AngularJS served from S3 bucket

Hello,
Wondering how to use the service in that instance? My backend server is rails, but only serves json to the angular app running on S3.
Thanks.

Did anything change from the last comment? I was looking to migrate the app to the S3, but does not want to lose prerender.

Would the following help?  CloudFlare seems to provide the conditional logic for url forwarding. Haven't tested it yet, just a brainstorm. cc: @thoop @aeldaly

Hmm, I don't think that would work because it looks like it would send a 301 redirect. You want the proxy to be invisible to the crawlers. Also, this wouldn't detect facebook, twitter, baidu, linkedin, etc since they don't follow the escaped fragment protocol.
The suggestion I still give is to use nginx in front of S3 until the day comes where they will allow you to proxy using rules that you determine :(

Ok, got it. Thanks for bringing up these points.

Okay I have a suggestion...
How about we put the index.html (the main angular file, whatever you may call it) on the nginx/apache server but all the resources are reffered from the s3 bucket. We still serve the templates/js/css/images/what-have-you from the s3 bucket, but we can apply the routing logic too.
I'm facing a similar problem so will update if it works.

It doesn't really matter where the resources live. You just need to have a server in front of the S3 bucket to do the Prerender check first.

Google has officially deprecated the escaped fragment protocol since it's bots understands your SPA anyway: https://webmasters.googleblog.com/2015/10/deprecating-our-ajax-crawling-scheme.html

@motin That's a good resource to post but it's not just Google. If you want link shares from your site to show up properly on platforms like Facebook, Twitter, LinkedIn and if you care about Bing then you still need to prerender.

@motin That's a good resource to post but it's not just Google. If you want link shares from your site to show up properly on platforms like ..

Facebook, Twitter, LinkedIn

True

if you care about Bing then you still need to prerender.

Bing also supports escaped fragment, does it mean that @websirnik's solution works for Bing?
That is, in total for statis sites served on static hosting with Cloudflare in front, it would potentially work with at least Google and Bing?

http://searchengineland.com/can-now-trust-google-crawl-ajax-sites-235267
Google still supports the escaped fragment crawling protocol just as they did before that announcement. Make sure to test your site with Google crawling the javascript because we've seen that they really slow down their crawl speed when they are executing the javascript. If you have a medium/large website then we recommend using prerender to make sure Google can crawl through your pages quickly and get everything in their index.
You don't want a send a 301 redirect so the cloudflare solution is not recommended. It needs to be a proxy to the prerender server.

It's been about a year since this issue was last addressed.  Any updates on whether this will be a possibility in the near future?

Is there any new solution for the issue since the last comment?

Ended up going this route: https://medium.com/@damwhitaker/using-aws-ec2-nginx-and-prerender-io-as-a-proxy-for-a-single-page-app-2c3769689060

@damwhit Definitely going to try this. looks pretty straightforward solution. Will let you know the results.

@damwhit It did not work for me. Any chance we can connect?

Any solution from prerender since the last prerender-team comment?

@ayushguptawingify sure.
-David
On Thu, Jun 22, 2017 at 9:35 AM, ayushguptawingify<EMAIL_ADDRESS>
wrote:

@damwhit https://github.com/damwhit<EMAIL_ADDRESS>—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/prerender/prerender/issues/93#issuecomment-310417427,
or mute the thread
https://github.com/notifications/unsubscribe-auth/AMf5qSXy7BfU0FBh5f_Y_1QS8zBJGpKfks5sGonegaJpZM4CCRqv
.

For using Prerender with an S3 website, AWS is rolling our Lambda@Edge which would allow you to run a version of the prerender-node middleware at the CloudFront edge locations in order to test if the request should be proxied to Prerender.io. Last I heard, you had to request to opt into Lambda@Edge but it looks like that would be a great solution going forward!

allow you to run a version of the prerender-node middleware at the CloudFront edge locations in order to test if the request should be proxied to Prerender.io

We were trying to do exactly that. Unfortunately it look like the execution duration of lambda on edge functions is limited to 50ms, after which the request will timeout.
We contacted Amazon support about increasing the timeout for Lambda@Edge:

Robert here from AWS Premium Support, thanks for getting back in touch with us. I've received a response from the Lambda@Edge team this morning regarding your request to increase the timeout on your Lambda@Edge functions. I'm sorry for the delay in the Lambda@Edge team's response, they are under heavy development load at the minute as it's a very new product. I understand that this issue must be frustrating for you. You've said that increasing this timeout is important to you, is this blocking some new feature development?
The team have reported that it is not going to be feasible to raise the timeout limit during the limited preview phase of Lambda@Edge. But they have expressed that this is definitely something which they would like to support when Lambda@Edge when the services is made generally available for all AWS customers. They have asked if we could have some more information regarding your use case. Do you think you could give us an overview of how you intend to use Lambda@Edge and why the timeout needs to be extended? This will help them to develop and provide support for your use case going forward. I may also be able to suggest some workarounds which you can use for the moment until the limit can be increased.

We were then looking into something like this:

But getting a 404 the first time you do a request doesn't really work for us. So we'll probably try to prerender every page of our apps ahead of time and make sure those are cached on S3. Then lambda on edge can forward any bot requests to those cached files.

Thanks for the ideas, I recently had to get prerender.io working with cloudfront and made an example of how to "modify the origin of the request to point to service.prerender.io and add the original URL to the end of the URL" over here:
https://github.com/jinty/prerender-cloudfront/blob/master/prerender-cloudfront.yaml

@jinty hey was looking at your implementation but i'm confused with the steps, where do i need to add that file exactly ?

@jinty
Your solution worked.
You need to make a tiny change though... (imo)
if (user_agent && host) {
      if (/baiduspider|Facebot|facebookexternalhit|twitterbot|rogerbot|linkedinbot|embedly|quora link preview|showyoubot|outbrain|pinterest|slackbot|vkShare|W3C_Validator/i.test(user_agent[0].value)) {
       // ... other lines
      }
    }

/i you need the i - for case insensitive.

some bots are lowercase for instance... and I think listing all cases would be too much.
anyway I added the i and boom worked like a charm!

@marlonmantilla
This template goes into AWS CloudFormation

go to AWS cloud formation
click create stack
upload the yaml file
go through the simple form (at some point it will ask you for origin domain and prerender io token)
then it creates 2 lambda functions and a cloudfront distribution for you. The cloudfront distribution uses the lambda functions ad event triggers (see comment above for slight change you might need to make)
you actually don't need that cloudfront distribution if you already have one... just add the events (similar to how it was added in the new cloudfront distribution)
you are good to go
if you do make the function change as I stated above... you will need to publish a new version and append the version to the arn in the cloudfrontdistribution event. (heads up: it has something like :1 at the end...just change the digit to the new version)

Thanks @jinty for this... saved me having to rewrite my entire app just to prerender (at least for now)

@KenYinkz I have tried this, but have not been able to get it to work. Is there any configuration to do in cloudfront?

@KenYinkz I am having trouble with this solution. The cloudformation file creates an origin, by default, but it does not include my S3 bucket origin, so I have added that seperately. But when I go to my site I get a warning.
ERROR
The request could not be satisfied.
CloudFront wasn't able to connect to the origin.
Generated by cloudfront (CloudFront)
Request ID: YPwcVhHrsb-KjcoEiwvQIjFGLZFgVGUkJCc9AvLlmI_W6yaK991OUQ==

Any ideas why that might be? Any help would be greatly appreciated.

@danielptm
The tricky part here is I had a separate cloudfront already which connected to my S3.

Upon adding the new one (cloudformation created a new one for me, just like you) , all I had to do was create the events (the Viewer Request and Origin Request ) in my existing cloudfront and added the appropriate ARN ids to them.
You can do this by editing the cloudfront behaviour
Make sure to set your origin of the new one to the domain of you site (e.g. example.com)

PS:

You can test the lambda functions with some default test files AWS has
I think (cloudfront) caching might affect you seeing results immediately (I had to wait 3 hours to see the right result....not sure why)
You can also add some console.log("blah")' to your lambda functions... I added some logging to verify the user_agent` and pinged my site using Slack

@KenYinkz Thanks, so you basically have 2 cloudfront distributions then? One that talks with prerender and the other for your S3 site?

@KenYinkz I assume you mean the ARN of the generated lambda functions. Which lambda is associated with Viewer Request and which one Origin request? I would just try, but because it takes so long, I want to make sure I do it right.

@danielptm
Did you only add the View request and origin request and associated lambda functions or did you change the other settings in the original CF to match the new CF as well.

I just added the requests.

I just added the requests to. I just copy and pasted  the arn form the new CF and put into my old CF for my S3 with a new View Request and a new Origin Request. It also wouldnt let me add the behaviors without adding a path pattern. I just set that to *. But its still not working so just wanted to clarify any other details that I might have missed.

Path Pattern for mine is Default(*)
I did invaidate my CF... and waited for a while before it started working.

@KenYinkz Thanks I got it to work. I made a mistake in the code which was creating the wrong og:url link which was causing it not to work. Thanks for the help!

Awesome!
@danielptm

@jinty
I was looking into this some and had a question...does this already (or is there a way to) change the cache key so that prerendered pages don't get put into the cloudfront cache and subsequently get served to a user instead of a crawler? The prerendered pages should only get served to a crawler so they either shouldn't be cached at cloudfront or cached under a different cache key.

Here are the lambda functions that is created by cloud formation.
//Daniel

On Feb 19, 2018, at 7:42 PM, Todd Hooper<EMAIL_ADDRESS>wrote:
@jinty https://github.com/jinty
I was looking into this some and had a question...does this already (or is there a way to) change the cache key so that prerendered pages don't get put into the cloudfront cache and subsequently get served to a user instead of a crawler? The prerendered pages should only get served to a crawler so they either shouldn't be cached at cloudfront or cached under a different cache key.
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub https://github.com/prerender/prerender/issues/93#issuecomment-366774910, or mute the thread https://github.com/notifications/unsubscribe-auth/AKnoyzuQ_38u05n8Z7PJMxN9dyJOsnuGks5tWcCsgaJpZM4CCRqv.

**********************One lambda function
'use strict';
/* change the version number below whenever this code is modified /
exports.handler = (event, context, callback) => {
const request = event.Records[0].cf.request;
console.log('****************** Redirecting to prerender //Daniel');
if (request.headers['x-prerender-token'] && request.headers['x-prerender-host']) {
request.origin = {
custom: {
domainName: 'service.prerender.io',
port: 443,
protocol: 'https',
readTimeout: 20,
keepaliveTimeout: 5,
customHeaders: {},
sslProtocols: ['TLSv1', 'TLSv1.1'],
path: '/https%3A%2F%2F' + request.headers['x-prerender-host'][0].value
}
};
}
callback(null, request);
};
**********************Second lambda function
'use strict';
/* change the version number below whenever this code is modified */
exports.handler = (event, context, callback) => {
const request = event.Records[0].cf.request;
const headers = request.headers;
const user_agent = headers['user-agent'];
const host = headers['host'];
if (user_agent && host) {
if (/baiduspider|Facebot|facebookexternalhit|twitterbot|rogerbot|linkedinbot|embedly|quora link preview|showyoubot|outbrain|pinterest|slackbot|vkShare|W3C_Validator/.test(user_agent[0].value)) {
headers['x-prerender-token'] = [{ key: 'X-Prerender-Token', value: 'VYHWvDB00eYWvrxcJ90w'}];
headers['x-prerender-host'] = [{ key: 'X-Prerender-Host', value: host[0].value}];
}
}
callback(null, request);
};

@KenYinkz for this: Make sure to set your origin of the new one to the domain of your site (e.g. example.com) ... i have added Lambda Function Associations (Viewer/Origin Request) to my old CF, but the origin of that one is the S3 bucket do i need to change that ?

