[FEATURE REQ] Convenient method to generate SAS url from user delegation key

Library or service name.
Azure.Storage.Blobs
Is your feature request related to a problem? Please describe.
For storage clients created from account key, there is a convenient GenerateSasUri method to generate a blob SAS url. The security best practice suggests to use MSI for authentication, thus the code need to switch to use user delegation key. There are some common problems about user delegation key that needs taken care for each consumer:

For best performance, a user delegation key could be cached in memory to sign subsequent requests until expiry.
The cache refresh should consider user delegation key expiration as well as SAS url expiration.
Handle request burst scenario so we don't make excessive user delegation key get requests.

This feature request asks the blob client SDK to provider a helper method that allows developers to generate SAS urls easily and efficiently using user delegation key, providing a similar experience as GenerateSasUri today, with the above details encapsulated underneath.

Very similar to this feature request, can probably be done in conjunction.
https://github.com/Azure/azure-sdk-for-net/issues/16470


add style support and fix twice-click to pick one

@kiliwalk Thanks a lot. It's merged and pusht to npm.


Add ZIP-321 Payment Request URI creation and parsing

Codecov Report

Merging #53 (b956f40) into main (db6d92b) will decrease coverage by 0.51%.
Report is 3 commits behind head on main.
The diff coverage is 88.82%.

@@            Coverage Diff             @@
##             main      #53      +/-   ##
==========================================
- Coverage   95.46%   94.95%   -0.51%
==========================================
  Files          95       97       +2
  Lines        4340     4715     +375
==========================================
+ Hits         4143     4477     +334
- Misses        197      238      +41

Flag
Coverage Δ

LinuxHost
94.95% <88.82%> (-0.51%)
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Release
94.95% <88.82%> (-0.51%)
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macOSHost
94.95% <88.82%> (-0.51%)
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Files Changed
Coverage Δ

src/Nerdbank.Zcash/TransparentP2SHAddress.cs
88.46% <0.00%> (-3.54%)
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src/Nerdbank.Zcash/ZcashAddress.cs
96.22% <ø> (ø)

src/Nerdbank.Zcash/Zip321PaymentRequestUris.cs
83.46% <83.46%> (ø)

src/Nerdbank.Zcash/CompoundUnifiedAddress.cs
68.42% <100.00%> (+1.75%)
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src/Nerdbank.Zcash/FixedLengthStructs.cs
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src/Nerdbank.Zcash/OrchardAddress.cs
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src/Nerdbank.Zcash/SaplingAddress.cs
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src/Nerdbank.Zcash/SproutAddress.cs
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src/Nerdbank.Zcash/TransparentP2PKHAddress.cs
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src/Nerdbank.Zcash/ZcashUtilities.cs
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Guides – Visualizing big datasets: aggregations and clustering

Related to #971
Guide at staging:

http://carto-vl-971-guides-aggregation.developers.carto-staging.com/developers/carto-vl/guides/aggregations/

This is a new guide, related to aggregations and clustering.
For the "General doc restructure" see https://github.com/CartoDB/carto-vl/issues/950
Tasks
Writing

[x] Global aggregation
[x] Viewport aggregation
[x] Resolution
[x] Clustering

Revision

[x] Name, files & folders structure
[x] Deploy to staging for global revision (typos, links...)
[ ] Merge to master

This PR also includes several fixes and improvements for other guides, mainly Sources (02) and Interactivity (09)

This guide would need to be updated in the future if https://github.com/CartoDB/carto-vl/issues/1054 is developed

Thx for your feedback @elenatorro
I have included all your suggestions and merged master into the branch

Thx @makella I really appreciate your review!
Regarding to your questions:

blend. I didn't know about that... I was using it as shortcut for a quick conditional styling. I have tried replacing it with ramp, but the result is not exactly the same, unless a little fix is applied. You can have a look at it here

commented lines. True! I have removed unused properties, simplifying the vizs. I tried them to be a help, but they were not working as clear as a I expected. In the future maybe we could have a better style for our CARTO_VL_Viz snippets to distinguish comments.

Hi @VictorVelarde!
I reviewed the guide (nice job!) as a first pass, I did a proofread and made some minor modifications to the guide text here and there (feel free to accept or reject).
I had a couple of questions:

for the examples that use blend... I think we are trying to stay away from blend in the examples (right?) replacing with ramp should give the same results. I didn't make any edits there because I wanted to ask you first
I'm wondering if you think it is worth simplifying the styling in the different steps by not showing unused/commented out lines (?) and/or maybe we can figure out a way to style "what's changed"? inside of the viz code. The only reason I say this is after the @g_ and @v_ styling and bringing them together in the resolution example, could be a little overwhelming

We have decided to keep the blend for the styling, and the PR has been merged


dim in ndfunc_arg_in_t

In my observation, "dim" field in ndfunc_arg_in_t is always 0.  What's this field?

It is the number of dimensions handled in a user iterator. If the argument is a matrix, dim=2. See Numo::Linalg https://github.com/ruby-numo/linalg/blob/master/ext/numo/linalg/gen/tmpl/matmul.c

Thank you for your reply.
For example, when input array is ndim=3 and dim=2, the input array is considered to be a sequence of matrices. Is that correct?

Yes, right. It accepts array of matrix.

Thank you.
I hope that tests for this functionality are added to the test suite of numo-narray.
Please close this issue.

Thank you for comments.
Testing and documentation are next issues.


sparse matrix support

Should be easy, most functions should already work on sparse matrices but we will need to update our typechecking in several places and write tests to make sure.
Also J1c says that one of the SVDs does not work on sparse
Possibly could include support for rank 1 + sparse matrices where rather than many 0s they have many of some constant

https://scikit-learn.org/stable/modules/generated/sklearn.utils.extmath.safe_sparse_dot.html#sklearn.utils.extmath.safe_sparse_dot

Never really understood the point of that function.
def safe_sparse_dot(a, b, dense_output=False):
    """Dot product that handle the sparse matrix case correctly
    Uses BLAS GEMM as replacement for numpy.dot where possible
    to avoid unnecessary copies.
    Parameters
    ----------
    a : array or sparse matrix
    b : array or sparse matrix
    dense_output : boolean, default False
        When False, either ``a`` or ``b`` being sparse will yield sparse
        output. When True, output will always be an array.
    Returns
    -------
    dot_product : array or sparse matrix
        sparse if ``a`` or ``b`` is sparse and ``dense_output=False``.
    """
    if sparse.issparse(a) or sparse.issparse(b):
        ret = a * b
        if dense_output and hasattr(ret, "toarray"):
            ret = ret.toarray()
        return ret
    else:
        return np.dot(a, b)

Just does * instead of @, which I think is equivalent in later versions of python.
import numpy as np
from scipy.sparse import csr_matrix

X = csr_matrix(np.random.normal(size=(100, 4)))
U = X * X.T
V = X @ X.T

(U != V).nnz == 0
>>> True

TODO:

[ ] ASE should require no changes
[ ] LSE might require changes to to_laplace
[ ] Omni requires change in omnibus matrix creation
[ ] cmds requires change for matrix pairwise distance computation, but no change for vector pairwise distance computation

More TODO:

[ ] Change PTR to output sparse matrix if input is sparse
[ ] Changes to simulations to output sparse matrix similar to link

This is lots of work

Need to check the following if output is sparse if input is sparse

[ ] LCC functions
[ ] symmetrize
[ ] augment_diagonal
[ ] remove_loops


How do I pull the formData from the finished callback?

