JS only reports crash on next boot after native crash

Platform:

[x]  iOS
[ ]  Android

paranoid redacted npm ls:
<EMAIL_ADDRESS>├── UNMET PEER DEPENDENCY<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>├──<EMAIL_ADDRESS>
Config:
Sentry.config(__CONFIG__.sentry.dsn, {
  deactivateStacktraceMerging: false,
  logLevel: SentryLog.Verbose,
  disableNativeIntegration: false,
  ignoreModulesExclude: [],
  ignoreModulesInclude: ["RNSentry"],
}).install();

As mentioned here: https://github.com/getsentry/react-native-sentry/issues/187#issuecomment-322896741  I am only seeing JS crashes being uploaded after native crashes on 1.17.1 on iOS. This is with disableNativeIntegration: false.
How to reproduce:

boot app with xcode in simulator
close xcode because debugger mode nothing will report
open app, cause JS crash
re-open app
check sentry web app
expected: a JS bug to be reported
actual: no bugs reported
re-open app
cause native crash
re-open app
expected: Native crash in sentry web app
actual: sentry web app has both JS and native crash.

update: I'm using CocoaPods to install sentry. This is the the podfile.lock
  - Sentry (3.4.2):
    - Sentry/Core (= 3.4.2)
  - Sentry/Core (3.4.2)
  - Sentry/KSCrash (3.4.2):
    - KSCrash/Core (~> 1.15.11)
  - SentryReactNative (0.17.1):
    - React
    - Sentry (~> 3.4.2)
    - Sentry/KSCrash (~> 3.4.2)

I downgraded to 1.70.0 and I'm seeing this as well:
- Sentry (3.4.2):
  - Sentry/Core (= 3.4.2)
- Sentry/Core (3.4.2)
- Sentry/KSCrash (3.4.2):
  - KSCrash/Core (~> 1.15.11)
- SentryReactNative (0.17.0):
  - React
  - Sentry (~> 3.4.2)
  - Sentry/KSCrash (~> 3.4.2)

Also something I've notice is that you've bumped Bump sentry-cocoa to 3.4.3 but podspec wasn't updated? Is this where the fix is?

hmmm manually bumped to 3.4.3 via forking, but that didn't seem to do the trick

Well I spent a full day trying to figure out why it suddenly started working and trying to figure out why it was originally broken, but I cannot figure it out. I'll close this for now.

I've learned that deleting node_modules from time to time when working with react-native helps a lot, so I am guessing that this could have been the issue.
Still, if you encounter it again, feel free to reopen it.


Users app provided in the app cannot migrate

I am using this current repo with docker for my Django project. The build runs fine but when I issue docker-compose up, the migration fails with following stacktrace

Traceback (most recent call last):
File "manage.py", line 23, in
execute_from_command_line(sys.argv)
File "/usr/local/lib/python3.5/site-packages/django/core/management/init.py", line 367, in execute_from_command_line
utility.execute()
File "/usr/local/lib/python3.5/site-packages/django/core/management/init.py", line 359, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "/usr/local/lib/python3.5/site-packages/django/core/management/base.py", line 294, in run_from_argv
self.execute(*args, **cmd_options)
File "/usr/local/lib/python3.5/site-packages/django/core/management/base.py", line 345, in execute
output = self.handle(*args, **options)
File "/usr/local/lib/python3.5/site-packages/django/core/management/commands/migrate.py", line 86, in handle
executor.loader.check_consistent_history(connection)
File "/usr/local/lib/python3.5/site-packages/django/db/migrations/loader.py", line 292, in check_consistent_history
connection.alias,
django.db.migrations.exceptions.InconsistentMigrationHistory: Migration admin.0001_initial is applied before its dependency users.0001_initial on database 'default'.

I am not understanding what is going wrong with it. Is there any other step involved in getting the application up and ready?

It was my mistake that to report this as an issue. But given that it was my first time trying this repository with docker there were lot many things I was not able to figure out. One among them was "what was happening with my db?" when I was removing containers and images. I found it hard way that despite deleting the images the DB persisted. It was my inexperience that led to this stupidity.
As far as issue, because of the above mentioned thing, I tried the whole setup as described on the landing page of the repo yesterday, so a DB was created yesterday and had successful migrations. I decided to remove all images and containers to retry everything. Now in this case the DB persisted and when migrations were being applied the above migration exception popped up.
Probably, for some one who is just trying to give cookiecutter django with docker a go, this might be helpful.

Probably, for some one who is just trying to give cookiecutter django with docker a go, this might be helpful.

It is, thanks!
I'm currently working on a full doc rewrite. If you want to help out, take a look here: https://github.com/pydanny/cookiecutter-django/pull/1051
Your input is probably something for the FAQ/Troubeshooting section.

@jayfk I will. Sure.


Handle date search parameters when the data type isn't date

the data type could be

date
dateTime
instant
Period
Timing

See https://www.hl7.org/fhir/search.html#date. At the moment we only index the date values. We need to handle the other 4 types of values.

Can I work on this?

Btw are we not indexing the instant values as well?
https://github.com/google/android-fhir/blob/85a4e853e597b0ec75c6f27bf467e3ec7789330a/core/src/main/java/com/google/android/fhir/index/ResourceIndexer.kt#L125-L134


Actions without title gets dropped in JavaScript

Platform
What platform is your issue or question related to? (Delete other platforms).

JavaScript

Related to #1883.

@khouzam this should be fixed - did you establish that it wasn't?

You're right. I jhad misclosed it when I saw the merge, but the merge didn't seem to mention this.
Anyway, you are right, the visualizer works as expected.
Thanks.


Update build.cmd

Quote expansion of MSBUILD_PATH to allow for spaces in the path.

Thanks for this fix!


deploy.yml: Add deploy to heroku

Adds a Github Actions job to deploy to Heroku

This PR introduces 2 checks: Build and Deploy. Build builds the Docker container and Deploy deploys the container to Heroku.


Reference values in evidence bundle

The IETF RATS working group is standardizing a Conceptual Message Wrapper format that allows an attester to bundle different "conceptual messages" to send along the attestation conversation.
Concepts include evidence, endorsement, reference values, and attestation results.
The TCG PC Client Platform Firmware Profile allows for an event log to include unmeasured events to point the verifier to the signed reference measurements of the firmware through an event named after NIST Special Publication 800-155. I've written the extraction logic that can interpret raw data, UEFI variable pointers, and URI pointers. I haven't added UEFI local device path support.
It's often beneficial for an attester to send along any node-cached reference values since there could be updates that haven't made their way to the RVPS before attestation, but are signed by a trusted authority.
The SP800155 event is but one pathway to provide reference measurements. For VMs that don't have mount efivarfs for whatever reason, the AMD extended guest request ABI allows for the host to provide extra data with GUIDed entries of their own (e.g., https://github.com/google/gce-tcb-verifier/blob/main/sev/endorsement.go#L31)
The format I've proposed for signed firmware measurements is a couple years old at this point, and I've been working with the IETF to get CoRIM to a better state for us to use, so let me know if Trustee would accept any GCE-specific logic for interpreting our signed protobuf thing or if you'll wait until we deploy CoRIMs.
We haven't had much of an industry discussion on what CoRIM profile we should use for SEV-SNP and TDX anyway, so with that format comes further interpretation that's still undecided.

The extraction logic that needs to touch the network is a fallback option if you don't have the reference values forwarded by the attester, that's true, but that requires the reference values to be served online rather than only through presentation to the guest via cert chain or UEFI variable. That's not always the case.

I'm probably asking for a big protocol change to use CMWs to allow for more media type and conceptual message type freedom, yeah.. :-/

I think this makes sense in some cases where attesters send fresh evidence along with signed reference values. At the same time, we should also offer enough flexibility for users to determine whether or not to accept such kind of reference value source and also the verification granularity (like signer, expired/ , etc).
Do you have any plan or concrete design for this?

Our attestation flow has been homebrewed to link up to the existing vTPM tool we had for Shielded VMs in Google Compute Engine, but I'm looking at how we can better support the more open ecosystem of CNCF and CCC projects.
The concrete plan for us has been to multivariate. I publish our signed measurements to a cloud storage bucket with an object name derived from the golden measurements. The object is our own VMLaunchEndorsement protobuf message format that has signed golden measurements for a single firmware release. There can be multiple measurements because both TDX's TDVF and AMD SEV-SNP without SVSM have different measurements depending on the size of the machine (ick). We might be able to change that later, but for now I copy-paste for all expected measurements.
I provide the same signed document to the VM (or will, when I can finally flip the flag) in the AMD SEV-SNP extended guest request aux_blob at a specific GUID.
For TDX there is no aux_blob, and the TCG just published a new spec last December that allows writing an unmeasured event that has a RimLocatorType that actually directs a verifier to how to get the reference measurements. I post two such events. One is an event that points to a UEFI variable we inject, and another with a URI that points to the firmware signature in the cloud storage bucket.
The derived object name is no longer a required strategy with this SP800155 event, but I haven't gotten rid of it yet. I'm still trying to upstream the opt/org.tianocode/sp800155evts fw_cfg passthrough to get events easily posted from the VMM side https://github.com/tianocore/edk2/pull/5738

@deeglaze Have you ever considered another way, s.t. add Google attester/verifier plugins in both AA and AS? In this way, you can implement any claims of the attester environment, thus on the verifier side any policy could be written with proper golden reference value.
Like what Azure did


GitHub workshop: Add citation to "Natural Language Processing"

GitHub for Collaboration Workshop
This issue accompanies the GitHub for Collaboration Workshop developed by Eirini Zormpa, Sophia Batchelor and Rachael Stickland for the AIM RSF. We're so glad to have you here! 🎉
Below you'll find some instructions for how to contribute to the AIM RSF Glossary of Terms and develop collaborative practices on GitHub. If you have any questions, please let @RayStick or @eirini-zormpa know on Zoom so that we can assist you.
Summary
Terms that were identified and discussed during the September Collaboration Cafe need to be added to the Glossary of Terms.
Guide to Contribution
You will be making 2 commits to a branch and then making a Pull Request that adds a citation to a term in the Glossary. Please follow the steps detailed below to complete this task.

Go to the glossary file in this repository to address the issue: https://github.com/aim-rsf/Glossary-of-Terms/blob/main/docs/glossary.md

Click 'Edit this file' and find line 40

Use Markdown format to add the following description at the end of the sentence

{cite}`telus2021`

Scroll down to the 'Propose changes' section at the bottom of the page: edit the title and the description of the issue to describe your update to the community.

Select "New Branch" and give your new branch a descriptive name.

Select the "Propose Changes" button. You will then be taken to a new screen that submits a Pull Request. Don't fill this out yet as we need to add the reference to the bibliography first.

Navigate to the references.bib file which contains all the references according to BibTeX formatting: https://github.com/aim-rsf/Glossary-of-Terms/blob/main/docs/references.bib

On line 43, paste the following text. Please be careful and ensure that the white space has also been copied as the line indentation is really important.

@misc{telus2021
,	title	= {50 {AI} {Terms} {Every} {Beginner} {Should} {Know}}
,	author	= {{TELUS International}}
,	year	= {2021}
,	month	= {March}
,	url	= {https://www.telusinternational.com/articles/50-beginner-ai-terms-you-should-know}
,	urldate	= {2022-10-17}
}

Scroll down to the 'Propose changes' section at the bottom of the page: and add a descriptive title (for example: "Added python citation to bibtex file").

