3Box DB Speed

Make openBox & getProfile faster

How?
Do you just want to create the actual initialization faster, and if so what's the best place I can start diving into to help?
Additionally, thoughts on providing a caching mechanism to provide the appearance of instant loading? It might not provide any significant for small amounts of data, but what about diffing cached data with data references on IPFS to only request data if it's been changed in circumstances where a significant amount of data is being requested?

@KamesCG This is an epic. If you open it in zenhub you will see a lot of stories associated with it. Building a caching layer is something that we are considering to do later on.


@bufbuild/connect-web -> @connectrpc/connect-web

@bufbuild/connect-web was deprecated. We have to use the new location.
See: https://github.com/connectrpc/connect-es/releases/tag/v0.13.1

Yes, you are right, i am aware of this but was not able to migrate buf.gen.yaml to generate the ts/js code to use connectrpc/connect-es instead.
Maybe we could fix this together this week


TestRunner0607_Orsay.zip - Not Work Orsay 2014

Hi,
we triedto install the TestRunner0607_Orsay.zip and it failed on device:
Samsung Smart TV Orsay
Model UE55F7000
Software version : T-FXPDEUC-1118.0
We hope in your help
Thank you ad best regards

Hello, Belsim77,
It is difficult to check the exact reason with your question.
so plz give it to me, ".zip" file.
Thank you.


Problems with SB3 and Gist on Mac OS El Capitan

I have Mac OS X 10.11.5 (El Capitan ) , Sublime Text Editor 3 (3114) and I just installed Gist. I'm getting the following exception:
unloading plugin Gist.gist reloading settings Packages/Gist/Gist.sublime-settings unloading plugin Gist.helpers unloading plugin Gist.request unloading plugin Gist.settings reloading settings Packages/User/Package Control.sublime-settings reloading settings Packages/User/Preferences.sublime-settings reloading /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Packages/User/Preferences.sublime-settings Package Control: The package Gist has been removed reloading settings Packages/User/Package Control.sublime-settings ignored packages updated to: [] reloading settings Packages/User/Package Control.sublime-settings reloading settings Packages/User/Preferences.sublime-settings reloading /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Packages/User/Preferences.sublime-settings reloading settings Packages/User/Preferences.sublime-settings reloading /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Packages/User/Preferences.sublime-settings reloading settings Packages/User/Git.sublime-settings reloading settings Packages/User/Git.sublime-settings ignored packages updated to: ["Gist"] reloading settings Packages/User/Package Control.sublime-settings reloading settings Packages/User/Preferences.sublime-settings reloading /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Packages/User/Preferences.sublime-settings ignored packages updated to: [] reloading settings Packages/User/Package Control.sublime-settings reloading settings Packages/User/Package Control.sublime-settings reloading settings Packages/User/Preferences.sublime-settings reloading plugin Gist.gist reloading settings Packages/Gist/Gist.sublime-settings reloading plugin Gist.helpers reloading plugin Gist.request reloading plugin Gist.settings reloading /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Packages/User/Preferences.sublime-settings reloading settings Packages/User/Preferences.sublime-settings reloading /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Packages/User/Preferences.sublime-settings Traceback (most recent call last):   File "gist in /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Installed Packages/Gist.sublime-package", line 37, in _fn   File "gist in /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Installed Packages/Gist.sublime-package", line 327, in run   File "request in /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Installed Packages/Gist.sublime-package", line 135, in api_request   File "request in /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Installed Packages/Gist.sublime-package", line 47, in api_request_native   File "request in /Users/robertovazquezgonzalez/Library/Application Support/Sublime Text 3/Installed Packages/Gist.sublime-package", line 37, in token_auth_string Gist.request.MissingCredentialsException error: Gist: unknown error (please, report a bug!)
I have created the /Users/user/Library/Application Support/Sublime Text 3/Packages/User/Git.sublime-settings file and added the token generated on github, but still the exception stay.
Also I have re-installed it a couples time with the same result.
If someone can help here will be very appreciated.
Thanks in advance.

It should be Gist.sublime-settings, not Git.sublime-settings. It is useful to use menu Sublime Text -> Preferences -> Package Settings -> Gist -> Settings - User instead of manually creating the files.


Remove gRPC tool related code from gRPC repo

Description:

The gRPC tool has been moved to a separate repo[1]. Therefore, the gRPC tool-related code needs to be removed from the gRPC repo.
Related task: https://github.com/ballerina-platform/ballerina-standard-library/issues/3019
[1] https://github.com/ballerina-platform/protoc-tools

Closing since this is completed.


Remove BootstrapIconsAsset::class.

Q
A

Is bugfix?
✔

New feature?
❌

Breaks BC?
❌

@terabytesoftw Hi. Why BootstrapIconsAsset::class was it removed. It would be convenient for Bootstrap to go along with the icons.

@terabytesoftw hola. Por qué bootstrapiconsasset::class se eliminó. Sería conveniente para Bootstrap ir junto con los iconos.

If that was the idea at first, but they commented that BS5 can use any icon pack, then they did not see it as consistent, and they proceeded to remove it.


Smaller Calendar-nav

Hi,
The Calendar-nav is awesome and beautiful but way too big imo: could we make it smaller so it takes less space? Or a little snippet to change its size?

As part of v2 update I plan to make navigation blocks highly configurable - with possibility to show/hide some rows and adjust styles to some degree


CASSANDRA-19118 Add support of vector type to COPY command

CASSANDRA-19118
This patch adds a converter that allows parsing vector literals passed via csv files to the COPY command.

@szymon-miezal I agree with all what @Maxwell-Guo wrote. Please address and ping me on the ticket.

@adelapena I think the PR is ready for a second round, once it's approved I will squash the history and attach patches to the jira ticket for the sake of running tests and merging them further.

Looks good to me, running CI for 5.0:

j11
j17

I'll run it for the trunk patch too when it's ready.

That failure is surprising: https://app.circleci.com/pipelines/github/adelapena/cassandra/3359/workflows/68cca061-02e3-419c-88f9-0062f42e1b3e/jobs/96153

I suspect it's because https://github.com/datastax/python-driver/tree/cassandra-test - a branch used by cqlshlib test - does not support vector type.

Yes, it seems we are going to need to update that branch before we proceed with this, probably in a separate ticket.

We could work around it by using this hated literal instead of a reference to VectorType but running tests for https://github.com/apache/cassandra/tree/trunk/pylib directory with a not-compatible driver will hit us again eventually.
I doubt we will be able to afford the luxury of updating this particular branch as that will break old versions that do not support python 3. More likely we will have to create yet another branch or use master.

I have upgraded python-driver to 3.28.0.
When running cassandra-cqlsh-tests.sh locally I can see the number of failures is the same on trunk and on my branch.
@adelapena I think it would be useful to rerun the CI for this patch.


Trustmark entity type

Title
trustmark_entity_type
Content
Change the label 'entity_type' for trust mark with trustmark_entity_type
Review

[X] Ensure your files are written following RST specs (not MD!)
[X] Italian version
[X] English version
[ ] Example files
[X] Ask for review

In OIDC Federation we have the Entity Types, corresponding at the roles the participant have in the federation.
Considering that every participant may issue TM, but only which are recognized by the TA should be considered valid, a federation entity may be a trust mark issuer
we don't have the role trustmark_entity_type in Federation 1.0
I'd use instead this PR to fix this typo, we define the role intermediary in the table, but federation_entity in the examples

and also:, for the english version the term Intermediary should be changed to Intermediate

So, can you confirm that the entity_type classification in trust mark
https://github.com/italia/spid-cie-oidc-docs/blame/versione-corrente/docs/en/trust_marks.rst#L73
should be equal to the classification of metadata
https://github.com/italia/spid-cie-oidc-docs/blame/versione-corrente/docs/en/entity_configuration.rst#L57

It's just a convention, if we say that that node in the path MUST be one of the possibile entity type we SHOULD use the entity type following the metadata types, considering that intermediary is not an entity type but a defined term in the specs
also: Intermediary should be changed in Intermediate, this is an english typo.
If AgID or IPZS wants use a custom id o change the patterns I'm ok with this, you have the power for do that, I just ask that both CIE and SPID uses the same pattern and possibily the same TM id. That would be great

For this reason, and for avoid ambiguity, I believe that it'is better to use in the description, a term other than entity_type. So I proposed trustmark_entity_type

A trust mark is issued to give additiona and administrave information about a participant, if it is a intermediate, RP, OP or AA.
What's the meaning and the achievent of having trustmark_entity_type? Considering that the TA publishes the "trust_mark_issuers" in its EC?

PS = the english typo related to the term Intermediate is fixed here: https://github.com/italia/spid-cie-oidc-docs/pull/157

Is the entity_type classification:

openid_relying_party
openid_provider
federation_entity
oauth_authorization_server
oauth_resource

or:

openid_relying_party
openid_provider
intermediate
oauth_resource

?
Maybe we could simply clarify that the type of the entities defined for trust mark are not strictly related to entity_type of metadata

I'm ok, we'll discuss it tomorrow :-)


CliRunner and multiple inputs

Hi all,
When using something like:
@click.command()
@click.password_option()
def cli(password): ...

It is not possible to test both the first Password prompt, and its confirmation prompt with CliRunner. CliRunner will enter the first input, but then the confirmation prompt remains unnoticed. Is there something else that needs to be used with CliRunner, or is this behavior unintended?

I am wondering the same thing; is it not possible to pass multiple inputs to the CliRunner?

It is possible to pass multiple inputs to CliRunner see the docs
If you are still having issues could you post a specific verifiable example and re-open the issue.

@jcrotts this is an example taken from the docs:
import click
from click.testing import CliRunner

def test_encrypt():
    @click.command()
    @click.password_option()
    def encrypt(password):
        click.echo('The password is {}' .format(password))

    runner = CliRunner()
    result = runner.invoke(encrypt, input='ABC')
    assert result.exit_code == 0
    assert result.output == 'ABC'

When the test runs, the input hangs. I'm unsure if this is the same scenario I ran across back in 2016 but hopefully it puts us on the right track.

how to test:
@click.password_option()
yes please @jcrotts


Lack of documentation

Having just stumbled upon Gerbera, there is an off-putting lack of documentation. While plenty of information is present to install Gerbera, there is no easily-discoverable instruction on how to use/configure the program, especially as a service. The closest I can find to any actual documentation is the old readme for MediaTomb.
This issue was created on the gerbera.io repo rather than gerbera itself, as the manpage directs the user (rather unhelpfully) to gerbera.io .

There is stuff on docs.gerbera.io now 👍


Race condition when creating multi BalancedConsumer

    def _add_self(self):
        """Register this consumer in zookeeper.
        This method ensures that the number of participants is at most the
        number of partitions.
        """
        participants = self._get_participants()
        # NOTE: Race condition here
        if len(self._topic.partitions) <= len(participants):
            raise KafkaException("Cannot add consumer: more consumers than partitions")

        self._zookeeper.create(
            self._path_self, self._topic.name, ephemeral=True, makepath=True)

As shown above, there is a race condition when multi processes create BalancedConsumer at the same time with the same consumer_group.
When a race condition occurred, the consumer instance holds empty partition, and the internal _consumer  is not inited.
Because of the null _consumer, there seems to be no way to stop it.
May be we can stop the consumer and raise an exception when calling _decide_partitions returns empty partition?