Hello,
Could you please help me out. I'm trying to basically upload a blog image and associate it with one individual blog post. I'm assigning the blog _id to formData on the template. Is there a way that I can get this data in the finished callback? That way I could update the blog record with the correct image url. Below is the source:
{{> upload_bootstrap formData=_id}}

  UploadServer.init({
    tmpDir: process.env.PWD + '/.uploads/tmp',
    uploadDir: process.env.PWD + '/.uploads/uploads',
    finished: function(fileInfo, formData) {
    	console.log(formData);
    	Campaigns.update({_id: formData}, {set: {image: fileInfo.path}});
    }
  })

Any suggestions would be great. Thanks for all your help.

formData parameter is string Json. So ethe best way to go is described in the documentation:
<template name="myTemplate">
{{> upload_bootstrap formData=myFormData}}
</template>

Template.myTemplate.helpers({
  myFormData: function() { return { id: this._id }; }
})

Thank you so much.

Heh, thanks. Glad I could help. I'll close this issue, please reopen if necessary. I have also updated my response for future reference.


Recommended R version?

Hey,
Thank you for creating and sharing such an important program. I am running into issues with dependencies on my R environment using my university cluster. I see that you specify BiocManager 3.10 on this github which would imply R version 3.6. On the actual publication, R version 3.5 is listed. Which R version do you recommend for Viral-Track?
Thanks,
Seth

Hi Seth,
Thank you for this heartwarming message :) So we tested Viral-Track on various computer configurations, inlcuding R 3.5 and R 3.6 so I don't think it would really affect how Viral-Track works. What kinds of problems are you facing ?
Best
Pierre

Hey Pierre,
Thanks for the quick response. So I was able to solve my R problem by using conda to download the r-XML package, which otherwise I couldn't update for some reason. After that I was able to install the R packages and ran Viral-Tracker on several PBMC samples, revealing mostly bacteriophages and retroviruses. However, I'm getting an error on the last step, demultiplexing. It's unclear to me exactly what's supposed to be in the target and parameters files for this step. Are they the identical files used in the viral scanning step?  I'm getting the following error when I run the demultiplexing step using the same 2 files as before:
Error in file(file, "rt") : cannot open the connection Calls: read.table -> file In addition: Warning message: In file(file, "rt") :   cannot open file '~output_dir//~sample///QC_filtered.txt': No such file or directory Execution halted
The multiple backslashes seem to be throwing off the path to the filtered virus file. Looking at the Viral_Track_cell_demultiplexing.R file, it appears this path is created by joining strings from the Output_directory, the path from the target.txt file, and the characters "/QC_filtered.txt". I'm not sure why the extra slashes are being added when they're joined. Any idea what's going on here?
Thanks again for the help!
Seth

I think R 4.0 breaks the code at line 343 of Viral-track-scanning.R, now matrix objects inherit the "array" class as well.


disallow newline between function return type and LBRACE

Addresses #341.

I'm afraid checking for INDENTIFIER is not enough:
val f: () -> () -> Unit = {
    val x = 1
    val y = x
    {
        println(y)
    }
}

Fixed in https://github.com/pinterest/ktlint/pull/360 so closing this.


Fix issue with missing nodejs-legacy package

Starting with Ubuntu 18.04 and Debian 10 the nodejs-legacy package is no
longer available/necessary. With these changes ansible checks if the nodejs-legacy package needs to be installed or not.

fixes #51


New version: Aserto.Topaz version 0.31.5

Pull request has been created with komac v2.1.1 :rocket:
Microsoft Reviewers: Open in CodeFlow

0.31.5 released has been removed

For moderators
This account is automated by Github Actions and the source code was created by CoolPlayLin. If you have any questions about any pull request, don't hesitate to ping Exorcism0666.

[!warning]
With the new version of Komac, numerous Pull Requests may contain bugs or unwanted elements. If such issues arise, please tag russellbanks so that these bugs can be addressed in future updates.

[!important]
Please carefully review these Pull Request before merging. If it is a Pull Request for removing incorrect content and the URLs are issue, free upon manual checking, please close this Pull Request directly. (It is best to inform Exorcism0666 of the closure.)

良い一日をお過ごしください！


Add Nim language

this is a pretty biased request .. but i would like the nim language to be added to the role's on the discord server

go too perhaps 🙃

go too perhaps 🙃

Sure these can be added 👍 - once there is a PR, I can create the roles on Discord

Sure these can be added 👍 - once there is a PR, I can create the roles on Discord

I think this issue can be closed, since the PR related to this was merged. (#411)

I think this issue can be closed, since the PR related to this was merged. (#411)

Yep 👍 - thanks @Vyvy-vi

Yep 👍 - thanks @Vyvy-vi


Fixed bundle audit issues

Summary
Fixed bundle audit vulnerabilities.
Type of change

[x] This change requires a documentation update

@swaathi Test cases passed on GH action. Pls review once again.
thanks in advance


Updated formatting for switch statements

Pretty self explanatory, we briefly talked about it at some point.

I'm getting ready to merge and updating the change log - please @me if any other changes are pushed.


Dependencies needed for Scala 3.0.0-RC1

[x] cats-effect
[x] log4s
[x] cats-parse
[x] fs2
[x] vault
[x] scodec-bits
[x] case-insensitive
[x] ip4s
[x] cats
[ ] scalafix (we should hack around this)
[x] keypool
[x] log4cats
[x] unique
[x] jawn
[x] jawn-fs2
[ ] circe
[ ] play-json
[x] scala-xml
[ ] boopickle
[ ] twirl
[ ] scalatags
[ ] blaze

I'll make sure play-json gets published soon. (and I started work on Twirl, but not sure yet on timeframe to finish)

Amazing initiative :-)
This is like the core library for those of us wanting to move into Scala 3 sooner than later

We're very close on 3.0.0-M3 just as RC1 arrives.  I expect we'll publish a mostly full milestone for M3, plus whatever we manage to already have working on RC1.

play-json 2.10.0-RC2 has been published with 3.0.0-RC1 support, as per https://github.com/playframework/play-json/issues/570

Yep, already integrated play-json. Thanks!

We released on RC1 today.  I think we can retire this ticket.


Added placeholder to RE landing page

Added full list of tools from the procurement status report.
Added paragraph to Reliability Engineering site explaining remit.

These are all meant to be placeholders,  with suggested comments, but if
it’s going to cause potential confusion perhaps just remove the comments
and use ‘content  in development’ or something similar?
On Mon, 5 Feb 2018 at 18:49, Tom<EMAIL_ADDRESS>wrote:

@tomnatt requested changes on this pull request.
Couple of requests for clarity.
In source/index.html.md.erb
https://github.com/alphagov/reliability-engineering/pull/5#discussion_r166072478
:

+Jira is an approved tool for GDS service teams to use.
+
+### Hosted Graphite
+
+Hosted Graphite is an approved tool for GDS service teams to use.
+
+### Sentry
+
+Sentry is an approved tool for GDS service teams to use.
+
+### PagerDuty
+
+PagerDuty is an approved tool for GDS service teams to use.
+
+### Zendesk - Verify
Why Verify? Is this only approved for Verify?
In source/index.html.md.erb
https://github.com/alphagov/reliability-engineering/pull/5#discussion_r166072741
:

Send logs securely to Logit.io

The PaaS docs document
how to send logs from PaaS to logit.
+### Confluence
+
+Confluence is an approved tool for GDS service teams to use.
What does "approved" mean? Do we have a hosted solution? Are teams ok to
procure their own solution? What actions can a team take with this
information?
—
You are receiving this because you authored the thread.
Reply to this email directly, view it on GitHub
https://github.com/alphagov/reliability-engineering/pull/5#pullrequestreview-94099270,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AWmqkW4Ak38Vb6g00nVVwwseLkZ29LNHks5tR001gaJpZM4R5r_y
.

--
[image: Cabinet Office - Government Digital Service]
Peter Thornton-Grimes
Technical Writer
Government Digital Service I The White Chapel Building, 10 Whitechapel High
Street, E1 8QS
T: 07748 368 982

Could we mark it as "tools in use in GDS" or something similar, and just have a list for the moment?

