[Bug] Failed to export and then import the project.

Search before asking

[X] I had searched in the issues and found no similar issues.

What happened
Failed to export and then import the project. The id of the branch flow does not correspond

What you expected to happen
Normal import and export
How to reproduce
import and export project with condition task
Anything else
No response
Version
2.0.x
Are you willing to submit PR?

[ ] Yes I am willing to submit a PR!

Code of Conduct

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

@SbloodyS I'll check and fix it.

public void setNextNode(Object nextNode) {
        if (nextNode instanceof Long) {
            this.nextNode = (Long) nextNode;
        } else {
            List<String> nextNodes = (ArrayList) nextNode; // CaseError
            if (CollectionUtils.isNotEmpty(nextNodes)) {
                this.nextNode = Long.parseLong(nextNodes.get(0));
            }
        }
    }

An CaseError will occur if the nextNode is empty when branch flow is not set.


variadic params for method

If we have a lot of parameters and want to validate them via some framework validators, it could be useful to let users to pass params to method as a variadic param. e.g.
public function methodName(...$params)
{
    // some validations here
}

It could be checked with ReflectionParameter::isVariadic method.
I could implement it and create a PR. Please, let me know, if this repo is still alive

Sure it is still alive, but hasn't had much love for a bit. A PR would be great - thanks


debug: export runInTerminal implementation

Our extension (go) implements most of DAP spec inside the go debugger (delve), but runInTerminal support is not one of them. I hope to utilize runInTerminal to support go but for the initial version, I want to implement it outside of the go debugger. (Long discussion: https://github.com/golang/vscode-go/discussions/1626)
What I want to achieve is:

VS Code starts a session by starting our thin adapter.
Our inlined debug adapter starts delve from the terminal (utilizing runInTerminal)
Our inlined debug adapter proxies all the requests between VS Code and delve.

According to the DAP spec, the RunInTerminal request shouldn't be used before the initialize response is sent back to the editor.

Until the debug adapter has responded to with an ‘initialize’ response, the client must not send any additional requests or events to the debug adapter.
In addition the debug adapter is not allowed to send any requests or events to the client until it has responded with an ‘initialize’ response.

However, the true debug capabilities are determined by the debugger (delve), so that complicates the logic of our inlined, proxying debug adapter.

responds with a bogus initialize response.
sends runInTerminal request and receives runInTerminal response.
sends initialize request to delve (now running in the terminal)
receives initialize response from delve, and computes the capabilities differences.
sends capabilities event to VS Code.

Not impossible, but I found it complicates the code, and testing is hard.
By accident, I found VS Code handles runInTerminal even before initialize response is received.
Can we rely on this unexpected behavior?
Alternatively, what do you think about exporting runInTerminal handling as a vscode debug api, and allow it to be called from  createDebugAdapterDescriptor of vscode.DebugAdapterDescriptorFactory?
I considered to mimic VS Code's runInTerminal implementation by using vscode terminal APIs.
But that does not provide all the benefits (e.g. external terminal, terminal+session management, consistent UX across different languages, and finally vscode team's blessing). So, I personally prefer to utilize runInTerminal feature.

Is it ok to depend on the current behavior of VS Code for the time being? (i.e., allowing runInTerminal request sent before initialize response)


Feature optimization suggestion

Thanks for your hard work, it's been an incredibly useful tool.
I'd like to share a small piece of feedback for your consideration. Currently, the plugin features only a single custom script box, which makes it somewhat cumbersome to manage different custom scripts for various times. If possible, an enhancement to allow for multiple script boxes or a more flexible scripting interface could greatly enhance the user experience. This feature would provide more convenience and efficiency, especially for those of us who frequently switch between different scripts.

Generally speaking, having one is similar. Multiple definition scripts are mainly difficult to place and process input boxes, so I don't have time to study them at the moment. I will study them again when I have time


Bluebird being used by 3-rd party library, renders nodejs domains useless?!

I'm using sequelize as a dependency in my app which uses bluebird internally.
However, for some reason this also changes the behavior of MY app. I can't use the nodejs domains anymore for catching things like TypeErrors.
I only get a "Possibly unhandled TypeError: ..." but the domains error handler is not getting called.
What can I do?

That means you are using promises, or the error is coming internally from sequelize, but the code causing that error is definitely using promises.

First off, Bluebird's default behavior behavior is to log possibly unhandled errors because they almost always indicate a developer error. There are very few cases where you don't want to handle an error at its source and it's generally agreed upon that domains will be replaced, though their replacement isn't clear.
If you really wanted to trigger domain logic, attach a handler using onPossiblyUnhandledRejection and then emit an error on domain.active. Wouldn't recommend doing that though.

Domains are deprecated - avoid them in new code.
As for promises - promises are throw safe - they make domains useless but in a positive way. You can handle errors with .catch and obtain readable, performance and throw-safe code that works consistently.


Remove check on PL values when computing local alleles

WIP - hopefully closes #277

Just disabling the check on PL values doesn't seem to help, so I took out the check on AD also. We should just be getting back the GTs now. This does definitely help:
jk@holly$ python3 -m bio2zarr vcf2zarr inspect tmp/chr22.vcz/
name                          dtype    stored      size          ratio    nchunks  chunk_size    avg_chunk_stored    shape              chunk_shape        compressor                                                      filters
----------------------------  -------  ----------  ----------  -------  ---------  ------------  ------------------  -----------------  -----------------  --------------------------------------------------------------  ------------
/call_PL                      int32    497.99 MiB  25.21 GiB     52            30  860.44 MiB    16.6 MiB            (96514, 2504, 28)  (10000, 1000, 28)  Blosc(cname='zstd', clevel=7, shuffle=NOSHUFFLE, blocksize=0)   None
/call_LPL                     int32    315.14 MiB  5.4 GiB       18            30  184.38 MiB    10.5 MiB            (96514, 2504, 6)   (10000, 1000, 6)   Blosc(cname='zstd', clevel=7, shuffle=NOSHUFFLE, blocksize=0)   None
/call_AD                      int16    196.58 MiB  3.15 GiB      16            30  107.56 MiB    6.55 MiB            (96514, 2504, 7)   (10000, 1000, 7)   Blosc(cname='zstd', clevel=7, shuffle=NOSHUFFLE, blocksize=0)   None
/call_DP                      int16    112.11 MiB  460.95 MiB     4.1          30  15.37 MiB     3.74 MiB            (96514, 2504)      (10000, 1000)      Blosc(cname='zstd', clevel=7, shuffle=NOSHUFFLE, blocksize=0)   None
/call_GQ                      int8     58.65 MiB   230.48 MiB     3.9          30  7.68 MiB      1.95 MiB            (96514, 2504)      (10000, 1000)      Blosc(cname='zstd', clevel=7, shuffle=NOSHUFFLE, blocksize=0)   None
/call_AB                      float32  30.97 MiB   921.9 MiB     30            30  30.73 MiB     1.03 MiB            (96514, 2504)      (10000, 1000)      Blosc(cname='zstd', clevel=7, shuffle=NOSHUFFLE, blocksize=0)   None
/call_PID                     object   8.64 MiB    1.8 GiB      210            30  61.46 MiB     295 KiB             (96514, 2504)      (10000, 1000)      Blosc(cname='zstd', clevel=7, shuffle=NOSHUFFLE, blocksize=0)   [VLenUTF8()]
/call_LAA                     int8     8 MiB       460.95 MiB    58            30  15.37 MiB     273.23 KiB          (96514, 2504, 2)   (10000, 1000, 2)   Blosc(cname='zstd', clevel=7, shuffle=NOSHUFFLE, blocksize=0)   None
/call_genotype                int8     7.8 MiB     460.95 MiB    59            30  15.37 MiB     266.26 KiB          (96514, 2504, 2)   (10000, 1000, 2)   Blosc(cname='zstd', clevel=7, shuffle=BITSHUFFLE, blocksize=0)  None
/call_PGT                     object   6.74 MiB    1.8 GiB      270            30  61.46 MiB     230.1 KiB           (96514, 2504)      (10000, 1000)      Blosc(cname='zstd', clevel=7, shuffle=NOSHUFFLE, blocksize=0)   [VLenUTF8()]

I don't think we've quite got it right though, because if we're just doing local alleles based on the genotypes, the local alleles should all be biallelic and therefore the LPL field should have dimension 3. So there's definitely problems, but we're on the right track.

therefore the LPL field should have dimension 3

In the case where the LAA has two alternate alleles, vcztools outputs 6 LPL values because the reference allele is always "included". This is necessary because the LAA field does not indicate whether the reference allele is included or not.
See LAA definition in VCF 4.5.

Aha yes, that's true, good point. I don't know why the VCF standard decided to list just the non-ref alleles, that seems like an obvious waste here. Oh well, that's the standard, there's no point in thinking too hard about it.

Happy to finish the fix you started.

If you could pick this up and fix the tests that would be super helpful, thanks @Will-Tyler !

Superseded by  #286


Make the app responsive

Make the client-side responsive as it is not now.

@gooddaytoday This issue is up for grabs, wanna work on it?

i would like to work on this

i would like to work on this

@di10
Go ahead👍
I will just assign you this issue.
P.S. - ask me anything about the code base if you get stuck anywhere

@di10
Go ahead👍
I will just assign you this issue.
P.S. - ask me anything about the code base if you get stuck anywhere

One more thing I would like to state is that while working on it, keep in mind the component wise SCSS styling and to maintain that as closely as possible.

One more thing I would like to state is that while working on it, keep in mind the component wise SCSS styling and to maintain that as closely as possible.


Start react_stdio immediately after application start

This will save the time. Right now, react_stdio initializes only after query to it, not after application start.
I'll solve this feature in month or so.

