download script complains about yq usage

Environmental Info:
K3s Version:
~/gd/dalsi/k3s [master|✔]$ git pull
Current branch master is up to date.
~/gd/dalsi/k3s [master|✔]$ git reset --hard HEAD
HEAD is now at 4d1f9eda Etcd Snapshot/Restore to/from S3 Compatible Backends (#2902)

Node(s) CPU architecture, OS, and Version:
~/gd/dalsi/k3s [master|✚ 30]$ uname -a
Linux mjlaptop 5.10.19-200.fc33.x86_64 #1 SMP Fri Feb 26 16:21:30 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

Describe the bug:
When I run
mkdir -p build/data && ./scripts/download

I got errors such as
yq: error: argument files: can't open 'name': [Errno 2] No such file or directory: 'name'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]

Detailed steps
~/gd/dalsi/k3s [master|✔]$ pip3 install yq
Defaulting to user installation because normal site-packages is not writeable
Requirement already satisfied: yq in /home/mj/.local/lib/python3.9/site-packages (2.12.0)
~/gd/dalsi/k3s [master|✔]$ which yq
~/.local/bin/yq
~/gd/dalsi/k3s [master|✔]$ yq --version
yq 2.12.0

~/gd/dalsi/k3s [master|✔]$ mkdir -p build/data && ./scripts/download
Downloading Traefik Helm chart from https://helm.traefik.io/traefik/traefik-9.14.2.tgz
Uncompress build/static/charts/tmp.GpG4gC4QyO/traefik-9.14.2.tgz
Prepare traefik CRD
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'name': [Errno 2] No such file or directory: 'name'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'apiVersion': [Errno 2] No such file or directory: 'apiVersion'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'version': [Errno 2] No such file or directory: 'version'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.group': [Errno 2] No such file or directory: 'spec.group'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.names.kind': [Errno 2] No such file or directory: 'spec.names.kind'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.version': [Errno 2] No such file or directory: 'spec.version'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.versions[0].name': [Errno 2] No such file or directory: 'spec.versions[0].name'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.group': [Errno 2] No such file or directory: 'spec.group'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.names.kind': [Errno 2] No such file or directory: 'spec.names.kind'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.version': [Errno 2] No such file or directory: 'spec.version'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.versions[0].name': [Errno 2] No such file or directory: 'spec.versions[0].name'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.group': [Errno 2] No such file or directory: 'spec.group'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.names.kind': [Errno 2] No such file or directory: 'spec.names.kind'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.version': [Errno 2] No such file or directory: 'spec.version'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.versions[0].name': [Errno 2] No such file or directory: 'spec.versions[0].name'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.group': [Errno 2] No such file or directory: 'spec.group'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.names.kind': [Errno 2] No such file or directory: 'spec.names.kind'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.version': [Errno 2] No such file or directory: 'spec.version'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.versions[0].name': [Errno 2] No such file or directory: 'spec.versions[0].name'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.group': [Errno 2] No such file or directory: 'spec.group'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.names.kind': [Errno 2] No such file or directory: 'spec.names.kind'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.version': [Errno 2] No such file or directory: 'spec.version'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.versions[0].name': [Errno 2] No such file or directory: 'spec.versions[0].name'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.group': [Errno 2] No such file or directory: 'spec.group'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.names.kind': [Errno 2] No such file or directory: 'spec.names.kind'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.version': [Errno 2] No such file or directory: 'spec.version'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.versions[0].name': [Errno 2] No such file or directory: 'spec.versions[0].name'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.group': [Errno 2] No such file or directory: 'spec.group'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.names.kind': [Errno 2] No such file or directory: 'spec.names.kind'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.version': [Errno 2] No such file or directory: 'spec.version'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.versions[0].name': [Errno 2] No such file or directory: 'spec.versions[0].name'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.group': [Errno 2] No such file or directory: 'spec.group'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.names.kind': [Errno 2] No such file or directory: 'spec.names.kind'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.version': [Errno 2] No such file or directory: 'spec.version'
usage: yq [-h] [--yaml-output] [--yaml-roundtrip] [--width WIDTH]
          [--indentless-lists] [--in-place] [--version]
          [jq_filter] [files ...]
yq: error: argument files: can't open 'spec.versions[0].name': [Errno 2] No such file or directory: 'spec.versions[0].name'
gzip: warning: GZIP environment variable is deprecated; use an alias or script
gzip: warning: GZIP environment variable is deprecated; use an alias or script

Expected behavior:
yq will not complain (report errors).
Actual behavior:
See description and the output above.

Newer binary (export VERSION=v4.6.1) also doesn't work
export BINARY=yq_linux_amd64
wget https://github.com/mikefarah/yq/releases/download/${VERSION}/${BINARY}.tar.gz -O - |  tar xz && mv ${BINARY} /usr/bin/yq

/gd/dalsi/k3s [master|✔]$ mkdir -p build/data && ./scripts/download
Downloading Traefik Helm chart from https://helm.traefik.io/traefik/traefik-9.14.2.tgz
Uncompress build/static/charts/tmp.CwUEypim7Q/traefik-9.14.2.tgz
Prepare traefik CRD
Error: unknown command "r" for "yq"
Run 'yq --help' for usage.
...

Seems that https://github.com/mikefarah/yq/releases/tag/3.4.1 works fine. But there should be some instructions how to get exactly this dependency/version.

I spend some time debugging and reporting this issue. So if it is up to me to decide. I vote for another half year.

The script now requires an up-to-date version of yq, instead of an old one. Closing.


Retrieve list of revoced location-ids

Your Question

Discussion: https://github.com/Digitaler-Impfnachweis/covpass-ios/issues/19#issuecomment-966123865
Question:
In above linked comment @oliver-steinbrecher mentions how the revoking of specific DCCs works for Germany. I am currently working on a custom DCC validation and I was not able to find the source for the list of location-ids. Is this list of revoked location ids publicly available and if so where can I find it?

Hi Christoph,
I looked in the CovPass Code, it seems that the the locations are hardcoded at the moment.
Please see: https://github.com/Digitaler-Impfnachweis/covpass-ios/blob/8ebcb284504c22d40235435cd609409163221ca9/Source/CovPassCommon/Sources/CovPassCommon/Repository/VaccinationRepository.swift#L360
Another open approach, but 4 months old and not in master, has been made via the business rules. https://github.com/eu-digital-green-certificates/dgc-business-rules-testdata/tree/feat/de-invalidation-rule/DE/IR-DE-0001
Hope it helps!
Greetings from Hamburg

additional to my comment above, it seems that the invalidation is sending a push to affected users it's done via the BoosterNotification rules published here: https://distribution.dcc-rules.de/bnrules/b75771eb841a3e17205d590170ff30dd5998299cd67af72ce508f3d57062eda8

Thanks a lot for your valuable input @arnebr!
Not really the most elegant way to revoke certificates, but let's see how this will evolve.


ROS Control for THORMANG3

We would like to see official support for the famous ROS Control framework http://wiki.ros.org/ros_control. This is the backport of our version that we are successfully using on Johnny#5. ROS Control enables to share advanced controls methods across the community, such as our bilateral tele-operation system:
https://www.youtube.com/watch?v=PxDxUY0QzfM
https://www.youtube.com/watch?v=qot0_3341i0
or compliant control based on wrist FT sensors (to be published).
Features:

Adds full ROS Control support on joint level
Sensor interfaces implemented
Joint Position/Trajectory controller pre-configured

Requirements:

Installed ROS Control (e.g. sudo apt-get install ros-kinetic-ros-control ros-kinetic-ros-controllers)
ROBOTIS-GIT/ROBOTIS-Framework#26
ROBOTIS-GIT/ROBOTIS-THORMANG-MPC#16
ROBOTIS-GIT/ROBOTIS-THORMANG-OPC#6

Usage:

Start up robot as used to (real or simulated)
Switch to ros_control_module mode in Demo UI (requires ROBOTIS-GIT/ROBOTIS-THORMANG-OPC#6)
Start rqt
Add trajectory controller plugin (Plugins->Robot Tools->Joint trajectory controller)
Select any trajectory controller from list (using controller manager namespace '/')
Enable it and have fun!

Limitations:

Although lMU and FT sensor interfaces are already implemented, we haven't verified the correctness of sensor data by now.

Thank you for your consideration and supports. This issue will be closed since there were no actions for a while. You can reopen this issue to show this issue to the users whenever. Thanks.


[#91921114] Fix assertion on error message

This exception now returns DISALLOWED_OPERATIONS [ com.vmware.vcloud.entity.vdc:12345678-1234-1234-1234-123456789012 ]
rather than a No access to entity message, so update the test
accordingly.
I don't believe there to be any functional difference between the to
messages and I think it's sufficient to check for a Forbidden
exception type.
Prevents this error:
1) Vcloud::Core::Vdc.new when instantiating with a valid UUID, that does not refer to a Vdc throws a Forbidden error when trying to access the #name of the Vdc
  Failure/Error: expect { subject.name }.to raise_error(
    expected Fog::Compute::VcloudDirector::Forbidden with message matching /No access to entity/, got #<Fog::Compute::VcloudDirector::Forbidden: DISALLOWED_OPERATIONS [ com.vmware.vcloud.entity.vdc:12345678-1234-1234-1234-123456789012 ]> with backtrace:
      # ./lib/vcloud/core/fog/service_interface.rb:33:in `get_vdc'
      # ./lib/vcloud/core/vdc.rb:34:in `vcloud_attributes'
      # ./lib/vcloud/core/vdc.rb:41:in `name'
      # ./spec/integration/core/vdc_spec.rb:83:in `block (5 levels) in <top (required)>'
      # ./spec/integration/core/vdc_spec.rb:83:in `block (4 levels) in <top (required)>'
  # ./spec/integration/core/vdc_spec.rb:83:in `block (4 levels) in <top (required)>'

The build failure here should be fixed by https://github.com/gds-operations/vcloud-core/pull/182.


