text:
added unit test for subscribe and unsubscribe stack

Fixes #137
Changes proposed in the pull request

Added unit tests for subscribe and unsubscribe stack endpoints

Other information

Check if you have done the following before creating the PR

[x] console logs have been deleted
[x] No commented code (If commented the reasons are given)

@agentmilindu @psnmissaka  Can you please review this PR?

repo: scorelab/Stackle


text:
How to manage errors like on demo

Hi,
Thank you so much for your project, it's awesome and really helped me in my work. But I would like to display errors (image too small with outerwidth etc..) like on the demo website. I didn't find any documentation about it.
Can you help me, tell me how did you do ? I'm not a pro with API :$
Thank you !

I'd also like this

Haha, I tried this afternoon, and got approximately the same code :P

Difference is I verify the error.code, i don't know if it's right, but it's working actually.
If the author can show us something which is "more official" because right now, it's only some merged codes, not really clean :)

Hello i did it but not working, why you configuationnot same like in doc,

It's just the Jquery part, here the css and html i used like the demo :
.cropit-image-preview .error-msg {
    position: absolute;
    top: 0;
    left: 0;
    width: 100%;
    padding: 10px 20px;
    color: #fff;
    background: rgba(210,65,72,0.8);
    line-height: 1.5;
    opacity: 0;
    -ms-filter: "progid:DXImageTransform.Microsoft.Alpha(Opacity=0)";
    filter: alpha(opacity=0);
    -webkit-transition: opacity 0.25s;
    -moz-transition: opacity 0.25s;
    -o-transition: opacity 0.25s;
    -ms-transition: opacity 0.25s;
    transition: opacity 0.25s;
}

.cropit-image-preview.has-error .error-msg {
    opacity: 1;
    -ms-filter: none;
    filter: none;
}

Hope it'll help you, waiting for the author's help :)

Hello thanks for respon @Keenjix will digging after this write comment done, i have a lot of question about crop and resize ?

Did you tested in mobile about crop images !
the errors came from because setting in css, am i right ? please correct ya this script

width: 250px;
height: 250px;

by the way code you posted above what name file in demo folder is that bassic.html or form.html or image_background.html or pisca.html, thanks for respond

Nop, i'm not in that case, i don't need a mobile compatibility
I'm not sure of what you wanted to say sorry :x

At first, i used the basic one, and when I tried to manage errors, I checked the author's demo page, I looked at his JS and I tinked the code above. There is no "true" code, and this is what I regret and asking for :)

oh oke you use bassic.html ya, then who is the right js, did you posted above or someone commnet above ?
the reason why errors came from ? cause i read doc configuration images can handle by css, if the images less than width 450px and height 450px the erorrs came,but tried uplopad images more than 450px images can accept, please answer complete ya, Thanks

It's the same code for both of us, my code checking what kind of error is : (e.code ===1) means "image too small"
This is what you have in the documentation :
onImageError function
Called when image cannot be loaded.

{object} error - Error object.
{number} error.code - Error code. 0 means generic image loading failure. 1 means image is too small.
{string} error.message - A message explaining the error.

If the uploaded image size if smaller than the preview area, then the error message is displayed EXCEPT if you allow "smallImage".

Please paste your whole code if you don't mind cause i got blank upload images, thanks
i use bassic.html thanks

Thanks for your support already solved, but i use this plugin in modal bootsrap for the first time click why errors already came up the fact i make more than height and width in css

src: base_url + "asset/img/default-product.png",

source: gharchive/issue

authors: Keenjix pjb493 sidaurukfreddy

repo: scottcheng/cropit

license: mit

license_type: permissive

license_source: bigquery


text:
Cannot open the RibbonWorkbench in XRMToolBox

Hi,
After the new update of XRMToolBox, i cannot open the RibbonWorkbench and i'm getting the error

as one of the new feature in the lateset XRMToolBox update was

You will need to update to the latest version of the RWB.

it's not showing any update in the plugin store

Hmm - I don't know what that is. The latest version in Nuget is 3.1.325.1
https://www.nuget.org/packages/RibbonWorkbench2016/

Hi,
I meant XRMToolBox Store, thanks for the link

repo: scottdurow/RibbonWorkbench


text:
Need to have the Tiler level copyMetadata and copyMask functions

Need to add the following functions to Tiler

ErrorType copyMetadata(Tiler& referenceTiler);
ErrorType copyMask(const Tiler& referenceTiler);

completed with b8a35029fb2fd3718c0420d8b61c41316c70ea57

repo: scottgs/cvtile


text:
How do I use SASS?

CSS Tricks makes it sound easy, but there is no connection to real app interfaces like Scout. SASS Basics http://sass-lang.com/guide is TOTALLY NOT BASIC. Latter resource, read the Import section without knowledge of how-to, and it is gibberish. SASS is like @media WIX dumps at Envato: a plague of creepy de-liquefied liquid @margin chunkies in a bondage club. Please don't refer me to slurred speech 'Getting Started with Scout App in 2 minutes HD - YouTube' - yet more steroids and Heavens knows what! Hint for teacher: CSS Tricks (started) with a working example, but as with 99.999% of the bondage culture, sample lost in transit. btw I am happy building my boxing.css per Paul Irish 2004. SASS could be curiosity, or sincere medical concern. Can anyone in the SASS club slow down enough to explain with absolute calm sobriety, how to Scout Sass?

Issue resolved. Closing this ticket.

Scout-App.io

authors: TheJaredWilcurt riverleaf

repo: scout-app/scout-app

license: MIT

license_source: github-api


text:
Update Compass Mixin

The version shipped is outdated and has a compact function that is deprecated in newer versions of LibSass.
Compass mixin needs updated.
Issue reported by: @zayyarphone in the Scout-App Chatroom

Bower.json has been updated in the master branch. This issue will be resolved in the next release of Scout-App.

@zayyarphone
There is a new release of Scout-App available for download.

Scout-App.io
Release Notes


text:
Email compliance

https://help.mailgun.com/hc/en-us/articles/20263554449179-Enhancing-Email-Compliance-A-Guide-To-The-2024-Gmail-And-Yahoo-Changes-For-Optimal-Deliverability

DMARC set up

repo: scoutplan/scoutplan


text:
WIP - Stream based file reader

This introduces the concept of a "Stream" based reader, where the
underlying storage backend operates in files/bytes (like S3) as opposed
to structured objects (like hubstorage).
Having binary/stream based readers allows us to have pluggable
decompressors and deserializers, instead of hardcoding them in the
readers.
This reuses the same get_read_streams method that the stream bypass uses
Also adds a CSV desserializer.
Improvements planned:

Tests
Use the same naming convenction as in the rest of the exporters modules
Config checker should fail if a compressor/deserializer module is used alongside an non-stream reader

I like where this is going, looks like a good way of addressing #298 :+1:

So, I've been testing this and it's working pretty fine, I'm quite happy with it -- awesome work, @Youwotma ! :)
I have only a couple comments, but they're really small things:

It's assuming ZLibDecompressor by default, which is good because of backwards compatibility, but nothing is being shown in the log to indicate that. It would be nice to have some message in the logs to help users trying to use it with uncompressed files -- currently one just gets a stacktrace with:
ERROR:export-pipeline: -- EXPORTMANAGER -- Error -3 while decompressing: incorrect header check

Logging No decompressor configured, using default ZLibDecompressor is a good start.
Catching that exception and appending a message like (use NoDecompressor if you're using uncompressed input) is even better

The same applies for deserializers, which the assumed default is JSON lines (albeit probably a lesser problem, since).

source: gharchive/pull-request

authors: Youwotma eliasdorneles

repo: scrapinghub/exporters


text:
Save as mhtml format?

Is there any methods to save web page as mhtml?
I found that Puppeteer and Playwright use CDP to save mhtml, and can I use CDP in Splash?

Switch to Playwright.

repo: scrapinghub/splash


text:
Shift directly

Thanks to recent improvements, we can shift expressions by constants directly.
Inspired by an observation from https://github.com/scroll-tech/ceno/pull/660

Most of this is now in https://github.com/scroll-tech/ceno/pull/660
So this PR served its purpose of showing what's possible.

repo: scroll-tech/ceno


text:
Training and Inference discussion for baseline model

What is the baseline model
The model which was trained on ✅ as per the QCs mentioned in #25 is the baseline model. A total of 96 images were used in the training of this model. A list of subjects (for later reference) is below:
participants_baseline.csv
The model was trained in 6 different settings - 5 models for the 5 fold cross-validation and 1 fold_all model (discussion can be found here - https://github.com/MIC-DKFZ/nnUNet/issues/1364#issuecomment-1492075312). The config (containing preprocessing, hyperparameters) for nnUNetv2 training is: plans.json
After the model was trained, the inference was run on the ❌  (failed segmentations) from #25. Below are the QCs from all the folds and fold_all:
qc_fold_0.zip
qc_fold_1.zip
qc_fold_2.zip
qc_fold_3.zip
qc_fold_4.zip
qc_fold_all.zip
The steps to reproduce the above QC results (/run inference) are the following:

Clone this repos
cd fmri-segmentation
Download the model weights from the link: https://drive.google.com/drive/folders/1WSn-15wGWz6i2_aZeQTwKls2sZ6dpfHf?usp=share_link
Install dependencies

pip install -r run_nnunet_inference_requirements.txt

Run the command:

python run_nnunet_inference.py --path-dataset <PATH TO FOLDER CONTAINING IMAGES, SUFFIXED WITH _0000> --path-out <PATH TO O/P FOLDER> --path-model <PATH TO DOWNLOADED WEIGHTS FOLDER>

Next steps:

[x] Choose the fold whose inference results will be used for the next round of training
[x] Choose and correct ~30 segmentations and include it in the next training round along with the ones that have good segmentation after inference.
[ ]  Get metric by running evaluation on the held-out test set (#33)

I chose 30 subjects from the fold_all inference that I manually corrected. The list of 30 chosen subjects is below:
qc_report_fold_all.zip
I manually corrected the segmentation for these subjects and attaching the QC for the same below:
qc_fold_all_corrected.zip
After @jcohenadad approves these segmentations, I'll add these images to the training set and start the re-training.

review: qc_fail.yml.zip
details:
spinefmri-sub-genevaR104_003_0000.nii.gz

spinefmri-sub-genevaR106_005_0000.nii.gz

spinefmri-sub-genevaR108_007_0000.nii.gz

spinefmri-sub-genevaR202_018_0000.nii.gz

spinefmri-sub-genevaR207_023_0000.nii.gz

spinefmri-sub-genevaR209_025_0000.nii.gz

spinefmri-sub-genevaR211_027_0000.nii.gz

spinefmri_sub-nwM09_task-motor_bold_0000.nii.gz
overseg:
spinefmri_sub-nwM16_task-motor_bold_0000.nii.gz

"Download all" button is not there-- please make sure to use the latest version of SCT:

Closing the issue since the baseline model training was successfully completed (including running inference and manual correction)

authors: jcohenadad rohanbanerjee

repo: sct-pipeline/fmri-segmentation


text:
No Gap Ack Blocks when TSN + offset > UINT32_MAX

What should be the correct behaviour when the current TSN is near uint32_max and there is gap ack blocks reported? I cannot find anything in the RFC but the logical way would be to still get relative offsets in the SACKs but i observe a different behaviour:
What i observe:
TSN=UINT32_MAX, no gaps reported when relative offset + TSN > UINT32_MAX
Example: (expected)
TSN=UINT32_MAX, GAP_START=4, GAP_END=5
This should still work because when using serial number arithmetics the gap TSNs should wrap around and still give us the correct report.

