core: Cleanup & Housekeeping

Add model tests
Remove Kafka components
Clean up Cassandra aborts

Codecov Report

Merging #66 into master will increase coverage by 3.69%.
The diff coverage is 95.01%.

@@             Coverage Diff              @@
##             master      #66      +/-   ##
============================================
+ Coverage     81.79%   85.49%   +3.69%
- Complexity      698      778      +80
============================================
  Files           114      112       -2
  Lines          3581     3474     -107
  Branches        202      211       +9
============================================
+ Hits           2929     2970      +41
+ Misses          551      455      -96
+ Partials        101       49      -52

Impacted Files
Coverage Δ
Complexity Δ

...rc/main/java/edu/berkeley/ground/GroundServer.java
0% <ø> (ø)
0 <0> (ø)
:arrow_down:

.../main/java/edu/berkeley/ground/db/Neo4jClient.java
96.26% <ø> (+5.91%)
29 <0> (ø)
:arrow_down:

...n/java/edu/berkeley/ground/model/models/Graph.java
100% <100%> (+41.66%)
9 <0> (+5)
:arrow_up:

...ao/models/cassandra/CassandraStructureFactory.java
100% <100%> (+13.04%)
7 <2> (ø)
:arrow_down:

.../edu/berkeley/ground/model/usage/LineageGraph.java
100% <100%> (+41.66%)
9 <0> (+5)
:arrow_up:

...in/java/edu/berkeley/ground/model/models/Edge.java
100% <100%> (+31.25%)
13 <0> (+7)
:arrow_up:

...va/edu/berkeley/ground/model/models/Structure.java
100% <100%> (+41.66%)
9 <0> (+5)
:arrow_up:

...a/edu/berkeley/ground/model/usage/LineageEdge.java
100% <100%> (+41.66%)
9 <0> (+5)
:arrow_up:

.../usage/cassandra/CassandraLineageGraphFactory.java
100% <100%> (+7.69%)
6 <2> (ø)
:arrow_down:

...in/java/edu/berkeley/ground/model/models/Node.java
100% <100%> (+41.66%)
9 <0> (+5)
:arrow_up:

... and 27 more

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Enable ClearLinux as a supported distro

This PR enables ClearLinux as a supported distribution with ceph-deploy. ClearLinux primarily only contains python3 which prompted another commit to add python3 support.

Can one of the admins verify this patch?

Hi @ganeshmaharaj ! Thanks for your commit!
I'm not an admin but just a contributor, so don't take my word like any more than just a suggestion.
I reviewed your code, yet I haven't tested it, and seems good. Just one detail I marked as dangerous that really needs amending, the rest is mere style. I would recommend running flake8 over your new code.
Cheers!

@HacKanCuBa no worries. All reviews are welcome. I have cleaned up the code as best as i can addressing your comments. Let me know how they look this time.

@HacKanCuBa no worries. All reviews are welcome. I have cleaned up the code as best as i can addressing your comments. Let me know how they look this time.

Awesome! I'll be reviewing ASAP :)

@ganeshmaharaj  Could you please solve this confict issues and move it forward?

@ganeshmaharaj the python3 bits in this changeset do not apply anymore. could you let me know if you want update this PR and move it forwards, i'd like to cut a new release in couple weeks. otherwise i will close this PR.

@tchaikov will work on fixing up the patch this week. Apologies for any delay on my end. Had been on a hiatus from github for a while.

@ganeshmaharaj no worries. sorry for the short notice. the previous maintainer of this project does not work on it anymore.  i feel it would help the community if we can have another release of ceph-deploy in a predictable timeline mainly to address python3 support and the pending PRs.

jenkins test this please.


Unable to play multiplayer

After installing this software, use steam to open the option of not displaying the module, if you open the installed version, you cannot play multiplayer, and there is no response when you click the Host table button

This probably is due to GodotSteam not working anymore after unpacking and repacking the Godot game.

Guess this can be closed then.


Revert "fix: handle.NewHandle() now accepts map instead of any (#26)"

This reverts commit 3def4df1c4a7aea6acfe8b80afad5e0f814c0654.

/merge


upcoming / past error

upcoming and past events show the same content - unless I missed that we are in the singularity now I would consider this a bug

Fixed


Crash on 1.20.1 on start of the game

crash-2024-06-18_12.35.24-client.txt

...you opened this issue already: https://github.com/mim1q/MineCells/issues/111
Just wait for a Connector update


WRP-3054: Fix loading of images in 'all-samples' sample apps

Enact-DCO-1.0-Signed-off-by: Alexandru Morariu<EMAIL_ADDRESS>Checklist

[X] I have read and understand the contribution guide
[ ] A CHANGELOG entry is included
[ ] At least one test case is included for this feature or bug fix
[X] Documentation was added or is not needed
[ ] This is an API breaking change

Issue Resolved / Feature Added
Added the images in all-samples and base folder for the all-samples app to be able to find them.
Resolution
Additional Considerations
On my local enviroment the images load properly but on git I do receive the message 'Unable to render rich display' for more than half of them.
Links
WRP-3054
Comments

@alexandrumorariu, Pattern Layout from all-samples also cannot load image files. Could you please check it too?


Update Request: test

Please provide the tool name
testing model 2
Description
blah blah
Code of Conduct

[X] I agree to follow the FIT's Code of Conduct

try commenting


Home page failure

Environment
The homepage of the Nitro project is not loading
Reproduction
Go to Nitro homepage :
https://nitro.unjs.io
Describe the bug

Additional context
Chrome:

Safari:

Logs
No response

Looks fine for me again

@manniL Not for me
Still getting 500's

This is a cache hit for me 🤔

Hi @vejja and @manniL
I'm experiencing the same issue, I'm unable to access any pages.

@manniL Probably the deploy process failed for that file
Should you reopen so that people know that the issue has been flagged ?
The whole nitro.unjs.io website is down right now

cc @pi0

Thanks for the reports. It is interesting because even when checking cf pages build logs, reported chunks are generated!

It might be a regional issue with CDN, will try a new deployment and report it to the team.

Hi @pi0
The missing file is Da0YM-yw
I'm able to fetch VeUX0XyX from the CDN, the issue seems to be that when VeUV tries to fetch DaOY, it does not find it

Interesting, Frankfort, and Syndey are failing:

I'm located in Paris, guess that resolves to Frankfurt

Made a new deployment, can you please refresh the website or check https://d94994da.nitropack.pages.dev/ ?

Solved 🚀🚀🚀
Thanks

@pi0 : fun fact, no more hyphens - in any of the chunk names
Can't see how this would be related in any possible way though

(/cc @danielroe just to be on context too)

Hmm not true though
There is one BL-MyqLX.js in the build...


Add bio function to Person module

https://github.com/faker-js/faker/blob/c2b952347e1f952cf379807a3c456fed65075d11/src/locales/en/person/bio_pattern.ts#L4
https://github.com/faker-js/faker/tree/c2b952347e1f952cf379807a3c456fed65075d11/src/locales/en/person

Hi i would like to work on this, can you assign it to me?

Sure, assigned :)


I cant understand the Shader 、ComputeShader how to defined with "HideInInspector" in this project

Example ： VolumetircFog——ComputeShader——m_Scatter。 The Code Working Well。But I Cant Rename the Variable Name，It will throw NullRef。I want to know the m_Scatter
how to defined . others like it?

If you select the VolumetricFog.cs script in the project view, the inspector shows the compute shader that m_Scatter is referencing.
Also this is handy for renaming serialized properties:
https://docs.unity3d.com/ScriptReference/Serialization.FormerlySerializedAsAttribute.html


Add Timelinr to JavaScript table

It's still very used, specially in some WordPress themes https://github.com/juanbrujo/jQuery-Timelinr

Please create a pull request for this.


Add GNO token being visible by default on Gnosis/Xdai

Hey @hboon,
I had a chat with Gnosis chain and they asked if we can add GNO (https://gnosisscan.io/token/0x9c58bacc331c9aa871afd802db6379a98e80cedb) to be visible by default when Gnosis/Xdai chain is selected - still keep the Xdai token (have both being visible even if the value is 0).
Is it possible to do it? Thank you!

It's easy and sensible, but wouldn't it already show up if the wallet has a non-zero GNO balance? Or do they want it to show up even when it is 0?

They want it to show natively even if its 0 (although its not the native token).

Yes of course.


Servicebus dev version in 'unreleased' folder

Just to plug the Swagger update system and begin some tests.

Coverage remained the same at 55.738% when pulling b063faba0d6c2ed278f3d84f1e81651ecf8c8d4a on lmazuel:servibus-arm into cf9b2f30901f7adb6c661ec32e3a5875dbf79add on Azure:master.

Coverage remained the same at 55.738% when pulling b063faba0d6c2ed278f3d84f1e81651ecf8c8d4a on lmazuel:servibus-arm into cf9b2f30901f7adb6c661ec32e3a5875dbf79add on Azure:master.


Fix HMR issues with routeData and server functions

There are a bunch of HMR related issues with routeData and server functions that need special consideration. @ghalle has been working on some fixes but this probably requires additional thought about how to approach this.
These PRs are contributing towards this:

[ ] #149

I'm seeing '"request" is not available on the client. Use it within an if (isServer)'-errors while playing with the with-auth-example when not server-rendering. Is this known/expected? As this error-description is a bit vague, I'm unsure if this needs an issue or would be a duplicate.

This is a weird issue with vite codesplitting..should be fixed by https://github.com/solidjs/solid-start/commit/aae4836fbebba7315de3a2a8bc4321bad8829e29

Can confirm! Fixed for me in 0.1.0-alpha.92. Thank you!

In setting up for SolidStarts next Beta Phase built on Nitro and Vinxi we are closing all PRs/Issues that will not be merged due to the system changing. If you feel your issue was closed in mistake. Feel free to re-open it after updating/testing against 0.4.x release. Thank you for your patience.

See https://github.com/solidjs/solid-start/pull/1139 for more details.


mobile compatibility

Currently on mobile (Android Marshmellow using Chrome or Firefox) the javascript seems to run fine (there is a blinking cursor), but the field is not accessible to input and the keyboard won't appear for input.

The problem as far as I can tell is that mobile keyboards only show up when a textbox has focus. Since josh emulates its own input for the shell, it's just listening to keypresses, but mobile browsers do not know that.

That makes sense. Looking over the code I can only come up with one possible solution (and it's hacky).
It might be possible to have a text input field in the foreground over the console that sets readline to active when focused. Meanwhile js would intercept the input and pass it to readline.


⚠ Bofrost.at has degraded performance

In 5e58160, Bofrost.at (https://www.bofrost.at) experienced degraded performance:

HTTP code: 200
Response time: 1099 ms

Resolved: Bofrost.at performance has improved in 7146551.


How to completely UNinstall?

Since this project is no longer working, how can I completely UNinstall everything that it installed on my system using the .bat file?

I'm sorry it's not working. There appears to be a recent upgrade in whisperx that makes this not working, I still have to solve it.
To uninstall this project completely, it's simple:

Remove the conda environment:

conda env remove --name whisperx

Remove the repository folder of this project: Just go to the directory where you have this whisper-gui repository and delete it.

Since this project only installs dependencies on its own conda environment, this is enough.
Thanks anyway for trying my project!