@tomnatt @soupdragon99 I'm not sure what the benefit of listing out these things here at all is. What is the objective - for teams to see what other teams are doing or to find out what they should be doing? If it's the former then a list of "things that have gone through IA and procurement" might be useful, but if it's the latter then that list would be different.
I think Tom's suggestion of a list is good, and I think we should unpack "approved" to "has been procured for use by GDS teams".

@tomnatt I have made some changes to the RE landing page based on our catchup yesterday.


[BUG] When uninstalling the Rancher gMSA CCG Plugin chart, not all registry keys are removed from the Windows worker nodes

Rancher Server Setup

Rancher version: v2.7.7
Installation option (Docker install/Helm Chart): Docker

If Helm Chart, Kubernetes Cluster and version (RKE1, RKE2, k3s, EKS, etc):

Proxy/Cert Details:

Information about the Cluster

Kubernetes version: v1.26.8+rke2r1
Cluster Type (Local/Downstream): Downstream

If downstream, what type of cluster? (Custom/Imported or specify provider for Hosted/Infrastructure Provider): Azure

User Information

What is the role of the user logged in? (Admin/Cluster Owner/Cluster Member/Project Owner/Project Member/Custom) Standard

If custom, define the set of permissions:

Describe the bug

When uninstalling the Rancher gMSA CCG Plugin chart, the cleanup logic should remove created registry keys in the Windows worker nodes. Specifically, these two:

HKLM:System\CurrentControlSet\Control\CCG\COMClasses{e4781092-f116-4b79-b55e-28eb6a224e26}
HKCR:CLSID{E4781092-F116-4B79-BFFE-28E6A224E26

However, in each of the supported Windows worker nodes, I noted that only the second registry key was removed rather than both.
To Reproduce

NOTE: An Azure Active Directory server needs to be configured and setup with Rancher as a prerequisite.

Provision a downstream RKE2 v1.26.8+rke2r1 custom cluster w/Windows nodes (I had 3 etcd, 1 cp, 2 Linux workers, 4 Windows workers).
Navigate to Cluster explorer > cluster > Apps > Repositories.
Add the https://github.com/rancher/Rancher-Plugin-gMSA repo with the main branch.
Install the Windows GMSA and Rancher gMSA CCG Plugin charts.
RDP into each of the Windows worker nodes and validate that both the above registry keys exists.
Navigate back to Rancher and uninstall the Rancher gMSA CCG Plugin chart.
RDP back into each of the Windows worker nodes and validate that only the following registry key is removed:

HKCR:CLSID{E4781092-F116-4B79-BFFE-28E6A224E26

Result
Both registry keys should be removed in each of the Windows worker nodes.
Expected Result

Only HKCR:CLSID{E4781092-F116-4B79-BFFE-28E6A224E26 is removed in each of the Windows worker nodes. Registry key HKLM:System\CurrentControlSet\Control\CCG\COMClasses{e4781092-f116-4b79-b55e-28eb6a224e26} still remains.

Validated that this has been addressed. See below:
SCREENSHOT OF ISSUE DESCRIPTION
ENVIRONMENT DETAILS

Rancher version: v2.7.7
Rancher install: Docker
Browser: Chrome

TEST RESULT

Scenario
Test Case
Result

1
Uninstall the Rancher gMSA CCG Plugin chart and validate the CCG-related registry keys are removed
:white_check_mark:

VALIDATION STEPS

Provisioned a downstream RKE2 v1.26.8+rke2r1 custom cluster w/Windows nodes (I had 3 etcd, 1 cp, 2 Linux workers, 4 Windows workers).
Navigated to Cluster explorer > cluster > Apps > Repositories.
Added the https://github.com/rancher/Rancher-Plugin-gMSA repo with the main branch.
Installed the Windows GMSA and Rancher gMSA CCG Plugin charts.
RDP'ed into each of the Windows worker nodes and validate that both the above registry keys exists.
Navigated back to Rancher and uninstall the Rancher gMSA CCG Plugin chart.
RDP back into each of the Windows worker nodes and validated that both of the CCG-related registry keys have been removed.


Small textual tweaks.

Again, some of this might just be personal preference. No offense taken if PR is denied 🙃.

A bit delayed of a review, but thank you!


External Variant Evidence Sources Ingestion and Display

We have an existing ticket specifically for bringing in CIViC data for display in the VCI (via the LDH): see #1769 . The purpose of this overarching ticket will be to construct a general workflow that allows for evidence from various different external resources to be automatically displayed in the VCI. CIViC is just one exemplar dataset, but when scoping and specifying this project we need several other exemplar data sets so that we can make sure this project will support multiple different types of data and have maximal utility.
Scoping for this feature provided by Deb:
Scoping for this feature includes:
Display Location: Linked Data Hub (LDH) content could be displayed as a row similar to ClinVar in the Basic Information tab.
Row Content: The row would summarize the content of the Linked Data Hub for that variant. It would provide either a link to the LDH for further exploration, or a direct link to the content LDH obtains (CIViC in this case).
With CIViC data as an example, and as a first step to integration, a user could know from looking at the LDH row in the Basic Information tab, if a variant under curation is (1) present in CIViC and (2) display the evidence available (Evidence IDs, evidence statements or Assertions) in CIViC. The format or specific items to display may change based on the dataset, but the row would be designed to hold some common elements from LDH datasets and minimize development of specific items for additional datasets.
Need to find out from Sai: For datasets LDH would contain, what are some of the common elements? Name of Dataset? Allele Registry ID (Are all variants in the LDH linked by Allele Registry ID?) Other elements?

Replaced https://github.com/ClinGen/clincoded/issues/2177

SP ticket: https://broadinstitute.atlassian.net/browse/CSP-115

From Sharon on 7/11/22:  - Also could consider bringing in AllofUs data separately rather than via gnomAD:
Note that in the reply to the ESP there was a comment about the AllofUs data that will eventually make it into gnomAD but we also talked about bringing it in like we did the PAGE data years ago. Here is the quote - “The ClinGen Variant Curation Interface will then ingest these updated data from gnomAD and directly incorporate these allele counts into the VCI. This will bring awareness of the existence of phenotype data in AoU for any variant with allele counts, allowing curators to access this case-level data for curation with appropriate permissions. This is similar to our prior ingest of the earlier PAGE genotype frequency data into the VCI.”

Closing to be replaced by #250


AccessDeniedException breaks if an S3 resource policy denies read access

Describe the bug
We have 100s of bucket in which few buckets are very critical and have a resource policy to restrict access to every IAM user/role except few. In such an environment, trying to run select * from aws_s3_bucket gives an error Error: AccessDenied: Access Denied status code: 403, request id: XXXXXXX, host id: XXXXXXXXXX along with unreliable results.
The results include buckets until it reaches 403 error. The number of results might not be constant.
Steampipe version (steampipe -v)
steampipe version 0.15.4
Plugin version (steampipe plugin list)
+--------------------------------------------------+---------+-------------+
| Name                                             | Version | Connections |
+--------------------------------------------------+---------+-------------+
| hub.steampipe.io/plugins/turbot/aws@latest       | 0.71.0  | aws         |
| hub.steampipe.io/plugins/turbot/steampipe@latest | 0.5.0   | steampipe   |
+--------------------------------------------------+---------+-------------+

