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/oplog_manager.py", line 668, in do_dump
upsert_all(dm)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/oplog_manager.py", line 651, in upsert_all
dm.bulk_upsert(docs_to_dump(from_coll), mapped_ns, long_ts)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/util.py", line 44, in wrapped
raise new_type(str(exc_value)).with_traceback(exc_tb)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/util.py", line 33, in wrapped
return f(*args, **kwargs)
File "/home/leveridge/.local/lib/python3.6/site-packages/mongo_connector/doc_managers/neo4j_doc_manager.py", line 78, in bulk_upsert
tx = self.graph.cypher.begin()
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 661, in cypher
metadata = self.resource.metadata
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 213, in metadata
self.get()
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/core.py", line 267, in get
raise_from(self.error_class(message, **content), error)
File "/home/leveridge/.local/lib/python3.6/site-packages/py2neo/util.py", line 235, in raise_from
raise exception
mongo_connector.doc_managers.error_handler.Neo4jOperationFailed: HTTP GET returned response 404
2020-10-22 14:55:18,225 [ERROR] mongo_connector.oplog_manager:723 - OplogThread: Failed during dump collection cannot recover! Collection(Database(MongoClient(host=['localhost:27017'], document_class=dict, tz_aware=False, connect=True, replicaset='replica01'), 'local'), 'oplog.rs')
2020-10-22 14:55:19,197 [ERROR] mongo_connector.connector:411 - MongoConnector: OplogThread <OplogThread(Thread-2, started<PHONE_NUMBER>24576)> unexpectedly stopped! Shutting down"

would love a review of this .. most puzzling

@johnda98 I just ran through this exact issue! As far as I can tell, it looks like neo4j changed up their data endpoint with version 4.0 on! Downgrading neo4j to 3.5 (3.5.25 is the latest version) works. This looks to be an issue with the neo4j_doc_manager plugin that has sat seemingly unmaintained for the last 5 years or so: https://github.com/neo4j-contrib/neo4j_doc_manager
So yeah, use neo4j 3.5.x or someone needs to fix the doc manager to work with 4.x.


Update readme

What:
I’ve made some minor grammar fixes in the section about the Docker image and added links to what is included in the Docker image.
I’ve also changed the reference to a Slack channel be changed to the Discord server invite link.
Why:
I feel that it’s important that developers and admins have the right links easily accessible from the README.me file, because it enhances usability.
Also, there is a lot of active discussion on Discord server, and I cannot find a Slack invite when I search online.

Hi @zbraiterman, could you add a "what" and "why" to the PR description to provide context on why the change is needed. Thanks!

Hi @zbraiterman, could you add a "what" and "why" to the PR description to provide context on why the change is needed. We try and include it on changes to this repository. Thanks!

Hi @leighmcculloch.  I've just done so.  Thank you for the reminder.

It's my pleasure. :)


Wallaroo Release 0.5.4 Testing

This issue will serve as a checklist for the release testing process for Wallaroo 0.5.4 and for tracking any issues related to that release.
Target Dates
Release Target
We're targeting to release on the 10/31
Phase 1 Target
Phase 1 should be completed by EOD Friday 10/26
Phase 2 Target
Phase 2 is expected to be complete by EOD Tuesday 10/30
Phase 1
Phase 1 consists of a modified set of tests runs of "Installing from Source" for the Python API (Machida 3), "Running an Application" for Python in Docker + Vagrant, and running of example applications for Machida3.
Issues
Any issues that arise during testing should be created using the following format: Release testing: + issue description and should reference this issue and be added to the 0.5.4 Milestone. Issues are NOT to be addressed until Phase 2.
Checklist
Wallaroo Up automated distribution testing
Run the misc/wallaroo-up-tester.bash script that test the RC version of Wallaroo Up and automagically runs the examples using the misc/example-tester.bash script to confirm everything works successfully for all officially supported Wallaroo Up distributions.

[ ] Automated Wallaroo Up Release Tester script - Jonathan

Review new documentation in details for errors/grammar/etc
New Machida3 docs
When running through the testing for your distribution, verify that there are no spelling errors or typos that were added as part of the mentions of machida3

[ ] Rachel
[ ] Dipin
[ ] Erik

Wallaroo Performance Testing

[ ] Jonathan

Docker for Python3/Machida3
Docker Installation Instructions
Follow the instructions for setting up and installing Wallaroo.

