Gene Page Specification, External references

Currently we have

Add screenshots of any other MODS or resources which could be emulated

[ ] List new links to be added

[ ]  List links to be removed or replaced

[ ] List New links to be added (provide descriptions)
[ ]  List links to be updated or removed (provide descriptions for new links)

Changes required to  external links section

[ ]  Discuss. Maybe we should group the db-xrefs within the  gene page section  displaying data that they are relevant to (this might already be in a ticket?).

[ ]  Make it clearer what  type of data they are (sometimes it non obvious). Group links by "type" (ortholog interaction etc)

Do we want to have these links associated with relevant page sections?

[ ]  For external links relevant to a page section, we have a landing page and list
(what detail?)

curators need to make a list for each site with

[ ]  database
[ ]  types (which section?)
[ ]  Id if relevant
[ ]  base URL or mapping file
[ ]  Description (what it is)
[ ] provider

Val, there are 18 tickboxes in this ticket xD what's to be done here?

Just the final task above for now

We can do this on a curator meeting.
Will be quickest.
I'll add discuss back so we can find it easily.

OK we have a plan.
We need a config file with the following headings:
Type (classifier for grouping)
Name (name of the resource , hyperlink)
Description (what the user will find when they get there)
LINK format will be either base URL or details of hwere the lookup/mapping file lives
So far we have:
Strain and reagents || National BioResource Project (NBRP)|| Strains and clones|| http://viewer.shigen.info/yeastvw/wordsearch/search?word=SPBC11B10.09&fuzzy=y&action=mapview&ysttype=f
Strain and reagents ||SPD / RIKEN||Orfeome Localization Data||Mapping_file
Interactions || BioGRID ||Physical and genetic interactions||https://thebiogrid.org/276415/summary/schizosaccharomyces-pombe/cdc2.html
Interaction|| STRING|| Network display of known and predicted interactions and functional associations||
Expression||Gene Expression Omnibus||https://www.ncbi.nlm.nih.gov/geoprofiles/?term=SPBC11B10.09
Expression||pombeTV|| tiling array & illumina sequencing profiles||http://bahlerweb.cs.ucl.ac.uk/cgi-bin/pombetv/pombetv?condition=13&genename=SPBC11B10.09&action=display
Expression||expression viewer cell cycle, stress, meiosis, or mating||http://bahlerweb.cs.ucl.ac.uk/cgi-bin/SPGE/geexview?group=4&scale=log2&scale_min=-2&scale_max=2&q=SPBC1215.02c
Proteomics||PeptideAtlas||Peptides identified in tandem mass spectrometry ||https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProtein?action=QUERY&atlas_build_id=355&protein_name=SPBC11B10.09
Structure	Comparative protein structure models
Orthologs
Sequence resources UniProtKB/SwissProt	protein database Mapping_file
Sequence resources NCBI	Query all NCBI databases	URL

The file may need some tweaking but otherwise ready to go...

@mah11

[ ] put URL in if not one in GO
[ ] if there is one put ID in
[ ] use same format for URL as GO file

@ValWood
chase up mapping file sources with Mark

I mailed Mark. He thinks these mappings are in Canto already, I think he might be correct as one place they are stored is in Artemis.
He provided a text file from 2011, but he didn't use it.
Maybe it would be good to do a quick check to make sure everything in the original file is still in Artemis/Canto, but not critical

Config file edits as done as they can be for the moment (i.e. until/unless Kim has feedback or we have new entries).
For the "query all NCBI databases" I put yes for mapping file, because the search terms should include the gene systematic ID, standard name, and any synonyms.

I've added a basic external references section.  It's not finished - the two links that need to use the go_xrfs file aren't wired up yet.
The configuration is in the section called "external_gene_references" in:
pombe-embl/website/pombase_v2_config.json
I hope the syntax makes sense.  Here's an example:
{
  "ref_type": "Expression",
  "name": "Gene Expression Omnibus",
  "description": "GEO profiles",
  "url": "https://www.ncbi.nlm.nih.gov/geoprofiles/?term=<<uniquename>>"
},

In the URL the "<>" will be replaced with the systematic ID of the gene.  Other possibilities are "<<uniprot_identifier>>", "<<orfeome_identifier>>" and "<<NCBI_ALL_IDS>>".
"<<NCBI_ALL_IDS>>" tells the web code to retrieve all IDs and synonyms and join them together in a way suitable for the NCBI query.
For now, if you make any config changes I'll need to manually re-release the site.  It's quick though, less than 60 seconds.
I wasn't sure what you wanted to do with the "Type" from the config file so for now it's the first column.
I've added "External references" to the menu on the left of the gene pages.
As usual, a shift-reload might be needed.

Looks great!

All of the config file items are now displayed and the external links work.
I have simplified the config a bit.  It now looks like:
{
  "ref_type": "Expression",
  "name": "Gene Expression Omnibus",
  "description": "GEO profiles",
  "field_name": "uniquename",
  "url": "https://www.ncbi.nlm.nih.gov/geoprofiles/?term=<<IDENTIFIER>>"
},

The <<IDENTIFIER>> is all the URLs.  The "field_name" can be "identifier", "uniprot_identifier", "orfeome_identifier" or "NCBI_ALL_IDS" as described above.
What else needs doing?

I'll close this.  Please open new issues for problems.


Error msg after install Anaconda

Description
What steps will reproduce the problem?
after install anaconda, then shows this error,
Ipython console keep connecting to kernal, but there is no responding
Is there something wrong?
Please provide any additional information below
File "C:\Users\morris\Anaconda3\lib\site-packages\spyder\plugins_init_.py", line 511, in
toggled=lambda checked: self.toggle_view(checked),
File "C:\Users\morris\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole.py", line 713, in toggle_view
self.create_new_client(give_focus=False)
File "C:\Users\morris\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole.py", line 1009, in create_new_client
self.connect_client_to_kernel(client)
File "C:\Users\morris\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole.py", line 1035, in connect_client_to_kernel
stderr_file)
File "C:\Users\morris\Anaconda3\lib\site-packages\spyder\plugins\ipythonconsole.py", line 1440, in create_kernel_manager_and_kernel_client
kernel_manager.start_kernel(stderr=stderr)
File "C:\Users\morris\Anaconda3\lib\site-packages\jupyter_client\manager.py", line 257, in start_kernel
**kw)
File "C:\Users\morris\Anaconda3\lib\site-packages\jupyter_client\manager.py", line 203, in _launch_kernel
return launch_kernel(kernel_cmd, **kw)
File "C:\Users\morris\Anaconda3\lib\site-packages\jupyter_client\launcher.py", line 128, in launch_kernel
proc = Popen(cmd, **kwargs)
File "C:\Users\morris\

Thanks for reporting. The error message is incomplete; please copy and paste the entire thing here so we can properly diagnose the error. Without that, we won't be able to fix it, and so we'll have to close this issue in a week (7 days) from now. Thanks.

Is there something wrong?

Well, yes, otherwise you would not be receiving an error message.
As a naive guess, you can try spyder --reset from the anaconda prompt to fix this, and if that doesn't help, try a clean uninstall and reinstall of Anaconda. There might be also be something particular to your machine, OS or environment that is causing this error, but we won't be able to tell without the full error message, along with information from you about anything special or non-standard with your setup.

thanks a lot, I solved the problem after reset spyder


How can I get longer answers

All answers get cut off short. I am running docsgpt locally. How could I increase the token limit in the response?

Go to your application/app.py file
somewhere in the /stream endpoint you will find this line
completion = openai.ChatCompletion.create(model="gpt-3.5-turbo", messages=messages_combine, stream=True,
                                                  max_tokens=500, temperature=0)

adjust max_tokens accrodingly, to 750 for example


amdgpu driver crashes after using OpenCL in Mandelbulber

Please see this issue for reference:
https://github.com/buddhi1980/mandelbulber2/issues/663
When rendering reflective or transparent images using ROCm's OpenCL implementation, the amdgpu Linux kernel driver crashes.
This leaves the desktop unusable - "X is wedged". In my case, I saw heavy graphical artifacts, a crashed KDE session and the desktop left in an unresponsive state.
Multiple users reported this issue with at least these cards:
AMD Radeon RX 580
AMD Radeon RX 570

Works fine for me on AMD Radeon R9 Fury X (FIJI, GFX8), with ROCm 3.8 and ROCm 3.9. I tested Mandelbulber 2.23 appimage from the github.
Looks like it is related to specific GPU and kernel.
Could you try again with most recent kernel you can try, and ROCm 3.9?

Thanks @clavinet
Not able to reproduce this issue with the latest ROCm 3.10.
Recommend to try with the latest ROCm 3.10.
Thank you.


Finnish unit tests added

Hi all.
Finnish language Faker was missing unit tests so I decided to start creating some.
Thank you.

Thanks!


Re-introduce call to acquireTokenSilent in DOCS-CODE-030

Reverts the decision to remove the token cache.
Adds the doc code to the README as a comment, required by styleguide.

For response


Testing adapter

I am integrating the adapter with fastify-casbin.
When creating a unit test for the adapter I get the error "PrismaClientInitializationError: error: Environment variable not found: DATABASE_URL."
I am mocking prisma client using vitest-mock-extended

@rgarcia3pillar can you give more details?

@rgarcia3pillar then define the DATABASE_URL env var in your test?

Closed as stale


Single JSON Output Schema

After making a release announcement on Twitter, the maintainers of YARA joined the conversation and mentioned that they're writing a Go implementation of the YARA parser that will provide JSON output as an option. Also, in the same thread, I learned that there is already a Go implementation here:
https://github.com/Northern-Lights/yara-parser
I've opened an issue on their repo for this same topic here:
https://github.com/Northern-Lights/yara-parser/issues/17
Here is my proposal:
Let's coordinate on one single schema for data structure and JSON output format. We can definitely have local variation, but I think having a single schema that is interoperable among all three projects is a good thing. As a first step, I can post an annotated copy of our full JSON schema along with the reasoning behind various decisions. The short term goal would be to have both annotated schemas sent over to the core YARA developers. An ideal situation would be that core adopts as much of our "unified" schema as makes sense. They would then release the official schema when ready. We would then produce JSON that conforms to that official schema. If there are fields that we can't all agree on, we would then have a flag to enable additional local/optional fields in our output.

https://github.com/VirusTotal/gyp

It's great they finally released that. Will need to take a look at its output and see if we can output the same thing.

From the new repo, it looks like it's based on the Northern Lights Golang repo.

This will be a feature of 3.0.0. The schema of the new JSON format is not finalized (here at least). I want it to be informed by the output from both gyp and yara-python.


[incubator/fluentd] Promote fluentd to stable

What this PR does / why we need it:
Which issue this PR fixes (optional, in fixes #<issue number>(, fixes #<issue_number>, ...) format, will close that issue when PR gets merged): fixes #
Special notes for your reviewer:

Thanks @paulczar I will get that sorted soon.

