Results problems

Hi,
I used proovread to correct my Nanopore Direct RNA sequencing data with illumina sequencing data, but the output .trimmed.f[aq] data is so small. The ori long-reads fastq data is 788M, however, the output .trimmed.fastq only 27M, the output .trimmed.fasta only 14M , and the .untrimmed.fq is 674M.
In  .untrimmed.fq, the sequence contains a large number of "N" as following:
"""
@0a0a1a5d-1c34-49eb-8bbc-d2373b5bf9d5_Basecall_1D_template
CACAANNNNCAGANACNCNGAANCGAAGCNAAAGANNCGCNGCCANGGACGCCNNGCNGANNCCGNCGNANNGANCCACCAGAGACNNCGCNNAAGGANAGNANNCGNNCGNNAAGCGNNGCCACAAGCCAGANCGCAAAAGAANNNGAAAGNNGCAGNNNGNCNGCGANNAAGNNNGNGGNAAANAGGANACNNGCGNNCNNNGNGAAGCNGNNNCANNNCCGANCAACAACANCANCGNCGGNGCCACNNAGAAAGCAAAGGANACACCANGGNNCGGNNNANGNNNGAGAAGGAAGANNNGAGGNNANCGNGNNNNNAGNGAAAGGCACCGGNNNCAGNNNGNGNNNNGNGNAANGGANCCGNNNNGNNCAANGNNNNNNNGGNNCNNNNGNNNACNGAAAANCGACGNNNNGAANGNAAAGAGCAAACNAANNNAAAGCNGNGGGANNCGCNGANGCCAGCNNGGNCNGNNCACNAANCCCCACACACNCCCACCANNNANNCCNCGCCCANCCAAANCCAGG
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@0a0a5b3d-3ae7-41c8-a9f9-231ca7fc22d4_Basecall_1D_template
CNGAAAACCAAAAGAAGAAGAGAAACAACAAGAAGAAGNAANGGTGNCTTCCTCTATGTTCTCCTCCACCGCNGNGGNNACCCTCCCCGGCNCAAGCCACCATGGNCGCNCCATTCACCGGCTTGAAGTCATCCGCTTCTTTNCCCGGTCACCCGCAAGGCCAACAACGACNACTGCCATCACAAGCAACGGAGGAAGAGTTANGCNGCATGAAGGGTGGCCACCAATCGGAAAGAAGAAGNNGAGACTCNANCNCCCNGACCNNCNGGNGACGNNGAANNGGCNAAGGGAAGNNGACNACCNCNCCGCANCAAGNGGANNCCNGNGNNGAANCAGNNGGAGCACGGANNNGCGGNCCNNGAGCACGGAAAACACNCCCGGANACNANGANGGACGANACNGGACAANGNGGAAGCNNCCAACNGNNCGGANGCACCACCGACNCCGCNCNGAGNGNNGAAGGAAGNNGAAGAAAACGGCAAGAAGGAGNACCNGGCGCCNNNANGGGANCANCGGANNNCCGACAACACCCGNCAAGNCCAANGCANCAGNNNNCANNGCCCNAAGCCCCAGCNNCNCCNNGGGNCNAANCCCCNNCNGGAANANNCAGCGNNGANNANNANNCNGGAACACCANNNCNANGNGGNCAANGCAAANNNAAGAAANNANNNGCCGANCGCAGNNGAGGAACNANNGNNNGAAAGNGAAAANGNNANNCCNANCAGNNNCNAANNANAGNNANCANNCAAANCCCANCCCANNNCANCCANCCCANCCCNANCCAAAANCCCNCAGG
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@0a0a6f37-23c3-466c-baef-d43fff52a4de_Basecall_1D_template
NGGAGAGNAAAGNAGAACAANGCCGAANCCNNANGNNCCGCANANNGNNGCCAAACGGGCCNNNANAGCACGCNCCACAACGGACNNAAGNCCNCGCNGCACCNNCCCCAGCCACCCGCAGGCNAACCNACAGGCNACNNCCAACACAAGCAACGGCGGAGNNANNGCANANGCAGGNGNGGCACCACGNGANNGGAAAAGNAGAGNNNGAGACNCNNNNCCNNCCNGACCNNNCGANNCCNAANNGGGCNAAGGAAGNNGNANCACCCNCANCCGCCAACAAGNNGGANNCCNNGNGNNGAANNCGAGNGGGAAAANACGGANNNANNGNACCGNGAGCACGGNAACNNNCCCGGANANCGNGANGGACGGNACNGGACAANGNGAAGCNNCCCCNGNNCGGNNGCACCGAACNCCGCNCNAAGNGNNGAAGGAAGNAGAAGAGNGCAAGAAGGAGNACCCCAANGCCNNNANGGAGNACANGGANNNCGACAACACCCGNCAAGNCCAGNGCANCAGNNNANNGCCNCACAAGCCACCAAGCNNCGGNNAANNNCCCNNCNGCNNNGNGNAAACCNCAANANNNNANCCCCCCANNGANNNNANCCCNNGNNNNNCNGCNNNNNCNNNNGAGGNNNNAANCNCCGGACNNAACGNNNGNNNNCCACGGNNGCGAGNNNANNNANCGGANNCNCANNGNNNAGCGCAANAANANGNNGNNNAANCCCCAACCCCNACNCCANCCCACCANNNANCCNNCANNACANCCANCCCACCAANNNACACNCCAANCCANN
+
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
"""
I used illumina short-read data is 150bp and Illumina reads 1 and 2 were merged into fragments
using FLASH at least 30X.
I don't know what the problem is. Can you give me some advice?  Thanks

Can you send me the log from the proovread run. That would help me understand where things might have gone wrong.

col0_1qf.log
This is the log, thanks.

Have a look at https://github.com/BioInf-Wuerzburg/proovread#log-and-statistics, which explains how to read the proovread log. In you case there seems to be an issue with mapping to the nanopore reads.
[Wed Sep 11 10:27:28 2019] Running mode: mr
[Wed Sep 11 10:31:37 2019] Running task bwa-mr-1
[Thu Sep 12 13:22:14 2019] Masked : 26.8%
[Thu Sep 12 13:22:14 2019] Running task bwa-mr-2
[Fri Sep 13 11:18:02 2019] Masked : 27.9%
[Fri Sep 13 11:18:57 2019] Running task bwa-mr-finish
[Sat Sep 14 01:55:09 2019] Masked : 30.0%

These values should be on the order of 80% in good runs. proovread is optimized for PacBio, not for Nanopore. The error profiles between the technologies differ, and it seems here, the mapping is just not sensitive enough for your data. Unfortunately, I don't think there is a good way to increase proovread's sensitivity enough to get good results for your data. You might want to look at other programs that deal with nanopore data specifically.


Add SET PARAMS operator for test purposes

SET PARAMS = {
	foo:'bar',
	fromId:1,
	toId:2
};

CREATE EDGE link from (select from Owner where id = :fromId)
TO (select from Owner where id = :toId) SET foo = :foo;

ASSERT 1;

Additional syntax to change properties in params:
   alasql('SELECT VALUE $0;  SET $0 = 200; SELECT VALUE $0',[100]);
   // [100,1,200]

Currently AlaSQL supports SET for params values, like:
    var mypar = {mydata:200};
    alasql('SET $mydata = $mydata+100', mypar);
    console.log(mypar.mydata);
    // returns 300

This $-like assignments done for compatibility with OrientDB, which uses $ for local variables (instead @, as many other databases do).

The more I think about it - the better it sounds with plugin system for flavour specific behaviour...


Issue #224: Handling single-value appends

Fixes #224
Changes:
IdentityToZeroTransformation:

it should always be superseded except by another IdentityToZeroTransformation with the same identityValue
IdentityToZeroTransformation.merge(other) = other

NullToZeroTransformation:

it should always be superseded except by another NullToZeroTransformation
NullToZeroTransformation.merge(other) = other

Both IdentityToZeroTransformation and NullToZeroTransformation are deprecated.
IdentityTranformation(identityValue) is used as a replacement.

it maps both null and identityValue to zero
IdentityTranformation(a).merge(IdentityTranformation(b)), with a < b, returns LinearTransformation(a, b)
IdentityTranformation(null).merge(IdentityTranformation(a)) returns IdentityTranformation(a)

LinearTransformation can only be superseded by

another LinearTransformation
an IdentityTranformation
an IdentityToZeroTransformation

LinearTransformer can only create either a LinearTransformation or an IdentityTransformation
Checklist:
Here is the list of things you should do before submitting this pull request:

[x] New feature / bug fix has been committed following the Contribution guide.
[ ] Add logging to the code following the Contribution guide.
[ ] Add comments to the code (make it easier for the community!).
[ ] Change the documentation.
[x] Add tests.
[x] Your branch is updated to the main branch (dependent changes have been merged).

Just missing a doc file or section describing briefly the Transformations. Then I would merge


chore(main): release 1.251.1

When this PR is merged, a new tagged release will be created with the notes below.
1.251.1 (2024-01-29)
Bug Fixes

Fix deferred Session Replay payloads (#868) (f69e4b0)
Pass unload options to simultaneous harvests in Session Replay (#870) (655aa5d)

This PR was generated with Release Please. See documentation.

:robot: Release is at https://github.com/newrelic/newrelic-browser-agent/releases/tag/v1.251.1 :sunflower:


new feature for file reupload

Is possible to do something like ?
Images.update(_id, { file: file })
I need reupload previously uploaded file without change of _id, but in docs i dont find recipe. Thanks

Hello @mizsha ,
Currently this is not possible.
I'll keep it as feature request.

Discussion at: #309 , please participate if you need this feature, see this comment
Related #291


java.unil.Date.toString() result is missing dd part

just to report, according to
http://docs.oracle.com/javase/7/docs/api/java/util/Date.html#toString()

Converts this Date object to a String of the form:
dow mon dd hh:mm:ss zzz yyyy

but the  implementation is missing the dd part:
https://github.com/scala-js/scala-js/blob/master/javalib/src/main/scala/java/util/Date.scala#L119

Duh. Thanks for the report.


Should vendor-prefixer load before the camel-case plugin?

Just want to double check. I'm currently loading vendor-prefixer, then camel-case.

thanks for checking, just realized the order in readme is wrong, vendor prefixer expects dasherized syntax and so if camel case is used  camel-case plugin needs to be applied first

Maybe plugins can specify certain plugins that they should run after, if present.

This would mean plugins know each other and this is bad.

I don't know a better way than documentation. Middelware serverside can also depend on order.


Do you think this project could collect more money to push it forward if it was written on Scala?

Question really.
Just wondering. Would it be good reason to start writing this project on Scala. It is not that I want sabotage it on any way (or to be a troll) - more just personal wonder. But I guess the author of FP on Scala might show nice example of what might be done in scala, and I believe there will be much more people willing to contribute or argue to/on this project that seems has nice ideas in it anyway, to push it forward. Or Scala is not good enough for that type of project not FP-pure enough maybe.

