Create new Gene2Phenotype evidence table in rewrite version

On the evidence page in the rewrite, can we please create a new data table that displays the Gene2Phenotype evidence data?
Example GraphQL API query
BRAF and Cardiofaciocutaneous syndrome
Data table

Data table column
Disease/phenotype
Reported disease/phenotype
Allelic requirement
Confidence
Literature

GraphQL API field
evidences.rows[x].disease.name
evidences.rows[x].diseaseFromSource
evidences.rows[x].allelicRequirement
evidences.rows[x].confidence
evidences.rows[x].literature

Sample data
Cardiofaciocutaneous syndrome
Cardiofaciocutaneous syndrome
monoallelic
confirmed
1 publication

Within the data table, can we please do the following?

Link the value in the "Disease/phenotype" column to the relevant profile page in the Platform
Transform the string value in the "Reported disease/phenotype" category from ALL CAPS to Sentence case
Link the value in the "Confidence" column to the gene search results page on the Gene2Phenoytpe portal using the following construct - https://www.ebi.ac.uk/gene2phenotype/search?panel=ALL&search_term= + evidences.rows[x].target.approvedSymbol (e.g. confirmed)
In the "Literature" column, please show the number of publications and link the value to the EuropePMC search results page using the following construct, assuming evidences.rows[x].literature returns an array of PubMed IDs - https://europepmc.org/search?query= + EXT_ID: + evidences.rows[x].literature[y] + EXT_ID: + evidences.rows[x].literature[y] ... and so on (e.g. 7 publications)

QC checks

GNAS (ENSG00000087460) and cataract (EFO_0001059)
SMPD1 (ENSG00000166311) and Niemann-Pick disease type B (Orphanet_77293)
ERCC2 (ENSG00000104884) and skin disease (EFO_0000701)

The graphql example shows clinGen as data source. Should that be gene2phenotype?

Yes @javfg, my apologies! I've updated the query here

The work on #1226 will provide a literature field as well for this datasource (null at the moment).
Feel free to include it, even if the API returns nulls at the moment.

Will do - thanks @d0choa!
@javfg I have updated the table to add the literature field, but it will be null until the work on #1226 is complete

With the latest iteration of the GraphQL API, can we please make a small adjustment to the data table?

[ ] Update "Allelic requirement" column as previously, the field was a string evidences.rows[x].allelicRequirement; however, it is now an array called evidences.rows[x].allelicRequirements with an "s". Within the column, if there is only one entry in evidences.rows[x].allelicRequirements, please display the string. If there are two or more entries in evidences.rows[x].allelicRequirements, please list the entries in an unordered list

As discussed:

[ ] Move reported disease/phenotype as tooltip in disease column. The tooltip content would be “Reported disease or phenotype:\n{diseaseFromSource}”

On the latest API there is a minor change in this widget regarding studyId. Example GraphQL query.
This minor change implies that we might need to do some small fixes:

[ ] Add a new column named Panel containing the content of studyId
[ ] The link that currently is built in the confidence column will be moved to the Panel column and include the panel on it:
https://www.ebi.ac.uk/gene2phenotype/search?panel=+ studyId + &search_term= + target.approvedSymbol -> Example

[ ] can we put the new Panel column between the Allelic requirement and the Confidence columns? It will help with consistency with other tables.

This was fixed in PR 271 (merged) https://github.com/opentargets/platform-app/pull/271


build: upload arm64 macOS files with different filenames

This is necessary for my solution https://github.com/replayio/backend/pulls?q=is:pr+is:open+sort:updated-desc to work


WorldWind getScreenCapture returns blank PNG

This currently requires a modification to how the webgl context is initialized in WorldWind
The preserveDrawingBuffer flag must be enabled when creating the context.


ENH: faster linear_sum_assignment for small cost matrices

For small cost matrices, linear_sum_assignment spends more time on input validation and bookkeeping than on finding the solution. Here I have moved some of this code into the C module.
Here is a benchmark:

Additional information

This may make linear_sum_assignment more attractive for some applications. There is some discussion in these benchmarks.

Thanks @pmla, merged.

Thanks for the review and assistance @peterbell10


Buid failed on windows with cuda

When enabling cuda on Windows it failed with the error
error: could not find native static library `onnxruntime`, perhaps an -L flag is missing?

Although I already link it. seems like it doesn't produce libonnxruntime?
Or maybe it produce it in different foldeR?
Action run:
https://github.com/thewh1teagle/sherpa-rs/actions/runs/9881675671/job/27292952044
Build options:
https://github.com/thewh1teagle/sherpa-rs/blob/main/sys/build.rs
You can see that without cuda it build sueccessfuly.
Another action with debug steps:
https://github.com/thewh1teagle/sherpa-rs/actions/runs/9882452000/job/27295323663
You can see that it produce onnxruntime.lib but in the nvidia action there it's not there.

To give you an idea the difference between shared and static lib, CPU enabled and cuda enable lib,
CPU (static)
ls -lh onnxruntime-win-x64-static_lib-1.18.1/lib

-rw-r--r-- 1<PHONE_NUMBER>21 266M Jul 10 07:21 onnxruntime.lib

CPU (shared)
ls -lh onnxruntime-win-x64-1.18.1/lib

-rw-r--r-- 1 root root  11M Jun 27 18:24 onnxruntime.dll
-rw-r--r-- 1 root root 2.1K Jun 27 17:49 onnxruntime.lib
-rw-r--r-- 1 root root 274M Jun 27 17:53 onnxruntime.pdb
-rw-r--r-- 1 root root  22K Jun 27 18:24 onnxruntime_providers_shared.dll
-rw-r--r-- 1 root root 2.3K Jun 27 17:41 onnxruntime_providers_shared.lib
-rw-r--r-- 1 root root 404K Jun 27 17:41 onnxruntime_providers_shared.pdb

GPU (shared)
ls -lh  onnxruntime-win-x64-gpu-1.18.1/lib

-rw-r--r-- 1 root root  12M Jun 27 18:31 onnxruntime.dll
-rw-r--r-- 1 root root 2.8K Jun 27 18:09 onnxruntime.lib
-rw-r--r-- 1 root root 274M Jun 27 18:11 onnxruntime.pdb
-rw-r--r-- 1 root root 392M Jun 27 18:32 onnxruntime_providers_cuda.dll
-rw-r--r-- 1 root root 2.0K Jun 27 18:15 onnxruntime_providers_cuda.lib
-rw-r--r-- 1 root root 126M Jun 27 18:15 onnxruntime_providers_cuda.pdb
-rw-r--r-- 1 root root  21K Jun 27 18:30 onnxruntime_providers_shared.dll
-rw-r--r-- 1 root root 2.3K Jun 27 17:42 onnxruntime_providers_shared.lib
-rw-r--r-- 1 root root 404K Jun 27 17:42 onnxruntime_providers_shared.pdb
-rw-r--r-- 1 root root 730K Jun 27 18:31 onnxruntime_providers_tensorrt.dll
-rw-r--r-- 1 root root 2.1K Jun 27 17:45 onnxruntime_providers_tensorrt.lib
-rw-r--r-- 1 root root  18M Jun 27 17:45 onnxruntime_providers_tensorrt.pdb