Since we're promoting to stable we should version it to 1.0.0

Closing in favour of #8477


[@azure/graph] getServicePrincipalsIdByAppId return MissingSubscription

Package Name: "@azure/graph"
Package Version: "5.0.0"
Operating system:
[ ] nodejs

version: 10.51

[ ] browser

name/version:

[ ] typescript

version:

Is the bug related to documentation in

[ ] README.md
[ ] source code documentation
[ ] SDK API docs on https://docs.microsoft.com

Describe the bug
A clear and concise description of what the bug is.
getServicePrincipalsIdByAppId return 404 error
'{"error":{"code":"MissingSubscription","message":"The request did not have a subscription or a valid tenant level resource provider."}}'
To Reproduce
Steps to reproduce the behavior:
1 import pacakge:
const {GraphRbacManagementClient} = require('@azure/graph')
const msRestNodeAuth = require("@azure/ms-rest-nodeauth");
2. sign in with serviceprincipal
msRestNodeAuth.loginWithServicePrincipalSecret(clientId, secret, domain)
3 create graphic client GraphRbacManagementClient
const graphClient = new GraphRbacManagementClient(credentials, domain)
4. get service principalsIdByAppId
graphClient.applications.getServicePrincipalsIdByAppId(clientId,  servicecallback)
Expected behavior
A clear and concise description of what you expected to happen.
expect to get service principalsId
Screenshots
If applicable, add screenshots to help explain your problem.
Additional context
Add any other context about the problem here.
{ Error: The request did not have a subscription or a valid tenant level resource provider.
at new RestError (/home/local/TERADICI/fwang/repos/CAM/ms_authorization/node_modules/@azure/ms-rest-js/dist/msRest.node.js:2400:28)
at /home/local/TERADICI/fwang/repos/CAM/ms_authorization/node_modules/@azure/ms-rest-js/dist/msRest.node.js:3544:37
at process._tickCallback (internal/process/next_tick.js:68:7)
code: 'MissingSubscription',
statusCode: 404,
request:
WebResource {
streamResponseBody: false,
url:
'https://management.azure.com/xxxxxx/servicePrincipalsByAppId/xxxxxx/objectId?api-version=1.6',
method: 'GET',
headers: HttpHeaders { _headersMap: [Object] },
body: undefined,
query: undefined,
formData: undefined,
withCredentials: false,
abortSignal: undefined,
timeout: 0,
onUploadProgress: undefined,
onDownloadProgress: undefined,
proxySettings: undefined,
keepAlive: undefined,
operationSpec:
{ httpMethod: 'GET',
path:
'{tenantID}/servicePrincipalsByAppId/{applicationID}/objectId',
urlParameters: [Array],
queryParameters: [Array],
headerParameters: [Array],
responses: [Object],
serializer: [Serializer] } },
response:
{ body:
'{"error":{"code":"MissingSubscription","message":"The request did not have a subscription or a valid tenant level resource provider."}}',
headers: HttpHeaders { _headersMap: [Object] },
status: 404 },
body:
{ error:
{ code: 'MissingSubscription',
message:
'The request did not have a subscription or a valid tenant level resource provider.' } } }

Thanks for the feedback. I have routed to the appropriate team for follow-up.

How is this issue going? Feel free to let us know if further help is needed.

Hi @fwang-teradici ,
How is this issue going? Feel free to let us know if further help is needed.

We are going to close this issue because we haven’t heard from you in a few days, but please re-open it if the issue still persists.


Convention for deriving Archive for Copy types in the ecosystem?

Hi,
I'm currently trying to improve rkyv support within chrono -- you can see my pull request here: https://github.com/chronotope/chrono/pull/762
With Copy types it would be convenient to use Self as the Archived type so that all the traits and methods carry over. However, this does not work if rkyv was configured to use a specific endianness. I was wondering whether you have any thoughts or recommendations on how other projects can add support for rkyv while maintaining compatibility throughout the ecosystem.

In the linked PR, I don't think you should have archive_be and archive_le features for chrono. These features should be chosen by whatever the final binary is by enabling those features in rkyv, and that choice should propagate through all of the libraries that support rkyv.
I'm not sure how to support this kind of conditional attribute you'd like to add. The only way that comes to mind is to move the conditional into the argument for rkyv (i.e. #[archive_cfg(not(any(feature = "archive_le", feature = "archive_be"), as = "Self")]). This seems like a reasonable way to address this specific issue.
Having separate archived and unarchived types is currently a pain point that is difficult to address. My goal for the next major revision is to address this by adding more functionality to archived types so that you can use them for everything, instead of having to deserialize to the native type and use that.

Yeah that sounds like it would work. Support for archive_cfg will have to be added to rkyv itself, correct?

Yes, this would require adding a new feature to rkyv's derive macro. Because this is additive, we should be able to release it in a bugfix (minor) point release. Would you be interested in helping out with this work?

I've made some decisions on technical direction for the future of rkyv which impact this issue:

Archived types must now implement Portable, so we can't get around using rend's primitive types
Developers should not care whether rkyv uses little-endian or big-endian types by default, and so rkyv won't do more than export the choices it made for archived primitives
"Archived types everywhere" has turned out to be too much work and complexity for me. I think it's still possible, but it's not a place where I can responsibly invest my time or effort.

I think the opportunity for archived-self types is pretty limited and requires a significant amount of legwork to cover all possible bases. With those in mind, I'm going to close this issue and say that if you want to support rkyv you'll have to provide a separate archived type in most cases.

For anyone else who ended here from a search, see https://github.com/rkyv/rkyv/issues/167


where is dynamic ntk and local attention?

local attention is not implemented now. Search dynamic_ntk in config.json and modeling_qwen.py can help.


File permissions/ownership for /mnt/hdd/* wrong in 1.6rc3?

Hi,
when setting up a fresh 1.6rc3 with a clean hdd (formated as ext4) on a Raspberry Pi 3 I got a permission denied error during setup for /mnt/hdd/raspiblitz.conf with the request to report the issue in https://github.com/rootzoll/raspiblitz/issues/293 (which I did, please see that issue for details). I just realized that issue 293 is already closed so I create this new issue. With 1.5.1 and the same hdd (but now formated as FAT as mentioned in the documentation) I didn't have any issues.
I did have the same permission denied issue for /mnt/hdd/raspiblitz.conf when updating my Raspberry Pi 4 from 1.3 to 1.6rc3 where I copied the files from the old hdd to a new ssd and I thought I just messed up the ownership of the files/directories, but apparently it is an issue with 1.6rc3 since it happened with a fresh install as well.

Thanks I will take a look again at this and make a testrun before v1.6 final ... so to reproduce this I would use:

1TB HDD freshly formatted as ext4 (formatted from a linux laptop)
A RaspberryPi 3
Anything else I should take into account to get as closer to your setup?

Did a new test:
Raspberry Pi 4 with 500GB USB HDD freshly formated as FAT32 with 1.6rc3:
Got an error after formating happened on the Raspiblitz:

# Wiping all partitions (sfdisk/wipefs)
# Creating the one big partition
# waiting until the partion gets available
# Formatting
mke2fs 1.44.5 (15-Dec-2018)
# waiting until formatted drives gets available
# OK EXT 4 format done
/dev/fd/63: line 2: The: command not found
/dev/fd/63: line 3: syntax error near unexpected token `('

/dev/fd/63: line 3: `Calling ioctl() to re-read partition table.'
-# OK

and generating the dhparam.pem took about an hour(!) on the RPI4 but the permissions/ownership seems to be fine. After the setup the Raspberry Pi script complains about a non running bitcoind although the service is actually running (but in the state "Loading block index"):

*****************************************
* The bitcoind service is not running.
*****************************************
If you just started some config/setup, this might be OK.
More Error Detail:
error code: -28 error message: Loading block index...
-> Use command 'repair' and then choose 'RESET-CHAIN' to try downloading new blockchain.
-> Use command 'debug' for more log output you can use for getting support.
-> Use command 'menu' to open main menu.
-> Have you tried to turn it off and on again? Use command 'restart'
Use CTRL+c to EXIT to Terminal
bitcoin error: error code: -28
error message:
Loading block index...

The permissions/ownership look like this:

admin@raspberrypi:~ $ ls -alh /mnt/hdd/
total 2.1G
drwxr-xr-x 10 root    root    4.0K Jul 29 19:09 .
drwxr-xr-x  4 root    root    4.0K Jul 29 17:41 ..
drwxr-xr-x  5 bitcoin bitcoin 4.0K Jul 29 19:10 app-data
drwxr-xr-x  2 bitcoin bitcoin 4.0K Jul 29 17:42 app-storage
drwxr-xr-x  4 bitcoin bitcoin 4.0K Jul 29 19:11 bitcoin
drwxr-xr-x  2 bitcoin bitcoin 4.0K Jul 29 17:41 litecoin
drwxr-xr-x  4 bitcoin bitcoin 4.0K Jul 29 19:09 lnd
drwx------  2 root    root     16K Jul 29 17:40 lost+found
-rwxrwxrwx  1 root    root     272 Jul 29 19:09 raspiblitz.conf
drwxr-xr-x  2 root    root    4.0K Jul 29 17:41 ssh
-rw-------  1 root    root    2.0G Jul 29 19:07 swapfile
drwxrwxrwx  2 bitcoin bitcoin 4.0K Jul 29 19:11 temp

Next test again with Raspberry 4, a fresh SD card with 1.6rc3 but now the 500GB HDD cleanly formated as ext4:
After setting the passwords in the setup it fails with this message:

bitcoin still not running
ls: cannot access '/mnt/hdd/raspiblitz.conf': Permission denied

!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
FAIL: /mnt/hdd/raspiblitz.conf should exists at this point, but not found!
Please report to: https://github.com/rootzoll/raspiblitz/issues/293
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
Press ENTER to EXIT.

And the ownership of /mnt/hdd belongs to pi:pi instead of root:root:

admin@raspberrypi:~ $ ls -alh /mnt/hdd/
ls: cannot open directory '/mnt/hdd/': Permission denied
admin@raspberrypi:~ $ sudo ls -alh /mnt/hdd/
total 52K
drwx------ 10 pi      pi      4.0K Jul 29 19:41 .
drwxr-xr-x  4 root    root    4.0K Jul 20 01:15 ..
drwxr-xr-x  2 bitcoin bitcoin 4.0K Jul 29 19:41 app-data
drwxr-xr-x  2 bitcoin bitcoin 4.0K Jul 29 19:41 app-storage
drwxr-xr-x  2 bitcoin bitcoin 4.0K Jul 29 19:38 bitcoin
drwxr-xr-x  2 bitcoin bitcoin 4.0K Jul 29 19:38 litecoin
drwxr-xr-x  2 bitcoin bitcoin 4.0K Jul 29 19:38 lnd
drwx------  2 root    root     16K Jul 29 19:21 lost+found
-rwxrwxrwx  1 root    root       0 Jul 29 19:41 raspiblitz.conf
drwxr-xr-x  2 root    root    4.0K Jul 29 19:41 ssh
drwxrw-rw-  2 bitcoin bitcoin 4.0K Jul 29 19:41 temp
admin@raspberrypi:~ $

So it is fails with a Raspberry Pi 4 as well, no need to try it with a Raspberry 3 :)

dhparam.pem took about an hour
@frennkie I havent seen taking this long on my test runs, but it always delays the setup quite a bit ... at least keep in mind for a v1.6.1 update?

OK the v1.6 will also format ext4 fresh of they dont contain a blockchain and I improved the initial writing of the raspiblitz.conf.


Sync stalls at epoch boundary

When moving to epoch 241 noticed a > 10 minute stall as the epoch rewards were retrieved and inserted into the database.

I can confirm. The db sync instances were all they were deleting 1 block, the instances that were restarted did not want to delete any block but still took a lot of time. In my case, the total outage was 17 min.

