toDataURL not working properly on rotated canvas

Hi to all.
I'm trying to use a rotated signature pad. Signature pad is drawn properly, i'm able to sign on a rotated canvas, but when calling toDataURLl, the resulting image is cut where the original, unrotated, canvas where placed initially, seems that toDataURL doesn't honor the rotation.
This is the code that I'm using to rotate the canvas:
var canvas = document.querySelector("canvas");

canvas.setAttribute("width", $$(window).height());
canvas.setAttribute("height", divSignature.height());

context = canvas.getContext("2d");

context.rotate(1.5 * Math.PI);
context.translate(-canvas.height, 0);

canvas is inside a <div class='signature'> rotated via CSS:
.rotate90right {
    -webkit-transform: rotate(90deg);
    -webkit-transform-origin: left bottom;
    transform: rotate(90deg);
    transform-origin: left bottom;

    width: 100vh;
    height: 100vw;
    overflow-x: hidden;
    position: absolute;
    top: -100vw;
    left: 0;
}

After all rotations, i'm initializing the signaturepad:
        var signaturePad = new SignaturePad(document.getElementById('signature-pad'), {
            backgroundColor: 'rgb(255, 255, 255)',
            penColor: 'rgb(0, 0, 0)'
        });
        signaturePad.clear();

and, as wrote above, i'm able to sign properly. The only missing thing is how to properly use the signaturePad.toDataURL horing the rotated canvas.
I don't need to support multiple rotations, this page starts rotated and the mobile app that i'm developing can't change orientation (is fixed in portrait), that's why I need to rotate everything via CSS
Any idea ?

Any hint ? I'm using v2, latest version.

bump

m


Project not run with version 2.6.8

Version

Vue version: 3

Description
When I install version 2.6.8, I am not able to run the project successfully

Should now be fixed in 2.6.9


Travis won't accept pull requests

Travis Continuous Integration won't accept full requests for this project, because of some infrastructure problem. The actual message reported is:
$ rake
rake aborted!
No Rakefile found (looking for: rakefile, Rakefile, rakefile.rb, Rakefile.rb)

e.g. [https://travis-ci.org/remy/inliner/builds/21471899]

This is supported @ 1.0.0.


hide the releases section from navigation

This PR hides the releases section from the navigation, but allows there to be an index page for the releases page that is rendered like the rest of our index pages are. It essentially:

Hides the Releases section from the left nav, but keeps the structure of the content in that directory in tact so it can be used to render the Releases section index page, so /builders/build/releases (with list of all the releases)
Hides the Releases section from the index page of the Build section, so /builders/build

I debated doing this with CSS, but it doesn't look good when the item shows up then disappears.
If you have questions about this, cause it's a weird one, let me know. Or suggestions to improve this flow would be great, but I didn't want to spend a whole lot of time on it as I don't know what the chances are of us needing another hidden section—I assume slim.
Goes with: https://github.com/moonbeam-foundation/moonbeam-docs/pull/882

No longer need this as we won't be moving forward with the runtime release notes on the docs, closing this PR.


Make shell script pass linter shellcheck.

Description
This shell script is used to install the dependencies of the project.
Currently it does not pass checks by the linter shellcheck https://www.shellcheck.net/
https://github.com/konveyor/move2kube/blob/abea0c90ef78dc12fefd1d3cbf711b562170efa0/scripts/installdeps.sh#L22
Line 22:
elif [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then
          ^-- SC2003: expr is antiquated. Consider rewriting this using $((..)), ${} or [[ ]].
                      ^-- SC2046: Quote this to prevent word splitting.

How to get started
❗ Please read the contribution guidelines first https://github.com/konveyor/move2kube/blob/master/contributing.md
As the error says rewrite the expression using one of $((..)), ${} or [[ ]]
Also make sure there are no other errors.
You can run shellcheck locally: https://github.com/koalaman/shellcheck
or as a vscode extension: https://marketplace.visualstudio.com/items?itemName=timonwong.shellcheck
Guidelines

Bash tutorial: https://mywiki.wooledge.org/BashGuide
FAQ about common tasks: https://mywiki.wooledge.org/BashFAQ
Things NOT to do: https://mywiki.wooledge.org/BashPitfalls
Bash reference: https://mywiki.wooledge.org/BashSheet

Hi @HarikrishnanBalagopal! I would love to try and fix that. Just to make sure, you want me to edit the file so that it passes the linter check?

Sorry for the silly question, I somehow managed to miss the huge title

@chrisgoutzi if you have done any work on this feel free to submit a PR.
Otherwise I would like to takeover.


Added TODO for OLS-679

Description
Added TODO for OLS-679
Type of change

[ ] Refactor
[ ] New feature
[ ] Bug fix
[ ] CVE fix
[ ] Optimization
[x] Documentation Update
[ ] Configuration Update
[ ] Bump-up dependent library
[ ] Bump-up library or tool used for development (does not change the final image)

Related Tickets & Documents

Related Issue #OLS-679
Closes #

/approve


Error when trying to run send-forgot-password-email.php

Hi, I'm getting an error with the App\Message\SendForgotPasswordEmail class not found when trying to run send-forgot-password-email.php. Although I do not see an issue with the namespace there. What seems to be causing the issue here?
Here's the full error I get:

I:\Misc. projects\elegant-background-job-php-demo>php bin/send-forgot-password-email.php
PHP Fatal error:  Class 'App\Message\SendForgotPasswordEmail' not found in I:\Misc. projects\elegant-background-job-php-demo\bin\send-forgot-password-email.php on line 20

Fatal error: Class 'App\Message\SendForgotPasswordEmail' not found in I:\Misc. projects\elegant-background-job-php-demo\bin\send-forgot-password-email.php on line 20

Thanks for the issue. Fixed in fd42f8552b0781c5bd9cba581626fe314fd2acd1

Thanks for the issue. Fixed in fd42f85

Great! Much thanks for the quick fix. All is good now :)


MX8 - Developer Portal Release Note for name change

April 30 Release Note - Product name change in Dev Portal

This supports Deployment issue DEP-1524

Should be released on morning of 30 April after 7:00 (assuming that release is successful).


DTS files are importing TS files - v3

Hi there, I'm migrating from 2.x to 3.0-alpha. I added a single line of code:
import type * as from from "@legendapp/state";

When I run tsc to type-check my code, I get a bunch of errors originating from node_modules/@legendapp/state. If I take a look at<EMAIL_ADDRESS>as it is currently in 3.0.0-alpha.1, here's what I see:
export { batch, beginBatch, endBatch } from './src/batching';
export { computed } from './src/computed';
export { linked } from './src/linked';
export { configureLegendState } from './src/config';
export { event } from './src/event';
// more imports...

The issue is that these files living in src are actually .ts files instead of .d.ts files. Because of this, when I run tsc those are pulled in for type-checking which causes type errors because for my own code I use a stricter tsconfig.json than the one @legendapp/state uses. Try setting verbatimModuleSyntax or noUncheckedIndexedAccess to true and you'll see what I mean.
Let me know if you need more info. Love the library by the way! So convenient and pleasant to work with.

#300

Forked the repo, and added these two typescript rules. This is what I have found:

@Asha20 Why are the files typechecked in the first place. I know that they are .ts files but I did exclude node_modules in my tsconfig

Looks like that's just how TypeScript works: https://github.com/microsoft/TypeScript/issues/41883#issuecomment-1758692340
I also intuitively expected being able to use exclude to side-step the issue, but apparently it doesn't work.

I have a question: What if before the code is published on npm, it gets fully compiled down to js so typescript does not check it? Is that a solution?

Sorry for the delay on this! I was mostly offline for a few days while going to an out of town family thing. I just released a new alpha.2 which should fix this.
I had at some point in the @next versions changed the build to include the src folder alongside the built files, and that worked great in every environment I tested, and nobody testing that version seemed to have any issues with it. But it seems like some environments do check against node_modules. I don’t know why it would have all those failures though… I’ve seen other packages include their src folder with no issues. Package building is hard 😅
So I removed src from the published package and changed the build to use tsup instead of rollup, which reduced file sizes too. So I think that should fix all of this. Let me know if it’s working better for you in alpha.2?

Think this is fixed now! At least I can deploy again with the newer versions (alpha.2 and alpha.3)

Great! I’ll close the issue but please let me know if it’s not totally fixed. Thanks for the report!


Crashes when select paths on Android TV

Android TV box
When I try to add a path for any system, Dai will crush as soon I select Add.

#72


Task #25064: Python SDK Data sampling implementation

This adds the capability for the Python SDK to sample in-flight elements. The implementation modifies the ProcessBundleDescriptor when received by the BundleProcessor to create additional DataSampling PTransforms on PCollections. The samples are then returned when the SDK receives a SampleDataRequest.
Task #25064

Thank you for your contribution! Follow this checklist to help us incorporate your contribution quickly and easily:

[x] Mention the appropriate issue in your description (for example: addresses #123), if applicable. This will automatically add a link to the pull request in the issue. If you would like the issue to automatically close on merging the pull request, comment fixes #<ISSUE NUMBER> instead.
[ ] Update CHANGES.md with noteworthy changes.
[ ] If this contribution is large, please file an Apache Individual Contributor License Agreement.

See the Contributor Guide for more tips on how to make review process smoother.
To check the build health, please visit https://github.com/apache/beam/blob/master/.test-infra/BUILD_STATUS.md
GitHub Actions Tests Status (on master branch)

See CI.md for more information about GitHub Actions CI.

R: pabloem this includes the proto changes from PR/25065, I'll clean up the commits before merge

R: @pabloem

LMK if you want me to split up the PR, most of the code deltas are in tests however.

lgtm thanks!


feat: Add --no-withdrawl flag for "canister delete" for when the canister is out of cycles

Note: the reject enum is too small (ReplicaError is all we get) to differentiate when a call fails because
the canister is out of cycycles.
If instead we passed from the ic repo: rs/types/error_types/src/lib.rs ErrorCode::OutOfCycles (code 501) back
we could use that to handle that case and automatically fallback to a simple delete.
Signed-off-by: John Plevyak<EMAIL_ADDRESS>

Would you please add an entry to the changelog?

Added changelog entry.