Add option to show data labels of Plot

Basically copy over gotop's linechart labels.

Are you planning to include the superior braille and line colors that gotop uses? Would love to see that get merged in.

What do you mean by superior? :D

The lines can be different colors depending on their height? I'll have to try that out thank you

Yah, you should be able to change the color values in your plot widget by checking if incoming data meets a certain threshold.

Thank you I was able to get the LineColors threshold bit working, although I noticed if you instantiate multiple plots when you control the LineColors of  one plot, it applies the same line color to all of the plots. Each plot only has one line so perhaps it has something to do with it. I was able to control the LineColors when there were more than one line (but only one plot instance).
Also, I'm really looking forward to the data label addition. Currently the labels only appear as numbers despite datalabels [] being set.

Thank you I was able to get the LineColors threshold bit working, although I noticed if you instantiate multiple plots when you control the LineColors of one plot, it applies the same line color to all of the plots. Each plot only has one line so perhaps it has something to do with it. I was able to control the LineColors when there were more than one line (but only one plot instance).

Huh that sounds strange. What should be happening is that you can set the default Plot LineColors in the Theme, but otherwise the plots should be independent. If that's not the case then feel free to create a bug report, and an example of the bug would be good too.

Also, I'm really looking forward to the data label addition. Currently the labels only appear as numbers despite datalabels [] being set.

So it looks like the DataLabels field of the Plot doesn't actually do anything atm, but I'll try to get the datalabels going soon!


@kanaabe: Added noindex meta tags to articles tagged with  noindex

RE: https://artsy.slack.com/archives/C083S2Y57/p1492191534419513

Nice and useful!


Crash on exit in SceneShaderForwardClustered destructor

Godot version
4.1.dev (094e88416ab84cc4e391703453fb46528739cd69)
System information
Mageia 9, Linux
Issue description
I'm seeing a crash on exit in one of my test projects, which seems to be a recent regression.
The crash happens when quitting the 3D gameplay in https://github.com/team-godog/NGJ2023_Godog
There are errors about leaking GodotBody3D and GodotShape3D, and then leaking two shaders:
ERROR: 5 RID allocations of type 'P11GodotBody3D' were leaked at exit.
ERROR: 4 RID allocations of type 'P12GodotShape3D' were leaked at exit.
ERROR: Pages in use exist at exit in PagedAllocator: N33RendererSceneRenderImplementation22RenderForwardClustered32GeometryInstanceSurfaceDataCacheE
   at: ~PagedAllocator (./core/templates/paged_allocator.h:170)
ERROR: Pages in use exist at exit in PagedAllocator: N33RendererSceneRenderImplementation22RenderForwardClustered32GeometryInstanceForwardClusteredE
   at: ~PagedAllocator (./core/templates/paged_allocator.h:170)
ERROR: 2 shaders of type SceneForwardClusteredShaderRD were never freed
   at: ~ShaderRD (servers/rendering/renderer_rd/shader_rd.cpp:708)
ERROR: FATAL: DEV_ASSERT failed  "_first == nullptr" is false.
   at: ~List (./core/templates/self_list.h:114)

Thread 1 "godot-git" received signal SIGILL, Illegal instruction.
0x0000000009c2e943 in SelfList<RendererSceneRenderImplementation::SceneShaderForwardClustered::ShaderData>::List::~List (this=0xd048958, __in_chrg=<optimized out>) at ./core/templates/self_list.h:114
114                             DEV_ASSERT(_first == nullptr);

(gdb) bt
#0  0x0000000009c2e943 in SelfList<RendererSceneRenderImplementation::SceneShaderForwardClustered::ShaderData>::List::~List (this=0xd048958, __in_chrg=<optimized out>) at ./core/templates/self_list.h:114
#1  0x0000000009c29747 in RendererSceneRenderImplementation::SceneShaderForwardClustered::~SceneShaderForwardClustered (this=0xd048958, __in_chrg=<optimized out>)
    at servers/rendering/renderer_rd/forward_clustered/scene_shader_forward_clustered.cpp:473
#2  0x0000000009c0fc10 in RendererSceneRenderImplementation::RenderForwardClustered::~RenderForwardClustered (this=0xd046d40, __in_chrg=<optimized out>)
    at servers/rendering/renderer_rd/forward_clustered/render_forward_clustered.cpp:4026
#3  0x0000000009b60da2 in memdelete<RendererSceneRenderRD> (p_class=0xd046d40) at ./core/os/memory.h:109
#4  0x0000000009b5f396 in RendererCompositorRD::finalize (this=0xcc78be0) at servers/rendering/renderer_rd/renderer_compositor_rd.cpp:149
#5  0x0000000009a64601 in RenderingServerDefault::_finish (this=0xcc368b0) at servers/rendering/rendering_server_default.cpp:217
#6  0x0000000009a64839 in RenderingServerDefault::finish (this=0xcc368b0) at servers/rendering/rendering_server_default.cpp:244
#7  0x000000000584fee4 in finalize_display () at main/main.cpp:313
#8  0x0000000005868d56 in Main::cleanup (p_force=false) at main/main.cpp:3597
#9  0x00000000057dae8a in main (argc=1, argv=0x7fffffffd688) at platform/linuxbsd/godot_linuxbsd.cpp:75

The crash is on a DEV_ASSERT (so dev_build=yes), might not happen in a non-dev build.
Doesn't happen in 4.0.3-stable, and I don't remember seeing it a couple of weeks ago, so I expect this is a recent regression.
Steps to reproduce

Clone https://github.com/team-godog/NGJ2023_Godog
Edit it with latest Godot master, game commit 212feb11867bb4468b357e96756fef40d904e614
Press "Play", watch the intro (or skip with Esc), wait for the gameplay to start (takes a while to load in a dev build)
When in game (sliding dog on a slope), press Esc to show the pause menu, and press Quit - it should crash

Minimal reproduction project
See Steps to reproduce. It's not really minimal, I might try to narrow it down further but this is a relatively simple open source project and I think the regression can be easily pinpointed to recent changes to shader freeing.
CC @BastiaanOlij @clayjohn

Regression from #77341

Regression from #77341

Right, the crash is caused by the change from a simple error to a DEV_ASSERT.
But what causes this assert doesn't seem to be a recent regression in the end, here's the log output from 4.1 dev 1 (seems similar in 4.1 dev 2):
ERROR: 5 RID allocations of type 'P11GodotBody3D' were leaked at exit.
ERROR: 4 RID allocations of type 'P12GodotShape3D' were leaked at exit.
ERROR: Pages in use exist at exit in PagedAllocator: N33RendererSceneRenderImplementation22RenderForwardClustered32GeometryInstanceSurfaceDataCacheE
   at: ~PagedAllocator (./core/templates/paged_allocator.h:140)
ERROR: Pages in use exist at exit in PagedAllocator: N33RendererSceneRenderImplementation22RenderForwardClustered32GeometryInstanceForwardClusteredE
   at: ~PagedAllocator (./core/templates/paged_allocator.h:140)
ERROR: 2 shaders of type SceneForwardClusteredShaderRD were never freed
   at: ~ShaderRD (servers/rendering/renderer_rd/shader_rd.cpp:708)
ERROR: Condition "_first != nullptr" is true.
   at: ~List (./core/templates/self_list.h:106)
ERROR: 10 RID allocations of type 'N10RendererRD11MeshStorage4MeshE' were leaked at exit.
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
ERROR: Condition "_first != nullptr" is true.
   at: ~List (./core/templates/self_list.h:106)
ERROR: 7 RID allocations of type 'N10RendererRD15MaterialStorage8MaterialE' were leaked at exit.
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
WARNING: Leaked instance dependency: Bug - did not call instance_notify_deleted when freeing.
     at: ~Dependency (servers/rendering/storage/utilities.cpp:56)
ERROR: 2 RID allocations of type 'N10RendererRD15MaterialStorage6ShaderE' were leaked at exit.
ERROR: 4 RID allocations of type 'N10RendererRD14TextureStorage7TextureE' were leaked at exit.
ERROR: 13 RID allocations of type 'N17RendererSceneCull8InstanceE' were leaked at exit.
WARNING: 7 RIDs of type "UniformBuffer" were leaked.
     at: _free_rids (drivers/vulkan/rendering_device_vulkan.cpp:8970)
WARNING: 30 RIDs of type "IndexArray" were leaked.
     at: _free_rids (drivers/vulkan/rendering_device_vulkan.cpp:8970)
WARNING: 30 RIDs of type "IndexBuffer" were leaked.
     at: _free_rids (drivers/vulkan/rendering_device_vulkan.cpp:8970)
WARNING: 4 RIDs of type "VertexArray" were leaked.
     at: _free_rids (drivers/vulkan/rendering_device_vulkan.cpp:8970)
WARNING: 16 RIDs of type "VertexBuffer" were leaked.
     at: _free_rids (drivers/vulkan/rendering_device_vulkan.cpp:8970)
WARNING: 8 RIDs of type "Texture" were leaked.
     at: finalize (drivers/vulkan/rendering_device_vulkan.cpp:9300)
WARNING: ObjectDB instances leaked at exit (run with --verbose for details).
     at: cleanup (core/object/object.cpp:1993)
ERROR: Resources still in use at exit (run with --verbose for details).
   at: clear (core/io/resource.cpp:489)

While 4.0.3-stable doesn't seem to report any leaks.

Was trying to bisect what was causing the _first != nullptr error a bit ago but failed to identify anything specific

Could it be because this shader is freed after the scene is deleted?
https://github.com/godotengine/godot/blob/094e88416ab84cc4e391703453fb46528739cd69/servers/rendering/renderer_rd/renderer_compositor_rd.cpp#L149-L160C48

I don't think this is related to Bastiaan's recent PRs, the first objects shown as leaking are physics objects. Bastiaan's changes only impacted freeing specific shaders in the RD renderer. His material-dependency PR did not change how  materials are freed.
I'll do a quick bisect and see if I can spot the culprit

ab5fc22f67a19eee27f2a6dbdde903aa3b6e4ef8 is the first bad commit

#75627

Not sure how that causes these issues tho.

Minimized project: Test_77430.zip
The problem is that in Level.tscn the Level2 node (which is an instantiation of Leval.tsnc) has a child with the name BackgroundModels, which also exists in Level.tscn at the same level, overwriting the one from the packed scene causing it to leak, and as the packed node has meshes as children they and their resources in rendering server get leaked as well, ultimately causing this crash.

I have to check deeper, but this may be one of those cases that the switch from ERR_FAIL_COND to DEV_ASSERT has helped discovering an issue that was already there.

I have to check deeper, but this may be one of those cases that the switch from ERR_FAIL_COND to DEV_ASSERT has helped discovering an issue that was already there.

Indeed, the crash was highlighted by the change to DEV_ASSERT. The actual issue it highlighted was caused by Juan's #75627 it seems.


M1 Mac

Is there any work of a port for native M1 Mac?
I saw something early for Anaconda, but I have a homebrew installation.