@marlonmantilla  No. Leave the existing CF origin as it is. It sometimes takes a few hours or so to reflect.

On Sat, Feb 17, 2018 at 08:10:38PM +0000, Daniel wrote:

@KenYinkz I am having trouble with this solution. The cloudformation file creates an origin, by default, but it does not include my S3 bucket origin, so I have added that seperately. But when I go to my site I get a warning.
ERROR
The request could not be satisfied.
CloudFront wasn't able to connect to the origin.
Generated by cloudfront (CloudFront)
Request ID: YPwcVhHrsb-KjcoEiwvQIjFGLZFgVGUkJCc9AvLlmI_W6yaK991OUQ==

@danielptm I meant this repository as an example where others could
build easily and extract some of the code from. Particularly I found
that not all origins are created equal and that different settings will
be required for each one.
I had the same error as you with the current settings when trying a few
different origins.  CloudFront doesn't make it easy to figure out what
the root cause is.
Hmm, I suppose I could change the example so that it is specific for an
SPA served from an S3 bucket. I'll try find the time to do that.
--
Brian Sutherland

On Mon, Feb 19, 2018 at 06:42:54PM +0000, Todd Hooper wrote:

@jinty
I was looking into this some and had a question...does this already (or is there a way to) change the cache key so that prerendered pages don't get put into the cloudfront cache and subsequently get served to a user instead of a crawler? The prerendered pages should only get served to a crawler so they either shouldn't be cached at cloudfront or cached under a different cache key.

@thoop Ah, yes, that shouldn't be too hard.  I've made an issue and will
have a look at it as I have the time:
https://github.com/jinty/prerender-cloudfront/issues/2

If this is a behaviour you really don't want, it might be better for you
to specify a Cache-Control header directly from prerender.io?
--
Brian Sutherland

Prerender.io tries to return the exact headers that the domain returns without modifying them, so ideally this would be handled by the Lambda function if it's possible.

On Wed, Feb 21, 2018 at 12:33:23PM -0800, Todd Hooper wrote:

Prerender.io tries to return the exact headers that the domain returns without modifying them, so ideally this would be handled by the Lambda function if it's possible.

Not sure I entirely agree, but thankfully not y decision. I updated the
example with a cachebusting header which avoids the Cloudfront cache for
prerender.io destined requests.
I have also added a simple SPA and expanded the README to make the
example more self-contained.
see https://github.com/jinty/prerender-cloudfront
I am still doubting whether to use case-insensitive regexes...
--
Brian Sutherland


Errors on non standard node installs like nvm

script/server: line 9: /usr/local/bin/forever: No such file or directory after a bootstrap because not everyone's node install and binaries live at /usr/local/bin/.
The simplest fix for this is to call forever in the shell scripts with $(which forever). I changed it locally, and output works with this fix.

I am getting this same error even tho see forever in usr/local/bin


[BUG]: Fetch failed error for a PDF document loaded on workspace

How are you running AnythingLLM?
AnythingLLM desktop app
What happened?
Hello, I obtain a Fetch failed error after I loaded a PDF document to a workspace.

The error log is showing nothing  related , Is this the correct place to read the logs ?

Are there known steps to reproduce?
I'm using Linux mint Cinnamom and the desktop app. Im using ollama on the same machine (slow but it works for normal chat) and the model is llama3:8b-instruct-q8_0
To reproduce I simply created a workspace, loaded a pdf file to workpace and started the agent...
After I asked something related to the pdf I obtain the error above.

Can you send a basic non-agent chat on a workspace? or does that not work as well?

Hi,
I am experiencing a similar issue. I'm using Ubuntu Server 22.04, and while the chat function works well with various LLMs (like Mistral, Llama, etc.), I encounter an error when uploading documents to the workspace—specifically, I receive a "fetch failed" error. Although I can upload and organize documents in the "My Documents" section without any issues, the problem arises when I try to upload them to the workspace. I would greatly appreciate your assistance in resolving this issue.

Hi,
The default embedding template for anythingLLM didn't seem to work for me. I installed a different embedding template from Ollama, updated the configuration in anythingLLM, and this resolved the issue. I hope this information helps anyone facing similar problems.


entgql: Non-string enum types produce code that does not compile

entgql treatment of enums assumes all enum GoTypes are strings. This results in generated ent code that does not compile.

[ ] The issue is present in the latest release.
[x] I have searched the issues of this repository and believe that this is not a duplicate.

Current Behavior 😯
An enum with a non-string GoType results in generated ent code that creates the enum using an empty string rather than the enum's type. The compilation failure occurs in the graphql.Marshaler check, where the enum is created using an empty string to assign back to the graphql.Marshaler.
Expected Behavior 🤔
The generated code for an enum always compiles.
Steps to Reproduce 🕹
Given an enum like
type IntEnum int

var (
  UnknownIntEnum IntEnum = iota
  ValidIntEnum
)

// Implement ValueScanner methods for enum...

and a schema like
type FooSchema struct {
  ent.Schema
}

func (FooSchema) Fields() []ent.Field {
  return []ent.Field{
    field.Enum("int_enum").
      GoType(IntEnum(UnknownIntEnum)),
  }
}

the code generated from entgql fails to compile, with error on line with the graphql.Marshaler interface assertion:
 _ graphql.Marshaler = IntEnum("")    // Fails to compile because IntEnum is not a string!