To reproduce
Create an S3 bucket in AWS account containing few S3 buckets. For this new bucket, set the resource policy like the following:
NOTE: Please update the account ID, rolename and the bucket name before adding this resource policy.
{
    "Version": "2012-10-17",
    "Statement": [
        {
            "Effect": "Allow",
            "Principal": {
                "AWS": "arn:aws:iam::111111111111:role/ROLENAME"
            },
            "Action": "s3:ListBucket",
            "Resource": "arn:aws:s3:::MyExampleBucket"
        },
        {
            "Effect": "Allow",
            "Principal": {
                "AWS": "arn:aws:iam::111111111111:role/ROLENAME"
            },
            "Action": [
                "s3:GetObject",
                "s3:PutObject",
                "s3:DeleteObject"
            ],
            "Resource": "arn:aws:s3:::MyExampleBucket/*"
        },
        {
            "Effect": "Deny",
            "Principal": "*",
            "Action": "s3:*",
            "Resource": [
                "arn:aws:s3:::MyExampleBucket",
                "arn:aws:s3:::MyExampleBucket/*"
            ],
            "Condition": {
                "StringNotLike": {
                    "aws:userId": [
                        "AROAEXAMPLEID:*",
                        "111111111111"
                    ]
                }
            }
        }
    ]
}

Setup IAM credentials having ReadOnly access across the account, open steampipe query and then execute select * from aws_s3_bucket. Or you don't want to use * then execute select tags from aws_s3_bucket.
Expected behavior
Allow fetching all buckets for which the IAM user has access. Maybe having a user variable in the plugin to ignore access denied errors and fetch all the accessible resource also helps.

@Chan9390 Sorry to hear that you are running into issues with the AWS S3 bucket table.
We do have a provision to ignore the access denied errors. Please take a look at the configuration section - https://hub.steampipe.io/plugins/turbot/aws#configuration
If you use the ignore_error_codes config argument, you can ignore all the access denied errors.
You can uncomment the ignore_error_codes config argument in your aws.spc file to be able to use this feature.
Hopefully, this solves your issue. Please let us know in case you have more questions about this.

Thank you @misraved, this solved my issue. 💯


Internet Archive stores a file not found message

Tested with https://soundcloud.com/circushomonovus/almereyda-theres-no-rest-for-the-wicked

I contacted them about whether this was fixable and haven't gotten a reply back yet.


Release 5.0.1

I've added a bunch more stuff to the changelog that has been merged since February: https://github.com/castleproject/Windsor/compare/v5.0.0...master
I doubt anyone objects, but I'll make a release in a day if all good.
/cc @castleproject/committers @dariuslf @Yitzchok

Tagged v5.0.1
Confirmed successfully pushed to nuget.org
Tweeted


Upgrade go from 1.16 to 1.17

Upgraded go version to 1.17
Signed-off-by: Zheng Xi Zhou<EMAIL_ADDRESS>

Maybe the GO_VERSION of format.yml in .github/workflow should be upgraded to 1.17.


Untitled database: Table 1 - AppSheet databases

https://www.appsheet.com/dbs/database/ELZ90lVZKU4ryLu-do4b_7/table/xCH5C1fAql4_QfzQnK6Rp6

/language en

Please provide some details on the issue that you are facing.
/triage needs-information

@BothHybrid2022 Is it the accurate description of the issue you wish to report? It would be beneficial to include the correct details (here). Currently, it appears to resemble spam or or an unintentional creation of an issue in the wrong repository.

/close not-planned
Closing this issue for now. Please feel free to reopen it and provide the accurate details for the issue encountered in the documentation at https://kubernetes.io.


feat: add civic TR submission examples

Currently making a draft PR because I still need to create prognostic/diagnostic examples. @wesleygoar The TR examples are ready for review and all return 204 status code when doing a dry run with the test api.

@wesleygoar I'll probably wait for your review to submit to test API?

@wesleygoar for batch, I only did evidence items with the same molecular profile. Lmk if this is an issue

@Kuzma, @.***> can we do a second batch submission test as well with multiple genes included?
Thanks,
Wesley Goar PhD
Senior Bioinformatics Scientist
Institute for Genomic Medicine
Nationwide Children's Hospital

From: Kori Kuzma @.>
Sent: Tuesday, May 7, 2024 5:53:36 PM
To: ga4gh/gks-clinvar @.>
Cc: Goar, Wesley @.>; Mention @.>
Subject: Re: [ga4gh/gks-clinvar] feat: add civic TR submission examples (PR #8)
@wesleygoar for batch, I only did evidence items with the same molecular profile. Lmk if this is an issue — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned. Message ID:
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@korikuzma can we do a second batch submission test as well with multiple genes included?

@wesleygoar added

@wesleygoar I'm cleaning up my script if it makes it easier for your review.

@wesleygoar added nb. lmk if you have any qs

@wesleygoar okay, I think it's officially ready for review. README was added in addition to diagnostic/prognostic (manually created).

What we can put in ClinVar, but doesn't work with GKS

Things found in GKS extensions

Normalizer information (label and ID). The reason why we do not store the normalized ID/label in the GKS model is because in MetaKB, we use the source provided id/label. A solution for this is to swap our current solution and stick source provided information in the extensions?
Indication information. We use this to map CIViC evidence level to AMP/ASCO/CAP tiers.

@korikuzma we should use the mappings field for this (inherited from MappableEntity instead of the old descriptor approach.

What we can put in ClinVar, but doesn't work with GKS

Things found in GKS extensions

Normalizer information (label and ID). The reason why we do not store the normalized ID/label in the GKS model is because in MetaKB, we use the source provided id/label. A solution for this is to swap our current solution and stick source provided information in the extensions?
Indication information. We use this to map CIViC evidence level to AMP/ASCO/CAP tiers.

@korikuzma we should use the mappings field for this (inherited from MappableEntity) instead of the old descriptor approach.

@ahwagner Ah okay, we already have mappings but I didn't pull from there. I can stick in the normalizer information there. Not sure about the indication data though...

@ahwagner It's also not guaranteed that the system will be the same across GKS representations. For example, some people could use a URL whereas others could use a free text string

but from the file the CIViC team provided I think they are planning to submit CIViC Assertions. This PR should reflect that.

That was my bad. I thought CIViC team was testing out the assertions. I included assertion data in the most recent commits

We should also be evaluating the deletes

I added dummy example of deletes. I couldn't find our SCV accession for the single submission that was actually submitted to the test API

Hrm. This PR shows how we would submit CIViC Evidence Items (this is okay for testing), but from the file the CIViC team provided I think they are planning to submit CIViC Assertions. This PR should reflect that. I have asked the CIViC team to see if they want Evidence Items supported.
We should also be evaluating the deletes

@ahwagner can you expand on what you mean by this please?

Which part would you like expanded upon? CIViC Assertions vs. Evidence, or the deletes? Or both?

@ahwagner the deletes

We should also be evaluating the deletes

I added dummy example of deletes. I couldn't find our SCV accession for the single submission that was actually submitted to the test API

This was me being blind. I found the corresponding SCV accession and upated


Show only subdomain handle for the user whose domain corresponds to the domain of the server

Is your feature request related to a problem? Please describe.
I think that handle are taking too much place on a post particularly because of the "bsky.app" at the end of 90% of the handle, this is problematic because it concentrates us with is glowing blue color from the real information that is the content, moreover sometimes due to long username, the handle takes half of the width of a post.
Describe the solution you'd like
It would be interesting if the handle could be displayed without the domain name (just showing subdomain) when we are on the server with the domain name, for example username.bsky.social would be displayed username if we are on https://bsky.app or an application that has decided to hide handles ending in bsky.social. In this way we can see handles coming from other servers and those using domain names directly.
Describe alternatives you've considered
Alternatively, we could suggest reducing handles with an ellipsis if they exceed a certain size, as with urls, with the option of activating it in the parameters.

Now that I can see the Threads application, I think it would be good to have something like this :

Any updates on this? With the influx of new users who are not used to having a full handle with domain, I think it would be a nice feature to have. A lot of users really seems to hate on having the full domain name.

