Support structured logging

There have been cases recently where the availability of structured logging output (e.g. JSON), rather than plain text output, would have potentially made diagnosing issues drastically simpler. This is because tooling could be written to analyse the output and provide additional diagnostics (e.g. in the complex cases of AMQP messaging, various visualisations could be written to more clearly see the series of events that happen).
We need to investigate and enable end-to-end structured logging in all Azure SDK for Java libraries. At a high level I would like to see the following as the outcome of this issue:

Documentation on docs.microsoft.com about how to enable structured logging output for all logging implementations that support this mode.
Updates to our ClientLogger API to enable the provision of key / value inputs that will find their way to the logging implementation and output as structured JSON output. Care needs to be taken to ensure that performance is kept as a high priority - no perf degradation should be acceptable when logging is disabled or from the provision of key / value pairs.
Updates to our critical libraries that would most benefit from key / value pairs being output in structured output. At a first pass, this should include at least all azure-core libraries, as well as our AMQP-based libraries (Event Hubs and Service Bus).
Socialisation of this functionality with partner teams so that they may make decisions about inclusion of this in their future revisions.

Updates to our ClientLogger API to enable the provision

done in #25247

Documentation on docs.microsoft.com about how to enable structured logging

Decided not to do it, summary https://gist.github.com/lmolkova/04f6484595fdd7edded9f4d82619291f

Event Hubs is done:

https://github.com/Azure/azure-sdk-for-java/pull/26561

TODO:

[ ] SerivceBus
[ ]  https://github.com/Azure/azure-sdk-for-java/issues/26396


Need way to auto-create topics in kafka

Right now you have to manually create kafka topics when doing local development, need to be able to auto create them.  There is a setting that allows this, but not sure how to enable in confluent local.

Closed by #50


[ARCTIC-938][Optimize] Deleting invalid data files when the major optimize commit throw ValidationException #939

Why are the changes needed?
fix #938
Brief change log

remove the logic of deleting the files produced by minor optimize
check whether the data files are valid before deleting files

How was this patch tested?

[x] Add some test cases that check the changes thoroughly including negative and positive cases if possible

[ ] Add screenshots for manual tests if appropriate

[ ] Run test locally before making a pull request

Documentation

Does this pull request introduces a new feature? (no)
If yes, how is the feature documented? (not documented)

LGTM. same as https://github.com/NetEase/arctic/pull/939


nbody readme update

Updated Nbody with instructions for how to run on Devcloud.
Existing Sample Changes
Description
Added instructions for how to run in batch mode on Devcloud.
Fixes Issue#
External Dependencies
List any external dependencies created as a result of this change.
Type of change
Please delete options that are not relevant. Add a 'X' to the one that is applicable.

[ ] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Implement fixes for ONSAM Jiras
[ x] Documentation

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] Command Line
[ ] oneapi-cli
[ ] Visual Studio
[ ] Eclipse IDE
[ ] VSCode
[ ] When compiling the compliler flag "-Wall -Wformat-security -Werror=format-security" was used

@mpanoop please review and comment if you find anything that needs changes. If no changes needed, please approve the PR.


feat: Ubsan for GoblinRecursionTests.Vanilla

Please read contributing guidelines and remove this line.

Benchmark results
Metrics with a significant change:

protocol_circuit_witness_generation_time_in_ms (private-kernel-reset-small): 2,278 (+17%)
protocol_circuit_proving_time_in_ms (private-kernel-init): 22,113 (-17%)
protocol_circuit_proving_time_in_ms (private-kernel-tail): 35,250 (-19%)
protocol_circuit_proving_time_in_ms (root-rollup): 19,218 (-19%)

Detailed results
All benchmarks are run on txs on the Benchmarking contract on the repository. Each tx consists of a batch call  to create_note and increment_balance, which guarantees that each tx has a private call, a nested private call, a public call, and a nested public call, as well as an emitted private note, an unencrypted log, and public storage read and write.
This benchmark source data is available in JSON format on S3 here.
Proof generation
Each column represents the number of threads used in proof generation.

Metric
1 threads
4 threads
16 threads
32 threads
64 threads

proof_construction_time_sha256
5,682
1,531 (-1%)
704 (-1%)
754 (-3%)
781 (+1%)

L2 block published to L1
Each column represents the number of txs on an L2 block published to L1.

Metric
8 txs
32 txs
64 txs

l1_rollup_calldata_size_in_bytes
1,412
1,412
1,412

l1_rollup_calldata_gas
9,452
9,464
9,476

l1_rollup_execution_gas
616,093
616,105
616,117

l2_block_processing_time_in_ms
1,281 (-1%)
4,810
9,576 (+1%)

l2_block_building_time_in_ms
44,785 (-1%)
177,269 (-1%)
354,610 (-1%)

l2_block_rollup_simulation_time_in_ms
44,614 (-1%)
176,633 (-1%)
353,371 (-1%)

l2_block_public_tx_process_time_in_ms
24,076 (-1%)
100,498
205,829 (-1%)

L2 chain processing
Each column represents the number of blocks on the L2 chain where each block has 16 txs.

Metric
3 blocks
5 blocks

node_history_sync_time_in_ms
9,429 (-1%)
14,351 (-1%)

node_database_size_in_bytes
14,471,248
21,360,720

pxe_database_size_in_bytes
18,071
29,868

Circuits stats
Stats on running time and I/O sizes collected for every kernel circuit run across all benchmarks.

Metric
1 leaves
16 leaves
64 leaves
128 leaves
512 leaves
1024 leaves
2048 leaves
4096 leaves
32 leaves

batch_insert_into_append_only_tree_16_depth_ms
10.7 (+2%)
17.0
N/A
N/A
N/A
N/A
N/A
N/A
N/A

batch_insert_into_append_only_tree_16_depth_hash_count
16.7
31.8
N/A
N/A
N/A
N/A
N/A
N/A
N/A

batch_insert_into_append_only_tree_16_depth_hash_ms
0.620 (+2%)
0.521
N/A
N/A
N/A
N/A
N/A
N/A
N/A

batch_insert_into_append_only_tree_32_depth_ms
N/A
N/A
49.8 (+3%)
76.1 (-1%)
246
473
930
1,853 (+1%)
N/A

batch_insert_into_append_only_tree_32_depth_hash_count
N/A
N/A
95.9
159
543
1,055
2,079
4,127
N/A

batch_insert_into_append_only_tree_32_depth_hash_ms
N/A
N/A
0.509 (+3%)
0.469 (-1%)
0.446
0.442
0.440
0.441 (+1%)
N/A

batch_insert_into_indexed_tree_20_depth_ms
N/A
N/A
60.2 (+3%)
113 (+1%)
357 (+1%)
697
1,392 (+1%)
2,776 (+1%)
N/A

batch_insert_into_indexed_tree_20_depth_hash_count
N/A
N/A
106
208
692
1,363
2,707
5,395
N/A

batch_insert_into_indexed_tree_20_depth_hash_ms
N/A
N/A
0.520 (+3%)
0.504
0.483
0.479
0.481
0.481 (+1%)
N/A

batch_insert_into_indexed_tree_40_depth_ms
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
63.1 (+1%)

batch_insert_into_indexed_tree_40_depth_hash_count
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
107

batch_insert_into_indexed_tree_40_depth_hash_ms
N/A
N/A
N/A
N/A
N/A
N/A
N/A
N/A
0.560 (+2%)

Miscellaneous
Transaction sizes based on how many contract classes are registered in the tx.

Metric
0 registered classes
1 registered classes

tx_size_in_bytes
83,794
665,117

Transaction size based on fee payment method
| Metric |  |
| - |  |

A bit wary here of turning off alignas as it can have threading improvements, putting this off until we gain more confidence this wont regress anything


MAID-3120: docs/license: update LICENSE details

made license text in readme more consitent with other repos

I'll be sending a PR with this change included since this has been inactive for long now.


Allow linking to individual rules

Adds an id to each rule to allow linking directly to the rule.
Closes #3420

You could also link the individual rules mentioned elsewhere to the links you created.
In task-tags setting, ERA and E501 are mentioned and could link back to the links you added in this PR.
They all seem to follow the regex \(`[A-Z]{1,3}[0-9]{0,4}`\).

You could also link the individual rules mentioned elsewhere to the links you created. In task-tags setting, ERA and E501 are mentioned and could link back to the links you added in this PR. They all seem to follow the regex \(`[A-Z]{1,3}[0-9]{0,4}`\).

Thanks for the suggestion @JonathanPlasse. I wonder if doing this automatically might lead to quite a few false positives and, therefore, if it might be better to do this manually in the specific documentation sections.
An example of a false positive could be if V101 in the external settings section was linked to https://beta.ruff.rs/docs/rules/#V101, which is currently not valid a valid rule section. Another example that matches your provided regex is "(key)" in the invalid-envvar-value (PLE1507) rules; this would direct users to https://beta.ruff.rs/docs/rules/#key, which is also not currently a valid rule section.

You could also link the individual rules mentioned elsewhere to the links you created. In task-tags setting, ERA and E501 are mentioned and could link back to the links you added in this PR. They all seem to follow the regex \(`[A-Z]{1,3}[0-9]{0,4}`\).

Thanks for the suggestion @JonathanPlasse. I wonder if doing this automatically might lead to quite a few false positives and, therefore, if it might be better to do this manually in the specific documentation sections.
An example of a false positive could be if V101 in the external settings section was linked to https://beta.ruff.rs/docs/rules/#V101, which is currently not valid a valid rule section. Another example that matches your provided regex is "(key)" in the invalid-envvar-value (PLE1507) rules; this would direct users to https://beta.ruff.rs/docs/rules/#key, which is also not currently a valid rule section.

To avoid false positives like V101 we could check if the rule exists.
(`key`) should not match the regex as it uses lower cases.

Checking the rule exists seems reasonable.
To be honest, this might be beyond my Rust skills. @JonathanPlasse, would you consider working on this, or should I open an issue as a feature request?

You can open an issue.
I may work on it if I have some time.

Tests are failing due to not being able to install "black[d]"'s dependencies. Would it be possible to rerun to check that this is not just a random error?

Tests are failing due to not being able to install "black[d]"'s dependencies. Would it be possible to rerun to check that this is not just a random error?

I triggered a re-run of the failing tests.

Should we include some kind of visual indicator, e.g., make it a link? (Is that even possible?) I'm also wondering if we should use the human-readable rule name for the URL, rather than the code, but then it becomes kind of duplicative with the standalone rule pages, like:

I'm also wondering if we should use the human-readable rule name for the URL, rather than the code, but then it becomes kind of duplicative with the standalone rule pages, like:

I consider this a workaround for the time being until we have standalone rule pages for every rule.


Add ledger close dates to transaction, operation, and effect resources

This will allow someone to, for example, build a transaction history with age display without having to load date data afterwards

Can we try to close this issue? I'm building an app that has a view with 200 recent operations. Loading tx time for each operation is an issue because it generates another 200 requests to horizon what makes the app very slow. It wouldn't be that big problem if it was a single page but my view also allows to go to the next page of operations. Then, if user navigates to the next page while the current page is still loading, live requests to /transactions should be cancelled and it's a pain.
@nullstyle I can do it if you don't have time (in a similar way to https://github.com/stellar/horizon/pull/345).

That seems smart to me.  I can build this today @bartekn.  IMO we need to separate the ledger loader/cache out of the trade endpoint and reuse it across the others.

I'm just finishing up this issue today... the ledger caching system I'm building needs some tests and then I can roll it out to other actions quite easily.