Queue concurrent feature branch builds at Codeship

How can we handle the following scenario when an organization has >1 concurrent build for their Codeship account:

User A pushes feature/User-A-Code branch on repo my_package
Codeship starts build of feature/User-A-Code to the my_package.feature org
User B pushes feature/User-B-Code branch on repo my_package
Codeship starts a concurrent build of feature/User-B-Code to the my_package.feature org
feature/User-B-Code build fails due to the my_package.feature org is still deploying feature/User-A-Code branch

@almostthor just stumbled upon this - did you mean something like this: https://blog.codeship.com/flexible-deployment-pipelines/ ?

Cleaning up as part of clearing out old issues.
CumulusCI does not intend to solve any concurrency challenges.  The purpose of CumulusCI is to run a single build operation against a single org.  The CI application is what should be responsible for handling concurrency of builds.
If anyone's interested, CumulusCI has a new related project, mrbelvedereci, which we're now using for production builds (as of a week ago).  It is a Salesforce specific CI app and thus is able to properly handle concurrency by queuing builds against persistent orgs and running builds against scratch orgs concurrently.  Our instance is at https://mrbelvedereci.herokuapp.com for reference.


Revision_count mismatch and version reconcilation

Describe the task
UI needs to be updated to alert users when 2 or more people are editing the same form. The user to save first, becomes the source of truth and the second user needs to be notified that they are not using the most up to date data and need to reload. The second users needs to be prevented from over-riding the changes of the 1st by accident.

Acceptance Criteria

[ ] what is required for this task to be complete?
what is the finishing point or end state of this task?
[ ] what is the output of this task?

SME/User Contact
(may want to use a persona to fill this in)
Additional context

any additional details that could not be captured above

file at: Figma


Variables being displayed instead of Values

Reinstall did not alleviate the issue, cropped up when the addon was updated 6/22
Downloaded via WoWUp.io. Running version 2.56.

Can you share what your search pattern setting screen looks like? Same with localization

I have this problem too. Version 2.57.

and the view:

and some error related:

Ah it looks like there is a conflict with another add on from the looks of it with Attune and/or RClootCouncil. Can you confirm if it works if it’s the only add on running ?

Good call on the other addon.
Mine was caused by Titan Panel Classic [Raid Lockout]
https://www.curseforge.com/wow/addons/titan-panel-classic-raid-lockout
Didn't quite achieve what I was looking for so into the bin it goes.
Thanks for putting out this addon, it's an absolute god send.

Yes seems this addon shares some constants/namespace or something like that with a few other addons. Disabling Titan Panel Classic [Raid Lockout] solved this issue for me also but it would be benefitial to find out why and what is causing leakage since I'm getting errors on some other addons as well.
error:

Haven't experienced any conflict with TSM. But I am aware there is a rare sorting error that happens but doesn't spam
In general I suggest to just turn off lua errors to everyone (nothing to do with this addon) as it's annoying as hell, by typing
/console scriptErrors 0

Closing this as this is a conflict between variable names in two add-ons. Since Lua sucks as it defaults variables to be global this is bound to happen. In future when I noticed things are global without needing to be I will make appropriate updates to limit the scope but not going to actively figure out what conflicts with what add-on and who is not accessing the correct data


About Experiences in Section 4.2 (Performance on Synthetic Long Context Tasks) in the paper

Dear authors,
Regarding the experimental results in Section 4.2, I noticed that the authors compared the performance of models using SWA and models using the SelfExtend method on the passkey retrieval task. Although SWA limits the attention window size between tokens, there are many layers in the LLM. It is possible that the last token do not attend to the tokens where the passkey is located in the first layer, but the tokens at the passkey position can propagate backward to the tokens within the SWA window size. This backward propagation continues layer by layer until the final layer. Why can't the passkey information be propagated to the tokens that need to be generated? I am really curious about this question and look forward to your response!

I also observed that the SelfExtend method causes tokens related to the passkey, when placed far from the last token, to have nearly the same distance to the last token. Why doesn’t this lead to the token order of the passkey being reversed in the output?


Update to the newer virtuals plugin

The old lib got deprecated and now throws warnings.
This doesn't affect the functionality and fully tested it in my local project.

Nothing game-breaking, but it works around deprecation warnings on the newest bookshelf version.
Although nothing broke yet, it likely will in the next major bookshelf release :)

Bump

Bump!

Is this project confirmed dead?

Thanks @Mindgamesnl

Released as v5.0.0

Awesome, thanks! :heart:


adding protectionsState to breakage form

Reviewer:

Description:

Steps to test this PR:

Automated tests:

[ ] Unit tests
[ ] Integration tests

Reviewer Checklist:

[ ] Ensure the PR solves the problem
[ ] Review every line of code
[ ] Ensure the PR does no harm by testing the changes thoroughly
[ ] Get help if you're uncomfortable with any of the above!
[ ] Determine if there are any quick wins that improve the implementation

PR Author Checklist:

[ ] Get advice or leverage existing code
[ ] Agree on technical approach with reviewer (if the changes are nuanced)
[ ] Ensure that there is a testing strategy (and documented non-automated tests)
[ ] Ensure there is a documented monitoring strategy (if necessary)
[ ] Consider systems implications

Current dependencies on/for this PR:

main

PR #2313   👈

This stack of pull requests is managed by Graphite.


How to use EMI with IC2C mod?

I am playing on my modpack on version 1.19.2 Forge which has Industrial Craft 2 Classic (IC2C) mod and EMI does not show the craft recipes in most of the blocks from this mod, but I want to use EMI because of the quick craft function and craft history. Can I make to have only these two functions of the mod and use JEI to view the crafts?
(I apologize for my English and the structure of the text, this is the first time I use the Issues button and I used a translator)

No. You can install both mods at the same time and have JEI give recipes to EMI.


Expand alert threshold detection to include vector data

Currently alerts work on raster data sets only. We also need alerts for hazard layers based on vector data such as tropical storms (and earthquakes in the future).
Example: Return an alert if a tropical storm’s wind buffer (a polygon) exceeds 90 km/h for any district in Myanmar. In this case, there isn’t a spatial analysis, just an event that is observed where a vector dataset above 90 km/h is found within an admin area. The screenshot below shows an example where the yellow polygon is 60 km/h and the orange/red is 90 km/h

As discussed with @JorgeMartinezG, we need to differentiate between wind speed buffers and nodes


WIP adding Envoy to the image

this is what I think the initial commit for envoy into the image would look like. Envoy would be turned off and not in the same slice as other services but this commit would allow me to test easier moving forward.

@darora @supaPatrick Can you share the rationale for introducing envoy?

@darora @supaPatrick Can you share the rationale for introducing envoy?

Hey Steve, in our testing it is using significantly less footprint in memory which was the desired outcome of replacing nginx/kong.

@supaPatrick Oh, I see. Are the tests public? Or is there an internal Notion link?

@supaPatrick Oh, I see. Are the tests public? Or is there an internal Notion link?

Here are some of the difference when running envoy other then kong
# ps eo user,pid,vsz,rss $(pgrep -f 'nginx')
USER       PID    VSZ   RSS
root     61413<PHONE_NUMBER>4
kong     61414<PHONE_NUMBER>2
kong     61415<PHONE_NUMBER>6
kong     61416<PHONE_NUMBER>2
kong     61417<PHONE_NUMBER>4
kong     61418<PHONE_NUMBER>8
kong     61419<PHONE_NUMBER>6
# kong stop
Kong stopped
# supervisorctl start envoy
envoy: started
# ps eo user,pid,vsz,rss $(pgrep -f 'envoy')
USER       PID    VSZ   RSS
envoy    62854   6692  2972
envoy    62855 2320208 47844

CONTAINER ID   NAME                           CPU %     MEM USAGE / LIMIT     MEM %     NET I/O           BLOCK I/O         PIDS
5bae4572c390   infrastructure-gotrue-1        0.00%     4.746MiB / 7.667GiB   0.06%     32.1kB / 26kB     32.6MB / 7.04MB   11
f273cdcfbfee   infrastructure-stripe-sync-1   0.00%     4.77MiB / 7.667GiB    0.06%     5.71kB / 1.88kB   107MB / 48.1MB    22
82324f7d55c4   infrastructure-envoy-1         0.71%     11.3MiB / 7.667GiB    0.14%     590kB / 619kB     2.86GB / 10.7MB   21
579351ef40e9   infrastructure-monitoring-1    0.01%     42.67MiB / 7.667GiB   0.54%     1.45MB / 1.96MB   23.4GB / 1.62GB   6
d2596899c88b   infrastructure-kong-1          7.24%     346.8MiB / 7.667GiB   4.42%     2.9MB / 3.26MB    1.4GB / 175MB     7
21812133eee9   infrastructure-rest-1          0.30%     30.82MiB / 7.667GiB   0.39%     6.59MB / 5.04MB   1.85GB / 11MB     39
6c4ed216a190   infrastructure-db-1            0.02%     100.2MiB / 7.667GiB   1.28%     32.7MB / 27.8MB   2.38GB / 29.5MB   22
1d3f1e652bef   infrastructure-pg-api-1        0.61%     61.87MiB / 7.667GiB   0.79%     1.88kB / 0B       2.11GB / 40.5MB   23

Looks good once we resolve https://github.com/supabase/postgres/pull/743#discussion_r1348095430


Class cannot be read from Sqlite3 database

Error: Class cannot be read from Sqlite3 database. Please check the type of field usersReviewList(java.util.ArrayList)
Hi, sugarORM can not read from the database fields stored in a custom object called UserReview in practice in my code I have an object called appWatched and for each object can have multiple objects UserReview which for convenience are saved in a list , when I try to read data stored in the database sugar fails to read the values stored in the table USER_REVIEW , how do I fix ? an extract from the code of java objects :
public class AppWatched extends SugarRecord{
private String appPackageName;
private String appName;
private String appLogoUrl;
private String vote;
private String numPeapleRating;
private String numStarsRatingFive;
private String numStarsRatingFour;
private String numStarsRatingThree;
private String numStarsRatingTwo;
private String numStarsRatingOne;
private List<UserReview> usersReviewList;

public AppWatched(){ }

}
public class UserReview extends SugarRecord{
private String userAvatarUrl;
private String userName;
private String currentRation;
private String reviewDate;
private String reviewTitle;
private String reviewBody;

public UserReview() {}

}
Used Version:
compile 'com.github.satyan:sugar:1.3'