Your Environment 🌎

Tech
Version

Go
1.17.2

entgo.io/contrib
v0.2.1-0.20220428181328-4512fb39812e

Database
MySQL

Driver
https://github.com/go-sql-driver/mysql

Noteworthy that the interface assertion for graphql.Unmarshaler works because it is asserting the pointer type is valid, which does not require creating the type - e.g.
_ graphql.Unmarshaler = (*schema.IntEnum)(nil)
```.

A possible solution for the `graphql.Marshaler` interface assertion is to change to assert the same pointer type satisfies the interface. This seems like it might be a better solution than the existing implementation, anyway, to allow for the pointer type to implement the `MarshalGQL` method instead of only allowing the value type to do so. I'm not sure if there's some inherent restriction in gqlgen that the implementing type must be the value type, though.


hubble: Hubble metrics server conflicts with cilium metrics

It seems like it is currently not possible to enable both the Cilium and the embeded Hubble metrics server. When using the helm option global.prometheus.enabled=true together with global.hubble.metricsServer=":19999", cilium-agent panics due to some conflict with the /metrics endpoint:
level=info msg="Starting Hubble Metrics server" address=":19999" metrics="[dns:query;ignoreAAAA drop tcp flow port-distribution icmp http]" subsys=hubble
time="2020-04-20T13:55:36Z" level=info msg="Configured metrics plugin" name=icmp status=
time="2020-04-20T13:55:36Z" level=info msg="Configured metrics plugin" name=http status=
time="2020-04-20T13:55:36Z" level=info msg="Configured metrics plugin" name=dns status="query,ignoreAAAA,"
time="2020-04-20T13:55:36Z" level=info msg="Configured metrics plugin" name=drop status=
time="2020-04-20T13:55:36Z" level=info msg="Configured metrics plugin" name=tcp status=
time="2020-04-20T13:55:36Z" level=info msg="Configured metrics plugin" name=flow status=
time="2020-04-20T13:55:36Z" level=info msg="Configured metrics plugin" name=port-distribution status=
level=info msg="Beginning to read perf buffer" startTime="2020-04-20 13:55:36.509912077 +0000 UTC m=+9.873313357" subsys=monitor-agent
level=info msg="Starting gRPC server on listener" listener="unix:///var/run/cilium/hubble.sock" subsys=hubble
level=info msg="Starting gRPC server on listener" listener="<IP_ADDRESS>:50051" subsys=hubble
panic: http: multiple registrations for /metrics

goroutine 569 [running]:
net/http.(*ServeMux).Handle(0x39e71a0, 0x22c2ba7, 0x8, 0x26c7b20, 0xc0001fa3f0)
	/usr/local/go/src/net/http/server.go:2403 +0x2b6
net/http.Handle(...)
	/usr/local/go/src/net/http/server.go:2446
github.com/cilium/cilium/pkg/hubble/metrics.Init.func1(0xc00049c720, 0xc0004f4620, 0x6)
	/go/src/github.com/cilium/cilium/pkg/hubble/metrics/metrics.go:59 +0xa6
created by github.com/cilium/cilium/pkg/hubble/metrics.Init
	/go/src/github.com/cilium/cilium/pkg/hubble/metrics/metrics.go:58 +0xd6

Not entirely sure why it conflicts, since I would expect the two metrics servers to be served on distinct ports.

Thanks for creating this issue. Will monitor it.


Update long_read_tools_master.csv

miniasm citation fixed
The following instructions are for pull requests related to tool entries.
If your pull request is about something else they can be ignored.
Please describe your pull request below and fill out the check list:
Add your description here:
Please check whether you could check following boxes. Else it will break the build of the database!

[ ] Only (manually) edited long_read_tools_master.csv
[ ] Tool/pipeline names were added using only "[a-z],{a-}, [0-9], _, -" characters (e.g. no spaces, slashes or tabs
[ ] Add relevant multiple publications separated by ;
[ ] Add "NOT-MAINTAINED:: " or "DEPRECIATED:: " to the beginning of the description column of long_read_tools_master.csv
[ ] Completed all columns that needs logical values(i.e. TRUE, FALSE)
[ ] Have at least one functional category marked as TRUE per tool
[ ] Add multiple Programming_Language separated by commas
[ ] Check the link of the Source you are noting points to the root of the repository only
[ ] Either have peer-reviewed journal DOI or preprint DOI. Leave reference as blank for unpublished tools
[ ] Run build_lrs_db.R (optional)

Thanks @QGouil ....
This correction is now applied outside the pull request! :)

Thanks @QGouil ....
This correction is now applied outside the pull request! :)


Non-reactive monthsOfYear with daysOfWeek

I observe strange behaviour in case daysOfWeek and monthsOfYear both are dynamic: only monthsOfYear reacts on change.
<Datepicker
   weekStart={app_state.dateLocale === 'en' ? 0 : 1}
   monthsOfYear={Calendar[app_state.dateLocale].monthsOfYear}
   daysOfWeek={Calendar[app_state.dateLocale].daysOfWeek}/>

Calendar is just a const which contains localised arrays, arrays are correct. The component receives initial locale and updates both months and days (and weekStart, btw), but when locale changes - only months update correct, days (and weekStart) still use initial values.
If wrap the component in some dynamic code which will hide it and re-render on locale changes - everything works fine.

Localization has been overhauled in the latest release of svelte-calendar (v3.x).  Please check out the localization example on this page.  Localization is still not reactive but I have called this out more clearly in the documentation.  Do you think there's a realistic need to change locales for an already-initialized calendar?


[Cherry-pick-2.1] [BugFix] Fix bug of master exit wrong when adding follower

Set the BDB-JE electable group size to (the_total_number_of_followers - the_number_of_adding_followers). After the follower is joined successfully, reset the electable group size to the_total_number_of_followers.

run starrocks_fe_unittest

run starrocks_fe_unittest


About page - content

Prepare content for the About page for the Project Catalogue.
(finish up the user story)

I am pasting here the list @mshadbolt made about the source of the information for the Catalogue, as this will probably be a source for the content on this page.
======
Wanted to note down currently where publications have come from:

Anything in the official HCA publications list https://www.humancellatlas.org/publications/
Anything that has been wrangled, awaiting export but project info can be public
Anything that has been wrangled and is currently in the HCA Portal/Browser (DCP)
Any primary data publications that were used in any of the integrative analysis papers in HCA publications
Any datasets identified as suitable by wranglers and in the backlog of datasets to wrangle, potential sources being:

Valentine single cell database - https://www.nxn.se/single-cell-studies
GEO
ArrayExpress
Single Cell Expression Atlas
incidental discovery of a paper with suitable data by any other means
Any datasets with a funding connection to the HCA
WSSS
MRC Developmental Cell Atlas
Organoid H2020 project
CZI seed networks
CZI biological networks
covidcellatlas papers https://www.covid19cellatlas.org/

I am pasting here the list @mshadbolt made about the source of the information for the Catalogue, as this will probably be a source for the content on this page.
======
Wanted to note down currently where publications have come from:

Anything in the official HCA publications list https://www.humancellatlas.org/publications/
Anything that has been wrangled, awaiting export but project info can be public
Anything that has been wrangled and is currently in the HCA Portal/Browser (DCP)
Any primary data publications that were used in any of the integrative analysis papers in HCA publications
Any datasets identified as suitable by wranglers and in the backlog of datasets to wrangle, potential sources being:

Valentine single cell database - https://www.nxn.se/single-cell-studies
GEO
ArrayExpress
Single Cell Expression Atlas
incidental discovery of a paper with suitable data by any other means
Any datasets with a funding connection to the HCA
WSSS
MRC Developmental Cell Atlas
Organoid H2020 project
CZI seed networks
CZI biological networks
covidcellatlas papers https://www.covid19cellatlas.org/

HI, @mshadbolt, @lauraclarke, @tburdett
I am pasting here my first idea about the copy on this page, it's in the layout, but the copy is here, and is open for feedback.
I have made a point of the different things we might want to say to potential contributors...
https://docs.google.com/document/d/1ih-nf4zPnyreugr7K6bbLwEX4vKAEn5iqrqq7FsdUGE/edit?usp=sharing

Gabs

@gabsie is this ticket being Open means the content of the About page still requires work?

hi, @amnonkhen and @jacobwindsor
For now, there's just a short block on the Criteria section. What I suggest is that we remove for now the Criteria paragraph (I am asking my participants anyway on their opinions on that), and we publish this on prod.
I expect to go back and just add that paragraph shortly..
Gabs

@gabsie sounds good. Is that something that can be done today?

I think please go ahead and publish on prod, yeah!


Simplify Api::LogEntriesController#index action

Previously, we were returning differently formatted JSON data, depending on whether the request was for the log entries of a single log or the log entries of all of the current user's logs.
This change simplifies the controller action by always returning the log entries data in the same format, regardless of whether we are returning the logs entries of one log or many logs.
This basically just moves the complexity from the backend to the frontend... but that feels slightly better. This complexity sort of feels like something that the frontend should manage.

I think that this change probably entails a performance penalty, for at least two reasons:

we are now doing some extra work on the client side that we weren't doing before
the response payload when requesting all logs will be larger

I don't really care, though. I'm guessing that the performance penalty is negligible. Additionally, this scenario happens "in the background", anyway, basically proactively cacheing all of the user's log data locally before they need it, so performance isn't a major concern (unless the slowdown is significant enough that the cacheing now doesn't finish before the user needs the data, i.e. before the user views their first log or a different log than the initial log).


version v1.11.2 failed to build on docker hub

https://hub.docker.com/r/boot2docker/boot2docker/builds/b6jswrmusnnqwbvkwnrbp7k/
latest is still only v1.11.1

this has been fixed now.


Add addAllIf method to Map<K, V>

What about adding a new addAllIf method to the Map<K, V> class?
Its signature could be something like:
void addAllIf(bool test(), Map<K, V> other);

This could be useful for example when we have a function that expects a Map because we could use the the cascade notation on the argument itself without having to store the map in a temporary variable.
void doSomethingWithTheMap(Map<String, dynamic> m) {
  // Do something with m...
}

final bool anyCondition = true;

So we could use this:
doSomethingWithTheMap({ 'a': 'abc', 'b': 15 }..addAllIf(() => anyCondition, {'c': 10}));

instead of this:
final Map<String, dynamic> m = { 'a': 'abc', 'b': 15 };
if (anyCondition) m['c'] =  10;
doSomethingWithTheMap(m);

Well, at the end it is just syntactic sugar. Not really sure if it is worth it.
Currently I'm using an extension in order to accomplish that:
extension AddAllIf<K,V> on Map<K,V> {
  void addAllIf(bool test(), Map<K,V> other) {
    if (test()) this.addAll(other);
  }
}

Anyway, looking forward to getting your opinion on this.

You might consider the following:
Adding an empty map:
doSomethingWithTheMap({ 'a': 'abc', 'b': 15 }..addAll(anyCondition ? {'c': 10} : {})

Constructing the map with conditional elements:
doSomethingWithTheMap(
  { 'a': 'abc',
    'b': 15,
    if (anyCondition) 'c': 10
  });

The second one is described here and here.

Perfect, these alternatives are great. Thanks for your suggestion @rakudrama!


Missing image for a Tabs example

Description
The Naruto image link is invalid as shown below.
Page: https://chakra-ui.com/docs/components/tabs#make-a-tab-initially-active

Fixed!


Not getting all of the tiles when iterating?

Testing this on a hex grid with 5 tiles placed. From (0,0) to (4,0). Left most tile you see is at (0,0)

I'm want to iterate through the tiles placed on the map and note down their positions. When I try:
    if let TileLayer::Infinite(layer) = map.get_layer(0).unwrap().as_tile_layer().unwrap() {
        for chunk in layer.chunks() {
            println!("{:?}", chunk);
            println!("#################")
        }
