Pie chart left align

G2 Version: 4.1.7

Platform: macos

Mini Showcase(like screenshots):

CodePen Link: NA

I have a container inside of which I have a pie chart rendered. On a wider viewport, the pie is looking fine at the center with the legend being at the right. But if I start to look at in a smaller device or I shrink the browser width, then the legend starts overlapping on the chart
I am using media queries to decrease the font-size of the legend text, setting offsetX values and trying different things, just wanted to check, if we can left align the chart using any existing config
Any help will be greatly appreciated
TIA

Determine the position of the legend based on the width of your screen.

When on a wider viewport, show legend right
Else bottom


MediaPlayer - The stream is in the wrong format

Hi AVS team,
I saw the release note for 1.1.0, it mentioned :  IMPORTANT NOTE FOR LINUX: GStreamer 1.8 does not work.
Last week, we still can test AVS for basic test, but today, we got "The stream is in the wrong format" while asking some basic questions. Is it related to GStreamer update requirements ?
Last week, in our test, we use GS 1.8.2 .
Thanks,

Hi @zeusshang, to help us diagnose down the issues, would you be able to give us the DEBUG9 logs?  Do do this you will need to build with -DCMAKE_BUILD_TYPE=DEBUG and enabling DEBUG9 mode in your SampleApp by:
TZ=UTC ./SampleApp ....../AlexaClientSDKConfig.json DEBUG9
Thanks,
Kenneth

Hi AVS team,
Sorry, I forgot to attached the log , please help to check the following log.
And I have another question here, if failed at MIC received speech, or failed at the response audio from the cloud ?
              #    #     #  #####      #####  ######  #    #
             # #   #     # #     #    #     # #     # #   #
            #   #  #     # #          #       #     # #  #
           #     # #     #  #####      #####  #     # ###
           #######  #   #        #          # #     # #  #
           #     #   # #   #     #    #     # #     # #   #
           #     #    #     #####      #####  ######  #    #

   #####                                           #
  #     #   ##   #    # #####  #      ######      # #   #####  #####
  #        #  #  ##  ## #    # #      #          #   #  #    # #    #
   #####  #    # # ## # #    # #      #####     #     # #    # #    #
        # ###### #    # #####  #      #         ####### #####  #####
  #     # #    # #    # #      #      #         #     # #      #
   #####  #    # #    # #      ###### ######    #     # #      #

+----------------------------------------------------------------------------+
|                                  Options:                                  |
| Tap to talk:                                                               |
|       Press 't' and Enter followed by your query (no need for the 'Alexa').|
| Hold to talk:                                                              |
|       Press 'h' followed by Enter to simulate holding a button.            |
|       Then say your query (no need for the 'Alexa').                       |
|       Press 'h' followed by Enter to simulate releasing a button.          |
| Stop an interaction:                                                       |
|       Press 's' and Enter to stop an ongoing interaction.                  |
| Info:                                                                      |
|       Press 'i' followed by Enter at any time to see the help screen.      |
| Quit:                                                                      |
|       Press 'q' followed by Enter at any time to quit the application.     |
+----------------------------------------------------------------------------+
t
2017-10-03 22:36:24.849 [  a] 0 AudioInputProcessor:setState:from=IDLE,to=RECOGNIZING
2017-10-03 22:36:24.855 [  7] 0 ContextManager:buildContextSuccessful:context={"context":[{"header":{"namespace":"Alerts","name":"AlertsState"},"payload":{"allAlerts":[],"activeAlerts":[]}},{"header":{"namespace":"AudioPlayer","name":"PlaybackState"},"payload":{"token":"","offsetInMilliseconds":0,"playerActivity":"IDLE"}},{"header":{"namespace":"SpeechSynthesizer","name":"SpeechState"},"payload":{"token":"","offsetInMilliseconds":0,"playerActivity":"FINISHED"}},{"header":{"namespace":"SpeechRecognizer","name":"RecognizerState"},"payload":{"wakeword":""}}]}
2017-10-03 22:36:24.852 [  b] 0 DialogUXStateAggregator:setState:from=IDLE,to=LISTENING
2017-10-03 22:36:24.858 [  a] 0 AudioInputProcessor:executeOnContextAvailable:jsonContext={"context":[{"header":{"namespace":"Alerts","name":"AlertsState"},"payload":{"allAlerts":[],"activeAlerts":[]}},{"header":{"namespace":"AudioPlayer","name":"PlaybackState"},"payload":{"token":"","offsetInMilliseconds":0,"playerActivity":"IDLE"}},{"header":{"namespace":"SpeechSynthesizer","name":"SpeechState"},"payload":{"token":"","offsetInMilliseconds":0,"playerActivity":"FINISHED"}},{"header":{"namespace":"SpeechRecognizer","name":"RecognizerState"},"payload":{"wakeword":""}}]}
############################
Listening...
############################
2017-10-03 22:36:24.862 [  a] I DirectiveProcessor:setDialogRequestIdLocked:oldValue=,newValue=361542b0-7c9b-448f-9def-682df8ec6fef
2017-10-03 22:36:24.863 [  a] 0 DirectiveProcessor:scrubDialogRequestIdLocked:reason=emptyDialogRequestId
2017-10-03 22:36:24.868 [  a] 0 EventBuilder:buildJsonEventString:messageId=9a47fa44-7a95-417f-8ab0-627be0b2b764,namespace=SpeechRecognizer,name=Recognize
2017-10-03 22:36:24.875 [  a] 0 AudioInputProcessor:executeOnFocusChanged:newFocus=FOREGROUND
2017-10-03 22:36:27.396 [  6] 0 MessageInterpreter:receive:messageId=5875f644-f339-467b-8f70-4d866de2281c:No dialogRequestId attached to message.
2017-10-03 22:36:27.399 [  6] I DirectiveSequencer:onDirective:directive={"namespace:"SpeechRecognizer",name:"StopCapture",messageId:"5875f644-f339-467b-8f70-4d866de2281c",dialogRequestId:""}
2017-10-03 22:36:27.401 [  c] I DirectiveRouter:preHandleDirective:messageId=5875f644-f339-467b-8f70-4d866de2281c,action=calling
2017-10-03 22:36:27.402 [  c] 0 CapabilityAgent:addingMessageIdToMap:messageId=5875f644-f339-467b-8f70-4d866de2281c
2017-10-03 22:36:27.407 [  d] I DirectiveRouter:handleDirective:messageId=5875f644-f339-467b-8f70-4d866de2281c,action=calling
2017-10-03 22:36:27.408 [  a] 0 AudioInputProcessor:stopCapture:stopImmediately=true
2017-10-03 22:36:27.408 [  a] 0 AudioInputProcessor:setState:from=RECOGNIZING,to=BUSY
2017-10-03 22:36:27.409 [  a] 0 DirectiveProcessor:onHandlingCompeted:messageId=5875f644-f339-467b-8f70-4d866de2281c,directiveBeingPreHandled=(nullptr)
2017-10-03 22:36:27.409 [  a] 0 CapabilityAgent:removingMessageIdFromMap:messageId=5875f644-f339-467b-8f70-4d866de2281c
2017-10-03 22:36:27.411 [  b] 0 DialogUXStateAggregator:setState:from=LISTENING,to=THINKING
2017-10-03 22:36:27.412 [  5] I InProcessAttachmentReader:readFailed:reason=SDS is closed
###########################
Thinking...
###########################
2017-10-03 22:36:27.812 [  5] 0 HTTP2Stream:receivedRequestId:value=x-amzn-requestid: 0ee7e3fffeeffd64-00006183-0003f817-3f824a1d9c795ecd-a51bc290-5
2017-10-03 22:36:27.817 [  6] I DirectiveSequencer:onDirective:directive={"namespace:"Speaker",name:"SetMute",messageId:"959bb737-a8f0-4dd5-9258-f4cd0e63296d",dialogRequestId:"361542b0-7c9b-448f-9def-682df8ec6fef"}
2017-10-03 22:36:27.818 [  c] W DirectiveRouter:preHandleDirectiveFailed:messageId=959bb737-a8f0-4dd5-9258-f4cd0e63296d,reason=noHandlerRegistered
2017-10-03 22:36:27.818 [  c] I DirectiveSequencer:sendingExceptionEncountered:messageId=959bb737-a8f0-4dd5-9258-f4cd0e63296d
2017-10-03 22:36:27.819 [  c] 0 EventBuilder:buildJsonEventString:messageId=be1d72a2-c1cd-49c9-aa33-f44d03d49da5,namespace=System,name=ExceptionEncountered
2017-10-03 22:36:27.821 [  6] I DirectiveSequencer:onDirective:directive={"namespace:"SpeechSynthesizer",name:"Speak",messageId:"b13962ff-f85a-4249-a74b-be2f517e04a4",dialogRequestId:"361542b0-7c9b-448f-9def-682df8ec6fef"}
2017-10-03 22:36:27.822 [  c] I DirectiveRouter:preHandleDirective:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4,action=calling
2017-10-03 22:36:27.822 [  c] 0 CapabilityAgent:addingMessageIdToMap:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4
2017-10-03 22:36:27.823 [  c] 9 SpeechSynthesizer:preHandleDirective:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4
2017-10-03 22:36:27.823 [  8] 0 SpeechSynthesizer:executePreHandle:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4
2017-10-03 22:36:27.827 [  d] I DirectiveRouter:handleDirective:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4,action=calling
2017-10-03 22:36:27.827 [  d] 9 SpeechSynthesizer:handleDirective:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4
2017-10-03 22:36:27.834 [  8] 0 SpeechSynthesizer:executeHandle:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4
2017-10-03 22:36:27.835 [  a] 0 AudioInputProcessor:executeOnFocusChanged:newFocus=NONE
2017-10-03 22:36:27.836 [  e] 0 SpeechSynthesizer:onFocusChanged:newFocus=FOREGROUND
2017-10-03 22:36:27.836 [  a] 0 AudioInputProcessor:executeOnFocusChanged:reason=Lost focus
2017-10-03 22:36:27.836 [  a] 0 AudioInputProcessor:setState:from=BUSY,to=IDLE
2017-10-03 22:36:27.836 [  8] 0 SpeechSynthesizer:executeStateChange:newState=PLAYING
2017-10-03 22:36:27.837 [  8] 9 SpeechSynthesizer:startPlaying
2017-10-03 22:36:27.837 [  8] 9 MediaPlayer:setSourceCalled:sourceType=AttachmentReader
2017-10-03 22:36:27.838 [  2] 0 MediaPlayer:handleSetSourceCalled
2017-10-03 22:36:27.838 [  2] 9 MediaPlayer:tearDownPipeline
2017-10-03 22:36:27.884 [  8] 9 MediaPlayer:playCalled
2017-10-03 22:36:27.885 [  2] 0 MediaPlayer:handlePlayCalled
2017-10-03 22:36:27.885 [  2] 0 MediaPlayer:doStopSuccess:reason=alreadyStopped
2017-10-03 22:36:27.885 [  2] 9 MediaPlayer:doStopSuccess
2017-10-03 22:36:27.885 [  2] 0 MediaPlayer:handlePlay:supportsBuffering=0
2017-10-03 22:36:27.901 [  2] 0 MediaPlayer:handlePlay:stateReturn=ASYNC
2017-10-03 22:36:27.902 [  f] 9 BaseStreamSource:onNeedDataCalled:size=4096
2017-10-03 22:36:27.903 [  2] 9 BaseStreamSource:handleNeedDataCalled
2017-10-03 22:36:27.903 [  2] 9 BaseStreamSource:installOnReadDataHandler:action=newSourceId,sourceId=9
2017-10-03 22:36:27.903 [  2] 9 AttachmentReaderSource:read:size=4096,status=0
2017-10-03 22:36:27.904 [  2] 9 AttachmentReaderSource:read:size=4096,status=0
2017-10-03 22:36:27.904 [  2] 9 AttachmentReaderSource:read:size=1645,status=0
2017-10-03 22:36:27.904 [  2] I InProcessAttachmentReader:readFailed:reason=SDS is closed
2017-10-03 22:36:27.905 [  2] 9 AttachmentReaderSource:read:size=0,status=3
2017-10-03 22:36:27.905 [  2] 9 BaseStreamSource:signalEndOfDataCalled
2017-10-03 22:36:27.906 [  2] 9 BaseStreamSource:clearOnReadDataHandlerCalled:sourceId=9
2017-10-03 22:36:27.985 [  f] 9 MediaPlayer:onPadAddedCalled
2017-10-03 22:36:27.986 [  2] 9 MediaPlayer:handlePadAddedSignalCalled
2017-10-03 22:36:27.994 [  f] 9 BaseStreamSource:onNeedDataCalled:size=4096
2017-10-03 22:36:27.995 [  2] 9 BaseStreamSource:handleNeedDataCalled
2017-10-03 22:36:28.000 [  2] E MediaPlayer:handleBusMessageError:source=audio_sink-actual-sink-alsa,error=The stream is in the wrong format.,debug=gstaudiobasesink.c(1142): gst_audio_base_sink_wait_event (): /GstPipeline:audio-pipeline/GstAutoAudioSink:audio_sink/GstAlsaSink:audio_sink-actual-sink-alsa:
Sink not negotiated before eos event.
2017-10-03 22:36:28.000 [  2] 0 MediaPlayer:callingOnPlaybackError:error=The stream is in the wrong format.
2017-10-03 22:36:28.001 [  2] 9 SpeechSynthesizer:onPlaybackError
2017-10-03 22:36:28.001 [  8] 0 SpeechSynthesizer:executePlaybackError:error=The stream is in the wrong format.
2017-10-03 22:36:28.001 [  8] 0 SpeechSynthesizer:executeProvideState:stateRequestToken=0
2017-10-03 22:36:28.002 [  8] 0 ContextManager:updateStateLocked:action=updatedState,state={"token":"amzn1.as-ct.v1.Domain:Application:Notifications#ACRI#DeviceTTSRenderer_c669a741-10a5-4ea0-ae2d-345e17a8bbeb","offsetInMilliseconds":0,"playerActivity":"FINISHED"},namespace=SpeechSynthesizer,name=SpeechState
2017-10-03 22:36:28.002 [  8] 9 SpeechSynthesizer:releaseForegroundFocus
2017-10-03 22:36:28.004 [  8] 0 EventBuilder:buildJsonEventString:messageId=0ef9a880-8d36-4383-bcf4-44a8cb907a6f,namespace=System,name=ExceptionEncountered
2017-10-03 22:36:28.005 [  8] 0 DirectiveProcessor:onHandlingFailed:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4,directiveBeingPreHandled=(nullptr),description=The stream is in the wrong format.
2017-10-03 22:36:28.005 [  8] 0 DirectiveProcessor:scrubDialogRequestIdLocked:dialogRequestId=361542b0-7c9b-448f-9def-682df8ec6fef
2017-10-03 22:36:28.006 [  8] 0 CapabilityAgent:removingMessageIdFromMap:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4
2017-10-03 22:36:28.007 [  8] 0 CapabilityAgent:removingMessageIdFromMap:messageId=b13962ff-f85a-4249-a74b-be2f517e04a4
2017-10-03 22:36:28.025 [  b] 0 DialogUXStateAggregator:transitionFromThinkingTimedOut
2017-10-03 22:36:28.025 [  b] 0 DialogUXStateAggregator:setState:from=THINKING,to=IDLE
########################################
Alexa is currently idle!
########################################
2017-10-03 22:36:28.055 [  5] 0 HTTP2Stream:receivedRequestId:value=x-amzn-requestid: 0ee7e3fffeeffd64-00006183-0003f817-3f824a1d9c795ecd-a51bc290-7
2017-10-03 22:36:28.055 [  5] 0 CurlEasyHandleWrapper:reset:responseCode=HTTP_RESPONSE_SUCCESS_NO_CONTENT
2017-10-03 22:36:28.281 [  5] 0 HTTP2Stream:receivedRequestId:value=x-amzn-requestid: 0ee7e3fffeeffd64-00006183-0003f817-3f824a1d9c795ecd-a51bc290-9
2017-10-03 22:36:28.281 [  5] 0 CurlEasyHandleWrapper:reset:responseCode=HTTP_RESPONSE_SUCCESS_NO_CONTENT
2017-10-03 22:36:29.836 [  e] E SpeechSynthesizer:onFocusChangeFailed:reason=stateChangeTimeout,messageId=b13962ff-f85a-4249-a74b-be2f517e04a4
2017-10-03 22:36:29.837 [  e] 0 SpeechSynthesizer:onFocusChanged:newFocus=NONE