The TSNs and the SSNs are using serial number arithmetic. See https://tools.ietf.org/html/rfc4960#section-1.6. So the numbers just wrap around.

That is what i am saying :D
But what i see is that gap ack blocks are no longer reported when the TSN is near UINT32_MAX

I'll attach a pcap

sctp.zip
N° 378 SACK with gap ack blocks
TSN wraps around to 0
N° 380 SACK with no gap ack blocks

OK. I see. Let me try to reproduce this.

For info: the SACK reporter is Firefox for Windows 75.0 if that helps

I have used packetdrill to create a script which triggers this behaviour on the FreeBSD kernel stack (usrsctp is the SCTP kernel stack of  FreeBSD running in userland):
--tolerance_usecs=50000

 0.0 socket(..., SOCK_STREAM, IPPROTO_SCTP) = 3
+0.0 fcntl(3, F_GETFL) = 0x2 (flags O_RDWR)
+0.0 fcntl(3, F_SETFL, O_RDWR|O_NONBLOCK) = 0
+0.0 connect(3, ..., ...) = -1 EINPROGRESS (Operation now in progress)
+0.0 > sctp: INIT[flgs=0, tag=1, a_rwnd=..., os=..., is=..., tsn=1, ...]
+0.1 < sctp: INIT_ACK[flgs=0, tag=2, a_rwnd=1500, os=1, is=1, tsn=4294967290, STATE_COOKIE[len=4, val=...]]
+0.0 > sctp: COOKIE_ECHO[flgs=0, len=4, val=...]
+0.1 < sctp: COOKIE_ACK[flgs=0]
+0.0 getsockopt(3, SOL_SOCKET, SO_ERROR, [0], [4]) = 0
+0.0 < sctp: DATA[flgs=BE, len=1416, tsn=4294967290, sid=0, ssn=0, ppid=0]
+0.0 > sctp: SACK[flgs=0, cum_tsn=4294967290, a_rwnd=..., gaps=[], dups=[]]
+0.0 recv(3, ..., 2000,0) = 1400
+0.0 < sctp: DATA[flgs=BE, len=1416, tsn=4294967292, sid=0, ssn=2, ppid=0]
+0.0 > sctp: SACK[flgs=0, cum_tsn=4294967290, a_rwnd=..., gaps=[2:2], dups=[]]
+0.0 < sctp: DATA[flgs=BE, len=1416, tsn=4294967293, sid=0, ssn=3, ppid=0]
+0.0 > sctp: SACK[flgs=0, cum_tsn=4294967290, a_rwnd=..., gaps=[2:3], dups=[]]
+0.0 < sctp: DATA[flgs=BE, len=1416, tsn=4294967295, sid=0, ssn=5, ppid=0]
+0.0 > sctp: SACK[flgs=0, cum_tsn=4294967290, a_rwnd=..., gaps=[2:3, 5:5], dups=[]]
+0.0 < sctp: DATA[flgs=BE, len=1416, tsn=1, sid=0, ssn=7, ppid=0]
+0.0 > sctp: SACK[flgs=0, cum_tsn=4294967290, a_rwnd=..., gaps=[2:3, 5:5, 7:7], dups=[]]

The scripts fails with:
tuexen@head:~ % sudo packetdrill --verbose --tun_dev=tun0 --persistent_tun_dev issue-462.pkt
outbound sniffed packet:  0.000107 sctp: INIT[flgs=0x00, tag=1618459559, a_rwnd=1864135, os=10, is=2048, tsn=2938908013, ECN_CAPABLE[], FORWARD_TSN_SUPPORTED[], SUPPORTED_EXTENSIONS[types=[FORWARD_TSN, AUTH, ASCONF, ASCONF_ACK, RECONFIG]], PARAMETER[type=0x8002, value=[0xb1, 0xaf, 0xef, 0x25, 0xec, 0x4f, 0x85, 0x4e, 0x10, 0xbd, 0xf8, 0xd5, 0x28, 0x91, 0x56, 0x98, 0xa6, 0x22, 0xfe, 0x81, 0x1a, 0x4e, 0x4c, 0x84, 0xe6, 0x03, 0xa9, 0x20, 0x76, 0x69, 0x79, 0x23]], HMAC_ALGO[ids=[SHA-256, SHA-1]], CHUNKS[types=[ASCONF_ACK, ASCONF]], SUPPORTED_ADDRESS_TYPES[types=[IPv4]]]
inbound injected packet:  0.100427 sctp: INIT_ACK[flgs=0x00, tag=2, a_rwnd=1500, os=1, is=1, tsn=4294967290, STATE_COOKIE[len=4, val=...]]
outbound sniffed packet:  0.100619 sctp: COOKIE_ECHO[flgs=0x00, len=4]
inbound injected packet:  0.201611 sctp: COOKIE_ACK[flgs=0x00]
inbound injected packet:  0.201835 sctp: DATA[flgs=BE, len=1416, tsn=4294967290, sid=0, ssn=0, ppid=0]
outbound sniffed packet:  0.201871 sctp: SACK[flgs=0x00, cum_tsn=4294967290, a_rwnd=1862479, gaps=[], dups=[]]
inbound injected packet:  0.201995 sctp: DATA[flgs=BE, len=1416, tsn=4294967292, sid=0, ssn=2, ppid=0]
outbound sniffed packet:  0.202044 sctp: SACK[flgs=0x00, cum_tsn=4294967290, a_rwnd=1862479, gaps=[2:2], dups=[]]
inbound injected packet:  0.202102 sctp: DATA[flgs=BE, len=1416, tsn=4294967293, sid=0, ssn=3, ppid=0]
outbound sniffed packet:  0.202127 sctp: SACK[flgs=0x00, cum_tsn=4294967290, a_rwnd=1860823, gaps=[2:3], dups=[]]
inbound injected packet:  0.202176 sctp: DATA[flgs=BE, len=1416, tsn=4294967295, sid=0, ssn=5, ppid=0]
outbound sniffed packet:  0.202209 sctp: SACK[flgs=0x00, cum_tsn=4294967290, a_rwnd=1859167, gaps=[2:3, 5:5], dups=[]]
inbound injected packet:  0.202290 sctp: DATA[flgs=BE, len=1416, tsn=1, sid=0, ssn=7, ppid=0]
outbound sniffed packet:  0.202328 sctp: SACK[flgs=0x00, cum_tsn=4294967290, a_rwnd=1857511, gaps=[], dups=[]]
issue-462.pkt:24: error handling packet: live packet field sctp_chunk_length: expected: 28 (0x1c) vs actual: 16 (0x10)
script packet:  0.202336 sctp: SACK[flgs=0x00, cum_tsn=4294967290, a_rwnd=0, gaps=[2:3, 5:5, 7:7], dups=[]]
actual packet:  0.202328 sctp: SACK[flgs=0x00, cum_tsn=4294967290, a_rwnd=1857511, gaps=[], dups=[]]

which is just what you are observing. I'll look into it.

The issue should be fixed in https://github.com/sctplab/usrsctp/commit/f7e0852148d579e12d0fc0b8236241386d2ba138.
Thanks for finding and reporting the issue. It is very appreciated!

authors: paniksystem tuexen

repo: sctplab/usrsctp


text:
AnnData cannot open file that was opened with JHDF5 before

Please make sure these conditions are met

[X] I have checked that this issue has not already been reported.
[X] I have confirmed this bug exists on the latest version of anndata.
[ ] (optional) I have confirmed this bug exists on the master branch of anndata.

Report
I noticed that AnnData throws an error while trying to read a .h5ad file that was opened with JHDF5 (with write permissions) before. This means that AnnData is currently not able to open HDF5 files created from a Java program, even if the files conform to the AnnData on-disk format.
The problem most likely occurs because JHDF5 adds a /__DATA_TYPES__ group (presumably for internal reasons), which can be seen by using h5dump before and after the access from Java and comparing with diff. AnnData tries to read that group, but fails because the datasets stored in this group have no valid AnnData-encoding type. I guess that this problem can be circumvented by making AnnData only read groups that are part of its on-disk schema, i.e., X, layers, uns, obs[m|p], var[m|p].
Steps to reproduce
This is a minimal python program failing on the last line if the file was opened from the Java-side in between write and read from the Python-side.
import numpy as np
import anndata as ad

adata = ad.AnnData(np.zeros((2,2)))
adata.write('test.h5ad')

# There is a conditional error on this line:
# * without external interference: works
# * if opened with JHDF5 before: throws error
bdata = ad.read('test.h5ad')

Also, here is Java program causing the last line to fail. Note that it doesn't change the file, but just opens it with write permissions.
import ch.systemsx.cisd.hdf5.HDF5Factory;

public class App {
	public static void main(String[] args) {
		HDF5Factory.open("test.h5ad");
	}
}

To get the necessary dependencies and execute the Java file, I suggest using maven with this pom.xml:

<?xml version="1.0" encoding="UTF-8"?>

<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
  <modelVersion>4.0.0</modelVersion>

  <parent>
    <groupId>org.scijava</groupId>
    <artifactId>pom-scijava</artifactId>
    <version>32.0.0-beta-5</version>
    <relativePath />
  </parent>

  <groupId>mwe</groupId>
  <artifactId>mwe</artifactId>
  <version>1.0-SNAPSHOT</version>

  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
    <maven.compiler.source>1.7</maven.compiler.source>
    <maven.compiler.target>1.7</maven.compiler.target>
  </properties>

  <dependencies>
    <dependency>
      <groupId>cisd</groupId>
      <artifactId>jhdf5</artifactId>
    </dependency>
  </dependencies>

  <repositories>
    <repository>
	  <id>scijava.public</id>
  	  <url>https://maven.scijava.org/content/groups/public</url>
	</repository>
  </repositories>

  <build>
    <pluginManagement>
      <plugins>
        <plugin>
          <groupId>org.apache.maven.plugins</groupId>
          <artifactId>maven-compiler-plugin</artifactId>
          <version>3.8.1</version>
        </plugin>
      </plugins>
    </pluginManagement>
  </build>
</project>

Traceback

Traceback (most recent call last):
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/utils.py", line 202, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/specs/registry.py", line 230, in read_elem
    read_func = self.registry.get_reader(
                ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/specs/registry.py", line 143, in get_reader
    raise IORegistryError._from_read_parts(
anndata._io.specs.registry.IORegistryError: No read method registered for IOSpec(encoding_type='', encoding_version='') from <class 'h5py._hl.datatype.Datatype'>. You may need to update your installation of anndata.