If you want to use CUDA enabled onnxruntime for Windows, you need to use BUILD_SHARED_LIBS=ON.
https://github.com/k2-fsa/sherpa-onnx/blob/5a2603ff5c4315a77c7b03d88698eadbcf648d56/cmake/onnxruntime.cmake#L97
    else()
      # for 64-bit windows (x64)
      if(BUILD_SHARED_LIBS)
        message(STATUS "Use dynamic onnxruntime libraries")
        if(SHERPA_ONNX_ENABLE_GPU)
          include(onnxruntime-win-x64-gpu)
        else()
          include(onnxruntime-win-x64)
        endif()
      else()
        # static libraries for windows x64
        message(STATUS "Use static onnxruntime libraries")
        if(CMAKE_BUILD_TYPE STREQUAL Release)
          include(onnxruntime-win-x64-static)
        elseif(CMAKE_BUILD_TYPE STREQUAL Debug OR CMAKE_BUILD_TYPE STREQUAL RelWithDebInfo OR CMAKE_BUILD_TYPE STREQUAL MinSizeRel)
          include(onnxruntime-win-x64-static-debug)
        else()
          message(FATAL_ERROR "Support only CMAKE_BUILD_TYPE being Release, Debug, RelWithDebInfo, or MinSizeRel. Given: ${CMAKE_BUILD_TYPE}")
        endif()

You can try to use static lib for sherpa-onnx while dynamic lib for cuda-enabled onnxruntime, but we have not tried that.
You need to update the above onnxruntime.cmake to do that.


Does shaka support playback of trickmode frames?

Have you read the Tutorials?
yes
Have you read the FAQ and checked for duplicate open issues?
yes
What version of Shaka Player are you using?
2.5.10 and tested in latest version(3.0.5)
Please ask your question
We have Adaptation set for trickmode included in the dash manifest  to enable thumbnails and when we try to playback the mpd file, shaka does not seem to download the keyframe segments. So does shaka support trick mode keyFrame playback ?
If shaka has the support already, then what is the configuration or step that has to be followed to enable the playback of keyFrames ?
Please see the below trick mode AdaptationSet used in dash manifest
<AdaptationSet maxHeight="144" maxWidth="256" mimeType="video/mp4" id="7" segmentAlignment="true" startWithSAP="1">         <EssentialProperty         				schemeIdUri="http://dashif.org/guidelines/trickmode"         				value="1"/>         <SegmentTemplate duration="6000" initialization="$RepresentationID$/i-frame/init.mp4" media="$RepresentationID$_184201/segment_$Number$.m4s" startNumber="0" timescale="1000" />         <Representation bandwidth="81216" codecs="avc1.64001F" height="144" width="256" maxPlayoutRate="10" id="3mbps_i-frame.idx~i-frame~481~avc" scanType="progressive" />     </AdaptationSet>

Yes we support it, but only during trick-mode playback.  You enable this with player.trickPlay(speed).  (Also, is this the same as #2949?)
Also, the value of the trickmode property is the AdaptationSet@id property that this is associated with. We can only play that trick mode track when we are playing the associated AdaptationSet streams.

Yes, Thanks for the quick reply
On Mon, 2 Nov 2020, 11:51 pm Shaka Bot<EMAIL_ADDRESS>wrote:

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questions? Can we close the issue?
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Create a Git Pre Commit Hook to run ESLint

Let's create a Git Pre Commit Hook to run ESLint in our NodeCloud repos to avoid ourselves pushing codes with lint errors.
Follow these steps:

Create a file in .git/hooks as pre-commit
Add these contents https://gist.github.com/agentmilindu/b61f4f8e23742d7cc394290d8a8c2378
chmod +x .git/hooks/pre-commit

Image Source: http://www.sterlinghamilton.com/git-hook-pre-commit-for-debug-comments/

Commits with no lint errors

Commits with lint errors

For others: To know more about creating git hooks, refer this-
https://scotch.io/tutorials/using-git-hooks-in-your-development-workflow


Fix header links on Github Pages

Links were not working when navigating from Contents ➡  Header sections and vice versa. Just added the correct id attributes to the headers so <a href="blah"> link tags worked correctly.

This page is supposed to be updated by an external tool, but it's been a while since the last update.
The index.html you changed is outdated by several weeks.
@bnb What should we do about this?

@darahak I think i'm ready to disable the external tool. It's not being maintained well enough and it's hard for us to update. Are you +1 for that? 🤔

@bnb Sure, go ahead :+1:
Hopefully, we'll find a better solution.

Closing this since the website will be disabled.


PDX blacklist

We have made a (rather trivial but fully reproducible) VCF blacklist of artifactual PDX variants by aligning a couple of mouse strains to the human reference using bcbio. The resulting VCF can be used by vcfanno to mark such artifactual variants in PDX samples that remain (due to high human-mouse homology) even after disambiguation. Perhaps it is of interest to others as well.
Paper: https://www.biorxiv.org/content/early/2017/08/25/180752
Repository: https://github.com/MaxSalm/pdxBlacklist

Sven-Eric -- nice, thank you for sharing this. This would be great to integrate for PDX runs and I know @mjafin should have a lot of interest. Sorry if I missed this, but are the VCFs publicly available in addition to the pipeline? Thanks again for this work.

Hi Sven-Eric, this is so awesome.

+1

Sven-Eric, just double checking, have you seen these variants in multiple captures (or other confounders) because different captures have different artefacts?

No, it's really a rather basic approach that just looks at publicly available sequencing data from mice lines (some of which are used for PDX) to generate variants that are being called from their alignment to the human reference.
The data mostly is from various WES kits but we also have WGS for some of the most important lines. However, we did not include the latter here due to size.
I agree that there are obvious ways to improve the product much and more like a mini-gnomad for artifactual mice variants in humans, but that wasn't in they budget for this iteration.
A next step could be to make VCFs for specific caller+reference combinations and add vcfanno definitions to have these annotations automatically added to disambiguation variant calls. Would that make sense to you, @mjafin, or would you recommend another course of action?

A next step could be to make VCFs for specific caller+reference combinations and add vcfanno definitions to have these annotations automatically added to disambiguation variant calls.

IMO that would be a great start. One of the lines of research at my institution relies heavily on PDX, and this would help a lot in reducing the noise.

Great; I could contribute VCFs for caller+reference combinations of interest. Anyone volunteering for writing the vcfanno config files?

Can do.

We're on this and I'll report back once we're done.


Use graphp package

Can you also tag a new version with this change, please?

@sandrokeil Thank you for looking into this! I've recently filed https://github.com/graphp/graphviz/pull/40 to show what is required to update this to the upcoming graphp/graph package. This can probably be used as a base for this PR as well. I will look into this again once the graph package API is stable.

@clue Any news on this?

We've made some significant progress with GraPHP, but it's API changes are still work in process. Accordingly, this PR will need an update for the improved APIs.
As much as I'd like to commit to specific date, I can only say that we will get to this feature as soon as time permits.
If you want to help sponsor this feature, feel free to reach out :+1:


Enabling lto and codegen-units = 1 breaks zeroizing key::rschnorr::test::sk_zeroed test

It seems that zeroizing for schnorr keys breaks when
[profile.release]
lto = true
codegen-units = 1

are enabled in the root cargo. We have to understand this and see whether we want to ban LTO.

This isn't relevant anymore since we don't use tari crypto anymore. However, we have to keep in mind that LTO can lead to eliminating zeroization.