Hi @zeusshuang, thanks for attaching the logs.  The error does indicate something wrong with the gstreamer.  Would it be possible for you to upgrade the gstreamer to version 1.10.4 and try again.  We have used 1.10.4 in our testings and we have verified that version to be working correctly.

Hi Kenneth ,
Thanks for the response, I am also thinking it and starts to move to new GS.
However, it's actually working last week with 1.8.2 (I filed another question for "last news" not working about TLS issue).
Could you advise the audio format is actually different after upgraded to V1.1.0 this Monday ?
(Last Friday, it's working with old GS 1.8.2 here).
Thanks,

Hi Kenneth ,
I have another question related to this fail log, is it failed at Cloud's response audio format, or failed at microphone's input audio format ?

Hi @zeusshuang, based on the log, it failed in the MediaPlayer where it was trying to play something from the Cloud.  I've found #196 to have the same errors as you've reported, so please try to upgrade to GS v1.10.4.  Thanks!

Hi Kenneth,
Thanks! I will work on it.

Closing this ticket.  Please reopen if you are still seeing issues after upgrading the GS to v1.10.4.  Thanks.


Allow generics in Signatures

Potential fix to #610
I was applying the fix as part of this PR locally on my PR tildeio/ember-element-helper#107 and see if in my type-test-component:
import Component from '@glimmer/component';
import type { ElementSignature, ElementFromTagName } from 'ember-element-helper';

interface ElementReceiverSignature<T extends string = 'article'> {
  Element: ElementFromTagName<T>;
  Args: {
    tag: ElementSignature<T>['Return'];
  };
  Blocks: {
    default: [];
  }
}

export default class ElementReceiver<T extends string> extends Component<ElementReceiverSignature<T>> {}

{{#let @tag as |Tag|}}
  {{!@glint-ignore}}
  <Tag id="content" ...attributes>{{yield}}</Tag>
{{/let}}

I was able to remove the line {{!@glint-ignore}} and if the type linting still passes, which is the case.
So, yes this is a potential fix, but I share the same concerns as @dfreeman this might come with side-effects.
So I'll make it a draft PR.

Thanks for opening this! The fact that CI is ✅ is a great initial sign – one of us will try to review in detail shortly.

This should include, at a minimum, a new test case for the scenario this is intended to fix. Otherwise there's nothing to prevent us from flipping this back in the future and causing the same problem again
(I'd also recommend coming up with a more specific title for this PR, since that's what will go in the release notes—we clearly already "allow generics in signatures" in the general case, since many built-ins like let and each require that 😉)

I added some tests. I copied over all the relevant types from (element) helper as well as a component receiving it. Feels a lot, but makes it accurate. If this can be less types, please let me know.
I also left comments where I got stuck. I think, I need to test broken/invalid types, in a environment with correct types?


TypeError: Cannot read property 'members' of undefined

TypeError: Cannot read property 'members' of undefined
at /home/runner/Bot-with-Advanced-Dashboard/dashboard/dashboard.js:640:25
at Layer.handle [as handle_request] (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/layer.js:95:5)
at next (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/route.js:137:13)
at checkAuth (/home/runner/Bot-with-Advanced-Dashboard/dashboard/dashboard.js:138:41)
at Layer.handle [as handle_request] (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/layer.js:95:5)
at next (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/route.js:137:13)
at Route.dispatch (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/route.js:112:3)
at Layer.handle [as handle_request] (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/layer.js:95:5)
at /home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:281:22
at Function.process_params (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:335:12)
at next (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:275:10)
at urlencodedParser (/home/runner/Bot-with-Advanced-Dashboard/node_modules/body-parser/lib/types/urlencoded.js:91:7)
at Layer.handle [as handle_request] (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/layer.js:95:5)
at trim_prefix (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:317:13)
at /home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:284:7
at Function.process_params (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:335:12)
at next (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:275:10)
at jsonParser (/home/runner/Bot-with-Advanced-Dashboard/node_modules/body-parser/lib/types/json.js:110:7)
at Layer.handle [as handle_request] (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/layer.js:95:5)
at trim_prefix (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:317:13)
at /home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:284:7
at Function.process_params (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:335:12)
at next (/home/runner/Bot-with-Advanced-Dashboard/node_modules/express/lib/router/index.js:275:10)
at SessionStrategy.strategy.pass (/home/runner/Bot-with-Advanced-Dashboard/node_modules/passport/lib/middleware/authenticate.js:343:9)
at /home/runner/Bot-with-Advanced-Dashboard/node_modules/passport/lib/strategies/session.js:69:12
at pass (/home/runner/Bot-with-Advanced-Dashboard/node_modules/passport/lib/authenticator.js:337:31)
at deserialized (/home/runner/Bot-with-Advanced-Dashboard/node_modules/passport/lib/authenticator.js:349:7)
at /home/runner/Bot-with-Advanced-Dashboard/dashboard/dashboard.js:76:45

see pins in support channel in support guild


ci: don't register repository if in Github actions

Check if the build is running in Github actions. That it is when the GITHUB_RUN_ID environment variable is present.
If it is running in github actions unless the system properties 'aws.accessKeyId' / 'aws.secretAccessKey' or the environment variables AWS_ACCESS_KEY_ID / AWS_SECRET_ACCESS_KEY don't register the code artifact repository
see: https://docs.aws.amazon.com/sdk-for-java/latest/developer-guide/ec2-iam-roles.html
see: see: https://metadata.atlassian.net/browse/EX-4472

This will make the build pass in Github action, since it will not register the publishing repository.


Provisioning

Add facilities to ease provisioning of a new gateway.
WiFi?
BT?

This is being covered outside the scope of this repo


Remove LICENSE

Addresses https://github.com/kubernetes/kubernetes/issues/54398.
The README.md is already present in staging and is not authoritative here.
/cc @sttts

do we need to wait until the corresponding PR merges the changes to staging?

@DirectXMan12 technically no. Only downside: no LICENSE file until we have created new branches to publish and @eparis has run the script again to do the actual push.

I'd prefer not to be missing a license for any significant period of time, but if you anticipate this'll go fairly quickly, I'll merge it now.

Will synchronize this with @eparis and the 1.8.2 tag. Eric can merge as well. Then we minimize that time.