I can confirm. The db sync instances were all they were deleting 1 block, the instances that were restarted did not want to delete any block but still took a lot of time. In my case, the total outage was 17 min.

were all saying they were deleting 1 block

I saw this too, but it was after the stall and therefore not the cause of the stall. The cause of the stall is that at the epoch boundary there is a large amount of data to be pulled out of the ledger-state and inserted into the database.

were all saying they were deleting 1 block

I saw this too, but it was after the stall and therefore not the cause of the stall. The cause of the stall is that at the epoch boundary there is a large amount of data to be pulled out of the ledger-state and inserted into the database.

Strangely enough, my instances logged this and they proceeded to be frozen for another several minutes though.

Strangely enough, my instances logged this and they proceeded to be frozen for another several minutes though.

I can confirm that epoch boundaries are very slow. Not sure if something changed on Allegra or it was the same before.  For each reward we run a very composite query queryStakeAddressAndPool. It's very possible that we need to add Indexes to make this faster.

I can confirm that epoch boundaries are very slow. Not sure if something changed on Allegra or it was the same before.  For each reward we run a very composite query queryStakeAddressAndPool. It's very possible that we need to add Indexes to make this faster.

We are looking at adding more indicies.

We are looking at adding more indicies.

Indexes eventually didn't help much for this. But I saw good results with this pr https://github.com/input-output-hk/cardano-db-sync/pull/489

Indexes eventually didn't help much for this. But I saw good results with this pr https://github.com/input-output-hk/cardano-db-sync/pull/489

A third idea: for each reward we run this query:
SELECT "stake_address"."id","delegation"."pool_hash_id"
FROM "stake_address"
    INNER JOIN "delegation" ON "stake_address"."id" = "delegation"."addr_id"
    INNER JOIN "tx" ON "delegation"."tx_id" = "tx"."id"
    INNER JOIN "block" ON "block"."id" = "tx"."block_id"
WHERE ("stake_address"."hash_raw" = '\xe12f6f594d58d056098962d163854177cff6d612e7ac2e6800de5e22ad')
AND ("delegation"."active_epoch_no" <= 240)
ORDER BY "block"."slot_no" DESC

We could create a view to speed this up (I suspect postgresql already does some optimizations here or else this would be much slower).

A third idea: for each reward we run this query:
SELECT "stake_address"."id","delegation"."pool_hash_id"
FROM "stake_address"
    INNER JOIN "delegation" ON "stake_address"."id" = "delegation"."addr_id"
    INNER JOIN "tx" ON "delegation"."tx_id" = "tx"."id"
    INNER JOIN "block" ON "block"."id" = "tx"."block_id"
WHERE ("stake_address"."hash_raw" = '\xe12f6f594d58d056098962d163854177cff6d612e7ac2e6800de5e22ad')
AND ("delegation"."active_epoch_no" <= 240)
ORDER BY "block"."slot_no" DESC

We could create a view to speed this up (I suspect postgresql already does some optimizations here or else this would be much slower).

On current master (46b89294ab0650b9946b74d7ba76c8c8e5dcd05f) at the epoch boundary:
[2021-02-04 21:46:00.97 UTC] insertShelleyBlock(Allegra): epoch 246, slot 20908800, block 5300189, hash b5e181f2b79c62cdb2d5235d09d51caf79e893af9ce34f653e55ec9e3756036c
[2021-02-04 21:46:01.05 UTC] Finishing epoch 245: 141412 rewards, 213 orphaned_rewards, 165252 stakes.
[2021-02-04 21:50:47.20 UTC] Starting epoch 246
[2021-02-04 21:50:49.14 UTC] epochPluginInsertBlock: epoch 246

so inserting rewards took just under 5 minutes.

[2021-02-09 21:45:19.82 UTC] Finishing epoch 246: 148679 rewards, 257 orphaned_rewards, 176740 stakes.
[2021-02-09 21:52:40.53 UTC] Starting epoch 247

I ran some benchmarks and most of the time is spent on the 4 table join above. We join
address ⋈ delegation ⋈ tx ⋈ block
but we only use the block to sort results by the SlotNo.
By replacing it with a 2 table join:
address ⋈ delegation
I saw some good results.
before 5:11
[db-sync-node:Info:56] [2021-02-14 15:24:29.43 UTC] Finishing epoch 243: 123607 rewards, 88 orphaned_rewards, 150785 stakes.
[db-sync-node:Info:56] [2021-02-14 15:29:40.06 UTC] Starting epoch 244

after 2:09
[db-sync-node:Info:56] [2021-02-14 14:51:46.68 UTC] Finishing epoch 243: 123607 rewards, 88 orphaned_rewards, 150785 stakes.
[db-sync-node:Info:56] [2021-02-14 14:53:55.04 UTC] Starting epoch 244

The simplest solution is to replicate the SlotNo of the block to the Delegation, so that the multi-table joins are unnecessary.

This has 2 improvements

https://github.com/input-output-hk/cardano-db-sync/pull/489
more recent https://github.com/input-output-hk/cardano-db-sync/pull/528

Maybe we can close it?

Yeah, lest close this for now.

TransportError: Failed to sign with Ledger device: U2F DEVICE_INELIGIBLE.If you are using a hardware wallet, please make sure you are using the latest version of the Cardano application.

@timdug I am more than 100% certain the issue you have has nothing to do with an code in this repo. I suspect it actually belongs in https://github.com/vacuumlabs/adalite/ .


Tabalonia Licence

Hi, thanks a lot for the great project!
Under which licence is the package released? I could not find any licence file in the repos... Unless I missed it, it's worth adding a LICENCE file so that people (me included!) are confident using the library in there project.
FYI, I see Dragablz is MIT
Thanks a lot again!

Hi)
I added MIT license

That's amazing! Thanks for that


at_c: atclient monitor

Implement the bits that allow you to monitor in at_c:
The likely interface for monitor as it stands:
int atclient_start_monitor(...);
int atclient_send_heartbeat(...); // send a noop:0\r\n to keep the connection alive
int atclient_read_monitor(...);  // read what could either be a (data:ok, error:msg, notification:json)
                                 // utility struct provided to help with parsing each possibility

Writing down some of my thoughts around this:
It is really hard to come up with a clean solution that doesn't involve much work from the end developer. One can assume that the end developer is using the pthread library, but, we also want to support embedded devices, which means the possibility of RTOS's which don't implement a pthread interface.


Document cycle_basis() doesn't work with multigraphs

As was pointed out in #505 the cycle_basis() function doesn't work with
multigraphs, but this was missing in the documentation. This commit adds
a note to the docstring that it won't work correctly if a multigraph is
used with it.

Pull Request Test Coverage Report for Build<PHONE_NUMBER>

0 of 0   changed or added relevant lines in 0 files are covered.
No unchanged relevant lines lost coverage.
Overall coverage remained the same at 98.511%

Totals

Change from base Build<PHONE_NUMBER>:
0.0%

Covered Lines:
11114

Relevant Lines:
11282

💛  - Coveralls


Add configuration file support for Nuget feeds and packages

Currently configuration file supports the configuration of Assembly and Folder catalogs.
Add support for configuring feed and package catalogs.

Currently the IConfiguration support is provided using the following two classes:
FolderCatalogConfigurationConverter
AssemblyCatalogConfigurationCoverter
When implementing this feature we should add one for nuget feeds and one for nuget packages. These should be added into Weikio.PluginFramework.Catalogs.Nuget.
The converters must be registered into the DI before they can be used:
        services.AddTransient(typeof(IConfigurationToCatalogConverter), typeof(NugetFeedCatalogConfigurationConverter));
        services.AddTransient(typeof(IConfigurationToCatalogConverter), typeof(NugetPackageCatalogConfigurationCoverter));

Currently the IConfiguration support is provided using the following two classes:
FolderCatalogConfigurationConverter
AssemblyCatalogConfigurationCoverter
When implementing this feature we should add one for nuget feeds and one for nuget packages. These should be added into Weikio.PluginFramework.Catalogs.Nuget.
The converters must be registered into the DI before they can be used:
        services.AddTransient(typeof(IConfigurationToCatalogConverter), typeof(NugetFeedCatalogConfigurationConverter));
        services.AddTransient(typeof(IConfigurationToCatalogConverter), typeof(NugetPackageCatalogConfigurationCoverter));


@clientName does not impact x-ms-enum.name in typespec-autorest

When representing union types using x-ms-enum,  the @clientName  decorator does not impact the x-ms-enum.name field.  Since this field determines the name of any generated enum type, the clientName should change this value.
Here is a playground sample showing the issue.
Note that, @encodedName  does not work, either, but that is ok, since the x-ms-enum.name field does not impact the API on the wire.

Happens to both union and enum

est: 3


--image-endpoint does not use --runtime-endpoint as documented in crictl usage

What happened:
Setting --runtime-endpoint or $CONTAINER_RUNTIME_ENDPOINT does not appear to set the image endpoint to the same value as suggested in the usage text:

--image-endpoint value, -i value    Endpoint of CRI image manager service (default: uses 'runtime-endpoint' setting) [$IMAGE_SERVICE_ENDPOINT]

What you expected to happen:
I should be able to set --runtime-endpoint and not bother with --image-endpoint
How to reproduce it (as minimally and precisely as possible):
[maybe@karma cri-o]$ crictl images
FATA[0002] connect: connect endpoint 'unix:///var/run/crio/crio.sock', make sure you are running as root and the endpoint has been started: context deadline exceeded
[maybe@karma cri-o]$ crictl --runtime-endpoint unix:///run/user/1337/usernetes/crio/crio.sock images
FATA[0002] connect: connect endpoint 'unix:///var/run/crio/crio.sock', make sure you are running as root and the endpoint has been started: context deadline exceeded
[maybe@karma cri-o]$ CONTAINER_RUNTIME_ENDPOINT=unix:///run/user/1337/usernetes/crio/crio.sock crictl images
FATA[0002] connect: connect endpoint 'unix:///var/run/crio/crio.sock', make sure you are running as root and the endpoint has been started: context deadline exceeded
[maybe@karma cri-o]$ crictl --image-endpoint unix:///run/user/1337/usernetes/crio/crio.sock images
IMAGE                       TAG                 IMAGE ID            SIZE
docker.io/library/busybox   1.31.0              19485c79a9bbd       1.44MB
k8s.gcr.io/pause            3.2                 80d28bedfe5de       688kB
[maybe@karma cri-o]$ IMAGE_SERVICE_ENDPOINT=unix:///run/user/1337/usernetes/crio/crio.sock crictl images
IMAGE                       TAG                 IMAGE ID            SIZE
docker.io/library/busybox   1.31.0              19485c79a9bbd       1.44MB
k8s.gcr.io/pause            3.2                 80d28bedfe5de       688kB

Anything else we need to know?:
Environment:

Container runtime or hardware configuration: CRI-O 1.20.0 (d388528dbed26b93c5bc1c89623607a1e597aa57)
OS (e.g: cat /etc/os-release): Fedora 33
Kernel (e.g. uname -a): 5.10.15-200.fc33
Others:

This probably caused by incorrect ImageEndpoint set in crictl.yaml.
If you have ImageEndpoint set in config yaml, and you only overrides the RuntimeEndpoint with CLI flags, the ImageEndpoint will not automatically changed to RuntimeEndpoint as you already have it explicitly defined in config yaml.
Check your crictl.yaml at /etc/crictl.yaml


Transition from internal.py defaults in config.py to schema defaults.