Implement Full Metrics Options

Proposal
Maesh should provide full metrics options based on the Traefik Proxy.
This would require the following metrics providers:

[x] Prometheus
[ ] Datadog
[ ] InfluxDB
[ ] StatsD

much needed feature, it could be nice to get traditional metrics such as number of backend endpoints per service, open connections per backend, avg latency per backend, status codes per backend, session rate per backend, retry count per backend.
we are using maesh almost from the launch, but we fail to see a big benefit over the native kube-proxy besides the retry attempts and basic circuit breaker.


MM-37455: fix misplaced channel header info popover

Summary
conditionally adds the global header height value to the channel header info topOffset value (if global header is enabled)
Ticket Link
MM-37455
Screenshots

before
after

Release Note
NONE

Thanks @michelengelen
Another instance where the announcement banner is causing an issue. I can file separately. Without the banner, channel header is positioned correctly.

@jgilliam17 that is strange... it should calculate the offset automatically (this was in place even before my PR. I will have a look locally and try to resolve it here.

Hi @jgilliam17 I found the problem with and fixed it accordingly. Now the Popover should be placed correctly with enabled and disabled banners.

/cherry-pick cloud

Cherry pick is scheduled.


Window not opening after unlock from sleep

Tested versions

Reproducible in 4.2 stable, 4.2.1 stable, 4.3-dev2 (All non-C# builds)

System information
OS  Pop!Os 22.04 LTS  GPU  RTX 3060M  CPU  Intel 12700h
Issue description
The game play window instantly closes upon attempting to run in the editor after unlocking from sleep / suspend.
Quit to project list does not work either after unlock, as it just closes the editor without opening the project list.
Reloading the project also just closes the editor window without opening anything again.
Steps to reproduce
In Pop!Os, Open a game in the editor,
put the device in a sleep cycle, try to run the game after unlocking from sleep, trying to quit to project list, or reloading the project.
Minimal reproduction project (MRP)
WindowBugTest.zip

Thanks for the report! Consolidating in https://github.com/godotengine/godot/issues/52738. This is a NVIDIA issue we can't fix on our end without large sweeping changes. All other applications using Vulkan on Linux run into the same issue unless they can restart their rendering context entirely in a clean manner (preferably without losing any data).
You may try following the advice on this page at your own risk: https://wiki.archlinux.org/title/NVIDIA/Tips_and_tricks#Preserve_video_memory_after_suspend

Duplicate of #52738 which is documented here:
https://docs.godotengine.org/en/stable/tutorials/troubleshooting.html#the-editor-project-freezes-or-displays-glitched-visuals-after-resuming-the-pc-from-suspend


Table Format

I've been reviewing this sink for usage in our applications. One big issue we have identified is that the chosen scheme for the rowkey messes up the order in table storage when lots happens at the 'same' time (also when using batching). I have made the modifications to the sink by adjusting the code in this repository, would you be interested in PR for this or should I keep this a separate sink (since the table format changes) and package it myself?

Hi @bjorncoltof - it sounds like it'd be a possible inclusion here, but others are more familiar with the format than I am. If you can post a PR it's definitely got a good chance!
Thanks for the heads-up, either way :+1:

:+1: to this - it is annoying

This issue has been solved by #9 for us.


A word of thank you

Hey James,
This not a bug or feature request, this is a thank you. The components in this library are among the easiest I've ever used and so far everything works amazingly well.
Happy new year!

Thanks for the kind words @jordyvandomselaar! Feel free to post in #277 with what you're working on, and keep spreading the word. It's gonna be a big year for RMWC, excited about whats coming down the pipe.


human3.6 mosh_data

Could you please provided the mosh_data including pose and shape parameters separately? It is critical to reproduce the best performance mentioned in your paper. Thanks.

Unfortunately, I would like to but I cannot due to legal reasons that are beyond my control. Please obtain permission from the authors of Human3.6M who have the rights. Thanks.

@junhaozhang98  你知道如何得到H3.6m泥参数现在？如果你知道，请告诉我。谢谢！！！


Sample sheet support for new SampleContext section

This is the first piece of the new mulit-project plate support.  It adds a new kind of sample sheet that contains a new SampleContext section holding explicit details on "technical samples" in the sheet and what project(s) they belong to.

Reviewed the latest changes and additions to support replicates, mainly to ensure I know what's going on. For what it's worth, I approve and I apologize for my untimeliness.


JSON LD Contexts in JWT VCs

Currently JSON LD contexts in JWT VCs are required, but that doesn't clearly enforces contexts beyond Verifiable Credential data model. In simple words https://www.w3.org/2018/credentials/v1 is required but any additional contexts for custom properties inside credential subject can be optional.
Example: https://github.com/decentralized-identity/jwt-vc-presentation-profile/pull/52/files#diff-76909e03d654c1deb30b8258103972c9fa20ccb9411e72f0dc2436151c70ddc9R2-R4
Objective of this task:
For JWT VCs,

[ ] make VC data model context as required and other contexts can be optional
[ ] If strict validation option enabled while parsing JWT VCs, then JSON LD  data model should be performed

@mishasizov-SK

PR: https://github.com/hyperledger/aries-framework-go/pull/3357


Feature request: action nothing

Hi,
Will be great if you will add a "nothing" action on this resource.
Thanks

Disregard this, was a bag setting.


Dev -> Main

Action console issues fix: Showing action console when new action comes on the frontend
Adding separate classes for resource manager and using the same inside tools
SuperCoder: New tools for Spec, Code, Test
Fixing the breaking unit tests and adding it as part github actions
Adding docs for slack and stable diffusion

I can not have all the extra stuff on this app and or the people that have added code to this. If I have to I’ll change my route
Sent from my iPhone
On Jun 22, 2023, at 9:35 AM, I’m @.***> wrote:

Merged #447https://github.com/TransformerOptimus/SuperAGI/pull/447 into main.
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Will the docs show previous versions of the task or only the current version?

Is there a way in the docs to see the previous task version or will they only ever publish the current task version?

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

ID: b03d67d0-8738-72e6-dbe7-324c1784d4fc
Version Independent ID: bbb4d774-cd98-3ecb-7ccf-5f49e6f2b425
Content: Download Pipeline Artifact task - Azure Pipelines
Content Source: docs/pipelines/tasks/utility/download-pipeline-artifact.md
Product: devops
GitHub Login: @steved0x
Microsoft Alias: midenn

@jafin Thank you for the question. There are some issues with older versions of the tasks and will be deprecated in the future. As of right now, we are only supporting the current version of a task. If you have an more questions or feedback. Feel free to reach out!


Fix a typo in agent.yml

Got it, right now the comparison treats 7.48.0-rcx as older than v7.48.0, sounds like it's the expected behavior

Yes It is, we even have a test that ensure it : https://github.com/DataDog/system-tests/blob/main/tests/test_the_test/test_version.py#L43


Create search and filter bar in the projects page

[ ] Search bar at the top of the page, that does a string search for project name, description etc.
[ ] Filter UI that filters (and potentially sorts) the project according to tags, collaborators, last updated etc.

BLOCKED BY #2

Closing all BETA-RELEASE till after launch.


THANK YOU

I came across this here, and it just saved me hours of untold grief. The web app is particularly nice. Thank you! You should add a "buy me a coffee" link.

I also came across this here after so many annotations I made on a draft were not saved by Preview! I will try and avoid Preview in the future but today your script recovered my annotations and prevented hours of work from being wasted!! The web app is awesome. Thank you so much!

Thank you sooooo much! I made tons of annotations in hours but they were not saved by Preview. All annotations were successfully recovered using your web app.  Awesome work!

same here bro! thank you, it happened to me before and I thought I did a mistake not saving properly
now I was 100% careful and sure I had saved, still it was forgotten so I went nuts, hopefully I found your tool and it recovered everything
now I am done with this crap of preview, thanks for saving me this time!