No patience :-)

heh, whoops, I misunderstood your comment ;-)

@DirectXMan12 no problem, trying to get @eparis to merge the other PRs for the other repos. If you happen to be at the same place, tell him how easy this is :)


Create consensus sequences from BAM file

Hi,
I have run the epi2me-labs/wf-single-cell workflow on my nanopore data but would like to create consensus sequences for reads tagged with the same cell barcode, UMI and gene and then do SNV calling.
Is it possible to use sicelore to create the consensus sequence from the BAM file, re-align and call SNVs?
The SAM flags differ and I am a bit confused what parameters I would have to set to make the pipeline take the epi2me BAM file.
It is single-cell 5' 10X data with PCR amplification (no polyA expected).
Below an example BAM record. If I subset the reads to my genes of interest, I have 3,928,283 reads and 248,167 UMI.
146f227d-5167-4c40-97c5-027a0e9c4652_0  2048    chr11   237007  60      2H138M1853N79M4964N35M85N56M209N44M205N65M1D21M2515N172M1327N80M76N60M2D25M1D38M1745N63M680N81M193N25M1D91M568N175M1466H        *       0       0       GACATCCCGGTTGTTCTTCTGTGCCGGGGGTCTTCCTGCTGTCATGAAGGACGTACCGGGCTTCCTACAGCAGAGCCAGAGCTCCGGGCCCGGGCAGCCCGCTGTGTGGCACCGTCTGGAGGAGCTCTACACGAAGAAGTTGTGGCATCAGCTGACACTTCAGGTGCTTGATTTTGTGCAGGATCCGTGCTTTGCCCAAGGAGATGGTCTCATTAAGCTTTATGAAAACTTTATCAGTGAATTTGAACACAGGGTGAATCCTCTGTCCCTCGTGGAAATCATTCTTCACGTCGTTAGACAGATGACTGATCCTAATGTGGCTCTTACTTTTCTGGAAAAGACTCGTGAGAAGGTGAAAAGTAGTGATGAGGCAGTGATCCTGTGTAAAACAGCAATTGGAGCTCTAAAATTAAACATGGGGACCTACAGGTTACAAAGGAAACAATTGAAGATGTTGAAGAAATGCTCAACAACCTTCCTGGTGTGACATCGGTTCACAGTCGTTTCTATGATCTCTCCAGTAAATACTATCAAACAATCGGAAACCACGCGTCCTACTACAAAGATGCTCTGCGGTTTTTGGGCTGTGTTGACATCAAGGATCTACCAGTGTCTGAGCAGCAGGAGAGAGCCTTCACGCTGGGGCTAGCAGGACTTCTCGGCGAGGGAGTTTTTAACTTTGGAGAACTCCTCATGCACCCTGTGCTGGAGTCCCTGAGGAATACTGACCGGCAGTGGCTGATTGACACCCTATGCCTTCAACAGTGGCAACGTAAGCGGTCCCAGACTCTGAAGACTGCCTGGGGCCAGCAGCCTGATTTAGCAGCTAATGAAGCCCAGCTTCTGAGGAAAATTCAGTTGTTGTGCCTCATGGAGATGACTTTCACACGACCTGCCAATCACAGACAACTCACTTTTGAAGAAATTGCCAAAAGTGCTAAAATCACAGTGAATGAGGTGGAGCTTCTGGTGATGAAGGCCCTTCGGTGGGGCTGGTGAAAGGCAGTATAGACGAGGTGGACAAACGAGTCCACATGACCTGGGTGCAGCCCCGAGTGTTGGATTTGCAACAGATCAAGGGAATGAAGGACCGCCTGGAGTTCTGGTGCACGGATGTGAAGAGCATGGAGATGCTGGTGGAGCACCAGGCCCATGACATCCTCACCTAGGGCCCCCTGGTTCCCCGTCGTGTCTCCTTTGACTCACCTGAGAGAGGCGTTTGCAGCCAATGAAGCTGGCTGCTCAGAC      >?=>ACA><;;<>@BAABAACCBB97666<;<=ABBFDDDCA@@AAEEA>><::::;;;;;=?@AB????@EBCDCBDB;;<?><8899;<:;<<@BB@<::;;?ECCAAA@?;;;;<@@?:::9:==>@>?411,78:;;;;<<<==>ABACA@A<<<=:;;::;<???@AA>429898>?BCB?<<<;=???B>98DDBBA@AA>>=<=?@DDCC=<<==E.((((;>>?9=1/.-,,-++++,:=CBC@=;;:;=@?>?>>?A??;867888@DGDCBBA>>>>>@9821100444;;????@@>@@@??@?ACB@=<<9:;<:?>>:9:A@ABDFE@?>=:9:;<@A@>?>?@CGH>><<=>>BB?====?AA@>>>>>AAABCEDA>=>>?BA=<;;;>=?ABGGJEEED97((('())))))78;;@@???>A?@CADBCCCDDBA@??AA@CCCEEFF@@???CCD><==<>>>=@@@?@???=:::;<CBB>=<::;<>CBA@@AAACDBCBCCBG@@?==>><=>?CBDB@77778>??>88889@A@=>???CEAAA@?EDCD>;;;;9BCB=;;<;?CBCCAABC?@?@??<<<<A>===@AAA@ABBCCCDB>>?>@@@@=>>>>?=>=>?@>=<<<==?>?>=>>??76655::<@>@@BBEEEBBBB@@CBAA??=<<==ADBA?>=>?ADDDA??@BBA?=:<?>?BBBCEDCD=88889ACBBEABB@===<:::-((?BBABABEEEDCC????>>>311347778889>>>>BBFHGCBCA@@A@?=<;<<?ACBBCDDDEGFECCCB@BAABBCDA???>@A@>>>;9:966AFEFDDCAAA@AA@@?===>@A@?<<===@@ACCDBA855559=>@@BBCEFFDBABB>????CDFH@GNGIGIIHA@?<=@BEDCA@ABBGIIGDDBBBEDDDE@<<<;=@>?@???>=@ABBBB?=<<:78));<<=<<<<=@BBBCFDA>>>?@@@AC?;;;;<EFFF?@?>;776453231.//0668979:21122<1----=@;:;>@@@?<<<<?BBBCFB@97<7,,,+243311228;>><=<<<>==<<<33347CEFFBA@???@AA???A@?====>>>>>@ABB@A?>???BE??>>>>>>=>3432113112+,,=?>>:7875678;>>?3//(.AC?22222@?@A@=;:889:<BCDAABABCCCAA@@AAAA??<<<88 NM:i:11 ms:i:1217       AS:i:1049       nn:i:0  ts:A:+  tp:A:P  cm:i:176        s1:i:987        s2:i:0  de:f:0.008      SA:Z:chr11,86250326,+,1333S1375M27014D8S,60,8;  MD:Z:80A177C3T25T2A125^C333^CT25^G6T200^T266rl:i:0   CB:Z:CGGACACTCTTGGGTA   CR:Z:CGGACACTCTTGGGTA   CY:Z:B???@787775,,,88   UB:Z:CGTAACTCGA UR:Z:CGTAACTCGA UY:Z:>===>?A=;; GN:Z:EED        TR:Z:ENST00000263360

If it is not possible to concatenate the 2 workflows, I would run sicelore start-to-finish with the nextflow pipeline, and then Step5 SNV calling.
What parameters do I have to set in the nextflow pipeline for PCR amplified 5' 10X data?
Would it make sense to specify the filtered cell barcode list of non-empty droplets from cellranger from matched short-read scRNA-seq data?
Thanks a lot for your help!
Best,
Henrietta

So, I'm trying to run the whole nextflow pipeline on my data.
I've adjusted the config.xml to
umi_length 10
fileWithAllPossibleTenXbarcodes 737k-august-2016.txt
And I've modified the nextflow pipeline to accept parameters for 5' sequencing in step 1 and 3
--noPolyARequired and --fivePbc
The pipeline completes on a small subset of my data and 04b.matrices/molecules.tags.GE.bam contains 88,481 reads, which is reasonable.
However, I cannot manage to run the SNV calling. It tells me that "nothing has been detected".
Below are some BAM records from 04b.matrices/molecules.tags.GE.bam. Could you please confirm that this is the correct input format for the SNV calling? Maybe I'm still not using the pipeline correctly for 5' data?
Thanks!
TGAGGGAAGTGCCAGA-AGAGCTCTGG-1   2048    chr17   30636139        60      31H20M6I1M1I2M1I5M133705N2M1I10M4D1M3D9M1I10M1D3M1D50M6331N106M182H     *       0       0       AATACTTACACTCTTTCCCTACACGACGCTCTTCCTATCTTGAGGGAAGTGCCAGAAGAGCTCTGGTTTCTTATATGGGGGAAAGACATTTGTTGCACAAATGACAGTATTTGATAAAAACAGGCGCTTACAGCTTTTAGATGGGGAATATGAAGTAGCCATGCAGGAAATGGAAGAATGTCCAATAAGCAAGAGAGAAGCAACATGGGAGACTATTCTTGATGGGAAG        $$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$$        s1:i:130        s2:i:0  U8:Z:AGAGCTCTGG SA:Z:chr17,31976566,+,105S304M11600D33S,60,12;  BC:Z:TGAGGGAAGTGCCAGA        GE:Z:LRRC37BP1,SUZ12P1  XF:Z:UTR        NM:i:35 RN:i:1  AS:i:87 GS:Z:+,+        de:f:0.1096     rl:i:0  cm:i:45 nn:i:0  tp:A:P  ms:i:143        ts:A:+
AGGTCATTCCTCCTAG-AGAGTTTCAC-1   256     chr17   30731643        0       128S64M1I34M1I37M1D189M12I85M21I71M2773N47M89N65M8203N69M16121N28M1I21M6963N66M2D2M1D3M1D11M3283N27M1D52M1D13M6331N70M1D14M164S *       0       0       *       *       s1:i:681     U8:Z:AGAGTTTCAC BC:Z:AGGTCATTCCTCCTAG   GE:Z:SUZ12P1    XF:Z:UTR        NM:i:72 RN:i:1  AS:i:718        GS:Z:+  de:f:0.0408     rl:i:15 cm:i:184        nn:i:0  tp:A:S  ms:i:841        ts:A:+
CGGACGTGTTACGACT-CCATGCCTCA-1   256     chr17   30731652        0       62S51M1D2M1I97M1D11M1I3M1D2M2D113M8D24M12I80M22I76M2773N47M89N65M24393N28M1I21M6963N50M1D1M4I34M2245N78M1I141M1I12M807N47M1I47M6331N70M1D31M179S        *       0       0   **       s1:i:906        U8:Z:CCATGCCTCA BC:Z:CGGACGTGTTACGACT   GE:Z:SUZ12P1    XF:Z:UTR        NM:i:75 RN:i:1  AS:i:894        GS:Z:+  de:f:0.0279     rl:i:30 cm:i:243        nn:i:0  tp:A:S  ms:i:1025       ts:A:+
AAGTCTGCACCGGAAA-GTAAACGCAT-2   256     chr17   30731657        0       110S61M1D145M1D51M1D7M1D3M1I29M3D6M2D85M21I19M1D51M2773N47M89N65M8203N69M16121N28M1I21M6963N86M2245N219M1I12M807N94M6331N79M5I27M182S   *       0       0       *       *   s1:i:940 U8:Z:GTAAACGCAT BC:Z:AAGTCTGCACCGGAAA   GE:Z:SUZ12P1    XF:Z:UTR        NM:i:65 RN:i:2  AS:i:951        GS:Z:+  de:f:0.0312     rl:i:0  cm:i:269        nn:i:0  tp:A:S  ms:i:1083       ts:A:+
CGATTGAAGTATCTCG-TACGGCTACG-1   256     chr17   30731658        0       118S19M1D29M2I34M1I14M2D21M1D60M1D10M1I12M1D5M1D10M2D1M1I28M1D57M12I80M12I5M12I24M1D5M1D40M2773N47M89N65M8203N37M1D2M1D28M16121N28M1I21M6963N86M2245N219M1I12M807N94M6331N48M*       0       0       *       *       s1:i:799        U8:Z:TACGGCTACG BC:Z:CGATTGAAGTATCTCG   GE:Z:SUZ12P1    XF:Z:UTR        NM:i:85 RN:i:1  AS:i:846        GS:Z:+  de:f:0.0422     rl:i:30 cm:i:214        nn:i:0  tp:A:S  ms:i:984        ts:A:+

Hi. I have the same problem running de sicelore pipeline from polyA data. Have you found something?

it seems read number per UMI is always 1 or 2, for SNV calling, RN default is 3 i guess, you have to change it to integrate the molecules having 1 or 2 reads. Please be sure to have some signal on the SNVs you are calling, visualiing the bam fil ein IGV prior to calling. The format of the .csv SNV file is also important but it shoud works.

