[InsufficientNetworkMode - no *.ripple.com peers] (Version: [1.6.0])

Issue Description
I have two machines running rippled. Since Friday I have been getting InsufficientNetworkMode responses for e.g. account_info calls on both of them. This started to happen without my interaction.
Steps to Reproduce
Start rippled, wait for consensus.
server_info > server_state is "full"
To troubleshoot I added this to my existing config:
...
[ips_fixed]
xrpl.ws 443
r.ripple.com 51234
s1.ripple.com 51234
s2.ripple.com 51234
zaphod.alloy.ee 51235
...

If I check rippled peers it only returns <IP_ADDRESS>: and ...51235 addresses that are - accoding to dig -x - from zaphod.alloy.ee.
I tried rippled connect <ip> 51234 to add s2.ripple.com but although it returns success the new address is not added to the peers list.
I have also tried to open the peer port but it had no effect.
Is there any problem with *.ripple.com addresses?
Expected Result
Account_info should return the info.
Actual Result
I get a "InsufficientNetworkMode" error message.

"InsufficientNetworkMode" means that your rippled node is not able to get in sync or stay in sync with the rest of the network. The two most common causes are insufficient connectivity / networking issues, and insufficient computing resources. Sometimes, this happens during transaction spikes when an otherwise sufficient system gets overwhelmed. Most of the time the issue will resolve itself, and the node will backfill any ledgers it missed.
A good starting point is to check the system requirements page to ensure you have sufficient resources available. If you're still unable to stay synced, then post the output of rippled server_info here, and carefully scrub your rippled.cfg file to remove any secrets and post the scrubbed version of that here, too.

"InsufficientNetworkMode" means that your rippled node is not able to get in sync or stay in sync with the rest of the network. The two most common causes are insufficient connectivity / networking issues, and insufficient computing resources. Sometimes, this happens during transaction spikes when an otherwise sufficient system gets overwhelmed. Most of the time the issue will resolve itself, and the node will backfill any ledgers it missed.
A good starting point is to check the system requirements page to ensure you have sufficient resources available. If you're still unable to stay synced, then post the output of rippled server_info here, and carefully scrub your rippled.cfg file to remove any secrets and post the scrubbed version of that here, too.

hi @ximinez , thank you for your advices.
I know what can be the reasons but I don't understand why it happened on both of my machines without me changing anything and why don't I have *.ripple.com peers? And this has been the situation for 3 days now.
I have 23 GB Ram and 6 cores - I guess it should be enough.
Here's my server_info:
{
  "result": {
    "info": {
      "build_version": "1.6.0",
      "complete_ledgers": "60828267-60828272",
      "hostid": "******",
      "io_latency_ms": 1,
      "jq_trans_overflow": "0",
      "last_close": {
        "converge_time_s": 2.001,
        "proposers": 0
      },
      "load": {
        "job_types": [
          {
            "job_type": "untrustedValidation",
            "peak_time": 1,
            "per_second": 81
          },
          {
            "job_type": "untrustedProposal",
            "per_second": 1
          },
          {
            "avg_time": 39,
            "in_progress": 1,
            "job_type": "ledgerData",
            "peak_time": 541,
            "per_second": 3
          },
          {
            "in_progress": 1,
            "job_type": "clientCommand",
            "per_second": 1
          },
          {
            "in_progress": 1,
            "job_type": "updatePaths"
          },
          {
            "job_type": "advanceLedger",
            "peak_time": 3,
            "per_second": 9
          },
          {
            "job_type": "fetchTxnData",
            "per_second": 43
          },
          {
            "job_type": "trustedValidation",
            "peak_time": 2,
            "per_second": 26
          },
          {
            "job_type": "writeObjects",
            "peak_time": 1,
            "per_second": 24
          },
          {
            "job_type": "trustedProposal",
            "per_second": 36
          },
          {
            "job_type": "peerCommand",
            "per_second": 365
          },
          {
            "job_type": "SyncReadNode",
            "peak_time": 8,
            "per_second": 1715
          },
          {
            "job_type": "AsyncReadNode",
            "peak_time": 5,
            "per_second": 3398
          },
          {
            "job_type": "WriteNode",
            "per_second": 56
          }
        ],
        "threads": 6
      },
      "load_factor": 1,
      "peer_disconnects": "558",
      "peer_disconnects_resources": "0",
      "peers": 10,
      "pubkey_node": "******",
      "pubkey_validator": "none",
      "published_ledger": 60828272,
      "server_state": "connected",
      "server_state_duration_us": "1548579243",
      "state_accounting": {
        "connected": {
          "duration_us": "4871418631",
          "transitions": 6
        },
        "disconnected": {
          "duration_us": "79361085",
          "transitions": 4
        },
        "full": {
          "duration_us": "0",
          "transitions": 0
        },
        "syncing": {
          "duration_us": "10043647",
          "transitions": 2
        },
        "tracking": {
          "duration_us": "0",
          "transitions": 0
        }
      },
      "time": "2021-Jan-11 14:11:46.813513 UTC",
      "uptime": 4960,
      "validated_ledger": {
        "age": 1608,
        "base_fee_xrp": 1e-05,
        "hash": "49E517A8BB2D37F4A74B1E929209210E381B477D66EEE74E8E9A6C2913455AAC",
        "reserve_base_xrp": 20,
        "reserve_inc_xrp": 5,
        "seq": 60828289
      },
      "validation_quorum": 31,
      "validator_list": {
        "count": 1,
        "expiration": "2021-Feb-21 00:00:00.000000000 UTC",
        "status": "active"
      }
    },
    "status": "success"
  }
}

hi @ximinez , thank you for your advices.
I know what can be the reasons but I don't understand why it happened on both of my machines without me changing anything and why don't I have *.ripple.com peers? And this has been the situation for 3 days now.
I have 23 GB Ram and 6 cores - I guess it should be enough.
Here's my server_info:
{
  "result": {
    "info": {
      "build_version": "1.6.0",
      "complete_ledgers": "60828267-60828272",
      "hostid": "******",
      "io_latency_ms": 1,
      "jq_trans_overflow": "0",
      "last_close": {
        "converge_time_s": 2.001,
        "proposers": 0
      },
      "load": {
        "job_types": [
          {
            "job_type": "untrustedValidation",
            "peak_time": 1,
            "per_second": 81
          },
          {
            "job_type": "untrustedProposal",
            "per_second": 1
          },
          {
            "avg_time": 39,
            "in_progress": 1,
            "job_type": "ledgerData",
            "peak_time": 541,
            "per_second": 3
          },
          {
            "in_progress": 1,
            "job_type": "clientCommand",
            "per_second": 1
          },
          {
            "in_progress": 1,
            "job_type": "updatePaths"
          },
          {
            "job_type": "advanceLedger",
            "peak_time": 3,
            "per_second": 9
          },
          {
            "job_type": "fetchTxnData",
            "per_second": 43
          },
          {
            "job_type": "trustedValidation",
            "peak_time": 2,
            "per_second": 26
          },
          {
            "job_type": "writeObjects",
            "peak_time": 1,
            "per_second": 24
          },
          {
            "job_type": "trustedProposal",
            "per_second": 36
          },
          {
            "job_type": "peerCommand",
            "per_second": 365
          },
          {
            "job_type": "SyncReadNode",
            "peak_time": 8,
            "per_second": 1715
          },
          {
            "job_type": "AsyncReadNode",
            "peak_time": 5,
            "per_second": 3398
          },
          {
            "job_type": "WriteNode",
            "per_second": 56
          }
        ],
        "threads": 6
      },
      "load_factor": 1,
      "peer_disconnects": "558",
      "peer_disconnects_resources": "0",
      "peers": 10,
      "pubkey_node": "******",
      "pubkey_validator": "none",
      "published_ledger": 60828272,
      "server_state": "connected",
      "server_state_duration_us": "1548579243",
      "state_accounting": {
        "connected": {
          "duration_us": "4871418631",
          "transitions": 6
        },
        "disconnected": {
          "duration_us": "79361085",
          "transitions": 4
        },
        "full": {
          "duration_us": "0",
          "transitions": 0
        },
        "syncing": {
          "duration_us": "10043647",
          "transitions": 2
        },
        "tracking": {
          "duration_us": "0",
          "transitions": 0
        }
      },
      "time": "2021-Jan-11 14:11:46.813513 UTC",
      "uptime": 4960,
      "validated_ledger": {
        "age": 1608,
        "base_fee_xrp": 1e-05,
        "hash": "49E517A8BB2D37F4A74B1E929209210E381B477D66EEE74E8E9A6C2913455AAC",
        "reserve_base_xrp": 20,
        "reserve_inc_xrp": 5,
        "seq": 60828289
      },
      "validation_quorum": 31,
      "validator_list": {
        "count": 1,
        "expiration": "2021-Feb-21 00:00:00.000000000 UTC",
        "status": "active"
      }
    },
    "status": "success"
  }
}

I see you have 10 peers, but I also notice you have 558 peer disconnects. Some disconnects are normal, so that number will increase over time, but with an uptime of only 4960 seconds, that's one disconnect about every 9 seconds. It's also taking an average of 39 seconds to process ledger data. Those both seem pretty high.
My best guess right now is that you don't have sufficient IOPS to keep up when things get busy. What kind of hard drive are you using? We recommend an SSD drive with a minimum of 1000 IOPS.  It's also possible that your network connection is having trouble. Can you run some kind of network speed and latency test?

I see you have 10 peers, but I also notice you have 558 peer disconnects. Some disconnects are normal, so that number will increase over time, but with an uptime of only 4960 seconds, that's one disconnect about every 9 seconds. It's also taking an average of 39 seconds to process ledger data. Those both seem pretty high.
My best guess right now is that you don't have sufficient IOPS to keep up when things get busy. What kind of hard drive are you using? We recommend an SSD drive with a minimum of 1000 IOPS.  It's also possible that your network connection is having trouble. Can you run some kind of network speed and latency test?

Replying really late, apologies! The [ips_fixed] entries are the problem. xrpl.ws is a websocket cluster, not a peer cluster. And the other servers' peer port should be 51235 not 51234
[ips_fixed]
r.ripple.com 51235
s1.ripple.com 51235
s2.ripple.com 51235
zaphod.alloy.ee 51235

may yield you better results. If you don't have [peer_private] set to 1, then you can actually comment out this entire section.


[Bug Report]: The workflow .Platform: Update ReadMe Module Tables fails

Describe the bug
The workflow .Platform: Update ReadMe Module Tables (https://github.com/Azure/ResourceModules/actions/workflows/platform.updateReadMe.yml) fails.
To reproduce
Run https://github.com/Azure/ResourceModules/actions/workflows/platform.updateReadMe.yml
Code snippet
No response
Relevant log output
No response

Fixed by commit 'Fixed logic by introducing api name fetching'.


Comments for Chapter 11 Linear regression Part 2 (June 5, 2021)

Hi Kevin, I am sending few remaining comments for Chapter 11 Linear regression (Part 2)
cerno_comments_on_pmlv2_c11_linreg_part2.pdf
Thanks!
Cheers,
Peter

very helpful, as usual - thanks!. All fixed now.