We currently rely on internal.py defaults to specify optional keys in the configuration through a manually-set config dictionary:
https://github.com/CABLE-LSM/benchcab/blob/a44e9862ee3ebf43ad2c9840e6ad705824010288/src/benchcab/config.py#L74
We can get around doing this by setting the defaults via the Cerberus config schema.

Duplicate issue: https://github.com/CABLE-LSM/benchcab/issues/284


How can I run a pipelined training job on 16 GPUs and 4 nodes in a cluster

Is your feature request related to a problem? Please describe.
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
I have created a 4 node cluster and I am setting GPU ids to be 0..3.
How can I either change train.py or my pipeline_run.py which uses PythonScriptStep with minimal changes so it can take advantage of all of the 4 nodes in my compute cluster and not just one of the nodes?

Currently, each node only has 4 GPUs so I am hoping to get access to 16 GPUs to run my job.
A few lines of code for GPU setup in train.py:
parser.add_argument('--gpuids',
    nargs='+',
    type=int,
    default=[0,1,2,3],
    help='GPUs to use')
net = torch.nn.DataParallel(net,device_ids=opt.gpuids).cuda()

in my pipeline_run.py I have:
train_cfg = ScriptRunConfig(source_directory=script_path,
                     script='train.py',
                     arguments=script_args,
                     compute_target=compute_target,
                     environment=env)

train_step = PythonScriptStep(
    name="train step",
    arguments=script_args,
    source_directory=train_cfg.source_directory,
    script_name=train_cfg.script,
    runconfig=train_cfg.run_config,
)
pipeline = Pipeline(ws, steps=[train_step])
run = exp.submit(pipeline)

Describe the solution you'd like
A clear and concise description of what you want to happen.
Describe alternatives you've considered
A clear and concise description of any alternative solutions or features you've considered.
Additional context
Add any other context or screenshots about the feature request here.

Hi @monajalal, could you please share the SDK library you are using? As well as the version? Thanks!

Hi @catalinaperalta thanks a lot for your time.
Here is the libraries used in train.py
import mlflow
import mlflow.pytorch

from azureml.core.authentication import ServicePrincipalAuthentication
from azureml.core import Workspace
and the libraries used in pipeline_run.py are:
import os
import azureml.core

from azureml.data import OutputFileDatasetConfig
from azureml.core.compute import AmlCompute
from azureml.core.compute_target import ComputeTargetException
from azureml.pipeline.steps import PythonScriptStep
from azureml.pipeline.core import Pipeline

# You can find tenant id under azure active directory->properties

from azureml.core.authentication import ServicePrincipalAuthentication

from azureml.core import (
    Workspace,
    Experiment,
    Dataset,
    Datastore,
    ComputeTarget,
    Environment,
    ScriptRunConfig
)

The versions:
In [1]: import mlflow

In [2]: mlflow.__version__
Out[2]: '2.1.1'

$ pip show azureml-core
Name: azureml-core
Version: 1.48.0
Summary: Azure Machine Learning core packages, modules, and classes
Home-page: https://docs.microsoft.com/python/api/overview/azure/ml/?view=azure-ml-py
Author: Microsoft Corp
Author-email:
License: https://aka.ms/azureml-sdk-license
Location: /anaconda/envs/jupyter_env/lib/python3.8/site-packages
Requires: adal, argcomplete, azure-common, azure-core, azure-graphrbac, azure-mgmt-authorization, azure-mgmt-containerregistry, azure-mgmt-keyvault, azure-mgmt-resource, azure-mgmt-storage, backports.tempfile, contextlib2, cryptography, docker, humanfriendly, jmespath, jsonpickle, knack, msal, msal-extensions, msrest, msrestazure, ndg-httpsclient, packaging, paramiko, pathspec, pkginfo, PyJWT, pyopenssl, python-dateutil, pytz, requests, SecretStorage, urllib3
Required-by: azureml-pipeline-core, azureml-telemetry, azureml-train-automl-client, azureml-train-core, azureml-widgets

Is this helpful for you?
Please note that I am intending to run my job as pipeline steps inside pipeline_run.py  from the submit_node which is a VM inside Azure to a GPU cluster with 4 nodes where each node has 4 GPUs not via jupyter notebook.
pipeline = Pipeline(ws, steps=[train_step, inference_step])

Thanks for the info @monajalal! Re-routing to the appropriate team to investigate.


hal-push: Hal push module is implemented.

Ref: #1642

@oguzdemirbasci looks good, just the comments!


Patient Search: search for multiple words

Heather mentioned that it would be nice if searches for things like "Smith John" would match correctly.
Currently, typing a space will break matching.
Server side should split terms using a whitespace delimiter (space and probably ,) and prefix search with and terms.

At a certain point it may just make more sense to look at postgresql full text search￼—if we're going to approach that point, probably better to identify it up front and save some intermediate steps.

Related https://github.com/cdcgov/prime-simplereport/issues/96

Will be difficult to maintain when we scale; if we implement it, may not have capacity to manage.

While I don't disagree with closing this bug, maybe we should display a warning on the client if they type in multiple words (e.g. type a space)?


ARROW-7428: [Format][C++] Add serialization for CSF sparse tensors

This is to solve ARROW-7428.

@pitrou @mrkn - I'm tying to serialize vectors of Buffers but I'm getting wrong buffer offsets and lengths on deserializing. Any idea why this is? I'm a bit stuck.

@rok I've begun to look it.

I think this is ready for review.

Ping.

Thanks for the review @wesm and @mrkn. I've pushed another commit.

Thanks @wes @mrkn and @pitrou!


Give liveness epoch same "shape" as attester duties

https://github.com/ethereum/beacon-APIs/pull/131 introduced a new liveness endpoint - the request is similar to attester duties in that we query a list of validators for data pertaining to a particular epoch - as such, it seems reasonable to keep the two requests similar in terms of their URL/postdata structure.

cc @paulhauner

my understanding was that it's not really something we can query for anything but current or previous epoch... it seems that the epoch field is just going to result in false unless it's very carefully used...

it's not really something we can query for anything but current or previous epoch

it's allowed, just not required - the data could be synthesized from a state for example, or if a client wants to implement "deep" doppelganger protection (ie more than 2 epochs of silence)

to me this makes sense overall, just would like to hear from @paulhauner and potentially @mehdi-aouadi to get opinions of people implementing...

Change looks good to me :+1:


When i open it, it closes immediatly

My system should meet the limitations listed on your page. I went on gamebanana and saw someone experiencing the same problem, however they have not openend an issue yet.
My PC information:
Operating system: Windows 10, 64-bit
GPU: nvidia 940M
(CPU: Intel(R) Core(TM) i5-4210H CPU @ 2.90GHz   2.90 GHz)
please do not let it be the gpu :'''')

There are two main issues that could cause this. The first issue is that you don't have the C++ 2015 runtime installed required by Rust, which is required for Rust programs to work on Windows. You can download it from https://www.microsoft.com/en-us/download/details.aspx?id=52685. I'll update the documentation since I forgot to mention this. You may already have this installed, but it's worth double checking.
The second issue is GPU compatibility issues. Your system has an integrated GPU (intel) and a discrete GPU (Nvidia). These should both be modern enough to run Vulkan or DX12.

i actually have all of these runtimes installed, also tried changing the gpu which runs the program, still no success

okay after deinstalling the .net core 3.1 runtimes i have installed prior for crossmodgui, upgrading to the 6.0 version and installing the ms visual c++ it SOMEHOW worked out. i cannot tell you how i got it and i actually tried it before commenting a second time but now it suddenly works.

SSBH Editor doesn't require .NET Core like Cross Mod. It sounds like reinstalling the c++ runtime did the trick. If you're still having problems, you can reopen this issue or create a new issue. I've updated the installation instructions on the release and updated the system requirements.

i guess so. thank you for your support!


[connector-v2][iceberg sink] add iceberg sink connector

Purpose of this pull request

Check list

[ ] Code changed are covered with tests, or it does not need tests for reason:
[ ] If any new Jar binary package adding in your PR, please add License Notice according
New License Guide
[ ] If necessary, please update the documentation to describe the new feature. https://github.com/apache/seatunnel/tree/dev/docs
[ ] If you are contributing the connector code, please check that the following files are updated:

Update change log that in connector document. For more details you can refer to connector-v2
Update plugin-mapping.properties and add new connector information in it
Update the pom file of seatunnel-dist

[ ] Update the release-note.

你会继续推进这个 iceberg sink的完成吗？
Will you continue to push for the completion of this iceberg sink?

你会继续推进这个 iceberg sink的完成吗？
Will you continue to push for the completion of this iceberg sink?

同问，用了比较久的seatunnel，一直卡在sink iceberg的功能，啥时候可以出来呢？
By the same token, I have been using seatunnel for a long time and have been stuck in the sink iceberg function. When will it be available?

I will refine this pr in the next few days

I will refine this pr in the next few days

大佬，sink iceberg的功能有计划什么时候可以在dev上测试呢？
When is there a plan to test the functionality of sink iceberg on dev?

pr #6265 merged


Searching by typing misses keypresses after 0810250b3ad27a850033fd57d1519008f0828cd7

As per title, this commit seems to introduce some regression on the search-by-typing functionality.
Sometimes keypresses are not registered at all, some other times, after typing one letter, the focus is grabbed by the first available entry.
This causes the second letter to be lost. A third letter is again appended to the input. Rinse and repeat.
I specified the first entry 'cause if there is no entry, the input field doesn't lose focus.

You're right. I had to change the key event from key-press to key-release for Esc key. I shouldn't have done it for other keys. Will fix it, thanks.

I cannot find any issue anymore. Thanks for the quick fix!


SET search_path TO {self._schema} is executing by SQLDatabase for all databases except 'snowflake' and 'bigquery'.

System Info
LangChain Version- 0.0.235, Windows, Python Version-3.9.16
As per below source code of SQLDatabase, before executing any sql query, connection.exec_driver_sql(f"SET search_path TO {self._schema}") is executed for all database except 'snowflake' and 'bigquery'.
if self._schema is not None:
if self.dialect == "snowflake":
connection.exec_driver_sql(
f"ALTER SESSION SET search_path='{self._schema}'"
)
elif self.dialect == "bigquery":
connection.exec_driver_sql(f"SET @@dataset_id='{self._schema}'")
else:
connection.exec_driver_sql(f"SET search_path TO {self._schema}")
cursor = connection.execute(text(command))
As per my knowledge, The SET search_path command is specific to PostgreSQL, not Oracle. This is why I am getting the following error.
sqlalchemy.exc.DatabaseError: (oracledb.exceptions.DatabaseError) ORA-00922: missing or invalid option
[SQL: SET search_path TO evr1]
(Background on this error at: https://sqlalche.me/e/20/4xp6)
Oracle does not recognize this command.
I think it is better to use SCHEMA.TABLE in all sql queries.
Who can help?
No response
Information

[ ] The official example notebooks/scripts
[X] My own modified scripts

Related Components

[ ] LLMs/Chat Models
[ ] Embedding Models
[ ] Prompts / Prompt Templates / Prompt Selectors
[ ] Output Parsers
[ ] Document Loaders
[ ] Vector Stores / Retrievers
[ ] Memory
[ ] Agents / Agent Executors
[X] Tools / Toolkits
[ ] Chains
[ ] Callbacks/Tracing
[ ] Async

Reproduction
oracle_connection_str = f"oracle+oracledb://{username}:{password}@{hostname}:{port}/?service_name={service_name}"
db = SQLDatabase.from_uri(
oracle_connection_str,
schema="evr1",
include_tables=[ ],
sample_rows_in_table_info=3,
)
llm = ChatOpenAI(model_name=GPT_MODEL, temperature=0, openai_api_key=OpenAI_API_KEY)
toolkit = SQLDatabaseToolkit(
db=db,
llm=llm,
)
agent_executor = create_sql_agent(
llm=llm,
toolkit=toolkit,
agent_type=AgentType.ZERO_SHOT_REACT_DESCRIPTION,
return_intermediate_steps=True,
handle_parsing_errors=_handle_error,
verbose=True,
)
response = agent_executor(user_input)
Expected behavior
Should not execute SET search_path TO {self._schema} for Oracle

I have pull the source BUT did not get the changes.