Missing p315 data in DATASET_MatchaTTS/train directory, but referenced in train.txt

It seems that the data for p315 is missing in the DATASET_MatchaTTS/train/ directory. However, p315 is still referenced in the train.txt file. Could you please check if the p315 data has been misplaced or omitted, and update the dataset accordingly?

Hi, I have removed the list of spoof data for speaker p315 from train.txt.
As for why spoofed data for p315 is not generated, it's because Matcha TTS requires a speaker mapping list to perform VCTK voice inference, but the official repo does not provide this list. I found a similar file list (https://github.com/jaywalnut310/vits/blob/main/filelists/vctk_audio_sid_text_train_filelist.txt) to use for speaker mapping. In this file list, p315 is not included.


Fhir docs

Create documentation around performing FHIR-related queries and authentication.

@DanPaseltiner that makes sense... I won't be on the standup tomorrow to discuss unfortunately, but perhaps the team could discuss and I can update accordingly.

Moved to: https://github.com/usds/PRIME-PHDI-Internal/pull/17


Better handling of Opus tags

tagutil backend on an Ogg Opus file returns TagLib, and as expected only the basic tags are returned.
opustags uses libogg and can display and manipulate all tags.
I'm not at all aware of the technical details, but would it be a good idea to switch from libvorbis to libogg so Opus file could be better handled or is there something that libvorbis does better?

Hi @haplo and thanks for the report.
To clarify: we're using both libogg and libvorbis. We need libogg to find/replace the vorbis comment packet (and potentially re-write all following packet), libvorbis is used to extract / build tags from / into the comment packet.
I didn't look into details, but I guess to implement opus we would need to use libogg in about the same way as for ogg/vorbis, and then either write our own code to handle the comment packet (like opustags) or use another library like libopusenc (see this example).
Unfortunately I don't have the time to look further into an implementation, but I'll gladly review a PR if someone is willing to pick it up :pray:

Thank you for your reply @kaworu.
I cannot commit at this moment to work on this feature, but it's encouraging to know that libogg is already integrated and that the parsing should be similar that to that of ogg/vorbis files.
I will be relying on opustags for the time being, but tagutil is a great one-stop shop and I wish this feature gets implemented at some point.


[BUG]

:bug: Bug report
Current Behavior

I am having a problem entering an order and clicking on "Get Payment Update", as I am receiving an error from the "ParadoxLabs/TokenBase" module
Error: Call to a member function setAdditionalInformation() on bool in /var/www/vhosts/domain.com/httpdocs/app/code/ParadoxLabs/TokenBase/Model/AbstractMethod.php:749
Expected Behavior

What I hope is that when I enter an order and click "Get Payment Update", it doesn't give me any Paradox errors and allows me to continue.
Minimal reproduction of the problem with instructions

Go to Magento Admin -> Sales -> Order -> Select any order paid by "paradox" -> click to "Get Payment Update"
What is the motivation / use case for changing the behavior?

Environment

TokenBase version: 4.1.0
Magento version: 2.4.5
PHP version: 8.1.2

Others:

Thanks for reporting this! It looks like this will happen if there is no open authorization transaction on the order. Could you give a screenshot of the 'Transactions' tab on the admin order view? (Without any identifying info)
That will help us confirm the cause.
Do you have the payment method configured to capture at checkout?

Hello, I already solved the error.
The error was that a transaction was not recorded in that order.
Thank you anyway.

Okay, thank you @gustahthorres. Just to confirm, was the issue that caused that unrecorded transaction something outside our payment modules?
I think I'll still make a code change to prevent this PHP error under these particular circumstances.


Update window-focus-refetching.md for React Native

:tada: This PR is included in version 3.9.0 :tada:
The release is available on:

npm package (@latest dist-tag)
GitHub release

Your semantic-release bot :package::rocket:


Need to abstract out access control for TruflationFeedRegistry

closed.  The adapter/registry interface has been abstracted out by ITruflationFeedRegistry.


Chapters 5/6 unicon version of j0 parser does not run

In chapters 5 and 6, so far, when I run the unicon version of the j0 compiler using the hello.java file as input, I receive an error during the parse.
Here is the command-line I run on Ubuntu Linux 21.10 with KDE:
./j0 hello.java
and this is the error messages that I receive:
Run-time error 102
File j0gram.y; Line 30
numeric expected
offending value: tree_11
Traceback:
main(list_1 = ["hello.java"])
yyparse() from line 9 in j0.icn
action_21() from line 581 in j0gram.icn
{tree_11 = tree_14} from line 30 in j0gram.y
I even ran the compiler/parser in debug mode, but it did not give me any useful information.
It seems to be failing on lines 28/29 of the j0gram.y file:
VarDeclarator: IDENTIFIER | VarDeclarator '[' ']' {
$$=j0.node("VarDeclarator",1060,$1); };
The java version of the parser for j0 runs fine.
Does anyone have any ideas on how to fix this?

FYI, I built the unicon and java parsers for chapter 7, and now the unicon parser is working.  I will compare the grammars from chapters 5/6 with chapter 7 and see what the differences are.

Thank you for this report. Assuming all turns out as reported, I will apply a comparable fix to the Ch5-6 code as was apparently made during the development of Ch7.


bug-config player comes out empty if player does not choose any option

Player choice is getting set to empty string if player does not choose any option. Need to persist previous choice.

This bug will be fixed in the above mentioned PR

Fixed the bug in the latest commit. Closing the issue.


Bypass URLs which are not included

Hello,
I want to monitor only google URLs, So I have included only google's URLs.
But still other URLs which are not included, not decrypting, are also going through Titanium Proxy.
Is there any way, not to use Titanium proxy for all other URLs(not included). Please help me.

You can crete ProxyAutoConfig file:
https://en.wikipedia.org/wiki/Proxy_auto-config
for example:
function FindProxyForURL(url, host) {
	if (shExpMatch(host, "*.google.com"))
	{
		return "PROXY <IP_ADDRESS>:8080";
	}

	return "DIRECT";
}

Thanks, I will try with this.
But I couldn't understand, Even I am including only google's URLs, why some of the applications are not working properly with titanium proxy.

The Included/ExcludedHttpsHostNameRegex (which is now obsolete) means that the given encrypted communication will be forwarded without decrypting it. But it still goes through the proxy.

In webex, after clicking on "start meeting" it is having issue.
https://indiafreetrial.webex.com

Do you mean '"Host a meeting?"

yes, Host meeting.
After login you will find "start meeting" option in My WebEx tab.

I can't login to this website. Is there any PUBLIC website were you can reproduce the issue?

WebEx is public website.
Please try with below URL:
https://www.webex.co.in/

I can't reproduce the issue with this URL:(

Did you tried relaying the site? could be certificate pinning.
proxyServer.ExcludeTunnelConnect = async (hostname) => {
                if (hostname.Contains("webex"))
                {
                    //exclude webex
                    return await Task.FromResult(true);
                }
                else
                {
                    return await Task.FromResult(false);
                }
            };

I am not including webex and it is not going to decrypt the URL, still it is not working properly.
Please try again the URL, I have updated.

I don't have a problem visiting https://www.webex.co.in using the proxy.

Problem is not in visiting the webex, but in "start meeting".
Please follow the steps to reproduce the issue:

Go to the URL and Try it free. Once you are done with signup, login with the given credentials.
After login you will find My WebEx tab, click on that and then go to "Start Meeting".
After clicking on start meeting, new window will open and it will show an error message after sometime.

For me it is stopped after completion of 86%.
During debug I found that all webex URLs are throwing exception in HandleClient() in RequestHandler

"Unable to read data from the transport connection: An existing connection was forcibly closed by the remote host."

I think I've reproduced the issue, but not in the browser, it is a native addon which was instelled by this site (Cisco_WebEx_Add-On.exe), it opens in a new (non browser) window.

That's what I thought it was. Did you tried relaying all the requests? @honfika Non-browser addons/apps may use ceritificate pinning like dropbox client.

I tried with the latest beta from nuget.
When I set
            explicitEndPoint.BeforeTunnelConnect = async hostname =>
            {
                return true;
            };

Then is works.
When I set:
            explicitEndPoint.BeforeTunnelConnect = async hostname =>
            {
                return false;
            };

It stucks at 10%
So @harrip12 you should set the following (@justcoding121 's sample was old):
            explicitEndPoint.BeforeTunnelConnect = async hostname =>
            {
                return hostname.EndsWith("webex.com");
            };

I tried this and it seems to work. Do not forget to upgrade to the latest beta package.

Or if you want to decrypt only the google urls, you can use this:
explicitEndPoint.BeforeTunnelConnect = async hostname =>
{
return !hostname.EndsWith("google.com");
};


Ubuntu toolchain setup script fails

Describe the bug
When running the Ubuntu setup script (Tools/setup/ubuntu.sh) on Ubuntu 20.04, the script stops running at this line: https://github.com/PX4/Firmware/blob/0a4e7142ee7baa14cc50ea86d5a13b1933d5d5e4/Tools/setup/ubuntu.sh#L144
To Reproduce
Run the script on Ubuntu 20.04, after installing the NuttX dependencies it stops. When replacing the line linked above with GCC_FOUND_VER=0, the installation continues as expected.

@Franky333 can you check again?

@julianoes Not sure why but now I get this error before the toolchain installation:
./ubuntu.sh: line 149: [: missing ]'
And then the toolchain gets installed even though I already have it installed.
It seems like I had the same problem in my original report (where I didn't have the toolchain already installed) but instead of printing the error message the script just finished without doing anything else.

I just tried this in a fresh Ubuntu 18.04 docker and it worked just fine.
How did you download your ubuntu.sh file? Can you try the one downloaded with the repository?

I used a fresh download of the repository and launched the script from there.
Maybe the version of bash I am using (5.0.16(1)-release) behaves differently than yours?

@julianoes I can reproduce in a VM - see duplicate https://github.com/PX4/Firmware/issues/14916
I think it is something to do with the Grep of the version and the addition of "+x" but I don't understand this bit of the code. Hoping you can work out why it is falling over.

Sorry, I overlooked the error. Now I can reproduce it.


Repo transferred to apache and renamed

Hi all,
This project now belongs to apache, and has a new repo path at: https://github.com/apache/mesatee-sgx
Currently if one uses the forked crates, he/she still needs to use the old repo URL as git = "https://github.com/baidu/rust-sgx-sdk", rev = "v1.0.9", because all the forked crates are using the old repo URL.
Now, mixed usage of this SDK, like the following Cargo.toml would trigger collision between two sgx_tstd:
sgx_tstd = { rev = "v1.0.9", git = "https://github.com/apache/mesatee-sgx.git" }
wasmi = { git = "https://github.com/mesalock-linux/wasmi-sgx" }

You'll see
error: the `#[global_allocator]` in sgx_tstd conflicts with this global allocator in: sgx_tstd
error: duplicate lang item in crate `sgx_tstd`: `f32_runtime`.
  |
  = note: first defined in crate `sgx_tstd`.

error: duplicate lang item in crate `sgx_tstd`: `f64_runtime`.
  |
  = note: first defined in crate `sgx_tstd`.

error: duplicate lang item in crate `sgx_tstd`: `panic_impl`.
  |
  = note: first defined in crate `sgx_tstd`.

error: duplicate lang item in crate `sgx_tstd`: `begin_panic`.
  |
  = note: first defined in crate `sgx_tstd`.

error: duplicate lang item in crate `sgx_tstd`: `oom`.
  |
  = note: first defined in crate `sgx_tstd`.

error: aborting due to 6 previous errors

error: Could not compile `Helloworldsampleenclave`.