There was a problem installing LTI

Hello
I got an error when installing LTI. I have reinstalled it several times. Every time I installed it to the 10th step, there would be a problem. It seems to be a bug. How can I solve it?
First stage

Log-30-11-2021-09-55-08.log
Transcript-30-11-2021-09-55-08.log
second stage
I deleted all resource groups and all resources on Azure, and after redeploying LTI, the following problems occurred in the sixth step of deployment:

Log-30-11-2021-10-41-49.log
Transcript-30-11-2021-10-41-49.log

So the error looks like you have NOT installed the prerequisites of .NETcore SDK or the version you have is less than 2.0.3 the latest version is 3.1 simply download and install it using the link below.. Please ensure you have all the other items also.
see https://github.com/microsoft/Learn-LTI/blob/main/docs/DEPLOYMENT_GUIDE.md
To begin, you will need:
Prerequisites
To begin, you will need:
Azure CLI
DotNet Core SDK
Node.js
Powershell
Git
An Azure subscription
See https://github.com/microsoft/Learn-LTI/blob/main/docs/DEPLOYMENT_GUIDE.md
Please follow the guide to ensure you delete your resources and redeploy https://github.com/microsoft/Learn-LTI/blob/main/docs/TROUBLESHOOTING.md
Again if you look at closed issues this issue is if you have not installed at the prerequirements
Typical issue is people NOT installing .NETCORE SDK please ensure you have installed all the prerequirements and restarted the machine https://github.com/microsoft/Learn-LTI/issues?q=install+error

Your initial log had this error which indicates the wrong SDK being installed for .NET Core Please ensure you delete all resources using the cleanup script and ensure the resource group is deleted.
???? .NET 6.0!
SDK ??: 6.0.100
??
.NET ?????????,??????????????? Microsoft ??,??????????????????,??????????,? DOTNET_CLI_TELEMETRY_OPTOUT ??????? '1' ? 'true' ???
?????? .NET CLI ???????: https://aka.ms/dotnet-cli-telemetry

??? ASP.NET Core HTTPS ?????
??????,??? 'dotnet dev-certs https --trust' (?? Windows ? macOS )?
???? HTTPS: https://aka.ms/dotnet-https
?????????: https://aka.ms/dotnet-hello-world
??????: https://aka.ms/dotnet-whats-new
????: https://aka.ms/dotnet-docs
? GitHub ?????????: https://github.com/dotnet/core
Use 'dotnet --help' ??????????: https://aka.ms/dotnet-cli
??????????...

@a00110110  I will close this issue as its a known issue of not installing the prerequisites if you need any more assistance please reopen the issue

@pfurgal5 Thanks for the comment made this is correct its the .NET Core SDK https://dotnet.microsoft.com/en-us/download/dotnet/3.1
I have updated the docs to reflect this.

Your initial log had this error which indicates the wrong SDK being installed for .NET Core Please ensure you delete all resources using the cleanup script and ensure the resource group is deleted.
???? .NET 6.0!
@a00110110
Error in the log
SDK ??: 6.0.100
??
.NET ?????????,??????????????? Microsoft ??,??????????????????,??????????,? DOTNET_CLI_TELEMETRY_OPTOUT ??????? '1' ? 'true' ???
?????? .NET CLI ???????: https://aka.ms/dotnet-cli-telemetry
??? ASP.NET Core HTTPS ?????
??????,??? 'dotnet dev-certs https --trust' (?? Windows ? macOS )?
???? HTTPS: https://aka.ms/dotnet-https
?????????: https://aka.ms/dotnet-hello-world
??????: https://aka.ms/dotnet-whats-new
????: https://aka.ms/dotnet-docs
? GitHub ?????????: https://github.com/dotnet/core
Use 'dotnet --help' ??????????: https://aka.ms/dotnet-cli
??????????...

Please ensure you download and install the .NET Core SDK current version is 3.1 see https://dotnet.microsoft.com/en-us/download/dotnet/3.1


depictured, abandon (logical-conflict)

This pull request was generated by the 'mq' tool

/trunk merge


Add migration manager

#143
Pre-submission Checklist

For tests to work you need a working neo4j and redis instance with the example dataset in docker/db-graph

[ ] Testing: Implement and pass new tests for the new features/fixes, cargo test.
[ ] Performance: Ensure new code has relevant performance benchmarks, cargo bench

Is this inteded only for Redis keys/cache migration?
If so, can we first create an MVP "migration" with the minimal amount of complexity and code keeping it extremely simple?
What's the overall flow and usage? I'd say we can do something straight forward. E.g:
I'd say we need to version the Redis schemas. The current version will always be availble as a Redis value. On service/watcher setup (start-up), we check whether current version is the latest. If it's not latest, apply migrations.


Check for Separate Security and Privacy sections

It has been common to have a single section for this, for example:
<h2 id="priv-sec">
Security and Privacy Considerations
</h2>

No new security or privacy considerations have been raised on this specification.

This is no longer allowed. The horizontal review guidelines mentions separate Security Considerations and Privacy Considerations sections.

Before requesting privacy and security reviews from the Privacy Interest Group (PING) and security reviewers, respectively, authors must write both "Security Considerations" and "Privacy Considerations" sections for their documents,
https://w3ctag.github.io/security-questionnaire/#reviews

Furthermore, the issue template for Privacy review states:

Does your document have an in-line Privacy Considerations section, separate from Security Considerations?  If not, corrrect that before proceeding further.

which is an annoying thing to discover, the day you publish a CRD to get wide review, given that pubrules give no complaint for this.

Sigh, it would be great to actually see these changes somewhere before they're live. Would also be nice to see what the actual reasoning was for "priv and sec must be separate sections".
Oh well, I'll fix the check to make this disallowed, I suppose.


libxx/libcxx: select PTHREAD_MUTEX_TYPES to support recursive mutex

Summary
libxx/libcxx: select PTHREAD_MUTEX_TYPES to support recursive mutex
Impact
fix recursive mutex issue for c++
Testing
local test

Please because PR to fix CI failure


Custom delimiter function

Proposal
Support passing (string, string) => string function as a delimiter option.
For example, for object:
{
  first: {
    second: "hello"
  }
}

and delimiter:
(left, right) => left + right.charAt(0).toUpperCase() + right.slice(1);

it will produce camel case names:
{
  firstSecond: "hello"
}

@hughsk WDYT if I'll prepare such PR?

I need the camel case option as well. We need this functionality for better customisation of key names than a simple separator!

There is a snake case variant here

I complete rewrote flat as flat2 here: https://github.com/kristianmandrup/flat2
Includes loads of customisation options for custom key generation and transforms to fit any such scenario. Now snakecase and camelCase options come built in as well ;)

@mxl how would you handle the case where the object looks like so?
{
  first: {
    second: "hello",
    Third: "world",
    fOurth: "foo"
  }
}

Now you have the key-value pair
firstFOurth: "foo"
How will this be unflattened? Or, how will you determine whether or not this is first.fOurth or first.f.ourth?


General discrepancies between ProteinNet and mmCIF/PDB files (biopython)

I have some code that fetches mmCIF files for each entry in CASP11 using BioPython. A substantial proportion of examples fail the various checks, though some pass. Many of them are missing the corresponding model, and most that have the given model disagree on primary sequence length. Perhaps there is an obvious explanation for this, and I simply overlooked it. Subtracting one from model_id allows most of the models to be resolved, but many of the primary sequences have significant length mismatch. Most of the files only have the one model, so it's unclear what is exactly is going on here.
#!/usr/bin/python

# imports
import sys
import re

# Constants
NUM_DIMENSIONS = 3

# Functions for conversion from Mathematica protein files to TFRecords
_aa_dict = {
    'A': '0',
    'C': '1',
    'D': '2',
    'E': '3',
    'F': '4',
    'G': '5',
    'H': '6',
    'I': '7',
    'K': '8',
    'L': '9',
    'M': '10',
    'N': '11',
    'P': '12',
    'Q': '13',
    'R': '14',
    'S': '15',
    'T': '16',
    'V': '17',
    'W': '18',
    'Y': '19'
}
_dssp_dict = {
    'L': '0',
    'H': '1',
    'B': '2',
    'E': '3',
    'G': '4',
    'I': '5',
    'T': '6',
    'S': '7'
}
_mask_dict = {'-': '0', '+': '1'}

class switch(object):
    """Switch statement for Python, based on recipe from Python Cookbook."""
    def __init__(self, value):
        self.value = value
        self.fall = False

    def __iter__(self):
        """Return the match method once, then stop"""
        yield self.match

    def match(self, *args):
        """Indicate whether or not to enter a case suite"""
        if self.fall or not args:
            return True
        elif self.value in args:  # changed for v1.5
            self.fall = True
            return True
        else:
            return False

def letter_to_num(string, dict_):
    """ Convert string of letters to list of ints """
    patt = re.compile('[' + ''.join(dict_.keys()) + ']')
    num_string = patt.sub(lambda m: dict_[m.group(0)] + ' ', string)
    num = [int(i) for i in num_string.split()]
    return num

def read_record(file_, num_evo_entries):
    """ Read a Mathematica protein record from file and convert into dict. """

    dict_ = {}

    while True:
        next_line = file_.readline()
        for case in switch(next_line):
            if case('[ID]' + '\n'):
                id_ = file_.readline()[:-1]
                dict_.update({'id': id_})
            elif case('[PRIMARY]' + '\n'):
                primary = letter_to_num(file_.readline()[:-1], _aa_dict)
                dict_.update({'primary': primary})
            elif case('[EVOLUTIONARY]' + '\n'):
                evolutionary = []
                for residue in range(num_evo_entries):
                    evolutionary.append(
                        [float(step) for step in file_.readline().split()])
                dict_.update({'evolutionary': evolutionary})
            elif case('[SECONDARY]' + '\n'):
                secondary = letter_to_num(file_.readline()[:-1], _dssp_dict)
                dict_.update({'secondary': secondary})
            elif case('[TERTIARY]' + '\n'):
                tertiary = []
                for axis in range(NUM_DIMENSIONS):
                    tertiary.append(
                        [float(coord) for coord in file_.readline().split()])
                dict_.update({'tertiary': tertiary})
            elif case('[MASK]' + '\n'):
                mask = letter_to_num(file_.readline()[:-1], _mask_dict)
                dict_.update({'mask': mask})
            elif case('\n'):
                return dict_
            elif case(''):
                return None

if __name__ == '__main__':
    from Bio.PDB.MMCIFParser import MMCIFParser
    from Bio.PDB.PDBParser import PDBParser
    from Bio.PDB import PDBIO, PDBList
    from Bio.PDB.Structure import Structure, Entity
    from Bio.PDB.Model import Model
    from Bio.PDB.Residue import Residue
    from Bio.PDB.Chain import Chain
    from Bio.PDB.Atom import Atom
    import numpy as np

