Seperated Books and Screencasts and added Code School course

Jeremy suggested I add the new course to the list and separate these two sections.

Thanks.


Changing HardDeleter to use DiskIOScheduler instead of Throttler

Built and formatted

Formatted and built

Looks good. Merging.


change ?= to an ifeq in the Makefiles for issue #284

Convert all ?= lines in the Makefiles of the codes (which will not work if the variable is set but empty) into 3 lines with ifeq.

I think this is overkill (makes a lot of Makefiles ugly to read)..better to fix few cases where it matters (if it ever does, simplex case I don't think qualifies because the root cause was the config failing (which could be set by hand))
in any case: there are errors in the conversion...

I think the better alternative is to not export unset variables in config.mk, or to check whether variables that should be set, are....
(really, the resulting makefiles are clearly not written by/for humans..)

Well yes, the configure could not find the libs. And if you then change the Makefile in testing you get very hard to understand and debug behavior. (I.E. your change will not be used for an unknown reason)

also I am not sure if the original behaviour is in many cases not the exact desired behaviour, e.g. some flag being empty can be the desired contents of the flag...

Well yes, that's also true. Lets bin this pull request.

ok, lets do that;-)


Issues starting on wrong page

I think comic issues should start on the last page they were on when the comic was closed instead of the furthest page reached in the comic like it is doing now.

So say you skip to page 20, but then you skip back and read up only to page 15, page 15 should be stored as your bookmark?

Yah i think what ever page you physically left off at should be the one thats saved as the bookmark.


error: [Errno 111] Connection refused

problem description
For Hello case
./wsk action invoke /whisk.system/samples/echo -p message hello --blocking --result
returns   "error: [Errno 111] Connection refused"
steps to reproduce

Clone openwhisk
git clone --depth=1 https://github.com/openwhisk/openwhisk.git

Change directory to tools/vagrant/simple
cd openwhisk/tools/vagrant/simple

Run script to create vm and run hello action
vagrant up
./wsk action invoke /whisk.system/samples/echo -p message hello --blocking --result

I try the quickcase following  the guide         https://github.com/openwhisk/openwhisk

I run it locally on my laptop

Hi @lfzCarlosC could you provide more info on your environment to be able to reproduce?
I tried today with latest hash bf3fe240ff56f772837f7c9ccf909483b1893a8c
I'm using Mac OSX El Capitan
$ uname -a
Darwin carlosmacbookpro.raleigh.ibm.com 15.5.0 Darwin Kernel Version 15.5.0: Tue Apr 19 18:36:36 PDT 2016; root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64

$ vagrant -v
Vagrant 1.8.1

Virtual Box Version 5.0.20 r106931

I clean ~/.vagrant.d/ just in case
I made sure no whisk VMs are listed or running on Virtual Box
No other VMs are running
Steps:
$ rm -rf ~/.vagrant.d/
$ git clone --depth=1 https://github.com/openwhisk/openwhisk.git
$ cd openwhisk/tools/vagrant/simple/
$ ./hello

wait for a while, downloading new vagrant ubuntu to cache (10 minutes) then whisk setup (20 minutes)

==> default: ++ bin/wsk action invoke /whisk.system/samples/echo -p message hello --blocking --result
==> default: {
==> default:     "message": "hello"
==> default: }
{
    "message": "hello"
}

$ git log
commit bf3fe240ff56f772837f7c9ccf909483b1893a8c
Author: Perry Cheng<EMAIL_ADDRESS>Date:   Wed Jun 8 21:34:48 2016 -0400

I clean all the things and re-ran the whole steps,This time the behaviour is a little bit different. Hello action work fine the first time when vagrant vm is created , but then if I try to restart vm(via GUI from virtual box) and run hello action , the error happens.I will attach the log info then

@csantanapr I have run a travis build that does install a vagrant box. It would work in theory, however you need to install virtualbox first which in conjunction with our own build + test flow takes longer than travis allows on the free tier and the build gets killed. I suggest making a build on our Jenkins that does a vagrant up and checks the output.

@lfzCarlosC Ah I think you are hitting some of the UX, we are seeing and working on fixing.
Restarting I think will cause problems, since you have to deploy ant deploy but the inmortal DB is not up. @houshengbo is working on fixing this workflow.
For now don't restart the VM, just suspend it and then up (not resume). you can use vagrant cli, we have that in the [simple/README.md(https://github.com/openwhisk/openwhisk/blob/master/tools/vagrant/simple/README.md)

@domdom82 thanks for volunteering 😆

I suggest making a build on our Jenkins that does a vagrant up and checks the output.

I would prefer to see something externally test this, but I guess for now we will use an internal server, but even with that I will suggest to have all the scripts in open (i.e. tools/travis/test-vagrant.sh)

I don't think you can run vagrant inside an SL VM.   Virtualization inside virtualization usually doesn't work.

relate issue #311

But I was considering a real development case.If I developed new updates for action/trigger/rule and test it on local vagrant env,  next time these updates are not useful because I am not allowed to restart the vm? Or what is the process of development based on local vagrant env?

I don't understand the last comment. If you restart the vm you expect the whisk deployment to still be up?

let us consider a case. If I develop an action A on vagrant vm from my host machine, and then the vm for some reasons dump ,so how should I do to make action A rerun?

Suspending the machine is like shutting it down. It doesn't take resources. Just suspend , when you start the VM your actions, rules, etc are still available.
We also have a custom setup where you can use a persistent remote DB like cloudant or a remote CouchDB
Regardless if you restart the VM the whisk system doesn't start automatically, you need to deploy/start the whisk system.

So, can I use this guide https://developer.ibm.com/open/2016/02/22/openwhisk-a-quick-tech-preview/  if I want to deploy whisk system once I need?

Regardless if you restart the VM the whisk system doesn't start automatically, you need to deploy/start the whisk system.

@csantanapr not entirely true. The system should come back up in general. Ephemeral couch is a different story, however. If you use cloudant or other peristent db it should recover from a reboot. Part of our RAS strategy.

@csantanapr  I clean all and try today's build. This is my log info:
$ uname -a
MINGW64_NT-6.1 BPK1MZ87 2.5.0(0.295/5/3) 2016-03-31 18:47 x86_64 Msys
$ vagrant -v
Vagrant 1.8.1
virtual box 5.0.10 r104061
$ rm -rf ~/.vagrant.d/
$ git clone --depth=1 https://github.com/openwhisk/openwhisk.git
$ cd openwhisk/tools/vagrant/simple/
$ ./hello
.........
==> default: ++ bin/wsk action invoke /whisk.system/samples/echo -p message hello --blocking --result
==> default: {
==> default:     "message": "hello"
==> default: }
error: name 'C:' contains illegal characters (code 29)
wsk failed, build might be broken try running ./resume_build
$vagrant ssh   //to the vagrant vm
Then:
create js file hello.js:
function main() {
return {payload: 'Hello world'};
}
wsk action create hello hello.js
wsk action invoke --blocking hello
vagrant@vagrant-ubuntu-trusty-64:~$ error: org.apache.kafka.common.errors.NetworkException: The server disconnected before a response was received. (code 63)

I'm working on providing instructions on how to re-deploy openwhisk after restarting the Vagrant VM.