Educational aircraft design example - step-by-step

Educational example that steps through aircraft design models, building up from very simple to increasingly complex.

I can work on this this week, however, it may lack @bqpd's special touches...

I made a quick fuel / range example with the interactive web widgets: not sure where it fits on the complexity scale, though. :)

With the new modular example we've got a nicer framework for incremental complexity!

Should this be in gpkit-model?

yes.

Moved to https://github.com/aeroa/gpkit-models/issues/7


Add exports.types to package.json

Added the types file path to exports.types in package.json to prevent the following error:
Could not find a declaration file for module '@mondaycom/apps-sdk'. <EMAIL_ADDRESS>implicitly has an 'any' type.
  There are types at<EMAIL_ADDRESS>but this result could not be resolved when respecting package.json "exports". The '@mondaycom/apps-sdk' library may need to update its package.json or typings.

The reason behind this error is that node will ignore the types field if the package has an exports field. And since the exports didn't include an exports.types, node would not be able to find the relevant types .
Docs & stackoverflow here –
https://stackoverflow.com/a/76212193
https://www.typescriptlang.org/docs/handbook/esm-node.html#packagejson-exports-imports-and-self-referencing

closing because its stale

Hey, reopening this because someone brought it up again in the dev community.
We are using an outdated package.json structure: as of Typescript 4.7, the types field in package.json will no longer be used. We need to move the types field under exports
See this StackOverflow - https://stackoverflow.com/questions/76211877/the-xxxx-library-may-need-to-update-its-package-json-or-typings-ts/76212193#76212193


Documentation is wrong and does not work get this error

Any information would be helpful in solving these errors.
Event ID 7211 - The Secondary Account Primary Refresh Token prerequisite check failed.
Followed by
Event ID 7206 - Windows Hello for Business failed to locate a certificate registration authority.

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

ID: 49d45db5-5172-45cb-2c4d-d73a9e15d699
Version Independent ID: fa08e81d-3307-514e-129a-843e812e97a9
Content: Hybrid Windows Hello for Business key trust Provisioning (Windows Hello for Business)
Content Source: windows/security/identity-protection/hello-for-business/hello-hybrid-key-whfb-provision.md
Product: w10
GitHub Login: @MikeStephens-MS
Microsoft Alias: mstephen

Hello @JonBrekhus , Thank you for your feedback. For Event ID 7211, please refer to the following link (https://social.technet.microsoft.com/Forums/en-US/7625faf1-1641-4293-b629-51a56595a1b1/helloforbusiness-the-secondary-account-primary-refresh-token-prerequisite-check-failed-id-7211?forum=win10itprosecurity)
Also, can you please share details for Event ID 7206 so that we can further help you.
Thanks.

@JonBrekhus - We appreciate any feedback that improves the content in the Microsoft docs but we haven't had any response from you so we are going to close this issue.
Please feel free to re-open this issue if there is a specific area of the docs that we can improve or make better. Thank you.

@JonBrekhus - We would like to follow up on this. Can you please respond to the query of joinimran?
Thank you.

@JonBrekhus - We appreciate any feedback that improves the content in the Microsoft docs but we haven't had any response from you so we are going to close this issue.
Please feel free to re-open this issue if there is a specific area of the docs that we can improve or make better. Thank you.

@officedocsbot close

Hi can we reopen this case ?
I'm having exactly the same issue :)
Event ID 7211 - The Secondary Account Primary Refresh Token prerequisite check failed.
Followed by
Event ID 7206 - Windows Hello for Business failed to locate a certificate registration authority.

@EdgeSN : did you read the TechNet forum post provided by joinimran ?

https://social.technet.microsoft.com/Forums/en-US/7625faf1-1641-4293-b629-51a56595a1b1/helloforbusiness-the-secondary-account-primary-refresh-token-prerequisite-check-failed-id-7211?forum=win10itprosecurity

Judging by the posts there, it could either be caused by a missing entry for “https://login.windows.net” which needs to be added to the “IE trusted site” list, or it could be a time-out issue, solved by waiting and new retry attempts.

Same problem. "Login.windows.net" is in IE trusted sites.


[ButteflyAspect] Typos and spelling errors fixed

Changes / Comments
Typos and spelling errors fixed
Roll20 Requests
Comments are very helpful for reviewing the code changes. Please answer the relevant questions below in your comment.

[ ] Does the pull request title have the sheet name(s)? Include each sheet name.
[ ] Is this a bug fix?

Character Sheet Info Roll20 Internal Use only.


Speedup inside kernel

Unless I messed up, I think you can get a pretty nice speedup inside the kernel with this one simple trick
instead of
filterArr = weightArr * signalSeg
filterSeg = np.sum(filterArr, axis=1)
# print(idx, m+1 + idx)
filterPoint = filterSeg[m + 1]
sgFilter[idx] = filterPoint

try
sgFilter[idx] = np.sum(weightArr[m+1] * signalSeg)

Since you're only using the m+1 element of filterSeg, you might as well not compute the matrix vector produt.

This should mainly affect cases where you have a large stencil, because of the time saving going from a mat-vec to a vec-vec product.


Slow page loading with federated icons enabled

Description
Apparently I misidentified the real culprit in #28074 and thought that the slowdown is caused by Gravatar.
Opening a PR page is very slow because the user avatars take aeons to load:

The problem is solved by simply turning of the Enable Federated Avatars option.
Apparently gitea is constantly querying them via SRV record lookups on every request to the /avatar endpoint:

Gitea Version
1.21.0
Can you reproduce the bug on the Gitea demo site?
No
Log Gist
No response
Screenshots
No response
Git Version
No response
Operating System
No response
How are you running Gitea?
Binary started via systemd behind a caddy reverse proxy.
Database
None

That SRV lookup needs to at least honor DNS TTL and cache with that time.

I think this depends on your network?

If those SRV queries come out of gitea, then it's our responsibility to respect DNS TTL.

In our case, the records didn't exist as the feature was most likely turned on by mistake.
Honoring the TTL is still the way to go. Additionally, a minimum TTL should be enforced in case of DNS servers that do not properly implement negative caching for NXDOMAIN responses.


enable public notes on Wizard's Den servers

About the PR

Requires #14228 and some policy or interim policy stuff
Media

[X] I have added screenshots/videos to this PR showcasing its changes ingame, or this PR does not require an ingame showcase

Just doublechecking. Is this allowing the player to see their own notes, or allowing other players to see each others notes?

I'm not an admin so perhaps my opinion means jack here, but having had bad behavior in the past and wanting to be a better player, seeing things I did wrong or right would be nice to know if I've actually gotten better.

how would one see their own notes?


Fix issues of e2e tests for Egress and ServiceExternalIP

Signed-off-by: Xu Liu<EMAIL_ADDRESS>

Codecov Report

Merging #3234 (ccf8122) into main (df6094b) will decrease coverage by 20.27%.
The diff coverage is n/a.

@@             Coverage Diff             @@
##             main    #3234       +/-   ##
===========================================
- Coverage   58.76%   38.48%   -20.28%
===========================================
  Files         331      330        -1
  Lines       28437    39652    +11215
===========================================
- Hits        16711    15262     -1449
- Misses       9894    22873    +12979
+ Partials     1832     1517      -315

Flag
Coverage Δ

integration-tests
34.05% <ø> (?)

kind-e2e-tests
?

unit-tests
41.34% <ø> (-0.02%)
:arrow_down:

Flags with carried forward coverage won't be shown. Click here to find out more.

 Thanks @xliuxu

/test-e2e

Closing this PR as sudo is available on jenkins testbeds. https://github.com/antrea-io/antrea/pull/3948


Move Chronos to Marathon

https://github.com/CiscoCloud/microservices-infrastructure/issues/792
I made some changes due to this issue.

Adding in @ryane.
Should we just use the mesosphere package for chronos and launch it via mantl-api?

I tend to think so. We are doing some duplicate work by using ansible to run frameworks on marathon + it seems a little less modular. I think this applies to the elasticsearch framework too

@ryane i guess it's not completely correct since Chronos is supposed to be core part of Mantl and actually requires way more actions then just running the framework. I guess we can refactor the code to use Mantl-API for framework installation, but we also have to deal with proxying, healthchecks and so on.
How all those should be deployed with Mantl-API?

@ryane I think it is nice idea, but I need more information about deploying process.
I can install chronos by this command:
curl -X POST -d "{"name": "chronos"}" http://mantl-worker-003:4001/1/packages
but I don't understand how to specify parameters for marthon.
I found something in consul KV by this path MANTL-INSTALL/REPOSITORY/0/REPO/PACKAGES/C/CHRONOS/0/.
is this what I am looking for ?
if it so, could you please describe how to configure it in a right way?

@dmitriybondr this currently doesn't build for me on vagrant:
=> default: failed: [default] => {"attempts": 10, "changed": true, "cmd": "curl marathon.service.consul:8080/v2/apps/chronos/tasks | awk ' {print $3} '", "delta": "0:00:00.157471", "end": "2015-12-09 12:46:15.368143", "failed": true, "rc": 0, "start": "2015-12-09 12:46:15.210672", "warnings": ["Consider using get_url module rather than running curl"]}
==> default: stderr:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
==> default:
==> default:            Dload  Upload   Total   Spent    Left  Speed
0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (6) Could not resolve host: marathon.service.consul; Name or service not known

The reason your Mantl API command failed was because we had not created a support chronos package yet. There are a few issues with the Chronos package PR that need to be addressed but we should have a working package very soon.
@corebug you're right. if we move chronos to marathon, we need to maintain (or improve) the integration we already have. One thing we still need to do before we can make this switch is to update the UI to properly reflect a valid chronos health check (see CiscoCloud/mantl-ui-frontend#4).

there is now a working chronos package as of CiscoCloud/mantl-universe#15

the chronos package required a few small changes to mantl-api so I bumped the version number. I know this PR will likely change a lot to use the package but I added some additional comments to what is already here.

@ryane  I found unexpected behaviour, trying to run chronos. I got this error:
"[scallop] Error: Bad arguments for option 'cassandra ttl': '3.1536e+07' - wrong arguments format "
I think it is because mantl-api having faced with some large integers tries to convert it to exponential format.

@dmitriybondr this should be fixed in mantl-api 0.1.2 (see 5925df9da5aa69cd97651e58f15be0961d91bfa8 in this PR). are you still seeing that with 0.1.2?

@ryane I still see this this with new version of mantl-api (0.1.2)

@dmitriybondr that's strange. I cannot repro the error with 0.1.2 (but I can with 0.1.1). Do you want to try and setup a time where we can go over your setup?

@ryane  I decided to  destroy my cluster and rebuild it from scratch with new mantl-api. And it works ! it awesome. Thank you. )

@dmitriybondr What's the status of this PR?

I'm going to close this for now since there hasn't been a commit since December. Please reopen if there's more interest, or we can create an issue tracking the movement of Chronos to Marathon.


To navigate back you have to press Esc twice

Describe the bug
When there is a link inside a tooltip, during reverse navigation via Shift + Tab, the tooltip opens again and grabs focus, which leads to navigation blocking on this element
Code example
Open codesandbox
To Reproduce
Steps to reproduce the behavior:

Go to Tooltip.Popper
Press on Esc
Press Shift+Tab
See Tooltip.Popper again

Expected behavior
When you first hit the tooltip it should open, after pressing Esc it should be possible to direct the focus both forward and backward

Fixed in https://github.com/semrush/intergalactic/releases/tag/v15.57.0


Big File

Hello,
I should import a big file with 19K entries,
but only 14K are imported.