    input_path = 'D:/casp11/training_30'
    print(f'Reading data from {input_path}')
    num_evo_entries = int(sys.argv[2]) if len(
        sys.argv) == 3 else 20  # default number of evo entries

    input_file = open(input_path, 'r')
    pdbl = PDBList()

    while True:
        record = read_record(input_file, num_evo_entries)
        if record is not None:
            id = record["id"]
            primary = record['primary']
            primary_len = len(primary)
            parts = id.split('_')
            if len(parts) != 3:
                # https://github.com/aqlaboratory/proteinnet/issues/1#issuecomment-375270286
                continue
            pdb_id = parts[0]
            path = pdbl.retrieve_pdb_file(pdb_id, pdir='pdb/', file_format='mmCif')
            parser = MMCIFParser()
            structure = parser.get_structure(pdb_id, path)
            model_id = int(parts[1])
            assert model_id >= 0
            chain_id = parts[2]
            if not model_id in structure.child_dict:
                print(f'{pdb_id} lacks model {model_id}, models: {structure.child_dict}')
                continue
            model = structure.child_dict[model_id]
            assert isinstance(model, Model)
            chain = model.child_dict[chain_id]
            if not chain_id in model.child_dict:
                print(f'{pdb_id} model {model_id} lacks chain {chain_id}, chains: {model.child_dict}')
                continue
            chain_len = len(chain.child_list)
            assert isinstance(chain, Chain)
            if chain_len != primary_len:
                print(f'{pdb_id} chain ({chain_len}) and primary ({primary_len}) lengths mismatch')
            else:
                print(f'{pdb_id} is all good!')
        else:
            input_file.close()
            break

Sampled output:
Reading data from D:/casp11/training_30
Structure exists: 'pdb/2yo0.cif'
2YO0 lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/4jrn.cif'
4JRN lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/4hxf.cif'
4HXF lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/2l0e.cif'
2L0E is all good!
Structure exists: 'pdb/2kxi.cif'
2KXI is all good!
Structure exists: 'pdb/2o57.cif'
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 8744.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 9031.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 9318.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 9580.
  warnings.warn(
2O57 lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/4lhr.cif'
4LHR lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/3zrg.cif'
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 1020.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 1024.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 1027.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 1097.
  warnings.warn(
3ZRG lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/2k0m.cif'
2K0M is all good!
Structure exists: 'pdb/4hhx.cif'
4HHX lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/4ld3.cif'
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 1362.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 1382.
  warnings.warn(
4LD3 lacks model 2, models: {0: <Model id=0>}
Structure exists: 'pdb/3wo6.cif'
3WO6 lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/2kkp.cif'
2KKP is all good!
Structure exists: 'pdb/4jja.cif'
4JJA lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/4h5s.cif'
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 1565.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 1733.
  warnings.warn(
4H5S lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/4aez.cif'
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 16578.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 16692.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 16725.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 16758.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 16819.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain F is discontinuous at line 16820.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain G is discontinuous at line 16868.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain H is discontinuous at line 16889.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain I is discontinuous at line 16895.
  warnings.warn(
4AEZ lacks model 3, models: {0: <Model id=0>}
Structure exists: 'pdb/4gdo.cif'
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 3247.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 3295.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 3336.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain D is discontinuous at line 3362.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 3401.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain F is discontinuous at line 3403.
  warnings.warn(
4GDO lacks model 1, models: {0: <Model id=0>}
Structure exists: 'pdb/3up6.cif'
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 4854.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 4927.
  warnings.warn(
3UP6 lacks model 1, models: {0: <Model id=0>}
Downloading PDB structure '3UKW'...
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 3473.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain C is discontinuous at line 3717.
  warnings.warn(
3UKW lacks model 2, models: {0: <Model id=0>}
Downloading PDB structure '3SEO'...
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 3510.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 3511.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain A is discontinuous at line 3519.
  warnings.warn(
C:\Users\tlhavlik\AppData\Local\Programs\Python\Python38\lib\site-packages\Bio\PDB\StructureBuilder.py:89: PDBConstructionWarning: WARNING: Chain B is discontinuous at line 3539.
  warnings.warn(
3SEO lacks model 1, models: {0: <Model id=0>}

Related issue https://github.com/aqlaboratory/proteinnet/issues/13
Thanks for all the good work.

@thavlik did you ever find out what was going on here?

I have not. Right now I'm preferring the information in the PDB files over what is supplied by ProteinNet.

@thavlik oh noes :( is there a nice place where you can download all the PDBs used by Casp12 in one compressed file?

@lucidrains if you'd like to download the original raw PDBs for CASP12 (just what CASP released, i.e. the ProteinNet test set), you can grab them from the CASP site itself, here.
@thavlik without seeing specific examples of the discrepancy (i.e. a sequence you're getting versus what ProteinNet has), it's difficult to tell what the issue is. My best guess is that you're taking the sequence of the resolved residues in a PDB file--i.e. you're concatenating a bunch of discontiguous segments. This would be incorrect and non-physical. Virtually all PDB files have missing residues and so the sequence in the PDB file has gaps in it. ProteinNet entries have the full sequences, which is the physical object that actually folds, along with mask fields that indicate which residues are missing from the structure, so that you can correctly map the sequence to the structure and also account for the missing residues in the loss function, etc. I am not 100% sure this is what's going on, but that's my best guess like I said. If you can paste a specific sequence from ProteinNet and your pipeline it would be easier to compare the two, and see if you are in fact concatenating discontiguous segments.

@thavlik without seeing specific examples of the discrepancy (i.e. a sequence you're getting versus what ProteinNet has), it's difficult to tell what the issue is. My best guess is that you're taking the sequence of the resolved residues in a PDB file--i.e. you're concatenating a bunch of discontiguous segments. This would be incorrect and non-physical.

Code with example output is in the original issue. Some structures agree (e.g. 2KKP, 2L0E) but some (e.g. 4LHR) do not have the model specified by ProteinNet. In the examples specifying model id=1, is this referencing a modified version of ?
You bring up a very good point about naively concatenating the residues in the PDB file together. I think we've just been operating on the assumption that a specific ID should have immediate structural correspondence between the training example and PDB file. I will investigate more this weekend.
Thanks again

In the examples specifying model id=1, is this referencing a modified version of ?

After more digging, this turned out to be correct. Many PDBs have waters and other garbage residues included in Model0ChainA. The ProteinNet record will reference a Model1ChainA, which does not exist in the PDB. It can be derived by normalizing Model0ChainA according to the primary sequence / mask. Here is a concrete example with 4JRN_1_A:
PDB primary sequence, followed by ProteinNet's primary sequence and mask:
GAHMSELVFEKADSGCVIGKRILAHMQEQIGQPQALENSERLDRILTVAAWPPDVPKRFVSVTTGETRTLVRGAPLGSGGFATVYEATDVETNEELAVKVFMSEKEPTDETMLDLQRESSCYRNFSLAKTAKDAQESCRFMVPSDVVMLEGQPASTEVVIGLTTRWVPNYFLLMMRAEADMSKVISWVFGDASVNKSEFGLVVRMYLSSQAIKLVANVQAQGIVHTDIKPANFLLLKDGRLFLGDFGTYRINNSVGRAIGTPGYEPPERPFQATGITYTFPTDAWQLGITLYCIWCKERPTPADGIWDYLHFADCPSTPELVQDLIRSLLNRDPQKRMLPLQALETAAFKEMDSVVKGAAQNFEQQEHLHTE

SELVFEKADSGCVIGKRILAHMQELENSERLDRILTVAAWPPDVPKRFVSVTTGETRTLVRGAPLGSGGFATVYEATDVETNEELAVKVFMSEKEPTDETMLDLQRESSCYRNFSLAKTAKDAQESCRFMVPSDVVMLEGQPASTEVVIGLTTRWVPNYFLLMMRAEADMSKVISWVFGDASVNKSEFGLVVRMYLSSQAIKLVANVQAQGIVHTDIKPANFLLLKDGRLFLGDFGTYRINNSVGRGTPGYEPPERPGITYTFPTDAWQLGITLYCIWCKERPTPADGIWDYLHFADCPSTPELVQDLIRSLLNRDPQKRMLPLQALETAAFKEMDSVVKGAAQNFEQQ

----++++++++++++++++++++++++-------++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++--+++++++++++----++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++------

Put these all on one line in a text editor, visualize the relationship. The length of the normalized chain should be equal to the number of + signs in the mask.
HUGE thank you, @alquraishi. ProteinNet is a significant contribution to the community. I'll open another issue if there is any additional confusion.

@thavlik @alquraishi thank you both!


Error: Operation timed out

I am trying to use the action to run a .sh file to sync and build a Laravel/React app.
The action successfully connects via ssh and runs the file but there is no output and after 30sec it exits with timeout error.
I start running a couple of tests I got the same error just copying and paste your example code.
I am trying to connect to a Ubuntu 18 server.
Any tips?
Action out put:
Warning: This action does not currently support host verification; verification is disabled.

/home/***/deploy/deploy_dev.sh
Start Run Command
Pseudo-terminal will not be allocated because stdin is not a terminal.
ssh: connect to host *** port 22: Operation timed out
##[error]Docker run failed with exit code 255

Hi,There may be two possibilities
1、Blocked by firewall
2、Try ssh -t -t(or ssh -tt for short) to force pseudo-tty allocation even if stdin isn't a terminal.
https://stackoverflow.com/questions/7114990/pseudo-terminal-will-not-be-allocated-because-stdin-is-not-a-terminal
For the second problem, I added a args parameter to pass the extra parameters of SSH
See https://github.com/fifsky/ssh-action#options
- name: ls -a via ssh
  uses: fifsky/ssh-action@master
  with:
    command: |
      cd /tmp
      ls -a
    host: ${{ secrets.HOST }}
    user: root
    key: ${{ secrets.PRIVATE_KEY}}
    args:"-tt"

Thanks for the quick reply =]
I added the args and the Pseudo-terminal alert is gone but the result is the same.
cd /var/www
ls -a
 exit
Start Run Command
ssh: connect to host *** port 22: Operation timed out
##[error]Docker run failed with exit code 255

You can add parameters to see more error information, such as
args:"-tt -vvv"

Thanks for the reply! Added the arg -vvv and managed to identify the error.
Turns out it was a typo in the secret configuration.
I am embarrassed for this silly mistake but also relieved that all works now.
Thanks!


How to manage memory with blasr ?