This is fix now instructions in vagrant/README.md


Support opening application from the path editbox

What's the Problem?
In explorer.exe, you can start a new cmd at the current folder by typing "cmd.exe" in the path editbox. I also like to open IntelliJ at the current folder using "idea .".
This is what I mean in explorer.exe:

In the files app, "cmd" actually works somehow. But typing other things on the path, like idea gives an error:

Solution/Idea
Match the behaviour of explorer.exe and open the application. I am pretty sure this could be achieved by running
using System.Diagnostics;
...
Process.Start("process.exe");

But I am not 100% sure if that is the exact logic / recognizing that the user is actually trying to do that. Probably involves manually verifying that the provided application name is actually an executable on the path.
Alternatives
As a workaround I have to start a terminal at the current location and type the command in there.
Priorities

Capability
Priority

Start applications entered in the path editbox
Must

Pass the arguments to it
Must

Keep the launched application open when files closes
Must

Files Version
<IP_ADDRESS>
Windows Version
Edition	Windows 10 Enterprise Version	21H2 Installiert am	04.08.2020 Betriebssystembuild	19044.1415 Leistung	Windows Feature Experience Pack 120.2212.3920.0
Comments
No response

@StefanLobbenmeier that sample would work but it would need to open the application in the current directory. Do you want to work on this?

I do not have a development environment setup, but I think Azure can build it and I test it after fixing it with a text editor 😄

Tracked in #5677


SSO using Authelia

Describe the bug
I have setup my Authelia for the SSO authentication, below is a screenshot of the config in Memos instance

This is the Authelia configuration.yml
      - id: memos
        description: Memos
        secret: yM************************N6K...
        authorization_policy: two_factor
        redirect_uris:
          - https://memos.*********.com/auth/callback
        scopes:
          - openid

Steps to reproduce
All mentioned above
The version of Memos you're using
0.18.1
Screenshots or additional context
This is after I login using my usual Authelia credentials (username and password and then I pass through the PIN using my Google Authenticator)

Got it resolved. Just changed the Identifier to preferred_username


only seed if there's no data.

when we delete, update bestie we don't want to seed data again because it will fail.

Fixed #26
Updated and changed app flask seeding to seed only if the data doesn't already exist
New Image : "quay.io/mkong/bestiev2:2.0"


chore: Remove old way of adding feature flags

Description
Removes optimizely package from Appsmith client.
Rationale:

[ ] We now have a different mechanism for feature flags
[ ] We need to put in additional effort maintaining optimizely keys, with no apparent benefit

What has changed? (Reviewer Checklist)

[ ] Appsmith configs which used optimizely for feature flags, no longer have any references
[ ] Nginx templates do not have optimizely references
[ ] Vercel configs do not have optimizely references
[ ] Netlify configs do not have optimizely references
[ ] docker scripts do not have optimizely references
[ ] index.html does not expect optimizely key

Fixes # (issue) TBD
Type of change

Bug fix (non-breaking change which fixes an issue)

How Has This Been Tested?
This is not supposed to change anything in the application, as a result we expect that if all tests pass, the changes are valid.
Checklist:

[x] My code follows the style guidelines of this project
[ ] I have performed a self-review of my own code
[ ] 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

/ok-to-test sha=e310cb2


[FLINK-30903][runtime] Fix the max parallelism used in adaptive batch scheduler doesn't fallbacks to default parallelism

What is the purpose of the change
In FLINK-30684 we mark the vertices which use the default parallelism, and in AdaptiveBatchScheduler we allow users to use parallelism.default as the max parallelism if they don't configure the configuration item "execution.batch.adaptive.auto-parallelism.max-parallelism". This issue will fix the fallback logic.
Brief change log
Fallback the max pararallelism to default parallelism in DefaultVertexParallelismAndInputInfosDecider if the max parallelism haven't been configured.
Verifying this change
This change is a trivial rework / code cleanup without any test coverage.
Does this pull request potentially affect one of the following parts:

Dependencies (does it add or upgrade a dependency): (yes / no)
The public API, i.e., is any changed class annotated with @Public(Evolving): (yes / no)
The serializers: (yes / no / don't know)
The runtime per-record code paths (performance sensitive): (yes / no / don't know)
Anything that affects deployment or recovery: JobManager (and its components), Checkpointing, Kubernetes/Yarn, ZooKeeper: (yes / no / don't know)
The S3 file system connector: (yes / no / don't know)

Documentation

Does this pull request introduce a new feature? (yes / no)
If yes, how is the feature documented? (not applicable / docs / JavaDocs / not documented)

@zhuzhurk Thanks for CR, I've addressed comment. PTAL!

@flinkbot run azure

@flinkbot run azure


aws-sdk-go upgrade to v1.42.0 for ACK repositories

Update aws-sdk-go dependency to v1.42.0 in ACK core libraries and controllers.
I will create a separate issue for automation of aws-sdk-go upgrades

I am planning to use following strategy:

Update ACK runtime to aws-sdk-go v1.42.35 , which is the latest version. Locally testing code generation for some cheery-picked controllers will give confidence that there are no major issues with this aws-sdk-go version
Create new release of ACK runtime v0.16.2
Update code-generator to new ACK runtime version. This will update aws-sdk-go dependency transitively inside ACK code-generator
Create new release of code-generator v0.16.2
This will autogenerate PRs for all service controller with automated aws-sdk-go upgrades

If there are no new resources added, and e2e tests are passing, merge the controller
If there are new resources added, ignore them in generator.yaml and update automated PR
If the code-generation failed, infer the auto generated issue and manually update the aws-sdk-go for service controller

cc: @haarchri

There was a delay in rolling out this upgrade because of multiple e2e test failures due to new v0.16.0-v0.16.2 releases. Working on this now.

aws-sdk-go now updated in runtime and code-gen. Waiting for some OLM bug-fixes before cutting a new code-generator v0.16.4 release

ACK core libraries are now updated to aws-sdk-go v1.42.0 . Cheers!


malformed universal file: GSgnI-5.0.2

I get the error below which seems to be coming from the GoogleSignIn package:
malformed universal file: slice extends beyond end of file file '/Users/usermac/Library/Caches/Xamarin/mtbs/builds/App.iOS/762012bfafecf6ef89b2cdf969e045de167b578bc9fa4e51c8a84f59f661233c/C:/Users/userwindows/AppData/Local/XamarinBuildDownloadCache/GSgnI-5.0.2/Frameworks/GoogleSignIn.framework/GoogleSignIn' App.iOS
The project does not build.

do you resovle this problem?


Linux area mmap type is not sufficiently virtualized

In GitLab by @perarnau on Mar 26, 2018, 17:19
aml_area_linux_mmap_fd_destroy() or aml_area_linux_mmap_tmpfile_destroy() are never invoked. Instead, aml_area_linux_destroy() contains a hardcoded invocation of aml_area_linux_mmap_anonymous_destroy() (which is a no-op).
This looks fixable by expanding struct aml_area_linux_mmap_ops (which currently contains just mmap) to include the destroy function and picking the right variant in aml_area_linux_vinit(), as with mbind type.

In GitLab by @perarnau on Mar 25, 2019, 11:14
mentioned in merge request !38
By Swann Perarnau on 2019-03-25T16:14:30 (imported from GitLab project)

In GitLab by @perarnau on Mar 27, 2019, 13:55
mentioned in merge request !43
By Swann Perarnau on 2019-03-27T18:55:51 (imported from GitLab project)

In GitLab by @perarnau on Mar 27, 2019, 13:56
mentioned in commit 4c6b449000f806ecd035adb1124eb77fb28e7d3d
By Swann Perarnau on 2019-03-27T18:56:39 (imported from GitLab project)

In GitLab by @perarnau on Mar 27, 2019, 13:56
closed via merge request !43
By Swann Perarnau on 2019-03-27T18:56:41 (imported from GitLab project)

In GitLab by @perarnau on Aug 6, 2019, 13:56
mentioned in commit 4c6b449000f806ecd035adb1124eb77fb28e7d3d


Projected result of a SELECT query is too big

We are using the spark-riak-connector to query a riakTS cluster and getting a  com.basho.riak.client.core.netty.RiakResponseException: Projected result of a SELECT query is too big.
We thought that by increasing the number of executors we would avoid this error but this does not seem to be the case.
Is the query range divided into several smaller range queries and then distributed to each of the executors ?
We are trying to avoid having to segment the range into several smaller ranges within in our code.