Mostly probably not performant enough. Scala has bad optimisation problems. No tail call recursion. Plus it runs on the JVM and not in "native" code.
Technically maybe. But the effort required would not justify it, I think, even if Scala was an equally good choice from a performance standpoint.

https://reddit.com/r/haskell/comments/1pjjy5/odersky_the_trouble_with_types_strange_loop_2013/cd3bgcu

The project won't be switching to Scala. Maybe it would attract more attention if it used Scala, dunno, but I much prefer using Haskell for a project like this. Let's just leave it at that. :)


Is this package still maintained?

There are 24 open PRs, some of which could be very easily merged, and 28 issues. @jossmac seems to be pretty active on Github with other packages, yet is nowhere to be found on this repo. The last time he replied to an issue was in February 2018 !
Why can't other core maintainers be added ? Or let's fork ?

Indeed the last merge was back in June. Do we know if @jossmac has been contacted about adding more maintainers through methods other than on here?
I'd say if that is tried and we don't hear anything then fork and carry on ¯_(ツ)_/¯

I've forked this and pushed it to NPM.
I've also merged some PRs into the fork.
https://github.com/davwheat/react-images-maintained

As mentioned, I'm not very active with this repo anymore. I still believe in Open Source, but got really burnt out. I have to prioritise my family.
Please raise your hand if you'd like to be a maintainer 👋
Or, obviously just fork / take want you like from the lib.

✋ I'd happily (try my best) to maintain it!

@davwheat invitation sent. What's your username for npm?

Thanks a bunch. Npm username is the exact same as on here.
On Sun, 24 Nov 2019, 22:50 Joss Mackison<EMAIL_ADDRESS>wrote:

@davwheat https://github.com/davwheat invitation sent. What's your
username for npm?
—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/jossmac/react-images/issues/331?email_source=notifications&email_token=ABYQJZVKUKRDL7Z6NZG3H3TQVMAMHA5CNFSM4JLSXCOKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFAW6ZI#issuecomment-557936485,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/ABYQJZVBRCYLJQ7NWWTLQ7DQVMAMHANCNFSM4JLSXCOA
.

@jossmac Thanks for stopping by :-) Family comes before everything else! Take care! 💪

Hey guys! A pinch to zoom feature for mobile devices would be very appreciated =)!

I completely agree with you. Could you open up another issue as this one
has been closed and is unrelated?
Thanks!
On Thu, 28 Nov 2019, 21:57 mhedengren<EMAIL_ADDRESS>wrote:

Hey guys! A pinch to zoom feature for mobile devices would be very
appreciated =)!
—
You are receiving this because you modified the open/close state.
Reply to this email directly, view it on GitHub
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or unsubscribe
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.


/events: Move WithClock to unit build tagged file

Reverts https://github.com/dapr/kit/pull/62
WithClock should be moved to unit build tagged files to not pollute implementation non-test builds. Developers wanting to override the clock in testing can do so by go testing with the unit build tag.

Codecov Report
All modified lines are covered by tests :white_check_mark:

:exclamation: No coverage uploaded for pull request base (main@a043330). Click here to learn what that means.

Additional details and impacted files
@@           Coverage Diff           @@
##             main      #63   +/-   ##
=======================================
  Coverage        ?   81.05%
=======================================
  Files           ?       40
  Lines           ?     2328
  Branches        ?        0
=======================================
  Hits            ?     1887
  Misses          ?      317
  Partials        ?      124

Files
Coverage Δ

events/batcher/batcher.go
87.50% <ø> (ø)

events/batcher/batcher_unit.go
100.00% <100.00%> (ø)

events/queue/processor.go
90.21% <100.00%> (ø)

events/queue/processor_unit.go
100.00% <100.00%> (ø)

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

#62 was made on purpose. Please don’t reverse this.

I don't see the technical reason for needing WithClock in the implementation code. The mock code is still available in tests with the unit build tag.

@JoshVanL please resolve the conflict

@yaron2 Done

#62 was made on purpose. Please don’t reverse this.

I don't see the technical reason for needing WithClock in the implementation code. The mock code is still available in tests with the unit build tag.

@ItalyPaleAle please review this comment so we can decide how to move forward with this PR


Invoke-WebRequest should save the file name with the name in Content-Disposition

How to get a file name from the server when downloading a file?
The server has a Content-Disposition property, how to get it, and is used when downloading files
Steps to reproduce
$URL=@'
https://skydrive.live.com/download?resid=A78ACCAEBB24EDD7!37948&authkey=!AKjXpDoxgONjhUw
'@

Iwr $URL -outfile ./
Or
$a=Iwr $URL -outfile ./sss

Expected behavior
Autoaddfilename
Or
PS >$a.headers
  Key                 Value
---                 -----
x-amz-id-2          {XAI956ZLVN5q12SAfXINuiiU6rUrLD0w88mtCcMt1uLcwwv…
x-amz-request-id    {3EE4C53FE4416D0E}
Date                {Fri, 24 Jan 2020 08:36:04 GMT}
ETag                {"c4ac8566c3831011ab981c9662b33183"}
Accept-Ranges       {bytes}
Server              {AmazonS3}
Last-Modified       {Wed, 18 Dec 2019 08:27:16 GMT}
Content-Disposition {attachment; filename=OpenSSH-Win32.zip}
Content-Type        {application/octet-stream}
Content-Length      {3018600}

Actual behavior
Error or null

Environment data

@CarloToso has graciously tackled an implementation, in the following PR:

https://github.com/PowerShell/PowerShell/pull/19007

New information has since come to light, which requires further discussion:

While Content-Disposition is worth supporting - while it not may be all-too common, it is used in practice, notably on GitHub (for instance, the Content-Disposition file name for https://github.com/mklement0/ttab/archive/stable.zip is ttab-stable.zip, which is more useful than using just the last URI segment, stable.zip) - but perhaps better on an opt-in basis, which is what curl and wget offer, given the following warning from curl's man page:

WARNING: Exercise judicious use of this option, especially on
Windows. A rogue server could send you the name of a DLL or
other file that could be loaded automatically by Windows or some
third party software.

At this point, the implementation in the PR (exclusively) uses the ultimately redirected-to target URI's last segment as the file name.

This is defensible, but differs from how curl handles this with its -O parameter, in that it uses the input URI's last segment (while also requiring -L in order to follow redirections).

If we stick with the current approach, there's a discoverability problem, which would also apply to a Content-Disposition opt-in: how will the user learn what file name was ultimately used, short of examining the output directory for the most recently added file (which is cumbersome and not fully robust).

My suggestion is as follows:

Provide a Content-Disposition opt-in via a  new switch, say -UseSuggestedFileName, which would have to report an error if the -OutFile argument targets a file.

I know there are concerns over having too many parameters, but I don't seen another option.

As for the discoverability problem:

At the very least, -Verbose should include the file name ultimately used.
-PassThru should use an ETS instance member to decorate the passed-through Microsoft.PowerShell.Commands.BasicHtmlWebResponseObject instance with a .FullName property that reflects the output file's full path.

This would preserve backward-compatibility, but may still be obscure.
Ideally, a [System.IO.FileInfo] instance representing the output file would be returned if -PassThru is combined with -OutFile; while this amounts to a breaking change, it strikes me as the more sensibly behavior, and perhaps it falls into bucket 3.

As for how to parse Content-Disposition and fallback behavior:

Based on the description of the Content-Disposition header field, the C# equivalent of the following is probably good enough in practice, though the recommendation is to give precedence to filename* (sic) entries:

<value-of-Content-Disposition-field(s)> -replace '^.*\bfilename\*?="?([^;"]+)?.*', '$1'
If there's no Content-Disposition field or if the file-name extraction fails, fall back to the last-URI-segment approach

@mklement0 Thank you for your thorough review.

In my opinion the usage of this new feature (let's call it autonaming) intrinsecally exposes the user to a some risk wether we use the last segment or the content-disposition. The last segment of the original uri is safer but often less informative and so less useful.
I wouldn't use an opt in, too many parameters and discoverability problem.
I don't think the users need to remember these rules, they are delegating the choice of the name to PowerShell. If they wanted to control the output they would have added a name string to outfile
Erroring out would be a breaking change, I would prefer to avoid it (we could look for a better naming scheme)

I will wait for @SteveL-MSFT to decide the best course of action before continuing.

@SteveL-MSFT friendly ping

Oh, finally, thank you for this @CarloToso 🥇

@CarloToso The provided code looks more-or-less the same as what Chromium is doing, sans some sanitization: https://github.com/chromium/chromium/blob/11a147047d7ed9d429b53e536fe1ead54fad5053/net/base/filename_util_internal.cc#L219 In general, it would make sense to me to stay close to the behavior of major browsers as much as possible, since that's what most users likely expect as the default.

@CarloToso Note that both the Content-Disposition filename value and the URL decoded last segment may contain invalid chars (especially / and , which could lead to nasty path traversal issues, and also the usual set of forbidden characters (Path.GetInvalidFileNameChars())) and should also be checked for DOS special files (COM0-9, AUX,...).

This is what I have now (Windows-only, although only minor modifications should be needed to make it work on Linux), seems to work reasonably intuitively from my testing:
using System;
using System.IO;
using System.Linq;
using System.Net.Http.Headers;
using System.Text.RegularExpressions;
using System.Web;

namespace Pog.Utils.Http;

/// <summary>
/// Utility class for getting the server-provided file name for a downloaded file.
/// </summary>
public static class HttpFileNameParser {
    /// <param name="resolvedUri">Resolved URI (after redirects) of the downloaded file.</param>
    /// <param name="contentDisposition">The Content-Disposition header from the server response, if any.</param>
    public static string GetDownloadedFileName(Uri resolvedUri, ContentDispositionHeaderValue? contentDisposition) {
        // link to a similar function in Chromium:
        // https://github.com/chromium/chromium/blob/11a147047d7ed9d429b53e536fe1ead54fad5053/net/base/filename_util_internal.cc#L219
        // Chromium also takes into account the mime type of the response, we're not doing that for now

        // try available names in the order of preference, use the first one found that is valid
        string? fileName = null;

        // if Content-Disposition is set and valid, use the specified filename
        fileName ??= SanitizeDownloadedFileName(GetRawDispositionFileName(contentDisposition));

        // use the last segment of the resolved URL
        var lastSegment = resolvedUri.Segments.LastOrDefault();
        fileName ??= SanitizeDownloadedFileName(HttpUtility.UrlDecode(lastSegment));

        // use the hostname
        fileName ??= SanitizeDownloadedFileName(resolvedUri.Host);

        // fallback default name
        fileName ??= "download";

        return fileName;
    }

    private static string? GetRawDispositionFileName(ContentDispositionHeaderValue? contentDisposition) {
        if (contentDisposition is not {DispositionType: "attachment"}) {
            return null;
        }

        var headerVal = contentDisposition switch {
            {FileNameStar: not null} => contentDisposition.FileNameStar,
            {FileName: not null} => contentDisposition.FileName,
            _ => null,
        };

        if (headerVal == null) {
            return null;
        }

        if (headerVal.StartsWith("\"") && headerVal.EndsWith("\"")) {
            // ContentDispositionHeaderValue parser leaves the quotes in the parsed filename, strip them
            headerVal = headerVal.Substring(1, headerVal.Length - 2);
        }

        return headerVal;
    }

    private static readonly Regex InvalidDosNameRegex = new Regex(@"^(CON|PRN|AUX|NUL|COM\d|LPT\d)(\..+)?$",
            RegexOptions.Compiled | RegexOptions.IgnoreCase | RegexOptions.CultureInvariant);

    private static string? SanitizeDownloadedFileName(string? fileName) {
        // sources for relevant functions in Chromium:
        // GetFileNameFromURL: https://github.com/chromium/chromium/blob/11a147047d7ed9d429b53e536fe1ead54fad5053/net/base/filename_util_internal.cc#L119
        // GenerateSafeFileName: https://github.com/chromium/chromium/blob/bf9e98c98e8d7e79befeb057fde42b0e320d9b19/net/base/filename_util.cc#L163
        // SanitizeGeneratedFileName: https://github.com/chromium/chromium/blob/11a147047d7ed9d429b53e536fe1ead54fad5053/net/base/filename_util_internal.cc#L79