Hi,
I'm trying to align subreads (5 .bam files from PacBio Sequel) to a draft genome assembly (400Mo) in order to polish my assembly with arrow. I use blasr from pbbioconda.
blasr --bam --hitPolicy randombest --nproc 4 --maxAnchorsPerPosition 1000 --minMatch 12 --bestn 10 --minPctAccuracy 75 --minPctSimilarity 75 --minSubreadLength 500 --out raw_vs_draft.bam subreads.fofn my_draft_genome.fasta
I always obtain an out of memory error, even with 128Go of RAM.
Is there a way to limit the memory use by blasr or to manage the memory differently ?
Thank you in advance for your help.
Stephane

Here is the trick, you use pbmm2. Blasr is end of life and had been fully replaced in all workflows.

OK, I will try it, thanks for the quick answer.


[SPARK-31786][K8S][BUILD] Upgrade kubernetes-client to 4.9.2

What changes were proposed in this pull request?
This PR aims to upgrade kubernetes-client library to bring the JDK8 related fixes. Please note that JDK11 works fine without any problem.

https://github.com/fabric8io/kubernetes-client/releases/tag/v4.9.2

JDK8 always uses http/1.1 protocol (Prevent OkHttp from wrongly enabling http/2)

Why are the changes needed?
OkHttp "wrongly" detects the Platform as Jdk9Platform on JDK 8u251.

https://github.com/fabric8io/kubernetes-client/issues/2212
https://stackoverflow.com/questions/61565751/why-am-i-not-able-to-run-sparkpi-example-on-a-kubernetes-k8s-cluster

Does this PR introduce any user-facing change?
No. This will recover the failures on JDK 8u252.
How was this patch tested?
Pass the Jenkins with the old K8s and do the manual testing on K8s 1.17.3.

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Since there is a revert on master branch (https://github.com/apache/spark/commit/db5e5fce68f7e3a724eb4516908c4ba9786b0db3), I'll rebase once more to make it sure.

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Retest this please.

The one failure in the last K8s IT is a known flaky one.
KubernetesSuite:
- Run SparkPi with no resources *** FAILED ***
  The code passed to eventually never returned normally. Attempted 130 times over 2.0017359222166666 minutes. Last failure message: false was not true. (KubernetesSuite.scala:370)
- Run SparkPi with a very long application name.
- Use SparkLauncher.NO_RESOURCE
- Run SparkPi with a master URL without a scheme.
- Run SparkPi with an argument.
- Run SparkPi with custom labels, annotations, and environment variables.
- All pods have the same service account by default
- Run extraJVMOptions check on driver
- Run SparkRemoteFileTest using a remote data file
- Run SparkPi with env and mount secrets.
- Run PySpark on simple pi.py example
- Run PySpark with Python2 to test a pyfiles example
- Run PySpark with Python3 to test a pyfiles example
- Run PySpark with memory customization
- Run in client mode.
- Start pod creation from template
- PVs with local storage
- Launcher client dependencies
- Test basic decommissioning
- Run SparkR on simple dataframe.R example
Run completed in 14 minutes, 43 seconds.
Total number of tests run: 20
Suites: completed 2, aborted 0
Tests: succeeded 19, failed 1, canceled 0, ignored 0, pending 0
*** 1 TEST FAILED ***

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cc @dbtsai and @holdenk

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WorkerDecommissionSuite is irrelevant to this PR.
org.apache.spark.scheduler.WorkerDecommissionSuite.verify a task with all workers decommissioned succeeds

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@dongjoon-hyun
Any reason of not using kubernetes-client 4.10.1?

@dongjoon-hyun, I have the same question as above, why not upgrade to 4.10.1 ?
Looks good otherwise.

Thank you for review, @maver1ck and @ScrapCodes .
In this PR, I tried 4.10.1 and 4.10.0 first. However, the dependency change was too huge. And, kubernetes-model was split into many jars in 4.10.x. Given the risk and complexity of 4.10.x, 4.9.2 is more safer option which having a minimal change for this issue. Since we need backport this PR to 3.0.0 RC3 and 2.4.6 RC4, minimizing risk is important. We can revisit 4.10.x later for the other issues.

https://github.com/apache/spark/pull/28601/commits/760030bbb2f50569ef1d2c5427b14d53d2996ef1

Jenkins retest this please.
LGTM pending Jenkins

Retest this please.

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Yeah a minor update for now, esp if being backported, seems prudent.

Thank you all. Merged to master/branch-3.0

Due to the conflicts on dependency file, I need to make a backporting PR separately.
BTW, branch-3.0 is currently broken by https://github.com/apache/spark/pull/28604.
The backporting PR will fail due the above failure.

This is tested with the latest JDK8 and K8s 1.17.x manually and backported to branch-3.0.


Syntax error in generated dot file

The generated visualization dot file contains an syntax error if the character < or > is placed inside an HTML table within an label.
Steps to reproduce:
Run this exemple modified from https://textx.github.io/textX/stable/visualization/
from textx import metamodel_from_str
from textx.export import metamodel_export

grammar = '''

Comment:
    "<:" ( !"*/" /./ )* ":>"
;

EntityModel:
  entities+=Entity    // each model has one or more entities
;

Entity:
  'entity' name=ID '{'
    attributes+=Attribute     // each entity has one or more attributes
  '}'
;

Attribute:
  name=ID ':' type=[Entity]   // type is a reference to an entity. There are
                              // built-in entities registered on the meta-model
                              // for primitive types (integer, string)
;
'''

entity_mm = metamodel_from_str(grammar)

metamodel_export(entity_mm, 'entity_model.dot')

Now execute:
$ dot -Tpng -O entity_model.dot

When parsed graphviz will return an syntax error and that will be solved only if all > and < are removed. An possible solution is to replace them with their respective Unicode character as > and < respectively.
OS: Ubuntu 20.04 LTS
Python: Python 3.8.5
textX: 2.2.0

@hlouzada Thanks for the detailed report.

@hlouzada : the bug should be fixed. You can have a look at the current master.

Thanks for the fix. It's working now.


Add Guides to Docs

All current guides can be found here , in addition to the git good slides from our latest workshop.

Follow-up: https://github.com/techstartucalgary/tsu-website/issues/397

I'm going to close this one in favor of more granular issues, to track progress better


stripped angular example with html package

sorry about the delay i can only work on this on the weekend - stripped angular added html package in reference to the last PR 867

Thank you for taking time to update this! Some notes
Core notes

React is still used in the example, should not be the case i.e this should be a pure angular example

Overal notes

I can still some extra dependencies in the source i.e.react-dom, @wagmi/chains, react types etc. (this one is part of wagmi/core)
Could you remove any extra un-necessary files like editorconfig / tests etc... ideally leaving minimal ammout of these
Files like package-lock need to be removed in favour of using setup in this monorepo (yarn and there is only one lockfile at the root)
Example should be renamed to just angular
Similarly to other examples, some commands need to be exposed in root package json workspaces i.e. dev:angular
Remove readme (as per other examples)
Update .gitignore to de-duplicate entries from root .gitignore and only include rules specific to angular and this example
All package.json dependencies should be strict i.e no ^ in versions
Remove duplicate packages like typescript that are already present in the root of the monorepo, also is tslib/ tsx needed?
tsconfig.json should extend root one and only include extra rules / overrides needed for this example
There are some files that are empty

😅 Sorry for the extensive list, but these should be complete to keep this example inline with practices established in a repo and make it simpler for people to get started with.

😅 Sorry for the extensive list, but these should be complete to keep this example inline with practices established in a repo and make it simpler for people to get started with.

ok, no problem. i'll work on this

hi so far:
Core notes

React is still used in the example, should not be the case i.e this should be a pure angular example
+done

Overal notes

I can still some extra dependencies in the source i.e.react-dom, @wagmi/chains, react types etc. (this one is part of wagmi/core)
+done

Could you remove any extra un-necessary files like editorconfig / tests etc... ideally leaving minimal ammout of these
+done

Files like package-lock need to be removed in favour of using setup in this monorepo (yarn and there is only one lockfile at the root)
+done

Example should be renamed to just angular
+done

I had to add a couple duplicates in tsconfig angular, wouldn't build without this config. Could be missing something possible on your list but from root ... yarn, yarn dev:angular and you're good to go

This is awesome 🔥 will be reviewing during the week, but can already tell there was a lot of cleanup and simplification done, thank you!

Sorry for taking too long on this, we were super busy with bringing V2 of web3modal to stable and are now focusing on V3 which will have entirely new architecture. Plan is to add more framework support there, thus I'll be closing this pr as it is no longer portable.


Enable chat-template for vLLM

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fastled bug fixes

If you’re using Fastled with WLED, you might want to look at the work I did a couple years ago to make Fastled patterns more easily portable to WLED. (Probably after the burn, it’s not in a state to use right now without significant work)
https://github.com/embedded-creations/WLED/tree/FastLED_2D/usermods/FastLED_Compatibility
I really like your project and would love to collaborate at some point in the future when I have a bit more time. In the meantime I’m just following your repo


Could not resolve dependency: peer<EMAIL_ADDRESS>from<EMAIL_ADDRESS>

Upon executing npm install against a fresh clone of this repository, NPM fails with the following output:

npm resolution error report
While resolving<EMAIL_ADDRESS>Found<EMAIL_ADDRESS>node_modules/@babel/core
dev<EMAIL_ADDRESS>from the root project
Could not resolve dependency:
peer<EMAIL_ADDRESS>from<EMAIL_ADDRESS>node_modules/@babel/eslint-parser
dev<EMAIL_ADDRESS>from the root project
Fix the upstream dependency conflict, or retry
this command with --force or --legacy-peer-deps
to accept an incorrect (and potentially broken) dependency resolution.

hi @Wounded-Knee thank you for bringing this up, the repository has a yarn.lock file so we recommend running yarn install instead of npm install this should run the install command successfully


Add BitCanna chain

On block 4490420 authz module will be activated. ;)
Please edit name, change bitcanna-1 by bitcanna and wait next upgrade is passed.  🙏
Aug 11th at 16.15.
Thanks

Thanks @RaulBernal ! Can you tell me - does the chain ID change in this update? Ultimately REStake is driven by the Chain Registry so we shouldn't need any updates to networks.json. Cosmos.directory will recognise that Authz has been enabled and REStake will update accordingly.
Assuming all the info in Chain Registry is correct (code version doesn't matter in the context of REStake), then it should 'just work' (famous last words).
https://github.com/cosmos/chain-registry/blob/master/bitcanna/chain.json