Thanks for reporting this! Just to make sure I fully understand the issue: the fact that _add_self may raise an exception is expected behaviour for your use case, but the problem is that such an instance cannot be properly cleaned up afterwards, is that right?
Would changing BalancedConsumer.stop() so that it has
if self._consumer is not None:
    self._consumer.stop()

be a sufficient solution in that case? (That's probably a useful change anyway.)

From the comments so far, I gather that the issue is essentially that there exists a situation in which the BalancedConsumer can assign itself no partitions (in particular, this race condition), which causes a bunch of other problems. Assuming that's an accurate assessment, what can we do to ensure that this never happens? I think we should avoid adding more locks to the mix if possible. Maybe we can check here whether new_partitions is empty and simply call stop() if so.


CWL runners with TES support (like rabix bunny) are needed

Is your feature request related to a problem? Please describe.
In our use case, we would like to implement end2end where it is possible to find a computational pipeline via TRS and send it to the execution using TES with data described in DRS. So far, I found Dockstore (local cli client for now) but have some hard time using it with a rabix bunny cwl launcher (because it supports TES) and a funnel as an execution engine. It seems that rabix support was dropped a while ago, so I downgraded dockstore-cli and replaced rabix-1.0.3 with 1.0.5 (which supports TES). After that, I could do a simple end2end run, but I don't this approach is sustainable.
Describe the solution you'd like
I wonder if there are plans to bring support for more CWL runners or bring back rabix? Or anybody else is interested in executing DRS->CWL->TES use case.
Describe alternatives you've considered
As I see where only two CWL runners are supported, I need to check Toil if it works with TES.
Additional context
Our next steps are to move pipeline execution into Trusted Execution Environment by utilizing Intel SGX technology in Azure cloud and eventually provide secure execution as a service.
┆Issue is synchronized with this Jira Story
┆Issue Number: DOCK-1744
┆Sprint: Backlog
┆Issue Type: Story

@superbsky for Rabix bunny, we dropped support roughly when Bunny became a legacy project, pointing users at cwltool
https://github.com/rabix/bunny#summary
For cwltool, we haven't tried this but with could try https://github.com/ohsu-comp-bio/cwl-tes/releases/tag/0.3.0 with some hacking.
Both:
We've toyed with Arvados in #1671 but, agreed that GA4GH support seems like a larger project.

I try to summarise my finding so far:

Arvados is possible to use only as WES backend (--wes-url)
dockstore has no TES support like WES
cwltool is supported but has no TES support
cwl-tes is not supported but has TES support
rabix dropped as a legacy project

I was using this table to navigate around possible options but it seems there is not a lot with TES support:
https://github.com/common-workflow-language/cwltool/blob/main/cwltool/schemas/README.md
What would be a better way to approach this issue? What hack can be applied to cwltool to support TES? Any other options? Or maybe I am missing something on the bigger scale, and this use case is not feasible?

I think that is a reasonable summary so far but my knowledge of TES is limited. It might be worth poking around the discussion groups for https://github.com/ohsu-comp-bio/funnel or https://github.com/elixir-cloud-aai/TEStribute to see what is being used currently in the TES community.

Toil runs CWL and has a WES prototype now and TES support on the roadmap: https://github.com/DataBiosphere/toil/issues/2830
This is another WES-based CWL runner: https://github.com/uc-cdis/mariner
Not aware of any CLI app that integrates clients for all the GA4GH Cloud APIs and makes it easy to conveniently run workflows or start tasks on WES and TES, respectively.
Possibly a combination of these may help:

https://github.com/ohsu-comp-bio/tesseract (remotely execute Python code on TES)
https://github.com/ohsu-comp-bio/py-tes (TES client also used in cwl-tes and tesseract)
https://github.com/elixir-cloud-aai/TRS-cli (TRS client)
https://github.com/elixir-cloud-aai/DRS-cli (DRS client)
https://github.com/elixir-cloud-aai/WES-cli (WES client)

Thank you! I ended-up testing a combination of TRS (dockstore via dockstore-cli) WES (cwl-WES) TES (funnel) and it seemed promised before I stuck on malformed request from TRS to WES:

wes_1         | [2021-03-30 13:20:22,268: ERROR   ] Required parameter 'workflow_params' not in request body. [cwl_wes.ga4gh.wes.endpoints.run_workflow]
wes_1         | [2021-03-30 13:20:22,269: ERROR   ] POST request does not conform to schema. [cwl_wes.ga4gh.wes.endpoints.run_workflow]

not sure what happens here, but I will keep posting my updates here

I have stuck with debugging this issue because have no a lot of experience in Java. Barely compiled the app but not quite sure where the wrong parameter binding is going but I think it should be somewhere in ApiClientExtended.java or AbstractEntryClient.java. I also noticed a comment regarding wrong code generation by swagger itself that is why it using an extended client. Please advise who can.
In the meanwhile, I am looking for other WES/TES implementations to combine them together so if anyone aware of working dockstore<->WES combination please suggest.

Which branch are you building from and is there a reason you aren't using the compiled jar from https://github.com/dockstore/dockstore-cli/releases/tag/1.10.0
Also pinging @wshands who has more experience working on the WES portion of the CLI

@denis-yuen yes, I am using this release branch and it works like a charm then I run just mvn package and then something like this:

/usr/bin/env /usr/lib/jvm/java-11-openjdk-amd64/bin/java -cp dockstore-client/target/dockstore-client-1.10.0-shaded.jar io.dockstore.client.cli.Client workflow wes launch --entry github.com/briandoconnor/dockstore-workflow-md5sum:1.4.0 --json /media/temp/cwl_wes/app/test.json --wes-url http://localhost:8080/ga4gh/wes/v1

But I am having a hard time running the project in the IDE (VSCode) because it is messing somehow with the source code, and the project would not compile; thus, I can't debug it properly.
Sorry, I understand that this is a freshman problem and not related to the project. I will give it another shot and maybe I can find a root cause for this missing parameter issue.

Okay, I was able to debug (the old way using stdout) and found that everything is actually in place:

15:28:38.421 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES getMediaType param: workflow_attachment media type: Optional[application/octet-stream]
15:28:38.423 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES createBodyPart key: workflow_attachment media type: application/octet-stream content disp: form-data; filename="md5sum.cwl"; size=251; name="workflow_attachment"
15:28:38.423 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES getMediaType param: workflow_attachment media type: Optional[application/octet-stream]
15:28:38.423 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES createBodyPart key: workflow_attachment media type: application/octet-stream content disp: form-data; filename="dockstore-tool-md5sum.cwl"; size=1505; name="workflow_attachment"
15:28:38.423 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES getMediaType param: workflow_attachment media type: Optional[application/octet-stream]
15:28:38.423 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES createBodyPart key: workflow_attachment media type: application/octet-stream content disp: form-data; filename="md5sum.cwl.json"; size=84; name="workflow_attachment"
15:28:38.423 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES getMediaType param: workflow_engine_parameters media type: Optional[application/json]
15:28:38.423 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES createBodyPart key: workflow_engine_parameters media type: application/json
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES getMediaType param: workflow_url media type: Optional[text/plain]
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES createBodyPart key: workflow_url media type: text/plain
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES serialize key: workflow_params value: /tmp/parameter1751458891458327565json
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES getMediaType param: workflow_params media type: Optional[application/json]
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES createBodyPart key: workflow_params media type: application/json content disp: form-data; filename="parameter1751458891458327565json"; size=156; name="workflow_params"
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES getMediaType param: workflow_type media type: Optional[text/plain]
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES createBodyPart key: workflow_type media type: text/plain
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES getMediaType param: workflow_type_version media type: Optional[text/plain]
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES createBodyPart key: workflow_type_version media type: text/plain
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES getMediaType param: tags media type: Optional[application/json]
15:28:38.424 [main] INFO io.dockstore.client.cli.nested.ApiClientExtended - WES createBodyPart key: tags media type: application/json

I also realized that it would be also helpful to use tcpdump to check an actual HTTP header (it could have saved a lot of time!) and it looks just fine:

Content-Type: application/octet-stream
Content-Disposition: form-data; filename="md5sum.cwl.json"; size=84; name="workflow_attachment"
Content-Type: application/json
Content-Disposition: form-data; name="workflow_engine_parameters"
Content-Type: text/plain
Content-Disposition: form-data; name="workflow_url"
Content-Type: application/json
Content-Disposition: form-data; filename="parameter1751458891458327565json"; size=156; name="workflow_params"
Content-Type: text/plain
Content-Disposition: form-data; name="workflow_type"
Content-Type: text/plain
Content-Disposition: form-data; name="workflow_type_version"
Content-Type: application/json
Content-Disposition: form-data; name="tags"

Maybe something on the WES side (I am using Elixir implementation), but it is undergoing major refactoring and improvements, so I guess it is better to check again once it is done.
@wshands, please suggest if you know any other WES implementation to test with dockstore WES backend.

Just a quick update - I was able to combine dockstore-cli execution with this WES implementation https://github.com/common-workflow-language/workflow-service
cwl-tes was using as a runner in WES pointing to the Funnel TES.
I also found this implementation and will try to run it as well - https://github.com/ddbj/sapporo

Hi @superbsky,
Here is a link to documentation for some WES implementations I have worked with; however it only outlines CURL commands to use to access WES APIs; you can use these to verify the inputs needed for the WES implementations.
I have used the current Dockstore CLI to successfully (albeit several months ago) run WES commands for the Arvados, Illumina, and DNAStack WES implementations
Here are some others (I believe you know some of them):
https://gitlab.com/one-touch-pipeline/wesnake (to be renamed WESkit and will support Nextflow & Snakemake at least)
https://github.com/elixir-cloud-aai/cwl-WES (built on cwl-tes)
https://github.com/elixir-cloud-aai/proWES (sort of; it’s a WES gateway, rather, doesn’t do any actual compute)
https://github.com/icgc-argo/workflow-management
https://github.com/Duke-GCB/calrissian (CWL; not 100% sure it’s a WES, but I heard it is)
https://github.com/uc-cdis/mariner (another CWL one, possibly with TES support?)
Toil has working prototype
https://github.com/ddbj/sapporo-service
I can help you setup debugging in Intellij for the Dockstore CLI but I don't know VSCode.
Let me know if this helps and anything else you need.
Walt

thank you very much @wshands ! I went over the projects you mentioned and it was very informative.
a few comments on that:
wesnake - it may be useful for us because we have our pipeline written using Snakemake. I also tried their recent TES implementation and it works well
cwl-WES - this is actually the WES implementation I tried first not no luck with the combination with dockstore. I talked to @uniqueg and learn that it would be a major refactoring for this project in the upcoming months so I will wait till then
proWES etc - we may use it later once we have more than one WES instance as well as other tools supporting workflow management and k8s
I would also mention https://github.com/microsoft/tes-azure project which is quite interesting since we have an Azure backend at the moment and plans to integrate TES (or even WES) into Trusted Execution Environment using Confidential Computing to protect data in use.