I think it would be nice as a setting, I could see something like
Show Handles: [ Always | Exclude default | Never ]
I hope this gets addressed in some form. Hiding the default domain would also make "unique" domains way easier to spot/notice.

I don't think that's a good idea.
If you hide the default domain, then there's no way to differentiate between the user "example.com.bsky.social" (with the "bsky.social" part hidden) and the actual "example.com" user.
For example, if you see a post from<EMAIL_ADDRESS>you wouldn't know if it's actually from them or if it's actually from someone named<EMAIL_ADDRESS>with the "bsky.social" part being hidden.
The only thing that might make sense might be a slightly smaller font for the "bsky.social" or a slightly less visible font color, but even that I don't think is a good idea.

I don't think that's a good idea.
If you hide the default domain, then there's no way to differentiate between the user "example.com.bsky.social" (with the "bsky.social" part hidden) and the actual "example.com" user.
For example, if you see a post from<EMAIL_ADDRESS>you wouldn't know if it's actually from them or if it's actually from someone named<EMAIL_ADDRESS>with the "bsky.social" part being hidden.
The only thing that might make sense might be a slightly smaller font for the "bsky.social" or a slightly less visible font color, but even that I don't think is a good idea.

This makes sense, yeah.

I don't think that's a good idea.
If you hide the default domain, then there's no way to differentiate between the user "example.com.bsky.social" (with the "bsky.social" part hidden) and the actual "example.com" user.
For example, if you see a post from<EMAIL_ADDRESS>you wouldn't know if it's actually from them or if it's actually from someone named<EMAIL_ADDRESS>with the "bsky.social" part being hidden.
The only thing that might make sense might be a slightly smaller font for the "bsky.social" or a slightly less visible font color, but even that I don't think is a good idea.

Is it possible to have a dot in a handle? In this case, it could be problematic, but it can be put into perspective as you can hover over the handle and see the profile in more detail.

It definitely is possible to have a dot inside a handle in general.
For example, this profile has quite a few dots in their name, so the protocol itself definitely supports it. Whether bsky.app itself supports it, I don't know.
But A), even if bsky.app doesn't support it, other servers will (and then their users will be vulnerable to this kind of spoofing, and B) it's not even that simple to figure out where the username begins and where the domain ends.
If a user is named "test.account.example.com" - is the handle "test" and the domain "account.example.com" or is the handle "test.account" and the domain is example.com?
Also, there's already issues with people impersonating others, only showing part of the handle is only causing more of these, even if you show the full handle in the hover popup, nobody is going to check that and it's not going to show up in screenshots.


Add support for HTTP checks

Newer versions of Consul support built-in HTTP+interval checks (https://consul.io/docs/agent/checks.html). This adds support for http as an alternative to script in the service_def LWRP so we can do e.g.
consul_service_def "service" do
  check(
    id: "service",
    name: "service on port 80",
    http: "http://localhost:80/",
    interval: "10s",
    timeout: "1s"
  )
  notifies :reload, "service[consul]"
end

Coverage remained the same at 100.0% when pulling 7f44766b9eb24ce3c9e1ec22b3cd21098711e1de on mydrive:http-checks into 60e3072a3db35657747a608c83b2209e0101f23b on johnbellone:master.


Helm chart repo is broken

apiVersion: v1
entries:
  tigera-operator:
  - apiVersion: v2
    appVersion: v3.21.1
    created: "2021-12-02T17:13:12.449037905-08:00"
    description: Installs the Tigera operator for Calico
    digest: 6b55d4377b0d842c0a7685b3982bb9c144e019f024ad49e68f8f650a39a892af
    name: tigera-operator
    urls:
    - https://github.com/projectcalico/calico/releases/download/v3.21.1/tigera-operator-v3.21.1-0.tgz
    version: v3.21.1-0
  - apiVersion: v2
    appVersion: v3.21.0
    created: "2021-12-02T17:13:12.447301449-08:00"
    description: Installs the Tigera operator for Calico
    digest: 23c37c695c2a41a603bc7fd6196326fa9b5e93a8f9472ce577992aff402739d8
    name: tigera-operator
    urls:
    - https://github.com/projectcalico/calico/releases/download/others/tigera-operator-v3.21.0-0.tgz
    version: v3.21.0

the versions are inconsistent v3.21.1-0 vs v3.21.0, Helm treats v3.21.0 as latest one
excepts v3.21.1-0 version, the urls are invalid and lead to 404

Yep, our pipelines are broken as we can't pull any charts

I just re-ran make helm-index and I think that's fixed it up.  Can you confirm please?
I'll investigate what happened here and get back to you, but I think someone manually pushed a broken helm index in error.

It is ok now @lwr20 .

Seems to be working now, thanks!

Looks like it's broken again

Worked for me?  But I did find an error in the docs - the version should be v3.21.2, not v3.21.2-0 (the -0 upsets our release tooling, I think semver defines the -n suffix as a pre-release)
lance@lwr20:~/scratch$ kind create cluster --config kind-config.yaml
Creating cluster "kind" ...
 ✓ Ensuring node image (kindest/node:v1.21.1) 🖼
 ✓ Preparing nodes 📦 📦
 ✓ Writing configuration 📜
 ✓ Starting control-plane 🕹
 ✓ Installing StorageClass 💾
 ✓ Joining worker nodes 🚜
Set kubectl context to "kind-kind"
You can now use your cluster with:

kubectl cluster-info --context kind-kind

Not sure what to do next? 😅  Check out https://kind.sigs.k8s.io/docs/user/quick-start/

lance@lwr20:~/scratch$ kubectl get no
NAME                 STATUS     ROLES                  AGE   VERSION
kind-control-plane   NotReady   control-plane,master   38s   v1.21.1
kind-worker          NotReady   <none>                 9s    v1.21.1

lance@lwr20:~/scratch$ helm repo update
Hang tight while we grab the latest from your chart repositories...
...Successfully got an update from the "projectcalico" chart repository
Update Complete. ⎈Happy Helming!⎈

lance@lwr20:~/scratch$ helm install calico projectcalico/tigera-operator --version v3.21.2
W1207 09:47:20.273337  129294 warnings.go:70] policy/v1beta1 PodSecurityPolicy is deprecated in v1.21+, unavailable in v1.25+
W1207 09:47:20.353424  129294 warnings.go:70] policy/v1beta1 PodSecurityPolicy is deprecated in v1.21+, unavailable in v1.25+
NAME: calico
LAST DEPLOYED: Tue Dec  7 09:47:20 2021
NAMESPACE: default
STATUS: deployed
REVISION: 1
TEST SUITE: None

@lwr20 I'm using the terraform helm_release to deploy the operator:
resource "helm_release" "tigera-operator" {
  name = "tigera-operator"

  repository = "https://docs.projectcalico.org/charts"
  chart      = "tigera-operator"
  version    = "v3.21.1"

  max_history = 10

  values = [
    file("${path.module}/tigera-operator/values.yaml")
  ]
}

values.yaml
installation:
  # Configures Calico networking.
  calicoNetwork:
    mtu: 1400
    nodeAddressAutodetectionV4:
      firstFound: false
      cidrs:
        - 172.xx.yy.0/24
        - 172.xx.zz.0/24
    # Note: The ipPools section cannot be modified post-install.
    ipPools:
    - blockSize: 26
      cidr: 10.xx.0.0/16
      encapsulation: IPIPCrossSubnet
      natOutgoing: Enabled
      nodeSelector: all()

if update the version to v3.21.2, it will break with the error i posted 😕

Can you raise a separate issue please?  I think that isn't really covered by this closed issue "Helm chart repo is broken"

resource "helm_release" "tigera_operator" {
name       = "tigera-operator"
repository = "https://docs.tigera.io/calico/charts"
chart      = "tigera-operator"
namespace  = "tigera-operator"
create_namespace = true
set {
name  = "image.tag"
value = "v3.21.1"
}
set {
name  = "kubernetesProvider"
value = "eks"
}
depends_on = [
aws_eks_cluster.atarim_eks_cluster
]
}
Install Calico
resource "helm_release" "calico" {
name       = "calico"
repository = "https://docs.tigera.io/calico/charts"
chart      = "calico"
namespace  = "tigera-operator"
depends_on = [
helm_release.tigera_operator
]
}
Applying above terraform code. i get below error.
Error: could not download chart: chart "calico" not found in https://docs.tigera.io/calico/charts repository
How to fix it?