    }

I got only 1 chunk with width: 2 and height: 2 positioned at (0,0). Where are the rest of the tiles? A more general question is what's the easiest way to iterate through all of the tiles on an infinite layer?

I got only 1 chunk with width: 2 and height: 2 positioned at (0,0). Where are the rest of the tiles? A more general question is what's the easiest way to iterate through all of the tiles on an infinite layer?

Hmm, chunks actually don't have an individual width and height, so I'm not sure which width and height you're referring to there? Since chunks are currently always 16x16, it is at least expected that for that map there is only a single chunk.
The documentation for InfiniteTileLayer::chunks provides an example showing how to iterate the tiles in a chunk.

I want to load a tmx map async. What would be the easiest way to do that? an async reader?

Since the crate has no async support (it'd require an entire rewrite of the interface) the best option is to either block or load the map on another thread and then send it over via a channel or some other send  mechanism.

@feelingsonice I guess we can close this issue now, but I'm still curious, where did you see the "width: 2 and height: 2" reported in the original question?

I think it was referring to the width and height in that screenshot.

Hmm, yes, that looks quite confusing. Since the map is marked as Infinite, the map's Width and Height properties are meaningless / not actually used. Would be nice to reflect this better in Tiled's UI.


Scheduling directives with an "after" variant should have a "before" variant, too

Scheduling directives with an "after" variant should have a "before" variant, too.
IIRC @yamaguchi1024 was telling me about some weird case where we need to manually write a pass in the starting code to schedule after it... we could also just schedule before the next statement.
We should also have a pattern for inserting into the very beginning and very end of the function.

Yup. Another possibility is to rethink the pointing mechanism altogether to better convey before between and after uniformly.

On Nov 15, 2021, at 11:11 AM, Alex Reinking @.***> wrote:

Scheduling directives with an "after" variant should have a "before" variant, too.
IIRC @yamaguchi1024 was telling me about some weird case where we need to manually write a pass in the starting code to schedule after it... we could also just schedule before the next statement.
We should also have a pattern for inserting into the very beginning and very end of the function.
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[Proposal] Restructuring repository

I propose to align the repository/solution to the following structure:
\
  Fido2.sln
  Directory.Build.props     (Common for all projects)
  \src
    Directory.Build.props   (Common for all src projects)
    \Fido2.csproj
    \Fido2.AspNetCore. ...
    \...
  \test
    Directory.Build.props   (Common for all test projects)
    \Fido2.Tests
    \Fido2.IntegrationTests
    \…

The reason why I propose it, is to help new developers that are used to other dotnet projects to get into the work (e.g. aspnetcore). A benefit from the build perspective is the MSBuild built-in extensibility hook that could be effectively used. Sure, this is also a matter of taste, rather than functionality.
What do you think?

Makes sense, and we probably should have done this a long time ago.  I have been much more focused on passing conformance tests than external consumability.

@aseigler If this is a "yes, do it" - then I would propose a PR accordingly :)

I will defer to @abergs as this is really outside of my area of expertise.

LGTM.
However Demo should probably not be in src. In way Demo should be moved out from the library BUT it makes conformance testing a lot more tedious and harder, so i'm against it. But let's not place it in src.

@abergs Could you please elaborate how would place the library into src lead to tedious conformance testing?

Sorry. What I meant was that Demo should optimally not be in project/src (since it's not part of the library) and we should put it in project/demo/.
So we have:
Project/
  .sln
  demo/
  src/
  test/

@abergs Got it! It‘s exactly what I proposed. Sorry, that I didn‘t outlined the demo project as well in the initial post. I will do a PR.

If possible use git mv so that we don't nuke git blame on the files.


macOS Unable to build

When i open it in VS for mac i can get it to build but it throws an error when it tries to launch, as well as 60+ warnings about the code.
I also cannot use .NET 5.0 because its unsupported, so when i try to up it to 6.0 it seems to work but i'm guessing thats where the warnings come from.

I also got it to build with the console command but the program will not open at all. i followed the instructions but "remove signature" isn't an item in the plst file

Akorin is no longer in development. Any interested users should use RecStar instead.
https://github.com/sdercolin/recstar/


[🐛 BUG]: Could not find any available RoadRunner binary version which meets criterio     n

No duplicates 🥲.

[X] I have searched for a similar issue in our bug tracker and didn't find any solutions.

What happened?
A bug happened!
vendor/bin/rr get-binary -f 2.5.*

Version
2.5.*
Relevant log output
Environment:
   - Version:          2.5.*
   - Stability:        stable
   - Operating System: linux
   - Architecture:     amd64

In GetBinaryCommand.php line 299:

  Could not find any available RoadRunner binary version which meets criterio
  n (--os=linux --arch=amd64 --stability=stable). Available: v2.5.3, v2.5.2,
  v2.5.1, v2.5.0

get-binary [-o|--os [OS]] [-a|--arch [ARCH]] [-f|--filter [FILTER]] [-l|--location [LOCATION]] [-s|--stability [STABILITY]]

Hey @Yurunsoft. What roadrunner-cli version do you use?

I use v2.1.0
Why: Starting from the roadrunner-cli v2.1.0 versions of roadrunner binary lower than 2.7.0 are not supported.

I use v2.1.0
Why: Starting from the roadrunner-cli v2.1.0 versions of roadrunner binary lower than 2.7.0 are not supported.

We moved to the new organization.
We support only the latest stable release.

RR doesn't contain BC's, except configuration for the KV described in the 2.5.0 release notes. So, you can safely upgrade to 2.7.3 (latest release)

If you still wanted to use the previous versions, please, use the previous roadrunner-cli version.

@Yurunsoft Feel free to reopen this issue if you have any questions about it. Thanks.


Put specific scene on top of the stack

May i know how can i achieve this? I have the following Scenes below as example.
Scene A > Scene B > Scene C > Scene D
Scene A is the initial scene and Scene D is the one on top of the stack. The question is, how can i move Scene B on the top of the stack and will have something like this.
SceneA > Scene C > Scene D > Scene B

Not sure you want this, but you could try popTo()
https://github.com/aksonov/react-native-router-flux/blob/master/docs/API.md#actions

@delia-m popTo() will close the scenes along the way.

It is not supported at this moment


Turn On / Turn Off Bluetooth

I only need know if is possible to turning on and turning off the Bluetooth from the flutter_blue lib.
If it is possible I need some examples to do this issue.
I have searched during several hours but I did not finded anything !
Can someone  help me, please?

Find out the state:

FlutterBlue.instance.isAvailable
FlutterBlue.instance.isOn
Then use a package like: https://pub.dev/packages/system_setting and open settings.
Or a popup dialog to inform user to do something with the bluetooth.

Thanks.
I hope got it feature in the lib soon. Is the most important and will be friendly if the user could turning on or turning off the Bluetooth from the app and not from the Android Settings Screen.
@JUREXT  Does you know if the options you gave me are supported by iOS ?

Thanks.
I hope got it feature in the lib soon. Is the most important and will be friendly if the user could turning on or turning off the Bluetooth from the app and not from the Android Settings Screen.
@JUREXT Does you know if the options you gave me are supported by iOS ?

If it helps someone, i will respond to myself...  Yes, the system_settings is supported to iOS


Update qgs with hot

This updates the qgs template to the HOT style.

Coverage remained the same at 82.489% when pulling cadc4f1753a326aa9a2a2f5c99cb5b166beb3337 on update-qgs-with-hot into ff5648c410fbcd5c6649c873986ace1cf9e1c292 on master.


[SourceKit NameLookup] Don't walk into inactive clauses.

Don't do lookups in inactive #if clauses as long as ASTScopes do not support them.
Addresses rdar://56760957

@swift-ci please smoke test

@nathawes This PR addresses the issue by not walking into inactive clauses. I realize that this fix may reduce the utility of SourceKit in these cases. Is this limitation acceptable? If not, I see two alternatives:

Disable ASTScopes for these activities and fall back to the declaration-context-based lookup system. This change will work for the short term, but will require more thought when we completely replace the old context-based lookups. Or,

Change ASTScopes to support lookups into inactive clauses. This change will not be easy because of the way that inactive clauses are currently handled in the AST. In addition, @DougGregor  has expressed the intuition that the compiler should not be in the business of lookups into inactive clauses, but I don't know if he would change his mind for this use case.

So, please take a gander at this PR and let me know what you think.
Thanks!

@nathawes Never mind--I think this fix is too draconian. Let me see what I can come up with.

@swift-ci please smoke test

@nathawes OK, I've got something that just forestalls the problematic lookups. If it tests acceptably, I think it's good. Check it out and let me know. Tx.

@swift-ci please smoke test osx platform

@swift-ci please clean smoke test os x platform

@swift-ci please smoke test

@swift-ci please smoke test

@swift-ci please smoke test os x platform

@swift-ci please clean smoke test os x platform


Reduce reactive computations for app.

App is currently starting up with 1754 computations. Some basic use will take it up to 5000+.
We should optimize to reduce number of computations. By stopping template subscriptions once data has been gathered and replicating them in memory, the system can stop listening to the server nonstop via ddp and hence reduce reactive computations potentially to < 1000 at startup. This will impact perception in mobile experience.

This was a major refactor, now completed across the board. It will improve speed of app significantly.


Append ?raw=true to image URLs within Readmes

Thanks in advance for your bug report!

[X] Have you reproduced this issue in incognito/private browsing?
[X] Have you made sure you issue doesn't already exist?

Where is the URL that this occurs?
https://web.pulsar-edit.dev/packages/pulsar-column-select-mode
What's your issue?
Seems for some reason images may sometimes not be properly loaded when given a path within the repo, rather than say githubusercontent.
I'm not totally sure of the cause, but at the very least a simple resolution here would be adding ?raw=true to the end of the content to ensure we get an image back rather than HTML.
Which OS/Browser/Version does this happen on?
N/A
Steps to Reproduce/Additional Details:
No response

That's really weird, never noticed that before with GitHub. It seems that in this case the .git refers to the file ending within the GH source tree and not the actual file itself as the browser wants to see it. If you click the below you can see it takes you to an entire github page and not a link. (Not teaching you to suck eggs @confused-Techie, more for if other people see this).
https://github.com/tom-power/pulsar-column-select-mode/blob/main/assets/demo.gif
Honestly I don't see a better solution than what you propose unless we substitute the url to githubusercontent.
i.e.
https://github.com/tom-power/pulsar-column-select-mode/blob/main/assets/demo.gif
to
https://raw.githubusercontent.com/tom-power/pulsar-column-select-mode/main/assets/demo.gif

@Daeraxa yeah converting this links would be really cool, but since I wouldn't want to accidentally break any links (Since presumably we can append the raw value from above to nearly any link without repercussions) I'd want to make sure we get it totally right.
As I'm not currently aware of any module that's able to interact with GitHub links like this, but if we can find a spec on how they are created we more than likely could implement one ourselves.