Are you using as a lib or cli tool?
What errors do you received with error event?
~Keyang

I'm using as cli tool and I don't receive errors
..only that,  the created json entries are  as less then in csv file

Is there any line breaks in any csv columns as one csv row could contains multiple lines .
also if you set --checkColumn=true see if it gives any errors.

facing a similiar issue. Not using cmd line but my entire file is not being parsed.

Close due to no activity
Please try with latest csvtojson tool


[BUG] App crashes when trying to load tags tab with a particular view created

Steps to reproduce:

Run fiftyone quickstart
Add a SortBy("uniqueness", reverse=False) stage
Click on Tags tab

The error page will appear, but if you refresh, the Tags page then loads properly.
I can't get this to happen when creating other views... Limit(10) and Exists("predictions", bool=True) work fine, for example.
Here's the error in the App:
ViewStageParameter.tsx:231 Uncaught TypeError: Cannot read property 'removeEventListener' of null
    at ViewStageParameter.tsx:231
    at HTMLUnknownElement.callCallback (/Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:188)
    at Object.invokeGuardedCallbackDev (/Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:237)
    at invokeGuardedCallback (/Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:292)
    at safelyCallDestroy (/Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:19617)
    at /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:20090
    at unstable_runWithPriority (/Users/Brian/dev/fiftyone/electron/app/node_modules/scheduler/cjs/scheduler.development.js:653)
    at runWithPriority$1 (/Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:11039)
    at commitUnmount (/Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:20083)
    at commitNestedUnmounts (/Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:20163)
(anonymous) @ ViewStageParameter.tsx:231
callCallback @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:188
invokeGuardedCallbackDev @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:237
invokeGuardedCallback @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:292
safelyCallDestroy @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:19617
(anonymous) @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:20090
unstable_runWithPriority @ /Users/Brian/dev/fiftyone/electron/app/node_modules/scheduler/cjs/scheduler.development.js:653
runWithPriority$1 @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:11039
commitUnmount @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:20083
commitNestedUnmounts @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:20163
unmountHostComponents @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:20443
commitDeletion @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:20500
commitMutationEffects @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:22782
callCallback @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:188
invokeGuardedCallbackDev @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:237
invokeGuardedCallback @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:292
commitRootImpl @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:22509
unstable_runWithPriority @ /Users/Brian/dev/fiftyone/electron/app/node_modules/scheduler/cjs/scheduler.development.js:653
runWithPriority$1 @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:11039
commitRoot @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:22381
finishSyncRender @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:21807
performSyncWorkOnRoot @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:21793
(anonymous) @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:11089
unstable_runWithPriority @ /Users/Brian/dev/fiftyone/electron/app/node_modules/scheduler/cjs/scheduler.development.js:653
runWithPriority$1 @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:11039
flushSyncCallbackQueueImpl @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:11084
flushSyncCallbackQueue @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:11072
discreteUpdates$1 @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:21893
discreteUpdates @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:806
dispatchDiscreteEvent @ /Users/Brian/dev/fiftyone/electron/app/node_modules/react-dom/cjs/react-dom.development.js:4168
react_devtools_backend.js:6 The above error occurred in the <ObjectEditor> component:
    in ObjectEditor (at ViewStageParameter.tsx:350)
    in div (created by styled.div)
    in styled.div (at ViewStageParameter.tsx:342)
    in Component (at ViewStage.tsx:376)
    in div (created by styled.div)
    in styled.div (created by ForwardRef)
    in ForwardRef (at ViewStage.tsx:304)
    in Component (at ViewBar.tsx:122)
    in div (created by styled.div)
    in styled.div (at ViewBar.tsx:101)
    in div (created by styled.div)
    in styled.div (at ViewBar.tsx:99)
    in ViewBar (at SamplesContainer.tsx:162)
    in div (created by Sticky)
    in div (created by Sticky)
    in Sticky (at SamplesContainer.tsx:155)
    in div (created by styled.div)
    in styled.div (at SamplesContainer.tsx:154)
    in SamplesContainer (at Dataset.tsx:140)
    in Route (at Dataset.tsx:139)
    in Switch (at Dataset.tsx:133)
    in div (created by Container)
    in Container (at Dataset.tsx:128)
    in Dataset (created by ConnectFunction)
    in ConnectFunction (at Routes.tsx:36)
    in Route (at Routes.tsx:46)
    in Switch (at Routes.tsx:41)
    in div (at App.tsx:125)
    in ErrorBoundary (at App.tsx:119)
    in App (created by ConnectFunction)
    in ConnectFunction (at Routes.tsx:40)
    in Routes (created by ConnectFunction)
    in ConnectFunction (at Root.tsx:26)
    in RecoilRoot (at Root.tsx:25)
    in Router (created by ConnectedRouter)
    in ConnectedRouter (created by Context.Consumer)
    in ConnectedRouterWithContext (created by ConnectFunction)
    in ConnectFunction (at Root.tsx:24)
    in Provider (at Root.tsx:23)
    in ThemeProvider (at Root.tsx:21)
    in Root (created by HotExportedRoot)
    in AppContainer (created by HotExportedRoot)
    in HotExportedRoot
    in AppContainer (at app/index.tsx:20)

React will try to recreate this component tree from scratch using the error boundary you provided, ErrorBoundary.

This is resolved as of v0.7.

This is resolved as of v0.7.


Improve error messages + add release.me requirements

When requesting a non-existing cursor with pagination, the returned error was "Something went wrong". Not a very transparent error message.  This PR addresses this issue.
If there other conditions under which the before_type and after_type would be incorrect, do please let me know.
Also, as the release.md file was a requirement for my last PR. I have taken the liberty to adding it to the README.md file to educate others.
I did see that the tests are failing locally, but the tests seems to be failing for the project on GitHub as well. Not sure if that's desirable.

[ ] Core
[x] Bugfix
[ ] New feature
[ ] Enhancement/optimization
[x] Documentation

Checklist

[x] My code follows the code style of this project.
[ ] My change requires a change to the documentation.
[x] I have updated the documentation accordingly.
[x] I have read the CONTRIBUTING document.
[ ] I have added tests to cover my changes.
[ ] I have tested the changes and verified that they work and don't break anything (as well as I can manage).

Thanks for adding the RELEASE.md file!

Here's a preview of the changelog:

Improved error message when supplying in incorrect before or after argument with using relay and pagination.
Add extra PR requirement in README.md

Here's the tweet text:
🆕 Release (next) is out! Thanks to SD for the PR 👏

Get it here 👉 https://beta.strawberry.rocks/release/(next)

Thanks for adding the RELEASE.md file!

Here's a preview of the changelog:

Improved error message when supplying in incorrect before or after argument with using relay and pagination.
Add extra PR requirement in README.md

Here's the tweet text:
🆕 Release (next) is out! Thanks to SD for the PR 👏

Get it here 👉 https://beta.strawberry.rocks/release/(next)

LGTM :)
Would be nice to add a test for those if possible. Should be simples!

Sure, why not.  Not very familiar with pytest, but I added a couple of tests that fail the before and after.  The response did seem to yield a different content then in my Django environment.  But at least it's covered.

I changed the README again to refer to the CONTRIBUTE page.  Never realised it was there.

Hmm, that didn't take, the tests are skipping the TypeErrors.  I'll have to take another look on another day.

@bellini666 test are covering the change now.  Seems I had used a special query rather than the simple one.

@bellini666 test are covering the change now. Seems I had used a special query rather than the simple one.

Thanks! :)


Can't lazy-load polymorphic relationships with different primary key columns

Laravel Version: 5.6.26
PHP Version: 7.2.6
Database Driver & Version: MySQL 5.7.22

Description:
You cannot lazy-load models of a polymorphic relationship that have different primary key columns.
This functionality broke with #21310.
Scenario:
$comments = Comment::all();
$comments->load('commentable'); // this fails if you have the below schema

posts

post_id
title
body

111
Test Post
hello world

videos

video_id
title
video

222
Test Video
my-video.mov

comments

id
commentable_type
commentable_id
body

1
App\Post
111
"comment on a post"

2
App\Video
222
"comment on a video"

// This works (eager loading):
$comments = App\Comment::with('commentable')->get();

// This fails (lazy loading):
$comments = App\Comment::all();
$comments->load('commentable');
// > Results in "no such column: videos.post_id"

Steps To Reproduce:
I created a failing integration test to demonstrate.
## Pull down my fork
git clone -b polymorphic-diff-keys git@github.com:fitztrev/framework.git polymorphic-diff-keys

cd polymorphic-diff-keys
composer install

## Run the tests
## These 2 work
./vendor/bin/phpunit --filter testWithNoEagerOrLazyLoad
./vendor/bin/phpunit --filter testItCanEagerLoad

## This 1 fails
./vendor/bin/phpunit --filter testItCanLazyLoad

#24063 has an explanation for this bug.
Currently, the only approach to fixing this is analyzing the backtrace. Since this is rather terrible, we are still looking for better ideas.


Are there any more updates to the code?

Thank you for your excellent work! I'm wondering if there will be an update to the code? If not, I will start reproducing it immediately. If there is still an update, I will wait for you to finish updating it before reproducing it. @KorMachine

After the ECCV 2024, I'll release the pretrained model weights for all categories so stay tuned!
Except for the release of the pretrained model weights, all other components have already been released, so feel free to reproduce the results!
However, please note that due to the randomness in the superpoint generation step (part of the preprocessing process), the superpoint results may vary each time, causing the final results to differ slightly.

Thank you for your excellent work! I'm wondering if there will be an update to the code? If not, I will start reproducing it immediately. If there is still an update, I will wait for you to finish updating it before reproducing it. @KorMachine

After the ECCV 2024, I'll release the pretrained model weights for all categories so stay tuned!
Except for the release of the pretrained model weights, all other components have already been released, so feel free to reproduce the results!
However, please note that due to the randomness in the superpoint generation step (part of the preprocessing process), the superpoint results may vary each time, causing the final results to differ slightly.

If I use a custom dataset, how should I get a finetuned GLIP checkpoint? @KorMachine

@LinLin1031 Thank you for pointing out! I'll update demo_examples.tar.xz in a week!
Also for the custom dataset, GLIP finetuning is a part of PartSLIP which is the previous work or ours. Thus, you can finetune with your custom dataset using the code from PartSLIP.


Backfill ended subscriptions updated_at

In this PR a bug was introduced which stopped updating the
updated_at when all of a users subscriptions were ended. This had a
knock on effect of breaking a report.

Thanks for the review @benthorner. I've also redefined the Subscription class in the migration to make the migration resilient against future model changes.

I've also redefined the Subscription class in the migration to make the migration resilient against future model changes.

This is an excellent argument for not using migrations for this sort of thing 😆. To that end, perhaps we should just cut the not-great practice now and just do it with a temporary rake task.
What do you think?

