text:
Support for hexadecimal passwords of System.Data.SQLite/RC4

System.Data.SQLite supported hexadecimal passwords, like this: data source=mydb.sqlite;hexpassword=6d696c6b. In case I'm playing in sandbox, and those four bytes are 'milk' in ASCII encoidng, I can also access such database with data source=mydb.sqlite;password=milk, and respectively later with SQLite3MultipleCiphers PRAGMA cipher = rc4 and PRAGMA key = 'milk'.
It's reasonable to assume that under the hood there is just binary key used by the algorithm whatsoever, so it's just a matter of finding a way to pass it down.
Problem is that when it comes to real world databases encrypted with random sets of 32 bytes, just straight decoding them into ASCII (or in local code page, or something similar), chances of getting string valid from the point of view of SQLite are pretty slim. Furthermore, SQLite doesn't let any operators left of pragma's equal, so CASTs, CHARs and ||s are out of option, and there are no variables in SQLite that I know of. So I was not able to access such databases using SQLite3MultipleCiphers. Still I tried passing the key using both special ways (SQLCipher and sqleet) too, but obviously it didn't work.
It would be really handy if it was possible to pass hex passwords in similar way for RC4.

[...] It's reasonable to assume that under the hood there is just binary key used by the algorithm whatsoever, so it's just a matter of finding a way to pass it down.

Typically, a hash algorithm is used to derive the actual encryption key. For the cipher schemes sqleet (ChaCha20) and SQLCipher there exist methods to use a special key syntax to circumvent the key derivation. Those methods are supported by SQLite3MultipleCiphers as well to be compatible with the original implementations of the ciphers.

It would be really handy if it was possible to pass hex passwords in similar way for RC4.

Currently, SQLite3MultipleCiphers allows to specify hex passwords via URI parameter hexkey (see URI parameters). However, I have to admit that it would be convenient to be able to specify hex passwords via pragma as well.
I will add pragma support for hex passwords with the next release of SQLite3MultipleCiphers.

Thank you. I thought I missed something. In paticular, all the URI parameters went under radar for me :)

Release 1.3.10 now includes this enhancement.

Thank you, much appreciated! (and separate thank you for fix with 40 bytes)

authors: professor-k utelle


text:
Decode LoR's dock code

This revision includes:

Decode LoR's dock code (#18)

References

https://github.com/RiotGames/LoRDeckCodes
https://github.com/EvanKaraf/LoRDeckpp

Add library 'cppcodec' as submodule
Refactor code

Delete 'std::unique_ptr' of the variable 'm_cards'

Create classes

Deck: This class stores deck information that contains exactly 40 cards. Players can only have 40 cards in their deck, of which 6 can be champion cards. All cards have a max limit of 3 copies per deck
DeckCode: This class encodes/decodes Legend of Runeterra decks to/from simple strings

Add constants

MAX_KNOWN_VERSION: he max known version
MAX_ALLOWED_IN_DECK: The maximum number of cards that is allowed in the deck
START_DECK_SIZE: The number of cards that can be stored in the deck at game start

Add utility functions

GetNextVarInt(): Gets next int variable
RegionToString(): Converts enum value region to string

The reason of 'dockercloud-stage' failure is gitsubmodule. Please ignore it.

source: gharchive/pull-request

repo: utilForever/Runeterra

license: MIT

license_type: permissive

license_source: github-api


text:
The cursor is not changing symbols

The cursor is not changing symbols – they overlap.
It happens usually when I'm opening a text/code editor.

When I enable the Capture Mouse option, the cursor stack halfway.
https://user-images.githubusercontent.com/50456099/150654405-241ea6b1-5b4a-46b0-8005-bd353610bc66.mov
Configuration

UTM Version: 3.0.3
OS Version: 12.1
Apple Silicon
Spice guest tools: 0.164.3
windows 11 build 22000.438

I've experienced this as well. The problem is with the SPICE drivers and how Windows 10/11 handles the cursor. It seems like Windows isn't always passing the right cursor image to the driver. But it needs to be debugged some more.

If I disable the mouse driver, it doesn't overlap, so it is a good temporary solution :)

source: gharchive/issue

authors: idoio osy

repo: utmapp/UTM


text:
Ubuntu Server 22.04.1 installer freezing after selecting "Install Ubuntu Server" (Mac M1 PRO Ventura 13.0, UTM 3.0.4)

Describe the issue
So, I am trying to install Ubuntu Server 22.04.01, on my Mac M1 Pro, UTM 3.0.4, I've made sure to download the ARM version from the UTM Gallery, and after starting the virtual machine and selecting "Install Ubuntu Server" I get stuck in a frozen black screen with a cursor and nothing else happens (screenshot attached). I've tried the same with Fedora, and Ubuntu Desktop, with the same results. Checked the Console Crash Reports to search for any log, and it's empty.
I then decided to download the x64 version and installed it using emulation, and had no issues installing, however, emulation is frustratingly slow. Is there any way you could recommend me to know why the ARM boot is freezing and not advancing, or how to fix this?
I've seen similar threads with the same debug log warning (however it's a warning, not an error), and none of those threads seem to be consistent on a solution.
Thank you very much!
Configuration

UTM Version:  3.0.4
macOS Version:  Ventura 13.0
Mac Chip: M1 Pro 2021

Crash log
No crash log registered, log is empty.
Debug log
qemu-aarch64-softmmu: warning: Spice: playback:0 (0x14c02b940): setsockopt failed, Operation not supported on socket
qemu-aarch64-softmmu: warning: Spice: record:0 (0x14c02b9f0): setsockopt failed, Operation not supported on socket


text:
I can't show control bar when system boot up

I can't show control bar when system boot up
When I turn on the system and try to press the Show control bar button > it doesn't work.
Or rather, when you click on it, the widgets do not appear. I tried on iPhone 11 OS 16.3.1. Hope the problem is clear
Configuration (required)

UTM Version: v4.2.5
OS Version: 15.4.1, 16.3.1
Device Model: Xr jailbreak, 11 without jailbreak
Is it jailbroken (name jailbreak used)? Dopamine
How did you install UTM? Github

Can you provide a screen capture?


text:
Manually specify TZ

This manually specifies a TimeZone so that it is not blank.

gonna try merging this and see if it works on staging


text:
Improve readme; improve scope handling; support multiple namespaces per file; add tests

Fixes #1 and #2.

Codecov Report
Attention: Patch coverage is 85.52632% with 11 lines in your changes missing coverage. Please review.

Project coverage is 78.17%. Comparing base (77fecec) to head (3943353).

Files
Patch %
Lines

src/PhpImportsParser.php
71.42%
6 Missing :warning:

src/PhpImportsFile.php
86.66%
2 Missing :warning:

src/TypeResolver.php
81.81%
2 Missing :warning:

src/PhpImportsResolver.php
88.88%
1 Missing :warning:

:exclamation: Your organization needs to install the Codecov GitHub app to enable full functionality.
Additional details and impacted files
@@             Coverage Diff              @@
##               main       #5      +/-   ##
============================================
+ Coverage     74.23%   78.17%   +3.93%
- Complexity       97      112      +15
============================================
  Files             4        7       +3
  Lines           295      307      +12
============================================
+ Hits            219      240      +21
+ Misses           76       67       -9

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.


text:
factor::miller_rabin: Minor improvements

[x] Remove duplicate computation.
[x] Mark miller_rabbin::Result as #[must_use] to ensure no useless
computation is performed.

Will conflict with #1554, but the merge should be pretty trivial.

Rebased post #1554

repo: uutils/coreutils


text:
Mg/document upload

Notion ticket link

Ticket Name
https://user-images.githubusercontent.com/35342787/136640674-e92824af-82ed-48aa-a8c2-af77b045b074.mp4

Implementation description

Created 2 components

DragAndDrop.tsx

uses a FileUploadButton
NO drag and drop functionality yet will look into 3rd party package most likely https://www.npmjs.com/package/dropzone

FileUploadButton.tsx

Uses a button and an input (ref on input so when button clicked we add files to the input
Multiple files are supported if you uncomment the multiple keyword on the input (though formatting may get messed up)

Created document-upload page

Checks sessions, redirects to home if no valid session
gets query parameter of /document-upload?type=SOMETHING

valid types are "", "criminal-check", "income-proof", "curriculum-plans"

if no parameter, s3 bucket folder will be sent to "other"
if invalid parameter type, 404 returned in console (no error page yet) from backend
if query parameter is not type redirected back to /document-upload
if query parameter type is not set redirected to  /document-upload

gets presigned s3 url for posting from /api/upload/url?path=TYPE}&file=PREFIXED_FILENAME

filename currently prefixed with user info as email-session_id-filename

will transition from this prefix to another method after demo (ticket)

uploads file as FormData to presigned url

Created backend api /api/upload/url?path=TYPE}&file=PREFIXED_FILENAME

checks valid session
checks valid upload types
creates presigned url with key (s3 path) from type and filename
max 5MB file currently

Simple terraform configuration for s3 creation

creates folders in s3
upload types/folder names specified in terraform.tfvars --> decoupled from type checks in api backend

would be good to centralize

Steps to test

Try using an invalid query parameter (?xxxx=...) --> redirect back to /document-upload'
Try not assigning query parameter ?type to anything --> redirected back to  /document-upload
Try uploading without logging in (should be redirected back to home)
Try uploading with invalid value not support query parameters (404 returned from backend)
Try uploading logging in
Check S3 bucket for file

What should reviewers focus on?

Dev: File uploading for supported types ("",  "criminal-check",  "income-proof",   "curriculum-plans")
Dev: Logic of eligibility
Dev: Code style
Design: Look and feel of upload process

TODO

route to 404 page
drag and drop functionality
better error handling
store s3 filenames for each uploader in database

Checklist

[x] My PR name is descriptive and in imperative tense
[x] I have run the linter
[x] I have requested a review from the PL, and/or other devs who have background knowledge on this PR or who will be building on top of this PR

I think we also want some close button on the top right to return to the page below we redirected to the upload page. We might need a thumbs up from the designers.
It's to support flows like this:

authors: MatoPlus matthewgeng


text:
Commits missing the Change-ID

Commits with the plugins are not attaching the Change-Id

If you do not use the IntelliJ plugin to checkout your project for Gerrit, you need to install the commit message hook manually, see: https://gerrit-review.googlesource.com/Documentation/user-changeid.html#creation
Though the plugin could show a warning when this hook is not installed and offer an option to manually install it.

It appears there is no support for Change-ID on Windows git clients by Gerrit: https://github.com/civiccc/gerrit/issues/9#issuecomment-454640547

@HenkPoley : Not sure if I understand correctly: can you please explain how the linked issue is related to this IntelliJ Gerrit plugin?

Maybe it isn't.
A colleague managed to get a 'run Git hooks' checkbox working in the get Commit sidepane on Windows via a Laragon supplied bash. So I guess now it does work. Even though gerrit only supports hooks in bash scripts for their basic operations, which you will need install separately on Windows.

authors: HenkPoley lssilva uwolfer

repo: uwolfer/gerrit-intellij-plugin

license_source: bigquery


text:
[Enhancement] remove convert_to_supported function

Description
As part of the array_api rollout, moving the capability of convert_to_supported in the table creation is desired. As checking for datatypes for oneDAL should occur on the tables, and not on the arrays before they become tables.  When they become tables, they can be converted to the supported type via the queue supplied to them.  This logic only currently occurs with numpy arrays, as sycl_usm_ndarrays are not allowed in _device_offload.dispatch to be moved off their current device (i.e. when queue devices don't match, an error is thrown). Given they are on their current device, they are already in a supported format. Dlpack will be handled separately in its own PR.