Try to get nbsite to build website...

Consider merging only if https://travis-ci.org/ioam/param/builds/440314750 passes and then https://ioam-docs.github.io/param-dev starts working again.
Then could push website tag so param.pyviz.org gets re-built.

Coverage remained the same at 76.713% when pulling c7ffb755ccc4ebe3783e62b67205909722076209 on nbsite_fixup into 51c78a6601416a6a75a9f491fe3a1fd0a2dcee9c on master.

https://ioam-docs.github.io/param-dev has started to work again.
So I guess merge and then push websitetag to re-build param.pyviz.org?

I've pushed a tag named website; fingers crossed...


can we publish message to queue in rabbit mq instead of a topic?

i am trying to use rabbit mq pubsub component and try to send a message to queue directly instead of using a topic
i have a few queues already created, i tried using bindings but it was causing some overflow when i was trying to define ttlInSeconds of "2592000" (30 days), according to RabbitMQ documentation if we pass a empty string as exchange and pass a routingKey
https://www.rabbitmq.com/tutorials/amqp-concepts#exchange-default
i am trying to send it like below
d.client.PublishEvent(ctx, "rabbit-mq-pubsub", "", data.Message, 			client.PublishEventWithMetadata( 				map[string]string{ 					"priority":   fmt.Sprint(data.Priority), 					"routingKey": queueName, 				}, 			))
any pointers will be helpful

I am not sure. I don't believe we currently have any active contributor with deep RabbitMQ knowledge (through I could be wrong). If you'd like to look through the code we have it's here. PRs welcome to improve things.
The SDK we use: github.com/rabbitmq/amqp091-go (currently on v1.8.1)
Dapr PubSub code:
https://github.com/dapr/components-contrib/tree/main/pubsub/rabbitmq/
and
Dapr Binding code
https://github.com/dapr/components-contrib/blob/main/bindings/rabbitmq/

@isaacnikon93 see this: https://docs.dapr.io/reference/components-reference/supported-pubsub/setup-rabbitmq/#use-topic-exchange-to-route-messages


lodash: signatures of the method _.difference changed

https://lodash.com/docs#difference
https://lodash.com/docs#_ (description of the chainable wrapper)

thanks mate!


Projects migrated previous to RC2 should be disallowed from loading

We should disallow projects that have been migrated previous to RC2 from loading. They can get into a bad state when you have projects migrated before and projects migrated after, they can conflict and get into a bad state. /cc @davkean @piotrpMSFT @livarcocc.

At this point, given the backlog of issues, I don't think this is worth the cost.


[BUG] Edit Config not saving changes

Environment
Self-Hosted (Docker)
Version
2.1.0
Describe the problem
Updating the config with the "old" editor tree/code doesn't save changes to the config file on disk, just writes the config again with same data. Using the interactive editor it saves it fine. Looking at the POST request send when trying to save, in case of the interactive editor the value passed includes the config with the changes. But when looking at the same POST with the other editor it just passes on the same config as before it was edited.
Tested on my config and also a fresh container. Tried clearing cookies and rebuild, but I'm guessing that doesn't matter much if data doesn't reach the config anyway. Also saving to local doesn't work either in the "old" editor. If you preview the changes it writes changes instantly, I'm guessing it uses the same layout and functions as the interactive editor. Most likely related to #603, opened this as that had no real info.
Additional info
Interactive edit writes new data to config

"Old" editor writes same/old data to config

Edit using "Old" editor, text in the notepad is the config value found in the save POST request

Config value passed to the POST request when edited with interactive editor

Please tick the boxes

[X] You are using a supported version of Dashy (check the first two digits of the version number)
[X] You've checked that this issue hasn't already been raised
[X] You've checked the docs and troubleshooting guide
[X] You agree to the code of conduct

I am also having this same issue.

I am working on a complete re-work of how config is managed to make things faster, and that should also fix this issue.
I think duplicate of #603, but this ticket is much clearer with lots of really good info, so keeping open.

See https://github.com/Lissy93/dashy/discussions/799

See #799

I'll go ahead and close this one you already got it planned in #799, to prevent having to reply it to every 6 weeks and save you having to close it in the future anyway. Thanks for the hard work :)


Watch changes crash

Hello,
The --watch option seems to crash after some saves on my mjml file.
> mjml --watch test.mjml --output test.html
produces:

Error: [MJMLError] EmptyMJMLError: Null element found in mjmlElementParser at MJMLError.Error (native)
at new MJMLError (C:[...]\AppData\Roaming\npm\node_modules\mjml\lib\Error.js:24:85)
at Object.mjmlElementParser (C:[...]\AppData\Roaming\npm\node_modules\mjml\lib\documentParser.js:24:13)
at documentParser (C:[...]\AppData\Roaming\npm\node_modules\mjml\lib\documentParser.js:65:22)
at mjml2html (C:[...]\AppData\Roaming\npm\node_modules\mjml\lib\mjml2html.js:49:52)
at C:[...]\AppData\Roaming\npm\node_modules\mjml\lib\cli.js:88:12

No problem with:
> mjml -r test.mjml --output test.html
I'm using Node v4.3.0, NPM v2.14.12 & MJML v1.0.3
Thank you

Hey @laurent-bientz !
This should be solved by the last release. Can you make sure it works on your side?
Regards,
Guillaume

Hey @laurent-bientz !
This is probably when you save the file with an empty body, I will try to make the error appear without crashing for the next release tomorrow!
Regards,
Guillaume

@GuillaumeBadi : I believe you're correct about it being empty tags. I can confirm that using --watch with the following causes an error:
<mj-body>
  <mj-section>
    <mj-column>
      <mj-text align='left'></mj-text>
    </mj-column>
    <mj-column>
      <mj-text align='right'></mj-text>
    </mj-column>
  </mj-section>
</mj-body>

However, adding text to the mj-text element fixes the problem and an error is not thrown. The error I'm receiving is different though:
Warning: React.renderToStaticMarkup is deprecated. Please use ReactDOMServer.renderToStaticMarkup from require('react-dom/server') instead.
Invariant Violation: renderToStaticMarkup(): You must pass a valid ReactElement.

Hello and thank u for your feedback.
I can't test today but to reproduce the glitch, just put some spaces in your file.
For me, it's crashed and no memories about an empty <mj-body> or <mj-text>.
Btw, i can remember that empty <mj-text> also crashed with basic command line (mjml -r test.mjml --output test.html), so I don't think it's linked to the same pb, maybe i'm wrong.
I'll check next mon

Empty mj-text is now fixed ! Please reopen if you're still having the issue with 1.2.0

Plus the client won't crash anymore and simply log the error message if any :smile:

:+1:


NetJSONGraph map elements animation

Fixed  #32

Combined with echarts-leaflet, use leaflet as basemap coordinate system and echarts element rendering.
Support dynamic effects.

go ahead :+1:

No more updates at this point. 😄
I've made a new branch focus on nodes expand or fold.
Should we open a new one or just update here?

I'd suggest opening up a new pull request if the next updates are not relating to this feature.

Sorry, I have updated. :cold_sweat:


Keeps prompting for sign-in

Issue Type: Bug
Install live share.
Sign in to a Microsoft account.
Just wait - it'll prompt you to sign in to GitHub as well.
Extension version: 1.0.4836
VS Code version: Code 1.60.0 (e7d7e9a9348e6a8cc8c03f877d39cb72e5dfb1ff, 2021-09-01T10:54:53.442Z)
OS version: Darwin x64 19.6.0
Restricted Mode: No

System Info

Item
Value

CPUs
Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz (8 x 2600)

GPU Status
2d_canvas: enabledgpu_compositing: enabledmetal: disabled_offmultiple_raster_threads: enabled_onoop_rasterization: enabledopengl: enabled_onrasterization: enabledskia_renderer: disabled_off_okvideo_decode: enabledwebgl: enabledwebgl2: enabled

Load (avg)
2, 2, 2

Memory (System)
16.00GB (0.46GB free)

Process Argv
. --crash-reporter-id 48469422-ab52-4128-86cb-70acdb293239

Screen Reader
no

VM
0%

A/B Experiments
vsliv368:30146709
vsreu685:30147344
python383:30185418
vspyt653:30270858
pythonvspyt602:30300191
vspor879:30202332
vspor708:30202333
vspor363:30204092
vstes627:30244334
pythonvspyt639:30300192
pythontb:30283811
pythonptprofiler:30281270
vshan820:30294714
vstes263:30335439
vscorecescf:30358481
pythondataviewer:30285071
pythonvsuse255:30340121
vscod805cf:30301675
pythonvspyt200:30340761
vscextlang:30333561
binariesv615:30325510
vsccppwtct:30364498
pythonvssor306:30344512
bridge0708:30335490
pygetstartedt2:30360495
bridge0723:30353136
pythonrunftest32cf:30365367
pythonf5test824:30361777
javagetstartedc:30364665
pythonvspyt187cf:30365362
pydsgst2:30361792
vscus224cf:30358040
vssid140:30363603
vssur157:30365996

The only way I have made it go away, is by performing an elaborate series of actions, none of which I have determined to be the exact way to make it go away, but here they are: disabling Git (git.enabled = false), logging off of Live Share from all accounts. uninstalling Live Share, reinstalling Live Share, signing into Live Share from only Microsoft (the sign-in must be prompted from the command prompt), start a Live Share session, get a Windows Firewall prompt for access and approve needed access, stop the Live Share session, close VS Code, restart VS Code, and sometimes this stops GitHub from ever prompting a login request, and sometimes it doesn't, but this has worked most of time...
"60% of the time it works every time"
~Brian Fantana

We’ve made improvements in this area since this issue was filed. We believe this may have improved your experience and are closing this issue. If this issue still persists for you, please comment on the issue and let us know. Thank you.


enable-geopm-profiling

Enable performance profiling of the geopm code itself.
Determine the overhead the run-time requires and enable
reporting at different levels of granularity.

https://review.gerrithub.io/#/c/303295/


Add Chronicle charges to Daily Task Indicator

You are allowed to buy up to 100 chronicle charges a day.
Having a notifier if possible would be useful.