So I'm planning to have thorough update on all of the forked crates to use the new repo URL, and it would affect all of the projects which are depending on the old URL.
Any ideas?
Best,
Yu

Congratulations for the Apache tribute. Any chance you can update mesalock crates along with the next version bump? However, this is a delicate issue for us. We'd be blocked if this transition doesn't work smoothly. However, we did lock down our mesalock dependencies to specific git commits, so this might be less of an issue

Thanks @brenzi !
I'm thinking of use a permanent (at least I think it's permanent) domain to host the redirect. I have a candidate rustsgx.com which triggers 301 redirect to https://github.com/apache/mesatee-sgx now. So the following git clone command works:
$ git clone https://rustsgx.com
Cloning into 'rustsgx.com'...
warning: redirecting to https://github.com/apache/mesatee-sgx/
remote: Enumerating objects: 363, done.
remote: Counting objects: 100% (363/363), done.
remote: Compressing objects: 100% (256/256), done.
remote: Total 15613 (delta 125), reused 212 (delta 71), pack-reused 15250
Receiving objects: 100% (15613/15613), 40.78 MiB | 4.87 MiB/s, done.
Resolving deltas: 100% (8118/8118), done.

Seems that git can work with HTTP 301 redirect. However, cargo does not allow me to do that. If I have sgx_types = { git = "http://rustsgx.com" } in Cargo.toml, error would be:
    Updating git repository `http://rustsgx.com/`
warning: spurious network error (2 tries remaining): cross host redirect not allowed; class=Net (12)
warning: spurious network error (1 tries remaining): cross host redirect not allowed; class=Net (12)
error: failed to load source for a dependency on `sgx_tstd`

Caused by:
  Unable to update http://rustsgx.com/

Caused by:
  failed to fetch into /home/ding/.cargo/git/db/_empty-f3f08613514edcc1

Caused by:
  cross host redirect not allowed; class=Net (12)

Any ideas?

Just find a flag in .cargo/config which enables command line git instead of the built-in libgit-sys:
[net]
git-fetch-with-cli = true

If we enable this, we can directly use git = "https://rustsgx.com"
cargo build --release
    Updating git repository `https://rustsgx.com/`
    Updating crates.io index
   Compiling cc v1.0.46
   Compiling sgx_types v1.0.9 (https://rustsgx.com/#1d8a9f87)
   Compiling sgx_build_helper v0.1.0 (https://rustsgx.com/#1d8a9f87)
   Compiling sgx_tstd v1.0.9 (https://rustsgx.com/#1d8a9f87)
   Compiling sgx_demangle v1.0.9 (https://rustsgx.com/#1d8a9f87)
   Compiling sgx_libc v1.0.9 (https://rustsgx.com/#1d8a9f87)
   Compiling sgx_unwind v0.0.1 (https://rustsgx.com/#1d8a9f87)
   Compiling sgx_trts v1.0.9 (https://rustsgx.com/#1d8a9f87)
   Compiling sgx_alloc v1.0.9 (https://rustsgx.com/#1d8a9f87)
   Compiling sgx_tprotected_fs v1.0.9 (https://rustsgx.com/#1d8a9f87)
   Compiling sgx_backtrace_sys v1.0.9 (https://rustsgx.com/#1d8a9f87)
   Compiling Helloworldsampleenclave v1.0.0 (/home/ding/rust-sgx-sdk/samplecode/hello-rust/enclave)
    Finished release [optimized] target(s) in 15.09s

Is this a good choice?

@moriab @avishaiw

I would prefer don't change global settings, actually developers no need to do anything after you transferred the repo, GitHub will do the redirection automatically . if the project staying at GitHub, it will auto redirect to the correct repo after you transferred, so developer

I would prefer don't change global settings,
if I remember correctly, developers no need to do anything after you transferred the repo, GitHub will do the redirection automatically.

@jasl You're right about git.  It'll lead to panic handler collisions and mess up the dependency tree.

This is a patch which you guys can apply to hello-rust sample. It shows some usage on "sdk.rustsgx.com" and "repo.rustsgx.com"
diff --git a/samplecode/hello-rust/enclave/.cargo/config b/samplecode/hello-rust/enclave/.cargo/config
new file mode 100644
index 0000000..c91c3f3
--- /dev/null
+++ b/samplecode/hello-rust/enclave/.cargo/config
@@ -0,0 +1,2 @@
+[net]
+git-fetch-with-cli = true
diff --git a/samplecode/hello-rust/enclave/Cargo.toml b/samplecode/hello-rust/enclave/Cargo.toml
index abd6c59..4c932cc 100644
--- a/samplecode/hello-rust/enclave/Cargo.toml
+++ b/samplecode/hello-rust/enclave/Cargo.toml
@@ -10,32 +10,36 @@ crate-type = ["staticlib"]
 [features]
 default = []

+[dependencies]
+log = { git = "https://repo.rustsgx.com/log-sgx" }
+
 [target.'cfg(not(target_env = "sgx"))'.dependencies]
 sgx_types = { git = "https://github.com/baidu/rust-sgx-sdk.git" }
-sgx_tstd = { git = "https://github.com/baidu/rust-sgx-sdk.git" }
+sgx_tstd  = { git = "https://github.com/baidu/rust-sgx-sdk.git" }
+
 [patch.'https://github.com/baidu/rust-sgx-sdk.git']
-sgx_alloc = { path = "../../../sgx_alloc" }
-sgx_build_helper = { path = "../../../sgx_build_helper" }
-sgx_cov = { path = "../../../sgx_cov" }
-sgx_crypto_helper = { path = "../../../sgx_crypto_helper" }
-sgx_libc = { path = "../../../sgx_libc" }
-sgx_rand = { path = "../../../sgx_rand" }
-sgx_rand_derive = { path = "../../../sgx_rand_derive" }
-sgx_serialize = { path = "../../../sgx_serialize" }
-sgx_serialize_derive = { path = "../../../sgx_serialize_derive" }
-sgx_serialize_derive_internals = { path = "../../../sgx_serialize_derive_internals" }
-sgx_tcrypto = { path = "../../../sgx_tcrypto" }
-sgx_tcrypto_helper = { path = "../../../sgx_tcrypto_helper" }
-sgx_tdh = { path = "../../../sgx_tdh" }
-sgx_tkey_exchange = { path = "../../../sgx_tkey_exchange" }
-sgx_tprotected_fs = { path = "../../../sgx_tprotected_fs" }
-sgx_trts = { path = "../../../sgx_trts" }
-sgx_tse = { path = "../../../sgx_tse" }
-sgx_tseal = { path = "../../../sgx_tseal" }
-sgx_tservice = { path = "../../../sgx_tservice" }
-sgx_tstd = { path = "../../../sgx_tstd" }
-sgx_tunittest = { path = "../../../sgx_tunittest" }
-sgx_types = { path = "../../../sgx_types" }
-sgx_ucrypto = { path = "../../../sgx_ucrypto" }
-sgx_unwind = { path = "../../../sgx_unwind" }
-sgx_urts = { path = "../../../sgx_urts" }
+sgx_alloc                       = { git = "https://sdk.rustsgx.com" }
+sgx_build_helper                = { git = "https://sdk.rustsgx.com" }
+sgx_cov                         = { git = "https://sdk.rustsgx.com" }
+sgx_crypto_helper               = { git = "https://sdk.rustsgx.com" }
+sgx_libc                        = { git = "https://sdk.rustsgx.com" }
+sgx_rand                        = { git = "https://sdk.rustsgx.com" }
+sgx_rand_derive                 = { git = "https://sdk.rustsgx.com" }
+sgx_serialize                   = { git = "https://sdk.rustsgx.com" }
+sgx_serialize_derive            = { git = "https://sdk.rustsgx.com" }
+sgx_serialize_derive_internals  = { git = "https://sdk.rustsgx.com" }
+sgx_tcrypto                     = { git = "https://sdk.rustsgx.com" }
+sgx_tcrypto_helper              = { git = "https://sdk.rustsgx.com" }
+sgx_tdh                         = { git = "https://sdk.rustsgx.com" }
+sgx_tkey_exchange               = { git = "https://sdk.rustsgx.com" }
+sgx_tprotected_fs               = { git = "https://sdk.rustsgx.com" }
+sgx_trts                        = { git = "https://sdk.rustsgx.com" }
+sgx_tse                         = { git = "https://sdk.rustsgx.com" }
+sgx_tseal                       = { git = "https://sdk.rustsgx.com" }
+sgx_tservice                    = { git = "https://sdk.rustsgx.com" }
+sgx_tstd                        = { git = "https://sdk.rustsgx.com" }
+sgx_tunittest                   = { git = "https://sdk.rustsgx.com" }
+sgx_types                       = { git = "https://sdk.rustsgx.com" }
+sgx_ucrypto                     = { git = "https://sdk.rustsgx.com" }
+sgx_unwind                      = { git = "https://sdk.rustsgx.com" }
+sgx_urts                        = { git = "https://sdk.rustsgx.com" }

the .cargo/config only affects the enclave itself, because it locates in the "enclave" folder, along with enclave's Cargo.toml. with the help of "sdk.rustsgx.com" and "repo.rustsgx.com", I can make all of the forked crates depends on a permanent "repo" address "sdk.rustsgx.com", no matter where the git repo is.

if this solution is acceptable, I can try if a shorter domain name is affordable. it'll be more ergonomic.

Yes, that cargo issue crosses me all the time. I'd be happy for some endorsing comments (or critique) on my suggestion to resolve this properly:
https://github.com/rust-lang/cargo/issues/7497
I'm not sure a custom domain will resolve the underlying problem. It's just a workaround. I could live with changing the global setting but I don't think this is elegant because it might change other behaviour as well as a side effect

@brenzi Yeah I've seen your comments and I agree with you.
btw, the  .cargo/config can be local and no need to be global. it can only affect the enclave itself by just putting it together with the enclave's Cargo.toml

the other choice is sgx.rs, sdk.sgx.rs and repo.sgx.rs

given that this project is now under the apache org, i don't see any reason why you'd want to transfer repos again.  apache is pretty prestigious.  So, why not just go with https://github.com/apache/mesatee-sgx in the forked crates?

@nabilschear The reason is that "mesatee" is a brand name owned by Baidu, and Baidu does not donate it to Apache. So we have to change it soon.
besides, we may have option to make this sdk an isolated project and get rid of the prefix in a couple of years. in this case, we have to change the repo name again. don't know what to do is right.

understood.  Whatever the solution to the path problem, when will it roll out to all the forked crates?

@nabilschear I will do this next week after I get back in town.
A new problem is that MesaTEE is being renamed... which means that the repo has to change its repo name again. So should we use the "sgx.rs" jumper, or keep up with every renaming? How do you think?

What about creating a registery?
https://doc.rust-lang.org/cargo/reference/registries.html

@elichai Yes I'm thinking about it seriously!
I have done a lot of experiment on that. I think it should be do-able, but with less transparency of porting. Currently, the forked crates can be "compared" directly with the upstream, and the diff reveals the difference clearly just in one click.
Another though is that some crates are forked while some others are not. Does Cargo supports "partially overrided"

Well you can still keep them on github.
Just publish them afterwards.
What do you mean partially ovrrided?
(btw I would first spend time reaserching the --sysroot new feature I linked before, I still have hopes for that)

In the previous crates.io design, a create published on crates.io can only depends on crates.io crates.
So can I publish a crate on sgx's crates.io, but make it depends on crates hosted on official crates.io?

regarding to the --sysroot feature, I'm trying it as well :-)

@dingelish that's a great question. Can we use 2 separate crates.io together? Idk.