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/h5ad.py", line 243, in read_h5ad
    adata = read_dispatched(f, callback=callback)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/experimental/__init__.py", line 58, in read_dispatched
    return reader.read_elem(elem)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/utils.py", line 204, in func_wrapper
    re_raise_error(e, elem)
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/utils.py", line 185, in re_raise_error
    raise e
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/utils.py", line 202, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/specs/registry.py", line 235, in read_elem
    return self.callback(read_func, elem.name, elem, iospec=get_spec(elem))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/h5ad.py", line 224, in callback
    **{
      ^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/h5ad.py", line 227, in <dictcomp>
    k: read_dispatched(elem[k], callback)
       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/experimental/__init__.py", line 58, in read_dispatched
    return reader.read_elem(elem)
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/utils.py", line 204, in func_wrapper
    re_raise_error(e, elem)
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/utils.py", line 185, in re_raise_error
    raise e
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/utils.py", line 202, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/specs/registry.py", line 235, in read_elem
    return self.callback(read_func, elem.name, elem, iospec=get_spec(elem))
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/h5ad.py", line 241, in callback
    return func(elem)
           ^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/specs/methods.py", line 94, in read_basic
    return {k: _reader.read_elem(v) for k, v in elem.items()}
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/specs/methods.py", line 94, in <dictcomp>
    return {k: _reader.read_elem(v) for k, v in elem.items()}
               ^^^^^^^^^^^^^^^^^^^^
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/utils.py", line 204, in func_wrapper
    re_raise_error(e, elem)
  File "/home/innerbergerm@hhmi.org/Software/mambaforge/envs/anndata/lib/python3.11/site-packages/anndata/_io/utils.py", line 188, in re_raise_error
    raise AnnDataReadError(
anndata._io.utils.AnnDataReadError: Above error raised while reading key '/__DATA_TYPES__/Enum_Boolean' of type <class 'h5py._hl.datatype.Datatype'> from /.

Versions
anndata             0.9.1
session_info        1.0.0
-----
Python 3.11.4 | packaged by conda-forge | (main, Jun 10 2023, 18:08:17) [GCC 12.2.0]
Linux-5.19.0-46-generic-x86_64-with-glibc2.35
-----
Session information updated at 2023-07-11 05:25

I can reproduce with:
import anndata as ad, numpy as np, h5py

a = ad.AnnData(np.ones((5, 5)))
a.write("tmp.h5ad")

with h5py.File("tmp.h5ad", "w") as f:
    f.create_group("__DATA_TYPES__")

ad.read_h5ad("tmp.h5ad")

You can get around this right now with:
with h5py.File("tmp.h5ad", "r") as f:
    result = ad.experimental.read_elem(f)

It would be great, though, if this could be the default behavior in future versions to facilitate collaboration across language boundaries.

Is this a common feature in java hdf5 readers? It seems like there are multiple (like JHDF), and it's not easy for me to judge their popularity.

even if the files conform to the AnnData on-disk format.

The specification says which entries are required, and a number of entries that MAY be included. It doesn't say you can put other entries in the anndata group, though it also doesn't specifically say you can't.
This should probably be clarified. Though the which direction the clarification goes would need some thought and consideration. I don't think netcdf would be permissive about this, for example.

Does this being in the ad.experimental namespace mean that this is already planned for a future release?

Not neccesarily, but read_elem and write_elem will definitely move to the permanent API. However, read_elem should basically do the same thing as read_h5ad for new enough file formats.

Is this a common feature in java hdf5 readers? It seems like there are multiple (like JHDF), and it's not easy for me to judge their popularity.

To be honest, my experience with HDF5 readers in Java is pretty limited, too, and it's not clear to me how wide-spread this behavior is. However, the particular library I'm using is featured on the website of the HDF group and is a wrapper around the official Java-bindings. Furthermore, also the HDF5 version of the N5 API uses this particular library, so there is definitely a non-vanishing number of users potentially affected by this issue.

The specification says which entries are required, and a number of entries that MAY be included. It doesn't say you can put other entries in the anndata group, though it also doesn't specifically say you can't.

I agree that this needs clarification. However, for the reasons above, providing a means of reading files with a __DATA_TYPES__ group would be beneficial.

Not neccesarily, but read_elem and write_elem will definitely move to the permanent API. However, read_elem should basically do the same thing as read_h5ad for new enough file formats.

Awesome! I expect that most files that are affected by this issue will conform to a sufficiently recent file format such that read_elem provides a viable solution.

I don't think any recent version of anndata would have allowed reading this file, so I'm hesitant to change that precedent.
Do you think you could confirm if the n5 implementation has this behavior? I'd thought that people had made anndata readers/ writers using n5 (though possibly only the zarr format) and this hasn't come up before.

I think it would be fine to ignore things like __dunder__ or .dotfile groups in /. Not saying we should, but maybe.
That’s because /X, /obs, … are our (limited) entry points. We’ll never start adding arbitrary things in /. But deeper inside the structure, groups actually mean things like dicts stored in uns or so, so users adding things there means something and IO should definitely complain when there’s groups without metadata there.

Do you think you could confirm if the n5 implementation has this behavior? I'd thought that people had made anndata readers/ writers using n5 (though possibly only the zarr format) and this hasn't come up before.

Implementing AnnData readers/writers using N5 is exactly where I'm coming from (as I said, N5 is using JHDF5 for it's HDF5 implementation), so I can confirm this. The reason why this hasn't come up earlier is a grossly negligent lack of testing on my side: I only properly tested Python -> Java and Java -> Java, where '->' means '-generated files can be read from'.

edit: Actually it's not totally clear to me if the n5 library is a good point of reference, since it has it's own data model.

I agree. But that applies to the storage format (which, confusingly, is also named N5). I'm only using the N5 API to read/write HDF5 and Zarr.
Don't get me wrong, I can see the pitfalls of allowing arbitrary data in AnnData files and I don't think this should be the default behavior. Even generally allowing __*__ or .* is perhaps not a good idea.
I'm just asking for a 'Java-switch' which recognizes and ignores this particular group. For the time being, the prospect of having a non-experimental way (i.e., h5py and read_elem) of reading these files is already sufficient to me.

Hm, unfortunately, it’s configurable too: IHDF5WriterConfigurator.houseKeepingNameSuffix(String)

Oh, that's not good news. Thanks for digging into the code that deeply. I guess that ignoring the standard names would be sufficient.

I wouldn't want to special case a specific hdf5 implementation. But I think this sort of case would be covered by the aforementioned "permissive reader", though that wouldn't be the default behavior. I think an interim fix would be warning very loudly about this, saying it will error by default in the future, but allowing it.
@minnerbe (or maybe @bogovicj), do you have any sense of whether this behavior could be changed on the n5 side? Also what does this do?

unfortunately, it’s configurable too: IHDF5WriterConfigurator.houseKeepingNameSuffix(String)

nasty.

whether this behavior could be changed on the n5 side

Perhaps.  It's strange, because jhdf5 seems to create that group immediately when making a writer.  Strange...
I think this line triggers the creation of that group, and I'm not immediately seeing any flags or other way to disable that.

Also what does this do?

Not clear (to me).  We can certainly read h5 data without the __DATA_TYPES__ group, so its not essential.  I suppose we could just manually delete the group for the AnnData h5's we create, but I don't know what the consequences will be if any.

Also what does this do?

I'm not sure either. It looks like it's trying to consolidate some data type meta-information  into a single place. Other HDF5 implementations seem to be able to read it, but it doesn't look essential.

But I think this sort of case would be covered by the aforementioned "permissive reader", though that wouldn't be the default behavior.

I think having a permissive-mode reader is a very viable long-term solution. For now, having a means of reading such files with [experimental.]read_elem is fine, I think.
Another possible (albeit very laborious and invasive) long-term approach would be to try to switch out JHDF5 in N5 for some other HDF5 Java bindings, since it seems like JHDF5 is not actively maintained right now. What's your take on this @bogovicj?

it seems like JHDF5 is not actively maintained right now

seems like you eventually want to get rid of it, and until then a stopgap solution dealing with its quirks right now (either on your side by deleting the groups or our side by ignoring it) is viable.

I suppose we could just manually delete the group for the AnnData h5's we create

It looks like some other users of this library do that:

https://github.com/DeplanckeLab/ASAP/blob/23dbabf6281b7dc3c5c4c97ff172687a5937a232/Java/src/hdf5/loom/LoomFile.java#L1012

But searching for "hdf5 __DATA_TYPES__" mostly looks like people trying to work around this being added.

try to switch out JHDF5 in N5 for some other HDF5 Java bindings, since it seems like JHDF5 is not actively maintained right now.

certainly possible.  There would have to be a pretty compelling reason, and I'm not sure that this (unwanted __DATA_TYPES__ group) is enough to justify the effort.  Lack of maintenance eventually might be enough of a reason though - if there are clearly better alternatives.

Since there are some viable options to circumvent this problem (reading with a lower level API from AnnData or just deleting the group after writing from Java), I'm going to close this issue.
Thanks for your help!

authors: bogovicj flying-sheep ivirshup minnerbe

repo: scverse/anndata


text:
Create issue templates

I think this repo should provide sensible default issue templates and link to the scverse discourse for help requests.

I tried setting that up for scirpy. Feedback welcome!
https://github.com/scverse/scirpy/issues/new/choose

One issue I'm having is that I didn't find a way to make the version info collapsible. Either there's still some need for a markdown template within the form, or it won't be collapsed.

Once we are happy with it there, I'll copy it over to this repo.

Link to a demo bug report:
https://github.com/scverse/scirpy/issues/340
The section Version Information is quite unusable atm... maybe better to just use a plain text field. This might result in a very long issue, but :shrug:

Great!
"plase paste the output between the backticks "
Typo
I'm a fan of the background text that you have in the other cells. Maybe this would also be something for the version information?
But this seems to be a decent version

Not collapsible, but I don't know how to make that work either.