Check that you are committing your changes to the branch you created in the previous steps. Select the "Propose changes" button.

Navigate to the Pull Requests page and select "New Pull Request".

Fill in any relevant information, including the issue that the pull request fixes. You can connect the pull request and the issue it addressed using a#. You can find the issue number next to the title of this issue (this one is 32).

For example: this pull request fixes #32
Including this sentence in the body of your pull request will automagically close the issue once the pull request is merged 🪄✨

Click 'Create Pull Request'! And Congratulations! 🎉 You're done!

Navigate to the  "Reviewers" section to the top righthand side of your Pull Request. Click on the cogwheel and select @eirini-zormpa, @RayStick, and @BrainonSilicon from the list. A reviewer will review your pull request, and ask you if you need to make any changes before it can be approved.

Once your pull request is approved and the checks are complete, you can merge your change into the repository! ✅

Updated Glossary with Topic specific layout and addressed this issue in this commit


[#2096] fix: Direct memory is used too much due to each GrpcClient create one allocator.

What changes were proposed in this pull request?
Use static allocator for GrpcClient
Why are the changes needed?
Fix: #2096
Does this PR introduce any user-facing change?
No.
How was this patch tested?
test in real cluster.

Codecov Report
Attention: Patch coverage is 20.00000% with 4 lines in your changes missing coverage. Please review.

Project coverage is 53.04%. Comparing base (3cf820b) to head (6421f36).
Report is 12 commits behind head on master.

Files with missing lines
Patch %
Lines

...org/apache/uniffle/common/util/GrpcNettyUtils.java
0.00%
3 Missing :warning:

...client/impl/grpc/ShuffleServerGrpcNettyClient.java
0.00%
1 Missing :warning:

Additional details and impacted files
@@             Coverage Diff              @@
##             master    #2098      +/-   ##
============================================
+ Coverage     52.95%   53.04%   +0.09%
+ Complexity     3208     2678     -530
============================================
  Files           487      430      -57
  Lines         26461    19872    -6589
  Branches       2457     1801     -656
============================================
- Hits          14012    10542    -3470
+ Misses        11548     8664    -2884
+ Partials        901      666     -235

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


Update CRI-O to v1.28.0

What type of PR is this?
/kind cleanup
What this PR does / why we need it:
Updated CRI-O to the latest release.
Which issue(s) this PR fixes:

None
Does this PR have test?
None

Special notes for your reviewer:
None
Does this PR introduce a user-facing change?

None

Codecov Report

Merging #1847 (eea380d) into main (52cc43e) will decrease coverage by 0.10%.
The diff coverage is n/a.

Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1847      +/-   ##
==========================================
- Coverage   49.23%   49.13%   -0.10%
==========================================
  Files          71       71
  Lines        7024     7024
==========================================
- Hits         3458     3451       -7
- Misses       3432     3438       +6
- Partials      134      135       +1

This may require https://github.com/kubernetes-sigs/security-profiles-operator/pull/1846

/retest

@kubernetes-sigs/security-profiles-operator-maintainers PTAL


Investigate why our covid data doesn't match CDC's covid tracker

CDC covid tracker: https://covid.cdc.gov/covid-data-tracker/#demographics

This is a known issue turns out, see https://satcherinstitute.github.io/analysis/cdc_case_data#Comparison-to-CDC-COVID-Data-Tracker
We are following up with the CDC on this, moving to backlog for now as this shouldn't block launch as it doesn't seem to be an issue with the tracker

Closing as comparing current data on tracker (which is from March) against a web archive of the same data from the CDC tracker (https://web.archive.org/web/20210318000606/https://covid.cdc.gov/covid-data-tracker/#demographics) things seem to line up pretty closely


[Proposal] API Exception Handler

Since we now have API support in App\Providers\RouteServiceProvider via the mapWebRoutes and mapApiRoutes methods I believe a great new feature would to also have matching API support in exception handling. Right now all of the handling is designed for websites (inc. form posts and ajax) and it isn't entirely obvious how or where API handling should be implemented. E.g. a developer may try to reuse as much of the built-in handling as possible, may see the calls to expectsJson, however that would be a mistake. Instead, and to keep them on the right track this could be achieved with the following modification to App\Exceptions\Handler
public function render($request, Exception $exception)
    {
        // by checking the url and not expectsJson we can differentiate between API requests and form posts, e.g. ajax that might return validation errors, see  convertValidationExceptionToResponse.
        // api/* matches the default implementation of mapApiRoutes
        if($request->is('api/*')){
            return $this->renderForApi($request, $exception);
        }
        return parent::render($request, $exception);
    }

public function renderForApi($request, Exception $exception){
   // some default json returned, see below
}

This is my current implementation of this method, some or all of it could be used. It doesn't follow any official spec just what I think is suitable for a default implementation. The spec is that error key will always appear in the case of an exception, with the name of the exception. A validation key will appear if that was the exception and it will contain the error messages array. The message key contains the exception message if it isn't empty, in case of a QueryException it will contain the database error message without including the SQL if not in debug mode. Status codes are the same as the web renderer. Lots of APIs, e.g. Facebooks always return 200 so we could also just do that for the default implementation to keep it simple.
   public function renderForApi($request, Exception $exception){
        $statusCode = 500;

        if ($exception instanceof HttpExceptionInterface) {
            $statusCode = $exception->getStatusCode();
        }

        $error = ['error' => class_basename($exception)];
        $message = $exception->getMessage();

        if($exception instanceof ValidationException){
            $error['validation'] = $exception->validator->errors()->getMessages();
            $statusCode = 422;
        }
        else if($exception instanceof QueryException){
            // hide the sql and bindings if not in debug.
            if(!config('app.debug')) {
                $message = $exception->getPrevious()->getMessage();
            }
        }
        else if($exception instanceof AuthorizationException){
            $statusCode = 403;
        }

        if(!empty($message)) {
            $error['reason'] = $message;
        }

        return response()->json($error, $statusCode);
    }

Note, FlattenException::create used in convertExceptionToResponse does some of this and more so could be reused, e.g. if not an HttpException it uses 500, and it builds a stack trace if app.debug is on. Unfortunately its toArray method isn't suitable for a JSON response because it uses a indexed array instead of the associative we need.
Illuminate\Foundation\Exceptions\Handler could also be refactored to achieve some of this or tidy it up, e.g. the following issues in it could also be fixed on the way:
Doesn't match naming scheme of other methods, convertExceptionToResponse and convertValidationExceptionToResponse:
protected function unauthenticated($request, AuthenticationException $exception)
Missing the request param:

protected function convertExceptionToResponse(Exception $e)
Not required in case of an API error since we don't want to lose the info that it was a AuthorizationException:
protected function prepareException(Exception $e)

There are already lots of ways people do this, so we've kept the core minimal. Feel free to check out https://github.com/GrahamCampbell/Laravel-Exceptions. It looks like it could do what you want.


Delta protocol version upgrade is allowing any invalid version number for minWriterVersion value

Issue:
I have tried to upgrade the delta protocol on a newly created delta table by providing a invalid bigger 3 digit minWriterVersion number  and surprisingly it accepted and updated on the<PHONE_NUMBER>0000000001.json . This will make entire delta table unusable after upgrade.
Though it rejecting further upgrades with any value with below exception :
com.databricks.sql.transaction.tahoe.actions.InvalidProtocolVersionException: Delta protocol version is too new for this version of the Databricks Runtime. Please upgrade to a newer release.
Tested on:
Databricks Runtime : DBR 9.1 LTS , SPARK 3.1.2 (on Azure)
Delta created on : Azure Gen 2 storage
Delta Lake : 1.0.0
Steps to reproduce:

Create sample dataframe and written as delta :

df=spark.createDataFrame(

  [(1,'test1',33,'Q1'),

   (2,'test2',48,'Q1'),

   (3,'test3',22,'Q1'),

   (4,'test4',88,'Q2'),

   (5,'test5',None,'Q2'),

   (6,'test6',42,'Q2')

  ],'id int,test_name string,score int,quarter string'

)

 df_to_write=df.repartition(1,['id'])

<EMAIL_ADDRESS>

Read the written data using python delta library's  class method delta.tables.DeltaTable.forPath:

from delta.tables import DeltaTable

<EMAIL_ADDRESS>

Upgraded the delta table protocol version:

dt.upgradeTableProtocol(1,101)

The invalid minWriter version is updated on<PHONE_NUMBER>0000000001.json:

Good catch. This is an oversight. Should be easy to fix.

Hey @zsxwing, I would like to contribute to this project and this feature seems like a good one to start out. Can you assign it to me?

@Orpheuz done!

@Orpheuz : It will be great if you can give an overview of the fix you will be doing once you have done that.  so that will introduce me to the portion that handles this check and exceptions

@Orpheuz : It will be great if you can give an overview of the fix you will be doing once you have done that. so that will introduce me to the portion that handles this check and exceptions (I am the one who has raised this bug , with a different profile)

Hey @YetAnotherDataGuy no worries!
I just took a look at the code and I'll try my best to explain what I learned.
When you run
ALTER TABLE delta.`delta_path`
SET TBLPROPERTIES (delta.minWriterVersion=version)

it gets checked and validated at DeltaConfig for both reader and writer versions. It makes use of this protocol that by default is created with all the current features the client supports (thus having both read and write max allowed versions).
When you try to update the versions using the DeltaTable API
table.upgradeTableProtocol(readerVersion, writerVersion)

it is validated by the prepareCommit function that validates and modifies all the actions that will be part of the transaction.
Currently, only non-negative values requirements are implemented. The solution is to verify the upper bounds with Action.supportedProtocolVersion() as well.
@scottsand-db would you please validate this is correct? Also, do you think it would be better to move these checks to the creation of the AlterTableSetPropertiesDeltaCommand in upgradeTableProtocol instead of verifying them later (similar to what is done in the DeltaCatalog)?


Change hh.mutually_broadcastable_shapes() defaults to generate more interesting shapes

Changes the defaulting of max_dims and max_side so that more interesting shapes get generated. Also defaults min_side to 0.

I guess this doesn't end up being that different for us because the hypothesis shapes strategy is also based on limiting the side length, whereas in ndindex I just use tuples(integer()) and filter across the total size.

I guess this doesn't end up being that different for us because the hypothesis shapes strategy is also based on limiting the side length, whereas in ndindex I just use tuples(integer()) and filter across the total size.

Ah so you're saying #73 is limited as-is? Does this PR fair well? Maybe can bump up the defaults a bit more too.
My impression is that the defaults from Hypothesis might be too low, but I also think relying on st.integers().filter(<below max size>) is overkill (i.e. seemingly won't be finding interesting bugs for the big performance cost when making/manipulating arrays).