@mdecaro the conda-forge distribution of spiceypy natively supports M1 macs so I recommend using that version if you can for now. I have PR #424 that is attempting to add the support to the project, although I am running into issues with setuptools/pip that I haven't been able to fix yet. Once that PR is fully working wheels will be provided for all platforms including M1/arm macs.
Until then, if you are able to compile cspice from source yourself you can provide the shared library to spiceypy using the offline installation option https://spiceypy.readthedocs.io/en/main/installation.html#offline-installation. The steps to compile cspice itself can be sorted out from the code in #424, so you can probably clone the branch locally and just run python get_spice.py to generate the shared library and then pass the path to the file using the environment variable described in the docs


Salesforce.Common.ForceException: npsp.TDTM_Contact: System.LimitException: npsp:Too many query rows: 50001

We have an external system using a .NET integration via SOAP to create and update records in a SF Instance  running NPSP 3.84.  The integration is updating / inserting contacts. The current contacts object has  74,798 records. Contacts carry an external id related to the integration (Personify Record Id). We are receiving the following message:
2016-11-21 08:05:53.5056 ERROR SmeInterface.Job Failed to update contact '000011916878' Salesforce.Common.ForceException: npsp.TDTM_Contact: System.LimitException: npsp:Too many query rows: 50001
It appears the integration is attempting to update the contact with the associated Personify Id '000011916878'  and is somehow tripping a query limit in npsp.TDTM_Contact which I gather is a trigger leading to a trigger handler. This seems to be happening on a contact by contact update/insert basis for all contacts in the integration.
Can you provide any insight into what might be causing this inside the npsp code? Is there a way to switch to- / use batch apex to avoid the query limit issue?

I'm afraid we can't debug this issue for you.  I'd look into how you have your org set up, and compare what happens when you insert a single contact in the UI vs. insert a single contact through your integration.  Things to consider are that when a new contact is inserted without an account, NPSP will automatically create an account for it, assuming your are using the One-to-One or Household Account model.  You should make sure that your integration profile has full permissions to the various account and contact fields, as well as any record types being used.  If you want to refer to our source code, its all here in gitHub at https://github.com/SalesforceFoundation/Cumulus/tree/dev/src/classes


Add get_rule_group method

Description
This PR adds a get_rule_group method to the AlertProvisioning API, which uses the /v1/provisioning/folder/%s/rule-groups/%s endpoint.
It also renames update_rule_group_interval to update_rule_group for consistency while maintaining the previous method for backward compatibility. I'm happy to revert this change if you'd rather avoid it.
I also attempted to add tests to this. However, I'm unfamiliar with your mocking library and am unsure where to register the  API path, and thus got a requests_mock.exceptions.NoMockAddress exception. If this change requires test coverage, I'd be happy to try and add it, but I'd need to be pointed in the right direction.

Thank you very much.


add javascript podcast

What does this PR do?
Add Resource(s)
For resources
Description
Why is this valuable (or not)
it's a web development podcast.
How do we know it's really free?
For book lists, is it a book?
Checklist:

[x ] Not a duplicate
[ ] Included author(s) if appropriate
[ ] Lists are in alphabetical order
[ ] Needed indications added (PDF, access notes, under construction)

Thanks!


Cannot connect to OpenSearch after update to 9.0.0-rc1: The client noticed that the server is not Elasticsearch and we do not support this unknown product.

After upgrading from package 9.0.0-beta7 to 9.0.0-rc1, I am not able to connect to a remote OpenSearch 2.3 instance any more.
Using 9.0.0-beta7, the logs were sent correctly. After upgrading to 9.0.0-rc1, we see multiple UnsupportedProductException errors with message The client noticed that the server is not Elasticsearch and we do not support this unknown product. coming from inside the Elasticsearch.Net package.
I tried changing multiple options with no changes, the current options I set are:
...
sinkOptions.AutoRegisterTemplate = true;
sinkOptions.AutoRegisterTemplateVersion = AutoRegisterTemplateVersion.ESv7;
sinkOptions.TypeName = null;

Rolling back to 9.0.0-beta7 "fixes" the issue.
Looking at the code in the ElasticSearch client, it throws the exception when it get a ProductCheckStatus.InvalidProduct from the "product check" logic:

It seems to be testing if the server product name contains "Elasticsearch" explicitly:

Sorry I only have a screenshot for this part of the code when trying to diagnose with a debugger attached
I'm not sure what would explain this regression: it seems that this version of ElasticSearch.Net can never be compatible with something other than ElasticSearch itself. But serilog-sinks-elasticsarch used to work fine with OpenSearch until the recent updates?
Is this change expected or is it an unexpected regression due to adding support for ES8 ? If support for OpenSearch is dropped it would be a potentially big issue for us.
Edit:
Setting DetectElasticsearchVersion to true or false does not change the behavior.

That is the message coming from Elasticseach.NET client version 7.16+. It explicitly checks that the product is Elasticserach and major version between 6 and 8, before it allows any client request to be executed.

Yes that is what I observed, but this did not happen with previous version of the serilog-sinks-elasticsearch package. What can I do to workaround this issue? If v9 of this package is no longer compatible with OpenSearch this will break everyone who was using v8 when upgrading?

I found this comment here https://github.com/elastic/elasticsearch-net/issues/5950#issuecomment-902658200 that explicitly confirm that the v7.14+ of ESNET are not compatible anymore with OpenSearch and equivalent.
Does this mean that this Serilog sink is no longer compatible as well, unless support is added explicitly for OpenSearch, using the OpenSearch .NET library (https://github.com/opensearch-project/opensearch-net) ?

Hmm, I was not aware of Opensearch and the Elasticsearch story, so sorry if this is breaking at the moment.
But in essence; this sink is for Elasticsearch and uses their client libraries, which we did upgrade and will keep updating for sure. There is also no test case against open search.
So either stick with an older version, or use an alternative implementation to access open search would be my suggestion.

I ran into the same issue - since this is the only Serilog sink that (intentionally or unintentionally) supported Opensearch -
I would suggest adding a note about this in the Breaking Changes section of Version 9 (Updated Elasticsearch packages no longer support server versions < ESv7 and that includes Opensearch)

That is indeed good to mention. Thanks for the PR!

We also ran into this issue, so we created a nuget package that implements the Serilog's ILogEventSink: https://github.com/appfacterp/AppFact.SerilogOpenSearchSink


Call information tip update

Updating Call Information tip to say Call information is not supported for all .NET Core, not just ASP.NET Core.

@deborahc,
Thanks for your contribution as a Microsoft full-time employee or intern. You do not need to sign a CLA.
Thanks,
Microsoft Pull Request Bot

:white_check_mark: Validation status: passed

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docs/debugger/intellitrace-features.md
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Allow alternate 'close' icon/content for FAB menu

In some of Google's Material Design examples they show a floating action button transition to a close "X" when the menu is shown. Would you please consider adding this feature to Materialize?
https://material-design.storage.googleapis.com/publish/material_v_4/material_ext_publish/0Bzhp5Z4wHba3LWNhZHZ0WDVpems/components-buttons-fab-transition_speeddial_02.mp4

I believe that it shouldn't be enforced, but could be a good addition, Added to the feature request board.

https://github.com/Dogfalo/materialize/pull/3836


Fix "x-dns-prefectch-control" typo

Correct x-dns-prefectch-control top where x-dns-prefetch-control was intended.

@KraigWalker : Thanks for your contribution! The author(s) have been notified to review your proposed change.

@KraigWalker : Thanks for your contribution! The author(s) have been notified to review your proposed change.

The typo fix looks good; thanks @KraigWalker.

The typo fix looks good; thanks @KraigWalker.


snazy: 0.50.0 -> 0.51.2

Diff: https://github.com/chmouel/snazy/compare/0.50.0...0.51.2
Changelog: https://github.com/chmouel/snazy/releases/tag/0.51.2
Description of changes

Things done

Built on platform(s)

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

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

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

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

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

[x] Fits CONTRIBUTING.md.

Result of nixpkgs-review pr 240363 run on x86_64-linux 1

1 package built:

snazy


Documentation meta-ticket

I have an open ticket at work to improve the docs, and we've had a couple people offer to help.  From Gitter:

Can somebody who knows the library quite well create tickets for parts that need documentation? I could then try them out and try to document them. I think many people would want to benefit from http4s but it's hard to get started.

[x] request matching in http4s-dsl
[x] JSON codecs, including how to make them work with case classes
[x] basic client operations
[ ] how to configure a client (IMO, SimpleHttpClient is almost always a bad choice)
[x] adding headers to a request
[x] creating and manipulating URIs
[ ] what's the difference between Request and Task[Request]?
[ ] Websockets
[x] Serve static files
[ ] Interruptable ServerApp
[x] how to get cookies from a request
[ ] how to "reload like Play" (we don't, but sbt-revolver is cool)

If you want to work on one of these, please comment and claim it.
If you want to propose something else, please comment and we'll add it.

Could you please add (or point me to) how to deal with handling a route, e.g. POST /foobar that has a payload?
Perhaps JSON codecs, including how to make them work with case classes covers this case.

@kevinmeredith: Here's an example of decoding a UrlForm from a POST.  The key concept is the EntityDecoder.  You can get one for JSON like this, and then you'd be able to req.decode[Foo].  I welcome a debate on whether fooDecoder should be optional in that example at #660.

There is also the documentation label, which shows a few related issues for us to tackle.

@reactormonk is improving the JSON and URI situation over on #689.

I'd like to chime in, perhaps, adding headers to a request and #568
Is there some info on where the documentation is stored and how to compile it with tut?

Docs live here, with a readme on roughly what goes where and how to preview it.

A few things:

[ ] Websockets
[ ] Serve static files
[ ] Interruptable ServerApp

Added those from the comment above.  By Interruptable ServerApp, you mean the cancelable in Global and ^C trick?  That's come up a few times.  Also, fork := true.

Exactly the ^C stuff.

Here are some of my thoughts wrt documentation from the perspective of someone just starting to use http4s.
First, it'd be nice to have an overview of the architecture of http4s so the user could see where their code fits into the picture. This could be fairly high level.
An explanation of Task might be appropriate since it is so integral, and, for me at least, was an important reason for wanting to use http4s. Maybe include some references to other documentation for Task, and explanations of the benefits over Future.
After the descriptions of the pieces (Request, Response, Service, Middleware, etc)., I would really like to see some explanations of how these pieces compose and how you can build up more complex routes and services. Documentation for request pattern matching (already mentioned above) would also be very useful.

@toddburnside I had a crack the other day coming at it from the angle you described. It's super rough, but I guess it might be useful as inspiration or something:
https://gist.github.com/dbousamra/f58354b0b3f273649dbf782ddd17b32c

I'm going to see if I can work some of @dbousamra's ideas into #782 while I'm on an airplane this weekend.  Watch this space.

@dbousamra Yes, that's the kind of think I was thinking of. I'm glad Ross is running with it. :smile:
@rossabaker I need to do some proof-reading,  but I'm just about done with some docs on middleware in general, and CORS and GZip in particular. Given the documentation churn at the moment, would it be simpler if I waited until the dust settled before putting in a PR?

@toddburnside: I'd say topic/hugo is where the fun is happening right now.  I would suggest targeting that.  If that branch turns into a flaming wreckage, I can rescue any markdown you contribute.

Closed in favour of https://github.com/http4s/http4s/projects/1


Clean up how player's animation node is set

 assert(animations)

This is a good improvement. Might be better to use vm.report_errors() though, to provide the developer with a more helpful error message?