@wshands @denis-yuen
sorry to bother you again but I have a question regarding Cromwell support in dockstore-cli
I wonder if you plan to add support for the remote Cromwell API instead of just local runner?
In my case, I would like to post a job for the remote Cromwell installation.


Error merging of paths

I'am use SVGO(5.0.1, all defaults) for SVG in SVG set file and result has several error on "camcorder_pro", "left_up2", "positive_dynamic", "process", "refresh", "right_up2", "workflow" icons. (Each icon has been optimized separately, before building icon set.)
![Broken SVG set file]
(https://cdn.rawgit.com/icons8/svg-sets/9896b4d4651024569384248180de05a75e458fca/libs/flat-color-icons/1.0.2/flat-color-icons.min.svg)
SVG set from original SVG files (SVG set created only with nodes manipulation without any transformation)

v0.5.2 with the fix has been just released.

Thank you very much!


The function multiple starts immediately after add into cron

I'm trying to add function into CRON to running every minute:
c.AddFunc("*/1 * * * *", func() { log.Println("Run every minute") })
If I do it immediately after cron object was created, then code works as expected - the function will be executed every minute, starting at the beginning of the next minute.
But if I will add the function in a minute after the current (or later - after 2, 3 and more minutes), it begins to execute immediately after you add into the cron.
In addition, it executed as many times as the minutes passed between the creation of the cron and function was added.
For example, if you try to run the following code:
package main

import (
        "log"
        "time"
        "gopkg.in/robfig/cron.v2"
)

func main() {
        c := cron.New()
        c.Start()
        log.Println("Start CRON.")
        time.Sleep(2 * time.Minute)
        log.Println("Add function into CRON.")
        c.AddFunc("*/1 * * * *", func() { log.Println("Run every minute") })
        time.Sleep(5 * time.Second)
        c.Stop()
}

So, the function will call exactly 2 times immediately after adding into cron, because it took 2 minutes between the start of the cron (12:31:36) and adding the function into it (12:33:36).
2017/05/29 12:31:36 Start CRON.
2017/05/29 12:33:36 Add function into CRON.
2017/05/29 12:33:36 Run every minute
2017/05/29 12:33:36 Run every minute

If between execute c.Start() and c.AddFunc took 3 minutes, then we would see in the logs three calls Run every minute.
In my opinion, the first time the function should be executed at the beginning of the next minute - 12:34:00 and repeat every minute.

Excuse me, it was fixed in master, but not in v2.
Would you fix it in v2?

I agree that it is a bug. v3 branch has this fix, and it has other fixes too. I recommend upgrading to it.


Adding unit tests for the existing code #97

For testing, Vitest is used with the combination of React Testing Library, as this application runs with React and Vite. The tests are located in the test folder and can be started with the command pnpm run test. I have written simple tests for now, which can of course be extended by the community as more features are being implemented.
This issue closes #97

For testing, Vitest is used with the combination of React Testing Library, as this application runs with React and Vite. The tests are located in the test folder and can be started with the command pnpm run test. I have written simple tests for now, which can of course be extended by the community as more features are being implemented.
This issue closes #97

Sounds like a solid testing strategy, I'm sure the community will contribute more tests as more features get added. Thank you for contributing!


[enhancement]: Add a metadata recall option for the Guidance FLux parameter

Is there an existing issue for this?

[X] I have searched the existing issues

Contact Details
skunkworxdark
What should this feature add?
It should add the ability to recall the Flux Guidance value that is stored in an image metadata.
in the attached images taken from 5.0.0 rc2 the guidance is missing from the recall option but is in the metadata

Alternatives
No response
Additional Content
No response

In a related issue,  Flux Guidance and Denoising Strength are not recalled when you use the "Use All" on an image.


feat: scans to csv report

are there any differences between #1 ?

You're right, there's no difference


Proper test of ssh client and add upload/download

Resolves #121 and introduces functions that can upload from a reader and download to a writer.
Counterfeiter was used to generate the fake for the client instead of updating the existing one by hand.
/cc @maximilien

@sykesm Travis is not happy. Ill review when that is fixed

Fixed. An incorrect import was generated by counterfeiter because I was working out of the release tree and there's an .envrc that incorrectly sets the GOPATH.  (As described in https://github.com/cloudfoundry-incubator/bosh-softlayer-cpi-release/issues/22)

Good work @sykesm. I have a few comments but based on the fact that we are moving from nothing to some tests, I defer these feedback as non-important...
I am merging so we can start having this pass in CI. Thanks, cheers 👍


⚠ Fortnite has degraded performance

In f3a2983, Fortnite (https://fortnite.com) experienced degraded performance:

HTTP code: 200
Response time: 1621 ms

Resolved: Fortnite performance has improved in 6eaab0d.


Fix the issue of extract_frames_as_images destory input frame

fixes #302

@1192119703jzx could you also some sanity checks (and maybe some edge case handling?) to the test suite, around here https://github.com/clamsproject/mmif-python/blob/0e6dbbb05b816861eb8342beaa592c49fd8d33db/tests/test_utils.py#L107-L108?


Phone Number Metadata

@qubixes
This is what the metadata for phone number column looks like. This metadata was created when I used "metadata = MetaDataset.from_dataframe(df)"
{
"name": "emp_phone_no",
"type": "continuous",
"dtype": "Float64",
"prop_missing": 0.23655913978494625,
"distribution": {
"implements": "core.exponential",
"provenance": "builtin",
"class_name": "ExponentialDistribution",
"parameters": {
"rate": 3.1744290032716335e-07
}
}
},
Can you please share instruction on how I can create metadata manually for Phone number, name, email id ,ssn, credit_card_number so that it fetches samples from faker? As we can see in this example, the code in the backend is translating phone number as exponential continuous distribution.
My intention is to pass "metadata.json" file to synthesize data for various columns."synthetic_data = metadata.synthesize(500) "
The outputs that I am getting from synthesize function, does not resemble phone numbers at all.
Eg:
617914.509611
3.2832e6
null
495603.009907

Hey @Mrin7, great to see that you're actively using MetaSynth!
You have probably noticed that we are still actively developing this software, and it will become more stable over the coming months. The answer to your question is not yet in the official documentation, but you can find it here:
https://github.com/sodascience/metasynth/blob/main/examples/advanced_tutorial.ipynb
in short, either manually specify a RegexDistribution with regex "\d{9}", or specify a FakerDistribution with "phone_number" as its provider.
How to do this can be found in the section "Specifying the distribution of structured strings".

Hi @Mrin7,
It seems like the column you're trying to synthesize has the wrong data type. Are you using pandas or polars to create the dataframe? With pandas, be sure to convert the column to a nullable integer type, otherwise you'll get floating point numbers. Hope that helps.


IKEv1 can't be used in AzS

https://docs.microsoft.com/en-us/azure/azure-stack/user/azure-stack-vpn-gateway-about-vpn-gateways#site-to-site
"A site-to-site (S2S) VPN gateway connection is a connection over IPsec/IKE (IKEv1 or IKEv2) VPN tunnel." --> Remove IKEv1

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

ID: f780e2ad-c126-43e9-2596-848115d09fa7
Version Independent ID: f4794385-4948-b927-9205-398fd63896a7
Content: About VPN gateway for Azure Stack
Content Source: articles/azure-stack/user/azure-stack-vpn-gateway-about-vpn-gateways.md
Service: azure-stack
GitHub Login: @sethmanheim
Microsoft Alias: sethm

@weyCC81 Thanks for the feedback! I have assigned the issue to the content author to evaluate and update as appropriate.

@weyCC81 Thank you for your feedback, we will incorporate this change ASAP. #please-close

@weyCC81 We will now proceed to close this thread. If there are further questions regarding this matter, please tag me in your reply. We will gladly continue the discussion and we will reopen the issue.


docker: 20.10.7 -> 20.10.8

Motivation for this change
https://docs.docker.com/engine/release-notes/#20108
Opening as a draft, as docker needs to have its own docker-containerd derivation for now, until they switch to containerd >=1.5.x - this is due to containerd only switching to go modules as of 1.5.0, and docker still using the 1.4.x tree right now. See:

Update static binaries and containerd.io rpm and deb packages to containerd v1.4.9 and runc v1.0.1:

This is technically a "downgrade" of containerd, however it matches the version upstream intends to use. This also fixes two CVEs against containerd-1.5.1, as they are fixed both in >=1.5.4 and >=1.4.8.
I'll be finishing this up when I have a little more time than just late night cleanup, I just wanted to open this PR proactively, to fix the pinned docker-specific versions of containerd and runc :)
Things done

[x] Tested using sandboxing (nix.useSandbox on NixOS, or option sandbox in nix.conf on non-NixOS linux)
Built on platform(s)

[x] NixOS
[ ] macOS
[ ] other Linux distributions

[x] Tested via one or more NixOS test(s) if existing and applicable for the change (look inside nixos/tests)
[ ] Tested compilation of all pkgs that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review wip"
[x] Tested execution of all binary files (usually in ./result/bin/)
21.11 Release Notes (or backporting 21.05 Relase notes)

[ ] (Package updates) Added a release notes entry if the change is major or breaking
[ ] (Module updates) Added a release notes entry if the change is significant
[ ] (Module addition) Added a release notes entry if adding a new NixOS module

[x] Fits CONTRIBUTING.md.

I'm not sure if this is the best way to resolve the problem in nix. We need 1.4.x for the sake of docker, but support for go modules was only introduced in 1.5.0, hence the extra derivation. Would appreciate pointers if this isn't the best way to solve it, e.g. if we can not expose 1.4 at all beyond docker :)
Once docker 21.x is out we can drop containerd_1_4.

Result of nixpkgs-review pr 132717 run on x86_64-linux 1

1 package blacklisted:

tests.nixos-functions.nixos-test

1 package failed to build:

nixos-install-tools

13 packages built:

charliecloud
containerd_1_4
docker (docker-edge ,docker_20_10)
docker-client
docker-gc
fn-cli
grype
nvidia-docker
out-of-tree
pipework
python38Packages.jupyter-repo2docker
python39Packages.jupyter-repo2docker
tarsum

Not sure what the nixos-install-tools failure was, building again from the branch it succeeded.


Added 3d pose estimation file

Title: Add Real-Time 3D Pose Estimation with UDP Data Transmission
Description: This PR introduces a real-time 3D pose estimation feature using MediaPipe and OpenCV. The main functionalities include:
Pose Detection: Utilizes MediaPipe to detect and extract 3D pose landmarks from webcam video feed.
Visualization: Draws detected landmarks on the video feed for real-time monitoring.
UDP Data Transmission: Sends the 3D landmark coordinates to a specified Unity application via UDP for further processing.
User Interaction: Allows users to terminate the program using the 'q' key.
Changes Made:

@iamwatchdogs are any changes required?

Sorry for the delay @mahipalimkar, Your work is being reviewed by me. Please be patient.

@iamwatchdogs sorry about that, I had the readme ready, I suppose there was an issue in the original commit. Please check now

@iamwatchdogs made necessary changes. Please check.