Yeah, I think I'm gonna get rid of the template for making it collapsible.
Should we still advertise for putting the full list of versions returned by
sc.logging.print_versions() or rather ask for a few specific ones (the
package itself and maybe numpy/pandas)?
On Fri, May 20, 2022, 11:27 Lukas Heumos @.***> wrote:

Great!
"plase paste the output between the backticks "
Typo
I'm a fan of the background text that you have in the other cells. Maybe
this would also be something for the version information?
But this seems to be a decent version
[image: image]
https://user-images.githubusercontent.com/21954664/169498695-5ee67db1-d295-46c2-b695-1ad3f579357c.png
Not collapsible, but I don't know how to make that work either.
—
Reply to this email directly, view it on GitHub
https://github.com/scverse/cookiecutter-scverse/issues/57#issuecomment-1132683340,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/ABVZRV4VSCIFWIJNV4HV42DVK5LJRANCNFSM5V54W6LA
.
You are receiving this because you were assigned.Message ID:
@.***>

Not sure whether all of our ecosystem packages require scanpy as a dependency. Some people may not know where this command comes from. I'd go with a "manual" approach (what you suggested)

New version: https://github.com/scverse/scirpy/blob/9665b2d5d011ce1df230809050c800f264dba095/.github/ISSUE_TEMPLATE/bug_report.yml

MuData version might also be relevant. Maybe we should ask users to run https://pypi.org/project/session-info/ ? This might be the most general version.

sc.logging.print_versions() is just session-info.
Lesson learned from scanpy: get people to report all imported packages in the session where the bug occurred. This will save many hours of debugging.

Stuff eventually got fixed, but there is also https://github.com/IBM/import-tracker (which I haven't tried)

Another one
https://pypi.org/project/depinfo/
On Mon, May 30, 2022, 21:31 Isaac Virshup @.***> wrote:

Stuff eventually got fixed, but there is also
https://github.com/IBM/import-tracker (which I haven't tried)
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or unsubscribe
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.
You are receiving this because you were assigned.Message ID:
@.***>

authors: Zethson grst ivirshup

repo: scverse/cookiecutter-scverse


text:
TypeError: Can't implicitly convert non-string objects to strings

Describe the bug
I couldn't write h5ad  after concating multi samples and defining clonotypes. I tried adata.obs['IR_VDJ_2_consensus_count'] = adata.obs['IR_VDJ_2_consensus_count'].astype(str) but it didn't work. I found some similar issues but no specific solution was given.
So how can I save adata properly?
To Reproduce
def get_tcr_adata(df_sampleinfo):
    lst = []
    for sample_id in df_sampleinfo.index:
        tcr_file = df_sampleinfo.loc[sample_id, 'TCR']
        # read 10x vdj file into adata
        _adata = ir.io.read_10x_vdj(tcr_file)
        _adata.obs.insert(0, 'sample_id', sample_id)
        _adata.obs.index = sample_id + '_' + _adata.obs.index
        lst.append(_adata)
    # concat into one adata
    adata = sc.concat(lst)
    # qc: add receptor_type, receptor_subtype, chain_pairing
    ir.tl.chain_qc(adata)
    # calculate distance matrix: default identity
    ir.pp.ir_dist(adata, sequence='aa')
    # define clonotype
    ir.tl.define_clonotype_clusters(adata, sequence="aa", receptor_arms="all", dual_ir="primary_only")
    # clonotype network
    ir.tl.clonotype_network(adata, min_cells=50, sequence="aa")
    return adata

adata_tcr = get_tcr_adata(df_sampleinfo)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
File /opt/conda/lib/python3.10/site-packages/anndata/_io/utils.py:246, in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
    245 try:
--> 246     return func(*args, **kwargs)
    247 except Exception as e:

File /opt/conda/lib/python3.10/site-packages/anndata/_io/specs/registry.py:311, in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
    310 else:
--> 311     return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)

File /opt/conda/lib/python3.10/site-packages/anndata/_io/specs/registry.py:52, in write_spec.<locals>.decorator.<locals>.wrapper(g, k, *args, **kwargs)
     50 @wraps(func)
     51 def wrapper(g, k, *args, **kwargs):
---> 52     result = func(g, k, *args, **kwargs)
     53     g[k].attrs.setdefault("encoding-type", spec.encoding_type)

File /opt/conda/lib/python3.10/site-packages/anndata/_io/specs/methods.py:359, in write_vlen_string_array(f, k, elem, _writer, dataset_kwargs)
    358 str_dtype = h5py.special_dtype(vlen=str)
--> 359 f.create_dataset(k, data=elem.astype(str_dtype), dtype=str_dtype, **dataset_kwargs)

File /opt/conda/lib/python3.10/site-packages/h5py/_hl/group.py:183, in Group.create_dataset(self, name, shape, dtype, data, **kwds)
    181         group = self.require_group(parent_path)
--> 183 dsid = dataset.make_new_dset(group, shape, dtype, data, name, **kwds)
    184 dset = dataset.Dataset(dsid)

File /opt/conda/lib/python3.10/site-packages/h5py/_hl/dataset.py:168, in make_new_dset(parent, shape, dtype, data, name, chunks, compression, shuffle, fletcher32, maxshape, compression_opts, fillvalue, scaleoffset, track_times, external, track_order, dcpl, dapl, efile_prefix, virtual_prefix, allow_unknown_filter, rdcc_nslots, rdcc_nbytes, rdcc_w0)
    167 if (data is not None) and (not isinstance(data, Empty)):
--> 168     dset_id.write(h5s.ALL, h5s.ALL, data)
    170 return dset_id

File h5py/_objects.pyx:54, in h5py._objects.with_phil.wrapper()

File h5py/_objects.pyx:55, in h5py._objects.with_phil.wrapper()

File h5py/h5d.pyx:280, in h5py.h5d.DatasetID.write()

File h5py/_proxy.pyx:145, in h5py._proxy.dset_rw()

File h5py/_conv.pyx:444, in h5py._conv.str2vlen()

File h5py/_conv.pyx:95, in h5py._conv.generic_converter()

File h5py/_conv.pyx:249, in h5py._conv.conv_str2vlen()

TypeError: Can't implicitly convert non-string objects to strings

The above exception was the direct cause of the following exception:

TypeError                                 Traceback (most recent call last)
Cell In[32], line 1
----> 1 adata_tcr.write('01.data/01.all_tcr.h5ad')

File /opt/conda/lib/python3.10/site-packages/anndata/_core/anndata.py:1951, in AnnData.write_h5ad(self, filename, compression, compression_opts, as_dense)
   1948 if filename is None:
   1949     filename = self.filename
-> 1951 _write_h5ad(
   1952     Path(filename),
   1953     self,
   1954     compression=compression,
   1955     compression_opts=compression_opts,
   1956     as_dense=as_dense,
   1957 )
   1959 if self.isbacked:
   1960     self.file.filename = filename

File /opt/conda/lib/python3.10/site-packages/anndata/_io/h5ad.py:92, in write_h5ad(filepath, adata, as_dense, dataset_kwargs, **kwargs)
     90 elif adata.raw is not None:
     91     write_elem(f, "raw", adata.raw, dataset_kwargs=dataset_kwargs)
---> 92 write_elem(f, "obs", adata.obs, dataset_kwargs=dataset_kwargs)
     93 write_elem(f, "var", adata.var, dataset_kwargs=dataset_kwargs)
     94 write_elem(f, "obsm", dict(adata.obsm), dataset_kwargs=dataset_kwargs)

File /opt/conda/lib/python3.10/site-packages/anndata/_io/specs/registry.py:353, in write_elem(store, k, elem, dataset_kwargs)
    329 def write_elem(
    330     store: GroupStorageType,
    331     k: str,
   (...)
    334     dataset_kwargs: Mapping = MappingProxyType({}),
    335 ) -> None:
    336     """
    337     Write an element to a storage group using anndata encoding.
    338
   (...)
    351         E.g. for zarr this would be `chunks`, `compressor`.
    352     """
--> 353     Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)

File /opt/conda/lib/python3.10/site-packages/anndata/_io/utils.py:248, in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
    246     return func(*args, **kwargs)
    247 except Exception as e:
--> 248     re_raise_error(e, elem, key)

File /opt/conda/lib/python3.10/site-packages/anndata/_io/utils.py:246, in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
    244         break
    245 try:
--> 246     return func(*args, **kwargs)
    247 except Exception as e:
    248     re_raise_error(e, elem, key)

File /opt/conda/lib/python3.10/site-packages/anndata/_io/specs/registry.py:311, in Writer.write_elem(self, store, k, elem, dataset_kwargs, modifiers)
    302     return self.callback(
    303         write_func,
    304         store,
   (...)
    308         iospec=self.registry.get_spec(elem),
    309     )
    310 else:
--> 311     return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)

File /opt/conda/lib/python3.10/site-packages/anndata/_io/specs/registry.py:52, in write_spec.<locals>.decorator.<locals>.wrapper(g, k, *args, **kwargs)
     50 @wraps(func)
     51 def wrapper(g, k, *args, **kwargs):
---> 52     result = func(g, k, *args, **kwargs)
     53     g[k].attrs.setdefault("encoding-type", spec.encoding_type)
     54     g[k].attrs.setdefault("encoding-version", spec.encoding_version)

File /opt/conda/lib/python3.10/site-packages/anndata/_io/specs/methods.py:579, in write_dataframe(f, key, df, _writer, dataset_kwargs)
    574 _writer.write_elem(
    575     group, index_name, df.index._values, dataset_kwargs=dataset_kwargs
    576 )
    577 for colname, series in df.items():
    578     # TODO: this should write the "true" representation of the series (i.e. the underlying array or ndarray depending)
--> 579     _writer.write_elem(
    580         group, colname, series._values, dataset_kwargs=dataset_kwargs
    581     )

File /opt/conda/lib/python3.10/site-packages/anndata/_io/utils.py:248, in report_write_key_on_error.<locals>.func_wrapper(*args, **kwargs)
    246     return func(*args, **kwargs)
    247 except Exception as e:
--> 248     re_raise_error(e, elem, key)

File /opt/conda/lib/python3.10/site-packages/anndata/_io/utils.py:229, in report_write_key_on_error.<locals>.re_raise_error(e, elem, key)
    227 else:
    228     parent = _get_parent(elem)
--> 229     raise type(e)(
    230         f"{e}\n\n"
    231         f"Above error raised while writing key {key!r} of {type(elem)} "
    232         f"to {parent}"
    233     ) from e

TypeError: Can't implicitly convert non-string objects to strings

Above error raised while writing key 'IR_VDJ_2_consensus_count' of <class 'h5py._hl.group.Group'> to /