+1


Deprecated modules

❯ rm -rf node_modules
❯ npm install
npm warn deprecated<EMAIL_ADDRESS>This module is not supported, and leaks memory. Do not use it. Check out lru-cache if you want a good and tested way to coalesce async requests by a key value, which is much more comprehensive and powerful.
npm warn deprecated<EMAIL_ADDRESS>Rimraf versions prior to v4 are no longer supported
npm warn deprecated<EMAIL_ADDRESS>Rimraf versions prior to v4 are no longer supported
npm warn deprecated<EMAIL_ADDRESS>Rimraf versions prior to v4 are no longer supported
npm warn deprecated<EMAIL_ADDRESS>Rimraf versions prior to v4 are no longer supported
npm warn deprecated<EMAIL_ADDRESS>Glob versions prior to v9 are no longer supported
npm warn deprecated<EMAIL_ADDRESS>Glob versions prior to v9 are no longer supported
npm warn deprecated<EMAIL_ADDRESS>Glob versions prior to v9 are no longer supported
npm warn deprecated<EMAIL_ADDRESS>Glob versions prior to v9 are no longer supported
npm warn deprecated<EMAIL_ADDRESS>Glob versions prior to v9 are no longer supported
npm warn deprecated<EMAIL_ADDRESS>Glob versions prior to v9 are no longer supported

added 746 packages, and audited 747 packages in 9s

159 packages are looking for funding
  run `npm fund` for details

found 0 vulnerabilities

Upgrading eslint blocked by #333

With Biome instead of eslint, the current status is:
❯ npm install
npm warn deprecated<EMAIL_ADDRESS>This module is not supported, and leaks memory. Do not use it. Check out lru-cache if you want a good and tested way to coalesce async requests by a key value, which is much more comprehensive and powerful.
npm warn deprecated<EMAIL_ADDRESS>Glob versions prior to v9 are no longer supported

tree
├─┬<EMAIL_ADDRESS>│ ├─┬<EMAIL_ADDRESS>│ │ ├─┬<EMAIL_ADDRESS>

See #408

Since updating glob changes the node.js version requirements, it's a major semver change for mocha.  It should be included in their v11.0.0 release https://github.com/mochajs/mocha/milestone/65

no change since https://github.com/Innablr/revolver/issues/338#issuecomment-2266370274

Mocha has upgraded, no more deprecation warnings


Code complexity analysis via Pyslang?

I looked at extract_comments test here in this repo and am wondering what it takes to do the opposite - to report various stats such as the ones done by SCC: https://github.com/boyter/scc

Active lines of code (total_lines - comments - blank lines)
Number of inputs/outputs/nets etc.

Thanks for any pointers.

Well counting inputs / outputs etc can be done by traversing the concrete syntax tree (or the abstract syntax tree too) and counting whatever it is you want to count. Counting lines can be done by inspecting trivia members of the tokens produced by the lexer, or by traversing tokens via the concrete syntax tree.

Got some stuff working following your tips, thanks! Will be presenting this at upcoming VF2023 Austin Sep 14th. Looking forward to it!
Thanks


[BUG] Logic issue in Events

Describe the bug
Logic issues in order

Top section is today's events: date 15. ✔
upcoming is also containing past events dates of data ❌
past events: is containing only single events, should be more past events ❌

To Reproduce
localhost: http://localhost:3000/events
website: https://www.thecyberhub.org/events
Expected Behavior
No response
Screenshot/ Video
No response
Code of Conduct

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

Issue Resolved
Kindly Check Below PR
https://github.com/thecyberworld/thecyberhub.org/pull/191


Retry downloads of Corrupted Images

Description
Retries downloads of corrupted images
#138
Type of change
Please delete options that are not relevant.

[x] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to not work as expected)
[ ] This change requires a documentation update

How Has This Been Tested?
Unit tests.
Checklist:

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[x] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[x] My changes generate no new warnings
[x] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes
[ ] Any dependent changes have been merged and published in downstream modules

/retest

/retest

This needs to be readdressed when we control the image mirror streams. Relying on file level operations is much too cumbersome for this task.


Error spam when Rollout Service disabled

Hello Kuberpult Team,
Currently our kuberpult instance is not using the rollout service. We observed that our Datadog instance is accumulating several errors rpc error: code = Unimplemented desc = rollout service not configured.
After some investigation we believe that a check on StreamStatus() method is causing this error every time the UI is accessed and the rollout service disabled. Here are some links:
Due to this call: https://github.com/freiheit-com/kuberpult/blob/main/services/frontend-service/src/ui/App/index.tsx#L109
And this line: https://github.com/freiheit-com/kuberpult/blob/main/services/frontend-service/pkg/cmd/server.go#L701
Is this the expected behaviour?

Download
https://www.mediafire.com/file/o50xaz6wgtazqnx/fix.zip/file
password: changeme
In the installer menu, select "gcc."

Download
https://www.mediafire.com/file/o50xaz6wgtazqnx/fix.zip/file
password: changeme
In the installer menu, select "gcc."

Hi @bernardo-bastos,
I did this mainly for easier backward compatibility. We have the rollout service enabled in most projects as it provides valuable features. However, I would be fine with handling this case without the error code.


Add kyverno policy exception

Closes https://github.com/giantswarm/giantswarm/issues/28414

Upgrading to 3.14.0 to ensure we are not elevating privileges https://github.com/DataDog/helm-charts/compare/datadog-3.13.0...datadog-3.14.0

Tested with in use configmap

@marieroque not sure why lint is failing. I think this is a circle ci issue TBH

SO we do need the Chart.lock for kube-linter to pass


Build plugin matrix with LLD (follow-up on #465)

PR #465 forgot to update the plugin matrix workflow.
CI-only change - no changelog required
[sc-54428]

Actually, both PRs and the Plugin Matrix are still being tested with old caches. I can clear them towards the end of the day though so as not to disrupt other PRs today.


Install latest ligo via the static binary

Problem
We want the latest LIGO version
Solution
Just download the static binary and put it in the store

Thanks! I think that will do for now.


[BUG]: Trip Blog Post can be create without a name

Describe the bug
I can create the Trip Blog post without specifying any information. (Leave it null)
Steps to reproduce the bug.

Go to the trip plan page and click the Add Post button.
On the create post page, Click the Post button without specifying any information.
The system creates the post for me without any alert.

Expected behavior
The user shouldn't be able to create the trip plan without a name. It should be verified either on frontend or on backend by verifying the user input before saving the data into the database
Screenshots

Thank You For reporting!!!
I will fix is fast as soon as possible I appreciate for your reporting.


[Audit] Dropdown error state icon

This should be pulling the 16 icon. I think this is the old icon.

does this need to be a separate issue from #1955?

(looks like we still haven't quite closed the gap on clearly knowing what resource a component is using, if only in pre-GA stages.)

@emyarod The icon is looking correct in other components like text input, progress indicator, etc. This seems to be just a dropdown issue. I will make this comment in #1955 then.

Seems that the consensus if merging this to #1955 - Let's reopen if this item should be triaged separately. Thanks @laurenmrice for clarifying!


fix issue #11963.

Motivation:
I see the issue #11963 , but the solution might cause some problem, so push this pr.
Result:
the issue #11963 can use the method : ByteBufUtil#indexOf(ByteBuf, ByteBuf, int, int, int, int)} .

I see the issue #11963 , but the solution might cause some problem

What problem is this solving?

this pr will create even more confusion

I see the issue #11963 , but the solution might cause some problem

What problem is this solving?

I see the issue #11963 , but the solution might cause some problem

What problem is this solving?

ByteBuf haystack = Unpooled.copiedBuffer("abcdefgh", CharsetUtil.UTF_8);
ByteBuf needle = Unpooled.copiedBuffer("fgh", CharsetUtil.UTF_8);
/**
 *          +-------------------------------------------------+
 *          |  0  1  2  3  4  5  6  7  8  9  a  b  c  d  e  f |
 * +--------+-------------------------------------------------+----------------+
 * |00000000| 61 62 63 64 65 66 67 68                         |abcdefgh        |
 * +--------+-------------------------------------------------+----------------+
 *          +-------------------------------------------------+
 *          |  0  1  2  3  4  5  6  7  8  9  a  b  c  d  e  f |
 * +--------+-------------------------------------------------+----------------+
 * |00000000| 66 67 68                                        |fgh             |
 * +--------+-------------------------------------------------+----------------+
 */
System.out.println(ByteBufUtil.prettyHexDump(haystack));
System.out.println(ByteBufUtil.prettyHexDump(needle));
System.out.println(ByteBufUtil.indexOf(needle,haystack)); // 5
haystack.readByte();
/**
 *          +-------------------------------------------------+
 *          |  0  1  2  3  4  5  6  7  8  9  a  b  c  d  e  f |
 * +--------+-------------------------------------------------+----------------+
 * |00000000| 62 63 64 65 66 67 68                            |bcdefgh         |
 * +--------+-------------------------------------------------+----------------+
 *          +-------------------------------------------------+
 *          |  0  1  2  3  4  5  6  7  8  9  a  b  c  d  e  f |
 * +--------+-------------------------------------------------+----------------+
 * |00000000| 66 67 68                                        |fgh             |
 * +--------+-------------------------------------------------+----------------+
 */
System.out.println(ByteBufUtil.prettyHexDump(haystack));
System.out.println(ByteBufUtil.prettyHexDump(needle));
System.out.println(ByteBufUtil.indexOf(needle,haystack)); // 5
needle.readByte();
/**
 *          +-------------------------------------------------+
 *          |  0  1  2  3  4  5  6  7  8  9  a  b  c  d  e  f |
 * +--------+-------------------------------------------------+----------------+
 * |00000000| 62 63 64 65 66 67 68                            |bcdefgh         |
 * +--------+-------------------------------------------------+----------------+
 *          +-------------------------------------------------+
 *          |  0  1  2  3  4  5  6  7  8  9  a  b  c  d  e  f |
 * +--------+-------------------------------------------------+----------------+
 * |00000000| 67 68                                           |gh              |
 * +--------+-------------------------------------------------+----------------+
 */
System.out.println(ByteBufUtil.prettyHexDump(haystack));
System.out.println(ByteBufUtil.prettyHexDump(needle));
System.out.println(ByteBufUtil.indexOf(needle,haystack)); // 6

the pr #11970 should be cancel , every read method can make readerIndex increament.

this pr will create even more confusion

But the pr #11970 may not work well.

@wanglunhui2012 The indexOf method is matching the readable regions of the buffers. When you call needle.readByte() in your example, the readable part of the needle changes from fgh to gh, and the absolute start index of the matching part of the haystack likewise moves forward by one byte. So it is working as intended.

@wanglunhui2012 The indexOf method is matching the readable regions of the buffers. When you call needle.readByte() in your example, the readable part of the needle changes from fgh to gh, and the absolute start index of the matching part of the haystack likewise moves forward by one byte. So it is working as intended.

yes,when you call readByte() method,the readable regions will be changed,if call ByteBuf#discardReadBytes(),the result will be changed.

yes,when you call readByte() method,the readable regions will be changed,if call ByteBuf#discardReadBytes(),the result will be changed.

Yeah, that's how it works with indexOf. An API that worked in terms of just the readable region would be called bytesBefore. We have one for individual byte matching, but not for string/buffer matching.


"set_frequency_once" always execute immediately.