PR should start as a draft, then move to ready for review state after CI is passed and all applicable checkboxes are closed.
This approach ensures that reviewers don't spend extra time asking for regular requirements.
You can remove a checkbox as not applicable only if it doesn't relate to this PR in any way.
For example, PR with docs update doesn't require checkboxes for performance while PR with any change in actual code should have checkboxes and justify how this code change is expected to affect performance (or justification should be self-evident).
Checklist to comply with before moving PR from draft:
PR completeness and readability

[ ] I have reviewed my changes thoroughly before submitting this pull request.
[ ] I have commented my code, particularly in hard-to-understand areas.
[ ] I have updated the documentation to reflect the changes or created a separate PR with update and provided its number in the description, if necessary.
[ ] Git commit message contains an appropriate signed-off-by string (see CONTRIBUTING.md for details).
[ ] I have added a respective label(s) to PR if I have a permission for that.
[ ] I have resolved any merge conflicts that might occur with the base branch.

Testing

[ ] I have run it locally and tested the changes extensively.
[ ] All CI jobs are green or I have provided justification why they aren't.
[ ] I have extended testing suite if new functionality was introduced in this PR.

Performance

[ ] I have measured performance for affected algorithms using scikit-learn_bench and provided at least summary table with measured data, if performance change is expected.
[ ] I have provided justification why performance has changed or why changes are not expected.
[ ] I have provided justification why quality metrics have changed or why changes are not expected.
[ ] I have extended benchmarking suite and provided corresponding scikit-learn_bench PR if new measurable functionality was introduced in this PR.

/intelci: run

/intelci: run

/intelci: run

Why is sklearn 1.6 being installed?

/intelci: run

Failure in private CI unrelated.

authors: ethanglaser icfaust

repo: uxlfoundation/scikit-learn-intelex


text:
Rendering of frame and events in Multi Objects 2D renderer are not in sync

In the Multi Objects 2D renderer, there seems  to be an offset between the position of the object(in this case rugby ball) to the corresponding events that must be generated. This effect happens both while running the code on my system and in the demo video given in the wiki (https://www.youtube.com/watch?v=Yre8iS2LqPc&feature=youtu.be). Shouldn't the frame and events generated be in sync?

Hi,
This time offset is normal.
To simulate a real DAVIS camera, the framerate of the camera images is artifically throttled to 40 fps (https://github.com/uzh-rpg/rpg_esim/blob/master/event_camera_simulator/esim_ros/cfg/multi_objects.conf#L24). This causes the events to be always "in advance" compared to the frames. This is also what you would observe with a real DAVIS sensor.
You can disable throttling the framerate of the images by setting the variable ros_publisher_frame_rate to a very high value (say, 1000000000).


text:
Set homepage as Blog (broken with beta 16 update)

With the latest version of the extension the configuration of the homepage as Blog is broken, it picks up discussions instead of blog category posts.
To see the live bug you can go to flarumes or brickdose. To see the posts that are actually from the blog category add /blog to the url (it's a bit weird, when you go to e.g. brickdose.com/blog it shows the correct blog posts but automatically deletes /blog from the url) Edit: this cannot be done as a guest user (it gives you error) only if you are logged in, I have also temporarily removed the blog as a homepage on flarum.es because of the bug.
With /all in the url (brickdose.com/all) you can see that it is actually taking posts from discussions (with categories not added to the blog extension).
After a lot of testing I get no errors in console or logs. I rule out that this is an incompatibility with other extensions, the error occurred equally with about 60 extensions as with 4 extensions.
I leave some details of the server in case they are useful, anyway I could replicate the error on a xampp server (Windows) so I do not know how useful they will be...
Operating System: CentOS Linux 8
Kernel: Linux 4.18.0-240.15.1.el8_3.x86_64
Flarum core 0.1.0-beta.16
nginx version: nginx/1.18.0
10.3.28-MariaDB
PHP version: 8.0.3
Loaded extensions: Core, date, libxml, openssl, pcre, zlib, filter, hash, pcntl, readline, Reflection, SPL, session, standard, bz2, calendar, ctype, curl, dom, mbstring, fileinfo, ftp, gd, gettext, iconv, intl, json, exif, mysqlnd, PDO, Phar, SimpleXML, sockets, sodium, sqlite3, tokenizer, xml, xmlwriter, xsl, mysqli, pdo_mysql, pdo_sqlite, xmlreader, Zend OPcache

When I first got the error the server is running PHP 7.4.16 I decided to upgrade to PHP 8.0.3 for that was the problem, but the issue persists in the same way.

I noticed the same during my test today. Unfortunately for me it renders it unusable in the meantime :(

Thanks for reporting, I'll look at it this weekend

Thanks for reporting, I'll look at it this weekend

Thank you Jasper! I've edited the initial post with some more information after the tests I did yesterday, I hope it's helpful 😀

I had the same problem when I upgraded to beta 16, I went back to beta 15 which works, I don't know what happened with the upgrade

Wow thanks Jasper! I'm sorry to waste your time, of course our first instinct is to start looking at the extension.
What is odd is that users on discuss report blog as homepage working. I'm not sure why it would differ for people.
Anyways, looks like you cracked the case again 👍  At least I now know that my upgrade to beta 16 will not be happening so I can stop worrying about and wait for the next RC or stable :)

There isn't much we can do about this, but I'm still exploring some options... If anyone has some feedback/ideas, please let me know

Thank you very much for your dedication, it seemed such a weird bug that I really thought it was my server's fault.
With the possible breaking changes in beta 17-1.0 it's possible that I'll be on beta 16 for a while, in the issue the user says he has patched the bug by applying the commints, is it possible to do that in production from the server? Do you think it's too complicated or impossible to do that in my case?

Fortunately this has automatically been fixed in the new Flarum v1.0.0 version 🎉
I'll close this issue :)

authors: IamDarkle ctml91 ihhddis jaspervriends


text:
x509: certificate has expired or is not yet valid 同样一份配置文件，有的机器可以有的不行

我自己购买域名配置基于h2+nginx配置了，在windows电脑上稳定使用3年。
目前将客户端配置复制到mac上以后，使用V2RayU（core版本3.2）报错，具体为：
2022/05/03 18:35:36 [Info] [4057736577] proxy/socks: TCP Connect request to tcp:www.google.com:443 2022/05/03 18:35:36 [Info] [4057736577] app/dispatcher: default route for tcp:www.google.com:443 2022/05/03 18:35:36 [Info] [4057736577] common/mux: dispatching request to tcp:www.google.com:443 2022/05/03 18:35:36 tcp:127.0.0.1:50596 accepted tcp:www.google.com:443 [proxy] 2022/05/03 18:35:37 [Error] transport/internet/http: failed to dial to myserver.online:443 > x509: certificate has expired or is not yet valid: current time 2022-05-03T18:35:37+08:00 is after 2020-12-27T03:40:14Z 2022/05/03 18:35:37 [Error] transport/internet/http: failed to dial to myserver.online:443 > x509: certificate has expired or is not yet valid: current time 2022-05-03T18:35:37+08:00 is after 2020-12-27T03:40:14Z 2022/05/03 18:35:38 [Error] transport/internet/http: failed to dial to myserver.online:443 > x509: certificate has expired or is not yet valid: current time 2022-05-03T18:35:38+08:00 is after 2020-12-27T03:40:14Z 2022/05/03 18:35:39 [Warning] failed to handler mux client connection > proxy/vmess/outbound: failed to find an available destination > common/retry: [transport/internet/http: failed to dial to tcp:myserveronline:443 > Put "https://myserver.online:443/ray": x509: certificate has expired or is not yet valid: current time 2022-05-03T18:35:36+08:00 is after 2020-12-27T03:40:14Z transport/internet/http: failed to dial to tcp:myserver.online:443 > Put "https://myserver.online:443/ray": x509: certificate has expired or is not yet valid: current time 2022-05-03T18:35:37+08:00 is after 2020-12-27T03:40:14Z transport/internet/http: failed to dial to tcp:myserver.online:443 > Put "https://myserver.online:443/ray": x509: certificate has expired or is not yet valid: current time 2022-05-03T18:35:38+08:00 is after 2020-12-27T03:40:14Z] > common/retry: all retry attempts failed 2022/05/03 18:35:39 [Info] common/mux: failed to read metadata > io: read/write on closed pipe 2022/05/03 18:35:40 [Info] [2216922927] app/proxyman/inbound: connection ends > proxy/socks: connection ends > context canceled
我的服务器端配置文件为：
{     "port": 443,     "protocol": "vmess",     "settings": {       "clients": [         {            "id": "xxxxxxxx",            "alterId": 64          }       ]     },     "streamSettings": {       "network": "h2",       "httpSettings": {         "path": "/ray"       },       "security": "tls",       "tlsSettings": {         "certificates": [           {             "certificateFile": "/etc/v2ray/v2ray.crt",             "keyFile": "/etc/v2ray/v2ray.key"           }         ]       }     }   }
我的mac客户端的配置文件为：
outbounds": [     {       "mux": {         "enabled": true,         "concurrency": 8       },       "protocol": "vmess",       "streamSettings": {         "tlsSettings": {           "allowInsecure": true         },         "security": "tls",         "httpSettings": {           "path": "/ray",           "host": [             ""           ]         },         "network": "h2"       },       "tag": "proxy",       "settings": {         "vnext": [           {             "address": "myserver.online",             "users": [               {                 "id": "xxxxxxxx",                 "alterId": 64,                 "level": 0,                 "security": "auto"               }             ],             "port": 443           }         ]       }     },

是自签证书吗?

是的
kingwilliam @.***> 于2022年5月5日周四 07:15写道：

是自签证书吗?
—
Reply to this email directly, view it on GitHub
https://github.com/v2fly/v2ray-core/issues/1767#issuecomment-1118017571,
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{
  "outbounds": [
    {
      "mux": {
        "enabled": true,
        "concurrency": 8
      },
      "protocol": "vmess",
      "streamSettings": {
        "tlsSettings": {
          "allowInsecure": true
        },
        "security": "tls",
        "httpSettings": {
          "path": "/ray",
          "host": [
            ""
          ]
        },
        "network": "h2"
      },
      "tag": "proxy",
      "settings": {
        "vnext": [
          {
            "address": "myserver.online",
            "users": [
              {
                "id": "xxxxxxxx",
                "alterId": 64,
                "level": 0,
                "security": "auto"
              }
            ],
            "port": 443
          }
        ]
      }
    }
  ]
}

試試: 在 "httpSettings" 的 "host" 加入您的fqdn 如:"host": ["myserver.online"]
建議1: h2本身已包含mux功能, 所以 "mux"可以刪除
建議2: outbounds已有TLS, 為何不轉用vless

authors: Vargnatt kingwilliam


text:
cannot be installed as binary package and must be built from source

Hi
I tried to install via homebrew but seem formula is broken
Updating Homebrew...
==> Installing v2ray-core from v2ray/v2ray
==> Downloading https://github.com/v2ray/v2ray-core/releases/download/v4.25.0/v2ray-macos.zip
==> Downloading from https://github-production-release-asset-2e65be.s3.amazonaws.com/41912791/06a49580-b287-11ea-97cc-891edf5aa2b6?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=
######################################################################## 100.0%
Error: The following formula
  v2ray-core
cannot be installed as binary package and must be built from source.
Install the Command Line Tools:
  xcode-select --install```

Please help

It's seem that was a homebrew problem. you can do that run xcode-select --install. If that doesn't fix it, Run brew doctor and check output.

authors: Doublemine pindank


text:
如果是在防火墙后面  能不能配置中转服务器使用的本地端口  默认是绑定随机的本地端口吗？

由于防火墙限制 只开通了几个端口  无法对外访问  可以用这个软件作为代理吗？

嗯，目前不支持绑定本地的特定端口用于发送数据。而且由于并发连接，设置固定端口可以肯定是无法使用的。请确定你的防火墙限制了本地的端口，而不是远程主机的端口。

Closing due to inactivity.

authors: DarienRaymond sngths


text:
linter周りをどうするか

efm-language-server
none-ls

none-lsを採用


text:
0067 - Add Binary

Description of the Problem
Given two binary strings, return their sum (also a binary string).
The input strings are both non-empty and contains only characters 1 or 0.
Example 1:
Input: a = "11", b = "1"
Output: "100"

Example 2:
Input: a = "1010", b = "1011"
Output: "10101"

Constraints:
Each string consists only of '0' or '1' characters.
1 <= a.length, b.length <= 10^4
Each string is either "0" or doesn't contain any leading zero.
Code
PR

Link To The LeetCode Problem
LeetCode

please assign this problem to me!