        // list of invalid filenames on Windows: https://stackoverflow.com/a/62888

        if (fileName == null) {
            return null;
        }

        // Win32 does not like trailing '.' and ' ', remove it
        fileName = fileName.TrimEnd('.', ' ');
        // replace any invalid characters with _
        fileName = string.Join("_", fileName.Split(Path.GetInvalidFileNameChars()));

        if (InvalidDosNameRegex.IsMatch(fileName)) {
            // is a DOS file name, prefix with _ to lose the special meaning
            fileName = "_" + fileName;
        }

        // if fileName is empty or only consists of invalid chars (or _), skip it
        if (fileName.All(c => c == '_')) {
            return null;
        }
        return fileName;
    }
}

Unit tests:
using System.Net.Http.Headers;
using Pog.Utils.Http;
using Xunit;

namespace Pog.Tests;

// list of test cases for Content-Disposition parsing: http://test.greenbytes.de/tech/tc2231/
public class HttpFileNameParserTests {
    [Fact]
    public void TestDosNames() {
        TestSingle("_aux", "https://example.com/aux");
        TestSingle("_AUX.txt", "https://example.com/AUX.txt");
        TestSingle("_COM9", "https://example.com/COM9");
    }

    [Fact]
    public void TestPriority() {
        TestSingle("header", "https://host/segment", "attachment; filename=header");
        TestSingle("segment", "https://host/segment");
        TestSingle("segment", "https://host/segment", "attachment; filename=_");
        TestSingle("host", "https://host/");
        TestSingle("host", "https://host/_", "attachment; filename=_");
    }

    [Fact]
    public void TestSanitization() {
        // filename*
        TestSingle("hello_world.txt", "https://host/segment", "attachment; filename*=utf-8''hello%2Fworld.txt");
        // filename
        TestSingle("hello_world.txt", "https://host/segment", "attachment; filename=\"hello/world.txt\"");
        // segment
        TestSingle(".._hello_world.txt", "https://host/..%2Fhello%2Fworld.txt");
        TestSingle("invalid_chars_.txt", "https://host/invalid%2fchars%0a.txt");
    }

    private static void TestSingle(string expected, string url, string? dispositionHeader = null) {
        var disposition = dispositionHeader == null ? null : ContentDispositionHeaderValue.Parse(dispositionHeader);
        Assert.Equal(expected, HttpFileNameParser.GetDownloadedFileName(new Uri(url), disposition));
    }
}

This remains a valid issue that should be addressed.


TEM2015 Test 02:  Intelligence SIGINT dashboard video widgets not available

Downloaded and opened Intelligence/SIGINT dashboard
Item 4b66154bc0c54ec08e0f195cfc73651c
Two panels say "The Custom widget VideoWidget is not accessible"

Other widgets look good.

It appears that the dashboard has a reference to the AddIn id:D9E73D85E0874CC4A192A6873BE71E3D
The new id for this AddIn is
id:aae674686c5d4564b390fa2ba8afd560
The dashboard config json has an array of ids that need to be updated during the copy process.
addInIds: [
"D9E73D85E0874CC4A192A6873BE71E3D"
]

99.9% sure that they issue is that the publishing script didn't update the GUIDS because the addInIds are stored in uppercase and not lowercase. Looking into modifying update logic to search for both uppercase and lowercase guids.

I've updated the PortalContentPost.py, UpdatePortalGUIDs.py, and UpdateWebApps.py scripts to search for uppercase, lowercase versions of the search string as well as the original search string.

Fixed in Esri\ops-server-config v.next. Will verify if scripts modifications solved the widget issue when testing Ops Server install on "TEM2015 Test 03" machine.

Verified on TEM2015 Test 03 server. Closing issue.


Add interface for UUID-related exceptions

Description
As the exception thrown during the creating of an instance of a UUID requires intimate knowledge of the codec/builder relationship, I had a delve, and thought the simplest answer would be to give them an interface. This allows catching a UuidExceptionInterface $e which will keep the necessary knowledge lighter in the enclosing class.
Motivation and context

How has this been tested?

I ran the existing test suite, after seeing you are catching on specific exceptions. Because the use of the interface to catch is optional, it didn't look like I needed to refactor there, as the tests are after the more specific detail of the exception anyway.
Types of changes

[ ] Bug fix (non-breaking change which fixes an issue)
[x] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist:

[x] My code follows the code style of this project.
[ ] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly.
[x] I have read the CONTRIBUTING.md document.
[x] I have added tests to cover my changes.
[x] All new and existing tests passed.
[x] I have run composer run-script test locally, and there were no failures or errors. (Well there was one but not related, phan complained about Method Ramsey\Uuid\Converter\Number\GenericNumberConverter::fromHex() should return string&numeric but returns string. So it's not my fault ;-)

@ramsey Oh mighty god of uuids, what do you think?

Well, I'm not a fan of being acknowledged as a deity. I'm more of a demigod. 😉
I like the feature. I need to decide whether this goes into the next major version or the current 4.x series. Since it introduces an interface and doesn't change one, I think it still fits semver to go into the next minor.

Morning saviour.
While it’s a bit early for more Monty Python quotes, my coffee-withdrawn brain agrees with you that it fits the minor version semver definition, because it’s a backwards compatible feature.

@shrikeh I've released this in v4.2.0. Thanks!


C implementation uses a lot of memory (for use on a microcontroller)

The C implementation has 5 look-up tables, which combined use 4352 bytes of memory:
// Forward S-box & tables
static uint8_t FSb[256];
static uint32_t FT0[256];
static uint32_t FT1[256];
static uint32_t FT2[256];
static uint32_t FT3[256];

This might not seem like a lot on desktop/laptop/mobile, but is a lot in the context of embedded microcontrollers, which sometimes only have 38 KB of RAM memory in total.
This could be done more efficiently by making the lookup tables static const and having them populated at compile-time. The disadvantage of this is that the hardcoded constants will be harder to audit (but then again, if the constants are wrong, the tests won't pass).

Hello,
Thank you for your suggestion, as you mentioned, we were not targeting MCU at first, so we didn't face the issue. But as you mentioned, it can be easily fixed with static const tables.
We will add the possibility to use precomputed tables with a preprocessor macro that can be enabled at compile time.
We're currently fixing another unrelated issue, which we will merge soon, so we will also include the ROM tables in the next release.
Thank you.

Thanks for the quick reply! I've added a comment in the PR, I think it's possible to save even more memory :)

The feature has been added, with feature flags for both having ROM tables and limiting the number of tables used. We're about to merge it to master and make a new release version.


Conform to IAM reporting of negative emissions

I accidently pushed to main, then reverted and with this PR will reapply the commit.
The changes are to conform with how negative emissions are accounted in the Ariadne database. Most importantly:
Supply side
1. DACCS and BECCS is regarded as negative emissions
2a. DACCU and BECCU are regarded as neutral
2b. BE and fossilCCS are regarded as neutral
3. fossilCCU is regarded as emissions
Demand side
4. CCU (e-fuels) is neutral

Before asking for a review for this PR make sure to complete the following checklist:

[ ] Workflow with target rule ariadne_all completes without errors
[ ] The logic of export_ariadne_variables has been adapted to the changes
[ ] One or several figures that validate the changes in the PR have been posted as a comment
[ ] A brief description of the changes has been added to Changelog.md
[ ] The latest main has been merged into the PR
[ ] The config has a new prefix of the format YYYYMMDDdescriptive_title

Before:

After:

Before:

After:


Helm Chart: Add support for affinity and tolerations

Adds support for setting the node affinity and tolerations scheduling options
Add support for node affinity and tolerations in Helm chart

Nice, thank you @kiall

/test all

Can you also run ./hack/update-deploy-sh.sh and commit the changes made to the docs/deploy directory? These let users deploy cert-manager without using Helm 😄

Can you also run ./hack/update-deploy-sh.sh and commit the changes made to the docs/deploy directory? These let users deploy cert-manager without using Helm smile

Done.

/retest

/retest

/lgtm
/approve

/retest


\email{} no longer working on Feb-2022 build

With the latest install of moderncv from MikTeX I get this warning "academicons requires xetex/luatex to work. Using alternatives" and I am not able to compile a document using \email{}. I asked the question on StackExchange, but now see this is back in development. I will work on a work-around or fix it and see what I can find.
StackExchange question https://tex.stackexchange.com/questions/649938/modern-cv-no-longer-compiles-with-email

I updated MikTeX as an admin and it worked. Sorry about that.


Use imperative commit message

Following these guidelines.

Thank you for the contribution. It needed some fixes, so they were made in b837f1c334c8582e1a112947c64167c350405e25. Your contribution is still included (and still credited to you), with the appropriate modifications. Please feel free to ask about any of the changes.


feat: APM-APPLICATION to INFRA-AWSMSKTOPIC relationship rule

Relevant information

Rename the relationship rule for consistency with the rest of the rules that are related to INFRA .
Use the proper candidate for the synthesis lookup

Checklist

[ ] I've read the guidelines and understand the acceptance criteria.
[ ] The value of the attribute marked as identifier will be unique and valid.
[ ] I've confirmed that my entity type wasn't already defined. If it is I'm providing an explanation above.

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.dsankaraganti seems not to be a GitHub user. You need a GitHub account to be able to sign the CLA. If you have already a GitHub account, please add the email address used for this commit to your account.You have signed the CLA already but the status is still pending? Let us recheck it.

closing as stale. Feel free to re-open once the feedback has been addressed.


Fix checks for vlan parameters

Add check to not allow non default values of qos and proto when vlan is zero.
Remove check when vlan is zero and qos and proto are not in config since default values are now set.

@adrianchiris, @SchSeba, @zeeke, could you please review this? The sriov network operator sets vlan and vlanQoS equal to zero by default which is a valid config. I'm removing the check that prevents that and adding back a check that I omitted in my last PR.

what about vlan proto == 802.1ad and vlan==0  ?

nothing happens, it is ignored when vlan is set to 0 (checked with ice and mlx5 drivers).

so its invalid  ? maybe we want to block it in cni ? currently 802.1ad and vlan=0 is allowed and as you say will work and be ignored.

Just to clarify, the drivers for all cases effectively set the vlan to 0. With ignore I mean the other parameters, i.e. if the qos is set to 5 and vlan to 0, the ice driver sets vlan 0 and qos 0, whereas the mlx5 sets vlan 0 and qos 5.