I have an implementation for this written in this branch. I will be testing it to make sure it works properly and open a PR when I'm confident it has no issues.
Anyone feel free to clone my branch and try to find issues with it, it'd be much appreciated.


x/crypto/ssh: TestSSHCLIAuth fails on Windows

Not sure how I didn't notice this until today. See #60981 previously.
Example: http://ci.chromium.org/b/8763261739598890561:
sign_and_send_pubkey: signing using rsa-sha2-512 SHA256:Anr3LjZK8YVpjrxu79myrW9Hrb/wpcMNpVvTq/RcBm8\r\nBad permissions. Try removing permissions for user: UNKNOWN\\\\UNKNOWN (S-1-15-2-2) on file C:/b/s/w/ir/x/t/TestSSHCLIAuth1586735692/001/rsa.
Seems like a bug in the test so for now I'm going to skip.
cc @drakkan @golang/security @FiloSottile @rolandshoemaker

uhmm... I cannot reproduce on Windows 10

This is currently the only Windows VM I have access to.
It appears that 0600 is not enough to make the private key file not accessible by other users on some versions of Windows


Position picker sometimes shows NaN

This happens on the first use. The displayed coordinates are NaN,NaN.
Also default should be center of screen, 80,60

Position picker shows NaN when an expression is used.
Also, if you pick a value outside the screen, the value shows as the max, not the user input value.

This is fixed.


Inventory variables should appear in JSON format if --format json requested

Stumbled across this one while looking into a support issue via RedHat support (01894363).
Steps to reproduce:

Create an inventory, and add some variables in YAML format
Query the inventory via tower-cli and observe the structure of the variables field
Go back to the inventory via the UI and hit the json toggle and then save
Perform step 2 again and notice the change of format of the variables field

Expected behaviour
I expected that the toggle boxes were just changing a visual representation of the same underlying data. It seems that it is more than that though. Asking for --format json sounds to me like even the inventory variables should be as json.
I'm writing a playbook that can upsert specific variables in an inventory. To do this I need to read the inventory variables in as a variable, with code like this:
- hosts: localhost
  tasks:

   - name: Get inventory
     command: tower-cli inventory get 3 --format json
     register: inventory

   - name: Access inventory variable variables
     debug:
       var: ((inventory.stdout|from_json).variables|from_json).fooagain

It seems the second from_json will work if the variables are in a json form, otherwise I guess I need from_yaml (I'll test now).
It'd be nice to not need to know how the variables are saved - maybe just my opinion though!

This isn't great, but unfortunately, it's something that I think should be considered on the Tower side as opposed to the tower-cli side.
One thing we can do is hit the endpoint /api/v1/inventories/N/variable_data/ instead. This will parse the data and return it as valid JSON data. You can also get YAML by passing ?format=yaml when visiting that endpoint, although converting from one to the other is so trivial that I doubt this would be useful.
I have considered that we could introduce a new command like tower-cli inventory variables which would return the variables, but it's a very narrow use case.

Not sure if this is also related, but the extra-vars of a job template if empty are also a blank string in the tower-cli output with --format json, and though the UI shows them as an empty JSON block (i.e. {}) in the json view. This makes it slightly more difficult to parse the extra vars of a template as json without needing to check first whether it is a blank string.

This would be very nice. Right now I'm running tower-cli host list -a -f json but in variables I get a string with YAML which is quite impossible to parse with tools like jq.


[Feature]: Allow widget navigation through anchors

Is there an existing issue for this?

[X] I have searched the existing issues

Summary
We need to support widget navigation through either URL or a widely used method of anchors
Why should this be worked on?
Use Case 1:
I have 5 containers placed one below another and 5 buttons configured to navigate to specific containers based on user choice
Use Case 2:
I have a form on Page 1 and want to navigate users to a specific section of the canvas on Page 2 based on user response on the form

This can also belong to action selector where the navigateTo function address the enhancement requested for

Duplicate of #8314


fix TimePlot tz problems #1454

Default timezone has been changed to the 'UTC'. Typo in the XYChartSerializer has been fixed. Also algorithm for an extraction common part from time values has been improved (see https://github.com/twosigma/beaker-notebook/issues/2081).
Notebook for tests https://www.dropbox.com/s/sipau5hou3hlywx/1454.bkr?dl=0

:+1:


Test issue

[Enter feedback here]

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

ID: bcbccfee-331a-ac88-2026-1a056031208b
Version Independent ID: 455839ad-dbdc-92cb-23ee-103d3b623982
Content: What is Custom Vision? - Azure AI services
Content Source: articles/ai-services/custom-vision-service/overview.md
Service: azure-ai-custom-vision
GitHub Login: @PatrickFarley
Microsoft Alias: pafarley

@nitinme
It's test case, Glad to know you have self-resolved the issue.

@nitinme
Duplicate of #https://github.com/MicrosoftDocs/azure-docs/issues/116728


Refactor (Fisher)LDA solvers into separate class

This includes:

refactor LDA binary classification and dimension reduction solvers in two separate classes: LDASolver, centers data w.r.t. class, compute within cov matrix (shared by bin. class. and dim. red. llt/eigen solvers); LDACanVarSolver, inherits from LDASolver and computes the solution through canonical variates algorithm (shared by bin class. and dim. red. canvar solvers)
fix bias calculation in LDA #3886
option to compute SVD by bidiagonalization divide and conquer algorithm (with Eigen >= 3.3)
MulticlassLabels constructor from BinaryLabels (I know there is already some work going on labels, so let me know if there is a better way)
LDA benchmarks: https://gist.github.com/micmn/d4b51bf39676621afca563b55bdb9a98 :dancer:

Certainly some docs are missing, I'll double check.

@micmn great! now the only thing that's left is to update the shogun-data repo with the new integration test data for binary lda (this is why all the jobs on travis failed). lemme know if you need help how to do it

@micmn there are some formatting errors: https://travis-ci.org/shogun-toolbox/shogun/jobs/250312428#L807


Question about the architecture (graphTransformer)

I was looking at your implementation of attention here :
https://github.com/cvignac/DiGress/blob/main/src/models/transformer_model.py#L158
I have some question about the code :
Q = Q.unsqueeze(2)  # (bs, 1, n, n_head, df)
K = K.unsqueeze(1)  # (bs, n, 1, n head, df)

# Compute unnormalized attentions. Y is (bs, n, n, n_head, df)
Y = Q * K

Here I have a question because in the classic attention mecanism we have Y which have a dimension of (bs, n, n, n_head) not feature specific. I don't know if this what the author wanted (this is not proper outer product this is element wise multiplication).
Also a few line after we have :
attn = masked_softmax(Y, softmax_mask, dim=2)  # bs, n, n, n_head
print("attn.shape : ", attn.shape) # i add this

As the attention shape I obtain (bs, n, n, n_head, df) dimension (contrary to the comment).
The code is not really implementing "real" graph transformer attention like other code like  :
https://docs.dgl.ai/_modules/dgl/nn/pytorch/gt/egt.html#EGTLayer
But as your code give me better results than the one above (with a proper attention mecanism) I wonder if this is something that the authors made intentionnally.

Copying the answer from https://github.com/cvignac/DiGress/issues/47
your observation is correct. It’s not exactly the standard attention
mechanism. I’ve not thoroughly compared the two, but current code was
written on purpose. The reason for this is that we have to manipulate
features of size (bs, n, n, de) anyway, so using vector attention scores
instead of scalar does not create a strong memory bottleneck. I would be
interesting to investigate this further, though.
Clement
Le mar. 30 janv. 2024 à 14:59, Adrien B @.***> a écrit :

I was looking at your implementation of attention here :
https://github.com/cvignac/DiGress/blob/main/src/models/transformer_model.py#L158
I have some question about the code :
Q = Q.unsqueeze(2)  # (bs, 1, n, n_head, df)K = K.unsqueeze(1)  # (bs, n, 1, n head, df)
Compute unnormalized attentions. Y is (bs, n, n, n_head, df)Y = Q * K
Here I have a question because in the classic attention mecanism we have Y
which have a dimension of (bs, n, n, n_head) not feature specific. I don't
know if this what the author wanted (this is not proper outer product this
is element wise multiplication).
Also a few line after we have :
attn = masked_softmax(Y, softmax_mask, dim=2)  # bs, n, n, n_headprint("attn.shape : ", attn.shape) # i add this
As the attention shape I obtain (bs, n, n, n_head, df) dimension (contrary
to the comment).
The code is not really implementing "real" graph transformer attention
like other code like :
https://docs.dgl.ai/_modules/dgl/nn/pytorch/gt/egt.html#EGTLayer
But as your code give me better results than the one above (with a proper
attention mecanism) I wonder if this is not something that the authors made
intentionnally.
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--
Clément Vignac

I am doing some experiment on my own graph dataset. Your implementation seems to be more performant that the standard graph transformer (at least the one I tried from DGL library). Yours clearly achieve to generate more plausible edges.
I am doing more experiements to confirm this (I currently only have "visual" clues and noisy loss curves).
Your implementation is equivalent of having a classic graph transformer but with as many head as original dimension, so you ends up having heads of only one dimension (I mean if df = 1 you will obtain the same results).


The name of the city is not same with description.

URL: https://admin.peviitor.ro/
Browser: Chrome
Device: Laptop
OS: Windows 10
STEPS TO REPRODUCE:
1.Open the URL in the browser
2.Search for company "Smarttech"
3.Click on "Vizualizeaza joburi"
EXPECTED RESULTS:
The name of the city must be same with description.
ACTUAL RESULTS:
The name of the city is not same with description.

Aici au fost harcodate. :))))


(profiles, pipeline) Add workload identity binding for service account. Partial #227

Partial #227
Need some help validating GCS access after applying this change.
Profile controller is validated to be working to access gcp resources.

/LGTM
Note, when we move workload identity bindings to each package, it's clearer that we might want to also move the corresponding GSA to its package. These actions continue to push each package towards installable by itself and not depend on common settings

/LGTM
Note, when we move workload identity bindings to each package, it's clearer that we might want to also move the corresponding GSA to its package. These actions continue to push each package towards installable by itself and not depend on common settings

Thank you Yuan! I added a card in release 1.3 to track this change.


Max of 200 documents when querying Cloudant

Is it possible I get a maximum of 200 documents when querying a Cloudant database? I'm using pouchdb as a client to the Cloudant database.

I don't really understand your question. But you can use limit to limit the number of documents retrieved.
All misspelling thanks to my iPhone

On 04 Nov 2015, at 4:56 PM, arnoutaertgeerts<EMAIL_ADDRESS>wrote:
Is it possible I get a maximum of 200 documents when querying a Cloudant database? I'm using pouchdb as a client to the Cloudant database.
—
Reply to this email directly or view it on GitHub.

When I use the plugin to query my Cloudant database the maximum amount of docs that are returned is 200 although I did not specify a limit. I'm expecting a lot more documents :)

You need to test and see if when using curl or the cloudant dadhboard if you get the same number of docs or more.
All misspelling thanks to my iPhone

On 04 Nov 2015, at 4:59 PM, arnoutaertgeerts<EMAIL_ADDRESS>wrote:
When I use the plugin to query my Cloudant database the maximum amount of docs that are returned is 200 although I did not specify a limit. I'm expecting a lot more documents :)
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When I execute the exact same query in the cloudant dashboard I get all the documents (so > 200). I tested this for several different databases.

Can you share your query syntax.
All misspelling thanks to my iPhone

On 04 Nov 2015, at 6:06 PM, arnoutaertgeerts<EMAIL_ADDRESS>wrote:
When I execute the exact same query in the cloudant dashboard I get all the documents (so > 200). I tested this for several different databases.
—
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        "selector": {
          "offtake": {
            "$exists": true
          }
        },
        "fields": [
          "_id",
          "offtake"
        ]
      }```

If I do something like this
db.find({
   "selector": {
    "_id": {
      "$gt": 0
    },
    "myfield": {
      "$exists": true
    }
  },
  "fields": [
    "_id",
    "_rev"
  ],
  "sort": [
    {
      "_id": "asc"
    }
  ]
})

With a Cloudant database I get more than 200 documents. Using just $exists shouldn't work with Cloudant as you need to provide another field to query off. As the docs say:
You cannot use combination or array logical operators such as $regex as the basis of a query when using indexes of type json. Only equality operators such as $eq, $gt, $gte, $lt, and $lte (but not $ne) can be used as the basis of a query for json indexes.