I suppose the negative of doing it with a rake task is that it disappears when we remove it meaning we lose visibility of the change, although it would be present through Github with some searching.
However we've now done subscriber list migrations in rake tasks so it seems consistent with that approach so I'll close this PR and resurrect as a rake task @benthorner  😄


Add Package edit support for packages with unsafe flags

Fixes #8079
Allows unsafe flags for edited packages
Motivation:
Edited packages in SwiftPM should be allowed to use unsafe flags.
Modifications:
Adjusted logic in unsafeAllowedPackages to add .edited packages to the allowed list, alongside the root package and .fileSystem packages
Result:
After this change, edited packages will be permitted to use unsafe flags.

Awesome. That really annoyed me :).
@swift-ci please test


[ANDROID] Menu Item Profile within menu_feeds.xml not displaying user's profile picture.

From @patricknasc on December 20, 2016 9:27
I guess it was expected that this menu item should also display the user's profile. I think that menu items doesn't allow to customize the icon format, so that probably it won't be possible to repeat the circle format for profile pictures that are being used throughout the app. The options I see are:

Use a square format profile picture and keep using a menu item.
Change the menu item for a ImageView/CircleImageView.

Copied from original issue: firebase/friendlypix#60

Cleaning up issue fixed in upcoming v2.


Change interest calc to continous compounding

The interests are now calculated with a taylor approximation of
continous compounding to match the calculation in the contracts
Also add some tests to test that the calculation is the same as in the
smart contracts

During that I refactored some parts of the code:

Refactor trustline access

It was a hugh mess how we accessed the trustline data. I tried to
clean it up a bit with some getter setter functions

Refactor call to time.time() to be now within graph.py.
This makes the code easier to reuse and test
We should probably refactor that further and move it even more up so
that it is within the trustlinesrelay so that the cached graph only
dependes on its own state.

Closes #214

Codecov Report

Merging #216 into develop will increase coverage by 0.46%.
The diff coverage is 95.28%.

@@             Coverage Diff             @@
##           develop     #216      +/-   ##
===========================================
+ Coverage    62.06%   62.53%   +0.46%
===========================================
  Files           45       46       +1
  Lines         2979     2987       +8
===========================================
+ Hits          1849     1868      +19
+ Misses        1130     1119      -11

Impacted Files
Coverage Δ

relay/network_graph/dijkstra_weighted.py
90.15% <100%> (+0.49%)
:arrow_up:

relay/network_graph/interests.py
100% <100%> (ø)
:arrow_up:

relay/network_graph/trustline_data.py
100% <100%> (ø)

relay/network_graph/graph.py
81.85% <89.13%> (+2.15%)
:arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
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Remove use of errors.Trace for package internal/locate

seems no errors.Trace found in this package.


[Model] Update MPT model with GLU and rope and add low precision layer norm

This PR does the following like #4116

Update the MPT model to match the latest in https://github.com/mosaicml/llm-foundry/tree/main/llmfoundry/models/mpt
Add low precision layer norm
Allow MPT model to select layer norm algorithms

differents from #4116 is

Uses MergedColumnParallelLinear instead of  two separated ColumnParallelLinear
Uses torch.get_autocast_dtype instead of old APIs (get_autocast_gpu_dtype / get_autocast_cpu_dtype)
Reduces redundants code.

BEFORE SUBMITTING, PLEASE READ THE CHECKLIST BELOW AND FILL IN THE DESCRIPTION ABOVE

 PR Checklist (Click to Expand)
Thank you for your contribution to vLLM! Before submitting the pull request, please ensure the PR meets the following criteria. This helps vLLM maintain the code quality and improve the efficiency of the review process.
PR Title and Classification
Only specific types of PRs will be reviewed. The PR title is prefixed appropriately to indicate the type of change. Please use one of the following:

[Bugfix] for bug fixes.
[CI/Build] for build or continuous integration improvements.
[Doc] for documentation fixes and improvements.
[Model] for adding a new model or improving an existing model. Model name should appear in the title.
[Frontend] For changes on the vLLM frontend (e.g., OpenAI API server, LLM class, etc.)
[Kernel] for changes affecting CUDA kernels or other compute kernels.
[Core] for changes in the core vLLM logic (e.g., LLMEngine, AsyncLLMEngine, Scheduler, etc.)
[Hardware][Vendor] for hardware-specific changes. Vendor name should appear in the prefix (e.g., [Hardware][AMD]).
[Misc] for PRs that do not fit the above categories. Please use this sparingly.

Note: If the PR spans more than one category, please include all relevant prefixes.
Code Quality
The PR need to meet the following code quality standards:

We adhere to Google Python style guide and Google C++ style guide.
Pass all linter checks. Please use format.sh to format your code.
The code need to be well-documented to ensure future contributors can easily understand the code.
Include sufficient tests to ensure the project to stay correct and robust. This includes both unit tests and integration tests.
Please add documentation to docs/source/ if the PR modifies the user-facing behaviors of vLLM. It helps vLLM user understand and utilize the new features or changes.

Adding or changing kernels
Each custom kernel needs a schema and one or more implementations to be registered with PyTorch.

Make sure custom ops are registered following PyTorch guidelines: Custom C++ and CUDA Operators and The Custom Operators Manual
Custom operations that return Tensors require meta-functions. Meta-functions should be implemented and registered in python so that dynamic dims can be handled automatically. See above documents for a description of meta-functions.
Use torch.libary.opcheck() to test the function registration and meta-function for any registered ops.  See tests/kernels for examples.
When changing the C++ signature of an existing op, the schema must be updated to reflect the changes.
If a new custom type is needed, see the following document: Custom Class Support in PT2.

Notes for Large Changes
Please keep the changes as concise as possible. For major architectural changes (>500 LOC excluding kernel/data/config/test), we would expect a GitHub issue (RFC) discussing the technical design and justification. Otherwise, we will tag it with rfc-required and might not go through the PR.
What to Expect for the Reviews
The goal of the vLLM team is to be a transparent reviewing machine. We would like to make the review process transparent and efficient and make sure no contributor feel confused or frustrated. However, the vLLM team is small, so we need to prioritize some PRs over others. Here is what you can expect from the review process:

 After the PR is submitted, the PR will be assigned to a reviewer. Every reviewer will pick up the PRs based on their expertise and availability.
 After the PR is assigned, the reviewer will provide status update every 2-3 days. If the PR is not reviewed within 7 days, please feel free to ping the reviewer or the vLLM team.
 After the review, the reviewer will put an  action-required label on the PR if there are changes required. The contributor should address the comments and ping the reviewer to re-review the PR.
 Please respond to all comments within a reasonable time frame. If a comment isn't clear or you disagree with a suggestion, feel free to ask for clarification or discuss the suggestion.

Thank You
 Finally, thank you for taking the time to read these guidelines and for your interest in contributing to vLLM. Your contributions make vLLM a great tool for everyone!

I rebased it because it was conflicting with the current main branch.

I rebased. Some tests have failed, but this PR is not the cause.

rebased


Open case [Source]

I am going to share my code with you guys next week i just wanna finish this code (i have added latest protobuf to make it work with the inventory)

smash a like if you like it.
If you let me some more days after release i will try my best to make it savable with config.

maybe do the same thing with "fake unbox" option? like searching for the knifes/skins, automatic nick in game switching or something (sorry for trash eng)

Nice

waw is that inventory change?? the equip from inventory is an inventory changer?
and good luck bro :)

+rep
how you add an image to imgui?

+rep
how you add an image to imgui?

ImGui::Image(texture_id, size);
Ez as that

oh thx men

Did you implement the full protobuf? I've been struggling to implement myself. I am trying to make a translator for ingame chat as outlined here.  Add real items to my inventory? naaah

@GenTapDude it's gonna be an inventory changer but with a case opener that's awesome asf

any progress?  The button text aint even alligned the same

yh this is fake 100%


Adding a new example to the list

Closing all example blogs PR for now. Will be cleaning things up and migrating to a v2 version with react server components based on the app dir structure. Happy to accept new additions after that.


Viewer Width and Height on Safari iOS

Guys,
There's a simple fix for the view width and height, which will allow OpenJsCad to display correctly on devices running iOS.
Reference:
http://www.w3schools.com/js/js_window.asp
Fix createElements()...
var myWidth = window.innerWidth || document.documentElement.clientWidth || document.body.clientWidth;
var myHeight = window.innerHeight || document.documentElement.clientHeight || document.body.clientHeight;
FYI, these values change if the window is resized.

This was corrected by commit e262bec33168fce099a612044c715f89b80287a2


Y-axis label formatter for LineChart

This PR fixes #187
Adds the ability to set custom labels on the Y-axis using a value formatter that accepts a numeric value (float64) and returns the corresponding label to this value (string).
The PR is in WIP state. I'll update the PR accordingly.
Steps:

[x] Set the Linechart Y-axis option with the ValueFormatter.
[x] Use the formatter on the Value if is present.
[ ] Create formatter for most common time units.
[ ] Create formatter to round values (#95).

This approach seems to work fine, I put an image of the project that I'm developing (a Grafana for terminal that I'll make it public soon) using this feature.

Hi @mum4k!
I've added the first step of defining the API (I have a first implementation but I would like your feedback on the API option before pushing those changes to the PR).

Hi @slok, this all looks good, I don't have any comments at this time. Looks like we are on the same page.
Also I had no idea we could do draft PRs on GitHub, thank you for teaching me something new and for making the review easy by splitting it to small pieces.

Hi @mum4k, I just pushed the code that implements the usage of the formatter option.
I've been struggling a bit (did some iterations and I was not happy with the results haha) on the design of how to pass the formatter around, the approach that I selected is the least invasive I could think of (without knowing the design decisions you have taken of the linechart internals).
I would have preferred to remove Value.Rounded, Value.ZeroDecimals and Value.NonZeroDecimals struct attributes, and use a default formatter that takes the Value.Value and calculates this rounded float, but I've seen that Value.Rounded is not only used as a way of text representation but also used on internal logic of length, positions... so I didn't want to alter how this works.

Wow! that was an awesome review, many thanks!
I'll check in detail, answer and solve in a few days. I don't have much time these coming days, sorry.
Best!

Thanks @slok, no worries feel free to get back to this whenever it suits. There are no time commitments for pet projects.

Hey @slok,
me and @keithknott26 were wondering how you got the legend under the LineChart in your screenshot up in this PR. Is this just a Text widget under the LineChart widget or are you planning to implement support for a legend?
Keith opened #191 so assuming you're not working on the legend, one of us (me or Keith) could work on supporting it in the LineChart directly.
Please let us know.

Hi @mum4k!
Yes, is composed of a lineachart and a text. On the app I'm creating a widget is an element that can be composed of multiple widgets/elements.
This way I can customize a legend that can be at any side and scrolls also.
Some examples:

Thanks @slok, that's a great usage of the Text widget. I will continue discussion around the legend in #191 in order to not derail this thread.

Hey @mum4k, Ready for a new check!
Thanks for all your feedback and time, your tips, corner cases and pointing to the correct code paths have been a HUGE  help.

I pushed the changes to allow empty labels on the Y-axis

Wow that was fast, looks good. Thank you.