Unable to run zipline example with fresh install

Dear Zipline Maintainers,
Before I tell you about my issue, let me describe my environment:
Environment

Operating System: (4.4.0-53-generic #74-Ubuntu SMP Fri Dec 2 15:59:10 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux)
Python Version: $ python --version  3.5.2
Python Bitness: `$ 64
How did you install Zipline: (Tried pip, install completed successfully, then I ran into this issue, so I cloned the git repo and did sudo python3 setup.py install. It reported as completed successfully)
Python packages: $ pip freeze or $ conda list
Pip freeze of virtualenv
alembic==0.9.6
bcolz==0.12.1
Bottleneck==1.2.1
certifi==2<IP_ADDRESS>
chardet==3.0.4
click==6.7
contextlib2==0.5.5
cyordereddict==1.0.0
Cython==0.27.2
decorator==4.1.2
empyrical==0.3.2
idna==2.6
intervaltree==2.1.0
Logbook==1.1.0
lru-dict==1.1.6
Mako==1.0.7
MarkupSafe==1.0
multipledispatch==0.4.9
networkx==2.0
numexpr==2.6.4
numpy==1.13.3
pandas==0.18.1
pandas-datareader==0.5.0
patsy==0.4.1
python-dateutil==2.6.1
python-editor==1.0.3
pytz==2017.3
requests==2.18.4
requests-file==1.4.2
requests-ftp==0.3.1
scipy==1.0.0
six==1.11.0
sortedcontainers==1.5.7
SQLAlchemy==1.1.14
statsmodels==0.8.0
tables==3.4.2
toolz==0.8.2
urllib3==1.22
zipline==1.1.1

Now that you know a little about me, let me tell you about the issue I am
having:
Description of Issue

What did you expect to happen? > I expected the buyapple example to work
What happened instead?

EDIT
It appears I missed part of the traceback when I pasted here the first time, the originating problem seems to be an SSL Error?:
[2017-10-30 15:20:04.461962] WARNING: Loader: Refusing to download new benchmark data because a download succeed
ed at 2017-10-30 14:47:39.200223+00:00.
[2017-10-30 15:20:04.462134] INFO: Loader: Cache at /home/crews/.zipline/data/treasury_curves.csv does not have
data from 1990-01-02 00:00:00+00:00 to 2017-10-26 00:00:00+00:00.
[2017-10-30 15:20:04.462206] INFO: Loader: Downloading treasury data for 'SPY'.
[2017-10-30 15:20:04.703224] ERROR: Loader: failed to cache treasury data
Traceback (most recent call last):
File "/usr/lib/python3.5/urllib/request.py", line 1254, in do_open
h.request(req.get_method(), req.selector, req.data, headers)
File "/usr/lib/python3.5/http/client.py", line 1106, in request
self._send_request(method, url, body, headers)
File "/usr/lib/python3.5/http/client.py", line 1151, in _send_request
self.endheaders(body)
File "/usr/lib/python3.5/http/client.py", line 1102, in endheaders
self._send_output(message_body)
File "/usr/lib/python3.5/http/client.py", line 934, in _send_output
self.send(msg)
File "/usr/lib/python3.5/http/client.py", line 877, in send
self.connect()
File "/usr/lib/python3.5/http/client.py", line 1260, in connect
server_hostname=server_hostname)
File "/usr/lib/python3.5/ssl.py", line 377, in wrap_socket
_context=self)
File "/usr/lib/python3.5/ssl.py", line 752, in init
self.do_handshake()
File "/usr/lib/python3.5/ssl.py", line 988, in do_handshake
self._sslobj.do_handshake()
File "/usr/lib/python3.5/ssl.py", line 633, in do_handshake
self._sslobj.do_handshake()
ssl.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:645)
During handling of the above exception, another exception occurred:
/usr/local/lib/python3.5/dist-packages/zipline/data/loader.py in has_data_for_dates(series_or_df, first_date, last_date)
85     last_date?
86     """
---> 87     dts = series_or_df.index
88     if not isinstance(dts, pd.DatetimeIndex):
89         raise TypeError("Expected a DatetimeIndex, but got %s." % type(dts))
AttributeError: 'NoneType' object has no attribute 'index'
Here is how you can reproduce this issue on your machine:
Reproduction Steps

install zipline
zipline ingest
try to run the buyapple example. Both the notebook and the commandline interface are giving the same error to me.
...

What steps have you taken to resolve this already?
From the notebook, I tried to fall back to shell, same error
Tried running 'zipline ingest' again
Tried pulling zipline from git rather than pip
created a virtualenv, installed zipline from pip hoping it was my dirty pip env.
updated system time via NTP in case it was an ssl error related to time
...
Anything else?
I see a few other issues with the same SSLError related to the demise of Yahoo finance, but I judging from the comments, it appeared to me as though those problems had been fixed.
I may try conda on linux as a workaround, but I'd rather not have to resort to that permanently
...
Sincerely,
Andrew(PS thanks for your time)
PPS, I have downloaded zipline onto my Windows machine with pip and it does seem to work. Any ideas on what in my environment could cause this sort of an error?

Hi @Mandrewoid can you try running the example with a shorter start date, such as 2017-08-01?
There's a PR open that addresses benchmark data errors.

Thanks for your input @freddiev4. Unfortunately no matter what dates I enter I get the same errors. It appears that whatever code is called after "INFO: Loader: Downloading treasury data for 'SPY'" fails to download that data.

@Mandrewoid try this solution https://github.com/quantopian/zipline/issues/1965#issuecomment-352715830 . It's works for me.

Merged that IEX PR above ^^ you (hopefully) should be able to run a backtest up to 5 years from the current date using zipline master


[Documentation] What are the message types supported by JMS services?

What are the message types (Text, ObjectMessage etc) a JMS service can receive? There is no documentation available on this.

This is tracked at: https://github.com/ballerinalang/connector-jms/issues/4


"ERROR: Could not refill buffer" for BGPStream v2

I'm getting the following error while using pybgpstrea for BGPStream v2:

Unexpected EOF while reading compressed file -- file is probably incomplete
2018-09-26 23:24:37 1518: bgpstream_parsebgp_common.c:495: ERROR: Could not refill buffer
Unexpected EOF while reading compressed file -- file is probably incomplete
2018-09-26 23:24:38 1518: bgpstream_parsebgp_common.c:495: ERROR: Could not refill buffer
Unexpected EOF while reading compressed file -- file is probably incomplete
2018-09-26 23:24:39 1518: bgpstream_parsebgp_common.c:495: ERROR: Could not refill buffer

After this error happens the code hangs and if I don't kill the program it keeps running without progressing. The actual code is very simple:
start = "2018-04-25 00:00:00"
end = "2018-05-25 09:00:00 UTC"

stream = pybgpstream.BGPStream(
    from_time=start,
    until_time=end,
    record_type="ribs",
)

for elem in stream:
    print elem

ping


Overly specific implicit requirements

Any binary package currently yields e.g..
platform-windows/os-windows-10/python-3.7

Whereby platform-windows and os-windows-10 isn't providing unique value. Let's remove platform-windows.

Fixed


Grpc+RDMA problem

For RDMA, when start the ps server, it will do RDMA connect to worker server, but failed because worker still not started:
# python tf_rdma.py --ps_hosts='workernode2:1111' --worker_hosts='workernode3:2222' --job_name=ps --task_id=0
....
2018-04-04 11:23:38.912680: I tensorflow/core/distributed_runtime/rpc/grpc_server_lib.cc:324] Started server with target: grpc://localhost:1111
2018-04-04 11:23:38.920106: E tensorflow/contrib/verbs/rdma_mgr.cc:119] Connecting to /job:worker/replica:0/task:0: Got Transport closed. Retrying (1/5)...
2018-04-04 11:23:41.920544: E tensorflow/contrib/verbs/rdma_mgr.cc:119] Connecting to /job:worker/replica:0/task:0: Got OS Error. Retrying (2/5)...
2018-04-04 11:23:43.921039: E tensorflow/contrib/verbs/rdma_mgr.cc:119] Connecting to /job:worker/replica:0/task:0: Got OS Error. Retrying (3/5)...
2018-04-04 11:23:46.922376: E tensorflow/contrib/verbs/rdma_mgr.cc:119] Connecting to /job:worker/replica:0/task:0: Got OS Error. Retrying (4/5)...
2018-04-04 11:23:48.922817: E tensorflow/contrib/verbs/rdma_mgr.cc:119] Connecting to /job:worker/replica:0/task:0: Got OS Error. Retrying (5/5)...
2018-04-04 11:23:48.922848: I tensorflow/contrib/verbs/rdma_mgr.cc:128] Connected to remote node /job:worker/replica:0/task:0

Then start the worker server:
# python tf_rdma.py --ps_hosts='workernode2:1111' --worker_hosts='workernode3:2222' --job_name=worker --task_id=0
...
2018-04-04 14:12:38.008214: I tensorflow/core/distributed_runtime/rpc/grpc_channel.cc:215] Initialize GrpcChannelCache for job ps -> {0 -> workernode2:1111}
2018-04-04 14:12:38.008256: I tensorflow/core/distributed_runtime/rpc/grpc_channel.cc:215] Initialize GrpcChannelCache for job worker -> {0 -> localhost:2222}
2018-04-04 14:12:38.013784: I tensorflow/core/distributed_runtime/rpc/grpc_channel.cc:215] Initialize GrpcChannelCache for job ps -> {0 -> workernode2:1111}
2018-04-04 14:12:38.013803: I tensorflow/core/distributed_runtime/rpc/grpc_channel.cc:215] Initialize GrpcChannelCache for job worker -> {0 -> localhost:2222}
2018-04-04 14:12:38.019732: I tensorflow/core/distributed_runtime/rpc/grpc_server_lib.cc:324] Started server with target: grpc://localhost:2222
2018-04-04 14:12:38.028558: I tensorflow/contrib/verbs/rdma_mgr.cc:128] Connected to remote node /job:ps/replica:0/task:0

the worker server can do RDMA connect successfully. But hanged up with the follows:
(gdb) bt
#0  0x00007fbdcc4f7a54 in mlx4_poll_cq () from /lib64/libmlx4-rdmav2.so
#1  0x00007fbdf16301d8 in tensorflow::RdmaMgr::ConnectivityCheck() () from /usr/lib/python2.7/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so
#2  0x00007fbdf1628874 in tensorflow::VerbsServer::Start() () from /usr/lib/python2.7/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so
#3  0x00007fbdf12abf9b in _wrap_PyServer_Start () from /usr/lib/python2.7/site-packages/tensorflow/python/_pywrap_tensorflow_internal.so
#4  0x00007fbe01542aa4 in PyEval_EvalFrameEx () from /lib64/libpython2.7.so.1.0

I think ps server should wait worker server setup before connect worker server.
Am I right?

Thank you for your post. We noticed you have not filled out the following field in the issue template. Could you update them if they are relevant in your case, or leave them as N/A? Thanks.
Have I written custom code
OS Platform and Distribution
TensorFlow installed from
TensorFlow version
Bazel version
CUDA/cuDNN version
GPU model and memory
Exact command to reproduce

It has been 14 days with no activity and the awaiting response label was assigned. Is this still an issue?

It has been 22 days with no activity and the awaiting response label was assigned. Is this still an issue?

It has been 14 days with no activity and the awaiting response label was assigned. Is this still an issue?


Issue running ant build it was failing on modules/fibers and modules/express because they weren't in the source path

Modifying ant build.xml to include source directory for modules/fibers and modules/express.
I also added Apache Ivy to the build.xml to bootstrap the dependencies (GWT, Junit). This will allow you to not have to check-in the large jar files into the repository.
Apache Ivy is itself bootstrapped and downloaded simply by Apache Ant. So no further setup instructions needed other than:
ant build

I will review this sometime within the next couple of days. I am tied up at the moment. Thanks for the contribution!

Merged. I like removing the JAR dependencies from the app and I much prefer Ivy over Maven. Thanks again.


Make release v23.5

WAIT TO MERGE UNTIL WE ARE HAPPY WITH THE RELEASE CANDIDATE
I wasn't sure whether to have v23.5 or v23.5rc0 in the CHANGELOG and the CITATION. Everywhere else it is 23.5rc0 which should make a pre-release in PyPI.