ArrayList or other collections aren't supported yet :-(
Only solution and then create a report 1 to n between my items , thanks

you model a 1:n relationship, put a AppWatched member into the UserReview class at first to have that relation. i would then put a @Ignore to the usersReviewList and fill that list when needed. code like:
usersReviewList = UserReview.find(UserReview.class, "appWatched = ?", Long.toString(getId()));
(i hope i did not mix something ;) )

this one is serious, and should be supported

@emdete I thinked column names are snack cased as in appWatched maps to "app_watched". Please correct me if I am wrong

Is this still on-going? Are collections of any kind not supported? This is a massive deal-breaker

Okay, it's 2018 and it's crazy how such an important thing is missing.
I found this way to be quite helpful: Basically storing it as a string json
https://stackoverflow.com/a/46543631/3520157


Repo Mountie should sign PRs

Many repos in open source communities require that all PRs be signed for DCO purposes.  For a background, see this GitHub link and this page that has the declaration. Our projects that often wind up being moved to the Linux Foundation require DCOs on all commits and it's at best a painful git exercise to retroactively sign PRs.  For now, we can accept repomountie PRs and have to manually add equivalent PRs.
Please add signing to each repo mountie PRs.  Signing in this case just means adding a blank line and name/email address to the commit message:
This is my commit message

Signed-off-by: Random J Developer<EMAIL_ADDRESS>

@swcurran We're just rolling this feature out now. If it's still not doing this correctly LMK.
Duplicate of #101

Awesome - I should have known Wade would have put one in :-).  I should have looked in the closed issues first - doh!


rename join-pairs to merge-pairs

Addresses #84
Ready for review, all feedback welcome!

@lizgehret, would you like to include this in 2022.11 or wait for now?
The full discussion around this PR is here: https://github.com/qiime2/q2-vsearch/issues/84


Fix a bug with unnecessary kwargs unpacking

Proposed changes:

fix a bug with unnecessary kwargs unpacking in rasa.test.test_core call from rasa.test.test (see issue https://github.com/RasaHQ/rasa/issues/4798)

Status (please check what you already did):

[x] made PR ready for code review
[ ] added some tests for the functionality
[ ] updated the documentation
[x] updated the changelog
[x] reformat files using black (please check Readme for instructions)

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

Thanks for the PR, we'll give it a review as soon as possible.

@imLew does this have to do with https://github.com/RasaHQ/rasa/issues/4458?

@erohmensing it's the same underlying issue (having an argument called kwargs which is not the typical catch-all-additional-keyword-args, ie **kwargs), but it is not the what that issue was referring to.
Looking at this function, I think this PR fixes the superficial issue resulting from using the name kwargs as an argument name. Right now test_core will complain about "unexpected keyword argument" if kwargs is unpacked and is not empty. But this should should addressed in more comprehensive way, either changing the name kwargs or rewritting it to use **kwargs.


Shell linters and github action

Adds and refactors existing shell based linters and adds a github workflow to run static analysis.
Closes #10392

./main.sh: 141: test_static_analysis: not found

./main.sh: 141: test_static_analysis: not found

@tomponline I've removed this from test/main.sh now

@markylaing any ideas why the workflows dont seem to be running on github anymore?

@markylaing any ideas why the workflows dont seem to be running on github anymore?

@tomponline not a clue :unamused:


free(): invalid pointer Aborted (core dumped)

This is basically the same issue as https://github.com/DjDeveloperr/skia_canvas/issues/67 but I fixed the part that was user error (I hope), now I'm seeing this:
root@ubuntu-s-1vcpu-512mb-10gb-nyc1-01:~# deno run -A --unstable-ffi captcha.ts
free(): invalid pointer
Aborted (core dumped)

Reproduction:
import { createCaptcha } from<EMAIL_ADDRESS>import { createCanvas } from 'jsr<EMAIL_ADDRESS>
const canvas = createCanvas(300, 100);
const ctx = canvas.getContext('2d') as unknown as CanvasRenderingContext2D;

const { text } = createCaptcha({ ctx });

const uri = canvas.toDataURL();

console.log(text);
console.log(uri);

I tried to look at the core dump and it's a 548MB ELF file.

Thanks for reporting this, I've identified the bug in native code. A local structure's pointer was stored in context state which is wrong. I will release a fix ASAP.

Fixed in 0.5.7


Can't download mac app from http://gitify.io site

When click on Mac OSX button, the API request fails so nothing is downloaded.
Here's the API that's returning 403: https://api.github.com/repos/manosim/gitify/releases/latest
Error message:
{
"message": "API rate limit exceeded for <IP_ADDRESS>. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)",
"documentation_url": "https://developer.github.com/v3/#rate-limiting"
}

This link works fine for me. Have you tried it again since then? If so, is this still an issue?

I just tried it again, everything seems to be working fine now!


[FLINK-8421] [DataStream] Make timer serializers reconfigurable on restore

What is the purpose of the change
Previously, key and namespace serializers of the HeapInternalTimerService were not reconfigured on restore.
In Flink 1.4.0, we removed Avro dependency, and on restore if the Avro dependency is not present, a DummyAvroKryoSerializerClass was registered to Kryo as a placeholder, which altered the base Kryo registrations in the KryoSerializer. This change required a serializer reconfiguration in order for restores to work. Effectively, this allowed the issue in the HeapInternalTimerService to surface.
This PR fixes this by writing also the TypeSerializerConfigSnapshots of the key and namespace serializer of the HeapInternalTimerService into savepoints, and use them to reconfigure new serializers on restore.
Since this would change the binary format of the written timer services, this PR also uses this opportunity to properly make the format versioned.
This needs to be merged for release-1.4 also.
More details of the change is explained below.
Brief change log

1bc3cd0: A preliminary migration test that took a savepoint of a WindowOperator with keys that required serialization using the KryoSerializer. Savepoints were taken for Flink versions 1.2 and 1.3. Restoring from this savepoint in Flink 1.4 fails, and requires the following commits to pass.

e1fd1fc: Always use the FailureTolerantObjectInputStream to read objects in the InstantiationUtil.deserializeObject(...) methods. That special stream avoids restore failures with ClassNotFoundException if Avro is not present, but there were leaks where during the restore process, that special input stream was not used.

a078eed and dfa3e82: Introduced ByteArrayPrependedInputStream and PostVersionedIOReadableWritable. These are utility classes that were required to migrate the serialization format of the timer services from non-versioned to versioned.

4e27a4b: The main change, which adds key / namespace serializer config snapshots and use them for serializer reconfiguration on restore. This commit also makes the format versioned.

Verifying this change

The migration test added in 1bc3cd0 will not pass without all fixes.
Unit tests are added for the new ByteArrayPrependedInputStream and PostVersionedIOReadableWritable classes.
The testSnapshotAndRestore and testSnapshotAndRebalancedRestore tests in HeapInternalTimerServiceTest are adapted to test both versioned and previous non-versioned formats.

Does this pull request potentially affect one of the following parts:

Dependencies (does it add or upgrade a dependency): (yes / no)
The public API, i.e., is any changed class annotated with @Public(Evolving): (yes / no)
The serializers: (yes / no / don't know)
The runtime per-record code paths (performance sensitive): (yes / no / don't know)
Anything that affects deployment or recovery: JobManager (and its components), Checkpointing, Yarn/Mesos, ZooKeeper: (YES / no / don't know)
The S3 file system connector: (yes / no / don't know)

Documentation

Does this pull request introduce a new feature? (yes / no)
If yes, how is the feature documented? (not applicable / docs / JavaDocs / not documented)

@aljoscha As discussed offline, I've:

replaced ByteArrayPrependedInputStream with Java's PushbackInputStream
use negative values in VERSIONED_IDENTIFIER to be extra safe

I think this is good to go now. 👍 😃

Thanks for the reviews!
Will merge after Travis gives green.


Feature Request?

Hi would like a featured to download deleted accounts/arts is that possible?

That is not actually possible, sorry! For that sort of thing, you'll wanna look at a project like this: https://furarchiver.net/
It archives most every account that's been on FA, so it has all of that past info; my program can only gather what's already currently there. It doesn't keep a history of past/deleted accounts.


Pop switch expression  correctly

This PR fixes a small behaviour bug with the switch statement. Prior to this, the switch expression was never popped out of stack at the end of the case statements, polluting the stack and leading to problems.
Type of change:

[X] Bug fix

I think this could be more noticible when there is a switch statement inside a loop and taking a look at the traced instructions.
Here a basic example:
for(var i = 1; i <= 3; i += 1)
{
    switch(i)
    {
        case 1:
        {
            print("One");
            break;
        }
        case 2:
        {
            print("Two");
            break;
        }
        case 3:
        {
            print("Three");
            break;
        }
    }
    print("Other");
}

With a longer and intense loop it could be noticed better, but after all the compare jumps you should see the switch expression left up on the stack.


Please update the github documentation posted in this page with latest changes on Azure portal

[Enter feedback here]

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

ID: 714f2c6b-3bc4-9e14-7f0a-7b56d52ac1fa
Version Independent ID: 7a00b7d7-f46b-1aa3-f2ea-7fd0bcee3f95
Content: Configure authentication in a sample web application using Azure Active Directory B2C
Content Source: articles/active-directory-b2c/configure-authentication-sample-web-app.md
Service: active-directory
Sub-service: b2c
GitHub Login: @msmimart
Microsoft Alias: mimart

@mehdijalal
Thanks for your feedback! I've assigned this issue to the author who will investigate and update as appropriate.