Could you please provide a querying example?

Query is as follows:
_sc.riakTSTable(ts_table_name).sql(s"SELECT * FROM $ts_table_name WHERE  time ><PHONE_NUMBER>500 and time <<PHONE_NUMBER>500 and source = '123' and instance = 'instance1'")
table is as follow:
"CREATE TABLE FloatStream " +
"(source     varchar     not null, " +
"instance     varchar     not null, " +
"time         timestamp   not null, " +
"val   double    not null," +
"PRIMARY KEY ( " +
"(source, instance, quantum(time, 1, 'd')), " +
" source, instance, time )) WITH (n_val=1);
The query spans 10 quanta

Additional info:
I also tried to query using dataframes. My query is as follows:
val df = sqlContext.read.option("spark.riak.input.split.count", "100").option("spark.riak.connection.host","myhost.media.com:8087").format("org.apache.spark.sql.riak").load(ts_table_name).select("time", "source", "instance").filter(s"time >= $from ) AND time $to AND source= 'mysource' AND instance='myinstance'")
I received the following error:
coveragePlanResult - CoveragePlanOperation returns at least one coverage entry: 'CoverageEntry [host=<IP_ADDRESS>, port=8087, fieldName=time, lowerBound=1382846337500, lowerBoundInclusive=true, upperBound=1382918400000, upperBoundInclusive=false, description=FloatStream / time >=<PHONE_NUMBER>500 and time <<PHONE_NUMBER>000]' -- with IP address '<IP_ADDRESS>'.
Execution will be failed due to the imposibility of using IP '<IP_ADDRESS>' for querying data from the remote Riak.
java.lang.RuntimeException: CoveragePlanOperation returns at least one coverage entry with ip '<IP_ADDRESS>'.

Managed to get past that one as well. Apparently I did not have the partitioning field configured. I added option("spark.riak.partitioning.ts-range-field-name", "time") and now the dataframe is created successfully. However, when I try to create an additional dataframe using the existing spark context I get the following error:
Caused by: java.util.concurrent.ExecutionException: com.basho.riak.client.core.netty.RiakResponseException: overload
at com.basho.riak.client.core.FutureOperation.throwExceptionIfSet(FutureOperation.java:325)
at com.basho.riak.client.core.FutureOperation.get(FutureOperation.java:311)
at com.basho.riak.spark.query.QueryTS$$anonfun$nextChunk$2.apply(QueryTS.scala:66)
at com.basho.riak.spark.query.QueryTS$$anonfun$nextChunk$2.apply(QueryTS.scala:65)
at com.basho.riak.spark.rdd.connector.RiakConnector$$anonfun$withSessionDo$1.apply(RiakConnector.scala:58)
at com.basho.riak.spark.rdd.connector.RiakConnector$$anonfun$withSessionDo$1.apply(RiakConnector.scala:58)
at com.basho.riak.spark.rdd.connector.RiakConnector.closeSessionAfterUse(RiakConnector.scala:63)
at com.basho.riak.spark.rdd.connector.RiakConnector.withSessionDo(RiakConnector.scala:58)
at com.basho.riak.spark.query.QueryTS.nextChunk(QueryTS.scala:65)
at com.basho.riak.spark.query.TSDataQueryingIterator.prefetch(TSDataQueryingIterator.scala:58)
at com.basho.riak.spark.query.TSDataQueryingIterator.columnDefs(TSDataQueryingIterator.scala:44)
at com.basho.riak.spark.rdd.RiakTSRDD.computeTS(RiakTSRDD.scala:73)
at com.basho.riak.spark.rdd.RiakTSRDD.compute(RiakTSRDD.scala:105)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)
at org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:306)
at org.apache.spark.rdd.RDD.iterator(RDD.scala:270)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:73)
at org.apache.spark.scheduler.ShuffleMapTask.runTask(ShuffleMapTask.scala:41)
at org.apache.spark.scheduler.Task.run(Task.scala:89)
at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:227)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

@yadid The reason of the error you've got for for the first DF case is a default Riak TS configuration. You just need to re-configure Riak TS to use real IPs instead of providing <IP_ADDRESS> for the PB listener. Here is an example http://docs.basho.com/riak/kv/2.2.3/using/running-a-cluster/#select-an-ip-address-and-port


Enable ccache on CI by default

This PR enables ccache on Tensile builds by default.
It's currently a draft, as I'm testing a few improvements to the robustness of our ccache configuration. When I'm done, I'll mark it ready for review.

This PR was useful for testing out a few things, but there's more work here than I expected. ccache is enabled via changes to environment variables (PATH, CCACHE_*, *_COMPILER_LAUNCHER) and tox undoes those changes. I'm not familiar enough with the Tensile tests or with tox to feel comfortable changing its configuration, so I'm going to drop this for now.


intergate others

[x] https://github.com/aybabtme/untilitworks
[x] https://github.com/sethgrid/pester
[x] https://github.com/eapache/go-resiliency/tree/master/retrier

added to research.yml


Integrate OpenStreetMap (OSM) camera data

OpenStreetMap.org has data containing a webcam's url as well as geographic coordinates. Showing these on a map would be useful and automate part of the task of adding webcams. Querying the OSM database the data can be done through Overpass turbo, using this guide. Objects in the OSM database are tagged with a key value system. For example this object has the key of "contact:webcam" and the value of "http://cmhimg01.dot.state.oh.us/images/CMH/Dublin-Sawmill.jpg" Knowing which tags to query using overpass turbo will help you find useful data (geotagged webcam urls).
Below are some example queries to extract webcam data from OpenStreetMap using overpass turbo.
Query: "contact:webcam":".jpg"
Meaning: find all objects tagged with the key=contact:webcam and the fragment ".jpg" in the value. Note that not all links may be valid, but it narrows down the options and excludes things your app doesn't currently support such as .mjpg.
URL: http://overpass-turbo.eu/s/860
Query: man_made=surveillance and image:".jpg"
Meaning: find surveillance cameras with public feeds. The key "image" is more broad than "contact:webcam" and as such will contain values other than webcam feeds unless coupled with the "man_made=surveillance" tag.
URL: http://overpass-turbo.eu/s/861
Query: man_made=surveillance and url:".jpg"
Meaning: Same as above but with the key "url" (OSM data is based on a free-tagging system so there are sometimes multiple ways of tagging the same thing.)
URL:http://overpass-turbo.eu/s/862
After the query has been loaded, you can export the data ina variety of formats using a button in the top left.
You can also combine queries in overpass turbo. The following query includes ALL of the above queries and some additonal ones. There are about 500 webcams tagged with .jpg web addresses, but not all are guaranteed to be active.
Query:man_made=surveillance and url:".jpg" or man_made=surveillance and image:".jpg" or man_made=surveillance and "url:webcam":".jpg" or man_made=surveillance and "website":".jpg" or "contact:webcam":".jpg"
Meaning: The "or" function serves to chain together distinct queries.
URL:http://overpass-turbo.eu/s/864 (note may take a short while to load)
These examples are not exhaustive or even the most efficient means of extracting data from OpenStreetMap, but I hope they can be of some use.
If you choose to include this data be sure to provide proper attribution to OSM contributors and the data license.
OSMcamera is a web application that displays surveillance cameras on an OSM map, some are tagged with publicly accessible URLs. I'm not sure if it will be helpful, but the source code of that is public.