23.5 in the changelog is good, but we need to change the date

23.5 in the changelog is good, but we need to change the date

Fair point. I have updated the date now, I will try to make the release and publish to pypi, but I am not sure if I have the permissions to trigger the action and actually push to pypi. I will let you know if not and you can trigger it.


Glue wrappers to create @overload from split typing and lowering.

As title.

Buildfarm ID: numba_smoketest_cpu_yaml_11.

Buildfarm ID: numba_smoketest_cpu_yaml_11.

This passed.


Missing browser.wait() function in typings

Bug report

Node Version: 8.8.1
Protractor Version: 5.2.0
Angular Version: ``
Browser(s): chrome 63
Operating System and Version: Windows 10
Your protractor configuration file
A relevant example test
Output from running the test
Steps to reproduce the bug
The URL you are running your tests against (if relevant)
Typescript version: 2.6.1

Looks like, the similar issue has appeared again. The code below
async isOpened(url: string = null): Promise<boolean> {
        try {
            const timeout = await PageObject.getPageTimeout();
            return await browser.wait(EC.or(EC.urlIs(this.url), EC.urlContains(url)), timeout, 'Page is not opened.');
        } catch (e) {
            console.log(e);
        }
    }

after running tsc --alwaysStrict produces the error message Type '{}' is not assignable to type 'boolean' for the line return await browser.wait(EC.or(EC.urlIs(this.url), EC.urlContains(url)), timeout, 'Page is not opened.');

That happens since browser.wait returns promise.Promise<T> but you specified return function type - Promise<boolean>
Rewrite to something like this:
async isOpened(url: string = null): Promise<boolean> {
        try {
            const timeout = await PageObject.getPageTimeout();
            await browser.wait(EC.or(EC.urlIs(this.url), EC.urlContains(url)), timeout, 'Page is not opened.');
            return true
        } catch (e) {
            console.log(e)
            return false
        }
    }


pdomOrder has a memory leak

In https://github.com/phetsims/density-buoyancy-common/issues/168 we found that pdomOrder has a memory leak. When a Node is disposed, it does not remove itself from the pdomOrder that it might be in. For example, in this bit:
    const massViewAdded = ( massView: MassView ) => {
      if ( massView.mass === model.primaryMass ) {
        primaryCubeLayer.pdomOrder = [ ...primaryCubeLayer.pdomOrder!, massView.focusablePath ];
        // nothing to do for removal since disposal of the node will remove it from the pdom order
      }
      else if ( massView.mass === model.secondaryMass ) {
        secondaryCubeLayer.pdomOrder = [ ...secondaryCubeLayer.pdomOrder!, massView.focusablePath ];
        // nothing to do for removal since disposal of the node will remove it from the pdom order
      }
    };

These comments are reasonable but not correct at the moment! We should fix this.
@zepumph noted that we can use pdomParent to remove a Node from a pdomOrder when it is disposed. I will give this a try.

This was made in the above commit with some unit tests, @zepumph would you mind reviewing?

Review:

I see that Node.children asserts that there aren't duplicates in the list, I think we should do that for setting pdomOrder too. https://github.com/phetsims/scenery/blob/b3e6c15d2ab4d2db60371ec1729da840395bfaa8/js/nodes/Node.ts#L874. Commits above.
I don't love the closure for filter in such a low level function. I committed a fix to use arrayRemove() instead.
I wanted some tests that also ensure that the PDOM HTML elements were behaving correctly, also committed above.

I ran fuzzing for the new uniq assertion locally, but we should still be on the look out on CT. Can you please review. Anything else you can think of?

Those changes are great thanks! I fixed a bug with slice using arrayRemove, but otherwise that makes sense. Ill watch CT for one more column.

CT looks OK, closing.


[Bug]: The logical database name is incorrectly generated

ODC version
odc 4.3.2
OB version
no related
What happened?

The logical database name is incorrectly generated
What did you expect to happen?
If the logical database name is generated incorrectly, the logical database name should be generated according to the physical database name and related rules
How can we reproduce it (as minimally and precisely as possible)?
Configure and commit a logic library
Anything else we need to know?
No response

Fixed In Commit c1469755bb913bc85ab7c9b46b43e454079713fd
------
畅晚
Fri Sep 20 18:48:17 2024 +0800

pass


reduce opacity for disable button #23390

Reduce opacity for disable button to differentiate between disable and normal button as per #23390

This would break color contrast requirements, thanks though.


_create_categorical_colors returns duplicate colors

Calling cellrank.tl._colors._create_categorical_colors returns duplicate colors when more than 10 colors are requested. That's becasue we use both cm.tab10 as well as cm.tab20 which partly overlap.

can we use scanpy's default color palette?

Yes, we can start with vega_20 (modified version of tab20). Do you want by default colorblind-friendly version?

yes, sure, sounds good. We just need to make sure that the colormaps we combine don't have repeated colors, e.g. if we do
[cm.tab10, cm.tab20, cm.Paired, cm.Accent, cm.Set1, cm.Set2, cm.Set3]
than this is useless if tab 10 and tab20 have repeated colors. It makes more sense to desing say three different colormaps, one with 10 colors, one with 20 and one with 30. And for all of these, we make sure that colors are not repeated. I think Volker has designed some colormaps we can use here. This would be the nicest solution.

thanks.


tooltip over time rail to show time

As a user I want to be able to hover over the time rail and see a tooltip for the time I will be jumping to if I click in that location.

Fixed in #68


Add checkbox_tree component to supplier app

This pull request:

pulls in the latest frontend-toolkit with the checkbox_tree pattern
pulls in the latest frameworks with the new service categories
pulls in the latest content-loader which knows how to process checkbox_tree data
adds a wrapper macro for a checkbox_tree question
brings in the ability to chain show/hide questions

gifs
no child categories (looks like a flat list)

parent and child categories (has an open/close widget)

:+1:


Replace the full path to 'Jou'?

Before:
D:\jou-main\jou-main\jou.exe: missing Jou file name (try "D:\jou-main\jou-main\jou.exe --help")

After:
Jou: missing Jou file name (try "D:\jou-main\jou-main\jou.exe --help")

This could be confusing if someone has two installations of jou.
How are you running jou? Jou uses argv[0] for these messages, and usually argv[0] is set to a shorter string, something like "jou.exe" (Windows) or "./jou" (MacOS and Linux).

It seems that the argv[0] didn't set to "./jou".

Here's what it's supposed to look like:

Apparently this is a windows thing: https://stackoverflow.com/questions/7941536/windows-vs-linux-gcc-argv0-value
Using argv[0] to refer to "this program" is a standard thing to do in C, and almost all other programs do it, so changing it could be a bad idea. That said, I can't think of anything that would go wrong practically if we just use "jou" instead of argv[0]. Even if someone has two jous installed, there are other ways to check which jou is being used.

Ok. Sorry to interrupt.

No problem, it was a good question and I didn't know argv[0] is the full path on Windows :)


Compute nodes are not showing up in sinfo

I have a cluster up and running with a custom_ami. Cluster creation is successful according to the message on the command prompt. Both master and compute nodes are spun up and they can be seen in the console. Compute nodes are not showing up sinfo or on ganglia. What could be the problem? Where should I look for potential errors?
Thanks
Santi

After slurmctld restart status message is as follows:
sudo service slurmctld status
● slurmctld.service - Slurm controller daemon
   Loaded: loaded (/etc/systemd/system/slurmctld.service; enabled; vendor preset: enabled)
   Active: active (running) since Tue 2018-03-27 00:48:12 UTC; 1min 10s ago
  Process: 13648 ExecStart=/opt/slurm/sbin/slurmctld $SLURMCTLD_OPTIONS (code=exited, status=0/SUCCESS)
 Main PID: 13652 (slurmctld)
    Tasks: 5
   Memory: 1.5M
      CPU: 25ms
   CGroup: /system.slice/slurmctld.service
           └─13652 /opt/slurm/sbin/slurmctld

Mar 27 00:48:12 ip-172-31-17-29 systemd[1]: Starting Slurm controller daemon...
Mar 27 00:48:12 ip-172-31-17-29 systemd[1]: slurmctld.service: PID file /var/run/slurmctld.pid not readable (yet?) after start: No such file or directory
Mar 27 00:48:12 ip-172-31-17-29 systemd[1]: Started Slurm controller daemon.

Looks like PID file /var/run/slurmctld.pid not readable (yet?) after start: No such file or directory is not readable. I think slurm is not recognizing the compute nodes because of this.


/tmp folder clean up needed

Hello,
I have found some kind of bug in undouble lib.
After using undouble lib. many times like millions, tons of empty temporary folders are made in /tmp (in linux) and never removed.
It leads to system fail because of lack of free inode (in linux).
It is because of "tempfile.mkdtemp()" in your source code from clustimage.py.
I think you have to remove temp folder in destructor in the class.
Thanks.

Thank you for this good suggestion and created some changes in the new version.

The temp directory is not a random new dirname anymore but is "clustimage" in the systems temp directory.
Files for the specific run can easily be removed using the .clean_files() functionality.
The entire temp directory can removed setting the parameter .clean_files(clean_tempdir=True).

Let me know and/or re-open if this issue if required.


Commands didnt work

Hey so i installed the magic plugin and when i typed in any of the commands it just kept bring up the same list of commands could someone please tell me what im doing wrong

Please check your server logs when your server starts up. There is probably an error in there, most likely to be a server/plugin compatibility issue. If in doubt, paste your logs into http://www.pastebin.com and paste the link here.

http://pastebin.com/X7g1Figy
And the plugins I have are
commandbook
craftbook
deathchest
factions
headslite
magic
massive core
multiverse core
multiverse portals
mythicmobs

The most recent version of Magic require Spigot 1.8.8. You'll need to go back to Magic 5.4 or update your server.
[11:44:35] [Server thread/INFO]: [Magic] Enabling Magic v5.4.5
[11:44:35] [Server thread/WARN]: java.lang.NoSuchMethodException: net.minecraft.server.v1_8_R1.EntityArmorStand.n(boolean)
[11:44:35] [Server thread/WARN]:    at java.lang.Class.getDeclaredMethod(Class.java:2130)
[11:44:35] [Server thread/WARN]:    at com.elmakers.mine.bukkit.utility.NMSUtils.<clinit>(NMSUtils.java:351)
[11:44:35] [Server thread/WARN]:    at com.elmakers.mine.bukkit.magic.MagicPlugin.onEnable(MagicPlugin.java:155)
[11:44:35] [Server thread/WARN]:    at org.bukkit.plugin.java.JavaPlugin.setEnabled(JavaPlugin.java:321)
[11:44:35] [Server thread/WARN]:    at org.bukkit.plugin.java.JavaPluginLoader.enablePlugin(JavaPluginLoader.java:335)
[11:44:35] [Server thread/WARN]:    at org.bukkit.plugin.SimplePluginManager.enablePlugin(SimplePluginManager.java:405)
[11:44:35] [Server thread/WARN]:    at org.bukkit.craftbukkit.v1_8_R1.CraftServer.loadPlugin(CraftServer.java:356)
[11:44:35] [Server thread/WARN]:    at org.bukkit.craftbukkit.v1_8_R1.CraftServer.enablePlugins(CraftServer.java:316)
[11:44:35] [Server thread/WARN]:    at net.minecraft.server.v1_8_R1.MinecraftServer.q(MinecraftServer.java:402)
[11:44:35] [Server thread/WARN]:    at net.minecraft.server.v1_8_R1.MinecraftServer.k(MinecraftServer.java:370)
[11:44:35] [Server thread/WARN]:    at net.minecraft.server.v1_8_R1.MinecraftServer.a(MinecraftServer.java:325)
[11:44:35] [Server thread/WARN]:    at net.minecraft.server.v1_8_R1.DedicatedServer.init(DedicatedServer.java:211)
[11:44:35] [Server thread/WARN]:    at net.minecraft.server.v1_8_R1.MinecraftServer.run(MinecraftServer.java:505)
[11:44:35] [Server thread/WARN]:    at java.lang.Thread.run(Thread.java:745)
[11:44:35] [Server thread/WARN]: [Magic] Something went wrong with some Deep Magic, plugin will not load.
[11:44:35] [Server thread/WARN]: [Magic] Please make sure you are running a compatible version of CraftBukkit or Spigot!