Editing an environment with a new Docker image might duplicate the environment on Grafana

Today, I was adding a new environment to CodeOcean. Unfortunately, I had to adjust the settings a few times and also switched the Docker image I used. As a result, our Grafana dashboards duplicated the environment (which has the ID 33). We should ensure that only the newest environment details are shown (based on the ID which is unique and the timestamp).

Good catch, before it was the latest environment detail based on id, image, and stage; now it's only id and stage - by adding
  |> group(columns: ["id", "stage"], mode:"by")

Awesome, thanks! I just checked the dashboard again and made similar changes. This time, updated Docker images are correctly processed and shown expected.


This repo is mentioned for classification only, so it cant be used to semantic segmentation yet?

At the last layer of Axial attention, there is the implementation of the Linear fc layer, which gives the classification output. But, I need to work on semantic segmentation. So usingn axial attention as encoder, should I use this for unet decoder or else how can I proceed for segmentation task?

Right. It does not support segmentation yet.
I would suggest to use it as an encoder. Please have a look at section 3.2 axial-deeplab for details. If you would like to use it as a decoder also, Appendix B provides our decoder design and the performance of it.

keeping this as encoder can other decoders (eg unet ) be used for performing semantic segmentation?

Yes.

Are you planning to upload the code for the axial decoder anytime soon?

No, but you could convert a block to a decoder block easily by inserting one or two upsamplings and 1x1 convolutions.

I am getting this error. MY N=8, group planes =8/2=4, H-64, W-64
what might be the possible reason for this?

It seems that the sizes of q and q_embedding do not match. Could you please provide more information? Did you make any changes of the code?

Can you please check if this network design is correct or not while using axial deeplab encoder with decoder. Also after the decoder reaches 1,32,56,56 which are N,C,H,W what can be done to produce the output as exact size as of its image ?

It seems OK

Can you please check if this network design is correct or not while using axial deeplab encoder with decoder. Also after the decoder reaches 1,32,56,56 which are N,C,H,W what can be done to produce the output as exact size as of its image ?

In the decoder block, we go 3,4,6,3 blocks in each layer as in encoder side, or else we have only one block in each layer as shown in figure above?

@shrutishrestha Have you completed the decoder block?

In the paper it is written "Firstly, to extract dense feature maps, DeepLab [13] changes the stride and
atrous rates of the last one or two stages in ResNet [32]. Similarly, we remove the
stride of the last stage but we do not implement the `atrous' attention module,
since our axial-attention already captures global information for the whole input."
Does this mean for the last layer we don't need to do the downsampling and the output size of the last layer will be [1, 1024, 14, 14]? @csrhddlam

Right, it will be [1, 1024, 14, 14], although in practice, the input resolution for semantic segmentation is usually larger than 224x224.

Yes right. I was assuming 224x224 for calculation. Thanks.

Can you please check if this network design is correct or not while using axial deeplab encoder with decoder. Also after the decoder reaches 1,32,56,56 which are N,C,H,W what can be done to produce the output as exact size as of its image ?

I see the skip connection will be passed through conv1x1, would you please explain why you design in this way?
The second thing I notice is that in the decoder (in the right down corner), the input size is 1x1024x7x7, but somehow it becomes 1x512x7x7 before conv and upsample without any operation?
Thank you


Align default seccomp profile with selected capabilities

Currently the default seccomp profile is fixed. This changes it
so that it varies depending on the Linux capabilities selected with
the --cap-add and --cap-drop options. Without this, if a user adds
privileges, eg to allow ptrace with --cap-add sys_ptrace then still
cannot actually use ptrace as it is still blocked by seccomp, so
they will probably disable seccomp or use --privileged. With this
change the syscalls that are needed for the capability are also
allowed by the seccomp profile based on the selected capabilities.
While this patch makes it easier to do things with for example
cap_sys_admin enabled, as it will now allow creating new namespaces
and use of mount, it still allows less than --cap-add cap_sys_admin
--security-opt seccomp:unconfined would have previously. It is not
recommended that users run containers with cap_sys_admin as this does
give full access to the host machine.
It also cleans up some architecture specific system calls to be
only selected when needed.
Signed-off-by: Justin Cormack<EMAIL_ADDRESS>Note this patch is currently missing the needed documentation changes,
but I thought I would put it out for review first.
cc @jfrazelle

There is I think an issue with checking the generated json profile on the tests on non amd64 architectures that I need to work out a way to resolve or tests on arm will probably fail.

cc @rhatdan @cpuguy83

15:38:53 ----------------------------------------------------------------------
15:38:53 FAIL: docker_cli_run_unix_test.go:947: DockerSuite.TestRunSeccompDefaultProfile
15:38:53
15:38:53 docker_cli_run_unix_test.go:989:
15:38:53     c.Assert(err, checker.IsNil)
15:38:53 ... value *errors.errorString = &errors.errorString{s:"expected Operation not permitted, got: acct failed: No such file or directory\n"} ("expected Operation not permitted, got: acct failed: No such file or directory\n")
15:38:53

Failure on simple janky

@LK4D4 actually it might be, will investigate further

@justincormack no, I saw failures in two other PRs :/

@LK4D4 yes, that test will be broken with this patch as acct is allowed now with --cap-add all, will fix the test. So where else did you see it fail?

:+1:  I like this

This is cool! Looks good to me, maybe just needs some tests for adding the specific caps :)

Added docs changes and test fixes, maybe might pass CI now...

I am fine with this, I like the idea, I think there is a chance of this being buggy where a seccomp filter continues to block access that would be allowed with the modified caps.  But this at least gives users the ability to adjust the permissions based on --cap-add/--cap-drop without needing to drop seccomp filters all together or switching to --privileged.

I think we can move it to code-review.

@rhatdan yes there are probably some cases, but I have been pretty broad with the added yscalls, eg SYS_ADMIN will allow mount and namespace creation, SYS_BOOT will allow reboot etc, as the aim is to avoid people having to disable seccomp. I can re-review eg SYS_ADMIN as there are a lot of calls that it allows.

Yes, but to give you an example of a potential bug from a user point of view.  reboot inside of a container depending on the namespaces will only effect the PID1 of the container not necessarily reboot the host system.

There is an issue in the default seccomp profile tests with "panic: sync: negative WaitGroup counter" which I am looking into. @LK4D4 is that what you saw elsewhere?

1 test still failing, will examine.

Rebase/rebuild seems to have fixed the test failure, which I could not replicate, maybe that is the occasional failure @LK4D4 was seeing before?

sigh..
E: Failed to fetch http://cdn-fastly.deb.debian.org/debian/pool/main/g/gcc-4.9/gcc-4.9_4.9.2-10_amd64.deb  503  backend read error

retest this please

It's green now
ping @jfrazelle @LK4D4 PTAL 👍

looks good to me! I like the tests :)

LGTM

LGTM

docs LGTM - @thaJeztah

oh! forgot to add my LGTM. Here it is \o/


One Play Per Turn

Is there a way to allow only 1 play when the board becomes visible?  I am trying to set up a correspondence chess game but cannot have one person playing both sides.  White plays then should not be able to do anything further until black plays.
I tried adding this to the end of onDrop but it didn't work:
var childNodes = document.getElementById("board1").getElementsByTagName('*');
for (var node of childNodes) {
node.disabled = true;
}

I think Example 4002 might be similar to what you are looking for.