[verilator] How to dump wave in verilator?

Hi, I'm testing verilog with verilator flow, according to the verilator's user guide, the wave dump methods are in C files. How can i integrate these methods in SVUnit?

Seems that you can also do it from SystemVerilog code: https://veripool.org/guide/latest/faq.html#how-do-i-generate-waveforms-traces-in-c

Pass the --trace option to Verilator. Then you may use $dumpfile and $dumpvars to enable traces, the same as with any Verilog simulator.

So, when running with SVUnit, you'd need something like runSVUnit -r_args "--trace".

Thanks ^_^

I'm trying to do this but I'm not sure where to add the $dumpfile and $dumpvars in the verilog code.  If I just have one unit_test.sv file I can put it in the build function, but if I have multiple unit_test.sv files, each with their own $dumpfile then it seems only dump waves for one of them.

@krupan You should be able to use the unit test names to make the file names unique of the dump files unique.


typo in FC layer

Hello,
In resnet.py:283 you use FC_WEIGHT_STDDEV even for weight decay which looks wrong for me. Probably just a copy-paste bug.

Out of curiosity, what should it be?

FC_WEIGHT_DECAY. Which already exists, but just isn't used. For equivalent code in conv layers CONV_WEIGHT_DECAY is used.


File Exists Problem

(ET-BERT) ymx@5950x-3090:~/ET-BERT$ bash user.sh
Traceback (most recent call last):
File "/home/ymx/ET-BERT/fine-tuning/run_classifier.py", line 9, in
from uer.encoders import *
File "/home/ymx/ET-BERT/uer/encoders/init.py", line 1, in
from uer.encoders.transformer_encoder import TransformerEncoder
File "/home/ymx/ET-BERT/uer/encoders/transformer_encoder.py", line 3, in
from uer.layers.transformer import TransformerLayer
File "/home/ymx/ET-BERT/uer/layers/transformer.py", line 3, in
from uer.layers.position_ffn import PositionwiseFeedForward, GatedFeedForward
File "/home/ymx/ET-BERT/uer/layers/position_ffn.py", line 2, in
from uer.utils import *
File "/home/ymx/ET-BERT/uer/utils/init.py", line 1, in
from uer.utils.dataset import *
File "/home/ymx/ET-BERT/uer/utils/dataset.py", line 6, in
from uer.utils.constants import *
File "/home/ymx/ET-BERT/uer/utils/constants.py", line 4, in
with open("models/special_tokens_map.json", mode="r", encoding="utf-8") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'models/special_tokens_map.json'
I exactly did not find the file. Hope that I can get it. Thanks.

Thanks for your excellent work.


Failed to install it with luarocks on Ubuntu 16.04

I tried to install luamqtt with luarocks on Ubuntu 16.04, but I failed with the following logs:
daniel@memory:~/mqtt $ sudo luarocks install luamqtt
Installing https://rocks.moonscript.org/luamqtt-1.4.3-1.rockspec...
Using https://rocks.moonscript.org/luamqtt-1.4.3-1.rockspec... switching to 'build' mode
Cloning into 'luamqtt'...
remote: Enumerating objects: 29, done.
remote: Counting objects: 100% (29/29), done.
remote: Compressing objects: 100% (26/26), done.
remote: Total 29 (delta 2), reused 18 (delta 1), pack-reused 0
Receiving objects: 100% (29/29), 25.08 KiB | 0 bytes/s, done.
Resolving deltas: 100% (2/2), done.
Checking connectivity... done.
Note: checking out 'e2e16e029ff06f622d4750463ba64c18674d8d1f'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

Updating manifest for /usr/local/lib/luarocks/rocks
luamqtt 1.4.3-1 is now built and installed in /usr/local (license: MIT)

No code is installed:
daniel@memory:~/mqtt $ ls /usr/local/lib/luarocks/rocks/
index.html  luabitop  luafilesystem  luamqtt  luasec  luasocket  manifest  manifest-5.1  manifest-5.2  manifest-5.3  penlight
daniel@memory:~/mqtt $ ls /usr/local/lib/luarocks/rocks/luamqtt/
1.4.3-1
daniel@memory:~/mqtt $ ls /usr/local/lib/luarocks/rocks/luamqtt/1.4.3-1/
doc  luamqtt-1.4.3-1.rockspec  rock_manifest
daniel@memory:~/mqtt $

Oh sorry, I'm new to lua, it's installed some where else.


Fix an error when incomplete S3Client is destroyed

If an error occurs during initialization of the S3Client instance, the initializer for the Client superclass is never called. This could happen, for example, when the S3Client has a bad profile name passed which botocore doesn't understand. The specific error is that the file_cache_mode attribute is not set because the superclass initializer is not called in the S3Client initializer if an error occurs during S3 session setup. This commit moves the superclass initializer to the top of the S3Client initializer to ensure that all superclass attributes are defined if/when any errors occur.
The same fix is applied for the Google client and the local client.
Closes #372

Contributor checklist:

[X] I have read and understood CONTRIBUTING.md
[X] Confirmed an issue exists for the PR, and the text Closes #issue appears in the PR summary (e.g., Closes #123).
[X] Confirmed PR is rebased onto the latest base
[x] Confirmed failure before change and success after change
[X] Any generic new functionality is replicated across cloud providers if necessary
[ ] Tested manually against live server backend for at least one provider
[ ] Added tests for any new functionality
[ ] Linting passes locally
[ ] Tests pass locally
[x] Updated HISTORY.md with the issue that is addressed and the PR you are submitting. If the top section is not `## UNRELEASED``, then you need to add a new section to the top of the document for your change.

I don't have a Windows machine available and all the tests pass locally for me on my Mac. I think I'll need some help to debug and fix that.

@bryanwweber I have a preference to do this with getattr in the __del__ method, which will be a little more resilient to future changes and not depend on order of execution.
E.g.,
    def __del__(self) -> None:
        # remove containing dir, even if a more aggressive strategy
        # removed the actual files
        if getattr(self, "file_cache_mode", None) in [
            FileCacheMode.tmp_dir,
            FileCacheMode.close_file,
            FileCacheMode.cloudpath_object,
        ]:
            self.clear_cache()

            if self._local_cache_dir.exists():
                self._local_cache_dir.rmdir()

🎉 great idea @pjbull! I'll make that change

@pjbull Change is made, sorry for the delay!

@bryanwweber I don't think the Windows failure is due to your change. Going to merge into a repo-local branch to see if that passes, and if not tweak the test on that branch.

This one is maybe back in 0.18.1:
Exception ignored in: <function CloudPath.__del__ at 0x7f0ace1ef420>
Traceback (most recent call last):
  File "/virtualenv/.venv/lib/python3.12/site-packages/cloudpathlib/cloudpath.py", line 250, in __del__
    and self.client.file_cache_mode == FileCacheMode.cloudpath_object
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'S3Client' object has no attribute 'file_cache_mode'
Exception ignored in: <function CloudPath.__del__ at 0x7f0ace1ef420>
Traceback (most recent call last):
  File "/virtualenv/.venv/lib/python3.12/site-packages/cloudpathlib/cloudpath.py", line 250, in __del__
    and self.client.file_cache_mode == FileCacheMode.cloudpath_object
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'S3Client' object has no attribute 'file_cache_mode'


How do I manage repos ?

Maybe I am just missing something in the docs, but is there a way to delete repos? What is the proper way to insure restic forgets a repo ?

Ok , I get that, but restic itself has no way of doing that , correct ? I'd have to manually purge the files that restic created in the repo whether it be s3 b2 or local storage, correct ?

Yes, I believe so.
However, you could try running a very aggressive prune, although I'm not sure that will delete every single snapshot.

You can forget all snapshots with restic forget --keep-last; restic forget latest and then run restic prune, but this will keep the directories and a few files e.g. in keys/ in the backend. There's no way to let restic delete a repository completely. I think having a way to delete an entire repo is not so important...

+1 for this feature...

@tnatanael On GitHub and other platforms, please do not comment "+1, me too" and more. Instead use the reaction "+1" on the original comment.

I'm closing this. It won't happen in the foreseeable future from what I can tell due to activity and previous comments.

@asche77 Please open a new issue if you think there is still a problem. From the log snippet you provided, everything looks as it should. After deleting a repository, restic obviously won't be able to read from it.


Support for Backblaze B2 Cloud storage

I want to start by saying you have done an amazing job with imgproxy, I love the idea and the execution!
I would like to propose adding support for Backblaze B2 Cloud storage as a source option. It's a great and cheaper alternative to AWS S3.

Hi Emil,
As far as I see, Backblaze has access to the files by URL. if you need access to private files, you can set the Authorization header with IMGPROXY_CUSTOM_REQUEST_HEADERS (supported only by Pro version though).
If you want a dedicated URL schema for Backblaze B2, you can make a PR. I'm pretty loaded with other tasks right now, and this feature request may wait for my attention a pretty long time.

Backblaze has s3 compatible API.
So you can use your backblaze creds with imgproxy as follows:
AWS_ACCESS_KEY_ID=keyID
AWS_SECRET_ACCESS_KEY=applicationKey
IMGPROXY_S3_ENDPOINT=s3.us-west-000.backblazeb2.com
IMGPROXY_USE_S3=true

Access your image:
http://imgproxy.sample.com/[signature]/fill/300/400/sm/0/plain/s3://[backblaze bucket name]/0000011.jpg

Backblaze has s3 compatible API.
So you can use your backblaze creds with imgproxy as follows:
AWS_ACCESS_KEY_ID=keyID
AWS_SECRET_ACCESS_KEY=applicationKey
IMGPROXY_S3_ENDPOINT=s3.us-west-000.backblazeb2.com
IMGPROXY_USE_S3=true

Access your image:
http://imgproxy.sample.com/[signature]/fill/300/400/sm/0/plain/s3://[backblaze bucket name]/0000011.jpg


bug:  background-activated css property is not working for ion-tab-button

Hi,
--background-activated css property is not working for ion-tab-button.
ion-tab-button{
--background-activated:rgb(73, 177, 187,0.2);
}

@rajiramamoorthi There isn't a background-activated property for this component according to the official docs and according to github's readme.

Thanks for the issue! @NikolaPeevski is correct, tabs does not have this CSS variable. We do have an issue open here to update these components to have the variables they need: https://github.com/ionic-team/ionic/issues/18279. Please subscribe to this issue for updates!
Note that the activated class is only added on press in iOS, and in Material Design it uses a ripple upon activation/press.


Error on running: you are using an empty matrix

These are the last few lines of the output before it crashed with an error:
Reading in super matrix file now... Done... Required 0 seconds
Reading in SR file now... Done
Going through iteration 1 now... variance is -nan
Going through iteration 2 now... variance is -nan
.
.
.
Going through iteration 45 now... variance is -nan
Going through iteration 46 now... variance is -nan
Going through iteration 47 now... variance is -nan
Going through iteration 48 now... variance is -nan
Going through iteration 49 now... variance is -nan
Going through iteration 50 now... variance is -nan
Reading in super matrix file now... Done
Construction matrix now...  done
Creating covariance matrix now...  done
Finding eigenvectors now... hic_breakfinder: hic_breakfinder/eigen/eigen-git-mirror/Eigen/src/Core/Redux.h:401: typename Eigen::internal::traits::Scalar Eigen::DenseBase::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_max_op<double, double>; Derived = Eigen::CwiseUnaryOp<Eigen::internal::scalar_abs_op, const Eigen::Matrix<double, -1, -1> >; typename Eigen::internal::traits::Scalar = double]: Assertion `this->rows()>0 && this->cols()>0 && "you are using an empty matrix"' failed.
Why might this be happening?