Typo in locale/*/meta.lua

In meta files we have this typo:
https://github.com/sumneko/lua-language-server/blob/8b3e2f7597fb267f70362903d2fbe285edde03c1/locale/en-us/meta.lua#L50
https://github.com/sumneko/lua-language-server/blob/8b3e2f7597fb267f70362903d2fbe285edde03c1/locale/zh-cn/meta.lua#L50
and also here
https://github.com/sumneko/lua-language-server/blob/8b3e2f7597fb267f70362903d2fbe285edde03c1/meta/template/basic.lua#L135
But it supposed to be pairs

@jefersonf I have added the topic hacktoberfest, is this enough?


Do not enable SyncCuratorRecommendedFeed by default

Running app should not try and download 1000 songs as a default setting

I fixed the release zip to have the config ini disable Curator Recommended, when I get the motivation I'll be doing a big overhaul to bring it more in line with BeatSync.


Harmonise pharmacogenetics associations that refer to star alleles

As a developer I want to integrate and harmonise star allele data from PharmGKB into the Platform because these are clinically relevant associations that our users expect to see in our widgets.
Background
Star alleles are a widely used notation within the pharmacogenetics field.
For 23.12 we won't show this information because of the complexities of standardising this notation to our variant IDs. @apriltuesday has explored its complexities in this notebook.
For the next iteration, we want to integrate them as part of the pharmacogenetics dataset.
Tasks

[ ] Consolidate strategy to harmonise star allele nomenclature
[ ] Validate the presence of key drug associations with the corresponding star alleles.

Acceptance tests
Ellie has shared with us some key drug associations that we should use to validate the data. As it can be seen, most of the key associations using star alleles are lost (see column In OT).

Gene
Chromosome
Position
Reference
Alternative
RsID
Legacy Name
Alleles
Star allele
Key drug association
In OT

DPYD
1
97450058
C
T
rs3918290
c.1905+1G>A
*2A
*2A
capecitabine/fluorouracil
Yes

DPYD
1
97515787
A
C
rs55886062
c.1679T>G
*13
*13
capecitabine/fluorouracil
Yes

DPYD
1
97573863
C
T
rs56038477
c.1236G>A
HapB3
HapB3
capecitabine/fluorouracil
Yes

DPYD
1
97579893
G
C
rs75017182
c.1129-5923C>G
HapB3
HapB3
capecitabine/fluorouracil
Yes

UGT1A1
2
233760233
C
CAT
rs3064744
NC_000002.11:g.234668881TA[6]>TA[7]
*28
*28
Irinotecan
No

UGT1A1
2
233760498
G
A
rs4148323
211G>A
*6
*6
Irinotecan
No

TPMT
6
18130687
T
C
rs1142345
719A>G
*3C
*3A/*3C
thiopurine/mercaptopurine/azathioprine
No

TPMT
6
18130781
C
T
rs1800584
626-1G>A
*4
*4
thiopurine/mercaptopurine/azathioprine
No

TPMT
6
18138997
C
T
rs1800460
460G>A
*3B
*3A/*3B
thiopurine/mercaptopurine/azathioprine
No

CYP2D6

rs3892097

*4

codeine
No

CYP2C19

rs28399504

*4

clopidogrel
No

HLA

any variants?

abacavir/allopurinol
No

CYP2C9

rs1799853

*2

phenytoin/warfarin
No

Context
Metrics extracted by @apriltuesday and based on the 2023-10-05 data dump:
Total clinical annotations: 5073
        With RS: 4477 (88.25%)
                1. Exploded by allele: 13497 (3.0x)
                2. Exploded by drug: 18830 (1.4x)
                3. Exploded by phenotype: 23086 (1.2x)
Total evidence strings: 24641
        With CHEBI: 20451 (83.00%)
        With EFO phenotype: 8139 (33.03%)
        With functional consequence: 15633 (63.44%)
        With VEP gene: 15633 (63.44%)
Gene comparisons per annotation
        With PGKB genes: 4220 (83.19%)
        With VEP genes: 4099 (80.80%)
        PGKB genes != VEP genes: 770 (15.18%)
Total RS: 2794
        With parsed alleles: 2771 (99.18%)
                With >2 alleles: 31 (1.12%)

EVA will update the Pharmacogenetics dataset they provide to include star allele/gene associations so that we can display them in the widget. Our next meeting with them is on Jan 22nd.
For reference, the genes of the current pharmacogenetics dataset are the ones assigned by VEP. So the implicated variant requires to be normalised so that VEP can consume it.
This is not possible for star alleles, however PharmGKB does have gene information. The intention is to show these associations as is, without the extra annotation from VEP.

Useful issue tracking the investigations made by @apriltuesday: https://github.com/EBIvariation/opentargets-pharmgkb/issues/28

After the discussion with EVA today, we have agreed that we want to maintain the star allele notation because it's well established in the field.
This means that we need to introduce a new ID field in the schema to accommodate this. I propose haplotypeId.
In the end, we'll have:

haplotypeId: for example CYP2C9*3, the name of the haplotype that comprises multiple variants.
variantRId: one of the variants in that haplotype, for example rs1057910. This information will come from PharmGKB, so that we can extract the most severe consequence.
genotypeId: each of the possible alleles in the variantId, for example 10_94981296_A_C

Hello! Some thoughts on these questions (and one question of my own)...

Linking to the haplotype page is surprisingly tricky as I think we'd need to find the PGKB ID for the haplotype (e.g. PA165816542, from which you can construct the URL), and this ID isn't in the data tables I'm currently using. I will look into it and keep you posted.
variantRsId and genotypeId can (actually must) be left blank here, we just need to remove the variant ID from the required fields in the schema...
We can get the allele function annotations (decreased function etc.), the annotation is technically available for all records but in my experience is only present for these named alleles. In theory the only possible values are documented in Table 2 here, but in a quick glance I see some variability in the PGKB data, so for now I would make this a generic string field - maybe alleleFunction?

On a separate note, for the genotype field - we currently fill this with the first column in PGKB's annotation table (rsid example, star example), which is labelled Allele but can be either allele or genotype. We can continue to do this for named alleles, as in both cases it would document the raw text that we use to create the genotype OR haplotype ID, or we could do something else.  Do you guys use this field at all?  Do you have a preference?

Hi @emcdonagh-OT @ireneisdoomed @DSuveges -  Getting the information to link to a haplotype page from the haplotypeId will not be possible in general, as sometimes the annotation is actually for a genotype and not a haplotype at all... (example here).
However it should be achievable for the majority of cases, so perhaps can be added as a non-required field. This would be PGKB's internal identifier for the haplotype - for example (field name pending):
{
    ...
    "haplotypeId": "CYP2C9*1",
    "internalHaplotypeId": "PA165816542"
    ...
}

from which you can get the URL as https://www.pharmgkb.org/haplotype/PA165816542.
Does this seem reasonable?

@apriltuesday Apologies for the late reply, I'd missed this.
That is absolutely reasonable, we expect that haplotypes won't be available for many evidence.
Using this ID to link back to PharmGKB is a nice to have, but not essential since we already link the whole evidence. Is it complex to extract?
As for the field name, I'd suggest haplotypeFromSourceId. Let me know if this is OK and we'll update our schema.

@ireneisdoomed thanks, haplotypeFromSourceId sounds good, it's not complicated to extract for the majority of cases so should be fine.
The other schema changes I think are needed are:

variantRsId needs to be not required - you could make it so that either variantRsId or haplotypeId are required though
alleleFunction (or another name) to be added - if you want the "decreased function" etc. annotation to be included in this submission

Sorry for the delay @apriltuesday
We have a new schema version under the tag 2.6.1 with the changes you have requested:

variantRsId is now optional (all IDs are now optional)
haplotypeFromSourceId will contain PGKB's haplotype ID to link to
directionality contains the allele function annotation

And one more:

drugFromSourceId will contain the CHEBI identifiers. This used to be stored in drugId, but we want to leave this field blank. Is this possible?

Let me know if you have any problems, thank you so much!

The latest EVA submission (cttv012-2024-02-02_pgkb.json.gz) contain the evidence from the haplotypes in the table above.

Gene
Chromosome
Position
Reference
Alternative
RsID
Legacy Name
Alleles
Star allele
Key drug association
In OT 23.12
In OT 24.02

DPYD
1
97450058
C
T
rs3918290
c.1905+1G>A
*2A
*2A
capecitabine/fluorouracil
Yes
Yes

DPYD
1
97515787
A
C
rs55886062
c.1679T>G
*13
*13
capecitabine/fluorouracil
Yes
Yes

DPYD
1
97573863
C
T
rs56038477
c.1236G>A
HapB3
HapB3
capecitabine/fluorouracil
Yes
Yes

DPYD
1
97579893
G
C
rs75017182
c.1129-5923C>G
HapB3
HapB3
capecitabine/fluorouracil
Yes
Yes

UGT1A1
2
233760233
C
CAT
rs3064744
NC_000002.11:g.234668881TA[6]>TA[7]
*28
*28
Irinotecan
No
Yes<PHONE_NUMBER>)

UGT1A1
2
233760498
G
A
rs4148323
211G>A
*6
*6
Irinotecan
No
Yes<PHONE_NUMBER>)

TPMT
6
18130687
T
C
rs1142345
719A>G
*3C
*3A/*3C
thiopurine/mercaptopurine/azathioprine
No
Yes<PHONE_NUMBER>)

TPMT
6
18130781
C
T
rs1800584
626-1G>A
*4
*4
thiopurine/mercaptopurine/azathioprine
No
Yes<PHONE_NUMBER>)

TPMT
6
18138997
C
T
rs1800460
460G>A
*3B
*3A/*3B
thiopurine/mercaptopurine/azathioprine
No
Yes<PHONE_NUMBER>)

CYP2D6

rs3892097

*4

codeine
No
Yes<PHONE_NUMBER>)

CYP2C19

rs28399504

*4

clopidogrel
No
Yes<PHONE_NUMBER>)

HLA

any variants?

abacavir/allopurinol
No
Yes (981419257/981419260)

CYP2C9

rs1799853

*2

phenytoin/warfarin
No
Yes<PHONE_NUMBER>/982047500)

This is an example of how CYP2C9*2 and warfarin is represented:
-RECORD 0----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
 datasourceId                   | pharmgkb
 datasourceVersion              | 2024-01-05
 datatypeId                     | clinical_annotation
 directionality                 | Decreased function
 drugFromSource                 | warfarin
 drugFromSourceId               | CHEBI_10033
 evidenceLevel                  | 1A
 genotype                       | *2
 genotypeAnnotationText         | The CYP2C9*2 allele is assigned as a decreased function allele by CPIC. Patients with CYP2C9*2 in combination with another normal function allele, a decreased function allele, or a no function allele may have increased risk of bleeding when treated with warfarin as compared to patients with two normal function alleles. However, conflicting evidence has been reported. Other genetic and clinical factors may also influence the risk of warfarin-induced bleeding.
 genotypeId                     | NULL
 haplotypeFromSourceId          | PA165816543
 haplotypeId                    | CYP2C9*2
 literature                     | [29432897, 10509530, 31186542, 29432897, 17653141, 17653141, 17653141, 17653141, 17653141, 18756910, 24503627, 24503627, 11926893, 10509530, 18574025, 24503627, 24503627, 24474498, 25001883, 25001883, 23932037, 23932037, 23774101, 23104259, 23104259, 25521356, 25521356, 24602049, 25769357, 25858232, 14676821, 17955230, 18690342, 22571356, 19297219, 23602689, 21148049, 25244877, 15714076, 23348161, 18570163, 26777610, 27488176, 27581200, 28033245, 28033245, 28689179]
 pgxCategory                    | toxicity
 phenotypeFromSourceId          | MP_0001914
 phenotypeText                  | Hemorrhage
 studyId                        |<PHONE_NUMBER>
 targetFromSourceId             | ENSG00000138109
 variantFunctionalConsequenceId | NULL
 variantRsId                    | NULL

Unless there are any comments, I consider this work done.
Thanks again @apriltuesday for your effort!