Gallery::Imagery Layers Split

Hi,
A little suggestion:
https://pasu.github.io/ExamplesforCesium/examples/examples.html#Visualization-Planet
I make this demo Imagery Layers Split, which is similiar with Cesiums'.
One day I browsed this demo and found it did not support touch event
Here is my modification and I tested it was fine:
document.getElementById('slider').addEventListener('mousedown', mouseDown, false);
document.getElementById('slider').addEventListener('touchstart', mouseDown, false);
window.addEventListener('mouseup', mouseUp, false);
window.addEventListener('touchend', mouseUp, false);
function mouseUp() {
  window.removeEventListener('mousemove', sliderMove, true);
  window.removeEventListener('touchmove', sliderMove, true);
}

function mouseDown(e) {
  var slider = document.getElementById('slider');
  var nPos = e.clientX != undefined?e.clientX:e.changedTouches[0].clientX;
  dragStartX = nPos - slider.offsetLeft;
  window.addEventListener('mousemove', sliderMove, true);
  window.addEventListener('touchmove', sliderMove, true);
}

function sliderMove(e) {
  var slider = document.getElementById('slider');
  var nPos = e.clientX != undefined?e.clientX:e.changedTouches[0].clientX;
  var splitPosition = (nPos - dragStartX) / slider.parentElement.offsetWidth;
  slider.style.left = 100.0 * splitPosition + "%";
  viewer.scene.imagerySplitPosition = splitPosition;
}

Good suggestion, thanks @pasu!

The above update doesn't support PointerEvents.  Maybe use ScreenSpaceEventHandler instead?

Well, I will try and test  this idea later, thanks

I got this new skill, @emackey
Here is my update and I test it in Chrome, iPhone 6s and Android(Huawei P9)
it is ok.
var handler = new Cesium.ScreenSpaceEventHandler(slider);
var bMoveActive = false;
function move(movement){
	if(!bMoveActive)
		return;
	var nMove = movement.endPosition.x ;//- movement.startPosition.x;
	var splitPosition = (slider.offsetLeft + nMove) / slider.parentElement.offsetWidth;
	slider.style.left = 100.0 * splitPosition + "%";
	viewer.scene.imagerySplitPosition = splitPosition;
}
handler.setInputAction(function(movement) {
	bMoveActive = true;
}, Cesium.ScreenSpaceEventType.LEFT_DOWN);
handler.setInputAction(function(movement) {
	bMoveActive = true;
}, Cesium.ScreenSpaceEventType.PINCH_START);
handler.setInputAction(function(movement) {
	move(movement);
}, Cesium.ScreenSpaceEventType.MOUSE_MOVE);
handler.setInputAction(function(movement) {
	move(movement);
}, Cesium.ScreenSpaceEventType.PINCH_MOVE);
handler.setInputAction(function(movement) {
	bMoveActive = false;
}, Cesium.ScreenSpaceEventType.LEFT_UP);
handler.setInputAction(function(movement) {
	bMoveActive = false;
}, Cesium.ScreenSpaceEventType.PINCH_END);

@pasu Awesome!  Would you be willing to contribute this back to the Sandcastle demo for us?  We would need a CLA (unless you work for a company that already signed a Cesium CLA).

We have a CLA from @pasu already 😄

Yes, I registered CLA:smile:
Now, I am pulling another request #5780 .
When I committed this html page, it would cause errors for the CI test, so I had to rollback the code for the Reviewers. And I largely believe there is nothing wrong with my code.
So would you like to commit this for me or when cesium close the current request #5780, I promise to commit it later. Either is OK to me. I really hope to make more contributions to this great team.
Attachment is Imagery Layers Split.html.
Imagery Layers Split.html.txt

I think the Sandcastle cleanup could be separate from #5780.  Sounds like it should wait for that one to get merged first.

Fixed in #5781.  Thanks @pasu!

Unrelated to this issue:
@pasu Any chance you're looking to PR that Vector Tile stuff? I'd be glad to assist if so. :)


[E0277]: the trait bound i32: diesel::types::FromSqlRow<diesel::types::Nullable<diesel::types::Integer>, diesel::pg::Pg> is not satisfied

Hello, when I try to use diesel to build my first orm, and error is come. My way is exactly same  to your getting-start doc.
up.sql:
CREATE TABLE USERS (
    uid VARCHAR PRIMARY KEY,
    realname VARCHAR NOT NULL,
    age INTEGER,
    sex VARCHAR
);

down.sql:
DROP TABLE USERS;

.env:
DATABASE_URL=postgres://postgres:postgres@localhost/simllsan

and the command diesel migration redo has been executed successfully :
fuying@fuying-linux:~/rustprojs/simtraining$ diesel migration redo
Rolling back migration<PHONE_NUMBER>0851
Running migration<PHONE_NUMBER>0851

lib.rs:
#![feature(custom_derive, custom_attribute, plugin)]
#![plugin(serde_macros, diesel_codegen, dotenv_macros)]

#[macro_use]
extern crate diesel;
extern crate dotenv;

extern crate serde;
extern crate serde_json;

extern crate time;
extern crate rand;
extern crate libc;
extern crate mio;
#[cfg(windows)]
extern crate winapi;
#[cfg(windows)]
extern crate ws2_32;

pub mod jizu;
pub mod simctrl;
pub mod util;
pub mod zhiling;
pub mod dianzhan;
pub mod duanluqi;
pub mod fuzai;
pub mod node;
pub mod zhilu;
pub mod xitong;

pub mod schema;
pub mod user;
// pub mod evaluation;
// pub mod projects;
// pub mod station;
// pub mod training;
use diesel::prelude::*;
use diesel::pg::PgConnection;
use dotenv::dotenv;
use std::env;
use diesel::result::Error;
use user::{User, NewUser};

pub fn establish_connection() -> PgConnection {
    dotenv().ok();

    let database_url = env::var("DATABASE_URL")
        .expect("DATABASE_URL must be set");
    PgConnection::establish(&database_url)
        .expect(&format!("Error connecting to {}", database_url))
}

pub fn create_user<'a>(conn: &PgConnection,
                  _uid: &'a str,
                  _realname: &'a str,
                  _age: i32,
                  _sex: &'a str)
                  -> QueryResult<User> {
    use schema::users;
    let uid_s = String::from(_uid);

    let result = users::table.find(uid_s).first(conn);
    match result {
        Err(NotFound) => {
            let new_user = NewUser {
                uid: _uid,
                realname: _realname,
                age : _age,
                sex : _sex,
            };
            return diesel::insert(&new_user).into(users::table)
                .get_result(conn);
        }
        Ok(_) => return Err(Error::DatabaseError("此用户名已存在".to_string())),
    }
}

schema.rs:
infer_schema!(dotenv!("DATABASE_URL"));

user.rs:
use super::schema::users;
#[derive(PartialEq, Copy, Clone, Debug, Serialize, Deserialize)]
pub enum Sex {
    Male,
    Female,
    Unisex,
}
#[derive(PartialEq, Clone, Debug, Serialize, Deserialize, Queryable)]
pub struct User {
    pub uid: String,
    pub realname: String,
    pub age: i32,
    pub sex: String,
}

#[insertable_into(users)]
pub struct NewUser<'a> {
    pub uid: &'a str,
    pub realname: &'a str,
    pub age: i32,
    pub sex: &'a str,
}

impl User {
    pub fn new(_id: &str, _realname: &str) -> User {
        User {
            uid: String::from(_id),
            realname: String::from(_realname),
            age: 0,
            sex: "".to_string(),
        }
    }

}

I use ubuntu 15.10, and the version of rust is:
fuying@fuying-linux:~/rustprojs/simtraining$ rustc --version
rustc 1.10.0-nightly (d91f8ab0f 2016-05-07)
fuying@fuying-linux:~/rustprojs/simtraining$ cargo --version
cargo 0.11.0-nightly (b304305 2016-05-06)

cargo.toml:
[package]
name = "simtraining"
version = "0.1.0"
authors = ["fuying"]

[dependencies]
time = "^0.1"
rand = "^0.3"
libc = "^0.2"
mio = "^0.5"
serde = "^0.7.0"
serde_json = "^0.7.0"
serde_macros = "^0.7.0"
iron = "^0.3.0"
router = "^0.1.1"
diesel = { git = "https://github.com/diesel-rs/diesel.git" }
diesel_codegen = { git = "https://github.com/diesel-rs/diesel.git", default-features = false, features = ["nightly", "postgres"] }
dotenv = "^0.8.0"
dotenv_macros = "^0.8.0"

[dev-dependencies]
rand = "^0.3"

[target.x86_64-pc-windows-msvc.dependencies]
winapi = "^0.2"
ws2_32-sys = "^0.2"
[target.x86_64-pc-windows-gnu.dependencies]
winapi = "^0.2"
ws2_32-sys = "^0.2"
[target.i686-pc-windows-msvc.dependencies]
winapi = "^0.2"
ws2_32-sys = "^0.2"

[[example]]
name = "test-router"
path = "examples/testrouter.rs"

[[example]]
name = "test-create-user"
path = "examples/testcreateuser.rs"

This is correct. You cannot deserialize a column of type Nullable<Integer> into an i32. You'll either need to use an Option<i32> on the Rust side, or change the field to be NOT NULL on the SQL side.

@sgrif
thank you very much

@sgrif
sorry to bother you. Another question is how can i deserialize an embedded struct obiect? It likes this:
#[derive(Queryable)]
#[insert_into(users)]
struct User {
//...
}
#[derive(Queryable)]
#[insert_into(posts)]
struct Post {
//...
user : User
}
Does it correct? Because I am outside and can't test it. So if you are not busy, please help me.
By the way, does diesel support json or jsonb type? And if diesel can support it, where can I find its docs and how to use it? Thank you very much.

We don't really have support for embedded structs at the moment. When you're querying against two tables, you'd get back a (Post, User) instead of embedding the parent record inside of the child. If you really want to embed a struct, you'll need to implement FromSqlRow for your User struct manually. It'd look something like this:
use diesel::prelude::*;
use diesel::backend::Backend;
use diesel::types::{FromSqlRow + HasSqlType};
use diesel::row::Row;
use std::error::Error;

impl<ST, DB> FromSqlRow<ST, DB> for User where
    DB: Backend + HasSqlType<ST>,
    User: Queryable<ST, DB>,
    <User as Queryable<ST, DB>>::Row: FromSqlRow<ST, DB>,
{
    fn build_from_row<T: Row<DB>>(row: &mut T) -> Result<Self, Box<Error + Send + Sync>> {
        let row = try!(<<User as Queryable<ST, DB>>::Row as FromSqlRow<ST, DB>>::build_from_row(row));
        Ok(User::build(row))
    }
}

Note: Haven't tried that exact code, that's just from memory of what it'd roughly look like.
We don't support the JSON type yet, but it's on the radar for something we'd like to support. https://github.com/diesel-rs/diesel/issues/44 is the tracking issue, and I've mentioned how you could use it today in your app if needed in the comments there.

@sgrif
thank you very much.

@sgrif
thank you very much.

Just a note, I faced similar issue. it's important that after you've made changes to the migration, run
cargo clean
From my limited understanding, I assume the custom code generator does not update the generated code and uses the old database definition, So we need to clean the generated code
I am sorry, for least clear explanation as I'm sleepy and just figured out the problem. I hope it helps someone.