I've pushed the code for a single unit time duration value formatter.
It's a factory method that returns a value formatter that It can be customized with the number of decimals and the time unit.
I've added also a helper for second based 0 decimals value formatter, that is a common case for RPC based services like GRPC or HTTP latency graphs.
What do you think?

Ready for a new check.
I've also added the check for NaN values.
Thanks @mum4k!

Looks good @slok.
Good catch about checking for the NaN values, I completely missed that.

I pushed the last step. Add a simple round formatter.
I've added also suffix and decimal based formatter that I think that can be helpful for the users in lots of simple cases where you only want to add a suffix and limit the decimals so it shows pretty on the line chart.
I've also updated the changelog.
When we are finished with this last step I'll remove the draft state from the PR and would be ready :tada:

Ready! :)

For some reason the automated checks didn't trigger. I will try to cause a Travis run by closing and reopening this PR.

Pull Request Test Coverage Report for Build 1136

120 of 120 (100.0%)  changed or added relevant lines in 8 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage increased (+0.1%) to 92.6%

Totals

Change from base Build 1126:
0.1%

Covered Lines:
7383

Relevant Lines:
7973

💛  - Coveralls

I forgot about the permission, sorry!
You have permission to merge this PR into master branch.

Looks good, thanks a lot @slok, I have really enjoyed working with you on this feature.

Same here! Thanks for your time and effort in explaining things. I hope to contribute more!

Anytime, looking forward to it already. How is your project going, are you approaching a release? Are there any other major features you are missing?

I'm implementing the unit formatters inside the app at this moment (maybe we could port some of them to termdash), when finished, next will be a little bit of documentation, clean up the readme, add some flags that I think that will be handy and I'll be ready for the first release, depending on how many hours I can spend this weekend I think that next week I'll have it!
At this moment for the first release of grafterm I think that the required ones are already implemented, if people like this app and start asking for features I'll have a better priority vision.
In mind, I have lot's of features apart from the ones we discussed in the other PR (the table and the selector are the ones that I think are the most important ones). Maybe are a little crazy xD but I give you some of them in case you like or you think that will be fun to implement.

Stacked graph series, this can be done calculating the final value aggregating the different values by the users of termdash, but using a simple flag on the graph widget would be the easiest way for the user (I don't know if this is worth).
Legend over a graph (I don't know if this is possible)
Fill the graph lines area (render all area instead of only a line, this could come with Z-axis score/value, to set the depth of series so the known smallest ones can be over the highest ones, this way they are not hidden, e.g. percentiles).

Example all these on the same graph in Grafana

Heatmap widget.
A more feature-rich bar gauge (check the ideas here).

horizontal, vertical.
Multiple colors on the bar based on the bar percent.

Like I said, some maybe are crazy ideas :)
I'll notify you when Grafterm is released!

That sounds great @slok, looking forward to the first release of grafterm. Feel free to circle back and open issues if you find anything wrong or missing. Meanwhile I will continue working on the table and the selector, same as you it is a continuous fight in trying to find enough hours during the weekend.
No ideas are crazy and brainstorming really helps, so feel free to propose anything that comes to mind, worst case we will agree that it isn't doable or worth it ;)
The stacked graph series and filled graph areas look really good, but might not be doable on terminal due to limitations that I didn't find a way around yet. Even though with the braille unicode characters we get sub-character resolution, each cell is still limited to only one set of cell options. This becomes a problem especially when two series share a cell, the entire cell would be of a single color (series 1 or series2). You can already observe this in cells where multiple series cross, when we start filling them it might look bad or the differences / borders between series might get lost. If you have ideas how to overcome this - please let me know.
The legend over a graph is absolutely doable once we have #104. Same as above, we can only let users click on a full cell, rather than a braille point within a cell, but that shouldn't be a large issue. If you have some spare time - please do file an issue briefly describing the functionality (what should be displayed in the pop-up).
The heatmap might also suffer from the single-color-per-cell issue, unless we create a cell based heatmap which might have too low of a resolution? What do you think?
More features for bar chart sound good, I was already planning a #9. As with the legend - if you get some spare cycles, please file an issue describing what features we should add.
Thanks for all the ideas and support!

Hey @mum4k, I've been lucky and manage to get the time and have a productive weekend :tada: https://github.com/slok/grafterm

Looks amazing, great work and congratulations @slok. Glad to see this come together.
I took this opportunity and listed grafterm in the README, however if you would prefer I don't, please let me know.
Alternatively feel free to send a PR against master adding a short description next to the link if you would like.

Many thanks for adding a link to grafterm on the readme!


style: change endDrawer search box color

Changes search box color to pull from the theme

This PR is dependent on #510 which adds the fillColor for light mode.


ENHANCEMENT: Added onBeforeRender extension point to form fields that call renderWith (fixes #4790)

This pull request adds the onBeforeRender extension point to the following form fields, the other built in form fields that are not listed either don't seem to call renderWith and instead use raw html or already have the onBeforeRender extension point in the Field method,.

CheckboxSetField
OptionsetField
TreedropdownField
TreeMultiselectField
UploadField
ListboxField

Is this an enhancement or a bug fix? Should it be in 3.2 release line or just 3?

Ya I'm not sure, given that it adds something previously not available I'd call it a feature. But then again its also possible it could be considered a bug because they probably should have had it when that was originally added. Not sure it's kind of a grey area ;)

Well, the intention of adding this hook to the parent class must have been to make it available to "all" field types, right?
If there are modules that rely on this hook, then it's a broken feature and therefore a bug imo.
Waiting for thoughts from @silverstripe/core-team

why is returning parent::Field() not working? It looks like it should from a brief inspection of the code?
I don't like having to add the hook to each child class that overrides the method

Is this an enhancement or a bug fix? Should it be in 3.2 release line or just 3?

I think this is fine for a patch release.

OK - @kinglozzer agrees it's suitable to be a patch release.
I'd really prefer if we can get this working by calling parent::Field() instead - is that something that's realistic? I'm not sure why it'd make tests fail from first glance.
@UndefinedOffset are you ok to reopen this against 3.2 potentially with them calling the parent method?

@dhensby can do I'll make the changes, and open a new pull request. I'll also see if I can figure out that test failure that was spotted in #5780.

@UndefinedOffset much appreciated - if you can't get to the bottom of it, I'll probably accept this as a stop-gap solution and it'd be good to get it working "properly" later


Resolve deprecations on Patient Module

All deprecations in the patient module need to be resolved.
@zinyando is working on this with PR #181

I believe all of the patient specific deprecations are now addressed.
Thanks to @zinyando for contributing his PR.


Fixed can't get sa token secret when secret name is long

Signed-off-by: xuezhaojun<EMAIL_ADDRESS>Relevant issue: https://github.com/open-cluster-management-io/registration-operator/issues/196

/assign @zhujian7
/assign @zhiweiyin318

/lgtm

/approve

@zhiweiyin318 Hello, Zhiwei, would you like to have a review?

/approve


No autocomplete popup in closures

Version of VSCode: 1.12.2
Version of the extension: 0.3.14
OS: macOs Sierra
Description:
In the following
    let pwd = path::Path::new(".");
    let output = pwd
                .read_dir()
                .unwrap()
                .map(|entry| entry.$) // cursor here
                .collect::<Vec<_>>();

It seems rls successfully infers the type of entry, but provides no autocomplete when I press ".".

@KalitaAlexey improve it, please! :disappointed:


Fix PSAvoidGlobalVars

Summary of new feature
There are 2 cmdlets breaking the PSAvoidGlobalVars script analyzer rule, which could be impacting cmdlet use as well as our BOH. This rule states that creating global variables may cause conflicts or unexpected changes in the environment.
ScriptName                Line Extent
----------                ---- ------
Export-DbaDacPackage.ps1   227 $global:output
Export-DbaDacPackage.ps1   228 $global:output
Export-DbaDacPackage.ps1   251 $global:output
Publish-DbaDacPackage.ps1  283 $global:output
Publish-DbaDacPackage.ps1  284 $global:output
Publish-DbaDacPackage.ps1  319 $global:output

See PSAvoidGlobalVars.md for more details
Proposed technical details (if applicable)
Reading the code, it seems to need this to pass information from the -Action parameter of Register-ObjectEvent back out to the dbatools cmdlet. However, it seems like we could remove global variable, but maintain the same functionality by using the -MessageData parameter to pass information back to a [Systems.Collections.ArrayList] object. An example of this would look something like this:
$output = New-object System.Collections.arraylist
Register-ObjectEvent -InputObject $dacSvc -EventName "Message" -SourceIdentifier "msg" -Action { [void]$MessageData.output.Add($EventArgs.Message.Message) } -MessageData $output | Out-Null

Would like some feedback from @RichieBzzzt on this cmdlet as he was the original author of both cmdlets in question.

Hello!
Providing it outputs the messages from the deployment/exporting, I'm more than happy for this change.

Awesome! I am not as familiar with the use of this cmdlet. I tried some of the examples, but they seem incomplete. And the Integration tests pass, so I don't know if they are testing this section of the code. Do you have some examples that I could use to test this section of the code?

I'll get in touch with you on Slack, we can have a chat there.


mailcap hash change infinite recursion

Steps To Reproduce
Steps to reproduce the behavior:

try to build mailcap (needed for python3.9, needed for various other things)

Build log
$ nix-instantiate '<nixpkgs>' -A mailcap
warning: you did not specify '--add-root'; the result might be removed by the garbage collector
/nix/store/2km7xxdp57ylsh8p9jm8zykz2v6cfmbp-mailcap-2.1.53.drv
$ nix-store -r --check /nix/store/2km7xxdp57ylsh8p9jm8zykz2v6cfmbp-mailcap-2.1.53.drv
checking outputs of '/nix/store/2km7xxdp57ylsh8p9jm8zykz2v6cfmbp-mailcap-2.1.53.drv'...

trying https://releases.pagure.org/mailcap/mailcap-2.1.53.tar.xz
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 24636  100 24636    0     0  56589      0 --:--:-- --:--:-- --:--:-- 56634
unpacking source archive /build/mailcap-2.1.53.tar.xz
tar: /build/file: Cannot open: No such file or directory
tar: Error is not recoverable: exiting now
error: builder for '/nix/store/2km7xxdp57ylsh8p9jm8zykz2v6cfmbp-mailcap-2.1.53.drv' failed with exit code 2

Additional context
https://github.com/NixOS/nixpkgs/pull/173430 changes what postFetch means in fetchzip; mailcap https://github.com/NixOS/nixpkgs/blob/master/pkgs/data/misc/mailcap/default.nix#L13 expects the downloaded file still to be in $downloadedFile, but the new fetchzip has moved it to $renamed https://github.com/NixOS/nixpkgs/blob/master/pkgs/build-support/fetchzip/default.nix#L47.
looks like mailcap's postFetch really does intend to replace fetchzip's. maybe it would be better to change to plain fetchurl?
Notify maintainers
@c0bw3b @Artturin , if I may
Metadata
$ nix-shell -p nix-info --run "nix-info -m"
...
 - system: `"x86_64-linux"`
 - host os: `Linux 5.10.109+, Debian GNU/Linux, 11 (bullseye), nobuild`
 - multi-user?: `no`
 - sandbox: `yes`
 - version: `nix-env (Nix) 2.9.0`
 - channels(...): `"nixpkgs"`
 - nixpkgs: `/home/.../.nix-defexpr/channels/nixpkgs`