[ ] MacOS - Rachel

Docker "Run a Wallaroo Application" Instructions
Follow the instructions for Run a Wallaroo Application in Docker for Python3/Machida3.

[ ] MacOS - Rachel

Docker Python Examples for Machida3
Run through all the Python examples and make sure they work for Machida3. This means manually running everything in examples/python using Machida3 except for the connectors example.

[ ] MacOS - Rachel

Resilience example
Follow the steps in Resilience to run the "Recovery in Practice" example application using Machida3 and confirm it works.

[ ] MacOS - Rachel

Python3/Machida3 From Wallaroo Up
Installing From Wallaroo Up for Python Instructions
Follow the instructions for setting up and installing Wallaroo's Machida3.

[ ] Ubuntu Xenial - Dipin

Python3/Machida3 From Wallaroo Up "Run a Wallaoo Application" Instructions
Follow the instructions for the Python From Wallaroo Up Run a Wallaroo Application for Machida3.

[ ] Ubuntu Xenial - Dipin

From Wallaroo Up Python Examples
Run through all the Python examples and make sure they work for Machida3. This means manually running everything in examples/python using Machida3 except for the connectors example.
Making Sure it Works:
- Building and running all examples/python applications using Machida3 (to be done by following the replacement edit mentioned in the README)
- verifying all applications build and run as expected using Machida3

[ ] Ubuntu Xenial - Dipin

Resilience example
Follow the steps in Resilience to run the "Recovery in Practice" example application using Machida3 and confirm it works.

[ ] Ubuntu Xenial - Dipin

Python3/Machida3 From Source
Installing From Source for Python Instructions
Follow the instructions for setting up and installing Wallaroo for Machida3.

[ ] Bionic - Jonathan

Python3/Machida3 From Source "Run a Wallaoo Application" Instructions
Follow the instructions for the Python From Source Run a Wallaroo Application for Machida3.

[ ] Bionic - Jonathan

From Source Python Examples
Run through all the Python examples and make sure they work for Machida3. This means manually running everything in examples/python using Machida3 except for the connectors example.
Making Sure it Works:
- Building and running all examples/python applications using Machida3 (to be done by following the replacement edit mentioned in the README)
- verifying all applications build and run as expected using Machida3

[ ] Bionic - Jonathan

Resilience example
Follow the steps in Resilience to run the "Recovery in Practice" example application using Machida3 and confirm it works.

[ ] Bionic - Jonathan

Vagrant for Python3/Machida3
Vagrant Installation Instructions
Follow the instructions for setting up and installing Wallaroo for Machida3.

[ ] MacOS - Erik

Vagrant "Run a Wallaroo Application" Instructions
Follow the instructions for Run a Wallaroo Application in Vagrant for Machida3.

[ ] MacOS - Erik

Vagrant Python3/Machida3 Examples
Run through all the Python examples and make sure they work for Machida3. This means manually running everything in examples/python using Machida3 except for the connectors example.
Making Sure it Works:
- Building and running all examples/python applications using Machida3 (to be done by following the replacement edit mentioned in the README)
- verifying all applications build and run as expected using Machida3

[ ] MacOS - Erik

Resilience example
Follow the steps in Resilience to run the "Recovery in Practice" example application using Machida3 and confirm it works.

[ ] MacOS - Erik

Phase 2
Review all issues that arise from Phase 1. Address issues that we feel are worth including or can be included to meet release target date. Dependent on the issues addressed, another round of testing may be needed.

Vagrant Notes
If you are testing with Vagrant, you'll want to give at least 4 gigs of memory to virtualbox, this is done by adding the following to your Vagrantfile:
  config.vm.provider "virtualbox" do |v|
    v.memory = 4084
  end

Should we be testing cosmic(18.10) too?

@enilsen16 cosmic was released on 10/18 and there are too many unknowns to consider it a supported distribution for this release. an issue should be opened for adding support in a future release

@JONBRWN Should this be closed?