Cannot map RelationshipEntity from Custom Query

Relationship Entity
@RelationshipEntity(type = "MEMBER")
public class Member
{
    @GraphId
     Long graphId;
    @Property(name = "id")
    private String id;
    @StartNode
    private User user;
    @EndNode
    private Group group;
    @Property(name = "since")
    private long since;
}

Retrieving records
String query = "MATCH (u:User)-[m:MEMBER]->(g:Group) RETURN u,g,m";
Iterable<Member> members = session.query(Member.class,query,properties);

After executing the above statement, members size is 0.But when the following statement is executed, I am successfully able to get records.
Result result = session.query(query,properties);

Can we not map query result to RelationshipEntity?

Closing. Feel free to reopen if problem still here.


--watch not working on 4.6.x

It works with "node-sass": "4.5.x".

NPM version (npm -v): 5.5.1
Node version (node -v): 8.9.1
Node Process (node -p process.versions):

    {
      http_parser: '2.7.0',
      node: '8.9.1',
      v8: '6.1.534.47',
      uv: '1.15.0',
      zlib: '1.2.11',
      ares: '1.10.1-DEV',
      modules: '57',
      nghttp2: '1.25.0',
      openssl: '1.0.2m',
      icu: '59.1',
      unicode: '9.0',
      cldr: '31.0.1',
      tz: '2017b'
    }

Node Platform (node -p process.platform): darwin

Node architecture (node -p process.arch): x64

node-sass version (node -p "require('node-sass').info"):
node-sass 4.5.3 (Wrapper) [JavaScript]
libsass   3.5.0.beta.2  (Sass Compiler) [C/C++]

npm node-sass versions (npm ls node-sass):

Please search before opening new issues.

Sorry about that; I did search, but couldn't find a similar issue.
Which issue can I track?

The original tracking issue is #2139. The problems should be resolve din 4.7.1


security / privacy issues

keybase does not automatically log out
messages show when offline if did not logout. (does not update newer messages but older ones show)
making paper key makes account vulnerable since hard coded set of phrases and only that one set instead of default generated random set of phrases. should not annoy users to make one in people tab. once that one key is compromised people would be able to add devices as wish.
keybase makes public directories of /keybase /keybase/public /keybase/private /keybase/team so if you are on a shared computer or network others will know you have keybase installed which could lead to searches of your computer. should make those directories on login and remove them on logout.

+bump


Broken Link for Feature Sets

The documentation on the Microsoft website under the below link has a broken link.
https://docs.microsoft.com/en-us/azure/machine-learning/team-data-science-process/lifecycle-modeling#feedback
The Github link for 'Feature Sets' is broken.
[Enter feedback here]

Document Details
⚠ Do not edit this section. It is required for docs.microsoft.com ➟ GitHub issue linking.

ID: 703809ca-6dcb-930c-d806-bf341def4de6
Version Independent ID: d1ca5a92-a403-f43c-ccc6-07458b259342
Content: Modeling stage of the Team Data Science Process lifecycle
Content Source: articles/machine-learning/team-data-science-process/lifecycle-modeling.md
Service: machine-learning
Sub-service: team-data-science-process
GitHub Login: @marktab
Microsoft Alias: tdsp

@umeshmsachdev thanks for bringing this to our attention, we will review it and get back to you shortly.

@umeshmsachdev changes should be visible soon (next day or two). Thanks.


Documentation error

In your doc string and documentation for Timezone you instruct that:
"Timezone[...]`` (the ellipsis literal) expresses that the datetime must be tz-aware but any timezone is allowed."
This should be corrected to:
"Timezone(...)`` (the ellipsis literal) expresses that the datetime must be tz-aware but any timezone is allowed."
Replacing square brackets with normal brackets. This is used correctly in your test_cases here:
yield Case(
Annotated[datetime, at.Timezone(...)], [datetime(2000, 1, 1, tzinfo=timezone.utc)], [datetime(2000, 1, 1)]
)

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

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

Could you please submit a PR? Thanks


Fix google native provider packages

Description

Fixes #381
Checklist

[ ] I have added tests that prove my fix is effective or that my feature works

[ ] I have updated the CHANGELOG-PENDING file with my change

[ ] Yes, there are changes in this PR that warrants bumping the Pulumi Service API version

missing codegen, until I figure out how to update the shema in the upstream repo

Why is the dirty check failing? I fear the google-native generated code is not up to date, and the example hasn't been fixed up.

TBH I'm not sure, maybe I should use the 0.18.2 instead of updating to latest

For this check it versions don't matter, it just means maybe you did not run make provider.gcp.generate? Let me check it out and try.

merged the missing codegen, rebased on master

LGTM if tests pass ok to merge.

thank you, ideally upstream PR would be merged before this one:
https://github.com/pulumi/pulumi-google-native/pull/554

rebased

LGTM let's merge up.


AzCopy quit unexpectedly uploading files other than pictures into Blob Storage

Storage Explorer Version: 1.7.0
Platform/OS: Windows 10
Architecture: x64
Regression From: No
Bug description
When uploading files other than pictures into my Azure Blob Storage using Azure Storage Explorer, AzCopy quits unexpectedly all the time, whether I try to upload a complete Folder or just a File. PNG, JPEG, uploads fine, but CSV, JSON, XML, XLSX, all fail... with the new version 1.7.0 I had hoped the problem would have been solved, but it still remains. I only started using Azure Storage Explorer recently and this has never worked for me. Loading files in File Storage and Table Storage does work. It is a Blob Storage on a Azure Data Lake Storage Gen2.
Transfer from 'C:\Users*****' to 'powerbi/TestFolder/' complete with errors: 0 completed, 0 failed (used name and key, discovery not completed), error: AzCopy quit unexpectedly
Steps to Reproduce

Select the Blob Storage in your Blob Container using Azure Storage Explorer
Select from the menu above: 'Upload' and then 'Upload Files...'
Select a file from my local drive
Click 'Upload'

Expected Experience
I expect a Transfer completed (used name and key)
Actual Experience
Transfer failed with error message complete with errors: 0 completed, 0 failed (used name and key, discovery not completed), error: AzCopy quit unexpectedly
Additional Context
None that I see relevant...

This is awkward... when selecting files from my local drive that are a sync of my OneDrive it gives the described error except when being pictures and pdf, but when I load from my C:\Documents folder it does load. Very strange... I guess I found a workaround for myself, but I wonder if this behavior is to be expected...

I have the same error. The command-line that StorageExplorer creates to run AzCopy is incorrect. Mine looks like so:
$env:AZCOPY_CRED_TYPE = "Anonymous";
./azcopy copy "https://account.blob.core.windows.net/container/*?shared_access_key" "C:\Users\name\Downloads" --overwrite=false --recursive --fromTo=BlobLocal --list-of-files "C:\Users\name\AppData\Local\Temp\stg-exp-azcopy-202dd503-8552-4725-8577-17c6e8ee9317.json"
$env:AZCOPY_CRED_TYPE = "";
Notice the lack of space or semi-colon immediately after the ".json" file and the reset of the environement variable at the end. If I add a semi-colon and a space to separate those two instructions, the command-line runs correctly.
Hope this helps.

Thanks for the tip springcomp, but when comparing the AzCopy command generated by Azure Storage Explorer, between the file upload from my local C: drive and my C:\Users\me\OneDrive then both miss the semicolon and space, but the first one is working and the second one causes AzCopy to quit unexpectedly...
How can I modify the AzCopy command in Azure Storage Explorer and run it again?

I think we need a PR to fix this error. I'm not knowledgeable enough in electron/JavaScript to do this though...

Hey y'all, we recently updated the integrated AzCopy version. If y'all are willing could you give it a try and let us know if you're still having issues? Here's a link to a private build of Storage Explorer:

macOS: https://storageexplorerpublish.blob.core.windows.net/privatebuilds/AzCopy-v10-0-9/StorageExplorer-darwin-x64.zip
Windows https://storageexplorerpublish.blob.core.windows.net/privatebuilds/AzCopy-v10-0-9/StorageExplorer-ia32.exe
Linux: https://storageexplorerpublish.blob.core.windows.net/privatebuilds/AzCopy-v10-0-9/StorageExplorer-linux-x64.tar.gz

Let us know if AzCopy works for you now. If not, we can take a look at your AzCopy logs to find out more.

Hi M, thanks for the update. I ran the installation and at finish, launched the application. Unfortunately it still gives an error, although a different one this time...
{
"message": ""failed to perform copy command due to error: cannot start job due to error: nothing can be uploaded, please use --recursive to upload directories.\n""
}
It still does upload files from my local C: drive, but nothing from any of the synced OneDrive or SharePoint folders yet...
Hope this will help you fix the issue further.
Regards,
Hilko

Hi @MRayermannMSFT  thank you very much for this private build.
Unfortunately, no, it does not work.
Now I get the following error:

Ok, let's work through these then!
@hulkje
If you're uploading multiple items then copy the AzCopy command to your clipboard. Paste it into a text editor (ideally not Notepad because Notepad handles new lines weirdly) and look for something like this:
--list-of-files "C:\Users\matt\AppData\Local\Temp\stg-exp-azcopy-29a381c8-64f8-481b-9eed-cf579cd4633d.json".
Drag and drop that file here Feel free to redact file and folder names in it, I just want to make sure it looks right.
Also, regardless of how many things you are uploading, can you share the log file with me? You'll find it at C:\Users\<your username>\.azcopy. If there's lots of logs in there, then just delete all of them, reproduce the failure, and then copy the single log that is now in the folder. Please read through the log and redact any sensitive information you do not want others to see (account keys, account names, etc.) before uploading the log file.
@springcomp , I think your issue should be a little easier to diagnose and fix. If you could do the following steps that'd be great:

Open Storage Explorer
Open Dev Tools (F12 or via the Help menu)
Reproduce your issue
Go to the dev tools and open the console

In the filter field, put in "AzCopy.Blob.uploadBlobs", after doing show, the console should have much fewer things in it.
Look for a message that looks like this:
FROM CHILD PROCESS 16812: {"id":"MessagePassingProviderProxy4353","args":{"type":"UploadFiles","defaultDestinationBlobFolder":"","connection":{"type":"blobContainer","serviceEndpoint":"https://REDACTED.blob.core.windows.net/","container":"1millionblobsdivided","credentials":[{"type":"key","accountKey":"REDACTED","accountName":"stgexp"},{"type":"auth","accountId":"REDACTED","tenantId":"REDACTED"}]}},"messageType":"FunctionCall","providerNamespace":"se-az-copy-extension","functionNamespace":"AzCopy.Blob.uploadBlobs"}
Copy and paste that to a reply to me.