+1 for restricting this for now until there is a use-case for it.
its not the first time we see different behavior between drivers around VF configuration such as this.


Missing Helm release secrets cause ListHelmReleases to return an error, and to list no releases

Hey friends! @amulyakish and I encountered what we're pretty sure is a corner-case in WGO's rendering of deployed HelmReleases.
The behavior is similar to what was seen in #2016 and a few other issues. The associated fix for #2016 , #2042 , introduced behavior that requires all Helm releases in ListHelmReleases to be "complete", i.e. to have a Helm release secret created for a given release revision. Without the Helm release secret, WGO is not able to read the details of the release. Without the details of the release, WGO does not render any HelmReleases, renders a stack trace instead, and yields an error about a missing Helm secret.
Describe the bug
If a Flux HelmRelease receives a new Helm revision number, but the associated Helm release at that revision did not complete and did not create a release secret, then there is no release to read. WGO therefore does not render the entire list of HelmReleases. We also see a stack trace, and a console message like "secrets \"sh.helm.release.v1.myapp8v9np.v1\" not found".
Environment

Weave-Gitops Version: 0.9.3 and main HEAD
Flux Version: v0.28.5
Kubernetes version: 1.22

To Reproduce
Steps to reproduce the behavior:
Introduce a Flux HelmRelease with a Helm revision number that doesn't exist. This may be due to a Helm upgrade that is attempted, but that fails due to Kubernetes validation rules.
We saw an example of this in our own cluster. Following one cluster's upgrade to Kubernetes 1.22, the Ingress object at extensions/v1beta1 was deprecated. One application had not updated their Helm chart for this, causing a Helm upgrade failure. Some sample outputs:
$ kubectl get hr -n this-namespace
NAME                     AGE    READY   STATUS
this-service   355d   False   Helm upgrade failed: current release manifest contains removed kubernetes api(s) for this kubernetes version and it is therefore unable to build the kubernetes objects for performing the diff. error from kubernetes: unable to recognize "": no matches for kind "Ingress" in version "extensions/v1beta1"

$ kubectl describe hr -n this-namespace this-service
apiVersion: helm.toolkit.fluxcd.io/v2beta1
kind: HelmRelease
metadata:
  creationTimestamp: "2021-09-08T01:29:15Z"
  finalizers:
  - finalizers.fluxcd.io
  generation: 50
  labels:
    kustomize.toolkit.fluxcd.io/name: applications
    kustomize.toolkit.fluxcd.io/namespace: internal-system
  managedFields:
  ...
spec:
  ...
status:
  conditions:
  - lastTransitionTime: "2022-08-25T21:22:42Z"
    message: 'Helm upgrade failed: current release manifest contains removed kubernetes
      api(s) for this kubernetes version and it is therefore unable to build the kubernetes
      objects for performing the diff. error from kubernetes: unable to recognize
      "": no matches for kind "Ingress" in version "extensions/v1beta1"'
    reason: UpgradeFailed
    status: "False"
    type: Ready
  - lastTransitionTime: "2022-08-25T21:22:42Z"
    message: |-
      Helm upgrade failed: current release manifest contains removed kubernetes api(s) for this kubernetes version and it is therefore unable to build the kubernetes objects for performing the diff. error from kubernetes: unable to recognize "": no matches for kind "Ingress" in version "extensions/v1beta1"

      Last Helm logs:

      preparing upgrade for this-service
      resetting values to the chart's original version
      performing update for this-service
    reason: UpgradeFailed
    status: "False"
    type: Released
  failures: 1
  ...
  lastReleaseRevision: 35 ## <----- NOTICE HERE!
  observedGeneration: 50
  upgradeFailures: 1

Compare the above lastReleaseRevision to the following REVISION:
$ helm list -n this-namespace
NAME          NAMESPACE                 REVISION        UPDATED                                      STATUS          CHART                    APP VERSION
this-service  this-namespace            34              2022-07-21 16:29:31.442591761 +0000 UTC      deployed        this-service-1.0.0       1.0.0
...

Expected behavior
WGO Applications lists all HelmReleases, regardless of deployment state.
Actual Behavior
WGO Applications lists no HelmReleases, regardless of deployment state. WGO instead shows an error message.

Additional Context (screenshots, logs, etc)
What might we do about this? In the short term, there is at least one relatively simple fix, and I'll have a PR open shortly to show. The logic in ListHelmReleases may be amended to append err to respErrors on failure to getHelmReleaseInventory, instead of returning early: https://github.com/weaveworks/weave-gitops/blob/main/core/server/helm_release.go#L58-L67
This will cause the Helm Release listing in WGO to omit the failing release in its list view. Not great, but it permits the Helm Release list view to render overall in the case identified in this issue, thereby satisfying this issue. Users will not see entries that do not have releases at their specified revision. This is confusing for users, and users will need to a) notice that their release is missing, and then b) manually dig into kubectl and helm in their clusters to figure out what happened to their missing entry. It is however arguably better than one failing release causing WGO to not render any releases, which is the current state.
In the long-term, however, I'm not sure what you all might want to do with error handling and messaging, and I don't mean to presume at this stage. The inner-loop error handling logic in most of the other List methods looked fine for now. I saw a couple of spots in both List and Get methods that seemed like they would push stack traces back to the user (return nil, err being the indicator). All of those are out of scope of this Issue.
There is at least one other List endpoint that might warrant a similar review as here, in ListKustomizations: https://github.com/weaveworks/weave-gitops/blob/main/core/server/kustomization.go#L66-L69
Thank you for your consideration here! PR for ListHelmReleases coming shortly.

^ Just to put context to this close-reopen dance, #2665 was a stop-gap measure as mentioned above. It isn't a fully baked solution to this issue.

This was fixed by #2765 - helmreleases now show up even if they don't have a secret.


Refined ProofsTest to be more expressively.

issueCredential function changed slightly to make it easier to read.

Looks good. Thanks.


Use TitleContainer.OpenStream instead of File.OpenRead()

Purpose
For platform specific context, such as Android, File.OpenRead() is not well suited.  MonoGame already offers a TitleContainer.OpenStream() method that considers the platform context when opening a file stream.
Motivation
Not using the TitleContainer could lead to issues for users.  This request is also being opened to track #47

Implemented in #47


Feature: Improve UX on Create New List Feature

Type of feature
🍕 Feature
Current behavior
The current design of the New List Creation has a few elements that could potentially disrupt the user flow:

The title input is wrapped in a border, which visually separates it from the other elements.
The "Make Public" button comes after the title but before the "Add People" component.

Because of the lines and the spacing, it's not clear that the user needs to do anything beyond create a list name. But if the user presses enter after inputing a list name, nothing happens.

Suggested solution

Remove the bottom border on the title input: The border around the title input creates a visual break that can disrupt the user's focus.

Switch the positions of the "Add Contributors" component and the "Make Public" radio button: The current order can be confusing. Users are more likely to decide on the list's privacy settings after they've added people to it.

Something like this:

Additional context
No response
Code of Conduct

[X] I agree to follow this project's Code of Conduct

Contributing Docs

[X] I agree to follow this project's Contribution Docs

+1 on the suggestions @BekahHW, i think this doesn’t needs a redesign for now... It should be a quick UI fix
adding the easy win and style label to it

@5hraddha we need to get @isabensusan to give her thoughts first

hey @5hraddha ! Thanks for looking into this :)
I'm on board with most changes, except for changing the "Page Visibility" option. Since both "Import your Github Following" and "Explore Contributors" take you to a different page, by placing the "Page Visibility" part on the bottom users will never get a chance to adjust it before moving on to the next screen.
Intended Changes

Normalize spacing between items: The current padding / gap / margin situation is all over the place, and it'd be great to normalize it. Ideally strip all spacing classes (for margins and paddings) and re-do it using the same logic.
Remove confusing separator

An ideal final look could be something like this:

With this type of spacing (use Tailwind classes as needed to achieve the spacing):

Thank you!!

Sure @isabensusan . Thanks for providing details. I'll start working in it.


SvelteKit on AWS does not support PUT, POST, PATCH, DELETE for API routes

When deploying a SvelteKit app on AWS, the generated CloudFront distribution does not route PUT, POST, PATCH, and DELETE requests to the server lambda, which breaks certain SvelteKit features like API routes. 3rd party integrations auch as Auth.js for SvelteKit using server hooks might also rely on these HTTP methods.
This issue sounds related to #196 but there seems to be no straight-forward way to explicitly define server routes for SvelteKit apps. My workaround looks similar to this:
async run() {
  const serverRoutes = ["/auth/*", "/api/*"];
  new sst.aws.SvelteKit("SvelteApp", {
    transform: {
      cdn(cdnArgs) {
        cdnArgs.transform = {
          distribution(distArgs) {
            const behaviors = distArgs.orderedCacheBehaviors!;
            const newBehaviors = serverRoutes.map((pattern) => {
              const behavior = { ...behaviors[0] };
              behavior.pathPattern = pattern;
              behavior.targetOriginId = "server";
              behavior.allowedMethods = ["GET", "HEAD", "OPTIONS", "PUT", "POST", "PATCH", "DELETE"];
              return behavior;
            });
            distArgs.orderedCacheBehaviors = newBehaviors.concat(behaviors);
          }
        }
      },
    },
  });
}

Used versions:

@sveltejs/kit: 2.5.28
sst: 3.1.31
svelte-kit-sst: 2.43.5

I'm sorry if this is a known limitation but I have not found anything in the docs or the issues so far.

https://github.com/sst/ion/compare/v3.1.19...v3.1.20
Seems like this is what broke it.
Up to 3.1.19 works 3.1.20 and after breaks Svelte's SSR magic due to the CF behavior.

Thanks for catching this!
Releasing v3.1.35 reverting the change.


Change prefix from / to =

Example: /n -> name=

Codecov Report

Merging #42 (9559671) into master (416bb3c) will not change coverage.
The diff coverage is 100.00%.

@@            Coverage Diff            @@
##             master      #42   +/-   ##
=========================================
  Coverage     72.15%   72.15%
  Complexity      399      399
=========================================
  Files            70       70
  Lines          1232     1232
  Branches        125      125
=========================================
  Hits            889      889
  Misses          311      311
  Partials         32       32

Impacted Files
Coverage Δ

...ain/java/seedu/address/logic/parser/CliSyntax.java
83.33% <100.00%> (ø)

Continue to review full report at Codecov.

Legend - Click here to learn more
Δ = absolute <relative> (impact), ø = not affected, ? = missing data
Powered by Codecov. Last update 416bb3c...9559671. Read the comment docs.


Incomplete wide strings in .NET binaries

Wide strings found in .NET binaries are incomplete. Sometimes the first letter is missing, sometimes the ending letter.
>>> bv.get_string_at(0x411308).value
'&Cance'
>>> bv.get_string_at(0x411308).raw
b'&\x00C\x00a\x00n\x00c\x00e\x00'

I'm not seeing this in any binaries I have, can you share one that shows this behavior? You can post it here or message me in slack.

Closing since I haven't found a sample of this happening - I'm assuming it was fixed when unicode handling got refactored.