I can't seem to find anything official in their docs unfortunately but the approach I mentioned seems to be pretty stable and well known.
For example https://github.com/orgs/community/discussions/22537 and an npm package https://www.npmjs.com/package/rawbot.
Not fussed what approach we take, just offering an alternative.

I do like the approach taken by the package you've linked. It's super simple, but seems to be rather effective, testing it on the problem link above worked without issue.
So might be a totally valid way forward.

i'm always using
https://github.com/tom-power/pulsar-column-select-mode/raw/main/assets/demo.gif
instead
https://github.com/tom-power/pulsar-column-select-mode/blob/main/assets/demo.gif
and working as desired. blob -> raw


can't find googletest/confu.yaml

Hi, @Maratyszcza I am trying to build nnpack  and compiler output :

No such file or directory: '/home/deep/work/NNPACK_rel/NNPACK/pthreadpool/deps/googletest/confu.yaml'

Can you tell me where to find confu version of googletest? Thank you .

You seem to have a strange directory structure. Did you follow the README instructions?
I think you need to run confu setup in top-level NNPACK directory, then ./configure.py and ninja.

Thank you . It's the confu setup.

Hi, @Maratyszcza. I get the similar error when building nnpack, and the output is:
$ confu setup Reuse dependency pthreadpool from /root/nnpack/NNPACK/deps/pthreadpool Reuse dependency pthreadpool:fxdiv from  /root/nnpack/NNPACK/deps/fxdiv Reuse dependency pthreadpool:fxdiv:googletest from /root/nnpack/NNPACK/deps/googletest Fatal error: failed to read project manifest /root/nnpack/NNPACK/deps/googletest/confu.yaml:  Traceback (most recent call last):   File "/usr/local/bin/confu", line 6, in <module>     main()   File "/usr/local/lib/python2.7/site-packages/confu/__main__.py", line 84, in main     options.process(options, unparsed_args)   File "/usr/local/lib/python2.7/site-packages/confu/__main__.py", line 70, in setup_deps     setup_project_deps(root_dir, root_dir)   File "/usr/local/lib/python2.7/site-packages/confu/__main__.py", line 65, in setup_project_deps     namespace=dep.name if not namespace else namespace + ":" + dep.name)   File "/usr/local/lib/python2.7/site-packages/confu/__main__.py", line 65, in setup_project_deps     namespace=dep.name if not namespace else namespace + ":" + dep.name)   File "/usr/local/lib/python2.7/site-packages/confu/__main__.py", line 65, in setup_project_deps     namespace=dep.name if not namespace else namespace + ":" + dep.name)   File "/usr/local/lib/python2.7/site-packages/confu/__main__.py", line 34, in setup_project_deps     project = confu.manifest.Project.from_root(project_dir)   File "/usr/local/lib/python2.7/site-packages/confu/manifest.py", line 29, in from_root     with open(manifest_path) as manifest_file: IOError: [Errno 2] No such file or directory: '/root/nnpack/NNPACK/deps/googletest/confu.yaml'
Thank you in advance for your help.

Something is messed up in your deps directory, removing it and doing confu setup again should fix it.


[QUERY] Azure SDK guidelines for partial error

Hi,
I am working on an API that will serve long-running operations in our service and I want to follow azure sdk guidelines.
I am trying to understand what are the guidelines for partial success. I don't see any reference to it in azure-sdk-general-guidelines nor in microsoft-azure-rest-api-guidelines.
We are using autorest code generator for our clients, and the auto generated code throws a RequestFailedException for all HTTP responses, except 200/201/204. This means that in a case of 206 - partial content, a RequestFailedException is being thrown.
What is the expected behavior in a case of partial success?
Are we expected to return status code 200, with a response body that will describe the partial success or - are we expected to return 206 that eventually throws a RequestFailedException to the user?
Thanks,
Violet.
Environment:
Windows 11 .NET Framework 4.8
Visual Studio 17.0.0

Thank you for your inquiry.  Tagging and routing to the team member best able to assist.


feat: Adding Core UI Dep

Adding @incutonez/core-ui dep for UI components
Changing vite configs to TS

:tada: This PR is included in version 1.6.0 :tada:
The release is available on GitHub release
Your semantic-release bot :package::rocket:


Craig find

I need to find and replace thousands of strings (sequence names) in a file.  I was not sure how to do this with *nix tools without doing many passes over the file (which is large), so I wrote a small program to do this with a single pass over the file.

There is already a cmd in gonomics called "FindAndReplace". Is it possible to make this function an option of the other one, or can we find a more descriptive name for either of these to avoid confusion going forward?

That is a good point.  Let me see if I can incorporate this functionality into the existing program

I am closing this to instead add functionality to an existing program


HydroServerWebsite:  Data query date selection

pamaishlin[CodePlex] I find inability to manually type in date selection lacking in Hydroserver data query. The calendar wizard that appears is inefficient, particularly as it seems to require selection back/forward only one month at a time. This is problematic when needing
to select a date many years in advance of the given month and year.

horsburgh[CodePlex] Re-opening with a status of fixed.

ravivegiraju[CodePlex] ** Closed by ravivegiraju 5/6/2011 11:56 AM

pamaishlin[CodePlex] Ravi, Thank you. If I update to the latest version of HydroServer, will all remain intact as is on my Hydroserver Website? I will not have to redo any of my website configurations, either basic or those involving HydroServerCapabilities?

ravivegiraju[CodePlex] It is fixed on the current release for HydroServer Website. The calendar wizard has been done away with, date selection is now done by manually entering a date and then verified to make sure the input is valid. Please update your HydroServer Website to
the latest version to use these options.

horsburgh[CodePlex] I believe this has already been fixed. I am assigning to Ravi to make sure.


Refactor https://github.com/apache/beam/pull/30847

Instead of commenting on https://github.com/apache/beam/pull/30847, I am submitting a PR of utility_cluster. I tested both .test-infra/terraform/google-cloud-platform/google-kubernetes-engine and .test-infra/kafka/strimzi and a new Google Cloud project. I was able to provision both the GKE cluster and the strimzi helm chart, but I didn't see any further Kubernetes artifacts other than the operator deployment. Listed below is what this PR suggests. Below is a list of what remains.

Replaces .test-infra/kafka/strimzi with what you had as strimzi-operator
Simplifies README instructions
Moves default variable values to common.tfvars or start tfvars such as .test-infra/terraform/google-cloud-platform/google-kubernetes-engine/us-central1.apache-beam-testing.tfvars
Fixes gcloud command output

What remains

It wasn't clear from the strimzi helm chart documentation what happens after the helm chart is applied. I only saw a strimzi operator deployment and no other Kubernetes artifacts such as a service, etc.
I left a TODO comment in .test-infra/kafka/strimzi/README.md. See .test-infra/kafka/bitnami/README.md as an example for how to help people connect to the Kafka cluster. I hope we can see the same for the strimzi README.
I hope we will see an internally load balanced Service associated with the Kafka cluster. It wasn't clear if this was available from the helm documentation. See .test-infra/kafka/bitnami/kafka.tf for an example of how I added the load balancer annotations so that it is internally load balanced in GKE.

Think that its not clear what #30847 tries to do. Its purpose is to have terraform for a cluster that will serve as part of the test infra for all the needed utilities on for the workflows in apache/beam repo.In this case we start with kafka which should use terraform to build a cluster and then install a strimzi operator chart. The workflow then should use the kafka kustomization already present in the repo.
With that it clarifies couple of remains:

It wasn't clear from the strimzi helm chart documentation what happens after the helm chart is applied. I only saw a
strimzi operator deployment and no other Kubernetes artifacts such as a service, etc.
The purpose was to install a operator on the cluster and then test can use }/.test-infra/kafka/strimzi/02-kafka-persistent/overlays/gke-internal-load-balanced to instantiate its own kafka for the test purpose

I hope we will see an internally load balanced Service associated with the Kafka cluster. It wasn't clear if this was
vailable from the helm documentation. See .test-infra/kafka/bitnami/kafka.tf for an example of how I added the load
balancer annotations so that it is internally load balanced in GKE.
Given that we are to reuse the customization the balancing will be internal

Also note that:

we should not remove kafka persistent kustomization files from the repo as its intended to use them in workflows.
We should not also remove operator kustomization as perhaps in manual setups people still can use that
the common tfvars in strimzi kafka terrraform - should we have it - The purpose of this terraform is to install strimzi to apache-beam-testing project to be used by the workflows there
Why is strimzi terraform moved to .test-infra/kafka. This terraform only installs the operator for the cluster and it makes more sense to keep it in terrafrom folder, close to the tfvars of its cluster
Why are tfvars files for clusters named by regions eg. region.apache-beam-testing.tfvars . We are building clusters not regions so it makes sense to have by cluster name. beam-utility.apache-beam-testing.tfvars in my example

we should not remove kafka persistent kustomization files from the repo as its intended to use them in workflows.

This makes sense, I agree.

We should not also remove operator kustomization as perhaps in manual setups people still can use that

I think we should either use one or the other. I prefer the helm terraform solution; it seems cleaner.

the common tfvars in strimzi kafka terrraform - should we have it

I personally prefer to default using tfvars instead of using variable defaults. Individuals are more likely to notice a variable this way and are not suprised.

Why is strimzi terraform moved to .test-infra/kafka

https://github.com/akvelon/beam/tree/utility_cluster places it under google_cloud_platform. I'd argue it makes more sense under kafka. The compromise is to just place it directly under terraform instead of google_cloud_platform.

This terraform only installs the operator for the cluster and it makes more sense to keep it in terrafrom folder, close to the tfvars of its cluster

The tfvars should be in the same directory as the module to which it applies. This convention is understood by IDEs that will autocomplete the variables when editing tfvars files.

Why are tfvars files for clusters named by regions eg. region.apache-beam-testing.tfvars . We are building clusters not regions so it makes sense to have by cluster name. beam-utility.apache-beam-testing.tfvars in my example

Auto pilot GKE cluster is isolated by region. The two region tfvars files that already exist are helpful starters because the subnetwork name is different between the two regions.

Ok so,

I think we should either use one or the other. I prefer the helm terraform solution; it seems cleaner.

Terraform it is then, it is cleaner.

The tfvars should be in the same directory as the module to which it applies. This convention is understood by IDEs that will >autocomplete the variables when editing tfvars files.

Yeah, makes sense.

Auto pilot GKE cluster is isolated by region. The two region tfvars files that already exist are helpful starters because the > subnetwork name is different between the two regions.

Also makes sense. What is unclear is can i later upload the utility-beam.apache-beam-testing.tfvar alongside these starter files. I want it source controlled.
Rest i agree without issue. Let me know when you merge changes so i can figure out the change how backends are handled

Also makes sense. What is unclear is can i later upload the utility-beam.apache-beam-testing.tfvar alongside these starter files. I want it source controlled.

Yes, please version control the tfvars and note that the expected format is <cluster-id-prefix>.<region>.<project>.tfvars. I would expect the the cluster-id-prefix to be something more specific that utility-beam but rather strimzi or strimzi-kafka.