 (Or send you a donation)
I almost cried when 2.5 hours of already annoying work disappeared and this really saved me.
Thank you! x10

Thank you bro! But why apple still didn't fix these issues!

thank you SO much. almost lost all my work on an exam very shortly before the deadline. lifesaver!


Update

could you update this to 1.16.4 pls

it should work in 1.16.4

doesn't for me

I found out why it didn't work


Where does the data in resource.rar come from?

Hi, julian,
Your work is great. Thanks for sharing.
I download the resource.rar and there are several folders including different data. As far as I know, the data of the folder 'luna16_annotations' is from LUNA16 and LIDC-IDRI ，and the data of the folders 'luna16_manual_labels' and 'ndsb3_manual_labels' are generated manually. How about other folders? Such as annotations_excluded.csv of the folder 'luna16_annotations', candidates_V2.csv of the folder 'luna16_annotations' , the folder 'luna16_falsepos_labels' and the folder 'segmenter_traindata'.
Thanks
Cao jiehui

It's in the blog under Preprocessing and creating a trainset


[SPARK-33790][CORE] Reduce the rpc call of getFileStatus in SingleFileEventLogFileReader

What changes were proposed in this pull request?
FsHistoryProvider#checkForLogs already has FileStatus when constructing SingleFileEventLogFileReader, and there is no need to get the FileStatus again when SingleFileEventLogFileReader#fileSizeForLastIndex.
Why are the changes needed?
This can reduce a lot of rpc calls and improve the speed of the history server.
Does this PR introduce any user-facing change?
No
How was this patch tested?
exist ut

Can one of the admins verify this patch?

ok to test.

Test build #132827 has started for PR 30780 at commit 7dae56f.

Test build #132827 has finished for PR 30780 at commit 7dae56f.

This patch fails Scala style tests.
This patch merges cleanly.
This patch adds no public classes.

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This patch merges cleanly.
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cc @HeartSaVioR FYI

current
FsHistoryProvider#checkForLogs - Takes 23 minutes
20/12/16 10:27:13,152 [log-replay-executor-44] INFO FsHistoryProvider: Finished parsing hdfs://XXXX.lz4
20/12/16 10:50:36,897 [log-replay-executor-85] INFO FsHistoryProvider: Parsing hdfs://XXXX.lz4 for listing data...

fix
FsHistoryProvider#checkForLogs - Takes 5 minutes
20/12/16 12:17:09,109 [log-replay-executor-62] INFO FsHistoryProvider: Finished parsing hdfs://XXXX.lz4
20/12/16 12:23:56,765 [log-replay-executor-43] INFO FsHistoryProvider: Parsing hdfs://XXXX.lz4 for listing data...

I agree this is a good improvement. Thanks!
Regardless of approval of the PR, I wonder your experiment result, though. rootPath is supposed to be just a file, so 17 minutes to get status of the file sounds really odd.
Could you add log message around lazy val to ensure the experiment is only affected by your change? Like,

Before

private lazy val status = {
  val startNs = System.nanoTime()
  val s = fileSystem.getFileStatus(rootPath)
  println(s"DEBUG: elapsed = ${System.nanoTime() - startNs} ns")
  s
}

After

private lazy val status = {
  val startNs = System.nanoTime()
  val s = maybeStatus.getOrElse(fileSystem.getFileStatus(rootPath))
  println(s"DEBUG: elapsed = ${System.nanoTime() - startNs} ns")
  s
}

Again I'll approve this even the gain is not that significant. Just curious about the accurate measurement of the change.

FsHistoryProvider#checkForLogs currently gets the file status of each application. If the number of applications is large, for example, there are 10,000, this will add 10,000 rpc calls to obtain file status.
23 minutes is not the time it takes to get the file status of an applicaton, but the approximate time it takes for a single call to checkForLogs.
Because the FsHistoryProvider#checkForLogs call has no logs, I can only use the last completion time of the last round of process tasks and the initial start time of this round of tasks to estimate the duration.

OK it makes sense if you have a bunch of event log files. I've seen 50000+ in SPARK-29043 so won't be surprised anymore. :)

retest this, please

Will merge to master once the build passes.

Test build #132907 has started for PR 30780 at commit 4d1d5e4.

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Test build #132907 has finished for PR 30780 at commit 4d1d5e4.

This patch fails Spark unit tests.
This patch merges cleanly.
This patch adds no public classes.

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retest this, please

I forgot I also reran the Github Action build. Given that is passing, I'm merging to master.

Test build #132915 has started for PR 30780 at commit 4d1d5e4.

Thanks @cxzl25 I merged into master (3.2.0).

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Test build #132915 has finished for PR 30780 at commit 4d1d5e4.

This patch fails Spark unit tests.
This patch merges cleanly.
This patch adds no public classes.

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Container stats tables not sorting correctly

portainer 1.15.0 is not correctly sorting the tables. When I click any column, it re-sorts the table, but I'm not really sure how it sorting, as the end results makes no sense. Take a look at this screenshot:

I'll try to reproduce this on a Windows platform, as it's working fine on Linux (you can check on http://demo.portainer.io)

I can not reproduce the problem with Portainer 1.19.2

@deviantony The table is not sortable anymore. Is this correct?

@ricardona Correct.
Closing this issue.


Add note when upgrading Rancher 1.6 HA clusters

Please add the following note to page https://rancher.com/docs/rancher/v1.6/en/upgrading/#multi-nodes
NOTE:
Ensure Rancher server containers, as they are brought up, are allowed sufficient "settling-down" time before starting the next Rancher server container.  A baseline for the database's CPU usage could be used as a gauge to determine how much time is sufficient time. As a new Rancher server comes up, watch spikes in CPU usage to settle down to near-baseline levels before starting the next Rancher server. Additionally, Rancher logs can be monitored to see if a server has had sufficient time to settle down before starting the next one.

It has been my experience that not giving sufficient time causes DB spikes and can potentially cause the upgrade to be stuck due to a non-responsive db. The workaround being to stop all Rancher server containers and restart the upgrade process with a longer delay.
Also, this mainly impacts larger environments with a large number of clusters, hosts, and workloads.


Maybe it don't work

@arcticlion See this. Contributions graph went fishy also. :smile:

@arcticlion See this. Contributions graph went fishy also. :smile:

Oh, I see. It’s Github bug. No wonder, I submit the code today, it don’t show.
--
Finch
Sent with Airmail
在 2015年1月1日 下午10:59:54, Ionică Bizău<EMAIL_ADDRESS>写到:
@arcticlion See this. Contributions graph went fishy also.
—
Reply to this email directly or view it on GitHub.

Oh, I see. It’s Github bug. No wonder, I submit the code today, it don’t show.
--
Finch
Sent with Airmail
在 2015年1月1日 下午10:59:54, Ionică Bizău<EMAIL_ADDRESS>写到:
@arcticlion See this. Contributions graph went fishy also.
—
Reply to this email directly or view it on GitHub.


Add auth

https://app.clickup.com/t/8695e0h70
Adds auth from old api (mostly moved over)

All good. @liviuba to make minor change to .env_compose and fix logs in future PR

Just realised that the readme does mention a .env, but it doesn't explicitly mention the usecase where we start the api with docker compose up and want to run the tests from the host.
In this case, what we would need to do is to cp .env_compose .env and change the biaint_mongo host in the connstring to be localhost. WIll add to the readme.