Important: Please redact sensitive information before clicking "Comment." It is likely that what I'm having you paste includes things such as storage account name, account key, tenant ID, AAD account ID, etc. In my above example, you can see how I replaced those items with REDACTED. I advise you to do the same/similar. Thanks!

 Ok, what I thought is indeed the case (there isn't a blob service endpoint in the args to our azcopy code). I will get a fix for this in for 1.8.0.

Ok checked in the fix today. You can try it here:

macOS: https://storageexplorerpublish.blob.core.windows.net/privatebuilds/1.8.0-RC1/StorageExplorer-darwin-x64.zip
Windows https://storageexplorerpublish.blob.core.windows.net/privatebuilds/1.8.0-RC1/StorageExplorer-ia32.exe
Linux: https://storageexplorerpublish.blob.core.windows.net/privatebuilds/1.8.0-RC1/StorageExplorer-linux-x64.tar.gz

Hopefully that gets things working for you @springcomp 🤞

Hi M, sorry for the late reply.
The AzCopy command for a single file is like this:
./azcopy.exe copy "C:\Users\Hilko\OneDrive\Project\Data Lake\Azure_BlobFiles\SalesLT.Customer.csv"
or this when selecting a whole foler:
./azcopy.exe copy "C:\Users\Hilko\OneDrive\Project\Data Lake\Azure_BlobFiles"
When I look in that log folder you mention, I only see another folder called 'plans'. In here I have only one file of the type STEV6... is that what you are looking for?
Thanks again for your support.
Regards,
Hilko

@hulkje ,some follow-ups:

Do you have issues if you move what you're trying to upload out of your onedrive folder?
Are the files sync'ed to be on your machine? Or more specifically, if you go and look at say SalesLT.Customer.csv in file explorer, which of these three icons does it have?

Are you able to open the files if you double click on them in File Explorer?
The commands you copied, is that the entire command, or did you trim off some parts? Because the command should have looked something like:
./azcopy.exe copy "C:\Users\Hilko\OneDrive\Project\Data Lake\Azure_BlobFiles\SalesLT.Customer.csv" "https://someaccount.blob.core.windows.net/somecontainer/?SASCREDENTIAL" --overwrite=false --follow-symlinks --recursive --fromTo=LocalBlob --blobType=BlockBlob

And no, that folder should be filled with text files:

Hi Matt,

Hope I read your question right, but yes, I can move files from the OneDrive folder on my local machine to another non-OneDrive folder on my machine.
That does not seem to matter. As soon as I select a file with the cloud pictogram it downloads it first to my local machine before I can start the upload to the Blob storage. In neither case does it works.
Yep, files open fine in their application
Sorry, you are right. This is the complete command.
./azcopy.exe copy "C:\Users\Hilko\OneDrive\Project\Data Lake\Azure_BlobFiles\SalesLT.Customer.csv" "https://datalake.dfs.core.windows.net/testblobcontainer/SalesLT.Customer.csv" --overwrite=false --follow-symlinks --recursive --from-to=LocalBlobFS --put-md5;

Hmmm, I am afraid no log files appear in that C:\Users\Hilko.azcopy folder...
Hope this information helps.
Regards,
Hilko

Bit of miscommunication on question #1. I wanted to know if you could upload your SalesLT.Customer.csv file from a non-OneDrive location. So for example, if you placed SalesLT.Customer.csv on your desktop, does the upload work? Also I tried replicating your upload today and unfortunatley I'm still not seeing any issue. ☹
Command I ended up trying:
./azcopy.exe copy "C:\Users\matthew\OneDrive\Project\Data Lake\Azure_BlobFiles\SalesLT.Customer.csv" "https://dfsdfstest01.dfs.core.windows.net/fstest/SalesLT.Customer.csv" --overwrite=false --follow-symlinks --recursive --from-to=LocalBlobFS --put-md5
Let me contact the AzCopy folks and see if they have any ideas. Unfortunatley I'm out of ideas at this point.

Ah, ok, yes this works fine. I found out later and mentioned this in my second comment on this post.
Maybe the problem is with my laptop or the way our OneDrive / Office 365 is configured...?

Yes, something weird is going on with OneDrive unfortuately. The AzCopy team is looking into this.

@MRayermannMSFT
Sorry for the delayed answer, I was on vacation :-).
Yes, the latest private build works correctly with AzCopy.
Thank you very much.

Is this latest private build a part of the 1.9.0 release?  I have just taken that release but am receiving failuer when performing an upload:
{
"message": ""failed to perform copy command due to error: cannot start job due to error: nothing can be uploaded, please use --recursive to upload directories.\n""
}

@ticklen Could you tell us a bit more on what you were trying to do when the error occured?  Thanks.

Move an excel spreadsheet from my onedrive folder into gen2 blob storage.
Nancy Tickle – Enterprise Architect
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@ticklenhttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fticklen&data=02|01||40014c0b74774a0dba2a08d7145ab13f|05609332b9054a6bbf744807fa89857d|1|0|637000252062901579&sdata=CgrwmSdZoGRcQm7qtHrWX%2FxGUwPUWcpnjcZqzOhOecQ%3D&reserved=0 Could you tell us a bit more on what you were trying to do when the error occured? Thanks.
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@ticklen can you share with us the AzCopy log file. There should be an action in the activity log to go to it. You can then attach it to a new comment on this issue.


No video or voice calls possible

Operating system: Manjaro KDE 16.10 Fringilla, Kernel, x86_64 Linux 4.9.9-1-MANJARO, KDE 5.31.0 / Plasma 5.9.2
Messenger for Desktop version: 2.0.4-1 from AUR

In the past calls and video connections were possible. Now when I click on call, I see pop-up window: Error - KIOExec, Missing file: about:blank.
Here is screen of that window:
https://puu.sh/ua5re/844d713fed.png
Other then that, application seems to work fine, maybe except the fact that it global menu on Plasma shows but is not clickable on the panel.

Fixed in 2.0.5, will be released soon

Thanks, will wait for the update.


Updates Proxy TrustedCA godocs

https://github.com/openshift/api/pull/377 added the trustedCA field to the proxy api type. However, the godocs for this field referenced namespace openshift-config-manaed instead of openshift-config. This PR fixes the godoc namespace reference.
cc @abhinavdahiya @bparees @jcpowermac

/lgtm
/approve


Close after page refresh

Hi,
Everytime I refresh a page after the remodal box was launched the modal box is in open state. How do I default the modal box to a close state even after a page refresh?

I'm also having this issue

Use the hashTrack options your modal window. data-remodal-options="hashTracking: false, closeOnOutsideClick: false"
As long as you are calling remodal normally (event based), this will work. if you call it from an instance, options do no seem to work (which is the issue I present in another issue).

I am using remodal right now like this, and it works.
var modalSms = this.$('[data-remodal-id=modalSms]').remodal({
			'hashTracking': false,
                        'closeOnOutsideClick': false
		});
modalSms.open();


feat: WebAssembly filter chains, coming in Kong Gateway 3.4

This PR introduces the FilterChains entity, a new entity coming in Kong Gateway 3.4 (OSS and Enterprise) to manage WebAssembly filters ("filters" are the WebAssembly analog to Lua plugins — we call them filters because it's the already-established terminology used by the proxy-wasm API we implemented, which is also implemented by other WebAssembly-enabled gateways such as Envoy).

Codecov Report
Patch coverage: 0.54% and project coverage change: -35.03% :warning:

Comparison is base (5236d86) 52.53% compared to head (09168b8) 17.51%.
Report is 5 commits behind head on main.

Additional details and impacted files
@@             Coverage Diff             @@
##             main     #362       +/-   ##
===========================================
- Coverage   52.53%   17.51%   -35.03%
===========================================
  Files          69       71        +2
  Lines        5158     5360      +202
===========================================
- Hits         2710      939     -1771
- Misses       1872     4328     +2456
+ Partials      576       93      -483

Flag
Coverage Δ

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community
17.51% <0.54%> (-20.41%)
:arrow_down:

enterprise
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enterprise-nightly
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integration
17.51% <0.54%> (-35.03%)
:arrow_down:

nightly
17.51% <0.54%> (-19.87%)
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Files Changed
Coverage Δ

kong/filter_chain.go
0.00% <0.00%> (ø)

kong/filter_chain_service.go
0.00% <0.00%> (ø)

kong/client.go
64.66% <100.00%> (-1.65%)
:arrow_down:

... and 42 files with indirect coverage changes

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

Regarding the failing test: we probably need KONG_WASM=on set on the 3.4/nightly tests for the filter chain operations to work, and probably KONG_WASM_FILTERS_PATH=filters/ as well, containing a dummy filters/example-filter.wasm

CI problems...
The nightly tests were using an old tag (master-alpine), so those tests were broken for filter chains. I updated this to master. However, now some other tests are failing now that they are being executed against a real nightly image:
=== RUN   TestFillPluginDefaults/no_config_no_protocols
    plugin_service_test.go:671:   &kong.Plugin{
          	... // 6 identical fields
          	Consumer:      nil,
          	ConsumerGroup: nil,
          	Config: kong.Configuration{
          		"anonymous":        nil,
          		"hide_credentials": bool(false),
        - 		"realm":            string("service"),
          	},
          	Enabled: &true,
          	RunOn:   &"test",
          	... // 3 identical fields
          }

Lint fixes are in #421

I had to fix a host of testing problems in order to get CI working against Kong nightly/master, so there are a bunch of additional commits in this PR. I can move them to another PR if desired.

@hishamhm who is a good person to tag for review on this?

https://github.com/Kong/go-kong/pull/362#issuecomment-2010158479 is being addressed in https://github.com/Kong/go-kong/pull/432


Conversion from RGB to HSV preserves HSV color space range

Description

Per title
Types of Changes

[ ] Core
[x] Bugfix
[ ] New feature
[ ] Enhancement/optimization
[x] Documentation

Issues Fixed or Closed by This PR

Fixes:

Checklist

[x] My code follows the code style of this project.
[x] My change requires a change to the documentation.
[x] I have updated the documentation accordingly.
[x] I have read the CONTRIBUTING document.
[x] I have added tests to cover my changes.
[x] I have tested the changes and verified that they work and don't break anything (as well as I can manage).

#339 to be merged first


move tracing helper into its own package

Moved tracing helper into its own package
Add extra span attributes
Aligned existing tracing

resolves #18

resolves #18


FreeBSD config dir params

Fix a typo in variables for config dir perms and ownership for FreeBSD

Sorry, pull request doesn't include actual changes. Clearly I am unfamiliar with the Github way of doing things.


Change eval batch size

Description
Surfaces extra options for eval step: number of eval batches and number of sequences per eval batch. Adds an optional parameter to activations_store.get_batch_tokens to make this clean: now get_batch_tokens can get a number of sequences that differs from the value defined at init.
Type of change
Please delete options that are not relevant.