Let me know when you merge changes so i can figure out the change how backends are handled

Will target updating my changes tomorrow Thursday PST time. Thank you for responding and being open to my suggestions.

Just regarding the name:
Idea is that not only kafka operator is there but perhaps more stuff. Perhaps we can find operators or use exiting manifests for hadoop, postgres, mongo, rabbitmq etc., whatever workflows need


Plugin Err on Firefox - Pihole Admin Panel behind Traefik and with SSO Boreale for traefik

Describe the bug
Plugin still red with Err
Expected behavior
I have my pi-hole Admin panel behind Traefik v1 Reverse Proxy and SSO Boreale (https://github.com/lewazo/boreale). I remembered during the first version of the plugin I was able to use it and one day it stopped working.
I correctly setuped the API token (no space etc..) I have the good URL with the one I access to my Pihole Admin.
Screenshots

Desktop (please complete the following information):

Switch for PiHole: 2.2.8
Operating System: Win32
Browser: Mozilla Firefox 78.0

Additional context
Add any other context about the problem here.

If you can call the URL that you have set in the settings in your browser without everything, then it should work with the extension. How the extension accesses the PiHole has never changed and is even relatively identical to the first version.
 I would recommend you to install the extension again 1:1 in chrome with your settings.
Then open the popup and right-click into the popup and press " inspect". In the new window go to the console and put a screenshoot of it here in the issue.

Hi,
Thanks for your help.
So I tried on Chrome to inspect and I had an error 401 because of I was not authentified through SSO boreale. After being authentified I was able to use the plugin.
That's remind me that I'm using Firefox Multi-Account Containers and I put my personal domain in another "container" so your plugin can't read the cookie for the SSO. After disable Firefox Multi-Account Containers the plugin works well.
I don't think if it's possible to interact with Firefox Multi-Account Containers in order to permit Pihole Swith to have access to a "container" ?
Thanks.

The extension won't access anything in the containers directly. This extension is a low level feature that is deeply implemented in firefox that won't allow this.
But if you open a new tab that is not a container, shouldn't it work then? Bcs you then have a normal tab and the cookie should be available globally.

The extension won't access anything in the containers directly. This extension is a low level feature that is deeply implemented in firefox that won't allow this.
But if you open a new tab that is not a container, shouldn't it work then? Bcs you then have a normal tab and the cookie should be available globally.

Hi,
Yes. That's right. It works
It was just an interrogation.

Cool, I close the issue here. Enjoy the extension.
For any other problem, open another issue.


Underlined cursor line number in gutter

Hi,
I'm using Nord theme for VIM 8 on iTerm2 (also using Nord theme) and recently (my guess is after the last major iTerm2 update) I noticed that my line number gutter started appearing underlined on highlight.

Any ideas how to resolve? I mean, remove the underline from the line number.
Regards.

Hi @alexandremjacques :wave:, thanks for your contribution :+1:
Maybe this is also related to https://github.com/arcticicestudio/nord-iterm2/issues/9. I'll try to reproduce this when updating to the latest iTerm2 version.

This might be related to latest Vim defaulting to underline for CursorLineNr:
https://github.com/vim/vim/blob/017ba07fa2cdc578245618717229444fd50c470d/src/highlight.c#L256

@nixtrace Really nice catch :tada:
Comparing with the parent commit shows that underline attribute was explicitly set for cterm.
The question is if this was done on purpose or should be reported as bug.
If this is a change that'll stay in Vim itself I'll update Nord Vim to explicitly disable the cterm attribute for the CursorLineNr group.
I haven't updated to the latest iTerm2 version yet (only running macOS at my job), but I guess this is superfluous now anyway. I'll also see if this is reproducible on my personal system (Arch Linux) using the latest Vim version.

:+1: I can see the underline on Arch and Ubuntu running Vim version 8.1.2105. Thanks!


GCDS Q2 Product update presentation

📇 User story
Add here context on why we have to work on that
As a PM, I want to create and share the work done for the Q2 quarter, in order to show progress, gain trust and show accountability towards our committed goals and OKRs.
✅ Definition of Done / Outcomes

[ ] A presentation in EN
[ ] A presentation in FR

📜 Acceptance criteria
Add here the list of assumed steps that will be needed to complete the task

[ ] Check in on status of work done
[ ] Prepare presentation with evidence of work
[ ] Translation
[ ] Demo to GCWP
[ ] Demo at Platform Townhall

Slides in EN are done here
@EliseKa  Need a translation please.

@adorayi Translation complete - slides in FR


Indexing of RNA sequences suddenly treats them as protein sequences

Expected Behavior

indexdb command should process RNA sequences and report k-mers of size 15
a search with a RNA sequence on this database should finish gracefully

Current Behavior

indexdb on RNA sequences treats them as protein sequence (?) and creates k-mers of size 6
a search with a RNA sequence on this database results in an error

Steps to Reproduce (for bugs)

Install v5-2e4efbf of MMseqs2-App

cd /opt/mmseqs
git clone https://github.com/soedinglab/MMseqs2-App.git
cd MMseqs2-App
git checkout v5-2e4efbf

Create /opt/mmseqs/MMseqs2-App/docker-compose/databases/pdb_rna_sequence.fasta with some test RNA sequences:

>4QEI_2
GCGCCGCUGGUGUAGUGGUAUCAUGCAAGAUUCCCAUUCUUGCGACCCGGGUUCGAUUCCCGGGCGGCG
>6Q8V_1
GGCGAAGAACCGGGGAGCC
>5DO4_3
GGGAAXAAAGXUGAAGUXXUUAXXX
>1VQL_1
UUGGCUACUAUGCCAGCUGGUGGAUUGCUCGGCUCAGGCGCUGAUGAAGGACGUGCCAAGCUGCGAUAAGCCAUGGGGAGCCGCACGGAGGCGAAGAACCAUGGAUUUCCGAAUGAGAAUCUCUCUAACAAUUGCUUCGCGCAAUGAGGAACCCCGAGAACUGAAACAUCUCAGUAUCGGGAGGAACAGAAAACGCAAUGUGAUGUCGUUAGUAACCGCGAGUGAACGCGAUACAGCCCAAACCGAAGCCCUCACGGGCAAUGUGGUGUCAGGGCUACCUCUCAUCAGCCGACCGUCUCGACGAAGUCUCUUGGAACAGAGCGUGAUACAGGGUGACAACCCCGUACUCGAGACCAGUACGACGUGCGGUAGUGCCAGAGUAGCGGGGGUUGGAUAUCCCUCGCGAAUAACGCAGGCAUCGACUGCGAAGGCUAAACACAACCUGAGACCGAUAGUGAACAAGUAGUGUGAACGAACGCUGCAAAGUACCCUCAGAAGGGAGGCGAAAUAGAGCAUGAAAUCAGUUGGCGAUCGAGCGACAGGGCAUACAAGGUCCCUCGACGAAUGACCGACGCGCGAGCGUCCAGUAAGACUCACGGGAAGCCGAUGUUCUGUCGUACGUUUUGAAAAACGAGCCAGGGAGUGUGUCUGCAUGGCAAGUCUAACCGGAGUAUCCGGGGAGGCACAGGGAAACCGACAUGGCCGCAGGGCUUUGCCCGAGGGCCGCCGUCUUCAAGGGCGGGGAGCCAUGUGGACACGACCCGAAUCCGGACGAUCUACGCAUGGACAAGAUGAAGCGUGCCGAAAGGCACGUGGAAGUCUGUUAGAGUUGGUGUCCUACAAUACCCUCUCGUGAUCUAUGUGUAGGGGUGAAAGGCCCAUCGAGUCCGGCAACAGCUGGUUCCAAUCGAAACAUGUCGAAGCAUGACCUCCGCCGAGGUAGUCUGUGAGGUAGAGCGACCGAUUGGUGUGUCCGCCUCCGAGAGGAGUCGGCACACCUGUCAAACUCCAAACUUACAGACGCCGUUUGACGCGGGGAUUCCGGUGCGCGGGGUAAGCCUGUGUACCAGGAGGGGAACAACCCAGAGAUAGGUUAAGGUCCCCAAGUGUGGAUUAAGUGUAAUCCUCUGAAGGUGGUCUCGAGCCCUAGACAGCCGGGAGGUGAGCUUAGAAGCAGCUACCCUCUAAGAAAAGCGUAACAGCUUACCGGCCGAGGUUUGAGGCGCCCAAAAUGAUCGGGACUCAAAUCCACCACCGAGACCUGUCCGUACCACUCAUACUGGUAAUCGAGUAGAUUGGCGCUCUAAUUGGAUGGAAGUAGGGGUGAAAACUCCUAUGGACCGAUUAGUGACGAAAAUCCUGGCCAUAGUAGCAGCGAUAGUCGGGUGAGAACCCCGACGGCCUAAUGGAUAAGGGUUCCUCAGCACUGCUGAUCAGCUGAGGGUUAGCCGGUCCUAAGUCAUACCGCAACUCGACUAUGACGAAAUGGGAAACGGGUUAAUAUUCCCGUGCCACUAUGCAGUGAAAGUUGACGCCCUGGGGUCGAUCACGCUGGGCAUUCGCCCAGUCGAACCGUCCAACUCCGUGGAAGCCGUAAUGGCAGGAAGCGGACGAACGGCGGCAUAGGGAAACGUGAUUCAACCUGGGGCCCAUGAAAAGACGAGCAUAGUGUCCGUACCGAGAACCGACACAGGUGUCCAUGGCGGCGAAAGCCAAGGCCUGUCGGGAGCAACCAACGUUAGGGAAUUCGGCAAGUUAGUCCCGUACCUUCGGAAGAAGGGAUGCCUGCUCCGGAACGGAGCAGGUCGCAGUGACUCGGAAGCUCGGACUGUCUAGUAACAACAUAGGUGACCGCAAAUCCGCAAGGACUCGUACGGUCACUGAAUCCUGCCCAGUGCAGGUAUCUGAACACCUCGUACAAGAGGACGAAGGACCUGUCAACGGCGGGGGUAACUAUGACCCUCUUAAGGUAGCGUAGUACCUUGCCGCAUCAGUAGCGGCUUGCAUGAAUGGAUUAACCAGAGCUUCACUGUCCCAACGUUGGGCCCGGUGAACUGUACAUUCCAGUGCGGAGUCUGGAGACACCCAGGGGGAAGCGAAGACCCUAUGGAGCUUUACUGCAGGCUGUCGCUGAGACGUGGUCGCCGAUGUGCAGCAUAGGUAGGAGACACUACACAGGUACCCGCGCUAGCGGGCCACCGAGUCAACAGUGAAAUACUACCCGUCGGUGACUGCGACUCUCACUCCGGGAGGAGGACACCGAUAGCCGGGCAGUUUGACUGGGGCGGUACGCGCUCGAAAAGAUAUCGAGCGCGCCCUAUGGCUAUCUCAGCCGGGACAGAGACCCGGCGAAGAGUGCAAGAGCAAAAGAUAGCUUGACAGUGUUCUUCCCAACGAGGAACGCUGACGCGAAAGCGUGGUCUAGCGAACCAAUUAGCCUGCUUGAUGCGGGCAAUUGAUGACAGAAAAGCUACCCUAGGGAUAACAGAGUCGUCACUCGCAAGAGCACAUAUCGACCGAGUGGCUUGCUACCUCGAUGUCGGUUCCCUCCAUCCUGCCCGUGCAGAAGCGGGCAAGGGUGAGGUUGUUCGCCUAUUAAAGGAGGUCGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUCGGCUGCUAUCUACUGGGUGUGUAAUGGUGUCUGACAAGAACGACCGUAUAGUACGAGAGGAACUACGGUUGGUGGCCACUGGUGUACCGGUUGUUCGAGAGAGCACGUGCCGGGUAGCCACGCCACACGGGGUAAGAGCUGAACGCAUCUAAGCUCGAAACCCACUUGGAAAAGAGACACCGCCGAGGUCCCGCGUACAAGACGCGGUCGAUAGACUCGGGGUGUGCGCGUCGAGGUAACGAGACGUUAAGCCCACGAGCACUAACAGACCAAAGCCAUCAU
>1VQL_2
UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCGGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAACCCGGUUCGCCGCCACC
>3ADD_2
GGCCGCCGCCACCGGGGUGGUCCCCGGGCCGGACUUCAGAUCCGGCGCGCCCCGAGUGGGGCGCGGGGUUCAAUUCCCCGCGGCGGCCGCCA
>5U33_2
GGUCUAGAGGACAGAAUUUUUCAACGGGUGUGCCAAUGGCCACUUUCCAGGUGGCAAAGCCCGUUGAGCUUCUCAAAUCUGAGAAGUGGCACCAGAACCGGAGGACAAAGUC
>6LQU_1
GUCGACGUACUUCAUAGGAUCAUUUCUAUAGGAAUCGUCACUCUUUGACUCUUCAAAAGAGCCACUGAAUCCAACUUGGUUGAUGAGUCCCAUAACCUUUGUACCCCAGAGUGAGAAACCGAAAUUGAAUCUAAAUUAGCUUGGUCCGCAAUCCUUAGCGGUUCGGCCAUCUAUAAUUUUGAAUAAAAAUUUUGCUUUGCCGUUGCAUUUGUAGUUUUUUCCUUUGGAAGUAAUUACAAUAUUUUAUGGCGCGAUGAUCUUGACCCAUCCUAUGUACUUCUUUUUUGAAGGGAUAGGGCUCUAUGGGUGGGUACAAAUGGCAGUCUGACAAGU
>6LQU_2
AUGCGAAAGCAGUUGAAGACAAGUUCGAAAAGAGUUUGGAAACGAAUUCGAGUAGGCUUGUCGUUCGUUAUGUUUUUGUAAAUGGCCUCGUCAAACGGUGGAGAGAGUCGCUAGGUGAUCGUCAGAUCUGCCUAGUCUCUAUACAGCGUGUUUAAUUGACAUGGGUUGAUGCGUAUUGAGAGAUACAAUUUGGGAAGAAAUUCCCAGAGUGUGUUUCUUUUGCGUUUAACCUGAACAGUCUCAUCGUGGGCAUCUUGCGAUUCCAUUGGUGAGCAGCGAAGGAUUUGGUGGAUUACUAGCUAAUAGCAAUCUAUUUCAAAGAAUUCAAACUUGGGGGAAUGCCUUGUUGAAUAGCCGGUCGCAAGACUGUGAUUCUUCAAGUGUAACCUCCUCUCAAAUCAGCGAUAUCAAACGUACCAUUCCGUGAAACACCGGGGUAUCUGUUUGGUGGAACCUGAUUAGAGGAAACUCAAAGAGUGCUAUGGUAUGGUGACGGAGUGCGCUGGUCAAGAGUGUAAAAGCUUUUUGAACAGAGAGCAUUUCCGGCAGCAGAGAGACCUGAAAAAGCAAUUUUUCUGGAAUUUCAGCUGUUUCCAAACUCAAUAAGUAUCUUCUAGCAAGAGGGAAUAGGUGGGAAAAAAAAAAAGAGAUUUCGGUUUCUUUCUUUUUUACUGCUUGUUGCUUCUUCUUUUAAGAUAGU
>6LQU_3
AAGAUAGUUAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCGAUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGUGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA
>2G1G_1
ACGGGCUCAUAACCCGU
>6VZJ_8
AUGUUUUUUUUUUUUUUUGAUUUGGUGAGAGG

Create /opt/mmseqs/MMseqs2-App/docker-compose/databases/pdb_rna_sequence.params:

{
  "display": {
    "name": "PDB RNA sequence (seqres)",
    "version": "2022-09-22",
    "default": false,
    "order": 2,
    "index": "--search-type 3",
    "search": "--max-seqs 2000 --search-type 3 --strand 1"
  }
}

Call docker-compose up --no-color

MMseqs Output (for bugs)
/usr/lib/python3/dist-packages/requests/__init__.py:89: RequestsDependencyWarning: urllib3 (1.26.12) or chardet (3.0.4) doesn't match a supported version!
  warnings.warn("urllib3 ({}) or chardet ({}) doesn't match a supported "
Creating network "docker-compose_default" with the default driver
Creating volume "docker-compose_redis-volume" with default driver
Pulling mmseqs-web-redis (redis:alpine)...
alpine: Pulling from library/redis
Digest: sha256:dc1b954f5a1db78e31b8870966294d2f93fa8a7fba5c1337a1ce4ec55f311bc3
Status: Downloaded newer image for redis:alpine
Pulling mmseqs-web-api (soedinglab/mmseqs2-app-backend:version-5)...
version-5: Pulling from soedinglab/mmseqs2-app-backend
Digest: sha256:cb3937c294b3e666af4f4a424af0b7c4adc4f5469e2f309651b9a852731d786d
Status: Downloaded newer image for soedinglab/mmseqs2-app-backend:version-5
Pulling mmseqs-web-webserver (soedinglab/mmseqs2-app-frontend:version-5)...
version-5: Pulling from soedinglab/mmseqs2-app-frontend
Digest: sha256:30690f07999e0d1d7eccfe63c40df2b11d246590f094014e16987ed5d74d06d9
Status: Downloaded newer image for soedinglab/mmseqs2-app-frontend:version-5
Creating docker-compose_mmseqs-web-redis_1 ...
Creating docker-compose_mmseqs-web-redis_1 ... done
Creating docker-compose_mmseqs-web-api_1   ...
Creating docker-compose_mmseqs-web-api_1   ... done
Creating docker-compose_mmseqs-web-webserver_1 ...
Creating docker-compose_mmseqs-web-worker_1    ...
Creating docker-compose_mmseqs-web-worker_1    ... done
Creating docker-compose_mmseqs-web-webserver_1 ... done
Attaching to docker-compose_mmseqs-web-redis_1, docker-compose_mmseqs-web-api_1, docker-compose_mmseqs-web-worker_1, docker-compose_mmseqs-web-webserver_1