Fixed checkbox read for preview

Tasks:

[ ] gather feedback for my changes

Informations:

Q
A

Tests pass?
yes => no changes

Fixed tickets
fixes #647

BC Breaks
none

Doc
none

Falsy values do not produce preview update

@danrot fixed

After clicking on a checkbox you still have to  click somewhere else for the preview to update, I guess that's because there is no focus out event otherwise. Maybe we should adapt the dom filter for checkboxes?

@danrot i have added a changed event for radio and checkbox


User can add item to shelf

As user
I want to add an item to some shelf
So that it is listed there in my shopping view
NOTE this is postponed from MVP because the same functionality will be achieved though "edit item"
Acceptance criteria:

[ ] For each shelf in the shelves view: The user has an "add item to shelf" dialog
[ ] This dialog allows to select from existing items or create a new item (dropdown with text input)

[ ] if not supported by UI framework, just dropdown is ok for now

[ ] Title of the dialog includes the shelf name
[ ] User can add item to shelf with button (no selection of shelves)

Fully covered by #58


Feature: Add mod update checker

Resolves #84.
Replaces #235. Thanks @JoeZwet for all the work you have done to make this a reality.
I'm opening this pull request as the original author has said themselves they're caught up in work and not have much time to maintain this and there's not been any updates again for nearly a month. I hope they don't have anything against me taking over the work. I'm up to further maintain this and fix related issues.
New features in this PR:

[x] Fixed many major issues in the original codebase.
[x] A update notification toast on the title screen. (Can be disable through the settings)
[x] Can now read ModUpdater's custom mod json data.
[x] In addition to the CurseForge, GitHub, Maven and Modrinth update providers, I have added a GitLab update provider.
[ ] A custom, user-defined JSON file that can be used to provide update information for mods that don't add support themselves without the user having to edit the JAR or rebase and recompile the mod every update.

I have gone ahead and cleaned up some formatting, addressed some minor code issues and made the code properly compatible with JDK 16 and newer. I have also rewritten a large chunk of the update providers for more modularity and better using the fact Java is a object oriented language with generics. We sadly cannot use records for the data classes each ModUpdateProvider uses, because Gson doesn't natively support using records and adding a custom JSON factory just for a few classes seems like unnecessary work for realistically no gain.
Note: I'm thinking of adding more compatibility layers, so that more other mod updater mods other than ModUpdater also automatically work with this. What's your opinions on this?

bruh

@JoeZwet You have any issues with this PR?
Btw, this is what the update notification looks like.

@JoeZwet You have any issues with this PR? You can hit me up on discord if you want to: seΛn#6338
Btw, this is what the update notification looks like.

Looks good. Though you could always just commit to the original pr

Looks good. Though you could always just commit to the original pr

As the first PR to your fork took a full month and there's been a lot of inactivity on your end, I decided to open a separate PR so that the updates get through quicker. There was a lot wrong in the original code and opening so many PRs and possibly needing to wait a month would substantially slow down the development and sorry, but I really couldn't be bothered. I hope you can agree that this might be the better (I'm active daily) solution but if you really want it to go through your original PR I would still be happy to PR my current changes into your fork.

I've reimplemented this as a stand-alone mod and haven't rebased this fork in a while because of the lack of attention from the maintainers, they don't seem like they care much about this feature or simply don't have the time to review & test. I'd be perfectly happy to rebase, get feedback, and work on this feature.

Superseded by #546. Thank you for your work on this, we would've used your work but a lot has changed in the last year and a half so we decided to go with a different approach.


Newbie question about defining interface for a com object

Hello, there
First of all, Thanks for your great job.
As a newbie for com technology, I would like to ask few questions about how to use the crate.

Defining interface
Should Interface contain all member functions of com server? I tried to define one member of com object, however I always got compile error from macro.

Does camel case matter to define interface when com object provides functions eg.”AbcDef”?

Hey 👋.
1.) ComInterfaces care about the amount and order of their methods because methods are really just offsets into a VTable. That means you must ensure that all methods of parent interfaces are declared and that all methods of the interface in question are declared. Again order matters here. It's important to note that "declaring" methods you're not actually going to use only means you need to have some place holder (e.g., unsafe fn placeholder0(&self)). It just matters that the method "slot" is occupied.
2.) Yes our implementation expects "snake_case" and will not work if CamelCase is used. So for a function declared in C++ as MyFunction you would declare it in Rust as my_function. It should be noted that method names actually don't matter and you can name functions whatever you want (as long as it's snake case). COM only cares about method ordering, and method signatures, not method names.

Thanks a lot for your answers!!
It helps a lot :)


Additional to_fhir informational exports

NOTE: to be merged after to_fhir_slicing
This PR adds in some additional "informational" data to the JSON exported by toFHIR():

For entries, it adds an ID (as pulled from entryId on the object) when exporting
For all objects, it adds a meta field with the profile the object is being exported for

Migrated this to merge into to_fhir_slicing, so I can update test methods there before getting that PR merged.

Closing as we are no longer actively maintaining this repo.


Bug: Opening dataset while another one is open freezes client.

When you have dataset open, and then proceed to open another one, the app freezes. If you manually close it first, it works just fine.
There are two variants of this bug, if you open another dataset, it freezes while opening. If you open the same dataset, it freezes while closing. In both cases it opens the progress dialog, but never progresses beyond that.
This can probably just be fixed by closing the dataset first in DatasetOpenAction.
I noticed that the CloseDatasetAction doesn't actually contain the logic for closing either, as it's included in EmailDatasetBrowser. It'd probably be a worthwhile endeavor to move this logic too when fixing this bug.

Fixed as of version 2.7.4.


NO MERGE: testing appveyor

Coverage decreased (-0.3%) to 87.873% when pulling edb71ec00f2c62cd30d1080a2677b13d4afa2cf7 on gidden:test-appveyor into 4ba54fad56ebd407c79dbb6276ee0c3d55bbbfa1 on IAMconsortium:master.

Merging to keep things going on my end..


Korean Translation

I completed the Korean translation work through Crowdin. Could you merge it for me?

I'll gladly merge a PR that enables Korean! For reference: https://github.com/olistic/warriorjs/pulls?q=is%3Apr+is%3Aclosed+languages

Thank you~!!!


newly added test_size::test_proc_macro2_wrapper_size_without_locations test fails on i686

I noticed that the proc-macro2 crate's test suite started to fail on Fedora Linux - from the build logs:
     Running `/builddir/build/BUILD/proc-macro2-1.0.84/target/rpm/deps/test_size-05b53b4047993840 --skip src/lib.rs`
running 5 tests
test test_proc_macro2_fallback_size_with_locations ... ignored
test test_proc_macro2_fallback_size_without_locations ... ignored
test test_proc_macro2_wrapper_size_with_locations ... ignored
test test_proc_macro_size ... ok
test test_proc_macro2_wrapper_size_without_locations ... FAILED
failures:
---- test_proc_macro2_wrapper_size_without_locations stdout ----
thread 'test_proc_macro2_wrapper_size_without_locations' panicked at tests/test_size.rs:52:5:
assertion `left == right` failed
  left: 20
 right: 24
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
failures:
    test_proc_macro2_wrapper_size_without_locations
test result: FAILED. 1 passed; 1 failed; 3 ignored; 0 measured; 0 filtered out; finished in 0.00s
error: test failed, to rerun pass `--test test_size`

The output points to this assertion:
https://github.com/dtolnay/proc-macro2/blob/1.0.84/tests/test_size.rs#L52
Looks like the size of proc_macro2::Group is 4 bytes smaller on i686 than on other architectures.
Possibly this affects all 32-bit architectures, but i686 is the only one that we still partially support in Fedora Linux.
As far as I can tell, the size difference is harmless (probably you just added it to make sure the size doesn't accidentally grow?), so I have ignored this test in our builds for now, but I still wanted to file an issue in case you want to add an additional not(target_pointer_width = "64") clause to the test's #[ignore] cases.