Thank you @ejabbsrh for the tip,
I will think about this feature. But I'm not sure if this is the way that I would like to go.

Thanks, I meant this more as an idea than a demand or formal request. If anyone knows of a simpler method that would be better.


Version 4.0.0 listed pypi but not on Github or documentation

On pypi we see: https://pypi.org/project/django-tinymce/4.0.0/#history with a date of "Mar 27, 2024".
However, there's no Github release (https://github.com/jazzband/django-tinymce/releases) or documentation update (https://django-tinymce.readthedocs.io/en/latest/history.html).
What is changed in 4.0.0? Are there breaking changes?

The release is here: https://github.com/jazzband/django-tinymce/releases/tag/4.0.0
The changelog is here: https://raw.githubusercontent.com/jazzband/django-tinymce/master/CHANGELOG.rst

Thank you!


Support for key repetition

When keeping a key pressed for a long time, the character was only entered once.
Not sure if this is an OS feature or something wrong in the firmware. Maybe the key up event is send independently of effective key up???
(only tested on Android phone, I need to check another OS)

Yes, this is OS-dependent, on Windows you get the auto-repeat as long as you hold the key.


prepares v4

_Fixes #336_
Changes proposed:

[ ] Add
[X] Prepare
[X] Delete
[ ] Fix

Things I've done:

[X] I've pulled the latest master branch
[ ] I've run npm install to install all the dependenies
[X] I've checked my code, it is clean.
[ ] I've run ESLint.
[X] My pull request fixes an issue, I referenced the issue.
[X] My pull request is not too big, otherwise I've already squashed it.
[ ] I've run npm run build to build the extension. (If I had done something with the extension.)

removes settings and commands.
P.S.: The branch was created by me. (I don't want to merge it in next, I don't know wether we're going to create more subreleases.)

@robertohuertasm I think, when submitting this PR, it was not merged... Anyway...

@jens1o, I'm closing this as this is already done in my latest merge.


[Pipeline filtering] Mechanism to share which pipelines will be excluded or analyzed by build analysis

As part of the pipeline filtering we need to create a mechanism for the repositories to communicate to the build analysis which pipelines needs to be analyzed or which pipelines needs to be excluded
I think we have couple of option of doing this via some configuration on the service side, or on the repository.
Additionally, the ideal objective is to integrate the Opt-in mechanism for behavior of build analysis check · Issue #23 · dotnet/dnceng (github.com) so we only have one mechanism

Release Note Category

[x] Feature changes/additions
[ ] Bug fixes
[ ] Internal Infrastructure Improvements

Release Note Description

Added mechanism to share build analysis settings file

PR: https://dev.azure.com/dnceng/internal/_git/dotnet-helix-service/pullrequest/35814

rolled out


Fixed README demo bug

Thanks for awesome react plugin !
When I use it and copy README.MD code. It is have any error. below code.

Fixed - thanks.


[Feat] Metadata discovery loop prevention

during the build of the trust chain a loop may occour due to a bad configurations on entities in a federation.
In this case the trust chain builder have to break that short circuit :)

we need also to add new unit test with many auth hints to cover critical mechanisms of the real world and also some evil behaviour/misconfiguration of a third party related to the authority_hints claim

Closed by https://github.com/peppelinux/spid-cie-oidc-django/commit/76e499f943e609acf9f77acfc2a000081759343b


i18n: ja Raidbos config update

ヾ(*’Ｏ’*)/

Could you rebase this on top of main and fix the conflicts? Somehow everybody decided to submit translations all at once for this!

Done! 😂


(enhancement) Release DXVK on 2x 3.5" floppy disks

The title was shameless clickbait (or perhaps gibberish for younger folk), but now that I've got your attention I'm going to argue my case.
Since dlls are (usually) highly compressible, why not use XZ Utils for packaging releases?
Here are some comparisons with DXVK 1.6 on compression:

tar -czvf dxvk-1.6.tar.gz dxvk-1.6
time (real):  0m1,655s
size: 7708662

tar -cJvf dxvk-1.6.tar.xz dxvk-1.6
time (real): 0m10,913s
size: 2861040

... and on decompression:

tar -xzvf dxvk-1.6.tar.gz
time (real): 0m0,220s

tar -xJvf dxvk-1.6.tar.xz
time (real): 0m0,367s

The xz package size is only 37.1% of the gz, and the difference in decompression time is negligible.
This enhancement request was brought to you by:

       _     _
      (')-=-(')
    __(   V   )__
   / _/'-----'\_ \
___\\ \\     // //___
>____)/_\---/_\(____<

The highly efficient packaging frogs consortium

How does zstd compare?

How does zstd compare?

It's tuned for speed by default:

tar -I zstd -cvf dxvk-1.6.tar.zst dxvk-1.6
time (real): 0m0,378s
size: 7693867

tar -I zstd -xvf dxvk-1.6.tar.zst
time (real): 0m0,122s

... but doesn't make the two floppy disk mark even on max compression:

tar -I 'zstd --ultra -22' -cvf dxvk-1.6.tar.zst dxvk-1.6
time (real): 0m18,922s
size: 3173229

tar -I zstd -xvf dxvk-1.6.tar.zst
time (real): 0m0,131s

But I assume you're pulling the consortium's frog legs, since zstd is not (yet) widely available or recognized by the average user.
I'll close this, since the seeds of high compression rates have been planted in the right spots, come rain or drought. The frogs made me do it, I swear.
Carry on with the stellar work :wink:


LocalDevEnv.ps1 doesn't assignPremiumPlan

I have the following AL-Go-Settings.json
{
  "type": "AppSource App",
  "templateUrl": "https://github.com/freddydk/AL-Go-AppSource@issue328",
  "useProjectDependencies": true,
  "assignPremiumPlan": true
}

But part of the log shows its not passed to the Run-AlPipeline
  _____                               _
 |  __ \                             | |
 | |__) |_ _ _ __ __ _ _ __ ___   ___| |_ ___ _ __ ___
 |  ___/ _` | '__/ _` | '_ ` _ \ / _ \ __/ _ \ '__/ __|
 | |  | (_| | | | (_| | | | | | |  __/ |_  __/ |  \__ \
 |_|   \__,_|_|  \__,_|_| |_| |_|\___|\__\___|_|  |___/

Pipeline name                   localDevEnv
Container name                  bcserver
Image name
ArtifactUrl                     https://bcartifacts.azureedge.net/sandbox/21.3.51409.51913/de
SasToken                        Not Specified
BcAuthContext                   Not Specified
Environment
ReUseContainer                  False
KeepContainer                   True
Auth                            UserPassword
Credential                      Specified
CompanyName
MemoryLimit                     8G
FailOn                          error
TreatTestFailuresAsWarnings     False
Enable Task Scheduler           False
Assign Premium Plan             False

I don't have overriding configuration in .Al-Go\settings.json

AssignPremiumPlan is not part of issue328 – is in a different branch.
Will be in preview later today (probably tonight)

Is AssignPremiumPlan a new feature? I thought it was already supported before you opened the branch issue328.
What will be in preview tonight? #328 or/and AssignPremiumPlan? Because I don't think I can update before #328 is resolved.