Thanks @mehdijalal for taking time to share your valuable feedback. The GitHub document now points to the Azure AD B2C doc.
#please-close


Failing to run main because of SQLEngine

I would like to get some assistance with a small issue I am facing (not strong in python). I have tried using pip install SQLEngine and even went on to install SQLAlchemy but I can't seem to go past this stage when I run python main.py
Can you please help
└> python2.7 main.py Traceback (most recent call last):   File "main.py", line 4, in <module>     from securitybot.bot import SecurityBot   File "/Users/pathXXXX/securitybot/securitybot/bot.py", line 9, in <module>     from securitybot.user import User   File "/Users/pathXXXX/securitybot/securitybot/user.py", line 11, in <module>     import securitybot.ignored_alerts as ignored_alerts   File "/Users/pathXXXX/securitybot/securitybot/ignored_alerts.py", line 6, in <module>     from securitybot.sql import SQLEngine   File "/Users/pathXXXX/securitybot/securitybot/sql.py", line 7, in <module>     from typing import Any, Sequence ImportError: No module named typing

Try pip install typing.
On Mon, 20 Mar 2017, 03:00 Hatitye<EMAIL_ADDRESS>wrote:

I would like to get some assistance with a small issue I am facing (not
strong in python). I have tried using pip install SQLEngine and even went
on to install SQLAlchemy but I can't seem to go past this stage when I
run python main.py
Can you please help
└> python2.7 main.py Traceback (most recent call last): File "main.py",
line 4, in  from securitybot.bot import SecurityBot File
"/Users/pathXXXX/securitybot/securitybot/bot.py", line 9, in  from
securitybot.user import User File
"/Users/pathXXXX/securitybot/securitybot/user.py", line 11, in
import securitybot.ignored_alerts as ignored_alerts File
"/Users/pathXXXX/securitybot/securitybot/ignored_alerts.py", line 6, in
 from securitybot.sql import SQLEngine File
"/Users/pathXXXX/securitybot/securitybot/sql.py", line 7, in  from
typing import Any, Sequence ImportError: No module named typing
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/dropbox/securitybot/issues/16, or mute the thread
https://github.com/notifications/unsubscribe-auth/AAEewvwxz6mTYFebgDemgIQFnWdkpRnKks5rnk4pgaJpZM4MiNwE
.

👍 Had missed the requirements.txt file 😞


Lacking support of JSON fields

Describe the bug
No data appears for MySQL JSON fields when using Prisma.
Installed libraries and their versions

<EMAIL_ADDRESS><EMAIL_ADDRESS><EMAIL_ADDRESS>
To Reproduce
Steps to reproduce the behavior:

Have JSON field in one of your resources
View it in dashboard
No data appears

Expected behavior
JSON field is supported (its data appears in the dashbord & is editable).
Screenshots
https://prnt.sc/SIEr4FMIR48a
AdminJSOptions with schema
Exactly as in docs:
https://docs.adminjs.co/installation/adapters/prisma

In non-mongoose adapters we're unable to retrieve JSON objects and determine their types automatically.
You would have to modify this property's type in your resource options to be either:

mixed - it requires you to define subfields and doesn't have a dynamic structure but you're able to save JSONs with specific types conversion:

properties: {
  meta: { type: 'mixed' },
  'meta.name': { type: 'string' },
  'meta.timestamp': { type: 'number' },
  // etc
}

key-value - it loads your JSON from database as it is and allows you to add new keys, but all values are saved as text

properties: {
  meta: { type: 'key-value' },
}

@dziraf
Okay, I tried this and was able to make the JSON data display correctly. To show nested JSON you need to combine 'mixed' with 'key-value', e.g:
meta: { type: 'mixed' }, 'meta.request': { type: 'key-value' },
There are however several important issues with JSON fields right now.
1. You can't update resource if one of JSON fields is null.
Error: Argument X for data.X must not be null. Please use undefined instead.
Fix: This happens because you use null instead of Prisma's null values (e.g. Prisma.DbNull):
https://www.prisma.io/docs/concepts/components/prisma-client/working-with-fields/working-with-json-fields#inserting-null-values
2. When you update a JSON field, all primitves are cast to string.
true ends up being "true", null becomes "", 25 changes to "25". This is very bad.
Fix: see #3

You are required to define the JSON tree beforehand it order to work with it.

Instead of defining the type once for nested JSON you need to describe the tree as described in the beginning.
Fix: Add 'json' property type. When showing the value in the client, show it as is and only beautify the JSON. This is how Laravel Nova does it and it works perfectly (https://prnt.sc/9-qwjPSF1gQH).


Added Git Lint gem

Submission Requirements

[x] I've reviewed the contribution guidelines.
[x] This is an awesome CLI that I've used and cannot live without.

Describe the CLI app

Repository/Homepage link: Git Lint
Description: A Git commit linter and code quality tool. Ensures you maintain a clean, easy to read, debuggable, and maintainable project history.

Why is this CLI app awesome?

Enforces a Git Rebase Workflow.
Enforces a clean and consistent Git commit history.
Supports Git default branch configuration.
Provides a customizable suite of analyzers.
Provides Git Hook support for local use.
Provides Continuous Integration (CI) support.

How does this CLI compare with other similar tools?
I don't know of any other CLI that is solely focused on being customizable while easily hooked into your Git workflow along with auto-detection support for various build systems. I suppose Overcommit and/or Pronto come close.

Hi Brooke 👋
Thank you for your submission.
I've tried to make the contribution guides as concise, precise and straightforward as possible without being too prescriptive. One of the things I mention is significant download numbers. GitHub stars, downloads, releases are some of the metrics that help to estimate if a tool is used by other devs.
Your project has really great documentation and good potential to become a must-have tool. But as things stand currently, it has very few download numbers and is rather 'fresh'. I'd like for the list to contain tools that are more widely used. So for now I'm afraid I won't be able to include git-lint into the list. I'd like to see your project grow a bit more and then I'm sure it will find its way into the list. It's on my radar now.


Filename Pattern not working as expected.

Azure DevOps Extension you are using
Version Angular Environment.TS File
Where are you running it?
You can run the extensions in the cloud or on-premise

Azure DevOps Server (on-premise TFS, Version 15.117.26714.0)

Version of Extension/Task
v2.11.2
Expected behaviour and actual behaviour
We have multiple environment files used for prod and test (environment.prod.ts). Using the file pattern does not work as expected. This means a patterns like "environment*.ts" will not work and does not find the file.

2019-05-22T07:30:21.5881330Z Filename Pattern: environment*.ts
2019-05-22T07:30:21.5881330Z Version Number/Build Number: ZBJ Tablet Manager CI <IP_ADDRESS>
2019-05-22T07:30:21.5881330Z Version Filter to extract build number: \d+.\d+.\d+.\d+
2019-05-22T07:30:21.5881330Z Version Format for JSON File: {1}.{2}.{3}.{4}
2019-05-22T07:30:21.5881330Z Field to update (all if empty): version
2019-05-22T07:30:21.5881330Z Inject Version: false
2019-05-22T07:30:21.5881330Z Output: Version Number Parameter Name: OutputedVersion
2019-05-22T07:30:21.5881330Z Extracting version number from build number
2019-05-22T07:30:21.5881330Z Extracted Build Version: <IP_ADDRESS>
2019-05-22T07:30:21.5881330Z Angular Version Name will be: <IP_ADDRESS>
2019-05-22T07:30:26.0256692Z ##[warning]Found no files.

Looking at the code it does an endsWith compare and not an actual pattern compare.
        if (file.toLowerCase().endsWith(filename.toLowerCase())) {
          filelist.push(path.join(dir, file));
        }

Steps to reproduce the problem

Use a node project with multiple environment files.
Use a file pattern of "environment*.ts".
Run the build.

Good catch, that shoould be a more complext match, paybe some regrex. I will have a look at it

Looking forward to a fix. These tasks are very handy 👍

@martijnvanschie This has been fixed in 2.12.1
You can now enter the filename as environmen.ts regex environment.(.*).ts
If this issue remains a problem please do not hesitate to re-open it

Just tested it. Works like a charm.
Many thank :)
👍


[KO] Translation of Umbrella Projects Lesson.

Related #201.
I had busy days. I apologize for being late for finalizing Korean Translations. :pray:
You can compare this with original text at devleoper/elixir-school#5
Feel free to review. @Dalgona @malkoG @riseshia

Nice :+1:


Master to live

Docs Build status updates of commit b01cd8c:
:white_check_mark: Validation status: passed

File
Status
Preview URL
Details

academic-services/graph/network-similarity.md
:white_check_mark:Succeeded

academic-services/knowledge-exploration-service/reference-get-interpret.md
:white_check_mark:Succeeded

academic-services/knowledge-exploration-service/reference-post-interpret.md
:white_check_mark:Succeeded

academic-services/project-academic-knowledge/TOC.yml
:white_check_mark:Succeeded

academic-services/project-academic-knowledge/reference-interpret-method.md
:white_check_mark:Succeeded

For more details, please refer to the build report.
Note: If you changed an existing file name or deleted a file, broken links in other files to the deleted or renamed file are listed only in the full build report.


tilemap problems

A problem with my own code ( i think )

when I switch out tilemaps / tilelayers, they update visually, but not if i begin to move tiles around.
basically i am trying to switch out tilemaps or tilemap layers for different levels of the game.
It's just not working as expected, I will be happy to give more detail if needed
also the shuffle method on the tilemap isn't working properly, it swaps the tiles around visually but doesn't retain their properties

I have been destroying/creating new layers. Maybe I should create all of the layers, and switch between them by changing opacity/bring to front, something like that?

a layer seems to only work as long as it is first in the array of layers

update: i got everything working except for shuffle, described here by someone with the same question, they never got an answer http://www.html5gamedevs.com/topic/12946-tilemap-shuffle/

I think you should be able to switch TilemapLayers on and off with exists.