MINOR: demonstrate migrating Produced config to an interface

I was wondering about the impact of changing our config objects to be interfaces on the public side. This is just a sketch of the idea for discussion.
Committer Checklist (excluded from commit message)

[ ] Verify design and implementation
[ ] Verify test coverage and CI build status
[ ] Verify documentation (including upgrade notes)

I'd have to test binary compatibility, but I think this would be both binary and source compatible with existing user code, so I don't think we would need KIPs to make changes like this.
It could be my prejudice, but I think that this arrangement is a little cleaner for users to be able to look at the interface instead of a class. And I also think it's a bit more ergonomic for us to deal with just one class, rather than having the setters in one class and the getters in another, as well as having to make the fields protected rather than private.
That said, I don't know if it matters that much either way...


add sendout extrinsic hash and block number to confignft attributes

@niklasp can you help me do this please


Resolver preferring ts file imported from d.ts even-though d.ts is available

TypeScript Version:  2.0.3
Code
See minimal repro https://github.com/Bobris/tscbug.git
When compiling with tsc it will show resolving details:
c:\tscbug>tsc
======== Resolving module 'lib' from 'c:/tscbug/main.ts'. ========
Explicitly specified module resolution kind: 'NodeJs'.
Loading module 'lib' from 'node_modules' folder.
File 'c:/tscbug/node_modules/lib.ts' does not exist.
File 'c:/tscbug/node_modules/lib.tsx' does not exist.
File 'c:/tscbug/node_modules/lib.d.ts' does not exist.
Found 'package.json' at 'c:/tscbug/node_modules/lib/package.json'.
'package.json' has 'types' field 'index.d.ts' that references 'c:/tscbug/node_modules/lib/index.d.ts'.
File 'c:/tscbug/node_modules/lib/index.d.ts' exist - use it as a name resolution result.
Resolving real path for 'c:/tscbug/node_modules/lib/index.d.ts', result 'C:/tscbug/node_modules/lib/index.d.ts'
======== Module name 'lib' was successfully resolved to 'C:/tscbug/node_modules/lib/index.d.ts'. ========
======== Resolving module './nested' from 'C:/tscbug/node_modules/lib/index.d.ts'. ========
Explicitly specified module resolution kind: 'NodeJs'.
Loading module as file / folder, candidate module location 'C:/tscbug/node_modules/lib/nested'.
File 'C:/tscbug/node_modules/lib/nested.ts' exist - use it as a name resolution result.
Resolving real path for 'C:/tscbug/node_modules/lib/nested.ts', result 'C:/tscbug/node_modules/lib/nested.ts'
======== Module name './nested' was successfully resolved to 'C:/tscbug/node_modules/lib/nested.ts'. ========

Expected behavior:
import ./nested from lib/index.d.ts should resolve to lib/nested.d.ts
Actual behavior:
import ./nested from lib/index.d.ts was resolved to lib/nested.ts
Compilation works but it is just probably slower than needed because full source needs to be parsed instead of just declaration file.
Solution would be to not publish original source code, but only declaration files, but I need it for other use-cases.

.ts files always have precedence. We have, for a while, only picked up .d.ts files from node_modules, and that broke scenarios where ppl are developing multiple modules in conjunction, and using npm link to link their sources.
So the recommendation, assuming you own the sources of the library, is to keep your .d.ts files in a separate folder than your .ts files. possibly use --declarationDir to specify that.

Thanks, I will try declarationDir that looks like it could work.


feat: CompiledBinding StringFormat without curly braces

What does the pull request do?

Allow using binding StringFormat like {Binding Value,StringFormat=c} or {Binding Value,StringFormat=c2}
What is the current behavior?

What is the updated/expected behavior with this PR?

How was the solution implemented (if it's not obvious)?

Checklist

[x] Added unit tests (if possible)?
[ ] Added XML documentation to any related classes?
[ ] Consider submitting a PR to https://github.com/AvaloniaUI/Documentation with user documentation

Breaking changes

Obsoletions / Deprecations

Fixed issues

Fixes #11258

You can test this PR using the following package version. 11.0.999-cibuild0034553-beta. (feed url: https://pkgs.dev.azure.com/AvaloniaUI/AvaloniaUI/_packaging/avalonia-all/nuget/v3/index.json) [PRBUILDID]

You can test this PR using the following package version. 11.0.999-cibuild0034561-beta. (feed url: https://pkgs.dev.azure.com/AvaloniaUI/AvaloniaUI/_packaging/avalonia-all/nuget/v3/index.json) [PRBUILDID]

this needs to be updated in the 11.0 docs as well, see: https://docs.avaloniaui.net/docs/data-binding/bindings#binding-stringformat


197379 Owen Creek notes on write up

          photos are now in the 197379 directory on the onedrive.