Good one! It started off as protection against me forgetting to set the
animations, but of course it's more useful if we use the correct error
reporting.
I'll do this as soon as I have real computer time.

Is this better now?

Looks good; thank you, @mjtorn. 🙂


Add updates to CMS Editor Article Features

Fixes #25
Changed done in this PR:

Added Tags to Articles
Added Tags on the Article Detail Page
Added Recommended Articles in Article Admin
Added (hyperlinked) Recommended Articles in the Article Detail Page
Added Recommended Sections in Article Admin
Added (hyperlinked) Recommended Sections in the Article Detail Page
Added CSS for Recommended content

@istride Can you go through this whenever you have time?
cc: @dannyparsons

I think the code is fine, I just have a problem with the purpose of these changes. I can understand the need for recommended articles, which I can see are currently used in v1 sites, and Laurie used it in the walkthrough video. However, tags and recommended sections were glossed over in the video, and I can't confirm whether they are used in v1.
@dannyparsons do we know how article tags are used or will be used?
Do we need to treat articles and sections separately, or can we lump them together and make the order in which they are presented an editorial decision (like the homepage)?
Would it be beneficial to be able to link to other types of content from the 'recommended' section, such as surveys/polls/quizzes, or an external link?

@istride I think recommended articles have to be shown with their image/title. Same for surveys/polls/quizzes (i think). External link wouldn't let us do that easily. Thoughts?

Going by #25 description, tags and recommended sections have been noted to keep - I don't see Recommended Sections having any effect in the v1 demo site and I can't find any examples on live sites, I've queried this on #25 and whether recommended articles/section could be together. I think tags are useful to have, even if not used much currently.
I don't think recommended surveys/polls/quizzes would be needed as these would be featured in the body as I understand from the current use.

Okay, this PR can wait till Laurie replies on #25

Sorry I forgot to update on this, I added the response from Laurie https://github.com/unicef/iogt/issues/25#issuecomment-851390241

@ehmadzubair  I think this PR is waiting for more work to be done on it. Can this be completed before any new task is started?

@istride There wasn't anything left to be done in this. The current functionality (recommended articles and recommended sections in Article Admin) is consistent with what Laurie is expecting.
Resolving the conflicts however was a long exercise :(. This PR can be merged now
cc: @dannyparsons


Review use of output_dataset_id in workflow_apply

This should be an optional argument

As part of the new 1.3 fractal-server, this becomes a required argument


Add AcmSearchbar component

Issue: https://github.com/open-cluster-management/backlog/issues/6461

The placeholder "Search items" never gets removed.  I expect it to disappear after I start typing.

I expect the placeholer text ("Search items") to be a lighter color. Similar to our current UI and OCP.


Make OS functions an option. (use it at your own risk)

Funni.
You can completely disable os, only use the non-malicious ones, or use every os function.
Time for da funni kids 2 cry.

 No, we’re only using non-malicious functions and that’s all, clearly, all the other functions aren’t worth the risk

ok lol


Add Kaniko test case that requires advanced permissions

We are currently testing how well builds work with restrictions through a pod security policy for the Tekton pods. The added test case is the result. The test case succeeds against a "normal" k8s cluster. It fails with a psp in place and we are checking which permissions it needs or if certain Dockerfile constructs (RUN something after USER root) can only work with privileged containers.

/assign @sbose78

/ok-to-test

The test case succeeds against a "normal" k8s cluster. Are you running this PR against something where you would expect a reproduction of the issue?

Hi @sbose78, sry, "normal" was not a good wording. We are trying to let the builds run with a pod security policy that is as restrictive as possible. For the test case I am currently adding it is too restrictive and causes the build to fail. Without it, the build just passes fine.

Thanks, let me know.

@sbose78 we tested some more Dockerfiles and did not notice further issue. The rational for requiring SETGID and SETUID for Kaniko is:

When you have a USER user:group command in your Dockerfile, Kaniko will remember that information in config.User see user.go
If you then do a RUN anything, then Kaniko will check config.User and if it is set, will set cmd.SysProcAttr.Credential which requires these two capabilities, see run.go

@sbose78 anything else needed to merge this?

/lgtm
/approve


Nested Journal Page Links lose their link data

I've built a complex web of inline tables.  tables that roll on other tables and so on..
All functions as expected except that journal links that pass through more than 1 inline roll, lose their correct linkage.
The correct journal will still open up, but it has forgotten which page it was supposed to open.
Since I'm using this to create easy links to random encounter journals as we hex crawl, I'd like to be able to click the link and open the associated page without having to search through the document for the correct page.

Nevermind.. it doesn't even matter if they're nested.
I have a rolltable filled with text options.  each option is a link to a journal page in my compendium.
If I roll it with Inline Table Rolls, it loses the specific page data and only launches the first page of the journal.
If I roll it normally or with a macro, it will link to the journal page correctly.

Just some additional info on this:
Inline Table Rolls will not properly link to pages in Compendium journals, but it DOES work on Journals inside the world.
This isn't ideal since I'll have to import everything in and redo all the links for hundreds of entries.


Structure Markdown pages using Obsidian properties

This may be limited, because properties are key/value pairs that don't allow multiline content.

Here's an overview of a plug-in for Obsidian called "RPG Manager" and it somehow works to create both links and longer content in properties. Unsure how, but there is a link to their github and maybe it'll help?
https://www.youtube.com/watch?v=NLvzfOWI4aE

Thank you for the hint. But please, do not link external content here.
it looks like the rpg manager provides a syntax to use Obsidian as a sort of database for RPG definitions.
You can think of going that way and define something similar for the Aeon Timeline data structure, if you see a benefit.


"variable length arrays in C++ are a Clang extension"

When using installed fpl2cc:
In file included from src/rage.cc:3:
src/util/utf8_buffer.h:59:19: warning: variable length arrays in C++ are a Clang extension [-Wvla-cxx-extension]
59 |     utf8_byte buf[filesize + 1];
|                   ^~~~~~~~~~~~

e8903b9dc5834b387d723f2227840d7e7ab972ca fixes


Restrict access for shared projects to published projects only

Follow up fix for #72 to prevent access to unpublished shared projects.

Thanks for reviewing @co0lsky. Good point, I’ll refactor it.


Code block breaks if the scrolled to view more contents.

Browser: Version 56.0.2924.87 (64-bit), OS X.

Should be fixed by #314

Can you check @deekoder with the PR.

Spoke too soon the PR #314 doesn't address that.

This is css issue.

@deekoder Can we close this?


Consent & Permission API?

@brockallen try to morph consent store/service into the new grant API

done.

Need to consider an API/service to allow the UI to list user's consent, and revoke user's consent.

done


settings: Fix bad alignment in organization profile for non-English languages.

Due to differences in length of the words for different languages there were alignment issues in organization profile settings.
We fix this using flexbox to ensure that the alignment stays correct for any changes in language/word length; this is realised by merging the css properties of all the image upload widgets and branching to specific ids/classes for individual component adjustments.
see #21385 for context

Testing Plan:

Goto Organisation > Organisation Profile.
Check for any alignment issues when display language is English (incl. hover states).
Change to different non-English languages.
Check for any alignment issues (incl. hover states).

GIFs or screenshots:

Before
After

@sayamsamal changes look good to me. I see you have made some changes that are tangential to the issue. I would be nice to have them in a separate commit.

I played with the PR -- looks great!

@amanagr I have separated the commits into distinct incremental changes, thanks.

This is great, merged, thanks @sayamsamal!
I really appreciate the attention to detail and effort towards deduplicating the CSS for these components -- it was sorta a leftover TODO from making the JS/HTML somewhat shared.
https://github.com/zulip/zulip/issues/14730 might be worth looking at -- I'm not sure whether this PR should close that, but perhaps you can look and then post your recommendation in #frontend.
You could also consider browsing https://github.com/zulip/zulip/issues?q=is%3Aopen+is%3Aissue+label%3A"area%3A+settings+UI" for similar issues that we can dispatch relatively quickly.

@timabbott thank you for the valuable information, I was looking at CSS deduplication and structuring for this year's GSOC and it is reassuring to know that it was a part of the leftover TODO.


gitlab: source /etc/profile instead of ~/.bashrc

What does this PR do?
This PR sources /etc/profile instead of /root/.bashrc for jobs runnings on k8s

Motivation
/etc/profile will source the user's .bashrc as well, and will in addition source /etc/profile.d/*.sh
In most cases it doesn't make much difference, but RVM puts its configuration in /etc/profile.d, causing k8s runners not to be able to find ruby tools (as they ignore entrypoints, which was executing the commands through a login shell, which sources /etc/profile automatically)

Additional Notes

Possible Drawbacks / Trade-offs

Describe how to test/QA your changes

Reviewer's Checklist

[ ] If known, an appropriate milestone has been selected; otherwise the Triage milestone is set.
[ ] Use the major_change label if your change either has a major impact on the code base, is impacting multiple teams or is changing important well-established internals of the Agent. This label will be use during QA to make sure each team pay extra attention to the changed behavior. For any customer facing change use a releasenote.
[ ] A release note has been added or the changelog/no-changelog label has been applied.
[ ] Changed code has automated tests for its functionality.
[ ] Adequate QA/testing plan information is provided if the qa/skip-qa label is not applied.
[ ] At least one team/.. label has been applied, indicating the team(s) that should QA this change.
[ ] If applicable, docs team has been notified or an issue has been opened on the documentation repo.
[ ] If applicable, the need-change/operator and need-change/helm labels have been applied.
[ ] If applicable, the k8s/<min-version> label, indicating the lowest Kubernetes version compatible with this feature.
[ ] If applicable, the config template has been updated.

Closed since I somehow assumed that /etc/bash.bashrc would source ~/.bashrc while it definitely doesn't


Feature/issue 21 server credentials

@maweck
ready for review and merge
#21

@pdehnel
Ready for merge #21


Add CLI for users to manage/query databases

For #18
Control logs with
RUST_LOG=debug cargo run -- server --host <IP_ADDRESS> --port 8000
or
RUST_LOG=actix_web=debug cargo run -- server --host <IP_ADDRESS> --port 8000

To solve: Failed to extract Data<&sqlx_core::pool::Pool<sqlx_core::postgres::database::Postgres>>forcreate_databasehandler. For the Data extractor to work correctly, wrap the data withData::new()and pass it toApp::app_data(). Ensure that types align in both the set and retrieve calls.

Next: pass sqlx errors in crud.rs through server.rs as error_strings

Next: Better reporting on CRUD errors for creating entities. Then implement create_entity.