@samme thanks if i run into any more problems I will try exists, i've got everything working now though


Add Directory Mention provider for Cody

Closes: https://linear.app/sourcegraph/issue/SRCH-892/support-mentioning-dirs-and-better-monorepo-support-overall
This PR adds @Directories and @Remote Directories mention providers for Cody.
Merge it only after this commit is merged & deployed on sourcegraph.sourcegraph.com: https://github.com/sourcegraph/sourcegraph/commit/0684b550cb318e9cbe3d68790ea15dda156b410e
It requires a new filesPattern filter on getCodyContext API. Therefore the providers are limited to SG version 5.7.0 and the insider builds.
Test plan
Demo: https://www.loom.com/share/e55afcb2a5064a708a08f7851a618b2e?sid=8d68a39c-521a-4b47-9e5d-fb769f3975f4
Changelog

Add @-mention directories & remote directories provider for enterprise Cody users.

Backend PR here

This is awesome. When @-mentioning a directory in your current workspace, you mention it's fetching context from the server. This means it will lack any local changes and won't get the entire files. This could be confusing to users:

What if the dir they want doesn't exist remotely?
What if it exists remotely on a non-default branch?
What if the files have changed?
I understand that relying on the server is necessary for big dirs where we need to context-search inside of them to select context snippets, but if it's just a few files, users might want the entire contents to be included (not just snippets).

I think we can break down the use cases for directory @-mentions into:

(A) I want to use relevant context (but not the entire contents) from a big directory that I haven't made local changes to. I don't know which specific files or snippets that I want to use.
(B) I want to use the entire contents from all files in a small directory that I may have made local changes to.

This PR addresses (A) but not (B). So, definitely worth merging as this is a huge step forward, but I think we need to solve for (B) as well and remove user confusion about what is happening. I'll get @rrhyne's help here.

@sqs from the loom, I think this covers both local and remote directories. I will say I was a bit surprised at the distinction though.
On that topic, I think we should have a single directory provider that can accept a local or remote URL.
@thenamankumar One way to accomplish this is to add a top-level item to the @directory menu with a label that reads "Enter remote directory URL". I believe you could then trigger your RemoteDirectory functionality.
Question: What kind of directories? Does it support many code hosts, or is this only GitHub? We should consider strategic scale and code host support before this is enterprise-ready.

@rrhyne:

@sqs from the loom, I think this covers both local and remote directories.

It supports directories in the current repo, but the directory list and the contents are both pulled from the server, which means it won't include local changes.

Does it support many code hosts, or is this only GitHub?

The remote directories are pulled from a Sourcegraph instance, not directly from GitHub, so it should support any code host supported by Sourcegraph. We do not support naming an arbitrary remote directory because this is implemented as a filter on the context search, and we cannot do a context search on an arbitrarily-large directory on a codehost.

Thanks for the feedback @sqs, all of it makes sense. I have moved the conversation to linear. Will work with @rrhyne to figure out how we can solve the usecase B. As it is more like a UX problem than a technical one, I'll merge this PR and do the further needful as an incremental improvement. Anyways it will be released to enterprise customers in September.


Accessibility issue in "Forms → Autocomplete" (contrast issue)

Describe the bug
The grey hover state has a contrast ratio of 1.1:1 on the white background making it less than the sufficient 3.0:1. In accordance with WCAG 2.1, this does not satisfy the 1.4.3 Contrast (minimum).

How to fix
Leave it up to the UI designers. Inverting the colours is usually a good starting point.

Reminder to myself. Make text bold.

Reminder to myself. Make text bold.


merge_snp issue still exist

Hi,
From your command line history midas2_output/LRDYA/snps/145629.snps.tsv.lz4, can you make sure the the sample name provided to the merge_snps command --samples_list list_of_samples.tsv is LRDYA?
Thanks,
Chunyu
Originally posted by @zhaoc1 in https://github.com/czbiohub/MIDAS2/issues/88#issuecomment-1150724995
i reference this issue but this kind of bug still exist.
command：
midas2 merge_snps   --samples_list list_of_samples.tsv --midasdb_name uhgg --midasdb_dir ~/database/midas2/ midas2/  --debug
issue：
1661742862.8:  Across samples population SNV calling in subcommand merge_snps with args
1661742862.8:  {
1661742862.8:      "subcommand": "merge_snps",
1661742862.8:      "force": false,
1661742862.8:      "debug": true,
1661742862.8:      "zzz_worker_mode": false,
1661742862.8:      "batch_branch": "master",
1661742862.8:      "batch_memory": 378880,
1661742862.8:      "batch_vcpus": 48,
1661742862.8:      "batch_queue": "pairani",
1661742862.8:      "batch_ecr_image": "pairani:latest",
1661742862.8:      "midas_outdir": "midas2/",
1661742862.8:      "samples_list": "list_of_samples.tsv",
1661742862.8:      "midasdb_name": "uhgg",
1661742862.8:      "midasdb_dir": "/home/lbl/database/midas2/",
1661742862.8:      "species_list": null,
1661742862.8:      "genome_depth": 5.0,
1661742862.8:      "genome_coverage": 0.4,
1661742862.8:      "sample_counts": 2,
1661742862.8:      "site_depth": 5,
1661742862.8:      "site_ratio": 3.0,
1661742862.8:      "site_prev": 0.9,
1661742862.8:      "snv_type": "common",
1661742862.8:      "snp_pooled_method": "prevalence",
1661742862.8:      "snp_maf": 0.05,
1661742862.8:      "snp_type": "bi, tri, quad",
1661742862.8:      "locus_type": "any",
1661742862.8:      "num_cores": 16,
1661742862.8:      "chunk_size": 1000000,
1661742862.8:      "advanced": false,
1661742862.8:      "robust_chunk": false
1661742862.8:  }
1661742863.7:  248 species pass the filter
1661742863.7:  Create OUTPUT directory.
1661742863.7:  'rm -rf midas2/snps'
1661742863.7:  'mkdir -p midas2/snps'
1661742863.7:  Create TEMP directory.
1661742863.7:  'rm -rf midas2/temp/snps'
1661742863.7:  'mkdir -p midas2/temp/snps'
1661742870.0:  MIDAS2::write_species_summary::start
1661742870.0:  MIDAS2::write_species_summary::finish
1661742870.6:  MIDAS2::design_chunks::start
Traceback (most recent call last):
File "/home/lbl/miniconda3/envs/midas2.0/bin/midas2", line 8, in
sys.exit(main())
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/main.py", line 24, in main
return subcommand_main(subcommand_args)
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 664, in main
merge_snps(args)
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 658, in merge_snps
raise error
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 639, in merge_snps
arguments_list = design_chunks(species_ids_of_interest, midas_db)
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 220, in design_chunks
all_site_chunks = multithreading_map(design_chunks_per_species, [(sp, midas_db) for sp in dict_of_species.values()], num_cores) #<---
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/common/utils.py", line 540, in multithreading_map
return _multi_map(func, items, num_threads, ThreadPool)
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/common/utils.py", line 520, in _multi_map
return p.map(func, items, chunksize=1)
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 205, in design_chunks_per_species
return sp.compute_snps_chunks(midas_db, chunk_size, "merge")
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/models/species.py", line 84, in compute_snps_chunks
chunks_of_sites = load_chunks_cache(local_file)
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/site-packages/midas2/models/species.py", line 181, in load_chunks_cache
chunks_dict = json.load(stream)
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/json/init.py", line 296, in load
parse_constant=parse_constant, object_pairs_hook=object_pairs_hook, **kw)
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/json/init.py", line 348, in loads
return _default_decoder.decode(s)
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/json/decoder.py", line 337, in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
File "/home/lbl/miniconda3/envs/midas2.0/lib/python3.7/json/decoder.py", line 355, in raw_decode
raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
how to fix it？

Hi,
The error message suggested the error happened during load_chunks_cache() step. Can you make sure the provided local copy of MIDASDB ~/database/midas2/ has been properly downloaded? Please refer to https://midas2.readthedocs.io/en/latest/download_midasdb.html for downloading MIDASDB.
Thanks.
Chunyu