[Pick 2.1](inverted index) add inverted index reader memory size into searcher cache

Proposed changes
Issue Number: close #xxx
Pick from #35149

run buildall


A problem

Hello, I would like to ask the carbon generated pictures, how to restore the code in the picture back. This problem is due to the lack of my code, thanks to the pictures generated by carbon, thank you.

If you saved your code in SVG format then it's easy. Just open the file into a text editor and copy and paste it out again.
If you saved it as a PNG, you're out of luck. Either type it in again or try looking at some OCR software.
There's no way Carbon itself should support this imho.

Thanks @photonstorm . I will pay attention to this problem next time.
Thanks @mfix22, I have an idea: now there are a lot of picture scanning technology, this technology is often used in the translation of the contents of the content, I think you may be able to refer to my idea to try to solve such problems, to prevent new users from downloading the SVG problem. Thank you


[Bug]: post-processing variables require pybamm.Symbol to have a mesh

PyBaMM Version
develop
Python Version
3.10
Describe the bug
Adding a variable to a pre-built pybamm model causes a failure in pybamm.solvers.processed_variable.py::process_variable() because it doesn't have a mesh attribute
Steps to Reproduce

create a pybamm model (e.g. SPM)
manually add a new variable (model.variables.update({"name": expression}))
solve the model then try and access the variable (sol["name"])

Relevant log output
  File "/home/mrobins/git/PyBOP/pybop/problems/fitting_problem.py", line 133, in evaluate
    return {
  File "/home/mrobins/git/PyBOP/pybop/problems/fitting_problem.py", line 134, in <dictcomp>
    signal: sol[signal].data
  File "/home/mrobins/git/PyBOP/env/lib/python3.10/site-packages/pybamm/solvers/solution.py", line 710, in __getitem__
    self.update(key)
  File "/home/mrobins/git/PyBOP/env/lib/python3.10/site-packages/pybamm/solvers/solution.py", line 590, in update
    self._update_variable(variable)
  File "/home/mrobins/git/PyBOP/env/lib/python3.10/site-packages/pybamm/solvers/solution.py", line 640, in _update_variable
    var = pybamm.process_variable(
  File "/home/mrobins/git/PyBOP/env/lib/python3.10/site-packages/pybamm/solvers/processed_variable.py", line 881, in process_variable
    mesh = base_variables[0].mesh
AttributeError: 'Power' object has no attribute 'mesh'

this doesn't normally pop up as we seem to add mesh somewhere in the pipeline, but it seems to occur if you add the new variable after the model is discretised

I think the main issue with our current approach is that mesh is not an attribute of the Symbol class, its just something that gets added somewhere along the line, which is not good. In general all class attribute should be created in the __init__, not afterwards. I would suggest just adding self.mesh = None in Symbol.__init__

Got it, makes sense. There are a lot of places where attributes get added outside of the __init__…

Got it, makes sense. There are a lot of places where attributes get added outside of the __init__…

I know :( but this was a particularly blatent example that I thought we should clean up

Agreed!


How to quit a SlidePrompt ?

Hi, I'm currently trying to understand how to quit a SlidePrompt during the inputs. I saw you did a keyhandler.register but I can't implement it.
Does it have to be in the SlidePrompt class ? Can I put an keyhandler on my functions ?
For example, I have a login "form" and I want to cancel the process
def logIn():
    form = SlidePrompt([
        Input("Enter your username: ",
            word_color=_YELLOW
        ),
        Input("Enter your password: ",
            word_color=_YELLOW
        ),
    ])
    result = form.launch()

I tested to add @keyhandler.register(charDef.INTERRUPT_KEY) above the function but it didn't work, so maybe a clearer explanation on how to achieve this could be great !
Thanks 😄

Hi @pommepommee , you could refer to DOCUMENTATION.md and ./examples/check.py to see how keyhandler works in the general case.
However, after playing with your example for a while, I found that the keyhandler could not solve your case.
The main reason is that Input calls myInput function, and myInput calls utils.getchar. The getchar function essentially captures all keyboard events.
# in client.myInput
def input(self):
        while True:
            c = utils.getchar()
            i = c if c == UNDEFINED_KEY else ord(c)

            if i == NEWLINE_KEY:
                utils.forceWrite('\n')
                return self.getInput()

I believe the only thing you could do (for now) is modify the input function of myInput so that it handles charDef.INTERRUPT_KEY, probably like the following:
# in client.myInput
def input(self):
        while True:
            c = utils.getchar()
            i = c if c == UNDEFINED_KEY else ord(c)

            if i == INTERRUPT_KEY:
                #do something
            if i == NEWLINE_KEY:
                utils.forceWrite('\n')
                return self.getInput()

I plan to completely rewrite the myInput function to solve your issue for good. Please stay tuned for the latest release.


webkit_server processes lingering

Hi there,
When I run my suite of tests, by the end I have tons of webkit_server processes running, even when a test is only using one session.  I've read a few other issues about this, but everything seems to say the issues have been resolved in 1.6.0.  I'm using 1.6.0 and am still having the issue, so I'm wondering if there may still be something wrong, or if it's complete user error.
Here's what I'm doing... in some tests, I initialize several sessions by doing something like: supplier_session, buyer_session = new_session, new_session, where new_session is defined as:
def new_session
  Capybara::Session.new(Capybara.javascript_driver)
end

Then I structure my tests as:
using_session(supplier_session) { do_something }
using_session(buyer_session) { check_what_was_done}

At the end of the test, there then 2 webkit_server processes that don't close until the very end of the entire suite.
Any idea what the issue may be?
Thanks,
Zach

The webkit_server process will not be reaped until the end of the test suite, so what you're seeing is expected behavior. There's no mechanism via the Capybara API to clean up the processes, so we rely on Ruby closing its file descriptors to determine when to terminate the process.

This would not be terribly difficult for us to implement, but it's not something that's generally supported by Capybara. If you got buy-in from the Capybara team on a general stop or shutdown command for sessions, we'd implement it in capybara-webkit. However, I'm not sure how likely that is, because I don't think there's much cost in keeping the extra connection open for the remainder of the test suite.
I'm going to close this, because I don't believe this is a bug and there isn't anything related to this we plan to implement. However, feel free to continue discussing on this thread if you have further thoughts.

Awesome... thanks for the info!  Glad it wasn't just me doing something wrong.  I'm pretty new to this, so that was a very real possibility :-)

@iastazach Why are you attempting to generate new sessions for every test?  Capybaras using_session takes the name of a session, so
using_session(:buyer_session) { do something }

should automatically create a new session, associate it to the name :buyer_session, and then reuse the server process created in that session in any other test where you use the session :buyer_session.  In fact, unless you're using your own custom using_session, you may very well be creating 2 sessions each time you use using_session - the one you're creating, and then the one capybara creates based off the text value "name" of the session you created

@twalpole Thanks for the tip!  It's working exactly the way you described, and I'm updating my tests now.


Fix:Button Styling in Home.css

Issue #56
Fixed the styling of buttons in Home page
Before:
https://github.com/user-attachments/assets/4502baf5-227d-4975-a6fe-00449eb75c0c
After:
https://github.com/user-attachments/assets/5f334b0c-3755-4c26-acd9-bfea6aad2cb8
PS: Please merge this pr under hackothon-accepted label. Thank you

@Shinu-ster , and lmk soon!


feat(build): using semantic-release

Thanks @DianaSuvorova!
Uses semantic-release to trigger build from Travis CI on push to master (if all tests pass). Semantic release will take care of the version and publish steps, however you'll need to use Angular commit message conventions. See https://github.com/semantic-release/semantic-release/ for more information.
Why is this a feat?
Well, I'm hoping semantic-release will augment by a minor version to account for the alwaysUse2dCanvas option we just added. :)
Wait a minute...why does this seem suspicious? >_>
This is using my GH and NPM tokens to push to the npm repository. I think you guys can set this up with a different set of tokens. Let me know if you can't access the Travis CI options for this repo to change it yourselves.

:tada: This PR is included in version 1.4.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Ventura Compatibility?

Awesome app; thank you!!!
Any hope of getting an update that will work with Ventura?

The app should already work with Ventura. What kind of problems are you seeing?

Hi Sasindu:
Thanks for taking the time to reply, and for coding such a nifty little app!
I had some issues with upgrading to Ventura, but after a reinstall of 13.3.1 and some restarts, Spaceman is working fairly well now. The only issue I’ve noted is that it doesn’t play optimally with Bartender, but I’ve found some work arounds for that.
Again, thank you for coding such a fun and useful piece of software!
All the best. Tom
On 4/2/23, 23:27, "Sasindu Jayasinghe" @.***> wrote:
The app should already work with Ventura. What kind of problems are you seeing?
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you authored the thread.Message ID: @.***>


Add a note about v-else caveat with components and v-show

Refers to https://github.com/vuejs/vue/issues/2639

Should I add a not to the API too?

Just a link in the API should be enough

I noticed there's already a See also link in the api that refers to the v-else guide. Nevertheless I added a second one because it looks more explicit to me and draws user attention because of the word caveat


Create simple documentation landing page

I think this is the only missing thing before we do a release. We can use the setup from http://fsprojects.github.io/ProjectScaffold/writing-docs.html which means just modifying docs/content/index.fsx for now.

Closed by #25


What's The difference !

Hello What's the difference between this package and loopback-connector-firestore is it a clone ?

Really its just clone @dyaa


Add a number to indicate number of accidents on the map

Add a number to indicate number of accidents on the map

Duplicate of putting the number of marker group members on aggregated icons #515


Where to add custom commands?

Hello!
I red the wiki but I'm unable to understand where I can add a simple notification.
I want to use telegram to select next pages with this module: https://github.com/edward-shen/MMM-pages
Thank you

Yes, I can

Insert belows in MMM-pages.js. I think line 18 is good place to insert.
getCommands: function(commander) {
  return [
    {command: 'PAGE_CHANGED'},
    {command: 'PAGE_INCREMENT'},
    {command: 'PAGE_DECREMENT'},
  ]
},

Now you can get commands

/PAGE_CHANGED number
/PAGE_INCREMENT
/PAGE_DECREMENT

More detailed information is here;
https://github.com/eouia/MMM-TelegramBot/wiki/How-to-add-commands


How to see a list of methods/fields in a class?

How to see a list of methods/fields in a class and quickly jump to selected method/field?

How to see a list of methods/fields in a class and quickly jump to selected method/field?

Key options: The semantic view : https://basarat.gitbooks.io/alm/content/features/semantic-view.html
Alternatively the symbol search : https://basarat.gitbooks.io/alm/content/features/omni-search.html#symbol-search :rose:


Usage example in Readme has syntax error

In the Usage section of the Readme, it contains a syntax error. The line:
if ((verifyAppProxyHmac(req.query), process.env.SHOPIFY_SECRET)) {
should be:
if (verifyAppProxyHmac(req.query, process.env.SHOPIFY_SECRET)) {

I'd also recommend changing process.env.SHOPIFY_SECRET to process.env.SHOPIFY_API_SECRET, since that's what it is named by default.

Changes have been made, thank you for pointing this out.

Thanks for the fix, but it looks like you accidentally introduced another error! You need to remove the extra if.