@tmahmood thank you :)

If you ever land here looking for solution to not implemented traits compilation errors make sure that your model declaration fields follow exact order of fields in your table.

This is correct. You cannot deserialize a column of type Nullable<Integer> into an i32. You'll either need to use an Option<i32> on the Rust side, or change the field to be NOT NULL on the SQL side.

This solution solves my issue! Thanks!!

@mplebanski Thank you for your comment! I have tried to understand and solve a similar issue for an hour now, and randomly I saw your comment which fixed it all 🎉
I simply changed the field order in my struct to match my up.sql migration and everthing compiles.
That the field order matters should be written in capital letters somewhere.

@skovmand That is already mentioned in multiple locations like the getting started guide or the documentation of the Queryable derive
If you have another location in mind where you expect this information please open a PR.

Thank you for the reference, which explains it clearly 👍 . Perhaps I was overwhelmed by new information :-)

If you ever land here looking for solution to not implemented traits compilation errors make sure that your model declaration fields follow exact order of fields in your table.

I owe you lunch.


tacoRepo.findAll(PageRequest page).getContent() in Chapter 6?

The updated TacoRepository please? What's the return type of findAll(PageRequest page) ?
Please release your example code. We can QA for you.

Adding Page findAll(Pageable page) to TacoRepository would make the code work.
But still, please provide the example code. Time flying. Maybe wait and wait, a new version of software or dependency would come out.


got a bus error on raspberry pi

I trained my network on my mac, and predict something on my raspberry pi with keras, but I got a bus error.
OS: Raspbian GNU/Linux 9
tensorflow: 1.9.0
keras: 2.2.2
log info:
Using TensorFlow backend.
/usr/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: compiletime version 3.4 of module 'tensorflow.python.framework.fast_tensor_util' does not match runtime version 3.5
return f(*args, **kwds)
/usr/lib/python3.5/importlib/_bootstrap.py:222: RuntimeWarning: builtins.type size changed, may indicate binary incompatibility. Expected 432, got 412
return f(*args, **kwds)
2018-08-28 14:31:25.554008: W tensorflow/core/framework/allocator.cc:108] Allocation of 63539200 exceeds 10% of system memory.
2018-08-28 14:31:26.177700: W tensorflow/core/framework/allocator.cc:108] Allocation of 63539200 exceeds 10% of system memory.
2018-08-28 14:31:26.345901: W tensorflow/core/framework/allocator.cc:108] Allocation of 63539200 exceeds 10% of system memory.
2018-08-28 14:31:36.619646: W tensorflow/core/framework/allocator.cc:108] Allocation of 63539200 exceeds 10% of system memory.
2018-08-28 14:31:36.850119: W tensorflow/core/framework/allocator.cc:108] Allocation of 63539200 exceeds 10% of system memory.
Bus error

Hello, I am having the same problem. Has anyone found a solution?
I am using another network on raspberry and it works fine, but not this one.
In my case the error looks like this:
2018-08-14 09:56:59.250458: W tensorflow/core/framework/allocator.cc:108] Allocation of 5677056 exceeds 10% of system memory.
2018-08-14 09:56:59.288605: W tensorflow/core/framework/allocator.cc:108] Allocation of 5677056 exceeds 10% of system memory.
Bus error

@Anto95 Are you using keras? Maybe it's an error about keras.

I'm sorry I didn't  specify.
I'm using tensorflow. The model which works is a 2D Cnn in pure tensorflow 1.9.0, the one which gives  the error is a 3D Cnn implemented with tensorflow but using Slim. Maybe that could be the problem.

have the same issue @Anto95

@aselle - who can address Raspberry Pi issues?

I also had this issue, using keras and tensorflow. The problem for me was that I trained my model with tensorflow 1.10 but had 1.9 on my raspberry. I only had the "Bus error" log, though
You can get a prebuilt 1.10 version for raspbian stretch from https://github.com/lhelontra/tensorflow-on-arm/releases

Nagging Assignee @karmel: It has been 14 days with no activity and this issue has an assignee. Please update the label and/or status accordingly.

Nagging Assignee @aselle: It has been 14 days with no activity and this issue has an assignee. Please update the label and/or status accordingly.


PT-154173362 VM/chain API (rebased on master)

This is PR #894 without the consensus protocol version changes (to be addressed in separate PR re hard fork). I tested in this CI workflow including Python UAT tests and aevm-test.
I am running further check as this is meant to be the first consensus breaking change since v0.11.0.

I checked that node with this PR is able to verify testnet chain up to height 5254 (I did not check further - current height is 5718).


ActionController::InvalidAuthenticityToken

I have tested ng-token-auth in my app, but when I connect to rails 4 backend it show this errors.
in rails app i have used rack-cors gem.
Parameters<EMAIL_ADDRESS>"password"=>"[FILTERED]", "password_confirmation"=>"[FILTERED]", "confirm_success_url"=>"http://localhost:9000/#/sign_up", "config_name"=>"default"<EMAIL_ADDRESS>"password"=>"[FILTERED]", "password_confirmation"=>"[FILTERED]", "confirm_success_url"=>"http://localhost:9000/#/sign_up", "config_name"=>"default"}}
Can't verify CSRF token authenticity
Completed 422 Unprocessable Entity in 55ms

ActionController::InvalidAuthenticityToken (ActionController::InvalidAuthenticityToken):
  actionpack (4.1.6) lib/action_controller/metal/request_forgery_protection.rb:176:in `handle_unverified_request'
  actionpack (4.1.6) lib/action_controller/metal/request_forgery_protection.rb:202:in `handle_unverified_request'
  devise (3.4.1) lib/devise/controllers/helpers.rb:251:in `handle_unverified_request'
  actionpack (4.1.6) lib/action_controller/metal/request_forgery_protection.rb:197:in `verify_authenticity_token'
  activesupport (4.1.6) lib/active_support/callbacks.rb:424:in `block in make_lambda'
  activesupport (4.1.6) lib/active_support/callbacks.rb:160:in `call'
  activesupport (4.1.6) lib/active_support/callbacks.rb:160:in `block in halting'
  activesupport (4.1.6) lib/active_support/callbacks.rb:166:in `call'
  activesupport (4.1.6) lib/active_support/callbacks.rb:166:in `block in halting'
  activesupport (4.1.6) lib/active_support/callbacks.rb:86:in `call'
  activesupport (4.1.6) lib/active_support/callbacks.rb:86:in `run_callbacks'
  actionpack (4.1.6) lib/abstract_controller/callbacks.rb:19:in `process_action'
  actionpack (4.1.6) lib/action_controller/metal/rescue.rb:29:in `process_action'
  actionpack (4.1.6) lib/action_controller/metal/instrumentation.rb:31:in `block in process_action'
  activesupport (4.1.6) lib/active_support/notifications.rb:159:in `block in instrument'
  activesupport (4.1.6) lib/active_support/notifications/instrumenter.rb:20:in `instrument'
  activesupport (4.1.6) lib/active_support/notifications.rb:159:in `instrument'
  actionpack (4.1.6) lib/action_controller/metal/instrumentation.rb:30:in `process_action'
  actionpack (4.1.6) lib/action_controller/metal/params_wrapper.rb:250:in `process_action'
  activerecord (4.1.6) lib/active_record/railties/controller_runtime.rb:18:in `process_action'
  actionpack (4.1.6) lib/abstract_controller/base.rb:136:in `process'
  actionview (4.1.6) lib/action_view/rendering.rb:30:in `process'
  actionpack (4.1.6) lib/action_controller/metal.rb:196:in `dispatch'
  actionpack (4.1.6) lib/action_controller/metal/rack_delegation.rb:13:in `dispatch'
  actionpack (4.1.6) lib/action_controller/metal.rb:232:in `block in action'
  actionpack (4.1.6) lib/action_dispatch/routing/route_set.rb:82:in `call'
  actionpack (4.1.6) lib/action_dispatch/routing/route_set.rb:82:in `dispatch'
  actionpack (4.1.6) lib/action_dispatch/routing/route_set.rb:50:in `call'
  actionpack (4.1.6) lib/action_dispatch/routing/mapper.rb:45:in `call'
  actionpack (4.1.6) lib/action_dispatch/journey/router.rb:73:in `block in call'
  actionpack (4.1.6) lib/action_dispatch/journey/router.rb:59:in `each'
  actionpack (4.1.6) lib/action_dispatch/journey/router.rb:59:in `call'
  actionpack (4.1.6) lib/action_dispatch/routing/route_set.rb:678:in `call'
  warden (1.2.3) lib/warden/manager.rb:35:in `block in call'
  warden (1.2.3) lib/warden/manager.rb:34:in `catch'
  warden (1.2.3) lib/warden/manager.rb:34:in `call'
  rack (1.5.2) lib/rack/etag.rb:23:in `call'
  rack (1.5.2) lib/rack/conditionalget.rb:35:in `call'
  rack (1.5.2) lib/rack/head.rb:11:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/params_parser.rb:27:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/flash.rb:254:in `call'
  rack (1.5.2) lib/rack/session/abstract/id.rb:225:in `context'
  rack (1.5.2) lib/rack/session/abstract/id.rb:220:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/cookies.rb:560:in `call'
  dragonfly (0.9.15) lib/dragonfly/cookie_monster.rb:9:in `call'
  activerecord (4.1.6) lib/active_record/query_cache.rb:36:in `call'
  activerecord (4.1.6) lib/active_record/connection_adapters/abstract/connection_pool.rb:621:in `call'
  activerecord (4.1.6) lib/active_record/migration.rb:380:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/callbacks.rb:29:in `block in call'
  activesupport (4.1.6) lib/active_support/callbacks.rb:82:in `run_callbacks'
  actionpack (4.1.6) lib/action_dispatch/middleware/callbacks.rb:27:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/reloader.rb:73:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/remote_ip.rb:76:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/debug_exceptions.rb:17:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/show_exceptions.rb:30:in `call'
  railties (4.1.6) lib/rails/rack/logger.rb:38:in `call_app'
  railties (4.1.6) lib/rails/rack/logger.rb:20:in `block in call'
  activesupport (4.1.6) lib/active_support/tagged_logging.rb:68:in `block in tagged'
  activesupport (4.1.6) lib/active_support/tagged_logging.rb:26:in `tagged'
  activesupport (4.1.6) lib/active_support/tagged_logging.rb:68:in `tagged'
  railties (4.1.6) lib/rails/rack/logger.rb:20:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/request_id.rb:21:in `call'
  rack (1.5.2) lib/rack/methodoverride.rb:21:in `call'
  rack (1.5.2) lib/rack/runtime.rb:17:in `call'
  activesupport (4.1.6) lib/active_support/cache/strategy/local_cache_middleware.rb:26:in `call'
  rack (1.5.2) lib/rack/lock.rb:17:in `call'
  actionpack (4.1.6) lib/action_dispatch/middleware/static.rb:64:in `call'
  rack (1.5.2) lib/rack/sendfile.rb:112:in `call'
  rack-cors (0.2.9) lib/rack/cors.rb:54:in `call'
  dragonfly (0.9.15) lib/dragonfly/middleware.rb:13:in `call'
  rack-cache (1.2) lib/rack/cache/context.rb:136:in `forward'
  rack-cache (1.2) lib/rack/cache/context.rb:143:in `pass'
  rack-cache (1.2) lib/rack/cache/context.rb:155:in `invalidate'
  rack-cache (1.2) lib/rack/cache/context.rb:71:in `call!'
  rack-cache (1.2) lib/rack/cache/context.rb:51:in `call'
  railties (4.1.6) lib/rails/engine.rb:514:in `call'
  railties (4.1.6) lib/rails/application.rb:144:in `call'
  rack (1.5.2) lib/rack/lock.rb:17:in `call'
  rack (1.5.2) lib/rack/content_length.rb:14:in `call'
  rack (1.5.2) lib/rack/handler/webrick.rb:60:in `service'
  /home/luandk/.rvm/rubies/ruby-2.1.2/lib/ruby/2.1.0/webrick/httpserver.rb:138:in `service'
  /home/luandk/.rvm/rubies/ruby-2.1.2/lib/ruby/2.1.0/webrick/httpserver.rb:94:in `run'
  /home/luandk/.rvm/rubies/ruby-2.1.2/lib/ruby/2.1.0/webrick/server.rb:295:in `block in start_thread'

  Rendered<EMAIL_ADDRESS>(0.5ms)
  Rendered<EMAIL_ADDRESS>(0.9ms)
  Rendered<EMAIL_ADDRESS>(0.8ms)
  Rendered<EMAIL_ADDRESS>within rescues/layout (13.2ms)
cache: [POST /api/auth] invalidate, pass

Would you still expect to see "Can't verify CSRF token authenticity" warnings in the console after modifying the controller as you suggested above?