E00435:54:H3LH5CCXY:5:1103:17462:65564/1	0	chr1	9999	0	49S60M42S	*	0	0	CCCAAGTATGAGTTGCCTAGAACAGCTCTTCCTTTATTTTCTTTTTCTGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGAGATAACTATTGATACAACACCTTCATGACCCTAAGGTAC	AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJAAFFJFJFJFJJJFJJJFFJJA-7-7FJ<FFJFF7<AAF-A7	NM:i:0	MD:Z:6AS:i:60	XS:i:59	SA:Z:chr5,18606943,-,93S58M,0,0;chr5,18606892,-,44M107S,0,0;
E00435:54:H3LH5CCXY:5:2103:13240:59763/1	0	chr1	9999	0	49S60M42S	*	0	0	CCCAAGTATGAGTTGCCTAGAACAGCTCTTCCTTTATTTTCTTTTTCTGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGAGATAACTATTGATACAACACCTTCATGACCCTAAGGTAC	AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJFJJJJJJJJJFJJJJJFJJJFJJJJJ7	NM:i:0	MD:Z:6AS:i:60	XS:i:59	SA:Z:chr5,18606943,-,93S58M,0,0;chr5,18606892,-,44M107S,0,0;
E00435:54:H3LH5CCXY:6:1118:13646:20805/1	2048	chr1	9999	0	78H47M26H	*	0	0	GATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA	JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ<J	NM:i:0	MD:Z:47	AS:i:47	XS:i:46	SA:Z:chr5,18606943,-,64S87M,42,0;
E00435:54:H3LH5CCXY:5:1103:17462:65564/2	16	chr1	9999	0	44S60M47S	*	0	0	GTATGAGTTGCCTAGAACAGCTCTTCCTTTATTTTCTTTTTCTGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGAGATAACTATTGATACAACACCTTCATGACCCTAAGGTACTATCA	FF<F7FJJFA7JJJJJA<JJFJJJJJJJFFAJJJJFJFFJJFFFAFJJJJJJJFFJJJJJJJJJJJFJJJJJJJJJJAJJJJJJAJJJJAFJJFF-FJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJ<JJJJJJJJJJ<FFFAA	NM:i:0	MD:Z:6AS:i:60	XS:i:59	SA:Z:chr5,18606943,+,98S53M,0,0;chr5,18606887,+,49M102S,0,0;
E00435:54:H3LH5CCXY:5:2103:13240:59763/2	16	chr1	9999	0	44S60M47S	*	0	0	GTATGAGTTGCCTAGAACAGCTCTTCCTTTATTTTCTTTTTCTGGATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACAGAGATAACTATTGATACAACACCTTCATGACCCTAAGGTACTATCA	FJA<JFJJJJJJJFJJJFFJF<JJ<JJF<F-FFFJJJJJJJJFFJFJF7JJJJJJJJJJJJJJJJAAJJJJJJJJFJJFJJJFJAJJJAJFJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFFFAA	NM:i:0	MD:Z:6AS:i:60	XS:i:59	SA:Z:chr5,18606943,+,98S53M,0,0;chr5,18606887,+,49M102S,0,0;
E00435:54:H3LH5CCXY:6:1118:13646:20805/2	2064	chr1	9999	0	104H47M	*	0	0	GATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAA	FJFJFAJFJJJJFAJJFFJJJJJJJJFJJFJJFJAJJJJFJAAFAAA	NM:i:0	MD:Z:47	AS:i:47	XS:i:45	SA:Z:chr5,18606943,+,38S87M26S,42,0;
E00435:54:H3LH5CCXY:6:2116:22323:12877/1	0	chr1	10000	0	69S82M	*	0	0	GATCGGAAGAGCACACGTCTGAACTCCAGTCACTATGAGTATCCCGTATGCCGTCTTCTGCTTGAAAAAATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCAACCCTAACGCTCACCCTAA	AAAF-FJAFJFFJJFJJAAFAJFJJJJ-7F<FJAFAA7AFFF--<<FJFJJJF<FA-FJF<<---AJA7-<<<AJJAJ7FFFA<<FJ-AF-<-<7<AFFA7FJJJJFF-AJFFF-A<AF<--<AF--7-7)-)-F)--77-<-)))77)--	NM:i:3	MD:Z:61T9C2A7	AS:i:67	XS:i:66
E00435:54:H3LH5CCXY:5:1101:18375:73299/2	16	chr1	10000	6	48S58M1I44M	*	0	0	CTACACTATTTCCCTACACGACGCTATTCCGATCTCCCTACCCCAACCATAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC	-AFA<A7--<-A7-<-7)-)AAF<---7--AF77-)A<)<AF<<7<A7-----A--7-<F7AF-7-A-AFJJJFFF<-F<JAFJJ7JJA7F-7JFJF-7FJFF-J<AJJJJJFJJFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJFFAAA	NM:i:1	MD:Z:102	AS:i:95	XS:i:91
E00435:54:H3LH5CCXY:7:2104:29244:38860/2	16	chr1	10000	0	43S108M	*	0	0	CCTAACCCCAACCCTACCCCTCCCCCCACCCCCACCCCTACCCATAACCCTAACCCTAACCCTAACCCTAACCCTACCCCCAACCCTAACCCTACCCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACC	77-))AA<)--F<7)7<<)<-)---))-)))-)-)J7<7---7--77777---7AA7A-A7--7-<-----7-F---AA7--A<---<-FF-77-<<<7--JJFFFJJFFAF7JJJFFFF7FJJJJJJJJFJJJJJJJJJJJJJJJFFFAA	NM:i:3	MD:Z:33A3T13A5AS:i:93	XS:i:92
E00435:54:H3LH5CCXY:7:2113:16001:28048/2	16	chr1	10000	0	72S79M	*	0	0	CTCCCACAATACAAACACACAATCCCCACAATAACCCTCACCCTCACCCTATCCTTACCACTCCCCCTAAACATAACCCTACCCCTAACCCTAACACGAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCCTAACCA	-)7-A----77---F<7<-77)7-)--<<-7--7)7)))))FF7--7-A<7-----7---7-7--7-77-----F7-7<AF--A<-----<-AA<7--J<-<--7-AA--<---JJJJJJJJJJJFJJJ<JJJJJFFF<-JFJJJJFFFAA	NM:i:4	MD:Z:9A13C1T52C0	AS:i:63	XS:i:62

Thanks for sharing this. Is it possible to also share the command/software for generating the bam file? I suspect this is a formatting issue.
-Jesse

Ah! I just ran the Picard ValidateSamFile and it seems that there might be Read Group related problems in the bam file. I will attempt to fix that and re-run and let you know if the above error persists. Thanks much!

Hi!
I ran the bam file through picard MarkDuplicates, and then added read groups with AddOrReplaceReadGroups and finally ran ValidateSamFile which gave no errors.
The hic_breakfinder run on this bam file again ended with this error:
Going through iteration 46 now... variance is -nan
Going through iteration 47 now... variance is -nan
Going through iteration 48 now... variance is -nan
Going through iteration 49 now... variance is -nan
Going through iteration 50 now... variance is -nan
Reading in super matrix file now... Done
Construction matrix now...  done
Creating covariance matrix now...  done
Finding eigenvectors now... hic_breakfinder: hic_breakfinder/eigen/eigen-git-mirror/Eigen/src/Core/Redux.h:401: typename Eigen::internal::traits::Scalar Eigen::DenseBase::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_max_op<double, double>; Derived = Eigen::CwiseUnaryOp<Eigen::internal::scalar_abs_op, const Eigen::Matrix<double, -1, -1> >; typename Eigen::internal::traits::Scalar = double]: Assertion `this->rows()>0 && this->cols()>0 && "you are using an empty matrix"' failed.
How can we go about fixing this?
Thanks!

Also, what pipeline/software have you used in the past to generate the BAM files? Perhaps I can use that to prevent any software incompatibility issues that might have led to some missing flags in the bam file perhaps?

Hi Sanjit,
I am not totally sure about this, but I suspect this is a bam file formatting issue. The lines in the bam file that you posted don't have any information about the pair information for each read, which is something the tool will be looking for. I suspect this is why the matrix is empty, is that it believe you are giving it a bunch of single ended reads. When you made this bam file, did you merge two files together that were originally aligned as read1 and read2? Or can you share the specific command you used to make these files? Thanks.
-Jesse

Hi Sanjit,
Please see the https://github.com/dixonlab/bwa_mem_hic_aligner directory for the scripts we have used for alignment/post-processing of the Hi-C data. I think that the problem is the lack of pair information for each read (at least from what I can tell from the lines of the bam file you posted). Please let me know if this helps. Thanks for your input.
-Jesse

@sanjitsbatra
Was this ever resolved for you?
I am encountering the same error even after generating BAMs via the dixonlab/bwa_mem_hic_aligner  scripts.
.
.
.
Going through iteration 49 now... variance is -nan
Going through iteration 50 now... variance is -nan
Reading in super matrix file now... Done
Construction matrix now...  done
Creating covariance matrix now...  done
Finding eigenvectors now... hic_breakfinder: /home/mjohnston/software/miniconda3/envs/breakfinder/include/eigen3/Eigen/s
rc/Core/Redux.h:413: typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [wi
th BinaryOp = Eigen::internal::scalar_max_op<double, double>; Derived = Eigen::CwiseUnaryOp<Eigen::internal::scalar_abs_
op<double>, const Eigen::Matrix<double, -1, -1> >; typename Eigen::internal::traits<T>::Scalar = double]: Assertion `thi
s->rows()>0 && this->cols()>0 && "you are using an empty matrix"' failed.
Aborted (core dumped)

I notice that the Eigen error message is slightly different.
Is it possibly an Eigen version issue? Is there a recommended version number for hic_breakfinder?
My software versions used for bwa_mem_hic_aligner and hic_breakfinder are as follows:
  - bamtools = 2.4.0
  - bwa = 0.7.17
  - eigen = 3.3.7
  - samtools = 1.6

Thanks for any advice!

I got the same problem with you all.
but when I try to run the  two_read_bam_combiner.pl in dixonlab/bwa_mem_hic_aligner scripts.
I got error like this
AGAATCTTAAGAGCTGTGAGACAGAAGTACCAGGTAACCTATAAAAGAAAACCTATCAGATTAACAGCAGATTTCTC   AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ    AS:i:0  XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:150       YT:Z:UU          RG:Z:BMG ST-E00493:381:HL3Y2CCXY:1:1101:16904:19135      147     chr16   24413027        42     25M              chr1     236126711       0       CTGAGTCATCGACAGACCCATTCTC       JJJJJJJJJJJJJJJJJJFJFFFAA               AS:i:0   XN:i:0  XM:i:0  XO:i:0  XG:i:0  NM:i:0  MD:Z:25 YT:Z:UU RG:Z:BMG The IDs don't match up
May the 'IDs' be the  missing information in the bam file ? or just something wrong with Eigen or bamtools ?
hope for some advice .
Thank you so much !

Just to clarify, the error of "The IDs don't match up" is when you run the two_read_bam_combiner.pl script?