Fix for immutable HttpParams in build url search params

Hi Asad
I've added a small fix for buildUrlSearchParams.
Currently HttpParams is immutable so you should set params as below:
// for set method
let params: HttpParams = new HttpParams().set('something', 'hello');
// for append method
let params: HttpParams = new HttpParams().append('something', 'hello');
Here is the topic on stackoverflow
https://stackoverflow.com/questions/45500264/angular-4-3-httpclient-get-params-empty
Best regards,
Krzysztof

Thanks @kmiskiewicz


Inefficetive paratial complement of Brazil recovered data

Summary
As discussed in #423, partial complement of Brazil recovered data is ineffective. The number of recovered cases increased sharply on 27Oct2020.
https://gist.github.com/lisphilar/7a737c7ceefb47316cac2010d34b5238
(Optional) Related classes

covsirphy.JHUData
covsirphy.JHUDataComplementHandler

Codes and outputs:
import covsirphy as cs
# Dataset preparation
data_loader = cs.DataLoader("input")
jhu_data = data_loader.jhu()
population_data = data_loader.population()
# Show complemented records
snl = cs.Scenario(jhu_data, population_data, "Brazil")
_ = snl.records()

This code creates the next figure.

Environment

CovsirPhy version: 2.13.0-alpha.fix.417
Python version; 3.6
Installation: pip
System: Google Colaboratory

As I see the data, I think that the original source data show a jump of 400.000 recovered cases, this is not caused by any kind of our complement methods.

Is it unnecessary to create new complement methods to jump?

Since the data are valid values and they are provided as such formally, I don't think they should be handled somehow for the moment. They don't cause any trouble and they show the real cataloguing behaviour of the country. If we do handle jumps, then we smooth too much the data (what is considered as a jump?). Similar jumps for example can happen in confirmed and fatal (characteristic example is the fatal cases jump in China back in April out of sudden). We should keep these as they are, because it gets too complicated otherwise. If the jumps cause irregularities or problems we can revise this.

OK, I will mark this issue as invalid. If we or users find new problems related to these jumps, we may return to this issue.

Not "invalid", "wontfix" is correct.


undefined reference

Hello,
I am trying to compile a test application in windows with  mingw-w64 and encountered a linking issue.
g++ -Wall -Werror -DBUILDING_EXAMPLE_DLL -c  main.cpp  libs\mem\mem.cpp
g++ -shared -m64 -o main.dll mem.o main.o  -Wl,--out-implib,main.a

any help would be greatly appreciated.

Can you compile a DLL with multiple source files or is this problem specific to the memory lib?

Yes I have another test library which linked successfully but this is unable to.
test.h
#ifndef TEST_H #define TEST_H int adds(int); #endif
test.cpp
#include "test.h" int adds(int a){     return a; }
Command line parameters:
g++ -Wall -Werror -DBUILDING_EXAMPLE_DLL -c  main.cpp   libs\test\test.cpp g++ -shared -m64 -o main.dll main.o test.o -Wl,--out-implib,main.a

What is the code of main.cpp?

`#include
#include
#include "libs/mem/mem.hpp"
#include <windows.h>
void (ActualFunction)(void, std::string a2, std::string a3);
uintptr_t  BaseAddress;
void MyFunction(void* handle, std::string const& a2, int64_t a3) {
return;
}
int init(){
ActualFunction= (decltype(ActualFunction))(BaseAddress + 0xf30);
mem::in::detour_trampoline((mem::voidptr_t)&ActualFunction, (mem::voidptr_t)&MyFunction, (mem::int_t)0x9);
return true;
}
extern "C" BOOL WINAPI DllMain(HINSTANCE hinstDLL, DWORD fdwReason, LPVOID lpvReserved)
{
BaseAddress = (uintptr_t)GetModuleHandle(0);
switch (fdwReason)
{
case DLL_PROCESS_ATTACH:
return init();
case DLL_PROCESS_DETACH:
case DLL_THREAD_ATTACH:

case DLL_THREAD_DETACH:

default:

    break;
}

return TRUE;

}`
This is the code which throws the undefined reference.

I am on Linux rn and I also never used g++ on Windows, so I'll just give my last shot. Try this:
g++ -c -m64 -fPIC main.cpp libs\test\test.cpp g++ -shared -m64 -o main.dll main.o test.o
If it doesn't work, then I'll install a Windows VM and check it out

The commands do work and produce an injectable dll but upon using your library it gives the same error with the throwbin code above.
I am using the following compiler for windows: https://sourceforge.net/projects/mingw-w64/files/Toolchains targetting Win32/Personal Builds/mingw-builds/installer/mingw-w64-install.exe/download
Windows 10 19041

Just a note in case you want to finish what you're doing without having to wait for my response: it probably works on Visual Studio without any problems, as long as the project is set up properly.

Just a note in case you want to finish what you're doing without having to wait for my response
That's alright as I really want to compile this on GCC.
it seems like MEM_COMPATIBLE does not even get defined at all.

If MEM_COMPATIBLE is not defined then it could be:

Neither MEM_WIN nor MEM_LINUX is being defined
Neither MEM_86 not MEM_64 is being defined
As you're using Windows and compiling as 64 bit, then this would force MEM_WIN and MEM_64 to be defined:
#define _WIN32
#define _M_X64
(you have to put those before including mem.hpp)

Well with a bit of investigation, it turned out that neither MEM_64 and MEM_86 were being defined. Forcing that resulted in errors which looked like typos(maybe?) and were fixed. The program compiles and runs just fine( with a bunch of warnings).
Updated linker:  -shared -m64 -o main.dll mem.o main.o -Wl,--out-implib,main.a -L. -lPsapi
in function mem::int_t mem::ex::load_library(process_t process, lib_t libpath)
the following changes were made:

You're right, that variable was supposed to be called "lib". I probably overwrote something on VSCode using CTRL+D. That is fixed now on the master branch.

(hopefully nothing else broke)

Absolutely.
Alright I am going to close this issue as it seems to be resolved (currently). Thanks for the amazing library!

Thank you for letting me know about this MINGW definitions, gonna add them to the project.
Also, the size parameter in detour trampoline is used to return a gateway that constains the original bytes of the hooked area.

One more thing. It seems like the definitions on a 64-bit machine defines both __MINGW32__  and __MINGW64__. This may or may not cause problems.


Update example extension name

Update the example extension name from vscode.csharp to ms-dotnettools.csharp.
While adding an extensions.json to a project of my own, I noticed that the "Intellisense" for the schema was suggesting an extension that no longer exists, so this updates it to the current Id.

Thanks for the PR. The example mentioned in the code is just for a reference of extension id which is pub.name and not intended to point to a specific extension that exists. So it's fine to have a dummy extension id like this.


Add camera_rate param.

Add a ros param that sets a timer frequency that teensy uses to trigger the camera at a given frame rate.

Great.  Definitely interested to hear your thoughts on the project as a whole.  I know there are a lot of rough edges and barely implemented functionality.  One foot in front of the other, though.


Dockerfile: Remove ~/.cache dirs created by Pip and Pipenv

This directory was getting created as root during image build which then made it unwriteable by non-root users at run time.  This wasn't an issue for a while, but Snakemake, as of newer versions¹, now uses the same user cache dir for its own subdir (~/.cache/snakemake, i.e. /nextstrain/.cache/snakemake).  Snakemake fails to create its own subdir if the user cache dir is owned by root.
Like most in-image caching, these are not useful and only serve to increase image size.
It's easiest to remove the directories explicitly rather than disable their creation (possible for Pip with --no-cache-dir or PIP_NO_CACHE_DIR=1, not possible for Pipenv).
An alternative would be to set HOME differently during build, but that seems like a potential source of other unforeseen issues.  Maybe in the future when we have a more general "derivative image" recipe.
¹ https://github.com/nextstrain/docker-base/issues/135
https://github.com/nextstrain/docker-base/pull/136
Testing

[x] Locally builds and no longer has the ~/.cache dir.
[x] Checks pass

CI-built image looks good too. Merging now to address current breakage following the Snakemake upgrade in the nextstrain/base image.


galactolipid

Would be better to do galactolipid.  They assessed cerebrosides and sulfatides which I’d put under galactolipids, no?.  (Note was to remind myself what I put where and why.)
Galactolipids are not limited to myelin...
but I could add galactocerebroside (GalC) which is myelin-specific?
Melissa Berry wrote:
> Abnormal galactolipid level
> This is cerebrosides and sulfatides and they are part of myelin.
>
> Note to self: J:5170, I put it under abnormal myelin.
Reported by: *anonymous
Original Ticket: obo/mammalian-phenotype-requests/677

According to https://en.wikipedia.org/wiki/Galactocerebroside galactocerebroside is  oligodendrocyte specific not myelin specific

MP:0020380 abnormal galatolipid level


[Packaging] Create a git smudge filter for project.json

Needed so that the in repo version of samples etc uses "*" for package versions while the checked out version can automagically change to the "latest" in any branch that isn't master.
This additionally will need some cross-repo work / environment variable overrides so that other repos like winobjc-samples can also automatically use the right package version.

Change of plans to use packageReference instead.


DrpDwn of custom filter gets stucked on Accounts page.

To Reproduce
Steps to reproduce the behavior:

Go to 'Accounts Page'
Click on '+' btn of custom filter.
Click on drpdwn of custom filter.
Click on 'x' clear btn of Past query/New Name.

Screenshots

Not able to reproduce

Not able to reproduce

Open Custom filter and leave it till token refresh, or 2, 3 minutes, parameter dropdown popup stuck,

attempted to solve. Please check


How to create process with args

I could not handle to handle creating process with arguments.  For example: I wanna create process with portable chrome. But i wanna open a html file in kiosk mode. How can i open sample.html file in portable chrome exe with --kiosk argument?

So what's the problem?

I have a html file in same directory and wanna open this html file in kiosk mode.  i'm trying to do something like that:
string url = @System.AppDomain.CurrentDomain.BaseDirectory + "updater.html ";
string kioskMode = url + " --kiosk --incognito --disable-pinch --overscroll-history-navigation=0 ";

StartProcessAsCurrentUser("C:\\Chrome\\PortableChrome.exe", kioskMode);

At this rate google start in kiosk mode but doesnt open html file.

Does it open the html file with exactly the same parameters when run by the same user from the command line?


not possible to insert null values

I have a c# backend with nullable type and with swift I am able to insert null values but with Android is not possible. I have also tried to pull data using postman and it works perfect but when I use the insert method of MobileServiceSyncTable and MobileServiceJsonSyncTable is not possible. I have tried to add values manually into the json object with value JSONObject.NULL but is also not possible.

Hi @erikmompean
Could you provide more details (code snippet, model structure) on how are you trying to insert an item into the table? I tried inserting records with null values and it worked as expected.