Errors a little clearer. Created create_entity. Next:

Finish create_entity/Handle null ID issue when creating entity
Add create_query
Integration tests

Entity / DB creation works! Next:

Add query to CLI / Client API
Clean up client API (make it return instantiated entities rather than printing, leave that to CLI)
Integration tests

Queries work! Next:

Review/merge PR
Integration tests


credible set data for backend integration

Similar to the work on variant index (#3350) and study index (#3357), we would like to serve a credible_set dataset through OS + API.
This dataset is created by different upstream ETL processes (gentropy), but they all write to the exact location and contain a shared schema. So effectively, they can be considered one single dataset that we would like to load:
❯ gsutil ls gs://genetics_etl_python_playground/releases/24.06/credible_set/
gs://genetics_etl_python_playground/releases/24.06/credible_set/eqtl_catalogue_susie/
gs://genetics_etl_python_playground/releases/24.06/credible_set/finngen_susie/
gs://genetics_etl_python_playground/releases/24.06/credible_set/gwas_catalog_PICSed_curated_associations/
gs://genetics_etl_python_playground/releases/24.06/credible_set/gwas_catalog_PICSed_summary_statistics/

Note that these datasets are currently pending validation and will be implemented in the gentropy layer. Records are expected to have:

Unique studyLocusId
variantId and locus.variantId available in the variant index
studyId available in the study index

(This has been discussed with @DSuveges but there is not ticket yet)
The credible sets use the study_locus as the reference schema.
Some stats (they might float in future iterations but not significantly):
Parquet size: 4.1 GiB
Rows (credible sets): 2_982_370
I'm making some comments in the next schema:
root
 |-- variantId: string (nullable = true) => Resolve using new variant index (#3350)
 |-- chromosome: string (nullable = true)
 |-- position: integer (nullable = true)
 |-- region: string (nullable = true)
 |-- studyId: string (nullable = true) => Resolve using new study index (#3357)
 |-- beta: double (nullable = true)
 |-- pValueMantissa: float (nullable = true)
 |-- pValueExponent: integer (nullable = true)
 |-- standardError: double (nullable = true)
 |-- finemappingMethod: string (nullable = true)
 |-- credibleSetIndex: integer (nullable = true)
 |-- locus: array (nullable = true)
 |    |-- element: struct (containsNull = true)
 |    |    |-- variantId: string (nullable = true) => Resolve using new variant index (#3350)
 |    |    |-- posteriorProbability: double (nullable = true)
 |    |    |-- pValueMantissa: float (nullable = true)
 |    |    |-- pValueExponent: integer (nullable = true)
 |    |    |-- logBF: double (nullable = true)
 |    |    |-- beta: double (nullable = true)
 |    |    |-- standardError: double (nullable = true)
 |    |    |-- is95CredibleSet: boolean (nullable = true)
 |    |    |-- is99CredibleSet: boolean (nullable = true)
 |    |    |-- r2Overall: double (nullable = true)
 |-- studyLocusId: long (nullable = true) => This will define unique schemas
 |-- credibleSetlog10BF: double (nullable = true)
 |-- effectAlleleFrequencyFromSource: float (nullable = true)
 |-- zScore: double (nullable = true)
 |-- subStudyDescription: string (nullable = true)
 |-- qualityControls: array (nullable = true)
 |    |-- element: string (containsNull = true)
 |-- purityMeanR2: double (nullable = true)
 |-- purityMinR2: double (nullable = true)
 |-- sampleSize: integer (nullable = true)
 |-- ldSet: array (nullable = true)
 |    |-- element: struct (containsNull = true)
 |    |    |-- tagVariantId: string (nullable = true)
 |    |    |-- r2Overall: double (nullable = true)

We want a top-level credible_set endpoint, but this dataset will need to be queried in additional ways, which we can define later.

If we want to ensure uniqueness of the dataset based on studyLocusId, it should be the generated from the following fields:

variantId - Identifier of the lead variant
studyId - Identifier of the study the locus belongs to
credibleSetIndex - as one locus might have multiple credible sets.
finemappingMethod - as one locus might be fine-mapped by multiple methods as well.

However, the process is not clear eg. the window based clumping would generate study locus with some id, but then it should be overwritten once a downstream finemapping process picks up and does the finemapping.

@DSuveges could you help me with a copy of the data in json format please

Some planned changes to data/schema are expected on this front. @DSuveges will list them here when plan is finalised.

Some updates on the credible set schema:

[x] adding maximum l2g score.
[x] adding geneId for maximum l2g score.
[ ] adding study type that allows sorting credible sets between gwas and qtl widget.
[ ] adding EFO of the gwas study that allow showing credible sets on the disease page.
[ ] adding target id from qtl studies that allows showing credible sets on target profile page.

There's an updated credible set dataset in json for the backend team to ingest: gs://ot-team/dsuveges/credible_sets.json
Number of credible sets: 3,019,002
The distribution of credible sets across study types:
+---------+-------+
|studyType|  count|
+---------+-------+
|    tuqtl| 411170|
|     gwas| 876691|
|     sqtl| 234066|
|     pqtl|   1772|
|     eqtl|1495303|
+---------+-------+

Schema
Changes

I though it would be better to rename field l2g to strongestLocus2gene
The geneId from QTLs are named as qtlGeneId to make it more obvious.

root
 |-- studyId: string (nullable = true)
 |-- studyLocusId: string (nullable = true)
 |-- variantId: string (nullable = true)
 |-- chromosome: string (nullable = true)
 |-- position: integer (nullable = true)
 |-- region: string (nullable = true)
 |-- beta: double (nullable = true)
 |-- zScore: double (nullable = true)
 |-- pValueMantissa: float (nullable = true)
 |-- pValueExponent: integer (nullable = true)
 |-- effectAlleleFrequencyFromSource: float (nullable = true)
 |-- standardError: double (nullable = true)
 |-- subStudyDescription: string (nullable = true)
 |-- qualityControls: array (nullable = true)
 |    |-- element: string (containsNull = true)
 |-- finemappingMethod: string (nullable = true)
 |-- credibleSetIndex: integer (nullable = true)
 |-- credibleSetlog10BF: double (nullable = true)
 |-- purityMeanR2: double (nullable = true)
 |-- purityMinR2: double (nullable = true)
 |-- locusStart: integer (nullable = true)
 |-- locusEnd: integer (nullable = true)
 |-- sampleSize: integer (nullable = true)
 |-- locus: array (nullable = true)
 |    |-- element: struct (containsNull = true)
 |    |    |-- is95CredibleSet: boolean (nullable = true)
 |    |    |-- is99CredibleSet: boolean (nullable = true)
 |    |    |-- logBF: double (nullable = true)
 |    |    |-- posteriorProbability: double (nullable = true)
 |    |    |-- variantId: string (nullable = true)
 |    |    |-- pValueMantissa: float (nullable = true)
 |    |    |-- pValueExponent: integer (nullable = true)
 |    |    |-- beta: double (nullable = true)
 |    |    |-- standardError: double (nullable = true)
 |    |    |-- r2Overall: double (nullable = true)
 |-- strongestLocus2gene: struct (nullable = true)
 |    |-- geneId: string (nullable = true)
 |    |-- score: double (nullable = true)
 |-- studyType: string (nullable = true)
 |-- traitFromSourceMappedIds: array (nullable = true)
 |    |-- element: string (containsNull = true)
 |-- qtlGeneId: string (nullable = true)

How the data looks like: PICS credible sets
For clarity, the number of tag variants are truncated.
{
  "studyId": "GCST90105038",
  "studyLocusId": "-9221662644183536443",
  "variantId": "3_50557710_C_T",
  "chromosome": "3",
  "position": 50557710,
  "region": null,
  "beta": 0.0134335,
  "zScore": null,
  "pValueMantissa": 6.0,
  "pValueExponent": -15,
  "effectAlleleFrequencyFromSource": null,
  "standardError": null,
  "subStudyDescription": null,
  "qualityControls": [],
  "finemappingMethod": "pics",
  "credibleSetIndex": null,
  "credibleSetlog10BF": null,
  "purityMeanR2": null,
  "purityMinR2": null,
  "locusStart": null,
  "locusEnd": null,
  "sampleSize": null,
  "locus": [
    {
      "is95CredibleSet": true,
      "is99CredibleSet": true,
      "logBF": null,
      "posteriorProbability": 0.8281915098204469,
      "variantId": "3_50557710_C_T",
      "pValueMantissa": null,
      "pValueExponent": null,
      "beta": null,
      "standardError": 0.9999996011812708,
      "r2Overall": 1.0000000000000027
    },
    {
      "is95CredibleSet": true,
      "is99CredibleSet": true,
      "logBF": null,
      "posteriorProbability": 0.018635570174451596,
      "variantId": "3_50972004_C_T",
      "pValueMantissa": null,
      "pValueExponent": null,
      "beta": null,
      "standardError": 0.0387769970112231,
      "r2Overall": 0.7735468485352232
    },
  ],
  "strongestLocus2gene": {
    "geneId": "ENSG00000088538",
    "score": 0.7871325016021729
  },
  "studyType": "gwas",
  "traitFromSourceMappedIds": [
    "EFO_0011015"
  ],
  "qtlGeneId": null
}

How the data looks like: SuSiE credible sets

For clarity, the number of tag variants are truncated.
Only finngen, at this point without disease

{
  "studyId": "FINNGEN_R10_C3_RECTUM_ADENO_MUCINO_EXALLC",
  "studyLocusId": "-9131389010760691102",
  "variantId": "18_48925503_G_A",
  "chromosome": "18",
  "position": 48925503,
  "region": "chr18:47425503-50425503",
  "beta": -0.19892,
  "zScore": null,
  "pValueMantissa": 2.0810000896453857,
  "pValueExponent": -12,
  "effectAlleleFrequencyFromSource": 0.49358999729156494,
  "standardError": 0.0283,
  "subStudyDescription": null,
  "qualityControls": null,
  "finemappingMethod": "SuSie",
  "credibleSetIndex": 1,
  "credibleSetlog10BF": 5.91695653245,
  "purityMeanR2": null,
  "purityMinR2": null,
  "locusStart": null,
  "locusEnd": null,
  "sampleSize": null,
  "locus": [
    {
      "is95CredibleSet": true,
      "is99CredibleSet": true,
      "logBF": 22.2531357731279,
      "posteriorProbability": 0.254337321094081,
      "variantId": "18_48925503_G_A",
      "pValueMantissa": 2.0810000896453857,
      "pValueExponent": -12,
      "beta": -0.19892,
      "standardError": 0.0283,
      "r2Overall": null
    },
    {
      "is95CredibleSet": true,
      "is99CredibleSet": true,
      "logBF": 22.1759052599176,
      "posteriorProbability": 0.23543406807608,
      "variantId": "18_48925435_C_CG",
      "pValueMantissa": 2.255000114440918,
      "pValueExponent": -12,
      "beta": -0.198598,
      "standardError": 0.0282994,
      "r2Overall": null
    }
  ],
  "strongestLocus2gene": {
    "geneId": "ENSG00000101665",
    "score": 0.9262983798980713
  },
  "studyType": "gwas",
  "traitFromSourceMappedIds": null,
  "qtlGeneId": null
}

How the data looks like: QTL studies

For clarity, the number of tag variants are truncated.