Just to clarify, the error of "The IDs don't match up" is when you run the two_read_bam_combiner.pl script?

yes , that error only happens when I run the two_read_bam_combiner.pl script .
I tried it a lot of times in yesterday( the error still exist). And I ruled out dependent software  or environment configuration issues.

OK got it. Just to explain that script a bit, it assumes that the input bam files for read1 and read2 are name sorted and that the paired reads appear in the same order. The error that you listed appears when the script recognizes that the read IDs are not the same, meaning the files are not in the same order for some reason. The times that this happens tend to be that 1) there was some prior filtering of reads, most likely at the fastq stage prior to alignment, 2) there was some kind of error where the bam file was truncated, or 3) The aligner/fastq files have some way it labels the read ID differently for read1 and read2.
To help sort this out, I modified the script so that it will print out the read IDs that don't match. If you can re-download the script and re-run and post the error it will help to figure out what is going on.

It's greatly helpful.  My problem has been solved with  your new code.  Thank you very much !


Event Details Page: Add edit , delete, archive, and attend buttons (UI only)

Satisfies #207
Related to #206
Would like feedback on styling or code.

Reference from docs:

The buttons are looking good! I would suggest a bit more space between the icon and the text for each of the buttons, but other than that, I think this PR is ready for review.


'UserWarning: Version mistmatch between Java ZMQ server and Python client.' with pycro-manager version 0.4.5

Hi,
I got the warning 'UserWarning: Version mistmatch between Java ZMQ server and Python client.  Java ZMQ server version: 2.5.0
Python client expected version: 2.6.0'.
This happened with the updated pycro-manager version 0.4.5 but not with an older version 0.3.6.

This means you have to update to the latest micro-manager nighly build in addition to pycromanager 0.4.5. I added an better error message to clarify this in the future


Add cacheOnly option to StoreReadRequest

I took a stab at implementing the cache-only reads for the StoreReadRequest. I thought sending back NoNewData made more sense than Error since reading from an empty or invalid cache isn't exactly a problem per-se. Of note is that this doesn't hit the disk either, but I think that's fine since the original request was to only hit the cache
This closes #457

@matt-ramotar I seem to be unable to request a review from you for some reason. Sorry if this is already on your radar, just wanted to make sure you saw it!


Bundle not included in RDF seralisation

Hi @trungdong, @satra,
With the RDF exporter, it looks like bundles are exported as if they were entities. Here is a minimal example:
import prov.model as prov

document = prov.ProvDocument()

document.set_default_namespace('http://example.org/0/')
document.add_namespace('ex1', 'http://example.org/1/')
document.add_namespace('ex2', 'http://example.org/2/')

document.entity('e001')

bundle = document.bundle('e001')
bundle.set_default_namespace('http://example.org/2/')
bundle.entity('e001')

print(document.get_provn())

print('---')

print(document.serialize(format='rdf', rdf_format='turtle'))

And the output is:
document
  default <http://example.org/0/>
  prefix ex2 <http://example.org/2/>
  prefix ex1 <http://example.org/1/>

  entity(e001)
  bundle e001
    default <http://example.org/2/>

    entity(e001)
  endBundle
endDocument
---
@prefix ex1: <http://example.org/1/> .
@prefix ex2: <http://example.org/2/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

<http://example.org/0/e001> a prov:Entity .

ex2:e001 a prov:Entity .

There is no formal representation of bundles in turtle (we should use trig instead) but I was nevertheless expecting ex001 entity to be declared as a prov:Bundle in the RDF-turtle serialisation, i.e.:
@prefix ex1: <http://example.org/1/> .
@prefix ex2: <http://example.org/2/> .
@prefix prov: <http://www.w3.org/ns/prov#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix xml: <http://www.w3.org/XML/1998/namespace> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .

ex:e001 a prov:Bundle .

ex2:e001 a prov:Entity .

What are you thought on this? Thanks in advance for your feedback!

Hi  @cmaumet
In my opinion, the fact that a URI is used as the identifier of a bundle does not automatically mean that it is asserted as a prov:Bundle. I don't think that there is an inference defined for that.
This example in PROV-DM, for instance, explicitly asserts the prov:Bundle type for the entities.
In fact, if you did not assert ex:e001 as an entity, we would only know it as a normal URI. Suppose I use a URI as an RDF graph's identifier, I wonder if there is a rule to say that the URI is a graph.
Dong.


Make COUNT_ALIGNMENT_DUPLICATES use more clever parent selection.

Currently, our duplication analysis using Bowtie2 alignments assigns the parent of the duplicate reads as the one with the highest average phred quality score. However, as Mike pointed out there are better solutions. In the future, we may decide to implement this.

I expect this will shortly be rendered moot by https://github.com/naobservatory/mgs-workflow/issues/122, which will involve removing deduplication from the core pipeline. However, a very similar issue might be inherited by whatever downstream script or pipeline takes on that functionality.
Moving this down to priority 3 for now.


Version env variable for inso artifact name in test workflow

The test workflow creating run artifacts should suffix the run number onto artifacts, but that wasn't happening because the environment variable was not correctly set. Previously, the inso-package and inso-package:artifacts steps were combined, but on separation this was missed.
This screenshot is current behavior. The zip file should also have the -run.1234 suffix.

Superseeded by #4108


Librarify TAS so it can be used with other projects

Added new server and config methods to construct server objects
Removed everything from the main file and moved main server example
to examples/tas-server.go
Updated README.md to reflect the changes
Updated to ZMQ3 (2.x is very old)

@faizanchango mind taking a look?

@jessicachango I did not re-write any of the internals other than re-grouping them into types and functions. I will fix the print, but the other ones are exactly as they were before.

Looks good to me.


chore: add timeout for 2d projections

Adds a configurable timeout for 2D projections (default no timeout). If a timeout is set, we run the projection in a child process and kill it if it does not finish within the allotted time.

thanks - i'm happy to make this more general but want to try this as is first to see what kinds of overheads we incur from it. projection2d is a good op to start with since it takes a long time anyway


Upgrade to azurerm v4.0 provider

Description

Increase min azurerm ver to 4.0.0 (breaking change).
Replace retention_policy block with retention_policy_in_days (breaking change).
Use trust_policy_enabled property. Module variable enable_trust_policy remains the same.
Remove use of the network_rule_set.virtual_network block.

Type of Change

[ ] Non-module change (e.g. CI/CD, documentation, etc.)
[x] Azure Verified Module updates:

[ ] Bugfix containing backwards compatible bug fixes

[ ] Someone has opened a bug report issue, and I have included "Closes #{bug_report_issue_number}" in the PR description.
[ ] The bug was found by the module author, and no one has opened an issue to report it yet.

[ ] Feature update backwards compatible feature updates.
[x] Breaking changes.
[x] Update to documentation

Checklist

[x] I'm sure there are no other open Pull Requests for the same update/change
[x] My corresponding pipelines / checks run clean and green without any errors or warnings
[x] I did run all  pre-commit checks

@alefteris - We're going to hold off on 4.0 updates until the core team can agree on handling deprecated items that aren't forward compatible.  I'm hoping to be able to add this functionality next week.

@jchancellor-ms, looks like #95 was merged so would be nice to see if we can proceed with this PR to get the v4 provider supposed :)

Closing, as it has been replaced by the now merged https://github.com/Azure/terraform-azurerm-avm-res-containerregistry-registry/pull/95


Override field's name attribute?

I need compatibility with some existing HTML that uses dashes in the name attribute, but I have yet to find a way to override it with wtforms. The documentation for wtforms.fields.core.Field mentions the following about _name:

The name of this field, passed by the enclosing form during its construction. You should never pass this value yourself.

This makes me think that I should be able to override the name in the enclosing form. But in that case - where? Here's a failing test that shows what I'm expecting to be able to do:
import wtforms
from werkzeug.datastructures import ImmutableMultiDict

class MyForm(wtforms.Form):
    my_field_id = wtforms.IntegerField('My field', id='my-field',
                                       _name='my-field')

my_data = ImmutableMultiDict([('my-field', '2')])
my_form = MyForm(my_data)
assert my_form.my_field_id.name == 'my-field'  # Instead `my_field_id`
assert my_form.my_field_id.data == 2  # Instead `None`

Instead I have to use this custom field to get what I'm looking for:
import wtforms
class MyCustomIntegerField(wtforms.IntegerField):

    def __init__(self, *args, **kwargs):
        name = kwargs.pop('name', None)
        super().__init__(*args, **kwargs)
        if name:
            self.name = name

Am I missing something here?

I noticed this is mentioned in #154:

De-couple attribute names from field names
Allow users to have fields with names containing "special" characters while still allowing the field to >function, just like SQLAlchemy with attribute vs column names.
Default case (when attribute name unspecified) is still using attribute name munging for maximum >compatibility

Hopefully we can get it earlier though :wink:

Just ran across this today when integrating with a third-party that requires special characters in the form submission. Primarily [ and ].

Will be supported in 3.0 as you mentioned
https://github.com/wtforms/wtforms/issues/154

@jmagnusson a workaround is to override form meta when binding a field.
from wtforms.meta import DefaultMeta

class BindNameMeta(DefaultMeta):
    def bind_field(self, form, unbound_field, options):
        if 'custom_name' in unbound_field.kwargs:
            options['name'] = unbound_field.kwargs.pop('custom_name')
        return unbound_field.bind(form=form, **options)

This allows you to provide a parameter custom_name to any field you want to override a name for.
class PostForm(Form):
    my_title = StringField(custom_name='my-title')

Just keep in mind that you have to subclass from your own Form that uses new meta:
import wtforms

class Form(wtforms.Form):
    meta = BindNameMeta

thanks bmwant, i just needed to change meta to Meta.
import wtforms

class Form(wtforms.Form):
    Meta = BindNameMeta

I Wonder how dose it work in

FormFiled


Redundant linebreaks in Insert mode (when using Jupyter Notebooks)

I am editing a Jupyter / IPython notebook, and it seems that when hitting the Return key in Insert mode, Pentadactyl inserts redundant linebreaks. This, however, does not happen when editing in Pass-Through mode (C-z). For example, the first case would look like:
foo

bar

While in Pass-Through mode the result is (as it should be):
foo
bar

Any idea what might be going on in Insert mode compared to Pass-Through mode and how I could fix this?

I've noticed this happens on a few front-end JS heavy websites (facebook.com, messenger.com are notable ones I've noticed this problem with), it's likely because of the way pentadactyl and the JS for that particular website end up interacting and not something that's wrong with penta in particular.

shift+enter usually works as well

It's a bug with very long history: http://code.google.com/p/dactyl/issues/detail?id=616
The temporary solution:
:set pk+=.*:<CR>

Some recent update fixed this, it seems. Not sure which one. Maybe 4904fb5bff72e0d45fea353372ccf9c3061722f8 ?


Detect unused imports in dry-run mode

Detecting and reporting unused library and resource imports in dry-run mode would ease maintaining test data. Resource file should be considered used also if it contains any additional imports.
Unfortunately we cannot really detect unused variable file imports because dry-run doesn't validate variables in general. Similarly resource files containing only variables will be incorrectly reported as unused. Need to think are these false positives so big a problem that it should be possible to somehow disable this functionality.
This functionality has been requested by Zhang Yu from NSN.

@pekkaklarck how do You propose could we crunch it? Since @jussimalinen closed #1998 We could use that just to create set of libraries from which all parsed keywords originated and later compare it with all imports, right?
What I'm thinking is we need three things:

place to create set of all used imports
add items to the set witch from each keyword
compare the set with *** Settings ***

Should I think about it as a new listener, or should this happen some other place?