Notes in the writeup of this site should include a bit of detail about:

[x] - CGL remote camp adjacent to stream (see google earth).  See if there is a way to find out about oil and gas liscencing of water extraction site (I don't think they register in the same place as water extraction liscences on bc data catalogue)
[x] - waterfall with photo, distance from culvert and estimated height
[x] - area of wetlands upstream and rough assessment of land degradation way upstream (ie. does google and bing show that perhaps there a bunch of rangeland up there that may have management activities leading to beaver and riparian removal?
[x] note that there appeared to be some rb and ct hybrids
[x] note that stream was mostly dry in 2022 with fish concentrated in pools
[x] tagging data as attachment linked to in data folder
[x] note that coho captured downsstream of crossing but not upstream
[x] note that design is underway by Mark Dewit from MoF. Can prob find his deets in the bc gov directory

Originally posted by @NewGraphEnvironment in https://github.com/NewGraphEnvironment/fish_passage_skeena_2022_reporting/issues/44#issuecomment-1421781316

This site was re visited in 2023. Tag reader was used to search for tagged fish from 2022 surveyed areas. Notes on survey found below.

closed with https://github.com/NewGraphEnvironment/fish_passage_skeena_2022_reporting/commit/b5808b3da27ffeebdd053aa55f7b6e2759ec1a47


[EasyDocker] Use .easy directory for easy-docker generated parameter & manifest files

Q
A

Bug fix?
no

New feature?
yes

BC breaks?
no

Deprecations?
no

Tests pass?
yes

Fixed tickets

By default, a .easy directory will be assumed for parameter and manifest files generated by this tool
Backwards compatibility is present, this will only affect new projects using the tool, when a manifest/params file does not already exist

❤


Code of Conduct is missing

The repo is also missing the Code of Conduct that defines standards for how to engage in a community. If you want to add that in your repo, then I would also add another pull request for that.

Sure go ahead @FahimFBA

Closing wrt #56


CM install of Chef failure

vmware-iso: https://opscode-omnibus-packages.s3.amazonaws.com/windows/2008r2/x86_64/chef-windows-12.4.3.windows.msi:
vmware-iso: ==> Downloading "https://opscode-omnibus-packages.s3.amazonaws.com/windows/2008r2/x86_64/chef-windows-12.4.3.windows.msi" to "C:\Users\vagrant\AppData\Local\Temp\chef\chef-client-latest.msi"
vmware-iso: 2015-12-17 11:04:53 ERROR 404: Not Found.

Reviewing the Chef Download site between versions 12.4.1 and 12.4.2 they changed the download URL:

https://opscode-omnibus-packages.s3.amazonaws.com/windows/2008r2/x86_64/chef-client-12.4.1-1.msi
https://opscode-omnibus-packages.s3.amazonaws.com/windows/2012r2/i386/chef-client-12.4.2-1-x86.msi

Looks like /script/cmtool.bat needs to be modified to handle the change in URL.

The problem here is cmtool.bat is assuming there is an x64 version of chef client available but that is not always the case.  x64 builds are not available until chef-client 12.7.2.  cmtool.bat needs to be fixed to default to x86 versions of Chef if the CM_VER is less than 12.7.2.

Quick and dirty fix, edit script/cmtool.bat:
REM if not defined CHEF_URL set CHEF_64_URL=https://packages.chef.io/stable/windows/2008r2/chef-client-%CM_VERSION%-x64.msi
REM if not defined CHEF_URL set CHEF_32_URL=https://packages.chef.io/stable/windows/2008r2/chef-client-%CM_VERSION%-x86.msi

REM if defined ProgramFiles(x86) (
REM   SET CHEF_URL=%CHEF_64_URL%
REM ) else (
REM   SET CHEF_URL=%CHEF_32_URL%
REM )

if not defined CHEF_URL set CHEF_URL=https://packages.chef.io/stable/windows/2008r2/chef-client-%CM_VERSION%-x86.msi

Fixed by PR #86

Fixed and future proofed by PR #187
Is there anybody out there?