@erikmompean We haven't heard back from you. I am closing the issue for now but please feel free to reach out to us if you have any questions. Thanks!


table 5077 "Segment Line" - new integration event in OnDelete Trigger

To delete additional records from tables in our product knkPublishing depending on the confirm-dialog, we would like to have an additional event:
change in OnDelete Trigger
trigger OnDelete()
    var
        SegLine: Record "Segment Line";
        SegmentCriteriaLine: Record "Segment Criteria Line";
        SegmentHistory: Record "Segment History";
        SegInteractLanguage: Record "Segment Interaction Language";
        Task: Record "To-do";
    begin
        [...]
        SegLine.SetRange("Segment No.", "Segment No.");
        SegLine.SetFilter("Line No.", '<>%1', "Line No.");
        if SegLine.IsEmpty() then begin
            if SegHeader.Get("Segment No.") then
                SegHeader.CalcFields("No. of Criteria Actions");
            if SegHeader."No. of Criteria Actions" > 1 then
                if Confirm(Text006, true) then begin
                    SegmentCriteriaLine.SetRange("Segment No.", "Segment No.");
                    //Call of new event
                    OnDeleteOnBeforeSegmentCriteriaLineDeleteAll(Rec, SegmentCriteriaLine);
                    SegmentCriteriaLine.DeleteAll();
                    SegmentHistory.SetRange("Segment No.", "Segment No.");
                    SegmentHistory.DeleteAll();
                end;
        end;
        [...]
    end;

New Integration Event
[IntegrationEvent(false, false)]
local procedure OnDeleteOnBeforeSegmentCriteriaLineDeleteAll(SegmentLine: Record "Segment Line"; SegmentCriteriaLine: Record "Segment Criteria Line")
begin
end;

Thanks for reporting this. We agree, and we’ll publish a fix asap, either in an update for the current version or in the next major release. Please do not reply to this, as we do not monitor closed issues. If you have follow-up questions or requests, please create a new issue where you reference this one.
Build ID: 52831.


Snapshot API call

Read from framebuffer directly in core library and add an API call for it (used in tizen related work).

Looks good. Merging.


id -> galtileid?

Hi David,
I'm looking through some of this code to try and figure out why Ismael's getting weird results.  I came across this line: https://github.com/DarkEnergyScienceCollaboration/WeakLensingDeblending/blob/master/descwl/catalog.py#L87
I'm guessing this should be
if self.only_id and entry['galtileid'] not in self.only_id:

but wanted to make sure I'm interpreting your intentions right.  Can you confirm?

Yes!  (and the same two lines below).  I renamed 'id' to 'galtileid' at some point and obviously didn't test this option after the change.  Can you make a PR with just this fix or should I do it?


Show parsing-errors in error-list

Installed product versions

Visual Studio: 2017 professional
This extension: just installed

Description
Parsing errors are only shown in the output-window.
Steps to recreate
Create a js-file with only a single line: 1==0?;
Current behavior
The error-list in VS is empty, the error is only shown in the output-window.
Expected behavior
I think it would be more intuitive to see the parsing-error in the error-list. The code will not execute after all. Why let the developer execute the code if VisualLinter does already know it won't run?

Hi @Epaminaidos Thank you for your suggestion!
I agree that it would indeed be more intuitive to show this error in the error list instead of the output window.
I'll update back here once I've gotten around fixing it!

I've reverted the changes made to catch the parser error message in version 1.0.223, I honestly don't remember why I did this in the first place, but I'm sure we'll find out soon enough. (in before revert revert)
The new version will soon be available on the Market place.


readme describing overall repository contents

Would like to get a thumbs up from everyone on the PR to confirm that my descriptions are an accurate representation of what you know to be contained in each folder!

@amsnyder dataset_processing looks good


.query() should not mix up KeyConditionExpression and FilterExpression

The core idea would be to make clear that query:

Requires a hashKey
A hashKey can have conditions (KeyConditionExpression)
Optionally can have a rangeKey
A rangeKey can have conditions (KeyConditionExpression)
A query can be done on a secondary local index or a secondary global index
The result of a query can be filtered by attributes with conditions (FilterExpression)

Proposal, example:
Cat
.query({
  hashKey: 'breed',
})
.filter([
  {
     attribute: 'age'
     condition: {between: {5, 8}}
  }
],
[
  {
     attribute: 'age'
     condition: {between: {5, 8}}
  }
])
.exec()

query() accepts an object with where rangeKey is optional: query({hashKey: string | number, rangeKey?: string | number, useIndex?: string})
.filter() may have OR between each array and AND inside of each array: filter(...conditions: AndConditon[])
.using() I would remove in favor of defining the index in query()

This would would have the benefit of:

Make it clear that there is a difference between selecting items with the range key / sort key and filtering the result of that selection
Make the use of hashKey, rangeKey and indexes more clear and testable (e.g. a query requires at least a hashKey)
No need for endless piping
Making the user a little bit more thoughtful that filtering a large amount of items is not very performant and may result in high costs
Documentation can be very on point and explain things easily. Currently everything is very loose with mixed types(string, object, class) etc.

Other operations should be refactored too for consistency. Also see https://github.com/dynamoosejs/dynamoose/issues/795

Curious to hear others thoughts on this.

I'm gonna close this due to no activity. If anyone else has more thoughts on this feel free to comment and we can consider this further.


chore: update to 10.3

Update to 10.3 and 7.3 for component package
Update left nav override styles to be compatible with new shell updates
fixes some console errors

closes #1639

Updating from 7.2 to 7.3 for carbon-components-react is breaking the Gatsby build. This is related to the tab/tabs component but beyond narrowing it down to that I'm not sure how to fix.
This is the build error https://reactjs.org/docs/error-decoder.html/?invariant=130&args[]=undefined

Element type is invalid: expected a string (for built-in components) or a class/function (for composite components) but got: undefined.[missing argument]

Any ideas on what might have changed with the React library from 7.2 to 7.3 ?

Could this be cut into a new alpha release? Our addons site depends on this as it's not yet on the new gatsby theme.
We're attempting to update our breakpoint mixin usage to have the prefix. Our build is failing without the breakpoint fix to _typeface-sub-families.scss.

Just published 0.0.1-alpha.24 @tay1orjones, hopefully, that works ok for you guys and doesn't break stuff. 🙏 Let me know if you want help converting your site to use the theme. We're in the middle of moving the Design Language site and Carbon to use it right now. 😅


[Schema Registry] No longer return an undefined and throw instead

Related issue: https://github.com/Azure/azure-sdk-for-js/issues/17697
Let's throw instead of returning an undefined in getSchema and getSchemaProperties, since the avro package will throw anyway and to be consistent with other languages.

I was out when this came in. Are folks aware that this originally threw, then we changed it to not throw based on a customer request?
See https://github.com/Azure/azure-sdk-for-js/issues/15130

@nguerrera sorry for the back and forth. I wish I had remembered the source of this change during the board review. Could you start an e-mail thread with the arch board about this issue to see if this information sways any hearts?

@xirzec No worries, and sure thing.

@nguerrera could you please add me to that thread as well?

Yep, will do, I didn't send it yet.


Flyway swallows the error and dies with unhelpful stack trace when trying to create a partitioned table on Oracle XE

What version of Flyway are you using?
4.0.3
Which client are you using? (Command-line, Java API, Maven plugin, Gradle plugin, SBT plugin, ANT tasks)
Command-line
What database are you using (type & version)?
Oracle Database 11g Express Edition Release <IP_ADDRESS>.0 - 64bit Production
What operating system are you using?
Mac OS X 10.11.5 (client)
Ubuntu 14.04.4 LTS (Oracle server, inside Docker container)
What did you do?
Ran
flyway migrate
with this config:
flyway.driver=oracle.jdbc.OracleDriver
flyway.url=jdbc:oracle:thin:SYSTEM/oracle@//localhost:42161/XE
flyway.user=SYSTEM
flyway.password=oracle
flyway.schemas=FLYWAY_DEMO
flyway.table=SCHEMA_HISTORY
and this migration:
create table partition_demo (pk number) partition by list(pk) (partition p1 values (1), partition p2 values (2));
What did you expect to see?
ERROR at line 1:
ORA-00439: feature not enabled: Partitioning
That's the error message I get when running the script from the SQL/Plus command line.
What did you see instead?
$ ./flyway migrate
Flyway 4.0.3 by Boxfuse
Database: jdbc:oracle:thin:SYSTEM/oracle@//localhost:42161/XE (Oracle 11.2)
Successfully validated 1 migration (execution time 00:00.007s)
Creating Metadata table: "FLYWAY_DEMO"."SCHEMA_HISTORY"
Current version of schema "FLYWAY_DEMO": << Empty Schema >>
Migrating schema "FLYWAY_DEMO" to version 1 - Create table
ERROR: Unable to rollback transaction
java.sql.SQLRecoverableException: Getrennte Verbindung
at oracle.jdbc.driver.PhysicalConnection.rollback(PhysicalConnection.java:3933)
at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:81)
at org.flywaydb.core.internal.command.DbMigrate.applyMigration(DbMigrate.java:305)
at org.flywaydb.core.internal.command.DbMigrate.access$1000(DbMigrate.java:47)
at org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:230)
at org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:173)
at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:173)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:959)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:917)
at org.flywaydb.core.Flyway.execute(Flyway.java:1373)
at org.flywaydb.core.Flyway.migrate(Flyway.java:917)
at org.flywaydb.commandline.Main.executeOperation(Main.java:139)
at org.flywaydb.commandline.Main.main(Main.java:102)
ERROR: Unable to restore autocommit to original value for connection
java.sql.SQLRecoverableException: Getrennte Verbindung
at oracle.jdbc.driver.PhysicalConnection.setAutoCommit(PhysicalConnection.java:3775)
at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:96)
at org.flywaydb.core.internal.command.DbMigrate.applyMigration(DbMigrate.java:305)
at org.flywaydb.core.internal.command.DbMigrate.access$1000(DbMigrate.java:47)
at org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:230)
at org.flywaydb.core.internal.command.DbMigrate$2.doInTransaction(DbMigrate.java:173)
at org.flywaydb.core.internal.util.jdbc.TransactionTemplate.execute(TransactionTemplate.java:72)
at org.flywaydb.core.internal.command.DbMigrate.migrate(DbMigrate.java:173)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:959)
at org.flywaydb.core.Flyway$1.execute(Flyway.java:917)
at org.flywaydb.core.Flyway.execute(Flyway.java:1373)
at org.flywaydb.core.Flyway.migrate(Flyway.java:917)
at org.flywaydb.commandline.Main.executeOperation(Main.java:139)
at org.flywaydb.commandline.Main.main(Main.java:102)
ERROR: Migration of schema "FLYWAY_DEMO" to version 1 - Create table failed! Please restore backups and roll back database and code!
ERROR: Error restoring current schema to its original setting

No idea why the connection to your DB got severed, this is however something you should check in your networking setup. When this is working properly Flyway does clearly return and display any error that is returned by the database.


fix(lists): do not double parse sub lists

Nested lists we're passed through inlineBlock n-times where n is the nesting level. This fix passes a to inlineBlock separate from the list tail (b).
Hopefully this doesn't break any other use cases :)
🌴

Thanks for the PR :)
This too seems right on first glance, I will double check when I find the time.