Assuming listeners actually work in dry-run, using them to collect information about used libs and resources is a good idea. The listener should also get information about imports somehow. I haven't looked at that, but assume that the info is somehow available through namespace that ought to be accessible through context (see e.g. BuiltIn).

One thing to decide is do we want to enable this functionality automatically or should we have a separate command line option like --detectunusedimports or --unusedimportwarning. If we have an option, it would be good to have it available also when running tests normally (which is probably also easier than having it available only in dry-run). We then should also decided should the option be enabled automatically in dry-run or not. Because there can be false positives (i.e. a resource containing only other imports and/or variables but no keywords), having it off by default might actually be a good idea.

We have decided to implement this using listeners. They already get a notification when a keyword is called, but they don't know what libraries or resource files are imported. Issue #2030 covers adding a new listener method to get that information and this issue is basically blocked until it has been implemented.

We discussed this further with @pekkaklarck and realized that there are a lot of open questions on how exactly this should work.
Obviously if a test suite file contains an import for a library or a resource which is not used at all, there should be a warning.
But what about these cases:

What if a resource does not implement any keywords itself, but imports other resources, from which keywords are used? (This is actually a fairly common use case and I dont there should be a warning.)
What if two resource files both dont directly provide a keyword that is used, but both import the same library, which is used. Should there be a warning?
What if a suite imports a resource file which contains imports that that specific suite does not use? Should there be a warning? (I dont think so.)
What if a resource file contains imports which none of the suites which import it use? (I think yes.)
What if a resource file imports only variables (which are used) but no keywords are used from it? (Probably we still have to warn, as it is impossible to track variable use currently.)

To track the transitive use of resources, the listener interface in issue #2030 will require some kind of origin information for import events.
As this is clearly quite complicated issue, we have to drop this from 2.9. It can very well come in a minor version after 2.9 release, so that we have more time to test different options and design this properly.


Update initialize_bouncer_middleware.stub

🔗 Linked issue

❓ Type of change

[x] 🐞 Bug fix (a non-breaking change that fixes an issue)
[ ] 👌 Enhancement (improving an existing functionality like performance)
[ ] ✨ New feature (a non-breaking change that adds functionality)
[ ] ⚠ Breaking change (fix or feature that would cause existing functionality to change)

📚 Description

There is a typescript build problem in this code. I don't know if this is the best way to do it, but it is resolves the problem.

📝 Checklist

[ ] I have linked an issue or discussion.
[ ] I have updated the documentation accordingly.

Hey, thanks for the PR, but I think you are just missing this provider in your adonisrc.ts file :
  providers: [
     // ... others providers
    () => import('@adonisjs/core/providers/edge_provider'),
  ],

So we should add that to configure command?

Oh wait sorry. Indeed a fix is needed, because maybe you are not using Edge. And so, ctx.view type will be unknown. But using a as any will not be the best way.
There is no need to modify the stub.

So this should be explicit in the docs, right? So that we don't have this same issue in the future.

Yeah, we can update the docs to mention to remove this line if you are not using Edge.

What about conditionally add this line only if edge.js is installed on the user's application? I mean, in configure.ts we could have a check like that
It should be easy to do

What about conditionally add this line in the middleware only if edge.js is installed on the user's application? I mean, in configure.ts we could have a check like that It should be easy to do

If we do that, people will install Edge.js afterward will have an issue. I believe we are better off documenting it and leave it to the user.

i was thinking about that : if Edge is not installed, we add the middleware with commented code. that way, if people need to install edge afterward, they can simply uncomment the code

    /**
     * Uncomment if you need Edge helpers
     */
   // if ('view' in ctx) {
   //  ctx.view.share(ctx.bouncer.edgeHelpers)
   // }

Having to manually update the bouncer middleware seems a bit boring. But it's not the end of the world either

I think, we are trying to serve individuals who do not want to understand the surrounding ecosystem of the framework. They will always struggle to use the framework.

But you ignore the docs, do not understand the error in the first place and start with an issue, then its a problem with you and not with anything else.
Also, I do not want to make these configure commands complicated like in v5 and then create a mess for ourselves in order to maintain them.

Documented. https://github.com/adonisjs/v6-docs/commit/0912db42d5165fc2efa6c2a998100a6faf8239f6
https://docs.adonisjs.com/guides/authorization#the-initialize-bouncer-middleware


Meetup Suggestion: Honolulu BitDevs

Required:

Name of Meetup: Honolulu Bitcoin Developers
Location Of Meetup: Honolulu
At least one of the following:

Meetup Page (or similar): https://meetu.ps/c/4SS7m/M2dkz/a
Telegram Group (or similar): https://t.me/+Uh9gbHO9EHFkZWJh
Website: http://www.honolulubitdevs.com/

Optional

Name of Organiser(s) & Twitter Handle: Robby (@RawBTC) and Michael (@MichaelHawaii)
Links showing public support: Commitment tweet

ok - please make a pull request


DOC-1847 and editorial revisions

Harness Developer Pull Request
Thanks for helping us make the Developer Hub better. The PR will be looked at
by the maintainers.
What Type of PR is This?

[ ] Issue
[ ] Feature
[x ] Maintenance/Chore

If tied to an Issue, list the Issue(s) here:

Issue(s)

House Keeping
Some items to keep track of. Screen shots of changes are optional but would help the maintainers review quicker.

[x ] Tested Locally
[ ] Optional Screen Shoot.

Preview environment: https://ci.pr.harness.io/pr-632

Comments are added

Maybe a comment on this page with the link to Docker registry. And then mention anonymous access on the Connector page
(https://developer.harness.io/docs/platform/Connectors/connect-to-harness-container-image-registry-using-docker-connector).

Preview environment: https://ci.pr.harness.io/pr-632

Preview environment: https://ci.pr.harness.io/pr-632


Click on list view row/card to show event details

Add generic way to handle row click action
Implement show event details with it

This issue was moved to cloudfoundry-incubator/stratos#1470


There are no toggle for fire rule

When a vehicle is on fire, there isn't a way to note it on the sheet.
(clearing hazards should untoggle fire automatically)
I suggest a faint fire icon in a corner that you can tap to enable, lighting it up in red.

done


coordinating OBO terms for OHD

Hello Bill,
following our editorial working group call,
looking at OHD, to see where I can contribute.
I've included below a few OBO Foundry ontology terms, that may be of use for this project.  As we discussed on the call today, DO would welcome collaboration on this branch of the DO with your project. We don't currently have carious lesion in the DO. Have you considered carious lesion as a phenotype ?
To get us started, can you share the authoritative resources you are using ?,
so that we can align our definitions and include citations to your sources.
Looking around for sources, which of these do you recommend:
(Caton et al. 2018)
A new classification scheme for periodontal and peri‐implant diseases and conditions – Introduction and key changes from the 1999 classification
https://onlinelibrary.wiley.com/doi/full/10.1111/jcpe.12935
https://www.ncbi.nlm.nih.gov/pubmed/29926489
Professional Dental Terminology for the Dental Assistant and Hygienist
https://www.dentalcare.com/en-us/professional-education/ce-courses/ce542/a-c
-- glossary of terms
ADA: Glossary of Dental Clinical and Administrative Terms
https://www.ada.org/en/publications/cdt/glossary-of-dental-clinical-and-administrative-ter#c
OBO Ontology terms:
from the Symptom Ontology:
symptom:  SYMP:0000462
pain: SYMP:0000099
A sensation perception where there is an unpleasant sensation that usually indicates the body is threatened or damaged. The sensation may be sharp or dull, short-lived or chronic, intermittent or continual, confined to one area or spread over the entire body.
http://www.nationalpainfoundation.org/MyTreatment/articles/Cancer_PainDefinitions.asp
DO: Disease Ontology
disease [DOID:4]
tooth disease [DOID:1091]
dental caries  [DOID:216]
Cheers,
Lynn

Hi Lynn.
Sorry my response was so slow. As you know, I've had a lot happen in my life the last two years.
I cannot comment on the quality of the references you mention. I typically work with a dentist for adding particular disease grade terms.
Other comments:

We use OGMS's pain term. The reason for this is that we are/were following the OGMS model of disease, and pain was already in the OGMS. In the future, we may switch to the emotion ontology's feeling of pain term. It depends on what we end up doing with the concept of pain in the future.

OHD's dental caries term was originally added by Alan (I think). It may have originally used the DOID:216 IRI. For some reason (which is hard to discern) it seems that I changed the IRI in 2015. The definitions in the OHD and DO are also different. This may be the reason why the IRI was changed.

Perhaps in the future, we may make use of the DO tooth disease hierarchy. It depends what exactly is meant by 'disease'. In the dental context, I am finding that most of what is called a 'disease' by a dentist would be classified as either a disorder (e.g, carious lesion of tooth or a disease course in the OGMS framework.

Hello Bill,
Good to hear from you.
Would be happy to coordinate the dental diseases with you.
BTW: DO includes both diseases and disorders.
Cheers,
Lynn
Sent from my iPhone

On Dec 7, 2022, at 9:28 AM, Bill Duncan @.***> wrote:

Hi Lynn.
Sorry my response was so slow. As you know, I've had a lot happen in my life the last two years.
I cannot comment on the quality of the references you mention. I typically work with a dentist for adding particular disease grade terms.
Other comments:
We use OGMS's pain term. The reason for this is that we are/were following the OGMS model of disease, and pain was already in the OGMS. In the future, we may switch to the emotion ontology's feeling of pain term. It depends on what we end up doing with the concept of pain in the future.
OHD's dental caries term was originally added by Alan (I think). It may have originally used the DOID:216 IRI. For some reason (which is hard to discern) it seems that I changed the IRI in 2015. The definitions in the OHD and DO are also different. This may be the reason why the IRI was changed.
Perhaps in the future, we may make use of the DO tooth disease hierarchy. It depends what exactly is meant by 'disease'. In the dental context, I am finding that most of what is called a 'disease' by a dentist would be classified as either a disorder (e.g, carious lesion of tooth or a disease course in the OGMS framework.
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you authored the thread.


Check for previous/existing GitHub issues/module proposals

[X] I have checked for previous/existing GitHub issues/module proposals.

Check this module doesn't already exist in the module indexes

[X] I have checked for that this module doesn't already exist in the module indexes; or I'm proposing the module to be migrated from CARML/TFVM.

Bicep or Terraform?
Bicep
Module Classification?
Resource Module
Module Name
avm/res/managed-identity/user-assigned-identity
Module Details
Migrate from CARML to AVM
Do you want to be the owner of this module?
Yes
Module Owner's GitHub Username (handle)
elanzel
(Optional) Secondary Module Owner's GitHub Username (handle)
No response

Hi @elanzel ,
Thanks for requesting/proposing to be an AVM module owner!
We just want to confirm you agree to the below pages that define what module ownership means:

Team Definitions & RACI
Shared Specification (Bicep & Terraform)
Module Support

Any questions or clarifications needed, let us know!
If you agree, please just reply to this issue with the exact sentence below (as this helps with our automation 👍):
"I CONFIRM I WISH TO OWN THIS AVM MODULE AND UNDERSTAND THE REQUIREMENTS AND DEFINITION OF A MODULE OWNER"
Thanks,
The AVM Core Team
#RR

NOTE:

This Module Proposal issue MUST remain open until the module is fully developed, tested and published to the relevant registry. Do NOT close the issue before the successful publication is confirmed!
Once the module is fully developed, tested and published to the relevant registry, and the Module Proposal issue was closed, it MUST remain closed.