I would like to work on this one

Issue with Problem 67 is already open - please find another Problem you want to solve 😸

authors: mkiglics vJechsmayr vmgmreddy

repo: vJechsmayr/PythonAlgorithms


text:
Nothing works

Describe the bug
Only 3 out of 8 mirrors let me mount.
Only 2 show any directories.
Only 1 seems to contain any apk files.
0 of them let me install anything
Only get this error:
Error: EIO: i/o error, copyfile '/tmp/mnt/Quest Games/République VR v127622+1.2 -QU (b)/Republique VR ['1.2'.127622] S3.0.2.apk' -> '/tmp/Republique VR ['1.2'.127622] S3.0.2.apk.part'
To Reproduce
Steps to reproduce the behavior:

Try installing any game. For example "Republique VR"

Expected behavior
All mirrors let me mount, contain directories and apks and let me install something.
Desktop (please complete the following information):

OS: ArcoLinux
Started via downloaded AppImage
Version 0.6.0 - 0.7.3 (Didn't test older versions)

Server issue not sidenoder issue.... Since this program uses others mirrors this is out of the devs control. Also consider upgrading to the new program and mirrors a t.me/sidenoder or his other repository named sidenoder (instead of quest-sidenoder. All config may help since it has 2 sets of mirrors

Yeah, I'm sorry.
For some reason I didn't realize the mirrors are out of the dev's control.
Thanks for still being cool.
Will download the new program and mirrors.
Thanks again :)

authors: KaladinDMP TheBlackEntity

repo: vKolerts/quest-sidenoder


text:
[autocrud] Deep linking support for editing

Crud should out of the box be able to support urls like
/myview - shows crud
/myview/edit/foobar12 - selects the item with id 'foobar12' in the grid and shows the values in the form

What is the use case? I don’t think auto grid even enables selection automatically

One use case is an AutoGrid with an attached selection listener that, upon selection, populates a non-form component. As the end user of such AutoGrid, I sometimes want to share a URL with my colleagues that automatically highlights a specific row and opens the related component.

authors: Artur- tarekoraby

repo: vaadin/hilla


text:
Adding description file for Vaadin Directory

Connected to vaadin/components-team-tasks#328

This change is

Applying  and merging since it's already in skeleton and other elements.

Reviewed 1 of 1 files at r1.
Review status: all files reviewed at latest revision, all discussions resolved.

Comments from Reviewable

repo: vaadin/vaadin-date-picker


text:
RLN: Use arkworks field arithmetic only

Problem
Currently, zerokit RLN uses both semaphore-rs Field and ark-ec Fr data types to carry field arithmetic, in order to use natively primitives from dependencies implemented for one type and the other.
However, while the semaphore-rs Field type corresponds to a big-endian byte vector without Montgomery reduction, the arkworks Fr type does operations directly in the more efficient Montgomery form, hence modulo p reduction is implicit.
This issue partially overlaps with the second item of https://github.com/vacp2p/zerokit/issues/31: while, in the latter, we ask to maximize usage of the Fr type, here we aim to exclusively use Fr along the whole module. Such refactor might require much more time than what is expected for zerokit v0.1 release.
Acceptance Criteria

[x] Use exclusively the arkworks Fr field type to perform arithmetic in zerokit RLN

Can we please solve this in a normal PR and not bundle everything up into a mega PR for release.


text:
Vue组件缓存后 resize 一直在计算

Vue组件缓存后 resize 一直在计算
autoResize文件中加入以下代码可解决
 onActivated(autoResizeMixinInit)
 onDeactivated(unbindDomResizeCallback)

官网在哪里？

已经在最新版本 1.7.3 中加上了 5b7f8d4

authors: anyedapingguo chg122345 vaemusic


text:
[REQUEST] clean up subtitles

FYI, this tool can clean up subtitles. https://github.com/icza/srtgears
maybe the source code is interesting to add this functionality to subsearch too. not high prio.

FYI, this tool can clean up subtitles. https://github.com/icza/srtgears
maybe the source code is interesting to add this functionality to subsearch too. not high prio.

It has some interesting features that could be nice to have. But I don't know GO which would make it very hard for me to implement / maintain.

authors: eikaramba vagabondHustler

repo: vagabondHustler/subsearch


text:
Target Java 8 Rather than 17

The Kotlin compiler targets Java 8 by default as this makes it compatible with most existing ecosystems. Is there a good reason to target Java 17 here? I would like to use this library for my project but due to historical limitations the ecosystem at my company is on Java 8.

java17 cannot be used in the android system


text:
Add named text color parsing

Adds parsing color names in the text module, resolves #21

Thanks

repo: valence-rs/valence


text:
Added exclude to the options

This allows the user to exclude characters from the string, as proposed in #3.
Note: You must implicitly state the characters you want to remove, lowercase letters will not remove uppercase letters

great idea, ty for that.
i will merge if you remove the console.log-statements and add the option to the readme

Sorry, that was for debugging. Will do.

Done.

authors: bjskistad hereandnow

repo: valiton/node-random-string

license: mit


text:
Suggestion : move CurrentListingFocused from UILobbyListing to UIGameServers

Haven't had time to look at much but I noticed something about the way server listings are selected that could potentially cause problems later.

Finally this solves the problem for the join button in the server list's button bar

Thank you
The following commit has applied these changes --> b8530df059f228a2e0b3e8dd53e02040b01a7f28

authors: LazerGoat valkyrienyanko

repo: valkyrienyanko/GodotModules


text:
Multiple Mesh Renderer Question

Does every mesh in Unity need its own mesh filter and mesh renderer component?

Yes

repo: valkyrienyanko/Space-RPG-Game


text:
Bump open-aea plugins to post release

Proposed changes
This PR updates the plugin versions to post1 to address the ripemd160 issue
Types of changes
What types of changes does your code introduce? (A breaking change is a fix or feature that would cause existing functionality and APIs to not work as expected.)
Put an x in the box that applies

[ ] Non-breaking fix (non-breaking change which fixes an issue)
[ ] Breaking fix (breaking change which fixes an issue)
[ ] Non-breaking feature (non-breaking change which adds functionality)
[ ] Breaking feature (breaking change which adds functionality)
[ ] Refactor (non-breaking change which changes implementation)
[ ] Messy (mixture of the above - requires explanation!)

Checklist
Put an x in the boxes that apply.

[ ] I have read the CONTRIBUTING doc
[ ] I am making a pull request against the main branch (left side). Also you should start your branch off our main.
[ ] Lint and unit tests pass locally with my changes
[ ] I have added tests that prove my fix is effective or that my feature works
[ ] I have locally run services that could be impacted and they do not present failures derived from my changes

Thanks, now we have this logging, and the retry, this puts us in a much better position to go ahead and try to implement a server side solution.
Based on the errors retrieved from this;
it looks like I have a few more settings I can tweak;

The client is trying to send more data than the server is configured to accept.

The server is experiencing high load and is unable to keep up with the number of incoming requests.
(Maybe heavy load from the contribution service?)

The client is closing the connection unexpectedly, possibly due to a network issue or an error on the client side. In this case, there may not be anything we can do on the server side to fix the issue.

Are these particularly large packages? have we added anything into the release which would increase the size of the packages?

repo: valory-xyz/open-autonomy


text:
Refactoring "parser" to separate package

This refactors the parser into a separate package, so that it can be used by third-party build tools that also use quicktemplate. This eliminates the need to build a binary for generating Go code.

Changed.

The test breaks under 1.10.x when using build.Default.GOPATH. I pushed another update that removes 1.10.x from the travis configuration, and adds 1.12.x.
The broken 1.10.x build is here: https://travis-ci.org/valyala/quicktemplate/jobs/514931152

Added an additional commit that cleans up the go.mod and go.sum files (ie, ran `go mod tidy').

Any feedback on this PR?

@kenshaw , I'm going to merge the PR soon.

Manually merged the PR in https://github.com/valyala/quicktemplate/commit/d15c553841f6c9710bebc4e6be64a2e31dda53d2 . Thanks for the contribution, @kenshaw !

@valyala greatly appreciate it. Thanks for this package, as I much prefer this over the horrible Go template syntax.

authors: kenshaw valyala

repo: valyala/quicktemplate


text:
README.md in the project root.

The readme file is moved to the web/ folder. We need a new one at the root level.

I created a new root README file so that something would show up in our github repository, but not closing this because I think more details of the design document should probably be added.

authors: jwnichls yyoon

repo: vanadium/reader


text:
Added global $auth_meth_global

New branch with change

Merged & deploy to the test server!

repo: vanderbilt/redcap-external-modules


text:
row does not fit on page

I want to generate a pdf based on a form filled in by the user. This text might be longer than one page.
Now I get an error
org.vandeseer.easytable.RowIsTooHighException: There is a row that is too high to be drawn on a single page
I can't find any clues in the docs or tests. How can I handle this?

Hi @djcanard,
the exception itself conveys the message already: The height of the text (according to the specific settings like font, font size, line spacing etc.) is simply higher than what can be drawn on the page (again according to the settings like the starting point of the table etc.).
So how can you handle this? What you need to do is to check the text height beforehand and add another row should it be necessary. You can use methods from PdfUtil.java and check how it's done in the text cells.
Hope this helps,
Stefan

Thanks for your quick response! I looked into it but I find it quite hard to wrap my head around the non-intuitive building of the pdf content with PDFBox :)

Hi @djcanard,
the exception itself conveys the message already: The height of the text (according to the specific settings like font, font size, line spacing etc.) is simply higher than what can be drawn on the page (again according to the settings like the starting point of the table etc.).
So how can you handle this? What you need to do is to check the text height beforehand and add another row should it be necessary. You can use methods from PdfUtil.java and check how it's done in the text cells.
Hope this helps,
Stefan

@vandeseer,
The cell height can be calculated and we can make a decision whether to split the row or not. This works fine for regular tables. Won't this cause issues with tables having multiple columns with rowSpan ? Please let us know how we can handle this.

How can I use the getTextHeight() from AbstractTextCell without getting nullpointer? I guess that this method is initialized during cell building process but I need to split the cell before that happens. Any clue? I'd be very thankful for tips

authors: Pandoors djcanard pradhan-v vandeseer

repo: vandeseer/easytable


text:
jsbayesviz.fromGraph(g) | TypeError: Cannot read property 'length' of undefined

When construct the network viz, with the method: jsbayesviz.fromGraph(g); return a TypeError:

TypeError: Cannot read property 'length' of undefined

When construct the network viz, with the method: jsbayesviz.fromGraph(g); return a TypeError:

TypeError: Cannot read property 'length' of undefined

Hi @BogdanStanciu did you sort this out? I'm getting the same error. Thanks

authors: BogdanStanciu acarioca

repo: vangj/jsbayes-viz


text:
NtH: Update docs to Markdown

Currently the documentation of AFLplusplus is writing in plain text.
I suggest to reformat the docs/*.txt files to markdown.
What are your thoughts?

if you want to do that - sure, go for it :)

Alright, I made a start. Could you provide access so that I can push my docs_to_md branch?

Just fork the repo and open a pull request

@ThomasTNO just click fork repo - make your changes in your fork, and then click "create pull request" on your fork. super easy.

This was mostly fixed with commit 89088035322c8b3ddb07f29367f62cdb590fb8f5

authors: ThomasTNO andreafioraldi domenukk vanhauser-thc

repo: vanhauser-thc/AFLplusplus


text:
color issue for validation text

Can't change the color of the validation text (0/8, 0/10 etc.)

Simply add a TextStyle to the counterStyle property of the InputDecoration object of the IntlPhoneField decoration property.
This is an example, where the counter text will be displayed in red :
IntlPhoneField(
decoration: InputDecoration(
counterStyle: TextStyle(color: Colors.red),
...
),
...
),


text:
🛑 CityMarket is down

In e23677d, CityMarket (https://citymarket.zakaz.ua) was down:

HTTP code: 0
Response time: 0 ms

Resolved: CityMarket is back up in a9530f3.

repo: vanyakosmos/zakaz-uptime


text:
API/Fluent: White text on white background

Describe the bug
White text on white background is not readable.
To Reproduce
Go to https://api.vapor.codes/fluent/documentation/fluent/
Expected behavior
Expect some contrast between the text and the background.
Environment

Vapor Framework version: current https://api.vapor.codes/ website
Vapor Toolbox version: N/A
OS version: N/A

Additional context
Unknown if this is an issue on other api pages. A sampling of other API pages looked ok.