I'm very sorry. I was mixing chromosome names as you suggested also for @HenriettaHolze . I did write the wrong chromosomes for the SNPs file. Now it's working.
Besides, is the tool able to genotype small indels?

Yes I was also able to resolve the issue, I specified the wrong strand in the csv.
I got the consensus sequence from sicelore but had to use cellsnv-lite for SNV calling because it was too resource intensive with sicelore.
@cartof I'm also looking for a small indel caller, please let me know if you've found something :)


Supporting mongodb

Excuse me, the business needs to support mongodb, how to add secondary functions in it? How to achieve it?

while this is more advanced.. here is an example of an externally developed
storage module.
https://github.com/adriancole/zipkin-voltdb
for Mongo to happen we need both interest and someone to help. right now
seems missing help. if you can try to create an external repo I can help
review
On Fri, Feb 22, 2019, 8:46 AM qiufeng001<EMAIL_ADDRESS>wrote:

Excuse me, the business needs to support mongodb, how to add secondary
functions in it? How to achieve it?
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/openzipkin/zipkin/issues/2408, or mute the thread
https://github.com/notifications/unsubscribe-auth/AAD613RLzjHjq89dSUwaMO9Fr0FTgN0Zks5vPz3PgaJpZM4bIoBw
.

while this is more advanced.. here is an example of an externally developed storage module. https://github.com/adriancole/zipkin-voltdb for Mongo to happen we need both interest and someone to help. right now seems missing help. if you can try to create an external repo I can help review
…
On Fri, Feb 22, 2019, 8:46 AM qiufeng001 @.***> wrote: Excuse me, the business needs to support mongodb, how to add secondary functions in it? How to achieve it? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2408>, or mute the thread https://github.com/notifications/unsubscribe-auth/AAD613RLzjHjq89dSUwaMO9Fr0FTgN0Zks5vPz3PgaJpZM4bIoBw .

I will study hard. Thank you very much.

Duplicate of #2275

If there is an old version of the mongodb module, I would like to refer to it, because I just started IT, technical ability is not enough, I hope to help, thank you!

while this is more advanced.. here is an example of an externally developed storage module. https://github.com/adriancole/zipkin-voltdb for Mongo to happen we need both interest and someone to help. right now seems missing help. if you can try to create an external repo I can help review
…
On Fri, Feb 22, 2019, 8:46 AM qiufeng001 @.***> wrote: Excuse me, the business needs to support mongodb, how to add secondary functions in it? How to achieve it? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2408>, or mute the thread https://github.com/notifications/unsubscribe-auth/AAD613RLzjHjq89dSUwaMO9Fr0FTgN0Zks5vPz3PgaJpZM4bIoBw .

If there is an old version of the mongodb module, I would like to refer to it, because I just started IT, technical ability is not enough, I hope to help, thank you!

If there is an old version of the mongodb module, I would like to refer to it, because I just started IT, technical ability is not enough, I hope to help, thank you!

Here is the last commit, but I think it will more likely distract than
help as the server was completely different, as is the data design. It
is likely closer to elasticsearch than this commit. Anyway, I wanted
to answer you
https://github.com/openzipkin/zipkin/tree/c963f8915e1d4b21cea20e97f0864c717b63a79c

If there is an old version of the mongodb module, I would like to refer to it, because I just started IT, technical ability is not enough, I hope to help, thank you!
Here is the last commit, but I think it will more likely distract than help as the server was completely different, as is the data design. It is likely closer to elasticsearch than this commit. Anyway, I wanted to answer you https://github.com/openzipkin/zipkin/tree/c963f8915e1d4b21cea20e97f0864c717b63a79c

I am grateful for your answers and help.

If there is an old version of the mongodb module, I would like to refer to it, because I just started IT, technical ability is not enough, I hope to help, thank you!
Here is the last commit, but I think it will more likely distract than help as the server was completely different, as is the data design. It is likely closer to elasticsearch than this commit. Anyway, I wanted to answer you https://github.com/openzipkin/zipkin/tree/c963f8915e1d4b21cea20e97f0864c717b63a79c

I like technology very much, so I hope I can ask you some ways to do technology, how to do it well, thank you.

I like technology very much, so I hope I can ask you some ways to do
technology, how to do it well, thank you.

ok probably best to use chat from now on so that we can reduce the amount
of email people get on this issue :) see you soon
https://gitter.im/openzipkin/zipkin


incorrect response information for docker swarm init command

incorrect response information for docker swarm init command

Sorry @lixiaobing10051267, I'll have to close this, per my comment above


Double join not working

The double join is made using correctly the aliases, but it fails adding the second join.
  I'd suggest checking if the Distance related EntitySet in your Context derived class is named "DistanceSet". If that is not the problem, I'll need more information to reproduce the error.


Should I need to use copy-webpack-plugin for schema.prisma in a monorepo?

I've used serverless-webpack-prisma before in another codebase and it worked fine without giving it any specific help to find schema.prisma. Once I started to use it in a yarn workspaces monorepo test project, I initially got errors like this:
Error: ENOENT: no such file or directory, open '/Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/services/backend/.webpack/service/src/schema.prisma'

Only after I explicitly copied it over using copy-webpack-plugin (based on this comment) with this as part of my webpack.config.js, the error went away:
module.exports = {
  // ...
  plugins: [
    new CopyWebpackPlugin({
      patterns: [
        {
          from: '../../packages/prisma/prisma/schema.prisma',
          to: 'src',
        },
      ],
    }),
  ],
  // ...
}

Even using prismaPath in serverless.yml doesn't seem to help:
custom:
  webpack:
    packager: yarn     # not sure if this is needed?
    includeModules: true
  prisma:
    installDeps: false # or this?
    prismaPath: ../../packages/prisma

So, it works, but I thought the point of @pcrodrigues0's #6 was that you can just give it the path and it shouldn't need anything else?
I say it 'works', but I am still dealing with a Prisma engine/generator error. While there is a general issue with a similar error on the main Prisma repo, I think this is more related to my serverless-webpack-prisma implementation, since in my test monorepo project, Next.js also uses the same Prisma client and it works fine there.
PrismaClientInitializationError:
Invalid `prisma.video.findMany()` invocation:

  Query engine library for current platform "darwin-arm64" could not be found.
You incorrectly pinned it to darwin-arm64

This probably happens, because you built Prisma Client on a different platform.
(Prisma Client looked in "/Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/services/backend/.webpack/service/src/libquery_engine-darwin-arm64.dylib.node")

Searched Locations:

  /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/services/backend/.prisma/client
  /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/node_modules/@prisma/client
  /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/services/backend/.webpack/service
  /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/services/backend/.webpack/service/src
  /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/services/backend/.webpack/service/src
  /tmp/prisma-engines
  /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/services/backend/.webpack/service/src

You already added the platform "darwin-arm64" to the "generator" block
in the "schema.prisma" file as described in https://pris.ly/d/client-generator,
but something went wrong. That's suboptimal.

For the second part of this issue, looking at the paths it is trying to use, specifically that it does mention both the project root node_modules/@prisma/client and services/backend/.prisma/client, my guess is that wherever directory the engine is being written to is not compatible with what this plugin does?
Here's the full debug output from prisma generate:
DEBUG="*" yarn prisma:generate                                                                                13:32 Lise
  prisma:engines  binaries to download libquery-engine, migration-engine, introspection-engine, prisma-fmt +0ms
  prisma:loadEnv  project root found at /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/packages/prisma/package.json +0ms
  prisma:tryLoadEnv  Environment variables loaded from /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/packages/prisma/.env +0ms
Environment variables loaded from .env
Prisma schema loaded from prisma/schema.prisma
  prisma:getConfig  Using CLI Query Engine (Node-API Library) at: /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/node_modules/prisma/libquery_engine-darwin-arm64.dylib.node +0ms
  prisma:getConfig  Loaded Node-API Library +5ms
  prisma:getConfig  config data retrieved without errors in getConfigNodeAPI +1ms
  prisma:getDMMF  Using CLI Query Engine (Node-API Library) at: /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/node_modules/prisma/libquery_engine-darwin-arm64.dylib.node +0ms
  prisma:getDMMF  Loaded Node-API Library +0ms
  prisma:getDMMF  unserialized dmmf result ready +6ms
  prisma:getDMMF  dmmf retrieved without errors in getDmmfNodeAPI +2ms
  prisma:generator  prismaCLIDir /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/node_modules/prisma +0ms
  prisma:generator  prismaClientDir /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/node_modules/@prisma/client +0ms
  prisma:generator  baseDir /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/packages/prisma/prisma +0ms
  prisma:generator  typescriptPath /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/node_modules/typescript +1ms
  prisma:GeneratorProcess  2022-08-09T12:32:27.879Z prisma:client:generator  requiredEngine: libqueryEngine +0ms
  prisma:getGenerators  neededVersions {
  "8d8414deb360336e4698a65aa45a1fbaf1ce13d8": {
    "engines": [
      "libqueryEngine"
    ],
    "binaryTargets": [
      {
        "fromEnvVar": null,
        "value": "darwin-arm64"
      },
      {
        "fromEnvVar": null,
        "value": "rhel-openssl-1.0.x"
      }
    ]
  }
} +0ms
  prisma:getGenerators  {
  generatorBinaryPaths: {
    libqueryEngine: {
      'darwin-arm64': '/Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/node_modules/prisma/libquery_engine-darwin-arm64.dylib.node',
      'rhel-openssl-1.0.x': '/Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/node_modules/prisma/libquery_engine-rhel-openssl-1.0.x.so.node'
    }
  }
} +107ms
  prisma:GeneratorProcess  2022-08-09T12:32:28.008Z prisma:loadEnv  project root found at /Users/joostschuur/Code/Personal/_Tests/yarn-workspaces-prisma-nextjs-serverless/package.json +127ms

✔ Generated Prisma Client (4.1.1 | library) to ./../../node_modules/@prisma/client in 90ms
You can now start using Prisma Client in your code. Reference: https://pris.ly/d/client

import { PrismaClient } from '@prisma/client'
const prisma = new PrismaClient()
  prisma:getConfig  Using CLI Query Engine (Node-API Library) at<EMAIL_ADDRESS>+425ms
  prisma:getConfig  Loaded Node-API Library +3ms
  prisma:getConfig  config data retrieved without errors in getConfigNodeAPI +1ms

hello.
I appreciate for your interest.
Sorry, but that library doesn't support yarn monorepo function yet.
We are working hard to support you, but we are having difficulties in applying because of the lack of professional knowledge about monorepo. If you have solved the problem, could you please send me a pull request?
thank you

I had the same issue with M1 using npm workspaces. Seems like Prisma is looking at the wrong directory to search for the binary. I tried @jschuur solution by adding the specific output location and it did work! Thanks @jschuur


Placeholder text in add-spogeoadministrator

https://docs.microsoft.com/en-us/powershell/module/sharepoint-online/add-spogeoadministrator?view=sharepoint-ps
has placeholder text like
{{Fill in the Description}}
{{Fill in the Synopsis}}
and
{{ Add example description here }}

@tomresing Thanks for your feedback. We are working on this.