Hi @elanzel ,
Thanks for confirming that you wish to own this AVM module and understand the related requirements and responsibilities!
We just want to ask you to double check a few important things and take the next steps before you start the development.
Please use the following values explicitly as provided in the module index page:

For your module:

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Repository name and folder path are defined in RepoURL
Create the GitHub teams defined in the ModuleOwnersGHTeam and ModuleContributorsGHTeam columns and grant them permissions as described here.

In case of a Bicep module, please let the AVM core team know when you created these teams, and we'll help you with assigning the necessary permissions as described here.
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Grant the right level of permissions for  the AVM core team and PG teams on your GitHub repo as described here.
You can now start the development of this module! ✅ Happy coding! 🎉
Please respond to this comment, once your module is ready to be published! 🙏
Any further questions or clarifications needed, let us know!
Thanks,
The AVM Core Team

NOTE:

This Module Proposal issue MUST remain open until the module is fully developed, tested and published to the relevant registry. Do NOT close the issue before the successful publication is confirmed!
Once the module is fully developed, tested and published to the relevant registry, and the Module Proposal issue was closed, it MUST remain closed.

@elanzel,
Due to a recent change in the naming convention for AVM Bicep modules, this module is getting an updated name.
The title and description of this GH issue has been updated to reflect the name change. Please make sure you adhere to the new naming convention when publishing your module!
Please see the new naming convention in:

RMNFR1 for resource modules
PMNFR1 for pattern modules

Please note that the Telemetry ID and name of GitHub Teams haven't changed.
If you feel uncertain about any details, please check the Bicep modules indexes.

PR merged.
Owners and contributors teams created and added to their respective parent.
CODEOWNERS file updated in BRM.

Thank you for your work @elanzel! Closing the issue.


RTD Programmer error with S25FS-S Family Serial flash

Dear Bernard Black and ghent360,
I am using S25FS-S Family serial flash.
rtd266x_programmer/main.cpp
Line 19 in e83f32e
static const FlashDesc FlashDevices[] = {
in ghent360 code:
https://github.com/ghent360/RTD-2660-Programmer/blob/94a74bcd6586c71c160da4bdcc47fdff2b518b90/RTD Programmer/main.cpp#L21
but this SPI flash not listed in your program. Can you please tell me how can i add this device to list , i checked the datasheet some registers are differnet but maximum are same.

Which part is confusing?
It is just a table with the device ID and some parameters. Just print what
device Id you are reading, then add a line to the table with the device
name, the device ID and the rest of the parameters from the datasheet.
On Sep 25, 2017 9:53 PM, "Bhura Malik"<EMAIL_ADDRESS>wrote:
Dear Bernard Black and ghent360,
I am using S25FS-S Family serial flash.
rtd266x_programmer/main.cpp
Line 19 in e83f32e
static const FlashDesc FlashDevices[] = {
in ghent360 code:
https://github.com/ghent360/RTD-2660-Programmer/blob/
94a74bcd6586c71c160da4bdcc47fdff2b518b90/RTD%20Programmer/main.cpp#L21
but this SPI flash not listed in your program. Can you please tell me how
can i add this device to list , i checked the datasheet some registers are
differnet but maximum are same.
—
You are receiving this because you are subscribed to this thread.
Reply to this email directly, view it on GitHub
https://github.com/ghent360/RTD-2660-Programmer/issues/8, or mute the
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.

http://www.mouser.com/ds/2/380/S25FS-S_00-271247.pdf
page - 137
i couldn't understand how can i read this device jedec Id
can you please help me out

I have answered this here: https://github.com/static-void/rtd266x_programmer/issues/2
@ghent360 don't know if you've seen my code previously, I modified yours to use the I2C on the VGA port of Linux machines (so on my board I can use a standard VGA cable). It's based on your code - thank you.

I modified yours to use the I2C on the VGA port of Linux machines (so on my board I can use a standard VGA cable). @static-void
I am using normal Monitor VGA  cable,it's works or not ?


Adds support for sharedworker

Copied from https://github.com/GoogleChromeLabs/worker-plugin/pull/42/files since this has not been landed in master

Rebased #42 with master since there we merge conflicts.

Sorry for the delay. I merged #42.

Really appreciate the help @developit
Great work on the plugin, BTW. Would love to help. Are there any bugs/issues where you're looking for more collaborators?


Try Travis caching of jars

should speed up builds, potentially.

You can check if it worked once the tests pass by running travis cache at the command line.

Well, I guess the tests have been erroring for quite some time. Maybe this isn't the best project to test this opt on.

yeah, right now the tests are pretty hosed. fracking storm.

realtime is the future. Any negativity or inference that there might be a problem with Storm is a sign of impending codgerhood.

@johnynek merged develop since tests now pass. Pushed again.

@sritchie thanks old friend.

I'm seeing
Setting up build cache
$ export CASHER_DIR=$HOME/.casher
0.03s$ Installing caching utilities
0.48sattempting to download cache archive
found cache

Unclear how much time's getting saved on the build.

total of this run was 58 min, whereas this was 57 min: https://github.com/twitter/summingbird/pull/601
So far, no evidence of a win.

Or if your metric is "distance away from a 1 hour run time", I'm seeing 50% improvement.

:)

 Thank you for your submission, we really appreciate it. Like many open source projects, we ask that you all sign our Contributor License Agreement before we can accept your contribution.1 out of 2 committers have signed the CLA.:white_check_mark: johnynek:x: sritchieYou have signed the CLA already but the status is still pending? Let us recheck it.


nodejs-functions: add monitoring support and timeoutSeconds in app-deploy

Checklist:

[x] Read the Code of Conduct and Contributing Guidelines.

[x] Followed the commit message guidelines.

[x] Stack adheres to Appsody stack structure.

Modifying an existing stack:

[x] Updated the stack version in stack.yaml

Implements creating a ServiceMonitor CR for deployed applications (for stacks that use Prometheus). Also adds timeoutSeconds under the readiness probe to avoid Knative error.
Contributing a new stack:

Describe how application dependencies are managed:

Explain how Appsody file watcher is utilized:

Describe other Appsody environment variables defined by the stack image:

Describe any limitations and known issues:

Related Issues:
Related to: https://github.com/appsody/stacks/issues/313 and https://github.com/appsody/stacks/issues/391

Closing for now - Will reopen after more testing.


mingw libs missing in glfw-3.3.3.bin.WIN64.zip

Duplicate of https://github.com/glfw/glfw/issues/1852


Adaptive noise cancellation using reference signal

Hi,
Thanks for the wonderful repo. Could you please tell me how we can perform the Adaptive noise cancellation using a reference signal (reference noise signal)?
The example you provided here  only makes use of the past value of the signal. Can we adjust it to make use of the reference signal to update the filter coefficients?

Please elaborate. Do you mean the case where you can measure some global noise - for example with second sensor next to your measured process? Can you reference some paper/tutorial/blog post where this situation is presented?

Thanks for the quick reply. Here is the paper (link) that uses Acceleration data as a reference signal to remove the noise from PPG sensor.
The workflow of ANC (from the above paper) is shown below

I was working on similar problem recently with no success. So I will gladly investigate the paper. Be patient, I will try to process the topic.

Hi,
Is there any progress ? we are facing the same issue!
this is the paper which describe such a method:
https://www.diva-portal.org/smash/get/diva2:1456739/FULLTEXT01.pdf ( chapter 2.3.1)

In case it helps, here is another one ( much clearer one) with Matlab code:
https://arajhans.github.io/files/papers/GuptaJR_ESE531Report06.pdf
another Matlab code:
https://github.com/ADataDate/Acoustic_Noise_Cancellation
P.S: they have different variable names ( d - signal , v1- noise , v2-noise_reference,  x- observation)

Hi,
Thanks for your recommendations. I have actually implemented the LMS filter from the first link in python. There is not much progress (the error is reduced by only 25%). I am yet to try NLMS and RLS filters from the same paper.
Thanks a lot for your comments.


Update team pic on homepage (quarterly)

Update the team pic on the homepage every quarter (or at least review every quarter and update as needed).

[x] #190
[x] Q2 / April
[ ] Q3 / July
[ ] Q4 / October

Closing since Kimberly was the only one involved in the issue and is no long at ODI.


reference.txt not found error

reference.txt file not found error after importing and converting the python file to exe file

Please provide context. Tell me more, about what application and which converting method is used?

I have experienced a similar issue when converting a python file to .exe using PyInstaller. This issue prevents me from launching the .exe file.
Error Message: FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\sophi\AppData\Local\Temp\_MEI264762\AppOpener\reference.txt'

I have experienced a similar issue when converting a python file to .exe using PyInstaller. This issue prevents me from launching the .exe file.
Error Message: FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\sophi\AppData\Local\Temp_MEI264762\AppOpener\reference.txt'

Okay fixing this issue, tonight!

@merksk8 can you look into this??

Hello,
the problem is this:
Traceback (most recent call last):
  File "appopener_test.py", line 7, in <module>
  File "<frozen importlib._bootstrap>", line 991, in _find_and_load
  File "<frozen importlib._bootstrap>", line 975, in _find_and_load_unlocked
  File "<frozen importlib._bootstrap>", line 671, in _load_unlocked
  File "PyInstaller\loader\pyimod02_importers.py", line 499, in exec_module
  File "AppOpener\__init__.py", line 4, in <module>
  File "AppOpener\check.py", line 53, in check_reference
FileNotFoundError: [Errno 2] No such file or directory: 'C:\\Users\\Merk\\AppData\\Local\\Temp\\_MEI346282\\AppOpener\\reference.txt'

When creating an exe file, using  main_path = os.path.dirname(__file__) to get the path to the folder of the exe file doesn't seems to work.
The solution is to get it like this:
if getattr(sys, 'frozen', False):
    main_path = os.path.dirname(sys.executable)
elif __file__:
    main_path = os.path.dirname(__file__)

I would recommend to make a function to get the main_path instead using this if-else everywhere it's used( check.py, update_list.py, init.py, probably others) so if there's a problem with it we can modify easier in the future.
Please double check the solution, and I'm sorry but I don't have too much time this week to create the pull request and do more checkings.
Cheers!

i have only one file which i want to convert which is main.py so what solution should i use ? should i create a function in main.py file and give it the location of the exe file?

Yo bro! rolling AppOpener v1.4 today to fix #7 and #6

i have only one file which i want to convert which is main.py so what solution should i use ? should i create a function in main.py file and give it the location of the exe file?

Yo bro! rolling AppOpener v1.4 today to fix #7 and #6

thanks a bunch can i message u anywhere i want to get in touch with u if possible could u provide ur insta handle ?

Hey bruhhhh, its been a while since you rised this issue...
AppOpener version 1.4 rolls today, with the release of it this issue might have been fixed. You may close this issue now if your problem is solved 🤗
Install AppOpener v1.4
pip install AppOpener==1.4

Converting to standalone file (EXE)
Follow any Example from here.
pyinstaller -F Tkinter.py --hidden-import AppOpener --exclude-module _bootlocale

If you had any problem, Iam always here bruhhhhh

thanks a bunch can i message u anywhere i want to get in touch with u if possible could u provide ur insta handle ?

Tip:  Real programmers prefer Discord to interact
Stay connected 🤝

Mail
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Discord

yes thanks a ton

hello

FileNotFoundError: [Errno 2] No such file or directory: 'C:\Users\aadhi\AppData\Local\Programs\Python\Python310\lib\site-packages\AppOpener\Data\reference.txt'
IAM NOT ABBLE TO IMPORT APPOPENER