AssignPremiumPlan was in Run-AlPipeline - but forgotten in AL-Go
Will be there tonight (incl. 328)

update AL-Go system files with microsoft/AL-Go-PTE@preview or microsoft/AL-Go-Appsource@preview and you should have #328 and this

Duplicate of #319

Hi @jonaswre - let me know when you have moved away from freddydk@issue328 - as I want to clean up orpheant branches
Thanks

I'll switch tonight.
But go ahead and delete it.

I've moved
Thanks

I'll try to reproduce this tomorrow in test repo. But after updating to preview this doesn't seem to be fixed for me.

I can confirm this is not fixed.
Aleast not for me.
Please check https://github.com/byndit/AL-Go-Issue138 to see if its reproducible for you.
I've executed AppA.AL-Go\localDevEnv.ps1
And setting is set in .github\AL-Go-Settings.json

BTW - AssignPremiumPlan is a project setting, but you can set it in the repo setting (like you did), to take effect in all projects.

Could you try again? I applied a hotfix with a fix.

Didn't help
Downloading BcContainerHelper preview version from Blob Storage
Using 7zip
BcContainerHelper version 4.0.10-preview848
BC.HelperFunctions emits usage statistics telemetry to Microsoft
Reading ..\.github\AL-Go-Settings.json
Reading .AL-Go\settings.json
Checking type
Checking appFolders and testFolders
Application Dependency <IP_ADDRESS>
Checking artifact setting
Downloading artifacts from https://bcartifacts.azureedge.net/sandbox/21.3.51409.51979/de
Updating app- and test Dependencies
Analyzing Test App Dependencies
Checking project dependencies
Checking appDependencyProbingPaths
WARNING: No performance test apps found in bcptTestFolders in .AL-Go\settings.json
WARNING: No test apps found in testFolders in .AL-Go\settings.json
  _____                               _
 |  __ \                             | |
 | |__) |_ _ _ __ __ _ _ __ ___   ___| |_ ___ _ __ ___
 |  ___/ _` | '__/ _` | '_ ` _ \ / _ \ __/ _ \ '__/ __|
 | |  | (_| | | | (_| | | | | | |  __/ |_  __/ |  \__ \
 |_|   \__,_|_|  \__,_|_| |_| |_|\___|\__\___|_|  |___/

Pipeline name                   localDevEnv
Container name                  bcserver
Image name
ArtifactUrl                     https://bcartifacts.azureedge.net/sandbox/21.3.51409.51979/de
SasToken                        Not Specified
BcAuthContext                   Not Specified
Environment
ReUseContainer                  False
KeepContainer                   True
Auth                            UserPassword
Credential                      Specified
CompanyName
MemoryLimit                     8G
FailOn                          error
TreatTestFailuresAsWarnings     False
Enable Task Scheduler           False
Assign Premium Plan             False

BTW - AssignPremiumPlan is a project setting, but you can set it in the repo setting (like you did), to take effect in all projects.

Just do be sure I tried in both.

Clumsy me - it is fixed now.

It works now!


Fix #2005-Provide Ascending/Descending option in sorting.

Fixes #2005
Changes: Add buttons to Sort dialog box for ascending / descending option.
Screenshots for the change:

@heysadboy Didn't get you. You mean it should be a part of the menu ?

@mayank8318 use image button instead of text. Like ↑ for ascending. What's your view about it?

@heysadboy Using Image Button in place of a text buttons in an alert dialog does't look intuitive for the user. Maybe we can use the arrows in the menu or something like in any normal website or sorting thing?
But I guess the text buttons looks better.


Primitives – Fix typo on styling page

polymoprhism to polymorphism.
This pull request:

[ ] Fixes a bug
[ ] Adds additional features/functionality
[X] Updates documentation or example code
[ ] Other

Thanks @feute !


Remove version: Google.CloudSDK version 461.0.0

Checklist for Pull Requests

[X] Have you signed the Contributor License Agreement?
[ ] Is there a linked Issue?

Manifests

[X] Have you checked that there aren't other open pull requests for the same manifest update/change?
[X] This PR only modifies one (1) manifest
[ ] Have you validated your manifest locally with winget validate --manifest <path>?
[ ] Have you tested your manifest locally with winget install --manifest <path>?
[ ] Does your manifest conform to the 1.6 schema?

Note: <path> is the name of the directory containing the manifest you're submitting.

Google.CloudSDK installer is a vanity installer. It will always install the latest version. Therefore this package is incorrect/outdated.

Microsoft Reviewers: Open in CodeFlow

URL: https://dl.google.com/dl/cloudsdk/channels/rapid/GoogleCloudSDKInstaller.exe
OK
(Automated message - build 888)

Hijacking momentarily for testing.

Hi @aisgbnok,
This manifest has the highest version number for this package. Is it available from another location? (This might be in error if the version is switching from semantic to string, or string to semantic.)
(Automated response - build 881.)

https://github.com/microsoft/winget-pkgs/pull/154823


Crash When Uploading File on a Server

When I try to upload a file to any server, XPipe disconnects me from the SFTP window after the upload is completed, and I receive the error Wait for process exit timed out.
Error details:
io.xpipe.core.process.ProcessOutputException: Wait for process exit timed out
    at io.xpipe.core.process.ProcessOutputException.of(ProcessOutputException.java:53)
    at io.xpipe.ext.proc.c.close(SourceFile:107)
    at io.xpipe.ext.proc.dialect.e$1.close(SourceFile:279)
    at io.xpipe.ext.proc.a$2.close(SourceFile:120)
    at io.xpipe.app.browser.file.BrowserFileTransferOperation.handleSingleAcrossFileSystems(BrowserFileTransferOperation.java:263)
    at io.xpipe.app.browser.file.BrowserFileTransferOperation.execute(BrowserFileTransferOperation.java:127)
    at io.xpipe.app.browser.fs.OpenFileSystemModel.lambda$dropFilesIntoAsync$15(OpenFileSystemModel.java:376)
    at io.xpipe.app.util.BooleanScope.executeExclusive(BooleanScope.java:18)
    at io.xpipe.app.browser.fs.OpenFileSystemModel.lambda$dropFilesIntoAsync$16(OpenFileSystemModel.java:369)
    at io.xpipe.app.util.ThreadHelper.lambda$runFailableAsync$1(ThreadHelper.java:42)
    at io.xpipe.app.util.ThreadHelper.lambda$wrap$0(ThreadHelper.java:19)
    at java.lang.VirtualThread.run(VirtualThread.java:309)

System details:

OS: Windows 11 version 23H2 (OS Build 22631.3810)
XPipe Version: 10.0.4

Hardware specifications:

CPU: 12th Gen Intel(R) Core(TM) i5-12600K (Virtualization: Enabled)
GPU: AMD Radeon RX 6700 XT

Driver version: 31.0.24033.1003
Driver date: 5/8/2024
DirectX version: 12 (FL 12.1)

I've tested this on multiple Ubuntu servers. Here is one example:
            .-/+oossssoo+/-.                                                                       r
        `:+ssssssssssssssssss+:`           -------------
      -+ssssssssssssssssssyyssss+-         OS: Ubuntu 22.04.4 LTS x86_64
    .ossssssssssssssssssdMMMNysssso.       Kernel: 5.15.0-107-generic
   /ssssssssssshdmmNNmmyNMMMMhssssss/      Uptime: 45 days, 13 hours, 54 mins
  +ssssssssshmydMMMMMMMNddddyssssssss+     Packages: 1042 (dpkg), 5 (snap)
 /sssssssshNMMMyhhyyyyhmNMMMNhssssssss/    Shell: bash 5.1.16
.ssssssssdMMMNhsssssssssshNMMMdssssssss.   Terminal: /dev/pts/0
+sssshhhyNMMNyssssssssssssyNMMMysssssss+   CPU: AMD Ryzen 7 3800X (16) @ 3.900GHz
ossyNMMMNyMMhsssssssssssssshmmmhssssssso   GPU: 22:00.0 ASPEED Technology, Inc. ASPEED Graphics Fami
ossyNMMMNyMMhsssssssssssssshmmmhssssssso   Memory: 30317MiB / 64184MiB
+sssshhhyNMMNyssssssssssssyNMMMysssssss+
.ssssssssdMMMNhsssssssssshNMMMdssssssss.
 /sssssssshNMMMyhhyyyyhdNMMMNhssssssss/
  +sssssssssdmydMMMMMMMMddddyssssssss+
   /ssssssssssshdmNNNNmyNMMMMhssssss/
    .ossssssssssssssssssdMMMNysssso.
      -+sssssssssssssssssyyyssss+-
        `:+ssssssssssssssssss+:`
            .-/+oossssoo+/-.