This is actually fixed by PR #180. @daxgames, if you're still interested in getting that merged..do you mind re-basing it? Lmk, if it's too much trouble.

I will look at this today

@arizvisa #180 is rebased.  It rebased cleanly and I have not tested it since rebasing.
I am not actively using it at this point but glad to see your involvement and passion.

Thx man. I'll work on integrating it.

This issue has been fixed by PR #200. If chef installations don't download and install due to a url issue, lmk and I'll re-open this.


getPrice can return non-integer "Too Many Requests", should throw

https://github.com/ArweaveTeam/arweave-js/blob/a07243c0e418a4e8d7ecc4afa0a1aa55e8fb2acc/src/common/transactions.ts#L55

you could determine if it's parseable to an int? if you need an error, you could then create one, would this be reasonable? :
const price = parseInt(await getPrice(123))
if(isNaN(price)) throw new Error("error fetching price")

getPrice call is inside createTransaction
https://github.com/ArweaveTeam/arweave-js/blob/a07243c0e418a4e8d7ecc4afa0a1aa55e8fb2acc/src/common/common.ts#L124
So I need check each createTransaction for if (isNaN(tx.reward)) in all places. I preffer createTransaction which should either generate valid transaction or throw exception

Also this bug is actually not a bug of library but bug on arweave.net gateway, because it should have error code 429, but normal code returned

I've made this fix for my purposes https://github.com/virdpool/arweave-js/commit/91a7e04628d2aad94baa1cf81dc65b6be665ae04

This ties in with 2 or 3 other open issues regarding lack of error propagation. It's not a quick fix, so someone needs to spend a few hours on this.

right, so in switching over to fetch it has become apparent why this was set up in this way. some work had already been done in preparing for a switch over, fetch doesn't throw errors for status codes.
i was trying to recreate your error, and i realised that there is an incredibly high rate limit for this endpoint.
what are you doing that requires creating more than 30,000 transactions every 5 minutes @vird ? it's not possible to post them, that's for sure!

Global rate limit among all routes - 100 per second (30,000 per 5min)
I don't create too much transactions, but other endpoints are heavily used. So transaction creation could fail.
Usually there is no problem with 5 min limit, but there is problem with per second limit. Imagine pool found a block and block is confirmed. In worst case I need to send transaction to all miners. If there is more than 100 miners (different addresses) I need to send 100 transactions. And I need store that transactions to calculate fee for each transaction to make sure that there is no problem with balance overuse (otherwise last tx will fail).

But actually I didn't make deep investigation how many request I do to arweave.net. I have no monitoring inside or outside arweave-js. And now I can't recheck that because pool hashrate is low

hmm. ok. i'll leave this issue open for now, there's another unhandled error issue opened. likely they will both get looked at at the same time when someone has free time.

putting in a fix for this now. stole your regex, thanks!


MGDCTRS-516 : health check and error handler not working when kafka instance is del…

…eted
Jira : https://issues.redhat.com/browse/MGDCTRS-516

@lburgazzoli Could you please review the PR


How do I use Magic

I have magic but I don't know how to use it

i wonder if this is abandoned

@c0dyb-0 Unfortunately I have abandoned this project because the code is written with ReactJS Class Components. I built it in order to learn ReactJS but now I have moved on to functional components. Migrating the code is possible but when trying it I found it to be too much effort. Everyone is free to pick up the project and build something better out of it. It's unfortunate that it got stranded but it served the purpose of learning React for me and that was honestly all that I wanted to get out of it.


allow optional disk sync for download_object()

Add an argument to allow not syncing the file to disk after get_object_old()  and leave it to the operating system's cache strategy. This is useful in performance sensitive scenarios.

Btw, this breaks API compatibility


adc state machine

wrap the adc into a state machine

automatic schedule alignment

build some infrastructure for non-homogeneous schedules

also refactor the AdcPhy usage and InputChannel functionality

add AdcChannel to enumerate the ad7172 config "channel"

clean up some temperature conversion math and remove unnecessary parentheses

remove unnecessary and redundant comments

clean up imports and make them more explicit to avoid ambiguities

use enum iterators

[ ] not tested on hardware, especially interrupt setup/initial clear/enable

Should I explicitly test something else?

Not particularly.
Check that it doesn't lock/panic. I'd add a few debug to trace the state machine through its first few rounds and then check whether the data is fine compared to before this PR.