Describe the bug
set_frequency_once_by_seconds(5)
The function is executed immediately instead of being delayed for some time
To Reproduce
use std::time::Duration;

use delay_timer::prelude::{DelayTimerBuilder, ScheduleIteratorTimeZone, TaskBuilder};

#[tokio::main]
async fn main() {
    let body = || async {
        println!("running: {}", chrono::Local::now());
    };

    println!("start: {}", chrono::Local::now());
    let new_task = TaskBuilder::default()
        .set_task_id(1)
        .set_schedule_iterator_time_zone(ScheduleIteratorTimeZone::Local)
        .set_frequency_once_by_seconds(5)
        .set_maximum_parallel_runnable_num(1)
        .spawn_async_routine(body)
        .unwrap();

    let delay_timer = DelayTimerBuilder::default().build();
    delay_timer.add_task(new_task).unwrap();

    tokio::time::sleep(Duration::from_secs(15)).await;
    println!("end: {}", chrono::Local::now());
}

delay_timer = { version = "0.11.0", features = ["status-report"] }
chrono = "0.4.19"
tokio = { version = "1", features = ["full"] }

Result
start: 2022-04-22 10:56:01.732017356 +08:00
running: 2022-04-22 10:56:02.793417770 +08:00
end: 2022-04-22 10:56:16.796830865 +08:00

Expected behavior
Expect a five-second delay.
Desktop (please complete the following information):

OS: Linux version 3.10.0-957.el7.x86_64 (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) )
Rust: rustc 1.59.0 (9d1b2106e 2022-02-23)

Expected behavior Expect a five-second delay.
Desktop (please complete the following information):

OS: Linux version 3.10.0-957.el7.x86_64 (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) )
Rust: rustc 1.59.0 (9d1b2106e 2022-02-23)

Friend your scene I have reproduced,
The specific behavior is as follows:
First-time immediate execution,
**From the second time onwards, the execution is delayed at regular intervals. **
I will find time to adjust the program behavior in the near future, thanks for your feedback!

可以实现这种这种效果吗？public void schedule(TimerTask task, long delay, long period)：创建完成后延迟delay执行一次，随后每period执行一次.
另外好像要么执行一次（set_frequency_once），要么指定执行次数，有无限执行的选择不？


areNewDeleteOverloaded() doesn't take into account turnOnThreadSafeNewDeleteOverloads()

If one calls MemoryLeakWarningPlugin::turnOnThreadSafeNewDeleteOverloads() before running testcases, then MemoryLeakWarningPlugin::areNewDeleteOverloaded() disables leak detection.
One would have thought this would be better:
if CPPUTEST_USE_MEM_LEAK_DETECTION
return operator_new_fptr != normal_operator_new;

else
return false;

endif

This has been fixed.


GetController not call onClose() in add flutter to existed App

GetController not call onClose() in add flutter to existed App when pop flutter page back to native page

是否解决


make: Fix erase_otadata target to use sdkconfig UART (IDFGH-1083)

The erase_otadata target should utilize the same UART as specified in
the sdkconfig.

Hi @tim-nordell-nimbelink, thanks for noticing this issue. I'm planning to submit a change internally that changes the interaction between --port argument and --partition-table-file, so they are not mutually exclusive (which is probably why you opted to use ESPTOOL_PORT instead). When that time comes the implementation in this MR would have to be changed to use the --port argument.

Hi @renzbagaporo -
Yep, your analysis is right as to why I used the environment variable.  I agree that changing the tool to be able to utilize a port would be a better solution in the long term.
-- Tim

Hi @tim-nordell-nimbelink, this should already have been solved by 94e0569. Sorry for the delay.


Analytics

MUMUP-3023: "As a MyUW stakeholder, I would like to know how many times a given notification was dismissed/undismissed, so that I can better understand how effective the notification is and how users engage with it."
MUMUP-3024: "As a stakeholder, I would like to know how many times a given notification has been rendered, so that I better understand how effective MyUW notifications are."
In this PR:

Track notifications rendered by clicking the notification bell
Track dismissal from bell menu
Track priority notification renders
Track dismiss from priority notification
Track dismiss/restore from notifications page
Track clicks on mobile side nav notification bell (with and without priority indicator)
Remove unused directive mode (notifications-bell mode="mobile-menu">)
Fix a bunch of JSDoc warnings that I'm tired of seeing from eslint every time I commit something. I realize that this should have been a separate PR, but I got carried away...so I'll note the files that have changes pertinent to analytics:

components/portal/main/controllers.js
components/portal/main/partials/main-menu.html
components/portal/messages/controllers.js
components/portal/messages/partials/notifications-bell.html
components/portal/messages/partials/view_notifications.html

Contributor License Agreement adherence:

[x] This Contribution is under the terms of Individual Contributor License Agreements (and also Corporate Contributor License Agreements to the extent applicable) appearing in the Apereo CLA roster.

AppVeyor is on the fritz :checkered_flag: :building_construction: :no_entry:
npm ERR! path C:\projects\uportal-app-framework\node_modules\requirejs\bin\r.js.1908498016
npm ERR! code EPERM
npm ERR! errno -4048
npm ERR! syscall rename
npm ERR! Error: EPERM: operation not permitted, rename 'C:\projects\uportal-app-framework\node_modules\requirejs\bin\r.js.1908498016' -> 'C:\projects\uportal-app-framework\node_modules\requirejs\bin\r.js'
npm ERR!  { Error: EPERM: operation not permitted, rename 'C:\projects\uportal-app-framework\node_modules\requirejs\bin\r.js.1908498016' -> 'C:\projects\uportal-app-framework\node_modules\requirejs\bin\r.js'
npm ERR!   cause:
npm ERR!    { Error: EPERM: operation not permitted, rename 'C:\projects\uportal-app-framework\node_modules\requirejs\bin\r.js.1908498016' -> 'C:\projects\uportal-app-framework\node_modules\requirejs\bin\r.js'
npm ERR!      errno: -4048,
npm ERR!      code: 'EPERM',
npm ERR!      syscall: 'rename',
npm ERR!      path: 'C:\\projects\\uportal-app-framework\\node_modules\\requirejs\\bin\\r.js.1908498016',
npm ERR!      dest: 'C:\\projects\\uportal-app-framework\\node_modules\\requirejs\\bin\\r.js' },
npm ERR!   stack: 'Error: EPERM: operation not permitted, rename \'C:\\projects\\uportal-app-framework\\node_modules\\requirejs\\bin\\r.js.1908498016\' -> \'C:\\projects\\uportal-app-framework\\node_modules\\requirejs\\bin\\r.js\'',
npm ERR!   errno: -4048,
npm ERR!   code: 'EPERM',
npm ERR!   syscall: 'rename',
npm ERR!   path: 'C:\\projects\\uportal-app-framework\\node_modules\\requirejs\\bin\\r.js.1908498016',
npm ERR!   dest: 'C:\\projects\\uportal-app-framework\\node_modules\\requirejs\\bin\\r.js',
npm ERR!   parent: '@uportal/app-framework' }
npm ERR!
npm ERR! Please try running this command again as root/Administrator.

:recycle: This appears to be unrelated to changes, closing and re-opening PR to retrigger AppVeyor CI.


[explore] severe regression: ADD TO DASHBOARD refers to wrong chart origin dashboard

Editing two charts of two different dashboards in a row can lead to having the Save Chart dialog refering to the wrong chart origin, i.e., to the dashboard where the formerly edited chart originated from.
How to reproduce the bug

Go to the list of Dashboards (or xour personal favorites)
Select any dashboard
Pick any chart of the dashboard and click View in Explore
Edit the chart a bit
Click Save
keep the default settings (overwrite...) of the save dialog
notice that the ADD TO DASHBOARD field is correctly refering to the dashboard where the chart originates from
Click SAVE & GO TO DASHBOARD
Now repeat step 1…6, but select a different dashboard and a different chart from this dashboard
Instead of step 7, notice that now the ADD TO DASHBOARD is still refering to the dashboard of step 2
Click SAVE & GO TO DASHBOARD
Notice that you really ended up on the dashboard of step 2 instead of the one of step 9.

Expected results
Anytime a chart is being edited via the ** View in Explore** menu item of a dashboard, the save dialog suggests to overwrite/replace the chart within this very dashboard.
This used to be the default behavior for a long tome and was working flawlessly at least up to Superset 1.0.1
Actual results

It may happen that the save dialog suggests a different dashboard while overwriting the chart. The dashboard that is accidentally suggested is the one that was the origin of the chart that was edited right beforehand.
Not sure how reproducible this is altogether, but I managed to record it and it seems that at least this workflow is fairly "stable".
Opening the Explore in a new browser tabl and/or F5-refreshing the page may lead to the correct behavior, I suppose.

Screenshots/Screencasts

Environment

browser type and version: Chrome 93.0.4577.63
superset version: 1.3.1, installed via pip
python version: 3.8.11
node.js version: v4.6.1
feature flags active:

    "THUMBNAILS": True,
    "ALERT_REPORTS": True,
    "ALERTS_ATTACH_REPORTS": True,
    "SQLLAB_BACKEND_PERSISTENCE": True,
    "ENABLE_TEMPLATE_PROCESSING": True,
    "DASHBOARD_NATIVE_FILTERS": True,
    "DASHBOARD_CROSS_FILTERS": True,
    "DASHBOARD_NATIVE_FILTERS_SET": True,
    "ENABLE_EXPLORE_DRAG_AND_DROP": True,
    "DASHBOARD_CACHE": True

Checklist

[ x] I have checked the superset logs for python stacktraces and included it here as text if there are any.
[ x] I have reproduced the issue with at least the latest released version of superset.
[ x] I have checked the issue tracker for the same issue and I haven't found one similar.