{
  "studyId": "GTEx_esophagus_muscularis_ENSG00000105483.grp_2.upstream.ENST00000391898",
  "studyLocusId": "-9223054931290123158",
  "variantId": "19_48204408_G_A",
  "chromosome": "19",
  "position": 48204408,
  "region": "chr19:47255946-49255946",
  "beta": -0.274482,
  "zScore": null,
  "pValueMantissa": 1.0399999618530273,
  "pValueExponent": -7,
  "effectAlleleFrequencyFromSource": null,
  "standardError": 0.0507531,
  "subStudyDescription": null,
  "qualityControls": null,
  "finemappingMethod": "SuSie",
  "credibleSetIndex": 1,
  "credibleSetlog10BF": 14.906432151794434,
  "purityMeanR2": null,
  "purityMinR2": null,
  "locusStart": null,
  "locusEnd": null,
  "sampleSize": null,
  "locus": [
    {
      "is95CredibleSet": true,
      "is99CredibleSet": true,
      "logBF": 12.9898148734311,
      "posteriorProbability": 0.143881970498929,
      "variantId": "19_48204408_G_A",
      "pValueMantissa": 1.0399999618530273,
      "pValueExponent": -7,
      "beta": -0.274482,
      "standardError": 0.0507531,
      "r2Overall": null
    },
    {
      "is95CredibleSet": true,
      "is99CredibleSet": true,
      "logBF": 12.9898148734311,
      "posteriorProbability": 0.143881970498929,
      "variantId": "19_48204483_G_A",
      "pValueMantissa": 1.0399999618530273,
      "pValueExponent": -7,
      "beta": -0.274482,
      "standardError": 0.0507531,
      "r2Overall": null
    }
  ],
  "strongestLocus2gene": null,
  "studyType": "tuqtl",
  "traitFromSourceMappedIds": null,
  "qtlGeneId": "ENSG00000105483"
}

@remo87 @jdhayhurst : In this schema there are a handful of identifiers to resolve:

variantId -> Resolve in the variant index.
locus.variantId  ->  Resolve in the variant index.
strongestLocus2gene. geneId -> Resolve in target index
qtlGeneId -> Resolve in target index
studyId  -> Resolve in study index

Some notes with @jdhayhurst on the credible set endpoints
Study page:

Fixed entity: studyId

Variant page:

Fixed entity: all credible sets that contain page variant in the locus.variantId list
Filtering by studyType. it should be an enum. We need to provide a list with all the qualifying studyType (e.g. ['eqtl', 'pqtl', 'sqtl'])

Disease page:

Fixed entity: diseaseIds (currently not available in the data) cc @DSuveges
Filtering by studyType. it should be an enum. We need to provide a list with all the qualifying studyType (e.g. ['eqtl', 'pqtl', 'sqtl'])

Root-level endpoint:

credibleSetId: [String]
diseaseId: [String]
studyId: [String]
variantId: [String]
study_type: [String]
region [String]

I don't think we are missing anything obvious but it might be good to have a look @addramir & @DSuveges

Update 14/08: Hoping for a first iteration by Friday

New iteration of the credible set dataset
@remo87  The JSON formatted data is here: gs://ot-team/dsuveges/credible_sets.json.
Schema change: instead of traitFromSourceMappedIds field there's a diseaseIds field containing a list of validated EFO IDs, that should be resolvable against the disease index.
Important - Although the dataset was generated in a validation step, the flagged credible sets are still in the dataset except those, which don't have variantId.
Schema:
root
 |-- studyId: string (nullable = true)
 |-- studyLocusId: string (nullable = true)
 |-- variantId: string (nullable = true)
 |-- chromosome: string (nullable = true)
 |-- position: integer (nullable = true)
 |-- region: string (nullable = true)
 |-- beta: double (nullable = true)
 |-- zScore: double (nullable = true)
 |-- pValueMantissa: float (nullable = true)
 |-- pValueExponent: integer (nullable = true)
 |-- effectAlleleFrequencyFromSource: float (nullable = true)
 |-- standardError: double (nullable = true)
 |-- subStudyDescription: string (nullable = true)
 |-- qualityControls: array (nullable = true)
 |    |-- element: string (containsNull = true)
 |-- finemappingMethod: string (nullable = true)
 |-- credibleSetIndex: integer (nullable = true)
 |-- credibleSetlog10BF: double (nullable = true)
 |-- purityMeanR2: double (nullable = true)
 |-- purityMinR2: double (nullable = true)
 |-- locusStart: integer (nullable = true)
 |-- locusEnd: integer (nullable = true)
 |-- sampleSize: integer (nullable = true)
 |-- locus: array (nullable = true)
 |    |-- element: struct (containsNull = true)
 |    |    |-- is95CredibleSet: boolean (nullable = true)
 |    |    |-- is99CredibleSet: boolean (nullable = true)
 |    |    |-- logBF: double (nullable = true)
 |    |    |-- posteriorProbability: double (nullable = true)
 |    |    |-- variantId: string (nullable = true)
 |    |    |-- pValueMantissa: float (nullable = true)
 |    |    |-- pValueExponent: integer (nullable = true)
 |    |    |-- beta: double (nullable = true)
 |    |    |-- standardError: double (nullable = true)
 |    |    |-- r2Overall: double (nullable = true)
 |-- strongestLocus2gene: struct (nullable = true)
 |    |-- geneId: string (nullable = true)
 |    |-- score: double (nullable = true)
 |-- studyType: string (nullable = true)
 |-- diseaseIds: array (nullable = true)
 |    |-- element: string (containsNull = true)
 |-- qtlGeneId: string (nullable = true)

Question about studyTypes:
For the enum, these are the current values of study types: tuqtl, gwas, sqtl, pqtl, eqtl the distribution of the labels:
+---------+-------+
|studyType|  count|
+---------+-------+
|    tuqtl| 411170|
|     gwas| 793759|
|     sqtl| 234066|
|     pqtl|   1772|
|     eqtl|1495303|
+---------+-------+

Discussed on slack: we should change field name studyLocusId(all occurrences) to credibleSetId in credibleSet API to avoid confusion (especially for FE development)

Based on discussion with @d0choa and @jdhayhurst : as part of planning evidence and l2g integration, some updates are proposed on the credible set data ingestion and modelling:

A new l2g dataset is proposed with studyLocusId, targetId, l2g prediction and potentially features.
In the credible set widget on the variant page, the top l2g prediction and gene is expected to be resolved against the planned l2g dataset based on studyLocusId and pulling the highest l2g score.

All possible list of studyTypes are: ['tuqtl', 'pqtl', 'eqtl', 'sqtl', 'sctuqtl', 'scpqtl', 'sceqtl', 'scsqtl', 'gwas']


Add support for embedded version information on Windows

From @alexandervrs on December 5, 2016 22:45
It'd be great to have Windows-only version information for Windows executables.
If I compile with hxcpp, I get an executable with the icon but it is missing the version information:

I also tried with several ways to attach a .rc file with this info:
1 VERSIONINFO
FILEVERSION 1,0,0,0
PRODUCTVERSION 1,0,0,0
FILEOS 0x4
FILETYPE 0x2
{
	BLOCK "StringFileInfo"
	{
		BLOCK "040904E4"
		{
			VALUE "CompanyName", ""
			VALUE "FileVersion", "<IP_ADDRESS>"
			VALUE "FileDescription", "Sample"
			VALUE "InternalName", ""
			VALUE "LegalCopyright", "Author Name"
			VALUE "LegalTrademarks", ""
			VALUE "OriginalFilename", "Sample.exe"
			VALUE "ProductName", "Sample"
			VALUE "ProductVersion", "<IP_ADDRESS>"
		}
	}
	BLOCK "VarFileInfo"
	{
		VALUE "Translation", 0x0409, 1252
	}
}

Some fields like File Description are important in Windows Applications, as it is used as description in the taskbar and system tray and the others are informative to the user and enrich some other Windows dialogs.
Could there be any way to specify these?
I'd expect something like,
<config:windows version-information="productname" value="test" />
<config:windows version-information="productversion" value="<IP_ADDRESS>" /> (also affects PRODUCTVERSION 1,0,0,0)
<config:windows version-information="companyname" value="test" />
<config:windows version-information="fileversion" value="<IP_ADDRESS>" /> (also affects FILEVERSION 1,0,0,0)
<config:windows version-information="filedescription" value="test" />
<config:windows version-information="legalcopyright" value="test" />
<config:windows version-information="legaltrademarks" value="test" />
<config:windows version-information="internalname" value="test" />
<config:windows version-information="originalfilename" value="test.exe" />

in the project.xml file
Copied from original issue: openfl/openfl#1370

Looked into whether Lime had this feature and found a 7 year old issue.

This feature can be achieved by defining resourceFile which makes it able to assign the resource.rc file. This feature has been added on hxcpp since this commit.


Allow defining an EventDispatcher service in the container

This patch adds logic to the ApplicationFactory to test for a Laminas\Cli\SymfonyEventDispatcher instance and, if found, use it to populate the symfony/console instance (if not found, we instantiate one directly, as we did before).
We require that the service returned implement Symfony\Component\EventDispatcher\EventDispatcherInterface to ensure that we can add our ConsoleEvents::TERMINATE event.
Users who want to supply additional listeners or subscribers can do so by defining the service and optionally adding delegators to it.
Fixes #47

Note: this patch does not contain the fixes found in #53, so tests will fail until that patch is merged.

Note: this patch does not contain the fixes found in #53, so tests will fail until that patch is merged.

Pushed all QA changes into separate PRs that are now in the 0.1.x branch, which allows tests for this to run; ready to review now, @michalbundyra .

Pushed all QA changes into separate PRs that are now in the 0.1.x branch, which allows tests for this to run; ready to review now, @michalbundyra .

I'd like to see full example here, so it's clear what is our recommended way of adding listeners.

Comprehensible examples are a must! 👍

I'd like to see full example here, so it's clear what is our recommended way of adding listeners.

Comprehensible examples are a must! 👍

@froschdesign and @michalbundyra — Updated the events.md to provide a full example!

@froschdesign and @michalbundyra — Updated the events.md to provide a full example!


Add GitHub check reporter

This PR adds the possibility to report checks to GitHub.

The WebHookReceiver now creates a check as soon as a web hook is received.
CheckReporter gets request details from GitHubApi and makes the request.

It generally looks good to me, but it's kind of a puzzle to figure out what gets called when and by whom. I think documentation of the behaviour would be of great help, in particular of the internal classes and methods.

Codecov Report

Merging #197 into master will decrease coverage by 2.46%.
The diff coverage is 54.26%.

@@             Coverage Diff              @@
##             master     #197      +/-   ##
============================================
- Coverage     79.67%   77.21%   -2.47%
- Complexity      376      451      +75
============================================
  Files            46       51       +5
  Lines           930     1185     +255
  Branches        174      227      +53
============================================
+ Hits            741      915     +174
- Misses          113      182      +69
- Partials         76       88      +12

Impacted Files
Coverage Δ
Complexity Δ

...ojo/schaapi/githubtestreporter/CustomHttpClient.kt
0% <0%> (ø)
0 <0> (?)

...jojo/schaapi/githubtestreporter/WebHookReceiver.kt
0% <0%> (ø)
0 <0> (ø)
:arrow_down:

...jojo/schaapi/githubtestreporter/CheckSuiteEvent.kt
0% <0%> (ø)
0 <0> (ø)
:arrow_down:

...jojo/schaapi/githubtestreporter/AppKeyGenerator.kt
93.75% <100%> (ø)
3 <1> (ø)
:arrow_down:

...jo/schaapi/githubtestreporter/FuelConfiguration.kt
100% <100%> (ø)
1 <1> (?)

...jo/schaapi/githubtestreporter/JsonObjectBuilder.kt
100% <100%> (ø)
3 <3> (?)

...fejojo/schaapi/githubtestreporter/CheckReporter.kt
84.61% <84.61%> (ø)
5 <5> (?)