(some info redacted)

this has exposed a larger problem which is infinite recursions
error: infinite recursion encountered

       at //builtin/derivation.nix:19:19:
       … while evaluating 'optionalString'

       at /nix/store/1ljgyxz46vh768ya2djkmf3cqsn3ln1p-source/lib/strings.nix:203:5:

          202|     # String to return if condition is true
          203|     string: if cond then string else "";
             |     ^
          204|

       … from call site

       at /nix/store/1ljgyxz46vh768ya2djkmf3cqsn3ln1p-source/pkgs/development/interpreters/python/cpython/default.nix:278:8:

          277|       --replace "'/bin/sh'" "'${bash}/bin/sh'"
          278|   '' + optionalString mimetypesSupport ''
             |        ^
          279|     substituteInPlace Lib/mimetypes.py \

       … while evaluating the attribute 'postPatch' of the derivation 'python3-3.9.13'

       at /nix/store/1ljgyxz46vh768ya2djkmf3cqsn3ln1p-source/pkgs/stdenv/generic/make-derivation.nix:278:7:

          277|     // (lib.optionalAttrs (attrs ? name || (attrs ? pname && attrs ? version)) {
          278|       name =
             |       ^
          279|         let

       … while evaluating the attribute 'nativeBuildInputs' of the derivation 'python3.9-buildcatrust-0.1.3'

       at /nix/store/1ljgyxz46vh768ya2djkmf3cqsn3ln1p-source/pkgs/stdenv/generic/make-derivation.nix:278:7:

          277|     // (lib.optionalAttrs (attrs ? name || (attrs ? pname && attrs ? version)) {
          278|       name =
             |       ^
          279|         let

       … while evaluating the attribute 'nativeBuildInputs' of the derivation 'nss-cacert-3.77'

       at /nix/store/1ljgyxz46vh768ya2djkmf3cqsn3ln1p-source/pkgs/stdenv/generic/make-derivation.nix:278:7:

          277|     // (lib.optionalAttrs (attrs ? name || (attrs ? pname && attrs ? version)) {
          278|       name =
             |       ^
          279|         let

       … while evaluating the attribute 'SSL_CERT_FILE' of the derivation 'mailcap-2.1.53'

       at /nix/store/1ljgyxz46vh768ya2djkmf3cqsn3ln1p-source/pkgs/stdenv/generic/make-derivation.nix:278:7:

          277|     // (lib.optionalAttrs (attrs ? name || (attrs ? pname && attrs ? version)) {
          278|       name =
             |       ^
          279|         let

https://github.com/NixOS/nixpkgs/pull/176291

where are you getting this error so we'll know if this needs to go in to master

nixpkgs unstable and nixos 22.05

Fix got reverted in #177541

Wasn't this solved by switching to fetchurl?

This issue has been mentioned on NixOS Discourse. There might be relevant details there:
https://discourse.nixos.org/t/nix-macos-monthly/12330/29


Check if a lifespan is given when setting an out going context

The previous check couldn’t handle 0 as a lifespan, using isset resolves this issue

Thanks for merging, any timeline on when a new release will be available with this fix?


[Feature] Open Graph improvements and customization for the central server.

Allow for full customization of all open graph elements.
Also enable open graph for non-musiqpad links. i.e. mypad.com

On hold until #104 / #39 gets finished


Issue 004

seems good to merge. Should we have the user input their name during sign up or have them add it into their profile after signing up?


Move repo under PistonDevelopers?

I feel like this should (eventually?) be moved into PistonDevelopers for more visibility, but it's your call, @viperscape

If we move it to piston, I can get TravisCI set up and have it automatically deploy docs to https://github.com/PistonDevelopers/docs

Yes sure, what is involved?

I'll see if I can get you added as a PistonDevelopers admin.., then it's just simply transferring ownership of the repo to PistonDevelopers

Okay great

Completed

sweet!


Generating Alternative Reference

Hi,
I have a hemizygous genome and I have detected SVs on the main reference genome using dysgu. I wanted to confirm that the filtering parameters I am using would make sense in this case, and also to check if you knew of any good tools that can create an alternative reference genome using the vcf output file from dysgu.
I ran dysgu as follows:
dysgu run -p$cpus --mode pacbio --pl pacbio --drop-gaps False --verbosity 2 --metrics --clean --overwrite $ref temp_${name} $file -o ${name}.vcf
dysgu filter -p$cpus --min-prob 0.5 -o ${name}.flt.vcf ${name}.vcf
I am merging the results from dysgu with the results from deepvariant to obtain an full alt vcf.
I was using gatk to generate the alternate reference but the issue is that it only can process SNPs INS and DELs but not DUP, TRA and INV
gatk IndexFeatureFile -I 3.chr.vcf
gatk CreateSequenceDictionary -R ${ref}.fasta -O ${ref}.dict
gatk FastaAlternateReferenceMaker -R ${ref}.fasta -O reference_alt.fasta -V 3.chr.vcf
is there any good alternative for this that you could recommend?
Thanks

Hi @grpiccoli,
I think the filtering looks OK, you should remove most false-positives. Lowering the --min-prob will increase sensitivity though.
Making a new fasta sequence is not something I have tried myself, so can't claim any expertise. I image creating a new reference from SNPs + indels + symbolic SVs (,  etc, that dont have exact sequences) would be quite a challenge. The SVs can lead to non-trivial genome structure. DNA assembly/scaffolding programs might be worth checking out?

@kcleal thank you for your reply.
What min-prob would you recommend?
about the alternative assembly I am trying bcftools consensus I think it should work for more complex variant types, I'll let you know how it goes. I have an alternative assembly and I would like to compare it to the alternate assembly from the SV analysis.
Thanks

Thank you for the software solutions! gw looks really good. I will close the ticket for now and update it if I find a way to get the alternative reference, just in case someone else might need it.

Hello, I'm also working on the same task, but I'm using bcftools consensus. My mutation data comes from two sources: 1. GATK germline mutations pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels/) mainly for SNPs and short indels. 2. Using dysgu to find structural variants.
I believe that a combination of these two types of mutations represents an individual's mutations.
Methods for generating ALT sequences I used
I downloaded WGS data from GEO, ran BWA to get sorted BAM files, and then used dysgu as follows:
sample = SRR10129631
samtools index  $sample"_sorted.bam"
dysgu run -x -p8 /data/wenyuhao/55/CCLE/raw/resources/genome.fasta tmp $sample"_sorted.bam" > $sample"_dysgu.vcf"
dysgu filter --min-prob 0.75 --support-fraction 0.2 SRR10129632_dysgu.vcf

The VCF files generated by dysgu contain ALT values like <DEL>,<DUP>, <INS>, <INV> ,<TRA>, which are not supported by bcftools consensus. Therefore, I want to extract all possible variants from the ALT field.
I referred to two issues issues 10, issues 63 and came up with the following strategy:

For DEL mutations, I delete the sequence of SVLEN length after the ref, keeping the ref unchanged and changing alt to genome[chrom][pos:pos+SVLEN].
For INS mutations, there are two cases. A. If the ALT field is not <INS>, then no changes are needed. B. If the ALT field is <INS>, I change ALT to 'LEFT_SVINSSEQ' + ref + 'RIGHT_SVINSSEQ'
For <DUP>, <INV>, <TRA> mutations, I'm not sure how to handle them yet.

I've written a script process_dysgu.py for this purpose. Could you please confirm if the above process is correct? If not, kindly point out the corrections needed. If it's correct, could you also provide guidance on how to handle the <DUP>, <INV>, and <TRA> mutations?
eg.
python process_dysgu.py -i SRR10129632_dysgu.vcf -r /data/wenyuhao/55/CCLE/raw/resources/genome.fasta | bgzip -c > test.vcf.gz && tabix -p vcf test.vcf.gz
bcftools consensus -f /data/wenyuhao/55/CCLE/raw/resources/genome.fasta  test.vcf.gz > test.fa

question About INFO['END'] and INFO['SVLEN'] for INS
Generally speaking，‘END‘ must be in INFO in SV vcf file, if some rows are missing END field, need to add. I counted the missing END field, usually INS mutation. bcftools consensus will check whether the insertion sequence and SVLEN match, and throw an exception if they do not match
The fasta sequence does not match the REF allele at 1:886224:
   REF .vcf: [T]
   ALT .vcf: [TGCCCTTTGGCAGAGCAGGTGTGCTGTGCTG]
   REF .fa : [TGCCCTTTGGCAGAGCAGGTGTGCTGTGCTG]TGCTGA

However, during the process, I found that the length of the insertion sequence ('LEFT_SVINSSEQ' + ref + 'RIGHT_SVINSSEQ') is not equal to SVLEN. It is either greater than or rarely equal to SVLEN, which has left me puzzled. I am unsure whether SVLEN is meaningful for INS mutations. As a result, I removed the END field, but I am uncertain if this is the correct approach.
If the length of the insertion sequence is greater than SVLEN, I can trim a portion of lowercase letters and a portion of uppercase letters. However, if the length of the insertion sequence is less than SVLEN, how should I handle it?
Supplementary Note
1，The insert sequence ('LEFT_SVINSSEQ' + ref + 'RIGHT_SVINSSEQ') is longer than SVLEN
{'#CHROM': '1',
 'POS': 1478003,
 'ID': 514531,
 'REF': 'C',
 'ALT': '<INS>',
 'FORMAT': 'GT:GQ:MAPQP:SU:WR:PE:SR:SC:BND:COV:NEIGH10:PS:MS:RMS:RED:BCC:FCC:ICN:OCN:PROB',
 'SRR10129632': '1/1:25:41:16:0:0:4:16:10:37.7:4:5:15:90:0:1:0.53:1.402:0.744:0.835',
 'SVTYPE': 'INS',
 'END': '1478003',
 'CT': '3to5',
 'SVLEN': '133',
 'CONTIGA': 'AATGTTGTATTTTAGTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCTAACTCCCGACCTCAGGTGATCCACCCGCCTCGGCCTCTCAAACTGTTGGGATTACAGGCATGTGCCACCACGCCTGGCtaatgttgtattttagtagagacggggtttctccatgttggtcag',
 'CONTIGB': 'GTAGAGACGGGGTTTCTCCATGTTGGTCAGGCTGGTCTCTAACTCCCGACCTCAGGTGATCCACCCGCCTCGGCCTCTCAAACTGTTGGGATTACAGGCATGTGCCACCACGCCTGGCtaatgttgtattttagtagagacggggtttctc',
 'RIGHT_SVINSSEQ': 'taatgttgtattttagtagagacggggtttctccatgttggtcag',
 'LEFT_SVINSSEQ': nan}

2，INS but ALT is not <INS>
1	886225	302472	T	GCCCTTTGGCAGAGCAGGTGTGCTGTGCTG	.	PASS
	SVMETHOD=DYSGUv1.5.0;SVTYPE=INS;END=886226;CHR2=1;GRP=302472;NGRP=1;

CT=3to5;CIPOS95=12;CIEND95=12;SVLEN=30;KIND=extra-regional;GC=58.75;NEXP=0;STRIDE=0;