This has already been addressed; the API docs site will update shortly. For an example, see http://api.vapor.codes/postgreskit/documentation/postgreskit/, which has already updated

authors: gwynne marc-medley

repo: vapor/api-docs


text:
[Do not merge] Add Repro fro #405

Code to replicate issue #405.
The repro crashes in 5.8.1 after 100 iterations:
Backtrace
    frame #0: 0x0000fffff696c584 libc.so.6`___lldb_unnamed_symbol3383 + 1348
libc.so.6`___lldb_unnamed_symbol3383:
->  0xfffff696c584 <+1348>: ldr    x8, [x6, #0x10]
    0xfffff696c588 <+1352>: cmp    x8, x2
    0xfffff696c58c <+1356>: b.ne   0xfffff696c888            ; <+2120>
    0xfffff696c590 <+1360>: ldr    x8, [x2, #0x10]
Target 0: (Repro) stopped.
(lldb) bt
* thread #2, name = 'NIO-ELT-0-#0', stop reason = signal SIGSEGV: invalid address (fault address: 0xfffdf00000a0)
  * frame #0: 0x0000fffff696c584 libc.so.6`___lldb_unnamed_symbol3383 + 1348
    frame #1: 0x0000fffff696e548 libc.so.6`__libc_calloc + 216
    frame #2: 0x0000fffff75c05b8 libdispatch.so`_dispatch_continuation_alloc_from_heap + 20
    frame #3: 0x0000fffff75d2b88 libdispatch.so`_dispatch_continuation_redirect_push + 316
    frame #4: 0x0000fffff7336690 libswift_Concurrency.so`resumeTaskAfterContinuation(swift::AsyncTask*, swift::ContinuationAsyncContext*) + 380
    frame #5: 0x0000aaaaaace1358 Repro`partial apply for specialized closure #1 in closure #1 in EventLoopFuture.get() at <compiler-generated>:0 [opt]
    frame #6: 0x0000aaaaaad1be70 Repro`merged generic specialization <()> of closure #1 @Sendable () -> NIOCore.CallbackList in NIOCore.EventLoopFuture._publicWhenComplete(@Sendable (Swift.Result<τ_0_0, Swift.Error>) -> ()) -> () + 92
    frame #7: 0x0000aaaaaad1bd94 Repro`merged generic specialization <()> of closure #1 @Sendable () -> () in NIOCore.EventLoopFuture._internalWhenComplete(@Sendable () -> NIOCore.CallbackList) -> () + 68
    frame #8: 0x0000aaaaaadc1390 Repro`SelectableEventLoop.run() [inlined] closure #4 () -> () in NIOPosix.SelectableEventLoop.run() throws -> () at SelectableEventLoop.swift:518:30 [opt]
    frame #9: 0x0000aaaaaadc138c Repro`SelectableEventLoop.run() [inlined] generic specialization <()> of NIOPosix.withAutoReleasePool<τ_0_0>(() throws -> τ_0_0) throws -> τ_0_0 at SelectableEventLoop.swift:29:16 [opt]
    frame #10: 0x0000aaaaaadc138c Repro`SelectableEventLoop.run(self=0x0000fffff0001170) at SelectableEventLoop.swift:517:21 [opt]
    frame #11: 0x0000aaaaaada60fc Repro`closure #1 in static MultiThreadedEventLoopGroup.setupThreadAndEventLoop(name:parentGroup:selectorFactory:initializer:) at MultiThreadedEventLoopGroup.swift:97:22 [opt]
    frame #12: 0x0000aaaaaada60d8 Repro`closure #1 in static MultiThreadedEventLoopGroup.setupThreadAndEventLoop(t=<unavailable>, parentGroup=<unavailable>, selectorFactory=0x0000aaaaaada631c Repro`implicit closure #1 () throws -> NIOPosix.Selector<NIOPosix.NIORegistration> in NIOPosix.MultiThreadedEventLoopGroup.init(numberOfThreads: Swift.Int) -> NIOPosix.MultiThreadedEventLoopGroup, initializer=<unavailable>, lock=NIOConcurrencyHelpers.NIOLock @ x19, loopUpAndRunningGroup=0x0000aaaaab16d7c0) at MultiThreadedEventLoopGroup.swift:118:41 [opt]
    frame #13: 0x0000aaaaaada8d64 Repro`partial apply for closure #1 in static MultiThreadedEventLoopGroup.setupThreadAndEventLoop(name:parentGroup:selectorFactory:initializer:) at <compiler-generated>:0 [opt]
    frame #14: 0x0000aaaaaadaab38 Repro`thunk for @escaping @callee_guaranteed (@guaranteed NIOThread) -> () at <compiler-generated>:0 [opt]
    frame #15: 0x0000aaaaaaddbe2c Repro`closure #1 in static ThreadOpsPosix.run($0=0xaaaaab16d950) at ThreadPosix.swift:112:13 [opt]
    frame #16: 0x0000fffff695d5c8 libc.so.6`___lldb_unnamed_symbol3291 + 724
    frame #17: 0x0000fffff69c5d1c libc.so.6`___lldb_unnamed_symbol3659 + 12

Codecov Report

Merging #406 (8f9a39d) into main (d89a723) will decrease coverage by 0.13%.
The diff coverage is n/a.

Additional details and impacted files
@@            Coverage Diff             @@
##             main     #406      +/-   ##
==========================================
- Coverage   49.13%   49.01%   -0.13%
==========================================
  Files         108      108
  Lines        8841     8841
==========================================
- Hits         4344     4333      -11
- Misses       4497     4508      +11

see 2 files with indirect coverage changes

authors: codecov-commenter fabianfett

repo: vapor/postgres-nio


text:
🛑 Vcoud is down

In 57f85d4, Vcoud (https://vcoud.com) was down:

HTTP code: 0
Response time: 0 ms

Resolved: Vcoud is back up in b83ff4b after 9 minutes.

repo: vcoud/upptime


text:
🛑 Criptodolar & Covid API is down

In 44a27fe, Criptodolar & Covid API (https://exchange.vcoud.com/) was down:

HTTP code: 502
Response time: 15957 ms

Resolved: Criptodolar & Covid API is back up in 9e8ce17 after 11 minutes.


text:
BUG - CI is failing

should investigate and fix the build on the CI
https://github.com/vczb/sagu-ui/actions/runs/4365660452/jobs/7634591925

Fixed :pray:

repo: vczb/sagu-ui


text:
barline missing, alter and accidentals doesnt include arabic quarter notes

hello,, i have notice the barline is not included.. and the quarter notes will raise an exception since its alter value is double and the alter type in the parser is int.
i modified the code.. how i can upload the modifications here ?

sorry,, if forgot to say congrats for the nice work.. it is really nice library. thx

Hi @ahmedabuomar, send me a pull request

You can find documentation here : https://help.github.com/articles/creating-a-pull-request/

Hi @vdaron, sorry for being late. I will make a pull request now.

Hi @ahmedabuomar , I do not see any pull request... sorry

authors: ahmedabuomar vdaron


text:
missing function SDL_GetWindowID(SDL_Window * ptr)

SDL_GetWindowID(SDL_Window * ptr)
is missing

Hi @LifeSoftServ, you can use https://godoc.org/github.com/veandco/go-sdl2/sdl#Window.GetID

authors: LifeSoftServ veeableful


text:
static build for linux produces dynamically linked executable

$ CGO_ENABLED=1 CC=gcc GOOS=linux GOARCH=amd64 go build -tags static -ldflags '-s -w'  foo.go
$ ldd foo
	linux-vdso.so.1 (0x00007ffea0d18000)
	libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007effa257a000)
	libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007effa2376000)
	libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007effa2157000)
	librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007effa1f4f000)
	libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007effa1b5e000)
	/lib64/ld-linux-x86-64.so.2 (0x00007effa2918000)

I tried using -extldflags "-static"  but that produces a binary that either crashes or hangs forever. It could be something to do with Alsa lib.
Would it be possible to support fully statically linked binaries?

Perhaps doesn't have to be with musl, but just static.

I can still reproduce the issue.
$ CGO_ENABLED=1 CC=gcc GOOS=linux GOARCH=amd64 go build -tags static -ldflags "-s -w"

$ ldd guitest
        linux-vdso.so.1 (0x00007fffba277000)
        libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f8355263000)
        libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f835525d000)
        libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f835523b000)
        libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f8355051000)
        /lib64/ld-linux-x86-64.so.2 (0x00007f83553da000)

Is there a way to compile with static libs?

Hi @gcstr, I believe SDL2 is compiled with glibc which is why it can't be fully static. I could be wrong though.
Do you have a specific issue that is caused by this behavior?

Sorry, I couldn't figure out how to make it completely static. The sdl2-config --static-libs command still defines some dynamic libraries though they should be available on most Linux platform.
$ sdl2-config --static-libs
-L/usr/local/lib -lSDL2 -Wl,--no-undefined -lm -ldl -lpthread -lrt

If anyone knows how to make it completely static, please let me know!

@gcstr It is not really recommended to build a fully static binary with Glibc, you will get a big fat warning from Glibc, and you will have issues with Alsa, which is hard to compile statically (probably some patches are needed).
If you really want this, you need to use musl toolchain to build SDL and all dependencies fully static, and again apply some patches to Alsa (probably Alpine distro have some). Also, Musl recommends linking libC statically, with Glibc you get a warning not to do that.


text:
Rename corpus to index

Renamed corpus to index in 4 topics

I fixed the typos in the latest commit

@pwoznic Great work!
Only addition is I think we should introduce index/indicies verbiage in the body of creating a corpus
https://deploy-preview-77--luxury-shortbread-acee05.netlify.app/docs/console-ui/creating-a-corpus
Noteably the first line of text
"To get begin searching your data, you first have to create a corpus. A corpus is a container where you upload all your data to be indexed and grouped together in a single location for querying."
You may want to consider lightly adjusting some of the follow on text regarding corpus vs. index when it comes to what users should be clicking on and removing images as well, perhaps just including a single one.
This document is directly linked to from the console. This way the flow from console -> docs for create corpus can be tied together in a minimal way.

@pwoznic Great work! Only addition is I think we should introduce index/indicies verbiage in the body of creating a corpus https://deploy-preview-77--luxury-shortbread-acee05.netlify.app/docs/console-ui/creating-a-corpus
Noteably the first line of text "To get begin searching your data, you first have to create a corpus. A corpus is a container where you upload all your data to be indexed and grouped together in a single location for querying."
You may want to consider lightly adjusting some of the follow on text regarding corpus vs. index when it comes to what users should be clicking on and removing images as well, perhaps just including a single one.
This document is directly linked to from the console. This way the flow from console -> docs for create corpus can be tied together in a minimal way.

Done :)

Updated topics for more clarifications

authors: danielone pwoznic

repo: vectara/vectara-docs


text:
Sometimes userpic is not shown in the notifications

Yes, thanks for reporting. I'm aware of this limitation.
This issue has been fixed on RiotX, you may consider switching to this application, which can be installed along with Riot-Android.
Unfortunately this issue as low chance to get fixed on the legacy application

Benoit, yes, I know. Really I doubted to report it, but later decided it's better to let you know. (As you can see the screenshot date is Dec 14).
I use RiotX but only with matrix.org homeserver, as there are no voice and several accounts support.

repo: vector-im/riot-android


text:
Optionally decrypt pushes for e2e rooms to display them as notifications

This means treating the push as a wake-up request to sync the real encrypted message, and then decrypting it via olm.

This can be closed

indeed! :))

repo: vector-im/riot-ios


text:
Update README.md

added telegram group link for community part

@mrfarhadir thanks for your contribution. I noticed there is only one member in the group. Is this true?