System
-----
anndata     0.9.1
scanpy      1.9.3
-----
Bio                         1.81
Levenshtein                 0.21.0
PIL                         9.5.0
adjustText                  NA
airr                        1.4.1
anyio                       NA
arrow                       1.2.3
asttokens                   NA
attr                        22.2.0
babel                       2.12.1
backcall                    0.2.0
beta_ufunc                  NA
binom_ufunc                 NA
bottleneck                  1.3.7
cairo                       1.23.0
certifi                     2023.05.07
cffi                        1.15.1
changeo                     1.0.2
chardet                     4.0.0
charset_normalizer          3.1.0
cloudpickle                 2.2.1
colorama                    0.3.9
comm                        0.1.3
cycler                      0.10.0
cython_runtime              NA
cytoolz                     0.12.0
dandelion                   0.3.1
dask                        2023.4.1
dateutil                    2.8.2
debugpy                     1.6.7
decorator                   5.1.1
defusedxml                  0.7.1
distance                    NA
executing                   1.2.0
fastjsonschema              NA
fontTools                   4.39.3
fqdn                        NA
gi                          3.44.1
gio                         NA
glib                        NA
gobject                     NA
google                      NA
gtk                         NA
h5py                        3.8.0
hypergeom_ufunc             NA
idna                        3.4
igraph                      0.10.3
invgauss_ufunc              NA
ipykernel                   6.22.0
ipython_genutils            0.2.0
ipywidgets                  8.0.6
isoduration                 NA
jedi                        0.18.2
jinja2                      3.1.2
joblib                      1.2.0
json5                       NA
jsonpointer                 2.0
jsonschema                  4.17.3
jupyter_events              0.5.0
jupyter_server              2.5.0
jupyterlab_server           2.22.1
kiwisolver                  1.4.4
leidenalg                   0.9.1
llvmlite                    0.39.1
lz4                         4.3.2
markupsafe                  2.1.2
matplotlib                  3.7.1
matplotlib_inline           0.1.6
mizani                      0.9.0
mpl_toolkits                NA
natsort                     8.3.1
nbformat                    5.8.0
nbinom_ufunc                NA
ncf_ufunc                   NA
nct_ufunc                   NA
ncx2_ufunc                  NA
networkx                    3.1
numba                       0.56.4
numexpr                     2.8.4
numpy                       1.23.5
packaging                   23.1
palettable                  3.3.3
pandas                      1.3.5
parasail                    1.3.3
parso                       0.8.3
patsy                       0.5.3
pexpect                     4.8.0
pickleshare                 0.7.5
pkg_resources               NA
platformdirs                3.5.0
plotnine                    0.10.1
polyleven                   NA
presto                      0.7.1
prometheus_client           NA
prompt_toolkit              3.0.38
psutil                      5.9.5
ptyprocess                  0.7.0
pure_eval                   0.2.2
pvectorc                    NA
pyarrow                     11.0.0
pycparser                   2.21
pydev_ipython               NA
pydevconsole                NA
pydevd                      2.9.5
pydevd_file_utils           NA
pydevd_plugins              NA
pydevd_tracing              NA
pygments                    2.15.1
pynndescent                 0.5.10
pyparsing                   3.0.9
pyrsistent                  NA
pythonjsonlogger            NA
pytz                        2023.3
rapidfuzz                   2.15.1
requests                    2.29.0
rfc3339_validator           0.1.4
rfc3986_validator           0.1.1
ruamel                      NA
scipy                       1.10.1
scirpy                      0.12.0
seaborn                     0.12.2
send2trash                  NA
session_info                1.0.0
setuptools                  67.7.2
setuptools_scm              NA
six                         1.16.0
skewnorm_ufunc              NA
sklearn                     1.2.2
sniffio                     1.3.0
socks                       1.7.1
squarify                    NA
stack_data                  0.6.2
statsmodels                 0.13.5
tblib                       1.7.0
texttable                   1.6.7
threadpoolctl               3.1.0
tlz                         0.12.0
toolz                       0.12.0
tornado                     6.3
tqdm                        4.65.0
tracerlib                   NA
traitlets                   5.9.0
typing_extensions           NA
umap                        0.5.3
uri_template                NA
urllib3                     1.23
wcwidth                     0.2.6
webcolors                   1.13
websocket                   1.5.1
yaml                        6.0
yamlordereddictloader       NA
zipp                        NA
zmq                         25.0.2
zoneinfo                    NA
-----
IPython             8.13.1
jupyter_client      8.2.0
jupyter_core        5.3.0
jupyterlab          3.6.3
notebook            6.5.4
-----
Python 3.10.10 | packaged by conda-forge | (main, Mar 24 2023, 20:08:06) [GCC 11.3.0]
Linux-3.10.0-1160.81.1.el7.x86_64-x86_64-with-glibc2.35
-----
Session information updated at 2023-07-04 02:33

Hi, thanks for reporting.
I currently don't see how this could be happening, especially after .astype(str).
Could you please share (the relevant parts of) your obs data frame, e.g.
adata.obs.loc[:, ['IR_VDJ_2_consensus_count']].to_pickle("test_obs.pickle"),

?
As an additional remark: scirpy updated the data structure in v0.13. Unless you are working with a legacy project, I would strongly encourage to switch to v0.13 and the new data structure. This would also bypass your current problem, as all the different variables are not stored in .obs anymore.

Thanks for replying! I'm sorry that I couldn't reproduce this error maybe due to upgrade of packages. I retried adata.obs['IR_VDJ_2_consensus_count'] = adata.obs['IR_VDJ_2_consensus_count'].astype(str), then I can save adata successfully.
I have tried v0.13 and it is great!
Current enviroment:
-----
anndata     0.9.1
scanpy      1.9.3
-----
Bio                         1.81
Levenshtein                 0.21.0
PIL                         9.5.0
adjustText                  NA
airr                        1.4.1
anyio                       NA
arrow                       1.2.3
asttokens                   NA
attr                        22.2.0
babel                       2.12.1
backcall                    0.2.0
beta_ufunc                  NA
binom_ufunc                 NA
bottleneck                  1.3.7
cairo                       1.23.0
certifi                     2023.05.07
cffi                        1.15.1
changeo                     1.0.2
chardet                     4.0.0
charset_normalizer          3.1.0
cloudpickle                 2.2.1
colorama                    0.3.9
comm                        0.1.3
cycler                      0.10.0
cython_runtime              NA
cytoolz                     0.12.0
dandelion                   0.3.1
dask                        2023.4.1
dateutil                    2.8.2
debugpy                     1.6.7
decorator                   5.1.1
defusedxml                  0.7.1
distance                    NA
executing                   1.2.0
fastjsonschema              NA
fontTools                   4.39.3
fqdn                        NA
gi                          3.44.1
gio                         NA
glib                        NA
gobject                     NA
google                      NA
gtk                         NA
h5py                        3.8.0
hypergeom_ufunc             NA
idna                        3.4
igraph                      0.10.3
invgauss_ufunc              NA
ipykernel                   6.22.0
ipython_genutils            0.2.0
ipywidgets                  8.0.6
isoduration                 NA
jedi                        0.18.2
jinja2                      3.1.2
joblib                      1.2.0
json5                       NA
jsonpointer                 2.0
jsonschema                  4.17.3
jupyter_events              0.5.0
jupyter_server              2.5.0
jupyterlab_server           2.22.1
kiwisolver                  1.4.4
leidenalg                   0.9.1
llvmlite                    0.39.1
lz4                         4.3.2
markupsafe                  2.1.2
matplotlib                  3.7.1
matplotlib_inline           0.1.6
mizani                      0.9.0
mpl_toolkits                NA
natsort                     8.3.1
nbformat                    5.8.0
nbinom_ufunc                NA
ncf_ufunc                   NA
nct_ufunc                   NA
ncx2_ufunc                  NA
networkx                    3.1
numba                       0.56.4
numexpr                     2.8.4
numpy                       1.23.5
packaging                   23.1
palettable                  3.3.3
pandas                      1.3.5
parasail                    1.3.3
parso                       0.8.3
patsy                       0.5.3
pexpect                     4.8.0
pickleshare                 0.7.5
pkg_resources               NA
platformdirs                3.5.0
plotnine                    0.10.1
polyleven                   NA
presto                      0.7.1
prometheus_client           NA
prompt_toolkit              3.0.38
psutil                      5.9.5
ptyprocess                  0.7.0
pure_eval                   0.2.2
pvectorc                    NA
pyarrow                     11.0.0
pydev_ipython               NA
pydevconsole                NA
pydevd                      2.9.5
pydevd_file_utils           NA
pydevd_plugins              NA
pydevd_tracing              NA
pygments                    2.15.1
pyparsing                   3.0.9
pyrsistent                  NA
pythonjsonlogger            NA
pytz                        2023.3
rapidfuzz                   2.15.1
requests                    2.29.0
rfc3339_validator           0.1.4
rfc3986_validator           0.1.1
ruamel                      NA
scipy                       1.10.1
scirpy                      0.12.0
seaborn                     0.12.2
send2trash                  NA
session_info                1.0.0
setuptools                  67.7.2
setuptools_scm              NA
six                         1.16.0
skewnorm_ufunc              NA
sklearn                     1.2.2
sniffio                     1.3.0
socks                       1.7.1
squarify                    NA
stack_data                  0.6.2
statsmodels                 0.13.5
tblib                       1.7.0
texttable                   1.6.7
threadpoolctl               3.1.0
tlz                         0.12.0
toolz                       0.12.0
tornado                     6.3
tqdm                        4.65.0
tracerlib                   NA
traitlets                   5.9.0
typing_extensions           NA
uri_template                NA
urllib3                     1.23
wcwidth                     0.2.6
webcolors                   1.13
websocket                   1.5.1
yaml                        6.0
yamlordereddictloader       NA
zipp                        NA
zmq                         25.0.2
zoneinfo                    NA
-----
IPython             8.13.1
jupyter_client      8.2.0
jupyter_core        5.3.0
jupyterlab          3.6.3
notebook            6.5.4
-----
Python 3.10.10 | packaged by conda-forge | (main, Mar 24 2023, 20:08:06) [GCC 11.3.0]
Linux-3.10.0-1160.81.1.el7.x86_64-x86_64-with-glibc2.35
-----
Session information updated at 2023-07-04 12:35

Can I close this issue, or is there still anything open?

yes，please close this issue. Thanks！
Get Outlook for iOShttps://aka.ms/o0ukef

From: Gregor Sturm @.>
Sent: Wednesday, July 5, 2023 3:57:00 PM
To: scverse/scirpy @.>
Cc: ZhouZhendiao @.>; Author @.>
Subject: Re: [scverse/scirpy] TypeError: Can't implicitly convert non-string objects to strings (Issue #427)
Can I close this issue, or is there still anything open?
―
Reply to this email directly, view it on GitHubhttps://github.com/scverse/scirpy/issues/427#issuecomment-1621233716, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AC5ZUF4RQNTOEDRXPP6CN2DXOUM4ZANCNFSM6AAAAAAZ5DE7PM.
You are receiving this because you authored the thread.Message ID: @.***>

authors: grst zhouzhendiao

repo: scverse/scirpy


text:
Update template to v0.3.0 (#773)

IMPORTANT: Please search among the Pull requests before creating one.
Description

How has this been tested?

Closes

Codecov Report

Merging #777 (c9fedb5) into main (0dcbc48) will not change coverage.
The diff coverage is n/a.