Awesome!
BTW the chain ID remains as bitcanna-1

Closing as Bitcanna update works fine and this info is sourced from Chain Registry

Thanks


Webapp no more starting

Please provide us with the following information:

This issue is for a: (mark with an x)
- [X] bug report -> please search issues before submitting
- [ ] feature request
- [ ] documentation issue or request
- [ ] regression (a behavior that used to work and stopped in a new release)

Minimal steps to reproduce

Deploy the app with last version and start it
Sounds like an issue with opentelemetry packages

Any log messages given by the failure

2024-04-17T11:30:59.947657554Z [2024-04-17 11:30:59 +0000] [128] [ERROR] Exception in worker process
2024-04-17T11:30:59.947701854Z Traceback (most recent call last):
2024-04-17T11:30:59.947708454Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/arbiter.py", line 609, in spawn_worker
2024-04-17T11:30:59.947713454Z     worker.init_process()
2024-04-17T11:30:59.947717453Z   File "/tmp/8dc5ec898960094/antenv/lib/python3.11/site-packages/uvicorn/workers.py", line 66, in init_process
2024-04-17T11:30:59.947721453Z     super(UvicornWorker, self).init_process()
2024-04-17T11:30:59.947725453Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/workers/base.py", line 134, in init_process
2024-04-17T11:30:59.947729553Z     self.load_wsgi()
2024-04-17T11:30:59.947733253Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/workers/base.py", line 146, in load_wsgi
2024-04-17T11:30:59.947737653Z     self.wsgi = self.app.wsgi()
2024-04-17T11:30:59.947741553Z                 ^^^^^^^^^^^^^^^
2024-04-17T11:30:59.947745453Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/base.py", line 67, in wsgi
2024-04-17T11:30:59.947749553Z     self.callable = self.load()
2024-04-17T11:30:59.947753353Z                     ^^^^^^^^^^^
2024-04-17T11:30:59.947757153Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 58, in load
2024-04-17T11:30:59.947761253Z     return self.load_wsgiapp()
2024-04-17T11:30:59.947771553Z            ^^^^^^^^^^^^^^^^^^^
2024-04-17T11:30:59.947775253Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 48, in load_wsgiapp
2024-04-17T11:30:59.947800652Z     return util.import_app(self.app_uri)
2024-04-17T11:30:59.947804752Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:30:59.947808652Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/util.py", line 371, in import_app
2024-04-17T11:30:59.947812652Z     mod = importlib.import_module(module)
2024-04-17T11:30:59.947816552Z           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:30:59.947820352Z   File "/opt/python/3.11.7/lib/python3.11/importlib/init.py", line 126, in import_module
2024-04-17T11:30:59.947824452Z     return _bootstrap._gcd_import(name[level:], package, level)
2024-04-17T11:30:59.947828252Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:30:59.947832152Z   File "", line 1204, in _gcd_import
2024-04-17T11:30:59.947846051Z   File "", line 1176, in _find_and_load
2024-04-17T11:30:59.947850651Z   File "", line 1147, in _find_and_load_unlocked
2024-04-17T11:30:59.947854651Z   File "", line 690, in _load_unlocked
2024-04-17T11:30:59.947858651Z   File "", line 940, in exec_module
2024-04-17T11:30:59.947862751Z   File "", line 241, in _call_with_frames_removed
2024-04-17T11:30:59.947867751Z   File "/tmp/8dc5ec898960094/main.py", line 1, in
2024-04-17T11:30:59.947872051Z     from app import create_app
2024-04-17T11:30:59.947875851Z   File "/tmp/8dc5ec898960094/app.py", line 23, in
2024-04-17T11:30:59.947879851Z     from opentelemetry.instrumentation.aiohttp_client import AioHttpClientInstrumentor
2024-04-17T11:30:59.947883951Z   File "/tmp/8dc5ec898960094/antenv/lib/python3.11/site-packages/opentelemetry/instrumentation/aiohttp_client/init.py", line 96, in
2024-04-17T11:30:59.947888251Z     from opentelemetry.instrumentation.utils import (
2024-04-17T11:30:59.947892151Z ImportError: cannot import name 'is_instrumentation_enabled' from 'opentelemetry.instrumentation.utils' (/agents/python/opentelemetry/instrumentation/utils.py)
2024-04-17T11:30:59.947896251Z [2024-04-17 11:30:59 +0000] [128] [INFO] Worker exiting (pid: 128)
2024-04-17T11:30:59.957741696Z [2024-04-17 11:30:59 +0000] [108] [ERROR] Exception in worker process
2024-04-17T11:30:59.957768196Z Traceback (most recent call last):
2024-04-17T11:30:59.957774596Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/arbiter.py", line 609, in spawn_worker
2024-04-17T11:30:59.957779296Z     worker.init_process()
2024-04-17T11:30:59.957783096Z   File "/tmp/8dc5ec898960094/antenv/lib/python3.11/site-packages/uvicorn/workers.py", line 66, in init_process
2024-04-17T11:30:59.957787496Z     super(UvicornWorker, self).init_process()
2024-04-17T11:30:59.957791295Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/workers/base.py", line 134, in init_process
2024-04-17T11:30:59.957795395Z     self.load_wsgi()
2024-04-17T11:30:59.957799195Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/workers/base.py", line 146, in load_wsgi
2024-04-17T11:30:59.957821695Z     self.wsgi = self.app.wsgi()
2024-04-17T11:30:59.957825795Z                 ^^^^^^^^^^^^^^^
2024-04-17T11:30:59.957829795Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/base.py", line 67, in wsgi
2024-04-17T11:30:59.957833995Z     self.callable = self.load()
2024-04-17T11:30:59.957837895Z                     ^^^^^^^^^^^
2024-04-17T11:30:59.957841795Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 58, in load
2024-04-17T11:30:59.957855494Z     return self.load_wsgiapp()
2024-04-17T11:30:59.957859894Z            ^^^^^^^^^^^^^^^^^^^
2024-04-17T11:30:59.957863794Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 48, in load_wsgiapp
2024-04-17T11:30:59.957868094Z     return util.import_app(self.app_uri)
2024-04-17T11:30:59.957872094Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:30:59.957875894Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/util.py", line 371, in import_app
2024-04-17T11:30:59.957879994Z     mod = importlib.import_module(module)
2024-04-17T11:30:59.957883894Z           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:30:59.957887794Z   File "/opt/python/3.11.7/lib/python3.11/importlib/init.py", line 126, in import_module
2024-04-17T11:30:59.957891994Z     return _bootstrap._gcd_import(name[level:], package, level)
2024-04-17T11:30:59.957895994Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:30:59.957899994Z   File "", line 1204, in _gcd_import
2024-04-17T11:30:59.957904794Z   File "", line 1176, in _find_and_load
2024-04-17T11:30:59.957908894Z   File "", line 1147, in _find_and_load_unlocked
2024-04-17T11:30:59.957912994Z   File "", line 690, in _load_unlocked
2024-04-17T11:30:59.957917094Z   File "", line 940, in exec_module
2024-04-17T11:30:59.957921393Z   File "", line 241, in _call_with_frames_removed
2024-04-17T11:30:59.957926293Z   File "/tmp/8dc5ec898960094/main.py", line 1, in
2024-04-17T11:30:59.957930593Z     from app import create_app
2024-04-17T11:30:59.957934493Z   File "/tmp/8dc5ec898960094/app.py", line 23, in
2024-04-17T11:30:59.957938693Z     from opentelemetry.instrumentation.aiohttp_client import AioHttpClientInstrumentor
2024-04-17T11:30:59.957942793Z   File "/tmp/8dc5ec898960094/antenv/lib/python3.11/site-packages/opentelemetry/instrumentation/aiohttp_client/init.py", line 96, in
2024-04-17T11:30:59.957947093Z     from opentelemetry.instrumentation.utils import (
2024-04-17T11:30:59.957950993Z ImportError: cannot import name 'is_instrumentation_enabled' from 'opentelemetry.instrumentation.utils' (/agents/python/opentelemetry/instrumentation/utils.py)
2024-04-17T11:30:59.967453044Z [2024-04-17 11:30:59 +0000] [108] [INFO] Worker exiting (pid: 108)
2024-04-17T11:31:00.025989626Z [2024-04-17 11:31:00 +0000] [118] [ERROR] Exception in worker process
2024-04-17T11:31:00.026028125Z Traceback (most recent call last):
2024-04-17T11:31:00.026034425Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/arbiter.py", line 609, in spawn_worker
2024-04-17T11:31:00.026039025Z     worker.init_process()
2024-04-17T11:31:00.026056025Z   File "/tmp/8dc5ec898960094/antenv/lib/python3.11/site-packages/uvicorn/workers.py", line 66, in init_process
2024-04-17T11:31:00.026060825Z     super(UvicornWorker, self).init_process()
2024-04-17T11:31:00.026064725Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/workers/base.py", line 134, in init_process
2024-04-17T11:31:00.026068925Z     self.load_wsgi()
2024-04-17T11:31:00.026073025Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/workers/base.py", line 146, in load_wsgi
2024-04-17T11:31:00.026077225Z     self.wsgi = self.app.wsgi()
2024-04-17T11:31:00.026081225Z                 ^^^^^^^^^^^^^^^
2024-04-17T11:31:00.026085125Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/base.py", line 67, in wsgi
2024-04-17T11:31:00.026089324Z     self.callable = self.load()
2024-04-17T11:31:00.026093124Z                     ^^^^^^^^^^^
2024-04-17T11:31:00.026097024Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 58, in load
2024-04-17T11:31:00.026101624Z     return self.load_wsgiapp()
2024-04-17T11:31:00.026105724Z            ^^^^^^^^^^^^^^^^^^^
2024-04-17T11:31:00.026109624Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 48, in load_wsgiapp
2024-04-17T11:31:00.026113824Z     return util.import_app(self.app_uri)
2024-04-17T11:31:00.026117724Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:31:00.026121624Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/util.py", line 371, in import_app
2024-04-17T11:31:00.026125724Z     mod = importlib.import_module(module)
2024-04-17T11:31:00.026129624Z           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:31:00.026133524Z   File "/opt/python/3.11.7/lib/python3.11/importlib/init.py", line 126, in import_module
2024-04-17T11:31:00.026137724Z     return _bootstrap._gcd_import(name[level:], package, level)
2024-04-17T11:31:00.026141724Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:31:00.026145624Z   File "", line 1204, in _gcd_import
2024-04-17T11:31:00.026150124Z   File "", line 1176, in _find_and_load
2024-04-17T11:31:00.026154323Z   File "", line 1147, in _find_and_load_unlocked
2024-04-17T11:31:00.026158323Z   File "", line 690, in _load_unlocked
2024-04-17T11:31:00.026162423Z   File "", line 940, in exec_module
2024-04-17T11:31:00.026166523Z   File "", line 241, in _call_with_frames_removed
2024-04-17T11:31:00.026171723Z   File "/tmp/8dc5ec898960094/main.py", line 1, in
2024-04-17T11:31:00.026176023Z     from app import create_app
2024-04-17T11:31:00.026183623Z   File "/tmp/8dc5ec898960094/app.py", line 23, in
2024-04-17T11:31:00.026188023Z     from opentelemetry.instrumentation.aiohttp_client import AioHttpClientInstrumentor
2024-04-17T11:31:00.026192123Z   File "/tmp/8dc5ec898960094/antenv/lib/python3.11/site-packages/opentelemetry/instrumentation/aiohttp_client/init.py", line 96, in
2024-04-17T11:31:00.026196523Z     from opentelemetry.instrumentation.utils import (
2024-04-17T11:31:00.026200523Z ImportError: cannot import name 'is_instrumentation_enabled' from 'opentelemetry.instrumentation.utils' (/agents/python/opentelemetry/instrumentation/utils.py)
2024-04-17T11:31:00.031780135Z [2024-04-17 11:31:00 +0000] [118] [INFO] Worker exiting (pid: 118)
2024-04-17T11:31:00.193856594Z [2024-04-17 11:31:00 +0000] [131] [ERROR] Exception in worker process
2024-04-17T11:31:00.193897793Z Traceback (most recent call last):
2024-04-17T11:31:00.193904793Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/arbiter.py", line 609, in spawn_worker
2024-04-17T11:31:00.193909693Z     worker.init_process()
2024-04-17T11:31:00.193913693Z   File "/tmp/8dc5ec898960094/antenv/lib/python3.11/site-packages/uvicorn/workers.py", line 66, in init_process
2024-04-17T11:31:00.193918093Z     super(UvicornWorker, self).init_process()
2024-04-17T11:31:00.193922893Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/workers/base.py", line 134, in init_process
2024-04-17T11:31:00.193927193Z     self.load_wsgi()
2024-04-17T11:31:00.193930992Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/workers/base.py", line 146, in load_wsgi
2024-04-17T11:31:00.193935092Z     self.wsgi = self.app.wsgi()
2024-04-17T11:31:00.193938992Z                 ^^^^^^^^^^^^^^^
2024-04-17T11:31:00.193942892Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/base.py", line 67, in wsgi
2024-04-17T11:31:00.193947792Z     self.callable = self.load()
2024-04-17T11:31:00.193951692Z                     ^^^^^^^^^^^
2024-04-17T11:31:00.193955592Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 58, in load
2024-04-17T11:31:00.193959692Z     return self.load_wsgiapp()
2024-04-17T11:31:00.193963592Z            ^^^^^^^^^^^^^^^^^^^
2024-04-17T11:31:00.193967592Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/app/wsgiapp.py", line 48, in load_wsgiapp
2024-04-17T11:31:00.193971892Z     return util.import_app(self.app_uri)
2024-04-17T11:31:00.193975892Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:31:00.193979892Z   File "/opt/python/3.11.7/lib/python3.11/site-packages/gunicorn/util.py", line 371, in import_app
2024-04-17T11:31:00.193984092Z     mod = importlib.import_module(module)
2024-04-17T11:31:00.193987992Z           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:31:00.193991892Z   File "/opt/python/3.11.7/lib/python3.11/importlib/init.py", line 126, in import_module
2024-04-17T11:31:00.194009791Z     return _bootstrap._gcd_import(name[level:], package, level)
2024-04-17T11:31:00.194014191Z            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
2024-04-17T11:31:00.194018091Z   File "", line 1204, in _gcd_import
2024-04-17T11:31:00.194022791Z   File "", line 1176, in _find_and_load
2024-04-17T11:31:00.194026791Z   File "", line 1147, in _find_and_load_unlocked
2024-04-17T11:31:00.194030891Z   File "", line 690, in _load_unlocked
2024-04-17T11:31:00.194034991Z   File "", line 940, in exec_module
2024-04-17T11:31:00.194039091Z   File "", line 241, in _call_with_frames_removed
2024-04-17T11:31:00.194044991Z   File "/tmp/8dc5ec898960094/main.py", line 1, in
2024-04-17T11:31:00.194049191Z     from app import create_app
2024-04-17T11:31:00.194053091Z   File "/tmp/8dc5ec898960094/app.py", line 23, in
2024-04-17T11:31:00.194057190Z     from opentelemetry.instrumentation.aiohttp_client import AioHttpClientInstrumentor
2024-04-17T11:31:00.194061290Z   File "/tmp/8dc5ec898960094/antenv/lib/python3.11/site-packages/opentelemetry/instrumentation/aiohttp_client/init.py", line 96, in
2024-04-17T11:31:00.194065690Z     from opentelemetry.instrumentation.utils import (
2024-04-17T11:31:00.194069690Z ImportError: cannot import name 'is_instrumentation_enabled' from 'opentelemetry.instrumentation.utils' (/agents/python/opentelemetry/instrumentation/utils.py)
2024-04-17T11:31:00.208234368Z [2024-04-17 11:31:00 +0000] [131] [INFO] Worker exiting (pid: 131)