@veelenga I mean, if you join it, it's already two :smile:
Good idea to have a Telegram Chat, but I'd prefer to join one moderated by known members of Crystal Community :thinking:

@mrfarhadir if you feel comfortable to moderate it, please suggest/announce the room to the community first.

authors: mrfarhadir veelenga vladfaust

repo: veelenga/awesome-crystal


text:
First pass of all priority transaction receipts

Story
As a user
I want to see the basic view of transactions for all types
So that I can review my Txs
Acceptance Criteria

[ ] I can see the basic info for all priority types (below)
[ ] I can NOT yet see nicely formatted price etc

Tasks

[ ] UX (if needed)
[ ] Design (if needed)
[ ] Team and stakeholder review
[ ] Specs reviewed and created or adjusted
[ ] Implementation
[ ] Testing (unit and/or e2e)
[ ] Code review
[ ] QA review

Sketch
Additional details / background info
Transaction types supported:

Order submission
Order amendement
Order cancellation
Transfer
Withdrawal
Batch market instructions
Stop order submission
Stop order cancellation

So types NOT supported:

Amend liquidity provision order
Cancel liquidity provision order
Cancel transfer funds
Create liquidity provider order
Delegate
Proposal
Submit oracle data
Undelegate
Vote on proposal
Chain event
Ethereum key rotation submission
Issue signatures
Key rotate submission
Node signature
Node vote
Protocol upgrade
Register new node
State variabel proposal
Validator heartbeat

Still needs:

Stop order submission
Add price components to existing views (where possible)
Batch market instructions

Need some Dale eyes on stop orders, pegged orders, and batch markets.
And do a final sweep.

repo: vegaprotocol/vegawallet-browser


text:
On documenting sealed secrets usage in README (and its proper usage)

Hi Vegard,
I already outlined in another issue (https://github.com/vehagn/homelab/issues/106#issuecomment-2424077149) that I'd like to contribute to the READMEs.  One area where I'm lacking knowledge is sealed secrets, hence the f. 2 questions:

Bootstrap: How do you create your sealed secrets initially?  Please see some snippets I've gathered so far.  Maybe you have some other commands handy -- maybe more elegant than my approach?
Regarding proper usage: It looks like you prefer storing the secrets in VCS permanently.  That helps when in the need for re-creating the cluster (may it be for trial-and-error start from scratch or in case of disaster recovery).  I will prepare a PR for storing the openssl key+crt in a SOPS-proteced file.  So one doesn't depend on storing the openssl key locally (without VCS or backup).  I'm contemplating this approach for terragrunt, at least, because using local files (not stored in VCS) is more tricky.  What do you think?
How do you facilitate key rotation (mentioned in one of your blog articles)?  As far as I understood the documentation, one could also create the K8S secrets first and then let the Controller generate/update the sealed secret upon.  That would mean one could just assing a new ssl key to the controller and let K8S update all sealed secrets without the need to update the secrets

General approach
Do you create the sealed secret first which then creates a K8s secret or the other way round.  Documentation for sealed secrets mentions both approaches.  I'm using the generic pipeline approach based on kubeseal:
echo -n bar | kubectl create secret generic mysecret --dry-run=client --from-file=foo=/dev/stdin -o yaml | kubeseal --controller-namespace sealed-secrets -o yaml -n <namespace> --merge-into <existing or new sealed secrets>.yaml
CloudFlare API Token
I first created a local-managed CF tunnel and then piped it into kubectl-kubeseal chain:
cat ~/.cloudflared/<my-tunnel-id>.json | kubectl create secret generic tunnel-credentials --dry-run=client --from-file=credentials.json=/dev/stdin -o yaml | kubeseal --controller-namespace sealed-secrets -o yaml -n cloudflared --merge-into ~/src/vehagn-homelab/k8s/infra/network/cloudflared/tunnel-credentials.yaml
AdGuard
I just leveraged the users.yaml from another instance:
cat users.yaml | kubectl create secret generic users --dry-run=client --from-file=users.yaml=/dev/stdin -o yaml | kubeseal --controller-namespace sealed-secrets -o yaml -n dns --merge-into infra/network/dns/adguard/secret-users.yaml
Kind regards -- Sebastian

Bootstrap: How do you create your sealed secrets initially?

It should be explained in this section.
I'm running
openssl req -x509 -days 365 -nodes -newkey rsa:4096 -keyout sealed-secrets.key -out sealed-secrets.cert -subj "/CN=sealed-secret/O=sealed-secret"

to create the certificate.

It looks like you prefer storing the secrets in VCS permanently

That's correct. I'll be the first to admit it's not the best way of doing it, but it's practical! I also store some of the secrets in clear-text in my local copy of this repo, though making sure I don't accidentally  commit them.

How do you facilitate key rotation

Short answer; I don't. Again, this is not how it should be done! Without reading the whole thing, I think this is what you're looking for.

Do you create the sealed secret first which then creates a K8s secret or the other way round.

I use the kubernetes provider with this config.

CloudFlare API Token

Manually create a Secret
apiVersion: v1
kind: Secret
metadata:
  name: cloudflare-api-token
  namespace: cert-manager
stringData:
  api-token: 'SECRET_API_TOKEN'

and run
kubeseal -o yaml --controller-namespace=sealed-secrets < secret-cert-manager-cloudflare-api.yaml > k8s/infra/controllers/cert-manager/cloudflare-api-token.yaml

AdGuard

apiVersion: v1
kind: Secret
metadata:
  name: users
  namespace: dns
data:
  users.yaml: "BASE64_ENCODED_STRING"

The BASE64_ENCODED_STRING looks like
users:
  - name: admin
    password: secret_passw0rd

And then a similar command as with the CF API token.
To summarise: I've made some security sacrifices for the sake of convenience. I have a note to address these in the future™.

authors: sebiklamar vehagn

repo: vehagn/homelab


text:
Validated 0 intron ?!