EXPSEQ;RPOLY=10;OL=0;SU=49;WR=7;PE=12;SR=6;SC=23;BND=0;LPREC=1;RT=pe

GT:GQ:MAPQP:SU:WR:PE:SR:SC:BND:COV:NEIGH10:PS:MS:RMS:RED:BCC:FCC:ICN:OCN:PROB

0/1:200:48.15:49:7:12:6:23:0:45.12:18:19:17:0:0:7:0.745:1.146:0.854:0.771

In fact, bcftools consensus does not entirely lack support for SV VCF files. It only supports three fields: <DEL>, <*> or <NON_REF>, and it cannot handle the <INS>,<DUP>, <INV>, and <TRA> fields. Therefore, in this case, I only dealt with the <INS> field.
└─(21:17:51)──> bcftools consensus -f /data/wenyuhao/55/CCLE/raw/resources/genome.fasta  wnm.vcf.gz > wnm.fa                             ──(Thu,Aug17)─┘
Symbolic alleles other than <DEL>, <*> or <NON_REF> are currently not supported, e.g. "<DUP>" at 1:231202004.
Please use filtering expressions to exclude such sites, for example by running with: -e 'ALT~"<.*>"'

Hi @wenyuhaokikika it looks like we are "phasing" the same problem (pun intended). I am working on a very similar script in python that deals with DEL DUP INS INV BND|TRA.
An alternative that did not work for me was to split the reads by haplotype using longphase and then assembling them separately. I mention it just in case that could work for you.
Please let me know if we can cooperate in developing this python script
Thanks

Hello, the author provides a script convert2bnd.py to split the reads by haplotype using longphase, but even if separated , I still don't know how to assemble them separately.

Hi, that's my issue as well. I have the two phased bam files and I was able to assemble them into a very fragmented assembly using HiFiasm but then when I try to scaffold them it fails, I am still trying to figure out why, but it looks that because the coverage was halved somehow the RAM that it takes to scaffold the assembly grew exponentially and even at 1T of RAM it still runs out of memory.
What type of reads are you using? maybe you won't face the same issue if you have already obtained the phased bam files.

Another alternative is to use RagTag to scaffold your reads with the assembly you already have as a template, that might be what you are looking for

I was able to solve my issue by reassembling in the end, with a custom algorithm based on the two approaches mentioned above, I don't think I'll pursue trying to phase the assembly based on the vcf any longer but you can find a very rough draft of what I was working on here https://github.com/grpiccoli/vcf2haplotypes/blob/master/phasedvcf2haplotypes.vcf in case it might be useful to anyone else

Hello, I have a few questions about your script:

Regarding handling DEL. During the first FOR loop, after processing the first DEL, all the positions after the mutation have changed. Won't this cause a shift in the sequence for the subsequent positions? How do you ensure that positions beyond the first DEL remain aligned?
I understand that allelic mutations indicate whether mutations occur on the positive or negative strand. If it's 0/0, it means there are no mutations on either strand. If it's 0/1, it means there's no mutation on the positive strand, but a mutation on the negative strand. And if it's 1/1, it indicates mutations on both the positive and negative strands.The following is from chatGPT

Q:The allelic mutation in vcf is 0/0, 1/1, 0/1. If it is 0/0, it means that there is no mutation on the positive and negative chains, and 0/1 means that the positive chain is not mutated, and the negative chain is mutated. , 1/1 means that both positive and negative are mutated, is that what it means?
A:Yes, your understanding is correct. In the VCF file, allelic mutations are represented using numeric genotypes. The numbers 0, 1, and 2 are commonly used to represent different genotypes. Specifically:

    0/0: Both alleles on the positive and negative strands are the same as the reference allele, indicating no mutation.
    1/1: Both alleles on the positive and negative strands are different from the reference allele, indicating a homozygous mutation.
    0/1: The allele on the positive strand is the reference allele, while the allele on the negative strand is different, indicating a heterozygous mutation.

So, your interpretation of the genotypes is accurate.

If it's a positive and negative strand scenario, why are the same operations performed on both strands? Shouldn't the operations be performed in reverse complement on the negative strand?
From my perspective, multiple mutations occurring on a chromosome are independent events, but their effects are not independent. This issue is complex, and by relying on bcftools consensus, we can generate the corresponding VCF with complete ALT fields.

Hi @wenyuhaokikika, yes it will you are right about your first point, and even if it did work there is no clear way to deal with unphased variants, so you will most likely end up with highly chimeric haplotypes either way.
/ <-- this indicates that it does not know which strand it occurs in
| <-- this indicates it does
0 <-- this means it is the "reference" haplotype (i.e. if it is / it means that it is whatever you used as a reference, in the case of '|' all '1s' will be in the same haplotig)
That's why I was trying to reassemble so hard as it is the recommended option in this case.
In my case I need to get the phased haplotypes in separate fasta files so only associated variants are grouped on the same file. If your case is different and you don't mind somewhat chimeric haplotypes, then a python script might be what you are after.
Let me know if I can help with anything, cheers

Sorry @kcleal this might not related to the original issue any longer.
I suspect @wenyuhaokikika and I might be trying to do a different thing.
@wenyuhaokikika,
Is your ultimate goal to obtain phased fastas, one per haplotype?
What type of reads do you have?
What type of reference do you have?
Is your reference genome already phased?
Do you have an LD mapping for your haplotypes?
What ploidy does the organism have?
Cheers

Thank you for your patient response.
I've reviewed the literature and realized my mistake regarding mutations occurring in two Haplotypes. Mutations don't need to consider reverse complementarity, but rather whether they are in the same phase, as you pointed out. I greatly appreciate you pointing out this oversight, and I apologize for the confusion in my previous statement.
While obtaining consensus sequences is just a part of my work, my main focus lies in cancer proteomics. I've summarized the issues I'm facing in hopes of receiving your guidance. I also aim to clarify all aspects before I proceed with coding.

My work revolves around WGS data from human cell lines, with read lengths of 126 and a sequencing depth of around 45X.
Currently, my data isn't phased, but I need to consider phased alleles.

I've researched tools for phasing mutations, including HaplotypeTools, Beagle, and SHAPEIT, among others. Ultimately, I've chosen SHAPEIT4 for phasing, based on SHAPEIT and the paper "Integrating sequence and array data to create an improved 1000 Genomes Project haplotype reference panel" (IF=14.92, date=2019).
I've run the following code:
mamba install shapeit4
bam=/data/wenyuhao/55/CCLE/raw/hct116/sorted.bam
vcf=/data/wenyuhao/55/CCLE/raw/hct116/SRR8639145_germline_filter.vcf

bgzip -c $vcf > unphased.vcf.gz
bcftools index unphased.vcf.gz

shapeit4 --input unphased.vcf.gz \
--map shapeit4/maps/chr1.b38.gmap.gz \
--region 1 \
--seed 123 \
--output phased.vcf.gz \
--sequencing \
--reference /data/wenyuhao/55/CCLE/raw/hct116/phase/reference/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5b.20130502.genotypes.vcf.gz \
--thread 8 \
--log shapeit_chr1.log

Utilizing GATK-generated mutation data, comprising approximately 100,000 variants, I've only obtained 1383 phased mutations. SHAPEIT4 necessitates a reference (e.g., 1000 Genomes Project) for phasing small sample sizes, rendering it unable to phase mutations absent in the reference. I've noticed a similar issue in the shapeit4-issues68 thread. However, I'm hesitant to discard any mutation data. In this scenario, what approach would you recommend? If no alternative exists, I might need to phase all mutations as 1|1.
I appreciate your assistance and guidance in resolving this matter. Thank you in advance for your support.

Hi @wenyuhaokikika thank you for your detailed answer.
I am working with a longread de novo assembly of a hemizygous organism, so the structural variants are between the two copies of "the same" chromosome, this results in only 2 haplotypes in my case.
I think in your case you are working with a virtually haploid reference plus a single diploid sample.
Could you confirm this?
If this is the case then it is possible to have multiallelic variants i.e., 0 would be your reference always, and 1 and 2 would be randomly assigned to a mixture of either one of your diploid sample two haplotypes.
Separating variants of 0 from 1,2 should be easy as 0 will always represent the reference in your case, but to separate 1 from 2 you might run into the issue I am describing.
Only if you need to separate 1 from 2 then you require phasing (assuming there is only one sample).
In the case you do not need phasing of your sample haplotypes, but you still need to generate the two FASTA consensus then you will run into the issue that most tools like "bcftools consensus" will not take into account complex structural variants when generating the consensus.
If this is your case and you have a decent genome coverage the best solution would be to do either a reference guided assembly or a de novo assembly, I checked google scholar and in cancer skim WGS they are using supernova assembler for humans, you would need to check the literature for the best assembler though.
Now if you need to phase multiple samples from a population then that's a whole different issue (like with HaplotypeTools).
Could you confirm if the assumptions are correct and why do you need a FASTA consensus?
If all you need is to visualize your variants, then just use the vcf file from dysgu and feed it to something like Ribbon for example and that's all


fix: Fix/js object ads issues

This PR addresses issues raised when migrating JsObjects to new design system.
Issue link here: https://www.notion.so/appsmith/f353d8c6bd664f79ad858a42010cdfc8?v=f04cde23f6424aeb9d5a6e389cd172bd&p=6ff9af061f354a569b160157453bfb3f&pm=s

Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?

Please describe the tests that you ran to verify your changes. Provide instructions, so we can reproduce.
Please also list any relevant details for your test configuration.
Delete anything that is not important

Manual
Jest
Cypress

Test Plan

Add Testsmith test cases links that relate to this PR

Issues raised during DP testing

Link issues raised during DP testing for better visiblity and tracking (copy link from comments dropped on this PR)

Checklist:
Dev activity

[ ] My code follows the style guidelines of this project
[ ] I have performed a self-review of my own code
[ ] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[ ] My changes generate no new warnings
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] New and existing unit tests pass locally with my changes
[ ] PR is being merged under a feature flag

QA activity:

[ ] Test plan has been approved by relevant developers
[ ] Test plan has been peer reviewed by QA
[ ] Cypress test cases have been added and approved by either SDET or manual QA
[ ] Organized project review call with relevant stakeholders after Round 1/2 of QA
[ ] Added Test Plan Approved label after reveiwing all Cypress test

/build-deploy-preview env=release

Removing of the logo background and border should not have been done because it doesn't match the entity explorer + the contrast doesn't work.


Add functional dependencies a la polysemy-plugin

polysemy-plugin is a godsend for working with polysemy, and it's possible its functional dependencies component could be adapted to work with in-other-words.

It was easier than expected.
https://github.com/KingoftheHomeless/in-other-words-plugin

It was easier than expected.
https://github.com/KingoftheHomeless/in-other-words-plugin


Can't easily drag mutiple node into property shared by multiple node

Tested versions
409c71bdfd8e0a08fd726225ebdce16bc60a4570
System information
macOS 13.3.0 - Vulkan (Forward+) - integrated Apple M1 Pro - Apple M1 Pro (8 Threads)
Issue description
Since #90378 you can now easily drag and drop a batch of node inside a property of a node. Unfortunately this doesn't work for putting it in properties in multiple nodes. This is a small usability issue which is not urgent especially since improving this will most likely be hard. Maybe here the good solution would be to be able to pin the Inspector.
Steps to reproduce
N/A
Minimal reproduction project (MRP)
N/A

This sounds like a proposal, not a bug

Yeah you might be right I thought of it has a bug as the workaround would allow it if I remember correctly.