Refactor rpc. Split lib-rpc into lib-rpc-app and lib-rpc-core

I am proposing to move agent_rpc.rs, conv_rpc.rs which are like a demo implementation on top of the core macro: generate_common_rpc_fns.
This will allow me to create a new crates/lib-rpc-myapp along the lines of crates/lib-rpc-app. Since I will not be editing framework (meaning rust10x/rust-web-app) syncing my fork from upstream will not demand careful look at diffs.
If @jeremychone would rather I take a different approach, I am happy to oblige. I am hoping you find this acceptable or are able to guide me along to a different approach more acceptable to you.

I like the direction of the PR. From a quick first scan, it looks pretty good.
I might need some time to review this, but thanks, this is good work, and I will definitely merge it if everything makes sense.

Glad you were able to take a quick look. I updated the comment with more notes.
As a first pass, I also want to separate out the rest of the demo items as well. Potentially

lib-model-demo (to take agent.rs, conv_msg.rs, conv.rs, conv_user.rs out of lib-core)
lib-web-core (potentially take reusable bits out of services/web-server)

Additionally, i feel that the lib-core/_dev_utils/dev_db.rs might be better taken out into it's own lib-core-demo-db or some such.

Allows less critical attention to PRs affecting those files in the future
Stick that dependency under a [profile.dev] so that even accidentally, it never makes it to staging/prod.

If you have any guidance along these lines, suggestions for lib names etc. I will be happy to make changes accordingly and send them your way.

@vamsi-juvvi the lib-core/_dev_utils/... uses some lib-core and is used by lib-core, so something will have to remain there.
Let's leave it there for now. In theory, I agree, but from a pragmatic point of view, I think we have a better net value/complexity ratio like this. We can move it somewhere else when needed. In my way, only lib-core should need those db-utils, as all data calls should go through the model. So, it's not that bad.

@vamsi-juvvi
Ok, I just saw the latest commit, and it adds React, which is interesting but not related to the initial intent of the PR.
The React addition is pretty cool, but React is not something I am familiar with (or intend to be familiar with), so it will be hard for me to maintain it when I update the codebase. This is a trick one.
Anyway, the fact that those two are in the same PR makes this PR tricky to merge. So, I am going to close this PR, but feel free to split them.
I might merge the rpc-core/app PR.
Regarding the ReactJS addition, I would be more comfortable adding a link to a fork/branch for people to look at.

Hah! Didn't realize I pushed the react stuff into the same branch. Will redo the PRs cleanly and send them back out.
Thanks for taking a look.


Upgrades for Node v13

These are API upgrades for Node version 13. I haven't checked older versions, can't remember how far back is supported.

I updated this PR to only apply the new API for Node versions 12+. This should maintain backwards compatibility for older Node versions.

Merged. Thanks for your contribution!

When might these changes be released? It seems it is currently preventing us from upgrading to electron 7


fix for issue 181 and updating the connection

This resolves #181 as well as issues with the DefaultDevicePortalConnection implementation of UpdateConnection.
The UpdateConnection change is to add a third parameter to specify whether or not to preserve the original connection's port. On HoloLens and Mobile, the port number is not preserved as the most common use of this is to switch from USB (port 10080) to WiFi (port number based on scheme)
Also implemented are methods to get the correctly formatted URI for accessing the Mixed Reality Capture live stream data on HoloLens.

Hi @davidkline-ms, I'm your friendly neighborhood Microsoft Pull Request Bot (You can call me MSBOT). Thanks for your contribution!

It looks like you're a Microsoft contributor (David Kline (XBOX)). If you're full-time, we DON'T require a Contribution License Agreement. If you are a vendor, please DO sign the electronic Contribution License Agreement. It will take 2 minutes and there's no faxing! https://cla.microsoft.com.

TTYL, MSBOT;

Except for the open question about StyleCop, looks great to me, thanks!

I'm having trouble connecting to the Hololens via USB on a new computer. I can connect to this device from another computer so I know it's possible, but the new computer must be missing a setting or something. I've copied every proxy setting, internet options settings, etc I can think of, but still cannot connect. When I go to http://<IP_ADDRESS> (or http://<IP_ADDRESS>:10080), I get this chrome browser message: "This site can’t be reached. <IP_ADDRESS> refused to connect." and ERR_CONNECTION_REFUSED
I have WiFi disabled (not allowed to use WiFi behind company firewalls), I have proxy settings correct, developer mode on, Device portal on. As I said, I can connect to this HoloLens from another computer but not my new one.
###What setting am I missing??????


Sender: Reply-To values override email template values even when empty

Even when empty, Email sender's reply-to-name and reply-to-email-address values will override the email template's values. It should be discussed if this should only happen when both values are explicitely set (i.e. not empty).

Thinking more about this I come to the conclusion that the values should indeed always be overriden. Closing this.


chore: remove needsTools param

Cherry-pick of https://github.com/microsoft/vscode-python/pull/24494 to test more APIScan developments.

@rzhao271 Can you cherry pick this commit as well: https://github.com/microsoft/vscode-python/commit/5508de4bdad1e4056d86a852a31806102209e926
That should unblock the linting.


Unable to download results

Hello
I uploaded my fasta and metadata.txt files into the online pipeline v 2.2
The process completed in one second, i am not able to download my data when i press the button download, nothing happen

when i tried to do stage-2 on command line. i got this error:
File "pandas/_libs/index.pyx", line 136, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/index.pyx", line 163, in pandas._libs.index.IndexEngine.get_loc
File "pandas/_libs/hashtable_class_helper.pxi", line 5198, in pandas._libs.hashtable.PyObjectHashTable.get_item
File "pandas/_libs/hashtable_class_helper.pxi", line 5206, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'CellNumber'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/root/esraa/miniconda3/envs/args_oap/lib/python3.10/site-packages/args_oap/argoap_pipeline_stagetwo_version3.py", line 177, in
result1_type["percell"] = result1_type["ratio"] / result1_type["CellNumber"]
File "/root/esraa/miniconda3/envs/args_oap/lib/python3.10/site-packages/pandas/core/frame.py", line 3505, in getitem
indexer = self.columns.get_loc(key)
File "/root/esraa/miniconda3/envs/args_oap/lib/python3.10/site-packages/pandas/core/indexes/base.py", line 3623, in get_loc
raise KeyError(key) from err
KeyError: 'CellNumber'

Hi,
Is column 'CellNumber' in your meta-data-online.txt empty? Did you try to run both stageone and stagetwo locally using the latest version of args_oap (>3.0)?
Xi

Hi,
Is column 'CellNumber' in your meta-data-online.txt empty? Did you try to run both stageone and stagetwo locally using the latest version of args_oap (>3.0)?
Xi

I used bioconda version beta
Cell number column is not empty

Metadata for stage one doesn't contain Cell number because i don't now cell number in this metagenomic data. Metadata_online for stage two has Cell number
Should i add 'cell number' column in the first metadata file (for stage one) and leave its cells empty?

Should i add 'cell number' column in the first metadata file (for stage one) and leave its cells empty?

No, this is not needed.
What command did you use for stagetwo? Is parameter -m meta-data.txt or -m meta-data-online.txt?

-m Metadata_online.txt which which i attached its screenshot above
في الأربعاء، ٢٤ أغسطس ٢٠٢٢ ٩:٥٠ ص Xi Chen @.***> كتب:

Should i add 'cell number' column in the first metadata file (for stage
one) and leave its cells empty?
No, this is not needed.
What command did you use for stagetwo? Is parameter -m meta-data.txt or -m
meta-data-online.txt?
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@.***>

Similar issue encountered.
I uploaded my fasta and metadata.txt files into the online pipeline v 2.2
The process completed in one second, i am not able to download my data when i press the button download, nothing happen
Is there something wrong with the webserver?


Allow Cutter to use Python plugins

One cannot use Python plugins with radare2-cutter.
As stated in their documentation:

The support for Python plugins is only available if Cutter was built with the options CUTTER_ENABLE_PYTHON and CUTTER_ENABLE_PYTHON_BINDINGS enabled.

I tried to add it myself, but after making very tiny progress, I can't figure why the compilation is stubbornly failing, and feel completely stuck...
What I have so far is available here: https://github.com/Pamplemousse/nixpkgs/tree/cutter .
Any suggestions @Mic92, @dtzWill?
Thanks!

@Pamplemousse Could you open this as a PR? Than I can checkout the branch and push fixes as necessary.

@Mic92 Done!
See #101571 .

I amended the PR.

Closing because NixOS/nixpkgs#101571 has been merged.


Add option to use vhs for animated gifs

The charmbracelet/vhs tool is super slick and creates gorgeous animated gifs from very simple instruction sets.
It could be nice to make use of the code that rich-codex has to find commands to run and then pipe to vhs instead of using the normal rich code to make animated gifs instead of svgs.
Shouldn't be too tricky to auto-generate the .tape instructions on the fly, and could also package that in the config for added customisation.

Another really nice looking one that makes animated SVGs: https://github.com/marionebl/svg-term-cli


Error on delete QuickAdmin

Please check delete option on the Admin Panel,

P.S.: Now I got the screen..

Hello,
Thank you for reporting this bug. We will check what was wrong with it. In the mean time, could you please provide us some details:
When was this CRUD created?
Which fields it has?
This will help us to check what is wrong.

@ModestasV sorry my late reply...
For the versions 5.3 it´s working ok, but still remains the issue with my old one, which I would like to delete it.
Here it is:

It only has a menu created... trying to delete or add anything comes with error messages as well.

@evertramos thank you for reporting that. The issue with our online version in general that some older adminpanels are now "broken" cause new features didn't regenerate it successfully. Will investigate your particular case in upcoming days.

@evertramos Hello, no worries about the reply, it is still great to hear more from you!
As for this specific case, we have a safety mechanism in our system which checks if the cruds are not "broker" (for example, a bug caused database table to be deleted but then something messed up). This is the case with older panels as we honestly had some unexpected cases/failures. We are sorry for this error as you can't delete your panel. If you want to remove it completely - confirm that here or write us an email at<EMAIL_ADDRESS>with your registration email and we will delete it manually.
Again, sorry for this, we are constantly trying to improve the system and whoopsies like this happen..

@PovilasKorop  @ModestasV  Thanks guys!
Yes you can remove it for me, thanks for that!
I will try to keep the tests up on my side.
Cheers!

@evertramos Removed your panel and changed its name a bit, to clarify that it is broken. Have fun testing!