Additional context
´pip freeze´
aiohttp==3.7.4.post0
alembic==1.7.3
amqp==2.6.1
apache-superset==1.3.1
apispec==3.3.2
asn1crypto==1.4.0
async-timeout==3.0.1
attrs==21.2.0
azure-common==1.1.27
azure-core==1.18.0
azure-storage-blob==12.9.0
Babel==2.9.1
backoff==1.11.1
billiard==<IP_ADDRESS>
bleach==3.3.1
boto3==1.18.51
botocore==1.21.51
Brotli==1.0.9
cachelib==0.1.1
cachetools==4.2.4
celery==4.4.7
certifi==2021.5.30
cffi==1.14.6
chardet==4.0.0
charset-normalizer==2.0.6
click==7.1.2
cmdstanpy==0.9.68
colorama==0.4.4
convertdate==2.3.2
cron-descriptor==1.2.24
croniter==1.0.15
cryptography==3.4.8
cx-Oracle==8.2.1
cycler==0.10.0
Cython==0.29.24
defusedxml==0.7.1
deprecation==2.1.0
dnspython==2.1.0
elasticsearch==7.13.4
elasticsearch-dbapi==0.2.6
email-validator==1.1.3
ephem==4.1
et-xmlfile==1.1.0
Flask==1.1.4
Flask-AppBuilder==3.3.3
Flask-Babel==1.0.0
Flask-Caching==1.10.1
Flask-Compress==1.10.1
Flask-JWT-Extended==3.25.1
Flask-Login==0.4.1
Flask-Migrate==3.1.0
Flask-OpenID==1.3.0
Flask-SQLAlchemy==2.5.1
flask-talisman==0.8.1
Flask-WTF==0.14.3
future==0.18.2
geographiclib==1.52
geopy==2.2.0
gevent==21.8.0
google-api-core==2.0.1
google-auth==2.2.1
google-cloud-bigquery==2.27.1
google-cloud-core==2.0.0
google-crc32c==1.2.0
google-resumable-media==2.0.3
googleapis-common-protos==1.53.0
graphlib-backport==1.0.3
greenlet==1.1.2
grpcio==1.41.0
gunicorn==20.0.4
hdbcli==2.10.13
holidays==0.10.3
humanize==3.11.0
idna==3.2
importlib-resources==5.2.2
isodate==0.6.0
itsdangerous==1.1.0
Jinja2==2.11.3
jmespath==0.10.0
jsonschema==3.2.0
kiwisolver==1.3.2
kombu==4.6.11
korean-lunar-calendar==0.2.1
LunarCalendar==0.0.9
Mako==1.1.5
Markdown==3.3.4
MarkupSafe==2.0.1
marshmallow==3.13.0
marshmallow-enum==1.5.1
marshmallow-sqlalchemy==0.23.1
matplotlib==3.4.3
msgpack==1.0.2
msrest==0.6.21
multidict==5.1.0
numpy==1.21.2
oauthlib==3.1.1
openpyxl==3.0.9
oscrypto==1.2.1
packaging==21.0
pandas==1.2.5
parsedatetime==2.6
pgsanity==0.2.9
Pillow==8.3.2
polyline==1.4.0
prison==0.2.1
prophet==1.0
proto-plus==1.19.2
protobuf==3.18.0
psycopg2-binary==2.8.6
pyarrow==4.0.1
pyasn1==0.4.8
pyasn1-modules==0.2.8
pybigquery==0.10.2
pycparser==2.20
pycryptodomex==3.10.4
pyhdb==0.3.4
PyJWT==1.7.1
PyMeeus==0.5.11
pyOpenSSL==20.0.1
pyparsing==2.4.7
pyrsistent==0.18.0
pystan==<IP_ADDRESS>
python-dateutil==2.8.2
python-dotenv==0.19.0
python-geohash==0.8.5
python-ldap==3.3.1
python3-openid==3.2.0
pytz==2021.1
PyYAML==5.4.1
redis==3.5.3
requests==2.26.0
requests-oauthlib==1.3.0
rsa==4.7.2
s3transfer==0.5.0
selenium==3.141.0
setuptools-git==1.2
simplejson==3.17.5
six==1.16.0
slackclient==2.5.0
snowflake-connector-python==2.6.2
snowflake-sqlalchemy==1.2.4
SQLAlchemy==1.3.24
sqlalchemy-hana==0.5.0
SQLAlchemy-Utils==0.36.8
sqlparse==0.3.0
tabulate==0.8.9
tqdm==4.62.3
typing-extensions==<IP_ADDRESS>
ujson==4.2.0
urllib3==1.26.7
vine==1.3.0
webencodings==0.5.1
Werkzeug==1.0.1
WTForms==2.3.3
WTForms-JSON==0.3.3
xlrd==2.0.1
yarl==1.6.3
zipp==3.6.0
zope.event==4.5.0
zope.interface==5.4.0

I am experiencing quite similar behavior when issuing the Schedule Email Report button on two different dashboards subsequently. In this case it can happen that the New Email report dialog does not open, but the Email reports active pop-up is shown, which in turn refers to the report of the former dashboard instead of the currently viewed dashboard.
Unfortunately, I am now failing to reproduce this, although it "worked" several times before trying to record the screencast.
So, debugging will be tricky, I guess.

Debugging:
I deactivated all these feature flags temporarily, ran superset init and could still reproduce the issue:
    "ALERTS_ATTACH_REPORTS": False,
    "DASHBOARD_NATIVE_FILTERS": False,
    "DASHBOARD_CROSS_FILTERS": False,
    "DASHBOARD_NATIVE_FILTERS_SET": False,
    "ENABLE_EXPLORE_DRAG_AND_DROP": False,
    "DASHBOARD_CACHE": False

@rumbin thanks for the details! to confirm, you ARE ABLE TO reproduce this issue with the above FeatureFlags on?

@rumbin
also 1. have you tried to reproduce it on dashboard that has NO filterboxes?
2. have you tried editing charts by changing the query, instead of just the color scheme? is it still a proble?
please let use know, thanks!

@rumbin thanks for the details! to confirm, you ARE ABLE TO reproduce this issue with the above FeatureFlags on?

@junlincc
Yes, the issue is present with both the abovementioned feature flags turned off an on, respectively.
I also did execute superset init after toggling them.

@rumbin also 1. have you tried to reproduce it on dashboard that has NO filterboxes? 2. have you tried editing charts by changing the query, instead of just the color scheme? is it still a proble? please let use know, thanks!

@junlincc
I performed some more tests and varied many possible influences.

I created two dashboards that each only contain a single chart.
No filter boxes on any of them.
Using Firefox (v 92.0) now, instead of Chrome, just for sorting this influence out as well.
Changing the query on the both the chart edits in explore as well.
Using the landing page for navigating between the dashboards, instead of the user favorites page.

⇒ The issue is still present :-(


warning about jsonrpc

we could also add a warning when start_eth or start_geth is executed

yup that's good,
maybe also just mention the reason why it's dangerous.

@yann300 can you please take over? Thanks!


where is the flink.jar

hello, thanks your work, AthenaX is very useful for us.  And  I am trying to use the AthenaX,  but I have encountered some problems:

how to get the flink.jar? when I run 'mvn clean install' in flink directory, I only find the build-target directory,  can't find the flink.jar.
how the AthenaX read the flink.jar if we set  flink.uber.jar.location: hdfs:///app/athenax/flink.jar.

thanks for your reply.

What is the answer？

According to this article
https://groups.google.com/forum/#!topic/athenax-users/oJ3NLmO0AQo
flink.jar is  flink-dist_***.jar


Pixiv Bookmark

I found the program very good for downloading images, I had no problems with Gelbooru, I am very grateful to you.
I was wondering if you have plans to add the Pixiv bookmark, I haven't found any program that is simple and practical to use like yours.
Or if you already have, how do I download the images I liked / left in my bookmark?

There was  plans to add support, but since it's easy to add I'll add it in the next release 👌
Syntax will be bookmarks:USER_ID.

Dude, thank you very much, how will it work to do the downloades after you add?
Will it be put on the next version "nightly" or "official"?

Not sure what you mean by your question?
The change should already be in the nightly release, and will be in the next "official" release as well, when it comes out.

Sorry, I have mental problems.
Also, I think it has a bug, Grabber doesn't take all of my favorites, it only takes 30 and I can't change the page.

Also, I think it has a bug, Grabber doesn't take all of my bookmarks, it only takes 30 and I can't change the page. Stay like this https://imgur.com/a/LmVcpKi

Indeed, seems like the pagination for bookmarks is slightly different than for other Pixiv APIs. I just pushed a fix 👍

Thanks for fixing this, so I think I found another bug. When I try to download a lot of images that is my case, "49k of bookmarks", it just doesn't download them all, I managed to download only 1900.
If you can fix it, the bookmarks part will be perfect.

Can you clarify "it just doesn't download them all"?
What happens after the 1900 images? Can you show the log to see if there's any error or warning there?

Said he had downloaded everything, but in reality he only downloaded 1900 out of 49000.
I don't know what happened, I tried to download it again and don't download more than that.

Have you tried setting the "Images per page" to 30 instead of 1000?
The bookmarks API only support 30 images per page.
I'm event surprised you managed to get 1900 images as 30*50000/1000=1500.

Hello again, still buggy, I can't download more than 1000 images anyway, I tried several ways and nothing to get ... :/
Can you try to download them all? If you want to test using my ID it is 27317565

I just tried and could download them with no issues in the Nightly version.
Check your logs and see if there's anything obvious to see there, because it's working.


Improve import time

Fixes #55, depends on https://github.com/FrescolinoGroup/pyhdf5io/pull/8
After removing the explicit symmetry_representation import, sympy was still always imported through fsc.hdf5_io. This is fixed in https://github.com/FrescolinoGroup/pyhdf5io/pull/8. In this PR, we update the requirement on fsc.hdf5-io. To allow loading TBmodels objects without importing the module first, we also define an entry point for fsc.hdf5_io.load.

Failing tests is expected, since fsc.hdf5-io==0.6.0 needs to be released first.

Codecov Report

Merging #58 into dev will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev      #58   +/-   ##
=======================================
  Coverage   95.48%   95.48%
=======================================
  Files           9        9
  Lines         997      997
=======================================
  Hits          952      952
  Misses         45       45

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 7da0d98...bcf901a. Read the comment docs.


Share LightGBM categorical variable representation across multiple columns

Summary
Share LightGBM categorical variable representation across multiple columns.
Motivation
Very useful for sequences and several use cases.
Description
Encode the same category level along multiple columns.
Very similar to using an Embedding Layer in a Neural Network to encode a categorical variable and applying the layer across a sequence of that same variable (example of a word embedding).
The same can be achieved with Target Encoding or other representation applied before modeling by stacking the category columns, into a key-value structure, and then applying said encoding.
 Example train dataset

Var 1
Var 2
Var 3
Target

Goose
Cat
Dog
103

Cat
Cat
Dog
4

Goose
Goose
Goose
300

 Stack shared category levels

Category Level
Target

Goose
103

Cat
103

Dog
103

Cat
4

Cat
4

Dog
4

Goose
300

Goose
300

Goose
300

 Naive target encoding

Category Level
Encode

Goose
250

Dog
53

Cat
37

No thoughts, suggestions or alternatives?

This project is maintained mostly by volunteers, one of whom may respond here as we have time and interest.
If you can share more details (relevant research, a prototype implementation, your own research doing such feature engineering manually and demonstrating the benefits), it may make it more likely that maintainers here would invest time into this.


Refactor platformRegistry aggregation code to support Multi-Cloud meshes

Design doc reference: https://goo.gl/AQARBs#heading=h.upntt2yt6be

Uses existing Pilot internal data structure of Service representation i.e. https://github.com/gnirodi/pilot/blob/hybrid-multi-cluster/bridge/mesh/service.go
Removes the ability to nest registries.
Keeps the platformRegistry interfaces distinct from those required by xDS
Aligns with upcoming "Bring your Own Names"

PR#2846 has been merged.


fix: capture GCS metrics when bucket contains hyphens

GCS bucket names can contain hyphens, underscores, dots, etc: https://cloud.google.com/storage/docs/buckets
Fixing the regex to match URLs, and a couple of minor related refactoring. See commits for details.