Dynamic indexing fix typos

If tests were quicker, then developers would be more likely to run tests before committing.

I had fixed these typos (except for the optional inclusion of {} for a one-line body in an if statement already but hadn't pushed.  So please pull my changes and go from there. I think this PR can be deleted.


  I would prefer to see a peek of IStructure.

This feature is powered by the TypeScript project. Please file a feature request upstream


[FABN-1555] Update EventListener typedef and document

add RegistrationOpts definition to type.js

Signed-off-by: david<EMAIL_ADDRESS>

@hyperledger/fabric-test-toolchain-maintainers ready for review

@bestbeforetoday would you mind triggering the builder again? My local test result show green.

Before I work on rebasing with solving a simple conflict.
I have to highlight that in this change I add back the npm callsite which is a critical fix.
Without this package we could not create HSMCryptoSuite with fabric-common only! (at least for current published version)


Feature / Generators and Iterators (instad of Files) in API

Closes #532 by removing any occurence of adiar::shared_file<label_t> in the public API. This also removes bdd_counter and zdd_sized_set until I have found a way to implement them anew.

System tests are breaking, because of the Adiar adapter uses the broken part of the API (specifically, it uses zdd_powerset(...). I have added bdd_top(), bdd_bot(), zdd_top(), and zdd_bot() to address this usecase.


CNS-593: fix "make proto-gen" breakage

The build 'make proto-gen' stopped working because the 'proto-build' docker image from cosmos no longer supports bash. Fix by adjusting the script to be compatible with 'sh' instead of 'bash'.

using this branch, trying protogenc.sh on my env doesnt work:
./scripts/protocgen.sh
./scripts/protocgen.sh: 3: source: not found
./scripts/protocgen.sh: 5: command_exists: not found

using this branch, trying protogenc.sh on my env doesnt work:

sigh, that was incomplete commit. fixed.

Not a must, but when I'm running ./scripts/protocgen.sh from this branch, it prints "option" strings like this: option go_package = "github.com/lavanet/lava/common/types";
Can you make it not print that (like before)?

Done.


Adding API keys

You should add bot API keys. Example: import Client from "msgroom";
const client = new Client("TestBot", "APIKey", [ "!" ]);
await client.connect();

This feature already exists, it works like this:
const client = new Client("[!] TestBot", "!", {
    apikey: "api key here"
});

You can get an apikey from ctrlz.
One problem though: it hasn't been implemented in the msgroom server.
We have no idea how this stuff would even work and what the difference would be between using an apikey and not using one.
Ctrlz still has to figure this out and probably isn't going to anytime soon.
You might also want to look into code formatting in markdown 😃

Also if you're only using one prefix, youc an turn [ "!" ] into "!"

Oh, ok


fix and enhance cni (re)provisioning

with this PR :

issue #113 is solved by performing reboot of master and minions on --provision-with cleanup (instructions added in the README.md)
it is possible not to configure any CNI plugin after configuration of kubernetes, useful for debug (kubernetes_network_plugin=no-cni-plugin)
Vagrantfile checks that a correct plugin identifier is provided, otherwise exits explaining the error and suggesting the allowed plugins
README.md is modified, also adding the instruction to Show verbose output of Ansible operations

The last feature is a bit off-topic, but as it is a minor enhancement, may be it easier not to add a separate PR...

I have added a --provision-with mount-shared, because after the the reboot, the shared folders are not automatically mounted. I am documenting the procedure on the README.md
In principle, it is possible to use "vagrant reload --no-provision" instead of doing the reboot inside the shell command and then --provision-with mount-shared, but it takes 4x the time, because the vagrant reload is very slow

I've updated the initial description of this PR


cmd/compile: not compiled

Processor architecture arm5, OS Synelogy+ipkg(optware may be)
Install from gvm.
Log errors:

Building C bootstrap tool.
cmd/dist

Building compilers and Go bootstrap tool for host, linux/arm.
lib9
libbio
liblink
cmd/cc
cmd/gc
cmd/5l
cmd/5a
cmd/5c
cmd/5g
runtime
go tool dist: FAILED: /root/.gvm/gos/go1.4/pkg/tool/linux_arm/5g -pack -o $WORK/go.a -p main -+ /root/.gvm/gos/go1.4/src/runtime/alg.go /root/.gvm/gos/go1.4/src/runtime/arch_arm.go /root/.gvm/gos/go1.4/src/runtime/atomic_arm.go /root/.gvm/gos/go1.4/src/runtime/cgocall.go /root/.gvm/gos/go1.4/src/runtime/cgocallback.go /root/.gvm/gos/go1.4/src/runtime/chan.go /root/.gvm/gos/go1.4/src/runtime/compiler.go /root/.gvm/gos/go1.4/src/runtime/complex.go /root/.gvm/gos/go1.4/src/runtime/cpuprof.go /root/.gvm/gos/go1.4/src/runtime/debug.go /root/.gvm/gos/go1.4/src/runtime/env_posix.go /root/.gvm/gos/go1.4/src/runtime/error.go /root/.gvm/gos/go1.4/src/runtime/extern.go /root/.gvm/gos/go1.4/src/runtime/hashmap.go /root/.gvm/gos/go1.4/src/runtime/hashmap_fast.go /root/.gvm/gos/go1.4/src/runtime/iface.go /root/.gvm/gos/go1.4/src/runtime/lock_futex.go /root/.gvm/gos/go1.4/src/runtime/malloc.go /root/.gvm/gos/go1.4/src/runtime/mem.go /root/.gvm/gos/go1.4/src/runtime/mgc0.go /root/.gvm/gos/go1.4/src/runtime/mprof.go /root/.gvm/gos/go1.4/src/runtime/netpoll.go /root/.gvm/gos/go1.4/src/runtime/netpoll_epoll.go /root/.gvm/gos/go1.4/src/runtime/noasm_arm.go /root/.gvm/gos/go1.4/src/runtime/os_linux.go /root/.gvm/gos/go1.4/src/runtime/panic.go /root/.gvm/gos/go1.4/src/runtime/print1.go /root/.gvm/gos/go1.4/src/runtime/proc.go /root/.gvm/gos/go1.4/src/runtime/race0.go /root/.gvm/gos/go1.4/src/runtime/rdebug.go /root/.gvm/gos/go1.4/src/runtime/rune.go /root/.gvm/gos/go1.4/src/runtime/runtime.go /root/.gvm/gos/go1.4/src/runtime/select.go /root/.gvm/gos/go1.4/src/runtime/sema.go /root/.gvm/gos/go1.4/src/runtime/signal_unix.go /root/.gvm/gos/go1.4/src/runtime/sigpanic_unix.go /root/.gvm/gos/go1.4/src/runtime/sigqueue.go /root/.gvm/gos/go1.4/src/runtime/slice.go /root/.gvm/gos/go1.4/src/runtime/softfloat64.go /root/.gvm/gos/go1.4/src/runtime/sqrt.go /root/.gvm/gos/go1.4/src/runtime/stack.go /root/.gvm/gos/go1.4/src/runtime/string.go /root/.gvm/gos/go1.4/src/runtime/stubs.go /root/.gvm/gos/go1.4/src/runtime/symtab.go /root/.gvm/gos/go1.4/src/runtime/time.go /root/.gvm/gos/go1.4/src/runtime/traceback.go /root/.gvm/gos/go1.4/src/runtime/typekind.go /root/.gvm/gos/go1.4/src/runtime/vlrt.go /root/.gvm/gos/go1.4/src/runtime/zgoarch_arm.go /root/.gvm/gos/go1.4/src/runtime/zgoos_linux.go /root/.gvm/gos/go1.4/src/runtime/zruntime_defs_linux_arm.go /root/.gvm/gos/go1.4/src/runtime/zversion.go

This output looks truncated, can you please include the full output if possible.

Also, have you tried building without gvm?

Also, have you tried building without gvm?

Yes.Same.

This output looks truncated, can you please include the full output if possible.

Tell me how to do it?

Download the go 1.4 sources. cd go/src ./make.bash

If I downloaded from the desired site (https://go.googlesource.com/go/+/go1.4), the output is almost the same.

I think it's time to go back to basics.
What is the platform you are using? How much memory does it have, does it have any swap? You will need more than 256mb of ram to run ./make.bash. Don't bother running all.bash, it won't pass without extra twiddling for you.
Have you checked dmesg, is the Oom killer stomping on your process?

On 1 Apr 2016, at 20:15, indariums<EMAIL_ADDRESS>wrote:
If I downloaded from the desired site (https://go.googlesource.com/go/+/go1.4), the output is almost the same.

Reply to this email directly or view it on GitHub

Platform -  Synology USB Station 2. Memory 128mb. Then the matter is the lack of memory.
Thank you.

The first Go asm builder was a similar platform. Sadly it was outgrown by
Go 1.0. You won't be able to compile locally on that system. However you
can cross compile from another platform with one command
http://dave.cheney.net/2015/08/22/cross-compilation-with-go-1-5
I recommend that.
On Fri, Apr 1, 2016 at 9:32 PM, indariums<EMAIL_ADDRESS>wrote:

Platform - Synology USB Station 2. Memory 128mb. Then the matter is the
lack of memory.
Thank you.
—
You are receiving this because you commented.
Reply to this email directly or view it on GitHub
https://github.com/golang/go/issues/15058#issuecomment-204342712

Closing, since there isn't anything actionable here for us to do.


Add api to the pin update system

Description

Todos

[ ] Tests
[ ] Documentation
[ ] Release note

Release Note

None required

/merge-when-ready delete-branch

/merge-when-ready delete-branch

/merge-when-ready delete-branch

/merge-when-ready delete-branch

/merge-when-ready delete-branch

OK, I will merge the pull request when it's ready, leave the commits as is when I merge it, and delete the branch after I've merged it.

I'm sorry but I failed delete the branch after merging the pull request.


Add try/catch protection for ~LocalAdmissionController

What problem does this PR solve?
Issue Number: close #8459
Problem Summary:
What is changed and how it works?
Check List
Tests

[ ] Unit test
[ ] Integration test
[ ] Manual test (add detailed scripts or steps below)
[ ] No code

Side effects

[ ] Performance regression: Consumes more CPU
[ ] Performance regression: Consumes more Memory
[ ] Breaking backward compatibility

Documentation

[ ] Affects user behaviors
[ ] Contains syntax changes
[ ] Contains variable changes
[ ] Contains experimental features
[ ] Changes MySQL compatibility

Release note

None

/run-all-tests


Add optional expiration height to tx

It can be useful to declare that a tx will be invalid after a certain height before signing it.
For example, to if a malicious node wants to delay a tx for hours and send it when you already sent another.  Or a multisig tx that you start, but is never finalized, can't show up weeks later.
Add this to the Chain middleware that enforces the proper chain, which can also enforce this, as it is a stateful validity check that doesn't need to touch the db.

Resolved with PR #165