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

Checklist:

[x] I have commented my code, particularly in hard-to-understand areas
[ ] I have made corresponding changes to the documentation
[x] My changes generate no new warnings
[] I have added tests that prove my fix is effective or that my feature works
[x] New and existing unit tests pass locally with my changes
[x] I have not rewritten tests relating to key interfaces which would affect backward compatibility

I've checked these locally but not added tests.
You have tested formatting, typing and unit tests (acceptance tests not currently in use)

[x] I have run make check-ci to check format and linting. (you can run make format to format code if needed.)

Yeah, the reason I called it this was that the batch size here is the
number of sequences, but the batch size produced for the SAEs is #
sequences * context length. Having an ‘eval_batch_size=4’ in the config
seemed like it would be surprising next to a batch size of (say) 4096.
On Wed, 8 May 2024 at 16:40, Joseph Bloom @.***> wrote:

@.**** commented on this pull request.
In sae_lens/training/config.py
https://github.com/jbloomAus/SAELens/pull/128#discussion_r1594247562:

@@ -106,6 +106,10 @@ class LanguageModelSAERunnerConfig:

 dead_feature_threshold: float = 1e-8

Evals

n_eval_batches: int = 10
n_eval_seqs: int | None = None  # useful if evals cause OOM

True. Feel free to make a PR for this.
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👍 makes sense!

@tomMcGrath  @tomMcGrath We previously has "train_batch_size" which is a token batch size for the SAE and a "store batch size" which was a prompts batch size for generating activations. The latter was then reused during evaluations, but we've now seperated them out. I think the following names might be best:

train_batch_size_tokens
store_batch_size_prompts
eval_batch_size_prompts
I generally like longer names if they are sufficiently clear but will admit these names are long and this could be annoying.

That rename makes sense to me, I feel like that makes it more clear what's going on and reduces confusion around the difference between a "batch" of prompts vs tokens

I like that rename - I just put a quick issue in to remind me to do the rename.


Support store decimal as integer for parquet writer

Parquet support store decimal as integer, rules are

int32: for 1 <= precision <= 9.
int64: for 10 <= precision <= 18.
fixed_len_byte_array: for precision > 18.

Presto support this behavior by default, https://github.com/prestodb/presto/blob/master/presto-parquet/src/main/java/com/facebook/presto/parquet/writer/valuewriter/DecimalValueWriter.java.
Spark has a config for it spark.sql.parquet.writeLegacyFormat, default behavior same as Presto, https://github.com/apache/spark/blob/df4d489b67a95c78b22d4def4ffdaf86fefb8931/sql/catalyst/src/main/scala/org/apache/spark/sql/internal/SQLConf.scala#L1106-L1114.
Arrow related config, https://arrow.apache.org/docs/cpp/api/formats.html#_CPPv4N7parquet16WriterProperties7Builder31enable_store_decimal_as_integerEv.

@majetideepak @yingsu00 @Yuhta would you help review this patch? thanks!

would someone help review/import? @pedroerp @kgpai


can i get access to waymo_dataset_val.yaml, it does not seem to exist in dataset_configs anymore

For validation, you are looking for waymo_dataset.yaml.
Please let me know if you have further questions!


Adds back #574

Summary
#620 reverted #574 and this adds it back.
Test Plan
Looks clean to me :)
Issues
Closes #622

Lol I was wondering why it was broken


Fixed some minor typos

Very nice review!   Fixed a few typos.

Thanks for all of these comments, @ericagol!! We'll incorporate them all soon!

I've merged these into the Overleaf document separately. Thanks!


GC cannot be triggered when no service exists.

Bug Report
1. Describe the bug
If no service exists in service group, 0 wil be returned as the safepoint. In this case, should use gc-worker safepoint to update the gc safepoint.
2. Minimal reproduce step (Required)
Run gc-worker and no service is registered to pd.

3. What did you see instead (Required)
0 is always the safepoint and gc cannot be triggered.
4. What did you expect to see? (Required)
use gc-worker safepoint to update the gc safepoint.
5. What is your migration tool and TiKV version? (Required)
GC-Worker

Still get & pass revision to update GC safe point interface.
p.s. In this scenario, revision will be `-1.

@pingyu What revision is returned from GetGCMinServiceSafePointByServiceGroup interface in this scenario? Could gc-worker pass the returned revision to UpdateGCSafePointByServiceGroup or need hard code to -1?

@pingyu What revision is returned from GetGCMinServiceSafePointByServiceGroup interface in this scenario?

-1. See here.

Could gc-worker pass the returned revision to UpdateGCSafePointByServiceGroup or need hard code to -1?

Yes. No hard code is needed.

ok, get it.


Discussion ticket: POC to use atprotocol for secrets management

Is your feature request related to a problem? Please describe.
I believe a solution around atProtocol will be a cost-efficient solution for secrets management.
Describe the solution you'd like

A secondary server can be used as a vault for secrets (passwords, API keys etc..)
A secondary server can be made to accept connections from selected atSigns (clients)
Each client can get its secrets through their respective atSigns
Change in secrets can be propagated to the clients using reshare/notification

Describe alternatives you've considered
No response
Additional context
No response

A rough representation of the idea.


Supporting mutating node values in GraphInfo

Our current GraphInfo stores GraphInfo.value in a NamedTuple which prevents mutation.
https://github.com/TuringLang/AbstractPPL.jl/blob/469252618fd6ea85dc911b0999b4614fcca45f2f/src/graphinfo.jl#L25
One simple improvement is to use Ref to store values inside NamedTupe. It does not influence type stability and keep the overall design intact. For example:
julia> Model(
               s2 = (0.0, () -> InverseGamma(2.0,3.0), :Stochastic),
               μ = (1.0, () -> 1.0, :Logical),
               y = (0.0, (μ, s2) -> MvNormal(μ, sqrt(s2)), :Stochastic)
           )

becomes
julia> Model(
               s2 = (Ref(0.0), () -> InverseGamma(2.0,3.0), :Stochastic),
               μ = (Ref(1.0), () -> 1.0, :Logical),
               y = (Ref(0.0), (μ, s2) -> MvNormal(μ, sqrt(s2)), :Stochastic)
           )

Then we can do
# support mutation for stochastic variables
m[@varname s2] = 5.0

# this should result in an error since we can't mutate logical variables (and hyperparameters)
m[@varname μ] = 2.0

Note that we only need to change the internal model constructor and accessor functions and keep the user-facing Model constructor the same.

Fixed by #57


Consider a way to prevent enum values from being at the top level of a package

Maybe use Jeff's enum package or @jhendrixMSFT might have an idea with generics.

Current thinking is to expose enum values as methods on the enum type.  We'd then export a constant for easy access.
type IntEnum string

// IntEnumVals provides access to the predefined values of IntEnum.
const IntEnumVals = IntEnum("")

// One - This is a really long comment to see what wrapping looks like. This comment is really long and it should wrap for
// readability. Please wrap. This should wrap.
func (IntEnum) One() IntEnum { return IntEnum("1") }

// Three - three
func (IntEnum) Three() IntEnum { return IntEnum("3") }

// Two - two
func (IntEnum) Two() IntEnum { return IntEnum("2") }

// Values returns the predefined values for the IntEnum type.
func (IntEnum) Values() []IntEnum {
	return []IntEnum{
		"1",
		"3",
		"2",
	}
}

// ToPtr returns a *IntEnum pointing to the current value.
func (c IntEnum) ToPtr() *IntEnum {
	return &c
}

Consumers we access the values via IntEnumVals (how to name these constants is still being discussed).
e := IntEnumVals.One()

Other option would be to move the const types and their values into a sub-package.  This would have to be done along-side the models.

I like the "type per enum" idea, but here are a few things to consider:

This doesn't address plain old consts. In the azblob package, the majority (8 of 15) const values fall into this category.  So for azblob, the "type per enum" approach would only reduce the number of top-level symbols from 15 to 14.  Maybe that's okay, because in other packages we'll get big wins, but I thought it was worth mentioning.

The large number of top level symbols is really an intellisense problem.  It does not affect the docs in pkg.go.dev, because all the constants are grouped together in one index entry called "Constants" (not expandable). And converting constants to types will increase the sub-index under "Types".  Again, maybe that's okay but worthing noting. And if we thought about this as an intellisense issue, maybe other solutions would pop up -- like could we do something in the Go Plugin to VSCode to hide constants by default, or always group them at the end? (Now that I typed that I kinda like that last idea.)

Even if we do the function enums could we still put them into a sub package? That would at least keep them from being at the "top level types" area, which would be nice but since we wouldn't have to have a sub-package per enum it wouldn't be too horrible.
Also, if we call the subpackage 'enum' or similar we wouldn't need to suffix each thing with enum.

We could, and if fact I have a prototype of that here.  This was the next thing on the list to discuss once we landed on our enums design.

We will be keeping our present const pattern for enumerations.


Add myentry to AUTHORS.

Hi. Django Authors.
I'm a contributor to the following ticket.
I would like to have me added to AUTHORS.
https://code.djangoproject.com/ticket/34788
I have also just signed and sent you the Individual Contributor License Agreement.
Please feel free to merge it.
Thanks.

@felixxm
I moved my entry.
Please check it agin.
Thanks.


Setup MiMa for ensuring binary compatibility

Maybe have a look at https://github.com/scalacenter/sbt-version-policy

Noticed this issue. You may find sbt-typelevel helpful, highly recommended 😉
https://typelevel.org/sbt-typelevel/

For sbt-typelevel to be stable? Whether I like it or not it has to be stable now, because there are too many builds using it and I don't want to redo them 😆

https://github.com/typelevel/sbt-typelevel/issues/83

Ok sorry last time I checked it was still in early stages, I will try the migration.

Closed by #315


Action hangs running on Windows/Edge

I'm not sure why, but it happens pretty often. We've tried a bunch of things (using different images included) but we were not able to solve this issue. We had to set a timeout-minutes on our workflow, otherwise if it happens the action would run forever until manually canceled.

The logs don't have any useful information:

As far as we can notice for some reason after finishing that last test(it's kinda random, it's not always the same test) nothing happened for 9min until the operation timed out and got canceled. The same test suite is running fine on Linux machines, testing with Chrome and Firefox.
Any tips here? Thanks so much!

Having this same issue

Having same issue on ubuntu too

Is this issue still happening with current versions?
GitHub window-2022 (latest) currently bundles Microsoft Edge 108.0.1462.46. Same for the GitHub Ubuntu runners.
I have run cypress-io/github-action@v5 on ubuntu-20.04, windows-latest & macos-latest with Cypress 9.6.1 and 10.0.0 against the Microsoft Edge browser and I did not see any problem.

TBH I'm not using Cypress anymore as I've been focusing on React Native lately - should we just close this issue then?

@felippepuhle
Thanks for responding! There haven't been any more comments in this issue for almost a year, and if the issue is not relevant to you any more then closing it would be the best.

Sounds good, thanks!


Projects Made With Roots

It would be great if there was an example page demonstrating Roots.  I found your globtester example but that is pretty simple.  Something more advanced like carrot.is would be inspirational.

This will now live here: http://roots.cx/articles/built-with-roots :tada:


Improvement : Email and phone number verification in user creation using SCIM 2.0 REST API

Description:
When creating a user using SCIM 2.0 REST API, user's emails and phone numbers aren't validated at the server.

This issue is being closed due to extended inactivity. Please feel free to reopen it if further attention is needed. Thank you for helping us keep the issue list relevant and focused!


Catch and show error in soundcard setup

Can help debugging problems like in issue #340

Thank you!