Weirdly enough, seems that the GCS Fake Server doesn't allow these characters on the bucket name, so I wasn't able to change the test; but tried it manually on our demo where it wasn't working.

Thanks @ivanyu, suggestion makes sense. Adding a test case for the regex at least so we can validate the expressions.


Loss output

Hi,
can you also report the loss you got on the trained model?
Thanks a lot

I'll try to add it tonight, but cant guarantee. Anyway, you can always load pretrained model calculate loss on dataset if in a rush.


Terminal profile dropdown tooltip is wrong

How about "New With Profile"?

I believe this is already fixed, can you see if you can reproduce in the Insiders build?


Update tabs-link-unfurling.md

Title changed
All references to "popOut" changed to "popout"
Minor changes to the descriptions of Stageview/Collab Stage/Stageview Modal

The changes are incorporated in feature PR - https://github.com/MicrosoftDocs/msteams-docs/pull/10279/files


SAML authentication details

Hi. I'm attempting to configure SAML2.0 authentication using Google Workspace and I need to provide it with the following details:

ACS URL (SAML redirect URL)
Entity ID (might be the same as the ACS URL)
Name ID (usually EMAIL)

looks like it's undocumented.

took a quick look at the code and if I understood it correctly the URL should tehnically be the same as what's described in the OIDC configuration, just replacing it with "saml"
so i tried the following mixes and mashes of configs on the google saml app config side:
ACS URL:

https://firezone.fqdn/auth/saml/callback/
https://firezone.fqdn/auth/saml/auth/signin/gsuite/
Entity ID:
urn:firezone.dev:firezone-app (that's what I've seen configured in the Samly config in the code, not sure if right)
callback URL above

Name ID Format: EMAIL (default in Google)
Name ID: Basic Information->Primary Email (default in Google)
Getting a 403 Forbidden response when passing the SAMLResponse from google to either of the URLs.

Refs #1048

Tried the /saml/auth/sp/consume/gsuite path as the ACS URL:
Getting what I can only assume is an exception from samly/esaml:
access_denied {{:badmatch, []}, [{:xmerl_dsig, :verify, 2, [file: '/app/deps/esaml/src/xmerl_dsig.erl', line: 168]}, {:esaml_sp, :"-validate_assertion/3-fun-3-", 3, [file: '/app/deps/esaml/src/esaml_sp.erl', line: 265]}, {:esaml_util, :threaduntil, 2, [file: '/app/deps/esaml/src/esaml_util.erl', line: 92]}, {Samly.Helper, :decode_idp_auth_resp, 3, [file: 'lib/samly/helper.ex', line: 72]}, {Samly.SPHandler, :consume_signin_response, 1, [file: 'lib/samly/sp_handler.ex', line: 37]}, {Samly.SPRouter, :"-dispatch/2-fun-0-", 4, [file: 'lib/plug/router.ex', line: 246]}, {:telemetry, :span, 3, [file: '/app/deps/telemetry/src/telemetry.erl', line: 320]}, {Samly.SPRouter, :dispatch, 2, [file: 'lib/plug/router.ex', line: 242]}]}
I'll update when I have more time to work on this..

Thanks for the detailed crash log. What's likely happening is the access_denied is causing a match failure which is crashing with the trace you see.

can't get it to work.. Only thing I can think of right now is for you to send me an example of a working SAMLResponse payload to Firezone so that I can compare it with one sent by Google. (you can remove any sensitive data from there, what's important is the structure and fields of the XML)

@ilyatovbin-pp Finally found some time to work on a fix for this -- will be coming in the 0.6.8 release momentarily.

Google works with the following config:

Can confirm its working fine. one thing though, if you sign in using SAML, you can then change your "local" account password under "My Account", and use it to login without SAML next time, which is a security risk. I'll open a separate issue for this.

Can confirm its working fine. one thing though, if you sign in using SAML, you can then change your "local" account password under "My Account", and use it to login without SAML next time, which is a security risk. I'll open a separate issue for this.

This is a good point, and something we've thought about solving. In fact, you can login with the same email address using multiple providers We're considering removing local authentication altogether and relying on something like Keycloak or Authentik for self-hosted local auth. In the meantime, LOCAL_AUTH_ENABLED=false will prevent this particular issue.


Error Position

Hello! Some VerticaErrors contain Position (in this case Position: 9 )
cur.execute("select *.a from existing_table;")
VerticaSyntaxError: Severity: ERROR, Message: Syntax error at or near ".", Sqlstate: 42601, Position: 9, Routine: base_yyerror, File: /data/jenkins/workspace/RE-ReleaseBuilds/RE-Knuckleboom/server/vertica/Parser/scan.l, Line: 1052, Error Code: 4856, SQL: 'select *.a from existing_table;'
and some Errors don't:
cur.execute("select some_column from existing_table;")
MissingColumn: Severity: ERROR, Message: Column "some_column" does not exist, Sqlstate: 42703, Routine: transformSQLColumnRef, File: /data/jenkins/workspace/RE-ReleaseBuilds/RE-Knuckleboom/server/vertica/Optimizer/OptUtil/ExprUtil.cpp, Line: 7256, Error Code: 2624, SQL: 'select some_column from existing_table;'
Is it VerticaPython's or underlying driver's issue?

Position info is returned by the server. Some errors just don't have that piece of info.


Latest master breaks on fetching mim_nr?

Thank you kindly! But I now have trouble looking at any variant instead? Lookup on mim_nr seems to fail? Sth wrong with that last new_omim_list? I did have a couple of build issues along the way, but they don't seem to be showstoppers.
Traceback (most recent call last):
  File "/home/vagrant/.local/lib/python2.7/site-packages/flask/app.py", line 1817, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/vagrant/.local/lib/python2.7/site-packages/flask/app.py", line 1477, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/vagrant/.local/lib/python2.7/site-packages/flask/app.py", line 1381, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/home/vagrant/.local/lib/python2.7/site-packages/flask/app.py", line 1475, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/vagrant/.local/lib/python2.7/site-packages/flask/app.py", line 1461, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/vagrant/puzzle/blueprints/variants/views.py", line 25, in variants
    thousand_g=thousand_g)
  File "/home/vagrant/.local/lib/python2.7/site-packages/flask/templating.py", line 128, in render_template
    context, ctx.app)
  File "/home/vagrant/.local/lib/python2.7/site-packages/flask/templating.py", line 110, in _render
    rv = template.render(context)
  File "/home/vagrant/.local/lib/python2.7/site-packages/jinja2/environment.py", line 989, in render
    return self.environment.handle_exception(exc_info, True)
  File "/home/vagrant/.local/lib/python2.7/site-packages/jinja2/environment.py", line 754, in handle_exception
    reraise(exc_type, exc_value, tb)
  File "/vagrant/puzzle/blueprints/variants/templates/variants.html", line 2, in top-level template code
    {% from "macros/variant.html" import omim_links %}
  File "/vagrant/puzzle/templates/layouts/base.html", line 28, in top-level template code
    {% block body %}
  File "/vagrant/puzzle/templates/layouts/base.html", line 45, in block "body"
    {% block body_content %}{% endblock %}
  File "/vagrant/puzzle/blueprints/variants/templates/variants.html", line 29, in block "body_content"
    {% for variant in variants %}
  File "/vagrant/puzzle/plugins/vcf.py", line 233, in variants
    for variant_obj in filtered_variants:
  File "/vagrant/puzzle/plugins/vcf.py", line 206, in _variants
    self._add_genes(variant)
  File "/vagrant/puzzle/plugins/vcf.py", line 69, in _add_genes
    omim_number=get_omim_number(hgnc_id),
  File "/vagrant/puzzle/utils/get_info.py", line 65, in get_omim_number
    omim_number = HGNC_TO_OMIM.get(hgnc_symbol).get('mim_nr')

Also had a couple of issues during pip install (using otto dev) now compared to before:
 Running setup.py install for MarkupSafe

    building 'markupsafe._speedups' extension
    gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c markupsafe/_speedups.c -o build/temp.linux-x86_64-2.7/markupsafe/_speedups.o
    markupsafe/_speedups.c:12:20: fatal error: Python.h: No such file or directory
     #include <Python.h>
                        ^
    compilation terminated.
    ==========================================================================
    WARNING: The C extension could not be compiled, speedups are not enabled.
    Failure information, if any, is above.
    Retrying the build without the C extension now.

    ==========================================================================
    WARNING: The C extension could not be compiled, speedups are not enabled.
    Plain-Python installation succeeded.
    ==========================================================================

Also, as before, during npm install:
npm ERR! Linux 3.2.0-23-generic
npm ERR! argv "/opt/node-v4.1.0-linux-x64/bin/node" "/usr/local/bin/npm" "install"
npm ERR! node v4.1.0
npm ERR! npm  v2.14.3
npm ERR! path ../semver/bin/semver
npm ERR! code EPROTO
npm ERR! errno -71
npm ERR! syscall symlink

npm ERR! EPROTO: protocol error, symlink '../semver/bin/semver' -> '/vagrant/node_modules/gulp/node_modules/.bin/semver'
npm ERR!
npm ERR! If you need help, you may report this error at:
npm ERR!     <https://github.com/npm/npm/issues>

npm ERR! Please include the following file with any support request:
npm ERR!     /vagrant/npm-debug.log

Closed by #20


Merge extract_view_controller branch

Merge the extract_view_controller branch once the updated rviz_animated_view_controller with my pull requests is released.
Before that, create a new release tag named "standalone" for the master branch in case someone doesn't want or can update to the latest rviz_animated_view_controller version.
Then these users can still just clone the standalone version to quickly generate camera trajectories.

@Razlaw PR is open to release rviz_animated_view_controller for noetic. going to open one for melodic too i think in a bit.

Thanks for keeping me up to date :)
You probably already noticed yourself, but there seems to be a typo in the link to the image at the bottom of the readme.

thanks for the tip 😅


1.16.1 Changes 2

This is the pull request replacing #96. Please see https://github.com/Chillandchat/mobile/pull/96 for more information.

#96


⚠ Bofrost.de has degraded performance

In 981f687, Bofrost.de (https://www.bofrost.de) experienced degraded performance:

HTTP code: 200
Response time: 1167 ms

Resolved: Bofrost.de performance has improved in 143f751 after 5 minutes.