IndexError: list index out of range

Traceback (most recent call last):
File "main.py", line 8, in
myserv = atservers[0]
IndexError: list index out of range
whenever i try to use this it always does this
main.py:
from python_aternos import Client
aternos = Client('testyname1', password='***')
atservers = aternos.get_servers()
print(atservers)
myserv = atservers[0]
print(atservers)
myserv.start()
myserv.stop()
Find server by IPx
testserv = None
for serv in atservers:
if serv.address == 'testyname1.aternos.me':
testserv = serv
if testserv != None:
# Prints a server softaware and its version
# (for example, "Vanilla 1.12.2")
print(testserv.software, testserv.version)
# Starts server
testserv.start()

Hello. Send, please, print(atservers) output.


Support for Thundbird 60

It would be good were this extension to support Thunderbird 60. True, I can tell TB 60 to disable compatibility checking, and that does enable the extension to work, but that workaround will cause some people problems. It will cause some people problems because disabling the compatibility allows the operation of many extensions that break TB 60. I had to disable all the problematic extensions before TB 60, and your extension, would work.

It still doesn't work in version 60.3.1

I've just submitted a new version for a review yesterday, it should be up and running in a few days. Sorry for the delay though.


Array to XML converison getting error "Namespace prefix pkg on package is not defined"

Hello Guys,
I am facing issue with array to xml converion, On xml file I am getting below errors:
This page contains the following errors:
error on line 3 at column 15: Namespace prefix pkg on package is not defined
error on line 4 at column 14: Namespace prefix pkg on part is not defined
error on line 5 at column 19: Namespace prefix pkg on xmlData is not defined
error on line 37 at column 14: Namespace prefix pkg on part is not defined
error on line 38 at column 19: Namespace prefix pkg on xmlData is not defined
error on line 274 at column 14: Namespace prefix pkg on part is not defined
error on line 275 at column 16: Namespace prefix pkg on name is not defined
error on line 276 at column 23: Namespace prefix pkg on contentType is not defined
error on line 277 at column 19: Namespace prefix pkg on padding is not defined
error on line 279 at column 14: Namespace prefix pkg on part is not defined
error on line 280 at column 19: Namespace prefix pkg on xmlData is not defined
error on line 281 at column 20: Namespace prefix w on document is not defined
error on line 282 at column 18: Namespace prefix w on body is not defined
error on line 283 at column 17: Namespace prefix w on p is not defined
error on line 284 at column 19: Namespace prefix w on r is not defined
error on line 285 at column 24: Namespace prefix w on pict is not defined
error on line 286 at column 26: Namespace prefix v on rect is not defined
error on line 287 at column 28: Namespace prefix v on fill is not defined
error on line 288 at column 33: Namespace prefix v on fill_attr is not defined
error on line 290 at column 42: Namespace prefix o on detectmouseclick is not defined
error on line 292 at column 30: Namespace prefix v on stroke is not defined
error on line 293 at column 35: Namespace prefix v on stroke_attr is not defined
error on line 296 at column 31: Namespace prefix v on textbox is not defined
error on line 297 at column 37: Namespace prefix w on txbxContent is not defined
error on line 298 at column 29: Namespace prefix w on p is not defined
Below is a rendering of the page up to the first error.``

You need to post more information. Which Agent are you using, how is the Agent  configuration, what is the actual and expected output?


How to use Weights and Biases with AutoGluon?

Discussed in https://github.com/autogluon/autogluon/discussions/2527

Originally posted by pj-mathematician December  6, 2022
I am using MultiModal predictor to classify images. I want to use wandb with it, so that I can use its features along with autogluon. Can you please guide me if this is possible without customizing the source code?
Since multimodal image prediction primarily uses PyTorch and PyTorch lightning, the example codes are as follows:
PyTorch:
import wandb
# 1. Start a new run
wandb.init(project="gpt-3")
# 2. Save model inputs and hyperparameters
config = wandb.config
config.learning_rate = 0.01
# 3. Log gradients and model parameters
wandb.watch(model)
for batch_idx, (data, target) in enumerate(train_loader):
    if batch_idx % args.log_interval == 0:
    # 4. Log metrics to visualize performance
    wandb.log({"loss": loss})

PyTorch Lightning:
from pytorch_lightning.loggers import WandbLogger
from pytorch_lightning import Trainer

wandb_logger = WandbLogger()
trainer = Trainer(logger=wandb_logger)

If this isnt currently possible then can you guide me a bit of the technicalities of the predictors and the frameworks they use so that I can fork and edit it accordingly 🙂
Thanks

I've posted a message in another issue describing how to use wandb's native tensorboard support: https://github.com/autogluon/autogluon/issues/420#issuecomment-2088320893

Closing this issue in favor of #420


Suppress Generation of Controller / Decorator for specific endpoints

Hi currently use our RAML for two purposes. 1 to generate API model for our spring boot apps and 2. To provide “contract validation” in a mulesoft gateway (ensure that all incoming requests match raml before being passed to our API).
We would like to expose “standard” spring endpoints (metrics / health) and as such add them to our RAML but not autogen controllers / decorators for these. This would allow the downstream gateway to forward to them and let spring boot do the rest.
Is there a way to suppress autogeneration for specific end points?

At the moment, no.
But this is a valid feature request.
What do you think, what will be the best way to introduce this?
Maybe the best way will be to recognize certain annotation, e.g. endpoints with skipCodeGeneration annotation will be ignored.

Hi - thanks for the quick response. Just looked at a work around using the maven-antrun-plugin. You can specify files to delete during build with that (generated sources and classes). It’s a workaround for the moment ...

I introduced dontGenerateForAnnotation configuration option. The value is annotation name.
When defined annotation is found on resource or method - code generation will be skipped.
Keep in mind that when defined on resource - all methods in that resources and all of the subresources will be ignored (code will not be generated for them).


MAINT: add license texts to binary distributions

Ensure license texts are present also in binary distributions: either
contained in LICENSE.txt, or added as data files and referred to in
LICENSE.txt
Also reorder the bundled library list in alphabetical order vs. file names.

Nice, thanks!


Self DM - Self DM is not bolded in LHN after it is marked as unread

If you haven’t already, check out our contributing guidelines for onboarding and email<EMAIL_ADDRESS>to request to join our Slack channel!

Version Number: 9.0.53-0
Reproducible in staging?: Y
Reproducible in production?: Y
If this was caught on HybridApp, is this reproducible on New Expensify Standalone?: N/A
If this was caught during regression testing, add the test name, ID and link from TestRail: N/A
Email or phone of affected tester (no customers): javascript:
Issue reported by: Applause - Internal Team
Action Performed:

Go to staging.new.expensify.com
Log in with a new account
Go to self DM
Send a few messages
Right click on the self DM in LHN
Click Mark as unread

Expected Result:
Self DM will be bolded in LHN after it is marked as unread
Actual Result:
Self DM is not bolded in LHN after it is marked as unread
Workaround:
Unknown
Platforms:

Which of our officially supported platforms is this issue occurring on?

[ ] Android: Standalone
[ ] Android: HybridApp
[x] Android: mWeb Chrome
[ ] iOS: Standalone
[ ] iOS: HybridApp
[x] iOS: mWeb Safari
[x] MacOS: Chrome / Safari
[x] MacOS: Desktop

Screenshots/Videos

Add any screenshot/video evidence

https://github.com/user-attachments/assets/2ab7faa2-1f6e-4584-a211-96902e97ade5
View all open jobs on GitHub

I have a meeting right now but will look into this right after the meeting

Caused by this: https://github.com/Expensify/App/pull/51212. Tested reverting it locally.

Demoting

Gonna mark this as external since I don't know what PR caused it. @NJ-2020 as part of your proposal can you state what PR caused this regression in the first place?

We have the same issue before here too


Auth0.OidcClient.Tokens.IdTokenValidationException: 'Issuer (iss) claim mismatch in the ID token; expected "https://Domain.com/", found "https://Domain.com".

I tried with the provided sample and it fails with error in mismatching the issuer url . It automatically adds extra "/" in the domain url.
Further check could notice its happening because of the below dll code which i cant change.
protected Auth0ClientBase(Auth0ClientOptions options, string platformName)
{
_options = options;
_idTokenRequirements = new IdTokenRequirements("https://" + _options.Domain + "/", _options.ClientId, options.Leeway, options.MaxAge);
_userAgent = CreateAgentString(platformName);
_idTokenValidator = new IdTokenValidator(options.BackchannelHandler);
}

I have the same issue


Importing a nonexistent module/type using from syntax does not yield any errors

Repro
Run the following code:
from Standard.Base import Something_That_Does_Not_Exist

main = 423

Expected Behaviour
Import resolution should fail and tell me that Something_That_Does_Not_Exist does not exist.
Actual Behaviour
Instead the code runs OK and prints 423 on output.

It's even more suspicious if you run the following code:
from Standard.Base import Something_That_Does_Not_Exist

main =
    Something_That_Does_Not_Exist.do_a_thing_for_me 42

It yields:
In module nonexist:
Compiler encountered errors:
nonexist.enso[4:5-4:33]: The name `Something_That_Does_Not_Exist` could not be found.
Aborting due to 1 errors and 0 warnings.
Execution finished with an error: Compilation aborted due to errors.