Hmm I am aware of some rare issues on Windows of this but not on Linux systems. Does this happen every time or just sometimes? Also how large are the files you are dropping?

When I upload any file larger than approximately half a megabyte from my local machine to a remote server, it crashes every time after the upload is complete. However, it works fine for smaller files, such as YAML configurations. The files I tested were usually around 2MB in size, with an average upload speed of 120KB/s.

Let me think about how to debug this, I can release a build at https://github.com/xpipe-io/xpipe-ptb once it's ready.

Alright, you can try out the latest PTB build. That one is intended to determine where the issue lies. For Windows systems, it now prefers pwsh to powershell when doing file io. So you can try to install pwsh core from https://github.com/PowerShell/PowerShell and do the same file transfer again. If it works then I know where the issue is.
If not, you can go to Settings -> Troubleshoot -> Launch in debug mode and send me the logs somewhere, e.g. email or discord, after the file transfer fails.

It didn't work. Can you send me your discord id so I can share the debug log with you?

There is a discord server that you can find me on: https://github.com/xpipe-io/xpipe?tab=readme-ov-file#more-links

The issue has been resolved in the latest PBT version.


7.17.1 potential Bug in Locking Dashboards (apps)

I think I have found a bug in the locking of dashboards:
User 1 creates dashboard and shares it.
Admin gives access to User 2 (by way of groups).
User 2 loads dashboard and dashboard is unlocked.
User 1 (the dashboard owner), locks the dashboard and then shares it.
User 2 refreshes page, dashboard remains unlocked.
User 2 restores the dashboard and the dashboard is UNLOCKED.
Is this a bug, or am I missing something?
Thanks!!

That does sound like it would be a bug.  Thanks for finding it.

If it helps, we are configured to use ldap security option, if you need any details please let me know!

The fix has been verified, dashboard sharing now keeps the dashboard locked when the setting is set and a restore happens.


Example uses webpack-dev-server which is presently in a maintenance-only mode

Please note that webpack-dev-server is presently in a maintenance-only mode and will not be accepting any additional features in the near term. Most new feature requests can be accomplished with Express middleware; please look into using the before and after hooks in the documentation.
For reference https://github.com/webpack/webpack-dev-server
Mostly I created this issue because I want to have a discussion on what the alternative "Express middleware" would be

Would the example below from @yzrzya1 helps?
https://github.com/me-12/single-spa-portal-example/issues/68#issuecomment-462451301


⚠ Bofrost.at has degraded performance

In 49ecc83, Bofrost.at (https://www.bofrost.at) experienced degraded performance:

HTTP code: 200
Response time: 1871 ms

Resolved: Bofrost.at performance has improved in 1398f0f after 6 minutes.


Common specs fixes

This checklist is used to make sure that common issues in a pull request are addressed. This will expedite the process of getting your pull request merged and avoid extra work on your part to fix issues discovered during the review process.
PR information

[ ] The title of the PR is clear and informative.
[ ] There are a small number of commits, each of which have an informative message. This means that previously merged commits do not appear in the history of the PR. For information on cleaning up the commits in your pull request, see this page.
[ ] Except for special cases involving multiple contributors, the PR is started from a fork of the main repository, not a branch.
[ ] If applicable, the PR references the bug/issue that it fixes.
[ ] Swagger files are correctly named (e.g. the api-version in the path should match the api-version in the spec).

Quality of Swagger

[ ] I have read the contribution guidelines.
[ ] My spec meets the review criteria:

[ ] The spec conforms to the Swagger 2.0 specification.
[ ] The spec follows the guidelines described in the Swagger checklist document.
[ ] Validation tools were run on swagger spec(s) and have all been fixed in this PR.

@ajinkyapotdarvjti,
Thanks for your contribution as a Microsoft full-time employee or intern. You do not need to sign a CLA.
Thanks,
Microsoft Pull Request Bot

@ajinkyapotdarvjti have you shipped SDK with this API version?

@sergey-shandar  the PR looks good to me.
And no, we have not shipped sdk with this new api version (2017-09-01)

No modification for AutorestCI/azure-sdk-for-node

 https://github.com/Azure/azure-sdk-for-ruby/pull/947

 https://github.com/Azure/azure-sdk-for-python/pull/1415


test-lib: add binary availability in Dockerfile check

Required-by: s2i-nodejs-container#230

[test]

[test]

rhel CI failing because of:
stderr: fatal: unable to connect to github.com:
github.com[0: <IP_ADDRESS>]: errno=Connection timed out

[test]

[test]

nodejs PR needed rebasing for centos fixes, one more [test]

Made the test more generic so we can now check any binary not only npm.
[test]

[test]

[test]

[test]

[test]

Thanks for review, tests are green now so merging


Ingress and LB Service with NCP 2.3.2

Under review. Not ready for merge. Applicable to next 1.3.x release and 1.4/master. Thanks.

Received approval from dev. Please merge for 1.3.4. Thanks.
Hi Lorenzo,
The write-up covers the issues in 2.3.2. Looks good.

Thanks @lparis! Merged to master, as well as the 1.3 patch branch here: https://github.com/pivotal-cf/docs-pks/commit/31f6937eed0f24b7de529828afadf0ad43ac9482


OR patterns in let chains are formatted without indentation

        let hir = tcx.hir();
        if let Some(body_id) = tcx.hir_node_by_def_id(def_id).body_id() {
            tcx.arena.alloc_from_iter(hir.body_param_names(body_id))
        } else if let Node::TraitItem(&TraitItem {
            kind: TraitItemKind::Fn(_, TraitFn::Required(idents)),
            ..
        })
        | Node::ForeignItem(&ForeignItem {
            kind: ForeignItemKind::Fn(_, idents, _),
            ..
        }) = tcx.hir_node(tcx.local_def_id_to_hir_id(def_id))
        {
            idents
        } else {
            span_bug!(
                hir.span(tcx.local_def_id_to_hir_id(def_id)),
                "fn_arg_names: unexpected item {:?}",
                def_id
            );
        }