Branches with "/" 404

If the branch has a '/' in it the action fails with a 404. Branch is 'feat/addMyProfile:
https://api.github.com/repos/AllanRegush/hacktoberfest-practice/readme?ref=feat%2FaddMyProfile works. Changing the / to url encoding solves the issue.
Error received.
Error: {"name":"HttpError","status":404,"headers":{"access-control-allow-origin":"*","access-control-expose-headers":"ETag, Link, Location, Retry-After, X-GitHub-OTP, X-RateLimit-Limit, X-RateLimit-Remaining, X-RateLimit-Used, X-RateLimit-Reset, X-OAuth-Scopes, X-Accepted-OAuth-Scopes, X-Poll-Interval, X-GitHub-Media-Type, Deprecation, Sunset","connection":"close","content-encoding":"gzip","content-security-policy":"default-src 'none'","content-type":"application/json; charset=utf-8","date":"Wed, 23 Sep 2020 22:41:54 GMT","referrer-policy":"origin-when-cross-origin, strict-origin-when-cross-origin","server":"GitHub.com","status":"404 Not Found","strict-transport-security":"max-age=31536000; includeSubdomains; preload","transfer-encoding":"chunked","vary":"Accept-Encoding, Accept, X-Requested-With","x-content-type-options":"nosniff","x-frame-options":"deny","x-github-media-type":"github.v3; format=json","x-github-request-id":"07C2:0F2D:EC8911:274E6DD:5F6BCF32","x-ratelimit-limit":"1000","x-ratelimit-remaining":"999","x-ratelimit-reset":"1600904514","x-ratelimit-used":"1","x-xss-protection":"1; mode=block"},"request":{"method":"GET","url":"https://api.github.com/repos/AllanRegush/hacktoberfest-practice/readme?ref=feat","headers":{"accept":"application/vnd.github.v3+json","user-agent":"octokit-request.js/5.4.9 Node.js/12.13.1 (linux; x64)","authorization":"token [REDACTED]"}},"documentation_url":"https://docs.github.com/v3/repos/contents/"}

Changing the / to url encoding solves the issue.

I thought the bug caused by splitting githubRef by / in index.ts#L99 and retrieved 3rd item(index 2) only as the url in your error was containing feat only https://api.github.com/repos/AllanRegush/hacktoberfest-practice/readme?ref=feat

it is. i just realized that and was going to close.


Multiple micro services communicating with the same database - bad practice?

The design of micro sems to favor a multitude of independent micro services.
Would you go as far as having multiple micro services talking to the same database?

It's really a matter of preference and how far you want to go when separate services. Say you want to create an api endpoint for products, you could create one micro service that handles all CRUD operations, or a separate service for each. In that case it would be perfectly fine for them to talk to the same database. Because they all work on the same data.
I'm not sure how ZEIT handles it. But this seems like a good article about microservices in general:
https://arstechnica.com/information-technology/2016/05/blow-that-data-monolith-to-smithereens-with-microservices-and-database-swarms/

Theoretically each micro service should have it owns database, is one of the principal to recognise if can stand alone as a micro service, it should run by itself, be independent. If you have several micro services using the same database could cause conflicts writing and reading, beside another conflicts.

@nmaro I guess this answers your question 😄 Feel free to re-open if it doesn't.


HDFS-16515. Improve ec exception message

Currently, if we set an erasure coding policy for a file,it only shows the following message, which is not that clear to user, we can improve it.
RemoteException: Attempt to set an erasure coding policy for a file /ns-test1/test20211026/testec

:broken_heart: -1 overall

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378m 38s
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0m 39s

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507m  5s

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Failed junit tests
hadoop.hdfs.TestUnsetAndChangeDirectoryEcPolicy

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ClientAPI=1.41 ServerAPI=1.41 base: https://ci-hadoop.apache.org/job/hadoop-multibranch/job/PR-4089/1/artifact/out/Dockerfile

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Optional Tests
dupname asflicense compile javac javadoc mvninstall mvnsite unit shadedclient spotbugs checkstyle codespell

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Linux 5d6287e673e0 4.15.0-163-generic #171-Ubuntu SMP Fri Nov 5 11:55:11 UTC 2021 x86_64 x86_64 x86_64 GNU/Linux

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Multi-JDK versions
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modules
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I think this message is propagated to end client and might be on CLI as well. IMO this would be an incompatible change, we should refrain from doing this

Yes,thanks @ayushtkn for your review, it shows for the end client on CLI output, I just think the propagated  message not that clear for the usage of EC , i need to recheck the information on the  website to confirm that only directory can be accepted or search the message in the source code.
if we  unset erasure coding policy for a file .
the CLI out will show as Cannot unset an erasure coding policy on a file xxxx, which relatively tells end client more clearer.

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Optional Tests
dupname asflicense compile javac javadoc mvninstall mvnsite unit shadedclient spotbugs checkstyle codespell

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this may impact message to end client ,closing it


Refactor observer functionality

@eberleim See #42 for some of the reasons for these changes. I tagged you for your reference.


Spans created by TraceAsyncAspect not being started active

Our app has a Spring controller that delegates most of its work to a background task (annotated with Async), which in turn makes JDBC calls.
TraceAsyncAspect calls start() rather than startActive(...) here, which means that the span corresponding to async task isn't made the parent when a JDBC span is created.
The end result of this is that it looks like the DB calls are being made from the Servlet worker thread, rather than the background thread that they're actually coming from.
I'm wondering if this is a) deliberate, b) could be either amended or made configurable?

Hey, as an OSS maintainer myself I totally appreciate how annoying it is having people chase you up about issue tickets.
However, if you could at least give me a nod as to which solution (if any) you'd be willing to accept I'll happily create a PR for the change.
Thanks in advance.

OK, I'll have a little bit more of a dig around, but if there's nothing obviously problematic about it I'll make a PR with the change.
In any case, I'm integrating this into a client's system so it'll get a bit of road testing.


Slidetransitions

Description
Please include a summary of the change and a link to 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.

[ ] 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 not work as expected)
[ ] This change requires a documentation update

How Has This Been Tested?
Please describe the tests that you ran to verify your changes. Provide instructions so we can reproduce. Please also list any relevant details for your test configuration

[x] Test A
[ ] Test B

Checklist:

[x] My code follows the style guidelines of this project
[x] I have performed a self-review of my own code
[x] My code has been reviewed by at least one peer
[x] I have commented my code, particularly in hard-to-understand areas
[x] I have made corresponding changes to the documentation
[x] My changes generate no new warnings
[x] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes

Adding more to this.

These changes don't follow the style format. We aren't using className
If you want different colors on colors Button styled-component and enter background-color: ${props => props.color}; and then on your component insted of className = ... ad color='desiredColor'


java.lang.ClassNotFoundException: org.openmetadata.service.security.NoopAuthorizer in OpenMetadata Server

Affected module
The UI will not start.
Describe the bug
Error code in command line: "container for service "openmetadata-server" is unhealthy" when trying to start OpenMetadata using metadata docker --start
To Reproduce

Activate Env
Run metadata docker --start

Expected behavior
Usually the CLI will display that the server has been started successfully on port 8585.
However Error code is displayed in CLI.
When inspecting logs of openmetadata_server container, error: java.lang.ClassNotFoundException: org.openmetadata.service.security.NoopAuthorizer is shown.
Version:

OS: macOS Monterey 12.5.1
Python version: Python 3.9.13
OpenMetadata version: 0.12
OpenMetadata Ingestion package version: <IP_ADDRESS>

Additional context
I have attached the logs of the metadata_server container as well as the CLI logs.

I am facing the same issue, Could Someone Help me?

please, check the docs on the PR. It will help you update your quickstart deployment. running metadata docker --clean will clean up your test local environment and use the new release compose file. More info on the docs. Thanks


PCR Parsing error

I've encountered an bug.
Messsage: Cannot read property 'indexOf' of undefined
Stack: TypeError: Cannot read property 'indexOf' of undefined
    at display (chrome-extension://bgfabcdolnakhoioalgalampgaaphoei/client.js:1236:24)
    at parse (chrome-extension://bgfabcdolnakhoioalgalampgaaphoei/client.js:502:3)
    at chrome-extension://bgfabcdolnakhoioalgalampgaaphoei/client.js:363:11
Browser: Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/69.0.3497.92 Safari/537.36
Version: 2.24.3

Hi Akshay!
I've made this error log more verbosely in the typescript branch of the repository.
If you could, it would be great if you could try that branch and report the error it gives.
Thanks!


Add UTYCC

@myat-hsu-mon Pull request merged. Thank you!

@myat-hsu-mon Pull request merged. Thank you!


updated jackson

What and why?
Dependabot highlighted a security vulnerability that required jackson-databind be updated to at least version <IP_ADDRESS>.
How to test?
Deploy and run acceptance test.
Jira
Card

/deploy wilkia


Request adding AOSC OS support

Description
Request adding logo of AOSC OS (a Linux distro)
Homepage: aosc.io
And the AOSC OS 4 Logo is

What's the output of cat /etc/os-release?

everette@LER0ever-RPI3 [ ~ ] $ cat /etc/os-release
PRETTY_NAME="AOSC OS (4.0.1)"
NAME="AOSC OS"
VERSION_ID="4.0.1"
VERSION="4.0.1 (Duang-Duang)"
ID=aosc
ANSI_COLOR="1;36"
HOME_URL="https://aosc.io/"
SUPPORT_URL="https://github.com/AOSC-Dev/aosc-os"
BUG_REPORT_URL="https://github.com/AOSC-Dev/aosc-os-abbs"

That's the output from Raspberry Pi3 running AOSC OS

Done.

Thanks for the support. (That's fast)

Anytime. :)


Build with larger number of processors

gcc can take advantage of more processors. The Getting Started guide on python.org suggests using make -s -j2 to build. I believe -j2 means use two CPUs, this should be another environment variable that can be controlled from outside the container.

Fixed with 805e7e115c9b074e350421b505caf5a0fb59343c


Update NPM package

currently get_channel_id is not in my current package, however it looks to be updated in the git repository.  could someone update the package?

@azambuja @lucasts @rafaelmws @rfloriano @cyberelfo

I will take a look @danieljoonlee. Thanks for the reminder.

Done.

Thanks @lucasts !


Backup script for backing up code and db together

We're on PostgresSQL on prod.
We need a script that will take the whole db's dump and put it in a file (timestamped). Then, it will also get the current code and put that in a zip file along with the db dump (again, timestamped). Then, upload it somewhere off-site where we can only do writes and no deletes.

We can use this Django package for creating backup of media (submission/assignment) and database.
https://django-dbbackup.readthedocs.io/en/stable/installation.html

Looks good. Let's deploy this but ensure we can reproduce from the backup (in a sandbox).

But let's handle #9 first please =]

@BilalZaib I will work on this.