...g/cafejojo/schaapi/githubtestreporter/GitHubApi.kt
95.83% <95.83%> (ø)
2 <2> (?)

...pipeline/patterndetector/ccspan/PatternDetector.kt
75% <0%> (-25%)
3% <0%> (ø)

...cafejojo/schaapi/models/CustomEqualsCollections.kt
93.67% <0%> (-2.33%)
0% <0%> (ø)

... and 13 more

Continue to review full report at Codecov.

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Generator for flags.dart, updated

pushed to wrong branch and make new pull request by mistake

Is it normal that the builder is in the src folder ? I'm used to using build

Is it normal that the builder is in the src folder ? I'm used to using build

paths in build.yaml  use lib dir as root directory, if you want to use path outside of lib you need to use subpackage... afaik (but maybe i wrong - didn't test other variants....)

Yes using a subpackage would be a better solution


Update Kafka Scaler to check for ActivationLagThreshold below 0

Signed-off-by: Vicky Ledsom<EMAIL_ADDRESS>
We were experiencing issues when not providing ActivationLagThreshold, the value is then defaulted to 0 but the logic was checking for a value of less or equal to 0. Which would always fail with must be positive number when using the default. If the plan to keep the default as 0 then this logic needs changing. Hence this PR.
Checklist

[ ] When introducing a new scaler, I agree with the scaling governance policy
[x] I have verified that my change is according to the deprecations & breaking changes policy
[x] Tests have been added
[x] Changelog has been updated and is aligned with our changelog requirements
[ ] A PR is opened to update our Helm chart (repo) (if applicable, ie. when deployment manifests are modified)
[ ] A PR is opened to update the documentation on (repo) (if applicable)
[x] Commits are signed with Developer Certificate of Origin (DCO - learn more)

fixed in : https://github.com/kedacore/keda/pull/4143


Excel xlsx reader returns blank values for rows

Hi Mark,
I have an xlsx file whereby the read returns no values. I've debugged the issue and it's deep in the xml reading. I need to transfer the file privately, do you have a contact email, perhaps you could message me privately? charliedurrant at gmail dot com
Charlie

Took a look at the file and I see roughly where the issue is. It looks like the Apache POI tool creates a slightly strange format where it inlines string values in a way that I don't properly handle. It is definitely fixable, but it will take me a bit of time to figure out a solution that doesn't break other scenarios.
In the meantime, you can open the file in Excel and "Save as" a copy, the copy should then be able to be processed correctly.

Just pushed 0.1.12 to nuget with a fix for this.

@charles-durrant-tr I did notice one issue in the files you sent. There was an odd formatting style being applied in one of them that wasn't handled correctly, it ended up throwing an exception in the formatting code. I fixed that so that it will fallback to a standard format in those scenarios. This is pushed with 0.2.0-b0001 (prerelease). Give a try and see if it fixed the issues you saw. Anything still failing please create a new issue with specific details and I can take a look.


Error when invoking explorer.newFile while explorer viewlet is collapsed

VSCode Version: From sources

Steps to Reproduce:

Open a folder in vscode
Collapse explorer viewlet
Invoke explorer.newFile or explorer.newFolder command
Error Command 'File: New Folder' resulted in an error (TreeError [FileExplorer] Data tree node not found: [object Object]) shows in notifications

@jeanp413 good catch, thanks for reporting this.
I believe this was like that since we shipped stable and our changes to the view / viewlet infrastucture.
Issue was that open viewlet does not exapnd the explorer view which makes sense since a viewlet is a superset.


App::with_defaults pulls clap's author and version

Using the new App:with_defaults displays clap's author and version number.
This is with clap version 2.11.0

Interesting, I hadn't thought about that happenig. Thanks for reporting!

This still happens in 2.11.2, maybe that commit was meant to close #643 instead?

@clux yes, that was a mistake. Thanks!

From @RoPP

Cargo.toml :

[package]
name = "plop"
version = "0.1.0"
authors = ["Plop<EMAIL_ADDRESS>
[dependencies]
clap = "2.9"

src/main.rs :

extern crate clap;
use clap::App;

fn main() {
    App::with_defaults("plop").get_matches();
}

cargo run -- --help
     Running `target/debug/plop --help`
Plop 2.14.0        <-------------------
Kevin K<EMAIL_ADDRESS><--------

USAGE:
    plop

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

After a couple of iterations I've approached this from a different angle: what if instead the above src/main.rs looked like this:
#[macro_use]
extern crate clap;
use clap::App;

fn main() {
    defaulted_app!("plop").get_matches();
}

Name to be improved, of course/

@nabijaczleweli perhaps. I'm not against that, but also don't want to confuse people with the clap_app! macro, or macro builders.
At this point, I'm also not really against simply deprecating App::with_defaults as broken until we can decide something more elegant during the v3 build up. Because I think the with_defaults doesn't add a whole ton, and can be very easily worked around by using crate_version! and crate_authors!

App::with_defaults() in its current state has 100% no chance of working and tbh I don't really see its value, either.

Agreed.

Darn it, I guess if it doesn't work it doesn't work.

Yeah its deprecated as basically unfixable at this time. :(
On Oct 28, 2016 7:26 AM, "Roman A. Taycher"<EMAIL_ADDRESS>wrote:

Darn it, I guess if it doesn't work it doesn't work.
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub
https://github.com/kbknapp/clap-rs/issues/638#issuecomment-256897413,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AGntttf68UczkpzFhPLif23H984eG0U1ks5q4dvNgaJpZM4Ju5rb
.

It's because it pulls the info from the compilation of the clap-rs crate right?
And a macro like @nabijaczleweli proposed would work, right?
I was wondering if I could start a ticket to discuss re-design or if there's another place I could put it(forum?)?
I had some other ideas, like possibly putting CARGO_PKG_DESCRIPTION in about.

@rtaycher I'm all for opening an issue/PR which either fixes this, or discusses new ways to accomplish it. There are just other issues which are are a higher priority for myself right now, but if you'd like to open the discussion and try out some fixes I'm all for it :+1:

#778


Documentation: Running Kata CI offline

Running Kata CI offline
Given that the Kata CI can take time to run and flag errors it will save developers time to run the CI offline.
This can be done easily using ccloudvm in a non destructive way. Here are some early instruction
Setup ccloudvm
For more info https://github.com/intel/ccloudvm
go get github.com/intel/ccloudvm/...
$ ccloudvm setup

Create a ccloud fedora VM
ccloudvm create fedora28 --cpus 8 --disk 40 --mem 8192 --name kata-ci

Log into the VM and set it up for CI
ccloudvm connect kata-ci

sudo gpasswd -a $USER kvm
sudo dnf -y update
sudo dnf install -y git gcc dnf-plugins-core patch || ( sudo apt-get update -y && sudo apt-get install -y gcc git patch)
sudo mkdir /etc/docker
curl -LOk https://dl.google.com/go/go1.11.1.linux-amd64.tar.gz
sudo tar -xf go1.11.1.linux-amd64.tar.gz -C /usr/local
sudo sync
rm -rf go1.11.1.linux-amd64.tar.gz
mkdir -p ~/go
echo export GOPATH=~/go >> .bashrc
echo export GOROOT=\"/usr/local/go\" >> .bashrc
echo export PATH=\"\$PATH:\$GOROOT/bin\" >> .bashrc
echo export KUBECONFIG=/etc/kubernetes/admin.conf >> .bashrc
source .bashrc
go get -d github.com/kata-containers/tests
pushd go/src/github.com/kata-containers/tests/
export CI=true
.ci/setup.sh
sudo -E gpasswd -a $USER docker

Run the CI on your code
cd ~/go/src/github.com/kata-containers/runtime
export PATH=${GOPATH}/bin:/usr/local/go/bin:/usr/sbin:${PATH}
export CI=true
.ci/run.sh

/cc @chavafg @GabyCT @devimc please feel to correct/amend the issue directly.

@mcastelino , I will try to reproduce these steps

@GabyCT we also ensure we should be able to run the CI multiple times. So if we need to do any clean between runs we should document it.

@mcastelino - that could be tricky - a CI run can mess up your system (by that I mean, if a test fails it is possible for it to leave a container, docker or some other item in a state that is hard to clean up - think hung up container or runtime etc.) For the bare metal servers we have a set of scripts at https://github.com/kata-containers/tests/blob/master/.ci/lib.sh#L291 that try to clean the machine up, by removing all relevant items - but - you might not want to do that to your dev desktop for instance. So, just beware a little ;-)

@mcastelino , currently I am doing the setting and then I will run the tests to see possible failures and if we can run them multiply times, however, from the steps above,  I will modify the following:
After creating the ccloudvm fedora VM, I will add a note saying that sometimes you need to do
sudo gpasswd -a $USER kvm

I will add this as I got the error of failed to initialize KVM: Permission denied
Then for the setup of the CI, I will modify:
sudo dnf -y update

Now, we do not need to install manually docker as this will be install (with the version that we are supporting) by just simply running the .ci/setup.sh from the test repository (https://github.com/kata-containers/tests/blob/master/.ci/setup.sh#L126 and https://github.com/kata-containers/tests/blob/master/cmd/container-manager/manage_ctr_mgr.sh#L83) , so we can remove those steps. Also, I will do the export CI=true before running the .ci/setup.sh.

@mcastelino - that could be tricky - a CI run can mess up your system (by that I mean, if a test fails it is possible for it to leave a container, docker or some other item in a state that is hard to clean up - think hung up container or runtime etc.) For the bare metal servers we have a set of scripts at https://github.com/kata-containers/tests/blob/master/.ci/lib.sh#L291 that try to clean the machine up, by removing all relevant items - but - you might not want to do that to your dev desktop for instance. So, just beware a little ;-)

@grahamwhaley exactly the reason why this will run in a ccloudvm. So the user can run the CI non destructively.

@mcastelino , I can not run properly the docker tests, I am getting the following error
$ docker run -ti --runtime kata-runtime busybox sh
docker: Error response from daemon: OCI runtime create failed: Failed to check if grpc server is working: rpc error: code = Unavailable desc = transport is closing: unknown.

I am going to try to use an ubuntu image. @chavafg have you ever try to running the tests using ccloudvm?

Looks like this recipe is ripe for converting into a one-liner like we have for the automated install:

https://github.com/kata-containers/documentation/blob/master/install/installing-with-kata-manager.md

All the user would need to do is specify the name of the particular Kata repo they want to test (say runtime):
$ bash -c "$(curl -fsSL $url) runtime"

We'd need to determine golang version without hard-coding though so the script should query https://github.com/kata-containers/runtime/blob/master/versions.yaml.

@mcastelino , I run the ccloudvm using ubuntu, all the functional tests passed, only one of docker integration failed, CRI-O all passed, however, kubernetes only one failed and shimv2 failed (I could not run them).

I just ran this on a fedora-28 machine and all the tests seem to pass and complete without issues. This is what i see at the end of the run, sharing here to make sure that is what is expected.
Install Openshift
Install Openshift Origin
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   648    0   648    0     0   1417      0 --:--:-- --:--:-- --:--:--  1417
100  181M  100  181M    0     0  2699k      0  0:01:08  0:01:08 --:--:-- 3085k
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
tar: Ignoring unknown extended header keyword 'LIBARCHIVE.xattr.security.selinux'
Openshift installed successfully
Disable systemd-journald rate limit
Drop caches

I also saw a note that says  that k8s is only tested on ubuntu.
Install Kubernetes components
Currently this script only works for Ubuntu. Skipped Kubernetes Setup

it would be nice to test this on fedora and others distros too.