The indentation on this else if let is very confusing as it looks like the if else ends because we are at "normal" indentation for statements in the body, which makes it look like someone has written an assignment with a pattern with a leading | which is then somehow followed up by a block with an else on the end of it (?)
Something like the following would be significantly clearer as the indentation signifies that this is inside of the else condition:
        let hir = tcx.hir();
        if let Some(body_id) = tcx.hir_node_by_def_id(def_id).body_id() {
            tcx.arena.alloc_from_iter(hir.body_param_names(body_id))
        } else if let Node::TraitItem(&TraitItem {
                kind: TraitItemKind::Fn(_, TraitFn::Required(idents)),
                ..
            })
            | Node::ForeignItem(&ForeignItem {
                kind: ForeignItemKind::Fn(_, idents, _),
                ..
            }) = tcx.hir_node(tcx.local_def_id_to_hir_id(def_id))
        {
            idents
        } else {
            span_bug!(
                hir.span(tcx.local_def_id_to_hir_id(def_id)),
                "fn_arg_names: unexpected item {:?}",
                def_id
            );
        }

Relatedly consider the following two code examples:
else if let Node::TraitItem(&TraitItem {
    kind: TraitItemKind::Fn(..),
}) | Node::ForeignItem(&ForeignItem {
    kind: ForeignItemKind::Fn(..),
}) = tcx.hir_node()
{
    x
}

and
else if Node::TraitItem {
    kind: TraitItemKind::Fn(..),
} else if let Node::ForeignItem(&ForeignItem {
    kind: ForeignItemKind::Fn(..),
}) = tcx.hir_node()
{
    x
}

The former has incredibly similar structure to the latter despite having incredibly different meaning and the only distinction is | let which is very easy to miss when skimming the code.


i18n Locale Switcher

added a web component (to be used inside the API Default Box) showing a list of flag icons for the different locales configured for an API.

Merged with another commit.


Azure Functions API Reference doesn't offer documentation for FunctionApp and Blueprint classes

Type of issue
Missing information
Description
Azure Functions Python v2 projects use the azure.functions.Blueprint and FunctionApp classes, as well as a number of standard decorators, but there is no documentation for those classes and their decorators in the API reference.
They should be included in the Classes  and methods section of the package reference.
Page URL
https://learn.microsoft.com/en-us/python/api/azure-functions/azure.functions?view=azure-python
Content source URL
https://github.com/MicrosoftDocs/azure-docs-sdk-python/blob/main/docs-ref-autogen/azure-functions/azure.functions.yml
Document Version Independent Id
33be62d6-06f4-9c93-ba62-df4dfd96ddca
Article author
@lmazuel
Metadata

ID: 27839837-0e98-4389-b589-0562936f436c
Service: azure-functions

There is a related issue with durable functions in #34983

Hi @metamoof, this repo is for the Azure Python SDK. For items related to Azure Functions issues need to be opened here


Hard coded filters in VarDict remove true variant calls

I am trying to get to the bottom of why VarDict has some false negatives in my high-coverage amplicon samples. I noted that VarDict performs a number of filters which are documented in the VCF header:
##FILTER=<ID=AMPBIAS,Description="Indicate the variant has amplicon bias.">
##FILTER=<ID=Bias,Description="Strand Bias">
##FILTER=<ID=Cluster0bp,Description="Two variants are within 0 bp">
##FILTER=<ID=InGap,Description="The variant is in the deletion gap, thus likely false positive">
##FILTER=<ID=InIns,Description="The variant is adjacent to an insertion variant">
##FILTER=<ID=LongMSI,Description="The somatic variant is flanked by long A/T (>=14)">
##FILTER=<ID=MSI12,Description="Variant in MSI region with 12 non-monomer MSI or 13 monomer MSI">
##FILTER=<ID=NM4.25,Description="Mean mismatches in reads >= 4.25, thus likely false positive">
##FILTER=<ID=PASS,Description="All filters passed">
##FILTER=<ID=Q10,Description="Mean Mapping Quality Below 10">
##FILTER=<ID=SN1.5,Description="Signal to Noise Less than 1.5">
##FILTER=<ID=d3,Description="Total Depth < 3">
##FILTER=<ID=f0.1,Description="Allele frequency < 0.1">
##FILTER=<ID=p8,Description="Mean Position in Reads Less than 8">
##FILTER=<ID=pSTD,Description="Position in Reads has STD of 0">
##FILTER=<ID=q25,Description="Mean Base Quality Below 25">
##FILTER=<ID=v2,Description="Var Depth < 2">

Unfortunately, only a fraction of them seem to be accessible through the command line. I am particularly interested in modifying Cluster0bp and NM4.25. I assume that VarDict is not aware of phasing. I suspect Cluster0bp to remove variants on the second allele which are neatly called by freebayes and clearly visible to the eye like this one:
chr7	117199644	.	ATCT	GTCT,A

I wonder why Cluster0bp was introduced in the first place. I cannot imagine that it made much of a difference when optimizing for TP/FP ratios in gold standard data sets. Could you shine some light on that?

Hi @gabeng, VarDict does pay attention to whether adjacent variants are mutually exclusive or not in reads i.e. whether there is a more complex variant on the same allele.
Both of the two options you highlight are available in var2vcf_valid.pl if you look at the -c and -m options. The default for Clusterxbp is 0 i.e. it's off

The variants I am referring to are located on different alleles. They are not mutually exclusive. This is quite evident when you look at the reads.
This is the output of vardict-java:
S-NA21551_S45_L001_R1_001       -       chr7    117199644       117199644       A       G       1309    638     313     353     327     311     A/G     0.4874  2;2     36.8    1       36.9    1       60.0    24.520  0.4888  0       0       1.000   1       2.8     613     1254    GCACCATTAAAGAAAATATC    TCTTTGGTGTTTCCTATGAT    chr7:117199604-117199805        SNV     2       2       0       0
S-NA21551_S45_L001_R1_001       -       chr7    117199644       117199647       ATCT    A       1128    574     292     251     296     278     T/-3    0.5089  2;2     50.5    1       38.5    1       60.0    142.500 0.5263  0.0027  1       3.000   1       1.6     570     1083    GCACCATTAAAGAAAATATC    TTGGTGTTTCCTATGATGAA    chr7:117199495-117199708        Deletion        2       2       0       0

Once I pipe that through
teststrandbias.R| var2vcf_valid.pl -N S-NA21551_S45_L001_R1_001 -E -f 0.1

the SNV is gone.
This is the entire command:
vardict-java -G /home/ubuntu/local/share/bcbio/genomes/Hsapiens/hg19/seq/hg19.fa -f 0.1 -N S-NA21551_S45_L001_R1_001 -b /bioinf-data/10123-eval-testrun-4/work/prealign/S-NA21551_S45_L001_R1_001/S-NA21551_S45_L001_R1_001-ready.bam -c 1 -S 2 -E 3 -g 4 -Q 10 /bioinf-data/10123-eval-testrun-4/work/vardict/chr7/S-NA21551_S45_L001_R1_001-chr7_117119975_159138663-unmerged-regions-regionlimit.bed | teststrandbias.R| var2vcf_valid.pl -N S-NA21551_S45_L001_R1_001 -E -f 0.1 -c 1 > /bioinf-data/vardict-variants-1.vcf

The SNV should not be filtered out. Can you indicate which setting in var2vcf_valid.pl filters the SNV?

Just noted that there is an option -A in the (current) March 2016 version of var2vcf_valid.pl. I will ask Brad to bump up the version in bcbio.

The version in bcbio is the latest release 1.4.8 from December 2016 actually

I just made a bcbio_nextgen.py upgrade -u development and this is what appears in manifest/python-packages.yaml:
vardict:
  name: vardict
  version: 2016.02.19
vardict-java:
  name: vardict-java
  version: 1.4.8

The installed var2vcf_valid.pl is not the version from March that I can see on github.

Ben and Miika -- sorry about the out of date version in bcbio. I'll bump the perl version with the var2vcf_valid.pl script and follow up when it's finished in chapmanb/bcbio-nextgen#1768 Thanks much for the heads up.