Additional details and impacted files
@@           Coverage Diff           @@
##             main     #777   +/-   ##
=======================================
  Coverage   69.87%   69.87%
=======================================
  Files          39       39
  Lines        5481     5481
  Branches     1025     1025
=======================================
  Hits         3830     3830
  Misses       1363     1363
  Partials      288      288

authors: codecov-commenter giovp

repo: scverse/squidpy


text:
不支持SmartRefreshLayout 2.0.0-alpha-1

貌似包名冲突了

升级下2.0吧，更新了包名，不能一起使用

已经更新

authors: JunhuaLin liangjingkanji scwang90


text:
Fix table compression

Currently setting table compression fails with
Missing sub-option 'sstable_compression' for the 'compression' option.. This is due to Cassandra using now 'class' sub-option and Scylla using 'sstable_compression'. Resolved by calling with customized 'withOption' instead of directly 'withCompression'.
Upgrades snappy to 1.1.10.5. This technically also requires upping the driver version to the one using snappy 1.1.10.5.

No issues observed when running with LZ4, Deflate, Snappy and no table compression. No issues observed with snappy protocol compression.

repo: scylladb/kafka-connect-scylladb


text:
cloud-init[387]: 2023-04-29 17:05:45,277 - init.py[WARNING]: Unhandled unknown content-type (x-scylla/json) userdata: 'b'{'...'

Saw in a log file:
2023-04-29T17:05:51+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | cloud-init[387]: 2023-04-29 17:05:45,277 - __init__.py[WARNING]: Unhandled unknown content-type (x-scylla/json) userdata: 'b'{'...'
...
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: 2023-04-29 17:06:23,619 - [user_data] - INFO - Got user-data: Content-Type: multipart/mixed; boundary="===============1212770131587456580=="
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: MIME-Version: 1.0
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: --===============1212770131587456580==
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: Content-Type: x-scylla/json
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: MIME-Version: 1.0
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: Content-Disposition: attachment; filename="scylla_machine_image.json"
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: {
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:     "cluster_name": "longevity-lwt-3h-2023-1-db-cluster-8f772d9e",
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:     "data_device": "instance_store",
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:     "raid_level": 0,
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:     "scylla_yaml": {
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:         "cluster_name": "longevity-lwt-3h-2023-1-db-cluster-8f772d9e"
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:     },
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:     "start_scylla_on_first_boot": false
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: }
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: --===============1212770131587456580==
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: Content-Type: text/cloud-config
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: MIME-Version: 1.0
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: Content-Disposition: attachment; filename="cloud-config.txt"
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:         #cloud-config
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:         cloud_final_modules:
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:         - [scripts-user, always]
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]:
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: --===============1212770131587456580==
2023-04-29T17:06:23+00:00 longevity-lwt-3h-2023-1-db-node-8f772d9e-3     !INFO | scylla_post_start.py[904]: Content-Type: text/x-shellscript

Should the Content-Type be json/x-scylla? or application/json ?

Yeah, we should do better here.
But I suggest doing it gradually, and with advancing smi_version

@roydahan How is it related to us? it's in SCT,

authors: fruch mykaul yaronkaikov

repo: scylladb/scylla-machine-image


text:
Nodetool status reports 'UN' status for an initializing node during replace-node operation

During the nodetool operation of replace node, the replacing node is reported with a status of "UN" when it is still not really normal but rather in initializing state. it should report a different status like "UJ" for example.
see example in this comment:
https://github.com/scylladb/scylla/issues/9629#issuecomment-998926636
The original scylla issues with details are:
https://github.com/scylladb/scylla/issues/9629#issuecomment-1046703526
and:
https://github.com/scylladb/scylla/issues/1793

@slivne who should look at it?

@asias / @bhalevy ?

What's the direction for the fix?
Add a "R" status for replacing?

@asias / this maybe related to repair-based-node-operations as we moved replace to use repair=-based-node-operations

authors: bhalevy roydahan slivne yarongilor

repo: scylladb/scylla-tools-java


text:
Install Instructions Fail

./scripts/install-plugin.sh
-> Installing file:./target/releases/elasticsearch-simple-similarity-2.1.1.zip...
Trying http://download.elasticsearch.org/file:./target/target-releases.zip...
Trying http://search.maven.org/remotecontent?filepath=file://target/releases/target-releases.zip...
Trying https://oss.sonatype.org/service/local/repositories/releases/content/file://target/releases/target-releases.zip...
Trying https://github.com/file:./target/archive/releases.zip...
Trying https://github.com/file:./target/archive/master.zip...
Failed to install file:./target/releases/elasticsearch-simple-similarity-2.1.1.zip, reason: failed to download out of all possible locations..., use --verbose to get detailed information

Would you please release the plugin so it can be installed?

You need to build it first.
mvn clean package

authors: brupm sdauletau


text:
【无限滚动】间隔线位置变化问题

按住向上拖的时候，间隔线和内容的位置会有所变化，虽然关系不大，不知道可否解决？

刚试了下没有复现，麻烦提供下系统、机型、浏览器型号等信息。

微信自带浏览器，系统都是安卓5.0，试过小米4、魅族MX4都有这问题，试过，自带浏览器没有这个问题。

你好，我测试了mx3和米4,系统安卓4.4.4，没复现这个问题，我的测试地址是http://m.sui.taobao.org/demos/list/contacts-list，你试试看这个地址在你的手机中是否还有问题，如果没有，你可以放出你的demo地址，我去帮你看下定位问题，如果这个地址也有问题，麻烦也告诉我们一下，我去找一样的机型系统重测，谢谢～

红米note2 ，5.0也是好的～

@xiaran113 可以试试看用微信会不会？我用uc也是没问题的，开始微信一打开就这样了，同样地址。

你好，发现了，安卓5.0版本以上都有问题，5.0以下没有问题，这个问题我后面定位下原因，有进展了告诉你，谢谢～

authors: Mickey- muchard xiaran113

repo: sdc-alibaba/SUI-Mobile


text:
Error messages take too much space / hard to read

I think error messages should take only a single line (instead of 4+ like above).
See https://github.com/sdispater/pastel/issues/1 for the readability issue.

As per https://github.com/sdispater/pastel/issues/1#issuecomment-383604180 this sounds to be a wont-fix unfortunately.
I've had some hopes regarding poetry fixing the mess with pipenv, but obfuscating error messages like this really reminds me of the CLI issues with pipenv itself.
btw: I've used click for an own project and really liked it, but always found that pipenv does not get it right.  poetry using cleo made me look briefly at it, but as for poetry's CLI it wasn't much for the better.

Well, for me they are unreadable (i.e. "hidden"), and I've meant obfuscated in the sense of decorating them (with 2 lines above and below).
For me it's easier to parse
ERROR: foo

than

  ERROR
  foo

(disregarding the colors)

That's a matter of preferences, I guess. I prefer how it's currently formatted so I won't change it.
But if that's what turns you off poetry, so be it. I just think it's a pity to disregard the features poetry brings just for a matter of color choice and error formatting.

I just think it's a pity to disregard the features poetry brings just for a matter of color choice and error formatting.

I agree.  That's why I am pointing them out explicitly - I think others might agree eventually - espcially when considering pastel as a lib (https://github.com/sdispater/pastel/issues/1).
And with regard to "just for a matter of color choice": it's just unreadable for me, and therefore not accessible - it's like a webpage that is not accessible (due to missing alt texts or just outputting audio by default, and not providing any text).
Anyway, I'll be watching this project and really like it for trying to fix the things with pipenv already.

authors: blueyed sdispater

repo: sdispater/poetry


text:
Rename pull_request_tempalte.md to pull_request_template.md

#1248 = fix typo

Thanks for fixing!

repo: sdkman/sdkman-cli


text:
Script error

Below the error:
raspberrypi:~ $ curl -sL https://raw.githubusercontent.com/sdr-enthusiasts/Buster-Docker-Fixes/main/libseccomp2-checker.sh | bash
Welcome to the libseccomp2 upgrade script for Debian Stretch and Buster. This script is meant to be run on Raspberry Pi Buster/Stretch-based systems that have Docker containers
that run Debian Bullseye or later. For this, the "libseccomp2" library version must be 2.4 or later.
This script will check this, and upgrade the library as necessary.
Once upgraded, you can always stay up to date by typing "sudo apt update && sudo apt upgrade" on your command line.
Your system is "BUSTER" based, and it has libseccomp2 v2.3. Upgrade is recommended.
We will first update your system with the latest package versions. Please be patient, this may take a while.
Press ENTER to the upgrade or Control-C to cancel
Scaricamento di:1 http://deb.debian.org/debian buster-backports InRelease [51,4 kB]
Scaricamento di:2 http://httpredir.debian.org/debian buster-backports InRelease [51,4 kB]
Trovato:3 http://raspbian.raspberrypi.org/raspbian buster InRelease
Trovato:4 http://archive.raspberrypi.org/debian buster InRelease
Scaricamento di:5 http://giteduberger.fr rpimonitor/ InRelease [1.933 B]
Trovato:6 https://download.docker.com/linux/raspbian buster InRelease
Ignorato:1 http://deb.debian.org/debian buster-backports InRelease
Errore:2 http://httpredir.debian.org/debian buster-backports InRelease
Le seguenti firme non sono state verificate perché la chiave pubblica non è disponibile: NO_PUBKEY 0E98404D386FA1D9 NO_PUBKEY 6ED0E7B82643E131
Lettura elenco dei pacchetti...
W: Errore GPG: http://deb.debian.org/debian buster-backports InRelease: Le seguenti firme non sono state verificate perché la chiave pubblica non è disponibile: NO_PUBKEY 0E98404D386FA1D9 NO_PUBKEY 6ED0E7B82643E131
W: Errore GPG: http://httpredir.debian.org/debian buster-backports InRelease: Le seguenti firme non sono state verificate perché la chiave pubblica non è disponibile: NO_PUBKEY 0E98404D386FA1D9 NO_PUBKEY 6ED0E7B82643E131
E: Il repository "http://httpredir.debian.org/debian buster-backports InRelease" non è firmato.
Now upgrading libseccomp2...
Executing: /tmp/apt-key-gpghome.E5QaS7sVBS/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC 648ACFD622F3D138
gpg: connecting dirmngr at '/tmp/apt-key-gpghome.E5QaS7sVBS/S.dirmngr' failed: IPC connect call failed
gpg: ricezione dal keyserver fallita: No dirmngr
[ERROR] Error in line 80 when executing: sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC 648ACFD622F3D138. Please fix the issue and run the script again.
pi@raspberrypi:~ $
Many thanks

Your Apt Keys are out of date - this is not a script error, but a configuration issue of your machine.
You can try fixing it like this:
sudo apt-key adv --keyserver http://keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9
sudo apt-key adv --keyserver http://keyserver.ubuntu.com --recv-keys 6ED0E7B82643E131

Then run the script again
If that works, feel free to close this issue.