Hi velocyto team,
I have run velocyto on a smartseq2 sample and got the expected loom file output. But in the log of the run, I have a weird message :
"Summarizing the results of intron validation.
Validated 0 introns (of which unique intervals 0) out of 984652 total possible introns (considering each possible transcript models)."
It sounds very unlikely that there is no spliced situation in my data.
I have run the command :
velocyto run_smartseq2 -e velocyto STAR_mapping/cell1.sorted.bam gencode.v25.annotation.gtf
(I have tried with and without masking, the result was the same)
The genome annotation file is from https://www.gencodegenes.org/human/release_25.html (used the same version for the STAR mapping)
Log of the run :
2020-01-22 19:20:31,776 - WARNING - Each bam file will be interpreted as a DIFFERENT cell
2020-01-22 19:20:31,776 - INFO - No OUTPUTFOLDER specified, find output files inside /scbio1/marion/Charles_spleen/STAR_mapping/velocyto
2020-01-22 19:20:31,776 - DEBUG - Using logic: SmartSeq2
2020-01-22 19:20:31,777 - DEBUG - Cell barcodes will be determined while reading the .bam file
2020-01-22 19:20:31,796 - WARNING - The file /scbio1/marion/Charles_spleen/STAR_mapping/RHM5691.sorted.bam already exists. The sorting step will be skipped and the existing file will be used.
2020-01-22 19:20:31,797 - WARNING - The file /scbio1/marion/Charles_spleen/STAR_mapping/RHM5692.sorted.bam already exists. The sorting step will be skipped and the existing file will be used.
...
...
2020-01-22 19:20:31,831 - INFO - Load the annotation from /home/marion/scripts/reference_genome/GRCh38_gencode_v25_gtf/gencode.v25.annotation.gtf
2020-01-22 19:20:39,092 - DEBUG - Parsing Chromosome 1 strand - [line 0]
2020-01-22 19:20:39,794 - DEBUG - Done with 1- [line 111685]
2020-01-22 19:20:39,795 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:39,808 - DEBUG - Seen 2573 genes until now
2020-01-22 19:20:39,808 - DEBUG - Parsing Chromosome 1 strand + [line 111686]
2020-01-22 19:20:40,780 - DEBUG - Done with 1+ [line 232137]
2020-01-22 19:20:40,780 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:40,795 - DEBUG - Seen 5194 genes until now
2020-01-22 19:20:40,795 - DEBUG - Parsing Chromosome 10 strand - [line 232138]
2020-01-22 19:20:40,989 - DEBUG - Done with 10- [line 277419]
2020-01-22 19:20:40,989 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:40,996 - DEBUG - Seen 6256 genes until now
2020-01-22 19:20:40,996 - DEBUG - Parsing Chromosome 10 strand + [line 277420]
2020-01-22 19:20:41,187 - DEBUG - Done with 10+ [line 322747]
2020-01-22 19:20:41,187 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:41,192 - DEBUG - Seen 7398 genes until now
2020-01-22 19:20:41,192 - DEBUG - Parsing Chromosome 11 strand - [line 322748]
2020-01-22 19:20:41,759 - DEBUG - Done with 11- [line 398779]
2020-01-22 19:20:41,759 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:41,768 - DEBUG - Seen 9000 genes until now
2020-01-22 19:20:41,768 - DEBUG - Parsing Chromosome 11 strand + [line 398780]
2020-01-22 19:20:42,372 - DEBUG - Done with 11+ [line 478704]
2020-01-22 19:20:42,372 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:42,383 - DEBUG - Seen 10633 genes until now
2020-01-22 19:20:42,383 - DEBUG - Parsing Chromosome 12 strand - [line 478705]
2020-01-22 19:20:42,728 - DEBUG - Done with 12- [line 555117]
2020-01-22 19:20:42,728 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:42,738 - DEBUG - Seen 12096 genes until now
2020-01-22 19:20:42,738 - DEBUG - Parsing Chromosome 12 strand + [line 555118]
2020-01-22 19:20:43,077 - DEBUG - Done with 12+ [line 631946]
2020-01-22 19:20:43,078 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,369 - DEBUG - Seen 13573 genes until now
2020-01-22 19:20:43,369 - DEBUG - Parsing Chromosome 13 strand - [line 631947]
2020-01-22 19:20:43,452 - DEBUG - Done with 13- [line 650590]
2020-01-22 19:20:43,452 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,454 - DEBUG - Seen 14224 genes until now
2020-01-22 19:20:43,454 - DEBUG - Parsing Chromosome 13 strand + [line 650591]
2020-01-22 19:20:43,541 - DEBUG - Done with 13+ [line 670483]
2020-01-22 19:20:43,541 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,544 - DEBUG - Seen 14877 genes until now
2020-01-22 19:20:43,544 - DEBUG - Parsing Chromosome 14 strand - [line 670484]
2020-01-22 19:20:43,731 - DEBUG - Done with 14- [line 714647]
2020-01-22 19:20:43,731 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,737 - DEBUG - Seen 15954 genes until now
2020-01-22 19:20:43,737 - DEBUG - Parsing Chromosome 14 strand + [line 714648]
2020-01-22 19:20:43,940 - DEBUG - Done with 14+ [line 763579]
2020-01-22 19:20:43,940 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,947 - DEBUG - Seen 17101 genes until now
2020-01-22 19:20:43,947 - DEBUG - Parsing Chromosome 15 strand - [line 763580]
2020-01-22 19:20:44,169 - DEBUG - Done with 15- [line 814433]
2020-01-22 19:20:44,169 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:44,175 - DEBUG - Seen 18165 genes until now
2020-01-22 19:20:44,175 - DEBUG - Parsing Chromosome 15 strand + [line 814434]
2020-01-22 19:20:44,689 - DEBUG - Done with 15+ [line 860822]
2020-01-22 19:20:44,689 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:44,696 - DEBUG - Seen 19253 genes until now
2020-01-22 19:20:44,696 - DEBUG - Parsing Chromosome 16 strand - [line 860823]
2020-01-22 19:20:44,939 - DEBUG - Done with 16- [line 916752]
2020-01-22 19:20:44,939 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:44,948 - DEBUG - Seen 20469 genes until now
2020-01-22 19:20:44,948 - DEBUG - Parsing Chromosome 16 strand + [line 916753]
2020-01-22 19:20:45,240 - DEBUG - Done with 16+ [line 985772]
2020-01-22 19:20:45,240 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:45,250 - DEBUG - Seen 21764 genes until now
2020-01-22 19:20:45,250 - DEBUG - Parsing Chromosome 17 strand - [line 985773]
2020-01-22 19:20:45,614 - DEBUG - Done with 17- [line 1071727]
2020-01-22 19:20:45,614 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:45,626 - DEBUG - Seen 23294 genes until now
2020-01-22 19:20:45,627 - DEBUG - Parsing Chromosome 17 strand + [line 1071728]
2020-01-22 19:20:46,309 - DEBUG - Done with 17+ [line 1150792]
2020-01-22 19:20:46,309 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:46,319 - DEBUG - Seen 24759 genes until now
2020-01-22 19:20:46,320 - DEBUG - Parsing Chromosome 18 strand - [line 1150793]
2020-01-22 19:20:46,418 - DEBUG - Done with 18- [line 1173822]
2020-01-22 19:20:46,419 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:46,422 - DEBUG - Seen 25333 genes until now
2020-01-22 19:20:46,422 - DEBUG - Parsing Chromosome 18 strand + [line 1173823]
2020-01-22 19:20:46,514 - DEBUG - Done with 18+ [line 1195468]
2020-01-22 19:20:46,515 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:46,518 - DEBUG - Seen 25929 genes until now
2020-01-22 19:20:46,518 - DEBUG - Parsing Chromosome 19 strand - [line 1195469]
2020-01-22 19:20:46,854 - DEBUG - Done with 19- [line 1276363]
2020-01-22 19:20:46,854 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:46,865 - DEBUG - Seen 27362 genes until now
2020-01-22 19:20:46,865 - DEBUG - Parsing Chromosome 19 strand + [line 1276364]
2020-01-22 19:20:47,206 - DEBUG - Done with 19+ [line 1358881]
2020-01-22 19:20:47,206 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:47,217 - DEBUG - Seen 28855 genes until now
2020-01-22 19:20:47,217 - DEBUG - Parsing Chromosome 2 strand - [line 1358882]
2020-01-22 19:20:48,242 - DEBUG - Done with 2- [line 1455119]
2020-01-22 19:20:48,243 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,255 - DEBUG - Seen 30827 genes until now
2020-01-22 19:20:48,255 - DEBUG - Parsing Chromosome 2 strand + [line 1455120]
2020-01-22 19:20:48,662 - DEBUG - Done with 2+ [line 1551251]
2020-01-22 19:20:48,662 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,675 - DEBUG - Seen 32826 genes until now
2020-01-22 19:20:48,675 - DEBUG - Parsing Chromosome 20 strand - [line 1551252]
2020-01-22 19:20:48,787 - DEBUG - Done with 20- [line 1577072]
2020-01-22 19:20:48,787 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,791 - DEBUG - Seen 33525 genes until now
2020-01-22 19:20:48,791 - DEBUG - Parsing Chromosome 20 strand + [line 1577073]
2020-01-22 19:20:48,917 - DEBUG - Done with 20+ [line 1607038]
2020-01-22 19:20:48,917 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,922 - DEBUG - Seen 34212 genes until now
2020-01-22 19:20:48,922 - DEBUG - Parsing Chromosome 21 strand - [line 1607039]
2020-01-22 19:20:48,985 - DEBUG - Done with 21- [line 1621229]
2020-01-22 19:20:48,985 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,987 - DEBUG - Seen 34639 genes until now
2020-01-22 19:20:48,987 - DEBUG - Parsing Chromosome 21 strand + [line 1621230]
2020-01-22 19:20:49,054 - DEBUG - Done with 21+ [line 1635954]
2020-01-22 19:20:49,054 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:49,057 - DEBUG - Seen 35047 genes until now
2020-01-22 19:20:49,057 - DEBUG - Parsing Chromosome 22 strand - [line 1635955]
2020-01-22 19:20:49,174 - DEBUG - Done with 22- [line 1662909]
2020-01-22 19:20:49,174 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:49,178 - DEBUG - Seen 35644 genes until now
2020-01-22 19:20:49,178 - DEBUG - Parsing Chromosome 22 strand + [line 1662910]
2020-01-22 19:20:49,303 - DEBUG - Done with 22+ [line 1692214]
2020-01-22 19:20:49,303 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:49,307 - DEBUG - Seen 36365 genes until now
2020-01-22 19:20:49,308 - DEBUG - Parsing Chromosome 3 strand - [line 1692215]
2020-01-22 19:20:49,650 - DEBUG - Done with 3- [line 1772867]
2020-01-22 19:20:49,650 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:49,661 - DEBUG - Seen 37878 genes until now
2020-01-22 19:20:49,661 - DEBUG - Parsing Chromosome 3 strand + [line 1772868]
2020-01-22 19:20:50,439 - DEBUG - Done with 3+ [line 1852274]
2020-01-22 19:20:50,439 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:50,449 - DEBUG - Seen 39375 genes until now
2020-01-22 19:20:50,449 - DEBUG - Parsing Chromosome 4 strand - [line 1852275]
2020-01-22 19:20:50,657 - DEBUG - Done with 4- [line 1901817]
2020-01-22 19:20:50,658 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:50,664 - DEBUG - Seen 40607 genes until now
2020-01-22 19:20:50,664 - DEBUG - Parsing Chromosome 4 strand + [line 1901818]
2020-01-22 19:20:50,885 - DEBUG - Done with 4+ [line 1952043]
2020-01-22 19:20:50,885 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:50,892 - DEBUG - Seen 41880 genes until now
2020-01-22 19:20:50,892 - DEBUG - Parsing Chromosome 5 strand - [line 1952044]
2020-01-22 19:20:51,125 - DEBUG - Done with 5- [line 2006650]
2020-01-22 19:20:51,125 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:51,134 - DEBUG - Seen 43309 genes until now
2020-01-22 19:20:51,134 - DEBUG - Parsing Chromosome 5 strand + [line 2006651]
2020-01-22 19:20:51,384 - DEBUG - Done with 5+ [line 2066704]
2020-01-22 19:20:51,384 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:51,396 - DEBUG - Seen 44748 genes until now
2020-01-22 19:20:51,396 - DEBUG - Parsing Chromosome 6 strand - [line 2066705]
2020-01-22 19:20:51,648 - DEBUG - Done with 6- [line 2126597]
2020-01-22 19:20:51,648 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:51,656 - DEBUG - Seen 46169 genes until now
2020-01-22 19:20:51,656 - DEBUG - Parsing Chromosome 6 strand + [line 2126598]
2020-01-22 19:20:51,884 - DEBUG - Done with 6+ [line 2182757]
2020-01-22 19:20:51,884 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:51,892 - DEBUG - Seen 47611 genes until now
2020-01-22 19:20:51,892 - DEBUG - Parsing Chromosome 7 strand - [line 2182758]
2020-01-22 19:20:52,143 - DEBUG - Done with 7- [line 2240775]
2020-01-22 19:20:52,143 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:52,151 - DEBUG - Seen 48949 genes until now
2020-01-22 19:20:52,151 - DEBUG - Parsing Chromosome 7 strand + [line 2240776]
2020-01-22 19:20:52,420 - DEBUG - Done with 7+ [line 2304934]
2020-01-22 19:20:52,420 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:52,429 - DEBUG - Seen 50478 genes until now
2020-01-22 19:20:52,429 - DEBUG - Parsing Chromosome 8 strand - [line 2304935]
2020-01-22 19:20:53,146 - DEBUG - Done with 8- [line 2354546]
2020-01-22 19:20:53,146 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,152 - DEBUG - Seen 51692 genes until now
2020-01-22 19:20:53,153 - DEBUG - Parsing Chromosome 8 strand + [line 2354547]
2020-01-22 19:20:53,339 - DEBUG - Done with 8+ [line 2399113]
2020-01-22 19:20:53,339 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,346 - DEBUG - Seen 52831 genes until now
2020-01-22 19:20:53,346 - DEBUG - Parsing Chromosome 9 strand - [line 2399114]
2020-01-22 19:20:53,528 - DEBUG - Done with 9- [line 2442260]
2020-01-22 19:20:53,528 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,534 - DEBUG - Seen 53931 genes until now
2020-01-22 19:20:53,534 - DEBUG - Parsing Chromosome 9 strand + [line 2442261]
2020-01-22 19:20:53,736 - DEBUG - Done with 9+ [line 2489998]
2020-01-22 19:20:53,737 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,743 - DEBUG - Seen 55073 genes until now
2020-01-22 19:20:53,743 - DEBUG - Parsing Chromosome M strand - [line 2489999]
2020-01-22 19:20:53,743 - DEBUG - Done with M- [line 2490027]
2020-01-22 19:20:53,743 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,743 - DEBUG - Seen 55082 genes until now
2020-01-22 19:20:53,743 - DEBUG - Parsing Chromosome M strand + [line 2490028]
2020-01-22 19:20:53,743 - DEBUG - Done with M+ [line 2490141]
2020-01-22 19:20:53,744 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,744 - DEBUG - Seen 55110 genes until now
2020-01-22 19:20:53,744 - DEBUG - Parsing Chromosome X strand - [line 2490142]
2020-01-22 19:20:53,907 - DEBUG - Done with X- [line 2530278]
2020-01-22 19:20:53,907 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,913 - DEBUG - Seen 56259 genes until now
2020-01-22 19:20:53,913 - DEBUG - Parsing Chromosome X strand + [line 2530279]
2020-01-22 19:20:54,077 - DEBUG - Done with X+ [line 2570672]
2020-01-22 19:20:54,077 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:54,082 - DEBUG - Seen 57469 genes until now
2020-01-22 19:20:54,083 - DEBUG - Parsing Chromosome Y strand - [line 2570673]
2020-01-22 19:20:54,101 - DEBUG - Done with Y- [line 2574613]
2020-01-22 19:20:54,101 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:54,102 - DEBUG - Seen 57751 genes until now
2020-01-22 19:20:54,102 - DEBUG - Parsing Chromosome Y strand + [line 2574614]
2020-01-22 19:20:54,126 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:54,127 - DEBUG - Done with Y+ [line 2579815]
2020-01-22 19:20:54,127 - DEBUG - Fixing corner cases of transcript models containg intron longer than 1000Kbp
2020-01-22 19:20:55,832 - DEBUG - Generated 2167397 features corresponding to 198093 transcript models from /home/marion/scripts/reference_genome/GRCh38_gencode_v25_gtf/gencode.v25.annotation.gtf
2020-01-22 19:20:55,856 - INFO - Scan /scbio1/marion/Charles_spleen/STAR_mapping/RHM5691.sorted.bam /scbio1/marion/Charles_spleen/STAR_mapping/RHM5692.sorted.bam
...
...
/scbio1/marion/Charles_spleen/STAR_mapping/RHP4888.sorted.bam to validate intron intervals
2020-01-22 19:20:55,856 - DEBUG - Start molecule counting!
2020-01-22 19:20:59,702 - DEBUG - Features available for chromosomes : ['1-', '1+', '10-', '10+', '11-', '11+', '12-', '12+', '13-', '13+', '14-', '14+', '15-', '15+', '16-', '16+', '17-', '17+', '18-', '18+', '19-', '19+', '2-', '2+', '20-', '20+', '21-', '21+', '22-', '22+', '3-', '3+', '4-', '4+', '5-', '5+', '6-', '6+', '7-', '7+', '8-', '8+', '9-', '9+', 'M-', 'M+', 'X-', 'X+', 'Y-', 'Y+']
2020-01-22 19:20:59,702 - DEBUG - Mask available for chromosomes : []
2020-01-22 19:20:59,702 - DEBUG - Summarizing the results of intron validation.
2020-01-22 19:20:59,983 - DEBUG - Validated 0 introns (of which unique intervals 0) out of 984652 total possible introns (considering each possible transcript models).
2020-01-22 19:20:59,984 - DEBUG - Reading /scbio1/marion/Charles_spleen/STAR_mapping/RHM5691.sorted.bam
2020-01-22 19:20:59,985 - DEBUG - Read first 0 million reads
2020-01-22 19:21:46,626 - DEBUG - Counting for batch 1, containing 1 cells and 2153426 reads
2020-01-22 19:23:03,180 - DEBUG - 0 reads in repeat masked regions
2020-01-22 19:23:03,180 - DEBUG - 1096039 reads overlapping with features on plus strand
2020-01-22 19:23:03,180 - DEBUG - 1191030 reads overlapping with features on minus strand
2020-01-22 19:23:03,180 - DEBUG - 215962 reads overlapping with features on both strands
2020-01-22 19:23:21,903 - WARNING - The barcode selection mode is off, no cell events will be identified by <80 counts
2020-01-22 19:23:21,904 - WARNING - 0 of the barcodes where without cell
2020-01-22 19:23:22,362 - DEBUG - Reading /scbio1/marion/Charles_spleen/STAR_mapping/RHM5692.sorted.bam
2020-01-22 19:23:22,363 - DEBUG - Read first 0 million reads
2020-01-22 19:23:52,265 - DEBUG - Counting for batch 2, containing 1 cells and 1509092 reads
2020-01-22 19:24:45,763 - DEBUG - 0 reads in repeat masked regions
2020-01-22 19:24:45,763 - DEBUG - 787641 reads overlapping with features on plus strand
2020-01-22 19:24:45,763 - DEBUG - 819703 reads overlapping with features on minus strand
2020-01-22 19:24:45,763 - DEBUG - 177739 reads overlapping with features on both strands
2020-01-22 19:24:57,948 - WARNING - The barcode selection mode is off, no cell events will be identified by <80 counts
2020-01-22 19:24:57,948 - WARNING - 0 of the barcodes where without cell
...
...
2020-01-23 01:25:23,753 - DEBUG - 0 reads were skipped because no apropiate cell or umi barcode was found
2020-01-23 01:25:23,753 - DEBUG - Counting done!
2020-01-23 01:25:23,754 - DEBUG - Example of barcode: RHM5824.sorted.bam and cell_id: Charles_velocyto3:RHM5824.sorted.bam
2020-01-23 01:25:23,754 - DEBUG - Generating output file /scbio1/marion/Charles_spleen/STAR_mapping/velocyto/Charles_velocyto3.loom
2020-01-23 01:25:23,754 - DEBUG - Collecting row attributes
2020-01-23 01:25:23,950 - DEBUG - Generating data table
2020-01-23 01:25:24,019 - DEBUG - Writing loom file
2020-01-23 01:25:25,449 - DEBUG - Terminated Succesfully!
Does anyone has already encountered this weird issue ?
Regards,
Marion