An audit is currently underway for all Skype cmdlets along with adding missing content where found. I will continue on to SPO cmdlets after.

@tomresing Thank you for this feedback.
I am creating a backlog item for this for the PowerShell team so we can track to progress and get you updated once it's complete.
I was able to get this into the backlog for the PowerShell team. The team will get this prioritized into a sprint plan. Thank you for reporting and making the docs better. Much appreciated.
I made a note to request the team to update this when the work is complete.

@tomresing Thank you for the feedback. The Placeholder text's have been replaced with accurate information pertaining to the document.
Thank you for reporting and making the docs better.

@msbemba  Thank you very much for the contribution and sharing this explanation. @tomresing
Hope this comment is helpful for you. Thanks for taking out some time to open the issue. Appreciate and encourage you to do the same in future also.


Split dockerfiles for better maintenance

We need to split the big docker file into all the dependencies for Gazebo, other for subprojects like manifold and ignition libraries so as to improve docker hub compilation and use it in Bitbucket Pipelines.

Working on Docker Hub to see if I can compile everything.

The process in Docker Hub lasts more than 2 hours and it timeouts. It has only two large steps, one for cloning the repository and the other one for compiling Gazebo. It reaches only half of the process.

@Shokman I couldn't make Docker Hub to compile Gazebo. What do you think about leaving two dockerfiles? One for developing purposes and the other one as the latests stable version, as we still need to push the images it isn't worth to have half the process made by Docker Hub and the other by us.
I think we can use the following tags:

latest: the stable version
dev: developing version

If you agree, I will make a new issue and close this one to tackle this change in requirements.

I agree. It is ok. Although it is a pity we couldn't get the automate buildings running, since we don't update the Dockefiles that often I don't think that it is going to be an issue to push them manually. I also think that it is ok to have a development branch. We can close this issue.

This issue is closed, and work will continue in #146 with new requirements.


PageStorage: Optimize the critical region when removing a BlobFile from disk

What problem does this PR solve?
Issue Number: close https://github.com/pingcap/tiflash/issues/8650
Problem Summary:
When all page data in a BlobFile gets removed in the GC thread, removePosFromStats will remove the BlobFile from disk. However, it holds a lock on mtx_blob_files when removing the file from disk. If BlobStore::write happens to write a page data to a new BlobFile, BlobStore::getBlobFile will be blocked by the GC thread.
According to local tests, removing a BlobFile takes tens of milliseconds. Thus introducing performance jitter.
https://github.com/pingcap/tiflash/blob/63eb295f0664ec4251907f00f335976225ddf337/dbms/src/Storages/Page/V3/BlobStore.cpp#L803-L814
https://github.com/pingcap/tiflash/blob/63eb295f0664ec4251907f00f335976225ddf337/dbms/src/Storages/Page/V3/BlobStore.cpp#L632-L636
https://github.com/pingcap/tiflash/blob/63eb295f0664ec4251907f00f335976225ddf337/dbms/src/Storages/Page/V3/BlobStore.cpp#L1494-L1503
What is changed and how it works?
Keep a pointer within the lock on mtx_blob_files, and remove the blob file from disk without the lock
Check List
Tests

[ ] Unit test
[ ] Integration test
[x] 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

Reduce the effect of background GC tasks on foreground write

/run-all-tests


Add automatic access token refreshment when expired

Is your feature request related to a problem? Please describe.
Currently when the access token expires the API can no longer make any request to the Spotify Web API. There is no system in place that detects whether the access token has expired and refreshes the token when necessary.
The feature request is to implement a system that will refresh the access token automatically when expired using the already existing AuthorizationRefreshToken.
Describe the solution you'd like
The system should be able to detect when the token has expired. When it has detected that the token has expired it will make a request to Spotify Authorization API for a new access token. When the new access token has been obtained it should update all services that use that token to make requests.
Describe alternatives you've considered
None at the moment.
Additional context
This feature should be implemented in SpotifyApi, or somewhere else if it is more fitting but should be well substantiated why it is done that way.

Attempting issue

Attempting issue #1

Any update on the progress of this issue?


BUG: openapi docs break where two pydantic models have the same name

Describe the bug
Using a domain-centric app pattern, I'll have a single module or sub-package specific to a domain element and within that namespace have a set of common tools, all named consistently, e.g., books.Service, books.Model, books.Schema, and authors.Service, authors.Model, authors.Schema, etc. I prefer to have all components for a type grouped together rather than having services.Books, services.Authors, models.Books, models.Authors etc.
To Reproduce
Run this example: https://github.com/starlite-api/starlite-hello-world/tree/domain-scoped-models
$ poetry install
$ poetry run uvicorn app.main:app
Then navigate to localhost:8000/schema.
Additional context
Redoc stacktrace:

Notice the schema names get scoped with their path, e.g., app__domain__authors__Model, yet the $ref for the paths is                 $ref: '#/components/schemas/Model'
components:
  schemas:
    app__domain__authors__Model:
      properties:
        dead:
          title: Dead
          type: boolean
        name:
          title: Name
          type: string
      required:
      - name
      - dead
      title: Model
      type: object
    app__domain__books__Model:
      properties:
        genre:
          title: Genre
          type: string
        name:
          title: Name
          type: string
      required:
      - name
      - genre
      title: Model
      type: object
info:
  title: Starlite API
  version: 1.0.0
openapi: 3.1.0
paths:
  /authors:
    get:
      deprecated: false
      operationId: Get Authors
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Model'
          description: Request fulfilled, document follows
          headers: {}
  /books:
    get:
      deprecated: false
      operationId: Get Books
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Model'
          description: Request fulfilled, document follows
          headers: {}
servers:
- url: /

My workaround has been to instantiate the model with a unique name and then alias it:
# domain/authors.py

class Author(BaseModel): ...

Model = Author

why are you reusing the namespaces?

Do you mean why do I reuse names like Model? Grouping components by namespace is my preferred pattern. The example is obviously quite simplistic, however as applications grow, it is nice to have the consistency.
Not sure if I've answered your question though.

Maybe this is more of a pydantic-openapi-schema issue??

Maybe this is more of a pydantic-openapi-schema issue??

I'm pretty sure it is technically.
How about we add support to some special ClassVar - __schema_name__ for example. Pydantic ignores it, and we can use this value to allow the user to customize the schema key.

I really have no idea how to approach it. I've been sitting on the issue for a while cause my workaround has been fine and I haven't had the time to dig into it. So I'll take whatever solution you think is viable for a spin.
I always had the pydantic schema customization hook in the back of my mind, but no idea if I could actually make it work:
from typing import Any
from pydantic import BaseModel

class Person(BaseModel):
    name: str
    age: int

    class Config:
        @staticmethod
        def schema_extra(schema: dict[str, Any], model: type['Person']) -> None:
            for prop in schema.get('properties', {}).values():
                prop.pop('title', None)

print(Person.schema_json(indent=2))


Plugin example does not compile

Bug Description
The plugin example as of 3cfa04fa9179647fb78e54a32e9488617f6fbbe9 does not compile.
Steps to Reproduce

cd examples/plugin
cargo run

Backtrace
Compiling plugin_example v0.1.0 (C:\Users\\Documents\GitHub\pyo3\examples\plugin)
error[E0277]: the trait bound `&PyList: FromPyObjectBound<'_, '_>` is not satisfied
   --> src/main.rs:16:67
    |
16  |         let syspath: &PyList = py.import("sys")?.getattr("path")?.extract()?;
    |                                                                   ^^^^^^^ the trait `PyClass` is not implemented for `&PyList`, which is required by `&PyList: FromPyObjectBound<'_, '_>`
    |
    = help: the following other types implement trait `FromPyObjectBound<'a, 'py>`:
              &'a [u8]
              &'a str
              Cow<'a, [u8]>
              Cow<'a, str>
    = note: required for `&PyList` to implement `FromPyObject<'_>`
    = note: required for `&PyList` to implement `FromPyObjectBound<'_, '_>`
note: required by a bound in `pyo3::types::PyAnyMethods::extract`
   --> C:\Users\\Documents\GitHub\pyo3\src\types\any.rs:815:12
    |
813 |     fn extract<'a, T>(&'a self) -> PyResult<T>
    |        ------- required by a bound in this associated function
814 |     where
815 |         T: FromPyObjectBound<'a, 'py>;
    |            ^^^^^^^^^^^^^^^^^^^^^^^^^^ required by this bound in `PyAnyMethods::extract`

error[E0599]: no method named `insert` found for reference `&PyList` in the current scope
  --> src/main.rs:17:17
   |
17 |         syspath.insert(0, &path)?;
   |                 ^^^^^^ method not found in `&PyList`

error[E0277]: `PyList` doesn't implement `Debug`
  --> src/main.rs:18:42
   |
18 |         println!("Import path is: {:?}", syspath);
   |                                          ^^^^^^^ `PyList` cannot be formatted using `{:?}` because it doesn't implement `Debug`
   |
   = help: the trait `Debug` is not implemented for `PyList`, which is required by `&PyList: Debug`
   = note: this error originates in the macro `$crate::format_args_nl` which comes from the expansion of the macro `println` (in Nightly builds, run with -Z macro-backtrace for more info)

Some errors have detailed explanations: E0277, E0599.
For more information about an error, try `rustc --explain E0277`.
error: could not compile `plugin_example` (bin "plugin_example") due to 3 previous errors

### Your operating system and version

Windows 11

### Your Python version (`python --version`)

Python 3.12.5

### Your Rust version (`rustc --version`)

rustc 1.80.1 (3f5fd8dd4 2024-08-06)

### Your PyO3 version

0.22.2

### How did you install python? Did you use a virtualenv?

python.org. no virtualenv

### Additional Info

_No response_

Indeed. Looks like our CI does not build all examples? :scream:


Korean translation locale added

Korean is added to Streamus language support.
Let me know if there are messages that need to be shorter.

Thank you! I'll review at some point or just address naming as issues arise in the wild. :)


Installation seemingly worked - maestral not starting

Hi, so I installed everything following these instructions (https://www.linuxuprising.com/2019/07/maestral-is-new-open-source-dropbox.html
(I am on kubuntu 20.04)
but running maestral gui just results in maestral: command not found
If I run it from Pycharm terminal it works ...
Am I missing something?
All the best,
K

I suspect that this is an issue with the location of the CLI tool not being in your path. Did you install it globally or only for the current user?
From the PyCharm terminal, which maestral will return the location of the command. You'll need to make sure that this is in on the paths returned by echo $PATH.

I installed it for my user (only one on this machine)
which maestral returns obvsly the Pycharm/project/venv/bin/maestral
whereas
echo $PATH returns nothing

Ahh, that explains things! You installed Maestral in a virtual environment of a PyCharm project. It will therefore only be found when that environment is active, for example from the PyCharm terminal in that particular project.
For it to be available in a standard terminal, you'll either need add Pycharm/project/venv/bin to your PATH, as you have done, or install it outside of the venv.

added it to PATH, now whenever I enter maestral gui the cursor jumps to next line & nothing happens :-D

Nothing at all, not even an error message? This could again be an environment problem...
Can you install it regularly for the current user by running pip3 install --user maestral[gui] from a standard terminal, outside of a venv?

nope, nothing:

Not even a system tray icon showing up?