Many thanks I will update. In the meanwhile I obtain this error:
pi@raspberrypi:/etc/apt/sources.list.d $ sudo apt-key adv --keyserver http://keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9
Executing: /tmp/apt-key-gpghome.KRAiYfIC6O/gpg.1.sh --keyserver http://keyserver.ubuntu.com --recv-keys 0E98404D386FA1D9
gpg: Non sono stati trovati dati OpenPGP validi.
gpg: Numero totale esaminato: 0
pi@raspberrypi:/etc/apt/sources.list.d $ sudo apt-key adv --keyserver http://keyserver.ubuntu.com --recv-keys 6ED0E7B82643E131
Executing: /tmp/apt-key-gpghome.ttZUJhQkar/gpg.1.sh --keyserver http://keyserver.ubuntu.com --recv-keys 6ED0E7B82643E131
gpg: Non sono stati trovati dati OpenPGP validi.
gpg: Numero totale esaminato: 0
pi@raspberrypi:/etc/apt/sources.list.d $
I really appreciate if you can help me.
Many thanks.

I did some more digging -- try this one? I am not sure if it will work, I found it here:
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138

Many thanks. Unfortunately the result is the same:
pi@raspberrypi:~ $ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC
Executing: /tmp/apt-key-gpghome.ihS9063k3W/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC
gpg: key E0B11894F66AEC98: public key "Debian Archive Automatic Signing Key (9/stretch) ftpmaster@debian.org" imported
gpg: Numero totale esaminato: 1
gpg:              importate: 1
pi@raspberrypi:~ $ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138
Executing: /tmp/apt-key-gpghome.kELKfSAjP9/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 648ACFD622F3D138
gpg: key DC30D7C23CBBABEE: public key "Debian Archive Automatic Signing Key (10/buster) ftpmaster@debian.org" imported
gpg: Numero totale esaminato: 1
gpg:              importate: 1
pi@raspberrypi:~ $ curl -sL https://raw.githubusercontent.com/sdr-enthusiasts/Buster-Docker-Fixes/main/libseccomp2-checker.sh | bash
Welcome to the libseccomp2 upgrade script for Debian Stretch and Buster. This script is meant to be run on Raspberry Pi Buster/Stretch-based systems that have Docker containers
that run Debian Bullseye or later. For this, the "libseccomp2" library version must be 2.4 or later.
This script will check this, and upgrade the library as necessary.
Once upgraded, you can always stay up to date by typing "sudo apt update && sudo apt upgrade" on your command line.
Your system is "BUSTER" based, and it has libseccomp2 v2.3. Upgrade is recommended.
We will first update your system with the latest package versions. Please be patient, this may take a while.
Press ENTER to the upgrade or Control-C to cancel
Scaricamento di:1 http://deb.debian.org/debian buster-backports InRelease [51,4 kB]
Trovato:2 http://raspbian.raspberrypi.org/raspbian buster InRelease
Trovato:4 http://archive.raspberrypi.org/debian buster InRelease
Ignorato:3 http://giteduberger.fr rpimonitor/ InRelease
Errore:5 http://giteduberger.fr rpimonitor/ Release
Redirection loop encountered
Errore:1 http://deb.debian.org/debian buster-backports InRelease
Le seguenti firme non sono state verificate perché la chiave pubblica non è disponibile: NO_PUBKEY 0E98404D386FA1D9 NO_PUBKEY 6ED0E7B82643E131
Lettura elenco dei pacchetti...
E: Il repository "http://giteduberger.fr rpimonitor/ Release" non ha più un file Release.
W: Errore GPG: http://deb.debian.org/debian buster-backports InRelease: Le seguenti firme non sono state verificate perché la chiave pubblica non è disponibile: NO_PUBKEY 0E98404D386FA1D9 NO_PUBKEY 6ED0E7B82643E131
E: Il repository "http://deb.debian.org/debian buster-backports InRelease" non è firmato.
Now upgrading libseccomp2...
Executing: /tmp/apt-key-gpghome.P2Wrxqh4kA/gpg.1.sh --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC 648ACFD622F3D138
gpg: key DC30D7C23CBBABEE: "Debian Archive Automatic Signing Key (10/buster) ftpmaster@debian.org" not changed
gpg: key E0B11894F66AEC98: "Debian Archive Automatic Signing Key (9/stretch) ftpmaster@debian.org" not changed
gpg: Numero totale esaminato: 2
gpg:         non modificate: 2
deb [trusted=yes] http://deb.debian.org/debian buster-backports main
E: Impostati valori in conflitto per l'opzione Trusted riguardo alla sorgente http://deb.debian.org/debian/ buster-backports
E: Impossibile leggere l'elenco dei sorgenti.
[ERROR] Error in line 83 when executing: sudo apt update. Please fix the issue and run the script again.
pi@raspberrypi:~ $ A

Solved.
Get signing keys to verify the new packages, otherwise they will not install
rpi ~$ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 04EE7237B7D453EC 648ACFD622F3D138
Add the Buster backport repository to apt sources.list
rpi ~$ echo 'deb http://httpredir.debian.org/debian buster-backports main contrib non-free' | sudo tee -a /etc/apt/sources.list.d/debian-backports.list
rpi ~$ sudo apt update
rpi ~$ sudo apt install libseccomp2 -t buster-backports
from   https://blog.samcater.com/fix-workaround-rpi4-docker-libseccomp2-docker-20/?source=post_page-----fbde9574cad8--------------------------------

many thanks

:) Glad to see - happy holidays!

repo: sdr-enthusiasts/Buster-Docker-Fixes


text:
Add github-env-vars-action.

GitHub Environment Variables Action is a GitHub Action to expose useful environment variables.

@sdras Sure. I removed the emoji. Ready for re-review :)

repo: sdras/awesome-actions


text:
Create wireframe mock up in html or powerpoint

Steve

Complete and merge request submitted.


text:
fix(norway): add support for VAT registered legal entities

As described in the following article
https://vatstack.com/articles/norway-vat-number-validation
Norway has two VAT formats

999999999 (legal entity)
999999999MVA (VAT-registered legal entity)

This PR adds support for the 2nd type

@smilovanovic Merged. Thank you for the improvement

authors: se-panfilov smilovanovic

repo: se-panfilov/jsvat


text:
Update build configuration

The build configuration of this project is outdated and may no longer work.
This pull request will be merged automatically if there are no conflicts.

:tada: This PR is included in version 3.1.2 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:

repo: sealsystems/node-mongo


text:
on postgresql, trying to put strings into integer fields fails confusingly

upsert(foo: 0)

if foo is a string field, it will blow up confusingly

@seamusabshere Do you want to catch this at the Upsert level (specifically check the types of the fields being inserted, which seems slow) or try to catch the exception from Postgres and turn it in to something useful?

I took a look and unfortunately pg doesn't let you register an error handler, which means we're going to need to wrap every upsert call in a rescue block ... which is going to introduce a slight bit of slowdown, although I'm not sure how much.
I think that rather than trying to present a useful error message we instead add a note to the README indicating that mis-matched types are going to result in cryptic error messages.

authors: pnomolos seamusabshere

repo: seamusabshere/upsert


text:
overflow: hidden on html-tag?

Hi,
Why is the <html>-tag get the overflow: hidden css-property? Is there some way to not make it apply it via props?
Kind regards

This is so your page behind the overlay doesn't scroll while it's open. Seemed like a good default to me because otherwise it results in buggy behaviour.
But I can see the case for making this configurable. I'm flat out atm so would happily take a PR, otherwise I'll try and add it when I have spare time

repo: seaneking/react-portal-overlay


text:
added my name to guestbook.md

Thanks for the course! I'm learning a lot, and enjoying it!

Thank you!

authors: seankross zeebear

repo: seankross/the-unix-workbench


text:
发现使用converttoutf8插件导致乱码的一种可能

最近使用sublime配合converttoutf8，发现一种可能导致乱码的操作方式。
文件是GB2312编码的，添加若干字符保存文件后，如果用户使用ctrl+y前进，则中文部分会变成乱码，如果用户未注意到乱码继续编辑并保存，则会出现错误弹框并且乱码不能恢复。
总之，频繁将ctrl+z或ctrl+y与ctrl+s搭配使用易导致乱码并不可恢复。

这是因为保存后文件会被插件改写，造成ST重载文档，插件会回退这个重载，一旦再次使用CTRL+Y又会再次重载造成乱码。我再考虑下是否有办法防止。你可以临时将lazy_reload设置为true来减少这个问题的发生。

发现同样的问题，lazy_reload设置为true后试了几次没再发生，期待早日解决

使用了lazy_reload选项后之前问题没有了，但又出现个新问题。
保存文件后必须切换到其他软件，再切换到sublime让文件重载才能关闭sublime。否则如果保存后直接关闭sublime，再次打开后中文乱码，如果此时没注意到乱码而继续修改文件并再次保存，则sublime报错并不可恢复。