So yeah, it does report that the module was not found at usage site. But I can see I have an import that did not fail. Now I'm confused - I successfully imported this module, it should be here. If the module name does not have a weird name, I have no clue that it actually didn't exist instead.
Note that if I'd run the import without the from form:
import Standard.Base.Something_That_Does_Not_Exist

main =
    Something_That_Does_Not_Exist.do_a_thing_for_me 42

Then I get:
In module nonexist:
Compiler encountered errors:
nonexist.enso[1:1-1:50]: The module Standard.Base.Something_That_Does_Not_Exist does not exist.
nonexist.enso[4:5-4:33]: The name `Something_That_Does_Not_Exist` could not be found.
Aborting due to 2 errors and 0 warnings.
Execution finished with an error: Compilation aborted due to errors.

So it correctly points out that it was unable to import the module and now I know why it is later not found.
With from I do not know why it is not found, assuming that as I did not get any import resolution errors, the import must have succeeded.
cc: @hubertp you may be interested in this, as you know the imports resolution well

cc: @hubertp you may be interested in this, as you know the imports resolution well

Yup. I think @hubertp will need to take a look when not occupied with other pressing stuff.

Yes, it's been like that forever.

Shouldn't
from Standard.Base import Something_That_Does_Not_Exist

main = 412

yield a warning? Something Something_That_Does_Not_Exist isn't used`? That would be way simpler check than trying to resolve symbols from other modules...

If the imported module does not exist, there should be a warning about it (explicitly telling that it does not exist). Warning is better than error, as it is less error-prone - more projects will work. If this happens and the graph still works, for the user it give a way more "stable" feeling than crashing with an error. I know this is not how IDEs work, but Enso is not an IDE and we should be as error-prone as possible.


Fix session init - cannot run several times in a row

Quickfix: done, merge the exercises only on the instructions.
More robust approach soon: merge a random seed node in the graph + match exercise length* if there is none and generate random ID on which MERGE is done.
Problem out of scope: pre-existence of some workshop data in the DB.


define "zoom reset" for VSCode

The default value for "zoom reset"  defined in edit_win.py is "ctrl-0".  This does not work in VS Code. The PR  attempts to fix this.

The keyboard shortcut in VS Code is "ctrl-numpad_0". An alternative solution may thus be to change the default keyboard shortcut in edit_win.py.  but that  may run the risk of breaking things elsewhere.


Script List sometimes displays class reference name incorrectly.

Godot version
4.0.dev (b76dfde32)
System information
Windows 10, Vulkan, GTX 1050 mobile 471.11
Issue description
When you click "Search Help" button in Script Editor and select any children of EditorPlugin and then open the same script from FileSystem the class reference on the left changes from full path to file name with a double quote at the end.
E.g.:
"addons/addon_name/main.gd" changes to main.gd"   <--- notice the double quote

Steps to reproduce

Go to Project -> Project Settings -> Plugins -> Create
Give the plugin name, subfolder and main script (e.g. main.gd)
Click "Search Help" and open main.gd (It will be a children of EditorPlugin Node)
Notice that full path of the class refence is shown on the left
Open main.gd script from FileSystem
Now the class reference name is main.gd"

Minimal reproduction project
ScriptDisplayBug.zip

Also the Label showing currently selected item displays path with striped slashes (image 1)

@NeqsTech Can you reproduce this in 3.3.2?

@Calinou I don't think this can be reproduced in 3.3.2. When I click "Search Help" there are no children under "Editor Plugin" node.
I guess documentation generation for user-defined scripts wasn't cherry-picked for 3.3.2-stable or at all.

I guess documentation generation for user-defined scripts wasn't cherry-picked for 3.3.2-stable or at all.

Indeed, this was added by https://github.com/godotengine/godot/pull/41095 which relies on GDScript 2.0.

Doesn't happen in 4.3


Deploy path given to deployPush func gets indeterminately confused by old temp folder

Very low priority bug / very easy to fix for the user but I kept receiving the error that
'src-ba29225b8893dd3a/' does not have a commit checked out
Which I believe to be a temp dir from Obelisk that never got cleaned up. Weird part is that I had another temp directory 'src-355ad1892cc46de4/' that had existed for much longer and has definitely existed for past commits.

Quite possibly https://github.com/obsidiansystems/obelisk/issues/923

If I understand correctly then my bet is the same
I also see more temp directories have been left behind from yesterdays unpacking/ packing


transactionHistory is missing a field identifying DIP15 / Dashpay transactions

sending a dashpay tx makes it show up in the transactionHistory in the sender (but without a field to identify it as a dashpay tx) but it doesn't yet show up in the transactionHistory of the receiver (because that address is not added to the transaction stream).
Most wallets will want to handle dashpay txs differently from normal L1 transaction, separating those histories or at least adding metadata to identify them makes sense. I suggest a method to get only the normal L1 transactions and to get dashpay txs per identityId, and a wildcard to clobber all txs together, e.g. for export

We should get back to that in 2-4 weeks since this work is planned to be finished with the scope of Platform v0.23 - the Team needs bit more time to develop this.

retest failed - issue persists.

@mayoreee as discussed on the weekly triage, please investigate a fix for this.

@mayoreee dev blocked due to Testnet issues

I have no idea what's that but I will keep it for now


How do I tell if IgDiscover has hung?

How long should IgDiscover take to run on ~1M sequences? The display hasn't changed in the 24 hours now. Most recent output:
[Thu Jun  6 10:32:39 2019]
rule 20:
    input: reads/4-trimmed.fastq.gz, stats/trimming-successful
    output: reads/sequences.fasta.gz, stats/groups.json
    jobid: 45

igdiscover dereplicate --trim-g --json=stats/groups.json --minimum-length=300 reads/4-trimmed.fastq.gz | gzip > reads/sequences.fasta.gz
INFO: 1729883 sequences processed
INFO: 1078607 sequences long enough
INFO: 1048469 dereplicated sequences written
INFO: CPU time 00:00:37.4. Maximum memory usage 1.807 GB
[Thu Jun  6 10:33:46 2019]
Finished job 45.
20 of 63 steps (32%) done

[Thu Jun  6 10:33:46 2019]
rule igdiscover_igblast:
    input: reads/sequences.fasta.gz, iteration-01/database/V.fasta, iteration-01/database/D.fasta, iteration-01/database/J.fasta
    output: iteration-01/assigned.tab.gz, iteration-01/stats/assigned.json
    log: iteration-01/igblast.log
    jobid: 52
    wildcards: dir=iteration-01
    threads: 16

time igdiscover igblast --sequence-type=Ig --threads=16 --stats=iteration-01/stats/assigned.json iteration-01/database reads/sequences.fasta.gz | gzip 2>&1 > iteration-01/assigned.tab.gz | tee iteration-01/igblast.log >&2
WARNING: Length 104 of FR3 region in 'IGLV3-ACB*03' is not divisible by three; region info for this gene will not be available
WARNING: Length 104 of FR3 region in 'IGLV3-AAJ*01' is not divisible by three; region info for this gene will not be available

This is not normal. From the output above, it seems IgDiscover is doing the IgBLAST step. Although it is the slowest, it should be finished within a couple of hours for one million sequences, especially if it is using 16 CPU cores.
Also, a progress report should be printed every minute, something like this:
...
INFO: Processed    500,000 sequences at 32.3 ms/sequence

Do you run any other CPU-intense jobs on the machine? You can check your load average by running uptime. If IgDiscover is still running, the last three numbers should be at your number of CPU cores (16) or higher. If the numbers are below 1, it’s probably doing nothing and you should cancel it. Just try igdiscover run again and see if it works this time. I don’t know how, yet, but I can try to help more after the weekend.

I am running on a cluster where I have only reserved one core, though IgDiscover has autodetected that the node has 16 total cores. Could that be causing the issue? Is there a way to tell IgDiscover to restrict itself to N cores even if the machine has more?

Oh ok, that explains it. IgDiscover tries to be smart when it detects how many cores to use, so it should actually take into account how many cores are available vs how many cores the node actually has. It seems that this logic has failed here. You can tell it to use only one core with igdiscover run -j 1.

That indeed fixed it, thanks!

If you have time, could you run these two commands within a batch job for which you reserved only one core:
grep pus_allowed /proc/self/status

and
python3 -c 'import os; print(len(os.sched_getaffinity(0)))'

and send me the output?

schrammca@ai-hpcn021:~$ grep pus_allowed /proc/self/status
Cpus_allowed:	000000,00000000,00000000,0000ffff
Cpus_allowed_list:	0-15
schrammca@ai-hpcn021:~$ python3 -c 'import os; print(len(os.sched_getaffinity(0)))'
16

Also, it turns out that IgDiscover is still hanging after a few tens or hundreds of thousands of sequences. I tried reserving 8 cores and then using -j 6, which may possibly have resulted in the program getting a little farther before hanging, but it still said it had used 6 hrs of CPU time when I killed it 3.5 days later. It also seems to get through more sequences in a light chain sample than heavy chain, but again, I haven't tested that rigorously.

Ok, it seems that your cluster is not using the cpuset mechanism to restrict the number of CPU cores to use. You’ll have to continue to use -j.
Regarding the hangs: Did you now get a progress report (`Processed ... sequences at ... ms/sequence')? Or how did you assess that it got through more sequences?
I need to know at which stage the hang occurs. Is it consistently the igdiscover igblast step? If so, can you SSH into the node and tell how many igblastn subprocess are running when IgDiscover appears to hang? Do they just sit there idle at 0% CPU (they shouldn’t)? igdiscover igblast spawns as many igblastn subprocesses as specified with -j. I could imagine that for some reason the igblastn subprocesses are the ones that hang.
It’s hard for me to debug this remotely without access to the cluster, but I’m guessing it’s either some pecularity of your cluster system (possibly exposing an IgDiscover bug) or something in your data. I don’t know how much time you’re willing to spend on this since you obviously have your own pipeline doing similar things, but to find out which of the two is the problem, you could try to 1) run IgDiscover on a separate machine (a laptop with enough RAM should be fine) and/or 2) run IgDiscover on ERR1760498, which I’m using for testing all the time and which I’m very sure should work.
I can also prepare a new release of IgDiscover to see whether that fixes it, but this is going to take a bit.

Yes, getting the progress messages now. Yesterday it hung on ERR1760498, too. Today, it seems to be working on my sample after all --at least, I've made it to the second iteration... I've gone down now to -j 3 (on a session with 4 cores reserved). I wonder if it's possible that threads are getting into conflict somehow if there are too many of them, regardless of the number of cores I've reserved. In any event, for now I think I've got what I need.

Ok, thanks. A couple of days ago, I got an out of memory error myself that made the igblast step hang, but I hadn’t seen that before nor could I reproduce it afterwards. Anyway, I’ll keep this in mind fo the future.


Replace all org.spine3 occurrences by io.spine

This PR updates package names and advances Spine version to 0.9.16-SNAPSHOT.

@armiol PTAL.

@armiol PTAL.


Radio button bouncing up and down in nexus 5x-6.0.0 API 23

I have debug into RadioButton.js In that file onLayout is calling repetitively . Which is causing issue.
It is togging width from 20 to 19 and then 19 to 20. Which causing bubbling issue.

Having the same issue. This results in a shaky effect on radio button.

I'm seeing this for checkboxes on Nexus 5 and Pixel 2, so I'm not sure it is device-specific. In my case,  the height and width of the <Ripple> component keep increasing/decreasing inside <Checkbox>.

Hy, having the same issue with radio buttons on nexus 5x and 6p.
Any workarounds?