That looks like it would work, but I use the following code and I can still seem to move the other side's pieces after I move.
function onDragStart (source, piece, position, orientation) {
// do not pick up pieces if the game is over
if (game.game_over()) return false;
// only allow pieces to be dragged when the board is oriented in their direction
if ((orientation === 'white' && piece.search(/^w/) === -1) ||
    (orientation === 'black' && piece.search(/^b/) === -1)) {
    return false;
}

// only pick up pieces for the side to move
if ((game.turn() === 'w' && piece.search(/^b/) !== -1) ||
    (game.turn() === 'b' && piece.search(/^w/) !== -1)) {
    return false;
}

}

Yeah that did it.  It didn't seem to work at first until I did a hard refresh on my page to correct for the updated js file.  Thanks again.


add sexratio to rebuilder

Resolves issue #512
attn:  @brianlangseth-NOAA
#What tests have been done?
none
#Where are the relevant files?
[x] No test files are required for this pull request.
#What tests/review still need to be done?
none

Is there an input change for users to Stock Synthesis?
[x] No, there was no input change.
Additional information (optional).

Thanks Chantel.  Please check the review box with approval


Unable to setup typedoc in a nx monorepo

Search terms
monorepo, nx
Question
Hey, I am having a similiar setup as in https://github.com/TypeStrong/typedoc/issues/2061 - a pretty large project as nx monorepo, which contains both web (React) apps and some standalone libraries.
I want to generate docs for the libraries which are located at path libs/data
The typedoc config is following, I've added one package products just for sake of testing/simplicity, but there are more:
{
  "out": "docs",
  "entryPointStrategy": "packages",
  "entryPoints": [
    "libs/data/products"
  ]
}

The package.json for the products package is following:
{
  "name": "@mycompany/products",
  "version": "0.0.1",
  "main": "./src/index.ts",
  "typedoc": {
    "entryPoint": "./src/index.ts",
    "readmeFile": "./README.md",
    "displayName": "@mycompany/products"
  }
}

However I am getting these errors:
error TS6305: Output file '...../libs/data/products/src/service.d.ts' has not been built from source file '..../libs/data/products/src/service.ts'.
  The file is in the program because:
    Root file specified for compilation

error TS6306: Referenced project '....../libs/data/products/tsconfig.lib.json' must have setting "composite": true
error TS6306: Referenced project '....../libs/data/products/tsconfig.spec.json' must have setting "composite": true

Any advices on how to fix it? Thanks in advance.
Please note, that I cannot apply same solution of renaming every tsconfig file as mentioned in the linked issue above - the project is too large for that.
Node v.14.18.2
yarn 1.22.19
nx 13.1.2
typedoc 0.23
typescript 4.5.5 (I am aware of compatibiltiy issues with that typedoc version, however<EMAIL_ADDRESS>seems to be lack of the child package.json setup)

Sounds like you need the feature in #2061 to me. You could probably work around this with a script that generates a tsconfig that extends the "real" tsconfig, runs typedoc, then removes it.

@Gerrit0 thanks for reply! Do you mean to generate the tsconfig.json for every child package before running typedoc?

Yeah, very hacky way of getting around it, but...

@Gerrit0 Got it, I'll try to make a work around and post here if I have any success or failures, maybe someone will find it useful until further resolve

@Gerrit0 ah, sorry, just found, that nx already generates a tsconfig file in child packages with contents like that:
{
  "extends": "../../../../tsconfig.base.json",
  "files": [],
  "include": ["./src"],
  "references": [
    {
      "path": "./tsconfig.lib.json"
    },
    {
      "path": "./tsconfig.spec.json"
    }
  ],
  "compilerOptions": {
    "forceConsistentCasingInFileNames": true,
    "strict": true,
    "noImplicitReturns": true,
    "noFallthroughCasesInSwitch": true
  }
}

Just to confirm:

Does npx tsc -p path/to/tsconfig.lib.json --noEmit exit with no errors?
Does npx tsc -p path/to/tsconfig.json --noEmit exit with the same errors as TypeDoc?

@Gerrit0

Fails with other errors like error TS2591: Cannot find name 'process'. Do you need to install type definitions for node? Try npm i --save-dev @types/node and then add 'node' to the types field in your tsconfig
Yea, though the error output is a little bit more verbose, but the errors are the same

Given that, even with a tsconfig option it sounds like TypeDoc will still fail to build. Your project needs to be able to compile in order for TypeDoc to work correctly...

@Gerrit0 correct, but there is catch.
If I run yarn nx build <my project name> it successfully builds it without any error. So I suppose nx is doing some 'magic' under the hood to make the project build successfully.
Moreover, by default nx generates package tsconfig with empty includes: [] option, so if I run typedoc without adding ./src to it, the error would be as following:
Entry point "libs/data/products/src/index.ts" does not appear to be built by/included in the tsconfig found at "libs/data/products/tsconfig.json"

On other hand, If I include src folders for build, the errors described in first comment appear.
nx build succeds with any setting of the includes option in tsconfig.json

Hmm... could you by chance create an example project that is similar to your real project that I could poke at? If it's really doing magic, can't promise I'll support that, but if I can figure out how to get a successful build with tsc, might be able to provide better guidance.

Trying to create as similiar but minimal example to reproduce the error

@Gerrit0 here is minimal example, typedoc gives the same error as in my main project.
Project was setup under node 14.18.2 and yarn 1.22.19, using next commands:
yarn global add nx
yarn create nx-workspace
yarn nx generate @nrwl/web:lib products-service --directory=data/services --buildable --importPath=@myapp/products-service --publishable

Update: I've tried updating to latest typedoc version with tsconfig option support for separate packages and setting it to 'tsconfig.lib.json', but it didn't work too:
TypeError: context.checker.getTypeOfSymbol is not a function
    at Object.convertProperty (.../node_modules/typedoc/dist/lib/converter/symbols.js:362:25)

Can confirm the behavior.
When entryPointsStrategy is set to packages I get the error:
error Tried to set an option (entryPointsStrategy) that was not declared.

But it is declared like this:
{
  "tsconfig": "./tsconfig.base.json",
  "entryPoints": [
    "packages/time/src/index.ts",
    "packages/ui/src/index.ts",
    "packages/utils/src/index.ts"
  ],
  "entryPointsStrategy": "packages",
  "exclude": [],
  "out": "docs",
  "name": "Insided Packages",
  "pretty": true
}

By any configuration it does not use child (leaf) package.jsons typedoc property. For example, I would like to use tsconfig.json files per package (some packages are react-based, some not).
And I would like to use a custom .md (in  my case Changelog by Conventional Commits) on page of each package.

Just to confirm:

Does npx tsc -p path/to/tsconfig.lib.json --noEmit exit with no errors?
Does npx tsc -p path/to/tsconfig.json --noEmit exit with the same errors as TypeDoc?

They work fine for me.

@Gerrit0 here is minimal example: https://github.com/MrOnlineCoder/typedoc_nx_issue

With the following changes, documentation generates as expected.
diff --git a/libs/data/services/products-service/package.json b/libs/data/services/products-service/package.json
index 5e81c08..7281d96 100644
--- a/libs/data/services/products-service/package.json
+++ b/libs/data/services/products-service/package.json
@@ -4,6 +4,7 @@
   "typedoc": {
     "entryPoint": "./src/index.ts",
     "readmeFile": "./README.md",
-    "displayName": "@myapp/products-service"
+    "displayName": "@myapp/products-service",
+    "tsconfig": "tsconfig.lib.json"
   }
 }

Update: I've tried updating to latest typedoc version with tsconfig option support for separate packages and setting it to 'tsconfig.lib.json', but it didn't work too:
TypeError: context.checker.getTypeOfSymbol is not a function
    at Object.convertProperty (.../node_modules/typedoc/dist/lib/converter/symbols.js:362:25)

Apparently I need to make the warning about running with unsupported versions of TypeDoc louder. TypeScript 4.5 is not supported. If you upgrade TypeScript, this error will go away.