mmseqs-web-api_1        | 2022/09/22 16:09:10 MMseqs2 Webserver
mmseqs-web-redis_1      | 1:C 22 Sep 2022 16:09:10.002 # oO0OoO0OoO0Oo Redis is starting oO0OoO0OoO0Oo
mmseqs-web-redis_1      | 1:C 22 Sep 2022 16:09:10.002 # Redis version=7.0.4, bits=64, commit=00000000, modified=0, pid=1, just started
mmseqs-web-redis_1      | 1:C 22 Sep 2022 16:09:10.002 # Warning: no config file specified, using the default config. In order to specify a config file use redis-server /path/to/redis.conf
mmseqs-web-redis_1      | 1:M 22 Sep 2022 16:09:10.002 * monotonic clock: POSIX clock_gettime
mmseqs-web-redis_1      | 1:M 22 Sep 2022 16:09:10.003 * Running mode=standalone, port=6379.
mmseqs-web-redis_1      | 1:M 22 Sep 2022 16:09:10.003 # Server initialized
mmseqs-web-redis_1      | 1:M 22 Sep 2022 16:09:10.003 # WARNING overcommit_memory is set to 0! Background save may fail under low memory condition. To fix this issue add 'vm.overcommit_memory = 1' to /etc/sysctl.conf and then reboot or run the command 'sysctl vm.overcommit_memory=1' for this to take effect.
mmseqs-web-redis_1      | 1:M 22 Sep 2022 16:09:10.003 * Ready to accept connections
mmseqs-web-worker_1     | 2022/09/22 16:09:10 MMseqs2 worker
mmseqs-web-worker_1     | createdb /opt/mmseqs-web/databases/pdb_rna_sequence.fasta /opt/mmseqs-web/databases/pdb_rna_sequence
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | MMseqs Version:       	e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Converting sequences
mmseqs-web-worker_1     | [=
mmseqs-web-worker_1     | Time for merging to pdb_rna_sequence_h: 0h 0m 0s 12ms
mmseqs-web-worker_1     | Time for merging to pdb_rna_sequence: 0h 0m 0s 9ms
mmseqs-web-worker_1     | Database type: Aminoacid
mmseqs-web-worker_1     | Time for merging to pdb_rna_sequence.lookup: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 60ms
mmseqs-web-worker_1     | indexdb /opt/mmseqs-web/databases/pdb_rna_sequence /opt/mmseqs-web/databases/pdb_rna_sequence --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -k 0 --alph-size 21 --comp-bias-corr 1 --max-seq-len 65535 --max-seqs 300 --mask 1 --mask-lower-case 0 --spaced-kmer-mode 1 -s 7.5 --k-score 0 --check-compatible 1 --search-type 3 --split 0 --split-memory-limit 0 -v 3 --threads 2
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Estimated memory consumption: 1023M
mmseqs-web-worker_1     | Write VERSION (0)
mmseqs-web-worker_1     | Write META (1)
mmseqs-web-worker_1     | Write SCOREMATRIX3MER (4)
mmseqs-web-worker_1     | Write SCOREMATRIX2MER (3)
mmseqs-web-worker_1     | Write SCOREMATRIXNAME (2)
mmseqs-web-worker_1     | Write SPACEDPATTERN (23)
mmseqs-web-worker_1     | Write DBR1INDEX (5)
mmseqs-web-worker_1     | Write DBR1DATA (6)
mmseqs-web-worker_1     | Write HDR1INDEX (18)
mmseqs-web-worker_1     | Write HDR1DATA (19)
mmseqs-web-worker_1     | Write GENERATOR (22)
mmseqs-web-worker_1     | Index table: counting k-mers
mmseqs-web-worker_1     | [=================================================================] 10.79K 0s 918ms
mmseqs-web-worker_1     | Index table: Masked residues: 4422171
mmseqs-web-worker_1     | Index table: fill
mmseqs-web-worker_1     | [=================================================================] 10.79K 0s 61ms
mmseqs-web-worker_1     | Index statistics
mmseqs-web-worker_1     | Entries:          40961
mmseqs-web-worker_1     | DB size:          488 MB
mmseqs-web-worker_1     | Avg k-mer size:   0.000640
mmseqs-web-worker_1     | Top 10 k-mers
mmseqs-web-worker_1     |     AAGAGA	872
mmseqs-web-worker_1     |     CGGACA	532
mmseqs-web-worker_1     |     AAGACG	524
mmseqs-web-worker_1     |     AGAGCC	460
mmseqs-web-worker_1     |     AAGCGC	453
mmseqs-web-worker_1     |     AAAGGG	440
mmseqs-web-worker_1     |     CGAGGG	403
mmseqs-web-worker_1     |     AGCCAG	386
mmseqs-web-worker_1     |     GCGCAG	385
mmseqs-web-worker_1     |     AACAGG	323
mmseqs-web-worker_1     | Write ENTRIES (9)
mmseqs-web-worker_1     | Write ENTRIESOFFSETS (10)
mmseqs-web-worker_1     | Write SEQINDEXDATASIZE (15)
mmseqs-web-worker_1     | Write SEQINDEXSEQOFFSET (16)
mmseqs-web-worker_1     | Write SEQINDEXDATA (14)
mmseqs-web-worker_1     | Write ENTRIESNUM (12)
mmseqs-web-worker_1     | Write SEQCOUNT (13)
mmseqs-web-worker_1     | Time for merging to pdb_rna_sequence.idx: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for processing: 0h 0m 3s 688ms
mmseqs-web-worker_1     | touchdb /opt/mmseqs-web/databases/pdb_rna_sequence
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | MMseqs Version:	e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 47ms
mmseqs-web-worker_1     | 2022/09/22 16:09:14 Process finished gracefully without error

For comparison, logs looked like this when the RNA indexing was working:
mmseqs-web-worker_1     | indexdb /tmp/16248551593497607411/nucl_split_seq /opt/mmseqs-web/databases/pdb_rna_sequence --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -k 15 --alph-size 21 --comp-bias-corr 1 --max-seq-len 10000 --max-seqs 300 --mask 1 --mask-lower-case 0 --spaced-kmer-mode 1 -s 7.5 --k-score 0 --check-compatible 1 --search-type 3 --split 0 --split-memory-limit 0 -v 3 --threads 2
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Estimated memory consumption: 8G
mmseqs-web-worker_1     | Write VERSION (0)
mmseqs-web-worker_1     | Write META (1)
mmseqs-web-worker_1     | Write SCOREMATRIX3MER (4)
mmseqs-web-worker_1     | Write SCOREMATRIX2MER (3)
mmseqs-web-worker_1     | Write SCOREMATRIXNAME (2)
mmseqs-web-worker_1     | Write SPACEDPATTERN (23)
mmseqs-web-worker_1     | Write DBR1INDEX (5)
mmseqs-web-worker_1     | Write DBR1DATA (6)
mmseqs-web-worker_1     | Write DBR2INDEX (7)
mmseqs-web-worker_1     | Write DBR2DATA (8)
mmseqs-web-worker_1     | Write HDR1INDEX (18)
mmseqs-web-worker_1     | Write HDR1DATA (19)
mmseqs-web-worker_1     | Write HDR2INDEX (20)
mmseqs-web-worker_1     | Write HDR2DATA (21)
mmseqs-web-worker_1     | Write GENERATOR (22)
mmseqs-web-worker_1     | Index table: counting k-mers
mmseqs-web-worker_1     | [=================================================================] 10.75K 1s 426ms
mmseqs-web-worker_1     | Index table: Masked residues: 29698
mmseqs-web-worker_1     | Index table: fill
mmseqs-web-worker_1     | [=================================================================] 10.75K 0s 783ms
mmseqs-web-worker_1     | Index statistics
mmseqs-web-worker_1     | Entries:          6377423
mmseqs-web-worker_1     | DB size:          8228 MB
mmseqs-web-worker_1     | Avg k-mer size:   0.005939
mmseqs-web-worker_1     | Top 10 k-mers
mmseqs-web-worker_1     |     GAGTGGTTAGGCGGA	1170
mmseqs-web-worker_1     |     TGAAACGGCCCCCAC	886
mmseqs-web-worker_1     |     CCCCCAAGGGACAGT	883
mmseqs-web-worker_1     |     GGGTAGTCCGCAGGC	882
mmseqs-web-worker_1     |     TTGGTAAGCCACGGC	882
mmseqs-web-worker_1     |     GGGGCAGCGTGATTT	882
mmseqs-web-worker_1     |     TGGTAAGTCCAGACG	882
mmseqs-web-worker_1     |     AACGATTAATCGGAG	865
mmseqs-web-worker_1     |     ATTAGGGGCCAAACG	855
mmseqs-web-worker_1     |     TTCAGCAAGCGACTT	854
mmseqs-web-worker_1     | Write ENTRIES (9)
mmseqs-web-worker_1     | Write ENTRIESOFFSETS (10)
mmseqs-web-worker_1     | Write SEQINDEXDATASIZE (15)
mmseqs-web-worker_1     | Write SEQINDEXSEQOFFSET (16)
mmseqs-web-worker_1     | Write SEQINDEXDATA (14)
mmseqs-web-worker_1     | Write ENTRIESNUM (12)
mmseqs-web-worker_1     | Write SEQCOUNT (13)
mmseqs-web-worker_1     | Time for merging to pdb_rna_sequence.idx: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for processing: 0h 0m 29s 698ms
mmseqs-web-worker_1     | Remove temporary files
mmseqs-web-worker_1     | rmdb /tmp/16248551593497607411/nucl_split_seq
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | touchdb /opt/mmseqs-web/databases/pdb_rna_sequence

Please note the difference wrt the first argument, -k 15, and --max-seq-len 10000.

When I run any RNA query, e.g.:
>unnamed
UUUUUUUUUUUUUUUUUUUUUUUUU

The result is this:
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:04:37 +0000] "POST /ticket HTTP/1.0" 200 67
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:04:37 +0000] "POST /tickets HTTP/1.0" 200 69
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:04:37 +0000] "GET /ticket/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g HTTP/1.0" 200 67
mmseqs-web-worker_1     | Tmp /opt/mmseqs-web/jobs/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g/tmp folder does not exist or is not a directory.
mmseqs-web-worker_1     | createdb /opt/mmseqs-web/jobs/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g/job.fasta /opt/mmseqs-web/jobs/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g/tmp/5203697948948418300/query --dbtype 0 --shuffle 0 --createdb-mode 0 --id-offset 0 --compressed 0 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Converting sequences
mmseqs-web-worker_1     | [
mmseqs-web-worker_1     | Time for merging to query_h: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for merging to query: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Database type: Nucleotide
mmseqs-web-worker_1     | Time for merging to query.lookup: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Tmp /opt/mmseqs-web/jobs/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g/tmp/5203697948948418300/search_tmp folder does not exist or is not a directory.
mmseqs-web-worker_1     | extractorfs /opt/mmseqs-web/jobs/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g/tmp/5203697948948418300/query /opt/mmseqs-web/jobs/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g/tmp/5203697948948418300/search_tmp/10674843733463968173/q_orfs_aa --min-length 30 --max-length 32734 --max-gaps<PHONE_NUMBER> --contig-start-mode 2 --contig-end-mode 2 --orf-start-mode 1 --forward-frames 1,2,3 --reverse-frames 1,2,3 --translation-table 1 --translate 1 --use-all-table-starts 0 --id-offset 0 --create-lookup 0 --threads 2 --compressed 0 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | [=================================================================] 1 0s 5ms
mmseqs-web-worker_1     | Time for merging to q_orfs_aa_h: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for merging to q_orfs_aa: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 6ms
mmseqs-web-worker_1     | prefilter /opt/mmseqs-web/jobs/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g/tmp/5203697948948418300/search_tmp/10674843733463968173/q_orfs_aa /opt/mmseqs-web/databases/pdb_rna_sequence.idx /opt/mmseqs-web/jobs/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g/tmp/5203697948948418300/search_tmp/10674843733463968173/search/pref_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -k 0 --k-score<PHONE_NUMBER> --alph-size 21 --max-seq-len 65535 --max-seqs 2000 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --diag-score 1 --exact-kmer-matching 0 --mask 1 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 2 --pca 1 --pcb 1.5 --threads 2 --compressed 0 -v 3 -s 5.7
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Index version: 16
mmseqs-web-worker_1     | Generated by:  e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     | ScoreMatrix:  VTML80.out
mmseqs-web-worker_1     | Query database size: 0 type: Aminoacid
mmseqs-web-worker_1     | split was set to 1 but the db to split has only 0 sequences. Please run with default paramerters
mmseqs-web-worker_1     | Error: Prefilter died
mmseqs-web-worker_1     | Error: Search step died
mmseqs-web-worker_1     | Error: Search died
mmseqs-web-worker_1     | 2022/09/22 23:04:37 Execution Error: exit status 1
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:04:38 +0000] "GET /ticket/2_V_MA3apsJrv4zAPrfZqMF1rM88nxIsLoPD9g HTTP/1.0" 200 65

This is the healthy state:
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:07:17 +0000] "POST /ticket HTTP/1.0" 200 67
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:07:17 +0000] "POST /tickets HTTP/1.0" 200 137
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:07:17 +0000] "GET /ticket/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A HTTP/1.0" 200 67
mmseqs-web-worker_1     | Tmp /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp folder does not exist or is not a directory.
mmseqs-web-worker_1     | createdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/job.fasta /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/query --dbtype 0 --shuffle 0 --createdb-mode 0 --id-offset 0 --compressed 0 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Converting sequences
mmseqs-web-worker_1     | [
mmseqs-web-worker_1     | Time for merging to query_h: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for merging to query: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Database type: Nucleotide