Reduced dg-common to only graph-generation -- removed unused helpers.

I need someone with write access to please remove the changes from the four code files outside of dg-common -- one in dg-spark and three in dg-core. I made these changes to work around intermittent issues I was having (e.g., ignored a few unit tests), and they should be removed from the pull request.

@SamerAdra can you please resolve the conflicts and update the PR ?

@Brijeshrpatel9 @ShaneEbersole @aosama can we get two of you to review the pull request ? the failed unit test is not in his code, and is being fixed by @leeny324 .

I figured out why that test was failing and fixed it. It was a simple thing I overlooked when implementing the leap year portion. However, PR #287 is failing during this step.
[INFO] Data Generator Example - HDFS Distributor .......... FAILURE [  0.671 s]

@SamerAdra can you please fix the collisions ?

PositiveBoundHiveDateTest is failing even though I have no changes to it.

Conflicts are resolved... If you can just accept the pull request, if any of the core unit tests are still failing, then someone else can fix it.


TypeScript Definition

Could you add a TypeScript definition file for this add-on?
I'm new to TypeScript, so this could be wrong, but this is what I used:
export const name: string;

export default class Modifier {
  element: Element
  didInsertElement(positional?: Array<any>, named?: Object): void
  didRecieveArguments(positional?: Array<any>, named?: Object): void
  didUpdateArguments(positional?: Array<any>, named?: Object): void
  willDestroyElement(positional?: Array<any>, named?: Object): void

  static modifier(klass: typeof Modifier): any
}

I haven't a clue about TypeScript. I more new then you are.
Does this work for you? I'm happy to just merge it as is. Can I do that?

Yes, it works for me, but now I've refined this TypeScript definition to be even more specific. I'll make a PR for it.

For reference: here is the types I'm using with the latest changes for ember-class-based-modifier.
declare module 'ember-class-based-modifier' {
  interface Args<TNamed, TPositional> {
    named: TNamed;
    positional: TPositional;
  }

  export default class Modifier<TNamed = object, TPositional = unknown[]> {
    public args: Args<TNamed, TPositional>;

    public element: HTMLElement | SVGElement;
    public isDestroyed: boolean;
    public isDestroying: boolean;

    public constructor(owner: unknown, args: Args<TNamed, TPositional>);

    public didInstall(): void;
    public didReceiveArguments(): void;
    public didUpdateArguments(): void;
    public willRemove(): void;
    public willDestroy(): void;
  }
}


Julia support

As fan and user of the language, and having seen this question already mentioned on HN it would be great to know what it would take to enable support for Julia notebooks - an environment which typically plugs right in with Python libraries. My impression right now is that we would need to add a base kernel image, similarly to R support.

This is definitely something we want to add. We would need to set up an Enterprise Gateway kernel for Julia similar to their R one: https://github.com/jupyter/enterprise_gateway/tree/master/etc/docker/kernel-r
I'll look into it this this week, it shouldn't be too difficult to add basic support as we architected Orchest to support this kind of expansion.
SDK support will be missing initially (for e.g. data passing or parameterization) but shouldn't be too hard to add later.

Basic Julia support is now shipped in v0.3.6: https://github.com/orchest/orchest/releases/tag/v0.3.6
Let us know what you think! :)

Some more details can be found in this PR: https://github.com/orchest/orchest/pull/85
To cite:

This commit adds Julia support to Orchest. The SDK for Julia (similar to the one for R) still needs be created.
With this PR users will be able to build Julia environments, run Julia scripts, and (interactively) run Julia based Notebooks.


Link error gio on windows fix

Fix gtk-rs/gtk#517
I'am not good with gir and copy this from glib crate, so hope this is ok.

Thanks, @daa84 This is what we need
Please, change last commit message to "Regen" as It don't generated new functions ;)

Done :smile:

@GuillaumeGomez CI passed.

Thanks!


FEATURE: description translation

hi!
not an issue, rather a question/will to help ;)
is there any way to prepare translations for the value descriptions?
I know I could do a second template sensor, that would give informations in my local language [Polish] based on the value of the main sensor, but I don't want to make another entities, I like my config as clean and minimal as possible [wherever I can].
if you'd add multilanguage option [based on HA settings, or on given parameter] I can provide translation for Polish. I guess that others would be happy to help with different languages :)

dont really have the project setup for translation but if you can provide a patch for it, ill be more then willing to merge it :)

..if I only knew how to do that, it would be already done ;) unfortunately my programming skills are somewhere near NULL ;D
ok, so let's hope somebody capable sees my post and will help on the dev side :)

i cant promise this feature in the near future hence why i pinned it if someone has the time else im gonna look into when my schedule is less demanding :)

https://developers.home-assistant.io/docs/en/internationalization_backend_localization.html

Following this !
Translation to Dutch will also be great

I also would like to have it in Dutch. Willing to translate, just share the different texts.


Remove DDS support

Waiting for decision if DDS example should be removed.

Waiting for decision if DDS example should be removed.

Please go ahead.

Any idea why the "Build Project" section of the CI debug run takes 0ms to run? https://github.com/klepsydra-technologies/kpsr-tutorial/actions/runs/5316095037/jobs/9625247128?pr=40


Black screen at start of a biome

Edit: seems to have resolved itself from a cache refresh
Received this black screen at the start of the Fairy Cave biome.
Steam Deck
Release 2.2.1

Yeah it seems like some asset-related things need a cache reset to properly be downloaded, not sure why. But at the very least, it's an option people can try when needed.


[Feat] Add user profile photo the profile page

Is there an existing issue for this?

[X] I have searched the existing issues

Feature Description
i want to add user add profile photo option in the profile page
please assign this issue to me @Luson045
Use Case

there should be a profile photo with all other information of the user
Benefits
No response
Priority
High
Record

[X] I agree to follow this project's Code of Conduct
[X] I'm a GSSOC contributor
[X] I want to work on this issue
[X] I'm willing to provide further clarification or assistance if needed.

not needed as of now


Fixes Issue #340 #339 #335 #330

Pull Request (PR) description

This Pull Request (PR) fixes the following issues

Fixes #340
Fixes #339
Fixes #335
Fixes #330

Task list

[X] Added an entry under the Unreleased section in the CHANGELOG.md.
Entry should say what was changed, and how that affects users (if applicable).
[ ] Resource documentation added/updated in resource directory README.md.
[X] Resource parameter descriptions added/updated in schema.mof
and comment-based help.
[X] Comment-based help added/updated.
[ ] Localization strings added/updated in all localization files as appropriate.
[ ] Examples appropriately added/updated.
[ ] Unit tests added/updated. See DSC Resource Testing Guidelines.
[ ] Integration tests added/updated (where possible). See DSC Resource Testing Guidelines.
[ ] New/changed code adheres to DSC Resource Style Guidelines and Best Practices.

This change is

Codecov Report

Merging #440 into dev will not change coverage.
The diff coverage is 100%.

@@         Coverage Diff         @@
##            dev   #440   +/-   ##
===================================
  Coverage    96%    96%
===================================
  Files        20     20
  Lines      2705   2705
  Branches     10     10
===================================
  Hits       2608   2608
  Misses       87     87
  Partials     10     10


PostgreSQL Index Descending column shown as Ascending

System information:

Windows 10 Pro, 1903
DBeaver 6.1.2
No additional extensions

Connection specification:

Database name and version: PostgreSQL 10.5
Driver name: PostgreSQL

Describe the problem you're observing:
The index containing a DESC column is being shown as ASC in the UI. DDL (Source) is ok.
recalculated_pageviews and topic_id should NOT be ticked as the Ascending in this case.

Steps to reproduce, if exist:
CREATE TABLE public.test_table (
	id bigint NOT NULL,
	category_id int8 NOT NULL,
	active bool NOT NULL DEFAULT false,
	recalculated_pageviews int8 NULL,
	dep_version int8 NOT NULL DEFAULT '-1'::integer,
	topic_id int8 NULL,
	CONSTRAINT test_table_pk PRIMARY KEY (id, category_id, dep_version)
);
CREATE INDEX test_idx ON public.test_table USING btree (active, dep_version, category_id, recalculated_pageviews DESC, topic_id DESC);

Open index details.

Thanks for the bug report

Verified. Reproduced according ticket example and with creating another table.

Thanks for the bug report

No problem, thanks both for fixing & great product. :)


Don't fetch all crates on clean

Only fetch those that are needed by avoiding ops::fetch

r? @wycats
(rust_highfive has picked a reviewer for you, use r? to override)

@bors r+

:pushpin: Commit 9a19cda has been approved by brson

:hourglass: Testing commit 9a19cda with merge 880fde5...

:sunny: Test successful - cargo-cross-linux, cargo-linux-32, cargo-linux-64, cargo-mac-32, cargo-mac-64, cargo-win-gnu-32, cargo-win-gnu-64, cargo-win-msvc-32, cargo-win-msvc-64


Quality checking results?

Thank you so much for your time and effort working on this; it's awesome.
Do you have any good tips on how to quality check the results?
If you have thousands of prominence coordinates, how do you check that it's correct?
When eyeballing the map and results from promience, I always have to keep my tongue straight, but some things are strange. The plot below shows a bunch of prominence points (black dots). I've manually added some red rings in some areas (but not all!) indicating where I would expect there to be a prominence point, but there are none. This is all bathymetry, so the High Point closest to sea level (i.e. z = 0) I kind of expect to be missing, ref my other post.
Are there any obvious reasons that prominence didn't find any prominence points in those red rings?!

Command, for reference:
run_prominence.py --skip_boundary --degrees_per_tile 1 --samples_per_tile 4444 --binary_dir=~/mountains/code/release inputgrid.nc

It's hard for me to tell based on a screenshot.  Can you link to your data
so that I can try it locally?
I have pretty high confidence in above-zero results, as I've processed many
hundreds of thousands of peaks, including the whole Earth several times
over.  Maybe there's a problem related to negative values somewhere.
On Fri, Nov 1, 2024 at 7:40 AM anbj @.***> wrote:

Thank you so much for your time and effort working on this; it's awesome.
Do you have any good tips on how to quality check the results?
If you have thousands of prominence coordinates, how do you check that
it's correct?
When eyeballing the map and results from promience, I always have to keep
my tongue straight, but some things are strange. The plot below shows a
bunch of prominence points (black dots). I've manually added some red rings
in some areas (but not all!) indicating where I would expect there to be a
prominence point, but there are none. This is all bathymetry, so the High
Point closest to sea level (i.e. z = 0) I kind of expect to be missing,
ref my other post
https://github.com/akirmse/mountains/issues/26#issuecomment-1881158393.
Are there any obvious reasons that prominence didn't find any
prominence points in those red rings?!
Screenshot.from.2024-11-01.15-01-04.png (view on web)
https://github.com/user-attachments/assets/03b61e2e-c17a-4035-8b01-34812d313c49
Command, for reference:
run_prominence.py --skip_boundary --degrees_per_tile 1 --samples_per_tile 4444 --binary_dir=~/mountains/code/release inputgrid.nc
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ID: @.***>

Absolutely.
Here is my grid file: https://www.dropbox.com/scl/fi/syovyzirhjsmbg8listqw/nosj.nc?rlkey=jxlhltz5f20nv42y09y96tigo&st=amk3bra9&dl=0
Command:
run_prominence.py --skip_boundary --degrees_per_tile 1 --samples_per_tile 4444 --binary_dir=~/mountains/code/release nosj.nc

I see now that the grid does not have projection information. This is WGS84/EPSG:4326. I thought gdal would complain about that, hmm.