GH-35240: [Go][FlightRPC] Fix crash in client middleware

Rationale for this change
The Go interceptor API includes a provision for errors from trying to start an RPC. The handler for this in the Flight code was trying to use a nil pointer as a result.
What changes are included in this PR?
Fix a crash when those errors are encountered.
Are these changes tested?
New tests were added.
Are there any user-facing changes?
There are no user-facing changes.

Closes: #35240

Looks like the failures are the usual release-time things, unrelated to the PR


Fix: Nav Drawer UI Improved

Please make sure these boxes are checked before submitting your pull request - thanks!

[x] Apply the AndroidStyle.xml style template to your code in Android Studio.

[x] Run the checks with ./gradlew check to make sure you didn't break anything

[x] If you have multiple commits please combine them into one commit by squashing them.

Pressing Back button first closes the Navigation drawer(if its open) and does not directly exit the app.

@saketkumar95
Thanks for the review.

@nitish1211
Thanks for the PR


bcbio for panels

Hello,
We have several samples that were created using "Trusight RapidCapture Cancer Panel" on which I ran the default configuration of bcbio for variant calling (see example of the config below). This is ~100 genes panel.
When comparing the results to other pipeline (I believe Illumina's) the results were not concordant. Some regions were not covered properly for example while they should have.
Are there any best practices on how to tweak the bcbio to support high-depth panels? Any other recommendations?
Regards,
Y.
details:

algorithm:
aligner: bwa
mark_duplicates: true
platform: illumina
quality_format: standard
recalibrate: gatk
variantcaller:

gatk-haplotype
freebayes
analysis: variant2
description: mysample
files:
/encrypted/data/mysample1.fq.gz
/encrypted/data/mysample2.fq.gz
genome_build: hg19
metadata:
batch: Sample_batch
phenotype: ''

Thanks for the discussion, happy to figure out the right settings for your analysis and I have a couple of clarifying questions:

Is this a somatic sample where you want to identify low frequency variants? If so, you currently have a germline calling setup which will only call homozygous and heterozygous mutations. To do somatic calling, add phenotype: tumor and swap the callers to use somatic callers. vardict is a good choice for panels. You could also use freebayes and mutect or mutect2 if you want a GATK-based caller.

Which sample pipeline are you comparing the outputs to? How are you determining concordance?

You mention a coverage issue and I'm not sure what you mean. Could you provide an example of an issue you're finding?

Hope this helps.

Hello Brad and thanks for the prompt reply.

This is not somatic sample - this is a panel aimed for finding germline (inherited) cancer mutations.
I'm comparing with Illumina's pipeline. I'll gather the relevant info and share for concordance and coverage

Thanks again

Closing for now since there hasn't been any action on it and the suggests were for Ion Torrent which we don't support. We can open up a separate issue if there are other improvements that could be made to panel sequencing.


[demo] Add docker-compose for collector and jaeger

When running the demo app, the telemetry data should have somewhere to go.
We can use docker-compose and create a docker-compose.yml that spins up a configured collector and jaeger. We might not need the collector, and could just ingest directly to jaeger for the demo purposes....but I think it might be nice to have the collector as a place to wire up additional logging and/or other pipeline components.
When this issue is done, it should be easy to start the demo app and see some telemetry in the collector logs and in jaeger.
The README should be updated with the simple/clear instructions on how to start the "backend" and launch the demo via emulator.

I've started on this work.


Missing PATH description in INSTALL.rst

I find that one has to add %SCIPOPTDIR%\bin to path variable on Windows as well, not just the lib directory. Otherwise, I get an error complaining about cannot find dll.

Thank you for telling us!


Camera

DoD: Movable camera(hold rmb + drag) with centering function on double click

Review required


overwrite does wrong checksum validation

Describe the bug
When setting the overwrite it will do a checksum test but it does the sha2 checksum and not the md5 that is being used in the iRODS instance I have access to.
To Reproduce
Make sure your irods uses the md5 checksum
Download a file with overwrite...
        if not (
            local_path.is_file() and (calc_checksum(irods_path) == calc_checksum(local_path))
        ):

# Will call

    if isinstance(filepath, IrodsPath):
        return filepath.checksum
    f_hash=sha256()
    memv=memoryview(bytearray(128*1024))
    with open(filepath, 'rb', buffering=0) as file:
        for item in iter(lambda : file.readinto(memv), 0):
            f_hash.update(memv[:item])
    return f"sha2:{str(base64.b64encode(f_hash.digest()), encoding='utf-8')}"

Provide some information:

OS: Mac osx
Software version or branch you are working on
python version 3.12.4
iRODS version
python-irodsclient version (python -c "import irods; print(irods.__version__)" )

@jjkoehorst Thanks for noticing this. I will work on this before our next release.