Hi velocyto team,
I have run velocyto on a smartseq2 sample and got the expected loom file output. But in the log of the run, I have a weird message :
"Summarizing the results of intron validation.
Validated 0 introns (of which unique intervals 0) out of 984652 total possible introns (considering each possible transcript models)."
It sounds very unlikely that there is no spliced situation in my data.
I have run the command :
velocyto run_smartseq2 -e velocyto STAR_mapping/cell1.sorted.bam gencode.v25.annotation.gtf
(I have tried with and without masking, the result was the same)
The genome annotation file is from https://www.gencodegenes.org/human/release_25.html (used the same version for the STAR mapping)
Log of the run :
2020-01-22 19:20:31,776 - WARNING - Each bam file will be interpreted as a DIFFERENT cell
2020-01-22 19:20:31,776 - INFO - No OUTPUTFOLDER specified, find output files inside /scbio1/marion/Charles_spleen/STAR_mapping/velocyto
2020-01-22 19:20:31,776 - DEBUG - Using logic: SmartSeq2
2020-01-22 19:20:31,777 - DEBUG - Cell barcodes will be determined while reading the .bam file
2020-01-22 19:20:31,796 - WARNING - The file /scbio1/marion/Charles_spleen/STAR_mapping/RHM5691.sorted.bam already exists. The sorting step will be skipped and the existing file will be used.
2020-01-22 19:20:31,797 - WARNING - The file /scbio1/marion/Charles_spleen/STAR_mapping/RHM5692.sorted.bam already exists. The sorting step will be skipped and the existing file will be used.
...
...
2020-01-22 19:20:31,831 - INFO - Load the annotation from /home/marion/scripts/reference_genome/GRCh38_gencode_v25_gtf/gencode.v25.annotation.gtf
2020-01-22 19:20:39,092 - DEBUG - Parsing Chromosome 1 strand - [line 0]
2020-01-22 19:20:39,794 - DEBUG - Done with 1- [line 111685]
2020-01-22 19:20:39,795 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:39,808 - DEBUG - Seen 2573 genes until now
2020-01-22 19:20:39,808 - DEBUG - Parsing Chromosome 1 strand + [line 111686]
2020-01-22 19:20:40,780 - DEBUG - Done with 1+ [line 232137]
2020-01-22 19:20:40,780 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:40,795 - DEBUG - Seen 5194 genes until now
2020-01-22 19:20:40,795 - DEBUG - Parsing Chromosome 10 strand - [line 232138]
2020-01-22 19:20:40,989 - DEBUG - Done with 10- [line 277419]
2020-01-22 19:20:40,989 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:40,996 - DEBUG - Seen 6256 genes until now
2020-01-22 19:20:40,996 - DEBUG - Parsing Chromosome 10 strand + [line 277420]
2020-01-22 19:20:41,187 - DEBUG - Done with 10+ [line 322747]
2020-01-22 19:20:41,187 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:41,192 - DEBUG - Seen 7398 genes until now
2020-01-22 19:20:41,192 - DEBUG - Parsing Chromosome 11 strand - [line 322748]
2020-01-22 19:20:41,759 - DEBUG - Done with 11- [line 398779]
2020-01-22 19:20:41,759 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:41,768 - DEBUG - Seen 9000 genes until now
2020-01-22 19:20:41,768 - DEBUG - Parsing Chromosome 11 strand + [line 398780]
2020-01-22 19:20:42,372 - DEBUG - Done with 11+ [line 478704]
2020-01-22 19:20:42,372 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:42,383 - DEBUG - Seen 10633 genes until now
2020-01-22 19:20:42,383 - DEBUG - Parsing Chromosome 12 strand - [line 478705]
2020-01-22 19:20:42,728 - DEBUG - Done with 12- [line 555117]
2020-01-22 19:20:42,728 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:42,738 - DEBUG - Seen 12096 genes until now
2020-01-22 19:20:42,738 - DEBUG - Parsing Chromosome 12 strand + [line 555118]
2020-01-22 19:20:43,077 - DEBUG - Done with 12+ [line 631946]
2020-01-22 19:20:43,078 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,369 - DEBUG - Seen 13573 genes until now
2020-01-22 19:20:43,369 - DEBUG - Parsing Chromosome 13 strand - [line 631947]
2020-01-22 19:20:43,452 - DEBUG - Done with 13- [line 650590]
2020-01-22 19:20:43,452 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,454 - DEBUG - Seen 14224 genes until now
2020-01-22 19:20:43,454 - DEBUG - Parsing Chromosome 13 strand + [line 650591]
2020-01-22 19:20:43,541 - DEBUG - Done with 13+ [line 670483]
2020-01-22 19:20:43,541 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,544 - DEBUG - Seen 14877 genes until now
2020-01-22 19:20:43,544 - DEBUG - Parsing Chromosome 14 strand - [line 670484]
2020-01-22 19:20:43,731 - DEBUG - Done with 14- [line 714647]
2020-01-22 19:20:43,731 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,737 - DEBUG - Seen 15954 genes until now
2020-01-22 19:20:43,737 - DEBUG - Parsing Chromosome 14 strand + [line 714648]
2020-01-22 19:20:43,940 - DEBUG - Done with 14+ [line 763579]
2020-01-22 19:20:43,940 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:43,947 - DEBUG - Seen 17101 genes until now
2020-01-22 19:20:43,947 - DEBUG - Parsing Chromosome 15 strand - [line 763580]
2020-01-22 19:20:44,169 - DEBUG - Done with 15- [line 814433]
2020-01-22 19:20:44,169 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:44,175 - DEBUG - Seen 18165 genes until now
2020-01-22 19:20:44,175 - DEBUG - Parsing Chromosome 15 strand + [line 814434]
2020-01-22 19:20:44,689 - DEBUG - Done with 15+ [line 860822]
2020-01-22 19:20:44,689 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:44,696 - DEBUG - Seen 19253 genes until now
2020-01-22 19:20:44,696 - DEBUG - Parsing Chromosome 16 strand - [line 860823]
2020-01-22 19:20:44,939 - DEBUG - Done with 16- [line 916752]
2020-01-22 19:20:44,939 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:44,948 - DEBUG - Seen 20469 genes until now
2020-01-22 19:20:44,948 - DEBUG - Parsing Chromosome 16 strand + [line 916753]
2020-01-22 19:20:45,240 - DEBUG - Done with 16+ [line 985772]
2020-01-22 19:20:45,240 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:45,250 - DEBUG - Seen 21764 genes until now
2020-01-22 19:20:45,250 - DEBUG - Parsing Chromosome 17 strand - [line 985773]
2020-01-22 19:20:45,614 - DEBUG - Done with 17- [line 1071727]
2020-01-22 19:20:45,614 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:45,626 - DEBUG - Seen 23294 genes until now
2020-01-22 19:20:45,627 - DEBUG - Parsing Chromosome 17 strand + [line 1071728]
2020-01-22 19:20:46,309 - DEBUG - Done with 17+ [line 1150792]
2020-01-22 19:20:46,309 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:46,319 - DEBUG - Seen 24759 genes until now
2020-01-22 19:20:46,320 - DEBUG - Parsing Chromosome 18 strand - [line 1150793]
2020-01-22 19:20:46,418 - DEBUG - Done with 18- [line 1173822]
2020-01-22 19:20:46,419 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:46,422 - DEBUG - Seen 25333 genes until now
2020-01-22 19:20:46,422 - DEBUG - Parsing Chromosome 18 strand + [line 1173823]
2020-01-22 19:20:46,514 - DEBUG - Done with 18+ [line 1195468]
2020-01-22 19:20:46,515 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:46,518 - DEBUG - Seen 25929 genes until now
2020-01-22 19:20:46,518 - DEBUG - Parsing Chromosome 19 strand - [line 1195469]
2020-01-22 19:20:46,854 - DEBUG - Done with 19- [line 1276363]
2020-01-22 19:20:46,854 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:46,865 - DEBUG - Seen 27362 genes until now
2020-01-22 19:20:46,865 - DEBUG - Parsing Chromosome 19 strand + [line 1276364]
2020-01-22 19:20:47,206 - DEBUG - Done with 19+ [line 1358881]
2020-01-22 19:20:47,206 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:47,217 - DEBUG - Seen 28855 genes until now
2020-01-22 19:20:47,217 - DEBUG - Parsing Chromosome 2 strand - [line 1358882]
2020-01-22 19:20:48,242 - DEBUG - Done with 2- [line 1455119]
2020-01-22 19:20:48,243 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,255 - DEBUG - Seen 30827 genes until now
2020-01-22 19:20:48,255 - DEBUG - Parsing Chromosome 2 strand + [line 1455120]
2020-01-22 19:20:48,662 - DEBUG - Done with 2+ [line 1551251]
2020-01-22 19:20:48,662 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,675 - DEBUG - Seen 32826 genes until now
2020-01-22 19:20:48,675 - DEBUG - Parsing Chromosome 20 strand - [line 1551252]
2020-01-22 19:20:48,787 - DEBUG - Done with 20- [line 1577072]
2020-01-22 19:20:48,787 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,791 - DEBUG - Seen 33525 genes until now
2020-01-22 19:20:48,791 - DEBUG - Parsing Chromosome 20 strand + [line 1577073]
2020-01-22 19:20:48,917 - DEBUG - Done with 20+ [line 1607038]
2020-01-22 19:20:48,917 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,922 - DEBUG - Seen 34212 genes until now
2020-01-22 19:20:48,922 - DEBUG - Parsing Chromosome 21 strand - [line 1607039]
2020-01-22 19:20:48,985 - DEBUG - Done with 21- [line 1621229]
2020-01-22 19:20:48,985 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:48,987 - DEBUG - Seen 34639 genes until now
2020-01-22 19:20:48,987 - DEBUG - Parsing Chromosome 21 strand + [line 1621230]
2020-01-22 19:20:49,054 - DEBUG - Done with 21+ [line 1635954]
2020-01-22 19:20:49,054 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:49,057 - DEBUG - Seen 35047 genes until now
2020-01-22 19:20:49,057 - DEBUG - Parsing Chromosome 22 strand - [line 1635955]
2020-01-22 19:20:49,174 - DEBUG - Done with 22- [line 1662909]
2020-01-22 19:20:49,174 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:49,178 - DEBUG - Seen 35644 genes until now
2020-01-22 19:20:49,178 - DEBUG - Parsing Chromosome 22 strand + [line 1662910]
2020-01-22 19:20:49,303 - DEBUG - Done with 22+ [line 1692214]
2020-01-22 19:20:49,303 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:49,307 - DEBUG - Seen 36365 genes until now