Also, please try installing in outside of a virtual environment, as recommended above!

I think I just used pip install instead when installing it outside venv ...

Hrmp, in that case I am really not sure what the issue is. The following steps might help to narrow it down:

Did the GUI appear when running from the PyCharm environment? From your first comment, I understand that it did appear. If yes, did it also show a system tray icon?
Did you complete the setup dialog previously? If yes, any subsequent launches of the GUI will not open any windows but just create a system tray icon. This tray icon might not be visible to under some configurations / conditions. I'm not very familiar with KDE settings though I do regularly test that the GUI works in KDE Neon.
Is the sync daemon running properly? You can test this for example by running maestral status in another terminal.

Ah, sorry, I could have been clearer:
After I installed it outside the pycharm env it worked, once I used pip3 install maestral ...
before I only had tried pip ...
Thanks for your personalised help and time :-)


change up bmark/forecast settings in models

Most of the models in the test set use the same benchmark and forecast settings. It would be easy to improve code coverage by modifying benchmarks and forecasts so that they are different by model.

good idea


Can't deploy to a .net 8 isolated Function App in Linux

[x] Make sure you've installed the latest version using instructions in the wiki

Output from azd version
Run azd version and copy and paste the output here:
azd version 1.5.1 (commit 3856d1e98281683b8d112e222c0a7c7b3e148e96)
Describe the bug
Deploying an Azure Function in dotnet 8 isolated doesn't work from a Linux machine.
To Reproduce

Clone the following repo.
Run azd up from the root of the repo
Check the Overview panel of the Function App from the portal, no function has been deployed.

Expected behavior
We should see a HelloWorldFunction in the list of deployed functions. Deploying from vs code works fine.
Environment
Information on your environment:
* Language name and version: C#, dotnet isolated 8
* IDE and version : Visual Studio Code 1.85.1
Additional context
I guess my problem is related to the "run from a package" feature as described here in the docs.
Deploying from vs code adds the WEBSITE_RUN_FROM_PACKAGE setting to my Function App with a URL to a zip file in my storage account. I don't manage this setting in my Bicep code, I was expecting azd to handle it as vs code does (but it might be wrong).
The package created by azd in the /tmp folder looks correct.
I have also tried to use a file share (with the WEBSITE_CONTENTAZUREFILECONNECTIONSTRING and WEBSITE_CONTENTSHARE settings) but no content is pushed to the file share when deploying (except the host.json file).
Has anyone already deployed to a Linux Azure Function in .NET 8 isolated using azd ? I would like to know which method is supported, if any. I haven't found information about this in the docs, sorry if I missed it.
I am open to workarounds/suggestions, if there is anything I should try, please tell me !
Thanks and happy holidays !

@xaviermignot thanks for reporting
@wbreza can you triage this?

Unfortunately, azd only supports zip deploy deployment today for function and web apps.  RUN_FROM_PACKAGE is not supported at this time.

For the record, and for anyone having the same issue, I found a workaround by adding the setting SCM_DO_BUILD_DURING_DEPLOYMENT with the value False explicitely in my Bicep code.
I found this by deploying this sample and comparing both Function Apps.
I have no idea if that disables the "run from package" feature though :-/

I faced similar issue in nodejs function. I am having dependencies in parent directory
  "devDependencies": {
    "types": "file:../types",
  },

When using azd deploy it said successfully deployed but it didn't happen. Nothing out of place in debug logs. Adding SCM_DO_BUILD_DURING_DEPLOYMENT fixed my issue, thanks @xaviermignot . azd should atleast give an error that deployment failed.


Improving navigation in the docs

I find it hard to navigate in Electron's documentation without using CTRL-F often or going back and forth between different pages.
Since the content width is fixed, the remaining space could be used to include a navigation panel.
The best example I found is the Vue.js docs.
The highlight is updated as you scroll through and the search engine is great.
@kevinsawicki Thanks for taking the time to reply to me. I should have come here first instead of complaining on Twitter.

Great suggestion, @darahak. I've been thinking the same thing: a sidebar which lists all the APIs and their methods, properties, etc.
It's a common pattern on API docs sites, and it seems to work pretty well.

https://stripe.com/docs/api
https://lodash.com/docs/4.17.2

I hope to find time to work on this soon!

These are good examples too.

Stripe has a nice layout, but there's too much stuff on screen (scrolling is really slow). I think it could work really well if you don't render all the docs at the same time.
For lodash, I think the contents panel is too large and should have a reduced width (I have a 27" screen, which emphasizes the problem). The search field a really great addition though.

A while an app awhile back called microscope: http://github.com/simonhochrein/microscope
Which allows searching electron apps

Neat idea, @simonhochrein. A little off-topic, but note that (as of yesterday) you can now consume all the apps as a module from GitHub:
npm i electron/electron-apps

https://github.com/electron/electron-apps

Just hacked a simple one into the page:

And the gist for code you need to run in console every time: electron-doc-read-help.js

Love it!

That would be very much appreciated. To add to that:

It is hard to tell where one method/property ends and another begins. Since all APIs are code they don't look like proper titles. Consider changing font size to make them look like a title. Also consider adding more margin between entries. I just used DevTools to make the h4's 200% and that makes a huge difference when scanning. I don't think it's the final answer, but it's a start...

Add a table of contents to the top of every page so you can see, at a glance, what the module contains. Node does this in their docs.


Installation prints out compile errors

I get the following when trying to install:
$ go get npf.io/gorram
# npf.io/gorram/run
../go/src/npf.io/gorram/run/command.go:18: cannot use buf (type "golang.org/x/tools/go/types".Type) as type "go/types".Type in argument to "go/types".NewPointer:
        "golang.org/x/tools/go/types".Type does not implement "go/types".Type (wrong type for Underlying method)
                have Underlying() "golang.org/x/tools/go/types".Type
                want Underlying() "go/types".Type
../go/src/npf.io/gorram/run/command.go:21: cannot use prog.Package("io").Pkg.Scope().Lookup("Reader").Type() (type "golang.org/x/tools/go/types".Type) as type "go/types".Type in assignment:
        "golang.org/x/tools/go/types".Type does not implement "go/types".Type (wrong type for Underlying method)
                have Underlying() "golang.org/x/tools/go/types".Type
                want Underlying() "go/types".Type
../go/src/npf.io/gorram/run/command.go:22: cannot use prog.Package("io").Pkg.Scope().Lookup("Writer").Type() (type "golang.org/x/tools/go/types".Type) as type "go/types".Type in assignment:
        "golang.org/x/tools/go/types".Type does not implement "go/types".Type (wrong type for Underlying method)
                have Underlying() "golang.org/x/tools/go/types".Type
                want Underlying() "go/types".Type
../go/src/npf.io/gorram/run/command.go:121: cannot use pkg (type *"golang.org/x/tools/go/types".Package) as type *"go/types".Package in argument to getFunc

$ go version
go version go1.7 darwin/amd64

You need to update "golang.org/x/tools/go/loader"   It's been updated to point to go/types now.
Really, what I should do is start vendoring, so this kind of thing can't  trip people up.

Ah, thanks. Yeah, go vendoring is still painful sometimes.

Glad that fixed it!

Really, what I should do is start vendoring, so this kind of thing can't trip people up.

A much smaller hammer that prevents this problem is to add -u flag to your installation instructions.


go get fails with SECURITY ERROR for v4

Go get fails to download the dependency.
go get  github.com/dafny-lang/DafnyRuntimeGo/v4
go: downloading github.com/dafny-lang/DafnyRuntimeGo/v4 v4.7.0
go<EMAIL_ADDRESS>verifying module: checksum mismatch
        downloaded: h1:KmvAzhE8UDDSW22pntVGTFtErhFe27xdTdRz3qWajQk=
        sum.golang.org: h1:NeCXJa+Uyw1nLh8sWZcr2GPobEGLUqoZEG4vu9YKqVc=

SECURITY ERROR
This download does NOT match the one reported by the checksum server.
The bits may have been replaced on the origin server, or an attacker may
have intercepted the download attempt.

For more information, see 'go help module-auth'.

Suspect we moved the v4.7.0 tag which would have caused this. Fixed by pushing a fresh v4.8.0 tag, and https://github.com/dafny-lang/dafny/pull/5826 confirms the runtime works in an integration test now.


Sharing cache key refresh results among JuiceFS Hadoop SDK running in one NodeManager instead of refreshing individually

What would you like to be added:
Hadoop SDK refreshes cache key when initing cache and every 5 minute individually. I think it's better to share refresh results among JuiceFS Hadoop SDK running in one NodeManager than refreshing individually.
Why is this needed:
If there are many containers running with JuiceFS Hadoop SDK in NodeManager, refreshing cache key individually will generate many meta IO requests to cache disk. And it will be worse for shared cache dir, such as NFS or SMB.

This is non-trivial, we have no plan for it.


Added InsecureSkipVerify for self signed cert

Coverage increased (+0.6%) to 10.859% when pulling 5889e573fbfb47b9b1be4221a233e181a0e45e96 on scopelemanuele:master into c41ed1c32f62c8bc8679577537fd93c9bd78f61a on processone:master.

Coverage increased (+0.4%) to 10.67% when pulling 483c072eedec1654317b1d59ad24b48203a1864b on scopelemanuele:master into c41ed1c32f62c8bc8679577537fd93c9bd78f61a on processone:master.


Bash lint/cleanup

Breaking change

Proposed change

Type of change

[ ] Dependency upgrade
[ ] Bugfix (non-breaking change which fixes an issue)
[ ] New feature (which adds functionality to an existing integration)
[ ] Breaking change (fix/feature causing existing functionality to break)
[x] Code quality improvements to existing code or addition of tests

Additional information

This PR fixes or closes issue: fixes #
This PR is related to issue:
Link to documentation pull request:

Checklist

[ ] The code change is tested and works locally.
[ ] Local tests pass. Your PR cannot be merged unless tests pass
[ ] There is no commented out code in this PR.
[ ] I have followed the [development checklist][dev-checklist]
[ ] The code compiles without warnings (code quality chek)
[ ] Tests have been added to verify that the new code works.

If user exposed functionality or configuration variables are added/changed:

[ ] Documentation added/updated for www.home-assistant.io

Codecov Report

Merging #640 (9809893) into dev (fdecb37) will increase coverage by 0.10%.
The diff coverage is n/a.