Add app installation counter to website

Feature description
Add an actual counter for the number of installed apps to the website.

Problem and motivation
A lot of people are probably interested in this number, because it also gives an indication of how much of a difference the app can possibly make.
I know this can be roughly seen in the play store but the granularity decreases with increasing installs (next value above 10M is 50M). I think this info is not public in the AppStore at all.

It would probably motivate people to install the app if they see how many others have already  installed it as well and could be shared on social media to motivate others.
Is this something you're interested in working on
This can only be done by people with access to the publisher accounts in the AppStores

Please see this link for the daily installation numbers.
Numbers from yesterday:

We leave the sharing of this information to the app publisher (RKI) and focus on the open source project on this page.


How do I set cpu affinity explicitly for each logging thread?

Also is there a thread pool maintained internally? Could you kindly point me to the right place of the code? Thanks!

fmtlog won't create any threads implicitely, it's driven by user's hreads.


Discussion: style override

Related issues: #7.
A reusable component may need to set a style that it wants to be overridable. For instance,
function MyComponent({style, ...rest}) {
  return

}

Structurally it may be important for the component to have an outline. At the same time, provided it's substituted safely, it should be overridable. The example above allows override by passing the style prop. But that would only work with inline styling. A styled-components, for instance, would be unable to override it because it works via stylesheet.
Some possible options:

Try again to find a safe way to deploy stylesheets for components and use the predefined classes, e.g. className={${props.className || ''} amp-component}. So far, however, we didn't find a non-fragile way to deploy stylesheets.
Cancel default styles. E.g. <AmpComponent disableDefaultStyles>. This is a very rough flag however. The user may want to override only some of the styles.
Cancel style-by-style. E.g. <AmpComponent className="myclass" style={{outline: ''}}>. This will work, but a bit cryptic and also fragile. E.g. for now styles may use outline and tomorrow decide to switch to outline-color. CSS is smart enough to override it all. But style map may or may not work well for this. And even then, this is not very ergonomic. Basically, the component user must cancel the same styles on every use.

In @ampproject/wg-ui-and-a11y past discussions, we have often preferred some way to do (2). The underlying principle is that for every component that comes with default functionally crucial and visually enhancing styles, the visually enhancing styles should follow an "all or none" opt-in model. The reasoning is publishers should not rely on some combination of our styles and their styles to achieve the look on the page -- if so, we become locked into our non-critical styling because changes to these will break publishers in unanticipated ways.

In this case, we may also need to reclassify all styles into two categories: "essential structure" vs "pure styling". E.g. if an element must have overflow:hidden, it's not the same if it also recommends outline: 1px. Removing a structural style will likely break the component in some major ways.

Yes that's right, the document linked earlier discusses this:

As an additional point of reference, default styles tend to either be (1) functionally crucial or (2) visually enhancing. The former generally make the component "work", configuring DOM structure i.e. positionality of the element or the laying out of its children. The latter generally make the component "pretty", identifying a common visual language across components that shouldn't require additional styling on the publisher's part by default.
There is currently no way of distinguishing between the two types of default styles within our codebase other than ideologically, and in the past this has created obstacles for making changes to styles in AMP. In general this has been due to the assumption that publishers who use custom styles rely on the exact intersection between AMP's default styles and their custom styles to produce the experience on their page.
In this regard, establishing a styling heuristic in Bento not only addresses an unresolved technical challenge but also offers an opportunity to deviate from the existing pattern by defining a clear boundary between default and custom styles going forward.

Do we have an issue on wg-bento that lists the document and some key points from it? If not, could we create it and link it here?

Created #15

Related Web proposal: https://github.com/w3c/csswg-drafts/issues/3890


Populate metric details and access times only if stats are enabled

are enabled. Otherwise, its just a waste of memory and computation.

Thanks, @gksinghjsr