Expected/desired behavior

OS and Version?

Windows 7, 8 or 10. Linux (which distribution). macOS (Yosemite? El Capitan? Sierra?)

azd version?

run azd version and copy paste here.

Versions

Mention any other details that might be useful

Thanks! We'll be in touch soon.

omg!! I literally spent 8 hours trying to figure out the issue. Thanks to this post. I just remembered, after reading the post that the error began right after I enabled app insights!! 👎


API Gateway only has ProxyEndpoint

I'm fiddling with zappa, and I have followed through with the basic installation, and deployment.
The issue that I am having is although I have defined paths on my my_app.app,  Zappa generates a proxy handler. Not /test, /hello/user
`from flask import Flask
from messages import person
app = Flask(name)
@app.route("/")
def hello():
p = person.Person()
return p.get_message()
@app.route("/test")
def test():
return "test"
@app.route("/hello/user")
def test_1():
return "hello, jomar"
if name == 'main':
app.run()
`
Upon deploying the app. the api gateway has this result.
https://imgur.com/a/Gvt9Y
I was expecting that /test, and /hello/user will be automatically defined in the API gateway
[Edit URL –@scoates]

Zappa uses the proxy+ integration so that it can forward all requests to the lambda function that it uses to harness your app.
If it tried to do individual routes, the API gateway integration would need to change every time routes change, and Zappa would also need to know how to figure out an exhaustive list of all routes defined in the app.
Is there a specific problem you're trying to solve, here, or was it just unexpected?

Since your application can have dynamic routes, that wouldn't be very good.
In fact, before proxy+ existed, that's how Zappa worked - we literally enumerated 9-deep paths. Deploying took forever. Proxy+ was pretty much implemented by Amazon for us.

When "iam_authorization" is set to true, API Gateway expects headers with V4 signature, however, according to this thread, https://github.com/aws-amplify/amplify-js/issues/3168 , API signing doesn't work with proxy. Is there any workaround for this issue?

@masayang iam signing does work with proxy integration of api gateway. What it doesn't work is using proxy in front of api gw.
Amplify actually uses the same approach, it uses proxy events on api gateway and signs the requests.

We are using our own internal API Gateway using Gloo. It can discover our Lambdas, but we're having trouble invoking our Zappa Lambdas through it, though they work fine with AWS API Gateway and proxy+ ANY.
Gloo uses the Go AWS SDK to invoke, and I'm wondering if there is any documentation on what Zappa Lambdas expect in the InvokeInput ClientContext string ( https://docs.aws.amazon.com/sdk-for-go/api/service/lambda/#InvokeInput ) ?
Assuming the AWS API Gateway proxy+ invocation has some secret sauce in terms of the app.route that gets triggered, by passing in the request route in some way.


Use algolia search in docs

Motivation: Default search box kinda sucks, Mendable is slow
Played around with Algolia search box, kinda nice? 🤷

Some issues:

searchbar doesn't turn dark mode when page turns dark mode
command + K shortcut clashes with Mendable 😢

Possible dark mode hacks? https://discourse.algolia.com/t/dynamic-dark-mode-support-a-la-media-prefers-color-scheme-dark/15004/6

Yea the dark mode is unfortunate. I'll quickly try to see if I can hack it
The search is also slightly outdated (some links are 404). Not sure how it works for refreshing

There we go, CSS should be much nicer in dark mode now

huh weird, it works locally but not on the docs preview 🤔


Receiving 405 for deleting the Multi-Variate Flags value

I was exploring the open-source version of the flagsmith. While exploring I created a feature flag with a 'multi-variate' value.
I was trying to delete one of the existing variation values from the admin UI.
When I'm triggering the deletion request it's failing with an HTTP error-code 405 which is of the 'DELETE' type.  How can I delete the existing variation data?
Attaching the screenshot for reference.

@kyle-ssg I think this would be resolved if you add the trailing slash to the delete request. At the moment, it's trying to redirect to DELETE /api/v1/projects/1/features/3/mv-options/6/ and perhaps being routed elsewhere by the node proxy that's used in the open source version?