:exclamation: Current head 9809893 differs from pull request most recent head 510eaf4. Consider uploading reports for the commit 510eaf4 to get more accurate results

@@            Coverage Diff             @@
##              dev     #640      +/-   ##
==========================================
+ Coverage   80.08%   80.19%   +0.10%
==========================================
  Files         111      111
  Lines        2898     2898
  Branches      311      311
==========================================
+ Hits         2321     2324       +3
+ Misses        450      447       -3
  Partials      127      127

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unittests
80.19% <ø> (+0.10%)
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Impacted Files
Coverage Δ

...mon.HassClient/Internal/HomeAssistantConnection.cs
85.71% <0.00%> (-0.96%)
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...sClient/Internal/Net/WebSocketTransportPipeline.cs
91.22% <0.00%> (+0.87%)
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69.44% <0.00%> (+8.33%)
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DioError [DioErrorType.response]: Http status error [403]

CODE
await _dio.download(
urlPath,
'${dir.path}/Download/$filename.mkv}',
cancelToken: _cancel,
onReceiveProgress: (count, total) {
progress = ((count / total) * 100).toInt();
filesize = total ~/ 1024;
downlaodResponse(progress, filesize);
},
);
} catch (e) {
print(e);
}
ERROR
url :-https://eduid01-my.sharepoint.com/personal/mi_eduid01_onmicrosoft_com/_layouts/15/download.aspx?UniqueId=aab222da-9e79-4389-bc27-5a90e4bd2823
I/flutter ( 5002): DioError [DioErrorType.response]: Http status error [403]
I/flutter ( 5002): #0      DioMixin.assureDioError
package:dio/src/dio_mixin.dart:819
I/flutter ( 5002): #1      DioMixin._dispatchRequest
package:dio/src/dio_mixin.dart:678
I/flutter ( 5002):
I/flutter ( 5002): #2      DioMixin.fetch.. (package:dio/src/dio_mixin.dart)
package:dio/src/dio_mixin.dart:1

I am too getting this issue

please reopen the issue

I'm getting the same error when trying to download a file via the download function.
I'm using it with Flutter Linux, but the code is the same for Android etc. (dio_for_native)
The error is fixed for me as soon as I comment this line with cancelToken in dio_for_native.dart:
response = await request<ResponseBody>(
        urlPath,
        data: data,
        options: options,
        queryParameters: queryParameters,
        // cancelToken: cancelToken ?? CancelToken(),
      );

This call is in the implementations of the download functions.
I guess the http call / stream can not be cancelled after doing this.
But otherwise the HTTP 403 is not letting me download files.
Maybe it's server specific, but for me this workaround works.
Maybe I don't understand enough, but the expression cancelToken ?? CancelToken() doesn't make much sense anyway, since we don't have a reference to this cancelToken then right? Shouldn't we do something like
cancelToken = cancelToken ?? CancelToken();
[...]
request(..., cancelToken: cancelToken, ...)

So we have a reference to the token?


Persistent filter state

I'm building a small wrapper to connect the table to our redux-store and persist sort and filter state. This way the state of the table will remain even if navigating somewhere else and then coming back to the table.
For sorting this was really easy:

Add a handler to onSortChange which persists sortName and sortOrder to the store.
Add sortName and sortOrder from the redux-store to the options of the table.

Now I wanted to add filtering in the same way, but it seems that is not possible, because the options object does not allow setting the filters, correct? The only way I see to set the filters from outside the table is using a ref on each column and calling applyFilter, but I really would like a generic approach, without having to touch each column.
Any suggestions how this could be done?

I just found out that I can set all filters at once by calling handleFilterData(filterState) on a ref to the table, but this has two problems:

The filters are applied correctly, but the input fields are not set. They remain empty.

And it seems that I can not call handleFilterData immediately on render:
setFilterState(tableRef) {
    tableRef.handleFilterData(filterState); // does not work, filters are cleared
    setTimeout(() => tableRef.handleFilterData(filterState), 2000); // works...
}
<BootstrapTable ref={tableRef => this.setFilterState(tableRef)} .... />

The input fields not getting set can be reproduced using the example here:
https://github.com/AllenFang/react-bootstrap-table/blob/master/examples/js/column-filter/text-filter-programmatically.js#L29
applyFilter on the column ref works, while `handleFilterData´ on the table ref does not.

@JcBernack sorry for lately reply. Firstly, applyFilter is only way to do it now, handleFilterData is also work but it's legacy way before. I usually suggest to use applyFilter.
The other solution is use filter.defaultValue, check this example for text filter. Let me know if you have any question :)  thanks

Both methods you suggest would need changes on the columns, but I would really like to get/set the filter state at the table and not touch the columns.
Here is my redux connected table, which works perfectly for sorting. It can be used as a direct replacement for the BootstrapTable as it will pass through all props. This component does not know about the columns actually used, it will just catch any changes to sorting and fire a redux action.
import React, { Component, PropTypes } from 'react';
import { BootstrapTable } from 'react-bootstrap-table';
import { connect } from 'react-redux';
import { setOrderBy } from '../../../redux/actions/reduxBootstrapTable';

@connect((state, props) => ({
  tableState: state.reduxBootstrapTable[props.tableKey],
}), {
  setOrderBy,
})
export default class ReduxBootstrapTable extends Component {
  static propTypes = {
    tableKey: PropTypes.string.isRequired,
    tableState: PropTypes.object,
    children: PropTypes.node,
    setOrderBy: PropTypes.func,
  };

  handleSortChange = (sortName, sortOrder) => {
    this.props.setOrderBy(this.props.tableKey, sortName, sortOrder);
  };

  render() {
    const { tableState, options, children, ...rest } = this.props;
    // prevent passthrough to BootstrapTable
    delete rest.tableKey;
    delete rest.setOrderBy;
    return (
      <BootstrapTable
        options={{
          ...tableState,
          onSortChange: this.handleSortChange,
          ...options,
        }}
        {...rest}
      >
        {children}
      </BootstrapTable>
    );
  }
}

I don't see a way to do the same with filtering with you suggestions.

The only two solutions are mentioned above, if you use props.children, i think you can still use React.Children API to operate on them, but sometime, it's not a good practice, but anyway, it depends


Add directional arrows to edges in graph view

It would make the flow of the graph more easy to understand in a single glance when the edge direction would be visible in the graph view. @Charlottevm suggested to add small arrows to the edges to achieve this.

Maybe something like this? idk what the most simple method is but this would visually be the most minimal but still effective adjustment?


Fix #1331, Add Almalinux OS support

What this PR does / why we need it:
Provide scan support AlmaLinux OS.
Which issue this PR fixes
Fixes #1331, replacing #1326

Update init.py
Update mappers.py
Update test_namespaces.py
Update utils.py
Update test_distro_mapping.py
Update test_mappers.py

Signed-off-by: Bala Raman<EMAIL_ADDRESS>

@zhill this PR replaces #1326, please review

Fixed two scripts lint errors

@zhill Is it possible to add AlmaLinux support on next release?

Hi @srbala , thanks for the contribution! We'll take a look!


nufmt produces corrupted code

Describe the bug

Each invocation of nufmt corrupts the code.
nufmt inserts a line break at the start of the file if no shebang is present.

Steps To Reproduce

$ touch test.nu ; chmod +x test.nudef greet [name] {
  ["hello" $name]
}

greet "world"

$ cargo install --git https://github.com/nushell/nufmt
$ ~/.cargo/bin/nufmt test.nu

Result
(Note: I had to insert space for line breaks to be shown with Gitbub Markdown)

def greet [name]
{["hello" $name ]}greet "world"

> nu test.nu

Error: nu::parser::missing_positional

  × Missing required positional argument.
   ╭─[/home/user/me/test.nu:2:17]
 1 │
 2 │ def greet [name]
   ·                 ▲
   ·                 ╰── missing block
 3 │ {["hello" $name ]}greet "world"
   ╰────
  help: Usage: def {flags} <def_name> <params> <block> . Use `--help` for more information.

Executing nufmt again results in:

def greet [name]
{["hello" $name
]greet
greet
"world"
"world"

Expected behavior
Formatted code with a consistent structure, even across subsequent runs
Environment
Arch Linux
> rustc --version
rustc 1.82.0 (f6e511eec 2024-10-15)

> nu --version
0.100.0

Agreed. This is why the readme says, This project is still very much in beta. Expect bugs, inconsistent behavior. Do not use in productive nushell scripts! I wouldn't even call it alpha or beta. It's very premature. We're looking for people to come along side us and work on it.


getting dead code following this construct warning while using macroRW

case class TcpConnection(name: String, host: String, port: String)
object TcpConnection {
      implicit val tcpConnectionRw: RW[TcpConnection] = macroRW
}

This code generate following warnings:
dead code following this construct
[warn]   implicit val tcpConnectionRw: RW[TcpConnection]   = macroRW

We are seeing a lot of these warnings due to which it has become easy to miss out on real warnings on the project. Is there a way to suppress them?

I'm also seeing these warnings and hoping to suppress them


clarify Toolbox install per Nathan's comments

Updated Toolbox uninstall instructions for both Mac and Windows to include more comments from @nathanleclaire on Issue #650
Related issues
Issue #650
Reviewers
@nathanleclaire @friism
Signed-off-by: Victoria Bialas<EMAIL_ADDRESS>

LGTM


Add cmake to setup.py install requirements

Now that ChainerX is part of the base build, we should add cmake to the requirements.

After discussion, decided to add this to Chainer install docs. Closing, to replace with new PR.


Moved prepending the index and registry name to the client, added the re...

...levant information to the json returned by the search call to the daemon, added --no-index option to avoid listing the index

I incorporated the feedback, thanks. Please take a look now. One thing I am a bit unsure about is the part where cmpSearchResults compares the STARS field. Is there even a situation where that makes sense? Different stars on the same name in the same registry?

LGTM, good job! However, I'm still concerned about omitting index column, which may produce some duplicate entries and make them appear unsorted. I'll take a stab at it.

On 03/12/2015 03:32 AM, Michal Minar wrote:

LGTM, good job! However, I'm still concerned about omitting index
column, which may produce some duplicate entries and make them appear
unsorted. I'll take a stab at it.

I think it should be straight forward to add a filter for dupes. I am
only aware of one scenario where it would happen though: if e.g. there
is an image that we certify and that is hosted on docker.io.
In that case, the stars, OFFICIAL and AUTOMATED rating even will be
different, while the gully qualified URL will be identical.
Regards,
Daniel

@llunved please see the current commit


Add support for HD6301 and HD6303 microcontrollers

HD6303 is a Hitachi clone of 6803. This implementation has been done based on the Hitachi HD6301V1/HD6303R User's Manual. The ISA differs from 6805 and 6809.
The flags are implemented as pseudo-registers for better decompilation support. The logic for setting the result flags has been optimized to not produce extra reads from the source address to improve decompilation of volatile data accesses.
I have tested this implementation by reverse-engineering one 8kb firmware image that utilizes most of the opcodes.

To fix build errors:
diff --git a/Ghidra/Processors/MC6800/certification.manifest b/Ghidra/Processors/MC6800/certification.manifest
index f639a320c4..38ab353b57 100644
--- a/Ghidra/Processors/MC6800/certification.manifest
+++ b/Ghidra/Processors/MC6800/certification.manifest
@@ -21,6 +21,10 @@ data/languages/H6309.slaspec||GHIDRA||||END|
 data/languages/mc146805e2.pspec||GHIDRA||||END|
 data/languages/mc146805e2.slaspec||GHIDRA||||END|
 data/manuals/6809.idx||GHIDRA||||END|
+data/languages/HD6303.cspec||GHIDRA||||END|
+data/languages/HD6303.ldefs||GHIDRA||||END|
+data/languages/HD6303.pspec||GHIDRA||||END|
+data/languages/HD6303.slaspec||GHIDRA||||END|
 data/languages/mc6800.cspec||GHIDRA||||END|
 data/languages/mc6800.ldefs||GHIDRA||||END|
 data/languages/mc6800.pspec||GHIDRA||||END|

Thank you, added the files to the manifest in a new commit.