@GabyCT @jodh-intel @mcastelino what are the next steps here? i have been using these steps consistently to test things locally and they work fairly well. Should we call this an experimental try at your own risk doc?

@ganeshmaharaj - sounds good to me. Once this is documented, my only concern is how we ensure it continues to work. We either have a separate CI test for offline mode that we run periodically and/or we add a big red warning as you're suggesting. Let's start with a doc (that conforms to https://github.com/kata-containers/documentation/blob/master/Documentation-Requirements.md) plus a nice juicy warning ;)


Extend gslb object print columns with HOSTS

For the sake of readability, it would be good to extend gslb CRD print columns with HOSTS column,
similar to the one displayed for an ingress object in kubectl output, e.g:
❯ kubectl get gslb -n test-gslb test-gslb
NAME        STRATEGY    GEOTAG   HOSTS
test-gslb   roundRobin  eu       notfound.k8gb-test-nonprod.gslb.test.com,unhealthy.k8gb-test-nonprod.gslb.test.com,roundrobin.k8gb-test-nonprod.gslb.test.com

Isn't it done by @ytsarev already?

@k0da from what I see, it has been done for STRATEGY and GEOTAG only:
https://github.com/k8gb-io/k8gb/blob/master/api/v1beta1/gslb_types.go#L69-L70

@somaritane right.
https://github.com/k8gb-io/k8gb/pull/425#issuecomment-812684552

btw. the print column can also have a priority number assigned to it so that those with some high values are not displayed by default (i don't know the threshold from top of my head), but one can still show them by -o wide.

the closest I was able to get with the standard print column approach + simple json path was this
    - jsonPath: .spec.ingress.rules[*].host
      name: hosts
      type: string

get gslbs.k8gb.absa.oss test-gslb-failover
NAME                 STRATEGY   GEOTAG   HOSTS
test-gslb-failover   failover   us       failover.cloud.example.com

However, there were more hosts present on the gslb, it displays only one.
k get gslb test-gslb-failover -ntest-gslb -o=jsonpath="{.spec.ingress.rules[*].host}"
failover.cloud.example.com foo.bar blahbla.com

or
k get gslb test-gslb-failover -ntest-gslb -o=jsonpath="{range .spec.ingress.rules[*]}{.host},{end}"
failover.cloud.example.com,foo.bar,blahbla.com

Standard approach would be to duplicate some stuff from .spec under .status that will be consumed by the printer columns simple jsonpath. Because these doesn't support ranges or any other form of iteration.

Interesting, I wonder how ingress printer does that?
because I don't see hosts duplicated in status for ingress, but it displays all hostnames for simple k get

@somaritane good question, but I don't have an answer ;) I think that Ingress is treat differently than CRDs (no CRD manifest, perhaps some better love in kubectl)


Mumble Crash Error

I've been having this issue for months now, I have reinstalled my entire computer many times GTA V, FiveM, even went as far as buying a new audio output device!
An error caused FiveM to stop working. A crash report is being uploaded to the FiveM developers.
Stack trace:
0x0
voip-mumble.dll!MumbleAudioOutput::InitializeAudioDevice (0x26e) (MumbleAudioOutput.cpp:1217)
voip-mumble.dll!MumbleAudioOutput::ThreadFunc (0xd2) (MumbleAudioOutput.cpp:1046)
voip-mumble.dll!::operator() (0x101) (MumbleAudioOutput.cpp:202)
voip-mumble.dll!std::invoke< > (0x8) (type_traits:1596)
voip-mumble.dll!std::thread::_Invoke<std::tuple< >,0> (0x3b) (thread:43)
ucrtbase.dll!beginthreadex (0x141)

@FrazzIe

@FrazzIe

im having this same problem rn, and I cant find a fix.

@FrazzIe did you manage to find a fix? i've also reinstalled GTA V and Five M many times but found no solution.


Feature Request - Custom path for models folder

It is possible to specify custom path for migrations folder via --path flag. It would be neat if there was a way to specify custom path to models folder, when creating model with soda generate model.

@GrigoriyMikhalkin @stanislas-m In case the folder is specified, i get that that model should be generated in the specified folder, but should the folder name be used as the name of the package as well?

@paganotoni That's a legit question. :) I'd say yes?


Refactor ZoneUtils class

Refactoring in a way that only uses StringUtils.split

Codecov Report

Merging #1732 into master will decrease coverage by -0.02%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #1732      +/-   ##
==========================================
- Coverage   75.21%   75.19%   -0.02%
==========================================
  Files         199      199
  Lines        6205     6200       -5
  Branches      777      777
==========================================
- Hits         4667     4662       -5
- Misses       1198     1199       +1
+ Partials      340      339       -1

Impacted Files
Coverage Δ

...amework/cloud/netflix/ribbon/eureka/ZoneUtils.java
66.66% <100%> (+4.16%)
:white_check_mark:

...a/server/EurekaServerInitializerConfiguration.java
72.41% <ø> (-6.9%)
:x:

Continue to review full report at Codecov.

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How to publish angular2 webpack and lumen application to hostgator

I find some demo and want to make with that angular2 application. I start with this demo which use angular2, webpack and lumen as backend api. I see that I can run it localy when run
php artisan run

but I can't find the way how to run it in shared hosting (like hostgator). Did maybe anybody know how to do that?

If someone need it. Publish all files included public files when run webpack but before change in env file that APP_ENV=production and all works in public servers. TNX to all!


WIP: Remove MDAnalysis

Added 4 parsers (PDB, LAMMPS, XYZ, GROMACS)
Added 4 savers
Replaced UniverseManager with ViewerMemoryManager to avoid MDAnalysis dependency
Added command line file argument
Updated builder for gamma graphyne (graphyne-1). Other graphyne types and builders still depend on MDA.

Hi @fyffep,
Thank you for creating the PR.
Next time, please do not create a PR from your master branch. Create different branch.
Before I look into the code, I found these bugs:

Features such as graphene, single-wall and multi-walls do not work. This is the error when I open them:
"AttributeError: 'Viewer3D' object has no attribute 'load_universe'"

In Graphyne feature, only grahydine_1 works, the rest (such as grahydine_2, twin-graphene) have errors:
"UnboundLocalError: local variable 'builder' referenced before assignment"
"AttributeError: 'NoneType' object has no attribute 'particle_resolution'"
"The style" section does not work."

I think this happened since you didn't connect the rest of features.

In delete atoms, only atoms are deleted, the bonds that are connected to the atom will not be deleted. You can see the GIF file and compare it with latest version:

Delete bond also does not work.
I understand this is WIP PR. I wanted to make sure you are aware these bugs :)
I start look into the code.

@nasimanousheh Thanks for your comments. I used master so that the PR would not be inundated with your own recent changes. Bond deletion was fixed on a different branch specialized for the delete key shortcut. I think I will open as a separate PR after this one. Lastly, the rest of the graphyne builders have been implemented but the other builders will take time.

I updated this PR with my recent changes and will continue to use it, but future PRs will not use my master branch.


[BUG] grav-tabs-state generates a 403 error with mod_security

The mod_security configuration in Apache, on the CWP7.admin, generates a 403 access denied error when running Grav CMS:

[Thu Mar 21 15:40:47.967502 2019] [:error] [pid 21727:tid<PHONE_NUMBER>46304] [client <IP_ADDRESS>:57900] [client <IP_ADDRESS>] ModSecurity: Access denied with code 403 (phase 2). Pattern match "([\~\!\@\#\$\%\^\&\\(\)\-\+\=\{\}\[\]\|\:\;"\'\\xc2\xb4\\xe2\x80\x99\\xe2\x80\x98\`\<\>].?){8,}" at REQUEST_COOKIES:grav-tabs-state. [file "/usr/local/apache/modsecurity-owasp-old/base_rules/modsecurity_crs_41_sql_injection_attacks.conf"] [line "157"] [id "981172"] [rev "2"] [msg "Restricted SQL Character Anomaly Detection Alert - Total # of special characters exceeded"] [data "Matched Data: \x22 found within REQUEST_COOKIES:grav-tabs-state: {\x22tab-content.options.advanced\x22:\x22data.content\x22,\x22tab-content.options\x22:\x22data.content\x22,\x22tab-content.options.advanced.blog\x22:\x22data.options\x22}"] [ver "OWASP_CRS/2.2.9"] [maturity "9"] [accuracy "8"] [tag "OWASP_CRS/WEB_ATTACK/SQL_INJECTION"] [hostname "xxxxxxxx.com"] [uri "/favicon.ico"] [unique_id "XJOwf0cQATwA6mgjE8O7AwAAANc"], referer: http://xxxxxxxx.com/

This error only happens when visiting the website a second time, making it very hard to solve.
I manage to solve the issue setting up a special omission to the mod_security rule for grav, but this is only posible if you have access to the apache configuration.
I think this must be solved in the cookie.

That cookie is, as the name states, to remember and restore the active tab in admin.
Of course nothing malicious can happen with that nor is to be considered insecure but I get the annoyance of it being logged.
The value I’m storing is in json format, do you think base64 encoding it all would prevent mod security from yelling?

Of course nothing malicious can happen with that nor is to be considered insecure but I get the annoyance of it being logged.

Maybe I'm not being clear: the entire site —admin and frontend— gives an error 403 (access denied).
ModSecurity: Access denied with code 403
I was able to reproduce the error in the same server with two different installations of Grav. Readers from Argentina and Brazil got in touch with me to tell me that the website was down.

The value I’m storing is in json format, do you think base64 encoding it all would prevent mod security from yelling?

Maybe, look at the pattern match. I think it does not like the special characters
````Pattern match "([\\~\\!\\@\\#\\$\\%\\^\\&\\\\(\\)\\-\\+\\=\\{\\}\\[\\]\\|\\:\\;\"\\'\\\xc2\xb4\\\xe2\x80\x99\\\xe2\x80\x98\\`\\<\\>].?){8,}


Language Server Crashing and VS Code is hanged when opening Laravel 8 project with PHP 8.0

In ububtu 18.04 64 bit system, when opening a Laravel 8 project in PHP 8.0, the PHP language server is getting crashed and the whole system is getting hanged.
To reproduce the issue, you need to check in ubuntu 18.04 system. Install PHP 8.0 and enable it. Setup a Laravel 8 project. And open it. Open the terminal in VS code. You may not get the time to open it. But if you hurry then you can open the terminal. In the PROBLEMS tab there it is showing 4k+ issues. Then in OUTPUT tag it is showing some message, somethig is exited. Then you can't do anything.
It should work like normal. The extension is working perfect in PHP 7.4 but when u enabling PHP 8.0 then you are doomed.
Platform and version
OS: ubuntu 18.04
PHP: 8.0
Laravel: 8
Intelephense version: v1.7.1

If you are lucky and your PHP isn't new enough (like not 8.1 that doesn't work) you can go to the plugin folder in ~/.vscode/extensions and run compose update that should make it work with 8.0.
https://github.com/felixfbecker/php-language-server/issues/779