2020-01-22 19:20:49,308 - DEBUG - Parsing Chromosome 3 strand - [line 1692215]
2020-01-22 19:20:49,650 - DEBUG - Done with 3- [line 1772867]
2020-01-22 19:20:49,650 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:49,661 - DEBUG - Seen 37878 genes until now
2020-01-22 19:20:49,661 - DEBUG - Parsing Chromosome 3 strand + [line 1772868]
2020-01-22 19:20:50,439 - DEBUG - Done with 3+ [line 1852274]
2020-01-22 19:20:50,439 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:50,449 - DEBUG - Seen 39375 genes until now
2020-01-22 19:20:50,449 - DEBUG - Parsing Chromosome 4 strand - [line 1852275]
2020-01-22 19:20:50,657 - DEBUG - Done with 4- [line 1901817]
2020-01-22 19:20:50,658 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:50,664 - DEBUG - Seen 40607 genes until now
2020-01-22 19:20:50,664 - DEBUG - Parsing Chromosome 4 strand + [line 1901818]
2020-01-22 19:20:50,885 - DEBUG - Done with 4+ [line 1952043]
2020-01-22 19:20:50,885 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:50,892 - DEBUG - Seen 41880 genes until now
2020-01-22 19:20:50,892 - DEBUG - Parsing Chromosome 5 strand - [line 1952044]
2020-01-22 19:20:51,125 - DEBUG - Done with 5- [line 2006650]
2020-01-22 19:20:51,125 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:51,134 - DEBUG - Seen 43309 genes until now
2020-01-22 19:20:51,134 - DEBUG - Parsing Chromosome 5 strand + [line 2006651]
2020-01-22 19:20:51,384 - DEBUG - Done with 5+ [line 2066704]
2020-01-22 19:20:51,384 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:51,396 - DEBUG - Seen 44748 genes until now
2020-01-22 19:20:51,396 - DEBUG - Parsing Chromosome 6 strand - [line 2066705]
2020-01-22 19:20:51,648 - DEBUG - Done with 6- [line 2126597]
2020-01-22 19:20:51,648 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:51,656 - DEBUG - Seen 46169 genes until now
2020-01-22 19:20:51,656 - DEBUG - Parsing Chromosome 6 strand + [line 2126598]
2020-01-22 19:20:51,884 - DEBUG - Done with 6+ [line 2182757]
2020-01-22 19:20:51,884 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:51,892 - DEBUG - Seen 47611 genes until now
2020-01-22 19:20:51,892 - DEBUG - Parsing Chromosome 7 strand - [line 2182758]
2020-01-22 19:20:52,143 - DEBUG - Done with 7- [line 2240775]
2020-01-22 19:20:52,143 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:52,151 - DEBUG - Seen 48949 genes until now
2020-01-22 19:20:52,151 - DEBUG - Parsing Chromosome 7 strand + [line 2240776]
2020-01-22 19:20:52,420 - DEBUG - Done with 7+ [line 2304934]
2020-01-22 19:20:52,420 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:52,429 - DEBUG - Seen 50478 genes until now
2020-01-22 19:20:52,429 - DEBUG - Parsing Chromosome 8 strand - [line 2304935]
2020-01-22 19:20:53,146 - DEBUG - Done with 8- [line 2354546]
2020-01-22 19:20:53,146 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,152 - DEBUG - Seen 51692 genes until now
2020-01-22 19:20:53,153 - DEBUG - Parsing Chromosome 8 strand + [line 2354547]
2020-01-22 19:20:53,339 - DEBUG - Done with 8+ [line 2399113]
2020-01-22 19:20:53,339 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,346 - DEBUG - Seen 52831 genes until now
2020-01-22 19:20:53,346 - DEBUG - Parsing Chromosome 9 strand - [line 2399114]
2020-01-22 19:20:53,528 - DEBUG - Done with 9- [line 2442260]
2020-01-22 19:20:53,528 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,534 - DEBUG - Seen 53931 genes until now
2020-01-22 19:20:53,534 - DEBUG - Parsing Chromosome 9 strand + [line 2442261]
2020-01-22 19:20:53,736 - DEBUG - Done with 9+ [line 2489998]
2020-01-22 19:20:53,737 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,743 - DEBUG - Seen 55073 genes until now
2020-01-22 19:20:53,743 - DEBUG - Parsing Chromosome M strand - [line 2489999]
2020-01-22 19:20:53,743 - DEBUG - Done with M- [line 2490027]
2020-01-22 19:20:53,743 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,743 - DEBUG - Seen 55082 genes until now
2020-01-22 19:20:53,743 - DEBUG - Parsing Chromosome M strand + [line 2490028]
2020-01-22 19:20:53,743 - DEBUG - Done with M+ [line 2490141]
2020-01-22 19:20:53,744 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,744 - DEBUG - Seen 55110 genes until now
2020-01-22 19:20:53,744 - DEBUG - Parsing Chromosome X strand - [line 2490142]
2020-01-22 19:20:53,907 - DEBUG - Done with X- [line 2530278]
2020-01-22 19:20:53,907 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:53,913 - DEBUG - Seen 56259 genes until now
2020-01-22 19:20:53,913 - DEBUG - Parsing Chromosome X strand + [line 2530279]
2020-01-22 19:20:54,077 - DEBUG - Done with X+ [line 2570672]
2020-01-22 19:20:54,077 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:54,082 - DEBUG - Seen 57469 genes until now
2020-01-22 19:20:54,083 - DEBUG - Parsing Chromosome Y strand - [line 2570673]
2020-01-22 19:20:54,101 - DEBUG - Done with Y- [line 2574613]
2020-01-22 19:20:54,101 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:54,102 - DEBUG - Seen 57751 genes until now
2020-01-22 19:20:54,102 - DEBUG - Parsing Chromosome Y strand + [line 2574614]
2020-01-22 19:20:54,126 - DEBUG - Assigning indexes to genes
2020-01-22 19:20:54,127 - DEBUG - Done with Y+ [line 2579815]
2020-01-22 19:20:54,127 - DEBUG - Fixing corner cases of transcript models containg intron longer than 1000Kbp
2020-01-22 19:20:55,832 - DEBUG - Generated 2167397 features corresponding to 198093 transcript models from /home/marion/scripts/reference_genome/GRCh38_gencode_v25_gtf/gencode.v25.annotation.gtf
2020-01-22 19:20:55,856 - INFO - Scan /scbio1/marion/Charles_spleen/STAR_mapping/RHM5691.sorted.bam /scbio1/marion/Charles_spleen/STAR_mapping/RHM5692.sorted.bam
...
...
/scbio1/marion/Charles_spleen/STAR_mapping/RHP4888.sorted.bam to validate intron intervals
2020-01-22 19:20:55,856 - DEBUG - Start molecule counting!
2020-01-22 19:20:59,702 - DEBUG - Features available for chromosomes : ['1-', '1+', '10-', '10+', '11-', '11+', '12-', '12+', '13-', '13+', '14-', '14+', '15-', '15+', '16-', '16+', '17-', '17+', '18-', '18+', '19-', '19+', '2-', '2+', '20-', '20+', '21-', '21+', '22-', '22+', '3-', '3+', '4-', '4+', '5-', '5+', '6-', '6+', '7-', '7+', '8-', '8+', '9-', '9+', 'M-', 'M+', 'X-', 'X+', 'Y-', 'Y+']
2020-01-22 19:20:59,702 - DEBUG - Mask available for chromosomes : []
2020-01-22 19:20:59,702 - DEBUG - Summarizing the results of intron validation.
2020-01-22 19:20:59,983 - DEBUG - Validated 0 introns (of which unique intervals 0) out of 984652 total possible introns (considering each possible transcript models).
2020-01-22 19:20:59,984 - DEBUG - Reading /scbio1/marion/Charles_spleen/STAR_mapping/RHM5691.sorted.bam
2020-01-22 19:20:59,985 - DEBUG - Read first 0 million reads
2020-01-22 19:21:46,626 - DEBUG - Counting for batch 1, containing 1 cells and 2153426 reads
2020-01-22 19:23:03,180 - DEBUG - 0 reads in repeat masked regions
2020-01-22 19:23:03,180 - DEBUG - 1096039 reads overlapping with features on plus strand
2020-01-22 19:23:03,180 - DEBUG - 1191030 reads overlapping with features on minus strand
2020-01-22 19:23:03,180 - DEBUG - 215962 reads overlapping with features on both strands
2020-01-22 19:23:21,903 - WARNING - The barcode selection mode is off, no cell events will be identified by <80 counts
2020-01-22 19:23:21,904 - WARNING - 0 of the barcodes where without cell
2020-01-22 19:23:22,362 - DEBUG - Reading /scbio1/marion/Charles_spleen/STAR_mapping/RHM5692.sorted.bam
2020-01-22 19:23:22,363 - DEBUG - Read first 0 million reads
2020-01-22 19:23:52,265 - DEBUG - Counting for batch 2, containing 1 cells and 1509092 reads
2020-01-22 19:24:45,763 - DEBUG - 0 reads in repeat masked regions
2020-01-22 19:24:45,763 - DEBUG - 787641 reads overlapping with features on plus strand
2020-01-22 19:24:45,763 - DEBUG - 819703 reads overlapping with features on minus strand
2020-01-22 19:24:45,763 - DEBUG - 177739 reads overlapping with features on both strands
2020-01-22 19:24:57,948 - WARNING - The barcode selection mode is off, no cell events will be identified by <80 counts
2020-01-22 19:24:57,948 - WARNING - 0 of the barcodes where without cell
...
...
2020-01-23 01:25:23,753 - DEBUG - 0 reads were skipped because no apropiate cell or umi barcode was found
2020-01-23 01:25:23,753 - DEBUG - Counting done!
2020-01-23 01:25:23,754 - DEBUG - Example of barcode: RHM5824.sorted.bam and cell_id: Charles_velocyto3:RHM5824.sorted.bam
2020-01-23 01:25:23,754 - DEBUG - Generating output file /scbio1/marion/Charles_spleen/STAR_mapping/velocyto/Charles_velocyto3.loom
2020-01-23 01:25:23,754 - DEBUG - Collecting row attributes
2020-01-23 01:25:23,950 - DEBUG - Generating data table
2020-01-23 01:25:24,019 - DEBUG - Writing loom file
2020-01-23 01:25:25,449 - DEBUG - Terminated Succesfully!
Does anyone has already encountered this weird issue ?
Regards,
Marion

I met the same problem. Have you solved it?

Hi
I met the same problem. Have you solved it?

authors: Sonric marionchvr


text:
Should support "Enter" keyboard action in Security Answer page

Steps to Reproduce:

Enter the accept flow
Enter some characters into the Security Answer text field
Press "Enter" key
The page is refreshed with incorrect url

repo: ventureum/Chainsfer


text:
Profile photo model

Design in progress.
https://www.figma.com/proto/XTQwnQ8SZGGDYo2w5nFqH9/Chainsfr_v1.3?node-id=926%3A353&viewport=-1815%2C-1590%2C0.5764328837394714&scaling=min-zoom

Design done. @InVincible2016

repo: ventureum/Chainsfr