We ended up just using the native Android checkboxes since the issue wasn't present on iOS. Not really a solution but it was good enough for our purposes.
function PlatformSpecificCheckbox({ isChecked, style }) {
  PlatformSpecificCheckbox({ isChecked, style }) {
    return Platform.select({
      ios: (
        <MKCheckbox disabled checked={isChecked} />
      ),
      android: (
        <CheckBox disabled value={isChecked} />
      ),
    });
  }
}

The other approach we considered was forking or copying the the source code for MKCheckbox (here) and removing the  from the render function, which also works but would not be fun to maintain.
I'm not sure if the issue is with the library or if something in our app state is causing the onLayout event to be called repeatedly. Either way, it would be nice to be able to disable the Ripple effect through props!

@xinthink Any update on this issue? The radio button's _onLayout is continuously being triggered.
if (width === this.state.width && height === this.state.height) {
return;
}
is always false and hence setState is always triggered. I was able to fix it by modifying function in the following way
_onLayout = ({ nativeEvent: { layout: { width, height } } }) => {
const padding = this.props.extraRippleRadius || DEFAULT_EXTRA_RIPPLE_RADII;
if (parseInt(width+padding - this.state.width) < 1 && parseInt(height+padding - this.state.height) < 1) {
  return;
}
this.setState({
  width: width + padding,
  height: height + padding,
});

};
I am not sure if this is the way to do it but it works. Let me know. I can open a PR if the above solution is a feasible one.


Update Windows logo to 11 version

Also I think it would be nice to add a start menu icon:
Source

Updated in 608007b99fab1d55be5de9f9ec2c75bcc80a438c
Thanks


Head urdf fix for cob4-8

fixes head urdf configuration on the cob-aalto (cob4-8)

@fmessmer @floweisshardt Do you have any objections merging this? I do not have any.

there is more messed up on the head urdf...see https://github.com/ipa320/cob_common/pull/284
as we currently have the robot for repair anyway, we'll finalize the issue in #795


Allow configurable initial capacity for IndexedTable

One of the bottleneck for combining group-by results is to grow the IndexedTable as we are adding groups. To reduce the re-hashing, we can initialize it with a larger capacity:

The size of IndexedTable won't go over trimThreshold
The size of IndexedTable should at least be able to hold the groups from the first map to be merged
Allow user to config a min capacity by query option or instance config

Release Notes
Min initial indexed table capacity is 128 by default, and can be configured with:

Query option: minInitialIndexedTableCapacity
Server instance config: pinot.server.query.executor.min.init.indexed.table.capacity
Broker instance config: pinot.broker.min.init.indexed.table.capacity

Codecov Report
All modified and coverable lines are covered by tests :white_check_mark:

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integration
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integration2
3
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temurin
12
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java-21
7
1

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3
0

skip-bytebuffers-false
7
1

unittests
5
0

unittests1
2
0

java-11
5
0

unittests2
3
0

integration1
2
0

custom-integration1
2
0

Additional details and impacted files
@@              Coverage Diff              @@
##             master   #14620       +/-   ##
=============================================
- Coverage     61.75%    0.00%   -61.76%
=============================================
  Files          2436        3     -2433
  Lines        133233        6   -133227
  Branches      20636        0    -20636
=============================================
- Hits          82274        0    -82274
+ Misses        44911        6    -44905
+ Partials       6048        0     -6048

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integration
0.00% <ø> (-0.01%)
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0.00% <ø> (ø)

java-11
?

java-21
0.00% <ø> (-61.63%)
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skip-bytebuffers-false
0.00% <ø> (-61.75%)
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0.00% <ø> (-61.76%)
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Dynamic title

See #75

Likely will not merge. UI redesign is being done in #79 and this will be redone. That PR is branched off of this dynamic-title branch, but the work likely won't be kept.


browse feature updates

Coverage remained the same at 27.608% when pulling 5e2e555c0ab795aea31e12942bc07277b443dc36 on theseyi:browse-updates into 981b084c1b19933a92f229f1e5b9cb66bb8f8f4e on linkedin:master.

Codecov Report

Merging #1010 into master will increase coverage by 0.09%.
The diff coverage is 39.47%.

@@            Coverage Diff             @@
##           master    #1010      +/-   ##
==========================================
+ Coverage   29.03%   29.12%   +0.09%
==========================================
  Files         173      174       +1
  Lines        4587     4614      +27
  Branches     1202     1216      +14
==========================================
+ Hits         1332     1344      +12
- Misses       3255     3270      +15

Impacted Files
Coverage Δ

wherehows-web/app/utils/build-url.ts
0% <ø> (ø)

wherehows-web/app/utils/validators/urn.ts
84.21% <ø> (ø)
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wherehows-web/app/components/dataset-compliance.ts
22.22% <ø> (-0.07%)
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wherehows-web/app/utils/api/datasets/shared.ts
27.77% <0%> (-1.64%)
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wherehows-web/app/utils/api/datasets/dataset.ts
80% <100%> (+9.41%)
:arrow_up:

.../components/browser/containers/browser-viewport.ts
21.87% <20.83%> (+11.87%)
:arrow_up:

...pp/utils/encode-decode-uri-component-with-space.ts
66.66% <66.66%> (ø)

...ows-web/app/components/browser/browser-viewport.ts
85.71% <83.33%> (ø)

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Can you add approvers to github?


feature: Adding Typescript block

IMPORTANT: Please do not create a Pull Request without creating an issue first.
Any change needs to be discussed before proceeding. Failure to do so may result in the rejection of the pull request.

Adding Typescript block

What kind of change does this PR introduce?
Possibility to handle Typsecript

Does this PR introduce a breaking change?
No

What needs to be documented once your changes are merged?
The new block

Closing issues
closes #17

@c3dr0x Any comments or remarks ?


option to replace email message body contents

Is there is any option to replace email message body contents ?
 gmail.observe.before('send_message', function (url, body, data, xhr) {
    var body_params = xhr.xhrParams.body_params;
    var body_overwritten = body.replace(/[{(.*?)}]/g,' ');
    body_params.body = body_overwritten ;
 });

this is not works

Personally I've never had the need for this kind of functionality, but I think some people have tried this before, and there have been various suggestions which may or may not work.
Try searching issues, open and closed.

You checking your solution on new Gmail UI? If yes, then it's doesn't working, because new gmail data layer doesn't have a body field. Instead we see a protobuf spaghetti, which must be disassembled :(

using old Gmail UI
 gmail.observe.before('send_message', function (url, body, data, xhr) {
    var body_params = xhr.xhrParams.body_params;
    var oldCmml = xhr.xhrParams.url.cmml;
    var string = 'body_overwritten_message';

        if (string.length > oldCmml) {
            xhr.xhrParams.url.cmml = string.length;
        } else {
            string += '<div>';
            while(string.length<oldCmml){
                string += ' ';
            }
            string += '</div>';
            xhr.xhrParams.url.cmml = string.length;
        }

        body_params.body = string;
 });


Warning when importing via webpack

I'm getting this warning for a while in my project:
client:148 ./node_modules/comparators/dist/comparators.js 3:24-31
Critical dependency: require function is used in a way in which dependencies cannot be statically extracted

I love your lib a lot, it helps me to write way prettier code. Is there any reason or fix for this message?
I'm importing via webpack, babel and npm :)

Hi @luanpotter! Sorry it took me so long to get back to this -- for some reason, I don't get notified by Github about issues. I probably need to fix my notification settings somewhere.
I'll take a look when I get a chance to see if I can clean this up.
Glad you like this lib, and thanks for using it!

For an update here: I'm still looking into the best route here. That warning appears because this library is distributed as a "UMD" module (one that works "isometrically", of sorts, in "module-less" browser, AMD, and CommonJS environments without requiring separate versions of the file. The "wrapper" that is generated around a UMD module looks for the existence of a "require" function, and uses it if it exists, which is why webpack/babel are complaining.
As such, making that warning go away is a bit more involved of a fix, as it requires coming up with a different strategy for distributing this library. I'm still trying to figure out what the best approach is. Theoretically, ES6 modules are "the standard", but in practice, they don't work out-of-the-box with Node.js (unless you enable a command-line flag), so that option seems like a regression for nodejs users. I don't want to require people (pun intended) to install multiple dependencies to use this smallish library, so I'd like to avoid a route where I just go with ES6 and tell users to set up babel.
In your setup, is there a way you can set up your build pipeline to recognize a UMD module? If so, I may add that to the documentation of this module so that others who see the same warning can resolve it.

@luanpotter Version 3.0.1 is published now; in it, you'll find a purely-Commonjs format that should make Webpack happy, and a UMD format that can be used pretty much anywhere. I'm going to go ahead and close this issue, as the problem should be resolved now, but if you run into more problems, feel free to reopen it.

Thanks, I'll update right away!


Mac app does not open

Downloaded from https://scourhead.com/.

Hi there, thanks for letting me know. Looks like I need to get the app notarized by Apple, which I submitted a few days ago but unfortunately got stuck in their queue and hasn't processed yet.
I have an open support ticket and dev forum post on the topic: https://developer.apple.com/forums/thread/771580
I'll keep this issue open until the support ticket is resolved so folks can be kept up to date.
If you're up for it, running the build in development mode will work around this. Instructions are in the repo readme


Customize the baseUrl for debrid service?

Is there a way to customize the baseUrl of a debrid service? If not, I can open a PR to contribute the changes necessary if you're open to it.

This is not a local addon, so I dont see a use case where this would be needed. If some debrid url changes then most likely it will need code changes as well, and having just changing url is very niche and obscure setting.

This would've been useful if somebody sets up a reverse proxy for debrid service.


[Master ticket] [QA wait for #3318] Implement mechanism for making error objects serializable and refactor user module

Problem
ngrx8 introduced some strict runtime checks, such as strictStateImmutability, strictActionImmutability, strictStateSerializability and strictActionSerializability.
In #2813 we enabled all of them expect the strictActionSerializability.
strictActionSerializability flag checks whether the action is serializable. Currently, almost every *FailAction is NOT serializable because it takes an http error object which is not serializable (i.e. contains Map).
To solve this, we can create a utility function makeSerializable<T>(obj: T): T that will convert the non-serializable object into a serializable one.
The implementation is yet to be decided. It can be something as simple as using JSON.stringify and JSON.parse, or a completely custom one.
This ticket will require changing a lot of files. While we are at it, we should take care of all occurences of error.json().
Other tickets
In this ticket user module should be refactored. For the rest see these tickets:

[x] auth - #3260
[x] cart - #3262
[x] checkout - #3263
[x] cms - #3264
[x] global-messages - #3265
[x] kyma - #3270
[x] product - #3266
[x] routing - #3267
[x] site-context - #3268
[x] store-finder - #3269

QA
We can QA all the tickets when all the work is done. Since this is just a refactor, the goal is that app should look and feel as before.

To QA:
We can QA all the tickets when all the work is done. Since this is just a refactor, the goal is that app should look and feel as before.

Tested on dev2. Haven't seen anything broken so far.
I did notice that the product carousels on homepage have disappeared. Maybe not related to this ticket? Will need to confirm.
Will do a few more tests...

Updated dev2 again today. Carousels are back. Everything looks ok.