You inferred correctly, we don't need the types to be a particular size, I just need to be cognizant of when they change size because it impacts syn's performance. And for that purpose, I personally only care about 64-bit.
Thanks for reporting the issue. I have added #[cfg_attr(not(target_pointer_width = "64"), ignore)] in proc-macro2 1.0.85.
$ cargo miri test --test test_size --target i686-unknown-linux-gnu
    Finished `test` profile [unoptimized + debuginfo] target(s) in 0.04s
     Running tests/test_size.rs (target/miri/i686-unknown-linux-gnu/debug/deps/test_size-b5488b1435a7fdbe)

running 5 tests
test test_proc_macro2_fallback_size_with_locations ... ignored
test test_proc_macro2_fallback_size_without_locations ... ignored
test test_proc_macro2_wrapper_size_with_locations ... ignored
test test_proc_macro2_wrapper_size_without_locations ... ignored
test test_proc_macro_size ... ignored

test result: ok. 0 passed; 0 failed; 5 ignored; 0 measured; 0 filtered out; finished in 0.35s

Great, thank you!


QoD 0.9 - inline documentation problems

Problem description
Hello, I noticed that we moved to inline documentation. This poses a problem for stakeholders/Product folks or even Devs who just to understand the API quickly without using a tool.
Also, I believe this doesn't meet the check-list requirement for documentation: https://github.com/camaraproject/WorkingGroups/blob/main/Commonalities/documentation/API-Readiness-Checklist.md

Comparatively, 0.8.1 is so much nicer to consume:
https://github.com/camaraproject/QualityOnDemand/blob/release-0.8.1/documentation/API_documentation/QoD_API.md
Expected action
Expose documentation that is easy to consume like 0.8.1
Additional context
<none - see description>

cc: @gmuratk

Hi @murthygorty,
Have you tried swagger online editor ?
As a developer, I prefer all-in-one specs/docs over separate docs because separate always introduce consistency issues.

Hi @murthygorty,
Sorry, I was not clear.
I meant as a consumer developer...not as developper of the spec.
I always doubt the accuracy/consistency when I find multiple documents because I know it's hard to maintain.
And yes, we have already included the Markdown documentation in the oas file...so we could include more.

Besides, I always generate the models and the API from the OAS to be sure not to miss anything.

ahaa, thanks @patrice-conil  - so, if I understood you correctly, are you suggesting that

API Developers include all the documentation, markdown (pictures too?) in OAS.
before an API is released a tool is run to generate a non-Dev consumable documentation as part of release checklist?

if so, that is perfectly fine, imo.
Without #2 above, I am sorry I cannot agree. CAMARA consumption cannot be for developers only. CAMARA releasechecklist we have is really good and caters to the appropriate audience (including Technical Product Managers in customer organizations who need to create requirements towards Customer Development teams).
If we agree on #1 and #2 above, we still need to fix this issue so that there is a document that is part if 0.9 release :-), don't you agree?
cc: @hdamker @gmuratk

Hi @murthygorty,
I was just suggesting (1)...but if you really need (2), which I can understand, I don't feel competent to answer.

For (2) it would make sense to explore some way to generate a HTML formatted version of the yaml spec, with tools such as redocly/redoc, and provide that output as part of the project. This is something transversal to all WGs.

I don't think we should go back to what we did in 0.8.x, as that implies duplicating the effort to maintain doc in two different places. If the problem is to provide a non-dev friendly version of the yaml spec, there are some simple ways to provide that in the short term, until we decide to build a proper web hosting of our html versions of the APIs.
For example we could add the URL to the API version (raw) as parameter to
https://redocly.github.io/redoc/?url=<url>&nocors

and use that in the links in the README.md, as in
Status and released versions
...

Release 0.9.0 of the API is available within the release-0.9.0 branch:

API definition with inline documentation
For changes see CHANGELOG.md

The previous version v0.8.1 of the QoD API is available within the release-0.8.1 branch.

API definition with inline documentation for 0.8.1
...

To avoid external dependencies, another option could be to build the html doc with some Github actions host the files in Github Pages. Similar to this

Shouldn't we take this discussion to the Commonalities subproject to get an explicit guideline for all subprojects?
@shilpa-padgaonkar

Thinking about some more, I completely agree with @gmuratk .

is the current 0.9.1 compliant with commonalities? If yes, cool! If not, this needs to be fixed (as hotfix?). In parallel, commonalities can be improved as smart here give inputs.

There are two other considerations for merging CAMARA documentation with OAI spec:

During my active coding days, in companies where we had inline documentation standard, we kept up well with documenting the interface endpoint and parameters, but the overall documentation at the top of the interface including 'user guide's still had serious bugs from time to time, with inconsistencies.
with inline documentation, Carriers may need to upskill tech-writers to write/wordsmith inline documentation. The premise is the OAI developer is not the best at producing final documentation, which is definitely true in my case.
cc: @shilpa-padgaonkar @gmuratk @hdamker

The Swagger editor also supports linking to external documentation, for example:
https://editor.swagger.io/?url=https://raw.githubusercontent.com/camaraproject/QualityOnDemand/release-0.9.0/code/API_definitions/qod-api.yaml
I agree such links should be added to the release notes for each release.
With regard to the documentation itself, we need to distinguish between the mechanism by which APIs are documented, and the quality of that documentation. The introductory blurb (under info: description:) will always be the hardest to keep up to date, whether it is embedded in the API specification or a standalone markdown document.
But the value of using the API specification as the documentation is that OAS allows individual schema to have descriptions and examples, and good examples and descriptions can be included when the schema is introduced. So this stops documentation being viewed as something to be done right at the end when a new version of the API is otherwise ready.
So I think using these OAS features is the way to go towards keeping documentation up to date. Other tools, such as cucumber, will help to formalise the documentation of expected API behaviour. And whilst I agree that there is an obligation on API developers to try to keep inline documentation up to date and accessible to less technical viewers, I think there is also an obligation on those interested in such details to understand the way in which the associated tooling presents that information.

Agreed at meeting on 11th August to include links to release notes and README. Also raise in Commonalities.

@hdamker
The meeting consensus was to add links to the ReDoc and Swagger Editor formatted versions of a release to both the version release notes, and to the README (for the latest release). So something like:

Formatted documentation (Swagger Editor) (ReDoc)

Can you make the necessary changes? Thanks.

If it helps, in HomeDevicesQoD we have this PR https://github.com/camaraproject/HomeDevicesQoD/pull/54 (ready to be merged) that you might want to use as a reference or example. @hdamker @eric-murray @jlurien.

Can you make the necessary changes? Thanks.

Yes, will prepare a PR for that. Thanks for driving the issue to a conclusion.

If it helps, in HomeDevicesQoD we have this PR camaraproject/HomeDevicesQoD#54 (ready to be merged) that you might want to use as a reference or example.