When entryPointsStrategy is set to packages I get the error:

The option is entryPointStrategy, not entryPointsStrategy. For packages mode, you should also specify package directories containing package.json as your entry points, not files.

@Gerrit0 oh! thank you! My bad. The part: or packages mode, you should also specify package directories containing package.json as your entry points, not files. is super crucial as well. I could not figure it out when I used the correct spelling of this flag. Now I understand, why were there two different error messages.

@Gerrit0 thanks for investing time into my issue. I'll try to update the Typescript - though I've seen the warning, I didn't want to update it because of unknown consequences of that on other apps in the project. And it said it may work, but it might break - and thus I tried my luck

@Gerrit0 thanks for help again, issue seems to be resolved, upgrading typescript and adding tsconfig to package.json was the way for fixing.


[MB-7623] Switch the connection for the Job Runner to use HTTPS to GEX

Description
I took the GEX connection code from post_file_to_gex.go, updated it a bit, and used it to change places where we were using SFTP to send files to Syncada to use HTTP to send to GEX instead.
I left in the ability to switch back to using SFTP to send to Syncada. If we determine that we will not need this in the future, we should add a story to remove it.
I also added an ICN to the filenames that we send, to avoid having a file name collision if we sent multiple files at the same second. The new format is: <timestamp>_<ICN>_edi858.txt.
Reviewer Notes
Setup
This section is incomplete.
I think we might need to test this on experimental, and I haven't done that before.
go run ./cmd/milmove-tasks process-edis --send-to-syncada true

sendtosyncada.json
{
  "body": {
    "sendToSyncada": true,
    "readFromSyncada": false,
    "deleteFromSyncada": false
  }
}

prime-api-client --insecure support-reviewed-payment-requests --filename sendtosyncada.json

Code Review Verification Steps

[ ] Code follows the guidelines for Logging
[ ] Tested in the Experimental environment (for changes to containers, app startup, or connection to data stores)
[ ] Have the Jira acceptance criteria been met for this change?

References

Jira story for this change

Messages

:book:
:link: MB-7623

  Generated by :no_entry_sign: dangerJS against df45f6e0b4b8a6e01325044590b14a9c660b1e01


override the hard coded sign in error message

Hi,
How can you display custom error messages given in the server response on a failed sign in ?
Looking at the code it seems the promise is rejected with an hard coded message (Invalid credentials) but in my case I want to use the error message my API is giving back for i18n purposes.
I've tried to search for a similar issue, #38 was close but doesn't apply in my case or I'm missing something.
The server side code looks like
render json: { errors: ["my custom error message in whatever lang"] }, status: 401

Cheers!

Hello, I have the same issue, in my overrided method in my controller, I have
def render_create_error_bad_credentials
  render json: { errors: {
    email: [_("and password you entered did not match. Please double-check and try again.")] }
  }, status: 401
end

In the response of my api, I have the good result.
I can get the right response from the api via the auth:login-error, on the second argument.
But I would like to have it right from the catch response
$auth.submitLogin(loginForm).then( (response) ->
  ...
).catch( (response) ->
  ...
)

You can access the original error messages with :
    $rootScope.$on('auth:login-error', (context, data) ->
      console.log data.errors
    )

You can change in the src code this line:
 {
                 reason: 'unauthorized',
                  errors: ['Invalid credentials']
 }

to this:
_this.rejectDfd(resp);

I'll accept a PR for this change, provided there's some fallback to the existing message response (resp) if the existing response is lacking the proper messaging.

Something I also noticed might prove helpful is passing through the HTTP status; this way, a developer handling a login error might at least get some information on the type of problem that occured.
For now, I handled this by adding an interceptor to my application that attaches the HTTP status to the response payload, as follows:
$httpProvider.interceptors.push([
  '$injector', function($injector) {
    return {
      responseError: function(resp) {
        $injector.invoke([
          '$http', '$auth', function($http, $auth) {
            if (resp.config.url.match($auth.apiUrl())) {
              if(resp.data) {
                resp.data.httpstatus = resp.status;
              }
            }
          }
        ]);
        return $injector.get('$q').reject(resp);
      }
    };
  }
]);

This allows me to retrieve said HTTP status later on, when the actual login error occurs, by intercepting the event the that plugin fires (where the actual HTTP response is attached, and not the hardcoded object):
this.rootScope.$on('auth:login-error', (context, response) => {
  var errorLabel = 'login.error-login';
  if(response && response.httpstatus === 401) {
    errorLabel = 'login.invalid-credentials';
  }
  console.log(errorLabel);
});

If you deem it purposeful, I might provide a pull request that simply adds the HTTP status to the response like this:
.error((resp, status) =>
  @rejectDfd({
    reason: 'unauthorized'
    errors: ['Invalid credentials']
  })
  resp.httpstatus = status
  $rootScope.$broadcast('auth:login-error', resp)
)

Does this make sense?
Cheers!


Lines are "sticking" to the top

First: Thanks for this nice extension! I love the option the have both, relative and absolute line numbers. :+1:
Since the last update, however, something is off. When I scroll down, some lines tend to "stick at the top" and accumulate while scrolling. They also disappear again, when I scroll passed the region where the line got stuck.
I think a video explains it better: Screencast
System:

Arch Linux
VS Code 1.86.2
I also disable all other extensions (not seen in the video), but that didn't change the behavior.

Oh my, false alert. This seems to be a new "feature" of 1.86.2. :see_no_evil:
Sorry, I don't even no why I attributed it to your extension...


when the datepicker is disabled, I can delete the value with the clear button

Hi,
when you have the following config:
<datepicker placeholder="Select Date" :clearButton="true" :disabled="true" v-model="testDate"></datepicker>
you can clear the date with the "clear button", but I think the clear button should be disabled, too
example:
https://codesandbox.io/s/vue-datepicker-demo-iuljq?fontsize=14&module=%2Fcomponents%2FDemo.vue
(the first example, with "Disabled with clear button" name)

FYI I ran into this too. Was able to work around this as I was using a property for allowing edit
                                  :clear-button="editing"
                                  :disabled="!editing"


Add light map shader

Add a implementation of light map shader to render baked light map from Beast SDK.
I have tried to simplify this API to not add complexity to GearVRf. But further more
we could add support to apply different types of atlas texture to the scene, not just light map.
Because of this  I placed some methods with the prefix "[set,get]TextureAtlas" at Material class.
You may use latest updated branch  https://github.com/gearvrf/GearVRf-Demos/pull/15
to test it.
GearVRf-DCO-1.0-Signed-off-by: Ragner Magalhaes<EMAIL_ADDRESS>

Thanks for the update. Just a quick feedback: the FPS is about 24 on S6. Is it expected?
I will take a closer look when I have time.

Hi all,
I updated this branch with your suggestions last week ...

To me this looks ok. Tried it with the updated sample. loadTextureAtlasInformations still does an assertGLThread() though.

Looks good to me. I need thumbs up by someone else before merging this one though.

i know it sounds nit picky, but please correct the informations -> information everywhere it's needed.  otherwise, code looks fine.  haven't tested yet though.

I agree with you @thomasflynn...  I have fixed it at my last updated.
Thank you.

ok, looks good.  tested with the associated sample as well.