This would make sense since the SaaS version doesn't experience this, this has been adjusted now, please feel free to reopen if this doesn't solve your issue @ram2104

It's working as per expected. Thanks @kyle-ssg  & @matthewelwell


SAK-31768 - Upgrade JavaMail from 1.4.5 to 1.6.2

The current Java Mail library is from 2012!
I think it could be good to upgrade it to a newer version, I upgraded it locally and tested all the modules with a FakeSMTP server, it's working fine, this is an example of the SMTP debug:
`DEBUG: JavaMail version 1.6.2
DEBUG: successfully loaded resource: /META-INF/javamail.default.address.map
DEBUG: getProvider() returning javax.mail.Provider[TRANSPORT,smtp,com.sun.mail.smtp.SMTPTransport,Oracle]
DEBUG SMTP: useEhlo true, useAuth false
DEBUG SMTP: trying to connect to host "localhost", port 25, isSSL false
220 host.docker.internal ESMTP SubEthaSMTP null
DEBUG SMTP: connected to host "localhost", port: 25
EHLO host.docker.internal
250-host.docker.internal
250-8BITMIME
250-AUTH LOGIN
250 Ok
DEBUG SMTP: Found extension "8BITMIME", arg ""
DEBUG SMTP: Found extension "AUTH", arg "LOGIN"
DEBUG SMTP: Found extension "Ok", arg ""
DEBUG SMTP: use8bit false
MAIL<EMAIL_ADDRESS>250 Ok
DEBUG SMTP: sendPartial set
RCPT<EMAIL_ADDRESS>250 Ok
RCPT<EMAIL_ADDRESS>250 Ok
DEBUG SMTP: Verified Addresses
DEBUG SMTP<EMAIL_ADDRESS>DEBUG SMTP<EMAIL_ADDRESS>DATA
354 End data with .
Date: Fri, 16 Oct 2020 11:27:59 +0200 (CEST)
From: "On behalf of<EMAIL_ADDRESS><EMAIL_ADDRESS>Reply-To<EMAIL_ADDRESS>Message-ID<EMAIL_ADDRESS>Subject: TESTING THE LIBRARY :DDD
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Content-Type: text/html; charset=utf-8
----------------------This forwarded message was sent via WebLearn Messages from the  "TESTING_SITE" site.
To reply to this message click this link to access Messages for this site: TESTING_SITE----------------------To: All ParticipantsFrom: Sakai Administrator -<EMAIL_ADDRESS>:DDD
.
250 Ok
DEBUG SMTP: message successfully delivered to mail server
QUIT
221 Bye
16-Oct-2020 11:27:59.183 INFO [http-nio-8080-exec-1] org.sakaiproject.email.impl.BasicEmailService.sendToUsers sendToUsers: headers[ Content-Type: text/html; charset=utf-8 From<EMAIL_ADDRESS>Subject: TESTING :DDD] to[<EMAIL_ADDRESS><EMAIL_ADDRESS>`

Can one of the admins verify this patch?


Highest Severity in report summary reported as "Unknown"

Describe the bug
There is a situation where the "Highest Severity" in the report summary is reported as "Unknown" when details shown that it's in fact HIGH or CRITICAL. CVSS is higher than 7.

Version of dependency-check used
The problem occurs using version 6.5.3 of the Maven plugin.
Log file
[INFO] --- dependency-check-maven:6.5.3:aggregate (default-cli) @ cucumber ---
[INFO] Checking for updates
[...]

Dependency-Check is an open source tool performing a best effort analysis of 3rd party dependencies; false positives and false negatives may exist in the analysis performed by the tool. Use of the tool and the reporting provided constitutes acceptance for use in an AS IS condition, and there are NO warranties, implied or otherwise, with regard to the analysis or its use. Any use of the tool and the reporting provided is at the user’s risk. In no event shall the copyright holder or OWASP be held liable for any damages whatsoever arising out of or in connection with the use of this tool, the analysis performed, or the resulting report.

   About ODC: https://jeremylong.github.io/DependencyCheck/general/internals.html
   False Positives: https://jeremylong.github.io/DependencyCheck/general/suppression.html

💖 Sponsor: https://github.com/sponsors/jeremylong

[INFO] Analysis Started
[INFO] Finished Archive Analyzer (0 seconds)
[INFO] Finished File Name Analyzer (0 seconds)
[INFO] Finished Jar Analyzer (0 seconds)
[INFO] Finished Dependency Merging Analyzer (0 seconds)
[INFO] Finished Version Filter Analyzer (0 seconds)
[INFO] Finished Hint Analyzer (0 seconds)
[INFO] Created CPE Index (1 seconds)
[INFO] Finished CPE Analyzer (2 seconds)
[INFO] Finished False Positive Analyzer (0 seconds)
[INFO] Finished NVD CVE Analyzer (0 seconds)
[INFO] Finished RetireJS Analyzer (1 seconds)
[INFO] Finished Sonatype OSS Index Analyzer (1 seconds)
[INFO] Finished Vulnerability Suppression Analyzer (0 seconds)
[INFO] Finished Dependency Bundling Analyzer (0 seconds)
[INFO] Analysis Complete (5 seconds)
[INFO] Writing report to: /Users/marcelstoer/*********/target/dependency-check-report.html
[WARNING]

One or more dependencies were identified with known vulnerabilities in Cucumber to AsciiDoc Generator:

commons-io-2.6.jar<EMAIL_ADDRESS>cpe:2.3:a:apache:commons_io:2.6:*:*:*:*:*:*:*) : CVE-2021-29425
junit-4.12.jar<EMAIL_ADDRESS>cpe:2.3:a:junit:junit4:4.12:*:*:*:*:*:*:*) : CVE-2020-15250
messages-14.0.1.jar/META-INF/maven/com.google.guava/guava/pom.xml<EMAIL_ADDRESS>cpe:2.3:a:google:guava:29.0:*:*:*:*:*:*:*) : CVE-2020-8908
messages-14.0.1.jar/META-INF/maven/com.google.protobuf/protobuf-java/pom.xml<EMAIL_ADDRESS>cpe:2.3:a:google:protobuf-java:3.14.0:*:*:*:*:*:*:*) : CVE-2021-22569
plexus-utils-1.5.15.jar<EMAIL_ADDRESS>cpe:2.3:a:plexus-utils_project:plexus-utils:1.5.15:*:*:*:*:*:*:*) : CVE-2017-1000487, Directory traversal in org.codehaus.plexus.util.Expand, Possible XML Injection

See the dependency-check report for more details.

[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  09:25 min
[INFO] Finished at: 2022-02-25T09:43:18+01:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.owasp:dependency-check-maven:6.5.3:aggregate (default-cli) on project cucumber:
[ERROR]
[ERROR] One or more dependencies were identified with vulnerabilities that have a CVSS score greater than or equal to '7.0':
[ERROR]
[ERROR] plexus-utils-1.5.15.jar: CVE-2017-1000487
[ERROR]
[ERROR] See the dependency-check report for more details.

To Reproduce
Steps to reproduce the behavior:

Not sure...I think adding plexus-utils-1.5.15.jar to any Maven project should yield this.

Expected behavior
"Highest Severity" should always report the highest that was found.
Additional context
See reported details (for the relevant dependency) below. I am not sure how to correctly interpret this but I see both HIGH & CRITICAL and "Unscored".

"Highest Severity" should always report the highest that was found.

An unknown (because not CVSS-scored) severity level in my view should always be assumed to be the worst possible score - until proven otherwise by assigning it the appropriate CVSS score, so I tend to say that 'unknown' is properly labeled as the highest found severity (base score 10.0 until proven otherwise)

Understood, thanks. Looks like a corner case then. If the scored vulnerability is CRITICAL then it's irrelevant what the unscored ones are effectively. The overall severity should be CRITICAL.

@jeremylong @marcelstoer Have taken a look how we might improve here and as a proof-of-concept updated the vulnerability natural order and updated the HTML report to take advantage of it in branch issue-4112 would like to hear your thoughts on this.
The code on the branch will list plexus-utils appropriately as highest severity CRITICAL (based on the fact that the highest ranking severity of 'known severiy' issues is already a CVSS v3 CRITICAL issue)


Support new bump dependencies label

https://github.com/conan-io/conan-center-index/labels/Bump dependencies
Was added

Checking out

The bot needs to:

Modified lines always have requires
Support multiple conanfile.py (exclusive file)


adding ability to remove framework cruft

from cluster along with zook…eeper nodes
This seems best in packages since it is frameworks that leave this behind.

This is ready for review / merge.  I've tested it working.


New "unit": Count per square meter

I don't know at what level this could be implemented, but there is a need for a count per square meter (for example, plant population) as a unit. How could this be handled?

This unit can be requested of the Unit Ontology: https://www.ebi.ac.uk/ols/search?q=count&ontology=uo at their issues board: https://github.com/bio-ontology-research-group/unit-ontology/issues .  They have an additional curator so things should move along a bit more.

Added PR in bio-ontology-research-group/unit-ontology#40 including term 'count per square meter'


Asynchronous job submission and removal

This solution is using asyncio.create_subprocess_exec and similar to what was done in PR #473.
However, this other PR lacked an update job removal, which is included here.
The test_jobqueue_job_call required an overhaul to make it compatible with the async code. Its form is basically the same as the other async tests now.
In issue #470 another solution using run_in_executor was proposed. I consider the solution with create_subprocess_exec more rigorous though, because with create_subprocess_exec the code is fully using the async API, instead of wrapping non-async functionality in a run_in_executor call.

I have removed the weakref.finalize call here, which was one way to remove jobs at program exit. This is because finalize interferes with the fact that _close_job is a coroutine now. At program exit, Distributed already takes care of job removal here
https://github.com/dask/distributed/blob/8e0c79bb82b5d9e3f4f9538935520da960588df6/distributed/deploy/spec.py#L692C1-L692C1
In fact, before this PR, jobs were removed twice, which made the program exit unnecessary lengthy.
There is one issue left however: As you can see in the linked Distributed code, there is a timeout of 10 seconds. This is not enough to remove much more than 350 jobs (at least in my tests with HTCondor). One may want to ask to increase this timeout.

@jacobtomlinson could you take a quick look at this? I'm not familiar enough with asyncio to give a good advice.

Hi @jrueb, sorry again for the delay... It looks there is formatting problem in the source code, which sounds a little weird considering you didn't touch some of these files...
Could you check flake8 and black output?

I adjusted the 8 files black was complaining about (removal of blank lines). The PR did not touch the files before though, meaning these blank lines where there before.

It is unclear what the CI's issue is. The black of pre-commit run --all-files is passing for me and besides core.py this PR does not touch any of these files.

The PR did not touch the files before though, meaning these blank lines where there before.

this PR does not touch any of these files.

Yeah, I know, you are totally right. I won't block here because CI fixing is unrelated to your changes. I shouldn't have asked you to fix it in the first place.  Sorry it messes up a bit your changes.
Would you prefer to revert your last commit? Or are you OK that I merge as is?

Would you prefer to revert your last commit? Or are you OK that I merge as is?

Either is fine for me. If it's the easiest to merge as is, I'm okay with that.

Is anything else needed for this PR?

Sorry for the lack of follow-up, I'll merge this one as is, as we opened an issue to fix the CI.


added function to validate credentials

New function will allow users to validate their credentials and return a bool depending on validity

Very useful. I would love to see a snippet added to the README.md on how to use it. If you're feeling up to it, you could also add support for it in the cli.py. If not, that will probably have to be added to the roadmap


Clean up stale binary after name change with windows msi updater

Recent beta builds are no longer renaming the binary in a bundle to productName, keeping the rust crate name.
The issue we're facing at KittyCAD/Zoo is that running the updater installs our new zoo-modeling-app.exe binary (new name) in the Zoo Modeling App directory, but doesn't remove the existing Zoo Modeling App.exe (old name), leaving it stale for the user to potentially get confused about.