Error connection:   net::ERR_INVALID_HTTP_RESPONSE

I have a backend server grpc serve with port: 50051
When using connect-es config

const clientUser = createPromiseClient(       UserService,       createConnectTransport({ 	      baseUrl: 'http://<IP_ADDRESS>:50051',       }) );
It has an error:  net::ERR_INVALID_HTTP_RESPONSE
The same status with https://github.com/grpc/grpc-web/issues/622

I run your demo with config
const transport = createConnectTransport({ baseUrl: "https://demo.connectrpc.com", });  ---> It's ok

Hey! If you are serving gRPC from the backend then you need to use createGrpcTransport from @connectrpc/connect-node package. If you are running the client on the browser, then the backend needs to support gRPC-Web or Connect. gRPC protocol doesn't work in the browser (due to browser api limitations).

oh. I use backend grpc with Golang language. Not use  connect-go . I think, i should use the same connect-go at Backend and connect-es at FE.
Thank so much.


Fix queueNoWorkerDataFilter display by using Redux

Summary
Per the feature readme, the queueNoWorkerDataFilter actually is a facade and it is just setting skill filters under the hood. Because of this, Flex clears out the queue filter component when applying filters, which is a pretty confusing UX.
This fixes that by storing the selected queue in Redux, and then applying it when Flex clears the component.
Also disabled the agent skills filter by default, as it conflicts with the queueNoWorkerDataFilter if both are enabled (due to the queue filter also setting skill filters). It can be enabled instead of queueNoWorkerDataFilter, or can also be enabled in tandem with a more robust queue filter solution (i.e. queueWorkerDataFilter).
This hack seems to work a bit better than I was expecting, so please give it a spin to make sure I didn't miss anything 😄
Checklist

[x] Tested changes end to end
[x] Added PR Label "ready-for-review"
[x] Requested one or more reviewers for the PR

it's definitely looking a lot better.  Im not sure if this is a new bug or not but when you use a queue that has an OR'd expression, a notification is posted that the queue filter will be removed and ignored because its not supported.  This doesn't behave as intended, instead it seems to return to whatever was selected last, which on the first instance is blank so it returns to blank but on the second instance is stuck on the queue its supposed to remove  Alternatively i you first select. a working queue then a disqualified queue, it goes back to the working queue.


Add user_rf_pre_init() function to fix build error with SDK-1.1.0

This patch fixes below build error with SDK-1.1.0:
esp-open-sdk/sdk/lib/libmain.a(app_main.o): In function user_uart_wait_tx_fifo_empty': (.irom0.text+0x34c): undefined reference to user_rf_pre_init'
According to esp_iot_sdk_v1.1.0_15_05_26 Release Note:
user_rf_pre_init has to be added in user_main.c, user can call
system_phy_set_rfoption to set configuration of RF in it.

thanks


ConvTranspose2d gives inaccurate results

Hello!
I have an upsample pytorch model that uses torch.nn.ConvTranspose2d(1024, 40, kernel_size=2, stride=2). IREE outputs differ from PyTorch by a lot just on this operation. Any ideas on what could be wrong here? Thanks!
from einops import rearrange  # 0.7.0
class UpsampleModel(torch.nn.Module):
    def __init__(self):
        super().__init__()
        self.upsample = torch.nn.ConvTranspose2d(1024, 40, kernel_size=2, stride=2)

    def forward(self, triplanes):  # 1, 3, 1024, 32, 32
        triplanes_up = rearrange(
            self.upsample(rearrange(triplanes, "B Np Ci Hp Wp -> (B Np) Ci Hp Wp", Np=3)),
            "(B Np) Co Hp Wp -> B Np Co Hp Wp",
            Np=3,
        )
        return triplanes_up  # 1, 3, 40, 64, 64

Here is the full reproducible export and runner code to generate the mlir and vmfb using turbine.

upsample_export.py
upsample_runner.py
model weights in pytorch to load: upsample.pth
MLIR file: upsample.mlir

Versions
# torch                     2.3.0.dev20240308+cpu
# iree-compiler             20240226.813
# iree-runtime              20240226.813

einops==0.7.0 and shark-turbine are the other packages installed.
x is pytorch, y is turbine
AssertionError:
Arrays are not almost equal to 3 decimals

Mismatched elements: 245760 / 491520 (50%)
Max absolute difference: 3.9600449
Max relative difference: 26.276382
 x: array([[[[[-0.656,  0.393, -0.656, ...,  0.393, -0.656,  0.393],
          [ 1.201, -1.596,  1.201, ..., -1.596,  1.201, -1.596],
          [-0.656,  0.393, -0.656, ...,  0.393, -0.656,  0.393],...
 y: array([[[[[ 1.201,  0.393,  1.201, ...,  0.393,  1.201,  0.393],
          [-0.556, -1.596, -0.556, ..., -1.596, -0.556, -1.596],
          [ 1.201,  0.393,  1.201, ...,  0.393,  1.201,  0.393],...

Could you add an implementation with fixed values? I took your implementation and exported it to the torch test suite but when I used the torch.nn.functional variation it passed. I am concerned that the comparisons are initializing different weights matrices.

Hi @rsuderman , I'm getting errors without loading any weights too. I'm quite new the turbine workflow here.
Does this code work that has no loading of weights work on your machine? I'm getting consistently like 50% error rate on the results. Let me know what I'm doing wrong here... thanks!
# torch                     2.3.0.dev20240308+cpu
# iree-compiler             20240226.813
# iree-runtime              20240226.813

import torch
import numpy as np
from shark_turbine.aot import *
from einops import rearrange
import iree.runtime as rt

class UpsampleModel(torch.nn.Module):
    def __init__(self):
        super().__init__()
        self.upsample = torch.nn.ConvTranspose2d(1024, 40, kernel_size=2, stride=2)

    def forward(self, triplanes):  # 1, 3, 1024, 32, 32
        triplanes_up = rearrange(
            self.upsample(rearrange(triplanes, "B Np Ci Hp Wp -> (B Np) Ci Hp Wp", Np=3)),
            "(B Np) Co Hp Wp -> B Np Co Hp Wp",
            Np=3,
        )
        return triplanes_up  # 1, 3, 40, 64, 64

def shark_infer(x, mod):
    config = rt.Config("local-task")
    vmm = rt.load_vm_module(
        rt.VmModule.wrap_buffer(config.vm_instance, mod.map_memory()),
        config,
    )
    y = vmm.main(x)
    return y

def upsample_export(device="cpu", target_triple="", max_alloc="4294967296"):
    model = UpsampleModel()
    example_input = torch.ones(1, 3, 1024, 32, 32)
    # model.load_state_dict(torch.load("upsample.pth"))  # FAILS on random weights on my machine

    torch_output = model(example_input)
    torch_output = torch_output.detach().numpy()

    # Code from Resnet-18 example
    # build an mlir module with 1-shot exporter
    exported = export(model, example_input)
    compiled_binary = exported.compile(save_to=None)
    turbine_output = shark_infer(example_input, compiled_binary)
    turbine_output = turbine_output.to_host()

    print("TURBINE OUTPUT:", turbine_output, turbine_output.shape, turbine_output.dtype)
    print("TORCH OUTPUT:", torch_output, torch_output.shape, torch_output.dtype)

    np.testing.assert_almost_equal(torch_output, turbine_output, decimal=3)

upsample_export()

AssertionError:
Arrays are not almost equal to 3 decimals
Mismatched elements: 245760 / 491520 (50%)
Max absolute difference: 6.009089
Max relative difference: 16.23158
x: array([[[[[ 2.601,  2.268,  2.601, ...,  2.268,  2.601,  2.268],
[ 3.063, -0.461,  3.063, ..., -0.461,  3.063, -0.461],
[ 2.601,  2.268,  2.601, ...,  2.268,  2.601,  2.268],...
y: array([[[[[ 3.063,  2.268,  3.063, ...,  2.268,  3.063,  2.268],
[ 0.635, -0.461,  0.635, ..., -0.461,  0.635, -0.461],
[ 3.063,  2.268,  3.063, ...,  2.268,  3.063,  2.268],...

After debugging around the testing framework quirks, looks like IREE at head is fine. I would guess the version you have installed had an issue with padded, strided insertions given the numerical issues.

# torch                     2.1.0+cpu
# iree-compiler             20240311.828
# iree-runtime              20240311.828
# shark-turbine             0.9.7.dev1

Got it working after following the developer instructions to install shark-turbine dev version now. All good, thanks!!


Implemented TabStripPlacement to TabControlTemplate to allow tabs to …

…exist on the left, right and bottom in addition to the top. Also Added attached property in TabControlAssist for settings vertical alignment since it might need to be set when using left/right tabs.
Note: I added the property TabControlAssist.TabHeaderVerticalAlignment, TabControlAssist.TabHeaderAlignment should probably be renamed to TabHeaderHorizontalAlignment but that would be a breaking change for existing users.

@Awsmolak Thank you


Expression was too complex to be solved in reasonable time; consider breaking up the expression into distinct sub-expressions

Has been solved


[2.2.x] Add support for SLF4J 2.0 (with Logback 1.3.x)

Log4j2 has only log4j-slf4j18-impl artifact which was using long-in-development SLF4J 1.8.0-beta versions. There's no binding (actually service provider now) for SLF4J 2.0 in Log4j2.
The most important change in SLF4J2 is the removal of static binding, which historically was a brilliant idea by the way after the hellish configuration of commons-logging discovery mechanisms... See<EMAIL_ADDRESS>
SLF4J does not rely on any special class loader machinery. In fact, the binding between SLF4J and a given logging API implementation is performed statically at compile time of each binding. Each binding is hardwired to use one and only one specific logging API implementation. Each binding corresponds to one jar file. In your code, in addition to slf4j-api.jar, you simply drop the binding of your choice, that is a jar file, onto the appropriate class path location. As a consequence of this simple approach, SLF4J suffers from none of the class loader problems or memory leaks observed with Jakarta Commons Logging (JCL).

SLF4J 2 now relies on Java Service Loader (META-INF/services/org.slf4j.spi.SLF4JServiceProvider).

See https://jira.qos.ch/browse/LOGBACK-1716


update Helm instructions for k8s 1.16.0

See https://github.com/cockroachdb/docs/issues/5654

This change is

Online preview: http://cockroach-docs-review.s3-website-us-east-1.amazonaws.com/1301939800e59f0e7a1cb41f2d5cb107ba503db7/


IE 11 input displays the entire file path, not just file name

In Chrome/FF, the input field displays the filename only.  In IE11, it's displaying the whole path.  I don't want the path to be displayed.  Is there a way to correct this?

Use button and show the file name by {{file.name}}

@dhintze This link might help
http://stackoverflow.com/questions/2200100/input-type-file-for-ie-gives-full-path-need-file-name-only


[GH-490] Fix connect link on /jira info output

Summary
This PR removes the extra / from the connect URL indicated in /jira info output when a Jira instance is not yet connected. That seems to be the only place where this URL is constructed so I thought adding new method on Plugin wouldn't be necessary.
Alternative solution: strings.TrimLeft on routeUserConnect.
Ticket Link
Fixes #490

Codecov Report

Merging #523 into master will not change coverage.
The diff coverage is 0.00%.

@@           Coverage Diff           @@
##           master     #523   +/-   ##
=======================================
  Coverage   34.14%   34.14%
=======================================
  Files          37       37
  Lines        4581     4581
=======================================
  Hits         1564     1564
  Misses       2868     2868
  Partials      149      149

Impacted Files
Coverage Δ

server/command.go
23.86% <0.00%> (ø)

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I believe this is a personal preference concern, but can be achieved in multiple ways.  Personally, I prefer the response to include the (%s/%s) and modifying the variable that is prefixed, or suffixed with the additional /.
Your proposal works fine also and I'm approving.  Thanks, @promulo!

Thanks! I did think about that and was pretty undecided to be honest. :sweat_smile:
In the end I just went with the smallest possible diff but would be glad to change it if that makes it more sense.