authors: hyjbrave seanliang zzkiob


text:
Adjusted frame length exceeds 8388608: 791339008 - discarded

`2021-06-12 02:28:33.318  INFO --- [NIOWorker_1_1_2] i.s.c.r.n.AbstractNettyRemotingServer    : channel:[id: 0xd5e9c670, L:/10.244.2.50:8091 - R:/10.244.2.1:55830] read idle.
2021-06-12 02:28:33.318  INFO --- [NIOWorker_1_1_2] i.s.c.r.n.AbstractNettyRemotingServer    : 10.244.2.1:55830 to server channel inactive.
2021-06-12 02:28:33.318  INFO --- [NIOWorker_1_1_2] i.s.c.r.n.AbstractNettyRemotingServer    : remove unused channel:[id: 0xd5e9c670, L:/10.244.2.50:8091 - R:/10.244.2.1:55830]
2021-06-12 02:28:33.318  INFO --- [NIOWorker_1_1_2] i.s.c.r.n.AbstractNettyRemotingServer    : closeChannelHandlerContext channel:[id: 0xd5e9c670, L:/10.244.2.50:8091 - R:/10.244.2.1:55830]
2021-06-12 02:28:33.318  INFO --- [NIOWorker_1_1_2] i.s.c.r.n.AbstractNettyRemotingServer    : 10.244.2.1:55830 to server channel inactive.
2021-06-12 02:28:33.318  INFO --- [NIOWorker_1_1_2] i.s.c.r.n.AbstractNettyRemotingServer    : remove unused channel:[id: 0xd5e9c670, L:/10.244.2.50:8091 ! R:/10.244.2.1:55830]
2021-06-13 09:33:11.742  INFO --- [NIOWorker_1_2_2] i.s.c.r.n.AbstractNettyRemotingServer    : channel exx:Adjusted frame length exceeds 8388608: 791339008 - discarded,channel:[id: 0xc71255bf, L:/10.244.2.50:8091 - R:/10.244.0.0:50741]
2021-06-13 09:33:11.743  WARN --- [NIOWorker_1_2_2] io.netty.channel.DefaultChannelPipeline  : An exceptionCaught() event was fired, and it reached at the tail of the pipeline. It usually means the last handler in the pipeline did not handle the exception.
==>
io.netty.handler.codec.TooLongFrameException: Adjusted frame length exceeds 8388608: 791339008 - discarded
at io.netty.handler.codec.LengthFieldBasedFrameDecoder.fail(LengthFieldBasedFrameDecoder.java:522) ~[netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.handler.codec.LengthFieldBasedFrameDecoder.failIfNecessary(LengthFieldBasedFrameDecoder.java:500) ~[netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.handler.codec.LengthFieldBasedFrameDecoder.exceededFrameLength(LengthFieldBasedFrameDecoder.java:387) ~[netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.handler.codec.LengthFieldBasedFrameDecoder.decode(LengthFieldBasedFrameDecoder.java:430) ~[netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.seata.core.rpc.netty.v1.ProtocolV1Decoder.decode(ProtocolV1Decoder.java:82) ~[seata-core-1.3.0.jar:na]
at io.netty.handler.codec.LengthFieldBasedFrameDecoder.decode(LengthFieldBasedFrameDecoder.java:343) ~[netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.handler.codec.ByteToMessageDecoder.decodeRemovalReentryProtection(ByteToMessageDecoder.java:502) ~[netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.handler.codec.ByteToMessageDecoder.callDecode(ByteToMessageDecoder.java:441) ~[netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:278) ~[netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:340) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:286) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:340) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1434) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:362) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:348) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:965) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:163) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:644) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:579) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:496) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:458) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:897) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30) [netty-all-4.1.30.Final.jar:4.1.30.Final]
at java.lang.Thread.run(Thread.java:748) [na:1.8.0_212]
<==
2021-06-13 09:33:26.755  INFO --- [NIOWorker_1_2_2] i.s.c.r.n.AbstractNettyRemotingServer    : channel:[id: 0xc71255bf, L:/10.244.2.50:8091 - R:/10.244.0.0:50741] read idle.
2021-06-13 09:33:26.756  INFO --- [NIOWorker_1_2_2] i.s.c.r.n.AbstractNettyRemotingServer    : 10.244.0.0:50741 to server channel inactive.
2021-06-13 09:33:26.756  INFO --- [NIOWorker_1_2_2] i.s.c.r.n.AbstractNettyRemotingServer    : remove unused channel:[id: 0xc71255bf, L:/10.244.2.50:8091 - R:/10.244.0.0:50741]
2021-06-13 09:33:26.756  INFO --- [NIOWorker_1_2_2] i.s.c.r.n.AbstractNettyRemotingServer    : closeChannelHandlerContext channel:[id: 0xc71255bf, L:/10.244.2.50:8091 - R:/10.244.0.0:50741]
2021-06-13 09:33:26.756  INFO --- [NIOWorker_1_2_2] i.s.c.r.n.AbstractNettyRemotingServer    : 10.244.0.0:50741 to server channel inactive.
2021-06-13 09:33:26.756  INFO --- [NIOWorker_1_2_2] i.s.c.r.n.AbstractNettyRemotingServer    : remove unused channel:[id: 0xc71255bf, L:/10.244.2.50:8091 ! R:/10.244.0.0:50741]`

去掉健康检查试试


text:
springcloud-eureka-seata 无法注册GlobalTransactionScanner 组件.需要手动注册

@Bean
    public GlobalTransactionScanner getScanner() {
        return new GlobalTransactionScanner("my_test_tx_group");
    }

需要手动将组件注入spring.

加了程序报错
2019-07-23 19:04:04.611 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : Failed to get available servers: null
2019-07-23 19:04:04.611 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : no available server to connect.
2019-07-23 19:04:04.651 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : Failed to get available servers: null
2019-07-23 19:04:04.651 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : no available server to connect.
2019-07-23 19:04:09.611 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : Failed to get available servers: null
2019-07-23 19:04:09.612 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : no available server to connect.
2019-07-23 19:04:09.652 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : Failed to get available servers: null
2019-07-23 19:04:09.652 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : no available server to connect.
2019-07-23 19:04:14.612 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : Failed to get available servers: null
2019-07-23 19:04:14.612 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : no available server to connect.
2019-07-23 19:04:14.653 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : Failed to get available servers: null
2019-07-23 19:04:14.653 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : no available server to connect.
2019-07-23 19:04:19.611 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : Failed to get available servers: null
2019-07-23 19:04:19.611 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : no available server to connect.
2019-07-23 19:04:19.652 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : Failed to get available servers: null
2019-07-23 19:04:19.652 ERROR 22439 --- [imeoutChecker_1] i.s.c.r.netty.NettyClientChannelManager  : no available server to connect.

seatea-server已经启动

我这边是有个jar包maven构建失败 spring-cloud-alibaba-seata-0.9.1.BUILD-SNAPSHOT.jar.从同事那拷了一份扔到本地仓库后可以起来了.你可以看一下本地仓库有没有这个包.

authors: Switcherman shibd

repo: seata/seata-samples


text:
i.s.c.r.netty.AbstractRpcRemotingClient  : 0318

[ ] I have searched the issues of this repository and believe that this is not a duplicate.

Ⅰ. Issue Description
23:13:38.630  INFO 558444 --- [lector_RMROLE_1] i.s.c.r.netty.NettyClientChannelManager  : return to pool, rm channel:[id: 0xe62a788e, L:/192.168.30.128:54099 - R:/192.168.30.130:8091]
2019-11-24 23:13:38.630  INFO 558444 --- [lector_RMROLE_1] i.s.c.r.netty.AbstractRpcRemotingClient  : remove exception rm channel:[id: 0xe62a788e, L:/192.168.30.128:54099 - R:/192.168.30.130:8091]
2019-11-24 22:21:11.451 ERROR 561200 --- [lector_RMROLE_1] i.s.c.r.netty.AbstractRpcRemotingClient  : 0318
io.netty.handler.codec.DecoderException: java.lang.IllegalArgumentException: not support typeCode,111
at io.netty.handler.codec.ByteToMessageDecoder.callDecode(ByteToMessageDecoder.java:472) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.handler.codec.ByteToMessageDecoder.channelRead(ByteToMessageDecoder.java:278) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.handler.timeout.IdleStateHandler.channelRead(IdleStateHandler.java:287) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.AbstractChannelHandlerContext.fireChannelRead(AbstractChannelHandlerContext.java:352) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.DefaultChannelPipeline$HeadContext.channelRead(DefaultChannelPipeline.java:1408) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:374) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.AbstractChannelHandlerContext.invokeChannelRead(AbstractChannelHandlerContext.java:360) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.DefaultChannelPipeline.fireChannelRead(DefaultChannelPipeline.java:930) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.nio.AbstractNioByteChannel$NioByteUnsafe.read(AbstractNioByteChannel.java:163) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.nio.NioEventLoop.processSelectedKey(NioEventLoop.java:682) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.nio.NioEventLoop.processSelectedKeysOptimized(NioEventLoop.java:617) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.nio.NioEventLoop.processSelectedKeys(NioEventLoop.java:534) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.channel.nio.NioEventLoop.run(NioEventLoop.java:496) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.util.concurrent.SingleThreadEventExecutor$5.run(SingleThreadEventExecutor.java:906) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.util.internal.ThreadExecutorMap$2.run(ThreadExecutorMap.java:74) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.util.concurrent.FastThreadLocalRunnable.run(FastThreadLocalRunnable.java:30) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at java.base/java.lang.Thread.run(Thread.java:834) ~[na:na]
Caused by: java.lang.IllegalArgumentException: not support typeCode,111
at io.seata.codec.seata.MessageCodecFactory.getMergeResponseInstanceByCode(MessageCodecFactory.java:318) ~[seata-all-0.7.1.jar:0.7.1]
at io.seata.codec.seata.MessageCodecFactory.getMessage(MessageCodecFactory.java:260) ~[seata-all-0.7.1.jar:0.7.1]
at io.seata.codec.seata.SeataCodec.decode(SeataCodec.java:78) ~[seata-all-0.7.1.jar:0.7.1]
at io.seata.core.rpc.netty.v1.ProtocolV1Decoder.decodeFrame(ProtocolV1Decoder.java:125) ~[seata-all-0.7.1.jar:0.7.1]
at io.seata.core.rpc.netty.v1.ProtocolV1Decoder.decode(ProtocolV1Decoder.java:78) ~[seata-all-0.7.1.jar:0.7.1]
at io.netty.handler.codec.LengthFieldBasedFrameDecoder.decode(LengthFieldBasedFrameDecoder.java:334) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.handler.codec.ByteToMessageDecoder.decodeRemovalReentryProtection(ByteToMessageDecoder.java:502) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
at io.netty.handler.codec.ByteToMessageDecoder.callDecode(ByteToMessageDecoder.java:441) ~[netty-all-4.1.36.Final.jar:4.1.36.Final]
... 21 common frames omitted
Ⅱ. Describe what happened
If there is an exception, please attach the exception trace:
Just paste your stack trace here!

Ⅲ. Describe what you expected to happen
Ⅳ. How to reproduce it (as minimally and precisely as possible)

xxx
xxx
xxx

Ⅴ. Anything else we need to know?
Ⅵ. Environment:

JDK version :11
OS :win
Others:

有测试用例用来重现么？

authors: cmonkey yuerspring

repo: seata/seata


text:
Could not retrieve transation read-only status server

Ⅰ. Issue Description
接口调用报Could not retrieve transation read-only status server
Ⅱ. Describe what happened
seata版本0.8.1，在方法配置@GlobalTransactional(name = "platform-designer-edit",rollbackFor = Exception.class)，数据库采用的阿里云RDS MySQL 8.0，测试环境自己搭建的mysql,没有出现此问题。

驱动版本


text:
Seata server 無法在 Openshift container platform (OCP) 上 register TM 和 RM (TooLongFrameException)

Exception capture:

但client 能curl server的7091

Prerequisite:

Client 和 Server version: 1.5.2

Client Java version: 11
registry type: file
config type: file
file.conf 使用default settings

Additional Information:

已在local(windows with seata-server.bat), docker 環境試過，未有該異常，能成功執行transaction
client和server在同namespace (poc-demo) 下，grouplist.default: seats-server.poc-demo:8091

Disable istio could solve the problem, but how to use both istio and Seata?

8091端口是否被envoy代理导致此问题？

8091端口是否被envoy代理导致此问题？

解決了，謝謝
https://github.com/seata/seata/issues/2927#issuecomment-754997927


text:
Update universal-application-tool-0.0.1 to server in unit test setup

Description
Please explain the changes you made here.
Checklist

[ ] Created tests which fail without the change (if possible)
[ ] Extended the README / documentation, if necessary

Issue(s)
Fixes #<issue_number>; Fixes #<issue_number>; Fixes #<issue_number>...

duplicate of https://github.com/seattle-uat/civiform/pull/2440

authors: bion shanemc-goog

repo: seattle-uat/civiform