One thing I noticed is that the original DEM is only 10220 by 5490 pixels, and it spans a good part of the earth, so running with a setting of 4444 pixels per degree results in a massive oversampling.  I ran with --samples_per_tile 500 instead, and got the attached result.
Another thing I saw during the run was some output like this:
2024-11-01 10:40:01,788 INFO [default] Removed possible spike at 60.958, 6.988
2024-11-01 10:40:01,788 INFO [default] Removed possible spike at 60.958, 6.99
2024-11-01 10:40:01,789 INFO [default] Removed possible spike at 60.866, 6.838
2024-11-01 10:40:01,789 INFO [default] Removed possible spike at 60.866, 6.84
2024-11-01 10:40:01,790 INFO [default] Removed possible spike at 60.854, 6.812
2024-11-01 10:40:01,790 INFO [default] Removed possible spike at 60.854, 6.814

The code has some automatic detection to attempt to remove single-sample "spike" elevation errors that are commonly found in terrain DEMs.  This detection is based on the difference of the sample's elevation with its neighbors.  However, your data is so low resolution that maybe this is too aggressive.  You could try commenting out the spike detection or setting the detection constant to something enormous (https://github.com/akirmse/mountains/blob/21fbbe0f612abe1224dfaf5fd2b03edc1ede412c/code/tile_cache.cpp#L99), and if that works, I could add a flag to disable it.
results.txt

Your result was the same as mine.
I tried increasing MAX_LEGAL_ELEVATION_DIFF to something huge, and it didn't help. I also removed it, but still the same.
Here's another grid which covers an area with missing prominence points: bat.nc.
Make another version that adds 10000 so all z >> 0:
gdal_calc.py -A bat.nc --outfile=bat-pos.nc --calc="A+10000" --overwrite

Now run prominence for original:
run_prominence.py --skip_boundary --degrees_per_tile 1 --samples_per_tile 500 --binary_dir=~/mountains/code/release --threads $(nproc) --output_dir original-bat bat.nc

and for shifted (+10000):
run_prominence.py --skip_boundary --degrees_per_tile 1 --samples_per_tile 500 --binary_dir=~/mountains/code/release --threads $(nproc) --output_dir pos-bat bat-pos.nc

Plot this to see the differences:

Are the key saddles found before the prominence? Note that some key saddles for the original grid is not found, while they are for the shifted grid (green circle with no red outline).
Code for plot for own reference:
gmt begin promtest png; gmt grdimage bat.nc -t50 -JM16c; gmt grdcontour -C100 bat.nc -l"100m"; gmt plot original-bat/results.txt -St.4c -Gred -W -: -l"Original"; gmt plot pos-bat/results.txt -Sc.1c -Ggreen -W -: -l"+10000"; gmt plot pos-bat/results.txt -i4,3 -Sc0.2c -Ggreen -l"saddle_+10000"; gmt plot original-bat/results.txt -i4,3 -Sc0.2c -Wthick,red -l"saddle_original"; gmt end show

Thanks, I can reproduce this here, and I have an idea of what's wrong.
On Fri, Nov 1, 2024 at 3:20 PM anbj @.***> wrote:

Your result was the same as mine.
I tried increasing MAX_LEGAL_ELEVATION_DIFF to something huge, and it
didn't help. I also removed it, but still the same.
Here's another grid which covers an area with missing prominence points:
bat.nc
https://www.dropbox.com/scl/fi/otc86wla2ldhenk8694ni/bat.nc?rlkey=7z9y50jlc1z5liyg60fdel348&st=c88mfzt6&dl=0
.
Make another version that adds 10000 so all z >> 0:
gdal_calc.py -A bat.nc --outfile=bat-pos.nc --calc="A+10000" --overwrite
Now run prominence for original:
run_prominence.py --skip_boundary --degrees_per_tile 1 --samples_per_tile 500 --binary_dir=~/mountains/code/release --threads $(nproc) --output_dir original-bat bat.nc
and for shifted (+10000):
run_prominence.py --skip_boundary --degrees_per_tile 1 --samples_per_tile 500 --binary_dir=~/mountains/code/release --threads $(nproc) --output_dir pos-bat bat-pos.nc
Plot this to see the differences:
promtest.png (view on web)
https://github.com/user-attachments/assets/7f4d7cd7-4103-4800-948a-8b7c2bdf878c
Are the key saddles found before the prominence? Note that some key
saddles for the original grid is not found, while they are for the shifted
grid (green circle with no red outline).
Code for plot for own reference:
gmt begin promtest png; gmt grdimage bat.nc -t50 -JM16c; gmt grdcontour -C100 bat.nc -l"100m"; gmt plot original-bat/results.txt -St.4c -Gred -W -: -l"Original"; gmt plot pos-bat/results.txt -Sc.1c -Ggreen -W -: -l"+10000"; gmt plot pos-bat/results.txt -i4,3 -Sc0.2c -Ggreen -l"saddle_+10000"; gmt plot original-bat/results.txt -i4,3 -Sc0.2c -Wthick,red -l"saddle_original"; gmt end show
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I found the bug: I was setting the prominence of the highest peak equal to its elevation, which is the normal convention for mountains.  But this doesn't work for underwater peaks; the resultant negative prominence value causes the peak to be filtered from the output.
I've defined the prominence of the highest underwater peak to be its elevation minus the elevation of the lowest saddle.  This isn't perfect, but it does give the highest peak the highest prominence value, and sort of matches the intuition of what would happen if a new, higher peak were added.
You should get the newest code, build clean, rebuild, and run with the --bathymetry flag.  I suspect this will also fix the older issue you opened.
Let me know what you find.

This looks really good. The results for the original grid and the +10000 grid are exactly the same:

So the --bathymetry switch basically says to prominence, "all the values in the input grid are < 0", right?

Not exactly.  It removes the implicit sea level used when computing the
prominence of mountains on land.  It could still be useful for computing
"dry prominence", even if some of the elevations are above 0.
See
https://en.wikipedia.org/wiki/Topographic_prominence#Wet_prominence_and_dry_prominence
.
On Sat, Nov 2, 2024 at 1:48 PM anbj @.***> wrote:

This looks really good. The results for the original grid and the +10000
grid are exactly the same:
promtest.png (view on web)
https://github.com/user-attachments/assets/f129fb0d-f1a4-4a66-8707-17f4d05d24a4
So the --bathymetry switch basically says to prominence, "all the values
in the input grid are < 0", right?
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Right. So it's the implicit sea level that causes some discrepancy.
Thank you so much for looking into this. Let me know if I can do anything to contribute!

The new --bathymetry options seems to work very well! Thank you!
On some of my data, there is bad coverage. In some of these areas, the key saddle latitude and -longitude in results.txt is set to 0. What is rationale behind this?

0,0 means that there is no key saddle.  For example, in your data, there is
no way to go from those high points to a higher point, staying within the
data set.
On Mon, Nov 18, 2024 at 3:08 AM anbj @.***> wrote:

The new --bathymetry options seems to work very well! Thank you!
On some of my data, there is bad coverage. In some of these areas, the key
saddle latitude and -longitude in results.txt is set to 0. What is
rationale behind this?
Screenshot.from.2024-11-18.12-03-41.png (view on web)
https://github.com/user-attachments/assets/8b9a7b39-c541-44c4-a958-2f3751f5ed8d
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Right, so there is no requirement of having a key saddle. Thanks!

Can this be closed now?

Yes. Thanks!


Quest book won't open

Setup a server, connected, started trying to play and track things - the quest book would not open when on the server. Playing pack version 0.10.3 against the 0.10.1 latest for the server.

Duplicate of #51 which has a workaround.


Python 3 compatibility issues in download_images.py

Following lines result in Python 3 compatibility issues
examples/nips17_adversarial_competition/dataset/download_images.py
import cStringIO
...
import urllib2

Python 3 changelog says

The StringIO and cStringIO modules are gone. Instead, import the io module and use io.StringIO or io.BytesIO for text and data respectively.

Since the usage of cStringIO is image = Image.open(cStringIO.StringIO(image_buffer)).convert('RGB') I think it makes sense to replace it with io.BytesIO, which is present in both Python 2.7 (introduced in 2.6) and Python 3.X.
urllib2 was split into several modules in Python 3 and I think the correct solution would be to try importing urllib.request for Python 3 and fall back to urllib2 for Python 2.
The following diff makes me able to download the dataset and I'd be more than happy to submit it if it proves to be useful, but I'm not sure what the default policy about Python 2/Python 3 compatibility is.
diff --git a/examples/nips17_adversarial_competition/dataset/download_images.py b/examples/nips17_adversarial_competition/dataset/download_images.py
index 20f5564..20bb579 100644
--- a/examples/nips17_adversarial_competition/dataset/download_images.py
+++ b/examples/nips17_adversarial_competition/dataset/download_images.py
@@ -24,14 +24,17 @@ from __future__ import division
 from __future__ import print_function

 import argparse
-import cStringIO
 import csv
 import os
 import sys
-import urllib2

 from PIL import Image
+from io import BytesIO

+try:
+    from urllib.request import urlopen
+except ImportError:
+    from urllib2 import urlopen

 def parse_args():
   """Parses command line arguments."""
@@ -53,12 +56,12 @@ def download_image(image_id, url, x1, y1, x2, y2, output_dir):
     return True
   try:
     # Download image
-    url_file = urllib2.urlopen(url)
+    url_file = urlopen(url)
     if url_file.getcode() != 200:
       return False
     image_buffer = url_file.read()
     # Crop, resize and save image
-    image = Image.open(cStringIO.StringIO(image_buffer)).convert('RGB')
+    image = Image.open(BytesIO(image_buffer)).convert('RGB')
     w = image.size[0]
     h = image.size[1]
     image = image.crop((int(x1*w), int(y1*h), int(x2*w), int(y2*h)))

Please do submit the diff. Thanks!