Sorry, for the late response.
Sadly your code breaks multi line list elements.
Code like this should still work:
1. Lists can be structured and layered
  does this still work
  **inline code in lists work**
  Link [test](test)


How to register a different object displayer

Describe the bug
My widget - Buckaroo, is meant to be a better experience for viewing dataframes in notebook environments.  In jupyter, I can register displayers.
It is unclear how to do that in Marimo.  Your built in dataframe viewer is already registered.  Do you plan to let people register their own object displayers?
FWIW here is the code to do that in jupyter, adapted from my library
from IPython.core.getipython import get_ipython
try:
    def _display_as_buckaroo(df):
        from IPython.display import display
        try:
            bw = buckaroo_kls(df, debug=debug)
            return display(bw)
        except:
            if debug:
                traceback.print_exc()
                return
            # returning NotImplementedError causes IPython to find the
            # next registered formatter for the type
            raise NotImplementedError
    ip = get_ipython()
    ip_formatter = ip.display_formatter.ipython_display_formatter
    ip_formatter.for_type(pd.DataFrame, _display_as_buckaroo)

except:
    pass

Environment
N/A
Code to reproduce
N/a

Sorry.  I just found the docs
https://docs.marimo.io/guides/integrating_with_marimo/displaying_objects.html#option-4-add-a-formatter-to-the-marimo-repo


How to reload model and predict?

Hi GMvandeVen,  the model will be saved after run
./main_cl.py --experiment=splitMNIST --scenario=class --replay=generative --brain-inspired --pdf
is there any command to load trained model and use the model to predict?

Hi, you can use the option --test to load a previously trained model and evaluate its performance.
If you initially used this command to train the model:
./main_cl.py --experiment=splitMNIST --scenario=class --replay=generative --brain-inspired --pdf
Then you can use the following command to load that model and test it:
./main_cl.py --experiment=splitMNIST --scenario=class --replay=generative --brain-inspired --pdf --test

works great, thanks.


Update linux-install-manually.md

Updated steps to enable realtime protectoin

Issue#https://github.com/MicrosoftDocs/microsoft-365-docs/issues/7514

@mjcaparas Please merge this PR. Thanks


Fast lsa deberta large error

My code is:
import random
import torch
from pyabsa.functional import Trainer
from pyabsa.functional import APCConfigManager
from pyabsa.functional import ABSADatasetList
from pyabsa.functional import APCModelList
import warnings
warnings.filterwarnings('ignore')
seeds = [random.randint(0, 10000) for _ in range(2)]
apc_config_english = APCConfigManager.get_apc_config_english()
apc_config_english.model = APCModelList.FAST_LSA_T
apc_config_english.lcf = 'cdw'
apc_config_english.similarity_threshold = 1
apc_config_english.max_seq_len = 80
apc_config_english.dropout = 0
apc_config_english.cache_dataset = False
apc_config_english.patience = 10
apc_config_english.optimizer = 'radam'
apc_config_english.pretrained_bert = 'microsoft/deberta-v3-large'
apc_config_english.hidden_dim = 1024
apc_config_english.embed_dim = 1024
apc_config_english.num_epoch = 1
apc_config_english.log_step = 50
apc_config_english.learning_rate = 1e-5
apc_config_english.batch_size = 16
apc_config_english.evaluate_begin = 0
apc_config_english.l2reg = 1e-8
apc_config_english.seed = seeds
apc_config_english.cross_validate_fold = -1  # disable cross_validate
CryptoDataset = ABSADatasetList.CryptoCustom
sent_classifier = Trainer(config=apc_config_english,
dataset=CryptoDataset,  # train set and test set will be automatically detected
checkpoint_save_mode=2,  # =None to avoid save model
auto_device=True  # automatic choose CUDA or CPU
).load_trained_model()
Error happens in the end of training:
Traceback (most recent call last):
File "/home/ubuntu/nlp/PyABSA/demos/aspect_polarity_classification/train_apc_crypto_lsa_deberta_large.py", line 39, in
sent_classifier = Trainer(config=apc_config_english,
File "/home/ubuntu/nlp/PyABSA/pyabsa/functional/trainer/trainer.py", line 135, in init
self.train()
File "/home/ubuntu/nlp/PyABSA/pyabsa/functional/trainer/trainer.py", line 163, in train
if os.path.exists(max(model_path)):
TypeError: '>' not supported between instances of 'APCEnsembler' and 'APCEnsembler'
Please help.

I can not reproduce your problem, can you reproduce this issue with provided datasets?

I think i found the problem. It happens because I give it only 1 training epoch (apc_config_english.num_epoch = 1), and during training there is no accuracy shown (it was for testing purposes). So I increased the num_epochs and it works.


Running the Unit Tests

Trying to tun the unit tests from the pygccxm source unitests dir, used to  able to do so, now with python2/python3.
python decl_string_tester.py
Traceback (most recent call last):
File "decl_string_tester.py", line 9, in
from . import autoconfig
ValueError: Attempted relative import in non-package

Hi. Yes, I changed that lately. You can use python3 -m unittests.decl_string_tester.
I documented this in the readme too: cbba23503c37e204266daf1e2c91eab91fb61a27

Sorry I missed (i.e. didn't read) the updated readme.

I updated the readme after you opened this bug, so no blame here. Feel free to ask questions, feedback is always welcome.


a Simple and Fun Quiz App

Description
Please include a summary of the change and which issue is fixed. Please also include relevant motivation and context. List any dependencies that are required for this change.
Fixes # (issue)
Type of change
Please delete options that are not relevant.
How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce.
Checklist:

[x] I have performed a self-review of my own code
[x] My changes generate no new warnings
[x] I have added tests that prove my fix is effective or that my feature works

Its really a dirty work and dirty code also.

This is one of the most incredible play I've seen! I shall start doing code reviews soon.

This is one of the most incredible play I've seen! I shall start doing code reviews soon.

Give me the reviewing i am free

This is one of the most incredible play I've seen! I shall start doing code reviews soon.

Thanks. I see a bug. Will fix at next push.

sorry i was mistaken about the bug. i think its working good. although i fixed a "key" was missing while mapping array.

@Angryman18 Could you please create an issue for the play and associate with the PR to start the review?

@Angryman18 Could you please create an issue for the play and associate with the PR to start the review?

Created sir.

@Angryman18 Could you please create an issue for the play and associate with the PR to start the review?

Created sir.

Thanks but it was not done correctly.
So next time,

You need to create a play request if it is a play, else a bug or feature.
After creating the issue you can attach it to a PR(if already exist) from the right side setting of an issue.

ah. sorry about that. not very good on github yet but i learned a lot in recent days.

This is one of the most incredible play I've seen! I shall start doing code reviews soon.

Give me the reviewing and merging i am free

Please go ahead and finish the review

LGTM

Thanks, @koustov please finish your review too.

Started reviewing. I will finish it soon.

@Angryman18 this is a great play ❤. I am fully energized to see the granularity maintained here.

ok i will fix by night

i dont see any issue with hover. we only want to show pointer when its hovered. so eitherway it works the same.
and i believe only questions would be coming from the api so i didnt add additional validiation there.
and for nullable, i dont understand if you are talking about current question if so then current question cannot be null. its defined with a value and some certain conditions are applied for updating it's value  (when timer gets timed out or user clicks "confirm" button or at veryfirst clicking "Let start" button).

i dont see any issue with hover. we only want to show pointer when its hovered. so eitherway it works the same. and i believe only questions would be coming from the api so i didnt add additional validiation there. and for nullable, i dont understand if you are talking about current question if so then current question cannot be null. its defined with a value and some certain conditions are applied for updating it's value (when timer gets timed out or user clicks "confirm" button or at veryfirst clicking "Let start" button).

Look like we are close to getting done with the comments. Can't wait to see this one crossing the border...
@Angryman18 @koustov

@Angryman18 is it ready to be reviewed one last time?

i think the required changes are made.


Update Browser & Device Support docs

Select one ...  (check one with "x")
[ ] bug
[ ] feature request
[x] enhancement

Expected behavior
Clearer documentation on what browsers we support.
Questions to answer

How do we define a version? Should this be release or something else?
We show that we support mobile devices

Does this mean that we also support all of the listed browsers that are available on mobile devices?
Is this all mobile devices?

Actual behavior
As of now, we say

Clarity only supports the latest two versions of the listed browsers, with the exception of Internet Explorer.

We are getting questions/issues on support for Safari 9.1 and Mobile Safari.
Reproduction of behavior

Environment details

Clarity version: 0.10.0

Browser: all

We should try to get this into the 4.0 website work. I think it involves a different graphical treatment and not much else. #4005

We've revised our documentation with the new website for more depth and it is available now.

We've revised our documentation with the new website for more depth and it is available now.


What format should the 'event' variable take in client events

I've noticed a few different versions of the event variable already:
We've got:
function (e) { ... }

function (event) {...}

function (event, template) { ... } // admittedly me, and probably not common or necessary

The Meteor Style Guide doesn't give a preference here, but it should be consistent.

It should be event.

It's not in their style guide, but it is in their contribution guide.

One thing to take note of is that Blaze Components event handlers don't have the second argument being the template instance.
this is the template instance.


Pretrained Checkpoints

Hi,
Do you have the pretrained checkpoints available yet?
Regards,
Gaurav

Sry for a delayed response. The pretrained checkpoints are now available. Also since the results have been updated, a new arxiv version of the manuscript will be available soon (depending on arxiv processing times). Closing this for now!


How to use threadx on the basis of freertos

Like threadx provides freertos api

We have a FreeRTOS conversion layer here: https://github.com/azure-rtos/threadx/tree/master/utility/rtos_compatibility_layers/FreeRTOS

@goldscott I wasn't accurate enough. It should be like linux port or win port, provide a freertos port

I don't understand what you are asking for. ThreadX is a different operating system than FreeRTOS. In my previous comment, I linked to a conversion layer that allows you to use a FreeRTOS application with ThreadX as the actual RTOS.

@goldscott I want to use threadx on esp32s2. esp32s2 is developed using esp-idf, and some functions are bound to freertos provided by esp-idf, I want to use threadx on top of this.
Although ports/xtensa is provided, this is not the best solution for esp32s2.
What I expect like is ports/linux or ports/win32 to simulate the basic functions of threadx with the system's api. In this way, the original function can not be affected to the greatest extent, and threadx can also be used.

The only ThreadX port we have for esp32 is the xtensa port, so you'd have to use that.
I'm still not sure what you are trying to do. You are trying to simulate ThreadX with FreeRTOS? Or a conversion layer that converts ThreadX to underlying FreeRTOS?

@goldscott
Add a threadx/ports/freertos
If the role of threadx/ports/linux is to make threadx work on linux, then threadx/ports/freertos is to make threadx work on freertos

ThreadX on Linux is a special port compared to the rest of the ports. ThreadX actually uses posix pthreads for each ThreadX thread, and the ThreadX scheduler runs in a high priority pthread. This scheme will not work on FreeRTOS.


Kicad project not in root folder

I am setting a project to use the info from here as a starting point.
Does this tool work if the Kicad project is inside a folder instead of the root path of the repo?

Of course you can have the files in another folder.
If you take a look at all the regression tests for the KiPlot and kicad-automation-scripts you'll see that the KiCad files are always in another folder.
You just need to specify the KiCad file and the YAML file using -b and -c command line options.
KiPlot tries to be "smart" by guessing what you want, so another option is to change the current directory to where you files are located and run KiPlot there.
A more complex case is this project:
https://gitlab.com/set-soft/kicad-ci-test-spora/
Here 3 PCBs are included. The solution is quite clean, using makefiles to contain the commands.