@mjafin, there is certainly a reason why you remove one of two heterozygous variant calls at a certain position. What is that? Does the -A switch change the performance of VarDict in your reference data sets?

Ben, I'd have to refer to @zhongwulai for the design decision, bear with us.

I was able to verify that the -A option retains my verified SNP from above. Therefore, I would like to ask Brad to add this option to the bcbio vardict standard workflow, if this does not impact the overall FP rate in his validation.
I have another example in the same exon, though, where I need your help, since I cannot figure out why this variant is not called with the standard settings.
These are the genomic facts (NA21551): https://catalog.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM21551&PgId=166
ATGTGTGTGTGTGTGTGTGTGTGTTTTTTT (Reference/Wildtype)
A  TGTGTGTGTGTGTGTGTGTGTTTTTTT (Allele 1)
ATGTGTGTGTGTGTGTGTGTGTTTTTTTTT (Allele 2)

Depth is more than 1000x. Freebayes calls both variants correctly:
chr7	117188660	.	ATG	A	21700.2	PASS	AC=1;AF=0.5;AN=2;DECOMPOSED;LEN=2;NS=1;TYPE=del	GT:GQ:DP:AD:RO:QR:AO:QA:GL	1|0:127:1718:26,510,405:26:933:510,405:16471,14806:-2453.57,-1133.32,-1055.89,-1251.99,0,-1206.17
chr7	117188682	.	G	T	21700.2	PASS	AC=1;AF=0.5;AN=2;DECOMPOSED;LEN=1;NS=1;TYPE=snp	GT:GQ:DP:AD:RO:QR:AO:QA:GL	0|1:127:1718:26,510,405:26:933:510,405:16471,14806:-2453.57,-1133.32,-1055.89,-1251.99,0,-1206.17

Vardict only calls:
chr7	117188660	rs4646205	ATG	A	346	PASS	ADJAF=0.0075;AF=0.4284;AMPFLAG=0;BIAS=2:2;DP=1592;GDAMP=1;HIAF=0.4479;HICNT=654;HICOV=1460;LSEQ=AAACTCATCTTTTATTTTTG;MQ=58.2;MSI=11;MSILEN=2;NCAMP=0;NM=2.4;ODDRATIO=1.16393;PMEAN=51.8;PSTD=1;QSTD=1;QUAL=36.8;REFBIAS=346:322;RSEQ=TGTGTGTGTGTGTGTGTGTG;SAMPLE=S-NA21551_S45_L001_R1_001;SBF=0.17251;SHIFT3=21;SN=23.357;TLAMP=1;TYPE=Deletion;VARBIAS=379:303;VD=682;rs_ids=rs4646205	GT:DP:VD:AD:AF:RD:ALD	0/1:1592:682:668,682:0.4284:346,322:379,303

I tried to use the debug option  -D in vardict-java but I do not see any trace of the G>T call anywhere. Is there any way to figure out why this call is not made?

I have not found any parameter to modify the local realignment behaviour. It seems that local realignment is not working well (or not producing the desired results) in repetitive regions. I will turn it off in for my samples. What would be the global impact of using -k 0 with vardict-java in validation testing against GiB, @chapmanb?

 My assumption would be that this would hurt generally as it's going to ruin resolution in other less repetitive regions, but we could look along with the -A suggestion. I'm running DREAM synthetic 4 validation benchmarks now with the current version as a baseline to start to test these tweaks.
If you could share a slice of the BAM file in your problem region as a reproducible case, I think it would be worth looking at the underlying issue and trying to fix that. Would that be possible?

Brad,
thanks for running the validation so quickly. I was wondering if there is a parameter to tell vardict to consider a longer stretch of bp for local re-alignment. This may impact performance but may solve the issue at least for repetitive regions of certain length. Just a thought from an outsider without any knowledge of the code.
I would be happy to share a slice of the BAM file. Where should I put it?

Just a quick note, I would be cautious about changing global settings based on a single missed variant

You are absolutely right about being cautious. That is why Brad's validation is so valuable.
Regarding my specific application I am left with two choices: use both options mentioned above with vardict or go back to freebayes. Unfortunately, the missed variant is clinically relevant. When I have some time, I will take a broader look at variants where vardict and freebayes disagree.

Hi @gabeng, FreeBayes is absolutely brilliant for germline whereas VarDict was always tuned for cancer applications. FreeBayes isn't that great with longer, more complex and subclonal indels you see in tumours.
For your specific case and why the realigner dismisses the other variant we'd need to hear back from @zhongwulai, however I know he's been up to his eyeballs with other stuff lately.

Ben and Miika;
Thanks again for this discussion. We ran whole genome validation of these options against NA12878 (http://imgur.com/a/SF2a8) and have a comparison to discuss from:

The -A option provides a slight increase in sensitivity with corresponding small decrease in precision but does not have a big impact. Based on Ben's analysis above, it's worth adding this as a default.
The -k 0 option is more difficult. It does help with SNP sensitivity, likely in cases like Ben identified above, but it makes indel resolution much worse. The best thing to do here is to try and debug the problem case and see if there's a fix we can get into VarDict to do better at resolving these variants. Ben, how big are your sliced BAM files? You can likely attach them to a message or upload to S3 as a way to share them. Would that work?

Brad, thanks for the performance comparison, that's very interesting. I will share the data through S3 by early next week, since I am travelling.

@gabeng, hello!
I guess I can close this issue because it is quite old, and local realignment was significantly changed from that time. There is also -X option in VarDict to change the extension of bp to look for mismatches after insertion or deletion (default is 2), that can be helpful.
If there are still some problems with local realignment on your samples, please reopen this issue and we can work on it.
Thank you!


fix(http): fix doc label not found error

Closes https://github.com/influxdata/influxdb/issues/12860

LGTM, only thing I think that would be good is to add a test for this behavior.

Done 👍


0.12.0

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Merging #177 (b2fce46) into master (41bd6dc) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #177      +/-   ##
==========================================
+ Coverage   99.43%   99.45%   +0.01%
==========================================
  Files          15       14       -1
  Lines         177      183       +6
  Branches       36       43       +7
==========================================
+ Hits          176      182       +6
  Misses          1        1

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Redo Styling

Related PR on adi-website: https://github.com/adicu/adi-website/pull/280
This changes the way we do SCSS:

All SCSS files are now imported from one place: eventum.scss, instead of using some import tree.
We now have one big CSS file.
default profile picture / event image
remove scripts

Probably should update Readme

lgtm otherwise


IA-3338: Add fiter "Project" on Form statistics

Explain what problem this PR is resolving

Add fiter "Project" on Form statistics
Related JIRA tickets : IA-3338

Self proofreading checklist

[x] Did I use eslint and black formatters
[ ] Is my code clear enough and well documented
[ ] Are my typescript files well typed
[ ] New translations have been added or updated if new strings have been introduced in the frontend
[ ] My migrations file are included
[ ] Are there enough tests
[ ] Documentation has been included (for new feature)

Doc

Tell us where the doc can be found (docs folder, wiki, in the code...)

Changes

Added projects filter on front-end form stats page
Add projects filter in back-end on form stats api

How to test

Forms --> Form statistics
Check if the projects filter works where

Print screen / video
Screencast from 2024-09-02 16-59-12.webm
Notes
Things that the reviewers should know: known bugs that are out of the scope of the PR, other trade-offs that were made.
If the PR depends on a PR in bluesquare-components, or merges into another PR (i.o. main), it should also be mentioned here

The alignment of the filter and the button is off.

Code com

ments are for style/good practice.