Chapter 6 deployment build fails

following the instructions on chapter 6 to deploy on vercel the following errors occur
Warnings:
Warning: Detected "engines": { "node": ">=20.12.0" } in your package.json that will automatically upgrade when a new major Node.js Version is released. Learn More: http://vercel.link/node-version
Errors:
Collecting page data ...
tl [VercelPostgresError]: VercelPostgresError - 'missing_connection_string': You did not supply a 'connectionString' and no 'POSTGRES_URL' env var was found.
    at tf (/vercel/path0/.next/server/app/seed/route.js:60:5026)
    at Object.get (/vercel/path0/.next/server/app/seed/route.js:60:6072)
    at /vercel/path0/.next/server/app/seed/route.js:1:3957
    at t.a (/vercel/path0/.next/server/webpack-runtime.js:1:866)
    at 8854 (/vercel/path0/.next/server/app/seed/route.js:1:3850)
    at t (/vercel/path0/.next/server/webpack-runtime.js:1:127)
    at /vercel/path0/.next/server/app/seed/route.js:1:1177
    at t.a (/vercel/path0/.next/server/webpack-runtime.js:1:866)
    at 3113 (/vercel/path0/.next/server/app/seed/route.js:1:967)
    at t (/vercel/path0/.next/server/webpack-runtime.js:1:127) {
  code: 'missing_connection_string'
}
> Build error occurred
Error: Failed to collect page data for /seed
    at /vercel/path0/node_modules/.pnpm/next@15.0.0-rc.0_@babel+core@7.24.7_react-dom@19.0.0-rc-f994737d14-20240522_react@19.0.0-rc-f_tdi4orn62rfjbymsd33ya6r2le/node_modules/next/dist/build/utils.js:1274:15
    at process.processTicksAndRejections (node:internal/process/task_queues:95:5) {
  type: 'Error'
}
 ELIFECYCLE  Command failed with exit code 1.
Error: Command "pnpm run build" exited with 1

Try https://github.com/vercel/next-learn/issues/768#issuecomment-2190168439

The Vercel deployment error I-m getting is from a starter code file (./app/ui/acme-logo.tsx:2:26), saying Type error: Cannot find module '@/app/ui/fonts' or its corresponding type declarations.

https://github.com/vercel/next-learn/commit/d379162091cac7ea4d0e3054a9fb527c00596264


Update bracket rake task to populate entire bracket

@trevorghess I think there's a way to ignore whitespace on the pull request, which will help a lot


Is it possible to specify charset and collation for table creation?

Hi,
I'm wondering if it's possible to specify charset and collation for table creation?
I searched existing issues and found one answer that allows to set it at the column level
sql:"type:VARCHAR(5) CHARACTER SET utf8 COLLATE utf8_general_ci"
What is I'd like to specify the entire table charset/collation?
Thanks

Your Question
Is it possible to specify charset and collation for table creation?
The document you expected this should be explained
Consdier following struct
type Contract struct {
	gorm.Model
        code int64
        rate float64
}

By default db.AutoMigrate(&Contract{}) creates the database table using default charset and collation (Mysql)
Expected answer
Expect a way to specify charset and collation at the struct level so that the corresponding table schema will be created using specified charset and collation

Your Question
Is it possible to specify charset and collation for table creation?
The document you expected this should be explained
Consdier following struct
type Contract struct {
	gorm.Model
        code int64
        rate float64
}

By default db.AutoMigrate(&Contract{}) creates the database table using default charset and collation (Mysql)
Expected answer
Expect a way to specify charset and collation at the struct level so that the corresponding table schema will be created using specified charset and collation

db.Set("gorm:table_options", xxx)

db.Set("gorm:table_options", xxx)

db = db.Set("gorm:table_options", "ENGINE=InnoDB CHARSET=utf8 COLLATE=utf8_bin")
Note: new db has to be stored as it is cloned by SET()


Decode json errors

I'm occasionally getting spurious json decode errors when trying to run larger numbers of pods.
kubectl kboom generate --mode=scale:60 --load=pods:1000

<snip>
2019/04/27 04:10:35 Can't create pod scale-sleeper-936: decode error status 429: decode json: invalid character 'T' looking for beginning of value
2019/04/27 04:10:35 Can't create pod scale-sleeper-1176: decode error status 429: decode json: invalid character 'T' looking for beginning of value
2019/04/27 04:10:35 Can't create pod scale-sleeper-767: decode error status 429: decode json: invalid character 'T' looking for beginning of value
2019/04/27 04:10:35 Can't create pod scale-sleeper-275: decode error status 429: decode json: invalid character 'T' looking for beginning of value
2019/04/27 04:10:35 Can't create pod scale-sleeper-896: decode error status 429: decode json: invalid character 'T' looking for beginning of value
2019/04/27 04:10:35 Can't create pod scale-sleeper-160: decode error status 429: decode json: invalid character 'T' looking for beginning of value
2019/04/27 04:10:35 Can't create pod scale-sleeper-376: decode error status 429: decode json: invalid character 'T' looking for beginning of value
2019/04/27 04:10:35 Can't create pod scale-sleeper-130: decode error status 429: decode json: invalid character 'T' looking for beginning of value
2019/04/27 04:10:35 Can't create pod scale-sleeper-921: decode error status 429: decode json: invalid character 'T' looking for beginning of value
2019/04/27 04:10:35 Can't create pod scale-sleeper-403: decode error status 429: decode json: invalid character 'T' looking for beginning of value
<snip>

Thanks a lot for reporting this @lachie83, much appreciated!
A quick look at the responsible code segment suggests that I'm overloading the API server with requests, hence the HTTP 429 response code and due to that, rather than sending JSON back the API server sends some error message in plain-text that the library tries to decode because it thinks it's actually JSON.
This is not super surprising since I don't have any rate limiting in the code creation part. My hunch (or working hypothesis, if you prefer): adding some short, random delays in the ms range after go pr.launch() should address this issue.

This sounds like a reasonable approach. Just out of interest would it be better to make the go routine handle a 429 from api server?

Yeah, handling 429 from API server, in addition, wouldn't hurt. Nevertheless, not hammering the API server like a berserker would prolly not be a bad thing to do, in the first place ;)

Or, even better, three scale testing strategies: berserker (the current implementation), good-citizen (rate limiting), and graceful (handling 429s). WDYT?

I agree but it's probably quickest to implement the good-citizen based on your original proposal and ship it.

@lachie83 are you working on this? We also see this issue in our test setup (and would like to fix it).

Thanks for the reminder, will try to put a fix together for this over the weekend

@johscheuer given your overall contributions, I mean, if you wanna fix that as well … :)

I can take a look next week :)

OK, super @johscheuer … let's see who's faster, LOL ;)


Visual indication of file's read-only status

Those of us using Perforce often browse files that are read-only because they're not checked out yet (unlike Git, which always keeps files writable).
It would be very useful to have a visual indication of a file's read-only vs. read-write status, e.g., a lock icon next to the filename in the title bar or the "Working Files" list.

I had a look and apparently Brackets doesn't expose the read-only (or other attributes) status in the file API.
My starting point was the Various Improvements plugin which fetches the file date / time and display it.
https://github.com/Dammmien/brackets-various-improvements.git
I found something better (somehow): the Perforce plugin:
https://github.com/JoshGalvin/brackets-perforce.git
Very primitive (just checkout to default CL the file if dirty / add it if new / delete it if removed) but already eases my life.
Having a read-only indicator can still be useful ("it is file in a CL?").

I made an extension for this - https://github.com/mseiler025/show-read-only

Thanks @mseiler025 .
Could you post a screenshot in the GitHub readme.md page in the extension repo?

@abose posted screenshot

There is more work to be done on this extension, but I wanted to get something out there for now.
Things that I can think of that could be done:
-handle listed known limitations
-optionally, use addClassProvider to make file names for read only files another color, etc (might be useful if you have another icon provider and don't want to see multiple icons)
-as @isonno mentioned, add visual indication at that top (title bar) of current open document
-as @1for mentioned, have an option to make the read only file writable (possibly through a context menu item), or make a copy of the read only file to write to it

Thanks @mseiler025 For updating.
Closing as extension available.


VRG: status to keep updating on last sync time per PVC/VR

Enables application owner to look at the latest replica across peers
(from HackMD list)

Marking as duplicate; already covered in #66


Update chain-list

[x] Set SubWallet Official 3 as the default pool for Vara
[x] https://github.com/Koniverse/SubWallet-ChainList/issues/213
[x] Add Block Explorer for Enjin Relaychain https://enjin.subscan.io/
[x] Add Block Explorer for Enjin Relaychain https://matrix.subscan.io/
[x] https://github.com/Koniverse/SubWallet-ChainList/issues/212
[x] https://github.com/Koniverse/SubWallet-ChainList/issues/215

[ ]  Remove price WeHMND. Because eHMND and WeHMND coexist but not be summed up by $ value in wallet

Version test : http://file.cdmteck.com/s/r5mXRTwRRjLJ7yX
Validation passed in case :

Set SubWallet Official 3 as the default pool for Vara

[Commune AI] [COMAI] Add support for Commune AI blockchain and COMAI token (Mainnet)

=> Discuss more about price

Add Block Explorer for Enjin Relaychain https://enjin.subscan.io/

Add Block Explorer for Enjin Relaychain https://matrix.subscan.io/

[DBChain] [DBC && DLC] Integrate DBC and DLC tokens from the DBChain network into Subwallet #212

[Avail Turing] Support Avail Turing

=> Staking : improve later

Remove price WeHMND. Because eHMND and WeHMND coexist but not be summed up by $ value in wallet


Update README.md

Added Feature Tokenizer Transformer (Tabular Deep Learning)

Hi @Ritvik19. The notebook seems to be in private mode. You might need to enable public sharing.

Hi @omarsar I have made few changes in the notebook and made it public as well


AIRFLOW-296: template_ext is being treated as a string rather than a tuple in qubole operator

Dear Airflow Maintainers,
Please accept this PR that addresses the following issues:

https://issues.apache.org/jira/browse/AIRFLOW-296

LGTM


Detect storybook

In auto-installed sites we may have detected that the site is using Next.js, but the site may actually be building the Storybook. This currently causes the build to fail. This is a common enough scenario to deserve special handling, where we check the build command and if it's calling build-storybook then skip the plugin.

@ascorbic I just upgraded to the latest version of this plugin and now my builds are failing. I have a bit of a unique use case where I'm building a Next.js site and Storybook, outputting the storybook static files into the out directory on build. So I'm actually building a Next.js site, but due to my build command containing build-storybook as well, this plugin gives the "Site seems to be building a Storybook rather than the Next.js site, so the Essential Next.js plugin will not run." error and does not deploy.
We have a very aggressive deadline, so I may need to downgrade to the version prior to this change for now, but I'd like to see the ability to disable this somehow. While we're on an enterprise plan, I'm not sure it's worth going through the trouble of setting up a second site specifically for storybook.

Hello @KyleRoss,
This sounds like a job for an env var, which I'm planning to add probably this week. You'll be able to set something like NEXT_STATIC_EXPORT=false. I'd agree that the short-term fix is to downgrade, and then you can switch to the env var when we release that soon.


Fix unclosed console.group and overhaul logging in loader.ts

Pull Request Description

Fixes #6899

Important Notes
The linked issue is actually a combination of two issues - but the other (the cloud IDE using a different version of pkg.wasm) is unsolvable as that is intended behavior
Checklist
Please ensure that the following checklist has been satisfied before submitting the PR:

[x] The documentation has been updated, if necessary.
[x] Screenshots/screencasts have been attached, if there are any visual changes. For interactive or animated visual changes, a screencast is preferred.
[x] All code follows the
Scala,
Java,
and
Rust
style guides. In case you are using a language not listed above, follow the Rust style guide.
All code has been tested:

[x] Unit tests have been written where possible.
[x] If GUI codebase was changed, the GUI was tested when built using ./run ide build.

Still performing the QA.