i use right chunks，but issue still happen. And i am sure  MIDASDB  has been properly downloaded
command:
midas2 merge_snps   --samples_list list_of_samples.tsv --midasdb_name uhgg --midasdb_dir ~/database/midas2/ midas2/   --chunk_size 500000 --sample_counts 40
issue:
1661822975.2:  Across samples population SNV calling in subcommand merge_snps with args
1661822975.2:  {
1661822975.2:      "subcommand": "merge_snps",
1661822975.2:      "force": false,
1661822975.2:      "debug": false,
1661822975.2:      "zzz_worker_mode": false,
1661822975.2:      "batch_branch": "master",
1661822975.2:      "batch_memory": 378880,
1661822975.2:      "batch_vcpus": 48,
1661822975.2:      "batch_queue": "pairani",
1661822975.2:      "batch_ecr_image": "pairani:latest",
1661822975.2:      "midas_outdir": "midas2/",
1661822975.2:      "samples_list": "list_of_samples.tsv",
1661822975.2:      "midasdb_name": "uhgg",
1661822975.2:      "midasdb_dir": "/home/lbl/database/midas2/",
1661822975.2:      "species_list": null,
1661822975.2:      "genome_depth": 5.0,
1661822975.2:      "genome_coverage": 0.4,
1661822975.2:      "sample_counts": 40,
1661822975.2:      "site_depth": 5,
1661822975.2:      "site_ratio": 3.0,
1661822975.2:      "site_prev": 0.9,
1661822975.2:      "snv_type": "common",
1661822975.2:      "snp_pooled_method": "prevalence",
1661822975.2:      "snp_maf": 0.05,
1661822975.2:      "snp_type": "bi, tri, quad",
1661822975.2:      "locus_type": [
1661822975.2:          "CDS"
1661822975.2:      ],
1661822975.2:      "num_cores": 16,
1661822975.2:      "chunk_size": 500000,
1661822975.2:      "advanced": false,
1661822975.2:      "robust_chunk": false
1661822975.2:  }
1661822976.1:  3 species pass the filter
1661822976.1:  Create OUTPUT directory.
1661822976.1:  'rm -rf midas2/snps'
1661822976.1:  'mkdir -p midas2/snps'
1661822976.1:  Create TEMP directory.
1661822976.1:  'rm -rf midas2/temp/snps'
1661822976.1:  'mkdir -p midas2/temp/snps'
1661822976.2:  MIDAS2::write_species_summary::start
1661822976.2:  MIDAS2::write_species_summary::finish
1661822976.8:  MIDAS2::design_chunks::start
1661822976.9:  ================= Total number of compute chunks: 24
1661822976.9:  MIDAS2::design_chunks::finish
1661822976.9:  MIDAS2::multiprocessing_map::start
1661822977.0:    MIDAS2::process::102478-0::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-0::start accumulate_samples
1661822977.0:    MIDAS2::process::102478-1::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-1::start accumulate_samples
1661822977.0:    MIDAS2::process::102478-2::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-2::start accumulate_samples
1661822977.0:    MIDAS2::process::102478-3::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-3::start accumulate_samples
1661822977.0:    MIDAS2::process::102478-4::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-4::start accumulate_samples
1661822977.0:    MIDAS2::process::102478-5::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-5::start accumulate_samples
1661822977.0:    MIDAS2::process::102478-6::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-6::start accumulate_samples
1661822977.0:    MIDAS2::process::102478-7::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-7::start accumulate_samples
1661822977.0:    MIDAS2::process::102478-8::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-8::start accumulate_samples
1661822977.0:    MIDAS2::process::102478-9::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::102478-9::start accumulate_samples
1661822977.0:    MIDAS2::process::101346-0::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::101346-0::start accumulate_samples
1661822977.0:    MIDAS2::process::101346-1::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::101346-1::start accumulate_samples
1661822977.0:    MIDAS2::process::101346-2::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::101346-2::start accumulate_samples
1661822977.0:    MIDAS2::process::101346-3::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::101346-3::start accumulate_samples
1661822977.0:    MIDAS2::process::101346-4::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::101346-4::start accumulate_samples
1661822977.0:    MIDAS2::process::101346-5::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::101346-5::start accumulate_samples
1661822977.0:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822977.0:    MIDAS2::process::101346-6::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::101346-6::start accumulate_samples
1661822977.0:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/101346.snps.tsv.lz4.
1661822977.0:    MIDAS2::process::101346-7::start snps_worker
1661822977.0:      MIDAS2::chunk_worker::101346-7::start accumulate_samples
1661822977.1:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/101346.snps.tsv.lz4.
1661822977.1:    MIDAS2::process::102492-0::start snps_worker
1661822977.1:      MIDAS2::chunk_worker::102492-0::start accumulate_samples
1661822977.1:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822977.1:    MIDAS2::process::102492-1::start snps_worker
1661822977.1:      MIDAS2::chunk_worker::102492-1::start accumulate_samples
1661822977.1:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102492.snps.tsv.lz4.
1661822977.1:    MIDAS2::process::102492-2::start snps_worker
1661822977.1:      MIDAS2::chunk_worker::102492-2::start accumulate_samples
1661822977.2:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/101346.snps.tsv.lz4.
1661822977.2:    MIDAS2::process::102492-3::start snps_worker
1661822977.2:      MIDAS2::chunk_worker::102492-3::start accumulate_samples
1661822977.2:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822977.2:    MIDAS2::process::102492-4::start snps_worker
1661822977.2:      MIDAS2::chunk_worker::102492-4::start accumulate_samples
1661822977.3:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/101346.snps.tsv.lz4.
1661822977.3:    MIDAS2::process::102492-5::start snps_worker
1661822977.3:      MIDAS2::chunk_worker::102492-5::start accumulate_samples
1661822977.3:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102492.snps.tsv.lz4.
1661822977.3:    MIDAS2::process::102478--1::wait collect_chunks
1661822977.3:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822977.3:    MIDAS2::process::101346--1::wait collect_chunks
1661822977.4:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/101346.snps.tsv.lz4.
1661822977.4:    MIDAS2::process::102492--1::wait collect_chunks
1661822977.4:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/101346.snps.tsv.lz4.
1661822977.4:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102492.snps.tsv.lz4.
1661822977.4:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822977.5:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/101346.snps.tsv.lz4.
1661822977.5:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/101346.snps.tsv.lz4.
1661822977.5:    MIDAS2::process::101346--1::start collect_chunks
cat: midas2/temp/snps/101346/cid.0_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/101346/cid.1_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/101346/cid.2_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/101346/cid.3_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/101346/cid.4_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/101346/cid.5_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/101346/cid.6_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/101346/cid.7_snps_info.tsv.lz4: No such file or directory
1661822977.6:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822977.6:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102492.snps.tsv.lz4.
1661822977.7:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822977.8:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102492.snps.tsv.lz4.
1661822977.8:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822977.9:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822977.9:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102492.snps.tsv.lz4.
1661822977.9:    MIDAS2::process::102492--1::start collect_chunks
cat: midas2/temp/snps/102492/cid.0_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102492/cid.1_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102492/cid.2_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102492/cid.3_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102492/cid.4_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102492/cid.5_snps_info.tsv.lz4: No such file or directory
1661822978.0:  WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
1661822978.0:    MIDAS2::process::102478--1::start collect_chunks
cat: midas2/temp/snps/102478/cid.0_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102478/cid.1_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102478/cid.2_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102478/cid.3_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102478/cid.4_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102478/cid.5_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102478/cid.6_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102478/cid.7_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102478/cid.8_snps_info.tsv.lz4: No such file or directory
cat: midas2/temp/snps/102478/cid.9_snps_info.tsv.lz4: No such file or directory
1661822978.0:  Bugs in the codes, keep the outputs for debugging purpose.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 270, in process
snps_worker(species_id, chunk_id)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 293, in snps_worker
chunk_worker(chunks_of_sites[chunk_id][0])
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 345, in chunk_worker
accumulate(accumulator, proc_args)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 378, in accumulate
for row in select_from_tsv(stream, schema=curr_schema, selected_columns=snps_pileup_basic_schema, result_structure=dict):
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/common/utils.py", line 392, in select_from_tsv
assert False, f"Line {i + j} has {len(values)} columns;  was expecting {len(headers)}."
AssertionError: Line 0 has 13 columns;  was expecting 8.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/lbl/miniconda3/envs/midas2/bin/midas2", line 8, in
sys.exit(main())
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/main.py", line 24, in main
return subcommand_main(subcommand_args)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 664, in main
merge_snps(args)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 653, in merge_snps
raise error
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/merge_snps.py", line 643, in merge_snps
proc_flags = multiprocessing_map(process, arguments_list, args.num_cores)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/common/utils.py", line 532, in multiprocessing_map
return _multi_map(func, items, num_procs, multiprocessing.Pool)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/common/utils.py", line 520, in _multi_map
return p.map(func, items, chunksize=1)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
AssertionError: Line 0 has 13 columns;  was expecting 8.

Hi,
I can see a different error message was reported here.
WARNING: Non-zero exit code 141 from reader of midas2/HC1/snps/102478.snps.tsv.lz4.
AND
AssertionError: Line 0 has 13 columns; was expecting 8.
This seems like for single sample SNP (midas run_snps), you passed the --advanced , can you try to pass the --advanced in your merge_snps command? The basic SNP output files have 8 columns while the advanced SNP output files have 13 columns.
Chunyu

Thanks ，this issue is already fix. Now i have another issue. I use pre-build pangenome to call snp.
Here is my command:
midas2 run_snps --sample_name HC1
-1 ~/HCCMicrobiome/HCC/HC1_R1.fastq.gz
-2 ~/HCCMicrobiome/HCC/HC1_R2.fastq.gz --num_cores 60
--chunk_size 500000
--prebuilt_bowtie2_indexes midas2/bt2_indexes/pangenomes
--prebuilt_bowtie2_species midas2/bt2_indexes/pangenomes.species
--midasdb_name uhgg  --midasdb_dir ~/database/midas2/ ~/HCCMicrobiome/midas2/ --debug
And issue:
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/multiprocessing/pool.py", line 44, in mapstar
return list(map(*args))
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/run_snps.py", line 469, in filter_bam
reads_stats = filter_bam_by_single_read(species_id, repgenome_bamfile, filtered_bamfile)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/run_snps.py", line 309, in filter_bam_by_single_read
for aln in infile.fetch(contig_id):
File "pysam/libcalignmentfile.pyx", line 1091, in pysam.libcalignmentfile.AlignmentFile.fetch
File "pysam/libchtslib.pyx", line 685, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid contig gnl|Prokka|UHGG239728_1
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/lbl/miniconda3/envs/midas2/bin/midas2", line 8, in
sys.exit(main())
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/main.py", line 24, in main
return subcommand_main(subcommand_args)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/run_snps.py", line 861, in main
run_snps(args)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/run_snps.py", line 855, in run_snps
raise error
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/subcommands/run_snps.py", line 827, in run_snps
list_of_contig_aln_stats = multiprocessing_map(filter_bam, args_list, args.num_cores)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/common/utils.py", line 532, in multiprocessing_map
return _multi_map(func, items, num_procs, multiprocessing.Pool)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/site-packages/midas2/common/utils.py", line 520, in _multi_map
return p.map(func, items, chunksize=1)
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/multiprocessing/pool.py", line 268, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/home/lbl/miniconda3/envs/midas2/lib/python3.7/multiprocessing/pool.py", line 657, in get
raise self._value
ValueError: invalid contig gnl|Prokka|UHGG239728_1

Hmmm, may I ask did you build your pangenome database with midas2 build_bowtie2db command?
Also, can you check if the contig id gnl|Prokka|UHGG239728_1 is present in the midas2/bt2_indexes/pangenomes.fa (or which ever fasta file you used to build the pangenomes?