@jpengar thanks a lot, copied with pride 👍

@hdamker Happy to hear that my PR was useful :)
Remember that the PR updates the README and CHANGELOG files, but you also need to update the release notes accordingly.
https://github.com/camaraproject/QualityOnDemand/releases

thank you so much everyone. I feel like we can use QoD as the leading example of CAMARA APIs :-) - it is also very popular for usage as far as I can tell.


events.py: rename event counters

rename events_prev to event_counters for clarity.
Initialize event_counters as an empty dictionary for faster initialization.
Simplified the clear method for improved efficiency by updating only the counters of existing events, rather than rebuilding the counters for all events in EVENTS.keys().

Is this a substantial difference? The result is slightly more confusing at first glance. Just going to merge the rename for now.


docs(haskell): add lsp predicate to format check

So that if someone follows the advice of the warning, it will then go
away

Thanks for your help!


Cp 1205 1

Changelog category :

New Feature
Bug Fix
Improvement
Performance Improvement
Backward Incompatible Change
Build/Testing/Packaging Improvement
Documentation (changelog entry is not required)
Other
Not for changelog (changelog entry is not required)

Changelog entry (a user-readable short description of the changes that goes to CHANGELOG.md):
...
Documentation entry for user-facing changes

[ ] Documentation is written (mandatory for new features)

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you all sign our Contributor License Agreement before we can accept your contribution.2 out of 3 committers have signed the CLA.:white_check_mark: fky2015:white_check_mark: nudles:x: compassesYou have signed the CLA already but the status is still pending? Let us recheck it.


OneShot, and presumably other MKXP-based RPG Maker games are not detected

SteamDB link to the game
https://steamdb.info/app/420530
OneShot is an RPG Maker XP game that uses a fork of the custom open-source RGSS interpreter 'MKXP' for performance, cross-platform support, and interfacing with native libraries.
For information, their fork is located here https://github.com/elizagamedev/mkxp-oneshot
What should it be detected as?
RPG Maker

.rxdata is rpg maker proprietary file so i guess it can be just added to a rule? idk


bug: lun channel needs to be initialized at the right place

What type of PR is this?

What this PR does / why we need it:
Which issue(s) this PR fixes:

Fixes #
Special notes for your reviewer:
Does this PR introduce a user-facing change?

Additional documentation e.g., KEPs (Kubernetes Enhancement Proposals), usage docs, etc.:

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

3 of 3 (100.0%)  changed or added relevant lines in 1 file are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.04%) to 80.451%

Totals

Change from base Build<PHONE_NUMBER>:
0.04%

Covered Lines:
15729

Relevant Lines:
19551

💛  - Coveralls


Avoid scalastyle check as part assembly

Hey guys,
my build.sbt has following statements to execute scalastyle check as part of compilation:
lazy val compileScalastyle = taskKey[Unit]("compileScalastyle") compileScalastyle := scalastyle.in(Compile).toTask("").value (Keys.compile in Compile) := ((Keys.compile in Compile) dependsOn compileScalastyle).value
How do I avoid this scalastyle during assembly phase like when i run assemblyPackageDependency

https://github.com/sbt/sbt-assembly/blob/master/CONTRIBUTING.md#where-to-file-a-bug-report


feat: bump runner version

Bumping the runner version

Hi @dhruv-4  appreciate the PR however we have a few things to bump so we are going to do them together in this PR https://github.com/actions-runner-controller/actions-runner-controller/pull/730


kafka sink log improvment

The https://github.com/optiopay/kafka driver used for kafka sink, that has a configuration to provide logs via a Logger interface. This contains useful information, but by default those logs are thrown away.
This modification contains an implementation of that Logger calling glog directly.

This change is

I've signed it.

This seems reasonable to me. Assigning to the Kafka sink maintainer for a second review.

LGTM since the maintainer isn't responding.  Merging.


Changing the width and height of textboxes based on window size

can i work on this?

Right now the issue is open assignment
all of you can work on it

can i work on this

Could i work on this??

i have the code for this please assiign it to me
Y L Krishna Pani
PES2UG21CS616

can anyone assign this issue #6 to me @nishtha981

Can this be assigned to me pls

Can this be assigned to me @nishtha981 #6

can u please assign this to me
Y L Krishna Pani
pes2ug21cs616


feat: added /getuserid command that replies to the message of the author their user id

Allows a user to get their user id. Can be useful for always matching the user of beta applications, even when they change their username or discriminator

I will do that instead. Thanks


Try to have GitHub actions instead of travis

We will live without CoverityScan for the moment.

FYI @slavysis This is now complete, so as you can see only .travis.yml needs to be removed.


Image upload for wiki pages

This is the frontend counterpart issue to https://github.com/icebreaker-science/backend/issues/35
The user should be able to upload an image, when creating a new wiki page (for now only devices).
However, this is not a mandatory field in the form.

@chaoran-chen Only the person who is creating the page should be able to add a picture? What if several users add availability and like to show a pic alongside their device. Is the backend running some form of authentification on the request?

Hmm. The question is whether a picture should belong to the device or to the device-availability. For simplicity, I have currently defined that only a device can own a single picture which can only be uploaded during the initial creation of the device.


Add possibility to load credentials automatically for majordomo asm/gsm

Google Cloud and AWS both support to load credential via metadata service without any interaction if IAM roles/sa are attached to VM.
Current it's impossible to use because dirk pass only credentialPath, and majordomo strictly use only that too (gsm, asm).
I think it could be a good idea to make the default way getting credentials from metadata service work

It turns out that ASM support that right now due to non-mandatory path config option, which passed like empty string "", and GSM was fixed by https://github.com/attestantio/dirk/pull/31, so I close this issue


PluginException "ActionUpdateThread.OLD_EDT" thrown in IntelliJ with 0.0.78

Before submitting your bug report

[X] I believe this is a bug. I'll try to join the Continue Discord for questions
[X] I'm not able to find an open issue that reports the same bug
[X] I've seen the troubleshooting guide on the Continue Docs

Relevant environment info
- OS: MacOS 15.1
- Continue version: 0.0.78
- IDE version: IntelliJ
IntelliJ IDEA 2024.2.4 (Ultimate Edition)
Build #IU-242.23726.103, built on October 23, 2024

Runtime version: 21.0.4+13-b509.26 aarch64 (JCEF 122.1.9)
VM: OpenJDK 64-Bit Server VM by JetBrains s.r.o.
Toolkit: sun.lwawt.macosx.LWCToolkit
macOS 15.1
Kotlin plugin: K2 mode (Beta)
GC: G1 Young Generation, G1 Concurrent GC, G1 Old Generation
Memory: 4096M
Cores: 12
Metal Rendering is ON
Registry:
  ide.balloon.shadow.size=0
  ide.browser.jcef.jsQueryPoolSize=200
  ide.browser.jcef.contextMenu.devTools.enabled=true
  ide.experimental.ui=true
  i18n.locale=
Non-Bundled Plugins:
  com.github.continuedev.continueintellijextension (0.0.78)
  org.intellij.plugins.hcl (242.23339.11)
  PythonCore (242.23726.103)
  org.jetbrains.plugins.go-template (242.20224.155)
  Pythonid (242.23726.103)
  PlantUML integration (7.11.2-IJ2023.2)
  mobi.hsz.idea.gitignore (4.5.4)
Kotlin: 242.23726.103-IJ

- Model: all
- config.json:

{
  "models": [
    {
      "apiKey": "",
      "engine": "gpt-4o",
      "apiBase": "",
      "apiType": "azure",
      "model": "gpt-4o",
      "title": "GPT-4o",
      "systemMessage": "You are an expert software developer. You give helpful and concise responses. Omit greetings.",
      "provider": "azure",
      "apiVersion": "2024-08-01-preview"
    }
  ],
  "tabAutocompleteModel": {
    "title": "codeqwen",
    "provider": "ollama",
    "model": "codeqwen:latest"
  },
  "embeddingsProvider": {
    "title": "text-embedding-3-large",
    "provider": "openai",
    "model": "text-embedding-3-large",
    "apiBase": "",
    "engine": "text-embedding-3-large",
    "apiVersion": "2023-05-15",
    "apiType": "azure",
    "apiKey": ""
  },
  "customCommands": [
    {
      "name": "test",
      "prompt": "{{{ input }}}\n\nWrite a comprehensive set of unit tests for the selected code. It should setup, run tests that check for correctness including important edge cases, and teardown. Ensure that the tests are complete and sophisticated. Give the tests just as chat output, don't edit any file.",
      "description": "Write unit tests for highlighted code"
    }
  ],
  "contextProviders": [
    {
      "name": "diff",
      "params": {}
    },
    {
      "name": "folder",
      "params": {}
    },
    {
      "name": "codebase",
      "params": {}
    }
  ],
  "slashCommands": [
    {
      "name": "edit",
      "description": "Edit selected code"
    },
    {
      "name": "comment",
      "description": "Write comments for the selected code"
    },
    {
      "name": "share",
      "description": "Export the current chat session to markdown"
    },
    {
      "name": "commit",
      "description": "Generate a git commit message"
    }
  ],
  "allowAnonymousTelemetry": false
}

Description
When starting IntelliJ, I see an exception:
com.intellij.diagnostic.PluginException: ActionUpdateThread.OLD_EDT is deprecated and going to be removed soon. 'com.github.continuedev.continueintellijextension.autocomplete.CancelAutocompleteAction' must override getActionUpdateThread() and chose EDT or BGT. See ActionUpdateThread javadoc. [Plugin: com.github.continuedev.continueintellijextension]
at com.intellij.diagnostic.PluginProblemReporterImpl.createPluginExceptionByClass(PluginProblemReporterImpl.java:23)
at com.intellij.diagnostic.PluginException.createByClass(PluginException.java:90)
at com.intellij.diagnostic.PluginException.reportDeprecatedUsage(PluginException.java:125)
at com.intellij.openapi.actionSystem.ActionUpdateThreadAware.getActionUpdateThread(ActionUpdateThreadAware.java:21)
at com.intellij.openapi.actionSystem.AnAction.getActionUpdateThread(AnAction.java:201)
No helpful completions are shown, it only suggests "{" inline.
To reproduce

Install Plugin
Start IDE

Log output
[2024-10-29T15:38:43] [info] Starting Continue core...
[2024-10-29T15:38:43] Setup
[2024-10-29T15:38:43] Core started
[2024-10-29T15:38:43] Error loading remote config:  Error: ENOENT: no such file or directory, open '/Users/me/.continue/.configs/localhost/config.json'
[2024-10-29T15:38:43] Error loading remotely set config.js:  Error [ERR_MODULE_NOT_FOUND]: Cannot find module '/Users/me/.continue/.configs/localhost/config.js' imported from /snapshot/continue/binary/out/index.js
[2024-10-29T15:38:43] (node:45671) ExperimentalWarning: The Fetch API is an experimental feature. This feature could change at any time
(Use `continue-binary --trace-warnings ...` to show where the warning was created)
[2024-10-29T15:38:43] Failed to retrieve from remote cache TypeError: fetch failed
[2024-10-29T15:38:44] Chunk to delete wasn't found in the table:  /Users/me/Documents/Projekte/.../build.gradle.kts
[2024-10-29T15:38:44] Failed to retrieve from remote cache TypeError: fetch failed

Confirmed I see this a lot when refactoring file names / editing project window.
com.intellij.diagnostic.PluginException: `ActionUpdateThread.OLD_EDT` is deprecated and going to be removed soon. 'com.github.continuedev.continueintellijextension.autocomplete.CancelAutocompleteAction' must override `getActionUpdateThread()` and chose EDT or BGT. See ActionUpdateThread javadoc. [Plugin: com.github.continuedev.continueintellijextension]
	at com.intellij.diagnostic.PluginProblemReporterImpl.createPluginExceptionByClass(PluginProblemReporterImpl.java:23)
	at com.intellij.diagnostic.PluginException.createByClass(PluginException.java:90)
	at com.intellij.diagnostic.PluginException.reportDeprecatedUsage(PluginException.java:125)
	at com.intellij.openapi.actionSystem.ActionUpdateThreadAware.getActionUpdateThread(ActionUpdateThreadAware.java:21)
	at com.intellij.openapi.actionSystem.AnAction.getActionUpdateThread(AnAction.java:201)


Add enhancer/promoter, repressor, and squelcher tracks

Adds Enhancer / Promoter, Repressor, and Squelcher tracks

Adds Enhancer / Promoter, Repressor, and Squelcher tracks

Small typo in Candidate Enhancer / Promotors (--> Promoters).
Besides that, I think there is quite a bit of redundancy in the tracks, which might create some confusion and also have difficulty scaling as we add more data / expand the search. I understand each source is independent in the portal, even if they represent the same candidate regulatory element. Also the same elements might show up multiple times in the same track, like in the screenshot, if significantly linked to more than one target.  I think this shows the limits of the genome browser visualizations, which creates "long" views of the results if wanting to show all connections.
I'm fine with that for now, but I would prefer to include the elements in the "Tested" tracks into the "Candidate" tracks, perhaps in grey to separate them to the sig. hits. That way you can reduce the number of tracks, which should help simplifying the view.


Pod services: replace actorUri with podOwner

Make it more clear that we want to do some actions on a specific Pod.

In fact, if in the future we want to allow users (webIds) to have multiple Pods, which would mean every user can have multiple Pods, and some special Pods (Cods) can be owned by several users, it would be better to pass the link of the Pod storage (https://mypod.store/alice/data`) in addition to the webId.


Add open panel config and quick action

This PR adds config to change when Violations panel is shown, fixes #6.
It also introduces code action to show panel from code actions panel.
Needs https://github.com/kubeshop/vscode-sarif/pull/6 and https://github.com/kubeshop/vscode-sarif/pull/7 to be merged first.

Changes

As above.

Fixes

None.

Checklist

[x] tested locally
[ ] added new dependencies
[ ] updated the docs
[ ] added a test

There appear to be a bunch of conflicts though. I might have to re-review after you resolved those.

Sure, feel free to take another look. Conflicts were due to the fact that both this PR and autofix one (which was merged earlier) registered code actions related stuff (event, registering, etc) in the exact same lines.

Hmmm, autofix related tests started failing, I need to take a look on this.


Allow Test Print

Issue #, if available:
Description of changes:
By submitting this pull request, I confirm that you can use, modify, copy, and redistribute this contribution, under the terms of your choice.

Neither.
I agree that properly completed and merged tests should not print.
Back in my C++ days, I had my CI enforce that.
However, during development it is SUPER useful to be able to throw in a quick eprintln! to try to figure out what is happening.
As a side benefit, if our tests should not be printing, then this will at least allow the possibility that we notice that a test is printing.