mmseqs-web-worker_1     | Time for merging to query.lookup: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Tmp /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp folder does not exist or is not a directory.
mmseqs-web-worker_1     | splitsequence /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/query /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/query_seqs_split --max-seq-len 10000 --sequence-overlap 0 --sequence-split-mode 1 --create-lookup 0 --threads 2 --compressed 0 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | prefilter /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/query_seqs_split /opt/mmseqs-web/databases/pdb_rna_sequence.idx /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/search/pref_0 --sub-mat nucl:nucleotide.out,aa:blosum62.out --seed-sub-mat nucl:nucleotide.out,aa:VTML80.out -k 15 --k-score<PHONE_NUMBER> --alph-size 21 --max-seq-len 10000 --max-seqs 2000 --split 0 --split-mode 2 --split-memory-limit 0 -c 0 --cov-mode 0 --comp-bias-corr 1 --diag-score 1 --exact-kmer-matching 1 --mask 1 --mask-lower-case 0 --min-ungapped-score 15 --add-self-matches 0 --spaced-kmer-mode 1 --db-load-mode 2 --pca 1 --pcb 1.5 --threads 2 --compressed 0 -v 3 -s 5.7
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Index version: 16
mmseqs-web-worker_1     | Generated by:  e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     | ScoreMatrix:  nucleotide.out
mmseqs-web-worker_1     | Query database size: 1 type: Nucleotide
mmseqs-web-worker_1     | Estimated memory consumption: 8G
mmseqs-web-worker_1     | Target database size: 10754 type: Nucleotide
mmseqs-web-worker_1     | Process prefiltering step 1 of 1
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | k-mer similarity threshold: 0
mmseqs-web-worker_1     | Starting prefiltering scores calculation (step 1 of 1)
mmseqs-web-worker_1     | Query db start 1 to 1
mmseqs-web-worker_1     | Target db start 1 to 10754
mmseqs-web-worker_1     | [=================================================================] 1 0s 4ms
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | 0.120000 k-mers per position
mmseqs-web-worker_1     | 0 DB matches per sequence
mmseqs-web-worker_1     | 0 overflows
mmseqs-web-worker_1     | 0 queries produce too much hits (truncated result)
mmseqs-web-worker_1     | 0 sequences passed prefiltering per query sequence
mmseqs-web-worker_1     | 0 median result list length
mmseqs-web-worker_1     | 1 sequences with 0 size result lists
mmseqs-web-worker_1     | Time for merging to pref_0: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 5ms
mmseqs-web-worker_1     | align /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/query_seqs_split /opt/mmseqs-web/databases/pdb_rna_sequence.idx /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/search/pref_0 /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/aln --sub-mat nucl:nucleotide.out,aa:blosum62.out -a 1 --alignment-mode 3 --wrapped-scoring 0 -e 0.001 --min-seq-id 0 --min-aln-len 0 --seq-id-mode 0 --alt-ali 0 -c 0 --cov-mode 0 --max-seq-len 10000 --comp-bias-corr 1 --realign 0 --max-rejected<PHONE_NUMBER> --max-accept<PHONE_NUMBER> --add-self-matches 0 --db-load-mode 2 --pca 1 --pcb 1.5 --score-bias 0 --gap-open 5 --gap-extend 2 --zdrop 40 --threads 2 --compressed 0 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Index version: 16
mmseqs-web-worker_1     | Generated by:  e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     | ScoreMatrix:  nucleotide.out
mmseqs-web-worker_1     | Compute score, coverage and sequence identity
mmseqs-web-worker_1     | Query database size: 1 type: Nucleotide
mmseqs-web-worker_1     | Target database size: 10754 type: Nucleotide
mmseqs-web-worker_1     | Calculation of alignments
mmseqs-web-worker_1     | [=================================================================] 1 0s 2ms
mmseqs-web-worker_1     | Time for merging to aln: 0h 0m 0s 0ms
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | 0 alignments calculated.
mmseqs-web-worker_1     | 0 sequence pairs passed the thresholds (-nan of overall calculated).
mmseqs-web-worker_1     | 0.000000 hits per query sequence.
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 37ms
mmseqs-web-worker_1     | Remove temporary files
mmseqs-web-worker_1     | rmdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/search/pref_0 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | rmdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/search/aln_0 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | rmdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/search/input_0 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | rmdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/search/aln_merge -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | offsetalignment /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/query /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/query_seqs_split /opt/mmseqs-web/databases/pdb_rna_sequence.idx /opt/mmseqs-web/databases/pdb_rna_sequence.idx /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/aln /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/result --chain-alignments 0 --merge-query 1 --search-type 3 --threads 2 --compressed 0 --db-load-mode 2 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Index version: 16
mmseqs-web-worker_1     | Generated by:  e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     | ScoreMatrix:  nucleotide.out
mmseqs-web-worker_1     | Index version: 16
mmseqs-web-worker_1     | Generated by:  e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     | ScoreMatrix:  nucleotide.out
mmseqs-web-worker_1     | Index version: 16
mmseqs-web-worker_1     | Generated by:  e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     | ScoreMatrix:  nucleotide.out
mmseqs-web-worker_1     | Computing ORF lookup
mmseqs-web-worker_1     | Computing contig offsets
mmseqs-web-worker_1     | Computing contig lookup
mmseqs-web-worker_1     | Time for contig lookup: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Writing results to: /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/result
mmseqs-web-worker_1     | [=================================================================] 1 0s 0ms
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for merging to result: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 1ms
mmseqs-web-worker_1     | Remove temporary files
mmseqs-web-worker_1     | rmdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/q_orfs
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | rmdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/q_orfs_aa
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | rmdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/t_orfs
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | rmdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/search_tmp/7042327585447941378/t_orfs_aa
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | convertalis /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/query /opt/mmseqs-web/databases/pdb_rna_sequence.idx /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/result /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/alis_pdb_rna_sequence --sub-mat nucl:nucleotide.out,aa:blosum62.out --format-mode 0 --format-output query,target,pident,alnlen,mismatch,gapopen,qstart,qend,tstart,tend,evalue,bits,qlen,tlen,qaln,taln --translation-table 1 --gap-open 11 --gap-extend 1 --db-output 1 --db-load-mode 2 --search-type 3 --threads 2 --compressed 0 -v 3
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Index version: 16
mmseqs-web-worker_1     | Generated by:  e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     | ScoreMatrix:  nucleotide.out
mmseqs-web-worker_1     | Index version: 16
mmseqs-web-worker_1     | Generated by:  e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     | ScoreMatrix:  nucleotide.out
mmseqs-web-worker_1     | Index version: 16
mmseqs-web-worker_1     | Generated by:  e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249
mmseqs-web-worker_1     | ScoreMatrix:  nucleotide.out
mmseqs-web-worker_1     | [=================================================================] 1 0s 0ms
mmseqs-web-worker_1     | Time for merging to alis_pdb_rna_sequence: 0h 0m 0s 0ms
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 33ms
mmseqs-web-worker_1     | Removing temporary files
mmseqs-web-worker_1     | rmdb /opt/mmseqs-web/jobs/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/tmp/4977427893312161071/result
mmseqs-web-worker_1     |
mmseqs-web-worker_1     | Time for processing: 0h 0m 0s 0ms
mmseqs-web-worker_1     | 2022/09/22 23:07:17 Process finished gracefully without error
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:07:18 +0000] "GET /ticket/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A HTTP/1.0" 200 68
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:07:18 +0000] "GET /ticket/type/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A HTTP/1.0" 200 18
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:07:18 +0000] "POST /tickets HTTP/1.0" 200 138
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:07:18 +0000] "GET /result/queries/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/7/0 HTTP/1.0" 200 63
mmseqs-web-api_1        | <IP_ADDRESS> - - [22/Sep/2022:23:07:18 +0000] "GET /result/qRNpiMtH372WZ-C_jMFQJKscz01WKcG1y9ej0A/0 HTTP/1.0" 200 126

Context
On a weekly basis, some new sequences are added to the FASTA file. This week, RNA searching stopped working and seems to report errors for all queries. We didn't make any version changes and have been using mmseqs via MMseqs2-App v5 for a long time. Last week's data now shows the same behavior (but was fine a week ago).
Indexing for protein and DNA sequences still works as expected. DNA k-mers have size 15. I find it peculiar that the top k-mers for RNA sequences don't contain any U (or T), as it was the case previously.
Your Environment
Include as many relevant details about the environment you experienced the bug in.

Git commit used (The string after "MMseqs Version:" when you execute MMseqs without any parameters):
e1a1c1226ef22ac3d0da8e8f71adb8fd2388a249

Which MMseqs version was used (Statically-compiled, self-compiled, Homebrew, etc.):
docker image distributed by MMseqs2-App

For self-compiled and Homebrew: Compiler and Cmake versions used and their invocation:
N/A

Server specifications (especially CPU support for AVX2/SSE and amount of system memory):
2 CPUs, 16 GB memory

flags		: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss syscall nx pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology cpuid tsc_known_freq pni pclmulqdq vmx ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm 3dnowprefetch cpuid_fault invpcid_single ssbd ibrs ibpb stibp ibrs_enhanced tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid mpx avx512f avx512dq rdseed adx smap clflushopt clwb avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves arat umip pku ospke avx512_vnni md_clear arch_capabilities

Operating system and version:
Ubuntu 20.04

Thank you in advance!

It's a new week and we serve new (RNA) data. Now it's working again for our production data.
However, the example above is still broken. Is there some auto-detect step that determine the database type from the provided sequences? The only thing that changed is the sequence file.

I think this sequence broke the nucl-prot detection:
>5DO4_3
GGGAAXAAAGXUGAAGUXXUUAXXX

MMseqs2 assumes that the unknown residue for nucleotides is N and not X. The heuristic for differing between the two is as follows:

check the first 10 sequences if they are all nucleotide sequences
check every 100th sequence
check that all of these are at least 90% composed of ATGCUN

if all of these are nucleotide sequences, declare the database to be a nucleotide database.
You can disable the heuristic and fix the database to be a nucleotide db by passing --dbtype 2 to easy-search (in this case the search entry in the .params file.

Thanks for the pointer to use --dbtype 2. I've tried it (and a combination of other options & software versions) but no luck. The behavior doesn't change, the database is still indexed as amino acid sequences and search is still failing.
For now, I can try to sort the sequence file in a fashion that prevents problematic sequences from appearing at the top.

I think the issue here is that the detection of NA/prot goes wrong at indexing time. So what is also needed is the equivalent to --dbtype 2 but for indexing.