Here is my command for pangeome
midas2 build_bowtie2db
--midasdb_name uhgg
--midasdb_dir ~/database/midas2/
--species_profile midas2/species/species_prevalence.tsv
--select_by mean_coverage
--select_threshold 5 --num_cores 60
--bt2_indexes_name pangenomes
--bt2_indexes_dir midas2/bt2_indexes
and i use  this pangenome in cnv calling success
midas2 run_genes --sample_name $a
-1 ~/HCCMicrobiome/HCC/$a.R1.fastq.gz
-2 ~/HCCMicrobiome/HCC/$a.R2.fastq.gz
--midasdb_name uhgg --midasdb_dir ~/database/midas2/
--select_threshold=-1 --num_cores 60
--prebuilt_bowtie2_indexes midas2/bt2_indexes/pangenomes
--prebuilt_bowtie2_species midas2/bt2_indexes/pangenomes.species
~/HCCMicrobiome/midas2/
Should i rebuild this pangenome for snp calling ?

Thanks,this help me a lot.

No problem. I am gonna close this issue. Please let me know if you have more questions.


Security Update for Jumpbox

I noticed a security issue on one of the Network Security Group created by CAF terraform
vnet-hub-re1> jumpbox > SSH port 22 is exposed to internet.
The recommendation is:
SSH port 22 is exposed to the Internet. This is only recommended for testing. For production environments, we recommend using a VPN or private connection.
Recommendation

port 2222
add secure cyphers

add this to /etc/ssh/sshd_config
ClientAliveInterval 120
Port 2222
Ciphers chacha20-poly1305@openssh.com,aes256-gcm@openssh.com,aes128-gcm@openssh.com,aes256-ctr,aes192-ctr,aes128-ctr

We do not have a VM, this was a network security group warning

This issue was updated and fixe by PR https://github.com/retaildevcrews/caf-terraform-landingzones-starter/pull/8


Book rooms for September - December 2019

We're back!
Try to book Lovelace room when possible, and David Blackwell otherwise.

Bookings have been made for the following:
16th September: Lovelace
30th September: Lovelace
14th October: David Blackwell
28th October: David Blackwell
11th November: David Blackwell
25th November: Lovelace
9th December: No room booking made due to DSG

Great stuff! Closing this issue, we can continue in #19


Feature:  Create issues about the feature or bug you want to fix.

Feature description
Feature:  Create issues about the feature or bug you want to fix.
👀 Have you spent some time to check if this issue has been raised before?

[X] I checked and didn't find similar issue

🏢 Have you read the Code of Conduct?

[X] I have read the Code of Conduct

Can you assign this to me pls? I really need that t-shirt. I am basically living for it. I will be really grateful to you.

Can you please explain this a bit more, I would like to work upon this issue.

Hi @SauravMukherjee44 ,
can i work on this issue?

Hi @SauravMukherjee44 , I have created a new issue #911 . Please assign it to me

Should I create the issues or features needed and also work on it and create PR?


merge from konsum-frontend-svelte,template-svelte-app

package.json

chore(deps): add ^14.16.1 remove ^14.16.0 (devDependencies.stylelint)

:tada: This PR is included in version 1.35.0 :tada:
The release is available on:

npm package (@latest dist-tag)
v1.35.0
GitHub release

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Custom server doesn´t work in recent version.

Custom server doesn´t work in recent version.
brunch-config.coffee
server:
command: "php -S <IP_ADDRESS>:3000 -t public"
command: brunch watch -s
error: Initialization error - ReferenceError: server is not defined

works perfectly on 2.2.3

Thanks for the report, I'll take a look!

Thanks a bunch!


Adapt to path change of Newtonsoft.Json.dll from #2024 (see f0a15886)

The move of the Newtonsoft.Json.dll breaks the virustotal subcommand.  This PR fixes it.
Other similar PRs in the buckets versions and extras are forthcoming.
Thanks in advance,
Philippe Crama

Oh shit, forgot about the tests... Thanks for fixing it :+1:


confusing

can you add numbers to the tables in relation to the order of the potion? it highlights tables that aren't correct for the potion in your inventory and can end up making the wrong thing and causing a lot of xp loss.

can you add numbers to the tables in relation to the order of the potion? it highlights tables that aren't correct for the potion in your inventory and can end up making the wrong thing and causing a lot of xp loss.

With all the changes to the minigame within the last week, there are bound to be bugs. The one you're experiencing right now, is that when there are 2 orders with the same recipe, but different table. It will always prioritize one of the two tables, even when making both potions. I expect the next update will fix all these issues as the current iteration of the plugin only checks the levers' for the recipe, and not the item in your inventory / unfinished potions

This should be fixed with inventory ordering


remove availableSpace from BlobStats

Calling getFreeSpace causes access denied errors
("java.lang.RuntimePermission" "getFileSystemAttributes") due to the new
SecurityManager in ES
Since availableSpace was unused it can be removed completely.

ack


HHH-11215 - Fix NullPointerException when collection of embeddables reference an unaudited entity.

https://hibernate.atlassian.net/browse/HHH-11215

Applied upstream.


Add XR_FB_face_tracking support

This pull request adds support for the XR_FB_face_tracking extension to the Meta vendor plugin. Users can:

Select face-tracking features of None, Optional, and Required
Access the tracking data through the OpenXRFbFaceTrackingExtensionWrapper singleton
Test if face-tracking is enabled by the is_enabled() method
Get all 63x expression weights using the get_weights() method (indexed via enums)
Get the 2x tracking confidences using the get_confidences() method (indexed via enums)

It includes a face model from https://booth.pm/en/items/5420804 which contains almost all the blend-shapes necessary to test the face-tracking feature; although the files are quite large for this.
https://github.com/GodotVR/godot_openxr_vendors/assets/1863707/7a37bb99-86f5-4136-9ba9-11e112feb1f0

Wow, this looks so cool! I'll review in depth when I have a chance :-)

@Malcolmnixon Just to confirm, this only works on the Quest Pro, right?

In my testing, it only works on the Quest Pro. I also tried on the Quest 3, but it does nothing there - it doesn't even show the permission overlay about face tracking

@Malcolmnixon Just to confirm, this only works on the Quest Pro, right?

I believe only the Quest Pro has the face-tracking cameras necessary to do this.

@Malcolmnixon We should consider updating the implementation to use XR_FB_face_tracking2 instead.

@Malcolmnixon We should consider updating the implementation to use XR_FB_face_tracking2 instead.

That will need us to update openxr to 1.0.34 first. I'll get a separate PR ready for that.


Error - Unable to fetch image (a webcam that is not always on)

My tileboard stopped to work without doing anyting. All I did was to upgrade tileboard code.
Starting from the beggining, with default config.js, I could identify that the error that I was getting was related to a webcam that is not always on. And when it's off, I get this error (see the link below):
https://imgur.com/SS2xozu
After removing the camera from the config, now tileboard it's working again. This was not happening before. I don't know if a new update broke something.

This is a HA error, you need to look at your HA's log.

Ok, i got it. Please tell me what the state of camera when it's off?

Can you please try fetching latest code and try again?

Yes. Give me some minutes.

I still get the same error "Unable to fetch image.", but now tileboard loads, giving this error in the bottom right of the screen. Also, as the refered camera is in the second page, the error only appears if show the second page. If I come back to the first page, the error are still there, but they disappear as their timeout finish.

Are you sure that you are using the latest code? You might want to clear browser's cache.

Yes, latest code. And cleaned cache too.

Do you use CAMERA_THUMBNAIL tile type? Try to replace it with just CAMERA and set refresh as a
2000

The errors are gone changing to CAMERA and refresh 2000.  I was using CAMERA_THUMBNAIL.
You may take a look with cam below, also getting those errors. It's a public cam for testing.
   position: [0, 0],    id: 'camera.bekescsaba_hungria',    type: TYPES.CAMERA_THUMBNAIL,    bgSize: 'cover',    width: 2,    state: false,    fullscreen: {       type: TYPES.CAMERA,       refresh: 1000, // can be number in milliseconds       bgSize: 'contain'    },
  - platform: mjpeg     mjpeg_url: http://<IP_ADDRESS>:8080/axis-cgi/mjpg/video.cgi?resolution=640x480     name: Bekescsaba, Hungria

HA wasn't able to handle thumbnail for this camera.
Btw, if camera source already in "mjpeg" format, then you don't need refresh field.

Thanks for clarifying this.

If everything is ok i'm closing it

Thank you.


Windows version?

I am using inkscape 0.91 and I read in a stackexchange article about the scour tool and how it can reduce file sizes of .svg files significantly and that it was already an extension in inkscape.   But I do not see it within inkscape.
Is there a windows version of scour?
Does the windows version of inkscape come with scour and I'm not seeing it?

Scour is written in Python, so it is platform independent. You have to install the Python interpreter if you want to use it as a standalone program.
However what you read is correct: Inkscape for Windows ships with a bundled version of Scour. To use it you have to use "Save as" and choose "Optimized SVG" as output format.
If everything works as it's supposed to, a dialog should then appear that allows you to set Scour settings.

@4evermaat pip install scour should do on Windows too ..

Can you put it in the documentation that it is bundled with inkscape and how to access it?  I had no idea how to do it until you just said something.


Default Behavior of ${import.meta.env.BASE_URL} documentation

https://docs.astro.build/en/reference/configuration-reference/#base
Example says to use the import statement like this:
In most cases this results in a output URL of /base//image.png
Will open a pull request to update the example to  With a note that if you have trailing slash set to 'never' then you need to add the slash yourself.

#3349

Thanks for this @r-southworth! This seems like more helpful advice in the docs!  :partying_face:

Looks like this was done in https://github.com/withastro/astro/pull/7392
Thanks again @r-southworth!


chore: clarified assert message

Describe your changes
the path does not include the root
Checklist before requesting a review

Repo forked and branch created from next according to naming convention.
Commit messages and codestyle follow conventions.
Relevant issues are linked in the PR description.
Tests added for new functionality.
Documentation/comments updated according to changes.