Is there a hook we could use to run some type of clean up script for that stale executable as we forge ahead with the tauri dependency bump that requires this binary executable name change? I'm assuming other tauri users would be in the same boat as the rust crate names are much more restrictive on what characters they allow (for instance, no space).
Thank you!

I agree it's nice to have an easy way of setting beta/dev names so they can be installed alongside release versions.

Related for tracking:

https://github.com/tauri-apps/tauri/issues/10548
https://github.com/tauri-apps/tauri/pull/9375
https://github.com/gitbutlerapp/tauri/pull/1

Closed by #10962


Authorization only for a certain room or namespace

Hi,
I'd like to send both authorized and unauthorized data with one connection. E.g.
on connect:
  push public data
  if authorized:
    also push private data

Is this possible with the current implementation?

This is possible now, check the latest version and this example:
https://github.com/auth0/socketio-jwt/blob/master/test/fixture/namespace.js
sorry for the delay


feature request: add seperate function for full-text-search for filters

We are attempting to use qdrant's full text filters in order to be able to move our filtering logic to solely qdrant, however we were facing issues with the fact that qdrant's rust client only support full text matching when there is a space added to the end.
We want to be able to use qdrant's full text and substring filtering as a replacement for the LIKE queries that we perform in pg as of rn, however, in certain cases where we have multi word filters or single word filters, the logic would behave unpredictably.
Here is a link the the gist that contains our filtering logic: https://gist.github.com/skeptrunedev/3ede217aa78d6462c5c52c63d0318764.
The easiest solution to this issue is probably adding a separate full text match function like python does.
Thank you so much for a first class rust client and an amazing SVD!!

Resolved with #86.


Add Victoria Hochschule

@MxMartin lib/domains/de/victoria-hochschule: this request has an incorrect file path format, please ensure that you are familiar with     this repository rules located at the bottom of this page and change     your request accordingly. If you don't know how to change request, close it and open a new one.     If you are not able to make the pull request according the instructions, please send us an email to<EMAIL_ADDRESS>Please mention this request URL in the message.

@philipto Ah, dang, thanks for pointing that out! I updated the pull request

@MxMartin First stage of verification passed, official domain is victoria-hochschule.de as far as I verified. This is just an informational note. Pull request is still in the review. I appreciate your patience while waiting for the final decision.

@philipto  If that helps: The university changed its name from hwtk to Victoria in 2020 and there is an approved domain from the old name here: https://github.com/JetBrains/swot/tree/master/lib/domains/de/hwtk
You can find the official announcement here: https://www.victoria-hochschule.de/umbenennung-aus-der-hwtk-wird-victoria/

@MxMartin Thank you for your patience while waiting for a review and processing your request. Pull request merged.


Fixes indestructible mop buckets

About the PR
fixes #24992, mop buckets are now destructible
Why / Balance
immersion I guess? Idk.
Media

[x] I have added screenshots/videos to this PR showcasing its changes ingame, or this PR does not require an ingame showcase

Changelog
:cl:

fix: fixes mop buckets being indestructible.

why it made of wood
Wooden mop bucket yucky plastic mop bucket :godo:

why it made of wood Wooden mop bucket yucky plastic mop bucket :godo:

removed all the wood.


Tools to analyze smart contract immutability

A subcategory of smart contracts is library smart contracts.
Library contracts have common functionalities that are deployed once to the blockchain and multiple contracts can rely on them by calling their functions.
Given a library contract how do we know if their behavior is completely static?
This issue lists tools that analyze smart contract immutability.

Given a library contract how do we know if their behavior is completely static?

A easy case if when they declare no state/variable.

https://github.com/a16z/metamorphic-contract-detector pointed by Karolina
is definitely related, we should give it a try and look how it's implemented

In Code We Trust? DPM 2017

See "In Code We Trust? Measuring the Control Flow Immutability of All Smart Contracts Deployed on Ethereum" DPM 2017
No tool available.


Socket.IO Java/Android

Hello,
for my project (https://github.com/Schnup89/ioBroker_WearV2) I've used the iobroker socket.io adapter and I want to migrate it to the websocket adapter.
I've used socket.io java client (v1.0.1) for android to get the data from socket.io (v2.x) iobroker server.
https://socketio.github.io/socket.io-client-java/installation.html
This adapter is installed and running on port 8085, but with the socket.io client v1.0.1 or v2.0.1 I always get "parse error".
Should it be possible with socket.io library out of the box or is there any modification necessary?

In fact for socket.io pöease use the socket.io adapter :-) Pure ebsockets are more simple and you simply connect using anwebsocket and NOT socket.io. (For your info: socket.io is using websockets but also having long polling fallbacks and such things and these are NOT existent on "pure websocket adapter"

Thank you for your fast answer.
Let me ask two more questions:
I have some trouble getting SocketIO (v1.01) working stable/reliable on android and I'm currently reworking the code so would you advice to change to this websockets adapter?
If yes, is there any documentation which url has to be requested?
http://iobroker.lan:8084/ always gives me "Not Implemented"
With socket.io on Port 8085 it respond on http://iobroker.lan:8085/socket.io/

but in fact socket.io 1 is veeery old and outdated!

That's exaclty my problem, Socket.IO Java Client v1 is outdated and Socket.IO Java Client v2 is only compatible with Socket.IO Server 3.x and 4.x which is not provied by the iobroker socket.io adapter.
Because of this I would rewrite my code to use this (the iobroker websockets adapter) but I don't know how start/call the websockets api

But then the 1.x client should work with the 2.x server in the adapter ... whats exactly the issues?

Since 1.x Client is outdated and I can not use the 2.x Client with the "ioBroker Socket.IO-Adapter" or "ioBroker WS-Adapter" I would like to know how I can make http request (over websockets) to get data from through this adapter

In fact use a websocket client and connect against the port of the ws adapter with kind of ws://ip:port ... there should be nothing more needed. There is a javscript browser example in https://github.com/ioBroker/ioBroker.ws/blob/main/example/conn.js#L259

Thanks you! First connection was successfull, I hope the connection is more stable with the native websockets.


using -g option and embedding on a webpage, is it possible to have the correct download filename for the name of the video

Please follow the guide below

You will be asked some questions and requested to provide some information, please read them carefully and answer honestly
Put an x into all the boxes [ ] relevant to your issue (like that [x])
Use Preview tab to see how your issue will actually look like

Make sure you are using the latest version: run youtube-dl --version and ensure your version is 2017.02.16. If it's not read this FAQ entry and update. Issues with outdated version will be rejected.

[ x] I've verified and I assure that I'm running youtube-dl 2017.02.16

Before submitting an issue make sure you have:

[x ] At least skimmed through README and most notably FAQ and BUGS sections
[x ] Searched the bugtracker for similar issues including closed ones

What is the purpose of your issue?

[ ] Bug report (encountered problems with youtube-dl)
[ ] Site support request (request for adding support for a new site)
[ ] Feature request (request for a new functionality)
[x ] Question
[ ] Other

The following sections concretize particular purposed issues, you can erase any section (the contents between triple ---) not applicable to your issue

If the purpose of this issue is a bug report, site support request or you are not completely sure provide the full verbose output as follows:
Add -v flag to your command line you run youtube-dl with, copy the whole output and insert it here. It should look similar to one below (replace it with your log inserted between triple ```):
$ youtube-dl -v <your command line>
[debug] System config: []
[debug] User config: []
[debug] Command-line args: [u'-v', u'http://www.youtube.com/watch?v=BaW_jenozKcj']
[debug] Encodings: locale cp1251, fs mbcs, out cp866, pref cp1251
[debug] youtube-dl version 2017.02.16
[debug] Python version 2.7.11 - Windows-2003Server-5.2.3790-SP2
[debug] exe versions: ffmpeg N-75573-g1d0487f, ffprobe N-75573-g1d0487f, rtmpdump 2.4
[debug] Proxy map: {}
...
<end of log>

If the purpose of this issue is a site support request please provide all kinds of example URLs support for which should be included (replace following example URLs by yours):

Single video: https://www.youtube.com/watch?v=BaW_jenozKc
Single video: https://youtu.be/BaW_jenozKc
Playlist: https://www.youtube.com/playlist?list=PL4lCao7KL_QFVb7Iudeipvc2BCavECqzc

Note that youtube-dl does not support sites dedicated to copyright infringement. In order for site support request to be accepted all provided example URLs should not violate any copyrights.

Description of your issue, suggested solution and other information
Hi, I'm trying to embed a video i'm hosting on youtube on a webpage that i'm hosting. So far it's working fine by using the -g option and taking that url and embedding it into my site with the  tag. The problem is that when i right click and say "save as" under the video i get a file named videoplayback.mp4 Basically is there a way of auto naming the file to the right one on youtube, rather than videoplayback. Basically what i'm trying to do is so when a user right clicks and says save as it's automatically the right name, and not videoplayback. I understand how the -g option works, but so far i haven't found a solution for this. I've tried with the -o option but combined with the -g option gives an error for youtube-dl  saying that no valid url was entered. again my main goal is to have the correct filename when a user right clicks and says "save as". I'm not sure if this is possible, but for my website it is necessary. If anyone has any other ideas on how to change the filename automatically, with or without using youtube-dl please let me know.
Thanks,
Brian
Explanation of your issue in arbitrary form goes here. Please make sure the description is worded well enough to be understood. Provide as much context and examples as possible.
If work on your issue requires account credentials please provide them or explain how one can obtain them.

Parse the result of -j and add Content-Disposition header.


docs: fix typo

Description
Nitpick - fairly trivial, missing word makes the sentence a tiny bit more confusing.
Also, a first commit and PR just to get familiar. Thanks!
Issue

Closes: # N/A

Closing to reopen a clean PR after signing agreement, etc.


TF-A build failed on Pine64-A64+

ARM-Trusted-Firmware build will fail on Pine64 A64 plus.

https://github.com/buildroot/buildroot/blob/a7bf844813e2527267cb0a98eb73a0e4bdf04f99/boot/arm-trusted-firmware/arm-trusted-firmware.mk#L112-L118
Buildroot set ENABLE_STACK_PROTECTOR option according to project SSP configuration.