Looks good! Thank you!


Use's password overwritten on server boot?

For some reason Waterline is overwriting a hashed password with a hash of the hashed password on init.  Proposed solution would be to add a check to see if the password is already hashed, maybe by checking the length?  There must be a more bulletproof solution though.
libs/user-model.js
function hash_password(values, next) {
  // If no password was provided, just move on and exit.
  if (!values.password || values.password.length > 1000) {
    return next()
  }

I think this is actually an issue in the jwt module itself. Closing as invalid.


Code Review - Code

https://github.com/lisaoude/browser-technologies-2021/blob/203cb83bf7e0fc46e41def51c99e070bef27d5ec/views/details.ejs#L12
Maybe you can still make your variable names in English (has nothing to do with PE, but more because the rest is all in English 😄 )

Should have done this, but it will take too much time to change these names in both EJS, JS and Schema (for DB) files that I won't do it for this project. Will make sure to do this for my next project however!


NullPointerException when the claim doesn't exist in the token

Description
I am not sure this behaviour is the one expected. When I try to verify a token with a claim that is not present in the token I got a NullPointerException.
Reproduction
I got it in my own code and here's a scratch to reproduce it:
import com.auth0.jwt.JWT;
import com.auth0.jwt.JWTVerifier;
import com.auth0.jwt.algorithms.Algorithm;

class Scratch {
    public static void main(String[] args) {
        String token = JWT
                .create()
                .withArrayClaim("array", new Integer[]{1, 2, 3})
                .sign(Algorithm.HMAC256("secret"));

        JWTVerifier verifier = JWT
                .require(Algorithm.HMAC256("secret"))
                .withArrayClaim("arrtay", 1, 2, 3).build(); // <== arrtay is not array

        verifier.verify(token);
    }
}

StackTrace
Exception in thread "main" java.lang.NullPointerException
	at java.util.Objects.requireNonNull(Objects.java:203)
	at java.util.Arrays$ArrayList.<init>(Arrays.java:3813)
	at java.util.Arrays.asList(Arrays.java:3800)
	at com.auth0.jwt.JWTVerifier.assertValidClaim(JWTVerifier.java:412)
	at com.auth0.jwt.JWTVerifier.verifyClaims(JWTVerifier.java:391)
	at com.auth0.jwt.JWTVerifier.verify(JWTVerifier.java:355)
	at Scratch.main(scratch_1.java:17)

Environment

Version of this library used: 3.4.0

Personally I would expect to get a JWTVerificationException or InvalidClaimException.

Sorry I m just realizing that there is more recent version now. I ll test tomorrow if you have changed this behaviour in the latest version and will close it if yes otherwise no.

Correct, it should throw an InvalidClaimException at least. I'll look into it. Thanks for reaching out!


Pod shattering request

Def: A fruit quality trait (TO:0002728) that is associated with the opening of the pod (PO:0009001).

You should never use the 'is associated with' -- it has no meaning.
Also, I don't see how a request can be a quality.
BS
On Thu, Nov 12, 2015 at 7:20 PM, Rex Nelson<EMAIL_ADDRESS>wrote:

Def: A fruit quality trait (TO:0002728) that is associated with the
opening of the pod (PO:0009001).
—
Reply to this email directly or view it on GitHub
https://github.com/Planteome/plant-trait-ontology/issues/333.


[SMALLFIX] Better upload configurations for S3

Prevents the client from prematurely timing out and uses multipart upload more aggressively to saturate the upload to S3.

Overall LGTM, left one question.

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LGTM

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a high level question: it seems we keep adding supporting alluxio properties for jet3et in recent releases. Alternatively, we could simply forward all jet3et properties ?

+1 for @apc999 suggestion to support all jets3t properties. But in order to keep backwards-compatibility, do we want to limit the scope to be "Advanced" (or Alluxio-not-supported) jets3t properties only? otherwise setting Alluxio s3 properties might conflict with setting jets3t properties directly.

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LGTM

one minor comment let. thanks

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LGTM


[BUG] PR #251 makes torch a requirement causing installs to fail

Memgraph version gqlalchemy >=1.13.1,<2.0.0
Environment
Python 3.11.1
Ubuntu 22.04
Running in Docker
Describe the bug A clear and concise description of what the bug is.
To Reproduce Steps to reproduce the behavior:

have a pyproject.toml and require gqlalchemy >=1.13.1,<2.0.0

Expected behavior

Library continues to install and run as expected
If torch functionality is desired there should be a method for pointing to smaller binary files (if this is caused by an out of space issue)

Additional context The torch requirement is too strict forcing nvidia-cuda-* packages to install which fail when there is no valid GPU available.
There is a slight chance this could be a system space issue but if that is the case it is because the nvidia-cuda-* packages are requiring more than 1.5GB of space during install

@matroscoe Thanks for reporting an issue. We got a similar request on optional dependencies install.   https://github.com/memgraph/gqlalchemy/issues/226
We will take a look into this in the following days.


add API views for schema versioning

Purpose

Changes

QA Notes
Please make verification statements inspired by your code and what your code touches.

Verify
Verify

What are the areas of risk?
Any concerns/considerations/questions that development raised?
Documentation

Side Effects

Ticket

Still needs to add RelationShipField to schema_responses on the RegistrationSerializer. Should probably be a HideIfWithdrawn.


JsRunScript not available on OSX build

I am trying to use ChakraCore on a C# .netcore console app on the Mac.
So I built ChakraCore on OSX as dynamic library (libChakraCore.dylib) but got an error when calling the API JsRunScript. Looking a Jsrt.cpp the API JsRunScript (and some related ones) are within a _WIN32 preprocessor ifdef.
Out of curiosity I moved the API out of the ifdef. Not only does it find the API now, it even successfully executes the javascript :).
What is the reason JsRunScript is only enabled for windows?
As side question, I was not able to load the static lib (libChakraCoreStatic.a). Where should the static lib be placed and what should DllImport specify?

For cross platform you should use JsParse and JsRun.  The other APIs use Windows-specific types, so they are not cross platform compatible.
I'm not familiar with .Net Core on Mac, but on Windows you aren't able to load a static library (*.a on Mac, .lib on Windows).  You should be using a dynamic library (.dylib on Mac, equivalent to *.dll on Windows) for this purpose.

Thanks, works great with JsRun.

Thanks for the confirmation!  Out of curiosity, what was the reason to try and load the static library from .NET Core?

There is no reason. Dynamic library works fine. Just followed the first Hello World example on chakra-samples that shows building a static library.

Ok, thanks for the follow up!

I'll close this issue, but don't hesitate to open another one if you run into any issues.


Expand Contributor's Guide and README

PR Summary
Related Tickets & Documents
Closes #50 and #21
PR Checklist
General

[x] PR includes a summary of changes
[x] Link relevant issues, make one if none exist

I still have the Receipts page treated as its own kind of page. It is kind of its own type of page, but it is part of the NCL entry, so should I combine them to the same section?

I still have the Receipts page treated as its own kind of page. It is kind of its own type of page, but it is part of the NCL entry, so should I combine them to the same section?

I lean towards leaving them in their own section because they are separate files with their own processes. Also, theoretically I think we could "publish" a receipt before an NCL entry.

Should there be a separate option for receipt in the feature_request.yml then? As part of the drop-down options for an application template

Should there be a separate option for receipt in the feature_request.yml and PULL_REQUEST_TEMPLATE.md then? As part of the drop-down options for an application template

I don't think we need one in feature_request.yml because those templates are aimed at external folks and I don't think somebody requesting a receipt makes functional sense. I think I did suggest adding it to the PR template, though in my PR review a second ago.

Notes for further discussions:

Potentially changing the name of the Feature Request template
Workflow process for internal vs. external collaborators (when to make an issue and increasing clarity of the templates)
Add additional citations information (#59)

I modified the receipts_template to reveal the placeholder text. It will need to be removed/hidden for new notebooks, but when I was working on a receipt I missed the text since it was hidden so I expect others will too

I updated the background section into bullet-points that direct to relevant sections in Pythia


feat: fallback to slotted trigger when query fails #28

Alaska Airlines Pull Request
Fixes #28
Summary:
When auro-button was used as the popover trigger in a Svelte application, the trigger would not be initialized properly. This is because the button id was being set as a property, so querySelector didn't work.
At first I tried reflecting id to an attribute on auro-button so that querySelector could find it, but that was not reflected by the button until after popover had initialized the trigger, and the same problem occurred.
Instead, I chose to get the node assigned to the trigger slot, and use that if we couldn't find the trigger using querySelector. It could be possible to use this as our primary method of finding the trigger; however, I wasn't 100% confident that this wouldn't break existing uses of popover.
Type of change:
Please delete options that are not relevant.

[x] New capability
[x] Revision of an existing capability

Checklist:

[x] My update follows the CONTRIBUTING guidelines of this project
[x] I have performed a self-review of my own update

By submitting this Pull Request, I confirm that my contribution is made under the terms of the Apache 2.0 license.
Pull Requests will be evaluated by their quality of update and whether it is consistent with the goals and values of this project. Any submission is to be considered a conversation between the submitter and the maintainers of this project and may require changes to your submission.
Thank you for your submission!
-- Auro Design System Team

@blackfalcon good callout. Should all of the demo examples be updated to not use the for attribute and rely on the slot placement? I think that makes for a cleaner API. I can update the tests too.
We can have a single example of the for / id pair on the demo page and mention that it's no longer necessary, but is still supported for the time being.

@geoffrich please update the demo examples per your suggestion.

:tada: This PR is included in version 2.2.0 :tada:
The release is available on:

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GitHub release

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Add sound effects

Fixes #5

@virtosubogdan Sorry, I thought I merged the Travis integration PR, but i didn't - I merged it just now
If you merge master in this branch then I think Travis status will be reported